plateform
stringclasses 1
value | repo_name
stringlengths 13
113
| name
stringlengths 3
74
| ext
stringclasses 1
value | path
stringlengths 12
229
| size
int64 23
843k
| source_encoding
stringclasses 9
values | md5
stringlengths 32
32
| text
stringlengths 23
843k
|
|---|---|---|---|---|---|---|---|---|
github
|
cocoanlab/humanfmri_preproc_bids-master
|
nii_tool.m
|
.m
|
humanfmri_preproc_bids-master/external/dicm2nii/nii_tool.m
| 48,496 |
utf_8
|
b25318c88e1f9bee05462b06ac0f8cca
|
function varargout = nii_tool(cmd, varargin)
% Basic function to create, load and save NIfTI file.
%
% rst = nii_tool('cmd', para);
%
% To list all command, type
% nii_tool ?
%
% To get help information for each command, include '?' in cmd, for example:
% nii_tool init?
% nii_tool('init?')
%
% Here is a list of all command:
%
% nii_tool('default', 'version', 1, 'rgb_dim', 1);
% nii = nii_tool('init', img);
% nii = nii_tool('update', nii);
% nii_tool('save', nii, filename, force_3D);
% hdr = nii_tool('hdr', filename);
% img = nii_tool('img', filename_or_hdr);
% ext = nii_tool('ext', filename_or_hdr);
% nii = nii_tool('load', filename_or_hdr);
% nii = nii_tool('cat3D', filenames);
% nii_tool('RGBStyle', 'afni');
%
% Detail for each command is described below.
%
% oldVal = nii_tool('default', 'version', 1, 'rgb_dim', 1);
% oldVal = nii_tool('default', struct('version', 1, 'rgb_dim', 1));
%
% - Set/query default NIfTI version and/or rgb_dim. To check the setting, run
% nii_tool('default') without other input. The input for 'default' command can
% be either a struct with fields of 'version' and/or 'rgb_dim', or
% parameter/value pairs. See nii_tool('RGBstyle') for meaning of rgb_dim.
%
% Note that the setting will be saved for future use. If one wants to change the
% settting temporarily, it is better to return the oldVal, and to restore it
% after done:
%
% oldVal = nii_tool('default', 'version', 2); % set version 2 as default
% % 'init' and 'save' NIfTI using above version
% nii_tool('default', oldVal); % restore default setting
%
% The default version setting affects 'init' command only. If you 'load' a NIfTI
% file, modify it, and then 'save' it, the version will be the same as the
% original file, unless it is changed explicitly (see help for 'save' command).
% All 'load' command ('load', 'hdr', 'ext', 'img') will read any version
% correctly, regardless of version setting.
%
%
% nii = nii_tool('init', img, RGB_dim);
%
% - Initialize nii struct based on img, normally 3D or 4D array. Most fields in
% the returned nii.hdr contain default values, and need to be updated based on
% dicom or other information. Important ones include pixdim, s/qform_code and
% related parameters.
%
% The NIfTI datatype will depend on data type of img. Most Matlab data types are
% supported, including 8/16/32/64 bit signed and unsigned integers, single and
% double floating numbers. Single/double complex and logical array are also
% supported.
%
% The optional third input, RGB_dim, is needed only if img contains RGB/RGBA
% data. It specifies which dimension in img encodes RGB or RGBA. In other words,
% if a non-empty RGB_dim is provided, img will be interpreted as RGB/RGBA data.
%
% Another way to signify RGB/RGBA data is to permute color dim to 8th-dim of img
% (RGB_dim of 8 can be omitted then). Since NIfTI img can have up to 7 dim,
% nii_tool chooses to store RGB/RGBA in 8th dim. Although this looks lengthy
% (4th to 7th dim are often all ones), nii_tool can deal with up to 7 dim
% without causing any confusion. This is why the returned nii.img always stores
% RGB in 8th dim.
%
%
% nii = nii_tool('update', nii);
%
% - Update nii.hdr according to nii.img. This is useful if one changes nii.img
% type or dimension. The 'save' command calls this internally, so it is not
% necessary to call this before 'save'. A useful case to call 'update' is that
% one likes to use nii struct without saving it to a file, and 'update' will
% make nii.hdr.dim and others correct.
%
%
% hdr = nii_tool('hdr', filename);
%
% - Return hdr struct of the provided NIfTI file. This is useful to check NIfTI
% hdr, and it is much faster than 'load', especially for .gz file.
%
%
% img = nii_tool('img', filename_or_hdr);
%
% - Return image data in a NIfTI file. The second input can be NIfTI file name,
% or hdr struct returned by nii_tool('hdr', filename).
%
%
% ext = nii_tool('ext', filename_or_hdr);
%
% - Return NIfTI extension in a NIfTI file. The second input can be NIfTI file
% name, or hdr struct returned by nii_tool('hdr', filename). The returned ext
% will have field 'edata_decoded' if 'ecode' is of known type, such as dicom
% (2), text (4 or 6) or Matlab (40).
%
% Here is an example to add data in myFile.mat as extension to nii struct, which
% can be from 'init' or 'load':
%
% fid = fopen('myFile.mat'); % open the MAT file
% myEdata = fread(fid, inf, '*uint8'); % load all bytes as byte column
% fclose(fid);
% len = int32(numel(myEdata)); % number of bytes in int32
% myEdata = [typecast(len, 'uint8')'; myEdata]; % include len in myEdata
% nii.ext.ecode = 40; % 40 for Matlab extension
% nii.ext.edata = myEdata; % myEdata must be uint8 array
%
% nii_tool will take care of rest when you 'save' nii to a file.
%
% In case a NIfTI ext causes problem (for example, some FSL builds have problem
% in reading NIfTI img with ecode>30), one can remove the ext easily:
%
% nii = nii_tool('load', 'file_with_ext.nii'); % load the file with ext
% nii.ext = []; % or nii = rmfield(nii, 'ext'); % remove ext
% nii_tool('save', nii, 'file_without_ext.nii'); % save it
%
%
% nii = nii_tool('load', filename_or_hdr);
%
% - Load NIfTI file into nii struct. The returned struct includes NIfTI 'hdr'
% and 'img', as well as 'ext' if the file contains NIfTI extension.
%
% nii_tool returns nii.img with the same data type as stored in the file, while
% numeric values in hdr are in double precision for convenience.
%
%
% nii_tool('save', nii, filename, force_3D);
%
% - Save struct nii into filename. The format of the file is determined by the
% file extension, such as .img, .nii, .img.gz, .nii.gz etc. If filename is not
% provided, nii.hdr.file_name must contain a file name. Note that 'save' command
% always overwrites file in case of name conflict.
%
% If filename has no extension, '.nii' will be used as default.
%
% If the 4th input, force_3D, is true (default false), the output file will be
% 3D only, which means multiple volume data will be split into multiple files.
% This is the format SPM likes. You can use this command to convert 4D into 3D
% by 'load' a 4D file, then 'save' it as 3D files. The 3D file names will have
% 5-digit like '_00001' appended to indicate volume index.
%
% The NIfTI version can be set by nii_tool('default'). One can override the
% default version by specifying it in nii.hdr.version. To convert between
% versions, load a NIfTI file, specify new version, and save it. For example:
%
% nii = nii_tool('load', 'file_nifti1.nii'); % load version 1 file
% nii.hdr.version = 2; % force to NIfTI-2
% nii_tool('save', nii, 'file_nifti2.nii'); % save as version 2 file
%
% Following example shows how to change data type of a nii file:
% nii = nii_tool('load', 'file_int16.nii'); % load int16 type file
% nii.img = single(nii.img); % change data type to single/float32
% nii_tool('save', nii, 'file_float.nii'); % nii_tool will take care of hdr
%
%
% nii = nii_tool('cat3D', files);
%
% - Concatenate SPM 3D files into a 4D dataset. The input 'files' can be cellstr
% with file names, or char with wildcards (* or ?). If it is cellstr, the volume
% order in the 4D data corresponds to those files. If wildcards are used, the
% volume order is based on alphabetical order of file names.
%
% Note that the files to be concatenated must have the same datatype, dim, voxel
% size, scaling slope and intercept, transformation matrix, etc. This is
% normally true if files are for the same dicom series.
%
% Following example shows how to convert a series of 3D files into a 4D file:
%
% nii = nii_tool('cat3D', './data/fSubj2-0003*.nii'); % load files for series 3
% nii_tool('save', nii, './data/fSubj2-0003_4D.nii'); % save as a 4D file
%
%
% oldStyle = nii_tool('RGBStyle', 'afni');
%
% - Set/query the method to read/save RGB or RGBA NIfTI file. The default method
% can be set by nii_tool('default', 'rgb_dim', dimN), where dimN can be 1, 3 or
% 4, or 'afni', 'mricron' or 'fsl', as explained below.
%
% The default is 'afni' style (or 1), which is defined by NIfTI standard, but is
% not well supported by fslview till v5.0.8 or mricron till v20140804.
%
% If the second input is set to 'mricron' (or 3), nii_tool will save file using
% the old RGB fashion (dim 3 for RGB). This works for mricron v20140804 or
% earlier.
%
% If the second input is set to 'fsl' (or 4), nii_tool will save RGB or RGBA
% layer into 4th dimension, and the file is not encoded as RGB data, but as
% normal 4D NIfTI. This violates the NIfTI rule, but it seems it is the only way
% to work for fslview (at least till fsl v5.0.8).
%
% If no new style (second input) is provided, it means to query the current
% style (one of 'afni', 'mricron' and 'fsl').
%
% The GUI method to convert between different RGB style can be found in
% nii_viewer. Following shows how to convert other style into fsl style:
%
% nii_tool('RGBStyle', 'afni'); % we are loading afni style RGB
% nii = nii_tool('load', 'afni_style.nii'); % load RGB file
% nii_tool('RGBStyle', 'fsl'); % switch to fsl style for later save
% nii_tool('save', nii, 'fslRGB.nii'); % fsl can read it as RGB
%
% Note that, if one wants to convert fsl style (non-RGB file by NIfTI standard)
% to other styles, an extra step is needed to change the RGB dim from 4th to 8th
% dim before 'save':
%
% nii = nii_tool('load', 'fslStyleFile.nii'); % it is normal NIfTI
% nii.img = permute(nii.img, [1:3 5:8 4]); % force it to be RGB data
% nii_tool('RGBStyle', 'afni'); % switch to NIfTI RGB style if needed
% nii_tool('save', nii, 'afni_RGB.nii'); % now AFNI can read it as RGB
%
% Also note that the setting by nii_tool('RGBStyle') is effective only for
% current Matlab session. If one clears all or starts a new Matlab session, the
% default style by nii_tool('default') will take effect.
%
% See also NII_VIEWER, NII_XFORM, DICM2NII
% More information for NIfTI format:
% Official NIfTI website: http://nifti.nimh.nih.gov/
% Another excellent site: http://brainder.org/2012/09/23/the-nifti-file-format/
% History (yymmdd)
% 150109 Write it based on Jimmy Shen's NIfTI tool ([email protected])
% 150202 Include renamed pigz files for Windows
% 150203 Fix closeFile and deleteTmpFile order
% 150205 Add hdr.machine: needed for .img fopen
% 150208 Add 4th input for 'save', allowing to save SPM 3D files
% 150210 Add 'cat3D' to load SPM 3D files
% 150226 Assign all 8 char for 'magic' (version 2 needs it)
% 150321 swapbytes(nByte) for ecode=40 with big endian
% 150401 Add 'default' to set/query version and rgb_dim default setting
% 150514 read_ext: decode txt edata by dicm2nii.m
% 150517 func_handle: provide a way to use gunzipOS etc from outside
% 150617 auto detect rgb_dim 1&3 for 'load' etc using ChrisR method
% 151025 Change subfunc img2datatype as 'update' for outside access
% 151109 Include dd.exe from WinAVR-20100110 for partial gz unzip
% 151205 Partial gunzip: fix fname with space & unknown pigz | dd error.
% 151222 Take care of img for intent_code 2003/2004: anyone uses it?
% 160110 Use matlab pref method to replace para file.
% 160120 check_gzip: use "" for included pigz; ignore dd error if err is false.
% 160326 fix setpref for older Octave: set each parameter separately.
% 160531 fopen uses 'W' for 'w': performance benefit according to Yair.
% 160701 subFuncHelp: bug fix for mfile case.
% 161018 gunzipOS: use unique name for outName, to avoid problem with parfor.
% 161025 Make included linux pigz executible; fix "dd" for windows.
% 161031 gunzip_mem(), nii_bytes() for hdr/ext read: read uint8 then parse;
% Replace hdr.machine with hdr.swap_endian.
% 170212 Extract decode_ext() from 'ext' cmd so call it in 'update' cmd.
% 170215 gunzipOS: use -c > rather than copyfile for performance.
% 170322 gzipOS: stop using background gz to avoid file not exist error.
% 170410 read_img(): turn off auto RGB dim detection, and use rgb_dim.
% 170714 'save': force to version 2 if img dim exceeds 2^15-1.
% 170716 Add functionSignatures.json file for tab auto-completion.
% 171031 'LocalFunc' makes eaiser to call local functions.
% 171206 Allow file name ext other than .nii, .hdr, .img.
% 180104 check_gzip: add /usr/local/bin to PATH for unix if needed.
% 180119 use jsystem for better speed.
% 180710 bug fix for cal_max/cal_min in 'update'.
persistent C para; % C columns: name, length, format, value, offset
if isempty(C)
[C, para] = niiHeader;
if exist('OCTAVE_VERSION', 'builtin')
warning('off', 'Octave:fopen-mode'); % avoid 'W' warning
more off;
end
end
if ~ischar(cmd)
error('Provide a string command as the first input for nii_tool');
end
if any(cmd=='?'), subFuncHelp(mfilename, cmd); return; end
if strcmpi(cmd, 'init')
if nargin<2, error('nii_tool(''%s'') needs second input', cmd); end
nii.hdr = cell2struct(C(:,4), C(:,1));
nii.img = varargin{1};
if numel(size(nii.img))>8
error('NIfTI img can have up to 7 dimension');
end
if nargin>2
i = varargin{2};
if i<0 || i>8 || mod(i,1)>0, error('Invalid RGB_dim number'); end
nii.img = permute(nii.img, [1:i-1 i+1:8 i]); % RGB to dim8
end
varargout{1} = nii_tool('update', nii); % set datatype etc
elseif strcmpi(cmd, 'save')
if nargin<2, error('nii_tool(''%s'') needs second input', cmd); end
nii = varargin{1};
if ~isstruct(nii) || ~isfield(nii, 'hdr') || ~isfield(nii, 'img')
error(['nii_tool(''save'') needs a struct from nii_tool(''init'')' ...
' or nii_tool(''load'') as the second input']);
end
% Check file name to save
if nargin>2
fname = varargin{2};
if ~ischar(fname), error('Invalid name for NIfTI file: %s', fname); end
elseif isfield(nii.hdr, 'file_name')
fname = nii.hdr.file_name;
else
error('Provide a valid file name as the third input');
end
if ~ispc && strncmp(fname, '~/', 2) % matlab may err with this abbrevation
fname = [getenv('HOME') fname(2:end)];
end
[pth, fname, fext] = fileparts(fname);
do_gzip = strcmpi(fext, '.gz');
if do_gzip
[~, fname, fext] = fileparts(fname); % get .nii .img .hdr
end
if isempty(fext), fext = '.nii'; end % default single .nii file
fname = fullfile(pth, fname); % without file ext
isNii = strcmpi(fext, '.nii'); % will use .img/.hdr if not .nii
% Deal with NIfTI version and sizeof_hdr
niiVer = para.version;
if isfield(nii.hdr, 'version'), niiVer = nii.hdr.version; end
if niiVer==1 && any(nii.hdr.dim(2:end) > 32767), niiVer = 2; end
if niiVer == 1
nii.hdr.sizeof_hdr = 348; % in case it was loaded from other version
elseif niiVer == 2
nii.hdr.sizeof_hdr = 540; % version 2
else
error('Unsupported NIfTI version: %g', niiVer);
end
if niiVer ~= para.version
C0 = niiHeader(niiVer);
else
C0 = C;
end
% Update datatype/bitpix/dim in case nii.img is changed
[nii, fmt] = nii_tool('update', nii);
% This 'if' block: lazy implementation to split into 3D SPM files
if nargin>3 && ~isempty(varargin{3}) && varargin{3} && nii.hdr.dim(5)>1
if do_gzip, fext = [fext '.gz']; end
nii0 = nii;
for i = 1:nii.hdr.dim(5)
fname0 = sprintf('%s_%05g%s', fname, i, fext);
nii0.img = nii.img(:,:,:,i,:,:,:,:); % one vol
if i==1 && isfield(nii, 'ext'), nii0.ext = nii.ext;
elseif i==2 && isfield(nii0, 'ext'), nii0 = rmfield(nii0, 'ext');
end
nii_tool('save', nii0, fname0);
end
return;
end
% re-arrange img for special datatype: RGB/RGBA/Complex.
if any(nii.hdr.datatype == [128 511 2304]) % RGB or RGBA
if para.rgb_dim == 1 % AFNI style
nii.img = permute(nii.img, [8 1:7]);
elseif para.rgb_dim == 3 % old mricron style
nii.img = permute(nii.img, [1 2 8 3:7]);
elseif para.rgb_dim == 4 % for fslview
nii.img = permute(nii.img, [1:3 8 4:7]); % violate nii rule
dim = size(nii.img);
if numel(dim)>6 % dim7 is not 1
i = find(dim(5:7)==1, 1, 'last') + 4;
nii.img = permute(nii.img, [1:i-1 i+1:8 i]);
end
nii = nii_tool('update', nii); % changed to non-RGB datatype
end
elseif any(nii.hdr.datatype == [32 1792]) % complex single/double
nii.img = [real(nii.img(:))'; imag(nii.img(:))'];
end
% Check nii extension: update esize to x16
nExt = 0; esize = 0;
nii.hdr.extension = [0 0 0 0]; % no nii ext
if isfield(nii, 'ext') && isstruct(nii.ext) ...
&& isfield(nii.ext(1), 'edata') && ~isempty(nii.ext(1).edata)
nExt = numel(nii.ext);
nii.hdr.extension = [1 0 0 0]; % there is nii ext
for i = 1:nExt
if ~isfield(nii.ext(i), 'ecode') || ~isfield(nii.ext(i), 'edata')
error('NIfTI header ext struct must have ecode and edata');
end
n0 = numel(nii.ext(i).edata) + 8; % 8 byte for esize and ecode
n1 = ceil(n0/16) * 16; % esize: multiple of 16
nii.ext(i).esize = n1;
nii.ext(i).edata(end+(1:n1-n0)) = 0; % pad zeros
esize = esize + n1;
end
end
% Set magic, vox_offset, and open file for .nii or .hdr
if isNii
% version 1 will take only the first 4
nii.hdr.magic = sprintf('n+%g%s', niiVer, char([0 13 10 26 10]));
nii.hdr.vox_offset = nii.hdr.sizeof_hdr + 4 + esize;
fid = fopen([fname fext], 'W');
else
nii.hdr.magic = sprintf('ni%g%s', niiVer, char([0 13 10 26 10]));
nii.hdr.vox_offset = 0;
fid = fopen([fname '.hdr'], 'W');
end
% Write nii hdr
for i = 1:size(C0,1)
if isfield(nii.hdr, C0{i,1})
val = nii.hdr.(C0{i,1});
else % niiVer=2 omit some fields, also take care of other cases
val = C0{i,4};
end
n = numel(val);
len = C0{i,2};
if n>len
val(len+1:n) = []; % remove extra, normally for char
elseif n<len
val(n+1:len) = 0; % pad 0, normally for char
end
fwrite(fid, val, C0{i,3});
end
% Write nii ext: extension is in hdr
for i = 1:nExt % nExt may be 0
fwrite(fid, nii.ext(i).esize, 'int32');
fwrite(fid, nii.ext(i).ecode, 'int32');
fwrite(fid, nii.ext(i).edata, 'uint8');
end
if ~isNii
fclose(fid); % done with .hdr
fid = fopen([fname '.img'], 'W');
end
% Write nii image
fwrite(fid, nii.img, fmt);
fclose(fid); % all written
% gzip if asked
if do_gzip
if isNii
gzipOS([fname '.nii']);
else
gzipOS([fname '.hdr']); % better not to compress .hdr
gzipOS([fname '.img']);
end
end
elseif strcmpi(cmd, 'hdr')
if nargin<2, error('nii_tool(''%s'') needs second input', cmd); end
if ~ischar(varargin{1})
error('nii_tool(''hdr'') needs nii file name as second input');
end
fname = nii_name(varargin{1}, '.hdr'); % get .hdr if it is .img
[b, fname] = nii_bytes(fname, 600); % v2: 544+10 gzip header
varargout{1} = read_hdr(b, C, fname);
elseif any(strcmpi(cmd, {'img' 'load'}))
if nargin<2, error('nii_tool(''%s'') needs second input', cmd); end
if ischar(varargin{1}) % file name input
fname = nii_name(varargin{1}, '.hdr');
nii = struct;
elseif isstruct(varargin{1}) && isfield(varargin{1}, 'file_name')
nii.hdr = varargin{1};
fname = nii.hdr.file_name;
else
error(['nii_tool(''%s'') needs a file name or hdr struct from ' ...
'nii_tool(''hdr'') as second input'], cmd);
end
if strcmpi(cmd, 'load')
[ext, nii.hdr] = nii_tool('ext', varargin{1});
if ~isempty(ext), nii.ext = ext; end
elseif ~isfield(nii, 'hdr')
nii.hdr = nii_tool('hdr', fname);
end
nii.img = read_img(nii.hdr, para);
if strcmpi(cmd, 'load')
varargout{1} = nii;
else % img
varargout{1} = nii.img;
end
elseif strcmpi(cmd, 'ext')
if nargin<2, error('nii_tool(''%s'') needs second input', cmd); end
if ischar(varargin{1}) % file name input
fname = nii_name(varargin{1}, '.hdr');
hdr = nii_tool('hdr', fname);
elseif isstruct(varargin{1}) && isfield(varargin{1}, 'file_name')
hdr = varargin{1};
fname = hdr.file_name;
else
error(['nii_tool(''%s'') needs a file name or hdr struct from ' ...
'nii_tool(''hdr'') as second input'], cmd);
end
if isempty(hdr.extension) || hdr.extension(1)==0
varargout{1} = [];
else
if hdr.vox_offset>0, nByte = hdr.vox_offset + 64; % .nii arbituary +64
else, nByte = inf;
end
b = nii_bytes(fname, nByte);
varargout{1} = read_ext(b, hdr);
end
if nargout>1, varargout{2} = hdr; end
elseif strcmpi(cmd, 'RGBStyle')
styles = {'afni' '' 'mricron' 'fsl'};
curStyle = styles{para.rgb_dim};
if nargin<2, varargout{1} = curStyle; return; end % query only
irgb = varargin{1};
if isempty(irgb), irgb = 1; end % default as 'afni'
if ischar(irgb)
if strncmpi(irgb, 'fsl', 3), irgb = 4;
elseif strncmpi(irgb, 'mricron', 4), irgb = 3;
else, irgb = 1;
end
end
if ~any(irgb == [1 3 4])
error('nii_tool(''RGBStyle'') can have 1, 3, or 4 as second input');
end
if nargout, varargout{1} = curStyle; end % return old one
para.rgb_dim = irgb; % no save to pref
elseif strcmpi(cmd, 'cat3D')
if nargin<2, error('nii_tool(''%s'') needs second input', cmd); end
fnames = varargin{1};
if ischar(fnames) % guess it is like run1*.nii
f = dir(fnames);
f = sort({f.name});
fnames = strcat([fileparts(fnames) '/'], f);
end
n = numel(fnames);
if n<2 || ~iscellstr(fnames)
error('Invalid input for nii_tool(''cat3D''): %s', varargin{1});
end
nii = nii_tool('load', fnames{1}); % all for first file
nii.img(:,:,:,2:n) = 0; % pre-allocate
% For now, omit all consistence check between files
for i = 2:n, nii.img(:,:,:,i) = nii_tool('img', fnames{i}); end
varargout{1} = nii_tool('update', nii); % update dim
elseif strcmpi(cmd, 'default')
flds = {'version' 'rgb_dim'}; % may add more in the future
pf = getpref('nii_tool_para');
for i = 1:numel(flds), val.(flds{i}) = pf.(flds{i}); end
if nargin<2, varargout{1} = val; return; end % query only
if nargout, varargout{1} = val; end % return old val
in2 = varargin;
if ~isstruct(in2), in2 = struct(in2{:}); end
nam = fieldnames(in2);
for i = 1:numel(nam)
ind = strcmpi(nam{i}, flds);
if isempty(ind), continue; end
para.(flds{ind}) = in2.(nam{i});
setpref('nii_tool_para', flds{ind}, in2.(nam{i}));
end
if val.version ~= para.version, C = niiHeader(para.version); end
elseif strcmpi(cmd, 'update') % old img2datatype subfunction
if nargin<2, error('nii_tool(''%s'') needs second input', cmd); end
nii = varargin{1};
if ~isstruct(nii) || ~isfield(nii, 'hdr') || ~isfield(nii, 'img')
error(['nii_tool(''save'') needs a struct from nii_tool(''init'')' ...
' or nii_tool(''load'') as the second input']);
end
dim = size(nii.img);
ndim = numel(dim);
dim(ndim+1:7) = 1;
if ndim == 8 % RGB/RGBA data. Change img type to uint8/single if needed
valpix = dim(8);
if valpix == 4 % RGBA
typ = 'RGBA'; % error info only
nii.img = uint8(nii.img); % NIfTI only support uint8 for RGBA
elseif valpix == 3 % RGB, must be single or uint8
typ = 'RGB';
if max(nii.img(:))>1, nii.img = uint8(nii.img);
else, nii.img = single(nii.img);
end
else
error('Color dimension must have length of 3 for RGB and 4 for RGBA');
end
dim(8) = []; % remove color-dim so numel(dim)=7 for nii.hdr
ndim = find(dim>1, 1, 'last'); % update it
elseif isreal(nii.img)
typ = 'real';
valpix = 1;
else
typ = 'complex';
valpix = 2;
end
if islogical(nii.img), imgFmt = 'ubit1';
else, imgFmt = class(nii.img);
end
ind = find(strcmp(para.format, imgFmt) & para.valpix==valpix);
if isempty(ind) % only RGB and complex can have this problem
error('nii_tool does not support %s image of ''%s'' type', typ, imgFmt);
elseif numel(ind)>1 % unlikely
error('Non-unique datatype found for %s image of ''%s'' type', typ, imgFmt);
end
fmt = para.format{ind};
nii.hdr.datatype = para.datatype(ind);
nii.hdr.bitpix = para.bitpix(ind);
nii.hdr.dim = [ndim dim];
mx = double(max(nii.img(:)));
mn = double(min(nii.img(:)));
if nii.hdr.cal_min>mx || nii.hdr.cal_max<mn % reset wrong value
nii.hdr.cal_min = 0;
nii.hdr.cal_max = 0;
end
if nii.hdr.sizeof_hdr == 348
nii.hdr.glmax = round(mx); % we may remove these
nii.hdr.glmin = round(mn);
end
if isfield(nii, 'ext')
try swap = nii.hdr.swap_endian; catch, swap = false; end
nii.ext = decode_ext(nii.ext, swap);
end
varargout{1} = nii;
if nargout>1, varargout{2} = fmt; end
elseif strcmp(cmd, 'func_handle') % make a local function avail to outside
varargout{1} = str2func(varargin{1});
elseif strcmp(cmd, 'LocalFunc') % call local function from outside
[varargout{1:nargout}] = feval(varargin{:});
else
error('Invalid command for nii_tool: %s', cmd);
end
% End of main function
%% Subfunction: all nii header in the order in NIfTI-1/2 file
function [C, para] = niiHeader(niiVer)
pf = getpref('nii_tool_para');
if isempty(pf)
setpref('nii_tool_para', 'version', 1);
setpref('nii_tool_para', 'rgb_dim', 1);
pf = getpref('nii_tool_para');
end
if nargin<1 || isempty(niiVer), niiVer = pf.version; end
if niiVer == 1
C = {
% name len format value offset
'sizeof_hdr' 1 'int32' 348 0
'data_type' 10 'char*1' '' 4
'db_name' 18 'char*1' '' 14
'extents' 1 'int32' 16384 32
'session_error' 1 'int16' 0 36
'regular' 1 'char*1' 'r' 38
'dim_info' 1 'uint8' 0 39
'dim' 8 'int16' ones(1,8) 40
'intent_p1' 1 'single' 0 56
'intent_p2' 1 'single' 0 60
'intent_p3' 1 'single' 0 64
'intent_code' 1 'int16' 0 68
'datatype' 1 'int16' 0 70
'bitpix' 1 'int16' 0 72
'slice_start' 1 'int16' 0 74
'pixdim' 8 'single' zeros(1,8) 76
'vox_offset' 1 'single' 352 108
'scl_slope' 1 'single' 1 112
'scl_inter' 1 'single' 0 116
'slice_end' 1 'int16' 0 120
'slice_code' 1 'uint8' 0 122
'xyzt_units' 1 'uint8' 0 123
'cal_max' 1 'single' 0 124
'cal_min' 1 'single' 0 128
'slice_duration' 1 'single' 0 132
'toffset' 1 'single' 0 136
'glmax' 1 'int32' 0 140
'glmin' 1 'int32' 0 144
'descrip' 80 'char*1' '' 148
'aux_file' 24 'char*1' '' 228
'qform_code' 1 'int16' 0 252
'sform_code' 1 'int16' 0 254
'quatern_b' 1 'single' 0 256
'quatern_c' 1 'single' 0 260
'quatern_d' 1 'single' 0 264
'qoffset_x' 1 'single' 0 268
'qoffset_y' 1 'single' 0 272
'qoffset_z' 1 'single' 0 276
'srow_x' 4 'single' [1 0 0 0] 280
'srow_y' 4 'single' [0 1 0 0] 296
'srow_z' 4 'single' [0 0 1 0] 312
'intent_name' 16 'char*1' '' 328
'magic' 4 'char*1' '' 344
'extension' 4 'uint8' [0 0 0 0] 348
};
elseif niiVer == 2
C = {
'sizeof_hdr' 1 'int32' 540 0
'magic' 8 'char*1' '' 4
'datatype' 1 'int16' 0 12
'bitpix' 1 'int16' 0 14
'dim' 8 'int64' ones(1,8) 16
'intent_p1' 1 'double' 0 80
'intent_p2' 1 'double' 0 88
'intent_p3' 1 'double' 0 96
'pixdim' 8 'double' zeros(1,8) 104
'vox_offset' 1 'int64' 544 168
'scl_slope' 1 'double' 1 176
'scl_inter' 1 'double' 0 184
'cal_max' 1 'double' 0 192
'cal_min' 1 'double' 0 200
'slice_duration' 1 'double' 0 208
'toffset' 1 'double' 0 216
'slice_start' 1 'int64' 0 224
'slice_end' 1 'int64' 0 232
'descrip' 80 'char*1' '' 240
'aux_file' 24 'char*1' '' 320
'qform_code' 1 'int32' 0 344
'sform_code' 1 'int32' 0 348
'quatern_b' 1 'double' 0 352
'quatern_c' 1 'double' 0 360
'quatern_d' 1 'double' 0 368
'qoffset_x' 1 'double' 0 376
'qoffset_y' 1 'double' 0 384
'qoffset_z' 1 'double' 0 392
'srow_x' 4 'double' [1 0 0 0] 400
'srow_y' 4 'double' [0 1 0 0] 432
'srow_z' 4 'double' [0 0 1 0] 464
'slice_code' 1 'int32' 0 496
'xyzt_units' 1 'int32' 0 500
'intent_code' 1 'int32' 0 504
'intent_name' 16 'char*1' '' 508
'dim_info' 1 'uint8' 0 524
'unused_str' 15 'char*1' '' 525
'extension' 4 'uint8' [0 0 0 0] 540
};
else
error('Nifti version %g is not supported', niiVer);
end
if nargout<2, return; end
% class datatype bitpix valpix
D = {
'ubit1' 1 1 1 % neither mricron nor fsl support this
'uint8' 2 8 1
'int16' 4 16 1
'int32' 8 32 1
'single' 16 32 1
'single' 32 64 2 % complex
'double' 64 64 1
'uint8' 128 24 3 % RGB
'int8' 256 8 1
'single' 511 96 3 % RGB, not in NIfTI standard?
'uint16' 512 16 1
'uint32' 768 32 1
'int64' 1024 64 1
'uint64' 1280 64 1
% 'float128' 1536 128 1 % long double, for 22nd century?
'double' 1792 128 2 % complex
% 'float128' 2048 256 2 % long double complex
'uint8' 2304 32 4 % RGBA
};
para.format = D(:,1)';
para.datatype = [D{:,2}];
para.bitpix = [D{:,3}];
para.valpix = [D{:,4}];
para.rgb_dim = pf.rgb_dim; % dim of RGB/RGBA in NIfTI FILE
para.version = niiVer;
%% Subfunction: use pigz or system gzip if available (faster)
function gzipOS(fname)
persistent cmd; % command to gzip
if isempty(cmd)
cmd = check_gzip('gzip');
if ischar(cmd)
cmd = @(nam){cmd '-nf' nam};
elseif islogical(cmd) && ~cmd
fprintf(2, ['None of system pigz, gzip or Matlab gzip available. ' ...
'Files are not compressed into gz.\n']);
end
end
if islogical(cmd)
if cmd, gzip(fname); deleteFile(fname); end
return;
end
[err, str] = jsystem(cmd(fname));
if err && ~exist([fname '.gz'], 'file')
try
gzip(fname); deleteFile(fname);
catch
fprintf(2, 'Error during compression: %s\n', str);
end
end
%% Deal with pigz/gzip on path or in nii_tool folder, and matlab gzip/gunzip
function cmd = check_gzip(gz_unzip)
m_dir = fileparts(mfilename('fullpath'));
% away from pwd, so use OS pigz if both exist. Avoid error if pwd changed later
if strcmpi(pwd, m_dir), cd ..; clnObj = onCleanup(@() cd(m_dir)); end
if isunix
pth1 = getenv('PATH');
if isempty(strfind(pth1, '/usr/local/bin'))
pth1 = [pth1 ':/usr/local/bin'];
setenv('PATH', pth1);
end
end
% first, try system pigz
[err, ~] = jsystem({'pigz' '-V'});
if ~err, cmd = 'pigz'; return; end
% next, try pigz included with nii_tool
cmd = [m_dir '/pigz'];
if ismac % pigz for mac is not included in the package
if strcmp(gz_unzip, 'gzip')
fprintf(2, [' Please install pigz for fast compression: ' ...
'http://macappstore.org/pigz/\n']);
end
elseif isunix % linux
[st, val] = fileattrib(cmd);
if st && ~val.UserExecute, fileattrib(cmd, '+x'); end
end
[err, ~] = jsystem({cmd '-V'});
if ~err, return; end
% Third, try system gzip/gunzip
[err, ~] = jsystem({gz_unzip '-V'}); % gzip/gunzip on system path?
if ~err, cmd = gz_unzip; return; end
% Lastly, use Matlab gzip/gunzip if java avail
cmd = usejava('jvm');
%% check dd command, return empty if not available
function dd = check_dd
m_dir = fileparts(mfilename('fullpath'));
if strcmpi(pwd, m_dir), cd ..; clnObj = onCleanup(@() cd(m_dir)); end
[err, ~] = jsystem({'dd' '--version'});
if ~err, dd = 'dd'; return; end % dd with linix/mac, and maybe windows
if ispc % rename it as exe
dd = [m_dir '\dd'];
[err, ~] = jsystem({dd '--version'});
if ~err, return; end
end
dd = '';
%% Try to use in order of pigz, system gunzip, then matlab gunzip
function outName = gunzipOS(fname, nByte)
persistent cmd dd pth uid; % command to run gupzip, dd tool, and temp_path
if isempty(cmd)
cmd = check_gzip('gunzip'); % gzip -dc has problem in PC
if ischar(cmd)
cmd = @(nam)sprintf('"%s" -nfdc "%s" ', cmd, nam); % f for overwrite
elseif islogical(cmd) && ~cmd
cmd = [];
error('None of system pigz, gunzip or Matlab gunzip is available');
end
dd = check_dd;
if ~isempty(dd)
dd = @(n,out)sprintf('| "%s" count=%g of="%s"', dd, ceil(n/512), out);
end
if ispc % matlab tempdir could be slow due to cd in and out
pth = getenv('TEMP');
if isempty(pth), pth = pwd; end
else
pth = getenv('TMP');
if isempty(pth), pth = getenv('TMPDIR'); end
if isempty(pth), pth = '/tmp'; end % last resort
end
uid = @()sprintf('_%s_%03x', datestr(now, 'yymmddHHMMSSfff'), randi(999));
end
if islogical(cmd)
outName = gunzip(fname, pth);
outName = outName{1};
return;
end
[~, outName, ext] = fileparts(fname);
if strcmpi(ext, '.gz') % likely always true
[~, outName, ext1] = fileparts(outName);
outName = [outName uid() ext1];
else
outName = [outName uid()];
end
outName = fullfile(pth, outName);
if ~isempty(dd) && nargin>1 && ~isinf(nByte) % unzip only part of data
try
[err, ~] = system([cmd(fname) dd(nByte, outName)]);
if err==0, return; end
end
end
[err, str] = system([cmd(fname) '> "' outName '"']);
% [err, str] = jsystem({'pigz' '-nfdc' fname '>' outName});
if err
try
outName = gunzip(fname, pth);
catch
error('Error during gunzip:\n%s', str);
end
end
%% cast bytes into a type, swapbytes if needed
function out = cast_swap(b, typ, swap)
out = typecast(b, typ);
if swap, out = swapbytes(out); end
out = double(out); % for convenience
%% subfunction: read hdr
function hdr = read_hdr(b, C, fname)
n = typecast(b(1:4), 'int32');
if n==348, niiVer = 1; swap = false;
elseif n==540, niiVer = 2; swap = false;
else
n = swapbytes(n);
if n==348, niiVer = 1; swap = true;
elseif n==540, niiVer = 2; swap = true;
else, error('Not valid NIfTI file: %s', fname);
end
end
if niiVer>1, C = niiHeader(niiVer); end % C defaults for version 1
for i = 1:size(C,1)
try a = b(C{i,5}+1 : C{i+1,5});
catch
if C{i,5}==numel(b), a = [];
else, a = b(C{i,5} + (1:C{i,2})); % last item extension is in bytes
end
end
if strcmp(C{i,3}, 'char*1')
a = deblank(char(a));
else
a = cast_swap(a, C{i,3}, swap);
a = double(a);
end
hdr.(C{i,1}) = a;
end
hdr.version = niiVer; % for 'save', unless user asks to change
hdr.swap_endian = swap;
hdr.file_name = fname;
%% subfunction: read ext, and decode it if known ecode
function ext = read_ext(b, hdr)
ext = []; % avoid error if no ext but hdr.extension(1) was set
nEnd = hdr.vox_offset;
if nEnd == 0, nEnd = numel(b); end % .hdr file
swap = hdr.swap_endian;
j = hdr.sizeof_hdr + 4; % 4 for hdr.extension
while j < nEnd
esize = cast_swap(b(j+(1:4)), 'int32', swap); j = j+4; % x16
if isempty(esize) || mod(esize,16), return; end % just to be safe
i = numel(ext) + 1;
ext(i).esize = esize; %#ok<*AGROW>
ext(i).ecode = cast_swap(b(j+(1:4)), 'int32', swap); j = j+4;
ext(i).edata = b(j+(1:esize-8))'; % -8 for esize & ecode
j = j + esize - 8;
end
ext = decode_ext(ext, swap);
%% subfunction
function ext = decode_ext(ext, swap)
% Decode edata if we know ecode
for i = 1:numel(ext)
if isfield(ext(i), 'edata_decoded'), continue; end % done
if ext(i).ecode == 40 % Matlab: any kind of matlab variable
nByte = cast_swap(ext(i).edata(1:4), 'int32', swap); % MAT data
tmp = [tempname '.mat']; % temp MAT file to save edata
fid1 = fopen(tmp, 'W');
fwrite(fid1, ext(i).edata(5:nByte+4)); % exclude padded zeros
fclose(fid1);
deleteMat = onCleanup(@() deleteFile(tmp)); % delete temp file after done
ext(i).edata_decoded = load(tmp); % load into struct
elseif any(ext(i).ecode == [4 6 32]) % 4 AFNI, 6 plain text, 32 CIfTI
str = char(ext(i).edata(:)');
if isempty(strfind(str, 'dicm2nii.m'))
ext(i).edata_decoded = deblank(str);
else % created by dicm2nii.m
ss = struct;
ind = strfind(str, [';' char([0 10])]); % strsplit error in Octave
ind = [-2 ind]; % -2+3=1: start of first para
for k = 1:numel(ind)-1
a = str(ind(k)+3 : ind(k+1));
a(a==0) = []; % to be safe. strtrim wont remove null
a = strtrim(a);
if isempty(a), continue; end
try
eval(['ss.' a]); % put all into struct
catch
try
a = regexp(a, '(.*?)\s*=\s*(.*?);', 'tokens', 'once');
ss.(a{1}) = a{2};
catch me
fprintf(2, '%s\n', me.message);
fprintf(2, 'Unrecognized text: %s\n', a);
end
end
end
flds = fieldnames(ss); % make all vector column
for k = 1:numel(flds)
val = ss.(flds{k});
if isnumeric(val) && isrow(val), ss.(flds{k}) = val'; end
end
ext(i).edata_decoded = ss;
end
elseif ext(i).ecode == 2 % dicom
tmp = [tempname '.dcm'];
fid1 = fopen(tmp, 'W');
fwrite(fid1, ext(i).edata);
fclose(fid1);
deleteDcm = onCleanup(@() deleteFile(tmp));
ext(i).edata_decoded = dicm_hdr(tmp);
end
end
%% subfunction: read img
% memory gunzip may be slow and error for large img, so use file unzip
function img = read_img(hdr, para)
ind = para.datatype == hdr.datatype;
if ~any(ind)
error('Datatype %g is not supported by nii_tool.', hdr.datatype);
end
dim = hdr.dim(2:8);
dim(hdr.dim(1)+1:7) = 1; % avoid some error in file
dim(dim<1) = 1;
valpix = para.valpix(ind);
fname = nii_name(hdr.file_name, '.img'); % in case of .hdr/.img pair
fid = fopen(fname);
sig = fread(fid, 2, '*uint8')';
if isequal(sig, [31 139]) % .gz
fclose(fid);
fname = gunzipOS(fname);
cln = onCleanup(@() deleteFile(fname)); % delete gunzipped file
fid = fopen(fname);
end
% if ~exist('cln', 'var') && valpix==1 && ~hdr.swap_endian
% m = memmapfile(fname, 'Offset', hdr.vox_offset, ...
% 'Format', {para.format{ind}, dim, 'img'});
% nii = m.Data;
% return;
% end
if hdr.swap_endian % switch between LE and BE
[~, ~, ed] = fopen(fid); % default endian: almost always ieee-le
fclose(fid);
if isempty(strfind(ed, '-le')), ed = strrep(ed, '-be', '-le'); %#ok<*STREMP>
else, ed = strrep(ed, '-le', '-be');
end
fid = fopen(fname, 'r', ed); % re-open with changed endian
end
fseek(fid, hdr.vox_offset, 'bof');
img = fread(fid, prod(dim)*valpix, ['*' para.format{ind}]); % * to keep original class
fclose(fid);
if any(hdr.datatype == [128 511 2304]) % RGB or RGBA
% a = reshape(single(img), valpix, n); % assume rgbrgbrgb...
% d1 = abs(a - a(:,[2:end 1])); % how similar are voxels to their neighbor
% a = reshape(a, prod(dim(1:2)), valpix*prod(dim(3:7))); % rr...rgg...gbb...b
% d2 = abs(a - a([2:end 1],:));
% j = (sum(d1(:))>sum(d2(:)))*2 + 1; % 1 for afni, 3 for mricron
j = para.rgb_dim; % auto detection may get wrong for noisy background
dim = [dim(1:j-1) valpix dim(j:7)]; % length=8 now
img = reshape(img, dim);
img = permute(img, [1:j-1 j+1:8 j]); % put RGB(A) to dim8
elseif any(hdr.datatype == [32 1792]) % complex single/double
img = reshape(img, [2 dim]);
img = complex(permute(img(1,:,:,:,:,:,:,:), [2:8 1]), ... % real
permute(img(2,:,:,:,:,:,:,:), [2:8 1])); % imag
else % all others: valpix=1
if hdr.datatype==1, img = logical(img); end
img = reshape(img, dim);
end
% RGB triplet in 5th dim OR RGBA quadruplet in 5th dim
c = hdr.intent_code;
if (c == 2003 && dim(5) == 3) || (c == 2004 && dim(5) == 4)
img = permute(img, [1:4 6:8 5]);
end
%% Return requested fname with ext, useful for .hdr and .img files
function fname = nii_name(fname, ext)
if strcmpi(ext, '.img')
i = regexpi(fname, '.hdr(.gz)?$');
if ~isempty(i), fname(i(end)+(0:3)) = ext; end
elseif strcmpi(ext, '.hdr')
i = regexpi(fname, '.img(.gz)?$');
if ~isempty(i), fname(i(end)+(0:3)) = ext; end
end
%% Read NIfTI file as bytes, gunzip if needed, but ignore endian
function [b, fname] = nii_bytes(fname, nByte)
if nargin<2, nByte = inf; end
[fid, err] = fopen(fname); % system default endian
if fid<1, error([err ': ' fname]); end
b = fread(fid, nByte, '*uint8')';
fname = fopen(fid);
fclose(fid);
if isequal(b(1:2), [31 139]) % gz, tgz file
b = gunzip_mem(b, fname, nByte)';
end
%% subfunction: get help for a command
function subFuncHelp(mfile, cmd)
str = fileread(which(mfile));
i = regexp(str, '\n\s*%', 'once'); % start of 1st % line
str = regexp(str(i:end), '.*?(?=\n\s*[^%])', 'match', 'once'); % help text
str = regexprep(str, '\r?\n\s*%', '\n'); % remove '\r' and leading %
dashes = regexp(str, '\n\s*-{1,4}\s+') + 1; % lines starting with 1 to 4 -
if isempty(dashes), disp(str); return; end % Show all help text
prgrfs = regexp(str, '(\n\s*){2,}'); % blank lines
nTopic = numel(dashes);
topics = ones(1, nTopic+1);
for i = 1:nTopic
ind = regexpi(str(1:dashes(i)), [mfile '\s*\(']); % syntax before ' - '
if isempty(ind), continue; end % no syntax before ' - ', assume start with 1
ind = find(prgrfs < ind(end), 1, 'last'); % previous paragraph
if isempty(ind), continue; end
topics(i) = prgrfs(ind) + 1; % start of this topic
end
topics(end) = numel(str); % end of last topic
cmd = strrep(cmd, '?', ''); % remove ? in case it is in subcmd
if isempty(cmd) % help for main function
disp(str(1:topics(1))); % subfunction list before first topic
return;
end
expr = [mfile '\s*\(\s*''' cmd ''''];
for i = 1:nTopic
if isempty(regexpi(str(topics(i):dashes(i)), expr, 'once')), continue; end
disp(str(topics(i):topics(i+1)));
return;
end
fprintf(2, ' Unknown command for %s: %s\n', mfile, cmd); % no cmd found
%% gunzip bytes in memory if possible. 2nd/3rd input for fallback file gunzip
% Trick: try-block avoid error for partial file unzip.
function bytes = gunzip_mem(gz_bytes, fname, nByte)
bytes = [];
try
bais = java.io.ByteArrayInputStream(gz_bytes);
try, gzis = java.util.zip.GZIPInputStream(bais); %#ok<*NOCOM>
catch, try, gzis = java.util.zip.InflaterInputStream(bais); catch me; end
end
buff = java.io.ByteArrayOutputStream;
try org.apache.commons.io.IOUtils.copy(gzis, buff); catch me; end
gzis.close;
bytes = typecast(buff.toByteArray, 'uint8');
if isempty(bytes), error(me.message); end
catch
if nargin<3 || isempty(nByte), nByte = inf; end
if nargin<2 || isempty(fname)
fname = [tempname '.gz']; % temp gz file
fid = fopen(fname, 'W');
if fid<0, return; end
cln = onCleanup(@() deleteFile(fname)); % delete temp gz file
fwrite(fid, gz_bytes, 'uint8');
fclose(fid);
end
try %#ok<*TRYNC>
fname = gunzipOS(fname, nByte);
fid = fopen(fname);
bytes = fread(fid, nByte, '*uint8');
fclose(fid);
deleteFile(fname); % unzipped file
end
end
%% Delete file in background
function deleteFile(fname)
if ispc, system(['start "" /B del "' fname '"']);
else, system(['rm "' fname '" &']);
end
%% faster than system: based on https://github.com/avivrosenberg/matlab-jsystem
function [err, out] = jsystem(cmd)
% cmd is cell str, no quotation marks needed for file names with space.
try
pb = java.lang.ProcessBuilder(cmd);
pb.redirectErrorStream(true); % ErrorStream to InputStream
process = pb.start();
scanner = java.util.Scanner(process.getInputStream).useDelimiter('\A');
if scanner.hasNext(), out = char(scanner.next()); else, out = ''; end
err = process.exitValue; % err = process.waitFor() may hang
if err, error('java.lang.ProcessBuilder error'); end
catch % fallback to system() if java fails like for Octave
cmd = regexprep(cmd, '.+? .+', '"$0"'); % double quotes if with middle space
[err, out] = system(sprintf('%s ', cmd{:}));
end
%%
|
github
|
cocoanlab/humanfmri_preproc_bids-master
|
dicm2nii.m
|
.m
|
humanfmri_preproc_bids-master/external/dicm2nii/dicm2nii.m
| 128,433 |
utf_8
|
9017400933423c6f35d9ec43a688b5d3
|
function varargout = dicm2nii(src, niiFolder, fmt, varargin)
% Convert dicom and more into nii or img/hdr files.
%
% DICM2NII(dcmSource, niiFolder, outFormat)
%
% The input arguments are all optional:
% 1. source file or folder. It can be a zip or tgz file, a folder containing
% dicom files, or other convertible files. It can also contain wildcards
% like 'run1_*' for all files start with 'run1_'.
% 2. folder to save result files.
% 3. output file format:
% 0 or '.nii' for single nii uncompressed.
% 1 or '.nii.gz' for single nii compressed (default).
% 2 or '.hdr' for hdr/img pair uncompressed.
% 3 or '.hdr.gz' for hdr/img pair compressed.
% 4 or '.nii 3D' for 3D nii uncompressed (SPM12).
% 5 or '.nii.gz 3D' for 3D nii compressed.
% 6 or '.hdr 3D' for 3D hdr/img pair uncompressed (SPM8).
% 7 or '.hdr.gz 3D' for 3D hdr/img pair compressed.
% 'bids' for bids data structure (http://bids.neuroimaging.io/)
%
% Typical examples:
% DICM2NII; % bring up user interface if there is no input argument
% DICM2NII('D:/myProj/zip/subj1.zip', 'D:/myProj/subj1/data'); % zip file
% DICM2NII('D:/myProj/subj1/dicom/', 'D:/myProj/subj1/data'); % folder
%
% Less useful examples:
% DICM2NII('D:/myProj/dicom/', 'D:/myProj/subj2/data', 'nii'); % no gz compress
% DICM2NII('D:/myProj/dicom/run2*', 'D:/myProj/subj/data'); % convert run2 only
% DICM2NII('D:/dicom/', 'D:/data', '3D.nii'); % SPM style files
%
% If there is no input, or any of the first two input is empty, the graphic user
% interface will appear.
%
% If the first input is a zip/tgz file, such as those downloaded from a dicom
% server, DICM2NII will extract files into a temp folder, create NIfTI files
% into the data folder, and then delete the temp folder. For this reason, it is
% better to keep the compressed file as backup.
%
% If a folder is the data source, DICM2NII will convert all files in the folder
% and its subfolders (there is no need to sort files for different series).
%
% The output file names adopt SeriesDescription or ProtocolName of each series
% used on scanner console. If both original and MoCo series are present, '_MoCo'
% will be appended for MoCo series. For phase image, such as those from field
% map, '_phase' will be appended to the name. If multiple subjects data are
% mixed (highly discouraged), subject name will be in file name. In case of name
% conflict, SeriesNumber, such as '_s005', will be appended to make file names
% unique. It is suggested to use short, descriptive and distinct
% SeriesDescription on the scanner console.
%
% For SPM 3D files, the file names will have volume index in format of '_00001'
% appended to above name.
%
% Please note that, if a file in the middle of a series is missing, the series
% will normally be skipped without converting, and a warning message in red text
% will be shown in Command Window. The message will also be saved into a text
% file under the data folder.
%
% A Matlab data file, dcmHeaders.mat, is always saved into the data folder. This
% file contains dicom header from the first file for created series and some
% information from last file in field LastFile. Some extra information is also
% saved into this file. For MoCo series, motion parameters (RBMoCoTrans and
% RBMoCoRot) are also saved.
%
% Slice timing information, if available, is stored in nii header, such as
% slice_code and slice_duration. But the simple way may be to use the field
% SliceTiming in dcmHeaders.mat. That timing is actually those numbers for FSL
% when using custom slice timing. This is the universal method to specify any
% kind of slice order, and for now, is the only way which works for multiband.
% Slice order is one of the most confusing parameters, and it is recommended to
% use this method to avoid mistake. Following shows how to convert this timing
% into slice timing in ms and slice order for SPM:
%
% load('dcmHeaders.mat'); % or drag and drop the MAT file into Command Window
% s = h.myFuncSeries; % field name is the same as nii file name
% spm_ms = (0.5 - s.SliceTiming) * s.RepetitionTime;
% [~, spm_order] = sort(-s.SliceTiming);
%
% Some information, such as TE, phase encoding direction and effective dwell
% time, are stored in descrip of nii header. These are useful for fieldmap B0
% unwarp correction. Acquisition start time and date are also stored, and this
% may be useful if one wants to align the functional data to some physiological
% recording, like pulse, respiration or ECG.
%
% If there is DTI series, bval and bvec files will be generated for FSL etc.
% bval and bvec are also saved in the dcmHeaders.mat file.
%
% Starting from 20150514, the converter stores some useful information in NIfTI
% text extension (ecode=6). nii_tool can decode these information easily:
% ext = nii_tool('ext', 'myNiftiFile.nii'); % read NIfTI extension
% ext.edata_decoded contains all above mentioned information, and more. The
% included nii_viewer can show the extension by Window->Show NIfTI ext.
%
% Several preference can be set from dicm2nii GUI. The preference change will
% take effect until it is changed next time.
%
% One of preference is to save a .json file for each converted NIfTI. For more
% information about the purpose of json file, check
% http://bids.neuroimaging.io/
%
% By default, the converter will use parallel pool for dicom header reading if
% there are +2000 files. User can turn this off from GUI.
%
% By default, the PatientName is stored in NIfTI hdr and ext. This can be turned
% off from GUI.
%
% Please note that some information, such as the slice order information, phase
% encoding direction and DTI bvec are in image reference, rather than NIfTI
% coordinate system. This is because most analysis packages require information
% in image space. For this reason, in case the image in a NIfTI file is flipped
% or re-oriented, these information may not be correct anymore.
%
% Please report any bug to [email protected] or at
% http://www.mathworks.com/matlabcentral/fileexchange/42997
%
% To cite the work and for more detail about the conversion, check the paper at
% http://www.sciencedirect.com/science/article/pii/S0165027016300073
%
% See also NII_VIEWER, NII_MOCO, NII_STC
% Thanks to:
% Jimmy Shen's Tools for NIfTI and ANALYZE image,
% Chris Rorden's dcm2nii pascal source code,
% Przemyslaw Baranski for direction cosine matrix to quaternions.
% History (yymmdd):
% 130512 Publish to CCBBI users (Xiangrui Li).
% 130513 Convert img from uint16 to int16 if range allows;
% Support output file format of img/hdr/mat.
% 130515 Change creation order to acquisition order (more natural).
% If MoCo series is included, append _MoCo in file names.
% 130516 Use SpacingBetweenSlices, if exists, for SliceThickness.
% 130518 Use NumberOfImagesInMosaic in CSA header (work for some old data).
% 130604 Add scl_inter/scl_slope and special naming for fieldmap.
% 130614 Work out the way to get EffectiveEchoSpacing for B0 unwarp.
% 130616 Add needed dicom field check, so it won't err later.
% 130618 Reorient if non-mosaic or slice_dim is still 3 and no slice flip.
% 130619 Simplify DERIVED series detection. No '_mag' in fieldmap name.
% 130629 Improve the method to get phase direction;
% Permute img dim1&2 (no -90 rotation) & simplify xform accordingly.
% 130711 Make MoCoOption smarter: create nii if only 1 of 2 series exists.
% 130712 Remove 5th input (allHeader). Save memory by using partial header.
% 130712 Bug fix: dim_info with reorient. No problem since no EPI reorient.
% 130715 Use 2 slices for xform. No slice flip needed except revNum mosaic.
% 130716 Take care of lower/upper cases for output file names;
% Apply scl_slope and inter to img if range allows and no rounding;
% Save motion parameters, if any, into dcmHeader.mat.
% 130722 Ugly fix for isMos, so it works for '2004A 4VA25A' phase data;
% Store dTE instead of TE if two TE are used, such as fieldmap.
% 130724 Add two more ways for dwell time, useful for '2004A 4VA25A' dicom.
% 130801 Can't use DERIVED since MoCoSeries may be labeled as DERIVED.
% 130807 Check PixelSpacing consistency for a series;
% Prepare to publish to Matlab Central.
% 130809 Add 5th input for subjName, so one can choose a subject.
% 130813 Store ImageComments, if exists and is meaningful, into aux_file.
% 130818 Expand source to dicom file(s) and wildcards like run1*.dcm.
% Update fields in dcmHeader.mat, rather than overwriting the file.
% Include save_nii etc in the code for easy distribution.
% 130821 Bug fix for cellstr input as dicom source.
% Change file name from dcm2nii.m to reduce confusion from MRICron.
% GUI implemented into the single file.
% 130823 Remove dependency on Image Processing Toolbox.
% 130826 Bug fix for '*' src input. Minor improvement for dicm_hdr.
% 130827 Try and suggest to use pigz for compression (thanks Chris R.).
% 130905 Avoid the missing-field error for DTI data with 2 excitations.
% Protect GUI from command line plotting.
% 130912 Use lDelayTimeInTR for slice_dur, possibly useful for old data.
% 130916 Store B_matrix for DTI image, if exists.
% 130919 Work for GE and Philips dicom at Chris R website.
% 130922 Remove dependence on normc from nnet toolbox (thank Zhiwei);
% 130923 Work for Philips PAR/REC pair files.
% 130926 Take care of non-mosaic DTI for Siemens (img/bval/bvec);
% 130930 Use verify_slice_dir subfun to get slice_dir even for a single file.
% 131001 dicm_hdr can deal with VR of SQ. This slows down it a little.
% 131002 Avoid fullfile for cellstr input (not supported in old matlab).
% 131006 Tweak dicm_hdr for multiframe dicom (some bug fixes);
% First working version for multiframe (tested with Philips dicom).
% 131009 Put dicm_hdr, dicm_img, dicm_dict outside this file;
% dicm_hdr can read implicit VR, and is faster with single fread;
% Fix problem in gzipOS when folder name contains space.
% 131020 Make TR & ProtocolName non-mandatory; Set cal_min & cal_max.
% 131021 Implement conversion for AFNI HEAD/BRIK.
% 131024 Bug fix for dealing with current folder as src folder.
% 131029 Bug fix: Siemens, 2D, non-mosaic, rev-num slices were flipped.
% 131105 DTI parameters: field names more consistent across vendors;
% Read DTI flds in save_dti_para for GE/Philips (make others faster);
% Convert Philips bvec from deg into vector (need to be verified).
% 131114 Treak for multiframe dicm_hdr: MUCH faster by using only 1,2,n frames;
% Bug fix for Philips multiframe DTI parameters;
% Split multiframe Philips B0 map into mag and phase nii.
% 131117 Make the order of phase/mag image in Philips B0 map irrelevant.
% 131219 Write warning message to a file in data folder (Gui's suggestion).
% 140120 Bug fix in save_dti_para due to missing Manufacturer (Thank Paul).
% 140121 Allow missing instance at beginning of a series.
% 140123 save_nii: bug fix for gzip.m detection, take care of ~ as home dir.
% 140206 bug fix: MoCo detetion bug introduced by removing empty cell earlier.
% 140223 add missing-file check for Philips data by slice locations.
% 140312 use slice timing to set slice_code for both GE and Siemens.
% Interleaved order was wrong for GE data with even number of slices.
% 140317 Use MosaicRefAcqTimes from last vol for multiband (thank Chris).
% Don't re-orient fieldmap, so make FSL happy in case of non_axial.
% Ugly fix for wrong dicom item VR 'OB': Avoid using main header
% in csa_header(), convert DTI parameters to correct type.
% 140319 Store SliceTiming field in dcmHeaders.mat for FSL custom slice timing.
% Re-orient even if flipping slices for 2D MRAcquisitionType.
% 140324 Not set cal_min, cal_max anymore.
% 140327 Return unconverted subject names in 2nd output.
% 140401 Always flip image so phase dir is correct.
% 140409 Store nii extension (not enabled due to nifti ext issue).
% 140501 Fix for GE: use LocationsInAcquisition to replace ImagesInAcquisition;
% isDTI=DiffusionDirection>0; Gradient already in image reference.
% 140505 Always re-orient DTI. bvec fix for GE DTI (thx Chris).
% 140506 Remove last DTI vol if it is computed ADC (as dcm2niix);
% Use SeriesDescription to replace ProtocolName for file name;
% Improved dim_info and phase direction.
% 140512 Decode GE ProtocolDataBlock for phase direction;
% strtrim SeriesDescription for nii file name.
% 140513 change stored phase direction to image reference for FSL unwarp;
% Simplify code for dim_info.
% 140516 Switch back to ProtocolName for SIEMENS to take care of MOCO series;
% Detect Philips XYTZ (for multi files) during dicom check;
% Work for GE interleaved slices even if InstanceNumber is in time order;
% Do ImagePositionPatient check for all vendors;
% Simplify code for save_dti_para.
% 140517 Store img with first dim flipped, to take care of DTI bvec problems.
% 140522 Use SliceNormalVector for mosaic slice_dir, so no worry for revNumb;
% Bug fix for interleaved descending slice_code.
% 140525 xform sliceCenter to SliceLocation in verify_slice_dir.
% 140526 Take care of non-unique ixyz.
% 140608 Bug fix for GE interleaved slices;
% Take care all ixyz, put verify_slice_dir into xform_mat.
% 140610 Compute readout time for DTI, rather than dwell time.
% 140621 Support tgz file as data source.
% 140716 Bug fix due to empty src for GUI subject option.
% 140808 Simplify mosaic detection, and remove isMosaic.
% 140816 Simplify DTI detection.
% 140911 Minor fix for Siemens ProtocolName for error message.
% 141016 Remember GUI settings from last conversion;
% Make multi-subject error message friendly.
% 141023 Get LocationsInAcquisition for GE multiframe dicom.
% 141024 Use unique ImagePositionPatient to determine LocationsInAcquisition.
% 141028 Use matlabpool if available and worthy.
% 141125 Store NumberOfTemporalPositions in dicom header.
% 141128 Minor tweaks for Octave 3.8.1 command line (GUI not working).
% 141216 Use ImagePositionPatient to derive SliceThickness if possible.
% 141217 Override LocationsInAcquisition with computed nSL (thx Luigi);
% Check RescaleIntercept and RescaleSlope consistency.
% 141218 Allow 1e-4 diff for ImagePositionPatient of same slice location.
% 141223 multiFrameFields: return earlier if only single frame (thx Sander);
% No re-orient for single slice (otherwise problem for mricron to read).
% 141224 mos2vol: use nSL loop (faster unless many slices).
% 141229 Save nii ext (ecode=40) if FSL is detected & it is not 5.0.5/5.0.6.
% 141230 nojvm: no matlabpool; no dicm_hdr progress due to '\b' issue for WIN.
% 150109 dicm_img(s, 0) to follow the update for dicm_img.
% 150112 Use nii_tool.m, remove make_nii, save_nii etc from this file.
% 150115 Allow SamplesPerPixel>1, but likely not very useful.
% 150117 Store seq name in intent_name.
% 150119 Add phase img detection for Philips.
% 150120 No fieldmap file skip by EchoTime: keep all data by using EchoNumber.
% 150209 Add more output format for SPM style: 3D output;
% GUI includes SPM 3D, separates GZ option.
% 150211 No missing file check for all vendors, relying on ImagePosition check;
% csa_header() relies on dicm_hdr decoding (avoid error on old data);
% Deal with dim3-RGB and dim4-frames due to dicm_img.m update.
% 150222 Remove useless, mis-used TriggerTime for partial hdr; also B_matrix.
% 150302 No hardcoded sign change for DTI bvec, except for GE;
% set_nii_hdr: do flip only once after permute;
% 150303 Bug fix for phPos: result was right by lucky mistake;
% Progress shows nii dim, more informative than number of files.
% 150305 Replace null with cross: null gives inconsistent signs;
% Use SPM method for xform: account for shear; no qform setting if shear.
% 150306 GE: fully sort slices by loc to ease bvec sign (test data needed);
% bvec sign simplified by above sort & corrected R for Philips/Siemens.
% 150309 GUI: added the little popup for 'about/license'.
% 150323 Siemens non-mosaic: timing from ucMode, AcquisitionTime(disabled).
% 150324 mandatory flds reduced to 5; get info by asc_header if possible;
% 150325 Use SeriesInstanceUID to take care of multiple Study and PatientName;
% Remove 5th input (subj); GUI updated; subjName in file name if needed;
% Deal with MoCo series by output file names;
% Convert GLM and DTI junk too; no Manufacturer check in advance.
% 150405 Implement BrainVoyager dmr/fmr/vmr conversion; GUI updated accordingly.
% 150413 InstanceNumber is not mandatory (now total 4);
% Check missing files for non-DTI mosaic by InstanceNumber.
% 150418 phaseDirection: bug fix for Philips, simplify for others.
% 150423 fix matlabpool for later matlab versions; no auto-close anymore;
% GUI figure handle can't be uint32 for matlab 2015;
% Turn off saveExt40: FSL 5.0.8 may read vox_offset as 352.
% 150430 xform_mat: GE, no LastScanLoc needed since sorted by ImagePosition.
% 150508 csa2pos: bug fix for revNum, iSL==1; treat dInPlaneRot specially.
% 150514 set_nii_ext: start to store txt edata (ecode=6).
% Avoid dict change in dicm_hdr due to vendor change (GE/Philips faster);
% 150517 Octave compatibility fix in multiple files.
% 150526 multiFrameFields: LocationsInAcquisition by ImagePosition if needed.
% 150531 Check slice loc for all volumes to catch missing files (thx CarloR).
% 150604 phaseDirection: typo fix for Philips 'RLAPFH'; Show converter version.
% 150606 csa_header read both CSA image/series header.
% 150609 No t_unit and SliceTiming for DTI.
% 150613 mb_slicetiming: try to fix SOME broken multiband slice timing.
% 150620 use 'bval' for nii.ext and dcmHeaders.mat, so keep original B_value.
% 150910 bug fix for scl_slope/inter: missing double for max/min(nii.img(:)).
% 150924 PAR: fix weird SliceNumber; fix mean-ADC removal if not last vol.
% 150925 Bug fix for nSL=1 (vol-dim was at slice-dim);
% 150926 multiFrameFields: add SliceNumber & simplify code;
% save_dti_para: tidy format; try to avoid genvarname.
% 150927 Repalce misused length with numel in all files.
% 150928 checkImagePosition: skip most irregular spacing.
% 150929 Take care of SL order for regular dicom: GE no longer special case.
% 150930 Remove slice_dir guess; Use NiftiName for error info.
% 151115 GUI: remove srcType; Implement drag&drop for src and dst.
% 151117 save_json proposed by ChrisG; won't flush nii_viewer para.
% 151212 Bug fix for missing pref_file.
% 151217 gui callback uses subfunc directly, also include fh as argument.
% 151221 dim_info stores phaseDir at highest 2 bits (1 pos, 2 neg, 0 unknown).
% 160110 Implement "Check update" based on findjobj; Preference method updated.
% 160112 SeriesInstanceUID & SeriesNumber only need one (thx DavidR).
% 160115 checkUpdate: fix problem to download & unzip to pwd.
% 160127 dicm_hdr & dicm_img: support big endian dicom.
% 160229 flip now makes det<0, instead negative 1st axis (cor slice affected).
% 160304 undo some changes on 140808 so it works for syngo 2004 phase masaic.
% 160309 nMosaic(): use CSAHeader to detect above unlabeled mosaic.
% 160324 nMosaic(): unsecure fix for dicom without CSA header.
% 160329 GUI: add link to the JNM paper about dicom to nifti conversion.
% 160330 nMosaic(): take care of case of uc2DInterpolation.
% 160404 Bug fix: put back nFile<2 continue for series check.
% 160405 Remove 4th input arg MoCoOption: always convert all series.
% 160405 nMosaic(): get nMos by finding zeros in img.
% 160407 remove ang2vec: likely never used and may be wrong.
% 160409 multi .m files: use sscanf/strfind/regexp, avoid str2double/strtok.
% 160504 asc_header: ignore invalid CSASeriesHeaderInfo in B15 (thx LaureSA).
% 160512 get_dti_para: fix bvec sign for GE cor/sag slices (thx paul for data).
% 160514 csa2pos: make it safer so it won't err.
% 160516 checkImagePosition: assign isTZ for missing files (thx TanH).
% 160519 set nii.hdr.slice_duration for MB although it is useless.
% 160601 Update ReadoutSeconds, and store it even if ~isDTI.
% 160607 Avoid skipping series by ignoring empty-image dicom (thx QR).
% 160610 Add pref save_patientName and use_parfor; simplify save_json flag.
% 160807 Store InversionTime for nii ext and json.
% 160826 Add pref use_seriesUID to take care of missed-up SeriesIntanceUID.
% 160829 fix problem with large SeriesNumber; only 3 dicm fields are must.
% 160901 Put pref onto GUI.
% 160920 Convert series with varying Rescale slope/inter.
% 160921 Quick bug fix introduced on 160920: slope/inter applied for 2nd+ files.
% 161129 Bug fix for irregular slice order in Philips multiframe dicm.
% 161216 xform_mat: only override SliceThickness if it is >1% off.
% 161227 Convert a series by ignoring the only inconsistent file;
% checkImagePositions(): allow 10% error for gantry tilt (thx Qinwan).
% 161229 xform CT img with gantry tilt; add some flds in ext for CT.
% 170202 nMosaic(): bug fix for using LocationsInAcquisition.
% 170211 implement no_save for nii_viewer: return first nii without saving;
% Bug fix: double(val) for fldsCk (needed for Rows and Columns).
% 170225 nMosaic: minor fix.
% 170320 check_ipp: slice tol = max(diff(sort(ipp)))/100. Thx navot.
% 170322 split_philips_phase: bug fix for vol>2. Thx RobertW.
% 170403 save_jason: add DelayTime for BIDS.
% 170404 set MB slice_code to 0 to avoid FreeSurfer error. Thx JacobM.
% 170417 checkUpdate(): use 'user_version' due to Matlab Central web change.
% 170625 phaseDirection(): GE VIEWORDER update due to dicm_hdr() update.
% 170720 Allow regularly missing InstanceNumbers, like CMRR ISSS.
% 170810 Use GE SLICEORDER for SliceTiming if needed (thx PatrickS).
% 170826 Use 'VolumeTiming' for missing volumes based on BIDS.
% 170923 Correct readout (thx Chris R and MH); Always store readout in descrip;
% 170924 Bug fix for long file name (avoid genvarname now).
% 170927 Store TE in descrip even if multiple TEs.
% 171211 Make it work for Siemens multiframe dicom (seems 3D only).
% 180116 Bug fix for EchoTime1 for phase image (thx DylanW)
% 180219 json: PhaseEncodingDirection use ijk, fix pf.save_PatientName (thx MichaelD)
% 180312 json: ImageType uses BIDS format (thx ChrisR).
% 180419 bug fix for long file name (thx NedaK).
% 180430 store VolumeTiming from FrameReferenceTime (thx ChrisR).
% 180519 get_dti_para: bug fix to remove Philips ADC vol (thx ChrisR).
% 180520 Make copy for vida CSA, so asc_header/csa_header faster if non-Siemens.
% 180523 set_nii_hdr: use MRScaleSlope for Philips, same as dcm2niiX default.
% 180526 split_philips_phase: fix the long time slope/inter bug for phase image;
% move some code (eg SliceTiming related) out of main function.
% 180527 fix vida SliceTiming unit, but now turn it off, and rely on ucMode.
% 180530 store EchoTimes and CardiacTriggerDelayTimes;
% split_components: not only phase, json for each file (thx ChrisR).
% 180601 use SortFrames for multiframe and PAR (thx JulienB & ChrisR);
% 180602 extract sort_frames() for multiFrameFields() and philips_par()
% 180605 multiFrameFields: B=0 to first vol.
% 180614 Implement scale_16bit: free precision for tools using 16-bit datatype.
% 180619 use GetFullPath from Jan: (thx JulienB).
% 180721 accept mixture of files and folders as input; GUI uses jFileChooser().
% 180914 support UIH dicm, both GRID (mosaic) and regular.
% 180922 fix for UIH masaic -1 col; GE phPos from dcm2niix.
% 190122 add BIDS support. [email protected]
% TODO: need testing files to figure out following parameters:
% flag for MOCO series for GE/Philips
% GE non-axial slice (phase: ROW) bvec sign
% Phase image flag for GE
if nargout, varargout{1} = ''; end
if nargin==3 && ischar(fmt) && strcmp(fmt, 'func_handle') % special purpose
varargout{1} = str2func(niiFolder);
return;
end
%% Deal with output format first, and error out if invalid
if nargin<3 || isempty(fmt), fmt = 1; end % default .nii.gz
no_save = ischar(fmt) && strcmp(fmt, 'no_save');
if no_save, fmt = 'nii'; end
bids = false;
if ischar(fmt) && strcmpi(fmt,'BIDS')
bids = true;
fmt = '.nii.gz';
end
if ischar(fmt) && strcmpi(fmt,'BIDSNII')
bids = true;
fmt = '.nii';
end
if bids && verLessThan('matlab','9.4')
fprintf('BIDS conversion requires MATLAB R2018a or more. return.')
end
if (isnumeric(fmt) && any(fmt==[0 1 4 5])) || ...
(ischar(fmt) && ~isempty(regexpi(fmt, 'nii')))
ext = '.nii';
elseif (isnumeric(fmt) && any(fmt==[2 3 6 7])) || (ischar(fmt) && ...
(~isempty(regexpi(fmt, 'hdr')) || ~isempty(regexpi(fmt, 'img'))))
ext = '.img';
else
error(' Invalid output file format (the 3rd input).');
end
if (isnumeric(fmt) && mod(fmt,2)) || (ischar(fmt) && ~isempty(regexpi(fmt, '.gz')))
ext = [ext '.gz']; % gzip file
end
rst3D = (isnumeric(fmt) && fmt>3) || (ischar(fmt) && ~isempty(regexpi(fmt, '3D')));
if nargin<1 || isempty(src) || (nargin<2 || isempty(niiFolder))
create_gui; % show GUI if input is not enough
return;
end
%% Deal with niiFolder
if ~isdir(niiFolder), mkdir(niiFolder); end
niiFolder = [GetFullPath(niiFolder) filesep];
converter = ['dicm2nii.m ' getVersion];
if errorLog('', niiFolder) && ~no_save % remember niiFolder for later call
more off;
disp(['Xiangrui Li''s ' converter ' (feedback to [email protected])']);
end
%% Deal with data source
tic;
if isnumeric(src)
error('Invalid dicom source.');
elseif iscellstr(src) % multiple files/folders
fnames = {};
for i = 1:numel(src)
if isdir(src{i})
fnames = [fnames filesInDir(src{i})];
else
a = dir(src{i});
if isempty(a), continue; end
dcmFolder = fileparts(GetFullPath(src{i}));
fnames = [fnames fullfile(dcmFolder, a.name)];
end
end
elseif isdir(src) % folder
fnames = filesInDir(src);
elseif ~exist(src, 'file') % like input: run1*.dcm
fnames = dir(src);
if isempty(fnames), error('%s does not exist.', src); end
fnames([fnames.isdir]) = [];
dcmFolder = filepars(GetFullPath(src));
fnames = strcat(dcmFolder, filesep, {fnames.name});
elseif ischar(src) % 1 dicom or zip/tgz file
dcmFolder = fileparts(GetFullPath(src));
unzip_cmd = compress_func(src);
if isempty(unzip_cmd)
fnames = dir(src);
fnames = strcat(dcmFolder, filesep, {fnames.name});
else % unzip if compressed file is the source
[~, fname, ext1] = fileparts(src);
dcmFolder = sprintf('%stmpDcm%s/', niiFolder, fname);
if ~isdir(dcmFolder)
mkdir(dcmFolder);
delTmpDir = onCleanup(@() rmdir(dcmFolder, 's'));
end
disp(['Extracting files from ' fname ext1 ' ...']);
if strcmp(unzip_cmd, 'unzip')
cmd = sprintf('unzip -qq -o %s -d %s', src, dcmFolder);
err = system(cmd); % first try system unzip
if err, unzip(src, dcmFolder); end % Matlab's unzip is too slow
elseif strcmp(unzip_cmd, 'untar')
if isempty(which('untar'))
error('No untar found in matlab path.');
end
untar(src, dcmFolder);
end
fnames = filesInDir(dcmFolder);
end
else
error('Unknown dicom source.');
end
nFile = numel(fnames);
if nFile<1, error(' No files found in the data source.'); end
%% user preference
pf.save_patientName = getpref('dicm2nii_gui_para', 'save_patientName', true);
pf.save_json = getpref('dicm2nii_gui_para', 'save_json', false);
pf.use_parfor = false; % getpref('dicm2nii_gui_para', 'use_parfor', true);
pf.use_seriesUID = getpref('dicm2nii_gui_para', 'use_seriesUID', true);
pf.lefthand = getpref('dicm2nii_gui_para', 'lefthand', true);
pf.scale_16bit = getpref('dicm2nii_gui_para', 'scale_16bit', false);
%% Parsing out varargin (optional input) if there is any: added by Wani, 10/2/2017
addtask = false;
for i = 1:length(varargin)
if ischar(varargin{i})
switch varargin{i}
case 'save_json'
pf.save_json = true;
case 'taskname'
addtask = true;
taskname = varargin{i+1};
case 'use_parfor'
pf.use_parfor = true;
end
end
end
%% Check each file, store partial header in cell array hh
% first 2 fields are must. First 10 indexed in code
flds = {'Columns' 'Rows' 'BitsAllocated' 'SeriesInstanceUID' 'SeriesNumber' ...
'ImageOrientationPatient' 'ImagePositionPatient' 'PixelSpacing' ...
'SliceThickness' 'SpacingBetweenSlices' ... % these 10 indexed in code
'PixelRepresentation' 'BitsStored' 'HighBit' 'SamplesPerPixel' ...
'PlanarConfiguration' 'EchoTime' 'RescaleIntercept' 'RescaleSlope' ...
'InstanceNumber' 'NumberOfFrames' 'B_value' 'DiffusionGradientDirection' ...
'RTIA_timer' 'RBMoCoTrans' 'RBMoCoRot' 'AcquisitionNumber'};
dict = dicm_dict('SIEMENS', flds); % dicm_hdr will update vendor if needed
% read header for all files, use parpool if available and worthy
if ~no_save, fprintf('Validating %g files ...\n', nFile); end
hh = cell(1, nFile); errStr = cell(1, nFile);
doParFor = pf.use_parfor && nFile>2000 && useParTool;
for k = 1:nFile
[hh{k}, errStr{k}, dict] = dicm_hdr(fnames{k}, dict);
if doParFor && ~isempty(hh{k}) % parfor wont allow updating dict
parfor i = k+1:nFile
[hh{i}, errStr{i}] = dicm_hdr(fnames{i}, dict);
end
break;
end
end
%% sort headers into cell h by SeriesInstanceUID, EchoTime and InstanceNumber
h = {}; % in case of no dicom files at all
errInfo = '';
seriesUIDs = {}; ETs = {};
for k = 1:nFile
s = hh{k};
if isempty(s) || any(~isfield(s, flds(1:2))) || ~isfield(s, 'PixelData') ...
|| (isstruct(s.PixelData) && s.PixelData.Bytes<1)
if ~isempty(errStr{k}) % && isempty(strfind(errInfo, errStr{k}))
errInfo = sprintf('%s\n%s\n', errInfo, errStr{k});
end
continue; % skip the file
end
if isfield(s, flds{4}) && (pf.use_seriesUID || ~isfield(s, 'SeriesNumber'))
sUID = s.SeriesInstanceUID;
else
if isfield(s, 'SeriesNumber'), sN = s.SeriesNumber;
else, sN = fix(toc*1e6);
end
sUID = num2str(sN); % make up UID
if isfield(s, 'SeriesDescription')
sUID = [s.SeriesDescription sUID];
end
end
m = find(strcmp(sUID, seriesUIDs));
if isempty(m)
m = numel(seriesUIDs)+1;
seriesUIDs{m} = sUID;
ETs{m} = [];
end
% EchoTime is needed for Siemens fieldmap mag series
et = tryGetField(s, 'EchoTime');
if isempty(et), i = 1;
else
i = find(et == ETs{m}); % strict equal?
if isempty(i)
i = numel(ETs{m}) + 1;
ETs{m}(i) = et;
if i>1
[ETs{m}, ind] = sort(ETs{m});
i = find(et == ETs{m});
h{m}{end+1}{1} = [];
h{m} = h{m}(ind);
end
end
end
j = tryGetField(s, 'InstanceNumber');
if isempty(j) || j<1
try j = numel(h{m}{i}) + 1;
catch, j = 1;
end
end
h{m}{i}{j} = s; % sort partial header
end
clear hh errStr;
%% Check headers: remove dim-inconsistent series
nRun = numel(h);
if nRun<1 % no valid series
errorLog(sprintf('No valid files found:\n%s.', errInfo));
return;
end
keep = true(1, nRun); % true for useful runs
subjs = cell(1, nRun); vendor = cell(1, nRun);
sNs = ones(1, nRun); studyIDs = cell(1, nRun);
fldsCk = {'ImageOrientationPatient' 'NumberOfFrames' 'Columns' 'Rows' ...
'PixelSpacing' 'RescaleIntercept' 'RescaleSlope' 'SamplesPerPixel' ...
'SpacingBetweenSlices' 'SliceThickness'}; % last for thickness
for i = 1:nRun
h{i} = [h{i}{:}]; % concatenate different EchoTime
ind = cellfun(@isempty, h{i});
h{i}(ind) = []; % remove all empty cell for all vendors
s = h{i}{1};
if ~isfield(s, 'LastFile') % avoid re-read for PAR/HEAD/BV file
s = dicm_hdr(s.Filename); % full header for 1st file
end
if ~isfield(s, 'Manufacturer'), s.Manufacturer = 'Unknown'; end
subjs{i} = PatientName(s);
vendor{i} = s.Manufacturer;
if isfield(s, 'SeriesNumber'), sNs(i) = s.SeriesNumber;
else, sNs(i) = fix(toc*1e6);
end
studyIDs{i} = tryGetField(s, 'StudyID', '1');
series = sprintf('Subject %s, %s (Series %g)', subjs{i}, ProtocolName(s), sNs(i));
s = multiFrameFields(s); % no-op if non multi-frame
if isempty(s), keep(i) = 0; continue; end % invalid multiframe series
s.isDTI = isDTI(s);
if ~isfield(s, 'AcquisitionDateTime') % assumption: 1st instance is earliest
try s.AcquisitionDateTime = [s.AcquisitionDate s.AcquisitionTime]; end
end
h{i}{1} = s; % update record in case of full hdr or multiframe
nFile = numel(h{i});
if nFile>1 && tryGetField(s, 'NumberOfFrames', 1) > 1 % seen in vida
for k = 2:nFile % this can be slow
h{i}{k} = dicm_hdr(h{i}{k}.Filename); % full header
h{i}{k} = multiFrameFields(h{i}{k});
end
if ~isfield(s, 'EchoTimes') && isfield(s, 'EchoTime')
h{i}{1}.EchoTimes = nan(1, nFile);
for k = 1:nFile, h{i}{1}.EchoTimes(k) = h{i}{k}.EchoTime; end
end
end
% check consistency in 'fldsCk'
nFlds = numel(fldsCk);
if isfield(s, 'SpacingBetweenSlices'), nFlds = nFlds - 1; end % check 1 of 2
for k = 1:nFlds*(nFile>1)
if isfield(s, fldsCk{k}), val = s.(fldsCk{k}); else, continue; end
val = repmat(double(val), [1 nFile]);
for j = 2:nFile
if isfield(h{i}{j}, fldsCk{k}), val(:,j) = h{i}{j}.(fldsCk{k});
else, keep(i) = 0; break;
end
end
if ~keep(i), break; end % skip silently
ind = any(abs(bsxfun(@minus, val, val(:,1))) > 1e-4, 1);
if sum(ind)>1 % try 2nd, in case only 1st is inconsistent
ind = any(abs(bsxfun(@minus, val, val(:,2))) > 1e-4, 1);
end
if ~any(ind), continue; end % good
if any(strcmp(fldsCk{k}, {'RescaleIntercept' 'RescaleSlope'}))
h{i}{1}.ApplyRescale = true;
continue;
end
if numel(ind)>2 && sum(ind)==1 % 2+ files but only 1 inconsistent
h{i}(ind) = []; % remove first or last, but keep the series
nFile = nFile - 1;
if ind(1) % re-do full header for new 1st file
s = dicm_hdr(h{i}{1}.Filename);
s.isDTI = isDTI(s);
h{i}{1} = s;
end
else
errorLog(['Inconsistent ''' fldsCk{k} ''' for ' series '. Series skipped.']);
keep(i) = 0; break;
end
end
nSL = nMosaic(s); % nSL>1 for mosaic
if ~isempty(nSL) && nSL>1
h{i}{1}.isMos = true;
h{i}{1}.LocationsInAcquisition = nSL;
if s.isDTI, continue; end % allow missing directions for DTI
a = zeros(1, nFile);
for j = 1:nFile, a(j) = tryGetField(h{i}{j}, 'InstanceNumber', 1); end
if any(diff(a) ~= 1) % like CMRR ISSS seq or multi echo. Error for UIH
errorLog(['InstanceNumber discontinuity detected for ' series '.' ...
'See VolumeTiming in NIfTI ext or dcmHeaders.mat.']);
dict = dicm_dict('', {'AcquisitionDate' 'AcquisitionTime'});
vTime = nan(1, nFile);
for j = 1:nFile
s2 = dicm_hdr(h{i}{j}.Filename, dict);
dt = [s2.AcquisitionDate s2.AcquisitionTime];
vTime(j) = datenum(dt, 'yyyymmddHHMMSS.fff');
end
vTime = vTime - min(vTime);
h{i}{1}.VolumeTiming = vTime * 86400; % day to seconds
end
continue; % no other check for mosaic
end
if ~keep(i) || nFile<2 || ~isfield(s, 'ImagePositionPatient'), continue; end
if tryGetField(s, 'NumberOfFrames', 1) > 1, continue; end % Siemens Vida
ipp = zeros(nFile, 1);
iSL = xform_mat(s); iSL = iSL(3);
for j = 1:nFile, ipp(j,:) = h{i}{j}.ImagePositionPatient(iSL); end
gantryTilt = abs(tryGetField(s, 'GantryDetectorTilt', 0)) > 0.1;
[err, nSL, sliceN, isTZ] = checkImagePosition(ipp, gantryTilt);
if ~isempty(err)
errorLog([err ' for ' series '. Series skipped.']);
keep(i) = 0; continue; % skip
end
h{i}{1}.LocationsInAcquisition = uint16(nSL); % best way for nSL?
nVol = nFile / nSL;
if isTZ % Philips
ind = reshape(1:nFile, [nVol nSL])';
h{i} = h{i}(ind(:));
end
% re-order slices within vol. No SliceNumber since files are organized
if all(diff(sliceN, 2) == 0), continue; end % either 1:nSL or nSL:-1:1
if sliceN(end) == 1, sliceN = sliceN(nSL:-1:1); end % not important
inc = repmat((0:nVol-1)*nSL, nSL, 1);
ind = repmat(sliceN(:), nVol, 1) + inc(:);
h{i} = h{i}(ind); % sorted by slice locations
if sliceN(1) == 1, continue; end % first file kept: following update h{i}{1}
h{i}{1} = dicm_hdr(h{i}{1}.Filename); % read full hdr
s = h{i}{sliceN==1}; % original first file
fldsCp = {'AcquisitionDateTime' 'isDTI' 'LocationsInAcquisition'};
for j = 1:numel(fldsCp)
if isfield(h{i}{1}, fldsCk{k}), h{i}{1}.(fldsCp{j}) = s.(fldsCp{j}); end
end
end
h = h(keep); sNs = sNs(keep); studyIDs = studyIDs(keep);
subjs = subjs(keep); vendor = vendor(keep);
%% sort h by PatientName, then StudyID, then SeriesNumber
% Also get correct order for subjs/studyIDs/nStudy/sNs for nii file names
[subjs, ind] = sort(subjs);
subj = unique(subjs);
h = h(ind); sNs = sNs(ind); studyIDs = studyIDs(ind); % by subjs now
nStudy = ones(1, nRun); % one for each series
for i = 1:numel(subj)
iSub = find(strcmp(subj{i}, subjs));
study = studyIDs(iSub);
[study, iStudy] = sort(study); % by study for each subject
a = h(iSub); h(iSub) = a(iStudy);
a = sNs(iSub); sNs(iSub) = a(iStudy);
studyIDs(iSub) = study; % done for h/sNs/studyIDs by studyIDs for a subj
uID = unique(study);
nStudy(iSub) = numel(uID);
for k = 1:numel(uID) % now sort h/sNs by sNs for each studyID
iStudy = strcmp(uID{k}, study);
ind = iSub(iStudy);
[sNs(ind), iSN] = sort(sNs(ind));
a = h(ind); h(ind) = a(iSN);
end
end
%% Generate unique result file names
% Unique names are in format of SeriesDescription_s007. Special cases are:
% for phase image, such as field_map phase, append '_phase' to the name;
% for MoCo series, append '_MoCo' to the name if both series are present.
% for multiple subjs, it is SeriesDescription_subj_s007
% for multiple Study, it is SeriesDescription_subj_Study1_s007
nRun = numel(h); % update it, since we have removed some
if nRun<1
errorLog('No valid series found');
return;
end
rNames = cell(1, nRun);
multiSubj = numel(subj)>1;
j_s = nan(nRun, 1); % index-1 for _s003. needed if 4+ length SeriesNumbers
maxLen = namelengthmax - 3;
for i = 1:nRun
s = h{i}{1};
sN = sNs(i);
a = strtrim(ProtocolName(s));
if isPhase(s), a = [a '_phase']; end % phase image
if i>1 && sN-sNs(i-1)==1 && isType(s, '\MOCO\'), a = [a '_MoCo']; end
if multiSubj, a = [a '_' subjs{i}]; end
if nStudy(i)>1, a = [a '_Study' studyIDs{i}]; end
if ~isstrprop(a(1), 'alpha'), a = ['x' a]; end % genvarname behavior
a(~isstrprop(a, 'alphanum')) = '_'; % make str valid for field name
a = regexprep(a, '_{2,}', '_'); % remove repeated underscore
if sN>100 && strncmp(s.Manufacturer, 'Philips', 7)
sN = tryGetField(s, 'AcquisitionNumber', floor(sN/100));
end
j_s(i) = numel(a);
rNames{i} = sprintf('%s_s%03.0f', a, sN);
d = numel(rNames{i}) - maxLen;
if d>0, rNames{i}(j_s(i)+(-d+1:0)) = ''; j_s(i) = j_s(i)-d; end % keep _s007
end
vendor = strtok(unique(vendor));
if nargout>0, varargout{1} = subj; end % return converted subject IDs
% After following sort, we need to compare only neighboring names. Remove
% _s007 if there is no conflict. Have to ignore letter case for Windows & MAC
fnames = rNames; % copy it, reserve letter cases
[rNames, iRuns] = sort(lower(fnames));
j_s = j_s(iRuns);
for i = 1:nRun
if i>1 && strcmp(rNames{i}, rNames{i-1}) % truncated StudyID to PatientName
a = num2str(i);
rNames{i}(j_s(i)+(-numel(a)+1:0)) = a; % not 100% unique
end
a = rNames{i}(1:j_s(i)); % remove _s003
% no conflict with both previous and next name
if nRun==1 || ... % only one run
(i==1 && ~strcmpi(a, rNames{2}(1:j_s(2)))) || ... % first
(i==nRun && ~strcmpi(a, rNames{i-1}(1:j_s(i-1)))) || ... % last
(i>1 && i<nRun && ~strcmpi(a, rNames{i-1}(1:j_s(i-1))) ...
&& ~strcmpi(a, rNames{i+1}(1:j_s(i+1)))) % middle ones
fnames{iRuns(i)}(j_s(i)+1:end) = [];
end
end
if numel(unique(fnames)) < nRun % may happen to user-modified dicom/par
fnames = matlab.lang.makeUniqueStrings(fnames); % since R2014a
end
fmtStr = sprintf(' %%-%gs %%dx%%dx%%dx%%d\n', max(cellfun(@numel, fnames))+12);
%% Now ready to convert nii series by series
subjStr = sprintf('''%s'', ', subj{:}); subjStr(end+(-1:0)) = [];
vendor = sprintf('%s, ', vendor{:}); vendor(end+(-1:0)) = [];
if ~no_save
fprintf('Converting %g series (%s) into %g-D %s: subject %s\n', ...
nRun, vendor, 4-rst3D, ext, subjStr);
end
%% Parse BIDS
if bids
if multiSubj
fprintf('Multiple subjects detected!!!!! Skipping...\nPlease convert subjects one by one with BIDS options\n')
fprintf('%s\n',subj{:})
return;
end
% Table: subject Name
try
asciiInds=[1:47 58:64 91:96 123:127];
for j=1:numel(asciiInds)
subj=strrep(subj,char(asciiInds(j)),'');
end
Subject = subj;
catch
Subject = {'01'};
end
Session = {'01'};
S = table(Subject,Session);
% Table: Type/Modality
valueset = {'skip','skip';
'anat','T1w';
'anat','T2w';
'anat','T1rho';
'anat','T1map';
'anat','T2map';
'anat','T2star';
'anat','FLAIR';
'anat','FLASH';
'anat','PD';
'anat','PDmap';
'dwi' ,'dwi';
'fmap','phasediff';
'fmap','phase1';
'fmap','phase2';
'fmap','magnitude1';
'fmap','magnitude2';
'fmap','fieldmap'};
Modality = categorical(repmat({'skip'},[length(fnames),1]),valueset(:,2));
Type = categorical(repmat({'skip'},[length(fnames),1]),unique(valueset(:,1)));
Name = fnames';
T = table(Name,Type,Modality);
ModalityTablePref = getpref('dicm2nii_gui_para', 'ModalityTable', T);
for i = 1:nRun
match = strcmp(T{i,1},ModalityTablePref{:,1});
if any(match)
T{i,2:3} = ModalityTablePref{match,2:3};
end
end
% GUI
scrSz = get(0, 'ScreenSize');
clr = [1 1 1]*206/256;
hf = uifigure('bids' * 256.^(0:3)','Position',[min(scrSz(4)+420,620) scrSz(4)-600 420 300],'Color', clr);
set(hf,'Name', 'dicm2nii - BIDS Converter', 'NumberTitle', 'off')
% tables
TS = uitable(hf,'Data',S,'Position',[20 hf.Position(4)-110 hf.Position(3)-160 90]);
TT = uitable(hf,'Data',T,'Position',[20 20 hf.Position(3)-160 hf.Position(4)-120]);
TS.ColumnEditable = [true true];
TT.ColumnEditable = [false true true];
setappdata(0,'ModalityTable',TT.Data)
setappdata(0,'SubjectTable',TS.Data)
% button
B = uibutton(hf,'Position',[hf.Position(3)-120 20 100 30]);
B.Text = 'OK';
B.ButtonPushedFcn = @(btn,event) BtnModalityTable(hf,TT, TS);
waitfor(hf);
% get results
ModalityTable = getappdata(0,'ModalityTable');
SubjectTable = getappdata(0,'SubjectTable');
% setpref
ModalityTableSavePref = ModalityTable(~any(ismember(ModalityTable{:,2:3},'skip'),2),:);
for imod = 1:size(ModalityTableSavePref,1)
match = strcmp(ModalityTableSavePref{imod,1},ModalityTablePref{:,1});
if any(match) % replace old pref
ModalityTablePref{match,2:3} = ModalityTableSavePref{imod,2:3};
else % append new pref
ModalityTablePref{end+1,1} = ModalityTableSavePref{imod,1};
ModalityTablePref{end,2:3} = ModalityTableSavePref{imod,2:3};
end
end
setpref('dicm2nii_gui_para', 'ModalityTable', ModalityTablePref);
end
%% Convert
for i = 1:nRun
if bids
if any(ismember(ModalityTable{i,2:3},'skip')), continue; end
if isempty(char(SubjectTable{1,2})) % no session
ses = '';
else
ses = ['ses-' char(SubjectTable{1,2})];
end
% folder
modalityfolder = fullfile(['sub-' char(SubjectTable{1,1})],...
ses,...
char(ModalityTable{i,2}));
mkdir(fullfile(niiFolder, modalityfolder));
% filename
fnames{i} = fullfile(modalityfolder,...
['sub-' char(SubjectTable{1,1}) '_' ses '_' char(ModalityTable{i,3})]);
fnames{i} = strrep(fnames{i},'__','_');
end
nFile = numel(h{i});
h{i}{1}.NiftiName = fnames{i}; % for convenience of error info
s = h{i}{1};
if nFile>1 && ~isfield(s, 'LastFile')
h{i}{1}.LastFile = h{i}{nFile}; % store partial last header into 1st
end
for j = 1:nFile
if j==1
img = dicm_img(s, 0); % initialize img with dicm data type
if ndims(img)>4 % err out, likely won't work for other series
error('Image with 5 or more dim not supported: %s', s.NiftiName);
end
applyRescale = tryGetField(s, 'ApplyRescale', false);
if applyRescale, img = single(img); end
else
if j==2, img(:,:,:,:,nFile) = 0; end % pre-allocate for speed
img(:,:,:,:,j) = dicm_img(h{i}{j}, 0);
end
if applyRescale
slope = tryGetField(h{i}{j}, 'RescaleSlope', 1);
inter = tryGetField(h{i}{j}, 'RescaleIntercept', 0);
img(:,:,:,:,j) = img(:,:,:,:,j) * slope + inter;
end
end
if strcmpi(tryGetField(s, 'DataRepresentation', ''), 'COMPLEX')
img = complex(img(:,:,:,1:2:end,:), img(:,:,:,2:2:end,:));
end
[~, ~, d3, d4, ~] = size(img);
if strcmpi(tryGetField(s, 'SignalDomainColumns', ''), 'TIME') % no permute
elseif d3<2 && d4<2, img = permute(img, [1 2 5 3 4]); % remove dim3,4
elseif d4<2, img = permute(img, [1:3 5 4]); % remove dim4: Frames
elseif d3<2, img = permute(img, [1 2 4 5 3]); % remove dim3: RGB
end
nSL = double(tryGetField(s, 'LocationsInAcquisition'));
if tryGetField(s, 'SamplesPerPixel', 1) > 1 % color image
img = permute(img, [1 2 4:8 3]); % put RGB into dim8 for nii_tool
elseif tryGetField(s, 'isMos', false) % mosaic
img = mos2vol(img, nSL, strncmpi(s.Manufacturer, 'UIH', 3));
elseif ndims(img)==3 && ~isempty(nSL) % may need to reshape to 4D
if isfield(s, 'SortFrames'), img = img(:,:,s.SortFrames); end
dim = size(img);
dim(3:4) = [nSL dim(3)/nSL]; % verified integer earlier
img = reshape(img, dim);
end
if any(~isfield(s, flds(6:8))) || ~any(isfield(s, flds(9:10)))
h{i}{1} = csa2pos(h{i}{1}, size(img,3));
end
if isa(img, 'uint16') && max(img(:))<32768
img = int16(img); % use int16 if lossless
end
h{i}{1}.ConversionSoftware = converter;
nii = nii_tool('init', img); % create nii struct based on img
[nii, h{i}] = set_nii_hdr(nii, h{i}, pf); % set most nii hdr
% Save bval and bvec files after bvec perm/sign adjusted in set_nii_hdr
fname = fullfile(niiFolder,fnames{i}); % name without ext
if s.isDTI && ~no_save, save_dti_para(h{i}{1}, fname); end
nii = split_components(nii, h{i}{1}); % split Philips vol components
if no_save % only return the first nii
nii(1).hdr.file_name = [fnames{i} '_no_save.nii'];
nii(1).hdr.magic = 'n+1';
varargout{1} = nii_tool('update', nii(1));
if nRun>1, fprintf(2, 'Only one series is converted.\n'); end
return;
end
for j = 1:numel(nii)
nam = fnames{i};
if numel(nii)>1, nam = nii(j).hdr.file_name; end
fprintf(fmtStr, nam, nii(j).hdr.dim(2:5));
nii(j).ext = set_nii_ext(nii(j).json); % NIfTI extension
if addtask, nii(j).json.TaskName = taskname; end % *** Modified for cocoanlab ***
if pf.save_json, save_json(nii(j).json, fname); end % *** Modified for cocoanlab ***
nii_tool('save', nii(j), fullfile(niiFolder,[nam ext]), rst3D);
end
if isfield(nii(1).hdr, 'hdrTilt')
nii = nii_xform(nii(1), nii.hdr.hdrTilt);
fprintf(fmtStr, [fnames{i} '_Tilt'], nii.hdr.dim(2:5));
nii_tool('save', nii, fullfile(fname, ['_Tilt' ext]), rst3D); % save xformed nii
end
h{i} = h{i}{1}; % keep 1st dicm header only
if isnumeric(h{i}.PixelData), h{i} = rmfield(h{i}, 'PixelData'); end % BV
end
if ~bids
h = cell2struct(h, fnames, 2); % convert into struct
fname = [niiFolder 'dcmHeaders.mat'];
if exist(fname, 'file') % if file exists, we update fields only
S = load(fname);
for i = 1:numel(fnames), S.h.(fnames{i}) = h.(fnames{i}); end
h = S.h;
end
save(fname, 'h', '-v7'); % -v7 better compatibility
else
rmappdata(0,'ModalityTable');
rmappdata(0,'SubjectTable');
end
fprintf('Elapsed time by dicm2nii is %.1f seconds\n\n', toc);
return;
%% Subfunction: return PatientName
function subj = PatientName(s)
subj = tryGetField(s, 'PatientName');
if isempty(subj), subj = tryGetField(s, 'PatientID', 'Anonymous'); end
%% Subfunction: return SeriesDescription
function name = ProtocolName(s)
name = tryGetField(s, 'SeriesDescription');
if isempty(name) || (strncmp(s.Manufacturer, 'SIEMENS', 7) && any(regexp(name, 'MoCoSeries$')))
name = tryGetField(s, 'ProtocolName');
end
if isempty(name), [~, name] = fileparts(s.Filename); end
%% Subfunction: return true if keyword is in s.ImageType
function tf = isType(s, keyword)
typ = tryGetField(s, 'ImageType', '');
tf = ~isempty(strfind(typ, keyword)); %#ok<*STREMP>
%% Subfunction: return true if series is DTI
function tf = isDTI(s)
tf = isType(s, '\DIFFUSION'); % Siemens, Philips
if tf, return; end
if isfield(s, 'ProtocolDataBlock') % GE, not labeled as \DIFFISION
IOPT = tryGetField(s.ProtocolDataBlock, 'IOPT');
if isempty(IOPT), tf = tryGetField(s, 'DiffusionDirection', 0)>0;
else, tf = ~isempty(regexp(IOPT, 'DIFF', 'once'));
end
elseif strncmpi(s.Manufacturer, 'Philips', 7)
tf = strcmp(tryGetField(s, 'MRSeriesDiffusion', 'N'), 'Y');
elseif isfield(s, 'ApplicationCategory') % UIH
tf = ~isempty(regexp(s.ApplicationCategory, 'DTI', 'once'));
elseif isfield(s, 'AcquisitionContrast') % Bruker
tf = ~isempty(regexpi(s.AcquisitionContrast, 'DIFF', 'once'));
else % Some Siemens DTI are not labeled as \DIFFUSION
tf = ~isempty(csa_header(s, 'B_value'));
end
%% Subfunction: return true if series is phase img
function tf = isPhase(s)
tf = isType(s, '\P\') || ...
strcmpi(tryGetField(s, 'ComplexImageComponent', ''), 'PHASE'); % Philips
%% Subfunction: get field if exist, return default value otherwise
function val = tryGetField(s, field, dftVal)
if isfield(s, field), val = s.(field);
elseif nargin>2, val = dftVal;
else, val = [];
end
%% Subfunction: Set most nii header and re-orient img
function [nii, h] = set_nii_hdr(nii, h, pf)
dim = nii.hdr.dim(2:4); nVol = nii.hdr.dim(5);
fld = 'NumberOfTemporalPositions';
if ~isfield(h{1}, fld) && nVol>1, h{1}.(fld) = nVol; end
% Transformation matrix: most important feature for nii
[ixyz, R, pixdim, xyz_unit] = xform_mat(h{1}, dim); % R: dicom xform matrix
R(1:2,:) = -R(1:2,:); % dicom LPS to nifti RAS, xform matrix before reorient
% Compute bval & bvec in image reference for DTI series before reorienting
if h{1}.isDTI, [h, nii] = get_dti_para(h, nii); end
% Store CardiacTriggerDelayTime
fld = 'CardiacTriggerDelayTime';
if ~isfield(h{1}, 'CardiacTriggerDelayTimes') && nVol>1 && isfield(h{1}, fld)
if numel(h) == 1 % multi frames
iFrames = 1:dim(3):dim(3)*nVol;
if isfield(h{1}, 'SortFrames'), iFrames = h{1}.SortFrames(iFrames); end
s2 = struct(fld, nan(1,nVol));
s2 = dicm_hdr(h{1}, s2, iFrames);
tt = s2.(fld);
else
tt = zeros(1, nVol);
inc = numel(h) / nVol;
for j = 1:nVol
tt(j) = tryGetField(h{(j-1)*inc+1}, fld, 0);
end
end
if ~all(diff(tt)==0), h{1}.CardiacTriggerDelayTimes = tt; end
end
% Get EchoTime for each vol
if ~isfield(h{1}, 'EchoTimes') && nVol>1 && isfield(h{1}, 'EchoTime')
if numel(h) == 1 % 4D multi frames
iFrames = 1:dim(3):dim(3)*nVol;
if isfield(h{1}, 'SortFrames'), iFrames = h{1}.SortFrames(iFrames); end
s2 = struct('EffectiveEchoTime', nan(1,nVol));
s2 = dicm_hdr(h{1}, s2, iFrames);
ETs = s2.EffectiveEchoTime;
else % regular dicom. Vida done previously
ETs = zeros(1, nVol);
inc = numel(h) / nVol;
for j = 1:nVol
ETs(j) = tryGetField(h{(j-1)*inc+1}, 'EchoTime', 0);
end
end
if ~all(diff(ETs)==0), h{1}.EchoTimes = ETs; end
end
% set TR and slice timing related info before re-orient
[h, nii.hdr] = sliceTiming(h, nii.hdr);
nii.hdr.xyzt_units = xyz_unit + nii.hdr.xyzt_units; % normally: mm (2) + sec (8)
s = h{1};
% Store motion parameters for MoCo series
if all(isfield(s, {'RBMoCoTrans' 'RBMoCoRot'})) && nVol>1
inc = numel(h) / nVol;
trans = zeros(nVol, 3);
rotat = zeros(nVol, 3);
for j = 1:nVol
trans(j,:) = tryGetField(h{(j-1)*inc+1}, 'RBMoCoTrans', [0 0 0]);
rotat(j,:) = tryGetField(h{(j-1)*inc+1}, 'RBMoCoRot', [0 0 0]);
end
s.RBMoCoTrans = trans;
s.RBMoCoRot = rotat;
end
% Store FrameReferenceTime: seen in Philips PET
if isfield(s, 'FrameReferenceTime') && nVol>1
inc = numel(h) / nVol;
vTime = zeros(1, nVol);
dict = dicm_dict('', 'FrameReferenceTime');
for j = 1:nVol
s2 = dicm_hdr(h{(j-1)*inc+1}.Filename, dict);
vTime(j) = tryGetField(s2, 'FrameReferenceTime', 0);
end
if vTime(1) > vTime(end) % could also re-read sorted h{i}{1}
vTime = flip(vTime);
nii.img = flip(nii.img, 4);
end
s.VolumeTiming = vTime / 1000; % ms to seconds
end
% dim_info byte: freq_dim, phase_dim, slice_dim low to high, each 2 bits
[phPos, iPhase] = phaseDirection(s); % phPos relative to image in FSL feat!
if iPhase == 2, fps_bits = [1 4 16];
elseif iPhase == 1, fps_bits = [4 1 16];
else, fps_bits = [0 0 16];
end
% Reorient if MRAcquisitionType==3D || isDTI && nSL>1
% If FSL etc can read dim_info for STC, we can always reorient.
[~, perm] = sort(ixyz); % may permute 3 dimensions in this order
if (strcmp(tryGetField(s, 'MRAcquisitionType', ''), '3D') || s.isDTI) && ...
dim(3)>1 && (~isequal(perm, 1:3)) % skip if already XYZ order
R(:, 1:3) = R(:, perm); % xform matrix after perm
fps_bits = fps_bits(perm);
ixyz = ixyz(perm); % 1:3 after perm
dim = dim(perm);
pixdim = pixdim(perm);
nii.hdr.dim(2:4) = dim;
nii.img = permute(nii.img, [perm 4:8]);
if isfield(s, 'bvec'), s.bvec = s.bvec(:, perm); end
end
iSL = find(fps_bits==16);
iPhase = find(fps_bits==4); % axis index for phase_dim in re-oriented img
nii.hdr.dim_info = (1:3) * fps_bits'; % useful for EPI only
nii.hdr.pixdim(2:4) = pixdim; % voxel zize
flp = R(ixyz+[0 3 6])<0; % flip an axis if true
d = det(R(:,1:3)) * prod(1-flp*2); % det after all 3 axis positive
if (d>0 && pf.lefthand) || (d<0 && ~pf.lefthand)
flp(1) = ~flp(1); % left or right storage
end
rotM = diag([1-flp*2 1]); % 1 or -1 on diagnal
rotM(1:3, 4) = (dim-1) .* flp; % 0 or dim-1
R = R / rotM; % xform matrix after flip
for k = 1:3, if flp(k), nii.img = flip(nii.img, k); end; end
if flp(iPhase), phPos = ~phPos; end
if isfield(s, 'bvec'), s.bvec(:, flp) = -s.bvec(:, flp); end
if flp(iSL) && isfield(s, 'SliceTiming') % slices flipped
s.SliceTiming = flip(s.SliceTiming);
sc = nii.hdr.slice_code;
if sc>0, nii.hdr.slice_code = sc+mod(sc,2)*2-1; end % 1<->2, 3<->4, 5<->6
end
% sform
frmCode = all(isfield(s, {'ImageOrientationPatient' 'ImagePositionPatient'}));
frmCode = tryGetField(s, 'TemplateSpace', frmCode);
nii.hdr.sform_code = frmCode; % 1: SCANNER_ANAT
nii.hdr.srow_x = R(1,:);
nii.hdr.srow_y = R(2,:);
nii.hdr.srow_z = R(3,:);
R0 = normc(R(:, 1:3));
sNorm = null(R0(:, setdiff(1:3, iSL))');
if sign(sNorm(ixyz(iSL))) ~= sign(R(ixyz(iSL),iSL)), sNorm = -sNorm; end
shear = norm(R0(:,iSL)-sNorm) > 0.01;
R0(:,iSL) = sNorm;
% qform
nii.hdr.qform_code = frmCode;
nii.hdr.qoffset_x = R(1,4);
nii.hdr.qoffset_y = R(2,4);
nii.hdr.qoffset_z = R(3,4);
[q, nii.hdr.pixdim(1)] = dcm2quat(R0); % 3x3 dir cos matrix to quaternion
nii.hdr.quatern_b = q(2);
nii.hdr.quatern_c = q(3);
nii.hdr.quatern_d = q(4);
if shear
nii.hdr.hdrTilt = nii.hdr; % copy all hdr for tilt version
nii.hdr.qform_code = 0; % disable qform
gantry = tryGetField(s, 'GantryDetectorTilt', 0);
nii.hdr.hdrTilt.pixdim(iSL+1) = norm(R(1:3, iSL)) * cosd(gantry);
R(1:3, iSL) = sNorm * nii.hdr.hdrTilt.pixdim(iSL+1);
nii.hdr.hdrTilt.srow_x = R(1,:);
nii.hdr.hdrTilt.srow_y = R(2,:);
nii.hdr.hdrTilt.srow_z = R(3,:);
end
% store some possibly useful info in descrip and other text fields
str = tryGetField(s, 'ImageComments', '');
if isType(s, '\MOCO\'), str = ''; end % useless for MoCo
foo = tryGetField(s, 'StudyComments');
if ~isempty(foo), str = [str ';' foo]; end
str = [str ';' sscanf(s.Manufacturer, '%s', 1)];
foo = tryGetField(s, 'ProtocolName');
if ~isempty(foo), str = [str ';' foo]; end
nii.hdr.aux_file = str; % char[24], info only
seq = asc_header(s, 'tSequenceFileName'); % like '%SiemensSeq%\ep2d_bold'
if isempty(seq)
seq = tryGetField(s, 'ScanningSequence');
else
ind = strfind(seq, '\');
if ~isempty(ind), seq = seq(ind(end)+1:end); end % like 'ep2d_bold'
end
if pf.save_patientName, nii.hdr.db_name = PatientName(s); end % char[18]
nii.hdr.intent_name = seq; % char[16], meaning of the data
foo = tryGetField(s, 'AcquisitionDateTime');
descrip = sprintf('time=%s;', foo(1:min(18,end)));
TE0 = asc_header(s, 'alTE[0]')/1000; % s.EchoTime stores only 1 TE
if isempty(TE0), TE0 = tryGetField(s, 'EchoTime'); end % GE, philips
TE1 = asc_header(s, 'alTE[1]')/1000;
if ~isempty(TE1), s.SecondEchoTime = TE1; s.EchoTime = TE0; end
dTE = abs(TE1 - TE0); % TE difference
if isempty(dTE) && tryGetField(s, 'NumberOfEchoes', 1)>1
dTE = tryGetField(s, 'SecondEchoTime') - TE0; % need to update
end
if ~isempty(dTE)
descrip = sprintf('dTE=%.4g;%s', dTE, descrip);
s.deltaTE = dTE;
end
if ~isempty(TE0), descrip = sprintf('TE=%.4g;%s', TE0, descrip); end
% Get dwell time
if ~strcmp(tryGetField(s, 'MRAcquisitionType'), '3D') && ~isempty(iPhase)
dwell = double(tryGetField(s, 'EffectiveEchoSpacing')) / 1000; % GE
% http://www.spinozacentre.nl/wiki/index.php/NeuroWiki:Current_developments
if isempty(dwell) % Philips
wfs = tryGetField(s, 'WaterFatShift');
epiFactor = tryGetField(s, 'EPIFactor');
dwell = wfs ./ (434.215 * (double(epiFactor)+1)) * 1000;
end
if isempty(dwell) % Siemens
hz = csa_header(s, 'BandwidthPerPixelPhaseEncode');
dwell = 1000 ./ hz / dim(iPhase); % in ms
end
if isempty(dwell) % true for syngo MR 2004A
% ppf = [1 2 4 8 16] represent [4 5 6 7 8] 8ths PartialFourier
% ppf = asc_header(s, 'sKSpace.ucPhasePartialFourier');
lns = asc_header(s, 'sKSpace.lPhaseEncodingLines');
dur = csa_header(s, 'SliceMeasurementDuration');
dwell = dur ./ lns; % ./ (log2(ppf)+4) * 8;
end
if isempty(dwell) % next is not accurate, so as last resort
dur = csa_header(s, 'RealDwellTime') * 1e-6; % ns to ms
dwell = dur * asc_header(s, 'sKSpace.lBaseResolution');
end
if isempty(dwell) && strncmpi(s.Manufacturer, 'UIH', 3)
try dwell = s.AcquisitionDuration; % not confirmed yet
catch
try dwell = s.MRVFrameSequence.Item_1.AcquisitionDuration; end
end
if ~isempty(dwell), dwell = dwell / dim(iPhase); end
end
if ~isempty(dwell)
s.EffectiveEPIEchoSpacing = dwell;
% https://github.com/rordenlab/dcm2niix/issues/130
readout = dwell * (dim(iPhase)- 1) / 1000; % since 170923
s.ReadoutSeconds = readout;
descrip = sprintf('readout=%.3g;dwell=%.3g;%s', readout, dwell, descrip);
end
end
if ~isempty(iPhase)
if isempty(phPos), pm = '?'; b67 = 0;
elseif phPos, pm = ''; b67 = 1;
else, pm = '-'; b67 = 2;
end
nii.hdr.dim_info = nii.hdr.dim_info + b67*64;
axes = 'xyz'; % actually ijk
phDir = [pm axes(iPhase)];
s.UnwarpDirection = phDir;
descrip = sprintf('phase=%s;%s', phDir, descrip);
end
nii.hdr.descrip = descrip; % char[80], drop from end if exceed
% slope and intercept: apply to img if no rounding error
sclApplied = tryGetField(s, 'ApplyRescale', false);
if any(isfield(s, {'RescaleSlope' 'RescaleIntercept'})) && ~sclApplied
slope = tryGetField(s, 'RescaleSlope', 1);
inter = tryGetField(s, 'RescaleIntercept', 0);
if isfield(s, 'MRScaleSlope') % Philips: see PAR file for detail
inter = inter / (slope * double(s.MRScaleSlope));
slope = 1 / double(s.MRScaleSlope);
end
val = sort(double([max(nii.img(:)) min(nii.img(:))]) * slope + inter);
dClass = class(nii.img);
if isa(nii.img, 'float') || (mod(slope,1)==0 && mod(inter,1)==0 ...
&& val(1)>=intmin(dClass) && val(2)<=intmax(dClass))
nii.img = nii.img * slope + inter; % apply to img if no rounding
else
nii.hdr.scl_slope = slope;
nii.hdr.scl_inter = inter;
end
elseif sclApplied && isfield(s, 'MRScaleSlope')
slope = tryGetField(s, 'RescaleSlope', 1) * s.MRScaleSlope;
nii.img = nii.img / slope;
end
if pf.scale_16bit && any(nii.hdr.datatype==[4 512]) % like dcm2niix
if nii.hdr.datatype == 4 % int16
scale = floor(32000 / double(max(abs(nii.img(:)))));
else % datatype==512 % uint16
scale = floor(64000 / double((max(nii.img(:)))));
end
nii.img = nii.img * scale;
nii.hdr.scl_slope = nii.hdr.scl_slope / scale;
end
h{1} = s;
% Possible patient position: HFS/HFP/FFS/FFP / HFDR/HFDL/FFDR/FFDL
% Seems dicom takes care of this, and maybe nothing needs to do here.
% patientPos = tryGetField(s, 'PatientPosition', '');
flds = { % store for nii.ext and json
'ConversionSoftware' 'SeriesNumber' 'SeriesDescription' 'ImageType' 'Modality' ...
'AcquisitionDateTime' 'bval' 'bvec' 'VolumeTiming' ...
'ReadoutSeconds' 'DelayTimeInTR' 'SliceTiming' 'RepetitionTime' ...
'UnwarpDirection' 'EffectiveEPIEchoSpacing' 'EchoTime' 'deltaTE' 'EchoTimes' ...
'SecondEchoTime' 'InversionTime' 'CardiacTriggerDelayTimes' ...
'PatientName' 'PatientSex' 'PatientAge' 'PatientSize' 'PatientWeight' ...
'PatientPosition' 'SliceThickness' 'FlipAngle' 'RBMoCoTrans' 'RBMoCoRot' ...
'Manufacturer' 'SoftwareVersion' 'MRAcquisitionType' ...
'InstitutionName' 'InstitutionAddress' 'DeviceSerialNumber' ...
'ScanningSequence' 'SequenceVariant' 'ScanOptions' 'SequenceName' ...
'TableHeight' 'DistanceSourceToPatient' 'DistanceSourceToDetector'};
if ~pf.save_patientName, flds(strcmp(flds, 'PatientName')) = []; end
for i = 1:numel(flds)
if ~isfield(s, flds{i}), continue; end
nii.json.(flds{i}) = s.(flds{i});
end
%% Subfunction, reshape mosaic into volume, remove padded zeros
function vol = mos2vol(mos, nSL, isUIH)
nMos = ceil(sqrt(nSL)); % nMos x nMos tiles for Siemens, maybe nMos x nMos-1 UIH
[nr, nc, nv] = size(mos); % number of row, col and vol in mosaic
nr = nr / nMos; nc = nc / nMos; % number of row and col in slice
if isUIH && nMos*(nMos-1)>=nSL, nc = size(mos,2) / (nMos-1); end % one col less
vol = zeros([nr nc nSL nv], class(mos));
for i = 1:nSL
r = mod(i-1, nMos) * nr + (1:nr); % 2nd slice is tile(2,1)
c = floor((i-1)/nMos) * nc + (1:nc);
vol(:, :, i, :) = mos(r, c, :);
end
%% subfunction: set slice timing related info
function [h, hdr] = sliceTiming(h, hdr)
s = h{1};
TR = tryGetField(s, 'RepetitionTime'); % in ms
if isempty(TR), TR = tryGetField(s, 'TemporalResolution'); end
if isempty(TR), return; end
hdr.pixdim(5) = TR / 1000;
if tryGetField(s, 'isDTI', 0), return; end
hdr.xyzt_units = 8; % seconds
if hdr.dim(5)<3, return; end % skip structual, fieldmap etc
nSL = hdr.dim(4);
delay = asc_header(s, 'lDelayTimeInTR')/1000; % in ms now
if isempty(delay), delay = 0;
else, h{1}.DelayTimeInTR = delay;
end
TA = TR - delay;
% Siemens mosaic
t = csa_header(s, 'MosaicRefAcqTimes'); % in ms
if ~isempty(t) && isfield(s, 'LastFile') && max(t)-min(t)>TA % MB wrong vol 1
try t = mb_slicetiming(s, TA); end %#ok<*TRYNC>
end
if isempty(t) && strncmpi(s.Manufacturer, 'UIH', 3)
t = zeros(nSL, 1);
if isfield(s, 'MRVFrameSequence') % mosaic
for j = 1:nSL
item = sprintf('Item_%g', j);
str = s.MRVFrameSequence.(item).AcquisitionDateTime;
t(j) = datenum(str, 'yyyymmddHHMMSS.fff');
end
else
dict = dicm_dict('', 'AcquisitionDateTime');
for j = 1:nSL
s1 = dicm_hdr(h{j}.Filename, dict);
t(j) = datenum(s1.AcquisitionDateTime, 'yyyymmddHHMMSS.fff');
end
end
t = (t - min(t)) * 24 * 3600 * 1000; % day to ms
end
if isempty(t) && isfield(s, 'RTIA_timer') % GE
t = zeros(nSL, 1);
nFile = numel(h);
% seen problem for 1st vol, so use last vol
for j = 1:nSL, t(j) = tryGetField(h{nFile-nSL+j}, 'RTIA_timer', 0); end
if all(diff(t)==0), t = [];
else
t = t - min(t);
ma = max(t) / TA;
if ma>1, t = t / 10; % was ms*10, old dicom
elseif ma<1e-3, t = t * 1000; % was sec, new dicom?
end
end
end
if isempty(t) && isfield(s, 'ProtocolDataBlock') && ...
isfield(s.ProtocolDataBlock, 'SLICEORDER') % GE with invalid RTIA_timer
SliceOrder = s.ProtocolDataBlock.SLICEORDER;
t = (0:nSL-1)' * TA/nSL;
if strcmp(SliceOrder, '1') % 0/1: sequential/interleaved based on limited data
t([1:2:nSL 2:2:nSL]) = t;
elseif ~strcmp(SliceOrder, '0')
errorLog(['Unknown SLICEORDER (' SliceOrder ') for ' s.NiftiName]);
return;
end
end
% Siemens multiframe: read TimeAfterStart from last file
if isempty(t) && strncmpi(s.Manufacturer, 'SIEMENS', 7)
% Use TimeAfterStart, not FrameAcquisitionDatetime. See
% https://github.com/rordenlab/dcm2niix/issues/240#issuecomment-433036901
try
s.PerFrameFunctionalGroupsSequence.Item_1.CSAImageHeaderInfo.Item_1.TimeAfterStart;
% s2 = struct('FrameAcquisitionDatetime', {cell(nSL,1)});
% s2 = dicm_hdr(h{end}, s2, 1:nSL); % avoid 1st volume
% t = datenum(s2.FrameAcquisitionDatetime, 'yyyymmddHHMMSS.fff');
% t = (t - min(t)) * 24 * 3600 * 1000; % day to ms
s2 = struct('TimeAfterStart', nan(1, nSL));
s2 = dicm_hdr(h{end}, s2, 1:nSL); % avoid 1st volume
t = s2.TimeAfterStart; % in secs
t = (t - min(t)) * 1000;
end
end
% Get slice timing for non-mosaic Siemens file. Could remove Manufacturer
% check, but GE/Philips AcquisitionTime seems useless
if isempty(t) && ~tryGetField(s, 'isMos', 0) && strncmpi(s.Manufacturer, 'SIEMENS', 7)
dict = dicm_dict('', {'AcquisitionDate' 'AcquisitionTime'});
t = zeros(nSL, 1);
for j = 1:nSL
s1 = dicm_hdr(h{j}.Filename, dict);
str = [s1.AcquisitionDate s1.AcquisitionTime];
t(j) = datenum(str, 'yyyymmddHHMMSS.fff');
end
t = (t - min(t)) * 24 * 3600 * 1000; % day to ms
end
if isempty(t) % non-mosaic Siemens: create 't' based on ucMode
ucMode = asc_header(s, 'sSliceArray.ucMode'); % 1/2/4: Asc/Desc/Inter
if isempty(ucMode), return; end
t = (0:nSL-1)' * TA/nSL;
if ucMode==2
t = t(nSL:-1:1);
elseif ucMode==4
if mod(nSL,2), t([1:2:nSL 2:2:nSL]) = t;
else, t([2:2:nSL 1:2:nSL]) = t;
end
end
if asc_header(s, 'sSliceArray.ucImageNumb'), t = t(nSL:-1:1); end % rev-num
end
if numel(t)<2, return; end
t = t - min(t); % it may be relative to 1st slice
t1 = sort(t);
dur = sum(diff(t1)) / (nSL-1);
dif = sum(diff(t)) / (nSL-1);
if dur==0 || (t1(end)>TA), sc = 0; % no useful info, or bad timing MB
elseif t1(1) == t1(2), sc = 0; t1 = unique(t1); % was 7 for MB but error in FS
elseif abs(dif-dur)<1e-3, sc = 1; % ascending
elseif abs(dif+dur)<1e-3, sc = 2; % descending
elseif t(1)<t(3) % ascending interleaved
if t(1)<t(2), sc = 3; % odd slices first
else, sc = 5; % Siemens even number of slices
end
elseif t(1)>t(3) % descending interleaved
if t(1)>t(2), sc = 4;
else, sc = 6; % Siemens even number of slices
end
else, sc = 0; % unlikely to reach
end
h{1}.SliceTiming = 0.5 - t/TR; % as for FSL custom timing
hdr.slice_code = sc;
hdr.slice_end = nSL-1; % 0-based, slice_start default to 0
hdr.slice_duration = min(diff(t1))/1000;
%% subfunction: extract bval & bvec, store in 1st header
function [h, nii] = get_dti_para(h, nii)
nDir = nii.hdr.dim(5);
if nDir<2, return; end
bval = nan(nDir, 1);
bvec = nan(nDir, 3);
s = h{1};
nSL = nii.hdr.dim(4);
nFile = numel(h);
if isfield(s, 'bvec_original') % from BV or PAR file
bval = s.B_value;
bvec = s.bvec_original;
elseif isfield(s, 'PerFrameFunctionalGroupsSequence')
if nFile== 1 % all vol in 1 file, for Philips
iDir = 1:nSL:nSL*nDir;
if isfield(s, 'SortFrames'), iDir = s.SortFrames(iDir); end
s2 = struct('B_value', bval', 'DiffusionGradientDirection', bvec');
s2 = dicm_hdr(s, s2, iDir); % call search_MF_val
bval = s2.B_value';
bvec = s2.DiffusionGradientDirection';
% if all(isnan(bvec(:))) % Bruker
% a = nan(1, nDir);
% s2 = struct('DiffusionB_ValueXX', a, 'DiffusionB_ValueXY', a, ...
% 'DiffusionB_ValueXZ', a, 'DiffusionB_ValueYY', a, ...
% 'DiffusionB_ValueYZ', a, 'DiffusionB_ValueZZ', a);
% s2 = dicm_hdr(s, s2, iDir);
% bm = reshape(struct2array(s2), [nDir 6]);
% a = zeros(3);
% for i = 1:nDir % https://github.com/rordenlab/dcm2niix/issues/265
% a(:) = bm(i, [1:3 2 4 5 3 5 6]);
% [V, ~] = eig(a);
% bvec(i,:) = V(:,3);
% end
% end
% if isfield(s, 'Private_0177_1101') && all(isnan(bvec(:))) % Bruker
% str = char(s.Private_0177_1101');
% expr = 'DiffusionBMatrix\s*=\s*\(\s*(\d+),\s*(\d+)\s*\)\s+';
% [C, ind] = regexp(str, expr, 'tokens', 'end', 'once');
% if isequal(str2double(C), [nDir 9])
% bm = sscanf(str(ind:end), '%f', nDir*9);
% bm = reshape(bm, 3, 3, []);
% [~, i] = sort(iDir); bm(:,:,i) = bm;
% for i = 1:nDir
% [V, ~] = eig(bm(:,:,i));
% bvec(i,:) = V(:,3);
% end
% % errorLog('bvec is from B-matrix, so sign may be wrong.');
% end
% end
if isfield(s, 'Private_0177_1100') && all(isnan(bvec(:))) % Bruker
str = char(s.Private_0177_1100');
expr = 'DwGradVec\s*=\s*\(\s*(\d+),\s*(\d+)\s*\)\s+'; % DwDir incomplete
[C, ind] = regexp(str, expr, 'tokens', 'end', 'once');
if isequal(str2double(C), [nDir 3])
bvec = sscanf(str(ind+1:end), '%f', nDir*3);
bvec = normc(reshape(bvec, 3, []))';
[~, i] = sort(iDir); bvec(i,:) = bvec;
end
end
else % 1 vol per file, e.g. Siemens
for i = 1:nFile
bval(i) = MF_val('B_value', h{i}, 1);
bvec(i,:) = MF_val('DiffusionGradientDirection', h{i}, 1);
end
end
elseif nFile>1 % multiple files: order already in slices then volumes
dict = dicm_dict(s.Manufacturer, {'B_value' 'B_factor' 'SlopInt_6_9' ...
'DiffusionDirectionX' 'DiffusionDirectionY' 'DiffusionDirectionZ'});
iDir = (0:nDir-1) * nFile/nDir + 1; % could be mosaic
for j = 1:nDir % no bval/bvec for B0 volume
s2 = h{iDir(j)};
val = tryGetField(s2, 'B_value');
if val == 0, continue; end
vec = tryGetField(s2, 'DiffusionGradientDirection'); % Siemens/Philips/UIH
if isempty(val) || isempty(vec) % likely GE
s2 = dicm_hdr(s2.Filename, dict);
end
if isempty(val), val = tryGetField(s2, 'B_factor'); end % old Philips
if isempty(val) && isfield(s2, 'SlopInt_6_9') % GE
val = s2.SlopInt_6_9(1);
end
if isempty(val), val = 0; end % may be B_value=0
bval(j) = val;
if isempty(vec) % GE, old Philips
vec(1) = tryGetField(s2, 'DiffusionDirectionX', 0);
vec(2) = tryGetField(s2, 'DiffusionDirectionY', 0);
vec(3) = tryGetField(s2, 'DiffusionDirectionZ', 0);
end
bvec(j,:) = vec;
end
end
if all(isnan(bval)) && all(isnan(bvec(:)))
errorLog(['Failed to get DTI parameters: ' s.NiftiName]);
return;
end
bval(isnan(bval)) = 0;
bvec(isnan(bvec)) = 0;
if strncmpi(s.Manufacturer, 'Philips', 7)
% Remove computed ADC: it may not be the last vol
ind = find(bval>1e-4 & sum(abs(bvec),2)<1e-4);
if ~isempty(ind) % DiffusionDirectionality: 'ISOTROPIC'
bval(ind) = [];
bvec(ind,:) = [];
nii.img(:,:,:,ind) = [];
nii.hdr.dim(5) = nDir - numel(ind);
end
end
h{1}.bvec_original = bvec; % original from dicom
% http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
[ixyz, R] = xform_mat(s, nii.hdr.dim(2:4)); % R takes care of slice dir
if strncmpi(s.Manufacturer, 'UIH', 3) || strncmpi(s.Manufacturer, 'Bruker', 6)
% assume real image reference: unlike confusing GE scheme
elseif strncmpi(s.Manufacturer, 'GE', 2) % GE bvec already in image reference
if strcmp(tryGetField(s, 'InPlanePhaseEncodingDirection'), 'ROW')
bvec = bvec(:, [2 1 3]); % dicom bvec in Freq/Phase/Slice order
bvec(:, 2) = -bvec(:, 2); % because of transpose?
if ixyz(3)<3
errorLog(sprintf(['%s: bvec sign for non-axial acquisition with' ...
' ROW phase direction not tested.\n Please check ' ...
'the result and report problem to author.'], s.NiftiName));
end
end
flp = R(ixyz+[0 3 6]) < 0; % negative sign
flp(3) = ~flp(3); % GE slice dir opposite to LPS for all sag/cor/tra
if ixyz(3)==1, flp(1) = ~flp(1); end % Sag slice: don't know why
bvec(:, flp) = -bvec(:, flp);
else % Siemens/Philips
R = normc(R(:, 1:3));
bvec = bvec * R; % dicom plane to image plane
end
% bval may need to be scaled by norm(bvec)
% https://mrtrix.readthedocs.io/en/latest/concepts/dw_scheme.html
nm = sum(bvec .^ 2, 2);
if any(nm>1e-4 & nm<0.999) % this check may not be necessary
h{1}.bval_original = bval; % before scaling
bval = bval .* nm;
nm(nm<1e-4) = 1; % remove zeros after correcting bval
bvec = bsxfun(@rdivide, bvec, sqrt(nm));
end
h{1}.bval = bval; % store all into header of 1st file
h{1}.bvec = bvec; % computed bvec in image ref
%% subfunction: save bval & bvec files
function save_dti_para(s, fname)
if ~isfield(s, 'bvec') || all(s.bvec(:)==0), return; end
if isfield(s, 'bval')
fid = fopen([fname '.bval'], 'w');
fprintf(fid, '%.5g\t', s.bval); % one row
fclose(fid);
end
str = repmat('%9.6f\t', 1, size(s.bvec,1));
fid = fopen([fname '.bvec'], 'w');
fprintf(fid, [str '\n'], s.bvec); % 3 rows by # direction cols
fclose(fid);
%% Subfunction, return a parameter from CSA Image/Series header
function val = csa_header(s, key)
val = [];
fld = 'CSAImageHeaderInfo';
if isfield(s, fld) && isfield(s.(fld), key), val = s.(fld).(key); return; end
fld = 'CSASeriesHeaderInfo';
if isfield(s, fld) && isfield(s.(fld), key), val = s.(fld).(key); return; end
%% Subfunction, Convert 3x3 direction cosine matrix to quaternion
% Simplied from Quaternions by Przemyslaw Baranski
function [q, proper] = dcm2quat(R)
% [q, proper] = dcm2quat(R)
% Retrun quaternion abcd from normalized matrix R (3x3)
proper = sign(det(R));
if proper<0, R(:,3) = -R(:,3); end
q = sqrt([1 1 1; 1 -1 -1; -1 1 -1; -1 -1 1] * diag(R) + 1) / 2;
if ~isreal(q(1)), q(1) = 0; end % if trace(R)+1<0, zero it
[mx, ind] = max(q);
mx = mx * 4;
if ind == 1
q(2) = (R(3,2) - R(2,3)) /mx;
q(3) = (R(1,3) - R(3,1)) /mx;
q(4) = (R(2,1) - R(1,2)) /mx;
elseif ind == 2
q(1) = (R(3,2) - R(2,3)) /mx;
q(3) = (R(1,2) + R(2,1)) /mx;
q(4) = (R(3,1) + R(1,3)) /mx;
elseif ind == 3
q(1) = (R(1,3) - R(3,1)) /mx;
q(2) = (R(1,2) + R(2,1)) /mx;
q(4) = (R(2,3) + R(3,2)) /mx;
elseif ind == 4
q(1) = (R(2,1) - R(1,2)) /mx;
q(2) = (R(3,1) + R(1,3)) /mx;
q(3) = (R(2,3) + R(3,2)) /mx;
end
if q(1)<0, q = -q; end % as MRICron
%% Subfunction: get dicom xform matrix and related info
function [ixyz, R, pixdim, xyz_unit] = xform_mat(s, dim)
haveIOP = isfield(s, 'ImageOrientationPatient');
if haveIOP, R = reshape(s.ImageOrientationPatient, 3, 2);
else, R = [1 0 0; 0 1 0]';
end
R(:,3) = cross(R(:,1), R(:,2)); % right handed, but sign may be wrong
foo = abs(R);
[~, ixyz] = max(foo); % orientation info: perm of 1:3
if ixyz(2) == ixyz(1), foo(ixyz(2),2) = 0; [~, ixyz(2)] = max(foo(:,2)); end
if any(ixyz(3) == ixyz(1:2)), ixyz(3) = setdiff(1:3, ixyz(1:2)); end
if nargout<2, return; end
iSL = ixyz(3); % 1/2/3 for Sag/Cor/Tra slice
signSL = sign(R(iSL, 3));
try
pixdim = s.PixelSpacing([2 1]);
xyz_unit = 2; % mm
catch
pixdim = [1 1]'; % fake
xyz_unit = 0; % no unit information
end
thk = tryGetField(s, 'SpacingBetweenSlices');
if isempty(thk), thk = tryGetField(s, 'SliceThickness', pixdim(1)); end
pixdim = [pixdim; thk];
haveIPP = isfield(s, 'ImagePositionPatient');
if haveIPP, ipp = s.ImagePositionPatient; else, ipp = -(dim'.* pixdim)/2; end
% Next is almost dicom xform matrix, except mosaic trans and unsure slice_dir
R = [R * diag(pixdim) ipp];
% rest are former: R = verify_slice_dir(R, s, dim, iSL)
if dim(3)<2, return; end % don't care direction for single slice
if s.Columns>dim(1) && ~strncmpi(s.Manufacturer, 'UIH', 3) % Siemens mosaic
R(:,4) = R * [ceil(sqrt(dim(3))-1)*dim(1:2)/2 0 1]'; % real slice location
vec = csa_header(s, 'SliceNormalVector'); % mosaic has this
if ~isempty(vec) % exist for all tested data
if sign(vec(iSL)) ~= signSL, R(:,3) = -R(:,3); end
return;
end
elseif isfield(s, 'LastFile') && isfield(s.LastFile, 'ImagePositionPatient')
R(:, 3) = (s.LastFile.ImagePositionPatient - R(:,4)) / (dim(3)-1);
thk = norm(R(:,3)); % override slice thickness if it is off
if abs(pixdim(3)-thk)/thk > 0.01, pixdim(3) = thk; end
return; % almost all non-mosaic images return from here
end
% Rest of the code is almost unreachable
if isfield(s, 'CSASeriesHeaderInfo') % Siemens both mosaic and regular
ori = {'Sag' 'Cor' 'Tra'}; ori = ori{iSL};
sNormal = asc_header(s, ['sSliceArray.asSlice[0].sNormal.d' ori]);
if asc_header(s, ['sSliceArray.ucImageNumb' ori]), sNormal = -sNormal; end
if sign(sNormal) ~= signSL, R(:,3) = -R(:,3); end
if ~isempty(sNormal), return; end
end
pos = []; % volume center we try to retrieve
if isfield(s, 'LastScanLoc') && isfield(s, 'FirstScanLocation') % GE
pos = (s.LastScanLoc + s.FirstScanLocation) / 2; % mid-slice center
if iSL<3, pos = -pos; end % RAS convention!
pos = pos - R(iSL, 1:2) * (dim(1:2)'-1)/2; % mid-slice location
end
if isempty(pos) && isfield(s, 'Stack') % Philips
ori = {'RL' 'AP' 'FH'}; ori = ori{iSL};
pos = tryGetField(s.Stack.Item_1, ['MRStackOffcentre' ori]);
pos = pos - R(iSL, 1:2) * dim(1:2)'/2; % mid-slice location
end
if isempty(pos) % keep right-handed, and warn user
if haveIPP && haveIOP
errorLog(['Please check whether slices are flipped: ' s.NiftiName]);
else
errorLog(['No orientation/location information found for ' s.NiftiName]);
end
elseif sign(pos-R(iSL,4)) ~= signSL % same direction?
R(:,3) = -R(:,3);
end
%% Subfunction: get a parameter in CSA series ASC header: MrPhoenixProtocol
function val = asc_header(s, key)
val = [];
csa = 'CSASeriesHeaderInfo';
if ~isfield(s, csa), return; end
if isfield(s.(csa), 'MrPhoenixProtocol')
str = s.(csa).MrPhoenixProtocol;
elseif isfield(s.(csa), 'MrProtocol') % older version dicom
str = s.(csa).MrProtocol;
else % in case of failure to decode CSA header
str = char(s.(csa)(:)');
str = regexp(str, 'ASCCONV BEGIN(.*)ASCCONV END', 'tokens', 'once');
if isempty(str), return; end
str = str{1};
end
% tSequenceFileName = ""%SiemensSeq%\gre_field_mapping""
expr = ['\n' regexptranslate('escape', key) '.*?=\s*(.*?)\n'];
str = regexp(str, expr, 'tokens', 'once');
if isempty(str), return; end
str = strtrim(str{1});
if strncmp(str, '""', 2) % str parameter
val = str(3:end-2);
elseif strncmp(str, '"', 1) % str parameter for version like 2004A
val = str(2:end-1);
elseif strncmp(str, '0x', 2) % hex parameter, convert to decimal
val = sscanf(str(3:end), '%x', 1);
else % decimal
val = sscanf(str, '%g', 1);
end
%% Subfunction: return matlab decompress command if the file is compressed
function func = compress_func(fname)
func = '';
if any(regexpi(fname, '\.mgz$')), return; end
fid = fopen(fname);
if fid<0, return; end
sig = fread(fid, 2, '*uint8')';
fclose(fid);
if isequal(sig, [80 75]) % zip file
func = 'unzip';
elseif isequal(sig, [31 139]) % gz, tgz, tar
func = 'untar';
end
% ! "c:\program Files (x86)\7-Zip\7z.exe" x -y -oF:\tmp\ F:\zip\3047ZL.zip
%% Subfuction: for GUI callbacks
function gui_callback(h, evt, cmd, fh)
hs = guidata(fh);
drawnow;
switch cmd
case 'do_convert'
src = get(fh, 'UserData');
dst = hs.dst.Text;
if isempty(src) || isempty(dst)
str = 'Source folder/file(s) and Result folder must be specified';
errordlg(str, 'Error Dialog');
return;
end
rstFmt = (get(hs.rstFmt, 'Value') - 1) * 2; % 0 or 2
if rstFmt == 4
if verLessThan('matlab','9.4')
warndlg('BIDS conversion requires MATLAB R2018a or more.','MATLAB outdated');
return;
end
if get(hs.gzip, 'Value')
rstFmt = 'bids';
else
rstFmt = 'bidsnii';
end % 1 or 3
else
if get(hs.gzip, 'Value'), rstFmt = rstFmt + 1; end % 1 or 3
if get(hs.rst3D, 'Value'), rstFmt = rstFmt + 4; end % 4 to 7
end
set(h, 'Enable', 'off', 'string', 'Conversion in progress');
clnObj = onCleanup(@()set(h, 'Enable', 'on', 'String', 'Start conversion'));
drawnow;
dicm2nii(src, dst, rstFmt);
% save parameters if last conversion succeed
pf = getpref('dicm2nii_gui_para');
pf.rstFmt = get(hs.rstFmt, 'Value');
pf.rst3D = get(hs.rst3D, 'Value');
pf.gzip = get(hs.gzip, 'Value');
pf.src = hs.src.Text;
ind = strfind(pf.src, '{');
if ~isempty(ind), pf.src = strtrim(pf.src(1:ind-1)); end
pf.dst = hs.dst.Text;
setpref('dicm2nii_gui_para', fieldnames(pf), struct2cell(pf));
case 'dstDialog'
folder = hs.dst.Text; % current folder
if ~isdir(folder), folder = hs.src.Text; end
if ~isdir(folder), folder = fileparts(folder); end
if ~isdir(folder), folder = pwd; end
dst = uigetdir(folder, 'Select a folder for result files');
if isnumeric(dst), return; end
hs.dst.Text = dst;
case 'srcDir'
folder = hs.src.Text; % initial folder
if ~isdir(folder), folder = fileparts(folder); end
if ~isdir(folder), folder = pwd; end
src = jFileChooser(folder, 'Select folders/files to convert');
if isnumeric(src), return; end
set(hs.fig, 'UserData', src);
txt = src{1};
if numel(src) > 1, txt = [txt ' {and more}']; end
hs.src.Text = txt;
case 'set_src'
str = hs.src.Text;
ind = strfind(str, '{');
if ~isempty(ind), return; end % no check with multiple files
if ~isempty(str) && ~exist(str, 'file')
val = dir(str);
folder = fileparts(str);
if isempty(val)
val = get(fh, 'UserData');
if iscellstr(val)
val = [fileparts(val{1}), sprintf(' {%g files}', numel(val))];
end
if ~isempty(val), hs.src.Text = val; end
errordlg('Invalid input', 'Error Dialog');
return;
end
str = {val.name};
str = strcat(folder, filesep, str);
end
set(fh, 'UserData', str);
case 'set_dst'
str = hs.dst.Text;
if isempty(str), return; end
if ~exist(str, 'file') && ~mkdir(str)
hs.dst.Text = '';
errordlg(['Invalid folder name ''' str ''''], 'Error Dialog');
return;
end
case 'SPMStyle' % turn off compression
if get(hs.rst3D, 'Value'), set(hs.gzip, 'Value', 0); end
case 'about'
item = get(hs.about, 'Value');
if item == 1 % about
str = sprintf(['dicm2nii.m by Xiangrui Li\n\n' ...
'Feedback to: [email protected]\n\n' ...
'Last updated on %s\n'], getVersion);
helpdlg(str, 'About dicm2nii')
elseif item == 2 % license
try
str = fileread([fileparts(mfilename('fullpath')) '/LICENSE']);
catch
str = 'license.txt file not found';
end
helpdlg(strtrim(str), 'License')
elseif item == 3
doc dicm2nii;
elseif item == 4
checkUpdate(mfilename);
elseif item == 5
web('www.sciencedirect.com/science/article/pii/S0165027016300073', '-browser');
end
set(hs.about, 'Value', 1);
case 'drop_src' % Java drop source
try
if strcmp(evt.DropType, 'file')
n = numel(evt.Data);
if n == 1
hs.src.Text = evt.Data{1};
set(hs.fig, 'UserData', evt.Data{1});
else
hs.src.Text = sprintf('%s {%g files}', ...
fileparts(evt.Data{1}), n);
set(fh, 'UserData', evt.Data);
end
else % string
hs.src.Text = strtrim(evt.Data);
gui_callback([], [], 'set_src', fh);
end
catch me
errordlg(me.message);
end
case 'drop_dst' % Java drop dst
try
if strcmp(evt.DropType, 'file')
nam = evt.Data{1};
if ~isdir(nam), nam = fileparts(nam); end
hs.dst.Text = nam;
else
hs.dst.Text = strtrim(evt.Data);
gui_callback([], [], 'set_dst', fh);
end
catch me
errordlg(me.message);
end
otherwise
create_gui;
end
%% Subfuction: create GUI or bring it to front if exists
function create_gui
fh = figure('dicm' * 256.^(0:3)'); % arbitury integer
if strcmp('dicm2nii_fig', get(fh, 'Tag')), return; end
scrSz = get(0, 'ScreenSize');
fSz = 9; % + ~(ispc || ismac);
clr = [1 1 1]*206/256;
clrButton = [1 1 1]*216/256;
cb = @(cmd) {@gui_callback cmd fh}; % callback shortcut
uitxt = @(txt,pos) uicontrol('Style', 'text', 'Position', pos, 'FontSize', fSz, ...
'HorizontalAlignment', 'left', 'String', txt, 'BackgroundColor', clr);
getpf = @(p,dft)getpref('dicm2nii_gui_para', p, dft);
chkbox = @(parent,val,str,cbk,tip) uicontrol(parent, 'Style', 'checkbox', ...
'FontSize', fSz, 'HorizontalAlignment', 'left', 'BackgroundColor', clr, ...
'Value', val, 'String', str, 'Callback', cbk, 'TooltipString', tip);
set(fh, 'Toolbar', 'none', 'Menubar', 'none', 'Resize', 'off', 'Color', clr, ...
'Tag', 'dicm2nii_fig', 'Position', [200 scrSz(4)-600 420 300], 'Visible', 'off', ...
'Name', 'dicm2nii - DICOM to NIfTI Converter', 'NumberTitle', 'off');
uitxt('Move mouse onto button, text box or check box for help', [8 274 400 16]);
str = sprintf(['Browse convertible files or folders (can have subfolders) ' ...
'containing files.\nConvertible files can be dicom, Philips PAR,' ...
' AFNI HEAD, BrainVoyager files, or a zip file containing those files']);
uicontrol('Style', 'Pushbutton', 'Position', [6 235 112 24], ...
'FontSize', fSz, 'String', 'DICOM folder/files', 'Background', clrButton, ...
'TooltipString', str, 'Callback', cb('srcDir'));
jSrc = javaObjectEDT('javax.swing.JTextField');
hs.src = javacomponent(jSrc, [118 234 294 24], fh);
hs.src.FocusLostCallback = cb('set_src');
hs.src.Text = getpf('src', pwd);
% hs.src.ActionPerformedCallback = cb('set_src'); % fire when pressing ENTER
hs.src.ToolTipText = ['<html>This is the source folder or file(s). You can<br>' ...
'Type the source folder name into the box, or<br>' ...
'Click DICOM folder/files button to browse, or<br>' ...
'Drag and drop a folder or file(s) into the box'];
uicontrol('Style', 'Pushbutton', 'Position', [6 199 112 24], ...
'FontSize', fSz, 'String', 'Result folder', 'Background', clrButton, ...
'TooltipString', 'Browse result folder', 'Callback', cb('dstDialog'));
jDst = javaObjectEDT('javax.swing.JTextField');
hs.dst = javacomponent(jDst, [118 198 294 24], fh);
hs.dst.FocusLostCallback = cb('set_dst');
hs.dst.Text = getpf('dst', pwd);
hs.dst.ToolTipText = ['<html>This is the result folder name. You can<br>' ...
'Type the folder name into the box, or<br>' ...
'Click Result folder button to set the value, or<br>' ...
'Drag and drop a folder into the box'];
uitxt('Output format', [8 166 82 16]);
hs.rstFmt = uicontrol('Style', 'popup', 'Background', 'white', 'FontSize', fSz, ...
'Value', getpf('rstFmt',1), 'Position', [92 162 82 24], 'String', {' .nii' ' .hdr/.img' ' BIDS (http://bids.neuroimaging.io)'}, ...
'TooltipString', 'Choose output file format');
hs.gzip = chkbox(fh, getpf('gzip',true), 'Compress', '', 'Compress into .gz files');
sz = get(hs.gzip, 'Extent'); set(hs.gzip, 'Position', [220 166 sz(3)+24 sz(4)]);
hs.rst3D = chkbox(fh, getpf('rst3D',false), 'SPM 3D', cb('SPMStyle'), ...
'Save one file for each volume (SPM style)');
sz = get(hs.rst3D, 'Extent'); set(hs.rst3D, 'Position', [330 166 sz(3)+24 sz(4)]);
hs.convert = uicontrol('Style', 'pushbutton', 'Position', [104 8 200 30], ...
'FontSize', fSz, 'String', 'Start conversion', ...
'Background', clrButton, 'Callback', cb('do_convert'), ...
'TooltipString', 'Dicom source and Result folder needed before start');
hs.about = uicontrol('Style', 'popup', 'String', ...
{'About' 'License' 'Help text' 'Check update' 'A paper about conversion'}, ...
'Position', [326 12 88 20], 'Callback', cb('about'));
ph = uipanel(fh, 'Units', 'Pixels', 'Position', [4 50 410 102], 'FontSize', fSz, ...
'BackgroundColor', clr, 'Title', 'Preferences (also apply to command line and future sessions)');
setpf = @(p)['setpref(''dicm2nii_gui_para'',''' p ''',get(gcbo,''Value''));'];
p = 'lefthand';
h = chkbox(ph, getpf(p,true), 'Left-hand storage', setpf(p), ...
'Left hand storage works well for FSL, and likely doesn''t matter for others');
sz = get(h, 'Extent'); set(h, 'Position', [4 60 sz(3)+24 sz(4)]);
p = 'save_patientName';
h = chkbox(ph, getpf(p,true), 'Store PatientName', setpf(p), ...
'Store PatientName in NIfTI hdr, ext and json');
sz = get(h, 'Extent'); set(h, 'Position', [180 60 sz(3)+24 sz(4)]);
p = 'use_parfor';
h = chkbox(ph, getpf(p,true), 'Use parfor if needed', setpf(p), ...
'Converter will start parallel tool if necessary');
sz = get(h, 'Extent'); set(h, 'Position', [4 36 sz(3)+24 sz(4)]);
p = 'use_seriesUID';
h = chkbox(ph, getpf(p,true), 'Use SeriesInstanceUID if exists', setpf(p), ...
'Only uncheck this if SeriesInstanceUID is messed up by some third party archive software');
sz = get(h, 'Extent'); set(h, 'Position', [180 36 sz(3)+24 sz(4)]);
p = 'save_json';
h = chkbox(ph, getpf(p,false), 'Save json file', setpf(p), ...
'Save json file for BIDS (http://bids.neuroimaging.io/)');
sz = get(h, 'Extent'); set(h, 'Position', [4 12 sz(3)+24 sz(4)]);
p = 'scale_16bit';
h = chkbox(ph, getpf(p,false), 'Use 16-bit scaling', setpf(p), ...
'Losslessly scale 16-bit integers to use dynamic range');
sz = get(h, 'Extent'); set(h, 'Position', [180 12 sz(3)+24 sz(4)]);
hs.fig = fh;
guidata(fh, hs); % store handles
drawnow; set(fh, 'Visible', 'on', 'HandleVisibility', 'callback');
try % java_dnd is based on dndcontrol by Maarten van der Seijs
java_dnd(jSrc, cb('drop_src'));
java_dnd(jDst, cb('drop_dst'));
catch me
fprintf(2, '%s\n', me.message);
end
gui_callback([], [], 'set_src', fh);
%% subfunction: return phase positive and phase axis (1/2) in image reference
function [phPos, iPhase] = phaseDirection(s)
phPos = []; iPhase = [];
fld = 'InPlanePhaseEncodingDirection';
if isfield(s, fld)
if strncmpi(s.(fld), 'COL', 3), iPhase = 2; % based on dicm_img(s,0)
elseif strncmpi(s.(fld), 'ROW', 3), iPhase = 1;
else, errorLog(['Unknown ' fld ' for ' s.NiftiName ': ' s.(fld)]);
end
end
if isfield(s, 'CSAImageHeaderInfo') % SIEMENS
phPos = csa_header(s, 'PhaseEncodingDirectionPositive'); % image ref
% elseif isfield(s, 'ProtocolDataBlock') % GE
% try % VIEWORDER "1" == bottom_up
% phPos = s.ProtocolDataBlock.VIEWORDER == '1';
% end
elseif isfield(s, 'UserDefineData') % GE
% https://github.com/rordenlab/dcm2niix/issues/163
try
b = s.UserDefineData;
i = typecast(b(25:26), 'uint16'); % hdr_offset
v = typecast(b(i+1:i+4), 'single'); % 5.0 to 40.0
if v >= 25.002, i = i + 76; flag2_off = 777; else, flag2_off = 917; end
sliceOrderFlag = bitget(b(i+flag2_off), 2);
phasePolarFlag = bitget(b(i+49), 3);
phPos = ~xor(phasePolarFlag, sliceOrderFlag);
end
else
if isfield(s, 'Stack') % Philips
try d = s.Stack.Item_1.MRStackPreparationDirection(1); catch, return; end
elseif isfield(s, 'PEDirectionDisplayed') % UIH
try d = s.PEDirectionDisplayed(1); catch, return; end
elseif isfield(s, 'Private_0177_1100') % Bruker
expr ='(?<=\<\+?)[LRAPSI]{1}(?=;\s*phase\>)';
d = regexp(char(s.Private_0177_1100'), expr, 'match', 'once');
id = regexp('LRAPSI', d);
id = id + mod(id,2)*2-1;
str = 'LRAPFH'; d = str(id);
else % unknown Manufacturer
return;
end
try R = reshape(s.ImageOrientationPatient, 3, 2); catch, return; end
[~, ixy] = max(abs(R)); % like [1 2]
if isempty(iPhase) % if no InPlanePhaseEncodingDirection
iPhase = strfind('RLAPFH', d);
iPhase = ceil(iPhase/2); % 1/2/3 for RL/AP/FH
iPhase = find(ixy==iPhase); % now 1 or 2
end
if any(d == 'LPH'), phPos = false; % in dicom ref
elseif any(d == 'RAF'), phPos = true;
end
if R(ixy(iPhase), iPhase)<0, phPos = ~phPos; end % tricky! in image ref
end
%% subfunction: extract useful fields for multiframe dicom
function s = multiFrameFields(s)
if isfield(s, 'MRVFrameSequence') % not real multi-frame dicom
try
s.ImagePositionPatient = s.MRVFrameSequence.Item_1.ImagePositionPatient;
s.AcquisitionDateTime = s.MRVFrameSequence.Item_1.AcquisitionDateTime;
item = sprintf('Item_%g', s.LocationsInAcquisition);
s.LastFile.ImagePositionPatient = s.MRVFrameSequence.(item).ImagePositionPatient;
end
return;
end
pffgs = 'PerFrameFunctionalGroupsSequence';
sfgs = 'SharedFunctionalGroupsSequence';
if any(~isfield(s, {sfgs pffgs})), return; end
try nFrame = s.NumberOfFrames; catch, nFrame = numel(s.(pffgs).FrameStart); end
% check slice ordering (Philips often needs SortFrames)
n = numel(MF_val('DimensionIndexValues', s, 1));
if n>0 && nFrame>1
s2 = struct('InStackPositionNumber', nan(1, nFrame), ...
'TemporalPositionIndex', nan(1, nFrame), ...
'DimensionIndexValues', nan(n, nFrame), ...
'B_value', zeros(1, nFrame));
s2 = dicm_hdr(s, s2, 1:nFrame);
if ~isnan(s2.InStackPositionNumber(1))
SL = s2.InStackPositionNumber';
VL = [s2.TemporalPositionIndex' s2.DimensionIndexValues([3:end 1],:)'];
else % use DimensionIndexValues as backup (seen in GE)
SL = s2.DimensionIndexValues(2,:)'; % Bruker slice dim in (3,:)?
VL = s2.DimensionIndexValues([3:end 1],:)';
end
[ind, nSL] = sort_frames([SL s2.B_value'], VL);
if ~isequal(ind, 1:nFrame) % && strncmpi(s.Manufacturer, 'Philips', 7)
if ind(1) ~= 1 || ind(end) ~= nFrame
s = dicm_hdr(s.Filename, [], ind([1 end])); % re-read new frames [1 end]
end
s.SortFrames = ind; % will use to sort img and get iVol/iSL for PerFrameSQ
end
if ~isfield(s, 'LocationsInAcquisition'), s.LocationsInAcquisition = nSL; end
end
% copy important fields into s
flds = {'EchoTime' 'PixelSpacing' 'SpacingBetweenSlices' 'SliceThickness' ...
'RepetitionTime' 'FlipAngle' 'RescaleIntercept' 'RescaleSlope' ...
'ImageOrientationPatient' 'ImagePositionPatient' ...
'InPlanePhaseEncodingDirection' 'MRScaleSlope' 'CardiacTriggerDelayTime'};
iF = 1; if isfield(s, 'SortFrames'), iF = s.SortFrames(1); end
for i = 1:numel(flds)
if isfield(s, flds{i}), continue; end
a = MF_val(flds{i}, s, iF);
if ~isempty(a), s.(flds{i}) = a; end
end
if ~isfield(s, 'EchoTime')
a = MF_val('EffectiveEchoTime', s, iF);
if ~isempty(a), s.EchoTime = a;
else, try s.EchoTime = str2double(s.EchoTimeDisplay); end
end
end
% for Siemens: the redundant copy makes non-Siemens code faster
if isfield(s.(sfgs).Item_1, 'CSASeriesHeaderInfo')
s.CSASeriesHeaderInfo = s.(sfgs).Item_1.CSASeriesHeaderInfo.Item_1;
end
fld = 'CSAImageHeaderInfo';
if isfield(s.(pffgs).Item_1, fld)
s.(fld) = s.(pffgs).(sprintf('Item_%g', iF)).(fld).Item_1;
end
% check ImageOrientationPatient consistency for 1st and last frame only
if nFrame<2, return; end
iF = nFrame; if isfield(s, 'SortFrames'), iF = s.SortFrames(iF); end
a = MF_val('ImagePositionPatient', s, iF);
if ~isempty(a), s.LastFile.ImagePositionPatient = a; end
fld = 'ImageOrientationPatient';
val = MF_val(fld, s, iF);
if ~isempty(val) && isfield(s, fld) && any(abs(val-s.(fld))>1e-4)
s = []; return; % inconsistent orientation, skip
end
%% subfunction: return value from Shared or PerFrame FunctionalGroupsSequence
function val = MF_val(fld, s, iFrame)
pffgs = 'PerFrameFunctionalGroupsSequence';
switch fld
case 'EffectiveEchoTime'
sq = 'MREchoSequence';
case {'DiffusionDirectionality' 'B_value'}
sq = 'MRDiffusionSequence';
case 'ComplexImageComponent'
sq = 'MRImageFrameTypeSequence';
case {'DimensionIndexValues' 'InStackPositionNumber' 'TemporalPositionIndex' ...
'FrameReferenceDatetime' 'FrameAcquisitionDatetime'}
sq = 'FrameContentSequence';
case {'RepetitionTime' 'FlipAngle'}
sq = 'MRTimingAndRelatedParametersSequence';
case 'ImagePositionPatient'
sq = 'PlanePositionSequence';
case 'ImageOrientationPatient'
sq = 'PlaneOrientationSequence';
case {'PixelSpacing' 'SpacingBetweenSlices' 'SliceThickness'}
sq = 'PixelMeasuresSequence';
case {'RescaleIntercept' 'RescaleSlope' 'RescaleType'}
sq = 'PixelValueTransformationSequence';
case {'InPlanePhaseEncodingDirection' 'MRAcquisitionFrequencyEncodingSteps' ...
'MRAcquisitionPhaseEncodingStepsInPlane'}
sq = 'MRFOVGeometrySequence';
case 'CardiacTriggerDelayTime'
sq = 'CardiacTriggerSequence';
case {'SliceNumberMR' 'EchoTime' 'MRScaleSlope'}
sq = 'PrivatePerFrameSq'; % Philips
case 'DiffusionGradientDirection' %
sq = 'MRDiffusionSequence';
try
s2 = s.(pffgs).(sprintf('Item_%g', iFrame)).(sq).Item_1;
val = s2.DiffusionGradientDirectionSequence.Item_1.(fld);
catch, val = [0 0 0]';
end
if nargin>1, return; end
otherwise
error('Sequence for %s not set.', fld);
end
if nargin<2
val = {'SharedFunctionalGroupsSequence' pffgs sq fld 'NumberOfFrames'};
return;
end
try
val = s.SharedFunctionalGroupsSequence.Item_1.(sq).Item_1.(fld);
catch
try
val = s.(pffgs).(sprintf('Item_%g', iFrame)).(sq).Item_1.(fld);
catch
val = [];
end
end
%% subfunction: split nii components into multiple nii
function nii = split_components(nii, s)
fld = 'ComplexImageComponent';
if ~strcmp(tryGetField(s, fld, ''), 'MIXED'), return; end
if ~isfield(s, 'Volumes') % PAR file and single-frame file have this
nSL = nii.hdr.dim(4); nVol = nii.hdr.dim(5);
iFrames = 1:nSL:nSL*nVol;
if isfield(s, 'SortFrames'), iFrames = s.SortFrames(iFrames); end
s1 = struct(fld, {cell(1, nVol)}, 'MRScaleSlope', nan(1,nVol), ...
'RescaleSlope', nan(1,nVol), 'RescaleIntercept', nan(1,nVol));
s.Volumes = dicm_hdr(s, s1, iFrames);
end
if ~isfield(s, 'Volumes'), return; end
% suppose scl not applied in set_nii_hdr, since MRScaleSlope is not integer
flds = {'EchoTimes' 'CardiacTriggerDelayTimes'}; % to split
s1 = s.Volumes;
nii0 = nii;
% [c, ia] = unique(s.Volumes.(fld), 'stable'); % since 2013a?
[~, ia] = unique(s1.(fld));
ia = sort(ia);
c = s1.(fld)(ia);
for i = 1:numel(c)
nii(i) = nii0;
ind = strcmp(c{i}, s1.(fld));
nii(i).img = nii0.img(:,:,:,ind);
slope = s1.RescaleSlope(ia(i)); if isnan(slope), slope = 1; end
inter = s1.RescaleIntercept(ia(i)); if isnan(inter), inter = 0; end
if ~isnan(s1.MRScaleSlope(ia(i)))
inter = inter / (slope * s1.MRScaleSlope(ia(i)));
slope = 1 / s1.MRScaleSlope(ia(i));
end
nii(i).hdr.scl_inter = inter;
nii(i).hdr.scl_slope = slope;
nii(i).hdr.file_name = [s.NiftiName '_' lower(c{i})];
nii(i) = nii_tool('update', nii(i));
for j = 1:numel(flds)
if ~isfield(nii(i).json, flds{j}), continue; end
nii(i).json.(flds{j}) = nii(i).json.(flds{j})(ind);
end
end
%% Write error info to a file in case user ignores Command Window output
function firstTime = errorLog(errInfo, folder)
persistent niiFolder;
if nargin>1, firstTime = isempty(niiFolder); niiFolder = folder; end
if isempty(errInfo), return; end
fprintf(2, ' %s\n', errInfo); % red text in Command Window
fid = fopen([niiFolder 'dicm2nii_warningMsg.txt'], 'a');
fseek(fid, 0, -1);
fprintf(fid, '%s\n', errInfo);
fclose(fid);
%% Ger version in from file: version yyyy.mm.dd
function dStr = getVersion(str)
dStr = '20130101';
if nargin<1 || isempty(str)
pth = fileparts(mfilename('fullpath'));
fname = fullfile(pth, 'README.md');
if ~exist(fname, 'file'), return; end
str = fileread(fullfile(pth, 'README.md'));
end
a = regexp(str, 'version\s(\d{4}\.\d{2}\.\d{2})', 'tokens', 'once');
if ~isempty(a), dStr = a{1}([1:4 6:7 9:10]); end
%% Get position info from Siemens CSA ASCII header
% The only case this is useful for now is for DTI_ColFA, where Siemens omit
% ImageOrientationPatient, ImagePositionPatient, PixelSpacing.
% This shows how to get info from Siemens CSA header.
function s = csa2pos(s, nSL)
ori = {'Sag' 'Cor' 'Tra'}; % 1/2/3
sNormal = zeros(3,1);
for i = 1:3
a = asc_header(s, ['sSliceArray.asSlice[0].sNormal.d' ori{i}]);
if ~isempty(a), sNormal(i) = a; end
end
if all(sNormal==0); return; end % likely no useful info, give up
isMos = tryGetField(s, 'isMos', false);
revNum = ~isempty(asc_header(s, 'sSliceArray.ucImageNumb'));
[cosSL, iSL] = max(abs(sNormal));
if isMos && (~isfield(s, 'CSAImageHeaderInfo') || ...
~isfield(s.CSAImageHeaderInfo, 'SliceNormalVector'))
a = sNormal; if revNum, a = -a; end
s.CSAImageHeaderInfo.SliceNormalVector = a;
end
pos = zeros(3,2);
sl = [0 nSL-1];
for j = 1:2
key = sprintf('sSliceArray.asSlice[%g].sPosition.d', sl(j));
for i = 1:3
a = asc_header(s, [key ori{i}]);
if ~isempty(a), pos(i,j) = a; end
end
end
if ~isfield(s, 'SpacingBetweenSlices')
if all(pos(:,2)==0) % like Mprage: dThickness & sPosition for volume
a = asc_header(s, 'sSliceArray.asSlice[0].dThickness') ./ nSL;
if ~isempty(a), s.SpacingBetweenSlices = a; end
else
s.SpacingBetweenSlices = abs(diff(pos(iSL,:))) / (nSL-1) / cosSL;
end
end
if ~isfield(s, 'PixelSpacing')
a = asc_header(s, 'sSliceArray.asSlice[0].dReadoutFOV');
a = a ./ asc_header(s, 'sKSpace.lBaseResolution');
interp = asc_header(s, 'sKSpace.uc2DInterpolation');
if interp, a = a ./ 2; end
if ~isempty(a), s.PixelSpacing = a * [1 1]'; end
end
R(:,3) = sNormal; % ignore revNum for now
if isfield(s, 'ImageOrientationPatient')
R(:, 1:2) = reshape(s.ImageOrientationPatient, 3, 2);
else
if iSL==3
R(:,2) = [0 R(3,3) -R(2,3)] / norm(R(2:3,3));
R(:,1) = cross(R(:,2), R(:,3));
elseif iSL==2
R(:,1) = [R(2,3) -R(1,3) 0] / norm(R(1:2,3));
R(:,2) = cross(R(:,3), R(:,1));
elseif iSL==1
R(:,1) = [-R(2,3) R(1,3) 0] / norm(R(1:2,3));
R(:,2) = cross(R(:,1), R(:,3));
end
rot = asc_header(s, 'sSliceArray.asSlice[0].dInPlaneRot');
if isempty(rot), rot = 0; end
rot = rot - round(rot/pi*2)*pi/2; % -45 to 45 deg, is this right?
ca = cos(rot); sa = sin(rot);
R = R * [ca sa 0; -sa ca 0; 0 0 1];
s.ImageOrientationPatient = R(1:6)';
end
if ~isfield(s, 'ImagePositionPatient')
dim = double([s.Columns s.Rows]');
if all(pos(:,2) == 0) % pos(:,1) for volume center
if any(~isfield(s,{'PixelSpacing' 'SpacingBetweenSlices'})), return; end
R = R * diag([s.PixelSpacing([2 1]); s.SpacingBetweenSlices]);
x = [-dim/2*[1 1]; (nSL-1)/2*[-1 1]];
pos = R * x + pos(:,1) * [1 1]; % volume center to slice 1&nSL position
else % this may be how Siemens sets unusual mosaic ImagePositionPatient
if ~isfield(s, 'PixelSpacing'), return; end
R = R(:,1:2) * diag(s.PixelSpacing([2 1]));
pos = pos - R * dim/2 * [1 1]; % slice centers to slice position
end
if revNum, pos = pos(:, [2 1]); end
if isMos, pos(:,2) = pos(:,1); end % set LastFile same as first for mosaic
s.ImagePositionPatient = pos(:,1);
s.LastFile.ImagePositionPatient = pos(:,2);
end
%% subfuction: check whether parpool is available
% Return true if it is already open, or open it if available
function doParal = useParTool
doParal = usejava('jvm');
if ~doParal, return; end
if isempty(which('parpool')) % for early matlab versions
try
if matlabpool('size')<1 %#ok<*DPOOL>
try
matlabpool;
catch me
fprintf(2, '%s\n', me.message);
doParal = false;
end
end
catch
doParal = false;
end
return;
end
% Following for later matlab with parpool
try
if isempty(gcp('nocreate'))
try
parpool;
catch me
fprintf(2, '%s\n', me.message);
doParal = false;
end
end
catch
doParal = false;
end
%% subfunction: return nii ext from dicom struct
% The txt extension is in format of: name = parameter;
% Each parameter ends with [';' char(0 10)]. Examples:
% Modality = 'MR'; % str parameter enclosed in single quotation marks
% FlipAngle = 72; % single numeric value, brackets may be used, but optional
% SliceTiming = [0.5 0.1 ... ]; % vector parameter enclosed in brackets
% bvec = [0 -0 0
% -0.25444411 0.52460458 -0.81243353
% ...
% 0.9836791 0.17571079 0.038744]; % matrix rows separated by char(10) and/or ';'
function ext = set_nii_ext(s)
flds = fieldnames(s);
ext.ecode = 6; % text ext
ext.edata = '';
for i = 1:numel(flds)
try val = s.(flds{i}); catch, continue; end
if ischar(val)
str = sprintf('''%s''', val);
elseif numel(val) == 1 % single numeric
str = sprintf('%.8g', val);
elseif isvector(val) % row or column
str = sprintf('%.8g ', val);
str = sprintf('[%s]', str(1:end-1)); % drop last space
elseif isnumeric(val) % matrix, like DTI bvec
fmt = repmat('%.8g ', 1, size(val, 2));
str = sprintf([fmt char(10)], val');
str = sprintf('[%s]', str(1:end-2)); % drop last space and char(10)
else % in case of struct etc, skip
continue;
end
ext.edata = [ext.edata flds{i} ' = ' str ';' char([0 10])];
end
% % Matlab ext: ecode = 40
% fname = [tempname '.mat'];
% save(fname, '-struct', 's', '-v7'); % field as variable
% fid = fopen(fname);
% b = fread(fid, inf, '*uint8'); % data bytes
% fclose(fid);
% delete(fname);
%
% % first 4 bytes (int32) encode real data length, endian-dependent
% if exist('ext', 'var'), n = numel(ext)+1; else n = 1; end
% ext(n).edata = [typecast(int32(numel(b)), 'uint8')'; b];
% ext(n).ecode = 40; % Matlab
% % Dicom ext: ecode = 2
% if isfield(s, 'SOPInstanceUID') % make sure it is dicom
% if exist('ext', 'var'), n = numel(ext)+1; else n = 1; end
% ext(n).ecode = 2; % dicom
% fid = fopen(s.Filename);
% ext(n).edata = fread(fid, s.PixelData.Start, '*uint8');
% fclose(fid);
% end
%% Fix some broken multiband sliceTiming. Hope this won't be needed in future.
% Odd number of nShot is fine, but some even nShot may have problem.
% This gives inconsistent result to the following example in PDF doc, but I
% would rather believe the example is wrong:
% nSL=20; mb=2; nShot=nSL/mb; % inc=3
% In PDF: 0,10 - 3,13 - 6,16 - 9,19 - 1,11 - 4,14 - 7,17 - 2,12 - 5,15 - 8,18
% result: 0,10 - 3,13 - 6,16 - 9,19 - 2,12 - 5,15 - 8,18 - 1,11 - 4,14 - 7,17
function t = mb_slicetiming(s, TA)
dict = dicm_dict(s.Manufacturer, 'MosaicRefAcqTimes');
s2 = dicm_hdr(s.LastFile.Filename, dict);
t = s2.MosaicRefAcqTimes; % try last volume first
% No SL acc factor. Not even multiband flag. This is UGLY
nSL = double(s.LocationsInAcquisition);
mb = ceil((max(t) - min(t)) ./ TA); % based on the wrong timing pattern
if isempty(mb) || mb==1 || mod(nSL,mb)>0, return; end % not MB or wrong mb guess
nShot = nSL / mb;
ucMode = asc_header(s, 'sSliceArray.ucMode'); % 1/2/4: Asc/Desc/Inter
if isempty(ucMode), return; end
t = linspace(0, TA, nShot+1)'; t(end) = [];
t = repmat(t, mb, 1); % ascending, ucMode==1
if ucMode == 2 % descending
t = t(nSL:-1:1);
elseif ucMode == 4 % interleaved
if mod(nShot,2) % odd number of shots
inc = 2;
else
inc = nShot / 2 - 1;
if mod(inc,2) == 0, inc = inc - 1; end
errorLog([s.NiftiName ': multiband interleaved order, even' ...
' number of shots.\nThe SliceTiming information may be wrong.']);
end
% % This gives the result in the PDF doc for example above
% ind = nan(nShot, 1); j = 0; i = 1; k = 0;
% while 1
% ind(i) = j + k*inc;
% if ind(i)+(mb-1)*nShot > nSL-1
% j = j + 1; k = 0;
% else
% i = i + 1; k = k + 1;
% end
% if i>nShot, break; end
% end
ind = mod((0:nShot-1)*inc, nShot)'; % my guess based on chris data
if nShot==6, ind = [0 2 4 1 5 3]'; end % special case
ind = bsxfun(@plus, ind*ones(1,mb), (0:mb-1)*nShot);
ind = ind + 1;
t = zeros(nSL, 1);
for i = 1:nShot
t(ind(i,:)) = (i-1) / nShot;
end
t = t * TA;
end
if csa_header(s, 'ProtocolSliceNumber')>0, t = t(nSL:-1:1); end % rev-num
%% subfunction: check ImagePostionPatient from multiple slices/volumes
function [err, nSL, sliceN, isTZ] = checkImagePosition(ipp, gantryTilt)
a = diff(sort(ipp));
tol = max(a)/100; % max(a) close to SliceThichness. 1% arbituary
if nargin>1 && gantryTilt, tol = tol * 10; end % arbituary
nSL = sum(a > tol) + 1;
err = ''; sliceN = []; isTZ = false;
nVol = numel(ipp) / nSL;
if mod(nVol,1), err = 'Missing file(s) detected'; return; end
if nSL<2, return; end
isTZ = nVol>1 && all(abs(diff(ipp(1:nVol))) < tol);
if isTZ % Philips XYTZ
a = ipp(1:nVol:end);
b = reshape(ipp, nVol, nSL);
else
a = ipp(1:nSL);
b = reshape(ipp, nSL, nVol)';
end
[~, sliceN] = sort(a); % no descend since wrong for PAR/singleDicom
if any(abs(diff(a,2))>tol), err = 'Inconsistent slice spacing'; return; end
if nVol>1
b = diff(b);
if any(abs(b(:))>tol), err = 'Irregular slice order'; return; end
end
%% Save JSON file, proposed by Chris G
% matlab.internal.webservices.toJSON(s)
function save_json(s, fname)
flds = fieldnames(s);
fid = fopen([fname '.json'], 'w'); % overwrite silently if exist
fprintf(fid, '{\n');
for i = 1:numel(flds)
nam = flds{i};
if ~isfield(s, nam), continue; end
val = s.(nam);
% this if-elseif block takes care of name/val change for BIDS json
if any(strcmp(nam, {'RepetitionTime' 'InversionTime' 'EchoTimes' 'CardiacTriggerDelayTimes'}))
val = val / 1000; % in sec now
elseif strcmp(nam, 'UnwarpDirection')
nam = 'PhaseEncodingDirection';
if val(1) == '-' || val(1) == '?', val = val([2 1]); end
if val(1) == 'x', val(1) = 'i'; % BIDS spec
elseif val(1) == 'y', val(1) = 'j';
elseif val(1) == 'z', val(1) = 'k';
end
elseif strcmp(nam, 'EffectiveEPIEchoSpacing')
nam = 'EffectiveEchoSpacing';
val = val / 1000;
elseif strcmp(nam, 'ReadoutSeconds')
nam = 'TotalReadoutTime';
elseif strcmp(nam, 'SliceTiming')
val = (0.5 - val) * s.RepetitionTime / 1000; % FSL style to secs
elseif strcmp(nam, 'SecondEchoTime')
nam = 'EchoTime2';
val = val / 1000;
elseif strcmp(nam, 'EchoTime')
% if there are two TEs we are dealing with a fieldmap
if isfield(s, 'SecondEchoTime')
nam = 'EchoTime1';
end
val = val / 1000;
elseif strcmp(nam, 'bval')
nam = 'DiffusionBValue';
elseif strcmp(nam, 'bvec')
nam = 'DiffusionGradientOrientation';
elseif strcmp(nam, 'DelayTimeInTR')
nam = 'DelayTime';
val = val / 1000; % secs
elseif strcmp(nam, 'ImageType')
val = regexp(val, '\\', 'split');
end
fprintf(fid, '\t"%s": ', nam);
if isempty(val)
fprintf(fid, 'null,\n');
elseif ischar(val)
fprintf(fid, '"%s",\n', strrep(val, '\', '\\'));
elseif iscellstr(val)
fprintf(fid, '[');
fprintf(fid, '"%s", ', val{:});
fseek(fid, -2, 'cof'); % remove trailing comma and space
fprintf(fid, '],\n');
elseif numel(val) == 1 % scalar numeric
fprintf(fid, '%.8g,\n', val);
elseif isvector(val) % row or column
fprintf(fid, '[\n');
fprintf(fid, '\t\t%.8g,\n', val);
fseek(fid, -2, 'cof');
fprintf(fid, '\t],\n');
elseif isnumeric(val) % matrix
fprintf(fid, '[\n');
fmt = repmat('%.8g ', 1, size(val, 2));
fprintf(fid, ['\t\t[' fmt(1:end-1) '],\n'], val');
fseek(fid, -2, 'cof');
fprintf(fid, '\n\t],\n');
else % in case of struct etc, skip
fprintf(2, 'Unknown type of data for %s.\n', nam);
fprintf(fid, 'null,\n');
end
end
fseek(fid, -2, 'cof'); % remove trailing comma and \n
fprintf(fid, '\n}\n');
fclose(fid);
%% Check for newer version for 42997 at Matlab Central
% Simplified from checkVersion in findjobj.m by Yair Altman
function checkUpdate(mfile)
verLink = 'https://github.com/xiangruili/dicm2nii/blob/master/README.md';
webUrl = 'https://www.mathworks.com/matlabcentral/fileexchange/42997';
try
str = webread(verLink);
catch me
try
str = urlread(verLink); %#ok
catch
str = sprintf('%s.\n\nPlease download manually.', me.message);
errordlg(str, 'Web access error');
web(webUrl, '-browser');
return;
end
end
latestStr = getVersion(str);
if datenum(getVersion(), 'yyyymmdd') >= datenum(latestStr, 'yyyymmdd')
msgbox([mfile ' and the package are up to date.'], 'Check update');
return;
end
msg = ['Update to the newer version (' latestStr ')?'];
answer = questdlg(msg, ['Update ' mfile], 'Yes', 'Later', 'Yes');
if ~strcmp(answer, 'Yes'), return; end
url = ['https://www.mathworks.com/matlabcentral/mlc-downloads/'...
'downloads/e5a13851-4a80-11e4-9553-005056977bd0/' ...
'80e748a3-0ae1-48a5-a2cb-b8380dac0232/packages/zip'];
tmp = tempdir;
try
fname = websave('dicm2nii_github.zip', url); % 2014a
unzip(fname, tmp); delete(fname);
a = dir([tmp 'xiangruili*']);
if isempty(a), tdir = tmp; else, tdir = [tmp a(1).name '/']; end
catch
% system('git clone https://github.com/xiangruili/dicm2nii.git')
url = 'https://github.com/xiangruili/dicm2nii/archive/master.zip';
try
fname = [tmp 'dicm2nii_github.zip'];
urlwrite(url, fname); %#ok
unzip(fname, tmp); delete(fname);
tdir = [tmp 'dicm2nii-master/'];
catch me
errordlg(['Error in updating: ' me.message], mfile);
web(webUrl, '-browser');
return;
end
end
movefile([tdir '*.*'], [fileparts(which(mfile)) '/.'], 'f');
rmdir(tdir, 's');
rehash;
warndlg(['Package updated successfully. Please restart ' mfile ...
', otherwise it may give error.'], 'Check update');
%% Subfunction: return NumberOfImagesInMosaic if Siemens mosaic, or [] otherwise.
% If NumberOfImagesInMosaic in CSA is >1, it is mosaic, and we are done.
% If not exists, it may still be mosaic due to Siemens bug seen in syngo MR
% 2004A 4VA25A phase image. Then we check EchoColumnPosition in CSA, and if it
% is smaller than half of the slice dim, sSliceArray.lSize is used as nMos. If
% no CSA at all, the better way may be to peek into img to get nMos. Then the
% first attempt is to check whether there are padded zeros. If so we count zeros
% either at top or bottom of the img to decide real slice dim. In case there is
% no padded zeros, we use the single zero lines along row or col seen in most
% (not all, for example some phase img, derived data like moco series or tmap
% etc) mosaic. If the lines are equally spaced, and nMos is divisible by mosaic
% dim, we accept nMos. Otherwise, we fall back to NumberOfPhaseEncodingSteps,
% which is used by dcm2nii, but is not reliable for most mosaic due to partial
% fourier or less 100% phase fov.
function nMos = nMosaic(s)
nMos = csa_header(s, 'NumberOfImagesInMosaic'); % healthy mosaic dicom
if ~isempty(nMos), return; end % seen 0 for GLM Design file and others
% The next fix detects mosaic which is not labeled as MOSAIC in ImageType, nor
% NumberOfImagesInMosaic exists, seen in syngo MR 2004A 4VA25A phase image.
res = csa_header(s, 'EchoColumnPosition'); % half or full of slice dim
if ~isempty(res)
dim = max([s.Columns s.Rows]);
interp = asc_header(s, 'sKSpace.uc2DInterpolation');
if ~isempty(interp) && interp, dim = dim / 2; end
if dim/res/2 >= 2 % nTiles>=2
nMos = asc_header(s, 'sSliceArray.lSize'); % mprage lSize=1
end
return; % Siemens non-mosaic returns here
end
% The fix below is for dicom labeled as \MOSAIC in ImageType, but no CSA.
if ~isType(s, '\MOSAIC') && ~isType(s, '\VFRAME'), return; end % non-mosaic
try nMos = s.LocationsInAcquisition; return; end % try Siemens/UIH private tag
try nMos = numel(fieldnames(s.MRVFrameSequence)); return; end % UIH
dim = double([s.Columns s.Rows]); % slice or mosaic dim
img = dicm_img(s, 0) ~= 0; % peek into img to figure out nMos
nP = tryGetField(s, 'NumberOfPhaseEncodingSteps', 4); % sliceDim >= phase steps
c = img(dim(1)-nP:end, dim(2)-nP:end); % corner at bottom-right
done = false;
if all(~c(:)) % at least 1 padded slice: not 100% safe
c = img(1:nP+1, dim(2)-nP:end); % top-right
if all(~c(:)) % all right tiles padded: use all to determine
ln = sum(img);
else % use several rows at bottom to determine: not as safe as all
ln = sum(img(dim(1)-nP:end, :));
end
z = find(ln~=0, 1, 'last');
nMos = dim(2) / (dim(2) - z);
done = mod(nMos,1)==0 && mod(dim(1),nMos)==0;
end
if ~done % this relies on zeros along row or col seen in most mosaic
ln = sum(img, 2) == 0;
if sum(ln)<2
ln = sum(img) == 0; % likely PhaseEncodingDirectionPositive=0
i = find(~ln, 1, 'last'); % last non-zero column in img
ln(i+2:end) = []; % leave only 1 true for padded zeros
end
nMos = sum(ln);
done = nMos>1 && all(mod(dim,nMos)==0) && all(diff(find(ln),2)==0);
end
if ~done && isfield(s, 'NumberOfPhaseEncodingSteps')
nMos = min(dim) / nP;
done = nMos>1 && mod(nMos,1)==0 && all(mod(dim,nMos)==0);
end
if ~done
errorLog([ProtocolName(s) ': NumberOfImagesInMosaic not available.']);
nMos = []; % keep mosaic as it is
return;
end
nMos = nMos * nMos; % not work for UIH
img = mos2vol(uint8(img), nMos, 0); % find padded slices: useful for STC
while 1
a = img(:,:,nMos);
if any(a(:)), break; end
nMos = nMos - 1;
end
%% Get sorting index for multi-frame and PAR/XML (also called by dicm_hdr)
function [ind, nSL] = sort_frames(sl, ic)
% sl is for slice index, and has B_value as 2nd column for DTI.
% ic contains other possible identifiers which will be converted into index.
% The ic column order is important.
nSL = max(sl(:, 1));
nFrame = size(sl, 1);
if nSL==nFrame, ind = 1:nSL; ind(sl(:,1)) = ind; return; end % single vol
nVol = floor(nFrame / nSL);
badVol = nVol*nSL < nFrame; % incomplete volume
id = zeros(size(ic));
for i = 1:size(ic,2)
[~, ~, id(:,i)] = unique(ic(:,i)); % entries to index
end
n = max(id); id = id(:, n>1); n = n(n>1);
i = find(n == nVol+badVol, 1);
if ~isempty(i) % most fMRI/DTI
id = id(:, i); % use a single column for sorting
elseif ~badVol && numel(n)>1
[j, i] = find(tril(n' * n, -1) == nVol, 1); % need to ignore diag
if ~isempty(i)
id = id(:, [i j]); % 2 columns make nVol
elseif numel(n)>2
i = find(cumprod(n) == nVol, 1);
if ~isempty(i), id = id(:, 1:i); end % first i columns make nVol
end
end
[~, ind] = sortrows([sl id]); % this sort idea is from julienbesle
if badVol % only seen in Philips
try lastV = id(ind,1) > nVol; catch, lastV = []; end
if sum(lastV) == nFrame-nSL*nVol
ind(lastV) = []; % remove incomplete volume
else % suppose extra later slices are from bad volume
for i = 1:nSL
a = ind==i;
if sum(a) <= nVol, continue; end % shoule be ==
ind(find(a, 'last')) = []; % remove last extra one
if numel(ind) == nSL*nVol, break; end
end
end
end
ind = reshape(ind, [], nSL)'; % XYTZ to XYZT
ind = ind(:)';
%% this can be removed for matlab 2013b+
function y = flip(varargin)
if exist('flip', 'builtin')
y = builtin('flip', varargin{:});
else
if nargin<2, varargin{2} = find(size(varargin{1})>1, 1); end
y = flipdim(varargin); %#ok
end
%% return all file names in a folder, including in sub-folders
function files = filesInDir(folder)
dirs = genpath(folder);
dirs = regexp(dirs, pathsep, 'split');
files = {};
for i = 1:numel(dirs)
if isempty(dirs{i}), continue; end
curFolder = [dirs{i} filesep];
a = dir(curFolder); % all files and folders
a([a.isdir]) = []; % remove folders
a = strcat(curFolder, {a.name});
files = [files a]; %#ok<*AGROW>
end
%% Select both folders and files
function out = jFileChooser(folder, prompt, multi, button)
if nargin<4 || isempty(button), button = 'Select'; end
if nargin<3 || isempty(multi), multi = true; end
if nargin<2 || isempty(prompt)
if multi, prompt = 'Choose files and/or folders';
else, prompt = 'Choose file or folder';
end
end
if nargin<1 || isempty(folder), folder = pwd; end
jFC = javax.swing.JFileChooser(folder);
jFC.setFileSelectionMode(jFC.FILES_AND_DIRECTORIES);
set(jFC, 'MultiSelectionEnabled', logical(multi));
set(jFC, 'ApproveButtonText', button);
set(jFC, 'DialogTitle', prompt);
returnVal = jFC.showOpenDialog([]);
if returnVal ~= jFC.APPROVE_OPTION, out = returnVal; return; end % numeric
if multi
files = jFC.getSelectedFiles();
n = numel(files);
out = cell(1, n);
for i = 1:n, out{i} = char(files(i)); end
else
out = char(jFC.getSelectedFile());
end
%%
function v = normc(M)
den = sqrt(sum(M .* M));
den(den==0) = 1;
v = bsxfun(@rdivide, M, den);
%%
function BtnModalityTable(h,TT,TS)
if all(any(ismember(TT.Data{:,2:3},'skip'),2))
warndlg('All images are skipped... Please select the type and modality for all scans','No scan selected');
return;
end
setappdata(0,'ModalityTable',TT.Data)
setappdata(0,'SubjectTable',TS.Data)
delete(h)
|
github
|
cocoanlab/humanfmri_preproc_bids-master
|
dicm_hdr.m
|
.m
|
humanfmri_preproc_bids-master/external/dicm2nii/dicm_hdr.m
| 62,090 |
utf_8
|
b5094a6d10aab8edfae3dea1bff32612
|
function [s, info, dict] = dicm_hdr(fname, dict, iFrames)
% Return header of a dicom file in a struct.
%
% [s, err] = DICM_HDR(dicomFileName, dict, iFrames);
%
% The mandatory 1st input is the dicom file name.
%
% The optional 2nd input is a dicom dictionary returned by dicm_dict. It may
% have only part of the full dictionary, which can speed up header read
% considerably. See rename_dicm for example.
%
% The optional 3rd intput is useful for multi-frame dicom. When there are many
% frames, it may be slow to read all frames in PerFrameFunctionalGroupsSequence.
% The 3rd input specifies the frames to read. By default, items for only 1st,
% 2nd and last frames are read.
%
% The optional 2nd output contains information in case of error, and will be
% empty if there is no error.
%
% The optional 3rd output is rarely needed. It returns the dicom dictionary
% which may be updated from the input dict if the dicom vendor is different from
% that in the input dict.
%
% DICM_HDR is like Matlab dicominfo, but is independent of Image Processing
% Toolbox. The advantage is that it decodes most private and shadow tags for
% Siemens, GE and Philips dicom, and runs faster, especially for partial header
% and multi-frame dicom.
%
% DICM_HDR can also read Philips PAR/XML file, AFNI HEAD file, Freesurfer MGH
% file and some BrainVoyager files, and return needed fields for dicm2nii to
% convert into nifti.
%
% See also DICM_DICT, DICM2NII, DICM_IMG, RENAME_DICM, SORT_DICM, ANONYMIZE_DICM
% History (yymmdd):
% 130823 Write it for dicm2nii.m ([email protected]).
% 130912 Extend private tags, automatically detect vendor.
% 130923 Call philips_par, so make dicm2nii easier.
% 131001 Decode SQ, useful for multiframe dicom and Philips Stack.
% 131008 Load then typecast. Faster than multiple fread.
% 131009 Work for implicit VR.
% 131010 Decode Siemens CSA header (slow), so it is human readable.
% 131019 PAR file: read image col labels, and use it for indexing.
% 131023 Implement afni_hdr.
% 131102 Use last tag for partial hdr, so return if it is non-exist fld.
% 131107 Search tags if only a few fields: faster than regular way.
% 131114 Add 3rd input: only 1,2,last frames hdr read. 0.4 vs 38 seconds!
% Store needed fields in LastFile for PAR MIXED image type.
% 140123 Support dicom without meta info (thanks Paul).
% 140213 afni_head: IJK_TO_DICOM_REAL replaces IJK_TO_DICOM.
% 140502 philips_par: don't use FOV for PixelSpacing and SpacingBetweenSlices.
% 140506 philips_par: use PAR file name as SeriesDescription.
% 140512 decode GE ProtocolDataBlock (gz compressed).
% 140611 No re-do if there are <16 extra bytes after image data.
% 140724 Ignore PAR/HEAD ext case; fix philips_par: Patient Position.
% 140924 Use dict VR if VR==OB/UN (thx Macro R). Could be bad in theory.
% 141006 philips_par: take care of char(13 10) issue (thx Hye).
% 141021 Store fields in dict, so it can be used for changed vendor.
% 141023 checkManufacturer for fast search approach too.
% 141128 Minor tweaks (len-1 in read_csa) for Octave 3.8.1.
% 150114 Siemens CSA str is not always len=1. Fix it (runs slower).
% 150128 Use memory gunzip for GE ProtocolDataBlock (0.5 vs 43 ms).
% 150222 Avoid repeatedly reading .REC .BRIK file for hdr.
% 150227 Avoid error due to empty file (thx Kushal).
% 150316 Avoid error due to empty item dat for search method (thx VG).
% 150324 philips_par/afni_head: make up SeriesInstanceUID for dicm2nii.
% 150405 Implement bv_file to read non-transformed BV fmr/vmr/dmr.
% 150504 bv_file: fix multiple STCdata; bug fix for VMRData.
% 150513 return dict as 3rd output for dicm2nii in case of vendor change.
% 150517 fix manufacturer check problem for Octave: no re-read.
% 150522 PerFrameSQ ind: fix the case if numel(ind)~=nFrame.
% 150526 read_sq: use ItemDelimitationItem instead of empty dat1 as SQ end.
% 150924 philips_par: store SliceNumber if not acsending/decending order.
% 151001 check Manufacturer in advance for 'search' method.
% 160105 Bug fix for b just missing iPixelData (Thx Andrew S).
% 160127 Support big endian dicom; Always return TransferSyntaxUID for dicm_img.
% 160310 Fix problem of failing to update allRead with Inf bytes read.
% 160410 philips_par: check IndexInREC, and minor improvement.
% 160412 add read_val() for search method, but speed benefit is minor.
% 160414 Skip GEIIS SQ: not dicom compliant.
% 160418 Add search_MF_val(); need FrameStart in PerFrameSQ.
% 160422 Performance: avoid nestedFunc (big), use uint8, avoid typecast (minor).
% 160527 philips_par: center of slice 1 for slice dir; (dim-1)/2 for vol center.
% 160608 read_sq: n=nEnd (j>2) with PerFrameSQ (needed if length is not inf).
% 160825 can read dcm without PixelData, by faking p.iPixelData=fSize+1.
% 160829 no make-up SeriesNumber/InstanceUID in afni_head/philips_par/bv_file.
% 160928 philips_par: fix para table ind; treat type 17 as phase img. Thx SS.
% 161130 check i+n-1<=p.iPixelData in search method to avoid error. Thx xLei.
% 170127 Implement mgh_file: read FreeSurfer mgh or mgz.
% 170618 philips_par(): use regexp (less error prone); ignore keyname case.
% 170618 afni_head(): make MSB_FIRST (BE) BRIK work; fix negative PixelSpacing.
% 170625 read_ProtocolDataBlock(): decompress only to avoid datatype guess.
% 170803 par_key(): bug fix introduced on 170618.
% 170910 regexp tweak to work for Octave.
% 170921 read_ProtocolDataBlock: decode into struct with better performance.
% 171228 philips_par: bug fix for possible slice flip. thx ShereifH.
% 170309 philips_par: take care of incomplete volume if not XYTZ. thx YiL.
% 180507 read_val: keep bytes if typecast fails. thx JillM.
% 180528 remove reversed search so allow to get item from 1st PerFrame.
% 180531 philips_par: use SortFrames to solve XYTZ and incomplete volume.
% 180605 philips_xml: much faster than xml2par;
% philips_par: start to support V3 (thx ChrisR); fix (ap,fh,rl) issue.
% 180612 philips_par & xml: take care of IndexInREC (may never be tested).
% 180615 Avoid error for dicm without PixelData for search method (thx LucaT).
% 180620 philips_xml: bug fix to convert str to num for sort_frames.
% 180712 bug fix for implict VR in search method (thx LorenaF).
persistent dict_full;
s = []; info = '';
if nargin<2 || isempty(dict)
if isempty(dict_full), dict_full = dicm_dict; end
p.fullHdr = true;
p.dict = dict_full;
else
p.fullHdr = false; % p updated in main func
p.dict = dict;
end
if nargin==3 && isstruct(fname) % wrapper
s = search_MF_val(fname, dict, iFrames); % s, s1, iFrames
return;
end
if nargin<3, iFrames = []; end
p.iFrames = iFrames;
fid = fopen(fname, 'r', 'l');
if fid<0, info = ['File not exists: ' fname]; return; end
closeFile = onCleanup(@() fclose(fid)); % auto close when done or error
fseek(fid, 0, 1); fSize = ftell(fid); fseek(fid, 0, -1);
if fSize<140 % 132 + one empty tag, ignore truncated
info = ['Invalid file: ' fname];
return;
end
b8 = fread(fid, 130000, 'uint8=>uint8')'; % enough for most dicom
iTagStart = 132; % start of first tag
isDicm = isequal(b8(129:132), 'DICM');
if ~isDicm % truncated dicom: is first group 2 or 8? not safe
group = ch2int16(b8(1:2), 0);
isDicm = group==2 || group==8; % truncated dicm always LE
iTagStart = 0;
end
if ~isDicm % may be PAR/HEAD/BV file
[~, ~, ext] = fileparts(fname);
try
if strcmpi(ext, '.PAR')
[s, info] = philips_par(fname);
elseif strcmpi(ext, '.xml')
[s, info] = philips_xml(fname);
elseif strcmpi(ext, '.HEAD') % || strcmpi(ext, '.BRIK')
[s, info] = afni_head(fname);
elseif any(strcmpi(ext, {'.mgh' '.mgz'}))
[s, info] = mgh_file(fname);
elseif any(strcmpi(ext, {'.vmr' '.fmr' '.dmr'})) % BrainVoyager
[s, info] = bv_file(fname);
else
info = ['Unknown file type: ' fname];
end
catch me
info = me.message;
end
return;
end
p.expl = false; % default for truncated dicom
p.be = false; % little endian by default
% Get TransferSyntaxUID first, so find PixelData
i = strfind(char(b8), [char([2 0 16 0]) 'UI']); % always explicit LE
tsUID = '';
if ~isempty(i) % empty for truncated
i = i(1) + 6;
n = ch2int16(b8(i+(0:1)), 0);
tsUID = deblank(char(b8(i+1+(1:n))));
p.expl = ~strcmp(tsUID, '1.2.840.10008.1.2'); % may be wrong for some
p.be = strcmp(tsUID, '1.2.840.10008.1.2.2');
end
% find s.PixelData.Start so avoid search in img
% We verify iPixelData+bytes=fSize. If bytes=2^32-1, read all and use last tag
tg = char([224 127 16 0]); % PixelData, VR can be OW/OB even if expl
if p.be, tg = tg([2 1 4 3]); end
found = false;
for nb = [0 2e6 20e6 fSize] % if not enough, read more till all read
b8 = [b8 fread(fid, nb, 'uint8=>uint8')']; %#ok
i = strfind(char(b8), tg);
i = i(mod(i,2)==1); % must be odd number
if isempty(i) && feof(fid)
tg = char([00 86 32 0]); % SpectroscopyData, VR = 'OF'
if p.be, tg = tg([2 1 4 3]); end
i = strfind(char(b8), tg); i = i(mod(i,2)==1);
end
for k = i(end:-1:1) % last is likely real PixelData
if p.expl, p.VR = char(b8(k+(4:5))); end
p.iPixelData = k + p.expl*4 + 7; % s.PixelData.Start: 0-based
if numel(b8)<p.iPixelData, b8 = [b8 fread(fid, 12, '*uint8')']; end %#ok
p.bytes = ch2int32(b8(p.iPixelData+(-3:0)), p.be);
if p.bytes==4294967295 && feof(fid), break; end % 2^32-1 compressed
d = fSize - p.iPixelData - p.bytes; % d=0 most of time
if d>=0 && d<16, found = true; break; end % real PixelData
end
if found, break; end
if feof(fid)
if isempty(i), p.iPixelData = fSize+1; end % fake it: no PixelData
break;
end
end
s.Filename = fopen(fid);
s.FileSize = fSize;
nTag = numel(p.dict.tag); % always search if only one tag: can find it in any SQ
toSearch = nTag<2 || (nTag<30 && ~any(strcmp(p.dict.vr, 'SQ')) && p.iPixelData<1e6);
if toSearch % search each tag if header is short and not many tags asked
if ~isempty(tsUID), s.TransferSyntaxUID = tsUID; end % hope it is 1st tag
bc = char(b8(1:min(end, p.iPixelData)));
if ~isempty(p.dict.vendor) && any(mod(p.dict.group, 2)) % private group
tg = char([8 0 112 0]); % Manufacturer
if p.be, tg = tg([2 1 4 3]); end
if p.expl, tg = [tg 'LO']; end
i = strfind(bc, tg);
i = i(mod(i,2)==1);
if ~isempty(i)
i = i(1) + 4 + p.expl*2; % Manufacturer should be the earliest one
[n, nvr] = val_len('LO', b8(i+(0:5)), p.expl, p.be); i = i + nvr;
if i+n<p.iPixelData
dat = deblank(bc(i+(0:n-1)));
[p, dict] = updateVendor(p, dat);
end
end
end
tg = char([40 0 8 0]); % NumberOfFrames
if p.be, tg = tg([2 1 4 3]); end
if p.expl, tg = [tg 'IS']; end
i = strfind(bc, tg);
i = i(mod(i,2)==1);
if ~isempty(i)
i = i(1) + 4 + p.expl*2; % take 1st
[n, nvr] = val_len('IS', b8(i+(0:5)), p.expl, p.be); i = i + nvr;
if i+n<p.iPixelData, p.nFrames = str2double(bc(i+(0:n-1))); end
end
for k = 1:numel(p.dict.tag)
group = p.dict.group(k);
swap = p.be && group~=2;
hasVR = p.expl || group==2;
tg = char(typecast([group p.dict.element(k)], 'uint8'));
if swap, tg = tg([2 1 4 3]); end
i = strfind(bc, tg);
i = i(mod(i,2)==1);
if isempty(i), continue; % no this tag, next
elseif isfield(p, 'nFrames') && mod(numel(i), p.nFrames)<2, i = i(1);
% elseif strcmp('SeriesInstanceUID', p.dict.name{k}), i = i(end);
elseif numel(i)>1 % +1 tags found, add vr to try again if expl
if hasVR
tg = [tg p.dict.vr{k}]; %#ok
i = strfind(bc, tg);
i = i(mod(i,2)==1);
if numel(i)~=1, toSearch = false; break; end
else
toSearch = false; break; % switch to regular way
end
end
i = i + 4; % tag
if hasVR
vr = bc(i+(0:1)); i = i+2;
if any(vr>'Z') || any(vr<'A'), toSearch = false; break; end
if strcmp(vr, 'UN') || strcmp(vr, 'OB'), vr = p.dict.vr{k}; end
else
vr = p.dict.vr{k};
end
[n, nvr] = val_len(vr, b8(i+(0:5)), hasVR, swap); i = i+nvr;
if n<1 || mod(n,2) || i+n-1>p.iPixelData, continue; end % skip this tag
[dat, info] = read_val(b8(i+(0:n-1)), vr, swap);
if ~isempty(info), toSearch = false; break; end % re-do in regular way
if ~isempty(dat), s.(p.dict.name{k}) = dat; end
end
end
i = iTagStart + 1;
while ~toSearch
if i >= p.iPixelData
if strcmp(name, 'PixelData') % iPixelData might be in img
p.iPixelData = iPre + p.expl*4 + 7; % overwrite previous
p.bytes = ch2int32(b8(p.iPixelData+(-3:0)), p.be);
elseif p.iPixelData < fSize % has PixelData
info = ['End of file reached: likely error: ' s.Filename];
end
break; % done or give up
end
iPre = i; % back it up for PixelData
[dat, name, info, i, tg] = read_item(b8, i, p);
if ~isempty(info), break; end
if ~p.fullHdr && tg>p.dict.tag(end), break; end % done for partial hdr
if isempty(dat) || isnumeric(name), continue; end
s.(name) = dat;
if strcmp(name, 'Manufacturer')
[p, dict] = updateVendor(p, dat);
elseif tg>=2621697 && ~isfield(p, 'nFrames') % BitsAllocated
p = get_nFrames(s, p, b8); % only make code here cleaner
end
end
if p.iPixelData < fSize+1
s.PixelData.Start = p.iPixelData;
s.PixelData.Bytes = p.bytes;
if isfield(p, 'VR'), s.PixelData.Format = vr2fmt(p.VR); end
end
if isfield(s, 'CSAImageHeaderInfo') % Siemens CSA image header
s.CSAImageHeaderInfo = read_csa(s.CSAImageHeaderInfo);
end
if isfield(s, 'CSASeriesHeaderInfo') % series header
s.CSASeriesHeaderInfo = read_csa(s.CSASeriesHeaderInfo);
end
if isfield(s, 'ProtocolDataBlock') % GE
s.ProtocolDataBlock = read_ProtocolDataBlock(s.ProtocolDataBlock);
end
%% nested function: update Manufacturer
function [p, dict] = updateVendor(p, vendor)
if ~isempty(p.dict.vendor) && strncmpi(vendor, p.dict.vendor, 2)
dict = p.dict; % in case dicm_hdr asks 3rd output
return;
end
dict_full = dicm_dict(vendor);
if ~p.fullHdr && isfield(p.dict, 'fields')
dict = dicm_dict(vendor, p.dict.fields);
else
dict = dict_full;
end
p.dict = dict;
end
end % main func
%% subfunction: read dicom item. Called by dicm_hdr and read_sq
function [dat, name, info, i, tag] = read_item(b8, i, p)
dat = []; name = nan; info = ''; vr = 'CS'; % vr may be used if implicit
group = b8(i+(0:1)); i=i+2;
swap = p.be && ~isequal(group, [2 0]); % good news: no 0x0200 group
group = ch2int16(group, swap);
elmnt = ch2int16(b8(i+(0:1)), swap); i=i+2;
tag = group*65536 + elmnt;
if tag == 4294893581 % || tag == 4294893789 % FFFEE00D or FFFEE0DD
i = i+4; % skip length
return; % return in case n is not 0
end
swap = p.be && group~=2;
hasVR = p.expl || group==2;
if hasVR, vr = char(b8(i+(0:1))); i = i+2; end % 2-byte VR
[n, nvr] = val_len(vr, b8(i+(0:5)), hasVR, swap); i = i + nvr;
if n==0, return; end % empty val
% Look up item name in dictionary
ind = find(p.dict.tag == tag, 1);
if ~isempty(ind)
name = p.dict.name{ind};
if strcmp(vr, 'UN') || strcmp(vr, 'OB') || ~hasVR, vr = p.dict.vr{ind}; end
elseif tag==524400 % in case not in dict
name = 'Manufacturer';
elseif tag==131088 % need TransferSyntaxUID even if not in dict
name = 'TransferSyntaxUID';
elseif tag==593936 % 0x0009 0010 GEIIS not dicom compliant
i = i+n; return; % seems n is not 0xffffffff
elseif p.fullHdr
if elmnt==0, i = i+n; return; end % skip GroupLength
if mod(group,2), name = sprintf('Private_%04x_%04x', group, elmnt);
else, name = sprintf('Unknown_%04x_%04x', group, elmnt);
end
if ~hasVR, vr = 'UN'; end % not in dict, will leave as uint8
elseif n<4294967295 % no skip for SQ with length 0xffffffff
i = i+n; return;
end
% compressed PixelData, n can be 0xffffffff
if ~hasVR && n==4294967295, vr = 'SQ'; end % best guess
if n+i>p.iPixelData && ~strcmp(vr, 'SQ'), i = i+n; return; end % PixelData or err
% fprintf('(%04x %04x) %s %6.0f %s\n', group, elmnt, vr, n, name);
if strcmp(vr, 'SQ')
nEnd = min(i+n, p.iPixelData); % n is likely 0xffff ffff
[dat, info, i] = read_sq(b8, i, nEnd, p, tag==1375769136); % isPerFrameSQ?
else
[dat, info] = read_val(b8(i+(0:n-1)), vr, swap); i=i+n;
end
% if group==33
% fprintf('\t''%04X'' ''%04X'' ''%s'' ''%s'' ', group, elmnt, vr, name);
% if numel(dat)>99, fprintf('''%s ...''', dat(1:9));
% elseif ischar(dat), fprintf('''%s''', dat);
% elseif isnumeric(dat), fprintf('%g ', dat);
% else, fprintf('''SQ''');
% end
% fprintf('\n');
% end
end
%% Subfunction: decode SQ, called by read_item (recursively)
% SQ structure:
% while isItem (FFFE E000, Item) % Item_1, Item_2, ...
% loop tags under the Item till FFFE E00D, ItemDelimitationItem
% return if FFFE E0DD SequenceDelimitationItem (not checked)
function [rst, info, i] = read_sq(b8, i, nEnd, p, isPerFrameSQ)
rst = []; info = ''; tag1 = []; j = 0; % j is SQ Item index
while i<nEnd % loop through multi Item under the SQ
tag = b8(i+([2 3 0 1])); i = i+4;
if p.be, tag = tag([2 1 3 4]); end
tag = ch2int32(tag, 0);
if tag ~= 4294893568, i = i+4; return; end % only do FFFE E000, Item
n = ch2int32(b8(i+(0:3)), p.be); i = i+4; % n may be 0xffff ffff
n = min(i+n, nEnd);
j = j + 1;
% This 'if' block deals with partial PerFrameSQ: j and i jump to a frame.
% The 1/2/nf frame scheme will have problem in case that tag1 in 1st frame
% is not the first tag in other frames. Then the tags before tag1 in other
% frames will be treated as for previous frame. This is very unlikely since
% the 1st tag is almost always a SQ, like MREchoSequence
if isPerFrameSQ
if ischar(p.iFrames) % 'all' frames
if j==1 && ~isnan(p.nFrames), rst.FrameStart = nan(1, p.nFrames); end
rst.FrameStart(j) = i-9;
elseif j==1 % always read 1st frame, save i0 in case of re-do
i0 = i-8; rst.FrameStart = i-9;
elseif j==2 % always read 2nd frame, and find start ind for all frames
if isnan(p.nFrames) || isempty(tag1) % 1st frame has no asked tag
p.iFrames = 'all'; rst = []; j = 0; i = i0; % re-do the SQ
continue; % re-do
end
tag1 = char(typecast(uint32(tag1), 'uint8'));
tag1 = tag1([3 4 1 2]);
if p.be && ~isequal(tag1(1:2),[2 0]), tag1 = tag1([2 1 4 3]); end
ind = strfind(char(b8(i0:p.iPixelData)), tag1) + i0 - 1;
ind = ind(mod(ind,2)==1);
nInd = numel(ind);
if nInd ~= p.nFrames
tag1PerF = nInd / p.nFrames;
if mod(tag1PerF, 1) > 0 % not integer, read all frames
p.iFrames = 'all'; rst = []; j = 0; i = i0; % re-do SQ
fprintf(2, ['Failed to determine indice for frames. ' ...
'Reading all frames. Maybe slow ...\n']);
continue;
elseif tag1PerF>1 % more than one ind for each frame
ind = ind(1:tag1PerF:nInd);
nInd = p.nFrames;
end
end
rst.FrameStart = ind-9; % 0-based
iItem = 2; % initialize here. Increase when j>2
iFrame = unique([1 2 round(p.iFrames) nInd]);
else % overwrite j with asked iFrame, overwrite i with start ind
iItem = iItem + 1;
j = iFrame(iItem);
i = ind(j); % start of tag1 for asked frame
n = nEnd; % use very end of the sq
end
end
Item_n = sprintf('Item_%g', j);
while i<n % loop through multi tags under one Item
[dat, name, info, i, tag] = read_item(b8, i, p);
if tag == 4294893581, break; end % FFFE E00D ItemDelimitationItem
if isempty(tag1), tag1 = tag; end % first detected tag for PerFrameSQ
if isempty(dat) || isnumeric(name), continue; end % 0-length or skipped
rst.(Item_n).(name) = dat;
end
end
end
%% subfunction: cast uint8/char to double. Better performance than typecast
function d = ch2int32(u8, swap)
if swap, u8 = u8([4 3 2 1]); end
d = double(u8);
d = d(1) + d(2)*256 + d(3)*65536 + d(4)*16777216; % d = d * 256.^(0:3)';
end
function d = ch2int16(u8, swap)
if swap, u8 = u8([2 1]); end
d = double(u8);
d = d(1) + d(2)*256;
end
%% subfunction: return value length, numel(b)=6
function [n, nvr] = val_len(vr, b, expl, swap)
len16 = 'AE AS AT CS DA DS DT FD FL IS LO LT PN SH SL SS ST TM UI UL US';
if ~expl % implicit, length irrevalent to vr (faked as CS)
n = ch2int32(b(1:4), swap);
nvr = 4; % bytes of VR
elseif ~isempty(strfind(len16, vr)) %#ok<*STREMP> % length in uint16
n = ch2int16(b(1:2), swap);
nvr = 2;
else % length in uint32 and skip 2 bytes
n = ch2int32(b(3:6), swap);
nvr = 6;
end
if n==13, n = 10; end % ugly bug fix for some old dicom file
end
%% subfunction: read value, called by search method and read_item
function [dat, info] = read_val(b, vr, swap)
if strcmp(vr, 'DS') || strcmp(vr, 'IS')
dat = sscanf(char(b), '%f\\'); % like 1\2\3
elseif ~isempty(strfind('AE AS CS DA DT LO LT PN SH ST TM UI UT', vr)) % char
dat = deblank(char(b));
else % numeric data, UN. SQ taken care of
fmt = vr2fmt(vr);
if isempty(fmt)
dat = [];
info = sprintf('Given up: Invalid VR (%d %d)', vr);
return;
end
dat = b'; % keep as bytes in case typecast fails
try dat = typecast(dat, fmt); end
if swap, dat = swapbytes(dat); end
end
info = '';
end
%% subfunction: numeric format str from VR
function fmt = vr2fmt(vr)
switch vr
case 'US', fmt = 'uint16';
case 'OB', fmt = 'uint8';
case 'FD', fmt = 'double';
case 'SS', fmt = 'int16';
case 'UL', fmt = 'uint32';
case 'SL', fmt = 'int32';
case 'FL', fmt = 'single';
case 'AT', fmt = 'uint16';
case 'OW', fmt = 'uint16';
case 'OF', fmt = 'single';
case 'OD', fmt = 'double';
case 'UN', fmt = 'uint8';
otherwise, fmt = '';
end
end
%% subfunction: get nFrames into p.nFrames
function p = get_nFrames(s, p, ch)
if isfield(s, 'NumberOfFrames')
p.nFrames = s.NumberOfFrames; % useful for PerFrameSQ
elseif all(isfield(s, {'Columns' 'Rows' 'BitsAllocated'})) && p.bytes<4294967295
if isfield(s, 'SamplesPerPixel'), spp = double(s.SamplesPerPixel);
else, spp = 1;
end
n = p.bytes * 8 / double(s.BitsAllocated);
p.nFrames = n / (spp * double(s.Columns) * double(s.Rows));
else
% FFFE E0DD, 4-byte len (zeros), 0020 9111 (FrameContentSequence)
% GE has no FFFE E0DD 0000 0000. Only FrameContentSequence tag is not safe
tg = char([254 255 221 224 0 0 0 0 32 0 17 145]);
if p.be, tg = tg([2 1 4 3 5:8 10 9 12 11]); end
if p.expl, tg = [tg 'SQ']; end
p.nFrames = numel(strfind(char(ch), tg));
if p.nFrames<1, p.nFrames = nan; end
end
end
%% subfunction: decode Siemens CSA image and series header
function csa = read_csa(csa)
b = csa';
if numel(b)<4 || ~strcmp(char(b(1:4)), 'SV10'), return; end % no op if not SV10
chDat = 'AE AS CS DA DT LO LT PN SH ST TM UI UN UT';
i = 8; % 'SV10' 4 3 2 1
try % in case of error, we return the original csa
nField = ch2int32(b(i+(1:4)), 0); i=i+8;
for j = 1:nField
i=i+68; % name(64) and vm(4)
vr = char(b(i+(1:2))); i=i+8; % vr(4), syngodt(4)
n = ch2int32(b(i+(1:4)), 0); i=i+8;
if n<1, continue; end % skip name decoding, faster
nam = regexp(char(b(i-84+(1:64))), '\w+', 'match', 'once');
isNum = isempty(strfind(chDat, vr));
% fprintf('%s %3g %s\n', vr, n, nam);
dat = [];
for k = 1:n % n is often 6, but often only the first contains value
len = ch2int32(b(i+(1:4)), 0); i=i+16;
if len<1, i = i+(n-k)*16; break; end % rest are empty too
foo = char(b(i+(1:len-1))); % exclude nul, need for Octave
i = i + ceil(len/4)*4; % multiple 4-byte
if isNum
tmp = sscanf(foo, '%f', 1); % numeric to double
if ~isempty(tmp), dat(k,1) = tmp; end %#ok
else
dat{k} = deblank(foo); %#ok
end
end
if ~isNum
dat(cellfun(@isempty, dat)) = []; %#ok
if isempty(dat), continue; end
if numel(dat)==1, dat = dat{1}; end
end
rst.(nam) = dat;
end
csa = rst;
end
end
%% subfunction: decode GE ProtocolDataBlock
function ch = read_ProtocolDataBlock(ch)
n = typecast(ch(1:4), 'int32') + 4; % nBytes, zeros may be padded to make 4x
if ~all(ch(5:6) == [31 139]') || n>numel(ch), return; end % gz signature
ch = nii_tool('LocalFunc', 'gunzip_mem', ch(5:n))';
ch = regexp(char(ch), '(\w*)\s+"(.*?)"\n', 'tokens');
ch = [ch{:}];
ch = struct(ch{:});
end
%% subfunction: get fields for multiframe dicom
function s1 = search_MF_val(s, s1, iFrame)
% s1 = search_MF_val(s, s1, iFrame);
% Arg 1: the struct returned by dicm_hdr for a multiframe dicom
% Arg 2: a struct with fields to search, and with initial value, such as
% zeros or nans. The number of rows indicates the number of values for the
% tag, and columns for frames indicated by iFrame, Arg 3.
% Arg 3: frame indice, length consistent with columns of s1 field values.
% Example:
% s = dicm_hdr('multiFrameFile.dcm'); % read only 1,2 and last frame by default
% s1 = struct('ImagePositionPatient', nan(3, s.NumberOfFrames)); % define size
% s1 = search_MF_val(s, s1, 1:s.NumberOfFrames); % get values
% This is MUCH faster than asking all frames by dicm_hdr, and avoid to get into
% annoying SQ levels under PerFrameFuntionalGroupSequence. In case a tag is not
% found in PerFrameSQ, the code will search SharedSQ and common tags, and will
% ignore the 3th arg and duplicate the same value for all frames.
if ~isfield(s, 'PerFrameFunctionalGroupsSequence'), return; end
expl = false;
be = false;
if isfield(s, 'TransferSyntaxUID')
expl = ~strcmp(s.TransferSyntaxUID, '1.2.840.10008.1.2');
be = strcmp(s.TransferSyntaxUID, '1.2.840.10008.1.2.2');
end
fStart = s.PerFrameFunctionalGroupsSequence.FrameStart; % error if no FrameStart
fid = fopen(s.Filename);
b0 = fread(fid, fStart(1), 'uint8=>char')'; % before 1st frame in PerFrameSQ
b = fread(fid, s.PixelData.Start-fStart(1), 'uint8=>char')'; % within PerFrameSQ
fclose(fid);
fStart(end+1) = s.PixelData.Start; % for later ind search
fStart = fStart - fStart(1) + 1; % 1-based index in b
flds = fieldnames(s1);
dict = dicm_dict(s.Manufacturer, flds);
len16 = 'AE AS AT CS DA DS DT FD FL IS LO LT PN SH SL SS ST TM UI UL US';
chDat = 'AE AS CS DA DT LO LT PN SH ST TM UI UT';
nf = numel(iFrame);
for i = 1:numel(flds)
k = find(strcmp(dict.name, flds{i}), 1, 'last'); % GE has another ipp tag
if isempty(k), continue; end % likely private tag for another vendor
vr = dict.vr{k};
group = dict.group(k);
isBE = be && group~=2;
isEX = expl || group==2;
tg = char(typecast([group dict.element(k)], 'uint8'));
if isBE, tg = tg([2 1 4 3]); end
if isEX, tg = [tg vr]; end %#ok
ind = strfind(b, tg);
ind = ind(mod(ind,2)>0); % indice is odd
if isempty(ind) % no tag in PerFrameSQ, try tag before PerFrameSQ
ind = strfind(b0, tg);
ind = ind(mod(ind,2)>0);
if ~isempty(ind)
k = ind(1) + numel(tg); % take 1st in case of multiple
[n, nvr] = val_len(vr, uint8(b0(k+(0:5))), isEX, isBE); k = k + nvr;
a = read_val(uint8(b0(k+(0:n-1))), vr, isBE);
if ischar(a), a = {a}; end
s1.(flds{i}) = repmat(a, 1, nf); % all frames have the same value
end
continue;
end
len = 4; % bytes of tag value length (uint32)
if ~isEX % implicit, length irrevalent to VR
ind = ind + 4; % tg(4)
elseif ~isempty(strfind(len16, vr)) % data length in uint16
ind = ind + 6; % tg(4), vr(2)
len = 2;
else % length in uint32: skip 2 bytes
ind = ind + 8; % tg(4), vr(2), skip(2)
end
isCH = ~isempty(strfind(chDat, vr)); % char data
isDS = strcmp(vr, 'DS') || strcmp(vr, 'IS');
if ~isCH && ~isDS % numeric data, UN or SQ
fmt = vr2fmt(vr);
if isempty(fmt), continue; end % skip SQ
end
for k = 1:nf
j = iFrame(k); % asked frame index
j = find(ind>fStart(j) & ind<fStart(j+1), 1); % index in ind
if isempty(j), continue; end % no tag for this frame
if len==2, n = ch2int16(b(ind(j)+(0:1)), isBE);
else, n = ch2int32(b(ind(j)+(0:3)), isBE);
end
a = b(ind(j)+len+(0:n-1));
if isDS
a = sscanf(a, '%f\\'); % like 1\2\3
try s1.(flds{i})(:,k) = a; end %#ok<*TRYNC> ignore in case of error
elseif isCH
try s1.(flds{i}){k} = deblank(a); end
else
a = typecast(uint8(a), fmt)';
if isBE, a = swapbytes(a); end
try s1.(flds{i})(:,k) = a; end
end
end
end
end
%% subfunction: read PAR file, return struct like that from dicm_hdr.
function [s, err] = philips_par(fname)
err = '';
fid = fopen(fname);
if fid<0, s = []; err = ['File not exist: ' fname]; return; end
fullName = fopen(fid); % name with full path
[pth, nam] = fileparts(fullName);
str = fread(fid, inf, '*char')'; % read all as char
fclose(fid);
str = strrep(str, char([13 10]), char(10)); % remove char(13)
ch = regexp(str, '.*?(?=IMAGE INFORMATION DEFINITION)', 'match', 'once');
V = regexpi(ch, 'image export tool\s*(V[\d\.]+)', 'tokens', 'once');
if isempty(V), err = 'Not PAR file'; s = []; return; end
V = V{1};
s.SoftwareVersion = [V '\PAR'];
s.PatientName = par_attr(ch, 'Patient name', 0);
s.StudyDescription = par_attr(ch, 'Examination name', 0);
s.SeriesDescription = nam;
s.ProtocolName = par_attr(ch, 'Protocol name', 0);
a = par_attr(ch, 'Examination date/time', 0);
s.AcquisitionDateTime = a(isstrprop(a, 'digit'));
s.SeriesNumber = par_attr(ch, 'Acquisition nr');
% s.ReconstructionNumberMR = par_attr(ch, 'Reconstruction nr');
% s.MRSeriesScanDuration = par_attr(ch, 'Scan Duration');
s.NumberOfEchoes = par_attr(ch, 'Max. number of echoes');
a = par_attr(ch, 'Patient position', 0);
if isempty(a), a = par_attr(ch, 'Patient Position', 0); end
if ~isempty(a)
if numel(a)>4, s.PatientPosition = a(regexp(a, '\<.'));
else, s.PatientPosition = a;
end
end
s.MRAcquisitionType = par_attr(ch, 'Scan mode', 0);
s.ScanningSequence = par_attr(ch, 'Technique', 0); % ScanningTechnique
typ = par_attr(ch, 'Series Type', 0); typ(isspace(typ)) = '';
s.ImageType = ['PhilipsPAR\' typ '\' s.ScanningSequence];
s.RepetitionTime = par_attr(ch, 'Repetition time');
s.WaterFatShift = par_attr(ch, 'Water Fat shift');
s.EPIFactor = par_attr(ch, 'EPI factor');
% s.DynamicSeries = par_key(ch, 'Dynamic scan'); % 0 or 1
% Get list of para meaning for the table, and col index of each para
i1 = regexpi(str, 'IMAGE INFORMATION DEFINITION', 'once');
i2 = regexpi(str, '= IMAGE INFORMATION ='); i2 = i2(end);
ind = regexp(str(i1:i2), '\n#') + i1;
colLabel = {}; iColumn = [];
for i = 1:numel(ind)-1
a = str(ind(i)+1:ind(i+1)-2); % a line
i1 = regexp(a, '[<(]{1}'); % need first '<' or '(', and last '('
if isempty(i1), continue; end
nCol = sscanf(a(i1(end)+1:end), '%g');
if isempty(nCol), nCol = 1; end
colLabel{end+1} = strtrim(a(1:i1(1)-1)); %#ok para name
iColumn(end+1) = nCol; %#ok number of columns in the table for this para
end
iColumn = cumsum([1 iColumn]); % col start ind for corresponding colLabel
keyInLabel = @(key)strcmpi(colLabel, key);
colIndex = @(key)iColumn(keyInLabel(key));
i1 = regexp(str(i2:end), '\n\s*\d+', 'once') + i2;
n = iColumn(end)-1; % number of items each row, 41 for V4
para = sscanf(str(i1:end), '%g'); % read all numbers
nFrame = floor(numel(para) / n);
para = reshape(para(1:n*nFrame), n, nFrame)'; % whole table now
% SortFrames solves XYTZ, unusual slice order, incomplete volume etc
keys = {'dynamic scan number' 'gradient orientation number' 'echo number' ...
'cardiac phase number' 'image_type_mr' 'label type' 'scanning sequence'};
ic = []; for i = 1:numel(keys), ic = [ic colIndex(keys{i})]; end %#ok
sort_frames = dicm2nii('', 'sort_frames', 'func_handle');
sl = [para(:, colIndex('slice number')) para(:, colIndex('diffusion_b_factor'))];
[ind_sort, nSL] = sort_frames(sl, para(:, ic));
a = par_val('index in REC file', 1:nFrame); % always 0:nFrame-1 ?
a(a+1) = 1:nFrame; % [~, a] = sort(a);
a = a(ind_sort)';
if ~isequal(a, 1:nFrame), s.SortFrames = a; end % used only in dicm2nii
para = para(ind_sort, :); % XYZT order
s.LocationsInAcquisition = nSL;
s.NumberOfFrames = numel(ind_sort); % may be smaller than nFrame
s.NumberOfTemporalPositions = s.NumberOfFrames/nSL;
iVol = (0:s.NumberOfTemporalPositions-1)*nSL + 1; % already XYZT
fld = 'ComplexImageComponent';
typ = {'MAGNITUDE' 'REAL' 'IMAGINARY' 'PHASE'};
imgType = para(iVol, colIndex('image_type_mr'));
imgType(imgType==16) = 0;
imgType(imgType==17) = 3;
imgType(imgType==18) = 1;
ind = imgType + 1;
a = unique(imgType(imgType>3)); % unknown type
for i = 1:numel(a)
ind(imgType==a(i)) = i+4;
typ{i+4} = sprintf('image_type%g', a(i));
end
if numel(iVol) == 1
s.ComplexImageComponent = typ{ind(1)};
elseif any(diff(ind) ~= 0) % more than 1 type of image
s.(fld) = 'MIXED';
s.Volumes.(fld) = typ(ind); % one for each vol
s.Volumes.RescaleIntercept = para(iVol, colIndex('rescale intercept'));
s.Volumes.RescaleSlope = para(iVol, colIndex('rescale slope'));
s.Volumes.MRScaleSlope = para(iVol, colIndex('scale slope'));
else
s.ComplexImageComponent = typ(ind(1)); % cellstr
end
% These columns should be the same for nifti-convertible images:
cols = {'image pixel size' 'recon resolution' 'image angulation' ...
'slice thickness' 'slice gap' 'slice orientation' 'pixel spacing'};
if ~strcmp(s.((fld)), 'MIXED')
cols = [cols {'rescale intercept' 'rescale slope' 'scale slope'}];
end
ind = [];
for i = 1:numel(cols)
j = find(keyInLabel(cols{i}));
if isempty(j), continue; end % some not in V3
ind = [ind iColumn(j):iColumn(j+1)-1]; %#ok
end
a = para(:, ind);
a = abs(diff(a));
if any(a(:) > 1e-5)
err = sprintf('Inconsistent image size, bits etc: %s', fullName);
fprintf(2, ' %s. \n', err);
s = []; return;
end
% s.EchoNumber = getTableVal('echo number', 1:s.NumberOfFrames);
% 'pixel spacing' and 'slice gap' have poor precision for v<=4?
% It may be wrong to use FOV, maybe due to partial Fourier?
if strncmp(V, 'V3', 2)
s.BitsAllocated = par_attr(ch, 'Image pixel size', 1);
res = par_attr(ch, 'Recon resolution', 1);
s.SliceThickness = par_attr(ch, 'Slice thickness', 1);
gap = par_attr(ch, 'Slice gap', 1);
s.TurboFactor = par_attr('TURBO factor', 1);
s.NumberOfAverages = par_attr(ch, 'Number of averages', 1);
else
s.BitsAllocated = par_val('image pixel size');
res = par_val('recon resolution');
s.SliceThickness = par_val('slice thickness');
gap = par_val('slice gap');
s.TurboFactor = par_val('TURBO factor');
s.NumberOfAverages = par_val('number of averages');
end
s.Columns = res(1);
s.Rows = res(2);
if gap < 0, gap = 0; end
s.SpacingBetweenSlices = gap + s.SliceThickness;
a = par_val('pixel spacing');
s.PixelSpacing = a(:);
s.RescaleIntercept = par_val('rescale intercept');
s.RescaleSlope = par_val('rescale slope');
s.MRScaleSlope = par_val('scale slope');
s.EchoTimes = par_val('echo_time', iVol);
s.EchoTime = s.EchoTimes(1);
s.FlipAngle = par_val('image_flip_angle');
s.CardiacTriggerDelayTimes = par_val('trigger_time', iVol);
% s.TimeOfAcquisition = par_val('dyn_scan_begin_time', 1:s.NumberOfFrames);
posMid = par_attr(ch, 'Off Centre midslice'); % (ap,fh,rl) [mm]
posMid = posMid([3 1 2]); % better precision than those in the table
rotAngle = par_attr(ch, 'Angulation midslice'); % (ap,fh,rl) deg
a = rotAngle([3 1 2]) /180*pi; % always this order?
R = makehgtform('xrotate', a(1), 'yrotate', a(2), 'zrotate', a(3));
R = R(1:3, :);
iOri = par_val('slice orientation'); % 1/2/3 for TRA/SAG/COR
iOri = mod(iOri+1, 3) + 1;
a = {'SAGITTAL' 'CORONAL' 'TRANSVERSAL'};
s.SliceOrientation = a{iOri};
if iOri == 1
R(:,[1 3]) = -R(:,[1 3]);
R = R(:, [2 3 1 4]);
elseif iOri == 2
R(:,3) = -R(:,3);
R = R(:, [1 3 2 4]);
end
a = par_attr(ch, 'Preparation direction', 0); % Anterior-Posterior
if ~isempty(a)
a = a(regexp(a, '\<.')); % 'AP'
s.Stack.Item_1.MRStackPreparationDirection = a;
iPhase = strfind('LRAPFH', a(1));
iPhase = ceil(iPhase/2); % 1/2/3
if iPhase == (iOri==1)+1, a = 'ROW'; else, a = 'COL'; end
s.InPlanePhaseEncodingDirection = a;
end
s.ImageOrientationPatient = R(1:6)';
R = R * diag([s.PixelSpacing([2 1]); s.SpacingBetweenSlices; 1]);
R(:,4) = posMid; % 4th col is mid slice center position
a = par_val('image offcentre', [1 nSL]);
% Take axis with largest 'image offcentre' range as slice axis. This can be
% wrong in theory, but the fix based on PAR version do not work
[~, ind] = max(max(a)-min(a));
if ind==iOri, ax_order = 1:3; else, ax_order = [3 1 2]; end
s.SliceLocation = a(1, ax_order(iOri)); % center loc for 1st slice
if sign(R(iOri,3)) ~= sign(posMid(iOri)-s.SliceLocation)
R(:,3) = -R(:,3);
end
if par_attr(ch, 'Diffusion')>0 % DTI
s.ImageType = [s.ImageType '\DIFFUSION\'];
s.DiffusionEchoTime = par_attr(ch, 'Diffusion echo time'); % ms
s.B_value = par_val('diffusion_b_factor', iVol);
a = par_val('diffusion', iVol);
if ~isempty(a), s.bvec_original = a(:, ax_order); end
end
R(:,4) = R * [-([s.Columns s.Rows nSL]-1)/2 1]'; % vol center to corner of 1st
s.ImagePositionPatient = R(:,4);
s.LastFile.ImagePositionPatient = R * [0 0 nSL-1 1]'; % last slice
s.Manufacturer = 'Philips';
s.Filename = fullfile(pth, [nam '.REC']); % rest for dicm_img
s.PixelData.Start = 0;
s.PixelData.Bytes = s.Rows * s.Columns * nFrame * s.BitsAllocated / 8;
% nested function: set field if the key is in colTable
function val = par_val(key, iRow)
if nargin<2, iRow = 1; end
iCol = find(keyInLabel(key));
val = para(iRow, iColumn(iCol):iColumn(iCol+1)-1);
end
% subfunction: return value specified by key in PAR file
function val = par_attr(ch, key, isNum)
expr = ['\n.\s*' key '.*?:(.*?)\n']; % \n. key ... : val \n
val = strtrim(regexp(ch, expr, 'tokens', 'once'));
if isempty(val), val = ''; else, val = val{1}; end
if nargin<3 || isNum, val = sscanf(val, '%g'); end
end
end
%% subfunction: read AFNI HEAD file, return struct like that from dicm_hdr.
function [s, err] = afni_head(fname)
err = '';
fid = fopen(fname);
if fid<0, s = []; err = ['File not exist: ' fname]; return; end
str = fread(fid, inf, '*char')';
fname = fopen(fid);
fclose(fid);
i = strfind(str, 'DATASET_DIMENSIONS');
if isempty(i), s = []; err = 'Not brik header file'; return; end
% these make dicm_nii.m happy
[~, foo] = fileparts(fname);
% s.IsAFNIHEAD = true;
s.ProtocolName = foo;
s.ImageType = ['AFNIHEAD\' afni_key('TYPESTRING')];
foo = afni_key('BYTEORDER_STRING'); % "LSB_FIRST" or "MSB_FIRST".
if strcmpi(foo, 'MSB_FIRST'), s.TransferSyntaxUID = '1.2.840.10008.1.2.2'; end
foo = afni_key('BRICK_FLOAT_FACS');
if any(diff(foo)~=0), err = 'Inconsistent BRICK_FLOAT_FACS';
s = []; return;
end
if foo(1)==0, foo = 1; end
s.RescaleSlope = foo(1);
s.RescaleIntercept = 0;
foo = afni_key('BRICK_TYPES');
if any(diff(foo)~=0), err = 'Inconsistent DataType'; s = []; return; end
foo = foo(1);
if foo == 0
bpp = 8; s.PixelData.Format = '*uint8';
elseif foo == 1
bpp = 16; s.PixelData.Format = '*int16';
elseif foo == 3
bpp = 32; s.PixelData.Format = '*single';
else
error('Unsupported BRICK_TYPES: %g', foo);
end
hist = afni_key('HISTORY_NOTE');
i = strfind(hist, 'Time:') + 6;
if ~isempty(i)
dat = sscanf(hist(i:end), '%11c', 1); % Mar 1 2010
dat = datenum(dat, 'mmm dd yyyy');
s.AcquisitionDateTime = datestr(dat, 'yyyymmdd');
end
i = strfind(hist, 'Sequence:') + 9;
if ~isempty(i), s.ScanningSequence = strtok(hist(i:end), ' '); end
i = strfind(hist, 'Studyid:') + 8;
if ~isempty(i), s.StudyID = strtok(hist(i:end), ' '); end
% i = strfind(hist, 'Dimensions:') + 11;
% if ~isempty(i)
% dimStr = strtok(hist(i:end), ' ') % 64x64x35x92
% end
% i = strfind(hist, 'Orientation:') + 12;
% if ~isempty(i)
% oriStr = strtok(hist(i:end), ' ') % LAI
% end
i = strfind(hist, 'TE:') + 3;
if ~isempty(i), s.EchoTime = sscanf(hist(i:end), '%g', 1) * 1000; end
% foo = afni_key('TEMPLATE_SPACE'); % ORIG/TLRC
% INT_CMAP
foo = afni_key('SCENE_DATA');
s.TemplateSpace = foo(1)+1; %[0] 0=+orig, 1=+acpc, 2=+tlrc
if foo(2)==9, s.ImageType = [s.ImageType '\DIFFUSION\']; end
% ori = afni_key('ORIENT_SPECIFIC')+1;
% orients = [1 -1 -2 2 3 -3]; % RL LR PA AP IS SI
% ori = orients(ori) % in dicom/afni LPS,
% seems always [1 2 3], meaning AFNI re-oriented the volome
% no read/phase/slice dim info, so following 3D info are meaningless
dim = afni_key('DATASET_DIMENSIONS');
s.Columns = dim(1); s.Rows = dim(2); s.LocationsInAcquisition = dim(3);
R = afni_key('IJK_TO_DICOM_REAL'); % IJK_TO_DICOM is always straight?
if isempty(R), R = afni_key('IJK_TO_DICOM'); end
R = reshape(R, [4 3])';
s.ImagePositionPatient = R(:,4); % afni_key('ORIGIN') can be wrong
s.LastFile.ImagePositionPatient = R * [0 0 dim(3)-1 1]'; % last slice
R = R(1:3, 1:3);
R = bsxfun(@rdivide, R, sqrt(sum(R.^2)));
s.ImageOrientationPatient = R(1:6)';
foo = afni_key('DELTA');
s.PixelSpacing = abs(foo([2 1]));
% s.SpacingBetweenSlices = foo(3);
s.SliceThickness = abs(foo(3));
foo = afni_key('BRICK_STATS');
foo = reshape(foo, 2, []);
mn = min(foo(1,:)); mx = max(foo(2,:));
s.WindowCenter = (mx+mn)/2;
s.WindowWidth = mx-mn;
foo = afni_key('TAXIS_FLOATS'); %[0]:0;
if ~isempty(foo), s.RepetitionTime = foo(2)*1000; end
foo = afni_key('TAXIS_NUMS'); % [0]:nvals; [1]: 0 or nSL normally
if ~isempty(foo)
inMS = foo(3)==77001;
foo = afni_key('TAXIS_OFFSETS');
if inMS, foo = foo/1000; end
if ~isempty(foo), s.MosaicRefAcqTimes = foo; end
end
foo = afni_key('DATASET_RANK'); % [3 nvals]
dim(4) = foo(2);
s.NumberOfTemporalPositions = dim(4);
% s.NumberOfFrames = dim(4)*dim(3);
s.Manufacturer = '';
s.Filename = strrep(fname, '.HEAD', '.BRIK');
s.PixelData.Start = 0; % make it work for dicm_img.m
s.PixelData.Bytes = prod(dim(1:4)) * bpp / 8;
% subfunction: return value specified by key in afni header str
function val = afni_key(key)
i1 = regexp(str, ['\nname\s*=\s*' key '\n']); % line 'name = key'
if isempty(i1), val = []; return; end
i1 = i1(1) + 1;
typ = regexp(str(1:i1), 'type\s*=\s*(\w*)-attribute\n', 'tokens');
[n, i2] = regexp(str(i1:end), 'count\s*=\s*(\d+)', 'tokens', 'end', 'once');
n = sscanf(n{1}, '%g');
if strcmpi(typ{end}{1}, 'string')
val = regexp(str(i1:end), '(?<='').*?(?=~?\n)', 'match', 'once');
else
val = sscanf(str(i2+i1:end), '%g', n);
end
end
end
%% Subfunction: read BrainVoyager vmr/fmr/dmr. Call BVQXfile
function [s, err] = bv_file(fname)
s = []; err = '';
try
bv = BVQXfile(fname);
catch me
err = me.message;
if strfind(me.identifier, 'UndefinedFunction')
fprintf(2, 'Please download BVQXtools at \n%s\n', ...
'http://support.brainvoyager.com/available-tools/52-matlab-tools-bvxqtools.html');
end
return;
end
if ~isempty(bv.Trf)
for i = 1:numel(bv.Trf)
if ~isequal(diag(bv.Trf(i).TransformationValues), [1 1 1 1]')
err = 'Data has been transformed: skipped.';
return;
end
end
end
persistent subj folder % folder is used to update subj
if isempty(subj), subj = ''; folder = ''; end
s.Filename = bv.FilenameOnDisk;
fType = bv.filetype;
s.ImageType = ['BrainVoyagerFile\' fType];
% Find a fmr/dmr, and get subj based on dicom file name in BV format.
% Suppose BV files in the folder are for the same subj
[pth, nam] = fileparts(s.Filename);
s.SeriesDescription = nam;
if isempty(folder) || ~strcmp(folder, pth)
folder = pth;
subj = '';
if strcmp(fType, 'fmr') || strcmp(fType, 'dmr')
[~, nam] = fileparts(bv.FirstDataSourceFile);
nam = strtok(nam, '-');
if ~isempty(nam), subj = nam; end
else
fnames = dir([pth '/*.fmr']);
if isempty(fnames), fnames = dir([pth '/*.dmr']); end
if ~isempty(fnames)
bv1 = BVQXfile(fullfile(pth, fnames(1).name));
[~, nam] = fileparts(bv1.FirstDataSourceFile);
bv1.ClearObject;
nam = strtok(nam, '-');
if ~isempty(nam), subj = nam; end
end
end
end
if ~isempty(subj), s.PatientName = subj; end
s.SoftwareVersion = sprintf('%g/BV_FileVersion', bv.FileVersion);
s.Columns = bv.NCols;
s.Rows = bv.NRows;
s.SliceThickness = bv.SliceThickness;
R = [bv.RowDirX bv.RowDirY bv.RowDirZ; bv.ColDirX bv.ColDirY bv.ColDirZ]';
s.ImageOrientationPatient = R(:);
R(:,3) = cross(R(:,1), R(:,2));
[~, ixyz] = max(abs(R)); iSL =ixyz(3);
try
s.TemplateSpace = bv.ReferenceSpace; % 0/2/3: Scanner/ACPC/TAL
if s.TemplateSpace==0, s.TemplateSpace = 1; end
catch
s.TemplateSpace = 1;
end
pos = [bv.Slice1CenterX bv.Slice1CenterY bv.Slice1CenterZ
bv.SliceNCenterX bv.SliceNCenterY bv.SliceNCenterZ]'; % for real slices
if strcmpi(fType, 'vmr')
s.SpacingBetweenSlices = s.SliceThickness + bv.GapThickness;
s.PixelSpacing = [bv.VoxResX bv.VoxResY]'; % order correct?
if ~isempty(bv.VMRData16)
nSL = bv.DimZ;
s.PixelData = bv.VMRData16; % no padded zeros
else
v16 = [s.Filename(1:end-3) 'v16'];
if exist(v16, 'file')
bv16 = BVQXfile(v16);
nSL = bv16.DimZ;
s.PixelData = bv16.VMRData; % no padded zeros
bv16.ClearObject;
else % fall back the 8-bit data, and deal with padded zeros
ix = floor((bv.DimX - s.Columns)/2);
iy = floor((bv.DimY - s.Rows)/2);
R3 = abs(R(iSL,3)) * s.SpacingBetweenSlices;
nSL = round(abs(diff(pos(iSL,:))) / R3) + 1;
iz = floor((bv.DimZ - nSL)/2);
s.PixelData = bv.VMRData(ix+(1:s.Columns), iy+(1:s.Rows), iz+(1:nSL), :);
end
end
s.LocationsInAcquisition = nSL;
s.MRAcquisitionType = '3D'; % for dicm2nii to re-orient
elseif strcmpi(fType, 'fmr') || strcmpi(fType, 'dmr')
s.SpacingBetweenSlices = s.SliceThickness + bv.SliceGap;
s.PixelSpacing = [bv.InplaneResolutionX bv.InplaneResolutionY]'; % order?
nSL = bv.NrOfSlices;
s.LocationsInAcquisition = nSL;
s.NumberOfTemporalPositions = bv.NrOfVolumes;
s.RepetitionTime = bv.TR;
s.EchoTime = bv.TE;
if bv.TimeResolutionVerified
switch bv.SliceAcquisitionOrder % the same as NIfTI?
case 1, ind = 1:nSL;
case 2, ind = nSL:-1:1;
case 3, ind = [1:2:nSL 2:2:nSL];
case 4, ind = [nSL:-2:1 nSL-1:-2:1];
case 5, ind = [2:2:nSL 1:2:nSL];
case 6, ind = [nSL-1:-2:1 nSL:-2:1];
otherwise, ind = []; err = 'Unknown SliceAcquisitionOrder';
end
if ~isempty(ind)
t = (0:s.LocationsInAcquisition-1)' * bv.InterSliceTime; % ms
t(ind) = t;
s.SliceTiming = t;
end
end
if strcmpi(fType, 'fmr')
bv.LoadSTC;
s.PixelData = permute(bv.Slice(1).STCData , [1 2 4 3]);
for i = 2:numel(bv.Slice)
s.PixelData(:,:,i,:) = permute(bv.Slice(i).STCData , [1 2 4 3]);
end
else % dmr
s.ImageType = [s.ImageType '\DIFFUSION\'];
bv.LoadDWI;
s.PixelData = bv.DWIData;
if strncmpi(bv.GradientInformationAvailable, 'Y', 1)
a = bv.GradientInformation; % nDir by 4
s.B_value = a(:,4);
a = a(:,1:3); % bvec
% Following should be right in theory, but I would trust the grd
% table which should be in dicom coodinate system, rather than the
% confusing Gradient?DirInterpretation
% % 1:6 for LR RL AP PA IS SI. Default [2 3 5] by dicom LPS
% i1_6 = [bv.GradientXDirInterpretation ...
% bv.GradientYDirInterpretation ...
% bv.GradientZDirInterpretation];
% [xyz, ind] = sort(i1_6);
% if isequal(ceil(xyz/2), 1:3) % perm of 1/2/3
% a = a(:,ind);
% flip = xyz == [1 4 6]; % negative by dicom
% a(:,flip) = -a(:,flip);
% else
% str = sprintf(['Wrong Interpretation of gradient found: %s\n' ...
% 'Please check bvec and its sign.\n'], fname);
% fprintf(2, str);
% err = [err str];
% end
s.bvec_original = a;
end
end
% fmr/dmr are normally converted from uint16 to single
if isfloat(s.PixelData) && isequal(floor(s.PixelData), s.PixelData) ...
&& max(s.PixelData(:))<32768 && min(s.PixelData(:))>=-32768
s.PixelData = int16(s.PixelData);
end
else
err = ['Unknown BV file type: ' fType];
s = [];
return;
end
pos = pos - R(:,1:2) * diag(s.PixelSpacing([2 1])) * [s.Columns s.Rows]'/2 * [1 1];
s.ImagePositionPatient = pos(:,1);
s.LastFile.ImagePositionPatient = pos(:,2);
% Following make dicm2nii happy
s.SeriesInstanceUID = sprintf('%s_%03x', datestr(now, 'yymmddHHMMSSfff'), randi(999));
end
%% subfunction: read Freesurfer mgh or mgz file, return dicm info dicm_hdr.
function [s, err] = mgh_file(fname)
err = ''; s = [];
[~, ~, ext] = fileparts(fname);
isGZ = strcmpi(ext, '.mgz'); % .mgz = .mgh.gz
if isGZ
nam = nii_tool('LocalFunc', 'gunzipOS', fname);
fid = fopen(nam, 'r', 'b');
else
fid = fopen(fname, 'r', 'b'); % always big endian?
end
if fid<0, err = sprintf('File not exists: %s', fname); return; end
cln = onCleanup(@() close_mgh(fid, isGZ)); % close file, delete if isGZ
v = fread(fid, 1, 'int32');
if v ~= 1, err = sprintf('Not mgh file: %s', fname); return; end
dim = fread(fid, 4, 'int32')';
typ = fread(fid, 1, 'int32');
dof = fread(fid, 1, 'int32'); %#ok not used
s.Filename = fname;
s.Columns = dim(1);
s.Rows = dim(2);
s.LocationsInAcquisition = dim(3);
if dim(4)>1, s.NumberOfTemporalPositions = dim(4); end
have_ras = fread(fid, 1, 'int16');
if have_ras % 3+9+3=15 single
pixdim = fread(fid, 3, 'single');
R = fread(fid, [3 3], 'single'); % direction cosine matrix
c = fread(fid, 3, 'single'); % center xyz
R(1:2,:) = -R(1:2,:); c(1:2) = -c(1:2); % RAS to dicom LPS
s.PixelSpacing = pixdim([2 1]);
s.SliceThickness = pixdim(3);
s.ImageOrientationPatient = R(1:6)';
R = R * diag(pixdim);
s.ImagePositionPatient = R * -dim(1:3)'/2 + c;
s.LastFile.ImagePositionPatient = R * [-(dim(1:2))/2 dim(3)/2-1]' + c;
else
s.ImageOrientationPatient = [1 0 0 0 0 -1]'; % coronal
end
switch typ
case 0, fmt = 'uint8'; % MRI_UCHAR
case 1, fmt = 'int32'; % MRI_INT
case 2, fmt = 'int32'; % MRI_LONG
case 3, fmt = 'single'; % MRI_FLOAT
case 4, fmt = 'int16'; % MRI_SHORT
% case 5, fmt = 'uint8'; % MRI_BITMAP *3?
% case 6, fmt = 'uint8'; % MRI_TENSOR *5?
otherwise
err = sprintf('Unknown datatype: %s', fname);
s = []; return;
end
fseek(fid, 284, 'bof'); % start of img data
nv = prod(dim);
img = fread(fid, nv, ['*' fmt]);
if numel(img) ~= nv
err = ['Not enough data in file: ' fname];
s = []; return;
end
flds = {'RepetitionTime' 'FlipAngle' 'EchoTime' 'InversionTime'};
parms4 = fread(fid, 4, 'single');
for i = 1:numel(parms4), s.(flds{i}) = parms4(i); end
if isfield(s, 'FlipAngle'), s.FlipAngle = s.FlipAngle/pi*180; end % to deg
s.PixelData = reshape(img, dim);
function close_mgh(fid, isGZ)
if isGZ
uzip_nam = fopen(fid);
fclose(fid);
delete(uzip_nam);
else
fclose(fid);
end
end
end
%% similar to philips_par, inspired by Julien's xml2par
function [s, err] = philips_xml(fname)
err = '';
fid = fopen(fname);
if fid<0, s = []; err = ['File not exist: ' fname]; return; end
fullName = fopen(fid); % name with full path
ch = fread(fid, inf, '*char')'; % read all as char
fclose(fid);
[pth, nam] = fileparts(fullName);
i = regexp(ch, '</Series_Info>', 'once');
if isempty(i), s = []; err = 'Not valid Philips xml file'; return; end
ch1 = ch(1:i); ch = ch(i:end);
s.SoftwareVersion = regexp(ch1, '(?<=<)PRIDE.*?(?=>)', 'match', 'once');
s.PatientName = xml_attr(ch1, 'Patient Name');
s.StudyDescription = xml_attr(ch1, 'Examination Name');
s.SeriesDescription = nam;
s.ProtocolName = xml_attr(ch1, 'Protocol Name');
d = xml_attr(ch1, 'Examination Date'); d = d(isstrprop(d, 'digit'));
t = xml_attr(ch1, 'Examination Time'); t = t(isstrprop(t, 'digit'));
s.AcquisitionDateTime = [d t];
s.SeriesNumber = xml_attr(ch1, 'Ac?quisition Number', 1);
% s.ReconstructionNumberMR = xml_attr(ch1, 'Reconstruction Number', 1);
% s.MRSeriesScanDuration = xml_attr(ch1, 'Scan Duration', 1);
s.NumberOfEchoes = xml_attr(ch1, 'Max No Echoes', 1);
s.LocationsInAcquisition = xml_attr(ch1, 'Max No Slices', 1);
s.PatientPosition = xml_attr(ch1, 'Patient Position');
s.MRAcquisitionType = xml_attr(ch1, 'Scan Mode');
s.ScanningSequence = xml_attr(ch1, 'Technique'); % ScanningTechnique
typ = xml_attr(ch1, 'Series Data Type'); typ(isspace(typ)) = '';
s.ImageType = ['PhilipsXML\' typ '\' s.ScanningSequence];
s.RepetitionTime = xml_attr(ch1, 'Repetition Times?', 1);
if numel(s.RepetitionTime)>1, s.RepetitionTime = s.RepetitionTime(1); end
s.WaterFatShift = xml_attr(ch1, 'Water Fat Shift', 1);
s.EPIFactor = xml_attr(ch1, 'EPI factor', 1);
% s.DynamicSeries = xml_attr(ch1, 'Dynamic Scan', 1); % 0 or 1
isDTI = strncmpi(xml_attr(ch1, 'Diffusion'), 'Y', 1);
if isDTI
s.ImageType = [s.ImageType '\DIFFUSION\'];
s.DiffusionEchoTime = xml_attr(ch1, 'Diffusion echo time', 1); % ms
end
% SortFrames solves XYTZ, unusual slice order, incomplete volume etc
keys = {'Dynamic' 'Grad Orient' 'Echo' 'Phase' 'Type' 'Label Type' 'Sequence'};
id = [];
for i = 1:numel(keys)
[aa, ~, a] = unique(xml_raw(ch, keys{i}, i<5));
if numel(aa)>1, id = [id a]; end %#ok
end
sort_frames = dicm2nii('', 'sort_frames', 'func_handle');
sl = xml_raw(ch, 'Slice');
if isDTI, sl(:,2) = xml_raw(ch, 'Diffusion B Factor'); end
[ind_sort, nSL] = sort_frames(sl, id);
nFrame = size(sl, 1);
a = xml_raw(ch, 'Index'); % always 0:nFrame-1 ?
a(a+1) = 1:nFrame; % [~, a] = sort(a);
a = a(ind_sort)';
if ~isequal(a, 1:nFrame), s.SortFrames = a; end % used only in dicm2nii
s.NumberOfFrames = numel(ind_sort); % may be smaller than nFrame
s.NumberOfTemporalPositions = s.NumberOfFrames/nSL;
iVol = ind_sort((0:s.NumberOfTemporalPositions-1)*nSL + 1); % already XYZT
typ = {'MAGNITUDE' 'REAL' 'IMAGINARY' 'PHASE'};
imgType = xml_val(ch, 'Type', 0, iVol); % 'M'
for i = 1:numel(imgType), imgType{i} = find(strncmpi(typ, imgType{i}, 1), 1); end
imgType = cell2mat(imgType);
if numel(iVol) == 1
s.ComplexImageComponent = typ{imgType(1)};
elseif any(diff(imgType) ~= 0) % more than 1 type of image
s.ComplexImageComponent = 'MIXED';
s.Volumes.ComplexImageComponent = typ(imgType); % one for each vol
s.Volumes.RescaleIntercept = xml_val(ch, 'Rescale Intercept', 1, iVol);
s.Volumes.RescaleSlope = xml_val(ch, 'Rescale Slope', 1, iVol);
s.Volumes.MRScaleSlope = xml_val(ch, 'Scale Slope', 1, iVol);
else
s.ComplexImageComponent = typ(imgType(1));
end
% These columns should be the same for nifti-convertible images:
keys = {'Pixel Size' 'Resolution X' 'Resolution Y' 'Slice Orientation' ...
'Angulation AP' 'Angulation FH' 'Angulation RL' ...
'Slice Thickness' 'Slice Gap' 'Pixel Spacing'};
if ~strcmp(s.ComplexImageComponent, 'MIXED')
keys = [keys {'Rescale Intercept' 'Rescale Slope' 'Scale Slope'}];
end
for i = 1:numel(keys)
if numel(unique(xml_raw(ch, keys{i}, 0))) > 1
err = sprintf('Inconsistent %s for %s', keys{i}, fullName);
fprintf(2, ' %s. \n', err);
s = []; return;
end
end
v1 = ind_sort(1);
s.BitsAllocated = xml_val(ch, 'Pixel Size');
s.Columns = xml_val(ch, 'Resolution X');
s.Rows = xml_val(ch, 'Resolution Y');
s.RescaleIntercept = xml_val(ch, 'Rescale Intercept', 1, v1);
s.RescaleSlope = xml_val(ch, 'Rescale Slope', 1, v1);
s.MRScaleSlope = xml_val(ch, 'Scale Slope', 1, v1);
s.SliceThickness = xml_val(ch, 'Slice Thickness');
s.EchoTimes = xml_val(ch, 'Echo Time', 1, iVol);
s.EchoTime = s.EchoTimes(1);
s.FlipAngle = xml_val(ch, 'Image Flip Angle');
s.NumberOfAverages = xml_val(ch, 'No Averages');
s.CardiacTriggerDelayTimes = xml_val(ch, 'Trigger Time', 1, iVol);
if isDTI
s.B_value = xml_val(ch, 'Diffusion B Factor', 1, iVol);
s.bvec_original = [xml_val(ch, 'Diffusion RL', 1, iVol) ...
xml_val(ch, 'Diffusion AP', 1, iVol) ...
xml_val(ch, 'Diffusion FH', 1, iVol)];
end
s.TurboFactor = xml_val(ch, 'TURBO Factor');
a = [xml_attr(ch1, 'Angulation RL', 1)
xml_attr(ch1, 'Angulation AP', 1)
xml_attr(ch1, 'Angulation FH', 1)] /180*pi; % deg to radians
R = makehgtform('xrotate', a(1), 'yrotate', a(2), 'zrotate', a(3));
R = R(1:3, :);
s.SliceOrientation = upper(xml_val(ch, 'Slice Orientation', 0));
iOri = find(strncmp({'SAG' 'COR' 'TRA'}, s.SliceOrientation, 3));
if iOri == 1
R(:,[1 3]) = -R(:,[1 3]);
R = R(:, [2 3 1 4]);
elseif iOri == 2
R(:,3) = -R(:,3);
R = R(:, [1 3 2 4]);
end
s.PixelSpacing = xml_val(ch, 'Pixel Spacing')';
s.SpacingBetweenSlices = xml_val(ch, 'Slice Gap') + s.SliceThickness;
a = xml_attr(ch1, 'Preparation Direction'); % AP
s.Stack.Item_1.MRStackPreparationDirection = a;
iPhase = strfind('LRAPFH', a(1));
iPhase = ceil(iPhase/2); % 1/2/3
if iPhase == (iOri==1)+1, a = 'ROW'; else, a = 'COL'; end
s.InPlanePhaseEncodingDirection = a;
s.ImageOrientationPatient = R(1:6)';
R = R * diag([s.PixelSpacing([2 1]); s.SpacingBetweenSlices; 1]);
R(:,4) = [xml_attr(ch1, 'Off Center RL', 1)
xml_attr(ch1, 'Off Center AP', 1)
xml_attr(ch1, 'Off Center FH', 1)]; % vol center for now
ori = {'RL' 'AP' 'FH'}; ori = ori{iOri};
s.SliceLocation = xml_val(ch, ['Offcenter ' ori], 1, v1);
if sign(R(iOri,3)) ~= sign(R(iOri,4)-s.SliceLocation)
R(:,3) = -R(:,3);
end
R(:,4) = R * [-([s.Columns s.Rows nSL]-1)/2 1]'; % vol center to corner of 1st
s.ImagePositionPatient = R(:,4);
s.LastFile.ImagePositionPatient = R * [0 0 nSL-1 1]'; % last slice
s.Manufacturer = 'Philips';
s.Filename = fullfile(pth, [nam '.REC']); % rest for dicm_img
s.PixelData.Start = 0;
s.PixelData.Bytes = s.Rows * s.Columns * nFrame * s.BitsAllocated / 8;
% Return xml attribute value for key in Series_Info
function val = xml_attr(ch1, key, isnum)
expr = ['<Attribute\s+Name="' key '".*?>(.*?)</Attribute>'];
val = regexp(ch1, expr, 'tokens', 'once');
if isempty(val), val = ''; else, val = val{1}; end
if nargin>2 && isnum, val = str2num(val); end %#ok<*ST2NM>
end
% Return all values for key with original order in Image_Info
function val = xml_raw(ch, key, isnum)
expr = ['<Attribute\s+Name="' key '".*?>(.*?)</Attribute>'];
val = regexp(ch, expr, 'tokens');
val = [val{:}]';
if nargin<3 || isnum, val = str2num(char(val)); end
end
% Return values for key in Image_Info for volumes iVol
function val = xml_val(ch, key, isnum, iVol)
if nargin<3 || isempty(isnum), isnum = true; end
if nargin<4 || isempty(iVol), iVol = 1; end
expr = ['<Attribute\s+Name="' key '".*?>(.*?)</Attribute>'];
if isequal(iVol, 1), val = regexpi(ch, expr, 'tokens', 'once');
else, val = regexp(ch, expr, 'tokens'); val = [val{iVol}]';
end
if isnum, val = str2num(char(val));
elseif nargin<4, val = val{1};
end
end
end
|
github
|
cocoanlab/humanfmri_preproc_bids-master
|
nii_viewer.m
|
.m
|
humanfmri_preproc_bids-master/external/dicm2nii/nii_viewer.m
| 147,002 |
utf_8
|
9704a0e67438819449f6d0f5a1dc4334
|
function varargout = nii_viewer(fname, varargin)
% Basic tool to visualize NIfTI images.
%
% NII_VIEWER('/data/subj2/fileName.nii.gz')
% NII_VIEWER('background.nii', 'overlay.nii')
% NII_VIEWER('background.nii', {'overlay1.nii' 'overlay2.nii'})
%
% If no input is provided, the viewer will load included MNI_2mm brain as
% background NIfTI. Although the preferred format is NIfTI, NII_VIEWER accepts
% any files that can be converted into NIfTI by dicm2nii, including NIfTI,
% dicom, PAR/REC, etc. In case of CIfTI file, it will show the volume view, as
% well as surface view if GIfTI is available.
%
% Here are some features and usage.
%
% The basic use is to open a NIfTI file to view. When a NIfTI (background) is
% open, the display always uses the image plane close to xyz axes (voxel space)
% even for oblique acquisition. The possible confusion arises if the acquisition
% was tilted with a large angle, and then the orientation labels will be less
% accurate. The benefit is that no interpolation is needed for the background
% image, and there is no need to switch coordinate system when images with
% different systems are overlaid. The display is always in correct scale at
% three axes even with non-isotropic voxels. The displayed IJK always correspond
% to left -> right, posterior -> anterior and inferior -> superior directions,
% while the NIfTI data may not be saved in this order or along these directions.
% The I-index is increasing from left to right even when the display is flipped
% as radiological convention (right on left side).
%
% Navigation in 4D can be by mouse click, dialing IJK and volume numbers, or
% using keys (arrow keys and [ ] for 3D, and < > for volume).
%
% After the viewer is open, one can drag-and-drop a NIfTI file into the viewer
% to open as background, or drop a NIfTI with Control key down to add it as
% overlay.
%
% By default, the viewer shows full view of the background image data. The
% zoom-in always applies to three views together, and enlarges around the
% location of the crosshair. To zoom around a different location, set the
% crosshair to the interested location, and apply zoom again either by View ->
% Zoom in, or pressing Ctrl (Cmd) and +/-. View -> Set crosshair at -> center of
% view (or pressing key C) can set the crosshair to the center of display for
% all three views.
%
% Overlays are always mapped onto the coordinate of background image, so
% interpolation (nearest/linear/cubic/spline) is usually involved. The overlay
% makes sense only when it has the same coordinate system as the background
% image, while the resolution and dimension can be different. The viewer tries
% to match any of sform and qform between the images. If there is no match, a
% warning message will show up.
%
% A special overlay feature "Add aligned overlay" can be used to check the
% effect of registration, or overlay an image to a different coordinate system
% without creating a transformed file. It will ask for two files. The first is
% the overlay NIfTI file, and the second is either a transformation matrix file
% which aligns the overlay to the background image, or a warp file which
% transforms the overlay into the background reference.
%
% Here is an example to check FSL alignment. From a .feat/reg folder, Open
% "highres" as background image. "Add overlay" for "example_func". If there is
% head movement between the highres and the functional scans, the overlap will
% be off. Now "Add aligned overlay" for "example_func", and use
% example_func2highres.mat as the matrix. The two dataset should overlap well if
% the alignment matrix is accurate.
%
% Here is another example to overlay to a different coordinate system for FSL
% result. Open .feat/reg/standard.nii.gz as background. If an image like
% .feat/stats/zstat1.nii.gz is added as an overlay, a warning message will say
% inconsistent coordinate system since the zstat image is in Scanner Anat. The
% correct way is to "Add aligned overlay" for zstat1, and either use
% .feat/reg/example_func2standard.mat for linear transformation or better use
% .feat/reg/example_func2standard_warp.nii.gz if available for alignment.
%
% When the mouse pointer is moved onto a voxel, the x/y/z coordinates and voxel
% value will show on the panel. If there is an overlay, the overlay voxel value
% will also show up, unless its display is off. When the pointer moves onto the
% panel or out of an image, the information for the voxel at crosshair will be
% displayed. The display format is as following with val of the top image
% displayed first:
% (x,y,z): val_1 val_2 val_3 ...
%
% Note that although the x/y/z coordinates are shared by background and overlay
% images, IJK indices are always for background image (name shown on title bar).
%
% The mouse-over display can be turned on/off from Help -> Preferences ...
%
% If there is a .txt label file in the same folder as the NIfTI file, like for
% AAL, the labels will be shown instead of voxel value. The txt file should have
% a voxel value and ROI label pair per line, like
% 1 Precentral_L
% 2 Precentral_R
% 3 ...
%
% Image display can be smoothed in 3D (default is off). The smooth is slow when
% the image dimension is large, even when the current implementation of smooth
% does not consider voxel size.
%
% Background image and overlays are listed at the top-left of the panel. All
% parameters of the bottom row of the panel are for the selected image. This
% feature is indicated by a frame grouping these parameters. Each NIfTI file has
% its own set of parameters (display min and max value, LUT, alpha, whether to
% smooth, interpolation method, and volume number) to control its display.
% Moving the mouse onto a parameter will show the meaning of the parameter.
%
% The lastly added overlay is on the top of display and top of the file list.
% This also applies in case there is surface figure for CIfTI files. The
% background and overlay order can be changed by the two small arrows next to
% the list, or from Overlay -> Move selected image ...
%
% Each NIfTI display can be turned on/off by clicking the small checkbox at the
% left side of the file (or pressing spacebar for the selected NIfTI). This
% provides a way to turn on/off an overlay to view the overlap. Most operations
% are applied to the selected NIfTI in the list, such as Show NIfTI hdr/ext
% under Window menu, Move/Close overlay under Overlay menu, and most operations
% under File menu.
%
% A NIfTI mask can be applied to the selected image. Ideally, the mask should be
% binary, and the image corresponding to the non-zero part of the mask will be
% displayed. If non-binary mask is detected, a threshold to binarize will be
% asked. If the effect is not satisfied with the threshold, one can apply the
% mask with a different threshold without re-loading image. The way to remove a
% mask is to Remove, then Add overlay again. In case one likes to modulate the
% selected image with another NIfTI image (multiply two images), File -> Apply
% modulation will do it. If the mask image is not within 0 and 1, the lower and
% upper bound will be asked to normalize the range to [0 1]. A practical use of
% modulation is to use dti_FA map as weight for dti_V1 RGB image.
%
% For multi-volume data, one can change the Volume Number (the parameter at
% rightmost of the panel) to check the head motion. Click in the number dialer
% and or press < or > key, to simulate movie play. It is better to open the 4D
% data as background, since it may be slower to map it to the background image.
%
% Popular LUT options are implemented. Custom LUT can be added by Overlay ->
% Load LUT for selected overlay. The custom LUT file can be in text format (each
% line represents an RGB triplet, while the first line corresponds to the value
% 0 in the image data), or binary format (uint8 for all red, then green then
% blue). The color coding can be shown by View -> Show colorbar. There are
% several special LUTs. The "two-sided" allows to show both positive and
% negative data in one view. For example, if the display range is 3 to 10 for a
% t-map, positive T above 3 will be coded as red-yellow, and T below -3 will be
% coded as blue-green. This means the absolute display range values are used.
%
% One of the special LUT is "lines" in red text. This is for normalized vector
% display, e.g. for diffusion vector. The viewer will refuse the LUT selection
% if the data is not normalized vector. Under this LUT, all other parameters for
% the display are ignored. The color of the "lines" is the max color of previous
% LUT. For example, if one likes to show blue vector lines, choose LUT "blue"
% first, then change it to "lines".
%
% In case of complex image, most LUTs will display only the magnitude of the
% data, except the following three phase LUTs, where the magnitude is used as
% mask. Here is how the 3 phase LUTs encodes phase from 0 to 360 degree:
% phase: red-yellow monotonically,
% phase3: red-yellow-green-yellow-red circularly, and
% phase6: red-yellow-green/violet-blue-cyan, with sharp change at 180 degree.
% These LUTs are useful to visualize activation of periodic stimulus, such as
% those by expanding/shrinking ring or rotating wedge for retinotopy. To use
% this feature, one can save an complex NIfTI storing the Fourier component at
% the stimulus frequency.
%
% Note that, for RGB NIfTI, the viewer always displays the data as color
% regardless of the LUT option. The display min and max value also have no
% effect on RGB image. There is a special LUT, RGB, which is designed to display
% non-RGB NIfTI data as RGB, e.g. FSL-style 3-volome data.
%
% The viewer figure can be copied into clipboard (not available for Linux) or
% saved as variety of image format. For high quality picture, one can increase
% the output resolution by Help -> Preferences -> Resolution. Higher resolution
% will take longer time to copy or save, and result in larger file. If needed,
% one can change to white background for picture output. With white background,
% the threshold for the background image needs to be carefully selected to avoid
% strange effect with some background images. For this reason, white background
% is intended only for picture output.
%
% The selected NIfTI can also be saved as different format from File -> Save
% NIfTI as. For example, a file can be saved as a different resolution. With a
% transformation matrix, a file can also be saved into a different template. The
% latter is needed for FSLview since it won't allow overlay with different
% resolution or dimension at least till version 5.0.8.
%
% See also NII_TOOL DICM2NII NII_XFORM
%% By Xiangrui Li (xiangrui.li at gmail.com)
% History(yymmdd):
% 151021 Almost ready to publish.
% 151104 Include drag&drop by Maarten van der Seijs.
% 151105 Bug fix for Show NIfTI hdr/ext.
% 151106 Use p.interp to avoid unnecessary interp for overlay;
% Use check mark for colorbar/crosshair/background menu items.
% 151111 Take care of slope/inter of img; mask applies to DTI lines.
% 151114 Avoid see-thu for white background.
% 151119 Make smooth faster by using only 3 slices; Allow flip L/R.
% 151120 Implement key navigation and zoom in/out.
% 151121 Implement erode for white background; Add 'Show NIfTI essentials'.
% 151122 Bug fix for background img with sform=0.
% 151123 Show coordinate system in fig title; show masked/aligned in file list;
% Bug fix for alpha (0/1 only); Bug fix for background image R change.
% 151125 Avoid recursion for white background (failed under Linux).
% 151128 Change checkbox to radiobutton: looks better;
% Fix the bug in reorient dim(perm), introduced in last revision.
% 151129 Correct Center crosshair (was off by 0.5); Use evt.Key & add A/C/X/F1.
% 151201 Keep fig location & pref when 'open' & dnd: more user friendly.
% 151202 java robot trick allows to add overlay by Ctrl-dnd.
% 151207 Implement 'Add modulation'.
% 151208 Add xyz display for each view.
% 151217 Callback uses subfunc directly, and include fh as input.
% 151222 Show ROI labels (eg AAL) if .txt file with same name exists.
% 151224 Implement more matlab LUTs and custom LUT.
% 151230 Use listbox for files; Add stack buttons; file order reversed.
% 160102 Store p.R0 if need interp; No coordinate change for background.
% 160104 set_cdata: avoid indexing for single vol img: may be much faster!
% jscroll_handle from findjobj.m to set vertical scoll bar as needed.
% 160107 Rename XYZ label to IJK, implement "Set crosshair at XYZ".
% 160108 Fix the case of 2-form_code for background and addMask.
% 160109 Allow to turn off mouse-over display from Preferences;
% Implement Help -> Check update for easy update;
% Use Matlab built-in pref method for all files in the package.
% 160111 Use image ButtonDownFcn; Mouse down&move now is same as mouse move.
% 160112 Change back to line for crosshair: quiver is slow;
% Bug fix for white backgrnd & saveas backgrnd due to list order reverse.
% 160113 Implement time course for a cube.
% 160114 Figure visible avoids weird hanging problem for some matlab versions.
% 160119 Allow adding multiple overlays with cellstr as 2nd input.
% 160131 set_file: bug fix for cb(j); dnd: restore mouse location.
% 160208 Allow moving background image in stack.
% 160209 RGBA data supported; Background image can use lut "lines".
% 160218 "lines": Fix non-isovoxel display; Same-dim background not required.
% 160402 nii_xform_mat: make up R for possible Analyze file.
% 160506 phase LUT to map complex img: useful for retinotopy.
% 160509 Have 3 phase LUTs; Implement 'Open in new window'.
% 160512 KeyPressFcn bug fix: use the smallest axis dim when zoom in.
% 160517 KeyPressFcn: avoid double-dlg by Ctrl-A; phase6: bug fix for blue b3.
% 160531 use handle() for fh & others: allow dot convention for early matlab.
% 160601 Add cog and to image center, re-organize 'Set crosshair at' menu.
% 160602 bug fix for 'closeAll' files.String(ib); COG uses abs and excludes NaN.
% 160605 Add 'RGB' LUT to force RGB display: DTI_V1 or fsl style RGB file.
% 160608 javaDropFcn: 2 more method for ctlDn; bug fix for fh.xxx in Resize.
% 160620 Use JIDE CheckBoxList; Simplify KeyFcn by not focusing on active items.
% 160627 javaDropFcn: robot-click drop loc to avoid problem with vnc display.
% 160701 Implement hist for current volume; hs.value show top overlay first.
% 160703 bug fix for 'Add aligned' complex img: set p.phase after re-orient.
% 160710 Implement 'Create ROI file'; Time coure is for sphere, not cube.
% 160713 javaDropFnc for Linux: Robot key press replaces mouse click;
% Implement 'Set crosshair at' 'Smoothed maximum'.
% 160715 lut2img: bug fix for custom LUT; custom LUT uses rg [0 255]; add gap=0.
% 160721 Implement 'Set crosshair at' & 'a point with value of'.
% 160730 Allow to load single volume for large dataset.
% 161003 Add aligned overlay: accept FSL warp file as transformation.
% 161010 Implement 'Save volume as'; xyzr2roi: use valid q/sform.
% 161018 Take care of issue converting long file name to var name.
% 161103 Fix qform-only overlay, too long fig title, overlay w/o valid formCode.
% 161108 Implement "Crop below crosshair" to remove excessive neck tissue.
% 161115 Use .mat file for early spm Analyze file.
% 161216 Show more useful 4x4 R for both s/q form in nii essentials.
% 170109 bug fix: add .phase for background nifti.
% 170130 get_range: use nii as input, so always take care of slope/inter.
% 170210 Use flip for flipdim if available (in multiple files).
% 170212 Can open nifti-convertible files; Add Save NIfTI as -> a copy.
% 170421 java_dnd() changed as func, ControlDown OS independent by ACTION_LINK.
% 170515 Use area to normalize histogram.
% 171031 Implement layout. axes replace subplot to avoid overlap problem.
% 171129 bug fix save_nii_as(): undo img scale for no_save_nii.
% 171214 Try to convert back to volume in case of CIfTI (need anatomical gii).
% 171226 Store all info into sag img handle (fix it while it aint broke :)
% 171228 Surface view for gii (include HCP gii template).
% 171229 combine into one overlay for surface view.
% 180103 Allow inflated surface while mapping to correct location in volume.
% 180108 set_file back to nii_viewer_cb for cii_view_cb convenience.
% 180128 Preference stays for current window, and applies to new window only.
% 180228 'Add overlay' check nii struct in base workspace first.
% 180309 Implement 'Standard deviation' like for 'time course'.
% 180522 set_xyz: bug fix for display val >2^15.
% Later update history can be found at github.
%%
if nargin==2 && ischar(fname) && strcmp(fname, 'func_handle')
varargout{1} = str2func(varargin{1});
return;
elseif nargin>0 && ischar(fname) && strcmp(fname, 'LocalFunc')
[varargout{1:nargout}] = feval(varargin{:});
return;
end
if nargin<1 || isempty(fname) % open the included standard_2mm
fname = fullfile(fileparts(mfilename('fullpath')), 'example_data.mat');
fname = load(fname, 'nii'); fname = fname.nii;
end
nii = get_nii(fname);
[p, hs.form_code, rg, dim] = read_nii(nii); % re-oriented
p.Ri = inv(p.R);
nVol = size(p.nii.img, 4);
hs.bg.R = p.R;
hs.bg.Ri = p.Ri;
hs.bg.hdr = p.hdr0;
if ~isreal(p.nii.img)
p.phase = angle(p.nii.img); % -pi to pi
p.phase = mod(p.phase/(2*pi), 1); % 0~1
p.nii.img = abs(p.nii.img); % real now
end
hs.dim = single(dim); % single saves memory for ndgrid
hs.pixdim = p.pixdim;
hs.gap = min(hs.pixdim) ./ hs.pixdim * 3; % in unit of smallest pixdim
p.lb = rg(1); p.ub = rg(2);
p = dispPara(p);
[pName, niiName, ext] = fileparts(p.nii.hdr.file_name);
if strcmpi(ext, '.gz'), [~, niiName] = fileparts(niiName); end
if nargin>1 && any(ishandle(varargin{1})) % called by Open or dnd
fh = varargin{1};
hsN = guidata(fh);
pf = hsN.pref.UserData; % use the current pref for unless new figure
fn = get(fh, 'Number');
close(fh);
else
pf = getpref('nii_viewer_para');
if isempty(pf) || ~isfield(pf, 'layout') % check lastly-added field
pf = struct('openPath', pwd, 'addPath', pwd, 'interp', 'linear', ...
'extraV', NaN, 'dpi', '0', 'rightOnLeft', false, ...
'mouseOver', true, 'layout', 2);
setpref('nii_viewer_para', fieldnames(pf), struct2cell(pf));
end
set(0, 'ShowHiddenHandles', 'on');
a = handle(findobj('Type', 'figure', 'Tag', 'nii_viewer'));
set(0, 'ShowHiddenHandles', 'off');
if isempty(a)
fn = 'ni' * 256.^(1:2)'; % start with a big number for figure
elseif numel(a) == 1
fn = get(a, 'Number') + 1; % this needs handle() to work
else
fn = max(cell2mat(get(a, 'Number'))) + 1;
end
end
[siz, axPos, figPos] = plot_pos(dim.*hs.pixdim, pf.layout);
fh = figure(fn);
hs.fig = handle(fh); % have to use numeric for uipanel for older matlab
figNam = p.nii.hdr.file_name;
if numel(figNam)>40, figNam = [figNam(1:40) '...']; end
figNam = ['nii_viewer - ' figNam ' (' formcode2str(hs.form_code(1)) ')'];
set(fh, 'Toolbar', 'none', 'Menubar', 'none', 'Renderer', 'opengl', ...
'NumberTitle', 'off', 'Tag', 'nii_viewer', 'DockControls', 'off', ...
'Position', [figPos siz+[0 64]], 'Name', figNam);
cb = @(cmd) {@nii_viewer_cb cmd hs.fig}; % callback shortcut
xyz = [0 0 0]; % start cursor location
c = round(p.Ri * [xyz 1]'); c = c(1:3)' + 1; %
ind = c<=1 | c>=dim;
c(ind) = round(dim(ind)/2);
% c = round(dim/2); % start cursor at the center of images
xyz = round(p.R * [c-1 1]'); % take care of rounding error
%% control panel
pos = getpixelposition(fh); pos = [1 pos(4)-64 pos(3) 64];
hs.panel = uipanel(fh, 'Units', 'pixels', 'Position', pos, 'BorderType', 'none');
hs.focus = uicontrol(hs.panel, 'Style', 'text'); % dummy uicontrol for focus
% file list by JIDE CheckBoxList: check/selection independent
mdl = handle(javax.swing.DefaultListModel, 'CallbackProperties'); % dynamic item
mdl.add(0, niiName);
mdl.IntervalAddedCallback = cb('width');
mdl.IntervalRemovedCallback = cb('width');
mdl.ContentsChangedCallback = cb('width'); % add '(mask)' etc
h = handle(com.jidesoft.swing.CheckBoxList(mdl), 'CallbackProperties');
h.setFont(java.awt.Font('Tahoma', 0, 11));
% h.ClickInCheckBoxOnly = true; % it's default
h.setSelectionMode(0); % single selection
h.setSelectedIndex(0); % 1st highlighted
h.addCheckBoxListSelectedIndex(0); % check it
h.ValueChangedCallback = cb('file'); % selection change
h.MouseReleasedCallback = @(~,~)uicontrol(hs.focus); % move focus away
% h.Focusable = false;
h.setToolTipText(['<html>Select image to show/modify its display ' ...
'parameters.<br>Click checkbox to turn on/off image']);
jScroll = com.mathworks.mwswing.MJScrollPane(h);
width = h.getPreferredScrollableViewportSize.getWidth;
width = max(60, min(width+20, pos(3)-408)); % 20 pixels for vertical scrollbar
[~, hs.scroll] = javacomponent(jScroll, [2 4 width 60], hs.panel);
hCB = handle(h.getCheckBoxListSelectionModel, 'CallbackProperties');
hCB.ValueChangedCallback = cb('toggle'); % check/uncheck
hs.files = javaObjectEDT(h); % trick to avoid java error by Yair
% panel for controls except hs.files
pos = [width 1 pos(3)-width pos(4)];
ph = uipanel(hs.panel, 'Units', 'pixels', 'Position', pos, 'BorderType', 'none');
clr = get(ph, 'BackgroundColor');
hs.params = ph;
feature('DefaultCharacterSet', 'UTF-8'); % for old matlab to show triangles
hs.overlay(1) = uicontrol(ph, 'Style', 'pushbutton', 'FontSize', 7, ...
'Callback', cb('stack'), 'Enable', 'off', 'SelectionHighlight', 'off', ...
'String', char(9660), 'Position', [1 36 16 15], 'Tag', 'down', ...
'TooltipString', 'Move selected image one level down');
hs.overlay(2) = copyobj(hs.overlay(1), ph);
set(hs.overlay(2), 'Callback', cb('stack'), ...
'String', char(9650), 'Position', [1 50 16 15], 'Tag', 'up', ...
'TooltipString', 'Move selected image one level up');
hs.value = uicontrol(ph, 'Style', 'text', 'Position', [208 38 pos(3)-208 20], ...
'BackgroundColor', clr, 'FontSize', 8+(~ispc && ~ismac), ...
'TooltipString', '(x,y,z): top ... bottom');
% IJK java spinners
labls = 'IJK';
str = {'Left to Right' 'Posterior to Anterior' 'Inferior to Superior'};
pos = [38 44 22]; posTxt = [36 10 20];
for i = 1:3
loc = [(i-1)*64+34 pos];
txt = sprintf('%s, 1:%g', str{i}, dim(i));
hs.ijk(i) = java_spinner(loc, [c(i) 1 dim(i) 1], ph, cb('ijk'), '#', txt);
uicontrol(ph, 'Style', 'text', 'String', labls(i), 'BackgroundColor', clr, ...
'Position', [loc(1)-11 posTxt], 'TooltipString', txt, 'FontWeight', 'bold');
end
% Controls for each file
uipanel('Parent', ph, 'Units', 'pixels', 'Position', [1 2 412 34], ...
'BorderType', 'etchedin', 'BorderWidth', 2);
hs.lb = java_spinner([7 8 48 22], [p.lb -inf inf p.lb_step], ph, ...
cb('lb'), '#.##', 'min value (threshold)');
hs.ub = java_spinner([59 8 56 22], [p.ub -inf inf p.ub_step], ph, ...
cb('ub'), '#.##', 'max value (clipped)');
hs.lutStr = {'grayscale' 'red' 'green' 'blue' 'violet' 'yellow' 'cyan' ...
'red-yellow' 'blue-green' 'two-sided' '<html><font color="red">lines' ...
'parula' 'jet' 'hsv' 'hot' 'cool' 'spring' 'summer' 'autumn' 'winter' ...
'bone' 'copper' 'pink' 'prism' 'flag' 'phase' 'phase3' 'phase6' 'RGB' 'custom'};
hs.lut = uicontrol(ph, 'Style', 'popup', 'Position', [113 8 74 22], ...
'String', hs.lutStr, 'BackgroundColor', 'w', 'Callback', cb('lut'), ...
'Value', p.lut, 'TooltipString', 'Lookup table options for non-RGB data');
if p.lut==numel(hs.lutStr), set(hs.lut, 'Enable', 'off'); end
hs.alpha = java_spinner([187 8 44 22], [1 0 1 0.1], ph, cb('alpha'), '#.#', ...
'Alpha: 0 transparent, 1 opaque');
hs.smooth = uicontrol(ph, 'Style', 'checkbox', 'Value', p.smooth, ...
'Position', [231 8 60 22], 'String', 'smooth', 'BackgroundColor', clr, ...
'Callback', cb('smooth'), 'TooltipString', 'Smooth image in 3D');
hs.interp = uicontrol(ph, 'Style', 'popup', 'Position', [291 8 68 22], ...
'String', {'nearest' 'linear' 'cubic' 'spline'}, 'Value', p.interp, ...
'Callback', cb('interp'), 'Enable', 'off', 'BackgroundColor', 'w', ...
'TooltipString', 'Interpolation method for overlay');
hs.volume = java_spinner([361 8 44 22], [1 1 nVol 1], ph, cb('volume'), '#', ...
['Volume number, 1:' num2str(nVol)]);
hs.volume.setEnabled(nVol>1);
%% Three views: sag, cor, tra
% this panel makes resize easy: axes relative to panel
hs.frame = uipanel(fh, 'Units', 'pixels', 'Position', [1 1 siz], ...
'BorderType', 'none', 'BackgroundColor', 'k');
for i = 1:3
j = 1:3; j(j==i) = [];
hs.ax(i) = axes('Position', axPos(i,:), 'Parent', hs.frame);
hs.hsI(i) = handle(image(zeros(dim(j([2 1])), 'single')));
hold(hs.ax(i), 'on');
x = [c(j(1))+[-1 1 0 0]*hs.gap(j(1)); 0 dim(j(1))+1 c(j(1))*[1 1]];
y = [c(j(2))+[0 0 -1 1]*hs.gap(j(2)); c(j(2))*[1 1] 0 dim(j(2))+1];
hs.cross(i,:) = line(x, y);
hs.xyz(i) = text(0.02, 0.96, num2str(xyz(i)), 'Units', 'normalized', ...
'Parent', hs.ax(i), 'FontSize', 12);
end
set(hs.hsI, 'ButtonDownFcn', cb('mousedown'));
p.hsI = hs.hsI; % background img
p.hsI(1).UserData = p; % store everything in sag img UserData
labls='ASLSLP';
pos = [0.95 0.5; 0.47 0.96; 0 0.5; 0.47 0.96; 0 0.5; 0.47 0.05];
for i = 1:numel(labls)
hs.ras(i) = text(pos(i,1), pos(i,2), labls(i), 'Units', 'normalized', ...
'Parent', hs.ax(ceil(i/2)), 'FontSize', 12, 'FontWeight', 'bold');
end
% early matlab's colormap works only for axis, so ax(4) is needed.
hs.ax(4) = axes('Position', axPos(4,:), 'Parent', hs.frame);
try
hs.colorbar = colorbar(hs.ax(4), 'YTicks', [0 0.5 1], 'Color', [1 1 1], ...
'Location', 'West', 'PickableParts', 'none', 'Visible', 'off');
catch % for early matlab
colorbar('peer', hs.ax(4), 'Location', 'West', 'Units', 'Normalized');
hs.colorbar = findobj(fh, 'Tag', 'Colorbar');
set(hs.colorbar, 'Visible', 'off', 'HitTest', 'off', 'EdgeColor', [1 1 1]);
end
% image() reverses YDir. Turn off ax and ticks
set(hs.ax, 'YDir', 'normal', 'Visible', 'off');
set([hs.ras hs.cross(:)' hs.xyz], 'Color', 'b', 'UIContextMenu', '');
try set([hs.ras hs.cross(:)' hs.xyz], 'PickableParts', 'none'); % new matlab
catch, set([hs.ras hs.cross(:)' hs.xyz], 'HitTest', 'off'); % old ones
end
%% menus
h = uimenu(fh, 'Label', '&File');
uimenu(h, 'Label', 'Open', 'Accelerator', 'O', 'UserData', pName, 'Callback', cb('open'));
uimenu(h, 'Label', 'Open in new window', 'Callback', cb('open'));
uimenu(h, 'Label', 'Apply mask', 'Callback', @addMask);
uimenu(h, 'Label', 'Apply modulation', 'Callback', @addMask);
h_savefig = uimenu(h, 'Label', 'Save figure as');
h_saveas = uimenu(h, 'Label', 'Save NIfTI as');
uimenu(h, 'Label', 'Save volume as ...', 'Callback', cb('saveVolume'));
uimenu(h, 'Label', 'Crop below crosshair', 'Callback', cb('cropNeck'));
uimenu(h, 'Label', 'Create ROI file ...', 'Callback', cb('ROI'));
uimenu(h, 'Label', 'Close window', 'Accelerator', 'W', 'Callback', 'close gcf');
uimenu(h_saveas, 'Label', 'SPM 3D NIfTI (one file/pair per volume)', 'Callback', @save_nii_as);
uimenu(h_saveas, 'Label', 'NIfTI standard RGB (for AFNI, later mricron)', ...
'Callback', @save_nii_as, 'Separator', 'on');
uimenu(h_saveas, 'Label', 'FSL style RGB (RGB saved in dim 4)', 'Callback', @save_nii_as);
uimenu(h_saveas, 'Label', 'Old mricron style RGB (RGB saved in dim 3)', 'Callback', @save_nii_as);
uimenu(h_saveas, 'Label', 'a copy', 'Callback', @save_nii_as, 'Separator', 'on');
uimenu(h_saveas, 'Label', 'file with a new resolution', 'Callback', @save_nii_as);
uimenu(h_saveas, 'Label', 'file matching background', 'Callback', @save_nii_as);
uimenu(h_saveas, 'Label', 'file in aligned template space', 'Callback', @save_nii_as);
fmt = {'png' 'jpg' 'tif' 'bmp' 'pdf' 'eps'};
if ispc, fmt = [fmt 'emf']; end
for i = 1:numel(fmt)
uimenu(h_savefig, 'Label', fmt{i}, 'Callback', cb('save'));
end
if ispc || ismac
h = uimenu(fh, 'Label', '&Edit');
uimenu(h, 'Label', 'Copy figure', 'Callback', cb('copy'));
end
h_over = uimenu(fh, 'Label', '&Overlay');
uimenu(h_over, 'Label', 'Add overlay', 'Accelerator', 'A', 'Callback', cb('add'));
uimenu(h_over, 'Label', 'Add aligned overlay', 'Callback', cb('add'));
h = uimenu(h_over, 'Label', 'Move selected image', 'Enable', 'off');
uimenu(h, 'Label', 'to top', 'Callback', cb('stack'), 'Tag', 'top');
uimenu(h, 'Label', 'to bottom', 'Callback', cb('stack'), 'Tag', 'bottom');
uimenu(h, 'Label', 'one level up', 'Callback', cb('stack'), 'Tag', 'up');
uimenu(h, 'Label', 'one level down', 'Callback', cb('stack'), 'Tag', 'down');
hs.overlay(3) = h;
hs.overlay(5) = uimenu(h_over, 'Label', 'Remove overlay', 'Accelerator', 'R', ...
'Callback', cb('close'), 'Enable', 'off');
hs.overlay(4) = uimenu(h_over, 'Label', 'Remove overlays', ...
'Callback', cb('closeAll'), 'Enable', 'off');
uimenu(h_over, 'Label', 'Load LUT for current overlay', 'Callback', cb('custom'));
h_view = uimenu(fh, 'Label', '&View');
h = uimenu(h_view, 'Label', 'Zoom in by');
for i = [1 1.2 1.5 2 3 4 5 8 10 20]
uimenu(h, 'Label', num2str(i), 'Callback', cb('zoom'));
end
h = uimenu(h_view, 'Label', 'Layout', 'UserData', pf.layout);
uimenu(h, 'Label', 'one-row', 'Callback', cb('layout'));
uimenu(h, 'Label', 'two-row sag on right', 'Callback', cb('layout'));
uimenu(h, 'Label', 'two-row sag on left', 'Callback', cb('layout'));
uimenu(h_view, 'Label', 'White background', 'Callback', cb('background'));
hLR = uimenu(h_view, 'Label', 'Right on left side', 'Callback', cb('flipLR'));
uimenu(h_view, 'Label', 'Show colorbar', 'Callback', cb('colorbar'));
uimenu(h_view, 'Label', 'Show crosshair', 'Separator', 'on', ...
'Checked', 'on', 'Callback', cb('cross'));
h = uimenu(h_view, 'Label', 'Set crosshair at');
uimenu(h, 'Label', 'center of view', 'Callback', cb('viewCenter'));
uimenu(h, 'Label', 'center of image', 'Callback', cb('center'));
uimenu(h, 'Label', 'COG of image', 'Callback', cb('cog'));
uimenu(h, 'Label', 'Smoothed maximum', 'Callback', cb('maximum'));
uimenu(h, 'Label', 'a point [x y z] ...', 'Callback', cb('toXYZ'));
uimenu(h, 'Label', 'a point with value of ...', 'Callback', cb('toValue'));
uimenu(h_view, 'Label', 'Crosshair color', 'Callback', cb('color'));
h = uimenu(h_view, 'Label', 'Crosshair gap');
for i = [0 1 2 3 4 5 6 8 10 20 40]
str = num2str(i); if i==6, str = [str ' (default)']; end %#ok
uimenu(h, 'Label', str, 'Callback', cb('gap'));
end
h = uimenu(h_view, 'Label', 'Crosshair thickness');
uimenu(h, 'Label', '0.5 (default)', 'Callback', cb('thickness'));
for i = [0.75 1 2 4 8]
uimenu(h, 'Label', num2str(i), 'Callback', cb('thickness'));
end
h = uimenu(fh, 'Label', '&Window');
uimenu(h, 'Label', 'Show NIfTI essentials', 'Callback', cb('essential'));
uimenu(h, 'Label', 'Show NIfTI hdr', 'Callback', cb('hdr'));
uimenu(h, 'Label', 'Show NIfTI ext', 'Callback', cb('ext'));
uimenu(h, 'Label', 'DICOM to NIfTI converter', 'Callback', 'dicm2nii', 'Separator', 'on');
th = uimenu(h, 'Label', 'Time course ...', 'Callback', cb('tc'), 'Separator', 'on');
setappdata(th, 'radius', 6);
th = uimenu(h, 'Label', 'Standard deviation ...', 'Callback', cb('tc'));
setappdata(th, 'radius', 6);
uimenu(h, 'Label', 'Histogram', 'Callback', cb('hist'));
h = uimenu(fh, 'Label', '&Help');
hs.pref = uimenu(h, 'Label', 'Preferences', 'UserData', pf, 'Callback', @pref_dialog);
uimenu(h, 'Label', 'Key shortcut', 'Callback', cb('keyHelp'));
uimenu(h, 'Label', 'Show help text', 'Callback', 'doc nii_viewer');
checkUpdate = dicm2nii('', 'checkUpdate', 'func_handle');
uimenu(h, 'Label', 'Check update', 'Callback', @(~,~)checkUpdate('nii_viewer'));
uimenu(h, 'Label', 'About', 'Callback', cb('about'));
%% finalize gui
if isnumeric(fh) % for older matlab
fh = handle(fh);
schema.prop(fh, 'Number', 'mxArray'); fh.Number = fn;
hs.lut = handle(hs.lut);
hs.frame = handle(hs.frame);
hs.value = handle(hs.value);
hs.panel = handle(hs.panel);
hs.params = handle(hs.params);
hs.scroll = handle(hs.scroll);
hs.pref = handle(hs.pref);
end
guidata(fh, hs); % store handles and data
%% java_dnd based on dndcontrol at matlabcentral/fileexchange/53511
try % panel has JavaFrame in later matlab
jFrame = handle(hs.frame.JavaFrame.getGUIDEView, 'CallbackProperties');
catch
warning('off', 'MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
jFrame = fh.JavaFrame.getAxisComponent;
end
try java_dnd(jFrame, cb('drop')); catch me, disp(me.message); end
set(fh, 'ResizeFcn', cb('resize'), ... % 'SizeChangedFcn' for later matlab
'WindowKeyPressFcn', @KeyPressFcn, 'CloseRequestFcn', cb('closeFig'), ...
'PaperPositionMode', 'auto', 'InvertHardcopy', 'off', 'HandleVisibility', 'Callback');
nii_viewer_cb(fh, [], 'resize', fh); % avoid some weird problem
if pf.mouseOver, set(fh, 'WindowButtonMotionFcn', cb('mousemove')); end
if pf.rightOnLeft, nii_viewer_cb(hLR, [], 'flipLR', fh); end
set_cdata(hs);
set_xyz(hs);
if nargin>1
if ischar(varargin{1})
addOverlay(varargin{1}, fh);
elseif iscellstr(varargin{1})
for i=1:numel(varargin{1}), addOverlay(varargin{1}{i}, fh); end
end
end
if hs.form_code(1)<1
warndlg(['There is no valid form code in NIfTI. The orientation ' ...
'labeling is likely meaningless.']);
end
if isfield(p.nii, 'cii'), cii_view(hs); end
%% Get info from sag img UserData
function p = get_para(hs, iFile)
if nargin<2, iFile = hs.files.getSelectedIndex + 1; end
hsI = findobj(hs.ax(1), 'Type', 'image', '-or', 'Type', 'quiver');
p = get(hsI(iFile), 'UserData');
%% callbacks
function nii_viewer_cb(h, evt, cmd, fh)
hs = guidata(fh);
switch cmd
case 'ijk' % IJK spinner
ix = find(h == hs.ijk);
set_cdata(hs, ix);
set_cross(hs, ix);
xyz = set_xyz(hs);
for i = 1:3, set(hs.xyz(i), 'String', xyz(i)); end % need 3 if oblique
case 'mousedown' % image clicked
% if ~strcmp(get(fh, 'SelectionType'), 'normal'), return; end
ax = gca;
c = get(ax, 'CurrentPoint');
c = round(c(1, 1:2));
i = 1:3;
i(ax==hs.ax(1:3)) = [];
hs.ijk(i(1)).setValue(c(1));
hs.ijk(i(2)).setValue(c(2));
case {'lb' 'ub' 'lut' 'alpha' 'smooth' 'interp' 'volume'}
if ~strcmp(cmd, 'volume'), uicontrol(hs.focus); end % move away focus
p = get_para(hs);
val = get(h, 'Value');
if val == 11 && val~=p.lut
hs.lut.UserData = p.lut; % remember old lut
end
if strcmp(cmd, 'smooth')
if val==1 && numel(p.nii.img(:,:,:,1))<2
set(h, 'Value', 0); return;
end
elseif strcmp(cmd, 'lut')
err = false;
if val == 11 % error check for vector lines
err = true;
if size(p.nii.img,4)~=3
errordlg('Not valid vector data: dim4 is not 3');
else
a = sum(p.nii.img.^2, 4); a = a(a(:)>1e-4);
if any(abs(a-1)>0.1)
errordlg('Not valid vector data: squared sum is not 1');
else, err = false; % passed all checks
end
end
elseif any(val == 26:28) % error check for phase img
err = ~isfield(p, 'phase');
if err, warndlg('Seleced image is not complex data.'); end
elseif val == 29 % RGB
err = size(p.nii.img,4)~=3;
if err, errordlg('RGB LUT requres 3-volume data.'); end
elseif val == numel(hs.lutStr)
err = true;
errordlg('Custom LUT is used be NIfTI itself');
end
if err, hs.lut.Value = p.lut; return; end % undo selection
end
p.hsI(1).UserData.(cmd) = val;
if any(strcmp(cmd, {'lut' 'lb' 'ub' 'volume'})), set_colorbar(hs); end
if strcmp(cmd, 'volume'), set_xyz(hs); end
set_cdata(hs);
case 'resize'
if isempty(hs), return; end
cb = fh.ResizeFcn;
fh.ResizeFcn = []; drawnow; % avoid weird effect
clnObj = onCleanup(@() set(fh, 'ResizeFcn', cb)); % restore func
posP = getpixelposition(hs.panel); % get old height in pixels
posF = getpixelposition(fh); % asked position by user
posI = getpixelposition(hs.frame); % old size
siz = hs.frame.Position(3:4);
res = screen_pixels(1);
oldF = round([posI(3) posI(4)+posP(4)]); % previous fig size
if isequal(oldF, posF(3:4)), return; end % moving without size change
if all(posF(3:4) >= oldF) % enlarge
a = max([posF(3) posF(4)-posP(4)] ./ siz) * siz;
a(1) = min(a(1), res(1)-30); % leave space for MAC dock etc
a(2) = min(a(2), res(2)-92-posP(4)); % leave space for title bar etc
a = min(a ./ siz) * siz;
elseif all(posF(3:4) <= oldF) % shrink
a = min([posF(3) posF(4)-posP(4)] ./ siz) * siz;
else % one side enlarge, another side shrink: use old size
a = posI(3:4);
end
d = posF(1)+a(1)-res(1);
if d>0, posF(1) = posF(1) - d; end
d = posF(2)+a(2)+posP(4)+92-res(2);
if d>0, posF(2) = posF(2) - d; end
posF(1) = max(posF(1), 10);
posF(2) = max(posF(2), 50);
posF(3:4) = [a(1) a(2)+posP(4)]; % final figure size
fh.Position = posF; % done for fig
posP(2) = posF(4)-posP(4)+1;
posP(3) = posF(3);
hs.panel.Position = posP; % done for control panel
hs.frame.Position = [1 1 a]; % done for image panel
nii_viewer_cb([], [], 'width', fh);
case 'toggle' % turn on/off NIfTI
i = h.getAnchorSelectionIndex+1;
if i<1, return; end
checked = hs.files.getCheckBoxListSelectedIndices+1;
p = get_para(hs, i);
if p.show == any(checked==i), return; end % no change
p.show = ~p.show;
p.hsI(1).UserData = p;
states = {'off' 'on'};
try %#ok<*TRYNC>
set(p.hsI, 'Visible', states{p.show+1});
if p.show, set_cdata(hs); end
set_xyz(hs);
end
case 'mousemove'
% if ~strcmp(get(fh, 'SelectionType'), 'normal'), return; end
c = cell2mat(get(hs.ax(1:3), 'CurrentPoint'));
c = c([1 3 5], 1:2); % 3x2
x = cell2mat(get(hs.ax(1:3), 'XLim'));
y = cell2mat(get(hs.ax(1:3), 'YLim'));
I = cell2mat(get(hs.ijk, 'Value'))';
if c(1,1)>x(1,1) && c(1,1)<x(1,2) && c(1,2)>y(1,1) && c(1,2)<y(1,2)%sag
I = [I(1) c(1,:)];
elseif c(2,1)>x(2,1) && c(2,1)<x(2,2) && c(2,2)>y(2,1) && c(2,2)<y(2,2)%cor
I = [c(2,1) I(2) c(2,2)];
elseif c(3,1)>x(3,1) && c(3,1)<x(3,2) && c(3,2)>y(3,1) && c(3,2)<y(3,2)%tra
I = [c(3,:) I(3)];
end
set_xyz(hs, I);
case 'open' % open on current fig or new fig
pName = hs.pref.UserData.openPath;
[fname, pName] = uigetfile([pName '/*.nii; *.hdr;*.nii.gz; *.hdr.gz'], ...
'Select a NIfTI to view', 'MultiSelect', 'on');
if isnumeric(fname), return; end
fname = strcat([pName '/'], fname);
if strcmp(get(h, 'Label'), 'Open in new window'), nii_viewer(fname);
else, nii_viewer(fname, fh);
end
return;
case 'add' % add overlay
vars = evalin('base', 'who');
is_nii = @(v)evalin('base', ...
sprintf('isstruct(%s) && all(isfield(%s,{''hdr'',''img''}))', v, v));
for i = numel(vars):-1:1, if ~is_nii(vars{i}), vars(i) = []; end; end
if ~isempty(vars)
a = listdlg('SelectionMode', 'single', 'ListString', vars, ...
'ListSize', [300 100], 'CancelString', 'File dialog', ...
'Name', 'Select a NIfTI in the list or click File dialog');
if ~isempty(a), fname = evalin('base', vars{a}); end
end
pName = hs.pref.UserData.addPath;
label = get(h, 'Label');
if strcmp(label, 'Add aligned overlay')
if ~exist('fname', 'var')
[fname, pName] = uigetfile([pName '/*.nii; *.hdr;*.nii.gz;' ...
'*.hdr.gz'], 'Select overlay NIfTI');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
end
[mtx, pName] = uigetfile([pName '/*.mat;*_warp.nii;*_warp.nii.gz'], ...
'Select FSL mat file or warp file transforming the nii to background');
if ~ischar(mtx), return; end
mtx = fullfile(pName, mtx);
addOverlay(fname, fh, mtx);
else
if ~exist('fname', 'var')
[fname, pName] = uigetfile([pName '/*.nii; *.hdr;*.nii.gz;' ...
'*.hdr.gz'], 'Select overlay NIfTI', 'MultiSelect', 'on');
if ~ischar(fname) && ~iscell(fname), return; end
fname = get_nii(strcat([pName filesep], fname));
end
addOverlay(fname, fh);
end
setpref('nii_viewer_para', 'addPath', pName);
case 'closeAll' % close all overlays
for j = hs.files.getModel.size:-1:1
p = get_para(hs, j);
if p.hsI(1) == hs.hsI(1), continue; end
delete(p.hsI); % remove image
hs.files.getModel.remove(j-1);
end
hs.files.setSelectedIndex(0);
set_xyz(hs);
case 'close' % close selected overlay
jf = hs.files.getSelectedIndex+1;
p = get_para(hs, jf);
if p.hsI(1) == hs.hsI(1), return; end % no touch to background
delete(p.hsI); % 3 view
hs.files.getModel.remove(jf-1);
hs.files.setSelectedIndex(max(0, jf-2));
set_xyz(hs);
case {'hdr' 'ext' 'essential'} % show hdr ext or essential
jf = hs.files.getSelectedIndex+1;
p = get_para(hs, jf);
if strcmp(cmd, 'hdr')
hdr = p.hdr0;
elseif strcmp(cmd, 'ext')
if ~isfield(p.nii, 'ext')
errordlg('No extension for the selected NIfTI');
return;
end
hdr = {};
for i = 1:numel(p.nii.ext)
if ~isfield(p.nii.ext(i), 'edata_decoded'), continue; end
hdr{end+1} = p.nii.ext(i).edata_decoded; %#ok
end
if isempty(hdr)
errordlg('No known extension for the selected NIfTI');
return;
elseif numel(hdr) == 1, hdr = hdr{1};
end
elseif strcmp(cmd, 'essential')
hdr = nii_essential(p);
end
nam = hs.files.getModel.get(jf-1);
if ~isstrprop(nam(1), 'alpha'), nam = ['x' nam]; end % like genvarname
nam(~isstrprop(nam, 'alphanum')) = '_'; % make it valid for var name
nam = [nam '_' cmd];
nam = strrep(nam, '__', '_');
n = numel(nam); nm = namelengthmax;
if n>nm, nam(nm-4:n-4) = ''; end
assignin('base', nam, hdr);
evalin('base', ['openvar ' nam]);
case 'cross' % show/hide crosshairs and RAS labels
if strcmp(get(h, 'Checked'), 'on')
set(h, 'Checked', 'off');
set([hs.cross(:)' hs.ras hs.xyz], 'Visible', 'off');
else
set(h, 'Checked', 'on');
set([hs.cross(:)' hs.ras hs.xyz], 'Visible', 'on');
end
case 'color' % crosshair color
c = uisetcolor(get(hs.ras(1), 'Color'), 'Pick crosshair color');
if numel(c) ~= 3, return; end
set([hs.cross(:)' hs.ras hs.xyz], 'Color', c);
case 'thickness' % crosshair thickness
c = strtok(get(h, 'Label'));
set(hs.cross(:)', 'LineWidth', str2double(c));
case 'gap' % crosshair gap
c = str2double(strtok(get(h, 'Label')));
hs.gap = min(hs.pixdim) ./ hs.pixdim * c / 2;
guidata(fh, hs);
set_cross(hs, 1:3);
case 'copy' % copy figure into clipboard
fh1 = ancestor(h, 'figure');
if strncmp(get(fh1, 'Name'), 'nii_viewer', 10)
set(hs.panel, 'Visible', 'off');
clnObj = onCleanup(@() set(hs.panel, 'Visible', 'on'));
end
print(fh1, '-dbitmap', '-noui', ['-r' hs.pref.UserData.dpi]);
% print('-dmeta', '-painters');
case 'save' % save figure as picture
ext = get(h, 'Label');
fmt = ext;
if strcmp(ext, 'jpg'), fmt = 'jpeg';
elseif strcmp(ext, 'tif'), fmt = 'tiff';
elseif strcmp(ext, 'eps'), fmt = 'epsc';
elseif strcmp(ext, 'emf'), fmt = 'meta';
end
[fname, pName] = uiputfile(['*.' ext], 'Input file name to save figure');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
if any(strcmp(ext, {'eps' 'pdf' 'emf'})), render = '-painters';
else, render = '-opengl';
end
fh1 = ancestor(h, 'figure');
if strncmp(get(fh1, 'Name'), 'nii_viewer', 10)
set(hs.panel, 'Visible', 'off');
clnObj = onCleanup(@() set(hs.panel, 'Visible', 'on'));
end
print(fh1, fname, render, '-noui', ['-d' fmt], ['-r' hs.pref.UserData.dpi], '-cmyk');
case 'colorbar' % colorbar on/off
if strcmpi(get(hs.colorbar, 'Visible'), 'on')
set(hs.colorbar, 'Visible', 'off');
set(h, 'Checked', 'off');
else
set(hs.colorbar, 'Visible', 'on');
set(h, 'Checked', 'on');
set_colorbar(hs);
end
case 'about'
getVersion = dicm2nii('', 'getVersion', 'func_handle');
str = sprintf(['nii_viewer.m by Xiangrui Li\n\n' ...
'Last updated on %s\n\n', ...
'Feedback to: [email protected]\n'], getVersion());
helpdlg(str, 'About nii_viewer')
case 'stack'
uicontrol(hs.focus); % move focus out of buttons
jf = hs.files.getSelectedIndex+1;
p = get_para(hs, jf);
n = hs.files.getModel.size;
switch get(h, 'Tag') % for both uimenu and pushbutton
case 'up' % one level up
if jf==1, return; end
for j = 1:3, uistack(p.hsI(j)); end
ind = [1:jf-2 jf jf-1 jf+1:n]; jf = jf-1;
case 'down' % one level down
if jf==n, return; end
for j = 1:3, uistack(p.hsI(j), 'down'); end
ind = [1:jf-1 jf+1 jf jf+2:n]; jf = jf+1;
case 'top'
if jf==1, return; end
for j = 1:3, uistack(p.hsI(j), 'up', jf-1); end
ind = [jf 1:jf-1 jf+1:n]; jf = 1;
case 'bottom'
if jf==n, return; end
for j = 1:3, uistack(p.hsI(j), 'down', n-jf); end
ind = [1:jf-1 jf+1:n jf]; jf = n;
otherwise
error('Unknown stack level: %s', get(h, 'Tag'));
end
str = cell(hs.files.getModel.toArray);
str = str(ind);
for j = 1:n, hs.files.getModel.set(j-1, str{j}); end
chk = false(1,n);
chk(hs.files.getCheckBoxListSelectedIndices+1) = true;
chk = find(chk(ind)) - 1;
if ~isempty(chk), hs.files.setCheckBoxListSelectedIndices(chk); end
hs.files.setSelectedIndex(jf-1);
set_xyz(hs);
case 'zoom'
m = str2double(get(h, 'Label'));
a = min(hs.dim) / m;
if a<1, m = min(hs.dim); end
set_zoom(m, hs);
case 'background'
if strcmp(get(h, 'Checked'), 'on')
set(h, 'Checked', 'off');
hs.frame.BackgroundColor = [0 0 0];
set(hs.colorbar, 'EdgeColor', [1 1 1]);
else
set(h, 'Checked', 'on');
hs.frame.BackgroundColor = [1 1 1];
set(hs.colorbar, 'EdgeColor', [0 0 0]);
end
set_cdata(hs);
case 'flipLR'
hs.pref.UserData.rightOnLeft = strcmp(get(h, 'Checked'), 'on');
if hs.pref.UserData.rightOnLeft
set(h, 'Checked', 'off');
set(hs.ax([2 3]), 'XDir', 'normal');
set(hs.ras([3 5]), 'String', 'L');
else
set(h, 'Checked', 'on');
set(hs.ax([2 3]), 'XDir', 'reverse');
set(hs.ras([3 5]), 'String', 'R');
end
case 'layout'
submenu = {'one-row' 'two-row sag on right' 'two-row sag on left'};
layout = find(strcmp(get(h, 'Label'), submenu));
if hs.pref.UserData.layout == layout, return; end
cb = hs.fig.ResizeFcn;
hs.fig.ResizeFcn = ''; drawnow;
clnObj = onCleanup(@() set(hs.fig, 'ResizeFcn', cb));
[siz, axPos, figPos] = plot_pos(hs.dim.*hs.pixdim, layout);
hs.fig.Position = [figPos siz+[0 64]];
hs.frame.Position(3:4) = siz;
hs.panel.Position(2) = hs.fig.Position(4) - 64;
for i = 1:4, set(hs.ax(i), 'Position', axPos(i,:)); end
hs.pref.UserData.layout = layout;
case 'keyHelp'
str = sprintf([ ...
'Key press available when focus is not in a number dialer:\n\n' ...
'Left or Right arrow key: Move crosshair left or right.\n\n' ...
'Up or Down arrow key: Move crosshair superior or inferior.\n\n' ...
'[ or ] key: Move crosshair posterior or anterior.\n\n' ...
'< or > key: Decrease or increase volume number.\n\n' ...
'Ctrl + or - key: Zoom in or out by 10%% around crosshair.\n\n' ...
'A: Toggle on/off crosshair.\n\n' ...
'C: Crosshair to view center.\n\n' ...
'Space: Toggle on/off selected image.\n\n' ...
'F1: Show help text.\n']);
helpdlg(str, 'Key Shortcut');
case 'center' % image center
p = get_para(hs);
dim = p.nii.hdr.dim(2:4);
c = round(hs.bg.Ri * (p.R * [dim/2-1 1]')) + 1;
for i = 1:3, hs.ijk(i).setValue(c(i)); end
case 'viewCenter'
c(1) = mean(get(hs.ax(2), 'XLim'));
c(2) = mean(get(hs.ax(1), 'XLim'));
c(3) = mean(get(hs.ax(1), 'YLim'));
c = round(c-0.5);
for i = 1:3, hs.ijk(i).setValue(c(i)); end
case 'toXYZ'
c0 = cell2mat(get(hs.ijk, 'Value'));
c0 = hs.bg.R * [c0-1; 1];
c0 = sprintf('%g %g %g', round(c0(1:3)));
str = 'X Y Z coordinates in mm';
while 1
a = inputdlg(str, 'Crosshair to xyz', 1, {c0});
if isempty(a), return; end
c = sscanf(a{1}, '%g %g %g');
if numel(c) == 3, break; end
end
c = round(hs.bg.Ri * [c(:); 1]) + 1;
for i = 1:3, hs.ijk(i).setValue(c(i)); end
case 'toValue'
def = getappdata(h, 'Value');
if isempty(def), def = 1; end
def = num2str(def);
str = 'Input the voxel value';
while 1
a = inputdlg(str, 'Crosshair to a value', 1, {def});
if isempty(a), return; end
val = sscanf(a{1}, '%g');
if ~isnan(val), break; end
end
setappdata(h, 'Value', val);
jf = hs.files.getSelectedIndex+1;
p = get_para(hs, jf);
img = p.nii.img(:,:,:, hs.volume.getValue);
c = find(img(:)==val, 1);
if isempty(c)
nam = strtok(hs.files.getModel.get(jf-1), '(');
errordlg(sprintf('No value of %g found in %s', val, nam));
return;
end
dim = size(img); dim(numel(dim)+1:3) = 1;
[c(1), c(2), c(3)] = ind2sub(dim, c); % ijk+1
c = round(hs.bg.Ri * (p.R * [c(:)-1; 1])) + 1;
for i = 1:3, hs.ijk(i).setValue(c(i)); end
case 'cog' % crosshair to img COG
p = get_para(hs);
img = p.nii.img(:,:,:, hs.volume.getValue);
c = img_cog(img);
if any(isnan(c)), errordlg('No valid COG found'); return; end
c = round(hs.bg.Ri * (p.R * [c-1; 1])) + 1;
for i = 1:3, hs.ijk(i).setValue(c(i)); end
case 'maximum' % crosshair to img max
p = get_para(hs);
img = p.nii.img(:,:,:,hs.volume.getValue);
if sum(img(:)~=0) < 1
errordlg('All value are the same. No maximum!');
return;
end
img = smooth23(img, 'gaussian', 5);
img(isnan(img)) = 0;
img = abs(img);
[~, I] = max(img(:));
dim = size(img); dim(end+1:3) = 1;
c = zeros(3, 1);
[c(1), c(2), c(3)] = ind2sub(dim, I);
c = round(hs.bg.Ri * (p.R * [c-1; 1])) + 1;
for i = 1:3, hs.ijk(i).setValue(c(i)); end
case 'custom' % add custom lut
p = get_para(hs);
pName = fileparts(p.nii.hdr.file_name);
[fname, pName] = uigetfile([pName '/*.lut'], 'Select LUT file for current overlay');
if ~ischar(fname), return; end
fid = fopen(fullfile(pName, fname));
p.map = fread(fid, '*uint8');
fclose(fid);
if mod(numel(p.map),3)>0 || sum(p.map<8)<3 % guess text file
try, p.map = str2num(char(p.map'));
catch, errordlg('Unrecognized LUT file'); return;
end
if max(p.map(:)>1), p.map = single(p.map) / 255; end
else
p.map = reshape(p.map, [], 3);
p.map = single(p.map) / 255;
end
if isequal(p.nii.img, round(p.nii.img))
try, p.map = p.map(1:max(p.nii.img(:))+1, :); end
end
p.lut = numel(hs.lutStr);
p.hsI(1).UserData = p;
set(hs.lut, 'Value', p.lut, 'Enable', 'off');
set_cdata(hs);
set_colorbar(hs);
case 'tc' % time course or std
jf = hs.files.getSelectedIndex+1;
p = get_para(hs, jf);
nam = strtok(hs.files.getModel.get(jf-1), '(');
labl = strrep(get(h, 'Label'), ' ...', '');
r = num2str(getappdata(h, 'radius'));
r = inputdlg('Radius around crosshair (mm):', labl, 1, {r});
if isempty(r), return; end
r = str2double(r{1});
setappdata(h, 'radius', r);
for j = 3:-1:1, c(j) = get(hs.ijk(j), 'Value'); end % ijk for background
c = hs.bg.R * [c-1 1]'; % in mm now
c = c(1:3);
b = xyzr2roi(c, r, p.nii.hdr); % overlay space
img = p.nii.img;
dim = size(img);
img = reshape(img, [], prod(dim(4:end)))';
img = img(:, b(:));
fh1 = figure(mod(fh.Number,10)+jf);
if strcmp(labl, 'Time course')
img = mean(single(img), 2);
else
img = std(single(img), [], 2);
end
plot(img);
xlabel('Volume number');
c = sprintf('(%g,%g,%g)', round(c));
set(fh1, 'Name', [nam ' ' lower(labl) ' around voxel ' c]);
case 'hist' % plot histgram
jf =hs.files.getSelectedIndex+1;
if jf<1, return; end
p = get_para(hs, jf);
img = p.nii.img(:,:,:, hs.volume.getValue);
img = sort(img(:));
img(isnan(img)) = [];
img(img<hs.lb.getValue) = [];
img(img>hs.ub.getValue) = [];
nv = numel(img);
img0 = unique(img);
nu = numel(img0);
n = max([nv/2000 nu/20 10]);
n = min(round(n), nu);
if n == nu, edges = img0;
else, edges = linspace(0,1,n)*double(img(end)-img(1)) + double(img(1));
end
nam = strtok(hs.files.getModel.get(jf-1), '(');
fh1 = figure(mod(fh.Number,10)+jf);
set(fh1, 'NumberTitle', 'off', 'Name', nam);
[y, x] = hist(img, edges);
bar(x, y/sum(y)/(x(2)-x(1)), 'hist'); % probability density
xlabel('Voxel values'); ylabel('Probability density');
title('Histogram between min and max values');
case 'width' % adjust hs.scroll width
hs.files.updateUI;
width = hs.panel.Position(3);
x = hs.files.getPreferredScrollableViewportSize.getWidth;
x = max(60, min(x+20, width-408)); % 408 width of the little panel
hs.scroll.Position(3) = x;
hs.params.Position([1 3]) = [x+2 width-x-2];
hs.value.Position(3) = max(1, width-x-hs.value.Position(1));
case 'saveVolume' % save 1 or more volumes as a nifti
p = get_para(hs);
nam = p.nii.hdr.file_name;
t = p.volume;
while 1
a = inputdlg('Volume indice to save (2:4 for example)', ...
'Save Volume', 1, {num2str(t)});
if isempty(a), return; end
try
t = eval(['[' a{1} '];']);
break;
end
end
pName = fileparts(nam);
[fname, pName] = uiputfile([pName '/*.nii;*.nii.gz'], ...
'Input name to save volume as');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
nii = nii_tool('load', nam); % re-load to be safe
nii.img = nii.img(:,:,:,t);
nii_tool('save', nii, fname);
case 'ROI' % save sphere
c0 = cell2mat(get(hs.ijk, 'Value'));
c0 = hs.bg.R * [c0-1; 1];
c0 = sprintf('%g %g %g', round(c0(1:3)));
str = {'X Y Z coordinates in mm' 'Radius in mm'};
while 1
a = inputdlg(str, 'Sphere ROI', 1, {c0 '6'});
if isempty(a), return; end
c = sscanf(a{1}, '%g %g %g');
r = sscanf(a{2}, '%g');
if numel(c) == 3, break; end
end
p = get_para(hs);
pName = fileparts(p.nii.hdr.file_name);
[fname, pName] = uiputfile([pName '/*.nii;*.nii.gz'], ...
'Input file name to save ROI into');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
b = xyzr2roi(c, r, p.nii.hdr);
p.nii.img = single(b); % single better supported by FSL
nii_tool('save', p.nii, fname);
case 'cropNeck'
k0 = get(hs.ijk(3), 'Value') - 1;
p = get_para(hs);
nam = p.nii.hdr.file_name;
pName = fileparts(nam);
[fname, pName] = uiputfile([pName '/*.nii;*.nii.gz'], ...
'Input file name to save cropped image');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
d = single(p.hdr0.dim(2:4));
I = ones([d 4], 'single');
[I(:,:,:,1), I(:,:,:,2), I(:,:,:,3)] = ndgrid(0:d(1)-1, 0:d(2)-1, 0:d(3)-1);
I = permute(I, [4 1 2 3]);
I = reshape(I, 4, []); % ijk in 4 by nVox
R = nii_xform_mat(p.hdr0, hs.form_code); % original R
k = hs.bg.Ri * R * I; % background ijk
nii = nii_tool('load', nam);
d = size(nii.img);
nii.img = reshape(nii.img, prod(d(1:3)), []);
nii.img(k(3,:)<k0, :) = -nii.hdr.scl_inter / nii.hdr.scl_slope;
nii.img = reshape(nii.img, d);
nii_tool('save', nii, fname);
case 'closeFig'
try close(fh.UserData); end % cii_view
delete(fh); return;
case 'file'
if ~isempty(evt) && evt.getValueIsAdjusting, return; end
p = get_para(hs);
nam = {'lb' 'ub' 'alpha' 'volume' 'lut' 'smooth' 'interp' };
cb = cell(4,1);
for j = 1:4 % avoid firing spinner callback
cb{j} = hs.(nam{j}).StateChangedCallback;
hs.(nam{j}).StateChangedCallback = '';
end
for j = 1:numel(nam)
set(hs.(nam{j}), 'Value', p.(nam{j}));
end
set(hs.lb.Model, 'StepSize', p.lb_step);
set(hs.ub.Model, 'StepSize', p.ub_step);
nVol = size(p.nii.img, 4);
str = sprintf('Volume number, 1:%g', nVol);
set(hs.volume, 'Enable', nVol>1, 'ToolTipText', str);
set(hs.volume.Model, 'Maximum', nVol);
for j = 1:4 % restore spinner callback
hs.(nam{j}).StateChangedCallback = cb{j};
end
set_colorbar(hs);
off_on = {'off' 'on'};
set(hs.interp, 'Enable', off_on{isfield(p, 'R0')+1});
set(hs.overlay(1:4), 'Enable', off_on{(hs.files.getModel.size>1)+1}); % stack & Close overlays
set(hs.overlay(5), 'Enable', off_on{(p.hsI(1) ~= hs.hsI(1))+1}); % Close overlay
set(hs.lut, 'Enable', off_on{2-(p.lut==numel(hs.lutStr))});
case 'drop'
try
nii = get_nii(evt.Data);
if evt.ControlDown, addOverlay(nii, fh); % overlay
else, nii_viewer(nii, fh); return; % background
end
catch me
errordlg(me.message);
end
otherwise
error('Unknown Callback: %s', cmd);
end
try, cii_view_cb(fh.UserData, [], cmd); end
%% zoom in/out with a factor
function set_zoom(m, hs)
c = hs.dim(:) / 2;
if m <= 1, I = c; % full view regardless of crosshair location
else, I = cell2mat(get(hs.ijk, 'Value'));
end
lim = round([I I] + c/m*[-1 1]) + 0.5;
axis(hs.ax(1), [lim(2,:) lim(3,:)]);
axis(hs.ax(2), [lim(1,:) lim(3,:)]);
axis(hs.ax(3), [lim(1,:) lim(2,:)]);
%% KeyPressFcn for figure
function KeyPressFcn(fh, evt)
if any(strcmp(evt.Key, evt.Modifier)), return; end % only modifier
hs = guidata(fh);
if ~isempty(intersect({'control' 'command'}, evt.Modifier))
switch evt.Key
case {'add' 'equal'}
[dim, i] = min(hs.dim);
if i==1, d = get(hs.ax(2), 'XLim');
elseif i==2, d = get(hs.ax(1), 'XLim');
else, d = get(hs.ax(1), 'YLim');
end
d = abs(diff(d'));
if d<=3, return; end % ignore
m = dim / d * 1.1;
if round(dim/2/m)==d/2, m = dim / (d-1); end
set_zoom(m, hs);
case {'subtract' 'hyphen'}
d = abs(diff(get(hs.ax(2), 'XLim')));
m = hs.dim(1) / d;
if m<=1, return; end
m = m / 1.1;
if round(hs.dim(1)/2/m)==d/2, m = hs.dim(1) / (d+1); end
if m<1.01, m = 1; end
set_zoom(m, hs);
end
return;
end
switch evt.Key
case 'leftarrow'
val = max(get(hs.ijk(1), 'Value')-1, 1);
hs.ijk(1).setValue(val);
case 'rightarrow'
val = min(get(hs.ijk(1), 'Value')+1, hs.dim(1));
hs.ijk(1).setValue(val);
case 'uparrow'
val = min(get(hs.ijk(3),'Value')+1, hs.dim(3));
hs.ijk(3).setValue(val);
case 'downarrow'
val = max(get(hs.ijk(3),'Value')-1, 1);
hs.ijk(3).setValue(val);
case 'rightbracket' % ]
val = min(get(hs.ijk(2),'Value')+1, hs.dim(2));
hs.ijk(2).setValue(val);
case 'leftbracket' % [
val = max(get(hs.ijk(2),'Value')-1, 1);
hs.ijk(2).setValue(val);
case 'period' % . or >
val = min(get(hs.volume,'Value')+1, get(hs.volume.Model,'Maximum'));
hs.volume.setValue(val);
case 'comma' % , or <
val = max(get(hs.volume,'Value')-1, 1);
hs.volume.setValue(val);
case 'c'
nii_viewer_cb([], [], 'viewCenter', hs.fig);
case {'x' 'space'}
i = hs.files.getSelectedIndex;
checked = hs.files.getCheckBoxListSelectedIndices;
if any(i == checked)
hs.files.removeCheckBoxListSelectedIndex(i);
else
hs.files.addCheckBoxListSelectedIndex(i);
end
case 'a'
h = findobj(hs.fig, 'Type', 'uimenu', 'Label', 'Show crosshair');
nii_viewer_cb(h, [], 'cross', hs.fig);
case 'f1'
doc nii_viewer;
case 'tab' % prevent tab from cycling uicontrol
mousexy = get(0, 'PointerLocation'); % for later restore
posF = getpixelposition(fh);
posA = getpixelposition(hs.ax(4), true); % relative to figure
c = posF(1:2) + posA(1:2) + posA(3:4)/2; % ax(4) center xy
res = screen_pixels;
rob = java.awt.Robot();
rob.mouseMove(c(1), res(2)-c(2));
rob.mousePress(16); rob.mouseRelease(16); % BUTTON1
set(0, 'PointerLocation', mousexy); % restore mouse location
end
%% update CData/AlphaData for 1 or 3 of the sag/cor/tra views
function set_cdata(hs, iaxis)
if nargin<2, iaxis = 1:3; end
interStr = get(hs.interp, 'String');
for i = 1:hs.files.getModel.size
p = get_para(hs, i);
if ~p.show, continue; end % save time, but need to update when enabled
lut = p.lut;
if lut == 11 % "lines" special case: do it separately
vector_lines(hs, i, iaxis); continue;
elseif ~strcmpi(p.hsI(1).Type, 'image') % was "lines"
delete(p.hsI); % delete quiver
p.hsI = copyimg(hs);
p.hsI(1).UserData = p; % update whole UserData
if i>1, for j=1:3; uistack(p.hsI(j), 'down', i-1); end; end
end
t = round(p.volume);
img = p.nii.img;
isRGB = size(img, 8)>2;
if isRGB % avoid indexing for single vol img: could speed up a lot
img = permute(img(:,:,:,t,:,:,:,:), [1:3 8 4:7]);
elseif size(img,4)>1 && lut~=29
img = img(:,:,:,t);
end
if ~isfloat(img)
img = single(img);
if isfield(p, 'scl_slope')
img = img * p.scl_slope + p.scl_inter;
end
end
if isfield(p, 'mask')
img = bsxfun(@times, img, p.mask);
end
if isfield(p, 'modulation')
img = bsxfun(@times, img, p.modulation);
end
if any(lut == 26:28) % interp/smooth both mag and phase
img(:,:,:,2) = p.phase(:,:,:,t);
end
dim4 = size(img,4);
for ix = iaxis
ind = get(hs.ijk(ix), 'Value'); % faster than hs.ijk(ix).getValue
ind = round(ind);
if ind<1 || ind>hs.dim(ix), continue; end
ii = {':' ':' ':'};
io = ii;
d = hs.dim;
d(ix) = 1; % 1 slice at dim ix
im = zeros([d dim4], 'single');
if isfield(p, 'R0') % interp, maybe smooth
I = ones([d 4], 'single');
[I(:,:,:,1), I(:,:,:,2), I(:,:,:,3)] = ndgrid(0:d(1)-1, 0:d(2)-1, 0:d(3)-1);
I = permute(I, [4 1 2 3]);
I = reshape(I, 4, []); % ijk grids of background img
I(ix,:) = ind-1;
if isfield(p, 'warp')
iw = {':' ':' ':' ':'}; iw{ix} = ind;
warp = p.warp(iw{:});
warp = reshape(warp, [], 3)'; warp(4,:) = 0;
I = p.Ri * (p.R0 * I + warp) + 1;
else
I = p.Ri * p.R0 * I + 1; % ijk+1 for overlay img
end
for j = 1:dim4
if p.smooth
ns = 3; % number of voxels (odd) used for smooth
d3 = d; d3(ix) = ns; % e.g. 3 slices
b = zeros(d3, 'single');
I0 = I(1:3,:);
for k = 1:ns % interp for each slice
I0(ix,:) = I(ix,:) - (ns+1)/2 + k;
a = interp3a(img(:,:,:,j), I0, interStr{p.interp});
ii{ix} = k; b(ii{:}) = reshape(a, d);
end
b = smooth23(b, 'gaussian', ns);
io{ix} = (ns+1)/2;
im(:,:,:,j) = b(io{:}); % middle one
else
a = interp3a(img(:,:,:,j), I, interStr{p.interp});
im(:,:,:,j) = reshape(a, d);
end
end
elseif p.smooth % smooth only
ns = 3; % odd number of slices to smooth
ind1 = ind - (ns+1)/2 + (1:ns); % like ind+(-1:1)
if any(ind1<1 | ind1>hs.dim(ix)), ind1 = ind; end % 2D
ii{ix} = ind1;
io{ix} = mean(1:numel(ind1)); % middle slice
for j = 1:dim4
a = smooth23(img(ii{:},j), 'gaussian', ns);
im(:,:,:,j) = a(io{:});
end
else % no interp or smooth
io{ix} = ind;
im(:) = img(io{:}, :);
end
if ix == 1, im = permute(im, [3 2 4 1]);
elseif ix == 2, im = permute(im, [3 1 4 2]);
elseif ix == 3, im = permute(im, [2 1 4 3]);
end
if ~isRGB % not NIfTI RGB
[im, alfa] = lut2img(im, p, hs.lutStr{p.lut});
elseif dim4 == 3 % NIfTI RGB
if max(im(:))>2, im = im / 255; end % guess uint8
im(im>1) = 1; im(im<0) = 0;
alfa = sum(im,3) / dim4; % avoid mean
elseif dim4 == 4 % NIfTI RGBA
if max(im(:))>2, im = im / 255; end % guess uint8
im(im>1) = 1; im(im<0) = 0;
alfa = im(:,:,4);
im = im(:,:,1:3);
else
error('Unknown data type: %s', p.nii.hdr.file_name);
end
if p.hsI(1) == hs.hsI(1) && isequal(hs.frame.BackgroundColor, [1 1 1])
alfa = img2mask(alfa);
elseif dim4 ~= 4
alfa = alfa > 0;
end
alfa = p.alpha * alfa;
set(p.hsI(ix), 'CData', im, 'AlphaData', alfa);
end
end
%% Add an overlay
function addOverlay(fname, fh, mtx)
hs = guidata(fh);
frm = hs.form_code;
aligned = nargin>2;
R_back = hs.bg.R;
R0 = nii_xform_mat(hs.bg.hdr, frm(1)); % original background R
[~, perm, flp] = reorient(R0, hs.bg.hdr.dim(2:4), 0);
if aligned % aligned mtx: do it in special way
[p, ~, rg, dim] = read_nii(fname, frm, 0); % no re-orient
try
if any(regexpi(mtx, '\.mat$'))
R = load(mtx, '-ascii');
if ~isequal(size(R), [4 4])
error('Invalid transformation matrix file: %s', mtx);
end
else % see nii_xform
R = eye(4);
warp = nii_tool('img', mtx); % FSL warp nifti
if ~isequal(size(warp), [hs.bg.hdr.dim(2:4) 3])
error('warp file and template file img size don''t match.');
end
if det(R0(1:3,1:3))<0, warp(:,:,:,1) = -warp(:,:,:,1); end
if ~isequal(perm, 1:3)
warp = permute(warp, [perm 4]);
end
for j = 1:3
if flp(j), warp = flip(warp, j); end
end
p.warp = warp;
p.R0 = R_back; % always interp
end
catch me
errordlg(me.message);
return;
end
% see nii_xform for more comment on following method
R = R0 / diag([hs.bg.hdr.pixdim(2:4) 1]) * R * diag([p.pixdim 1]);
[~, i1] = max(abs(p.R(1:3,1:3)));
[~, i0] = max(abs(R(1:3,1:3)));
flp = sign(R(i0+[0 4 8])) ~= sign(p.R(i1+[0 4 8]));
if any(flp)
rotM = diag([1-flp*2 1]);
rotM(1:3,4) = (dim-1).* flp;
R = R / rotM;
end
[p.R, perm, p.flip] = reorient(R, dim); % in case we apply mask to it
if ~isequal(perm, 1:3)
dim = dim(perm);
p.pixdim = p.pixdim(perm);
p.nii.img = permute(p.nii.img, [perm 4:8]);
end
for j = 1:3
if p.flip(j), p.nii.img = flip(p.nii.img, j); end
end
p.alignMtx = mtx; % info only for NIfTI essentials
else % regular overlay
[p, frm, rg, dim] = read_nii(fname, frm);
% Silently use another background R_back matching overlay: very rare
if frm>0 && frm ~= hs.form_code(1) && any(frm == hs.form_code)
R = nii_xform_mat(hs.bg.hdr, frm); % img alreay re-oriented
R_back = reorient(R, hs.bg.hdr.dim(2:4));
elseif frm==0 && isequal(p.hdr0.dim(2:4), hs.bg.hdr.dim(2:4))
p.R = hs.bg.R; % best guess: use background xform
p.perm = perm;
p.nii.img = permute(p.nii.img, [p.perm 4:8]);
for i = 1:3
if p.flip(i) ~= flp(i)
p.nii.img = flip(p.nii.img, i);
end
end
p.flip = flp;
warndlg(['There is no valid coordinate system for the overlay. ' ...
'The viewer supposes the same coordinate as the background.'], ...
'Missing valid tranformation');
elseif frm ~= 2 && ~any(frm == hs.form_code)
warndlg(['There is no matching coordinate system between the overlay ' ...
'image and the background image. The overlay is likely meaningless.'], ...
'Transform Inconsistent');
end
end
singleVol = 0;
nv = size(p.nii.img, 4);
if nv>1 && numel(p.nii.img)>1e7 % load all or a single volume
if isfield(p.nii, 'NamedMap')
nams = cell(1, numel(p.nii.NamedMap));
for i = 1:numel(nams), nams{i} = p.nii.NamedMap{i}.MapName; end
a = listdlg('PromptString', 'Load "All" or one of the map:', ...
'SelectionMode', 'single', 'ListString', ['All' nams]);
if a==1, a = 'All'; else, a = a - 1; end
else
str = ['Input ''all'' or a number from 1 to ' num2str(nv)];
while 1
a = inputdlg(str, 'Volumes to load', 1, {'all'});
if isempty(a), return; end
a = strtrim(a{1});
if ~isstrprop(a, 'digit'), break; end
a = str2num(a);
if isequal(a,1:nv) || (numel(a)==1 && a>=1 && a<=nv && mod(a,1)==0)
break;
end
end
end
if isnumeric(a) && numel(a)==1
singleVol = a;
p.nii.img = p.nii.img(:,:,:,a);
if isfield(p.nii, 'cii')
p.nii.cii{1} = p.nii.cii{1}(:,a);
p.nii.cii{2} = p.nii.cii{2}(:,a);
end
if isfield(p.nii, 'NamedMap')
try, p.nii.NamedMap = p.nii.NamedMap(a); %#ok<*NOCOM>
catch, p.nii.NamedMap = p.nii.NamedMap(1);
end
try, p.map = p.nii.NamedMap{1}.map; end
end
rg = get_range(p.nii);
end
end
ii = [1 6 11 13:15]; % diag and offset: avoid large ratio due to small value
if ~isequal(hs.dim, dim) || any(abs(R_back(ii)./p.R(ii)-1) > 0.01)
p.R0 = R_back;
end
p.Ri = inv(p.R);
if ~isreal(p.nii.img)
p.phase = angle(p.nii.img); % -pi to pi
p.phase = mod(p.phase/(2*pi), 1); % 0~1
p.nii.img = abs(p.nii.img); % real now
end
mdl = hs.files.getModel;
luts = zeros(1, mdl.size);
for i = 1:mdl.size % overlay added
p0 = get_para(hs, i);
luts(i) = p0.lut;
end
p.hsI = copyimg(hs); % duplicate image obj for overlay: will be at top
p.lb = rg(1); p.ub = rg(2);
p = dispPara(p, luts);
p.hsI(1).UserData = p;
[pName, niiName, ext] = fileparts(p.nii.hdr.file_name);
if strcmpi(ext, '.gz'), [~, niiName] = fileparts(niiName); end
if aligned, niiName = [niiName '(aligned)']; end
if singleVol, niiName = [niiName '(' num2str(singleVol) ')']; end
try
checked = [0; hs.files.getCheckBoxListSelectedIndices+1];
mdl.insertElementAt(niiName, 0);
hs.files.setCheckBoxListSelectedIndices(checked);
hs.files.setSelectedIndex(0); hs.files.updateUI;
catch me
delete(p.hsI);
errordlg(me.message);
return;
end
hs.pref.UserData.addPath = pName;
set_cdata(hs);
set_xyz(hs);
if isfield(p.nii, 'cii'), cii_view(hs); end
%% Reorient 4x4 R
function [R, perm, flp] = reorient(R, dim, leftHand)
% [R, perm, flip] = reorient(R, dim, leftHand)
% Re-orient transformation matrix R (4x4), so it will be diagonal major and
% positive at diagonal, unless the optional third input is true, which requires
% left-handed matrix, where R(1,1) will be negative.
% The second input is the img space dimension (1x3).
% The perm output, like [1 2 3] or a permutation of it, indicates if input R was
% permuted for 3 axis. The third output, flip (1x3 logical), indicates an axis
% (AFTER perm) is flipped if true.
a = abs(R(1:3,1:3));
[~, ixyz] = max(a);
if ixyz(2) == ixyz(1), a(ixyz(2),2) = 0; [~, ixyz(2)] = max(a(:,2)); end
if any(ixyz(3) == ixyz(1:2)), ixyz(3) = setdiff(1:3, ixyz(1:2)); end
[~, perm] = sort(ixyz);
R(:,1:3) = R(:,perm);
flp = R([1 6 11]) < 0; % diag(R(1:3, 1:3))
if nargin>2 && leftHand, flp(1) = ~flp(1); end
rotM = diag([1-flp*2 1]);
rotM(1:3, 4) = (dim(perm)-1) .* flp; % 0 or dim-1
R = R / rotM; % xform matrix after flip
%% Load, re-orient nii, extract essential nii stuff
% nifti may be re-oriented, p.hdr0 stores original nii.hdr
function [p, frm, rg, dim] = read_nii(fname, ask_code, reOri)
if nargin<2, ask_code = []; end
if ischar(fname), p.nii = nii_tool('load', fname);
else, p.nii = fname; fname = p.nii.hdr.file_name;
end
p.hdr0 = p.nii.hdr; % original hdr
c = p.nii.hdr.intent_code;
if c>=3000 && c<=3099 && isfield(p.nii, 'ext') && any([p.nii.ext.ecode] == 32)
p.nii = cii2nii(p.nii);
end
if nargin<3 || reOri
[p.nii, p.perm, p.flip] = nii_reorient(p.nii, 0);
else
p.perm = 1:3;
p.flip = false(1,3);
end
dim = p.nii.hdr.dim(2:8);
dim(dim<1 | mod(dim,1)~=0) = 1;
if p.nii.hdr.dim(1)>4 % 4+ dim, put all into dim4
if sum(dim(4:7)>1)>1
warndlg([fname ' has 5 or more dimension. Dimension above 4 are ' ...
'all treated as volumes for visualization']);
end
dim(4) = prod(dim(4:7)); dim(5:7) = 1;
p.nii.img = reshape(p.nii.img, [dim size(p.nii.img, 8)]);
end
[p.R, frm] = nii_xform_mat(p.nii.hdr, ask_code);
dim = dim(1:3);
p.pixdim = p.nii.hdr.pixdim(2:4);
if size(p.nii.img,4)<4 && ~isfloat(p.nii.img)
p.nii.img = single(p.nii.img);
end
if p.nii.hdr.scl_slope==0, p.nii.hdr.scl_slope = 1; end
if p.nii.hdr.scl_slope~=1 || p.nii.hdr.scl_inter~=0
if isfloat(p.nii.img)
p.nii.img = p.nii.img * p.nii.hdr.scl_slope + p.nii.hdr.scl_inter;
else
p.scl_slope = p.nii.hdr.scl_slope;
p.scl_inter = p.nii.hdr.scl_inter;
end
end
% check if ROI labels available: the same file name with .txt extension
if c == 1002 % Label
[pth, nam, ext] = fileparts(p.nii.hdr.file_name);
nam1 = fullfile(pth, [nam '.txt']);
if strcmpi(ext, '.gz') && ~exist(nam1, 'file')
[~, nam] = fileparts(nam);
nam1 = fullfile(pth, [nam '.txt']);
end
if exist(nam1, 'file') % each line format: 1 ROI_1
fid = fopen(nam1);
while 1
ln = fgetl(fid);
if ~ischar(ln), break; end
[ind, a] = strtok(ln);
ind = str2double(ind);
try p.labels{ind} = strtrim(a); catch, end
end
fclose(fid);
end
end
rg = get_range(p.nii, isfield(p, 'labels'));
if isfield(p.nii, 'NamedMap')
try, p.map = p.nii.NamedMap{1}.map; end
end
%% Return xform mat and form_code: form_code may have two if not to ask_code
function [R, frm] = nii_xform_mat(hdr, ask_code)
% [R, form] = nii_xform_mat(hdr, asked_code);
% Return the transformation matrix from a NIfTI hdr. By default, this returns
% the sform if available. If the optional second input, required form code, is
% provided, this will try to return matrix for that form code. The second
% optional output is the form code of the actually returned matrix.
fs = [hdr.sform_code hdr.qform_code]; % sform preferred
if fs(1)==fs(2), fs = fs(1); end % sform if both are the same
f = fs(fs>=1 & fs<=4); % 1/2/3/4 only
if isempty(f) || ~strncmp(hdr.magic, 'n', 1) % treat it as Analyze
frm = 0;
try % try spm style Analyze
[pth, nam, ext] = fileparts(hdr.file_name);
if strcmpi(ext, '.gz'), [~, nam] = fileparts(nam); end
R = load(fullfile(pth, [nam '.mat']));
R = R.M;
catch % make up R for Analyze: suppose xyz order with left storage
R = [diag(hdr.pixdim(2:4)) -(hdr.dim(2:4).*hdr.pixdim(2:4)/2)'; 0 0 0 1];
R(1,:) = -R(1,:); % use left handed
end
return;
end
if numel(f)==1 || nargin<2 || isempty(ask_code) % only 1 avail or no ask_code
frm = f;
else % numel(f) is 2, numel(ask_code) can be 1 or 2
frm = f(f == ask_code(1));
if isempty(frm) && numel(ask_code)>1, frm = f(f == ask_code(2)); end
if isempty(frm) && any(f==2), frm = 2; end % use confusing code 2
if isempty(frm), frm = f(1); end % no match to ask_code, use sform
end
if frm(1) == fs(1) % match sform_code or no match
R = [hdr.srow_x; hdr.srow_y; hdr.srow_z; 0 0 0 1];
else % match qform_code
R = quat2R(hdr);
end
%%
function R = quat2R(hdr)
% Return 4x4 qform transformation matrix from nii hdr.
b = hdr.quatern_b;
c = hdr.quatern_c;
d = hdr.quatern_d;
a = sqrt(1-b*b-c*c-d*d);
if ~isreal(a), a = 0; end % avoid complex due to precision
R = [1-2*(c*c+d*d) 2*(b*c-d*a) 2*(b*d+c*a);
2*(b*c+d*a) 1-2*(b*b+d*d) 2*(c*d-b*a);
2*(b*d-c*a ) 2*(c*d+b*a) 1-2*(b*b+c*c)];
if hdr.pixdim(1)<0, R(:,3) = -R(:,3); end % qfac
R = R * diag(hdr.pixdim(2:4));
R = [R [hdr.qoffset_x hdr.qoffset_y hdr.qoffset_z]'; 0 0 0 1];
%% Create java SpinnerNumber
function h = java_spinner(pos, val, parent, callback, fmt, helpTxt)
% h = java_spinner(pos, val, parent, callback, fmt, helpTxt)
% pos: [left bottom width height]
% val: [curVal min max step]
% parent: figure or panel
% fmt: '#' for integer, or '#.#', '#.##'
mdl = javax.swing.SpinnerNumberModel(val(1), val(2), val(3), val(4));
% jSpinner = javax.swing.JSpinner(mdl);
jSpinner = com.mathworks.mwswing.MJSpinner(mdl);
h = javacomponent(jSpinner, pos, parent);
set(h, 'StateChangedCallback', callback, 'ToolTipText', helpTxt);
jEditor = javaObject('javax.swing.JSpinner$NumberEditor', h, fmt);
h.setEditor(jEditor);
h.setFont(java.awt.Font('Tahoma', 0, 11));
%% Estimate lower and upper bound of img display
function rg = get_range(nii, isLabel)
if size(nii.img, 8)>2 || any(nii.hdr.datatype == [128 511 2304]) % RGB / RGBA
if max(nii.img(:))>2, rg = [0 255]; else, rg = [0 1]; end
return;
elseif nii.hdr.cal_max~=0 && nii.hdr.cal_max>min(nii.img(:))
rg = [nii.hdr.cal_min nii.hdr.cal_max];
return;
end
img = nii.img(:,:,:,1);
img = img(:);
img(isnan(img) | isinf(img)) = [];
if ~isreal(img), img = abs(img); end
if ~isfloat(img)
slope = nii.hdr.scl_slope; if slope==0, slope = 1; end
img = single(img) * slope + nii.hdr.scl_inter;
end
mi = min(img); ma = max(img);
if nii.hdr.intent_code > 1000 || (nargin>1 && isLabel)
rg = [mi ma]; return;
end
ind = abs(img)>50;
if sum(ind)<numel(img)/10, ind = abs(img)>std(img)/2; end
im = img(ind);
mu = mean(im);
sd = std(im);
rg = mu + [-2 2]*sd;
if rg(1)<=0 && mu-sd>0, rg(1) = sd/5; end
if rg(1)<mi || isnan(rg(1)), rg(1) = mi; end
if rg(2)>ma || isnan(rg(2)), rg(2) = ma; end
if rg(1)==rg(2), rg(1) = mi; if rg(1)==rg(2), rg(1) = 0; end; end
% rg = round(rg, 2, 'significant'); % since 2014b
rg = str2num(sprintf('%.2g ', rg)); %#ok<*ST2NM>
if rg(1)==rg(2), rg(1) = mi; end
if abs(rg(1))>10, rg(1) = floor(rg(1)/2)*2; end % even number
if abs(rg(2))>10, rg(2) = ceil(rg(2)/2)*2; end % even number
%% Draw vector lines, called by set_cdata
function vector_lines(hs, i, iaxis)
p = get_para(hs, i);
d = single(size(p.nii.img));
pixdim = hs.bg.hdr.pixdim(2:4); % before reorient
if strcmpi(get(p.hsI(1), 'Type'), 'image') % just switched to "lines"
delete(p.hsI);
lut = hs.lut.UserData; % last lut
if isempty(lut), lut = 2; end % default red
clr = lut2map(p, hs.lutStr{lut}); clr = clr(end,:);
cb = get(hs.hsI(1), 'ButtonDownFcn');
for j = 1:3
p.hsI(j) = quiver(hs.ax(j), 1, 1, 0, 0, 'Color', clr, ...
'ShowArrowHead', 'off', 'AutoScale', 'off', 'ButtonDownFcn', cb);
end
crossFront(hs); % to be safe before next
if i>1, for j = 1:3, uistack(p.hsI(j), 'down', i-1); end; end
if isfield(p, 'R0') && ~isfield(p, 'ivec')
I = ones([d(1:3) 4], 'single');
[I(:,:,:,1), I(:,:,:,2), I(:,:,:,3)] = ndgrid(0:d(1)-1, 0:d(2)-1, 0:d(3)-1);
I = permute(I, [4 1 2 3]);
I = reshape(I, 4, []);
I = p.R0 \ (p.R * I) + 1;
p.ivec = reshape(I(1:3,:)', d);
R0 = normc(p.R0(1:3, 1:3));
R = normc(p.R(1:3, 1:3));
[pd, j] = min(p.pixdim);
p.Rvec = R0 / R * pd / pixdim(j);
end
p.hsI(1).UserData = p;
end
img = p.nii.img;
% This is needed since vec is in image ref, at least for fsl
img(:,:,:,p.flip) = -img(:,:,:,p.flip);
if isfield(p, 'mask') % ignore modulation
img = bsxfun(@times, img, p.mask);
end
if any(abs(diff(pixdim))>1e-4) % non isovoxel background
pd = pixdim / min(pixdim);
for j = 1:3, img(:,:,:,j) = img(:,:,:,j) / pd(j); end
end
if isfield(p, 'Rvec')
img = reshape(img, [], d(4));
img = img * p.Rvec;
img = reshape(img, d);
end
for ix = iaxis
I = round(get(hs.ijk(ix), 'Value'));
j = 1:3; j(ix) = [];
if isfield(p, 'ivec')
I = abs(p.ivec(:,:,:,ix) - I);
[~, I] = min(I, [], ix);
ii = {1:d(1) 1:d(2) 1:d(3)};
ii{ix} = single(1);
[ii{1}, ii{2}, ii{3}] = ndgrid(ii{:});
ii{ix} = single(I);
io = {':' ':' ':' ':'}; io{ix} = 1;
im = img(io{:});
for k = 1:2
im(:,:,:,k) = interp3(img(:,:,:,j(k)), ii{[2 1 3]}, 'nearest');
end
ind = sub2ind(d(1:3), ii{:});
X = p.ivec(:,:,:,j(1)); X = permute(X(ind), [j([2 1]) ix]);
Y = p.ivec(:,:,:,j(2)); Y = permute(Y(ind), [j([2 1]) ix]);
else
ii = {':' ':' ':'};
ii{ix} = I;
im = img(ii{:}, j);
[Y, X] = ndgrid(1:d(j(2)), 1:d(j(1)));
end
im = permute(im, [j([2 1]) 4 ix]);
im(im==0) = nan; % avoid dots in emf and eps
X = X - im(:,:,1)/2;
Y = Y - im(:,:,2)/2;
set(p.hsI(ix), 'XData', X, 'YData', Y, 'UData', im(:,:,1), 'VData', im(:,:,2));
end
%% Bring cross and label to front
function crossFront(hs)
for i = 1:3
txt = allchild(hs.ax(i));
ind = strcmpi(get(txt, 'Type'), 'text');
txt = txt(ind); % a number, two letters, plus junk text with matlab 2010b
uistack([txt' hs.cross(i,:)], 'top');
end
%% Compute color map for LUT
function map = lut2map(p, lutStr)
persistent parula64;
if isfield(p, 'map')
if isfield(p.nii, 'NamedMap')
try, map = p.nii.NamedMap{p.volume}.map; end
else, map = p.map;
end
return;
end
lut = p.lut;
map = linspace(0,1,64)'*[1 1 1]; % gray
if lut == 1, return; % gray
elseif lut == 2, map(:,2:3) = 0; % red
elseif lut == 3, map(:,[1 3]) = 0; % green
elseif lut == 4, map(:,1:2) = 0; % blue
elseif lut == 5, map(:,2) = 0; % violet
elseif lut == 6, map(:,3) = 0; % yellow
elseif lut == 7, map(:,1) = 0; % cyan
elseif any(lut == [8 19 26]), map(:,3) = 0; map(:,1) = 1; % red_yellow
elseif lut == 9, map(:,1) = 0; map(:,3) = flip(map(:,3)); % blue_green
elseif lut == 10 % two-sided
map = map(1:2:end,:); % half
map_neg = map;
map(:,3) = 0; map(:,1) = 1; % red_yellow
map_neg(:,1) = 0; map_neg(:,3) = flip(map_neg(:,3)); % blue_green
map = [flip(map_neg,1); map];
elseif lut == 11, map(:,2:3) = 0; % vector lines
elseif lut == 12 % parula not in old matlab, otherwise this can be omitted
if isempty(parula64)
fname = fullfile(fileparts(mfilename('fullpath')), 'example_data.mat');
a = load(fname, 'parula'); parula64 = a.parula;
end
map = parula64;
elseif lut < 26 % matlab LUT
map = feval(lutStr, 64);
elseif lut == 27 % phase3: red-yellow-green-yellow-red
a = map(:,1);
map(1:32,3) = 0; map(1:16,1) = 1; map(17:32,2) = 1;
map(1:16,2) = a(1:4:64); map(17:32,1) = a(64:-4:1);
map(33:64,:) = map(32:-1:1,:);
elseif lut == 28 % phase6: red-yellow-green/violet-blue-cyan
a = map(:,1);
map(1:32,3) = 0; map(1:16,1) = 1; map(17:32,2) = 1;
map(1:16,2) = a(1:4:64); map(17:32,1) = a(64:-4:1);
map(33:48,2) = 0; map(33:48,3) = 1; map(33:48,1) = a(64:-4:1);
map(49:64,1) = 0; map(49:64,3) = 1; map(49:64,2) = a(1:4:64);
elseif lut == 29 % RGB
end
%% Preference dialog
function pref_dialog(h, ~)
pf = getpref('nii_viewer_para');
d = dialog('Name', 'Preferences', 'Visible', 'off');
pos = getpixelposition(d);
pos(3:4) = [396 332];
hs.fig = ancestor(h, 'figure');
uicontrol(d, 'Style', 'text', 'Position', [8 306 300 22], ...
'String', 'Background (template) image folder:', 'HorizontalAlignment', 'left');
hs.openPath = uicontrol(d, 'Style', 'edit', 'String', pf.openPath, ...
'Position', [8 288 350 22], 'BackgroundColor', 'w', 'HorizontalAlignment', 'left', ...
'TooltipString', 'nii_viewer will point to this folder when you "Open" image');
uicontrol('Parent', d, 'Position', [358 289 30 22], 'Tag', 'browse', ...
'String', '...', 'Callback', @pref_dialog_cb);
hs.rightOnLeft = uicontrol(d, 'Style', 'popup', 'BackgroundColor', 'w', ...
'Position', [8 252 380 22], 'Value', pf.rightOnLeft+1, ...
'String', {'Neurological orientation (left on left side)' ...
'Radiological orientation (right on left side)'}, ...
'TooltipString', 'Display convention also applies to future use');
uicontrol(d, 'Style', 'text', 'Position', [8 210 40 22], ...
'String', 'Layout', 'HorizontalAlignment', 'left', ...
'TooltipString', 'Layout for three views');
% iconsFolder = fullfile(matlabroot,'/toolbox/matlab/icons/');
% iconUrl = strrep(['file:/' iconsFolder 'matlabicon.gif'],'\','/');
% str = ['<html><img src="' iconUrl '"/></html>'];
hs.layout = uicontrol(d, 'Style', 'popup', 'BackgroundColor', 'w', ...
'Position', [50 214 338 22], 'Value', pf.layout, ...
'String', {'one-row' 'two-row sag on right' 'two-row sag on left'}, ...
'TooltipString', 'Layout for three views');
hs.mouseOver = uicontrol(d, 'Style', 'checkbox', ...
'Position', [8 182 380 22], 'Value', pf.mouseOver, ...
'String', 'Show coordinates and intensity when mouse moves over image', ...
'TooltipString', 'Also apply to future use');
uipanel(d, 'Units', 'Pixels', 'Position', [4 110 390 56], 'BorderType', 'etchedin', ...
'BorderWidth', 2, 'Title', 'For "Save NIfTI as" if interpolation is applicable');
str = {'nearest' 'linear' 'cubic' 'spline'};
val = find(strcmp(str, pf.interp));
uicontrol('Parent', d, 'Style', 'text', 'Position', [8 116 140 22], ...
'String', 'Interpolation method:', 'HorizontalAlignment', 'right');
hs.interp = uicontrol(d, 'Style', 'popup', 'String', str, ...
'Position', [150 120 68 22], 'Value', val, 'BackgroundColor', 'w');
uicontrol('Parent', d, 'Style', 'text', 'Position', [230 116 90 22], ...
'String', 'Missing value:', 'HorizontalAlignment', 'right');
hs.extraV = uicontrol(d, 'Style', 'edit', 'String', num2str(pf.extraV), ...
'Position', [324 120 60 22], 'BackgroundColor', 'w', ...
'TooltipString', 'NaN or 0 is typical, but can be any number');
str = strtrim(cellstr(num2str([0 120 150 200 300 600 1200]')));
val = find(strcmp(str, pf.dpi));
uipanel(d, 'Units', 'Pixels', 'Position', [4 40 390 56], 'BorderType', 'etchedin', ...
'BorderWidth', 2, 'Title', 'For "Save figure as" and "Copy figure"');
uicontrol('Parent', d, 'Style', 'text', 'Position', [8 46 90 22], ...
'String', 'Resolution:', 'HorizontalAlignment', 'right');
hs.dpi = uicontrol(d, 'Style', 'popup', 'String', str, ...
'Position', [110 50 50 22], 'Value', val, 'BackgroundColor', 'w', ...
'TooltipString', 'in DPI (0 means screen resolution)');
uicontrol('Parent', d, 'Position', [300 10 70 24], 'Tag', 'OK', ...
'String', 'OK', 'Callback', @pref_dialog_cb);
uicontrol('Parent', d, 'Position',[200 10 70 24], ...
'String', 'Cancel', 'Callback', 'delete(gcf)');
set(d, 'Position', pos, 'Visible', 'on');
guidata(d, hs);
%% Preference dialog callback
function pref_dialog_cb(h, ~)
hs = guidata(h);
if strcmp(get(h, 'Tag'), 'OK') % done
fh = hs.fig;
pf = getpref('nii_viewer_para');
pf.layout = get(hs.layout, 'Value'); % 1:3
pf.rightOnLeft = get(hs.rightOnLeft, 'Value')==2;
pf.mouseOver = get(hs.mouseOver, 'Value');
if pf.mouseOver % this is the only one we update current fig
set(fh, 'WindowButtonMotionFcn', {@nii_viewer_cb 'mousemove' fh});
else
set(fh, 'WindowButtonMotionFcn', '');
end
i = get(hs.interp, 'Value');
str = get(hs.interp, 'String');
pf.interp = str{i};
pf.extraV = str2double(get(hs.extraV, 'String'));
pf.openPath = get(hs.openPath, 'String');
i = get(hs.dpi, 'Value');
str = get(hs.dpi, 'String');
pf.dpi = str{i};
setpref('nii_viewer_para', fieldnames(pf), struct2cell(pf));
delete(get(h, 'Parent'));
elseif strcmp(get(h, 'Tag'), 'browse') % set openPath
pth = uigetdir(pwd, 'Select folder for background image');
if ~ischar(pth), return; end
set(hs.openPath, 'String', pth);
end
%% Simple version of interp3
function V = interp3a(V, I, method)
% V = interp3a(V, I, 'linear');
% This is similar to interp3 from Matlab, but takes care of the Matlab version
% issue, and the input is simplified for coordinate. The coordinate input are in
% this way: I(1,:), I(2,:) and I(3,:) are for x, y and z.
persistent v;
if isempty(v)
try
griddedInterpolant(ones(3,3,3), 'nearest', 'none');
v = 2014;
catch
try
griddedInterpolant(ones(3,3,3), 'nearest');
v = 2013;
catch
v = 2011;
end
end
end
if strcmp(method, 'nearest') || any(size(V)<2), I = round(I); end
if size(V,1)<2, V(2,:,:) = nan; end
if size(V,2)<2, V(:,2,:) = nan; end
if size(V,3)<2, V(:,:,2) = nan; end
if v > 2011
if v > 2013
F = griddedInterpolant(V, method, 'none');
else
F = griddedInterpolant(V, method);
end
V = F(I(1,:), I(2,:), I(3,:)); % interpolate
else % earlier matlab
V = interp3(V, I(2,:), I(1,:), I(3,:), method, nan);
end
%% 2D/3D smooth wrapper: no input check for 2D
function im = smooth23(im, varargin)
% out = smooth23(in, varargin)
% This works the same as smooth3 from Matlab, but takes care of 2D input.
is2D = size(im,3) == 1;
if is2D, im = repmat(im, [1 1 2]); end
im = smooth3(im, varargin{:});
if is2D, im = im(:,:,1); end
%% Show xyz and value
function xyz = set_xyz(hs, I)
if nargin<2
for i=3:-1:1, I(i) = get(hs.ijk(i), 'Value'); end
end
I = round(I);
xyz = round(hs.bg.R * [I-1 1]');
xyz = xyz(1:3);
str = sprintf('(%i,%i,%i): ', xyz);
for i = 1:hs.files.getModel.size % show top one first
p = get_para(hs, i);
if p.show == 0, continue; end
t = round(p.volume);
if isfield(p, 'R0') % need interpolation
if isfield(p, 'warp')
warp = p.warp(I(1), I(2), I(3), :);
I0 = p.Ri * (p.R0 * [I-1 1]' + [warp(:); 0]);
else
I0 = p.Ri * p.R0 * [I-1 1]'; % overlay ijk
end
I0 = round(I0(1:3)+1);
else, I0 = I;
end
try
val = p.nii.img(I0(1), I0(2), I0(3), t, :);
if isfield(p, 'scl_slope')
val = single(val) * p.scl_slope + p.scl_inter;
end
catch
val = nan; % out of range
end
if isfield(p, 'labels')
try
labl = p.labels{val};
str = sprintf('%s %s', str, labl);
continue; % skip numeric val assignment
end
end
if isfield(p.nii, 'NamedMap')
try
labl = p.nii.NamedMap{p.volume}.labels{val};
str = sprintf('%s %s', str, labl);
continue;
end
end
fmtstr = '%.4g ';
if numel(val)>1
fmtstr = repmat(fmtstr, 1, numel(val));
fmtstr = ['[' fmtstr]; fmtstr(end) = ']'; %#ok
end
str = sprintf(['%s ' fmtstr], str, val);
end
hs.value.String = str;
%% nii essentials
function s = nii_essential(hdr)
% info = nii_essential(hdr);
% Decode important NIfTI hdr into struct info, which is human readable.
if isfield(hdr, 'nii') % input by nii_viewer
s.FileName = hdr.nii.hdr.file_name;
if isfield(hdr, 'mask_info'), s.MaskedBy = hdr.mask_info; end
if isfield(hdr, 'modulation_info'), s.ModulatdBy = hdr.modulation_info; end
if isfield(hdr, 'alignMtx'), s.AlignMatrix = hdr.alignMtx; end
hdr = hdr.nii.hdr;
else
s.FileName = hdr.file_name;
end
switch hdr.intent_code
case 2, s.intent = 'Correlation'; s.DoF = hdr.intent_p1;
case 3, s.intent = 'T-test'; s.DoF = hdr.intent_p1;
case 4, s.intent = 'F-test'; s.DoF = [hdr.intent_p1 hdr.intent_p2];
case 5, s.intent = 'Z-score';
case 6, s.intent = 'Chi squared'; s.DoF = hdr.intent_p1;
% several non-statistical intent_code
case 1002, s.intent = 'Label'; % e.g. AAL labels
case 2003, s.intent = 'RGB'; % triplet in the 5th dimension
case 2004, s.intent = 'RGBA'; % quadruplet in the 5th dimension
end
switch hdr.datatype
case 0
case 1, s.DataType = 'logical';
case 2, s.DataType = 'uint8';
case 4, s.DataType = 'int16';
case 8, s.DataType = 'int32';
case 16, s.DataType = 'single';
case 32, s.DataType = 'single complex';
case 64, s.DataType = 'double';
case 128, s.DataType = 'uint8 RGB';
case 256, s.DataType = 'int8';
case 511, s.DataType = 'single RGB';
case 512, s.DataType = 'uint16';
case 768, s.DataType = 'uint32';
case 1024, s.DataType = 'int64';
case 1280, s.DataType = 'uint64';
case 1792, s.DataType = 'double complex';
case 2304, s.DataType = 'uint8 RGBA';
otherwise, s.DataType = 'unknown';
end
s.Dimension = hdr.dim(2:hdr.dim(1)+1);
switch bitand(hdr.xyzt_units, 7)
case 1, s.VoxelUnit = 'meters';
case 2, s.VoxelUnit = 'millimeters';
case 3, s.VoxelUnit = 'micrometers';
end
s.VoxelSize = hdr.pixdim(2:4);
switch bitand(hdr.xyzt_units, 56)
case 8, s.TemporalUnit = 'seconds';
case 16, s.TemporalUnit = 'milliseconds';
case 24, s.TemporalUnit = 'microseconds';
case 32, s.TemporalUnit = 'Hertz';
case 40, s.TemporalUnit = 'ppm';
case 48, s.TemporalUnit = 'radians per second';
end
if isfield(s, 'TemporalUnit') && strfind(s.TemporalUnit, 'seconds')
s.TR = hdr.pixdim(5);
end
if hdr.dim_info>0
s.FreqPhaseSliceDim = bitand(hdr.dim_info, [3 12 48]) ./ [1 4 16];
a = bitand(hdr.dim_info, 192) / 64;
if a>0 && s.FreqPhaseSliceDim(2)>0
ax = 'xyz'; % ijk to be accurate
pm = ''; if a == 2, pm = '-'; end
s.PhaseEncodingDirection = [pm ax(s.FreqPhaseSliceDim(2))];
end
end
switch hdr.slice_code
case 0
case 1, s.SliceOrder = 'Sequential Increasing';
case 2, s.SliceOrder = 'Sequential Decreasing';
case 3, s.SliceOrder = 'Alternating Increasing 1';
case 4, s.SliceOrder = 'Alternating Decreasing 1';
case 5, s.SliceOrder = 'Alternating Increasing 2';
case 6, s.SliceOrder = 'Alternating Decreasing 2';
otherwise, s.SliceOrder = 'Multiband?';
end
if ~isempty(hdr.descrip), s.Notes = hdr.descrip; end
str = formcode2str(hdr.qform_code);
if ~isempty(str), s.qform = str; end
if hdr.qform_code>0, s.qform_mat = quat2R(hdr); end
str = formcode2str(hdr.sform_code);
if ~isempty(str), s.sform = str; end
if hdr.sform_code>0
s.sform_mat = [hdr.srow_x; hdr.srow_y; hdr.srow_z; 0 0 0 1];
end
%% decode NIfTI form_code
function str = formcode2str(code)
switch code
case 0, str = '';
case 1, str = 'Scanner Anat';
case 2, str = 'Aligned Anat';
case 3, str = 'Talairach';
case 4, str = 'mni_152';
otherwise, str = 'Unknown';
end
%% Get a mask based on image intensity, but with inside brain filled
function r = img2mask(img)
mn = mean(img(img(:)>0));
r = smooth23(img, 'box', 5) > mn/8; % smooth, binarize
if sum(r(:))==0, return; end
try
C = contourc(double(r), [1 1]);
i = 1; c = {};
while size(C,2)>2 % split C into contours
k = C(2,1) + 1;
c{i} = C(:, 2:k); C(:,1:k) = []; %#ok
i = i+1;
end
nc = numel(c);
rg = nan(nc, 4); % minX minY maxX maxY
for i = 1:nc
rg(i,:) = [min(c{i},[],2)' max(c{i},[],2)'];
end
ind = false(nc,1);
foo = min(rg(:,1)); ind = ind | foo==rg(:,1);
foo = min(rg(:,2)); ind = ind | foo==rg(:,2);
foo = max(rg(:,3)); ind = ind | foo==rg(:,3);
foo = max(rg(:,4)); ind = ind | foo==rg(:,4);
c = c(ind); % outmost contour(s)
len = cellfun(@(x) size(x,2), c);
[~, ind] = sort(len, 'descend');
c = c(ind);
C = c{1};
if isequal(C(:,1), C(:,end)), c(2:end) = []; end % only 1st if closed
nc = numel(c);
for i = nc:-1:2 % remove closed contours except one with max len
if isequal(c{i}(:,1), c{i}(:,end)), c(i) = []; end
end
nc = numel(c);
while nc>1 % +1 contours, put all into 1st
d2 = nan(nc-1, 2); % distance^2 from C(:,end) to other start/endpoint
for i = 2:nc
d2(i-1,:) = sum((C(:,end)*[1 1] - c{i}(:,[1 end])).^2);
end
[i, j] = find(d2 == min(d2(:)));
i = i + 1; % start with 2nd
if j == 1, C = [C c{i}]; %#ok C(:,1) connect to c{i}(:,1)
else C = [C c{i}(:,end:-1:1)]; %#ok C(:,end) to c{i}(:,end)
end
c(i) = []; nc = nc-1;
end
if ~isequal(C(:,1), C(:,end)), C(:,end+1) = C(:,1); end % close the contour
x = C(1, :);
y = C(2, :);
[m, n] = size(r);
% following is the method in Octave poly2mask
xe = [x(1:numel(x)-1); x(1, 2:numel(x))]; % edge x
ye = [y(1:numel(y)-1); y(1, 2:numel(y))]; % edge y
ind = ye(1,:) == ye(2,:);
xe(:,ind) = []; ye(:, ind) = []; % reomve horizontal edges
minye = min(ye);
maxye = max(ye);
t = (ye == [minye; minye]);
exminy = xe(:); exminy = exminy(t);
exmaxy = xe(:); exmaxy = exmaxy(~t);
maxye = maxye';
minye = minye';
m_inv = (exmaxy - exminy) ./ (maxye - minye);
ge = [maxye minye exmaxy m_inv];
ge = sortrows(ge, [1 3]);
ge = [-Inf -Inf -Inf -Inf; ge];
gei = size(ge, 1);
sl = ge(gei, 1);
ae = []; % active edge
while (sl == ge(gei, 1))
ae = [ge(gei, 2:4); ae]; %#ok
gei = gei - 1;
end
miny = min(y);
if miny < 1, miny = 1; end
while (sl >= miny)
if (sl <= m) % check vert clipping
ie = round(reshape(ae(:, 2), 2, size(ae, 1)/2));
ie(1, :) = ie(1, :) + (ie(1, :) ~= ie(2, :));
ie(1, (ie(1, :) < 1)) = 1;
ie(2, (ie(2, :) > n)) = n;
ie = ie(:, (ie(1, :) <= n));
ie = ie(:, (ie(2, :) >= 1));
for i = 1:size(ie,2)
r(sl, ie(1, i):ie(2, i)) = true;
end
end
sl = sl - 1;
ae = ae((ae(:, 1) ~= sl), :);
ae(:, 2) = ae(:, 2) - ae(:, 3);
while (sl == ge(gei, 1))
ae = [ae; ge(gei, 2:4)]; %#ok
gei = gei - 1;
end
if size(ae,1) > 0
ae = sortrows(ae, 2);
end
end
catch %me, fprintf(2, '%s\n', me.message); assignin('base', 'me', me);
end
%% update colorbar label
function set_colorbar(hs)
if strcmpi(get(hs.colorbar, 'Visible'), 'off'), return; end
p = get_para(hs);
map = lut2map(p, hs.lutStr{p.lut});
rg = sort([p.lb p.ub]);
tickLoc = [0 0.5 1];
if any(p.lut == 26:28)
labls = [0 180 360];
elseif p.lut==10
rg = sort(abs(rg));
labls = {num2str(-rg(2),'%.2g') num2str(rg(1),'+/-%.2g') num2str(rg(2),'%.2g')};
elseif p.lut==numel(hs.lutStr) % custom
im = p.nii.img(:,:,:,p.volume);
im(isnan(im) | im==0) = [];
im = unique(im);
if max(im)<=size(map,1) && isequal(im, round(im)) % integer
try, map = map(im+1, :); rg = [im(1) im(end)]; end
end
labls = [rg(1) rg(2)];
tickLoc = [0 1];
else
if rg(2)<0, rg = rg([2 1]); end
mn = str2double(num2str(mean(rg), '%.4g'));
labls = [rg(1) mn rg(2)];
end
% colormap in earlier matlab version changes values in colorbar.
% So we have to set those values each time.
colormap(hs.ax(end), map); % map must be double for old matlab
% set(hs.colorbar, 'YTickLabel', labls); % new matlab
set(get(hs.colorbar, 'Children'), 'YData', [0 1]); % Trick for old matlab
set(hs.colorbar, 'YTickLabel', labls, 'YTick', tickLoc, 'Ylim', [0 1]);
fh = hs.fig.UserData;
if isempty(fh) || ~ishandle(fh) || ~isfield(p.nii, 'cii'), return; end
hs = guidata(fh);
colormap(hs.ax(end), map);
set(get(hs.colorbar, 'Children'), 'YData', [0 1]);
set(hs.colorbar, 'YTickLabel', labls, 'YTick', tickLoc, 'Ylim', [0 1]);
%% return screen size in pixels
function res = screen_pixels(id)
res = get(0, 'MonitorPositions');
if size(res,1)<2, res = res(1, 3:4); return; end % single/duplicate monitor
if nargin, res = res(id,3:4); return; end
res = sortrows(res);
res = res(end,1:2) + res(end,3:4) - res(1,1:2);
%% add mask or modulation
function addMask(h, ~)
hs = guidata(h);
jf = hs.files.getSelectedIndex+1;
p = get_para(hs, jf);
pName = fileparts(p.nii.hdr.file_name);
[fname, pName] = uigetfile([pName '/*.nii;*.hdr;*.nii.gz;*.hdr.gz'], ...
'Select mask NIfTI');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
nii = nii_tool('load', fname);
hdr = p.nii.hdr;
codes = [hdr.sform_code hdr.qform_code];
[R, frm] = nii_xform_mat(nii.hdr, codes);
if ~any(frm == codes)
str = ['There is no matching coordinate system between the selected ' ...
'image and the mask image. Do you want to apply the mask anyway?'];
btn = questdlg(str, 'Apply mask?', 'Cancel', 'Apply', 'Cancel');
if isempty(btn) || strcmp(btn, 'Cancel'), return; end
R0 = nii_xform_mat(hdr, codes(1));
else
R0 = nii_xform_mat(hdr, frm); % may be the same as p.R
end
% R0 = reorient(R0, hdr.dim(2:4)); % do this since img was done when loaded
% if isfield(p, 'alignMtx'), R = R0 / p.R * R; end % inverse
% this wont work if lines is background & Mprage is overlay
if all(isfield(p, {'R0' 'alignMtx'})) % target as mask
R1 = reorient(R, nii.hdr.dim(2:4));
if all(abs(R1(:)-p.R0(:))<1e-4), R0 = p.R; end % not 100% safe
end
d = single(size(p.nii.img)); % dim for reoriented img
d(numel(d)+1:3) = 1; d = d(1:3);
I = ones([d 4], 'single');
[I(:,:,:,1), I(:,:,:,2), I(:,:,:,3)] = ndgrid(0:d(1)-1, 0:d(2)-1, 0:d(3)-1);
I = permute(I, [4 1 2 3]);
I = reshape(I, 4, []); % ijk grids of target img
I = inv(R) * R0 * I + 1; %#ok ijk+1 for mask
I = round(I * 100) / 100;
im = single(nii.img(:,:,:,1)); % first mask volume
slope = nii.hdr.scl_slope;
if slope==0, slope = 1; end
im = im * slope + nii.hdr.scl_inter;
im = interp3a(im, I, 'nearest');
im1 = im(~isnan(im)); % for threshold computation
im = reshape(im, d);
if strcmp(get(h, 'Label'), 'Apply mask') % binary mask
if numel(unique(im1))<3
thre = min(im1);
else
a = get_range(nii);
str = sprintf('Threshold for non-binary mask (%.3g to %.4g)', ...
min(im1), max(im1));
a = inputdlg(str, 'Input mask threshold', 1, {num2str(a(1), '%.3g')});
if isempty(a), return; end
thre = str2double(a{1});
fname = [fname ' (threshold = ' a{1} ')']; % info only
end
p.mask = ones(size(im), 'single');
p.mask(abs(im)<=thre) = nan;
p.mask_info = fname;
noteStr = '(masked)';
else % modulation
mi = min(im1); ma = max(im1);
if mi<0 || ma>1
str = {sprintf('Lower bound to clip to 0 (image min = %.2g)', mi) ...
sprintf('Upper bound to clip to 1 (image max = %.2g)', ma)};
def = strtrim(cellstr(num2str([mi;ma], '%.2g'))');
a = inputdlg(str, 'Input modulation range', 1, def);
if isempty(a), return; end
mi = str2double(a{1}); ma = str2double(a{2});
fname = [fname ' (range [' a{1} ' ' a{2} '])'];
end
im(im<mi) = mi; im(im>ma) = ma;
p.modulation = (im-mi) / (ma-mi);
p.modulation_info = fname;
noteStr = '(modulated)';
end
p.hsI(1).UserData = p;
set_cdata(hs);
str = hs.files.getModel.get(jf-1);
if ~any(regexp(str, [regexptranslate('escape', noteStr) '$']))
hs.files.getModel.set(jf-1, [str noteStr]);
end
%% update crosshair: ix correspond to one of the three spinners, not views
function set_cross(hs, ix)
h = hs.cross;
for i = ix
c = get(hs.ijk(i), 'Value');
g = hs.gap(i);
if i == 1 % I changed
set([h(2,3:4) h(3,3:4)], 'XData', [c c]);
set([h(2,1) h(3,1)], 'XData', [0 c-g]);
set([h(2,2) h(3,2)], 'XData', [c+g hs.dim(1)+1]);
elseif i == 2 % J
set(h(1,3:4), 'XData', [c c]);
set(h(1,1), 'XData', [0 c-g]);
set(h(1,2), 'XData', [c+g hs.dim(2)+1]);
set(h(3,1:2), 'YData', [c c]);
set(h(3,3), 'YData', [0 c-g]);
set(h(3,4), 'YData', [c+g hs.dim(2)+1]);
else % K
set([h(1,1:2) h(2,1:2)], 'YData', [c c]);
set([h(1,3) h(2,3)], 'YData', [0 c-g]);
set([h(1,4) h(2,4)], 'YData', [c+g hs.dim(3)+1]);
end
end
%% Duplicate image handles, inlcuding ButtonDownFcn for new matlab
function h = copyimg(hs)
h = hs.hsI;
for i = 1:3, h(i) = handle(copyobj(hs.hsI(i), hs.ax(i))); end
cb = get(hs.hsI(1), 'ButtonDownFcn');
set(h, 'Visible', 'on', 'ButtonDownFcn', cb); % cb needed for 2014b+
crossFront(hs);
%% Save selected nii as another file
function save_nii_as(h, ~)
hs = guidata(h);
c = get(h, 'Label');
p = get_para(hs);
nam = p.nii.hdr.file_name;
pName = fileparts(nam);
if isempty(pName), pName = pwd; end
try nii = nii_tool('load', nam); % re-load to be safe
catch % restore reoriented img
nii = p.nii;
for k = 1:3, if p.flip(k), nii.img = flip(nii.img, k); end; end
nii.img = permute(nii.img, [p.perm 4:8]); % all vol in dim(4)
slope = nii.hdr.scl_slope; if slope==0, slope = 1; end
nii.img = (single(nii.img) - nii.hdr.scl_inter) / slope; % undo scale
if nii.hdr.datatype == 4 % leave others as it is or single
nii.img = int16(nii.img);
elseif nii.hdr.datatype == 512
nii.img = uint16(nii.img);
elseif any(nii.hdr.datatype == [2 128 2304])
nii.img = uint8(nii.img);
end
end
if ~isempty(strfind(c, 'a copy')) %#ok<*STREMP> % a copy
[fname, pName] = uiputfile([pName '/*.nii'], 'Input name for FSL RGB file');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
nii_tool('save', nii, fname);
elseif ~isempty(strfind(c, 'dim 4')) % fsl RGB
if any(size(nii.img,8) == 3:4)
nii.img = permute(nii.img, [1:3 8 4:7]);
elseif ~any(nii.hdr.dim(5) == 3:4)
errordlg('Selected image is not RGB data.'); return;
end
[fname, pName] = uiputfile([pName '/*.nii'], 'Input name for FSL RGB file');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
nii_tool('save', nii, fname);
elseif ~isempty(strfind(c, 'dim 3')) % old mricron RGB
if any(nii.hdr.dim(5) == 3:4)
nii.img = permute(nii.img, [1:3 5:7 4]);
elseif ~any(size(nii.img,8) == 3:4)
errordlg('Selected image is not RGB data'); return;
end
[fname, pName] = uiputfile([pName '/*.nii'], 'Input name for old mricrom styte file');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
old = nii_tool('RGBStyle', 'mricron');
nii_tool('save', nii, fname);
nii_tool('RGBStyle', old);
elseif ~isempty(strfind(c, 'AFNI')) % NIfTI RGB
if any(nii.hdr.dim(5) == 3:4)
nii.img = permute(nii.img, [1:3 5:8 4]);
elseif ~any(size(nii.img,8) == 3:4)
errordlg('Selected image is not RGB data'); return;
end
nii.img = abs(nii.img);
[fname, pName] = uiputfile([pName '/*.nii'], ...
'Input name for NIfTI standard RGB file');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
old = nii_tool('RGBStyle', 'afni');
nii_tool('save', nii, fname);
nii_tool('RGBStyle', old);
elseif ~isempty(strfind(c, '3D')) % SPM 3D
if nii.hdr.dim(5)<2
errordlg('Selected image is not multi-volume data'); return;
end
[fname, pName] = uiputfile([pName '/*.nii'], 'Input base name for SPM 3D file');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
nii_tool('save', nii, fname, 1); % force 3D
elseif ~isempty(strfind(c, 'new resolution'))
str = 'Resolution for three dimension in mm';
a = inputdlg(str, 'Input spatial resolution', 1, {'3 3 3'});
if isempty(a), return; end
res = sscanf(a{1}, '%g %g %g');
if numel(res) ~= 3
errordlg('Invalid spatial resolution');
return;
end
if isequal(res, p.nii.hdr.pixdim(2:4))
warndlg('The input resolution is the same as current one');
return;
end
[fname, pName] = uiputfile([pName '/*.nii;nii.gz'], ...
'Input result name for the new resolution file');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
nii_xform(nii, res, fname, hs.pref.UserData.interp, hs.pref.UserData.extraV)
elseif ~isempty(strfind(c, 'matching background'))
if p.hsI(1) == hs.hsI(1)
errordlg('You selected background image');
return;
end
[fname, pName] = uiputfile([pName '/*.nii;*.nii.gz'], ...
'Input result file name');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
nii_xform(nii, hs.bg.hdr, fname, hs.pref.UserData.interp, hs.pref.UserData.extraV)
elseif ~isempty(strfind(c, 'aligned template'))
[temp, pName] = uigetfile([pName '/*.nii;*.nii.gz'], ...
'Select the aligned template file');
if ~ischar(temp), return; end
temp = fullfile(pName, temp);
[mtx, pName] = uigetfile([pName '/*.mat'], ['Select the text ' ...
'matrix file which aligns the nii to the template']);
if ~ischar(mtx), return; end
mtx = fullfile(pName, mtx);
[fname, pName] = uiputfile([pName '/*.nii;*.nii.gz'], ...
'Input result file name');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
nii_xform(nii, {temp mtx}, fname, hs.pref.UserData.interp, hs.pref.UserData.extraV)
else
errordlg(sprintf('%s not implemented yet.', c));
end
%% Return 3-layer RGB, called by set_cdata
function [im, alfa] = lut2img(im, p, lutStr)
rg = sort([p.lb p.ub]);
if isfield(p.nii, 'NamedMap')
try, p.map = p.nii.NamedMap{p.volume}.map; end
end
if any(p.lut == 26:28)
im = im(:,:,2) .* single(im(:,:,1)>min(abs(rg))); % mag as mask
end
if rg(2)<0 % asking for negative data
rg = -rg([2 1]);
if p.lut~=10, im = -im; end
end
alfa = single(0); % override for lut=10
if p.lut == 10 % two-sided, store negative value
rg = sort(abs(rg));
im_neg = -single(im) .* (im<0);
im_neg = (im_neg-rg(1)) / (rg(2)-rg(1));
im_neg(im_neg>1) = 1; im_neg(im_neg<0) = 0;
alfa = im_neg; % add positive part later
im_neg = repmat(im_neg, [1 1 3]); % gray now
end
if p.lut < 26 % no scaling for 3 phase LUTs, RGB, custom
im = (im-rg(1)) / (rg(2)-rg(1));
im(im>1) = 1; im(im<0) = 0;
end
alfa = im + alfa;
if p.lut ~= 29, im = repmat(im, [1 1 3]); end % gray now
switch p.lut
case 1 % gray do nothing
case 2, im(:,:,2:3) = 0; % red
case 3, im(:,:,[1 3]) = 0; % green
case 4, im(:,:,1:2) = 0; % blue
case 5, im(:,:,2) = 0; % violet
case 6, im(:,:,3) = 0; % yellow
case 7, im(:,:,1) = 0; % cyan
case {8 19} % red_yellow, autumn
a = im(:,:,1); a(a>0) = 1; im(:,:,1) = a;
im(:,:,3) = 0;
case 9 % blue_green
im(:,:,1) = 0;
a = im(:,:,3); a(a==0) = 1; a = 1 - a; im(:,:,3) = a;
case 10 % two-sided: combine red_yellow & blue_green
im(:,:,3) = 0;
a = im(:,:,1); a(a>0) = 1; im(:,:,1) = a;
im_neg(:,:,1) = 0;
a = im_neg(:,:,3); a(a==0) = 1; a = 1 - a; im_neg(:,:,3) = a;
im = im + im_neg;
case 15 % hot, Matlab colormap can be omitted, but faster than mapping
a = im(:,:,1); a = a/0.375; a(a>1) = 1; im(:,:,1) = a;
a = im(:,:,2); a = a/0.375-1;
a(a<0) = 0; a(a>1) = 1; im(:,:,2) = a;
a = im(:,:,3); a = a*4-3; a(a<0) = 0; im(:,:,3) = a;
case 16 % cool
a = im(:,:,2); a(a==0) = 1; a = 1 - a; im(:,:,2) = a;
a = im(:,:,3); a(a>0) = 1; im(:,:,3) = a;
case 17 % spring
a = im(:,:,1); a(a>0) = 1; im(:,:,1) = a;
a = im(:,:,3); a(a==0) = 1; a = 1 - a; im(:,:,3) = a;
case 18 % summer
a = im(:,:,2); a(a==0) = -1; a = a/2+0.5; im(:,:,2) = a;
a = im(:,:,3); a(a>0) = 0.4; im(:,:,3) = a;
case 20 % winter
im(:,:,1) = 0;
a = im(:,:,3); a(a==0) = 2; a = 1-a/2; im(:,:,3) = a;
case 22 % copper
a = im(:,:,1); a = a*1.25; a(a>1) = 1; im(:,:,1) = a;
im(:,:,2) = im(:,:,2) * 0.7812;
im(:,:,3) = im(:,:,3) * 0.5;
case 26 % phase, like red_yellow
im(:,:,1) = 1; im(:,:,3) = 0;
case 27 % phase3, red-yellow-green-yellow-red
a = im(:,:,1);
b1 = a<=0.25;
b2 = a>0.25 & a<=0.5;
b3 = a>0.5 & a<=0.75;
b4 = a>0.75;
a(b1 | b4) = 1;
a(b2) = (0.5-a(b2))*4;
a(b3) = (a(b3)-0.5)*4;
im(:,:,1) = a;
a = im(:,:,2);
a(b2 | b3) = 1;
a(b1) = a(b1)*4;
a(b4) = (1-a(b4))*4;
im(:,:,2) = a;
im(:,:,3) = 0;
case 28 % phase6, red-yellow-green/violet-blue-cyan
a = im(:,:,1);
b1 = a<=0.25;
b2 = a>0.25 & a<=0.5;
b3 = a>0.5 & a<=0.75;
b4 = a>0.75;
a(b2) = (0.5-a(b2))*4; a(b1) = 1;
a(b3) = (0.75-a(b3))*4; a(b4) = 0;
im(:,:,1) = a;
a = im(:,:,2);
a(b1) = a(b1)*4; a(b2) = 1;
a(b3) = 0; a(b4) = (a(b4)-0.75)*4;
im(:,:,2) = a;
a = im(:,:,3);
a(b1 | b2) = 0;
a(b3 | b4) = 1;
im(:,:,3) = a;
case 29 % disp non-NIfTI RGB as RGB
im = abs(im); % e.g. DTI V1
if max(im(:)) > 1, im = im / 255; end % it should be unit8
alfa = sum(im,3)/3;
otherwise % parula(12), jet(13), hsv(14), bone(21), pink(23), custom
if isfield(p, 'map') % custom
map = p.map;
else
try, map = feval(lutStr, 256);
catch me
if p.lut == 12, map = lut2map(p); % parula for old matlab
else, rethrow(me);
end
end
end
if p.lut ~= 30 % normalized previously
a = floor(im(:,:,1) * (size(map,1)-1)) + 1; % 1st for bkgrnd
elseif max(p.nii.img(:)) <= size(map,1)
alfa = alfa / max(alfa(:));
a = round(im(:,:,1)) + 1; % custom or uint8, round to be safe
else
a = (im(:,:,1) - rg(1)) / (rg(2)-rg(1));
a(a<0) = 0 ; a(a>1) = 1;
alfa = a;
a = round(a * (size(map,1)-1)) + 1;
end
a(isnan(a)) = 1;
aa = a;
for i = 1:3
aa(:) = map(a, i);
im(:,:,i) = aa;
end
end
%% Return binary sphere ROI from xyz and r (mm)
function b = xyzr2roi(c, r, hdr)
% ROI_img = xyzr2roi(center, radius, hdr)
% Return an ROI img based on the dim info in NIfTI hdr. The center and radius
% are in unit of mm.
d = single(hdr.dim(2:4));
I = ones([d 4], 'single');
[I(:,:,:,1), I(:,:,:,2), I(:,:,:,3)] = ndgrid(0:d(1)-1, 0:d(2)-1, 0:d(3)-1);
I = permute(I, [4 1 2 3]);
I = reshape(I, 4, []); % ijk in 4 by nVox
R = nii_xform_mat(hdr);
I = R * I; % xyz in 4 by nVox
b = bsxfun(@minus, I(1:3,:), c(:)); % dist in x y z direction from center
b = sum(b .* b); % dist to center squared, 1 by nVox
b = b <= r*r; % within sphere
b = reshape(b, d);
%% Return center of gravity of an image
function c = img_cog(img)
% center_ijk = img_cog(img)
% Return the index of center of gravity in img (must be 3D).
img(isnan(img)) = 0;
img = double(abs(img));
gs = sum(img(:));
c = ones(3,1);
for i = 1:3
if size(img,i)==1, continue; end
a = shiftdim(img, i-1);
a = sum(sum(a,3),2);
c(i) = (1:size(img,i)) * a / gs;
end
%% set up disp parameter for new nifti
function p = dispPara(p, luts)
if nargin<2, luts = []; end
p.show = true; % img on
if isfield(p, 'map')
p.lut = 30; % numel(hs.lutStr)
elseif any(p.nii.hdr.datatype == [32 1792]) % complex
p.lut = 26; % phase
p.lb = str2double(sprintf('%.2g', p.ub/2));
elseif any(p.nii.hdr.intent_code == [1002 3007]) % Label
p.lut = 24; % prism
elseif p.nii.hdr.intent_code > 0 % some stats
if p.lb < 0
p.lut = 10; % two-sided
p.lb = str2double(sprintf('%.2g', p.ub/2));
else
a = setdiff(8:9, luts); % red-yellow & blue-green
if isempty(a), a = 8; end % red-yellow
p.lut = a(1);
end
elseif isempty(luts)
p.lut = 1; % gray
else
a = setdiff(2:7, luts); % use smallest unused mono-color lut
if isempty(a), a = 2; end % red
p.lut = a(1);
end
p.lb_step = stepSize(p.lb);
p.ub_step = stepSize(p.ub);
p.alpha = 1; % opaque
p.smooth = false;
p.interp = 1; % nearest
p.volume = 1; % first volume
%% estimate StepSize for java spinner
function d = stepSize(val)
d = abs(val/10);
% d = round(d, 1, 'significant');
d = str2double(sprintf('%.1g', d));
d = max(d, 0.01);
if d>4, d = round(d/2)*2; end
%% Return nii struct from nii struct, nii fname or other convertible files
function nii = get_nii(fname)
if isstruct(fname), nii = fname; return;
elseif iscellstr(fname), nam = fname{1};
else, nam = fname;
end
try
nii = nii_tool('load', strtrim(nam));
catch me
try, nii = dicm2nii(fname, pwd, 'no_save');
catch, rethrow(me);
end
end
%% Get figure/plot position from FoV for layout
% siz is in pixels, while pos is normalized.
function [siz, axPos, figPos] = plot_pos(mm, layout)
if layout==1 % 1x3
siz = [sum(mm([2 1 1]))+mm(1)/4 max(mm(2:3))]; % image area width/height
y0 = mm(2) / siz(1); % normalized width of sag images
x0 = mm(1) / siz(1); % normalized width of cor/tra image
z0 = mm(3) / siz(2); % normalized height of sag/cor images
y1 = mm(2) / siz(2); % normalized height of tra image
if y1>z0, y3 = 0; y12 = (y1-z0)/2;
else, y3 = (z0-y1)/2; y12 = 0;
end
axPos = [0 y12 y0 z0; y0 y12 x0 z0; y0+x0 y3 x0 y1; y0+x0*2 0 mm(1)/4/siz(1) min(z0,y1)];
elseif layout==2 || layout==3 % 2x2
siz = [sum(mm(1:2)) sum(mm(2:3))]; % image area width/height
x0 = mm(1) / siz(1); % normalized width of cor/tra images
y0 = mm(2) / siz(2); % normalized height of tra image
z0 = mm(3) / siz(2); % normalized height of sag/cor images
if layout == 2 % 2x2 sag at (1,2)
axPos = [x0 y0 1-x0 z0; 0 y0 x0 z0; 0 0 x0 y0; x0 0 1-x0 y0];
else % ==3: 2x2 sag at (1,2)
axPos = [0 y0 1-x0 z0; 1-x0 y0 x0 z0; 1-x0 0 x0 y0; 0 0 1-x0 y0];
end
else
error('Unknown layout parameter');
end
siz = siz / max(siz) * 800;
res = screen_pixels(1); % use 1st screen
maxH = res(2) - 160;
maxW = res(1) - 100;
if siz(1)>maxW, siz = siz / siz(1) * maxW; end
if siz(2)>maxH, siz = siz / siz(2) * maxH; end
figPos = round((res-siz)/2);
if figPos(1)+siz(1) > res(1), figPos(1) = res(1)-siz(1)-10; end
if figPos(2)+siz(2) > res(2)-130, figPos(2) = min(figPos(2), 50); end
%% Return nii struct from cii and gii
function nii = cii2nii(nii)
persistent gii; % Anatomical surface
if nargin<1, nii = gii; return; end
ind = find([nii.ext.ecode]==32, 1);
xml = nii.ext(ind).edata_decoded;
expr = '(?<=((SurfaceNumberOfVertices)|(SurfaceNumberOfNodes))=").*?(?=")';
nVer = str2double(regexp(xml, expr, 'match', 'once'));
if isempty(nVer), error('SurfaceNumberOfVertices not found'); end
if isempty(gii), gii = get_surfaces(nVer, 'Anatomical'); end
if isempty(gii) || numel(gii.Vertices) ~=2, error('Not valid GIfTI'); end
if nVer ~= size(gii.Vertices{1},1), error('GIfTI and CIfTI don''t match'); end
if gii_attr(xml, 'CIFTI Version', 1) == 1
dim = size(nii.img);
nii.img = reshape(nii.img, dim([1:4 6 5]));
end
dim = gii_attr(xml, 'VolumeDimensions', 1);
if isempty(dim), dim = [91 109 91]; end % HCP 2x2x2 mm
TR = gii_attr(xml, 'SeriesStep', 1);
if ~isempty(TR), nii.hdr.pixdim(5) = TR; end
mat = gii_element(xml, 'TransformationMatrixVoxelIndicesIJKtoXYZ', 1);
if isempty(mat) % some cii miss 'mat' and 'dim'
mat = [-2 0 0 90; 0 2 0 -126; 0 0 2 -72; 0 0 0 1]; % best guess from HCP
else
pow = gii_attr(xml, 'MeterExponent', 1);
mat(1:3,:) = mat(1:3,:) / 10^(3+pow);
end
nii.hdr.sform_code = gii.DataSpace;
nii.hdr.srow_x = mat(1,:);
nii.hdr.srow_y = mat(2,:);
nii.hdr.srow_z = mat(3,:);
nii.hdr.pixdim(2:4) = sqrt(sum(mat(1:3,1:3).^2));
nVol = size(nii.img, 5);
imgG = permute(nii.img, [6 5 1:4]);
nii.img = zeros([prod(dim) nVol], class(imgG));
iMdl = regexp(xml, '<BrainModel[\s>]'); iMdl(end+1) = numel(xml);
for j = 1:numel(iMdl)-1
c = xml(iMdl(j):iMdl(j+1));
offset = gii_attr(c, 'IndexOffset', 1);
typ = gii_attr(c, 'ModelType');
if strcmp(typ, 'CIFTI_MODEL_TYPE_SURFACE')
a = gii_attr(c, 'BrainStructure');
ig = find(strcmp(a, {'CIFTI_STRUCTURE_CORTEX_LEFT' 'CIFTI_STRUCTURE_CORTEX_RIGHT'}));
if isempty(ig), warning('Unknown BrainStructure: %s', a); continue; end
ind = gii_element(c, 'VertexIndices', 1) + 1;
if isempty(ind), ind = 1:gii_attr(c, 'IndexCount', 1); end
nii.cii{ig} = zeros(nVer, nVol, 'single');
nii.cii{ig}(ind,:) = imgG((1:numel(ind))+offset, :);
elseif strcmp(typ, 'CIFTI_MODEL_TYPE_VOXELS')
a = gii_element(c, 'VoxelIndicesIJK', 1) + 1;
a = sub2ind(dim, a(:,1), a(:,2), a(:,3));
nii.img(a, :) = imgG((1:numel(a))+offset, :);
end
end
for ig = 1:2 % map surface back to volume
v = gii.Vertices{ig}'; v(4,:) = 1;
v = round(mat \ v) + 1; % ijk 1-based
ind = sub2ind(dim, v(1,:), v(2,:), v(3,:));
nii.img(ind, :) = nii.cii{ig};
end
nii.img = reshape(nii.img, [dim nVol]);
nii = nii_tool('update', nii);
expr = '<Label\s+Key="(.*?)"\s+Red="(.*?)"\s+Green="(.*?)"\s+Blue="(.*?)".*?>(.*?)</Label>';
ind = regexp(xml, '<NamedMap'); ind(end+1) = numel(xml);
for k = 1:numel(ind)-1
nii.NamedMap{k}.MapName = gii_element(xml(ind(k):ind(k+1)), 'MapName');
tok = regexp(xml(ind(k):ind(k+1)), expr, 'tokens');
if numel(tok)<2, continue; end
tok = reshape([tok{:}], 5, [])'; % Key R G B nam
a = str2double(tok(:, 1:4));
nii.NamedMap{k}.map(a(:,1)+1, :) = a(:,2:4);
if a(1,1) == 0 % key="0"
nii.NamedMap{k}.labels(a(2:end, 1)) = tok(2:end, 5); % drop Key="0"
else
nii.NamedMap{k}.map = [0 0 0; nii.NamedMap{k}.map];
nii.NamedMap{k}.labels(a(:, 1)) = tok(:, 5);
end
end
%% Return gii for both hemesperes
function gii = get_surfaces(nVer, surfType)
persistent pth;
if nargin>1 && strcmpi(surfType, 'Anatomical') && nVer == 32492 % HCP 2mm surface
fname = fullfile(fileparts(mfilename('fullpath')), 'example_data.mat');
a = load(fname, 'gii'); gii = a.gii;
return;
end
if nargin>1, surfType = [surfType ' ']; else, surfType = ''; end
prompt = ['Select ' surfType 'GIfTI surface files for both hemispheres'];
if isempty(pth), pth = pwd; end
[nam, pth] = uigetfile([pth '/*.surf.gii'], prompt, 'MultiSelect', 'on');
if isnumeric(nam), gii = []; return; end
nam = cellstr(strcat([pth '/'], nam));
for i = 1:numel(nam)
a = read_gii(nam{i});
if ~isempty(surfType) && ~strcmpi(surfType, a.GeometryType)
error('Surface is not of required type: %s', surfType);
end
gii.DataSpace = a.DataSpace;
if all(a.Vertices(:,3)==0), a.Vertices = a.Vertices(:,[3 1 2]); end % flat
if strcmp(a.AnatomicalStructurePrimary, 'CortexLeft')
gii.Vertices{1} = a.Vertices; gii.Faces{1} = a.Faces;
elseif strcmp(a.AnatomicalStructurePrimary, 'CortexRight')
gii.Vertices{2} = a.Vertices; gii.Faces{2} = a.Faces;
end
end
%% Return gii struct with DataSpace, Vertices and Faces.
function gii = read_gii(fname)
xml = fileread(fname); % text file basically
for i = regexp(xml, '<DataArray[\s>]') % often 2 of them
c = regexp(xml(i:end), '.*?</DataArray>', 'match', 'once');
[Data, i0] = gii_element(c, 'Data'); % suppose '<Data' is last element
c = regexprep(c(1:i0-1), '<!\[CDATA\[(.*?)\]\]>', '$1'); % rm CDADA thing
a = gii_attr(c, 'DataType');
if strcmp(a, 'NIFTI_TYPE_FLOAT32'), dType = 'single';
elseif strcmp(a, 'NIFTI_TYPE_INT32'), dType = 'int32';
elseif strcmp(a, 'NIFTI_TYPE_UINT8'), dType = 'uint8';
else, error('Unknown GIfTI DataType: %s', a);
end
nDim = gii_attr(c, 'Dimensionality', 1);
dim = ones(1, nDim);
for j = 1:nDim, dim(j) = gii_attr(c, sprintf('Dim%g', j-1), 1); end
Endian = gii_attr(c, 'Endian'); % LittleEndian or BigEndian
Endian = lower(Endian(1));
Encoding = gii_attr(c, 'Encoding');
if any(strcmp(Encoding, {'Base64Binary' 'GZipBase64Binary'}))
% Data = matlab.net.base64decode(Data); % since 2016b
Data = javax.xml.bind.DatatypeConverter.parseBase64Binary(Data);
Data = typecast(Data, 'uint8');
if strcmp(Encoding, 'GZipBase64Binary') % HCP uses this
Data = nii_tool('LocalFunc', 'gunzip_mem', Data);
end
Data = typecast(Data, dType);
if Endian == 'b', Data = swapbytes(Data); end
elseif strcmp(Encoding, 'ASCII') % untested
Data = str2num(Data);
elseif strcmp(Encoding, 'ExternalFileBinary') % untested
nam = gii_attr(c, 'ExternalFileName');
if isempty(fileparts(nam)), nam = fullfile(fileparts(fname), nam); end
fid = fopen(nam, 'r', Endian);
if fid==-1, error('ExternalFileName %s not exists'); end
fseek(fid, gii_attr(c, 'ExternalFileOffset', 1), 'bof');
Data = fread(fid, prod(dim), ['*' dType]);
fclose(fid);
else, error('Unknown Encoding: %s', Encoding);
end
if nDim>1
if strcmp(gii_attr(c, 'ArrayIndexingOrder'), 'RowMajorOrder')
Data = reshape(Data, dim(nDim:-1:1));
Data = permute(Data, nDim:-1:1);
else
Data = reshape(Data, dim);
end
end
Intent = gii_attr(c, 'Intent');
if strcmp(Intent, 'NIFTI_INTENT_TRIANGLE')
gii.Faces = Data; % 0-based
continue;
elseif ~strcmp(Intent, 'NIFTI_INTENT_POINTSET') % store Data only for now
if ~isfield(gii, 'Data'), gii.Data = []; gii.Intent = []; end
gii.Intent{end+1} = Intent;
gii.Data{end+1} = Data;
continue;
end
% now only for NIFTI_INTENT_POINTSET
gii.AnatomicalStructurePrimary = gii_meta(c, 'AnatomicalStructurePrimary');
gii.AnatomicalStructureSecondary = gii_meta(c, 'AnatomicalStructureSecondary');
gii.GeometricType = gii_meta(c, 'GeometricType');
frms = {'NIFTI_XFORM_UNKNOWN' 'NIFTI_XFORM_SCANNER_ANAT' ...
'NIFTI_XFORM_ALIGNED_ANAT' 'NIFTI_XFORM_TALAIRACH' 'NIFTI_XFORM_MNI_152'};
gii.DataSpace = find(strcmp(gii_element(c, 'DataSpace'), frms)) - 1;
gii.TransformedSpace = find(strcmp(gii_element(c, 'TransformedSpace'), frms)) - 1;
gii.MatrixData = gii_element(c, 'MatrixData', 1);
gii.Vertices = Data;
end
%% Return cii/gii attribute
function val = gii_attr(ch, key, isnum)
val = regexp(ch, ['(?<=' key '=").*?(?=")'], 'match', 'once');
if nargin>2 && isnum, val = str2num(val); end %#ok<*ST2NM>
%% Return cii/gii element
function [val, i0] = gii_element(ch, key, isnum)
i0 = regexp(ch, ['<' key '[\s>]'], 'once');
val = regexp(ch(i0:end), ['(?<=<' key '.*?>).*?(?=</' key '>)'], 'match', 'once');
if nargin>2 && isnum, val = str2num(val); end
%% Return MetaData value for cii/gii 'Name'
function val = gii_meta(ch, key)
val = regexp(ch, ['(?<=>' key '<.*?<Value>).*?(?=</Value>)'], 'match', 'once');
%% Open surface view or add cii to it
function cii_view(hsN)
fh = hsN.fig.UserData;
if isempty(fh) || ~ishandle(fh) % create surface figure
fh = figure(hsN.fig.Number+100);
set(fh, 'NumberTitle', 'off', 'MenuBar', 'none', 'Renderer', 'opengl', ...
'Color', 'k', 'HandleVisibility', 'Callback', 'InvertHardcopy', 'off');
if isnumeric(fh), fh = handle(fh); end
cMenu = uicontextmenu('Parent', fh);
uimenu(cMenu, 'Label', 'Reset view', 'Callback', {@cii_view_cb 'reset'});
uimenu(cMenu, 'Label', 'Zoom in' , 'Callback', {@cii_view_cb 'zoomG'});
uimenu(cMenu, 'Label', 'Zoom out', 'Callback', {@cii_view_cb 'zoomG'});
uimenu(cMenu, 'Label', 'Change cortex color', ...
'Callback', {@cii_view_cb 'cortexColor'}, 'Separator', 'on');
uimenu(cMenu, 'Label', 'Change surface', 'Callback', {@cii_view_cb 'changeSurface'});
saveAs = findobj(hsN.fig, 'Type', 'uimenu', 'Label', 'Save figure as');
m = copyobj(saveAs, cMenu);
set(m, 'Separator', 'on');
m = get(m, 'Children'); delete(m(1:3)); m = m(4:end); % pdf/eps etc too slow
set(m, 'Callback', {@nii_viewer_cb 'save' hsN.fig});
if ispc || ismac
uimenu(cMenu, 'Label', 'Copy figure', 'Callback', {@nii_viewer_cb 'copy' hsN.fig});
end
set(fh, 'UIContextMenu', cMenu);
r = 0.96; % width of two columns, remaining for colorbar
pos = [0 1 r 1; 0 0 r 1; r 1 r 1; r 0 r 1] / 2;
gii = cii2nii(); % get buffered Anatomical gii
for ig = 1:2
v = gii.Vertices{ig};
lim = [min(v)' max(v)'];
im = ones(size(v,1), 3, 'single') * 0.667;
for i = ig*2+[-1 0]
hs.ax(i) = axes('Parent', fh, 'Position', pos(i,:), 'CameraViewAngle', 6.8);
axis vis3d; axis equal; axis off;
set(hs.ax(i), 'XLim', lim(1,:), 'YLim', lim(2,:), 'ZLim', lim(3,:));
hs.patch(i) = patch('Parent', hs.ax(i), 'EdgeColor', 'none', ...
'Faces', gii.Faces{ig}+1, 'Vertices', v, ...
'FaceVertexCData', im, 'FaceColor', 'interp', 'FaceLighting', 'gouraud');
hs.light(i) = camlight('infinite'); material dull;
end
end
set(hs.patch, 'ButtonDownFcn', {@cii_view_cb 'buttonDownPatch'}, 'UIContextMenu', cMenu);
hs.ax(5) = axes('Position', [r 0.1 1-r 0.8], 'Visible', 'off', 'Parent', fh);
try
hs.colorbar = colorbar(hs.ax(5), 'PickableParts', 'none');
catch % for early matlab
colorbar('peer', hs.ax(5), 'Units', 'Normalized', 'HitTest', 'off');
hs.colorbar = findobj(fh, 'Tag', 'Colorbar');
end
set(hs.colorbar, 'Location', 'East', 'Visible', get(hsN.colorbar, 'Visible'));
fh.Position(3:4) = [1/r diff(lim(3,:))/diff(lim(2,:))] * 600;
srn = get(0, 'MonitorPositions');
dz = srn(1,4)- 60 - sum(fh.Position([2 4]));
if dz<0, fh.Position(2) = fh.Position(2) + dz; end
fh.ResizeFcn = {@cii_view_cb 'resizeG'};
fh.WindowButtonUpFcn = {@cii_view_cb 'buttonUp'};
fh.WindowButtonDownFcn = {@cii_view_cb 'buttonDown'};
fh.WindowButtonMotionFcn={@cii_view_cb 'buttonMotion'};
fh.WindowKeyPressFcn = {@cii_view_cb 'keyFcn'};
fh.UserData = struct('xy', [], 'xyz', [], 'hemi', [], 'deg', [-90 0], ...
'color', [1 1 1]*0.667);
hsN.fig.UserData = fh;
hs.gii = gii.Vertices;
hs.fig = fh;
hs.hsN = hsN;
guidata(fh, hs);
set_cii_view(hs, [-90 0]);
try % drawnow then set manual, not exist for earlier Matlab
set(hs.patch, 'VertexNormalsMode', 'auto');
drawnow; set(hs.patch, 'VertexNormalsMode', 'manual'); % faster update
end
end
set_colorbar(hsN);
cii_view_cb(fh, [], 'volume');
cii_view_cb(fh, [], 'background');
%% cii_view callbacks
function cii_view_cb(h, ev, cmd)
if isempty(h) || ~ishandle(h), return; end
hs = guidata(h);
switch cmd
case 'buttonMotion' % Rotate gii and set light direction
if isempty(hs.fig.UserData.xy), return; end % button not down
d = get(hs.fig, 'CurrentPoint') - hs.fig.UserData.xy; % location change
d = hs.fig.UserData.deg - d; % new azimuth and elevation
set_cii_view(hs, d);
hs.fig.UserData.xyz = []; % so not set cursor in nii_viewer
case 'buttonDownPatch' % get button xyz
if ~strcmpi(hs.fig.SelectionType, 'normal') % button 1 only
hs.fig.UserData.xyz = []; return;
end
hs.fig.UserData.hemi = 1 + any(get(h, 'Parent') == hs.ax(3:4));
try, hs.fig.UserData.xyz = ev.IntersectionPoint;
catch, hs.fig.UserData.xyz = get(gca, 'CurrentPoint'); % old Matlab
end
case 'buttonDown' % figure button down: prepare for rotation
if ~strcmpi(hs.fig.SelectionType, 'normal'), return; end % not button 1
hs.fig.UserData.xy = get(hs.fig, 'CurrentPoint');
hs.fig.UserData.deg = get(hs.ax(1), 'View');
case 'buttonUp' % set cursor in nii_viewer
hs.fig.UserData.xy = []; % disable buttonMotion
xyz = hs.fig.UserData.xyz;
if isempty(xyz), return; end
ig = hs.fig.UserData.hemi;
v = get(hs.patch(ig*2), 'Vertices');
% xyz = get(gca, 'CurrentPoint'); % test
if size(xyz,1) > 1 % for Matlab without IntersectionPoint
ln = [linspace(xyz(1,1), xyz(2,1), 200);
linspace(xyz(1,2), xyz(2,2), 200);
linspace(xyz(1,3), xyz(2,3), 200)]; % line between box edges
ln = permute(ln, [3 1 2]);
d = sum(bsxfun(@minus, v, ln) .^ 2, 2); % distance squared
a = permute(min(d), [3 1 2]); % min along the line
a = sum([a a([2:end end]) a([1 1:end-1])], 2) / 3; % smooth
i = find((diff(a)>0) & (a(1:end-1)<8), 1); % find 1st valley
i = max(1, i-1);
d = d(:,:, i:i+3); % use a couple of samples along the line
[~, ind] = min(d(:));
[iv, ~, ~] = ind2sub(size(d), ind);
xyz = v(iv,:); % may find 2nd intersection for Anatomical surface
% disp(xyz-hs.fig.UserData.xyz);
if ~isequal(v, hs.gii{ig}), xyz = hs.gii{ig}(iv,:); end
elseif ~isequal(v, hs.gii{ig})
v = bsxfun(@minus, v, xyz);
[~, iv] = min(sum(v.^2, 2));
xyz = hs.gii{ig}(iv,:);
end
c = round(hs.hsN.bg.Ri * [xyz(:); 1]) + 1;
for i = 1:3, hs.hsN.ijk(i).setValue(c(i)); end
case 'reset'
set_cii_view(hs, [-90 0]);
case 'cortexColor'
c = uisetcolor(hs.fig.UserData.color, 'Set cortical surface color');
if numel(c) ~= 3, return; end
hs.fig.UserData.color = c;
set_cdata_cii(hs);
case 'changeSurface'
gii = get_surfaces(size(hs.gii{1}, 1));
if isempty(gii), return; end
if size(gii.Vertices{1},1) ~= size(hs.gii{1},1)
errordlg('GIfTI has different number of vertices from CIfTI');
return;
end
ind = [isequal(gii.Vertices{1}, get(hs.patch(1), 'Vertices')) ...
isequal(gii.Vertices{2}, get(hs.patch(3), 'Vertices'))];
if all(ind), return; end % no change
for i = find(~ind)
ip = i*2+(-1:0);
set(hs.patch(ip), 'Vertices', gii.Vertices{i}, 'Faces', gii.Faces{i}+1);
lim = [min(gii.Vertices{i})' max(gii.Vertices{i})'];
set(hs.ax(ip), 'ZLim', lim(3,:), 'YLim', lim(2,:));
try, set(hs.ax(ip), 'XLim', lim(1,:)); end % avoid error for flat
end
set_cdata_cii(hs);
try
set(hs.patch, 'VertexNormalsMode', 'auto');
drawnow; set(hs.patch, 'VertexNormalsMode', 'manual');
end
case 'resizeG'
sz = getpixelposition(h); % asked position
cb = hs.fig.ResizeFcn;
hs.fig.ResizeFcn = []; drawnow; % avoid weird effect
r = get(hs.ax(5), 'Position');
r = diff(get(hs.ax(1), 'ZLim')) / diff(get(hs.ax(1), 'YLim')) * r(1);
if sz(3)/sz(4) < r, sz = sz(3) * [1 r];
else, sz = sz(4) * [1/r 1];
end
hs.fig.Position(3:4) = sz;
hs.fig.ResizeFcn = cb;
case 'zoomG'
va = get(hs.ax(1), 'CameraViewAngle');
if strcmp(get(h, 'Label'), 'Zoom in'), va = va * 0.9;
else, va = va * 1.1;
end
set(hs.ax(1:4), 'CameraViewAngle', va);
case 'keyFcn'
if any(strcmp(ev.Key, ev.Modifier)), return; end % only modifier
figure(hs.fig); % avoid focus to Command Window
if ~isempty(intersect({'control' 'command'}, ev.Modifier))
if any(strcmp(ev.Key, {'add' 'equal'}))
h = findobj(hs.fig, 'Type', 'uimenu', 'Label', 'Zoom in');
cii_view_cb(h, [], 'zoomG');
elseif any(strcmp(ev.Key, {'subtract' 'hyphen'}))
h = findobj(hs.fig, 'Type', 'uimenu', 'Label', 'Zoom out');
cii_view_cb(h, [], 'zoomG');
elseif any(strcmp(ev.Key, {'a' 'r'}))
figure(hs.hsN.fig);
key = java.awt.event.KeyEvent.(['VK_' upper(ev.Key)]);
java.awt.Robot().keyPress(key);
java.awt.Robot().keyRelease(key);
end
elseif any(strcmp(ev.Key, {'space' 'comma' 'period'}))
KeyPressFcn(hs.hsN.fig, ev);
end
% Rest cases not called by surface callback, but from nii_viewer_cb
case {'lb' 'ub' 'lut' 'toggle' 'alpha' 'volume' 'stack' 'close' 'closeAll'}
set_cdata_cii(hs);
if strcmp(cmd, 'volume'), cii_view_cb(h, [], 'file'); end
case 'file' % update MapName if available
p = get_para(hs.hsN);
try, mName = p.nii.NamedMap{p.volume}.MapName; catch, mName = ''; end
frm = formcode2str(p.nii.hdr.sform_code);
hs.fig.Name = ['cii_view - ' mName ' (' frm ')'];
case 'background'
clr = hs.hsN.frame.BackgroundColor;
hs.fig.Color = clr;
set(hs.colorbar, 'EdgeColor', 1-clr);
case 'colorbar' % colorbar on/off
set(hs.colorbar, 'Visible', get(hs.hsN.colorbar, 'Visible'));
otherwise, return; % ignore other nii_viewer_cb cmd
end
%% set surface FaceVertexCData
function set_cdata_cii(hs)
imP{1} = ones(size(hs.gii{1},1), 1, 'single') * hs.fig.UserData.color;
imP{2} = ones(size(hs.gii{2},1), 1, 'single') * hs.fig.UserData.color;
for j = hs.hsN.files.getModel.size:-1:1
p = get_para(hs.hsN, j);
if ~p.show || ~isfield(p.nii, 'cii'), continue; end
for i = 1:2 % hemispheres
[im, alfa] = lut2img(p.nii.cii{i}(:, p.volume), p, hs.hsN.lutStr{p.lut});
alfa = p.alpha * single(alfa>0);
im = permute(im, [1 3 2]); % nVertices x 3
im = bsxfun(@times, im, alfa);
imP{i} = bsxfun(@times, imP{i}, 1-alfa) + im;
end
end
set(hs.patch(1:2), 'FaceVertexCData', imP{1});
set(hs.patch(3:4), 'FaceVertexCData', imP{2});
% tic; drawnow; toc
%% set surface view
function set_cii_view(hs, ae)
ae = [ae; ae(1)+180 -ae(2); -ae(1) ae(2); -ae(1)-180 -ae(2)];
for i = 1:4
set(hs.ax(i), 'View', ae(i,:));
camlight(hs.light(i), 'headlight');
end
%% this can be removed for matlab 2013b+
function y = flip(varargin)
if exist('flip', 'builtin')
y = builtin('flip', varargin{:});
else
if nargin<2, varargin{2} = find(size(varargin{1})>1, 1); end
y = flipdim(varargin{:}); %#ok
end
%% normalize columns
function v = normc(M)
v = bsxfun(@rdivide, M, sqrt(sum(M .* M)));
% v = M ./ sqrt(sum(M .* M)); % since 2016b
%% reorient nii to diagnal major
function [nii, perm, flp] = nii_reorient(nii, leftHand)
[R, frm] = nii_xform_mat(nii.hdr);
dim = nii.hdr.dim(2:4);
pixdim = nii.hdr.pixdim(2:4);
[R, perm, flp] = reorient(R, dim, leftHand);
if ~isequal(perm, 1:3)
nii.hdr.dim(2:4) = dim(perm);
nii.hdr.pixdim(2:4) = pixdim(perm);
fps = bitand(nii.hdr.dim_info, [3 12 48]) ./ [1 4 16];
nii.hdr.dim_info = [1 4 16] * fps(perm)' + bitand(nii.hdr.dim_info, 192);
nii.img = permute(nii.img, [perm 4:8]);
end
sc = nii.hdr.slice_code;
if sc>0 && perm(3)~=3 && flp(perm==3)
nii.hdr.slice_code = sc+mod(sc,2)*2-1; % 1<->2, 3<->4, 5<->6
end
if ~isequal(perm, 1:3) || any(flp)
if frm(1) == nii.hdr.sform_code % only update matching form
nii.hdr.srow_x = R(1,:);
nii.hdr.srow_y = R(2,:);
nii.hdr.srow_z = R(3,:);
end
if frm(1) == nii.hdr.qform_code
nii.hdr.qoffset_x = R(1,4);
nii.hdr.qoffset_y = R(2,4);
nii.hdr.qoffset_z = R(3,4);
R0 = normc(R(1:3, 1:3));
dcm2quat = dicm2nii('', 'dcm2quat', 'func_handle');
[q, nii.hdr.pixdim(1)] = dcm2quat(R0);
nii.hdr.quatern_b = q(2);
nii.hdr.quatern_c = q(3);
nii.hdr.quatern_d = q(4);
end
end
for i = 1:3, if flp(i), nii.img = flip(nii.img, i); end; end
%% flip slice dir for nii hdr
% function hdr = flip_slices(hdr)
% if hdr.sform_code<1 && hdr.sform_code<1, error('No valid form_code'); end
% R = nii_xform_mat(hdr);
% [~, iSL] = max(abs(R(1:3,1:3))); iSL = find(iSL==3);
% if hdr.sform_code
% hdr.srow_x(iSL) = -hdr.srow_x(iSL);
% hdr.srow_y(iSL) = -hdr.srow_y(iSL);
% hdr.srow_z(iSL) = -hdr.srow_z(iSL);
% end
% if hdr.qform_code<1, return; end
% R = quat2R(hdr);
% R(:, iSL) = -R(:,iSL);
% R = normc(R(1:3, 1:3));
% dcm2quat = dicm2nii('', 'dcm2quat', 'func_handle');
% [q, hdr.pixdim(1)] = dcm2quat(R);
% hdr.quatern_b = q(2);
% hdr.quatern_c = q(3);
% hdr.quatern_d = q(4);
%%
|
github
|
cocoanlab/humanfmri_preproc_bids-master
|
nii_moco.m
|
.m
|
humanfmri_preproc_bids-master/external/dicm2nii/nii_moco.m
| 10,422 |
utf_8
|
4b02f2199b90d3823468dba1a430723e
|
function varargout = nii_moco(nii, out, ref)
% Perform motion correction to the input NIfTI data.
%
% Syntax:
% p = NII_MOCO(filename_in); % return correction parameter only
% NII_MOCO(filename_in, filename_out); % save corrected image file
% [p, nii_out] = NII_MOCO(nii_in); % also return correct NIfTI without saving
% [p, nii_out] = NII_MOCO(nii_in, fileName_out);
% [...] = NII_MOCO(nii_in, fileName_out, ref);
%
% The mandatory first input is a NIfTI file name or a struct returned by
% nii_tool('load').
%
% If the second optional input, the result NIfTI file name, is provided, the
% corrected data will be saved into the file (overwrite if exists). A .mat file
% with the same name is also saved for the correction parameters (see first
% output argument below for meaning of the parameters). If no reference volume
% is provided (see 3rd input below), a NIfTI file, with name in format of
% fileName_out_ref.nii, will also be saved.
%
% The third optional input is the reference to align to. It can be:
% omitted or empty: NII_MOCO will choose a good reference volume in the data;
% a single number: volume index to align to;
% nii struct or file name: its first volume will be used as reference.
% This argument is useful if one likes to align multiple runs to the same
% referece img. For example align all 3 runs to run1:
% p = NII_MOCO('run1.nii', 'run1_moco.nii'); % return ref info for run1
% NII_MOCO('run2.nii', 'run2_moco.nii', p.ref); % align run2 to ref vol of run1
% NII_MOCO('run3.nii', 'run3_moco.nii', p.ref); % align run3
% Then run1_moco_ref.nii can be used to align to structural image.
%
% The first optional output, if requested, returns the parameters of motion. It
% is a struct with following fields:
% ref: reference NIfTI name, or struct if no corrected img is saved.
% R: rigid xform matrix to correct the motion to ref volume, 4 by 4 by nVol
% mss: sum of squared diff between vol and ref img
% trans: translation in mm, nVol by 3
% rot: rotation in radian, nVol by 3
% FD: frame-wise displacement in mm, nVol by 1
%
% The second optional output is nii struct after motion correction.
%
% See also NII_STC, NII_VIEWER, NII_TOOL
% Xiangrui Li ([email protected])
% 161127 Wrote it by peeking into spm_realign.m.
% 170120 Use later ref vol: p.ref=p.ref+1
toSave = nargin>1 && ~isempty(out);
if toSave && ~ischar(out)
error('Second input must be nii file name to save data.');
end
if ~toSave && nargout<1
[out, pth] = uiputfile('*.nii;*.nii.gz', 'Input file name to save result');
if ~ischar(out), varargout(1:nargout) = {}; return; end
out = fullfile(pth, out);
toSave = true;
end
if ischar(nii), nii = nii_tool('load', nii); end % file name
if ~isstruct(nii) || ~all(isfield(nii, {'hdr' 'img'}))
error('Input must be nii struct or nii file name.');
end
d = nii.hdr.dim(2:7); d(d<1 | d>32768 | mod(d,1)) = 1;
nVol = prod(d(4:end));
if nVol<2, error('Not multi-volume NIfTI: %s', nii.hdr.file_name); end
d = d(1:3);
Rm = nii_viewer('LocalFunc', 'nii_xform_mat', nii.hdr, 1); % moving img R
sz = nii.hdr.pixdim(2:4);
if all(abs(diff(sz)/sz(1)))<0.05 && sz(1)>2 && sz(1)<4 % 6~12mm
sz = 3; % iso-voxel, 2~4mm res, simple fast smooth
else
sz = 9 ./ sz; % 9 mm seems good
end
% Deal with ref vol options
if nargin<3 || isempty(ref) % pick a good vol as ref: similar to next vol
n = min(10, nVol);
mss = double(nii.img(:,:,:,1:n));
mss = diff(mss, 1, 4) .^ 2;
mss = reshape(mss, [], n-1);
mss = sum(mss);
[~, p.ref] = min(mss);
p.ref = p.ref + 1; % later one less affected by spin history?
refV.hdr = nii.hdr; refV.img = nii.img(:,:,:,p.ref);
elseif isnumeric(ref) && numel(ref)==1 % ref vol index in moving nii
refV.hdr = nii.hdr; refV.img = nii.img(:,:,:,ref);
p.ref = ref;
else % ref NIfTI file or struct
if isstruct(ref) && isfield(ref, 'ref'), ref = ref.ref; end % p input
if ischar(ref) && exist(ref, 'file') % NIfTI file as ref
refV = nii_tool('load', ref);
elseif isstruct(ref) && isfield(ref, 'img') && isfield(ref, 'hdr')
refV = ref;
else
error('Invalid reference input: %s', inputname(3));
end
p.ref = ref; % simply pass the ref input
end
R0 = nii_viewer('LocalFunc', 'nii_xform_mat', refV.hdr, 1);
% resample ref vol to isovoxel (often lower-res)
res = 4; % use 4 mm grid for alignment
d0 = size(refV.img); d0 = [d0 1]; d0 = d0(1:3); d0 = d0-1;
ind = find(d0<4, 1);
if ~isempty(ind), res = refV.hdr.pixdim(ind+1); end % untested
dd = res ./ refV.hdr.pixdim(2:4);
[i, j, k] = ndgrid(0:dd(1):d0(1)-0.5, 0:dd(2):d0(2)-0.5, 0:dd(3):d0(3)-0.5);
I = [i(:) j(:) k(:)]'; clear i j k;
a = rng('default'); I = I + rand(size(I))*0.5; rng(a); % used by spm
sz1 = sz .* nii.hdr.pixdim(2:4) ./ refV.hdr.pixdim(2:4);
V = smooth_mc(refV.img(:,:,:,1), sz1);
F = griddedInterpolant({0:d0(1), 0:d0(2), 0:d0(3)}, V, 'linear', 'none');
V0 = F(I(1,:), I(2,:), I(3,:)); % ref: 1 by nVox
I(4,:) = 1; % 0-based ijk: 4 by nVox
I = R0 * I; % xyz of ref voxels
% compute derivative to each motion parameter in ref vol
dG = zeros(6, numel(V0));
dd = 1e-6; % delta of motion parameter, value won't affect dG much
R0i = inv(R0); % speed up a little
for i = 1:6
p6 = zeros(6,1); p6(i) = dd; % change only 1 of 6
J = R0i * rigid_mat(p6) * I; %#ok<*MINV>
dG(i,:) = F(J(1,:), J(2,:), J(3,:)) - V0; % diff now
end
dG = dG / dd; % derivative
% choose voxels with larger derivative for alignment: much faster
a = sum(dG.^2); % 6 derivatives has similar range
ind = a > std(a(~isnan(a)))/10; % arbituray threshold. Also exclude NaN
dG = dG(:, ind);
V0 = V0(ind);
I = I(:, ind);
F.GridVectors = {0:d(1)-1, 0:d(2)-1, 0:d(3)-1};
p.R = repmat(inv(Rm), [1 1 nVol]); % inv(R_rst)
for i = 1:nVol
% R = p.R(:,:,i);
if i>1, R = p.R(:,:,i-1); else, R = p.R(:,:,i); end % start w/ previous vol
F.Values = smooth_mc(nii.img(:,:,:,i), sz);
mss0 = inf;
for iter = 1:64
J = R * I; % R_rst*J -> R0*ijk
V = F(J(1,:), J(2,:), J(3,:));
ind = ~isnan(V); % NaN means out of range
V = V(ind);
dV = V0(ind); % ref
dV = dV - V * (sum(dV)/sum(V)); % diff now, sign affects p6 sign
mss = dV*dV' / numel(dV); % mean(dV.^2)
% % watch mss change over iterations
% if iter==1
% figure(33); pause(1*(i>1));
% hPlot = plot(nan(1,64), 'o-', 'MarkerFaceColor', 'r');
% title(['Volume ' num2str(i)]); set(gca, 'xtick', 1:64);
% xlabel('Iterations'); ylabel('mss');
% end
% try hPlot.YData(iter) = mss; drawnow; end %#ok
if mss > mss0, break; end % give up and use previous R
p.R(:,:,i) = R; % accecpt only if improving
p.mss(i) = mss;
if 1-mss/mss0 < 1e-6, break; end % little effect, stop
a = dG(:, ind);
p6 = (a * a') \ (a * dV'); % dG(:,ind)'\dV' estimate p6 from current R
R = R * rigid_mat(p6); % inv(inv(rigid_mat(p6)) * inv(R_rst))
mss0 = mss;
end
if iter==64
warning('Max iterations reached: %s, vol %g', nii.hdr.file_name, i);
end
end
doXform = toSave || nargout>1;
if doXform
nii.img = single(nii.img); % single for result nii
nii.hdr.sform_code = 2; % Aligned Anat
nii.hdr.descrip = ['nii_moco.m: orig ' nii.hdr.file_name];
F.Method = 'spline'; % much slower than linear
F.ExtrapolationMethod = 'nearest';
I = ones([d 4], 'single');
[I(:,:,:,1), I(:,:,:,2), I(:,:,:,3)] = ndgrid(0:d(1)-1, 0:d(2)-1, 0:d(3)-1);
I = permute(I, [4 1 2 3]);
I = reshape(I, 4, []); % ijk in 4 by nVox for original dim
I = Rm * I; % xyz now
end
% Compute p.trans and p.rot, then p.FD, and xform nii if needed
p.trans = zeros(nVol,3); p.rot = zeros(nVol,3);
for i = 1:nVol
if doXform % create xfrom 'ed nii
J = p.R(:,:,i) * I; % R_rst \ (Rm * ijk)
F.Values = nii.img(:,:,:,i);
a = F(J(1,:), J(2,:), J(3,:));
nii.img(:,:,:,i) = reshape(a, d(1:3));
end
R = Rm * p.R(:,:,i); % inv(R_rst / Rref)
p.trans(i,:) = -R(1:3, 4);
R = bsxfun(@rdivide, R, sqrt(sum(R.^2))); % to be safe
p.rot(i,:) = -[atan2(R(2,3), R(3,3)) asin(R(1,3)) atan2(R(1,2), R(1,1))];
p.R(:,:,i) = inv(p.R(:,:,i));
end
p.FD = diff([p.trans p.rot*50]); % 50 mm is radius of head
p.FD = [0; sum(abs(p.FD), 2)]; % Power et al method
% Update p.ref in case it is needed for other runs
if isnumeric(p.ref) % need to store p.ref
refV.hdr.descrip = sprintf('Ref: vol %g of %s', p.ref, nii.hdr.file_name);
if toSave
[pth, nam, ext] = fileparts(out);
if strcmpi(ext, '.gz'), [~, nam, e0] = fileparts(nam); ext = [e0 ext]; end
p.ref = fullfile(pth, [nam '_ref' ext]);
nii_tool('save', refV, p.ref);
else % store nii struct as ref in p: result large p
refV.hdr.file_name = ''; % just avoid overwrite accident
p.ref = nii_tool('update', refV); % override iRef for single vol nii
end
end
if ischar(p.ref) % file name, make it full name in case of relative path
[~, a] = fileattrib(p.ref);
p.ref = a.Name;
end
if toSave % save corrected nii and p
nii_tool('save', nii, out);
[pth, nam, ext] = fileparts(out);
if strcmpi(ext, '.gz'), [~, nam] = fileparts(nam); end
nam = fullfile(pth, [nam '.mat']);
save(nam, 'p'); % save a mat file with the same name as NIfTI
end
if nargout>0, varargout{1} = p; end
if nargout>1, varargout{2} = nii_tool('update', nii); end
%% Translation (mm) and rotation (deg) to 4x4 R. Order: ZYXT
function R = rigid_mat(p6)
ca = cosd(p6(4:6)); sa = sind(p6(4:6));
rx = [1 0 0; 0 ca(1) -sa(1); 0 sa(1) ca(1)]; % 3D rotation
ry = [ca(2) 0 sa(2); 0 1 0; -sa(2) 0 ca(2)];
rz = [ca(3) -sa(3) 0; sa(3) ca(3) 0; 0 0 1];
R = rx * ry * rz;
R = [R p6(1:3); 0 0 0 1];
%% Simple gaussian smooth for motion correction, sz in unit of voxels
function out = smooth_mc(in, sz)
out = double(in);
if all(abs(diff(sz)/sz(1))<0.05) && abs(sz(1)-round(sz(1)))<0.05 ...
&& mod(round(sz(1)),2)==1
out = smooth3(out, 'gaussian', round(sz)); % sz odd integer
return; % save time for special case
end
d = size(in);
I = {1:d(1) 1:d(2) 1:d(3)};
n = sz/3;
if numel(n)==1, n = n*[1 1 1]; end
J = {1:n(1):d(1) 1:n(2):d(2) 1:n(3):d(3)};
intp = 'linear';
F = griddedInterpolant(I, out, intp);
out = smooth3(F(J), 'gaussian'); % sz=3
F = griddedInterpolant(J, out, intp);
out = F(I);
|
github
|
cocoanlab/humanfmri_preproc_bids-master
|
java_dnd.m
|
.m
|
humanfmri_preproc_bids-master/external/dicm2nii/java_dnd.m
| 2,820 |
utf_8
|
b72dadc83df5d9f523b72cf084b3e056
|
function java_dnd(jObj, dropFcn)
% Set Matlab dropFcn for java object, like JavaFrame or JTextField.
% 170421 Xiangrui Li adapted from dndcontrol class by Maarten van der Seijs:
% https://www.mathworks.com/matlabcentral/fileexchange/53511
% Required: MLDropTarget.class under the same folder
if ~exist('MLDropTarget', 'class')
pth = fileparts(mfilename('fullpath'));
javaaddpath(pth); % dynamic for this session
fid = fopen(fullfile(prefdir, 'javaclasspath.txt'), 'a+');
if fid>0 % static path for later sessions: work for 2013+?
cln = onCleanup(@() fclose(fid));
fseek(fid, 0, 'bof');
classpth = fread(fid, inf, '*char')';
if isempty(strfind(classpth, pth)) %#ok<*STREMP> % avoid multiple write
fseek(fid, 0, 'bof');
fprintf(fid, '%s\n', pth);
end
end
end
dropTarget = handle(javaObjectEDT('MLDropTarget'), 'CallbackProperties');
set(dropTarget, 'DragEnterCallback', @DragEnterCallback, ...
'DragExitCallback', @DragExitCallback, ...
'DropCallback', {@DropCallback, dropFcn});
jObj.setDropTarget(dropTarget);
%%
function DropCallback(jSource, jEvent, dropFcn)
setComplete = onCleanup(@()jEvent.dropComplete(true));
% Following DropAction is for ~jEvent.isLocalTransfer, such as dropping file.
% For LocalTransfer, Linux seems consistent with other OS.
% DropAction: Neither ctrl nor shift Dn, PC/MAC 2, Linux 1
% All OS: ctrlDn 1, shiftDn 2, both Dn 1073741824 (2^30)
if ispc || ismac
evt.ControlDown = jEvent.getDropAction() ~= 2;
else % fails to report CtrlDn if user releases shift between DragEnter and Drop
evt.ControlDown = bitget(jEvent.getDropAction,31)>0; % ACTION_LINK 1<<30
java.awt.Robot().keyRelease(16); % shift up
end
% evt.Location = [jEvent.getLocation.x jEvent.getLocation.y]; % top-left [0 0]
if jSource.getDropType() == 1 % String dropped
evt.DropType = 'string';
evt.Data = char(jSource.getTransferData());
if strncmp(evt.Data, 'file://', 7) % files identified as string
evt.DropType = 'file';
evt.Data = regexp(evt.Data, '(?<=file://).*?(?=\r?\n)', 'match')';
end
elseif jSource.getDropType() == 2 % file(s) dropped
evt.DropType = 'file';
evt.Data = cell(jSource.getTransferData());
else, return; % No success
end
if iscell(dropFcn), feval(dropFcn{1}, jSource, evt, dropFcn{2:end});
else, feval(dropFcn, jSource, evt);
end
%%
function DragEnterCallback(~, jEvent)
try jEvent.acceptDrag(1); catch, return; end % ACTION_COPY
if ~ispc && ~ismac, java.awt.Robot().keyPress(16); end % shift down
%%
function DragExitCallback(~, jEvent)
if ~ispc && ~ismac, java.awt.Robot().keyRelease(16); end % shift up
try jEvent.rejectDrag(1); catch, end % ACTION_COPY
%%
|
github
|
cocoanlab/humanfmri_preproc_bids-master
|
nii_xform.m
|
.m
|
humanfmri_preproc_bids-master/external/dicm2nii/nii_xform.m
| 9,448 |
utf_8
|
f1220c195ff9723fdad045a1477dbf77
|
function varargout = nii_xform(src, target, rst, intrp, missVal)
% Transform a NIfTI into different resolution, or into a template space.
%
% NII_XFORM('source.nii', 'template.nii', 'result.nii')
% NII_XFORM(nii, 'template.nii', 'result.nii')
% NII_XFORM('source.nii', [1 1 1], 'result.nii')
% nii = NII_XFORM('source.nii', 'template.nii');
% NII_XFORM('source.nii', {'template.nii' 'source2template.mat'}, 'result.nii')
% NII_XFORM('source.nii', {'template.nii' 'source2template_warp.nii.gz'}, 'result.nii')
% NII_XFORM('source.nii', 'template.nii', 'result.nii', 'nearest', 0)
%
% NII_XFORM transforms the source NIfTI, so it has the requested resolution or
% has the same dimension and resolution as the template NIfTI.
%
% Input (first two mandatory):
% 1. source file (nii, hdr/img or gz versions) or nii struct to be transformed.
% 2. The second input determines how to transform the source file:
% (1) If it is numeric and length is 1 or 3, [2 2 2] for example, it will be
% treated as requested resolution in millimeter. The result will be in
% the same coordinate system as the source file.
% (2) If it is a nii file name, a nii struct, or nii hdr struct, it will be
% used as the template. The result will have the same dimension and
% resolution as the template. The source file and the template must have
% at least one common coordinate system, otherwise the transformation
% doesn't make sense, and it will err out. With different coordinate
% systems, a transformation to align the two dataset is needed, which is
% the next case.
% (3) If the input is a cell containing two file names, it will be
% interpreted as a template nii file and a transformation. The
% transformation can be a FSL-style .mat file with 4x4 transformation
% matrix which aligns the source data to the template, in format of:
% 0.9983 -0.0432 -0.0385 -17.75
% 0.0476 0.9914 0.1216 -14.84
% 0.0329 -0.1232 0.9918 111.12
% 0 0 0 1
% The transformation can also be a FSL-style warp nii file incorporating
% both linear and no-linear transformation from the source to template.
% 3. result file name. If not provided or empty, nii struct will be returned.
% This allows to use the returned nii in script without saving to a file.
% 4. interpolation method, default 'linear'. It can also be one of 'nearest',
% 'cubic' and 'spline'.
% 5. value for missing data, default NaN. This is the value assigned to the
% location in template where no data is available in the source file.
%
% Output (optional): nii struct.
% NII_XFORM will return the struct if the output is requested or result file
% name is not provided.
%
% Please note that, once the transformation is applied to functional data, it is
% normally invalid to perform slice timing correction. Also the data type is
% changed to single unless the interpolation is 'nearest'.
%
% See also NII_VIEWER, NII_TOOL, DICM2NII
% By Xiangrui Li ([email protected])
% History(yymmdd):
% 151024 Write it.
% 160531 Remove narginchk so work for early matlab.
% 160907 allow src to be nii struct.
% 160923 allow target to be nii struct or hdr; Take care of logical src img.
% 161002 target can also be {tempFile warpFile}.
% 170119 resolution can be singular.
% 180219 treat formcode 3 and 4 the same.
if nargin<2 || nargin>5, help('nii_xform'); error('Wrong number of input.'); end
if nargin<3, rst = []; end
if nargin<4 || isempty(intrp), intrp = 'linear'; end
if nargin<5 || isempty(missVal), missVal = nan; else, missVal = missVal(1); end
intrp = lower(intrp);
quat2R = nii_viewer('func_handle', 'quat2R');
if isstruct(src), nii = src;
else, nii = nii_tool('load', src);
end
if isstruct(target) || ischar(target) || (iscell(target) && numel(target)==1)
hdr = get_hdr(target);
elseif iscell(target)
hdr = get_hdr(target{1});
if hdr.sform_code>0, R0 = [hdr.srow_x; hdr.srow_y; hdr.srow_z; 0 0 0 1];
elseif hdr.qform_code>0, R0 = quat2R(hdr);
end
[~, ~, ext] = fileparts(target{2});
if strcmpi(ext, '.mat') % template and xform file names
R = load(target{2}, '-ascii');
if ~isequal(size(R), [4 4]), error('Invalid transformation file.'); end
else % template and warp file names
warp_img_fsl = nii_tool('img', target{2});
if ~isequal(size(warp_img_fsl), [hdr.dim(2:4) 3])
error('warp file and template file img size don''t match.');
end
R = eye(4);
end
if nii.hdr.sform_code>0
R1 = [nii.hdr.srow_x; nii.hdr.srow_y; nii.hdr.srow_z; 0 0 0 1];
elseif nii.hdr.qform_code>0
R1 = quat2R(nii.hdr);
end
% I thought it is something like R = R0 \ R * R1; but it is way off. It
% seems the transform info in src nii is irrevelant, but direction must be
% used: Left/right-handed storage of both src and target img won't affect
% FSL alignment R. Alignment R may not be diag-major, and can be negative
% for major axes (e.g. cor/sag slices).
% Following works for tested FSL .mat and warp.nii files: Any better way?
% R0: target; R1: source; R: xform; result is also R
R = R0 / diag([hdr.pixdim(2:4) 1]) * R * diag([nii.hdr.pixdim(2:4) 1]);
[~, i1] = max(abs(R1(1:3,1:3)));
[~, i0] = max(abs(R(1:3,1:3)));
flp = sign(R(i0+[0 4 8])) ~= sign(R1(i1+[0 4 8]));
if any(flp)
rotM = diag([1-flp*2 1]);
rotM(1:3,4) = (nii.hdr.dim(2:4)-1) .* flp;
R = R / rotM;
end
elseif isnumeric(target) && any(numel(target)==[1 3]) % new resolution in mm
if numel(target)==1, target = target * [1 1 1]; end
hdr = nii.hdr;
ratio = target(:)' ./ hdr.pixdim(2:4);
hdr.pixdim(2:4) = target;
hdr.dim(2:4) = round(hdr.dim(2:4) ./ ratio);
if hdr.sform_code>0
hdr.srow_x(1:3) = hdr.srow_x(1:3) .* ratio;
hdr.srow_y(1:3) = hdr.srow_y(1:3) .* ratio;
hdr.srow_z(1:3) = hdr.srow_z(1:3) .* ratio;
end
else
error('Invalid template or resolution input.');
end
if ~iscell(target)
s = hdr.sform_code;
q = hdr.sform_code;
sq = [nii.hdr.sform_code nii.hdr.qform_code];
if s>0 && (any(s == sq) || (s>2 && (any(sq==3) || any(sq==4))))
R0 = [hdr.srow_x; hdr.srow_y; hdr.srow_z; 0 0 0 1];
frm = s;
elseif any(q == sq) || (q>2 && (any(sq==3) || any(sq==4)))
R0 = quat2R(hdr);
frm = q;
else
error('No matching transformation between source and template.');
end
if sq(1) == frm || (sq(1)>2 && frm>2) || sq(2)<1
R = [nii.hdr.srow_x; nii.hdr.srow_y; nii.hdr.srow_z; 0 0 0 1];
else
R = quat2R(nii.hdr);
end
end
d = single(hdr.dim(2:4));
I = ones([d 4], 'single');
[I(:,:,:,1), I(:,:,:,2), I(:,:,:,3)] = ndgrid(0:d(1)-1, 0:d(2)-1, 0:d(3)-1);
I = permute(I, [4 1 2 3]);
I = reshape(I, [4 prod(d)]); % template ijk
if exist('warp_img_fsl', 'var')
warp_img_fsl = reshape(warp_img_fsl, [prod(d) 3])';
if det(R0(1:3,1:3))<0, warp_img_fsl(1,:) = -warp_img_fsl(1,:); end % correct?
warp_img_fsl(4,:) = 0;
I = R \ (R0 * I + warp_img_fsl) + 1; % ijk+1 (fraction) in source
else
I = R \ (R0 * I) + 1; % ijk+1 (fraction) in source
end
I = reshape(I(1:3,:)', [d 3]);
V = nii.img; isbin = islogical(V);
if any(size(V)<2) && ~strcmpi(intrp, 'nearest')
intrp = 'nearest';
warning('nii_xform:NotEnoughPoints', 'Not enough data. Switch to "nearest".');
end
d48 = size(V); % in case of RGB
d48(numel(d48)+1:4) = 1; d48(1:3) = [];
if isbin
intrp = 'nearest'; missVal = false;
nii.img = zeros([d d48], 'uint8');
elseif isinteger(V)
nii.img = zeros([d d48], 'single');
else
nii.img = zeros([d d48], class(V));
end
if ~isfloat(V), V = single(V); end
if strcmpi(intrp, 'nearest'), I = round(I); end % needed for edge voxels
if size(V,1)<2, V(2,:,:) = missVal; end
if size(V,2)<2, V(:,2,:) = missVal; end
if size(V,3)<2, V(:,:,2) = missVal; end
try
F = griddedInterpolant(V(:,:,:,1), intrp, 'none'); % since 2014?
for i = 1:prod(d48)
F.Values = V(:,:,:,i);
nii.img(:,:,:,i) = F(I(:,:,:,1), I(:,:,:,2), I(:,:,:,3));
end
if ~isnan(missVal), nii.img(isnan(nii.img)) = missVal; end
catch
for i = 1:prod(d48)
nii.img(:,:,:,i) = interp3(V(:,:,:,i), I(:,:,:,2), I(:,:,:,1), I(:,:,:,3), intrp, missVal);
end
end
if isbin, nii.img = logical(nii.img); end
% copy xform info from template to rst nii
nii.hdr.pixdim(1:4) = hdr.pixdim(1:4);
flds = {'qform_code' 'sform_code' 'srow_x' 'srow_y' 'srow_z' ...
'quatern_b' 'quatern_c' 'quatern_d' 'qoffset_x' 'qoffset_y' 'qoffset_z'};
for i = 1:numel(flds), nii.hdr.(flds{i}) = hdr.(flds{i}); end
if ~isempty(rst), nii_tool('save', nii, rst); end
if nargout || isempty(rst), varargout{1} = nii_tool('update', nii); end
%%
function hdr = get_hdr(in)
if iscell(in), in = in{1}; end
if isstruct(in)
if isfield(in, 'hdr') % nii input
hdr = in.hdr;
elseif isfield(in, 'sform_code') % hdr input
hdr = in;
else
error('Invalid input: %s', inputname(1));
end
else % template file name
hdr = nii_tool('hdr', in);
end
|
github
|
TREE-Ind/speaker-rec-skill-test-master
|
estimate_x_and_u.m
|
.m
|
speaker-rec-skill-test-master/jfa/estimate_x_and_u.m
| 5,477 |
utf_8
|
1f30c33b7f0eecda4b7fa1266a4b23ba
|
function [x u]=estimate_x_and_u(F, N, S, m, E, d, v, u, z, y, x, spk_ids)
% ESTIMATE_X_AND_U estimates channel factors and eigenchannels for
% joint factor analysis model
%
%
% [x u]=estimate_x_and_u(F, N, S, m, E, d, v, u, z, y, x, spk_ids)
%
% provides new estimates of channel factors, x, and 'eigenchannels', u,
% given zeroth and first order sufficient statistics (N. F), current
% hyper-parameters of joint factor analysis model (m, E, d, u, v) and
% current estimates of speaker and channel factors (x, y, z)
%
% F - matrix of first order statistics (not centered). The rows correspond
% to training segments. Number of columns is given by the supervector
% dimensionality. The first n collums correspond to the n dimensions
% of the first Gaussian component, the second n collums to second
% component, and so on.
% N - matrix of zero order statistics (occupation counts of Gaussian
% components). The rows correspond to training segments. The collums
% correspond to Gaussian components.
% S - NOT USED by this function; reserved for second order statistics
% m - speaker and channel independent mean supervector (e.g. concatenated
% UBM mean vectors)
% E - speaker and channel independent variance supervector (e.g. concatenated
% UBM variance vectors)
% d - Row vector that is the diagonal from the diagonal matrix describing the
% remaining speaker variability (not described by eigenvoices). Number of
% columns is given by the supervector dimensionality.
% v - The rows of matrix v are 'eigenvoices'. (The number of rows must be the
% same as the number of columns of matrix y). Number of columns is given
% by the supervector dimensionality.
% u - The rows of matrix u are 'eigenchannels'. (The number of rows must be
% the same as the number of columns of matrix x) Number of columns is
% given by the supervector dimensionality.
% y - matrix of speaker factors corresponding to eigenvoices. The rows
% correspond to speakers (values in vector spk_ids are the indices of the
% rows, therfore the number of the rows must be (at least) the highest
% value in spk_ids). The columns correspond to eigenvoices (The number
% of columns must the same as the number of rows of matrix v).
% z - matrix of speaker factors corresponding to matrix d. The rows
% correspond to speakers (values in vector spk_ids are the indices of the
% rows, therfore the number of the rows must be (at least) the highest
% value in spk_ids). Number of columns is given by the supervector
% dimensionality.
% x - NOT USED by this function; used by other JFA function as
% matrix of channel factors. The rows correspond to training
% segments. The columns correspond to eigenchannels (The number of columns
% must be the same as the number of rows of matrix u)
% spk_ids - column vector with rows corresponding to training segments and
% integer values identifying a speaker. Rows having same values identifies
% segments spoken by same speakers. The values are indices of rows in
% y and z matrices containing corresponding speaker factors.
%
%
% x=estimate_x_and_u(F, N, S, m, E, d, v, u, z, y, x, spk_ids)
%
% only the channels factors are estimated
%
%
% [x A C]=estimate_x_and_u(F, N, S, m, E, d, v, u, z, y, x, spk_ids)
%
% estimates channels factors and acumulators A and C. A is cell array of MxM
% matrices, where M is number of eigenchannels. Number of elements in the
% cell array is given by number of Gaussian components. C is of the same size
% at the matrix u.
%
%
% u=estimate_x_and_u(A, C)
%
% updates eigenchannels from accumulators A and C. Using F and N statistics
% corresponding to subsets of training segments, multiple sets of accumulators
% can be collected (possibly in parallel) and summed before the update. Note
% that segments of one speaker must not be split into different subsets.
if nargin == 2 && nargout == 1
% update u from acumulators A and C
x=update_u(F, N);
return
end
% this will just create a index map, so that we can copy the counts n-times (n=dimensionality)
dim = size(F,2)/size(N,2);
index_map = reshape(repmat(1:size(N,2), dim,1),size(F,2),1);
x = zeros(size(spk_ids,1), size(u,1));
if nargout > 1
for c=1:size(N,2)
A{c} = zeros(size(u,1));
end
C = zeros(size(u,1), size(F,2));
end
for c=1:size(N,2)
c_elements = ((c-1)*dim+1):(c*dim);
uEuT{c} = u(:,c_elements) .* repmat(1./E(c_elements), size(u,1), 1) * u(:,c_elements)';
end
for ii = unique(spk_ids)'
speakers_sessions = find(spk_ids == ii);
spk_shift = m + y(ii,:) * v + z(ii,:) .* d;
for jj = speakers_sessions'
Nh = N(jj, index_map);
Fh = F(jj,:) - Nh .* spk_shift;
% L = eye(size(u,1)) + u * diag(Nh./E) * u';
L = eye(size(u,1));
for c=1:size(N,2)
L = L + uEuT{c} * N(jj,c);
end
invL = inv(L);
x(jj,:) = ((Fh./E) * u') * invL;
if nargout > 1
invL = invL + x(jj,:)' * x(jj,:);
for c=1:size(N,2)
A{c} = A{c} + invL * N(jj,c);
end
C = C + x(jj,:)' * Fh;
end
end
end
if nargout == 3
% output new estimates of x and accumulators A and C
u = A;
elseif nargout == 2
% output new estimates of x and u
u=update_u(A, C);
end
%-------------------------------------------------
function u=update_u(A, C)
u = zeros(size(C));
dim = size(C,2)/length(A);
for c=1:length(A)
c_elements = ((c-1)*dim+1):(c*dim);
u(:,c_elements) = inv(A{c}) * C(:,c_elements);
end
|
github
|
TREE-Ind/speaker-rec-skill-test-master
|
estimate_y_and_v.m
|
.m
|
speaker-rec-skill-test-master/jfa/estimate_y_and_v.m
| 5,502 |
utf_8
|
1e4d706f8060302120ad648461d7a943
|
function [y v C]=estimate_y_and_v(F, N, S, m, E, d, v, u, z, y, x, spk_ids)
% ESTIMATE_Y_AND_V estimates speaker factors and eigenvoices for
% joint factor analysis model
%
%
% [y v]=estimate_y_and_v(F, N, S, m, E, d, v, u, z, y, x, spk_ids)
%
% provides new estimates of channel factors, x, and 'eigenchannels', u,
% given zeroth and first order sufficient statistics (N. F), current
% hyper-parameters of joint factor analysis model (m, E, d, u, v) and
% current estimates of speaker and channel factors (x, y, z)
%
% F - matrix of first order statistics (not centered). The rows correspond
% to training segments. Number of columns is given by the supervector
% dimensionality. The first n collums correspond to the n dimensions
% of the first Gaussian component, the second n collums to second
% component, and so on.
% N - matrix of zero order statistics (occupation counts of Gaussian
% components). The rows correspond to training segments. The collums
% correspond to Gaussian components.
% S - NOT USED by this function; reserved for second order statistics
% m - speaker and channel independent mean supervector (e.g. concatenated
% UBM mean vectors)
% E - speaker and channel independent variance supervector (e.g. concatenated
% UBM variance vectors)
% d - Row vector that is the diagonal from the diagonal matrix describing the
% remaining speaker variability (not described by eigenvoices). Number of
% columns is given by the supervector dimensionality.
% v - The rows of matrix v are 'eigenvoices'. (The number of rows must be the
% same as the number of columns of matrix y). Number of columns is given
% by the supervector dimensionality.
% u - The rows of matrix u are 'eigenchannels'. (The number of rows must be
% the same as the number of columns of matrix x) Number of columns is
% given by the supervector dimensionality.
% y - NOT USED by this function; used by other JFA function as
% matrix of speaker factors corresponding to eigenvoices. The rows
% correspond to speakers (values in vector spk_ids are the indices of the
% rows, therfore the number of the rows must be (at least) the highest
% value in spk_ids). The columns correspond to eigenvoices (The number
% of columns must the same as the number of rows of matrix v).
% z - matrix of speaker factors corresponding to matrix d. The rows
% correspond to speakers (values in vector spk_ids are the indices of the
% rows, therfore the number of the rows must be (at least) the highest
% value in spk_ids). Number of columns is given by the supervector
% dimensionality.
% x - matrix of channel factors. The rows correspond to training
% segments. The columns correspond to eigenchannels (The number of columns
% must be the same as the number of rows of matrix u)
% spk_ids - column vector with rows corresponding to training segments and
% integer values identifying a speaker. Rows having same values identifies
% segments spoken by same speakers. The values are indices of rows in
% y and z matrices containing corresponding speaker factors.
%
%
% y=estimate_y_and_v(F, N, S, m, E, d, v, u, z, y, x, spk_ids)
%
% only the speaker factors are estimated
%
%
% [y A C]=estimate_y_and_v(F, N, S, m, E, d, v, u, z, y, x, spk_ids)
%
% estimates speaker factors and acumulators A and C. A is cell array of MxM
% matrices, where M is number of eigenvoices. Number of elements in the
% cell array is given by number of Gaussian components. C is of the same size
% at the matrix v.
%
%
% v=estimate_y_and_v(A, C)
%
% updates eigenvoices from accumulators A and C. Using F and N statistics
% corresponding to subsets of training segments, multiple sets of accumulators
% can be collected (possibly in parallel) and summed before the update. Note
% that segments of one speaker must not be split into different subsets.
if nargin == 2 && nargout == 1
% update v from acumulators A and C
y=update_v(F, N);
return
end
% this will just create a index map, so that we can copy the counts n-times (n=dimensionality)
dim = size(F,2)/size(N,2);
index_map = reshape(repmat(1:size(N,2), dim,1),size(F,2),1);
y = zeros(max(spk_ids), size(v,1));
if nargout > 1
for c=1:size(N,2)
A{c} = zeros(size(v,1));
end
C = zeros(size(v,1), size(F,2));
end
for c=1:size(N,2)
c_elements = ((c-1)*dim+1):(c*dim);
vEvT{c} = v(:,c_elements) .* repmat(1./E(c_elements), size(v, 1), 1) * v(:,c_elements)';
end
for ii = unique(spk_ids)'
speakers_sessions = find(spk_ids == ii);
Fs = sum(F(speakers_sessions,:), 1);
Nss = sum(N(speakers_sessions,:), 1);
Ns = Nss(1,index_map);
Fs = Fs - (m + z(ii,:) .* d) .* Ns;
for jj = speakers_sessions'
Fs = Fs - (x(jj,:) * u) .* N(jj, index_map);
end
% L = eye(size(v,1)) + v * diag(Ns./E) * v';
L = eye(size(v,1));
for c=1:size(N,2)
L = L + vEvT{c} * Nss(c);
end
invL = inv(L);
y(ii,:) = ((Fs ./ E) * v') * invL;
if nargout > 1
invL = invL + y(ii,:)' * y(ii,:);
for c=1:size(N,2)
A{c} = A{c} + invL * Nss(c);
end
C = C + y(ii,:)' * Fs;
end
end
if nargout == 3
% output new estimates of y and accumulators A and C
v = A;
elseif nargout == 2
% output new estimates of y and v
v=update_v(A, C);
end
%-------------------------------------------------
function C=update_v(A, C)
dim = size(C,2)/length(A);
for c=1:length(A)
c_elements = ((c-1)*dim+1):(c*dim);
C(:,c_elements) = inv(A{c}) * C(:,c_elements);
end
|
github
|
nathanie/DataHack-2017-master
|
csv2kml.m
|
.m
|
DataHack-2017-master/visualiztion/csv2kml.m
| 3,175 |
utf_8
|
9c842c1e4597dfe89d1b5b200d7443bf
|
function csv2kml(mainDir,data2WorkOn,class2show,lines2show,nedOrigin,openFileWhenDone)
%%%%
% mainDir - Dir where train/test data is
% data2WorkOn - Name of the data CSV file
% class2show - Which class in CSV file to draw, or (-1) if using test set or lines2show parameter
% lines2show - Which lines in CSV file to draw
% nedOrigin - Geo coordinates where XYZ = 0
% openFileWhenDone - Open KML after it is ready (KML files have to be associated with Google Earth)
%%%%
if nargin == 0
mainDir = 'D:\DataHack2017\';
%data2WorkOn = 'test';
data2WorkOn = 'train';
class2show = -1; %for 'train' only
lines2show = 1:300; %for 'test' (or 'train if class2show == -1)
nedOrigin = [31.784491,35.214245,0];
openFileWhenDone = 1;
end
name = 'Rocket_Data_Science';
if class2show > 0
name = [name '_' num2str(class2show)];
end
kmlStrHeader = ['<kml xmlns:gx="http://www.google.com/kml/ext/2.2" xmlns:atom="http://www.w3.org/2005/Atom" xmlns="http://www.opengis.net/kml/2.2"> \n' ...
' <Document> \n' ...
' <name>' name '</name> \n'];
kmlStrFooter = ' </Document></kml>';
strUP = '';
strDN = '';
disp('Loading...');
csvSetTable = readtable([mainDir data2WorkOn '.csv']);
csvSet = table2array(csvSetTable(:,1:211));
disp('Working...');
if strfind(data2WorkOn,'train') && class2show > 0
lines2show = find(csvSet(:,end) == class2show);
end
for lll = lines2show(:)'
lla_str = ned2geodetic2String(csvSet,lll,nedOrigin);
velVal = round((norm( csvSet(lll,6:8) )/1500) * 255 );
velColor = dec2hex(velVal,2);
if csvSet(lll,8) > 0
clr_str = ['FF' velColor '0000'];
strUP = addPlacemark(strUP,['line_' num2str(lll-1)],lla_str,clr_str);
else
clr_str = ['FF0000' velColor];
strDN = addPlacemark(strDN,['line_' num2str(lll-1)],lla_str,clr_str);
end
end
finalStr = [kmlStrHeader '<Folder>\n <name>UP</name> \n' strUP ...
'</Folder><Folder>\n <name>DOWN</name> \n' strDN '</Folder>' kmlStrFooter];
disp('Saving...');
fid = fopen([mainDir name '_MATLAB.kml'],'w');
fprintf(fid,finalStr);
fclose(fid);
disp('Done!');
if openFileWhenDone
winopen( [mainDir name '_MATLAB.kml']);
end
end
function str = addPlacemark(str,name,lla_str,clr_str)
strTMP = [ ...
' <Placemark> \n' ...
' <name>' name '</name> \n' ...
' <Style> \n' ...
' <LineStyle> \n' ...
' <color>' clr_str '</color> \n' ...
' <width>4</width> \n' ...
' </LineStyle> \n' ...
' </Style> \n' ...
' <LineString> \n' ...
' <altitudeMode>absolute</altitudeMode> \n' ...
' <coordinates>' lla_str '</coordinates> \n' ...
' </LineString> \n' ...
' </Placemark> \n' ...
];
str = [str strTMP];
end
function lla_str = ned2geodetic2String(csvSet,line,nedOrigin)
lla_str = '';
for iii = 1:15
northCoor = csvSet(line,3+7*(iii-1));
eastCoor = csvSet(line,4+7*(iii-1));
downCoor = -csvSet(line,5+7*(iii-1));
if isnan(northCoor)
continue
end
[lat,lon,h] = ned2geodetic(northCoor,eastCoor,downCoor,nedOrigin(1),nedOrigin(2),nedOrigin(3),referenceEllipsoid('GRS 80'));
lla_str = [lla_str num2str([lon lat h],'%.10f,%.10f,%.10f') ' '];
end
end
|
github
|
risetarnished/VehicleDetection-master
|
getBWratio.m
|
.m
|
VehicleDetection-master/Meng/getBWratio.m
| 1,609 |
utf_8
|
91fdec4a7183e0a15d6dc1b484eb2cc2
|
function features1 = getBWratio(img)
% foregroundDetector = vision.ForegroundDetector('NumGaussians', 3, ...
% 'NumTrainingFrames', 50);
%foreground = step(foregroundDetector, img);
foreground = rgb2gray(img);
image=imresize(foreground, [256 256]);
imwrite(image, 'temp.jpg');
blockCount = 1;
xpixel = 1;
ypixel = 1;
blocksize = 16;
yblockCount = 1;
xblockCount = 1;
features1 = zeros(1,256);
while (blockCount <= blocksize*blocksize)
whitepixel = 0;
blackpixel = 0;
originalypixel = ypixel;
originalxpixel = xpixel;
for i = ypixel:(blocksize*yblockCount)
for j = xpixel:(blocksize*xblockCount)
if( image(i,j) <= 128)
blackpixel = blackpixel + 1;
else
whitepixel = whitepixel + 1;
end
end
end
if blackpixel == 0
blackpixel = 1;
end
if whitepixel == 0
whitepixel = 1;
end
features1(blockCount) = whitepixel / blackpixel;
if xblockCount == blocksize
xpixel = 1;
ypixel = blocksize*yblockCount;
xblockCount = 1;
yblockCount = yblockCount + 1;
elseif xblockCount < blocksize
ypixel = originalypixel;
xpixel = blocksize*xblockCount;
xblockCount = xblockCount + 1;
end
blockCount = blockCount + 1;
end
%hist(features);
end
|
github
|
rajaeipour/spatial-carrier-master
|
FTP10.m
|
.m
|
spatial-carrier-master/FTP10.m
| 47,519 |
utf_8
|
88ee2a3d9801c3ebcdbab29b2792bc10
|
function varargout = FTP10(varargin)
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @FTP10_OpeningFcn, ...
'gui_OutputFcn', @FTP10_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before FTP10 is made visible.
function FTP10_OpeningFcn(hObject, eventdata, handles, varargin)
% IMTEK Logo read
logo_im = imread('imtek-logo.png','BackgroundColor',[0.93 0.93 0.93]);
axes(handles.axes5);
imshow(logo_im, []);
% Define Zernike table size
% set(handles.ZernFitTable,'Data',cell(10,1));
% Camera input setting
handles.DepthVid = videoinput('linuxvideo', 1, 'RGB24_1920x1200');% 'YUY2_1920x1200'); % make object for depth camera
set(handles.DepthVid,'FramesPerTrigger',1); % capture 1 frame every time DepthVid is trigered
set(handles.DepthVid,'TriggerRepeat',Inf); % infinite amount of triggers
%set(handles.DepthVid, 'ReturnedColorspace', 'RGB');
triggerconfig(handles.DepthVid, 'Manual');% trigger Depthvid manually within program
% handles.DepthVid.LoggingMode = 'disk';
% diskLogger = VideoWriter('/home/pouya/Desktop/1.avi', 'Uncompressed AVI');
% handles.DepthVid.DiskLogger = diskLogger;
% diskLogger.FrameRate = 1;
% Define frame aquisition frequency
handles.FrameAquiFreq = 1;
writefreqtoedit = handles.FrameAquiFreq;
set(handles.FrameFreq, 'String', num2str(writefreqtoedit));
% Define algorithm timers
handles.t1 = timer('TimerFcn',{@FTP_MainFunc, gcf}, 'BusyMode', 'drop',...
'Period',1/handles.FrameAquiFreq,'executionMode','fixedRate');
handles.t2 = timer('TimerFcn',{@FTP_PlotFunc, gcf}, 'BusyMode', 'drop',...
'Period',1/handles.FrameAquiFreq,'executionMode','fixedRate');
% Define primary frequency filter diameter
set(handles.FilterDiam,'Value',0.12);
% Make axes1 units normalized
set(handles.axes1,'Units','normalized');
% Set sliders step values
set(handles.FilterDiam,'SliderStep',[0.001, 0.01]);
set(handles.FilterX,'SliderStep',[0.0005, 0.01]);
set(handles.FilterY,'SliderStep',[0.0005, 0.01]);
% Set realtime sign off
set(handles.realtime,'foregroundcolor',[1 1 1]);
% set (handles.ZernFitTable,'ColumnWidth', {100,52})
% Choose default command line output for FTP10
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes FTP10 wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = FTP10_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
handles.DepthVid.FramesAvailable
function LightWaveLength_Callback(hObject, eventdata, handles)
% hObject handle to LightWaveLength (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of LightWaveLength as text
% str2double(get(hObject,'String')) returns contents of LightWaveLength as a double
% --- Executes during object creation, after setting all properties.
function LightWaveLength_CreateFcn(hObject, eventdata, handles)
% hObject handle to LightWaveLength (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in SystemMode.
function SystemMode_Callback(hObject, eventdata, handles)
% hObject handle to SystemMode (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = cellstr(get(hObject,'String')) returns SystemMode contents as cell array
% contents{get(hObject,'Value')} returns selected item from SystemMode
% --- Executes during object creation, after setting all properties.
function SystemMode_CreateFcn(hObject, eventdata, handles)
% hObject handle to SystemMode (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: popupmenu controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on slider movement.
function FilterDiam_Callback(hObject, eventdata, handles)
% hObject handle to FilterDiam (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
% --- Executes during object creation, after setting all properties.
function FilterDiam_CreateFcn(hObject, eventdata, handles)
% hObject handle to FilterDiam (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor',[.9 .9 .9]);
end
% --- Executes on slider movement.
function FilterX_Callback(hObject, eventdata, handles)
% hObject handle to FilterX (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
% --- Executes during object creation, after setting all properties.
function FilterX_CreateFcn(hObject, eventdata, handles)
% hObject handle to FilterX (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor',[.9 .9 .9]);
end
% --- Executes on slider movement.
function FilterY_Callback(hObject, eventdata, handles)
% hObject handle to FilterY (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
% --- Executes during object creation, after setting all properties.
function FilterY_CreateFcn(hObject, eventdata, handles)
% hObject handle to FilterY (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor',[.9 .9 .9]);
end
function Crop4_Callback(hObject, eventdata, handles)
% hObject handle to Crop4 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of Crop4 as text
% str2double(get(hObject,'String')) returns contents of Crop4 as a double
% --- Executes during object creation, after setting all properties.
function Crop4_CreateFcn(hObject, eventdata, handles)
% hObject handle to Crop4 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function Crop3_Callback(hObject, eventdata, handles)
% hObject handle to Crop3 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of Crop3 as text
% str2double(get(hObject,'String')) returns contents of Crop3 as a double
% --- Executes during object creation, after setting all properties.
function Crop3_CreateFcn(hObject, eventdata, handles)
% hObject handle to Crop3 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function Crop1_Callback(hObject, eventdata, handles)
% hObject handle to Crop1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of Crop1 as text
% str2double(get(hObject,'String')) returns contents of Crop1 as a double
% --- Executes during object creation, after setting all properties.
function Crop1_CreateFcn(hObject, eventdata, handles)
% hObject handle to Crop1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function Crop2_Callback(hObject, eventdata, handles)
% hObject handle to Crop2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of Crop2 as text
% str2double(get(hObject,'String')) returns contents of Crop2 as a double
% --- Executes during object creation, after setting all properties.
function Crop2_CreateFcn(hObject, eventdata, handles)
% hObject handle to Crop2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function Crop7_Callback(hObject, eventdata, handles)
% hObject handle to Crop7 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of Crop7 as text
% str2double(get(hObject,'String')) returns contents of Crop7 as a double
% --- Executes during object creation, after setting all properties.
function Crop7_CreateFcn(hObject, eventdata, handles)
% hObject handle to Crop7 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function Crop5_Callback(hObject, eventdata, handles)
% hObject handle to Crop5 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of Crop5 as text
% str2double(get(hObject,'String')) returns contents of Crop5 as a double
% --- Executes during object creation, after setting all properties.
function Crop5_CreateFcn(hObject, eventdata, handles)
% hObject handle to Crop5 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function Crop6_Callback(hObject, eventdata, handles)
% hObject handle to Crop6 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of Crop6 as text
% str2double(get(hObject,'String')) returns contents of Crop6 as a double
% --- Executes during object creation, after setting all properties.
function Crop6_CreateFcn(hObject, eventdata, handles)
% hObject handle to Crop6 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in CropDone.
function CropDone_Callback(hObject, eventdata, handles)
% hObject handle to CropDone (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of CropDone
function Crop8_Callback(hObject, eventdata, handles)
% hObject handle to Crop8 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of Crop8 as text
% str2double(get(hObject,'String')) returns contents of Crop8 as a double
% --- Executes during object creation, after setting all properties.
function Crop8_CreateFcn(hObject, eventdata, handles)
% hObject handle to Crop8 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in Reset.
function Reset_Callback(hObject, eventdata, handles)
set(handles.Crop5,'String',num2str(0));
set(handles.Crop6,'String',num2str(0));
set(handles.Crop7,'String',num2str(1920));
set(handles.Crop8,'String',num2str(1200));
set(handles.CropDone,'Value',0);
set(handles.CropDone,'backgroundcolor',[0.93 0.93 0.93]);
set(handles.LoopTime,'String','');
set(handles.peak_valley,'String','');
set(handles.RMS,'String','');
% set(handles.ZernFitTable, 'Data', cell(size(get(handles.ZernFitTable,'Data'))));
set(handles.uibuttongroup2,'selectedobject',handles.AutoFilter)
set(handles.FourierPlot,'Value',0);
set(handles.FilterPlot,'Value',0);
set(handles.ReferencePlot,'Value',0);
% set(handles.WUTPlot,'Value',0);
set(handles.WrappedPlot,'Value',0);
set(handles.D2Plot,'Value',0);
set(handles.D3Plot,'Value',0);
set(handles.ZernikeTable,'Value',0);
cla(handles.axes2,'reset');
cla(handles.axes3,'reset');
cla(handles.axes4,'reset');
% --- Executes on button press in Apply.
function Apply_Callback(hObject, eventdata, handles)
stoppreview(handles.DepthVid)
crop_x = str2double(get(handles.Crop5,'String'));
crop_y = str2double(get(handles.Crop6,'String'));
crop_width = str2double(get(handles.Crop7,'String'));
crop_height = str2double(get(handles.Crop8,'String'));
set(handles.DepthVid,'ROIPosition',[crop_x crop_y crop_width crop_height]);
axes(handles.axes1)
videoRes = get(handles.DepthVid, 'VideoResolution');
numberOfBands = get(handles.DepthVid, 'NumberOfBands');
handleToImageInAxes = image( zeros([videoRes(2), videoRes(1), numberOfBands], 'uint8') );
preview(handles.DepthVid,handleToImageInAxes)
set(handles.axes1title,'String','Live View');
axis equal
% --- Executes on button press in FourierPlot.
function FourierPlot_Callback(hObject, eventdata, handles)
% hObject handle to FourierPlot (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of FourierPlot
% --- Executes on button press in WrappedPlot.
function WrappedPlot_Callback(hObject, eventdata, handles)
% hObject handle to WrappedPlot (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of WrappedPlot
% --- Executes on button press in D2Plot.
function D2Plot_Callback(hObject, eventdata, handles)
% hObject handle to D2Plot (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of D2Plot
% --- Executes on button press in D3Plot.
function D3Plot_Callback(hObject, eventdata, handles)
% hObject handle to D3Plot (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of D3Plot
% --- Executes on button press in ZernikeTable.
function ZernikeTable_Callback(hObject, eventdata, handles)
% hObject handle to ZernikeTable (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of ZernikeTable
% % --- Executes on button press in WUTPlot.
% function WUTPlot_Callback(hObject, eventdata, handles)
% % hObject handle to WUTPlot (see GCBO)
% % eventdata reserved - to be defined in a future version of MATLAB
% % handles structure with handles and user data (see GUIDATA)
%
% % Hint: get(hObject,'Value') returns toggle state of WUTPlot
% --- Executes on button press in FilterPlot.
function FilterPlot_Callback(hObject, eventdata, handles)
% hObject handle to FilterPlot (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of FilterPlot
% --- Executes on button press in ReferencePlot.
function ReferencePlot_Callback(hObject, eventdata, handles)
% hObject handle to ReferencePlot (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of ReferencePlot
% --- Executes on button press in LiveView.
function LiveView_Callback(hObject, eventdata, handles)
crop_x = str2double(get(handles.Crop5,'String'));
crop_y = str2double(get(handles.Crop6,'String'));
crop_width = str2double(get(handles.Crop7,'String'));
crop_height = str2double(get(handles.Crop8,'String'));
set(handles.DepthVid,'ROIPosition',[crop_x crop_y crop_width crop_height]);
axes(handles.axes1)
videoRes = get(handles.DepthVid, 'VideoResolution');
numberOfBands = get(handles.DepthVid, 'NumberOfBands');
handleToImageInAxes = image( zeros([videoRes(2), videoRes(1), numberOfBands], 'uint8') );
preview(handles.DepthVid,handleToImageInAxes)
set(handles.axes1title,'String','Live View');
axis equal
% --- Executes on button press in Crop.
function Crop_Callback(hObject, eventdata, handles)
window1 = figure;
window1.Units = 'pixels';
im_crop = getsnapshot(handles.DepthVid);
figure(window1)
imshow(im_crop)
set(gca,'units','normalized','position',[0,0,1,1],'xtick',[],'ytick',[]);
ROI_rect = imrect;
ROI_crop = wait(ROI_rect);
close(window1)
ROI_crop = round(ROI_crop);
ROI_crop_length = min([ROI_crop(3) ROI_crop(4)]);
handles.ReferenceFringe_axes4 = imcrop(im_crop,[ROI_crop(1) ROI_crop(2) ROI_crop_length ROI_crop_length]);
set(handles.Crop1, 'String', num2str(ROI_crop(1)));
set(handles.Crop2, 'String', num2str(ROI_crop(2)));
set(handles.Crop3, 'String', num2str(ROI_crop(3)));
set(handles.Crop4, 'String', num2str(ROI_crop(4)));
set(handles.Crop5, 'String', num2str(ROI_crop(1)));
set(handles.Crop6, 'String', num2str(ROI_crop(2)));
set(handles.Crop7, 'String', num2str(ROI_crop_length));
set(handles.Crop8, 'String', num2str(ROI_crop_length));
handles.reference_im = im_crop;
handles.output = hObject;
guidata(hObject, handles);
% --- Executes on button press in Measure.
function Measure_Callback(hObject, eventdata, handles)
set(handles.DepthVid,'ROIPosition',[0 0 1920 1200]) %%%% Bring ROI to default for capturing
start(handles.DepthVid); % Start Video
start(handles.t1) % Start measurement function
function realtime_Callback(hObject, eventdata, handles)
% hObject handle to realtime (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of realtime as text
% str2double(get(hObject,'String')) returns contents of realtime as a double
% --- Executes during object creation, after setting all properties.
function realtime_CreateFcn(hObject, eventdata, handles)
% hObject handle to realtime (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in Capture.
function Capture_Callback(hObject, eventdata, handles)
% handles = guidata(fignum);
check_timer1 = isvalid(handles.t1);
if check_timer1 == 1
stop(handles.DepthVid);
stop(handles.t1);
set(handles.realtime,'foregroundcolor',[0.9 0.9 0.9],'backgroundcolor',[0.9 0.9 0.9]);
end
check_timer2 = isvalid(handles.t2);
if check_timer2 == 1
stop(handles.t2);
end
% FTP_PlotFunc(hObject,eventdata,fignum) % Calling plot function
axes(handles.axes4)
colorbar
colormap jet
shading interp
h=rotate3d;
set(h,'Enable','on');
% assignin('base', 'Reference_fringe', handles.ReferenceFringe_axes4)
assignin('base', 'Captured_frame', handles.im_axes1)
% assignin('base', 'Fourier_Domain', handles.G_abs_axes2)
assignin('base', 'Frequency_Filter', handles.lobe1_axes3)
assignin('base', 'Wrapped_Phase', handles.Wrapped_axes3)
assignin('base', 'Deformation', handles.Deformation2D_axes3)
% --- Executes on button press in PLOT.
function PLOT_Callback(hObject, eventdata, handles)
start(handles.t2)
% --- Executes on button press in STOP.
function STOP_Callback(hObject, eventdata, handles)
check_timer1 = isvalid(handles.t1);
check_timer2 = isvalid(handles.t2);
if check_timer2 == 1
stop(handles.t2)
end
if check_timer1 == 1
stop(handles.DepthVid);
stop(handles.t1);
set(handles.realtime,'foregroundcolor',[0.9 0.9 0.9],'backgroundcolor',[0.9 0.9 0.9]);
set(handles.LoopTime, 'String', ' ');
stoppreview(handles.DepthVid)
else
stoppreview(handles.DepthVid)
end
function LoopTime_Callback(hObject, eventdata, handles)
% hObject handle to LoopTime (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of LoopTime as text
% str2double(get(hObject,'String')) returns contents of LoopTime as a double
% --- Executes during object creation, after setting all properties.
function LoopTime_CreateFcn(hObject, eventdata, handles)
% hObject handle to LoopTime (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function FrameFreq_Callback(hObject, eventdata, handles)
% hObject handle to FrameFreq (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of FrameFreq as text
% str2double(get(hObject,'String')) returns contents of FrameFreq as a double
% --- Executes during object creation, after setting all properties.
function FrameFreq_CreateFcn(hObject, eventdata, handles)
% hObject handle to FrameFreq (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function FTP_MainFunc(hObject, evendata, fignum)
tic;
handles = guidata(fignum);
set(handles.realtime,'foregroundcolor',[0 0 0],'backgroundcolor',[0 1 0]);
trigger(handles.DepthVid)%trigger DepthVid to capture image
im=getdata(handles.DepthVid,1);%
crop_x = str2double(get(handles.Crop5,'String'));
crop_y = str2double(get(handles.Crop6,'String'));
crop_width = str2double(get(handles.Crop7,'String'));
handles.ROI_P = [crop_x crop_y crop_width crop_width];
im = imcrop(im,[crop_x crop_y crop_width crop_width]);
handles.im_axes1 = im;
im = im(:,:,1); % reading only "red" values of the captured frame
check_crop_done = get(handles.CropDone, 'Value');
if check_crop_done == 1
set(handles.CropDone,'backgroundcolor',[0.93 0.93 0.93]);
K0 = get(handles.FilterDiam,'value'); % Radius of the filter as a fraction of pi
wave_length = str2double(get(handles.LightWaveLength,'String'))*10^(-9); % Wavelength of the light used for illumination
mode = get(handles.SystemMode,'Value'); % If the membrane is reflective: 'reflection' , if the membrane is transimissive: 'transmission'
img1=im2double(im);
[N,M]=size(img1); %[height, width]
% Preparing for applying hamming window
h_win=hamming(N);
hamm = zeros(N,N);
% Initialize windows along column direction
for n=1:N
hamm(:,n)=h_win;
end
% Apply windows along rows
hamm=hamm.*hamm';
% Apply hamming window to the image
img1=img1.*hamm;
% Compute fft2 of the windowed image
G=fft2(img1);
G=fftshift(G);
G_abs=abs(G);
handles.G_abs_axes2 = G_abs; % making a copy of fourier transform for plotting
% check for mode of finding the frequency filter position
Filter_Position_Auto = get(handles.AutoFilter,'value');
K0 = K0*pi;
dx = 1;
dy = 1;
if Filter_Position_Auto == 1
No_X_pixel = round(N/2);
No_Y_pixel = round(M/2);
G_abs_left = zeros(N,No_Y_pixel);
G_abs_left(1:N,35:No_Y_pixel-5) = G_abs(1:N,35:No_Y_pixel-5);
maxValue=max(G_abs_left(:));
[rowOfMax, colOfMax] = find(G_abs_left == maxValue);
X_index = colOfMax;
Y_index = rowOfMax;
shift_x = -(1-X_index / No_X_pixel)*pi; % Shift of the origin of the filter in spatial domain as a fraction of pi (Should be equal to carrier frequency)
shift_x_slider = shift_x/pi;
set(handles.FilterX,'Value',shift_x_slider);
shift_y = -(1-Y_index / No_Y_pixel)*pi;
shift_y_slider = shift_y/pi;
set(handles.FilterY,'Value',-shift_y_slider);
else
shift_x = get(handles.FilterX,'value');
shift_x = shift_x * pi;
shift_y = get(handles.FilterY,'value');
shift_y = -shift_y * pi;
end
handles.Filter_X = shift_x/pi;
handles.Filter_Y = shift_y/pi;
handles.Filter_D = K0/pi;
KX0 = (mod((1/2 + (0:(N-1))/N), 1) - 1/2);
KX1 = KX0 * (2*pi/dx);
KY0 = (mod((1/2 + (0:(M-1))/M), 1) - 1/2);
KY1 = KY0 * (2*pi/dy);
[KX,KY] = meshgrid(KX1,KY1);
%Filter formulation
lpf = ((KX-shift_x).^2 + (KY-shift_y).^2 < K0^2);
lpf = fftshift(lpf);
% Convoluting the filter with image
G=lpf.*G;
% Isolating the desired lobe
% Finding horizontal and vertical elements by scaning in 4 directions
help1=0;
scan1=zeros(N,1);
for kk=1:M
if help1==0
scan1=G(:,kk);
if mean(scan1) ~= 0
hor1=kk;
help1=1;
end
end
end
help1=0;
scan1=zeros(N,1);
for kk=1:M
if help1==0
scan1=G(:,M-kk);
if mean(scan1) ~= 0
hor2=M-kk;
help1=1;
end
end
end
help1=0;
scan2=zeros(1,hor2-hor1);
for kk=1:N
if help1 == 0
scan2=G(kk,:);
if mean(scan2) ~= 0
ver1=kk;
help1=1;
end
end
end
help1=0;
scan2=zeros(1,hor2-hor1);
for kk=1:N
if help1 == 0
scan2=G(N-kk,:);
if mean(scan2) ~= 0
ver2=N-kk;
help1=1;
end
end
end
lobe1_help=G(ver1:ver2,hor1:hor2);
[xxx,yyy]=size(lobe1_help);
zzz = min(xxx,yyy);
lobe1=zeros(zzz,zzz);
for ii=1:zzz
for jj=1:zzz
lobe1(ii,jj)=lobe1_help(ii,jj);
end
end
handles.lobe1_axes3 = abs(lobe1);
% Taking the inverse fourier transform of the lobe ifft2
lobe1 = fftshift(lobe1);
ifft_lobe=ifft2(lobe1);
% Extracting the imaginary part
imag_ifft_lobe=imag(ifft_lobe);
abs_lobe = abs(imag_ifft_lobe); % Wavefront under test
handles.WUT_axes1 = abs_lobe; % Making a copy of the wavefront under test
% Taking arc tan of the inverse Fourier transform of the 1st lobe
% phase_lobe=2.*atan(real(ifft_lobe)./imag(ifft_lobe));
phase_lobe = angle(ifft_lobe);
phase_lobe = mod(phase_lobe+pi,2*pi)-pi;
handles.Wrapped_axes3 = phase_lobe; % Making a copy of the wrapped phase
% Unwrapping
[unwrapped] = cunwrap_nodisp(phase_lobe);
switch mode
case 2
unwrapped_phase = unwrapped / 2; % Compensating for reflection path difference
case 1
unwrapped_phase = unwrapped;
end
Deformation = unwrapped_phase * (wave_length/(2*pi)) * 10^6; % Converting phase difference to deformations
handles.Deformation2D_axes3 = Deformation;
else % if crop is not done
set(handles.CropDone,'backgroundcolor',[1 0 0]);
end
set(handles.realtime,'foregroundcolor',[0.9 0.9 0.9],'backgroundcolor',[0.9 0.9 0.9]);
handles.TimeSpent = toc;
guidata(fignum, handles);
function FTP_PlotFunc(hObject,eventdata,fignum)
handles = guidata(fignum);
set(handles.LoopTime, 'String', num2str(handles.TimeSpent));
% Plotting the captured frame
imshow(handles.im_axes1,'Parent',handles.axes1)
set(handles.axes1title,'String','Captured Frame');
% Checking the output selection checkboxes
Fourier_Plot = get(handles.FourierPlot, 'Value');
Filter_Plot = get(handles.FilterPlot, 'Value');
Reference_Plot = get(handles.ReferencePlot, 'Value');
% Wavefront_Plot = get(handles.WUTPlot, 'Value');
Fit_Plot = get(handles.Deformation_fit, 'Value');
Wrapped_Plot = get(handles.WrappedPlot, 'Value');
Deform2D_Plot = get(handles.D2Plot, 'Value');
Deform3D_Plot = get(handles.D3Plot, 'Value');
Zernike_Table = get(handles.ZernikeTable, 'Value');
% low =0;
% high =50;
% max_handles_G_abs_axes2=handles.G_abs_axes2/(max(max(handles.G_abs_axes2)));
% max_handles_G_abs_axes2=max_handles_G_abs_axes2*255;
if Fourier_Plot == 1
GG = mat2gray(log(handles.G_abs_axes2+1));
imshow(GG,'Parent',handles.axes2,'colormap',jet)
set(handles.axes2title,'String','Fourier Transform');
end
if Filter_Plot == 1
GG_lobe = mat2gray(log(handles.lobe1_axes3+1));
% max_handles_lobe1=handles.lobe1_axes3/(max(max(handles.G_abs_axes2)));
% max_handles_lobe1=max_handles_lobe1*255;
imshow(GG_lobe,'Parent',handles.axes3,'colormap',jet)
set(handles.axes3title,'String','Frequency Filtered Area');
end
if Reference_Plot == 1
imshow(handles.ReferenceFringe_axes4,'Parent',handles.axes4)
set(handles.axes1title,'String','Reference Fringe');
end
% if Wavefront_Plot == 1
% set(handles.FourierPlot,'Value',0);
% set(handles.WrappedPlot,'Value',0);
% min_wavefront=min(min(handles.WUT_axes1));
% wavefront_plot=handles.Wrapped_axes3+abs(min_wavefront);
% wavefront_plot=wavefront_plot/max(max(wavefront_plot));
% imshow(wavefront_plot,'Parent',handles.axes2)%,'colormap',jet)
% set(handles.axes2title,'String','Wavefront under test');
% end
if Wrapped_Plot == 1
set(handles.FourierPlot,'Value',0);
min_wrapped=min(min(handles.Wrapped_axes3));
wrapped_plot=handles.Wrapped_axes3+abs(min_wrapped);
wrapped_plot=wrapped_plot/max(max(wrapped_plot));
imshow(wrapped_plot,'Parent',handles.axes2,'colormap',jet)
set(handles.axes2title,'String','Wrapped Phase');
end
if Deform2D_Plot == 1
set(handles.FilterPlot,'Value',0);
min_deform2d = min(min(handles.Deformation2D_axes3));
deform2d_plot = handles.Deformation2D_axes3 + abs(min_deform2d);
deform2d_plot = deform2d_plot/max(max(deform2d_plot));
imshow(deform2d_plot,'Parent',handles.axes3,'colormap',jet)
% colorbar(handles.axes4)
set(handles.axes3title,'String','Membrane Deformation 2D');
end
if Deform3D_Plot == 1
set(handles.ReferencePlot,'Value',0);
Deformation = handles.Deformation2D_axes3;
[nnn,mmm] = size(Deformation);
K0_unwrap_mask = pi/1.07; % Radius of circular area inside the square cropped frame
KX0 = (mod((1/2 + (0:(nnn-1))/nnn), 1) - 1/2);
KX1 = KX0 * (2*pi);
KY0 = (mod(1/2 + (0:(mmm-1))/mmm, 1) - 1/2);
KY1 = KY0 * (2*pi);
[KX,KY] = meshgrid(KX1,KY1);
% Unwrap mask formulation
unwrap_mask = ((KX).^2 + (KY).^2 < K0_unwrap_mask^2);
unwrap_mask = fftshift(unwrap_mask);
Deformation_mask = unwrap_mask .* Deformation;
X_UW = 1:nnn;
Y_UW = 1:mmm;
[AA,BB]=meshgrid(X_UW,Y_UW);
% Applying the mask to X & Y coordinates
AA = unwrap_mask .* AA;
BB = unwrap_mask .* BB;
length_x=nnn*mmm;
length_y=nnn*mmm;
length_z=nnn*mmm;
X=zeros(1,length_x);
Y=zeros(1,length_y);
Z=zeros(1,length_z);
PP=1;
for ii=1:nnn
X(1,PP:PP+mmm-1)=AA(ii,:);
PP=PP+mmm;
end
PP=1;
for ii=1:nnn
Y(1,PP:PP+mmm-1)=BB(ii,:);
PP=PP+mmm;
end
PP=1;
for ii=1:nnn
Z(1,PP:PP+mmm-1)=Deformation_mask(ii,:);
PP=PP+mmm;
end
% Extracting X & Y & Z coordinates of only the membrane
PP=1;
for ii=1:length_x
if X(ii) ~= 0
X_circ(PP) = X(ii);
PP = PP + 1;
end
end
PP=1;
for ii=1:length_y
if Y(ii) ~= 0
Y_circ(PP) = Y(ii);
PP = PP + 1;
end
end
PP=1;
for ii=1:length_z
if Z(ii) ~= 0
Z_circ(PP) = Z(ii);
PP = PP + 1;
end
end
mean_Z = mean(mean(Z_circ));
ZZ_circ = Z_circ-mean_Z;
tri = delaunay(X_circ,Y_circ);
plot(X_circ,Y_circ,'.', 'Parent',handles.axes4)
% Plot it with TRISURF
h = trisurf(tri, X_circ, Y_circ, ZZ_circ, 'Parent',handles.axes4);
az = 0;
el = 90;
view(handles.axes4,az, el);
colorbar(handles.axes4)
colormap(handles.axes4,'jet')
shading(handles.axes4,'flat')
caxis(handles.axes4,[-1,1])
set(handles.axes4, 'ZLim', [-5,5]);
set(handles.axes4title,'String','Membrane Deformation 3D [um]');
PeakValley = max(Z_circ) - min(Z_circ);
PeakValley = roundn(PeakValley,-2);
RMS_Z = rms(Z_circ);
RMS_Z = roundn(RMS_Z,-2);
set(handles.peak_valley, 'String', num2str(PeakValley));
set(handles.RMS, 'String', num2str(RMS_Z));
end
if Fit_Plot == 1
set(handles.D3Plot,'Value',0);
Deformation = handles.Deformation2D_axes3;
[nnn,mmm] = size(Deformation);
if mod(nnn,2) == 0
radious = nnn/2;
[AA,BB]=meshgrid(-radious:radious-1,-radious:radious-1);
else
radious = floor(nnn/2);
[AA,BB]=meshgrid(-radious:radious,-radious:radious);
end
% radious = round(nnn/2) - 1;
[THETA_pix,Rad_Pix] = cart2pol(AA,BB);
is_in_circle = Rad_Pix<=(radious);
Rad = Rad_Pix(is_in_circle) ./ (radious);
THETA = THETA_pix(is_in_circle);
N = []; M = []; %make zernicke indexes m,n up to 4,4
for n = 0:8
N = [N n*ones(1,n+1)];
M = [M -n:2:n];
end
zern_coeff = zernfun(N,M,Rad,THETA); %generate zernicke polynomial values at each pair of r,theta for each n,m index
ZernikeCoeff = zern_coeff\Deformation(is_in_circle); %fit data to Zernicke to estimate coefficient of data
ZernikeCoeff(1:3) = 0;
fit_def = getFitted_mod3(ZernikeCoeff,THETA,Rad); %make fit data so we can visualize
A = AA(is_in_circle);
B = BB(is_in_circle);
tri = delaunay(A,B);
plot(A,B,'.', 'Parent',handles.axes4)
h = trisurf(tri, A, B, fit_def, 'Parent',handles.axes4);
az = 0;
el = 90;
view(handles.axes4,az, el);
colorbar(handles.axes4)
colormap(handles.axes4,'jet')
shading(handles.axes4,'flat')
caxis(handles.axes4,[-1,1])
set(handles.axes4, 'ZLim', [-5,5]);
set(handles.axes4title,'String','Membrane Deformation Fit [um]');
PeakValley = max(fit_def) - min(fit_def);
PeakValley = roundn(PeakValley,-2);
RMS_Z = rms(fit_def);
RMS_Z = roundn(RMS_Z,-2);
set(handles.peak_valley, 'String', num2str(PeakValley));
set(handles.RMS, 'String', num2str(RMS_Z));
end
if Zernike_Table == 1
if Fit_Plot == 1
Column1 = ZernikeCoeff(4:15);
bar(Column1,0.5,'Parent',handles.axes6)
set(handles.axes6, 'YLim', [-2,2]);
set(handles.axes6,'XTickLabel',{'AST', 'DEF', 'AST', 'TFL','CMA','CMA','TFL','QUD','2AST','SPH','2AST','QUD'})
else
Deformation = handles.Deformation2D_axes3;
[nnn,mmm] = size(Deformation);
if mod(nnn,2) == 0
radious = nnn/2;
[AA,BB]=meshgrid(-radious:radious-1,-radious:radious-1);
else
radious = floor(nnn/2);
[AA,BB]=meshgrid(-radious:radious,-radious:radious);
end
% radious = round(nnn/2) - 1;
[THETA_pix,Rad_Pix] = cart2pol(AA,BB);
is_in_circle = Rad_Pix<=(radious);
Rad = Rad_Pix(is_in_circle) ./ (radious);
THETA = THETA_pix(is_in_circle);
N = []; M = []; %make zernicke indexes m,n up to 4,4
for n = 0:8
N = [N n*ones(1,n+1)];
M = [M -n:2:n];
end
zern_coeff = zernfun(N,M,Rad,THETA); %generate zernicke polynomial values at each pair of r,theta for each n,m index
ZernikeCoeff = zern_coeff\Deformation(is_in_circle); %fit data to Zernicke to estimate coefficient of data
% Column1 = zeros(10,1);
Column1 = ZernikeCoeff(4:15);
bar(Column1,0.5,'Parent',handles.axes6)
set(handles.axes6, 'YLim', [-2,2]);
set(handles.axes6,'XTickLabel',{'AST', 'DEF', 'AST', 'TFL','CMA','CMA','TFL','QUD','2AST','SPH','2AST','QUD'})
end
end
function peak_valley_Callback(hObject, eventdata, handles)
% hObject handle to peak_valley (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of peak_valley as text
% str2double(get(hObject,'String')) returns contents of peak_valley as a double
% --- Executes during object creation, after setting all properties.
function peak_valley_CreateFcn(hObject, eventdata, handles)
% hObject handle to peak_valley (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function RMS_Callback(hObject, eventdata, handles)
% hObject handle to RMS (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of RMS as text
% str2double(get(hObject,'String')) returns contents of RMS as a double
% --- Executes during object creation, after setting all properties.
function RMS_CreateFcn(hObject, eventdata, handles)
% hObject handle to RMS (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in SAVE.
function SAVE_Callback(hObject, eventdata, handles)
% hObject handle to SAVE (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
Captured_frame = evalin('base', 'Captured_frame');
% Fourier_Domain = evalin('base', 'Fourier_Domain');
Frequency_Filter = evalin('base', 'Frequency_Filter');
Wrapped_Phase = evalin('base', 'Wrapped_Phase');
Deformation = evalin('base', 'Deformation');
uisave({'Captured_frame','Frequency_Filter','Wrapped_Phase','Deformation'})
% --- Executes on button press in loadandplot.
function loadandplot_Callback(hObject, eventdata, handles)
% hObject handle to loadandplot (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
uiopen
f = figure('Position',[200 200 1000 450]);;
subplot(1,2,1)
min_wrapped=min(min(Wrapped_Phase));
wrapped_plot=Wrapped_Phase+abs(min_wrapped);
wrapped_plot=wrapped_plot/max(max(wrapped_plot));
imshow(wrapped_plot,'colormap',jet)
title('Wrapped Phase')
axis equal
[nnn,mmm] = size(Deformation);
K0_unwrap_mask = pi/1.07; % Radius of circular area inside the square cropped frame
KX0 = (mod((1/2 + (0:(nnn-1))/nnn), 1) - 1/2);
KX1 = KX0 * (2*pi);
KY0 = (mod(1/2 + (0:(mmm-1))/mmm, 1) - 1/2);
KY1 = KY0 * (2*pi);
[KX,KY] = meshgrid(KX1,KY1);
% Unwrap mask formulation
unwrap_mask = ((KX).^2 + (KY).^2 < K0_unwrap_mask^2);
unwrap_mask = fftshift(unwrap_mask);
Deformation_mask = unwrap_mask .* Deformation;
X_UW = 1:nnn;
Y_UW = 1:mmm;
[AA,BB]=meshgrid(X_UW,Y_UW);
% Applying the mask to X & Y coordinates
AA = unwrap_mask .* AA;
BB = unwrap_mask .* BB;
length_x=nnn*mmm;
length_y=nnn*mmm;
length_z=nnn*mmm;
X=zeros(1,length_x);
Y=zeros(1,length_y);
Z=zeros(1,length_z);
PP=1;
for ii=1:nnn
X(1,PP:PP+mmm-1)=AA(ii,:);
PP=PP+mmm;
end
PP=1;
for ii=1:nnn
Y(1,PP:PP+mmm-1)=BB(ii,:);
PP=PP+mmm;
end
PP=1;
for ii=1:nnn
Z(1,PP:PP+mmm-1)=Deformation_mask(ii,:);
PP=PP+mmm;
end
% Extracting X & Y & Z coordinates of only the membrane
PP=1;
for ii=1:length_x
if X(ii) ~= 0
X_circ(PP) = X(ii);
PP = PP + 1;
end
end
PP=1;
for ii=1:length_y
if Y(ii) ~= 0
Y_circ(PP) = Y(ii);
PP = PP + 1;
end
end
PP=1;
for ii=1:length_z
if Z(ii) ~= 0
Z_circ(PP) = Z(ii);
PP = PP + 1;
end
end
mean_Z = mean(mean(Z_circ));
ZZ_circ = Z_circ-mean_Z;
tri = delaunay(X_circ,Y_circ);
subplot(1,2,2)
plot(X_circ,Y_circ,'.')
% Plot it with TRISURF
h = trisurf(tri, X_circ, Y_circ, ZZ_circ);
title('Deformation [um]')
az = 0;
el = 90;
view(az, el);
colorbar
colormap jet
shading flat
axis off
caxis([-0.5,0.5])
colorbar('Ticks',[-2:0.5:2])
% create the data
PeakValley = max(Z_circ) - min(Z_circ);
PeakValley = roundn(PeakValley,-2);
radious = round(nnn/2) - 1;
[AA,BB]=meshgrid(-radious:radious,-radious:radious);
[THETA,Rad_Pix] = cart2pol(AA,BB);
is_in_circle = Rad_Pix<=(radious-1);
Rad = Rad_Pix(is_in_circle) ./ (radious);
N = []; M = []; %make zernicke indexes m,n up to 4,4
for n = 0:8
N = [N n*ones(1,n+1)];
M = [M -n:2:n];
end
zern_coeff = zernfun(N,M,Rad,THETA(is_in_circle)); %generate zernicke polynomial values at each pair of r,theta for each n,m index
ZernikeCoeff = zern_coeff\Deformation(is_in_circle); %fit data to Zernicke to estimate coefficient of data
ZernikeCoeff(1:13);
d = [PeakValley ZernikeCoeff(2) ZernikeCoeff(3) ZernikeCoeff(4) ZernikeCoeff(6) ZernikeCoeff(5) ZernikeCoeff(13)];
% Create the column and row names in cell arrays
cnames = {'Peak to Valley','Tilt X','Tilt Y','O-Astigmatism','V-Astigmatism','Defocus','Spherical'};
rnames = {'Value [um]'};
% Create the uitable
t = uitable(f,'Data',d,...
'ColumnName',cnames,...
'RowName',rnames);
% Set width and height
t.Position(3) = t.Extent(3);
t.Position(4) = t.Extent(4);
% --- Executes on button press in CharacData.
function CharacData_Callback(hObject, eventdata, handles)
% hObject handle to CharacData (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
assignin('base', 'Filter_X', handles.Filter_X)
assignin('base', 'Filter_Y', handles.Filter_Y)
assignin('base', 'Filter_D', handles.Filter_D)
assignin('base', 'Crop_Pix', handles.ROI_P)
Filter_X = evalin('base', 'Filter_X');
Filter_Y = evalin('base', 'Filter_Y');
Filter_D = evalin('base', 'Filter_D');
Crop_Pix = evalin('base', 'Crop_Pix');
% filename = fullfile('/home/pouya/meausre 31.05', 'Crop_and_Filter.mat');
uisave({'Filter_X','Filter_Y','Filter_D','Crop_Pix'},'Crop_and_Filter');
STOP_Callback(hObject, eventdata, handles)
% --- Executes on button press in Deformation_fit.
function Deformation_fit_Callback(hObject, eventdata, handles)
% hObject handle to Deformation_fit (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of Deformation_fit
|
github
|
rajaeipour/spatial-carrier-master
|
cunwrap_nodisp.m
|
.m
|
spatial-carrier-master/cunwrap_nodisp.m
| 16,666 |
utf_8
|
f64eda6acf71fe85dfd64078206275c3
|
function PhiUnwrap = cunwrap_nodisp(Psi, options)
% PhiUnwrap = cunwrap(Psi, options)
%
% Purpose: Costantini's 2D unwrapping based on Minimum Network Flow
%
% INPUTS:
% - Psi: 2D-array wrapped phase (radian)
% - options: optional structure used to modify the behavior of the
% unwrapping algorithm. All fields are optional.
% The fieldname does not need to exactly case-matched.
% Weight: array of same dimension as the Psi, with is used as
% the positive weight of the L1 norm of the residual (to be
% minimized). For example user can provide WEIGHT as function
% of the interference amplitude or function of phase
% measurement quality (e.g., fringe contrast).
% By default: all internal pixels have the same weight of 1,
% 0.5 for edge-pixels, and 0.25 for corner-pixels.
% CutSize: even integer scalar, default [4]: the width (in pixel) of
% the Gaussian kernel use to lower the weight around pixels
% that do not fulfill rotational relation.
% If CutSize is 0, no rotational-based weighting will be
% carried out.
% RoundK: Boolean, [false] by default. When ROUNDK is true, CUNWRAP
% forces the partial derivative residuals K1/K2 to be
% integers.
% MaxBlockSize: scalar default [125], target linear blocksize.
% Set to Inf for single-block global unwrapping.
% Note: network flow is costly in CPU for large size.
% Overlap: scalar default [0.25], fractional overlapping between two
% neighboring blocks.
% Verbose: logical [true], control printout information.
% LPoption: LINPROG option structure as return by OPTIMSET(...).
% OUTPUT:
% - Phi: 2D-array unwrapped phase (radian)
%
% Minimum network flow computation engine is Matlab LINPROG (optimization
% toolbox is required)
%
% References:
% - http://earth.esa.int/workshops/ers97/papers/costantini/
% - Costantini, M. (1998) A novel phase unwrapping method based on network
% programming. IEEE Tran. on Geoscience and Remote Sensing, 36, 813-821.
%
% Author: Bruno Luong <[email protected]>
% History:
% Orginal: 27-Aug-2009
% 28-Aug-2009: modification in block splitting, default size changes
% to 125 x 125
% 28-Aug-2009: correct a serious indexing bug
if nargin<2
options = struct();
end
if ndims(Psi)>2
error('CUNWRAP: input Psi must be 2D array.');
end
[ny nx] = size(Psi);
if nx<2 || ny<2
error('CUNWRAP: size of Psi must be larger than 2');
end
roundK = getoption(options, 'roundk', false);
verbose = getoption(options, 'verbose', true);
% Default weight
w1 = ones(ny,1); w1([1 end]) = 0.5;
w2 = ones(1,nx); w2([1 end]) = 0.5;
weight = w1*w2; % tensorial product
weight = getoption(options, 'weight', weight);
% Split in smaller block size
blocksize = getoption(options, 'maxblocksize', 125);
blocksize = max(blocksize,2);
% Overlapping fraction
p = getoption(options, 'overlap', 0.25);
p = max(min(p,1),0);
% Split the linear index for each dimension
[ix blk_x] = splitidx(blocksize, nx, p);
[iy blk_y] = splitidx(blocksize, ny, p);
nbblk = length(iy)*length(ix);
% Allocate arrays
% negative/positive parts of wrapped partial derivatives
x1p = nan(ny-1, nx, class(Psi));
x1m = nan(ny-1, nx, class(Psi));
x2p = nan(ny, nx-1, class(Psi));
x2m = nan(ny, nx-1, class(Psi));
%%
% Loop over the blocks
blknum = 0;
for i=1:length(iy)
iy0 = iy{i};
iy1 = iy0(1:end-1);
iy2 = iy0(1:end);
for j=1:length(ix)
ix0 = ix{j};
ix1 = ix0(1:end);
ix2 = ix0(1:end-1);
blknum = blknum + 1;
options.weight = weight(iy0,ix0);
options.blknum = blknum;
% Costantini's minimum network flow resolution for one block
[x1p(iy1,ix1) x1m(iy1,ix1) x2p(iy2,ix2) x2m(iy2,ix2)] = ...
cunwrap_blk(Psi(iy0,ix0), ...
x1p(iy1,ix1), x1m(iy1,ix1),...
x2p(iy2,ix2), x2m(iy2,ix2),...
options);
end
end
%%
% Compute partial derivative Psi1, eqt (1,3)
i = 1:(ny-1);
j = 1:nx;
[ROW_I ROW_J] = ndgrid(i,j);
I_J = sub2ind(size(Psi),ROW_I,ROW_J);
IP1_J = sub2ind(size(Psi),ROW_I+1,ROW_J);
Psi1 = Psi(IP1_J) - Psi(I_J);
% A priori knowledge that Psi1 is in [-pi,pi)
Psi1 = mod(Psi1+pi,2*pi)-pi;
% Compute partial derivative Psi2, eqt (2,4)
i = 1:ny;
j = 1:(nx-1);
[ROW_I ROW_J] = ndgrid(i,j);
I_J = sub2ind(size(Psi),ROW_I,ROW_J);
I_JP1 = sub2ind(size(Psi),ROW_I,ROW_J+1);
Psi2 = Psi(I_JP1) - Psi(I_J);
% A priori knowledge that Psi1 is in [-pi,pi)
Psi2 = mod(Psi2+pi,2*pi)-pi;
% Compute the derivative jumps, eqt (20,21)
k1 = x1p-x1m;
k2 = x2p-x2m;
% Round to integer solution (?)
if roundK
k1 = round(k1);
k2 = round(k2);
end
% Sum the jumps with the wrapped partial derivatives, eqt (10,11)
k1 = reshape(k1,[ny-1 nx]);
k2 = reshape(k2,[ny nx-1]);
k1 = k1+Psi1/(2*pi);
k2 = k2+Psi2/(2*pi);
%%
% Integrate the partial derivatives, eqt (6)
% Not sure why integrate this way is better than otherway around
% Integration order, not documented
intorder = getoption(options, 'IntOrder', 1);
if intorder==1
K = cumsum([0 k2(1,:)]);
K = [K; k1];
K = cumsum(K,1);
else
% Integration is this order does not work well (still mysterious for BL)
K = cumsum([0; k1(:,1)]);
K = [K k2];
K = cumsum(K,2);
end
PhiUnwrap = (2*pi)*K;
end % cunwrap
%%
function [x1p x1m x2p x2m] = cunwrap_blk(Psi, ...
X1p, X1m, X2p, X2m, options)
% function [x1p x1m x2p x2m] = cunwrap_blk(Psi, ...
% X1p, X1m, X2p, X2m, options)
% Costantini's minimum network flow resolution for one block
%%
% if getoption(options, 'blknum', NaN) == 8
% save('debug.mat', 'Psi', 'X1p', 'X1m', 'X2p', 'X2m', 'options');
% end
%%
[ny nx] = size(Psi);
verbose = getoption(options, 'verbose', true);
% the width (in pixel) of the Gaussian kernel to limit effect of
% patch that does not satisfy rotational relation
CutSize = getoption(options, 'cutsize', 4);
% Default weight
w1 = ones(ny,1); w1([1 end])=0.5;
w2 = ones(1,nx); w2([1 end])=0.5;
weight = w1*w2; % tensorial product
weight = getoption(options, 'weight', weight);
% Compute partial derivative Psi1, eqt (1,3)
i = 1:(ny-1);
j = 1:nx;
[ROW_I ROW_J] = ndgrid(i,j);
I_J = sub2ind(size(Psi),ROW_I,ROW_J);
IP1_J = sub2ind(size(Psi),ROW_I+1,ROW_J);
Psi1 = Psi(IP1_J) - Psi(I_J);
% A priori knowledge that Psi1 is in [-pi,pi)
Psi1 = mod(Psi1+pi,2*pi)-pi;
% Compute partial derivative Psi2, eqt (2,4)
i = 1:ny;
j = 1:(nx-1);
[ROW_I ROW_J] = ndgrid(i,j);
I_J = sub2ind(size(Psi),ROW_I,ROW_J);
I_JP1 = sub2ind(size(Psi),ROW_I,ROW_J+1);
Psi2 = Psi(I_JP1) - Psi(I_J);
% A priori knowledge that Psi1 is in [-pi,pi)
Psi2 = mod(Psi2+pi,2*pi)-pi;
%%
% The RHS is column-reshaping of a 2D array [ny-1] x [nx-1]
% Build the equality constraint RHS (eqt 17)
beq = 0;
% Compute beq
i = 1:(ny-1);
j = 1:(nx-1);
[ROW_I ROW_J] = ndgrid(i,j);
I_J = sub2ind(size(Psi1),ROW_I,ROW_J);
I_JP1 = sub2ind(size(Psi1),ROW_I,ROW_J+1);
beq = beq + (Psi1(I_JP1)-Psi1(I_J));
I_J = sub2ind(size(Psi2),ROW_I,ROW_J);
IP1_J = sub2ind(size(Psi2),ROW_I+1,ROW_J);
beq = beq - (Psi2(IP1_J)-Psi2(I_J));
beq = -1/(2*pi)*beq;
beq = round(beq);
beq = beq(:);
%%
% The vector of LP is arranged as following:
% x := (x1p, x1m, x2p, x2m).'
% x1p, x1m: reshaping of [ny-1] x [nx]
% x2p, x2m: reshaping of [ny] x [nx-1]
%
% Row index, used by all foure blocks in Aeq, beq
i = 1:(ny-1);
j = 1:(nx-1);
[ROW_I ROW_J] = ndgrid(i,j);
ROW_I_J = sub2ind([length(i) length(j)],ROW_I,ROW_J);
nS0 = (nx-1)*(ny-1);
% Use by S1p, S1m
[COL_I COL_J] = ndgrid(i,j);
COL_IJ_1 = sub2ind([length(i) length(j)+1],COL_I,COL_J);
[COL_I COL_JP1] = ndgrid(i,j+1);
COL_I_JP1 = sub2ind([length(i) length(j)+1],COL_I,COL_JP1);
nS1 = (nx)*(ny-1);
% Use by S2p, S2m
[COL_I COL_J] = ndgrid(i,j);
COL_IJ_2 = sub2ind([length(i)+1 length(j)],COL_I,COL_J);
[COL_IP1 COL_J] = ndgrid(i+1,j);
COL_IP1_J = sub2ind([length(i)+1 length(j)],COL_IP1,COL_J);
nS2 = (nx-1)*(ny);
% Build four indexes arrays that will be used to split x in four parts
% 29/08/09 bug corrected
offset1p = 0;
idx1p = offset1p+(1:nS1);
offset1m = idx1p(end);
idx1m = offset1m+(1:nS1);
offset2p = idx1m(end);
idx2p = offset2p+(1:nS2);
offset2m = idx2p(end);
idx2m = offset2m+(1:nS2);
% Equality constraint matrix (Aeq)
S1p = + sparse(ROW_I_J, COL_I_JP1,1,nS0,nS1) ...
- sparse(ROW_I_J, COL_IJ_1,1,nS0,nS1);
S1m = -S1p;
S2p = - sparse(ROW_I_J, COL_IP1_J,1,nS0,nS2) ...
+ sparse(ROW_I_J, COL_IJ_2,1,nS0,nS2);
S2m = -S2p;
% Matrix of the LHS of eqt (17)
Aeq = [S1p S1m S2p S2m];
nvars = size(Aeq,2);
% Clean up
clear S1p S1m S2p S2m
%%
% force to be even
CutSize = ceil(CutSize/2)*2;
% Modify weight to limit the effect of points that violate
% the rorational condition. The weight is graduataly increase
% around the points.
if CutSize>0
% mydisplay(verbose, '\tAdjust weight (CutSize = %d pixels)\n', CutSize);
% Truncated Gaussian Kernel
v = 1*linspace(-1,1,CutSize);
[x y] = meshgrid(v,v);
kernel = 1.1*exp(-(x.^2+y.^2));
rotdegradation = double(reshape(beq~=0, [ny nx]-1)); % 0 or 1
%mydisplay(verbose, '\tInconsistency = %d/%d\n', ...
% sum(rotdegradation(:)), numel(beq));
rotdegradation = conv2(rotdegradation, kernel, 'full');
rotdegradation = rotdegradation(CutSize/2 + (0:ny-1),...
CutSize/2 + (0:nx-1));
% mininum weight threshold
wmin = 1e-2; % weight never goes under this value, small positive value
rotdegradation = min(rotdegradation,1-wmin);
weight = weight .* (1-rotdegradation);
end
c1 = 0.5*(weight(1:ny-1,:)+weight(1:ny-1,:));
c2 = 0.5*(weight(:,1:nx-1)+weight(:,1:nx-1));
% Cost vector, eqt (16)
cost = zeros(nvars,1);
cost(idx1p) = c1(:);
cost(idx1m) = c1(:);
cost(idx2p) = c2(:);
cost(idx2m) = c2(:);
%%
% Lower and upper bound, eqt (18,19)
L = zeros(nvars,1);
U = Inf(size(L)); % No upper bound, U=[];
%%
% Lock the x values to prior computed value (from calculation on other
% blocks)
i1 = find(~isnan(X1p));
i2 = find(~isnan(X2p));
% Lock method, not documented
lockadd = 1;
lockremove = 2; %#ok
lockmethod = getoption(options, 'lockmethod', lockadd);
if lockmethod==lockadd
% Lock matrix and values, eqt (26, 27), larger system
L1p = sparse(1:length(i1), idx1p(i1), 1, length(i1), size(Aeq,2));
L1m = sparse(1:length(i1), idx1m(i1), 1, length(i1), size(Aeq,2));
L2p = sparse(1:length(i2), idx2p(i2), 1, length(i2), size(Aeq,2));
L2m = sparse(1:length(i2), idx2m(i2), 1, length(i2), size(Aeq,2));
AL = [L1p; L1m; L2p; L2m];
bL = [X1p(i1); X1m(i1); X2p(i2); X2m(i2)];
clear L1p L1m L2p L2m % clean up
% Find the rows in Aeq with all variables locked
ColPatch = [offset1p+COL_IJ_1(:) offset1p+COL_I_JP1(:) ...
offset2p+COL_IJ_2(:) offset2p+COL_IP1_J(:)];
[trash ColDone] = find(AL); %#ok
remove = all(ismember(ColPatch, ColDone),2);
Aeq = [Aeq(~remove,:); AL];
beq = [beq(~remove,:); bL];
% No need to bother with what already computed
cost(idx1p(i1)) = 0;
cost(idx1m(i1)) = 0;
cost(idx2p(i2)) = 0;
cost(idx2m(i2)) = 0;
L(idx1p(i1)) = -Inf;
L(idx1m(i1)) = -Inf;
L(idx2p(i2)) = -Inf;
L(idx2m(i2)) = -Inf;
clear AL bL trash ColPatch ColDone remove i1 i2 % clean up
else
% Lock by remove the overlapped variables, smaller system
% But *seems* more affected by error propagation
% BL think both method should be strictly equivalent (!)
% remove the equality contribution from the RHS
lock = zeros(nvars,1,class(Aeq));
lock(idx1p(i1)) = X1p(i1);
lock(idx1m(i1)) = X1m(i1);
lock(idx2p(i2)) = X2p(i2);
lock(idx2m(i2)) = X2m(i2);
beq = beq - Aeq*lock;
% Remove the variables
vremove = [idx1p(i1) idx1m(i1) idx2p(i2) idx2m(i2)];
% keep is use later to dispatch partial derivative
keep = true(nvars,1); keep(vremove) = false;
Aeq(:,vremove) = [];
L(vremove) = []; U(vremove) = [];
cost(vremove) = [];
% Find the rows in Aeq with all variables locked
ColPatch = [offset1p+COL_IJ_1(:) offset1p+COL_I_JP1(:) ...
offset2p+COL_IJ_2(:) offset2p+COL_IP1_J(:)];
% Remove the equations
eremove = all(ismember(ColPatch, vremove),2);
Aeq(eremove,:) = [];
beq(eremove,:) = [];
clear vremove eremove ColPatch lock % clean up
end
%%
% To do: implement Bertsekas/Tseng's relaxation method, ref. [20]
% Call LP solver
%mydisplay(verbose, '\tMinimum network flow resolution\n');
%mydisplay(verbose, '\t\tmatrix size = (%d,%d)\n', size(Aeq,1),size(Aeq,2));
if ~isempty(which('linprog'))
% Call Matlab Linprog
% Adjust optional LP options at your preference, see
% http://www.mathworks.com/access/helpdesk/help/toolbox/optim/ug/linprog.html
% http://www.mathworks.com/access/helpdesk/help/toolbox/optim/ug/optimset.html
%mydisplay(verbose, '\tLINPROG...\n');
% BL has not checked because he does not have the right toolbox
%LPoption = getoption(options, 'LPoption', {});
LPoptions = optimset('Display','none','Algorithm','interior-point');
% LPoption2 = getoption(options, 'Display', 'none');
if ~iscell(LPoptions)
LPoptions = {LPoptions};
end
% LPoption = {optimset(...)}
sol = linprog(cost,[],[],Aeq,beq,L,U,[],LPoptions{:});
elseif ~isempty(which('BuildMPS'))
% Here is BL Linprog, call Matlab linprog instead to get "SOL",
% the solution of the above LP problem
mpsfile='costantini.mps';
% mydisplay(verbose, '\tConversion to MPS file\n');
Contain = BuildMPS([], [], Aeq, beq, cost, L, U, 'costantini');
OK = SaveMPS(mpsfile,Contain);
if ~OK
error('CUNWRAP: Cannot write mps file');
end
PCxpath=App_path('PCx');
[OK outfile]=invokePCx(mpsfile,PCxpath,verbose==0);
if ~OK
% mydisplay(verbose, 'PCx path=%s\n', PCxpath);
%mydisplay(verbose, 'Cannot invoke LP solver, PCx not installed?\n');
error('CUNWRAP: Cannot invoke PCx');
end
[OK sol]=readPCxoutput(outfile);
if ~OK
error('CUNWRAP: Cannot read PCx outfile, L1 fit might fails.');
end
else
error('CUNWRAP: cannot detect network flow (LP) engine');
end
%%
% Displatch the LP solution
if lockmethod==lockadd
x = sol;
else
x = zeros(size(keep),class(sol));
x(keep) = sol;
end
x1p = reshape(x(idx1p), [ny-1 nx]);
x1m = reshape(x(idx1m), [ny-1 nx]);
x2p = reshape(x(idx2p), [ny nx-1]);
x2m = reshape(x(idx2m), [ny nx-1]);
end
%% Get defaut option
function value = getoption(options, name, defaultvalue)
% function value = getoption(options, name, defaultvalue)
value = defaultvalue;
fields = fieldnames(options);
found = strcmpi(name,fields);
if any(found)
i = find(found,1,'first');
if ~isempty(options.(fields{i}))
value = options.(fields{i});
end
end
end
%%
function [ilist blocksize] = splitidx(blocksize, n, p)
% function ilist = splitidx(blocksize, n, p)
%
% return the cell array, each element is subindex of (1:n)
% The union is (1:n) with overlapping fraction is p (0<p<1)
if blocksize>=n
ilist = {1:n};
blocksize = n;
else
q = 1-p;
% Number of blocks
k = (n/blocksize - p) / q;
k = ceil(k);
% Readjust the block size, float
blocksize = n/(k*q + p);
% first index
firstidx = round(linspace(1,n-ceil(blocksize)+1, k));
lastidx = round(firstidx+blocksize-1);
lastidx(end) = n;
% Make sure they are overlapped
lastidx(1:end-1) = max(lastidx(1:end-1),firstidx(2:end));
% Put the indexes of k blocks into cell array
ilist = cell(1,length(firstidx));
for k=1:length(ilist)
ilist{k} = firstidx(k):lastidx(k);
end
blocksize = round(blocksize);
end
end
|
github
|
EPFL-LCSB/matTFA-master
|
solveTFAmodelCplex.m
|
.m
|
matTFA-master/matTFA/solveTFAmodelCplex.m
| 5,589 |
utf_8
|
8ab7d957942db50f3dd288fbaa9e3c70
|
function sol = solveTFAmodelCplex(tModel,TimeInSec,manualScalingFactor,mipTolInt,emphPar,feasTol,scalPar,mipDisplay,CPXPARAMdisp)
% Solve a model using specific solver settings. More details in
% changeToCPLEX_WithOptions
%
% INPUTS
% tModel: a TFA-ready model (has a .A matrix)
% TimeInSec: timelimit for the solver.
% manualScalingFactor: manual scaling factor for the solver
% mipTolInt: Integer tolerance of the solver
% emphPar: Solver emphasis (trade-offs between speed, feasibility,
% optimality, and moving bounds in MIP - see https://www.ibm.com/support/knowledgecenter/en/SSSA5P_12.6.0/ilog.odms.cplex.help/CPLEX/Parameters/topics/MIPEmphasis.html)
% feasTol: solver tolerance for feasibility (error on constraints)
% mipDisplay: verbosity of the MIP info display
% CPXPARAMdisp: Turn on/off the cplex problem setup display
%
%% Changelog
% 2017/04/26 - Modified by Pierre on Georgios Fengos's base, to incorporate
% Vikash's Gurobi hooks in a more global fashion, in a similar way COBRA
% solvers are handled.
% Calls the global parameter TFA_MILP_SOLVER, and check if it set to
% something. If not, default to CPLEX using Fengos's code.
% In the long run, we should rename thins function to remove CPLEX from its
% name.
% TODO : Add parameter setting in gurobi call
%
global TFA_MILP_SOLVER
if ~exist('TFA_MILP_SOLVER','var') || isempty(TFA_MILP_SOLVER)
TFA_MILP_SOLVER = 'cplex_direct';
end
solver = TFA_MILP_SOLVER;
% solver = 'gurobi_direct';
if ~exist('manualScalingFactor','var') || isempty(manualScalingFactor)
manualScalingFactor = [];
end
if ~exist('mipTolInt','var') || isempty(mipTolInt)
mipTolInt = [];
end
if ~exist('emphPar','var') || isempty(emphPar)
emphPar = [];
end
if ~exist('feasTol','var') || isempty(feasTol)
feasTol = [];
end
if ~exist('scalPar','var') || isempty(scalPar)
scalPar = [];
end
if ~exist('TimeInSec','var') || isempty(TimeInSec)
TimeInSec = [];
end
if ~exist('mipDisplay','var') || isempty(mipDisplay)
mipDisplay = [];
end
if ~exist('CPXPARAMdisp','var') || isempty(CPXPARAMdisp)
CPXPARAMdisp = [];
end
switch solver
%% Case CPLEX
case 'cplex_direct'
if isempty(which('cplex.p'))
error('You need to add CPLEX to the Matlab-path!!')
end
sol = x_solveCplex(tModel,TimeInSec,manualScalingFactor,mipTolInt,emphPar,feasTol,scalPar,mipDisplay,CPXPARAMdisp);
%% Case GUROBI
case 'gurobi_direct'
if isempty(which('gurobi'))
error('You need to add Gurobi to the Matlab-path!!')
end
sol = x_solveGurobi(tModel,TimeInSec,manualScalingFactor,mipTolInt,emphPar,feasTol,scalPar,mipDisplay);
end
end
%% Private function for CPLEX solve
function sol = x_solveCplex(tModel,TimeInSec,manualScalingFactor,mipTolInt,emphPar,feasTol,scalPar,mipDisplay,CPXPARAMdisp)
% this function solves a TFBA problem using CPLEX
% if cplex is installed, and in the path
if isempty(which('cplex.m'))
error('cplex is either not installed or not in the path')
end
% Convert problem to cplex
cplex = changeToCPLEX_WithOptions(tModel,TimeInSec,manualScalingFactor,mipTolInt,emphPar,feasTol,scalPar,mipDisplay,CPXPARAMdisp);
% Optimize the problem
try
CplexSol = cplex.solve();
if isfield(cplex.Solution,'x')
x = cplex.Solution.x;
if ~isempty(x)
sol.x = cplex.Solution.x;
sol.val = cplex.Solution.objval;
sol.cplexSolStatus = cplex.Solution.status;
else
sol.x = [];
sol.val = [];
disp('Empty solution');
warning('Cplex returned an empty solution!')
sol.cplexSolStatus = 'Empty solution';
end
else
sol.x = [];
sol.val = [];
disp('No field cplex.Solution.x');
warning('The solver does not return a solution!')
sol.cplexSolStatus = 'No field cplex.Solution.x';
end
catch
sol.x = NaN;
sol.val = NaN;
sol.cplexSolStatus = 'Solver crashed';
end
delete(cplex)
end
%% Private function for GUROBI solve
function sol = x_solveGurobi(tModel,TimeInSec,manualScalingFactor,mipTolInt,emphPar,feasTol,scalPar,mipDisplay)
num_constr = length(tModel.constraintType);
num_vars = length(tModel.vartypes);
contypes = '';
vtypes = '';
% convert contypes and vtypes into the right format
for i=1:num_constr
contypes = strcat(contypes,tModel.constraintType{i,1});
end
for i=1:num_vars
vtypes = strcat(vtypes,tModel.vartypes{i,1});
end
% TODO: Add Solver settings
gmodel.A=tModel.A;
gmodel.obj=tModel.f;
gmodel.lb=tModel.var_lb;
gmodel.ub=tModel.var_ub;
gmodel.rhs=tModel.rhs;
gmodel.sense=contypes;
gmodel.vtype=vtypes;
gmodel.varnames=tModel.varNames;
if tModel.objtype==-1
gmodel.modelsense='max'
elseif tModel.objtype==1
gmodel.modelsense='min'
else
error(['No objective type specified ' ...
'(model.objtype should be in {-1,1})']);
end
try
result=gurobi(gmodel);
if isfield(result,'x')
x = result.x;
x(find(abs(x) < 1E-9))=0;
else
warning('The solver does not return a solution!')
result.x=[];
result.objval=[];
end
catch
result.status='0';
x=NaN;
result.x=NaN;
result.objval=NaN;
end
sol.x=result.x;
sol.val=result.objval;
sol.status=result.status;
% TODO: Add exitflag translation
end
|
github
|
EPFL-LCSB/matTFA-master
|
solveFBAmodelCplex.m
|
.m
|
matTFA-master/matTFA/solveFBAmodelCplex.m
| 30,450 |
utf_8
|
6e803c4720697333350bcd6e8563f5b5
|
function FBAsolution = solveFBAmodelCplex(model, scalPar, feasTol, emphPar, osenseStr)
%optimizeCbModel Solve a flux balance analysis problem
%
% Georgios Fengos 24/05/2016 Created this version of optimizeCbModel
% to be able to control externally the cplex parameters
%% Process arguments and set up problem
if ~exist('osenseStr','var')
osenseStr = 'max';
end
allowLoops = true;
if ~exist('scalPar','var') || isempty(scalPar)
scalPar = [];
end
if ~exist('feasTol','var') || isempty(feasTol)
feasTol = [];
end
if ~exist('emphPar','var') || isempty(emphPar)
emphPar = [];
end
[minNorm, printLevel, primalOnlyFlag, ~] = getCobraSolverParams('LP',{'minNorm','printLevel','primalOnly','saveInput'});
% Figure out objective sense
if strcmpi(osenseStr,'max')
LPproblem.osense = -1;
else
LPproblem.osense = +1;
end
[nMets,nRxns] = size(model.S);
% add csense
%Doing this makes csense a double array. Totally smart design move.
%LPproblem.csense = [];
if ~isfield(model,'csense')
% If csense is not declared in the model, assume that all
% constraints are equalities.
LPproblem.csense(1:nMets,1) = 'E';
else % if csense is in the model, move it to the lp problem structure
if length(model.csense)~=nMets,
warning('Length of csense is invalid! Defaulting to equality constraints.')
LPproblem.csense(1:nMets,1) = 'E';
else
model.csense = columnVector(model.csense);
LPproblem.csense = model.csense;
end
end
% Fill in the RHS vector if not provided
if (~isfield(model,'b'))
LPproblem.b = zeros(size(model.S,1),1);
else
LPproblem.b = model.b;
end
% Rest of the LP problem
LPproblem.A = model.S;
LPproblem.c = model.c;
LPproblem.lb = model.lb;
LPproblem.ub = model.ub;
%Double check that all inputs are valid:
if ~(verifyCobraProblem(LPproblem, [], [], false) == 1)
warning('invalid problem');
return;
end
%%
t1 = clock;
% Solve initial LP
% if allowLoops
solution = solveCobraLP_edited(LPproblem,scalPar,feasTol,emphPar);
% else
% MILPproblem = addLoopLawConstraints(LPproblem, model, 1:nRxns);
% solution = solveCobraMILP(MILPproblem);
% end
if (solution.stat ~= 1) % check if initial solution was successful.
if printLevel>0
warning('Optimal solution was not found');
end
FBAsolution.f = 0;
FBAsolution.x = [];
FBAsolution.stat = solution.stat;
FBAsolution.origStat = solution.origStat;
FBAsolution.solver = solution.solver;
FBAsolution.time = etime(clock, t1);
return;
end
objective = solution.obj; % save for later use.
% Store results
if (solution.stat == 1)
%solution found.
FBAsolution.x = solution.full(1:nRxns);
%this line IS necessary.
FBAsolution.f = model.c'*solution.full(1:nRxns); %objective from original optimization problem.
if abs(FBAsolution.f - objective) > .01
display('warning: objective appears to have changed while performing secondary optimization (minNorm)');
end
if (~primalOnlyFlag && allowLoops && any(~minNorm)) % rcost/dual only correct if not doing minNorm
FBAsolution.y = solution.dual;
FBAsolution.w = solution.rcost;
end
else
%some sort of error occured.
if printLevel>0
warning('Optimal solution was not found');
end
FBAsolution.f = 0;
FBAsolution.x = [];
end
FBAsolution.stat = solution.stat;
FBAsolution.origStat = solution.origStat;
FBAsolution.solver = solution.solver;
FBAsolution.time = etime(clock, t1);
end
function solution = solveCobraLP_edited(LPproblem,scalPar,feasTol,emphPar)
% solveCobraLP Solve constraint-based LP problems
% Georgios Fengos 24/05/2016 Created this version of solveCobraLP
% to be able to control externally the cplex parameters
global CBTLPSOLVER
if (~isempty(CBTLPSOLVER))
solver = CBTLPSOLVER;
else
error('No solver found. call changeCobraSolver(solverName)');
end
optParamNames = {'minNorm','printLevel','primalOnly','saveInput', ...
'feasTol','optTol','EleNames','EqtNames','VarNames','EleNameFun', ...
'EqtNameFun','VarNameFun','PbName','MPSfilename'};
parameters = '';
% if nargin ~=1
% if mod(length(varargin),2)==0
% for i=1:2:length(varargin)-1
% if ismember(varargin{i},optParamNames)
% parameters.(varargin{i}) = varargin{i+1};
% else
% error([varargin{i} ' is not a valid optional parameter']);
% end
% end
% elseif strcmp(varargin{1},'default')
% parameters = 'default';
% elseif isstruct(varargin{1})
% parameters = varargin{1};
% else
% display('Warning: Invalid number of parameters/values')
% solution=[];
% return;
% end
% end
[minNorm, printLevel, ~, saveInput, ~, ~] = ...
getCobraSolverParams('LP',optParamNames(1:6),parameters);
%Save Input if selected
if ~isempty(saveInput)
fileName = parameters.saveInput;
if ~find(regexp(fileName,'.mat'))
fileName = [fileName '.mat'];
end
display(['Saving LPproblem in ' fileName]);
save(fileName,'LPproblem')
end
% [A,b,c,lb,ub,csense,osense] = deal(LPproblem.A,LPproblem.b,LPproblem.c,LPproblem.lb,LPproblem.ub,LPproblem.csense,LPproblem.osense);
% if any(any(~isfinite(A)))
% error('Cannot perform LP on a stoichiometric matrix with NaN of Inf coefficents.')
% end
% Defaults in case the solver does not return anything
f = [];
x = [];
y = [];
w = [];
origStat = -99;
stat = -99;
t_start = clock;
switch solver
case 'cplex_direct'
%% Tomlab cplex.m direct
%Used with the current script, only some of the control affoarded with
%this interface is provided. Primarily, this is to change the print
%level and whether to minimise the Euclidean Norm of the internal
%fluxes or not.
%See solveCobraLPCPLEX.m for more refined control of cplex
%Ronan Fleming 11/12/2008
if isfield(LPproblem,'basis') && ~isempty(LPproblem.basis)
LPproblem.LPBasis = LPproblem.basis;
end
[solution LPprob] = solveCobraLPCPLEX_edited(LPproblem,printLevel,1,[],[],minNorm,scalPar,feasTol,emphPar);
solution.basis = LPprob.LPBasis;
solution.solver = solver;
case 'gurobi5'
%% Gurobi direct
% 2017/04/26 Added by Pierre
% TODO : Get the LP basis ?
if isfield(LPproblem,'basis') && ~isempty(LPproblem.basis)
LPproblem.LPBasis = LPproblem.basis;
end
[solution LPprob] = solveCobraLPGurobi(LPproblem,printLevel,1,[],[],minNorm,scalPar,feasTol,emphPar);
solution.basis = [];%LPprob.LPBasis;
solution.solver = solver;
otherwise
error(['Unknown solver: ' solver]);
end
if ~strcmp(solver,'cplex_direct') && ~strcmp(solver,'mps')
%% Assign solution
t = etime(clock, t_start);
if ~exist('basis','var'), basis=[]; end
[solution.full,solution.obj,solution.rcost,solution.dual,solution.solver,solution.stat,solution.origStat,solution.time,solution.basis] = ...
deal(x,f,w,y,solver,stat,origStat,t,basis);
end
end
function [solution,LPproblem] = solveCobraLPCPLEX_edited(LPproblem,printLevel,basisReuse,conflictResolve,contFunctName,minNorm,scalPar,feasTol,emphPar)
% [solution,LPproblem]=solveCobraLPCPLEX(LPproblem,printLevel,basisReuse,conflictResolve,contFunctName,minNorm)
% Georgios Fengos 24/05/2016 Created this version of solveCobraLPCPLEX
% to be able to control externally the cplex parameters
if ~exist('printLevel','var')
printLevel=2;
end
if ~exist('basisReuse','var')
basisReuse=0;
end
if ~exist('conflictResolve','var')
conflictResolve=0;
end
if ~exist('contFunctName','var')
cpxControl=[];
else
if isstruct(contFunctName)
cpxControl=contFunctName;
else
if ~isempty(contFunctName)
%calls a user specified function to create a CPLEX control structure
%specific to the users problem. A TEMPLATE for one such function is
%CPLEXParamSet
cpxControl=eval(contFunctName);
else
cpxControl=[];
end
end
end
if ~exist('minNorm','var')
minNorm=0;
end
if basisReuse
if isfield(LPproblem,'LPBasis')
basis=LPproblem.LPBasis;
%use advanced starting information when optimization is initiated.
cpxControl.ADVIND=1;
else
basis=[];
end
else
basis=[];
%do not use advanced starting information when optimization is initiated.
cpxControl.ADVIND=0;
end
if ~isfield(LPproblem,'A')
if ~isfield(LPproblem,'S')
error('Equality constraint matrix must either be a field denoted A or S.')
end
LPproblem.A=LPproblem.S;
end
if ~isfield(LPproblem,'csense')
nMet=size(LPproblem.A);
if printLevel>0
fprintf('%s\n','Assuming equality constraints, i.e. S*v=b');
end
%assuming equality constraints
LPproblem.csense(1:nMet,1)='E';
end
if ~isfield(LPproblem,'osense')
%assuming maximisation
LPproblem.osense=-1;
if printLevel>0
fprintf('%s\n','Assuming maximisation of objective');
end
end
%get data
[c,x_L,x_U,b,csense,osense] = deal(LPproblem.c,LPproblem.lb,LPproblem.ub,LPproblem.b,LPproblem.csense,LPproblem.osense);
%modify objective to correspond to osense
c=full(c*osense);
%cplex expects it dense
b=full(b);
%Conflict groups descriptor (cpxBuildConflict can be used to generate the input). Set this if
%conflict refinement is desired in the case that infeasibility is detected
%by CPLEX.
if conflictResolve
[m_lin,n]=size(LPproblem.A);
m_quad=0;
m_sos=0;
m_log=0;
%determines how elaborate the output is
mode='full';%'minimal';
fprintf('%s\n%s\n','Building Structure for Conflict Resolution...','...this slows CPLEX down so should not be used for repeated LP');
confgrps = cpxBuildConflict(n,m_lin,m_quad,m_sos,m_log,mode);
prefix=pwd;
suffix='LP_CPLEX_conflict_file.txt';
conflictFile=[prefix '\' suffix];
else
confgrps=[]; conflictFile=[];
end
%Name of file to write the CPLEX log information to. If empty, no log is
%written.
logfile=[];
%Name of a file to save the CPLEX problem object (Used for submitting
%possible bugs in CPLEX to ILOG)
savefile=[]; savemode=[];
% savefile='C:\CPLEX_possible_bug.txt';
% vector defining which callbacks to use in CPLEX. If the ith entry of the logical vector
% callback is set, the corresponding callback is defined. The callback calls the m-file specified
% in Table 7 below. The user may edit this file, or make a new copy, which is put in a directory
% that is searched before the cplex directory in the Matlab path.
callback=[]; %I'm not really sure what this option means as yet
%this is not a tomlab problem so this is not needed
Prob=[];
% variables not used in LP problems
IntVars=[]; PI=[]; SC=[]; SI=[]; sos1=[]; sos2=[];
%quadratic constraint matrix, size n x n
if sum(minNorm)~=0
if length(minNorm)==1
% same weighting of min norm for all variables
F=speye(length(c))*minNorm;
else
if length(minNorm)~=length(c)
error('Either minNorm is a scalar, or is an n x 1 vector')
else
% individual weighting of min norm for all variables
F=spdiags(minNorm,0,length(c),length(c));
end
end
else
F=[];
end
%Structure array defining quadratic constraints
qc=[];
%Structure telling whether and how you want CPLEX to perform a sensitivity analysis (SA).
%This may be useful in future but probably will have more meaning with an
%additional term in the objective
saRequest =[];
%Vector with MIP starting solution, if known
xIP=[];
%Logical constraints, i.e. an additional set of single-sided linear constraints that are controlled
%by a binary variable (switch) in the problem
logcon=[];
%call cplex
tic;
%tic;
%by default use the complex ILOG-CPLEX interface
ILOGcomplex=1;
tomlab_cplex=0; %by default DO NOT use the tomlab_cplex interface
if ~isempty(which('cplexlp')) && tomlab_cplex==0
if ILOGcomplex
%complex ibm ilog cplex interface
if ~isempty(csense)
%set up constant vectors for CPLEX
b_L(csense == 'E',1) = b(csense == 'E');
b_U(csense == 'E',1) = b(csense == 'E');
b_L(csense == 'G',1) = b(csense == 'G');
b_U(csense == 'G',1) = Inf;
b_L(csense == 'L',1) = -Inf;
b_U(csense == 'L',1) = b(csense == 'L');
else
b_L = b;
b_U = b;
end
% Initialize the CPLEX object
try
ILOGcplex = Cplex('fba');
catch ME
error('CPLEX not installed or licence server not up')
end
ILOGcplex.Model.sense = 'minimize';
% Now populate the problem with the data
ILOGcplex.Model.obj = c;
ILOGcplex.Model.lb = x_L;
ILOGcplex.Model.ub = x_U;
if isfield(ILOGcplex.Model,'S')
ILOGcplex.Model.A = LPproblem.S;
elseif isfield(ILOGcplex.Model,'A')
ILOGcplex.Model.A = LPproblem.A;
end
ILOGcplex.Model.lhs = b_L;
ILOGcplex.Model.rhs = b_U;
if ~isempty(F)
%quadratic constraint matrix, size n x n
ILOGcplex.Model.Q=F;
end
if ~isempty(cpxControl)
if isfield(cpxControl,'LPMETHOD')
%set the solver
ILOGcplex.Param.lpmethod.Cur=cpxControl.LPMETHOD;
end
end
if printLevel==0
ILOGcplex.DisplayFunc=[];
else
%print level
ILOGcplex.Param.barrier.display.Cur = printLevel;
ILOGcplex.Param.simplex.display.Cur = printLevel;
ILOGcplex.Param.sifting.display.Cur = printLevel;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%% EDITED BY GF >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
% |---------------------------|
% | SCALING (PRECONDITIONING) |
% |---------------------------|
% Sometimes it can happen that the solver finds a solution, but
% because of bad scaling (preconditioning) it does not return the
% actual solution to the user, but an empty solution instead.
% |-------------------------------------------|
% | Value : Meaning |
% |-------------------------------------------|
% | -1 : No scaling |
% | 0 : Equilibration scaling |
% | 1 : More aggressive scaling (default) |
% |-------------------------------------------|
% To avoid this, we change the default of these parameter to no
% scaling:
if ~exist('scalPar','var') || isempty(scalPar)
% LCSB default
scalPar = -1;
else
if ~ismember(scalPar,[-1 0 1])
error('Parameter value out of range!')
end
end
ILOGcplex.Param.read.scale.Cur = scalPar;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% |-----------------------|
% | FEASIBILITY TOLERANCE |
% |-----------------------|
% Specifies the feasibility tolerance, that is, the degree to which
% values of the basic variables calculated by the simplex method may
% violate their bounds. CPLEX? does not use this tolerance to relax the
% variable bounds nor to relax right hand side values. This parameter
% specifies an allowable violation. Feasibility influences the selection
% of an optimal basis and can be reset to a higher value when a problem is
% having difficulty maintaining feasibility during optimization. You can
% also lower this tolerance after finding an optimal solution if there is
% any doubt that the solution is truly optimal. If the feasibility tolerance
% is set too low, CPLEX may falsely conclude that a problem is infeasible.
% If you encounter reports of infeasibility during Phase II of the
% optimization, a small adjustment in the feasibility tolerance may
% improve performance.
% |-------------------------------------------|
% | Values : |
% |-------------------------------------------|
% | Range : from 1e-9 to 1e-1 |
% | Cplex-Default: 1e-06 |
% |-------------------------------------------|
if ~exist('feasTol','var') || isempty(feasTol)
% LCSB default
feasTol = 1e-9;
else
if feasTol < 1e-9 || feasTol > 1e-1
error('Parameter value out of range!')
end
end
ILOGcplex.Param.simplex.tolerances.feasibility.Cur = feasTol;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% |-----------------------|
% | EMPHASIS ON PRECISION |
% |-----------------------|
% Emphasizes precision in numerically unstable or difficult problems.
% This parameter lets you specify to CPLEX that it should emphParasize
% precision in numerically difficult or unstable problems, with
% consequent performance trade-offs in time and memory.
% |-----------------------------------------------------------|
% | Values : Meaning |
% |-----------------------------------------------------------|
% | 0 : Do not emphasize numerical precision; cplex-default |
% | 1 : Exercise extreme caution in computation |
% |-----------------------------------------------------------|
if ~exist('emphPar','var') || isempty(emphPar)
% LCSB default
emphPar = 1;
else
if ~ismember(emphPar,[0 1])
error('Parameter value out of range!')
end
end
ILOGcplex.Param.emphasis.numerical.Cur = emphPar;
%<<<<<<<<<<<<<< EDITED BY GF %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Optimize the problem
ILOGcplex.solve();
if isfield(ILOGcplex.Solution, 'objval')
solution.obj = osense*ILOGcplex.Solution.objval;
solution.full = ILOGcplex.Solution.x;
solution.rcost = ILOGcplex.Solution.reducedcost;
solution.dual = ILOGcplex.Solution.dual;
solution.nInfeas = NaN;
solution.sumInfeas = NaN;
%solution.stat = ILOGcplex.Solution.
solution.origStat = ILOGcplex.Solution.status;
solution.solver = ILOGcplex.Solution.method;
solution.time = ILOGcplex.Solution.time;
else
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%% EDITED BY GF >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
% I got this from somebody elses code, and thought it is a good
% idea to avoid crashing if it is infeasible
solution.obj = [];
solution.full = [];
solution.rcost = [];
solution.dual = [];
solution.nInfeas = NaN;
solution.sumInfeas = NaN;
%solution.stat = ILOGcplex.Solution.
solution.origStat = [];
solution.solver = [];
solution.time = [];
end
%<<<<<<<<<<<<<< EDITED BY GF %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
else
try
ILOGcplex = Cplex('fba');
catch ME
error('CPLEX not installed or licence server not up')
end
%simple ibm ilog cplex interface
options = cplexoptimset;
switch printLevel
case 0
options = cplexoptimset(options,'Display','off');
case 1
options = cplexoptimset(options,'Display','off');
case 1
options = cplexoptimset(options,'Display','off');
case 1
options = cplexoptimset(options,'Display','off');
end
if ~isempty(csense)
if sum(minNorm)~=0
Aineq = [LPproblem.A(csense == 'L',:); - LPproblem.A(csense == 'G',:)];
bineq = [b(csense == 'L',:); - b(csense == 'G',:)];
% min 0.5*x'*H*x+f*x or f*x
% st. Aineq*x <= bineq
% Aeq*x = beq
% lb <= x <= ub
[x,fval,exitflag,output,lambda] = cplexqp(F,c,Aineq,bineq,LPproblem.A(csense == 'E',:),b(csense == 'E',1),x_L,x_U,[],options);
else
Aineq = [LPproblem.A(csense == 'L',:); - LPproblem.A(csense == 'G',:)];
bineq = [b(csense == 'L',:); - b(csense == 'G',:)];
% min c*x
% st. Aineq*x <= bineq
% Aeq*x = beq
% lb <= x <= ub
[x,fval,exitflag,output,lambda] = cplexlp(c,Aineq,bineq,LPproblem.A(csense == 'E',:),b(csense == 'E',1),x_L,x_U,[],options);
end
%primal
solution.obj=osense*fval;
solution.full=x;
%this is the dual to the equality constraints but it's not the chemical potential
solution.dual=lambda.eqlin;
else
Aineq=[];
bineq=[];
if sum(minNorm)~=0
[x,fval,exitflag,output,lambda] = cplexqp(F,c,Aineq,bineq,LPproblem.A,b,x_L,x_U,[],options);
else
[x,fval,exitflag,output,lambda] = cplexlp(c,Aineq,bineq,LPproblem.A,b,x_L,x_U,[],options);
end
solution.obj=osense*fval;
solution.full=x;
%this is the dual to the equality constraints but it's not the chemical potential
solution.dual=sparse(size(LPproblem.A,1),1);
solution.dual(csense == 'E')=lambda.eqlin;
%this is the dual to the inequality constraints but it's not the chemical potential
solution.dual(csense == 'L')=lambda.ineqlin(1:nnz(csense == 'L'),1);
solution.dual(csense == 'G')=lambda.ineqlin(nnz(csense == 'L')+1:end,1);
end
%this is the dual to the simple ineequality constraints : reduced costs
solution.rcost=lambda.lower-lambda.upper;
solution.nInfeas = [];
solution.sumInfeas = [];
solution.origStat = output.cplexstatus;
end
%1 = (Simplex or Barrier) Optimal solution is available.
Inform = solution.origStat;
else
%tomlab cplex interface
if ~isempty(csense)
%set up constant vectors for CPLEX
b_L(csense == 'E',1) = b(csense == 'E');
b_U(csense == 'E',1) = b(csense == 'E');
b_L(csense == 'G',1) = b(csense == 'G');
b_U(csense == 'G',1) = Inf;
b_L(csense == 'L',1) = -Inf;
b_U(csense == 'L',1) = b(csense == 'L');
else
b_L = b;
b_U = b;
end
%tomlab cplex interface
% minimize 0.5 * x'*F*x + c'x subject to:
% x x_L <= x <= x_U
% b_L <= Ax <= b_U
[x, slack, v, rc, f_k, ninf, sinf, Inform, basis] = cplex(c, LPproblem.A, x_L, x_U, b_L, b_U, ...
cpxControl, callback, printLevel, Prob, IntVars, PI, SC, SI, ...
sos1, sos2, F, logfile, savefile, savemode, qc, ...
confgrps, conflictFile, saRequest, basis, xIP, logcon);
solution.full=x;
%this is the dual to the equality constraints but it's not the chemical potential
solution.dual=v;
%this is the dual to the simple ineequality constraints : reduced costs
solution.rcost=rc;
if Inform~=1
solution.obj = NaN;
else
if minNorm==0
solution.obj=f_k*osense;
else
solution.obj=c'*x*osense;
end
% solution.obj
% norm(x)
end
solution.nInfeas = ninf;
solution.sumInfeas = sinf;
solution.origStat = Inform;
end
%timeTaken=toc;
timeTaken=NaN;
if Inform~=1 && ~isempty(which('cplex'))
if conflictResolve ==1
if isfield(LPproblem,'mets') && isfield(LPproblem,'rxns')
%this code reads the conflict resolution file and replaces the
%arbitrary names with the abbreviations of metabolites and reactions
[nMet,nRxn]=size(LPproblem.A);
totAbbr=nMet+nRxn;
conStrFind=cell(nMet+nRxn,1);
conStrReplace=cell(nMet+nRxn,1);
%only equality constraint rows
for m=1:nMet
conStrFind{m,1}=['c' int2str(m) ':'];
conStrReplace{m,1}=[LPproblem.mets{m} ': '];
end
%reactions
for n=1:nRxn
conStrFind{nMet+n,1}=['x' int2str(n) ' '];
conStrReplace{nMet+n,1}=[LPproblem.rxns{n} ' '];
end
fid1 = fopen(suffix);
fid2 = fopen(['COBRA_' suffix], 'w');
while ~feof(fid1)
tline{1}=fgetl(fid1);
%replaces all occurrences of the string str2 within string str1
%with the string str3.
%str= strrep(str1, str2, str3)
for t=1:totAbbr
tline= strrep(tline, conStrFind{t}, conStrReplace{t});
end
fprintf(fid2,'%s\n', tline{1});
end
fclose(fid1);
fclose(fid2);
%delete other file without replacements
% delete(suffix)
else
warning('Need reaction and metabolite abbreviations in order to make a readable conflict resolution file');
end
fprintf('%s\n',['Conflict resolution file written to: ' prefix '\COBRA_' suffix]);
fprintf('%s\n%s\n','The Conflict resolution file gives an irreducible infeasible subset ','of constraints which are making this LP Problem infeasible');
else
if printLevel>0
fprintf('%s\n','No conflict resolution file. Perhaps set conflictResolve = 1 next time.');
end
end
solution.solver = 'cplex_direct';
end
% Try to give back COBRA Standardized solver status:
% 1 Optimal solution
% 2 Unbounded solution
% 0 Infeasible
% -1 No solution reported (timelimit, numerical problem etc)
if Inform==1
solution.stat = 1;
if printLevel>0
%use tomlab code to print out exit meassage
% [ExitText,ExitFlag] = cplexStatus(Inform);
% solution.ExitText=ExitText;
% solution.ExitFlag=ExitFlag;
% fprintf('\n%s%g\n',[ExitText ', Objective '], c'*solution.full*osense);
end
else
if Inform==2
solution.stat = 2;
%use tomlab code to print out exit meassage
% [ExitText,ExitFlag] = cplexStatus(Inform);
% solution.ExitText=ExitText;
% solution.ExitFlag=ExitFlag;
% fprintf('\n%s%g\n',[ExitText ', Objective '], c'*solution.full*osense);
else
if Inform==3
solution.stat = 0;
else
%this is a conservative view
solution.stat = -1;
%use tomlab code to print out exit meassage
% [ExitText,ExitFlag] = cplexStatus(Inform);
% solution.ExitText=ExitText;
% solution.ExitFlag=ExitFlag;
% fprintf('\n%s%g\n',[ExitText ', Objective '], c'*solution.full*osense);
end
end
end
solution.time = timeTaken;
%return basis
if basisReuse
LPproblem.LPBasis=basis;
end
if sum(minNorm)~=0
fprintf('%s\n','This objective corresponds to a flux with minimum Euclidean norm.');
fprintf('%s%d%s\n','The weighting for minimising the norm was ',minNorm,'.');
fprintf('%s\n','Check that the objective is the same without minimising the norm.');
end
end
function [solution,LPproblem] = solveCobraLPGurobi(LPproblem,printLevel,basisReuse,conflictResolve,contFunctName,minNorm,scalPar,feasTol,emphPar)
%% gurobi5 / gurobi_direct
% 2017/04/26 Pierre: Adding this as part of an effort to ad dgurobi hooks
% in our functions. Adapted code from cobra/OptimizeCbModel.m
% TODO: Add the same level of control as with the CPLEX interface written
% by Georgios Fengos
% Free academic licenses for the Gurobi solver can be obtained from
% http://www.gurobi.com/html/academic.html
solution = struct('x',[],'objval',[],'pi',[]);
LPproblem.A = deal(sparse(LPproblem.A));
clear params % Use the default parameter settings
if printLevel == 0
params.OutputFlag = 0;
params.DisplayInterval = 1;
else
params.OutputFlag = 1;
params.DisplayInterval = 5;
end
if exist('feasTol','var') & ~isempty(feasTol)
params.FeasibilityTol = feasTol;
end
% params.OptimalityTol = optTol;
if (isempty(LPproblem.csense))
clear LPproblem.csense
LPproblem.csense(1:length(b),1) = '=';
else
LPproblem.csense(LPproblem.csense == 'L') = '<';
LPproblem.csense(LPproblem.csense == 'G') = '>';
LPproblem.csense(LPproblem.csense == 'E') = '=';
LPproblem.csense = LPproblem.csense(:);
end
if LPproblem.osense == -1
LPproblem.osense = 'max';
else
LPproblem.osense = 'min';
end
LPproblem.modelsense = LPproblem.osense;
[LPproblem.rhs,LPproblem.obj,LPproblem.sense] = deal(LPproblem.b,double(LPproblem.c),LPproblem.csense);
solution = gurobi(LPproblem,params);
% if strcmp(solution.status,'OPTIMAL')
% stat = 1; % Optimal solution found
% [x,f,y] = deal(solution.x,solution.objval,solution.pi);
% elseif strcmp(solution.status,'INFEASIBLE')
% stat = 0; % Infeasible
% elseif strcmp(solution.status,'UNBOUNDED')
% stat = 2; % Unbounded
% elseif strcmp(solution.status,'INF_OR_UNBD')
% stat = 0; % Gurobi reports infeasible *or* unbounded
% else
% stat = -1; % Solution not optimal or solver problem
% end
end
|
github
|
EPFL-LCSB/matTFA-master
|
splitString.m
|
.m
|
matTFA-master/matTFA/utilities/splitString.m
| 1,729 |
utf_8
|
d9ebd7e1d412e1d0b9832c5f9c1f89f6
|
function fields = splitString(string,delimiter)
%splitString Splits a string Perl style
%
% fields = splitString(string,delimiter)
%
% string Either a single string or a cell array of strings
% delimiter Splitting delimiter
%
% fields Either a single cell array of fields or a cell array of cell
% arrays of fields
%
% Default delimiter is '\s' (whitespace)
% Delimiters are perl regular expression style, e.g. '|' has to be expressed
% as '\|'
% Results are returned in the cell array fields
%
% 07/14/04 Markus Herrgard
if (nargin < 2)
delimiter = '\s';
end
% Check if this is a list of strings or just a single string
if iscell(string)
stringList = string;
for i = 1:length(stringList)
fields{i} = splitOneString(stringList{i},delimiter);
end
else
fields = splitOneString(string,delimiter);
end
fields = columnVector(fields);
%%
function fields = splitOneString(string,delimiter)
% Internal function that splits one string
[startIndex,endIndex] = regexp(string,delimiter);
if (~isempty(startIndex))
cnt = 0;
for i = 1:length(startIndex)+1
if (i == 1)
if (endIndex(i) > 1)
cnt = cnt + 1;
fields{cnt} = string(1:endIndex(i)-1);
end
elseif (i == length(startIndex)+1)
if (startIndex(i-1) < length(string))
cnt = cnt + 1;
fields{cnt} = string(startIndex(i-1)+1:end);
end
else
cnt = cnt + 1;
fields{cnt} = string(startIndex(i-1)+1:endIndex(i)-1);
end
end
else
fields{1} = string;
end
fieldsOut = {};
cnt = 0;
for i = 1:length(fields)
if (~isempty(fields{i}))
cnt = cnt+1;
fieldsOut{cnt} = fields{i};
end
end
fields = fieldsOut;
|
github
|
EPFL-LCSB/matTFA-master
|
strescape.m
|
.m
|
matTFA-master/matTFA/utilities/MatlabBuiltInFunctions/strescape.m
| 1,148 |
utf_8
|
e50bfb2ad948fb14d6732ec00fbd2b6a
|
function escapedStr = strescape(str)
%STRESCAPE Escape control character sequences in a string.
% STRESCAPE(STR) converts the escape sequences in a string to the values
% they represent.
%
% Example:
%
% strescape('Hello World\n')
%
% See also SPRINTF.
% Copyright 2012 The MathWorks, Inc.
escapeFcn = @escapeChar; %#ok<NASGU>
escapedStr = regexprep(str, '\\(.|$)', '${escapeFcn($1)}');
end
%--------------------------------------------------------------------------
function c = escapeChar(c)
switch c
case '0' % Null.
c = char(0);
case 'a' % Alarm.
c = char(7);
case 'b' % Backspace.
c = char(8);
case 'f' % Form feed.
c = char(12);
case 'n' % New line.
c = char(10);
case 'r' % Carriage return.
c = char(13);
case 't' % Horizontal tab.
c = char(9);
case 'v' % Vertical tab.
c = char(11);
case '\' % Backslash.
case '' % Unescaped trailing backslash.
c = '\';
otherwise
warning(message('MATLAB:strescape:InvalidEscapeSequence', c, c));
end
end
|
github
|
EPFL-LCSB/matTFA-master
|
strsplit.m
|
.m
|
matTFA-master/matTFA/utilities/MatlabBuiltInFunctions/strsplit.m
| 4,356 |
utf_8
|
27145ac2a6cf2a3d7f3e9c0f300d34e3
|
function [c, matches] = strsplit(str, aDelim, varargin)
%STRSPLIT Split string at delimiter
% C = STRSPLIT(S) splits the string S at whitespace into the cell array
% of strings C.
%
% C = STRSPLIT(S, DELIMITER) splits S at DELIMITER into C. DELIMITER can
% be a string or a cell array of strings. If DELIMITER is a cell array of
% strings, STRSPLIT splits S along the elements in DELIMITER, in the
% order in which they appear in the cell array.
%
% C = STRSPLIT(S, DELIMITER, PARAM1, VALUE1, ... PARAMN, VALUEN) modifies
% the way in which S is split at DELIMITER.
% Valid parameters are:
% 'CollapseDelimiters' - If true (default), consecutive delimiters in S
% are treated as one. If false, consecutive delimiters are treated as
% separate delimiters, resulting in empty string '' elements between
% matched delimiters.
% 'DelimiterType' - DelimiterType can have the following values:
% 'Simple' (default) - Except for escape sequences, STRSPLIT treats
% DELIMITER as a literal string.
% 'RegularExpression' - STRSPLIT treats DELIMITER as a regular
% expression.
% In both cases, DELIMITER can include the following escape
% sequences:
% \\ Backslash
% \0 Null
% \a Alarm
% \b Backspace
% \f Form feed
% \n New line
% \r Carriage return
% \t Horizontal tab
% \v Vertical tab
%
% [C, MATCHES] = STRSPLIT(...) also returns the cell array of strings
% MATCHES containing the DELIMITERs upon which S was split. Note that
% MATCHES always contains one fewer element than C.
%
% Examples:
%
% str = 'The rain in Spain stays mainly in the plain.';
%
% % Split on all whitespace.
% strsplit(str)
% % {'The', 'rain', 'in', 'Spain', 'stays',
% % 'mainly', 'in', 'the', 'plain.'}
%
% % Split on 'ain'.
% strsplit(str, 'ain')
% % {'The r', ' in Sp', ' stays m', 'ly in the pl', '.'}
%
% % Split on ' ' and on 'ain' (treating multiple delimiters as one).
% strsplit(str, {' ', 'ain'})
% % ('The', 'r', 'in', 'Sp', 'stays',
% % 'm', 'ly', 'in', 'the', 'pl', '.'}
%
% % Split on all whitespace and on 'ain', and treat multiple
% % delimiters separately.
% strsplit(str, {'\s', 'ain'}, 'CollapseDelimiters', false, ...
% 'DelimiterType', 'RegularExpression')
% % {'The', 'r', '', 'in', 'Sp', '', 'stays',
% % 'm', 'ly', 'in', 'the', 'pl', '.'}
%
% See also REGEXP, STRFIND, STRJOIN.
% Copyright 2012-2014 The MathWorks, Inc.
narginchk(1, Inf);
% Initialize default values.
collapseDelimiters = true;
delimiterType = 'Simple';
% Check input arguments.
if ~ischar(str)
error(message('MATLAB:strsplit:InvalidStringType'));
end
if nargin < 2
delimiterType = 'RegularExpression';
aDelim = {'\s'};
elseif ischar(aDelim)
aDelim = {aDelim};
elseif ~iscellstr(aDelim)
error(message('MATLAB:strsplit:InvalidDelimiterType'));
end
if nargin > 2
funcName = mfilename;
p = inputParser;
p.FunctionName = funcName;
p.addParameter('CollapseDelimiters', collapseDelimiters);
p.addParameter('DelimiterType', delimiterType);
p.parse(varargin{:});
collapseDelimiters = verifyScalarLogical(p.Results.CollapseDelimiters, ...
funcName, 'CollapseDelimiters');
delimiterType = validatestring(p.Results.DelimiterType, ...
{'RegularExpression', 'Simple'}, funcName, 'DelimiterType');
end
% Handle DelimiterType.
if strcmp(delimiterType, 'Simple')
% Handle escape sequences and translate.
aDelim = strescape(aDelim);
aDelim = regexptranslate('escape', aDelim);
else
% Check delimiter for regexp warnings.
regexp('', aDelim, 'warnings');
end
% Handle multiple delimiters.
aDelim = strjoinTGL(aDelim, '|');
% Handle CollapseDelimiters.
if collapseDelimiters
aDelim = ['(?:', aDelim, ')+'];
end
% Split.
[c, matches] = regexp(str, aDelim, 'split', 'match');
end
%--------------------------------------------------------------------------
function tf = verifyScalarLogical(tf, funcName, parameterName)
if isscalar(tf) && isnumeric(tf) && any(tf == [0, 1])
tf = logical(tf);
else
validateattributes(tf, {'logical'}, {'scalar'}, funcName, parameterName);
end
end
|
github
|
EPFL-LCSB/matTFA-master
|
generateDoc.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/generateDoc.m
| 3,858 |
utf_8
|
fdb222d907785762dddb4a82c06b02f7
|
function generateDoc(pathname, graph)
%generateDoc uses m2html to create a set of html docs
%in the cba toolbox and place them in a directory called 'docs'.
%
% generateDoc(pathname, graph)
%
%OPTIONAL INPUTS
% pathname Path to folder to generate documents for
% graph Generate function dependcy graph (Default = off) Set to 'on'
%
%If the directory 'docs' exists, the user will be prompted
%for notice that the contents of the directory will be
%replaced with a new set of generated docs.
%
%This routine will exit if the user does not agree with this.
%If the directory 'docs' does not exist, then it will be created.
%
%generateDoc uses m2html, therefore m2html must be in the path.
%m2html will be located in the cba toolbox and added to the path
%if not found on the path.
%
% Wing Choi 1/17/08
% Richard Que (8/06/2010)
saveDir = pwd;
%BUGFIX: Updated to work on Unix systems in addition to MS Windows
%Do not remove this unless you've validated that your changes function
%on Mac OS X and GNU/Linux
if filesep == '/'
cbaDir = filesep;
else
cbaDir = '';
end
dN = '';
%locate the cbaToolbox from where matlab finds generateDoc
mFilePath = mfilename('fullpath');
cbaDir = mFilePath(1:end-length(mfilename)-1);
cd(cbaDir);
%if pathname was not an input argument
currentDir = pwd;
if(nargin<1)||isempty(pathname)
% parse out the current dir name, not the entire path
display (' ');
display(strcat('Creating html docs for --> ' , ' ' , currentDir));
reply = input('is this ok? y/n [n]: ', 's');
if ((isempty(reply)) || (reply ~= 'y'))
cd(saveDir);
return;
end
else
cbaDir = pathname;
end
%Get Directory Name
remain = currentDir;
while true
[str, remain] = strtok(remain,filesep);
if isempty(str), break; end
dirName = str;
end
if (exist('m2html','file') ~= 2)
disp('m2html not found, adding it to path');
addpath(strcat(cbaDir,filesep,'external',filesep,'m2html')); %changed to reflect new folder structure
end
if (isdir('docs'))
display ('The docs directory already exists')
display ('I will remove the existing docs directory')
display ('and replace its entire contents with newly')
display ('generated html docs.')
display (' ');
reply = input('Do you want to replace the contents of the directory? y/n [n]: ', 's');
if ((isempty(reply)) || (reply ~= 'y'))
cd(saveDir);
return;
end
end
preDirName = cbaDir(1:end-length(dirName));
if(nargin<2)||~strcmp(graph, 'on')
dirNames = getDir(cbaDir,{'.svn','obsolete','docs','private','@template','toolboxes','internal','testing'});
for i=1:length(dirNames), dirNames{i} = strrep(dirNames{i},preDirName,''); end
cd ..;
m2html('mfiles',dirNames,'htmldir',strcat(dirName,filesep,'docs'),'recursive','off', 'global','on','template','frame', 'index','menu', 'globalHypertextLinks', 'on');
else
dirNames = getDir(cbaDir,{'.svn','obsolete','docs','private','@template','internal','toolboxes','testing'});
for i=1:length(dirNames), dirNames{i} = strrep(dirNames{i},preDirName,''); end
% go up one dir
cd ..;
% call m2html
m2html('mfiles', dirNames, 'htmldir',strcat(dirName,filesep,'docs'),'recursive','off', 'global','on','template','frame', 'index','menu', 'globalHypertextLinks', 'on', 'graph', 'on');
end
% cd back to saveDir again
cd(saveDir);
function directories = getDir(directory,ignore)
%Get list of directories beneath the specified directory
directories = {directory};
currDir = dir([directory,filesep,'*']);
currDir = {currDir([currDir.isdir]).name};
currDir = currDir(~ismember(currDir,{'.','..',ignore{:}}));
%Loop through the directory list and recursively call this function
for i = 1:length(currDir)
tmp = getDir([directory,filesep,currDir{i}],ignore);
tmp = columnVector(tmp);
directories = [directories; tmp(:)];
end
|
github
|
EPFL-LCSB/matTFA-master
|
solveFBAmodelCplex.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/solveFBAmodelCplex.m
| 28,006 |
utf_8
|
6478764de59239a1782fac0520b6dc20
|
function FBAsolution = solveFBAmodelCplex(model, scalPar, feasTol, emphPar, osenseStr)
%optimizeCbModel Solve a flux balance analysis problem
%
% Georgios Fengos 24/05/2016 Created this version of optimizeCbModel
% to be able to control externally the cplex parameters
%% Process arguments and set up problem
if ~exist('osenseStr','var')
osenseStr = 'max';
end
allowLoops = true;
if ~exist('scalPar','var') || isempty(scalPar)
scalPar = [];
end
if ~exist('feasTol','var') || isempty(feasTol)
feasTol = [];
end
if ~exist('emphPar','var') || isempty(emphPar)
emphPar = [];
end
[minNorm, printLevel, primalOnlyFlag, ~] = getCobraSolverParams('LP',{'minNorm','printLevel','primalOnly','saveInput'});
% Figure out objective sense
if strcmpi(osenseStr,'max')
LPproblem.osense = -1;
else
LPproblem.osense = +1;
end
[nMets,nRxns] = size(model.S);
% add csense
%Doing this makes csense a double array. Totally smart design move.
%LPproblem.csense = [];
if ~isfield(model,'csense')
% If csense is not declared in the model, assume that all
% constraints are equalities.
LPproblem.csense(1:nMets,1) = 'E';
else % if csense is in the model, move it to the lp problem structure
if length(model.csense)~=nMets,
warning('Length of csense is invalid! Defaulting to equality constraints.')
LPproblem.csense(1:nMets,1) = 'E';
else
model.csense = columnVector(model.csense);
LPproblem.csense = model.csense;
end
end
% Fill in the RHS vector if not provided
if (~isfield(model,'b'))
LPproblem.b = zeros(size(model.S,1),1);
else
LPproblem.b = model.b;
end
% Rest of the LP problem
LPproblem.A = model.S;
LPproblem.c = model.c;
LPproblem.lb = model.lb;
LPproblem.ub = model.ub;
%Double check that all inputs are valid:
if ~(verifyCobraProblem(LPproblem, [], [], false) == 1)
warning('invalid problem');
return;
end
%%
t1 = clock;
% Solve initial LP
% if allowLoops
solution = solveCobraLP_edited(LPproblem,scalPar,feasTol,emphPar);
% else
% MILPproblem = addLoopLawConstraints(LPproblem, model, 1:nRxns);
% solution = solveCobraMILP(MILPproblem);
% end
if (solution.stat ~= 1) % check if initial solution was successful.
if printLevel>0
warning('Optimal solution was not found');
end
FBAsolution.f = 0;
FBAsolution.x = [];
FBAsolution.stat = solution.stat;
FBAsolution.origStat = solution.origStat;
FBAsolution.solver = solution.solver;
FBAsolution.time = etime(clock, t1);
return;
end
objective = solution.obj; % save for later use.
% Store results
if (solution.stat == 1)
%solution found.
FBAsolution.x = solution.full(1:nRxns);
%this line IS necessary.
FBAsolution.f = model.c'*solution.full(1:nRxns); %objective from original optimization problem.
if abs(FBAsolution.f - objective) > .01
display('warning: objective appears to have changed while performing secondary optimization (minNorm)');
end
if (~primalOnlyFlag && allowLoops && any(~minNorm)) % rcost/dual only correct if not doing minNorm
FBAsolution.y = solution.dual;
FBAsolution.w = solution.rcost;
end
else
%some sort of error occured.
if printLevel>0
warning('Optimal solution was not found');
end
FBAsolution.f = 0;
FBAsolution.x = [];
end
FBAsolution.stat = solution.stat;
FBAsolution.origStat = solution.origStat;
FBAsolution.solver = solution.solver;
FBAsolution.time = etime(clock, t1);
end
function solution = solveCobraLP_edited(LPproblem,scalPar,feasTol,emphPar)
% solveCobraLP Solve constraint-based LP problems
% Georgios Fengos 24/05/2016 Created this version of solveCobraLP
% to be able to control externally the cplex parameters
global CBTLPSOLVER
if (~isempty(CBTLPSOLVER))
solver = CBTLPSOLVER;
else
error('No solver found. call changeCobraSolver(solverName)');
end
optParamNames = {'minNorm','printLevel','primalOnly','saveInput', ...
'feasTol','optTol','EleNames','EqtNames','VarNames','EleNameFun', ...
'EqtNameFun','VarNameFun','PbName','MPSfilename'};
parameters = '';
% if nargin ~=1
% if mod(length(varargin),2)==0
% for i=1:2:length(varargin)-1
% if ismember(varargin{i},optParamNames)
% parameters.(varargin{i}) = varargin{i+1};
% else
% error([varargin{i} ' is not a valid optional parameter']);
% end
% end
% elseif strcmp(varargin{1},'default')
% parameters = 'default';
% elseif isstruct(varargin{1})
% parameters = varargin{1};
% else
% display('Warning: Invalid number of parameters/values')
% solution=[];
% return;
% end
% end
[minNorm, printLevel, ~, saveInput, ~, ~] = ...
getCobraSolverParams('LP',optParamNames(1:6),parameters);
%Save Input if selected
if ~isempty(saveInput)
fileName = parameters.saveInput;
if ~find(regexp(fileName,'.mat'))
fileName = [fileName '.mat'];
end
display(['Saving LPproblem in ' fileName]);
save(fileName,'LPproblem')
end
% [A,b,c,lb,ub,csense,osense] = deal(LPproblem.A,LPproblem.b,LPproblem.c,LPproblem.lb,LPproblem.ub,LPproblem.csense,LPproblem.osense);
% if any(any(~isfinite(A)))
% error('Cannot perform LP on a stoichiometric matrix with NaN of Inf coefficents.')
% end
% Defaults in case the solver does not return anything
f = [];
x = [];
y = [];
w = [];
origStat = -99;
stat = -99;
t_start = clock;
switch solver
case 'cplex_direct'
%% Tomlab cplex.m direct
%Used with the current script, only some of the control affoarded with
%this interface is provided. Primarily, this is to change the print
%level and whether to minimise the Euclidean Norm of the internal
%fluxes or not.
%See solveCobraLPCPLEX.m for more refined control of cplex
%Ronan Fleming 11/12/2008
if isfield(LPproblem,'basis') && ~isempty(LPproblem.basis)
LPproblem.LPBasis = LPproblem.basis;
end
[solution LPprob] = solveCobraLPCPLEX_edited(LPproblem,printLevel,1,[],[],minNorm,scalPar,feasTol,emphPar);
solution.basis = LPprob.LPBasis;
solution.solver = solver;
otherwise
error(['Unknown solver: ' solver]);
end
if ~strcmp(solver,'cplex_direct') && ~strcmp(solver,'mps')
%% Assign solution
t = etime(clock, t_start);
if ~exist('basis','var'), basis=[]; end
[solution.full,solution.obj,solution.rcost,solution.dual,solution.solver,solution.stat,solution.origStat,solution.time,solution.basis] = ...
deal(x,f,w,y,solver,stat,origStat,t,basis);
end
end
function [solution,LPProblem] = solveCobraLPCPLEX_edited(LPProblem,printLevel,basisReuse,conflictResolve,contFunctName,minNorm,scalPar,feasTol,emphPar)
% [solution,LPProblem]=solveCobraLPCPLEX(LPProblem,printLevel,basisReuse,conflictResolve,contFunctName,minNorm)
% Georgios Fengos 24/05/2016 Created this version of solveCobraLPCPLEX
% to be able to control externally the cplex parameters
if ~exist('printLevel','var')
printLevel=2;
end
if ~exist('basisReuse','var')
basisReuse=0;
end
if ~exist('conflictResolve','var')
conflictResolve=0;
end
if ~exist('contFunctName','var')
cpxControl=[];
else
if isstruct(contFunctName)
cpxControl=contFunctName;
else
if ~isempty(contFunctName)
%calls a user specified function to create a CPLEX control structure
%specific to the users problem. A TEMPLATE for one such function is
%CPLEXParamSet
cpxControl=eval(contFunctName);
else
cpxControl=[];
end
end
end
if ~exist('minNorm','var')
minNorm=0;
end
if basisReuse
if isfield(LPProblem,'LPBasis')
basis=LPProblem.LPBasis;
%use advanced starting information when optimization is initiated.
cpxControl.ADVIND=1;
else
basis=[];
end
else
basis=[];
%do not use advanced starting information when optimization is initiated.
cpxControl.ADVIND=0;
end
if ~isfield(LPProblem,'A')
if ~isfield(LPProblem,'S')
error('Equality constraint matrix must either be a field denoted A or S.')
end
LPProblem.A=LPProblem.S;
end
if ~isfield(LPProblem,'csense')
nMet=size(LPProblem.A);
if printLevel>0
fprintf('%s\n','Assuming equality constraints, i.e. S*v=b');
end
%assuming equality constraints
LPProblem.csense(1:nMet,1)='E';
end
if ~isfield(LPProblem,'osense')
%assuming maximisation
LPProblem.osense=-1;
if printLevel>0
fprintf('%s\n','Assuming maximisation of objective');
end
end
%get data
[c,x_L,x_U,b,csense,osense] = deal(LPProblem.c,LPProblem.lb,LPProblem.ub,LPProblem.b,LPProblem.csense,LPProblem.osense);
%modify objective to correspond to osense
c=full(c*osense);
%cplex expects it dense
b=full(b);
%Conflict groups descriptor (cpxBuildConflict can be used to generate the input). Set this if
%conflict refinement is desired in the case that infeasibility is detected
%by CPLEX.
if conflictResolve
[m_lin,n]=size(LPProblem.A);
m_quad=0;
m_sos=0;
m_log=0;
%determines how elaborate the output is
mode='full';%'minimal';
fprintf('%s\n%s\n','Building Structure for Conflict Resolution...','...this slows CPLEX down so should not be used for repeated LP');
confgrps = cpxBuildConflict(n,m_lin,m_quad,m_sos,m_log,mode);
prefix=pwd;
suffix='LP_CPLEX_conflict_file.txt';
conflictFile=[prefix '\' suffix];
else
confgrps=[]; conflictFile=[];
end
%Name of file to write the CPLEX log information to. If empty, no log is
%written.
logfile=[];
%Name of a file to save the CPLEX problem object (Used for submitting
%possible bugs in CPLEX to ILOG)
savefile=[]; savemode=[];
% savefile='C:\CPLEX_possible_bug.txt';
% vector defining which callbacks to use in CPLEX. If the ith entry of the logical vector
% callback is set, the corresponding callback is defined. The callback calls the m-file specified
% in Table 7 below. The user may edit this file, or make a new copy, which is put in a directory
% that is searched before the cplex directory in the Matlab path.
callback=[]; %I'm not really sure what this option means as yet
%this is not a tomlab problem so this is not needed
Prob=[];
% variables not used in LP problems
IntVars=[]; PI=[]; SC=[]; SI=[]; sos1=[]; sos2=[];
%quadratic constraint matrix, size n x n
if sum(minNorm)~=0
if length(minNorm)==1
% same weighting of min norm for all variables
F=speye(length(c))*minNorm;
else
if length(minNorm)~=length(c)
error('Either minNorm is a scalar, or is an n x 1 vector')
else
% individual weighting of min norm for all variables
F=spdiags(minNorm,0,length(c),length(c));
end
end
else
F=[];
end
%Structure array defining quadratic constraints
qc=[];
%Structure telling whether and how you want CPLEX to perform a sensitivity analysis (SA).
%This may be useful in future but probably will have more meaning with an
%additional term in the objective
saRequest =[];
%Vector with MIP starting solution, if known
xIP=[];
%Logical constraints, i.e. an additional set of single-sided linear constraints that are controlled
%by a binary variable (switch) in the problem
logcon=[];
%call cplex
tic;
%tic;
%by default use the complex ILOG-CPLEX interface
ILOGcomplex=1;
tomlab_cplex=0; %by default DO NOT use the tomlab_cplex interface
if ~isempty(which('cplexlp')) && tomlab_cplex==0
if ILOGcomplex
%complex ibm ilog cplex interface
if ~isempty(csense)
%set up constant vectors for CPLEX
b_L(csense == 'E',1) = b(csense == 'E');
b_U(csense == 'E',1) = b(csense == 'E');
b_L(csense == 'G',1) = b(csense == 'G');
b_U(csense == 'G',1) = Inf;
b_L(csense == 'L',1) = -Inf;
b_U(csense == 'L',1) = b(csense == 'L');
else
b_L = b;
b_U = b;
end
% Initialize the CPLEX object
try
ILOGcplex = Cplex('fba');
catch ME
error('CPLEX not installed or licence server not up')
end
ILOGcplex.Model.sense = 'minimize';
% Now populate the problem with the data
ILOGcplex.Model.obj = c;
ILOGcplex.Model.lb = x_L;
ILOGcplex.Model.ub = x_U;
if isfield(ILOGcplex.Model,'S')
ILOGcplex.Model.A = LPProblem.S;
elseif isfield(ILOGcplex.Model,'A')
ILOGcplex.Model.A = LPProblem.A;
end
ILOGcplex.Model.lhs = b_L;
ILOGcplex.Model.rhs = b_U;
if ~isempty(F)
%quadratic constraint matrix, size n x n
ILOGcplex.Model.Q=F;
end
if ~isempty(cpxControl)
if isfield(cpxControl,'LPMETHOD')
%set the solver
ILOGcplex.Param.lpmethod.Cur=cpxControl.LPMETHOD;
end
end
if printLevel==0
ILOGcplex.DisplayFunc=[];
else
%print level
ILOGcplex.Param.barrier.display.Cur = printLevel;
ILOGcplex.Param.simplex.display.Cur = printLevel;
ILOGcplex.Param.sifting.display.Cur = printLevel;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%% EDITED BY GF >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
% |---------------------------|
% | SCALING (PRECONDITIONING) |
% |---------------------------|
% Sometimes it can happen that the solver finds a solution, but
% because of bad scaling (preconditioning) it does not return the
% actual solution to the user, but an empty solution instead.
% |-------------------------------------------|
% | Value : Meaning |
% |-------------------------------------------|
% | -1 : No scaling |
% | 0 : Equilibration scaling |
% | 1 : More aggressive scaling (default) |
% |-------------------------------------------|
% To avoid this, we change the default of these parameter to no
% scaling:
if ~exist('scalPar','var') || isempty(scalPar)
% LCSB default
scalPar = -1;
else
if ~ismember(scalPar,[-1 0 1])
error('Parameter value out of range!')
end
end
ILOGcplex.Param.read.scale.Cur = scalPar;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% |-----------------------|
% | FEASIBILITY TOLERANCE |
% |-----------------------|
% Specifies the feasibility tolerance, that is, the degree to which
% values of the basic variables calculated by the simplex method may
% violate their bounds. CPLEX? does not use this tolerance to relax the
% variable bounds nor to relax right hand side values. This parameter
% specifies an allowable violation. Feasibility influences the selection
% of an optimal basis and can be reset to a higher value when a problem is
% having difficulty maintaining feasibility during optimization. You can
% also lower this tolerance after finding an optimal solution if there is
% any doubt that the solution is truly optimal. If the feasibility tolerance
% is set too low, CPLEX may falsely conclude that a problem is infeasible.
% If you encounter reports of infeasibility during Phase II of the
% optimization, a small adjustment in the feasibility tolerance may
% improve performance.
% |-------------------------------------------|
% | Values : |
% |-------------------------------------------|
% | Range : from 1e-9 to 1e-1 |
% | Cplex-Default: 1e-06 |
% |-------------------------------------------|
if ~exist('feasTol','var') || isempty(feasTol)
% LCSB default
feasTol = 1e-9;
else
if feasTol < 1e-9 || feasTol > 1e-1
error('Parameter value out of range!')
end
end
ILOGcplex.Param.simplex.tolerances.feasibility.Cur = feasTol;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% |-----------------------|
% | EMPHASIS ON PRECISION |
% |-----------------------|
% Emphasizes precision in numerically unstable or difficult problems.
% This parameter lets you specify to CPLEX that it should emphParasize
% precision in numerically difficult or unstable problems, with
% consequent performance trade-offs in time and memory.
% |-----------------------------------------------------------|
% | Values : Meaning |
% |-----------------------------------------------------------|
% | 0 : Do not emphasize numerical precision; cplex-default |
% | 1 : Exercise extreme caution in computation |
% |-----------------------------------------------------------|
if ~exist('emphPar','var') || isempty(emphPar)
% LCSB default
emphPar = 1;
else
if ~ismember(emphPar,[0 1])
error('Parameter value out of range!')
end
end
ILOGcplex.Param.emphasis.numerical.Cur = emphPar;
%<<<<<<<<<<<<<< EDITED BY GF %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Optimize the problem
ILOGcplex.solve();
if isfield(ILOGcplex.Solution, 'objval')
solution.obj = osense*ILOGcplex.Solution.objval;
solution.full = ILOGcplex.Solution.x;
solution.rcost = ILOGcplex.Solution.reducedcost;
solution.dual = ILOGcplex.Solution.dual;
solution.nInfeas = NaN;
solution.sumInfeas = NaN;
%solution.stat = ILOGcplex.Solution.
solution.origStat = ILOGcplex.Solution.status;
solution.solver = ILOGcplex.Solution.method;
solution.time = ILOGcplex.Solution.time;
else
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%% EDITED BY GF >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
% I got this from somebody elses code, and thought it is a good
% idea to avoid crashing if it is infeasible
solution.obj = [];
solution.full = [];
solution.rcost = [];
solution.dual = [];
solution.nInfeas = NaN;
solution.sumInfeas = NaN;
%solution.stat = ILOGcplex.Solution.
solution.origStat = [];
solution.solver = [];
solution.time = [];
end
%<<<<<<<<<<<<<< EDITED BY GF %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
else
try
ILOGcplex = Cplex('fba');
catch ME
error('CPLEX not installed or licence server not up')
end
%simple ibm ilog cplex interface
options = cplexoptimset;
switch printLevel
case 0
options = cplexoptimset(options,'Display','off');
case 1
options = cplexoptimset(options,'Display','off');
case 1
options = cplexoptimset(options,'Display','off');
case 1
options = cplexoptimset(options,'Display','off');
end
if ~isempty(csense)
if sum(minNorm)~=0
Aineq = [LPProblem.A(csense == 'L',:); - LPProblem.A(csense == 'G',:)];
bineq = [b(csense == 'L',:); - b(csense == 'G',:)];
% min 0.5*x'*H*x+f*x or f*x
% st. Aineq*x <= bineq
% Aeq*x = beq
% lb <= x <= ub
[x,fval,exitflag,output,lambda] = cplexqp(F,c,Aineq,bineq,LPProblem.A(csense == 'E',:),b(csense == 'E',1),x_L,x_U,[],options);
else
Aineq = [LPProblem.A(csense == 'L',:); - LPProblem.A(csense == 'G',:)];
bineq = [b(csense == 'L',:); - b(csense == 'G',:)];
% min c*x
% st. Aineq*x <= bineq
% Aeq*x = beq
% lb <= x <= ub
[x,fval,exitflag,output,lambda] = cplexlp(c,Aineq,bineq,LPProblem.A(csense == 'E',:),b(csense == 'E',1),x_L,x_U,[],options);
end
%primal
solution.obj=osense*fval;
solution.full=x;
%this is the dual to the equality constraints but it's not the chemical potential
solution.dual=lambda.eqlin;
else
Aineq=[];
bineq=[];
if sum(minNorm)~=0
[x,fval,exitflag,output,lambda] = cplexqp(F,c,Aineq,bineq,LPProblem.A,b,x_L,x_U,[],options);
else
[x,fval,exitflag,output,lambda] = cplexlp(c,Aineq,bineq,LPProblem.A,b,x_L,x_U,[],options);
end
solution.obj=osense*fval;
solution.full=x;
%this is the dual to the equality constraints but it's not the chemical potential
solution.dual=sparse(size(LPProblem.A,1),1);
solution.dual(csense == 'E')=lambda.eqlin;
%this is the dual to the inequality constraints but it's not the chemical potential
solution.dual(csense == 'L')=lambda.ineqlin(1:nnz(csense == 'L'),1);
solution.dual(csense == 'G')=lambda.ineqlin(nnz(csense == 'L')+1:end,1);
end
%this is the dual to the simple ineequality constraints : reduced costs
solution.rcost=lambda.lower-lambda.upper;
solution.nInfeas = [];
solution.sumInfeas = [];
solution.origStat = output.cplexstatus;
end
%1 = (Simplex or Barrier) Optimal solution is available.
Inform = solution.origStat;
else
%tomlab cplex interface
if ~isempty(csense)
%set up constant vectors for CPLEX
b_L(csense == 'E',1) = b(csense == 'E');
b_U(csense == 'E',1) = b(csense == 'E');
b_L(csense == 'G',1) = b(csense == 'G');
b_U(csense == 'G',1) = Inf;
b_L(csense == 'L',1) = -Inf;
b_U(csense == 'L',1) = b(csense == 'L');
else
b_L = b;
b_U = b;
end
%tomlab cplex interface
% minimize 0.5 * x'*F*x + c'x subject to:
% x x_L <= x <= x_U
% b_L <= Ax <= b_U
[x, slack, v, rc, f_k, ninf, sinf, Inform, basis] = cplex(c, LPProblem.A, x_L, x_U, b_L, b_U, ...
cpxControl, callback, printLevel, Prob, IntVars, PI, SC, SI, ...
sos1, sos2, F, logfile, savefile, savemode, qc, ...
confgrps, conflictFile, saRequest, basis, xIP, logcon);
solution.full=x;
%this is the dual to the equality constraints but it's not the chemical potential
solution.dual=v;
%this is the dual to the simple ineequality constraints : reduced costs
solution.rcost=rc;
if Inform~=1
solution.obj = NaN;
else
if minNorm==0
solution.obj=f_k*osense;
else
solution.obj=c'*x*osense;
end
% solution.obj
% norm(x)
end
solution.nInfeas = ninf;
solution.sumInfeas = sinf;
solution.origStat = Inform;
end
%timeTaken=toc;
timeTaken=NaN;
if Inform~=1 && ~isempty(which('cplex'))
if conflictResolve ==1
if isfield(LPProblem,'mets') && isfield(LPProblem,'rxns')
%this code reads the conflict resolution file and replaces the
%arbitrary names with the abbreviations of metabolites and reactions
[nMet,nRxn]=size(LPProblem.A);
totAbbr=nMet+nRxn;
conStrFind=cell(nMet+nRxn,1);
conStrReplace=cell(nMet+nRxn,1);
%only equality constraint rows
for m=1:nMet
conStrFind{m,1}=['c' int2str(m) ':'];
conStrReplace{m,1}=[LPProblem.mets{m} ': '];
end
%reactions
for n=1:nRxn
conStrFind{nMet+n,1}=['x' int2str(n) ' '];
conStrReplace{nMet+n,1}=[LPProblem.rxns{n} ' '];
end
fid1 = fopen(suffix);
fid2 = fopen(['COBRA_' suffix], 'w');
while ~feof(fid1)
tline{1}=fgetl(fid1);
%replaces all occurrences of the string str2 within string str1
%with the string str3.
%str= strrep(str1, str2, str3)
for t=1:totAbbr
tline= strrep(tline, conStrFind{t}, conStrReplace{t});
end
fprintf(fid2,'%s\n', tline{1});
end
fclose(fid1);
fclose(fid2);
%delete other file without replacements
% delete(suffix)
else
warning('Need reaction and metabolite abbreviations in order to make a readable conflict resolution file');
end
fprintf('%s\n',['Conflict resolution file written to: ' prefix '\COBRA_' suffix]);
fprintf('%s\n%s\n','The Conflict resolution file gives an irreducible infeasible subset ','of constraints which are making this LP Problem infeasible');
else
if printLevel>0
fprintf('%s\n','No conflict resolution file. Perhaps set conflictResolve = 1 next time.');
end
end
solution.solver = 'cplex_direct';
end
% Try to give back COBRA Standardized solver status:
% 1 Optimal solution
% 2 Unbounded solution
% 0 Infeasible
% -1 No solution reported (timelimit, numerical problem etc)
if Inform==1
solution.stat = 1;
if printLevel>0
%use tomlab code to print out exit meassage
[ExitText,ExitFlag] = cplexStatus(Inform);
solution.ExitText=ExitText;
solution.ExitFlag=ExitFlag;
fprintf('\n%s%g\n',[ExitText ', Objective '], c'*solution.full*osense);
end
else
if Inform==2
solution.stat = 2;
%use tomlab code to print out exit meassage
[ExitText,ExitFlag] = cplexStatus(Inform);
solution.ExitText=ExitText;
solution.ExitFlag=ExitFlag;
fprintf('\n%s%g\n',[ExitText ', Objective '], c'*solution.full*osense);
else
if Inform==3
solution.stat = 0;
else
%this is a conservative view
solution.stat = -1;
%use tomlab code to print out exit meassage
[ExitText,ExitFlag] = cplexStatus(Inform);
solution.ExitText=ExitText;
solution.ExitFlag=ExitFlag;
fprintf('\n%s%g\n',[ExitText ', Objective '], c'*solution.full*osense);
end
end
end
solution.time = timeTaken;
%return basis
if basisReuse
LPProblem.LPBasis=basis;
end
if sum(minNorm)~=0
fprintf('%s\n','This objective corresponds to a flux with minimum Euclidean norm.');
fprintf('%s%d%s\n','The weighting for minimising the norm was ',minNorm,'.');
fprintf('%s\n','Check that the objective is the same without minimising the norm.');
end
end
|
github
|
EPFL-LCSB/matTFA-master
|
geometricFBA.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/geometricFBA.m
| 6,629 |
utf_8
|
511013ff705cedf3231d79af4e99e023
|
function flux = geometricFBA(model,varargin)
%geometricFBA finds a unique optimal FBA solution that is (in some sense)
%central to the range of possible fluxes; as described in
% K Smallbone, E Simeonidis (2009). Flux balance analysis:
% A geometric perspective. J Theor Biol 258: 311-315
% http://dx.doi.org/10.1016/j.jtbi.2009.01.027
%
% flux = geometricFBA(model)
%
%INPUT
% model COBRA model structure
%
%OPTIONAL INPUTS
% Optional parameters can be entered as parameter name followed by
% parameter value: i.e. ...,'epsilon',1e-9)
% printLevel [default: 1] printing level
% = 0 silent
% = 1 show algorithm progress and times
% epsilon [default: 1e-6] convergence tolerance of algorithm,
% defined in more detail in paper above
% flexRel [default: 0] flexibility to flux bounds
% try e.g. 1e-3 if the algorithm has convergence problems
%
%OUTPUT
% flux unique centered flux
%
%kieran smallbone, 5 May 2010
%
% This script is made available under the Creative Commons
% Attribution-Share Alike 3.0 Unported Licence (see
% www.creativecommons.org).
param = struct('epsilon',1e-6,'flexRel',0,'printLevel',1);
field = fieldnames(param);
if mod(nargin,2) ~= 1 % require odd number of inputs
error('incorrect number of input parameters')
else
for k = 1:2:(nargin-1)
param.(field{strcmp(varargin{k},field)}) = varargin{k+1};
end
end
param.flexTol = param.flexRel * param.epsilon; % absolute flexibility
% determine optimum
FBAsolution = optimizeCbModel(model);
ind = find(model.c);
if length(ind) == 1
model.lb(ind) = FBAsolution.f;
end
A = model.S;
b = model.b;
L = model.lb;
U = model.ub;
% ensure column vectors
b = b(:); L = L(:); U = U(:);
% Remove negligible elements
J = any(A,2); A = A(J,:); b = b(J);
% presolve
v = nan(size(L));
J = (U-L < param.epsilon);
v(J) = (L(J)+U(J))/2;
J = find(isnan(v));
if param.printLevel
fprintf('%s\t%g\n\n%s\t@%s\n','# reactions:',length(v),'iteration #0',datestr(now,16));
end
L0 = L; U0 = U;
for k = J(:)'
f = zeros(length(v),1); f(k) = -1;
[dummy,opt,conv] = easyLP(f,A,b,L0,U0);
if conv
vL = max(-opt,L(k));
else
vL = L(k);
end
[dummy,opt,conv] = easyLP(-f,A,b,L0,U0);
if conv
vU = min(opt,U(k));
else vU = U(k);
end
if abs(vL) < param.epsilon
vL = 0;
end
if abs(vU) < param.epsilon
vU = 0;
end
vM = (vL + vU)/2;
if abs(vM) < param.epsilon
vM = 0;
end
if abs(vU - vL) < param.epsilon
vL = (1-sign(vM)* param.flexTol)*vM;
vU = (1+sign(vM)* param.flexTol)*vM;
end
L(k) = vL; U(k) = vU;
end
v = nan(size(L));
J = (U-L < param.epsilon);
v(J) = (L(J)+U(J))/2; v = v.*(abs(v) > param.epsilon);
if param.printLevel
fprintf('%s\t\t%g\n%s\t\t%g\n\n','fixed:',sum(J),'@ zero:',sum(v==0));
end
% iterate
J = find(U-L >= param.epsilon);
n = 1;
mu = [];
Z = [];
while ~isempty(J)
if param.printLevel
fprintf('%s #%g\t@%s\n','iteration',n,datestr(now,16));
end
if n == 1
M = zeros(size(L));
else
M = (L+U)/2;
end
mu(:,n) = M; %#ok<AGROW>
allL = L; allU = U; allA = A; allB = b;
[a1,a2] = size(A);
% build new matrices
for k = 1:(n-1)
[b1,b2] = size(allA);
f = sparse(b2+2*a2,1); f((b2+1):end) = -1;
opt = -Z(k);
allA = [allA,sparse(b1,2*a2);
speye(a2,a2),sparse(a2,b2-a2),-speye(a2),speye(a2);
f(:)']; %#ok<AGROW>
allB = [allB;mu(:,k);opt]; %#ok<AGROW>
allL = [allL;zeros(2*a2,1)]; %#ok<AGROW>
allU = [allU;inf*ones(2*a2,1)]; %#ok<AGROW>
end
[b1,b2] = size(allA);
f = zeros(b2+2*a2,1); f((b2+1):end) = -1;
allA = [allA,sparse(b1,2*a2);
speye(a2,a2),sparse(a2,b2-a2),-speye(a2),speye(a2)]; %#ok<AGROW>
allB = [allB;M]; %#ok<AGROW>
allL = [allL;zeros(2*a2,1)]; %#ok<AGROW>
allU = [allU;inf*ones(2*a2,1)]; %#ok<AGROW>
[v,opt,conv] = easyLP(f,allA,allB,allL,allU);
if ~conv, disp('error: no convergence'); flux = (L+U)/2; return; end
opt = ceil(-opt/eps)*eps;
Z(n) = opt; %#ok<AGROW>
allA = [allA; sparse(f(:)')]; %#ok<AGROW>
allB = [allB; -opt]; %#ok<AGROW>
for k = J(:)'
f = zeros(length(allL),1); f(k) = -1;
[dummy,opt,conv] = easyLP(f,allA,allB,allL,allU);
if conv
vL = max(-opt,L(k));
else
vL = L(k);
end
[dummy,opt,conv] = easyLP(-f,allA,allB,allL,allU);
if conv
vU = min(opt,U(k));
else
vU = U(k);
end
if abs(vL) < param.epsilon
vL = 0;
end
if abs(vU) < param.epsilon
vU = 0;
end
vM = (vL + vU)/2;
if abs(vM) < param.epsilon
vM = 0;
end
if abs(vU - vL) < param.epsilon
vL = (1-sign(vM)* param.flexTol)*vM;
vU = (1+sign(vM)* param.flexTol)*vM;
end
L(k) = vL;
U(k) = vU;
end
v = nan(size(L));
J = (U-L < param.epsilon);
v(J) = (L(J)+U(J))/2; v = v.*(abs(v) > param.epsilon);
if param.printLevel
fprintf('%s\t\t%g\n%s\t\t%g\n\n','fixed:',sum(J),'@ zero:',sum(v==0));
end
n = n+1;
J = find(U-L >= param.epsilon);
flux = v;
end
function [v,fOpt,conv] = easyLP(c,A,b,lb,ub)
%easyLP
%
% solves the linear programming problem:
% max c'x subject to
% A x = b
% lb <= x <= ub.
%
% Usage: [v,fOpt,conv] = easyLP(c,A,b,lb,ub)
%
% c objective coefficient vector
% A LHS matrix
% b RHS vector
% lb lower bound
% ub upper bound
%
% v solution vector
% fOpt objective value
% conv convergence of algorithm [0/1]
%
% the function is a wrapper for the "solveCobraLP" script.
%
%kieran smallbone, 5 may 2010
csense(1:length(b)) = 'E';
model = struct('A',A,'b',b,'c',full(c),'lb',lb,'ub',ub,'osense',-1,'csense',csense);
solution = solveCobraLP(model);
v = solution.full;
fOpt = solution.obj;
conv = solution.stat == 1;
|
github
|
EPFL-LCSB/matTFA-master
|
changeRxnMets.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/changeRxnMets.m
| 3,484 |
utf_8
|
a54ed5421c1d7e06d54c21d49c1dd01a
|
function [model ModifiedRxns] = changeRxnMets(model,Mets2change,NewMets,Rxn,NewStoich)
%changeRxnMets Change metabolites in a specified reaction, or
% randomly chosen reactions.
%
% [model ModifiedRxns] = changeRxnMets(model,Mets2change,NewMets,Rxn,NewStoich)
%
%INPUTS
% model COBRA model structure
% Mets2change Cell array of metabolites to change
% NewMets Cell array of replacement metabolites (must be in
% order of those that will be replaced
% Rxn reaction to change (string) or cell array, or if a number is put
% here, that number of reactions (with Mets2change) will
% be randomly chosen and the metabolites will be swapped
%
%OPTIONAL INPUT
% NewStoich Stoichiometry of new metabs (conserved from old mets by default).
% If multiple reactions are being changed, this must be
% a mets x rxns matrix,
% e.g. for 2 new reactions: Rxn = {'r1','r2'}
% r1: 2 A + 3 B -> 1 C
% r2: 4 A + 3 B -> 3 C
% where A and C are the new metabolites,
% NewMets = {'A', 'C'}
% NewStoich = [ 2 4; 1 3]
%
%OUTPUTS
% model COBRA model structure with changed reaction
% ModifiedRxns Rxns which were modified
%
% Nathan Lewis (Apr 24, 2009)
if nargin ==4
NewStoich = [];
end
%%% make sure metabolites are in the model
OldMetInd = findMetIDs(model,Mets2change);
NewMetInd = findMetIDs(model,NewMets);
if min(OldMetInd) == 0 || min(NewMetInd) == 0
error('A metabolite wasn''t found in your model!')
end
if ~all(isnumeric(Rxn))
%%% make sure rxns are in the model
RxnsInd = findRxnIDs(model,Rxn);
if min(RxnsInd == 0)
error('A reaction wasn''t found in your model!')
end
model = changeMets(model,OldMetInd,NewMetInd,RxnsInd,NewStoich);
ModifiedRxns = model.rxns(RxnsInd);
else
%%% find all reactions with the old mets, and choose the specified number of rxns
RxnsInd = 1:length(model.rxns);
tempS = full(model.S);
for i = 1:length(OldMetInd)
RxnsInd = intersect(find(tempS(OldMetInd(i),:)),RxnsInd);
end
if length(RxnsInd)<Rxn
warning('Fewer reactions have your metabolites than the number you wanted to randomly choose!')
RxnsToSwitch = RxnsInd(ceil(rand(length(RxnsInd),1)));
Rxn = length(RxnsToSwitch);
else
%%% chose the reactions to randomize
RxnsToSwitch = [];
Rxns2Exclude = findRxnIDs(model,{'DM_SC_PRECUSOR'});
for r=1:length(Rxns2Exclude)
tmp = find(RxnsInd==Rxns2Exclude(r));
if ~isempty(tmp)
RxnsInd(tmp) = [];
end
end
while length(unique(RxnsToSwitch))<Rxn
RxnsToSwitch = RxnsInd(ceil(rand(length(RxnsInd),1)*length(RxnsInd)));
RxnsToSwitch = RxnsToSwitch(1:Rxn);
end
end
model = changeMets(model,OldMetInd,NewMetInd,RxnsToSwitch,NewStoich);
ModifiedRxns = model.rxns(RxnsToSwitch);
end
end
function model = changeMets(model,OldMetInd,NewMetInd,RxnsInd,NewStoich)
if isempty(NewStoich)
NewStoich = model.S(OldMetInd,RxnsInd);
end
for i = 1:length(RxnsInd)
model.S(OldMetInd,RxnsInd(i))=0;
model.S(NewMetInd,RxnsInd(i))=NewStoich(:,i);
end
end
|
github
|
EPFL-LCSB/matTFA-master
|
convertModelToEX.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/convertModelToEX.m
| 2,482 |
utf_8
|
262c28a115d8194846f4c7562681fe0e
|
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% convert Matlab Model to XPA format
% Inputs:
% model Model Structure
% filename Filename of Output File (make sure to include '.txt' or
% '.xpa')
% rxnzero Matrix containing all no flux var rxns (to skip, set=0)
%
% Limitations:
% -Works properly with only integer value reaction coeff. (except for .5
% or -.5)
% Other non-integer value coeff. have to be edited manually
% -Exchange reactions have to be clumped together in model
% -If using rxnzero, make sure that EX reactions contain no compounds
% that are not used in the uncommented reactions
%
% Aarash Bordbar, 07/06/07
% Updated Aarash Bordbar 02/22/10
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function convertModelToEX(model,filename,rxnzero)
fid = fopen(filename,'w');
fprintf(fid,'(Internal Fluxes)\n');
EXrxns = [strmatch('EX_',model.rxns);strmatch('DM_',model.rxns)];
EXrxns = model.rxns(EXrxns);
checkEX = ismember(model.rxns,EXrxns);
% Reactions prior to exchange reactions
for i = 1:length(model.rxns)
if checkEX(i) == 0
for t = 1:size(rxnzero,1)
if i == rxnzero(t)
fprintf(fid,'// ');
end
end
fprintf(fid,'%s\t',model.rxns{i});
if model.rev(i) == 0
fprintf(fid,'I\t');
else
fprintf(fid,'R\t');
end
reactionPlace = find(model.S(:,i));
if abs(model.S(reactionPlace,i)) > 1 - 1e-2
for j = 1:size(reactionPlace,1)
fprintf(fid,'%i\t%s\t',model.S(reactionPlace(j),i),model.mets{reactionPlace(j)});
end
else
for j = 1:size(reactionPlace,1)
newS(j,i) = 2*model.S(reactionPlace(j),i);
fprintf(fid,'%i\t%s\t',newS(j,i),model.mets{reactionPlace(j)});
end
end
fprintf(fid,'\n');
end
end
% Exchange Reactions
fprintf(fid,'(Exchange Fluxes)\n');
for i = 1:length(model.rxns)
if checkEX(i) == 1
metabolitePlace = find(model.S(:,i));
fprintf(fid,'%s\t',model.mets{metabolitePlace});
if model.lb(i) >= 0 && model.ub(i) >= 0
fprintf(fid,'Output\n');
else if model.lb(i) <= 0 && model.ub(i) <= 0
fprintf(fid,'Input\n');
else
fprintf(fid,'Free\n');
end
end
end
end
fclose(fid);
|
github
|
EPFL-LCSB/matTFA-master
|
pFBA.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/pFBA.m
| 9,274 |
utf_8
|
ec4edfb9cb08758b017493c5cb612fcd
|
function [GeneClasses RxnClasses modelIrrevFM] = pFBA(model, varargin)
% Parsimoneous enzyme usage Flux Balance Analysis - method that optimizes
% the user's objective function and then minimizes the flux through the
% model and subsequently classifies each gene by how it contributes to the
% optimal solution. See Lewis, et al. Mol Syst Bio doi:10.1038/msb.2010.47
%
% Inputs:
% model COBRA model
%
% varargin:
% 'geneoption' 1 = only minimize the sum of the flux through
% gene-associated fluxes (default), 0 = minimize the
% sum of all fluxes in the network
% 'tol' tolerance (default = 1e-6)
% 'map' map structure from readCbMap.m (no map written if empty
% 'mapoutname' File Name for map
% 'skipclass' 1 = Don't classify genes and reactions. Only return
% model with the minimium flux set as upper bound.
% 0 = classify genes and reactions (default).
%
% Output:
% GeneClasses Structure with fields for each gene class
% RxnsClasses Structure with fields for each reaction class
% modelIrrevFM Irreversible model used for minimizing flux with
% the minimum flux set as a flux upper bound
%
%
%
% ** note on maps: Red (6) = Essential reactions, Orange (5) = pFBA optima
% reaction, Yellow (4) = ELE reactions, Green (3) = MLE reactions,
% blue (2) = zero flux reactions, purple (1) = blocked reactions,
% black (0) = not classified
%
% Example:
% [GeneClasses RxnClasses modelIrrevFM] = pFBA(model, 'geneoption',0, 'tol',1e-7)
%
% by Nathan Lewis Aug 25, 2010
%
if nargin < 2
tol = 1e-6;
GeneOption = 1;
map = []; % no map
mapOutName = 'pFBA_map.svg';
skipclass = 0;
end
if mod(length(varargin),2)==0
for i=1:2:length(varargin)-1
switch lower(varargin{i})
case 'geneoption', GeneOption = varargin{i+1};
case 'tol', tol = varargin{i+1};
case 'map', map = varargin{i+1};
case 'mapoutname', mapOutName = varargin{i+1};
case 'skipclass', skipclass = varargin{i+1};
otherwise, options.(varargin{i}) = varargin{i+1};
end
end
else
error('Invalid number of parameters/values');
end
if ~exist('GeneOption','var'), GeneOption = 1; end
if ~exist('tol','var'), tol = 1e-6; end
if ~exist('map','var'), map = []; end
if ~exist('mapOutName','var'), mapOutName = 'pFBA_map.svg'; end
if ~exist('skipclass','var'), skipclass = 0; end
if skipclass % skip the model reduction and gene/rxn classification
% minimize the network flux
FBAsoln = optimizeCbModel(model);
model.lb(model.c==1) = FBAsoln.f;
[ MinimizedFlux modelIrrevFM]= minimizeModelFlux_local(model,GeneOption);
modelIrrevFM = changeRxnBounds(modelIrrevFM,'netFlux',MinimizedFlux.f,'b');
GeneClasses = [];
RxnClasses = [];
else
% save a copy of the inputted model
model_sav = model;
% Remove all blocked reactions
[selExc,selUpt] = findExcRxns(model,0,0); % find and open up all exchanges
tempmodel = changeRxnBounds(model,model.rxns(selExc),-1000,'l');
tempmodel = changeRxnBounds(tempmodel,model.rxns(selExc),1000,'u');
tempmodel = reduceModel(tempmodel,tol); % reduce the model to find blocked reactions
Blocked_Rxns = setdiff(model.rxns,regexprep(tempmodel.rxns,'_r$',''));
model = removeRxns(model,setdiff(model.rxns,regexprep(tempmodel.rxns,'_r$',''))); % remove blocked reactions
Ind2Remove = find(~and(sum(full(model.rxnGeneMat),1),1));
Blocked_genes = model.genes(Ind2Remove);
model.genes(Ind2Remove)={'dead_end'}; % make sure genes that are unique to blocked reactions are tagged for removal
% find essential genes
grRatio = singleGeneDeletion(model);
grRatio(isnan(grRatio))=0;
pFBAEssential = model.genes(grRatio<tol);
if nargout > 1
% find essential reactions
RxnRatio = singleRxnDeletion(model);
RxnRatio(isnan(RxnRatio))=0;
pFBAEssentialRxns = model.rxns(RxnRatio<tol);
end
% remove zero flux rxns
tempmodel = reduceModel(model,tol);
ZeroFluxRxns = setdiff(model.rxns,regexprep(tempmodel.rxns,'_r$',''));
model = removeRxns(model,ZeroFluxRxns);
% find MLE reactions
FBAsoln = optimizeCbModel(model);
model.lb(model.c==1) = FBAsoln.f;
[minFlux,maxFlux] = fluxVariability(model,100);
for i = 1:length(minFlux)
tmp(i,1) = max([abs(minFlux(i)) abs(maxFlux(i))])<tol;
end
MLE_Rxns = setdiff(model.rxns(tmp),ZeroFluxRxns);
% minimize the network flux
[ MinimizedFlux modelIrrevFM]= minimizeModelFlux_local(model,GeneOption);
% separate pFBA optima rxns from ELE rxns
modelIrrevFM = changeRxnBounds(modelIrrevFM,'netFlux',MinimizedFlux.f,'b');
[minFlux,maxFlux] = fluxVariability(modelIrrevFM,100);
pFBAopt_Rxns = modelIrrevFM.rxns((abs(minFlux)+abs(maxFlux))>=tol);
ELE_Rxns = modelIrrevFM.rxns((abs(minFlux)+abs(maxFlux))<=tol);
pFBAopt_Rxns = unique(regexprep(pFBAopt_Rxns,'_[f|b]$',''));
ELE_Rxns = unique(regexprep(ELE_Rxns,'_[f|b]$',''));
ELE_Rxns = ELE_Rxns(~ismember(ELE_Rxns,pFBAopt_Rxns));
ELE_Rxns = ELE_Rxns(~ismember(ELE_Rxns,MLE_Rxns));
% determine pFBA optima genes
pFBAopt_Rxns(ismember(pFBAopt_Rxns,'netFlux'))=[];
[geneList]=findGenesFromRxns(model,pFBAopt_Rxns);
geneList2 = {};
for i = 1:length(geneList),
geneList2(end+1:end+length(geneList{i}),1) = columnVector( geneList{i});
end
pFBAOptima = unique(geneList2);
% determine Zero Flux genes
Ind2Remove = find(~and(sum(full(model.rxnGeneMat),1),1));
ZeroFluxGenes = unique(model.genes(Ind2Remove));
% determine ELE genes
[geneList]=findGenesFromRxns(model,ELE_Rxns);
geneList2 = {};
for i = 1:length(geneList)
geneList2(end+1:end+length(geneList{i}),1) = columnVector( geneList{i});
end
ELEGenes = unique(geneList2);
ELEGenes = setdiff(ELEGenes,[pFBAOptima;ZeroFluxGenes]);
% determine Met ineff genes
MLEGenes = setdiff(model.genes, [pFBAOptima;ZeroFluxGenes;ELEGenes]);
% clean up lists by removing non-genes
pFBAOptima(~cellfun('isempty',regexp(pFBAOptima,'dead_end')))=[];
ELEGenes(~cellfun('isempty',regexp(ELEGenes ,'dead_end')))=[];
MLEGenes(~cellfun('isempty',regexp(MLEGenes,'dead_end')))=[];
ZeroFluxGenes(~cellfun('isempty',regexp(ZeroFluxGenes,'dead_end')))=[];
pFBAOptima(cellfun('isempty',pFBAOptima))=[];
ELEGenes(cellfun('isempty',ELEGenes ))=[];
MLEGenes(cellfun('isempty',MLEGenes))=[];
ZeroFluxGenes(cellfun('isempty',ZeroFluxGenes))=[];
% filter out essential genes from pFBA optima
pFBAOptima(ismember(pFBAOptima,pFBAEssential))=[];
if nargout > 1
% filter out essential Rxns from pFBA optima
pFBAopt_Rxns(ismember(pFBAopt_Rxns,pFBAEssentialRxns))=[];
end
% prepare output variables
GeneClasses.pFBAEssential =pFBAEssential;
GeneClasses.pFBAoptima = pFBAOptima;
GeneClasses.ELEGenes = ELEGenes;
GeneClasses.MLEGenes = MLEGenes;
GeneClasses.ZeroFluxGenes = ZeroFluxGenes;
GeneClasses.Blockedgenes = Blocked_genes;
RxnClasses.Essential_Rxns = pFBAEssentialRxns;
RxnClasses.pFBAOpt_Rxns = pFBAopt_Rxns;
RxnClasses.ELE_Rxns = ELE_Rxns;
RxnClasses.MLE_Rxns = MLE_Rxns;
RxnClasses.ZeroFlux_Rxns = ZeroFluxRxns;
RxnClasses.Blocked_Rxns = Blocked_Rxns;
if ~isempty(map)
MapVector = zeros(length(model_sav.rxns),1);
MapVector(ismember(model_sav.rxns,Blocked_Rxns))= 1;
MapVector(ismember(model_sav.rxns,ZeroFluxRxns))= 2;
MapVector(ismember(model_sav.rxns,MLE_Rxns))= 3;
MapVector(ismember(model_sav.rxns,ELE_Rxns))= 4;
MapVector(ismember(model_sav.rxns,pFBAopt_Rxns))= 5;
MapVector(ismember(model_sav.rxns,pFBAEssentialRxns))= 6;
options.lb = 0;
options.ub = 6;
tmpCmap = hsv(18);
tmpCmap = [tmpCmap([1,3,4,6,11,14],:); 0 0 0;];
options.fileName = mapOutName;
options.colorScale = flipud(round(tmpCmap*255));
global CB_MAP_OUTPUT
if ~exist('CB_MAP_OUTPUT', 'var') || isempty(CB_MAP_OUTPUT)
changeCbMapOutput('svg');
end
drawFlux(map, model_sav, MapVector, options);
end
end
end
function [ MinimizedFlux modelIrrev]= minimizeModelFlux_local(model,GeneOption)
% This function finds the minimum flux through the network and returns the
% minimized flux and an irreversible model
% convert model to irrev
modelIrrev = convertToIrreversible(model);
% add pseudo-metabolite to measure flux through network
if nargin==1,GeneOption=0;
end
if GeneOption==0, % signal that you want to minimize the sum of all gene and non-gene associated fluxes
modelIrrev.S(end+1,:) = ones(size(modelIrrev.S(1,:)));
elseif GeneOption==1, % signal that you want to minimize the sum of only gene-associated fluxes
%find all reactions which are gene associated
Ind=find(sum(modelIrrev.rxnGeneMat,2)>0);
modelIrrev.S(end+1,:) = zeros(size(modelIrrev.S(1,:)));
modelIrrev.S(end,Ind) = 1;
end
modelIrrev.b(end+1) = 0;
modelIrrev.mets{end+1} = 'fluxMeasure';
% add a pseudo reaction that measures the flux through the network
modelIrrev = addReaction(modelIrrev,'netFlux',{'fluxMeasure'},[-1],false,0,inf,0,'','');
% set the flux measuring demand as the objective
modelIrrev.c = zeros(length(modelIrrev.rxns),1);
modelIrrev = changeObjective(modelIrrev, 'netFlux');
% minimize the flux measuring demand (netFlux)
MinimizedFlux = optimizeCbModel(modelIrrev,'min');
end
|
github
|
EPFL-LCSB/matTFA-master
|
reduceModel.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/reduceModel.m
| 8,348 |
utf_8
|
1d56cf233017a4d6aa106e6c8714ab94
|
function [modelRed,hasFlux,maxes,mins] = reduceModel(model,tol,irrevFlag,verbFlag,negFluxAllowedFlag,checkConsistencyFlag,changeBoundsFlag)
%reduceModel Removes from the model all of the reactions that are never used (max and
% min are < tol). Finds the minimal bounds for the flux through each reaction.
% Also returns the results for flux variability analysis (maxes, mins).
%
% [modelRed,hasFlux,maxes,mins] = reduceModel(model,tol,irrevFlag,verbFlag,negFluxAllowedFlag,checkConsistencyFlag,changeBoundsFlag)
%
%INPUT
% model COBRA model structure
%
%OPTIONAL INPUTS
% tol Tolerance for non-zero bounds - bounds smaller in absolute
% value than this value will be set to zero (Default = 1e-6)
% irrevFlag Determines if the models should be treated using
% the irreversible form. (Default = false)
% verbFlag Verbose output (Default = false)
% negFluxAllowedFlag Allow negative fluxes through irrev reactions
% (Default = false)
% checkConsistencyFlag Do a consistency check of the optimal solution
% (Default = true)
% changeBoundsFlag Change upper/lower bounds to the minimal bounds
% (Default = true)
%
%OUTPUTS
% modelRed Reduced model
% hasFlux The indexes of the reactions that are not blocked
% in the model
% maxes Maximum fluxes
% mins Minimum fluxes
%
% Gregory Hannum and Markus Herrgard 7/20/05
% Sets the tolerance for zero flux determination
if nargin < 2
global CBT_LP_PARAMS
if (exist('CBT_LP_PARAMS', 'var'))
if isfield(CBT_LP_PARAMS, 'objTol')
tol = CBT_LP_PARAMS.objTol;
else
tol = 1e-6
end
else
tol = 1e-6;
end
end
% Sets the irrevFlag to default
if nargin < 3
irrevFlag = false;
end
% Print out more stuff
if nargin < 4
verbFlag = false;
end
% Allow negative irreversible fluxes (default: reverse the reaction
% direction)
if (nargin < 5)
negFluxAllowedFlag = false;
end
% Check if the reduced model produces consistent results
if (nargin < 6)
checkConsistencyFlag = true;
end
% Change to minimal bounds
if (nargin < 7)
changeBoundsFlag = true;
end
%declare some variables
maxes = [];
mins = [];
%modelRed = model;
[nMets,nRxns]= size(model.S);
%obtain maxes and mins for the fluxes
rxnID = 1;
h = waitbar(0,'Model reduction in progress ...');
while rxnID <= nRxns
if mod(rxnID,10) == 0
waitbar(rxnID/nRxns,h);
end
rxnName = model.rxns{rxnID};
if (verbFlag)
fprintf('%s\t',rxnName);
end
% Set the objective function to the current reactiom
tempModel = changeObjective(model,rxnName);
if (irrevFlag && model.rev(rxnID))
% Make the forward reaction reversible temporarily
tempModel.lb(rxnID) = -tempModel.ub(rxnID+1);
% Disable the reverse reaction
tempModel.ub(rxnID+1) = 0;
end
%solve for the minimum and maximum for the current reaction
sol = optimizeCbModel(tempModel,'max',[]);
if (sol.stat > 0)
maxBound = sol.f;
else
maxBound = model.ub(rxnID);
end
sol = optimizeCbModel(tempModel,'min',[]);
if (sol.stat > 0)
minBound = sol.f;
else
minBound = model.lb(rxnID);
end
%eliminate very small boundaries and set predetermined reversible boundaries
if abs(maxBound) < tol
maxBound = 0;
end
% Ignore negative lower bounds for irrev reactions
if abs(minBound) < tol || (minBound < 0 && ~model.rev(rxnID))
minBound = 0;
end
%set the new appropriate bounds
if (irrevFlag && model.rev(rxnID))
if minBound < 0 && maxBound < 0 % Negative flux
mins(rxnID) = 0;
mins(rxnID+1) = -maxBound;
maxes(rxnID) = 0;
maxes(rxnID+1) = -minBound;
elseif minBound < 0 && maxBound >= 0 % Reversible flux
mins(rxnID:rxnID+1) = 0;
maxes(rxnID) = maxBound;
maxes(rxnID+1) = -minBound;
elseif minBound >= 0 && maxBound >= 0 % Positive flux
mins(rxnID) = minBound;
mins(rxnID+1) = 0;
maxes(rxnID) = maxBound;
maxes(rxnID+1) = 0;
end
if (verbFlag)
fprintf('%g\t%g\n',mins(rxnID),maxes(rxnID));
fprintf('%s\t',model.rxns{rxnID+1});
fprintf('%g\t%g\n',mins(rxnID+1),maxes(rxnID+1));
end
% Jump over the reverse direction
rxnID = rxnID + 1;
else
maxes(rxnID)=maxBound;
mins(rxnID)=minBound;
if (verbFlag)
fprintf('%g\t%g\n',minBound,maxBound);
end
end
rxnID = rxnID + 1;
end
if ( regexp( version, 'R20') )
close(h);
end
if (verbFlag)
fprintf('\n');
end
% Create a list of flux indexes that have non-zero flux (hasFlux)
hasFluxSel = (abs(maxes) > tol | abs(mins) > tol);
hasFlux = find(hasFluxSel);
hasFlux = columnVector(hasFlux);
% Remove reactions that are blocked
modelRed = removeRxns(model,model.rxns(~hasFluxSel),irrevFlag,true);
% Update bounds
if (changeBoundsFlag)
modelRed.lb = columnVector(mins(hasFlux));
modelRed.ub = columnVector(maxes(hasFlux));
selInconsistentBounds = (modelRed.ub < modelRed.lb);
modelRed.ub(selInconsistentBounds) = modelRed.lb(selInconsistentBounds);
%update the reversible list with new bounds
nRxnsNew = size(modelRed.S,2);
for rxnID = 1:nRxnsNew
if (~irrevFlag)
if (modelRed.lb(rxnID) >= 0)
% Only runs in positive direction
modelRed.rev(rxnID) = false;
end
if (modelRed.ub(rxnID) <= 0)
% Only runs in negative direction -> reverse the reaction
modelRed.rev(rxnID) = false;
if (~negFluxAllowedFlag)
ubTmp = modelRed.ub(rxnID);
lbTmp = modelRed.lb(rxnID);
modelRed.S(:,rxnID) = -modelRed.S(:,rxnID);
modelRed.ub(rxnID) = -lbTmp;
modelRed.lb(rxnID) = -ubTmp;
modelRed.c(rxnID) = -modelRed.c(rxnID);
modelRed.rxns{rxnID} = [modelRed.rxns{rxnID} '_r'];
end
end
end
end
if (checkConsistencyFlag)
fprintf('Perform model consistency check\n');
modelOK = checkConsistency(model,modelRed,tol);
if (~modelOK)
modelRed = expandBounds(model,modelRed,tol);
end
end
else
if (checkConsistencyFlag)
fprintf('Perform model consistency check\n');
modelOK = checkConsistency(model,modelRed,tol);
end
end
%%
function modelRed = expandBounds(model,modelRed,tol)
% Expand bounds to achieve the desired objective value
%
% modelRed = expandBounds(model,modelRed,tol)
%
modelOK = false;
cushion = tol;
tempModel = modelRed;
while (~modelOK)
narrowInd = find(modelRed.ub-modelRed.lb < cushion & modelRed.ub ~= modelRed.lb);
tempModel.lb(narrowInd) = tempModel.lb(narrowInd) - cushion;
narrowIrrevInd =intersect(narrowInd,find(~tempModel.rev));
tempModel.lb(narrowIrrevInd) = max(tempModel.lb(narrowIrrevInd),0);
tempModel.ub(narrowInd) = tempModel.ub(narrowInd) + cushion;
modelRed.lb(narrowInd) = tempModel.lb(narrowInd);
modelRed.ub(narrowInd) = tempModel.ub(narrowInd);
cushion = cushion*2;
modelOK = checkConsistency(model,tempModel,tol);
end
%%
function modelOK = checkConsistency(model,modelRed,tol)
%
% modelOK = checkConsistency(model,modelRed,tol)
%
if (sum(model.c ~= 0) > 0)
% Original model
solOrigMax = optimizeCbModel(model,'max',[]);
solOrigMin = optimizeCbModel(model,'min',[]);
% Reduced model
solRedMax = optimizeCbModel(modelRed,'max',[]);
solRedMin = optimizeCbModel(modelRed,'min',[]);
diffMax = abs(solRedMax.f - solOrigMax.f);
diffMin = abs(solRedMin.f - solOrigMin.f);
if (diffMax > tol || diffMin > tol)
fprintf('Inconsistent objective values %g %g %g %g\n',solOrigMax.f,solRedMax.f,solOrigMin.f,solRedMin.f);
modelOK = false;
else
fprintf('Model is consistent\n');
modelOK = true;
end
else
modelOK = true;
end
|
github
|
EPFL-LCSB/matTFA-master
|
drawLine.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/maps/tools/drawLine.m
| 6,310 |
utf_8
|
4e8f08121c24f5717852ff9ffa6451d7
|
function drawLine(node1,node2,map,edgeColor,edgeArrowColor,edgeWeight,nodeWeight,rxnDir,rxnDirMultiplier)
%drawLine
%
% drawLine(node1,node2,map,edgeColor,edgeArrowColor,edgeWeight,nodeWeight)
%
%INPUTS
% node1 start node
% node2 end node
% map COBRA map structure
% edgeColor Line color
% edgeArrowColor Arrowhead color
% edgeWeight Line width
%
%OPTIONAL INPUT
% nodeWeight Node size
%
%
if nargin < 9
rxnDirMultipler = 2;
end
if nargin < 8
rxnDir = 0;
end
if (nargin < 7)
rad = 20;
else
index1 = find(map.molIndex(:) == node1);
index2 = find(map.molIndex(:) == node2);
if length(index1) == 1
rad = nodeWeight(index1);
elseif length(index2) == 1
rad = nodeWeight(index2);
else
rad = 20;
end
end
if isnan(node1) || isnan(node2)
return;
end
[type1, nodePos(:,1)] = getType(node1, map);
[type2, nodePos(:,2)] = getType(node2, map);
p1 = nodePos(:,1);
p2 = nodePos(:,2);
if type1 == 1 && type2 == 1
drawVector(nodePos(:,1),nodePos(:,2),edgeColor,edgeWeight);
elseif type1 == 1 && type2 == 2
%drawCircle(p2, 3, 'r');
index1 = find(map.connection(:,1) == node2);
index2 = find(map.connection(:,2) == node2);
isend = 0;
if map.connectionReversible(index1) == 1
isend = 1;
end
if length(index1) == 1 && length(index2) == 1 % case metabolite to center reaction.
[point1,dir] = c2p(nodePos(:,1),nodePos(:,2),rad);
drawVector(point1, nodePos(:,2),edgeColor,edgeWeight);
if isend
if rxnDir < 0, rad = rad*rxnDirMultiplier; end
drawArrowhead(point1,dir,rad,edgeArrowColor);
end
elseif length(index1) > 1 && length(index2) == 1
display('blah'); % for some reason this doesn't happen. (metabolite node cannot have more than one point)
elseif length(index1) == 1 && length(index2) > 1
othernode = map.connection(index1,2);
[t3,p3] = getType(othernode, map);
%%%p3 = p3';
direction = p2-p3;
%direction = p3-p2;
if any(direction~=0)
dirnorm = direction/(norm(direction));
else
dirnorm = zeros(size(direction));
end
multiplier = dirnorm' * (p1-p2);
multiplier = max([.3*norm(p2-p1), multiplier]);
ptemp = p2 + multiplier*dirnorm;
distance = norm(ptemp-p1);
if distance < multiplier
multiplier = mean([multiplier, distance]);
end
ptemp = p2 + multiplier*dirnorm;
%drawCircle(ptemp,5,'m');
%drawCircle(p3,5,'g');
[p1,dir] = c2p(p1,ptemp,rad);
drawBezier([p2,ptemp,p1],edgeColor,edgeWeight);
if isend
if rxnDir < 0, rad = rad*rxnDirMultiplier; end
drawArrowhead(p1,dir,rad,edgeArrowColor)
end
else
display('oops');
end
elseif type1 == 2 && type2 == 1
%drawCircle(p1, 3, 'y');
index1 = find(map.connection(:,1) == node1);
index2 = find(map.connection(:,2) == node1);
% if length(index1) == 1 && length(index2) == 1 % case metabolite to center reaction.
% [point2,dir] = c2p(nodePos(:,2),nodePos(:,1),rad);
% drawVector(nodePos(:,1), point2,edgeColor,edgeWeight);
% drawArrowhead(point2,dir,rad,edgeArrowColor);
% elseif length(index1) > 1 && length(index2) == 1
othernode = map.connection(index2,1);
[t3,p3] = getType(othernode, map);
%%%p3 = p3';
direction = p1-p3;
if any(direction~=0)
dirnorm = direction/(norm(direction));
else
dirnorm = zeros(size(direction));
end
multiplier = dirnorm' * (p2-p1);
multiplier = max([ .3*norm(p2-p1), multiplier]);
ptemp = p1 + multiplier*dirnorm;
distance = norm(ptemp-p2);
if distance < multiplier
multiplier = mean([multiplier, distance]);
end
ptemp = p1 + multiplier*dirnorm;
%drawCircle(ptemp,5,'m');
%drawCircle(p3,5,'g');
[p2,dir] = c2p(p2,ptemp,rad);
drawBezier([p1,ptemp,p2],edgeColor,edgeWeight);
if rxnDir > 0, rad = rad*rxnDirMultiplier; end
drawArrowhead(p2,dir,rad,edgeArrowColor);
% elseif length(index1) == 1 && length(index2) > 1
% display('blah2');% for some reason this doesn't happen.
% else
% display('oops');
% end
elseif type1 ==2 && type2 == 2
drawVector(nodePos(:,1),nodePos(:,2),edgeColor,edgeWeight);
else
display('oops');
pause;
end
% % display the reaction label in case of a midpoint
% if rxnTextWeight ~= 0
% if type1 == 2
% index1 = find(map.rxnIndex == node1);
% if map.rxnLabelPosition(1,index1)~= 0
% index2 = find(map.connection(:,1) == node1);
% drawText(map.rxnLabelPosition(1,index1),map.rxnLabelPosition(2,index1),map.connectionAbb(index2),rxnTextWeight,'italic;');
% end
% end
% if type2 == 2
% index1 = find(map.rxnIndex == node1);
% if map.rxnLabelPosition(1,index1)~= 0
% index2 = find(map.connection(:,2) == node2);
% drawText(map.rxnLabelPosition(1,index1),map.rxnLabelPosition(2,index1),map.connectionAbb(index2),rxnTextWeight,'italic');
% end
% end
% end
end
function [type, position] = getType(node, map) % you could also have it output a third value which could be the index of the preceding node.
molIndex = find(map.molIndex == node);
rxnIndex = find(map.rxnIndex == node);
if ~isempty(molIndex)
type = 1; %molecule
position = map.molPosition(:,molIndex);
elseif ~isempty(rxnIndex)
type = 2; % reaction.
position = map.rxnPosition(:,rxnIndex);
%Add more code here to figure out subtype of reaction node.
else % should never get here, but go ahead and scan for errors.
display('errorXYZ in drawLine.m');
% pause;
end
if numel(molIndex) > 1 || numel(rxnIndex) > 1 % this means that it is not unique.
display('error2');
% pause;
end
end
% move p1 from the center of the circle to the pyrimid of the circle in the
% direction of p2
function [point,dir] = c2p(p1,p2,rad)
dir = p2-p1;
point = p1+rad*(dir/sqrt(dir(1)^2+dir(2)^2));
end
|
github
|
EPFL-LCSB/matTFA-master
|
calcGroupStats.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/tools/calcGroupStats.m
| 3,452 |
utf_8
|
06bebf75a99b8cf627b1054f5738961f
|
function [groupStat,groupList,groupCnt,zScore] = calcGroupStats(data,groups,statName,groupList,randStat,nRand)
%calcGroupStats Calculate statistics such as mean or standard deviation for
%subgroups of a population
%
% [groupStat,groupList,groupCnt,zScore] =
% calcGroupStats(data,groups,statName,groupList,randStat,nRand)
%
% data Matrix of data (individuals x variables)
% groups Group identifier for each individual
% statName Name of the statistic to be computed for each group:
% 'mean': mean value for group (default)
% 'std': standard deviation for group
% 'median': median for group
% 'count': sum total of variable values for group
% groupList List of group identifiers to be considered (optional, default
% all values occurring in groups)
% randStat Perform randomization analysis
% nRand # of randomizations
%
% Group identifier can be either strings or numerical values
%
% groupStat Matrix of group statistic values for each group and variable
% groupList List of group identifiers considered
% groupCount Number of individuals in a group
%
% Markus Herrgard 2006
[nItems,nSets] = size(data);
if (nargin < 3)
statName = 'mean';
end
if (nargin < 4)
groupList = unique(groups);
end
if (isempty(groupList))
groupList = unique(groups);
end
if (nargin < 5)
randStat = false;
end
if (nargin < 6)
nRand = 1000;
end
if iscell(groups)
cellFlag = true;
else
cellFlag = false;
end
for i = 1:length(groupList)
if (cellFlag)
selGroup = strcmp(groups,groupList{i});
else
selGroup = (groups == groupList(i));
end
selData = data(selGroup,:);
groupCnt(i) = sum(selGroup);
groupStat(i,:) = calcStatInternal(groupCnt(i),selData,statName,nSets);
end
groupCnt = groupCnt';
if (randStat)
groupCntList = unique(groupCnt);
zScore = zeros(length(groupList),nSets);
for i = 1:length(groupCntList)
thisGroupCnt = groupCntList(i);
selGroups = find(groupCnt == thisGroupCnt);
if (thisGroupCnt > 0)
for j = 1:nRand
randInd = randperm(nItems);
randData = data(randInd(1:thisGroupCnt),:);
groupStatRand(j,:) = calcStatInternal(thisGroupCnt,randData,statName,nSets);
end
groupStatRandMean = nanmean(groupStatRand);
groupStatRandStd = nanstd(groupStatRand);
nGroups = length(selGroups);
zScore(selGroups,:) = (groupStat(selGroups,:)-repmat(groupStatRandMean,nGroups,1))./repmat(groupStatRandStd,nGroups,1);
end
end
end
function groupStat = calcStatInternal(groupCnt,data,statName,nSets)
if (groupCnt > 0)
switch lower(statName)
case 'mean'
if (groupCnt > 1)
groupStat = nanmean(data);
else
groupStat = data;
end
case 'std'
if (groupCnt > 1)
groupStat = nanstd(data);
else
groupStat = zeros(1,nSets);
end
case 'median'
if (groupCnt > 1)
groupStat = nanmedian(data);
else
groupStat = data;
end
case 'count'
if (groupCnt > 1)
groupStat = nansum(data);
else
groupStat = data;
end
end
else
groupStat = ones(1,nSets)*NaN;
end
|
github
|
EPFL-LCSB/matTFA-master
|
solveBooleanRegModel.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/rFBA/solveBooleanRegModel.m
| 3,855 |
utf_8
|
c3c1af861606efb5eb37d3e177c748a7
|
function [finalState,finalInputs1States,finalInputs2States] = solveBooleanRegModel(model,initialState,inputs1States,inputs2States)
% solveBooleanRegModel - determines the next state of the regulatory
% network based on the current state. Called by optimizeRegModel and
% dynamicRFBA
%
% [finalState,finalInputs1States,finalInputs2States] =
% solveBooleanRegModel(model,initialState,inputs1States,inputs2States)
%
% model a regulatory COBRA model
% initialState initial state of regulatory network
% inputs1States initial state of type 1 inputs (metabolites)
% inputs2States initial state of type 2 inputs (reactions)
%
% finalState final state of regulatory network
% finalInputs1States final state of type 1 inputs
% finalInputs2States final state of type 2 inputs
%
% Jeff Orth 7/24/08
% determine state of inputs
% determine external metabolite levels from exchange rxn bounds (maybe change this later)
finalInputs1States = [];
[selExc,selUpt] = findExcRxns(model); %get all exchange rxns
for i = 1:length(model.regulatoryInputs1)
met = model.regulatoryInputs1{i};
fullS = full(model.S);
rxnID = intersect(find(fullS(findMetIDs(model,met),:)),find(selExc));
if model.lb(rxnID) < 0
finalInputs1States(i,1) = true;
else
finalInputs1States(i,1) = false;
end
end
% apply initialState to model, get rxn fluxes
drGenes = {};
for i = 1:length(model.regulatoryGenes)
if initialState(i) == false
drGenes{length(drGenes)+1} = model.regulatoryGenes{i};
end
end
drGenes = intersect(model.genes,drGenes); % remove genes not associated with rxns
modelDR = deleteModelGenes(model,drGenes); % set rxns to 0
fbasolDR = optimizeCbModel(modelDR,'max',true);
% if rxn flux = 0, set state to false
finalInputs2States = [];
if ~any(fbasolDR.x)
finalInputs2States = false.*ones(length(model.regulatoryInputs2),1);
else
for i = 1:length(model.regulatoryInputs2)
rxnFlux = fbasolDR.x(findRxnIDs(model,model.regulatoryInputs2{i}));
if rxnFlux == 0
finalInputs2States(i,1) = false;
else
finalInputs2States(i,1) = true;
end
end
end
% determine state of genes
ruleList = parseRegulatoryRules(model); %get the set of rules in a form that can be evaluated
geneStates = [];
for i = 1:length(model.regulatoryRules)
geneStates(i,1) = eval(ruleList{i});
end
finalState = geneStates;
%% parseRegulatoryRules
function ruleList = parseRegulatoryRules(model)
ruleList = cell(length(model.regulatoryRules),1); %preallocate array
for i = 1:length(model.regulatoryRules)
fields = splitString(model.regulatoryRules{i},'[\s~|&()]');
newFields = fields;
for j = 1:length(fields) %iterate through words and replace
word = fields{j};
if strcmp(word,'true')
newFields{j} = 'true';
elseif strcmp(word,'false')
newFields{j} = 'false';
else
if any(strcmp(word,model.regulatoryGenes))
index = find(strcmp(word,model.regulatoryGenes));
newFields{j} = ['initialState(',num2str(index),')'];
elseif any(strcmp(word,model.regulatoryInputs1))
index = find(strcmp(word,model.regulatoryInputs1));
newFields{j} = ['inputs1States(',num2str(index),')'];
elseif any(strcmp(word,model.regulatoryInputs2))
index = find(strcmp(word,model.regulatoryInputs2));
newFields{j} = ['inputs2States(',num2str(index),')'];
else
newFields{j} = ''; %no match, delete the invalid word
end
end
end
newRule = model.regulatoryRules{i};
for j = 1:length(fields)
newRule = strrep(newRule,fields{j},newFields{j});
end
ruleList{i} = newRule;
end
|
github
|
EPFL-LCSB/matTFA-master
|
readCbModel.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/io/readCbModel.m
| 12,794 |
utf_8
|
96786224cfdf9e5aa3330142d7524196
|
function model = readCbModel(fileName,defaultBound,fileType,modelDescription,compSymbolList,compNameList)
%readCbModel Read in a constraint-based model
%
% model = readCbModel(fileName,defaultBound,fileType,modelDescription)
%
% If no arguments are passed to the function, the user will be prompted for
% a file name.
%
%OPTIONAL INPUTS
% fileName File name for file to read in (optional)
% defaultBound Default value for maximum flux through a reaction if
% not given in the SBML file (Default = 1000)
% fileType File type for input files: 'SBML', 'SimPheny', or
% 'SimPhenyPlus', 'SimPhenyText' (Default = 'SBML')
% * SBML indicates a file in SBML format
% * SimPheny is a set of three files in SimPheny
% simulation output format
% * SimPhenyPlus is the same as SimPheny except with
% additionalfiles containing gene-protein-reaction
% associations andcompound information
% * SimPhenyText is the same as SimPheny except with
% additionaltext file containing gene-protein-reaction
% associations
% modelDescription Description of model contents
% compSymbolList Compartment Symbol List
% compNameList Name of compartments corresponding to compartment
% symbol list
%
%OUTPUT
% Returns a model in the COBRA format:
%
% model
% description Description of model contents
% rxns Reaction names
% mets Metabolite names
% S Stoichiometric matrix
% lb Lower bounds
% ub Upper bounds
% rev Reversibility vector
% c Objective coefficients
% subSystems Subsystem name for each reaction (opt)
% grRules Gene-reaction association rule for each reaction (opt)
% rules Gene-reaction association rule in computable form (opt)
% rxnGeneMat Reaction-to-gene mapping in sparse matrix form (opt)
% genes List of all genes (opt)
% rxnNames Reaction description (opt)
% metNames Metabolite description (opt)
% metFormulas Metabolite chemical formula (opt)
%
%EXAMPLES OF USE:
%
% 1) Load a file to be specified in a dialog box:
%
% model = readCbModel;
%
% 2) Load model named 'iJR904' in SBML format with maximum flux set
% at 1000 (requires file named 'iJR904.xml' to exist)
%
% model = readCbModel('iJR904',1000,'SBML');
%
% 3) Load model named 'iJR904' in SimPheny format with maximum flux set
% at 500 (requires files named 'iJR904.rxn', 'iJR904.met', and 'iJR904.sto' to exist)
%
% model = readCbModel('iJR904',500,'SimPheny');
%
% 4) Load model named 'iJR904' in SimPheny format with gpr and compound information
% (requires files named 'iJR904.rxn', 'iJR904.met','iJR904.sto',
% 'iJR904_gpr.txt', and 'iJR904_cmpd.txt' to exist)
%,
% model = readCbModel('iJR904',500,'SimPhenyPlus');
%
% Markus Herrgard 7/11/06
%
% Richard Que 02/08/10 - Added inptus for compartment names and symbols
%% Process arguments
if (nargin < 2)
defaultBound = 1000;
else
if (isempty(defaultBound))
defaultBound = 1000;
end
end
if (nargin < 3)
fileType = 'SBML';
if (isempty(fileType))
fileType = 'SBML';
end
end
% Open a dialog to select file
if (nargin < 1)
[fileNameFull,filePath] = uigetfile({'*.xml';'*.sto'});
if (fileNameFull)
[t1,t2,t3,t4,tokens] = regexp(fileNameFull,'(.*)\.(\w*)');
noPathName = tokens{1}{1};
fileTypeTmp = tokens{1}{2};
fileName = [filePath noPathName];
else
model = 0;
return;
end
switch fileTypeTmp
case 'xml'
fileType = 'SBML';
case 'sto'
fileType = 'SimPheny';
otherwise
error('Cannot process this file type');
end
end
if (nargin < 4)
if (exist('filePath'))
modelDescription = noPathName;
else
modelDescription = fileName;
end
end
if (nargin < 5)
compSymbolList = {};
compNameList = {};
end
switch fileType
case 'SBML',
if isempty(regexp(fileName,'\.xml$', 'once'))
model = readSBMLCbModel([fileName '.xml'],defaultBound,compSymbolList,compNameList);
else
model = readSBMLCbModel(fileName,defaultBound,compSymbolList,compNameList);
end
case 'SimPheny',
model = readSimPhenyCbModel(fileName,defaultBound,compSymbolList,compNameList);
case 'SimPhenyPlus',
model = readSimPhenyCbModel(fileName,defaultBound,compSymbolList,compNameList);
model = readSimPhenyGprCmpd(fileName,model);
case 'SimPhenyText',
model = readSimPhenyCbModel(fileName,defaultBound,compSymbolList,compNameList);
model = readSimPhenyGprText([fileName '_gpra.txt'],model);
otherwise,
error('Unknown file type');
end
% Check reversibility
model = checkReversibility(model);
% Check uniqueness of metabolite and reaction names
checkCobraModelUnique(model);
model.b = zeros(length(model.mets),1);
model.description = modelDescription;
% End main function
%% Make sure reversibilities are correctly indicated in the model
function model = checkReversibility(model)
selRev = (model.lb < 0 & model.ub > 0);
model.rev(selRev) = 1;
%% readSBMLCbModel Read SBML format constraint-based model
function model = readSBMLCbModel(fileName,defaultBound,compSymbolList,compNameList)
if ~(exist(fileName,'file'))
error(['Input file ' fileName ' not found']);
end
if isempty(compSymbolList)
compSymbolList = {'c','m','v','x','e','t','g','r','n','p'};
compNameList = {'Cytosol','Mitochondria','Vacuole','Peroxisome','Extra-organism','Pool','Golgi Apparatus','Endoplasmic Reticulum','Nucleus','Periplasm'};
end
% Read SBML
modelSBML = TranslateSBML(fileName);
% Convert
model = convertSBMLToCobra(modelSBML,defaultBound,compSymbolList,compNameList);
%%
function model = readSimPhenyCbModel(baseName,defaultBound,compSymbolList,compNameList)
%readSimPhenyCbModel Read a SimPheny metabolic model
%
% model = readSimPhenyCbModel(baseName,defaultBound)
%
% baseName Base filename for models
% vMax Maximum flux through a reaction
%
% model.mets Metabolite names
% model.rxns Reaction names
% model.rev Reversible (1)/Irreversible (0)
% model.lb Lower bound
% model.ub Upper bound
% model.c Objective coefficients
% model.S Stoichiometric matrix
%
% Markus Herrgard 8/3/04
if (nargin < 2)
defaultBound = 1000;
end
if ~(exist([baseName '.met'],'file') & exist([baseName '.rxn'],'file') & exist([baseName '.sto'],'file'))
error('One or more input files not found');
end
if isempty(compSymbolList)
compSymbolList = {'c','m','v','x','e','t','g','r','n','p'};
compNameList = {'Cytosol','Mitochondria','Vacuole','Peroxisome','Extra-organism','Pool','Golgi Apparatus','Endoplasmic Reticulum','Nucleus','Periplasm'};
end
% Get the metabolite names
fid = fopen([baseName '.met']);
cnt = 0;
while 1
tline = fgetl(fid);
if ~ischar(tline), break, end
if (~isempty(regexp(tline,'^\d', 'once')))
cnt = cnt + 1;
fields = splitString(tline,'\t');
mets{cnt} = fields{2};
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% mets{cnt} = strrep(mets{cnt}, '(', '[');
% mets{cnt} = strrep(mets{cnt}, ')', ']');
comp{cnt,1} = fields{4};
% compSymb = compSymbolList{strcmp(compNameList,comp{cnt})};
compSymb = 0;
TF = strcmp('comp{cnt}', compNameList);
for n = 1:length(compNameList)
if TF(n)
compSymb = compSymbolList{n};
end
end
if (isempty(compSymb))
compSymb = comp{cnt};
end
if (~isempty(regexp(mets{cnt},'\(', 'once')))
mets{cnt} = strrep(mets{cnt},'(','[');
mets{cnt} = strrep(mets{cnt},')',']');
else
mets{cnt} = [mets{cnt} '[' compSymb ']'];
end
metNames{cnt} = fields{3};
end
end
fclose(fid);
mets = columnVector(mets);
metNames = columnVector(metNames);
% Get the reaction names, lower/upper bounds, and reversibility
fid = fopen([baseName '.rxn']);
cnt = 0;
startRxns = false;
while 1
tline = fgetl(fid);
if ~ischar(tline), break, end
if (regexp(tline,'^REACTION'))
startRxns = true;
end
if (startRxns & ~isempty(regexp(tline,'^\d', 'once')))
cnt = cnt + 1;
fields = splitString(tline,'\t');
rxns{cnt} = fields{2};
rxnNames{cnt} = fields{3};
revStr{cnt} = fields{4};
lb(cnt) = str2num(fields{5});
ub(cnt) = str2num(fields{6});
c(cnt) = str2num(fields{7});
end
end
fclose(fid);
revStr = columnVector(revStr);
rev = strcmp(revStr,'Reversible');
rxns = columnVector(rxns);
rxnNames = columnVector(rxnNames);
lb = columnVector(lb);
ub = columnVector(ub);
c = columnVector(c);
lb(lb < -defaultBound) = -defaultBound;
ub(ub > defaultBound) = defaultBound;
% Get the stoichiometric matrix
fid = fopen([baseName '.sto']);
fid2 = fopen('load_simpheny.tmp','w');
while 1
tline = fgetl(fid);
if ~ischar(tline), break, end
% This here might give some problems, but it worked for the iJR904
% model
if (~isempty(regexp(tline,'^[-0123456789.]', 'once')))
fprintf(fid2,[tline '\n']);
else
% For debugging
%tline
end
end
fclose(fid);
fclose(fid2);
S = load('load_simpheny.tmp');
% tmp = regexp(rxns,'deleted');
% sel_rxn = ones(length(rxns),1);
% for i = 1:length(tmp)
% if (~isempty(tmp{i}))
% sel_rxn(i) = 0;
% end
% end
%
% tmp = regexp(mets,'deleted');
% sel_met = ones(length(mets),1);
% for i = 1:length(tmp)
% if (~isempty(tmp{i}))
% sel_met(i) = 0;
% end
% end
% Store the variables in a structure
model.mets = mets;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
model.metComps = comp;
model.metNames = metNames;
model.rxns = removeDeletedTags(rxns);
model.rxnNames = rxnNames;
model.rev = rev;
model.lb = lb;
model.ub = ub;
model.c = c;
model.S = sparse(S);
% Delete the temporary file
delete('load_simpheny.tmp');
%%
function list = removeDeletedTags(list)
%removeDeletedTags Get rid of the [deleted tags in the SimPheny files
%
% list = removeDeletedTags(list)
%
% 5/19/05 Markus Herrgard
for i = 1:length(list)
item = list{i};
ind = strfind(item,' [deleted');
if (~isempty(ind))
list{i} = item(1:(ind-1));
end
end
%% readSimPhenyGprCmpd Read SimPheny GPRA and compound data and integrate it
% with the model
function model = readSimPhenyGprCmpd(baseName,model)
[rxnInfo,rxns,allGenes] = readSimPhenyGPR([baseName '_gpr.txt']);
nRxns = length(model.rxns);
% Construct gene to rxn mapping
rxnGeneMat = sparse(nRxns,length(allGenes));
h = waitbar(0,'Constructing GPR mapping ...');
for i = 1:nRxns
rxnID = find(ismember(rxns,model.rxns{i}));
if (~isempty(rxnID))
if mod(i,10) == 0
waitbar(i/nRxns,h);
end
[tmp,geneInd] = ismember(rxnInfo(rxnID).genes,allGenes);
rxnGeneMat(i,geneInd) = 1;
rules{i} = rxnInfo(rxnID).rule;
grRules{i} = rxnInfo(rxnID).gra;
grRules{i} = regexprep(grRules{i},'\s{2,}',' ');
grRules{i} = regexprep(grRules{i},'( ','(');
grRules{i} = regexprep(grRules{i},' )',')');
subSystems{i} = rxnInfo(rxnID).subSystem;
for j = 1:length(geneInd)
%rules{i} = strrep(rules{i},['x(' num2str(j) ')'],['x(' num2str(geneInd(j)) ')']);
rules{i} = strrep(rules{i},['x(' num2str(j) ')'],['x(' num2str(geneInd(j)) '_TMP_)']);
end
rules{i} = strrep(rules{i},'_TMP_','');
else
rules{i} = '';
grRules{i} = '';
subSystems{i} = '';
end
end
if ( regexp( version, 'R20') )
close(h);
end
%% Read SimPheny cmpd output file
[metInfo,mets] = readSimPhenyCMPD([baseName '_cmpd.txt']);
baseMets = parseMetNames(model.mets);
nMets = length(model.mets);
h = waitbar(0,'Constructing metabolite lists ...');
for i = 1:nMets
if mod(i,10) == 0
waitbar(i/nMets,h);
end
metID = find(ismember(mets,baseMets{i}));
if (~isempty(metID))
metFormulas{i} = metInfo(metID).formula;
else
metFormulas{i} = '';
end
end
if ( regexp( version, 'R20') )
close(h);
end
model.rxnGeneMat = rxnGeneMat;
model.rules = columnVector(rules);
model.grRules = columnVector(grRules);
model.genes = columnVector(allGenes);
model.metFormulas = columnVector(metFormulas);
model.subSystems = columnVector(subSystems);
|
github
|
EPFL-LCSB/matTFA-master
|
convertCobraToSBML.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/io/convertCobraToSBML.m
| 10,266 |
utf_8
|
ff076a85c6b0755e496ccb290d0442e2
|
function sbmlModel = convertCobraToSBML(model,sbmlLevel,sbmlVersion,compSymbolList,compNameList,debug_function)
%convertCobraToSBML converts a cobra structure to an sbml
%structure using the structures provided in the SBML toolbox 3.1.0
%
% sbmlModel = convertCobraToSBML(model,sbmlLevel,sbmlVersion,compSymbolList,compNameList)
%
%INPUTS
% model COBRA model structure
%
%OPTIONAL INPUTS
% sbmlLevel SBML Level (default = 2)
% sbmlVersion SBML Version (default = 1)
% compSymbolList List of compartment symbols
% compNameList List of copmartment names correspoding to compSymbolList
%
%OUTPUT
% sbmlModel SBML MATLAB structure
%
%
%NOTE: The name mangling of reaction and metabolite ids is necessary
%for compliance with the SBML sID standard.
%
%NOTE: Sometimes the Model_create function doesn't listen to the
%sbmlVersion parameter, so it is essential that the items that
%are added to the sbmlModel are defined with the sbmlModel's level
%and version: sbmlModel.SBML_level,sbmlModel.SBML_version
%
%NOTE: Some of the structures are recycled to reduce to overhead for
%their creation. There's a chance this can cause bugs in the future.
%
%NOTE: Currently, I don't add in the boundary metabolites.
%
%NOTE: Speed could probably be improved by directly adding structures to
%lists in a struct instead of using the SBML _addItem function, but this
%could break in future versions of the SBML toolbox.
%
%POTENTIAL FUTURE BUG: To speed things up, sbml structs have been
%recycled and are directly appended into lists instead of using _addItem
if (~exist('sbmlLevel','var') || isempty(sbmlLevel))
sbmlLevel = 2;
end
if (~exist('sbmlVersion','var') || isempty(sbmlVersion))
sbmlVersion = 1;
end
if (~exist('debug_function','var') || isempty(debug_function))
debug_function = 0;
end
reaction_units = 'mmol_per_gDW_per_hr';
sbmlModel = Model_create(sbmlLevel, sbmlVersion);
sbmlModel.namespaces = struct();
sbmlModel.namespaces.prefix = '';
sbmlModel.namespaces.uri = 'http://www.sbml.org/sbml/level2';
if isfield(model,'description')
sbmlModel.id = strrep(strrep(strrep(model.description,'.','_'), filesep, '_'), ':','_');
else
sbmlModel.id = '';
end
%POTENTIAL FUTURE BUG: Create temporary structs to speed things up.
tmp_unit = Unit_create(sbmlModel.SBML_level, sbmlModel.SBML_version);
tmp_species = Species_create(sbmlModel.SBML_level, sbmlModel.SBML_version);
sbml_tmp_compartment = Compartment_create(sbmlModel.SBML_level, sbmlModel.SBML_version);
sbml_tmp_parameter = Parameter_create(sbmlModel.SBML_level, sbmlModel.SBML_version);
sbml_tmp_species_ref = SpeciesReference_create(sbmlModel.SBML_level, sbmlModel.SBML_version);
sbml_tmp_reaction = Reaction_create(sbmlModel.SBML_level, sbmlModel.SBML_version);
sbml_tmp_law = KineticLaw_create(sbmlModel.SBML_level, sbmlModel.SBML_version);
tmp_unit_definition = UnitDefinition_create(sbmlModel.SBML_level, sbmlModel.SBML_version);
%% Compartments
if ~exist('compSymbolList','var') || isempty(compSymbolList)
compSymbolList = {'c','m','v','x','e','t','g','r','n','p','l'};
compNameList = {'Cytoplasm','Mitochondrion','Vacuole','Peroxisome','Extracellular','Pool','Golgi','Endoplasmic_reticulum','Nucleus','Periplasm','Lysosome'};
end
%Create and add the unit definition to the sbml model struct.
tmp_unit_definition.id = reaction_units;
%The 4 following lists are in matched order for each unit.
unit_kinds = {'mole','gram','second'};
unit_exponents = [1 -1 -1];
unit_scales = [-3 0 0];
unit_multipliers = [1 1 1.0/60/60];
%Add the units to the unit definition
for i = 1:size(unit_kinds, 2)
tmp_unit.kind = unit_kinds{ i };
tmp_unit.exponent = unit_exponents(i);
tmp_unit.scale = unit_scales(i);
tmp_unit.multiplier = unit_multipliers(i);
tmp_unit_definition = UnitDefinition_addUnit(tmp_unit_definition, tmp_unit);
end
if debug_function
if ~isSBML_Unit(tmp_unit_definition)
error('unit definition failed')
end
end
sbmlModel = Model_addUnitDefinition(sbmlModel, tmp_unit_definition);
%List to hold the compartment ids.
the_compartments = {};
%separate metabolite and compartment
[tokens tmp_met_struct] = regexp(model.mets,'(?<met>.+)\[(?<comp>.+)\]|(?<met>.+)\((?<comp>.+)\)','tokens','names');
for (i=1:size(model.mets, 1))
tmp_notes='';
tmp_met = tmp_met_struct{i}.met;
%Change id to correspond to SBML id specifications
tmp_met = strcat('M_', (tmp_met), '_', tmp_met_struct{i}.comp);
model.mets{ i } = formatForSBMLID(tmp_met);
tmp_species.id = formatForSBMLID(tmp_met);
tmp_species.compartment = formatForSBMLID(tmp_met_struct{i}.comp);
if isfield(model, 'metNames')
tmp_species.name = (model.metNames{i});
end
if isfield(model, 'metFormulas')
tmp_notes = [tmp_notes '<p>FORMULA: ' model.metFormulas{i} '</p>'];
end
if isfield(model, 'metCharge')
%NOTE: charge is being removed in SBML level 3
% tmp_species.charge = model.metCharge(i);
% tmp_species.isSetCharge = 1;
tmp_notes = [tmp_notes '<p>CHARGE: ' num2str(model.metCharge(i)) '</p>'];
end
if ~isempty(tmp_notes)
tmp_species.notes = ['<body xmlns="http://www.w3.org/1999/xhtml">' tmp_notes '</body>'];
end
sbmlModel.species = [ sbmlModel.species tmp_species ];
%This is where the compartment symbols are aggregated.
the_compartments{ i } = tmp_species.compartment ;
end
if debug_function
for (i = 1:size(sbmlModel.species, 2))
if ~isSBML_Species(sbmlModel.species(i), sbmlLevel, sbmlVersion)
error('SBML species failed to pass test')
end
end
end
%Add the unique compartments to the model struct.
the_compartments = unique(the_compartments);
for (i=1:size(the_compartments,2))
tmp_id = the_compartments{1,i};
tmp_symbol_index = find(strcmp(formatForSBMLID(compSymbolList),tmp_id));
%Check that symbol is in compSymbolList
if ~isempty(tmp_symbol_index)
tmp_name = compNameList{tmp_symbol_index};
else
error(['Unknown compartment: ' tmp_id '. Be sure that ' tmp_id ' is specified in compSymbolList and compNameList.'])
end
tmp_id = formatForSBMLID(tmp_id);
sbml_tmp_compartment.id = tmp_id;
sbml_tmp_compartment.name = tmp_name;
sbmlModel = Model_addCompartment(sbmlModel, sbml_tmp_compartment);
end
if debug_function
for (i = 1:size(sbmlModel.compartment, 2))
if ~isSBML_Compartment(sbmlModel.compartment(i), sbmlLevel, sbmlVersion)
error('SBML compartment failed to pass test')
end
end
end
%Add the reactions to the model struct. Use the species references.
sbml_tmp_parameter.units = reaction_units;
sbml_tmp_parameter.isSetValue = 1;
for (i=1:size(model.rxns, 1))
tmp_id = strcat('R_', formatForSBMLID(model.rxns{i}));
model.rxns{i} = tmp_id;
met_idx = find(model.S(:, i));
sbml_tmp_reaction.notes = '';
%Reset the fields that have been filled.
sbml_tmp_reaction.reactant = [];
sbml_tmp_reaction.product = [];
sbml_tmp_reaction.kineticLaw = [];
sbml_tmp_reaction.id = tmp_id;
if isfield(model, 'rxnNames')
sbml_tmp_reaction.name = model.rxnNames{i};
end
if isfield(model, 'rev')
sbml_tmp_reaction.reversible = model.rev(i);
end
sbml_tmp_law.parameter = [];
sbml_tmp_law.formula = 'FLUX_VALUE';
sbml_tmp_parameter.id = 'LOWER_BOUND';
sbml_tmp_parameter.value = model.lb(i);
sbml_tmp_law.parameter = [ sbml_tmp_law.parameter sbml_tmp_parameter ];
sbml_tmp_parameter.id = 'UPPER_BOUND';
sbml_tmp_parameter.value = model.ub(i);
sbml_tmp_law.parameter = [ sbml_tmp_law.parameter sbml_tmp_parameter ];
sbml_tmp_parameter.id = 'FLUX_VALUE';
sbml_tmp_parameter.value = 0;
sbml_tmp_law.parameter = [ sbml_tmp_law.parameter sbml_tmp_parameter ];
sbml_tmp_parameter.id = 'OBJECTIVE_COEFFICIENT';
sbml_tmp_parameter.value = model.c(i);
sbml_tmp_law.parameter = [ sbml_tmp_law.parameter sbml_tmp_parameter ];
sbml_tmp_reaction.kineticLaw = sbml_tmp_law;
%Add in other notes
tmp_note = '';
if isfield(model, 'grRules')
tmp_note = [tmp_note '<p>GENE_ASSOCIATION: ' model.grRules{i} '</p>' ];
end
if isfield(model, 'subSystems')
tmp_note = [ tmp_note ' <p>SUBSYSTEM: ' model.subSystems{i} '</p>'];
end
if isfield(model, 'rxnECNumbers')
tmp_note = [ tmp_note ' <p>EC Number: ' model.rxnECNumbers{i} '</p>'];
end
if isfield(model, 'confidenceScores')
tmp_note = [ tmp_note ' <p>Confidence Level: ' model.confidenceScores{i} '</p>'];
end
if isfield(model, 'rxnReferences')
tmp_note = [ tmp_note ' <p>AUTHORS: ' model.rxnReferences{i} '</p>'];
end
if isfield(model, 'rxnNotes')
tmp_note = [ tmp_note ' <p>' model.rxnNotes{i} '</p>'];
end
if ~isempty(tmp_note)
sbml_tmp_reaction.notes = ['<body xmlns="http://www.w3.org/1999/xhtml">' tmp_note '</body>'];
end
%Add in the reactants and products
for (j_met=1:size(met_idx,1))
tmp_idx = met_idx(j_met,1);
sbml_tmp_species_ref.species = model.mets{tmp_idx};
met_stoich = model.S(tmp_idx, i);
sbml_tmp_species_ref.stoichiometry = abs(met_stoich);
if (met_stoich > 0)
sbml_tmp_reaction.product = [ sbml_tmp_reaction.product sbml_tmp_species_ref ];
else
sbml_tmp_reaction.reactant = [ sbml_tmp_reaction.reactant sbml_tmp_species_ref];
end
end
sbmlModel.reaction = [ sbmlModel.reaction sbml_tmp_reaction ];
end
if debug_function
for (i = 1:size(sbmlModel.reaction, 2))
if ~isSBML_Reaction(sbmlModel.reaction(i), sbmlLevel, sbmlVersion)
error('SBML reaction failed to pass test')
end
end
end
%% Format For SBML
function str = formatForSBMLID(str)
str = strrep(str,'-','_DASH_');
str = strrep(str,'/','_FSLASH_');
str = strrep(str,'\','_BSLASH_');
str = strrep(str,'(','_LPAREN_');
str = strrep(str,')','_RPAREN_');
str = strrep(str,'[','_LSQBKT_');
str = strrep(str,']','_RSQBKT_');
str = strrep(str,',','_COMMA_');
str = strrep(str,'.','_PERIOD_');
str = strrep(str,'''','_APOS_');
str = regexprep(str,'\(e\)$','_e');
str = strrep(str,'&','&');
str = strrep(str,'<','<');
str = strrep(str,'>','>');
str = strrep(str,'"','"');
|
github
|
EPFL-LCSB/matTFA-master
|
writeCbModel.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/io/writeCbModel.m
| 10,729 |
utf_8
|
0a6994071e50ffd3dc681e8043552a69
|
function writeCbModel(model,format,fileName,compSymbolList,compNameList,sbmlLevel,sbmlVersion)
%writeCbModel Write out COBRA models in various formats
%
% writeCbModel(model,format,fileName,compSymbolList,compNameList,sbmlLevel,sbmlVersion)
%
%INPUTS
% model Standard COBRA model structure
% format File format to be used ('text','xls' or 'sbml')
%
%OPTIONAL INPUTS
% fileName File name for output file (optional, default opens
% dialog box)
% compSymbolList List of compartment symbols
% compNameList List of compartment names corresponding to compSymbolList
% sbmlLevel SBML Level (default = 2)
% sbmlVersion SBML Version (default = 1)
%
% Markus Herrgard 2/5/07
% Ines Thiele 01/10 - Added more options for field to write in xls format
% Richard Que (3/17/10) Added ability to specify compartment names and
% symbols
if nargin < 4
compSymbolList = {};
compNameList = {};
end
if nargin < 6
sbmlLevel = 2;
sbmlVersion = 1;
end
[nMets,nRxns] = size(model.S);
formulas = printRxnFormula(model,model.rxns,false,false,false,1,false);
%% Open a dialog to select file name
if (nargin < 3 & ~strcmp(format,'sbml'))
switch format
case 'xls'
[fileNameFull,filePath] = uiputfile({'*.xls'});
case {'text','txt'}
[fileNameFull,filePath] = uiputfile({'*.txt'});
case 'xml'
[fileNameFull,filePath] = uiputfile({'*.xml'});
otherwise
[fileNameFull,filePath] = uiputfile({'*'});
end
if (fileNameFull)
[t1,t2,t3,t4,tokens] = regexp(fileNameFull,'(\w*)\.(\w*)');
fileName = [filePath tokens{1}{1}];
switch tokens{1}{2}
case 'xls'
format = 'xls';
case 'txt'
format = 'text';
fileName = [fileName '.txt'];
case 'xml'
format = 'sbml';
% fprintf('Note that you will be asked to supply the file name again (this is a feature, not a bug)');
otherwise
format = 'unknown';
end
else
return;
end
end
switch format
%% Text file
case {'text','txt'}
fid = fopen(fileName,'w');
fprintf(fid,'Rxn name\t');
if (isfield(model,'rxnNames'))
fprintf(fid,'Rxn description\t');
end
fprintf(fid,'Formula\t');
if (isfield(model,'grRules'))
fprintf(fid,'Gene-reaction association\t');
end
fprintf(fid,'Reversible\tLB\tUB\tObjective\n');
for i = 1:nRxns
fprintf(fid,'%s\t',model.rxns{i});
if (isfield(model,'rxnNames'))
fprintf(fid,'%s\t',model.rxnNames{i});
end
fprintf(fid,'%s\t',formulas{i});
if (isfield(model,'grRules'))
fprintf(fid,'%s\t',model.grRules{i});
end
fprintf(fid,'%d\t%6.2f\t%6.2f\t%6.2f\n',model.rev(i),model.lb(i),model.ub(i),model.c(i));
end
fprintf(fid,'Metabolite name\tMetabolite description\tMetabolite formula\n');
for i = 1:nMets
fprintf(fid,'%s',model.mets{i});
if isfield(model,'metNames')
fprintf(fid,'\t%s',model.metNames{i});
end
if isfield(model,'metFormulas')
fprintf(fid,'\t%s',model.metFormulas{i});
end
fprintf(fid,'\n');
end
fclose(fid);
%% Excel file
case 'xls'
tmpData{1,1} = 'Rxn name';
tmpData{1,2} = 'Rxn description';
baseInd = 3;
tmpData{1,baseInd} = 'Formula';
tmpData{1,baseInd+1} = 'Gene-reaction association';
tmpData{1,baseInd+2} = 'Genes';
tmpData{1,baseInd+3} = 'Proteins';
tmpData{1,baseInd+4} = 'Subsystem';
tmpData{1,baseInd+5} = 'Reversible';
tmpData{1,baseInd+6} = 'LB';
tmpData{1,baseInd+7} = 'UB';
tmpData{1,baseInd+8} = 'Objective';
tmpData{1,baseInd+9} = 'Confidence Score';
tmpData{1,baseInd+10} = 'EC Number';
tmpData{1,baseInd+11} = 'Notes';
tmpData{1,baseInd+12} = 'References';
for i = 1:nRxns
tmpData{i+1,1} = chopForExcel(model.rxns{i});
if (isfield(model,'rxnNames'))
tmpData{i+1,2} = chopForExcel(model.rxnNames{i});
else
tmpData{i+1,2} = '';
end
tmpData{i+1,baseInd} = chopForExcel(formulas{i});
if (isfield(model,'geneNameRules'))
tmpData{i+1,baseInd+1} = chopForExcel(model.geneNameRules{i});
elseif (isfield(model,'grRules'))
tmpData{i+1,baseInd+1} = chopForExcel(model.grRules{i});
else
tmpData{i+1,baseInd+1} = '';
end
if (isfield(model,'geneNames'))
geneNames = model.geneNames(model.rxnGeneMat(i,:) == 1);
tmpData{i+1,baseInd+2} = constructGeneStr(geneNames);
elseif (isfield(model,'genes'))
geneNames = model.genes(model.rxnGeneMat(i,:) == 1);
tmpData{i+1,baseInd+2} = constructGeneStr(geneNames);
else
tmpData{i+1,baseInd+2} = '';
end
if (isfield(model,'proteins'))
tmpData{i+1,baseInd+3} = chopForExcel(model.proteins{i});
else
tmpData{i+1,baseInd+3} = '';
end
if (isfield(model,'subSystems'))
tmpData{i+1,baseInd+4} = chopForExcel(char(model.subSystems{i}));
else
tmpData{i+1,baseInd+4} = '';
end
tmpData{i+1,baseInd+5} = model.rev(i)*1.0;
tmpData{i+1,baseInd+6} = model.lb(i);
tmpData{i+1,baseInd+7} = model.ub(i);
tmpData{i+1,baseInd+8} = model.c(i);
if (isfield(model,'confidenceScores'))
tmpData{i+1,baseInd+9} = chopForExcel(num2str(model.confidenceScores{i}));
else
tmpData{i+1,baseInd+9} = '';
end
if (isfield(model,'rxnECNumbers'))
tmpData{i+1,baseInd+10} = chopForExcel(model.rxnECNumbers{i});
else
tmpData{i+1,baseInd+10} = '';
end
if (isfield(model,'rxnNotes'))
tmpData{i+1,baseInd+11} = chopForExcel(char(model.rxnNotes{i}));
else
tmpData{i+1,baseInd+11} = '';
end
if (isfield(model,'rxnReferences'))
tmpData{i+1,baseInd+12} = chopForExcel(char(model.rxnReferences{i}));
else
tmpData{i+1,baseInd+12} = '';
end
end
%keyboard
xlswrite(fileName,tmpData,'reactions');
if isfield(model,'metNames')
tmpMetData{1,1} = 'Metabolite name';
tmpMetData{1,2} = 'Metabolite description';
tmpMetData{1,3} = 'Metabolite neutral formula';
tmpMetData{1,4} = 'Metabolite charged formula';
tmpMetData{1,5} = 'Metabolite charge';
tmpMetData{1,6} = 'Metabolite Compartment';
tmpMetData{1,7} = 'Metabolite KEGGID';
tmpMetData{1,8} = 'Metabolite PubChemID';
tmpMetData{1,9} = 'Metabolite CheBI ID';
tmpMetData{1,10} = 'Metabolite Inchi String';
tmpMetData{1,11} = 'Metabolite Smile';
for i = 1:nMets
tmpMetData{i+1,1} = chopForExcel(model.mets{i});
tmpMetData{i+1,2} = chopForExcel(model.metNames{i});
if isfield(model,'metFormulasNeutral')
tmpMetData{i+1,3} = chopForExcel(model.metFormulasNeutral{i});
else
tmpMetData{i+1,3} = '';
end
if isfield(model,'metFormulas')
tmpMetData{i+1,4} = chopForExcel(model.metFormulas{i});
else
tmpMetData{i+1,4} = '';
end
if isfield(model,'metCharge')
tmpMetData{i+1,5} = chopForExcel(model.metCharge(i));
else
tmpMetData{i+1,5} = '';
end
if isfield(model,'metCompartment')
tmpMetData{i+1,6} = chopForExcel(model.metCompartment{i});
else
tmpMetData{i+1,6} = '';
end
if isfield(model,'metKEGGID')
tmpMetData{i+1,7} = chopForExcel(model.metKEGGID{i});
else
tmpMetData{i+1,7} = '';
end
if isfield(model,'metPubChemID')
if iscell(model.metPubChemID(i))
tmpMetData{i+1,8} = chopForExcel(model.metPubChemID{i});
else
tmpMetData{i+1,8} = chopForExcel(model.metPubChemID(i));
end
else
tmpMetData{i+1,8} = '';
end
if isfield(model,'metChEBIID')
tmpMetData{i+1,9} = chopForExcel(model.metChEBIID(i));
else
tmpMetData{i+1,9} = '';
end
if isfield(model,'metInchiString')
tmpMetData{i+1,10} = chopForExcel(model.metInchiString{i});
else
tmpMetData{i+1,10} = '';
end
if isfield(model,'metSmiles')
tmpMetData{i+1,11} = chopForExcel(model.metSmiles{i});
else
tmpMetData{i+1,11} = '';
end
end
xlswrite(fileName,tmpMetData,'metabolites');
else
xlswrite(fileName,model.mets,'metabolites');
end
%% SBML
case 'sbml'
sbmlModel = convertCobraToSBML(model,sbmlLevel,sbmlVersion,compSymbolList,compNameList);
if exist('fileName','var')&&~isempty(fileName)
OutputSBML(sbmlModel,fileName);
else
OutputSBML(sbmlModel);
end
%% Unknown
otherwise
error('Unknown file format');
end
%% Chop strings for excel output
function strOut = chopForExcel(str)
if (length(str) > 5000)
strOut = str(1:5000);
fprintf('String longer than 5000 characters - truncated for Excel output\n%s\n',str);
else
strOut = str;
end
%% Construct gene name string
function geneStr = constructGeneStr(geneNames)
geneStr = '';
for i = 1:length(geneNames)
geneStr = [geneStr ' ' geneNames{i}];
end
geneStr = strtrim(geneStr);
|
github
|
EPFL-LCSB/matTFA-master
|
convertSBMLToCobra.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/io/convertSBMLToCobra.m
| 14,410 |
utf_8
|
ca4c9588a99e906f4a3636188d2c0574
|
function model = convertSBMLToCobra(modelSBML,defaultBound,compSymbolList,compNameList)
%convertSBMLToCobra Convert SBML format model (created using SBML Toolbox)
%to Cobra format
%
% model = convertSBMLToCobra(modelSBML,defaultBound)
%
%INPUTS
% modelSBML SBML model structure
%
%OPTIONAL INPUTS
% defaultBound Maximum bound for model (Default = 1000)
% compSymbolList List of compartment symbols
% compNameList List of compartment names corresponding to compSymbolList
%
%OUTPUT
% model COBRA model structure
% Markus Herrgard 1/25/08
%
% Ines Thiele 01/27/2010 - I added new field to be read-in from SBML file
% if provided in file (e.g., references, comments, metabolite IDs, etc.)
%
% Richard Que 02/08/10 - Properly format reaction and metabolite fields
% from SBML.
%
if (nargin < 2)
defaultBound = 1000;
end
if nargin < 3
compSymbolList = {};
compNameList = {};
end
nMetsTmp = length(modelSBML.species);
nRxns = length(modelSBML.reaction);
%% Construct initial metabolite list
formulaCount = 0;
speciesList = {};
chargeList = [];
metFormulas = {};
haveFormulasFlag = false;
tmpSpecies = [];
for i = 1:nMetsTmp
% Ignore boundary metabolites
if (~modelSBML.species(i).boundaryCondition)
%Check for the Palsson lab _b$ boundary condition indicator
if (isempty(regexp(modelSBML.species(i).id,'_b$')));
tmpSpecies = [ tmpSpecies modelSBML.species(i)];
speciesList{end+1} = modelSBML.species(i).id;
notesField = modelSBML.species(i).notes;
% Get formula if in notes field
if (~isempty(notesField))
[tmp,tmp,tmp,tmp,formula,tmp,tmp,tmp,tmp,charge] = parseSBMLNotesField(notesField);
tmpCharge = charge;
metFormulas {end+1} = formula;
formulaCount = formulaCount + 1;
haveFormulasFlag = true;
end
chargeList= [chargeList modelSBML.species(i).charge];
end
end
end
nMets = length(speciesList);
%% Construct stoichiometric matrix and reaction list
S = sparse(nMets,nRxns);
rev = zeros(nRxns,1);
lb = zeros(nRxns,1);
ub = zeros(nRxns,1);
c = zeros(nRxns,1);
rxns = cell(nRxns,1);
rules = cell(nRxns,1);
genes = cell(nRxns,1);
allGenes = {};
h = waitbar(0,'Reading SBML file ...');
hasNotesField = false;
for i = 1:nRxns
if mod(i,10) == 0
waitbar(i/nRxns,h);
end
% Read the gpra from the notes field
notesField = modelSBML.reaction(i).notes;
if (~isempty(notesField))
[geneList,rule,subSystem,grRule,formula,confidenceScore, citation, comment, ecNumber] = parseSBMLNotesField(notesField);
subSystems{i} = subSystem;
genes{i} = geneList;
allGenes = [allGenes geneList];
rules{i} = rule;
grRules{i} = grRule;
hasNotesField = true;
confidenceScores{i}= confidenceScore;
citations{i} = citation;
comments{i} = comment;
ecNumbers{i} = ecNumber;
end
rev(i) = modelSBML.reaction(i).reversible;
rxnNameTmp = regexprep(modelSBML.reaction(i).name,'^R_','');
rxnNames{i} = regexprep(rxnNameTmp,'_+',' ');
rxnsTmp = regexprep(modelSBML.reaction(i).id,'^R_','');
rxns{i} = cleanUpFormatting(rxnsTmp);
% Construct S-matrix
reactantStruct = modelSBML.reaction(i).reactant;
for j = 1:length(reactantStruct)
speciesID = find(strcmp(reactantStruct(j).species,speciesList));
if (~isempty(speciesID))
stoichCoeff = reactantStruct(j).stoichiometry;
S(speciesID,i) = -stoichCoeff;
end
end
productStruct = modelSBML.reaction(i).product;
for j = 1:length(productStruct)
speciesID = find(strcmp(productStruct(j).species,speciesList));
if (~isempty(speciesID))
stoichCoeff = productStruct(j).stoichiometry;
S(speciesID,i) = stoichCoeff;
end
end
if isfield(modelSBML.reaction(i).kineticLaw,'parameter')
parameters = modelSBML.reaction(i).kineticLaw.parameter;
else
parameters =[];
end
if (~isempty(parameters))
for j = 1:length(parameters)
paramStruct = parameters(j);
switch paramStruct.id
case 'LOWER_BOUND'
lb(i) = paramStruct.value;
if (lb(i) < -defaultBound)
lb(i) = -defaultBound;
end
case 'UPPER_BOUND'
ub(i) = paramStruct.value;
if (ub(i) > defaultBound)
ub(i) = defaultBound;
end
case 'OBJECTIVE_COEFFICIENT'
c(i) = paramStruct.value;
end
end
else
ub(i) = defaultBound;
if (rev(i) == 1)
lb(i) = -defaultBound;
else
lb(i) = 0;
end
end
end
%close the waitbar if this is matlab
if (regexp(version, 'R20'))
close(h);
end
allGenes = unique(allGenes);
%% Construct gene to rxn mapping
if (hasNotesField)
rxnGeneMat = sparse(nRxns,length(allGenes));
h = waitbar(0,'Constructing GPR mapping ...');
for i = 1:nRxns
if mod(i,10) == 0
waitbar(i/nRxns,h);
end
if iscell(genes{i})
[tmp,geneInd] = ismember(genes{i},allGenes);
else
[tmp,geneInd] = ismember(num2cell(genes{i}),allGenes);
end
rxnGeneMat(i,geneInd) = 1;
for j = 1:length(geneInd)
rules{i} = strrep(rules{i},['x(' num2str(j) ')'],['x(' num2str(geneInd(j)) '_TMP_)']);
end
rules{i} = strrep(rules{i},'_TMP_','');
end
%close the waitbar if this is matlab
if (regexp(version, 'R20'))
close(h);
end
end
%% Construct metabolite list
mets = cell(nMets,1);
compartmentList = cell(length(modelSBML.compartment),1);
if isempty(compSymbolList), useCompList = true; else useCompList = false; end
for i=1:length(modelSBML.compartment)
compartmentList{i} = modelSBML.compartment(i).id;
end
h = waitbar(0,'Constructing metabolite lists ...');
hasAnnotationField = 0;
for i = 1:nMets
if mod(i,10) == 0
waitbar(i/nMets,h);
end
% Parse metabolite id's
% Get rid of the M_ in the beginning of metabolite id's
metID = regexprep(speciesList{i},'^M_','');
metID = regexprep(metID,'^_','');
% Find compartment id
tmpCell = {};
if useCompList
for j=1:length(compartmentList)
tmpCell = regexp(metID,['_(' compartmentList{j} ')$'],'tokens');
if ~isempty(tmpCell), break; end
end
if isempty(tmpCell), useCompList = false; end
elseif ~isempty(compSymbolList)
for j = 1: length(compSymbolList)
tmpCell = regexp(metID,['_(' compSymbolList{j} ')$'],'tokens');
if ~isempty(tmpCell), break; end
end
end
if isempty(tmpCell), tmpCell = regexp(metID,'_(.)$','tokens'); end
if ~isempty(tmpCell)
compID = tmpCell{1};
metTmp = [regexprep(metID,['_' compID{1} '$'],'') '[' compID{1} ']'];
else
metTmp = metID;
end
%Clean up met ID
mets{i} = cleanUpFormatting(metTmp);
% Parse metabolite names
% Clean up some of the weird stuff in the sbml files
metNamesTmp = regexprep(tmpSpecies(i).name,'^M_','');
metNamesTmp = cleanUpFormatting(metNamesTmp);
metNamesTmp = regexprep(metNamesTmp,'^_','');
% metNamesTmp = strrep(metNamesTmp,'_','-');
metNamesTmp = regexprep(metNamesTmp,'-+','-');
metNamesTmp = regexprep(metNamesTmp,'-$','');
metNamesAlt{i} = metNamesTmp;
% Separate formulas from names
%[tmp,tmp,tmp,tmp,tokens] = regexp(metNamesTmp,'(.*)-((([A(Ag)(As)C(Ca)(Cd)(Cl)(Co)(Cu)F(Fe)H(Hg)IKLM(Mg)(Mn)N(Na)(Ni)OPRS(Se)UWXY(Zn)]?)(\d*)))*$');
if (~haveFormulasFlag)
[tmp,tmp,tmp,tmp,tokens] = regexp(metNamesTmp,'(.*)_((((A|Ag|As|C|Ca|Cd|Cl|Co|Cu|F|Fe|H|Hg|I|K|L|M|Mg|Mn|Mo|N|Na|Ni|O|P|R|S|Se|U|W|X|Y|Zn)?)(\d*)))*$');
if (isempty(tokens))
if length(metFormulas)<i||(metFormulas{i}=='')
metFormulas{i} = '';
end
metNames{i} = metNamesTmp;
else
formulaCount = formulaCount + 1;
metFormulas{i} = tokens{1}{2};
metNames{i} = tokens{1}{1};
end
else
metNames{i} = metNamesTmp;
end
if isfield(modelSBML.species(i),'annotation')
hasAnnotationField = 1;
[metCHEBI,metKEGG,metPubChem,metInChI] = parseSBMLAnnotationField(modelSBML.species(i).annotation);
metCHEBIID{i} = metCHEBI;
metKEGGID{i} = metKEGG;
metPubChemID{i} = metPubChem;
metInChIString{i} = metInChI;
end
end
if ( regexp( version, 'R20') )
close(h);
end
%% Collect everything into a structure
model.rxns = rxns;
model.mets = mets;
model.S = S;
model.rev = rev;
model.lb = lb;
model.ub = ub;
model.c = c;
model.metCharge = transpose(chargeList);
if (hasNotesField)
model.rules = rules;
model.genes = columnVector(allGenes);
model.rxnGeneMat = rxnGeneMat;
model.grRules = columnVector(grRules);
model.subSystems = columnVector(subSystems);
model.confidenceScores = columnVector(confidenceScores);
model.rxnReferences = columnVector(citations);
model.rxnECNumbers = columnVector(ecNumbers);
model.rxnNotes = columnVector(comments);
end
model.rxnNames = columnVector(rxnNames);
% Only include formulas if at least 90% of metabolites have them (otherwise
% the "formulas" are probably just parts of metabolite names)
if (formulaCount < 0.9*nMets)
model.metNames = columnVector(metNamesAlt);
else
model.metNames = columnVector(metNames);
model.metFormulas = columnVector(metFormulas);
end
if (hasAnnotationField)
model.metChEBIID = columnVector(metCHEBIID);
model.metKEGGID = columnVector(metKEGGID);
model.metPubChemID = columnVector(metPubChemID);
model.metInChIString = columnVector(metInChIString);
end
%%
function [genes,rule,subSystem,grRule,formula,confidenceScore,citation,comment,ecNumber,charge] = parseSBMLNotesField(notesField)
%parseSBMLNotesField Parse the notes field of an SBML file to extract
%gene-rxn associations
%
% [genes,rule] = parseSBMLNotesField(notesField)
%
% Markus Herrgard 8/7/06
% Ines Thiele 1/27/10 Added new fields
% Handle different notes fields
if isempty(regexp(notesField,'html:p', 'once'))
tag = 'p';
else
tag = 'html:p';
end
subSystem = '';
grRule = '';
genes = {};
rule = '';
formula = '';
confidenceScore = '';
citation = '';
ecNumber = '';
comment = '';
charge = [];
Comment = 0;
[tmp,fieldList] = regexp(notesField,['<' tag '>.*?</' tag '>'],'tokens','match');
for i = 1:length(fieldList)
fieldTmp = regexp(fieldList{i},['<' tag '>(.*)</' tag '>'],'tokens');
fieldStr = fieldTmp{1}{1};
if (regexp(fieldStr,'GENE_ASSOCIATION'))
gprStr = regexprep(strrep(fieldStr,'GENE_ASSOCIATION:',''),'^(\s)+','');
grRule = gprStr;
[genes,rule] = parseBoolean(gprStr);
elseif (regexp(fieldStr,'GENE ASSOCIATION'))
gprStr = regexprep(strrep(fieldStr,'GENE ASSOCIATION:',''),'^(\s)+','');
grRule = gprStr;
[genes,rule] = parseBoolean(gprStr);
elseif (regexp(fieldStr,'SUBSYSTEM'))
subSystem = regexprep(strrep(fieldStr,'SUBSYSTEM:',''),'^(\s)+','');
subSystem = strrep(subSystem,'S_','');
subSystem = regexprep(subSystem,'_+',' ');
if (isempty(subSystem))
subSystem = 'Exchange';
end
elseif (regexp(fieldStr,'EC Number'))
ecNumber = regexprep(strrep(fieldStr,'EC Number:',''),'^(\s)+','');
elseif (regexp(fieldStr,'FORMULA'))
formula = regexprep(strrep(fieldStr,'FORMULA:',''),'^(\s)+','');
elseif (regexp(fieldStr,'CHARGE'))
charge = str2num(regexprep(strrep(fieldStr,'CHARGE:',''),'^(\s)+',''));
elseif (regexp(fieldStr,'AUTHORS'))
if isempty(citation)
citation = strcat(regexprep(strrep(fieldStr,'AUTHORS:',''),'^(\s)+',''));
else
citation = strcat(citation,';',regexprep(strrep(fieldStr,'AUTHORS:',''),'^(\s)+',''));
end
elseif Comment == 1 && isempty(regexp(fieldStr,'genes:', 'once'))
Comment = 0;
comment = fieldStr;
elseif (regexp(fieldStr,'Confidence'))
confidenceScore = regexprep(strrep(fieldStr,'Confidence Level:',''),'^(\s)+','');
Comment = 1;
end
end
%%
function [metCHEBI,metKEGG,metPubChem,metInChI] = parseSBMLAnnotationField(annotationField)
%parseSBMLAnnotationField Parse the annotation field of an SBML file to extract
%metabolite information associations
%
% [genes,rule] = parseSBMLAnnotationField(annotationField)
%
% Ines Thiele 1/27/10 Added new fields
% Handle different notes fields
metPubChem = '';
metCHEBI = '';
metKEGG = '';
metPubChem = '';
metInChI='';
[tmp,fieldList] = regexp(annotationField,'<rdf:li rdf:resource="urn:miriam:(\w+).*?"/>','tokens','match');
%fieldTmp = regexp(fieldList{i},['<' tag '>(.*)</' tag '>'],'tokens');
for i = 1:length(fieldList)
fieldTmp = regexp(fieldList{i},['<rdf:li rdf:resource="urn:miriam:(.*)"/>'],'tokens');
fieldStr = fieldTmp{1}{1};
if (regexp(fieldStr,'obo.chebi'))
metCHEBI = strrep(fieldStr,'obo.chebi:CHEBI%','');
elseif (regexp(fieldStr,'kegg.compound'))
metKEGG = strrep(fieldStr,'kegg.compound:','');
elseif (regexp(fieldStr,'pubchem.substance'))
metPubChem = strrep(fieldStr,'pubchem.substance:','');
end
end
% get InChI string
fieldTmp = regexp(annotationField,'<in:inchi xmlns:in="http://biomodels.net/inchi" metaid="(.*?)">(.*?)</in:inchi>','tokens');
if ~isempty(fieldTmp)
fieldStr = fieldTmp{1}{2};
if (regexp(fieldStr,'InChI'))
metInChI = strrep(fieldStr,'InChI=','');
end
end
%% Cleanup Formatting
function str = cleanUpFormatting(str)
str = strrep(str,'-DASH-','-');
str = strrep(str,'_DASH_','-');
str = strrep(str,'_FSLASH_','/');
str = strrep(str,'_BSLASH_','\');
str = strrep(str,'_LPAREN_','(');
str = strrep(str,'_LSQBKT_','[');
str = strrep(str,'_RSQBKT_',']');
str = strrep(str,'_RPAREN_',')');
str = strrep(str,'_COMMA_',',');
str = strrep(str,'_PERIOD_','.');
str = strrep(str,'_APOS_','''');
str = regexprep(str,'_e_$','(e)');
str = regexprep(str,'_e$','(e)');
str = strrep(str,'&','&');
str = strrep(str,'<','<');
str = strrep(str,'>','>');
str = strrep(str,'"','"');
|
github
|
EPFL-LCSB/matTFA-master
|
lp_solve.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/solvers/lp_solve.m
| 2,708 |
utf_8
|
80baa061e65e08df66a4b417047cd713
|
%LP_SOLVE Solves mixed integer linear programming problems.
%
% SYNOPSIS: [obj,x,duals,stat] = lp_solve(f,a,b,e,vlb,vub,xint,scalemode,keep)
%
% solves the MILP problem
%
% max v = f'*x
% a*x <> b
% vlb <= x <= vub
% x(int) are integer
%
% ARGUMENTS: The first four arguments are required:
%
% f: n vector of coefficients for a linear objective function.
% a: m by n matrix representing linear constraints.
% b: m vector of right sides for the inequality constraints.
% e: m vector that determines the sense of the inequalities:
% e(i) = -1 ==> Less Than
% e(i) = 0 ==> Equals
% e(i) = 1 ==> Greater Than
% vlb: n vector of lower bounds. If empty or omitted,
% then the lower bounds are set to zero.
% vub: n vector of upper bounds. May be omitted or empty.
% xint: vector of integer variables. May be omitted or empty.
% scalemode: scale flag. Off when 0 or omitted.
% keep: Flag for keeping the lp problem after it's been solved.
% If omitted, the lp will be deleted when solved.
%
% OUTPUT: A nonempty output is returned if a solution is found:
%
% obj: Optimal value of the objective function.
% x: Optimal value of the decision variables.
% duals: solution of the dual problem.
function [obj, x, duals, stat] = lp_solve(f, a, b, e, vlb, vub, xint, scalemode, keep)
if nargin == 0
help lp_solve;
return;
end
[m,n] = size(a);
lp = mxlpsolve('make_lp', m, n);
mxlpsolve('set_verbose', lp, 3);
mxlpsolve('set_mat', lp, a);
mxlpsolve('set_rh_vec', lp, b);
mxlpsolve('set_obj_fn', lp, f);
mxlpsolve('set_maxim', lp); % default is solving minimum lp.
for i = 1:length(e)
if e(i) < 0
con_type = 1;
elseif e(i) == 0
con_type = 3;
else
con_type = 2;
end
mxlpsolve('set_constr_type', lp, i, con_type);
end
if nargin > 4
for i = 1:length(vlb)
mxlpsolve('set_lowbo', lp, i, vlb(i));
end
end
if nargin > 5
for i = 1:length(vub)
mxlpsolve('set_upbo', lp, i, vub(i));
end
end
if nargin > 6
for i = 1:length(xint)
mxlpsolve('set_int', lp, xint(i), 1);
end
end
if nargin > 7
if scalemode ~= 0
mxlpsolve('set_scaling', lp, scalemode);
end
end
result=mxlpsolve('solve', lp);
if result == 0 | result == 1 | result == 11 | result == 12
% [obj, x, duals, stat] = mxlpsolve('get_solution', lp), result;
[obj, x, duals] = mxlpsolve('get_solution', lp);
stat = result;
else
obj = [];
x = [];
duals = [];
stat = result;
end
if nargin < 9
mxlpsolve('delete_lp', lp);
end
|
github
|
EPFL-LCSB/matTFA-master
|
cpxcb_INCUMBENT.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/solvers/cpxcb_INCUMBENT.m
| 3,387 |
utf_8
|
c53a9437062846671fbafd7691e91c80
|
% function ret = cpxcb_INCUMBENT(x,f,Prob,cbxCBInfo)
%
% CPLEX MIP Incumbent callback
%
% Called from TOMLAB /CPLEX during mixed integer optimization when a new integer
% solution has been found but before this solution has replaced the current best known integer solution.
%
% This file can be used to perform any desired analysis of the new integer
% solution and return a status flag to the solver deciding whether to stop
% or continue the optimization, and also whether to accept or discard the newly
% found solution.
%
% This callback is enabled by setting callback(14)=1 in the call to
% cplex.m, or Prob.MIP.callback(14)=1 if using tomRun('cplex',...)
%
% cpxcb_INCUMBENT is called by the solver with three arguments:
%
% x - the new integer solution
% f - the objective value at x
% Prob - the Tomlab problem structure
%
% cpxcb_INCUMBENT should return one of the following scalar values:
%
% 0 Continue optimization and accept new integer solution
% 1 Continue optimization but discard new integer solution
% 2 Stop optimization and accept new integer solution
% 3 Stop optimization adn discard new integer solution
%
% Any other return value will be interpreted as 0.
%
% If modifying this file, it is recommended to make a copy of it which
% is placed before the original file in the MATLAB path.
%
% Anders Goran, Tomlab Optimization Inc., E-mail: [email protected]
% Copyright (c) 2002-2007 by Tomlab Optimization Inc., $Release: 10.1.0$
% Written Jun 1, 2007. Last modified Jun 1, 2007.
function ret = cpxcb_INCUMBENT(x,f,Prob)
% ADD USER CODE HERE.
% Accepted return values are:
%
% 0 Continue optimization and accept new integer solution
% 1 Continue optimization but discard new integer solution
% 2 Stop optimization and accept new integer solution
% 3 Stop optimization adn discard new integer solution
%
% Any other return value will be interpreted as 0.
global MILPproblemType;
switch MILPproblemType
case 'OptKnock'
% Allow printing intermediate OptKnock solutions
global cobraIntSolInd;
global cobraContSolInd;
global selectedRxnIndIrrev;
global rxnList;
global irrev2rev;
global biomassRxnID;
global solutionFileName;
global OptKnockKOrxnList;
global OptKnockObjective;
global OptKnockGrowth;
global solID;
% Initialize
if isempty(solID)
solID = 0;
OptKnockObjective = [];
OptKnockGrowth = [];
OptKnockKOrxnList = {};
end
solID = solID + 1;
% Get the reactions
OptKnockObjective(solID) = -f;
optKnockRxnInd = selectedRxnIndIrrev(x(cobraIntSolInd) < 1e-4);
optKnockRxns = rxnList(unique(irrev2rev(optKnockRxnInd)));
OptKnockKOrxnList{solID} = optKnockRxns;
% Get the growth rate
fluxes = x(cobraContSolInd);
growth = fluxes(biomassRxnID);
OptKnockGrowth(solID) = growth;
fprintf('OptKnock\t%f\t%f\t',-f,growth);
for i = 1:length(optKnockRxns)
fprintf('%s ',optKnockRxns{i});
end
fprintf('\n');
save(solutionFileName,'OptKnockKOrxnList','OptKnockObjective','OptKnockGrowth');
ret = 0;
otherwise
ret = 0;
end
|
github
|
EPFL-LCSB/matTFA-master
|
solveCobraLP.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/solvers/solveCobraLP.m
| 21,393 |
utf_8
|
015fc2b9bee21ee6eb4f30f6e94e39d8
|
function solution = solveCobraLP(LPproblem, varargin)
%solveCobraLP Solve constraint-based LP problems
%
% solution = solveCobraLP(LPproblem, parameters)
%
%INPUT
% LPproblem Structure containing the following fields describing the LP
% problem to be solved
% A LHS matrix
% b RHS vector
% c Objective coeff vector
% lb Lower bound vector
% ub Upper bound vector
% osense Objective sense (-1 max, +1 min)
% csense Constraint senses, a string containting the constraint sense for
% each row in A ('E', equality, 'G' greater than, 'L' less than).
%
%OPTIONAL INPUTS
% Optional parameters can be entered using parameters structure or as
% parameter followed by parameter value: i.e. ,'printLevel',3)
%
% parameters Structure containing optional parameters as fields.
% Setting parameters = 'default' uses default setting set in
% getCobraSolverParameters.
% printLevel Printing level
% = 0 Silent (Default)
% = 1 Warnings and Errors
% = 2 Summary information
% = 3 More detailed information
% > 10 Pause statements, and maximal printing (debug mode)
% saveInput Saves LPproblem to filename specified in field.
% i.e. parameters.saveInput = 'LPproblem.mat';
% minNorm {(0), scalar , n x 1 vector}, where [m,n]=size(S);
% If not zero then, minimise the Euclidean length
% of the solution to the LP problem. minNorm ~1e-6 should be
% high enough for regularisation yet maintain the same value for
% the linear part of the objective. However, this should be
% checked on a case by case basis, by optimization with and
% without regularisation.
% primalOnly {(0),1} 1=only return the primal vector (lindo solvers)
%
% optional parameters can also be set through the
% solver can be set through changeCobraSolver('LP', value);
% changeCobraSolverParames('LP', 'parameter', value) function. This
% includes the minNorm and the printLevel flags
%
%OUTPUT
% solution Structure containing the following fields describing a LP
% solution
% full Full LP solution vector
% obj Objective value
% rcost Reduced costs
% dual Dual solution
% solver Solver used to solve LP problem
%
% stat Solver status in standardized form
% 1 Optimal solution
% 2 Unbounded solution
% 0 Infeasible
% -1 No solution reported (timelimit, numerical problem etc)
%
% origStat Original status returned by the specific solver
% time Solve time in seconds
%
%
% Markus Herrgard 08/29/06
% Ronan Fleming 11/12/08 'cplex_direct' allows for more refined control
% of cplex than tomlab tomrun
% Ronan Fleming 04/25/09 Option to minimise the Euclidean Norm of internal
% fluxes using either 'cplex_direct' solver or 'pdco'
% Jan Schellenberger 09/28/09 Changed header to be much simpler. All parameters
% now accessed through
% changeCobraSolverParams(LP, parameter,value)
% Richard Que 11/30/09 Changed handling of optional parameters to use
% getCobraSolverParams().
% Ronan Fleming 12/07/09 Commenting of input/output
% Ronan Fleming 21/01/10 Not having second input, means use the parameters as specified in the
% global paramerer variable, rather than 'default' parameters
% Steinn Gudmundsson 03/03/10 Added support for the Gurobi solver
% Tim Harrington 05/18/12 Added support for the Gurobi 5.0 solver
%% Process arguments etc
global CBTLPSOLVER
if (~isempty(CBTLPSOLVER))
solver = CBTLPSOLVER;
else
error('No solver found. call changeCobraSolver(solverName)');
end
optParamNames = {'minNorm','printLevel','primalOnly','saveInput', ...
'feasTol','optTol','EleNames','EqtNames','VarNames','EleNameFun', ...
'EqtNameFun','VarNameFun','PbName','MPSfilename'};
parameters = '';
if nargin ~=1
if mod(length(varargin),2)==0
for i=1:2:length(varargin)-1
if ismember(varargin{i},optParamNames)
parameters.(varargin{i}) = varargin{i+1};
else
error([varargin{i} ' is not a valid optional parameter']);
end
end
elseif strcmp(varargin{1},'default')
parameters = 'default';
elseif isstruct(varargin{1})
parameters = varargin{1};
else
display('Warning: Invalid number of parameters/values')
solution=[];
return;
end
end
[minNorm, printLevel, primalOnlyFlag, saveInput, feasTol, optTol] = ...
getCobraSolverParams('LP',optParamNames(1:6),parameters);
%Save Input if selected
if ~isempty(saveInput)
fileName = parameters.saveInput;
if ~find(regexp(fileName,'.mat'))
fileName = [fileName '.mat'];
end
display(['Saving LPproblem in ' fileName]);
save(fileName,'LPproblem')
end
[A,b,c,lb,ub,csense,osense] = deal(LPproblem.A,LPproblem.b,LPproblem.c,LPproblem.lb,LPproblem.ub,LPproblem.csense,LPproblem.osense);
% if any(any(~isfinite(A)))
% error('Cannot perform LP on a stoichiometric matrix with NaN of Inf coefficents.')
% end
% Defaults in case the solver does not return anything
f = [];
x = [];
y = [];
w = [];
origStat = -99;
stat = -99;
t_start = clock;
switch solver
%% GLPK
case 'glpk'
params.msglev = printLevel; % level of verbosity
params.tolbnd = feasTol; %tolerance
params.toldj = optTol; %tolerance
if (isempty(csense))
clear csense
csense(1:length(b),1) = 'S';
else
csense(csense == 'L') = 'U';
csense(csense == 'G') = 'L';
csense(csense == 'E') = 'S';
csense = columnVector(csense);
end
%glpk needs b to be full, not sparse -Ronan
b=full(b);
[x,f,y,w,stat,origStat] = solveGlpk(c,A,b,lb,ub,csense,osense,params);
case {'lindo_new','lindo_old'}
%% LINDO
if (strcmp(solver,'lindo_new'))
% Use new API (>= 2.0)
[f,x,y,w,s,origStat] = solveCobraLPLindo(A,b,c,csense,lb,ub,osense,primalOnlyFlag,false);
% Note that status handling may change (see Lindo.h)
if (origStat == 1 || origStat == 2)
stat = 1; % Optimal solution found
elseif (origStat == 4)
stat = 2; % Unbounded
elseif (origStat == 3 || origStat == 6)
stat = 0; % Infeasible
else
stat = -1; % Solution not optimal or solver problem
end
else
% Use old API
[f,x,y,w,s,origStat] = solveCobraLPLindo(A,b,c,csense,lb,ub,osense,primalOnlyFlag,true);
% Note that status handling may change (see Lindo.h)
if (origStat == 2 || origStat == 3)
stat = 1; % Optimal solution found
elseif (origStat == 5)
stat = 2; % Unbounded
elseif (origStat == 4 || origStat == 6)
stat = 0; % Infeasible
else
stat = -1; % Solution not optimal or solver problem
end
end
%[f,x,y,s,w,stat] = LMSolveLPNew(A,b,c,csense,lb,ub,osense,0);
case 'lp_solve'
%% lp_solve
if (isempty(csense))
[f,x,y,origStat] = lp_solve(c*(-osense),A,b,zeros(size(A,1),1),lb,ub);
f = f*(-osense);
else
e(csense == 'E') = 0;
e(csense == 'G') = 1;
e(csense == 'L') = -1;
[f,x,y,origStat] = lp_solve(c*(-osense),A,b,e,lb,ub);
f = f*(-osense);
end
% Note that status handling may change (see lp_lib.h)
if (origStat == 0)
stat = 1; % Optimal solution found
elseif (origStat == 3)
stat = 2; % Unbounded
elseif (origStat == 2)
stat = 0; % Infeasible
else
stat = -1; % Solution not optimal or solver problem
end
s = [];
w = [];
case 'mosek'
%% mosek
%if mosek is installed, and the paths are added ahead of matlab's
%built in paths, then mosek linprog shaddows matlab linprog and
%is used preferentially
switch printLevel
case 0
options.Display='off';
case 1
options.Display='final';
case 2
options.Display='iter';
otherwise
% Ask for default options for a function.
options = optimset;
end
if (isempty(csense))
[x,f,origStat,output,lambda] = linprog(c*osense,[],[],A,b,lb,ub,[],options);
else
Aeq = A(csense == 'E',:);
beq = b(csense == 'E');
Ag = A(csense == 'G',:);
bg = b(csense == 'G');
Al = A(csense == 'L',:);
bl = b(csense == 'L');
clear A;
A = [Al;-Ag];
clear b;
b = [bl;-bg];
[x,f,origStat,output,lambda] = linprog(c*osense,A,b,Aeq,beq,lb,ub,[],options);
end
y = [];
if (origStat > 0)
stat = 1; % Optimal solution found
f = f*osense;
y = lambda.eqlin;
elseif (origStat < 0)
stat = 0; % Infeasible
else
stat = -1; % Solution did not converge
end
case 'gurobi'
%% gurobi
% Free academic licenses for the Gurobi solver can be obtained from
% http://www.gurobi.com/html/academic.html
%
% The code below uses Gurobi Mex to interface with Gurobi. It can be downloaded from
% http://www.convexoptimization.com/wikimization/index.php/Gurobi_Mex:_A_MATLAB_interface_for_Gurobi
clear opts % Use the default parameter settings
if printLevel == 0
% Version v1.10 of Gurobi Mex has a minor bug. For complete silence
% Remove Line 736 of gurobi_mex.c: mexPrintf("\n");
opts.Display = 0;
opts.DisplayInterval = 0;
else
opts.Display = 1;
end
opts.FeasibilityTol = feasTol;
opts.OptimalityTol = optTol;
if (isempty(csense))
clear csense
csense(1:length(b),1) = '=';
else
csense(csense == 'L') = '<';
csense(csense == 'G') = '>';
csense(csense == 'E') = '=';
csense = csense(:);
end
%gurobi_mex doesn't cast logicals to doubles automatically
c = double(c);
[x,f,origStat,output,y] = gurobi_mex(c,osense,sparse(A),b, ...
csense,lb,ub,[],opts);
if origStat==2
stat = 1; % Optimal solutuion found
elseif origStat==3
stat = 0; % Infeasible
elseif origStat==5
stat = 2; % Unbounded
elseif origStat==4
stat = 0; % Gurobi reports infeasible *or* unbounded
else
stat = -1; % Solution not optimal or solver problem
end
case 'gurobi5'
%% gurobi 5
% Free academic licenses for the Gurobi solver can be obtained from
% http://www.gurobi.com/html/academic.html
resultgurobi = struct('x',[],'objval',[],'pi',[]);
LPproblem.A = deal(sparse(LPproblem.A));
clear params % Use the default parameter settings
if printLevel == 0
params.OutputFlag = 0;
params.DisplayInterval = 1;
else
params.OutputFlag = 1;
params.DisplayInterval = 5;
end
params.FeasibilityTol = feasTol;
params.OptimalityTol = optTol;
if (isempty(LPproblem.csense))
clear LPproblem.csense
LPproblem.csense(1:length(b),1) = '=';
else
LPproblem.csense(LPproblem.csense == 'L') = '<';
LPproblem.csense(LPproblem.csense == 'G') = '>';
LPproblem.csense(LPproblem.csense == 'E') = '=';
LPproblem.csense = LPproblem.csense(:);
end
if LPproblem.osense == -1
LPproblem.osense = 'max';
else
LPproblem.osense = 'min';
end
LPproblem.modelsense = LPproblem.osense;
[LPproblem.rhs,LPproblem.obj,LPproblem.sense] = deal(LPproblem.b,double(LPproblem.c),LPproblem.csense);
resultgurobi = gurobi(LPproblem,params);
if strcmp(resultgurobi.status,'OPTIMAL')
stat = 1; % Optimal solution found
[x,f,y] = deal(resultgurobi.x,resultgurobi.objval,resultgurobi.pi);
elseif strcmp(resultgurobi.status,'INFEASIBLE')
stat = 0; % Infeasible
elseif strcmp(resultgurobi.status,'UNBOUNDED')
stat = 2; % Unbounded
elseif strcmp(resultgurobi.status,'INF_OR_UNBD')
stat = 0; % Gurobi reports infeasible *or* unbounded
else
stat = -1; % Solution not optimal or solver problem
end
case 'matlab'
%matlab is not a reliable LP solver
if (isempty(csense))
[x,f,origStat,output,lambda] = linprog(c*osense,[],[],A,b,lb,ub);
else
Aeq = A(csense == 'E',:);
beq = b(csense == 'E');
Ag = A(csense == 'G',:);
bg = b(csense == 'G');
Al = A(csense == 'L',:);
bl = b(csense == 'L');
clear A;
A = [Al;-Ag];
clear b;
b = [bl;-bg];
[x,f,origStat,output,lambda] = linprog(c*osense,A,b,Aeq,beq,lb,ub);
end
y = [];
if (origStat > 0)
stat = 1; % Optimal solution found
f = f*osense;
y = lambda.eqlin;
elseif (origStat < 0)
stat = 0; % Infeasible
else
stat = -1; % Solution did not converge
end
case 'tomlab_cplex'
%% Tomlab
if (~isempty(csense))
b_L(csense == 'E') = b(csense == 'E');
b_U(csense == 'E') = b(csense == 'E');
b_L(csense == 'G') = b(csense == 'G');
b_U(csense == 'G') = 1e6;
b_L(csense == 'L') = -1e6;
b_U(csense == 'L') = b(csense == 'L');
else
b_L = b;
b_U = b;
end
tomlabProblem = lpAssign(osense*c,A,b_L,b_U,lb,ub);
%Result = tomRun('cplex', tomlabProblem, 0);
% This is faster than using tomRun
%set parameters
tomlabProblem.optParam = optParamDef('cplex',tomlabProblem.probType);
tomlabProblem.QP.F = [];
tomlabProblem.PriLevOpt = printLevel;
%if basis is availible use it
if isfield(LPproblem,'basis') && ~isempty(LPproblem.basis)
tomlabProblem.MIP.basis = LPproblem.basis;
end
%set tolerance
tomlabProblem.MIP.cpxControl.EPRHS = feasTol;
tomlabProblem.MIP.cpxControl.EPOPT = optTol;
%solve
Result = cplexTL(tomlabProblem);
% Assign results
x = Result.x_k;
f = osense*sum(tomlabProblem.QP.c.*Result.x_k);
% [Result.f_k f]
origStat = Result.Inform;
w = Result.v_k(1:length(lb));
y = Result.v_k((length(lb)+1):end);
basis = Result.MIP.basis;
if (origStat == 1)
stat = 1;
elseif (origStat == 3)
stat = 0;
elseif (origStat == 2 || origStat == 4)
stat = 2;
else
stat = -1;
end
case 'cplex_direct'
%% Tomlab cplex.m direct
%Used with the current script, only some of the control affoarded with
%this interface is provided. Primarily, this is to change the print
%level and whether to minimise the Euclidean Norm of the internal
%fluxes or not.
%See solveCobraLPCPLEX.m for more refined control of cplex
%Ronan Fleming 11/12/2008
if isfield(LPproblem,'basis') && ~isempty(LPproblem.basis)
LPproblem.LPBasis = LPproblem.basis;
end
[solution LPprob] = solveCobraLPCPLEX(LPproblem,printLevel,1,[],[],minNorm);
solution.basis = LPprob.LPBasis;
solution.solver = solver;
case 'lindo'
error('Solver type lindo is obsolete - use lindo_new or lindo_old instead');
case 'pdco'
%-----------------------------------------------------------------------
% pdco.m: Primal-Dual Barrier Method for Convex Objectives (16 Dec 2008)
%-----------------------------------------------------------------------
% AUTHOR:
% Michael Saunders, Systems Optimization Laboratory (SOL),
% Stanford University, Stanford, California, USA.
%Interfaced with Cobra toolbox by Ronan Fleming, 27 June 2009
[nMet,nRxn]=size(LPproblem.A);
x0 = ones(nRxn,1);
y0 = ones(nMet,1);
z0 = ones(nRxn,1);
%setting d1 to zero is dangerous numerically, but is necessary to avoid
%minimising the Euclidean norm of the optimal flux. A more
%numerically stable way is to use pdco via solveCobraQP, which has
%a more reasonable d1 and should be more numerically robust. -Ronan
d1=0;
d2=1e-6;
options = pdcoSet;
options.FeaTol = 1e-12;
options.OptTol = 1e-12;
%pdco is a general purpose convex optization solver, not only a
%linear optimization solver. As such, much control over the optimal
%solution and the method for solution is available. However, this
%also means you may have to tune the various parameters here,
%especially xsize and zsize (see pdco.m) to get the real optimal
%objective value
xsize = 1000;
zsize = 10000;
options.Method=2; %QR
options.MaxIter=100;
options.Print=printLevel;
[x,y,w,inform,PDitns,CGitns,time] = ...
pdco(osense*c*10000,A,b,lb,ub,d1,d2,options,x0,y0,z0,xsize,zsize);
f= c'*x;
% inform = 0 if a solution is found;
% = 1 if too many iterations were required;
% = 2 if the linesearch failed too often;
% = 3 if the step lengths became too small;
% = 4 if Cholesky said ADDA was not positive definite.
if (inform == 0)
stat = 1;
elseif (inform == 1 || inform == 2 || inform == 3)
stat = 0;
else
stat = -1;
end
origStat=inform;
case 'mps'
%% BuildMPS
% This calls buildMPS and generates a MPS format description of the
% problem as the result
% Build MPS Author: Bruno Luong
% Interfaced with CobraToolbox by Richard Que (12/18/09)
display('Solver set to MPS. This function will output an MPS matrix string for the LP problem');
%Get optional parameters
[EleNames,EqtNames,VarNames,EleNameFun,EqtNameFun,VarNameFun,PbName,MPSfilename] = ...
getCobraSolverParams('LP',{'EleNames','EqtNames','VarNames','EleNameFun','EqtNameFun','VarNameFun','PbName','MPSfilename'},parameters);
%split A matrix for L and E csense
Ale = A(csense=='L',:);
ble = b(csense=='L');
Aeq = A(csense=='E',:);
beq = b(csense=='E');
%%%%Adapted from BuildMPS%%%%%
[neq nvar]=size(Aeq);
nle=size(Ale,1);
if isempty(EleNames)
EleNames=arrayfun(EleNameFun,(1:nle),'UniformOutput', false);
end
if isempty(EqtNames)
EqtNames=arrayfun(EqtNameFun,(1:neq),'UniformOutput', false);
end
if isempty(VarNames)
VarNames=arrayfun(VarNameFun,(1:nvar),'UniformOutput', false);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[solution] = BuildMPS(Ale, ble, Aeq, beq, c, lb, ub, PbName,'MPSfilename',MPSfilename,'EleNames',EleNames,'EqtNames',EqtNames,'VarNames',VarNames);
otherwise
error(['Unknown solver: ' solver]);
end
if ~strcmp(solver,'cplex_direct') && ~strcmp(solver,'mps')
%% Assign solution
t = etime(clock, t_start);
if ~exist('basis','var'), basis=[]; end
[solution.full,solution.obj,solution.rcost,solution.dual,solution.solver,solution.stat,solution.origStat,solution.time,solution.basis] = ...
deal(x,f,w,y,solver,stat,origStat,t,basis);
end
%% solveGlpk Solve actual LP problem using glpk and return relevant results
function [x,f,y,w,stat,origStat] = solveGlpk(c,A,b,lb,ub,csense,osense,params)
% Old way of calling glpk
%[x,f,stat,extra] = glpkmex(osense,c,A,b,csense,lb,ub,[],params);
[x,f,origStat,extra] = glpk(c,A,b,lb,ub,csense,[],osense,params);
y = extra.lambda;
w = extra.redcosts;
% Note that status handling may change (see glplpx.h)
if (origStat == 180 || origStat == 5)
stat = 1; % Optimal solution found
elseif (origStat == 182 || origStat == 183 || origStat == 3 || origStat == 110)
stat = 0; % Infeasible
elseif (origStat == 184 || origStat == 6)
stat = 2; % Unbounded
else
stat = -1; % Solution not optimal or solver problem
end
|
github
|
EPFL-LCSB/matTFA-master
|
optGeneFitnessTilt.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/design/optGeneFitnessTilt.m
| 4,526 |
utf_8
|
b9d818464262c0403801cde0424f0834
|
function [val] = optGeneFitnessTilt(rxn_vector_matrix, model, targetRxn, rxnListInput, isGeneList)
%optGeneFitnessTilt GeneOptFitness the fitness function
%
% [val] = optGeneFitnessTilt(rxn_vector_matrix, model, targetRxn, rxnListInput, isGeneList)
%
%INPUTS
% rxn_vector_matrix
% model
% targetRxn
% rxnListInput
% isGeneList
%
%OUTPUT
% val fitness value
%
%
global MaxKnockOuts
%size(rxn_vector_matrix)
popsize = size(rxn_vector_matrix,1);
val = zeros(1,popsize);
for i = 1:popsize
rxn_vector = rxn_vector_matrix(i,:);
rxnList = rxnListInput(logical(rxn_vector));
%see if we've done this before
val_temp = memoize(rxn_vector);
if ~ isempty(val_temp)
val(i) = val_temp;
continue;
end
% check to see if mutations is above the max number allowed
nummutations = sum(rxn_vector);
if nummutations > MaxKnockOuts
continue;
end
% generate knockout.
if isGeneList
modelKO = deleteModelGenes(model, rxnList);
else % is reaction list
[isValidRxn,removeInd] = ismember(rxnList,model.rxns);
removeInd = removeInd(isValidRxn);
modelKO = model;
modelKO.ub(removeInd) = 0;
modelKO.lb(removeInd) = 0;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% augment BOF (tilt)
[modelKO] = augmentBOF(modelKO, targetRxn, .001);
% find growthrate
if exist('LPBasis', 'var')
modelKO.LPBasis = LPBasis;
end
[slnKO, LPOUT] = solveCobraLPCPLEX(modelKO, 0,1);
LPBasis = LPOUT.LPBasis;
growthrate = slnKO.obj;
[tmp,tar_loc] = ismember(targetRxn,modelKO.rxns);
minProdAtSetGR = slnKO.full(tar_loc);
% check to ensure that GR is above a certain value
if growthrate < .10
continue;
end
% % display('second optimization');
% % find the lowesest possible production rate (a hopefully high number)
% % at the max growth rate minus some set factor gamma (a growth rate slightly
% % smaller than the max). A positive value will eliminate solutions where the
% % production envelope has a vertical line at the max GR, a "non-unique"
% % solution. Set value to zero if "non-unique" solutions are not an issue.
% gamma = 0.01; % proportional to Grwoth Rate (hr-1), a value around 0.5 max.
%
% %find indicies of important vectors
% indBOF = find(modelKO.c);
% indTar = findRxnIDs(modelKO, targetRxn);
% % generate a model with a fixed max KO growth rate
% modelKOsetGR = modelKO;
% modelKOsetGR.lb(indBOF) = growthrate - gamma; % this growth rate is required as lb.
% modelKOsetGR.c = zeros(size(modelKO.c));
% modelKOsetGR.c(indTar) = -1; % minimize for this variable b/c we want to look at the very minimum production.
%
% % find the minimum production rate for the targeted reaction.
%
% % slnKOsetGR = optimizeCbModel(modelKOsetGR);
% % minProdAtSetGR1 = -slnKOsetGR.f; % This should be a negative value b/c of the minimization setup, so -1 is necessary.
%
% if exist('LPBasis2', 'var')
% modelKOsetGR.LPBasis = LPBasis2;
% end
%
% [slnKOsetGR, LPOUT2] = solveCobraLPCPLEX(modelKOsetGR, 0,1);
% LPBasis2 = LPOUT2.LPBasis;
% minProdAtSetGR = -slnKOsetGR.obj;
% objective function for optGene algorithm = val (needs to be a negative value, since it is
% a minimization)
val(i) = -minProdAtSetGR;
% penalty for a greater number of mutations
%val(i) = -minProdAtSetGR * (.98^nummutations);
% select best substrate-specific productivity
% val(i) = -minProdAtSetGR * (.98^nummutations) * growthrate;
% check to prevent very small values from being considerered improvments
if val(i) > -1e-3
val(i) = 0;
end
memoize(rxn_vector, val(i));
end
return;
%% Memoize
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% MEMOIZE %%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% internal function to speed things up.
function [value] = memoize(gene_vector, value)
global HTABLE
hashkey = num2str(gene_vector);
hashkey = strrep(hashkey,' ',''); % cut out white space from string (more space efficient).
if nargin == 1
value = HTABLE.get(hashkey);
return;
else
if HTABLE.size() > 50000
HTABLE = java.util.Hashtable; %reset the hashtable if more than 50,000 entries.
end
HTABLE.put(hashkey, value);
value = [];
return;
end
return
|
github
|
EPFL-LCSB/matTFA-master
|
GDLS.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/design/GDLS.m
| 14,440 |
utf_8
|
217f0fb80c846b4d2bb8d8b633753282
|
function [gdlsSolution, bilevelMILPProblem, gdlsSolutionStructs] = GDLS(model, targetRxns, varargin)
%GDLS (Genetic Design through Local Search) attempts to find genetic
% designs with greater in silico production of desired metabolites.
%
% [gdlsSolution, bilevelMILPProblem, gdlsSolutionStructs] = GDLS(model, varargin)
%
%INPUTS
% model Cobra model structure
% targetRxn Reaction(s) to be maximized (Cell array of strings)
%
%OPTIONAL INPUTS
% varargin parameters entered using either a structure or list of
% parameter, parameter value
% List of optional parameters
% 'nbhdsz' Neighborhood size (default: 1)
% 'M' Number of search paths (default: 1)
% 'maxKO' Maximum number of knockouts (default: 50)
% 'koCost' Cost for knocking out a reaction, gene set, or gene
% A different cost can be set for each knockout.
% (default: 1 for each knockout)
% 'selectedRxns' List of reactions/geneSets that can be knocked out
% 'koType' What to knockout: reactions, gene sets, or genes
% {('rxns'), 'geneSets', 'genes'}
% 'iterationLimit' Maximum number of iterations (default: 70)
% 'timeLimit' Maximum run time in seconds (default: 252000)
% 'minGrowth' Minimum growth rate
%
%OUTPUTS
% gdlsSolution GDLS solution structure (similar to OptKnock sol struct)
% bilevelMILPProblem Problem structure used in computation
%
% Adapted from Desmond S Lun's gdls scripts.
% Richard Que (1/28/2010)
MAXFLUX = 1000;
MAXDUAL = 1000;
EPS = 1e-4;
gdlsSolutionStructs = [];
if nargin < 2
error('Model and target reaction(s) must be specified')
elseif mod((nargin-2),2)==0 %manual entry
options.targetRxns = targetRxns;
for i=1:2:(nargin-2)
if ismember(varargin{i},{'nbhdsz','M','maxKO','selectedRxns','koType','koCost','minGrowth', ...
'timeLimit','iterationLimit'})
options.(varargin{i}) = varargin{i+1};
else
display(['Unknown option ' varargin{i}]);
end
end
elseif isstruct(targetRxns) %options structure
options = varargin{1};
else
error('Invalid number of entries')
end
%Default Values
if ~isfield(options,'koType'), options.koType = 'rxns'; end
if ~isfield(options,'nbhdsz'), options.nbhdsz=1; end
if ~isfield(options,'M'), options.M=1; end
if ~isfield(options,'maxKO'), options.maxKO=50; end
if ~isfield(options,'iterationLimit'), options.iterationLimit=70; end
if ~isfield(options,'timeLimit'), options.timeLimit=252000 ; end
if isfield(options,'targetRxns')
selTargetRxns = logical(ismember(model.rxns,options.targetRxns));
if ~any(selTargetRxns)
error([options.targetRxns ' not found. Double check spelling.']);
end
else
error('No target reaction specified')
end
if isfield(options,'selectedRxns')
selSelectedRxns = logical(ismember(model.rxns,options.selectedRxns));
else
selSelectedRxns = true(length(model.rxns),1);
end
switch lower(options.koType)
case 'rxns'
%% Generate selection reaction matrix
model.selRxnMatrix = selMatrix(selSelectedRxns)';
possibleKOList = model.rxns(selSelectedRxns);
case 'genesets'
%% Generate reaction gene set mapping matrix
%remove biomass reaction from grRules and generate unique gene set list
possibleKOList = unique(model.grRules(selSelectedRxns));
if isempty(possibleKOList{1}), possibleKOList = possibleKOList(2:end); end
for i = 1:length(possibleKOList)
model.selRxnMatrix(:,i) = double(strcmp(possibleKOList{i},model.grRules));
end
case 'genes'
%% Use rxnGeneMat as selRxnMatrix
model.selRxnMatrix = model.rxnGeneMat;
possibleKOList = model.genes;
otherwise
error('Unrecognized KO type')
end
%% Generate koCost if not present
if ~isfield(options,'koCost')
if isfield(model,'koCost')
if length(model.koCost) == 1
options.koCost = ones(length(possibleKOList,1)) * model.koCost;
else
options.koCost = model.koCost;
end
else
options.koCost = ones(length(possibleKOList),1);
end
elseif length(model.koCost) == 1
options.koCost = ones(length(possibleKOList,1)) * model.koCost;
else
options.koCost = model.koCost;
end
%index exchange reactions
[selExc] = findExcRxns(model,true,true);
%% Setup model
model.ub(isinf(model.ub)) = MAXFLUX;
model.ub(model.ub>MAXFLUX) = MAXFLUX;
model.lb(isinf(model.lb)) = -MAXFLUX;
model.lb(model.lb<-MAXFLUX) = -MAXFLUX;
model.rxnsPresent = ones(length(model.rxns),1);
%% Create Baseline
solution0 = fluxBalance(model,selTargetRxns);
%% Create bi-level MILP problem
[nMets nRxns] = size(model.S);
nInt = size(model.selRxnMatrix,2);
jMu = find(~isinf(model.lb));
nMu = length(jMu);
jNu = find(~isinf(model.ub));
nNu = length(jNu);
y0 = (model.selRxnMatrix' * ~model.rxnsPresent) ~= 0;
y0 = repmat(y0,1,options.M);
y0p = y0;
iiter = 1;
change = true;
t1 = clock;
while change
change = false;
y = false(nInt, 0);
fmax = zeros(1, 0);
for istart = 1:size(y0, 2)
for irun = 1:options.M
c = [selTargetRxns;
zeros(nMets, 1);
zeros(nMu, 1);
zeros(nNu, 1);
zeros(nRxns, 1);
zeros(nInt, 1)];
%x= [ v lambda mu nu xi y ]
A = [ model.S sparse(nMets, nMets) sparse(nMets, nMu) sparse(nMets, nNu) sparse(nMets, nRxns) sparse(nMets, nInt);
sparse(nRxns, nRxns) model.S' -sparse(jMu, 1:nMu, ones(nMu, 1), nRxns, nMu) sparse(jNu, 1:nNu, ones(nNu, 1), nRxns, nNu) speye(nRxns) sparse(nRxns, nInt);
speye(nRxns) sparse(nRxns, nMets) sparse(nRxns, nMu) sparse(nRxns, nNu) sparse(nRxns, nRxns) model.selRxnMatrix .* repmat(model.lb, 1, nInt);
speye(nRxns) sparse(nRxns, nMets) sparse(nRxns, nMu) sparse(nRxns, nNu) sparse(nRxns, nRxns) model.selRxnMatrix .* repmat(model.ub, 1, nInt);
sparse(nRxns, nRxns) sparse(nRxns, nMets) sparse(nRxns, nMu) sparse(nRxns, nNu) speye(nRxns) model.selRxnMatrix * MAXDUAL;
sparse(nRxns, nRxns) sparse(nRxns, nMets) sparse(nRxns, nMu) sparse(nRxns, nNu) speye(nRxns) -model.selRxnMatrix * MAXDUAL;
model.c' sparse(1, nMets) model.lb(jMu)' -model.ub(jNu)' sparse(1, nRxns) sparse(1, nInt);
sparse(1, nRxns) sparse(1, nMets) sparse(1, nMu) sparse(1, nNu) sparse(1, nRxns) ((y0(:, istart) == 0) - (y0(:, istart) == 1))';
sparse(size(y, 2), nRxns) sparse(size(y, 2), nMets) sparse(size(y, 2), nMu) sparse(size(y, 2), nNu) sparse(size(y, 2), nRxns) ((y == 0) - (y == 1))';
sparse(1, nRxns) sparse(1, nMets) sparse(1, nMu) sparse(1, nNu) sparse(1, nRxns) options.koCost'; ];
b = [ zeros(nMets, 1);
model.c;
model.lb;
model.ub;
zeros(nRxns, 1);
zeros(nRxns, 1);
0;
options.nbhdsz - nnz(y0(:, istart));
ones(size(y, 2), 1) - sum((y ~= 0), 1)';
options.maxKO; ];
csense = char(['E' * ones(nMets, 1);
'E' * ones(nRxns, 1);
'G' * ones(nRxns, 1);
'L' * ones(nRxns, 1);
'G' * ones(nRxns, 1);
'L' * ones(nRxns, 1);
'E';
'L';
'G' * ones(size(y, 2), 1);
'L'; ]);
lb = [ model.lb;
-Inf * ones(nMets, 1);
zeros(nMu, 1);
zeros(nNu, 1);
-Inf * ones(nRxns, 1);
zeros(nInt, 1) ];
ub = [ model.ub;
Inf * ones(nMets, 1);
Inf * ones(nMu, 1);
Inf * ones(nNu, 1);
Inf * ones(nRxns, 1);
ones(nInt, 1) ];
vartype = char(['C' * ones(nRxns, 1);
'C' * ones(nMets, 1);
'C' * ones(nMu, 1);
'C' * ones(nNu, 1);
'C' * ones(nRxns, 1);
'B' * ones(nInt, 1); ]);
osense = -1; %maximize
if isfield(options,'minGrowth')
A = [A; model.c' sparse(1, nMets + nMu + nNu + nRxns + nInt)];
b = [b; options.minGrowth];
csense = [csense; 'G'];
end
[bilevelMILPProblem.c, bilevelMILPProblem.A,...
bilevelMILPProblem.b, bilevelMILPProblem.lb,...
bilevelMILPProblem.ub, bilevelMILPProblem.csense,...
bilevelMILPProblem.vartype, bilevelMILPProblem.osense,...
bilevelMILPProblem.x0] = ...
deal(c, A, b, lb, ub, csense, vartype, osense, []);
%solve
solution1 = solveCobraMILP(bilevelMILPProblem);
%check solver status
if solution1.stat~=1
continue; %non optimal solution
end
yt = solution1.full((end - nInt + 1):end) > EPS;
model.rxnsPresent = ~(model.selRxnMatrix * yt);
solution2 = fluxBalance(model,selTargetRxns,false);
if abs(solution2.obj - solution1.obj) > EPS
continue; %inconsistent
end
fmax(:, end + 1) = solution1.obj;
y(:, end + 1) = yt;
end
end
if size(y, 2) == 0
continue;
end
[fmaxsort, ifmaxsort] = sort(fmax);
y = y(:, ifmaxsort);
y = y(:, max([1 size(y, 2) - options.M + 1]):end);
y = shrinkKnockouts(y, model, selTargetRxns);
if size(y, 2) ~= size(y0, 2) || any(any(y~=y0))&&any(any(y~=y0p))
y0p=y0;
y0 = y;
change = true;
end
fprintf('Iteration %d\n', iiter);
fprintf('----------%s\n', char('-' * ones(1, floor(log10(iiter)) + 1)));
for iend = 1:size(y0, 2)
model.rxnsPresent = ~(model.selRxnMatrix * y0(:, iend));
[solSynMax solSynMin solBiomass] = fluxBalance(model,selTargetRxns);
fprintf('Knockout cost: %d\n', options.koCost' * y0(:, iend));
if nnz(y0) > 0
fprintf('Knockouts:\n%s', sprintf('\t%s\n', possibleKOList{y0(:, iend)}));
end
printLabeledData(model.rxns(selExc),solSynMax.full(selExc),true);
fprintf('\n');
%Save Solutions
gdlsSolutionStructs.(sprintf('Iteration_%d',iiter)).(sprintf('solution_%2',i)).solBiomass = solBiomass;
gdlsSolutionStructs.(sprintf('Iteration_%d',iiter)).(sprintf('solution_%2',i)).solSynMin = solSynMin;
gdlsSolutionStructs.(sprintf('Iteration_%d',iiter)).(sprintf('solution_%2',i)).solSynMax = solSynMax;
end
elapsed_time = etime(clock,t1)
iiter = iiter + 1;
if (elapsed_time >= options.timeLimit) || (iiter >= options.iterationLimit)
break;
end
end
%Generate Solution Structure
fprintf('\nGenerating Output\n');
gdlsSolution.int = y0;
gdlsSolutions.KOs = cell(max(sum(y0,2)),size(y0,2));
for i = 1:size(y0,2)
gdlsSolution.KOs(1:nnz(y0(:,i)),i) = possibleKOList(y0(:,i));
[solSynMax solSynMin solBiomass] = fluxBalance(model,selTargetRxns,false);
gdlsSolution.biomass(1,i) = solBiomass.obj;
gdlsSolution.minTargetProd(1,i) = solSynMin.obj;
gdlsSolution.maxTargetProd(1,i) = solSynMax.obj;
end
end
function y = shrinkKnockouts(y, model, selTargetRxns)
for iycol = 1:size(y, 2)
model.rxnsPresent = ~(model.selRxnMatrix * y(:, iycol));
solution1 = fluxBalance(model, selTargetRxns, false);
for i = find(y(:, iycol))'
yt = y(:, iycol);
yt(i) = 0;
model.rxnsPresent = ~(model.selRxnMatrix * yt);
solution2 = fluxBalance(model, selTargetRxns, false);
if solution2.obj >= solution1.obj
y(:, iycol) = yt;
y(:, iycol) = shrinkKnockouts(y(:, iycol), model, selTargetRxns);
end
end
end
y = unique(y', 'rows')';
end
function [solSynMax solSynMin solBiomass] = fluxBalance(model,selTargetRxns,verbFlag)
if nargin < 3
verbFlag = true;
end
model.x0 = [];
modelb = model;
model_syn = model;
[nMets nRxns] = size(model.S);
yt = model.rxnsPresent;
modelb.A = [ model.S;
sparse(1:nnz(~yt), find(~yt), ones(nnz(~yt), 1), nnz(~yt), nRxns) ];
modelb.b = [ zeros(nMets, 1);
zeros(nnz(~yt), 1) ];
modelb.csense = char('E' * ones(1, nMets + nnz(~yt)));
modelb.vartype = char('C' * ones(1, nRxns));
modelb.osense = -1;
solBiomass = solveCobraMILP(modelb);
model_syn.A = [ model.S;
sparse(1:nnz(~yt), find(~yt), ones(nnz(~yt), 1), nnz(~yt), nRxns);
model.c' ];
model_syn.b = [ zeros(nMets, 1);
zeros(nnz(~yt), 1);
solBiomass.obj ];
model_syn.c = selTargetRxns;
model_syn.csense = char('E' * ones(1, nMets + nnz(~yt) + 1));
model_syn.vartype = char('C' * ones(1, nRxns));
model_syn.osense = -1;
solSynMax = solveCobraMILP(model_syn);
model_syn.osense = 1;
solSynMin = solveCobraMILP(model_syn);
if verbFlag
fprintf('Biomass flux: %f\n', solBiomass.obj);
fprintf('Synthetic flux: [%f, %f]\n', solSynMin.obj, solSynMax.obj);
end
end
|
github
|
EPFL-LCSB/matTFA-master
|
optGene.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/design/optGene.m
| 10,378 |
utf_8
|
096047845ee9473fe011e1224eda05b7
|
function [x, population, scores, optGeneSol] = optGene(model, targetRxn, substrateRxn, generxnList, MaxKOs, population)
%OPTGENE implements the optgene algorithm.
%
% [x, population, scores, optGeneSol] = optGene(model, targetRxn, substrateRxn, generxnList, MaxKOs, population)
%
%INPTUS
% mode Model of reconstruction
% targetRxn String name of reaction which is to be maximized.
% generxnList List of genes or rxns which can be knocked out. The
% program will guess which of the two it is, based on the
% content in model.
%
%OPTIONAL INPUT
% population population matrix (binary matrix). Use this
% parameter to interrupt simulation and resume afterwards.
%
%OUTPUTS
% x best optimized value found
% population Population of individuals. Pass this back into optgene to
% continue simulating where you left off.
% scores An array of scores
% optGeneSol optGene solution strcture
%
% Jan Schellenberger and Adam Feist 04/08/08
% hash table for hashing results... faster than not using it.
global HTABLE
HTABLE = java.util.Hashtable;
global MaxKnockOuts
ngenes = length(generxnList);
% figure out if list is genes or reactions
rxnok = 1;
geneok = 1;
for i = 1:length(generxnList)
if(~ ismember(generxnList{i}, model.rxns)), rxnok = 0; end
if(~ ismember(generxnList{i}, model.genes)),geneok = 0; end
end
if geneok
display('assuming list is genes');
elseif rxnok
display('assuming list is reactions');
else
display('list appears to be neither genes nor reactions: aborting');
return;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% PARAMETERS - set parameters here %%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if nargin < 5
MaxKnockOuts = 10;
else
MaxKnockOuts = MaxKOs;
end
mutationRate = 1/ngenes; % paper: a mutation rate of 1/(genome size) was found to be optimal for both representations.
crossovermutationRate = mutationRate*.2; % the rate of mutation after a crossover. This value should probably be fairly low. It is only there to ensure that not every member of the population ends up with the same genotype.
CrossoverFraction = .80; % Percentage of offspring created by crossing over (as opposed to mutation). 0.7 - 0.8 were found to generate the highest mean, but this can be adjusted.
PopulationSize = [125 125 125 125]; % paper: it was found that an increase beyond 125 individuals did not improve the results significantly.
Generations = 10000; % paper: 5000. maximum number of generations to perform
TimeLimit = 3600*24*2; % global time limit in seconds
StallTimeLimit = 3600*24*1; % Stall time limit (terminate after this much time of not finding an improvement in fitness)
StallGenLimit = 10000; % terminate after this many generations of not finding an improvement
PlotFcns = {@gaplotscores, @gaplotbestf, @gaplotscorediversity, @gaplotstopping, @gaplotmutationdiversity}; % what to plot.
crossfun = @(a,b,c,d,e,f) crossoverCustom(a,b,c,d,e,f,crossovermutationRate);
MigrationFraction = .1; % how many individuals migrate (.1 * 125 ~ 12 individuals).
MigrationInterval = 100; % how often individuals migrate from one population to another.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% END PARAMETERS %%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
InitialPopulation = [];
if nargin > 5
InitialPopulation = double(population);
end
options = gaoptimset( ...
'PopulationType', 'bitstring', ...
'CreationFcn', @lowmutationcreation, ...
'MutationFcn', {@mutationUniformEqual, mutationRate}, ...
'PopulationSize', PopulationSize, ...
'StallTimeLimit', StallTimeLimit, ...
'TimeLimit', TimeLimit, ...
'PlotFcns', PlotFcns, ...
'InitialPopulation', InitialPopulation, ...
'CrossoverFraction', CrossoverFraction, ...
'CrossoverFcn', crossfun, ...
'StallGenLimit', StallGenLimit, ...
'Generations', Generations, ...
'TolFun', 1e-10, ...
'Vectorize', 'on', ...
'MigrationFraction', MigrationFraction, ...
'MigrationInterval', MigrationInterval ...
... % 'SelectionFcn', @selectionstochunif ...
);
% options
% pause;
%finess function call
%FitnessFunction = @(x) optGeneFitness(x,model,targetRxn, generxnList, geneok);
FitnessFunction = @(x) optGeneFitnessTilt(x,model,targetRxn, generxnList, geneok);
gap.fitnessfcn = FitnessFunction;
gap.nvars = ngenes;
gap.options = options;
[x,FVAL,REASON,OUTPUT,population, scores] = ga(gap);
% save the solution
[optGeneSol] = GetOptGeneSol(model, targetRxn, substrateRxn, generxnList, population, x, scores, geneok); % in case of genes
return;
%% Creation Function
% generates initial warmup with much lower number of mutations (on average
% one mutation per
function [Population] = lowmutationcreation(GenomeLength,FitnessFcn,options)
totalPopulation = sum(options.PopulationSize);
initPopProvided = size(options.InitialPopulation,1);
individualsToCreate = totalPopulation - initPopProvided;
% Initialize Population to be created
Population = true(totalPopulation,GenomeLength);
% Use initial population provided already
if initPopProvided > 0
Population(1:initPopProvided,:) = options.InitialPopulation;
end
% Create remaining population
Population(initPopProvided+1:end,:) = logical(1/GenomeLength > rand(individualsToCreate,GenomeLength));
return;
%% Mutation Function
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% mutation function %%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
function mutationChildren = mutationUniformEqual(parents,options,GenomeLength,FitnessFcn,state,thisScore,thisPopulation,mutationRate)
global MaxKnockOuts
if(nargin < 8)
mutationRate = 0.01; % default mutation rate
end
mutationChildren = zeros(length(parents),GenomeLength);
for i=1:length(parents)
child = thisPopulation(parents(i),:);
kos = sum(child);
mutationPoints = find(rand(1,length(child)) < mutationRate);
child(mutationPoints) = ~child(mutationPoints);
if MaxKnockOuts > 0
while(sum(child(:))> MaxKnockOuts)
ind2 = find(child);
removeindex = ind2(randint(1,1,length(ind2))+1);
child(removeindex) = 0;
end
end
% with 50% chance, you will have fewer knockouts after mutation
% than before. This is to stop aquiring so many mutations.
if rand > .5 && kos > 1
while(sum(child(:))>= kos)
ind2 = find(child);
removeindex = ind2(randint(1,1,length(ind2))+1);
child(removeindex) = 0;
end
end
mutationChildren(i,:) = child;
end
return;
%% Crossover Function
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% crossover function %%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function xoverKids = crossoverCustom(parents,options,GenomeLength,FitnessFcn,unused,thisPopulation, mutationRate)
nKids = length(parents)/2;
% Extract information about linear constraints
% Allocate space for the kids
xoverKids = zeros(nKids,GenomeLength);
global MaxKnockOuts;
% To move through the parents twice as fast as thekids are
% being produced, a separate index for the parents is needed
index = 1;
% for each kid...
for i=1:nKids
% get parents
r1 = parents(index);
index = index + 1;
r2 = parents(index);
index = index + 1;
% Randomly select half of the genes from each parent
% This loop may seem like brute force, but it is twice as fast as the
% vectorized version, because it does no allocation.
for j = 1:GenomeLength
if(rand > 0.5)
xoverKids(i,j) = thisPopulation(r1,j);
else
xoverKids(i,j) = thisPopulation(r2,j);
end
end
if MaxKnockOuts>0
while(sum(xoverKids(i,:))> MaxKnockOuts)
ind2 = find(xoverKids(i,:));
removeindex = ind2(randint(1,1,length(ind2))+1);
xoverKids(i,removeindex) = 0;
end
end
end
% also apply mutations to crossover kids...
xoverKids = mutationUniformEqual(1:size(xoverKids,1) ,[],GenomeLength,[],[],[],xoverKids,mutationRate);
return;
function state = gaplotmutationdiversity(options,state,flag,p1)
%GAPLOTSCOREDIVERSITY Plots a histogram of this generation's scores.
% STATE = GAPLOTSCOREDIVERSITY(OPTIONS,STATE,FLAG) plots a histogram of current
% generation's scores.
%
% Example:
% Create an options structure that uses GAPLOTSCOREDIVERSITY
% as the plot function
% options = gaoptimset('PlotFcns',@gaplotscorediversity);
% Copyright 2003-2007 The MathWorks, Inc.
% $Revision: 1.6.4.3 $ $Date: 2007/05/23 18:49:53 $
global MaxKnockOuts
if nargin < 4
p1 = 10;
end
p1 = MaxKnockOuts+1;
p1 = [0:(MaxKnockOuts)];
switch flag
case 'init'
title('Mutation Histogram','interp','none')
xlabel('number of mutations');
ylabel('Number of individuals');
case 'iter'
% Check if Rank is a field and there are more than one objectives, then plot for Rank == 1
if size(state.Score,2) > 1 && isfield(state,'Rank')
index = (state.Rank == 1);
% When there is one point hist will treat it like a vector
% instead of matrix; we need to add one more duplicate row
if nnz(index) > 1
set(gca,'ylimmode','auto');
hist(sum(state.Population(index,:)),p1);
else
set(gca,'ylim',[0 1]);
hist([sum(state.Population(index,:)); sum(state.Population(index,:))],p1);
end
% Legend for each function <min max> values on the Pareto front
nObj = size(state.Score,2);
fminval = min(state.Score(index,:),[],1);
fmaxval = max(state.Score(index,:),[],1);
legendText = cell(1,nObj);
for i = 1:nObj
legendText{i} = ['fun',num2str(i),' [',sprintf('%g ',fminval(i)), ...
sprintf('%g',fmaxval(i)),']'];
end
legend(legendText);
else % else plot all score
hist(sum(state.Population,2),p1);
end
end
|
github
|
EPFL-LCSB/matTFA-master
|
optGeneFitness.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/design/optGeneFitness.m
| 4,201 |
utf_8
|
af651aa05b3544eb6d725b9ac5cfa801
|
function [val] = optGeneFitness(rxn_vector_matrix, model, targetRxn, rxnListInput, isGeneList)
%optGeneFitness GeneOptFitness the fitness function
%
% [val] = optGeneFitness(rxn_vector_matrix, model, targetRxn, rxnListInput, isGeneList)
%
%INPUTS
% rxn_vector_matrix
% model
% targetRxn
% rxnListInput
% isGeneList
%
%OUTPUT
% val
%
%
global MaxKnockOuts
%size(rxn_vector_matrix)
popsize = size(rxn_vector_matrix,1);
val = zeros(1,popsize);
for i = 1:popsize
rxn_vector = rxn_vector_matrix(i,:);
rxnList = rxnListInput(logical(rxn_vector));
%see if we've done this before
val_temp = memoize(rxn_vector);
if ~ isempty(val_temp)
val(i) = val_temp;
continue;
end
% check to see if mutations is above the max number allowed
nummutations = sum(rxn_vector);
if nummutations > MaxKnockOuts
continue;
end
% generate knockout.
if isGeneList
modelKO = deleteModelGenes(model, rxnList);
else % is reaction list
[isValidRxn,removeInd] = ismember(rxnList,model.rxns);
removeInd = removeInd(isValidRxn);
modelKO = model;
modelKO.ub(removeInd) = 0;
modelKO.lb(removeInd) = 0;
end
% find growthrate;
% slnKO = optimizeCbModel(modelKO);
% growthrate1 = slnKO.f; %max growth rate.
if exist('LPBasis', 'var')
modelKO.LPBasis = LPBasis;
end
[slnKO, LPOUT] = solveCobraLPCPLEX(modelKO, 0,1);
LPBasis = LPOUT.LPBasis;
growthrate = slnKO.obj;
% check to ensure that GR is above a certain value
if growthrate < .10
continue;
end
% display('second optimization');
% find the lowesest possible production rate (a hopefully high number)
% at the max growth rate minus some set factor gamma (a growth rate slightly
% smaller than the max). A positive value will eliminate solutions where the
% production envelope has a vertical line at the max GR, a "non-unique"
% solution. Set value to zero if "non-unique" solutions are not an issue.
gamma = 0.01; % proportional to Grwoth Rate (hr-1), a value around 0.5 max.
%find indicies of important vectors
indBOF = find(modelKO.c);
indTar = findRxnIDs(modelKO, targetRxn);
% generate a model with a fixed max KO growth rate
modelKOsetGR = modelKO;
modelKOsetGR.lb(indBOF) = growthrate - gamma; % this growth rate is required as lb.
modelKOsetGR.c = zeros(size(modelKO.c));
modelKOsetGR.c(indTar) = -1; % minimize for this variable b/c we want to look at the very minimum production.
% find the minimum production rate for the targeted reaction.
% slnKOsetGR = optimizeCbModel(modelKOsetGR);
% minProdAtSetGR1 = -slnKOsetGR.f; % This should be a negative value b/c of the minimization setup, so -1 is necessary.
if exist('LPBasis2', 'var')
modelKOsetGR.LPBasis = LPBasis2;
end
[slnKOsetGR, LPOUT2] = solveCobraLPCPLEX(modelKOsetGR, 0,1);
LPBasis2 = LPOUT2.LPBasis;
minProdAtSetGR = -slnKOsetGR.obj;
% objective function for optGene algorithm = val (needs to be a negative value, since it is
% a minimization)
val(i) = -minProdAtSetGR;
% penalty for a greater number of mutations
% val(i) = -minProdAtSetGR * (.98^nummutations);
% select best substrate-specific productivity
% val(i) = -minProdAtSetGR * (.98^nummutations) * growthrate;
% check to prevent very small values from being considerered improvments
if val(i) > -1e-3
val(i) = 0;
end
memoize(rxn_vector, val(i));
end
return;
%% Memoize
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% MEMOIZE %%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% internal function to speed things up.
function [value] = memoize(gene_vector, value)
global HTABLE
hashkey = num2str(gene_vector);
hashkey = strrep(hashkey,' ',''); % cut out white space from string (more space efficient).
if nargin == 1
value = HTABLE.get(hashkey);
return;
else
if HTABLE.size() > 10000
HTABLE = java.util.Hashtable; %reset the hashtable if more than 10,000 entries.
end
HTABLE.put(hashkey, value);
value = [];
return;
end
return
|
github
|
EPFL-LCSB/matTFA-master
|
compareMultSamp.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/fluxomics/compareMultSamp.m
| 3,253 |
utf_8
|
2cdd10a7b9419f8d2af32bf86b455456
|
function [totalz,zscore,mdvs] = compareMultSamp(xglc,model,samps,measuredMetabolites)
% Compare the multiple sets of samples
% xglc is optional, a random sugar distribution is calculated if empty
% expects samp1 and samp2 to have a field named points containing
% an array of sampled points
% expects model.rxns to contain a list of rxn names
% measuredMetabolites is an optional parameter fed to calcMDVfromSamp.m
% which only calculates the MDVs for the metabolites listed in this
% array. e.g.
%
% totalz is the sum of all zscores
% zscore is the calculated difference for each mdv element distributed
% across all the points
% mdv1,mdv2 each containing fields:
% - mdv - the calculated mdv distribution converted from the idv
% solved from each point contained in their respective samples sampX
% - names - the names of the metabolites
% - ave - the average of each mdv element across all of the points
% - stdev - the standard dev for each mdv element across all points
% Wing Choi 2/11/08
%glc = zeros(62,1);
%glc = [.2 ;.8 ;glc];
if (nargin < 3)
disp '[totalz,zscore,mdvs] = compareMultSamp(xglc,model,samps,measuredMetabolites)';
return;
end
if (nargin < 4)
measuredMetabolites = [];
end
mdvs.ave = [];
mdvs.stdev = [];
if (isempty(xglc))
% random glucose
xglc = rand(64,1);
xglc = xglc/sum(xglc);
xglc = idv2cdv(6)*xglc;
end
% generate the translation index array
% can shave time by not regenerating this array on every call.
xltmdv = zeros(1,4096);
for i = 1:4096
xltmdv(i) = length(strrep(dec2base(i-1,2),'0',''));
end
% calculate mdv for samp1 and samp2
for i = 1:length(samps)
samp.points = samps(i).points;
mdv = calcMDVfromSamp(model,xglc,samp,measuredMetabolites);
l = length(mdv.ave);
mdvs.ave(1:l,i) = mdv.ave;
mdvs.stdev(1:l,i) = mdv.stdev;
%[mdv2] = calcMDVfromSamp(model,xglc,samp2,measuredMetabolites);
%[totalz,zscore] = compareTwoMDVs(mdv1,mdv2);
end
totalz = 0;
zscore = 0;
%mdvs = mdv;
return
end
%Here's what the function does.
%Apply slvrXXfast to each point
%for each field in the output, apply iso2mdv to get a much shorter vector.
%store all the mdv's for each point and for each metabolite in both sets.
%
%Compute the mean and standard deviation of each mdv and then get a z-score
% between them (=(mean1-mean2)/(sqrt(sd1^2+sd2^2))).
%Add up all the z-scores (their absolute value) and have this function return
% that value.
%
%Intuitively what we're doing here is comparing the two sets based on
% how different the mdv's appear.
%We're going to see if different glucose mixtures result in different values.
%I'm going to rewrite part of slvrXXfast so it doesn't return every metabolite
% but only those we can actually measure, but for now just make it generic.
function mdv = myidv2mdv (idv,xltmdv)
% generate the mdv
len = length(idv);
%disp(sprintf('idv is %d long',len));
mdv = zeros(1,xltmdv(len)+1);
%disp(sprintf('mdv is %d long',length(mdv)));
for i = 1:len
idx = xltmdv(i) + 1;
%disp(sprintf('idx is %d, currently on %d',idx,i));
mdv(idx) = mdv(idx) + idv(i);
end
return
end
|
github
|
EPFL-LCSB/matTFA-master
|
C13ConfidenceInterval.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/fluxomics/C13ConfidenceInterval.m
| 14,161 |
utf_8
|
4b5572a4c36fbfc32729f15f709e7683
|
function [vs, output, v0] = C13ConfidenceInterval(v0, expdata, model, max_score, directions, majorIterationLimit)
% v0 - set of flux vectors to be used as initial guesses. They may be
% valid or not.
% expdata - experimental data.
% model - The standard model. Additional field .N (= null(S)) should also
% be provided. This is a basis of the flux space.
% max score - maximum allowable data fit error.
% directions (optional) - ones and zeros of which reactions to compute (size = n
% x 1).
% OR
% numbers of reactions to use aka. [1;5;7;8;200]
% OR
% reaction strings aka. {'GPK', 'PGL'}. Ratios are possible with this
% input only. Default = [] meaning do FVA with no ratios.
% majorIterationLimit (optional) - default = 10000
if nargin < 5
directions = ones(size(v0,1),1);
end
if isempty(directions)
directions = ones(size(v0,1),1);
end
t_start = clock;
printLevel = 3;
if nargin < 6
majorIterationLimit = 1000; %max number of iterations
end
diffInterval = 1e-5; %gradient step size.
feasibilityTolerance = max_score/20; % how close you need to be to the max score.
logdirectory = strcat('temp', filesep);
% isratio(i): >0 indicates not a ratio and points to reaction#
% <0 indicates -numerator of ratio fraction. In this case,
% denom(i) stores the denominator
%
denom = zeros(size(directions));
if isnumeric(directions) %cannot be an actual ratio
if max(directions) == 1
isratio = find(directions);
else
isratio = directions;
end
else % might be a ratio. Gotta process strings
isratio = zeros(size(directions));
for i = 1:length(directions)
if findstr(directions{i}, '/')
[rxn1,rest] = strtok(directions{i}, '/');
rxnID = findRxnIDs(model,rxn1);
if rxnID == 0
display('unable to process rxn from list');
display(directions{i});
return;
else
isratio(i) = -rxnID;
end
rxn2 = rest(2:end);
rxnID = findRxnIDs(model,rxn2);
if rxnID == 0
display('unable to process rxn from list');
display(rest(2:end));
return;
else
denom(i) = rxnID;
end
else
rxnID = findRxnIDs(model,directions{i});
if rxnID == 0
display('unable to process rxn from list');
display(directions{i});
return;
else
isratio(i) = rxnID;
end
end
end
end
numdirections = length(isratio);
numpoints = size(v0,2);
numiterations = numdirections*numpoints*2; % total number of iterations.
x0 = model.N\v0; % back substitute
scores = zeros(numpoints,1);
tProb.user.expdata = expdata;
tProb.user.model = model;
for i = 1:numpoints
scores(i) = errorComputation2(x0(:,i),tProb);
end
% fit points if they are not currently feasible
v0(:,scores> max_score) = fitC13Data(v0(:,scores > max_score),expdata,model, majorIterationLimit);
if ~isfield(model, 'N')
model.N = null(model.S);
end
x0 = model.N\v0; % back substitute
% safety check:
if (max(abs(model.S*v0))> 1e-6)
display('v0 not quite in null space');
pause;
end
if(max(abs(model.N*x0 - v0)) > 1e-6)
display('null basis is weird');
pause;
end
Name = 't2';
nalpha = size(model.N, 2);
x_L = -1000*ones(nalpha,1);
x_U = 1000*ones(nalpha,1);
[A, b_L, b_U] = defineLinearConstraints(model);
scores = zeros(numpoints,1);
% compute scores for all points.
for i = 1:numpoints
scores(i) = errorComputation2(x0(:,i),tProb);
end
valid_index = scores < max_score + feasibilityTolerance;
fprintf('found %d valid points\n', sum(valid_index));
x0_valid = x0(:,valid_index);
x0_invalid = x0;
scores_valid = scores(valid_index);
% pre-compute unnecesary directions.
% if checkedbefore(i) ~= 0 then direction i is redundant
% if checkedbefore(i) = j then direction i and j are identical and do not
% need to be recomputed.
% checkedbefore(i) = j < 0 means that direction j is the same as i except
% for a sign switch.
checkedbefore = zeros(length(isratio),1);
for i = 2:length(isratio)
if(isratio(i) < 0) % meaning it actually IS a ratio and no simplification possible
continue
end
d = objective_coefficient(isratio(i), model);
for j = 1:i-1
if(isratio(j) < 0) % meaning it actually IS a ratio and no simplification possible
continue
end
dj = objective_coefficient(isratio(j), model);
if max(abs(dj - d))< 1e-4
checkedbefore(i) = j;
break;
elseif max(abs(dj + d))< 1e-4
checkedbefore(i) = -j;
break;
end
end
end
% initialize variables;
outputv = 222*ones(numiterations,1);
outputexitflag = -222*ones(numiterations,1);
outputfinalscore = -222*ones(numiterations,1);
outputstruct = cell(numiterations,1);
csense = '';
for mm = 1:length(b_L),csense(mm,1) = 'L';end
for mm = 1:length(b_L),csense(mm+length(b_L),1) = 'G';end
fLowBnds = zeros(length(isratio), 2); %initialize but fill in later.
for rxn = 1:length(isratio)
for direction = -1:2:1
if isratio(rxn) < 0
ration = objective_coefficient(-isratio(rxn),model);
ratiod = objective_coefficient(denom(rxn),model);
% in case RXN is a ratio
Result = solveCobraNLP(...
struct('lb', x_L, 'ub', x_U,...
'name', Name,...
'A', A,...
'b_L', b_L, 'b_U', b_U,...
'objFunction', 'ratioScore', 'g', 'ratioScore_grad',...
'userParams', struct(...
'ration', direction*ration, 'ratiod', ratiod,... % set direction here too.
'diff_interval', diffInterval,'useparfor', true)...
),...
'printLevel', 1, ...
'iterationLimit', 1000);
else
d = objective_coefficient(isratio(rxn),model);
Result = solveCobraLP(...
struct('A', [A;A],'b',[b_U;b_L],'csense', csense, ...
'c', direction*d, ...
'lb', x_L,'ub', x_U, ...
'osense', 1),...
'feasTol',1e-7,'optTol',1e-7);
if Result.stat ~= 1
Result
pause
end
end
fLowBnds(rxn, (direction+3)/2) = direction*Result.obj; % fill in
end
end
if ~exist (logdirectory, 'dir')
if ~mkdir(logdirectory)
display('unable to create logdirectory');
return;
end
end
clear d
%iterate through directions
parfor itnum = 1:numiterations
if exist('ttt.txt', 'file') % abort w/o crashing if file 'ttt.txt' found in current directory
fprintf('quitting due to file found\n');
continue;
end
[rxn, direction, point] = getValues(itnum, numpoints); % translate itnum to rxn, direction and point
% direction == 1 means minimize. direction == -1 means maximize
% (opposite of what you might think.
if checkedbefore(rxn) ~= 0 %if this reaction maps to a previous reaction, we can skip
continue;
end
fLowBnd = fLowBnds(rxn, (direction+3)/2); %get the absolute bound in the space w/o regards to C13 constraints.
fprintf('reaction %d of %d, direction %d, lowerbound %f point %d of %d\n', rxn ,length(isratio), direction, fLowBnd, point, numpoints);
% short circuit if x0 already close to a bound.
if isratio(rxn) > 0
di = objective_coefficient(isratio(rxn),model);
obj1 = di'*x0_valid;
else
rationi = objective_coefficient(-isratio(rxn),model);
ratiodi = objective_coefficient(denom(rxn),model);
obj1 = (rationi'*x0_valid) ./ (ratiodi'*x0_valid);
end
if(any(abs(obj1-fLowBnd)<.0001))
display('short circuiting');
[nil, min_index] = min(obj1);
outputv(itnum,1) = fLowBnd; % multiply by direction to correct sign.
outputexitflag(itnum,1) = 111;
outputfinalscore(itnum,1) = scores_valid(min_index);
else % gotta actually do the computation.
xinitial = x0_invalid(:,point);
if isratio(rxn) > 0
NLPsolution = solveCobraNLP(...
struct('x0', xinitial, ...
'lb', x_L, 'ub', x_U,...
'name', Name,...
'A', A, 'b_L', b_L, 'b_U', b_U,...
'd', 'errorComputation2', 'dd', 'errorComputation2_grad',...
'd_L', 0, 'd_U', max_score,...
'c', di*direction, ... % direction of optimization
'userParams', struct(...
'expdata', expdata,'model', model,'max_error', max_score,...
'diff_interval', diffInterval,'useparfor', true)...
),...
'printLevel', printLevel, ...
...%'intTol', 1e-7, ...
'iterationLimit', majorIterationLimit, ...
'logFile', strcat(logdirectory, 'ci_', num2str(rxn),'x',num2str(direction),'x', point, '.txt'));
else
NLPsolution = solveCobraNLP(...
struct('x0', xinitial, ...
'lb', x_L, 'ub', x_U,...
'name', Name,...
'A', A, 'b_L', b_L, 'b_U', b_U,...
'd', 'errorComputation2', 'dd', 'errorComputation2_grad',...
'd_L', 0, 'd_U', max_score,...
'objFunction', 'ratioScore', 'g', 'ratioScore_grad',...
'userParams', struct(...
'expdata', expdata,'model', model,'max_error', max_score,...
'ration', direction*rationi,...
'ratiod', ratiodi,...
'diff_interval', diffInterval,'useparfor', false)...
),...
'printLevel', printLevel, ...
...%'intTol', 1e-7, ...
'iterationLimit', majorIterationLimit, ...
'logFile', strcat(logdirectory, 'ci_', num2str(rxn),'x',num2str(direction),'x', point, '.txt'));
end
tscore = errorComputation2(NLPsolution.full, tProb);
tbest = NLPsolution.obj;
fprintf('reaction %d (%d), x %d; x=%f (%f); score=%f (%f)\n', rxn, length(isratio),direction, tbest,fLowBnd, tscore, max_score)
outputv(itnum,1) = direction*tbest; % multiply by direction to correct sign.
outputexitflag(itnum,1) = NLPsolution.origStat;
outputfinalscore(itnum,1) = tscore;
outputstruct{itnum,1} = NLPsolution;
end
end
for itnum = 1:numiterations
[rxn, direction, point] = getValues(itnum,numpoints);
if direction == 1;
output.minv(rxn,point) = outputv(itnum);
output.minexitflag(rxn,point) = outputexitflag(itnum);
output.minfinalscore(rxn,point) = outputfinalscore(itnum);
output.minstruct(rxn,point) = outputstruct(itnum);
else
output.maxv(rxn,point) = outputv(itnum);
output.maxexitflag(rxn,point) = outputexitflag(itnum);
output.maxfinalscore(rxn,point) = outputfinalscore(itnum);
output.maxstruct(rxn,point) = outputstruct(itnum);
end
end
for i = 1:length(isratio)
if checkedbefore(i) > 0 %short circuit if seen before.
output.minv(i) = output.minv(checkedbefore(i));
output.maxv(i) = output.maxv(checkedbefore(i));
output.minexitflag(i) = output.minexitflag(checkedbefore(i));
output.maxexitflag(i) = output.maxexitflag(checkedbefore(i));
output.minfinalscore(i) = output.minfinalscore(checkedbefore(i));
output.maxfinalscore(i) = output.maxfinalscore(checkedbefore(i));
output.minstruct(i) = output.minstruct(checkedbefore(i));
output.maxstruct(i) = output.maxstruct(checkedbefore(i));
elseif checkedbefore(i) < 0
output.minv(i) = -output.maxv(-checkedbefore(i));
output.maxv(i) = -output.minv(-checkedbefore(i));
output.minexitflag(i) = output.maxexitflag(-checkedbefore(i));
output.maxexitflag(i) = output.minexitflag(-checkedbefore(i));
output.minfinalscore(i) = output.maxfinalscore(-checkedbefore(i));
output.maxfinalscore(i) = output.minfinalscore(-checkedbefore(i));
output.minstruct(i) = output.maxstruct(-checkedbefore(i));
output.maxstruct(i) = output.minstruct(-checkedbefore(i));
end
end
vs = zeros(length(isratio), 2);
for i = 1:length(isratio)
validindex = output.minfinalscore(i,:) < max_score + feasibilityTolerance;
if any(validindex)
vs(i,1) = min(output.minv(i,validindex));
else
vs(i,1) = 222;
end
validindex = output.maxfinalscore(i,:) < max_score + feasibilityTolerance;
if any(validindex)
vs(i,2) = max(output.maxv(i,validindex));
else
vs(i,2) = -222;
end
end
elapsed_time = etime(clock, t_start)
return;
% function [index] = getIndex(rxn, direction, point, numpoints)
% % point goes from 1 .. NUMPOINTS
% % rxn goes from 1 .. NUMRXNS
% % direction is -1 or 1
% % index goes from 1 to NUMPOINTS*NUMRXNS*2
%
% rxn = rxn - 1;
% point = point -1;
% direction = (direction + 1)/2;
%
%
% index = rxn*numpoints*2 + direction*numpoints + point;
% index = index+1;
%
% return;
function [rxn, direction, point] = getValues(index, numpoints)
% point goes from 1 .. NUMPOINTS
% rxn goes from 1 .. NUMRXNS
% direction is -1 or 1
% index goes from 1 to NUMPOINTS*NUMRXNS*2
index = index - 1;
point = mod(index, numpoints);
index = index - point;
index = index/numpoints;
direction = mod(index,2);
index = index - direction;
index = index/2;
rxn = index;
point = point +1; % remap to 1..NUMPOINTS
direction = direction*2-1; % remap to -1,1
rxn = rxn+1; % remap to 1 .. number of rxns;
return;
% function that returns the proper objective coefficient for each reaction
% takes into account the reversibility of reactinos etc.
function [d] = objective_coefficient(i, model)
d = zeros(length(model.lb),1);
d(i) = 1;
if (model.match(i))
d(model.match(i)) = -1;
end
d = (d'*model.N)'; % transform to null space;
return
|
github
|
EPFL-LCSB/matTFA-master
|
runHiLoExp.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/fluxomics/runHiLoExp.m
| 10,864 |
utf_8
|
f754c1508023d127daf3b1f489af2798
|
function [experiment] = runHiLoExp(experiment)
% runHiLoExp
% takes an experiment with the following structure
% and splits the sample space at the median of a target flux
% solves the two spaces with a given sugar and compares the
% resulting mdvs to provide a z-score.
%
% experiment -
% model - S = the stoichiometric matrix
% - rxns = array of reaction names, corresponding the S
% - c = optimization target 1, or -1
% - ub,lb = upper and lower bounds of reactions
% points = a #fluxes X #samples (~2000) array of the solution space
% if missing or empty, will generate a sample
% glcs = an array of sugars in isotopomer format, each column a separate sugar.
% Should not be in MDV format. Conversion is done automatically.
% will default to generate 1 random sugar if set to []
% targets = an array of cells with string for the reaction to
% split on the solution space, defaults to 'PGL'
% thresholds = # targets X 1 array of thresholds
% metabolites = an optional parameter fed to calcMDVfromSamp.m
% which only calculates the MDVs for the metabolites listed in this
% array. e.g.
% - optionally, metabolites can also be a structure of fragments
% hilo = a #targets X #samples array of 0/1's, 0 id's the sample of
% fluxes as the lo side and 1 id's the sample for the hi side.
% hilo will only be calculated/recalculated if it's missing or
% if the targets have been replaced using the param list
% mdvs = structure of mdv results
% - (name) = name of the run = t + glc#
% e.g. t1, t2, glc# refers to the glc in the glcs array
% - mdv = array of mdv results
% - zscore = array of zscores from comparison btw the two mdvs
% - totalz
% Note that the split of mdvs are not stored,
% also since the only time mdvs should be regen'd is when glcs
% has changed, but we have no way of knowing when this happens,
% the user will have to manually empty out mdvs to have it
% regenerated.
% zscores = array of zscores from each run, targets X glcs
% rscores = array of ridge scores from each run, targets X glcs
%
% target is an optional string for a specific rxn to target.
% if supplied, it will override and replace the targets field in the
% experiment structure.
% threshold is an optional number to apply on the solution space fluxes
% if supplied, it will be applied to the hilo field and replace the
% hilo splits.
%
%
% outputs the experiment array.
%
% basically, this code will loop thru one experiment
% per sugar, per target
%
% Wing Choi 3/14/08
if (nargin < 1)
disp '[experiment] = runHiLoExp(experiment,target,threshold)';
return;
end
runzscore = true; %binary flag for z-scores
runrscore = false; %binary flag for r-scores
runkscore = false; %binary flag for k-scores
%% if no model, exit with error.
% if model exists, but no points
% then points are generated
% existing mdvs in experiment, if any, are wiped
if (not(isfield(experiment,'model')))
disp 'ERROR: input structure experiment lacks the requisite model in the model field';
return;
end
model = experiment.model;
points = [];
if (isfield(experiment,'points'))
points = experiment.points;
end
if (isempty(points))
disp 'WARN: experiment.points is empty or missing';
disp ' generating a sample and empty out mdvs';
pointSample = generateRandomSample(model,2000);
points = pointSample.point;
experiment.mfrac = pointSample.mf;
%points = m.points;
experiment.points = points;
%experiment.mfrac = mf;
% recalculate the mdvs since we have new points.
experiment.mdvs = [];
end
%% if the rxns array is inverted
% display error message indicating that rxns array is inverted
dr = size(model.rxns,2);
if (dr > 1),
disp 'ERROR: rxns array is inverted';
return;
end
if (isfield(experiment,'metabolites'))
metabolites = experiment.metabolites;
else
metabolites = [];
end
%% if no sugar, generate a random one and warn the user.
% existing mdvs are wiped
glcs = [];
if (isfield(experiment,'glcs'))
glcs = experiment.glcs;
end
if (isempty(glcs))
disp 'WARN: glcs not found, will generate 1 random sugar for experiment and empty out mdvs';
glcs = getRandGlc();
experiment.glcs = glcs;
experiment.mdvs = [];
end
%% set glucose mixture name description;
glcsnames = {};
for i = 1:size(glcs,2)
glcsnames{1,i} = '';
glci = glcs(:,i);
fglc = find(glci);
for j = 1:length(fglc)
if j ~=1
glcsnames{1,i} = strcat(glcsnames{1,i}, '+');
end
if round(100*glci(fglc(j))) < 100
glcsnames{1,i} = strcat(glcsnames{1,i}, num2str(round(100*glci(fglc(j)))), '% ');
end
if fglc(j)-1 == 0 % not labeled
glcsnames{1,i} = strcat(glcsnames{1,i}, 'C0');
elseif abs(log2(fglc(j)-1) - round(log2(fglc(j)-1)))<1e-8 % if it's a perfect power
glcsnames{1,i} = strcat(glcsnames{1,i}, 'C', num2str(6-round(log2(fglc(j)-1))) );
elseif fglc(j)-1 == 32+16 % C12
glcsnames{1,i} = strcat(glcsnames{1,i}, 'C12');
elseif fglc(j)-1 == 63 % fully labeled
glcsnames{1,i} = strcat(glcsnames{1,i}, 'CU');
else
glcsnames{1,i} = strcat(glcsnames{1,i}, '#', dec2bin(fglc(j)-1, 6));
end
end
end
experiment.glcsnames = glcsnames;
%% if hilo is defined in experiment
% then inform user and error out
if (not(isfield(experiment,'hilo')))
disp 'ERROR: hilo field not found in input structure experiment';
return;
else
hilo = experiment.hilo;
end
ntarget = size(hilo,1);
nglc = size(glcs,2);
%% we don't care about the thresholds field from this point on
if (not(isfield(experiment,'mdvs')))
experiment.mdvs = [];
end
mdvs = experiment.mdvs;
if (isempty(mdvs))
disp('no mdvs found, recalculating mdvs and emptying out zscores');
mdvs = struct;
for iglc = 1:nglc
fprintf('MDVS on glucose %d of %d\n',iglc, nglc);
glc = glcs(:,iglc);
% translate sugar from isotopomer to cuomer format
if abs(sum(glc)-1)>1e-6 || any(glc <0)
display('invalid glc. needs to be idv');
disp(iglc)
glc
pause;
end
mdv = calcMDVfromSamp(glc,experiment.points,metabolites);
name = sprintf('t%d',iglc);
mdvs.(name) = mdv;
end
experiment.mdvs = mdvs;
experiment.zscores = [];
end
%% regen the zscores
if (not(isfield(experiment,'zscores')))
experiment.zscores = [];
end
zscores = experiment.zscores;
if (isempty(zscores) && runzscore)
disp('calculating zscores');
for iglc = 1:nglc
fprintf('z-scores on glucose %d of %d\n',iglc, nglc);
for itgt = 1:ntarget
% target = char(targets(itgt));
hl = hilo(itgt,:);
name = sprintf('t%d',iglc);
mdv = mdvs.(name);
[hiset,loset] = splitMDVbyTarget(mdv,hl);
% if ((size(loset,1)) ~= (size(hiset,1)))
% zscores(itgt,iglc) = -1;
% disp('problem with the hi or lo set, cannot calculate zscore');
% continue;
% end
mdv1.names = mdv.names;
mdv1.ave = mean(loset,2);
mdv1.stdev = std(loset,0,2);
mdv2.ave = mean(hiset,2);
mdv2.stdev = std(hiset,0,2);
[totalz,zscore] = compareTwoMDVs(mdv1,mdv2);
zscores(itgt,iglc) = totalz;
end
end
experiment.zscores = zscores;
end
%% regen the ridge score
if (not(isfield(experiment,'rscores')))
experiment.rscores = [];
end
rscores = experiment.rscores;
if (isempty(rscores) && runrscore)
disp('calculating ridge scores');
for iglc = 1:nglc
fprintf('r-scores on glucose %d of %d\n',iglc, nglc);
for itgt = 1:ntarget
hl = hilo(itgt,:)';
name = sprintf('t%d',iglc);
mdv = mdvs.(name).mdv;
rscore = score_ridge(mdv,hl);
rscores(itgt,iglc) = rscore;
end
end
experiment.rscores = rscores;
end
%% regen the KS score
if (not(isfield(experiment,'kscores')))
experiment.kscores = [];
end
kscores = experiment.kscores;
if (isempty(kscores) && runkscore)
disp('calculating KS scores');
for iglc = 1:nglc
fprintf('KS-scores on glucose %d of %d\n',iglc, nglc);
for itgt = 1:ntarget
hl = hilo(itgt,:)';
name = sprintf('t%d',iglc);
mdv = mdvs.(name).mdv;
kscore = score_KS(mdv,hl);
kscores(itgt,iglc) = kscore;
end
end
experiment.kscores = kscores;
end
return;
end
%% findIndexToTarget
%
% function [targetind] = findIndexToTarget(model,target)
%
% % Given a model, find the index to the target in the model.rxns
%
% d = size(model.c);
% %find index to target flux
% found = false;
% for r = 1:d(1),
% if ~isempty(findstr(char(model.rxns(r)),target))
% found = true;
% break;
% end
% end
% if (~found)
% disp(sprintf('could not locate %s flux',target));
% targetind = -1;
% return;
% end
% targetind = r;
% disp(sprintf('found target flux for %s at: %d',target,targetind));
%
% return
% end
%% splitMDVbyTarget
%
function [hiset,loset] = splitMDVbyTarget(mdv,hilo)
% Given an mdv set and a hilo discriminator, split the
% mdvset into 2 sets: a lo and hi set each with numinset cols.
hiset = mdv.mdv(:,hilo==1);
loset = mdv.mdv(:,~hilo);
return;
% nmdv = size(mdv.mdv,2);
%
% hisetcount = 0;
% losetcount = 0;
% hiset = [];
% loset = [];
% mdva = mdv.mdv;
% mdvnan = mdv.mdvnan;
% cnan = size(mdvnan,2);
%
% % if ((2*numinset) > nmdv)
% % disp('WARN: insufficient number of points to cover split into hi and lo set');
% % end
%
%
%
% for i = 1:nmdv
% if (cnan >= i)
% % do nan check only if nan array is larger than i index
% if (sum(isnan(mdvnan(:,i))) > 1)
% continue;
% end
% end
% if (hilo(1,i) == 1)
% if (hisetcount <= numinset)
% hisetcount = hisetcount + 1;
% hiset(:,hisetcount) = mdva(:,i);
% end
% else
% if (losetcount <= numinset)
% losetcount = losetcount + 1;
% loset(:,losetcount) = mdva(:,i);
% end
% end
% if ((hisetcount >= numinset) && (losetcount >= numinset))
% break;
% end
% end
%
% % might have read thru the entire set but lots of nan for mdv's
% if ((hisetcount < numinset) || (losetcount < numinset))
% disp(sprintf('WARN: hisetcount = %d, losetcount = %d',hisetcount,losetcount));
% end
end
|
github
|
EPFL-LCSB/matTFA-master
|
compareTwoSamp.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/fluxomics/compareTwoSamp.m
| 3,031 |
utf_8
|
5a0c5086089c00108fbf0be445048674
|
function [totalz,zscore,mdv1,mdv2] = compareTwoSamp(xglc,model,samp1,samp2,measuredMetabolites)
% Compare the 2 sets of samples
% xglc is optional, a random sugar distribution is calculated if empty
% expects samp1 and samp2 to have a field named points containing
% an array of sampled points
% expects model.rxns to contain a list of rxn names
% measuredMetabolites is an optional parameter fed to calcMDVfromSamp.m
% which only calculates the MDVs for the metabolites listed in this
% array. e.g.
%
% totalz is the sum of all zscores
% zscore is the calculated difference for each mdv element distributed
% across all the points
% mdv1,mdv2 each containing fields:
% - mdv - the calculated mdv distribution converted from the idv
% solved from each point contained in their respective samples sampX
% - names - the names of the metabolites
% - ave - the average of each mdv element across all of the points
% - stdev - the standard dev for each mdv element across all points
% Wing Choi 2/11/08
%glc = zeros(62,1);
%glc = [.2 ;.8 ;glc];
if (nargin < 4)
disp '[totalz,zscore,mdv1,mdv2] = compareTwoSamp(xglc,model,samp1,samp2,measuredMetabolites)';
return;
end
if (nargin < 5)
measuredMetabolites = [];
end
if (isempty(xglc))
% random glucose
xglc = rand(64,1);
xglc = xglc/sum(xglc);
xglc = idv2cdv(6)*xglc;
end
% generate the translation index array
% can shave time by not regenerating this array on every call.
xltmdv = zeros(1,4096);
for i = 1:4096
xltmdv(i) = length(strrep(dec2base(i-1,2),'0',''));
end
% calculate mdv for samp1 and samp2
[mdv1] = calcMDVfromSamp(samp1.points,measuredMetabolites);
[mdv2] = calcMDVfromSamp(samp2.points,measuredMetabolites);
[totalz,zscore] = compareTwoMDVs(mdv1,mdv2);
return
end
%Here's what the function does.
%Apply slvrXXfast to each point
%for each field in the output, apply iso2mdv to get a much shorter vector.
%store all the mdv's for each point and for each metabolite in both sets.
%
%Compute the mean and standard deviation of each mdv and then get a z-score
% between them (=(mean1-mean2)/(sqrt(sd1^2+sd2^2))).
%Add up all the z-scores (their absolute value) and have this function return
% that value.
%
%Intuitively what we're doing here is comparing the two sets based on
% how different the mdv's appear.
%We're going to see if different glucose mixtures result in different values.
%I'm going to rewrite part of slvrXXfast so it doesn't return every metabolite
% but only those we can actually measure, but for now just make it generic.
function mdv = myidv2mdv (idv,xltmdv)
% generate the mdv
len = length(idv);
%disp(sprintf('idv is %d long',len));
mdv = zeros(1,xltmdv(len)+1);
%disp(sprintf('mdv is %d long',length(mdv)));
for i = 1:len
idx = xltmdv(i) + 1;
%disp(sprintf('idx is %d, currently on %d',idx,i));
mdv(idx) = mdv(idx) + idv(i);
end
return
end
|
github
|
EPFL-LCSB/matTFA-master
|
computeConfidenceInterval2.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/fluxomics/obsolete/computeConfidenceInterval2.m
| 9,292 |
utf_8
|
76f328a01a51b8ee184e498657e94f7e
|
function [vs, output, v0] = computeConfidenceInterval2(v0, expdata, model, max_score)
majorIterationLimit = 2000; %max number of iterations
minorIterationLimit = 1e7; % essentially infinity
diffInterval = 1e-5; %gradient step size.
feasibilityTolerance = max_score/20; % how close you need to be to the max score.
v0 = fitC13Data(v0,expdata,model);
if ~isfield(model, 'N')
model.N = null(model.S);
end
x0 = model.N\v0; % back substitute
% safety check:
if (max(abs(model.S*v0))> 1e-6)
display('v0 not quite in null space');
pause;
end
if(max(abs(model.N*x0 - v0)) > 1e-6)
display('null basis is weird');
pause;
end
nalpha = size(model.N, 2);
x_L = -1000*ones(nalpha,1);
x_U = 1000*ones(nalpha,1);
Name = 't2';
[A, b_L, b_U] = defineLinearConstraints(model);
numpoints = size(x0,2);
scores = zeros(numpoints,1);
% compute scores for all points.
tProb.user.expdata = expdata;
tProb.user.model = model;
for i = 1:numpoints
scores(i) = errorComputation2(x0(:,i),tProb);
end
valid_index = scores < max_score + feasibilityTolerance;
fprintf('found %d valid points\n', sum(valid_index));
x0_valid = x0(:,valid_index);
x0_invalid = x0;
scores_valid = scores(valid_index);
c = []; c_L = []; c_U = []; HessPattern = [];
f = 'errorComputation2';
g = 'errorComputation2_grad'; H = [];
%c = 'errorComputation2';
%c_L = 0;
%c_U = max_score;
dc = []; d2c = []; ConsPattern = [];
pSepFunc = [];
x_min = []; x_max = []; f_opt = []; x_opt = [];
Solver = 'snopt';
% pre-compute unnecesary directions.
% if checkedbefore(i) ~= 0 then direction i is redundant
% checkedbefore(i) < 0 means that the sign of all computations should be
% switched.
checkedbefore = zeros(length(model.lb),1);
for i = 2:length(model.lb)
d = objective_coefficient(i, model);
for j = 1:i-1
dj = objective_coefficient(j, model);
if max(abs(dj - d))< 1e-4
checkedbefore(i) = j;
break;
elseif max(abs(dj + d))< 1e-4
checkedbefore(i) = -j;
break;
end
end
end
% initialize variables;
numpoints = size(x0, 2);
outputminv = 222*ones(length(model.lb), numpoints);
outputminexitflag = -222*ones(length(model.lb), numpoints);
outputminfinalscore = -222*ones(length(model.lb), numpoints);
outputmaxv = -222*ones(length(model.lb), numpoints);
outputmaxexitflag = -222*ones(length(model.lb), numpoints);
outputmaxfinalscore = -222*ones(length(model.lb), numpoints);
outputminstruct = cell(length(model.lb), numpoints);
outputmaxstruct = cell(length(model.lb), numpoints);
%iterate through directions
parfor i = 1:length(model.lb)
if checkedbefore(i) ~= 0
continue;
end
for j = -1:2:1 % max and min
d = objective_coefficient(i,model)*j;
lbprob = lpAssign(d, A, b_L, b_U, x_L, x_U, [], 'linear_bound', [],[],[],[],[],[],[]);
lbresult = tomRun('cplex', lbprob, 0);
fLowBnd = lbresult.f_k;
fprintf('reaction %d of %d, direction %d, lowerbound %f\n', i,length(model.lb), j, fLowBnd);
% short circuit if x0 already close to a bound.
obj1 = d'*x0_valid;
if(any(abs(obj1-fLowBnd)<.0001))
display('short circuiting');
[nil, index1] = min(obj1);
if (j > 0)
outputminv(i,:) = j*fLowBnd; % multiply by j to correct sign.
outputminexitflag(i,:) = 111;
outputminfinalscore(i,:) = scores_valid(index1);
else
outputmaxv(i,:) = j*fLowBnd; % multiply by j to correct sign.
outputmaxexitflag(i,:) = 111;
outputmaxfinalscore(i,:) = scores_valid(index1);
end
else % gotta actually do the computation.
all_ds = d'*x0_invalid;
[nil, index2] = sort(all_ds);
% initialize temp variables to make parfor work.
v = j*222*ones(1,numpoints);
exitflag = -222*ones(1,numpoints);
finalscore = 222*ones(1,numpoints);
ostruct = cell(1,numpoints);
for k = 1:length(index2)
if exist('ttt.txt', 'file')
fprintf('quitting due to file found\n');
continue;
end
xinitial = x0_invalid(:,index2(k));
% Prob = lpconAssign(d, x_L, x_U, Name, xinitial,...
% A, b_L, b_U,...
% c, dc, d2c, ConsPattern, c_L, c_U,...
% fLowBnd, x_min, x_max, f_opt, x_opt);
Prob = conAssign(f, g, H, HessPattern, x_L, x_U, Name, xinitial, ...
pSepFunc, fLowBnd, ...
A, b_L, b_U, c, dc, d2c, ConsPattern, c_L, c_U, ...
x_min, x_max, f_opt, x_opt);
%Prob.NumDiff = 2; % central diff
%Prob.optParam.CentralDiff = 1e-5;
%pause;
Prob.user.expdata = expdata;
Prob.user.model = model;
Prob.user.objective = d;
Prob.user.max_error = max_score;
Prob.user.diff_interval = diffInterval;
Prob.user.multiplier = 10;
Prob.optParam.IterPrint = 0;
%Prob.optParam.cTol = .1*feasibilityTolerance;
Prob.PriLevOpt = 0;
Prob.SOL.PrintFile = strcat('temp/snoptp', num2str(i), 'x', num2str(j), 'x', num2str(k),'.txt');
Prob.SOL.SummFile = strcat('temp/snopts', num2str(i), 'x', num2str(j), 'x', num2str(k),'.txt');
Prob.SOL.optPar(35) = majorIterationLimit; %This is major iteration count.
Prob.SOL.optPar(30) = minorIterationLimit; %total iteration limit;
%Prob.SOL.optPar(11) = feasibilityTolerance; % feasibility tolerance
Result = tomRun(Solver, Prob, 5);
tscore = errorComputation2(Result.x_k, tProb);
tbest = Result.f_k;
fprintf('reaction %d (%d), x %d; x=%f (%f); score=%f (%f)\n', i,length(model.lb),j, tbest,fLowBnd, tscore, max_score)
v(k) = j*tbest;
exitflag(k) = Result.Inform;
finalscore(k) = tscore;
ostruct{k} = Result;
end
if (j > 0) %minimizing
outputminv(i,:) = v; % multiply by j to correct sign.
outputminexitflag(i,:) = exitflag;
outputminfinalscore(i,:) = finalscore;
outputminstruct(i,:) = ostruct;
else
outputmaxv(i,:) = v; % multiply by j to correct sign.
outputmaxexitflag(i,:) = exitflag;
outputmaxfinalscore(i,:) = finalscore;
outputmaxstruct(i,:) = ostruct;
end
end
end
end
output.minv = outputminv;
output.maxv = outputmaxv;
output.minexitflag = outputminexitflag;
output.maxexitflag = outputmaxexitflag;
output.minfinalscore = outputminfinalscore;
output.maxfinalscore = outputmaxfinalscore;
output.minstruct = outputminstruct;
output.maxstruct = outputmaxstruct;
for i = 1:length(model.lb)
if checkedbefore(i) > 0 %short circuit if seen before.
output.minv(i,:) = output.minv(checkedbefore(i),:);
output.maxv(i,:) = output.maxv(checkedbefore(i),:);
output.minexitflag(i,:) = output.minexitflag(checkedbefore(i),:);
output.maxexitflag(i,:) = output.maxexitflag(checkedbefore(i),:);
output.minfinalscore(i,:) = output.minfinalscore(checkedbefore(i),:);
output.maxfinalscore(i,:) = output.maxfinalscore(checkedbefore(i),:);
output.minstruct(i,:) = output.minstruct(checkedbefore(i),:);
output.maxstruct(i,:) = output.maxstruct(checkedbefore(i),:);
elseif checkedbefore(i) < 0
output.minv(i,:) = -output.maxv(-checkedbefore(i),:);
output.maxv(i,:) = -output.minv(-checkedbefore(i),:);
output.minexitflag(i,:) = output.maxexitflag(-checkedbefore(i),:);
output.maxexitflag(i,:) = output.minexitflag(-checkedbefore(i),:);
output.minfinalscore(i,:) = output.maxfinalscore(-checkedbefore(i),:);
output.maxfinalscore(i,:) = output.minfinalscore(-checkedbefore(i),:);
output.minstruct(i,:) = output.maxstruct(-checkedbefore(i),:);
output.maxstruct(i,:) = output.minstruct(-checkedbefore(i),:);
end
end
vs = zeros(length(model.lb), 2);
for i = 1:length(model.lb)
validindex = output.minfinalscore(i,:) < max_score + feasibilityTolerance;
if any(validindex)
vs(i,1) = min(output.minv(i,validindex));
else
vs(i,1) = 222;
end
validindex = output.maxfinalscore(i,:) < max_score + feasibilityTolerance;
if any(validindex)
vs(i,2) = max(output.maxv(i,validindex));
else
vs(i,2) = -222;
end
end
return;
% function that returns the proper objective coefficient for each reaction
% takes into account the reversibility of reactinos etc.
function [d] = objective_coefficient(i, model)
d = zeros(length(model.lb),1);
d(i) = 1;
if (model.match(i))
d(model.match(i)) = -1;
end
d = (d'*model.N)'; % transform to null space;
return
|
github
|
EPFL-LCSB/matTFA-master
|
computeRatioConfidenceInterval.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/fluxomics/obsolete/computeRatioConfidenceInterval.m
| 6,966 |
utf_8
|
910c32ca417673f241f14c0350b9c7a3
|
function [vs, output, v0] = computeRatioConfidenceInterval(v0, expdata, model, max_score, ratio)
% v0 - set of flux vectors to be used as initial guesses. They may be
% valid or not.
% expdata - experimental data.
% model - The standard model. Additional field .N (= null(S)) should also
% be provided. This is a basis of the flux space.
% max score - maximum allowable data fit error.
% ratio - which reactions to take the ratio of. positive values indicate
% reactions in the numerator and negative values, reactions in the
% denominator.
majorIterationLimit = 2000; %max number of iterations
minorIterationLimit = 1e7; % essentially infinity
diffInterval = 1e-5; %gradient step size.
feasibilityTolerance = max_score/20; % how close you need to be to the max score.
x0 = model.N\v0; % back substitute
numpoints = size(v0,2);
numratios = size(ratio,2);
scores = zeros(numpoints,1);
tProb.user.expdata = expdata;
tProb.user.model = model;
for i = 1:numpoints
scores(i) = errorComputation2(x0(:,i),tProb);
end
v0(:,scores > max_score) = fitC13Data(v0(:,scores > max_score),expdata,model);
if ~isfield(model, 'N')
model.N = null(model.S);
end
x0 = model.N\v0; % back substitute
% safety check:
if (max(abs(model.S*v0))> 1e-6)
display('v0 not quite in null space');
pause;
end
if(max(abs(model.N*x0 - v0)) > 1e-6)
display('null basis is weird');
pause;
end
nalpha = size(model.N, 2);
x_L = -1000*ones(nalpha,1);
x_U = 1000*ones(nalpha,1);
Name = 't2';
[A, b_L, b_U] = defineLinearConstraints(model);
scores = zeros(numpoints,1);
% compute scores for all points.
for i = 1:numpoints
scores(i) = errorComputation2(x0(:,i),tProb);
end
valid_index = scores < max_score + feasibilityTolerance;
fprintf('found %d valid points\n', sum(valid_index));
c = 'errorComputation2';
c_L = 0; c_U = max_score;
dc = 'errorComputation2_grad';
d2c = []; ConsPattern = [];
%pSepFunc = [];
x_min = []; x_max = []; f_opt = []; x_opt = [];
H = []; HessPattern = []; pSepFunc = []; fLowBnd = [];
Solver = 'snopt';
outputminv = 222*ones(numratios, numpoints);
outputminexitflag = -222*ones(numratios, numpoints);
outputminfinalscore = -222*ones(numratios, numpoints);
outputmaxv = -222*ones(numratios, numpoints);
outputmaxexitflag = -222*ones(numratios, numpoints);
outputmaxfinalscore = -222*ones(numratios, numpoints);
outputminstruct = cell(numratios, numpoints);
outputmaxstruct = cell(numratios, numpoints);
%iterate through directions
for i = 1:numratios
%for i = 10:200
for j = -1:2:1 % max and min
ration = zeros(size(objective_coefficient(1,model)));
ratiod = zeros(size(objective_coefficient(1,model)));
for m = 1:size(ratio,1);
if(ratio(m,i) > 0)
ration = ration + objective_coefficient(m,model)*j;
elseif(ratio(m,i) < 0)
ratiod = ratiod + objective_coefficient(m,model);
end
end
% initialize temp variables to make parfor work.
v = j*222*ones(1,numpoints);
exitflag = -222*ones(1,numpoints);
finalscore = 222*ones(1,numpoints);
ostruct = cell(1,numpoints);
for k = 1:numpoints
if exist('ttt.txt', 'file')
fprintf('quitting due to file found\n');
continue;
end
xinitial = x0(:,k);
% Prob = lpconAssign(d, x_L, x_U, Name, xinitial,...
% A, b_L, b_U,...
% c, dc, d2c, ConsPattern, c_L, c_U,...
% fLowBnd, x_min, x_max, f_opt,
% x_opt);
Prob = conAssign('ratioScore', 'ratioScore_grad', H, HessPattern, x_L, x_U, Name, xinitial, ...
pSepFunc, fLowBnd, ...
A, b_L, b_U, c, dc, d2c, ConsPattern, c_L, c_U, ...
x_min, x_max, f_opt, x_opt);
%Prob.NumDiff = 2; % central diff
%Prob.optParam.CentralDiff = 1e-5;
%pause;
Prob.user.expdata = expdata;
Prob.user.model = model;
Prob.user.ration = ration;
Prob.user.ratiod = ratiod;
Prob.user.max_error = max_score;
Prob.user.diff_interval = diffInterval;
Prob.user.useparfor = true;
Prob.optParam.IterPrint = 0;
%Prob.optParam.cTol = .1*feasibilityTolerance;
Prob.PriLevOpt = 1;
Prob.SOL.PrintFile = strcat('temp/snoptp', num2str(i), 'x', num2str(j), 'x', num2str(k),'.txt');
Prob.SOL.SummFile = strcat('temp/snopts', num2str(i), 'x', num2str(j), 'x', num2str(k),'.txt');
Prob.SOL.optPar(35) = majorIterationLimit; %This is major iteration count.
Prob.SOL.optPar(30) = minorIterationLimit; %total iteration limit;
%Prob.SOL.optPar(11) = feasibilityTolerance; % feasibility tolerance
Result = tomRun(Solver, Prob, 5);
tscore = errorComputation2(Result.x_k, tProb);
tbest = Result.f_k;
fprintf('reaction %d (%d), x %d; x=%f (%f); score=%f (%f)\n', i,length(model.lb),j, tbest,fLowBnd, tscore, max_score)
v(k) = j*tbest;
exitflag(k) = Result.Inform;
finalscore(k) = tscore;
ostruct{k} = Result;
end
if (j > 0) %minimizing
outputminv(i,:) = v; % multiply by j to correct sign.
outputminexitflag(i,:) = exitflag;
outputminfinalscore(i,:) = finalscore;
outputminstruct(i,:) = ostruct;
else
outputmaxv(i,:) = v; % multiply by j to correct sign.
outputmaxexitflag(i,:) = exitflag;
outputmaxfinalscore(i,:) = finalscore;
outputmaxstruct(i,:) = ostruct;
end
end
end
output.minv = outputminv;
output.maxv = outputmaxv;
output.minexitflag = outputminexitflag;
output.maxexitflag = outputmaxexitflag;
output.minfinalscore = outputminfinalscore;
output.maxfinalscore = outputmaxfinalscore;
output.minstruct = outputminstruct;
output.maxstruct = outputmaxstruct;
vs = zeros(numratios, 2);
for i = 1:numratios
validindex = output.minfinalscore(i,:) < max_score + feasibilityTolerance;
if any(validindex)
vs(i,1) = min(output.minv(i,validindex));
else
vs(i,1) = 222;
end
validindex = output.maxfinalscore(i,:) < max_score + feasibilityTolerance;
if any(validindex)
vs(i,2) = max(output.maxv(i,validindex));
else
vs(i,2) = -222;
end
end
return;
% function that returns the proper objective coefficient for each reaction
% takes into account the reversibility of reactinos etc.
function [d] = objective_coefficient(i, model)
d = zeros(length(model.lb),1);
d(i) = 1;
if (model.match(i))
d(model.match(i)) = -1;
end
d = (d'*model.N)'; % transform to null space;
return
|
github
|
EPFL-LCSB/matTFA-master
|
Combination.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/fluxomics/c13solver/Combination.m
| 1,354 |
utf_8
|
e737cd2414f521a8b1701de9c05cff10
|
function [out] = Combination(n,k)
% produces the array of combinations possible picking k from n
% adapted from Combinadics
% http://msdn.microsoft.com/en-us/library/aa289166(VS.71).aspx
if (n < 0 || k < 0) % normally n >= k
disp('Negative parameter in constructor');
return
end
data(k) = 0;
for i = 1:k;
data(i) = i;
end
% Combination(n,k)
out.choose = getNumberCombinations(n,k);
% determine the combinations
for i = 1:out.choose
out.all(:,i) = getCombination(n,k,i-1);
end
return;
function [m] = getNumberCombinations(n,k)
% find number of combinations by choose k items from n
if (n < k)
m = 0; % special case
else
if (n == k)
m = 1;
else
m = factorial(n) / (factorial(k) * factorial(n-k));
end
end
return;
function [c] = getCombination(n,k,index)
c(1) = 1;
x = 1;
for i = 1:n
if (k == 0)
return;
end
threshold = getNumberCombinations(n-i,k-1);
%disp(sprintf('index = %d, threshold = %d',index,threshold));
if (index < threshold)
c(x) = i;
x = x+1;
k = k-1;
else
if (index >= threshold)
index = index - threshold;
end
end
end
return;
|
github
|
EPFL-LCSB/matTFA-master
|
idv2mdv.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/fluxomics/c13solver/idv2mdv.m
| 1,629 |
utf_8
|
4602db4ffd72989e332f08b0d92cf05f
|
function [out] = idv2mdv(n, fragment)
% returns transofmation matrix from idv's (either Jennie's or Jan's order).
% MDV = idv2mdv(log2(length(idv)))*idv;
%
% fragment (optional): a vector of carbons to be included. [ 0, 0, 1,1,1]' = last 3 carbons.
global pseudohash1 pseudohash2
if isempty(pseudohash1)
pseudohash1 = sparse(15, 2048);
pseudohash2 = {};
end
if nargin == 1
out = sparse(1);
for i = 1:n
out = [[out;sparse(1, size(out,2))] [sparse(1, size(out,2));out]];
end
return;
end
if length(fragment) ~= n
display('error in fragment length');
return;
end
ncarbons = sum(fragment)+1;
out = sparse(ncarbons, 2^n);
fragment = fragment(n:-1:1); % reverse order fragment... faster than reversing order of idv's.
m = memoize(n, fragment);
if ~isempty(m)
out = m;
return;
end
for i = 0:(2^n-1)
t = dec2bin(i,n);
t(logical(fragment));
i2 = sum(t(logical(fragment)) == '1');
out(i2+1,i+1) = 1;
end
memoize(n, fragment, out);
return
function [matrix] = memoize(n, fragment, matrix)
global pseudohash1 pseudohash2
fragmentindex = 0;
for i = 1:length(fragment)
fragmentindex = fragmentindex*2;
fragmentindex = fragment(i) + fragmentindex;
end
tindex = pseudohash1(n, fragmentindex);
if tindex == 0
if nargin < 3
matrix = [];
return;
else % assign
tindex = length(pseudohash2)+1;
pseudohash1(n, fragmentindex) = tindex;
pseudohash2{tindex} = matrix;
end
else
matrix = pseudohash2{tindex};
return;
end
return
|
github
|
EPFL-LCSB/matTFA-master
|
createTissueSpecificModel.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/reconstruction/createTissueSpecificModel.m
| 22,833 |
utf_8
|
b1e36173def8a0675727e3d42c0bb7e9
|
function [tissueModel,Rxns] = createTissueSpecificModel(model, ...
expressionData,proceedExp,orphan,exRxnRemove,solver,options,funcModel)
%createTissueSpecificModel Create draft tissue specific model from mRNA expression data
%
% [tissueModel,Rxns] =
% createTissueSpecificModel(model,expressionData,proceedExp,orphan,exRxnRemove,solver,options,funcModel)
%
%INPUTS
% model global recon1 model
% expressionData mRNA expression Data structure
% Locus Vector containing GeneIDs
% Data Presence/Absence Calls
% Use: (1 - Present, 0 - Absent) when proceedExp = 1
% Use: (2 - Present, 1 - Marginal, 0 - Absent)
% when proceedExp = 0
% Transcript RefSeq Accession (only required if proceedExp = 0)
%
%OPTINAL INPUTS
% proceedExp 1 - data are processed ; 0 - data need to be
% processed (Default = 1)
% orphan 1 - leave orphan reactions in model for Shlomi Method
% 0 - remove orphan reactions
% (Default = 1)
% exRxnRemove Names of exchange reactions to remove
% (Default = [])
% solver Use either 'GIMME', 'iMAT', or 'Shlomi' to create tissue
% specific model. 'Shlomi' is the same as 'iMAT' the names
% are just maintained for historical purposes.
% (Default = 'GIMME')
% options If using GIMME, enter objectiveCol here
% Default: objective function with 90% flux cutoff,
% written as: [find(model.c) 0.9]
% funcModel 1 - Build a functional model having only reactions
% that can carry a flux (using FVA), 0 - skip this
% step (Default = 0)
%
%
%OUTPUTS
% tissueModel Model produced by GIMME or iMAT, containing only
% reactions carrying flux
% Rxns Statistics of test
% ExpressedRxns - predicted by mRNA data
% UnExpressedRxns - predicted by mRNA data
% unknown - unable to be predicted by mRNA
% data
% Upregulated - added back into model
% Downregulated - removed from model
% UnknownIncluded - orphans added
%
% NOTE: If there are multiple transcripts to one probe that have different
% expression patterns the script will ask what the locus is of the
% expressed and unexpressed transcripts
%
% Note: GIMME script matches objective functions flux, Shlomi algorithm is
% based on maintaining pathway length comparable to expression data, not flux
%
% Aarash Bordbar 05/15/2009
% Added proceedExp, IT 10/30/09
% Adjusted manual input for alt. splice form, IT 05/27/10
% Final Corba 2.0 Version, AB 08/05/10
% Define defaults
% Deal with hardcoded belief that all the genes will have human entrez
% ids and the user wants to collapse alternative constructs
if iscell(expressionData.Locus(1))
match_strings = true;
else
match_strings = false;
end
if ~exist('proceedExp','var') || isempty(proceedExp)
proceedExp = 1;
end
if ~exist('solver','var') || isempty(solver)
solver = 'GIMME';
end
if ~exist('exRxnRemove','var') || isempty(exRxnRemove)
exRxnRemove = [];
end
if ~exist('orphan','var') || isempty(orphan)
orphan = 1;
end
if ~exist('funcModel','var') || isempty(funcModel)
funcModel = 0;
end
% Extracting GPR data from model
[parsedGPR,corrRxn] = extractGPRs(model);
if proceedExp == 0
% Making presence/absence calls on mRNA expression data
[Results,Transcripts] = charExpData(expressionData);
x = ismember(Transcripts.Locus,[Transcripts.Expressed;Transcripts.UnExpressed]);
unkLocus = find(x==0);
AltSplice.Locus = Transcripts.Locus(unkLocus);
AltSplice.Transcripts = Transcripts.Data(unkLocus);
AltSplice.Expression = Transcripts.Expression(unkLocus);
fprintf('There are some probes that match up with different transcripts and expression patterns\n');
fprintf('Please elucidate these discrepancies below\n');
fprintf('To do so, look up the transcript in RefSeq and enter the proper locii below\n');
cnt1 = 1;
cnt2 = 1;
locusNE =[];
locusE = [];
for i = 1:length(AltSplice.Locus)
if length(AltSplice.Transcripts{i}) < 1
elseif AltSplice.Expression(i) == 0
fprintf('Probe: %i, Transcript: %s, Expression: %i\n',AltSplice.Locus(i),AltSplice.Transcripts{i},AltSplice.Expression(i));
% locusNE(cnt1,1) = input('What is the proper locii? ');
locusNE(cnt1,1) = AltSplice.Locus(i);%input('What is the proper locii? ');
cnt1=cnt1+1;
elseif AltSplice.Expression(i) == 1
fprintf('Probe: %i, Transcript: %s, Expression: %i\n',AltSplice.Locus(i),AltSplice.Transcripts{i},AltSplice.Expression(i));
% locusE(cnt2,1) = input('What is the proper locii? ');
locusE(cnt2,1) = AltSplice.Locus(i);% Hack by Maike %input('What is the proper locii? ');
cnt2=cnt2+1;
end
end
locusP = [Results.Expressed;Transcripts.Expressed;locusE];
locusNP = [Results.UnExpressed;Transcripts.UnExpressed;locusNE];
genePresenceP = ones(length(locusP),1);
genePresenceNP = zeros(length(locusNP),1);
locus = [locusP;locusNP];
genePresence = [genePresenceP;genePresenceNP];
else
locus = expressionData.Locus;
genePresence = zeros(length(locus),1);
genePresence(find(expressionData.Data(:,1))) = 1;
end
% Mapping probes to reactions in model
[ExpressedRxns,UnExpressedRxns,unknown] = mapProbes(parsedGPR,corrRxn,locus,genePresence,match_strings);
% Removing exchange reactions that are not in this specific tissue
% metabolome
if ~isempty(exRxnRemove)
model = removeRxns(model,exRxnRemove);
end
nRxns = length(model.lb);
% Determine reaction indices of expressed and unexpressed reactions
RHindex = findRxnIDs(model,ExpressedRxns);
RLindex = findRxnIDs(model,UnExpressedRxns);
if (strcmp(solver, 'iMAT'))
solver = 'Shlomi';
end
switch solver
case 'Shlomi'
S = model.S;
lb = model.lb;
ub = model.ub;
eps = 1;
% Creating A matrix
A = sparse(size(S,1)+2*length(RHindex)+2*length(RLindex),size(S,2)+2*length(RHindex)+length(RLindex));
[nConstr,nVar] = size(S);
[m,n,s] = find(S);
for i = 1:length(m)
A(m(i),n(i)) = s(i);
end
for i = 1:length(RHindex)
A(i+size(S,1),RHindex(i)) = 1;
A(i+size(S,1),i+size(S,2)) = lb(RHindex(i)) - eps;
A(i+size(S,1)+length(RHindex),RHindex(i)) = 1;
A(i+size(S,1)+length(RHindex),i+size(S,2)+length(RHindex)+length(RLindex)) = ub(RHindex(i)) + eps;
end
for i = 1:length(RLindex)
A(i+size(S,1)+2*length(RHindex),RLindex(i)) = 1;
A(i+size(S,1)+2*length(RHindex),i+size(S,2)+length(RHindex)) = lb(RLindex(i));
A(i+size(S,1)+2*length(RHindex)+length(RLindex),RLindex(i)) = 1;
A(i+size(S,1)+2*length(RHindex)+length(RLindex),i+size(S,2)+length(RHindex)) = ub(RLindex(i));
end
% Creating csense
csense1(1:size(S,1)) = 'E';
csense2(1:length(RHindex)) = 'G';
csense3(1:length(RHindex)) = 'L';
csense4(1:length(RLindex)) = 'G';
csense5(1:length(RLindex)) = 'L';
csense = [csense1 csense2 csense3 csense4 csense5];
% Creating lb and ub
lb_y = zeros(2*length(RHindex)+length(RLindex),1);
ub_y = ones(2*length(RHindex)+length(RLindex),1);
lb = [lb;lb_y];
ub = [ub;ub_y];
% Creating c
c_v = zeros(size(S,2),1);
c_y = ones(2*length(RHindex)+length(RLindex),1);
c = [c_v;c_y];
% Creating b
b_s = zeros(size(S,1),1);
lb_rh = lb(RHindex);
ub_rh = ub(RHindex);
lb_rl = lb(RLindex);
ub_rl = ub(RLindex);
b = [b_s;lb_rh;ub_rh;lb_rl;ub_rl];
% Creating vartype
vartype1(1:size(S,2),1) = 'C';
vartype2(1:2*length(RHindex)+length(RLindex),1) = 'B';
vartype = [vartype1;vartype2];
n_int = length(vartype2);
MILPproblem.A = A;
MILPproblem.b = b;
MILPproblem.c = c;
MILPproblem.lb = lb;
MILPproblem.ub = ub;
MILPproblem.csense = csense;
MILPproblem.vartype = vartype;
MILPproblem.osense = -1;
MILPproblem.x0 = [];
verboseFlag = true;
solution = solveCobraMILP(MILPproblem);
Rxns.solution = solution;
x = solution.cont;
for i = 1:length(x)
if abs(x(i)) < 1e-6
x(i,1) = 0;
end
end
removed = find(x==0);
% option to leave orphan reactions
if orphan == 1
orphans = findorphanRxns(model);
removed(find(ismember(model.rxns(removed),orphans)))=[];
end
rxnRemList = model.rxns(removed);
tissueModel = removeRxns(model,rxnRemList);
Rxns.Expressed = ExpressedRxns;
Rxns.UnExpressed = UnExpressedRxns;
Rxns.unknown = unknown;
x = ismember(UnExpressedRxns,tissueModel.rxns);
loc = find(x);
Rxns.UpRegulated = UnExpressedRxns(loc);
x = ismember(ExpressedRxns,tissueModel.rxns);
loc = find(x==0);
Rxns.DownRegulated = ExpressedRxns(loc);
x = ismember(model.rxns,[ExpressedRxns;UnExpressedRxns]);
loc = find(x==0);
x = ismember(tissueModel.rxns,model.rxns(loc));
loc = find(x);
Rxns.UnknownIncluded = tissueModel.rxns(loc);
case 'GIMME'
x = ismember(model.rxns,[ExpressedRxns;UnExpressedRxns]);
unk = find(x==0);
expressionCol = zeros(length(model.rxns),1);
for i = 1:length(unk)
expressionCol(unk(i)) = -1;
end
for i = 1:length(RHindex)
expressionCol(RHindex(i)) = 2;
end
if ~exist('options','var') || isempty(options)
loc = find(model.c);
sol = optimizeCbModel(model);
options = [loc 0.9];
end
cutoff = 1;
[reactionActivity,reactionActivityIrrev,model2gimme,gimmeSolution] = solveGimme(model,options,expressionCol,cutoff);
remove = model.rxns(find(reactionActivity == 0));
tissueModel = removeRxns(model,remove);
if funcModel ==1
c = tissueModel.c;
remove = [];
tissueModel.c = zeros(length(tissueModel.c),1);
for i = 1:length(tissueModel.rxns)
tissueModel.c(i) = 1;
sol1 = optimizeCbModel(tissueModel,'max');
sol2 = optimizeCbModel(tissueModel,'min');
if sol1.f == 0 & sol2.f == 0
remove = [remove tissueModel.rxns(i)];
end
tissueModel.c(i) = 0;
end
tissueModel.c = c;
tissueModel = removeRxns(tissueModel,remove);
end
Rxns.Expressed = ExpressedRxns;
Rxns.UnExpressed = UnExpressedRxns;
Rxns.unknown = unknown;
x = ismember(UnExpressedRxns,tissueModel.rxns);
loc = find(x);
Rxns.UpRegulated = UnExpressedRxns(loc);
x = ismember(ExpressedRxns,tissueModel.rxns);
loc = find(x==0);
Rxns.DownRegulated = ExpressedRxns(loc);
x = ismember(model.rxns,[ExpressedRxns;UnExpressedRxns]);
loc = find(x==0);
x = ismember(tissueModel.rxns,model.rxns(loc));
loc = find(x);
Rxns.UnknownIncluded = tissueModel.rxns(loc);
end
%% Internal Functions
function [reactionActivity,reactionActivityIrrev,model2gimme,gimmeSolution] = solveGimme(model,objectiveCol,expressionCol,cutoff)
nRxns = size(model.S,2);
%first make model irreversible
[modelIrrev,matchRev,rev2irrev,irrev2rev] = convertToIrreversible(model);
nExpressionCol = size(expressionCol,1);
if (nExpressionCol < nRxns)
display('Warning: Fewer expression data inputs than reactions');
expressionCol(nExpressionCol+1:nRxns,:) = zeros(nRxns-nExpressionCol, size(expressionCol,2));
end
nIrrevRxns = size(irrev2rev,1);
expressionColIrrev = zeros(nIrrevRxns,1);
for i=1:nIrrevRxns
% objectiveColIrrev(i,:) = objectiveCol(irrev2rev(i,1),:);
expressionColIrrev(i,1) = expressionCol(irrev2rev(i,1),1);
end
nObjectives = size(objectiveCol,1);
for i=1:nObjectives
objectiveColIrrev(i,:) = [rev2irrev{objectiveCol(i,1),1}(1,1) objectiveCol(i,2)];
end
%Solve initially to get max for each objective
for i=1:size(objectiveCol)
%define parameters for initial solution
modelIrrev.c=zeros(nIrrevRxns,1);
modelIrrev.c(objectiveColIrrev(i,1),1)=1;
%find max objective
FBAsolution = optimizeCbModel(modelIrrev);
if (FBAsolution.stat ~= 1)
not_solved=1;
display('Failed to solve initial FBA problem');
return
end
maxObjective(i)=FBAsolution.f;
end
model2gimme = modelIrrev;
model2gimme.c = zeros(nIrrevRxns,1);
for i=1:nIrrevRxns
if (expressionColIrrev(i,1) > -1) %if not absent reaction
if (expressionColIrrev(i,1) < cutoff)
model2gimme.c(i,1) = cutoff-expressionColIrrev(i,1);
end
end
end
for i=1:size(objectiveColIrrev,1)
model2gimme.lb(objectiveColIrrev(i,1),1) = objectiveColIrrev(i,2) * maxObjective(i);
end
gimmeSolution = optimizeCbModel(model2gimme,'min');
if (gimmeSolution.stat ~= 1)
%% gimme_not_solved=1;
% display('Failed to solve GIMME problem');
% return
gimmeSolution.x = zeros(nIrrevRxns,1);
end
reactionActivityIrrev = zeros(nIrrevRxns,1);
for i=1:nIrrevRxns
if ((expressionColIrrev(i,1) > cutoff) | (expressionColIrrev(i,1) == -1))
reactionActivityIrrev(i,1)=1;
elseif (gimmeSolution.x(i,1) > 0)
reactionActivityIrrev(i,1)=2;
end
end
%Translate reactionActivity to reversible model
reactionActivity = zeros(nRxns,1);
for i=1:nRxns
for j=1:size(rev2irrev{i,1},2)
if (reactionActivityIrrev(rev2irrev{i,1}(1,j)) > reactionActivity(i,1))
reactionActivity(i,1) = reactionActivityIrrev(rev2irrev{i,1}(1,j));
end
end
end
function [rxnExpressed,unExpressed,unknown] = mapProbes(parsedGPR,corrRxn,locus,genePresence,match_strings)
if ~exist('match_strings', 'var') || isempty(match_strings)
match_strings = false;
end
rxnExpressed = [];
unExpressed = [];
unknown = [];
for i = 1:size(parsedGPR,1)
cnt = 0;
for j = 1:size(parsedGPR,2)
if length(parsedGPR{i,j}) == 0
break
end
cnt = cnt+1;
end
test = 0;
for j = 1:cnt
if match_strings
loc = parsedGPR{i,j};
x = strmatch(loc, locus, 'exact');
else
loc = str2num(parsedGPR{i,j});
loc = floor(loc);
x = find(locus == loc);
end
if length(x) > 0 & genePresence(x) == 0
unExpressed = [unExpressed;corrRxn(i)];
test = 1;
break
elseif length(x) == 0
test = 2;
end
end
if test == 0
rxnExpressed = [rxnExpressed;corrRxn(i)];
elseif test == 2
unknown = [unknown;corrRxn(i)];
end
end
rxnExpressed = unique(rxnExpressed);
unExpressed = unique(unExpressed);
unknown = unique(unknown);
unknown = setdiff(unknown,rxnExpressed);
unknown = setdiff(unknown,unExpressed);
unExpressed = setdiff(unExpressed,rxnExpressed);
function [parsedGPR,corrRxn] = extractGPRs(model)
warning off all
parsedGPR = [];
corrRxn = [];
cnt = 1;
for i = 1:length(model.rxns)
if length(model.grRules{i}) > 1
% Parsing each reactions gpr
[parsing{1,1},parsing{2,1}] = strtok(model.grRules{i},'or');
for j = 2:1000
[parsing{j,1},parsing{j+1,1}] = strtok(parsing{j,1},'or');
if isempty(parsing{j+1,1})==1
break
end
end
for j = 1:length(parsing)
for k = 1:1000
[parsing{j,k},parsing{j,k+1}] = strtok(parsing{j,k},'and');
if isempty(parsing{j,k+1})==1
break
end
end
end
for j = 1:size(parsing,1)
for k = 1:size(parsing,2)
parsing{j,k} = strrep(parsing{j,k},'(','');
parsing{j,k} = strrep(parsing{j,k},')','');
parsing{j,k} = strrep(parsing{j,k},' ','');
end
end
for j = 1:size(parsing,1)-1
newparsing(j,:) = parsing(j,1:length(parsing(j,:))-1);
end
parsing = newparsing;
for j = 1:size(parsing,1)
for k = 1:size(parsing,2)
if length(parsing{j,k}) == 0
parsing{j,k} = '';
end
end
end
num = size(parsing,1);
for j = 1:num
sizeP = length(parsing(j,:));
if sizeP > size(parsedGPR,2)
for k = 1:size(parsedGPR,1)
parsedGPR{k,sizeP} = {''};
end
end
for l = 1:sizeP
parsedGPR{cnt,l} = parsing(j,l);
end
cnt = cnt+1;
end
for j = 1:num
corrRxn = [corrRxn;model.rxns(i)];
end
clear parsing newparsing
end
end
for i = 1:size(parsedGPR,1)
for j = 1:size(parsedGPR,2)
if isempty(parsedGPR{i,j}) == 1
parsedGPR{i,j} = {''};
end
end
end
i =1 ;
sizeP = size(parsedGPR,1);
while i < sizeP
if strcmp(parsedGPR{i,1},{''}) == 1
parsedGPR = [parsedGPR(1:i-1,:);parsedGPR(i+1:end,:)];
corrRxn = [corrRxn(1:i-1,:);corrRxn(i+1:end,:)];
sizeP = sizeP-1;
i=i-1;
end
i = i+1;
end
for i = 1:size(parsedGPR,1)
for j= 1:size(parsedGPR,2)
parsedGPR2(i,j) = cellstr(parsedGPR{i,j});
end
end
parsedGPR = parsedGPR2;
function [Results,Transcripts] = charExpData(ExpressionData)
n = length(ExpressionData.Locus);
Locus = ExpressionData.Locus;
ExpThreshold = floor(0.75*size(ExpressionData.Data,2))/size(ExpressionData.Data,2);
UnExpThreshold = ceil(0.25*size(ExpressionData.Data,2))/size(ExpressionData.Data,2);
Results.Expressed = [];
Results.UnExpressed = [];
Results.AltSplice = [];
Results.Total = 0;
for i = 1:n
if ExpressionData.Locus(i) > 0
locus = ExpressionData.Locus(i);
loc = find(ExpressionData.Locus == locus);
cap = length(loc)*size(ExpressionData.Data,2)*2;
for j = 1:length(loc)
total(j) = sum(ExpressionData.Data(loc(j),:));
ExpressionData.Locus(loc(j)) = 0;
end
transcripts = {};
for j = 1:length(loc)
if length(ExpressionData.Transcript{loc(j)}) > 0
transcripts = [transcripts;ExpressionData.Transcript{loc(j)}];
end
end
if length(unique(transcripts)) <= 1
% Overall expression patterns (> 75% in binary data, Expressed)
if sum(total)/cap >= ExpThreshold
Results.Expressed = [Results.Expressed;locus];
% If < 25% in binary data, UnExpressed
elseif sum(total)/cap <= UnExpThreshold
Results.UnExpressed = [Results.UnExpressed;locus];
% Accounting for different probes and their binding positions
else
cntP = 0;
for j = 1:length(total)
% Threshold once again, 75%
if total(j) >= floor(0.75*size(ExpressionData.Data,2))*2;
cntP = cntP+1;
end
end
% If 50% or more of the probes have met the threshold,
% expressed
if cntP/length(total) >= 0.5
Results.Expressed = [Results.Expressed;locus];
else
Results.UnExpressed = [Results.UnExpressed;locus];
end
end
else
% If different RefSeq Accession codes, different transcripts,
% must be manually curated
Results.AltSplice = [Results.AltSplice;locus];
end
Results.Total = Results.Total+1;
clear total
end
end
% Setting up different transcripts for manual curation
Transcripts.Locus = [];
Transcripts.Data = {};
for i = 1:length(Results.AltSplice)
num = find(Locus==Results.AltSplice(i));
transcripts = unique(ExpressionData.Transcript(num));
for j = 1:length(transcripts)
Transcripts.Locus = [Transcripts.Locus;Results.AltSplice(i)];
end
Transcripts.Data = [Transcripts.Data;transcripts];
end
% Determining each transcripts expression using a similar threshold as
% before
for i = 1:length(Transcripts.Data)
loc = strmatch(Transcripts.Data{i},ExpressionData.Transcript,'exact');
for j = 1:length(loc)
total(j) = sum(ExpressionData.Data(loc(j),:));
ExpressionData.Locus(loc(j)) = 0;
end
cap = length(loc)*11*2;
if sum(total)/cap >= ExpThreshold
Transcripts.Expression(i,1) = 1;
else
Transcripts.Expression(i,1) = 0;
end
end
% If expression of transcripts of one locus are the same, added as if no
% alternative splicing occurs for simplicity
Transcripts.Expressed = [];
Transcripts.UnExpressed = [];
mem_tran = Transcripts.Locus;
for i = 1:length(Transcripts.Locus)
if Transcripts.Locus(i) > 0
locus = Transcripts.Locus(i);
loc = find(Transcripts.Locus==locus);
sumExp = 0;
for j = 1:length(loc)
sumExp = sumExp+Transcripts.Expression(loc(j));
Transcripts.Locus(loc(j)) = 0;
end
if sumExp == 0
Transcripts.UnExpressed = [Transcripts.UnExpressed;locus];
elseif sumExp == length(loc)
Transcripts.Expressed = [Transcripts.Expressed;locus];
end
end
end
Transcripts.Locus = mem_tran;
|
github
|
EPFL-LCSB/matTFA-master
|
removeFieldEntriesForType.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/reconstruction/refinement/removeFieldEntriesForType.m
| 7,139 |
utf_8
|
702148175917ef57ddf13c5c8740e153
|
function model = removeFieldEntriesForType(model, indicesToRemove, type, fieldSize, varargin)
% Remove field entries at the specified indices from all fields associated
% with the given type
% USAGE:
% model = removeFieldEntriesForType(model, indicesToRemove, type, varargin)
%
% INPUTS:
%
% model: the model to update
% indicesToRemove: indices which should eb removed (either a logical array or double indices)
% type: the Type of field to update one of
% ('rxns','mets','comps','genes')
% fieldSize: The size of the original field before
% modification. This is necessary to identify fields
% from which entries have to be removed.
% OPTIONAL INPUTS:
% varargin: Additional Options as 'ParameterName', Value pairs. Options are:
% - 'excludeFields', fields which should not be
% adjusted but kkept how they are.
%
% OUTPUT:
%
% modelNew: the model in which all fields associated with the
% given type have the entries indicated removed. The
% initial check is for the size of the field, if
% multiple base fields have the same size, it is
% assumed, that fields named e.g. rxnXYZ are
% associated with rxns, and only those fields are
% adapted along with fields which are specified in the
% Model FieldDefinitions.
%
% .. Authors:
% - Thomas Pfau June 2017, adapted to merge all fields.
% - Georgios F. modification Aug 2017: There is a special case, when we have
% equal number of reactions and metabolites (lines 128-144)
%
PossibleTypes = {'rxns','mets','comps','genes'};
parser = inputParser();
parser.addRequired('model',@(x) isfield(x,type));
parser.addRequired('indicesToRemove',@(x) islogical(x) || isnumeric(x));
parser.addRequired('type',@(x) any(ismember(PossibleTypes,x)));
parser.addRequired('fieldSize',@isnumeric);
parser.addParameter('excludeFields',{},@iscell);
parser.parse(model,indicesToRemove,type,fieldSize,varargin{:});
fieldSize = parser.Results.fieldSize;
excludeFields = parser.Results.excludeFields;
if isnumeric(indicesToRemove)
res = false(fieldSize,1);
res(indicesToRemove) = 1;
indicesToRemove = res;
end
%We need a special treatment for genes, i.e. if we remove genes, we need to
%update all rules/gprRules
if strcmp(type,'genes')
removeRulesField = false;
genePos = find(indicesToRemove);
if ~ isfield(model,'rules') && isfield(model, 'grRules')% Only use grRules, if no rules field is present.
%lets make this easy. we will simply create the rules field and
%Then work on the rules field (removing that field again in the
%end.
model = generateRules(model);
removeRulesField = true;
end
%update the rules fields.
if isfield(model,'rules') %Rely on rules first
%However, we first normalize the rules.
model = normalizeRules(model);
%First, eliminate all removed indices
for i = 1:numel(genePos)
%Replace either a trailing &, or a leading &
rules = regexp(model.rules,['(?<pre>[\|&]?) *x\(' num2str(genePos(i)) '\) *(?<post>[\|&]?)'],'names');
matchingrules = find(~cellfun(@isempty, rules));
for elem = 1:numel(matchingrules)
cres = rules{matchingrules(elem)};
for pos = 1:numel(cres)
if isequal(cres(pos).pre,'&')
model.rules(matchingrules(elem)) = regexprep(model.rules(matchingrules(elem)),[' *& *x\(' num2str(genePos(i)) '\) *([ \)])'],'$1');
elseif isequal(cres(pos).post,'&')
model.rules(matchingrules(elem)) = regexprep(model.rules(matchingrules(elem)),['[ \(] *x\(' num2str(genePos(i)) '\) *& *'],'$1');
elseif isequal(cres(pos).post,'|')
%Make sure its not preceded by a &
model.rules(matchingrules(elem)) = regexprep(model.rules(matchingrules(elem)),['([^&]) *x\(' num2str(genePos(i)) '\) *\| *'],'$1 ');
elseif isequal(cres(pos).pre,'|')
%Make sure its not followed by a &
model.rules(matchingrules(elem)) = regexprep(model.rules(matchingrules(elem)),[' *\| *x\(' num2str(genePos(i)) '\) *([^&])'],' $1');
else
%This should only ever happen if there is only one gene.
model.rules(matchingrules(elem)) = regexprep(model.rules(matchingrules(elem)),['[\( ]*x\(' num2str(genePos(i)) '\)[\( ]*'],'');
end
end
end
end
%Now, replace all remaining indices.
oldIndices = find(~indicesToRemove);
for i = 1:numel(oldIndices)
if i ~= oldIndices(i)
%replace by new with an indicator that this is new.
model.rules = strrep(model.rules,['x(' num2str(oldIndices(i)) ')'],['x(' num2str(i) '$)']);
end
end
%remove the indicator.
model.rules = strrep(model.rules,'$','');
if isfield(model, 'grRules')
model = creategrRulesField(model);
end
end
if removeRulesField
model = rmfield(model,'rules');
end
end
fields = getModelFieldsForType(model, type, fieldSize);
fields = setdiff(fields,excludeFields);
for i = 1:numel(fields)
% Lets assume, that we only have 2 dimensional fields.
%%%%%%%%%%%%%%%%%%% ->->->->->->->->->->->->->->->->-> %%%%%%%%%%%%%%%%
% ATTENTION: Georgios F. modification: There is a special case, when we have
% equal number of reactions and metabolites
if (size(model.(fields{i}),1) == fieldSize) && (size(model.(fields{i}),2) == fieldSize) && strcmp(fields{i}, 'S')
if strcmp(type,'rxns')
if size(model.(fields{i}),2) == fieldSize
model.(fields{i}) = model.(fields{i})(:,~indicesToRemove);
end
elseif strcmp(type,'mets')
if size(model.(fields{i}),1) == fieldSize
model.(fields{i}) = model.(fields{i})(~indicesToRemove,:);
end
else
error('Something is wrong with the definition of the stoichiometric matrix!')
end
else
%%%%%%%%%%%%%%%%%%% -<-<-<-<-<-<-<-<-<-<-<-<-<-<-<-<-< %%%%%%%%%%%%%%%%
if size(model.(fields{i}),1) == fieldSize
model.(fields{i}) = model.(fields{i})(~indicesToRemove,:);
end
if size(model.(fields{i}),2) == fieldSize
model.(fields{i}) = model.(fields{i})(:,~indicesToRemove);
end
end
end
function model = normalizeRules(model)
origrules = model.rules;
model.rules = regexprep(model.rules,'\( *(x\([0-9]+\)) *\)','$1');
while ~all(strcmp(origrules,model.rules))
origrules = model.rules;
model.rules = regexprep(model.rules,'\( *(x\([0-9]+\)) *\)','$1');
end
|
github
|
EPFL-LCSB/matTFA-master
|
sparseNull.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/sparseNull.m
| 9,145 |
utf_8
|
a10b073ba5651689e2e10fa7a5e6ca65
|
function N = sparseNull(S, tol)
% sparseNull returns computes the sparse Null basis of a matrix
%
% N = sparseNull(S, tol)
%
% Computes a basis of the null space for a sparse matrix. For sparse
% matrixes this is much faster than using null. It does however have lower
% numerical accuracy. N is itself sparse and not orthonormal. So in this
% way it is like using N = null(S, 'r'), except of course much faster.
%
% Jan Schellenberger 10/20/2009
% based on this:
% http://www.mathworks.com/matlabcentral/fileexchange/11120-null-space-of-a-sparse-matrix
if nargin <2
tol = 1e-9;
end
[SpLeft, SpRight] = spspaces(S,2, tol);
N = SpRight{1}(:,SpRight{3});
N(abs(N) < tol) = 0;
%%%%%%%%%%%%%% code from website. I did not write this myself. -Jan
%%%%
function [SpLeft, SpRight] = spspaces(A,opt,tol)
% PURPOSE: finds left and right null and range space of a sparse matrix A
%
% ---------------------------------------------------
% USAGE: [SpLeft, SpRight] = spspaces(A,opt,tol)
%
% INPUT:
% A a sparse matrix
% opt spaces to calculate
% = 1: left null and range space
% = 2: right null and range space
% = 3: both left and right spaces
% tol uses the tolerance tol when calculating
% null subspaces (optional)
%
% OUTPUT:
% SpLeft 1x4 cell. SpLeft = {} if opt =2.
% SpLeft{1} an invertible matrix Q
% SpLeft{2} indices, I, of rows of the matrix Q that
% span the left range of the matrix A
% SpLeft{3} indices, J, of rows of the matrix Q that
% span the left null space of the matrix A
% Q(J,:)A = 0
% SpLeft{4} inverse of the matrix Q
% SpRight 1x4 cell. SpRight = {} if opt =1.
% SpLeft{1} an invertible matrix Q
% SpLeft{2} indices, I, of rows of the matrix Q that
% span the right range of the matrix A
% SpLeft{3} indices, J, of rows of the matrix Q that
% span the right null space of the matrix A
% AQ(:,J) = 0
% SpLeft{4} inverse of the matrix Q
%
% COMMENTS:
% uses luq routine, that finds matrices L, U, Q such that
%
% A = L | U 0 | Q
% | 0 0 |
%
% where L, Q, U are invertible matrices, U is upper triangular. This
% decomposition is calculated using lu decomposition.
%
% This routine is fast, but can deliver inaccurate null and range
% spaces if zero and nonzero singular values of the matrix A are not
% well separated.
%
% WARNING:
% right null and rang space may be very inaccurate
%
% Copyright (c) Pawel Kowal (2006)
% All rights reserved
% LREM_SOLVE toolbox is available free for noncommercial academic use only.
% [email protected]
if nargin<3
tol = max(max(size(A)) * norm(A,1) * eps,100*eps);
end
switch opt
case 1
calc_left = 1;
calc_right = 0;
case 2
calc_left = 0;
calc_right = 1;
case 3
calc_left = 1;
calc_right = 1;
end
[L,U,Q] = luq(A,0,tol);
if calc_left
if ~isempty(L)
LL = L^-1;
else
LL = L;
end
S = max(abs(U),[],2);
I = find(S>tol);
if ~isempty(S)
J = find(S<=tol);
else
J = (1:size(S,1))';
end
SpLeft = {LL,I,J,L};
else
SpLeft = {};
end
if calc_right
if ~isempty(Q)
QQ = Q^-1;
else
QQ = Q;
end
S = max(abs(U),[],1);
I = find(S>tol);
if ~isempty(S)
J = find(S<=tol);
else
J = (1:size(S,2))';
end
SpRight = {QQ,I,J,Q};
else
SpRight = {};
end
function [L,U,Q] = luq(A,do_pivot,tol)
% PURPOSE: calculates the following decomposition
%
% A = L |Ubar 0 | Q
% |0 0 |
%
% where Ubar is a square invertible matrix
% and matrices L, Q are invertible.
%
% ---------------------------------------------------
% USAGE: [L,U,Q] = luq(A,do_pivot,tol)
% INPUT:
% A a sparse matrix
% do_pivot = 1 with column pivoting
% = 0 without column pivoting
% tol uses the tolerance tol in separating zero and
% nonzero values
%
% OUTPUT:
% L,U,Q matrices
%
% COMMENTS:
% based on lu decomposition
%
% Copyright (c) Pawel Kowal (2006)
% All rights reserved
% LREM_SOLVE toolbox is available free for noncommercial academic use only.
% [email protected]
[n,m] = size(A);
if ~issparse(A)
A = sparse(A);
end
%--------------------------------------------------------------------------
% SPECIAL CASES
%--------------------------------------------------------------------------
if size(A,1)==0
L = speye(n);
U = A;
Q = speye(m);
return;
end
if size(A,2)==0
L = speye(n);
U = A;
Q = speye(m);
return;
end
%--------------------------------------------------------------------------
% LU DECOMPOSITION
%--------------------------------------------------------------------------
if do_pivot
[L,U,P,Q] = lu(A);
Q = Q';
else
[L,U,P] = lu(A);
Q = speye(m);
end
p = size(A,1)-size(L,2);
LL = [sparse(n-p,p);speye(p)];
L = [P'*L P(n-p+1:n,:)'];
U = [U;sparse(p,m)];
%--------------------------------------------------------------------------
% FINDS ROWS WITH ZERO AND NONZERO ELEMENTS ON THE DIAGONAL
%--------------------------------------------------------------------------
if size(U,1)==1 || size(U,2)==1
S = U(1,1);
else
S = diag(U);
end
I = find(abs(S)>tol);
Jl = (1:n)';
Jl(I) = [];
Jq = (1:m)';
Jq(I) = [];
Ubar1 = U(I,I);
Ubar2 = U(Jl,Jq);
Qbar1 = Q(I,:);
Lbar1 = L(:,I);
%--------------------------------------------------------------------------
% ELININATES NONZEZO ELEMENTS BELOW AND ON THE RIGHT OF THE
% INVERTIBLE BLOCK OF THE MATRIX U
%
% UPDATES MATRICES L, Q
%--------------------------------------------------------------------------
if ~isempty(I)
Utmp = U(I,Jq);
X = Ubar1'\U(Jl,I)';
Ubar2 = Ubar2-X'*Utmp;
Lbar1 = Lbar1+L(:,Jl)*X';
X = Ubar1\Utmp;
Qbar1 = Qbar1+X*Q(Jq,:);
Utmp = [];
X = [];
end
%--------------------------------------------------------------------------
% FINDS ROWS AND COLUMNS WITH ONLY ZERO ELEMENTS
%--------------------------------------------------------------------------
I2 = find(max(abs(Ubar2),[],2)>tol);
I5 = find(max(abs(Ubar2),[],1)>tol);
I3 = Jl(I2);
I4 = Jq(I5);
Jq(I5) = [];
Jl(I2) = [];
U = [];
%--------------------------------------------------------------------------
% FINDS A PART OF THE MATRIX U WHICH IS NOT IN THE REQIRED FORM
%--------------------------------------------------------------------------
A = Ubar2(I2,I5);
%--------------------------------------------------------------------------
% PERFORMS LUQ DECOMPOSITION OF THE MATRIX A
%--------------------------------------------------------------------------
[L1,U1,Q1] = luq(A,do_pivot,tol);
%--------------------------------------------------------------------------
% UPDATES MATRICES L, U, Q
%--------------------------------------------------------------------------
Lbar2 = L(:,I3)*L1;
Qbar2 = Q1*Q(I4,:);
L = [Lbar1 Lbar2 L(:,Jl)];
Q = [Qbar1; Qbar2; Q(Jq,:)];
n1 = length(I);
n2 = length(I3);
m2 = length(I4);
U = [Ubar1 sparse(n1,m-n1);sparse(n2,n1) U1 sparse(n2,m-n1-m2);sparse(n-n1-n2,m)];
|
github
|
EPFL-LCSB/matTFA-master
|
ezimplot3.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/ezimplot3.m
| 8,154 |
utf_8
|
7bbd5c9f9dba80200fd1fb799e7c8cb3
|
function h = ezimplot3(varargin)
% EZIMPLOT3 Easy to use 3D implicit plotter.
% EZIMPLOT3(FUN) plots the function FUN(X,Y,Z) = 0 (vectorized or not)
% over the default domain:
% -2*PI < X < 2*PI, -2*PI < Y < 2*PI, -2*PI < Z < 2*PI.
% FUN can be a string, an anonymous function handle, a .M-file handle, an
% inline function or a symbolic function (see examples below)
%
% EZIMPLOT3(FUN,DOMAIN)plots FUN over the specified DOMAIN instead of the
% default domain. DOMAIN can be vector [XMIN,XMAX,YMIN,YMAX,ZMIN,ZMAX] or
% vector [A,B] (to plot over A < X < B, A < Y < B, A < Z < B).
%
% EZIMPLOT3(..,N) plots FUN using an N-by-N grid. The default value for
% N is 60.
% EZIMPLOT3(..,'color') plots FUN with color 'color'. The default value
% for 'color' is 'red'. 'color' must be a valid Matlab color identifier.
%
% EZIMPLOT3(axes_handle,..) plots into the axes with handle axes_handle
% instead of into current axes (gca).
%
% H = EZIMPLOT3(...) returns the handle to the patch object this function
% creates.
%
% Example:
% Plot x^3+exp(y)-cosh(z)=4, between -5 and 5 for x,y and z
%
% via a string:
% f = 'x^3+exp(y)-cosh(z)-4'
% ezimplot3(f,[-5 5])
%
% via a anonymous function handle:
% f = @(x,y,z) x^3+exp(y)-cosh(z)-4
% ezimplot3(f,[-5 5])
%
% via a function .m file:
%------------------------------%
% function out = myfun(x,y,z)
% out = x^3+exp(y)-cosh(z)-4;
%------------------------------%
% ezimplot3(@myfun,[-5 5]) or ezimplot('myfun',[-5 5])
%
% via a inline function:
% f = inline('x^3+exp(y)-cosh(z)-4')
% ezimplot3(f,[-5 5])
%
% via a symbolic expression:
% syms x y z
% f = x^3+exp(y)-cosh(z)-4
% ezimplot3(f,[-5 5])
%
% Note: this function do not use the "ezgraph3" standard, like ezsurf,
% ezmesh, etc, does. Because of this, ezimplot3 only tries to imitate that
% interface. A future work must be to modify "ezgraph3" to include a
% routine for implicit surfaces based on this file
%
% Inspired by works of: Artur Jutan UWO 02-02-98 [email protected]
% Made by: Gustavo Morales UC 04-12-09 [email protected]
%
%%% Checking & Parsing input arguments:
if ishandle(varargin{1})
cax = varargin{1}; % User selected axes handle for graphics
axes(cax);
args{:} = varargin{2:end}; %ensuring args be a cell array
else
args = varargin;
end
[fun domain n color] = argcheck(args{:});
%%% Generating the volumetric domain data:
xm = linspace(domain(1),domain(2),n);
ym = linspace(domain(3),domain(4),n);
zm = linspace(domain(5),domain(6),n);
[x,y,z] = meshgrid(xm,ym,zm);
%%% Formatting "fun"
[f_handle f_text] = fix_fun(fun); % f_handle is the anonymous f-handle for "fun"
% f_text is "fun" ready to be a title
%%% Evaluating "f_handle" in domain:
% try
fvalues = f_handle(x,y,z); % fvalues: volume data
% catch ME
% error('Ezimplot3:Functions', 'FUN must have no more than 3 arguments');
% end
%%% Making the 3D graph of the 0-level surface of the 4D function "fun":
h = patch(isosurface(x,y,z,fvalues,0)); % "patch" handles the structure...
% sent by "isosurface"
isonormals(x,y,z,fvalues,h)% Recalculating the isosurface normals based...
% on the volume data
set(h,'FaceColor',color,'EdgeColor','none');
%%% Aditional graphic details:
xlabel('x');ylabel('y');zlabel('z');% naming the axis
alpha(0.7) % adjusting for some transparency
grid on; view([1,1,1]); axis equal; camlight; lighting gouraud
%%% Showing title:
title([f_text,' = 0']);
%
%--------------------------------------------Sub-functions HERE---
function [f dom n color] = argcheck(varargin)
%ARGCHECK(arg) parses "args" to the variables "f"(function),"dom"(domain)
%,"n"(grid size) and "c"(color)and TRIES to check its validity
switch nargin
case 0
error('Ezimplot3:Arguments',...
'At least "fun" argument must be given');
case 1
f = varargin{1};
dom = [-2*pi, 2*pi]; % default domain: -2*pi < xi < 2*pi
n = 60; % default grid size
color = 'red'; % default graph color
case 2
f = varargin{1};
if isa(varargin{2},'double') && length(varargin{2})>1
dom = varargin{2};
n = 60;
color = 'red';
elseif isa(varargin{2},'double') && length(varargin{2})==1
n = varargin{2};
dom = [-2*pi, 2*pi];
color = 'red';
elseif isa(varargin{2},'char')
dom = [-2*pi, 2*pi];
n = 60;
color = varargin{2};
end
case 3 % If more than 2 arguments are given, it's
f = varargin{1}; % assumed they are in the correct order
dom = varargin{2};
n = varargin{3};
color = 'red'; % default color
case 4 % If more than 2 arguments are given, it's
f = varargin{1}; % assumed they are in the correct order
dom = varargin{2};
n = varargin{3};
color = varargin{4};
otherwise
warning('Ezimplot3:Arguments', ...
'Attempt will be made only with the 4 first arguments');
f = varargin{1};
dom = varargin{2};
n = varargin{3};
color = varargin{4};
end
if length(dom) == 2
dom = repmat(dom,1,3); %domain repeated in all variables
elseif length(dom) ~= 6
error('Ezimplot3:Arguments',...
'Input argument "domain" must be a row vector of size 2 or size 6');
end
%
%--------------------------------------------
function [f_hand f_text] = fix_fun(fun)
% FIX_FUN(fun) Converts "fun" into an anonymous function of 3 variables (x,y,z)
% with handle "f_hand" and a string "f_text" to use it as title
types = {'char','sym','function_handle','inline'}; % cell array of 'types'
type = ''; %Identifing FUN object class
for i=1:size(types,2)
if isa(fun,types{i})
type = types{i};
break;
end
end
switch type
case 'char' % Formatting FUN if it is char type. There's 2 possibilities:
% A string with the name of the .m file
if exist([fun,'.m'],'file')
syms x y z;
if nargin(str2func(fun)) == 3
f_sym = eval([fun,'(x,y,z)']); % evaluating FUN at the sym point (x,y,z)
else
error('Ezimplot3:Arguments',...
'%s must be a function of 3 arguments or unknown function',fun);
end
f_text = strrep(char(f_sym),' ',''); % converting to char and eliminating spaces
f_hand = eval(['@(x,y,z)',vectorize(f_text),';']); % converting string to anonymous f_handle
else
% A string with the function's expression
f_hand = eval(['@(x,y,z)',vectorize(fun),';']); % converting string to anonymous f_handle
f_text = strrep(fun,'.',''); f_text = strrep(f_text,' ',''); % removing vectorization & spaces
end
case 'sym' % Formatting FUN if it is a symbolic object
f_hand = eval(['@(x,y,z)',vectorize(fun),';']); % converting string to anonymous f_handle
f_text = strrep(char(fun),' ',''); % removing spaces
case {'function_handle', 'inline'} % Formatting FUN if it is a function_handle or an inline object
syms x y z;
if nargin(fun) == 3 %&& numel(symvar(char(fun))) == 3 % Determining if # variables == 3
f_sym = fun(x,y,z); % evaluating FUN at the sym point (x,y,z)
else
error('Ezimplot3:Arguments',...
'%s must be function of 3 arguments or unknown function',char(fun));
end
f_text = strrep(char(f_sym),' ',''); % converting into string to removing spaces
f_hand = eval(['@(x,y,z)',vectorize(f_text),';']); % converting string to anonymous f_handle
otherwise
error('First argument "fun" must be of type character, simbolic, function handle or inline');
end
|
github
|
EPFL-LCSB/matTFA-master
|
m2html.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/m2html/m2html.m
| 38,334 |
utf_8
|
9e0ccc8f5147c96ff4bde2efa2b4787b
|
function m2html(varargin)
%M2HTML - Documentation System for Matlab M-files in HTML
% M2HTML by itself generates an HTML documentation of Matlab M-files in the
% current directory. HTML files are also written in the current directory.
% M2HTML('PropertyName1',PropertyValue1,'PropertyName2',PropertyValue2,...)
% sets multiple option values. The list of option names and default values is:
% o mFiles - Cell array of strings or character array containing the
% list of M-files and/or directories of M-files for which an HTML
% documentation will be built [ '.' ]
% o htmlDir - Top level directory for generated HTML files [ '.' ]
% o recursive - Process subdirectories [ on | {off} ]
% o source - Include Matlab source code in the HTML documentation
% [ {on} | off ]
% o syntaxHighlighting - Syntax Highlighting [ {on} | off ]
% o tabs - Replace '\t' (horizontal tab) in source code by n white space
% characters [ 0 ... {4} ... n ]
% o globalHypertextLinks - Hypertext links among separate Matlab
% directories [ on | {off} ]
% o todo - Create a TODO file in each directory summarizing all the
% '% TODO %' lines found in Matlab code [ on | {off}]
% o graph - Compute a dependency graph using GraphViz [ on | {off}]
% 'dot' required, see <http://www.research.att.com/sw/tools/graphviz/>
% o indexFile - Basename of the HTML index file [ 'index' ]
% o extension - Extension of generated HTML files [ '.html' ]
% o template - HTML template name to use [ 'blue' ]
% o save - Save current state after M-files parsing in 'm2html.mat'
% in directory htmlDir [ on | {off}]
% o load - Load a previously saved '.mat' M2HTML state to generate HTML
% files once again with possibly other options [ <none> ]
% o verbose - Verbose mode [ {on} | off ]
%
% Examples:
% >> m2html('mfiles','matlab', 'htmldir','doc');
% >> m2html('mfiles',{'matlab/signal' 'matlab/image'}, 'htmldir','doc');
% >> m2html('mfiles','matlab', 'htmldir','doc', 'recursive','on');
% >> m2html('mfiles','mytoolbox', 'htmldir','doc', 'source','off');
% >> m2html('mfiles','matlab', 'htmldir','doc', 'global','on');
% >> m2html( ... , 'template','frame', 'index','menu');
%
% See also HIGHLIGHT, MDOT, TEMPLATE.
% Copyright (C) 2003 Guillaume Flandin <[email protected]>
% $Revision: 1.2 $Date: 2003/31/08 17:25:20 $
% This program is free software; you can redistribute it and/or
% modify it under the terms of the GNU General Public License
% as published by the Free Software Foundation; either version 2
% of the License, or any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation Inc, 59 Temple Pl. - Suite 330, Boston, MA 02111-1307, USA.
% Suggestions for improvement and fixes are always welcome, although no
% guarantee is made whether and when they will be implemented.
% Send requests to [email protected]
% For tips on how to write Matlab code, see:
% * MATLAB Programming Style Guidelines, by R. Johnson:
% <http://www.datatool.com/prod02.htm>
% * For tips on creating help for your m-files 'type help.m'.
% * Matlab documentation on M-file Programming:
% <http://www.mathworks.com/access/helpdesk/help/techdoc/matlab_prog/ch10_pr9.shtml>
% This function uses the Template class so that you can fully customize
% the output. You can modify .tpl files in templates/blue/ or create new
% templates in a new directory.
% See the template class documentation for more details.
% <http://www.madic.org/download/matlab/template/>
% Latest information on M2HTML is available on the web through:
% <http://www.artefact.tk/software/matlab/m2html/>
% Other Matlab to HTML converters available on the web:
% 1/ mat2html.pl, J.C. Kantor, in Perl, 1995:
% <http://fresh.t-systems-sfr.com/unix/src/www/mat2html>
% 2/ htmltools, B. Alsberg, in Matlab, 1997:
% <http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=175>
% 3/ mtree2html2001, H. Pohlheim, in Perl, 1996, 2001:
% <http://www.pohlheim.com/perl_main.html#matlabdocu>
% 4/ MatlabToHTML, T. Kristjansson, binary, 2001:
% <http://www.psi.utoronto.ca/~trausti/MatlabToHTML/MatlabToHTML.html>
% 5/ Highlight, G. Flandin, in Matlab, 2003:
% <http://www.madic.org/download/matlab/highlight/>
% 6/ mdoc, P. Brinkmann, in Matlab, 2003:
% <http://www.math.uiuc.edu/~brinkman/software/mdoc/>
% 7/ Ocamaweb, Miriad Technologies, in Ocaml, 2002:
% <http://ocamaweb.sourceforge.net/>
% 8/ Matdoc, M. Kaminsky, in Perl, 2003:
% <http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=3498>
% 9/ Matlab itself, The Mathworks Inc, with HELPWIN and DOC
%-------------------------------------------------------------------------------
%- Set up options and default parameters
%-------------------------------------------------------------------------------
msgInvalidPair = 'Bad value for argument: ''%s''';
options = struct('verbose', 1,...
'mFiles', {{'.'}},...
'htmlDir', '.',...
'recursive', 0,...
'source', 1,...
'syntaxHighlighting', 1,...
'tabs', 4,...
'globalHypertextLinks', 0,...
'graph', 0,...
'todo', 0,...
'load', 0,...
'save', 0,...
'search', 0,...
'indexFile', 'index',...
'extension', '.html',...
'template', 'blue');
if nargin == 1 & isstruct(varargin{1})
paramlist = [ fieldnames(varargin{1}) ...
struct2cell(varargin{1}) ]';
paramlist = { paramlist{:} };
else
if mod(nargin,2)
error('Invalid parameter/value pair arguments.');
end
paramlist = varargin;
end
optionsnames = lower(fieldnames(options));
for i=1:2:length(paramlist)
pname = paramlist{i};
pvalue = paramlist{i+1};
ind = strmatch(lower(pname),optionsnames);
if isempty(ind)
error(['Invalid parameter: ''' pname '''.']);
elseif length(ind) > 1
error(['Ambiguous parameter: ''' pname '''.']);
end
switch(optionsnames{ind})
case 'verbose'
if strcmpi(pvalue,'on')
options.verbose = 1;
elseif strcmpi(pvalue,'off')
options.verbose = 0;
else
error(sprintf(msgInvalidPair,pname));
end
case 'mfiles'
if iscellstr(pvalue)
options.mFiles = pvalue;
elseif ischar(pvalue)
options.mFiles = cellstr(pvalue);
else
error(sprintf(msgInvalidPair,pname));
end
options.load = 0;
case 'htmldir'
if ischar(pvalue)
if isempty(pvalue),
options.htmlDir = '.';
else
options.htmlDir = pvalue;
end
else
error(sprintf(msgInvalidPair,pname));
end
case 'recursive'
if strcmpi(pvalue,'on')
options.recursive = 1;
elseif strcmpi(pvalue,'off')
options.recursive = 0;
else
error(sprintf(msgInvalidPair,pname));
end
options.load = 0;
case 'source'
if strcmpi(pvalue,'on')
options.source = 1;
elseif strcmpi(pvalue,'off')
options.source = 0;
else
error(sprintf(msgInvalidPair,pname));
end
case 'syntaxhighlighting'
if strcmpi(pvalue,'on')
options.syntaxHighlighting = 1;
elseif strcmpi(pvalue,'off')
options.syntaxHighlighting = 0;
else
error(sprintf(msgInvalidPair,pname));
end
case 'tabs'
if pvalue >= 0
options.tabs = pvalue;
else
error(sprintf(msgInvalidPair,pname));
end
case 'globalhypertextlinks'
if strcmpi(pvalue,'on')
options.globalHypertextLinks = 1;
elseif strcmpi(pvalue,'off')
options.globalHypertextLinks = 0;
else
error(sprintf(msgInvalidPair,pname));
end
options.load = 0;
case 'graph'
if strcmpi(pvalue,'on')
options.graph = 1;
elseif strcmpi(pvalue,'off')
options.graph = 0;
else
error(sprintf(msgInvalidPair,pname));
end
case 'todo'
if strcmpi(pvalue,'on')
options.todo = 1;
elseif strcmpi(pvalue,'off')
options.todo = 0;
else
error(sprintf(msgInvalidPair,pname));
end
case 'load'
if ischar(pvalue)
try
load(pvalue);
catch
error(sprintf('Unable to load %s.',pvalue));
end
options.load = 1;
[dummy options.template] = fileparts(options.template);
else
error(sprintf(msgInvalidPair,pname));
end
case 'save'
if strcmpi(pvalue,'on')
options.save = 1;
elseif strcmpi(pvalue,'off')
options.save = 0;
else
error(sprintf(msgInvalidPair,pname));
end
case 'search'
if strcmpi(pvalue,'on')
options.search = 1;
elseif strcmpi(pvalue,'off')
options.search = 0;
else
error(sprintf(msgInvalidPair,pname));
end
case 'indexfile'
if ischar(pvalue)
options.indexFile = pvalue;
else
error(sprintf(msgInvalidPair,pname));
end
case 'extension'
if ischar(pvalue) & pvalue(1) == '.'
options.extension = pvalue;
else
error(sprintf(msgInvalidPair,pname));
end
case 'template'
if ischar(pvalue)
options.template = pvalue;
else
error(sprintf(msgInvalidPair,pname));
end
otherwise
error(['Invalid parameter: ''' pname '''.']);
end
end
%-------------------------------------------------------------------------------
%- Get template files location
%-------------------------------------------------------------------------------
s = fileparts(which(mfilename));
options.template = fullfile(s,'templates',options.template);
if exist(options.template) ~= 7
error('[Template] Unknown template.');
end
%-------------------------------------------------------------------------------
%- Get list of M-files
%-------------------------------------------------------------------------------
if ~options.load
mfiles = getmfiles(options.mFiles,{},options.recursive);
if ~length(mfiles), fprintf('Nothing to be done.\n'); return; end
if options.verbose,
fprintf('Found %d M-files.\n',length(mfiles));
end
mfiles = sort(mfiles); % sort list of M-files in dictionary order
end
%-------------------------------------------------------------------------------
%- Get list of (unique) directories and (unique) names
%-------------------------------------------------------------------------------
if ~options.load
mdirs = {};
names = {};
for i=1:length(mfiles)
[mdirs{i}, names{i}] = fileparts(mfiles{i});
if isempty(mdirs{i}), mdirs{i} = '.'; end
end
mdir = unique(mdirs);
if options.verbose,
fprintf('Found %d unique Matlab directories.\n',length(mdir));
end
name = names;
%name = unique(names); % output is sorted
%if options.verbose,
% fprintf('Found %d unique Matlab files.\n',length(name));
%end
end
%-------------------------------------------------------------------------------
%- Create output directory, if necessary
%-------------------------------------------------------------------------------
if isempty(dir(options.htmlDir))
%- Create the top level output directory
if options.verbose
fprintf('Creating directory %s...\n',options.htmlDir);
end
if options.htmlDir(end) == filesep,
options.htmlDir(end) = [];
end
[pathdir, namedir] = fileparts(options.htmlDir);
if isempty(pathdir)
[status, msg] = mkdir(namedir);
else
[status, msg] = mkdir(pathdir, namedir);
end
if ~status, error(msg); end
end
%-------------------------------------------------------------------------------
%- Get synopsis, H1 line, script/function, subroutines, cross-references, todo
%-------------------------------------------------------------------------------
if ~options.load
synopsis = cell(size(mfiles));
h1line = cell(size(mfiles));
subroutine = cell(size(mfiles));
hrefs = sparse(length(mfiles),length(mfiles));
todo = struct('mfile',[],'line',[],'comment',{{}});
ismex = zeros(length(mfiles),length(mexexts));
for i=1:length(mfiles)
s = mfileparse(mfiles{i}, mdirs, names, options);
synopsis{i} = s.synopsis;
h1line{i} = s.h1line;
subroutine{i} = s.subroutine;
hrefs(i,:) = s.hrefs;
todo.mfile = [todo.mfile repmat(i,1,length(s.todo.line))];
todo.line = [todo.line s.todo.line];
todo.comment = {todo.comment{:} s.todo.comment{:}};
ismex(i,:) = s.ismex;
end
hrefs = hrefs > 0;
end
%-------------------------------------------------------------------------------
%- Save M-filenames and cross-references for further analysis
%-------------------------------------------------------------------------------
matfilesave = 'm2html.mat';
if options.save
if options.verbose
fprintf('Saving MAT file %s...\n',matfilesave);
end
save(fullfile(options.htmlDir,matfilesave), ...
'mfiles', 'names', 'mdirs', 'name', 'mdir', 'options', ...
'hrefs', 'synopsis', 'h1line', 'subroutine', 'todo', 'ismex');
end
%-------------------------------------------------------------------------------
%- Setup the output directories
%-------------------------------------------------------------------------------
for i=1:length(mdir)
if exist(fullfile(options.htmlDir,mdir{i})) ~= 7
ldir = splitpath(mdir{i});
for j=1:length(ldir)
if exist(fullfile(options.htmlDir,ldir{1:j})) ~= 7
%- Create the output directory
if options.verbose
fprintf('Creating directory %s...\n',...
fullfile(options.htmlDir,ldir{1:j}));
end
if j == 1
[status, msg] = mkdir(options.htmlDir,ldir{1});
else
[status, msg] = mkdir(options.htmlDir,fullfile(ldir{1:j}));
end
error(msg);
end
end
end
end
%-------------------------------------------------------------------------------
%- Write the master index file
%-------------------------------------------------------------------------------
tpl_master = 'master.tpl';
tpl_master_identifier_nbyline = 4;
%- Create the HTML template
tpl = template(options.template,'remove');
tpl = set(tpl,'file','TPL_MASTER',tpl_master);
tpl = set(tpl,'block','TPL_MASTER','rowdir','rowdirs');
tpl = set(tpl,'block','TPL_MASTER','idrow','idrows');
tpl = set(tpl,'block','idrow','idcolumn','idcolumns');
%- Open for writing the HTML master index file
curfile = fullfile(options.htmlDir,[options.indexFile options.extension]);
if options.verbose
fprintf('Creating HTML file %s...\n',curfile);
end
fid = openfile(curfile,'w');
%- Set some template variables
tpl = set(tpl,'var','DATE',[datestr(now,8) ' ' datestr(now,1) ' ' ...
datestr(now,13)]);
tpl = set(tpl,'var','MASTERPATH', './');
tpl = set(tpl,'var','DIRS', sprintf('%s ',mdir{:}));
%- Print list of unique directories
for i=1:length(mdir)
tpl = set(tpl,'var','L_DIR',...
fullurl(mdir{i},[options.indexFile options.extension]));
tpl = set(tpl,'var','DIR',mdir{i});
tpl = parse(tpl,'rowdirs','rowdir',1);
end
%- Print full list of M-files (sorted by column)
[sortnames, ind] = sort(names);
m_mod = mod(length(sortnames), tpl_master_identifier_nbyline);
ind = [ind zeros(1,tpl_master_identifier_nbyline-m_mod)];
m_floor = floor(length(ind) / tpl_master_identifier_nbyline);
ind = reshape(ind,m_floor,tpl_master_identifier_nbyline)';
for i=1:prod(size(ind))
if ind(i)
tpl = set(tpl,'var','L_IDNAME',...
fullurl(mdirs{ind(i)},[names{ind(i)} options.extension]));
tpl = set(tpl,'var','T_IDNAME',mdirs{ind(i)});
tpl = set(tpl,'var','IDNAME',names{ind(i)});
tpl = parse(tpl,'idcolumns','idcolumn',1);
else
tpl = set(tpl,'var','L_IDNAME','');
tpl = set(tpl,'var','T_IDNAME','');
tpl = set(tpl,'var','IDNAME','');
tpl = parse(tpl,'idcolumns','idcolumn',1);
end
if mod(i,tpl_master_identifier_nbyline) == 0
tpl = parse(tpl,'idrows','idrow',1);
tpl = set(tpl,'var','idcolumns','');
end
end
%- Print the template in the HTML file
tpl = parse(tpl,'OUT','TPL_MASTER');
fprintf(fid,'%s',get(tpl,'OUT'));
fclose(fid);
%-------------------------------------------------------------------------------
%- Copy template files (CSS, images, ...)
%-------------------------------------------------------------------------------
% Get list of files
d = dir(options.template);
d = {d(~[d.isdir]).name};
% Copy files
for i=1:length(d)
[p, n, ext] = fileparts(d{i});
if ~strcmp(ext,'.tpl') % do not copy .tpl files
if ~(exist(fullfile(options.htmlDir,d{i})))
if options.verbose
fprintf('Copying template file %s...\n',d{i});
end
[status, errmsg] = copyfile(fullfile(options.template,d{i}),...
options.htmlDir);
error(errmsg);
end
end
end
%-------------------------------------------------------------------------------
%- Write an index for each output directory
%-------------------------------------------------------------------------------
tpl_mdir = 'mdir.tpl';
tpl_mdir_link = '<a href="%s">%s</a>';
dotbase = 'graph';
%- Create the HTML template
tpl = template(options.template,'remove');
tpl = set(tpl,'file','TPL_MDIR',tpl_mdir);
tpl = set(tpl,'block','TPL_MDIR','row-m','rows-m');
tpl = set(tpl,'block','row-m','mexfile','mex');
tpl = set(tpl,'block','TPL_MDIR','othermatlab','other');
tpl = set(tpl,'block','othermatlab','row-other','rows-other');
tpl = set(tpl,'block','TPL_MDIR','subfolder','subfold');
tpl = set(tpl,'block','subfolder','subdir','subdirs');
tpl = set(tpl,'block','TPL_MDIR','todolist','todolists');
tpl = set(tpl,'block','TPL_MDIR','graph','graphs');
tpl = set(tpl,'var','DATE',[datestr(now,8) ' ' datestr(now,1) ' ' ...
datestr(now,13)]);
for i=1:length(mdir)
%- Open for writing each output directory index file
curfile = fullfile(options.htmlDir,mdir{i},...
[options.indexFile options.extension]);
if options.verbose
fprintf('Creating HTML file %s...\n',curfile);
end
fid = openfile(curfile,'w');
%- Set template fields
tpl = set(tpl,'var','INDEX', [options.indexFile options.extension]);
tpl = set(tpl,'var','MASTERPATH',backtomaster(mdir{i}));
tpl = set(tpl,'var','MDIR', mdir{i});
%- Display Matlab m-files, their H1 line and their Mex status
tpl = set(tpl,'var','rows-m','');
for j=1:length(mdirs)
if strcmp(mdirs{j},mdir{i})
tpl = set(tpl,'var','L_NAME', [names{j} options.extension]);
tpl = set(tpl,'var','NAME', names{j});
tpl = set(tpl,'var','H1LINE', h1line{j});
if any(ismex(j,:))
tpl = parse(tpl,'mex','mexfile');
else
tpl = set(tpl,'var','mex','');
end
tpl = parse(tpl,'rows-m','row-m',1);
end
end
%- Display other Matlab-specific files (.mat,.mdl,.p)
tpl = set(tpl,'var','other','');
tpl = set(tpl,'var','rows-other','');
w = what(mdir{i}); w = w(1);
w = {w.mat{:} w.mdl{:} w.p{:}};
for j=1:length(w)
tpl = set(tpl,'var','OTHERFILE',w{j});
tpl = parse(tpl,'rows-other','row-other',1);
end
if ~isempty(w)
tpl = parse(tpl,'other','othermatlab');
end
%- Display subsequent directories and classes
tpl = set(tpl,'var','subdirs','');
tpl = set(tpl,'var','subfold','');
d = dir(mdir{i});
d = {d([d.isdir]).name};
d = {d{~ismember(d,{'.' '..'})}};
for j=1:length(d)
if ismember(fullfile(mdir{i},d{j}),mdir)
tpl = set(tpl,'var','SUBDIRECTORY',...
sprintf(tpl_mdir_link,...
fullurl(d{j},[options.indexFile options.extension]),d{j}));
else
tpl = set(tpl,'var','SUBDIRECTORY',d{j});
end
tpl = parse(tpl,'subdirs','subdir',1);
end
if ~isempty(d)
tpl = parse(tpl,'subfold','subfolder');
end
%- Link to the TODO list if necessary
tpl = set(tpl,'var','todolists','');
if options.todo
if ~isempty(intersect(find(strcmp(mdir{i},mdirs)),todo.mfile))
tpl = set(tpl,'var','LTODOLIST',['todo' options.extension]);
tpl = parse(tpl,'todolists','todolist',1);
end
end
%- Link to the dependency graph if necessary
tpl = set(tpl,'var','graphs','');
if options.graph
tpl = set(tpl,'var','LGRAPH',[dotbase options.extension]);
tpl = parse(tpl,'graphs','graph',1);
end
%- Print the template in the HTML file
tpl = parse(tpl,'OUT','TPL_MDIR');
fprintf(fid,'%s',get(tpl,'OUT'));
fclose(fid);
end
%-------------------------------------------------------------------------------
%- Write a TODO list file for each output directory, if necessary
%-------------------------------------------------------------------------------
tpl_todo = 'todo.tpl';
if options.todo
%- Create the HTML template
tpl = template(options.template,'remove');
tpl = set(tpl,'file','TPL_TODO',tpl_todo);
tpl = set(tpl,'block','TPL_TODO','filelist','filelists');
tpl = set(tpl,'block','filelist','row','rows');
tpl = set(tpl,'var','DATE',[datestr(now,8) ' ' datestr(now,1) ' ' ...
datestr(now,13)]);
for i=1:length(mdir)
mfilestodo = intersect(find(strcmp(mdir{i},mdirs)),todo.mfile);
if ~isempty(mfilestodo)
%- Open for writing each TODO list file
curfile = fullfile(options.htmlDir,mdir{i},...
['todo' options.extension]);
if options.verbose
fprintf('Creating HTML file %s...\n',curfile);
end
fid = openfile(curfile,'w');
%- Set template fields
tpl = set(tpl,'var','INDEX',[options.indexFile options.extension]);
tpl = set(tpl,'var','MASTERPATH', backtomaster(mdir{i}));
tpl = set(tpl,'var','MDIR', mdir{i});
tpl = set(tpl,'var','filelists', '');
for k=1:length(mfilestodo)
tpl = set(tpl,'var','MFILE',names{mfilestodo(k)});
tpl = set(tpl,'var','rows','');
nbtodo = find(todo.mfile == mfilestodo(k));
for l=1:length(nbtodo)
tpl = set(tpl,'var','L_NBLINE',...
[names{mfilestodo(k)} ...
options.extension ...
'#l' num2str(todo.line(nbtodo(l)))]);
tpl = set(tpl,'var','NBLINE',num2str(todo.line(nbtodo(l))));
tpl = set(tpl,'var','COMMENT',todo.comment{nbtodo(l)});
tpl = parse(tpl,'rows','row',1);
end
tpl = parse(tpl,'filelists','filelist',1);
end
%- Print the template in the HTML file
tpl = parse(tpl,'OUT','TPL_TODO');
fprintf(fid,'%s',get(tpl,'OUT'));
fclose(fid);
end
end
end
%-------------------------------------------------------------------------------
%- Create a dependency graph for each output directory, if requested
%-------------------------------------------------------------------------------
tpl_graph = 'graph.tpl';
dot_exec = 'dot';
%dotbase defined earlier
if options.graph
%- Create the HTML template
tpl = template(options.template,'remove');
tpl = set(tpl,'file','TPL_GRAPH',tpl_graph);
tpl = set(tpl,'var','DATE',[datestr(now,8) ' ' datestr(now,1) ' ' ...
datestr(now,13)]);
for i=1:length(mdir)
mdotfile = fullfile(options.htmlDir,mdir{i},[dotbase '.dot']);
if options.verbose
fprintf('Creating dependency graph %s...',mdotfile);
end
ind = find(strcmp(mdirs,mdir{i}));
%ind = find(strncmp(mdirs,mdir{i},length(mdir{i}))); %R.F.
href1 = zeros(length(ind),length(hrefs));
for j=1:length(hrefs), href1(:,j) = hrefs(ind,j); end
href2 = zeros(length(ind));
for j=1:length(ind), href2(j,:) = href1(j,ind); end
mdot({href2,{names{ind}},options,{mfiles{ind}}}, mdotfile);
%mdot({href2,{names{ind}},options,{mfiles{ind}}},mdotfile,mdir{i});%R.F.
try
%- see <http://www.research.att.com/sw/tools/graphviz/>
% <dot> must be in your system path:
% - on Linux, modify $PATH accordingly
% - on Windows, modify the environment variable PATH like this:
% From the Start-menu open the Control Panel, open 'System' and activate the
% panel named 'Extended'. Open the dialog 'Environment Variables'. Select the
% variable 'Path' of the panel 'System Variables' and press the 'Modify button.
% Then add 'C:\GraphViz\bin' to your current definition of PATH, assuming that
% you did install GraphViz into directory 'C:\GraphViz'. Note that the various
% paths in PATH have to be separated by a colon. Her is an example how the final
% Path should look like: ...;C:\WINNT\System32;...;C:\GraphViz\bin
% (Note that this should have been done automatically during GraphViz installation)
eval(['!' dot_exec ' -Tcmap -Tpng ' mdotfile ...
' -o ' fullfile(options.htmlDir,mdir{i},[dotbase '.map']) ...
' -o ' fullfile(options.htmlDir,mdir{i},[dotbase '.png'])])
% use '!' rather than 'system' for backward compability
catch
fprintf('failed.');
end
fprintf('\n');
fid = openfile(fullfile(options.htmlDir,mdir{i},...
[dotbase options.extension]),'w');
tpl = set(tpl,'var','INDEX',[options.indexFile options.extension]);
tpl = set(tpl,'var','MASTERPATH', backtomaster(mdir{i}));
tpl = set(tpl,'var','MDIR', mdir{i});
tpl = set(tpl,'var','GRAPH_IMG', [dotbase '.png']);
fmap = openfile(fullfile(options.htmlDir,mdir{i},[dotbase '.map']),'r');
tpl = set(tpl,'var','GRAPH_MAP', fscanf(fmap,'%c'));
fclose(fmap);
tpl = parse(tpl,'OUT','TPL_GRAPH');
fprintf(fid,'%s', get(tpl,'OUT'));
fclose(fid);
end
end
%-------------------------------------------------------------------------------
%- Write an HTML file for each M-file
%-------------------------------------------------------------------------------
%- List of Matlab keywords (output from iskeyword)
matlabKeywords = {'break', 'case', 'catch', 'continue', 'elseif', 'else', ...
'end', 'for', 'function', 'global', 'if', 'otherwise', ...
'persistent', 'return', 'switch', 'try', 'while'};
%'keyboard', 'pause', 'eps', 'NaN', 'Inf'
tpl_mfile = 'mfile.tpl';
tpl_mfile_code = '<a href="%s" class="code" title="%s">%s</a>';
tpl_mfile_keyword = '<span class="keyword">%s</span>';
tpl_mfile_comment = '<span class="comment">%s</span>';
tpl_mfile_string = '<span class="string">%s</span>';
tpl_mfile_aname = '<a name="%s" href="#_subfunctions" class="code">%s</a>';
tpl_mfile_line = '%04d %s\n';
%- Delimiters used in strtok: some of them may be useless (% " .), removed '.'
strtok_delim = sprintf(' \t\n\r(){}[]<>+-*~!|\\@&/,:;="''%%');
%- Create the HTML template
tpl = template(options.template,'remove');
tpl = set(tpl,'file','TPL_MFILE',tpl_mfile);
tpl = set(tpl,'block','TPL_MFILE','pathline','pl');
tpl = set(tpl,'block','TPL_MFILE','mexfile','mex');
tpl = set(tpl,'block','TPL_MFILE','script','scriptfile');
tpl = set(tpl,'block','TPL_MFILE','crossrefcall','crossrefcalls');
tpl = set(tpl,'block','TPL_MFILE','crossrefcalled','crossrefcalleds');
tpl = set(tpl,'block','TPL_MFILE','subfunction','subf');
tpl = set(tpl,'block','subfunction','onesubfunction','onesubf');
tpl = set(tpl,'block','TPL_MFILE','source','thesource');
tpl = set(tpl,'var','DATE',[datestr(now,8) ' ' datestr(now,1) ' ' ...
datestr(now,13)]);
for i=1:length(mdir)
for j=1:length(mdirs)
if strcmp(mdirs{j},mdir{i})
curfile = fullfile(options.htmlDir,mdir{i},...
[names{j} options.extension]);
%- Open for writing the HTML file
if options.verbose
fprintf('Creating HTML file %s...\n',curfile);
end
fid = openfile(curfile,'w');
%- Open for reading the M-file
fid2 = openfile(mfiles{j},'r');
%- Set some template fields
tpl = set(tpl,'var','INDEX', [options.indexFile options.extension]);
tpl = set(tpl,'var','MASTERPATH', backtomaster(mdir{i}));
tpl = set(tpl,'var','MDIR', mdirs{j});
tpl = set(tpl,'var','NAME', names{j});
tpl = set(tpl,'var','H1LINE', h1line{j});
tpl = set(tpl,'var','scriptfile', '');
if isempty(synopsis{j})
tpl = set(tpl,'var','SYNOPSIS',get(tpl,'var','script'));
else
tpl = set(tpl,'var','SYNOPSIS', synopsis{j});
end
s = splitpath(mdir{i});
tpl = set(tpl,'var','pl','');
for k=1:length(s)
c = cell(1,k); for l=1:k, c{l} = filesep; end
cpath = {s{1:k};c{:}}; cpath = [cpath{:}];
if ~isempty(cpath), cpath = cpath(1:end-1); end
if ismember(cpath,mdir)
tpl = set(tpl,'var','LPATHDIR',[repmat('../',...
1,length(s)-k) options.indexFile options.extension]);
else
tpl = set(tpl,'var','LPATHDIR','#');
end
tpl = set(tpl,'var','PATHDIR',s{k});
tpl = parse(tpl,'pl','pathline',1);
end
%- Handle mex files
tpl = set(tpl,'var','mex', '');
samename = dir(fullfile(mdir{i},[names{j} '.*']));
samename = {samename.name};
for k=1:length(samename)
[dummy, dummy, ext] = fileparts(samename{k});
switch ext
case '.c'
tpl = set(tpl,'var','MEXTYPE', 'c');
case {'.cpp' '.c++' '.cxx' '.C'}
tpl = set(tpl,'var','MEXTYPE', 'c++');
case {'.for' '.f' '.FOR' '.F'}
tpl = set(tpl,'var','MEXTYPE', 'fortran');
end
end
[exts, platform] = mexexts;
mexplatforms = sprintf('%s, ',platform{find(ismex(j,:))});
if ~isempty(mexplatforms)
tpl = set(tpl,'var','PLATFORMS', mexplatforms(1:end-2));
tpl = parse(tpl,'mex','mexfile');
end
%- Set description template field
descr = '';
flagsynopcont = 0;
flag_seealso = 0;
while 1
tline = fgets(fid2);
if ~ischar(tline), break, end
tline = entity(fliplr(deblank(fliplr(tline))));
%- Synopsis line
if ~isempty(strmatch('function',tline))
if ~isempty(strmatch('...',fliplr(deblank(tline))))
flagsynopcont = 1;
end
%- H1 line and description
elseif ~isempty(strmatch('%',tline))
%- Hypertext links on the "See also" line
ind = findstr(lower(tline),'see also');
if ~isempty(ind) | flag_seealso
%- "See also" only in files in the same directory
indsamedir = find(strcmp(mdirs{j},mdirs));
hrefnames = {names{indsamedir}};
r = deblank(tline);
flag_seealso = 1; %(r(end) == ',');
tline = '';
while 1
[t,r,q] = strtok(r,sprintf(' \t\n\r.,;%%'));
tline = [tline q];
if isempty(t), break, end;
ii = strcmpi(hrefnames,t);
if any(ii)
jj = find(ii);
tline = [tline sprintf(tpl_mfile_code,...
[hrefnames{jj(1)} options.extension],...
synopsis{indsamedir(jj(1))},t)];
else
tline = [tline t];
end
end
tline = sprintf('%s\n',tline);
end
descr = [descr tline(2:end)];
elseif isempty(tline)
if ~isempty(descr), break, end;
else
if flagsynopcont
if isempty(strmatch('...',fliplr(deblank(tline))))
flagsynopcont = 0;
end
else
break;
end
end
end
tpl = set(tpl,'var','DESCRIPTION',...
horztab(descr,options.tabs));
%- Set cross-references template fields:
% Function called
ind = find(hrefs(j,:) == 1);
tpl = set(tpl,'var','crossrefcalls','');
for k=1:length(ind)
if strcmp(mdirs{j},mdirs{ind(k)})
tpl = set(tpl,'var','L_NAME_CALL', ...
[names{ind(k)} options.extension]);
else
tpl = set(tpl,'var','L_NAME_CALL', ...
fullurl(backtomaster(mdirs{j}), ...
mdirs{ind(k)}, ...
[names{ind(k)} options.extension]));
end
tpl = set(tpl,'var','SYNOP_CALL', synopsis{ind(k)});
tpl = set(tpl,'var','NAME_CALL', names{ind(k)});
tpl = set(tpl,'var','H1LINE_CALL', h1line{ind(k)});
tpl = parse(tpl,'crossrefcalls','crossrefcall',1);
end
% Callers
ind = find(hrefs(:,j) == 1);
tpl = set(tpl,'var','crossrefcalleds','');
for k=1:length(ind)
if strcmp(mdirs{j},mdirs{ind(k)})
tpl = set(tpl,'var','L_NAME_CALLED', ...
[names{ind(k)} options.extension]);
else
tpl = set(tpl,'var','L_NAME_CALLED', ...
fullurl(backtomaster(mdirs{j}),...
mdirs{ind(k)}, ...
[names{ind(k)} options.extension]));
end
tpl = set(tpl,'var','SYNOP_CALLED', synopsis{ind(k)});
tpl = set(tpl,'var','NAME_CALLED', names{ind(k)});
tpl = set(tpl,'var','H1LINE_CALLED', h1line{ind(k)});
tpl = parse(tpl,'crossrefcalleds','crossrefcalled',1);
end
%- Set subfunction template field
tpl = set(tpl,'var',{'subf' 'onesubf'},{'' ''});
if ~isempty(subroutine{j}) & options.source
for k=1:length(subroutine{j})
tpl = set(tpl, 'var', 'L_SUB', ['#_sub' num2str(k)]);
tpl = set(tpl, 'var', 'SUB', subroutine{j}{k});
tpl = parse(tpl, 'onesubf', 'onesubfunction',1);
end
tpl = parse(tpl,'subf','subfunction');
end
subname = extractname(subroutine{j});
%- Display source code with cross-references
if options.source & ~strcmpi(names{j},'contents')
fseek(fid2,0,-1);
it = 1;
matlabsource = '';
nbsubroutine = 1;
%- Get href function names of this file
indhrefnames = find(hrefs(j,:) == 1);
hrefnames = {names{indhrefnames}};
%- Loop over lines
while 1
tline = fgetl(fid2);
if ~ischar(tline), break, end
myline = '';
splitc = splitcode(entity(tline));
for k=1:length(splitc)
if isempty(splitc{k})
elseif ~isempty(strmatch('function',splitc{k}))
%- Subfunctions definition
myline = [myline ...
sprintf(tpl_mfile_aname,...
['_sub' num2str(nbsubroutine-1)],splitc{k})];
nbsubroutine = nbsubroutine + 1;
elseif splitc{k}(1) == ''''
myline = [myline ...
sprintf(tpl_mfile_string,splitc{k})];
elseif splitc{k}(1) == '%'
myline = [myline ...
sprintf(tpl_mfile_comment,deblank(splitc{k}))];
elseif ~isempty(strmatch('...',splitc{k}))
myline = [myline sprintf(tpl_mfile_keyword,'...')];
if ~isempty(splitc{k}(4:end))
myline = [myline ...
sprintf(tpl_mfile_comment,splitc{k}(4:end))];
end
else
%- Look for keywords
r = splitc{k};
while 1
[t,r,q] = strtok(r,strtok_delim);
myline = [myline q];
if isempty(t), break, end;
%- Highlight Matlab keywords &
% cross-references on known functions
if options.syntaxHighlighting & ...
any(strcmp(matlabKeywords,t))
if strcmp('end',t)
rr = fliplr(deblank(fliplr(r)));
icomma = strmatch(',',rr);
isemicolon = strmatch(';',rr);
if ~(isempty(rr) | ~isempty([icomma isemicolon]))
myline = [myline t];
else
myline = [myline sprintf(tpl_mfile_keyword,t)];
end
else
myline = [myline sprintf(tpl_mfile_keyword,t)];
end
elseif any(strcmp(hrefnames,t))
indt = indhrefnames(logical(strcmp(hrefnames,t)));
flink = [t options.extension];
ii = ismember({mdirs{indt}},mdirs{j});
if ~any(ii)
% take the first one...
flink = fullurl(backtomaster(mdirs{j}),...
mdirs{indt(1)}, flink);
else
indt = indt(logical(ii));
end
myline = [myline sprintf(tpl_mfile_code,...
flink, synopsis{indt(1)}, t)];
elseif any(strcmp(subname,t))
ii = find(strcmp(subname,t));
myline = [myline sprintf(tpl_mfile_code,...
['#_sub' num2str(ii)],...
['sub' subroutine{j}{ii}],t)];
else
myline = [myline t];
end
end
end
end
matlabsource = [matlabsource sprintf(tpl_mfile_line,it,myline)];
it = it + 1;
end
tpl = set(tpl,'var','SOURCECODE',...
horztab(matlabsource,options.tabs));
tpl = parse(tpl,'thesource','source');
else
tpl = set(tpl,'var','thesource','');
end
tpl = parse(tpl,'OUT','TPL_MFILE');
fprintf(fid,'%s',get(tpl,'OUT'));
fclose(fid2);
fclose(fid);
end
end
end
%===============================================================================
function mfiles = getmfiles(mdirs,mfiles,recursive)
%- Extract M-files from a list of directories and/or M-files
for i=1:length(mdirs)
if exist(mdirs{i}) == 2 % M-file
mfiles{end+1} = mdirs{i};
elseif exist(mdirs{i}) == 7 % Directory
w = what(mdirs{i});
w = w(1); %- Sometimes an array is returned...
for j=1:length(w.m)
mfiles{end+1} = fullfile(mdirs{i},w.m{j});
end
if recursive
d = dir(mdirs{i});
d = {d([d.isdir]).name};
d = {d{~ismember(d,{'.' '..'})}};
for j=1:length(d)
mfiles = getmfiles(cellstr(fullfile(mdirs{i},d{j})),...
mfiles,recursive);
end
end
else
fprintf('Warning: Unprocessed file %s.\n',mdirs{i});
end
end
%===============================================================================
function s = backtomaster(mdir)
%- Provide filesystem path to go back to the root folder
ldir = splitpath(mdir);
s = repmat('../',1,length(ldir));
%===============================================================================
function ldir = splitpath(p)
%- Split a filesystem path into parts using filesep as separator
ldir = {};
p = deblank(p);
while 1
[t,p] = strtok(p,filesep);
if isempty(t), break; end
if ~strcmp(t,'.')
ldir{end+1} = t;
end
end
if isempty(ldir)
ldir{1} = '.'; % should be removed
end
%===============================================================================
function name = extractname(synopsis)
if ischar(synopsis), synopsis = {synopsis}; end
name = cell(size(synopsis));
for i=1:length(synopsis)
ind = findstr(synopsis{i},'=');
if isempty(ind)
ind = findstr(synopsis{i},'function');
s = synopsis{i}(ind(1)+8:end);
else
s = synopsis{i}(ind(1)+1:end);
end
name{i} = strtok(s,[9:13 32 '(']);
end
if length(name) == 1, name = name{1}; end
%===============================================================================
function f = fullurl(varargin)
%- Build full url from parts (using '/' and not filesep)
f = strrep(fullfile(varargin{:}),'\','/');
%===============================================================================
function str = entity(str)
%- See http://www.w3.org/TR/html4/charset.html#h-5.3.2
str = strrep(str,'&','&');
str = strrep(str,'<','<');
str = strrep(str,'>','>');
str = strrep(str,'"','"');
%===============================================================================
function str = horztab(str,n)
%- For browsers, the horizontal tab character is the smallest non-zero
%- number of spaces necessary to line characters up along tab stops that are
%- every 8 characters: behaviour obtained when n = 0.
if n > 0
str = strrep(str,sprintf('\t'),blanks(n));
end
|
github
|
EPFL-LCSB/matTFA-master
|
qpsolng.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/glpkmex/qpsolng.m
| 2,447 |
utf_8
|
4b2e7f7c92565cb039eed9907693651d
|
% Core QP Solver. Use qpng.m instead.
%
% This routine solves the following optimization problem:
%
% min_x .5x' H x + q' x
% s.t. Aeq x = beq
% Ain x <= bin
%
% note that x0 is a feasible starting point.
%
% (C) Nicolo Giorgetti, 2006.
function [x, lam, k, status]=qpsolng(H, q, Aeq, beq, Ain, bin, x0)
nmax=200; % max number of iterations
tol=1e-6; % tolerance
neq=length(beq); % number of eqs
nin=length(bin); % number of ineqs
x=x0;
n=size(x);
Wact=[];
nact=0; % number of rows in Wact (only active inequalities)
status=1; % problem feasible
lam=zeros(neq+nin,1);
k=[];
for k=1:nmax
% Construct KKT
K=H;
r=-q-H*x;
if neq > 0
% Add equality constraints
A=Aeq;
end
if nin > 0
% Add active inequality constraints
for j=1:nact
i=Wact(j);
if j+neq==1
A=Ain(i,:);
else
A=[A; Ain(i,:)];
end
end
end
nneq=neq+nact;
if nneq>0
K=[K, A'; A, zeros(nneq,nneq)];
r=[r; zeros(nneq,1)];
end
y=K\r; %%%%%%%% Check this: we should use pinv instead. Possible numerical problems
p=y(1:n);
if norm(p)<tol
% check optimality or add to work set
if nact==0
x=x+p;
status=1;
return % successfully
else
lam=y(n+neq+1:n+neq+nact);
[lmin,arg]=min(lam);
if lmin >= 0
x=x+p;
status=1;
return; % successfully
else
% remove constraints from W
nact=nact-1;
for j=arg:nact
Wact(j)=Wact(j+1);
end
end
end
else % x is not the minimizer in W
count=nin+1;
val(1:count)=1.1;
for j=1:nin
if Ain(j,1:n)*p > max(tol^2,1e-15)
val(j)=(bin(j)-Ain(j,1:n)*x)/(Ain(j,1:n)*p);
end
end
val(count)=1;
[alpha,ind]=min(val); % this is the allowed step size
x=x+alpha*p;
if ind < count % there are blocking constraints, add one to W
nact=nact+1;
Wact(nact)=ind;
end
end
end
eq_infeas=0;
in_infeas=0;
if neq>0
eq_infeas = (norm(Aeq*x-beq) > rtol*(1+norm(beq)));
end
if nin>0
in_infeas = (any(Ain*x-bin > -rtol*(1+norm(bin))));
end
if eq_infeas | in_infeas
status=2; % Max iterations reached, no solution found.
else
status=3; % Max iterations reached but a feasible solution found.
end
return;
|
github
|
EPFL-LCSB/matTFA-master
|
qpng.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/glpkmex/qpng.m
| 8,266 |
utf_8
|
a76ee167df8e11072eea16b6f9407482
|
% Quadratic programming solver using a null-space active-set method.
%
% [x, obj, lambda, info] = qpng (H, q, A, b, ctype, lb, ub, x0)
%
% Solve the general quadratic program
%
% min 0.5 x'*H*x + q'*x
% x
%
% subject to
% A*x [ "=" | "<=" | ">=" ] b
% lb <= x <= ub
%
% and given x0 as initial guess.
%
% ctype = An array of characters containing the sense of each constraint in the
% constraint matrix. Each element of the array may be one of the
% following values
% 'U' Variable with upper bound ( A(i,:)*x <= b(i) ).
% 'E' Fixed Variable ( A(i,:)*x = b(i) ).
% 'L' Variable with lower bound ( A(i,:)*x >= b(i) ).
%
% status = an integer indicating the status of the solution, as follows:
% 0 The problem is infeasible.
% 1 The problem is feasible and convex. Global solution found.
% 2 Max number of iterations reached no feasible solution found.
% 3 Max number of iterations reached but a feasible solution found.
%
% If only 4 arguments are provided the following QP problem is solved:
%
% min_x .5 x'*H*x+x'*q s.t. A*x <= b
%
% Any bound (ctype, lb, ub, x0) may be set to the empty matrix []
% if not present. If the initial guess is feasible the algorithm is faster.
%
% See also: glpk.
%
% Copyright 2006-2007 Nicolo Giorgetti.
% This file is part of GLPKMEX.
%
% GLPKMEX is free software; you can redistribute it and/or modify it
% under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2, or (at your option)
% any later version.
%
% GLPKMEX is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with GLPKMEX; see the file COPYING. If not, write to the Free
% Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
% 02110-1301, USA.
function varargout = qpng (varargin)
% Inputs
H=[];
q=[];
A=[];
b=[];
lb=[];
ub=[];
x0=[];
ctype=[];
% Outputs
x=[];
obj=[];
lambda=[];
info=[];
if nargin < 1
disp('Quadratic programming solver using null-space active set method.');
disp('(C) 2006-2007, Nicolo Giorgetti. Version 1.0');
disp(' ');
disp('Syntax: [x, obj, lambda, info] = qpng (H, q, A, b, ctype, lb, ub, x0)');
return;
end
if nargin<4
error('At least 4 argument are necessary');
else
H=varargin{1};
q=varargin{2};
A=varargin{3};
b=varargin{4};
end
if nargin>=5
ctype=varargin{5};
end
if nargin>=7
lb=varargin{6};
ub=varargin{7};
end
if nargin>=8
x0=varargin{8};
end
if nargin>8
warning('qpng: Arguments more the 8th are omitted');
end
% Checking the quadratic penalty
[n,m] = size(H);
if n ~= m
error('qpng: Quadratic penalty matrix not square');
end
if H ~= H'
warning('qpng: Quadratic penalty matrix not symmetric');
H = (H + H')/2;
end
% Linear penalty.
if isempty(q)
q=zeros(n,1);
else
if length(q) ~= n
error('qpng: The linear term has incorrect length');
end
end
% Constraint matrices
if (isempty(A) || isempty(b))
error('qpng: Constraint matrices cannot be empty');
end
[nn, n1] = size(A);
if n1 ~= n
error('qpng: Constraint matrix has incorrect column dimension');
end
if length (b) ~= nn
error ('qpng: Equality constraint matrix and vector have inconsistent dimension');
end
Aeq=[];
beq=[];
Ain=[];
bin=[];
if nargin <= 4
Ain=A;
bin=b;
end
if ~isempty(ctype)
if length(ctype) ~= nn
tmp=sprintf('qpng: ctype must be a char valued vector of length %d', nn);
error(tmp);
end
indE=find(ctype=='E');
Aeq=A(indE,:);
beq=b(indE,:);
indU=find(ctype=='U');
Ain=A(indU,:);
bin=b(indU,:);
indL=find(ctype=='L');
Ain=[Ain; -A(indL,:)];
bin=[bin; -b(indL,:)];
end
if ~isempty(lb)
if length(lb) ~= n
error('qpng: Lower bound has incorrect length');
else
Ain = [Ain; -eye(n)];
bin = [bin; -lb];
end
end
if ~isempty(ub)
if length(ub) ~= n
error('qpng: Upper bound has incorrect length');
else
Ain = [Ain; eye(n)];
bin = [bin; ub];
end
end
% Discard inequality constraints that have -Inf bounds since those
% will never be active.
idx = isinf(bin) & (bin > 0);
bin(idx) = [];
Ain(idx,:) = [];
% Now we should have the following QP:
%
% min_x 0.5*x'*H*x + q'*x
% s.t. A*x = b
% Ain*x <= bin
% Checking the initial guess (if empty it is resized to the
% right dimension and filled with 0)
if isempty(x0)
x0 = zeros(n, 1);
elseif length(x0) ~= n
error('qpng: The initial guess has incorrect length');
end
% Check if the initial guess is feasible.
rtol = sqrt (eps);
n_eq=size(Aeq,1);
n_in=size(Ain,1);
eq_infeasible=0;
in_infeasible=0;
if n_eq>0
eq_infeasible = (norm(Aeq*x0-beq) > rtol*(1+norm(beq)));
end
if n_in>0
in_infeasible = any(Ain*x0-bin > 0);
end
status = 1;
% if (eq_infeasible | in_infeasible)
% % The initial guess is not feasible. Find one by solving an LP problem.
% % This function has to be improved by moving in the null space.
% Atmp=[Aeq; Ain];
% btmp=[beq; bin];
% ctmp=zeros(size(Atmp,2),1);
% ctype=char(['S'*ones(1,n_eq), 'U'*ones(1,n_in)]');
% [P, dummy, stat] = glpk (ctmp, Atmp, btmp, [], [], ctype);
%
% if (stat == 180 | stat == 181 | stat == 151)
% x0=P;
% else
% % The problem is infeasible
% status = 0;
% end
%
% end
if (eq_infeasible | in_infeasible)
% The initial guess is not feasible.
% First define xbar that is feasible with respect to the equality
% constraints.
if (eq_infeasible)
if (rank(Aeq) < n_eq)
error('qpng: Equality constraint matrix must be full row rank')
end
xbar = pinv(Aeq) * beq;
else
xbar = x0;
end
% Check if xbar is feasible with respect to the inequality
% constraints also.
if (n_in > 0)
res = Ain * xbar - bin;
if any(res > 0)
% xbar is not feasible with respect to the inequality
% constraints. Compute a step in the null space of the
% equality constraints, by solving a QP. If the slack is
% small, we have a feasible initial guess. Otherwise, the
% problem is infeasible.
if (n_eq > 0)
Z = null(Aeq);
if (isempty(Z))
% The problem is infeasible because A is square and full
% rank, but xbar is not feasible.
info = 0;
end
end
if info
% Solve an LP with additional slack variables to find
% a feasible starting point.
gamma = eye(n_in);
if (n_eq > 0)
Atmp = [Ain*Z, gamma];
btmp = -res;
else
Atmp = [Ain, gamma];
btmp = bin;
end
ctmp = [zeros(n-n_eq, 1); ones(n_in, 1)];
lb = [-Inf*ones(n-n_eq,1); zeros(n_in,1)];
ub = [];
ctype = repmat ('L', n_in, 1);
[P, dummy, status] = glpk (ctmp, Atmp, btmp, lb, ub, ctype);
if ((status == 180 | status == 181 | status == 151) & all (abs (P(n-n_eq+1:end)) < rtol * (1 + norm (btmp))))
% We found a feasible starting point
if (n_eq > 0)
x0 = xbar + Z*P(1:n-n_eq);
else
x0 = P(1:n);
end
else
% The problem is infeasible
info = 0;
end
end
else
% xbar is feasible. We use it a starting point.
x0 = xbar;
end
else
% xbar is feasible. We use it a starting point.
x0 = xbar;
end
end
if status
% The initial (or computed) guess is feasible.
% We call the solver.
t=cputime;
[x, lambda, iter, status]=qpsolng(H, q, Aeq, beq, Ain, bin, x0);
time=cputime-t;
else
iter = 0;
x = x0;
lambda = [];
time=0;
end
varargout{1}= x;
varargout{2}= 0.5 * x' * H * x + q' * x; %obj
varargout{3}= lambda;
info=struct('status', status, 'solveiter', iter, 'time', time);
varargout{4}=info;
|
github
|
EPFL-LCSB/matTFA-master
|
glpk.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/glpkmex/glpk.m
| 20,365 |
utf_8
|
d8e67c6977ba79760299289ebfca225f
|
% Matlab MEX interface for the GLPK library
%
% [xopt, fmin, status, extra] = glpk (c, a, b, lb, ub, ctype, vartype,
% sense, param)
%
% Solve an LP/MILP problem using the GNU GLPK library. Given three
% arguments, glpk solves the following standard LP:
%
% min C'*x subject to A*x <= b
%
% but may also solve problems of the form
%
% [ min | max ] C'*x
% subject to
% A*x [ "=" | "<=" | ">=" ] b
% x >= LB
% x <= UB
%
% Input arguments:
% c = A column array containing the objective function coefficients.
%
% A = A matrix containing the constraints coefficients.
%
% b = A column array containing the right-hand side value for each constraint
% in the constraint matrix.
%
% lb = An array containing the lower bound on each of the variables. If
% lb is not supplied (or an empty array) the default lower bound for the variables is
% minus infinite.
%
% ub = An array containing the upper bound on each of the variables. If
% ub is not supplied (or an empty array) the default upper bound is assumed to be
% infinite.
%
% ctype = An array of characters containing the sense of each constraint in the
% constraint matrix. Each element of the array may be one of the
% following values
% 'F' Free (unbounded) variable (the constraint is ignored).
% 'U' Variable with upper bound ( A(i,:)*x <= b(i)).
% 'S' Fixed Variable (A(i,:)*x = b(i)).
% 'L' Variable with lower bound (A(i,:)*x >= b(i)).
% 'D' Double-bounded variable (A(i,:)*x >= -b(i) and A(i,:)*x <= b(i)).
%
% vartype = A column array containing the types of the variables.
% 'C' Continuous variable.
% 'I' Integer variable
% 'B' Binary variable
%
% sense = If sense is 1, the problem is a minimization. If sense is
% -1, the problem is a maximization. The default value is 1.
%
% param = A structure containing the following parameters used to define the
% behavior of solver. Missing elements in the structure take on default
% values, so you only need to set the elements that you wish to change
% from the default.
%
% Integer parameters:
% msglev (default: 1)
% Level of messages output by solver routines:
% 0 - No output.
% 1 - Error messages only.
% 2 - Normal output.
% 3 - Full output (includes informational messages).
%
% scale (default: 1). Scaling option:
% 0 - No scaling.
% 1 - Equilibration scaling.
% 2 - Geometric mean scaling, then equilibration scaling.
% 3 - Geometric then Equilibrium scaling
% 4 - Round to nearest power of 2 scaling
%
% dual (default: 0). Dual simplex option:
% 0 - Do not use the dual simplex.
% 1 - If initial basic solution is dual feasible, use
% the dual simplex.
% 2- Use two phase dual simplex, or if primal simplex
% if dual fails
%
% price (default: 1). Pricing option (for both primal and dual simplex):
% 0 - Textbook pricing.
% 1 - Steepest edge pricing.
%
% r_test (default: 1). Ratio test Technique:
% 0 - stardard (textbook)
% 1 - Harris's two-pass ratio test
%
% round (default: 0). Solution rounding option:
%
% 0 - Report all primal and dual values "as is".
% 1 - Replace tiny primal and dual values by exact zero.
%
% itlim (default: -1). Simplex iterations limit.
% If this value is positive, it is decreased by one each
% time when one simplex iteration has been performed, and
% reaching zero value signals the solver to stop the search.
% Negative value means no iterations limit.
%
% itcnt (default: 200). Output frequency, in iterations.
% This parameter specifies how frequently the solver sends
% information about the solution to the standard output.
%
% presol (default: 1). If this flag is set, the routine
% lpx_simplex solves the problem using the built-in LP presolver.
% Otherwise the LP presolver is not used.
%
% lpsolver (default: 1) Select which solver to use.
% If the problem is a MIP problem this flag will be ignored.
% 1 - Revised simplex method.
% 2 - Interior point method.
% 3 - Simplex method with exact arithmatic.
%
% branch (default: 2). Branching heuristic option (for MIP only):
% 0 - Branch on the first variable.
% 1 - Branch on the last variable.
% 2 - Branch on the most fractional variable.
% 3 - Branch using a heuristic by Driebeck and Tomlin.
%
% btrack (default: 2). Backtracking heuristic option (for MIP only):
% 0 - Depth first search.
% 1 - Breadth first search.
% 2 - best local bound
% 3 - Backtrack using the best projection heuristic.
%
% pprocess (default: 2) Pre-processing technique option ( for MIP only ):
% 0 - disable preprocessing
% 1 - perform preprocessing for root only
% 2 - perform preprocessing for all levels
%
% usecuts (default: 1). ( for MIP only ):
% glp_intopt generates and adds cutting planes to
% the MIP problem in order to improve its LP relaxation
% before applying the branch&bound method
% 0 -> all cuts off
% 1 -> Gomoy's mixed integer cuts
% 2 -> Mixed integer rounding cuts
% 3 -> Mixed cover cuts
% 4 -> Clique cuts
% 5 -> all cuts
%
% binarize (default: 0 ) Binarizeation option ( for mip only ):
% ( used only if presolver is enabled )
% 0 -> do not use binarization
% 1 -> replace general integer variables by binary ones
%
% save (default: 0). If this parameter is nonzero save a copy of
% the original problem to file. You can specify the
% file name and format by using the 'savefilename' and 'savefiletype'
% parameters (see in String Parameters Section here below).
% If previous parameters are not defined the original problem
% is saved with CPLEX LP format in the default file "outpb.lp".
%
% mpsinfo (default: 1) If this is set,
% the interface writes to file several comment cards,
% which contains some information about the problem.
% Otherwise the routine writes no comment cards.
%
% mpsobj ( default: 2) This parameter tells the
% routine how to output the objective function row:
% 0 - never output objective function row
% 1 - always output objective function row
% 2 - output objective function row if the problem has
% no free rows
%
% mpsorig (default: 0) If this is set, the
% routine uses the original symbolic names of rows and
% columns. Otherwise the routine generates plain names
% using ordinal numbers of rows and columns.
%
% mpswide (default: 1) If this is set, the
% routine uses all data fields. Otherwise the routine
% keeps fields 5 and 6 empty.
%
% mpsfree (default: 0) If this is set, the routine
% omits column and vector names every time when possible
% (free style). Otherwise the routine never omits these
% names (pedantic style).
%
%
% Real parameters:
% relax (default: 0.07). Relaxation parameter used
% in the ratio test. If it is zero, the textbook ratio test
% is used. If it is non-zero (should be positive), Harris'
% two-pass ratio test is used. In the latter case on the
% first pass of the ratio test basic variables (in the case
% of primal simplex) or reduced costs of non-basic variables
% (in the case of dual simplex) are allowed to slightly violate
% their bounds, but not more than relax*tolbnd or relax*toldj
% (thus, relax is a percentage of tolbnd or toldj).
%
% tolbnd (default: 10e-7). Relative tolerance used
% to check ifthe current basic solution is primal feasible.
% It is not recommended that you change this parameter
% unless you have a detailed understanding of its purpose.
%
% toldj (default: 10e-7). Absolute tolerance used to
% check if the current basic solution is dual feasible. It
% is not recommended that you change this parameter unless
% you have a detailed understanding of its purpose.
%
% tolpiv (default: 10e-9). Relative tolerance used
% to choose eligible pivotal elements of the simplex table.
% It is not recommended that you change this parameter
% unless you have a detailed understanding of its purpose.
%
% objll ( default: -DBL_MAX). Lower limit of the
% objective function. If on the phase II the objective
% function reaches this limit and continues decreasing, the
% solver stops the search. This parameter is used in the
% dual simplex method only.
%
% objul (default: +DBL_MAX). Upper limit of the
% objective function. If on the phase II the objective
% function reaches this limit and continues increasing,
% the solver stops the search. This parameter is used in
% the dual simplex only.
%
% tmlim (default: -1.0). Searching time limit, in
% seconds. If this value is positive, it is decreased each
% time when one simplex iteration has been performed by the
% amount of time spent for the iteration, and reaching zero
% value signals the solver to stop the search. Negative
% value means no time limit.
%
% outdly (default: 0.0). Output delay, in seconds.
% This parameter specifies how long the solver should
% delay sending information about the solution to the standard
% output. Non-positive value means no delay.
%
% tolint (default: 10e-5). Relative tolerance used
% to check if the current basic solution is integer
% feasible. It is not recommended that you change this
% parameter unless you have a detailed understanding of
% its purpose.
%
% tolobj (default: 10e-7). Relative tolerance used
% to check if the value of the objective function is not
% better than in the best known integer feasible solution.
% It is not recommended that you change this parameter
% unless you have a detailed understanding of its purpose.
%
% mipgap (default: 0.0) The relative mip gap tolerance. If the
% relative mip gap for currently known best integer feasible
% solution falls below this tolerance, the solver terminates
% the search. This allows obtaining suboptimal interger
% feasible solutions if solving the problem to optimality
% takes too long.
%
% String Parameters:
% savefilename (default: "outpb"). Specify the name to use to
% save the original problem. MEX interface looks for
% this parameter if 'save' parameter is set to 1. If
% no name is provided "outpb" will be used.
% savefiletype (default: CPLEX format). Specify the format type
% used to save the file. Only the following options
% are allowed:
% 'fixedmps' - fixed MPS format (.mps).
% 'freemps' - free MPS format (.mps).
% 'cplex' - CPLEX LP format (.lp).
% 'plain' - plain text (.txt).
%
% Output values:
% xopt = The optimizer (the value of the decision variables at the optimum).
%
% fopt = The optimum value of the objective function.
%
% status = Status of the optimization.
% 1 solution is undefined
% 2 solution is feasible
% 3 solution is infeasible
% 4 no feasible solution exists
% 5 solution is optimal
% 6 solution is unbounded
%
% If an error occurs, status will contain one of the following
% codes.
% Simplex method:
% 101 invalid basis
% 102 singular matrix
% 103 ill-conditioned matrix
% 104 invalid bounds
% 105 solver failed
% 106 objective lower limit reached
% 107 objective upper limit reached
% 108 iteration limit exceeded
% 109 time limit exceeded
% 110 no primal feasible solution
%
% Interior point method, mixed integer problem:
% 204 Unable to start the search.
% 205 Objective function lower limit reached.
% 206 Objective function upper limit reached.
% 207 Iterations limit exhausted.
% 208 Time limit exhausted.
% 209 No feasible solution.
% 210 Numerical instability.
% 211 Problems with basis matrix.
% 212 No convergence (interior).
% 213 No primal feasible solution (LP presolver).
% 214 No dual feasible solution (LP presolver).
%
% extra = A data structure containing the following fields:
% lambda - Dual variables.
% redcosts - Reduced Costs.
% time - Time (in seconds) used for solving LP/MIP problem.
% mem - Memory (in Kbytes) used for solving LP/MIP problem.
%
% Example:
%
% c = [10, 6, 4]';
% a = [ 1, 1, 1;
% 10, 4, 5;
% 2, 2, 6];
% b = [100, 600, 300]';
% lb = [0, 0, 0]';
% ub = [];
% ctype = "UUU";
% vartype = "CCC";
% s = -1;
%
% param.msglev = 1;
% param.itlim = 100;
%
% [xmin, fmin, status, extra] = ...
% glpk (c, a, b, lb, ub, ctype, vartype, s, param);
%
% See also: qpng.
%
% Copyright 2005-2007 Nicolo' Giorgetti
% Email: Nicolo' Giorgetti <giorgetti __at __ ieee.org>
% updated by Niels Klitgord March 2009
% Email: Niels Klitgord <niels __at__ bu.edu>
% This file is part of GLPKMEX.
%
% GLPKMEX is free software; you can redistribute it and/or modify it
% under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2, or (at your option)
% any later version.
%
% This part of code is distributed with the FURTHER condition that it
% can be linked to the Matlab libraries and/or use it inside the Matlab
% environment.
%
% GLPKMEX is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with GLPKMEX; see the file COPYING. If not, write to the Free
% Software Foundation, 59 Temple Place - Suite 330, Boston, MA
% 02111-1307, USA.
function [xopt,fmin,status,extra] = glpk (c,a,b,lb,ub,ctype,vartype,sense,param)
% If there is no input output the version and syntax
if (nargin < 3 || nargin > 9)
disp('GLPK Matlab interface. Version: 2.7');
disp('(C) 2001-2007, Nicolo'' Giorgetti.');
disp('Maintained by Niels Klitgord');
disp(' ');
disp('Syntax: [xopt,fopt,status,extra]=glpk(c,a,b,lb,ub,ctype,vartype,sense,param)');
return;
end
if (all(size(c) > 1) || ~isreal(c) || ischar(c))
error('C must be a real vector');
end
% clears glpkcc mex function from memory to deal with param bug
% this is because params not specificly set default to the last used rather
% than internal defaults for some reason....
clear glpkcc;
nx = length (c);
% 1) Force column vector.
c = c(:);
% 2) Matrix constraint
if (isempty(a))
error('A cannot be an empty matrix');
end
[nc, nxa] = size(a);
if (~isreal(a) || nxa ~= nx)
tmp=sprintf('A must be a real valued %d by %d matrix', nc, nx);
error(tmp);
return;
end
% 3) RHS
if (isempty(b))
error('B cannot be an empty vector');
end
if (~isreal(b) || length(b) ~= nc)
tmp=sprintf('B must be a real valued %d by 1 vector', nc);
error (tmp);
return;
end
% 4) Vector with the lower bound of each variable
if (nargin > 3)
if (isempty(lb))
lb = repmat(-Inf, nx, 1);
elseif (~isreal(lb) || all(size(lb) > 1) || length(lb) ~= nx)
tmp=sprintf('LB must be a real valued %d by 1 column vector', nx);
error (tmp);
return;
end
else
lb = -Inf*ones(nx, 1);
end
% 5) Vector with the upper bound of each variable
if (nargin > 4)
if (isempty(ub))
ub = repmat(Inf, nx, 1);
elseif (~isreal(ub) || all(size(ub) > 1) || length(ub) ~= nx)
tmp=sprintf('UB must be a real valued %d by 1 column vector', nx);
error (tmp);
return;
end
else
ub = repmat(Inf, nx, 1);
end
% 6) Sense of each constraint
if (nargin > 5)
if (isempty (ctype))
ctype = repmat('U', nc, 1);
elseif (~ischar(ctype) || all(size(ctype) > 1) || length(ctype) ~= nc)
tmp=sprintf('CTYPE must be a char valued vector of length %d', nc);
error(tmp);
return;
else
for i=1:length(ctype)
switch(ctype(i))
case {'f','F'}, % do nothing
case {'u','U'}, % do nothing
case {'s','S'}, % do nothing
case {'l','L'}, % do nothing
case {'d','D'}, % do nothing
otherwise
tmp=sprintf('CTYPE must contain only F, U, S, L, or D');
error(tmp);
end
end
end
else
ctype= repmat('U', nc, 1);
end
% 7) Vector with the type of variables
if (nargin > 6)
if isempty(vartype)
vartype = repmat('C', nx, 1);
elseif (~ischar(vartype) || all(size(vartype) > 1) || length (vartype) ~= nx)
tmp=sprintf('VARTYPE must be a char valued vector of length %d', nx);
error(tmp);
return;
else
for i=1:length(vartype)
switch(vartype(i))
case {'c','C'}, % do nothing
case {'i','I'}, % do nothing
case {'b','B'}, % do nothing
otherwise
tmp=sprintf('VARTYPE must contain only C, I or B');
error(tmp);
end
end
end
else
% As default we consider continuous vars
vartype = repmat('C', nx, 1);
end
% 8) Sense of optimization
if (nargin >7)
if isempty(sense)
sense=1;
elseif (ischar(sense) || all(size(sense) > 1) || ~isreal(sense))
tmp=sprintf('SENSE must be an integer value');
error(tmp);
elseif sense>=0
sense=1;
else
sense=-1;
end
else
sense=1;
end
% 9) Parameters vector
if (nargin > 8)
if (~isstruct(param))
error('PARAM must be a structure');
end
else
if str2double(version('-release'))<36
param =struct;
else
param = struct([]);
end
end
[xopt, fmin, status, extra] = glpkcc(c, a, b, lb, ub, ctype, vartype, sense, param);
|
github
|
EPFL-LCSB/matTFA-master
|
glpkmex.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/glpkmex/glpkmex.m
| 3,052 |
utf_8
|
33b5f8ff88c0469e04a4e77cd09ef9da
|
% ***OBSOLETE*** GLPKMEX interface. Use glpk instead.
%
% [xmin,fmin,status,extra]=glpkmex(sense,c,a,b,ctype,lb,ub,vartype,param,lp,solver,save)
%
% This function is provided for compatibility with the old Matlab
% interface to the GNU GLPK library. You should use the glpk function
% instead.
%
% See also: glpk, qpng.
%
% Copyright 2001-2007, Nicolo' Giorgetti
% This file is part of GLPKMEX.
%
% Octave is free software; you can redistribute it and/or modify it
% under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2, or (at your option)
% any later version.
%
% This part of code is distributed with the FURTHER condition that it is
% possible to link it to the Matlab libraries and/or use it inside the Matlab
% environment.
%
% GLPKMEX is distributed in the hope that it will be useful, but
% WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
% General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with GLPKMEX; see the file COPYING. If not, write to the Free
% Software Foundation, 59 Temple Place - Suite 330, Boston, MA
% 02111-1307, USA.
function [xopt, fopt, status, extra] = glpkmex (varargin)
% If there is no input output the version and syntax
if (nargin < 4 || nargin > 11)
disp('***OLD*** GLPK Matlab interface.');
disp('(C) 2001-2007, Nicolo'' Giorgetti.');
disp(' ');
disp('[xopt,fopt,status,extra] = glpkmex(sense,c,a,b,ctype,lb,ub,vartype,param,lpsolver,savepb');
return;
end
% reorder args:
%
% glpkmex glpk
%
% 1 sense c
% 2 c a
% 3 a b
% 4 b lb
% 5 ctype ub
% 6 lb ctype
% 7 ub vartype
% 8 vartype sense
% 9 param param
% 10 lpsolver
% 11 savepb
sense = varargin{1};
c = varargin{2};
a = varargin{3};
b = varargin{4};
nx = length (c);
if (nargin > 4)
ctype = varargin{5};
else
ctype = repmat ('U', nx, 1);
end
if (nargin > 5)
lb = varargin{6};
else
lb = repmat (-Inf, nx, 1);
end
if (nargin > 6)
ub = varargin{7};
else
ub = repmat (Inf, nx, 1);
end
if (nargin > 7)
vartype = varargin{8};
else
vartype = repmat ('C', nx, 1);
end
if (nargin > 8)
param = varargin{9};
else
param = struct ();
end
if (nargin > 9 && ~isfield(param, 'lpsolver'))
param.lpsolver = varargin{10};
end
if (nargin > 10 && ~isfield(param, 'save'))
param.save = varargin{11};
end
if (nargout == 0)
glpk (c, a, b, lb, ub, ctype, vartype, sense, param);
elseif (nargout == 1)
xopt = glpk (c, a, b, lb, ub, ctype, vartype, sense, param);
elseif (nargout == 2)
[xopt, fopt] = glpk (c, a, b, lb, ub, ctype, vartype, sense, param);
elseif (nargout == 3)
[xopt, fopt, status] = ...
glpk (c, a, b, lb, ub, ctype, vartype, sense, param);
else
[xopt, fopt, status, extra] = ...
glpk (c, a, b, lb, ub, ctype, vartype, sense, param);
end
|
github
|
EPFL-LCSB/matTFA-master
|
isBindingInstalled.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/isBindingInstalled.m
| 3,030 |
utf_8
|
fd7bfb0254686f102c3dfc6170e65038
|
function installed = isBindingInstalled()
% installed = isBindingInstalled()
%
% Returns
%
% 1. installed =
% - 1 if the libSBML executables are installed
% - 0 otherwise
%
%
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
installed = 1;
if (~exist('OCTAVE_VERSION'))
filename = fullfile(tempdir, 'test.xml');
outFile = fullfile(tempdir, 'test-out.xml');
else
if isWindows()
filename = fullfile(pwd, 'test.xml');
outFile = [tempdir, 'temp', filesep, 'test-out.xml'];
else
filename = fullfile(pwd, 'test.xml');
outFile = [tempdir, 'test-out.xml'];
end;
end;
writeTempFile(filename);
try
M = TranslateSBML(filename);
catch
installed = 0;
return;
end;
if (installed == 1)
try
OutputSBML(M, outFile, 1);
catch
installed = 0;
return;
end;
end;
delete(filename);
delete(outFile);
%
%
% Is this windows
% Mac OS X 10.7 Lion returns true for a call to ispc()
% since we were using that to distinguish between windows and macs we need
% to catch this
% ------------------------------------------------------------------------
function y = isWindows()
y = 1;
if isunix()
y = 0;
return;
end;
if ismac()
y = 0;
return;
end;
if ~ispc()
message = sprintf('\n%s\n%s\n', ...
'Unable to determine the type of operating system in use.', ...
'Please contact [email protected] to help resolve this problem.');
error(message);
end;
% write out a temporary file
function writeTempFile(filename)
fout = fopen(filename, 'w');
fprintf(fout, '<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n');
fprintf(fout, '<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" ');
fprintf(fout, 'level=\"3\" version=\"1\">\n');
fprintf(fout, ' <model/>\n</sbml>\n');
fclose(fout);
|
github
|
EPFL-LCSB/matTFA-master
|
install.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/install.m
| 9,088 |
utf_8
|
881213623382d9ea90f52aa2142f33e7
|
function install
% install
%
% 1. reports whether the libsbml binding is installed
% 2. adds the toolbox dirctories to the Path
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
% =========================================================================
% Main loop.
% =========================================================================
disp(sprintf('\nInstalling the SBMLToolbox.\n'));
[matlab_octave, bit64] = check_system();
disp(sprintf('\nChecking for libSBML %s binding\n', matlab_octave));
if isBindingInstalled() == 1
disp(sprintf('libSBML %s binding found and working\n', matlab_octave));
else
disp(sprintf('libSBML %s binding not found\n\n%s\n%s\n%s', matlab_octave, ...
'NOTE: This is not a fatal error.', ...
'You will not be able to import or export SBML but can still use the toolbox', ...
'to create and manipulate MATLAB_SBML structures'));
end;
% add the current directory and all subdirectories to the MATLAB search
% path
ToolboxPath = genpath(pwd);
addpath(ToolboxPath);
s = savepath;
if (s ~= 0)
disp(sprintf('\nInstallation failed\n%s', ...
'The directories were not added to the Path'));
else
disp(sprintf('\nInstallation successful'));
end;
% =========================================================================
% Support functions.
% =========================================================================
%
% Assess our computing environment.
% -------------------------------------------------------------------------
function [matlab_octave, bit64] = check_system()
disp('* Doing preliminary checks of runtime environment ...');
if (~exist('OCTAVE_VERSION'))
matlab_octave = 'MATLAB';
disp(' - This appears to be MATLAB and not Octave.');
else
matlab_octave = 'Octave';
disp(' - This appears to be Octave and not MATLAB.');
end;
bit64 = 32;
if ispc()
if strcmp(computer(), 'PCWIN64') == 1
bit64 = 64;
disp(sprintf(' - %s reports the OS is Windows 64-bit.', matlab_octave));
else
disp(sprintf(' - %s reports the OS is Windows 32-bit.', matlab_octave));
end;
elseif ismac()
if strcmp(computer(), 'MACI64') == 1
bit64 = 64;
disp(sprintf(' - %s reports the OS is 64-bit MacOS.', matlab_octave));
else
% Reading http://www.mathworks.com/help/techdoc/ref/computer.html
% it is still not clear to me what a non-64-bit MacOS will report.
% Let's not assume the only other alternative is 32-bit, since we
% actually don't care here. Let's just say "macos".
%
disp(sprintf(' - %s reports the OS is MacOS.', matlab_octave));
end;
elseif isunix()
if strcmp(computer(), 'GLNXA64') == 1
bit64 = 64;
disp(sprintf(' - %s reports the OS is 64-bit Linux.', matlab_octave));
else
disp(sprintf(' - %s reports the OS is 32-bit Linux.', matlab_octave));
end;
end;
%
% Assess our location in the file system.
% -------------------------------------------------------------------------
% Possible values returned:
% LOCATION:
% 'installed' -> installation directory
% 'source' -> libsbml source tree
%
% WRITEACCESS:
% 1 -> we can write in this directory
% 0 -> we can't write in this directory
%
function [location, writeAccess, in_installer] = check_location(matlab_octave, ...
functioning)
myDisp('* Trying to establish our location ...', functioning);
% This is where things get iffy. There are a lot of possibilities, and
% we have to resort to heuristics.
%
% Linux and Mac: we look for 2 possibilities
% - installation dir ends in "libsbml/bindings/matlab"
% Detect it by looking for ../../VERSION.txt.
% Assume we're in .../share/libsbml/bindings/matlab and that our
% library is in .../lib/
%
% - source dir ends in "libsbml/src/bindings/matlab"
% Detect it by looking for ../../../VERSION.txt.
% Assume our library is in ../../
%
in_installer = 0;
[remain, first] = fileparts(pwd);
if strcmpi(matlab_octave, 'matlab')
if ~strcmp(first, 'matlab')
if ~ispc()
error_incorrect_dir('matlab');
else
in_installer = 1;
end;
else
myDisp(' - We are in the libSBML subdirectory for Matlab.', functioning);
end;
else
if ~strcmp(first, 'octave')
if ~ispc()
error_incorrect_dir('octave');
else
in_installer = 1;
end;
else
myDisp(' - We are in the libSBML subdirectory for Octave.', functioning);
end;
end;
location = '';
% if in_installer == 1 then we are in the windows installer but in
% path provided by the user
% checking further is pointless
if (in_installer == 0)
[above_bindings, bindings] = fileparts(remain);
if exist(fullfile(above_bindings, 'VERSION.txt'))
myDisp(' - We appear to be in the installation target directory.', functioning);
in_installer = 1;
if ispc()
location = above_bindings;
else
location = 'installed';
end;
else
[libsbml_root, src] = fileparts(above_bindings);
if exist(fullfile(libsbml_root, 'Makefile.in'))
myDisp(' - We appear to be in the libSBML source tree.', functioning);
if ispc()
location = libsbml_root;
else
location = 'source';
end;
else
if ispc()
% we might be in the windows installer but in a location the user chose
% for the bindings
% Makefile.in will not exist in this directory
if (exist([pwd, filesep, 'Makefile.in']) == 0)
in_installer = 1;
else
% We don't know where we are.
if strcmpi(matlab_octave, 'MATLAB')
error_incorrect_dir('matlab');
else
error_incorrect_dir('octave');
end;
end;
else
% We don't know where we are.
if strcmpi(matlab_octave, 'MATLAB')
error_incorrect_dir('matlab');
else
error_incorrect_dir('octave');
end;
end;
end;
end;
end;
% if we are in the windows installer but in a location the user chose
% for the bindings
% we need the user to tell use the root directory for the rest of libsbml
% unless we are already functioning
if (ispc() && functioning == 0 && in_installer == 1 && isempty(location))
count = 1;
while(exist(location, 'dir') == 0 && count < 3)
location = input(sprintf('%s: ', ...
'Please enter the location of the top-level libsbml directory'), 's');
count = count + 1;
end;
if (exist(location, 'dir') == 0)
error('Failed to find libsbml directory');
end;
end;
% Test that it looks like we have the expected pieces in this directory.
% We don't want to assume particular paths, because we might be
% getting run from the libSBML source tree or the installed copy of
% the matlab bindings sources. So, we test for just a couple of
% things: the tail of the name of the directory in which this file is
% located (should be either "matlab" or "octave") and the presence of
% another file, "OutputSBML.c", which became part of libsbml at the
% same time this new build scheme was introduced.
our_name = sprintf('%s.m', mfilename);
other_name = 'OutputSBML.c';
if ~exist(fullfile(pwd, our_name), 'file') ...
|| ~exist(fullfile(pwd, other_name), 'file')
error_incorrect_dir('matlab');
end;
% Check whether we have write access to this directory.
fid = fopen('temp.txt', 'w');
writeAccess = 1;
if fid == -1
myDisp(' - We do not have write access here -- will write elsewhere.', functioning);
writeAccess = 0;
else
myDisp(' - We have write access here! That makes us happy.', functioning);
fclose(fid);
delete('temp.txt');
end;
|
github
|
EPFL-LCSB/matTFA-master
|
isBindingFbcEnabled.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/fbc_package/isBindingFbcEnabled.m
| 2,265 |
utf_8
|
8cb0fb5729183cd42636bc97918fb7e8
|
function fbcEnabled = isBindingFbcEnabled()
% fbcEnabled = isBindingFbcEnabled()
%
% Returns
%
% 1. fbcEnabled =
% - 1 if the executables are enabled with fbc support
% - 0 otherwise
%
%
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
% assume not enabled
fbcEnabled = 0;
if isBindingInstalled() == 0
return;
end;
if (isoctave() == '0')
filename = fullfile(tempdir, 'fbc.xml');
else
filename = fullfile(pwd, 'fbc.xml');
end;
writeTempFile(filename);
try
[m, e] = TranslateSBML(filename, 1, 0);
if (length(e) == 0 && isfield(m, 'fbc_version') == 1 )
fbcEnabled = 1;
end;
delete(filename);
catch
delete(filename);
return
end;
function writeTempFile(filename)
fout = fopen(filename, 'w');
fprintf(fout, '<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n');
fprintf(fout, '<sbml xmlns=\"http://www.sbml.org/sbml/level3/version1/core\" ');
fprintf(fout, 'xmlns:fbc=\"http://www.sbml.org/sbml/level3/version1/fbc/version1\" ');
fprintf(fout, 'level=\"3\" version=\"1\" fbc:required=\"true\">\n');
fprintf(fout, ' <model/>\n</sbml>\n');
fclose(fout);
|
github
|
EPFL-LCSB/matTFA-master
|
bind_isSBML_Model.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Validate_MATLAB_SBML_Structures/bind_isSBML_Model.m
| 139,862 |
utf_8
|
6b19c286b430b99baed148584e663c49
|
function [valid, message] = isValidSBML_Model(SBMLStructure)
% [valid, message] = isValidSBML_Model(SBMLModel)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Model structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
% *NOTE:* The fields present in a MATLAB_SBML Model structure of the appropriate
% level and version can be found using getModelFieldnames(level, version)
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2011 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
%check the input arguments are appropriate
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
if ~isempty(SBMLStructure)
if isfield(SBMLStructure, 'SBML_level')
level = SBMLStructure.SBML_level;
else
level = 3;
end;
if isfield(SBMLStructure, 'SBML_version')
version = SBMLStructure.SBML_version;
else
version = 1;
end;
else
level = 3;
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_MODEL';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_MODEL', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
%check that any nested structures are appropriate
% functionDefinitions
if (valid == 1 && level > 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.functionDefinition))
[valid, message] = isSBML_FunctionDefinition( ...
SBMLStructure.functionDefinition(index), ...
level, version);
index = index + 1;
end;
end;
% unitDefinitions
if (valid == 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.unitDefinition))
[valid, message] = isSBML_UnitDefinition( ...
SBMLStructure.unitDefinition(index), ...
level, version);
index = index + 1;
end;
end;
% compartments
if (valid == 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.compartment))
[valid, message] = isSBML_Compartment(SBMLStructure.compartment(index), ...
level, version);
index = index + 1;
end;
end;
% species
if (valid == 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.species))
[valid, message] = isSBML_Species(SBMLStructure.species(index), ...
level, version);
index = index + 1;
end;
end;
% compartmentTypes
if (valid == 1 && level == 2 && version > 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.compartmentType))
[valid, message] = isSBML_CompartmentType(SBMLStructure.compartmentType(index), ...
level, version);
index = index + 1;
end;
end;
% speciesTypes
if (valid == 1 && level == 2 && version > 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.speciesType))
[valid, message] = isSBML_SpeciesType(SBMLStructure.speciesType(index), ...
level, version);
index = index + 1;
end;
end;
% parameter
if (valid == 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.parameter))
[valid, message] = isSBML_Parameter(SBMLStructure.parameter(index), ...
level, version);
index = index + 1;
end;
end;
% initialAssignment
if (valid == 1 && (level > 2 || (level == 2 && version > 1)))
index = 1;
while (valid == 1 && index <= length(SBMLStructure.initialAssignment))
[valid, message] = isSBML_InitialAssignment( ...
SBMLStructure.initialAssignment(index), ...
level, version);
index = index + 1;
end;
end;
% rule
if (valid == 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.rule))
[valid, message] = isSBML_Rule(SBMLStructure.rule(index), ...
level, version);
index = index + 1;
end;
end;
% constraints
if (valid == 1 && (level > 2 || (level == 2 && version > 1)))
index = 1;
while (valid == 1 && index <= length(SBMLStructure.constraint))
[valid, message] = isSBML_Constraint( ...
SBMLStructure.constraint(index), ...
level, version);
index = index + 1;
end;
end;
% reaction
if (valid == 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.reaction))
[valid, message] = isSBML_Reaction(SBMLStructure.reaction(index), ...
level, version);
index = index + 1;
end;
end;
% event
if (valid == 1 && level > 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.event))
[valid, message] = isSBML_Event(SBMLStructure.event(index), ...
level, version);
index = index + 1;
end;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Model structure\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_AlgebraicRule(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_ALGEBRAIC_RULE';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_ALGEBRAIC_RULE', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid AlgebraicRule\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_AssignmentRule(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_ASSIGNMENT_RULE';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (level > 1)
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
% check L1 types
typecode = SBMLStructure.typecode;
cvr = strcmp(typecode, 'SBML_COMPARTMENT_VOLUME_RULE');
pr = strcmp(typecode, 'SBML_PARAMETER_RULE');
scr = strcmp(typecode, 'SBML_SPECIES_CONCENTRATION_RULE');
if (cvr ~= 1 && pr ~= 1 && scr ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
elseif (strcmp(SBMLStructure.type, 'scalar') ~= 1)
valid = 0;
message = 'expected scalar type';
return;
end;
end;
else
valid = 0;
message = 'missing typecode';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames(typecode, level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid AssignmentRule\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_Compartment(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_COMPARTMENT';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_COMPARTMENT', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Compartment\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_CompartmentType(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_COMPARTMENT_TYPE';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_COMPARTMENT_TYPE', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid CompartmentType\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_CompartmentVolumeRule(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_COMPARTMENT_VOLUME_RULE';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_COMPARTMENT_VOLUME_RULE', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid CompartmentVolumeRule\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_Constraint(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_CONSTRAINT';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_CONSTRAINT', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Constraint\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_Delay(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_DELAY';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_DELAY', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Delay\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_Event(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_EVENT';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_EVENT', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
%check that any nested structures are appropriate
% eventAssignments
if (valid == 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.eventAssignment))
[valid, message] = isSBML_EventAssignment( ...
SBMLStructure.eventAssignment(index), ...
level, version);
index = index + 1;
end;
end;
% trigger/delay/priority
% these are level and version dependent
if (valid == 1)
if (level == 2 && version > 2)
if (length(SBMLStructure.trigger) > 1)
valid = 0;
message = 'multiple trigger elements encountered';
elseif (length(SBMLStructure.delay) > 1)
valid = 0;
message = 'multiple delay elements encountered';
end;
if (valid == 1 && length(SBMLStructure.trigger) == 1)
[valid, message] = isSBML_Trigger(SBMLStructure.trigger, level, version);
end;
if (valid == 1 && length(SBMLStructure.delay) == 1)
[valid, message] = isSBML_Delay(SBMLStructure.delay, level, version);
end;
elseif (level > 2)
if (length(SBMLStructure.trigger) > 1)
valid = 0;
message = 'multiple trigger elements encountered';
elseif (length(SBMLStructure.delay) > 1)
valid = 0;
message = 'multiple delay elements encountered';
elseif (length(SBMLStructure.priority) > 1)
valid = 0;
message = 'multiple priority elements encountered';
end;
if (valid == 1 && length(SBMLStructure.trigger) == 1)
[valid, message] = isSBML_Trigger(SBMLStructure.trigger, level, version);
end;
if (valid == 1 && length(SBMLStructure.delay) == 1)
[valid, message] = isSBML_Delay(SBMLStructure.delay, level, version);
end;
if (valid == 1 && length(SBMLStructure.priority) == 1)
[valid, message] = isSBML_Priority(SBMLStructure.priority, level, version);
end;
end;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Event\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_EventAssignment(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_EVENT_ASSIGNMENT';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_EVENT_ASSIGNMENT', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid EventAssignment\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_FunctionDefinition(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_FUNCTION_DEFINITION';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_FUNCTION_DEFINITION', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid FunctionDefinition\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_InitialAssignment(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_INITIAL_ASSIGNMENT';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_INITIAL_ASSIGNMENT', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid InitialAssignment\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_KineticLaw(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_KINETIC_LAW';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_KINETIC_LAW', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
%check that any nested structures are appropriate
% parameters
if (valid == 1 && level < 3)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.parameter))
[valid, message] = isSBML_Parameter(SBMLStructure.parameter(index), ...
level, version);
index = index + 1;
end;
end;
%check that any nested structures are appropriate
% localParameters
if (valid == 1 && level > 2)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.localParameter))
[valid, message] = isSBML_LocalParameter(SBMLStructure.localParameter(index), ...
level, version);
index = index + 1;
end;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid KineticLaw\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_LocalParameter(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_LOCAL_PARAMETER';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_LOCAL_PARAMETER', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid LocalParameter\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_ModifierSpeciesReference(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_MODIFIER_SPECIES_REFERENCE';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_MODIFIER_SPECIES_REFERENCE', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid ModifierSpeciesReference\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_Parameter(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_PARAMETER';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_PARAMETER', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Parameter\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_ParameterRule(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_PARAMETER_RULE';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_PARAMETER_RULE', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid ParameterRule\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_Priority(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_PRIORITY';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_PRIORITY', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Priority\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_RateRule(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_RATE_RULE';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (level > 1)
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
% check L1 types
typecode = SBMLStructure.typecode;
cvr = strcmp(typecode, 'SBML_COMPARTMENT_VOLUME_RULE');
pr = strcmp(typecode, 'SBML_PARAMETER_RULE');
scr = strcmp(typecode, 'SBML_SPECIES_CONCENTRATION_RULE');
if (cvr ~= 1 && pr ~= 1 && scr ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
elseif (strcmp(SBMLStructure.type, 'rate') ~= 1)
valid = 0;
message = 'expected rate type';
return;
end;
end;
else
valid = 0;
message = 'missing typecode';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames(typecode, level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid RateRule\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_Reaction(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_REACTION';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_REACTION', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
%check that any nested structures are appropriate
% reactants
if (valid == 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.reactant))
[valid, message] = isSBML_SpeciesReference(SBMLStructure.reactant(index), ...
level, version);
index = index + 1;
end;
end;
% products
if (valid == 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.product))
[valid, message] = isSBML_SpeciesReference(SBMLStructure.product(index), ...
level, version);
index = index + 1;
end;
end;
% modifiers
if (valid == 1 && level > 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.modifier))
[valid, message] = isSBML_ModifierSpeciesReference( ...
SBMLStructure.modifier(index), ...
level, version);
index = index + 1;
end;
end;
% kineticLaw
if (valid == 1 && length(SBMLStructure.kineticLaw) == 1)
[valid, message] = isSBML_KineticLaw(SBMLStructure.kineticLaw, level, version);
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Reaction\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_Rule(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
if ~isempty(SBMLStructure)
if isfield(SBMLStructure, 'typecode')
typecode = SBMLStructure.typecode;
else
valid = 0;
message = 'missing typecode';
return;
end;
else
typecode = 'SBML_ASSIGNMENT_RULE';
end;
switch (typecode)
case 'SBML_ALGEBRAIC_RULE'
[valid, message] = isSBML_AlgebraicRule(SBMLStructure, level, version);
case 'SBML_ASSIGNMENT_RULE'
[valid, message] = isSBML_AssignmentRule(SBMLStructure, level, version);
case 'SBML_COMPARTMENT_VOLUME_RULE'
[valid, message] = isSBML_CompartmentVolumeRule(SBMLStructure, level, version);
case 'SBML_PARAMETER_RULE'
[valid, message] = isSBML_ParameterRule(SBMLStructure, level, version);
case 'SBML_RATE_RULE'
[valid, message] = isSBML_RateRule(SBMLStructure, level, version);
case 'SBML_SPECIES_CONCENTRATION_RULE'
[valid, message] = isSBML_SpeciesConcentrationRule(SBMLStructure, level, version);
case 'SBML_RULE'
[valid, message] = checkRule(SBMLStructure, level, version);
otherwise
valid = 0;
message = 'Incorrect rule typecode';
end;
function [valid, message] = checkRule(SBMLStructure, level, version)
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_RULE';
if (valid == 1 && ~isempty(SBMLStructure))
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getAlgebraicRuleFieldnames(level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Rule\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_Species(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_SPECIES';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_SPECIES', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Species\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_SpeciesConcentrationRule(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_SPECIES_CONCENTRATION_RULE';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_SPECIES_CONCENTRATION_RULE', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid SpeciesConcentrationRule\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_SpeciesReference(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_SPECIES_REFERENCE';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_SPECIES_REFERENCE', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid SpeciesReference\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_SpeciesType(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_SPECIES_TYPE';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_SPECIES_TYPE', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid SpeciesType\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_StoichiometryMath(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_STOICHIOMETRY_MATH';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_STOICHIOMETRY_MATH', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid StoichiometryMath\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_Trigger(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_TRIGGER';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_TRIGGER', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Trigger\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_Unit(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_UNIT';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_UNIT', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Unit\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [valid, message] = isSBML_UnitDefinition(varargin)
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_UNIT_DEFINITION';
if (valid == 1 && ~isempty(SBMLStructure))
if isfield(SBMLStructure, 'typecode')
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
return;
end;
else
valid = 0;
message = 'missing typecode field';
return;
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getFieldnames('SBML_UNIT_DEFINITION', level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
%check that any nested structures are appropriate
% unit
if (valid == 1)
index = 1;
while (valid == 1 && index <= length(SBMLStructure.unit))
[valid, message] = isSBML_Unit(SBMLStructure.unit(index), ...
level, version);
index = index + 1;
end;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid UnitDefinition\n%s\n', message);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function valid = isValidLevelVersionCombination(level, version)
valid = 1;
if ~isIntegralNumber(level)
error('level must be an integer');
elseif ~isIntegralNumber(version)
error('version must be an integer');
end;
if (level < 1 || level > 3)
error('current SBML levels are 1, 2 or 3');
end;
if (level == 1)
if (version < 1 || version > 2)
error('SBMLToolbox supports versions 1-2 of SBML Level 1');
end;
elseif (level == 2)
if (version < 1 || version > 4)
error('SBMLToolbox supports versions 1-4 of SBML Level 2');
end;
elseif (level == 3)
if (version ~= 1)
error('SBMLToolbox supports only version 1 of SBML Level 3');
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function value = isIntegralNumber(number)
value = 0;
integerClasses = {'int8', 'uint8', 'int16', 'uint16', 'int32', 'uint32', 'int64', 'uint64'};
% since the function isinteger does not exist in MATLAB Rel 13
% this is not used
%if (isinteger(number))
if (ismember(class(number), integerClasses))
value = 1;
elseif (isnumeric(number))
% if it is an integer
if (number == fix(number))
value = 1;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getAlgebraicRuleFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'type', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 10;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 10;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getAssignmentRuleFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 10;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getCompartmentFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'name', ...
'volume', ...
'units', ...
'outside', ...
'isSetVolume', ...
};
nNumberFields = 8;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'spatialDimensions', ...
'size', ...
'units', ...
'outside', ...
'constant', ...
'isSetSize', ...
'isSetVolume', ...
};
nNumberFields = 13;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'compartmentType', ...
'spatialDimensions', ...
'size', ...
'units', ...
'outside', ...
'constant', ...
'isSetSize', ...
'isSetVolume', ...
};
nNumberFields = 14;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'compartmentType', ...
'spatialDimensions', ...
'size', ...
'units', ...
'outside', ...
'constant', ...
'isSetSize', ...
'isSetVolume', ...
};
nNumberFields = 15;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'compartmentType', ...
'spatialDimensions', ...
'size', ...
'units', ...
'outside', ...
'constant', ...
'isSetSize', ...
'isSetVolume', ...
};
nNumberFields = 15;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'spatialDimensions', ...
'size', ...
'units', ...
'constant', ...
'isSetSize', ...
'isSetSpatialDimensions', ...
};
nNumberFields = 13;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getCompartmentTypeFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
};
nNumberFields = 6;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
};
nNumberFields = 7;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
};
nNumberFields = 7;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getCompartmentVolumeRuleFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'type', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 10;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 2)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 3)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 4)
SBMLfieldnames = [];
nNumberFields = 0;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getConstraintFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
'message', ...
};
nNumberFields = 7;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
'message', ...
};
nNumberFields = 7;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
'message', ...
};
nNumberFields = 7;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
'message', ...
};
nNumberFields = 7;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getDelayFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 2)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
};
nNumberFields = 6;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
};
nNumberFields = 6;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
};
nNumberFields = 6;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getEventAssignmentFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'variable', ...
'math', ...
};
nNumberFields = 6;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'variable', ...
'sboTerm', ...
'math', ...
};
nNumberFields = 7;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'variable', ...
'math', ...
};
nNumberFields = 7;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'variable', ...
'math', ...
};
nNumberFields = 7;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'variable', ...
'math', ...
};
nNumberFields = 7;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getEventFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'trigger', ...
'delay', ...
'timeUnits', ...
'eventAssignment', ...
};
nNumberFields = 10;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'trigger', ...
'delay', ...
'timeUnits', ...
'sboTerm', ...
'eventAssignment', ...
};
nNumberFields = 11;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'trigger', ...
'delay', ...
'eventAssignment', ...
};
nNumberFields = 10;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'useValuesFromTriggerTime', ...
'trigger', ...
'delay', ...
'eventAssignment', ...
};
nNumberFields = 11;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'useValuesFromTriggerTime', ...
'trigger', ...
'delay', ...
'priority', ...
'eventAssignment', ...
};
nNumberFields = 12;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getFieldnames(typecode, ...
level, version)
done = 1;
switch (typecode)
case {'SBML_ALGEBRAIC_RULE', 'AlgebraicRule', 'algebraicRule'}
fhandle = str2func('getAlgebraicRuleFieldnames');
case {'SBML_ASSIGNMENT_RULE', 'AssignmentRule', 'assignmentRule'}
fhandle = str2func('getAssignmentRuleFieldnames');
case {'SBML_COMPARTMENT', 'Compartment', 'compartment'}
fhandle = str2func('getCompartmentFieldnames');
case {'SBML_COMPARTMENT_TYPE', 'CompartmentType', 'compartmentType'}
fhandle = str2func('getCompartmentTypeFieldnames');
case {'SBML_COMPARTMENT_VOLUME_RULE', 'CompartmentVolumeRule', 'compartmentVolumeRule'}
fhandle = str2func('getCompartmentVolumeRuleFieldnames');
case {'SBML_CONSTRAINT', 'Constraint', 'constraint'}
fhandle = str2func('getConstraintFieldnames');
case {'SBML_DELAY', 'Delay', 'delay'}
fhandle = str2func('getDelayFieldnames');
case {'SBML_EVENT', 'Event', 'event'}
fhandle = str2func('getEventFieldnames');
case {'SBML_EVENT_ASSIGNMENT', 'EventAssignment', 'eventAssignment'}
fhandle = str2func('getEventAssignmentFieldnames');
case {'SBML_FUNCTION_DEFINITION', 'FunctionDefinition', 'functionDefinition'}
fhandle = str2func('getFunctionDefinitionFieldnames');
case {'SBML_INITIAL_ASSIGNMENT', 'InitialAssignment', 'initialAssignment'}
fhandle = str2func('getInitialAssignmentFieldnames');
case {'SBML_KINETIC_LAW', 'KineticLaw', 'kineticLaw'}
fhandle = str2func('getKineticLawFieldnames');
case {'SBML_LOCAL_PARAMETER', 'LocalParameter', 'localParameter'}
fhandle = str2func('getLocalParameterFieldnames');
case {'SBML_MODEL', 'Model', 'model'}
fhandle = str2func('getModelFieldnames');
case {'SBML_MODIFIER_SPECIES_REFERENCE', 'ModifierSpeciesReference', 'modifierSpeciesReference'}
fhandle = str2func('getModifierSpeciesReferenceFieldnames');
case {'SBML_PARAMETER', 'Parameter', 'parameter'}
fhandle = str2func('getParameterFieldnames');
case {'SBML_PARAMETER_RULE', 'ParameterRule', 'parameterRule'}
fhandle = str2func('getParameterRuleFieldnames');
case {'SBML_PRIORITY', 'Priority', 'priority'}
fhandle = str2func('getPriorityFieldnames');
case {'SBML_RATE_RULE', 'RateRule', 'ruleRule'}
fhandle = str2func('getRateRuleFieldnames');
case {'SBML_REACTION', 'Reaction', 'reaction'}
fhandle = str2func('getReactionFieldnames');
case {'SBML_SPECIES', 'Species', 'species'}
fhandle = str2func('getSpeciesFieldnames');
case {'SBML_SPECIES_CONCENTRATION_RULE', 'SpeciesConcentrationRule', 'speciesConcentrationRule'}
fhandle = str2func('getSpeciesConcentrationRuleFieldnames');
case {'SBML_SPECIES_REFERENCE', 'SpeciesReference', 'speciesReference'}
fhandle = str2func('getSpeciesReferenceFieldnames');
case {'SBML_SPECIES_TYPE', 'SpeciesType', 'speciesType'}
fhandle = str2func('getSpeciesTypeFieldnames');
case {'SBML_STOICHIOMETRY_MATH', 'StoichiometryMath', 'stoichiometryMath'}
fhandle = str2func('getStoichiometryMathFieldnames');
case {'SBML_TRIGGER', 'Trigger', 'trigger'}
fhandle = str2func('getTriggerFieldnames');
case {'SBML_UNIT', 'Unit', 'unit'}
fhandle = str2func('getUnitFieldnames');
case {'SBML_UNIT_DEFINITION', 'UnitDefinition', 'unitDefinition'}
fhandle = str2func('getUnitDefinitionFieldnames');
otherwise
done = 0;
end;
if done == 1
[SBMLfieldnames, nNumberFields] = feval(fhandle, level, version);
else
switch (typecode)
case {'SBML_FBC_FLUXBOUND', 'FluxBound', 'fluxBound'}
fhandle = str2func('getFluxBoundFieldnames');
case {'SBML_FBC_FLUXOBJECTIVE', 'FluxObjective', 'fluxObjective'}
fhandle = str2func('getFluxObjectiveFieldnames');
case {'SBML_FBC_OBJECTIVE', 'Objective', 'objective'}
fhandle = str2func('getObjectiveFieldnames');
case {'SBML_FBC_MODEL', 'FBCModel'}
fhandle = str2func('getFBCModelFieldnames');
case {'SBML_FBC_SPECIES', 'FBCSpecies'}
fhandle = str2func('getFBCSpeciesFieldnames');
otherwise
error('%s\n%s', ...
'getFieldnames(typecode, level, version', ...
'typecode not recognised');
end;
[SBMLfieldnames, nNumberFields] = feval(fhandle, level, version, 1);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getFunctionDefinitionFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'math', ...
};
nNumberFields = 7;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'math', ...
};
nNumberFields = 8;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'math', ...
};
nNumberFields = 8;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'math', ...
};
nNumberFields = 8;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'math', ...
};
nNumberFields = 8;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getInitialAssignmentFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'symbol', ...
'math', ...
};
nNumberFields = 7;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'symbol', ...
'math', ...
};
nNumberFields = 7;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'symbol', ...
'math', ...
};
nNumberFields = 7;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'symbol', ...
'math', ...
};
nNumberFields = 7;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getKineticLawFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'formula', ...
'parameter', ...
'timeUnits', ...
'substanceUnits', ...
};
nNumberFields = 7;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'formula', ...
'math', ...
'parameter', ...
'timeUnits', ...
'substanceUnits', ...
};
nNumberFields = 9;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'formula', ...
'math', ...
'parameter', ...
'sboTerm', ...
};
nNumberFields = 8;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'math', ...
'parameter', ...
};
nNumberFields = 8;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'math', ...
'parameter', ...
};
nNumberFields = 8;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
'localParameter', ...
};
nNumberFields = 7;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getLocalParameterFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'value', ...
'units', ...
'isSetValue', ...
};
nNumberFields = 10;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getModelFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'SBML_level', ...
'SBML_version', ...
'name', ...
'unitDefinition', ...
'compartment', ...
'species', ...
'parameter', ...
'rule', ...
'reaction', ...
};
nNumberFields = 12;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'SBML_level', ...
'SBML_version', ...
'name', ...
'id', ...
'functionDefinition', ...
'unitDefinition', ...
'compartment', ...
'species', ...
'parameter', ...
'rule', ...
'reaction', ...
'event', ...
};
nNumberFields = 16;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'SBML_level', ...
'SBML_version', ...
'name', ...
'id', ...
'sboTerm', ...
'functionDefinition', ...
'unitDefinition', ...
'compartmentType', ...
'speciesType', ...
'compartment', ...
'species', ...
'parameter', ...
'initialAssignment', ...
'rule', ...
'constraint', ...
'reaction', ...
'event', ...
};
nNumberFields = 21;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'SBML_level', ...
'SBML_version', ...
'name', ...
'id', ...
'sboTerm', ...
'functionDefinition', ...
'unitDefinition', ...
'compartmentType', ...
'speciesType', ...
'compartment', ...
'species', ...
'parameter', ...
'initialAssignment', ...
'rule', ...
'constraint', ...
'reaction', ...
'event', ...
};
nNumberFields = 21;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'SBML_level', ...
'SBML_version', ...
'name', ...
'id', ...
'sboTerm', ...
'functionDefinition', ...
'unitDefinition', ...
'compartmentType', ...
'speciesType', ...
'compartment', ...
'species', ...
'parameter', ...
'initialAssignment', ...
'rule', ...
'constraint', ...
'reaction', ...
'event', ...
};
nNumberFields = 21;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'SBML_level', ...
'SBML_version', ...
'name', ...
'id', ...
'sboTerm', ...
'functionDefinition', ...
'unitDefinition', ...
'compartment', ...
'species', ...
'parameter', ...
'initialAssignment', ...
'rule', ...
'constraint', ...
'reaction', ...
'event', ...
'substanceUnits', ...
'timeUnits', ...
'lengthUnits', ...
'areaUnits', ...
'volumeUnits', ...
'extentUnits', ...
'conversionFactor', ...
};
nNumberFields = 26;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getModifierSpeciesReferenceFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'species', ...
};
nNumberFields = 5;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'species', ...
'id', ...
'name', ...
'sboTerm', ...
};
nNumberFields = 8;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'species', ...
'id', ...
'name', ...
};
nNumberFields = 8;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'species', ...
'id', ...
'name', ...
};
nNumberFields = 8;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'species', ...
'id', ...
'name', ...
};
nNumberFields = 8;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getParameterFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'name', ...
'value', ...
'units', ...
'isSetValue', ...
};
nNumberFields = 7;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'value', ...
'units', ...
'constant', ...
'isSetValue', ...
};
nNumberFields = 10;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'value', ...
'units', ...
'constant', ...
'sboTerm', ...
'isSetValue', ...
};
nNumberFields = 11;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'value', ...
'units', ...
'constant', ...
'isSetValue', ...
};
nNumberFields = 11;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'value', ...
'units', ...
'constant', ...
'isSetValue', ...
};
nNumberFields = 11;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'value', ...
'units', ...
'constant', ...
'isSetValue', ...
};
nNumberFields = 11;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getParameterRuleFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'type', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 10;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 2)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 3)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 4)
SBMLfieldnames = [];
nNumberFields = 0;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getPriorityFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
};
nNumberFields = 6;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getRateRuleFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 10;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getReactionFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'name', ...
'reactant', ...
'product', ...
'kineticLaw', ...
'reversible', ...
'fast', ...
};
nNumberFields = 9;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'reactant', ...
'product', ...
'modifier', ...
'kineticLaw', ...
'reversible', ...
'fast', ...
'isSetFast', ...
};
nNumberFields = 13;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'reactant', ...
'product', ...
'modifier', ...
'kineticLaw', ...
'reversible', ...
'fast', ...
'sboTerm', ...
'isSetFast', ...
};
nNumberFields = 14;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'reactant', ...
'product', ...
'modifier', ...
'kineticLaw', ...
'reversible', ...
'fast', ...
'isSetFast', ...
};
nNumberFields = 14;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'reactant', ...
'product', ...
'modifier', ...
'kineticLaw', ...
'reversible', ...
'fast', ...
'isSetFast', ...
};
nNumberFields = 14;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'reactant', ...
'product', ...
'modifier', ...
'kineticLaw', ...
'reversible', ...
'fast', ...
'isSetFast', ...
'compartment', ...
};
nNumberFields = 15;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getRuleFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'type', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 10;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 10;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 11;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getSpeciesConcentrationRuleFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'type', ...
'formula', ...
'variable', ...
'species', ...
'compartment', ...
'name', ...
'units', ...
};
nNumberFields = 10;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 2)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 3)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 4)
SBMLfieldnames = [];
nNumberFields = 0;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getSpeciesFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'name', ...
'compartment', ...
'initialAmount', ...
'units', ...
'boundaryCondition', ...
'charge', ...
'isSetInitialAmount', ...
'isSetCharge', ...
};
nNumberFields = 11;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'compartment', ...
'initialAmount', ...
'initialConcentration', ...
'substanceUnits', ...
'spatialSizeUnits', ...
'hasOnlySubstanceUnits', ...
'boundaryCondition', ...
'charge', ...
'constant', ...
'isSetInitialAmount', ...
'isSetInitialConcentration', ...
'isSetCharge', ...
};
nNumberFields = 18;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'speciesType', ...
'compartment', ...
'initialAmount', ...
'initialConcentration', ...
'substanceUnits', ...
'spatialSizeUnits', ...
'hasOnlySubstanceUnits', ...
'boundaryCondition', ...
'charge', ...
'constant', ...
'isSetInitialAmount', ...
'isSetInitialConcentration', ...
'isSetCharge', ...
};
nNumberFields = 19;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'speciesType', ...
'compartment', ...
'initialAmount', ...
'initialConcentration', ...
'substanceUnits', ...
'hasOnlySubstanceUnits', ...
'boundaryCondition', ...
'charge', ...
'constant', ...
'isSetInitialAmount', ...
'isSetInitialConcentration', ...
'isSetCharge', ...
};
nNumberFields = 19;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'speciesType', ...
'compartment', ...
'initialAmount', ...
'initialConcentration', ...
'substanceUnits', ...
'hasOnlySubstanceUnits', ...
'boundaryCondition', ...
'charge', ...
'constant', ...
'isSetInitialAmount', ...
'isSetInitialConcentration', ...
'isSetCharge', ...
};
nNumberFields = 19;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'compartment', ...
'initialAmount', ...
'initialConcentration', ...
'substanceUnits', ...
'hasOnlySubstanceUnits', ...
'boundaryCondition', ...
'constant', ...
'isSetInitialAmount', ...
'isSetInitialConcentration', ...
'conversionFactor', ...
};
nNumberFields = 17;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getSpeciesReferenceFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'species', ...
'stoichiometry', ...
'denominator', ...
};
nNumberFields = 6;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'species', ...
'stoichiometry', ...
'denominator', ...
'stoichiometryMath', ...
};
nNumberFields = 8;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'species', ...
'id', ...
'name', ...
'sboTerm', ...
'stoichiometry', ...
'stoichiometryMath', ...
};
nNumberFields = 10;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'species', ...
'id', ...
'name', ...
'stoichiometry', ...
'stoichiometryMath', ...
};
nNumberFields = 10;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'species', ...
'id', ...
'name', ...
'stoichiometry', ...
'stoichiometryMath', ...
};
nNumberFields = 10;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'species', ...
'id', ...
'name', ...
'stoichiometry', ...
'constant', ...
'isSetStoichiometry', ...
};
nNumberFields = 11;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getSpeciesTypeFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
};
nNumberFields = 6;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
};
nNumberFields = 7;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
};
nNumberFields = 7;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getStoichiometryMathFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 2)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
};
nNumberFields = 6;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
};
nNumberFields = 6;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getTriggerFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 2)
SBMLfieldnames = [];
nNumberFields = 0;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
};
nNumberFields = 6;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'math', ...
};
nNumberFields = 6;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'persistent', ...
'initialValue', ...
'math', ...
};
nNumberFields = 8;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getUnitDefinitionFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'name', ...
'unit', ...
};
nNumberFields = 5;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'unit', ...
};
nNumberFields = 7;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'name', ...
'id', ...
'unit', ...
};
nNumberFields = 7;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'unit', ...
};
nNumberFields = 8;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'unit', ...
};
nNumberFields = 8;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'name', ...
'id', ...
'unit', ...
};
nNumberFields = 8;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [SBMLfieldnames, nNumberFields] = getUnitFieldnames(level, ...
version)
if (~isValidLevelVersionCombination(level, version))
error ('invalid level/version combination');
end;
if (level == 1)
SBMLfieldnames = { 'typecode', ...
'notes', ...
'annotation', ...
'kind', ...
'exponent', ...
'scale', ...
};
nNumberFields = 6;
elseif (level == 2)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'kind', ...
'exponent', ...
'scale', ...
'multiplier', ...
'offset', ...
};
nNumberFields = 9;
elseif (version == 2)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'kind', ...
'exponent', ...
'scale', ...
'multiplier', ...
};
nNumberFields = 8;
elseif (version == 3)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'kind', ...
'exponent', ...
'scale', ...
'multiplier', ...
};
nNumberFields = 9;
elseif (version == 4)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'kind', ...
'exponent', ...
'scale', ...
'multiplier', ...
};
nNumberFields = 9;
end;
elseif (level == 3)
if (version == 1)
SBMLfieldnames = { 'typecode', ...
'metaid', ...
'notes', ...
'annotation', ...
'sboTerm', ...
'kind', ...
'exponent', ...
'scale', ...
'multiplier', ...
};
nNumberFields = 9;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
github
|
EPFL-LCSB/matTFA-master
|
isSBML_Rule.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Validate_MATLAB_SBML_Structures/isSBML_Rule.m
| 4,719 |
utf_8
|
82221b39c9f485c76bc0c4cb4425712d
|
function [valid, message] = isSBML_Rule(varargin)
% [valid, message] = isSBML_Rule(SBMLRule, level, version(optional))
%
% Takes
%
% 1. SBMLRule, an SBML Rule structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
%
% Returns
%
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Rule structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
% *NOTE:* the optional version defaults to a value of 1
%
% *NOTE:* The fields present in a MATLAB_SBML Rule structure of the appropriate
% level and version can be found using getRuleFieldnames(level, version)
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
%check the input arguments are appropriate
if (nargin < 2 || nargin > 3)
error('wrong number of input arguments');
end;
SBMLStructure = varargin{1};
if (length(SBMLStructure) > 1)
valid = 0;
message = 'cannot deal with arrays of structures';
return;
end;
level = varargin{2};
if (nargin == 3)
version = varargin{3};
else
version = 1;
end;
isValidLevelVersionCombination(level, version);
message = '';
if ~isempty(SBMLStructure)
if isfield(SBMLStructure, 'typecode')
typecode = SBMLStructure.typecode;
else
valid = 0;
message = 'missing typecode';
return;
end;
else
typecode = 'SBML_ASSIGNMENT_RULE';
end;
switch (typecode)
case 'SBML_ALGEBRAIC_RULE'
[valid, message] = isSBML_AlgebraicRule(SBMLStructure, level, version);
case 'SBML_ASSIGNMENT_RULE'
[valid, message] = isSBML_AssignmentRule(SBMLStructure, level, version);
case 'SBML_COMPARTMENT_VOLUME_RULE'
[valid, message] = isSBML_CompartmentVolumeRule(SBMLStructure, level, version);
case 'SBML_PARAMETER_RULE'
[valid, message] = isSBML_ParameterRule(SBMLStructure, level, version);
case 'SBML_RATE_RULE'
[valid, message] = isSBML_RateRule(SBMLStructure, level, version);
case 'SBML_SPECIES_CONCENTRATION_RULE'
[valid, message] = isSBML_SpeciesConcentrationRule(SBMLStructure, level, version);
case 'SBML_RULE'
[valid, message] = checkRule(SBMLStructure, level, version);
otherwise
valid = 0;
message = 'Incorrect rule typecode';
end;
function [valid, message] = checkRule(SBMLStructure, level, version)
message = '';
% check that argument is a structure
valid = isstruct(SBMLStructure);
% check the typecode
typecode = 'SBML_RULE';
if (valid == 1 && ~isempty(SBMLStructure))
if (strcmp(typecode, SBMLStructure.typecode) ~= 1)
valid = 0;
message = 'typecode mismatch';
end;
end;
% if the level and version fields exist they must match
if (valid == 1 && isfield(SBMLStructure, 'level') && ~isempty(SBMLStructure))
if ~isequal(level, SBMLStructure.level)
valid = 0;
message = 'level mismatch';
end;
end;
if (valid == 1 && isfield(SBMLStructure, 'version') && ~isempty(SBMLStructure))
if ~isequal(version, SBMLStructure.version)
valid = 0;
message = 'version mismatch';
end;
end;
% check that structure contains all the necessary fields
[SBMLfieldnames, numFields] = getAlgebraicRuleFieldnames(level, version);
if (numFields ==0)
valid = 0;
message = 'invalid level/version';
end;
index = 1;
while (valid == 1 && index <= numFields)
valid = isfield(SBMLStructure, char(SBMLfieldnames(index)));
if (valid == 0);
message = sprintf('%s field missing', char(SBMLfieldnames(index)));
end;
index = index + 1;
end;
% report failure
if (valid == 0)
message = sprintf('Invalid Rule\n%s\n', message);
end;
|
github
|
EPFL-LCSB/matTFA-master
|
AnalyseSpecies.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Simulation/AnalyseSpecies.m
| 14,715 |
utf_8
|
8b6973e0bfad96e3ccee4c6adb214328
|
function Species = AnalyseSpecies(SBMLModel)
% [analysis] = AnalyseSpecies(SBMLModel)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. a structure detailing the species and how they are manipulated
% within the model
%
%
% *EXAMPLE:*
%
% Using the model from toolbox/Test/test-data/algebraicRules.xml
%
% analysis = AnalyseSpecies(m)
%
% analysis =
%
% 1x5 struct array with fields:
% Name
% constant
% boundaryCondition
% initialValue
% hasAmountOnly
% isConcentration
% compartment
% ChangedByReaction
% KineticLaw
% ChangedByRateRule
% RateRule
% ChangedByAssignmentRule
% AssignmentRule
% InAlgebraicRule
% AlgebraicRule
% ConvertedToAssignRule
% ConvertedRule
%
% analysis(1) =
%
%
% Name: {'S1'}
% constant: 0
% boundaryCondition: 0
% initialValue: 0.0300
% hasAmountOnly: 0
% isConcentration: 0
% compartment: 'compartment'
% ChangedByReaction: 1
% KineticLaw: {' - (k*S1)'}
% ChangedByRateRule: 0
% RateRule: ''
% ChangedByAssignmentRule: 0
% AssignmentRule: ''
% InAlgebraicRule: 1
% AlgebraicRule: {{1x1 cell}}
% ConvertedToAssignRule: 0
% ConvertedRule: ''
%
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
if (~isValidSBML_Model(SBMLModel))
error('AnalyseSpecies(SBMLModel)\n%s', 'argument must be an SBMLModel structure');
end;
if length(SBMLModel.species) == 0
Species = [];
return;
end;
[name, KineticLaw] = GetRateLawsFromReactions(SBMLModel);
[n, RateRule] = GetRateLawsFromRules(SBMLModel);
[n, AssignRule] = GetSpeciesAssignmentRules(SBMLModel);
[n, AlgRules] = GetSpeciesAlgebraicRules(SBMLModel);
[n, Values] = GetSpecies(SBMLModel);
% create the output structure
for i = 1:length(SBMLModel.species)
Species(i).Name = name(i);
% species Type
if (SBMLModel.SBML_level == 2 && SBMLModel.SBML_version > 1)
if exist('OCTAVE_VERSION')
if isempty(SBMLModel.species(i).speciesType)
Species(i).speciesType = '';
else
Species(i).speciesType = SBMLModel.species(i).speciesType;
end;
else
Species(i).speciesType = SBMLModel.species(i).speciesType;
end;
end;
% boundary condition and constant
bc = SBMLModel.species(i).boundaryCondition;
if (SBMLModel.SBML_level > 1)
const = SBMLModel.species(i).constant;
else
const = 0;
end;
Species(i).constant = const;
Species(i).boundaryCondition = bc;
%initial value / amount/ concentration
Species(i).initialValue = Values(i);
if (SBMLModel.SBML_level > 1)
comp = Model_getCompartmentById(SBMLModel, SBMLModel.species(i).compartment);
if (comp.spatialDimensions == 0)
Species(i).hasAmountOnly = 1;
else
if (SBMLModel.species(i).hasOnlySubstanceUnits == 1)
Species(i).hasAmountOnly = 1;
else
Species(i).hasAmountOnly = 0;
end;
end;
if (SBMLModel.species(i).isSetInitialConcentration == 0 ...
&& SBMLModel.species(i).isSetInitialAmount == 0)
% value is set by rule/assignment thus will be concentration
% unless the compartment is 0D or species hasOnlySubstanceUnits
if (comp.spatialDimensions == 0 ...
|| SBMLModel.species(i).hasOnlySubstanceUnits == 1)
Species(i).isConcentration = 0;
else
Species(i).isConcentration = 1;
end;
elseif (SBMLModel.species(i).isSetInitialAmount == 1)
% species has a value given as amount
% but if overridden by assignment it will be in conc
if (abs(SBMLModel.species(i).initialAmount - Values(i)) > 1e-16)
Species(i).isConcentration = 1;
else
Species(i).isConcentration = 0;
end;
else
% here species has a value given as concentration
% if comp is 0D or species hasOnlySubstanceUnits this is not
% correct and needs to be converted
if (comp.spatialDimensions == 0 ...
|| SBMLModel.species(i).hasOnlySubstanceUnits == 1)
Species(i).isConcentration = 0;
if isnan(comp.size)
Species(i).initialvalue = NaN;
else
Species(i).initialValue = Values(i)/comp.size;
end;
else
Species(i).isConcentration = 1;
end;
end;
else
% level 1 species were in amounts
Species(i).isConcentration = 0;
end;
Species(i).compartment = SBMLModel.species(i).compartment;
if (strcmp(KineticLaw(i), '0'))
Species(i).ChangedByReaction = 0;
Species(i).KineticLaw = '';
else
Species(i).ChangedByReaction = 1;
Species(i).KineticLaw = KineticLaw(i);
end;
if (strcmp(RateRule(i), '0'))
Species(i).ChangedByRateRule = 0;
Species(i).RateRule = '';
else
Species(i).ChangedByRateRule = 1;
Species(i).RateRule = RateRule(i);
end;
if (strcmp(AssignRule(i), '0'))
Species(i).ChangedByAssignmentRule = 0;
Species(i).AssignmentRule = '';
else
Species(i).ChangedByAssignmentRule = 1;
Species(i).AssignmentRule = AssignRule(i);
end;
if (strcmp(AlgRules(i), '0'))
Species(i).InAlgebraicRule = 0;
Species(i).AlgebraicRule = '';
else
Species(i).InAlgebraicRule = 1;
Species(i).AlgebraicRule = AlgRules(i);
end;
if ((Species(i).constant == 0) ...
&& (Species(i).ChangedByReaction == 0) ...
&& (Species(i).ChangedByRateRule == 0) ...
&& (Species(i).ChangedByAssignmentRule == 0))
if (Species(i).InAlgebraicRule == 1)
Species(i).ConvertedToAssignRule = 1;
Rule = Species(i).AlgebraicRule{1};
% need to look at whether rule contains a user definined
% function
FunctionIds = Model_getFunctionIds(SBMLModel);
for f = 1:length(FunctionIds)
if (matchFunctionName(char(Rule), FunctionIds{f}))
Rule = SubstituteFunction(char(Rule), SBMLModel.functionDefinition(f));
end;
end;
SubsRule = SubsAssignmentRules(SBMLModel, char(Rule));
Species(i).ConvertedRule = Rearrange(SubsRule, name{i});
else
Species(i).ConvertedToAssignRule = 0;
Species(i).ConvertedRule = '';
end;
elseif ((isnan(Species(i).initialValue)) ...
&& (Species(i).InAlgebraicRule == 1) ...
&& (Species(i).ChangedByAssignmentRule == 0))
error ('The model is over parameterised and the simulation cannot make decisions regarding rules');
else
Species(i).ConvertedToAssignRule = 0;
Species(i).ConvertedRule = '';
end;
end;
function form = SubsAssignmentRules(SBMLModel, rule)
[species, AssignRule] = GetSpeciesAssignmentRules(SBMLModel);
form = rule;
% bracket the species to be replaced
for i = 1:length(species)
if (matchName(rule, species{i}))
if (~strcmp(AssignRule{i}, '0'))
form = strrep(form, species{i}, strcat('(', species{i}, ')'));
end;
end;
end;
for i = 1:length(species)
if (matchName(rule, species{i}))
if (~strcmp(AssignRule{i}, '0'))
form = strrep(form, species{i}, AssignRule{i});
end;
end;
end;
function output = Arrange(formula, x, vars)
ops = '+-';
f = LoseWhiteSpace(formula);
operators = ismember(f, ops);
OpIndex = find(operators == 1);
%--------------------------------------------------
% divide formula up into elements seperated by +/-
if (OpIndex(1) == 1)
% leading sign i.e. +x-y
NumElements = length(OpIndex);
j = 2;
index = 2;
else
NumElements = length(OpIndex) + 1;
j = 1;
index = 1;
end;
for i = 1:NumElements-1
element = '';
while (j < OpIndex(index))
element = strcat(element, f(j));
j = j+1;
end;
Elements{i} = element;
j = j + 1;
index = index + 1;
end;
% get last element
j = OpIndex(end)+1;
element = '';
while (j <= length(f))
element = strcat(element, f(j));
j = j+1;
end;
Elements{NumElements} = element;
%--------------------------------------------------
% check whether element contains x
% if does keep on lhs else move to rhs changing sign
output = '';
lhs = 1;
for i = 1:NumElements
if (matchName(Elements{i}, x))
% element contains x
LHSElements{lhs} = Elements{i};
if (OpIndex(1) == 1)
LHSOps(lhs) = f(OpIndex(i));
elseif (i == 1)
LHSOps(lhs) = '+';
else
LHSOps(lhs) = f(OpIndex(i-1));
end;
lhs = lhs + 1;
elseif (i == 1)
% first element does not contain x
if (OpIndex(1) == 1)
if (strcmp(f(1), '-'))
output = strcat(output, '+');
else
output = strcat(output, '-');
end;
else
% no sign so +
output = strcat(output, '-');
end;
output = strcat(output, Elements{i});
else
% element not first and does not contain x
if (OpIndex(1) == 1)
if (strcmp(f(OpIndex(i)), '-'))
output = strcat(output, '+');
else
output = strcat(output, '-');
end;
else
if (strcmp(f(OpIndex(i-1)), '-'))
output = strcat(output, '+');
else
output = strcat(output, '-');
end;
end;
output = strcat(output, Elements{i});
end;
end;
%------------------------------------------------------
% look at remaining LHS
for i = 1:length(LHSElements)
Mult{i} = ParseElement(LHSElements{i}, x);
end;
if (length(LHSElements) == 1)
% only one element with x
% check signs and multipliers
if (strcmp(LHSOps(1), '-'))
output = strcat('-(', output, ')');
end;
if (~strcmp(Mult{1}, '1'))
output = strcat(output, '/', Mult{1});
end;
else
divisor = '';
if (strcmp(LHSOps(1), '+'))
divisor = strcat(divisor, '(', Mult{1});
else
divisor = strcat(divisor, '(-', Mult{1});
end;
for i = 2:length(LHSElements)
divisor = strcat(divisor, LHSOps(i), Mult{i});
end;
divisor = strcat(divisor, ')');
output = strcat('(', output, ')/', divisor);
end;
function multiplier = ParseElement(element, x)
% assumes that the element is of the form n*x/m
% and returns n/m in simplest form
if (strcmp(element, x))
multiplier = '1';
return;
end;
VarIndex = matchName(element, x);
MultIndex = strfind(element, '*');
DivIndex = strfind(element, '/');
if (isempty(MultIndex))
MultIndex = 1;
end;
if (isempty(DivIndex))
DivIndex = length(element);
end;
if ((DivIndex < MultIndex) ||(VarIndex < MultIndex) || (VarIndex > DivIndex))
error('Cannot deal with formula in this form; %s', element);
end;
n = '';
m = '';
for i = 1:MultIndex-1
n = strcat(n, element(i));
end;
if (isempty(n))
n = '1';
end;
for i = DivIndex+1:length(element)
m = strcat(m, element(i));
end;
if (isempty(m))
m = '1';
end;
% if both m and n represenet numbers then they can be simplified
Num_n = str2num(n);
Num_m = str2num(m);
if (~isempty(Num_n) && ~isempty(Num_m))
multiplier = num2str(Num_n/Num_m);
else
if (strcmp(m, '1'))
multiplier = n;
else
multiplier = strcat(n, '/', m);
end;
end;
function y = LoseWhiteSpace(charArray)
% LoseWhiteSpace(charArray) takes an array of characters
% and returns the array with any white space removed
%
%----------------------------------------------------------------
% EXAMPLE:
% y = LoseWhiteSpace(' exa mp le')
% y = 'example'
%
%------------------------------------------------------------
% check input is an array of characters
if (~ischar(charArray))
error('LoseWhiteSpace(input)\n%s', 'input must be an array of characters');
end;
%-------------------------------------------------------------
% get the length of the array
NoChars = length(charArray);
%-------------------------------------------------------------
% create an array that indicates whether the elements of charArray are
% spaces
% e.g. WSpace = isspace(' v b') = [1, 1, 0, 1, 0]
% and determine how many
WSpace = isspace(charArray);
NoSpaces = sum(WSpace);
%-----------------------------------------------------------
% rewrite the array to leaving out any spaces
% remove any numbers from the array of symbols
if (NoSpaces > 0)
NewArrayCount = 1;
for i = 1:NoChars
if (~isspace(charArray(i)))
y(NewArrayCount) = charArray(i);
NewArrayCount = NewArrayCount + 1;
end;
end;
else
y = charArray;
end;
|
github
|
EPFL-LCSB/matTFA-master
|
WriteODEFunction.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Simulation/WriteODEFunction.m
| 29,879 |
utf_8
|
9d231760d2c9e73dd506f73078e5a7da
|
function WriteODEFunction(varargin)
% WriteODEFunction(SBMLModel, name(optional))
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
% 2. name, an optional string representing the name of the ode function to be used
%
% Outputs
%
% 1. a file 'name.m' defining a function that defines the ode equations of
% the model for use with the ode solvers
% (if no name supplied the model id will be used)
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
switch (nargin)
case 0
error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'must have at least one argument');
case 1
SBMLModel = varargin{1};
filename = '';
case 2
SBMLModel = varargin{1};
filename = varargin{2};
otherwise
error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'does not take more than two arguments');
end;
% check input is an SBML model
if (~isValidSBML_Model(SBMLModel))
error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'first argument must be an SBMLModel structure');
end;
% -------------------------------------------------------------
% check that we can deal with the model
% for i=1:length(SBMLModel.parameter)
% if (SBMLModel.parameter(i).constant == 0)
% error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'Cannot deal with varying parameters');
% end;
% end;
if SBMLModel.SBML_level > 2
if ~isempty(SBMLModel.conversionFactor)
error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'Cannot deal with conversion factors');
end;
for i=1:length(SBMLModel.species)
if ~isempty(SBMLModel.species(i).conversionFactor)
error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'Cannot deal with conversion factors');
end;
end;
end;
for i=1:length(SBMLModel.compartment)
if (SBMLModel.compartment(i).constant == 0)
error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'Cannot deal with varying compartments');
end;
end;
% if (length(SBMLModel.species) == 0)
% error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'Cannot deal with models with no species');
% end;
for i=1:length(SBMLModel.event)
if exist('OCTAVE_VERSION') && length(SBMLModel.event) > 0
error('Octave cannot deal with events');
end;
if (~isempty(SBMLModel.event(i).delay))
error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'Cannot deal with delayed events');
end;
if SBMLModel.SBML_level > 2
if (~isempty(SBMLModel.event(i).priority))
error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'Cannot deal with event priorities');
end;
if (~isempty(SBMLModel.event(i).trigger) && ...
(SBMLModel.event(i).trigger.initialValue == 1 || SBMLModel.event(i).trigger.persistent == 1))
error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'Cannot deal with persistent trigger');
end;
end;
end;
for i=1:length(SBMLModel.reaction)
if (SBMLModel.reaction(i).fast == 1)
error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'Cannot deal with fast reactions');
end;
end;
if (length(SBMLModel.compartment) > 1)
error('WriteODEFunction(SBMLModel, (optional) filename)\n%s', 'Cannot deal with multiple compartments');
end;
if (SBMLModel.SBML_level > 1 && ~isempty(SBMLModel.time_symbol))
for i=1:length(SBMLModel.rule)
if (strcmp(SBMLModel.rule(i).typecode, 'SBML_ASSIGNMENT_RULE'))
if (~isempty(matchName(SBMLModel.rule(i).formula, SBMLModel.time_symbol)))
error('Cannot deal with time in an assignment rule');
end;
end;
end;
end;
if (SBMLModel.SBML_level > 1 && ~isempty(SBMLModel.delay_symbol))
for i=1:length(SBMLModel.rule)
if (strcmp(SBMLModel.rule(i).typecode, 'SBML_ASSIGNMENT_RULE'))
if (~isempty(matchName(SBMLModel.rule(i).formula, SBMLModel.delay_symbol)))
error('Cannot deal with delay in an assignment rule');
end;
end;
end;
end;
%--------------------------------------------------------------
% get information from the model
[ParameterNames, ParameterValues] = GetAllParametersUnique(SBMLModel);
[VarParams, VarInitValues] = GetVaryingParameters(SBMLModel);
NumberParams = length(VarParams);
NumberSpecies = length(SBMLModel.species);
if NumberSpecies > 0
Species = AnalyseSpecies(SBMLModel);
Speciesnames = GetSpecies(SBMLModel);
end;
if NumberParams > 0
Parameters = AnalyseVaryingParameters(SBMLModel);
end;
if length(SBMLModel.compartment) > 0
[CompartmentNames, CompartmentValues] = GetCompartments(SBMLModel);
else
CompartmentNames = [];
end;
if (NumberParams + NumberSpecies) == 0
error('Cannot detect any variables');
end;
if (SBMLModel.SBML_level > 1)
NumEvents = length(SBMLModel.event);
NumFuncs = length(SBMLModel.functionDefinition);
% version 2.0.2 adds the time_symbol field to the model structure
% need to check that it exists
if (isfield(SBMLModel, 'time_symbol'))
if (~isempty(SBMLModel.time_symbol))
timeVariable = SBMLModel.time_symbol;
else
timeVariable = 'time';
end;
else
timeVariable = 'time';
end;
if ((SBMLModel.SBML_level == 2 &&SBMLModel.SBML_version > 1) || ...
(SBMLModel.SBML_level > 2))
if (length(SBMLModel.constraint) > 0)
error('Cannot deal with constraints.');
end;
end;
else
NumEvents = 0;
NumFuncs = 0;
timeVariable = 'time';
end;
%---------------------------------------------------------------
% get the name/id of the model
Name = '';
if (SBMLModel.SBML_level == 1)
Name = SBMLModel.name;
else
if (isempty(SBMLModel.id))
Name = SBMLModel.name;
else
Name = SBMLModel.id;
end;
end;
if (~isempty(filename))
Name = filename;
elseif (length(Name) > 63)
Name = Name(1:60);
end;
fileName = strcat(Name, '.m');
%--------------------------------------------------------------------
% open the file for writing
fileID = fopen(fileName, 'w');
% write the function declaration
% if no events and using octave
if (exist('OCTAVE_VERSION') && NumEvents == 0)
fprintf(fileID, 'function xdot = %s(x_values, %s)\n', Name, timeVariable);
else
fprintf(fileID, 'function xdot = %s(%s, x_values)\n', Name, timeVariable);
end;
% need to add comments to output file
fprintf(fileID, '%% function %s takes\n', Name);
fprintf(fileID, '%%\n');
fprintf(fileID, '%% either\t1) no arguments\n');
fprintf(fileID, '%% \t and returns a vector of the initial values\n');
fprintf(fileID, '%%\n');
fprintf(fileID, '%% or \t2) time - the elapsed time since the beginning of the reactions\n');
fprintf(fileID, '%% \t x_values - vector of the current values of the variables\n');
fprintf(fileID, '%% \t and returns a vector of the rate of change of value of each of the variables\n');
fprintf(fileID, '%%\n');
fprintf(fileID, '%% %s can be used with MATLABs odeN functions as \n', Name);
fprintf(fileID, '%%\n');
fprintf(fileID, '%%\t[t,x] = ode23(@%s, [0, t_end], %s)\n', Name, Name);
fprintf(fileID, '%%\n');
fprintf(fileID, '%%\t\t\twhere t_end is the end time of the simulation\n');
fprintf(fileID, '%%\n');
fprintf(fileID, '%%The variables in this model are related to the output vectors with the following indices\n');
fprintf(fileID, '%%\tIndex\tVariable name\n');
for i = 1:NumberSpecies
fprintf(fileID, '%%\t %u \t %s\n', i, char(Species(i).Name));
end;
for i = 1:NumberParams
fprintf(fileID, '%%\t %u \t %s\n', i+NumberSpecies, char(VarParams{i}));
end;
fprintf(fileID, '%%\n');
% write the variable vector
fprintf(fileID, '%%--------------------------------------------------------\n');
fprintf(fileID, '%% output vector\n\n');
fprintf(fileID, 'xdot = zeros(%u, 1);\n', NumberSpecies+NumberParams);
% write the compartment values
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% compartment values\n\n');
for i = 1:length(CompartmentNames)
fprintf(fileID, '%s = %g;\n', CompartmentNames{i}, CompartmentValues(i));
end;
% write the parameter values
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% parameter values\n\n');
for i = 1:length(ParameterNames)
fprintf(fileID, '%s = %g;\n', ParameterNames{i}, ParameterValues(i));
end;
% write the initial concentration values for the species
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% initial values of variables - these may be overridden by assignment rules\n');
fprintf(fileID, '%% NOTE: any use of initialAssignments has been considered in calculating the initial values\n\n');
fprintf(fileID, 'if (nargin == 0)\n');
% if time symbol is used in any subsequent formula it is undeclared
% for the initial execution of the function
% which would only happen when time = 0
fprintf(fileID, '\n\t%% initial time\n');
fprintf(fileID, '\t%s = 0;\n', timeVariable);
fprintf(fileID, '\n\t%% initial values\n');
for i = 1:NumberSpecies
if (Species(i).isConcentration == 1)
fprintf(fileID, '\t%s = %g;\n', char(Species(i).Name), Species(i).initialValue);
elseif (Species(i).hasAmountOnly == 1)
fprintf(fileID, '\t%s = %g;\n', char(Species(i).Name), Species(i).initialValue);
else
fprintf(fileID, '\t%s = %g/%s;\n', char(Species(i).Name), Species(i).initialValue, Species(i).compartment);
end;
end;
for i = 1:NumberParams
fprintf(fileID, '\t%s = %g;\n', char(Parameters(i).Name), Parameters(i).initialValue);
end;
fprintf(fileID, '\nelse\n');
fprintf(fileID, '\t%% floating variable values\n');
for i = 1:NumberSpecies
fprintf(fileID, '\t%s = x_values(%u);\n', char(Species(i).Name), i);
end;
for i = 1:NumberParams
fprintf(fileID, '\t%s = x_values(%u);\n', char(Parameters(i).Name), i+NumberSpecies);
end;
fprintf(fileID, '\nend;\n');
% write assignment rules
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% assignment rules\n');
AssignRules = Model_getListOfAssignmentRules(SBMLModel);
for i = 1:length(AssignRules)
rule = WriteRule(AssignRules(i));
fprintf(fileID, '%s\n', rule);
end;
% write algebraic rules
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% algebraic rules\n');
for i = 1:NumberSpecies
if (Species(i).ConvertedToAssignRule == 1)
fprintf(fileID, '%s = %s;\n', char(Species(i).Name), Species(i).ConvertedRule);
end;
end;
for i = 1:NumberParams
if (Parameters(i).ConvertedToAssignRule == 1)
fprintf(fileID, '%s = %s;\n', char(Parameters(i).Name), Parameters(i).ConvertedRule);
end;
end;
% write code to calculate concentration values
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% calculate concentration values\n\n');
fprintf(fileID, 'if (nargin == 0)\n');
fprintf(fileID, '\n\t%% initial values\n');
% need to catch any initial concentrations that are not set
% and case where an initial concentration is set but is incosistent with a
% later rule
for i = 1:NumberSpecies
if (Species(i).ChangedByAssignmentRule == 0)
% not set by rule - use value given
if (isnan(Species(i).initialValue))
error('WriteODEFunction(SBMLModel)\n%s', 'species concentration not provided or assigned by rule');
else
if (Species(i).isConcentration == 1)
fprintf(fileID, '\txdot(%u) = %g;\n', i, Species(i).initialValue);
elseif (Species(i).hasAmountOnly == 1)
fprintf(fileID, '\txdot(%u) = %g;\n', i, Species(i).initialValue);
else
fprintf(fileID, '\txdot(%u) = %g/%s;\n', i, Species(i).initialValue, Species(i).compartment);
end;
% fprintf(fileID, '\txdot(%u) = %g;\n', i, Species(i).initialValue);
end;
else
% initial concentration set by rule
fprintf(fileID, '\txdot(%u) = %s;\n', i, char(Species(i).Name));
end;
end; % for NumSpecies
% parameters
for i = 1:NumberParams
if (Parameters(i).ChangedByAssignmentRule == 0 && Parameters(i).ConvertedToAssignRule == 0)
% not set by rule - use value given
if (isnan(Parameters(i).initialValue))
error('WriteODEFunction(SBMLModel)\n%s', 'parameter not provided or assigned by rule');
else
fprintf(fileID, '\txdot(%u) = %g;\n', i+NumberSpecies, Parameters(i).initialValue);
end;
else
% initial concentration set by rule
fprintf(fileID, '\txdot(%u) = %s;\n', i+NumberSpecies, char(Parameters(i).Name));
end;
end; % for NumParams
fprintf(fileID, '\nelse\n');
fprintf(fileID, '\n\t%% rate equations\n');
NeedToOrderArray = 0;
for i = 1:NumberSpecies
if (Species(i).ChangedByReaction == 1)
% need to look for piecewise functions
if (isempty(matchFunctionName(char(Species(i).KineticLaw), 'piecewise')))
if (Species(i).hasAmountOnly == 0)
Array{i} = sprintf('\txdot(%u) = (%s)/%s;\n', i, char(Species(i).KineticLaw), Species(i).compartment);
else
Array{i} = sprintf('\txdot(%u) = %s;\n', i, char(Species(i).KineticLaw));
end;
else
var = sprintf('xdot(%u)', i);
Array{i} = WriteOutPiecewise(var, char(Species(i).KineticLaw));
end;
elseif (Species(i).ChangedByRateRule == 1)
% a rule will be in concentration by default
% if (Species(i).isConcentration == 1)
Array{i} = sprintf('\txdot(%u) = %s;\n', i, char(Species(i).RateRule));
% else
% Array{i} = sprintf('\txdot(%u) = (%s)*%s;\n', i, char(Species(i).RateRule), Species(i).compartment);
% end;
% Array{i} = sprintf('\txdot(%u) = %s;\n', i, char(Species(i).RateRule));
elseif (Species(i).ChangedByAssignmentRule == 1)
% here no rate law has been provided by either kinetic law or rate
% rule - need to check whether the species is in an
% assignment rule which may impact on the rate
%%% Checking for a piecewise in the assignment rule and
%%% handling it
%%% Change made by Sumant Turlapati, Entelos, Inc. on June 8th, 2005
if (isempty(matchFunctionName(char(Species(i).AssignmentRule), 'piecewise')))
DifferentiatedRule = DifferentiateRule(char(Species(i).AssignmentRule), Speciesnames, SBMLModel);
Array{i} = sprintf('\txdot(%u) = %s;\n', i, char(DifferentiatedRule));
NeedToOrderArray = 1;
else
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% TO DO NESTED PIECEWISE
Args = DealWithPiecewise(char(Species(i).AssignmentRule));
DiffRule1 = DifferentiateRule(char(Args{1}), Speciesnames, SBMLModel);
DiffRule2 = DifferentiateRule(char(Args{3}), Speciesnames, SBMLModel);
Array{i} = sprintf('\tif (%s) \n\t\txdot(%d) = %s;\n\telse\n\t\txdot(%u) = %s;\n\tend;\n', ...
Args{2}, i, char(DiffRule1), i, char(DiffRule2));
% NeedToOrderArray = 1;
end;
%DifferentiatedRule = DifferentiateRule(char(Species(i).AssignmentRule), Speciesnames);
%Array{i} = sprintf('\txdot(%u) = %s;\n', i, char(DifferentiatedRule));
%NeedToOrderArray = 1;
elseif (Species(i).ConvertedToAssignRule == 1)
% here no rate law has been provided by either kinetic law or rate
% rule - need to check whether the species is in an
% algebraic rule which may impact on the rate
DifferentiatedRule = DifferentiateRule(char(Species(i).ConvertedRule), Speciesnames, SBMLModel);
Array{i} = sprintf('\txdot(%u) = %s;\n', i, char(DifferentiatedRule));
NeedToOrderArray = 1;
else
% not set by anything
Array{i} = sprintf('\txdot(%u) = 0;\n', i);
end;
end; % for Numspecies
for i = 1:NumberParams
if (Parameters(i).ChangedByRateRule == 1)
Array{i+NumberSpecies} = sprintf('\txdot(%u) = %s;\n', i+NumberSpecies, char(Parameters(i).RateRule));
elseif (Parameters(i).ChangedByAssignmentRule == 1)
if (isempty(matchFunctionName(char(Parameters(i).AssignmentRule), 'piecewise')))
DifferentiatedRule = DifferentiateRule(char(Parameters(i).AssignmentRule), VarParams, SBMLModel);
Array{i+NumberSpecies} = sprintf('\txdot(%u) = %s;\n', i+NumberSpecies, char(DifferentiatedRule));
NeedToOrderArray = 1;
else
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% TO DO NESTED PIECEWISE
Args = DealWithPiecewise(char(Parameters(i).AssignmentRule));
DiffRule1 = DifferentiateRule(char(Args{1}), VarParams, SBMLModel);
DiffRule2 = DifferentiateRule(char(Args{3}), VarParams, SBMLModel);
Array{i+NumberSpecies} = sprintf('\tif (%s) \n\t\txdot(%d) = %s;\n\telse\n\t\txdot(%u) = %s;\n\tend;\n', ...
Args{2}, i+NumberSpecies, char(DiffRule1), i+NumberSpecies, char(DiffRule2));
% NeedToOrderArray = 1;
end;
elseif (Parameters(i).ConvertedToAssignRule == 1)
% here no rate law has been provided by either kinetic law or rate
% rule - need to check whether the species is in an
% algebraic rule which may impact on the rate
DifferentiatedRule = DifferentiateRule(char(Parameters(i).ConvertedRule), VarParams, SBMLModel);
Array{i+NumberSpecies} = sprintf('\txdot(%u) = %s;\n', i+NumberSpecies, char(DifferentiatedRule));
NeedToOrderArray = 1;
else
% not set by anything
Array{i+NumberSpecies} = sprintf('\txdot(%u) = 0;\n', i+NumberSpecies);
end;
end; % for Numparams
% need to check that assignments are made in appropriate order
% deals with rules that have been differentiated where xdot may occur on
% both sides of an equation
if (NeedToOrderArray == 1)
Array = OrderArray(Array);
end;
if (NumberSpecies + NumberParams) > 0
for i = 1:length(Array)
fprintf(fileID, '%s', Array{i});
end;
end;
fprintf(fileID, '\nend;\n');
% -----------------------------------------------------------------
if (NumEvents > 0)
% write two additional files for events
WriteEventHandlerFunction(SBMLModel, Name);
WriteEventAssignmentFunction(SBMLModel, Name);
end;
% ------------------------------------------------------------------
% put in any function definitions
if (NumFuncs > 0)
fprintf(fileID, '\n\n%%---------------------------------------------------\n%%Function definitions\n\n');
for i = 1:NumFuncs
Name = SBMLModel.functionDefinition(i).id;
Elements = GetArgumentsFromLambdaFunction(SBMLModel.functionDefinition(i).math);
fprintf(fileID, '%%function %s\n\n', Name);
fprintf(fileID, 'function returnValue = %s(', Name);
for j = 1:length(Elements)-1
if (j == length(Elements)-1)
fprintf(fileID, '%s', Elements{j});
else
fprintf(fileID, '%s, ', Elements{j});
end;
end;
if (isempty(matchFunctionName(Elements{end}, 'piecewise')))
fprintf(fileID, ')\n\nreturnValue = %s;\n\n\n', Elements{end});
else
pw = WriteOutPiecewise('returnValue', Elements{end});
fprintf(fileID, ')\n\n%s\n\n', pw);
end;
end;
end;
fclose(fileID);
%--------------------------------------------------------------------------
function y = WriteRule(SBMLRule)
y = '';
switch (SBMLRule.typecode)
case 'SBML_ASSIGNMENT_RULE'
if (isempty(matchFunctionName(char(SBMLRule.formula), 'piecewise')))
y = sprintf('%s = %s;', SBMLRule.variable, SBMLRule.formula);
else
var = sprintf('%s', SBMLRule.variable);
y = WriteOutPiecewise(var, char(SBMLRule.formula));
end;
case 'SBML_SPECIES_CONCENTRATION_RULE'
y = sprintf('%s = %s;', SBMLRule.species, SBMLRule.formula);
case 'SBML_PARAMETER_RULE'
y = sprintf('%s = %s;', SBMLRule.name, SBMLRule.formula);
case 'SBML_COMPARTMENT_VOLUME_RULE'
y = sprintf('%s = %s;', SBMLRule.compartment, SBMLRule.formula);
otherwise
error('No assignment rules');
end;
%--------------------------------------------------------------------------
function formula = DifferentiateRule(f, SpeciesNames, model)
if (model.SBML_level > 1 && ~isempty(model.time_symbol))
if (~isempty(matchName(f, model.time_symbol)))
error('Cannot deal with time in an assignment rule');
end;
end;
if (~isempty(matchFunctionName(f, 'piecewise')))
error('Cannot deal with nested piecewise in an assignment rule');
end;
% if the formula contains a functionDefinition
% need to get rid of it first
for i=1:length(model.functionDefinition)
id = model.functionDefinition(i).id;
if (~isempty(matchFunctionName(f, id)))
f = SubstituteFunction(f, model.functionDefinition(i));
% remove surrounding brackets
if (strcmp(f(1), '(') && strcmp(f(end), ')'))
f = f(2:end-1);
end;
end;
end;
Brackets = PairBrackets(f);
Dividers = '+-';
Divide = ismember(f, Dividers);
% dividers between brackets do not count
if (Brackets ~= 0)
[NumPairs,y] = size(Brackets);
for i = 1:length(Divide)
if (Divide(i) == 1)
for j = 1:NumPairs
if ((i > Brackets(j,1)) && (i < Brackets(j, 2)))
Divide(i) = 0;
end;
end;
end;
end;
end;
Divider = '';
NoElements = 1;
element = '';
for i = 1:length(f)
if (Divide(i) == 0)
element = strcat(element, f(i));
else
Divider = strcat(Divider, f(i));
Elements{NoElements} = element;
NoElements = NoElements + 1;
element = '';
end;
% catch last element
if (i == length(f))
Elements{NoElements} = element;
end;
end;
for i = 1:NoElements
% check whether element contains a species name
% need to catch case where element is number and
% species names use numbers eg s3 element '3'
found = 0;
for j = 1:length(SpeciesNames)
% j = 1;
A = matchName(Elements{i}, SpeciesNames{j});
if (~isempty(A))
if (length(Elements{i}) == length(SpeciesNames{j}))
found = 1; % exact match
else
% need to check what has been found
poscharAfter = A(1) + length(SpeciesNames{j});
poscharBefore = A(1) - 1;
if (poscharBefore > 0)
charBefore = Elements{i}(poscharBefore);
else
charBefore = '*';
end;
if (poscharAfter <= length(Elements{i}))
charAfter = Elements{i}(poscharAfter);
else
charAfter = '*';
end;
if ((charBefore == '*' || charBefore == '/') && ...
(charAfter == '*' || charAfter == '/'))
found = 1;
end;
end;
if (found == 1)
break;
end;
end;
end;
if (found == 0)
% this element does not contain a species
Elements{i} = strrep(Elements{i}, Elements{i}, '0');
else
% this element does contain a species
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% WHAT IF MORE THAN ONE SPECIES
% for moment assume this would not happen
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Power = strfind(Elements{i}, '^');
if (~isempty(Power))
Number = '';
Digits = isstrprop(Elements{i}, 'digit');
k = Power+1;
while ((k < (length(Elements{i})+1)) & (Digits(k) == 1))
Number = strcat(Number, Elements{i}(k));
k = k + 1;
end;
Index = str2num(Number);
Replace = sprintf('%u * %s^%u*xdot(%u)', Index, SpeciesNames{j}, Index-1, j);
Initial = sprintf('%s^%u', SpeciesNames{j}, Index);
Elements{i} = strrep(Elements{i}, Initial, Replace);
else
Replace = sprintf('xdot(%u)', j);
Elements{i} = strrep(Elements(i), SpeciesNames{j}, Replace);
end;
end;
end;
% put the formula back together
formula = '';
for i = 1:NoElements-1
formula = strcat(formula, Elements{i}, Divider(i));
end;
formula = strcat(formula, Elements{NoElements});
%--------------------------------------------------------------------------
% function to put rate assignments in appropriate order
% eg
% xdot(2) = 3
% xdot(1) = 3* xdot(2)
function Output = OrderArray(Array)
% if (length(Array) > 9)
% error('cannot deal with more than 10 species yet');
% end;
NewArrayIndex = 1;
TempArrayIndex = 1;
TempArray2Index = 1;
NumberInNewArray = 0;
NumberInTempArray = 0;
NumberInTempArray2 = 0;
TempArray2 = {};
% put any formula withoutxdot on RHS into new array
for i = 1:length(Array)
if (length(strfind(Array{i}, 'xdot'))> 2)
% xdot occurs more than once
% put in temp array
TempArray{TempArrayIndex} = Array{i};
TempArrayIndices(TempArrayIndex) = i;
% update
TempArrayIndex = TempArrayIndex + 1;
NumberInTempArray = NumberInTempArray + 1;
elseif (length(strfind(Array{i}, 'xdot'))==2)
% if it is piecewise it will be of form if x xdot() = else xdot()
% so xdot will occur twice but not necessarily on RHS
if (length(strfind(Array{i}, 'if (')) == 1 ...
&& strfind(Array{i}, 'if (') < 3)
% put in New array
NewArray{NewArrayIndex} = Array{i};
NewArrayIndices(NewArrayIndex) = i;
% update
NewArrayIndex = NewArrayIndex + 1;
NumberInNewArray = NumberInNewArray + 1;
else
TempArray{TempArrayIndex} = Array{i};
TempArrayIndices(TempArrayIndex) = i;
% update
TempArrayIndex = TempArrayIndex + 1;
NumberInTempArray = NumberInTempArray + 1;
% error('cannot deal with this function %s', Array{i});
end;
else
% no xdot on RHS
% put in New array
NewArray{NewArrayIndex} = Array{i};
NewArrayIndices(NewArrayIndex) = i;
% update
NewArrayIndex = NewArrayIndex + 1;
NumberInNewArray = NumberInNewArray + 1;
end;
end;
while (NumberInTempArray > 0)
% go thru temp array
for i = 1:NumberInTempArray
% find positions of xdot
Xdot = strfind(TempArray{i}, 'xdot');
% check whether indices of xdot on RHS are already in new array
Found = 0;
for j = 2:length(Xdot)
Number = str2num(TempArray{i}(Xdot(j)+5));
if (sum(ismember(NewArrayIndices, Number)) == 1)
Found = 1;
else
Found = 0;
end;
end;
% if all have been found put in new array
if (Found == 1)
% put in New array
NewArray{NewArrayIndex} = TempArray{i};
NewArrayIndices(NewArrayIndex) = TempArrayIndices(i);
% update
NewArrayIndex = NewArrayIndex + 1;
NumberInNewArray = NumberInNewArray + 1;
else
% put in temp array2
TempArray2{TempArray2Index} = TempArray{i};
TempArray2Indices(TempArray2Index) = TempArrayIndices(i);
% update
TempArray2Index = TempArray2Index + 1;
NumberInTempArray2 = NumberInTempArray2 + 1;
end;
end;
%Realloctate temp arrays
if (~isempty(TempArray2))
TempArray = TempArray2;
TempArrayIndices = TempArray2Indices;
NumberInTempArray = NumberInTempArray2;
TempArray2Index = 1;
NumberInTempArray2 = 0;
else
NumberInTempArray = 0;
end;
end; % of while NumInTempArray > 0
Output = NewArray;
function output = WriteOutPiecewise(var, formula)
Arguments = DealWithPiecewise(formula);
if (strfind('piecewise', Arguments{2}))
error('Cant do this yet!');
end;
Text1{1} = sprintf('\n\tif (%s)', Arguments{2});
if (matchFunctionName(Arguments{1}, 'piecewise'))
Text1{2} = WriteOutPiecewise(var, Arguments{1});
else
Text1{2} = sprintf('\n\t\t%s = %s;', var, Arguments{1});
end;
Text1{3} = sprintf('\n\telse');
if (matchFunctionName('piecewise', Arguments{3}))
Text1{4} = WriteOutPiecewise(var, Arguments{3});
else
Text1{4} = sprintf('\n\t\t%s = %s;\n\tend;\n', var, Arguments{3});
end;
output = Text1{1};
for (i = 2:4)
output = strcat(output, Text1{i});
end;
|
github
|
EPFL-LCSB/matTFA-master
|
WriteEventAssignmentFunction.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Simulation/WriteEventAssignmentFunction.m
| 9,101 |
utf_8
|
0b45ac0f8184fe7240a489b6399337d3
|
function WriteEventAssignmentFunction(SBMLModel, Name)
% WriteEventAssignmentFunction(SBMLModel, name)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
% 2. name, a string representing the name of the ode function being used
%
% Outputs
%
% 1. a file 'name_eventAssign.m' defining a function that assigns values following an event
% (for use with the event option of MATLABs ode solvers)
%
% *NOTE:* This function is called from WriteODEFunction when a model with
% events is encountered.
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
% check input is an SBML model
if (~isValidSBML_Model(SBMLModel))
error('WriteEventAssignmentFunction(SBMLModel)\n%s', 'argument must be an SBMLModel structure');
end;
% -------------------------------------------------------------
% get information from the model
% get information from the model
[ParameterNames, ParameterValues] = GetAllParametersUnique(SBMLModel);
[VarParams, VarInitValues] = GetVaryingParameters(SBMLModel);
NumberParams = length(VarParams);
[SpeciesNames, SpeciesValues] = GetSpecies(SBMLModel);
NumberSpecies = length(SBMLModel.species);
VarNames = [SpeciesNames, VarParams];
VarValues = [SpeciesValues, VarInitValues];
NumberVars = NumberSpecies + NumberParams;
NumFuncs = length(SBMLModel.functionDefinition);
Species = AnalyseSpecies(SBMLModel);
Params = AnalyseVaryingParameters(SBMLModel);
%---------------------------------------------------------------
% get the name/id of the model
% Name = '';
% if (SBMLModel.SBML_level == 1)
% Name = SBMLModel.name;
% else
% if (isempty(SBMLModel.id))
% Name = SBMLModel.name;
% else
% Name = SBMLModel.id;
% end;
% end;
% version 2.0.2 adds the time_symbol field to the model structure
% need to check that it exists
if (isfield(SBMLModel, 'time_symbol'))
if (~isempty(SBMLModel.time_symbol))
timeVariable = SBMLModel.time_symbol;
else
timeVariable = 'time';
end;
else
timeVariable = 'time';
end;
Name = strcat(Name, '_eventAssign');
fileName = strcat(Name, '.m');
%--------------------------------------------------------------------
% open the file for writing
fileID = fopen(fileName, 'w');
% write the function declaration
fprintf(fileID, 'function Values = %s(%s, VarValues, eventNo)\n', Name, timeVariable);
% need to add comments to output file
fprintf(fileID, '%% function %s takes\n', Name);
fprintf(fileID, '%%\n');
fprintf(fileID, '%% current simulation time\n');
fprintf(fileID, '%%\n');
fprintf(fileID, '%% vector of current species values\n');
fprintf(fileID, '%%\n');
fprintf(fileID, '%% the number of the event that has triggered\n');
fprintf(fileID, '%%\n');
fprintf(fileID, '%% and returns the values assigned by an event assignment\n');
fprintf(fileID, '%%\n');
fprintf(fileID, '%% %s should be used with MATLABs odeN functions\n', Name);
fprintf(fileID, '%% and called to reinitialise values when an event has stopped the integration\n');
fprintf(fileID, '%%\n');
fprintf(fileID, '\n');
% write the parameter values
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% parameter values\n\n');
for i = 1:length(ParameterNames)
fprintf(fileID, '%s = %g;\n', ParameterNames{i}, ParameterValues(i));
end;
% write the current species concentrations
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% floating variables\n');
for i = 1:NumberVars
fprintf(fileID, '%s = VarValues(%u);\n', VarNames{i}, i);
end;
% write the event assignments
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% event assignments\n\n');
fprintf(fileID, 'switch(eventNo)\n');
for i = 1:length(SBMLModel.event)
fprintf(fileID, '\tcase %u\n', i);
for j = 1:length(SBMLModel.event(i).eventAssignment)
% if a variable being assigned occurs in the math of a subsequent event
% assignment the value should be the original
assignment = SBMLModel.event(i).eventAssignment(j).math;
for s=1:NumberVars
if (~isempty(matchName(SBMLModel.event(i).eventAssignment(j).math, VarNames{s})))
speciesV = sprintf('VarValues(%u)', s);
assignment = strrep(assignment, VarNames{s}, speciesV);
end;
end;
fprintf(fileID, '\t\t%s = %s;\n', SBMLModel.event(i).eventAssignment(j).variable, assignment);
end;
end;
fprintf(fileID, '\totherwise\nend;\n');
% write assignment rules
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% assignment rules\n');
AssignRules = Model_getListOfAssignmentRules(SBMLModel);
for i = 1:length(AssignRules)
rule = WriteRule(AssignRules(i));
fprintf(fileID, '%s\n', rule);
end;
% write algebraic rules
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% algebraic rules\n');
for i = 1:NumberSpecies
if (Species(i).ConvertedToAssignRule == 1)
fprintf(fileID, '%s = %s;\n', char(Species(i).Name), Species(i).ConvertedRule);
end;
end;
for i = 1:NumberParams
if (Params(i).ConvertedToAssignRule == 1)
fprintf(fileID, '%s = %s;\n', char(Params(i).Name), Params(i).ConvertedRule);
end;
end;
% output values
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% output values\n\n');
for i = 1:NumberVars
fprintf(fileID, 'Values(%u) = %s;\n', i, VarNames{i});
end;
% put in any function definitions
if (NumFuncs > 0)
fprintf(fileID, '\n\n%%---------------------------------------------------\n%%Function definitions\n\n');
for i = 1:NumFuncs
Name = SBMLModel.functionDefinition(i).id;
Elements = GetArgumentsFromLambdaFunction(SBMLModel.functionDefinition(i).math);
fprintf(fileID, '%%function %s\n\n', Name);
fprintf(fileID, 'function returnValue = %s(', Name);
for j = 1:length(Elements)-1
if (j == length(Elements)-1)
fprintf(fileID, '%s', Elements{j});
else
fprintf(fileID, '%s, ', Elements{j});
end;
end;
fprintf(fileID, ')\n\nreturnValue = %s;\n\n\n', Elements{end});
end;
end;
fclose(fileID);
%--------------------------------------------------------------------------
function y = WriteRule(SBMLRule)
y = '';
switch (SBMLRule.typecode)
case 'SBML_ASSIGNMENT_RULE'
if (isempty(matchFunctionName(char(SBMLRule.formula), 'piecewise')))
y = sprintf('%s = %s;', SBMLRule.variable, SBMLRule.formula);
else
var = sprintf('%s', SBMLRule.variable);
y = WriteOutPiecewise(var, char(SBMLRule.formula));
end;
case 'SBML_SPECIES_CONCENTRATION_RULE'
y = sprintf('%s = %s;', SBMLRule.species, SBMLRule.formula);
case 'SBML_PARAMETER_RULE'
y = sprintf('%s = %s;', SBMLRule.name, SBMLRule.formula);
case 'SBML_COMPARTMENT_VOLUME_RULE'
y = sprintf('%s = %s;', SBMLRule.compartment, SBMLRule.formula);
otherwise
error('No assignment rules');
end;
%------------------------------------------------------------------------------
function output = WriteOutPiecewise(var, formula)
Arguments = DealWithPiecewise(formula);
if (strfind('piecewise', Arguments{2}))
error('Cant do this yet!');
end;
Text1{1} = sprintf('\n\tif (%s)', Arguments{2});
if (matchFunctionName(Arguments{1}, 'piecewise'))
Text1{2} = WriteOutPiecewise(var, Arguments{1});
else
Text1{2} = sprintf('\n\t\t%s = %s;', var, Arguments{1});
end;
Text1{3} = sprintf('\n\telse');
if (strfind('piecewise', Arguments{3}))
Text1{4} = WriteOutPiecewise(var, Arguments{3});
else
Text1{4} = sprintf('\n\t\t%s = %s;\n\tend;\n', var, Arguments{3});
end;
output = Text1{1};
for (i = 2:4)
output = strcat(output, Text1{i});
end;
|
github
|
EPFL-LCSB/matTFA-master
|
AnalyseVaryingParameters.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Simulation/AnalyseVaryingParameters.m
| 10,969 |
utf_8
|
eadb1635027fd7b7829377f0df6f9f66
|
function VaryingParameters = AnalyseVaryingParameters(SBMLModel)
% [analysis] = AnalyseVaryingParameters(SBMLModel)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. a structure detailing any parameters that are not constant and how they are manipulated
% within the model
%
% *EXAMPLE:*
%
% Using the model from toolbox/Test/test-data/algebraicRules.xml
%
% analysis = AnalyseVaryingParameters(m)
%
% analysis =
% Name: {'s2'}
% initialValue: 4
% ChangedByRateRule: 0
% RateRule: ''
% ChangedByAssignmentRule: 0
% AssignmentRule: ''
% InAlgebraicRule: 1
% AlgebraicRule: {{1x1 cell}}
% ConvertedToAssignRule: 1
% ConvertedRule: '-(-S2-S3)'
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
if (~isValidSBML_Model(SBMLModel))
error('AnalyseVaryingParameters(SBMLModel)\n%s', ...
'argument must be an SBMLModel structure');
end;
VaryingParameters = [];
if length(SBMLModel.parameter) == 0
return;
end;
[names, Values] = GetVaryingParameters(SBMLModel);
[n, AssignRule] = GetParameterAssignmentRules(SBMLModel);
[n, RateRule] = GetParameterRateRules(SBMLModel);
[n, AlgRules] = GetParameterAlgebraicRules(SBMLModel);
% create the output structure
index = 1;
for i = 1:length(SBMLModel.parameter)
% skip constant parameters
if SBMLModel.parameter(i).constant == 1
continue;
end;
VaryingParameters(index).Name = names(index);
VaryingParameters(index).initialValue = Values(index);
if (strcmp(RateRule(i), '0'))
VaryingParameters(index).ChangedByRateRule = 0;
VaryingParameters(index).RateRule = '';
else
VaryingParameters(index).ChangedByRateRule = 1;
VaryingParameters(index).RateRule = RateRule(i);
end;
if (strcmp(AssignRule(i), '0'))
VaryingParameters(index).ChangedByAssignmentRule = 0;
VaryingParameters(index).AssignmentRule = '';
else
VaryingParameters(index).ChangedByAssignmentRule = 1;
VaryingParameters(index).AssignmentRule = AssignRule(i);
end;
if (strcmp(AlgRules(i), '0'))
VaryingParameters(index).InAlgebraicRule = 0;
VaryingParameters(index).AlgebraicRule = '';
else
VaryingParameters(index).InAlgebraicRule = 1;
VaryingParameters(index).AlgebraicRule = AlgRules(i);
end;
if ((VaryingParameters(index).ChangedByRateRule == 0) && (VaryingParameters(index).ChangedByAssignmentRule == 0))
if (VaryingParameters(index).InAlgebraicRule == 1)
VaryingParameters(index).ConvertedToAssignRule = 1;
Rule = VaryingParameters(index).AlgebraicRule{1};
% need to look at whether rule contains a user definined
% function
FunctionIds = Model_getFunctionIds(SBMLModel);
for f = 1:length(FunctionIds)
if (matchFunctionName(char(Rule), FunctionIds{f}))
Rule = SubstituteFunction(char(Rule), SBMLModel.functionDefinition(f));
end;
end;
SubsRule = SubsAssignmentRules(SBMLModel, char(Rule));
VaryingParameters(index).ConvertedRule = Rearrange(SubsRule, names{index});
else
VaryingParameters(index).ConvertedToAssignRule = 0;
VaryingParameters(index).ConvertedRule = '';
end;
else
VaryingParameters(index).ConvertedToAssignRule = 0;
VaryingParameters(index).ConvertedRule = '';
end;
index = index + 1;
end;
function form = SubsAssignmentRules(SBMLModel, rule)
[VaryingParameters, AssignRule] = GetParameterAssignmentRules(SBMLModel);
form = rule;
% bracket the VaryingParameters to be replaced
for i = 1:length(VaryingParameters)
if (matchName(rule, VaryingParameters{i}))
if (~strcmp(AssignRule{i}, '0'))
form = strrep(form, VaryingParameters{i}, strcat('(', VaryingParameters{i}, ')'));
end;
end;
end;
for i = 1:length(VaryingParameters)
if (matchName(rule, VaryingParameters{i}))
if (~strcmp(AssignRule{i}, '0'))
form = strrep(form, VaryingParameters{i}, AssignRule{i});
end;
end;
end;
function output = Arrange(formula, x, vars)
ops = '+-';
f = LoseWhiteSpace(formula);
operators = ismember(f, ops);
OpIndex = find(operators == 1);
%--------------------------------------------------
% divide formula up into elements seperated by +/-
if (OpIndex(1) == 1)
% leading sign i.e. +x-y
NumElements = length(OpIndex);
j = 2;
index = 2;
else
NumElements = length(OpIndex) + 1;
j = 1;
index = 1;
end;
for i = 1:NumElements-1
element = '';
while (j < OpIndex(index))
element = strcat(element, f(j));
j = j+1;
end;
Elements{i} = element;
j = j + 1;
index = index + 1;
end;
% get last element
j = OpIndex(end)+1;
element = '';
while (j <= length(f))
element = strcat(element, f(j));
j = j+1;
end;
Elements{NumElements} = element;
%--------------------------------------------------
% check whether element contains x
% if does keep on lhs else move to rhs changing sign
output = '';
lhs = 1;
for i = 1:NumElements
if (matchName(Elements{i}, x))
% element contains x
LHSElements{lhs} = Elements{i};
if (OpIndex(1) == 1)
LHSOps(lhs) = f(OpIndex(i));
elseif (i == 1)
LHSOps(lhs) = '+';
else
LHSOps(lhs) = f(OpIndex(i-1));
end;
lhs = lhs + 1;
elseif (i == 1)
% first element does not contain x
if (OpIndex(1) == 1)
if (strcmp(f(1), '-'))
output = strcat(output, '+');
else
output = strcat(output, '-');
end;
else
% no sign so +
output = strcat(output, '-');
end;
output = strcat(output, Elements{i});
else
% element not first and does not contain x
if (OpIndex(1) == 1)
if (strcmp(f(OpIndex(i)), '-'))
output = strcat(output, '+');
else
output = strcat(output, '-');
end;
else
if (strcmp(f(OpIndex(i-1)), '-'))
output = strcat(output, '+');
else
output = strcat(output, '-');
end;
end;
output = strcat(output, Elements{i});
end;
end;
%------------------------------------------------------
% look at remaining LHS
for i = 1:length(LHSElements)
Mult{i} = ParseElement(LHSElements{i}, x);
end;
if (length(LHSElements) == 1)
% only one element with x
% check signs and multipliers
if (strcmp(LHSOps(1), '-'))
output = strcat('-(', output, ')');
end;
if (~strcmp(Mult{1}, '1'))
output = strcat(output, '/', Mult{1});
end;
else
divisor = '';
if (strcmp(LHSOps(1), '+'))
divisor = strcat(divisor, '(', Mult{1});
else
divisor = strcat(divisor, '(-', Mult{1});
end;
for i = 2:length(LHSElements)
divisor = strcat(divisor, LHSOps(i), Mult{i});
end;
divisor = strcat(divisor, ')');
output = strcat('(', output, ')/', divisor);
end;
function multiplier = ParseElement(element, x)
% assumes that the element is of the form n*x/m
% and returns n/m in simplest form
if (strcmp(element, x))
multiplier = '1';
return;
end;
VarIndex = matchName(element, x);
MultIndex = strfind(element, '*');
DivIndex = strfind(element, '/');
if (isempty(MultIndex))
MultIndex = 1;
end;
if (isempty(DivIndex))
DivIndex = length(element);
end;
if ((DivIndex < MultIndex) ||(VarIndex < MultIndex) || (VarIndex > DivIndex))
error('Cannot deal with formula in this form: %s', element);
end;
n = '';
m = '';
for i = 1:MultIndex-1
n = strcat(n, element(i));
end;
if (isempty(n))
n = '1';
end;
for i = DivIndex+1:length(element)
m = strcat(m, element(i));
end;
if (isempty(m))
m = '1';
end;
% if both m and n represenet numbers then they can be simplified
Num_n = str2num(n);
Num_m = str2num(m);
if (~isempty(Num_n) && ~isempty(Num_m))
multiplier = num2str(Num_n/Num_m);
else
if (strcmp(m, '1'))
multiplier = n;
else
multiplier = strcat(n, '/', m);
end;
end;
function y = LoseWhiteSpace(charArray)
% LoseWhiteSpace(charArray) takes an array of characters
% and returns the array with any white space removed
%
%----------------------------------------------------------------
% EXAMPLE:
% y = LoseWhiteSpace(' exa mp le')
% y = 'example'
%
%------------------------------------------------------------
% check input is an array of characters
if (~ischar(charArray))
error('LoseWhiteSpace(input)\n%s', 'input must be an array of characters');
end;
%-------------------------------------------------------------
% get the length of the array
NoChars = length(charArray);
%-------------------------------------------------------------
% create an array that indicates whether the elements of charArray are
% spaces
% e.g. WSpace = isspace(' v b') = [1, 1, 0, 1, 0]
% and determine how many
WSpace = isspace(charArray);
NoSpaces = sum(WSpace);
%-----------------------------------------------------------
% rewrite the array to leaving out any spaces
% remove any numbers from the array of symbols
if (NoSpaces > 0)
NewArrayCount = 1;
for i = 1:NoChars
if (~isspace(charArray(i)))
y(NewArrayCount) = charArray(i);
NewArrayCount = NewArrayCount + 1;
end;
end;
else
y = charArray;
end;
|
github
|
EPFL-LCSB/matTFA-master
|
WriteEventHandlerFunction.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Simulation/WriteEventHandlerFunction.m
| 12,176 |
utf_8
|
f5fbcd1778a9be55b55816f0d6e020a8
|
function WriteEventHandlerFunction(SBMLModel, Name)
% WriteEventHandlerFunction(SBMLModel, name)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
% 2. name, a string representing the name of the ode function being used
%
% Outputs
%
% 1. a file 'name_events.m' defining a function that tests whether events
% have been triggered
% (for use with the event option of MATLABs ode solvers)
%
% *NOTE:* This function is called from WriteODEFunction when a model with
% events is encountered.
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
% check input is an SBML model
if (~isValidSBML_Model(SBMLModel))
error('WriteEventHandlerFunction(SBMLModel)\n%s', 'argument must be an SBMLModel structure');
end;
% -------------------------------------------------------------
% get information from the model
[ParameterNames, ParameterValues] = GetAllParametersUnique(SBMLModel);
[VarParams, VarInitValues] = GetVaryingParameters(SBMLModel);
NumberParams = length(VarParams);
[SpeciesNames, SpeciesValues] = GetSpecies(SBMLModel);
NumberSpecies = length(SBMLModel.species);
VarNames = [SpeciesNames, VarParams];
VarValues = [SpeciesValues, VarInitValues];
NumberVars = NumberSpecies + NumberParams;
arrayVariable = 'var1';
if ismember(arrayVariable, VarNames)
arrayVariable = 'xyz_var1';
end;
if ismember(arrayVariable, VarNames)
error ('Unbelievable clash of variable names between model and event handling functions');
end;
%---------------------------------------------------------------
% get the name/id of the model
% Name = '';
% if (SBMLModel.SBML_level == 1)
% Name = SBMLModel.name;
% else
% if (isempty(SBMLModel.id))
% Name = SBMLModel.name;
% else
% Name = SBMLModel.id;
% end;
% end;
% version 2.0.2 adds the time_symbol field to the model structure
% need to check that it exists
if (isfield(SBMLModel, 'time_symbol'))
if (~isempty(SBMLModel.time_symbol))
timeVariable = SBMLModel.time_symbol;
else
timeVariable = 'time';
end;
else
timeVariable = 'time';
end;
if (min(VarValues) == 0)
degree = 1;
else
degree = round(log10(min(VarValues)));
end;
tol = 1e-10 * power(10, degree);
Name = strcat(Name, '_events');
fileName = strcat(Name, '.m');
%--------------------------------------------------------------------
% open the file for writing
fileID = fopen(fileName, 'w');
% write the function declaration
fprintf(fileID, 'function [value,isterminal,direction] = %s(%s, %s)\n', ...
Name, timeVariable, arrayVariable);
% need to add comments to output file
fprintf(fileID, '%% function %s takes\n', Name);
fprintf(fileID, '%%\n');
fprintf(fileID, '%%\t1) current elapsed time of integration\n');
fprintf(fileID, '%%\t2) vector of current output values\n');
fprintf(fileID, '%%\n');
fprintf(fileID, '%% and stops the integration if the value calculated is zero\n');
fprintf(fileID, '%%\n');
fprintf(fileID, '%% %s should be used with MATLABs odeN functions as \n', Name);
fprintf(fileID, '%% the events function option\n');
fprintf(fileID, '%%\n');
fprintf(fileID, '%%\ti.e. options = odeset(''Events'', @%s)\n', Name);
fprintf(fileID, '%%\n');
fprintf(fileID, '%%\t[t,x] = ode23(@function, [0, t_end], function, options)\n');
fprintf(fileID, '%%\n');
fprintf(fileID, '\n');
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% constant for use with < or >\neps = %g;\n\n', tol);
% write the parameter values
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% parameter values\n\n');
for i = 1:length(ParameterNames)
fprintf(fileID, '%s = %g;\n', ParameterNames{i}, ParameterValues(i));
end;
% write the current species concentrations
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% floating variables\n');
for i = 1:NumberVars
fprintf(fileID, '%s = %s(%u);\n', VarNames{i}, arrayVariable, i);
end;
% write the events
fprintf(fileID, '\n%%--------------------------------------------------------\n');
fprintf(fileID, '%% events - point at which value will return 0\n\n');
numOfFunctions = 0 ;
fprintf(fileID, 'value = [');
for i = 1:length(SBMLModel.event)
[Funcs, Ignored] = ParseTriggerFunction(SBMLModel.event(i).trigger,[]);
for j = 1:length(Funcs)
numOfFunctions = numOfFunctions + 1;
%fprintf(1, '%s\n', Funcs{j});
if ((i > 1) || (j > 1))
fprintf(fileID, ', %s', Funcs{j});
else
fprintf(fileID, '%s', Funcs{j});
end;
end;
end;
fprintf(fileID, '];\n');
fprintf(fileID, '\n%%stop integration\n');
fprintf(fileID, 'isterminal = [1');
for i = 2:numOfFunctions
fprintf(fileID, ', 1');
end;
fprintf(fileID, '];\n\n');
% this may depend on model
fprintf(fileID, '%%set direction at which event should be looked for\n');
fprintf(fileID, 'direction = [-1');
for i = 2:numOfFunctions
fprintf(fileID, ', -1');
end;
fprintf(fileID, '];\n\n');
fclose(fileID);
%--------------------------------------------------------------------------
% other functions
function [FunctionStrings, Trigger] = ParseTriggerFunction(Trigger, FunctionStrings)
%fprintf(1,'parsing: %s\n', Trigger);
if (isstruct(Trigger))
Trigger = LoseLeadingWhiteSpace(Trigger.math);
else
Trigger = LoseLeadingWhiteSpace(Trigger);
end;
% trigger has the form function(function(variable,constant), function(v,c))
% need to isolate each
OpenBracket = strfind(Trigger, '(');
Func = Trigger(1:OpenBracket-1);
Trigger = Trigger(OpenBracket+1:length(Trigger));
%fprintf(1,'got function: %s\n', Func);
switch (Func)
case 'and'
[FunctionStrings, Trigger] = ParseTwoArgumentsAndClose(Trigger, FunctionStrings);
case 'or'
[FunctionStrings, Trigger] = ParseTwoArgumentsAndClose(Trigger, FunctionStrings);
case 'lt'
[left, right, Trigger] = ParseTwoNumericArgumentsAndClose(Trigger);
FunctionString = sprintf('(%s) - (%s) + eps', left, right);
FunctionStrings{length(FunctionStrings)+1} = FunctionString;
case 'le'
[left, right, Trigger] = ParseTwoNumericArgumentsAndClose(Trigger);
FunctionString = sprintf('(%s) - (%s) + eps', left, right);
FunctionStrings{length(FunctionStrings)+1} = FunctionString;
case 'gt'
[left, right, Trigger] = ParseTwoNumericArgumentsAndClose(Trigger);
FunctionString = sprintf('(%s) - (%s) + eps', right, left);
FunctionStrings{length(FunctionStrings)+1} = FunctionString;
case 'ge'
[left, right, Trigger] = ParseTwoNumericArgumentsAndClose(Trigger);
FunctionString = sprintf('(%s) - (%s) + eps', right, left);
FunctionStrings{length(FunctionStrings)+1} = FunctionString;
otherwise
error(sprintf('unrecognised function %s in trigger', Func));
end;
function [FunctionStrings, Trigger] = ParseTwoArgumentsAndClose(Trigger, FunctionStrings)
%fprintf(1, 'In ParseTwoArgumentsAndClose parsing: %s\n', Trigger);
[FunctionStrings, Trigger] = ParseTriggerFunction(Trigger, FunctionStrings);
comma = strfind(Trigger, ',');
[FunctionStrings, Trigger] = ParseTriggerFunction(Trigger(comma+1:length(Trigger)), FunctionStrings);
closeBracket = strfind(Trigger, ')');
Trigger = Trigger(closeBracket+1:length(Trigger));
function [left, right, Trigger] = ParseTwoNumericArgumentsAndClose(Trigger)
[left, Trigger] = ParseNumericFunction(Trigger);
comma = strfind(Trigger, ',');
[right, Trigger] = ParseNumericFunction(Trigger(comma+1:length(Trigger)));
closeBracket = strfind(Trigger, ')');
Trigger = Trigger(closeBracket+1:length(Trigger));
function [func, Trigger] = ParseNumericFunction(Trigger)
%fprintf(1,'In ParseNumericFunction parsing: %s\n', Trigger);
openBracket = strfind(Trigger, '(');
comma = strfind(Trigger, ',');
closeBracket = strfind(Trigger, ')');
if (isempty(openBracket) || (length(comma)~=0 && comma(1) < openBracket(1)) ...
|| (length(closeBracket)~=0 && closeBracket(1) < openBracket(1)))
% simple case where no nesting
if (length(comma)~=0 && comma(1) < closeBracket(1))
% terminated by comma
func = Trigger(1:comma(1)-1);
Trigger = Trigger(comma(1):length(Trigger));
else
if (length(closeBracket)~=0)
% terminated by close bracket
func = Trigger(1:closeBracket(1)-1);
Trigger=Trigger(closeBracket(1):length(Trigger));
else
func=Trigger;
Trigger='';
end;
end;
else
% nested case
func = Trigger(1:openBracket-1);
Trigger = Trigger(openBracket+1:length(Trigger));
[subfunc, Trigger] = ParseNumericFunction(Trigger);
func = sprintf('%s(%s', func, subfunc);
Trigger = LoseLeadingWhiteSpace(Trigger);
comma = strfind(Trigger, ',');
while (length(comma) ~= 0 && comma(1) == 1)
[subfunc, Trigger] = ParseNumericFunction(Trigger);
func = sprintf('%s,%s', func, subfunc);
Trigger = LoseLeadingWhiteSpace(Trigger);
comma = strfind(Trigger, ',');
end
func=sprintf('%s)',func);
closeBracket=strfind(Trigger, ')');
Trigger = Trigger(closeBracket(1)+1:length(Trigger));
end;
%fprintf(1,'at end of ParseNumericFunction function: %s\n', func);
%fprintf(1,'at end of ParseNumericFunction parsing: %s\n', Trigger);
function y = LoseLeadingWhiteSpace(charArray)
% LoseLeadingWhiteSpace(charArray) takes an array of characters
% and returns the array with any leading white space removed
%
%----------------------------------------------------------------
% EXAMPLE:
% y = LoseLeadingWhiteSpace(' example')
% y = 'example'
%
%------------------------------------------------------------
% check input is an array of characters
if (~ischar(charArray))
error('LoseLeadingWhiteSpace(input)\n%s', 'input must be an array of characters');
end;
%-------------------------------------------------------------
% get the length of the array
NoChars = length(charArray);
%-------------------------------------------------------------
% determine the number of leading spaces
% create an array that indicates whether the elements of charArray are
% spaces
% e.g. WSpace = isspace(' v b') = [1, 1, 0, 1, 0]
WSpace = isspace(charArray);
% find the indices of elements that are 0
% no spaces equals the index of the first zero minus 1
% e.g. Zeros = find(WSpace == 0) = [3,5]
% NoSpaces = 2;
Zeros = find(WSpace == 0);
if (isempty(Zeros))
NoSpaces = 0;
else
NoSpaces = Zeros(1)-1;
end;
%-----------------------------------------------------------
% if there is leading white spaces rewrite the array to leave these out
if (NoSpaces > 0)
for i = 1: NoChars-NoSpaces
y(i) = charArray(i+NoSpaces);
end;
else
y = charArray;
end;
|
github
|
EPFL-LCSB/matTFA-master
|
SolveODEFunction.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Simulation/SolveODEFunction.m
| 13,085 |
utf_8
|
f779f53ab96b648094f18c546b0837c7
|
function [t, data] = SolveODEFunction(varargin)
% SolveODEFunction(varargin)
%
% Takes
%
% 1. a MATLAB_SBML model structure (required argument)
% 2. time limit (default = 10)
% 3. number of time steps (default lets the solver decide)
% 4. a flag to indicate whether to output species values in amount/concentration
% 1 amount, 0 concentration (default)
% 5. a flag to indicate whether to output the simulation data as
% a comma separated variable (csv) file
% 1 output 0 no output (default)
% 6. a filename (this is needed if WriteODEFunction was used with a
% filename)
%
% Returns
%
% 1. an array of time values
% 2. an array of the values of variables at each time point; species will
% be in concentration or amount as specified by input arguments
%
% Outputs
%
% 1. a file 'name.csv' with the data results (if the flag to output such a
% file is set to 1.
%
% *NOTE:* the results are generated using ode45 solver (MATLAB) or lsode
% (Octave)
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
% get inputs
if (nargin < 1)
error('SolveODEFunction(SBMLModel, ...)\n%s', 'must have at least one argument');
elseif (nargin > 6)
error('SolveODEFunction(SBMLModel, ...)\n%s', 'cannot have more than six arguments');
end;
% first argument
SBMLModel = varargin{1};
% check first input is an SBML model
if (~isValidSBML_Model(SBMLModel))
error('SolveODEFunction(SBMLModel)\n%s', 'first argument must be an SBMLModel structure');
end;
% put in default values
Time_limit = 10;
NoSteps = -1;
outAmt = 0;
outCSV = 1;
if (SBMLModel.SBML_level == 1)
Name = SBMLModel.name;
else
Name = SBMLModel.id;
end;
if (length(Name) > 63)
Name = Name(1:60);
end;
switch nargin
case 2
Time_limit = varargin{2};
case 3
Time_limit = varargin{2};
NoSteps = varargin{3};
case 4
Time_limit = varargin{2};
NoSteps = varargin{3};
outAmt = varargin{4};
case 5
Time_limit = varargin{2};
NoSteps = varargin{3};
outAmt = varargin{4};
outCSV = varargin{5};
case 6
Time_limit = varargin{2};
NoSteps = varargin{3};
outAmt = varargin{4};
outCSV = varargin{5};
if ~isempty(varargin{6})
Name = varargin{6};
end;
end;
% check values are sensible
if ((length(Time_limit) ~= 1) || (~isnumeric(Time_limit)))
error('SolveODEFunction(SBMLModel, time)\n%s', ...
'time must be a single real number indicating a time limit');
end;
if ((length(NoSteps) ~= 1) || (~isnumeric(NoSteps)))
error('SolveODEFunction(SBMLModel, time, steps)\n%s', ...
'steps must be a single real number indicating the number of steps');
end;
if (~isIntegralNumber(outAmt) || outAmt < 0 || outAmt > 1)
error('SolveODEFunction(SBMLModel, time, steps, concFlag)\n%s', ...
'concFlag must be 0 or 1');
end;
if (~isIntegralNumber(outCSV) || outCSV < 0 || outCSV > 1)
error('SolveODEFunction(SBMLModel, time, steps, concFlag, csvFlag)\n%s', ...
'csvFlag must be 0 or 1');
end;
if (~ischar(Name))
error('SolveODEFunction(SBMLModel, time, steps, concFlag, csvFlag, name)\n%s', ...
'name must be a string');
end;
fileName = strcat(Name, '.m');
%--------------------------------------------------------------
% check that a .m file of this name exists
% check whether file exists
fId = fopen(fileName);
if (fId == -1)
if (nargin < 6)
error('SolveODEFunction(SBMLModel)\n%s\n%s', ...
'You must use WriteODEFunction to output an ode function for this', ...
'model before using this function');
else
error('SolveODEFunction(SBMLModel)\n%s', 'You have not used this filename with WriteODEFunction');
end;
else
fclose(fId);
end;
%------------------------------------------------------------
% calculate values to use in iterative process
if (NoSteps ~= -1)
delta_t = Time_limit/NoSteps;
Time_span = [0:delta_t:Time_limit];
else
Time_span = [0, Time_limit];
end;
%--------------------------------------------------------------
% get variables from the model
[VarParams, VarInitValues] = GetVaryingParameters(SBMLModel);
NumberParams = length(VarParams);
[SpeciesNames, SpeciesValues] = GetSpecies(SBMLModel);
NumberSpecies = length(SBMLModel.species);
VarNames = [SpeciesNames, VarParams];
NumVars = NumberSpecies + NumberParams;
%---------------------------------------------------------------
% get function handle
fhandle = str2func(Name);
% get initial conditions
InitConds = feval(fhandle);
% set the tolerances of the odesolver to appropriate values
RelTol = min(InitConds(find(InitConds > 0))) * 1e-4;
if isempty(RelTol)
RelTol = 1e-6;
end;
if (RelTol > 1e-6)
RelTol = 1e-6;
end;
AbsTol = RelTol * 1e-4;
if exist('OCTAVE_VERSION')
[t, data] = runSimulationOctave(RelTol, AbsTol, fhandle, Time_span, InitConds);
else
if Model_getNumEvents(SBMLModel) == 0
[t, data] = runSimulation(RelTol, AbsTol, fhandle, Time_span, InitConds);
else
[t, data] = runEventSimulation(Name, NumVars, RelTol, AbsTol, fhandle, Time_span, InitConds);
end;
end;
if (outAmt == 1)
data = calculateAmount(SBMLModel, t, data);
end;
if (outCSV == 1)
outputData(t, data, Name, VarNames);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [TimeCourse, VarsCourse] = runSimulation(RelTol, AbsTol, ...
fhandle, Time_span, InitConds)
options = odeset('RelTol', RelTol, 'AbsTol', AbsTol);
[TimeCourse, VarsCourse] = runSimulator(options, fhandle, Time_span, InitConds);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [TimeCourse, VarsCourse] = runEventSimulation(Name, NumVars, RelTol, AbsTol, ...
fhandle, Time_span, InitConds)
eventName = strcat(Name, '_events');
afterEvent = strcat(Name, '_eventAssign');
eventHandle = str2func(eventName);
AfterEventHandle = str2func(afterEvent);
options = odeset('Events', eventHandle, 'RelTol', RelTol, 'AbsTol', AbsTol);
TimeCourse = [];
VarsCourse = [];
while ((~isempty(Time_span)) && (Time_span(1) < Time_span(end)))
[TimeCourse, VarsCourse, InitConds, Time_span] = ...
runEventSimulator(options, fhandle, Time_span, ...
InitConds, TimeCourse, VarsCourse, NumVars, ...
AfterEventHandle, Time_span(end));
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [TimeCourse, VarsCourse, InitConds, Time_span] ...
= runEventSimulator(options, fhandle, Time_span, InitConds, TimeCourse, ...
VarsCourse, NumVars, AfterEventHandle, Time_limit)
[TimeCourseA, VarsCourseA, eventTime, ab, eventNo] = ode45(fhandle, Time_span, InitConds, options);
% need to catch case where the time span entered was two sequential
% times from the original time-span
% e.g. original Time_span = [0, 0.1, ..., 4.9, 5.0]
% Time_span = [4.9, 5.0]
%
% ode solver will output points between
if (length(Time_span) == 2)
NewTimeCourse = [TimeCourseA(1); TimeCourseA(end)];
TimeCourseA = NewTimeCourse;
for i = 1:NumVars
NewVar(1,i) = VarsCourseA(1, i);
NewVar(2,i) = VarsCourseA(end, i);
end;
VarsCourseA = NewVar;
end;
% store current values of the varaiables at the time simulation ended
for i = 1:NumVars
CurrentValues(i) = VarsCourseA(end, i);
end;
% if we are not at the end of the time span remove the last point from
% each
if (TimeCourseA(end) ~= Time_span(end))
TimeCourseA = TimeCourseA(1:length(TimeCourseA)-1);
for i = 1:NumVars
VarsCourseB(:,i) = VarsCourseA(1:end-1, i);
end;
else
VarsCourseB = VarsCourseA;
end;
% adjust the time span
Time_spanA = Time_span - TimeCourseA(length(TimeCourseA));
Time_span_new = Time_spanA((find(Time_spanA==0)+1): length(Time_spanA));
Time_span = [];
Time_span = Time_span_new + TimeCourseA(length(TimeCourseA));
% if time span has not finished get new initial conditions
% need to integrate from the time the event stopped the solver to the
% next starting point to determine the new initial conditions
if (~isempty(Time_span))
InitConds = runCatchUpSimulation(AfterEventHandle, eventTime(end), ...
CurrentValues, eventNo(end), Time_span(1), Time_limit, options, fhandle, NumVars);
end;
% add the values from this iteration
TimeCourse = [TimeCourse;TimeCourseA];
VarsCourse = [VarsCourse;VarsCourseB];
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function InitConds = runCatchUpSimulation(AfterEventHandle, eventTime, ...
CurrentValues, eventNo, endTime, Time_limit, options, fhandle, NumVars)
CurrentValues = feval(AfterEventHandle, eventTime, CurrentValues, eventNo);
[t,NewValues, eventTime, ab, eventNo] = ode45(fhandle, ...
[eventTime, endTime], CurrentValues, options);
if ~isempty(eventTime)
% an event has been triggered in this small time span
for i = 1:NumVars
CurrentValues(i) = NewValues(end, i);
end;
InitConds = runCatchUpSimulation(AfterEventHandle, eventTime(end), ...
CurrentValues, eventNo(end), endTime, Time_limit, options, fhandle, NumVars);
else
for i = 1:NumVars
InitConds(i) = NewValues(length(NewValues), i);
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [TimeCourse, VarsCourse] = runSimulator(options, fhandle, ...
Time_span, InitConds)
[TimeCourse, VarsCourse] = ode45(fhandle, Time_span, InitConds, options);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [TimeCourse, VarsCourse] = runSimulationOctave(RelTol, AbsTol, ...
fhandle, Time_span, InitConds)
lsode_options('relative tolerance', RelTol);
lsode_options('absolute tolerance', AbsTol);
VarsCourse = lsode(fhandle, InitConds, Time_span);
TimeCourse = Time_span;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function amtData = calculateAmount(SBMLModel, TimeCourse, SpeciesCourse)
[compartments, comp_values] = GetCompartments(SBMLModel);
allOnes = 1;
for i=1:length(comp_values)
if comp_values(i) ~= 1
allOnes = 0;
end;
end;
amtData = SpeciesCourse;
if allOnes == 1
return;
else
for i = 1:length(TimeCourse)
for j = 1:length(SBMLModel.species)
% if the species hasOnlySubstanceUnits then it is already in amount
if (SBMLModel.species(j).hasOnlySubstanceUnits == 1)
amtData(i, j) = SpeciesCourse(i, j);
else
% need to deal with mutliple compartments
comp = Model_getCompartmentById(SBMLModel, SBMLModel.species(j).compartment);
comp_size = comp.size;
% catch any anomalies
if (isnan(comp_size))
comp_size = 1;
end;
amtData(i, j) = SpeciesCourse(i,j)*comp_size;
end;
end;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function outputData(TimeCourse, VarsCourse, Name, Vars)
fileName = strcat(Name, '.csv');
%--------------------------------------------------------------------
% open the file for writing
fileID = fopen(fileName, 'w');
numVars = length(Vars);
numdata = size(VarsCourse);
if (numVars ~= numdata(2)) || (length(TimeCourse) ~= numdata(1))
error ('%s\n%s', 'Incorrect numbers of data points from simulation', ...
'Please report the problem to libsbml-team @caltech.edu')
end;
% write the header
fprintf(fileID, 'time');
for i = 1: length(Vars)
fprintf(fileID, ',%s', Vars{i});
end;
fprintf(fileID, '\n');
% write each time course step values
for i = 1:length(TimeCourse)
fprintf(fileID, '%0.5g', TimeCourse(i));
for j = 1:length(Vars)
fprintf(fileID, ',%1.16g', VarsCourse(i,j));
end;
fprintf(fileID, '\n');
end;
fclose(fileID);
|
github
|
EPFL-LCSB/matTFA-master
|
SubstituteFunction.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Convenience/SubstituteFunction.m
| 5,155 |
utf_8
|
66c788cb09b115ecfad961f50a6ac138
|
function Formula = SubstituteFunction(OriginalFormula, SBMLFunctionDefinition)
% newExpression = SubstituteFunction(expression, SBMLFunctionDefinition)
%
% Takes
%
% 1. expression, a string representation of a math expression
% 2. SBMLFunctionDefinition, an SBML FunctionDefinition structure
%
% Returns
%
% 1. newExpression
% - the string representation of the expression when any instances of the
% functionDefinition have been substituted
% - an empty string if the functiondefinition is not in the original
% expression
%
% *EXAMPLE:*
%
% Consider fD to be an SBMLFunctionDefinition
% with id = 'g' and math = 'lambda(x,x+0.5)'
%
% formula = SubstituteFormula('g(y)', fD)
%
% formula = 'y+0.5'
%
%
% formula = SubstituteFormula('h(y)', fD)
%
% formula = ''
%
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
%check arguments are appropriate
if (~isstruct(SBMLFunctionDefinition))
error(sprintf('%s', ...
'first argument must be an SBML functionDefinition structure'));
end;
[sbmlLevel, sbmlVersion] = GetLevelVersion(SBMLFunctionDefinition);
if (~ischar(OriginalFormula))
error('SubstituteFunction(OriginalFormula, SBMLFunctionDefinition)\n%s', 'first argument must be a character array containing the id of the function definition');
elseif (~isSBML_FunctionDefinition(SBMLFunctionDefinition, sbmlLevel, sbmlVersion))
error('SubstituteFunction(OriginalFormula, SBMLFunctionDefinition)\n%s', 'second argument must be an SBML function definition structure');
end;
OriginalFormula = LoseWhiteSpace(OriginalFormula);
startPoint = matchFunctionName(OriginalFormula, SBMLFunctionDefinition.id);
if (isempty(startPoint))
Formula = '';
return;
end;
ElementsOfFuncDef = GetArgumentsFromLambdaFunction(SBMLFunctionDefinition.math);
% get the arguments of the application of the formula
Formula = '';
index = length(startPoint);
StartFunctionInFormula = startPoint(index);
j = StartFunctionInFormula + length(SBMLFunctionDefinition.id);
pairs = PairBrackets(OriginalFormula);
for i=1:length(pairs)
if (pairs(i, 1) == j)
endPt = pairs(i, 2);
break;
end;
end;
[NoElements, ElementsInFormula] = GetElementsOfFunction(OriginalFormula(j:endPt));
OriginalFunction = '';
for i = StartFunctionInFormula:endPt
OriginalFunction = strcat(OriginalFunction, OriginalFormula(i));
end;
% check got right number
if (NoElements ~= length(ElementsOfFuncDef) - 1)
error('SubstituteFunction(OriginalFormula, SBMLFunctionDefinition)\n%s', 'mismatch in number of arguments between formula and function');
end;
% check that same arguments have not been used
for i = 1:NoElements
for j = 1:NoElements
if (strcmp(ElementsInFormula{i}, ElementsOfFuncDef{j}))
newElem = strcat(ElementsInFormula{i}, '_new');
ElementsOfFuncDef{j} = newElem;
ElementsOfFuncDef{end} = strrep(ElementsOfFuncDef{end}, ElementsInFormula{i}, newElem);
end;
end;
end;
% replace the arguments in function definition with those in the formula
FuncFormula = '(';
FuncFormula = strcat(FuncFormula, ElementsOfFuncDef{end});
FuncFormula = strcat(FuncFormula, ')');
for i = 1:NoElements
FuncFormula = strrep(FuncFormula, ElementsOfFuncDef{i}, ElementsInFormula{i});
end;
Formula = strrep(OriginalFormula, OriginalFunction, FuncFormula);
% if the function occurred more than once
if (index - 1) > 0
Formula = SubstituteFunction(Formula, SBMLFunctionDefinition);
end;
function [NoElements, ElementsInFormula] = GetElementsOfFunction(OriginalFormula);
j = 2;
c = OriginalFormula(j);
element = '';
NoElements = 1;
ElementsInFormula = {};
while (j < length(OriginalFormula))
if (strcmp(c, ','))
ElementsInFormula{NoElements} = element;
element = '';
NoElements = NoElements + 1;
else
element = strcat(element, c);
end;
j = j + 1;
c = OriginalFormula(j);
end;
ElementsInFormula{NoElements} = element;
|
github
|
EPFL-LCSB/matTFA-master
|
RemoveDuplicates.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Convenience/RemoveDuplicates.m
| 2,898 |
utf_8
|
46f7aade9e3235449589d381f0890c24
|
function y = RemoveDuplicates(FullArray)
% newArray = RemoveDuplicates(array)
%
% Takes
%
% 1. array, any array
%
% Returns
%
% 1. the array with any duplicate entries removed
%
% *EXAMPLE:*
%
% newArray = RemoveDuplicates([2, 3, 4, 3, 2, 5])
% newArray = [2, 3, 4, 5]
%
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
% check whether array is a column vector
[size_x, size_y] = size(FullArray);
if (size_y == 1 && size_x ~= 1)
y = RemoveDuplicatesColumn(FullArray);
return;
end;
%-------------------------------------------------------------
% find number of elements in existing array
NoElements = length(FullArray);
if (NoElements == 0)
y = [];
return;
end;
% copy first element of the array to the new array
newArrayIndex = 1;
NewArray(1) = FullArray(1);
%loop through all elements
% if they do not already exist in new array copy them into it
for i = 2:NoElements
element = FullArray(i);
if (~ismember(element, NewArray))
newArrayIndex = newArrayIndex + 1;
NewArray(newArrayIndex) = element;
end;
end;
y = NewArray;
function y = RemoveDuplicatesColumn(FullArray)
% RemoveDuplicatesCell takes column vector
% and returns it with any duplicates removed
% find number of elements in existing array
[NoElements, x] = size(FullArray);
% copy first element of the array to the new array
newArrayIndex = 1;
NewArray(1,x) = FullArray(1);
%loop through all elements
% if they already exist in new array do not copy
for i = 2:NoElements
element = FullArray(i);
if (~ismember(element, NewArray))
newArrayIndex = newArrayIndex + 1;
NewArray(newArrayIndex,x) = element;
end;
end;
y = NewArray;
|
github
|
EPFL-LCSB/matTFA-master
|
Rearrange.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Convenience/Rearrange.m
| 11,479 |
utf_8
|
6ed57da4458b9e994a775fa3c990b46f
|
function output = Rearrange(formula, x)
% output = Rearrange(expression, name)
%
% Takes
%
% 1. expression, a string representation of a math expression
% 2. name, a string representing the name of a variable
%
% Returns
%
% 1. the expression rearranged in terms of the variable
%
% *EXAMPLE:*
%
% output = Rearrange('X + Y - Z', 'X')
%
% output = '-Y+Z'
%
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
f = LoseWhiteSpace(formula);
if (~isempty(strfind(f, '+-')))
f = strrep(f, '+-', '-');
end;
if (~isempty(strfind(f, '-+')))
f = strrep(f, '-+', '-');
end;
% if x is not in the formula just return the formula
if (~ismember(f, x))
output = f;
return;
end;
% if there are brackets these need to switch sides of the equation
% "intact" ie x+(y+z) rearranges to x = -(y+z)
brackets = PairBrackets(f);
num = 0;
if (length(brackets)>1)
[num, m] = size(brackets);
for b=1:num
group{b} = f(brackets(1): brackets(2));
if (sum(ismember(group{b}, x)) > 0)
error('Cannot deal with formula in this form: %s', f);
end;
newvar{b} = strcat('var', num2str(b));
f = strrep(f, group{b}, newvar{b});
end;
end;
ops = '+-';
operators = ismember(f, ops);
OpIndex = find(operators == 1);
if(~isempty(OpIndex))
%--------------------------------------------------
% divide formula up into elements seperated by +/-
if (OpIndex(1) == 1)
% leading sign i.e. +x-y
NumElements = length(OpIndex);
j = 2;
index = 2;
else
NumElements = length(OpIndex) + 1;
j = 1;
index = 1;
end;
for i = 1:NumElements-1
element = '';
while (j < OpIndex(index))
element = strcat(element, f(j));
j = j+1;
end;
Elements{i} = element;
j = j + 1;
index = index + 1;
end;
% get last element
j = OpIndex(end)+1;
element = '';
while (j <= length(f))
element = strcat(element, f(j));
j = j+1;
end;
Elements{NumElements} = element;
else
NumElements = 0;
LHSElements{1} = f;
LHSOps(1) = '+';
end;
%--------------------------------------------------
% check whether element contains x
% if does keep on lhs else move to rhs changing sign
output = '';
lhs = 1;
for i = 1:NumElements
if (matchName(Elements{i}, x))
% element contains x
LHSElements{lhs} = Elements{i};
if (OpIndex(1) == 1)
LHSOps(lhs) = f(OpIndex(i));
elseif (i == 1)
LHSOps(lhs) = '+';
else
LHSOps(lhs) = f(OpIndex(i-1));
end;
lhs = lhs + 1;
elseif (i == 1)
% first element does not contain x
if (OpIndex(1) == 1)
if (strcmp(f(1), '-'))
output = strcat(output, '+');
else
output = strcat(output, '-');
end;
else
% no sign so +
output = strcat(output, '-');
end;
output = strcat(output, Elements{i});
else
% element not first and does not contain x
if (OpIndex(1) == 1)
if (strcmp(f(OpIndex(i)), '-'))
output = strcat(output, '+');
else
output = strcat(output, '-');
end;
else
if (strcmp(f(OpIndex(i-1)), '-'))
output = strcat(output, '+');
else
output = strcat(output, '-');
end;
end;
output = strcat(output, Elements{i});
end;
end;
%------------------------------------------------------
% look at remaining LHS
for i = 1:length(LHSElements)
[Mult{i}, invert(i)] = ParseElement(LHSElements{i}, x);
end;
operators = '+-/*^';
if (length(LHSElements) == 1)
% only one element with x
% check signs and multipliers
if (strcmp(LHSOps(1), '-'))
output = strcat('-(', output, ')');
end;
if (~strcmp(Mult{1}, '1'))
if (isempty(output))
if (invert(1) == 0)
output = '0';
end;
else
if (sum(ismember(Mult{1}, '/')) > 0)
if (invert(1) == 0)
output = strcat(output, '*(', Invert(Mult{1}, x), ')');
else
output = strcat('(', Mult{1}, ')*(', Invert(output, x), ')');
end;
else
output = strcat(output, '/', Mult{1});
end;
end;
end;
else
if (isempty(output))
if (invert == 0)
output = '0';
end;
else
divisor = '';
if (strcmp(LHSOps(1), '+'))
divisor = strcat(divisor, '(', Mult{1});
else
divisor = strcat(divisor, '(-', Mult{1});
end;
for i = 2:length(LHSElements)
divisor = strcat(divisor, LHSOps(i), Mult{i});
end;
divisor = strcat(divisor, ')');
if (sum(ismember(output, operators)) > 0)
output = strcat('(', output, ')/', divisor);
else
output = strcat(output, '/', divisor);
end;
end;
end;
% replaced substituted vars
for b=1:num
output = strrep(output, newvar{b}, group{b});
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [multiplier, invert] = ParseElement(element, x)
if (strcmp(element, x))
multiplier = '1';
invert = 0;
return;
end;
multipliers = strfind(element, '*');
if (length(multipliers) > 2)
error('Too many multipliers');
end;
VarIndex = matchName(element, x);
if (isempty(multipliers))
MultIndex = 1;
else
if (length(multipliers) == 1)
MultIndex = multipliers(1);
else
if (VarIndex > multipliers(2))
MultIndex = multipliers(2);
else
MultIndex = multipliers(1);
end;
end;
end;
DivIndex = strfind(element, '/');
if (isempty(DivIndex))
DivIndex = length(element);
end;
% if we have x/5*b
if (DivIndex < MultIndex)
MultIndex = 1;
end;
% if we have b/x
if (VarIndex > DivIndex)
[element, noinvert] = Invert(element, x);
multiplier = ParseElement(element, x);
if (noinvert == 0)
multiplier = Invert(multiplier, x);
invert = 1;
else
invert = 0;
end;
return;
end;
% if we have x*c
if (VarIndex < MultIndex)
element = SwapMultiplier(element, x);
[multiplier, invert] = ParseElement(element, x);
return;
end;
if ((DivIndex < MultIndex) ||(VarIndex < MultIndex) || (VarIndex > DivIndex))
error('Cannot deal with formula in this form: %s', element);
end;
n = '';
m = '';
for i = 1:MultIndex-1
if (element(i) ~= '(' && element(i) ~= ')')
n = strcat(n, element(i));
end;
end;
if (isempty(n))
n = '1';
end;
for i = DivIndex+1:length(element)
m = strcat(m, element(i));
end;
if (isempty(m))
m = '1';
end;
% if both m and n represenet numbers then they can be simplified
Num_n = str2num(n);
Num_m = str2num(m);
if (~isempty(Num_n) && ~isempty(Num_m))
multiplier = num2str(Num_n/Num_m);
else
if (strcmp(m, '1'))
multiplier = n;
else
multiplier = strcat(n, '/', m);
end;
end;
invert = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [y, noinvert] = Invert(formula, x)
% need to consider a/x*b
% which is really (b*a)/x
operators = '+-/*^';
noinvert = 0;
divider = strfind(formula, '/');
if (length(divider) > 1)
error('Too many divide signs');
end;
if (isempty(divider))
nominator = formula;
denominator = '1';
else
nominator = formula(1:divider-1);
denominator = formula(divider+1:end);
end;
if (~IsSingleBracketed(denominator))
multiplier = strfind(denominator, '*');
if (length(multiplier) > 1)
error('Too may multiplication signs');
end;
if (~isempty(multiplier))
lhs = denominator(1:multiplier-1);
rhs = denominator(multiplier+1:end);
if (sum(ismember(nominator, operators)) > 0)
if (IsSingleBracketed(nominator))
nominator = strcat(nominator, '*', rhs);
else
nominator = strcat('(', nominator, ')*', rhs);
end;
else
nominator = strcat(nominator, '*', rhs);
end;
denominator = lhs;
end;
end;
% if x is now part of the nominator dont invert
if (matchName(nominator, x))
if (sum(ismember(nominator, operators)) > 0)
if (IsSingleBracketed(nominator))
y = strcat(nominator, '/');
else
y = strcat ('(', nominator, ')/');
end;
else
y = strcat(nominator, '/');
end;
if (sum(ismember(denominator, operators)) > 0)
if (IsSingleBracketed(denominator))
y = strcat(y, denominator);
else
y = strcat(y, '(', denominator, ')');
end;
else
y = strcat(y, denominator);
end;
noinvert = 1;
else
if (sum(ismember(denominator, operators)) > 0)
if (IsSingleBracketed(denominator))
y = strcat(denominator, '/');
else
y = strcat ('(', denominator, ')/');
end;
else
y = strcat(denominator, '/');
end;
if (sum(ismember(nominator, operators)) > 0)
if (IsSingleBracketed(nominator))
y = strcat(y, nominator);
else
y = strcat(y, '(', nominator, ')');
end;
else
y = strcat(y, nominator);
end;
end;
%y = strcat('(', denominator, ')/(', nominator, ')');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function y = IsSingleBracketed(formula)
y = 0;
Open = strfind(formula, '(');
if (isempty(Open) || length(Open)> 1)
return;
end;
if (Open ~= 1)
return;
end;
len = length(formula);
Close = strfind(formula, ')');
if (length(Close)> 1)
return;
end;
if (Close ~= len)
return;
end;
y = 1;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function y = SwapMultiplier(formula, x)
% formula will have only * and /
% x will occur before both
% * will occur before /
index = matchName(formula, x);
start = index(1);
index = strfind(formula, '*');
multiplier = index(1);
nextop = 0;
if (length(index) > 1)
nextop = index(2);
end;
index = strfind(formula, '/');
if (length(index) > 0)
end_after = index(1)-1;
else
if (nextop > 0)
end_after = nextop-1;
else
end_after = length(formula);
end;
end;
replace = '';
for i = multiplier+1:end_after
replace = strcat(replace, formula(i));
end;
newformula = replace;
newformula = strcat(newformula, '*');
newformula = strcat(newformula, x);
for i = end_after+1:length(formula)
newformula = strcat(newformula, formula(i));
end;
y = newformula;
|
github
|
EPFL-LCSB/matTFA-master
|
propagateLevelVersion.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/MATLAB_SBML_Structure_Functions/structFieldnames/propagateLevelVersion.m
| 2,729 |
utf_8
|
ac0c57fde5be4302fbf3241c14e3787e
|
function model = propagateLevelVersion(SBMLModel)
% SBMLModel = propagateLevelVersion(SBMLModel)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
%
% Returns
%
% 1. the SBML Model structure with level and version fields added to all
% sub structures
%
% *NOTE:* This function facilitates keeping track of the level and version
% of sub objects within a model
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
%get level and version and check the input arguments are appropriate
if ~isValidSBML_Model(SBMLModel)
error('first argument must be an SBMLModel structure');
end;
level = SBMLModel.SBML_level;
version = SBMLModel.SBML_version;
model = addLV('SBML_MODEL', SBMLModel, level, version);
function model = addLV(typecode, model, level, version)
fields = getFieldnames(typecode, level, version);
for i=1:length(fields)
subcomp = getfield(model, fields{i});
if isstruct(subcomp)
if length(subcomp) > 0
model = setfield(model, fields{i}, addLevelVersion(subcomp, level, version));
end;
end;
end;
function retStr = addLevelVersion(substr, level, version)
if length(substr) == 1
retStr = addLevelVersionStruct(substr, level, version);
retStr = addLV(substr.typecode, retStr, level, version);
else
for i=1:length(substr)
retStr(i) = addLevelVersionStruct(substr(i), level, version);
retStr(i) = addLV(substr(i).typecode, retStr(i), level, version);
end;
end;
function retStr = addLevelVersionStruct(substr, level, version)
retStr = substr;
retStr.level = level;
retStr.version = version;
|
github
|
EPFL-LCSB/matTFA-master
|
testObject.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/MATLAB_SBML_Structure_Functions/Test/testObject.m
| 10,178 |
utf_8
|
7294eab33dbb7ea5880923e3769a8072
|
function [fail, num, message] = testObject(obj, attributes, component, fail, num, message)
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
% different cases which indicate what type of attribute is being tested
% 1 string
% 2 sboTerm - ie integer with unset value = -1
% 3 double whose unset value is NaN
% 4 double - always set
% 5 boolean - with issetvalue
% 6 int - always set
% 7 boolean - no issetvalue
% 8 L1RuleType - always set
% 9 another structure - test add functions
% 10 SBMLlevel/version - always set - ignore
% if no attributes obj should be empty
if length(attributes) == 0
if (~isempty(obj))
fail = fail + 1;
num = num + 1;
m = sprintf('create%s created an invalid object', component);
disp(m);
message{length(message)+1} = m;
end;
end;
%remove any fbc prefix
for i = 1:length(attributes)
name = attributes{i}{1};
if length(name) > 4
if strcmp(name(1:4), 'Fbc_')
attributes{i}{1} = strcat(upper(name(5:5)), name(6:end));
end;
end;
end;
for i = 1:length(attributes)
switch (attributes{i}{2})
case 7
f = 0;
case 9
[f, m] = testEmpty(component, attributes{i}{1}, obj);
case {4, 6, 8, 10}
[f, m] = testAlwaysSet(component, attributes{i}{1}, obj);
otherwise
[f, m] = testIsNotSet(component, attributes{i}{1}, obj);
end;
num = num + 1;
if f > 0
fail = fail + f;
disp(m);
message{length(message)+1} = m;
end;
end;
for i = 1:length(attributes)
[f, m] = testSet(component, attributes{i}{1}, obj, attributes{i}{2});
num = num + 3;
if f > 0
fail = fail + f;
disp(m);
len = length(message);
for j = 1:length(m)
message{len+j} = m{j};
end;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [fail, message] = testEmpty(component, attribute, obj)
message = {};
singles = {'KineticLaw', 'Trigger', 'Delay', 'Priority', 'StoichiometryMath'};
if isIn(singles, attribute)
fhandle = sprintf('%s_isSet%s', component, attribute);
else
fhandle = sprintf('%s_getNum%ss', component, attribute);
end;
result = feval(fhandle, obj);
if result == 0
fail = 0;
else
fail = 1;
message{1} = sprintf('%s should return 0', fhandle);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [fail, message] = testIsNotSet(component, attribute, obj)
message = {};
fhandle = sprintf('%s_isSet%s', component, attribute);
result = feval(fhandle, obj);
if result == 0
fail = 0;
else
fail = 1;
message{1} = sprintf('%s_isSet%s should return 0', component, attribute);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [fail, message] = testAlwaysSet(component, attribute, obj)
message = {};
fhandle = sprintf('%s_isSet%s', component, attribute);
result = feval(fhandle, obj);
if result == 1
fail = 0;
else
fail = 1;
message{1} = sprintf('%s_isSet%s should return 1', component, attribute);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [fail, message] = testSet(component, attribute, obj, type)
testStr = 'abc';
testDouble = 3.3;
testInt = 2;
testBool = 1;
testL1RuleType = 'rate';
message = {};
fail = 0;
if (type == 9)
[fail, message] = testAdd(component, attribute, obj);
return;
elseif (type == 10) % level/version
return;
end;
fhandle_isSet = sprintf('%s_isSet%s', component, attribute);
fhandle_set = sprintf('%s_set%s', component, attribute);
fhandle_get = sprintf('%s_get%s', component, attribute);
fhandle_unset = sprintf('%s_unset%s', component, attribute);
% set and test that attribute is set
switch (type)
case 1
obj = feval(fhandle_set, obj, testStr);
case 2
obj = feval(fhandle_set, obj, testInt);
case 3
obj = feval(fhandle_set, obj, testDouble);
case 4
obj = feval(fhandle_set, obj, testDouble);
case 5
obj = feval(fhandle_set, obj, testBool);
case 6
obj = feval(fhandle_set, obj, testInt);
case 7
obj = feval(fhandle_set, obj, testBool);
case 8
obj = feval(fhandle_set, obj, testL1RuleType);
otherwise
end;
switch (type)
case 7
result = 1;
otherwise
result = feval(fhandle_isSet, obj);
end;
if result ~= 1
fail = fail + 1;
m = sprintf('%s_set%s failed', component, attribute);
message{length(message)+1} = m;
end;
%get the attribute and check it is correct
result = feval(fhandle_get, obj);
switch (type)
case 1
if ~strcmp(result, testStr)
fail = fail + 1;
m = sprintf('%s_get%s failed', component, attribute);
message{length(message)+1} = m;
end;
case 2
if result ~= testInt
fail = fail + 1;
m = sprintf('%s_get%s failed', component, attribute);
message{length(message)+1} = m;
end;
case 3
if result ~= testDouble
fail = fail + 1;
m = sprintf('%s_get%s failed', component, attribute);
message{length(message)+1} = m;
end;
case 4
if result ~= testDouble
fail = fail + 1;
m = sprintf('%s_get%s failed', component, attribute);
message{length(message)+1} = m;
end;
case 5
if result ~= testBool
fail = fail + 1;
m = sprintf('%s_get%s failed', component, attribute);
message{length(message)+1} = m;
end;
case 6
if result ~= testInt
fail = fail + 1;
m = sprintf('%s_get%s failed', component, attribute);
message{length(message)+1} = m;
end;
case 7
if result ~= testBool
fail = fail + 1;
m = sprintf('%s_get%s failed', component, attribute);
message{length(message)+1} = m;
end;
case 8
if ~strcmp(result, testL1RuleType)
fail = fail + 1;
m = sprintf('%s_get%s failed', component, attribute);
message{length(message)+1} = m;
end;
otherwise
end;
% unset and check it is unset
switch (type)
case {4, 6, 7, 8}
result = 0;
otherwise
obj = feval(fhandle_unset, obj);
result = feval(fhandle_isSet, obj);
end;
if result ~= 0
fail = fail + 1;
m = sprintf('%s_unset%s failed', component, attribute);
message{length(message)+1} = m;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [fail, message] = testAdd(component, attribute, obj)
fail = 0;
message = {};
singles = {'KineticLaw', 'Trigger', 'Delay', 'Priority', 'StoichiometryMath'};
if isIn(singles, attribute)
single = 1;
else
single = 0;
end;
if strcmp(attribute, 'Rule')
fhandle_create = 'AlgebraicRule_create';
elseif strcmp(attribute, 'Product') || strcmp(attribute, 'Reactant')
fhandle_create = 'SpeciesReference_create';
elseif strcmp(attribute, 'Modifier')
fhandle_create = 'ModifierSpeciesReference_create';
else
fhandle_create = sprintf('%s_create', attribute);
end;
fhandle_get = sprintf('%s_get%s', component, attribute);
if single == 1
fhandle_set = sprintf('%s_set%s', component, attribute);
fhandle_isset = sprintf('%s_isSet%s', component, attribute);
fhandle_unset = sprintf('%s_unset%s', component, attribute);
else
fhandle_set = sprintf('%s_add%s', component, attribute);
fhandle_isset = sprintf('%s_getNum%ss', component, attribute);
fhandle_getLO = sprintf('%s_getListOf%ss', component, attribute);
end;
fhandle_createSub = sprintf('%s_create%s', component, attribute);
if strcmp(obj.typecode, 'SBML_MODEL')
newObj = feval(fhandle_create, obj.SBML_level, obj.SBML_version);
else
newObj = feval(fhandle_create, obj.level, obj.version);
end;
% add new obj and check is now set
obj = feval(fhandle_set, obj, newObj);
result = feval(fhandle_isset, obj);
if result == 1
fail = 0;
else
fail = 1;
message{1} = sprintf('%s failed', fhandle_set);
end;
% get the obj and test
if single == 1
returnObj = feval(fhandle_get, obj);
else
returnObj = feval(fhandle_get, obj, 1);
end;
if areIdentical(returnObj, newObj)
fail = 0;
else
fail = 1;
message{1} = sprintf('%s failed', fhandle_set);
end;
% test unset single obj
if single
obj = feval(fhandle_unset, obj);
result = feval(fhandle_isset, obj);
if result == 0
fail = 0;
else
fail = 1;
message{1} = sprintf('%s failed', fhandle_unset);
end;
else
obj = feval(fhandle_set, obj, newObj);
lo = feval(fhandle_getLO, obj);
result = length(lo);
if result == 2
fail = 0;
else
fail = 1;
message{1} = sprintf('%s failed', fhandle_getLO);
end;
end;
% test create
if single
obj = feval(fhandle_createSub, obj);
result = feval(fhandle_isset, obj);
if result == 1
fail = 0;
else
fail = 1;
message{1} = sprintf('%s failed', fhandle_createSub);
end;
else
obj = feval(fhandle_createSub, obj);
lo = feval(fhandle_getLO, obj);
result = length(lo);
if result == 3
fail = 0;
else
fail = 1;
message{1} = sprintf('%s failed', fhandle_createSub);
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function value = isIn(array, thing)
value = sum(ismember(array, thing));
|
github
|
EPFL-LCSB/matTFA-master
|
Model_getListOfByTypecode.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/MATLAB_SBML_Structure_Functions/Model/Model_getListOfByTypecode.m
| 3,470 |
utf_8
|
3ee51ba7a44c4697be5cce017e9c2346
|
function array = Model_getListOfByTypecode(SBMLModel, SBMLTypecode)
% listOf = Model_getListOfByTypecode(SBMLModel, typecode)
%
% Takes
%
% 1. SBMLModel, an SBML Model structure
% 2. typecode; a string representing the typecode of SBML ListOf structure
%
% Returns
%
% 1. the SBML ListOf structure that has this typecode
%
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
% check that input is correct
if (~isValidSBML_Model(SBMLModel))
error(sprintf('%s\n%s', 'Model_getListOfByTypecode(SBMLModel, SBMLTypecode)', 'first argument must be an SBML model structure'));
elseif (~CheckTypecode(SBMLTypecode))
error(sprintf('%s\n%s', 'Model_getListOfByTypecode(SBMLModel, SBMLTypecode)', 'second argument must be a string representing an SBML typecode'));
end;
switch (SBMLTypecode)
case 'SBML_FUNCTION_DEFINITION'
array = SBMLModel.functionDefinition;
case 'SBML_UNIT_DEFINITION'
array = SBMLModel.unitDefinition;
case 'SBML_COMPARTMENT'
array = SBMLModel.compartment;
case 'SBML_SPECIES'
array = SBMLModel.species;
case 'SBML_PARAMETER'
array = SBMLModel.parameter;
case {'SBML_ASSIGNMENT_RULE', 'SBML_ALGEBRAIC_RULE', 'SBML_RATE_RULE', 'SBML_SPECIES_CONCENTRATION_RULE', 'SBML_COMPARTMENT_VOLUME_RULE', 'SBML_PARAMETER_RULE'}
array = SBMLModel.rule;
case 'SBML_REACTION'
array = SBMLModel.reaction;
case 'SBML_EVENT'
array = SBMLModel.event;
otherwise
array = [];
end;
%------------------------------------------------------------------------------------
function value = CheckTypecode(SBMLTypecode)
%
% CheckTypecode
% takes a string representing an SBMLTypecode
% and returns 1 if it is a valid typecode and 0 otherwise
%
% value = CheckTypecode('SBMLTypecode')
ValidTypecodes = {'SBML_COMPARTMENT', 'SBML_EVENT', 'SBML_FUNCTION_DEFINITION', 'SBML_PARAMETER', 'SBML_REACTION', 'SBML_SPECIES', ...
'SBML_UNIT_DEFINITION', 'SBML_ASSIGNMENT_RULE', 'SBML_ALGEBRAIC_RULE', 'SBML_RATE_RULE', 'SBML_SPECIES_CONCENTRATION_RULE', ...
'SBML_COMPARTMENT_VOLUME_RULE', 'SBML_PARAMETER_RULE'};
value = 1;
if (~ischar(SBMLTypecode))
value = 0;
elseif (~ismember(SBMLTypecode, ValidTypecodes))
value = 0;
end;
|
github
|
EPFL-LCSB/matTFA-master
|
GetRateLawsFromReactions.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/AccessModel/GetRateLawsFromReactions.m
| 17,010 |
utf_8
|
e123fc8f39c36d33d5ef39991f08688a
|
function [Species, RateLaws] = GetRateLawsFromReactions(SBMLModel)
% [species, rateLaws] = GetRateLawsFromReactions(SBMLModel)
%
% Takes
%
% 1. SBMLModel; an SBML Model structure
%
% Returns
%
% 1. an array of strings representing the identifiers of all species
% 2. an array of
%
% - the character representation of the rate law established from any reactions
% that determines the particular species
% - '0' if the particular species is not a reactant/product in any reaction
%
% *EXAMPLE:*
%
% model has 4 species (s1, s2, s3, s4)
% and 2 reactions; s1 -> s2 with kineticLaw 'k1*s1'
% s2 -> s3 with kineticLaw 'k2*s2'
%
% [species, rateLaws] = GetRateLawsFromReactions(model)
%
% species = ['s1', 's2', 's3', 's4']
% rateLaws = {'-k1*s1', 'k1*s1-k2*s2', 'k2*s2', '0'}
%
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
% check input is an SBML model
if (~isValidSBML_Model(SBMLModel))
error('GetRateLawsFromReactions(SBMLModel)\n%s', 'input must be an SBMLModel structure');
end;
%--------------------------------------------------------------
% get information from the model
Species = GetSpecies(SBMLModel);
NumberSpecies = length(SBMLModel.species);
NumReactions = length(SBMLModel.reaction);
% for each species loop through each reaction and determine whether the species
% takes part and in what capacity
for i = 1:NumberSpecies
output = '';
% if species is a boundary condition (or constant in level 2
% no rate law is required
boundary = SBMLModel.species(i).boundaryCondition;
if (SBMLModel.SBML_level > 1)
constant = SBMLModel.species(i).constant;
else
constant = -1;
end;
if (boundary == 1)
output = '0';
elseif (constant ==1)
output = '0';
else
%determine which reactions it occurs within
for j = 1:NumReactions
SpeciesRole = DetermineSpeciesRoleInReaction(SBMLModel.species(i), SBMLModel.reaction(j));
%--------------------------------------------------------------
% check that reaction has a kinetic law
if (isempty(SBMLModel.reaction(j).kineticLaw))
error('GetRateLawsFromReactions(SBMLModel)\n%s', 'NO KINETIC LAW SUPPLIED');
end;
%--------------------------------------------------------------
if (SBMLModel.SBML_level < 3)
kineticLawMath = SBMLModel.reaction(j).kineticLaw.formula;
else
kineticLawMath = SBMLModel.reaction(j).kineticLaw.math;
end;
TotalOccurences = 0;
% record numbers of occurences of species as reactant/product
% and check that we can deal with reaction
if (sum(SpeciesRole)>0)
NoReactants = SpeciesRole(2);
NoProducts = SpeciesRole(1);
TotalOccurences = NoReactants + NoProducts;
%--------------------------------------------------------------
% check that a species does not occur twice on one side of the
% reaction
if (NoReactants > 1 || NoProducts > 1)
error('GetRateLawsFromReactions(SBMLModel)\n%s', 'SPECIES OCCURS MORE THAN ONCE ON ONE SIDE OF REACTION');
end;
%--------------------------------------------------------------
% check that reaction has a kinetic law formula
if (isempty(SBMLModel.reaction(j).kineticLaw))
error('GetRateLawsFromReactions(SBMLModel)\n%s', 'NO KINETIC LAW SUPPLIED');
end;
%--------------------------------------------------------------
end;
% species has been found in this reaction
while (TotalOccurences > 0) %
% add the kinetic law to the output for this species
if(NoProducts > 0)
% Deal with case where parameter is defined within the reaction
% and thus the reaction name has been appended to the parameter
% name in the list in case of repeated use of same name
Param_Name = GetParameterFromReaction(SBMLModel.reaction(j));
if (~isempty(Param_Name))
ReviseParam_Name = GetParameterFromReactionUnique(SBMLModel.reaction(j));
formula = Substitute(Param_Name, ReviseParam_Name, kineticLawMath);
else
formula = kineticLawMath;
end;
% put in stoichiometry
if ((SBMLModel.SBML_level == 2 && SBMLModel.SBML_version > 1) ...
|| SBMLModel.SBML_level == 3)
stoichiometry = SBMLModel.reaction(j).product(SpeciesRole(4)).stoichiometry;
else
stoichiometry = SBMLModel.reaction(j).product(SpeciesRole(4)).stoichiometry/double(SBMLModel.reaction(j).product(SpeciesRole(4)).denominator);
end;
if ((SBMLModel.SBML_level == 2) && (~isempty(SBMLModel.reaction(j).product(SpeciesRole(4)).stoichiometryMath)))
if (SBMLModel.SBML_version < 3)
output = sprintf('%s + (%s) * (%s)', output, SBMLModel.reaction(j).product(SpeciesRole(4)).stoichiometryMath, formula);
else
output = sprintf('%s + (%s) * (%s)', output, SBMLModel.reaction(j).product(SpeciesRole(4)).stoichiometryMath.math, formula);
end;
elseif (SBMLModel.SBML_level == 3)
% level 3 stoichiometry may be assigned by
% rule/initialAssignment which will override any
% stoichiometry value
if (~isempty(SBMLModel.reaction(j).product(SpeciesRole(4)).id))
rule = Model_getAssignmentRuleByVariable(SBMLModel, SBMLModel.reaction(j).product(SpeciesRole(4)).id);
rrule = Model_getRateRuleByVariable(SBMLModel, SBMLModel.reaction(j).product(SpeciesRole(4)).id);
ia = Model_getInitialAssignmentBySymbol(SBMLModel, SBMLModel.reaction(j).product(SpeciesRole(4)).id);
if ~isempty(rule)
output = sprintf('%s + (%s) * (%s)', output, rule.formula, formula);
elseif ~isempty(ia)
output = sprintf('%s + (%s) * (%s)', output, ia.math, formula);
elseif ~isempty(rrule)
error('Cannot deal with stoichiometry in a rate rule');
elseif ~isnan(stoichiometry)
if (stoichiometry == 1)
output = sprintf('%s + (%s)', output, formula);
else
output = sprintf('%s + %g * (%s)', output, stoichiometry, formula);
end;
else
error('Cannot determine stoichiometry');
end;
elseif isnan(stoichiometry)
error ('Cannot determine stoichiometry');
else
if (stoichiometry == 1)
output = sprintf('%s + (%s)', output, formula);
else
output = sprintf('%s + %g * (%s)', output, stoichiometry, formula);
end;
end;
else
% if stoichiometry = 1 no need to include it in formula
if (stoichiometry == 1)
output = sprintf('%s + (%s)', output, formula);
else
output = sprintf('%s + %g * (%s)', output, stoichiometry, formula);
end;
end;
NoProducts = NoProducts - 1;
elseif (NoReactants > 0)
% Deal with case where parameter is defined within the reaction
% and thus the reaction name has been appended to the parameter
% name in the list in case of repeated use of same name
Param_Name = GetParameterFromReaction(SBMLModel.reaction(j));
if (~isempty(Param_Name))
ReviseParam_Name = GetParameterFromReactionUnique(SBMLModel.reaction(j));
formula = Substitute(Param_Name, ReviseParam_Name, kineticLawMath);
else
formula = kineticLawMath;
end;
% put in stoichiometry
if ((SBMLModel.SBML_level == 2 && SBMLModel.SBML_version > 1) ...
|| SBMLModel.SBML_level == 3)
stoichiometry = SBMLModel.reaction(j).reactant(SpeciesRole(5)).stoichiometry;
else
stoichiometry = SBMLModel.reaction(j).reactant(SpeciesRole(5)).stoichiometry/double(SBMLModel.reaction(j).reactant(SpeciesRole(5)).denominator);
end;
if ((SBMLModel.SBML_level == 2) && (~isempty(SBMLModel.reaction(j).reactant(SpeciesRole(5)).stoichiometryMath)))
if (SBMLModel.SBML_version < 3)
output = sprintf('%s - (%s) * (%s)', output, SBMLModel.reaction(j).reactant(SpeciesRole(5)).stoichiometryMath, formula);
else
output = sprintf('%s - (%s) * (%s)', output, SBMLModel.reaction(j).reactant(SpeciesRole(5)).stoichiometryMath.math, formula);
end;
elseif (SBMLModel.SBML_level == 3)
% level 3 stoichiometry may be assigned by
% rule/initialAssignment which will override any
% stoichiometry value
if (~isempty(SBMLModel.reaction(j).reactant(SpeciesRole(5)).id))
rule = Model_getAssignmentRuleByVariable(SBMLModel, SBMLModel.reaction(j).reactant(SpeciesRole(5)).id);
rrule = Model_getRateRuleByVariable(SBMLModel, SBMLModel.reaction(j).reactant(SpeciesRole(5)).id);
ia = Model_getInitialAssignmentBySymbol(SBMLModel, SBMLModel.reaction(j).reactant(SpeciesRole(5)).id);
if ~isempty(rule)
output = sprintf('%s - (%s) * (%s)', output, rule.formula, formula);
elseif ~isempty(ia)
output = sprintf('%s - (%s) * (%s)', output, ia.math, formula);
elseif ~isempty(rrule)
error('Cannot deal with stoichiometry in a rate rule');
elseif ~isnan(stoichiometry)
if (stoichiometry == 1)
output = sprintf('%s - (%s)', output, formula);
else
output = sprintf('%s - %g * (%s)', output, stoichiometry, formula);
end;
else
error('Cannot determine stoichiometry');
end;
elseif isnan(stoichiometry)
error ('Cannot determine stoichiometry');
else
if (stoichiometry == 1)
output = sprintf('%s - (%s)', output, formula);
else
output = sprintf('%s - %g * (%s)', output, stoichiometry, formula);
end;
end;
else
% if stoichiometry = 1 no need to include it in formula
if (stoichiometry == 1)
output = sprintf('%s - (%s)', output, formula);
else
output = sprintf('%s - %g * (%s)', output, stoichiometry, formula);
end;
end;
NoReactants = NoReactants - 1;
end;
TotalOccurences = TotalOccurences - 1;
end; % while found > 0
end; % for NumReactions
end; % if boundary condition
% finished looking for this species
% record rate law and loop to next species
% rate = 0 if no law found
if (isempty(output))
RateLaws{i} = '0';
else
RateLaws{i} = output;
end;
end; % for NumberSpecies
if NumberSpecies == 0
RateLaws = {};
end;
function y = Substitute(InitialCharArray, ReplacementParams, Formula)
% Allowed = {'(',')','*','/','+','-','^', ' ', ','};
if exist('OCTAVE_VERSION')
[g,b,c,e] = regexp(Formula, '[,+/*\^()-]');
len = length(Formula);
a{1} = Formula(1:b(1)-1);
for i=2:length(b)
a{i} = Formula(b(i-1)+1:b(i)-1);
end;
i = length(b)+1;
a{i} = Formula(b(i-1)+1:len);
else
[a,b,c,d,e] = regexp(Formula, '[,+*/()-]', 'split');
end;
num = length(a);
for i=1:length(InitialCharArray)
for j=1:num
if strcmp(a(j), InitialCharArray{i})
a(j) = regexprep(a(j), a(j), ReplacementParams{i});
end;
end;
end;
Formula = '';
for i=1:num-1
Formula = strcat(Formula, char(a(i)), char(e(i)));
end;
Formula = strcat(Formula, char(a(num)));
y = Formula;
% % get the number of parameters to be replced
% NumberParams = length(InitialCharArray);
%
%
% % want these in order of shortest to longest
% % since shorter may be subsets of longer
% % ie. 'alpha' is a subset of 'alpha1'
%
% % determine length of each parameter
% for i = 1:NumberParams
% NoCharsInParam(i) = length(InitialCharArray{i});
% end;
%
% % create an array of the index of the shortest to longest
% [NoCharsInParam, Index] = sort(NoCharsInParam);
%
% % rewrite the arrays of parameters from shortest to longest
% for i = 1:NumberParams
% OrderedCharArray{i} = InitialCharArray{Index(i)};
% OrderedReplacements{i} = ReplacementParams{Index(i)};
% end;
%
% RevisedFormula = Formula;
%
% for i = NumberParams:-1:1
% % before replacing a character need to check that it is not part of a
% % word etc
% NumOccurences = length(findstr(OrderedCharArray{i}, RevisedFormula));
% for j = 1:NumOccurences
% k = findstr(OrderedCharArray{i}, RevisedFormula);
% if (k(j) == 1)
% before = ' ';
% else
% before = RevisedFormula(k(j)-1);
% end;
% if ((k(j)+length(OrderedCharArray{i})) < length(RevisedFormula))
% after = RevisedFormula(k(j)+length(OrderedCharArray{i}));
% else
% after = ' ';
% end;
% % octave does not match ' ' using ismember
% if ((ismember(after, Allowed) || (after == Allowed{8})) ...
% && (ismember(before, Allowed) || (before == Allowed{8})))
% RevisedFormula = regexprep(RevisedFormula, OrderedCharArray{i}, ...
% OrderedReplacements{i}, j);
% end;
% end;
% end;
%
% y = RevisedFormula;
%
|
github
|
EPFL-LCSB/matTFA-master
|
TestFunction.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/external/toolboxes/SBMLToolbox-4.1.0/toolbox/Test/TestFunction.m
| 4,751 |
utf_8
|
20ffcfa9c79433da3fc9998246d20dd8
|
function y = TestFunction(varargin)
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2011 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
y = 0;
if (nargin < 3)
error('Need at least 3 inputs');
end;
func = varargin{1};
fhandle = str2func(func);
number_in = varargin{2};
number_out = varargin{3};
if (nargin < 3+number_in+number_out)
error('incorrect number of arguments');
end;
start_out = 4 + number_in;
fail = 0;
switch number_out
case 0
switch number_in
case 1
[a] = feval(fhandle, varargin{4});
case 2
[a] = feval(fhandle, varargin{4}, varargin{5});
case 3
[a] = feval(fhandle, varargin{4}, varargin{5}, varargin{6});
case 4
[a] = feval(fhandle, varargin{4}, varargin{5}, varargin{6}, varargin{7});
end;
fail = fail + ~testEquality(a);
case 1
switch number_in
case 1
[a] = feval(fhandle, varargin{4});
case 2
[a] = feval(fhandle, varargin{4}, varargin{5});
case 3
[a] = feval(fhandle, varargin{4}, varargin{5}, varargin{6});
case 4
[a] = feval(fhandle, varargin{4}, varargin{5}, varargin{6}, varargin{7});
end;
fail = fail + ~testEquality(a, varargin{start_out});
case 2
switch number_in
case 1
[a, b] = feval(fhandle, varargin{4});
case 2
[a, b] = feval(fhandle, varargin{4}, varargin{5});
case 3
[a] = feval(fhandle, varargin{4}, varargin{5}, varargin{6});
case 4
[a] = feval(fhandle, varargin{4}, varargin{5}, varargin{6}, varargin{7});
end;
fail = fail + ~testEquality(a, varargin{start_out});
fail = fail + ~testEquality(b, varargin{start_out+1});
case 3
switch number_in
case 1
[a, b, c] = feval(fhandle, varargin{4});
case 2
[a, b, c] = feval(fhandle, varargin{4}, varargin{5});
case 3
[a] = feval(fhandle, varargin{4}, varargin{5}, varargin{6});
case 4
[a] = feval(fhandle, varargin{4}, varargin{5}, varargin{6}, varargin{7});
end;
fail = fail + ~testEquality(a, varargin{start_out});
fail = fail + ~testEquality(b, varargin{start_out+1});
fail = fail + ~testEquality(c, varargin{start_out+2});
otherwise
error('too many output');
end;
if (fail > 0)
y = 1;
end;
function y = testEquality(array1, array2)
y = isequal(array1, array2);
if y == 1
return;
elseif length(array1) ~= length(array2)
y = 0;
return;
elseif issparse(array1)
array1_full = full(array1);
array2_full = full(array2);
y = testEquality(array1_full, array2_full);
else
y = 1;
i = 1;
% check whether we are dealing with a nan which will always fail equality
while (y == 1 && i <= length(array1))
if ~isstruct(array1)
if isnan(array1(i))
y = isnan(array2(i));
else
y = isequal(array1(i), array2(i));
end;
else
fields = fieldnames(array1(i));
j = 1;
while( y == 1 && j <= length(fields))
ff1 = getfield(array1(i), fields{j});
ff2 = getfield(array2(i), fields{j});
if (iscell(ff1))
ff1 = ff1{1};
ff2 = ff2{1};
end;
if isnan(ff1)
y = isnan(ff2);
else
y = isequal(ff1, ff2);
end;
j = j+1;
end;
end;
i = i + 1;
end;
end;
|
github
|
EPFL-LCSB/matTFA-master
|
sampleScatterMatrix.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/sampling/sampleScatterMatrix.m
| 4,767 |
utf_8
|
58deec35b12aa4bb50273bc36cd3f221
|
function sampleScatterMatrix(rxnNames,model,sample,nPoints,fontSize,dispRFlag,rxnNames2)
%sampleScatterMatrix Draws a scatterplot matrix with pairwise scatterplots
%for multiple reactions
%
% sampleScatterMatrix(rxnNames,model,sample,nPoints,dispRFlag,rxnNames2)
%
%INPUTS
% rxnNames Cell array of reaction names to be plotted
% model Model structure
% sample Samples to be analyzed (nRxns x nSamples)
%
%OPTIONAL INPUTS
% nPoints How many sample points to plot (Default 100)
% fontSize Font size for labels (Default calculated based on
% number of reactions)
% dispRFlag Display correlation coefficients (Default false)
% rxnNames2 Optional second set of reaction names
%
% Examples of usage:
%
% 1) sampleScatterMatrix({'PFK','PYK','PGL'},model,sample);
% Plots the scatterplots only between the three reactions listed -
% histograms for each reaction will be on the diagonal
%
% 2) sampleScatterMatrix({'PFK','PYK','PGL'},model,sample,100,10,true,{'ENO','TPI');
% Plots the scatterplots between each of the first set of reactions and
% each of the second set of reactions. No histograms will be shown.
%
% Markus Herrgard 9/14/06
[isInModel,rxnInd] = ismember(rxnNames,model.rxns);
rxnNames = rxnNames(isInModel);
rxnInd = rxnInd(isInModel);
nRxns = length(rxnNames);
if (nargin < 4)
nPoints = 100;
end
if (nargin < 6)
dispRFlag = false;
end
if (nargin > 6)
[isInModel2,rxnInd2] = ismember(rxnNames2,model.rxns);
rxnNames2 = rxnNames2(isInModel2);
rxnInd2 = rxnInd2(isInModel2);
nRxns2 = length(rxnNames2);
twoSetsFlag = true;
else
nRxns2 = nRxns;
rxnNames2 = rxnNames;
twoSetsFlag = false;
end
if (twoSetsFlag)
nRxns = nRxns+1;
nRxns2 = nRxns2+1;
end
if (nargin < 5)
nPanels = nRxns*nRxns2;
fontSize = 10+ceil(50/sqrt(nPanels));
end
height = 0.8/nRxns;
width = 0.8/nRxns2;
fontSize = 10;
clf
h = waitbar(0,'Drawing scatterplots ...');
for i = 1:nRxns
for j = 1:nRxns2
waitbar(((i-1)*nRxns+j)/(nRxns*nRxns2),h);
left = 0.1+(j-1)*width;
bottom = 0.9-i*height;
if (twoSetsFlag)
if (i == 1 & j == 1)
else
%subplot(nRxns,nRxns2,(i-1)*nRxns2+j);
subplot('position',[left bottom width height]);
if (j >1 & i >1)
sampleScatterPlot(sample,rxnInd2(j-1),rxnInd(i-1),nPoints,fontSize,dispRFlag);
elseif (i == 1)
sampleHistInternal(sample,rxnInd2(j-1),fontSize);
elseif (j == 1)
sampleHistInternal(sample,rxnInd(i-1),fontSize);
end
if (i == 1)
title(rxnNames2{j-1},'FontSize',fontSize);
end
if (j == 1)
ylabel(rxnNames{i-1},'FontSize',fontSize);
end
end
else
if (j == i)
%subplot(nRxns,nRxns2,(i-1)*nRxns2+j);
subplot('position',[left bottom width height]);
sampleHistInternal(sample,rxnInd(i),fontSize);
elseif (j > i)
%subplot(nRxns,nRxns2,(i-1)*nRxns2+j);
subplot('position',[left bottom width height]);
sampleScatterPlot(sample,rxnInd(j),rxnInd(i),nPoints,fontSize,dispRFlag);
end
if (i == 1)
title(rxnNames2{j},'FontSize',fontSize);
end
if (j == nRxns2)
set(gca,'YAxisLocation','right');
ylabel(rxnNames{i},'FontSize',fontSize);
end
end
end
end
close(h);
function sampleScatterPlot(sample,id1,id2,nPoints,fontSize,dispRFlag)
selPts = randperm(size(sample,2));
selPts = selPts(1:nPoints);
plot(sample(id1,selPts),sample(id2,selPts),'r.');
set(gca,'YTickLabel',[]);
set(gca,'XTickLabel',[]);
maxx = max(sample(id1,:));
maxy = max(sample(id2,:));
minx = min(sample(id1,:));
miny = min(sample(id2,:));
axis([minx maxx miny maxy]);
% Display correlation coefficients
if (dispRFlag)
r = corrcoef(sample(id1,:)',sample(id2,:)');
%h = text(minx+0.66*(maxx-minx),miny+0.2*(maxy-miny),num2str(round(100*r(1,2))/100));
%set(h,'FontSize',fontSize-5);
xlabel(num2str(round(100*r(1,2))/100),'FontSize',fontSize-5);
end
function sampleHistInternal(sample,id,fontSize)
[n,bins] = hist(sample(id,:),30);
if (exist('smooth'))
plot(bins,smooth(bins,n')/sum(n'));
else
plot(bins,n'/sum(n'));
end
maxx = max(bins);
minx = min(bins);
set(gca,'XTick',linspace(minx,maxx,4));
set(gca,'XTickLabel',round(10*linspace(minx,maxx,4))/10);
set(gca,'YTickLabel',[]);
set(gca,'FontSize',fontSize-5);
axis tight
|
github
|
EPFL-LCSB/matTFA-master
|
verifyPoints.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/sampling/verifyPoints.m
| 1,925 |
utf_8
|
51f9f4c742a6369a2be6b835d274e08f
|
% function [errorsA, errorsLUB] = verifyPoints(sampleStruct)
function [errorsA, errorsLUB, stuckPoints] = verifyPoints(sampleStruct)
%verifyPoints Verify that a set of points are in the solutoin space of sampleStruct.
% Typically, this method would be called to check a set of warmup points or
% points generated via gpSampler. Also verifies if points moved from
% warmup points.
%
% function [errorsA, errorsLUB, stuckPoints] = verifyPoints(sampleStruct)
%
%INPUT
% sampleStruct LPProblem containing points and warmup points
%
%OUTPUTS
% errorsA Row index of the constraint in sampleStruct that
% is not consistent with the given points
% errorsLUB Upper and lower bounds of the constraint + tolerance
% stuckPoints Index of points which did not move.
%
% Author: Ellen Tsai 2007
% Richard Que (12/1/09) Combined with checkWP.m
%check to see if warmup points moved
[warmupPts, points] = deal(sampleStruct.warmupPts, sampleStruct.points);
n=size(points,2);
len=size(n,1);
stuckPoints=zeros(0,1);
for i=1:n
len(i,1)=norm(warmupPts(:,i)-points(:,i));
if len(i,1)<10
stuckPoints=[stuckPoints; i];
end
end
minL = min(len);
%check to see if points are within solution space
[A,b,csense]=deal(sampleStruct.A,sampleStruct.b,sampleStruct.csense);
t=.01; %tolerance
npoints = size(points, 2);
LHS = A*points;
EIndex = (csense == 'E');
LIndex = (csense == 'L');
GIndex = (csense == 'G');
[errorsL(:,1), errorsL(:,2)] = find(LHS(LIndex,:) - b(LIndex)* ones(1, npoints) > t);
[errorsG(:,1), errorsG(:,2)] = find(b(GIndex)* ones(1, npoints) - LHS(GIndex,:) > t);
[errorsE(:,1), errorsE(:,2)] = find( abs(LHS(EIndex,:) - b(EIndex)* ones(1, npoints)) > t);
errorsUB = find(points > sampleStruct.ub*ones(1,npoints) + t);
errorsLB = find(points < sampleStruct.lb*ones(1,npoints) - t);
errorsA = [errorsL; errorsG; errorsE];
errorsLUB = [errorsLB; errorsUB];
end
|
github
|
EPFL-LCSB/matTFA-master
|
gpSampler_tFBAVersiontUsed.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/sampling/gpSampler_tFBAVersiontUsed.m
| 12,932 |
utf_8
|
e82b2581d217d3925c1a3fa2c4ff003e
|
function [sampleStructOut, mixedFrac] = gpSampler(sampleStruct, nPoints, bias, maxTime, maxSteps, threads, nPointsCheck)
%gpSampler Samples an arbitrary linearly constrained space using a fixed
%number of points that are moved in parallel
%
% [sampleStructOut, mixedFraction] = gpSampler(sampleStruct, nPoints, bias, maxTime, maxSteps)
%
% The space is defined by
% A x <=,==,>= b
% lb <= x <= ub
%
%INPUTS
% sampleStruct Structure describing the space to be sampled and
% previous point sets
% A LHS matrix (optionally, if not A script checks for S)
% b RHS vector
% lb Lower bound
% ub Upper bound
% csense Constraint type for each row in A ('G', 'L', 'E')
% warmupPoints Set of warmup points (optional, generated by default)
% points Currently sampled points (optional)
%
%OPTIONAL INPUTS
% nPoints Number of points used in sampling
% (default = 2*nRxns or 5000 whichever is greater)
% bias
% method Biasing distribution: 'uniform', 'normal'
% index The reaction indexes which to bias (nBias total)
% param nBias x 2 matrix of parameters (for uniform it's min
% max, for normal it's mu, sigma).
% maxTime Maximum time alloted for the sampling in seconds
% (default 600 s, pass an empty number [] to set maxSteps instead)
% maxSteps Maximum number of steps to take (default 1e10). Sampler
% will run until either maxStep or maxTime is reached.
% Set maxStep or maxTime to 0 and no sampling will occur
% (only warmup points generated).
% threads number of threads the sampler will use. If you have a
% dual core machine, you can set it to 2 etc. The speed
% up is almost linear w/ the number of cores.
% If using this feature and 2009a or newer, a futher
% speedup can be obtained by starting matlab from the
% command line by "typing matlab -singleCompThread"
% New feature: if threads < 0, use distributed toolbox.
% nPointsCheck Checks that minimum number of points (2*nRxns) are
% used. (Default = true).
%
%OUTPUT
% sampleStructOut The sampling structure with some extra fields.
% mixedFract The fraction mixed (relative to the warmupPts). A value of 1
% means not mixed at all. A value of .5 means completely mixed.
%% Parameter Processing / error checking
sampleStructOut = 0; % in case of returning early
mixedFrac = 1; % in case of returning early
if nargin < 2
nPoints = 5000;
end
if nargin < 3
bias = [];
end
if ~isempty(bias)
if ~isfield (bias, 'method')
display('bias does not have a method set');
return;
end
end
if nargin < 4 || (isempty(maxTime) && isempty(maxSteps))
maxTime = 10*60; % 10 minutes
end
if (nargin < 5) || isempty(maxSteps)
% Max time takes precedence
maxSteps = 1e10;
else
% Set max steps instead of max time
if (isempty(maxTime))
maxTime = 1e10;
end
end
if nargin < 6 || isempty(threads)
threads = 1;
end
if nargin < 7, nPointsCheck = true; end
% Sanity checking
if (~ isfield (sampleStruct, 'A'))
if isfield(sampleStruct, 'S')
display('A set to S');
sampleStruct.A = sampleStruct.S;
else
display('A and/or S not set');
return;
end
end
if (~ isfield (sampleStruct, 'b'))
sampleStruct.b = zeros(size(sampleStruct.A,1), 1);
display('Warning: b not set. Defaulting to zeros');
end
if (~ isfield (sampleStruct, 'csense'))
sampleStruct.csense(1:size(sampleStruct.A,1)) = 'E';
display('Warning: csense not set. Defaulting to all Equality constraints');
end
if (~isfield (sampleStruct, 'lb'))
display('lb not set');
return;
end
if (~isfield (sampleStruct, 'ub'))
display('ub not set');
return;
end
%% internal data generation
% make internal structure
[A, b, csense, lb, ub] = deal(sampleStruct.A, sampleStruct.b, sampleStruct.csense, sampleStruct.lb, sampleStruct.ub);
% constInd = (lb == ub);
% constVal = lb(constInd);
% Aconst = A(:,constInd);
% b = b - Aconst*constVal;
% A = A(:,~constInd);
% lb = lb(~constInd);
% ub = ub(~constInd);
% [sampleStruct.A, sampleStruct.b, sampleStruct.csense, sampleStruct.lb, sampleStruct.ub] = deal(A, b, csense, lb, ub);
[rA, dimx] = size(A);
if (~ isfield(sampleStruct, 'internal'))
Anew = sparse(0, dimx);
Cnew = sparse(0, dimx);
Bnew = zeros(rA, 1);
Dnew = zeros(rA, 1);
rAnew = 0;
rCnew = 0 ;
for i = 1:size(A, 1)
switch csense(i)
case 'E'
rAnew = rAnew+1;
Anew(rAnew,:) = A(i,:);
Bnew(rAnew,:) = b(i);
case 'G'
rCnew=rCnew+1;
Cnew(rCnew,:) = -A(i,:);
Dnew(rCnew,:) = -b(i);
case 'L'
rCnew=rCnew+1;
Cnew(rCnew,:) = A(i,:);
Dnew(rCnew,:) = b(i);
otherwise
display ('whoops. csense can only contain E, G, or L')
return;
end
end
%Anew = Anew(1:rAnew,:);
Bnew = Bnew(1:rAnew,:);
Dnew = Dnew(1:rCnew,:);
% calculate offset
if find(Bnew ~= 0)
offset = Anew\Bnew;
else
offset = zeros(size(Anew,2), 1);
end
% rescale Bnew, Dnew
Boffset = Bnew - Anew*offset;
if (max(abs(Boffset)) > .0000000001)
display('whoops. It looks like the offset calculation made a mistake. this should be zero.');
max(abs(Boffset))
return;
end
Doffset = Dnew - Cnew*offset;
lbnew = lb - offset;
ubnew = ub - offset;
sampleStruct.internal.offset = offset;
sampleStruct.internal.Anew = Anew;
sampleStruct.internal.Cnew = Cnew;
sampleStruct.internal.Dnew = Doffset;
sampleStruct.internal.lbnew = lbnew;
sampleStruct.internal.ubnew = ubnew;
if (isfield(sampleStruct, 'warmupPts'))
sampleStruct = rmfield(sampleStruct, 'warmupPts');
end
if ~isempty(bias)
sampleStruct.internal.fixed = bias.index;
else
sampleStruct.internal.fixed = [];
end
end
%% Generate warmup points
if (~ isfield(sampleStruct, 'warmupPts') )
fprintf('Generating warmup points\n');
% warmupPts = warmup(sampleStruct, nPoints, bias);
warmupPts = createHRWarmup(sampleStruct, nPoints, false, bias, nPointsCheck);
sampleStruct.warmupPts = warmupPts;
if (isfield(sampleStruct, 'points'))
sampleStruct = rmfield(sampleStruct, 'points');
end
if (isfield(sampleStruct, 'bias'))
sampleStruct = rmfield(sampleStruct, 'bias');
end
sampleStruct.steps = 0;
save sampleStructTmp sampleStruct
else
fprintf('Warmup points already present.\n');
% save sampleStructTmp sampleStruct
end
%% Do actual sampling
fprintf('Sampling\n');
if(maxTime > 0 && maxSteps > 0)
if threads < 0 %uses distributed toolbox.
sampleStruct = ACHRSamplerDistributedGeneral(sampleStruct, ceil(maxSteps/50), 50, maxTime);
else
sampleStruct = ACHRSamplerParallelGeneral(sampleStruct, ceil(maxSteps/50), 50, maxTime, threads);
end
mixedFrac = mixFraction(sampleStruct.points, sampleStruct.warmupPts, sampleStruct.internal.fixed);
else
mixedFrac = 1;
end
sampleStructOut = sampleStruct;
return;
%% warmup Point generator
function warmupPts = warmup(sampleProblem, nPoints, bias)
dimX = size(sampleProblem.A, 2);
warmupPts = zeros(dimX, nPoints);
[LPproblem.A,LPproblem.b,LPproblem.lb,LPproblem.ub,LPproblem.csense,LPproblem.osense] = ...
deal(sampleProblem.A,sampleProblem.b,sampleProblem.lb,sampleProblem.ub,sampleProblem.csense,1);
% Generate the correct parameters for the biasing reactions
if ~isempty(bias)
if (~ismember(bias.method,{'uniform','normal'}))
error('Biasing method not implemented');
end
for k = 1:size(bias.index)
ind = bias.index(k);
% Find upper & lower bounds for bias rxns to ensure that no
% problems arise with values out of bounds
LPproblem.c = zeros(size(LPproblem.A,2),1);
LPproblem.c(ind) = 1;
LPproblem.osense = -1;
sol = solveCobraLP(LPproblem);
maxFlux = sol.obj;
LPproblem.osense = 1;
sol = solveCobraLP(LPproblem);
minFlux = sol.obj;
if strcmp(bias.method, 'uniform')
upperBias = bias.param(k,2);
lowerBias = bias.param(k,1);
if (upperBias > maxFlux || upperBias < minFlux)
upperBias = maxFlux;
disp('Invalid bias bounds - using default bounds instead');
end
if (lowerBias < minFlux || lowerBias > maxFlux)
lowerBias = minFlux;
disp('Invalid bias bounds - using default bounds instead');
end
bias.param(k,1) = lowerBias;
bias.param(k,2) = upperBias;
elseif strcmp(bias.method, 'normal')
biasMean = bias.param(k,1);
if (biasMean > maxFlux || biasMean < minFlux)
bias.param(k,1) = (minFlux + maxFlux)/2;
disp('Invalid bias mean - using default mean instead');
end
biasFluxMin(k) = minFlux;
biasFluxMax(k) = maxFlux;
end
end
end
%Generate the points
i = 1;
while i <= nPoints/2
if mod(i,10) ==0
fprintf('%d\n',2*i);
end
if ~isempty(bias)
for k = 1:size(bias.index)
ind = bias.index(k);
if strcmp(bias.method, 'uniform')
diff = bias.param(k,2) - bias.param(k,1);
fluxVal = diff*rand() + bias.param(k,1);
elseif strcmp(bias.method, 'normal')
valOK = false;
% Try until get points inside the space
while (~valOK)
fluxVal = randn()*bias.param(k,2)+bias.param(k,1);
if (fluxVal <= biasFluxMax(k) && fluxVal >= biasFluxMin(k))
valOK = true;
end
end
end
LPproblem.lb(ind) = 0.99999999*fluxVal;
LPproblem.ub(ind) = 1.00000001*fluxVal;
end
end
% Pick the next flux to optimize, cycles though each reaction
% alternates minimization and maximization for each cycle
LPproblem.c = rand(dimX, 1)-.5;
validFlag = true;
for maxMin = [1, -1]
% Set the objective function
if i <= dimX
% LPproblem.c = rand(dimX, 1)-.5;
LPproblem.c(i) = 5000;
end
LPproblem.osense = maxMin;
% Determine the max or min for the rxn
sol = solveCobraLP(LPproblem);
x = sol.full;
if maxMin == 1
sol1 = sol;
else
sol2 = sol;
end
status = sol.stat;
if status ~= 1
display ('invalid solution')
validFlag = false;
display(status)
pause;
end
% Move points to within bounds
x(x > LPproblem.ub) = LPproblem.ub(x > LPproblem.ub);
x(x < LPproblem.lb) = LPproblem.lb(x < LPproblem.lb);
% Store point
% For non-random points just store a min/max point
if (maxMin == 1)
warmupPts(:,2*i-1) = x;
else
warmupPts(:,2*i) = x;
end
end
if validFlag
%postprocess(LPproblem, sol1, sol2)
i = i+1;
end
end
centerPoint = mean(warmupPts,2);
% Move points in
if isempty(bias)
warmupPts = warmupPts*.33 + .67*centerPoint*ones(1,nPoints);
else
warmupPts = warmupPts*.99 + .01*centerPoint*ones(1,nPoints);
end
% Permute point order
% if (permFlag)
% [nRxns,nPoints] = size(warmupPts);
% warmupPts = warmupPts(:,randperm(nPoints));
% end
return;
%% post processing for better warmup point generation.
% function out = postprocess(LPproblem, sol1, sol2)
% x1 = sol1.full;
% x2 = sol2.full;
% closetoboundary(LPproblem, x1)
% closetoboundary(LPproblem, x2)
%
% separation = sol2.obj - sol1.obj;
% if separation < .00001
% disp('low separation');
% pause;
% end
% LPproblem.A = [LPproblem.A; LPproblem.c];
% LPproblem.b(end+1) = sol1.obj + separation*.1;
% Lpproblem.csense(end+1) = 'L';
%
%
%
% pause;
% out = 2;
%
% return;
% function counter = closetoboundary(LPproblem, sol)
% etol = 1e-5;
% counter = 0;
% counter = counter + sum(LPproblem.A((LPproblem.csense == 'G'),:)*sol - LPproblem.b(LPproblem.csense =='G') < etol)
% counter = counter + sum(LPproblem.b(LPproblem.csense =='L') - LPproblem.A((LPproblem.csense == 'L'),:)*sol < etol)
% counter = counter + sum(LPproblem.ub - sol < etol)
% counter = counter + sum(sol - LPproblem.lb < etol)
% return;
|
github
|
EPFL-LCSB/matTFA-master
|
ACHRSamplerParallelGeneral.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/sampling/ACHRSamplerParallelGeneral.m
| 13,226 |
utf_8
|
a57266feeacacc3b5068e1cf4d95fc38
|
function [sampleStruct] = ACHRSamplerParallelGeneral(sampleStruct,nLoops,stepsPerPoint, maxtime, proc, fdirectory)
% ACHRSamplerParallelGeneral Artificial Centering Hit-and-Run sampler with in place (memory) point
% managmenet
%
% sampleStruct = ACHRSamplerParallelGeneral(sampleStruct,nLoops,stepsPerPoint)
%
%INPUTS
% sampleStruct Sampling structure
% nLoops Number of iterations
% stepsPerPoint Number of sampler steps per point saved
% maxtime Amount of time to spend on calculation (in seconds)
%
%OPTIONAL INPUTS
% proc Number of processes if > 0. Otherwise, the proces #.
% fdirectory Do not use this parameter when calling function directly.
%
%OUTPUT
% sampleStruct Sampling structure with sample points
%
% Jan Schellenberger 1/29/07
% (vaguely) based on code by:
% Markus Herrgard, Gregory Hannum, Ines Thiele, Nathan Price 4/14/06
warning off MATLAB:divideByZero;
%proc == 0 means master
%proc greater than 1 means slave.
if nargin < 5 % not parallel at all.
parallel = 0;
proc = 0;
elseif nargin >= 5 && proc == 1 % not parallel (explicit)
parallel = 0;
proc = 0;
else % parallel.
parallel = 1;
if proc < 0 % an indication that this is a slave process
proc = -proc;
else % indicator that you are a master process
numproc = proc;
proc = 0;
% clear all files that may exist
delete('xxMasterfil*.mat');
delete('xxRound*.mat');
delete('xxRoundDonePrint*.mat');
delete('xxRoundAck*.mat');
delete('xxDoneRound*.mat');
delete('xxDoneP*.mat');
delete('xxGlobalDone*.mat*');
end
end
% Minimum allowed distance to the closest constraint
maxMinTol = 1e-10;
% Ignore directions where u is really small
uTol = 1e-10;
safetycheck = false; % checks the direction of u for fixed directions.
totalStepCount = 0;
t0 = clock;
if proc == 0 % if master thread
if( ~ isfield(sampleStruct, 'points'))
points = sampleStruct.warmupPts; % start with warmup points
else
points = sampleStruct.points; % continue with points
end
offset = sampleStruct.internal.offset;
[dimX,nPoints] = size(points);
points = points - offset*ones(1, nPoints);
ub = sampleStruct.internal.ubnew;
lb = sampleStruct.internal.lbnew;
A = sampleStruct.internal.Anew;
C = sampleStruct.internal.Cnew;
D = sampleStruct.internal.Dnew;
fixed = union(sampleStruct.internal.fixed,find(ub==lb));
if (~isfield(sampleStruct.internal,'N'))
if size(A,1)==0
N=[];
sampleStruct.internal.N=N;
else
if issparse(A)
N = null(full(A));
else
N = null(A);
end
sampleStruct.internal.N = N;
end
else
N = sampleStruct.internal.N;
end
movable = (1:dimX)';
movable(fixed) = [];
if safetycheck
Nsmall = null(full(A(:, movable)));
else
Nsmall = [];
end
% Find the center of the space
centerPoint = mean(points, 2);
fidErr = fopen('ACHRParallelError.txt','w');
pointRange = 1:nPoints;
totalloops = nLoops;
if parallel
blah = 1;
display('saving master file.');
save('xxMasterfile', 'ub', 'lb', 'A', 'C', 'D', 'fixed', 'N', 'movable', 'Nsmall', 'numproc', 'nPoints' );
display('finished saving master file. spawning processes');
for i = 1:(numproc - 1) % goes from 1 to 7 if proc == 8
command = strcat('matlab -singleCompThread -automation -nojvm -r ACHRSamplerParallelGeneral([],',num2str(nLoops),',',num2str(stepsPerPoint),',0,', num2str(-i) ,',''' ,pwd, ''');exit; &' );
display(command)
system(command);
end
display('finished spawning processes');
end
end
if proc > 0 %slave threads only
cd (fdirectory);
load('xxMasterfile', 'ub', 'lb', 'A', 'C', 'D', 'fixed', 'N', 'movable', 'Nsmall', 'numproc', 'nPoints');
blah = 1;
end
for i = 1:nLoops
if parallel % this whole block only gets executed in parallel mode.
if proc == 0 %master thread does this.
% save points
display(strcat('distributing points round ', num2str(i)));
save(strcat('xxRound', num2str(i)), 'points', 'centerPoint');
save(strcat('xxRoundDonePrint', num2str(i)), 'blah');
display(strcat('finished distributing points round ', num2str(i)));
else % if slave threads do this.
display(strcat('reading in points round ', num2str(i)));
while exist(strcat('xxRoundDonePrint', num2str(i), '.mat'), 'file') ~= 2; % wait for other thread to finish.
%display(strcat('waiting for round ', num2str(i)));
fprintf(1, '.');
if exist('xxGlobalDone.mat', 'file') == 2
exit;
end
pause(.25);
end
fprintf(1,'\nloading files four next round.\n');
try load(strcat('xxRound', num2str(i)), 'points', 'centerPoint'); % load actual points
catch pause(15) % for some reason at round 64 it needs extra time to load
load(strcat('xxRound', num2str(i)), 'points', 'centerPoint'); % load actual points
end
save(strcat('xxRoundAck', num2str(i),'x', num2str(proc) ), 'blah'); % save acknowledgement
display(strcat('finished reading input and acknowledgment sent ', num2str(i)));
end
% divide up points. master thread (proc = 0) gets first chunk.
pointRange = subparts(nPoints, numproc, proc);
end
% actual sampling over pointRange
for pointCount = pointRange
% Create the random step size vector
randVector = rand(stepsPerPoint,1);
prevPoint = points(:,pointCount);
curPoint = prevPoint;
if mod(pointCount,200) == 0
display(pointCount);
end
saveCoords = prevPoint(fixed);
for stepCount = 1:stepsPerPoint
% Pick a random warmup point
randPointID = ceil(nPoints*rand);
randPoint = points(:,randPointID);
% Get a direction from the center point to the warmup point
u = (randPoint-centerPoint);
if ~isempty(fixed) % no need to reproject if there are no fixed reactions.
%ubefore = u;
if safetycheck
u(movable) = Nsmall * (Nsmall' * u(movable));
end
%uafter = u;
u(fixed) = 0; % takes care of biasing.
end
u = u/norm(u);
% Figure out the distances to upper and lower bounds
distUb = (ub - prevPoint);
distLb = (prevPoint - lb);
distD = (D-C*prevPoint);
% Figure out positive and negative directions
posDirn = (u > uTol);
negDirn = (u < -uTol);
move = C*u;
posDirn2 = (move > uTol);
negDirn2 = (move < -uTol);
% Figure out all the possible maximum and minimum step sizes
maxStepTemp = distUb./u;
minStepTemp = -distLb./u;
StepD = distD./move;
maxStepVec = [maxStepTemp(posDirn);minStepTemp(negDirn);StepD(posDirn2 )];
minStepVec = [minStepTemp(posDirn);maxStepTemp(negDirn);StepD(negDirn2 )];
% Figure out the true max & min step sizes
maxStep = min(maxStepVec);
minStep = max(minStepVec);
% Find new direction if we're getting too close to a constraint
if (abs(minStep) < maxMinTol && abs(maxStep) < maxMinTol) || (minStep > maxStep)
fprintf('Warning small step: %f %f\n',minStep,maxStep);
continue;
end
% Pick a rand out of list_of_rands and use it to get a random
% step distance
stepDist = minStep + randVector(stepCount)*(maxStep-minStep);
%fprintf('%d %d %d %f %f\n',i,pointCount,stepCount,minStep,maxStep);
% Advance to the next point
curPoint = prevPoint + stepDist*u;
% Reproject the current point into the null space
if mod (stepCount, 25) == 0
if ~isempty(N)
curPoint = N* (N' * curPoint);
end
curPoint(fixed) = saveCoords;
end
% Print out amount of constraint violation
if (mod(totalStepCount,1000)==0) && proc == 0 % only do for master thread
fprintf(fidErr,'%10.8f\t%10.8f\t',max(curPoint-ub),max(lb-curPoint));
end
% Move points inside the space if reprojection causes problems
overInd = (curPoint > ub);
underInd = (curPoint < lb);
if (sum(overInd)>0) || (sum(underInd)>0)
curPoint(overInd) = ub(overInd);
curPoint(underInd) = lb(underInd);
end
% Print out amount of constraint violation
if (mod(totalStepCount,1000) == 0) && proc == 0 % only do for master thread
fprintf(fidErr,'%10.8f\n',full(max(max(abs(A*curPoint)))));
end
prevPoint = curPoint;
% Count the total number of steps
totalStepCount = totalStepCount + 1;
end % Steps per point
% Final reprojection
if ~isempty(N)
curPoint = N* (N' * curPoint);
end
curPoint(fixed) = saveCoords;
centerPoint = centerPoint + (curPoint - points(:,pointCount))/nPoints; % only swapping one point... it's trivial.
% Swap current point in set of points.
points(:,pointCount) = curPoint;
end % Points per cycle
if parallel % do this block if in parallel mode (regather points)
if proc == 0 % if master
% look for acknowledgements.
display(strcat ('waiting for acknowledgement', num2str(i)));
donewaiting = 0;
while ~donewaiting
donewaiting = 1;
for k = 1:(numproc-1);
if exist(strcat('xxRoundAck',num2str(i), 'x', num2str(k),'.mat'), 'file') ~= 2
donewaiting = 0;
end
end
%display('waiting for acknowledgement');
fprintf(1, '.');
pause(.25)
end
% all other processes have received their information. delete temporary files.
fprintf(1, '\n');
for k = 1:(numproc-1)
delete (strcat('xxRoundAck', num2str(i), 'x', num2str(k), '.mat'));
end
delete(strcat('xxRound', num2str(i), '.mat'));
delete(strcat('xxRoundDonePrint', num2str(i), '.mat'));
% look for return values.
display(strcat ('waiting for return files ', num2str(i)));
donewaiting = 0;
while ~donewaiting
donewaiting = 1;
for k = 1:(numproc-1);
if exist(strcat('xxDoneP',num2str(i), 'x', num2str(k),'.mat'), 'file') ~= 2
donewaiting = 0;
end
end
pause(.25)
fprintf(1,'.');
end
fprintf(1, '\nAll processes finished. reading\n');
for k = 1:(numproc-1)
load (strcat('xxDoneRound', num2str(i), 'x', num2str(k)), 'points2');
r2 = subparts(nPoints, numproc, k);
points(:,r2) = points2;
delete (strcat('xxDoneRound', num2str(i), 'x', num2str(k), '.mat') );
delete (strcat('xxDoneP',num2str(i), 'x', num2str(k), '.mat'));
end
centerPoint = mean(points, 2); % recalculate center point after gathering all data.
display(strcat('done with round ', num2str(i)));
else % if slave
points2 = points(:, pointRange);
save (strcat('xxDoneRound', num2str(i), 'x', num2str(proc)), 'points2');
save (strcat('xxDoneP',num2str(i), 'x', num2str(proc)), 'blah');
end
end
t1 = clock();
fprintf('%10.0f s %d steps\n',etime(t1, t0),i*stepsPerPoint);
if etime(t1, t0) > maxtime && proc == 0 % only master thread can terminate due to time limits.
totalloops = i;
break;
end
end
if proc > 0 % slave threads terminate here.
return;
end
points = points + offset*ones(1, nPoints);
sampleStruct.points = points;
if ~ isfield(sampleStruct, 'steps')
sampleStruct.steps = 0;
end
sampleStruct.steps = sampleStruct.steps + stepsPerPoint*totalloops;
% flag for all other handles to terminate.
if parallel
save('xxGlobalDone', 'blah');
delete('xxMaster*.mat');
end
fclose(fidErr);
function out = subparts(nPoints, n, k)
out = (floor(nPoints*k/n)+1) : (floor(nPoints*(k+1)/n));
return
|
github
|
EPFL-LCSB/matTFA-master
|
generateSUXMatrix.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/gapFilling/growthExpMatch/generateSUXMatrix.m
| 3,883 |
utf_8
|
7765018ced7286373cb6eabb2a70249c
|
function MatricesSUX =generateSUXMatrix(model,dictionary, KEGGFilename, KEGGBlackList, compartment, addModel)
% generateSUXMatrix creates the matrices for matlab smiley -- > combines S, U
% (KEGG), X (transport)
%
% MatricesSUX =generateSUXMatrix(model,CompAbr, KEGGID,
% KEGGFilename, compartment)
%
% model model structure
% CompAbr List of compounds abreviation (non-compartelized)
% KEGGID List of KEGGIDs for compounds in CompAbr
% KEGGFilename File name containing KEGG database
% KEGGBlackList
% compartment [c] --> transport from cytoplasm [c] to extracellulat space
% [e] (default), [p] creates transport from [c] to [p] and from [p] to [c],
% if '' - no exchange reactions/transport will be added to the matrix.
% addModel model structure, containing an additional matrix or model
% that should be combined with SUX matrix.% Note that the naming of metabolites in this matrix has to be identical to
% model naming. Also, the list should be unique.
%
% 11-10-07 IT
%
if nargin < 6
addModel = '';
end
if nargin < 5
compartment = '[c]';
end
if nargin < 4
KEGGBlackList = {};
end
if nargin < 3
KEGGFilename = '11-20-08-KEGG-reaction.lst';
end
% checks if model.mets has () or [] for compartment, or adds cytosol to
% compounds if no compartment is specified
model = CheckMetName(model);
% create KEGG Matrix - U
KEGG = createUniversalReactionModel(KEGGFilename, KEGGBlackList);
KEGG = transformKEGG2Model(KEGG,dictionary);
%merge all 3 matrixes
% 1. S with U
model.RxnSubsystem = model.subSystems;
KEGG.RxnSubsystem = KEGG.subSystems;
[model_SU] = mergeTwoModels(model,KEGG,1);
% Adds an additional matrix if given as input
% Note that the naming of metabolites in this matrix has to be identical to
% model naming. Also, the list should be unique.
if isstruct(addModel)
addModel = CheckMetName(addModel);
[model_SU] = mergeTwoModels(model_SU,addModel,1);
end
if ~isempty(compartment)
ExchangeRxnMatrix = createXMatrix(model_SU.mets,1,compartment);
% 2. SU with X
ExchangeRxnMatrix.RxnSubsystem = ExchangeRxnMatrix.subSystems;
%model_SU.RxnSubsystem = model_SU.subSystems;
[MatricesSUX] = mergeTwoModels(model_SU,ExchangeRxnMatrix,1);
% creates a vector assigning the origin of the reactions to the parentfprintf(1,'Converting merged model into an irreversible model...');
else
MatricesSUX=model_SU;
end
MatricesSUX.rxnGeneMat(length(MatricesSUX.rxns),length(MatricesSUX.genes))=0;
MatricesSUX.rxnGeneMat = sparse(MatricesSUX.rxnGeneMat);
MatricesSUX = convertToIrreversible(MatricesSUX);
% MatrixPart indicates in which area of MatricesSUX the model reactions,
% kegg reactions, and exchange/transport reactions are located (ie. 1 -
% model, 2 - kegg, 3 - X)
tmp=find(model.rev);
MatricesSUX.MatrixPart(1:length(model.rxns)+length(tmp),1)=1; % model reactions
MatricesSUX.MatrixPart(length(MatricesSUX.MatrixPart)+1:length(MatricesSUX.MatrixPart)+length(KEGG.rxns)+length(find(KEGG.rev)),1)=2;%KEGG DB reactions
MatricesSUX.MatrixPart(length(MatricesSUX.MatrixPart)+1:length(MatricesSUX.rxns),1)=3; %exchange and transport reactions
function model = CheckMetName(model)
% checks if model.mets has () or [] for compartment
if ~isempty(strfind(model.mets,'(c)')) ||~isempty(strfind(model.mets,'(e)'))
for i = 1 :length(model.mets)
model.mets{i} = regexprep(model.mets{i},'(','[');
model.mets{i} = regexprep(model.mets{i},')',']');
end
end
% fixes metabolites names if no compartment has been added to metabolites.
% It assumes that the metabolites without compartment are in the cytosol
for i = 1 :length(model.mets)
if isempty(regexp(model.mets{i},'\(\w\)')) && isempty(regexp(model.mets{i},'\[\w\]'))
model.mets{i} = strcat(model.mets{i},'[c]');
end
end
|
github
|
EPFL-LCSB/matTFA-master
|
growthExpMatch.m
|
.m
|
matTFA-master/ext/Cobra205_vDec2014/gapFilling/growthExpMatch/growthExpMatch.m
| 6,053 |
utf_8
|
7b4d9288dec14e0b4979d70ba9f64043
|
function [solution]=growthExpMatch(model, KEGGFilename, compartment, iterations, dictionary, logFile, threshold)
%growExpMatch run the growthExpMatch algorythm
%
% [solution]=growthExpMatch(model, KEGGFilename, compartment, iterations, dictionary, logFile, threshold)
%
%INPUTS
% model COBRA model structure
% KEGGFilename File name containing Kegg database (.lst file with list of
% reactions: each listing is reaction name followed by colon
% followed by the reaction formula)
% compartment [c] --> transport from cytoplasm [c] to extracellulat space
% [e] (default), [p] creates transport from [c] to [p]
% and from [p] to [c]
% iterations Number of iterations to run
% dictionary n x 2 cell array of metabolites names for conversion from
% Kegg ID's to the compound abbreviations from BiGG database
% (1st column is compound abb. (non-compartmenalized) and
% 2nd column is Kegg ID) Both columns are the same length.
%
%OPTINAL INPUTS
% logFile solution is printed in this file (name of reaction added and
% flux of that particular reaction) (Default = GEMLog.txt)
%
% threshold threshold number for biomass reaction; model is considered
% to be growing when the flux of the biomass reaction is
% above threshold. (Default = 0.05)
%
%OUTPUT
% solution MILP solution that consists of the continuous solution, integer
% solution, objective value, stat, full solution, and
% imported reactions
%
%
%%Procedure to run SMILEY:
%(1) obtain all input files (ie. model, CompAbr, and KeggID are from BiGG, KeggList is from Kegg website)
%(2) remove desired reaction from model with removeRxns, or set the model
% on a particular Carbon or Nitrogen source
%(3) create an SUX Matrix by using the function MatricesSUX =
% generateSUXMatrix(model,dictionary, KEGGFilename,compartment)
%(4) run it through SMILEY using [solution,b,solInt]=Smiley(MatricesSUX)
%(5) solution.importedRxns contains the solutions to all iterations
%
% MILPproblem
% A LHS matrix
% b RHS vector
% c Objective coeff vector
% lb Lower bound vector
% ub Upper bound vector
% osense Objective sense (-1 max, +1 min)
% csense Constraint senses, a string containting the constraint sense for
% each row in A ('E', equality, 'G' greater than, 'L' less than).
% vartype Variable types
% x0 Initial solution
% Based on IT 11/2008
% Edited by xx
if nargin<2
MatricesSUX= model;
iterations=2;
else
MatricesSUX = generateSUXMatrix(model,dictionary, KEGGFilename,compartment);
end
if nargin <6
logFile='GEMLog';
end
if nargin <7
threshold= 0.05;
end
MatricesSUXori = MatricesSUX;
startKegg = find(MatricesSUX.MatrixPart ==2, 1, 'first');
stopKegg = find(MatricesSUX.MatrixPart ==2, 1, 'last');
lengthKegg = stopKegg -startKegg +1;
startEx = find(MatricesSUX.MatrixPart ==3, 1, 'first');
stopEx = find(MatricesSUX.MatrixPart ==3, 1, 'last');
lengthEx = stopEx -startEx +1;
if isempty(lengthEx)
lengthEx = 0;
end
vmax = 1000;
[a,b]=size(MatricesSUX.S);
cols = b + lengthKegg + lengthEx;
rows = a + lengthKegg + lengthEx;
[i1,j1,s1] = find(MatricesSUX.S);
% Kegg
%add rows
i2a=(a+1:a+lengthKegg)';
j2a=(startKegg:stopKegg)';
s2a=ones(lengthKegg,1);
%add cols
i2b=(a+1:a+lengthKegg)';
j2b=(b+1:b+lengthKegg)';
s2b=-vmax*ones(lengthKegg,1);
%Exchange
%add rows
i3a=(a+lengthKegg+1:rows)';
j3a=(startEx:stopEx)';
s3a=ones(lengthEx,1);
%add cols
i3b=(a+lengthKegg+1:rows)';
j3b=(b+lengthKegg+1:cols)';
s3b=-vmax*ones(lengthEx,1);
if isempty(MatricesSUX.c);
disp('No biomass reaction found');
else
biomass_rxn_loc = find(MatricesSUX.c);
end
i = [i1;i2a;i2b;i3a;i3b;rows+1];
j=[j1;j2a;j2b;j3a;j3b;biomass_rxn_loc];
s=[s1;s2a;s2b;s3a;s3b;1];
MatricesSUX.A = sparse(i,j,s);
MatricesSUX.b = zeros(size(MatricesSUX.A,1),1);
%%% Set the threshold to 0.05 %%%
MatricesSUX.b(size(MatricesSUX.A,1),1) = threshold;
MatricesSUX.cOuter = zeros(size(MatricesSUX.A,2),1);
MatricesSUX.cOuter(b+1:b+lengthKegg)=1;
MatricesSUX.cOuter(b+lengthKegg+1:cols)=2.1;
MatricesSUX.csense(1:a)='E';
MatricesSUX.csense(a+1:rows)='L';
MatricesSUX.csense(rows+1) = 'G';
MatricesSUX.lb(b+1:cols)=0;
MatricesSUX.ub(b+1:cols)=1;
MatricesSUX.rxns(b+1:cols)=strcat(MatricesSUX.rxns(startKegg:stopEx),'dummy');
MatricesSUX.MatrixPart(b+1:cols)=4;
Int= find(MatricesSUX.MatrixPart>=4);
spy(MatricesSUX.A)
x0=zeros(size(MatricesSUX.A,2),1);
solInt=zeros(length(Int),1);
%%% setting the MILPproblem %%%
vartype(b+1:cols) = 'B';
vartype(1:b) = 'C';
MILPproblem.A = MatricesSUX.A;
MILPproblem.b = MatricesSUX.b;
MILPproblem.c = MatricesSUX.cOuter;
MILPproblem.lb = MatricesSUX.lb;
MILPproblem.ub = MatricesSUX.ub;
MILPproblem.csense = MatricesSUX.csense;
MILPproblem.osense = 1;
MILPproblem.vartype = vartype;
MILPproblem.x0 = x0;
for i = 1: iterations
solution = solveCobraMILP(MILPproblem);
if(solution.obj~=0)
solInt(:,i+1)=solution.int;
printSolutionGEM(MatricesSUX, solution,logFile,i);
MILPproblem.A(rows+i+1,j2b(1):cols) = solInt(:,i+1)';
MILPproblem.b(rows+i+1) = sum(solInt(:,i+1))-.1;
MILPproblem.csense(rows+i+1) = 'L';
% save([logFile '_solution_' num2str(i)]);
end
solution.importedRxns = findImportedReactions(solInt, MatricesSUX);
tmp=find(solution.cont);
for j=1:length(tmp)
if(tmp(j)>=Int(1))
MILPproblem.ub(tmp(j))=solution.cont(tmp(j));%%%
end
end
if (solution.stat~=1)
break
end
end
printSolutionGEM(MatricesSUX, solution);
function importedRxns = findImportedReactions(solInt, MatricesSUX)
importedRxns= {};
stopModel = find((MatricesSUX.MatrixPart ==1), 1, 'last');
for i = 1: size(solInt,2)-1
[x,y] = find(solInt(:, i+1));
for j = 1: size(x)
importedRxns{i, j} = MatricesSUX.rxns(stopModel + x(j));
MatricesSUX.rxns(stopModel + x(j));
end
end
|
github
|
CollinGuo/GoDec_plus-master
|
SpectralClustering.m
|
.m
|
GoDec_plus-master/SpectralClustering.m
| 1,247 |
utf_8
|
21c3ecc5345706307b629c9e01180798
|
%--------------------------------------------------------------------------
% This function takes an adjacency matrix of a graph and computes the
% clustering of the nodes using the spectral clustering algorithm of
% Ng, Jordan and Weiss.
% CMat: NxN adjacency matrix
% n: number of groups for clustering
% groups: N-dimensional vector containing the memberships of the N points
% to the n groups obtained by spectral clustering
%--------------------------------------------------------------------------
% Copyright @ Ehsan Elhamifar, 2012
%--------------------------------------------------------------------------
function groups = SpectralClustering(CKSym,n)
warning off;
N = size(CKSym,1);
MAXiter = 1000; % Maximum number of iterations for KMeans
REPlic = 20; % Number of replications for KMeans
% Normalized spectral clustering according to Ng & Jordan & Weiss
% using Normalized Symmetric Laplacian L = I - D^{-1/2} W D^{-1/2}
DN = diag( 1./sqrt(sum(CKSym)+eps) );
LapN = speye(N) - DN * CKSym * DN;
[uN,sN,vN] = svd(LapN);
kerN = vN(:,N-n+1:N);
for i = 1:N
kerNS(i,:) = kerN(i,:) ./ norm(kerN(i,:)+eps);
end
groups = kmeans(kerNS,n,'maxiter',MAXiter,'replicates',REPlic,'EmptyAction','singleton');
|
github
|
walid1992/AndroidSpeexDenoise-master
|
echo_diagnostic.m
|
.m
|
AndroidSpeexDenoise-master/app/src/main/jni/libspeexdsp/echo_diagnostic.m
| 2,076 |
utf_8
|
8d5e7563976fbd9bd2eda26711f7d8dc
|
% Attempts to diagnose AEC problems from recorded samples
%
% out = echo_diagnostic(rec_file, play_file, out_file, tail_length)
%
% Computes the full matrix inversion to cancel echo from the
% recording 'rec_file' using the far end signal 'play_file' using
% a filter length of 'tail_length'. The output is saved to 'out_file'.
function out = echo_diagnostic(rec_file, play_file, out_file, tail_length)
F=fopen(rec_file,'rb');
rec=fread(F,Inf,'short');
fclose (F);
F=fopen(play_file,'rb');
play=fread(F,Inf,'short');
fclose (F);
rec = [rec; zeros(1024,1)];
play = [play; zeros(1024,1)];
N = length(rec);
corr = real(ifft(fft(rec).*conj(fft(play))));
acorr = real(ifft(fft(play).*conj(fft(play))));
[a,b] = max(corr);
if b > N/2
b = b-N;
end
printf ("Far end to near end delay is %d samples\n", b);
if (b > .3*tail_length)
printf ('This is too much delay, try delaying the far-end signal a bit\n');
else if (b < 0)
printf ('You have a negative delay, the echo canceller has no chance to cancel anything!\n');
else
printf ('Delay looks OK.\n');
end
end
end
N2 = round(N/2);
corr1 = real(ifft(fft(rec(1:N2)).*conj(fft(play(1:N2)))));
corr2 = real(ifft(fft(rec(N2+1:end)).*conj(fft(play(N2+1:end)))));
[a,b1] = max(corr1);
if b1 > N2/2
b1 = b1-N2;
end
[a,b2] = max(corr2);
if b2 > N2/2
b2 = b2-N2;
end
drift = (b1-b2)/N2;
printf ('Drift estimate is %f%% (%d samples)\n', 100*drift, b1-b2);
if abs(b1-b2) < 10
printf ('A drift of a few (+-10) samples is normal.\n');
else
if abs(b1-b2) < 30
printf ('There may be (not sure) excessive clock drift. Is the capture and playback done on the same soundcard?\n');
else
printf ('Your clock is drifting! No way the AEC will be able to do anything with that. Most likely, you''re doing capture and playback from two different cards.\n');
end
end
end
acorr(1) = .001+1.00001*acorr(1);
AtA = toeplitz(acorr(1:tail_length));
bb = corr(1:tail_length);
h = AtA\bb;
out = (rec - filter(h, 1, play));
F=fopen(out_file,'w');
fwrite(F,out,'short');
fclose (F);
|
github
|
brennankoopman/MTE204_Robot_Arm_Control-master
|
Jacobian.m
|
.m
|
MTE204_Robot_Arm_Control-master/Jacobian.m
| 575 |
utf_8
|
7231c1c63fd0e284853ed024883d2ea1
|
% calculates the jacobian based on the joint angles
function J = Jacobian(q);
len = [0 1 1];
dx1 = -(len(2)*cos(q(2)) + len(3)*cos(q(2)-q(3)))*sin(q(1));
dx2 = (-len(2)*sin(q(2))-len(3)*sin(q(2)-q(3)))*cos(q(1));
dx3 = (len(3)*sin(q(2)-q(3)))*cos(q(1));
dy1 = (len(2)*cos(q(2))+len(3)*cos(q(2)-q(3)))*cos(q(1));
dy2 = (-len(2)*sin(q(2))-len(3)*sin(q(2)-q(3)))*sin(q(1));
dy3 = len(3)*sin(q(2)-q(3))*sin(q(1));
dz1 = 0;
dz2 = len(2)*cos(q(2))+len(3)*cos(q(2)-q(3));
dz3 = -len(3)*cos(q(2)-q(3));
J = [dx1,dx2,dx3;
dy1,dy2,dy3;
dz1,dz2,dz3];
|
github
|
brennankoopman/MTE204_Robot_Arm_Control-master
|
timeOutputTest.m
|
.m
|
MTE204_Robot_Arm_Control-master/timeOutputTest.m
| 2,015 |
utf_8
|
4d5da938ce78aadae33aca4b8d618470
|
%{
%this times the numerical method verses n subintervals, the calculations in this function are the major ones a real
%time system would need to operate with our mething method
q - the initial position in angles of deg
t - the target position in cartesian coords, col vesctor
Jerr - the end case error on the Jacobian transpose method
n = number of steps you break the linear movement into
%}
function time = timeOutputTest(q, t, Jerr, n)
tic %this records the innitial time stamp for the time trials
q = q*(pi/180);
Q = [q,zeros(3,n)]; %list of all angles for each target point starting at the initial position
Points = sectionPath(t,q,n);
%CALCULATES THE ANGLES FOR EACH STEP POINT USING THE JACOBIAN TRANSPOSE METHOD
for a = 1:n
Q(:,a+1) = getQ( Points(:,a+1), Q(:,a),Jerr); % ERROR of Jerr
end
dQ = [zeros(3,n)]; %list of all differential angles
cPoints = [Points(:,1)]; %list of points, with 100 points for each arc, ie target point, here we just set the first entry the initial position
for a = 1:n %for each jump in angles
dQ(:,a+1) = Q(:,a+1) - Q(:,a); %finds the change in angle needed for this step
%it turns out that the rotations dont linearlize nicely when a path crosses
%the refrence axis, since the change in angle from 350 -> 10 should be 20,
% NOT -340, thus a single dq value cannot exceed 180 deg, as the smaller
% rotation value is preffered. note that angles are in RADIANS
if( abs(dQ(1,a))>pi)
dQ(1,a)= dQ(1,a)-2*pi*sign(dQ(1,a)); %takes the opposite of the sign of your dQ * 360, and adds your dQ to find your opposite rotation
end
if( abs(dQ(2,a))>pi)
dQ(2,a) = dQ(2,a)-2*pi*sign(dQ(2,a));
end
if( abs(dQ(3,a))>pi)
dQ(3,a) = dQ(3,a)-2*pi*sign(dQ(3,a));
end
end
%csvwrite('dQ.csv', transpose(dQ));
%csvwrite('Q.csv', transpose(Q));
time = toc; %return time stamp for the time the method took
|
github
|
brennankoopman/MTE204_Robot_Arm_Control-master
|
armFunction_midJoint.m
|
.m
|
MTE204_Robot_Arm_Control-master/armFunction_midJoint.m
| 387 |
utf_8
|
ef5a3716f0aca41119ee61b2002b8ec0
|
%this function calculates the postion of the midjoint with the inputs of
%q, which is the joint angles of the arm
%P is the reference point of the arm in 3D space, typically (0,0,0)
function [smid] = armFunction_midJoint (q, P)
len = [0;1;1];
y = (len(2)*cos(q(2)))*sin(q(1)) - P(1);
x = (len(2)*cos(q(2)))*cos(q(1)) - P(2);
z = len(2)*sin(q(2)) - P(3);
smid = [x;y;z];
endfunction
|
github
|
brennankoopman/MTE204_Robot_Arm_Control-master
|
armFunction.m
|
.m
|
MTE204_Robot_Arm_Control-master/armFunction.m
| 458 |
utf_8
|
af0cc0db3ec240f263d95ab51ab4835f
|
%this function calculates the postion of the end effector with the inputs of
%q, which is the joints angles of the arm
%P is the reference point of the arm in 3D space, typically (0,0,0)
function s = armFunction(q, P)
len = [0 1 1];
x = (len(2)*cos(q(2)) + len(3)*cos(q(2)-q(3)))*cos(q(1)) - P(1); % x
y = (len(2)*cos(q(2)) + len(3)*cos(q(2)-q(3)))*sin(q(1)) - P(2); % y
z = (len(2)*sin(q(2)) + len(3)*sin(q(2)-q(3))) - P(3); % z
s = [x;y;z];
|
github
|
brennankoopman/MTE204_Robot_Arm_Control-master
|
sectionPath.m
|
.m
|
MTE204_Robot_Arm_Control-master/sectionPath.m
| 764 |
utf_8
|
fc563b76c2ae1de650cea01e7498cf4d
|
%{
Version = Test
this version will be used for the analysis of the time efficiency of the algorithm
this function will take any linear path between s and t, and break it up into an
efficient number of smaller steps in order to make the path as straight as
possible
%}
%t is the target position, q is the initial position given in its angles
%n = number of steps
%sNew is a list of new positions to be outputted
function sNew = sectionPath(t, qi, n)
s = armFunction( qi, [0;0;0]);
e = t - s;
%n is the number of substeps we have per movement
eN = e / n;
sNew = [s,zeros(3, n)]; %set the first value to the initial position
for a = 1:n
sNew(:,a+1) = sNew(:,a) + eN; %the size of sNew is 3 x n+1
end
end
|
github
|
zeakey/edgeval-master
|
checkNumArgs.m
|
.m
|
edgeval-master/utils/checkNumArgs.m
| 3,796 |
utf_8
|
726c125c7dc994c4989c0e53ad4be747
|
function [ x, er ] = checkNumArgs( x, siz, intFlag, signFlag )
% Helper utility for checking numeric vector arguments.
%
% Runs a number of tests on the numeric array x. Tests to see if x has all
% integer values, all positive values, and so on, depending on the values
% for intFlag and signFlag. Also tests to see if the size of x matches siz
% (unless siz==[]). If x is a scalar, x is converted to a array simply by
% creating a matrix of size siz with x in each entry. This is why the
% function returns x. siz=M is equivalent to siz=[M M]. If x does not
% satisfy some criteria, an error message is returned in er. If x satisfied
% all the criteria er=''. Note that error('') has no effect, so can use:
% [ x, er ] = checkNumArgs( x, ... ); error(er);
% which will throw an error only if something was wrong with x.
%
% USAGE
% [ x, er ] = checkNumArgs( x, siz, intFlag, signFlag )
%
% INPUTS
% x - numeric array
% siz - []: does not test size of x
% - [if not []]: intended size for x
% intFlag - -1: no need for integer x
% 0: error if non integer x
% 1: error if non odd integers
% 2: error if non even integers
% signFlag - -2: entires of x must be strictly negative
% -1: entires of x must be negative
% 0: no contstraints on sign of entries in x
% 1: entires of x must be positive
% 2: entires of x must be strictly positive
%
% OUTPUTS
% x - if x was a scalar it may have been replicated into a matrix
% er - contains error msg if anything was wrong with x
%
% EXAMPLE
% a=1; [a, er]=checkNumArgs( a, [1 3], 2, 0 ); a, error(er)
%
% See also NARGCHK
%
% Piotr's Computer Vision Matlab Toolbox Version 2.0
% Copyright 2014 Piotr Dollar. [pdollar-at-gmail.com]
% Licensed under the Simplified BSD License [see external/bsd.txt]
xname = inputname(1); er='';
if( isempty(siz) ); siz = size(x); end;
if( length(siz)==1 ); siz=[siz siz]; end;
% first check that x is numeric
if( ~isnumeric(x) ); er = [xname ' not numeric']; return; end;
% if x is a scalar, simply replicate it.
xorig = x; if( length(x)==1); x = x(ones(siz)); end;
% regardless, must have same number of x as n
if( length(siz)~=ndims(x) || ~all(size(x)==siz) )
er = ['has size = [' num2str(size(x)) '], '];
er = [er 'which is not the required size of [' num2str(siz) ']'];
er = createErrMsg( xname, xorig, er ); return;
end
% check that x are the right type of integers (unless intFlag==-1)
switch intFlag
case 0
if( ~all(mod(x,1)==0))
er = 'must have integer entries';
er = createErrMsg( xname, xorig, er); return;
end;
case 1
if( ~all(mod(x,2)==1))
er = 'must have odd integer entries';
er = createErrMsg( xname, xorig, er); return;
end;
case 2
if( ~all(mod(x,2)==0))
er = 'must have even integer entries';
er = createErrMsg( xname, xorig, er ); return;
end;
end;
% check sign of entries in x (unless signFlag==0)
switch signFlag
case -2
if( ~all(x<0))
er = 'must have strictly negative entries';
er = createErrMsg( xname, xorig, er ); return;
end;
case -1
if( ~all(x<=0))
er = 'must have negative entries';
er = createErrMsg( xname, xorig, er ); return;
end;
case 1
if( ~all(x>=0))
er = 'must have positive entries';
er = createErrMsg( xname, xorig, er ); return;
end;
case 2
if( ~all(x>0))
er = 'must have strictly positive entries';
er = createErrMsg( xname, xorig, er ); return;
end
end
function er = createErrMsg( xname, x, er )
if(numel(x)<10)
er = ['Numeric input argument ' xname '=[' num2str(x) '] ' er '.'];
else
er = ['Numeric input argument ' xname ' ' er '.'];
end
|
github
|
zeakey/edgeval-master
|
edgesEvalDir.m
|
.m
|
edgeval-master/utils/edgesEvalDir.m
| 5,852 |
utf_8
|
b708b92045eaa75fa68d09e169447bb6
|
function varargout = edgesEvalDir( varargin )
% Calculate edge precision/recall results for directory of edge images.
%
% Enhanced replacement for boundaryBench() from BSDS500 code:
% http://www.eecs.berkeley.edu/Research/Projects/CS/vision/grouping/
% Uses same format for results and is fully compatible with boundaryBench.
% Given default prms results are *identical* to boundaryBench with the
% additional 9th output of R50 (recall at 50% precision).
%
% The odsF/P/R/T are results at the ODS (optimal dataset scale).
% The oisF/P/R are results at the OIS (optimal image scale).
% Naming convention: P=precision, R=recall, F=2/(1/P+1/R), T=threshold.
%
% In addition to the outputs, edgesEvalDir() creates three files:
% eval_bdry_img.txt - per image OIS results [imgId T R P F]
% eval_bdry_thr.txt - per threshold ODS results [T R P F]
% eval_bdry.txt - complete results (*re-ordered* copy of output)
% These files are identical to the ones created by boundaryBench.
%
% USAGE
% [odsF,odsP,odsR,odsT,oisF,oisP,oisR,AP,R50] = edgesEvalDir( prms )
% [ODS,~,~,~,OIS,~,~,AP,R50] = edgesEvalDir( prms )
%
% INPUTS
% prms - parameters (struct or name/value pairs)
% .resDir - ['REQ'] dir containing edge detection results (.png)
% .gtDir - ['REQ'] dir containing ground truth (.mat)
% .pDistr - [{'type','parfor'}] parameters for fevalDistr
% .cleanup - [0] if true delete temporary files
% .thrs - [99] number or vector of thresholds for evaluation
% .maxDist - [.0075] maximum tolerance for edge match
% .thin - [1] if true thin boundary maps
%
% OUTPUTS
% odsF/P/R/T - F-measure, precision, recall and threshold at ODS
% oisF/P/R - F-measure, precision, and recall at OIS
% AP - average precision
% R50 - recall at 50% precision
%
% EXAMPLE
%
% See also edgesEvalImg, edgesEvalPlot
%
% Structured Edge Detection Toolbox Version 3.01
% Code written by Piotr Dollar, 2014.
% Licensed under the MSR-LA Full Rights License [see license.txt]
% get additional parameters
dfs={ 'resDir','REQ', 'gtDir','REQ', 'pDistr',{{'type','parfor'}}, ...
'cleanup',0, 'thrs',99, 'maxDist',.0075, 'thin',1 };
p=getPrmDflt(varargin,dfs,1); resDir=p.resDir; gtDir=p.gtDir;
evalDir=[resDir '-eval/']; if(~exist(evalDir,'dir')), mkdir(evalDir); end
% check if results already exist, if so load and return
fNm = fullfile(evalDir,'eval_bdry.txt');
if(exist(fNm,'file')), R=dlmread(fNm); R=mat2cell2(R,[1 8]);
varargout=R([4 3 2 1 7 6 5 8]); if(nargout<=8), return; end;
R=dlmread(fullfile(evalDir,'eval_bdry_thr.txt')); P=R(:,3); R=R(:,2);
[~,o]=unique(P); R50=interp1(P(o),R(o),max(P(o(1)),.5));
varargout=[varargout R50]; return;
end
% perform evaluation on each image (this part can be very slow)
assert(exist(resDir,'dir')==7); assert(exist(gtDir,'dir')==7);
ids=dir(fullfile(gtDir,'*.mat')); ids={ids.name}; n=length(ids);
do=false(1,n); jobs=cell(1,n); res=cell(1,n);
for i=1:n, id=ids{i}(1:end-4);
res{i}=fullfile(evalDir,[id '_ev1.txt']); do(i)=~exist(res{i},'file');
im1=fullfile(resDir,[id '.png']); gt1=fullfile(gtDir,[id '.mat']);
jobs{i}={im1,gt1,'out',res{i},'thrs',p.thrs,'maxDist',p.maxDist,...
'thin',p.thin}; if(0), edgesEvalImg(jobs{i}{:}); end
end
fevalDistr('edgesEvalImg',jobs(do),p.pDistr{:});
% collect evaluation results
I=dlmread(res{1}); T=I(:,1);
Z=zeros(numel(T),1); cntR=Z; sumR=Z; cntP=Z; sumP=Z;
oisCntR=0; oisSumR=0; oisCntP=0; oisSumP=0; scores=zeros(n,5);
for i=1:n
% load image results and accumulate
I = dlmread(res{i});
cntR1=I(:,2); cntR=cntR+cntR1; sumR1=I(:,3); sumR=sumR+sumR1;
cntP1=I(:,4); cntP=cntP+cntP1; sumP1=I(:,5); sumP=sumP+sumP1;
% compute OIS scores for image
[R,P,F] = computeRPF(cntR1,sumR1,cntP1,sumP1); [~,k]=max(F);
[oisR1,oisP1,oisF1,oisT1] = findBestRPF(T,R,P);
scores(i,:) = [i oisT1 oisR1 oisP1 oisF1];
% oisCnt/Sum will be used to compute dataset OIS scores
oisCntR=oisCntR+cntR1(k); oisSumR=oisSumR+sumR1(k);
oisCntP=oisCntP+cntP1(k); oisSumP=oisSumP+sumP1(k);
end
% compute ODS R/P/F and OIS R/P/F
[R,P,F] = computeRPF(cntR,sumR,cntP,sumP);
[odsR,odsP,odsF,odsT] = findBestRPF(T,R,P);
[oisR,oisP,oisF] = computeRPF(oisCntR,oisSumR,oisCntP,oisSumP);
% compute AP/R50 (interpolating 100 values, has minor bug: should be /101)
if(0), R=[0; R; 1]; P=[1; P; 0]; F=[0; F; 0]; T=[1; T; 0]; end
[~,k]=unique(R); k=k(end:-1:1); R=R(k); P=P(k); T=T(k); F=F(k); AP=0;
if(numel(R)>1), AP=interp1(R,P,0:.01:1); AP=sum(AP(~isnan(AP)))/100; end
[~,o]=unique(P); R50=interp1(P(o),R(o),max(P(o(1)),.5));
% write results to disk
varargout = {odsF,odsP,odsR,odsT,oisF,oisP,oisR,AP,R50};
writeRes(evalDir,'eval_bdry_img.txt',scores);
writeRes(evalDir,'eval_bdry_thr.txt',[T R P F]);
writeRes(evalDir,'eval_bdry.txt',[varargout{[4 3 2 1 7 6 5 8]}]);
% optionally perform cleanup
if( p.cleanup ), delete([evalDir '/*_ev1.txt']);
delete([resDir '/*.png']); rmdir(resDir); end
end
function [R,P,F] = computeRPF(cntR,sumR,cntP,sumP)
% compute precision, recall and F measure given cnts and sums
R=cntR./max(eps,sumR); P=cntP./max(eps,sumP); F=2*P.*R./max(eps,P+R);
end
function [bstR,bstP,bstF,bstT] = findBestRPF(T,R,P)
% linearly interpolate to find best thr for optimizing F
if(numel(T)==1), bstT=T; bstR=R; bstP=P;
bstF=2*P.*R./max(eps,P+R); return; end
A=linspace(0,1,100); B=1-A; bstF=-1;
for j = 2:numel(T)
Rj=R(j).*A+R(j-1).*B; Pj=P(j).*A+P(j-1).*B; Tj=T(j).*A+T(j-1).*B;
Fj=2.*Pj.*Rj./max(eps,Pj+Rj); [f,k]=max(Fj);
if(f>bstF), bstT=Tj(k); bstR=Rj(k); bstP=Pj(k); bstF=f; end
end
end
function writeRes( alg, fNm, vals )
% write results to disk
k=size(vals,2); fNm=fullfile(alg,fNm); fid=fopen(fNm,'w');
if(fid==-1), error('Could not open file %s for writing.',fNm); end
frmt=repmat('%10g ',[1 k]); frmt=[frmt(1:end-1) '\n'];
fprintf(fid,frmt,vals'); fclose(fid);
end
|
github
|
zeakey/edgeval-master
|
fevalDistr.m
|
.m
|
edgeval-master/utils/fevalDistr.m
| 11,227 |
utf_8
|
7e4d5077ef3d7a891b2847cb858a2c6c
|
function [out,res] = fevalDistr( funNm, jobs, varargin )
% Wrapper for embarrassingly parallel function evaluation.
%
% Runs "r=feval(funNm,jobs{i}{:})" for each job in a parallel manner. jobs
% should be a cell array of length nJob and each job should be a cell array
% of parameters to pass to funNm. funNm must be a function in the path and
% must return a single value (which may be a dummy value if funNm writes
% results to disk). Different forms of parallelization are supported
% depending on the hardware and Matlab toolboxes available. The type of
% parallelization is determined by the parameter 'type' described below.
%
% type='LOCAL': jobs are executed using a simple "for" loop. This implies
% no parallelization and is the default fallback option.
%
% type='PARFOR': jobs are executed using a "parfor" loop. This option is
% only available if the Matlab *Parallel Computing Toolbox* is installed.
% Make sure to setup Matlab workers first using "matlabpool open".
%
% type='DISTR': jobs are executed on the Caltech cluster. Distributed
% queuing system must be installed separately. Currently this option is
% only supported on the Caltech cluster but could easily be installed on
% any Linux cluster as it requires only SSH and a shared filesystem.
% Parameter pLaunch is used for controller('launchQueue',pLaunch{:}) and
% determines cluster machines used (e.g. pLaunch={48,401:408}).
%
% type='COMPILED': jobs are executed locally in parallel by first compiling
% an executable and then running it in background. This option requires the
% *Matlab Compiler* to be installed (but does NOT require the Parallel
% Computing Toolbox). Compiling can take 1-10 minutes, so use this option
% only for large jobs. (On Linux alter startup.m by calling addpath() only
% if ~isdeployed, otherwise will get error about "CTF" after compiling).
% Note that relative paths will not work after compiling so all paths used
% by funNm must be absolute paths.
%
% type='WINHPC': jobs are executed on a Windows HPC Server 2008 cluster.
% Similar to type='COMPILED', except after compiling, the executable is
% queued to the HPC cluster where all computation occurs. This option
% likewise requires the *Matlab Compiler*. Paths to data, etc., must be
% absolute paths and available from HPC cluster. Parameter pLaunch must
% have two fields 'scheduler' and 'shareDir' that define the HPC Server.
% Extra parameters in pLaunch add finer control, see fedWinhpc for details.
% For example, at MSR one possible cluster is defined by scheduler =
% 'MSR-L25-DEV21' and shareDir = '\\msr-arrays\scratch\msr-pool\L25-dev21'.
% Note call to 'job submit' from Matlab will hang unless pwd is saved
% (simply call 'job submit' from cmd prompt and enter pwd).
%
% USAGE
% [out,res] = fevalDistr( funNm, jobs, [varargin] )
%
% INPUTS
% funNm - name of function that will process jobs
% jobs - [1xnJob] cell array of parameters for each job
% varargin - additional params (struct or name/value pairs)
% .type - ['local'], 'parfor', 'distr', 'compiled', 'winhpc'
% .pLaunch - [] extra params for type='distr' or type='winhpc'
% .group - [1] send jobs in batches (only relevant if type='distr')
%
% OUTPUTS
% out - 1 if jobs completed successfully
% res - [1xnJob] cell array containing results of each job
%
% EXAMPLE
% % Note: in this case parallel versions are slower since conv2 is so fast
% n=16; jobs=cell(1,n); for i=1:n, jobs{i}={rand(500),ones(25)}; end
% tic, [out,J1] = fevalDistr('conv2',jobs,'type','local'); toc,
% tic, [out,J2] = fevalDistr('conv2',jobs,'type','parfor'); toc,
% tic, [out,J3] = fevalDistr('conv2',jobs,'type','compiled'); toc
% [isequal(J1,J2), isequal(J1,J3)], figure(1); montage2(cell2array(J1))
%
% See also matlabpool mcc
%
% Piotr's Computer Vision Matlab Toolbox Version 3.26
% Copyright 2014 Piotr Dollar. [pdollar-at-gmail.com]
% Licensed under the Simplified BSD License [see external/bsd.txt]
dfs={'type','local','pLaunch',[],'group',1};
[type,pLaunch,group]=getPrmDflt(varargin,dfs,1); store=(nargout==2);
if(isempty(jobs)), res=cell(1,0); out=1; return; end
switch lower(type)
case 'local', [out,res]=fedLocal(funNm,jobs,store);
case 'parfor', [out,res]=fedParfor(funNm,jobs,store);
case 'distr', [out,res]=fedDistr(funNm,jobs,pLaunch,group,store);
case 'compiled', [out,res]=fedCompiled(funNm,jobs,store);
case 'winhpc', [out,res]=fedWinhpc(funNm,jobs,pLaunch,store);
otherwise, error('unkown type: ''%s''',type);
end
end
function [out,res] = fedLocal( funNm, jobs, store )
% Run jobs locally using for loop.
nJob=length(jobs); res=cell(1,nJob); out=1;
tid=ticStatus('collecting jobs');
for i=1:nJob, r=feval(funNm,jobs{i}{:});
if(store), res{i}=r; end; tocStatus(tid,i/nJob); end
end
function [out,res] = fedParfor( funNm, jobs, store )
% Run jobs locally using parfor loop.
nJob=length(jobs); res=cell(1,nJob); out=1;
parfor i=1:nJob, r=feval(funNm,jobs{i}{:});
if(store), res{i}=r; end; end
end
function [out,res] = fedDistr( funNm, jobs, pLaunch, group, store )
% Run jobs using Linux queuing system.
if(~exist('controller.m','file'))
msg='distributed queuing not installed, switching to type=''local''.';
warning(msg); [out,res]=fedLocal(funNm,jobs,store); return; %#ok<WNTAG>
end
nJob=length(jobs); res=cell(1,nJob); controller('launchQueue',pLaunch{:});
if( group>1 )
nJobGrp=ceil(nJob/group); jobsGrp=cell(1,nJobGrp); k=0;
for i=1:nJobGrp, k1=min(nJob,k+group);
jobsGrp{i}={funNm,jobs(k+1:k1),'type','local'}; k=k1; end
nJob=nJobGrp; jobs=jobsGrp; funNm='fevalDistr';
end
jids=controller('jobsAdd',nJob,funNm,jobs); k=0;
fprintf('Sent %i jobs...\n',nJob); tid=ticStatus('collecting jobs');
while( 1 )
jids1=controller('jobProbe',jids);
if(isempty(jids1)), pause(.1); continue; end
jid=jids1(1); [r,err]=controller('jobRecv',jid);
if(~isempty(err)), disp('ABORTING'); out=0; break; end
k=k+1; if(store), res{jid==jids}=r; end
tocStatus(tid,k/nJob); if(k==nJob), out=1; break; end
end; controller('closeQueue');
end
function [out,res] = fedCompiled( funNm, jobs, store )
% Run jobs locally in background in parallel using compiled code.
nJob=length(jobs); res=cell(1,nJob); tDir=jobSetup('.',funNm,'',{});
cmd=[tDir 'fevalDistrDisk ' funNm ' ' tDir ' ']; i=0; k=0;
Q=feature('numCores'); q=0; tid=ticStatus('collecting jobs');
while( 1 )
% launch jobs until queue is full (q==Q) or all jobs launched (i==nJob)
while(q<Q && i<nJob), q=q+1; i=i+1; jobSave(tDir,jobs{i},i);
if(ispc), system2(['start /B /min ' cmd int2str2(i,10)],0);
else system2([cmd int2str2(i,10) ' &'],0); end
end
% collect completed jobs (k1 of them), release queue slots
done=jobFileIds(tDir,'done'); k1=length(done); k=k+k1; q=q-k1;
for i1=done, res{i1}=jobLoad(tDir,i1,store); end
pause(1); tocStatus(tid,k/nJob); if(k==nJob), out=1; break; end
end
for i=1:10, try rmdir(tDir,'s'); break; catch,pause(1),end; end %#ok<CTCH>
end
function [out,res] = fedWinhpc( funNm, jobs, pLaunch, store )
% Run jobs using Windows HPC Server.
nJob=length(jobs); res=cell(1,nJob);
dfs={'shareDir','REQ','scheduler','REQ','executable','fevalDistrDisk',...
'mccOptions',{},'coresPerTask',1,'minCores',1024,'priority',2000};
p = getPrmDflt(pLaunch,dfs,1);
tDir = jobSetup(p.shareDir,funNm,p.executable,p.mccOptions);
for i=1:nJob, jobSave(tDir,jobs{i},i); end
hpcSubmit(funNm,1:nJob,tDir,p); k=0;
ticId=ticStatus('collecting jobs');
while( 1 )
done=jobFileIds(tDir,'done'); k=k+length(done);
for i1=done, res{i1}=jobLoad(tDir,i1,store); end
pause(5); tocStatus(ticId,k/nJob); if(k==nJob), out=1; break; end
end
for i=1:10, try rmdir(tDir,'s'); break; catch,pause(5),end; end %#ok<CTCH>
end
function tids = hpcSubmit( funNm, ids, tDir, pLaunch )
% Helper: send jobs w given ids to HPC cluster.
n=length(ids); tids=cell(1,n); if(n==0), return; end;
scheduler=[' /scheduler:' pLaunch.scheduler ' '];
m=system2(['cluscfg view' scheduler],0);
minCores=(hpcParse(m,'total number of nodes',1) - ...
hpcParse(m,'Unreachable nodes',1) - 1)*8;
minCores=min([minCores pLaunch.minCores n*pLaunch.coresPerTask]);
m=system2(['job new /numcores:' int2str(minCores) '-*' scheduler ...
'/priority:' int2str(pLaunch.priority)],1);
jid=hpcParse(m,'created job, id',0);
s=min(ids); e=max(ids); p=n>1 && isequal(ids,s:e);
if(p), jid1=[jid '.1']; else jid1=jid; end
for i=1:n, tids{i}=[jid1 '.' int2str(i)]; end
cmd0=''; if(p), cmd0=['/parametric:' int2str(s) '-' int2str(e)]; end
cmd=@(id) ['job add ' jid scheduler '/workdir:' tDir ' /numcores:' ...
int2str(pLaunch.coresPerTask) ' ' cmd0 ' /stdout:stdout' id ...
'.txt ' pLaunch.executable ' ' funNm ' ' tDir ' ' id];
if(p), ids1='*'; n=1; else ids1=int2str2(ids); end
if(n==1), ids1={ids1}; end; for i=1:n, system2(cmd(ids1{i}),1); end
system2(['job submit /id:' jid scheduler],1); disp(repmat(' ',1,80));
end
function v = hpcParse( msg, key, tonum )
% Helper: extract val corresponding to key in hpc msg.
t=regexp(msg,': |\n','split'); t=strtrim(t(1:floor(length(t)/2)*2));
keys=t(1:2:end); vals=t(2:2:end); j=find(strcmpi(key,keys));
if(isempty(j)), error('key ''%s'' not found in:\n %s',key,msg); end
v=vals{j}; if(tonum==0), return; elseif(isempty(v)), v=0; return; end
if(tonum==1), v=str2double(v); return; end
v=regexp(v,' ','split'); v=str2double(regexp(v{1},':','split'));
if(numel(v)==4), v(5)=0; end; v=((v(1)*24+v(2))*60+v(3))*60+v(4)+v(5)/1000;
end
function tDir = jobSetup( rtDir, funNm, executable, mccOptions )
% Helper: prepare by setting up temporary dir and compiling funNm
t=clock; t=mod(t(end),1); t=round((t+rand)/2*1e15);
tDir=[rtDir filesep sprintf('fevalDistr-%015i',t) filesep]; mkdir(tDir);
if(~isempty(executable) && exist(executable,'file'))
fprintf('Reusing compiled executable...\n'); copyfile(executable,tDir);
else
t=clock; fprintf('Compiling (this may take a while)...\n');
[~,f,e]=fileparts(executable); if(isempty(f)), f='fevalDistrDisk'; end
mcc('-m','fevalDistrDisk','-d',tDir,'-o',f,'-a',funNm,mccOptions{:});
t=etime(clock,t); fprintf('Compile complete (%.1f seconds).\n',t);
if(~isempty(executable)), copyfile([tDir filesep f e],executable); end
end
end
function ids = jobFileIds( tDir, type )
% Helper: get list of job files ids on disk of given type
fs=dir([tDir '*-' type '*']); fs={fs.name}; n=length(fs);
ids=zeros(1,n); for i=1:n, ids(i)=str2double(fs{i}(1:10)); end
end
function jobSave( tDir, job, ind ) %#ok<INUSL>
% Helper: save job to temporary file for use with fevalDistrDisk()
save([tDir int2str2(ind,10) '-in'],'job');
end
function r = jobLoad( tDir, ind, store )
% Helper: load job and delete temporary files from fevalDistrDisk()
f=[tDir int2str2(ind,10)];
if(store), r=load([f '-out']); r=r.r; else r=[]; end
fs={[f '-done'],[f '-in.mat'],[f '-out.mat']};
delete(fs{:}); pause(.1);
for i=1:3, k=0; while(exist(fs{i},'file')==2) %#ok<ALIGN>
warning('Waiting to delete %s.',fs{i}); %#ok<WNTAG>
delete(fs{i}); pause(5); k=k+1; if(k>12), break; end;
end; end
end
function msg = system2( cmd, show )
% Helper: wraps system() call
if(show), disp(cmd); end
[status,msg]=system(cmd); msg=msg(1:end-1);
if(status), error(msg); end
if(show), disp(msg); end
end
|
github
|
isamabdullah88/Visual-Inertial-Odometry-master
|
integrateIMU.m
|
.m
|
Visual-Inertial-Odometry-master/SourceCode/Functions/integrateIMU.m
| 3,116 |
utf_8
|
26979cd3549c449c0e7ca5da743e2957
|
function[xUpdate] = integrateIMU(xPrev, a, omega, dt, g_w)
%INTEGRATEIMUSTREAM Integrate IMU stream and return state and covariance
%estimates
%The state is given by :
%x =[p_I_G q_IG v_I_G b_g b_a];
%Set noise to 0
noise_params.sigma_g = 0;
noise_params.sigma_a = 0;
noise_params.sigma_bg = 0;
noise_params.sigma_ba = 0;
noise_params.tau = 10^12;
%Calculate xDot
w = getWhiteNoise(noise_params);
%RK4 Integration
% Given x' = f(x), RK4 integration proceeds as follows :
% x(n + 1) = x(n) + dt / 6 * (k1 + 2 * k2 + 2 * k3 + k4); where
% k1 = f(x);
% k2 = f(x + dt / 2 * k1)
% k3 = f(x + dt / 2 * k2)
% k4 = f(x + dt * k3)
k = {};
k_coeffs =[1 0.5 0.5 1];
b_coeffs =[1 / 6 1 / 3 1 / 3 1 / 6]; %RK4
%b_coeffs =[1 0 0 0]; %Forward Euler
k{1} = getxDot(xPrev, omega, a, w, noise_params, g_w);
for i_k = 2 : 4
xTemp.p_I_G = xPrev.p_I_G + (k{i_k - 1}.p_I_G) * k_coeffs(i_k) * dt;
xTemp.q_IG = xPrev.q_IG + (k{i_k - 1}.q_IG) * k_coeffs(i_k) * dt; %Possibly renormalize here
xTemp.v_I_G = xPrev.v_I_G + (k{i_k - 1}.v_I_G) * k_coeffs(i_k) * dt;
xTemp.b_g = xPrev.b_g + (k{i_k - 1}.b_g) * k_coeffs(i_k) * dt;
xTemp.b_a = xPrev.b_a + (k{i_k - 1}.b_a) * k_coeffs(i_k) * dt;
k{i_k} = getxDot(xTemp, omega, a, w, noise_params, g_w);
end
xUpdate.p_I_G = xPrev.p_I_G + dt * (b_coeffs(1) * k{1}.p_I_G + b_coeffs(2) * k{2}.p_I_G + b_coeffs(3) * k{3}.p_I_G + b_coeffs(4) * k{4}.p_I_G);
xUpdate.v_I_G = xPrev.v_I_G + dt * (b_coeffs(1) * k{1}.v_I_G + b_coeffs(2) * k{2}.v_I_G + b_coeffs(3) * k{3}.v_I_G + b_coeffs(4) * k{4}.v_I_G);
xUpdate.b_g = xPrev.b_g + dt * (b_coeffs(1) * k{1}.b_g + b_coeffs(2) * k{2}.b_g + b_coeffs(3) * k{3}.b_g + b_coeffs(4) * k{4}.b_g);
xUpdate.b_a = xPrev.b_a + dt * (b_coeffs(1) * k{1}.b_a + b_coeffs(2) * k{2}.b_a + b_coeffs(3) * k{3}.b_a + b_coeffs(4) * k{4}.b_a);
xUpdate.q_IG = quat_normalize(xPrev.q_IG + dt * (b_coeffs(1) * k{1}.q_IG + b_coeffs(2) * k{2}.q_IG + b_coeffs(3) * k{3}.q_IG + b_coeffs(4) * k{4}.q_IG)); %Note the renormalization
%Non linear kinematics
% x - state
% w - noise vector
% omega, a - ang. rates and accels.
% tau - time constant for accelerometer bias
function xdot = getxDot(x, omega, a, w, noise_params, g_w)
xdot.p_I_G = x.v_I_G;
xdot.q_IG = 0.5 * omegaMat(omega, zeros(3, 1), x.b_g) * x.q_IG;
xdot.v_I_G = rotmat_from_quat(quat_normalize(x.q_IG)) * (a - x.b_a) + rotmat_from_quat(quat_normalize(x.q_IG)) * g_w;
xdot.b_g = zeros(3, 1);
xdot.b_a = zeros(3, 1);
end
%White noise vector
function w = getWhiteNoise(sigma_params)
w.w_g = sigma_params.sigma_g. * randn(3, 1);
w.w_a = sigma_params.sigma_a. * randn(3, 1);
w.w_bg = sigma_params.sigma_bg. * randn(3, 1);
w.w_ba = sigma_params.sigma_ba. * randn(3, 1);
end
%Quaternion kinematic matrix
function bigOmega = omegaMat(omega_meas, w_g, b_g)
%Is it + w_g or - w_g? Does it matter?
omega_true = omega_meas + w_g - b_g;
ox = omega_true(1);
oy = omega_true(2);
oz = omega_true(3);
bigOmega =[0 - ox - oy - oz; ...
ox 0 oz - oy;
oy - oz 0 ox;
oz oy - ox 0;];
%See technical note on quaternions by Sola. Page 6.
%This formulation assumes that the quaternion has the scalar part
%at the start
end
end
|
github
|
isamabdullah88/Visual-Inertial-Odometry-master
|
calcGNPosEstTODO.m
|
.m
|
Visual-Inertial-Odometry-master/SourceCode/Functions/calcGNPosEstTODO.m
| 2,592 |
utf_8
|
79942d6dfc17224ece353c06cb16e2a5
|
function[p_f_G, cost, RCOND] = calcGNPosEst(camState, observations, noiseParams)
%CALCGNPOSEST Calculate the position estimate of the feature using Gauss
%Newton optimization
% INPUT :
% observations : 2xM matrix of pixel values of the current landmark
% camStates : Cell array of M structs of camera poses
% camera : intrinsic calibration
% OUTPUT :
% p_f_G : 3x1 feature vector in the global frame
%K is not needed if we assume observations are not pixels but x' = (u -
%c_u) / f_u
%K =[camera.f_u 0 camera.c_u; 0 camera.f_v camera.c_v; 0 0 1];
%% Actual Problem
%Get initial estimate through intersection
%Use the first 2 camStates
CnInd = length(camState);
C_1n = quatToRotMat(camState{CnInd}.q_CG)' * quatToRotMat(camState{1}.q_CG);
% t_21_1 = quatToRotMat(camState{secondViewIdx}.q_CG) * (camState{secondViewIdx}.p_C_G - camState{1}.p_C_G);
t_1n_1 = quatToRotMat(camState{1}.q_CG) * (camState{CnInd}.p_C_G - camState{1}.p_C_G);
p_f1_1_bar = triangulate(observations( :, 1), observations( : , CnInd), C_1n, t_1n_1);
x0 =[p_f1_1_bar(1) / p_f1_1_bar(3); p_f1_1_bar(2) / p_f1_1_bar(3); 1 / p_f1_1_bar(3)];
[params, cost] = lsqnonlin(@objFn, double(x0));
p_f_G = params;
RCOND = 1;
%% The Objective Function
function r = objFn(beta)
% beta =[X, Y, Z]of the feature position in global frame. These
% are our parameters to estimate
% r = f(X, beta) - Y : These are the list of residuals for all the
% data points
lastInd = length(camState);
for i = 2 : lastInd
C_1i = quatToRotMat(camState{i}.q_CG)' * quatToRotMat(camState{i}.q_CG);
% t_i1_1 = quatToRotMat(camState{1}.q_CG) * (camState{i}.p_C_G - camState{1}.p_C_G);
t_i1_1 = quatToRotMat(camState{1}.q_CG) * (camState{i}.p_C_G - camState{1}.p_C_G);
% C1 = C_1i( : , 1); C2 = C_1i( : , 2); C3 = C_1i( : , 3);
% B1 = beta(1); B2 = beta(2); B3 = beta(3);
% X1 = t_i1_1(1); X2 = t_i1_1(2); X3 = t_i1_1(3);
% Calculate f(X, B)
fXBVec = C_1i * (beta - (t_i1_1 * beta(3)));
f1XB = fXBVec(1) / fXBVec(3); f2XB = fXBVec(2) / fXBVec(3);
% Compute residual of norms
fXB =[f1XB, f2XB];
obs = double(observations( : , i));
y =[obs(1), obs(2)];
r(i - 1) = norm(y - fXB);
end
end
function[p_f1_1] = triangulate(obs1, obs2, C_12, t_21_1)
% triangulate Triangulates 3D points from two sets of feature vectors and a
% a frame - to - frame transformation
%Calculate unit vectors
v_1 =[obs1;1];
v_2 =[obs2;1];
v_1 = v_1 / norm(v_1);
v_2 = v_2 / norm(v_2);
A =[v_1 - C_12 * v_2];
b = t_21_1;
% disp(b);
scalar_consts = A\b;
p_f1_1 = scalar_consts(1) * v_1;
end
end
|
github
|
isamabdullah88/Visual-Inertial-Odometry-master
|
match.m
|
.m
|
Visual-Inertial-Odometry-master/SourceCode/Functions/match.m
| 1,927 |
utf_8
|
f7d5bf4c2b0a7056954aaa41a7ab575e
|
% num = match(image1, image2)
%
% This function reads two images, finds their SIFT features, and
% displays lines connecting the matched keypoints. A match is accepted
% only if its distance is less than distRatio times the distance to the
% second closest match.
% It returns the number of matches displayed.
%
% Example : match('scene.pgm', 'book.pgm');
function num = match(image1, image2)
% Find SIFT keypoints for each image
[im1, des1, loc1] = sift(image1);
[im2, des2, loc2] = sift(image2);
% For efficiency in Matlab, it is cheaper to compute dot products between
% unit vectors rather than Euclidean distances. Note that the ratio of
% angles (acos of dot products of unit vectors) is a close approximation
% to the ratio of Euclidean distances for small angles.
%
% distRatio : Only keep matches in which the ratio of vector angles from the
% nearest to second nearest neighbor is less than distRatio.
distRatio = 0.6;
% For each descriptor in the first image, select its match to second image.
des2t = des2'; % Precompute matrix transpose
for i = 1 : size(des1, 1)
dotprods = des1(i, : ) * des2t; % Computes vector of dot products
[vals, indx] = sort(acos(dotprods)); % Take inverse cosine and sort results
% Check if nearest neighbor has angle less than distRatio times 2nd.
if (vals(1) < distRatio * vals(2))
match(i) = indx(1);
else
match(i) = 0;
end
end
% Create a new image showing the two images side by side.
im3 = appendimages(im1, im2);
% Show a figure with lines joining the accepted matches.
figure('Position', [100 100 size(im3, 2) size(im3, 1)]);
colormap('gray');
imagesc(im3);
hold on;
cols1 = size(im1, 2);
for i = 1 : size(des1, 1)
if (match(i) > 0)
line([loc1(i, 2) loc2(match(i), 2)+ cols1], ...
[loc1(i, 1) loc2(match(i), 1)], 'Color', 'c');
end
end
hold off;
num = sum(match > 0);
fprintf('Found %d matches.\n', num);
|
github
|
isamabdullah88/Visual-Inertial-Odometry-master
|
loadImuData.m
|
.m
|
Visual-Inertial-Odometry-master/SourceCode/Functions/loadImuData.m
| 1,522 |
utf_8
|
376c7c00df767b65f51449e0d08648eb
|
function[ imuData, gpsData, velocity ] = loadImuData( imuDir )
%loadImuData loads the imu data from kitti dataset in required format i.e.
%gyro, accelerometer and timestamps
fileDir =[imuDir ' / data /'];
fileNames = dir(fullfile(fileDir, ' * .txt'));
dateStrings = loadTimestamps(imuDir);
len = size(dateStrings, 1);
wgs84 = wgs84Ellipsoid('meters');
% seperating required data
for i = 1 : len
dataF = dlmread([fileDir ' /' fileNames(i).name]);
tmpGps = dataF(1 : 3);
gpsLatLong(i, : ) = tmpGps;
[x, y, z] = geodetic2ecef(wgs84, tmpGps(1), tmpGps(2), tmpGps(3));
gpsData(i, : ) = [x, y, z];
acc(i, : ) = [dataF(12), dataF(13), dataF(14)];
omega(i, : ) = dataF(18 : 20);
velocity(i, : ) = [dataF(9), dataF(10), dataF(11)];
end
imuData.acc = acc;
imuData.omega = omega;
% Subtract GPS from first value and plot ground truth
gpsData( : , 1) = gpsData( : , 1) - gpsData(1, 1);
gpsData( : , 2) = gpsData( : , 2) - gpsData(1, 2);
gpsData( : , 3) = gpsData( : , 3) - gpsData(1, 3);
% tGPS = toGlobalCoords(gpsData);
% % tGPS = gpsData;
% figure; line(tGPS( :, 1), tGPS( : , 2), tGPS( : , 3), 'Color', 'm');
% title('Ground Truth GPS in x - y - z plot');
% xlabel('pos X'); ylabel('pos Y'); zlabel('pos Z');
% converting from date to time
for i = 1 : len
dataTs(i) = dateToTime(datenum(dateStrings(i)));
end
imuData.dT = diff(dataTs);
%%% Function to convert data to time --------------------------------------
function t = dateToTime(date)
t = (date - 719529) * 86400; %# 719529 == datenum(1970, 1, 1)
end
end
|
github
|
isamabdullah88/Visual-Inertial-Odometry-master
|
loadCalibrationCamToCam.m
|
.m
|
Visual-Inertial-Odometry-master/SourceCode/Utils/loadCalibrationCamToCam.m
| 1,837 |
utf_8
|
ab070dd26d9e2df2f7739d6d203c4547
|
function calib = loadCalibrationCamToCam(filename)
% open file
fid = fopen(filename, 'r');
if fid < 0
calib =[];
return;
end
% read corner distance
calib.cornerdist = readVariable(fid, 'corner_dist', 1, 1);
% read all cameras (maximum : 100)
for cam = 1 : 100
% read variables
S_ = readVariable(fid, ['S_' num2str(cam - 1, '%02d')], 1, 2);
K_ = readVariable(fid, ['K_' num2str(cam - 1, '%02d')], 3, 3);
D_ = readVariable(fid, ['D_' num2str(cam - 1, '%02d')], 1, 5);
R_ = readVariable(fid, ['R_' num2str(cam - 1, '%02d')], 3, 3);
T_ = readVariable(fid, ['T_' num2str(cam - 1, '%02d')], 3, 1);
S_rect_ = readVariable(fid, ['S_rect_' num2str(cam - 1, '%02d')], 1, 2);
R_rect_ = readVariable(fid, ['R_rect_' num2str(cam - 1, '%02d')], 3, 3);
P_rect_ = readVariable(fid, ['P_rect_' num2str(cam - 1, '%02d')], 3, 4);
% calibration for this cam completely found?
if isempty(S_) || isempty(K_) || isempty(D_) || isempty(R_) || isempty(T_)
break;
end
% write calibration
calib.S{cam} = S_;
calib.K{cam} = K_;
calib.D{cam} = D_;
calib.R{cam} = R_;
calib.T{cam} = T_;
% if rectification available
if ~ isempty(S_rect_) && ~ isempty(R_rect_) && ~ isempty(P_rect_)
calib.S_rect{cam} = S_rect_;
calib.R_rect{cam} = R_rect_;
calib.P_rect{cam} = P_rect_;
end
end
% close file
fclose(fid);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function A = readVariable(fid, name, M, N)
% rewind
fseek(fid, 0, 'bof');
% search for variable identifier
success = 1;
while success > 0
[str, success] = fscanf(fid, '%s', 1);
if strcmp(str, [name ' :'])
break;
end
end
% return if variable identifier not found
if ~ success
A = [];
return;
end
% fill matrix
A = zeros(M, N);
for m = 1 : M
for n = 1 : N
[val, success] = fscanf(fid, '%f', 1);
if success
A(m, n) = val;
else
A =[];
return;
end
end
end
|
github
|
isamabdullah88/Visual-Inertial-Odometry-master
|
loadCalibrationRigid.m
|
.m
|
Visual-Inertial-Odometry-master/SourceCode/Utils/loadCalibrationRigid.m
| 834 |
utf_8
|
f52ca08e93a8e8441acb81012628dfa4
|
function Tr = loadCalibrationRigid(filename)
% open file
fid = fopen(filename, 'r');
if fid < 0
error(['ERROR : Could not load : ' filename]);
end
% read calibration
R = readVariable(fid, 'R', 3, 3);
T = readVariable(fid, 'T', 3, 1);
Tr =[R T;0 0 0 1];
% close file
fclose(fid);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function A = readVariable(fid, name, M, N)
% rewind
fseek(fid, 0, 'bof');
% search for variable identifier
success = 1;
while success > 0
[str, success] = fscanf(fid, '%s', 1);
if strcmp(str, [name ' :'])
break;
end
end
% return if variable identifier not found
if ~ success
A = [];
return;
end
% fill matrix
A = zeros(M, N);
for m = 1 : M
for n = 1 : N
[val, success] = fscanf(fid, '%f', 1);
if success
A(m, n) = val;
else
A =[];
return;
end
end
end
|
github
|
isamabdullah88/Visual-Inertial-Odometry-master
|
simCamera.m
|
.m
|
Visual-Inertial-Odometry-master/Gauss Newton Simulation/simCamera.m
| 1,700 |
utf_8
|
25bcc63217dba70a35b10547d459fb33
|
function[ obs, camStates ] = simCamera( C1_p_f, camera, C1_p_C2, thetas, n )
%simCamera simulates a camera of n frames given the parameters and returns 2D feature
%coordinates in each frame
% C1_p_f : 3D position coordinates of feature in C1, which would be
% tracked in sub - sequent camera frames
% camera : The camera parameter matrix
% thetas : List of angles of each frame with respect to first frame
% n : The number of frames in which it is to track
% C1_p_Ci : List of poses of each frame from first frame
% obs : 2Xn matrix. Each column contains 3D coordinates of feature in
% each frame
% poseC1 : 3D poses of each camera frame in C1
% Note : The maximum number of frames would only be, in which the feature
% does not go out of view.
% Poses of i frame in C1
C1_p_Ci = C1_p_C2;
K = camera.K;
tmpP = K *[C1_p_f; 1];
obs( :, 1) = [tmpP(1) / tmpP(3); tmpP(2) / tmpP(3)];
for i = 1 : n
% camStates{i}.q_CG = (angle2quat(0, thetas(i), 0, 'XYZ'))';
camStates{i}.q_CG =[0;0;0;1];
if (i == 1)
camStates{i}.p_C_G =[0;0;0];
else
camStates{i}.p_C_G = C1_p_Ci;
% Translating camera Ci from Ci - 1
C1_p_Ci = C1_p_Ci + C1_p_C2;
end
C_C1_Ci = rotMat(thetas(i));
% 3D feature pos in Ci
Ci_p_f = C_C1_Ci * (C1_p_f - camStates{i}.p_C_G);
% 2D pos of feature in Ci
tmpPi = K *[Ci_p_f; 1];
obs( : , i + 1) = [tmpPi(1) / tmpPi(3); tmpPi(2) / tmpPi(3)];
end
% Coverting pixel coordinates to 'ideal' coordinates
obs(1, : ) = (obs(1, : ) - camera.px) / camera.mx;
obs(2, : ) = (obs(2, : ) - camera.py) / camera.my;
function C_C1_C2 = rotMat(theta)
C_C1_C2 =[cosd(theta) 0 sind(theta);
0 1 0
- sind(theta) 0 cosd(theta)];
end
end
|
github
|
epilepsyecosystem/1stplace_notsorandomanymore-master
|
spatFilt.m
|
.m
|
1stplace_notsorandomanymore-master/Andriy/code/spatFilt.m
| 1,113 |
utf_8
|
9e5d17114745661029930c1558855096
|
%James Ethridge , Will Weaver
%Spatial filtering function. Returns the filtered signal Y.
%
%Inputs:
%x: the input matrix where M rows are the channels and N columns are the
% time bins
%
%coef: the entire P' matrix of filter coefficients
%
%dimm: the number of dimensions the filter should attemp to reduce the
% output vector space to
function Y = spatFilt(x, coef, dimm)
[m n] = size(coef);
%check for valid dimensions
if(m<dimm)
disp('Cannot reduce to a higher dimensional space!');
return
end
%instantiate filter matrix
Ptild = zeros(dimm,n);
%create the n-dimensional filter by sorting
i=0;
for d = 1:dimm
if(mod(d,2)==0)
Ptild(d,:) = coef(m-i,:);
i=i+1;
else
Ptild(d,:) = coef(1+i,:);
end
end
%get length of input signal
T = length(x);
%instantiate output matrix
Y=zeros(dimm,T);
%filtering
for d = 1:dimm
for t = 1:T
Y(d,t) = dot(Ptild(d,:),x(:,t));
end
end
return
|
github
|
epilepsyecosystem/1stplace_notsorandomanymore-master
|
sub_pos.m
|
.m
|
1stplace_notsorandomanymore-master/Andriy/code/sub_pos.m
| 496 |
utf_8
|
12fb7f8d85bca88f653bf530a3e02f07
|
%
% Stephen Faul
% 21st July 2004
%
% SUB_POS: returns the starting positions of each subband of the
% resultant vector from wt
%
% input: data_len -- the length of the original signal
% num_coeffs -- the number of filter coefficients (2*order for Daubechie
%
% output: pos -- vector of the starting positions of each subband
%
function pos = sub_pos(data_len,num_coeffs)
for i=1:num_coeffs
pos(i)=data_len/(2^i)+1;
end
pos(i+1)=1;
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.