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stringlengths 13
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stringlengths 12
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stringclasses 9
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|---|---|---|---|---|---|---|---|---|
github
|
lcnbeapp/beapp-master
|
om_normals.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/openmeeg/om_normals.m
| 1,572 |
utf_8
|
ca0342ba8f9473f946c7df879e4a82c8
|
function [nrm] = normals(pos, tri, opt)
% NORMALS compute the surface normals of a triangular mesh
% for each triangle or for each vertex
%
% Use as
% nrm = normals(pos, tri, opt)
% where opt is either 'vertex' or 'triangle'
% Copyright (C) 2002-2007, Robert Oostenveld
if nargin<3
opt='vertex';
elseif (opt(1)=='v' | opt(1)=='V')
opt='vertex';
elseif (opt(1)=='t' | opt(1)=='T')
opt='triangle';
else
error('invalid optional argument');
end
npos = size(pos,1);
ntri = size(tri,1);
% shift to center
pos(:,1) = pos(:,1)-mean(pos(:,1),1);
pos(:,2) = pos(:,2)-mean(pos(:,2),1);
pos(:,3) = pos(:,3)-mean(pos(:,3),1);
% compute triangle normals
nrm_tri = zeros(ntri, 3);
for i=1:ntri
v2 = pos(tri(i,2),:) - pos(tri(i,1),:);
v3 = pos(tri(i,3),:) - pos(tri(i,1),:);
nrm_tri(i,:) = cross(v2, v3);
end
if strcmp(opt, 'vertex')
% compute vertex normals
nrm_pos = zeros(npos, 3);
for i=1:ntri
nrm_pos(tri(i,1),:) = nrm_pos(tri(i,1),:) + nrm_tri(i,:);
nrm_pos(tri(i,2),:) = nrm_pos(tri(i,2),:) + nrm_tri(i,:);
nrm_pos(tri(i,3),:) = nrm_pos(tri(i,3),:) + nrm_tri(i,:);
end
% normalise the direction vectors to have length one
nrm = nrm_pos ./ (sqrt(sum(nrm_pos.^2, 2)) * ones(1,3));
else
% normalise the direction vectors to have length one
nrm = nrm_tri ./ (sqrt(sum(nrm_tri.^2, 2)) * ones(1,3));
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% fast cross product to replace the Matlab standard version
function [c] = cross(a,b)
c = [a(2)*b(3)-a(3)*b(2) a(3)*b(1)-a(1)*b(3) a(1)*b(2)-a(2)*b(1)];
|
github
|
lcnbeapp/beapp-master
|
normals.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/openmeeg/private/normals.m
| 2,346 |
utf_8
|
fc0a8ff8ded57a42b7f5436338ed6788
|
function [nrm] = normals(pnt, tri, opt);
% NORMALS compute the surface normals of a triangular mesh
% for each triangle or for each vertex
%
% [nrm] = normals(pnt, tri, opt)
% where opt is either 'vertex' or 'triangle'
% Copyright (C) 2002-2007, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.ru.nl/neuroimaging/fieldtrip
% for the documentation and details.
%
% FieldTrip 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 3 of the License, or
% (at your option) any later version.
%
% FieldTrip 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 FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$
if nargin<3
opt='vertex';
elseif (opt(1)=='v' | opt(1)=='V')
opt='vertex';
elseif (opt(1)=='t' | opt(1)=='T')
opt='triangle';
else
error('invalid optional argument');
end
npnt = size(pnt,1);
ntri = size(tri,1);
% shift to center
pnt(:,1) = pnt(:,1)-mean(pnt(:,1),1);
pnt(:,2) = pnt(:,2)-mean(pnt(:,2),1);
pnt(:,3) = pnt(:,3)-mean(pnt(:,3),1);
% compute triangle normals
nrm_tri = zeros(ntri, 3);
for i=1:ntri
v2 = pnt(tri(i,2),:) - pnt(tri(i,1),:);
v3 = pnt(tri(i,3),:) - pnt(tri(i,1),:);
nrm_tri(i,:) = cross(v2, v3);
end
if strcmp(opt, 'vertex')
% compute vertex normals
nrm_pnt = zeros(npnt, 3);
for i=1:ntri
nrm_pnt(tri(i,1),:) = nrm_pnt(tri(i,1),:) + nrm_tri(i,:);
nrm_pnt(tri(i,2),:) = nrm_pnt(tri(i,2),:) + nrm_tri(i,:);
nrm_pnt(tri(i,3),:) = nrm_pnt(tri(i,3),:) + nrm_tri(i,:);
end
% normalise the direction vectors to have length one
nrm = nrm_pnt ./ (sqrt(sum(nrm_pnt.^2, 2)) * ones(1,3));
else
% normalise the direction vectors to have length one
nrm = nrm_tri ./ (sqrt(sum(nrm_tri.^2, 2)) * ones(1,3));
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% fast cross product to replace the Matlab standard version
function [c] = cross(a,b)
c = [a(2)*b(3)-a(3)*b(2) a(3)*b(1)-a(1)*b(3) a(1)*b(2)-a(2)*b(1)];
|
github
|
lcnbeapp/beapp-master
|
dipoli.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/dipoli/dipoli.m
| 4,457 |
utf_8
|
f2e2fe3dbd61e25b90d68adb9202f375
|
function [vol] = dipoli(vol, isolated)
% DIPOLI computes a BEM system matrix
%
% Use as
% [vol] = dipoli(vol, isolated)
% Copyright (C) 2005-2008, Robert Oostenveld
%
% $Log: dipoli.m,v $
% Revision 1.3 2008/12/24 10:25:41 roboos
% cleaned up the dipoli wrapper, replaced the binary by a better one and added a copy of the helper functions (from fileio)
%
% Revision 1.2 2008/12/24 09:20:11 roboos
% added subfunctions etc as dipoli_xxx and modified dipoli main function accordingly
%
% Revision 1.1.1.1 2008/12/24 08:52:28 roboos
% created new module that will hold the dipoli specific stuff for prepare_bemmodel
%
% Revision 1.2 2006/01/20 09:48:36 roboos
% fill remaining elements of matrix with zeros
% changed reshape and transpose
%
%$Id$
warning('DIPOLI is deprecated, please use FT_PREPARE_HEADMODEL with cfg.method = ''dipoli'' instead.')
% find the location of the binary
str = which('dipoli.m');
[p, f, x] = fileparts(str);
dipoli = fullfile(p, f); % without the .m extension
dipoli = checkplatformbinary(dipoli);
if ~isempty(dipoli)
skin = find_outermost_boundary(vol.bnd);
source = find_innermost_boundary(vol.bnd);
% the first compartment should be the skin, the last the source
if skin==1 && source==length(vol.bnd)
vol.skin = 1;
vol.source = length(vol.bnd);
elseif skin==length(vol.bnd) && source==1
% flip the order of the compartments
vol.bnd = fliplr(vol.bnd(:)');
vol.skin = 1;
vol.source = length(vol.bnd);
else
error('the first compartment should be the skin, the last the source');
end
if isolated
fprintf('using the isolated source approach\n');
else
fprintf('not using isolated source approach\n');
end
% write the triangulations to file
bnddip = vol.bnd;
bndfile = {};
for i=1:length(bnddip)
bndfile{i} = [tempname '.tri'];
% make sure that normals on the vertices point outwards
ok = checknormals(bnddip(i));
if ~ok, bnddip(i).tri = fliplr(bnddip(i).tri);end
write_tri(bndfile{i}, bnddip(i).pnt, bnddip(i).tri);
end
% these will hold the shell script and the inverted system matrix
exefile = [tempname '.sh'];
amafile = [tempname '.ama'];
fid = fopen(exefile, 'w');
fprintf(fid, '#!/bin/sh\n');
fprintf(fid, '\n');
fprintf(fid, '%s -i %s << EOF\n', dipoli, amafile);
for i=1:length(vol.bnd)
if isolated && vol.source==i
% the isolated potential approach should be applied using this compartment
fprintf(fid, '!%s\n', bndfile{i});
else
fprintf(fid, '%s\n', bndfile{i});
end
fprintf(fid, '%g\n', vol.cond(i));
end
fprintf(fid, '\n');
fprintf(fid, '\n');
fprintf(fid, 'EOF\n');
fclose(fid);
dos(sprintf('chmod +x %s', exefile));
try
% execute dipoli and read the resulting file
dos(exefile);
ama = loadama(amafile);
vol = ama2vol(ama);
catch
warning('an error ocurred while running dipoli');
disp(lasterr);
end
% delete the temporary files
for i=1:length(vol.bnd)
delete(bndfile{i})
end
delete(amafile);
delete(exefile);
else
error('Binary file not found or not implemented for this platform!')
end
function binname = checkplatformbinary(pathname)
binname = [];
% check for the appropriate platform dependent filename
c = computer;
is64 = ismember(lower(c),{'maci64' 'glnxa64' 'sol64' 'pcwin64'});
is32 = ismember(lower(c),{'maci' 'mac' 'pcwin'});
if ispc
binname = [pathname '.exe'];
elseif ismac
if is64
allowedbinnames = {[pathname '.maci64'] [pathname '.maci'] [pathname '.mac']};
else
allowedbinnames = {[pathname '.maci'] [pathname '.mac']};
end
elseif isunix
if is64
allowedbinnames = {[pathname '.glnxa64'] [pathname '.glnx86']};
else
allowedbinnames = [pathname '.glnx86'];
end
else
[pathname '.sol64'];
end
for i = 1:length(allowedbinnames)
if exist(allowedbinnames{i})
binname = allowedbinnames{i};
return
end
end
function ok = checknormals(bnd)
ok = 0;
pnt = bnd.pnt;
tri = bnd.tri;
% translate to the center
org = mean(pnt,1);
pnt(:,1) = pnt(:,1) - org(1);
pnt(:,2) = pnt(:,2) - org(2);
pnt(:,3) = pnt(:,3) - org(3);
w = sum(solid_angle(pnt, tri));
if w<0 && (abs(w)-4*pi)<1000*eps
% FIXME: this method is rigorous only for star shaped surfaces
warning('your normals are not oriented correctly')
ok = 0;
elseif w>0 && abs(w-4*pi)<1000*eps
ok = 1;
else
error('your surface probably is irregular')
ok = 0;
end
|
github
|
lcnbeapp/beapp-master
|
scpopen.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/biosig/private/scpopen.m
| 57,392 |
utf_8
|
efe5be2dea8235810f4b98539abfdbd1
|
function [HDR]=scpopen(arg1,CHAN,arg4,arg5,arg6)
% SCPOPEN reads and writes SCP-ECG files
%
% SCPOPEN is an auxillary function to SOPEN for
% opening of SCP-ECG files for reading ECG waveform data
%
% Use SOPEN instead of SCPOPEN
%
% See also: fopen, SOPEN,
% $Id$
% (C) 2004,2006,2007,2008 by Alois Schloegl <[email protected]>
% This is part of the BioSig-toolbox http://biosig.sf.net/
%
% BioSig 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 3 of the License, or
% (at your option) any later version.
if nargin<2, CHAN=0; end;
if isstruct(arg1)
HDR=arg1;
FILENAME=HDR.FileName;
elseif ischar(arg1);
HDR.FileName=arg1;
fprintf(2,'Warning SCPOPEN: the use of SCPOPEN is discouraged; please use SOPEN instead.\n');
end;
VER = version;
fid = fopen(HDR.FileName,HDR.FILE.PERMISSION,'ieee-le');
HDR.FILE.FID = fid;
if ~isempty(findstr(HDR.FILE.PERMISSION,'r')), %%%%% READ
tmpbytes = fread(fid,inf,'uchar');
tmpcrc = crc16eval(tmpbytes(3:end));
fseek(fid, 0, 'bof');
HDR.FILE.CRC = fread(fid,1,'uint16');
if (HDR.FILE.CRC ~= tmpcrc);
fprintf(HDR.FILE.stderr,'Warning: CRC check failed (%x vs %x)\n',tmpcrc,HDR.FILE.CRC);
end;
HDR.FILE.Length = fread(fid,1,'uint32');
if HDR.FILE.Length~=HDR.FILE.size,
fprintf(HDR.FILE.stderr,'Warning SCPOPEN: header information contains incorrect file size %i %i \n',HDR.FILE.Length,HDR.FILE.size);
end;
HDR.data = [];
DHT = [0,1,-1,2,-2,3,-3,4,-4,5,-5,6,-6,7,-7,8,-8,9,-9;0,1,5,3,11,7,23,15,47,31,95,63,191,127,383,255,767,511,1023]';
prefix = [1,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,10,10];
PrefixLength = prefix;
%PREFIX = [0,4,5,12,13,28,29,60,61,124,125,252,253,508,509,1020,1021,1022,1023];
PREFIX = [0,4,5,12,13,28,29,60,61,124,125,252,253,508,509,1020,1021,1022,1023]'.*2.^[32-prefix]';
codelength = [1,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,18,26];
mask = [1,7,7,15,15,31,31,63,63,127,127,255,255,511,511,1023,1023,1023,1023]'.*2.^[32-prefix]';
%MASK = dec2bin(mask);
%mask = [1,7,7,15,15,31,31,63,63,127,127,255,255,511,511,1023,1023,1023,1023]';
mask2 = [1,7,7,15,15,31,31,63,63,127,127,255,255,511,511,1023,1023,1023,1023]';
PREFIX2 = DHT(:,2);
HT19999 = [prefix',codelength',ones(length(prefix),1),DHT];
HT = [prefix',codelength',ones(length(prefix),1),DHT];
dd = [0:255]';
ACC = zeros(size(dd));
c = 0;
for k2 = 1:8,
ACC = ACC + (dd>127).*(2^c);
dd = mod(dd*2, 256);
c = c + 1;
end;
section.CRC = fread(fid,1,'uint16');
section.ID = fread(fid,1,'uint16');
section.Length = fread(fid,1,'uint32');
section.Version = fread(fid,[1,2],'uint8');
section.tmp = fread(fid,[1,6],'uint8');
NSections = min(11,(section.Length-16)/10);
for k = 1:NSections,
HDR.Block(k).id = k;
HDR.Block(k).length = 0;
HDR.Block(k).startpos = -1;
end;
for K = 1:NSections,
k = fread(fid,1,'uint16');
len = fread(fid,1,'uint32');
pos = fread(fid,1,'uint32');
if ((k > 0) && (k < NSections))
HDR.Block(k).id = k;
HDR.Block(k).length = len;
HDR.Block(k).startpos = pos-1;
%% [HDR.Block(k).id ,length(tmpbytes), HDR.Block(k).length, HDR.Block(k).length+HDR.Block(k).startpos]
%% FIXME: instead of min(...,FileSize) a warning or error message should be reported
tmpcrc = crc16eval(tmpbytes(HDR.Block(k).startpos+3:min(HDR.Block(k).startpos+HDR.Block(k).length,HDR.FILE.size)));
if (HDR.Block(k).length>0)
if (tmpcrc~=(tmpbytes(HDR.Block(k).startpos+(1:2))'*[1;256]))
fprintf(HDR.FILE.stderr,'Warning SCPOPEN: faulty CRC %04x in section %i\n',tmpcrc,k-1);
end;
end;
end;
end;
%%[[HDR.Block.id];[HDR.Block.length];[HDR.Block.startpos]]'
% default values - in case Section 6 is missing
HDR.NS = 0; HDR.SPR = 0; HDR.NRec = 0; HDR.Calib = zeros(1,0);
secList = find([HDR.Block.length]);
for K = secList(1:end),
if fseek(fid,HDR.Block(K).startpos,'bof');
fprintf(HDR.FILE.stderr,'Warning SCPOPEN: section %i not available, although it is listed in Section 0\n',secList(K+1));
end;
section.CRC = fread(fid,1,'uint16');
section.ID = fread(fid,1,'uint16');
section.Length = fread(fid,1,'uint32');
section.Version = fread(fid,[1,2],'uint8');
section.tmp = fread(fid,[1,6],'uint8');
HDR.SCP.Section{find(K==secList)} = section;
if (section.Length==0),
elseif section.ID==0,
NSections = (section.Length-16)/10;
for k = 1:NSections,
HDR.Block(k).id = fread(fid,1,'uint16');
HDR.Block(k).length = fread(fid,1,'uint32');
HDR.Block(k).startpos = fread(fid,1,'uint32')-1;
end;
elseif section.ID==1,
tag = 0;
k1 = 0;
Sect1Len = section.Length-16;
ListOfRequiredTags = [2,14,25,26];
ListOfRecommendedTags = [0,1,5,8,15,34];
while (tag~=255) & (Sect1Len>2),
tag = fread(fid,1,'uint8');
len = fread(fid,1,'uint16');
Sect1Len = Sect1Len - 3 - len;
%% [tag,len,Sect1Len], %% DEBUGGING information
field = fread(fid,[1,len],'uchar');
if tag == 0,
ListOfRecommendedTags(ListOfRecommendedTags==tag)=[];
HDR.Patient.Name = char(field); %% LastName
elseif tag == 1,
ListOfRecommendedTags(ListOfRecommendedTags==tag)=[];
HDR.Patient.FirstName = char(field);
elseif tag == 2,
ListOfRequiredTags(find(ListOfRequiredTags==2))=[];
HDR.Patient.Id = char(field);
elseif tag == 3,
HDR.Patient.LastName2 = char(field);
elseif tag == 4,
HDR.Patient.Age = field(1:2)*[1;256];
tmp = field(3);
if tmp==1, HDR.Patient.Age = HDR.Patient.Age; % unit='Y';
elseif tmp==2, HDR.Patient.Age = HDR.Patient.Age/12; % unit='M';
elseif tmp==3, HDR.Patient.Age = HDR.Patient.Age/52; % unit='W';
elseif tmp==4, HDR.Patient.Age = HDR.Patient.Age/365.25; % unit='d';
elseif tmp==5, HDR.Patient.Age = HDR.Patient.Age/(365.25*24); %unit='h';
else warning('units of age not specified');
end;
elseif (tag == 5)
ListOfRecommendedTags(ListOfRecommendedTags==tag)=[];
if any(field(1:4)~=0)
HDR.Patient.Birthday = [field(1:2)*[1;256],field(3:4),12,0,0];
end;
elseif (tag == 6)
if any(field(1:3)),
HDR.Patient.Height = field(1:2)*[1;256];
tmp = field(3);
if tmp==1, % unit='cm';
elseif tmp==2, HDR.Patient.Height = HDR.Patient.Height*2.54; %unit='inches';
elseif tmp==3, HDR.Patient.Height = HDR.Patient.Height*0.1; %unit='mm';
else warning('units of height not specified');
end;
end;
elseif (tag == 7)
if any(field(1:3)),
HDR.Patient.Weight = field(1:2)*[1;256];
tmp = field(3);
if tmp==1, % unit='kg';
elseif tmp==2, HDR.Patient.Weight = HDR.Patient.Weight/1000; %unit='g';
elseif tmp==3, HDR.Patient.Weight = HDR.Patient.Weight/2.2; %unit='pound';
elseif tmp==4, HDR.Patient.Weight = HDR.Patient.Weight*0.0284; %unit='ounce';
else warning('units of weight not specified');
end;
end;
elseif tag == 8,
ListOfRecommendedTags(ListOfRecommendedTags==tag)=[];
HDR.Patient.Sex = field;
elseif tag == 9,
HDR.Patient.Race = field;
elseif tag == 10,
if (field(1)~=0)
HDR.Patient.Medication = field;
else
HDR.Patient.Medication.Code = field(2:3);
HDR.Patient.Medication = field(4:end);
end;
elseif tag == 11,
HDR.Patient.BloodPressure.Systolic = field*[1;256];
elseif tag == 12,
HDR.Patient.BloodPressure.Diastolic = field*[1;256];
elseif tag == 13,
HDR.Patient.Diagnosis = char(field);
elseif tag == 14,
ListOfRequiredTags(ListOfRequiredTags==tag)=[];
HDR.SCP1.AcquiringDeviceID = char(field);
HDR.VERSION = field(15)/10;
elseif tag == 15,
ListOfRecommendedTags(ListOfRecommendedTags==tag)=[];
HDR.SCP1.AnalyisingDeviceID = char(field);
elseif tag == 16,
HDR.SCP1.AcquiringInstitution = char(field);
elseif tag == 17,
HDR.SCP1.AnalyzingInstitution = char(field);
elseif tag == 18,
HDR.SCP1.AcquiringDepartment = char(field);
elseif tag == 19,
HDR.SCP1.AnalyisingDepartment = char(field);
elseif tag == 20,
HDR.SCP1.Physician = char(field);
elseif tag == 21,
HDR.SCP1.LatestComfirmingPhysician = char(field);
elseif tag == 22,
HDR.SCP1.Technician = char(field);
elseif tag == 23,
HDR.SCP1.Room = char(field);
elseif tag == 24,
HDR.SCP1.Emergency = field;
elseif tag == 25,
ListOfRequiredTags(ListOfRequiredTags==tag)=[];
HDR.T0(1,1:3) = [field(1:2)*[1;256],field(3:4)];
elseif tag == 26,
ListOfRequiredTags(ListOfRequiredTags==tag)=[];
HDR.T0(1,4:6) = field(1:3);
elseif tag == 27,
HDR.Filter.HighPass = field(1:2)*[1;256]/100;
elseif tag == 28,
HDR.Filter.LowPass = field(1:2)*[1;256]/100;
elseif tag == 29,
if (field==0)
HDR.FILTER.Notch = NaN;
elseif bitand(field,1)
HDR.FILTER.Notch = 60; % 60Hz Notch
elseif bitand(field,2)
HDR.FILTER.Notch = 50; % 50Hz Notch
elseif bitand(field,3)==0
HDR.FILTER.Notch = -1; % Notch Off
end;
HDR.SCP1.Filter.BitMap = field;
elseif tag == 30,
HDR.SCP1.FreeText = char(field);
elseif tag == 31,
HDR.SCP1.ECGSequenceNumber = char(field);
elseif tag == 32,
HDR.SCP1.MedicalHistoryCodes = char(field);
elseif tag == 33,
HDR.SCP1.ElectrodeConfigurationCodes = field;
elseif tag == 34,
ListOfRecommendedTags(ListOfRecommendedTags==tag)=[];
HDR.SCP1.Timezone = field;
elseif tag == 35,
HDR.SCP1.MedicalHistory = char(field);
elseif tag == 255,
% section terminator
elseif tag >= 200,
% manufacturer specific - not standardized
else
fprintf(HDR.FILE.stderr,'Warning SCOPEN: unknown tag %i (section 1)\n',tag);
end;
end;
if ~isempty(ListOfRequiredTags)
fprintf(HDR.FILE.stderr,'Warning SCPOPEN: the following tags are required but missing in file %s\n',HDR.FileName);
disp(ListOfRequiredTags);
end;
if ~isempty(ListOfRecommendedTags)
fprintf(HDR.FILE.stderr,'Warning SCPOPEN: the following tags are recommended but missing in file %s\n',HDR.FileName);
disp(ListOfRecommendedTags);
end;
elseif section.ID==2, % Huffman tables
HDR.SCP2.NHT = fread(fid,1,'uint16');
HDR.SCP2.NCT = fread(fid,1,'uint16');
if HDR.SCP2.NHT~=19999,
NHT = HDR.SCP2.NHT;
else
NHT = 0;
end;
k3 = 0;
for k1 = 1:NHT,
HT1 = zeros(HDR.SCP2.NCT,5);
for k2 = 1:HDR.SCP2.NCT,
tmp = fread(fid,3,'uint8') ;
HDR.SCP2.prefix = tmp(1); % PrefixLength
HDR.SCP2.codelength = tmp(2); % CodeLength
HDR.SCP2.TableModeSwitch = tmp(3);
tmp(4) = fread(fid,1,'int16'); % BaseValue
tmp(5) = fread(fid,1,'uint32'); % BaseCode
k3 = k3 + 1;
HT (k3,:) = [tmp'];
HT1(k2,:) = [tmp'];
end;
HDR.SCP2.HTree{k1} = makeTree(HT1);
HDR.SCP2.HTs{k1} = HT1;
end;
if HDR.SCP2.NHT~=19999,
HDR.SCP2.HT = HT;
else
tmp = size(HT19999,1);
HDR.SCP2.HT = [ones(tmp,1),[1:tmp]',HT19999];
HDR.SCP2.HTree{1} = makeTree(HT19999);
HDR.SCP2.HTs{1} = HT19999;
end;
elseif section.ID==3,
HDR.NS = fread(fid,1,'uint8');
HDR.FLAG.Byte = fread(fid,1,'uint8');
if ~bitand(HDR.FLAG.Byte,4)
fprintf(HDR.FILE.stdout,'Warning SCPOPEN: not all leads simultaneously recorded - this mode is not supported.\n');
end;
HDR.FLAG.ReferenceBeat = mod(HDR.FLAG.Byte,2);
%HDR.NS = floor(mod(HDR.FLAG.Byte,128)/8);
for k = 1:HDR.NS,
HDR.LeadPos(k,1:2) = fread(fid,[1,2],'uint32');
HDR.LeadIdCode(k,1) = fread(fid,1,'uint8');
end;
HDR.N = max(HDR.LeadPos(:))-min(HDR.LeadPos(:))+1;
HDR.AS.SPR = HDR.LeadPos(:,2)-HDR.LeadPos(:,1)+1;
HDR.SPR = HDR.AS.SPR(1);
for k = 2:HDR.NS
HDR.SPR = lcm(HDR.SPR,HDR.AS.SPR(k));
end;
HDR = leadidcodexyz(HDR);
for k = 1:HDR.NS,
if 0,
elseif (HDR.LeadIdCode(k)==0),
HDR.Label{k} = 'unspecified lead';
elseif (HDR.VERSION <= 1.3) & (HDR.LeadIdCode(k) < 86),
% HDR.Label{k} = H.Label(H.LeadIdCode==HDR.LeadIdCode(k));
elseif (HDR.VERSION <= 1.3) & (HDR.LeadIdCode(k) > 99),
HDR.Label{k} = 'manufacturer specific';
elseif (HDR.VERSION >= 2.0) & (HDR.LeadIdCode(k) < 151),
% HDR.Label{k} = H.Label(H.LeadIdCode==HDR.LeadIdCode(k));
elseif (HDR.VERSION >= 2.0) & (HDR.LeadIdCode(k) > 199),
HDR.Label{k} = 'manufacturer specific';
else
HDR.Label{k} = 'reserved';
end;
end;
HDR.Label = strvcat(HDR.Label);
elseif section.ID==4,
HDR.SCP4.L = fread(fid,1,'int16');
HDR.SCP4.fc0 = fread(fid,1,'int16');
HDR.SCP4.N = fread(fid,1,'int16');
HDR.SCP4.type = fread(fid,[7,HDR.SCP4.N],'uint16')'*[1,0,0,0; 0,1,0,0;0,2^16,0,0; 0,0,1,0;0,0,2^16,0; 0,0,0,1;0,0,0,2^16];
tmp = fread(fid,[2*HDR.SCP4.N],'uint32');
HDR.SCP4.PA = reshape(tmp,2,HDR.SCP4.N)';
HDR.SCP4.pa = [0;tmp;HDR.N];
elseif any(section.ID==[5,6]),
SCP = [];
SCP.Cal = fread(fid,1,'int16')/1e6; % quant in nV, converted into mV
SCP.PhysDim = 'mV';
SCP.Dur = fread(fid,1,'int16');
SCP.SampleRate = 1e6/SCP.Dur;
SCP.FLAG.DIFF = fread(fid,1,'uint8');
SCP.FLAG.bimodal_compression = fread(fid,1,'uint8');
if isnan(HDR.NS),
HDR.ERROR.status = -1;
HDR.ERROR.message = sprintf('Error SCPOPEN: could not read %s\n',HDR.FileName);
fprintf(HDR.FILE.stderr,'Error SCPOPEN: could not read %s\n',HDR.FileName);
return;
end;
if CHAN==0, CHAN = 1:HDR.NS; end;
SCP.SPR = fread(fid,HDR.NS,'uint16');
HDR.InChanSelect = CHAN;
if section.ID==6,
HDR.HeadLen = ftell(fid);
HDR.FLAG.DIFF = SCP.FLAG.DIFF;
HDR.FLAG.bimodal_compression = SCP.FLAG.bimodal_compression;
HDR.data = [];
outlen = HDR.SPR;
HDR.Calib = sparse(2:HDR.NS+1, 1:HDR.NS, SCP.Cal);
elseif isfield(HDR,'SCP4') %% HACK: do no know whether it is correct
outlen = floor(1000*HDR.SCP4.L/SCP.Dur);
else
outlen = inf;
end;
if ~isfield(HDR,'SCP2'),
if any(SCP.SPR(1)~=SCP.SPR),
error('SCPOPEN: SPR do not fit');
else
S2 = fread(fid,[SCP.SPR(1)/2,HDR.NS],'int16');
end;
%S2 = S2(:,CHAN);
elseif (HDR.SCP2.NHT==1) && (HDR.SCP2.NCT==1) && (HDR.SCP2.prefix==0),
codelength = HDR.SCP2.HT(1,4);
if (codelength==16)
S2 = fread(fid,[HDR.N,HDR.NS],'int16');
elseif (codelength==8)
S2 = fread(fid,[HDR.N,HDR.NS],'int8');
else
fprintf(HDR.FILE.stderr,'Warning SCPOPEN: codelength %i is not supported yet.',codelength);
fprintf(HDR.FILE.stderr,' Contact <[email protected]>\n');
return;
end;
%S2 = S2(:,CHAN);
elseif 1, HDR.SCP2.NHT~=19999;
%% User specific Huffman table
%% a more elegant Huffman decoder is used here %%
for k = 1:HDR.NS,
SCP.data{k} = fread(fid,SCP.SPR(k),'uint8');
end;
% S2 = repmat(NaN,outlen,length(HDR.InChanSelect));
clear S2;
sz = inf;
for k3 = 1:length(HDR.InChanSelect), k = HDR.InChanSelect(k3); %HDR.NS,
outdata{k3} = DecodeHuffman(HDR.SCP2.HTree,HDR.SCP2.HTs,SCP.data{k},outlen);
sz = min(sz,length(outdata{k3}));
end;
for k3 = 1:length(HDR.InChanSelect), k = HDR.InChanSelect(k3); %HDR.NS,
S2(:,k) = outdata{k3}(1:sz);
end;
accu=0;
elseif HDR.SCP2.NHT==19999,
HuffTab = DHT;
for k = 1:HDR.NS,
SCP.data{k} = fread(fid,SCP.SPR(k),'uint8');
end;
%for k = 1:HDR.NS,
for k3 = 1:length(HDR.InChanSelect), k = HDR.InChanSelect(k3); %HDR.NS,
%for k = CHAN(:)',
s2 = SCP.data{k};
s2 = [s2; repmat(0,ceil(max(HDR.SCP2.HT(:,4))/8),1)];
k1 = 0;
l2 = 0;
accu = 0;
c = 0;
x = [];
HT = HDR.SCP2.HT(find(HDR.SCP2.HT(:,1)==1),3:7);
while (l2 < HDR.LeadPos(k,2)),
while ((c < max(HT(:,2))) & (k1<length(s2)-1));
k1 = k1 + 1;
dd = s2(k1);
accu = accu + ACC(dd+1)*(2^c);
c = c + 8;
if 0, %for k2 = 1:8,
accu = accu + (dd>127)*(2^c);
dd = mod(dd*2,256);
c = c + 1;
end;
end;
ixx = 1;
%acc = mod(accu,2^32); % bitand returns NaN if accu >= 2^32
acc = accu - 2^32*fix(accu*(2^(-32))); % bitand returns NaN if accu >= 2^32
while (bitand(acc,2^HT(ixx,1)-1) ~= HT(ixx,5)),
ixx = ixx + 1;
end;
dd = HT(ixx,2) - HT(ixx,1);
if HT(ixx,3)==0,
HT = HDR.SCP2.HT(find(HDR.SCP2.HT(:,1)==HT(ixx,5)),3:7);
fprintf(HDR.FILE.stderr,'Warning SCPOPEN: Switching Huffman Tables is not tested yet.\n');
elseif (dd==0),
l2 = l2 + 1;
x(l2) = HT(ixx,4);
else %if (HT(ixx,3)>0),
l2 = l2 + 1;
%acc2 = fix(accu*(2^(-HT(ixx,1))));
%tmp = mod(fix(accu*(2^(-HT(ixx,1)))),2^dd);
tmp = fix(accu*(2^(-HT(ixx,1)))); % bitshift(accu,-HT(ixx,1))
tmp = tmp - (2^dd)*fix(tmp*(2^(-dd))); % bitand(...,2^dd)
%tmp = bitand(accu,(2^dd-1)*(2^HT(ixx,1)))*(2^-HT(ixx,1));
% reverse bit-pattern
if dd==8,
tmp = ACC(tmp+1);
else
tmp = dec2bin(tmp);
tmp = [char(repmat('0',1,dd-length(tmp))),tmp];
tmp = bin2dec(tmp(length(tmp):-1:1));
end
x(l2) = tmp-(tmp>=(2^(dd-1)))*(2^dd);
end;
accu = fix(accu*2^(-HT(ixx,2)));
c = c - HT(ixx,2);
end;
x = x(:);
if k3==1,
S2=x(:,ones(1,k));
elseif size(x,1)==size(S2,1),
S2(:,k) = x;
else
fprintf(HDR.FILE.stderr,'Error SCPOPEN: Huffman decoding failed (%i) \n',size(x,1));
HDR.data = S2;
return;
end;
end;
elseif (HDR.SCP2.NHT==19999), % alternative decoding algorithm.
warning('this branch is experimental - it might be broken')
HuffTab = DHT;
for k = 1:HDR.NS,
SCP.data{k} = fread(fid,SCP.SPR(k),'uint8');
end;
%for k = 1:HDR.NS,
for k3 = 1:length(HDR.InChanSelect), k = HDR.InChanSelect(k3); %HDR.NS,
%for k = CHAN(:)',
tmp = SCP.data{k};
accu = [tmp(4)+256*tmp(3)+65536*tmp(2)+2^24*tmp(1)];
%accu = bitshift(accu,HDR.SCP2.prefix,32);
c = 0; %HDR.SCP2.prefix;
l = 4;
l2 = 0;
clear x;
Ntmp = length(tmp);
tmp = [tmp; zeros(4,1)];
while c <= 32, %1:HDR.SPR(k),
ixx = 1;
while (bitand(accu,mask(ixx)) ~= PREFIX(ixx)),
ixx = ixx + 1;
end;
if ixx < 18,
c = c + prefix(ixx);
%accu = bitshift(accu, prefix(ixx),32);
accu = mod(accu.*(2^prefix(ixx)),2^32);
l2 = l2 + 1;
x(l2) = HuffTab(ixx,1);
elseif ixx == 18,
c = c + prefix(ixx) + 8;
%accu = bitshift(accu, prefix(ixx),32);
accu = mod(accu.*(2^prefix(ixx)),2^32);
l2 = l2 + 1;
acc1 = mod(floor(accu*2^(-24)),256);
%accu = bitshift(accu, 8, 32);
accu = mod(accu*256, 2^32);
x(l2) = acc1-(acc1>=2^7)*2^8;
acc2 = 0;
for kk = 1:8,
acc2 = acc2*2 + mod(acc1,2);
acc1 = floor(acc1/2);
end;
elseif ixx == 19,
c = c + prefix(ixx);
%accu = bitshift(accu, prefix(ixx),32);
accu = mod(accu.*(2^prefix(ixx)),2^32);
l2 = l2 + 1;
while (c > 7) & (l < Ntmp),
l = l+1;
c = c-8;
accu = accu + tmp(l)*2^c;
end;
acc1 = mod(floor(accu*2^(-16)),2^16);
%accu = bitshift(accu, 16, 32);
accu = mod(accu.*(2^16), 2^32);
x(l2) = acc1-(acc1>=2^15)*2^16;
acc2 = 0;
for kk=1:16,
acc2 = acc2*2+mod(acc1,2);
acc1 = floor(acc1/2);
end;
%x(l2) = acc2;
c = c + 16;
end;
while (c > 7) & (l < Ntmp),
l = l+1;
c = c-8;
accu = accu + tmp(l)*(2^c);
end;
end;
x = x(1:end-1)';
if k3==1,
S2=x(:,ones(1,k));
elseif size(x,1)==size(S2,1),
S2(:,k) = x;
elseif 1,
fprintf(HDR.FILE.stderr,'Error SCPOPEN: length=%i of channel %i different to length=%i of channel 1 \n',size(x,1),k,size(S2,1));
return;
else
fprintf(HDR.FILE.stderr,'Error SCPOPEN: Huffman decoding failed (%i) \n',size(x,1));
HDR.data=S2;
return;
end;
end;
elseif HDR.SCP2.NHT~=19999,
%% OBSOLETE %%
fprintf(HDR.FILE.stderr,'Error SOPEN SCP-ECG: user specified Huffman Table not supported\n');
HDR.SCP = SCP;
return;
else
HDR.SCP2,
end;
% Decoding of Difference encoding
if SCP.FLAG.DIFF==2,
for k1 = 3:size(S2,1);
S2(k1,:) = S2(k1,:) + [2,-1] * S2(k1-(1:2),:);
end;
elseif SCP.FLAG.DIFF==1,
S2 = cumsum(S2);
end;
if section.ID==5,
HDR.SCP5 = SCP;
HDR.SCP5.data = S2;
HDR.SampleRate = SCP.SampleRate;
elseif section.ID==6,
HDR.SCP6 = SCP;
HDR.SampleRate = SCP.SampleRate;
HDR.PhysDim = repmat({HDR.SCP6.PhysDim},HDR.NS,1);
HDR.data = S2;
if HDR.FLAG.bimodal_compression,
%% FIXME: THIS IS A HACK - DO NOT KNOW WHETHER IT IS CORRECT.
% HDR.FLAG.bimodal_compression = isfield(HDR,'SCP5') & isfield(HDR,'SCP4');
HDR.FLAG.bimodal_compression = isfield(HDR,'SCP4');
end;
if HDR.FLAG.bimodal_compression,
if isfield(HDR,'SCP5')
F = HDR.SCP5.SampleRate/HDR.SCP6.SampleRate;
HDR.SampleRate = HDR.SCP5.SampleRate;
HDR.FLAG.F = F;
else
HDR.FLAG.F = 1;
end;
tmp=[HDR.SCP4.PA(:,1);HDR.LeadPos(1,2)]-[1;HDR.SCP4.PA(:,2)+1];
if ~all(tmp==floor(tmp))
tmp,
end;
t = (1:HDR.N) / HDR.SampleRate;
S1 = zeros(HDR.N, HDR.NS);
p = 1;
k2 = 1;
pa = [HDR.SCP4.PA;NaN,NaN];
flag = 1;
%% FIXME: accu undefined ##
accu = 0;
for k1 = 1:HDR.N,
if k1 == pa(p,2)+1,
flag = 1;
p = p+1;
accu = S2(k2,:);
elseif k1 == pa(p,1),
flag = 0;
k2 = ceil(k2);
end;
if flag,
S1(k1,:) = ((F-1)*accu + S2(fix(k2),:)) / F;
k2 = k2 + 1/F;
else
S1(k1,:) = S2(k2,:);
k2 = k2 + 1;
end;
end;
HDR.SCP.S2 = S2;
HDR.SCP.S1 = S1;
S2 = S1;
end;
if HDR.FLAG.ReferenceBeat & ~isfield(HDR,'SCP5')
fprintf(HDR.FILE.stderr,'Warning SOPEN SCP-ECG: Flag ReferenceBeat set, but no section 5 (containing the reference beat) is available\n');
elseif HDR.FLAG.ReferenceBeat,
tmp_data = HDR.SCP5.data*(HDR.SCP5.Cal/HDR.SCP6.Cal);
for k = find(~HDR.SCP4.type(:,1)'),
t1 = (HDR.SCP4.type(k,2):HDR.SCP4.type(k,4));
t0 = t1 - HDR.SCP4.type(k,3) + HDR.SCP4.fc0;
S2(t1,:) = S2(t1,:) + tmp_data(t0,:);
end;
end;
HDR.data = S2;
end;
elseif section.ID==7,
HDR.SCP7.byte1 = fread(fid,1,'uint8');
HDR.SCP7.Nspikes = fread(fid,1,'uint8');
HDR.SCP7.meanPPI = fread(fid,1,'uint16');
HDR.SCP7.avePPI = fread(fid,1,'uint16');
for k=1:HDR.SCP7.byte1,
HDR.SCP7.RefBeat{k} = fread(fid,16,'uint8');
%HDR.SCP7.RefBeat1 = fread(fid,16,'uint8');
end;
for k=1:HDR.SCP7.Nspikes,
tmp = fread(fid,16,'uint16');
tmp(1,2) = fread(fid,16,'int16');
tmp(1,3) = fread(fid,16,'uint16');
tmp(1,4) = fread(fid,16,'int16');
HDR.SCP7.ST(k,:) = tmp;
end;
for k=1:HDR.SCP7.Nspikes,
tmp = fread(fid,6,'uint8');
HDR.SCP7.ST2(k,:) = tmp;
end;
HDR.SCP7.Nqrs = fread(fid,1,'uint16');
HDR.SCP7.beattype = fread(fid,HDR.SCP7.Nqrs,'uint8');
HDR.SCP7.VentricularRate = fread(fid,1,'uint16');
HDR.SCP7.AterialRate = fread(fid,1,'uint16');
HDR.SCP7.QTcorrected = fread(fid,1,'uint16');
HDR.SCP7.TypeHRcorr = fread(fid,1,'uint8');
len = fread(fid,1,'uint16');
tag = 255*(len==0);
k1 = 0;
while tag~=255,
tag = fread(fid,1,'uchar');
len = fread(fid,1,'uint16');
field = fread(fid,[1,len],'uchar');
if tag == 0,
HDR.Patient.LastName = char(field);
elseif tag == 1,
end;
end;
HDR.SCP7.P_onset = fread(fid,1,'uint16');
HDR.SCP7.P_offset = fread(fid,1,'uint16');
HDR.SCP7.QRS_onset = fread(fid,1,'uint16');
HDR.SCP7.QRS_offset = fread(fid,1,'uint16');
HDR.SCP7.T_offset = fread(fid,1,'uint16');
HDR.SCP7.P_axis = fread(fid,1,'uint16');
HDR.SCP7.QRS_axis = fread(fid,1,'uint16');
HDR.SCP7.T_axis = fread(fid,1,'uint16');
elseif section.ID==8,
tmp = fread(fid,9,'uint8');
HDR.SCP8.Report = tmp(1);
HDR.SCP8.Time = [[1,256]*tmp(2:3),tmp(4:8)'];
HDR.SCP8.N = tmp(9);
for k = 1:HDR.SCP8.N,
ix = fread(fid,1,'uint8');
len = fread(fid,1,'uint16');
tmp = fread(fid,[1,len],'uchar');
HDR.SCP8.Statement{k,1} = char(tmp);
end
%elseif section.ID==9,
% HDR.SCP9.byte1 = fread(fid,1,'uint8');
elseif section.ID==10,
tmp = fread(fid,2,'uint16');
HDR.SCP10.NumberOfLeads = tmp(1);
HDR.SCP10.ManufacturerCode = tmp(2);
for k = []; 1:HDR.SCP10.NumberOfLeads,
tmp = fread(fid,2,'uint16')
LeadId = tmp(1);
LeadLen = tmp(2);
tmp = fread(fid,LeadLen/2,'uint16');
HDR.SCP10.LeadId(k)=LeadId;
HDR.SCP10.LeadLen(k)=LeadLen;
HDR.SCP10.Measurements{k}=tmp;
end;
elseif section.ID==11,
bytes = fread(fid,11,'uint8');
HDR.SCP11.T0 = [bytes(2)*256+bytes(3), bytes(4:8)];
HDR.SCP11.Confirmed = bytes(1);
HDR.SCP11.NumberOfStatements = bytes(9);
for k = 1:HDR.SCP11.NumberOfStatements,
SeqNo = fread(fid,1,'uint8');
len11 = fread(fid,1,'uint16');
typeID = fread(fid,1,'uint8');
Statement = fread(fid,len11-1,'uint8');
HDR.SCP11.Statement.SeqNo(k) = SeqNo;
HDR.SCP11.Statement.len11(k) = len11;
HDR.SCP11.Statement.typeID(k) = typeID;
HDR.SCP11.Statement.Statement{k} = Statement;
end;
end;
if ~section.Length,
HDR.ERROR.status = -1;
HDR.ERROR.message = 'Error SCPOPEN: \n';
return;
end;
end;
HDR.SPR = size(HDR.data,1);
HDR.NRec = 1;
HDR.AS.endpos = HDR.SPR;
HDR.FILE.OPEN = 0;
HDR.FILE.POS = 0;
HDR.TYPE = 'native';
fclose(HDR.FILE.FID);
else % writing SCP file
NSections = 12;
SectIdHdr = zeros(1,16);
VERSION = round(HDR.VERSION*10);
if ~any(VERSION==[10,13,20])
fprintf(HDR.FILE.stderr,'Warning SCPOPEN(WRITE): unknown Version number %4.2f\n',HDR.VERSION);
VERSION = 20;
end;
SectIdHdr(9:10) = VERSION; % Section and Protocol version number
POS = 6; B = zeros(1,POS);
for K = 0:NSections-1;
b = [];
if K==0,
% SECTION 0
b = [SectIdHdr(1:10),'SCPECG', zeros(1,NSections*10)];
b(16+(7:10)) = s4b(POS+1);
elseif K==1,
% SECTION 1
b = SectIdHdr;
% tag(1),len(1:2),field(1:len)
if isfield(HDR.Patient,'Name'),
b = [b, 0, s2b(length(HDR.Patient.Name)), HDR.Patient.Name];
end;
if isfield(HDR.Patient,'Id'),
b = [b, 2, s2b(length(HDR.Patient.Id)), HDR.Patient.Id];
end;
if isfield(HDR.Patient,'Age'),
%b = [b, 4, s2b(3), s2b(HDR.Patient.Age),1]; %% use birthday instead
end;
if isfield(HDR.Patient,'Birthday'),
b = [b, 5, s2b(4), s2b(HDR.Patient.Birthday(1)),HDR.Patient.Birthday(2:3)];
end;
if isfield(HDR.Patient,'Height'),
if ~isnan(HDR.Patient.Height),
b = [b, 6, s2b(3), s2b(HDR.Patient.Height),1];
end;
end;
if isfield(HDR.Patient,'Weight'),
if ~isnan(HDR.Patient.Weight),
b = [b, 7, s2b(3), s2b(HDR.Patient.Weight),1];
end;
end;
if isfield(HDR.Patient,'Sex'),
if ~isempty(HDR.Patient.Sex)
sex = HDR.Patient.Sex;
if 0,
elseif isnumeric(sex), sex = sex(1);
elseif strncmpi(sex,'male',1); sex = 1;
elseif strncmpi(sex,'female',1); sex = 2;
else sex = 9; % unspecified
end;
b = [b, 8, s2b(1), sex];
end;
end;
if isfield(HDR.Patient,'Race'),
b = [b, 9, s2b(1), HDR.Patient.Race(1)];
end;
if isfield(HDR.Patient,'BloodPressure'),
b = [b, 11, s2b(2), s2b(HDR.Patient.BloodPressure.Systolic)];
b = [b, 12, s2b(2), s2b(HDR.Patient.BloodPressure.Diastolic)];
end;
%% Tag 14
tag14.AnalyzingProgramRevisionNumber = ['',char(0)];
tag14.SerialNumberAcqDevice = ['',char(0)];
tag14.AcqDeviceSystemSoftware = ['',char(0)];
tag14.SCPImplementationSoftware = ['BioSig4OctMat v 1.76+',char(0)];
tag14.ManufactureAcqDevice = ['',char(0)];
t14 = [zeros(1,35), length(tag14.AnalyzingProgramRevisionNumber),tag14.AnalyzingProgramRevisionNumber,tag14.SerialNumberAcqDevice,tag14.AcqDeviceSystemSoftware,tag14.SCPImplementationSoftware,tag14.ManufactureAcqDevice];
t14(8) = 255; % Manufacturer
%%% ### FIXME ### t14(9:14) = % cardiograph model
t14(15) = VERSION; % Version
t14(16) = hex2dec('A0'); % Demographics and ECG rhythm data" (if we had also the reference beats we should change it in 0xC0).
t14(18) = hex2dec('D0'); % Capabilities of the ECG Device: 0xD0 (acquire, print and store).
b = [b, 14, s2b(length(t14)), t14];
b = [b, 25, s2b(4), s2b(HDR.T0(1)),HDR.T0(2:3)];
b = [b, 26, s2b(3), HDR.T0(4:6)];
if ~any(isnan(HDR.Filter.HighPass))
b = [b, 27, s2b(2), s2b(round(HDR.Filter.HighPass(1)*100))];
end;
if ~any(isnan(HDR.Filter.LowPass))
b = [b, 28, s2b(2), s2b(round(HDR.Filter.LowPass(1)))];
end;
b = [b, 255, 0, 0]; % terminator
b = b + (b<0)*256;
elseif K==3,
% SECTION 3
b = [SectIdHdr,HDR.NS,4+HDR.NS*8];
if ~isfield(HDR,'LeadIdCode'), HDR.LeadIdCode = zeros(1,HDR.NS); end;
if (numel(HDR.LeadIdCode)~=HDR.NS); warning('HDR.LeadIdCode does not have HDR.NS elements'); end;
if any(HDR.LeadIdCode>255), warning('invalid LeadIdCode'); end;
for k = 1:HDR.NS,
b = [b, s4b(1), s4b(HDR.SPR*HDR.NRec), mod(HDR.LeadIdCode(k),256)];
end;
elseif K==6,
% SECTION 6
Cal = full(HDR.Calib(2:end,:)); Cal = Cal - diag(diag(Cal));
if any(Cal(:))
fprintf(HDR.FILE.stderr,'Calibration is not a diagonal matrix.\n\tThis can result in incorrect scalings.\n');
end;
Cal = full(diag(HDR.Calib(2:end,:)));
if any(Cal~=Cal(1)),
fprintf(HDR.FILE.stderr,'scaling information is not equal for all channels; \n\tThis is not supported by SCP and can result in incorrect scalings.\n');
end;
[tmp,scale1] = physicalunits(HDR.PhysDim{1});
[tmp,scale2] = physicalunits('nV');
b = [SectIdHdr, s2b(round(Cal(1)*scale1/scale2)), s2b(round(1e6/HDR.SampleRate)), 0, 0];
for k = 1:HDR.NS,
b = [b, s2b(HDR.SPR*HDR.NRec*2)];
end;
data = HDR.data(:);
data = data + (data<0)*2^16;
tmp = s2b(round(data))';
b = [b,tmp(:)'];
else
b = [];
end;
if (length(b)>0)
if mod(length(b),2), % align to multiple of 2-byte blocks
b = [b,0];
end;
if (length(b)<16), fprintf(HDR.FILE.stderr,'section header %i less then 16 bytes %i', K,length(b)); end;
b(3:4) = s2b(K);
b(5:8) = s4b(length(b));
%b(1:2)= s4b(crc);
b(1:2) = s2b(crc16eval(b(3:end)));
% section 0: startpos in pointer field
B(22+K*10+(7:10)) = s4b(POS+1);
end;
B = [B(1:POS),b];
% section 0 pointer field
B(22+K*10+(1:2)) = s2b(K);
B(22+K*10+(3:6)) = s4b(length(b)); % length
POS = POS + length(b);
end
B(3:6) = s4b(POS); % length of file
B(7:8) = s2b(crc16eval(B(9:22+NSections*10))); % CRC of Section 0
B(1:2) = s2b(crc16eval(B(3:end)));
% fwrite(fid,crc,'int16');
count = fwrite(fid,B,'uchar');
fclose(fid);
end
end %% scpopen
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Auxillary functions
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function b2 = s2b(i)
% converts 16bit into 2 bytes
b2 = [bitand(i,255),bitand(bitshift(i,-8),255)];
return;
end %%%%% s2b %%%%%
function b4 = s4b(i)
% converts 32 bit into 4 bytes
b4 = [s2b(bitand(i,2^16-1)),s2b(bitand(bitshift(i,-16),2^16-1)) ];
return;
end %%%%% s4b %%%%%
function T = makeSubTree(T,bc,len,val)
if (len==0)
T.idxTable = val;
return
end;
if 1,
b = bitand(bc,1)+1;
if ~isfield(T,'branch') T.branch = {[],[]}; end;
T.branch{b} = makeSubTree(T.branch{b},bitshift(bc,-1),len-1,val);
else
if bitand(bc,1)
if ~isfield(T,'node1'),T.node1 = []; end;
T.node1 = makeSubTree(T.node1,bitshift(bc,-1),len-1,val);
else
if ~isfield(T,'node0'),T.node0 = []; end;
T.node0 = makeSubTree(T.node0,bitshift(bc,-1),len-1,val);
end;
end,
return;
end %%%%% makeSubTree %%%%%
function T = makeTree(HT)
T = [];
for k1 = 1:size(HT,1)
for k2 = 1:HT(k1,1) % CodeLength
T = makeSubTree(T,HT(k1,5),HT(k1,1),k1);
end;
end;
%save matlab T,pause
return;
end %%%%% makeTree %%%%%
function outdata = DecodeHuffman(HTrees,HTs,indata,outlen)
ActualTable = 1;
k1 = 1; r=0;
k2 = 0;
if ((outlen>0) && isfinite(outlen))
outdata = repmat(NaN,outlen,1);
else
outdata = [0;0]; %% make it a column vector
end;
Node = HTrees{ActualTable};
while ((k1*8+r <= 8*length(indata)) && (k2<outlen))
if ~isfield(Node,'idxTable')
r = r+1; if (r>8), k1=k1+1; r=1; end;
if 1,
b = bitand(bitshift(indata(k1),r-8),1)+1;
if ~isempty(Node.branch{b})
Node = Node.branch{b};
else
fprintf(2,'Warning SCPOPEN: empty node in Huffman table\n');
end;
else
if bitand(bitshift(indata(k1),r-8),1)
if isfield(Node,'node1')
Node = Node.node1;
else
fprintf(2,'Warning SCPOPEN: empty node in Huffman table\n');
end;
else
if isfield(Node,'node0')
Node = Node.node0;
else
fprintf(2,'Warning SCPOPEN: empty node in Huffman table\n');
end;
end;
end;
end;
if isfield(Node,'idxTable')
TableEntry = HTs{ActualTable}(Node.idxTable,:);
dlen = TableEntry(2)-TableEntry(1);
if (~TableEntry(3))
ActualTable = TableEntry(4);
elseif (dlen~=0)
acc = 0;
for k3 = 1:dlen,
r = r+1; if (r>8), k1=k1+1; r=1; end;
acc = 2*acc + bitand(bitshift(indata(k1),r-8), 1);
end;
if (acc>=bitshift(1,dlen-1))
acc = acc - bitshift(1,dlen);
end;
k2 = k2+1;
outdata(k2) = acc;
else
k2 = k2+1;
outdata(k2)=TableEntry(4);
end;
Node = HTrees{ActualTable};
end;
end;
return;
end %%%%%%%% DecodeHuffman %%%%%%%%%
function crc16 = crc16eval(D)
% CRC16EVAL cyclic redundancy check with the polynomiaL x^16+x^12+x^5+1
% i.e. CRC-CCITT http://en.wikipedia.org/wiki/Crc16
D = uint16(D);
crchi = 255;
crclo = 255;
t = '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';
crc16htab = hex2dec(reshape(t,2,length(t)/2)');
t = '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';
crc16ltab = hex2dec(reshape(t,2,length(t)/2)');
for k = 1:length(D),
ix = double(bitxor(crchi,D(k)))+1;
crchi = bitxor(crclo,crc16htab(ix));
crclo = crc16ltab(ix);
end;
crc16 = crchi*256+crclo;
end %%%%% crc16eval %%%%%
|
github
|
lcnbeapp/beapp-master
|
openxml.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/biosig/private/openxml.m
| 13,850 |
utf_8
|
a2522f85226716568c1d40ee7e6666f6
|
function [HDR]=openxml(arg1,CHAN,arg4,arg5,arg6)
% OPENXML reads XML files and tries to extract biosignal data
%
% This is an auxilary function to SOPEN.
% Use SOPEN instead of OPENXML.
%
%
% HDR = openxml(HDR);
%
% HDR contains the Headerinformation and internal data
%
% see also: SOPEN, SREAD, SSEEK, STELL, SCLOSE, SWRITE, SEOF
% 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 3
% of the License, or (at your option) any later version.
% $Id$
% Copyright 2006,2007,2008 by Alois Schloegl <[email protected]>
% This is part of the BIOSIG-toolbox http://biosig.sf.net/
if ischar(arg1);
HDR.FileName = arg1;
HDR.FILE.PERMISSION = 'r';
else
HDR = arg1;
end;
%if strncmp(HDR.TYPE,'XML',3),
% if any(HDR.FILE.PERMISSION=='r'),
fid = fopen(HDR.FileName,HDR.FILE.PERMISSION,'ieee-le');
s = char(fread(fid,[1,1024],'char'));
if all(s(1:2)==[255,254]) & all(s(4:2:end)==0)
HDR.TYPE='XML-UTF16';
elseif ~isempty(findstr(char(s),'?xml version'))
HDR.TYPE='XML-UTF8';
end;
fseek(fid,0,'bof');
if strcmp(HDR.TYPE,'XML-UTF16'),
magic = char(fread(fid,1,'uint16'));
HDR.XML = char(fread(fid,[1,inf],'uint16'));
elseif strcmp(HDR.TYPE,'XML-UTF8'),
HDR.XML = char(fread(fid,[1,inf],'uint8'));
end;
fclose(fid);
HDR.FILE.FID = fid;
if 0, ~exist('xmlstruct')
warning('XML toolbox missing')
end;
if 1,
HDR.XMLstruct = xmlstruct(HDR.XML,'sub');
HDR.XMLlist = xmlstruct(HDR.XML);
end;
try
XML = xmltree(HDR.XML);
XML = convert(XML);
HDR.XML = XML;
HDR.TYPE = 'XML';
catch
fprintf(HDR.FILE.stderr,'ERROR SOPEN (XML): XML-toolbox missing or invalid XML file.\n');
return;
end;
tmp = fieldnames(HDR.XML);
if any(strmatch('PatientDemographics',tmp)) & any(strmatch('TestDemographics',tmp)) & any(strmatch('RestingECGMeasurements',tmp)) & any(strmatch('Diagnosis',tmp)) & any(strmatch('Waveform',tmp)),
% GE-Marquette FDA-XML MAC5000
HDR.Patient.ID = HDR.XML.PatientDemographics.PatientID;
tmp = HDR.XML.PatientDemographics.Gender;
HDR.Patient.Sex = 2*(upper(tmp(1))=='F') + (upper(tmp(1))=='M');
HDR.Patient.Name = [HDR.XML.PatientDemographics.PatientLastName,', ',HDR.XML.PatientDemographics.PatientFirstName];
tmp = HDR.XML.TestDemographics.AcquisitionDate;
tmp(tmp=='-') = ' ';
HDR.T0([3,2,1])=str2double(tmp);
tmp = HDR.XML.TestDemographics.AcquisitionTime;
tmp(tmp==':') = ' ';
HDR.T0(4:6) = str2double(tmp);
HDR.NS = str2double(HDR.XML.Waveform.NumberofLeads);
HDR.SampleRate = str2double(HDR.XML.Waveform.SampleBase);
HDR.Filter.LowPass = str2double(HDR.XML.Waveform.LowPassFilter)*ones(1,HDR.NS);
HDR.Filter.HighPass = str2double(HDR.XML.Waveform.HighPassFilter)*ones(1,HDR.NS);
HDR.Filter.Notch = str2double(HDR.XML.Waveform.ACFilter)*ones(1,HDR.NS);
HDR.NRec = 1;
HDR.SPR = 1;
for k = 1:HDR.NS,
CH = HDR.XML.Waveform.LeadData{k};
HDR.AS.SPR(k) = str2double(CH.LeadSampleCountTotal);
HDR.SPR = lcm(HDR.SPR,HDR.AS.SPR(k));
HDR.Cal(k) = str2double(CH.LeadAmplitudeUnitsPerBit);
HDR.PhysDim{k} = CH.LeadAmplitudeUnits;
HDR.Label{k} = CH.LeadID;
t = radix64d(CH.WaveFormData);
t = 256*t(2:2:end) + t(1:2:end);
t = t - (t>=(2^15))*(2^16);
HDR.data(:,k) = t(:);
end;
HDR.TYPE = 'native';
elseif any(strmatch('component',tmp))
% FDA-XML Format
tmp = HDR.XML.component.series.derivation;
if isfield(tmp,'Series');
tmp = tmp.Series.component.sequenceSet.component;
else % Dovermed.CO.IL version of format
tmp = tmp.derivedSeries.component.sequenceSet.component;
end;
HDR.NS = length(tmp)-1;
HDR.NRec = 1;
HDR.Cal = 1;
HDR.PhysDim = {' '};
HDR.SampleRate = 1;
HDR.TYPE = 'XML-FDA'; % that's an FDA XML file
elseif any(strmatch('dataacquisition',tmp)) & any(strmatch('reportinfo',tmp)) & any(strmatch('patient',tmp)) & any(strmatch('documentinfo',tmp)),
% SierraECG 1.03 *.open.xml from PHILIPS
HDR.SampleRate = str2double(HDR.XML.dataacquisition.signalcharacteristics.samplingrate);
HDR.NS = str2double(HDR.XML.dataacquisition.signalcharacteristics.numberchannelsvalid);
HDR.Cal = str2double(HDR.XML.reportinfo.reportgain.amplitudegain.overallgain);
HDR.PhysDim = {'uV'};
HDR.Filter.HighPass = str2double(HDR.XML.reportinfo.reportbandwidth.highpassfiltersetting);
HDR.Filter.LowPass = str2double(HDR.XML.reportinfo.reportbandwidth.lowpassfiltersetting);
HDR.Filter.Notch = str2double(HDR.XML.reportinfo.reportbandwidth.notchfiltersetting);
t = HDR.XML.reportinfo.reportformat.waveformformat.mainwaveformformat;
k = 0;
HDR.Label={};
while ~isempty(t),
[s,t] = strtok(t,' ');
k = k+1;
HDR.Label{k, 1} = [s,' '];
end;
HDR.Patient.Id = str2double(HDR.XML.patient.generalpatientdata.patientid);
tmp = HDR.XML.patient.generalpatientdata.age;
if isfield(tmp,'years'),
HDR.Patient.Age = str2double(tmp.years);
end
if isfield(tmp,'dateofbirth')
tmp = tmp.dateofbirth;
tmp(tmp=='-')=' ';
HDR.Patient.Birthday([6,5,4]) = str2double(tmp);
end;
tmp = HDR.XML.patient.generalpatientdata.sex;
HDR.Patient.Sex = strncmpi(tmp,'Male',1) + strncmpi(tmp,'Female',1)*2;
HDR.Patient.Weight = str2double(HDR.XML.patient.generalpatientdata.weight.kg);
HDR.Patient.Height = str2double(HDR.XML.patient.generalpatientdata.height.cm);
HDR.VERSION = HDR.XML.documentinfo.documentversion;
HDR.TYPE = HDR.XML.documentinfo.documenttype;
elseif any(strmatch('component',tmp)) & any(strmatch('reportinfo',tmp)) & any(strmatch('patient',tmp)) & any(strmatch('documentinfo',tmp)),
% FDA-XML Format
tmp = HDR.XML.component.series.derivation;
if isfield(tmp,'Series');
tmp = tmp.Series.component.sequenceSet.component;
else % Dovermed.CO.IL version of format
tmp = tmp.derivedSeries.component.sequenceSet.component;
end;
HDR.NS = length(tmp)-1;
HDR.NRec = 1;
HDR.Cal = 1;
HDR.PhysDim = {' '};
HDR.SampleRate = 1;
HDR.TYPE = 'XML-FDA'; % that's an FDA XML file
elseif any(strmatch('StripData',tmp)) & any(strmatch('ClinicalInfo',tmp)) & any(strmatch('PatientInfo',tmp)) & any(strmatch('ArrhythmiaData',tmp)),
% GE Case8000 stress ECG
HDR.SampleRate = str2double(HDR.XML.StripData.SampleRate);
tmp = HDR.XML.ClinicalInfo.ObservationDateTime;
HDR.T0 = [str2double(tmp.Year), str2double(tmp.Month), str2double(tmp.Day), str2double(tmp.Hour), str2double(tmp.Minute), str2double(tmp.Second)];
HDR.Patient.Id = HDR.XML.PatientInfo.PID;
HDR.Patient.Name = 'X'; % [HDR.XML.PatientInfo.Name, ', ', HDR.XML.PatientInfo.GivenName];
HDR.Patient.Age = str2double(HDR.XML.PatientInfo.Age);
tmp = HDR.XML.PatientInfo.Gender;
HDR.Patient.Sex = any(tmp(1)=='Mm') + any(tmp(1)=='Ff')*2;
HDR.Patient.Height = str2double(HDR.XML.PatientInfo.Height);
HDR.Patient.Weight = str2double(HDR.XML.PatientInfo.Weight);
tmp = HDR.XML.PatientInfo.BirthDateTime;
HDR.Patient.Birthday = [str2double(tmp.Year), str2double(tmp.Month), str2double(tmp.Day),0,0,0];
tmp = HDR.XML.StripData.Strip;
HDR.NS = length(tmp{1}.WaveformData);
tmax = str2double(tmp{end}.Time.Minute)*60 + str2double(tmp{end}.Time.Second)+10;
data = repmat(NaN,tmax*HDR.SampleRate,HDR.NS);
for k = 1:length(tmp);
t = HDR.SampleRate*(str2double(tmp{k}.Time.Minute)*60 + str2double(tmp{k}.Time.Second));
for k2 = 1:HDR.NS,
x = str2double(tmp{k}.WaveformData{k2});
data(t+1:t+length(x),k2)=x(:);
end;
end;
tmp = HDR.XML.ArrhythmiaData.Strip;
for k = 1:length(tmp);
t = HDR.SampleRate*(str2double(tmp{k}.Time.Minute)*60 + str2double(tmp{k}.Time.Second));
for k2 = 1:HDR.NS,
x = str2double(tmp{k}.WaveformData{k2});
data(t+1:t+length(x),k2)=x(:);
end;
end;
HDR.data = data - 2^12*(data>2^11);
HDR.TYPE = 'native';
HDR.NRec = 1;
HDR.SPR = size(HDR.data,1);
HDR.Calib = sparse(2:HDR.NS,1:HDR.NS,1);
HDR.FLAG.UCAL = 1;
else
fprintf(HDR.FILE.stderr,'Warning SOPEN (XML): File %s is not supported.\n',HDR.FileName);
return;
end
try
tmp=HDR.XML.componentOf.timepointEvent.componentOf.subjectAssignment.subject.trialSubject.subjectDemographicPerson.name;
HDR.Patient.Name = sprintf('%s, %s',tmp.family, tmp.given);
catch
end;
HDR.Calib = sparse(2:HDR.NS+1,1:HDR.NS,HDR.Cal);
HDR.FILE.OPEN = 1;
HDR.FILE.POS = 0;
% end;
%end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Auxillary functions
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function y = radix64d(x);
% RADIX64D - decoding of radix64 encoded sequence
% 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 (at your option) 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 Place - Suite 330, Boston, MA 02111-1307, USA.
% $Id$
% (C) 2006 by Alois Schloegl <[email protected]>
% This is part of the BIOSIG-toolbox http://biosig.sf.net/
global BIOSIG_GLOBAL
if ~isfield(BIOSIG_GLOBAL,'R64E');
BIOSIG_GLOBAL.R64E = ['A':'Z','a':'z','0':'9','+','/'];
BIOSIG_GLOBAL.R64D = zeros(256,1)-1;
for k = 1:length(BIOSIG_GLOBAL.R64E),
BIOSIG_GLOBAL.R64D(BIOSIG_GLOBAL.R64E(k)) = k-1;
end;
end;
% http://www.faqs.org/rfcs/rfc2440.html
t = BIOSIG_GLOBAL.R64D(x);
t = [t(t>=0); zeros(3,1)];
N = floor(length(t)/4);
t = reshape(bitand(t(1:N*4),2^6-1),4,N);
y(1,:) = bitshift(t(1,:),2) + bitshift(t(2,:),-4);
y(2,:) = bitshift(mod(t(2,:),16),4) + bitshift(t(3,:),-2);
y(3,:) = bitshift(mod(t(3,:),4),6) + t(4,:);
y = y(:)';
y = y(1:end-sum(x=='=')); % remove possible pad characters
|
github
|
lcnbeapp/beapp-master
|
matread.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/biosig/private/matread.m
| 10,217 |
utf_8
|
0c42f4955d1ed526f04022f79b06fd87
|
function [HDR,data,t]=matread(HDR,arg2,idxlist)
% MATRREAD Loads (parts of) data stored in Matlab-format
%
% [HDR,data,timeindex]=matread(HDR,block_number, [startidx, endidx])
% This is the recommended use for Matlab-files generated from ADICHT data
% Before using MATREAD, HDR=MATOPEN(filename, 'ADI', ...) must be applied.
%
% [HDR,data,timeindex]=matread(HDR,Variable_Name, [startidx, endidx])
% can be used for other Matlab4 files.
% Variable name is a string which identifies a Matlab Variable.
% Before using MATREAD, HDR=MATOPEN(filename, 'r', ...) must be applied.
%
% see also: EEGREAD, FREAD, EEGOPEN, EEGCLOSE
% $Revision$
% $Id$
% Copyright (c) 1997-2003 by Alois Schloegl
% [email protected]
% This library is free software; you can redistribute it and/or
% modify it under the terms of the GNU Library General Public
% License as published by the Free Software Foundation; either
% Version 2 of the License, or (at your option) any later version.
%
% This library 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
% Library General Public License for more details.
%
% You should have received a copy of the GNU Library General Public
% License along with this library; if not, write to the
% Free Software Foundation, Inc., 59 Temple Place - Suite 330,
% Boston, MA 02111-1307, USA.
CHt=[];
if ~ischar(arg2)
if strcmp(HDR.TYPE,'ADI'); %HDR.ADI.Mode,
BlockNo=abs(arg2);
if isempty(BlockNo), BlockNo=1:length(HDR.ADI.DB); end;
if (isinf(BlockNo) | (length(BlockNo)~=1))
if nargout<3,
fprintf(2,'Warning MATREAD: missing output argument, time information cannot be returned\n');
end;
CHd=HDR.ADI.DB(BlockNo);
CHt=HDR.ADI.TB(BlockNo);
elseif ((BlockNo<1) | BlockNo>length(HDR.ADI.DB)),
fprintf(2,'Warning MATREAD: tried to read block %i, but only %i blocks in file %s\n',BlockNo,length(HDR.ADI.DB),HDR.FileName);
CHd=[];CHt=[];
else
CHd=HDR.ADI.DB(BlockNo);
CHt=HDR.ADI.TB(BlockNo);
end;
else
CHd=arg2;
fprintf(2,'Warning MATREAD: Variable identified by number\n');
end;
else %if ischar(arg2)
CHd=find(strcmp(arg2,{HDR.Var.Name}));
if isempty(CHd)
%HDR.ErrNo=-1;
fprintf(2,'Warning MATREAD: Variable %s not found\n',arg2);
data=[];
return;
end;
end;
if length(CHd)>1
fprintf(2,'Warning MATREAD: Only one block/variable can be read\n');
CHd=CHd(1);
end;
if nargin<4, end;
if nargin<3,
idxlist=[1,HDR.Var(CHd).Size(2)];
else
if ~all(isfinite(idxlist)),
idxlist=[1,HDR.Var(CHd).Size(2)];
end;
end
% if length(idxlist)<2,idxlist=idxlist*[1 1]; end;
if (idxlist(1)<1) %| (idxlist(length(idxlist))>HDR.Var(CHd).Size(2))),
fprintf(2,'Warning MATREAD #%i: Invalid File Position %f-%f\n',CHd,[idxlist(1)-1,idxlist(length(idxlist))]);
idxlist(1)=1;
%return;
end;
if idxlist(length(idxlist))>HDR.Var(CHd).Size(2),
fprintf(2,'Warning MATREAD #%i: endidx exceeds block length %f-%f\n',CHd,[HDR.Var(CHd).Size(2),idxlist(length(idxlist))]);
idxlist=[idxlist(1),HDR.Var(CHd).Size(2)];
%return;
end;
if 0; %((idxlist(1)<1) | (idxlist(length(idxlist))>HDR.Var(CHd).Size(2))),
fprintf(2,'ERROR MATREAD #%i: Invalid File Position %f-%f\n',CHd,[idxlist(1)-1,idxlist(length(idxlist))]);
return;
end;
Pos = (idxlist(1)-1) * HDR.Var(CHd).Size(1) * HDR.Var(CHd).SizeOfType;
Len = min(idxlist(length(idxlist)), HDR.Var(CHd).Size(2)) - idxlist(1) + 1;
fseek(HDR.FILE.FID, round(HDR.Var(CHd).Pos + Pos), -1); % round must be explicite, otherwise fseek does incorrect rounding
[msg,errno] = ferror(HDR.FILE.FID);
if errno, fprintf(2,'ERROR MATREAD: FSEEK does not work Pos=%f\n%s',HDR.Var(CHd).Pos+Pos,msg); return; end;
count = 0;
if ~any(CHd==HDR.ADI.DB), % for non-data blocks
data=repmat(nan,HDR.Var(CHd).Size(1),Len);
while (count<Len),
cc = min(2^12,Len-count);
% [CHd,idxlist(1),idxlist(length(idxlist)),Len,HDR.Var(CHd).Size(2)]
[dta,c] = readnextblock4(HDR.FILE.FID,HDR.Var(CHd),cc);
data(:,count+(1:size(dta,2))) = dta;
count = count + cc;
end;
else
BLOCKSIZE=64*3*25*4; % 2^12; % You can change this for optimizing on your platform
%HDR=mat_setfilter(HDR,BlockNo);% set filters for this block
for k=1:max(HDR.SIE.InChanSelect),
if k <= HDR.NS,
if HDR.SIE.FILT==1;
[tmp,HDR.Filter.Z(:,k)] = filter(HDR.Filter.B,HDR.Filter.A,zeros(length(HDR.Filter.B),1));
HDR.FilterOVG.Z = HDR.Filter.Z;
end;
end;
end;
if isfield(HDR,'iFs') & (HDR.iFs>0) & (HDR.iFs<inf),
Fs=HDR.SampleRate(find(CHd==HDR.ADI.DB))/HDR.iFs;
data = repmat(nan,ceil(Len*size(HDR.SIE.T,2)/size(HDR.SIE.T,1)/Fs),length(HDR.SIE.ChanSelect));
else
Fs=1;
data = repmat(nan,ceil(Len*size(HDR.SIE.T,2)/size(HDR.SIE.T,1)),length(HDR.SIE.ChanSelect));
end;
count=0; count2=0;
while (count2<Len),
cc = min(BLOCKSIZE,Len-count2);
% [Len, count2, count, Fs, (Len-count2)*Fs, cc]
% [CHd,idxlist(1),idxlist(length(idxlist)),Len,HDR.Var(CHd).Size(2)]
[dta,c] = readnextblock4(HDR.FILE.FID,HDR.Var(CHd),cc);
% ferror(HDR.FILE.FID)
% [Len,cc,count,BLOCKSIZE,HDR.FILE.Pos,ftell(HDR.FILE.FID)],
[nc,cc] = size(dta);
% if any postprocessing, resample to internal Sampling rate iFs=1000Hz)
if Fs~=1,
dta=rs(dta',Fs,1)'; %**************************************************************************************1
end;
if nc~=HDR.NS, % reorganizing of channels
dta=sparse(find(HDR.ADI.index{arg2}),1:sum(HDR.ADI.index{arg2}>0),1)*dta;
dta(find(~HDR.ADI.index{arg2}),:)=nan;
end;
for k = sort(HDR.SIE.InChanSelect), %1:size(data,2);
%k=HDR.SIE.chanselect(K),
if k<=HDR.NS,
if HDR.SIE.FILT,
[dta(k,:),HDR.Filter.Z(:,k)]=filter(HDR.Filter.B,HDR.Filter.A,dta(k,:),HDR.Filter.Z(:,k));
end;
end;
end;
if HDR.SIE.RS,
dta = rs(dta(HDR.SIE.ChanSelect,:)',HDR.SIE.T); %RS% ***********************************************2
else
dta = dta(HDR.SIE.ChanSelect,:)';
end;
data(count+(1:size(dta,1)),:) = dta;
count = count + size(dta,1);
count2 = count2 + cc;
end;
%%%%% Overflow Detection %%%%%
if HDR.SIE.TH,
for k=1:find(~isnan(sum(HDR.SIE.THRESHOLD,2))),
ch = phrchan(HDR.FILE.Name);
tmp = (data(:,k)<HDR.SIE.THRESHOLD(1,k)) | (data(:,ch)>HDR.SIE.THRESHOLD(2,k));
data(tmp,k) = NaN;
end;
end;
% load time vector
if nargout>2,
if ~isempty(CHt),
fseek(HDR.FILE.FID, round(HDR.Var(CHt).Pos + (idxlist(1)-1)*HDR.Var(CHt).SizeOfType),-1);
[t,c]=readnextblock4(HDR.FILE.FID,HDR.Var(CHt),idxlist(length(idxlist))-min(idxlist)+1);
if length(t)>1,
tmp=diff(t);
if any(abs(tmp-tmp(length(tmp)))>1000*eps)
fprintf(2,'Warning %s: Sampling is not equally spaced in %s [%i,%i]\n',mfilename,HDR.FileName,idxlist(1),idxlist(length(idxlist)));
end;
end;
%%%%% Delay of Filtering
if HDR.SIE.FILT,
t = t' + HDR.Filter.Delay;
else
t = t';
end;
% if any postprocessing, resample to internal Sampling rate iFs=1000Hz)
if isfield(HDR,'iFs') & (HDR.iFs>0) & (HDR.iFs<inf),
Fs=HDR.SampleRate(find(CHd==HDR.ADI.DB))/HDR.iFs;
if Fs~=1,
t=rs(t,Fs,1); %*********************************************************************3
end;
end;
%%%%% Resampling of the time
if HDR.SIE.RS,
t=rs(t,HDR.SIE.T); %RS% %******************************************************************4
end;
else
fprintf(2,'Warning %s: timeindex is not available \n',mfilename);
end;
end;
end;
function [data,c]=readnextblock4(fid,VarInfo,Len),
dt=VarInfo.Type(3);
if dt==0, type = 'float64';
elseif dt==6, type = 'uint8';
elseif dt==4, type = 'uint16';
elseif dt==3, type = 'int16';
elseif dt==2, type = 'int32';
elseif dt==1, type = 'float32';
else
fprintf(2,'Error %s: unknown data type\n',mfilename);
return;
end;
[data,c]=fread(fid,[VarInfo.Size(1),Len],type);
if VarInfo.Type(5);
%HDR.ErrNo=-1;
fprintf(2,'Warning %s: imaginary data not test\n',mfilename);
[di,c]=fread(fid,[VarInfo.Size(1),Len],type);
data=data+i*di;
end;
if VarInfo.Type(4)==1,data=char(data); end;
|
github
|
lcnbeapp/beapp-master
|
GE_createSPMmat.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/GE_createSPMmat.m
| 1,480 |
utf_8
|
9da4628d724922838247f14727e25722
|
%%%%%%%%%%%%%%%%%%%%%%%%
% %
% Write SPM mat file %
% %
%%%%%%%%%%%%%%%%%%%%%%%%
function M = GE_createSPMmat(im_hdr, scandir)
%
% Put the appropriate translations and rotations to the M matrix
% given the information in the image header and the direction of
% acquisition
%
% S. Inati
% Dartmouth College
% Apr. 2001
%
% The conversion from pixels to mm
Dims = diag( [im_hdr.pixsize_X, ...
im_hdr.pixsize_Y, ...
im_hdr.slthick + im_hdr.scanspacing ]);
% Compute the coordinate system in the image plane
tlhc = [ im_hdr.tlhc_R; im_hdr.tlhc_A; im_hdr.tlhc_S ]; % Top Left Hand Corner of Image
trhc = [ im_hdr.trhc_R; im_hdr.trhc_A; im_hdr.trhc_S ]; % Top Right Hand Corner of Image
brhc = [ im_hdr.brhc_R; im_hdr.brhc_A; im_hdr.brhc_S ]; % Bottom Right Hand Corner of Image
x = trhc - tlhc; x = x./sqrt(x'*x); % xhat
y = trhc - brhc; y = y./sqrt(y'*y); % yhat
% The normal to the plane
norm = [ im_hdr.norm_R; im_hdr.norm_A; im_hdr.norm_S ];
% The directional normal
z = scandir * norm; % zhat
% Build the M matrix for SPM
% M takes a voxel from the image and gives it a coordinate in mm
% On the scanner the voxels start in the top left hand corner of the
% first image. In SPM they start in the bottom left hand corner,
% so flip y and set the origin to tlhc.
% NB: The voxel (1,1,1) should have position tlhc
Rot = [x, -y, z];
M = eye(4);
M(1:3,1:3) = Rot * Dims;
M(1:3,4) = tlhc - Rot*Dims*[1;1;1];
return
|
github
|
lcnbeapp/beapp-master
|
NewCs.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/NewCs.m
| 20,018 |
utf_8
|
02f4f3b94b14be6adab8ee52224b2dc3
|
function [cs] = NewCs(Name, win, p1, p2, p3, p4, p5)
%
% [cs] = NewCs (Name, Con, P1, P2)
%
%Purpose:
% Create a command structure for passing to TellAfni
%
%
%Input Parameters:
% Name: Name of command, see AFNI's README.driver for all possibilities
% Example: SET_THRESHOLD
% To see a list of commands, try the function TellAfni_Commands
% To start AFNI, use the special Name: 'start_afni'
% Con : Index of controller where command is applied.
% Choose from 'A' to 'J'. Default if win = '' is controller 'A'
% P1 : First parameter passed to command. This can include the
% controller index in the form A. See AFNI's README.driver
% for information and Test_TellAfni for examples.
% P2 : All other parameters to pass to command. This would include
% any second parameters plus options.
%Output Parameters:
% cs : Returned structure to feed to AFNI with TellAfni
% .err: Error flag
% .w : AFNI controller
% .c : AFNI command (Name)
% .v : AFNI command value
%
%
%More Info :
% TellAfni
% TellAfni_Commands
% Test_TellAfni
% AFNI's README.driver
%
% Author : Ziad Saad
% Date : Tue Dec 6 12:05:09 EST 2005
% SSCC/NIMH/ National Institutes of Health, Bethesda Maryland
%Define the function name for easy referencing
FuncName = 'NewCs';
%Debug Flag
DBG = 1;
%initailize return variables
cs.err = 1;
cs.c = '';
cs.v = '';
cs.w = '';
np = nargin - 2; %number of p parameters
if (np == -1), win = ''; end
if (np == 0), p1 = ''; p2 = ''; p3 = ''; p4 = ''; p5 = ''; end
if (np == 1), p2 = ''; p3 = ''; p4 = ''; p5 = ''; end
if (np == 2), p3 = ''; p4 = ''; p5 = ''; end
if (np == 3), p4 = ''; p5 = ''; end
if (np == 4), p5 = ''; end
if (~isempty(win)),
win = upper(win);
uwin = win;
else
win = 'A';
uwin = '';
end
if (length(win) ~= 1 | win < 'A' | win > 'J'),
fprintf(2,'Bad window specifer %s\n', win);
return;
end
Name = upper(Name);
switch (Name),
case 'START_AFNI',
cs.c = sprintf('%s', Name);
if (~isempty(p1)),
if (NewCs_CheckFnames(p1) > 0),
cs.v = p1;
else
fprintf(2,'Command <%s> requires an existing directory or files for the first parameter\nSomething in %s not found\n', Name, p1)
end
end
cs.v = sprintf('%s %s', cs.v, p2);;
case 'ADD_OVERLAY_COLOR',
if (np ~= 2 | isnumeric(p1) | isnumeric(p2)),
fprintf(2,'Command <%s> requires two string parameters.\nHave %d in %s\n',...
Name, np);
return;
end
cs.c = Name;
cs.w = win;
cs.v = sprintf('%s %s', p1, p2);
case 'SET_THRESHOLD',
if (np < 1 | np > 2),
fprintf(2,'Command <%s> needs 1 or 2 parameters.\nHave %d\n', Name, np);
return;
end
if (~isnumeric(p1)),
if (upper(p1(1)) >= 'A' & upper(p1(1)) <= 'J'),
win = p1(1);
p1 = p1(2:length(p1));
end
p1 = str2double(p1);
end
if (p1 < 0 | p1 >= 1.0),
fprintf(2,'Command <%s> has a bad value for threshold (%s).\nThreshold must be between 0 and 1\n',...
Name, p1);
return;
end
if (np == 2),
if (p2 < 0 | p2 > 4),
fprintf(2,'Command <%s> has a bad value for decimal (%f).\nDecimal must be between 0 and 4\n',...
cs.c, p2);
end
return;
end
cs.v = sprintf('%c.%d %d', win, p1*10000, p2);
cs.w = win;
cs.c = Name;
case 'SET_THRESHNEW',
val = p1;
isp = '';
if (np == 1), dec = '';
elseif (np==2),
if (~isempty(find(p2 == '*'))), dec = '*';
else dec = '';
end
if (~isempty(find(p2 == 'p'))),
isp = 'p';
if (val < 0.0 | val > 1.0),
fprintf(2,'Command <%s> requires pvalues between 0 and 1.0\n',...
Name);
end
else
isp = '';
end
end
cs.w = win;
cs.c = Name;
cs.v = sprintf('%c %.14f %c%c', cs.w, val, dec, isp);
case 'SET_PBAR_NUMBER',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter\n', Name);
return;
end
if (~isnumeric(p1)),
if (upper(p1(1)) >= 'A' & upper(p1(1)) <= 'J'),
win = p1(1);
p1 = p1(2:length(p1));
end
p1 = str2double(p1);
end
if (p1 < 2 | p1 > 20),
fprintf(2,'Command <%s> requires a number between 2 and 20\nHave %f', Name, p1);
return;
end
cs.w = win;
cs.c = Name;
cs.v = sprintf('%c.%d', cs.w, p1);
case 'SET_PBAR_SIGN',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter\n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
if (p1(1) ~= '+' & p1(1) ~= '-'),
fprintf(2,'parameter must be either + or -\n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s', win, p1);
case 'SET_PBAR_ALL',
if (np ~= 2),
fprintf(2,'Command <%s> requires 2 parameters\n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
ps = p1(1); p1 = p1(2:length(p1));
if (ps ~= '+' & ps ~= '-'),
fprintf(2,'Missing sign for pbar\n', Name);
return;
end
ncol = str2num(p1);
if (ncol < 1 | ncol > 99),
fprintf(2,'Command <%s> needs num between 1 and 99\n', Name);
return;
end
if (ncol < 99),
%find out how many colors are specified in p2
if (WordCount(p2) ~= ncol),
fprintf(2,'Command <%s>: Mismatch between num (%d) and number of val=color strings (%d)\n', Name, ncol, WordCount(p2));
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%c%d %s', win, ps, ncol, p2);
else
%check on the topval
np2 = WordCount(p2);
if (np2 < 2 ),
fprintf(2,'Command <%s> needs 2 parameters in second string (topval colorscale_name)\n', Name);
return;
end
[err, topval] = GetWord(p2,1,' ');
topval = str2num(topval);
if (topval <= 0),
fprintf(2,'Command <%s> needs a positive topval\n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%c99 %s', win, ps, p2);
end
case 'PBAR_ROTATE',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter\n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
if (p1(1) ~= '+' & p1(1) ~= '-'),
fprintf(2,'parameter must be either + or -\n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s', win, p1);
case 'DEFINE_COLORSCALE',
if (np ~= 2),
fprintf(2,'Command <%s> requires 2 parametera\n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%s %s', p1, p2);
case 'SET_FUNC_AUTORANGE',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter\n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
if (p1(1) ~= '+' & p1(1) ~= '-'),
fprintf(2,'parameter must be either + or -\n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s', win, p1);
case 'SET_FUNC_RANGE',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter\n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
if (p1n < 0.0),
fprintf(2,'Command <%s> requires a positive parameter\n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%f', win, p1n);
case { 'SET_FUNC_VISIBLE', 'SEE_OVERLAY', 'SEE_FUNCTION'},
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter\n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
if (p1(1) ~= '+' & p1(1) ~= '-'),
fprintf(2,'parameter must be either + or -\n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s', win, p1);
case 'SET_FUNC_RESAM',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter\n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
[err,l1] = GetWord(p1,1,'.');
if (isempty(l1)),
fprintf(2,'Command <%s> has empty parameter\n', Name);
return;
end
err = NewCs_OKresam(l1);
if (err),
fprintf(2,'Function resampling mode %s not recognized.\nChoose from:\n%s\n',...
l1, NewCs_OKresam());
return;
end
[err, l2] = GetWord(p1,2,'.');
if (~isempty(l2)),
err = NewCs_OKresam(l2);
if (err),
fprintf(2,'Resampling mode %s not recognized.\nChoose from:\n%s\n',...
l2, NewCs_OKresam());
return;
end
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s.%s', win, l1, l2);
case 'OPEN_PANEL',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter\n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
err = NewCs_OKpanel(p1);
if (err),
fprintf(2,'Panel %s not recognized.\nChoose from:\n%s\n',...
p1, NewCs_OKpanel());
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s',win,p1);
case 'SYSTEM',
if (np < 1),
fprintf(2,'Command <%s> requires at least 1 parameter\n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%s %s', p1, p2);
case 'CHDIR',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter\n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%s', p1);
case 'RESCAN_THIS',
if (np > 1),
fprintf(2,'Command <%s> requires 1 parameter\n', Name);
return;
end
if (np),
if (p1(1) < 'A' | p1(1) > 'J'),
fprintf(2,'Command <%s> requires 1 parameter between A and J\n', Name);
return;
end
win = p1(1);
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c', win);
case {'SET_SESSION', 'SWITCH_SESSION', 'SWITCH_DIRECTORY'},
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter\n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s',win,p1);
case {'SET_SUBBRICKS','SET_SUB_BRICKS'},
if (np < 1),
fprintf(2,'Command <%s> requires at least 1 parameter\n', Name);
return;
end
if (np == 2), win = p1; p1 = p2; end
val = str2num(p1);
if (length(val) ~= 3),
fprintf(2,'Second string must contain 3 values.\n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c %d %d %d', win, val(1), val(2), val(3));
case {'SET_ANATOMY', 'SWITCH_ANATOMY', 'SWITCH_UNDERLAY'},
if (np < 1),
fprintf(2,'Command <%s> requires at least 1 parameter\n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
if (np == 2),
sb = str2num(p2);
if (length(sb) ~= 1),
fprintf(2,'Command <%s> requires one integer in the second parameter');
return;
end
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s %s', win, p1, p2);
case {'SET_FUNCTION', 'SWITCH_FUNCTION', 'SWITCH_OVERLAY'},
if (np < 1),
fprintf(2,'Command <%s> requires at least 1 parameter\n', Name);
return;
end
if (np == 2),
sb = str2num(p2);
if (length(sb) ~= 1 & length(sb) ~= 2),
fprintf(2,'Command <%s> requires one or two integers in the second parameter');
return;
end
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s %s', win, p1, p2);
case 'OPEN_WINDOW',
if (np < 1),
fprintf(2,'Command <%s> requires 1 parameter at least\n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
err = NewCs_OKwindowname(p1);
if (err),
fprintf(2,'Window name %s not recognized.\nChoose from:\n%s\n',...
p1, NewCs_OKwindowname());
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s %s', win, p1, p2);
case 'CLOSE_WINDOW',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter \n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
err = NewCs_OKwindowname(p1);
if (err),
fprintf(2,'Window name %s not recognized.\nChoose from:\n%s\n',...
p1, NewCs_OKwindowname());
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s', win, p1);
case 'SAVE_JPEG',
if (np ~= 2),
fprintf(2,'Command <%s> requires 2 parameters\n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
err = NewCs_OKwindowname(p1);
if (err),
fprintf(2,'Window name %s not recognized.\nChoose from:\n%s\n',...
p1, NewCs_OKwindowname());
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s %s', win, p1, p2);
case { 'SET_DICOM_XYZ', 'SET_SPM_XYZ', 'SET_IJK'},
if (np < 1),
fprintf(2,'Command <%s> requires at least 1 parameter\n', Name);
return;
end
if (np == 2), win = p1; p1 = p2; end
val = str2num(p1);
if (length(val) ~= 3),
fprintf(2,'Second string must contain 3 coordinates.\n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c %f %f %f', win, val(1), val(2), val(3));
case 'SET_XHAIRS',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter \n', Name);
return;
end
[win, p1, p1n] = NewCs_GetWin(p1, uwin);
err = NewCs_OKxhaircode(p1);
if (err),
fprintf(2,'Xhair code %s not recognized.\nChoose from:\n%s\n',...
p1, NewCs_OKxhaircode());
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%c.%s', win, p1);
case 'PURGE_MEMORY',
cs.w = win; cs.c = Name; cs.v = sprintf('%s', p1);
case 'QUIT',
cs.w = win; cs.c = Name; cs.v = '';
case 'SETENV',
cs.w = win; cs.c = Name; cs.v = sprintf('%s %s', p1, p2);
case 'REDISPLAY',
cs.w = win; cs.c = Name; cs.v = '';
case 'SLEEP',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter \n', Name);
return;
end
if (~isnumeric(p1)),
fprintf(2,'Command <%s> requires at 1 numeric value\n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%f', p1);
case 'OPEN_GRAPH_XY',
if (np ~= 2),
fprintf(2,'Command <%s> requires 2 parameters \n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%s %s', p1, p2);
case 'CLOSE_GRAPH_XY',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter \n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%s', p1);
case 'CLEAR_GRAPH_XY',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter \n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%s', p1);
case 'ADDTO_GRAPH_XY',
if (np ~= 2),
fprintf(2,'Command <%s> requires 2 parameters \n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%s %s', p1, p2);
case 'OPEN_GRAPH_1D',
if (np ~= 2),
fprintf(2,'Command <%s> requires 2 parameters \n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%s %s', p1, p2);
case 'CLOSE_GRAPH_1D',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter \n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%s', p1);
case 'CLEAR_GRAPH_1D',
if (np ~= 1),
fprintf(2,'Command <%s> requires 1 parameter \n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%s', p1);
case 'ADDTO_GRAPH_1D',
if (np ~= 2),
fprintf(2,'Command <%s> requires 2 parameters \n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%s %s', p1, p2);
case 'SET_GRAPH_GEOM',
if (np ~= 2),
fprintf(2,'Command <%s> requires 2 parameters \n', Name);
return;
end
cs.w = win; cs.c = Name; cs.v = sprintf('%s %s', p1, p2);
case 'MADMAG',
fprintf(2,'Command <%s> not implemented yet.\n', Name);
return;
otherwise,
fprintf(2,'Command <%s> not understood.\nTry function TellAfni_Commands for available commands.\n', Name);
return;
end
cs.err = 0;
return;
%%%%% Supporting functions below %%%%%%%%%%%%%%%%%
%figure out the window deal
function [win,p1,p1n] = NewCs_GetWin(p1, uwin)
win = uwin;
p1n = 0.0;
if (~isnumeric(p1)),
if (length(p1) > 1),
if ((p1(1)) >= 'A' & (p1(1)) <= 'J' & p1(2) == '.'),
win = p1(1);
if (~isempty(uwin) & uwin ~= win),
fprintf(2,...
'Warning: Conflict in window specification (%c vs %c).\nChoosing one in parameter (%c).\n',...
uwin, win, win);
end
p1 = p1(3:length(p1));
end
end
p1n = str2double(p1);
else
p1n = p1;
end
if (isempty(win)) win = 'A'; end
return
%check on windowname
function [err] = NewCs_OKwindowname(p1)
lcool = {'axialimage', 'sagittalimage', 'coronalimage',...
'axialgraph', 'sagittalgraph', 'coronalgraph'};
if (nargin == 1),
switch (p1),
case lcool,
err = 0;
return;
otherwise,
err = 1;
return;
end
else
err = '';
for (i=1:1:length(lcool)),
err = sprintf('%s %s\n', err, char(lcool(i)));
end
return;
end
return
%Check on xhaircode
function [err] = NewCs_OKxhaircode(p1)
lcool = {'OFF', 'SINGLE', 'MULTI',...
'LR_AP', 'LR_IS', 'AP_IS', 'LR', 'AP', 'IS'};
if (nargin == 1),
switch (p1),
case lcool,
err = 0;
return;
otherwise,
err = 1;
return;
end
else
err = '';
for (i=1:1:length(lcool)),
err = sprintf('%s %s\n', err, char(lcool(i)));
end
return;
end
return
%Check on resample
function [err] = NewCs_OKresam(p1)
lcool = {'NN', 'Li', 'Cu',...
'Bk'};
if (nargin == 1),
switch (p1),
case lcool,
err = 0;
return;
otherwise,
err = 1;
return;
end
else
err = '';
for (i=1:1:length(lcool)),
err = sprintf('%s %s\n', err, char(lcool(i)));
end
return;
end
return
%Check on panel
function [err] = NewCs_OKpanel(p1)
lcool = {'Define_Overlay', 'Define_Datamode', 'Define_Markers'};
if (nargin == 1),
switch (p1),
case lcool,
err = 0;
return;
otherwise,
err = 1;
return;
end
else
err = '';
for (i=1:1:length(lcool)),
err = sprintf('%s %s\n', err, char(lcool(i)));
end
return;
end
return
%check on input file names
function [k] = NewCs_CheckFnames(s)
[si, s] = strtok(s,' ');
k = 0;
if (exist(si,'dir') == 7 || filexist(si)),
k = k + 1;
else
k = -1;
end
return
|
github
|
lcnbeapp/beapp-master
|
New_HEAD.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/New_HEAD.m
| 8,432 |
utf_8
|
3213a4c8b09f49855cafdf9925e5b3d3
|
function [err,Info, opt] = New_HEAD (opt)
%
% [err,Info, Opt] = New_HEAD (Opt)
%
%Purpose:
% A function for the likes of Greg Detre.
% It makes the creation of an AFNI dataset
% from a 3 or 4 dimensional matrix in matlab a breeze.
%
%
%
%Input Parameters:
% opt is an options structure with the following fields:
% .prefix: A string containg the AFNI dataset's prefix
% .prefix and one of .dimen or .master must
% be used.
% .dimen: A string or array containing the dimensions of
% the dataset (at least 3 dimensions need be present).
% The following four options are from 3dUndump. See 3dUndump -help
% .view: '+orig' (default) or '+acpc' or '+tlrc'
% If you choose +tlrc, the resultant volume
% will fit the Talairach box.
% .master: Name of an existing AFNI dataset that would
% provide the needed matrix size, orientation etc.
% Do not mix .master with .dimen
% .datum: 'byte', 'short' (default), or 'float'
% .orient: Orientation of data in matrix. Default in 'RAI'
%
% .tr: a float specifying the TR in seconds.
% The presence of such a field necessitates a 4 dimensional
% .scale: 0/1 This is only meaningful with 'short' data where it
% defaults to 1. It defaults to 0 for other types. It is
% used when storing float data as shorts to minimize disk
% use while preserving numeric percision.
% .Overwrite: y/[n] allow header to be created even if one with
% similar name is found on disk
%Output Parameters:
% err : 0 No Problem
% : 1 Problems
% Info: The header structure, given the options specified
% Opt: A modified version of the input Opt. It will be passed
% along with the data array to WriteBrik for writing the
% dataset to disk. (See Examples below)
%
%Examples:
% Run New_HEAD('test') or see Test_New_HEAD.m for examples.
%
%More Info :
% AFNI programs 3drefit and 3dAttribute are your friends
% BrikLoad, BrikInfo, WriteBrik
% README.attributes
%
% The function makes heavy use of 3dUndump
%
%This function requires AFNI binaries postdating Feb. 12 2007
%
%
% Author : Ziad Saad [email protected]
% Date : Fri Feb 9 16:29:51 EST 2007
% SSCC/NIMH/ National Institutes of Health, Bethesda Maryland
%Define the function name for easy referencing
FuncName = 'New_HEAD';
%Debug Flag
DBG = 1;
%initailize return variables
err = 1;
Info = [];
%check on return parameters
if (nargout == 2),
fprintf(1, 'Notice %s:\nYou are not specifying a return argument for Opt.\n', FuncName);
fprintf(1, ' Be aware that some fields in Opt might have been modified inside\n');
fprintf(1, ' %s but these changes are not reflected in the Opt structure you\n', FuncName);
fprintf(1, ' will be passing to WriteBrik.\n');
fprintf(1, ' If this makes no sense to you, just use:\n');
fprintf(1, ' [err, Info, Opt] = New_HEAD(Opt);\n');
end
%work options
if (ischar(opt)), %perhaps test mode
Test_New_HEAD;
return;
end
%standardize input
if (isfield(opt,'dimen')),
if (ischar(opt.dimen)),
v = str2num(opt.dimen);
rmfield(opt, 'dimen');
opt.dimen = v;
end
end
%create command for -master option or non-tlrc views
if (~isfield(opt,'view') | ~strcmp(opt.view,'+tlrc') | isfield(opt,'master')),
tmp_suf = '___NeW_hEaD_';
sopt = '3dUndump -head_only';
if (isfield(opt,'dimen')),
sopt = sprintf('%s -dimen %s', sopt, num2str(opt.dimen(1:3)));
end
if (isfield(opt,'orient')),
sopt = sprintf('%s -orient %s', sopt, opt.orient);
end
if (isfield(opt,'master')),
[Status, mPrefix, mView] = PrefixStatus (opt.master);
sopt = sprintf('%s -master %s', sopt, opt.master);
else
mView = '+orig';
end
if (~isfield(opt,'datum')), opt.datum = 'short'; end
if (isfield(opt,'datum')),
if (~strcmp(opt.datum,'short') & ~strcmp(opt.datum, 'byte') & ~strcmp(opt.datum,'float')),
fprintf(1,'Error %s:\ndatum option must be one of ''byte'', ''short'', ''float''\nI have %s\n', FuncName, opt.datum);
return;
end
sopt = sprintf('%s -datum %s', sopt, opt.datum);
end
if (~isfield(opt,'view')),
opt.view = '+orig';
end
if (isfield(opt,'prefix')),
[Status, Prefix, View] = PrefixStatus (opt.prefix);
if (Status < 1 & strcmp(View,opt.view)),
if (isfield(opt,'overwrite') & ~strcmp(opt.overwrite,'y')),
fprintf(1,'Error %s:\nLooks like %s exists already.\n',...
FuncName, opt.prefix);
return;
end
end
opt.prefix = Prefix;
ohead = sprintf('%s%s', tmp_suf, opt.prefix);
sopt = sprintf('%s -prefix %s%s', sopt, ohead);
else
fprintf(1,'Error %s:\nNeed a .prefix option.\n', FuncName);
return;
end
[e,w] = unix(sopt);
if (e),
fprintf(1,'Error %s:\nHeader creating command %s failed.\nSee this function''s help and 3dUndump -help\n3dUndump''s output was:\n%s\n', ...
FuncName, sopt, w);
New_HEAD_CLEAN(tmp_suf);
return;
end
[err,Info] = BrikInfo(sprintf('%s%s', ohead,mView));
New_HEAD_CLEAN(tmp_suf);
else %have +tlrc and no master
mView = '+tlrc';
[e,d] = unix('which afni');
if (e),
fprintf(1,'Error %s:\nFailed to find afni!\n', FuncName);
return;
end
[e,pt] = GetPath(d);
templ = sprintf('%s/TT_N27+tlrc.HEAD', pt);
[e,Info] = BrikInfo(templ);
if (e),
fprintf(1,'Error %s:\nFailed to get header of %s!\n', FuncName, templ);
return;
end
%recalculate the origin (res. of template is 1x1x1mm)
oOrig = Info.ORIGIN;
oDelta = Info.DELTA;
oDimen = Info.DATASET_DIMENSIONS;
%Calculate dimension ratio and adjust so that volume fits in box.
rat = oDimen(1:3)./opt.dimen(1:3);
Info.DELTA = Info.DELTA .* rat;
Info.DATASET_DIMENSIONS(1:3) = opt.dimen(1:3);
%Now shift the origin so that the final volume still fits in the same box (edge to edge) of TLRC box
dOrig = 1./2*(Info.DELTA-oDelta);
Info.ORIGIN = Info.ORIGIN+dOrig;
%Have to deal with datum
if (isfield(opt,'datum')),
if (strcmp(opt.datum,'byte')),
Info.BRICK_TYPES(1) = 0;
elseif (strcmp(opt.datum,'short')),
Info.BRICK_TYPES(1) = 1;
elseif (strcmp(opt.datum,'float')),
Info.BRICK_TYPES(1) = 3;
else
fprintf(1,'Error %s: Bad data type %s\n', FuncName, opt.datum);
return;
end
else
opt.datum = 'short'
Info.BRICK_TYPES(1) = 1;
end
end
%the scaling option
if (isfield(opt,'scale')),
if (opt.scale & ~strcmp(opt.datum,'short')),
fprintf(1,'Warning %s:\n .scale option is only for ''short'' type data.\n Resetting it to 0.\n', FuncName);
opt.scale = 0;
end
else
if (strcmp(opt.datum,'short')),
opt.scale = 1;
else
opt.scale = 0;
end
end
%take care of prefix business
Info.RootName = sprintf('%s%s', opt.prefix, opt.view);
%take care of view
if (strcmp(mView, opt.view) == 0), %different
if (strcmp(opt.view,'+orig')) Info.SCENE_DATA(1) = 0;
elseif (strcmp(opt.view,'+acpc')) Info.SCENE_DATA(1) = 1;
elseif (strcmp(opt.view,'+tlrc')) Info.SCENE_DATA(1) = 2;
else
fprintf(1,'Error %s:\nBad view %s\n', FuncName, opt.view);
return;
end
end
%take care of 4th dimen
if (isfield(opt,'dimen')),
if (length(opt.dimen) > 3),
Info.DATASET_RANK(2) = opt.dimen(4);
Info.BRICK_TYPES = Info.BRICK_TYPES(1).*ones(1,opt.dimen(4));
Info.BRICK_FLOAT_FACS = Info.BRICK_FLOAT_FACS(1) .*ones(1, opt.dimen(4));
end
end
%take care of TR
if (isfield(opt,'tr')),
Info.TAXIS_NUMS(1) = Info.DATASET_RANK(2);
Info.TAXIS_NUMS(2) = 0; %no time offset for slices at the moment
Info.TAXIS_NUMS(3) = 77002; %units in seconds for tr (below)
Info.TAXIS_FLOATS(1) = 0; %time origin 0
Info.TAXIS_FLOATS(2) = opt.tr; %TR in units of Info.TAXIS_NUMS(3)
Info.TAXIS_FLOATS(3) = 0; %duration of acquisition
Info.TAXIS_FLOATS(4) = 0; %no time offset please
Info.TAXIS_FLOATS(5) = 0; %no time offset please
Info.TAXIS_OFFSETS = zeros(1,Info.TAXIS_NUMS(1)); %no bloody time offset
end
err = 0;
return;
function New_HEAD_CLEAN(sss)
unix(sprintf('rm -f %s*.HEAD >& /dev/null', sss));
return;
|
github
|
lcnbeapp/beapp-master
|
PeakFinder.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/PeakFinder.m
| 13,081 |
utf_8
|
2f79a40d4194ae7e9ad3a34c87589a80
|
function [R, e] = PeakFinder(vvec, Opt)
%Example: PeakFinder('Resp*.1D');
% or PeakFinder(v) where v is a column vector
% if v is a matrix, each column is processed separately.
%
%clear all but vvec (useful if I run this function as as script)
keep('vvec', 'Opt');
e = 0;
R = struct([]);
if (nargin < 2) Opt = struct(); end
if (~isfield(Opt,'PhysFS') | isempty(Opt.PhysFS)),
Opt.PhysFS= 1/0.025; %sampling frequency
end
if (~isfield(Opt,'zerophaseoffset') | isempty(Opt.zerophaseoffset) ),
Opt.zerophaseoffset = 0.5; %Fraction of the period that corresponds
%to a phase of 0
%0.5 means the middle of the period, 0 means the 1st peak
end
if (~isfield(Opt,'Quiet') | isempty(Opt.Quiet)),
Opt.Quiet = 0;
end
if (~isfield(Opt,'ResampFS') | isempty(Opt.ResampFS)),
Opt.ResampFS = Opt.PhysFS;
end
if (~isfield(Opt,'fcutoff') | isempty(Opt.fcutoff)),
Opt.fcutoff = 10;
end
if (~isfield(Opt,'FIROrder') | isempty(Opt.FIROrder)),
Opt.FIROrder = 80;
end
if (~isfield(Opt,'ResamKernel') | isempty(Opt.ResamKernel)),
Opt.ResamKernel = 'linear';
end
if (~isfield(Opt,'Demo') | isempty(Opt.Demo)),
Opt.Demo = 0;
end
if (~isfield(Opt,'as_windwidth') | isempty(Opt.as_windwidth)),
Opt.as_windwidth = 0;
end
if (~isfield(Opt,'as_percover') | isempty(Opt.as_percover)),
Opt.as_percover = 0;
end
if (~isfield(Opt,'as_fftwin') | isempty(Opt.as_fftwin)),
Opt.as_fftwin = 0;
end
if (Opt.Demo),
Opt.Quiet = 0;
else
pause off
end
%some filtering
fnyq = Opt.PhysFS./2;
%w(1) = 0.1/fnyq; %cut frequencies below 0.1Hz
%w(2) = Opt.fcutoff/fnyq; % upper cut off frequency normalized
%b = fir1(Opt.FIROrder, w, 'bandpass'); %FIR filter of order 40
w = Opt.fcutoff/fnyq; % upper cut off frequency normalized
b = fir1(Opt.FIROrder, w, 'low'); %FIR filter of order 40
NoDups = 1; % remove duplicates that might come up when improving peak location
if (ischar(vvec)),
l = zglobb(vvec);
nl = length(l);
if (isnumeric(l)),
fprintf(2,'File (%s) not found\n', vvec);
e = 1;
return;
end
else
l = [];
nl = size(vvec,2);
if (nl < 1),
fprintf(2,'No vectors\n', nl);
e = 1;
return;
end
end
clear R; %must clear it. Or next line fails
R(nl) = struct( 'vname', '',...
't', [], ...
'X', [],...
'iz', [],... %zero crossing (peak) locations
'ptrace', [], 'tptrace', [],...
'ntrace', [], 'tntrace', [],...
'prd', [], 'tmidprd', [], 'ptracemidprd', [],...
'phz', [],...
'RV', [], 'RVT', [] ...
);
for (icol = 1:1:nl),
if (~isempty(l) && ~l(icol).isdir),
R(icol).vname = sprintf('%s%s', l(icol).path, l(icol).name);
v = Read_1D(R(icol).vname);
else,
R(icol).vname = sprintf('vector input col %d', icol);
v = vvec(:,icol);
end
windwidth = 0.2; %window for adjusting peak location in seconds
%remove the mean
v = (v - mean(v));
R(icol).v = v; %store it for debugging
%filter both ways to cancel phase shift
v = filter(b,1,v); v = flipud(v); v = filter(b,1,v); v = flipud(v);
%get the analytic signal
R(icol).X = analytic_signal(v, Opt.as_windwidth.*Opt.PhysFS,...
Opt.as_percover, Opt.as_fftwin);
%using local version to illustrate, can use hilbert
%Doing ffts over smaller windows can improve peak detection
%in the few instances that go undetected but what value to use
%is not clear and there seems to be at times more errors introduced
%in the lower envelope .
nt = length(R(icol).X);
R(icol).t = [0:1/Opt.PhysFS:(nt-1)/Opt.PhysFS]; % FIX FIX FIX
iz = find( imag(R(icol).X(1:nt-1)).*imag(R(icol).X(2:nt)) <= 0);
polall = -sign(imag(R(icol).X(1:nt-1)) - imag(R(icol).X(2:nt)));
pk = real(R(icol).X(iz));
pol = polall(iz);
tiz = R(icol).t(iz);
ppp = find(pol>0);
ptrace = pk(ppp);
tptrace = tiz(ppp);
ppp = find(pol<0);
ntrace = pk(ppp);
tntrace = tiz(ppp);
if (~Opt.Quiet),
fprintf(2,[ '--> Load signal\n',...
'--> Smooth signal\n',...
'--> Calculate analytic signal Z\n',...
'--> Find zero crossing of imag(Z)\n',...
'\n']);
figure(1); clf
subplot(211);
plot (R(icol).t, real(R(icol).X),'g'); hold on
%plot (R(icol).t, imag(R(icol).X),'g');
plot (tptrace, ptrace, 'ro');
plot (tntrace, ntrace, 'bo');
%plot (R(icol).t, abs(R(icol).X),'k');
subplot (413);
vn = real(R(icol).X)./(abs(R(icol).X)+eps);
plot (R(icol).t, vn, 'g'); hold on
ppp = find(pol>0);
plot (tiz(ppp), vn(iz(ppp)), 'ro');
ppp = find(pol<0);
plot (tiz(ppp), vn(iz(ppp)), 'bo');
drawnow ;
if (Opt.Demo),
uiwait(msgbox('Press button to resume', 'Pausing', 'modal'));
end
end
%Some polishing
if (1),
nww = ceil(windwidth/2 * Opt.PhysFS);
pkp = pk;
R(icol).iz = iz;
for (i=1:1:length(iz)),
n0 = max(2,iz(i)-nww);
n1 = min(nt,iz(i)+nww);
if (pol(i) > 0),
[xx, ixx] = max((real(R(icol).X(n0:n1))));
else,
[xx, ixx] = min((real(R(icol).X(n0:n1))));
end
R(icol).iz(i) = n0+ixx-2;
pkp(i) = xx;
end
tizp = R(icol).t(R(icol).iz);
ppp = find(pol>0);
R(icol).ptrace = pkp(ppp);
R(icol).tptrace = tizp(ppp);
ppp = find(pol<0);
R(icol).ntrace = pkp(ppp);
R(icol).tntrace = tizp(ppp);
if (NoDups),
%remove duplicates
if (Opt.SepDups),
fprintf(2,'YOU SHOULD NOT BE USING THIS.\n');
fprintf(2,' left here for the record\n');
[R(icol).tptrace, R(icol).ptrace] = ...
remove_duplicates(R(icol).tptrace, R(icol).ptrace, Opt);
[R(icol).tntrace, R(icol).ntrace] = ...
remove_duplicates(R(icol).tntrace, R(icol).ntrace, Opt);
else,
[R(icol).tptrace, R(icol).ptrace,...
R(icol).tntrace, R(icol).ntrace] = ...
remove_PNduplicates(R(icol).tptrace, R(icol).ptrace,...
R(icol).tntrace, R(icol).ntrace, Opt);
end
if (length(R(icol).ptrace) ~= length(R(icol).ntrace)),
fprintf(1,'Bad news in tennis shoes. I''m outa here.\n');
e = 1;
return;
end
end
if (~Opt.Quiet),
fprintf(2,[ '--> Improved peak location\n',...
'--> Removed duplicates \n',...
'\n']);
subplot(211);
plot( R(icol).tptrace, R(icol).ptrace,'r+',...
R(icol).tptrace, R(icol).ptrace,'r');
plot( R(icol).tntrace, R(icol).ntrace,'b+',...
R(icol).tntrace, R(icol).ntrace,'b');
drawnow ;
if (Opt.Demo),
uiwait(msgbox('Press button to resume', 'Pausing', 'modal'));
end
end
else
tizp = tiz;
R(icol).iz = iz;
pkp = pk;
R(icol).ptrace = ptrace;
nR(icol).ptrace = nptrace;
end
%Calculate the period
nptrc = length(R(icol).tptrace);
R(icol).prd = (R(icol).tptrace(2:nptrc) - R(icol).tptrace(1:nptrc-1) );
R(icol).ptracemidprd = ( R(icol).ptrace(2:nptrc) ...
+ R(icol).ptrace(1:nptrc-1) ) ./2.0;
R(icol).tmidprd = ( R(icol).tptrace(2:nptrc) ...
+ R(icol).tptrace(1:nptrc-1)) ./2.0;
if (~Opt.Quiet),
fprintf(2,[ '--> Calculated the period (from beat to beat)\n',...
'\n']);
plot (R(icol).tmidprd, R(icol).ptracemidprd,'kx');
for (i=1:1:length(R(icol).prd)),
text( R(icol).tmidprd(i), R(icol).ptracemidprd(i),...
sprintf('%.2f', R(icol).prd(i)));
end
drawnow ;
if (Opt.Demo),
uiwait(msgbox('Press button to resume', 'Pausing', 'modal'));
end
end
if (~isempty(Opt.ResamKernel)),
%interpolate to slice sampling time grid:
R(icol).tR = [0:1./Opt.ResampFS:max(R(icol).t)];
R(icol).ptraceR = interp1( R(icol).tptrace', R(icol).ptrace, ...
R(icol).tR,Opt.ResamKernel);
R(icol).ntraceR = interp1( R(icol).tntrace', R(icol).ntrace, ...
R(icol).tR,Opt.ResamKernel);
R(icol).prdR = interp1(R(icol).tmidprd, R(icol).prd, ...
R(icol).tR,Opt.ResamKernel);
%you get NaN when tR exceeds original signal time, so set those
%to the last interpolated value
R(icol).ptraceR = clean_resamp(R(icol).ptraceR);
R(icol).ntraceR = clean_resamp(R(icol).ntraceR);
R(icol).prdR = clean_resamp(R(icol).prdR);
end
if (icol ~= nl), input ('Hit enter to proceed...','s'); end
end
if (~Opt.Quiet), plotsign2(1); end
return;
function v = clean_resamp(v)
inan = find(isnan(v)); %the bad
igood = find(isfinite(v)); %the good
for(i=1:1:length(inan)),
if (inan(i) < igood(1)),
v(inan(i))= v(igood(1));
elseif (inan(i) > igood(length(igood))),
v(inan(i))= v(igood(length(igood)));
else
fprintf(2,'Error: Unexpected NaN case\n');
v(inan(i))= 0;
end
end
return;
function [t,v] = remove_duplicates(t,v, Opt)
j = 1;
for (i=2:1:length(t)),
if ( t(i) ~= t(i-1) & ...
t(i) - t(i-1) > 0.3), %minimum time
%before next beat
j = j + 1;
t(j) = t(i);
v(j) = v(i);
else,
if (~Opt.Quiet),
fprintf(2,'Dropped peak at %g sec\n', t(i));
end
end
end
t = t(1:j);
v = v(1:j);
return;
function [tp,vp, tn, vn] = remove_PNduplicates(tp,vp, tn,vn, Opt)
ok=zeros(1,length(tp));
ok(1) = 1; j = 1;
for (i=2:1:min(length(tp), length(tn))),
if ( tp(i) ~= tp(i-1) & ...
tp(i) - tp(i-1) > 0.3), %minimum time
%before next beat
j = j + 1;
ok(j) = i;
else,
if (~Opt.Quiet),
fprintf(2,'Dropped peak at %g sec\n', tp(i));
end
end
end
ok = ok(1:j);
tp = tp(ok);
vp = vp(ok);
tn = tn(ok);
vn = vn(ok);
return;
function h = analytic_signal(vi, windwidth, percover, win),
nvi = length(vi);
h = zeros(size(vi));
[bli, ble, num] = fftsegs (windwidth, percover, nvi);
for (ii=1:1:length(bli)),
v = vi(bli(ii):ble(ii));
nv = length(v);
if (win == 1),
fv = fft(v.*hamming(nv));
else,
fv = fft(v);
end
wind = zeros(size(v));
%zero negative frequencies, double positive frequencies
if (iseven(nv)),
wind([1 nv/2+1]) = 1; %keep DC
wind([2:nv/2]) = 2; %double pos. freq
else
wind([1]) = 1;
wind([2:(nv+1)/2]) = 2;
end
h(bli(ii):ble(ii)) = h(bli(ii):ble(ii)) + ifft(fv.*wind);
end
h = h./num;
return
function [bli, ble, num] = fftsegs (ww, po, nv)
% Returns the segements that are to be used for fft
% calculations.
% ww: Segment width (in number of samples)
% po: Percent segment overlap
% nv: Total number of samples in original symbol
% Returns:
% bli, ble: Two Nblck x 1 vectors defining the segments'
% starting and ending indices
% num: An nv x 1 vector containing the number of segments
% each sample belongs to
%example
% [bli, ble, num] = fftsegs (100, 70, 1000);
if (ww==0),
po = 0;
ww = nv;
elseif (ww < 32 | ww > nv),
fprintf(2,'Error fftsegs: Bad value for window width of %d\n', ww);
return;
end
out = 0;
while (out == 0),
clear bli ble
%How many blocks?
jmp = floor((100-po)*ww/100); %jump from block to block
nblck = nv./jmp; %number of jumps
ib = 1;
cnt = 0;
while (cnt < 1 | ble(cnt)< nv),
cnt = cnt + 1;
bli(cnt) = ib;
ble(cnt) = min(ib+ww-1, nv);
ib = ib + jmp;
end
%if the last block is too small, spread the love
if (ble(cnt) - bli(cnt) < 0.1.*ww), % too small a last block, merge
ble(cnt-1) = ble(cnt); % into previous
cnt = cnt -1;
ble = ble(1:cnt); bli = bli(1:cnt);
out = 1;
elseif (ble(cnt) - bli(cnt) < 0.75.*ww), % too large to merge, spread it
ww = ww+floor((ble(cnt)-bli(cnt))./nblck);
out = 0;
else %last block big enough, proceed
out = 1;
end
%ble - bli + 1
%out
end
%bli
%ble
%ble - bli + 1
%now figure out the number of estimates each point of the time series gets
num = zeros(nv,1);
cnt = 1;
while (cnt <= length(ble)),
num(bli(cnt):ble(cnt)) = num(bli(cnt):ble(cnt))+ ones(ble(cnt)-bli(cnt)+1,1);
cnt = cnt + 1;
end
|
github
|
lcnbeapp/beapp-master
|
rgbdectohex.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/rgbdectohex.m
| 6,032 |
utf_8
|
fca22486bef72eb78e71977479b7940b
|
function [Cs] = rgbdectohex (Mrgb,strg)
%
% Mode 1:
% [Cs] = rgbdectohex (Mrgb,[string])
% Mode 2:
% rgbdectohex
%
% Mode 1:
%This function takes as an input the rgb matrix Mrgb (size is Nx3)
% where each row represents the rgb gun values of a color.
% gun values should be integers between 0 and 255
%
%the optional 'string' is placed before the #hex representation
%in a way VERY suitable for afni's .Xdefaults file stuff ...
%
% remember the magic command : xrdb -merge <colors filename>
%
% the function cyclmat helps you fix your color maps, check it out...
%
%The hex values are all padded to two characters, looks nice.
%
% The function first displays the map, then gives you the option of
% writing out the results:
% to an ascii file that can be (if you specified the right strg parameter) used
% directly in .Xdefaults
% to an ascii file that contains RGB values
% to an ascii file containing the definition of the colormap in a C-
% syntax that can be added to pbar.c and added with PBAR_define_bigmap( char *mapcmd );
%
%the result is written to stdout in a format used
%by .Xdefault files, to make importing them to
%.Xdefaults easy, just cut and paste.
%
%example: >> load hues_rygbr20 (this file is an ascii list of 3 integers per line specifying rgb colours)
% >> Mcyc = cyclmat (hues_rygbr20,-1,13); (changes the order of the loaded color file..)
% >> rgbdectohex (Mcyc,'AFNI*ovdef'); this displays the colour map, and asks if you want the results written out to a file
%
% If you sqaved the results to a file called junkmap
% from command line do : xrdb -merge junkmap and the colormap is set for afni to read.
%
% If you use the return parameters [Cs, sall] then you'll get a command structure vector
% that tells AFNI (TellAfni(Cs)) to load the newly created colorscale and switch to it.
% The colorscale is named string if one is supplied.
%
% Mode 2:
% Interactive mode for showing RGB colors. Enter RGB values to see color.
%
% see also MakeColorMap, TellAfni, ROIcmap
%
% Ziad Saad Nov 26 97/ Dec 4 97/ Jan 06
if (nargout), Cs = []; sall = ''; end
if (nargin == 2),
son = 1;
else
son = 0;
strg = '';
end
if (nargin == 0),
while (1),
strgb = input ('Enter rgb values (nothing to exit):','s');
if (isempty(strgb)) return; end
Mrgb = str2num(strgb);
ShowRGBcol(Mrgb);
fprintf(1,' Color: %s\n', RGBtoXhex(Mrgb, 0, ''));
end
end
if (size (Mrgb,2) ~= 3)
fprintf(2,'rgbdectohex : Wrong Mrgb matrix size')
Mhex = -1;
return;
end
if (max(abs(round(Mrgb(:))-Mrgb(:))) > 0.0001),
fprintf(2,'rgbdectohex : RGB values are not integers.\n');
Mhex = -1;
return;
end
if (max(Mrgb(:)) < 1.1),
fprintf(2,'rgbdectohex : Maximum RGB value < 1.1. Suspecting RGB to be between 0 and 1\nBe sure that color values are integers that can range between 0 and 255.')
input ('Hit enter to continue','s');
end
if (min(Mrgb(:)) < 0 | max(Mrgb(:)) > 255),
fprintf(2,'rgbdectohex : RGB value must range between 0 and 255.');
return;
end
ShowRGBcol(Mrgb);
for (i=1:1:size(Mrgb,1)),
fprintf(1,'%s\n',RGBtoXhex(Mrgb(i,:), son, strg));
end %i
chc = input ('Wanna write this to disk ? (y/n)','s');
if (chc == 'y'),
chc2 = input ('Write rgb version of map too ? (y/n)','s');
chc3 = input ('Write C-friendly version of map to include in AFNI''c code ? (y/n)','s');
rep = 1;
strout = strg;
while (rep == 1),
%strout = input ('Enter filename :','s');
rep = filexist (strout);
if (rep == 1),
fprintf (2,'rgdtodec : file %s exists, enter another name\n\a', strout);
end
end
strout2 = sprintf ('%s.rgb',strout);
strout3 = sprintf ('%s.love.c',strout);
fid = fopen (strout,'wt');
if (chc2 == 'y'),
fid2 = fopen (strout2,'wt');
end
if (chc3 == 'y'),
fid3 = fopen (strout3,'wt');
end
if (fid == -1 | (chc2 == 'y' & fid2 == -1) | (chc3 == 'y' & fid3 == -1)),
fprintf (2,'rgdtodec : Could not open %s or %s %s file for write operation\n',strout,strout2, strout3);
end
if (chc3 == 'y'),
fprintf (fid3,'static char %s_CMD[] = { \n "%s "\n "', upper(strg), strg);
end
for (i=1:1:size(Mrgb,1)),
s1 = pad_strn (lower(dec2hex(Mrgb(i,1))),'0',2,1);
s2 = pad_strn (lower(dec2hex(Mrgb(i,2))),'0',2,1);
s3 = pad_strn (lower(dec2hex(Mrgb(i,3))),'0',2,1);
if (son == 1),
cst = sprintf ('%g',i);
cpd = pad_strn (cst,'0',2,1);
fprintf (fid,'%s%s:\t#%s%s%s\n',strg,cpd,s1,s2,s3);
else
fprintf (fid,'#%s%s%s\n',s1,s2,s3);
end
if (chc2 == 'y'),
fprintf (fid2,'%g %g %g\n',Mrgb(i,1),Mrgb(i,2),Mrgb(i,3));
end
if (chc3 == 'y'),
if (rem(i, 5)==1 & i > 1),
fprintf (fid3,'"\n "');
end
fprintf (fid3,'#%s%s%s ',s1,s2,s3);
end
end %i
fclose (fid);
if (chc2 == 'y'),
fclose (fid2);
end
if (chc3 == 'y'),
fprintf (fid3,'"\n};');
fclose (fid3);
end
end
if (nargout),
sall = '';
for (i=1:1:size(Mrgb,1)),
s1 = pad_strn (lower(dec2hex(Mrgb(i,1))),'0',2,1);
s2 = pad_strn (lower(dec2hex(Mrgb(i,2))),'0',2,1);
s3 = pad_strn (lower(dec2hex(Mrgb(i,3))),'0',2,1);
sall = sprintf('%s#%s%s%s ',sall, s1,s2,s3);
end
if (son == 0), strg = 'rgbdectohex'; end
Cs = NewCs('DEFINE_COLORSCALE', '', strg, sall);
Cs(2) = NewCs('SET_PBAR_ALL', '' , '+99', sprintf('1.0 %s', strg));
end
return;
function ShowRGBcol(Mrgb)
figure (1);
colormap (Mrgb./255);
subplot 211;
image ([1:1:length(Mrgb(:,1))]);
title(sprintf('X11 Color in Hex: %s', RGBtoXhex(Mrgb, 0, '')));
%subplot 212;
%pie (ones(1,length(Mrgb(:,1))));
return;
function sret = RGBtoXhex(rgb, son, strg),
s1 = pad_strn (lower(dec2hex(rgb(1))),'0',2,1);
s2 = pad_strn (lower(dec2hex(rgb(2))),'0',2,1);
s3 = pad_strn (lower(dec2hex(rgb(3))),'0',2,1);
if (son == 1),
cst = sprintf ('%g',i);
cpd = pad_strn (cst,'0',2,1);
sret = sprintf ('%s%s:\t#%s%s%s',strg,cpd,s1,s2,s3);
else
sret = sprintf ('#%s%s%s',s1,s2,s3);
end
return;
|
github
|
lcnbeapp/beapp-master
|
afni_niml_writesimple.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/afni_niml_writesimple.m
| 4,503 |
utf_8
|
231807f9346f2bfcc56fa5f3eda8ff00
|
function D=afni_niml_writesimple(S,fn)
% writes surface data in a 'simple' struct in NIML format to a file.
%
% D=AFNI_NIML_WRITESIMPLE(fn,S) writes surface data S to the file FN.
% S should be a struct with a field S.data, and optionally S.stats,
% S.labels, S.history, S.types, and S.node_indices.
% This function returns the more complicated NIML-struct D that is
% written by afni_niml_write
%
% S.data a PxN struct for P nodes and N datapoints per node.
% S.node_indices (optional) a Nx1 vector with indices in base 0. If
% omitted, then it is assumed that all nodes have data.
% S.stats } Either a string (with ';'-separated elements for
% S.labels } S.stats and .labels: , or a cell with strings.
% S.history } In the latter case, if the number of elements in the
% cell is less than P, then elements are taken in cycles.
%
% Example:
% S=struct()
% S.data=randn(100002,4);
% S.labels={'A-mean','A-Tscore','B-mean','B-Tscore'};
% S.stats={'none','Ttest(15)'}; % each stat descriptor will be used twice
% afni_niml_writesimple('test.niml.dset',S)
%
% NNO Feb 2010 <[email protected]>
if isnumeric(S)
T=struct();
T.data=S;
S=T;
clear T;
end
if ischar(S) && isstruct(fn)
% swap struct and filename
T=fn;
fn=S;
S=T;
clear T;
end
if ~(isstruct(S) && isfield(S,'data'))
error('Illegal input: expected struct S with field S.data\n');
end
% main header
D=struct();
if isfield(S,'dset_type')
D.dset_type=S.dset_type;
else
D.dset_type='Node_Bucket'; % this is the default
end
% make new self_idcode, to keep SUMA happy
rand('twister',sum(100*clock));
D.self_idcode=['XYZ_' char(rand(1,24)*26+65)];
[path,f,ext]=fileparts(fn);
D.filename=[f ext];
D.label=D.filename;
D.name='AFNI_dataset';
D.ni_form='ni_group';
nodes=cell(7,1);
%data
nd=struct();
nd.data_type='Node_Bucket_data';
nd.name='SPARSE_DATA';
nd.data=S.data;
[nverts,ncols]=size(S.data);
nodes{1}=nd;
% node indices
nd=struct();
nd.data_type='Node_Bucket_node_indices';
if isfield(S,'node_indices')
idxs=S.node_indices;
else
idxs=0:(nverts-1);
end
if issorted(idxs)
nd.sorted_node_def='Yes';
else
nd.sorted_node_def='No';
end
if size(idxs,1)==1
idxs=idxs';
end
if numel(idxs) ~= nverts
error('The number of node indices (%d) does not match the number of rows (%d) in the data.',nverts,numel(idxs));
end
nd.data=idxs;
nd.COLMS_RANGE=data2range(idxs,0);
nd.COLMS_LABS='Node Indices';
nd.COLMS_TYPE='Node_Index';
nd.name='INDEX_LIST';
nodes{2}=nd;
% colum range
nd=struct();
nd.atr_name='COLMS_RANGE';
nd.name='AFNI_atr';
nd.data=data2range(S.data);
nodes{3}=nd;
% default labels for columns
defaultlabels=cell(1,ncols);
for k=1:ncols
defaultlabels{k}=sprintf('col_%d',k-1);
end
% default value for history; make call stack
st=dbstack();
stc=cell(numel(st));
for j=1:numel(st)
stc{j}=sprintf('%s (%d)',st(j).name,st(j).line);
end
defaulthistory=sprintf('Written %s using: %s',datestr(clock),unsplit_string(stc,' <- '));
if isfield(S,'history')
S.history=[S.history ';' defaulthistory];
end
nodes{4}=make_str_element('COLMS_LABS',S,'labels',defaultlabels,ncols);
nodes{5}=make_str_element('COLMS_TYPE',S,'types',{'Generic_Float'},ncols);
nodes{6}=make_str_element('COLMS_STATSYM',S,'stats',{'none'},ncols);
nodes{7}=make_str_element('HISTORY_NOTE',S,'history',defaulthistory,ncols);
D.nodes=nodes;
afni_niml_write(D,fn);
function elem=make_str_element(Nodefieldname,S,Sfieldname,default,ncols)
elem=struct();
elem.atr_name=Nodefieldname;
elem.name='AFNI_atr';
if isfield(S,Sfieldname)
vals=S.(Sfieldname);
else
vals=default;
end
if iscell(vals);
valcount=numel(vals);
v=cell(1,ncols);
for k=1:ncols
v{k}=vals{mod(k-1,valcount)+1}; %cyclically take elements
end
vals=unsplit_string(v,';');
elseif ~ischar(vals)
error('Unrecognized data type for field %s (%s)', Nodefieldname, Sfieldname);
end
elem.data=vals;
function r=data2range(data,precision)
% returns a string that defines the range of the data, and nodes where this
% range is found.
[rows,cols]=size(data);
rs=cell(cols,1);
for k=1:cols
datak=data(:,k);
[minv,mini]=min(datak);
[maxv,maxi]=max(datak);
if nargin<2
precision=get_required_precision(data(:,k));
end
pat=sprintf('%%.%df %%.%df %%d %%d', precision, precision);
rs{k}=sprintf(pat, minv, maxv, mini-1, maxi-1);
end
r=unsplit_string(rs,';');
|
github
|
lcnbeapp/beapp-master
|
zglobb.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/zglobb.m
| 3,946 |
utf_8
|
508195b45ee39c7296447826b75515f4
|
function [err,ErrMessage, NameList] = zglobb (Identifiers, Opt)
%
% [err, ErrMessage, List] = zglobb (Identifiers, [Opt])
%or
% [List] = zglobb (Identifiers, [Opt])
%Purpose:
% returns the list of files specified in Identifiers
%
%
%Input Parameters:
% Identifiers is a cellstr identifying which briks to use
% Identifiers = {'ADzst2r*ir.alnd2AAzs+orig.HEAD' , 'AFzst2r*ir.alnd2AAzs+orig.HEAD'}
% Opt is an optional Options structure
% .LsType : type of output List
% 'l' --> (default) Create a Nx1 structure vector with fields identical to those returned by dir
% '|' --> Create a | delimited string with al the filenames in it
% .NoExt : (default is '') a string containing a | delimited list of filename extensions to remove
% example '.HEAD|.BRIK'
%
%Output Parameters:
% err : 0 No Problem
% : 1 Mucho Problems
% ErrMessage : Any error or warning messages
% List is the list of files with a format depending on Opt.LsType
%
%Key Terms:
%
%More Info :
% ? as a wildcard now works on unix/OSX machines
%
%
%
% Author : Ziad Saad
% Date : Fri Feb 09 09:55:01 EST 2001
% LBC/NIMH/ National Institutes of Health, Bethesda Maryland
%Define the function name for easy referencing
FuncName = 'zglobb';
%Debug Flag
DBG = 1;
%initailize return variables
err = 1;
ErrMessage = 'Undetermined';
NameList = [];
if (nargin == 1),
Opt.LsType = 'l';
Opt.NoExt = '';
else
if (~isfield (Opt, 'LsType') | isempty(Opt.LsType)), Opt.LsType = 'l'; end
if (~isfield (Opt, 'NoExt') | isempty(Opt.NoExt)), Opt.NoExt = ''; end
end
switch Opt.LsType,
case 'l',
NameList = [];
case '|',
NameList = '';
otherwise,
ErrMessage = sprintf('%s is an unknown Opt.LsType value', Opt.LsType);
err = 1;
return;
end
if (ischar(Identifiers)),
Identifiers = cellstr(Identifiers);
end
%get the names of the BRIKS identified in Identifiers
N_ID = length(Identifiers);
cnt = 0;
i=1;
while (i<=length(Identifiers)),
% grab the path if it is there
[eee, ppp] = GetPath(char(Identifiers(i)));
if (ppp(length(ppp)) ~= filesep),
ppp = [ppp filesep];
end
if (~isempty (find(char(Identifiers(i)) == '?'))),
%have to go via ls!
com = sprintf('\\ls %s', char(Identifiers(i)));
[ee,ll] = unix(com);
if (ee),
i = i + 1;
continue;
end
cl = zstr2cell(ll);
if (length(Identifiers)>=i+1),
Identifiers = [ Identifiers(1:i-1) ...
cl ...
Identifiers(i+1:length(Identifiers))];
else
Identifiers = [ Identifiers(1:i-1) ...
cl ];
end
end
sd = dir (char(Identifiers(i)));
ns = length(sd);
for (j=1:1:ns)
if (~strcmp(sd(j).name, '.') & ~strcmp(sd(j).name, '..'))
cnt = cnt + 1;
if (~isempty(Opt.NoExt)),
sd(j).name = RemoveExtension (sd(j).name, Opt.NoExt);
end
switch Opt.LsType,
case 'l',
NameList(cnt).name = sd(j).name;
NameList(cnt).date = sd(j).date;
NameList(cnt).bytes = sd(j).bytes;
NameList(cnt).isdir = sd(j).isdir;
NameList(cnt).path = ppp;
case '|'
if (strcmp(ppp,'.') || strcmp(ppp,'./')),
NameList = sprintf('%s|%s',NameList,sd(j).name);
else
NameList = sprintf('%s|%s%s', ...
NameList,ppp,sd(j).name);
end
end
end
end
i = i + 1;
end
if (Opt.LsType == '|'),
NameList = NameList(2:length(NameList)); %get rid of first |
end
if (cnt == 0),
ErrMessage = 'No match';
return;
end
if (nargout <= 1),
err = NameList;
else,
err = 0;
ErrMessage = '';
end
return;
function cl = zstr2cell(ll)
sp = find(isspace(ll));
strt = 1;
cl = cellstr('');
for(i=1:1:length(sp)),
cl(i) = cellstr(ll(strt:sp(i)-1));
strt = sp(i)+1;
end
return;
|
github
|
lcnbeapp/beapp-master
|
afni_niml_parse.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/afni_niml_parse.m
| 4,013 |
utf_8
|
928c1d463779f609cd8549cfec5a0a37
|
function niml = afni_niml_parse(s)
% Simple parsing routine for AFNI NIML datasets
%
% N=AFNI_NIML_PARSE(S) parses the niml string S and returns a parsed
% structure P.
%
% P can either be an niml element, or a group of niml elements. In the
% formder case, P contains a field .data; in the latter, a cell .nodes.
%
% If S contains multiple niml datasets that are not in a group, then N will
% be a cell with the parsed datasets.
%
% This function is more or less the inverse of AFNI_NIML_PRINT.
%
% Many thanks to Ziad Saad, who wrote afni_niml_read and other routines
% that formed the basis of this function.
%
% Please note that this function is *VERY EXPERIMENTAL*
%
% NNO Dec 2009 <[email protected]>
% if the input is a string (i.e. not called recursively), parse header and
% body and put them in a struct s.
if ischar(s)
s=afni_nel_parseheaderbody(s);
end
% make sure we only have the fieldnames we expect
if ~isempty(setxor(fieldnames(s),{'headername','headertext','body'}))
error('Illegal struct s, expected s.headername, s.headertext, s.body');
end
% if more than 1 element, parse each of them seperately and put them in a
% cell.
scount=numel(s);
if scount>1
niml=cell(scount,1);
for k=1:scount
niml{k}=afni_niml_parse(s(k));
end
return
end
% parse the header part
niml=afni_nel_parsekeyvalue(s.headertext);
niml.name=s.headername;
if isfield(niml,'ni_form') && strcmp(niml.ni_form,'ni_group')
% this is a group of elements. parse each of the elements in the group
% and put the results in a field .nodes
nds=afni_niml_parse(s.body);
% for consistency, ensure that .nodes is always a cell
if iscell(nds)
niml.nodes=nds;
else
niml.nodes{1}=nds;
end
else
% this is a single element
% set a few fields
niml.vec_typ = afni_nel_getvectype(niml.ni_type);
niml.vec_len = str2num(niml.ni_dimen);
niml.vec_num = length(niml.vec_typ);
% parse only
if (~afni_ni_is_numeric_type(niml.vec_typ)),
%fprintf(2,'Data not all numeric, will not parse it');
niml.data = afni_nel_parse_nonnumeric(niml, s.body);
else
niml.data = afni_nel_parse_data(niml, s.body);
end
end
function p=afni_nel_parsekeyvalue(s)
% parses a string of the form "K1=V1 K2=V2 ...
expr='\s*(?<lhs>\w+)\s*=\s*"(?<rhs>[^"]+)"';
hh=regexp(s,expr,'names');
p = cell2struct({hh(:).rhs}, {hh(:).lhs},2); clear hh;
function p=afni_nel_parseheaderbody(s)
% parses a header and body
% in the form <HEADERNAME HEADERTEXT>BODY</HEADERNAME>
expr = '<(?<headername>\w+)(?<headertext>.*?)>(?<body>.*?)</\1>';
p = regexp(s, expr,'names');
function vec_typ=afni_nel_getvectype(tt)
% gets the vector type for a data element
vec_typ=zeros(1,1000);
nn=0;
while (~isempty(tt)),
[ttt,tt] = strtok(tt, ',');
%look for the N*type syntax
N = 1;
[tttt,ttt] = strtok(ttt,'*');
Ntttt = str2double(tttt);
if (~isnan(Ntttt)), %have a number, get the type
N = Ntttt;
tttt = strtok(ttt,'*');
end
vec_typ(nn+1:1:nn+N) = afni_ni_rowtype_name_to_code(tttt);
nn = nn + N;
end
vec_typ=vec_typ(1:nn)-1; % convert to base0, as in the niml.h.
%
% This is a point of concern as the
% afni_ni_rowtype_name_to_code function
% seems to prefer base1
%
% (if only matlab used base0 indexing...)
function p = afni_nel_parse_data(nel, data)
d=sscanf(data,'%f');
p = reshape(d, nel.vec_num, nel.vec_len)';
function p =afni_nel_parse_nonnumeric(nel,data)
if strcmp(nel.ni_type,'String')
p=strtrim(data);
if strcmp(p([1 end]),'""')
p=p(2:(end-1)); % remove surrounding quotes
end
else
p=data; %do nothing
end
|
github
|
lcnbeapp/beapp-master
|
afni_fig_interface.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/afni_fig_interface.m
| 3,035 |
utf_8
|
a6e27aaa75a4fe2aebabe4db5d20acfb
|
function afni_fig_interface(src, evnt)
cf = gcf;
figure(src);
% evnt
ud = get(src,'UserData');
if (isempty(ud) | ~isfield(ud,'axes_lock')),
ud = default_ud();
set(src,'UserData',ud);
end
if ( lower(evnt.Character) == 'l' ),
ud.axes_lock = ~ud.axes_lock;
set (src,'UserData',ud);
if ud.axes_lock, set (src,'Name','L');
else set (src,'Name','');
end
elseif ( lower(evnt.Character) == 'a' ),
if (ud.axes_lock),
reset_axis(evnt.Character, get_all_axes(src));
else
reset_axis(evnt.Character,gca); %can send arrays for characters and axes
end
elseif ( lower(evnt.Character) == 'x' |...
lower(evnt.Character) == 'y' |...
lower(evnt.Character) == 'z' ),
if (ud.axes_lock),
zoom_axis(evnt.Character, get_all_axes(src));
else
zoom_axis(evnt.Character,gca); %can send arrays for characters and axes
end
elseif ( strcmp(evnt.Key , 'leftarrow') |...
strcmp(evnt.Key , 'rightarrow') |...
strcmp(evnt.Key , 'uparrow') |...
strcmp(evnt.Key , 'downarrow')),
if (ud.axes_lock),
shift_axis(evnt, get_all_axes(src));
else
shift_axis(evnt, gca);
end
end
figure(cf);
return;
function reset_axis(a,h)
ca = gca;
for (ih=1:1:length(h)),
axes(h(ih));
axis auto;
end
axes(ca);
return
function zoom_axis(a,h)
ca = gca;
for (ia=1:1:length(a)),
for (ih=1:1:length(h)),
axes(h(ih));
dv = 4;
if ( ~(a(ia) - lower(a(ia))) ),
dv = 1;
end
if (~(lower(a(ia)) - 'x')), se = [1 2];
elseif (~(lower(a(ia)) - 'y')), se = [3 4];
elseif (~(lower(a(ia)) - 'z')), se = [5 6];
else
return;
end
v = axis;
if (length(v) < max(se)), return; end
vc = (v(se(1))+v(se(2)))/2;
vd = v(se(2))-v(se(1));
v(se(1)) = vc-vd/dv;
v(se(2)) = vc+vd/dv;
axis(v);
end
end
axes(gca);
return;
function shift_axis(e,h)
ca = gca;
for (ie=1:1:length(e)),
for (ih=1:1:length(h)),
axes(h(ih));
if (strcmp(e(ie).Key , 'leftarrow')),
se = [1 2]; dv = +0.1;
elseif (strcmp(e(ie).Key , 'rightarrow')),
se = [1 2]; dv = -0.1;
elseif (strcmp(e(ie).Key , 'downarrow')),
se = [3 4]; dv = -0.1;
elseif (strcmp(e(ie).Key , 'uparrow')),
se = [3 4]; dv = 0.1;
else
return;
end
v = axis
vd = v(se(2))-v(se(1));
v(se(1)) = v(se(1))+vd*dv;
v(se(2)) = v(se(2))+vd*dv;
axis(v);
end
end
axes(gca);
return;
function v = get_all_axes(f)
l = get(f, 'Children');
v = [];
for (i=1:1:length(l)),
if (strcmp(get(l(i),'Type'),'axes')), v = [v l(i)]; end
end
return
function ud = default_ud()
ud = struct('axes_lock', 0);
return
|
github
|
lcnbeapp/beapp-master
|
TellAfni.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/TellAfni.m
| 5,472 |
utf_8
|
77dce5f5339989af26f3e100da6bcfc3
|
function [err] = TellAfni (cs, opt)
%
% [err] = TellAfni (cs, opt)
%
%Purpose:
% Drive AFNI
%
%
%Input Parameters:
% cs: An Nx1 vector of communication command structures
% It is obtained using NewCs structure
% opt: An optional options structure
% .QuitOnErr (0/[1]): Return from function if any of cs(i) is malformed
% .Verbose (0/[1]/2): 0 = mute, 1 = Yak, Yak (default), 2 = YAK YAK
%Output Parameters:
% err : 0 No Problem
% : N N Problems
%
%
%More Info :
%
% NewCs
% TellAfni_Commands
% Test_TellAfni
% AFNI's README.driver file and the program plugout_drive
%
% Author : Ziad Saad
% Date : Tue Dec 6 10:38:23 EST 2005
% SSCC/NIMH/ National Institutes of Health, Bethesda Maryland
%Define the function name for easy referencing
FuncName = 'TellAfni';
%Debug Flag
DBG = 1;
%initailize return variables
err = 1;
LogFile = '.TellAfni.log';
if (nargin == 1) opt.QuitOnErr = []; end
if (~isfield(opt, 'QuitOnErr') | isempty(opt.QuitOnErr)) opt.QuitOnErr = 1; end
if (~isfield(opt, 'Verbose') | isempty(opt.Verbose)) opt.Verbose = 1; end
ncs = length(cs);
if (ncs == 0) err = 0; return; end
if (isempty(LogFile) | LogFile(1) ~= '.'),
fprintf(2,'Bad LogFile, whas happening?');
return;
end
com = '';
ComLast = '';
ncom = 0;
for (i=1:1:ncs),
if (cs(i).err),
fprintf(2,'Error in command structure %d (%s).\n', i,cs(i).c);
if (opt.QuitOnErr),
fprintf(2,'Quitting.\n');
return;
else
fprintf(2,'Ignoring command.\n');
cs(i).c = '';
end
end
if (cs(i).c),
switch (cs(i).c),
case 'START_AFNI',
if (exist(LogFile) == 2),
fprintf(2,'\nError: Log file %s found.\n', LogFile);
fprintf(2,'Make sure no other AFNI is running AND listening for plugouts.\n');
fprintf(2,'rm the logfile with:\n!rm -f %s \n', LogFile);
fprintf(2,'Then try your command again.\n\n');
return;
end
scom = sprintf('afni -yesplugouts %s |& tee %s &', cs(i).v, LogFile);
[s,w] = unix(scom);
if (opt.Verbose & ~isempty(w)),
fprintf(1,'Command output:\n%s\n', w);
end
if (s),
fprintf(2,'Error launching afni\n');
return;
end
%check on errors regarding connections
iserr = 1; Tel = 0;
while (Tel < 10 & iserr),
if ( (rem(Tel,1) < 0.0001) ) fprintf(2,'Checking on communication (%.1f/10)\n', Tel); end
iserr = TellAfni_CheckLog(LogFile, (rem(Tel,1)<0.0001));
pause (0.2); % wait to be sure AFNI launched
Tel = Tel+0.2;
end
if (iserr),
fprintf(2,'\nLaunched a new AFNI but failed to communicate.\n');
fprintf(2,'Close the failed AFNI and any other AFNI sessions\n');
fprintf(2,'that are listening to plugouts.\n\n');
scom = sprintf('rm -f %s >& /dev/null', LogFile);
unix(scom);
return;
end
case 'QUIT',
if (~isempty(LogFile)),
ComLast = sprintf('rm -f %s >& /dev/null', LogFile);
end
com = sprintf('%s -com ''%s %s''', com, cs(i).c, cs(i).v);
ncom = ncom+1;
otherwise,
com = sprintf('%s -com ''%s %s''', com, cs(i).c, cs(i).v);
ncom = ncom+1;
end
end
end
b = 0;
if (~isempty(com)),
scom = sprintf('plugout_drive -v %s -quit', com);
if (opt.Verbose > 1),
fprintf(1, 'making call:\n%s\n', scom);
end
[s,w] = unix(scom);
if (isempty(strfind(scom,'QUIT'))), %Do not check in cases of QUIT
[err, g, b] = TellAfniCheck(w);
if (ncom ~= err + g + b ),
fprintf(2,'Warning: Unexpected parsing trouble (ncom=%d, err+g+b=%d).\n', ncom, err+g+b);
end
if (err),
fprintf(2,'Warning: Failed in parsing plugout_drive output.\nCannot confirm how %d out of %d commands executed\n', err, ncom);
end
if (g & opt.Verbose),
fprintf(1,'%d out of %d commands OK\n', g, ncom);
end
if (b),
fprintf(2,'Warning: %d out of %d commands failed in AFNI.\n', b, ncom);
end
end
if (opt.Verbose > 1),
fprintf(1,'Command output:\n%s\n', w);
end
if (s),
fprintf(2,'Error telling afni\n');
return;
end
end
if (~isempty(ComLast)),
[s,w] = unix(ComLast);
end
err = b;
return;
function err = TellAfni_CheckLog(LogFile, verb)
err = 1;
if (exist(LogFile) ~= 2),
%no log file!
return;
end
fid = fopen(LogFile,'r');
if (fid < 0) return, end
c = fscanf(fid, '%c');
l = strfind(c,'Can''t bind? tcp_listen[bind]: Address already in use');
fclose(fid);
if (~isempty(l)),
if (verb)
fprintf(2,'Warning: Can''t listen. You probably have another AFNI listening.\nCommunication might fail.\nOnly one AFNI can communicate via plugouts\n');
end
return;
end
l = strfind(c,'Plugouts');
if (~isempty(l)),
l = strfind(c,'= listening for connections');
if (isempty(l)),
if (verb) fprintf(2,'Warning: pugouts not enabled. Communication might fail.\n'); end
return;
end
else
%not there yet
return;
end
err = 0;
return;
|
github
|
lcnbeapp/beapp-master
|
zinputdlg.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/zinputdlg.m
| 16,591 |
utf_8
|
63dc0806876466dc33fef8fbdfeb45c5
|
function Answer=zinputdlg(Prompt, Title, NumLines, DefAns, Resize)
% A copy of inputdlg.m , modified to have better looking font settings
%ZINPUTDLG Input dialog box.
% ANSWER = ZINPUTDLG(PROMPT) creates a modal dialog box that returns user
% input for multiple prompts in the cell array ANSWER. PROMPT is a cell
% array containing the PROMPT strings.
%
% ZINPUTDLG uses UIWAIT to suspend execution until the user responds.
%
% ANSWER = ZINPUTDLG(PROMPT,NAME) specifies the title for the dialog.
%
% ANSWER = ZINPUTDLG(PROMPT,NAME,NUMLINES) specifies the number of lines for
% each answer in NUMLINES. NUMLINES may be a constant value or a column
% vector having one element per PROMPT that specifies how many lines per
% input field. NUMLINES may also be a matrix where the first column
% specifies how many rows for the input field and the second column
% specifies how many columns wide the input field should be.
%
% ANSWER = ZINPUTDLG(PROMPT,NAME,NUMLINES,DEFAULTANSWER) specifies the
% default answer to display for each PROMPT. DEFAULTANSWER must contain
% the same number of elements as PROMPT and must be a cell array of
% strings.
%
% ANSWER = ZINPUTDLG(PROMPT,NAME,NUMLINES,DEFAULTANSWER,OPTIONS) specifies
% additional options. If OPTIONS is the string 'on', the dialog is made
% resizable. If OPTIONS is a structure, the fields Resize, WindowStyle, and
% Interpreter are recognized. Resize can be either 'on' or
% 'off'. WindowStyle can be either 'normal' or 'modal'. Interpreter can be
% either 'none' or 'tex'. If Interpreter is 'tex', the prompt strings are
% rendered using LaTeX.
%
% Examples:
%
% prompt={'Enter the matrix size for x^2:','Enter the colormap name:'};
% name='Input for Peaks function';
% numlines=1;
% defaultanswer={'20','hsv'};
%
% answer=zinputdlg(prompt,name,numlines,defaultanswer);
%
% options.Resize='on';
% options.WindowStyle='normal';
% options.Interpreter='tex';
%
% answer=zinputdlg(prompt,name,numlines,defaultanswer,options);
%
% See also DIALOG, ERRORDLG, HELPDLG, LISTDLG, MSGBOX,
% QUESTDLG, TEXTWRAP, UIWAIT, WARNDLG .
% Copyright 1994-2007 The MathWorks, Inc.
% $Revision$
%%%%%%%%%%%%%%%%%%%%
%%% Nargin Check %%%
%%%%%%%%%%%%%%%%%%%%
error(nargchk(0,5,nargin));
error(nargoutchk(0,1,nargout));
%%%%%%%%%%%%%%%%%%%%%%%%%
%%% Handle Input Args %%%
%%%%%%%%%%%%%%%%%%%%%%%%%
if nargin<1
Prompt='Input:';
end
if ~iscell(Prompt)
Prompt={Prompt};
end
NumQuest=numel(Prompt);
if nargin<2,
Title=' ';
end
if nargin<3
NumLines=1;
end
if nargin<4
DefAns=cell(NumQuest,1);
for lp=1:NumQuest
DefAns{lp}='';
end
end
if nargin<5
Resize = 'off';
end
WindowStyle='modal';
Interpreter='none';
Options = struct([]); %#ok
if nargin==5 && isstruct(Resize)
Options = Resize;
Resize = 'off';
if isfield(Options,'Resize'), Resize=Options.Resize; end
if isfield(Options,'WindowStyle'), WindowStyle=Options.WindowStyle; end
if isfield(Options,'Interpreter'), Interpreter=Options.Interpreter; end
end
[rw,cl]=size(NumLines);
OneVect = ones(NumQuest,1);
if (rw == 1 & cl == 2) %#ok Handle []
NumLines=NumLines(OneVect,:);
elseif (rw == 1 & cl == 1) %#ok
NumLines=NumLines(OneVect);
elseif (rw == 1 & cl == NumQuest) %#ok
NumLines = NumLines';
elseif (rw ~= NumQuest | cl > 2) %#ok
error('MATLAB:inputdlg:IncorrectSize', 'NumLines size is incorrect.')
end
if ~iscell(DefAns),
error('MATLAB:inputdlg:InvalidDefaultAnswer', 'Default Answer must be a cell array of strings.');
end
%%%%%%%%%%%%%%%%%%%%%%%
%%% Create InputFig %%%
%%%%%%%%%%%%%%%%%%%%%%%
FigWidth=175;
FigHeight=100;
FigPos(3:4)=[FigWidth FigHeight]; %#ok
FigColor=get(0,'DefaultUicontrolBackgroundcolor');
InputFig=dialog( ...
'Visible' ,'off' , ...
'KeyPressFcn' ,@doFigureKeyPress, ...
'Name' ,Title , ...
'Pointer' ,'arrow' , ...
'Units' ,'pixels' , ...
'UserData' ,'Cancel' , ...
'Tag' ,Title , ...
'HandleVisibility' ,'callback' , ...
'Color' ,FigColor , ...
'NextPlot' ,'add' , ...
'WindowStyle' ,WindowStyle, ...
'DoubleBuffer' ,'on' , ...
'Resize' ,Resize ...
);
%%%%%%%%%%%%%%%%%%%%%
%%% Set Positions %%%
%%%%%%%%%%%%%%%%%%%%%
DefOffset = 5;
DefBtnWidth = 53;
DefBtnHeight = 23;
TextInfo.Units = 'pixels' ;
TextInfo.FontSize = get(0,'FactoryUIControlFontSize');
TextInfo.FontWeight = get(InputFig,'DefaultTextFontWeight');
TextInfo.HorizontalAlignment= 'left' ;
TextInfo.HandleVisibility = 'callback' ;
StInfo=TextInfo;
StInfo.Style = 'text' ;
StInfo.BackgroundColor = FigColor;
EdInfo=StInfo;
EdInfo.FontWeight = get(InputFig,'DefaultUicontrolFontWeight');
EdInfo.Style = 'edit';
EdInfo.BackgroundColor = 'white';
BtnInfo=StInfo;
BtnInfo.FontWeight = get(InputFig,'DefaultUicontrolFontWeight');
BtnInfo.Style = 'pushbutton';
BtnInfo.HorizontalAlignment = 'center';
% Add VerticalAlignment here as it is not applicable to the above.
TextInfo.VerticalAlignment = 'bottom';
TextInfo.Color = get(0,'FactoryUIControlForegroundColor');
% adjust button height and width
btnMargin=1.4;
ExtControl=uicontrol(InputFig ,BtnInfo , ...
'String' ,'OK' , ...
'Visible' ,'off' ...
);
% BtnYOffset = DefOffset;
BtnExtent = get(ExtControl,'Extent');
BtnWidth = max(DefBtnWidth,BtnExtent(3)+8);
BtnHeight = max(DefBtnHeight,BtnExtent(4)*btnMargin);
delete(ExtControl);
% Determine # of lines for all Prompts
TxtWidth=FigWidth-2*DefOffset;
ExtControl=uicontrol(InputFig ,StInfo , ...
'String' ,'' , ...
'Position' ,[ DefOffset DefOffset 0.96*TxtWidth BtnHeight ] , ...
'Visible' ,'off' ...
);
WrapQuest=cell(NumQuest,1);
QuestPos=zeros(NumQuest,4);
for ExtLp=1:NumQuest
if size(NumLines,2)==2
[WrapQuest{ExtLp},QuestPos(ExtLp,1:4)]= ...
textwrap(ExtControl,Prompt(ExtLp),NumLines(ExtLp,2));
else
[WrapQuest{ExtLp},QuestPos(ExtLp,1:4)]= ...
textwrap(ExtControl,Prompt(ExtLp),80);
end
end % for ExtLp
delete(ExtControl);
QuestWidth =QuestPos(:,3);
QuestHeight=QuestPos(:,4);
TxtHeight=QuestHeight(1)/size(WrapQuest{1,1},1)+10;
EditHeight=TxtHeight*NumLines(:,1);
EditHeight(NumLines(:,1)==1)=EditHeight(NumLines(:,1)==1)+4;
FigHeight=(NumQuest+2)*DefOffset + ...
BtnHeight+sum(EditHeight) + ...
sum(QuestHeight);
TxtXOffset=DefOffset;
QuestYOffset=zeros(NumQuest,1);
EditYOffset=zeros(NumQuest,1);
QuestYOffset(1)=FigHeight-DefOffset-QuestHeight(1);
EditYOffset(1)=QuestYOffset(1)-EditHeight(1);
for YOffLp=2:NumQuest,
QuestYOffset(YOffLp)=EditYOffset(YOffLp-1)-QuestHeight(YOffLp)-DefOffset;
EditYOffset(YOffLp)=QuestYOffset(YOffLp)-EditHeight(YOffLp);
end % for YOffLp
QuestHandle=[]; %#ok
EditHandle=[];
AxesHandle=axes('Parent',InputFig,'Position',[0 0 1 1],'Visible','off');
inputWidthSpecified = false;
for lp=1:NumQuest,
if ~ischar(DefAns{lp}),
delete(InputFig);
error('MATLAB:inputdlg:InvalidInput', 'Default Answer must be a cell array of strings.');
end
EditHandle(lp)=uicontrol(InputFig , ...
EdInfo , ...
'Max' ,NumLines(lp,1) , ...
'Position' ,[ TxtXOffset EditYOffset(lp) TxtWidth EditHeight(lp) ], ...
'String' ,DefAns{lp} , ...
'Tag' ,'Edit' ...
);
%force the damned thing to respond on 'enter' too
if (NumLines(lp,1) == 1),
%set (EditHandle(lp), 'KeyPressFcn',@doEditKeyPress);
set (EditHandle(lp), 'Callback', @doCallback);
end
QuestHandle(lp)=text('Parent' ,AxesHandle, ...
TextInfo , ...
'Position' ,[ TxtXOffset QuestYOffset(lp)], ...
'String' ,WrapQuest{lp} , ...
'Interpreter',Interpreter , ...
'Tag' ,'Quest' ...
);
MinWidth = max(QuestWidth(:));
if (size(NumLines,2) == 2)
% input field width has been specified.
inputWidthSpecified = true;
EditWidth = setcolumnwidth(EditHandle(lp), NumLines(lp,1), NumLines(lp,2));
MinWidth = max(MinWidth, EditWidth);
end
FigWidth=max(FigWidth, MinWidth+2*DefOffset);
end % for lp
% fig width may have changed, update the edit fields if they dont have user specified widths.
if ~inputWidthSpecified
TxtWidth=FigWidth-2*DefOffset;
for lp=1:NumQuest
set(EditHandle(lp), 'Position', [TxtXOffset EditYOffset(lp) TxtWidth EditHeight(lp)]);
end
end
FigPos=get(InputFig,'Position');
FigWidth=max(FigWidth,2*(BtnWidth+DefOffset)+DefOffset);
FigPos(1)=0;
FigPos(2)=0;
FigPos(3)=FigWidth;
FigPos(4)=FigHeight;
set(InputFig,'Position',zgetnicedialoglocation(FigPos,get(InputFig,'Units')));
OKHandle=uicontrol(InputFig , ...
BtnInfo , ...
'Position' ,[ FigWidth-2*BtnWidth-2*DefOffset DefOffset BtnWidth BtnHeight ] , ...
'KeyPressFcn',@doControlKeyPress , ...
'String' ,'OK' , ...
'Callback' ,@doCallback , ...
'Tag' ,'OK' , ...
'UserData' ,'OK' ...
);
zsetdefaultbutton(InputFig, OKHandle);
CancelHandle=uicontrol(InputFig , ...
BtnInfo , ...
'Position' ,[ FigWidth-BtnWidth-DefOffset DefOffset BtnWidth BtnHeight ] , ...
'KeyPressFcn',@doControlKeyPress , ...
'String' ,'Cancel' , ...
'Callback' ,@doCallback , ...
'Tag' ,'Cancel' , ...
'UserData' ,'Cancel' ...
); %#ok
handles = guihandles(InputFig);
handles.MinFigWidth = FigWidth;
handles.FigHeight = FigHeight;
handles.TextMargin = 2*DefOffset;
guidata(InputFig,handles);
set(InputFig,'ResizeFcn', {@doResize, inputWidthSpecified});
% make sure we are on screen
movegui(InputFig)
% if there is a figure out there and it's modal, we need to be modal too
if ~isempty(gcbf) && strcmp(get(gcbf,'WindowStyle'),'modal')
set(InputFig,'WindowStyle','modal');
end
set(InputFig,'Visible','on');
drawnow;
if ~isempty(EditHandle)
uicontrol(EditHandle(1));
end
if ishandle(InputFig)
% Go into uiwait if the figure handle is still valid.
% This is mostly the case during regular use.
uiwait(InputFig);
end
% Check handle validity again since we may be out of uiwait because the
% figure was deleted.
if ishandle(InputFig)
Answer={};
if strcmp(get(InputFig,'UserData'),'OK'),
Answer=cell(NumQuest,1);
for lp=1:NumQuest,
Answer(lp)=get(EditHandle(lp),{'String'});
end
end
delete(InputFig);
else
Answer={};
end
function doFigureKeyPress(obj, evd) %#ok
switch(evd.Key)
case {'return','space'}
set(gcbf,'UserData','OK');
uiresume(gcbf);
case {'escape'}
delete(gcbf);
end
function doEditKeyPress(obj, evd) %#ok
switch(evd.Key)
case {'return'}
set(gcbf,'UserData','OK');
uiresume(gcbf);
case 'escape'
delete(gcbf)
end
function doControlKeyPress(obj, evd) %#ok
switch(evd.Key)
case {'return'}
if ~strcmp(get(obj,'UserData'),'Cancel')
set(gcbf,'UserData','OK');
uiresume(gcbf);
else
delete(gcbf)
end
case 'escape'
delete(gcbf)
end
function doCallback(obj, evd) %#ok
if ~strcmp(get(obj,'UserData'),'Cancel')
set(gcbf,'UserData','OK');
uiresume(gcbf);
else
delete(gcbf)
end
function doResize(FigHandle, evd, multicolumn) %#ok
% TBD: Check difference in behavior w/ R13. May need to implement
% additional resize behavior/clean up.
Data=guidata(FigHandle);
resetPos = false;
FigPos = get(FigHandle,'Position');
FigWidth = FigPos(3);
FigHeight = FigPos(4);
if FigWidth < Data.MinFigWidth
FigWidth = Data.MinFigWidth;
FigPos(3) = Data.MinFigWidth;
resetPos = true;
end
% make sure edit fields use all available space if
% number of columns is not specified in dialog creation.
if ~multicolumn
for lp = 1:length(Data.Edit)
EditPos = get(Data.Edit(lp),'Position');
EditPos(3) = FigWidth - Data.TextMargin;
set(Data.Edit(lp),'Position',EditPos);
end
end
if FigHeight ~= Data.FigHeight
FigPos(4) = Data.FigHeight;
resetPos = true;
end
if resetPos
set(FigHandle,'Position',FigPos);
end
% set pixel width given the number of columns
function EditWidth = setcolumnwidth(object, rows, cols)
% Save current Units and String.
old_units = get(object, 'Units');
old_string = get(object, 'String');
old_position = get(object, 'Position');
set(object, 'Units', 'pixels')
set(object, 'String', char(ones(1,cols)*'x'));
new_extent = get(object,'Extent');
if (rows > 1)
% For multiple rows, allow space for the scrollbar
new_extent = new_extent + 19; % Width of the scrollbar
end
new_position = old_position;
new_position(3) = new_extent(3) + 1;
set(object, 'Position', new_position);
% reset string and units
set(object, 'String', old_string, 'Units', old_units);
EditWidth = new_extent(3);
% A local version of matlab's getnicedialoglocation
function figure_size = zgetnicedialoglocation(figure_size, figure_units)
% adjust the specified figure position to fig nicely over GCBF
% or into the upper 3rd of the screen
% Copyright 1999-2006 The MathWorks, Inc.
% $Revision$
%%%%%% PLEASE NOTE %%%%%%%%%
%%%%%% This file has also been copied into:
%%%%%% matlab/toolbox/ident/idguis
%%%%%% If this functionality is changed, please
%%%%%% change it also in idguis.
%%%%%% PLEASE NOTE %%%%%%%%%
parentHandle = gcbf;
propName = 'Position';
if isempty(parentHandle)
parentHandle = 0;
propName = 'ScreenSize';
end
old_u = get(parentHandle,'Units');
set(parentHandle,'Units',figure_units);
container_size=get(parentHandle,propName);
set(parentHandle,'Units',old_u);
figure_size(1) = container_size(1) + 1/2*(container_size(3) - figure_size(3));
figure_size(2) = container_size(2) + 2/3*(container_size(4) - figure_size(4));
% A local version of matlab's setdefaultbutton
function zsetdefaultbutton(figHandle, btnHandle)
% WARNING: This feature is not supported in MATLAB and the API and
% functionality may change in a future release.
%SETDEFAULTBUTTON Set default button for a figure.
% SETDEFAULTBUTTON(BTNHANDLE) sets the button passed in to be the default button
% (the button and callback used when the user hits "enter" or "return"
% when in a dialog box.
%
% This function is used by inputdlg.m, msgbox.m, questdlg.m and
% uigetpref.m.
%
% Example:
%
% f = figure;
% b1 = uicontrol('style', 'pushbutton', 'string', 'first', ...
% 'position', [100 100 50 20]);
% b2 = uicontrol('style', 'pushbutton', 'string', 'second', ...
% 'position', [200 100 50 20]);
% b3 = uicontrol('style', 'pushbutton', 'string', 'third', ...
% 'position', [300 100 50 20]);
% setdefaultbutton(b2);
%
% Copyright 2005-2007 The MathWorks, Inc.
%--------------------------------------- NOTE ------------------------------------------
% This file was copied into matlab/toolbox/local/private.
% These two files should be kept in sync - when editing please make sure
% that *both* files are modified.
% Nargin Check
if nargin<1, error('MATLAB:setdefaultbutton:InvalidNumberOfArguments','Too few arguments for setdefaultbutton'); end
if nargin>2, error('MATLAB:setdefaultbutton:InvalidNumberOfArguments','Too many arguments for setdefaultbutton'); end
if (usejava('awt') == 1)
% We are running with Java Figures
useJavaDefaultButton(figHandle, btnHandle)
else
% We are running with Native Figures
useHGDefaultButton(figHandle, btnHandle);
end
function useJavaDefaultButton(figH, btnH)
% Get a UDD handle for the figure.
fh = handle(figH);
% Call the setDefaultButton method on the figure handle
fh.setDefaultButton(btnH);
function useHGDefaultButton(figHandle, btnHandle)
% First get the position of the button.
btnPos = getpixelposition(btnHandle);
% Next calculate offsets.
leftOffset = btnPos(1) - 1;
bottomOffset = btnPos(2) - 2;
widthOffset = btnPos(3) + 3;
heightOffset = btnPos(4) + 3;
% Create the default button look with a uipanel.
% Use black border color even on Mac or Windows-XP (XP scheme) since
% this is in natve figures which uses the Win2K style buttons on Windows
% and Motif buttons on the Mac.
h1 = uipanel(get(btnHandle, 'Parent'), 'HighlightColor', 'black', ...
'BorderType', 'etchedout', 'units', 'pixels', ...
'Position', [leftOffset bottomOffset widthOffset heightOffset]);
% Make sure it is stacked on the bottom.
uistack(h1, 'bottom');
|
github
|
lcnbeapp/beapp-master
|
afni_niml_read.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/afni_niml_read.m
| 2,791 |
utf_8
|
3da5cff1cf07ffd470bd42539f8078b9
|
function [p,s]=afni_niml_read(fn)
% simple function to read niml files
%
% P=AFNI_NIML_READ(FN) reads a file FN and returns a NIML structure P.
% [P,S]=AFNI_NIML_READ(FN) also returns the file contents S
%
% If FN refers to a file in another format than ASCII NIML, an attempt is
% made to convert the file to this format with AFNI's ConvertDset
%
% NNO Dec 2009 <[email protected]>
s=simpleread(fn);
[b1, ext]=is_non_niml_ascii(fn); % if the extension suggests that it is not ASCII NIML
if b1 || is_non_niml_ascii(s); % ... or the file contents suggest this
% then we try to convert the file
warning('Input file seems to be not a NIML ASCII file, will try to convert it to ascii');
s=binaryToASCII(s,ext);
end
p=afni_niml_parse(s);
function s=simpleread(fn)
fprintf('Reading %s\n', fn);
fid=fopen(fn);
if fid==-1
error('Error reading from file %s\n', fn);
end
s=fread(fid,inf,'char=>char');
fclose(fid);
s=s';
function sa=binaryToASCII(sb,ext)
% converts a non-ASCII NIML file to an ASCII NIML file
% ext is the extension of the input file
% keep looking for a temporary file name that does not exist yet
rand('twister',sum(100*clock)); % initialize random number generator
while true
idx=floor(rand()*1e6);
prefix=sprintf('__TMP_%d',idx);
tmpfn1=sprintf('%s_in%s',prefix,ext); % input
tmpfn2=sprintf('%s_out%s',prefix,'.niml.dset'); % output
if ~exist(tmpfn1,'file') && ~exist(tmpfn2,'file')
break;
end
end
fid=fopen(tmpfn1,'w');
if fid<0
error('Could not open temporary file for writing');
end
fwrite(fid,sb);
fclose(fid);
cmd=sprintf('ConvertDset -input %s -o_niml_asc -prefix %s', tmpfn1, tmpfn2);
fprintf('Running command: %s\n', cmd);
[a,w]=unix(cmd);
if a ~= 0
fprintf(w)
error('Error when trying to convert binary to ascii');
end
fprintf('Conversion was successful\n');
% read the output file
sa=simpleread(tmpfn2);
% clean up
delete(tmpfn1);
delete(tmpfn2);
function [b,ext]=is_non_niml_ascii(s)
% tries to determine whether the file is niml ascii or not
% - input argument can either be a filename or the contents of the file
% - ouput contains whether it's a NIML ASCII file, and the extension
[ffff,fn,ext1]=fileparts(s);
if exist(s,'file')
% s is a filename
exts={'.gii','1D'};
b=~isempty(strmatch(lower(ext1),exts));
[ffff,fffff,ext2]=fileparts(fn);
ext=[ext2 ext1]; % in case there is a double extension such as .niml.dset
else
% s contains the file contents
expr='<(?<h>\w+).*ni_form\s*=\s*"(?<rhs>[^"]+)".*</\1>';
hh=regexp(s,expr,'names');
b=false;
for k=1:numel(hh)
b=~isempty(findstr(hh(k).rhs,'binary.'));
if b
return
end
end
ext=NaN; %unknown
end
|
github
|
lcnbeapp/beapp-master
|
afni_nel_parse.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/afni_nel_parse.m
| 1,763 |
utf_8
|
62fbd076a3c4430f06f6385abc18b2d8
|
function [nel] = afni_nel_parse(nellcell)
%should really check that this is nel and not ngr ...
%assuming we have nel
%get the header part
cnel = char(nellcell); clear nellcell;
ncnel = length(cnel);
%break up into head and data
expr = '(?<head><(\w+).*?>)(?<data>.*)<';
%using expr = '(?<head><(\w+).*?>)(?<data>.*<.*>)';
%would get all of the data chunk including its closing tag
%but then I'd have to strip it...
[pp] = regexp(cnel,expr,'names');
%Now get the header fields into structs
hh = regexp(pp.head, '(?<lhs>\w*)="(?<rhs>\S*)"','names');
nel = cell2struct({hh(:).rhs}, {hh(:).lhs},2); clear hh;
tt = nel.ni_type;
nel.vec_typ=zeros(1,1000); nn=0;
while (~isempty(tt)),
[ttt,tt] = strtok(tt, ',');
%look for the N*type syntax
N = 1;
[tttt,ttt] = strtok(ttt,'*');
Ntttt = str2double(tttt);
if (~isnan(Ntttt)), %have a number, get the type
N = Ntttt;
tttt = strtok(ttt,'*');
end
nel.vec_typ(nn+1:1:nn+N) = afni_ni_rowtype_name_to_code(tttt);
nn = nn + N;
end
%interpret some things
nel.name = char(strtok(regexp(pp.head,'<\w+', 'match'),'<'));
nel.vec_typ = nel.vec_typ(1:nn);
nel.vec_len = str2num(nel.ni_dimen);
nel.vec_num = length(nel.vec_typ);
%Now parse the data
if (~afni_ni_is_numeric_type(nel.vec_typ)),
fprintf(2,'Data not all numeric, will not parse it');
nel.data = pp.data;
else
nel = afni_nel_parse_data(nel, pp.data);
end
clear pp
return;
function [nel] = afni_nel_parse_data(nel, data)
nel.data = reshape(sscanf(data,'%f'), nel.vec_num, nel.vec_len)';
return;
|
github
|
lcnbeapp/beapp-master
|
afni_niml_print.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/afni_niml_print.m
| 5,521 |
utf_8
|
9dbc69da949e82e64071c668290ac2da
|
function s=afni_niml_print(p)
% takes a NIML data structure and converts it to string representation
%
% S=AFNI_NIML_PRINT(P) takes an NIML datastructure P and returns a string
% representation S.
%
% This function is more or less the inverse of AFNI_NIML_PARSE.
%
% The current implementation will take any struct that has the required
% NIML fields; it does not check for any data consisentence.
%
% Please note that this function is *VERY EXPERIMENTAL*.
%
% NNO Dec 2009 <[email protected]>
if iscell(p)
ss=cell(1,numel(p));
% simple recursion
for k=1:numel(p)
ss{k}=afni_niml_print(p{k});
end
s=[ss{:}]; % concatenate
else
headername=p.name;
p=rmfield(p,'name'); % we don't want this as a field
if isfield(p,'nodes')
% is a group, do recursion
sbody=afni_niml_print(p.nodes);
p=rmfield(p,'nodes'); % 'nodes' is not a standard NIML field
elseif isfield(p,'data')
if ~isfield(p,'vec_typ')
% in case the type is not specified, we try
% to derive it based on the type of p.data
ps=derive_vec_type(p.data);
% set field names if not set
fns=fieldnames(ps);
for k=1:numel(fns)
if ~isfield(p,fns{k})
p.(fns{k})=ps.(fns{k});
end
end
elseif p.vec_typ<0;
error('vec_typ=%d not supported (yet)', p.vec_typ);
end
sbody=afni_niml_print_body(p);
% some fields are not standard NIML (I think), we remove these
removefields=strvcat('vec_typ','vec_len','vec_num','name','data');
fns=fieldnames(p);
for k=1:numel(fns)
fn=fns{k};
if ~isempty(strmatch(fn,removefields,'exact'))
p=rmfield(p,fn);
end
end
else
disp(p)
error('Do not understand this struct');
end
headertext=afni_niml_print_header(p);
s=sprintf('<%s\n%s >\n%s</%s>\n',headername,headertext,sbody,headername);
end
function s=afni_niml_print_body(p)
format=get_print_format(p.vec_typ,p.data);
if strcmp(format,'%s')
around='"'; %surround by quotes if it is a string - CHECKME is that according to the standard?
else
around='';
p.data=p.data'; %transpose to fix major row vs. major column order
end
s=sprintf([format '\n'],p.data);
s=[around s(1:(end-1)) around]; % remove last newline
function s=afni_niml_print_header(p)
pre=' '; % a bit of indendationn
post=sprintf('\n'); % every header gets a new line
fns=fieldnames(p);
n=numel(fns);
ss=cell(1,n);
for k=1:n
fn=fns{k};
val=strtrim(p.(fn));
if isnumeric(val)
warning('Converting numeric to string for field %s\n', fn);
val=num2str(val);
end
% surround by quotes, if that's not the case yet
if val(1) ~= '"' && val(end) ~= '"'
val=['"' val '"'];
end
if k==n
post=''; %no new line at the very end
end
ss{k}=sprintf('%s%s=%s%s',pre,fn,val,post);
end
s=[ss{:}]; % concatenate results
function p=derive_vec_type(data)
% sets the vector type, in case this is not given.
%
% data should be either a string or numeric
% TODO: support structs and cells, and mixed data types
% TODO: allow other fields missing (maybe use the whole struct rather than
% just the data so that we can be 'smart' and use converging
% evidence?
nidefs=afni_ni_defs();
if islogical(data)
data=single(data); % convert to numeric
end
if isnumeric(data)
if isequal(round(data),data)
tp=nidefs.NI_INT;
else
tp=nidefs.NI_FLOAT;
end
[ln,nm]=size(data);
elseif ischar(data)
tp=nidefs.NI_STRING;
ln=1;
nm=1;
else
disp(data)
error('Unknown data type');
end
if nm>1
prefix=sprintf('%d*',nm);
else
prefix='';
end
tps=strtrim(nidefs.type_name(tp+1,:)); % tricky base0 vs base1
p.ni_type=[prefix tps];
p.ni_dimen=sprintf('%d',ln); %NNO Jan 2010 fix
p.vec_typ=repmat(tp,1,nm); % tricky base0 vs base1 % Jan 2010: removed 'tp+1'
p.vec_len=ln;
p.vec_num=nm;
function f=get_print_format(vec_typ,data,nidefs)
% use vec_typ to create a format string for printf
% data is used in case we print floats; we use the least possible number of
% floating point positions
if nargin<3
nidefs=afni_ni_defs();
end
n=numel(vec_typ);
if n>1
if size(data,2) ~= n
error('Mismatch between data and vec_typ: %d ~= %d', n, size(data,2));
end
fs=cell(1,n);
for k=1:n
if k<n
addend=' '; % spacing between elements ...
else
addend=''; % ... except for the last element
end
% recursion
fs{k}=[get_print_format(vec_typ(k),data(:,k),nidefs) addend];
end
f=[fs{:}]; % concatenate result
else
vec_str=strtrim(nidefs.type_name(vec_typ+1,:)); %tricky again, base0 vs base1
switch vec_str
case 'String'
f='%s';
case {'byte','short','int'} % CHECKME don't know if this is ok for bytes and shorts...
f='%d';
otherwise
precision=get_required_precision(data);
f=sprintf('%%.%df',precision);
end
end
|
github
|
lcnbeapp/beapp-master
|
CA_EZ_Prep.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/CA_EZ_Prep.m
| 14,358 |
utf_8
|
af87e1ccd31dc096f0a411e877de8dd9
|
function [MapMPM, MapML, aur] = CA_EZ_Prep()
% A function to process a new Eickhoff, Amunts and Zilles CA toolbox
% The function creates new versions of AFNI's source files
% thd_ttatlas_CA_EZ.c and thd_ttatlas_CA_EZ.h .
% The new files created are called thd_ttatlas_CA_EZ-auto.c and thd_ttatlas_CA_EZ-auto.h
% must be inspected then moved and renamed into afni's src directory.
%
% See SUMA/Readme_Modify.log for info on sequence of execution
% search for: + How you install a new Zilles, Amunts, Eickhoff SPM toolbox:%
%
% See also scripts:
% @Prep_New_CA_EZ
% @Compare_CA_EZ
% @Create_suma_tlrc.tgz
% @Create_ca_ez_tlrc.tgz
% @DistArchives
% ZSS SSCC Feb 06
FuncName = 'CA_EZ_Prep';
MapMPM = [];
MapML = [];
toolbox_dir = '/Volumes/afni/home4/users/ziad/Programs/matlab/spm2/toolbox/Anatomy';
if (exist(toolbox_dir) ~= 7),
fprintf(2,'Toolbox directory %s not found\nPick a new one:', toolbox_dir);
toolbox = uigetdir(sprintf('.%c', filesep), 'Standard toobox dir not found. Pick a new one:');
if (exist(toolbox_dir) ~= 7),
fprintf(2,'Toolbox directory %s not found.', toolbox_dir);
return;
end
else
%get around the symbolic linc so that reference is to actual directory ...
curdir = pwd;
cd (toolbox_dir);
toolbox_dir = pwd;
cd (curdir);
[err,pt] = GetPath(toolbox_dir);
[err,sout] = unix(sprintf('ls -l %s', pt));
c = input(sprintf('Found toolbox here: %s\nDirectory Listing:\n%s\nEnter "y" to use it, anything else to quit.\n', toolbox_dir, sout),'s');
if (isempty(c) || ( c(1) ~= 'y' && c(1) ~= 'Y' ) ),
return;
end
end
fprintf(1,'Using toolbox directoy %s...\n', toolbox_dir);
%First get the MPM info
prf = sprintf('%s%cAllAreas*MPM.mat', toolbox_dir, filesep);
[err, ErrMessage, MPM_file] = zglobb ({prf});
if (size(MPM_file,1) ~= 1),
fprintf(2,'Could not find unique MPM map list\n', toolbox_dir);
for (i=1:1:size(MPM_file,1)), MPM_file(i), end
return;
end
%load the MPM map structure
MapMPM = load(MPM_file(1).name);
MapMPM = MapMPM.MAP;
%checks
if (~isstruct(MapMPM)),
fprintf(2,'MapMPM is not a struct\n');
return;
end
fld = 'name';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'GV';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'ref';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'smoothed';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'VOL';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'MaxMap';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'XYZ';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'XYZmm';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'orient';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'Z';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'LR';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'allXYZ';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'allZ';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
fld = 'allLR';
if (~isfield (MapMPM, fld)), fprintf(2,'%s field is not in MapMPM\n', fld); return; end
%Now the MacroLabels
prf = sprintf('%s%cMacro.mat', toolbox_dir, filesep);
[err, ErrMessage, ML_file] = zglobb ({prf});
if (size(ML_file,1) ~= 1),
fprintf(2,'Could not find unique ML map list\n', toolbox_dir);
for (i=1:1:size(ML_file,1)), ML_file(i), end
return;
end
%load the MacroLabels
MapML = load(ML_file(1).name);
MapML = MapML.Labels;
if (~iscellstr(MapML)),
fprintf(2,'MacroLabels variable not the expected cellstr\n');
return;
end
for (i=1:1:length(MapML)),
MapML(i) = cellstr(fix_string(char(MapML(i))));
end
MapML = char(MapML);
%Output files
cname = 'thd_ttatlas_CA_EZ-auto.c';
hname = 'thd_ttatlas_CA_EZ-auto.h';
rname = 'thd_ttatlas_CA_EZ-ref.h';
%Do the references
% a horrible mess of an if block below. One hopes for a better solution someday
if (~isempty(which('se_note'))),
fprintf(1,'\nNow trying to get at references using se_note\n');
se_note;
k = 0;
vers = '';
if (exist('fg')),
h = get(fg, 'Children');
cs = [];
nref = 0;
l = 1;
for (i=1:1:length(h)),
tmp = get(h(i),'String')
if (~isempty(tmp)),
k = k + 1;
cs(k).s = tmp;
if (iscellstr(cs(k).s) && length(cs(k).s) > 1),
if (length(cs(k).s) > 5), %papers
nref = nref + 1;
ref(nref) = k;
cs(k).typ = 1;
else
cs(k).typ = -1; %the authors's info
au = cellstr(cs(k).s);
end
else
cs(k).typ = 0; %other strings
ot(l) = cellstr(cs(k).s);
if (~isempty(strfind(char(ot(l)), 'Version'))),
vers = zdeblank(char(ot(l)));
end
l = l + 1;
end
end
end
if (isempty(vers)),
fprintf(2,'Version string not found!\n');
return;
else
fprintf(2,'Version set to %s\n', vers);
end
% find the corresponding references
ti = char(cs(ref(1)).s); ar = char(cs(ref(2)).s);
if (nref ~= 2 || (size(ar,1) ~= size(ti,1))),
fprintf(2,'Warning:\nUnexpected number of ref strings or some mismatch (%d, %d, %d)\nYou have to edit thd_ttat', nref, size(ar,1), size(ti,1));
sdecl = sprintf('char CA_EZ_REF_STR[128][256]');
sdecl2 = sprintf('char CA_EZ_VERSION_STR[128]');
%return;
else
k = 1;
l = 1;
ar_tmp = '';
ti_tmp = '';
while (k<=size(ar,1)),
if (sum(isspace(ar(k))) == size(k,2) && ~isempty(ar_tmp)), % all space, combine
ca(l) = cellstr([ar_tmp '-x->' ti_tmp]);
ar_tmp = '';
ti_tmp = '';
l = l + 1;
else %catenate
ar_tmp = [ar_tmp ' ' deblank(ar(k,:))];
ti_tmp = [ti_tmp ' ' deblank(ti(k,:))];
end
k = k + 1;
end
%Now fix up the looks of the list DO NOT CHANGE USAGE OF '-----> ' for padding, C function PrettyRef depends on them
imx = 0;
for (l=1:1:length(ca)),
isep = strfind(char(ca(l)), '-x->');
imx = max(isep, imx);
end
for (l=1:1:length(ca)),
isep = strfind(char(ca(l)), '-x->');
ca_tmp = char(ca(l));
c1 = pad_strn(ca_tmp(1:isep), '-', imx, -1);
c2 = ca_tmp(isep+4:length(ca_tmp));
ca(l) = cellstr([c1 '>' c2]);
end
aur = char(au);
iout = find (aur < 32 | aur > 127); %replace characters outside of basci ascii text
aur(iout) = '-'; %dunno what to do yet....
otr = flipud(char(ot));
car = char(ca);
sdecl = sprintf('char CA_EZ_REF_STR[%d][%d]', size(otr,1)+size(aur,1)+size(car,1)+10, max([size(otr,2)+15, size(aur,2)+15,size(car,2)+15]));
sdecl2 = sprintf('char CA_EZ_VERSION_STR[%d]',length(vers)+3);
%do someting nice
fida = fopen(rname,'w');
fprintf(fida, '%s = {\n',sdecl);
fprintf(fida, '"%s",\n"%s",\n"%s",\n',otr(1,:), otr(2,:), otr(3,:));
for (i=1:1:size(aur,1)), fprintf(fida, '" %s",\n', aur(i,:)); end
fprintf(fida, '"%s",\n', otr(4,:));
for (i=1:1:size(car,1)), fprintf(fida, '" %s",\n', car(i,:)); end
fprintf(fida, '"%s",\n', otr(5,:));
fprintf(fida, '" ",\n" ",\n"AFNI adaptation by",\n" Ziad S. Saad ([email protected], SSCC/NIMH/NIH)",\n');
fprintf(fida, '" Info automatically created with CA_EZ_Prep.m based on se_note.m",\n');
fprintf(fida, '""};/* Must be the only empty string in the array*/\n'); %Must be the only empty string in the array
fprintf(fida, '%s = { "%s" };\n', sdecl2, vers);
fclose(fida);
end
end
else
fprintf(2,'Failed to locate se_note.m\nNo new reference string created');
return;
end
%Prep C output files
fidc = fopen (cname,'w');
if (fidc < 0),
fprintf(2,'Failed to open output .c file\n');
return;
end
fidh = fopen (hname,'w');
if (fidh < 0),
fprintf(2,'Failed to open output .h file\n');
return;
end
str = sprintf('/*! Data for atlases from Eickhoff''s SPM toolbox.\nAutomatically compiled from: %s\n located at: %s\n by function %s\nDate: %s*/\n\n',...
MPM_file(1).name, toolbox_dir, which(FuncName), date);
fprintf(fidh,'%s', str);
fprintf(fidc,'%s', str);
%Add the references string file
fprintf(fidc,'/*! Leave the reference string in a separate file\nfor easy script parsing.*/\n#include "%s"\n\n', rname);
%Now do specifics to .h file
NLbl_ML = size(MapML,1);
MaxLbl_ML = size(MapML,2)+3;
NLbl_MPM = length(MapMPM);
MaxLbl_MPM = 0;
for (i=1:1:NLbl_MPM),
if (MaxLbl_MPM < length(MapMPM(i).name)), MaxLbl_MPM = length(MapMPM(i).name); end
end
MaxLbl_MPM = MaxLbl_MPM+3;
if (MaxLbl_MPM > 64),
fprintf(2,'Error: Labels longer than ATLAS_CMAX defined in AFNI src code.\nIncrease limit here and in thd_ttaltas_query.h\n');
return;
end
fprintf(fidh,'/* ----------- Macro Labels --------------------- */\n');
fprintf(fidh,'/* ----------- Based on: %s -------------*/\n', ML_file(1).name);
fprintf(fidh,'#define ML_EZ_COUNT %d\n\n', NLbl_ML);
fprintf(fidh,'extern ATLAS_point ML_EZ_list[ML_EZ_COUNT] ;\nextern char * ML_EZ_labels[ML_EZ_COUNT] ;\n');
fprintf(fidh,'extern int ML_EZ_labeled ;\nextern int ML_EZ_current ;\n');
fprintf(fidh,'/* ----------- Left Right --------------------- */\n');
fprintf(fidh,'/* ---- Based on my understanding -------------- */\n');
fprintf(fidh,'#define LR_EZ_COUNT 3\n\n');
fprintf(fidh,'extern ATLAS_point LR_EZ_list[LR_EZ_COUNT] ;\nextern char * LR_EZ_labels[LR_EZ_COUNT] ;\n');
fprintf(fidh,'extern int LR_EZ_labeled ;\nextern int LR_EZ_current ;\n\n');
fprintf(fidh,'/* ----------- MPM --------------------- */\n');
fprintf(fidh,'/* ----------- Based on: %s --------------*/\n', MPM_file(1).name);
fprintf(fidh,'#define CA_EZ_COUNT %d\n', NLbl_MPM);
fprintf(fidh,'#define CA_EZ_MPM_MIN 100 /*!< minimum meaningful value in MPM atlas */\n');
fprintf(fidh,'extern ATLAS_point CA_EZ_list[CA_EZ_COUNT] ;\nextern char * CA_EZ_labels[CA_EZ_COUNT] ;\n');
fprintf(fidh,'extern int CA_EZ_labeled ;\nextern int CA_EZ_current ;\n\n');
fprintf(fidh,'/* ----------- Refs --------------------- */\n');
fprintf(fidh,'/* ----------- Based on se_note.m --------------*/\n');
fprintf(fidh,'extern %s;\n', sdecl);
fprintf(fidh,'extern %s;\n', sdecl2);
%first create ML structure
fprintf(fidc,'/* ----------- Macro Labels --------------------- */\n');
fprintf(fidc,'/* ----------- Based on: %s -------------*/\n', ML_file(1).name);
fprintf(fidc,'ATLAS_point ML_EZ_list[ML_EZ_COUNT] = {\n');
for (i=1:1:size(MapML,1)),
%pad string by dots
fprintf(fidc,' { %-3d , "%s", 0, 0, 0, 0, ""}', i, pad_with_dot(MapML(i,:), 50));
if (i<size(MapML,1)) fprintf(fidc,',\n'); else fprintf(fidc,'\n'); end
end
fprintf(fidc,'};\n\n');
%Now create MPM structure
fprintf(fidc,'/* ----------- MPM --------------------- */\n');
fprintf(fidc,'/* ----------- Based on: %s --------------*/\n', MPM_file(1).name);
fprintf(fidc,'ATLAS_point CA_EZ_list[CA_EZ_COUNT] = { \n');
for (i=1:1:NLbl_MPM),
[err,PathString,FileString] = GetPath (MapMPM(i).ref, 1);
fprintf(fidc,' { %-3d, "%s", 0, 0, 0, 0, "%s" }', ...
MapMPM(i).GV, pad_with_dot(MapMPM(i).name,40), pad_with_dot(RemoveExtension(FileString,'.img|.mnc|.hdr'), 27));
if (i<NLbl_MPM) fprintf(fidc,',\n'); else fprintf(fidc,'\n'); end
end
fprintf(fidc,'};\n\n');
%Now create LR structure
fprintf(fidc,'/* ----------- Left Right --------------------- */\n');
fprintf(fidc,'/* ---- Based on my understanding -------------- */\n');
fprintf(fidc,'ATLAS_point LR_EZ_list[LR_EZ_COUNT] = {\n');
Lst = ['Non-Brain...'; 'Right Brain.'; 'Left Brain..'];
for (i=1:1:3),
fprintf(fidc,' { %-3d, "%s", 0, 0, 0, 0, "" }', ...
i-1, Lst(i, :));
if (i<3) fprintf(fidc,',\n'); else fprintf(fidc,'\n'); end
end
fprintf(fidc,'};\n\n');
fclose(fidh); fclose(fidc);
if (exist(rname) == 2),
lst = sprintf('%s, %s and %s', cname, hname, rname);
else
lst = sprintf('%s and %s (%s was not created!)', cname, hname, rname);
end
fprintf(1,'\nThe files:\n %s\n in %s\nare meant to replace\n thd_ttatlas_CA_EZ.c, thd_ttatlas_CA_EZ.h and %s\nin AFNI''s src code.\n',...
lst, pwd, rname) ;
return;
function str = fix_string(stri)
str = stri;
n_str = length(str);
%are you missing a ) ?
i = n_str;
broken = 0;
closed = 0;
while (i > 1 && ~broken),
if (str(i) == ')'),
closed = closed + 1;
elseif (str(i) == '('),
if (closed == 0),
broken = 1;
end
end
i = i - 1;
end
if (broken),
i = n_str;
fixed = 0;
while (i > 1 && ~fixed),
if (~isspace(str(i))),
if (i==n_str), str = [str,')'];
else str(i+1) = ')';
end
fixed = 1;
end
i = i - 1;
end
end
return;
function str = pad_with_dot(stri, ntot)
if (nargin == 2),
str = pad_strn(stri, ' ', ntot, -1);
else
str = stri;
end
n_str = length(str);
i = n_str;
while (i > 1 && isspace(str(i))),
str(i) = '.';
i = i - 1;
end
return;
|
github
|
lcnbeapp/beapp-master
|
ROIcmap.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/afni/ROIcmap.m
| 3,688 |
utf_8
|
93376acea9697c3dce4c73aea3838d9b
|
function [M] = ROIcmap(nc,opt)
% [M] = ROIcmap([nc],[opt]);
% creates a colormap with
% no color too close to grayscale,
% no two consecutive colors too close
% no colors exeedingly close to another in the map
% no colors too close to a background color (optional)
% nc: number of colors in map. Default is 64
% opt: optional options structure
% .show: Figure handle in which to show the map
% Default is 1. Set to 0 for no show.
% In show mode, you get to pick colors with mouse
% and read in their values. Hit enter to exit from
% this mode.
% .state: State of the random number generator.
% Default is 0.
% .write: Name of file to write colormap into
% Default is '', no writing. Use something like
% ROI64s0.1D.cmap, for a 64 cols, seed 0 colormap.
% .avoid: Color to avoid getting close to.
% .verb: verbosioty. 1 is default. 0 is for quiet
% returns
% M: The colormap.
%
%see also readXcol, rgbdectohex, and ScaleToMap
% Ziad S. Saad SSCC/NIMH/NIH, [email protected]
if (nargin == 0),
nc = 64;
opt.show = 1;
elseif (nargin == 1),
opt.show = 1;
end
if (isempty(nc)), nc = 64; end
if (~isfield(opt,'show') | isempty(opt.show)), opt.show = 1; end
if (~isfield(opt,'state') | isempty(opt.state)), opt.state = 0; end
if (~isfield(opt,'write') | isempty(opt.write)), opt.write = ''; end
if (~isfield(opt,'verb') | isempty(opt.verb)), opt.verb = 1; end
if (~isfield(opt,'avoid') | isempty(opt.avoid)), opt.avoid = []; end
%initialize rng
rand('state',opt.state);
M = zeros(nc,3);
alldiff_lim = 0.5; %between 0 and 1, controls how different all colors in map are.
%The first few colors can be quite different, high alldiff_lim
%The difference is adjusted as more colors are demanded.
g_lim = 0.2; %limit for too gray (0-1)
d_lim = 0.40; %limit for too dim (0-3)
b_lim = 2.2; %limit for too bright (0-3)
for (i=1:1:nc),
M(i,:) = rand(1,3);
cnt = 0;
%reject if too gray or too close to previous color
while (toogray(M(i,:), g_lim, d_lim, b_lim) | tooclose(M,i, 0.6, alldiff_lim) | (~isempty(opt.avoid) & (sum(abs(M(i,:)-opt.avoid)) < 0.6))),
M(i,:) = rand(1,3);
cnt = cnt + 1;
if (cnt > 2000), % too tight, relax
alldiff_lim = max([0.95.*alldiff_lim 0.1]) ;
d_lim = max([0.95.*d_lim 0.05]);
b_lim = min([b_lim*1.05, 3.0]);
if (opt.verb) fprintf(1,'Reduced alldiff_lim to %g, d_lim to %g, b_lim to %g\n', alldiff_lim, d_lim, b_lim); end
cnt = 0;
end
end
if (opt.verb) fprintf(1,'Color %d OK\n', i); end
end
if (opt.verb) fprintf(1,'alldiff_lim final was %g, d_lim final was %g, b_lim final was %g\n', alldiff_lim, d_lim, b_lim); end
if (~isempty(opt.write)),
optw.OverWrite = 'p';
wryte3(M, opt.write, optw);
end
if (opt.show),
ShowCmap(M, opt.show);
end
return;
function [a] = toogray(c, g_lim, d_lim, b_lim)
a = 0;
dc = abs(c - mean(c));
cs = sum(c);
if (dc(1) < g_lim & dc(2) < g_lim & dc(3) < g_lim), a = 1; return; end
if (cs < d_lim | cs > b_lim), a = 1; return; end
return;
function [a] = tooclose(M,i,prev_lim, alldiff_lim)
if (i==1), a = 0; return; end
a = 1;
%too close to previous ?
dc = abs(M(i,:)-M(i-1,:));
if (sum(dc) < prev_lim), return; end
%too close to one before?
if (i > 2),
for (j=1:1:i-2),
dc = abs(M(i,:)-M(j,:));
if (dc(1) < alldiff_lim & dc(2) < alldiff_lim & dc(3) < alldiff_lim), return; end
end
end
%OK if you get here
a = 0;
return;
|
github
|
lcnbeapp/beapp-master
|
bemcp_example.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/bemcp/bemcp_example.m
| 21,663 |
utf_8
|
ee954ecd4779bb13a017d139b7a6acb1
|
function bemcp_example
% Simple function to test/demonstrate how the Boundary element functions are
% used in combination with Fildtrip/Forwinv routines.
%
% 1. A model is created as 3 concentric meshed spheres (using FT's
% icosahedron routines),
% 2. then random electrodes are placed on the upper part of the outer
% sphere.
% 3. the model is then "prepared" with 'ft_prepare_bemmodel', this bits
% takes most time as it requires LOTS of calculation.
% 4. sensors and volumes are plugged together by 'forwinv_prepare_vol_sens'
% 5. Finally the leadfiled for 3 orthogonal sources placed at one location
% is calculated with 'forwinv_compute_leadfield.m'
% 6. Display the 3 leadfields
%
% NOTE:
% this bit of code needs access to low level fieldtrip/forwinv routines
% which have been copy/pasted here under.
% Be aware that this way of programming is generally NOT advisable!
% I used it only to ensure a quick & dirty check of the BEM module...
% Christophe Phillips
% $Id$
% create volume conductor starting from unit sphere
[pnt, tri] = icosahedron162;
vol = [];
vol.cond = [1 1/80 1];
vol.source = 1; % index of source compartment
vol.skin_surface = 3; % index of skin surface
% inner_skull_surface
vol.bnd(1).pnt = pnt*88;
vol.bnd(1).tri = tri;
% outer_skull_surface
vol.bnd(2).pnt = pnt*92;
vol.bnd(2).tri = tri;
% skin_surface
vol.bnd(3).pnt = pnt*100;
vol.bnd(3).tri = tri;
% create the BEM system matrix
cfg = [];
cfg.method = 'bemcp';
vol1 = ft_prepare_bemmodel(cfg, vol);
% create some random electrodes
pnt = randn(200,3);
pnt = pnt(pnt(:,3)>0, :); % only those on the upper half
sens = [];
for i=1:size(pnt,1)
sens.pnt(i,:) = pnt(i,:) / norm(pnt(i,:)); % scale towards the skin surface
sens.label{i} = sprintf('%02d', i);
end
% prepare the sensor array and volume conduction, i.e. set up the linear
% interpolation from vertices to electrodes
[vol2, sens] = forwinv_prepare_vol_sens(vol1, sens);
lf = forwinv_compute_leadfield([0 0 50], sens, vol2);
figure; triplot(sens.pnt, [], lf(:,1)); colorbar
figure; triplot(sens.pnt, [], lf(:,2)); colorbar
figure; triplot(sens.pnt, [], lf(:,3)); colorbar
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Subfunctions from FieldTrip
function [pnt, tri] = icosahedron162
% ICOSAHEDRON162 creates a 2-fold refined icosahedron
% Copyright (C) 2003, Robert Oostenveld
%
% $Log: icosahedron162.m,v $
% Revision 1.3 2003/11/28 09:40:12 roberto
% added a single help line
%
% Revision 1.2 2003/03/04 21:46:18 roberto
% added CVS log entry and synchronized all copyright labels
%
[pnt, tri] = icosahedron;
[pnt, tri] = refine(pnt, tri);
[pnt, tri] = refine(pnt, tri);
pnt = pnt ./ repmat(sqrt(sum(pnt.^2,2)), 1,3);
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [pnt, tri] = icosahedron
% ICOSAHEDRON creates an icosahedron
%
% [pnt, tri] = icosahedron
% creates an icosahedron with 12 vertices and 20 triangles
%
% See also OCTAHEDRON, ICOSAHEDRON42, ICOSAHEDRON162, ICOSAHEDRON642, ICOSAHEDRON2562
% Copyright (C) 2002, Robert Oostenveld
%
% $Log: icosahedron.m,v $
% Revision 1.4 2006/07/26 11:03:38 roboos
% added "see also octahedron"
%
% Revision 1.3 2003/03/11 15:35:20 roberto
% converted all files from DOS to UNIX
%
% Revision 1.2 2003/03/04 21:46:18 roberto
% added CVS log entry and synchronized all copyright labels
%
tri = [
1 2 3
1 3 4
1 4 5
1 5 6
1 6 2
2 8 3
3 9 4
4 10 5
5 11 6
6 7 2
7 8 2
8 9 3
9 10 4
10 11 5
11 7 6
12 8 7
12 9 8
12 10 9
12 11 10
12 7 11
];
pnt = zeros(12, 3);
rho=0.4*sqrt(5);
phi=2*pi*(0:4)/5;
pnt( 1, :) = [0 0 1]; % top point
pnt(2:6, 1) = rho*cos(phi)';
pnt(2:6, 2) = rho*sin(phi)';
pnt(2:6, 3) = rho/2;
pnt(7:11, 1) = rho*cos(phi - pi/5)';
pnt(7:11, 2) = rho*sin(phi - pi/5)';
pnt(7:11, 3) = -rho/2;
pnt(12, :) = [0 0 -1]; % bottom point
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [pntr, tri] = refine(pnt, tri, method, varargin)
% REFINE a 3D surface that is described by a triangulation
%
% Use as
% [pnt, tri] = refine(pnt, tri)
% [pnt, tri] = refine(pnt, tri, 'updown', numtri)
%
% The default method is to refine the mesh globally by inserting a vertex at
% each edge according to the algorithm described in Banks, 1983.
%
% The alternative 'updown' method refines the mesh a couple of times
% using Banks' algorithm, followed by a downsampling using the REDUCEPATCH
% function.
% The Banks method is a memory efficient implementation which remembers
% the previously inserted vertices. The refinement algorithm executes in
% linear time with the number of triangles.
% Copyright (C) 2002-2005, Robert Oostenveld
%
% $Log: refine.m,v $
% Revision 1.4 2005/05/06 08:54:31 roboos
% added 'updown method, using matlab reducepatch function
%
% Revision 1.3 2003/03/11 15:35:20 roberto
% converted all files from DOS to UNIX
%
% Revision 1.2 2003/03/04 21:46:19 roberto
% added CVS log entry and synchronized all copyright labels
%
if nargin<3
method = 'banks';
end
switch lower(method)
case 'banks'
npnt = size(pnt,1);
ntri = size(tri,1);
insert = spalloc(3*npnt,3*npnt,3*ntri);
tri = zeros(4*ntri,3); % allocate memory for the new triangles
pntr = zeros(npnt+3*ntri,3); % allocate memory for the maximum number of new vertices
pntr(1:npnt,:) = pnt; % insert the original vertices
current = npnt;
for i=1:ntri
if ~insert(tri(i,1),tri(i,2))
current = current + 1;
pntr(current,:) = (pnt(tri(i,1),:) + pnt(tri(i,2),:))/2;
insert(tri(i,1),tri(i,2)) = current;
insert(tri(i,2),tri(i,1)) = current;
v12 = current;
else
v12 = insert(tri(i,1),tri(i,2));
end
if ~insert(tri(i,2),tri(i,3))
current = current + 1;
pntr(current,:) = (pnt(tri(i,2),:) + pnt(tri(i,3),:))/2;
insert(tri(i,2),tri(i,3)) = current;
insert(tri(i,3),tri(i,2)) = current;
v23 = current;
else
v23 = insert(tri(i,2),tri(i,3));
end
if ~insert(tri(i,3),tri(i,1))
current = current + 1;
pntr(current,:) = (pnt(tri(i,3),:) + pnt(tri(i,1),:))/2;
insert(tri(i,3),tri(i,1)) = current;
insert(tri(i,1),tri(i,3)) = current;
v31 = current;
else
v31 = insert(tri(i,3),tri(i,1));
end
% add the 4 new triangles with the correct indices
tri(4*(i-1)+1, :) = [tri(i,1) v12 v31];
tri(4*(i-1)+2, :) = [tri(i,2) v23 v12];
tri(4*(i-1)+3, :) = [tri(i,3) v31 v23];
tri(4*(i-1)+4, :) = [v12 v23 v31];
end
% remove the space for the vertices that was not used
pntr = pntr(1:current, :);
case 'updown'
ntri = size(tri,1);
while ntri<varargin{1}
% increase the number of triangles by a factor of 4
[pnt, tri] = refine(pnt, tri, 'banks');
ntri = size(tri,1);
end
% reduce number of triangles using Matlab function
[tri, pntr] = reducepatch(tri, pnt, varargin{1});
otherwise
error(['unsupported method: ' method]);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [hs, hc, contour] = triplot(pnt, tri, val, mode, levels)
% TRIPLOT make 2D or 3D plot of triangulated surface and interpolated values
% The surface can be displayed with linear interpolated values or with
% linear interpolated contours of a potential distribution.
%
% Use as
% triplot(pnt, tri, value)
% triplot(pnt, tri, value, mode)
% triplot(pnt, tri, value, mode, levels)
% This will make a plot of value on the surface described by triangles
% tri with vertices pnt. The matrix tri can be [], in which case a
% it will be computed using a delaunay triangulation.
%
% The visualization mode can be
% 'surface' make interpolated plot of value on surface (default)
% 'faces' plot white triangles only (value can be [])
% 'faces_red' plot red triangles only (value can be [])
% 'faces_blue' plot blue triangles only (value can be [])
% 'faces_skin' plot skin-colored triangles only (value can be [])
% 'face_index' plot index of each triangle (value can be [])
% 'nodes' plot black vertices only (value can be [])
% 'node_index' plot index of each vertex (value can be [])
% 'node_label' plot label of each vertex (value should be cell array)
% 'edges' plot black edges only (value can be [])
% 'contour' make interpolated contour plot of value on surface
% 'contour_bw' make interpolated black-white contour plot
% 'contour_rb' make interpolated contour plot with red-blue
%
% With the optional levels, you can specify the levels at which contours will
% be plotted
%
% See also PATCH, COLORMAP, VIEW (general Matlab commands)
% updated on Mon Jul 23 12:41:44 MET DST 2001
% updated on Fri Jan 31 11:47:28 CET 2003
% Copyright (C) 2001=2006, Robert Oostenveld
%
% $Log: triplot.m,v $
% Revision 1.7 2008/06/24 13:37:51 roboos
% added option faces_blue
% always return handle to objects that were plotted
%
% Revision 1.6 2007/01/03 17:00:35 roboos
% updated documentation, changed layout of code and comments
%
% Revision 1.5 2006/09/19 16:11:35 roboos
% added support for line segments, removed "axis equal" at end
%
% Revision 1.4 2006/05/02 19:15:28 roboos
% added 'faces_red' style
%
% Revision 1.3 2004/06/28 07:51:39 roberto
% improved documentation, added faces_skin
%
% Revision 1.2 2003/03/17 10:37:29 roberto
% improved general help comments and added copyrights
%
% start with empty return values
hs = [];
hc = [];
contour = [];
% everything is added to the current figure
holdflag = ishold;
hold on
% check the input variables
if ~isempty(val)
val = val(:);
end
if nargin<4
mode = 'surface';
end
if isempty(tri) & ~strcmp(mode, 'nodes')
% no triangulation was specified but a triangulation is needed
if size(pnt,2)==2
% make a 2d triangulation of the points using delaunay
tri = delaunay(pnt(:,1), pnt(:,2));
else
% make a 2d triangulation of the projected points using delaunay
prj = elproj(pnt);
tri = delaunay(prj(:,1), prj(:,2));
end
end
if size(tri,2)==2
% lines are specified instead of triangles, convert to triangles
tri(:,3) = tri(:,2);
end
if nargin<3
warning('only displaying triangle edges')
mode='edges';
val = [];
elseif nargin<4
% warning('default displaying surface')
mode='surface';
elseif nargin<5
% determine contour levels
if ~isempty(val) & ~iscell(val)
absmax = max(abs([min(val) max(val)]));
levels = linspace(-absmax,absmax,21);
else
levels = [];
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% compute contours for 2D or 3D triangulation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmp(mode, 'contour') || strcmp(mode, 'contour_bw') || strcmp(mode, 'contour_rb')
triangle_val = val(tri);
triangle_min = min(triangle_val, [], 2);
triangle_max = max(triangle_val, [], 2);
for cnt_indx=1:length(levels)
cnt = levels(cnt_indx);
use = cnt>=triangle_min & cnt<=triangle_max;
counter = 0;
intersect1 = [];
intersect2 = [];
for tri_indx=find(use)'
pos = pnt(tri(tri_indx,:), :);
v(1) = triangle_val(tri_indx,1);
v(2) = triangle_val(tri_indx,2);
v(3) = triangle_val(tri_indx,3);
la(1) = (cnt-v(1)) / (v(2)-v(1)); % abcissa between vertex 1 and 2
la(2) = (cnt-v(2)) / (v(3)-v(2)); % abcissa between vertex 2 and 3
la(3) = (cnt-v(3)) / (v(1)-v(3)); % abcissa between vertex 1 and 2
abc(1,:) = pos(1,:) + la(1) * (pos(2,:) - pos(1,:));
abc(2,:) = pos(2,:) + la(2) * (pos(3,:) - pos(2,:));
abc(3,:) = pos(3,:) + la(3) * (pos(1,:) - pos(3,:));
counter = counter + 1;
sel = find(la>=0 & la<=1);
intersect1(counter, :) = abc(sel(1),:);
intersect2(counter, :) = abc(sel(2),:);
end
% remember the details for external reference
contour(cnt_indx).level = cnt;
contour(cnt_indx).n = counter;
contour(cnt_indx).intersect1 = intersect1;
contour(cnt_indx).intersect2 = intersect2;
end
% collect all different contourlevels for plotting
intersect1 = [];
intersect2 = [];
cntlevel = [];
for cnt_indx=1:length(levels)
intersect1 = [intersect1; contour(cnt_indx).intersect1];
intersect2 = [intersect2; contour(cnt_indx).intersect2];
cntlevel = [cntlevel; ones(contour(cnt_indx).n,1) * levels(cnt_indx)];
end
X = [intersect1(:,1) intersect2(:,1)]';
Y = [intersect1(:,2) intersect2(:,2)]';
C = [cntlevel(:) cntlevel(:)]';
if size(pnt,2)>2
Z = [intersect1(:,3) intersect2(:,3)]';
else
Z = zeros(2, length(cntlevel));
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% plot the desired detail
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
switch lower(mode)
case 'faces'
% plot the faces of the 2D or 3D triangulation
hs = patch('Vertices', pnt, 'Faces', tri);
set(hs, 'FaceColor', 'white');
set(hs, 'EdgeColor', 'none');
case 'faces_skin'
% plot the faces of the 2D or 3D triangulation
skin_surface = [255 213 119]/255;
inner_skull_surface = [202 100 100]/255;
cortex = [255 213 119]/255;
hs = patch('Vertices', pnt, 'Faces', tri);
set(hs, 'FaceColor', skin_surface);
set(hs, 'EdgeColor', 'none');
lighting gouraud
material shiny
camlight
case 'faces_red'
% plot the faces of the 2D or 3D triangulation
hs = patch('Vertices', pnt, 'Faces', tri);
set(hs, 'FaceColor', [1 0 0]);
set(hs, 'EdgeColor', 'none');
lighting gouraud
material shiny
camlight
case 'faces_blue'
% plot the faces of the 2D or 3D triangulation
hs = patch('Vertices', pnt, 'Faces', tri);
set(hs, 'FaceColor', [0 0 1]);
set(hs, 'EdgeColor', 'none');
lighting gouraud
material shiny
camlight
case 'face_index'
% plot the triangle indices (numbers) at each face
for face_indx=1:size(tri,1)
str = sprintf('%d', face_indx);
tri_x = (pnt(tri(face_indx,1), 1) + pnt(tri(face_indx,2), 1) + pnt(tri(face_indx,3), 1))/3;
tri_y = (pnt(tri(face_indx,1), 2) + pnt(tri(face_indx,2), 2) + pnt(tri(face_indx,3), 2))/3;
tri_z = (pnt(tri(face_indx,1), 3) + pnt(tri(face_indx,2), 3) + pnt(tri(face_indx,3), 3))/3;
h = text(tri_x, tri_y, tri_z, str, 'HorizontalAlignment', 'center', 'VerticalAlignment', 'middle');
hs = [hs; h];
end
case 'edges'
% plot the edges of the 2D or 3D triangulation
hs = patch('Vertices', pnt, 'Faces', tri);
set(hs, 'FaceColor', 'none');
set(hs, 'EdgeColor', 'black');
case 'nodes'
% plot the nodes (vertices) only as points
if size(pnt, 2)==2
hs = plot(pnt(:,1), pnt(:,2), 'k.');
else
hs = plot3(pnt(:,1), pnt(:,2), pnt(:,3), 'k.');
end
case 'nodes_blue'
% plot the nodes (vertices) only as points
if size(pnt, 2)==2
hs = plot(pnt(:,1), pnt(:,2), 'b.', 'MarkerSize', 20);
else
hs = plot3(pnt(:,1), pnt(:,2), pnt(:,3), 'b.', 'MarkerSize', 20);
end
case 'nodes_red'
% plot the nodes (vertices) only as points
if size(pnt, 2)==2
hs = plot(pnt(:,1), pnt(:,2), 'r.', 'MarkerSize', 20);
else
hs = plot3(pnt(:,1), pnt(:,2), pnt(:,3), 'r.', 'MarkerSize', 20);
end
case 'node_index'
% plot the vertex indices (numbers) at each node
for node_indx=1:size(pnt,1)
str = sprintf('%d', node_indx);
if size(pnt, 2)==2
h = text(pnt(node_indx, 1), pnt(node_indx, 2), str, 'HorizontalAlignment', 'center', 'VerticalAlignment', 'middle');
else
h = text(pnt(node_indx, 1), pnt(node_indx, 2), pnt(node_indx, 3), str, 'HorizontalAlignment', 'center', 'VerticalAlignment', 'middle');
end
hs = [hs; h];
end
case 'node_label'
% plot the vertex indices (numbers) at each node
for node_indx=1:size(pnt,1)
str = val{node_indx};
if ~isempty(str)
if size(pnt, 2)==2
h = text(pnt(node_indx, 1), pnt(node_indx, 2), str, 'HorizontalAlignment', 'center', 'VerticalAlignment', 'middle');
else
h = text(pnt(node_indx, 1), pnt(node_indx, 2), pnt(node_indx, 3), str, 'HorizontalAlignment', 'center', 'VerticalAlignment', 'middle');
end
else
h = -1;
end
hs = [hs; h];
end
case 'surface'
% plot a 2D or 3D triangulated surface with linear interpolation
if length(val)==size(pnt,1)
hs = patch('Vertices', pnt, 'Faces', tri, 'FaceVertexCData', val, 'FaceColor', 'interp');
else
hs = patch('Vertices', pnt, 'Faces', tri, 'CData', val, 'FaceColor', 'flat');
end
set(hs, 'EdgeColor', 'none');
case 'contour_bw'
% make black-white contours
hc = [];
for i=1:length(cntlevel)
if cntlevel(i)>0
linestyle = '-';
linewidth = 1;
elseif cntlevel(i)<0
linestyle = '--';
linewidth = 1;
else
linestyle = '-';
linewidth = 2;
end
h1 = patch('XData', X(:,i), 'Ydata', Y(:,i), ...
'ZData', Z(:,i), 'CData', C(:,i), ...
'facecolor','none','edgecolor','black', ...
'linestyle', linestyle, 'linewidth', linewidth, ...
'userdata',cntlevel(i));
hc = [hc; h1];
end
case 'contour_rb'
% make red-blue contours
hc = [];
for i=1:length(cntlevel)
if cntlevel(i)>0
edgecolor = 'red';
elseif cntlevel(i)<0
edgecolor = 'blue';
else
edgecolor = 'black';
end
h1 = patch('XData', X(:,i), 'Ydata', Y(:,i), ...
'ZData', Z(:,i), 'CData', C(:,i), ...
'facecolor','none','edgecolor',edgecolor, ...
'linestyle', '-', 'linewidth', 3, ...
'userdata',cntlevel(i));
hc = [hc; h1];
end
case 'contour'
% make full-color contours
hc = [];
for i=1:length(cntlevel)
h1 = patch('XData', X(:,i), 'Ydata', Y(:,i), ...
'ZData', Z(:,i), 'CData', C(:,i), ...
'facecolor','none','edgecolor','flat',...
'userdata',cntlevel(i));
hc = [hc; h1];
end
end % switch
axis off
axis vis3d
axis equal
if nargout==0
clear contour hc hs
end
if ~holdflag
hold off
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [proj] = elproj(pos, method);
% ELPROJ makes a azimuthal projection of a 3D electrode cloud
% on a plane tangent to the sphere fitted through the electrodes
% the projection is along the z-axis
%
% [proj] = elproj([x, y, z], 'method');
%
% Method should be one of these:
% 'gnomic'
% 'stereographic'
% 'ortographic'
% 'inverse'
% 'polar'
%
% Imagine a plane being placed against (tangent to) a globe. If
% a light source inside the globe projects the graticule onto
% the plane the result would be a planar, or azimuthal, map
% projection. If the imaginary light is inside the globe a Gnomonic
% projection results, if the light is antipodal a Sterographic,
% and if at infinity, an Orthographic.
%
% The default projection is a polar projection (BESA like).
% An inverse projection is the opposite of the default polar projection.
% Copyright (C) 2000-2008, Robert Oostenveld
%
% $Log: elproj.m,v $
% Revision 1.4 2008/05/15 10:54:24 roboos
% updated documentation
%
% Revision 1.3 2007/03/20 10:29:35 roboos
% renamed method 'default' into 'polar'
%
% Revision 1.2 2003/03/17 10:37:28 roberto
% improved general help comments and added copyrights
%
x = pos(:,1);
y = pos(:,2);
if size(pos, 2)==3
z = pos(:,3);
end
if nargin<2
method='polar';
end
if nargin<3
secant=1;
end
if strcmp(method, 'orthographic')
% this method compresses the lowest electrodes very much
% electrodes on the bottom half of the sphere are folded inwards
xp = x;
yp = y;
num = length(find(z<0));
str = sprintf('%d electrodes may be folded inwards in orthographic projection\n', num);
if num
warning(str);
end
proj = [xp yp];
elseif strcmp(method, 'gnomic')
% the lightsource is in the middle of the sphere
% electrodes on the equator are projected at infinity
% electrodes below the equator are not projected at all
rad = mean(sqrt(x.^2 + y.^2 + z.^2));
phi = cart2pol(x, y);
th = atan(sqrt(x.^2 + y.^2) ./ z);
xp = cos(phi) .* tan(th) .* rad;
yp = sin(phi) .* tan(th) .* rad;
num = length(find(th==pi/2 | z<0));
str = sprintf('removing %d electrodes from gnomic projection\n', num);
if num
warning(str);
end
xp(find(th==pi/2 | z<0)) = NaN;
yp(find(th==pi/2 | z<0)) = NaN;
proj = [xp yp];
elseif strcmp(method, 'stereographic')
% the lightsource is antipodal (on the south-pole)
rad = mean(sqrt(x.^2 + y.^2 + z.^2));
z = z + rad;
phi = cart2pol(x, y);
th = atan(sqrt(x.^2 + y.^2) ./ z);
xp = cos(phi) .* tan(th) .* rad * 2;
yp = sin(phi) .* tan(th) .* rad * 2;
num = length(find(th==pi/2 | z<0));
str = sprintf('removing %d electrodes from stereographic projection\n', num);
if num
warning(str);
end
xp(find(th==pi/2 | z<0)) = NaN;
yp(find(th==pi/2 | z<0)) = NaN;
proj = [xp yp];
elseif strcmp(method, 'inverse')
% compute the inverse projection of the default angular projection
[th, r] = cart2pol(x, y);
[xi, yi, zi] = sph2cart(th, pi/2 - r, 1);
proj = [xi, yi, zi];
else
% use default angular projection
[az, el, r] = cart2sph(x, y, z);
[x, y] = pol2cart(az, pi/2 - el);
proj = [x, y];
end
|
github
|
lcnbeapp/beapp-master
|
hcluster.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/icasso/hcluster.m
| 3,513 |
utf_8
|
4f1454878c289ef16d6355f9b24353ce
|
function [P,Z,order]=hcluster(D,link)
%function [P,Z,order] = hcluster(D,link)
%
%PURPOSE
%
%To perform a hierarchical agglomerative clustering on a distance
%matrix. Returns partition vectors for each level of the clustering
%hierarchy and information for visualizing the clustering hierarchy
%as a dendrogram.
%
%INPUT
%
% D (MxM matrix) distance matrix
% link (string) agglomeration strategy, (linkage)
% 'al' or 'average' (group average link.)
% 'sl' or 'single', (nearest neighbor link.)
% 'cl' or 'complete' (furthest neighbor link.)
%OUTPUT
%
% P (NxN matrix) contains the partitions on each level of the
% dendrogram (partition vectors)
% Z,order arguments returned by som_linkage. Needed for
% drawing dendrogram with function
% som_dendrogram. See also som_linkage.
%
%DETAILS
%
%A partition vector p represents division of objects into clusters,
%p(i) is the number of cluster that object i belongs to. Cluster
%numbers must be integers 1,2,...,k where k is the number of clusters.
%
%Function hcluster clusters hierarchically N objects according to an NxN
%dissimilarity matrix D. D(i,j) is the distance between objects i
%and j. The function applies a hierarchical agglomerative
%clustering (single, complete, or group average linkage). It
%returns matrix P (of size NxN) where each row is a partition
%vector. The partition vectors present the clustering of the
%objects on each level L=1,...,N of the dendrogram. Let c=P(L,i);
%Now, c is the cluster that object i belongs to at level L. On each
%row P(L,:), cluster labels are integers 1,2,...,L.
%
%Note, that the cluster labels cannot be compared over
%partitions. The same cluster may appear at different level(s) but
%it does not necessarily have the same label in every partition
%vector P(L,:).
%
%SEE ALSO
% som_linkage
% som_dendrogram
% icassoCluster
%COPYRIGHT NOTICE
%This function is a part of Icasso software library
%Copyright (C) 2003-2005 Johan Himberg
%
%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 Place - Suite 330, Boston, MA 02111-1307, USA.
% ver 1.21 johan 040305
switch lower(link),
case 'al'
link='average'; % Change Icasso name to SOM Toolbox name
case 'cl'
link='complete';% Change Icasso name to SOM Toolbox name
case 'sl'
link='single'; % Change Icasso name to SOM Toolbox name
end
N=size(D,1);
[Z,order]=som_linkage(ones(N,1),'linkage',link,'dist',D);
P=Z2partition(Z);
function partition=Z2partition(Z)
%
% function partition=Z2partition(Z)
%
% Recode SOM Toolbox presentation for hierachical clustering (Z)
% into partition vectors(s)
N=size(Z,1)+1;
C=zeros(N);
C(1,:)=1:N;
for i=2:N,
C(i,:)=C(i-1,:);
C(i,(Z(i-1,1)==C(i,:))|(Z(i-1,2)==C(i,:)))=N-1+i;
end
for i=1:size(C,1),
[u,tmp,newindex]=unique(C(i,:));
C(i,:)=newindex(:)';
end
partition=C(end:-1:1,:);
|
github
|
lcnbeapp/beapp-master
|
cca.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/icasso/cca.m
| 8,088 |
utf_8
|
b5659dc842e6c1fde35175caed2d8ea2
|
function [P] = cca(D, P, epochs, Mdist, alpha0, lambda0)
%CCA Projects data vectors using Curvilinear Component Analysis.
%
% P = cca(D, P, epochs, [Dist], [alpha0], [lambda0])
%
% P = cca(D,2,10); % projects the given data to a plane
% P = cca(D,pcaproj(D,2),5); % same, but with PCA initialization
% P = cca(D, 2, 10, Dist); % same, but the given distance matrix is used
%
% Input and output arguments ([]'s are optional):
% D (matrix) the data matrix, size dlen x dim
% (struct) data or map struct
% P (scalar) output dimension
% (matrix) size dlen x odim, the initial projection
% epochs (scalar) training length
% [Dist] (matrix) pairwise distance matrix, size dlen x dlen.
% If the distances in the input space should
% be calculated otherwise than as euclidian
% distances, the distance from each vector
% to each other vector can be given here,
% size dlen x dlen. For example PDIST
% function can be used to calculate the
% distances: Dist = squareform(pdist(D,'mahal'));
% [alpha0] (scalar) initial step size, 0.5 by default
% [lambda0] (scalar) initial radius of influence, 3*max(std(D)) by default
%
% P (matrix) size dlen x odim, the projections
%
% Unknown values (NaN's) in the data: projections of vectors with
% unknown components tend to drift towards the center of the
% projection distribution. Projections of totally unknown vectors are
% set to unknown (NaN).
%
% See also SAMMON, PCAPROJ.
% Reference: Demartines, P., Herault, J., "Curvilinear Component
% Analysis: a Self-Organizing Neural Network for Nonlinear
% Mapping of Data Sets", IEEE Transactions on Neural Networks,
% vol 8, no 1, 1997, pp. 148-154.
% Contributed to SOM Toolbox 2.0, February 2nd, 2000 by Juha Vesanto
% Copyright (c) by Juha Vesanto
% http://www.cis.hut.fi/projects/somtoolbox/
% juuso 171297 040100
% johan 170305: cca used error as a variable name which caused a
% warning, changed to error_
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Check arguments
error(nargchk(3, 6, nargin)); % check the number of input arguments
% input data
if isstruct(D),
if strcmp(D.type,'som_map'), D = D.codebook; else D = D.data; end
end
[noc dim] = size(D);
noc_x_1 = ones(noc, 1); % used frequently
me = zeros(1,dim); st = zeros(1,dim);
for i=1:dim,
me(i) = mean(D(find(isfinite(D(:,i))),i));
st(i) = std(D(find(isfinite(D(:,i))),i));
end
% initial projection
if prod(size(P))==1,
P = (2*rand(noc,P)-1).*st(noc_x_1,1:P) + me(noc_x_1,1:P);
else
% replace unknown projections with known values
inds = find(isnan(P)); P(inds) = rand(size(inds));
end
[dummy odim] = size(P);
odim_x_1 = ones(odim, 1); % this is used frequently
% training length
train_len = epochs*noc;
% random sample order
rand('state',sum(100*clock));
sample_inds = ceil(noc*rand(train_len,1));
% mutual distances
if nargin<4 | isempty(Mdist) | all(isnan(Mdist(:))),
fprintf(2, 'computing mutual distances\r');
dim_x_1 = ones(dim,1);
for i = 1:noc,
x = D(i,:);
Diff = D - x(noc_x_1,:);
N = isnan(Diff);
Diff(find(N)) = 0;
Mdist(:,i) = sqrt((Diff.^2)*dim_x_1);
N = find(sum(N')==dim); %mutual distance unknown
if ~isempty(N), Mdist(N,i) = NaN; end
end
else
% if the distance matrix is output from PDIST function
if size(Mdist,1)==1, Mdist = squareform(Mdist); end
if size(Mdist,1)~=noc,
error('Mutual distance matrix size and data set size do not match');
end
end
% alpha and lambda
if nargin<5 | isempty(alpha0) | isnan(alpha0), alpha0 = 0.5; end
alpha = potency_curve(alpha0,alpha0/100,train_len);
if nargin<6 | isempty(lambda0) | isnan(lambda0), lambda0 = max(st)*3; end
lambda = potency_curve(lambda0,0.01,train_len);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Action
k=0; fprintf(2, 'iterating: %d / %d epochs\r',k,epochs);
for i=1:train_len,
ind = sample_inds(i); % sample index
dx = Mdist(:,ind); % mutual distances in input space
known = find(~isnan(dx)); % known distances
if ~isempty(known),
% sample vector's projection
y = P(ind,:);
% distances in output space
Dy = P(known,:) - y(noc_x_1(known),:);
dy = sqrt((Dy.^2)*odim_x_1);
% relative effect
dy(find(dy==0)) = 1; % to get rid of div-by-zero's
fy = exp(-dy/lambda(i)) .* (dx(known) ./ dy - 1);
% Note that the function F here is e^(-dy/lambda))
% instead of the bubble function 1(lambda-dy) used in the
% paper.
% Note that here a simplification has been made: the derivatives of the
% F function have been ignored in calculating the gradient of error
% function w.r.t. to changes in dy.
% update
P(known,:) = P(known,:) + alpha(i)*fy(:,odim_x_1).*Dy;
end
% track
if rem(i,noc)==0,
k=k+1; fprintf(2, 'iterating: %d / %d epochs\r',k,epochs);
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% clear up
% calculate error
error_ = cca_error(P,Mdist,lambda(train_len));
fprintf(2,'%d iterations, error %f \n', epochs, error_);
% set projections of totally unknown vectors as unknown
unknown = find(sum(isnan(D)')==dim);
P(unknown,:) = NaN;
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% tips
% to plot the results, use the code below
%subplot(2,1,1),
%switch(odim),
% case 1, plot(P(:,1),ones(dlen,1),'x')
% case 2, plot(P(:,1),P(:,2),'x');
% otherwise, plot3(P(:,1),P(:,2),P(:,3),'x'); rotate3d on
%end
%subplot(2,1,2), dydxplot(P,Mdist);
% to a project a new point x in the input space to the output space
% do the following:
% Diff = D - x(noc_x_1,:); Diff(find(isnan(Diff))) = 0;
% dx = sqrt((Diff.^2)*dim_x_1);
% p = project_point(P,x,dx); % this function can be found from below
% tlen = size(p,1);
% plot(P(:,1),P(:,2),'bx',p(tlen,1),p(tlen,2),'ro',p(:,1),p(:,2),'r-')
% similar trick can be made to the other direction
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% subfunctions
function vals = potency_curve(v0,vn,l)
% curve that decreases from v0 to vn with a rate that is
% somewhere between linear and 1/t
vals = v0 * (vn/v0).^([0:(l-1)]/(l-1));
function error_ = cca_error(P,Mdist,lambda)
[noc odim] = size(P);
noc_x_1 = ones(noc,1);
odim_x_1 = ones(odim,1);
error_ = 0;
for i=1:noc,
known = find(~isnan(Mdist(:,i)));
if ~isempty(known),
y = P(i,:);
Dy = P(known,:) - y(noc_x_1(known),:);
dy = sqrt((Dy.^2)*odim_x_1);
fy = exp(-dy/lambda);
error_ = error_ + sum(((Mdist(known,i) - dy).^2).*fy);
end
end
error_ = error_/2;
function [] = dydxplot(P,Mdist)
[noc odim] = size(P);
noc_x_1 = ones(noc,1);
odim_x_1 = ones(odim,1);
Pdist = zeros(noc,noc);
for i=1:noc,
y = P(i,:);
Dy = P - y(noc_x_1,:);
Pdist(:,i) = sqrt((Dy.^2)*odim_x_1);
end
Pdist = tril(Pdist,-1);
inds = find(Pdist > 0);
n = length(inds);
plot(Pdist(inds),Mdist(inds),'.');
xlabel('dy'), ylabel('dx')
function p = project_point(P,x,dx)
[noc odim] = size(P);
noc_x_1 = ones(noc,1);
odim_x_1 = ones(odim,1);
% initial projection
[dummy,i] = min(dx);
y = P(i,:)+rand(1,odim)*norm(P(i,:))/20;
% lambda
lambda = norm(std(P));
% termination
eps = 1e-3; i_max = noc*10;
i=1; p(i,:) = y;
ready = 0;
while ~ready,
% mutual distances
Dy = P - y(noc_x_1,:); % differences in output space
dy = sqrt((Dy.^2)*odim_x_1); % distances in output space
f = exp(-dy/lambda);
fprintf(2,'iteration %d, error %g \r',i,sum(((dx - dy).^2).*f));
% all the other vectors push the projected one
fy = f .* (dx ./ dy - 1) / sum(f);
% update
step = - sum(fy(:,odim_x_1).*Dy);
y = y + step;
i=i+1;
p(i,:) = y;
ready = (norm(step)/norm(y) < eps | i > i_max);
end
fprintf(2,'\n');
|
github
|
lcnbeapp/beapp-master
|
icassoEst.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/icasso/icassoEst.m
| 8,817 |
utf_8
|
adb9102f63b02f7a42b3da5bdcf803ae
|
function sR=icassoEst(mode,X,M,varargin)
%function sR=icassoEst(mode,X,M,['FastICAparamName1',value1,'FastICAparamName2',value2,...])
%
%PURPOSE
%
%To compute randomized ICA estimates M times from data X. Output of
%this function (sR) is called 'Icasso result structure' (see
%icassoStruct). sR keeps the on all the methods, parameters, and
%results in the Icasso procedure.
%
%EXAMPLES OF BASIC USAGE
%
% sR=icassoEst('randinit', X, 30);
%
%estimates ICA for 30 times on data matrix X using Icasso
%default parameters for FastICA: symmetrical approach, kurtosis as
%contrast function. In maximum 100 iterations are used for
%estimating ICA in each round. Randomizes only initial conditions.
%
% sR=icassoEst('both', X, 30, 'g', 'tanh', 'approach', 'defl');
%
%estimates ICA for 15 times on data matrix X using 'tanh' as the
%contrast function and the deflatory approach in FastICA. Applies
%both bootstrapping the data and randomizing initial conditions.
%
%INPUT
%
% mode (string) 'randinit' | 'bootstrap | 'both'
% X (dxN matrix) data where d=dimension, N=number of vectors
% M (scalar) number of randomizations (estimation cycles)
%
%Optional input arguments are given as argument identifier - value
%pairs: 'identifier1', value1, 'identifier2', value2,...
%(case insensitive)
%
%FastICA parameters apply here (see function fastica)
%Default: 'approach', 'symm', 'g', 'pow3', 'maxNumIterations', 100
%
%OUTPUTS
%
% sR (struct) Icasso result data structure
%
%DETAILS
%
%Meaning of different choices for input arg. 'mode'
% 'randinit': different random initial condition each time.
% 'bootstrap': the same initial cond. each time, but data is
% bootstrapped. The initial condition can be explicitly
% specified using FastICA parameter 'initGuess'.
% 'both': use both data bootstrapping and randomization of
% initial condition.
%
%FASTICA PARAMETERS See function 'fastica' in FastICA toolbox for
%more information. Note that the following FastICA parameters
%cannot be used:
%
% In all modes ('randinit','bootstrap','both'):
% using 'interactivePCA','sampleSize', 'displayMode', 'displayInterval',
% and 'only' are not allowed for obvious reasons. In addition,
% in modes 'randinit' and 'both':
% using 'initGuess' is not allowed since initial guess is
% randomized, and
% in modes 'bootstrap' and 'both':
% using 'whiteMat', 'dewhiteMat', and 'whiteSig' are not allowed
% since they need to be computed for each bootstrap sample
% individually.
%
%ESTIMATE INDEXING CONVENTION: when function icassoEst is run
%each estimate gets a unique, integer label in order of
%appearance. The same order and indexing is used throughout the
%Icasso software. In many functions, one can pick a subset of
%estimates sR by giving vector whose elements refers to this unique
%label.
%
%SEE ALSO
% icasso
% fastica
% icassoStruct
% icassoExp
% icassoGet
% icassoShow
% icassoResult
%
%When icassoEst is accomplished, use icassoExp to obtain clustering
%results and to store them in sR After this, the results can be
%examined visually using icassoShow. Results and other information
%an be finally retrieved also by functions icassoResult and icassoGet.
%COPYRIGHT NOTICE
%This function is a part of Icasso software library
%Copyright (C) 2003-2005 Johan Himberg
%
%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 Place - Suite 330, Boston, MA 02111-1307, USA.
% ver 1.1 johan 210704
% Set the Icasso struct
sR=icassoStruct(X);
% Check compulsatory input arguments
if nargin<3,
error('At least three input args. required');
end
%% Check mode.
mode=lower(mode);
switch mode
case {'randinit','bootstrap','both'}
;
otherwise
error(['Randomization mode must be ''randinit'', ''bootstrap'' or' ...
' ''both''.']);
end
sR.mode=mode;
%% Set some values
num_of_args=length(varargin);
whitening='not done';
%% Default values for some FastICA options
fasticaoptions={'g','pow3','approach','symm',...
'maxNumIterations',100};
%% flag: initial conditions given (default: not given)
isInitGuess=0;
%% flag: elements for whitening given (default: not given)
isWhitesig=0; isWhitemat=0; isDewhitemat=0;
%% Check varargin & set defaults
fasticaoptions=processvarargin(varargin,fasticaoptions);
num_of_args=length(fasticaoptions);
%% Check fasticaoptions:
i=1;
while i<num_of_args,
switch fasticaoptions{i}
case {'approach','firstEig','lastEig','numOfIC','finetune','mu','g','a1','a2',...
'stabilization','epsilon','maxNumIterations','maxFinetune','verbose',...
'pcaE','pcaD'}
; % these are ok
%% Get explicit whitening if given & update flags; note that the
%% arguments are dropped away from fasticaoptions to avoid
%% duplicate storage in Icasso result struct & in FastICA input
case 'whiteSig'
w=fasticaoptions{i+1};
isWhitesig=1;
fasticaoptions(i:i+1)=[]; i=i-2; num_of_args=num_of_args-2;
case 'whiteMat'
White=fasticaoptions{i+1};
isWhitemat=1;
fasticaoptions(i:i+1)=[]; i=i-2; num_of_args=num_of_args-2;
case 'dewhiteMat'
deWhite=fasticaoptions{i+1};
isDewhitemat=1;
fasticaoptions(i:i+1)=[]; i=i-2; num_of_args=num_of_args-2;
case {'sampleSize','displayMode','displayInterval','only','interactivePCA'}
error(['You are not allowed to set FastICA option ''' fasticaoptions{i} ''' in Icasso.']);
% initGuess depends on mode
case 'initGuess'
switch mode
case {'randinit','both'}
error(['FastICA option ''initGuess'' cannot be used in sampling mode ''' ...
mode '''.']);
case 'bootstrap'
isInitGuess=1;
otherwise
error('Internal error!?');
end
otherwise
error(['Doesn''t recognize FastICA option ''' fasticaoptions{i} '''.']);
end
% add counter
i=i+2;
end
%% Whitening:
%% Check if some of whitening arguments have been given:
if (isWhitesig | isWhitemat | isDewhitemat),
%% both/bootstrap use each time different whitening... better to
%% give error
if (strcmp(mode,'bootstrap') | strcmp(mode,'both')),
error(['FastICA options ''whiteSig'',''whiteMat'',''dewhiteMat'' cannot be' ...
' used in modes ''bootstrap'' and ''both''.']);
end
%% FastICA expects that all of the three arguments are given (see
%help fastica): if not, error
if isWhitesig & isWhitemat & isDewhitemat,
disp('Using user specified whitening.');
else
error(['To prewhiten, each of ''whiteSig'',''whiteMat'',''dewhiteMat'' have to' ...
' be given (see help fastica)']);
end
else
% compute whitening for original data
[w,White,deWhite]=fastica(X,'only','white',fasticaoptions{:});
end
% store whitening for original data:
sR.whiteningMatrix=White;
sR.dewhiteningMatrix=deWhite;
% Icasso uses the same random initial condition for every sample in
% 'bootstrap'. It has to be computed if not given!!
if strcmp(mode,'bootstrap') & ~isInitGuess,
warning(sprintf('\n\n%s\n\n',['Initial guess not given for mode ''bootstrap'': I will' ...
' set a (fixed) random initial condition']));
% Randomize init conditions and add to fastica options: this
% keeps it fixed in every estimation round.
fasticaoptions{end+1}='initGuess';
fasticaoptions{end+1}=rand(size(White'))-.5;
end
% store options (except whitening which is
% stored separately)
sR.fasticaoptions=fasticaoptions;
%% Compute N times FastICA
k=0; index=[];
for i=1:M,
%clc;
fprintf('\n\n%s\n\n',['Randomization using FastICA: Round ' num2str(i) '/' ...
num2str(M)]);
switch mode
case 'randinit'
% data is fixed;
X_=X;
case {'bootstrap','both'}
% Bootstrap and compute whitening for _bootstrapped_ data
X_=bootstrap(X);
[w,White,deWhite]=fastica(X_,'only','white',fasticaoptions{:});
otherwise
error('Internal error?!');
end
% Estimate FastICA set displayMode off
[dummy,A_,W_]=fastica(X_,fasticaoptions{:},...
'whiteMat',White,'dewhiteMat',deWhite,'whiteSig',w,...
'sampleSize',1,'displayMode','off');
% Store results if any
n=size(A_,2);
if n>0,
k=k+1;
sR.index(end+1:end+n,:)=[repmat(k,n,1), [1:n]'];
sR.A{k}=A_; sR.W{k}=W_;
end
end
function X=bootstrap(X)
N=size(X,2);
index=round(rand(N,1)*N+.5);
X=X(:,index);
|
github
|
lcnbeapp/beapp-master
|
icassoStruct.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/icasso/icassoStruct.m
| 8,190 |
utf_8
|
d80e7670415d1867f114b16bebb620f6
|
function sR=icassoStruct(X)
%function sR=icassoStruct([X])
%
%PURPOSE
%
%To initiate an Icasso result data structure which is meant for
%storing and keeping organized all data, parameters and results
%when performing the Icasso procedure.
%
%EXAMPLE OF BASIC USAGE
%
% S=icassoStruct(X);
%
%creates an Icasso result structure in workspace variable S. Its
%fields are initially empty except field .signal that contains
%matrix X.
%
%INPUT
%
%[An argument in brackets is optional. If it isn't given or it's
% an empty matrix/string, the function will use a default value.]
%
%[X] (dxN matrix) the original data (signals) consisting of N
% d-dimensional vectors. Icasso centers the data (removes the
% sample mean from it) and stores it in field .signal.
% If the input argument is not given, or it is empty,
% the field is left empty.
%
%OUTPUT
%
% sR (struct) Icasso result structure that contains fields
%
% .mode (string)
% .signal (matrix)
% .index (matrix)
% .fasticaoptions (cell array)
% .A (cell array)
% .W (cell array)
% .whiteningMatrix (matrix)
% .dewhiteningMatrix (matrix)
% .cluster (struct)
% .projection (struct)
%
%DETAILS
%
%The following table presents the fields of Icasso result
%structure. Icasso is a sequential procedure that is split into
%several phases (functions). The table shows the order in which
%the fields are computed, the function that is used to change the
%parameters/results in the field, and lastly the phases that
%the result depends on.
%
%P=parameter that may be a explicit user input or a default parameter
%set by Icasso
%
%Phase Field Function depends on field(s)
%
%(1) .mode icassoEst P
%(1) .signal icassoEst P
%(1) .index icassoEst (ICA results)
%(1) .fasticaoptions icassoEst P
%(1) .A icassoEst (ICA results)
%(1a) .W icassoEst (ICA results)
%(1) .whiteningMatrix icassoEst (ICA results)
%(1b) .dewhiteningMatrix icassoEst (ICA results)
%
%(2a) .cluster.simfcn icassoCluster P
%(2b) .cluster.similarity icassoCluster 1a,1b,2a
%(2c) .cluster.s2d icassoCluster P
%(2d) .cluster.strategy icassoCluster P
%(2e) .cluster.partition icassoCluster 2b-d
%(2f) .cluster.dendrogram icassoCluster 2b-d
%(2g) .cluster.index.R icassoCluster 2b,2c,2e
%
%(3a) .projection.method icassoProjection P
%(3b) .projection.parameters icassoProjection P
%(3c) .projection.coordinates icassoProjection 2b,3a-b
%
%icasso performs the whole process with default parameters
%icassoEst performs phase 1
%icassoExp performs phases 2-3 with default parameters.
%
%(1) Data, ICA parameters, and estimation results
%
% .mode (string)
% type of randomization ('bootstrap'|'randinit'|'both')
%
% .signal (dxN matrix)
% the original data (signal) X (centered) where N is
% the number of samples and d the dimension
%
% .index (Mx2 matrix)
% the left column is the number of the estimation cycle, the
% right one is the number of the estimate on that cycle.
% See also function: icassoGet
%
%The following fields contain parameters and results of the ICA
%estimation using FastICA toolbox. More information can be found,
%e.g., from of function fastica in FastICA toolbox.
%
% .fasticaoptions (cell array)
% contains the options that FastICA uses in estimation.
%
% .A (cell array of matrices)
% contains mixing matrices from each estimation cycle
%
% .W (cell array of matrices)
% contains demixing matrices from each estimation cycle
%
% .whiteningMatrix (matrix)
% whitening matrix for original data (sR.signal)
%
% .dewhiteningMatrix (matrix)
% dewhitening matrix for original data (sR.signal).
%
%(2) Mutual similarities and clustering
%
%Parameters and results of
% -computing similarities S between the estimates, and
% -clustering the estimates
%are stored in field .cluster which has the following subfields:
%
% .cluster.simfcn (string)
% a string option for function icassoCluster
% (icassoSimilarity); it tells how the mutual similarities
% between estimates are computed.
%
% .cluster.similarity (MxM matrix)
% mutual similarities between estimates.
%
% .cluster.s2d (string)
% before clustering and computing the clustering validity index
% the similarity matrix S stored in .cluster.similarity is
% transformed into a dissimilarity matrix. This string is the
% name of the subfunction that makes the transformation: there
% is a function call
% D=feval(sR.cluster.s2d,sR.cluster.similarity);
% inside icassoCluster. Note that the dissimilarity matrix
% is not stored in the Icasso result data struct.
%
% .cluster.strategy (string)
% strategy that was used for hierarchical clustering which is
% done on dissimilarities D
% .cluster.partition (MxM matrix)
% stores the partitions resulting clustering. Each row
% partition(i,:), represents a division of M objects into K(i)
% clusters (classes). On each row, clusters must be labeled
% with integers 1,2,...,K(i), where K(i) is the number of
% clusters that may be different on each row Example:
% partition=[[1 2 3 4];[1 1 1 1];[1 1 2 2]] gives three
% different partitions where partition(1,:) means every object
% being in its own clusters; partition(2,:) means all objects
% being in a single cluster, and in partition(3,:) objects 1&2
% belong to cluster 1 and 3&4 to cluster 2.
%
% .cluster.dendrogram.Z and .cluster.dendrogram.order
% stores information needed for drawing dendrogram and
% similarity matrix visualizations. More details in function
% som_linkage
%
%The following subfields of .cluster contain heuristic validity
%scores for the partitions in .cluster.partition. If the score is
%NaN it means that the validity has not been (or can't be)
%computed.
%
% .cluster.index.R (Mx1 vector)
% computed by subfunction rindex
%
%(3) Projection for visualization
%
%Parameters for performing the visualization projection are results
%of the projection can be found in field .projection.
%
% .projection has the following subfields:
%
% .projection.method (string)
% projection method used in icassoProjection
%
% .projection.parameters (cell array)
% contains parameters used in icassoProjection
%
% .coordinates (Mx2 matrix)
% contains the coordinates of the projected estimates
%
%COPYRIGHT NOTICE
%This function is a part of Icasso software library
%Copyright (C) 2003-2005 Johan Himberg
%
%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 Place - Suite 330, Boston, MA
%02111-1307, USA.
% ver 1.2 johan 100105
if nargin<1|isempty(X),
X=[];
else
X=remmean(X);
end
sR.mode=[];
sR.signal=X;
sR.index=[];
sR.fasticaoptions=[];
sR.A=[];
sR.W=[];
sR.whiteningMatrix=[];
sR.dewhiteningMatrix=[];
sR.cluster=initClusterStruct;
sR.projection=initProjectionStruct;
function cluster=initClusterStruct
cluster.simfcn=[];
cluster.similarity=[];
cluster.s2d=[];
cluster.strategy=[];
cluster.partition=[];
cluster.dendrogram.Z=[];
cluster.dendrogram.order=[];
cluster.index.R=[];
function projection=initProjectionStruct
projection.method=[];
projection.parameters=[];
projection.coordinates=[];
|
github
|
lcnbeapp/beapp-master
|
som_dendrogram.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/icasso/som_dendrogram.m
| 9,039 |
utf_8
|
43f32770e95d19d4a12855bd8bfb91f3
|
function [h,Coord,Color,height] = som_dendrogram(Z,varargin)
%SOM_DENDROGRAM Visualize a dendrogram.
%
% [h,Coord,Color,height] = som_dendrogram(Z, [[argID,] value, ...])
%
% Z = som_linkage(sM);
% som_dendrogram(Z);
% som_dendrogram(Z,sM);
% som_dendrogram(Z,'coord',co);
%
% Input and output arguments ([]'s are optional):
% h (vector) handle to the arc lines
% Z (matrix) size n-1 x 1, the hierarchical cluster matrix
% returned by functions like LINKAGE and SOM_LINKAGE
% n is the number of original data samples.
% [argID, (string) See below. The values which are unambiguous can
% value] (varies) be given without the preceeding argID.
% Coord (matrix) size 2*n-1 x {1,2}, the coordinates of the
% original data samples and cluster nodes used
% in the visualization
% Color (matrix) size 2*n-1 x 3, the colors of ...
% height (vector) size 2*n-1 x 1, the heights of ...
%
% Here are the valid argument IDs and corresponding values. The values
% which are unambiguous (marked with '*') can be given without the
% preceeding argID.
% 'data' *(struct) map or data struct: many other optional
% arguments require this
% (matrix) data matrix
% 'coord' (matrix) size n x 1 or n x 2, the coordinates of
% the original data samples either in 1D or 2D
% (matrix) size 2*n-1 x {1,2}, the coordinates of both
% original data samples and each cluster
% *(string) 'SOM', 'pca#', 'sammon#', or 'cca#': the coordinates
% are calculated using the given data and the
% required projection algorithm. The '#' at the
% end of projection algorithms refers to the
% desired output dimension and can be either 1 or 2
% (2 by default). In case of 'SOM', the unit
% coordinates (given by SOM_VIS_COORDS) are used.
% 'color' (matrix) size n x 3, the color of the original data samples
% (matrix) size 2*n-1 x 3, the colors of both original
% data samples and each cluster
% (string) color specification, e.g. 'r.', used for each node
% 'height' (vector) size n-1 x 1, the heights used for each cluster
% (vector) size 2*n-1 x 1, the heights used for both original
% data samples and each cluster
% *(string) 'order', the order of combination determines height
% 'depth', the depth at which the combination
% happens determines height
% 'linecolor' (string) color specification for the arc color, 'k' by default
% (vector) size 1 x 3
%
% See also SOM_LINKAGE, DENDROGRAM.
% Copyright (c) 2000 by Juha Vesanto
% Contributed to SOM Toolbox on June 16th, 2000 by Juha Vesanto
% http://www.cis.hut.fi/projects/somtoolbox/
% Version 2.0beta juuso 160600
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% read the arguments
% Z
nd = size(Z,1)+1;
nc = size(Z,1);
% varargin
Coordtype = 'natural'; Coord = []; codim = 1;
Colortype = 'none'; Color = [];
height = [zeros(nd,1); Z(:,3)];
M = [];
linecol = 'k';
i=1;
while i<=length(varargin),
argok = 1;
if ischar(varargin{i}),
switch varargin{i},
case 'data', i = i + 1; M = varargin{i};
case 'coord',
i=i+1;
if isnumeric(varargin{i}), Coord = varargin{i}; Coordtype = 'given';
else
if strcmp(varargin{i},'SOM'), Coordtype = 'SOM';
else Coordtype = 'projection'; Coord = varargin{i};
end
end
case 'color',
i=i+1;
if isempty(varargin{i}), Colortype = 'none';
elseif ischar(varargin{i}), Colortype = 'colorspec'; Color = varargin{i};
else Colortype = 'given'; Color = varargin{i};
end
case 'height', i=i+1; height = varargin{i};
case 'linecolor', i=i+1; linecol = varargin{i};
case 'SOM',
Coordtype = 'SOM';
case {'pca','pca1','pca2','sammon','sammon1','sammon2','cca','cca1','cca2'},
Coordtype = 'projection'; Coord = varargin{i};
case {'order','depth'}, height = varargin{i};
end
elseif isstruct(varargin{i}), M = varargin{i};
else
argok = 0;
end
if ~argok,
disp(['(som_dendrogram) Ignoring invalid argument #' num2str(i+1)]);
end
i = i+1;
end
switch Coordtype,
case 'SOM',
if isempty(M) | ~any(strcmp(M.type,{'som_map','som_topol'})) ,
error('Cannot determine SOM coordinates without a SOM.');
end
if strcmp(M.type,'som_map'), M = M.topol; end
case 'projection',
if isempty(M), error('Cannot do projection without the data.'); end
if isstruct(M),
if strcmp(M.type,'som_data'), M = M.data;
elseif strcmp(M.type,'som_map'), M = M.codebook;
end
end
if size(M,1) ~= nd,
error('Given data must be equal in length to the number of original data samples.')
end
case 'given',
if size(Coord,1) ~= nd & size(Coord,1) ~= nd+nc,
error('Size of given coordinate matrix does not match the cluster hierarchy.');
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% initialization
% Coordinates
switch Coordtype,
case 'natural', o = leavesorder(Z)'; [dummy,Coord] = sort(o); codim = 1;
case 'SOM', Coord = som_vis_coords(M.lattice,M.msize); codim = 2;
case 'projection',
switch Coord,
case {'pca','pca2'}, Coord = pcaproj(M,2); codim = 2;
case 'pca1', Coord = pcaproj(M,1); codim = 1;
case {'cca','cca2'}, Coord = cca(M,2,20); codim = 2;
case 'cca1', Coord = cca(M,1,20); codim = 1;
case {'sammon','sammon2'}, Coord = sammon(M,2,50); codim = 2;
case 'sammon1', Coord = sammon(M,1,50); codim = 1;
end
case 'given', codim = min(size(Coord,2),2); % nill
end
if size(Coord,1) == nd,
Coord = [Coord; zeros(nc,size(Coord,2))];
for i=(nd+1):(nd+nc),
leaves = leafnodes(Z,i,nd);
if any(leaves), Coord(i,:) = mean(Coord(leaves,:),1); else Coord(i,:) = Inf; end
end
end
% Colors
switch Colortype,
case 'colorspec', % nill
case 'none', Color = '';
case 'given',
if size(Color,1) == nd,
Color = [Color; zeros(nc,3)];
for i=(nd+1):(nd+nc),
leaves = leafnodes(Z,i,nd);
if any(leaves), Color(i,:) = mean(Color(leaves,:),1);
else Color(i,:) = 0.8;
end
end
end
end
% height
if ischar(height),
switch height,
case 'order', height = [zeros(nd,1); [1:nc]'];
case 'depth', height = nodedepth(Z); height = max(height) - height;
end
else
if length(height)==nc, height = [zeros(nd,1); height]; end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% draw
% the arcs
lfrom = []; lto = [];
for i=1:nd+nc,
if i<=nd, ch = [];
elseif ~isfinite(Z(i-nd,3)), ch = [];
else ch = Z(i-nd,1:2)';
end
if any(ch),
lfrom = [lfrom; i*ones(length(ch),1)];
lto = [lto; ch];
end
end
% the coordinates of the arcs
if codim == 1,
Lx = [Coord(lfrom), Coord(lto), Coord(lto)];
Ly = [height(lfrom), height(lfrom), height(lto)];
Lz = [];
else
Lx = [Coord(lfrom,1), Coord(lto,1), Coord(lto,1)];
Ly = [Coord(lfrom,2), Coord(lto,2), Coord(lto,2)];
Lz = [height(lfrom), height(lfrom), height(lto)];
end
washold = ishold;
if ~washold, cla; end
% plot the lines
if isempty(Lz),
h = line(Lx',Ly','color',linecol);
else
h = line(Lx',Ly',Lz','color',linecol);
if ~washold, view(3); end
rotate3d on
end
% plot the nodes
hold on
switch Colortype,
case 'none', % nill
case 'colorspec',
if codim == 1, plot(Coord,height,Color);
else plot3(Coord(:,1), Coord(:,2), height, Color);
end
case 'given',
som_grid('rect',[nd+nc 1],'line','none','Coord',[Coord, height],...
'Markersize',10,'Markercolor',Color);
end
if ~washold, hold off, end
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% subfunctions
function depth = nodedepth(Z)
nd = size(Z,1)+1;
nc = size(Z,1);
depth = zeros(nd+nc,1);
ch = nc+nd-1;
while any(ch),
c = ch(1); ch = ch(2:end);
if c>nd & isfinite(Z(c-nd,3)),
chc = Z(c-nd,1:2);
depth(chc) = depth(c) + 1;
ch = [ch, chc];
end
end
return;
function inds = leafnodes(Z,i,nd)
inds = [];
ch = i;
while any(ch),
c = ch(1); ch = ch(2:end);
if c>nd & isfinite(Z(c-nd,3)), ch = [ch, Z(c-nd,1:2)]; end
if c<=nd, inds(end+1) = c; end
end
return;
function order = leavesorder(Z)
nd = size(Z,1)+1;
order = 2*nd-1;
nonleaves = 1;
while any(nonleaves),
j = nonleaves(1);
ch = Z(order(j)-nd,1:2);
if j==1, oleft = []; else oleft = order(1:(j-1)); end
if j==length(order), oright = []; else oright = order((j+1):length(order)); end
order = [oleft, ch, oright];
nonleaves = find(order>nd);
end
return;
|
github
|
lcnbeapp/beapp-master
|
corrw.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/icasso/corrw.m
| 1,654 |
utf_8
|
b24c05ddd84adfca75a0870878a9c0f7
|
function R=corrw(W,D)
%function R=corrw(W,D)
%
%PURPOSE
%
%To compute mutual linear correlation coefficients between M
%independent component estimates using the demixing matrix W and
%the dewhitening matrix D of the original data.
%
% R=W*D*D'*W';
%
%INPUT
%
% W (field W in Icasso struct: demixing matrices)
% D (field dewhiteningMatrix in Icasso struct) the dewhitening
% matrix of the data
%
%OUTPUT
%
% R (MxM matrix) of correlation coefficients
%
%SEE ALSO
% icassoSimilarity
% The normalization (rownorm) is a security measure: in some
% versions the FastICA has not normalized W properly if iteration
% stops prematurely
%COPYRIGHT NOTICE
%This function is a part of Icasso software library
%Copyright (C) 2003-2005 Johan Himberg
%
%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 Place - Suite 330, Boston, MA 02111-1307, USA.
% ver 1.2 100105
B=rownorm(W*D);
R=B*B';
function X=rownorm(X)
% normalize rows to unit length.
s=abs(sqrt(sum(X.^2,2)));
if any(s==0),
warning('Contains zero vectors: can''t normalize them!');
end
X=X./repmat(s,1,size(X,2));
|
github
|
lcnbeapp/beapp-master
|
reducesim.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/icasso/reducesim.m
| 3,056 |
utf_8
|
d2d2a37c6d316586dbfc3da7760af840
|
function S=reducesim(S,minLimit,partition,scatter,scatterLimit)
%function S=reducesim(S,minLimit)
% or
%function S=reducesim(S,minLimit,partition,scatter,scatterLimit)
%
%PURPOSE
%
%To reduce the number of lines that are drawn when the similarity
%matrix is visualized. That is, to set similarities below certain
%threshold to zero, and optionally, also within-cluster
%similarities above certain threshold to zero.
%
%INPUT
%
% Two input arguments:
%
% S (matrix) NxN similarity matrix
% minLimit (scalar) all values below this threshold in S are set to
% zero
%
% Five input arguments:
%
% S (matrix) NxN similarity matrix
% minLimit (scalar) all values below this threshold in S are set to
% zero
% partition (vector) Nx1 partition vector into K clusters (see
% explanation for 'partition vector' in function hcluster)
% scatter (vector) Kx1 vector that contains within-scatter for
% each cluster i=1,2,...,K implied by vector partition
% scatterLimit (scalar) threshold for within-cluster scatter.
%
%
%OUTPUT
%
% S (matrix) NxN similarity matrix with some entries cut to zero.
%
%SEE ALSO
% clusterstat
% icassoShow
%COPYRIGHT NOTICE
%This function is a part of Icasso software library
%Copyright (C) 2003-2005 Johan Himberg
%
%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 Place - Suite 330, Boston, MA 02111-1307, USA.
% ver 1.2 100105 johan
if nargin==2|nargin==5,
;
else
error('You must specify 2 or 5 input arguments!');
end
%%% Maximum number of lines
MAX_NLINES=5000;
%%% Set within-cluster similarities above certain threshold to zero
if nargin==5,
Ncluster=max(partition);
for i=1:Ncluster,
index=partition==i;
if scatter(i)>scatterLimit;
S(index,index)=0;
end
end
end
%%% We assume symmetric matrix and don't care about
%self-similarities upper diagonal is enough
S=tril(S); S(eye(size(S))==1)=0;
%% Number of lines to draw
Nlines=sum(sum(S>minLimit));
%%% If too many lines, try to set better minLimit
if Nlines>MAX_NLINES,
warning('Creates overwhelming number of lines');
warning('Tries to change the limit...');
minLimit=reduce(S,MAX_NLINES);
warning(['New limit =' num2str(minLimit)]);
end
%%% Set values below minLimit to zero
S(S<minLimit)=0;
function climit=reduce(c,N)
c(c==0)=[];
c=c(:);
if N==0,
warning('N=0 not allowed; setting N=1');
end
if N>length(c),
N=length(c);
end
climit=sort(-c); climit=-climit;
climit=climit(N);
|
github
|
lcnbeapp/beapp-master
|
clusterhull.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/icasso/clusterhull.m
| 5,149 |
utf_8
|
49c19208dafd1008be107e012aa6f36e
|
function [h_marker,txtcoord]=clusterhull(mode,coord,partition,color)
%function [h_marker,txtcoord]=clusterhull(mode,coord,partition,[color])
%
%PURPOSE
%
%To draw a cluster visualization where the objects (represented by
%points) belonging to the same cluster are presented by "cluster hulls",
%polygons where the edge of the polygon is the convex hull of the
%points that belong to the same cluster.
%
%INPUT
%
%%[An argument in brackets is optional. If it isn't given or it's
% an empty matrix/string, the function will use a default value.]
%
%mode (string) 'edge' | 'fill'
%coord (Mx2 matrix) coordinates of points (objects)
%partition (Mx1 vector) partition vector of objects (see
% explanation for 'partition vector' in function hcluster)
%[color] (Kx3 matrix) each line is a 1x3 RGB vector that defines
% color for each cluster. Default color is red for all
% clusters color(i,:)=[NaN NaN NaN] means that cluster(i)
% is not drawn at all.
%
%OUTPUT
%
% h_marker (vector) graphic handles to all clusters. h_marker(i)=NaN if
% color(i,:)=[NaN NaN NaN]
% txtcoord (Kx2 matrix) suggested coordinates for text labels.
% txtcoord(i,:)=[NaN NaN] if cluster i is not drawn.
% Meaningful only in mode 'edge', returns always a
% matrix of NaNs in mode 'fill'.
%
%DETAILS
%
%In mode 'edge' each cluster is represented by a convex hull if
%there are more than two points in the cluster. A two point cluster is
%represented by a line segment and a one point cluster by a small
%cross. The face of the convex hull is invisible.
%
%In mode 'fill' the cluster hulls are filled with the specified
%color. Clusters having less than three members are ignored.
%
%NOTE The function always adds to a plot (turns 'hold on' temporarily).
%
%USED IN
% icassoGraph
%COPYRIGHT NOTICE
%This function is a part of Icasso software library
%Copyright (C) 2003-2005 Johan Himberg
%
%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 Place - Suite 330, Boston, MA 02111-1307, USA.
% ver 1.2 100105 johan
holdStat=ishold;
hold on;
Ncluster=max(partition);
if nargin<4|isempty(color),
color=repmat([1 0 0],Ncluster,1);
end
switch mode
case 'edge'
[h_marker,txtcoord]=clusteredge(coord,partition,color);
case 'fill'
h_marker=clusterfill(coord,partition,color);
txtcoord=repmat(NaN,Ncluster,1);
otherwise
error('Unknown operation mode.');
end
% Some graphic settings
set(gca,'xtick',[],'ytick',[]);
axis equal;
if ~holdStat,
hold off;
end
function [h_marker,txtcoord]=clusteredge(coord,partition,color);
%% Number of clusters
Ncluster=max(partition);
%% Line width and +-sign size
LINEWIDTH=2;
MARKERSIZE=6;
for cluster=1:Ncluster,
hullCoord=[];
index=partition==cluster; Npoints=sum(index);
coord_=coord(index,:);
isVisible=all(isfinite(color(cluster,:)));
if isVisible,
if Npoints>=3,
I=convhull(coord_(:,1),coord_(:,2));
hullCoord=enlargehull([coord_(I,1) coord_(I,2)]);
h_marker(cluster,1)=patch(hullCoord(:,1),hullCoord(:,2),0);
set(h_marker(cluster,1),'edgecolor',color(cluster,:),'facecolor','none', ...
'linewidth',LINEWIDTH);
elseif size(coord_,1)==2,
hullCoord(:,1)=[coord_(1,1) coord_(2,1)]'; hullCoord(:,2)=[coord_(1,2) coord_(2,2)]';
h_marker(cluster,1)=plot(hullCoord(:,1)',hullCoord(:,2)','-');
set(h_marker(cluster,1),'color',color(cluster,:),'linewidth',LINEWIDTH);
else
hullCoord(:,1)=coord_(1,1); hullCoord(:,2)=coord_(1,2);
h_marker(cluster,1)=plot(coord_(1,1),coord_(1,2),'+');
set(h_marker(cluster),'color',color(cluster,:),'markersize',MARKERSIZE);
end
txtcoord(cluster,:)=gettextcoord(hullCoord);
else
txtcoord(cluster,1:2)=NaN; h_marker(cluster,1)=NaN;
end
end
function h_marker=clusterfill(coord,partition,color)
Ncluster=max(partition);
k=0;
for cluster=1:Ncluster,
hullCoord=[];
index=cluster==partition; Npoints=sum(index);
coord_=coord(index,:);
isVisible=all(isfinite(color(cluster,:)));
if Npoints>=3 & isVisible,
I=convhull(coord_(:,1),coord_(:,2));
hullCoord=enlargehull([coord_(I,1) coord_(I,2)]);
h_marker(cluster,1)=patch(hullCoord(:,1),hullCoord(:,2),0);
set(h_marker(cluster),'edgecolor','none','facecolor',color(cluster,:));
else
h_marker(cluster,1)=NaN;
end
end
function c=gettextcoord(coord)
[tmp,i]=min(coord(:,1));
c=coord(i,:);
function coord=enlargehull(coord)
S=1.1;
m=repmat(mean(coord(1:end-1,:),1),size(coord,1),1);
coord_=coord-m;
coord_=coord_.*S;
coord=coord_+m;
|
github
|
lcnbeapp/beapp-master
|
vis_valuetype.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/icasso/vis_valuetype.m
| 7,502 |
utf_8
|
cb7a373fcda9120d69231b2748371740
|
function flag=vis_valuetype(value, valid, str);
% VIS_VALUETYPE Used for type checks in SOM Toolbox visualization routines
%
% flag = vis_valuetype(value, valid, str)
%
% Input and output arguments:
% value (varies) variable to be checked
% valid (cell array) size 1xN, cells are strings or vectors (see below)
% str (string) 'all' or 'any' (default), determines whether
% all or just any of the types listed in argument 'valid'
% should be true for 'value'
%
% flag (scalar) 1 or 0 (true or false)
%
% This is an internal function of SOM Toolbox visualization. It makes
% various type checks. For example:
%
% % Return 1 if X is a numeric scalar otherwise 0:
% f=vis_valuetype(X,{'1x1'});
%
% % Return 1 if X is a ColorSpec, that is, a 1x3 vector presenting an RGB
% % value or any of strings 'red','blue','green','yellow','magenta','cyan',
% % 'white' or 'black' or their shortenings 'r','g','b','y','m','c','w','k':
% f=vis_valueype(X,{'1x3rgb','colorstyle'})
%
% % Return 1 if X is _both_ 10x3 size numeric matrix and has RGB values as rows
% f=vis_valuetype(X,{'nx3rgb',[10 3]},'all')
%
% Strings that may be used in argument valid:
% id is true if value is
%
% [n1 n2 ... nn] any n1 x n2 x ... x nn sized numeric matrix
% '1x1' scalar (numeric)
% '1x2' 1x2 vector (numeric)
% 'nx1' any nx1 numeric vector
% 'nx2' nx2
% 'nx3' nx3
% 'nxn' any numeric square matrix
% 'nxn[0,1]' numeric square matrix with values in interval [0,1]
% 'nxm' any numeric matrix
% '1xn' any 1xn numeric vector
% '1x3rgb' 1x3 vector v for which all(v>=0 & v<=1), e.g., a RGB code
% 'nx3rgb' nx3 numeric matrix that contains n RGB values as rows
% 'nx3dimrgb' nx3xdim numeric matrix that contains RGB values
% 'nxnx3rgb' nxnx3 numeric matrix of nxn RGB triples
% 'none' string 'none'
% 'xor' string 'xor'
% 'indexed' string 'indexed'
% 'colorstyle' strings 'red','blue','green','yellow','magenta','cyan','white'
% or 'black', or 'r','g','b','y','m','c','w','k'
% 'markerstyle' any of Matlab's marker chars '.','o','x','+','*','s','d','v',
% '^','<','>','p'or 'h'
% 'linestyle' any or Matlab's line style strings '-',':','--', or '-.'
% 'cellcolumn' a nx1 cell array
% 'topol_cell' {lattice, msize, shape}
% 'topol_cell_no_shape' {lattice, msize}
% 'string' any string (1xn array of char)
% 'chararray' any MxN char array
% Copyright (c) 1999-2000 by the SOM toolbox programming team.
% http://www.cis.hut.fi/projects/somtoolbox/
% Version 2.0beta Johan 201099 juuso 280800
if nargin == 2
str='any';
end
flag=0;
sz=size(value);
dims=ndims(value);
% isnumeric
numeric=isnumeric(value);
character=ischar(value);
% main loop: go through all types in arg. 'valid'
for i=1:length(valid),
if isnumeric(valid{i}), % numeric size for double matrix
if numeric & length(valid{i}) == dims,
flag(i)=all(sz == valid{i});
else
flag(i)=0; % not numeric or wrong dimension
end
else
msg=''; % for a error message inside try
try
switch valid{i}
% scalar
case '1x1'
flag(i)=numeric & dims == 2 & sz(1)==1 & sz(2) ==1;
% 1x2 numeric vector
case '1x2'
flag(i)=numeric & dims == 2 & sz(1)==1 & sz(2) == 2;
% 1xn numeric vector
case '1xn'
flag(i)=numeric & dims == 2 & sz(1) == 1;
% any numeric matrix
case 'nxm'
flag(i)=numeric & dims == 2;
% nx3 numeric matrix
case 'nx3'
flag(i)=numeric & dims == 2 & sz(2) == 3;
% nx2 numeric matrix
case 'nx2'
flag(i)=numeric & dims == 2 & sz(2) == 2;
% nx1 numeric vector
case 'nx1'
flag(i)=numeric & dims == 2 & sz(2) == 1;
% nx1xm numric matrix
case 'nx1xm'
flag(i)=numeric & dims == 3 & sz(2) == 1;
% nx3 matrix of RGB triples
case 'nx3rgb'
flag(i)=numeric & dims == 2 & sz(2) == 3 & in0_1(value);
% RGB triple (ColorSpec vector)
case '1x3rgb'
flag(i) = numeric & dims == 2 & sz(1)==1 & sz(2) == 3 & in0_1(value);
% any square matrix
case 'nxn'
flag(i)=numeric & dims == 2 & sz(1) == sz(2);
% nx3xdim array of nxdim RGB triples
case 'nx3xdimrgb'
flag(i)=numeric & dims == 3 & sz(2) == 3 & in0_1(value);
% nxnx3 array of nxn RGB triples
case 'nxnx3rgb'
flag(i)= numeric & dims == 3 & sz(1) == sz(2) & sz(3) == 3 ...
& in0_1(value);
% nxn matrix of values between [0,1]
case 'nxn[0,1]'
flag(i)=numeric & dims == 2 & sz(1) == sz(2) & in0_1(value);
% string 'indexed'
case 'indexed'
flag(i) = ischar(value) & strcmp(value,'indexed');
% string 'none'
case 'none'
flag(i) = character & strcmp(value,'none');
% string 'xor'
case 'xor'
flag(i) = character & strcmp(value,'xor');
% any string (1xn char array)
case 'string'
flag(i) = character & dims == 2 & sz(1)<=1;
% any char array
case 'chararray'
flag(i) = character & dims == 2 & sz(1)>0;
% ColorSpec string
case 'colorstyle'
flag(i)=(character & sz(1) == 1 & sz(2) == 1 & ...
any(ismember('ymcrgbwk',value))) | ...
(ischar(value) & any(strcmp(value,{'none','yellow','magenta',...
'cyan','red','green','blue','white','black'})));
% any valid Matlab's Marker
case 'markerstyle'
flag(i)=character & sz(1) == 1 & sz(2) == 1 & ...
any(ismember('.ox+*sdv^<>ph',value));
% any valid Matlab's LineStyle
case 'linestyle'
str=strrep(strrep(strrep(value,'z','1'),'--','z'),'-.','z');
flag(i)=character & any(ismember(str,'z-:')) & sz(1)==1 & (sz(2)==1 | sz(2)==2);
% any struct
case 'struct'
flag(i)=isstruct(value);
% nx1 cell array of strings
case 'cellcolumn_of_char'
flag(i)=iscell(value) & dims == 2 & sz(2)==1;
try, char(value); catch, flag(i)=0; end
% mxn cell array of strings
case '2Dcellarray_of_char'
flag(i)=iscell(value) & dims == 2;
try, char(cat(2,value{:})); catch, flag(i)=0; end
% valid {lattice, msize}
case 'topol_cell_no_shape'
flag(i)=1;
if ~iscell(value) | length(size(value)) ~= 2 | size(value,2)~=2
flag(i)=0;
else
if vis_valuetype(value{1},{'string'}),
switch value{1}
case { 'hexa','rect'}
;
otherwise
flag(i)=0;
end
end
if ~vis_valuetype(value{2},{'1xn'}),
flag(i)=0;
end
end
% valid {lattice, msize, shape}
case 'topol_cell'
flag(i)=1;
if ~iscell(value) | length(size(value)) ~= 2 | size(value,2) ~= 3,
flag(i)=0;
else
if vis_valuetype(value{1},{'string'}),
switch value{1}
case { 'hexa','rect'}
;
otherwise
flag(i)=0;
end
end
if ~vis_valuetype(value{2},{'1xn'})
flag(i)=0;
end
if ~vis_valuetype(value{3},{'string'})
flag(i)=0;
else
switch value{3}
case { 'sheet','cyl', 'toroid'}
;
otherwise
flag(i)=0;
end
end
end
otherwise
msg='Unknown valuetype!';
end
catch
% error during type check is due to wrong type of value:
% lets set flag(i) to 0
flag(i)=0;
end
% Unknown indetifier?
error(msg);
end
% set flag according to 3rd parameter (all ~ AND, any ~ OR)
if strcmp(str,'all');
flag=all(flag);
else
flag=any(flag);
end
end
function f=in0_1(value)
f=all(value(:) >= 0 & value(:)<=1);
|
github
|
lcnbeapp/beapp-master
|
icassoGet.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/icasso/icassoGet.m
| 5,635 |
utf_8
|
9a56d24c879fa67d054651240e964543
|
function out=icassoGet(sR,field,index)
%function out=icassoGet(sR,field,[index])
%
%PURPOSE
%
%Auxiliary function for obtaining various information from the
%Icasso result data structure. Using icassoGet, you can return
%information related to original data, e.g.: data matrix,
%(de)whitening matrix, total number of estimates, number of
%estimates on each round. You can also return specified estimated
%independent components (sources), and rows of demixing matrices
%from. (However, it is easier to use function icassoResult to return
%the final estimation results from the complete Icasso procedure.)
%
%EXAMPLES OF BASIC USAGE
%
% M=icassoGet(sR,'m');
%
%returns total number of estimates.
%
% nic=icassoGet(sR,'numOfIC')
%
%returns number of estimated IC components on each round in an Nx1
%vector (The number may differ in deflatory estimation mode due to
%convergence problems.)
%
% r=icassoGet(sR,'round',[25 17 126]);
%
%workspace variable r contains now a 3x2 matrix where the first
%column shows the number of estimation cycle. The second column
%is the order of appearance of the estimate within the cycle:
%e.g. 2 5 : estimate 25 was 5th estimate in cycle 2
% 1 17 : 17 1st 1
% 7 6 : 126 6th 7
%
% W=icassoGet(sR,'demixingmatrix',[25 17 126]);
%
%returns the demixing matrix rows for estimates 25, 17, and 126.
%
% s=icassoGet(sR,'source');
%
%returns _all_ M estimated independent components (sources), i.e.,
%estimates from all resampling cycles.
%
%INPUT
%
%[An argument in brackets is optional. If it isn't given or it's
% an empty matrix/string, the function will use a default value.]
%
% sR (struct) Icasso result data structure (from icassoEst).
% field (string) (case insensitive) determines what is returned:
% 'data' the original data centered
% 'N' the number of estimation cycles
% 'M' the total number of estimates available;
% equal to sum(icassoGet(sR,'numofic'));
% 'numofic' number of ICs extracted on each cycle (Nx1
% vector)
% 'odim' original data dimension
% 'rdim' reduced data dimension (after PCA)
% 'round' output is an Mx2 matrix that identifies from
% which estimation round each estimate
% originates:
% out(i,1) is the estimation round for
% estimate i,
% out(i,2) is the ordinal number of the
% estimate within the round.
% 'source' estimated source signals
% 'dewhitemat' dewhitening matrix for the original data
% 'whitemat' dewhitening matrix for the original data
% 'demixingmatrix' demixing matrix rows ('W' works as well)
%
% [index] (vector of integers) specifies which estimates to return
% Applies only for 'demixingmatrix', and 'source'
% Default: leaving this argument out corresponds to
% selecting all estimates, i.e., giving [1:M] as index
% vector.
%
%OUTPUT
%
% out (type and meaning vary according to input argument 'field')
%
%SEE ALSO
% icassoResult
%COPYRIGHT NOTICE
%This function is a part of Icasso software library
%Copyright (C) 2003-2005 Johan Himberg
%
%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 Place - Suite 330, Boston, MA 02111-1307, USA.
% ver 1.2 100105
M=size(sR.index,1);
if nargin<3,
index=1:M;
end
switch lower(field)
case 'm'
out=size(sR.index,1);
case 'n'
out=length(sR.A);
case 'odim'
out=size(sR.whiteningMatrix,2);
case 'rdim'
out=size(sR.whiteningMatrix,1);
case 'numofic'
for i=1:length(sR.A),
out(i,1)=size(sR.A{i},2);
end
case {'w','demixingmatrix'}
out=getDeMixing(sR,index);
case 'data'
out=sR.signal;
case {'dewhitemat'}
out=sR.dewhiteningMatrix;
case {'whitemat'}
out=sR.whiteningMatrix;
case 'source'
out=getSource(sR,index);
case 'round'
out=sR.index(index,:)
otherwise
error('Unknown operation.');
end
%function A=getMixing(sR,index);
%
%function A=getMixing(sR,index);
%
% reindex
%index2=sR.index(index,:);
%N=size(index2,1); A=[];
%for i=1:N,
% A(:,i)=sR.A{index2(i,1)}(:,index2(i,2));
%end
function W=getDeMixing(sR,index);
%
%function W=getDeMixing(sR,index);
%
% reindex
index2=sR.index(index,:);
N=size(index2,1); W=[];
for i=1:N,
W(i,:)=sR.W{index2(i,1)}(index2(i,2),:);
end
function S=getSource(sR,index)
%function S=getSource(sR,index)
%
X=sR.signal;
W=getDeMixing(sR,index);
S=W*X;
%% Old stuff
%function dWh=getDeWhitening(sR,index);
%
%function dWh=getDeWhitening(sR,index);
%
%
%index=sR.index(index,:);
%Nindex=size(index,1); W=[];
%for i=1:Nindex,
% dWh(:,i)=sR.dewhiteningMatrix{1}(:,index(i,2));
%end
%function W=getWhitening(sR,index);
%
%function W=getWhitening(sR,index);
%
%
%index=sR.index(index,:);
%Nindex=size(index,1); W=[];
%for i=1:Nindex,
% W(:,i)=sR.whiteningMatrix{index(i,1)}(:,index(i,2));
%end
|
github
|
lcnbeapp/beapp-master
|
spm_input.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_input.m
| 89,257 |
utf_8
|
74a73562f0562998a037c0c5d7a512c7
|
function varargout = spm_input(varargin)
% Comprehensive graphical and command line input function
% FORMATs (given in Programmers Help)
%_______________________________________________________________________
%
% spm_input handles most forms of interactive user input for SPM.
% (File selection is handled by spm_select.m)
%
% There are five types of input: String, Evaluated, Conditions, Buttons
% and Menus: These prompt for string input; string input which is
% evaluated to give a numerical result; selection of one item from a
% set of buttons; selection of an item from a menu.
%
% - STRING, EVALUATED & CONDITION input -
% For STRING, EVALUATED and CONDITION input types, a prompt is
% displayed adjacent to an editable text entry widget (with a lilac
% background!). Clicking in the entry widget allows editing, pressing
% <RETURN> or <ENTER> enters the result. You must enter something,
% empty answers are not accepted. A default response may be pre-specified
% in the entry widget, which will then be outlined. Clicking the border
% accepts the default value.
%
% Basic editing of the entry widget is supported *without* clicking in
% the widget, provided no other graphics widget has the focus. (If a
% widget has the focus, it is shown highlighted with a thin coloured
% line. Clicking on the window background returns the focus to the
% window, enabling keyboard accelerators.). This enables you to type
% responses to a sequence of questions without having to repeatedly
% click the mouse in the text widgets. Supported are BackSpace and
% Delete, line kill (^U). Other standard ASCII characters are appended
% to the text in the entry widget. Press <RETURN> or <ENTER> to submit
% your response.
%
% A ContextMenu is provided (in the figure background) giving access to
% relevant utilities including the facility to load input from a file
% (see spm_load.m and examples given below): Click the right button on
% the figure background.
%
% For EVALUATED input, the string submitted is evaluated in the base
% MatLab workspace (see MatLab's `eval` command) to give a numerical
% value. This permits the entry of numerics, matrices, expressions,
% functions or workspace variables. I.e.:
% i) - a number, vector or matrix e.g. "[1 2 3 4]"
% "[1:4]"
% "1:4"
% ii) - an expression e.g. "pi^2"
% "exp(-[1:36]/5.321)"
% iii) - a function (that will be invoked) e.g. "spm_load('tmp.dat')"
% (function must be on MATLABPATH) "input_cov(36,5.321)"
% iv) - a variable from the base workspace
% e.g. "tmp"
%
% The last three options provide a great deal of power: spm_load will
% load a matrix from an ASCII data file and return the results. When
% called without an argument, spm_load will pop up a file selection
% dialog. Alternatively, this facility can be gained from the
% ContextMenu. The second example assummes a custom funcion called
% input_cov has been written which expects two arguments, for example
% the following file saved as input_cov.m somewhere on the MATLABPATH
% (~/matlab, the matlab subdirectory of your home area, and the current
% directory, are on the MATLABPATH by default):
%
% function [x] = input_cov(n,decay)
% % data input routine - mono-exponential covariate
% % FORMAT [x] = input_cov(n,decay)
% % n - number of time points
% % decay - decay constant
% x = exp(-[1:n]/decay);
%
% Although this example is trivial, specifying large vectors of
% empirical data (e.g. reaction times for 72 scans) is efficient and
% reliable using this device. In the last option, a variable called tmp
% is picked up from the base workspace. To use this method, set the
% variables in the MatLab base workspace before starting an SPM
% procedure (but after starting the SPM interface). E.g.
% >> tmp=exp(-[1:36]/5.321)
%
% Occasionally a vector of a specific length will be required: This
% will be indicated in the prompt, which will start with "[#]", where
% # is the length of vector(s) required. (If a matrix is entered then
% at least one dimension should equal #.)
%
% Occasionally a specific type of number will be required. This should
% be obvious from the context. If you enter a number of the wrong type,
% you'll be alerted and asked to re-specify. The types are i) Real
% numbers; ii) Integers; iii) Whole numbers [0,1,2,3,...] & iv) Natural
% numbers [1,2,3,...]
%
% CONDITIONS type input is for getting indicator vectors. The features
% of evaluated input described above are complimented as follows:
% v) - a compressed list of digits 0-9 e.g. "12121212"
% ii) - a list of indicator characters e.g. "abababab"
% a-z mapped to 1-26 in alphabetical order, *except* r ("rest")
% which is mapped to zero (case insensitive, [A:Z,a:z] only)
% ...in addition the response is checked to ensure integer condition indices.
% Occasionally a specific number of conditions will be required: This
% will be indicated in the prompt, which will end with (#), where # is
% the number of conditions required.
%
% CONTRAST type input is for getting contrast weight vectors. Enter
% contrasts as row-vectors. Contrast weight vectors will be padded with
% zeros to the correct length, and checked for validity. (Valid
% contrasts are estimable, which are those whose weights vector is in
% the row-space of the design matrix.)
%
% Errors in string evaluation for EVALUATED & CONDITION types are
% handled gracefully, the user notified, and prompted to re-enter.
%
% - BUTTON input -
% For Button input, the prompt is displayed adjacent to a small row of
% buttons. Press the approprate button. The default button (if
% available) has a dark outline. Keyboard accelerators are available
% (provided no graphics widget has the focus): <RETURN> or <ENTER>
% selects the default button (if available). Typing the first character
% of the button label (case insensitive) "presses" that button. (If
% these Keys are not unique, then the integer keys 1,2,... "press" the
% appropriate button.)
%
% The CommandLine variant presents a simple menu of buttons and prompts
% for a selection. Any default response is indicated, and accepted if
% an empty line is input.
%
%
% - MENU input -
% For Menu input, the prompt is displayed in a pull down menu widget.
% Using the mouse, a selection is made by pulling down the widget and
% releasing the mouse on the appropriate response. The default response
% (if set) is marked with an asterisk. Keyboard accelerators are
% available (provided no graphic widget has the focus) as follows: 'f',
% 'n' or 'd' move forward to next response down; 'b', 'p' or 'u' move
% backwards to the previous response up the list; the number keys jump
% to the appropriate response number; <RETURN> or <ENTER> slelects the
% currently displayed response. If a default is available, then
% pressing <RETURN> or <ENTER> when the prompt is displayed jumps to
% the default response.
%
% The CommandLine variant presents a simple menu and prompts for a selection.
% Any default response is indicated, and accepted if an empty line is
% input.
%
%
% - Combination BUTTON/EDIT input -
% In this usage, you will be presented with a set of buttons and an
% editable text widget. Click one of the buttons to choose that option,
% or type your response in the edit widget. Any default response will
% be shown in the edit widget. The edit widget behaves in the same way
% as with the STRING/EVALUATED input, and expects a single number.
% Keypresses edit the text widget (rather than "press" the buttons)
% (provided no other graphics widget has the focus). A default response
% can be selected with the mouse by clicking the thick border of the
% edit widget.
%
%
% - Comand line -
% If YPos is 0 or global CMDLINE is true, then the command line is used.
% Negative YPos overrides CMDLINE, ensuring the GUI is used, at
% YPos=abs(YPos). Similarly relative YPos beginning with '!'
% (E.g.YPos='!+1') ensures the GUI is used.
%
% spm_input uses the SPM 'Interactive' window, which is 'Tag'ged
% 'Interactive'. If there is no such window, then the current figure is
% used, or an 'Interactive' window created if no windows are open.
%
%-----------------------------------------------------------------------
% Programers help is contained in the main body of spm_input.m
%-----------------------------------------------------------------------
% See : input.m (MatLab Reference Guide)
% See also : spm_select.m (SPM file selector dialog)
% : spm_input.m (Input wrapper function - handles batch mode)
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Andrew Holmes
% $Id$
%=======================================================================
% - FORMAT specifications for programers
%=======================================================================
% generic - [p,YPos] = spm_input(Prompt,YPos,Type,...)
% string - [p,YPos] = spm_input(Prompt,YPos,'s',DefStr)
% string+ - [p,YPos] = spm_input(Prompt,YPos,'s+',DefStr)
% evaluated - [p,YPos] = spm_input(Prompt,YPos,'e',DefStr,n)
% - natural - [p,YPos] = spm_input(Prompt,YPos,'n',DefStr,n,mx)
% - whole - [p,YPos] = spm_input(Prompt,YPos,'w',DefStr,n,mx)
% - integer - [p,YPos] = spm_input(Prompt,YPos,'i',DefStr,n)
% - real - [p,YPos] = spm_input(Prompt,YPos,'r',DefStr,n,mm)
% condition - [p,YPos] = spm_input(Prompt,YPos,'c',DefStr,n,m)
% contrast - [p,YPos] = spm_input(Prompt,YPos,'x',DefStr,n,X)
% permutation- [p,YPos] = spm_input(Prompt,YPos,'p',DefStr,P,n)
% button - [p,YPos] = spm_input(Prompt,YPos,'b',Labels,Values,DefItem)
% button/edit combo's (edit for string or typed scalar evaluated input)
% [p,YPos] = spm_input(Prompt,YPos,'b?1',Labels,Values,DefStr,mx)
% ...where ? in b?1 specifies edit widget type as with string & eval'd input
% - [p,YPos] = spm_input(Prompt,YPos,'n1',DefStr,mx)
% - [p,YPos] = spm_input(Prompt,YPos,'w1',DefStr,mx)
% button dialog
% - [p,YPos] = spm_input(Prompt,YPos,'bd',...
% Labels,Values,DefItem,Title)
% menu - [p,YPos] = spm_input(Prompt,YPos,'m',Labels,Values,DefItem)
% display - spm_input(Message,YPos,'d',Label)
% display - (GUI only) spm_input(Alert,YPos,'d!',Label)
%
% yes/no - [p,YPos] = spm_input(Prompt,YPos,'y/n',Values,DefItem)
% buttons (shortcut) where Labels is a bar delimited string
% - [p,YPos] = spm_input(Prompt,YPos,Labels,Values,DefItem)
%
% NB: Natural numbers are [1:Inf), Whole numbers are [0:Inf)
%
% -- Parameters (input) --
%
% Prompt - prompt string
% - Defaults (missing or empty) to 'Enter an expression'
%
% YPos - (numeric) vertical position {1 - 12}
% - overriden by global CMDLINE
% - 0 for command line
% - negative to force GUI
% - (string) relative vertical position E.g. '+1'
% - relative to last position used
% - overriden by global CMDLINE
% - YPos(1)=='!' forces GUI E.g. '!+1'
% - '_' is a shortcut for the lowest GUI position
% - Defaults (missing or empty) to '+1'
%
% Type - type of interrogation
% - 's'tring
% - 's+' multi-line string
% - p returned as cellstr (nx1 cell array of strings)
% - DefStr can be a cellstr or string matrix
% - 'e'valuated string
% - 'n'atural numbers
% - 'w'hole numbers
% - 'i'ntegers
% - 'r'eals
% - 'c'ondition indicator vector
% - 'x' - contrast entry
% - If n(2) or design matrix X is specified, then
% contrast matrices are padded with zeros to have
% correct length.
% - if design matrix X is specified, then contrasts are
% checked for validity (i.e. in the row-space of X)
% (checking handled by spm_SpUtil)
% - 'b'uttons
% - 'bd' - button dialog: Uses MatLab's questdlg
% - For up to three buttons
% - Prompt can be a cellstr with a long multiline message
% - CmdLine support as with 'b' type
% - button/edit combo's: 'be1','bn1','bw1','bi1','br1'
% - second letter of b?1 specifies type for edit widget
% - 'n1' - single natural number (buttons 1,2,... & edit)
% - 'w1' - single whole number (buttons 0,1,... & edit)
% - 'm'enu pulldown
% - 'y/n' : Yes or No buttons
% (See shortcuts below)
% - bar delimited string : buttons with these labels
% (See shortcuts below)
% - Defaults (missing or empty) to 'e'
%
% DefStr - Default string to be placed in entry widget for string and
% evaluated types
% - Defaults to ''
%
% n ('e', 'c' & 'p' types)
% - Size of matrix requred
% - NaN for 'e' type implies no checking - returns input as evaluated
% - length of n(:) specifies dimension - elements specify size
% - Inf implies no restriction
% - Scalar n expanded to [n,1] (i.e. a column vector)
% (except 'x' contrast type when it's [n,np] for np
% - E.g: [n,1] & [1,n] (scalar n) prompt for an n-vector,
% returned as column or row vector respectively
% [1,Inf] & [Inf,1] prompt for a single vector,
% returned as column or row vector respectively
% [n,Inf] & [Inf,n] prompts for any number of n-vectors,
% returned with row/column dimension n respectively.
% [a,b] prompts for an 2D matrix with row dimension a and
% column dimension b
% [a,Inf,b] prompt for a 3D matrix with row dimension a,
% page dimension b, and any column dimension.
% - 'c' type can only deal with single vectors
% - NaN for 'c' type treated as Inf
% - Defaults (missing or empty) to NaN
%
% n ('x'type)
% - Number of contrasts required by 'x' type (n(1))
% ( n(2) can be used specify length of contrast vectors if )
% ( a design matrix isn't passed )
% - Defaults (missing or empty) to 1 - vector contrast
%
% mx ('n', 'w', 'n1', 'w1', 'bn1' & 'bw1' types)
% - Maximum value (inclusive)
%
% mm ('r' type)
% - Maximum and minimum values (inclusive)
%
% m - Number of unique conditions required by 'c' type
% - Inf implies no restriction
% - Defaults (missing or empty) to Inf - no restriction
%
% P - set (vector) of numbers of which a permutation is required
%
% X - Design matrix for contrast checking in 'x' type
% - Can be either a straight matrix or a space structure (see spm_sp)
% - Column dimension of design matrix specifies length of contrast
% vectors (overriding n(2) is specified).
%
% Title - Title for questdlg in 'bd' type
%
% Labels - Labels for button and menu types.
% - string matrix, one label per row
% - bar delimited string
% E.g. 'AnCova|Scaling|None'
%
% Values - Return values corresponding to Labels for button and menu types
% - j-th row is returned if button / menu item j is selected
% (row vectors are transposed)
% - Defaults (missing or empty) to - (button) Labels
% - ( menu ) menu item numbers
%
% DefItem - Default item number, for button and menu types.
%
% -- Parameters (output) --
% p - results
% YPos - Optional second output argument returns GUI position just used
%
%-----------------------------------------------------------------------
% WINDOWS:
%
% spm_input uses the SPM 'Interactive' 'Tag'ged window. If this isn't
% available and no figures are open, an 'Interactive' SPM window is
% created (`spm('CreateIntWin')`). If figures are available, then the
% current figure is used *unless* it is 'Tag'ged.
%
%-----------------------------------------------------------------------
% SHORTCUTS:
%
% Buttons SHORTCUT - If the Type parameter is a bar delimited string, then
% the Type is taken as 'b' with the specified labels, and the next parameter
% (if specified) is taken for the Values.
%
% Yes/No question shortcut - p = spm_input(Prompt,YPos,'y/n') expands
% to p = spm_input(Prompt,YPos,'b','yes|no',...), enabling easy use of
% spm_input for yes/no dialogue. Values defaults to 'yn', so 'y' or 'n'
% is returned as appropriate.
%
%-----------------------------------------------------------------------
% EXAMPLES:
% ( Specified YPos is overriden if global CMDLINE is )
% ( true, when the command line versions are used. )
%
% p = spm_input
% Command line input of an evaluated string, default prompt.
% p = spm_input('Enter a value',1)
% Evaluated string input, prompted by 'Enter a value', in
% position 1 of the dialog figure.
% p = spm_input(str,'+1','e',0.001)
% Evaluated string input, prompted by contents of string str,
% in next position of the dialog figure.
% Default value of 0.001 offered.
% p = spm_input(str,2,'e',[],5)
% Evaluated string input, prompted by contents of string str,
% in second position of the dialog figure.
% Vector of length 5 required - returned as column vector
% p = spm_input(str,2,'e',[],[Inf,5])
% ...as above, but can enter multiple 5-vectors in a matrix,
% returned with 5-vectors in rows
% p = spm_input(str,0,'c','ababab')
% Condition string input, prompted by contents of string str
% Uses command line interface.
% Default string of 'ababab' offered.
% p = spm_input(str,0,'c','010101')
% As above, but default string of '010101' offered.
% [p,YPos] = spm_input(str,'0','s','Image')
% String input, same position as last used, prompted by str,
% default of 'Image' offered. YPos returns GUI position used.
% p = spm_input(str,'-1','y/n')
% Yes/No buttons for question with prompt str, in position one
% before the last used Returns 'y' or 'n'.
% p = spm_input(str,'-1','y/n',[1,0],2)
% As above, but returns 1 for yes response, 0 for no,
% with 'no' as the default response
% p = spm_input(str,4,'AnCova|Scaling')
% Presents two buttons labelled 'AnCova' & 'Scaling', with
% prompt str, in position 4 of the dialog figure. Returns the
% string on the depresed button, where buttons can be pressed
% with the mouse or by the respective keyboard accelerators
% 'a' & 's' (or 'A' & 'S').
% p = spm_input(str,-4,'b','AnCova|Scaling',[],2)
% As above, but makes "Scaling" the default response, and
% overrides global CMDLINE
% p = spm_input(str,0,'b','AnCova|Scaling|None',[1,2,3])
% Prompts for [A]ncova / [S]caling / [N]one in MatLab command
% window, returns 1, 2, or 3 according to the first character
% of the entered string as one of 'a', 's', or 'n' (case
% insensitive).
% p = spm_input(str,1,'b','AnCova',1)
% Since there's only one button, this just displays the response
% in GUI position 1 (or on the command line if global CMDLINE
% is true), and returns 1.
% p = spm_input(str,'+0','br1','None|Mask',[-Inf,NaN],0.8)
% Presents two buttons labelled "None" & "Mask" (which return
% -Inf & NaN if clicked), together with an editable text widget
% for entry of a single real number. The default of 0.8 is
% initially presented in the edit window, and can be selected by
% pressing return.
% Uses the previous GUI position, unless global CMDLINE is true,
% in which case a command-line equivalent is used.
% p = spm_input(str,'+0','w1')
% Prompts for a single whole number using a combination of
% buttons and edit widget, using the previous GUI position,
% or the command line if global CMDLINE is true.
% p = spm_input(str,'!0','m','Single Subject|Multi Subject|Multi Study')
% Prints the prompt str in a pull down menu containing items
% 'Single Subject', 'Multi Subject' & 'Multi Study'. When OK is
% clicked p is returned as the index of the choice, 1,2, or 3
% respectively. Uses last used position in GUI, irrespective of
% global CMDLINE
% p = spm_input(str,5,'m',...
% 'Single Subject|Multi Subject|Multi Study',...
% ['SS';'MS';'SP'],2)
% As above, but returns strings 'SS', 'MS', or 'SP' according to
% the respective choice, with 'MS; as the default response.
% p = spm_input(str,0,'m',...
% 'Single Subject|Multi Subject|Multi Study',...
% ['SS';'MS';'SP'],2)
% As above, but the menu is presented in the command window
% as a numbered list.
% spm_input('AnCova, GrandMean scaling',0,'d')
% Displays message in a box in the MatLab command window
% [null,YPos]=spm_input('Session 1','+1','d!','fMRI')
% Displays 'fMRI: Session 1' in next GUI position of the
% 'Interactive' window. If CMDLINE is 1, then nothing is done.
% Position used is returned in YPos.
%
%-----------------------------------------------------------------------
% FORMAT h = spm_input(Prompt,YPos,'m!',Labels,cb,UD,XCB);
% GUI PullDown menu utility - creates a pulldown menu in the Interactive window
% FORMAT H = spm_input(Prompt,YPos,'b!',Labels,cb,UD,XCB);
% GUI Buttons utility - creates GUI buttons in the Interactive window
%
% Prompt, YPos, Labels - as with 'm'enu/'b'utton types
% cb - CallBack string
% UD - UserData
% XCB - Extended CallBack handling - allows different CallBack for each item,
% and use of UD in CallBack strings. [Defaults to 1 for PullDown type
% when multiple CallBacks specified, 0 o/w.]
% H - Handle of 'PullDown' uicontrol / 'Button's
%
% In "normal" mode (when XCB is false), this is essentially a utility
% to create a PullDown menu widget or set of buttons in the SPM
% 'Interactive' figure, using positioning and Label definition
% conveniences of the spm_input 'm'enu & 'b'utton types. If Prompt is
% not empty, then the PullDown/Buttons appears on the right, with the
% Prompt on the left, otherwise the PullDown/Buttons use the whole
% width of the Interactive figure. The PopUp's CallBack string is
% specified in cb, and [optional] UserData may be passed as UD.
%
% For buttons, a separate callback can be specified for each button, by
% passing the callbacks corresponding to the Labels as rows of a
% cellstr or string matrix.
%
% This "different CallBacks" facility can also be extended to the
% PullDown type, using the "extended callback" mode (when XCB is
% true). % In addition, in "extended callback", you can use UD to
% refer to the UserData argument in the CallBack strings. (What happens
% is this: The cb & UD are stored as fields in the PopUp's UserData
% structure, and the PopUp's callback is set to spm_input('!m_cb'),
% which reads UD into the functions workspace and eval's the
% appropriate CallBack string. Note that this means that base
% workspace variables are inaccessible (put what you need in UD), and
% that any return arguments from CallBack functions are not passed back
% to the base workspace).
%
%
%-----------------------------------------------------------------------
% UTILITY FUNCTIONS:
%
% FORMAT colour = spm_input('!Colour')
% Returns colour for input widgets, as specified in COLOUR parameter at
% start of code.
% colour - [r,g,b] colour triple
%
% FORMAT [iCond,msg] = spm_input('!iCond',str,n,m)
% Parser for special 'c'ondition type: Handles digit strings and
% strings of indicator chars.
% str - input string
% n - length of condition vector required [defaut Inf - no restriction]
% m - number of conditions required [default Inf - no restrictions]
% iCond - Integer condition indicator vector
% msg - status message
%
% FORMAT hM = spm_input('!InptConMen',Finter,H)
% Sets a basic Input ContextMenu for the figure
% Finter - figure to set menu in
% H - handles of objects to delete on "crash out" option
% hM - handle of UIContextMenu
%
% FORMAT [CmdLine,YPos] = spm_input('!CmdLine',YPos)
% Sorts out whether to use CmdLine or not & canonicalises YPos
% CmdLine - Binary flag
% YPos - Position index
%
% FORMAT Finter = spm_input('!GetWin',F)
% Locates (or creates) figure to work in
% F - Interactive Figure, defaults to 'Interactive'
% Finter - Handle of figure to use
%
% FORMAT [PLoc,cF] = spm_input('!PointerJump',RRec,F,XDisp)
% Raise window & jump pointer over question
% RRec - Response rectangle of current question
% F - Interactive Figure, Defaults to 'Interactive'
% XDisp - X-displacement of cursor relative to RRec
% PLoc - Pointer location before jumping
% cF - Current figure before making F current.
%
% FORMAT [PLoc,cF] = spm_input('!PointerJumpBack',PLoc,cF)
% Replace pointer and reset CurrentFigure back
% PLoc - Pointer location before jumping
% cF - Previous current figure
%
% FORMAT spm_input('!PrntPrmpt',Prompt,TipStr,Title)
% Print prompt for CmdLine questioning
% Prompt - prompt string, callstr, or string matrix
% TipStr - tip string
% Title - title string
%
% FORMAT [Frec,QRec,PRec,RRec] = spm_input('!InputRects',YPos,rec,F)
% Returns rectangles (pixels) used in GUI
% YPos - Position index
% rec - Rectangle specifier: String, one of 'Frec','QRec','PRec','RRec'
% Defaults to '', which returns them all.
% F - Interactive Figure, Defaults to spm_figure('FindWin','Interactive')
% FRec - Position of interactive window
% QRec - Position of entire question
% PRec - Position of prompt
% RRec - Position of response
%
% FORMAT spm_input('!DeleteInputObj',F)
% Deltes input objects (only) from figure F
% F - Interactive Figure, Defaults to spm_figure('FindWin','Interactive')
%
% FORMAT [CPos,hCPos] = spm_input('!CurrentPos',F)
% Returns currently used GUI question positions & their handles
% F - Interactive Figure, Defaults to spm_figure('FindWin','Interactive')
% CPos - Vector of position indices
% hCPos - (n x CPos) matrix of object handles
%
% FORMAT h = spm_input('!FindInputObj',F)
% Returns handles of input GUI objects in figure F
% F - Interactive Figure, Defaults to spm_figure('FindWin','Interactive')
% h - vector of object handles
%
% FORMAT [NPos,CPos,hCPos] = spm_input('!NextPos',YPos,F,CmdLine)
% Returns next position index, specified by YPos
% YPos - Absolute (integer) or relative (string) position index
% Defaults to '+1'
% F - Interactive Figure, defaults to spm_figure('FindWin','Interactive')
% CmdLine - Command line? Defaults to spm_input('!CmdLine',YPos)
% NPos - Next position index
% CPos & hCPos - as for !CurrentPos
%
% FORMAT NPos = spm_input('!SetNextPos',YPos,F,CmdLine)
% Sets up for input at next position index, specified by YPos. This utility
% function can be used stand-alone to implicitly set the next position
% by clearing positions NPos and greater.
% YPos - Absolute (integer) or relative (string) position index
% Defaults to '+1'
% F - Interactive Figure, defaults to spm_figure('FindWin','Interactive')
% CmdLine - Command line? Defaults to spm_input('!CmdLine',YPos)
% NPos - Next position index
%
% FORMAT MPos = spm_input('!MaxPos',F,FRec3)
% Returns maximum position index for figure F
% F - Interactive Figure, Defaults to spm_figure('FindWin','Interactive')
% Not required if FRec3 is specified
% FRec3 - Length of interactive figure in pixels
%
% FORMAT spm_input('!EditableKeyPressFcn',h,ch)
% KeyPress callback for GUI string / eval input
%
% FORMAT spm_input('!ButtonKeyPressFcn',h,Keys,DefItem,ch)
% KeyPress callback for GUI buttons
%
% FORMAT spm_input('!PullDownKeyPressFcn',h,ch,DefItem)
% KeyPress callback for GUI pulldown menus
%
% FORMAT spm_input('!m_cb')
% Extended CallBack handler for 'p' PullDown utility type
%
% FORMAT spm_input('!dScroll',h,str)
% Scroll text string in object h
% h - handle of text object
% Prompt - Text to scroll (Defaults to 'UserData' of h)
%
%-----------------------------------------------------------------------
% SUBFUNCTIONS:
%
% FORMAT [Keys,Labs] = sf_labkeys(Labels)
% Make unique character keys for the Labels, ignoring case.
% Used with 'b'utton types.
%
% FORMAT [p,msg] = sf_eEval(str,Type,n,m)
% Common code for evaluating various input types.
%
% FORMAT str = sf_SzStr(n,l)
% Common code to construct prompt strings for pre-specified vector/matrix sizes
%
% FORMAT [p,msg] = sf_SzChk(p,n,msg)
% Common code to check (& canonicalise) sizes of input vectors/matrices
%
%_______________________________________________________________________
% @(#)spm_input.m 2.8 Andrew Holmes 03/03/04
%-Parameters
%=======================================================================
PJump = 1; %-Jumping of pointer to question?
TTips = 1; %-Use ToolTipStrings? (which can be annoying!)
ConCrash = 1; %-Add "crash out" option to 'Interactive'fig.ContextMenu
%-Condition arguments
%=======================================================================
if nargin<1|isempty(varargin{1}), Prompt=''; else, Prompt=varargin{1}; end
if ~isempty(Prompt) & ischar(Prompt) & Prompt(1)=='!'
%-Utility functions have Prompt string starting with '!'
Type = Prompt;
else %-Should be an input request: get Type & YPos
if nargin<3|isempty(varargin{3}), Type='e'; else, Type=varargin{3}; end
if any(Type=='|'), Type='b|'; end
if nargin<2|isempty(varargin{2}), YPos='+1'; else, YPos=varargin{2}; end
[CmdLine,YPos] = spm_input('!CmdLine',YPos);
if ~CmdLine %-Setup for GUI use
%-Locate (or create) figure to work in
Finter = spm_input('!GetWin');
COLOUR = get(Finter,'Color');
%-Find out which Y-position to use, setup for use
YPos = spm_input('!SetNextPos',YPos,Finter,CmdLine);
%-Determine position of objects
[FRec,QRec,PRec,RRec]=spm_input('!InputRects',YPos,'',Finter);
end
end
switch lower(Type)
case {'s','s+','e','n','w','i','r','c','x','p'} %-String and evaluated input
%=======================================================================
%-Condition arguments
if nargin<6|isempty(varargin{6}), m=[]; else, m=varargin{6}; end
if nargin<5|isempty(varargin{5}), n=[]; else, n=varargin{5}; end
if nargin<4, DefStr=''; else, DefStr=varargin{4}; end
if strcmp(lower(Type),'s+')
%-DefStr should be a cellstr for 's+' type.
if isempty(DefStr), DefStr = {};
else, DefStr = cellstr(DefStr); end
DefStr = DefStr(:);
else
%-DefStr needs to be a string
if ~ischar(DefStr), DefStr=num2str(DefStr); end
DefStr = DefStr(:)';
end
strM='';
switch lower(Type) %-Type specific defaults/setup
case 's', TTstr='enter string';
case 's+',TTstr='enter string - multi-line';
case 'e', TTstr='enter expression to evaluate';
case 'n', TTstr='enter expression - natural number(s)';
if ~isempty(m), strM=sprintf(' (in [1,%d])',m); TTstr=[TTstr,strM]; end
case 'w', TTstr='enter expression - whole number(s)';
if ~isempty(m), strM=sprintf(' (in [0,%d])',m); TTstr=[TTstr,strM]; end
case 'i', TTstr='enter expression - integer(s)';
case 'r', TTstr='enter expression - real number(s)';
if ~isempty(m), TTstr=[TTstr,sprintf(' in [%g,%g]',min(m),max(m))]; end
case 'c', TTstr='enter indicator vector e.g. 0101... or abab...';
if ~isempty(m) & isfinite(m), strM=sprintf(' (%d)',m); end
case 'x', TTstr='enter contrast matrix';
case 'p',
if isempty(n), error('permutation of what?'), else, P=n(:)'; end
if isempty(m), n = [1,length(P)]; end
m = P;
if ~length(setxor(m,[1:max(m)]))
TTstr=['enter permutation of [1:',num2str(max(m)),']'];
else
TTstr=['enter permutation of [',num2str(m),']'];
end
otherwise, TTstr='enter expression'; end
strN = sf_SzStr(n);
if CmdLine %-Use CmdLine to get answer
%-----------------------------------------------------------------------
spm_input('!PrntPrmpt',[Prompt,strN,strM],TTstr)
%-Do Eval Types in Base workspace, catch errors
switch lower(Type), case 's'
if ~isempty(DefStr)
Prompt=[Prompt,' (Default: ',DefStr,' )'];
end
str = input([Prompt,' : '],'s');
if isempty(str), str=DefStr; end
while isempty(str)
spm('Beep')
fprintf('! %s : enter something!\n',mfilename)
str = input([Prompt,' : '],'s');
if isempty(str), str=DefStr; end
end
p = str; msg = '';
case 's+'
fprintf(['Multi-line input: Type ''.'' on a line',...
' of its own to terminate input.\n'])
if ~isempty(DefStr)
fprintf('Default : (press return to accept)\n')
fprintf(' : %s\n',DefStr{:})
end
fprintf('\n')
str = input('l001 : ','s');
while (isempty(str) | strcmp(str,'.')) & isempty(DefStr)
spm('Beep')
fprintf('! %s : enter something!\n',mfilename)
str = input('l001 : ','s');
end
if isempty(str)
%-Accept default
p = DefStr;
else
%-Got some input, allow entry of additional lines
p = {str};
str = input(sprintf('l%03u : ',length(p)+1),'s');
while ~strcmp(str,'.')
p = [p;{str}];
str = input(sprintf('l%03u : ',length(p)+1),'s');
end
end
msg = '';
otherwise
if ~isempty(DefStr)
Prompt=[Prompt,' (Default: ',DefStr,' )'];
end
str = input([Prompt,' : '],'s');
if isempty(str), str=DefStr; end
[p,msg] = sf_eEval(str,Type,n,m);
while ischar(p)
spm('Beep'), fprintf('! %s : %s\n',mfilename,msg)
str = input([Prompt,' : '],'s');
if isempty(str), str=DefStr; end
[p,msg] = sf_eEval(str,Type,n,m);
end
end
if ~isempty(msg), fprintf('\t%s\n',msg), end
else %-Use GUI to get answer
%-----------------------------------------------------------------------
%-Create text and edit control objects
%---------------------------------------------------------------
hPrmpt = uicontrol(Finter,'Style','Text',...
'String',[strN,Prompt,strM],...
'Tag',['GUIinput_',int2str(YPos)],...
'UserData','',...
'BackgroundColor',COLOUR,...
'HorizontalAlignment','Right',...
'Position',PRec);
%-Default button surrounding edit widget (if a DefStr given)
%-Callback sets hPrmpt UserData, and EditWidget string, to DefStr
% (Buttons UserData holds handles [hPrmpt,hEditWidget], set later)
cb = ['set(get(gcbo,''UserData'')*[1;0],''UserData'',',...
'get(gcbo,''String'')),',...
'set(get(gcbo,''UserData'')*[0;1],''String'',',...
'get(gcbo,''String''))'];
if ~isempty(DefStr)
if iscellstr(DefStr), str=[DefStr{1},'...'];
else, str=DefStr; end
hDef = uicontrol(Finter,'Style','PushButton',...
'String',DefStr,...
'ToolTipString',...
['Click on border to accept default: ' str],...
'Tag',['GUIinput_',int2str(YPos)],...
'UserData',[],...
'BackgroundColor',COLOUR,...
'CallBack',cb,...
'Position',RRec+[-2,-2,+4,+4]);
else
hDef = [];
end
%-Edit widget: Callback puts string into hPrompts UserData
cb = 'set(get(gcbo,''UserData''),''UserData'',get(gcbo,''String''))';
h = uicontrol(Finter,'Style','Edit',...
'String',DefStr,...
'Max',strcmp(lower(Type),'s+')+1,...
'Tag',['GUIinput_',int2str(YPos)],...
'UserData',hPrmpt,...
'CallBack',cb,...
'Horizontalalignment','Left',...
'BackgroundColor','w',...
'Position',RRec);
set(hDef,'UserData',[hPrmpt,h])
uifocus(h);
if TTips, set(h,'ToolTipString',TTstr), end
%-Figure ContextMenu for shortcuts
hM = spm_input('!InptConMen',Finter,[hPrmpt,hDef,h]);
cb = [ 'set(get(gcbo,''UserData''),''String'',',...
'[''spm_load('''''',spm_select(1),'''''')'']), ',...
'set(get(get(gcbo,''UserData''),''UserData''),''UserData'',',...
'get(get(gcbo,''UserData''),''String''))'];
uimenu(hM,'Label','load from text file','Separator','on',...
'CallBack',cb,'UserData',h)
%-Bring window to fore & jump pointer to edit widget
[PLoc,cF] = spm_input('!PointerJump',RRec,Finter);
%-Setup FigureKeyPressFcn for editing of entry widget without clicking
set(Finter,'KeyPressFcn',[...
'spm_input(''!EditableKeyPressFcn'',',...
'findobj(gcf,''Tag'',''GUIinput_',int2str(YPos),''',',...
'''Style'',''edit''),',...
'get(gcbf,''CurrentCharacter''))'])
%-Wait for edit, do eval Types in Base workspace, catch errors
%---------------------------------------------------------------
waitfor(hPrmpt,'UserData')
if ~ishandle(hPrmpt), error(['Input window cleared whilst waiting ',...
'for response: Bailing out!']), end
str = get(hPrmpt,'UserData');
switch lower(Type), case 's'
p = str; msg = '';
case 's+'
p = cellstr(str); msg = '';
otherwise
[p,msg] = sf_eEval(str,Type,n,m);
while ischar(p)
set(h,'Style','Text',...
'String',msg,'HorizontalAlignment','Center',...
'ForegroundColor','r')
spm('Beep'), pause(2)
set(h,'Style','Edit',...
'String',str,...
'HorizontalAlignment','Left',...
'ForegroundColor','k')
%set(hPrmpt,'UserData','');
waitfor(hPrmpt,'UserData')
if ~ishandle(hPrmpt), error(['Input window cleared ',...
'whilst waiting for response: Bailing out!']),end
str = get(hPrmpt,'UserData');
[p,msg] = sf_eEval(str,Type,n,m);
end
end
%-Fix edit window, clean up, reposition pointer, set CurrentFig back
delete([hM,hDef]), set(Finter,'KeyPressFcn','')
set(h,'Style','Text','HorizontalAlignment','Center',...
'ToolTipString',msg,...
'BackgroundColor',COLOUR)
spm_input('!PointerJumpBack',PLoc,cF)
drawnow
end % (if CmdLine)
%-Return response
%-----------------------------------------------------------------------
varargout = {p,YPos};
case {'b','bd','b|','y/n','be1','bn1','bw1','bi1','br1',...
'-n1','n1','-w1','w1','m'} %-'b'utton & 'm'enu Types
%=======================================================================
%-Condition arguments
switch lower(Type), case {'b','be1','bi1','br1','m'}
m = []; Title = '';
if nargin<6, DefItem=[]; else, DefItem=varargin{6}; end
if nargin<5, Values=[]; else, Values =varargin{5}; end
if nargin<4, Labels=''; else, Labels =varargin{4}; end
case 'bd'
if nargin<7, Title=''; else, Title =varargin{7}; end
if nargin<6, DefItem=[]; else, DefItem=varargin{6}; end
if nargin<5, Values=[]; else, Values =varargin{5}; end
if nargin<4, Labels=''; else, Labels =varargin{4}; end
case 'y/n'
Title = '';
if nargin<5, DefItem=[]; else, DefItem=varargin{5}; end
if nargin<4, Values=[]; else, Values =varargin{4}; end
if isempty(Values), Values='yn'; end
Labels = {'yes','no'};
case 'b|'
Title = '';
if nargin<5, DefItem=[]; else, DefItem=varargin{5}; end
if nargin<4, Values=[]; else, Values =varargin{4}; end
Labels = varargin{3};
case 'bn1'
if nargin<7, m=[]; else, m=varargin{7}; end
if nargin<6, DefItem=[]; else, DefItem=varargin{6}; end
if nargin<5, Values=[]; else, Values =varargin{5}; end
if nargin<4, Labels=[1:5]'; Values=[1:5]; Type='-n1';
else, Labels=varargin{4}; end
case 'bw1'
if nargin<7, m=[]; else, m=varargin{7}; end
if nargin<6, DefItem=[]; else, DefItem=varargin{6}; end
if nargin<5, Values=[]; else, Values =varargin{5}; end
if nargin<4, Labels=[0:4]'; Values=[0:4]; Type='-w1';
else, Labels=varargin{4}; end
case {'-n1','n1','-w1','w1'}
if nargin<5, m=[]; else, m=varargin{5}; end
if nargin<4, DefItem=[]; else, DefItem=varargin{4}; end
switch lower(Type)
case {'n1','-n1'}, Labels=[1:min([5,m])]'; Values=Labels'; Type='-n1';
case {'w1','-w1'}, Labels=[0:min([4,m])]'; Values=Labels'; Type='-w1';
end
end
%-Check some labels were specified
if isempty(Labels), error('No Labels specified'), end
if iscellstr(Labels), Labels=char(Labels); end
%-Convert Labels "option" string to string matrix if required
if ischar(Labels) & any(Labels=='|')
OptStr=Labels;
BarPos=find([OptStr=='|',1]);
Labels=OptStr(1:BarPos(1)-1);
for Bar = 2:sum(OptStr=='|')+1
Labels=strvcat(Labels,OptStr(BarPos(Bar-1)+1:BarPos(Bar)-1));
end
end
%-Set default Values for the Labels
if isempty(Values)
if strcmp(lower(Type),'m')
Values=[1:size(Labels,1)]';
else
Values=Labels;
end
else
%-Make sure Values are in rows
if size(Labels,1)>1 & size(Values,1)==1, Values = Values'; end
%-Check numbers of Labels and Values match
if (size(Labels,1)~=size(Values,1))
error('Labels & Values incompatible sizes'), end
end
%-Numeric Labels to strings
if isnumeric(Labels)
tmp = Labels; Labels = cell(size(tmp,1),1);
for i=1:prod(size(tmp)), Labels{i}=num2str(tmp(i,:)); end
Labels=char(Labels);
end
switch lower(Type), case {'b','bd','b|','y/n'} %-Process button types
%=======================================================================
%-Make unique character keys for the Labels, sort DefItem
%---------------------------------------------------------------
nLabels = size(Labels,1);
[Keys,Labs] = sf_labkeys(Labels);
if ~isempty(DefItem) & any(DefItem==[1:nLabels])
DefKey = Keys(DefItem);
else
DefItem = 0;
DefKey = '';
end
if CmdLine
%-Display question prompt
spm_input('!PrntPrmpt',Prompt,'',Title)
%-Build prompt
%-------------------------------------------------------
if ~isempty(Labs)
Prmpt = ['[',Keys(1),']',deblank(Labs(1,:)),' '];
for i = 2:nLabels
Prmpt=[Prmpt,'/ [',Keys(i),']',deblank(Labs(i,:)),' '];
end
else
Prmpt = ['[',Keys(1),'] '];
for i = 2:nLabels, Prmpt=[Prmpt,'/ [',Keys(i),'] ']; end
end
if DefItem
Prmpt = [Prmpt,...
' (Default: ',deblank(Labels(DefItem,:)),')'];
end
%-Ask for user response
%-------------------------------------------------------
if nLabels==1
%-Only one choice - auto-pick & display
k = 1; fprintf('%s: %s\t(only option)',Prmpt,Labels)
else
str = input([Prmpt,'? '],'s');
if isempty(str), str=DefKey; end
while isempty(str) | ~any(lower(Keys)==lower(str(1)))
if ~isempty(str),fprintf('%c\t!Out of range\n',7),end
str = input([Prmpt,'? '],'s');
if isempty(str), str=DefKey; end
end
k = find(lower(Keys)==lower(str(1)));
end
fprintf('\n')
p = Values(k,:); if ischar(p), p=deblank(p); end
elseif strcmp(lower(Type),'bd')
if nLabels>3, error('at most 3 labels for GUI ''db'' type'), end
tmp = cellstr(Labels);
if DefItem
tmp = [tmp; tmp(DefItem)];
Prompt = cellstr(Prompt); Prompt=Prompt(:);
Prompt = [Prompt;{' '};...
{['[default: ',tmp{DefItem},']']}];
else
tmp = [tmp; tmp(1)];
end
k = min(find(strcmp(tmp,...
questdlg(Prompt,sprintf('%s%s: %s...',spm('ver'),...
spm('GetUser',' (%s)'),Title),tmp{:}))));
p = Values(k,:); if ischar(p), p=deblank(p); end
else
Tag = ['GUIinput_',int2str(YPos)]; %-Tag for widgets
%-Create text and edit control objects
%-'UserData' of prompt contains answer
%-------------------------------------------------------
hPrmpt = uicontrol(Finter,'Style','Text',...
'String',Prompt,...
'Tag',Tag,...
'UserData',[],...
'BackgroundColor',COLOUR,...
'HorizontalAlignment','Right',...
'Position',PRec);
if nLabels==1
%-Only one choice - auto-pick
k = 1;
else
%-Draw buttons and process response
dX = RRec(3)/nLabels;
if TTips, str = ['select with mouse or use kbd: ',...
sprintf('%c/',Keys(1:end-1)),Keys(end)];
else, str=''; end
%-Store button # in buttons 'UserData' property
%-Store handle of prompt string in buttons 'Max' property
%-Button callback sets UserData of prompt string to
% number of pressed button
cb = ['set(get(gcbo,''Max''),''UserData'',',...
'get(gcbo,''UserData''))'];
H = [];
XDisp = [];
for i=1:nLabels
if i==DefItem
%-Default button, outline it
h = uicontrol(Finter,'Style','Frame',...
'BackGroundColor','k',...
'ForeGroundColor','k',...
'Tag',Tag,...
'Position',...
[RRec(1)+(i-1)*dX ...
RRec(2)-1 dX RRec(4)+2]);
XDisp = (i-1/3)*dX;
H = [H,h];
end
h = uicontrol(Finter,'Style','Pushbutton',...
'String',deblank(Labels(i,:)),...
'ToolTipString',str,...
'Tag',Tag,...
'Max',hPrmpt,...
'UserData',i,...
'BackgroundColor',COLOUR,...
'Callback',cb,...
'Position',[RRec(1)+(i-1)*dX+1 ...
RRec(2) dX-2 RRec(4)]);
if i == DefItem, uifocus(h); end
H = [H,h];
end
%-Figure ContextMenu for shortcuts
hM = spm_input('!InptConMen',Finter,[hPrmpt,H]);
%-Bring window to fore & jump pointer to default button
[PLoc,cF]=spm_input('!PointerJump',RRec,Finter,XDisp);
%-Callback for KeyPress, to store valid button # in
% UserData of Prompt, DefItem if (DefItem~=0)
% & return (ASCII-13) is pressed
set(Finter,'KeyPressFcn',...
['spm_input(''!ButtonKeyPressFcn'',',...
'findobj(gcf,''Tag'',''',Tag,''',',...
'''Style'',''text''),',...
'''',lower(Keys),''',',num2str(DefItem),',',...
'get(gcbf,''CurrentCharacter''))'])
%-Wait for button press, process results
%-----------------------------------------------
waitfor(hPrmpt,'UserData')
if ~ishandle(hPrmpt)
error(['Input objects cleared whilst ',...
'waiting for response: Bailing out!'])
end
k = get(hPrmpt,'UserData');
%-Clean up
delete([H,hM]), set(Finter,'KeyPressFcn','')
spm_input('!PointerJumpBack',PLoc,cF)
end
%-Display answer
uicontrol(Finter,'Style','Text',...
'String',deblank(Labels(k,:)),...
'Tag',Tag,...
'Horizontalalignment','Center',...
'BackgroundColor',COLOUR,...
'Position',RRec);
drawnow
p = Values(k,:); if ischar(p), p=deblank(p); end
end
case {'be1','bn1','bw1','bi1','br1','-n1','-w1'}
%-Process button/entry combo types
%=======================================================================
if ischar(DefItem), DefStr=DefItem; else, DefStr=num2str(DefItem); end
if isempty(m), strM=''; else, strM=sprintf(' (<=%d)',m); end
if CmdLine
%-Process default item
%---------------------------------------------------------------
if ~isempty(DefItem)
[DefVal,msg] = sf_eEval(DefStr,Type(2),1);
if ischar(DefVal), error(['Invalid DefItem: ',msg]), end
Labels = strvcat(Labels,DefStr);
Values = [Values;DefVal];
DefItem = size(Labels,1);
end
%-Add option to specify...
Labels = strvcat(Labels,'specify...');
%-Process options
nLabels = size(Labels,1);
[Keys,Labs] = sf_labkeys(Labels);
if ~isempty(DefItem), DefKey = Keys(DefItem); else, DefKey = ''; end
%-Print banner prompt
%---------------------------------------------------------------
spm_input('!PrntPrmpt',Prompt) %-Display question prompt
if Type(1)=='-' %-No special buttons - go straight to input
k = size(Labels,1);
else %-Offer buttons, default or "specify..."
%-Build prompt
%-------------------------------------------------------
if ~isempty(Labs)
Prmpt = ['[',Keys(1),']',deblank(Labs(1,:)),' '];
for i = 2:nLabels
Prmpt=[Prmpt,'/ [',Keys(i),']',deblank(Labs(i,:)),' '];
end
else
Prmpt = ['[',Keys(1),'] '];
for i = 2:nLabels, Prmpt=[Prmpt,'/ [',Keys(i),'] ']; end
end
if DefItem, Prmpt = [Prmpt,...
' (Default: ',deblank(Labels(DefItem,:)),')']; end
%-Ask for user response
%-------------------------------------------------------
if nLabels==1
%-Only one choice - auto-pick & display
k = 1; fprintf('%s: %s\t(only option)',Prmpt,Labels)
else
str = input([Prmpt,'? '],'s');
if isempty(str), str=DefKey; end
while isempty(str) | ~any(lower(Keys)==lower(str(1)))
if ~isempty(str),fprintf('%c\t!Invalid response\n',7),end
str = input([Prmpt,'? '],'s');
if isempty(str), str=DefKey; end
end
k = find(lower(Keys)==lower(str(1)));
end
fprintf('\n')
end
%-Process response: prompt for value if "specify..." option chosen
%===============================================================
if k<size(Labels,1)
p = Values(k,:); if ischar(p), p=deblank(p); end
else
%-"specify option chosen: ask user to specify
%-------------------------------------------------------
switch lower(Type(2))
case 's', tstr=' string'; case 'e', tstr='n expression';
case 'n', tstr=' natural number';case 'w', tstr=' whole number';
case 'i', tstr='n integer'; case 'r', tstr=' real number';
otherwise, tstr=''; end
Prompt = sprintf('%s (a%s%s)',Prompt,tstr,strM);
if ~isempty(DefStr)
Prompt=sprintf('%s\b, default %s)',Prompt,DefStr); end
str = input([Prompt,' : '],'s');
if isempty(str), str=DefStr; end
%-Eval in Base workspace, catch errors
[p,msg] = sf_eEval(str,Type(2),1,m);
while ischar(p)
spm('Beep'), fprintf('! %s : %s\n',mfilename,msg)
str = input([Prompt,' : '],'s');
if isempty(str), str=DefStr; end
[p,msg] = sf_eEval(str,Type(2),1,m);
end
end
else
Tag = ['GUIinput_',int2str(YPos)]; %-Tag for widgets
nLabels = size(Labels,1); %-#buttons
%-Create text and edit control objects
%-'UserData' of prompt contains answer
%---------------------------------------------------------------
hPrmpt = uicontrol(Finter,'Style','Text',...
'String',[Prompt,strM],...
'Tag',Tag,...
'UserData',[],...
'BackgroundColor',COLOUR,...
'HorizontalAlignment','Right',...
'Position',PRec);
%-Draw buttons & entry widget, & process response
dX = RRec(3)*(2/3)/nLabels;
%-Store button # in buttons 'UserData'
%-Store handle of prompt string in buttons 'Max' property
%-Callback sets UserData of prompt string to button number.
cb = ['set(get(gcbo,''Max''),''UserData'',get(gcbo,''UserData''))'];
if TTips, str=sprintf('select by mouse or enter value in text widget');
else, str=''; end
H = [];
for i=1:nLabels
h = uicontrol(Finter,'Style','Pushbutton',...
'String',deblank(Labels(i,:)),...
'Max',hPrmpt,...
'ToolTipString',str,...
'Tag',Tag,...
'UserData',i,...
'BackgroundColor',COLOUR,...
'Callback',cb,...
'Position',[RRec(1)+(i-1)*dX+1 RRec(2) dX-2 RRec(4)]);
H = [H,h];
end
%-Default button surrounding edit widget (if a DefStr given)
%-Callback sets hPrmpt UserData, and EditWidget string, to DefStr
% (Buttons UserData holds handles [hPrmpt,hEditWidget], set later)
cb = ['set(get(gcbo,''UserData'')*[1;0],''UserData'',',...
'get(gcbo,''String'')),',...
'set(get(gcbo,''UserData'')*[0;1],''String'',',...
'get(gcbo,''String''))'];
if ~isempty(DefStr)
hDef = uicontrol(Finter,'Style','PushButton',...
'String',DefStr,...
'ToolTipString',['Click on border to accept ',...
'default: ' DefStr],...
'Tag',Tag,...
'UserData',[],...
'CallBack',cb,...
'BackgroundColor',COLOUR,...
'Position',...
[RRec(1)+RRec(3)*(2/3) RRec(2)-2 RRec(3)/3+2 RRec(4)+4]);
H = [H,hDef];
else
hDef = [];
end
%-Edit widget: Callback puts string into hPrompts UserData
cb = ['set(get(gcbo,''UserData''),''UserData'',get(gcbo,''String''))'];
h = uicontrol(Finter,'Style','Edit',...
'String',DefStr,...
'ToolTipString',str,...
'Tag',Tag,...
'UserData',hPrmpt,...
'CallBack',cb,...
'Horizontalalignment','Center',...
'BackgroundColor','w',...
'Position',...
[RRec(1)+RRec(3)*(2/3)+2 RRec(2) RRec(3)/3-2 RRec(4)]);
set(hDef,'UserData',[hPrmpt,h])
uifocus(h);
H = [H,h];
%-Figure ContextMenu for shortcuts
hM = spm_input('!InptConMen',Finter,[hPrmpt,H]);
%-Bring window to fore & jump pointer to default button
[PLoc,cF] = spm_input('!PointerJump',RRec,Finter,RRec(3)*0.95);
%-Setup FigureKeyPressFcn for editing of entry widget without clicking
set(Finter,'KeyPressFcn',[...
'spm_input(''!EditableKeyPressFcn'',',...
'findobj(gcf,''Tag'',''GUIinput_',int2str(YPos),''',',...
'''Style'',''edit''),',...
'get(gcbf,''CurrentCharacter''))'])
%-Wait for button press, process results
%---------------------------------------------------------------
waitfor(hPrmpt,'UserData')
if ~ishandle(hPrmpt), error(['Input objects cleared whilst waiting ',...
'for response: Bailing out!']), end
p = get(hPrmpt,'UserData');
if ~ischar(p)
k = p;
p = Values(k,:); if ischar(p), p=deblank(p); end
else
Labels = strvcat(Labels,'specify...');
k = size(Labels,1);
[p,msg] = sf_eEval(p,Type(2),1,m);
while ischar(p)
set(H,'Visible','off')
h = uicontrol('Style','Text','String',msg,...
'Horizontalalignment','Center',...
'ForegroundColor','r',...
'BackgroundColor',COLOUR,...
'Tag',Tag,'Position',RRec);
spm('Beep')
pause(2), delete(h), set(H,'Visible','on')
set(hPrmpt,'UserData','')
waitfor(hPrmpt,'UserData')
if ~ishandle(hPrmpt), error(['Input objects cleared ',...
'whilst waiting for response: Bailing out!']),end
p = get(hPrmpt,'UserData');
if ischar(p), [p,msg] = sf_eEval(p,Type(2),1,m); end
end
end
%-Clean up
delete([H,hM]), set(Finter,'KeyPressFcn','')
spm_input('!PointerJumpBack',PLoc,cF)
%-Display answer
uicontrol(Finter,'Style','Text',...
'String',num2str(p),...
'Tag',Tag,...
'Horizontalalignment','Center',...
'BackgroundColor',COLOUR,...
'Position',RRec);
drawnow
end % (if CmdLine)
case 'm' %-Process menu type
%=======================================================================
nLabels = size(Labels,1);
if ~isempty(DefItem) & ~any(DefItem==[1:nLabels]), DefItem=[]; end
%-Process pull down menu type
if CmdLine
spm_input('!PrntPrmpt',Prompt)
nLabels = size(Labels,1);
for i = 1:nLabels, fprintf('\t%2d : %s\n',i,Labels(i,:)), end
Prmpt = ['Menu choice (1-',int2str(nLabels),')'];
if DefItem
Prmpt=[Prmpt,' (Default: ',num2str(DefItem),')'];
end
%-Ask for user response
%-------------------------------------------------------
if nLabels==1
%-Only one choice - auto-pick & display
k = 1;
fprintf('Menu choice: 1 - %s\t(only option)',Labels)
else
k = input([Prmpt,' ? ']);
if DefItem & isempty(k), k=DefItem; end
while isempty(k) | ~any([1:nLabels]==k)
if ~isempty(k),fprintf('%c\t!Out of range\n',7),end
k = input([Prmpt,' ? ']);
if DefItem & isempty(k), k=DefItem; end
end
end
fprintf('\n')
else
Tag = ['GUIinput_',int2str(YPos)]; %-Tag for widgets
if nLabels==1
%-Only one choice - auto-pick
k = 1;
else
Labs=[repmat(' ',nLabels,2),Labels];
if DefItem
Labs(DefItem,1)='*';
H = uicontrol(Finter,'Style','Frame',...
'BackGroundColor','k',...
'ForeGroundColor','k',...
'Position',QRec+[-1,-1,+2,+2]);
else
H = [];
end
cb = ['if (get(gcbo,''Value'')>1),',...
'set(gcbo,''UserData'',''Selected''), end'];
hPopUp = uicontrol(Finter,'Style','PopUp',...
'HorizontalAlignment','Left',...
'ForegroundColor','k',...
'BackgroundColor',COLOUR,...
'String',strvcat([Prompt,'...'],Labs),...
'Tag',Tag,...
'UserData',DefItem,...
'CallBack',cb,...
'Position',QRec);
if TTips, set(hPopUp,'ToolTipString',['select with ',...
'mouse or type option number (1-',...
num2str(nLabels),') & press return']), end
%-Figure ContextMenu for shortcuts
hM = spm_input('!InptConMen',Finter,[hPopUp,H]);
%-Bring window to fore & jump pointer to menu widget
[PLoc,cF] = spm_input('!PointerJump',RRec,Finter);
%-Callback for KeyPresses
cb=['spm_input(''!PullDownKeyPressFcn'',',...
'findobj(gcf,''Tag'',''',Tag,'''),',...
'get(gcf,''CurrentCharacter''))'];
set(Finter,'KeyPressFcn',cb)
%-Wait for menu selection
%-----------------------------------------------
waitfor(hPopUp,'UserData')
if ~ishandle(hPopUp), error(['Input object cleared ',...
'whilst waiting for response: Bailing out!']),end
k = get(hPopUp,'Value')-1;
%-Clean up
delete([H,hM]), set(Finter,'KeyPressFcn','')
set(hPopUp,'Style','Text',...
'Horizontalalignment','Center',...
'String',deblank(Labels(k,:)),...
'BackgroundColor',COLOUR)
spm_input('!PointerJumpBack',PLoc,cF)
end
%-Display answer
uicontrol(Finter,'Style','Text',...
'String',deblank(Labels(k,:)),...
'Tag',Tag,...
'Horizontalalignment','Center',...
'BackgroundColor',COLOUR,...
'Position',QRec);
drawnow
end
p = Values(k,:); if ischar(p), p=deblank(p); end
otherwise, error('unrecognised type')
end % (switch lower(Type) within case {'b','b|','y/n'})
%-Return response
%-----------------------------------------------------------------------
varargout = {p,YPos};
case {'m!','b!'} %-GUI PullDown/Buttons utility
%=======================================================================
% H = spm_input(Prompt,YPos,'p',Labels,cb,UD,XCB)
%-Condition arguments
if nargin<7, XCB = 0; else, XCB = varargin{7}; end
if nargin<6, UD = []; else, UD = varargin{6}; end
if nargin<5, cb = ''; else, cb = varargin{5}; end
if nargin<4, Labels = []; else, Labels = varargin{4}; end
if CmdLine, error('Can''t do CmdLine GUI utilities!'), end
if isempty(cb), cb = 'disp(''(CallBack not set)'')'; end
if ischar(cb), cb = cellstr(cb); end
if length(cb)>1 & strcmp(lower(Type),'m!'), XCB=1; end
if iscellstr(Labels), Labels=char(Labels); end
%-Convert Labels "option" string to string matrix if required
if any(Labels=='|')
OptStr=Labels;
BarPos=find([OptStr=='|',1]);
Labels=OptStr(1:BarPos(1)-1);
for Bar = 2:sum(OptStr=='|')+1
Labels=strvcat(Labels,OptStr(BarPos(Bar-1)+1:BarPos(Bar)-1));
end
end
%-Check #CallBacks
if ~( length(cb)==1 | (length(cb)==size(Labels,1)) )
error('Labels & Callbacks size mismatch'), end
%-Draw Prompt
%-----------------------------------------------------------------------
Tag = ['GUIinput_',int2str(YPos)]; %-Tag for widgets
if ~isempty(Prompt)
uicontrol(Finter,'Style','Text',...
'String',Prompt,...
'Tag',Tag,...
'HorizontalAlignment','Right',...
'BackgroundColor',COLOUR,...
'Position',PRec)
Rec = RRec;
else
Rec = QRec;
end
%-Sort out UserData for extended callbacks (handled by spm_input('!m_cb')
%-----------------------------------------------------------------------
if XCB, if iscell(UD), UD={UD}; end, UD = struct('UD',UD,'cb',{cb}); end
%-Draw PullDown or Buttons
%-----------------------------------------------------------------------
switch lower(Type), case 'm!'
if XCB, UD.cb=cb; cb = {'spm_input(''!m_cb'')'}; end
H = uicontrol(Finter,'Style','PopUp',...
'HorizontalAlignment','Left',...
'ForegroundColor','k',...
'BackgroundColor',COLOUR,...
'String',Labels,...
'Tag',Tag,...
'UserData',UD,...
'CallBack',char(cb),...
'Position',Rec);
case 'b!'
nLabels = size(Labels,1);
dX = Rec(3)/nLabels;
H = [];
for i=1:nLabels
if length(cb)>1, tcb=cb(i); else, tcb=cb; end
if XCB, UD.cb=tcb; tcb = {'spm_input(''!m_cb'')'}; end
h = uicontrol(Finter,'Style','Pushbutton',...
'String',deblank(Labels(i,:)),...
'ToolTipString','',...
'Tag',Tag,...
'UserData',UD,...
'BackgroundColor',COLOUR,...
'Callback',char(tcb),...
'Position',[Rec(1)+(i-1)*dX+1 ...
Rec(2) dX-2 Rec(4)]);
H = [H,h];
end
end
%-Bring window to fore & jump pointer to menu widget
[PLoc,cF] = spm_input('!PointerJump',RRec,Finter);
varargout = {H};
case {'d','d!'} %-Display message
%=======================================================================
%-Condition arguments
if nargin<4, Label=''; else, Label=varargin{4}; end
if CmdLine & strcmp(lower(Type),'d')
fprintf('\n +-%s%s+',Label,repmat('-',1,57-length(Label)))
Prompt = [Prompt,' '];
while length(Prompt)>0
tmp = length(Prompt);
if tmp>56, tmp=min([max(find(Prompt(1:56)==' ')),56]); end
fprintf('\n | %s%s |',Prompt(1:tmp),repmat(' ',1,56-tmp))
Prompt(1:tmp)=[];
end
fprintf('\n +-%s+\n',repmat('-',1,57))
elseif ~CmdLine
if ~isempty(Label), Prompt = [Label,': ',Prompt]; end
figure(Finter)
%-Create text axes and edit control objects
%---------------------------------------------------------------
h = uicontrol(Finter,'Style','Text',...
'String',Prompt(1:min(length(Prompt),56)),...
'FontWeight','bold',...
'Tag',['GUIinput_',int2str(YPos)],...
'HorizontalAlignment','Left',...
'ForegroundColor','k',...
'BackgroundColor',COLOUR,...
'UserData',Prompt,...
'Position',QRec);
if length(Prompt)>56
pause(1)
set(h,'ToolTipString',Prompt)
spm_input('!dScroll',h)
uicontrol(Finter,'Style','PushButton','String','>',...
'ToolTipString','press to scroll message',...
'Tag',['GUIinput_',int2str(YPos)],...
'UserData',h,...
'CallBack',[...
'set(gcbo,''Visible'',''off''),',...
'spm_input(''!dScroll'',get(gcbo,''UserData'')),',...
'set(gcbo,''Visible'',''on'')'],...
'BackgroundColor',COLOUR,...
'Position',[QRec(1)+QRec(3)-10,QRec(2),15,QRec(4)]);
end
end
if nargout>0, varargout={[],YPos}; end
%=======================================================================
% U T I L I T Y F U N C T I O N S
%=======================================================================
case '!colour'
%=======================================================================
% colour = spm_input('!Colour')
varargout = {COLOUR};
case '!icond'
%=======================================================================
% [iCond,msg] = spm_input('!iCond',str,n,m)
% Parse condition indicator spec strings:
% '2 3 2 3', '0 1 0 1', '2323', '0101', 'abab', 'R A R A'
if nargin<4, m=Inf; else, m=varargin{4}; end
if nargin<3, n=NaN; else, n=varargin{3}; end
if any(isnan(n(:)))
n=Inf;
elseif (length(n(:))==2 & ~any(n==1)) | length(n(:))>2
error('condition input can only do vectors')
end
if nargin<2, i=''; else, i=varargin{2}; end
if isempty(i), varargout={[],'empty input'}; return, end
msg = ''; i=i(:)';
if ischar(i)
if i(1)=='0' & all(ismember(unique(i(:)),char(abs('0'):abs('9'))))
%-Leading zeros in a digit list
msg = sprintf('%s expanded',i);
z = min(find([diff(i=='0'),1]));
i = [zeros(1,z), spm_input('!iCond',i(z+1:end))'];
else
%-Try an eval, for functions & string #s
i = evalin('base',['[',i,']'],'i');
end
end
if ischar(i)
%-Evaluation error from above: see if it's an 'abab' or 'a b a b' type:
[c,null,i] = unique(lower(i(~isspace(i))));
if all(ismember(c,char(abs('a'):abs('z'))))
%-Map characters a-z to 1-26, but let 'r' be zero (rest)
tmp = c-'a'+1; tmp(tmp=='r'-'a'+1)=0;
i = tmp(i);
msg = [sprintf('[%s] mapped to [',c),...
sprintf('%d,',tmp(1:end-1)),...
sprintf('%d',tmp(end)),']'];
else
i = '!'; msg = 'evaluation error';
end
elseif ~all(floor(i(:))==i(:))
i = '!'; msg = 'must be integers';
elseif length(i)==1 & prod(n)>1
msg = sprintf('%d expanded',i);
i = floor(i./10.^[floor(log10(i)+eps):-1:0]);
i = i-[0,10*i(1:end-1)];
end
%-Check size of i & #conditions
if ~ischar(i), [i,msg] = sf_SzChk(i,n,msg); end
if ~ischar(i) & isfinite(m) & length(unique(i))~=m
i = '!'; msg = sprintf('%d conditions required',m);
end
varargout = {i,msg};
case '!inptconmen'
%=======================================================================
% hM = spm_input('!InptConMen',Finter,H)
if nargin<3, H=[]; else, H=varargin{3}; end
if nargin<2, varargout={[]}; else, Finter=varargin{2}; end
hM = uicontextmenu('Parent',Finter);
uimenu(hM,'Label','help on spm_input',...
'CallBack','spm_help(''spm_input.m'')')
if ConCrash
uimenu(hM,'Label','crash out','Separator','on',...
'CallBack','delete(get(gcbo,''UserData''))',...
'UserData',[hM,H])
end
set(Finter,'UIContextMenu',hM)
varargout={hM};
case '!cmdline'
%=======================================================================
% [CmdLine,YPos] = spm_input('!CmdLine',YPos)
%-Sorts out whether to use CmdLine or not & canonicalises YPos
if nargin<2, YPos=''; else, YPos=varargin{2}; end
if isempty(YPos), YPos='+1'; end
CmdLine = [];
%-Special YPos specifications
if ischar(YPos)
if(YPos(1)=='!'), CmdLine=0; YPos(1)=[]; end
elseif YPos==0
CmdLine=1;
elseif YPos<0
CmdLine=0;
YPos=-YPos;
end
CmdLine = spm('CmdLine',CmdLine);
if CmdLine, YPos=0; end
varargout = {CmdLine,YPos};
case '!getwin'
%=======================================================================
% Finter = spm_input('!GetWin',F)
%-Locate (or create) figure to work in (Don't use 'Tag'ged figs)
if nargin<2, F='Interactive'; else, F=varargin{2}; end
Finter = spm_figure('FindWin',F);
if isempty(Finter)
if any(get(0,'Children'))
if isempty(get(gcf,'Tag')), Finter = gcf;
else, Finter = spm('CreateIntWin'); end
else, Finter = spm('CreateIntWin'); end
end
varargout = {Finter};
case '!pointerjump'
%=======================================================================
% [PLoc,cF] = spm_input('!PointerJump',RRec,F,XDisp)
%-Raise window & jump pointer over question
if nargin<4, XDisp=[]; else, XDisp=varargin{4}; end
if nargin<3, F='Interactive'; else, F=varargin{3}; end
if nargin<2, error('Insufficient arguments'), else, RRec=varargin{2}; end
F = spm_figure('FindWin',F);
PLoc = get(0,'PointerLocation');
cF = get(0,'CurrentFigure');
if ~isempty(F)
figure(F)
FRec = get(F,'Position');
if isempty(XDisp), XDisp=RRec(3)*4/5; end
if PJump, set(0,'PointerLocation',...
floor([(FRec(1)+RRec(1)+XDisp), (FRec(2)+RRec(2)+RRec(4)/3)]));
end
end
varargout = {PLoc,cF};
case '!pointerjumpback'
%=======================================================================
% spm_input('!PointerJumpBack',PLoc,cF)
%-Replace pointer and reset CurrentFigure back
if nargin<4, cF=[]; else, F=varargin{3}; end
if nargin<2, error('Insufficient arguments'), else, PLoc=varargin{2}; end
if PJump, set(0,'PointerLocation',PLoc), end
cF = spm_figure('FindWin',cF);
if ~isempty(cF), set(0,'CurrentFigure',cF); end
case '!prntprmpt'
%=======================================================================
% spm_input('!PrntPrmpt',Prompt,TipStr,Title)
%-Print prompt for CmdLine questioning
if nargin<4, Title = ''; else, Title = varargin{4}; end
if nargin<3, TipStr = ''; else, TipStr = varargin{3}; end
if nargin<2, Prompt = ''; else, Prompt = varargin{2}; end
if isempty(Prompt), Prompt='Enter an expression'; end
Prompt = cellstr(Prompt);
if ~isempty(TipStr)
tmp = 8 + length(Prompt{end}) + length(TipStr);
if tmp < 62
TipStr = sprintf('%s(%s)',repmat(' ',1,70-tmp),TipStr);
else
TipStr = sprintf('\n%s(%s)',repmat(' ',1,max(0,70-length(TipStr))),TipStr);
end
end
if isempty(Title)
fprintf('\n%s\n',repmat('~',1,72))
else
fprintf('\n= %s %s\n',Title,repmat('~',1,72-length(Title)-3))
end
fprintf('\t%s',Prompt{1})
for i=2:prod(size(Prompt)), fprintf('\n\t%s',Prompt{i}), end
fprintf('%s\n%s\n',TipStr,repmat('~',1,72))
case '!inputrects'
%=======================================================================
% [Frec,QRec,PRec,RRec,Sz,Se] = spm_input('!InputRects',YPos,rec,F)
if nargin<4, F='Interactive'; else, F=varargin{4}; end
if nargin<3, rec=''; else, rec=varargin{3}; end
if nargin<2, YPos=1; else, YPos=varargin{2}; end
F = spm_figure('FindWin',F);
if isempty(F), error('Figure not found'), end
Units = get(F,'Units');
set(F,'Units','pixels')
FRec = get(F,'Position');
set(F,'Units',Units);
Xdim = FRec(3); Ydim = FRec(4);
WS = spm('WinScale');
Sz = round(22*min(WS)); %-Height
Pd = Sz/2; %-Pad
Se = 2*round(25*min(WS)/2); %-Seperation
Yo = round(2*min(WS)); %-Y offset for responses
a = 5.5/10;
y = Ydim - Se*YPos;
QRec = [Pd y Xdim-2*Pd Sz]; %-Question
PRec = [Pd y floor(a*Xdim)-2*Pd Sz]; %-Prompt
RRec = [ceil(a*Xdim) y+Yo floor((1-a)*Xdim)-Pd Sz]; %-Response
% MRec = [010 y Xdim-50 Sz]; %-Menu PullDown
% BRec = MRec + [Xdim-50+1, 0+1, 50-Xdim+30, 0]; %-Menu PullDown OK butt
if ~isempty(rec)
varargout = {eval(rec)};
else
varargout = {FRec,QRec,PRec,RRec,Sz,Se};
end
case '!deleteinputobj'
%=======================================================================
% spm_input('!DeleteInputObj',F)
if nargin<2, F='Interactive'; else, F=varargin{2}; end
h = spm_input('!FindInputObj',F);
delete(h(h>0))
case {'!currentpos','!findinputobj'}
%=======================================================================
% [CPos,hCPos] = spm_input('!CurrentPos',F)
% h = spm_input('!FindInputObj',F)
% hPos contains handles: Columns contain handles corresponding to Pos
if nargin<2, F='Interactive'; else, F=varargin{2}; end
F = spm_figure('FindWin',F);
%-Find tags and YPos positions of 'GUIinput_' 'Tag'ged objects
H = [];
YPos = [];
for h = get(F,'Children')'
tmp = get(h,'Tag');
if ~isempty(tmp)
if strcmp(tmp(1:min(length(tmp),9)),'GUIinput_')
H = [H, h];
YPos = [YPos, eval(tmp(10:end))];
end
end
end
switch lower(Type), case '!findinputobj'
varargout = {H};
case '!currentpos'
if nargout<2
varargout = {max(YPos),[]};
elseif isempty(H)
varargout = {[],[]};
else
%-Sort out
tmp = sort(YPos);
CPos = tmp(find([1,diff(tmp)]));
nPos = length(CPos);
nPerPos = diff(find([1,diff(tmp),1]));
hCPos = zeros(max(nPerPos),nPos);
for i = 1:nPos
hCPos(1:nPerPos(i),i) = H(YPos==CPos(i))';
end
varargout = {CPos,hCPos};
end
end
case '!nextpos'
%=======================================================================
% [NPos,CPos,hCPos] = spm_input('!NextPos',YPos,F,CmdLine)
%-Return next position to use
if nargin<3, F='Interactive'; else, F=varargin{3}; end
if nargin<2, YPos='+1'; else, YPos=varargin{2}; end
if nargin<4, [CmdLine,YPos]=spm_input('!CmdLine',YPos);
else, CmdLine=varargin{4}; end
F = spm_figure('FindWin',F);
%-Get current positions
if nargout<3
CPos = spm_input('!CurrentPos',F);
hCPos = [];
else
[CPos,hCPos] = spm_input('!CurrentPos',F);
end
if CmdLine
NPos = 0;
else
MPos = spm_input('!MaxPos',F);
if ischar(YPos)
%-Relative YPos
%-Strip any '!' prefix from YPos
if(YPos(1)=='!'), YPos(1)=[]; end
if strncmp(YPos,'_',1)
%-YPos='_' means bottom
YPos=eval(['MPos+',YPos(2:end)],'MPos');
else
YPos = max([0,CPos])+eval(YPos);
end
else
%-Absolute YPos
YPos=abs(YPos);
end
NPos = min(max(1,YPos),MPos);
end
varargout = {NPos,CPos,hCPos};
case '!setnextpos'
%=======================================================================
% NPos = spm_input('!SetNextPos',YPos,F,CmdLine)
%-Set next position to use
if nargin<3, F='Interactive'; else, F=varargin{3}; end
if nargin<2, YPos='+1'; else, YPos=varargin{2}; end
if nargin<4, [CmdLine,YPos]=spm_input('!CmdLine',YPos);
else, CmdLine=varargin{4}; end
%-Find out which Y-position to use
[NPos,CPos,hCPos] = spm_input('!NextPos',YPos,F,CmdLine);
%-Delete any previous inputs using positions NPos and after
if any(CPos>=NPos), h=hCPos(:,CPos>=NPos); delete(h(h>0)), end
varargout = {NPos};
case '!maxpos'
%=======================================================================
% MPos = spm_input('!MaxPos',F,FRec3)
%
if nargin<3
if nargin<2, F='Interactive'; else, F=varargin{2}; end
F = spm_figure('FindWin',F);
if isempty(F)
FRec3=spm('WinSize','Interactive')*[0;0;0;1];
else
%-Get figure size
Units = get(F,'Units');
set(F,'Units','pixels')
FRec3 = get(F,'Position')*[0;0;0;1];
set(F,'Units',Units);
end
end
Se = round(25*min(spm('WinScale')));
MPos = floor((FRec3-5)/Se);
varargout = {MPos};
case '!editablekeypressfcn'
%=======================================================================
% spm_input('!EditableKeyPressFcn',h,ch,hPrmpt)
if nargin<2, error('Insufficient arguments'), else, h=varargin{2}; end
if isempty(h), set(gcbf,'KeyPressFcn','','UserData',[]), return, end
if nargin<3, ch=get(get(h,'Parent'),'CurrentCharacter'); else, ch=varargin{3};end
if nargin<4, hPrmpt=get(h,'UserData'); else, hPrmpt=varargin{4}; end
tmp = get(h,'String');
if isempty(tmp), tmp=''; end
if iscellstr(tmp) & length(tmp)==1; tmp=tmp{:}; end
if isempty(ch) %- shift / control / &c. pressed
return
elseif any(abs(ch)==[32:126]) %-Character
if iscellstr(tmp), return, end
tmp = [tmp, ch];
elseif abs(ch)==21 %- ^U - kill
tmp = '';
elseif any(abs(ch)==[8,127]) %-BackSpace or Delete
if iscellstr(tmp), return, end
if length(tmp), tmp(length(tmp))=''; end
elseif abs(ch)==13 %-Return pressed
if ~isempty(tmp)
set(hPrmpt,'UserData',get(h,'String'))
end
return
else
%-Illegal character
return
end
set(h,'String',tmp)
case '!buttonkeypressfcn'
%=======================================================================
% spm_input('!ButtonKeyPressFcn',h,Keys,DefItem,ch)
%-Callback for KeyPress, to store valid button # in UserData of Prompt,
% DefItem if (DefItem~=0) & return (ASCII-13) is pressed
%-Condition arguments
if nargin<2, error('Insufficient arguments'), else, h=varargin{2}; end
if isempty(h), set(gcf,'KeyPressFcn','','UserData',[]), return, end
if nargin<3, error('Insufficient arguments'); else, Keys=varargin{3}; end
if nargin<4, DefItem=0; else, DefItem=varargin{4}; end
if nargin<5, ch=get(gcf,'CurrentCharacter'); else, ch=varargin{5}; end
if isempty(ch)
%- shift / control / &c. pressed
return
elseif (DefItem & ch==13)
But = DefItem;
else
But = find(lower(ch)==lower(Keys));
end
if ~isempty(But), set(h,'UserData',But), end
case '!pulldownkeypressfcn'
%=======================================================================
% spm_input('!PullDownKeyPressFcn',h,ch,DefItem)
if nargin<2, error('Insufficient arguments'), else, h=varargin{2}; end
if isempty(h), set(gcf,'KeyPressFcn',''), return, end
if nargin<3, ch=get(get(h,'Parent'),'CurrentCharacter'); else, ch=varargin{3};end
if nargin<4, DefItem=get(h,'UserData'); else, ch=varargin{4}; end
Pmax = get(h,'Max');
Pval = get(h,'Value');
if Pmax==1, return, end
if isempty(ch)
%- shift / control / &c. pressed
return
elseif abs(ch)==13
if Pval==1
if DefItem, set(h,'Value',max(2,min(DefItem+1,Pmax))), end
else
set(h,'UserData','Selected')
end
elseif any(ch=='bpu')
%-Move "b"ack "u"p to "p"revious entry
set(h,'Value',max(2,Pval-1))
elseif any(ch=='fnd')
%-Move "f"orward "d"own to "n"ext entry
set(h,'Value',min(Pval+1,Pmax))
elseif any(ch=='123456789')
%-Move to entry n
set(h,'Value',max(2,min(eval(ch)+1,Pmax)))
else
%-Illegal character
end
case '!m_cb' %-CallBack handler for extended CallBack 'p'ullDown type
%=======================================================================
% spm_input('!m_cb')
%-Get PopUp handle and value
h = gcbo;
n = get(h,'Value');
%-Get PopUp's UserData, check cb and UD fields exist, extract cb & UD
tmp = get(h,'UserData');
if ~(isfield(tmp,'cb') & isfield(tmp,'UD'))
error('Invalid UserData structure for spm_input extended callback')
end
cb = tmp.cb;
UD = tmp.UD;
%-Evaluate appropriate CallBack string (ignoring any return arguments)
% NB: Using varargout={eval(cb{n})}; gives an error if the CallBack
% has no return arguments!
if length(cb)==1, eval(char(cb)); else, eval(cb{n}); end
case '!dscroll'
%=======================================================================
% spm_input('!dScroll',h,Prompt)
%-Scroll text in object h
if nargin<2, return, else, h=varargin{2}; end
if nargin<3, Prompt = get(h,'UserData'); else, Prompt=varargin{3}; end
tmp = Prompt;
if length(Prompt)>56
while length(tmp)>56
tic, while(toc<0.1), pause(0.05), end
tmp(1)=[];
set(h,'String',tmp(1:min(length(tmp),56)))
end
pause(1)
set(h,'String',Prompt(1:min(length(Prompt),56)))
end
otherwise
%=======================================================================
error(['Invalid type/action: ',Type])
%=======================================================================
end % (case lower(Type))
%=======================================================================
%- S U B - F U N C T I O N S
%=======================================================================
function [Keys,Labs] = sf_labkeys(Labels)
%=======================================================================
%-Make unique character keys for the Labels, ignoring case
if nargin<1, error('insufficient arguments'), end
if iscellstr(Labels), Labels = char(Labels); end
if isempty(Labels), Keys=''; Labs=''; return, end
Keys=Labels(:,1)';
nLabels = size(Labels,1);
if any(~diff(abs(sort(lower(Keys)))))
if nLabels<10
Keys = sprintf('%d',[1:nLabels]);
elseif nLabels<=26
Keys = sprintf('%c',abs('a')+[0:nLabels-1]);
else
error('Too many buttons!')
end
Labs = Labels;
else
Labs = Labels(:,2:end);
end
function [p,msg] = sf_eEval(str,Type,n,m)
%=======================================================================
%-Evaluation and error trapping of typed input
if nargin<4, m=[]; end
if nargin<3, n=[]; end
if nargin<2, Type='e'; end
if nargin<1, str=''; end
if isempty(str), p='!'; msg='empty input'; return, end
switch lower(Type)
case 's'
p = str; msg = '';
case 'e'
p = evalin('base',['[',str,']'],'''!''');
if ischar(p)
msg = 'evaluation error';
else
[p,msg] = sf_SzChk(p,n);
end
case 'n'
p = evalin('base',['[',str,']'],'''!''');
if ischar(p)
msg = 'evaluation error';
elseif any(floor(p(:))~=p(:)|p(:)<1)|~isreal(p)
p='!'; msg='natural number(s) required';
elseif ~isempty(m) & any(p(:)>m)
p='!'; msg=['max value is ',num2str(m)];
else
[p,msg] = sf_SzChk(p,n);
end
case 'w'
p = evalin('base',['[',str,']'],'''!''');
if ischar(p)
msg = 'evaluation error';
elseif any(floor(p(:))~=p(:)|p(:)<0)|~isreal(p)
p='!'; msg='whole number(s) required';
elseif ~isempty(m) & any(p(:)>m)
p='!'; msg=['max value is ',num2str(m)];
else
[p,msg] = sf_SzChk(p,n);
end
case 'i'
p = evalin('base',['[',str,']'],'''!''');
if ischar(p)
msg = 'evaluation error';
elseif any(floor(p(:))~=p(:))|~isreal(p)
p='!'; msg='integer(s) required';
else
[p,msg] = sf_SzChk(p,n);
end
case 'p'
p = evalin('base',['[',str,']'],'''!''');
if ischar(p)
msg = 'evaluation error';
elseif length(setxor(p(:)',m))
p='!'; msg='invalid permutation';
else
[p,msg] = sf_SzChk(p,n);
end
case 'r'
p = evalin('base',['[',str,']'],'''!''');
if ischar(p)
msg = 'evaluation error';
elseif ~isreal(p)
p='!'; msg='real number(s) required';
elseif ~isempty(m) & ( max(p)>max(m) | min(p)<min(m) )
p='!'; msg=sprintf('real(s) in [%g,%g] required',min(m),max(m));
else
[p,msg] = sf_SzChk(p,n);
end
case 'c'
if isempty(m), m=Inf; end
[p,msg] = spm_input('!iCond',str,n,m);
case 'x'
X = m; %-Design matrix/space-structure
if isempty(n), n=1; end
%-Sort out contrast matrix dimensions (contrast vectors in rows)
if length(n)==1, n=[n,Inf]; else, n=reshape(n(1:2),1,2); end
if ~isempty(X) % - override n(2) w/ design column dimension
n(2) = spm_SpUtil('size',X,2);
end
p = evalin('base',['[',str,']'],'''!''');
if ischar(p)
msg = 'evaluation error';
else
if isfinite(n(2)) & size(p,2)<n(2)
tmp = n(2) -size(p,2);
p = [p, zeros(size(p,1),tmp)];
if size(p,1)>1, str=' columns'; else, str='s'; end
msg = sprintf('right padded with %d zero%s',tmp,str);
else
msg = '';
end
if size(p,2)>n(2)
p='!'; msg=sprintf('too long - only %d prams',n(2));
elseif isfinite(n(1)) & size(p,1)~=n(1)
p='!';
if n(1)==1, msg='vector required';
else, msg=sprintf('%d contrasts required',n(1)); end
elseif ~isempty(X) & ~spm_SpUtil('allCon',X,p')
p='!'; msg='invalid contrast';
end
end
otherwise
error('unrecognised type');
end
function str = sf_SzStr(n,l)
%=======================================================================
%-Size info string constuction
if nargin<2, l=0; else, l=1; end
if nargin<1, error('insufficient arguments'), end
if isempty(n), n=NaN; end
n=n(:); if length(n)==1, n=[n,1]; end, dn=length(n);
if any(isnan(n)) | (prod(n)==1 & dn<=2) | (dn==2 & min(n)==1 & isinf(max(n)))
str = ''; lstr = '';
elseif dn==2 & min(n)==1
str = sprintf('[%d]',max(n)); lstr = [str,'-vector'];
elseif dn==2 & sum(isinf(n))==1
str = sprintf('[%d]',min(n)); lstr = [str,'-vector(s)'];
else
str=''; for i = 1:dn
if isfinite(n(i)), str = sprintf('%s,%d',str,n(i));
else, str = sprintf('%s,*',str); end
end
str = ['[',str(2:end),']']; lstr = [str,'-matrix'];
end
if l, str=sprintf('\t%s',lstr); else, str=[str,' ']; end
function [p,msg] = sf_SzChk(p,n,msg)
%=======================================================================
%-Size checking
if nargin<3, msg=''; end
if nargin<2, n=[]; end, if isempty(n), n=NaN; else, n=n(:)'; end
if nargin<1, error('insufficient arguments'), end
if ischar(p) | any(isnan(n(:))), return, end
if length(n)==1, n=[n,1]; end
dn = length(n);
sp = size(p);
dp = ndims(p);
if dn==2 & min(n)==1
%-[1,1], [1,n], [n,1], [1,Inf], [Inf,1] - vector - allow transpose
%---------------------------------------------------------------
i = min(find(n==max(n)));
if n(i)==1 & max(sp)>1
p='!'; msg='scalar required';
elseif ndims(p)~=2 | ~any(sp==1) | ( isfinite(n(i)) & max(sp)~=n(i) )
%-error: Not2D | not vector | not right length
if isfinite(n(i)), str=sprintf('%d-',n(i)); else, str=''; end
p='!'; msg=[str,'vector required'];
elseif sp(i)==1 & n(i)~=1
p=p'; msg=[msg,' (input transposed)'];
end
elseif dn==2 & sum(isinf(n))==1
%-[n,Inf], [Inf,n] - n vector(s) required - allow transposing
%---------------------------------------------------------------
i = find(isfinite(n));
if ndims(p)~=2 | ~any(sp==n(i))
p='!'; msg=sprintf('%d-vector(s) required',min(n));
elseif sp(i)~=n
p=p'; msg=[msg,' (input transposed)'];
end
else
%-multi-dimensional matrix required - check dimensions
%---------------------------------------------------------------
if ndims(p)~=dn | ~all( size(p)==n | isinf(n) )
p = '!'; msg='';
for i = 1:dn
if isfinite(n(i)), msg = sprintf('%s,%d',msg,n(i));
else, msg = sprintf('%s,*',msg); end
end
msg = ['[',msg(2:end),']-matrix required'];
end
end
%==========================================================================
function uifocus(h)
try
if strcmpi(get(h, 'Style'), 'PushButton') == 1
uicontrol(gcbo);
else
uicontrol(h);
end
end
|
github
|
lcnbeapp/beapp-master
|
spm_write_sn.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_write_sn.m
| 20,195 |
utf_8
|
5bb2c4d938b07e035b1552465111fcf7
|
function VO = spm_write_sn(V,prm,flags,extras)
% Write Out Warped Images.
% FORMAT VO = spm_write_sn(V,matname,flags,msk)
% V - Images to transform (filenames or volume structure).
% matname - Transformation information (filename or structure).
% flags - flags structure, with fields...
% interp - interpolation method (0-7)
% wrap - wrap edges (e.g., [1 1 0] for 2D MRI sequences)
% vox - voxel sizes (3 element vector - in mm)
% Non-finite values mean use template vox.
% bb - bounding box (2x3 matrix - in mm)
% Non-finite values mean use template bb.
% preserve - either 0 or 1. A value of 1 will "modulate"
% the spatially normalised images so that total
% units are preserved, rather than just
% concentrations.
% prefix - Prefix for normalised images. Defaults to 'w'.
% msk - An optional cell array for masking the spatially
% normalised images (see below).
%
% Warped images are written prefixed by "w".
%
% Non-finite vox or bounding box suggests that values should be derived
% from the template image.
%
% Don't use interpolation methods greater than one for data containing
% NaNs.
% _______________________________________________________________________
%
% FORMAT msk = spm_write_sn(V,matname,flags,'mask')
% V - Images to transform (filenames or volume structure).
% matname - Transformation information (filename or structure).
% flags - flags structure, with fields...
% wrap - wrap edges (e.g., [1 1 0] for 2D MRI sequences)
% vox - voxel sizes (3 element vector - in mm)
% Non-finite values mean use template vox.
% bb - bounding box (2x3 matrix - in mm)
% Non-finite values mean use template bb.
% msk - a cell array for masking a series of spatially normalised
% images.
%
%
% _______________________________________________________________________
%
% FORMAT VO = spm_write_sn(V,prm,'modulate')
% V - Spatially normalised images to modulate (filenames or
% volume structure).
% prm - Transformation information (filename or structure).
%
% After nonlinear spatial normalization, the relative volumes of some
% brain structures will have decreased, whereas others will increase.
% The resampling of the images preserves the concentration of pixel
% units in the images, so the total counts from structures that have
% reduced volumes after spatial normalization will be reduced by an
% amount proportional to the volume reduction.
%
% This routine rescales images after spatial normalization, so that
% the total counts from any structure are preserved. It was written
% as an optional step in performing voxel based morphometry.
%
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id$
if isempty(V), return; end;
if ischar(prm), prm = load(prm); end;
if ischar(V), V = spm_vol(V); end;
if nargin==3 && ischar(flags) && strcmpi(flags,'modulate'),
if nargout==0,
modulate(V,prm);
else
VO = modulate(V,prm);
end;
return;
end;
def_flags = struct('interp',1,'vox',NaN,'bb',NaN,'wrap',[0 0 0],'preserve',0,...
'prefix','w');
if nargin < 3,
flags = def_flags;
else
fnms = fieldnames(def_flags);
for i=1:length(fnms),
if ~isfield(flags,fnms{i}),
flags.(fnms{i}) = def_flags.(fnms{i});
end;
end;
end;
[x,y,z,mat] = get_xyzmat(prm,flags.bb,flags.vox);
if nargin==4,
if ischar(extras) && strcmpi(extras,'mask'),
VO = get_snmask(V,prm,x,y,z,flags.wrap);
return;
end;
if iscell(extras),
msk = extras;
end;
end;
if nargout>0 && length(V)>8,
error('Too many images to save in memory');
end;
if ~exist('msk','var')
msk = get_snmask(V,prm,x,y,z,flags.wrap);
end;
if nargout==0,
if isempty(prm.Tr),
affine_transform(V,prm,x,y,z,mat,flags,msk);
else
nonlin_transform(V,prm,x,y,z,mat,flags,msk);
end;
else
if isempty(prm.Tr),
VO = affine_transform(V,prm,x,y,z,mat,flags,msk);
else
VO = nonlin_transform(V,prm,x,y,z,mat,flags,msk);
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function VO = affine_transform(V,prm,x,y,z,mat,flags,msk)
[X,Y] = ndgrid(x,y);
d = [flags.interp*[1 1 1]' flags.wrap(:)];
spm_progress_bar('Init',numel(V),'Resampling','volumes/slices completed');
for i=1:numel(V),
VO = make_hdr_struct(V(i),x,y,z,mat, flags.prefix);
if flags.preserve
VO.fname = prepend(VO.fname,'m');
end
detAff = det(prm.VF(1).mat*prm.Affine/prm.VG(1).mat);
if flags.preserve, VO.pinfo(1:2,:) = VO.pinfo(1:2,:)/detAff; end;
%Dat= zeros(VO.dim(1:3));
Dat = single(0);
Dat(VO.dim(1),VO.dim(2),VO.dim(3)) = 0;
C = spm_bsplinc(V(i),d);
for j=1:length(z), % Cycle over planes
[X2,Y2,Z2] = mmult(X,Y,z(j),V(i).mat\prm.VF(1).mat*prm.Affine);
dat = spm_bsplins(C,X2,Y2,Z2,d);
if flags.preserve, dat = dat*detAff; end;
dat(msk{j}) = NaN;
Dat(:,:,j) = single(dat);
if numel(V)<5, spm_progress_bar('Set',i-1+j/length(z)); end;
end;
if nargout~=0,
VO.pinfo = [1 0]';
VO.dt = [spm_type('float32') spm_platform('bigend')];
VO.dat = Dat;
else
spm_write_vol(VO, Dat);
end;
spm_progress_bar('Set',i);
end;
spm_progress_bar('Clear');
return;
%_______________________________________________________________________
%_______________________________________________________________________
function VO = nonlin_transform(V,prm,x,y,z,mat,flags,msk)
[X,Y] = ndgrid(x,y);
Tr = prm.Tr;
BX = spm_dctmtx(prm.VG(1).dim(1),size(Tr,1),x-1);
BY = spm_dctmtx(prm.VG(1).dim(2),size(Tr,2),y-1);
BZ = spm_dctmtx(prm.VG(1).dim(3),size(Tr,3),z-1);
if flags.preserve,
DX = spm_dctmtx(prm.VG(1).dim(1),size(Tr,1),x-1,'diff');
DY = spm_dctmtx(prm.VG(1).dim(2),size(Tr,2),y-1,'diff');
DZ = spm_dctmtx(prm.VG(1).dim(3),size(Tr,3),z-1,'diff');
end;
d = [flags.interp*[1 1 1]' flags.wrap(:)];
spm_progress_bar('Init',numel(V),'Resampling','volumes completed');
for i=1:numel(V),
VO = make_hdr_struct(V(i),x,y,z,mat, flags.prefix);
if flags.preserve
VO.fname = prepend(VO.fname,'m');
end
detAff = det(prm.VF(1).mat*prm.Affine/prm.VG(1).mat);
% Accumulate data
%Dat= zeros(VO.dim(1:3));
Dat = single(0);
Dat(VO.dim(1),VO.dim(2),VO.dim(3)) = 0;
C = spm_bsplinc(V(i),d);
for j=1:length(z), % Cycle over planes
% Nonlinear deformations
%----------------------------------------------------------------------------
tx = get_2Dtrans(Tr(:,:,:,1),BZ,j);
ty = get_2Dtrans(Tr(:,:,:,2),BZ,j);
tz = get_2Dtrans(Tr(:,:,:,3),BZ,j);
X1 = X + BX*tx*BY';
Y1 = Y + BX*ty*BY';
Z1 = z(j) + BX*tz*BY';
[X2,Y2,Z2] = mmult(X1,Y1,Z1,V(i).mat\prm.VF(1).mat*prm.Affine);
dat = spm_bsplins(C,X2,Y2,Z2,d);
dat(msk{j}) = NaN;
if ~flags.preserve,
Dat(:,:,j) = single(dat);
else
j11 = DX*tx*BY' + 1; j12 = BX*tx*DY'; j13 = BX*get_2Dtrans(Tr(:,:,:,1),DZ,j)*BY';
j21 = DX*ty*BY'; j22 = BX*ty*DY' + 1; j23 = BX*get_2Dtrans(Tr(:,:,:,2),DZ,j)*BY';
j31 = DX*tz*BY'; j32 = BX*tz*DY'; j33 = BX*get_2Dtrans(Tr(:,:,:,3),DZ,j)*BY' + 1;
% The determinant of the Jacobian reflects relative volume changes.
%------------------------------------------------------------------
dat = dat .* (j11.*(j22.*j33-j23.*j32) - j21.*(j12.*j33-j13.*j32) + j31.*(j12.*j23-j13.*j22)) * detAff;
Dat(:,:,j) = single(dat);
end;
if numel(V)<5, spm_progress_bar('Set',i-1+j/length(z)); end;
end;
if nargout==0,
if flags.preserve, VO = rmfield(VO,'pinfo'); end
VO = spm_write_vol(VO,Dat);
else
VO.pinfo = [1 0]';
VO.dt = [spm_type('float32') spm_platform('bigend')];
VO.dat = Dat;
end;
spm_progress_bar('Set',i);
end;
spm_progress_bar('Clear');
return;
%_______________________________________________________________________
%_______________________________________________________________________
function VO = modulate(V,prm)
spm_progress_bar('Init',numel(V),'Modulating','volumes completed');
for i=1:numel(V),
VO = V(i);
VO = rmfield(VO,'pinfo');
VO.fname = prepend(VO.fname,'m');
detAff = det(prm.VF(1).mat*prm.Affine/prm.VG(1).mat);
%Dat = zeros(VO.dim(1:3));
Dat = single(0);
Dat(VO.dim(1),VO.dim(2),VO.dim(3)) = 0;
[x,y,z,mat] = get_xyzmat(prm,NaN,NaN,VO);
if sum((mat(:)-VO.mat(:)).^2)>1e-7, error('Orientations not compatible'); end;
Tr = prm.Tr;
if isempty(Tr),
for j=1:length(z), % Cycle over planes
dat = spm_slice_vol(V(i),spm_matrix([0 0 j]),V(i).dim(1:2),0);
Dat(:,:,j) = single(dat);
if numel(V)<5, spm_progress_bar('Set',i-1+j/length(z)); end;
end;
else
BX = spm_dctmtx(prm.VG(1).dim(1),size(Tr,1),x-1);
BY = spm_dctmtx(prm.VG(1).dim(2),size(Tr,2),y-1);
BZ = spm_dctmtx(prm.VG(1).dim(3),size(Tr,3),z-1);
DX = spm_dctmtx(prm.VG(1).dim(1),size(Tr,1),x-1,'diff');
DY = spm_dctmtx(prm.VG(1).dim(2),size(Tr,2),y-1,'diff');
DZ = spm_dctmtx(prm.VG(1).dim(3),size(Tr,3),z-1,'diff');
for j=1:length(z), % Cycle over planes
tx = get_2Dtrans(Tr(:,:,:,1),BZ,j);
ty = get_2Dtrans(Tr(:,:,:,2),BZ,j);
tz = get_2Dtrans(Tr(:,:,:,3),BZ,j);
j11 = DX*tx*BY' + 1; j12 = BX*tx*DY'; j13 = BX*get_2Dtrans(Tr(:,:,:,1),DZ,j)*BY';
j21 = DX*ty*BY'; j22 = BX*ty*DY' + 1; j23 = BX*get_2Dtrans(Tr(:,:,:,2),DZ,j)*BY';
j31 = DX*tz*BY'; j32 = BX*tz*DY'; j33 = BX*get_2Dtrans(Tr(:,:,:,3),DZ,j)*BY' + 1;
% The determinant of the Jacobian reflects relative volume changes.
%------------------------------------------------------------------
dat = spm_slice_vol(V(i),spm_matrix([0 0 j]),V(i).dim(1:2),0);
dat = dat .* (j11.*(j22.*j33-j23.*j32) - j21.*(j12.*j33-j13.*j32) + j31.*(j12.*j23-j13.*j22)) * detAff;
Dat(:,:,j) = single(dat);
if numel(V)<5, spm_progress_bar('Set',i-1+j/length(z)); end;
end;
end;
if nargout==0,
VO = spm_write_vol(VO,Dat);
else
VO.pinfo = [1 0]';
VO.dt = [spm_type('float32') spm_platform('bigend')];
VO.dat = Dat;
end;
spm_progress_bar('Set',i);
end;
spm_progress_bar('Clear');
return;
%_______________________________________________________________________
%_______________________________________________________________________
function VO = make_hdr_struct(V,x,y,z,mat,prefix)
VO = V;
VO.fname = prepend(V.fname,prefix);
VO.mat = mat;
VO.dim(1:3) = [length(x) length(y) length(z)];
VO.pinfo = V.pinfo;
VO.descrip = 'spm - 3D normalized';
return;
%_______________________________________________________________________
%_______________________________________________________________________
function T2 = get_2Dtrans(T3,B,j)
d = [size(T3) 1 1 1];
tmp = reshape(T3,d(1)*d(2),d(3));
T2 = reshape(tmp*B(j,:)',d(1),d(2));
return;
%_______________________________________________________________________
%_______________________________________________________________________
function PO = prepend(PI,pre)
[pth,nm,xt,vr] = spm_fileparts(deblank(PI));
PO = fullfile(pth,[pre nm xt vr]);
return;
%_______________________________________________________________________
%_______________________________________________________________________
function Mask = getmask(X,Y,Z,dim,wrp)
% Find range of slice
tiny = 5e-2;
Mask = true(size(X));
if ~wrp(1), Mask = Mask & (X >= (1-tiny) & X <= (dim(1)+tiny)); end;
if ~wrp(2), Mask = Mask & (Y >= (1-tiny) & Y <= (dim(2)+tiny)); end;
if ~wrp(3), Mask = Mask & (Z >= (1-tiny) & Z <= (dim(3)+tiny)); end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function [X2,Y2,Z2] = mmult(X1,Y1,Z1,Mult)
if length(Z1) == 1,
X2= Mult(1,1)*X1 + Mult(1,2)*Y1 + (Mult(1,3)*Z1 + Mult(1,4));
Y2= Mult(2,1)*X1 + Mult(2,2)*Y1 + (Mult(2,3)*Z1 + Mult(2,4));
Z2= Mult(3,1)*X1 + Mult(3,2)*Y1 + (Mult(3,3)*Z1 + Mult(3,4));
else
X2= Mult(1,1)*X1 + Mult(1,2)*Y1 + Mult(1,3)*Z1 + Mult(1,4);
Y2= Mult(2,1)*X1 + Mult(2,2)*Y1 + Mult(2,3)*Z1 + Mult(2,4);
Z2= Mult(3,1)*X1 + Mult(3,2)*Y1 + Mult(3,3)*Z1 + Mult(3,4);
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function msk = get_snmask(V,prm,x,y,z,wrap)
% Generate a mask for where there is data for all images
%-----------------------------------------------------------------------
msk = cell(length(z),1);
t1 = cat(3,V.mat);
t2 = cat(1,V.dim);
t = [reshape(t1,[16 length(V)])' t2(:,1:3)];
Tr = prm.Tr;
[X,Y] = ndgrid(x,y);
BX = spm_dctmtx(prm.VG(1).dim(1),size(Tr,1),x-1);
BY = spm_dctmtx(prm.VG(1).dim(2),size(Tr,2),y-1);
BZ = spm_dctmtx(prm.VG(1).dim(3),size(Tr,3),z-1);
if numel(V)>1 && any(any(diff(t,1,1))),
spm_progress_bar('Init',length(z),'Computing available voxels','planes completed');
for j=1:length(z), % Cycle over planes
Count = zeros(length(x),length(y));
if isempty(Tr),
% Generate a mask for where there is data for all images
%----------------------------------------------------------------------------
for i=1:numel(V),
[X2,Y2,Z2] = mmult(X,Y,z(j),V(i).mat\prm.VF(1).mat*prm.Affine);
Count = Count + getmask(X2,Y2,Z2,V(i).dim(1:3),wrap);
end;
else
% Nonlinear deformations
%----------------------------------------------------------------------------
X1 = X + BX*get_2Dtrans(Tr(:,:,:,1),BZ,j)*BY';
Y1 = Y + BX*get_2Dtrans(Tr(:,:,:,2),BZ,j)*BY';
Z1 = z(j) + BX*get_2Dtrans(Tr(:,:,:,3),BZ,j)*BY';
% Generate a mask for where there is data for all images
%----------------------------------------------------------------------------
for i=1:numel(V),
[X2,Y2,Z2] = mmult(X1,Y1,Z1,V(i).mat\prm.VF(1).mat*prm.Affine);
Count = Count + getmask(X2,Y2,Z2,V(i).dim(1:3),wrap);
end;
end;
msk{j} = uint32(find(Count ~= numel(V)));
spm_progress_bar('Set',j);
end;
spm_progress_bar('Clear');
else
for j=1:length(z), msk{j} = uint32([]); end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function [x,y,z,mat] = get_xyzmat(prm,bb,vox,VG)
% The old voxel size and origin notation is used here.
% This requires that the position and orientation
% of the template is transverse. It would not be
% straitforward to account for templates that are
% in different orientations because the basis functions
% would no longer be seperable. The seperable basis
% functions mean that computing the deformation field
% from the parameters is much faster.
% bb = sort(bb);
% vox = abs(vox);
if nargin<4,
VG = prm.VG(1);
if all(~isfinite(bb(:))) && all(~isfinite(vox(:))),
x = 1:VG.dim(1);
y = 1:VG.dim(2);
z = 1:VG.dim(3);
mat = VG.mat;
return;
end
end
[bb0,vox0] = bbvox_from_V(VG);
if ~all(isfinite(vox(:))), vox = vox0; end;
if ~all(isfinite(bb(:))), bb = bb0; end;
msk = find(vox<0);
bb = sort(bb);
bb(:,msk) = flipud(bb(:,msk));
% Adjust bounding box slightly - so it rounds to closest voxel.
% Comment out if not needed.
%bb(:,1) = round(bb(:,1)/vox(1))*vox(1);
%bb(:,2) = round(bb(:,2)/vox(2))*vox(2);
%bb(:,3) = round(bb(:,3)/vox(3))*vox(3);
M = prm.VG(1).mat;
vxg = sqrt(sum(M(1:3,1:3).^2));
if det(M(1:3,1:3))<0, vxg(1) = -vxg(1); end;
ogn = M\[0 0 0 1]';
ogn = ogn(1:3)';
% Convert range into range of voxels within template image
x = (bb(1,1):vox(1):bb(2,1))/vxg(1) + ogn(1);
y = (bb(1,2):vox(2):bb(2,2))/vxg(2) + ogn(2);
z = (bb(1,3):vox(3):bb(2,3))/vxg(3) + ogn(3);
og = -vxg.*ogn;
% Again, chose whether to round to closest voxel.
%of = -vox.*(round(-bb(1,:)./vox)+1);
of = bb(1,:)-vox;
M1 = [vxg(1) 0 0 og(1) ; 0 vxg(2) 0 og(2) ; 0 0 vxg(3) og(3) ; 0 0 0 1];
M2 = [vox(1) 0 0 of(1) ; 0 vox(2) 0 of(2) ; 0 0 vox(3) of(3) ; 0 0 0 1];
mat = prm.VG(1).mat*inv(M1)*M2;
LEFTHANDED = true;
if (LEFTHANDED && det(mat(1:3,1:3))>0) || (~LEFTHANDED && det(mat(1:3,1:3))<0),
Flp = [-1 0 0 (length(x)+1); 0 1 0 0; 0 0 1 0; 0 0 0 1];
mat = mat*Flp;
x = flipud(x(:))';
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function [bb,vx] = bbvox_from_V(V)
vx = sqrt(sum(V.mat(1:3,1:3).^2));
if det(V.mat(1:3,1:3))<0, vx(1) = -vx(1); end;
o = V.mat\[0 0 0 1]';
o = o(1:3)';
bb = [-vx.*(o-1) ; vx.*(V.dim(1:3)-o)];
return;
%_______________________________________________________________________
%_______________________________________________________________________
function VO = write_dets(P,bb,vox)
if nargin==1,
job = P;
P = job.P;
bb = job.bb;
vox = job.vox;
end;
spm_progress_bar('Init',numel(P),'Writing','volumes completed');
for i=1:numel(V),
prm = load(deblank(P{i}));
[x,y,z,mat] = get_xyzmat(prm,bb,vox);
Tr = prm.Tr;
BX = spm_dctmtx(prm.VG(1).dim(1),size(Tr,1),x-1);
BY = spm_dctmtx(prm.VG(1).dim(2),size(Tr,2),y-1);
BZ = spm_dctmtx(prm.VG(1).dim(3),size(Tr,3),z-1);
DX = spm_dctmtx(prm.VG(1).dim(1),size(Tr,1),x-1,'diff');
DY = spm_dctmtx(prm.VG(1).dim(2),size(Tr,2),y-1,'diff');
DZ = spm_dctmtx(prm.VG(1).dim(3),size(Tr,3),z-1,'diff');
[pth,nam,ext,nm] = spm_fileparts(P{i});
VO = struct('fname',fullfile(pth,['jy_' nam ext nm]),...
'dim',[numel(x),numel(y),numel(z)],...
'dt',[spm_type('float32') spm_platform('bigend')],...
'pinfo',[1 0 0]',...
'mat',mat,...
'n',1,...
'descrip','Jacobian determinants');
VO = spm_create_vol(VO);
detAff = det(prm.VF(1).mat*prm.Affine/prm.VG(1).mat);
Dat = single(0);
Dat(VO.dim(1),VO.dim(2),VO.dim(3)) = 0;
for j=1:length(z), % Cycle over planes
% Nonlinear deformations
tx = get_2Dtrans(Tr(:,:,:,1),BZ,j);
ty = get_2Dtrans(Tr(:,:,:,2),BZ,j);
tz = get_2Dtrans(Tr(:,:,:,3),BZ,j);
%----------------------------------------------------------------------------
j11 = DX*tx*BY' + 1; j12 = BX*tx*DY'; j13 = BX*get_2Dtrans(Tr(:,:,:,1),DZ,j)*BY';
j21 = DX*ty*BY'; j22 = BX*ty*DY' + 1; j23 = BX*get_2Dtrans(Tr(:,:,:,2),DZ,j)*BY';
j31 = DX*tz*BY'; j32 = BX*tz*DY'; j33 = BX*get_2Dtrans(Tr(:,:,:,3),DZ,j)*BY' + 1;
% The determinant of the Jacobian reflects relative volume changes.
%------------------------------------------------------------------
dat = (j11.*(j22.*j33-j23.*j32) - j21.*(j12.*j33-j13.*j32) + j31.*(j12.*j23-j13.*j22)) * detAff;
Dat(:,:,j) = single(dat);
if numel(P)<5, spm_progress_bar('Set',i-1+j/length(z)); end;
end;
VO = spm_write_vol(VO,Dat);
spm_progress_bar('Set',i);
end;
spm_progress_bar('Clear');
return;
%_______________________________________________________________________
|
github
|
lcnbeapp/beapp-master
|
spm_imatrix.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_imatrix.m
| 1,499 |
utf_8
|
295b97abf7200bfd1af63c3e32aae6fd
|
function P = spm_imatrix(M)
% returns the parameters for creating an affine transformation
% FORMAT P = spm_imatrix(M)
% M - Affine transformation matrix
% P - Parameters (see spm_matrix for definitions)
%___________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner & Stefan Kiebel
% $Id$
% Translations and zooms
%-----------------------------------------------------------------------
R = M(1:3,1:3);
C = chol(R'*R);
P = [M(1:3,4)' 0 0 0 diag(C)' 0 0 0];
if det(R)<0, P(7)=-P(7);end % Fix for -ve determinants
% Shears
%-----------------------------------------------------------------------
C = diag(diag(C))\C;
P(10:12) = C([4 7 8]);
R0 = spm_matrix([0 0 0 0 0 0 P(7:12)]);
R0 = R0(1:3,1:3);
R1 = R/R0;
% This just leaves rotations in matrix R1
%-----------------------------------------------------------------------
%[ c5*c6, c5*s6, s5]
%[-s4*s5*c6-c4*s6, -s4*s5*s6+c4*c6, s4*c5]
%[-c4*s5*c6+s4*s6, -c4*s5*s6-s4*c6, c4*c5]
P(5) = asin(rang(R1(1,3)));
if (abs(P(5))-pi/2)^2 < 1e-9,
P(4) = 0;
P(6) = atan2(-rang(R1(2,1)), rang(-R1(3,1)/R1(1,3)));
else
c = cos(P(5));
P(4) = atan2(rang(R1(2,3)/c), rang(R1(3,3)/c));
P(6) = atan2(rang(R1(1,2)/c), rang(R1(1,1)/c));
end;
return;
% There may be slight rounding errors making b>1 or b<-1.
function a = rang(b)
a = min(max(b, -1), 1);
return;
|
github
|
lcnbeapp/beapp-master
|
spm_affreg.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_affreg.m
| 20,248 |
utf_8
|
431e3807877742bdec89d07ce61e87f8
|
function [M,scal] = spm_affreg(VG,VF,flags,M,scal)
% Affine registration using least squares.
% FORMAT [M,scal] = spm_affreg(VG,VF,flags,M0,scal0)
%
% VG - Vector of template volumes.
% VF - Source volume.
% flags - a structure containing various options. The fields are:
% WG - Weighting volume for template image(s).
% WF - Weighting volume for source image
% Default to [].
% sep - Approximate spacing between sampled points (mm).
% Defaults to 5.
% regtype - regularisation type. Options are:
% 'none' - no regularisation
% 'rigid' - almost rigid body
% 'subj' - inter-subject registration (default).
% 'mni' - registration to ICBM templates
% globnorm - Global normalisation flag (1)
% M0 - (optional) starting estimate. Defaults to eye(4).
% scal0 - (optional) starting estimate.
%
% M - affine transform, such that voxels in VF map to those in
% VG by VG.mat\M*VF.mat
% scal - scaling factors for VG
%
% When only one template is used, then the cost function is approximately
% symmetric, although a linear combination of templates can be used.
% Regularisation is based on assuming a multi-normal distribution for the
% elements of the Henckey Tensor. See:
% "Non-linear Elastic Deformations". R. W. Ogden (Dover), 1984.
% Weighting for the regularisation is determined approximately according
% to:
% "Incorporating Prior Knowledge into Image Registration"
% J. Ashburner, P. Neelin, D. L. Collins, A. C. Evans & K. J. Friston.
% NeuroImage 6:344-352 (1997).
%
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id$
if nargin<5, scal = ones(length(VG),1); end;
if nargin<4, M = eye(4); end;
def_flags = struct('sep',5, 'regtype','subj','WG',[],'WF',[],'globnorm',1,'debug',0);
if nargin < 2 || ~isstruct(flags),
flags = def_flags;
else
fnms = fieldnames(def_flags);
for i=1:length(fnms),
if ~isfield(flags,fnms{i}),
flags.(fnms{i}) = def_flags.(fnms{i});
end;
end;
end;
% Check to ensure inputs are valid...
% ---------------------------------------------------------------
if length(VF)>1, error('Can not use more than one source image'); end;
if ~isempty(flags.WF),
if length(flags.WF)>1,
error('Can only use one source weighting image');
end;
if any(any((VF.mat-flags.WF.mat).^2>1e-8)),
error('Source and its weighting image must have same orientation');
end;
if any(any(VF.dim(1:3)-flags.WF.dim(1:3))),
error('Source and its weighting image must have same dimensions');
end;
end;
if ~isempty(flags.WG),
if length(flags.WG)>1,
error('Can only use one template weighting image');
end;
tmp = reshape(cat(3,VG(:).mat,flags.WG.mat),16,length(VG)+length(flags.WG));
else
tmp = reshape(cat(3,VG(:).mat),16,length(VG));
end;
if any(any(diff(tmp,1,2).^2>1e-8)),
error('Reference images must all have the same orientation');
end;
if ~isempty(flags.WG),
tmp = cat(1,VG(:).dim,flags.WG.dim);
else
tmp = cat(1,VG(:).dim);
end;
if any(any(diff(tmp(:,1:3),1,1))),
error('Reference images must all have the same dimensions');
end;
% ---------------------------------------------------------------
% Generate points to sample from, adding some jitter in order to
% make the cost function smoother.
% ---------------------------------------------------------------
rand('state',0); % want the results to be consistant.
dg = VG(1).dim(1:3);
df = VF(1).dim(1:3);
if length(VG)==1,
skip = sqrt(sum(VG(1).mat(1:3,1:3).^2)).^(-1)*flags.sep;
[x1,x2,x3]=ndgrid(1:skip(1):dg(1)-.5, 1:skip(2):dg(2)-.5, 1:skip(3):dg(3)-.5);
x1 = x1 + rand(size(x1))*0.5; x1 = x1(:);
x2 = x2 + rand(size(x2))*0.5; x2 = x2(:);
x3 = x3 + rand(size(x3))*0.5; x3 = x3(:);
end;
skip = sqrt(sum(VF(1).mat(1:3,1:3).^2)).^(-1)*flags.sep;
[y1,y2,y3]=ndgrid(1:skip(1):df(1)-.5, 1:skip(2):df(2)-.5, 1:skip(3):df(3)-.5);
y1 = y1 + rand(size(y1))*0.5; y1 = y1(:);
y2 = y2 + rand(size(y2))*0.5; y2 = y2(:);
y3 = y3 + rand(size(y3))*0.5; y3 = y3(:);
% ---------------------------------------------------------------
if flags.globnorm,
% Scale all images approximately equally
% ---------------------------------------------------------------
for i=1:length(VG),
VG(i).pinfo(1:2,:) = VG(i).pinfo(1:2,:)/spm_global(VG(i));
end;
VF(1).pinfo(1:2,:) = VF(1).pinfo(1:2,:)/spm_global(VF(1));
end;
% ---------------------------------------------------------------
if length(VG)==1,
[G,dG1,dG2,dG3] = spm_sample_vol(VG(1),x1,x2,x3,1);
if ~isempty(flags.WG),
WG = abs(spm_sample_vol(flags.WG,x1,x2,x3,1))+eps;
WG(~isfinite(WG)) = 1;
end;
end;
[F,dF1,dF2,dF3] = spm_sample_vol(VF(1),y1,y2,y3,1);
if ~isempty(flags.WF),
WF = abs(spm_sample_vol(flags.WF,y1,y2,y3,1))+eps;
WF(~isfinite(WF)) = 1;
end;
% ---------------------------------------------------------------
n_main_its = 0;
ss = Inf;
W = [Inf Inf Inf];
est_smo = 1;
% ---------------------------------------------------------------
for iter=1:256,
pss = ss;
p0 = [0 0 0 0 0 0 1 1 1 0 0 0];
% Initialise the cost function and its 1st and second derivatives
% ---------------------------------------------------------------
n = 0;
ss = 0;
Beta = zeros(12+length(VG),1);
Alpha = zeros(12+length(VG));
if length(VG)==1,
% Make the cost function symmetric
% ---------------------------------------------------------------
% Build a matrix to rotate the derivatives by, converting from
% derivatives w.r.t. changes in the overall affine transformation
% matrix, to derivatives w.r.t. the parameters p.
% ---------------------------------------------------------------
dt = 0.0001;
R = eye(13);
MM0 = inv(VG.mat)*inv(spm_matrix(p0))*VG.mat;
for i1=1:12,
p1 = p0;
p1(i1) = p1(i1)+dt;
MM1 = (inv(VG.mat)*inv(spm_matrix(p1))*(VG.mat));
R(1:12,i1) = reshape((MM1(1:3,:)-MM0(1:3,:))/dt,12,1);
end;
% ---------------------------------------------------------------
[t1,t2,t3] = coords((M*VF(1).mat)\VG(1).mat,x1,x2,x3);
msk = find((t1>=1 & t1<=df(1) & t2>=1 & t2<=df(2) & t3>=1 & t3<=df(3)));
if length(msk)<32, error_message; end;
t1 = t1(msk);
t2 = t2(msk);
t3 = t3(msk);
t = spm_sample_vol(VF(1), t1,t2,t3,1);
% Get weights
% ---------------------------------------------------------------
if ~isempty(flags.WF) || ~isempty(flags.WG),
if isempty(flags.WF),
wt = WG(msk);
else
wt = spm_sample_vol(flags.WF(1), t1,t2,t3,1)+eps;
wt(~isfinite(wt)) = 1;
if ~isempty(flags.WG), wt = 1./(1./wt + 1./WG(msk)); end;
end;
wt = sparse(1:length(wt),1:length(wt),wt);
else
% wt = speye(length(msk));
wt = [];
end;
% ---------------------------------------------------------------
clear t1 t2 t3
% Update the cost function and its 1st and second derivatives.
% ---------------------------------------------------------------
[AA,Ab,ss1,n1] = costfun(x1,x2,x3,dG1,dG2,dG3,msk,scal^(-2)*t,G(msk)-(1/scal)*t,wt);
Alpha = Alpha + R'*AA*R;
Beta = Beta + R'*Ab;
ss = ss + ss1;
n = n + n1;
% t = G(msk) - (1/scal)*t;
end;
if 1,
% Build a matrix to rotate the derivatives by, converting from
% derivatives w.r.t. changes in the overall affine transformation
% matrix, to derivatives w.r.t. the parameters p.
% ---------------------------------------------------------------
dt = 0.0001;
R = eye(12+length(VG));
MM0 = inv(M*VF.mat)*spm_matrix(p0)*M*VF.mat;
for i1=1:12,
p1 = p0;
p1(i1) = p1(i1)+dt;
MM1 = (inv(M*VF.mat)*spm_matrix(p1)*M*VF.mat);
R(1:12,i1) = reshape((MM1(1:3,:)-MM0(1:3,:))/dt,12,1);
end;
% ---------------------------------------------------------------
[t1,t2,t3] = coords(VG(1).mat\M*VF(1).mat,y1,y2,y3);
msk = find((t1>=1 & t1<=dg(1) & t2>=1 & t2<=dg(2) & t3>=1 & t3<=dg(3)));
if length(msk)<32, error_message; end;
if length(msk)<32, error_message; end;
t1 = t1(msk);
t2 = t2(msk);
t3 = t3(msk);
t = zeros(length(t1),length(VG));
% Get weights
% ---------------------------------------------------------------
if ~isempty(flags.WF) || ~isempty(flags.WG),
if isempty(flags.WG),
wt = WF(msk);
else
wt = spm_sample_vol(flags.WG(1), t1,t2,t3,1)+eps;
wt(~isfinite(wt)) = 1;
if ~isempty(flags.WF), wt = 1./(1./wt + 1./WF(msk)); end;
end;
wt = sparse(1:length(wt),1:length(wt),wt);
else
wt = speye(length(msk));
end;
% ---------------------------------------------------------------
if est_smo,
% Compute derivatives of residuals in the space of F
% ---------------------------------------------------------------
[ds1,ds2,ds3] = transform_derivs(VG(1).mat\M*VF(1).mat,dF1(msk),dF2(msk),dF3(msk));
for i=1:length(VG),
[t(:,i),dt1,dt2,dt3] = spm_sample_vol(VG(i), t1,t2,t3,1);
ds1 = ds1 - dt1*scal(i); clear dt1
ds2 = ds2 - dt2*scal(i); clear dt2
ds3 = ds3 - dt3*scal(i); clear dt3
end;
dss = [ds1'*wt*ds1 ds2'*wt*ds2 ds3'*wt*ds3];
clear ds1 ds2 ds3
else
for i=1:length(VG),
t(:,i)= spm_sample_vol(VG(i), t1,t2,t3,1);
end;
end;
clear t1 t2 t3
% Update the cost function and its 1st and second derivatives.
% ---------------------------------------------------------------
[AA,Ab,ss2,n2] = costfun(y1,y2,y3,dF1,dF2,dF3,msk,-t,F(msk)-t*scal,wt);
Alpha = Alpha + R'*AA*R;
Beta = Beta + R'*Ab;
ss = ss + ss2;
n = n + n2;
end;
if est_smo,
% Compute a smoothness correction from the residuals and their
% derivatives. This is analagous to the one used in:
% "Analysis of fMRI Time Series Revisited"
% Friston KJ, Holmes AP, Poline JB, Grasby PJ, Williams SCR,
% Frackowiak RSJ, Turner R. Neuroimage 2:45-53 (1995).
% ---------------------------------------------------------------
vx = sqrt(sum(VG(1).mat(1:3,1:3).^2));
pW = W;
W = (2*dss/ss2).^(-.5).*vx;
W = min(pW,W);
if flags.debug, fprintf('\nSmoothness FWHM: %.3g x %.3g x %.3g mm\n', W*sqrt(8*log(2))); end;
if length(VG)==1, dens=2; else dens=1; end;
smo = prod(min(dens*flags.sep/sqrt(2*pi)./W,[1 1 1]));
est_smo=0;
n_main_its = n_main_its + 1;
end;
% Update the parameter estimates
% ---------------------------------------------------------------
nu = n*smo;
sig2 = ss/nu;
[d1,d2] = reg(M,12+length(VG),flags.regtype);
soln = (Alpha/sig2+d2)\(Beta/sig2-d1);
scal = scal - soln(13:end);
M = spm_matrix(p0 + soln(1:12)')*M;
if flags.debug,
fprintf('%d\t%g\n', iter, ss/n);
piccies(VF,VG,M,scal)
end;
% If cost function stops decreasing, then re-estimate smoothness
% and try again. Repeat a few times.
% ---------------------------------------------------------------
ss = ss/n;
if iter>1, spm_chi2_plot('Set',ss); end;
if (pss-ss)/pss < 1e-6,
est_smo = 1;
end;
if n_main_its>3, break; end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function [X1,Y1,Z1] = transform_derivs(Mat,X,Y,Z)
% Given the derivatives of a scalar function, return those of the
% affine transformed function
%_______________________________________________________________________
t1 = Mat(1:3,1:3);
t2 = eye(3);
if sum((t1(:)-t2(:)).^2) < 1e-12,
X1 = X;Y1 = Y; Z1 = Z;
else
X1 = Mat(1,1)*X + Mat(1,2)*Y + Mat(1,3)*Z;
Y1 = Mat(2,1)*X + Mat(2,2)*Y + Mat(2,3)*Z;
Z1 = Mat(3,1)*X + Mat(3,2)*Y + Mat(3,3)*Z;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function [d1,d2] = reg(M,n,typ)
% Analytically compute the first and second derivatives of a penalty
% function w.r.t. changes in parameters.
if nargin<3, typ = 'subj'; end;
if nargin<2, n = 13; end;
[mu,isig] = priors(typ);
ds = 0.000001;
d1 = zeros(n,1);
d2 = zeros(n);
p0 = [0 0 0 0 0 0 1 1 1 0 0 0];
h0 = penalty(p0,M,mu,isig);
for i=7:12, % derivatives are zero w.r.t. rotations and translations
p1 = p0;
p1(i) = p1(i)+ds;
h1 = penalty(p1,M,mu,isig);
d1(i) = (h1-h0)/ds; % First derivative
for j=7:12,
p2 = p0;
p2(j) = p2(j)+ds;
h2 = penalty(p2,M,mu,isig);
p3 = p1;
p3(j) = p3(j)+ds;
h3 = penalty(p3,M,mu,isig);
d2(i,j) = ((h3-h2)/ds-(h1-h0)/ds)/ds; % Second derivative
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function h = penalty(p,M,mu,isig)
% Return a penalty based on the elements of an affine transformation,
% which is given by:
% spm_matrix(p)*M
%
% The penalty is based on the 6 unique elements of the Hencky tensor
% elements being multinormally distributed.
%_______________________________________________________________________
% Unique elements of symmetric 3x3 matrix.
els = [1 2 3 5 6 9];
T = spm_matrix(p)*M;
T = T(1:3,1:3);
T = 0.5*logm(T'*T);
T = T(els)' - mu;
h = T'*isig*T;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function [mu,isig] = priors(typ)
% The parameters for this distribution were derived empirically from 227
% scans, that were matched to the ICBM space.
%_______________________________________________________________________
mu = zeros(6,1);
isig = zeros(6);
switch deblank(lower(typ)),
case 'mni', % For registering with MNI templates...
mu = [0.0667 0.0039 0.0008 0.0333 0.0071 0.1071]';
isig = 1e4 * [
0.0902 -0.0345 -0.0106 -0.0025 -0.0005 -0.0163
-0.0345 0.7901 0.3883 0.0041 -0.0103 -0.0116
-0.0106 0.3883 2.2599 0.0113 0.0396 -0.0060
-0.0025 0.0041 0.0113 0.0925 0.0471 -0.0440
-0.0005 -0.0103 0.0396 0.0471 0.2964 -0.0062
-0.0163 -0.0116 -0.0060 -0.0440 -0.0062 0.1144];
case 'rigid', % Constrained to be almost rigid...
mu = zeros(6,1);
isig = eye(6)*1e9;
case 'isochoric', % Volume preserving...
error('Not implemented');
case 'isotropic', % Isotropic zoom in all directions...
error('Not implemented');
case 'subj', % For inter-subject registration...
mu = zeros(6,1);
isig = 1e3 * [
0.8876 0.0784 0.0784 -0.1749 0.0784 -0.1749
0.0784 5.3894 0.2655 0.0784 0.2655 0.0784
0.0784 0.2655 5.3894 0.0784 0.2655 0.0784
-0.1749 0.0784 0.0784 0.8876 0.0784 -0.1749
0.0784 0.2655 0.2655 0.0784 5.3894 0.0784
-0.1749 0.0784 0.0784 -0.1749 0.0784 0.8876];
case 'none', % No regularisation...
mu = zeros(6,1);
isig = zeros(6);
otherwise,
error(['"' typ '" not recognised as type of regularisation.']);
end;
return;
%_______________________________________________________________________
function [y1,y2,y3]=coords(M,x1,x2,x3)
% Affine transformation of a set of coordinates.
%_______________________________________________________________________
y1 = M(1,1)*x1 + M(1,2)*x2 + M(1,3)*x3 + M(1,4);
y2 = M(2,1)*x1 + M(2,2)*x2 + M(2,3)*x3 + M(2,4);
y3 = M(3,1)*x1 + M(3,2)*x2 + M(3,3)*x3 + M(3,4);
return;
%_______________________________________________________________________
%_______________________________________________________________________
function A = make_A(x1,x2,x3,dG1,dG2,dG3,t)
% Generate part of a design matrix using the chain rule...
% df/dm = df/dy * dy/dm
% where
% df/dm is the rate of change of intensity w.r.t. affine parameters
% df/dy is the gradient of the image f
% dy/dm crange of position w.r.t. change of parameters
%_______________________________________________________________________
A = [x1.*dG1 x1.*dG2 x1.*dG3 ...
x2.*dG1 x2.*dG2 x2.*dG3 ...
x3.*dG1 x3.*dG2 x3.*dG3 ...
dG1 dG2 dG3 t];
return;
%_______________________________________________________________________
%_______________________________________________________________________
function [AA,Ab,ss,n] = costfun(x1,x2,x3,dG1,dG2,dG3,msk,lastcols,b,wt)
chunk = 10240;
lm = length(msk);
AA = zeros(12+size(lastcols,2));
Ab = zeros(12+size(lastcols,2),1);
ss = 0;
n = 0;
for i=1:ceil(lm/chunk),
ind = (((i-1)*chunk+1):min(i*chunk,lm))';
msk1 = msk(ind);
A1 = make_A(x1(msk1),x2(msk1),x3(msk1),dG1(msk1),dG2(msk1),dG3(msk1),lastcols(ind,:));
b1 = b(ind);
if ~isempty(wt),
wt1 = wt(ind,ind);
AA = AA + A1'*wt1*A1;
%Ab = Ab + A1'*wt1*b1;
Ab = Ab + (b1'*wt1*A1)';
ss = ss + b1'*wt1*b1;
n = n + trace(wt1);
clear wt1
else
AA = AA + A1'*A1;
%Ab = Ab + A1'*b1;
Ab = Ab + (b1'*A1)';
ss = ss + b1'*b1;
n = n + length(msk1);
end;
clear A1 b1 msk1 ind
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function error_message
% Display an error message for when things go wrong.
str = { 'There is not enough overlap in the images',...
'to obtain a solution.',...
' ',...
'Please check that your header information is OK.',...
'The Check Reg utility will show you the initial',...
'alignment between the images, which must be',...
'within about 4cm and about 15 degrees in order',...
'for SPM to find the optimal solution.'};
spm('alert*',str,mfilename,sqrt(-1));
error('insufficient image overlap')
%_______________________________________________________________________
%_______________________________________________________________________
function piccies(VF,VG,M,scal)
% This is for debugging purposes.
% It shows the linear combination of template images, the affine
% transformed source image, the residual image and a histogram of the
% residuals.
%_______________________________________________________________________
figure(2);
Mt = spm_matrix([0 0 (VG(1).dim(3)+1)/2]);
M = (M*VF(1).mat)\VG(1).mat;
t = zeros(VG(1).dim(1:2));
for i=1:length(VG);
t = t + spm_slice_vol(VG(i), Mt,VG(1).dim(1:2),1)*scal(i);
end;
u = spm_slice_vol(VF(1),M*Mt,VG(1).dim(1:2),1);
subplot(2,2,1);imagesc(t');axis image xy off
subplot(2,2,2);imagesc(u');axis image xy off
subplot(2,2,3);imagesc(u'-t');axis image xy off
%subplot(2,2,4);hist(b,50); % Entropy of residuals may be a nice cost function?
drawnow;
return;
%_______________________________________________________________________
|
github
|
lcnbeapp/beapp-master
|
spm_vol.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_vol.m
| 5,475 |
utf_8
|
41a73601c2e44259fb8f1f4f3e870558
|
function V = spm_vol(P)
% Get header information etc for images.
% FORMAT V = spm_vol(P)
% P - a matrix of filenames.
% V - a vector of structures containing image volume information.
% The elements of the structures are:
% V.fname - the filename of the image.
% V.dim - the x, y and z dimensions of the volume
% V.dt - A 1x2 array. First element is datatype (see spm_type).
% The second is 1 or 0 depending on the endian-ness.
% V.mat - a 4x4 affine transformation matrix mapping from
% voxel coordinates to real world coordinates.
% V.pinfo - plane info for each plane of the volume.
% V.pinfo(1,:) - scale for each plane
% V.pinfo(2,:) - offset for each plane
% The true voxel intensities of the jth image are given
% by: val*V.pinfo(1,j) + V.pinfo(2,j)
% V.pinfo(3,:) - offset into image (in bytes).
% If the size of pinfo is 3x1, then the volume is assumed
% to be contiguous and each plane has the same scalefactor
% and offset.
%__________________________________________________________________________
%
% The fields listed above are essential for the mex routines, but other
% fields can also be incorporated into the structure.
%
% The images are not memory mapped at this step, but are mapped when
% the mex routines using the volume information are called.
%
% Note that spm_vol can also be applied to the filename(s) of 4-dim
% volumes. In that case, the elements of V will point to a series of 3-dim
% images.
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id$
if nargin==0,
V = struct('fname', {},...
'dim', {},...
'dt', {},...
'pinfo', {},...
'mat', {},...
'n', {},...
'descrip', {},...
'private',{});
return;
end;
% If is already a vol structure then just return;
if isstruct(P), V = P; return; end;
V = subfunc2(P);
return;
%_______________________________________________________________________
%_______________________________________________________________________
function V = subfunc2(P)
if iscell(P),
V = cell(size(P));
for j=1:numel(P),
if iscell(P{j}),
V{j} = subfunc2(P{j});
else
V{j} = subfunc1(P{j});
end;
end;
else
V = subfunc1(P);
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function V = subfunc1(P)
if isempty(P),
V = [];
return;
end;
counter = 0;
for i=1:size(P,1),
v = subfunc(P(i,:));
[V(counter+1:counter+size(v, 2),1).fname] = deal('');
[V(counter+1:counter+size(v, 2),1).mat] = deal([0 0 0 0]);
[V(counter+1:counter+size(v, 2),1).mat] = deal(eye(4));
[V(counter+1:counter+size(v, 2),1).mat] = deal([1 0 0]');
if isempty(v),
hread_error_message(P(i,:));
error(['Can''t get volume information for ''' P(i,:) '''']);
end
f = fieldnames(v);
for j=1:size(f,1)
eval(['[V(counter+1:counter+size(v,2),1).' f{j} '] = deal(v.' f{j} ');']);
end
counter = counter + size(v,2);
end
return;
%_______________________________________________________________________
%_______________________________________________________________________
function V = subfunc(p)
[pth,nam,ext,n1] = spm_fileparts(deblank(p));
p = fullfile(pth,[nam ext]);
n = str2num(n1);
if ~spm_existfile(p),
%existance_error_message(p);
error('File "%s" does not exist.', p);
end
switch ext,
case {'.nii','.NII'},
% Do nothing
case {'.img','.IMG'},
if ~spm_existfile(fullfile(pth,[nam '.hdr'])) && ~spm_existfile(fullfile(pth,[nam '.HDR'])),
%existance_error_message(fullfile(pth,[nam '.hdr'])),
error('File "%s" does not exist.', fullfile(pth,[nam '.hdr']));
end
case {'.hdr','.HDR'},
ext = '.img';
p = fullfile(pth,[nam ext]);
if ~spm_existfile(p),
%existance_error_message(p),
error('File "%s" does not exist.', p);
end
otherwise,
error('File "%s" is not of a recognised type.', p);
end
if isempty(n),
V = spm_vol_nifti(p);
else
V = spm_vol_nifti(p,n);
end;
if isempty(n) && length(V.private.dat.dim) > 3
V0(1) = V;
for i = 2:V.private.dat.dim(4)
V0(i) = spm_vol_nifti(p, i);
end
V = V0;
end
if ~isempty(V), return; end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function hread_error_message(q)
str = {...
'Error reading information on:',...
[' ',spm_str_manip(q,'k40d')],...
' ',...
'Please check that it is in the correct format.'};
spm('alert*',str,mfilename,sqrt(-1));
return;
%_______________________________________________________________________
%_______________________________________________________________________
function existance_error_message(q)
str = {...
'Unable to find file:',...
[' ',spm_str_manip(q,'k40d')],...
' ',...
'Please check that it exists.'};
spm('alert*',str,mfilename,sqrt(-1));
return;
|
github
|
lcnbeapp/beapp-master
|
spm_jobman.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_jobman.m
| 21,324 |
utf_8
|
970b3aa24a514dea929b79722697efdc
|
function varargout = spm_jobman(varargin)
% Main interface for SPM Batch System
% This function provides a compatibility layer between SPM and matlabbatch.
% It translates spm_jobman callbacks into matlabbatch callbacks and allows
% to edit and run SPM5 style batch jobs.
%
% FORMAT job_id = spm_jobman
% job_id = spm_jobman('interactive')
% job_id = spm_jobman('interactive',job)
% job_id = spm_jobman('interactive',job,node)
% job_id = spm_jobman('interactive','',node)
% Runs the user interface in interactive mode. The job_id can be used to
% manipulate this job in cfg_util. Note that changes to the job in cfg_util
% will not show up in cfg_ui unless 'Update View' is called.
%
% FORMAT output_list = spm_jobman('serial')
% output_list = spm_jobman('serial',job[,'', input1,...inputN])
% output_list = spm_jobman('serial',job ,node[,input1,...inputN])
% output_list = spm_jobman('serial','' ,node[,input1,...inputN])
% Runs the user interface in serial mode. I job is not empty, then node
% is silently ignored. Inputs can be a list of arguments. These are
% passed on to the open inputs of the specified job/node. Each input should
% be suitable to be assigned to item.val{1}. For cfg_repeat/cfg_choice
% items, input should be a cell list of indices input{1}...input{k} into
% item.value. See cfg_util('filljob',...) for details.
%
% FORMAT output_list = spm_jobman('run',job)
% output_list = spm_jobman('run_nogui',job)
% Runs a job without X11 (as long as there is no graphics output from the
% job itself). The matlabbatch system does not need graphics output to run
% a job.
%
% node - indicates which part of the configuration is to be used.
% For example, it could be 'jobs.spatial.coreg'.
%
% job - can be the name of a jobfile (as a .m, .mat or a .xml), a
% cellstr of filenames, a 'jobs'/'matlabbatch' variable or a
% cell of 'jobs'/'matlabbatch' variables loaded from a jobfile.
%
% Output_list is a cell array and contains the output arguments from each
% module in the job. The format and contents of these outputs is defined in
% the configuration of each module (.prog and .vout callbacks).
%
% FORMAT spm_jobman('initcfg')
% Initialise cfg_util configuration and set path accordingly.
%
% FORMAT jobs = spm_jobman('spm5tospm8',jobs)
% Takes a cell list of SPM5 job structures and returns SPM8 compatible versions.
%
% FORMAT job = spm_jobman('spm5tospm8bulk',jobfiles)
% Takes a cell string with SPM5 job filenames and saves them in SPM8
% compatible format. The new job files will be MATLAB .m files. Their
% filenames will be derived from the input filenames. To make sure they are
% valid MATLAB script names they will be processed with
% genvarname(filename) and have a '_spm8' string appended to their
% filename.
%
% FORMAT spm_jobman('help',node)
% spm_jobman('help',node,width)
% Creates a cell array containing help information. This is justified
% to be 'width' characters wide. e.g.
% h = spm_jobman('help','jobs.spatial.coreg.estimate');
% for i=1:numel(h),fprintf('%s\n',h{i}); end;
%
% not implemented: FORMAT spm_jobman('defaults')
% Runs the interactive defaults editor.
%
% FORMAT [tag, job] = spm_jobman('harvest', job_id|cfg_item|cfg_struct)
% Take the job with id job_id in cfg_util and extract what is
% needed to save it as a batch job (for experts only). If the argument is a
% cfg_item or cfg_struct tree, it will be harvested outside cfg_util.
% tag - tag of the root node of the current job/cfg_item tree
% job - harvested data from the current job/cfg_item tree
%
% FORMAT spm_jobman('pulldown')
% Creates a pulldown 'TASKS' menu in the Graphics window.
%
% not implemented: FORMAT spm_jobman('jobhelp')
% Creates a cell array containing help information specific for a certain
% job. Help is only printed for items where job specific help is
% present. This can be used together with spm_jobman('help') to create a
% job specific manual. This feature is available only on MATLAB R14SP2
% and higher.
%
% not implemented: FORMAT spm_jobman('chmod')
% Changes the modality for the TASKS pulldown.
%
% This code is based on earlier versions by John Ashburner, Philippe
% Ciuciu and Guillaume Flandin.
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Copyright (C) 2008 Freiburg Brain Imaging
% Volkmar Glauche
% $Id$
if nargin==0
h = cfg_ui;
if nargout > 0, varargout = {h}; end
else
cmd = lower(varargin{1});
if any(strcmp(cmd, {'serial','interactive','run','run_nogui'}))
if nargin > 1
% sort out job/node arguments for interactive, serial, run cmds
if nargin>=2 && ~isempty(varargin{2})
% do not consider node if job is given
if ischar(varargin{2}) || iscellstr(varargin{2})
jobs = load_jobs(varargin{2});
elseif iscell(varargin{2})
if iscell(varargin{2}{1})
% assume varargin{2} is a cell of jobs
jobs = varargin{2};
else
% assume varargin{2} is a single job
jobs{1} = varargin{2};
end;
end;
[mljob comp] = canonicalise_job(jobs);
elseif any(strcmp(cmd, {'interactive','serial'})) && nargin>=3 && isempty(varargin{2})
% Node spec only allowed for 'interactive', 'serial'
arg3 = regexprep(varargin{3},'^spmjobs\.','spm.');
mod_cfg_id = cfg_util('tag2mod_cfg_id',arg3);
else
error('spm:spm_jobman:WrongUI', ...
'Don''t know how to handle this ''%s'' call.', lower(varargin{1}));
end;
end
end;
switch cmd
case 'help'
if (nargin < 2) || isempty(varargin{2})
node = 'spm';
else
node = regexprep(varargin{2},'^spmjobs\.','spm.');
end;
if nargin < 3
width = 60;
else
width = varargin{3};
end;
varargout{1} = cfg_util('showdocwidth', width, node);
case 'initcfg'
if ~isdeployed
addpath(fullfile(spm('Dir'),'matlabbatch'));
addpath(fullfile(spm('Dir'),'config'));
end
cfg_get_defaults('cfg_util.genscript_run', @genscript_run);
cfg_util('initcfg'); % This must be the first call to cfg_util
if ~spm('cmdline')
f = cfg_ui('Visible','off'); % Create invisible batch ui
f0 = findobj(f, 'Tag','MenuFile'); % Add entries to file menu
f2 = uimenu(f0,'Label','Load SPM5 job', 'Callback',@load_job, ...
'HandleVisibility','off', 'tag','jobs', ...
'Separator','on');
f3 = uimenu(f0,'Label','Bulk Convert SPM5 job(s)', ...
'Callback',@conv_jobs, ...
'HandleVisibility','off', 'tag','jobs');
end
case 'interactive',
if exist('mljob', 'var')
cjob = cfg_util('initjob', mljob);
elseif exist('mod_cfg_id', 'var')
if isempty(mod_cfg_id)
arg3 = regexprep(varargin{3},'^spmjobs\.','spm.');
warning('spm:spm_jobman:NodeNotFound', ...
['Can not find executable node ''%s'' - running '...
'matlabbatch without default node.'], arg3);
cjob = cfg_util('initjob');
else
cjob = cfg_util('initjob');
mod_job_id = cfg_util('addtojob', cjob, mod_cfg_id);
cfg_util('harvest', cjob, mod_job_id);
end;
else
cjob = cfg_util('initjob');
end;
cfg_ui('local_showjob', findobj(0,'tag','cfg_ui'), cjob);
if nargout > 0
varargout{1} = cjob;
end;
case 'serial',
if exist('mljob', 'var')
cjob = cfg_util('initjob', mljob);
else
cjob = cfg_util('initjob');
if nargin > 2
arg3 = regexprep(varargin{3},'^spmjobs\.','spm.');
[mod_cfg_id, item_mod_id] = cfg_util('tag2cfg_id', lower(arg3));
cfg_util('addtojob', cjob, mod_cfg_id);
end;
end;
sts = cfg_util('filljobui', cjob, @serial_ui, varargin{4:end});
if sts
cfg_util('run', cjob);
if nargout > 0
varargout{1} = cfg_util('getalloutputs', cjob);
end
end;
cfg_util('deljob', cjob);
case {'run','run_nogui'}
cjob = cfg_util('initjob', mljob);
cfg_util('run', cjob);
if nargout > 0
varargout{1} = cfg_util('getalloutputs', cjob);
end
cfg_util('deljob', cjob);
case {'spm5tospm8'}
varargout{1} = canonicalise_job(varargin{2});
case {'spm5tospm8bulk'}
conv_jobs(varargin{2});
case {'defaults'},
warning('spm:spm_jobman:NotImplemented', 'Not yet implemented.');
case {'pulldown'}
pulldown;
case {'chmod'}
warning('spm:spm_jobman:NotImplemented', 'Callback ''%s'' not implemented.', varargin{1});
case {'help'}
warning('spm:spm_jobman:NotImplemented', 'Not yet implemented.');
case {'jobhelp'}
warning('spm:spm_jobman:NotImplemented', 'Callback ''%s'' not implemented.', varargin{1});
case {'harvest'}
if nargin == 1
error('spm:spm_jobman:CantHarvest', ...
['Can not harvest job without job_id. Please use ' ...
'spm_jobman(''harvest'', job_id).']);
elseif cfg_util('isjob_id', varargin{2})
[tag job] = cfg_util('harvest', varargin{2});
elseif isa(varargin{2}, 'cfg_item')
[tag job] = harvest(varargin{2}, varargin{2}, false, false);
elseif isstruct(varargin{2})
% try to convert into class before harvesting
c = cfg_struct2cfg(varargin{2});
[tag job] = harvest(c,c,false,false);
else
error('spm:spm_jobman:CantHarvestThis', ['Can not harvest ' ...
'this argument.']);
end;
varargout{1} = tag;
varargout{2} = job;
otherwise
error(['"' varargin{1} '" - unknown option']);
end;
end;
return;
%------------------------------------------------------------------------
%------------------------------------------------------------------------
function [mljob, comp] = canonicalise_job(job)
% job: a cell list of job data structures.
% Check whether job is a SPM5 or matlabbatch job. In the first case, all
% items in job{:} should have a fieldname of either 'temporal', 'spatial',
% 'stats', 'tools' or 'util'. If this is the case, then job will be
% assigned to mljob{1}.spm, which is the tag of the SPM root
% configuration item.
comp = true(size(job));
mljob = cell(size(job));
for cj = 1:numel(job)
for k = 1:numel(job{cj})
comp(cj) = comp(cj) && any(strcmp(fieldnames(job{cj}{k}), ...
{'temporal', 'spatial', 'stats', 'tools', 'util'}));
if ~comp(cj)
break;
end;
end;
if comp(cj)
tmp = convert_jobs(job{cj});
for i=1:numel(tmp),
mljob{cj}{i}.spm = tmp{i};
end
else
mljob{cj} = job{cj};
end;
end;
%------------------------------------------------------------------------
%------------------------------------------------------------------------
function conv_jobs(varargin)
% Select a list of jobs, canonicalise each of it and save as a .m file
% using gencode.
spm('pointer','watch');
if nargin == 0 || ~iscellstr(varargin{1})
[fname sts] = spm_select([1 Inf], 'batch', 'Select job file(s)');
fname = cellstr(fname);
if ~sts, return; end;
else
fname = varargin{1};
end;
joblist = load_jobs(fname);
for k = 1:numel(fname)
if ~isempty(joblist{k})
[p n e v] = spm_fileparts(fname{k});
% Save new job as genvarname(*_spm8).m
newfname = fullfile(p, sprintf('%s.m', ...
genvarname(sprintf('%s_spm8', n))));
fprintf('SPM5 job: %s\nSPM8 job: %s\n', fname{k}, newfname);
cjob = cfg_util('initjob', canonicalise_job(joblist(k)));
cfg_util('savejob', cjob, newfname);
cfg_util('deljob', cjob);
end;
end;
spm('pointer','arrow');
%------------------------------------------------------------------------
%------------------------------------------------------------------------
function load_job(varargin)
% Select a single job file, canonicalise it and display it in GUI
[fname sts] = spm_select([1 Inf], 'batch', 'Select job file');
if ~sts, return; end;
spm('pointer','watch');
joblist = load_jobs(fname);
if ~isempty(joblist{1})
spm_jobman('interactive',joblist{1});
end;
spm('pointer','arrow');
return;
%------------------------------------------------------------------------
%------------------------------------------------------------------------
function newjobs = load_jobs(job)
% Load a list of possible job files, return a cell list of jobs. Jobs can
% be either SPM5 (i.e. containing a 'jobs' variable) or SPM8/matlabbatch
% jobs. If a job file failed to load, an empty cell is returned in the
% list.
if ischar(job)
filenames = cellstr(job);
else
filenames = job;
end;
newjobs = {};
for cf = 1:numel(filenames)
[p,nam,ext] = fileparts(filenames{cf});
switch ext
case '.xml',
spm('Pointer','Watch');
try
loadxml(filenames{cf},'jobs');
catch
try
loadxml(filenames{cf},'matlabbatch');
catch
warning('spm:spm_jobman:LoadFailed','LoadXML failed: ''%s''',filenames{cf});
end;
end;
spm('Pointer');
case '.mat'
try
S=load(filenames{cf});
if isfield(S,'matlabbatch')
matlabbatch = S.matlabbatch;
elseif isfield(S,'jobs')
jobs = S.jobs;
else
warning('spm:spm_jobman:JobNotFound','No SPM5/SPM8 job found in ''%s''', filenames{cf});
end
catch
warning('spm:spm_jobman:LoadFailed','Load failed: ''%s''',filenames{cf});
end;
case '.m'
try
fid = fopen(filenames{cf},'rt');
str = fread(fid,'*char');
fclose(fid);
eval(str);
catch
warning('spm:spm_jobman:LoadFailed','Load failed: ''%s''',filenames{cf});
end;
if ~(exist('jobs','var') || exist('matlabbatch','var'))
warning('spm:spm_jobman:JobNotFound','No SPM5/SPM8 job found in ''%s''', filenames{cf});
end;
otherwise
warning('Unknown extension: ''%s''', filenames{cf});
end;
if exist('jobs','var')
newjobs = [newjobs(:); {jobs}];
clear jobs;
elseif exist('matlabbatch','var')
newjobs = [newjobs(:); {matlabbatch}];
clear matlabbatch;
end;
end;
return;
%------------------------------------------------------------------------
%------------------------------------------------------------------------
function njobs = convert_jobs(jobs)
decel = struct('spatial',struct('realign',[],'coreg',[],'normalise',[]),...
'temporal',[],...
'stats',[],...
'meeg',[],...
'util',[],...
'tools',struct('dartel',[]));
njobs = {};
for i0 = 1:numel(jobs),
tmp0 = fieldnames(jobs{i0});
tmp0 = tmp0{1};
if any(strcmp(tmp0,fieldnames(decel))),
for i1=1:numel(jobs{i0}.(tmp0)),
tmp1 = fieldnames(jobs{i0}.(tmp0){i1});
tmp1 = tmp1{1};
if ~isempty(decel.(tmp0)),
if any(strcmp(tmp1,fieldnames(decel.(tmp0)))),
for i2=1:numel(jobs{i0}.(tmp0){i1}.(tmp1)),
njobs{end+1} = struct(tmp0,struct(tmp1,jobs{i0}.(tmp0){i1}.(tmp1){i2}));
end
else
njobs{end+1} = struct(tmp0,jobs{i0}.(tmp0){i1});
end
else
njobs{end+1} = struct(tmp0,jobs{i0}.(tmp0){i1});
end
end
else
njobs{end+1} = jobs{i0};
end
end
%------------------------------------------------------------------------
%------------------------------------------------------------------------
function pulldown
fg = spm_figure('findwin','Graphics');
if isempty(fg), return; end;
set(0,'ShowHiddenHandles','on');
delete(findobj(fg,'tag','jobs'));
set(0,'ShowHiddenHandles','off');
f0 = uimenu(fg,'Label','TASKS', ...
'HandleVisibility','off', 'tag','jobs');
f1 = uimenu(f0,'Label','BATCH', 'Callback',@cfg_ui, ...
'HandleVisibility','off', 'tag','jobs');
f4 = uimenu(f0,'Label','SPM (interactive)', ...
'HandleVisibility','off', 'tag','jobs', 'Separator','on');
cfg_ui('local_setmenu', f4, cfg_util('tag2cfg_id', 'spm'), ...
@local_init_interactive, false);
f5 = uimenu(f0,'Label','SPM (serial)', ...
'HandleVisibility','off', 'tag','jobs');
cfg_ui('local_setmenu', f5, cfg_util('tag2cfg_id', 'spm'), ...
@local_init_serial, false);
%------------------------------------------------------------------------
%------------------------------------------------------------------------
function local_init_interactive(varargin)
cjob = cfg_util('initjob');
mod_cfg_id = get(gcbo,'userdata');
cfg_util('addtojob', cjob, mod_cfg_id);
cfg_ui('local_showjob', findobj(0,'tag','cfg_ui'), cjob);
%------------------------------------------------------------------------
%------------------------------------------------------------------------
function local_init_serial(varargin)
mod_cfg_id = get(gcbo,'userdata');
cjob = cfg_util('initjob');
cfg_util('addtojob', cjob, mod_cfg_id);
sts = cfg_util('filljobui', cjob, @serial_ui);
if sts
cfg_util('run', cjob);
end;
cfg_util('deljob', cjob);
%------------------------------------------------------------------------
%------------------------------------------------------------------------
function [val sts] = serial_ui(item)
% wrapper function to translate cfg_util('filljobui'... input requests into
% spm_input/cfg_select calls.
sts = true;
switch class(item),
case 'cfg_choice',
labels = cell(size(item.values));
values = cell(size(item.values));
for k = 1:numel(item.values)
labels{k} = item.values{k}.name;
values{k} = k;
end;
val = spm_input(item.name, 1, 'm', labels, values);
case 'cfg_menu',
val = spm_input(item.name, 1, 'm', item.labels, item.values);
val = val{1};
case 'cfg_repeat',
labels = cell(size(item.values));
values = cell(size(item.values));
for k = 1:numel(item.values)
labels{k} = item.values{k}.name;
values{k} = k;
end;
% enter at least item.num(1) values
for k = 1:item.num(1)
val(k) = spm_input(sprintf('%s(%d)', item.name, k), 1, 'm', ...
labels, values);
end;
% enter more (up to varargin{3}(2) values
labels = {labels{:} 'Done'};
% values is a cell list of natural numbers, use -1 for Done
values = {values{:} -1};
while numel(val) < item.num(2)
val1 = spm_input(sprintf('%s(%d)', item.name, numel(val)+1), 1, ...
'm', labels, values);
if val1{1} == -1
break;
else
val(end+1) = val1;
end;
end;
case 'cfg_entry',
val = spm_input(item.name, 1, item.strtype, '', item.num, ...
item.extras);
case 'cfg_files',
[t,sts] = cfg_getfile(item.num, item.filter, item.name, '', ...
item.dir, item.ufilter);
if sts
val = cellstr(t);
else
val = {};
error('File selector was closed.');
end;
end;
%------------------------------------------------------------------------
%------------------------------------------------------------------------
function [code cont] = genscript_run
% Return code snippet to initialise SPM defaults and run a job generated by
% cfg_util('genscript',...) through spm_jobman.
modality = spm('CheckModality');
code{1} = sprintf('spm(''defaults'', ''%s'');', modality);
code{2} = 'spm_jobman(''serial'', jobs, '''', inputs{:});';
cont = false;
|
github
|
lcnbeapp/beapp-master
|
spm_eeg_inv_vbecd_disp.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_eeg_inv_vbecd_disp.m
| 22,913 |
UNKNOWN
|
d298cddd05dcda0aab1c23b6a9f98906
|
function spm_eeg_inv_vbecd_disp(action,varargin)
% Display the dipoles as obtained from VB-ECD
%
% FORMAT spm_eeg_inv_vbecd_disp('Init',D)
% Display the latest VB-ECD solution saved in the .inv{} field of the
% data structure D.
%
% FORMAT spm_eeg_inv_vbecd_disp('Init',D, ind)
% Display the ind^th .inv{} cell element, if it is actually a VB-ECD
% solution.
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Christophe Phillips
% $Id$
% Note:
% unfortunately I cannot see how to ensure that when zooming in the image
% the dipole location stays in place...
global st
Fig = spm_figure('GetWin','Graphics');
colors = {'y','b','g','r','c','m'}; % 6 possible colors
marker = {'o','x','+','*','s','d','v','p','h'}; % 9 possible markers
Ncolors = length(colors);
Nmarker = length(marker);
if nargin == 0, action = 'Init'; end;
switch lower(action),
%==========================================================================
case 'init'
%==========================================================================
% FORMAT spm_eeg_inv_vbecd_disp('init',D,ind)
% Initialise the variables with GUI
%--------------------------------------------------------------------------
if nargin<2
D = spm_eeg_load;
else
D = varargin{1};
end
if nargin<3
% find the latest inverse produced with vbecd
Ninv = length(D.inv);
lind = [];
for ii=1:Ninv
if isfield(D.inv{ii},'method') && ...
strcmp(D.inv{ii}.method,'vbecd')
lind = [lind ii];
end
end
ind = max(lind);
if ~ind,
spm('alert*','No VB-ECD solution found with this data file!',...
'VB-ECD display')
return
end
else
ind = varargin{3};
end
% Stash dipole(s) information in sdip structure
sdip = D.inv{ind}.inverse;
% if the exit flag is not in the structure, assume everything went ok.
if ~isfield(sdip,'exitflag')
sdip.exitflag = ones(1,sdip.n_seeds);
end
try
Pimg = spm_vol(D.inv{ind}.mesh.sMRI);
catch
Pimg = spm_vol(fullfile(spm('dir'), 'canonical', 'single_subj_T1.nii'));
end
spm_orthviews('Reset');
spm_orthviews('Image', Pimg, [0.0 0.45 1 0.55]);
spm_orthviews('MaxBB');
spm_orthviews('AddContext')
st.callback = 'spm_image(''shopos'');';
% remove clicking in image
for ii=1:3,
set(st.vols{1}.ax{ii}.ax,'ButtonDownFcn',';');
end
WS = spm('WinScale');
% Build GUI
%==========================================================================
% Location:
%--------------------------------------------------------------------------
uicontrol(Fig,'Style','Frame','Position',[60 25 200 325].*WS, ...
'DeleteFcn','spm_image(''reset'');');
uicontrol(Fig,'Style','Frame','Position',[70 250 180 90].*WS);
uicontrol(Fig,'Style','Text', 'Position',[75 320 170 016].*WS, ...
'String','Current Position');
uicontrol(Fig,'Style','Text', 'Position',[75 295 35 020].*WS,'String','mm:');
uicontrol(Fig,'Style','Text', 'Position',[75 275 35 020].*WS,'String','vx:');
uicontrol(Fig,'Style','Text', 'Position',[75 255 75 020].*WS,'String','Img Intens.:');
st.mp = uicontrol(Fig,'Style','Text', 'Position',[110 295 135 020].*WS,'String','');
st.vp = uicontrol(Fig,'Style','Text', 'Position',[110 275 135 020].*WS,'String','');
st.in = uicontrol(Fig,'Style','Text', 'Position',[150 255 85 020].*WS,'String','');
c = 'if get(gco,''Value'')==1, spm_orthviews(''Xhairs'',''off''), else, spm_orthviews(''Xhairs'',''on''); end;';
uicontrol(Fig,'Style','togglebutton','Position',[95 220 125 20].*WS,...
'String','Hide Crosshairs','Callback',c,'ToolTipString','show/hide crosshairs');
% Dipoles/seeds selection:
%--------------------------------------------------------------------------
uicontrol(Fig,'Style','Frame','Position',[300 25 180 325].*WS);
sdip.hdl.hcl = uicontrol(Fig,'Style','pushbutton','Position',[310 320 100 20].*WS, ...
'String','Clear all','CallBack','spm_eeg_inv_vbecd_disp(''ClearAll'')');
sdip.hdl.hseed=zeros(sdip.n_seeds,1);
for ii=1:sdip.n_seeds
if sdip.exitflag(ii)==1
sdip.hdl.hseed(ii) = uicontrol(Fig,'Style','togglebutton','String',num2str(ii),...
'Position',[310+rem(ii-1,8)*20 295-fix((ii-1)/8)*20 20 20].*WS,...
'CallBack','spm_eeg_inv_vbecd_disp(''ChgSeed'')');
else
sdip.hdl.hseed(ii) = uicontrol(Fig,'Style','Text','String',num2str(ii), ...
'Position',[310+rem(ii-1,8)*20 293-fix((ii-1)/8)*20 20 20].*WS) ;
end
end
uicontrol(Fig,'Style','text','String','Select dipole # :', ...
'Position',[310 255-fix((sdip.n_seeds-1)/8)*20 110 20].*WS);
txt_box = cell(sdip.n_dip,1);
for ii=1:sdip.n_dip, txt_box{ii} = num2str(ii); end
txt_box{sdip.n_dip+1} = 'all';
sdip.hdl.hdip = uicontrol(Fig,'Style','popup','String',txt_box, ...
'Position',[420 258-fix((sdip.n_seeds-1)/8)*20 40 20].*WS, ...
'Callback','spm_eeg_inv_vbecd_disp(''ChgDip'')');
% Dipoles orientation and strength:
%--------------------------------------------------------------------------
uicontrol(Fig,'Style','Frame','Position',[70 120 180 90].*WS);
uicontrol(Fig,'Style','Text', 'Position',[75 190 170 016].*WS, ...
'String','Dipole orientation & strength');
uicontrol(Fig,'Style','Text', 'Position',[75 165 65 020].*WS, ...
'String','x-y-z or.:');
uicontrol(Fig,'Style','Text', 'Position',[75 145 75 020].*WS, ...
'String','theta-phi or.:');
uicontrol(Fig,'Style','Text', 'Position',[75 125 75 020].*WS, ...
'String','Dip. intens.:');
sdip.hdl.hor1 = uicontrol(Fig,'Style','Text', 'Position', ...
[140 165 105 020].*WS,'String','a');
sdip.hdl.hor2 = uicontrol(Fig,'Style','Text', 'Position', ...
[150 145 85 020].*WS,'String','b');
sdip.hdl.int = uicontrol(Fig,'Style','Text', 'Position', ...
[150 125 85 020].*WS,'String','c');
st.vols{1}.sdip = sdip;
% First plot = all the seeds that converged !
l_conv = find(sdip.exitflag==1);
if isempty(l_conv)
error('No seed converged towards a stable solution, nothing to be displayed !')
else
spm_eeg_inv_vbecd_disp('DrawDip',l_conv,1)
set(sdip.hdl.hseed(l_conv),'Value',1); % toggle all buttons
end
%==========================================================================
case 'drawdip'
%==========================================================================
% FORMAT spm_eeg_inv_vbecd_disp('DrawDip',i_seed,i_dip,sdip)
% e.g. spm_eeg_inv_vbecd_disp('DrawDip',1,1,sdip)
% e.g. spm_eeg_inv_vbecd_disp('DrawDip',[1:5],1,sdip)
%--------------------------------------------------------------------------
if nargin < 2
i_seed = 1;
else
i_seed = varargin{1};
end
if nargin<3
i_dip = 1;
else
i_dip = varargin{2};
end
if nargin<4
if isfield(st.vols{1},'sdip')
sdip = st.vols{1}.sdip;
else
error('I can''t find sdip structure');
end
else
sdip = varargin{3};
st.vols{1}.sdip = sdip;
end
if any(i_seed>sdip.n_seeds) || i_dip>(sdip.n_dip+1)
error('Wrong i_seed or i_dip index in spm_eeg_inv_vbecd_disp');
end
% Note if i_dip==(sdip.n_dip+1) all dipoles are displayed simultaneously,
% The 3D cut will then be at the mean location of all sources !!!
if i_dip == (sdip.n_dip+1)
i_dip = 1:sdip.n_dip;
end
% if seed indexes passed is wrong (no convergence) remove the wrong ones
i_seed(sdip.exitflag(i_seed)~=1) = [];
if isempty(i_seed)
error('You passed the wrong seed indexes...')
end
if size(i_seed,2)==1, i_seed=i_seed'; end
% Display business
%--------------------------------------------------------------------------
loc_mm = sdip.loc{i_seed(1)}(:,i_dip);
if length(i_seed)>1
% unit = ones(1,sdip.n_dip);
for ii = i_seed(2:end)
loc_mm = loc_mm + sdip.loc{ii}(:,i_dip);
end
loc_mm = loc_mm/length(i_seed);
end
if length(i_dip)>1
loc_mm = mean(loc_mm,2);
end
% Place the underlying image at right cuts
spm_orthviews('Reposition',loc_mm);
if length(i_dip)>1
tabl_seed_dip = [kron(ones(length(i_dip),1),i_seed') ...
kron(i_dip',ones(length(i_seed),1))];
else
tabl_seed_dip = [i_seed' ones(length(i_seed),1)*i_dip];
end
% Scaling, according to all dipoles in the selected seed sets.
% The time displayed is the one corresponding to the maximum EEG power !
Mn_j = -1;
l3 = -2:0;
for ii = 1:length(i_seed)
for jj = 1:sdip.n_dip
Mn_j = max([Mn_j sqrt(sum(sdip.j{ii}(jj*3+l3,sdip.Mtb).^2))]);
end
end
st.vols{1}.sdip.tabl_seed_dip = tabl_seed_dip;
% Display all dipoles, the 1st one + the ones close enough.
% Run through the 6 colors and 9 markers to differentiate the dipoles.
% NOTA: 2 dipoles coming from the same set will have same colour/marker
ind = 1 ;
dip_h = zeros(9,size(tabl_seed_dip,1),1);
% each dipole displayed has 9 handles:
% 3 per view (2*3): for the line, for the circle & for the error
js_m = zeros(3,1);
% Deal with case of multiple i_seed and i_dip displayed.
% make sure dipole from same i_seed have same colour but different marker.
pi_dip = find(diff(tabl_seed_dip(:,2)));
if isempty(pi_dip)
% i.e. only one dip displayed per seed, use old fashion
for ii=1:size(tabl_seed_dip,1)
if ii>1
if tabl_seed_dip(ii,1)~=tabl_seed_dip(ii-1,1)
ind = ind+1;
end
end
ic = mod(ind-1,Ncolors)+1;
im = fix(ind/Ncolors)+1;
loc_pl = sdip.loc{tabl_seed_dip(ii,1)}(:,tabl_seed_dip(ii,2));
js = sdip.j{tabl_seed_dip(ii,1)}(tabl_seed_dip(ii,2)*3+l3,sdip.Mtb);
vloc = sdip.cov_loc{tabl_seed_dip(ii,1)}(tabl_seed_dip(ii,2)*3+l3,tabl_seed_dip(ii,2)*3+l3);
dip_h(:,ii) = add1dip(loc_pl,js/Mn_j*20,vloc, ...
marker{im},colors{ic},st.vols{1}.ax,Fig,st.bb);
js_m = js_m+js;
end
else
for ii=1:pi_dip(1)
if ii>1
if tabl_seed_dip(ii,1)~=tabl_seed_dip(ii-1,1)
ind = ind+1;
end
end
ic = mod(ind-1,Ncolors)+1;
for jj=1:sdip.n_dip
im = mod(jj-1,Nmarker)+1;
loc_pl = sdip.loc{tabl_seed_dip(ii,1)}(:,jj);
js = sdip.j{tabl_seed_dip(ii,1)}(jj*3+l3,sdip.Mtb);
vloc = sdip.cov_loc{tabl_seed_dip(ii,1)}(jj*3+l3,jj*3+l3);
js_m = js_m+js;
dip_h(:,ii+(jj-1)*pi_dip(1)) = ...
add1dip(loc_pl,js/Mn_j*20,vloc, ...
marker{im},colors{ic},st.vols{1}.ax,Fig,st.bb);
end
end
end
st.vols{1}.sdip.ax = dip_h;
% Display dipoles orientation and strength
js_m = js_m/size(tabl_seed_dip,1);
[th,phi,Ijs_m] = cart2sph(js_m(1),js_m(2),js_m(3));
Njs_m = round(js_m'/Ijs_m*100)/100;
Angle = round([th phi]*1800/pi)/10;
set(sdip.hdl.hor1,'String',[num2str(Njs_m(1)),' ',num2str(Njs_m(2)), ...
' ',num2str(Njs_m(3))]);
set(sdip.hdl.hor2,'String',[num2str(Angle(1)),'� ',num2str(Angle(2)),'�']);
set(sdip.hdl.int,'String',Ijs_m);
% Change the colour of toggle button of dipoles actually displayed
for ii=tabl_seed_dip(:,1)
set(sdip.hdl.hseed(ii),'BackgroundColor',[.7 1 .7]);
end
%==========================================================================
case 'clearall'
%==========================================================================
% Clears all dipoles, and reset the toggle buttons
%--------------------------------------------------------------------------
if isfield(st.vols{1},'sdip')
sdip = st.vols{1}.sdip;
else
error('I can''t find sdip structure');
end
disp('Clears all dipoles')
spm_eeg_inv_vbecd_disp('ClearDip');
for ii=1:st.vols{1}.sdip.n_seeds
if sdip.exitflag(ii)==1
set(st.vols{1}.sdip.hdl.hseed(ii),'Value',0);
end
end
set(st.vols{1}.sdip.hdl.hdip,'Value',1);
%==========================================================================
case 'chgseed'
%==========================================================================
% Changes the seeds displayed
%--------------------------------------------------------------------------
% disp('Change seed')
sdip = st.vols{1}.sdip;
if isfield(sdip,'tabl_seed_dip')
prev_seeds = p_seed(sdip.tabl_seed_dip);
else
prev_seeds = [];
end
l_seed = zeros(sdip.n_seeds,1);
for ii=1:sdip.n_seeds
if sdip.exitflag(ii)==1
l_seed(ii) = get(sdip.hdl.hseed(ii),'Value');
end
end
l_seed = find(l_seed);
% Modify the list of seeds displayed
if isempty(l_seed)
% Nothing left displayed
i_seed=[];
elseif isempty(prev_seeds)
% Just one dipole added, nothing before
i_seed=l_seed;
elseif length(prev_seeds)>length(l_seed)
% One seed removed
i_seed = prev_seeds;
for ii=1:length(l_seed)
p = find(prev_seeds==l_seed(ii));
if ~isempty(p)
prev_seeds(p) = [];
end % prev_seeds is left with the index of the one removed
end
i_seed(i_seed==prev_seeds) = [];
% Remove the dipole & change the button colour
spm_eeg_inv_vbecd_disp('ClearDip',prev_seeds);
set(sdip.hdl.hseed(prev_seeds),'BackgroundColor',[.7 .7 .7]);
else
% One dipole added
i_seed = prev_seeds;
for ii=1:length(prev_seeds)
p = find(prev_seeds(ii)==l_seed);
if ~isempty(p)
l_seed(p) = [];
end % l_seed is left with the index of the one added
end
i_seed = [i_seed ; l_seed];
end
i_dip = get(sdip.hdl.hdip,'Value');
spm_eeg_inv_vbecd_disp('ClearDip');
if ~isempty(i_seed)
spm_eeg_inv_vbecd_disp('DrawDip',i_seed,i_dip);
end
%==========================================================================
case 'chgdip'
%==========================================================================
% Changes the dipole index for the first seed displayed
%--------------------------------------------------------------------------
disp('Change dipole')
sdip = st.vols{1}.sdip;
i_dip = get(sdip.hdl.hdip,'Value');
if isfield(sdip,'tabl_seed_dip')
i_seed = p_seed(sdip.tabl_seed_dip);
else
i_seed = [];
end
if ~isempty(i_seed)
spm_eeg_inv_vbecd_disp('ClearDip')
spm_eeg_inv_vbecd_disp('DrawDip',i_seed,i_dip);
end
%==========================================================================
case 'cleardip'
%==========================================================================
% FORMAT spm_eeg_inv_vbecd_disp('ClearDip',seed_i)
% e.g. spm_eeg_inv_vbecd_disp('ClearDip')
% clears all displayed dipoles
% e.g. spm_eeg_inv_vbecd_disp('ClearDip',1)
% clears the first dipole displayed
%--------------------------------------------------------------------------
if nargin>2
seed_i = varargin{1};
else
seed_i = 0;
end
if isfield(st.vols{1},'sdip')
sdip = st.vols{1}.sdip;
else
return; % I don't do anything, as I can't find sdip strucure
end
if isfield(sdip,'ax')
Nax = size(sdip.ax,2);
else
return; % I don't do anything, as I can't find axes info
end
if seed_i==0 % removes everything
for ii=1:Nax
for jj=1:9
delete(sdip.ax(jj,ii));
end
end
for ii=sdip.tabl_seed_dip(:,1)
set(sdip.hdl.hseed(ii),'BackgroundColor',[.7 .7 .7]);
end
sdip = rmfield(sdip,'tabl_seed_dip');
sdip = rmfield(sdip,'ax');
elseif seed_i<=Nax % remove one seed only
l_seed = find(sdip.tabl_seed_dip(:,1)==seed_i);
for ii=l_seed
for jj=1:9
delete(sdip.ax(jj,ii));
end
end
sdip.ax(:,l_seed) = [];
sdip.tabl_seed_dip(l_seed,:) = [];
else
error('Trying to clear unspecified dipole');
end
st.vols{1}.sdip = sdip;
%==========================================================================
case 'redrawdip'
%==========================================================================
% spm_eeg_inv_vbecd_disp('RedrawDip')
% redraw everything, useful when zooming into image
%--------------------------------------------------------------------------
% spm_eeg_inv_vbecd_disp('ClearDip')
% spm_eeg_inv_vbecd_disp('ChgDip')
% disp('Change dipole')
sdip = st.vols{1}.sdip;
i_dip = get(sdip.hdl.hdip,'Value');
if isfield(sdip,'tabl_seed_dip')
i_seed = p_seed(sdip.tabl_seed_dip);
else
i_seed = [];
end
if ~isempty(i_seed)
spm_eeg_inv_vbecd_disp('ClearDip')
spm_eeg_inv_vbecd_disp('DrawDip',i_seed,i_dip);
end
%==========================================================================
otherwise
%==========================================================================
warning('Unknown action string');
end
% warning(sw);
return
%==========================================================================
% dh = add1dip(loc,js,vloc,mark,col,ax,Fig,bb)
%==========================================================================
function dh = add1dip(loc,js,vloc,mark,col,ax,Fig,bb)
% Plots the dipoles on the 3 views, with an error ellipse for location
% Then returns the handle to the plots
global st
is = inv(st.Space);
loc = is(1:3,1:3)*loc(:) + is(1:3,4);
% taking into account the zooming/scaling only for the location
% NOT for the dipole's amplitude.
% Amplitude plotting is quite arbitrary anyway and up to some scaling
% defined for better viewing...
loc(1,:) = loc(1,:) - bb(1,1)+1;
loc(2,:) = loc(2,:) - bb(1,2)+1;
loc(3,:) = loc(3,:) - bb(1,3)+1;
% +1 added to be like John's orthview code
% prepare error ellipse
vloc = is(1:3,1:3)*vloc*is(1:3,1:3);
[V,E] = eig(vloc);
VE = V*diag(sqrt(diag(E))); % use std
% VE = V*E; % or use variance ???
dh = zeros(9,1);
figure(Fig)
% Transverse slice, # 1
%----------------------
set(Fig,'CurrentAxes',ax{1}.ax)
set(ax{1}.ax,'NextPlot','add')
dh(1) = plot(loc(1),loc(2),[mark,col],'LineWidth',1);
dh(2) = plot(loc(1)+[0 js(1)],loc(2)+[0 js(2)],col,'LineWidth',2);
% add error ellipse
[uu,ss,vv] = svd(VE([1 2],:));
[phi] = cart2pol(uu(1,1),uu(2,1));
e = diag(ss);
t = (-1:.02:1)*pi;
x = e(1)*cos(t)*cos(phi)-e(2)*sin(t)*sin(phi)+loc(1);
y = e(2)*sin(t)*cos(phi)+e(1)*cos(t)*sin(phi)+loc(2);
dh(3) = plot(x,y,[':',col],'LineWidth',.5);
set(ax{1}.ax,'NextPlot','replace')
% Coronal slice, # 2
%----------------------
set(Fig,'CurrentAxes',ax{2}.ax)
set(ax{2}.ax,'NextPlot','add')
dh(4) = plot(loc(1),loc(3),[mark,col],'LineWidth',1);
dh(5) = plot(loc(1)+[0 js(1)],loc(3)+[0 js(3)],col,'LineWidth',2);
% add error ellipse
[uu,ss,vv] = svd(VE([1 3],:));
[phi] = cart2pol(uu(1,1),uu(2,1));
e = diag(ss);
t = (-1:.02:1)*pi;
x = e(1)*cos(t)*cos(phi)-e(2)*sin(t)*sin(phi)+loc(1);
y = e(2)*sin(t)*cos(phi)+e(1)*cos(t)*sin(phi)+loc(3);
dh(6) = plot(x,y,[':',col],'LineWidth',.5);
set(ax{2}.ax,'NextPlot','replace')
% Sagital slice, # 3
%----------------------
set(Fig,'CurrentAxes',ax{3}.ax)
set(ax{3}.ax,'NextPlot','add')
% dh(5) = plot(dim(2)-loc(2),loc(3),[mark,col],'LineWidth',2);
% dh(6) = plot(dim(2)-loc(2)+[0 -js(2)],loc(3)+[0 js(3)],col,'LineWidth',2);
dh(7) = plot(bb(2,2)-bb(1,2)-loc(2),loc(3),[mark,col],'LineWidth',1);
dh(8) = plot(bb(2,2)-bb(1,2)-loc(2)+[0 -js(2)],loc(3)+[0 js(3)],col,'LineWidth',2);
% add error ellipse
[uu,ss,vv] = svd(VE([2 3],:));
[phi] = cart2pol(uu(1,1),uu(2,1));
e = diag(ss);
t = (-1:.02:1)*pi;
x = -(e(1)*cos(t)*cos(phi)-e(2)*sin(t)*sin(phi))+bb(2,2)-bb(1,2)-loc(2);
y = e(2)*sin(t)*cos(phi)+e(1)*cos(t)*sin(phi)+loc(3);
dh(9) = plot(x,y,[':',col],'LineWidth',.5);
set(ax{3}.ax,'NextPlot','replace')
return
%==========================================================================
% pr_seed = p_seed(tabl_seed_dip)
%==========================================================================
function pr_seed = p_seed(tabl_seed_dip)
% Gets the list of seeds used in the previous display
ls = sort(tabl_seed_dip(:,1));
if length(ls)==1
pr_seed = ls;
else
pr_seed = ls([find(diff(ls)) ; length(ls)]);
end
%
% OLD STUFF
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Use it with arguments or not:
% - spm_eeg_inv_vbecd_disp('Init')
% The routine asks for the dipoles file and image to display
% - spm_eeg_inv_vbecd_disp('Init',sdip)
% The routine will use the avg152T1 canonical image
% - spm_eeg_inv_vbecd_disp('Init',sdip,P)
% The routines dispays the dipoles on image P.
%
% If multiple seeds have been used, you can select the seeds to display
% by pressing their index.
% Given that the sources could have different locations, the slices
% displayed will be the 3D view at the *average* or *mean* locations of
% selected sources.
% If more than 1 dipole was fitted at a time, then selection of source 1
% to N is possible through the pull-down selector.
%
% The location of the source/cut is displayed in mm and voxel, as well as
% the underlying image intensity at that location.
% The cross hair position can be hidden by clicking on its button.
%
% Nota_1: If the cross hair is manually moved by clicking in the image or
% changing its coordinates, the dipole displayed will NOT be at
% the right displayed location. That's something that needs to be improved...
%
% Nota_2: Some seeds may have not converged within the limits fixed,
% these dipoles are not displayed...
%
% Fields needed in sdip structure to plot on an image:
% + n_seeds: nr of seeds set used, i.e. nr of solutions calculated
% + n_dip: nr of fitted dipoles on the EEG time series
% + loc: location of fitted dipoles, cell{1,n_seeds}(3 x n_dip)
% remember that loc is fixed over the time window.
% + j: sources amplitude over the time window,
% cell{1,n_seeds}(3*n_dip x Ntimebins)
% + Mtb: index of maximum power in EEG time series used
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% % First point to consider
% loc_mm = sdip.loc{i_seed(1)}(:,i_dip);
%
% % PLace the underlying image at right cuts
% spm_orthviews('Reposition',loc_mm);
% % spm_orthviews('Reposition',loc_vx);
% % spm_orthviews('Xhairs','off')
%
% % if i_seed = set, Are there other dipoles close enough ?
% tabl_seed_dip=[i_seed(1) i_dip]; % table summarising which set & dip to use.
% if length(i_seed)>1
% unit = ones(1,sdip.n_dip);
% for ii = i_seed(2:end)'
% d2 = sqrt(sum((sdip.loc{ii}-loc_mm*unit).^2));
% l_cl = find(d2<=lim_cl);
% if ~isempty(l_cl)
% for jj=l_cl
% tabl_seed_dip = [tabl_seed_dip ; [ii jj]];
% end
% end
% end
% end
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% get(sdip.hdl.hseed(1),'Value')
% for ii=1:sdip.n_seeds, delete(hseed(ii)); end
% h1 = uicontrol(Fig,'Style','togglebutton','Position',[600 25 10 10].*WS)
% h2 = uicontrol(Fig,'Style','togglebutton','Position',[620 100 20 20].*WS,'String','1')
% h2 = uicontrol(Fig,'Style','checkbox','Position',[600 100 10 10].*WS)
% h3 = uicontrol(Fig,'Style','radiobutton','Position',[600 150 20 20].*WS)
% h4 = uicontrol(Fig,'Style','radiobutton','Position',[700 150 20 20].*WS)
% delete(h2),delete(h3),delete(h4),
% delete(hdip)
|
github
|
lcnbeapp/beapp-master
|
spm_figure.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_figure.m
| 32,150 |
utf_8
|
8f4bd924a038c03f7d509cc9e37b8395
|
function varargout=spm_figure(varargin)
% Setup and callback functions for Graphics window
% FORMAT varargout=spm_figure(varargin)
% - An embedded callback, multi-function function
% - For detailed programmers comments, see format specifications
% in main body of code
%_______________________________________________________________________
%
% spm_figure creates and manages the 'Graphics' window. This window and
% these facilities may be used independently of SPM, and any number of
% Graphics windows my be used within the same MATLAB session. (Though
% only one SPM 'Graphics' 'Tag'ed window is permitted.
%
% The Graphics window is provided with a menu bar at the top that
% facilitates editing and printing of the current graphic display,
% enabling interactive editing of graphic output prior to printing
% (e.g. selection of color maps, deleting, moving and editing graphics
% objects or adding text). (This menu is also provided as a figure
% background "ContextMenu" - right-clicking on the figure background
% should bring up the menu.)
%
% Print: Graphics windows with multi-page axes are printed page by page.
%
% Clear: Clears the Graphics window. If in SPM usage (figure 'Tag'ed as
% 'Graphics') then all SPM windows are cleared and reset.
%
% Colormap options:
% * gray, hot, pink: Sets the colormap to its default values and loads
% either a grayscale, 'hot metal' or color map.
% * gray-hot, etc: Creates a 'split' colormap {128 x 3 matrix}.
% The lower half is a gray scale and the upper half
% is 'hot metal' or 'pink'. This color map is used for
% viewing 'rendered' SPMs on a PET, MRI or other background images
%
% Colormap effects:
% * Invert: Inverts (flips) the current color map.
% * Brighten and Darken: Brighten and Darken the current colourmap
% using the MATLAB BRIGHTEN command, with beta's of +0.2 and -0.2
% respectively.
%
% Editing: Right button ('alt' button) cancels operations
% * Cut : Deletes the graphics object next selected (if deletable)
% Select with middle mouse button to delete blocks of text,
% or to delete individual elements from a plot.
% * Move : To re-position a text, uicontrol or axis object using a
% 'drag and drop' implementation (i.e. depress - move - release)
% Using the middle 'extend' mouse button on a text object moves
% the axes containing the text - i.e. blocks of text.
% * Size : Re-sizes the text, uicontrol or axis object next selected
% {left button - decrease, middle button - increase} by a factor
% of 1.24 (or increase/decrease FontSize by 2 dpi)
% * Text : Creates an editable text widget that produces a text object as
% its CallBack.
% The text object is provided with a ContextMenu, obtained by
% right-clicking ('alt') on the text, allowing text attributes
% to be changed. Alternatively, the edit facilities on the window
% menu bar or ContextMenu can be used.
% * Edit : To edit text, select a text object with the circle cursor,
% and edit the text in the editable text widget that appears.
% A middle 'extend' mouse click places a context menu on the text
% object, facilitating easy modification of text atributes.
%
% For SPM usage, the figure should be 'Tag'ed as 'Graphics'.
%
% For SPM power users, and programmers, spm_figure provides utility
% routines for using the SPM graphics interface. Of particular use are
% the GetWin, FindWin and Clear functions See the embedded callback
% reference in the main body of spm_figure, below the help text.
%
% See also: spm_print, spm_clf
%
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Andrew Holmes
% $Id$
%=======================================================================
% - FORMAT specifications for embedded CallBack functions
%=======================================================================
%( This is a multi function function, the first argument is an action )
%( string, specifying the particular action function to take. Recall )
%( MATLAB's command-function duality: `spm_figure Create` is )
%( equivalent to `spm_figure('Create')`. )
%
% FORMAT F = spm_figure
% [ShortCut] Defaults to Action 'Create'
%
% FORMAT F = spm_figure(F) - numeric F
% [ShortCut] Defaults to spm_figure('CreateBar',F)
%
% FORMAT F = spm_figure('Create',Tag,Name,Visible)
% Create a full length WhiteBg figure 'Tag'ed Tag (if specified),
% with a ToolBar and background context menu.
% Equivalent to spm_figure('CreateWin','Tag') and spm_figure('CreateBar')
% Tag - 'Tag' string for figure.
% Name - Name for window
% Visible - 'on' or 'off'
% F - Figure used
%
% FORMAT F = spm_figure('FindWin',F)
% Finds window with 'Tag' or figure numnber F - returns empty F if not found
% F - (Input) Figure to use [Optional] - 'Tag' string or figure number.
% - Defaults to 'Graphics'
% F - (Output) Figure number (if found) or empty (if not).
%
% FORMAT F = spm_figure('GetWin',Tag)
% Like spm_figure('FindWin',Tag), except that if no such 'Tag'ged figure
% is found and 'Tag' is recognized, one is created. Further, the "got"
% window is made current.
% Tag - Figure 'Tag' to get, defaults to 'Graphics'
% F - Figure number (if found/created) or empty (if not).
%
% FORMAT F = spm_figure('ParentFig',h)
% Finds window containing the object whose handle is specified
% h - Handle of object whose parent figure is required
% - If a vector, then first object handle is used
% F - Number or parent figure
%
% FORMAT spm_figure('Clear',F,Tags)
% Clears figure, leaving ToolBar (& other objects with invisible handles)
% Optional third argument specifies 'Tag's of objects to delete.
% If figure F is 'Tag'ged 'Interactive' (SPM usage), then the window
% name and pointer are reset.
% F - 'Tag' string or figure number of figure to clear, defaults to gcf
% Tags - 'Tag's (string matrix or cell array of strings) of objects to delete
% *regardless* of 'HandleVisibility'. Only these objects are deleted.
% '!all' denotes all objects
%
%
% FORMAT spm_figure('Print',F)
% F - [Optional] Figure to print. ('Tag' or figure number)
% Defaults to figure 'Tag'ed as 'Graphics'.
% If none found, uses CurrentFigure if avaliable.
% If objects 'Tag'ed 'NextPage' and 'PrevPage' are found, then the
% pages are shown and printed in order. In breif, pages are held as
% seperate axes, with ony one 'Visible' at any one time. The handles of
% the "page" axes are stored in the 'UserData' of the 'NextPage'
% object, while the 'PrevPage' object holds the current page number.
% See spm_help('!Disp') for details on setting up paging axes.
%
% FORMAT [hNextPage, hPrevPage, hPageNo] = spm_figure('NewPage',hPage)
% SPM pagination function: Makes objects with handles hPage paginated
% Creates pagination buttons if necessary.
% hPage - Handles of objects to stick to this page
% hNextPage, hPrevPage, hPageNo - Handles of pagination controls
%
% FORMAT spm_figure('TurnPage',move,F)
% SPM pagination function: Turn to specified page
%
% FORMAT spm_figure('DeletePageControls',F)
% SPM pagination function: Deletes page controls
% F - [Optional] Figure in which to attempt to turn the page
% Defaults to 'Graphics' 'Tag'ged window
%
% FORMAT n = spm_figure('#page')
% Returns the current number of pages.
%
% FORMAT n = spm_figure('CurrentPage');
% Return the current page number.
%
% FORMAT spm_figure('WaterMark',F,str,Tag,Angle,Perm)
% Adds watermark to figure windows.
% F - Figure for watermark. Defaults to gcf
% str - Watermark string. Defaults (missing or empty) to SPM
% Tag - Tag for watermark axes. Defaults to ''
% Angle - Angle for watermark. Defaults to -45
% Perm - If specified, then watermark is permanent (HandleVisibility 'off')
%
% FORMAT F = spm_figure('CreateWin',Tag,Name,Visible)
% Creates a full length WhiteBg figure 'Tag'ged Tag (if specified).
% F - Figure created
% Tag - Tag for window
% Name - Name for window
% Visible - 'on' or 'off'
%
% FORMAT WS = spm_figure('GetWinScale')
% Returns ratios of current display dimensions to that of a 1152 x 900
% Sun display. WS=[Xratio,Yratio,Xratio,Yratio]. Used for scaling other
% GUI elements.
% (Function duplicated in spm.m, repeated to reduce inter-dependencies.)
%
% FORMAT FS = spm_figure('FontSizes',FS)
% Returns fontsizes FS scaled for the current display.
% FS - (vector of) Font sizes to scale
% [default [08,09,11,13,14,6:36]]
%
% FORMAT spm_figure('CreateBar',F)
% Creates toolbar in figure F (defaults to gcf). F can be a 'Tag'
% If the figure is 'Tag'ed as 'Graphics' (SPM usage), then the Print button
% callback is set to attempt to clear an 'Interactive' figure too.
%
% FORMAT spm_figure('ColorMap')
% Callback for "ColorMap" buttons
%
% FORMAT h = spm_figure('GraphicsHandle',F)
% GUI choose object for handle identification. LeftMouse 'normal' returns
% handle, MiddleMouse 'extend' returns parents handle, RightMouse 'alt' cancels.
% F - figure to do a GUI "handle ID" in [Default gcbf]
%_______________________________________________________________________
%-Condition arguments
%-----------------------------------------------------------------------
if (nargin==0), Action = 'Create'; else Action = varargin{1}; end
switch lower(Action), case 'create'
%=======================================================================
% F = spm_figure('Create',Tag,Name,Visible)
%-Condition arguments
if nargin<4, Visible='on'; else Visible=varargin{4}; end
if nargin<3, Name=''; else, Name=varargin{3}; end
if nargin<2, Tag=''; else Tag=varargin{2}; end
F = spm_figure('CreateWin',Tag,Name,Visible);
spm_figure('CreateBar',F);
spm_figure('FigContextMenu',F);
varargout = {F};
case 'findwin'
%=======================================================================
% F=spm_figure('FindWin',F)
% F=spm_figure('FindWin',Tag)
%-Find window: Find window with FigureNumber# / 'Tag' attribute
%-Returns empty if window cannot be found - deletes multiple tagged figs.
if nargin<2, F='Graphics'; else F=varargin{2}; end
shh = get(0,'showhiddenhandles');
set(0,'showhiddenhandles','on');
if isempty(F)
% Leave F empty
elseif ischar(F)
% Finds Graphics window with 'Tag' string - delete multiples
Tag=F;
F = findobj(get(0,'Children'),'Flat','Tag',Tag);
if length(F) > 1
% Multiple Graphics windows - close all but most recent
close(F(2:end))
F = F(1);
end
else
% F is supposed to be a figure number - check it
if ~any(F==get(0,'Children')), F=[]; end
end
set(0,'showhiddenhandles',shh);
varargout = {F};
case 'getwin'
%=======================================================================
% F=spm_figure('GetWin',Tag)
if nargin<2, Tag='Graphics'; else Tag=varargin{2}; end
F = spm_figure('FindWin',Tag);
if isempty(F)
if ischar(Tag)
switch Tag
case 'Graphics'
F = spm_figure('Create','Graphics','Graphics');
case 'DEM'
F = spm_figure('Create','DEM','Dynamic Expectation Maximisation');
case 'DFP'
F = spm_figure('Create','DFP','Variational filtering');
case 'FMIN'
F = spm_figure('Create','FMIN','Function minimisation');
case 'MFM'
F = spm_figure('Create','MFM','Mean-field and neural mass models');
case 'MVB'
F = spm_figure('Create','MVB','Multivariate Bayes');
case 'SI'
F = spm_figure('Create','SI','System Identification');
case 'PPI'
F = spm_figure('Create','PPI','Physio/Psycho-Physiologic Interaction');
case 'Interactive'
F = spm('CreateIntWin');
otherwise
F = spm_figure('Create',Tag,Tag);
end
end
else
set(0,'CurrentFigure',F);
figure(F);
end
varargout = {F};
case 'parentfig'
%=======================================================================
% F=spm_figure('ParentFig',h)
if nargin<2, error('No object specified'), else h=varargin{2}; end
F = get(h(1),'Parent');
while ~strcmp(get(F,'Type'),'figure'), F=get(F,'Parent'); end
varargout = {F};
case 'clear'
%=======================================================================
% spm_figure('Clear',F,Tags)
%-Sort out arguments
%-----------------------------------------------------------------------
if nargin<3, Tags=[]; else Tags=varargin{3}; end
if nargin<2, F=get(0,'CurrentFigure'); else F=varargin{2}; end
F = spm_figure('FindWin',F);
if isempty(F), return, end
%-Clear figure
%-----------------------------------------------------------------------
if isempty(Tags)
%-Clear figure of objects with 'HandleVisibility' 'on'
pos = get(F,'Position');
delete(findobj(get(F,'Children'),'flat','HandleVisibility','on'));
drawnow
set(F,'Position',pos);
%-Reset figures callback functions
zoom(F,'off');
rotate3d(F,'off');
set(F,'KeyPressFcn','',...
'WindowButtonDownFcn','',...
'WindowButtonMotionFcn','',...
'WindowButtonUpFcn','')
%-If this is the 'Interactive' window, reset name & UserData
if strcmp(get(F,'Tag'),'Interactive')
set(F,'Name','','UserData',[]), end
else
%-Clear specified objects from figure
cSHH = get(0,'ShowHiddenHandles');
set(0,'ShowHiddenHandles','on')
if ischar(Tags); Tags=cellstr(Tags); end
if any(strcmp(Tags(:),'!all'))
delete(get(F,'Children'))
else
for tag = Tags(:)'
delete(findobj(get(F,'Children'),'flat','Tag',tag{:}));
end
end
set(0,'ShowHiddenHandles',cSHH)
end
set(F,'Pointer','Arrow')
movegui(F);
case 'print'
%=======================================================================
% spm_figure('Print',F,fname)
%-Arguments & defaults
if nargin<3, fname=''; else fname=varargin{3};end
if nargin<2, F='Graphics'; else F=varargin{2}; end
%-Find window to print, default to gcf if specified figure not found
% Return if no figures
if ~isempty(F), F = spm_figure('FindWin',F); end
if isempty(F), F = get(0,'CurrentFigure'); end
if isempty(F), return, end
%-Note current figure, & switch to figure to print
cF = get(0,'CurrentFigure');
set(0,'CurrentFigure',F)
%-See if window has paging controls
hNextPage = findobj(F,'Tag','NextPage');
hPrevPage = findobj(F,'Tag','PrevPage');
hPageNo = findobj(F,'Tag','PageNo');
iPaged = ~isempty(hNextPage);
%-Construct print command
%-----------------------------------------------------------------------
%-Temporarily change all units to normalized prior to printing
% (Fixes bizzarre problem with stuff jumping around!)
%-----------------------------------------------------------------------
H = findobj(get(F,'Children'),'flat','Type','axes');
if ~isempty(H),
un = cellstr(get(H,'Units'));
set(H,'Units','normalized')
end;
%-Print
%-----------------------------------------------------------------------
if ~iPaged
spm_print(fname)
else
hPg = get(hNextPage,'UserData');
Cpage = get(hPageNo, 'UserData');
nPages = size(hPg,1);
set([hNextPage,hPrevPage,hPageNo],'Visible','off')
if Cpage~=1
set(hPg{Cpage,1},'Visible','off'), end
for p = 1:nPages
set(hPg{p,1},'Visible','on');
spm_print(fname);
set(hPg{p,1},'Visible','off')
end
set(hPg{Cpage,1},'Visible','on')
set([hNextPage,hPrevPage,hPageNo],'Visible','on')
end
if ~isempty(H), set(H,{'Units'},un); end;
set(0,'CurrentFigure',cF)
case 'printto'
%=======================================================================
%spm_figure('PrintTo',F)
%-Arguments & defaults
if nargin<2, F='Graphics'; else F=varargin{2}; end
%-Find window to print, default to gcf if specified figure not found
% Return if no figures
F=spm_figure('FindWin',F);
if isempty(F), F = get(0,'CurrentFigure'); end
if isempty(F), return, end
[fn pn] = uiputfile('*.ps', 'Print to File');
if fn == 0
return;
end;
psname = fullfile(pn, fn);
spm_figure('Print',F,psname);
case 'newpage'
%=======================================================================
% [hNextPage, hPrevPage, hPageNo] = spm_figure('NewPage',h)
if nargin<2 || isempty(varargin{2}) error('No handles to paginate')
else h=varargin{2}(:)'; end
%-Work out which figure we're in
F = spm_figure('ParentFig',h(1));
hNextPage = findobj(F,'Tag','NextPage');
hPrevPage = findobj(F,'Tag','PrevPage');
hPageNo = findobj(F,'Tag','PageNo');
%-Create pagination widgets if required
%-----------------------------------------------------------------------
if isempty(hNextPage)
WS = spm('WinScale');
FS = spm('FontSizes');
SatFig = findobj('Tag','Satellite');
if ~isempty(SatFig)
SatFigPos = get(SatFig,'Position');
hNextPagePos = [SatFigPos(3)-25 15 15 15];
hPrevPagePos = [SatFigPos(3)-40 15 15 15];
hPageNo = [SatFigPos(3)-40 5 30 10];
else
hNextPagePos = [580 022 015 015].*WS;
hPrevPagePos = [565 022 015 015].*WS;
hPageNo = [550 005 060 015].*WS;
end
hNextPage = uicontrol(F,'Style','Pushbutton',...
'HandleVisibility','on',...
'String','>','FontSize',FS(10),...
'ToolTipString','next page',...
'Callback','spm_figure(''TurnPage'',''+1'',gcbf)',...
'Position',hNextPagePos,...
'ForegroundColor',[0 0 0],...
'Tag','NextPage','UserData',[]);
hPrevPage = uicontrol(F,'Style','Pushbutton',...
'HandleVisibility','on',...
'String','<','FontSize',FS(10),...
'ToolTipString','previous page',...
'Callback','spm_figure(''TurnPage'',''-1'',gcbf)',...
'Position',hPrevPagePos,...
'Visible','on',...
'Enable','off',...
'Tag','PrevPage');
hPageNo = uicontrol(F,'Style','Text',...
'HandleVisibility','on',...
'String','1',...
'FontSize',FS(6),...
'HorizontalAlignment','center',...
'BackgroundColor','w',...
'Position',hPageNo,...
'Visible','on',...
'UserData',1,...
'Tag','PageNo','UserData',1);
end
%-Add handles for this page to UserData of hNextPage
%-Make handles for this page invisible if PageNo>1
%-----------------------------------------------------------------------
mVis = strcmp('on',get(h,'Visible'));
mHit = strcmp('on',get(h,'HitTest'));
hPg = get(hNextPage,'UserData');
if isempty(hPg)
hPg = {h(mVis), h(~mVis), h(mHit), h(~mHit)};
else
hPg = [hPg; {h(mVis), h(~mVis), h(mHit), h(~mHit)}];
set(h(mVis),'Visible','off');
set(h(mHit),'HitTest','off');
end
set(hNextPage,'UserData',hPg)
%-Return handles to pagination controls if requested
if nargout>0, varargout = {[hNextPage, hPrevPage, hPageNo]}; end
case 'turnpage'
%=======================================================================
% spm_figure('TurnPage',move,F)
if nargin<3, F='Graphics'; else F=varargin{3}; end
if nargin<2, move=1; else move=varargin{2}; end
F = spm_figure('FindWin',F);
if isempty(F), error('No Graphics window'), end
hNextPage = findobj(F,'Tag','NextPage');
hPrevPage = findobj(F,'Tag','PrevPage');
hPageNo = findobj(F,'Tag','PageNo');
if isempty(hNextPage), return, end
hPg = get(hNextPage,'UserData');
Cpage = get(hPageNo, 'UserData');
nPages = size(hPg,1);
%-Sort out new page number
if ischar(move), Npage = Cpage+eval(move); else Npage = move; end
Npage = max(min(Npage,nPages),1);
%-Make current page invisible, new page visible, set page number string
set(hPg{Cpage,1},'Visible','off');
set(hPg{Cpage,3},'HitTest','off');
set(hPg{Npage,1},'Visible','on');
set(hPg{Npage,3},'HitTest','on');
set(hPageNo,'UserData',Npage,'String',sprintf('%d / %d',Npage,nPages))
for k = 1:length(hPg{Npage,1}) % VG
if strcmp(get(hPg{Npage,1}(k),'Type'),'axes')
axes(hPg{Npage,1}(k));
end;
end;
%-Disable appropriate page turning control if on first/last page (for neatness)
if Npage==1, set(hPrevPage,'Enable','off')
else set(hPrevPage,'Enable','on'), end
if Npage==nPages, set(hNextPage,'Enable','off')
else set(hNextPage,'Enable','on'), end
case 'deletepagecontrols'
%=======================================================================
% spm_figure('DeletePageControls',F)
if nargin<2, F='Graphics'; else F=varargin{2}; end
F = spm_figure('FindWin',F);
if isempty(F), error('No Graphics window'), end
hNextPage = findobj(F,'Tag','NextPage');
hPrevPage = findobj(F,'Tag','PrevPage');
hPageNo = findobj(F,'Tag','PageNo');
delete([hNextPage hPrevPage hPageNo])
case '#page'
%=======================================================================
% n = spm_figure('#Page',F)
if nargin<2, F='Graphics'; else F=varargin{2}; end
F = spm_figure('FindWin',F);
if isempty(F), error('No Graphics window'), end
hNextPage = findobj(F,'Tag','NextPage');
if isempty(hNextPage)
n = 1;
else
n = size(get(hNextPage,'UserData'),1)+1;
end
varargout = {n};
case 'currentpage'
%=======================================================================
% n = spm_figure('CurrentPage', F)
if nargin<2, F='Graphics'; else F=varargin{2}; end
F = spm_figure('FindWin',F);
if isempty(F), error('No Graphics window'), end
hPageNo = findobj(F,'Tag','PageNo');
Cpage = get(hPageNo, 'UserData');
varargout = {Cpage};
case 'watermark'
%=======================================================================
% spm_figure('WaterMark',F,str,Tag,Angle,Perm)
if nargin<6, HVis='on'; else HVis='off'; end
if nargin<5, Angle=-45; else Angle=varargin{5}; end
if nargin<4 || isempty(varargin{4}), Tag = 'WaterMark'; else Tag=varargin{4}; end
if nargin<3 || isempty(varargin{3}), str = 'SPM'; else str=varargin{3}; end
if nargin<2, if any(get(0,'Children')), F=gcf; else F=''; end
else F=varargin{2}; end
F = spm_figure('FindWin',F);
if isempty(F), return, end
%-Specify watermark color from background colour
%-----------------------------------------------------------------------
Colour = get(F,'Color');
%-Only mess with grayscale backgrounds
if ~all(Colour==Colour(1)), return, end
%-Work out colour - lighter unless grey value > 0.9
Colour = Colour+(2*(Colour(1)<0.9)-1)*0.02;
cF = get(0,'CurrentFigure');
set(0,'CurrentFigure',F)
Units=get(F,'Units');
set(F,'Units','normalized');
h = axes('Position',[0.45,0.5,0.1,0.1],...
'Units','normalized',...
'Visible','off',...
'Tag',Tag);
set(F,'Units',Units)
text(0.5,0.5,str,...
'FontSize',spm('FontSize',80),...
'FontWeight','Bold',...
'FontName',spm_platform('Font','times'),...
'Rotation',Angle,...
'HorizontalAlignment','Center',...
'VerticalAlignment','middle',...
'EraseMode','normal',...
'Color',Colour,...
'ButtonDownFcn',[...
'if strcmp(get(gcbf,''SelectionType''),''open''),',...
'delete(get(gcbo,''Parent'')),',...
'end'])
set(h,'HandleVisibility',HVis)
set(0,'CurrentFigure',cF)
case 'createwin'
%=======================================================================
% F=spm_figure('CreateWin',Tag,Name,Visible)
%-Condition arguments
%-----------------------------------------------------------------------
if nargin<4 || isempty(varargin{4}), Visible='on'; else Visible=varargin{4}; end
if nargin<3, Name=''; else Name = varargin{3}; end
if nargin<2, Tag=''; else Tag = varargin{2}; end
WS = spm('WinScale'); %-Window scaling factors
FS = spm('FontSizes'); %-Scaled font sizes
PF = spm_platform('fonts'); %-Font names (for this platform)
Rect = spm('WinSize','Graphics'); %-Graphics window rectangle
S0 = spm('WinSize','0',1); %-Screen size (of the current monitor)
F = figure(...
'Tag',Tag,...
'Position',[S0(1) S0(2) 0 0] + Rect,...
'Resize','off',...
'Color','w',...
'ColorMap',gray(64),...
'DefaultTextColor','k',...
'DefaultTextInterpreter','none',...
'DefaultTextFontName',PF.helvetica,...
'DefaultTextFontSize',FS(10),...
'DefaultAxesColor','w',...
'DefaultAxesXColor','k',...
'DefaultAxesYColor','k',...
'DefaultAxesZColor','k',...
'DefaultAxesFontName',PF.helvetica,...
'DefaultPatchFaceColor','k',...
'DefaultPatchEdgeColor','k',...
'DefaultSurfaceEdgeColor','k',...
'DefaultLineColor','k',...
'DefaultUicontrolFontName',PF.helvetica,...
'DefaultUicontrolFontSize',FS(10),...
'DefaultUicontrolInterruptible','on',...
'PaperType','A4',...
'PaperUnits','normalized',...
'PaperPosition',[.0726 .0644 .854 .870],...
'InvertHardcopy','off',...
'Renderer',spm_get_defaults('renderer'),...
'Visible','off',...
'Toolbar','none');
if ~isempty(Name)
set(F,'Name',sprintf('%s%s: %s',spm('ver'),...
spm('GetUser',' (%s)'),Name),'NumberTitle','off')
end
set(F,'Visible',Visible)
varargout = {F};
case 'getwinscale'
%=======================================================================
% WS = spm_figure('GetWinScale')
warning('spm_figure(''GetWinScale''... is Grandfathered: use spm(''WinScale''')
varargout = {spm('WinScale')};
case 'fontsizes'
%=======================================================================
% FS = spm_figure('FontSizes',FS)
warning('spm_figure(''FontSizes''... is Grandfathered: use spm(''FontSizes''')
if nargin<2, FS=[08,09,11,13,14,6:36]; else FS=varargin{2}; end
varargout = {round(FS*min(spm('WinScale')))};
%=======================================================================
case 'createbar'
%=======================================================================
% spm_figure('CreateBar',F)
if nargin<2, if any(get(0,'Children')), F=gcf; else F=''; end
else F=varargin{2}; end
F = spm_figure('FindWin',F);
if isempty(F), return, end
cSHH = get(0,'ShowHiddenHandles');
set(0,'ShowHiddenHandles','on')
t0 = findobj(get(F,'Children'),'Flat','Label','&Help');
if isempty(t0), t0 = uimenu( F,'Label','&Help'); end;
set(findobj(t0,'Position',1),'Separator','on');
uimenu(t0,'Position',1,...
'Label','SPM web',...
'CallBack','web(''http://www.fil.ion.ucl.ac.uk/spm/'');');
uimenu(t0,'Position',1,...
'Label','SPM help','ForegroundColor',[0 1 0],...
'CallBack','spm_help');
t0=uimenu( F,'Label','Colours','HandleVisibility','off');
t1=uimenu(t0,'Label','ColorMap');
uimenu(t1,'Label','Gray', 'CallBack','spm_figure(''ColorMap'',''gray'')');
uimenu(t1,'Label','Hot', 'CallBack','spm_figure(''ColorMap'',''hot'')');
uimenu(t1,'Label','Pink', 'CallBack','spm_figure(''ColorMap'',''pink'')');
uimenu(t1,'Label','Jet','CallBack','spm_figure(''ColorMap'',''jet'')');
uimenu(t1,'Label','Gray-Hot', 'CallBack','spm_figure(''ColorMap'',''gray-hot'')');
uimenu(t1,'Label','Gray-Cool','CallBack','spm_figure(''ColorMap'',''gray-cool'')');
uimenu(t1,'Label','Gray-Pink','CallBack','spm_figure(''ColorMap'',''gray-pink'')');
uimenu(t1,'Label','Gray-Jet', 'CallBack','spm_figure(''ColorMap'',''gray-jet'')');
t1=uimenu(t0,'Label','Effects');
uimenu(t1,'Label','Invert','CallBack','spm_figure(''ColorMap'',''invert'')');
uimenu(t1,'Label','Brighten','CallBack','spm_figure(''ColorMap'',''brighten'')');
uimenu(t1,'Label','Darken','CallBack','spm_figure(''ColorMap'',''darken'')');
uimenu( F,'Label','Clear','HandleVisibility','off','CallBack','spm_figure(''Clear'',gcbf)');
t0=uimenu( F,'Label','SPM-Print','HandleVisibility','off');
%uimenu( F,'Label','SPM-Print','HandleVisibility','off','CallBack','spm_figure(''Print'',gcbf)');
t1=uimenu(t0,'Label','default print file','HandleVisibility','off','CallBack','spm_figure(''Print'',gcbf)');
t1=uimenu(t0,'Label','other print file','HandleVisibility','off','CallBack','spm_figure(''PrintTo'',spm_figure(''FindWin'',''Graphics''))');
% ### CODE FOR SATELLITE FIGURE ###
% Code checks if there is a satellite window and if results are currently displayed
% It assumes that if hReg is invalid then there are no results currently displayed
% Modified by DRG to display a satellite figure 02/14/01.
cb = ['global SatWindow,',...
'try,',...
'tmp = get(hReg);,',...
'ResFlag = 1;',...
'catch,',...
'ResFlag = 0;',...
'end,',...
'if SatWindow,',...
'figure(SatWindow),',...
'else,',...
'if ResFlag,',...
'spm_setup_satfig,',...
'end,',...
'end'];
uimenu( F,'Label','Results-Fig','HandleVisibility','off','Callback',cb);
% ### END NEW CODE ###
set(0,'ShowHiddenHandles',cSHH)
try
spm_jobman('pulldown');
end
%=======================================================================
case 'figcontextmenu'
%=======================================================================
% h = spm_figure('FigContextMenu',F)
if nargin<2
F = get(0,'CurrentFigure');
if isempty(F), error('no figure'), end
else
F = spm_figure('FindWin',varargin{2});
if isempty(F), error('no such figure'), end
end
h = uicontextmenu('Parent',F,'HandleVisibility','CallBack');
cSHH = get(0,'ShowHiddenHandles');
set(0,'ShowHiddenHandles','on')
copy_menu(F,h);
set(0,'ShowHiddenHandles',cSHH)
set(F,'UIContextMenu',h)
varargout = {h};
case 'colormap'
%=======================================================================
% spm_figure('ColorMap',ColAction,h)
if nargin<3, h=[]; else h=varargin{3}; end
if nargin<2, ColAction='gray'; else ColAction=varargin{2}; end
switch lower(ColAction), case 'gray'
colormap(gray(64))
case 'hot'
colormap(hot(64))
case 'pink'
colormap(pink(64))
case 'jet'
colormap(jet(64))
case 'gray-hot'
tmp = hot(64 + 16); tmp = tmp((1:64) + 16,:);
colormap([gray(64); tmp]);
case 'gray-cool'
cool = [zeros(10,1) zeros(10,1) linspace(0.5,1,10)';
zeros(31,1) linspace(0,1,31)' ones(31,1);
linspace(0,1,23)' ones(23,1) ones(23,1) ];
colormap([gray(64); cool]);
case 'gray-pink'
tmp = pink(64 + 16); tmp = tmp((1:64) + 16,:);
colormap([gray(64); tmp]);
case 'gray-jet'
colormap([gray(64); jet(64)]);
case 'invert'
colormap(flipud(colormap));
case 'brighten'
colormap(brighten(colormap, 0.2));
case 'darken'
colormap(brighten(colormap, -0.2));
otherwise
error('Illegal ColAction specification');
end
case 'graphicshandle'
%=======================================================================
% h = spm_figure('GraphicsHandle',F)
if nargin<2, F=gcbf; else F=spm_figure('FindWin',varargin{2}); end
if isempty(F), return, end
tmp = get(F,'Name');
set(F,'Name',...
'Handle: Select item to identify, MiddleMouse=parent, RightMouse=cancel...');
set(F,'Pointer','CrossHair')
waitforbuttonpress;
h = gco(F);
hType = get(h,'Type');
SelnType = get(gcf,'SelectionType');
set(F,'Pointer','Arrow','Name',tmp)
if ~strcmp(SelnType,'alt') && ~isempty(h) && gcf==F
str = sprintf('Selected (%s) object',get(h,'Type'));
if strcmp(SelnType,'normal')
str = sprintf('%s: handle',str);
else
h = get(h,'Parent');
str = sprintf('%s: handle of parent (%s) object',str,get(h,'Type'));
end
if nargout==0
assignin('base','ans',h)
fprintf('\n%s: \n',str)
ans = h
else
varargout={h};
end
else
varargout={[]};
end
otherwise
%=======================================================================
warning(['Illegal Action string: ',Action])
end
return;
%=======================================================================
%=======================================================================
function copy_menu(F,G)
%=======================================================================
handles = findobj(get(F,'Children'),'Flat','Type','uimenu','Visible','on');
if isempty(handles), return; end;
for F1=handles',
if ~strcmp(get(F1,'Label'),'&Window'),
G1 = uimenu(G,'Label',get(F1,'Label'),...
'CallBack',get(F1,'CallBack'),...
'Position',get(F1,'Position'),...
'Separator',get(F1,'Separator'));
copy_menu(F1,G1);
end;
end;
return;
%=======================================================================
|
github
|
lcnbeapp/beapp-master
|
spm_smooth.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_smooth.m
| 3,654 |
utf_8
|
0f00684dc1b7cb99c88cd50e6a64a20a
|
function spm_smooth(P,Q,s,dtype)
% 3 dimensional convolution of an image
% FORMAT spm_smooth(P,Q,S,dtype)
% P - image to be smoothed
% Q - filename for smoothed image
% S - [sx sy sz] Gaussian filter width {FWHM} in mm
% dtype - datatype [default: 0 == same datatype as P]
%____________________________________________________________________________
%
% spm_smooth is used to smooth or convolve images in a file (maybe).
%
% The sum of kernel coeficients are set to unity. Boundary
% conditions assume data does not exist outside the image in z (i.e.
% the kernel is truncated in z at the boundaries of the image space). S
% can be a vector of 3 FWHM values that specifiy an anisotropic
% smoothing. If S is a scalar isotropic smoothing is implemented.
%
% If Q is not a string, it is used as the destination of the smoothed
% image. It must already be defined with the same number of elements
% as the image.
%
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner & Tom Nichols
% $Id$
%-----------------------------------------------------------------------
if length(s) == 1; s = [s s s]; end
if nargin<4, dtype = 0; end;
if ischar(P), P = spm_vol(P); end;
if isstruct(P),
for i=1:numel(P),
smooth1(P(i),Q,s,dtype);
end
else
smooth1(P,Q,s,dtype);
end
%_______________________________________________________________________
%_______________________________________________________________________
function smooth1(P,Q,s,dtype)
if isstruct(P),
VOX = sqrt(sum(P.mat(1:3,1:3).^2));
else
VOX = [1 1 1];
end;
if ischar(Q) && isstruct(P),
[pth,nam,ext,num] = spm_fileparts(Q);
q = fullfile(pth,[nam,ext]);
Q = P;
Q.fname = q;
if ~isempty(num),
Q.n = str2num(num);
end;
if ~isfield(Q,'descrip'), Q.descrip = sprintf('SPM compatible'); end;
Q.descrip = sprintf('%s - conv(%g,%g,%g)',Q.descrip, s);
if dtype~=0, % Need to figure out some rescaling.
Q.dt(1) = dtype;
if ~isfinite(spm_type(Q.dt(1),'maxval')),
Q.pinfo = [1 0 0]'; % float or double, so scalefactor of 1
else
% Need to determine the range of intensities
if isfinite(spm_type(P.dt(1),'maxval')),
% Integer types have a defined maximum value
maxv = spm_type(P.dt(1),'maxval')*P.pinfo(1) + P.pinfo(2);
else
% Need to find the max and min values in original image
mx = -Inf;
mn = Inf;
for pl=1:P.dim(3),
tmp = spm_slice_vol(P,spm_matrix([0 0 pl]),P.dim(1:2),0);
tmp = tmp(isfinite(tmp));
mx = max(max(tmp),mx);
mn = min(min(tmp),mn);
end
maxv = max(mx,-mn);
end
sf = maxv/spm_type(Q.dt(1),'maxval');
Q.pinfo = [sf 0 0]';
end
end
end
% compute parameters for spm_conv_vol
%-----------------------------------------------------------------------
s = s./VOX; % voxel anisotropy
s1 = s/sqrt(8*log(2)); % FWHM -> Gaussian parameter
x = round(6*s1(1)); x = -x:x; x = spm_smoothkern(s(1),x,1); x = x/sum(x);
y = round(6*s1(2)); y = -y:y; y = spm_smoothkern(s(2),y,1); y = y/sum(y);
z = round(6*s1(3)); z = -z:z; z = spm_smoothkern(s(3),z,1); z = z/sum(z);
i = (length(x) - 1)/2;
j = (length(y) - 1)/2;
k = (length(z) - 1)/2;
if isstruct(Q), Q = spm_create_vol(Q); end;
spm_conv_vol(P,Q,x,y,z,-[i,j,k]);
|
github
|
lcnbeapp/beapp-master
|
spm_smoothto8bit.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_smoothto8bit.m
| 2,377 |
utf_8
|
89653bff7e0591df6fa676885a830a16
|
function VO = spm_smoothto8bit(V,fwhm)
% 3 dimensional convolution of an image to 8bit data in memory
% FORMAT VO = spm_smoothto8bit(V,fwhm)
% V - mapped image to be smoothed
% fwhm - FWHM of Guassian filter width in mm
% VO - smoothed volume in a form that can be used by the
% spm_*_vol.mex* functions.
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id$
if nargin>1 & fwhm>0,
VO = smoothto8bit(V,fwhm);
else,
VO = V;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function VO = smoothto8bit(V,fwhm)
% 3 dimensional convolution of an image to 8bit data in memory
% FORMAT VO = smoothto8bit(V,fwhm)
% V - mapped image to be smoothed
% fwhm - FWHM of Guassian filter width in mm
% VO - smoothed volume in a form that can be used by the
% spm_*_vol.mex* functions.
%_______________________________________________________________________
vx = sqrt(sum(V.mat(1:3,1:3).^2));
s = (fwhm./vx./sqrt(8*log(2)) + eps).^2;
r = cell(1,3);
for i=1:3,
r{i}.s = ceil(3.5*sqrt(s(i)));
x = -r{i}.s:r{i}.s;
r{i}.k = exp(-0.5 * (x.*x)/s(i))/sqrt(2*pi*s(i));
r{i}.k = r{i}.k/sum(r{i}.k);
end;
buff = zeros([V.dim(1:2) r{3}.s*2+1]);
VO = V;
VO.dt = [spm_type('uint8') spm_platform('bigend')];
V0.dat = uint8(0);
V0.dat(VO.dim(1:3)) = uint8(0);
VO.pinfo = [];
for i=1:V.dim(3)+r{3}.s,
if i<=V.dim(3),
img = spm_slice_vol(V,spm_matrix([0 0 i]),V.dim(1:2),0);
msk = find(~isfinite(img));
img(msk) = 0;
buff(:,:,rem(i-1,r{3}.s*2+1)+1) = ...
conv2(conv2(img,r{1}.k,'same'),r{2}.k','same');
else,
buff(:,:,rem(i-1,r{3}.s*2+1)+1) = 0;
end;
if i>r{3}.s,
kern = zeros(size(r{3}.k'));
kern(rem((i:(i+r{3}.s*2))',r{3}.s*2+1)+1) = r{3}.k';
img = reshape(buff,[prod(V.dim(1:2)) r{3}.s*2+1])*kern;
img = reshape(img,V.dim(1:2));
ii = i-r{3}.s;
mx = max(img(:));
mn = min(img(:));
if mx==mn, mx=mn+eps; end;
VO.pinfo(1:2,ii) = [(mx-mn)/255 mn]';
VO.dat(:,:,ii) = uint8(round((img-mn)*(255/(mx-mn))));
end;
end;
|
github
|
lcnbeapp/beapp-master
|
spm_platform.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_platform.m
| 8,498 |
utf_8
|
9af699511e4e0bff6555d7a1e3fe0a23
|
function varargout=spm_platform(varargin)
% Platform specific configuration parameters for SPM
%
% FORMAT ans = spm_platform(arg)
% arg - optional string argument, can be
% - 'bigend' - return whether this architecture is bigendian
% - 0 - is little endian
% - 1 - is big endian
% - 'filesys' - type of filesystem
% - 'unx' - UNIX
% - 'win' - DOS
% - 'sepchar' - returns directory separator
% - 'user' - returns username
% - 'host' - returns system's host name
% - 'tempdir' - returns name of temp directory
% - 'drives' - returns string containing valid drive letters
%
% FORMAT PlatFontNames = spm_platform('fonts')
% Returns structure with fields named after the generic (UNIX) fonts, the
% field containing the name of the platform specific font.
%
% FORMAT PlatFontName = spm_platform('font',GenFontName)
% Maps generic (UNIX) FontNames to platform specific FontNames
%
% FORMAT PLATFORM = spm_platform('init',comp)
% Initialises platform specific parameters in persistent PLATFORM
% (External gateway to init_platform(comp) subfunction)
% comp - computer to use [defaults to MATLAB's `computer`]
% PLATFORM - copy of persistent PLATFORM
%
% FORMAT spm_platform
% Initialises platform specific parameters in persistent PLATFORM
% (External gateway to init_platform(computer) subfunction)
%
% ----------------
% SUBFUNCTIONS:
%
% FORMAT init_platform(comp)
% Initialise platform specific parameters in persistent PLATFORM
% comp - computer to use [defaults to MATLAB's `computer`]
%
%--------------------------------------------------------------------------
%
% Since calls to spm_platform will be made frequently, most platform
% specific parameters are stored as a structure in the persistent variable
% PLATFORM. Subsequent calls use the information from this persistent
% variable, if it exists.
%
% Platform specific definitions are contained in the data structures at
% the beginning of the init_platform subfunction at the end of this
% file.
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Matthew Brett
% $Id$
%-Initialise
%--------------------------------------------------------------------------
persistent PLATFORM
if isempty(PLATFORM), PLATFORM = init_platform; end
if nargin==0, return, end
switch lower(varargin{1}), case 'init' %-(re)initialise
%==========================================================================
init_platform(varargin{2:end});
varargout = {PLATFORM};
case 'bigend' %-Return endian for this architecture
%==========================================================================
varargout = {PLATFORM.bigend};
case 'filesys' %-Return file system
%==========================================================================
varargout = {PLATFORM.filesys};
case 'sepchar' %-Return file separator character
%==========================================================================
warning('use filesep instead (supported by MathWorks)')
varargout = {PLATFORM.sepchar};
case 'rootlen' %-Return length in chars of root directory name
%=======================================================================
varargout = {PLATFORM.rootlen};
case 'user' %-Return user string
%==========================================================================
varargout = {PLATFORM.user};
case 'host' %-Return hostname
%==========================================================================
varargout = {PLATFORM.host};
case 'drives' %-Return drives
%==========================================================================
varargout = {PLATFORM.drives};
case 'tempdir' %-Return temporary directory
%==========================================================================
twd = getenv('SPMTMP');
if isempty(twd)
twd = tempdir;
end
varargout = {twd};
case {'font','fonts'} %-Map default font names to platform font names
%==========================================================================
if nargin<2, varargout={PLATFORM.font}; return, end
switch lower(varargin{2})
case 'times'
varargout = {PLATFORM.font.times};
case 'courier'
varargout = {PLATFORM.font.courier};
case 'helvetica'
varargout = {PLATFORM.font.helvetica};
case 'symbol'
varargout = {PLATFORM.font.symbol};
otherwise
warning(['Unknown font ',varargin{2},', using default'])
varargout = {PLATFORM.font.helvetica};
end
otherwise %-Unknown Action string
%==========================================================================
error('Unknown Action string')
%==========================================================================
end
%==========================================================================
%- S U B - F U N C T I O N S
%==========================================================================
function PLATFORM = init_platform(comp) %-Initialise platform variables
%==========================================================================
if nargin<1, comp=computer; end
%-Platform definitions
%--------------------------------------------------------------------------
PDefs = {'PCWIN', 'win', 0;...
'PCWIN64', 'win', 0;...
'MAC', 'unx', 1;...
'MACI', 'unx', 0;...
'MACI64', 'unx', 0;...
'SOL2', 'unx', 1;...
'SOL64', 'unx', 1;...
'GLNX86', 'unx', 0;...
'GLNXA64', 'unx', 0};
PDefs = cell2struct(PDefs,{'computer','filesys','endian'},2);
%-Which computer?
%--------------------------------------------------------------------------
[issup, ci] = ismember(comp,{PDefs.computer});
if ~issup
error([comp ' not supported architecture for ' spm('Ver')]);
end
%-Set byte ordering
%--------------------------------------------------------------------------
PLATFORM.bigend = PDefs(ci).endian;
%-Set filesystem type
%--------------------------------------------------------------------------
PLATFORM.filesys = PDefs(ci).filesys;
%-File separator character
%--------------------------------------------------------------------------
PLATFORM.sepchar = filesep;
%-Username
%--------------------------------------------------------------------------
switch PLATFORM.filesys
case 'unx'
PLATFORM.user = getenv('USER');
case 'win'
PLATFORM.user = getenv('USERNAME');
otherwise
error(['Don''t know filesystem ',PLATFORM.filesys])
end
if isempty(PLATFORM.user), PLATFORM.user = 'anonymous'; end
%-Hostname
%--------------------------------------------------------------------------
[sts, Host] = system('hostname');
if sts
if strcmp(PLATFORM.filesys,'win')
Host = getenv('COMPUTERNAME');
else
Host = getenv('HOSTNAME');
end
Host = regexp(Host,'(.*?)\.','tokens','once');
else
Host = Host(1:end-1);
end
PLATFORM.host = Host;
%-Drives
%--------------------------------------------------------------------------
PLATFORM.drives = '';
if strcmp(PLATFORM.filesys,'win')
driveLett = cellstr(char(('C':'Z')'));
for i=1:numel(driveLett)
if exist([driveLett{i} ':\'],'dir')
PLATFORM.drives = [PLATFORM.drives driveLett{i}];
end
end
end
%-Fonts
%--------------------------------------------------------------------------
switch comp
case {'MAC','MACI','MACI64'}
PLATFORM.font.helvetica = 'TrebuchetMS';
PLATFORM.font.times = 'Times';
PLATFORM.font.courier = 'Courier';
PLATFORM.font.symbol = 'Symbol';
case {'SOL2','SOL64','GLNX86','GLNXA64'}
PLATFORM.font.helvetica = 'Helvetica';
PLATFORM.font.times = 'Times';
PLATFORM.font.courier = 'Courier';
PLATFORM.font.symbol = 'Symbol';
case {'PCWIN','PCWIN64'}
PLATFORM.font.helvetica = 'Arial Narrow';
PLATFORM.font.times = 'Times New Roman';
PLATFORM.font.courier = 'Courier New';
PLATFORM.font.symbol = 'Symbol';
end
|
github
|
lcnbeapp/beapp-master
|
spm_preproc.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_preproc.m
| 20,519 |
utf_8
|
c08f55c5a2eaeb3e30508750d366f52f
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function results = spm_preproc(varargin)
% Combined Segmentation and Spatial Normalisation
%
% FORMAT results = spm_preproc(V,opts)
% V - image to work with
% opts - options
% opts.tpm - n tissue probability images for each class
% opts.ngaus - number of Gaussians per class (n+1 classes)
% opts.warpreg - warping regularisation
% opts.warpco - cutoff distance for DCT basis functions
% opts.biasreg - regularisation for bias correction
% opts.biasfwhm - FWHM of Gausian form for bias regularisation
% opts.regtype - regularisation for affine part
% opts.fudge - a fudge factor
% opts.msk - unused
%
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id$
[dir,nam,ext] = fileparts(which(mfilename));
opts0.tpm = char(...
fullfile(dir,'tpm','grey.nii'),...
fullfile(dir,'tpm','white.nii'),...
fullfile(dir,'tpm','csf.nii'));
opts0.ngaus = [2 2 2 4];
opts0.warpreg = 1;
opts0.warpco = 25;
opts0.biasreg = 0.0001;
opts0.biasfwhm = 75;
opts0.regtype = 'mni';
opts0.fudge = 5;
opts0.samp = 3;
opts0.msk = '';
if nargin==0
V = spm_select(1,'image');
else
V = varargin{1};
end;
if ischar(V), V = spm_vol(V); end;
if nargin < 2
opts = opts0;
else
opts = varargin{2};
fnms = fieldnames(opts0);
for i=1:length(fnms)
if ~isfield(opts,fnms{i}), opts.(fnms{i}) = opts0.(fnms{i}); end;
end;
end;
if length(opts.ngaus)~= size(opts.tpm,1)+1,
error('Number of Gaussians per class is not compatible with number of classes');
end;
K = sum(opts.ngaus);
Kb = length(opts.ngaus);
lkp = [];
for k=1:Kb,
lkp = [lkp ones(1,opts.ngaus(k))*k];
end;
B = spm_vol(opts.tpm);
b0 = spm_load_priors(B);
d = V(1).dim(1:3);
vx = sqrt(sum(V(1).mat(1:3,1:3).^2));
sk = max([1 1 1],round(opts.samp*[1 1 1]./vx));
[x0,y0,o] = ndgrid(1:sk(1):d(1),1:sk(2):d(2),1);
z0 = 1:sk(3):d(3);
tiny = eps;
vx = sqrt(sum(V(1).mat(1:3,1:3).^2));
kron = inline('spm_krutil(a,b)','a','b');
% BENDING ENERGY REGULARIZATION for warping
%-----------------------------------------------------------------------
lam = 0.001;
d2 = max(round((V(1).dim(1:3).*vx)/opts.warpco),[1 1 1]);
kx = (pi*((1:d2(1))'-1)/d(1)/vx(1)).^2;
ky = (pi*((1:d2(2))'-1)/d(2)/vx(2)).^2;
kz = (pi*((1:d2(3))'-1)/d(3)/vx(3)).^2;
Cwarp = (1*kron(kz.^2,kron(ky.^0,kx.^0)) +...
1*kron(kz.^0,kron(ky.^2,kx.^0)) +...
1*kron(kz.^0,kron(ky.^0,kx.^2)) +...
2*kron(kz.^1,kron(ky.^1,kx.^0)) +...
2*kron(kz.^1,kron(ky.^0,kx.^1)) +...
2*kron(kz.^0,kron(ky.^1,kx.^1)) );
Cwarp = Cwarp*opts.warpreg;
Cwarp = [Cwarp*vx(1)^4 ; Cwarp*vx(2)^4 ; Cwarp*vx(3)^4];
Cwarp = sparse(1:length(Cwarp),1:length(Cwarp),Cwarp,length(Cwarp),length(Cwarp));
B3warp = spm_dctmtx(d(3),d2(3),z0);
B2warp = spm_dctmtx(d(2),d2(2),y0(1,:)');
B1warp = spm_dctmtx(d(1),d2(1),x0(:,1));
lmR = speye(size(Cwarp));
Twarp = zeros([d2 3]);
% GAUSSIAN REGULARISATION for bias correction
%-----------------------------------------------------------------------
fwhm = opts.biasfwhm;
sd = vx(1)*V(1).dim(1)/fwhm; d3(1) = ceil(sd*2); krn_x = exp(-(0:(d3(1)-1)).^2/sd.^2)/sqrt(vx(1));
sd = vx(2)*V(1).dim(2)/fwhm; d3(2) = ceil(sd*2); krn_y = exp(-(0:(d3(2)-1)).^2/sd.^2)/sqrt(vx(2));
sd = vx(3)*V(1).dim(3)/fwhm; d3(3) = ceil(sd*2); krn_z = exp(-(0:(d3(3)-1)).^2/sd.^2)/sqrt(vx(3));
Cbias = kron(krn_z,kron(krn_y,krn_x)).^(-2)*opts.biasreg;
Cbias = sparse(1:length(Cbias),1:length(Cbias),Cbias,length(Cbias),length(Cbias));
B3bias = spm_dctmtx(d(3),d3(3),z0);
B2bias = spm_dctmtx(d(2),d3(2),y0(1,:)');
B1bias = spm_dctmtx(d(1),d3(1),x0(:,1));
lmRb = speye(size(Cbias));
Tbias = zeros(d3);
% Fudge Factor - to (approximately) account for
% non-independence of voxels
ff = opts.fudge;
ff = max(1,ff^3/prod(sk)/abs(det(V.mat(1:3,1:3))));
Cwarp = Cwarp*ff;
Cbias = Cbias*ff;
ll = -Inf;
llr = 0;
llrb = 0;
tol1 = 1e-4; % Stopping criterion. For more accuracy, use a smaller value
d = [size(x0) length(z0)];
f = zeros(d);
for z=1:length(z0),
f(:,:,z) = spm_sample_vol(V,x0,y0,o*z0(z),0);
end;
[thresh,mx] = spm_minmax(f);
mn = zeros(K,1);
rand('state',0); % give same results each time
for k1=1:Kb,
kk = sum(lkp==k1);
mn(lkp==k1) = rand(kk,1)*mx;
end;
vr = ones(K,1)*mx^2;
mg = ones(K,1)/K;
if ~isempty(opts.msk),
VM = spm_vol(opts.msk);
if sum(sum((VM.mat-V(1).mat).^2)) > 1e-6 || any(VM.dim(1:3) ~= V(1).dim(1:3)),
error('Mask must have the same dimensions and orientation as the image.');
end;
end;
Affine = eye(4);
if ~isempty(opts.regtype),
Affine = spm_maff(V,{x0,y0,z0},b0,B(1).mat,Affine,opts.regtype,ff*100);
Affine = spm_maff(V,{x0,y0,z0},b0,B(1).mat,Affine,opts.regtype,ff);
end;
M = B(1).mat\Affine*V(1).mat;
nm = 0;
for z=1:length(z0),
x1 = M(1,1)*x0 + M(1,2)*y0 + (M(1,3)*z0(z) + M(1,4));
y1 = M(2,1)*x0 + M(2,2)*y0 + (M(2,3)*z0(z) + M(2,4));
z1 = M(3,1)*x0 + M(3,2)*y0 + (M(3,3)*z0(z) + M(3,4));
buf(z).msk = spm_sample_priors(b0{end},x1,y1,z1,1)<(1-1/512);
fz = f(:,:,z);
%buf(z).msk = fz>thresh;
buf(z).msk = buf(z).msk & isfinite(fz) & (fz~=0);
if ~isempty(opts.msk),
msk = spm_sample_vol(VM,x0,y0,o*z0(z),0);
buf(z).msk = buf(z).msk & msk;
end;
buf(z).nm = sum(buf(z).msk(:));
buf(z).f = fz(buf(z).msk);
nm = nm + buf(z).nm;
buf(z).bf(1:buf(z).nm,1) = single(1);
buf(z).dat = single(0);
if buf(z).nm,
buf(z).dat(buf(z).nm,Kb) = single(0);
end;
end;
clear f
finalit = 0;
spm_chi2_plot('Init','Processing','Log-likelihood','Iteration');
for iter=1:100,
if finalit,
% THIS CODE MAY BE USED IN FUTURE
% Reload the data for the final iteration. This iteration
% does not do any registration, so there is no need to
% mask out the background voxels.
%------------------------------------------------------------
llrb = -0.5*Tbias(:)'*Cbias*Tbias(:);
for z=1:length(z0),
fz = spm_sample_vol(V,x0,y0,o*z0(z),0);
buf(z).msk = fz~=0;
if ~isempty(opts.msk),
msk = spm_sample_vol(VM,x0,y0,o*z0(z),0);
buf(z).msk = buf(z).msk & msk;
end;
buf(z).nm = sum(buf(z).msk(:));
buf(z).f = fz(buf(z).msk);
nm = nm + buf(z).nm;
buf(z).bf(1:buf(z).nm,1) = single(1);
buf(z).dat = single(0);
if buf(z).nm,
buf(z).dat(buf(z).nm,Kb) = single(0);
end;
if buf(z).nm,
bf = transf(B1bias,B2bias,B3bias(z,:),Tbias);
tmp = bf(buf(z).msk);
llrb = llrb + sum(tmp);
buf(z).bf = single(exp(tmp));
end;
end;
% The background won't fit well any more, so increase the
% variances of these Gaussians in order to give it a chance
vr(lkp(K)) = vr(lkp(K))*8;
spm_chi2_plot('Init','Processing','Log-likelihood','Iteration');
end;
% Load the warped prior probability images into the buffer
%------------------------------------------------------------
for z=1:length(z0),
if ~buf(z).nm, continue; end;
[x1,y1,z1] = defs(Twarp,z,B1warp,B2warp,B3warp,x0,y0,z0,M,buf(z).msk);
for k1=1:Kb,
tmp = spm_sample_priors(b0{k1},x1,y1,z1,k1==Kb);
buf(z).dat(:,k1) = single(tmp);
end;
end;
for iter1=1:10,
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Estimate cluster parameters
%------------------------------------------------------------
for subit=1:40,
oll = ll;
mom0 = zeros(K,1)+tiny;
mom1 = zeros(K,1);
mom2 = zeros(K,1);
mgm = zeros(Kb,1);
ll = llr+llrb;
for z=1:length(z0),
if ~buf(z).nm, continue; end;
bf = double(buf(z).bf);
cr = double(buf(z).f).*bf;
q = zeros(buf(z).nm,K);
b = zeros(buf(z).nm,Kb);
s = zeros(buf(z).nm,1)+tiny;
for k1=1:Kb,
pr = double(buf(z).dat(:,k1));
b(:,k1) = pr;
s = s + pr*sum(mg(lkp==k1));
end;
for k1=1:Kb,
b(:,k1) = b(:,k1)./s;
end;
mgm = mgm + sum(b,1)';
for k=1:K,
q(:,k) = mg(k)*b(:,lkp(k)) .* exp((cr-mn(k)).^2/(-2*vr(k)))/sqrt(2*pi*vr(k));
end;
sq = sum(q,2)+tiny;
ll = ll + sum(log(sq));
for k=1:K, % Moments
p1 = q(:,k)./sq; mom0(k) = mom0(k) + sum(p1(:));
p1 = p1.*cr; mom1(k) = mom1(k) + sum(p1(:));
p1 = p1.*cr; mom2(k) = mom2(k) + sum(p1(:));
end;
end;
% Mixing proportions, Means and Variances
for k=1:K,
mg(k) = (mom0(k)+eps)/(mgm(lkp(k))+eps);
mn(k) = mom1(k)/(mom0(k)+eps);
vr(k) =(mom2(k)-mom1(k)*mom1(k)/mom0(k)+1e6*eps)/(mom0(k)+eps);
vr(k) = max(vr(k),eps);
end;
if subit>1 || (iter>1 && ~finalit),
spm_chi2_plot('Set',ll);
end;
if finalit, fprintf('Mix: %g\n',ll); end;
if subit == 1,
ooll = ll;
elseif (ll-oll)<tol1*nm,
% Improvement is small, so go to next step
break;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Estimate bias
%------------------------------------------------------------
if prod(d3)>0,
for subit=1:40,
% Compute objective function and its 1st and second derivatives
Alpha = zeros(prod(d3),prod(d3)); % Second derivatives
Beta = zeros(prod(d3),1); % First derivatives
ollrb = llrb;
oll = ll;
ll = llr+llrb;
for z=1:length(z0),
if ~buf(z).nm, continue; end;
bf = double(buf(z).bf);
cr = double(buf(z).f).*bf;
q = zeros(buf(z).nm,K);
for k=1:K,
q(:,k) = double(buf(z).dat(:,lkp(k)))*mg(k);
end;
s = sum(q,2)+tiny;
for k=1:K,
q(:,k) = q(:,k)./s .* exp((cr-mn(k)).^2/(-2*vr(k)))/sqrt(2*pi*vr(k));
end;
sq = sum(q,2)+tiny;
ll = ll + sum(log(sq));
w1 = zeros(buf(z).nm,1);
w2 = zeros(buf(z).nm,1);
for k=1:K,
tmp = q(:,k)./sq/vr(k);
w1 = w1 + tmp.*(mn(k) - cr);
w2 = w2 + tmp;
end;
wt1 = zeros(d(1:2)); wt1(buf(z).msk) = 1 + cr.*w1;
wt2 = zeros(d(1:2)); wt2(buf(z).msk) = cr.*(cr.*w2 - w1);
b3 = B3bias(z,:)';
Beta = Beta + kron(b3,spm_krutil(wt1,B1bias,B2bias,0));
Alpha = Alpha + kron(b3*b3',spm_krutil(wt2,B1bias,B2bias,1));
clear w1 w2 wt1 wt2 b3
end;
if finalit, fprintf('Bia: %g\n',ll); end;
if subit > 1 && ~(ll>oll),
% Hasn't improved, so go back to previous solution
Tbias = oTbias;
llrb = ollrb;
for z=1:length(z0),
if ~buf(z).nm, continue; end;
bf = transf(B1bias,B2bias,B3bias(z,:),Tbias);
buf(z).bf = single(exp(bf(buf(z).msk)));
end;
break;
else
% Accept new solution
spm_chi2_plot('Set',ll);
oTbias = Tbias;
if subit > 1 && ~((ll-oll)>tol1*nm),
% Improvement is only small, so go to next step
break;
else
% Use new solution and continue the Levenberg-Marquardt iterations
Tbias = reshape((Alpha + Cbias + lmRb)\((Alpha+lmRb)*Tbias(:) + Beta),d3);
llrb = -0.5*Tbias(:)'*Cbias*Tbias(:);
for z=1:length(z0),
if ~buf(z).nm, continue; end;
bf = transf(B1bias,B2bias,B3bias(z,:),Tbias);
tmp = bf(buf(z).msk);
llrb = llrb + sum(tmp);
buf(z).bf = single(exp(tmp));
end;
end;
end;
end;
if ~((ll-ooll)>tol1*nm), break; end;
end;
end;
if finalit, break; end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Estimate deformations
%------------------------------------------------------------
mg1 = full(sparse(lkp,1,mg));
ll = llr+llrb;
for z=1:length(z0),
if ~buf(z).nm, continue; end;
bf = double(buf(z).bf);
cr = double(buf(z).f).*bf;
q = zeros(buf(z).nm,Kb);
tmp = zeros(buf(z).nm,1)+tiny;
s = zeros(buf(z).nm,1)+tiny;
for k1=1:Kb,
s = s + mg1(k1)*double(buf(z).dat(:,k1));
end;
for k1=1:Kb,
kk = find(lkp==k1);
pp = zeros(buf(z).nm,1);
for k=kk,
pp = pp + exp((cr-mn(k)).^2/(-2*vr(k)))/sqrt(2*pi*vr(k))*mg(k);
end;
q(:,k1) = pp;
tmp = tmp+pp.*double(buf(z).dat(:,k1))./s;
end;
ll = ll + sum(log(tmp));
for k1=1:Kb,
buf(z).dat(:,k1) = single(q(:,k1));
end;
end;
for subit=1:20,
oll = ll;
A = cell(3,3);
A{1,1} = zeros(prod(d2));
A{1,2} = zeros(prod(d2));
A{1,3} = zeros(prod(d2));
A{2,2} = zeros(prod(d2));
A{2,3} = zeros(prod(d2));
A{3,3} = zeros(prod(d2));
Beta = zeros(prod(d2)*3,1);
for z=1:length(z0),
if ~buf(z).nm, continue; end;
[x1,y1,z1] = defs(Twarp,z,B1warp,B2warp,B3warp,x0,y0,z0,M,buf(z).msk);
b = zeros(buf(z).nm,Kb);
db1 = zeros(buf(z).nm,Kb);
db2 = zeros(buf(z).nm,Kb);
db3 = zeros(buf(z).nm,Kb);
s = zeros(buf(z).nm,1)+tiny;
ds1 = zeros(buf(z).nm,1);
ds2 = zeros(buf(z).nm,1);
ds3 = zeros(buf(z).nm,1);
p = zeros(buf(z).nm,1)+tiny;
dp1 = zeros(buf(z).nm,1);
dp2 = zeros(buf(z).nm,1);
dp3 = zeros(buf(z).nm,1);
for k1=1:Kb,
[b(:,k1),db1(:,k1),db2(:,k1),db3(:,k1)] = spm_sample_priors(b0{k1},x1,y1,z1,k1==Kb);
s = s + mg1(k1)* b(:,k1);
ds1 = ds1 + mg1(k1)*db1(:,k1);
ds2 = ds2 + mg1(k1)*db2(:,k1);
ds3 = ds3 + mg1(k1)*db3(:,k1);
end;
for k1=1:Kb,
b(:,k1) = b(:,k1)./s;
db1(:,k1) = (db1(:,k1)-b(:,k1).*ds1)./s;
db2(:,k1) = (db2(:,k1)-b(:,k1).*ds2)./s;
db3(:,k1) = (db3(:,k1)-b(:,k1).*ds3)./s;
pp = double(buf(z).dat(:,k1));
p = p + pp.*b(:,k1);
dp1 = dp1 + pp.*(M(1,1)*db1(:,k1) + M(2,1)*db2(:,k1) + M(3,1)*db3(:,k1));
dp2 = dp2 + pp.*(M(1,2)*db1(:,k1) + M(2,2)*db2(:,k1) + M(3,2)*db3(:,k1));
dp3 = dp3 + pp.*(M(1,3)*db1(:,k1) + M(2,3)*db2(:,k1) + M(3,3)*db3(:,k1));
end;
clear x1 y1 z1 b db1 db2 db3 s ds1 ds2 ds3
tmp = zeros(d(1:2));
tmp(buf(z).msk) = dp1./p; dp1 = tmp;
tmp(buf(z).msk) = dp2./p; dp2 = tmp;
tmp(buf(z).msk) = dp3./p; dp3 = tmp;
b3 = B3warp(z,:)';
Beta = Beta - [...
kron(b3,spm_krutil(dp1,B1warp,B2warp,0))
kron(b3,spm_krutil(dp2,B1warp,B2warp,0))
kron(b3,spm_krutil(dp3,B1warp,B2warp,0))];
b3b3 = b3*b3';
A{1,1} = A{1,1} + kron(b3b3,spm_krutil(dp1.*dp1,B1warp,B2warp,1));
A{1,2} = A{1,2} + kron(b3b3,spm_krutil(dp1.*dp2,B1warp,B2warp,1));
A{1,3} = A{1,3} + kron(b3b3,spm_krutil(dp1.*dp3,B1warp,B2warp,1));
A{2,2} = A{2,2} + kron(b3b3,spm_krutil(dp2.*dp2,B1warp,B2warp,1));
A{2,3} = A{2,3} + kron(b3b3,spm_krutil(dp2.*dp3,B1warp,B2warp,1));
A{3,3} = A{3,3} + kron(b3b3,spm_krutil(dp3.*dp3,B1warp,B2warp,1));
clear b3 b3b3 tmp p dp1 dp2 dp3
end;
Alpha = [A{1,1} A{1,2} A{1,3} ; A{1,2} A{2,2} A{2,3}; A{1,3} A{2,3} A{3,3}];
clear A
for subit1 = 1:3,
if iter==1,
nTwarp = (Alpha+lmR*lam + 10*Cwarp)\((Alpha+lmR*lam)*Twarp(:) - Beta);
else
nTwarp = (Alpha+lmR*lam + Cwarp)\((Alpha+lmR*lam)*Twarp(:) - Beta);
end;
nTwarp = reshape(nTwarp,[d2 3]);
nllr = -0.5*nTwarp(:)'*Cwarp*nTwarp(:);
nll = nllr+llrb;
for z=1:length(z0),
if ~buf(z).nm, continue; end;
[x1,y1,z1] = defs(nTwarp,z,B1warp,B2warp,B3warp,x0,y0,z0,M,buf(z).msk);
sq = zeros(buf(z).nm,1) + tiny;
b = zeros(buf(z).nm,Kb);
s = zeros(buf(z).nm,1)+tiny;
for k1=1:Kb,
b(:,k1) = spm_sample_priors(b0{k1},x1,y1,z1,k1==Kb);
s = s + mg1(k1)*b(:,k1);
end;
for k1=1:Kb,
sq = sq + double(buf(z).dat(:,k1)).*b(:,k1)./s;
end;
clear b
nll = nll + sum(log(sq));
clear sq x1 y1 z1
end;
if nll<ll,
% Worse solution, so use old solution and increase regularisation
lam = lam*10;
else
% Accept new solution
ll = nll;
llr = nllr;
Twarp = nTwarp;
lam = lam*0.5;
break;
end;
end;
spm_chi2_plot('Set',ll);
if (ll-oll)<tol1*nm, break; end;
end;
if ~((ll-ooll)>tol1*nm),
finalit = 1;
break; % This can be commented out.
end;
end;
spm_chi2_plot('Clear');
results = opts;
results.image = V;
results.tpm = B;
results.Affine = Affine;
results.Twarp = Twarp;
results.Tbias = Tbias;
results.mg = mg;
results.mn = mn;
results.vr = vr;
results.thresh = 0; %thresh;
results.ll = ll;
return;
%=======================================================================
%=======================================================================
function t = transf(B1,B2,B3,T)
if ~isempty(T),
d2 = [size(T) 1];
t1 = reshape(reshape(T, d2(1)*d2(2),d2(3))*B3', d2(1), d2(2));
t = B1*t1*B2';
else
t = zeros(size(B1,1),size(B2,1));
end;
return;
%=======================================================================
%=======================================================================
function [x1,y1,z1] = defs(Twarp,z,B1,B2,B3,x0,y0,z0,M,msk)
x1a = x0 + transf(B1,B2,B3(z,:),Twarp(:,:,:,1));
y1a = y0 + transf(B1,B2,B3(z,:),Twarp(:,:,:,2));
z1a = z0(z) + transf(B1,B2,B3(z,:),Twarp(:,:,:,3));
if nargin>=10,
x1a = x1a(msk);
y1a = y1a(msk);
z1a = z1a(msk);
end;
x1 = M(1,1)*x1a + M(1,2)*y1a + M(1,3)*z1a + M(1,4);
y1 = M(2,1)*x1a + M(2,2)*y1a + M(2,3)*z1a + M(2,4);
z1 = M(3,1)*x1a + M(3,2)*y1a + M(3,3)*z1a + M(3,4);
return;
%=======================================================================
|
github
|
lcnbeapp/beapp-master
|
spm_preproc_write.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_preproc_write.m
| 8,906 |
utf_8
|
9312486f72c3a8971ab0c9e847c3a465
|
function spm_preproc_write(p,opts)
% Write out VBM preprocessed data
% FORMAT spm_preproc_write(p,opts)
% p - results from spm_prep2sn
% opts - writing options. A struct containing these fields:
% biascor - write bias corrected image
% GM - flags for which images should be written
% WM - similar to GM
% CSF - similar to GM
%____________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id$
if nargin==1,
opts = struct('biascor',0,'GM',[0 0 1],'WM',[0 0 1],'CSF',[0 0 0],'cleanup',0);
end;
if numel(p)>0,
b0 = spm_load_priors(p(1).VG);
end;
for i=1:numel(p),
preproc_apply(p(i),opts,b0);
end;
return;
%=======================================================================
%=======================================================================
function preproc_apply(p,opts,b0)
%sopts = [opts.GM ; opts.WM ; opts.CSF];
nclasses = size(fieldnames(opts),1) - 2 ;
switch nclasses
case 3
sopts = [opts.GM ; opts.WM ; opts.CSF];
case 4
sopts = [opts.GM ; opts.WM ; opts.CSF ; opts.EXTRA1];
case 5
sopts = [opts.GM ; opts.WM ; opts.CSF ; opts.EXTRA1 ; opts.EXTRA2];
otherwise
error('######## unsupported number of classes....!!!')
end
[pth,nam,ext]=fileparts(p.VF.fname);
T = p.flags.Twarp;
bsol = p.flags.Tbias;
d2 = [size(T) 1];
d = p.VF.dim(1:3);
[x1,x2,o] = ndgrid(1:d(1),1:d(2),1);
x3 = 1:d(3);
d3 = [size(bsol) 1];
B1 = spm_dctmtx(d(1),d2(1));
B2 = spm_dctmtx(d(2),d2(2));
B3 = spm_dctmtx(d(3),d2(3));
bB3 = spm_dctmtx(d(3),d3(3),x3);
bB2 = spm_dctmtx(d(2),d3(2),x2(1,:)');
bB1 = spm_dctmtx(d(1),d3(1),x1(:,1));
mg = p.flags.mg;
mn = p.flags.mn;
vr = p.flags.vr;
K = length(p.flags.mg);
Kb = length(p.flags.ngaus);
for k1=1:size(sopts,1),
%dat{k1} = zeros(d(1:3),'uint8');
dat{k1} = uint8(0);
dat{k1}(d(1),d(2),d(3)) = 0;
if sopts(k1,3),
Vt = struct('fname', fullfile(pth,['c', num2str(k1), nam, ext]),...
'dim', p.VF.dim,...
'dt', [spm_type('uint8') spm_platform('bigend')],...
'pinfo', [1/255 0 0]',...
'mat', p.VF.mat,...
'n', [1 1],...
'descrip', ['Tissue class ' num2str(k1)]);
Vt = spm_create_vol(Vt);
VO(k1) = Vt;
end;
end;
if opts.biascor,
VB = struct('fname', fullfile(pth,['m', nam, ext]),...
'dim', p.VF.dim(1:3),...
'dt', [spm_type('float32') spm_platform('bigend')],...
'pinfo', [1 0 0]',...
'mat', p.VF.mat,...
'n', [1 1],...
'descrip', 'Bias Corrected');
VB = spm_create_vol(VB);
end;
lkp = []; for k=1:Kb, lkp = [lkp ones(1,p.flags.ngaus(k))*k]; end;
spm_progress_bar('init',length(x3),['Working on ' nam],'Planes completed');
M = p.VG(1).mat\p.flags.Affine*p.VF.mat;
for z=1:length(x3),
% Bias corrected image
f = spm_sample_vol(p.VF,x1,x2,o*x3(z),0);
cr = exp(transf(bB1,bB2,bB3(z,:),bsol)).*f;
if opts.biascor,
% Write a plane of bias corrected data
VB = spm_write_plane(VB,cr,z);
end;
if any(sopts(:)),
msk = (f==0) | ~isfinite(f);
[t1,t2,t3] = defs(T,z,B1,B2,B3,x1,x2,x3,M);
q = zeros([d(1:2) Kb]);
bt = zeros([d(1:2) Kb]);
for k1=1:Kb,
bt(:,:,k1) = spm_sample_priors(b0{k1},t1,t2,t3,k1==Kb);
end;
b = zeros([d(1:2) K]);
for k=1:K,
b(:,:,k) = bt(:,:,lkp(k))*mg(k);
end;
s = sum(b,3);
for k=1:K,
p1 = exp((cr-mn(k)).^2/(-2*vr(k)))/sqrt(2*pi*vr(k)+eps);
q(:,:,lkp(k)) = q(:,:,lkp(k)) + p1.*b(:,:,k)./s;
end;
sq = sum(q,3)+eps;
sw = warning('off','MATLAB:divideByZero');
for k1=1:size(sopts,1),
tmp = q(:,:,k1);
tmp(msk) = 0;
tmp = tmp./sq;
dat{k1}(:,:,z) = uint8(round(255 * tmp));
end;
warning(sw);
end;
spm_progress_bar('set',z);
end;
spm_progress_bar('clear');
if opts.cleanup > 0,
[dat{1},dat{2},dat{3}] = clean_gwc(dat{1},dat{2},dat{3}, opts.cleanup);
end;
if any(sopts(:,3)),
for z=1:length(x3),
for k1=1:size(sopts,1),
if sopts(k1,3),
tmp = double(dat{k1}(:,:,z))/255;
spm_write_plane(VO(k1),tmp,z);
end;
end;
end;
end;
for k1=1:size(sopts,1),
if any(sopts(k1,1:2)),
so = struct('wrap',[0 0 0],'interp',1,'vox',[NaN NaN NaN],...
'bb',ones(2,3)*NaN,'preserve',0);
ovx = abs(det(p.VG(1).mat(1:3,1:3)))^(1/3);
fwhm = max(ovx./sqrt(sum(p.VF.mat(1:3,1:3).^2))-1,0.1);
dat{k1} = decimate(dat{k1},fwhm);
fn = fullfile(pth,['c', num2str(k1), nam, ext]);
dim = [size(dat{k1}) 1];
VT = struct('fname',fn,'dim',dim(1:3),...
'dt', [spm_type('uint8') spm_platform('bigend')],...
'pinfo',[1/255 0]','mat',p.VF.mat,'dat',dat{k1});
if sopts(k1,2),
spm_write_sn(VT,p,so);
end;
so.preserve = 1;
if sopts(k1,1),
VN = spm_write_sn(VT,p,so);
VN.fname = fullfile(pth,['mwc', num2str(k1), nam, ext]);
spm_write_vol(VN,VN.dat);
end;
end;
end;
return;
%=======================================================================
%=======================================================================
function [x1,y1,z1] = defs(sol,z,B1,B2,B3,x0,y0,z0,M)
x1a = x0 + transf(B1,B2,B3(z,:),sol(:,:,:,1));
y1a = y0 + transf(B1,B2,B3(z,:),sol(:,:,:,2));
z1a = z0(z) + transf(B1,B2,B3(z,:),sol(:,:,:,3));
x1 = M(1,1)*x1a + M(1,2)*y1a + M(1,3)*z1a + M(1,4);
y1 = M(2,1)*x1a + M(2,2)*y1a + M(2,3)*z1a + M(2,4);
z1 = M(3,1)*x1a + M(3,2)*y1a + M(3,3)*z1a + M(3,4);
return;
%=======================================================================
%=======================================================================
function t = transf(B1,B2,B3,T)
if ~isempty(T)
d2 = [size(T) 1];
t1 = reshape(reshape(T, d2(1)*d2(2),d2(3))*B3', d2(1), d2(2));
t = B1*t1*B2';
else
t = zeros(size(B1,1),size(B2,1),size(B3,1));
end;
return;
%=======================================================================
%=======================================================================
function dat = decimate(dat,fwhm)
% Convolve the volume in memory (fwhm in voxels).
lim = ceil(2*fwhm);
x = -lim(1):lim(1); x = spm_smoothkern(fwhm(1),x); x = x/sum(x);
y = -lim(2):lim(2); y = spm_smoothkern(fwhm(2),y); y = y/sum(y);
z = -lim(3):lim(3); z = spm_smoothkern(fwhm(3),z); z = z/sum(z);
i = (length(x) - 1)/2;
j = (length(y) - 1)/2;
k = (length(z) - 1)/2;
spm_conv_vol(dat,dat,x,y,z,-[i j k]);
return;
%=======================================================================
%=======================================================================
function [g,w,c] = clean_gwc(g,w,c, level)
if nargin<4, level = 1; end;
b = w;
b(1) = w(1);
% Build a 3x3x3 seperable smoothing kernel
%-----------------------------------------------------------------------
kx=[0.75 1 0.75];
ky=[0.75 1 0.75];
kz=[0.75 1 0.75];
sm=sum(kron(kron(kz,ky),kx))^(1/3);
kx=kx/sm; ky=ky/sm; kz=kz/sm;
th1 = 0.15;
if level==2, th1 = 0.2; end;
% Erosions and conditional dilations
%-----------------------------------------------------------------------
niter = 32;
spm_progress_bar('Init',niter,'Extracting Brain','Iterations completed');
for j=1:niter,
if j>2, th=th1; else th=0.6; end; % Dilate after two its of erosion.
for i=1:size(b,3),
gp = double(g(:,:,i));
wp = double(w(:,:,i));
bp = double(b(:,:,i))/255;
bp = (bp>th).*(wp+gp);
b(:,:,i) = uint8(round(bp));
end;
spm_conv_vol(b,b,kx,ky,kz,-[1 1 1]);
spm_progress_bar('Set',j);
end;
th = 0.05;
for i=1:size(b,3),
gp = double(g(:,:,i))/255;
wp = double(w(:,:,i))/255;
cp = double(c(:,:,i))/255;
bp = double(b(:,:,i))/255;
bp = ((bp>th).*(wp+gp))>th;
g(:,:,i) = uint8(round(255*gp.*bp./(gp+wp+cp+eps)));
w(:,:,i) = uint8(round(255*wp.*bp./(gp+wp+cp+eps)));
c(:,:,i) = uint8(round(255*(cp.*bp./(gp+wp+cp+eps)+cp.*(1-bp))));
end;
spm_progress_bar('Clear');
return;
%=======================================================================
%=======================================================================
|
github
|
lcnbeapp/beapp-master
|
spm.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm.m
| 44,832 |
utf_8
|
d2d75e50e191a0c29cf483d58a754d7f
|
function varargout=spm(varargin)
% SPM: Statistical Parametric Mapping (startup function)
%_______________________________________________________________________
% ___ ____ __ __
% / __)( _ \( \/ )
% \__ \ )___/ ) ( Statistical Parametric Mapping
% (___/(__) (_/\/\_) SPM - http://www.fil.ion.ucl.ac.uk/spm/
%_______________________________________________________________________
%
% SPM (Statistical Parametric Mapping) is a package for the analysis
% functional brain mapping experiments. It is the in-house package of
% the Wellcome Trust Centre for Neuroimaging, and is available to the
% scientific community as copyright freeware under the terms of the
% GNU General Public Licence.
%
% Theoretical, computational and other details of the package are
% available in SPM's "Help" facility. This can be launched from the
% main SPM Menu window using the "Help" button, or directly from the
% command line using the command `spm_help`.
%
% Details of this release are available via the "About SPM" help topic
% (file spm.man), accessible from the SPM splash screen. (Or type
% `spm_help spm.man` in the MATLAB command window)
%
% This spm function initialises the default parameters, and displays a
% splash screen with buttons leading to the PET, fMRI and M/EEG
% modalities. Alternatively, `spm('pet')`, `spm('fmri')`, `spm('eeg')`
% (equivalently `spm pet`, `spm fmri` and `spm eeg`) lead directly to
% the respective modality interfaces.
%
% Once the modality is chosen, (and it can be toggled mid-session) the
% SPM user interface is displayed. This provides a constant visual
% environment in which data analysis is implemented. The layout has
% been designed to be simple and at the same time show all the
% facilities that are available. The interface consists of three
% windows: A menu window with pushbuttons for the SPM routines (each
% button has a 'CallBack' string which launches the appropriate
% function/script); A blank panel used for interaction with the user;
% And a graphics figure with various editing and print facilities (see
% spm_figure.m). (These windows are 'Tag'ged 'Menu', 'Interactive', and
% 'Graphics' respectively, and should be referred to by their tags
% rather than their figure numbers.)
%
% Further interaction with the user is (mainly) via questioning in the
% 'Interactive' window (managed by spm_input), and file selection
% (managed by spm_select). See the help on spm_input.m and spm_select.m for
% details on using these functions.
%
% If a "message of the day" file named spm_motd.man exists in the SPM
% directory (alongside spm.m) then it is displayed in the Graphics
% window on startup.
%
% Arguments to this routine (spm.m) lead to various setup facilities,
% mainly of use to SPM power users and programmers. See programmers
% FORMAT & help in the main body of spm.m
%
%_______________________________________________________________________
% SPM is developed by members and collaborators of the
% Wellcome Trust Centre for Neuroimaging
%-SVN ID and authorship of this program...
%-----------------------------------------------------------------------
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Andrew Holmes
% $Id$
%=======================================================================
% - FORMAT specifications for embedded CallBack functions
%=======================================================================
%( This is a multi function function, the first argument is an action )
%( string, specifying the particular action function to take. Recall )
%( MATLAB's command-function duality: `spm Welcome` is equivalent to )
%( `spm('Welcome')`. )
%
% FORMAT spm
% Defaults to spm('Welcome')
%
% FORMAT spm('Welcome')
% Clears command window, deletes all figures, prints welcome banner and
% splash screen, sets window defaults.
%
% FORMAT spm('AsciiWelcome')
% Prints ASCII welcome banner in MATLAB command window.
%
% FORMAT spm('PET') spm('FMRI') spm('EEG')
% Closes all windows and draws new Menu, Interactive, and Graphics
% windows for an SPM session. The buttons in the Menu window launch the
% main analysis routines.
%
% FORMAT spm('ChMod',Modality)
% Changes modality of SPM: Currently SPM supports PET & MRI modalities,
% each of which have a slightly different Menu window and different
% defaults. This function switches to the specified modality, setting
% defaults and displaying the relevant buttons.
%
% FORMAT spm('defaults',Modality)
% Sets default global variables for the specified modality.
%
% FORMAT [Modality,ModNum]=spm('CheckModality',Modality)
% Checks the specified modality against those supported, returns
% upper(Modality) and the Modality number, it's position in the list of
% supported Modalities.
%
% FORMAT Fmenu = spm('CreateMenuWin',Vis)
% Creates SPM menu window, 'Tag'ged 'Menu'
% F - handle of figure created
% Vis - Visibility, 'on' or 'off'
%
% Finter = FORMAT spm('CreateIntWin',Vis)
% Creates an SPM Interactive window, 'Tag'ged 'Interactive'
% F - handle of figure created
% Vis - Visibility, 'on' or 'off'
%
% FORMAT [Finter,Fgraph,CmdLine] = spm('FnUIsetup',Iname,bGX,CmdLine)
% Robust UIsetup procedure for functions:
% Returns handles of 'Interactive' and 'Graphics' figures.
% Creates 'Interactive' figure if ~CmdLine, creates 'Graphics' figure if bGX.
% Iname - Name for 'Interactive' window
% bGX - Need a Graphics window? [default 1]
% CmdLine - CommandLine usage? [default spm('CmdLine')]
% Finter - handle of 'Interactive' figure
% Fgraph - handle of 'Graphics' figure
% CmdLine - CommandLine usage?
%
% FORMAT WS=spm('WinScale')
% Returns ratios of current display dimensions to that of a 1152 x 900
% Sun display. WS=[Xratio,Yratio,Xratio,Yratio]. Used for scaling other
% GUI elements.
% (Function duplicated in spm_figure.m, repeated to reduce inter-dependencies.)
%
% FORMAT [FS,sf] = spm('FontSize',FS)
% FORMAT [FS,sf] = spm('FontSizes',FS)
% Returns fontsizes FS scaled for the current display.
% FORMAT sf = spm('FontScale')
% Returns font scaling factor
% FS - (vector of) Font sizes to scale [default [1:36]]
% sf - font scaling factor (FS(out) = floor(FS(in)*sf)
%
% Rect = spm('WinSize',Win,raw)
% Returns sizes and positions for SPM windows.
% Win - 'Menu', 'Interactive', 'Graphics', or '0'
% - Window whose position is required. Only first character is
% examined. '0' returns size of root workspace.
% raw - If specified, then positions are for a 1152 x 900 Sun display.
% Otherwise the positions are scaled for the current display.
%
% FORMAT [c,cName] = spm('Colour')
% Returns the RGB triple and a description for the current en-vogue SPM
% colour, the background colour for the Menu and Help windows.
%
% FORMAT F = spm('FigName',Iname,F,CmdLine)
% Set name of figure F to "SPMver (User): Iname" if ~CmdLine
% Robust to absence of figure.
% Iname - Name for figure
% F (input) - Handle (or 'Tag') of figure to name [default 'Interactive']
% CmdLine - CommandLine usage? [default spm('CmdLine')]
% F (output) - Handle of figure named
%
% FORMAT Fs = spm('Show')
% Opens all SPM figure windows (with HandleVisibility) using `figure`.
% Maintains current figure.
% Fs - vector containing all HandleVisible figures (i.e. get(0,'Children'))
%
% FORMAT spm('Clear',Finter, Fgraph)
% Clears and resets SPM-GUI, clears and timestamps MATLAB command window.
% Finter - handle or 'Tag' of 'Interactive' figure [default 'Interactive']
% Fgraph - handle or 'Tag' of 'Graphics' figure [default 'Graphics']
%
% FORMAT SPMid = spm('FnBanner', Fn,FnV)
% Prints a function start banner, for version FnV of function Fn, & datestamps
% FORMAT SPMid = spm('SFnBanner',Fn,FnV)
% Prints a sub-function start banner
% FORMAT SPMid = spm('SSFnBanner',Fn,FnV)
% Prints a sub-sub-function start banner
% Fn - Function name (string)
% FnV - Function version (string)
% SPMid - ID string: [SPMver: Fn (FnV)]
%
% FORMAT SPMdir = spm('Dir',Mfile)
% Returns the directory containing the version of spm in use,
% identified as the first in MATLABPATH containing the Mfile spm (this
% file) (or Mfile if specified).
%
% FORMAT [v,r] = spm('Ver',Mfile,ReDo)
% Returns the current version (v) and release (r) of file Mfile. This
% corresponds to the Last changed Revision number extracted from the
% Subversion Id tag.
% If Mfile is absent or empty then it returns the current SPM version (v)
% and release (r), extracted from the file Contents.m in the SPM directory
% (these information are cached in a persistent variable to enable repeat
% use without recomputation).
% If Redo [default false] is true, then the cached current SPM information
% are not used but recomputed (and recached).
%
% FORMAT v = spm('MLver')
% Returns MATLAB version, truncated to major & minor revision numbers
%
% FORMAT xTB = spm('TBs')
% Identifies installed SPM toolboxes: SPM toolboxes are defined as the
% contents of sub-directories of fullfile(spm('Dir'),'toolbox') - the
% SPM toolbox installation directory. For SPM to pick a toolbox up,
% there must be a single mfile in the directory whose name ends with
% the toolbox directory name. (I.e. A toolbox called "test" would be in
% the "test" subdirectory of spm('Dir'), with a single file named
% *test.m.) This M-file is regarded as the launch file for the
% toolbox.
% xTB - structure array containing toolbox definitions
% xTB.name - name of toolbox (taken as toolbox directory name)
% xTB.prog - launch program for toolbox
% xTB.dir - toolbox directory
%
% FORMAT spm('TBlaunch',xTB,i)
% Launch a toolbox, prepending TBdir to path if necessary
% xTB - toolbox definition structure (i.e. from spm('TBs')
% xTB.name - name of toolbox
% xTB.prog - name of program to launch toolbox
% xTB.dir - toolbox directory (prepended to path if not on path)
%
% FORMAT [v1,v2,...] = spm('GetGlobal',name1,name2,...)
% Returns values of global variables (without declaring them global)
% name1, name2,... - name strings of desired globals
% a1, a2,... - corresponding values of global variables with given names
% ([] is returned as value if global variable doesn't exist)
%
% FORMAT CmdLine = spm('CmdLine',CmdLine)
% Command line SPM usage?
% CmdLine (input) - CmdLine preference
% [defaults (missing or empty) to global defaults.cmdline,]
% [if it exists, or 0 (GUI) otherwise. ]
% CmdLine (output) - true if global CmdLine if true,
% or if on a terminal with no support for graphics windows.
%
% FORMAT spm('PopUpCB',h)
% Callback handler for PopUp UI menus with multiple callbacks as cellstr UserData
%
% FORMAT str = spm('GetUser',fmt)
% Returns current users login name, extracted from the hosting environment
% fmt - format string: If USER is defined then sprintf(fmt,USER) is returned
%
% FORMAT spm('Beep')
% Plays the keyboard beep!
%
% FORMAT spm('time')
% Returns the current time and date as hh:mm dd/mm/yyyy
%
% FORMAT spm('Pointer',Pointer)
% Changes pointer on all SPM (HandleVisible) windows to type Pointer
% Pointer defaults to 'Arrow'. Robust to absence of windows
%
% FORMAT h = spm('alert',Message,Title,CmdLine,wait)
% FORMAT h = spm('alert"',Message,Title,CmdLine,wait)
% FORMAT h = spm('alert*',Message,Title,CmdLine,wait)
% FORMAT h = spm('alert!',Message,Title,CmdLine,wait)
% Displays an alert, either in a GUI msgbox, or as text in the command window.
% ( 'alert"' uses the 'help' msgbox icon, 'alert*' the )
% ( 'error' icon, 'alert!' the 'warn' icon )
% Message - string (or cellstr) containing message to print
% Title - title string for alert
% CmdLine - CmdLine preference [default spm('CmdLine')]
% - If CmdLine is complex, then a CmdLine alert is always used,
% possibly in addition to a msgbox (the latter according
% to spm('CmdLine').)
% wait - if true, waits until user dismisses GUI / confirms text alert
% [default 0] (if doing both GUI & text, waits on GUI alert)
% h - handle of msgbox created, empty if CmdLine used
%
% FORMAT spm('GUI_FileDelete')
% CallBack for GUI for file deletion, using spm_select and confirmation dialogs
%
% FORMAT spm('Clean')
% Clear all variables, globals, functions, MEX links and class definitions.
%
% FORMAT spm('Help',varargin)
% Merely a gateway to spm_help(varargin) - so you can type "spm help"
%
% FORMAT spm('Quit')
% Quit SPM, delete all windows and clear the command window.
%
%_______________________________________________________________________
%-Parameters
%-----------------------------------------------------------------------
Modalities = {'PET','FMRI','EEG'};
%-Format arguments
%-----------------------------------------------------------------------
if nargin == 0, Action = 'Welcome'; else Action = varargin{1}; end
%=======================================================================
switch lower(Action), case 'welcome' %-Welcome splash screen
%=======================================================================
% spm('Welcome')
spm_check_installation('basic');
defaults = spm('GetGlobal','defaults');
if isfield(defaults,'modality')
spm(defaults.modality);
return
end
%-Open startup window, set window defaults
%-----------------------------------------------------------------------
Fwelcome = openfig(fullfile(spm('Dir'),'spm_Welcome.fig'),'new','invisible');
set(Fwelcome,'name',sprintf('%s%s',spm('ver'),spm('GetUser',' (%s)')));
set(get(findobj(Fwelcome,'Type','axes'),'children'),'FontName',spm_platform('Font','Times'));
set(findobj(Fwelcome,'Tag','SPM_VER'),'String',spm('Ver'));
RectW = spm('WinSize','W',1); Rect0 = spm('WinSize','0',1);
set(Fwelcome,'Units','pixels', 'Position',...
[Rect0(1)+(Rect0(3)-RectW(3))/2, Rect0(2)+(Rect0(4)-RectW(4))/2, RectW(3), RectW(4)]);
set(Fwelcome,'Visible','on');
%=======================================================================
case 'asciiwelcome' %-ASCII SPM banner welcome
%=======================================================================
% spm('AsciiWelcome')
disp( ' ___ ____ __ __ ');
disp( '/ __)( _ \( \/ ) ');
disp( '\__ \ )___/ ) ( Statistical Parametric Mapping ');
disp(['(___/(__) (_/\/\_) ',spm('Ver'),' - http://www.fil.ion.ucl.ac.uk/spm/']);
fprintf('\n');
%=======================================================================
case lower(Modalities) %-Initialise SPM in PET, fMRI, EEG modality
%=======================================================================
% spm(Modality)
spm_check_installation('basic');
try, feature('JavaFigures',0); end
%-Initialisation and workspace canonicalisation
%-----------------------------------------------------------------------
local_clc;
spm('AsciiWelcome'); fprintf('\n\nInitialising SPM');
Modality = upper(Action); fprintf('.');
delete(get(0,'Children')); fprintf('.');
%-Load startup global defaults
%-----------------------------------------------------------------------
spm_defaults; fprintf('.');
%-Setup for batch system
%-----------------------------------------------------------------------
spm_jobman('initcfg');
spm_select('prevdirs',[spm('Dir') filesep]);
%-Draw SPM windows
%-----------------------------------------------------------------------
if ~spm('CmdLine')
Fmenu = spm('CreateMenuWin','off'); fprintf('.');
Finter = spm('CreateIntWin','off'); fprintf('.');
else
Fmenu = [];
Finter = [];
end
Fgraph = spm_figure('Create','Graphics','Graphics','off'); fprintf('.');
spm_figure('WaterMark',Finter,spm('Ver'),'',45); fprintf('.');
Fmotd = fullfile(spm('Dir'),'spm_motd.man');
if exist(Fmotd,'file'), spm_help('!Disp',Fmotd,'',Fgraph,spm('Ver')); end
fprintf('.');
%-Setup for current modality
%-----------------------------------------------------------------------
spm('ChMod',Modality); fprintf('.');
%-Reveal windows
%-----------------------------------------------------------------------
set([Fmenu,Finter,Fgraph],'Visible','on'); fprintf('done\n\n');
%-Print present working directory
%-----------------------------------------------------------------------
fprintf('SPM present working directory:\n\t%s\n',pwd)
%=======================================================================
case 'chmod' %-Change SPM modality PET<->fMRI<->EEG
%=======================================================================
% spm('ChMod',Modality)
%-----------------------------------------------------------------------
%-Sort out arguments
%-----------------------------------------------------------------------
if nargin<2, Modality = ''; else Modality = varargin{2}; end
[Modality,ModNum] = spm('CheckModality',Modality);
%-Sort out global defaults
%-----------------------------------------------------------------------
spm('defaults',Modality);
%-Sort out visability of appropriate controls on Menu window
%-----------------------------------------------------------------------
Fmenu = spm_figure('FindWin','Menu');
if ~isempty(Fmenu)
if strcmpi(Modality,'PET')
set(findobj(Fmenu, 'Tag', 'FMRI'), 'Visible', 'off');
set(findobj(Fmenu, 'Tag', 'EEG'), 'Visible', 'off');
set(findobj(Fmenu, 'Tag', 'PETFMRI'), 'Visible', 'on' );
set(findobj(Fmenu, 'Tag', 'PET'), 'Visible', 'on' );
elseif strcmpi(Modality,'FMRI')
set(findobj(Fmenu, 'Tag', 'EEG'), 'Visible', 'off');
set(findobj(Fmenu, 'Tag', 'PET'), 'Visible', 'off');
set(findobj(Fmenu, 'Tag', 'PETFMRI'), 'Visible', 'on' );
set(findobj(Fmenu, 'Tag', 'FMRI'), 'Visible', 'on' );
else
set(findobj(Fmenu, 'Tag', 'PETFMRI'), 'Visible', 'off');
set(findobj(Fmenu, 'Tag', 'PET'), 'Visible', 'off');
set(findobj(Fmenu, 'Tag', 'FMRI'), 'Visible', 'off');
set(findobj(Fmenu, 'Tag', 'EEG'), 'Visible', 'on' );
end
set(findobj(Fmenu,'Tag','Modality'),'Value',ModNum,'UserData',ModNum);
else
warning('SPM Menu window not found');
end
%=======================================================================
case 'defaults' %-Set SPM defaults (as global variable)
%=======================================================================
% spm('defaults',Modality)
%-----------------------------------------------------------------------
if nargin<2, Modality=''; else Modality=varargin{2}; end
Modality = spm('CheckModality',Modality);
%-Re-initialise, load defaults (from spm_defaults.m) and store modality
%-----------------------------------------------------------------------
clear global defaults
spm_get_defaults('modality',Modality);
%-Addpath modality-specific toolboxes
%-----------------------------------------------------------------------
if strcmpi(Modality,'EEG') && ~isdeployed
addpath(fullfile(spm('Dir'),'external','fieldtrip'));
ft_defaults;
addpath(fullfile(spm('Dir'),'external','bemcp'));
addpath(fullfile(spm('Dir'),'external','ctf'));
addpath(fullfile(spm('Dir'),'external','eeprobe'));
addpath(fullfile(spm('Dir'),'toolbox', 'dcm_meeg'));
addpath(fullfile(spm('Dir'),'toolbox', 'spectral'));
addpath(fullfile(spm('Dir'),'toolbox', 'Neural_Models'));
addpath(fullfile(spm('Dir'),'toolbox', 'Beamforming'));
addpath(fullfile(spm('Dir'),'toolbox', 'MEEGtools'));
end
%-Return defaults variable if asked
%-----------------------------------------------------------------------
if nargout, varargout = {spm_get_defaults}; end
%=======================================================================
case 'checkmodality' %-Check & canonicalise modality string
%=======================================================================
% [Modality,ModNum] = spm('CheckModality',Modality)
%-----------------------------------------------------------------------
if nargin<2, Modality=''; else Modality=upper(varargin{2}); end
if isempty(Modality)
try
Modality = spm_get_defaults('modality');
end
end
if ischar(Modality)
ModNum = find(ismember(Modalities,Modality));
else
if ~any(Modality == 1:length(Modalities))
Modality = 'ERROR';
ModNum = [];
else
ModNum = Modality;
Modality = Modalities{ModNum};
end
end
if isempty(ModNum)
if isempty(Modality)
fprintf('Modality is not set: use spm(''defaults'',''MOD''); ');
fprintf('where MOD is one of PET, FMRI, EEG.\n');
end
error('Unknown Modality.');
end
varargout = {upper(Modality),ModNum};
%=======================================================================
case 'createmenuwin' %-Create SPM menu window
%=======================================================================
% Fmenu = spm('CreateMenuWin',Vis)
%-----------------------------------------------------------------------
if nargin<2, Vis='on'; else Vis=varargin{2}; end
%-Close any existing 'Menu' 'Tag'ged windows
%-----------------------------------------------------------------------
delete(spm_figure('FindWin','Menu'))
Fmenu = openfig(fullfile(spm('Dir'),'spm_Menu.fig'),'new','invisible');
set(Fmenu,'name',sprintf('%s%s: Menu',spm('ver'),spm('GetUser',' (%s)')));
S0 = spm('WinSize','0',1);
SM = spm('WinSize','M');
set(Fmenu,'Units','pixels', 'Position',[S0(1) S0(2) 0 0] + SM);
%-Set SPM colour
%-----------------------------------------------------------------------
set(findobj(Fmenu,'Tag', 'frame'),'backgroundColor',spm('colour'));
try
if ismac
b = findobj(Fmenu,'Style','pushbutton');
set(b,'backgroundColor',get(b(1),'backgroundColor')+0.002);
end
end
%-Set toolbox
%-----------------------------------------------------------------------
xTB = spm('tbs');
if ~isempty(xTB)
set(findobj(Fmenu,'Tag', 'Toolbox'),'String',{'Toolbox:' xTB.name });
set(findobj(Fmenu,'Tag', 'Toolbox'),'UserData',xTB);
else
set(findobj(Fmenu,'Tag', 'Toolbox'),'Visible','off')
end
set(Fmenu,'Visible',Vis);
varargout = {Fmenu};
%=======================================================================
case 'createintwin' %-Create SPM interactive window
%=======================================================================
% Finter = spm('CreateIntWin',Vis)
%-----------------------------------------------------------------------
if nargin<2, Vis='on'; else Vis=varargin{2}; end
%-Close any existing 'Interactive' 'Tag'ged windows
%-----------------------------------------------------------------------
delete(spm_figure('FindWin','Interactive'))
Finter = openfig(fullfile(spm('Dir'),'spm_Interactive.fig'),'new','invisible');
set(Finter,'name',spm('Ver'));
S0 = spm('WinSize','0',1);
SI = spm('WinSize','I');
set(Finter,'Units','pixels', 'Position',[S0(1) S0(2) 0 0] + SI);
set(Finter,'Visible',Vis);
varargout = {Finter};
%=======================================================================
case 'fnuisetup' %-Robust UI setup for main SPM functions
%=======================================================================
% [Finter,Fgraph,CmdLine] = spm('FnUIsetup',Iname,bGX,CmdLine)
%-----------------------------------------------------------------------
if nargin<4, CmdLine=spm('CmdLine'); else CmdLine=varargin{4}; end
if nargin<3, bGX=1; else bGX=varargin{3}; end
if nargin<2, Iname=''; else Iname=varargin{2}; end
if CmdLine
Finter = spm_figure('FindWin','Interactive');
if ~isempty(Finter), spm_figure('Clear',Finter), end
%if ~isempty(Iname), fprintf('%s:\n',Iname), end
else
Finter = spm_figure('GetWin','Interactive');
spm_figure('Clear',Finter)
if ~isempty(Iname)
str = sprintf('%s (%s): %s',spm('ver'),spm('GetUser'),Iname);
else
str = '';
end
set(Finter,'Name',str)
end
if bGX
Fgraph = spm_figure('GetWin','Graphics');
spm_figure('Clear',Fgraph)
else
Fgraph = spm_figure('FindWin','Graphics');
end
varargout = {Finter,Fgraph,CmdLine};
%=======================================================================
case 'winscale' %-Window scale factors (to fit display)
%=======================================================================
% WS = spm('WinScale')
%-----------------------------------------------------------------------
S0 = spm('WinSize','0',1);
if all(ismember(S0(:),[0 1]))
varargout = {[1 1 1 1]};
return;
end
tmp = [S0(3)/1152 (S0(4)-50)/900];
varargout = {min(tmp)*[1 1 1 1]};
% Make sure that aspect ratio is about right - for funny shaped screens
% varargout = {[S0(3)/1152 (S0(4)-50)/900 S0(3)/1152 (S0(4)-50)/900]};
%=======================================================================
case {'fontsize','fontsizes','fontscale'} %-Font scaling
%=======================================================================
% [FS,sf] = spm('FontSize',FS)
% [FS,sf] = spm('FontSizes',FS)
% sf = spm('FontScale')
%-----------------------------------------------------------------------
if nargin<2, FS=1:36; else FS=varargin{2}; end
offset = 1;
%try, if ismac, offset = 1.4; end; end
sf = offset + 0.85*(min(spm('WinScale'))-1);
if strcmpi(Action,'fontscale')
varargout = {sf};
else
varargout = {ceil(FS*sf),sf};
end
%=======================================================================
case 'winsize' %-Standard SPM window locations and sizes
%=======================================================================
% Rect = spm('WinSize',Win,raw)
%-----------------------------------------------------------------------
if nargin<3, raw=0; else raw=1; end
if nargin<2, Win=''; else Win=varargin{2}; end
Rect = [[108 466 400 445];...
[108 045 400 395];...
[515 015 600 865];...
[326 310 500 280]];
if isempty(Win)
%-All windows
elseif upper(Win(1))=='M'
%-Menu window
Rect = Rect(1,:);
elseif upper(Win(1))=='I'
%-Interactive window
Rect = Rect(2,:);
elseif upper(Win(1))=='G'
%-Graphics window
Rect = Rect(3,:);
elseif upper(Win(1))=='W'
%-Welcome window
Rect = Rect(4,:);
elseif Win(1)=='0'
%-Root workspace
Rect = get(0, 'MonitorPosition');
if all(ismember(Rect(:),[0 1]))
warning('SPM:noDisplay','Unable to open display.');
end
if size(Rect,1) > 1 % Multiple Monitors
%-Use Monitor containing the Pointer
pl = get(0,'PointerLocation');
Rect(:,[3 4]) = Rect(:,[3 4]) + Rect(:,[1 2]);
w = find(pl(1)>=Rect(:,1) & pl(1)<=Rect(:,3) &...
pl(2)>=Rect(:,2) & pl(2)<=Rect(:,4));
if numel(w)~=1, w = 1; end
Rect = Rect(w,:);
%-Make sure that the format is [x y width height]
Rect(1,[3 4]) = Rect(1,[3 4]) - Rect(1,[1 2]) + 1;
end
else
error('Unknown Win type');
end
if ~raw
WS = repmat(spm('WinScale'),size(Rect,1),1);
Rect = Rect.*WS;
end
varargout = {Rect};
%=======================================================================
case 'colour' %-SPM interface colour
%=======================================================================
% spm('Colour')
%-----------------------------------------------------------------------
%-Pre-developmental livery
% varargout = {[1.0,0.2,0.3],'fightening red'};
%-Developmental livery
% varargout = {[0.7,1.0,0.7],'flourescent green'};
%-Alpha release livery
% varargout = {[0.9,0.9,0.5],'over-ripe banana'};
%-Beta release livery
% varargout = {[0.9 0.8 0.9],'blackcurrant purple'};
%-Distribution livery
varargout = {[0.8 0.8 1.0],'vile violet'};
try
varargout = {spm_get_defaults('ui.colour'),'bluish'};
end
%=======================================================================
case 'figname' %-Robust SPM figure naming
%=======================================================================
% F = spm('FigName',Iname,F,CmdLine)
%-----------------------------------------------------------------------
if nargin<4, CmdLine=spm('CmdLine'); else CmdLine=varargin{4}; end
if nargin<3, F='Interactive'; else F=varargin{3}; end
if nargin<2, Iname=''; else Iname=varargin{2}; end
%if ~isempty(Iname), fprintf('\t%s\n',Iname), end
if CmdLine, varargout={[]}; return, end
F = spm_figure('FindWin',F);
if ~isempty(F) && ~isempty(Iname)
set(F,'Name',sprintf('%s (%s): %s',spm('ver'),spm('GetUser'),Iname))
end
varargout={F};
%=======================================================================
case 'show' %-Bring visible MATLAB windows to the fore
%=======================================================================
% Fs = spm('Show')
%-----------------------------------------------------------------------
cF = get(0,'CurrentFigure');
Fs = get(0,'Children');
Fs = findobj(Fs,'flat','Visible','on');
for F=Fs', figure(F), end
set(0,'CurrentFigure',cF)
spm('FnBanner','GUI show');
varargout={Fs};
%=======================================================================
case 'clear' %-Clear SPM GUI
%=======================================================================
% spm('Clear',Finter, Fgraph)
%-----------------------------------------------------------------------
if nargin<3, Fgraph='Graphics'; else Fgraph=varargin{3}; end
if nargin<2, Finter='Interactive'; else Finter=varargin{2}; end
spm_figure('Clear',Fgraph)
spm_figure('Clear',Finter)
spm('Pointer','Arrow')
spm_conman('Initialise','reset');
local_clc;
fprintf('\n');
%evalin('base','clear')
%=======================================================================
case {'fnbanner','sfnbanner','ssfnbanner'} %-Text banners for functions
%=======================================================================
% SPMid = spm('FnBanner', Fn,FnV)
% SPMid = spm('SFnBanner',Fn,FnV)
% SPMid = spm('SSFnBanner',Fn,FnV)
%-----------------------------------------------------------------------
time = spm('time');
str = spm('ver');
if nargin>=2, str = [str,': ',varargin{2}]; end
if nargin>=3
v = regexp(varargin{3},'\$Rev: (\d*) \$','tokens','once');
if ~isempty(v)
str = [str,' (v',v{1},')'];
else
str = [str,' (v',varargin{3},')'];
end
end
switch lower(Action)
case 'fnbanner'
tab = '';
wid = 72;
lch = '=';
case 'sfnbanner'
tab = sprintf('\t');
wid = 72-8;
lch = '-';
case 'ssfnbanner'
tab = sprintf('\t\t');
wid = 72-2*8;
lch = '-';
end
fprintf('\n%s%s',tab,str)
fprintf('%c',repmat(' ',1,wid-length([str,time])))
fprintf('%s\n%s',time,tab)
fprintf('%c',repmat(lch,1,wid)),fprintf('\n')
varargout = {str};
%=======================================================================
case 'dir' %-Identify specific (SPM) directory
%=======================================================================
% spm('Dir',Mfile)
%-----------------------------------------------------------------------
if nargin<2, Mfile='spm'; else Mfile=varargin{2}; end
SPMdir = which(Mfile);
if isempty(SPMdir) %-Not found or full pathname given
if exist(Mfile,'file')==2 %-Full pathname
SPMdir = Mfile;
else
error(['Can''t find ',Mfile,' on MATLABPATH']);
end
end
SPMdir = fileparts(SPMdir);
% if isdeployed
% ind = findstr(SPMdir,'_mcr')-1;
% if ~isempty(ind)
% % MATLAB 2008a/2009a doesn't need this
% SPMdir = fileparts(SPMdir(1:ind(1)));
% end
% end
varargout = {SPMdir};
%=======================================================================
case 'ver' %-SPM version
%=======================================================================
% [SPMver, SPMrel] = spm('Ver',Mfile,ReDo)
%-----------------------------------------------------------------------
if nargin > 3, warning('This usage of "spm ver" is now deprecated.'); end
if nargin ~= 3, ReDo = false; else ReDo = logical(varargin{3}); end
if nargin == 1 || (nargin > 1 && isempty(varargin{2}))
Mfile = '';
else
Mfile = which(varargin{2});
if isempty(Mfile)
error('Can''t find %s on MATLABPATH.',varargin{2});
end
end
v = spm_version(ReDo);
if isempty(Mfile)
varargout = {v.Release v.Version};
else
unknown = struct('file',Mfile,'id','???','date','','author','');
if ~isdeployed
fp = fopen(Mfile,'rt');
if fp == -1, error('Can''t read %s.',Mfile); end
str = fread(fp,Inf,'*uchar');
fclose(fp);
str = char(str(:)');
r = regexp(str,['\$Id: (?<file>\S+) (?<id>[0-9]+) (?<date>\S+) ' ...
'(\S+Z) (?<author>\S+) \$'],'names','once');
if isempty(r), r = unknown; end
else
r = unknown;
end
varargout = {r(1).id v.Release};
end
%=======================================================================
case 'mlver' %-MATLAB major & point version number
%=======================================================================
% v = spm('MLver')
%-----------------------------------------------------------------------
v = version; tmp = find(v=='.');
if length(tmp)>1, varargout={v(1:tmp(2)-1)}; end
%=======================================================================
case 'tbs' %-Identify installed toolboxes
%=======================================================================
% xTB = spm('TBs')
%-----------------------------------------------------------------------
% Toolbox directory
%-----------------------------------------------------------------------
Tdir = fullfile(spm('Dir'),'toolbox');
%-List of potential installed toolboxes directories
%-----------------------------------------------------------------------
if exist(Tdir,'dir')
d = dir(Tdir);
d = {d([d.isdir]).name};
d = {d{cellfun('isempty',regexp(d,'^\.'))}};
else
d = {};
end
%-Look for a "main" M-file in each potential directory
%-----------------------------------------------------------------------
xTB = [];
for i = 1:length(d)
tdir = fullfile(Tdir,d{i});
fn = cellstr(spm_select('List',tdir,['^.*' d{i} '\.m$']));
if ~isempty(fn{1}),
xTB(end+1).name = strrep(d{i},'_','');
xTB(end).prog = spm_str_manip(fn{1},'r');
xTB(end).dir = tdir;
end
end
varargout{1} = xTB;
%=======================================================================
case 'tblaunch' %-Launch an SPM toolbox
%=======================================================================
% xTB = spm('TBlaunch',xTB,i)
%-----------------------------------------------------------------------
if nargin < 3, i = 1; else i = varargin{3}; end
if nargin < 2, xTB = spm('TBs'); else xTB = varargin{2}; end
if i > 0
%-Addpath (& report)
%-------------------------------------------------------------------
if isempty(findstr(xTB(i).dir,path))
if ~isdeployed, addpath(xTB(i).dir,'-begin'); end
spm('alert"',{'Toolbox directory prepended to Matlab path:',...
xTB(i).dir},...
[xTB(i).name,' toolbox'],1);
end
%-Launch
%-------------------------------------------------------------------
evalin('base',xTB(i).prog);
end
%=======================================================================
case 'getglobal' %-Get global variable cleanly
%=======================================================================
% varargout = spm('GetGlobal',varargin)
%-----------------------------------------------------------------------
wg = who('global');
for i=1:nargin-1
if any(strcmp(wg,varargin{i+1}))
eval(['global ',varargin{i+1},', tmp=',varargin{i+1},';'])
varargout{i} = tmp;
else
varargout{i} = [];
end
end
%=======================================================================
case {'cmdline'} %-SPM command line mode?
%=======================================================================
% CmdLine = spm('CmdLine',CmdLine)
%-----------------------------------------------------------------------
if nargin<2, CmdLine=[]; else CmdLine=varargin{2}; end
if isempty(CmdLine)
defaults = spm('getglobal','defaults');
if isfield(defaults,'cmdline')
CmdLine = defaults.cmdline;
else
CmdLine = 0;
end
end
varargout = {CmdLine || (get(0,'ScreenDepth')==0)};
%=======================================================================
case 'popupcb' %-Callback handling utility for PopUp menus
%=======================================================================
% spm('PopUpCB',h)
%-----------------------------------------------------------------------
if nargin<2, h=gcbo; else h=varargin{2}; end
v = get(h,'Value');
if v==1, return, end
set(h,'Value',1)
CBs = get(h,'UserData');
evalin('base',CBs{v-1})
%=======================================================================
case 'getuser' %-Get user name
%=======================================================================
% str = spm('GetUser',fmt)
%-----------------------------------------------------------------------
str = spm_platform('user');
if ~isempty(str) && nargin>1, str = sprintf(varargin{2},str); end
varargout = {str};
%=======================================================================
case 'beep' %-Produce beep sound
%=======================================================================
% spm('Beep')
%-----------------------------------------------------------------------
beep;
%=======================================================================
case 'time' %-Return formatted date/time string
%=======================================================================
% [timestr, date_vec] = spm('Time')
%-----------------------------------------------------------------------
tmp = clock;
varargout = {sprintf('%02d:%02d:%02d - %02d/%02d/%4d',...
tmp(4),tmp(5),floor(tmp(6)),tmp(3),tmp(2),tmp(1)), tmp};
%=======================================================================
case 'memory'
%=======================================================================
% m = spm('Memory')
%-----------------------------------------------------------------------
maxmemdef = 200*1024*1024;
m = maxmemdef;
varargout = {m};
%=======================================================================
case 'pointer' %-Set mouse pointer in all MATLAB windows
%=======================================================================
% spm('Pointer',Pointer)
%-----------------------------------------------------------------------
if nargin<2, Pointer='Arrow'; else Pointer=varargin{2}; end
set(get(0,'Children'),'Pointer',Pointer)
%=======================================================================
case {'alert','alert"','alert*','alert!'} %-Alert dialogs
%=======================================================================
% h = spm('alert',Message,Title,CmdLine,wait)
%-----------------------------------------------------------------------
%- Globals
%-----------------------------------------------------------------------
if nargin<5, wait = 0; else wait = varargin{5}; end
if nargin<4, CmdLine = []; else CmdLine = varargin{4}; end
if nargin<3, Title = ''; else Title = varargin{3}; end
if nargin<2, Message = ''; else Message = varargin{2}; end
Message = cellstr(Message);
if isreal(CmdLine)
CmdLine = spm('CmdLine',CmdLine);
CmdLine2 = 0;
else
CmdLine = spm('CmdLine');
CmdLine2 = 1;
end
timestr = spm('Time');
SPMv = spm('ver');
switch(lower(Action))
case 'alert', icon = 'none'; str = '--- ';
case 'alert"', icon = 'help'; str = '~ - ';
case 'alert*', icon = 'error'; str = '* - ';
case 'alert!', icon = 'warn'; str = '! - ';
end
if CmdLine || CmdLine2
Message(strcmp(Message,'')) = {' '};
tmp = sprintf('%s: %s',SPMv,Title);
fprintf('\n %s%s %s\n\n',str,tmp,repmat('-',1,62-length(tmp)))
fprintf(' %s\n',Message{:})
fprintf('\n %s %s\n\n',repmat('-',1,62-length(timestr)),timestr)
h = [];
end
if ~CmdLine
tmp = max(size(char(Message),2),42) - length(SPMv) - length(timestr);
str = sprintf('%s %s %s',SPMv,repmat(' ',1,tmp-4),timestr);
h = msgbox([{''};Message(:);{''};{''};{str}],...
sprintf('%s%s: %s',SPMv,spm('GetUser',' (%s)'),Title),...
icon,'non-modal');
drawnow
set(h,'windowstyle','modal');
end
if wait
if isempty(h)
input(' press ENTER to continue...');
else
uiwait(h)
h = [];
end
end
if nargout, varargout = {h}; end
%=======================================================================
case 'gui_filedelete' %-GUI file deletion
%=======================================================================
% spm('GUI_FileDelete')
%-----------------------------------------------------------------------
[P, sts] = spm_select(Inf,'.*','Select file(s) to delete');
if ~sts, return; end
P = cellstr(P);
n = numel(P);
if n==0 || (n==1 && isempty(P{1}))
spm('alert"','Nothing selected to delete!','file delete',0);
return
elseif n<4
str=[{' '};P];
elseif n<11
str=[{' '};P;{' ';sprintf('(%d files)',n)}];
else
str=[{' '};P(1:min(n,10));{'...';' ';sprintf('(%d files)',n)}];
end
if spm_input(str,-1,'bd','delete|cancel',[1,0],[],'confirm file delete')
feval(@spm_unlink,P{:});
spm('alert"',P,'file delete',1);
end
%=======================================================================
case 'clean' %-Clean MATLAB workspace
%=======================================================================
% spm('Clean')
%-----------------------------------------------------------------------
evalin('base','clear all');
evalc('clear classes');
%=======================================================================
case 'help' %-Pass through for spm_help
%=======================================================================
% spm('Help',varargin)
%-----------------------------------------------------------------------
if nargin>1, spm_help(varargin{2:end}), else spm_help, end
%=======================================================================
case 'quit' %-Quit SPM and clean up
%=======================================================================
% spm('Quit')
%-----------------------------------------------------------------------
delete(get(0,'Children'));
local_clc;
fprintf('Bye for now...\n\n');
%=======================================================================
otherwise %-Unknown action string
%=======================================================================
error('Unknown action string');
%=======================================================================
end
%=======================================================================
function local_clc %-Clear command window
%=======================================================================
if ~isdeployed
clc;
end
%=======================================================================
function v = spm_version(ReDo) %-Retrieve SPM version
%=======================================================================
persistent SPM_VER;
v = SPM_VER;
if isempty(SPM_VER) || (nargin > 0 && ReDo)
v = struct('Name','','Version','','Release','','Date','');
try
fid = fopen(fullfile(spm('Dir'),'Contents.m'),'rt');
if fid == -1, error(str); end
l1 = fgetl(fid); l2 = fgetl(fid);
fclose(fid);
l1 = strtrim(l1(2:end)); l2 = strtrim(l2(2:end));
t = textscan(l2,'%s','delimiter',' '); t = t{1};
v.Name = l1; v.Date = t{4};
v.Version = t{2}; v.Release = t{3}(2:end-1);
catch
if isdeployed
% in deployed mode, M-files are encrypted
% (but first two lines of Contents.m should be preserved)
v.Name = 'Statistical Parametric Mapping';
v.Version = '8';
v.Release = 'SPM8';
v.Date = date;
else
error('Can''t obtain SPM Revision information.');
end
end
SPM_VER = v;
end
|
github
|
lcnbeapp/beapp-master
|
spm_orthviews.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_orthviews.m
| 77,288 |
utf_8
|
8878b323c3d77a20da9a6c983c6cb96a
|
function varargout = spm_orthviews(action,varargin)
% Display Orthogonal Views of a Normalized Image
% FORMAT H = spm_orthviews('Image',filename[,position])
% filename - name of image to display
% area - position of image
% - area(1) - position x
% - area(2) - position y
% - area(3) - size x
% - area(4) - size y
% H - handle for ortho sections
% FORMAT spm_orthviews('BB',bb)
% bb - bounding box
% [loX loY loZ
% hiX hiY hiZ]
%
% FORMAT spm_orthviews('Redraw')
% Redraws the images
%
% FORMAT spm_orthviews('Reposition',centre)
% centre - X, Y & Z coordinates of centre voxel
%
% FORMAT spm_orthviews('Space'[,handle[,M,dim]])
% handle - the view to define the space by, optionally with extra
% transformation matrix and dimensions (e.g. one of the blobs
% of a view)
% with no arguments - puts things into mm space
%
% FORMAT spm_orthviews('MaxBB')
% sets the bounding box big enough display the whole of all images
%
% FORMAT spm_orthviews('Resolution',res)
% res - resolution (mm)
%
% FORMAT spm_orthviews('Delete', handle)
% handle - image number to delete
%
% FORMAT spm_orthviews('Reset')
% clears the orthogonal views
%
% FORMAT spm_orthviews('Pos')
% returns the co-ordinate of the crosshairs in millimetres in the
% standard space.
%
% FORMAT spm_orthviews('Pos', i)
% returns the voxel co-ordinate of the crosshairs in the image in the
% ith orthogonal section.
%
% FORMAT spm_orthviews('Xhairs','off') OR spm_orthviews('Xhairs')
% disables the cross-hairs on the display.
%
% FORMAT spm_orthviews('Xhairs','on')
% enables the cross-hairs.
%
% FORMAT spm_orthviews('Interp',hld)
% sets the hold value to hld (see spm_slice_vol).
%
% FORMAT spm_orthviews('AddBlobs',handle,XYZ,Z,mat)
% Adds blobs from a pointlist to the image specified by the handle(s).
% handle - image number to add blobs to
% XYZ - blob voxel locations
% Z - blob voxel intensities
% mat - matrix from voxels to millimeters of blob.
% name - a name for this blob
% This method only adds one set of blobs, and displays them using a
% split colour table.
%
% FORMAT spm_orthviews('AddColouredBlobs',handle,XYZ,Z,mat,colour,name)
% Adds blobs from a pointlist to the image specified by the handle(s).
% handle - image number to add blobs to
% XYZ - blob voxel locations
% Z - blob voxel intensities
% mat - matrix from voxels to millimeters of blob.
% colour - the 3 vector containing the colour that the blobs should be
% name - a name for this blob
% Several sets of blobs can be added in this way, and it uses full colour.
% Although it may not be particularly attractive on the screen, the colour
% blobs print well.
%
% FORMAT spm_orthviews('AddColourBar',handle,blobno)
% Adds colourbar for a specified blob set
% handle - image number
% blobno - blob number
%
% FORMAT spm_orthviews('RemoveBlobs',handle)
% Removes all blobs from the image specified by the handle(s).
%
% FORMAT spm_orthviews('Register',hReg)
% hReg - Handle of HandleGraphics object to build registry in.
% See spm_XYZreg for more information.
%
% spm_orthviews('AddContext',handle)
% handle - image number to add context menu to
%
% spm_orthviews('RemoveContext',handle)
% handle - image number to remove context menu from
%
% CONTEXT MENU
% spm_orthviews offers many of its features in a context menu, which is
% accessible via the right mouse button in each displayed image.
%
% PLUGINS
% The display capabilities of spm_orthviews can be extended with
% plugins. These are located in the spm_orthviews subdirectory of the SPM
% distribution. Currently there are 3 plugins available:
% quiver Add Quiver plots to a displayed image
% quiver3d Add 3D Quiver plots to a displayed image
% roi ROI creation and modification
% The functionality of plugins can be accessed via calls to
% spm_orthviews('plugin_name', plugin_arguments). For detailed descriptions
% of each plugin see help spm_orthviews/spm_ov_'plugin_name'.
%
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner, Matthew Brett, Tom Nichols and Volkmar Glauche
% $Id$
% The basic fields of st are:
% n - the number of images currently being displayed
% vols - a cell array containing the data on each of the
% displayed images.
% Space - a mapping between the displayed images and the
% mm space of each image.
% bb - the bounding box of the displayed images.
% centre - the current centre of the orthogonal views
% callback - a callback to be evaluated on a button-click.
% xhairs - crosshairs off/on
% hld - the interpolation method
% fig - the figure that everything is displayed in
% mode - the position/orientation of the sagittal view.
% - currently always 1
%
% st.registry.hReg \_ See spm_XYZreg for documentation
% st.registry.hMe /
%
% For each of the displayed images, there is a non-empty entry in the
% vols cell array. Handles returned by "spm_orthviews('Image',.....)"
% indicate the position in the cell array of the newly created ortho-view.
% Operations on each ortho-view require the handle to be passed.
%
% When a new image is displayed, the cell entry contains the information
% returned by spm_vol (type help spm_vol for more info). In addition,
% there are a few other fields, some of which I will document here:
%
% premul - a matrix to premultiply the .mat field by. Useful
% for re-orienting images.
% window - either 'auto' or an intensity range to display the
% image with.
% mapping- Mapping of image intensities to grey values. Currently
% one of 'linear', 'histeq', loghisteq',
% 'quadhisteq'. Default is 'linear'.
% Histogram equalisation depends on the image toolbox
% and is only available if there is a license available
% for it.
% ax - a cell array containing an element for the three
% views. The fields of each element are handles for
% the axis, image and crosshairs.
%
% blobs - optional. Is there for using to superimpose blobs.
% vol - 3D array of image data
% mat - a mapping from vox-to-mm (see spm_vol, or
% help on image formats).
% max - maximum intensity for scaling to. If it
% does not exist, then images are auto-scaled.
%
% There are two colouring modes: full colour, and split
% colour. When using full colour, there should be a
% 'colour' field for each cell element. When using
% split colourscale, there is a handle for the colorbar
% axis.
%
% colour - if it exists it contains the
% red,green,blue that the blobs should be
% displayed in.
% cbar - handle for colorbar (for split colourscale).
%
% PLUGINS
% The plugin concept has been developed to extend the display capabilities
% of spm_orthviews without the need to rewrite parts of it. Interaction
% between spm_orthviews and plugins takes place
% a) at startup: The subfunction 'reset_st' looks for folders
% 'spm_orthviews' in spm('Dir') and each toolbox
% folder. Files with a name spm_ov_PLUGINNAME.m in any of
% these folders will be treated as plugins.
% For each such file, PLUGINNAME will be added to the list
% st.plugins{:}.
% The subfunction 'add_context' calls each plugin with
% feval(['spm_ov_', st.plugins{k}], ...
% 'context_menu', i, parent_menu)
% Each plugin may add its own submenu to the context
% menu.
% b) at redraw: After images and blobs of st.vols{i} are drawn, the
% struct st.vols{i} is checked for field names that occur in
% the plugin list st.plugins{:}. For each matching entry, the
% corresponding plugin is called with the command 'redraw':
% feval(['spm_ov_', st.plugins{k}], ...
% 'redraw', i, TM0, TD, CM0, CD, SM0, SD);
% The values of TM0, TD, CM0, CD, SM0, SD are defined in the
% same way as in the redraw subfunction of spm_orthviews.
% It is up to the plugin to do all necessary redraw
% operations for its display contents. Each displayed item
% must have set its property 'HitTest' to 'off' to let events
% go through to the underlying axis, which is responsible for
% callback handling. The order in which plugins are called is
% undefined.
global st;
if isempty(st), reset_st; end;
spm('Pointer','watch');
if nargin == 0, action = ''; end;
action = lower(action);
switch lower(action),
case 'image',
H = specify_image(varargin{1});
if ~isempty(H)
st.vols{H}.area = [0 0 1 1];
if numel(varargin)>=2, st.vols{H}.area = varargin{2}; end;
if isempty(st.bb), st.bb = maxbb; end;
bbox;
cm_pos;
end;
varargout{1} = H;
st.centre = mean(maxbb);
redraw_all
case 'bb',
if ~isempty(varargin) && all(size(varargin{1})==[2 3]), st.bb = varargin{1}; end;
bbox;
redraw_all;
case 'redraw',
redraw_all;
eval(st.callback);
if isfield(st,'registry'),
spm_XYZreg('SetCoords',st.centre,st.registry.hReg,st.registry.hMe);
end;
case 'reposition',
if isempty(varargin), tmp = findcent;
else tmp = varargin{1}; end;
if numel(tmp) == 3
h = valid_handles(st.snap);
if ~isempty(h)
tmp = st.vols{h(1)}.mat * ...
round(st.vols{h(1)}.mat\[tmp(:); 1]);
end
st.centre = tmp(1:3);
end
redraw_all;
eval(st.callback);
if isfield(st,'registry'),
spm_XYZreg('SetCoords',st.centre,st.registry.hReg,st.registry.hMe);
end
cm_pos;
case 'setcoords',
st.centre = varargin{1};
st.centre = st.centre(:);
redraw_all;
eval(st.callback);
cm_pos;
case 'space',
if numel(varargin)<1,
st.Space = eye(4);
st.bb = maxbb;
bbox;
redraw_all;
else
space(varargin{:});
bbox;
redraw_all;
end;
case 'maxbb',
st.bb = maxbb;
bbox;
redraw_all;
case 'resolution',
resolution(varargin{1});
bbox;
redraw_all;
case 'window',
if numel(varargin)<2,
win = 'auto';
elseif numel(varargin{2})==2,
win = varargin{2};
end;
for i=valid_handles(varargin{1}),
st.vols{i}.window = win;
end;
redraw(varargin{1});
case 'delete',
my_delete(varargin{1});
case 'move',
move(varargin{1},varargin{2});
% redraw_all;
case 'reset',
my_reset;
case 'pos',
if isempty(varargin),
H = st.centre(:);
else
H = pos(varargin{1});
end;
varargout{1} = H;
case 'interp',
st.hld = varargin{1};
redraw_all;
case 'xhairs',
xhairs(varargin{1});
case 'register',
register(varargin{1});
case 'addblobs',
addblobs(varargin{:});
% redraw(varargin{1});
case 'addcolouredblobs',
addcolouredblobs(varargin{:});
% redraw(varargin{1});
case 'addimage',
addimage(varargin{1}, varargin{2});
% redraw(varargin{1});
case 'addcolouredimage',
addcolouredimage(varargin{1}, varargin{2},varargin{3});
% redraw(varargin{1});
case 'addtruecolourimage',
% spm_orthviews('Addtruecolourimage',handle,filename,colourmap,prop,mx,mn)
% Adds blobs from an image in true colour
% handle - image number to add blobs to [default 1]
% filename of image containing blob data [default - request via GUI]
% colourmap - colormap to display blobs in [GUI input]
% prop - intensity proportion of activation cf grayscale [0.4]
% mx - maximum intensity to scale to [maximum value in activation image]
% mn - minimum intensity to scale to [minimum value in activation image]
%
if nargin < 2
varargin(1) = {1};
end
if nargin < 3
varargin(2) = {spm_select(1, 'image', 'Image with activation signal')};
end
if nargin < 4
actc = [];
while isempty(actc)
actc = getcmap(spm_input('Colourmap for activation image', '+1','s'));
end
varargin(3) = {actc};
end
if nargin < 5
varargin(4) = {0.4};
end
if nargin < 6
actv = spm_vol(varargin{2});
varargin(5) = {max([eps maxval(actv)])};
end
if nargin < 7
varargin(6) = {min([0 minval(actv)])};
end
addtruecolourimage(varargin{1}, varargin{2},varargin{3}, varargin{4}, ...
varargin{5}, varargin{6});
% redraw(varargin{1});
case 'addcolourbar',
addcolourbar(varargin{1}, varargin{2});
case 'rmblobs',
rmblobs(varargin{1});
redraw(varargin{1});
case 'addcontext',
if nargin == 1,
handles = 1:24;
else
handles = varargin{1};
end;
addcontexts(handles);
case 'rmcontext',
if nargin == 1,
handles = 1:24;
else
handles = varargin{1};
end;
rmcontexts(handles);
case 'context_menu',
c_menu(varargin{:});
case 'valid_handles',
if nargin == 1
handles = 1:24;
else
handles = varargin{1};
end;
varargout{1} = valid_handles(handles);
otherwise,
addonaction = strcmp(st.plugins,action);
if any(addonaction)
feval(['spm_ov_' st.plugins{addonaction}],varargin{:});
end;
end;
spm('Pointer');
return;
%_______________________________________________________________________
%_______________________________________________________________________
function addblobs(handle, xyz, t, mat, name)
global st
if nargin < 5
name = '';
end;
for i=valid_handles(handle),
if ~isempty(xyz),
rcp = round(xyz);
dim = max(rcp,[],2)';
off = rcp(1,:) + dim(1)*(rcp(2,:)-1 + dim(2)*(rcp(3,:)-1));
vol = zeros(dim)+NaN;
vol(off) = t;
vol = reshape(vol,dim);
st.vols{i}.blobs=cell(1,1);
mx = max([eps max(t)]);
mn = min([0 min(t)]);
st.vols{i}.blobs{1} = struct('vol',vol,'mat',mat,'max',mx, 'min',mn,'name',name);
addcolourbar(handle,1);
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function addimage(handle, fname)
global st
for i=valid_handles(handle),
if isstruct(fname),
vol = fname(1);
else
vol = spm_vol(fname);
end;
mat = vol.mat;
st.vols{i}.blobs=cell(1,1);
mx = max([eps maxval(vol)]);
mn = min([0 minval(vol)]);
st.vols{i}.blobs{1} = struct('vol',vol,'mat',mat,'max',mx,'min',mn);
addcolourbar(handle,1);
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function addcolouredblobs(handle, xyz, t, mat, colour, name)
if nargin < 6
name = '';
end;
global st
for i=valid_handles(handle),
if ~isempty(xyz),
rcp = round(xyz);
dim = max(rcp,[],2)';
off = rcp(1,:) + dim(1)*(rcp(2,:)-1 + dim(2)*(rcp(3,:)-1));
vol = zeros(dim)+NaN;
vol(off) = t;
vol = reshape(vol,dim);
if ~isfield(st.vols{i},'blobs'),
st.vols{i}.blobs=cell(1,1);
bset = 1;
else
bset = numel(st.vols{i}.blobs)+1;
end;
mx = max([eps maxval(vol)]);
mn = min([0 minval(vol)]);
st.vols{i}.blobs{bset} = struct('vol',vol, 'mat',mat, ...
'max',mx, 'min',mn, ...
'colour',colour, 'name',name);
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function addcolouredimage(handle, fname,colour)
global st
for i=valid_handles(handle),
if isstruct(fname),
vol = fname(1);
else
vol = spm_vol(fname);
end;
mat = vol.mat;
if ~isfield(st.vols{i},'blobs'),
st.vols{i}.blobs=cell(1,1);
bset = 1;
else
bset = numel(st.vols{i}.blobs)+1;
end;
mx = max([eps maxval(vol)]);
mn = min([0 minval(vol)]);
st.vols{i}.blobs{bset} = struct('vol',vol,'mat',mat,'max',mx,'min',mn,'colour',colour);
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function addtruecolourimage(handle,fname,colourmap,prop,mx,mn)
% adds true colour image to current displayed image
global st
for i=valid_handles(handle),
if isstruct(fname),
vol = fname(1);
else
vol = spm_vol(fname);
end;
mat = vol.mat;
if ~isfield(st.vols{i},'blobs'),
st.vols{i}.blobs=cell(1,1);
bset = 1;
else
bset = numel(st.vols{i}.blobs)+1;
end;
c = struct('cmap', colourmap,'prop',prop);
st.vols{i}.blobs{bset} = struct('vol',vol,'mat',mat,'max',mx, ...
'min',mn,'colour',c);
addcolourbar(handle,bset);
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function addcolourbar(vh,bh)
global st
if st.mode == 0,
axpos = get(st.vols{vh}.ax{2}.ax,'Position');
else
axpos = get(st.vols{vh}.ax{1}.ax,'Position');
end;
st.vols{vh}.blobs{bh}.cbar = axes('Parent',st.fig,...
'Position',[(axpos(1)+axpos(3)+0.05+(bh-1)*.1) (axpos(2)+0.005) 0.05 (axpos(4)-0.01)],...
'Box','on', 'YDir','normal', 'XTickLabel',[], 'XTick',[]);
if isfield(st.vols{vh}.blobs{bh},'name')
ylabel(st.vols{vh}.blobs{bh}.name,'parent',st.vols{vh}.blobs{bh}.cbar);
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function rmblobs(handle)
global st
for i=valid_handles(handle),
if isfield(st.vols{i},'blobs'),
for j=1:numel(st.vols{i}.blobs),
if isfield(st.vols{i}.blobs{j},'cbar') && ishandle(st.vols{i}.blobs{j}.cbar),
delete(st.vols{i}.blobs{j}.cbar);
end;
end;
st.vols{i} = rmfield(st.vols{i},'blobs');
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function register(hreg)
global st
tmp = uicontrol('Position',[0 0 1 1],'Visible','off','Parent',st.fig);
h = valid_handles(1:24);
if ~isempty(h),
tmp = st.vols{h(1)}.ax{1}.ax;
st.registry = struct('hReg',hreg,'hMe', tmp);
spm_XYZreg('Add2Reg',st.registry.hReg,st.registry.hMe, 'spm_orthviews');
else
warning('Nothing to register with');
end;
st.centre = spm_XYZreg('GetCoords',st.registry.hReg);
st.centre = st.centre(:);
return;
%_______________________________________________________________________
%_______________________________________________________________________
function xhairs(arg1)
global st
st.xhairs = 0;
opt = 'on';
if ~strcmp(arg1,'on'),
opt = 'off';
else
st.xhairs = 1;
end;
for i=valid_handles(1:24),
for j=1:3,
set(st.vols{i}.ax{j}.lx,'Visible',opt);
set(st.vols{i}.ax{j}.ly,'Visible',opt);
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function H = pos(arg1)
global st
H = [];
for arg1=valid_handles(arg1),
is = inv(st.vols{arg1}.premul*st.vols{arg1}.mat);
H = is(1:3,1:3)*st.centre(:) + is(1:3,4);
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function my_reset
global st
if ~isempty(st) && isfield(st,'registry') && ishandle(st.registry.hMe),
delete(st.registry.hMe); st = rmfield(st,'registry');
end;
my_delete(1:24);
reset_st;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function my_delete(arg1)
global st
% remove blobs (and colourbars, if any)
rmblobs(arg1);
% remove displayed axes
for i=valid_handles(arg1),
kids = get(st.fig,'Children');
for j=1:3,
if any(kids == st.vols{i}.ax{j}.ax),
set(get(st.vols{i}.ax{j}.ax,'Children'),'DeleteFcn','');
delete(st.vols{i}.ax{j}.ax);
end;
end;
st.vols{i} = [];
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function resolution(arg1)
global st
res = arg1/mean(svd(st.Space(1:3,1:3)));
Mat = diag([res res res 1]);
st.Space = st.Space*Mat;
st.bb = st.bb/res;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function move(handle,pos)
global st
for handle = valid_handles(handle),
st.vols{handle}.area = pos;
end;
bbox;
% redraw(valid_handles(handle));
return;
%_______________________________________________________________________
%_______________________________________________________________________
function bb = maxbb
global st
mn = [Inf Inf Inf];
mx = -mn;
for i=valid_handles(1:24),
bb = [[1 1 1];st.vols{i}.dim(1:3)];
c = [ bb(1,1) bb(1,2) bb(1,3) 1
bb(1,1) bb(1,2) bb(2,3) 1
bb(1,1) bb(2,2) bb(1,3) 1
bb(1,1) bb(2,2) bb(2,3) 1
bb(2,1) bb(1,2) bb(1,3) 1
bb(2,1) bb(1,2) bb(2,3) 1
bb(2,1) bb(2,2) bb(1,3) 1
bb(2,1) bb(2,2) bb(2,3) 1]';
tc = st.Space\(st.vols{i}.premul*st.vols{i}.mat)*c;
tc = tc(1:3,:)';
mx = max([tc ; mx]);
mn = min([tc ; mn]);
end;
bb = [mn ; mx];
return;
%_______________________________________________________________________
%_______________________________________________________________________
function space(arg1,M,dim)
global st
if ~isempty(st.vols{arg1})
num = arg1;
if nargin < 2
M = st.vols{num}.mat;
dim = st.vols{num}.dim(1:3);
end;
Mat = st.vols{num}.premul(1:3,1:3)*M(1:3,1:3);
vox = sqrt(sum(Mat.^2));
if det(Mat(1:3,1:3))<0, vox(1) = -vox(1); end;
Mat = diag([vox 1]);
Space = (M)/Mat;
bb = [1 1 1; dim];
bb = [bb [1;1]];
bb=bb*Mat';
bb=bb(:,1:3);
bb=sort(bb);
st.Space = Space;
st.bb = bb;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function H = specify_image(arg1)
global st
H=[];
if isstruct(arg1),
V = arg1(1);
else
try
V = spm_vol(arg1);
catch
fprintf('Can not use image "%s"\n', arg1);
return;
end;
end;
ii = 1;
while ~isempty(st.vols{ii}), ii = ii + 1; end;
DeleteFcn = ['spm_orthviews(''Delete'',' num2str(ii) ');'];
V.ax = cell(3,1);
for i=1:3,
ax = axes('Visible','off','DrawMode','fast','Parent',st.fig,'DeleteFcn',DeleteFcn,...
'YDir','normal','ButtonDownFcn',@repos_start);
d = image(0,'Tag','Transverse','Parent',ax,...
'DeleteFcn',DeleteFcn);
set(ax,'Ydir','normal','ButtonDownFcn',@repos_start);
lx = line(0,0,'Parent',ax,'DeleteFcn',DeleteFcn);
ly = line(0,0,'Parent',ax,'DeleteFcn',DeleteFcn);
if ~st.xhairs,
set(lx,'Visible','off');
set(ly,'Visible','off');
end;
V.ax{i} = struct('ax',ax,'d',d,'lx',lx,'ly',ly);
end;
V.premul = eye(4);
V.window = 'auto';
V.mapping = 'linear';
st.vols{ii} = V;
H = ii;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function repos_start(varargin)
% don't use right mouse button to start reposition
if ~strcmpi(get(gcbf,'SelectionType'),'alt')
set(gcbf,'windowbuttonmotionfcn',@repos_move, 'windowbuttonupfcn',@repos_end);
spm_orthviews('reposition');
end
%_______________________________________________________________________
%_______________________________________________________________________
function repos_move(varargin)
spm_orthviews('reposition');
%_______________________________________________________________________
%_______________________________________________________________________
function repos_end(varargin)
set(gcbf,'windowbuttonmotionfcn','', 'windowbuttonupfcn','');
%_______________________________________________________________________
%_______________________________________________________________________
function addcontexts(handles)
for ii = valid_handles(handles),
addcontext(ii);
end;
spm_orthviews('reposition',spm_orthviews('pos'));
return;
%_______________________________________________________________________
%_______________________________________________________________________
function rmcontexts(handles)
global st
for ii = valid_handles(handles),
for i=1:3,
set(st.vols{ii}.ax{i}.ax,'UIcontextmenu',[]);
st.vols{ii}.ax{i} = rmfield(st.vols{ii}.ax{i},'cm');
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function bbox
global st
Dims = diff(st.bb)'+1;
TD = Dims([1 2])';
CD = Dims([1 3])';
if st.mode == 0, SD = Dims([3 2])'; else SD = Dims([2 3])'; end;
un = get(st.fig,'Units');set(st.fig,'Units','Pixels');
sz = get(st.fig,'Position');set(st.fig,'Units',un);
sz = sz(3:4);
sz(2) = sz(2)-40;
for i=valid_handles(1:24),
area = st.vols{i}.area(:);
area = [area(1)*sz(1) area(2)*sz(2) area(3)*sz(1) area(4)*sz(2)];
if st.mode == 0,
sx = area(3)/(Dims(1)+Dims(3))/1.02;
else
sx = area(3)/(Dims(1)+Dims(2))/1.02;
end;
sy = area(4)/(Dims(2)+Dims(3))/1.02;
s = min([sx sy]);
offy = (area(4)-(Dims(2)+Dims(3))*1.02*s)/2 + area(2);
sky = s*(Dims(2)+Dims(3))*0.02;
if st.mode == 0,
offx = (area(3)-(Dims(1)+Dims(3))*1.02*s)/2 + area(1);
skx = s*(Dims(1)+Dims(3))*0.02;
else
offx = (area(3)-(Dims(1)+Dims(2))*1.02*s)/2 + area(1);
skx = s*(Dims(1)+Dims(2))*0.02;
end;
% Transverse
set(st.vols{i}.ax{1}.ax,'Units','pixels', ...
'Position',[offx offy s*Dims(1) s*Dims(2)],...
'Units','normalized','Xlim',[0 TD(1)]+0.5,'Ylim',[0 TD(2)]+0.5,...
'Visible','on','XTick',[],'YTick',[]);
% Coronal
set(st.vols{i}.ax{2}.ax,'Units','Pixels',...
'Position',[offx offy+s*Dims(2)+sky s*Dims(1) s*Dims(3)],...
'Units','normalized','Xlim',[0 CD(1)]+0.5,'Ylim',[0 CD(2)]+0.5,...
'Visible','on','XTick',[],'YTick',[]);
% Sagittal
if st.mode == 0,
set(st.vols{i}.ax{3}.ax,'Units','Pixels', 'Box','on',...
'Position',[offx+s*Dims(1)+skx offy s*Dims(3) s*Dims(2)],...
'Units','normalized','Xlim',[0 SD(1)]+0.5,'Ylim',[0 SD(2)]+0.5,...
'Visible','on','XTick',[],'YTick',[]);
else
set(st.vols{i}.ax{3}.ax,'Units','Pixels', 'Box','on',...
'Position',[offx+s*Dims(1)+skx offy+s*Dims(2)+sky s*Dims(2) s*Dims(3)],...
'Units','normalized','Xlim',[0 SD(1)]+0.5,'Ylim',[0 SD(2)]+0.5,...
'Visible','on','XTick',[],'YTick',[]);
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function redraw_all
redraw(1:24);
return;
%_______________________________________________________________________
function mx = maxval(vol)
if isstruct(vol),
mx = -Inf;
for i=1:vol.dim(3),
tmp = spm_slice_vol(vol,spm_matrix([0 0 i]),vol.dim(1:2),0);
imx = max(tmp(isfinite(tmp)));
if ~isempty(imx),mx = max(mx,imx);end
end;
else
mx = max(vol(isfinite(vol)));
end;
%_______________________________________________________________________
function mn = minval(vol)
if isstruct(vol),
mn = Inf;
for i=1:vol.dim(3),
tmp = spm_slice_vol(vol,spm_matrix([0 0 i]),vol.dim(1:2),0);
imn = min(tmp(isfinite(tmp)));
if ~isempty(imn),mn = min(mn,imn);end
end;
else
mn = min(vol(isfinite(vol)));
end;
%_______________________________________________________________________
%_______________________________________________________________________
function redraw(arg1)
global st
bb = st.bb;
Dims = round(diff(bb)'+1);
is = inv(st.Space);
cent = is(1:3,1:3)*st.centre(:) + is(1:3,4);
for i = valid_handles(arg1),
M = st.vols{i}.premul*st.vols{i}.mat;
TM0 = [ 1 0 0 -bb(1,1)+1
0 1 0 -bb(1,2)+1
0 0 1 -cent(3)
0 0 0 1];
TM = inv(TM0*(st.Space\M));
TD = Dims([1 2]);
CM0 = [ 1 0 0 -bb(1,1)+1
0 0 1 -bb(1,3)+1
0 1 0 -cent(2)
0 0 0 1];
CM = inv(CM0*(st.Space\M));
CD = Dims([1 3]);
if st.mode ==0,
SM0 = [ 0 0 1 -bb(1,3)+1
0 1 0 -bb(1,2)+1
1 0 0 -cent(1)
0 0 0 1];
SM = inv(SM0*(st.Space\M)); SD = Dims([3 2]);
else
SM0 = [ 0 -1 0 +bb(2,2)+1
0 0 1 -bb(1,3)+1
1 0 0 -cent(1)
0 0 0 1];
SM = inv(SM0*(st.Space\M));
SD = Dims([2 3]);
end;
try
imgt = spm_slice_vol(st.vols{i},TM,TD,st.hld)';
imgc = spm_slice_vol(st.vols{i},CM,CD,st.hld)';
imgs = spm_slice_vol(st.vols{i},SM,SD,st.hld)';
ok = true;
catch
fprintf('Image "%s" can not be resampled\n', st.vols{i}.fname);
ok = false;
end
if ok,
% get min/max threshold
if strcmp(st.vols{i}.window,'auto')
mn = -Inf;
mx = Inf;
else
mn = min(st.vols{i}.window);
mx = max(st.vols{i}.window);
end;
% threshold images
imgt = max(imgt,mn); imgt = min(imgt,mx);
imgc = max(imgc,mn); imgc = min(imgc,mx);
imgs = max(imgs,mn); imgs = min(imgs,mx);
% compute intensity mapping, if histeq is available
if license('test','image_toolbox') == 0
st.vols{i}.mapping = 'linear';
end;
switch st.vols{i}.mapping,
case 'linear',
case 'histeq',
% scale images to a range between 0 and 1
imgt1=(imgt-min(imgt(:)))/(max(imgt(:)-min(imgt(:)))+eps);
imgc1=(imgc-min(imgc(:)))/(max(imgc(:)-min(imgc(:)))+eps);
imgs1=(imgs-min(imgs(:)))/(max(imgs(:)-min(imgs(:)))+eps);
img = histeq([imgt1(:); imgc1(:); imgs1(:)],1024);
imgt = reshape(img(1:numel(imgt1)),size(imgt1));
imgc = reshape(img(numel(imgt1)+(1:numel(imgc1))),size(imgc1));
imgs = reshape(img(numel(imgt1)+numel(imgc1)+(1:numel(imgs1))),size(imgs1));
mn = 0;
mx = 1;
case 'quadhisteq',
% scale images to a range between 0 and 1
imgt1=(imgt-min(imgt(:)))/(max(imgt(:)-min(imgt(:)))+eps);
imgc1=(imgc-min(imgc(:)))/(max(imgc(:)-min(imgc(:)))+eps);
imgs1=(imgs-min(imgs(:)))/(max(imgs(:)-min(imgs(:)))+eps);
img = histeq([imgt1(:).^2; imgc1(:).^2; imgs1(:).^2],1024);
imgt = reshape(img(1:numel(imgt1)),size(imgt1));
imgc = reshape(img(numel(imgt1)+(1:numel(imgc1))),size(imgc1));
imgs = reshape(img(numel(imgt1)+numel(imgc1)+(1:numel(imgs1))),size(imgs1));
mn = 0;
mx = 1;
case 'loghisteq',
sw = warning('off','MATLAB:log:logOfZero');
imgt = log(imgt-min(imgt(:)));
imgc = log(imgc-min(imgc(:)));
imgs = log(imgs-min(imgs(:)));
warning(sw);
imgt(~isfinite(imgt)) = 0;
imgc(~isfinite(imgc)) = 0;
imgs(~isfinite(imgs)) = 0;
% scale log images to a range between 0 and 1
imgt1=(imgt-min(imgt(:)))/(max(imgt(:)-min(imgt(:)))+eps);
imgc1=(imgc-min(imgc(:)))/(max(imgc(:)-min(imgc(:)))+eps);
imgs1=(imgs-min(imgs(:)))/(max(imgs(:)-min(imgs(:)))+eps);
img = histeq([imgt1(:); imgc1(:); imgs1(:)],1024);
imgt = reshape(img(1:numel(imgt1)),size(imgt1));
imgc = reshape(img(numel(imgt1)+(1:numel(imgc1))),size(imgc1));
imgs = reshape(img(numel(imgt1)+numel(imgc1)+(1:numel(imgs1))),size(imgs1));
mn = 0;
mx = 1;
end;
% recompute min/max for display
if strcmp(st.vols{i}.window,'auto')
mx = -inf; mn = inf;
end;
if ~isempty(imgt),
tmp = imgt(isfinite(imgt));
mx = max([mx max(max(tmp))]);
mn = min([mn min(min(tmp))]);
end;
if ~isempty(imgc),
tmp = imgc(isfinite(imgc));
mx = max([mx max(max(tmp))]);
mn = min([mn min(min(tmp))]);
end;
if ~isempty(imgs),
tmp = imgs(isfinite(imgs));
mx = max([mx max(max(tmp))]);
mn = min([mn min(min(tmp))]);
end;
if mx==mn, mx=mn+eps; end;
if isfield(st.vols{i},'blobs'),
if ~isfield(st.vols{i}.blobs{1},'colour'),
% Add blobs for display using the split colourmap
scal = 64/(mx-mn);
dcoff = -mn*scal;
imgt = imgt*scal+dcoff;
imgc = imgc*scal+dcoff;
imgs = imgs*scal+dcoff;
if isfield(st.vols{i}.blobs{1},'max'),
mx = st.vols{i}.blobs{1}.max;
else
mx = max([eps maxval(st.vols{i}.blobs{1}.vol)]);
st.vols{i}.blobs{1}.max = mx;
end;
if isfield(st.vols{i}.blobs{1},'min'),
mn = st.vols{i}.blobs{1}.min;
else
mn = min([0 minval(st.vols{i}.blobs{1}.vol)]);
st.vols{i}.blobs{1}.min = mn;
end;
vol = st.vols{i}.blobs{1}.vol;
M = st.vols{i}.premul*st.vols{i}.blobs{1}.mat;
tmpt = spm_slice_vol(vol,inv(TM0*(st.Space\M)),TD,[0 NaN])';
tmpc = spm_slice_vol(vol,inv(CM0*(st.Space\M)),CD,[0 NaN])';
tmps = spm_slice_vol(vol,inv(SM0*(st.Space\M)),SD,[0 NaN])';
%tmpt_z = find(tmpt==0);tmpt(tmpt_z) = NaN;
%tmpc_z = find(tmpc==0);tmpc(tmpc_z) = NaN;
%tmps_z = find(tmps==0);tmps(tmps_z) = NaN;
sc = 64/(mx-mn);
off = 65.51-mn*sc;
msk = find(isfinite(tmpt)); imgt(msk) = off+tmpt(msk)*sc;
msk = find(isfinite(tmpc)); imgc(msk) = off+tmpc(msk)*sc;
msk = find(isfinite(tmps)); imgs(msk) = off+tmps(msk)*sc;
cmap = get(st.fig,'Colormap');
if size(cmap,1)~=128
figure(st.fig)
spm_figure('Colormap','gray-hot')
end;
redraw_colourbar(i,1,[mn mx],(1:64)'+64);
elseif isstruct(st.vols{i}.blobs{1}.colour),
% Add blobs for display using a defined
% colourmap
% colourmaps
gryc = (0:63)'*ones(1,3)/63;
actc = ...
st.vols{1}.blobs{1}.colour.cmap;
actp = ...
st.vols{1}.blobs{1}.colour.prop;
% scale grayscale image, not isfinite -> black
imgt = scaletocmap(imgt,mn,mx,gryc,65);
imgc = scaletocmap(imgc,mn,mx,gryc,65);
imgs = scaletocmap(imgs,mn,mx,gryc,65);
gryc = [gryc; 0 0 0];
% get max for blob image
if isfield(st.vols{i}.blobs{1},'max'),
cmx = st.vols{i}.blobs{1}.max;
else
cmx = max([eps maxval(st.vols{i}.blobs{1}.vol)]);
end;
if isfield(st.vols{i}.blobs{1},'min'),
cmn = st.vols{i}.blobs{1}.min;
else
cmn = -cmx;
end;
% get blob data
vol = st.vols{i}.blobs{1}.vol;
M = st.vols{i}.premul*st.vols{i}.blobs{1}.mat;
tmpt = spm_slice_vol(vol,inv(TM0*(st.Space\M)),TD,[0 NaN])';
tmpc = spm_slice_vol(vol,inv(CM0*(st.Space\M)),CD,[0 NaN])';
tmps = spm_slice_vol(vol,inv(SM0*(st.Space\M)),SD,[0 NaN])';
% actimg scaled round 0, black NaNs
topc = size(actc,1)+1;
tmpt = scaletocmap(tmpt,cmn,cmx,actc,topc);
tmpc = scaletocmap(tmpc,cmn,cmx,actc,topc);
tmps = scaletocmap(tmps,cmn,cmx,actc,topc);
actc = [actc; 0 0 0];
% combine gray and blob data to
% truecolour
imgt = reshape(actc(tmpt(:),:)*actp+ ...
gryc(imgt(:),:)*(1-actp), ...
[size(imgt) 3]);
imgc = reshape(actc(tmpc(:),:)*actp+ ...
gryc(imgc(:),:)*(1-actp), ...
[size(imgc) 3]);
imgs = reshape(actc(tmps(:),:)*actp+ ...
gryc(imgs(:),:)*(1-actp), ...
[size(imgs) 3]);
csz = size(st.vols{i}.blobs{1}.colour.cmap);
cdata = reshape(st.vols{i}.blobs{1}.colour.cmap, [csz(1) 1 csz(2)]);
redraw_colourbar(i,1,[cmn cmx],cdata);
else
% Add full colour blobs - several sets at once
scal = 1/(mx-mn);
dcoff = -mn*scal;
wt = zeros(size(imgt));
wc = zeros(size(imgc));
ws = zeros(size(imgs));
imgt = repmat(imgt*scal+dcoff,[1,1,3]);
imgc = repmat(imgc*scal+dcoff,[1,1,3]);
imgs = repmat(imgs*scal+dcoff,[1,1,3]);
cimgt = zeros(size(imgt));
cimgc = zeros(size(imgc));
cimgs = zeros(size(imgs));
colour = zeros(numel(st.vols{i}.blobs),3);
for j=1:numel(st.vols{i}.blobs) % get colours of all images first
if isfield(st.vols{i}.blobs{j},'colour'),
colour(j,:) = reshape(st.vols{i}.blobs{j}.colour, [1 3]);
else
colour(j,:) = [1 0 0];
end;
end;
%colour = colour/max(sum(colour));
for j=1:numel(st.vols{i}.blobs),
if isfield(st.vols{i}.blobs{j},'max'),
mx = st.vols{i}.blobs{j}.max;
else
mx = max([eps max(st.vols{i}.blobs{j}.vol(:))]);
st.vols{i}.blobs{j}.max = mx;
end;
if isfield(st.vols{i}.blobs{j},'min'),
mn = st.vols{i}.blobs{j}.min;
else
mn = min([0 min(st.vols{i}.blobs{j}.vol(:))]);
st.vols{i}.blobs{j}.min = mn;
end;
vol = st.vols{i}.blobs{j}.vol;
M = st.Space\st.vols{i}.premul*st.vols{i}.blobs{j}.mat;
tmpt = spm_slice_vol(vol,inv(TM0*M),TD,[0 NaN])';
tmpc = spm_slice_vol(vol,inv(CM0*M),CD,[0 NaN])';
tmps = spm_slice_vol(vol,inv(SM0*M),SD,[0 NaN])';
% check min/max of sampled image
% against mn/mx as given in st
tmpt(tmpt(:)<mn) = mn;
tmpc(tmpc(:)<mn) = mn;
tmps(tmps(:)<mn) = mn;
tmpt(tmpt(:)>mx) = mx;
tmpc(tmpc(:)>mx) = mx;
tmps(tmps(:)>mx) = mx;
tmpt = (tmpt-mn)/(mx-mn);
tmpc = (tmpc-mn)/(mx-mn);
tmps = (tmps-mn)/(mx-mn);
tmpt(~isfinite(tmpt)) = 0;
tmpc(~isfinite(tmpc)) = 0;
tmps(~isfinite(tmps)) = 0;
cimgt = cimgt + cat(3,tmpt*colour(j,1),tmpt*colour(j,2),tmpt*colour(j,3));
cimgc = cimgc + cat(3,tmpc*colour(j,1),tmpc*colour(j,2),tmpc*colour(j,3));
cimgs = cimgs + cat(3,tmps*colour(j,1),tmps*colour(j,2),tmps*colour(j,3));
wt = wt + tmpt;
wc = wc + tmpc;
ws = ws + tmps;
cdata=permute(shiftdim((1/64:1/64:1)'* ...
colour(j,:),-1),[2 1 3]);
redraw_colourbar(i,j,[mn mx],cdata);
end;
imgt = repmat(1-wt,[1 1 3]).*imgt+cimgt;
imgc = repmat(1-wc,[1 1 3]).*imgc+cimgc;
imgs = repmat(1-ws,[1 1 3]).*imgs+cimgs;
imgt(imgt<0)=0; imgt(imgt>1)=1;
imgc(imgc<0)=0; imgc(imgc>1)=1;
imgs(imgs<0)=0; imgs(imgs>1)=1;
end;
else
scal = 64/(mx-mn);
dcoff = -mn*scal;
imgt = imgt*scal+dcoff;
imgc = imgc*scal+dcoff;
imgs = imgs*scal+dcoff;
end;
set(st.vols{i}.ax{1}.d,'HitTest','off', 'Cdata',imgt);
set(st.vols{i}.ax{1}.lx,'HitTest','off',...
'Xdata',[0 TD(1)]+0.5,'Ydata',[1 1]*(cent(2)-bb(1,2)+1));
set(st.vols{i}.ax{1}.ly,'HitTest','off',...
'Ydata',[0 TD(2)]+0.5,'Xdata',[1 1]*(cent(1)-bb(1,1)+1));
set(st.vols{i}.ax{2}.d,'HitTest','off', 'Cdata',imgc);
set(st.vols{i}.ax{2}.lx,'HitTest','off',...
'Xdata',[0 CD(1)]+0.5,'Ydata',[1 1]*(cent(3)-bb(1,3)+1));
set(st.vols{i}.ax{2}.ly,'HitTest','off',...
'Ydata',[0 CD(2)]+0.5,'Xdata',[1 1]*(cent(1)-bb(1,1)+1));
set(st.vols{i}.ax{3}.d,'HitTest','off','Cdata',imgs);
if st.mode ==0,
set(st.vols{i}.ax{3}.lx,'HitTest','off',...
'Xdata',[0 SD(1)]+0.5,'Ydata',[1 1]*(cent(2)-bb(1,2)+1));
set(st.vols{i}.ax{3}.ly,'HitTest','off',...
'Ydata',[0 SD(2)]+0.5,'Xdata',[1 1]*(cent(3)-bb(1,3)+1));
else
set(st.vols{i}.ax{3}.lx,'HitTest','off',...
'Xdata',[0 SD(1)]+0.5,'Ydata',[1 1]*(cent(3)-bb(1,3)+1));
set(st.vols{i}.ax{3}.ly,'HitTest','off',...
'Ydata',[0 SD(2)]+0.5,'Xdata',[1 1]*(bb(2,2)+1-cent(2)));
end;
if ~isempty(st.plugins) % process any addons
for k = 1:numel(st.plugins),
if isfield(st.vols{i},st.plugins{k}),
feval(['spm_ov_', st.plugins{k}], ...
'redraw', i, TM0, TD, CM0, CD, SM0, SD);
end;
end;
end;
end;
end;
drawnow;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function redraw_colourbar(vh,bh,interval,cdata)
global st
if isfield(st.vols{vh}.blobs{bh},'cbar')
if st.mode == 0,
axpos = get(st.vols{vh}.ax{2}.ax,'Position');
else
axpos = get(st.vols{vh}.ax{1}.ax,'Position');
end;
% only scale cdata if we have out-of-range truecolour values
if ndims(cdata)==3 && max(cdata(:))>1
cdata=cdata./max(cdata(:));
end;
image([0 1],interval,cdata,'Parent',st.vols{vh}.blobs{bh}.cbar);
set(st.vols{vh}.blobs{bh}.cbar, ...
'Position',[(axpos(1)+axpos(3)+0.05+(bh-1)*.1)...
(axpos(2)+0.005) 0.05 (axpos(4)-0.01)],...
'YDir','normal','XTickLabel',[],'XTick',[]);
if isfield(st.vols{vh}.blobs{bh},'name')
ylabel(st.vols{vh}.blobs{bh}.name,'parent',st.vols{vh}.blobs{bh}.cbar);
end;
end;
%_______________________________________________________________________
%_______________________________________________________________________
function centre = findcent
global st
obj = get(st.fig,'CurrentObject');
centre = [];
cent = [];
cp = [];
for i=valid_handles(1:24),
for j=1:3,
if ~isempty(obj),
if (st.vols{i}.ax{j}.ax == obj),
cp = get(obj,'CurrentPoint');
end;
end;
if ~isempty(cp),
cp = cp(1,1:2);
is = inv(st.Space);
cent = is(1:3,1:3)*st.centre(:) + is(1:3,4);
switch j,
case 1,
cent([1 2])=[cp(1)+st.bb(1,1)-1 cp(2)+st.bb(1,2)-1];
case 2,
cent([1 3])=[cp(1)+st.bb(1,1)-1 cp(2)+st.bb(1,3)-1];
case 3,
if st.mode ==0,
cent([3 2])=[cp(1)+st.bb(1,3)-1 cp(2)+st.bb(1,2)-1];
else
cent([2 3])=[st.bb(2,2)+1-cp(1) cp(2)+st.bb(1,3)-1];
end;
end;
break;
end;
end;
if ~isempty(cent), break; end;
end;
if ~isempty(cent), centre = st.Space(1:3,1:3)*cent(:) + st.Space(1:3,4); end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function handles = valid_handles(handles)
global st;
if isempty(st) || ~isfield(st,'vols')
handles = [];
else
handles = handles(:)';
handles = handles(handles<=24 & handles>=1 & ~rem(handles,1));
for h=handles,
if isempty(st.vols{h}), handles(handles==h)=[]; end;
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function reset_st
global st
fig = spm_figure('FindWin','Graphics');
bb = []; %[ [-78 78]' [-112 76]' [-50 85]' ];
st = struct('n', 0, 'vols',[], 'bb',bb,'Space',eye(4),'centre',[0 0 0],'callback',';','xhairs',1,'hld',1,'fig',fig,'mode',1,'plugins',{{}},'snap',[]);
st.vols = cell(24,1);
xTB = spm('TBs');
if ~isempty(xTB)
pluginbase = {spm('Dir') xTB.dir};
else
pluginbase = {spm('Dir')};
end
for k = 1:numel(pluginbase)
pluginpath = fullfile(pluginbase{k},'spm_orthviews');
if isdir(pluginpath)
pluginfiles = dir(fullfile(pluginpath,'spm_ov_*.m'));
if ~isempty(pluginfiles)
if ~isdeployed, addpath(pluginpath); end
% fprintf('spm_orthviews: Using Plugins in %s\n', pluginpath);
for l = 1:numel(pluginfiles)
[p, pluginname, e, v] = spm_fileparts(pluginfiles(l).name);
st.plugins{end+1} = strrep(pluginname, 'spm_ov_','');
% fprintf('%s\n',st.plugins{k});
end;
end;
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function img = scaletocmap(inpimg,mn,mx,cmap,miscol)
if nargin < 5, miscol=1;end
cml = size(cmap,1);
scf = (cml-1)/(mx-mn);
img = round((inpimg-mn)*scf)+1;
img(img<1) = 1;
img(img>cml) = cml;
img(~isfinite(img)) = miscol;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function cmap = getcmap(acmapname)
% get colormap of name acmapname
if ~isempty(acmapname),
cmap = evalin('base',acmapname,'[]');
if isempty(cmap), % not a matrix, is .mat file?
[p, f, e] = fileparts(acmapname);
acmat = fullfile(p, [f '.mat']);
if exist(acmat, 'file'),
s = struct2cell(load(acmat));
cmap = s{1};
end;
end;
end;
if size(cmap, 2)~=3,
warning('Colormap was not an N by 3 matrix')
cmap = [];
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function item_parent = addcontext(volhandle)
global st;
%create context menu
fg = spm_figure('Findwin','Graphics');set(0,'CurrentFigure',fg);
%contextmenu
item_parent = uicontextmenu;
%contextsubmenu 0
item00 = uimenu(item_parent, 'Label','unknown image', 'Separator','on');
spm_orthviews('context_menu','image_info',item00,volhandle);
item0a = uimenu(item_parent, 'UserData','pos_mm', 'Callback','spm_orthviews(''context_menu'',''repos_mm'');','Separator','on');
item0b = uimenu(item_parent, 'UserData','pos_vx', 'Callback','spm_orthviews(''context_menu'',''repos_vx'');');
item0c = uimenu(item_parent, 'UserData','v_value');
%contextsubmenu 1
item1 = uimenu(item_parent,'Label','Zoom');
item1_1 = uimenu(item1, 'Label','Full Volume', 'Callback','spm_orthviews(''context_menu'',''zoom'',6);', 'Checked','on');
item1_2 = uimenu(item1, 'Label','160x160x160mm', 'Callback','spm_orthviews(''context_menu'',''zoom'',5);');
item1_3 = uimenu(item1, 'Label','80x80x80mm', 'Callback','spm_orthviews(''context_menu'',''zoom'',4);');
item1_4 = uimenu(item1, 'Label','40x40x40mm', 'Callback','spm_orthviews(''context_menu'',''zoom'',3);');
item1_5 = uimenu(item1, 'Label','20x20x20mm', 'Callback','spm_orthviews(''context_menu'',''zoom'',2);');
item1_6 = uimenu(item1, 'Label','10x10x10mm', 'Callback','spm_orthviews(''context_menu'',''zoom'',1);');
%contextsubmenu 2
checked={'off','off'};
checked{st.xhairs+1} = 'on';
item2 = uimenu(item_parent,'Label','Crosshairs');
item2_1 = uimenu(item2, 'Label','on', 'Callback','spm_orthviews(''context_menu'',''Xhair'',''on'');','Checked',checked{2});
item2_2 = uimenu(item2, 'Label','off', 'Callback','spm_orthviews(''context_menu'',''Xhair'',''off'');','Checked',checked{1});
%contextsubmenu 3
if st.Space == eye(4)
checked = {'off', 'on'};
else
checked = {'on', 'off'};
end;
item3 = uimenu(item_parent,'Label','Orientation');
item3_1 = uimenu(item3, 'Label','World space', 'Callback','spm_orthviews(''context_menu'',''orientation'',3);','Checked',checked{2});
item3_2 = uimenu(item3, 'Label','Voxel space (1st image)', 'Callback','spm_orthviews(''context_menu'',''orientation'',2);','Checked',checked{1});
item3_3 = uimenu(item3, 'Label','Voxel space (this image)', 'Callback','spm_orthviews(''context_menu'',''orientation'',1);','Checked','off');
%contextsubmenu 3
if isempty(st.snap)
checked = {'off', 'on'};
else
checked = {'on', 'off'};
end;
item3 = uimenu(item_parent,'Label','Snap to Grid');
item3_1 = uimenu(item3, 'Label','Don''t snap', 'Callback','spm_orthviews(''context_menu'',''snap'',3);','Checked',checked{2});
item3_2 = uimenu(item3, 'Label','Snap to 1st image', 'Callback','spm_orthviews(''context_menu'',''snap'',2);','Checked',checked{1});
item3_3 = uimenu(item3, 'Label','Snap to this image', 'Callback','spm_orthviews(''context_menu'',''snap'',1);','Checked','off');
%contextsubmenu 4
if st.hld == 0,
checked = {'off', 'off', 'on'};
elseif st.hld > 0,
checked = {'off', 'on', 'off'};
else
checked = {'on', 'off', 'off'};
end;
item4 = uimenu(item_parent,'Label','Interpolation');
item4_1 = uimenu(item4, 'Label','NN', 'Callback','spm_orthviews(''context_menu'',''interpolation'',3);', 'Checked',checked{3});
item4_2 = uimenu(item4, 'Label','Bilin', 'Callback','spm_orthviews(''context_menu'',''interpolation'',2);','Checked',checked{2});
item4_3 = uimenu(item4, 'Label','Sinc', 'Callback','spm_orthviews(''context_menu'',''interpolation'',1);','Checked',checked{1});
%contextsubmenu 5
% item5 = uimenu(item_parent,'Label','Position', 'Callback','spm_orthviews(''context_menu'',''position'');');
%contextsubmenu 6
item6 = uimenu(item_parent,'Label','Image','Separator','on');
item6_1 = uimenu(item6, 'Label','Window');
item6_1_1 = uimenu(item6_1, 'Label','local');
item6_1_1_1 = uimenu(item6_1_1, 'Label','auto', 'Callback','spm_orthviews(''context_menu'',''window'',2);');
item6_1_1_2 = uimenu(item6_1_1, 'Label','manual', 'Callback','spm_orthviews(''context_menu'',''window'',1);');
item6_1_2 = uimenu(item6_1, 'Label','global');
item6_1_2_1 = uimenu(item6_1_2, 'Label','auto', 'Callback','spm_orthviews(''context_menu'',''window_gl'',2);');
item6_1_2_2 = uimenu(item6_1_2, 'Label','manual', 'Callback','spm_orthviews(''context_menu'',''window_gl'',1);');
if license('test','image_toolbox') == 1
offon = {'off', 'on'};
checked = offon(strcmp(st.vols{volhandle}.mapping, ...
{'linear', 'histeq', 'loghisteq', 'quadhisteq'})+1);
item6_2 = uimenu(item6, 'Label','Intensity mapping');
item6_2_1 = uimenu(item6_2, 'Label','local');
item6_2_1_1 = uimenu(item6_2_1, 'Label','Linear', 'Checked',checked{1}, ...
'Callback','spm_orthviews(''context_menu'',''mapping'',''linear'');');
item6_2_1_2 = uimenu(item6_2_1, 'Label','Equalised histogram', 'Checked',checked{2}, ...
'Callback','spm_orthviews(''context_menu'',''mapping'',''histeq'');');
item6_2_1_3 = uimenu(item6_2_1, 'Label','Equalised log-histogram', 'Checked',checked{3}, ...
'Callback','spm_orthviews(''context_menu'',''mapping'',''loghisteq'');');
item6_2_1_4 = uimenu(item6_2_1, 'Label','Equalised squared-histogram', 'Checked',checked{4}, ...
'Callback','spm_orthviews(''context_menu'',''mapping'',''quadhisteq'');');
item6_2_2 = uimenu(item6_2, 'Label','global');
item6_2_2_1 = uimenu(item6_2_2, 'Label','Linear', 'Checked',checked{1}, ...
'Callback','spm_orthviews(''context_menu'',''mapping_gl'',''linear'');');
item6_2_2_2 = uimenu(item6_2_2, 'Label','Equalised histogram', 'Checked',checked{2}, ...
'Callback','spm_orthviews(''context_menu'',''mapping_gl'',''histeq'');');
item6_2_2_3 = uimenu(item6_2_2, 'Label','Equalised log-histogram', 'Checked',checked{3}, ...
'Callback','spm_orthviews(''context_menu'',''mapping_gl'',''loghisteq'');');
item6_2_2_4 = uimenu(item6_2_2, 'Label','Equalised squared-histogram', 'Checked',checked{4}, ...
'Callback','spm_orthviews(''context_menu'',''mapping_gl'',''quadhisteq'');');
end;
%contextsubmenu 7
item7 = uimenu(item_parent,'Label','Blobs');
item7_1 = uimenu(item7, 'Label','Add blobs');
item7_1_1 = uimenu(item7_1, 'Label','local', 'Callback','spm_orthviews(''context_menu'',''add_blobs'',2);');
item7_1_2 = uimenu(item7_1, 'Label','global', 'Callback','spm_orthviews(''context_menu'',''add_blobs'',1);');
item7_2 = uimenu(item7, 'Label','Add image');
item7_2_1 = uimenu(item7_2, 'Label','local', 'Callback','spm_orthviews(''context_menu'',''add_image'',2);');
item7_2_2 = uimenu(item7_2, 'Label','global', 'Callback','spm_orthviews(''context_menu'',''add_image'',1);');
item7_3 = uimenu(item7, 'Label','Add colored blobs','Separator','on');
item7_3_1 = uimenu(item7_3, 'Label','local', 'Callback','spm_orthviews(''context_menu'',''add_c_blobs'',2);');
item7_3_2 = uimenu(item7_3, 'Label','global', 'Callback','spm_orthviews(''context_menu'',''add_c_blobs'',1);');
item7_4 = uimenu(item7, 'Label','Add colored image');
item7_4_1 = uimenu(item7_4, 'Label','local', 'Callback','spm_orthviews(''context_menu'',''add_c_image'',2);');
item7_4_2 = uimenu(item7_4, 'Label','global', 'Callback','spm_orthviews(''context_menu'',''add_c_image'',1);');
item7_5 = uimenu(item7, 'Label','Remove blobs', 'Visible','off','Separator','on');
item7_6 = uimenu(item7, 'Label','Remove colored blobs','Visible','off');
item7_6_1 = uimenu(item7_6, 'Label','local', 'Visible','on');
item7_6_2 = uimenu(item7_6, 'Label','global','Visible','on');
for i=1:3,
set(st.vols{volhandle}.ax{i}.ax,'UIcontextmenu',item_parent);
st.vols{volhandle}.ax{i}.cm = item_parent;
end;
if ~isempty(st.plugins) % process any plugins
for k = 1:numel(st.plugins),
feval(['spm_ov_', st.plugins{k}], ...
'context_menu', volhandle, item_parent);
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function c_menu(varargin)
global st
switch lower(varargin{1}),
case 'image_info',
if nargin <3,
current_handle = get_current_handle;
else
current_handle = varargin{3};
end;
if isfield(st.vols{current_handle},'fname'),
[p,n,e,v] = spm_fileparts(st.vols{current_handle}.fname);
if isfield(st.vols{current_handle},'n')
v = sprintf(',%d',st.vols{current_handle}.n);
end;
set(varargin{2}, 'Label',[n e v]);
end;
delete(get(varargin{2},'children'));
if exist('p','var')
item1 = uimenu(varargin{2}, 'Label', p);
end;
if isfield(st.vols{current_handle},'descrip'),
item2 = uimenu(varargin{2}, 'Label',...
st.vols{current_handle}.descrip);
end;
dt = st.vols{current_handle}.dt(1);
item3 = uimenu(varargin{2}, 'Label', sprintf('Data type: %s', spm_type(dt)));
str = 'Intensity: varied';
if size(st.vols{current_handle}.pinfo,2) == 1,
if st.vols{current_handle}.pinfo(2),
str = sprintf('Intensity: Y = %g X + %g',...
st.vols{current_handle}.pinfo(1:2)');
else
str = sprintf('Intensity: Y = %g X', st.vols{current_handle}.pinfo(1)');
end;
end;
item4 = uimenu(varargin{2}, 'Label',str);
item5 = uimenu(varargin{2}, 'Label', 'Image dims', 'Separator','on');
item51 = uimenu(varargin{2}, 'Label',...
sprintf('%dx%dx%d', st.vols{current_handle}.dim(1:3)));
prms = spm_imatrix(st.vols{current_handle}.mat);
item6 = uimenu(varargin{2}, 'Label','Voxel size', 'Separator','on');
item61 = uimenu(varargin{2}, 'Label', sprintf('%.2f %.2f %.2f', prms(7:9)));
item7 = uimenu(varargin{2}, 'Label','Origin', 'Separator','on');
item71 = uimenu(varargin{2}, 'Label',...
sprintf('%.2f %.2f %.2f', prms(1:3)));
R = spm_matrix([0 0 0 prms(4:6)]);
item8 = uimenu(varargin{2}, 'Label','Rotations', 'Separator','on');
item81 = uimenu(varargin{2}, 'Label', sprintf('%.2f %.2f %.2f', R(1,1:3)));
item82 = uimenu(varargin{2}, 'Label', sprintf('%.2f %.2f %.2f', R(2,1:3)));
item83 = uimenu(varargin{2}, 'Label', sprintf('%.2f %.2f %.2f', R(3,1:3)));
item9 = uimenu(varargin{2},...
'Label','Specify other image...',...
'Callback','spm_orthviews(''context_menu'',''swap_img'');',...
'Separator','on');
case 'repos_mm',
oldpos_mm = spm_orthviews('pos');
newpos_mm = spm_input('New Position (mm)','+1','r',sprintf('%.2f %.2f %.2f',oldpos_mm),3);
spm_orthviews('reposition',newpos_mm);
case 'repos_vx'
current_handle = get_current_handle;
oldpos_vx = spm_orthviews('pos', current_handle);
newpos_vx = spm_input('New Position (voxels)','+1','r',sprintf('%.2f %.2f %.2f',oldpos_vx),3);
newpos_mm = st.vols{current_handle}.mat*[newpos_vx;1];
spm_orthviews('reposition',newpos_mm(1:3));
case 'zoom'
zoom_all(varargin{2});
bbox;
redraw_all;
case 'xhair',
spm_orthviews('Xhairs',varargin{2});
cm_handles = get_cm_handles;
for i = 1:numel(cm_handles),
z_handle = get(findobj(cm_handles(i),'label','Crosshairs'),'Children');
set(z_handle,'Checked','off'); %reset check
if strcmp(varargin{2},'off'), op = 1; else op = 2; end
set(z_handle(op),'Checked','on');
end;
case 'orientation',
cm_handles = get_cm_handles;
for i = 1:numel(cm_handles),
z_handle = get(findobj(cm_handles(i),'label','Orientation'),'Children');
set(z_handle,'Checked','off');
end;
if varargin{2} == 3,
spm_orthviews('Space');
for i = 1:numel(cm_handles),
z_handle = findobj(cm_handles(i),'label','World space');
set(z_handle,'Checked','on');
end;
elseif varargin{2} == 2,
spm_orthviews('Space',1);
for i = 1:numel(cm_handles),
z_handle = findobj(cm_handles(i),'label',...
'Voxel space (1st image)');
set(z_handle,'Checked','on');
end;
else
spm_orthviews('Space',get_current_handle);
z_handle = findobj(st.vols{get_current_handle}.ax{1}.cm, ...
'label','Voxel space (this image)');
set(z_handle,'Checked','on');
return;
end;
case 'snap',
cm_handles = get_cm_handles;
for i = 1:numel(cm_handles),
z_handle = get(findobj(cm_handles(i),'label','Snap to Grid'),'Children');
set(z_handle,'Checked','off');
end;
if varargin{2} == 3,
st.snap = [];
elseif varargin{2} == 2,
st.snap = 1;
else
st.snap = get_current_handle;
z_handle = get(findobj(st.vols{get_current_handle}.ax{1}.cm,'label','Snap to Grid'),'Children');
set(z_handle(1),'Checked','on');
return;
end;
for i = 1:numel(cm_handles),
z_handle = get(findobj(cm_handles(i),'label','Snap to Grid'),'Children');
set(z_handle(varargin{2}),'Checked','on');
end;
case 'interpolation',
tmp = [-4 1 0];
st.hld = tmp(varargin{2});
cm_handles = get_cm_handles;
for i = 1:numel(cm_handles),
z_handle = get(findobj(cm_handles(i),'label','Interpolation'),'Children');
set(z_handle,'Checked','off');
set(z_handle(varargin{2}),'Checked','on');
end;
redraw_all;
case 'window',
current_handle = get_current_handle;
if varargin{2} == 2,
spm_orthviews('window',current_handle);
else
if isnumeric(st.vols{current_handle}.window)
defstr = sprintf('%.2f %.2f', st.vols{current_handle}.window);
else
defstr = '';
end;
[w yp] = spm_input('Range','+1','e',defstr,[1 inf]);
while numel(w) < 1 || numel(w) > 2
uiwait(warndlg('Window must be one or two numbers','Wrong input size','modal'));
[w yp] = spm_input('Range',yp,'e',defstr,[1 inf]);
end
if numel(w) == 1
w(2) = w(1)+eps;
end
spm_orthviews('window',current_handle,w);
end;
case 'window_gl',
if varargin{2} == 2,
for i = 1:numel(get_cm_handles),
st.vols{i}.window = 'auto';
end;
else
current_handle = get_current_handle;
if isnumeric(st.vols{current_handle}.window)
defstr = sprintf('%d %d', st.vols{current_handle}.window);
else
defstr = '';
end;
[w yp] = spm_input('Range','+1','e',defstr,[1 inf]);
while numel(w) < 1 || numel(w) > 2
uiwait(warndlg('Window must be one or two numbers','Wrong input size','modal'));
[w yp] = spm_input('Range',yp,'e',defstr,[1 inf]);
end
if numel(w) == 1
w(2) = w(1)+eps;
end
for i = 1:numel(get_cm_handles),
st.vols{i}.window = w;
end;
end;
redraw_all;
case 'mapping',
checked = strcmp(varargin{2}, ...
{'linear', 'histeq', 'loghisteq', ...
'quadhisteq'});
checked = checked(end:-1:1); % Handles are stored in inverse order
current_handle = get_current_handle;
cm_handles = get_cm_handles;
st.vols{current_handle}.mapping = varargin{2};
z_handle = get(findobj(cm_handles(current_handle), ...
'label','Intensity mapping'),'Children');
for k = 1:numel(z_handle)
c_handle = get(z_handle(k), 'Children');
set(c_handle, 'checked', 'off');
set(c_handle(checked), 'checked', 'on');
end;
redraw_all;
case 'mapping_gl',
checked = strcmp(varargin{2}, ...
{'linear', 'histeq', 'loghisteq', 'quadhisteq'});
checked = checked(end:-1:1); % Handles are stored in inverse order
cm_handles = get_cm_handles;
for k = valid_handles(1:24),
st.vols{k}.mapping = varargin{2};
z_handle = get(findobj(cm_handles(k), ...
'label','Intensity mapping'),'Children');
for l = 1:numel(z_handle)
c_handle = get(z_handle(l), 'Children');
set(c_handle, 'checked', 'off');
set(c_handle(checked), 'checked', 'on');
end;
end;
redraw_all;
case 'swap_img',
current_handle = get_current_handle;
newimg = spm_select(1,'image','select new image');
if ~isempty(newimg)
new_info = spm_vol(newimg);
fn = fieldnames(new_info);
for k=1:numel(fn)
st.vols{current_handle}.(fn{k}) = new_info.(fn{k});
end;
spm_orthviews('context_menu','image_info',get(gcbo, 'parent'));
redraw_all;
end
case 'add_blobs',
% Add blobs to the image - in split colortable
cm_handles = valid_handles(1:24);
if varargin{2} == 2, cm_handles = get_current_handle; end;
spm_figure('Clear','Interactive');
[SPM,VOL] = spm_getSPM;
if ~isempty(SPM)
for i = 1:numel(cm_handles),
addblobs(cm_handles(i),VOL.XYZ,VOL.Z,VOL.M);
c_handle = findobj(findobj(st.vols{cm_handles(i)}.ax{1}.cm,'label','Blobs'),'Label','Remove blobs');
set(c_handle,'Visible','on');
delete(get(c_handle,'Children'));
item7_3_1 = uimenu(c_handle,'Label','local','Callback','spm_orthviews(''context_menu'',''remove_blobs'',2);');
if varargin{2} == 1,
item7_3_2 = uimenu(c_handle,'Label','global','Callback','spm_orthviews(''context_menu'',''remove_blobs'',1);');
end;
end;
redraw_all;
end
case 'remove_blobs',
cm_handles = valid_handles(1:24);
if varargin{2} == 2, cm_handles = get_current_handle; end;
for i = 1:numel(cm_handles),
rmblobs(cm_handles(i));
c_handle = findobj(findobj(st.vols{cm_handles(i)}.ax{1}.cm,'label','Blobs'),'Label','Remove blobs');
delete(get(c_handle,'Children'));
set(c_handle,'Visible','off');
end;
redraw_all;
case 'add_image',
% Add blobs to the image - in split colortable
cm_handles = valid_handles(1:24);
if varargin{2} == 2, cm_handles = get_current_handle; end;
spm_figure('Clear','Interactive');
fname = spm_select(1,'image','select image');
if ~isempty(fname)
for i = 1:numel(cm_handles),
addimage(cm_handles(i),fname);
c_handle = findobj(findobj(st.vols{cm_handles(i)}.ax{1}.cm,'label','Blobs'),'Label','Remove blobs');
set(c_handle,'Visible','on');
delete(get(c_handle,'Children'));
item7_3_1 = uimenu(c_handle,'Label','local','Callback','spm_orthviews(''context_menu'',''remove_blobs'',2);');
if varargin{2} == 1,
item7_3_2 = uimenu(c_handle,'Label','global','Callback','spm_orthviews(''context_menu'',''remove_blobs'',1);');
end;
end;
redraw_all;
end
case 'add_c_blobs',
% Add blobs to the image - in full colour
cm_handles = valid_handles(1:24);
if varargin{2} == 2, cm_handles = get_current_handle; end;
spm_figure('Clear','Interactive');
[SPM,VOL] = spm_getSPM;
if ~isempty(SPM)
c = spm_input('Colour','+1','m',...
'Red blobs|Yellow blobs|Green blobs|Cyan blobs|Blue blobs|Magenta blobs',[1 2 3 4 5 6],1);
colours = [1 0 0;1 1 0;0 1 0;0 1 1;0 0 1;1 0 1];
c_names = {'red';'yellow';'green';'cyan';'blue';'magenta'};
hlabel = sprintf('%s (%s)',VOL.title,c_names{c});
for i = 1:numel(cm_handles),
addcolouredblobs(cm_handles(i),VOL.XYZ,VOL.Z,VOL.M,colours(c,:),VOL.title);
addcolourbar(cm_handles(i),numel(st.vols{cm_handles(i)}.blobs));
c_handle = findobj(findobj(st.vols{cm_handles(i)}.ax{1}.cm,'label','Blobs'),'Label','Remove colored blobs');
ch_c_handle = get(c_handle,'Children');
set(c_handle,'Visible','on');
%set(ch_c_handle,'Visible',on');
item7_4_1 = uimenu(ch_c_handle(2),'Label',hlabel,'ForegroundColor',colours(c,:),...
'Callback','c = get(gcbo,''UserData'');spm_orthviews(''context_menu'',''remove_c_blobs'',2,c);',...
'UserData',c);
if varargin{2} == 1,
item7_4_2 = uimenu(ch_c_handle(1),'Label',hlabel,'ForegroundColor',colours(c,:),...
'Callback','c = get(gcbo,''UserData'');spm_orthviews(''context_menu'',''remove_c_blobs'',1,c);',...
'UserData',c);
end;
end;
redraw_all;
end
case 'remove_c_blobs',
cm_handles = valid_handles(1:24);
if varargin{2} == 2, cm_handles = get_current_handle; end;
colours = [1 0 0;1 1 0;0 1 0;0 1 1;0 0 1;1 0 1];
for i = 1:numel(cm_handles),
if isfield(st.vols{cm_handles(i)},'blobs'),
for j = 1:numel(st.vols{cm_handles(i)}.blobs),
if all(st.vols{cm_handles(i)}.blobs{j}.colour == colours(varargin{3},:));
if isfield(st.vols{cm_handles(i)}.blobs{j},'cbar')
delete(st.vols{cm_handles(i)}.blobs{j}.cbar);
end
st.vols{cm_handles(i)}.blobs(j) = [];
break;
end;
end;
rm_c_menu = findobj(st.vols{cm_handles(i)}.ax{1}.cm,'Label','Remove colored blobs');
delete(gcbo);
if isempty(st.vols{cm_handles(i)}.blobs),
st.vols{cm_handles(i)} = rmfield(st.vols{cm_handles(i)},'blobs');
set(rm_c_menu, 'Visible', 'off');
end;
end;
end;
redraw_all;
case 'add_c_image',
% Add truecolored image
cm_handles = valid_handles(1:24);
if varargin{2} == 2, cm_handles = get_current_handle;end;
spm_figure('Clear','Interactive');
fname = spm_select(1,'image','select image');
if ~isempty(fname)
c = spm_input('Colour','+1','m','Red blobs|Yellow blobs|Green blobs|Cyan blobs|Blue blobs|Magenta blobs',[1 2 3 4 5 6],1);
colours = [1 0 0;1 1 0;0 1 0;0 1 1;0 0 1;1 0 1];
c_names = {'red';'yellow';'green';'cyan';'blue';'magenta'};
hlabel = sprintf('%s (%s)',fname,c_names{c});
for i = 1:numel(cm_handles),
addcolouredimage(cm_handles(i),fname,colours(c,:));
addcolourbar(cm_handles(i),numel(st.vols{cm_handles(i)}.blobs));
c_handle = findobj(findobj(st.vols{cm_handles(i)}.ax{1}.cm,'label','Blobs'),'Label','Remove colored blobs');
ch_c_handle = get(c_handle,'Children');
set(c_handle,'Visible','on');
%set(ch_c_handle,'Visible',on');
item7_4_1 = uimenu(ch_c_handle(2),'Label',hlabel,'ForegroundColor',colours(c,:),...
'Callback','c = get(gcbo,''UserData'');spm_orthviews(''context_menu'',''remove_c_blobs'',2,c);','UserData',c);
if varargin{2} == 1
item7_4_2 = uimenu(ch_c_handle(1),'Label',hlabel,'ForegroundColor',colours(c,:),...
'Callback','c = get(gcbo,''UserData'');spm_orthviews(''context_menu'',''remove_c_blobs'',1,c);',...
'UserData',c);
end
end
redraw_all;
end
end;
%_______________________________________________________________________
%_______________________________________________________________________
function current_handle = get_current_handle
cm_handle = get(gca,'UIContextMenu');
cm_handles = get_cm_handles;
current_handle = find(cm_handles==cm_handle);
return;
%_______________________________________________________________________
%_______________________________________________________________________
function cm_pos
global st
for i = 1:numel(valid_handles(1:24)),
if isfield(st.vols{i}.ax{1},'cm')
set(findobj(st.vols{i}.ax{1}.cm,'UserData','pos_mm'),...
'Label',sprintf('mm: %.1f %.1f %.1f',spm_orthviews('pos')));
pos = spm_orthviews('pos',i);
set(findobj(st.vols{i}.ax{1}.cm,'UserData','pos_vx'),...
'Label',sprintf('vx: %.1f %.1f %.1f',pos));
set(findobj(st.vols{i}.ax{1}.cm,'UserData','v_value'),...
'Label',sprintf('Y = %g',spm_sample_vol(st.vols{i},pos(1),pos(2),pos(3),st.hld)));
end
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function cm_handles = get_cm_handles
global st
cm_handles = [];
for i=valid_handles(1:24),
cm_handles = [cm_handles st.vols{i}.ax{1}.cm];
end
return;
%_______________________________________________________________________
%_______________________________________________________________________
function zoom_all(op)
global st
cm_handles = get_cm_handles;
res = [.125 .125 .25 .5 1 1];
if op==6,
st.bb = maxbb;
else
vx = sqrt(sum(st.Space(1:3,1:3).^2));
vx = vx.^(-1);
pos = spm_orthviews('pos');
pos = st.Space\[pos ; 1];
pos = pos(1:3)';
if op == 5, st.bb = [pos-80*vx ; pos+80*vx] ;
elseif op == 4, st.bb = [pos-40*vx ; pos+40*vx] ;
elseif op == 3, st.bb = [pos-20*vx ; pos+20*vx] ;
elseif op == 2, st.bb = [pos-10*vx ; pos+10*vx] ;
elseif op == 1; st.bb = [pos- 5*vx ; pos+ 5*vx] ;
else disp('no Zoom possible');
end;
end
resolution(res(op));
redraw_all;
for i = 1:numel(cm_handles)
z_handle = get(findobj(cm_handles(i),'label','Zoom'),'Children');
set(z_handle,'Checked','off');
set(z_handle(op),'Checked','on');
end
if isfield(st.vols{1},'sdip')
spm_eeg_inv_vbecd_disp('RedrawDip');
end
return;
|
github
|
lcnbeapp/beapp-master
|
spm_maff.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_maff.m
| 11,287 |
utf_8
|
67d7a7a2de40e5f6a1c0c0e5e9f630f3
|
function [M,h] = spm_maff(varargin)
% Affine registration to MNI space using mutual information
% FORMAT M = spm_maff(P,samp,x,b0,MF,M,regtyp,ff)
% P - filename or structure handle of image
% x - cell array of {x1,x2,x3}, where x1 and x2 are
% co-ordinates (from ndgrid), and x3 is a list of
% slice numbers to use
% b0 - a cell array of belonging probability images
% (see spm_load_priors.m).
% MF - voxel-to-world transform of belonging probability
% images
% M - starting estimates
% regtype - regularisation type
% 'mni' - registration of European brains with MNI space
% 'eastern' - registration of East Asian brains with MNI space
% 'rigid' - rigid(ish)-body registration
% 'subj' - inter-subject registration
% 'none' - no regularisation
% ff - a fudge factor (derived from the one above)
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id$
[buf,MG] = loadbuf(varargin{1:2});
M = affreg(buf, MG, varargin{2:end});
return;
%_______________________________________________________________________
%_______________________________________________________________________
function [buf,MG] = loadbuf(V,x)
if ischar(V), V = spm_vol(V); end;
x1 = x{1};
x2 = x{2};
x3 = x{3};
% Load the image
V = spm_vol(V);
d = V(1).dim(1:3);
o = ones(size(x1));
d = [size(x1) length(x3)];
g = zeros(d);
spm_progress_bar('Init',V.dim(3),'Loading volume','Planes loaded');
for i=1:d(3)
g(:,:,i) = spm_sample_vol(V,x1,x2,o*x3(i),0);
spm_progress_bar('Set',i);
end;
spm_progress_bar('Clear');
% Convert the image to unsigned bytes
[mn,mx] = spm_minmax(g);
sw = warning('off','all');
for z=1:length(x3),
gz = g(:,:,z);
buf(z).msk = gz>mn & isfinite(gz);
buf(z).nm = sum(buf(z).msk(:));
gz = double(gz(buf(z).msk));
buf(z).g = uint8(round(gz*(255/mx)));
end;
warning(sw);
MG = V.mat;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function [M,h0] = affreg(buf,MG,x,b0,MF,M,regtyp,ff)
% Do the work
x1 = x{1};
x2 = x{2};
x3 = x{3};
[mu,isig] = priors(regtyp);
isig = isig*ff;
Alpha0 = isig;
Beta0 = -isig*mu;
sol = M2P(M);
sol1 = sol;
ll = -Inf;
nsmp = sum(cat(1,buf.nm));
pr = struct('b',[],'db1',[],'db2',[],'db3',[]);
spm_chi2_plot('Init','Registering','Log-likelihood','Iteration');
for iter=1:200
penalty = (sol1-mu)'*isig*(sol1-mu);
T = MF\P2M(sol1)*MG;
R = derivs(MF,sol1,MG);
y1a = T(1,1)*x1 + T(1,2)*x2 + T(1,4);
y2a = T(2,1)*x1 + T(2,2)*x2 + T(2,4);
y3a = T(3,1)*x1 + T(3,2)*x2 + T(3,4);
h0 = zeros(256,length(b0)-1)+eps;
for i=1:length(x3),
if ~buf(i).nm, continue; end;
y1 = y1a(buf(i).msk) + T(1,3)*x3(i);
y2 = y2a(buf(i).msk) + T(2,3)*x3(i);
y3 = y3a(buf(i).msk) + T(3,3)*x3(i);
for k=1:size(h0,2),
pr(k).b = spm_sample_priors(b0{k},y1,y2,y3,k==length(b0));
h0(:,k) = h0(:,k) + spm_hist(buf(i).g,pr(k).b);
end;
end;
h1 = (h0+eps);
ssh = sum(h1(:));
krn = spm_smoothkern(2,(-256:256)',0);
h1 = conv2(h1,krn,'same');
h1 = h1/ssh;
h2 = log2(h1./(sum(h1,2)*sum(h1,1)));
ll1 = sum(sum(h0.*h2))/ssh - penalty/ssh;
spm_chi2_plot('Set',ll1);
if ll1-ll<1e-5, break; end;
ll = ll1;
sol = sol1;
Alpha = zeros(12);
Beta = zeros(12,1);
for i=1:length(x3),
nz = buf(i).nm;
if ~nz, continue; end;
msk = buf(i).msk;
gi = double(buf(i).g)+1;
y1 = y1a(msk) + T(1,3)*x3(i);
y2 = y2a(msk) + T(2,3)*x3(i);
y3 = y3a(msk) + T(3,3)*x3(i);
dmi1 = zeros(nz,1);
dmi2 = zeros(nz,1);
dmi3 = zeros(nz,1);
for k=1:size(h0,2),
[pr(k).b, pr(k).db1, pr(k).db2, pr(k).db3] = spm_sample_priors(b0{k},y1,y2,y3,k==length(b0));
tmp = -h2(gi,k);
dmi1 = dmi1 + tmp.*pr(k).db1;
dmi2 = dmi2 + tmp.*pr(k).db2;
dmi3 = dmi3 + tmp.*pr(k).db3;
end;
x1m = x1(msk);
x2m = x2(msk);
x3m = x3(i);
A = [dmi1.*x1m dmi2.*x1m dmi3.*x1m...
dmi1.*x2m dmi2.*x2m dmi3.*x2m...
dmi1 *x3m dmi2 *x3m dmi3 *x3m...
dmi1 dmi2 dmi3];
Alpha = Alpha + A'*A;
Beta = Beta + sum(A,1)';
end;
drawnow;
Alpha = R'*Alpha*R;
Beta = R'*Beta;
% Gauss-Newton update
sol1 = (Alpha+Alpha0)\(Alpha*sol - Beta - Beta0);
end;
spm_chi2_plot('Clear');
M = P2M(sol);
return;
%_______________________________________________________________________
%_______________________________________________________________________
function P = M2P(M)
% Polar decomposition parameterisation of affine transform,
% based on matrix logs
J = M(1:3,1:3);
V = sqrtm(J*J');
R = V\J;
lV = logm(V);
lR = -logm(R);
if sum(sum(imag(lR).^2))>1e-6, error('Rotations by pi are still a problem.'); end;
P = zeros(12,1);
P(1:3) = M(1:3,4);
P(4:6) = lR([2 3 6]);
P(7:12) = lV([1 2 3 5 6 9]);
return;
%_______________________________________________________________________
%_______________________________________________________________________
function M = P2M(P)
% Polar decomposition parameterisation of affine transform,
% based on matrix logs
% Translations
D = P(1:3);
D = D(:);
% Rotation part
ind = [2 3 6];
T = zeros(3);
T(ind) = -P(4:6);
R = expm(T-T');
% Symmetric part (zooms and shears)
ind = [1 2 3 5 6 9];
T = zeros(3);
T(ind) = P(7:12);
V = expm(T+T'-diag(diag(T)));
M = [V*R D ; 0 0 0 1];
return;
%_______________________________________________________________________
%_______________________________________________________________________
function R = derivs(MF,P,MG)
% Numerically compute derivatives of Affine transformation matrix w.r.t.
% changes in the parameters.
R = zeros(12,12);
M0 = MF\P2M(P)*MG;
M0 = M0(1:3,:);
for i=1:12
dp = 0.000000001;
P1 = P;
P1(i) = P1(i) + dp;
M1 = MF\P2M(P1)*MG;
M1 = M1(1:3,:);
R(:,i) = (M1(:)-M0(:))/dp;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function [mu,isig] = priors(typ)
% The parameters for this distribution were derived empirically from 227
% scans, that were matched to the ICBM space.
%% Values can be derived by...
%sn = spm_select(Inf,'.*seg_inv_sn.mat$');
%X = zeros(size(sn,1),12);
%for i=1:size(sn,1),
% p = load(deblank(sn(i,:)));
% M = p.VF(1).mat*p.Affine/p.VG(1).mat;
% J = M(1:3,1:3);
% V = sqrtm(J*J');
% R = V\J;
% lV = logm(V);
% lR = -logm(R);
% P = zeros(12,1);
% P(1:3) = M(1:3,4);
% P(4:6) = lR([2 3 6]);
% P(7:12) = lV([1 2 3 5 6 9]);
% X(i,:) = P';
%end;
%mu = mean(X(:,7:12));
%XR = X(:,7:12) - repmat(mu,[size(X,1),1]);
%isig = inv(XR'*XR/(size(X,1)-1))
mu = zeros(6,1);
isig = zeros(6);
switch deblank(lower(typ))
case 'mni', % For registering with MNI templates...
mu = [0.0667 0.0039 0.0008 0.0333 0.0071 0.1071]';
isig = 1e4 * [
0.0902 -0.0345 -0.0106 -0.0025 -0.0005 -0.0163
-0.0345 0.7901 0.3883 0.0041 -0.0103 -0.0116
-0.0106 0.3883 2.2599 0.0113 0.0396 -0.0060
-0.0025 0.0041 0.0113 0.0925 0.0471 -0.0440
-0.0005 -0.0103 0.0396 0.0471 0.2964 -0.0062
-0.0163 -0.0116 -0.0060 -0.0440 -0.0062 0.1144];
case 'imni', % For registering with MNI templates...
mu = -[0.0667 0.0039 0.0008 0.0333 0.0071 0.1071]';
isig = 1e4 * [
0.0902 -0.0345 -0.0106 -0.0025 -0.0005 -0.0163
-0.0345 0.7901 0.3883 0.0041 -0.0103 -0.0116
-0.0106 0.3883 2.2599 0.0113 0.0396 -0.0060
-0.0025 0.0041 0.0113 0.0925 0.0471 -0.0440
-0.0005 -0.0103 0.0396 0.0471 0.2964 -0.0062
-0.0163 -0.0116 -0.0060 -0.0440 -0.0062 0.1144];
case 'rigid', % Constrained to be almost rigid...
mu = zeros(6,1);
isig = eye(6)*1e8;
case 'subj', % For inter-subject registration...
mu = zeros(6,1);
isig = 1e3 * [
0.8876 0.0784 0.0784 -0.1749 0.0784 -0.1749
0.0784 5.3894 0.2655 0.0784 0.2655 0.0784
0.0784 0.2655 5.3894 0.0784 0.2655 0.0784
-0.1749 0.0784 0.0784 0.8876 0.0784 -0.1749
0.0784 0.2655 0.2655 0.0784 5.3894 0.0784
-0.1749 0.0784 0.0784 -0.1749 0.0784 0.8876];
case 'eastern', % For East Asian brains to MNI...
mu = [0.0719 -0.0040 -0.0032 0.1416 0.0601 0.2578]';
isig = 1e4 * [
0.0757 0.0220 -0.0224 -0.0049 0.0304 -0.0327
0.0220 0.3125 -0.1555 0.0280 -0.0012 -0.0284
-0.0224 -0.1555 1.9727 0.0196 -0.0019 0.0122
-0.0049 0.0280 0.0196 0.0576 -0.0282 -0.0200
0.0304 -0.0012 -0.0019 -0.0282 0.2128 -0.0275
-0.0327 -0.0284 0.0122 -0.0200 -0.0275 0.0511];
case 'none', % No regularisation...
mu = zeros(6,1);
isig = zeros(6);
otherwise
error(['"' typ '" not recognised as type of regularisation.']);
end;
mu = [zeros(6,1) ; mu];
isig = [zeros(6,12) ; zeros(6,6) isig];
return;
%_______________________________________________________________________
%_______________________________________________________________________
function [h0,d1] = reg_unused(M)
% Try to analytically compute the first and second derivatives of a
% penalty function w.r.t. changes in parameters. It works for first
% derivatives, but I couldn't make it work for the second derivs - so
% I gave up and tried a new strategy.
T = M(1:3,1:3);
[U,S,V] = svd(T);
s = diag(S);
h0 = sum(log(s).^2);
d1s = 2*log(s)./s;
%d2s = 2./s.^2-2*log(s)./s.^2;
d1 = zeros(12,1);
for j=1:3
for i1=1:9
T1 = zeros(3,3);
T1(i1) = 1;
t1 = U(:,j)'*T1*V(:,j);
d1(i1) = d1(i1) + d1s(j)*t1;
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function M = P2M_unused(P)
% SVD parameterisation of affine transform, based on matrix-logs.
% Translations
D = P(1:3);
D = D(:);
% Rotation U
ind = [2 3 6];
T = zeros(3);
T(ind) = P(4:6);
U = expm(T-T');
% Diagonal zooming matrix
S = expm(diag(P(7:9)));
% Rotation V'
T(ind) = P(10:12);
V = expm(T'-T);
M = [U*S*V' D ; 0 0 0 1];
return;
%_______________________________________________________________________
%_______________________________________________________________________
|
github
|
lcnbeapp/beapp-master
|
spm_normalise.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_normalise.m
| 13,235 |
utf_8
|
5dfafbc96b6282a48b19ee3433a77167
|
function params = spm_normalise(VG,VF,matname,VWG,VWF,flags)
% Spatial (stereotactic) normalization
%
% FORMAT params = spm_normalise(VG,VF,matname,VWG,VWF,flags)
% VG - template handle(s)
% VF - handle of image to estimate params from
% matname - name of file to store deformation definitions
% VWG - template weighting image
% VWF - source weighting image
% flags - flags. If any field is not passed, then defaults are assumed.
% smosrc - smoothing of source image (FWHM of Gaussian in mm).
% Defaults to 8.
% smoref - smoothing of template image (defaults to 0).
% regtype - regularisation type for affine registration
% See spm_affreg.m (default = 'mni').
% cutoff - Cutoff of the DCT bases. Lower values mean more
% basis functions are used (default = 30mm).
% nits - number of nonlinear iterations (default=16).
% reg - amount of regularisation (default=0.1)
% ___________________________________________________________________________
%
% This module spatially (stereotactically) normalizes MRI, PET or SPECT
% images into a standard space defined by some ideal model or template
% image[s]. The template images supplied with SPM conform to the space
% defined by the ICBM, NIH P-20 project, and approximate that of the
% the space described in the atlas of Talairach and Tournoux (1988).
% The transformation can also be applied to any other image that has
% been coregistered with these scans.
%
%
% Mechanism
% Generally, the algorithms work by minimising the sum of squares
% difference between the image which is to be normalised, and a linear
% combination of one or more template images. For the least squares
% registration to produce an unbiased estimate of the spatial
% transformation, the image contrast in the templates (or linear
% combination of templates) should be similar to that of the image from
% which the spatial normalization is derived. The registration simply
% searches for an optimum solution. If the starting estimates are not
% good, then the optimum it finds may not find the global optimum.
%
% The first step of the normalization is to determine the optimum
% 12-parameter affine transformation. Initially, the registration is
% performed by matching the whole of the head (including the scalp) to
% the template. Following this, the registration proceeded by only
% matching the brains together, by appropriate weighting of the template
% voxels. This is a completely automated procedure (that does not
% require ``scalp editing'') that discounts the confounding effects of
% skull and scalp differences. A Bayesian framework is used, such that
% the registration searches for the solution that maximizes the a
% posteriori probability of it being correct. i.e., it maximizes the
% product of the likelihood function (derived from the residual squared
% difference) and the prior function (which is based on the probability
% of obtaining a particular set of zooms and shears).
%
% The affine registration is followed by estimating nonlinear deformations,
% whereby the deformations are defined by a linear combination of three
% dimensional discrete cosine transform (DCT) basis functions.
% The parameters represent coefficients of the deformations in
% three orthogonal directions. The matching involved simultaneously
% minimizing the bending energies of the deformation fields and the
% residual squared difference between the images and template(s).
%
% An option is provided for allowing weighting images (consisting of pixel
% values between the range of zero to one) to be used for registering
% abnormal or lesioned brains. These images should match the dimensions
% of the image from which the parameters are estimated, and should contain
% zeros corresponding to regions of abnormal tissue.
%
%
% Uses
% Primarily for stereotactic normalization to facilitate inter-subject
% averaging and precise characterization of functional anatomy. It is
% not necessary to spatially normalise the data (this is only a
% pre-requisite for intersubject averaging or reporting in the
% Talairach space).
%
% Inputs
% The first input is the image which is to be normalised. This image
% should be of the same modality (and MRI sequence etc) as the template
% which is specified. The same spatial transformation can then be
% applied to any other images of the same subject. These files should
% conform to the SPM data format (See 'Data Format'). Many subjects can
% be entered at once, and there is no restriction on image dimensions
% or voxel size.
%
% Providing that the images have a correct ".mat" file associated with
% them, which describes the spatial relationship between them, it is
% possible to spatially normalise the images without having first
% resliced them all into the same space. The ".mat" files are generated
% by "spm_realign" or "spm_coregister".
%
% Default values of parameters pertaining to the extent and sampling of
% the standard space can be changed, including the model or template
% image[s].
%
%
% Outputs
% All normalized *.img scans are written to the same subdirectory as
% the original *.img, prefixed with a 'n' (i.e. n*.img). The details
% of the transformations are displayed in the results window, and the
% parameters are saved in the "*_sn.mat" file.
%
%
%____________________________________________________________________________
% Refs:
% K.J. Friston, J. Ashburner, C.D. Frith, J.-B. Poline,
% J.D. Heather, and R.S.J. Frackowiak
% Spatial Registration and Normalization of Images.
% Human Brain Mapping 2:165-189(1995)
%
% J. Ashburner, P. Neelin, D.L. Collins, A.C. Evans and K. J. Friston
% Incorporating Prior Knowledge into Image Registration.
% NeuroImage 6:344-352 (1997)
%
% J. Ashburner and K. J. Friston
% Nonlinear Spatial Normalization using Basis Functions.
% Human Brain Mapping 7(4):in press (1999)
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id$
if nargin<2, error('Incorrect usage.'); end;
if ischar(VF), VF = spm_vol(VF); end;
if ischar(VG), VG = spm_vol(VG); end;
if nargin<3,
if nargout==0,
[pth,nm,xt,vr] = spm_fileparts(deblank(VF(1).fname));
matname = fullfile(pth,[nm '_sn.mat']);
else
matname = '';
end;
end;
if nargin<4, VWG = ''; end;
if nargin<5, VWF = ''; end;
if ischar(VWG), VWG=spm_vol(VWG); end;
if ischar(VWF), VWF=spm_vol(VWF); end;
def_flags = struct('smosrc',8,'smoref',0,'regtype','mni',...
'cutoff',30,'nits',16,'reg',0.1,'graphics',1);
if nargin < 6,
flags = def_flags;
else
fnms = fieldnames(def_flags);
for i=1:length(fnms),
if ~isfield(flags,fnms{i}),
flags = setfield(flags,fnms{i},getfield(def_flags,fnms{i}));
end;
end;
end;
fprintf('Smoothing by %g & %gmm..\n', flags.smoref, flags.smosrc);
VF1 = spm_smoothto8bit(VF,flags.smosrc);
% Rescale images so that globals are better conditioned
VF1.pinfo(1:2,:) = VF1.pinfo(1:2,:)/spm_global(VF1);
for i=1:numel(VG),
VG1(i) = spm_smoothto8bit(VG(i),flags.smoref);
VG1(i).pinfo(1:2,:) = VG1(i).pinfo(1:2,:)/spm_global(VG(i));
end;
% Affine Normalisation
%-----------------------------------------------------------------------
fprintf('Coarse Affine Registration..\n');
aflags = struct('sep',max(flags.smoref,flags.smosrc), 'regtype',flags.regtype,...
'WG',[],'WF',[],'globnorm',0);
aflags.sep = max(aflags.sep,max(sqrt(sum(VG(1).mat(1:3,1:3).^2))));
aflags.sep = max(aflags.sep,max(sqrt(sum(VF(1).mat(1:3,1:3).^2))));
M = eye(4); %spm_matrix(prms');
spm_chi2_plot('Init','Affine Registration','Mean squared difference','Iteration');
[M,scal] = spm_affreg(VG1, VF1, aflags, M);
fprintf('Fine Affine Registration..\n');
aflags.WG = VWG;
aflags.WF = VWF;
aflags.sep = aflags.sep/2;
[M,scal] = spm_affreg(VG1, VF1, aflags, M,scal);
Affine = inv(VG(1).mat\M*VF1(1).mat);
spm_chi2_plot('Clear');
% Basis function Normalisation
%-----------------------------------------------------------------------
fov = VF1(1).dim(1:3).*sqrt(sum(VF1(1).mat(1:3,1:3).^2));
if any(fov<15*flags.smosrc/2 & VF1(1).dim(1:3)<15),
fprintf('Field of view too small for nonlinear registration\n');
Tr = [];
elseif isfinite(flags.cutoff) && flags.nits && ~isinf(flags.reg),
fprintf('3D CT Norm...\n');
Tr = snbasis(VG1,VF1,VWG,VWF,Affine,...
max(flags.smoref,flags.smosrc),flags.cutoff,flags.nits,flags.reg);
else
Tr = [];
end;
clear VF1 VG1
flags.version = 'spm_normalise.m 2.12 04/11/26';
flags.date = date;
params = struct('Affine',Affine, 'Tr',Tr, 'VF',VF, 'VG',VG, 'flags',flags);
if flags.graphics, spm_normalise_disp(params,VF); end;
% Remove dat fields before saving
%-----------------------------------------------------------------------
if isfield(VF,'dat'), VF = rmfield(VF,'dat'); end;
if isfield(VG,'dat'), VG = rmfield(VG,'dat'); end;
if ~isempty(matname),
fprintf('Saving Parameters..\n');
if spm_matlab_version_chk('7') >= 0,
save(matname,'-V6','Affine','Tr','VF','VG','flags');
else
save(matname,'Affine','Tr','VF','VG','flags');
end;
end;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function Tr = snbasis(VG,VF,VWG,VWF,Affine,fwhm,cutoff,nits,reg)
% 3D Basis Function Normalization
% FORMAT Tr = snbasis(VG,VF,VWG,VWF,Affine,fwhm,cutoff,nits,reg)
% VG - Template volumes (see spm_vol).
% VF - Volume to normalize.
% VWG - weighting Volume - for template.
% VWF - weighting Volume - for object.
% Affine - A 4x4 transformation (in voxel space).
% fwhm - smoothness of images.
% cutoff - frequency cutoff of basis functions.
% nits - number of iterations.
% reg - regularisation.
% Tr - Discrete cosine transform of the warps in X, Y & Z.
%
% snbasis performs a spatial normalization based upon a 3D
% discrete cosine transform.
%
%______________________________________________________________________
fwhm = [fwhm 30];
% Number of basis functions for x, y & z
%-----------------------------------------------------------------------
tmp = sqrt(sum(VG(1).mat(1:3,1:3).^2));
k = max(round((VG(1).dim(1:3).*tmp)/cutoff),[1 1 1]);
% Scaling is to improve stability.
%-----------------------------------------------------------------------
stabilise = 8;
basX = spm_dctmtx(VG(1).dim(1),k(1))*stabilise;
basY = spm_dctmtx(VG(1).dim(2),k(2))*stabilise;
basZ = spm_dctmtx(VG(1).dim(3),k(3))*stabilise;
dbasX = spm_dctmtx(VG(1).dim(1),k(1),'diff')*stabilise;
dbasY = spm_dctmtx(VG(1).dim(2),k(2),'diff')*stabilise;
dbasZ = spm_dctmtx(VG(1).dim(3),k(3),'diff')*stabilise;
vx1 = sqrt(sum(VG(1).mat(1:3,1:3).^2));
vx2 = vx1;
kx = (pi*((1:k(1))'-1)/VG(1).dim(1)/vx1(1)).^2; ox=ones(k(1),1);
ky = (pi*((1:k(2))'-1)/VG(1).dim(2)/vx1(2)).^2; oy=ones(k(2),1);
kz = (pi*((1:k(3))'-1)/VG(1).dim(3)/vx1(3)).^2; oz=ones(k(3),1);
if 1,
% BENDING ENERGY REGULARIZATION
% Estimate a suitable sparse diagonal inverse covariance matrix for
% the parameters (IC0).
%-----------------------------------------------------------------------
IC0 = (1*kron(kz.^2,kron(ky.^0,kx.^0)) +...
1*kron(kz.^0,kron(ky.^2,kx.^0)) +...
1*kron(kz.^0,kron(ky.^0,kx.^2)) +...
2*kron(kz.^1,kron(ky.^1,kx.^0)) +...
2*kron(kz.^1,kron(ky.^0,kx.^1)) +...
2*kron(kz.^0,kron(ky.^1,kx.^1)) );
IC0 = reg*IC0*stabilise^6;
IC0 = [IC0*vx2(1)^4 ; IC0*vx2(2)^4 ; IC0*vx2(3)^4 ; zeros(prod(size(VG))*4,1)];
IC0 = sparse(1:length(IC0),1:length(IC0),IC0,length(IC0),length(IC0));
else
% MEMBRANE ENERGY (LAPLACIAN) REGULARIZATION
%-----------------------------------------------------------------------
IC0 = kron(kron(oz,oy),kx) + kron(kron(oz,ky),ox) + kron(kron(kz,oy),ox);
IC0 = reg*IC0*stabilise^6;
IC0 = [IC0*vx2(1)^2 ; IC0*vx2(2)^2 ; IC0*vx2(3)^2 ; zeros(prod(size(VG))*4,1)];
IC0 = sparse(1:length(IC0),1:length(IC0),IC0,length(IC0),length(IC0));
end;
% Generate starting estimates.
%-----------------------------------------------------------------------
s1 = 3*prod(k);
s2 = s1 + numel(VG)*4;
T = zeros(s2,1);
T(s1+(1:4:numel(VG)*4)) = 1;
pVar = Inf;
for iter=1:nits,
fprintf(' iteration %2d: ', iter);
[Alpha,Beta,Var,fw] = spm_brainwarp(VG,VF,Affine,basX,basY,basZ,dbasX,dbasY,dbasZ,T,fwhm,VWG, VWF);
if Var>pVar, scal = pVar/Var ; Var = pVar; else scal = 1; end;
pVar = Var;
T = (Alpha + IC0*scal)\(Alpha*T + Beta);
fwhm(2) = min([fw fwhm(2)]);
fprintf(' FWHM = %6.4g Var = %g\n', fw,Var);
end;
% Values of the 3D-DCT - for some bizarre reason, this needs to be done
% as two seperate statements in Matlab 6.5...
%-----------------------------------------------------------------------
Tr = reshape(T(1:s1),[k 3]);
drawnow;
Tr = Tr*stabilise.^3;
return;
|
github
|
lcnbeapp/beapp-master
|
spm_minmax.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_minmax.m
| 3,705 |
utf_8
|
58192721e506d5814be863bb8a7e2acf
|
function [mnv,mxv] = spm_minmax(g)
% Compute a suitable range of intensities for VBM preprocessing stuff
% FORMAT [mnv,mxv] = spm_minmax(g)
% g - array of data
% mnv - minimum value
% mxv - maximum value
%
% A MOG with two Gaussians is fitted to the intensities. The lower
% Gaussian is assumed to represent background. The lower value is
% where there is a 50% probability of being above background. The
% upper value is one that encompases 99.5% of the values.
%____________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id$
d = [size(g) 1];
mxv = double(max(g(:)));
mnv = double(min(g(:)));
h = zeros(256,1);
spm_progress_bar('Init',d(3),'Initial histogram','Planes loaded');
sw = warning('off','all');
for i=1:d(3)
h = h + spm_hist(uint8(round(g(:,:,i)*(255/mxv))),ones(d(1)*d(2),1));
spm_progress_bar('Set',i);
end;
warning(sw);
spm_progress_bar('Clear');
% Occasional problems with partially masked data because the first Gaussian
% just fits the big peak at zero. This will fix that one, but cause problems
% for skull-stripped data.
h(1) = 0;
h(end) = 0;
% Very crude heuristic to find a suitable lower limit. The large amount
% of background really messes up mutual information registration.
% Begin by modelling the intensity histogram with two Gaussians. One
% for background, and the other for tissue.
[mn,v,mg] = fithisto((0:255)',h,1000,[1 128],[32 128].^2,[1 1]);
pr = distribution(mn,v,mg,(0:255)');
%fg = spm_figure('FindWin','Interactive');
%if ~isempty(fg)
% figure(fg);
% plot((0:255)',h/sum(h),'b', (0:255)',pr,'r');
% drawnow;
%end;
% Find the lowest intensity above the mean of the first Gaussian
% where there is more than 50% probability of not being background
mnd = find((pr(:,1)./(sum(pr,2)+eps) < 0.5) & (0:255)' >mn(1));
if isempty(mnd) || mnd(1)==1 || mn(1)>mn(2),
mnd = 1;
else
mnd = mnd(1)-1;
end
mnv = mnd*mxv/255;
% Upper limit should get 99.5% of the intensities of the
% non-background region
ch = cumsum(h(mnd:end))/sum(h(mnd:end));
ch = find(ch>0.995)+mnd;
mxv = ch(1)/255*mxv;
return;
%_______________________________________________________________________
%_______________________________________________________________________
function [mn,v,mg,ll]=fithisto(x,h,maxit,n,v,mg)
% Fit a mixture of Gaussians to a histogram
h = h(:);
x = x(:);
sml = mean(diff(x))/1000;
if nargin==4
mg = sum(h);
mn = sum(x.*h)/mg;
v = (x - mn); v = sum(v.*v.*h)/mg*ones(1,n);
mn = (1:n)'/n*(max(x)-min(x))+min(x);
mg = mg*ones(1,n)/n;
elseif nargin==6
mn = n;
n = length(mn);
else
error('Incorrect usage');
end;
ll = Inf;
for it=1:maxit
prb = distribution(mn,v,mg,x);
scal = sum(prb,2)+eps;
oll = ll;
ll = -sum(h.*log(scal));
if it>2 && oll-ll < length(x)/n*1e-9
break;
end;
for j=1:n
p = h.*prb(:,j)./scal;
mg(j) = sum(p);
mn(j) = sum(x.*p)/mg(j);
vr = x-mn(j);
v(j) = sum(vr.*vr.*p)/mg(j)+sml;
end;
mg = mg + 1e-3;
mg = mg/sum(mg);
end;
%_______________________________________________________________________
%_______________________________________________________________________
function y=distribution(m,v,g,x)
% Gaussian probability density
if nargin ~= 4
error('not enough input arguments');
end;
x = x(:);
m = m(:);
v = v(:);
g = g(:);
if ~all(size(m) == size(v) & size(m) == size(g))
error('incompatible dimensions');
end;
for i=1:size(m,1)
d = x-m(i);
amp = g(i)/sqrt(2*pi*v(i));
y(:,i) = amp*exp(-0.5 * (d.*d)/v(i));
end;
return;
|
github
|
lcnbeapp/beapp-master
|
spm_create_vol.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_create_vol.m
| 4,914 |
utf_8
|
3d1ffa54c52618a0923d6642b8f5e471
|
function V = spm_create_vol(V,varargin)
% Create a volume
% FORMAT V = spm_create_vol(V)
% V - image volume information (see spm_vol.m)
%____________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id$
for i=1:numel(V),
if nargin>1,
v = create_vol(V(i),varargin{:});
else
v = create_vol(V(i));
end;
f = fieldnames(v);
for j=1:size(f,1),
V(i).(f{j}) = v.(f{j});
end;
end;
function V = create_vol(V,varargin)
if ~isstruct(V), error('Not a structure.'); end;
if ~isfield(V,'fname'), error('No "fname" field'); end;
if ~isfield(V,'dim'), error('No "dim" field'); end;
if ~all(size(V.dim)==[1 3]),
error(['"dim" field is the wrong size (' num2str(size(V.dim)) ').']);
end;
if ~isfield(V,'n'),
V.n = [1 1];
else
V.n = [V.n(:)' 1 1];
V.n = V.n(1:2);
end;
if V.n(1)>1 && V.n(2)>1,
error('Can only do up to 4D data (%s).',V.fname);
end;
if ~isfield(V,'dt'),
V.dt = [spm_type('float64') spm_platform('bigend')];
end;
dt{1} = spm_type(V.dt(1));
if strcmp(dt{1},'unknown'),
error(['"' dt{1} '" is an unrecognised datatype (' num2str(V.dt(1)) ').']);
end;
if V.dt(2), dt{2} = 'BE'; else dt{2} = 'LE'; end;
if ~isfield(V,'pinfo'), V.pinfo = [Inf Inf 0]'; end;
if size(V.pinfo,1)==2, V.pinfo(3,:) = 0; end;
V.fname = deblank(V.fname);
[pth,nam,ext] = fileparts(V.fname);
switch ext,
case {'.img'}
minoff = 0;
case {'.nii'}
minoff = 352;
otherwise
error(['"' ext '" is not a recognised extension.']);
end;
bits = spm_type(V.dt(1),'bits');
minoff = minoff + ceil(prod(V.dim(1:2))*bits/8)*V.dim(3)*(V.n(1)-1+V.n(2)-1);
V.pinfo(3,1) = max(V.pinfo(3,:),minoff);
if ~isfield(V,'descrip'), V.descrip = ''; end;
if ~isfield(V,'private'), V.private = struct; end;
dim = [V.dim(1:3) V.n];
dat = file_array(V.fname,dim,[dt{1} '-' dt{2}],0,V.pinfo(1),V.pinfo(2));
N = nifti;
N.dat = dat;
N.mat = V.mat;
N.mat0 = V.mat;
N.mat_intent = 'Aligned';
N.mat0_intent = 'Aligned';
N.descrip = V.descrip;
try
N0 = nifti(V.fname);
% Just overwrite if both are single volume files.
tmp = [N0.dat.dim ones(1,5)];
if prod(tmp(4:end))==1 && prod(dim(4:end))==1
N0 = [];
end;
catch
N0 = [];
end;
if ~isempty(N0),
% If the dimensions differ, then there is the potential for things to go badly wrong.
tmp = [N0.dat.dim ones(1,5)];
if any(tmp(1:3) ~= dim(1:3))
warning(['Incompatible x,y,z dimensions in file "' V.fname '" [' num2str(tmp(1:3)) ']~=[' num2str(dim(1:3)) '].']);
end;
if dim(5) > tmp(5) && tmp(4) > 1,
warning(['Incompatible 4th and 5th dimensions in file "' V.fname '" (' num2str([tmp(4:5) dim(4:5)]) ').']);
end;
N.dat.dim = [dim(1:3) max(dim(4:5),tmp(4:5))];
if ~strcmp(dat.dtype,N0.dat.dtype),
warning(['Incompatible datatype in file "' V.fname '" ' N0.dat.dtype ' ~= ' dat.dtype '.']);
end;
if single(N.dat.scl_slope) ~= single(N0.dat.scl_slope) && (size(N0.dat,4)>1 || V.n(1)>1),
warning(['Incompatible scalefactor in "' V.fname '" ' num2str(N0.dat.scl_slope) '~=' num2str(N.dat.scl_slope) '.']);
end;
if single(N.dat.scl_inter) ~= single(N0.dat.scl_inter),
warning(['Incompatible intercept in "' V.fname '" ' num2str(N0.dat.scl_inter) '~=' num2str(N.dat.scl_inter) '.']);
end;
if single(N.dat.offset) ~= single(N0.dat.offset),
warning(['Incompatible intercept in "' V.fname '" ' num2str(N0.dat.offset) '~=' num2str(N.dat.offset) '.']);
end;
if V.n(1)==1,
% Ensure volumes 2..N have the original matrix
nt = size(N.dat,4);
if nt>1 && sum(sum((N0.mat-V.mat).^2))>1e-8,
M0 = N0.mat;
if ~isfield(N0.extras,'mat'),
N0.extras.mat = zeros([4 4 nt]);
else
if size(N0.extras.mat,4)<nt,
N0.extras.mat(:,:,nt) = zeros(4);
end;
end;
for i=2:nt,
if sum(sum(N0.extras.mat(:,:,i).^2))==0,
N0.extras.mat(:,:,i) = M0;
end;
end;
N.extras.mat = N0.extras.mat;
end;
N0.mat = V.mat;
if strcmp(N0.mat0_intent,'Aligned'), N.mat0 = V.mat; end;
if ~isempty(N.extras) && isstruct(N.extras) && isfield(N.extras,'mat') &&...
size(N.extras.mat,3)>=1,
N.extras.mat(:,:,V.n(1)) = V.mat;
end;
else
N.extras.mat(:,:,V.n(1)) = V.mat;
end;
if ~isempty(N0.extras) && isstruct(N0.extras) && isfield(N0.extras,'mat'),
N0.extras.mat(:,:,V.n(1)) = N.mat;
N.extras = N0.extras;
end;
if sum((V.mat(:)-N0.mat(:)).^2) > 1e-4,
N.extras.mat(:,:,V.n(1)) = V.mat;
end;
end;
create(N);
V.private = N;
|
github
|
lcnbeapp/beapp-master
|
spm_check_installation.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_check_installation.m
| 19,147 |
utf_8
|
5500b12cea8521a513b4ff3226dc8f4d
|
function spm_check_installation(action)
% Check SPM installation
% FORMAT spm_check_installation('basic')
% Perform a superficial check of SPM installation [default].
%
% FORMAT spm_check_installation('full')
% Perform an in-depth diagnostic of SPM installation.
%
% FORMAT spm_check_installation('build')
% Build signature of SPM distribution as used by previous option.
% (for developers)
%__________________________________________________________________________
% Copyright (C) 2009 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id$
if isdeployed, return; end
%-Select action
%--------------------------------------------------------------------------
if ~nargin, action = 'basic'; end
switch action
case 'basic'
check_basic;
case 'full'
check_full;
case 'build'
build_signature;
otherwise
error('Unknown action to perform.');
end
%==========================================================================
% FUNCTION check_basic
%==========================================================================
function check_basic
%-Minimal MATLAB version required
%--------------------------------------------------------------------------
try
v = spm_matlab_version_chk('7.1');
catch
error('Where is spm_matlab_version_chk.m?');
end
if v < 0
error([...
'SPM8 requires MATLAB 7.1 onwards in order to run.\n'...
'This MATLAB version is %s\n'], version);
end
%-Check installation
%--------------------------------------------------------------------------
spm('Ver','',1);
d = spm('Dir');
%-Check the search path
%--------------------------------------------------------------------------
p = textscan(path,'%s','delimiter',pathsep); p = p{1};
if ~ismember(lower(d),lower(p))
error(sprintf([...
'You do not appear to have the MATLAB search path set up\n'...
'to include your SPM8 distribution. This means that you\n'...
'can start SPM in this directory, but if your change to\n'...
'another directory then MATLAB will be unable to find the\n'...
'SPM functions. You can use the editpath command in MATLAB\n'...
'to set it up.\n'...
' addpath %s\n'...
'For more information, try typing the following:\n'...
' help path\n help editpath'],d));
end
%-Ensure that the original release - as well as the updates - was installed
%--------------------------------------------------------------------------
if ~exist(fullfile(d,'spm_Npdf.m'),'file') % File that should not have changed
if isunix
error(sprintf([...
'There appears to be some problem with the installation.\n'...
'The original spm8.zip distribution should be installed\n'...
'and the updates installed on top of this. Unix commands\n'...
'to do this are:\n'...
' unzip spm8.zip\n'...
' unzip -o spm8_updates_r????.zip -d spm8\n'...
'You may need help from your local network administrator.']));
else
error(sprintf([...
'There appears to be some problem with the installation.\n'...
'The original spm8.zip distribution should be installed\n'...
'and the updates installed on top of this. If in doubt,\n'...
'consult your local network administrator.']));
end
end
%-Ensure that the files were unpacked correctly
%--------------------------------------------------------------------------
if ispc
try
t = load(fullfile(d,'Split.mat'));
catch
error(sprintf([...
'There appears to be some problem reading the MATLAB .mat\n'...
'files from the SPM distribution. This is probably\n'...
'something to do with the way that the distribution was\n'...
'unpacked. If you used WinZip, then ensure that\n'...
'TAR file smart CR/LF conversion is disabled\n'...
'(under the Miscellaneous Configuration Options).']));
end
if ~exist(fullfile(d,'toolbox','DARTEL','diffeo3d.c'),'file'),
error(sprintf([...
'There appears to be some problem with the installation.\n'...
'This is probably something to do with the way that the\n'...
'distribution was unbundled from the original .zip files.\n'...
'Please ensure that the files are unpacked so that the\n'...
'directory structure is retained.']));
end
end
%-Check the MEX files
%--------------------------------------------------------------------------
try
feval(@spm_bsplinc,1,ones(1,6));
catch
error([...
'SPM uses a number of MEX files, which are compiled functions.\n'...
'These need to be compiled for the various platforms on which SPM\n'...
'is run. At the FIL, where SPM is developed, the number of\n'...
'computer platforms is limited. It is therefore not possible to\n'...
'release a version of SPM that will run on all computers. See\n'...
' %s%csrc%cMakefile and\n'...
' http://en.wikibooks.org/wiki/SPM#Installation\n'...
'for information about how to compile mex files for %s\n'...
'in MATLAB %s.'],...
d,filesep,filesep,computer,version);
end
%==========================================================================
% FUNCTION check_full
%==========================================================================
function check_full
%-Say Hello
%--------------------------------------------------------------------------
disp( ' ___ ____ __ __ ' );
disp( '/ __)( _ \( \/ ) ' );
disp( '\__ \ )___/ ) ( Statistical Parametric Mapping ' );
disp(['(___/(__) (_/\/\_) SPM - http://www.fil.ion.ucl.ac.uk/spm/ ']);
fprintf('\n');
%-Detect SPM directory
%--------------------------------------------------------------------------
SPMdir = which('spm.m','-ALL');
if isempty(SPMdir)
fprintf('SPM is not in your MATLAB path.\n');
return;
elseif numel(SPMdir) > 1
fprintf('SPM seems to appear in several different folders:\n');
for i=1:numel(SPMdir)
fprintf(' * %s\n',SPMdir{i});
end
fprintf('Remove all but one with ''editpath'' or ''spm_rmpath''.\n');
return;
else
fprintf('SPM is installed in: %s\n',fileparts(SPMdir{1}));
end
SPMdir = fileparts(SPMdir{1});
%-Detect SPM version and revision number
%--------------------------------------------------------------------------
v = struct('Name','','Version','','Release','','Date','');
try
fid = fopen(fullfile(SPMdir,'Contents.m'),'rt');
if fid == -1
fprintf('Cannot open ''%s'' for reading.\n',fullfile(SPMdir,'Contents.m'));
return;
end
l1 = fgetl(fid); l2 = fgetl(fid);
fclose(fid);
l1 = strtrim(l1(2:end)); l2 = strtrim(l2(2:end));
t = textscan(l2,'%s','delimiter',' '); t = t{1};
v.Name = l1; v.Date = t{4};
v.Version = t{2}; v.Release = t{3}(2:end-1);
catch
fprintf('Cannot obtain SPM version & revision number.\n');
return;
end
fprintf('SPM version is %s (%s, %s)\n', ...
v.Release,v.Version,strrep(v.Date,'-',' '));
%-Detect SPM toolboxes
%--------------------------------------------------------------------------
officials = {'Beamforming', 'DARTEL', 'dcm_meeg', 'DEM', 'FieldMap', ...
'HDW', 'MEEGtools', 'mixture', 'Neural_Models', 'Seg', 'spectral', ...
'SRender'};
dd = dir(fullfile(SPMdir,'toolbox'));
dd = {dd([dd.isdir]).name};
dd(strmatch('.',dd)) = [];
dd = setdiff(dd,officials);
fprintf('SPM toolboxes:');
for i=1:length(dd)
fprintf(' %s',dd{i});
end
if isempty(dd), fprintf(' none'); end
fprintf('\n');
%-Detect MATLAB & toolboxes
%--------------------------------------------------------------------------
fprintf('MATLAB is installed in: %s\n',matlabroot);
fprintf('MATLAB version is %s\n',version);
fprintf('MATLAB toolboxes: '); hastbx = false;
if license('test','signal_toolbox') && ~isempty(ver('signal'))
vtbx = ver('signal'); hastbx = true;
fprintf('signal (v%s) ',vtbx.Version);
end
if license('test','image_toolbox') && ~isempty(ver('images'))
vtbx = ver('images'); hastbx = true;
fprintf('images (v%s) ',vtbx.Version);
end
if license('test','statistics_toolbox') && ~isempty(ver('stats'))
vtbx = ver('stats'); hastbx = true;
fprintf('stats (v%s)',vtbx.Version);
end
if ~hastbx, fprintf('none.'); end
fprintf('\n');
%-Detect Platform and Operating System
%--------------------------------------------------------------------------
[C, maxsize] = computer;
fprintf('Platform: %s (maxsize=%d)\n', C, maxsize);
if ispc
platform = [system_dependent('getos'),' ',system_dependent('getwinsys')];
elseif exist('ismac') && ismac
[fail, input] = unix('sw_vers');
if ~fail
platform = strrep(input, 'ProductName:', '');
platform = strrep(platform, sprintf('\t'), '');
platform = strrep(platform, sprintf('\n'), ' ');
platform = strrep(platform, 'ProductVersion:', ' Version: ');
platform = strrep(platform, 'BuildVersion:', 'Build: ');
else
platform = system_dependent('getos');
end
else
platform = system_dependent('getos');
end
fprintf('OS: %s\n', platform);
%-Detect Java
%--------------------------------------------------------------------------
fprintf('%s\n', version('-java'));
fprintf('Java support: ');
level = {'jvm', 'awt', 'swing', 'desktop'};
for i=1:numel(level)
if isempty(javachk(level{i})), fprintf('%s ',level{i}); end
end
fprintf('\n');
%-Detect Monitor(s)
%--------------------------------------------------------------------------
M = get(0,'MonitorPositions');
fprintf('Monitor(s):');
for i=1:size(M,1)
fprintf(' [%d %d %d %d]',M(i,:));
end
fprintf(' (%dbit)\n', get(0,'ScreenDepth'));
%-Detect OpenGL rendering
%--------------------------------------------------------------------------
S = opengl('data');
fprintf('OpenGL version: %s',S.Version);
if S.Software, fprintf('(Software)\n'); else fprintf('(Hardware)\n'); end
fprintf('OpenGL renderer: %s (%s)\n',S.Vendor,S.Renderer);
%-Detect MEX setup
%--------------------------------------------------------------------------
fprintf('MEX extension: %s\n',mexext);
try
cc = mex.getCompilerConfigurations('C','Selected');
if ~isempty(cc)
cc = cc(1); % can be C or C++
fprintf('C Compiler: %s (%s).\n', cc.Name, cc.Version);
fprintf('C Compiler settings: %s (''%s'')\n', ...
cc.Details.CompilerExecutable, cc.Details.OptimizationFlags);
else
fprintf('No C compiler is selected (see mex -setup)\n');
end
end
try
[sts, m] = fileattrib(fullfile(SPMdir,'src'));
m = [m.UserRead m.UserWrite m.UserExecute ...
m.GroupRead m.GroupWrite m.GroupExecute ...
m.OtherRead m.OtherWrite m.OtherExecute];
r = 'rwxrwxrwx'; r(~m) = '-';
fprintf('C Source code permissions: dir %s, ', r);
[sts, m] = fileattrib(fullfile(SPMdir,'src','spm_resels_vol.c'));
m = [m.UserRead m.UserWrite m.UserExecute ...
m.GroupRead m.GroupWrite m.GroupExecute ...
m.OtherRead m.OtherWrite m.OtherExecute];
r = 'rwxrwxrwx'; r(~m) = '-';
fprintf('file %s\n',r);
end
%-Get file details for local SPM installation
%--------------------------------------------------------------------------
fprintf('%s\n',repmat('-',1,70));
l = generate_listing(SPMdir);
fprintf('%s %40s\n','Parsing local installation...','...done');
%-Get file details for most recent public version
%--------------------------------------------------------------------------
fprintf('Downloading SPM information...');
url = sprintf('http://www.fil.ion.ucl.ac.uk/spm/software/%s/%s.xml',...
lower(v.Release),lower(v.Release));
try
p = [tempname '.xml'];
urlwrite(url,p);
catch
fprintf('\nCannot access URL %s\n',url);
return;
end
fprintf('%40s\n','...done');
%-Parse it into a Matlab structure
%--------------------------------------------------------------------------
fprintf('Parsing SPM information...');
tree = xmlread(p);
delete(p);
r = struct([]); ind = 1;
if tree.hasChildNodes
for i=0:tree.getChildNodes.getLength-1
m = tree.getChildNodes.item(i);
if strcmp(m.getNodeName,'signature')
m = m.getChildNodes;
for j=0:m.getLength-1
if strcmp(m.item(j).getNodeName,'file')
n = m.item(j).getChildNodes;
for k=0:n.getLength-1
o = n.item(k);
if ~strcmp(o.getNodeName,'#text')
try
s = char(o.getChildNodes.item(0).getData);
catch
s = '';
end
switch char(o.getNodeName)
case 'name'
r(ind).file = s;
case 'id'
r(ind).id = str2num(s);
otherwise
r(ind).(char(o.getNodeName)) = s;
end
end
end
ind = ind + 1;
end
end
end
end
end
fprintf('%44s\n','...done');
%-Compare local and public versions
%--------------------------------------------------------------------------
fprintf('%s\n',repmat('-',1,70));
compare_versions(l,r);
fprintf('%s\n',repmat('-',1,70));
%==========================================================================
% FUNCTION compare_versions
%==========================================================================
function compare_versions(l,r)
%-Uniformise file names
%--------------------------------------------------------------------------
a = {r.file}; a = strrep(a,'\','/'); [r.file] = a{:};
a = {l.file}; a = strrep(a,'\','/'); [l.file] = a{:};
%-Look for missing or unknown files
%--------------------------------------------------------------------------
[x,ir,il] = setxor({r.file},{l.file});
if isempty([ir il])
fprintf('No missing or unknown files\n');
else
if ~isempty(ir)
fprintf('File(s) missing in your installation:\n');
end
for i=1:length(ir)
fprintf(' * %s\n', r(ir(i)).file);
end
if ~isempty(ir) && ~isempty(il), fprintf('%s\n',repmat('-',1,70)); end
if ~isempty(il)
fprintf('File(s) not part of the current version of SPM:\n');
end
for i=1:length(il)
fprintf(' * %s\n', l(il(i)).file);
end
end
fprintf('%s\n',repmat('-',1,70));
%-Look for local changes or out-of-date files
%--------------------------------------------------------------------------
[tf, ir] = ismember({r.file},{l.file});
dispc = true;
for i=1:numel(r)
if tf(i)
if ~isempty(r(i).id) && (isempty(l(ir(i)).id) || (r(i).id ~= l(ir(i)).id))
dispc = false;
fprintf('File %s is not up to date (r%d vs r%d)\n', ...
r(i).file, r(i).id, l(ir(i)).id);
end
if ~isempty(r(i).md5) && ~isempty(l(ir(i)).md5) && ~strcmp(r(i).md5,l(ir(i)).md5)
dispc = false;
fprintf('File %s has been edited (checksum mismatch)\n', r(i).file);
end
end
end
if dispc
fprintf('No local change or out-of-date files\n');
end
%==========================================================================
% FUNCTION build_signature
%==========================================================================
function build_signature
[v,r] = spm('Ver','',1);
d = spm('Dir');
l = generate_listing(d);
fprintf('Saving %s signature in %s\n',...
v, fullfile(pwd,sprintf('%s_signature.xml',v)));
fid = fopen(fullfile(pwd,sprintf('%s_signature.xml',v)),'wt');
fprintf(fid,'<?xml version="1.0"?>\n');
fprintf(fid,'<!-- Signature for %s r%s -->\n',v,r);
fprintf(fid,'<signature>\n');
for i=1:numel(l)
fprintf(fid,' <file>\n');
fprintf(fid,' <name>%s</name>\n',l(i).file);
fprintf(fid,' <id>%d</id>\n',l(i).id);
fprintf(fid,' <date>%s</date>\n',l(i).date);
fprintf(fid,' <md5>%s</md5>\n',l(i).md5);
fprintf(fid,' </file>\n');
end
fprintf(fid,'</signature>\n');
fclose(fid);
%==========================================================================
% FUNCTION generate_listing
%==========================================================================
function l = generate_listing(d,r,l)
if nargin < 2
r = '';
end
if nargin < 3
l = struct([]);
end
%-List content of folder
%--------------------------------------------------------------------------
ccd = fullfile(d,r);
fprintf('%-10s: %58s','Directory',ccd(max(1,length(ccd)-57):end));
dd = dir(ccd);
f = {dd(~[dd.isdir]).name};
dispw = false;
for i=1:length(f)
[p,name,ext] = fileparts(f{i});
info = struct('file','', 'id',[], 'date','', 'md5','');
if ismember(ext,{'.m','.man','.txt','.xml','.c','.h',''})
info = extract_info(fullfile(ccd,f{i}));
end
info.file = fullfile(r,f{i});
try
try
info.md5 = md5sum(fullfile(ccd,f{i}));
catch
%[s, info.md5] = system(['md5sum "' fullfile(ccd,f{i}) '"']);
%info.md5 = strtok(info.md5);
end
end
if isempty(l), l = info;
else l(end+1) = info;
end
if isempty(r) && strcmp(ext,'.m')
w = which(f{i},'-ALL');
if numel(w) > 1 && ~strcmpi(f{i},'Contents.m')
if ~dispw, fprintf('\n'); end
dispw = true;
fprintf('File %s appears %d times in your MATLAB path:\n',f{i},numel(w));
for j=1:numel(w)
if j==1 && isempty(strmatch(d,w{1}))
fprintf(' %s (SHADOWING)\n',w{1});
else
fprintf(' %s\n',w{j});
end
end
end
end
end
if ~dispw, fprintf('%s',repmat(sprintf('\b'),1,70)); end
%-Recursively extract subdirectories
%--------------------------------------------------------------------------
dd = {dd([dd.isdir]).name};
dd(strmatch('.',dd)) = [];
for i=1:length(dd)
l = generate_listing(d,fullfile(r,dd{i}),l);
end
%==========================================================================
% FUNCTION extract_info
%==========================================================================
function svnprops = extract_info(f)
%Extract Subversion properties ($Id$ tag)
svnprops = struct('file',f, 'id',[], 'date','', 'md5','');
fp = fopen(f,'rt');
str = fread(fp,Inf,'*uchar');
fclose(fp);
str = char(str(:)');
r = regexp(str,['\$Id: (?<file>\S+) (?<id>[0-9]+) (?<date>\S+) ' ...
'(\S+Z) (?<author>\S+) \$'],'names');
if isempty(r)
%fprintf('\n%s has no SVN Id.\n',f);
else
svnprops.file = r(1).file;
svnprops.id = str2num(r(1).id);
svnprops.date = r(1).date;
[p,name,ext] = fileparts(f);
if ~strmatch(svnprops.file,[name ext],'exact')
warning('SVN Id for %s does not match filename.',f);
end
end
if numel(r) > 1
%fprintf('\n%s has several SVN Ids.\n',f);
end
|
github
|
lcnbeapp/beapp-master
|
spm_prep2sn.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/spm_prep2sn.m
| 7,345 |
utf_8
|
41b5744c0289cc48a8070de4648e82da
|
function [po,pin] = spm_prep2sn(p)
% Convert the output from spm_preproc into an sn.mat
% FORMAT [po,pin] = spm_prep2sn(p)
% p - the results of spm_preproc
% po - the output in a form that can be used by
% spm_write_sn.
% pin - the inverse transform in a form that can be
% used by spm_write_sn.
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id$
if ischar(p), p = load(p); end;
VG = p.tpm;
VF = p.image;
[Y1,Y2,Y3] = create_def(p.Twarp,VF,VG(1),p.Affine);
[Y1,Y2,Y3] = spm_invdef(Y1,Y2,Y3,VG(1).dim(1:3),eye(4),eye(4));
MT = procrustes(Y1,Y2,Y3,VG(1),VF.mat);
d = size(p.Twarp);
[Affine,Tr] = reparameterise(Y1,Y2,Y3,VG(1),VF.mat,MT,max(d(1:3)+2,[8 8 8]));
flags = struct(...
'ngaus', p.ngaus,...
'mg', p.mg,...
'mn', p.mn,...
'vr', p.vr,...
'warpreg', p.warpreg,...
'warpco', p.warpco,...
'biasreg', p.biasreg,...
'biasfwhm', p.biasfwhm,...
'regtype', p.regtype,...
'fudge', p.fudge,...
'samp', p.samp,...
'msk', p.msk,...
'Affine', p.Affine,...
'Twarp', p.Twarp,...
'Tbias', p.Tbias,...
'thresh', p.thresh);
if nargout==0,
[pth,nam,ext] = fileparts(VF.fname);
fnam = fullfile(pth,[nam '_seg_sn.mat']);
if spm_matlab_version_chk('7') >= 0,
save(fnam,'-V6','VG','VF','Tr','Affine','flags');
else
save(fnam,'VG','VF','Tr','Affine','flags');
end;
else
po = struct(...
'VG', VG,...
'VF', VF,...
'Tr', Tr,...
'Affine', Affine,...
'flags', flags);
end;
if nargout>=2,
% Parameterisation for the inverse
pin = struct(...
'VG', p.image,...
'VF', p.tpm(1),...
'Tr', p.Twarp,...
'Affine', p.tpm(1).mat\p.Affine*p.image.mat,...
'flags', flags);
% VG = p.image;
% VF = p.tpm(1);
% Tr = p.Twarp;
% Affine = p.tpm(1).mat\p.Affine*p.image.mat;
% save('junk_sn.mat','VG','VF','Tr','Affine');
end;
return;
%=======================================================================
%=======================================================================
function [Affine,Tr] = reparameterise(Y1,Y2,Y3,B,M2,MT,d2)
% Take a deformation field and reparameterise in the same form
% as used by the spatial normalisation routines of SPM
d = [size(Y1) 1];
[x1,x2,o] = ndgrid(1:d(1),1:d(2),1);
x3 = 1:d(3);
Affine = M2\MT*B(1).mat;
A = inv(Affine);
B1 = spm_dctmtx(d(1),d2(1));
B2 = spm_dctmtx(d(2),d2(2));
B3 = spm_dctmtx(d(3),d2(3));
pd = prod(d2(1:3));
AA = eye(pd)*0.01;
Ab = zeros(pd,3);
spm_progress_bar('init',length(x3),['Reparameterising'],'Planes completed');
mx = [0 0 0];
for z=1:length(x3),
y1 = double(Y1(:,:,z));
y2 = double(Y2(:,:,z));
y3 = double(Y3(:,:,z));
msk = isfinite(y1);
w = double(msk);
y1(~msk) = 0;
y2(~msk) = 0;
y3(~msk) = 0;
z1 = A(1,1)*y1+A(1,2)*y2+A(1,3)*y3 + w.*(A(1,4) - x1);
z2 = A(2,1)*y1+A(2,2)*y2+A(2,3)*y3 + w.*(A(2,4) - x2);
z3 = A(3,1)*y1+A(3,2)*y2+A(3,3)*y3 + w *(A(3,4) - z );
b3 = B3(z,:)';
Ab(:,1) = Ab(:,1) + kron(b3,spm_krutil(z1,B1,B2,0));
Ab(:,2) = Ab(:,2) + kron(b3,spm_krutil(z2,B1,B2,0));
Ab(:,3) = Ab(:,3) + kron(b3,spm_krutil(z3,B1,B2,0));
AA = AA + kron(b3*b3',spm_krutil(w, B1,B2,1));
spm_progress_bar('set',z);
end;
spm_progress_bar('clear');
Tr = reshape(AA\Ab,[d2(1:3) 3]); drawnow;
return;
%=======================================================================
%=======================================================================
function MT = procrustes(Y1,Y2,Y3,B,M2)
% Take a deformation field and determine the closest rigid-body
% transform to match it, with weighing.
%
% Example Reference:
% F. L. Bookstein (1997). "Landmark Methods for Forms Without
% Landmarks: Morphometrics of Group Differences in Outline Shape"
% Medical Image Analysis 1(3):225-243
M1 = B.mat;
d = B.dim(1:3);
[x1,x2,o] = ndgrid(1:d(1),1:d(2),1);
x3 = 1:d(3);
c1 = [0 0 0];
c2 = [0 0 0];
sw = 0;
spm_progress_bar('init',length(x3),['Procrustes (1)'],'Planes completed');
for z=1:length(x3),
y1 = double(Y1(:,:,z));
y2 = double(Y2(:,:,z));
y3 = double(Y3(:,:,z));
msk = find(isfinite(y1));
w = spm_sample_vol(B(1),x1(msk),x2(msk),o(msk)*z,0);
swz = sum(w(:));
sw = sw+swz;
c1 = c1 + [w'*[x1(msk) x2(msk)] swz*z ];
c2 = c2 + w'*[y1(msk) y2(msk) y3(msk)];
spm_progress_bar('set',z);
end;
spm_progress_bar('clear');
c1 = c1/sw;
c2 = c2/sw;
T1 = [eye(4,3) M1*[c1 1]'];
T2 = [eye(4,3) M2*[c2 1]'];
C = zeros(3);
spm_progress_bar('init',length(x3),['Procrustes (2)'],'Planes completed');
for z=1:length(x3),
y1 = double(Y1(:,:,z));
y2 = double(Y2(:,:,z));
y3 = double(Y3(:,:,z));
msk = find(isfinite(y1));
w = spm_sample_vol(B(1),x1(msk),x2(msk),o(msk)*z,0);
C = C + [(x1(msk)-c1(1)).*w (x2(msk)-c1(2)).*w ( z-c1(3))*w ]' * ...
[(y1(msk)-c2(1)) (y2(msk)-c2(2)) (y3(msk)-c2(3)) ];
spm_progress_bar('set',z);
end;
spm_progress_bar('clear');
[u,s,v] = svd(M1(1:3,1:3)*C*M2(1:3,1:3)');
R = eye(4);
R(1:3,1:3) = v*u';
MT = T2*R*inv(T1);
return;
%=======================================================================
%=======================================================================
function [Y1,Y2,Y3] = create_def(T,VG,VF,Affine)
% Generate a deformation field from its parameterisation.
d2 = size(T);
d = VG.dim(1:3);
M = VF.mat\Affine*VG.mat;
[x1,x2,o] = ndgrid(1:d(1),1:d(2),1);
x3 = 1:d(3);
B1 = spm_dctmtx(d(1),d2(1));
B2 = spm_dctmtx(d(2),d2(2));
B3 = spm_dctmtx(d(3),d2(3));
[pth,nam,ext] = fileparts(VG.fname);
spm_progress_bar('init',length(x3),['Creating Def: ' nam],'Planes completed');
for z=1:length(x3),
[y1,y2,y3] = defs(T,z,B1,B2,B3,x1,x2,x3,M);
Y1(:,:,z) = single(y1);
Y2(:,:,z) = single(y2);
Y3(:,:,z) = single(y3);
spm_progress_bar('set',z);
end;
spm_progress_bar('clear');
return;
%=======================================================================
%=======================================================================
function [x1,y1,z1] = defs(sol,z,B1,B2,B3,x0,y0,z0,M)
if ~isempty(sol),
x1a = x0 + transf(B1,B2,B3(z,:),sol(:,:,:,1));
y1a = y0 + transf(B1,B2,B3(z,:),sol(:,:,:,2));
z1a = z0(z) + transf(B1,B2,B3(z,:),sol(:,:,:,3));
else
x1a = x0;
y1a = y0;
z1a = z0;
end;
x1 = M(1,1)*x1a + M(1,2)*y1a + M(1,3)*z1a + M(1,4);
y1 = M(2,1)*x1a + M(2,2)*y1a + M(2,3)*z1a + M(2,4);
z1 = M(3,1)*x1a + M(3,2)*y1a + M(3,3)*z1a + M(3,4);
return;
%=======================================================================
%=======================================================================
function t = transf(B1,B2,B3,T)
d2 = [size(T) 1];
t1 = reshape(T, d2(1)*d2(2),d2(3)); drawnow;
t1 = reshape(t1*B3', d2(1), d2(2)); drawnow;
t = B1*t1*B2';
return;
%=======================================================================
|
github
|
lcnbeapp/beapp-master
|
cfg_getfile.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/matlabbatch/cfg_getfile.m
| 46,070 |
utf_8
|
3e6a6877315f1b08af13c88de5044295
|
function [t,sts] = cfg_getfile(varargin)
% File selector
% FORMAT [t,sts] = cfg_getfile(n,typ,mesg,sel,wd,filt,frames)
% n - Number of files
% A single value or a range. e.g.
% 1 - Select one file
% Inf - Select any number of files
% [1 Inf] - Select 1 to Inf files
% [0 1] - select 0 or 1 files
% [10 12] - select from 10 to 12 files
% typ - file type
% 'any' - all files
% 'batch' - SPM batch files (.m, .mat and XML)
% 'dir' - select a directory
% 'image' - Image files (".img" and ".nii")
% Note that it gives the option to select
% individual volumes of the images.
% 'mat' - Matlab .mat files or .txt files (assumed to contain
% ASCII representation of a 2D-numeric array)
% 'mesh' - Mesh files (".gii" and ".mat")
% 'nifti' - NIfTI files without the option to select frames
% 'xml' - XML files
% Other strings act as a filter to regexp. This means
% that e.g. DCM*.mat files should have a typ of '^DCM.*\.mat$'
% mesg - a prompt (default 'Select files...')
% sel - list of already selected files
% wd - Directory to start off in
% filt - value for user-editable filter (default '.*')
% frames - Image frame numbers to include (default '1')
%
% t - selected files
% sts - status (1 means OK, 0 means window quit)
%
% FORMAT [t,ind] = cfg_getfile('Filter',files,typ,filt,frames)
% filter the list of files (cell array) in the same way as the
% GUI would do. There is an additional typ 'extimage' which will match
% images with frame specifications, too. The 'frames' argument
% is currently ignored, i.e. image files will not be filtered out if
% their frame numbers do not match.
% When filtering directory names, the filt argument will be applied to the
% last directory in a path only.
% t returns the filtered list (cell array), ind an index array, such that
% t = files(ind).
%
% FORMAT cpath = cfg_getfile('CPath',path,cwd)
% function to canonicalise paths: Prepends cwd to relative paths, processes
% '..' & '.' directories embedded in path.
% path - string matrix containing path name
% cwd - current working directory [default '.']
% cpath - conditioned paths, in same format as input path argument
%
% FORMAT [files,dirs]=cfg_getfile('List',direc,filt)
% Returns files matching the filter (filt) and directories within dire
% direc - directory to search
% filt - filter to select files with (see regexp) e.g. '^w.*\.img$'
% files - files matching 'filt' in directory 'direc'
% dirs - subdirectories of 'direc'
% FORMAT [files,dirs]=cfg_getfile('ExtList',direc,filt,frames)
% As above, but for selecting frames of 4D NIfTI files
% frames - vector of frames to select (defaults to 1, if not
% specified). If the frame number is Inf, all frames for the
% matching images are listed.
% FORMAT [files,dirs]=cfg_getfile('FPList',direc,filt)
% FORMAT [files,dirs]=cfg_getfile('ExtFPList',direc,filt,frames)
% As above, but returns files with full paths (i.e. prefixes direc to each)
% FORMAT [files,dirs]=cfg_getfile('FPListRec',direc,filt)
% FORMAT [files,dirs]=cfg_getfile('ExtFPListRec',direc,filt,frames)
% As above, but returns files with full paths (i.e. prefixes direc to
% each) and searches through sub directories recursively.
%
% FORMAT cfg_getfile('prevdirs',dir)
% Add directory dir to list of previous directories.
% FORMAT dirs=cfg_getfile('prevdirs')
% Retrieve list of previous directories.
%
% This code is based on the file selection dialog in SPM5, with virtual
% file handling turned off.
%____________________________________________________________________________
% Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
%
% This code is part of a batch job configuration system for MATLAB. See
% help matlabbatch
% for a general overview.
%_______________________________________________________________________
% Copyright (C) 2007 Freiburg Brain Imaging
% John Ashburner and Volkmar Glauche
% $Id: cfg_getfile.m 6251 2014-10-30 13:58:44Z volkmar $
t = {};
sts = false;
if nargin > 0 && ischar(varargin{1})
switch lower(varargin{1})
case {'addvfiles', 'clearvfiles', 'vfiles'}
cfg_message('matlabbatch:deprecated:vfiles', ...
'Trying to use deprecated ''%s'' call.', ...
lower(varargin{1}));
case 'cpath'
cfg_message(nargchk(2,Inf,nargin,'struct'));
t = cpath(varargin{2:end});
sts = true;
case 'filter'
filt = mk_filter(varargin{3:end});
t = varargin{2};
if numel(t) == 1 && isempty(t{1})
sts = 1;
return;
end;
t1 = cell(size(t));
if any(strcmpi(varargin{3},{'dir','extdir'}))
% only filter last directory in path
for k = 1:numel(t)
t{k} = cpath(t{k});
if t{k}(end) == filesep
[p n] = fileparts(t{k}(1:end-1));
else
[p n] = fileparts(t{k});
end
if strcmpi(varargin{3},'extdir')
t1{k} = [n filesep];
else
t1{k} = n;
end
end
else
% only filter filenames, not paths
for k = 1:numel(t)
[p n e] = fileparts(t{k});
t1{k} = [n e];
end
end
[t1,sts1] = do_filter(t1,filt.ext);
[t1,sts2] = do_filter(t1,filt.filt);
sts = sts1(sts2);
t = t(sts);
case {'list', 'fplist', 'extlist', 'extfplist'}
if nargin > 3
frames = varargin{4};
else
frames = 1; % (ignored in listfiles if typ==any)
end;
if regexpi(varargin{1}, 'ext') % use frames descriptor
typ = 'extimage';
else
typ = 'any';
end
filt = mk_filter(typ, varargin{3}, frames);
[t sts] = listfiles(varargin{2}, filt); % (sts is subdirs here)
sts = sts(~(strcmp(sts,'.')|strcmp(sts,'..'))); % remove '.' and '..' entries
if regexpi(varargin{1}, 'fplist') % return full pathnames
direc = cfg_getfile('cpath', varargin{2});
% remove trailing path separator if present
direc = regexprep(direc, [filesep '$'], '');
if ~isempty(t)
t = strcat(direc, filesep, t);
end
if nargout > 1
% subdirs too
sts = cellfun(@(sts1)cpath(sts1, direc), sts, 'UniformOutput',false);
end
end
case {'fplistrec', 'extfplistrec'}
% list directory
[f1 d1] = cfg_getfile(varargin{1}(1:end-3),varargin{2:end});
f2 = cell(size(d1));
d2 = cell(size(d1));
for k = 1:numel(d1)
% recurse into sub directories
[f2{k} d2{k}] = cfg_getfile(varargin{1}, d1{k}, ...
varargin{3:end});
end
t = vertcat(f1, f2{:});
if nargout > 1
sts = vertcat(d1, d2{:});
end
case 'prevdirs',
if nargin > 1
prevdirs(varargin{2});
end;
if nargout > 0 || nargin == 1
t = prevdirs;
sts = true;
end;
otherwise
cfg_message('matlabbatch:usage','Inappropriate usage.');
end
else
[t,sts] = selector(varargin{:});
end
%=======================================================================
%=======================================================================
function [t,ok] = selector(n,typ,mesg,already,wd,filt,frames,varargin)
if nargin<1 || ~isnumeric(n) || numel(n) > 2
n = [0 Inf];
else
if numel(n)==1, n = [n n]; end;
if n(1)>n(2), n = n([2 1]); end;
if ~isfinite(n(1)), n(1) = 0; end;
end
if nargin<2 || ~ischar(typ), typ = 'any'; end;
if nargin<3 || ~(ischar(mesg) || iscellstr(mesg))
mesg = 'Select files...';
elseif iscellstr(mesg)
mesg = char(mesg);
end
if nargin<4 || isempty(already) || (iscell(already) && isempty(already{1}))
already = {};
else
% Add folders of already selected files to prevdirs list
pd1 = cellfun(@(a1)strcat(fileparts(a1),filesep), already, ...
'UniformOutput',false);
prevdirs(pd1);
end
if nargin<5 || isempty(wd) || ~ischar(wd)
if isempty(already)
wd = pwd;
else
wd = fileparts(already{1});
if isempty(wd)
wd = pwd;
end
end;
end
if nargin<6 || ~ischar(filt), filt = '.*'; end;
if nargin<7 || ~(isnumeric(frames) || ischar(frames))
frames = '1';
elseif isnumeric(frames)
frames = char(gencode_rvalue(frames(:)'));
elseif ischar(frames)
try
ev = eval(frames);
if ~isnumeric(ev)
frames = '1';
end
catch
frames = '1';
end
end
ok = 0;
t = '';
sfilt = mk_filter(typ,filt,eval(frames));
[col1,col2,col3,lf,bf] = colours;
% delete old selector, if any
fg = findobj(0,'Tag',mfilename);
if ~isempty(fg)
delete(fg);
end
% create figure
fg = figure('IntegerHandle','off',...
'Tag',mfilename,...
'Name',mesg,...
'NumberTitle','off',...
'Units','Pixels',...
'MenuBar','none',...
'DefaultTextInterpreter','none',...
'DefaultUicontrolInterruptible','on',...
'Visible','off');
cfg_onscreen(fg);
set(fg,'Visible','on');
sellines = min([max([n(2) numel(already)]), 4]);
[pselp pcntp pfdp pdirp] = panelpositions(fg, sellines+1);
uicontrol(fg,...
'style','text',...
'units','normalized',...
'position',posinpanel([0 sellines/(sellines+1) 1 1/(sellines+1)],pselp),...
lf,...
'BackgroundColor',get(fg,'Color'),...
'ForegroundColor',col3,...
'HorizontalAlignment','left',...
'string',mesg,...
'tag','msg');
% Selected Files
sel = uicontrol(fg,...
'style','listbox',...
'units','normalized',...
'Position',posinpanel([0 0 1 sellines/(sellines+1)],pselp),...
lf,...
'Callback',@unselect,...
'tag','selected',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'Max',10000,...
'Min',0,...
'String',already,...
'Value',1);
c0 = uicontextmenu('Parent',fg);
set(sel,'uicontextmenu',c0);
uimenu('Label','Unselect All', 'Parent',c0,'Callback',@unselect_all);
% get cwidth for buttons
tmp=uicontrol('style','text','string',repmat('X',[1,50]),bf,...
'units','normalized','visible','off');
fnp = get(tmp,'extent');
delete(tmp);
cw = 3*fnp(3)/50;
if strcmpi(typ,'image'),
uicontrol(fg,...
'style','edit',...
'units','normalized',...
'Position',posinpanel([0.61 0 0.37 .45],pcntp),...
'Callback',@update_frames,...
'tag','frame',...
lf,...
'BackgroundColor',col1,...
'String',frames,'UserData',eval(frames));
% 'ForegroundGolor',col3,...
end;
% Help
uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',posinpanel([0.02 .5 cw .45],pcntp),...
bf,...
'Callback',@heelp,...
'tag','?',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'String','?',...
'ToolTipString','Show Help');
uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',posinpanel([0.03+cw .5 cw .45],pcntp),...
bf,...
'Callback',@editwin,...
'tag','Ed',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'String','Ed',...
'ToolTipString','Edit Selected Files');
uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',posinpanel([0.04+2*cw .5 cw .45],pcntp),...
bf,...
'Callback',@select_rec,...
'tag','Rec',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'String','Rec',...
'ToolTipString','Recursively Select Files with Current Filter');
% Done
dne = uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',posinpanel([0.05+3*cw .5 0.45-3*cw .45],pcntp),...
bf,...
'Callback',@(h,e)delete(h),...
'tag','D',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'String','Done',...
'Enable','off',...
'DeleteFcn',@null);
if numel(already)>=n(1) && numel(already)<=n(2),
set(dne,'Enable','on');
end;
% Filter Button
uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',posinpanel([0.51 .5 0.1 .45],pcntp),...
bf,...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'Callback',@clearfilt,...
'String','Filt');
% Filter
uicontrol(fg,...
'style','edit',...
'units','normalized',...
'Position',posinpanel([0.61 .5 0.37 .45],pcntp),...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
lf,...
'Callback',@(ob,ev)update(ob),...
'tag','regexp',...
'String',filt,...
'UserData',sfilt);
% Directories
db = uicontrol(fg,...
'style','listbox',...
'units','normalized',...
'Position',posinpanel([0.02 0 0.47 1],pfdp),...
lf,...
'Callback',@click_dir_box,...
'tag','dirs',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'Max',1,...
'Min',0,...
'String','',...
'UserData',wd,...
'Value',1);
% Files
tmp = uicontrol(fg,...
'style','listbox',...
'units','normalized',...
'Position',posinpanel([0.51 0 0.47 1],pfdp),...
lf,...
'Callback',@click_file_box,...
'tag','files',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'UserData',n,...
'Max',10240,...
'Min',0,...
'String','',...
'Value',1);
c0 = uicontextmenu('Parent',fg);
set(tmp,'uicontextmenu',c0);
uimenu('Label','Select All', 'Parent',c0,'Callback',@select_all);
% Drives
if strcmpi(computer,'PCWIN') || strcmpi(computer,'PCWIN64'),
% get fh for lists
tmp=uicontrol('style','text','string','X',lf,...
'units','normalized','visible','off');
fnp = get(tmp,'extent');
delete(tmp);
fh = 2*fnp(4); % Heuristics: why do we need 2*
sz = get(db,'Position');
sz(4) = sz(4)-fh-2*0.01;
set(db,'Position',sz);
uicontrol(fg,...
'style','text',...
'units','normalized',...
'Position',posinpanel([0.02 1-fh-0.01 0.10 fh],pfdp),...
'HorizontalAlignment','left',...
lf,...
'BackgroundColor',get(fg,'Color'),...
'ForegroundColor',col3,...
'String','Drive');
uicontrol(fg,...
'style','popupmenu',...
'units','normalized',...
'Position',posinpanel([0.12 1-fh-0.01 0.37 fh],pfdp),...
lf,...
'Callback',@setdrive,...
'tag','drive',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'String',listdrives(false),...
'Value',1);
end;
[pd,vl] = prevdirs([wd filesep]);
% Previous dirs
uicontrol(fg,...
'style','popupmenu',...
'units','normalized',...
'Position',posinpanel([0.12 .05 0.86 .95*1/3],pdirp),...
lf,...
'Callback',@click_dir_list,...
'tag','previous',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'String',pd,...
'Value',vl);
uicontrol(fg,...
'style','text',...
'units','normalized',...
'Position',posinpanel([0.02 0 0.10 .95*1/3],pdirp),...
'HorizontalAlignment','left',...
lf,...
'BackgroundColor',get(fg,'Color'),...
'ForegroundColor',col3,...
'String','Prev');
% Parent dirs
uicontrol(fg,...
'style','popupmenu',...
'units','normalized',...
'Position',posinpanel([0.12 1/3+.05 0.86 .95*1/3],pdirp),...
lf,...
'Callback',@click_dir_list,...
'tag','pardirs',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'String',pardirs(wd));
uicontrol(fg,...
'style','text',...
'units','normalized',...
'Position',posinpanel([0.02 1/3 0.10 .95*1/3],pdirp),...
'HorizontalAlignment','left',...
lf,...
'BackgroundColor',get(fg,'Color'),...
'ForegroundColor',col3,...
'String','Up');
% Directory
uicontrol(fg,...
'style','edit',...
'units','normalized',...
'Position',posinpanel([0.12 2/3 0.86 .95*1/3],pdirp),...
lf,...
'Callback',@edit_dir,...
'tag','edit',...
'BackgroundColor',col1,...
'ForegroundColor',col3,...
'String','');
uicontrol(fg,...
'style','text',...
'units','normalized',...
'Position',posinpanel([0.02 2/3 0.10 .95*1/3],pdirp),...
'HorizontalAlignment','left',...
lf,...
'BackgroundColor',get(fg,'Color'),...
'ForegroundColor',col3,...
'String','Dir');
resize_fun(fg);
set(fg, 'ResizeFcn',@resize_fun);
update(sel,wd)
set(fg,'windowstyle', 'modal');
waitfor(dne);
drawnow;
if ishandle(sel),
t = get(sel,'String');
if isempty(t)
t = {''};
elseif sfilt.code == -1
% canonicalise non-empty folder selection
t = cellfun(@(t1)cpath(t1, pwd), t, 'UniformOutput',false);
end;
ok = 1;
end;
if ishandle(fg), delete(fg); end;
drawnow;
return;
%=======================================================================
%=======================================================================
function apos = posinpanel(rpos,ppos)
% Compute absolute positions based on panel position and relative
% position
apos = [ppos(1:2)+ppos(3:4).*rpos(1:2) ppos(3:4).*rpos(3:4)];
%=======================================================================
%=======================================================================
function [pselp, pcntp, pfdp, pdirp] = panelpositions(fg, sellines)
if nargin == 1
na = numel(get(findobj(fg,'Tag','selected'),'String'));
n = get(findobj(fg,'Tag','files'),'Userdata');
sellines = min([max([n(2) na]), 4]);
end
lf = cfg_get_defaults('cfg_ui.lfont');
bf = cfg_get_defaults('cfg_ui.bfont');
% Create dummy text to estimate character height
t=uicontrol('style','text','string','Xg','units','normalized','visible','off',lf);
lfh = 1.05*get(t,'extent');
delete(t)
t=uicontrol('style','text','string','Xg','units','normalized','visible','off',bf);
bfh = 1.05*get(t,'extent');
delete(t)
% panel heights
% 3 lines for directory, parent and prev directory list
% variable height for dir/file navigation
% 2 lines for buttons, filter etc
% sellines plus scrollbar for selected files
pselh = sellines*lfh(4) + 1.2*lfh(4);
pselp = [0 0 1 pselh];
pcnth = 2*bfh(4);
pcntp = [0 pselh 1 pcnth];
pdirh = 3*lfh(4);
pdirp = [0 1-pdirh 1 pdirh];
pfdh = 1-(pselh+pcnth+pdirh);
pfdp = [0 pselh+pcnth 1 pfdh];
%=======================================================================
%=======================================================================
function null(varargin)
%=======================================================================
%=======================================================================
function omsg = msg(ob,str)
ob = sib(ob,'msg');
omsg = get(ob,'String');
set(ob,'String',str);
if nargin>=3,
set(ob,'ForegroundColor',[1 0 0],'FontWeight','bold');
else
set(ob,'ForegroundColor',[0 0 0],'FontWeight','normal');
end;
drawnow;
return;
%=======================================================================
%=======================================================================
function setdrive(ob,varargin)
st = get(ob,'String');
vl = get(ob,'Value');
update(ob,st{vl});
return;
%=======================================================================
%=======================================================================
function resize_fun(fg,varargin)
% do nothing
return;
[pselp pcntp pfdp pdirp] = panelpositions(fg);
set(findobj(fg,'Tag','msg'), 'Position',pselp);
set(findobj(fg,'Tag','pcnt'), 'Position',pcntp);
set(findobj(fg,'Tag','pfd'), 'Position',pfdp);
set(findobj(fg,'Tag','pdir'), 'Position',pdirp);
return;
%=======================================================================
%=======================================================================
function [d,mch] = prevdirs(d)
persistent pd
if ~iscell(pd), pd = {}; end;
if nargin == 0
d = pd;
else
if ~iscell(d)
d = cellstr(d);
end
d = unique(d(:));
mch = cellfun(@(d1)find(strcmp(d1,pd)), d, 'UniformOutput',false);
sel = cellfun(@isempty, mch);
npd = numel(pd);
pd = [pd(:);d(sel)];
mch = [mch{~sel} npd+(1:nnz(sel))];
d = pd;
end
return;
%=======================================================================
%=======================================================================
function pd = pardirs(wd)
if ispc
fs = '\\';
else
fs = filesep;
end
pd1 = textscan(wd,'%s','delimiter',fs,'MultipleDelimsAsOne',1);
if ispc
pd = cell(size(pd1{1}));
pd{end} = pd1{1}{1};
for k = 2:numel(pd1{1})
pd{end-k+1} = fullfile(pd1{1}{1:k},filesep);
end
else
pd = cell(numel(pd1{1})+1,1);
pd{end} = filesep;
for k = 1:numel(pd1{1})
pd{end-k} = fullfile(filesep,pd1{1}{1:k},filesep);
end
end
%=======================================================================
%=======================================================================
function clearfilt(ob,varargin)
set(sib(ob,'regexp'),'String','.*');
update(ob);
return;
%=======================================================================
%=======================================================================
function click_dir_list(ob,varargin)
vl = get(ob,'Value');
ls = get(ob,'String');
update(ob,deblank(ls{vl}));
return;
%=======================================================================
%=======================================================================
function edit_dir(ob,varargin)
update(ob,get(ob,'String'));
return;
%=======================================================================
%=======================================================================
function c = get_current_char(lb)
fg = sib(lb, mfilename);
c = get(fg, 'CurrentCharacter');
if ~isempty(c)
% reset CurrentCharacter
set(fg, 'CurrentCharacter', char(13));
end
%=======================================================================
%=======================================================================
function click_dir_box(lb,varargin)
c = get_current_char(lb);
if isempty(c) || isequal(c,char(13))
vl = get(lb,'Value');
str = get(lb,'String');
pd = get(sib(lb,'edit'),'String');
while ~isempty(pd) && strcmp(pd(end),filesep)
pd=pd(1:end-1); % Remove any trailing fileseps
end
sel = str{vl};
if strcmp(sel,'..'), % Parent directory
[dr odr] = fileparts(pd);
elseif strcmp(sel,'.'), % Current directory
dr = pd;
odr = '';
else
dr = fullfile(pd,sel);
odr = '';
end;
update(lb,dr);
if ~isempty(odr)
% If moving up one level, try to set focus on previously visited
% directory
cdrs = get(lb, 'String');
dind = find(strcmp(odr, cdrs));
if ~isempty(dind)
set(lb, 'Value',dind(1));
end
end
end
return;
%=======================================================================
%=======================================================================
function re = getfilt(ob)
ob = sib(ob,'regexp');
ud = get(ob,'UserData');
re = struct('code',ud.code,...
'frames',get(sib(ob,'frame'),'UserData'),...
'ext',{ud.ext},...
'filt',{{get(sib(ob,'regexp'),'String')}});
return;
%=======================================================================
%=======================================================================
function update(lb,dr)
lb = sib(lb,'dirs');
if nargin<2 || isempty(dr) || ~ischar(dr)
dr = get(lb,'UserData');
end;
if ~(strcmpi(computer,'PCWIN') || strcmpi(computer,'PCWIN64'))
dr = [filesep dr filesep];
else
dr = [dr filesep];
end;
dr(strfind(dr,[filesep filesep])) = [];
[f,d] = listfiles(dr,getfilt(lb));
if isempty(d),
dr = get(lb,'UserData');
[f,d] = listfiles(dr,getfilt(lb));
else
set(lb,'UserData',dr);
end;
set(lb,'Value',1,'String',d);
set(sib(lb,'files'),'Value',1,'String',f);
set(sib(lb,'pardirs'),'String',pardirs(dr),'Value',1);
[ls,mch] = prevdirs(dr);
set(sib(lb,'previous'),'String',ls,'Value',mch);
set(sib(lb,'edit'),'String',dr);
if numel(dr)>1 && dr(2)==':',
str = char(get(sib(lb,'drive'),'String'));
mch = find(lower(str(:,1))==lower(dr(1)));
if ~isempty(mch),
set(sib(lb,'drive'),'Value',mch);
end;
end;
return;
%=======================================================================
%=======================================================================
function update_frames(lb,varargin)
str = get(lb,'String');
%r = get(lb,'UserData');
try
r = eval(['[',str,']']);
catch
msg(lb,['Failed to evaluate "' str '".'],'r');
beep;
return;
end;
if ~isnumeric(r),
msg(lb,['Expression non-numeric "' str '".'],'r');
beep;
else
set(lb,'UserData',r);
msg(lb,'');
update(lb);
end;
%=======================================================================
%=======================================================================
function select_all(ob,varargin)
lb = sib(ob,'files');
set(lb,'Value',1:numel(get(lb,'String')));
drawnow;
click_file_box(lb);
return;
%=======================================================================
%=======================================================================
function click_file_box(lb,varargin)
c = get_current_char(lb);
if isempty(c) || isequal(c, char(13))
vlo = get(lb,'Value');
if isempty(vlo),
msg(lb,'Nothing selected');
return;
end;
lim = get(lb,'UserData');
ob = sib(lb,'selected');
str3 = get(ob,'String');
str = get(lb,'String');
lim1 = min([max([lim(2)-numel(str3),0]),numel(vlo)]);
if lim1==0,
msg(lb,['Selected ' num2str(size(str3,1)) '/' num2str(lim(2)) ' already.']);
beep;
set(sib(lb,'D'),'Enable','on');
return;
end;
vl = vlo(1:lim1);
msk = false(size(str,1),1);
if vl>0, msk(vl) = true; else msk = []; end;
str1 = str( msk);
str2 = str(~msk);
dr = get(sib(lb,'edit'), 'String');
str1 = strcat(dr, str1);
set(lb,'Value',min([vl(1),numel(str2)]),'String',str2);
r = (1:numel(str1))+numel(str3);
str3 = [str3(:);str1(:)];
set(ob,'String',str3,'Value',r);
if numel(vlo)>lim1,
msg(lb,['Retained ' num2str(lim1) '/' num2str(numel(vlo))...
' of selection.']);
beep;
elseif isfinite(lim(2))
if lim(1)==lim(2),
msg(lb,['Selected ' num2str(numel(str3)) '/' num2str(lim(2)) ' files.']);
else
msg(lb,['Selected ' num2str(numel(str3)) '/' num2str(lim(1)) '-' num2str(lim(2)) ' files.']);
end;
else
if size(str3,1) == 1, ss = ''; else ss = 's'; end;
msg(lb,['Selected ' num2str(numel(str3)) ' file' ss '.']);
end;
if ~isfinite(lim(1)) || numel(str3)>=lim(1),
set(sib(lb,'D'),'Enable','on');
end;
end
return;
%=======================================================================
%=======================================================================
function obj = sib(ob,tag)
persistent fg;
if isempty(fg) || ~ishandle(fg)
fg = findobj(0,'Tag',mfilename);
end
obj = findobj(fg,'Tag',tag);
return;
%if isempty(obj),
% cfg_message('matlabbatch:usage',['Can''t find object with tag "' tag '".']);
%elseif length(obj)>1,
% cfg_message('matlabbatch:usage',['Found ' num2str(length(obj)) ' objects with tag "' tag '".']);
%end;
%return;
%=======================================================================
%=======================================================================
function unselect(lb,varargin)
vl = get(lb,'Value');
if isempty(vl), return; end;
str = get(lb,'String');
msk = true(numel(str),1);
if vl~=0, msk(vl) = false; end;
str2 = str(msk);
set(lb,'Value',min(vl(1),numel(str2)),'String',str2);
lim = get(sib(lb,'files'),'UserData');
if numel(str2)>= lim(1) && numel(str2)<= lim(2),
set(sib(lb,'D'),'Enable','on');
else
set(sib(lb,'D'),'Enable','off');
end;
if numel(str2) == 1, ss1 = ''; else ss1 = 's'; end;
%msg(lb,[num2str(size(str2,1)) ' file' ss ' remaining.']);
if numel(vl) == 1, ss = ''; else ss = 's'; end;
msg(lb,['Unselected ' num2str(numel(vl)) ' file' ss '. ' ...
num2str(numel(str2)) ' file' ss1 ' remaining.']);
return;
%=======================================================================
%=======================================================================
function unselect_all(ob,varargin)
lb = sib(ob,'selected');
set(lb,'Value',[],'String',{},'ListBoxTop',1);
msg(lb,'Unselected all files.');
lim = get(sib(lb,'files'),'UserData');
if lim(1)>0, set(sib(lb,'D'),'Enable','off'); end;
return;
%=======================================================================
%=======================================================================
function [f,d] = listfiles(dr,filt)
try
ob = sib(gco,'msg');
domsg = ~isempty(ob);
catch
domsg = false;
end
if domsg
omsg = msg(ob,'Listing directory...');
end
if nargin<2, filt = ''; end;
if nargin<1, dr = '.'; end;
de = dir(dr);
if ~isempty(de),
d = {de([de.isdir]).name};
if ~any(strcmp(d, '.'))
d = [{'.'}, d(:)'];
end;
if filt.code~=-1,
f = {de(~[de.isdir]).name};
else
% f = d(3:end);
f = d;
end;
else
d = {'.','..'};
f = {};
end;
if domsg
msg(ob,['Filtering ' num2str(numel(f)) ' files...']);
end
f = do_filter(f,filt.ext);
f = do_filter(f,filt.filt);
ii = cell(1,numel(f));
if filt.code==1 && (numel(filt.frames)~=1 || filt.frames(1)~=1),
if domsg
msg(ob,['Reading headers of ' num2str(numel(f)) ' images...']);
end
for i=1:numel(f),
try
ni = nifti(fullfile(dr,f{i}));
dm = [ni.dat.dim 1 1 1 1 1];
d4 = (1:dm(4))';
catch
d4 = 1;
end;
if all(isfinite(filt.frames))
msk = false(size(filt.frames));
for j=1:numel(msk), msk(j) = any(d4==filt.frames(j)); end;
ii{i} = filt.frames(msk);
else
ii{i} = d4;
end;
end
elseif filt.code==1 && (numel(filt.frames)==1 && filt.frames(1)==1),
for i=1:numel(f),
ii{i} = 1;
end;
end;
if domsg
msg(ob,['Listing ' num2str(numel(f)) ' files...']);
end
[f,ind] = sortrows(f(:));
ii = ii(ind);
msk = true(1,numel(f));
for i=2:numel(f),
if strcmp(f{i-1},f{i}),
if filt.code==1,
tmp = sort([ii{i}(:) ; ii{i-1}(:)]);
tmp(~diff(tmp,1)) = [];
ii{i} = tmp;
end;
msk(i-1) = false;
end;
end;
f = f(msk);
if filt.code==1,
% Combine filename and frame number(s)
ii = ii(msk);
nii = cellfun(@numel, ii);
c = cell(sum(nii),1);
fi = cell(numel(f),1);
for k = 1:numel(fi)
fi{k} = k*ones(1,nii(k));
end
ii = [ii{:}];
fi = [fi{:}];
for i=1:numel(c),
c{i} = sprintf('%s,%d', f{fi(i)}, ii(i));
end;
f = c;
elseif filt.code==-1,
fs = filesep;
for i=1:numel(f),
f{i} = [f{i} fs];
end;
end;
f = f(:);
d = unique(d(:));
if domsg
msg(ob,omsg);
end
return;
%=======================================================================
%=======================================================================
function [f,ind] = do_filter(f,filt)
t2 = false(numel(f),1);
filt_or = sprintf('(%s)|',filt{:});
t1 = regexp(f,filt_or(1:end-1));
if numel(f)==1 && ~iscell(t1), t1 = {t1}; end;
for i=1:numel(t1),
t2(i) = ~isempty(t1{i});
end;
ind = find(t2);
f = f(t2);
return;
%=======================================================================
%=======================================================================
function heelp(ob,varargin)
[col1,col2,col3,fn] = colours;
fg = sib(ob,mfilename);
t = uicontrol(fg,...
'style','listbox',...
'units','normalized',...
'Position',[0.01 0.01 0.98 0.98],...
fn,...
'BackgroundColor',col2,...
'ForegroundColor',col3,...
'Max',0,...
'Min',0,...
'tag','HelpWin',...
'String',' ');
c0 = uicontextmenu('Parent',fg);
set(t,'uicontextmenu',c0);
uimenu('Label','Done', 'Parent',c0,'Callback',@helpclear);
str = cfg_justify(t, {[...
'File Selection help. You can return to selecting files via the right mouse button (the "Done" option). '],...
'',[...
'The panel at the bottom shows files that are already selected. ',...
'Clicking a selected file will un-select it. To un-select several, you can ',...
'drag the cursor over the files, and they will be gone on release. ',...
'You can use the right mouse button to un-select everything.'],...
'',[...
'Directories are navigated by editing the name of the current directory (where it says "Dir"), ',...
'by going to one of the previously entered directories ("Prev"), ',...
'by going to one of the parent directories ("Up") or by navigating around ',...
'the parent or subdirectories listed in the left side panel.'],...
'',[...
'Files matching the filter ("Filt") are shown in the panel on the right. ',...
'These can be selected by clicking or dragging. Use the right mouse button if ',...
'you would like to select all files. Note that when selected, the files disappear ',...
'from this panel. They can be made to reappear by re-specifying the directory ',...
'or the filter. '],...
'',[...
'Both directory and file lists can also be browsed by typing the leading ',...
'character(s) of a directory or file name.'],...
'',[...
'Note that the syntax of the filter differs from that used by most other file selectors. ',...
'The filter works using so called ''regular expressions''. Details can be found in the ',...
'MATLAB help text on ''regexp''. ',...
'The following is a list of symbols with special meaning for filtering the filenames:'],...
' ^ start of string',...
' $ end of string',...
' . any character',...
' \ quote next character',...
' * match zero or more',...
' + match one or more',...
' ? match zero or one, or match minimally',...
' {} match a range of occurrances',...
' [] set of characters',...
' [^] exclude a set of characters',...
' () group subexpression',...
' \w match word [a-z_A-Z0-9]',...
' \W not a word [^a-z_A-Z0-9]',...
' \d match digit [0-9]',...
' \D not a digit [^0-9]',...
' \s match white space [ \t\r\n\f]',...
' \S not a white space [^ \t\r\n\f]',...
' \<WORD\> exact word match',...
'',[...
'Individual time frames of image files can also be selected. The frame filter ',...
'allows specified frames to be shown, which is useful for image files that ',...
'contain multiple time points. If your images are only single time point, then ',...
'reading all the image headers can be avoided by specifying a frame filter of "1". ',...
'The filter should contain a list of integers indicating the frames to be used. ',...
'This can be generated by e.g. "1:100", or "1:2:100".'],...
'',[...
'The recursive selection button (Rec) allows files matching the regular expression to ',...
'be recursively selected. If there are many directories to search, then this can take ',...
'a while to run.'],...
'',[...
'There is also an edit button (Ed), which allows you to edit your selection of files. ',...
'When you are done, then use the menu-button of your mouse to either cancel or accept your changes.'],''});
set(t,'String',str);
return;
%=======================================================================
%=======================================================================
function helpclear(ob,varargin)
ob = get(ob,'Parent');
ob = get(ob,'Parent');
ob = findobj(ob,'Tag','HelpWin');
delete(ob);
%=======================================================================
%=======================================================================
function t = cpath(t,d)
switch filesep,
case '/',
mch = '^/';
fs = '/';
fs1 = '/';
case '\',
mch = '^.:\\';
fs = '\';
fs1 = '\\';
otherwise;
cfg_message('matlabbatch:usage','What is this filesystem?');
end
if isempty(regexp(t,mch,'once')),
if (nargin<2)||isempty(d), d = pwd; end;
t = [d fs t];
end;
% Replace occurences of '/./' by '/' (problems with e.g. /././././././')
re = [fs1 '\.' fs1];
while ~isempty(regexp(t,re, 'once' )),
t = regexprep(t,re,fs);
end;
t = regexprep(t,[fs1 '\.' '$'], fs);
% Replace occurences of '/abc/../' by '/'
re = [fs1 '[^' fs1 ']+' fs1 '\.\.' fs1];
while ~isempty(regexp(t,re, 'once' )),
t = regexprep(t,re,fs,'once');
end;
t = regexprep(t,[fs1 '[^' fs1 ']+' fs1 '\.\.' '$'],fs,'once');
% Replace '//'
t = regexprep(t,[fs1 '+'], fs);
%=======================================================================
%=======================================================================
function editwin(ob,varargin)
[col1,col2,col3,lf,bf] = colours;
fg = gcbf;
lb = sib(ob,'selected');
str = get(lb,'String');
ac = allchild(fg);
acv = get(ac,'Visible');
h = uicontrol(fg,...
'Style','Edit',...
'units','normalized',...
'String',str,...
lf,...
'Max',2,...
'Tag','EditWindow',...
'HorizontalAlignment','Left',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'Position',[0.01 0.08 0.98 0.9],...
'Userdata',struct('ac',{ac},'acv',{acv}));
ea = uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',[.01 .01,.32,.07],...
bf,...
'Callback',@editdone,...
'tag','EditWindowAccept',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'String','Accept');
ee = uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',[.34 .01,.32,.07],...
bf,...
'Callback',@editeval,...
'tag','EditWindowEval',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'String','Eval');
ec = uicontrol(fg,...
'Style','pushbutton',...
'units','normalized',...
'Position',[.67 .01,.32,.07],...
bf,...
'Callback',@editclear,...
'tag','EditWindowCancel',...
'ForegroundColor',col3,...
'BackgroundColor',col1,...
'String','Cancel');
set(ac,'visible','off');
%=======================================================================
%=======================================================================
function editeval(ob,varargin)
ob = get(ob, 'Parent');
ob = sib(ob, 'EditWindow');
str = get(ob, 'String');
if ~isempty(str)
[out,sts] = cfg_eval_valedit(char(str));
if sts && (iscellstr(out) || ischar(out))
set(ob, 'String', cellstr(out));
else
fgc = get(ob, 'ForegroundColor');
set(ob, 'ForegroundColor', 'red');
pause(1);
set(ob, 'ForegroundColor', fgc);
end
end
%=======================================================================
%=======================================================================
function editdone(ob,varargin)
ob = get(ob,'Parent');
ob = sib(ob,'EditWindow');
str = cellstr(get(ob,'String'));
if isempty(str) || isempty(str{1})
str = {};
else
dstr = deblank(str);
if ~isequal(str, dstr)
c = questdlg(['Some of the filenames contain trailing blanks. This may ' ...
'be due to copy/paste of strings between MATLAB and the ' ...
'edit window. Do you want to remove any trailing blanks?'], ...
'Trailing Blanks in Filenames', ...
'Remove', 'Keep', 'Remove');
switch lower(c)
case 'remove'
str = dstr;
end
end
filt = getfilt(ob);
if filt.code >= 0 % filter files, but not dirs
[p,n,e] = cellfun(@fileparts, str, 'uniformoutput',false);
fstr = strcat(n, e);
[fstr1,fsel] = do_filter(fstr, filt.ext);
str = str(fsel);
end
end
lim = get(sib(ob,'files'),'UserData');
if numel(str)>lim(2),
msg(ob,['Retained ' num2str(lim(2)) ' of the ' num2str(numel(str)) ' files.']);
beep;
str = str(1:lim(2));
elseif isfinite(lim(2)),
if lim(1)==lim(2),
msg(ob,['Selected ' num2str(numel(str)) '/' num2str(lim(2)) ' files.']);
else
msg(ob,['Selected ' num2str(numel(str)) '/' num2str(lim(1)) '-' num2str(lim(2)) ' files.']);
end;
else
if numel(str) == 1, ss = ''; else ss = 's'; end;
msg(ob,['Specified ' num2str(numel(str)) ' file' ss '.']);
end;
if ~isfinite(lim(1)) || numel(str)>=lim(1),
set(sib(ob,'D'),'Enable','on');
else
set(sib(ob,'D'),'Enable','off');
end;
set(sib(ob,'selected'),'String',str,'Value',[]);
acs = get(ob,'Userdata');
fg = gcbf;
delete(findobj(fg,'-regexp','Tag','^EditWindow.*'));
set(acs.ac,{'Visible'},acs.acv);
%=======================================================================
%=======================================================================
function editclear(ob,varargin)
fg = gcbf;
acs = get(findobj(fg,'Tag','EditWindow'),'Userdata');
delete(findobj(fg,'-regexp','Tag','^EditWindow.*'));
set(acs.ac,{'Visible'},acs.acv);
%=======================================================================
%=======================================================================
function [c1,c2,c3,lf,bf] = colours
c1 = [1 1 1];
c2 = [1 1 1];
c3 = [0 0 0];
lf = cfg_get_defaults('cfg_ui.lfont');
bf = cfg_get_defaults('cfg_ui.bfont');
if isempty(lf)
lf = struct('FontName',get(0,'FixedWidthFontName'), ...
'FontWeight','normal', ...
'FontAngle','normal', ...
'FontSize',14, ...
'FontUnits','points');
end
if isempty(bf)
bf = struct('FontName',get(0,'FixedWidthFontName'), ...
'FontWeight','normal', ...
'FontAngle','normal', ...
'FontSize',14, ...
'FontUnits','points');
end
%=======================================================================
%=======================================================================
function select_rec(ob, varargin)
start = get(sib(ob,'edit'),'String');
filt = get(sib(ob,'regexp'),'Userdata');
filt.filt = {get(sib(ob,'regexp'), 'String')};
fob = sib(ob,'frame');
if ~isempty(fob)
filt.frames = get(fob,'Userdata');
else
filt.frames = [];
end;
ptr = get(gcbf,'Pointer');
try
set(gcbf,'Pointer','watch');
sel = select_rec1(start,filt);
catch
set(gcbf,'Pointer',ptr);
sel = {};
end;
set(gcbf,'Pointer',ptr);
already= get(sib(ob,'selected'),'String');
fb = sib(ob,'files');
lim = get(fb,'Userdata');
limsel = min(lim(2)-size(already,1),size(sel,1));
set(sib(ob,'selected'),'String',[already(:);sel(1:limsel)],'Value',[]);
msg(ob,sprintf('Added %d/%d matching files to selection.', limsel, size(sel,1)));
if ~isfinite(lim(1)) || size(sel,1)>=lim(1),
set(sib(ob,'D'),'Enable','on');
else
set(sib(ob,'D'),'Enable','off');
end;
%=======================================================================
%=======================================================================
function sel=select_rec1(cdir,filt)
sel={};
[t,d] = listfiles(cdir,filt);
if ~isempty(t)
sel = strcat([cdir,filesep],t);
end;
for k = 1:numel(d)
if ~any(strcmp(d{k},{'.','..'}))
sel1 = select_rec1(fullfile(cdir,d{k}),filt);
sel = [sel(:); sel1(:)];
end;
end;
%=======================================================================
%=======================================================================
function sfilt=mk_filter(typ,filt,frames)
if nargin<3, frames = 1; end;
if nargin<2, filt = '.*'; end;
if nargin<1, typ = 'any'; end;
switch lower(typ),
case {'any','*'}, code = 0; ext = {'.*'};
case {'image'}, code = 1; ext = {'.*\.nii(,\d+){0,2}$','.*\.img(,\d+){0,2}$','.*\.NII(,\d+){0,2}$','.*\.IMG(,\d+){0,2}$'};
case {'mesh'}, code = 0; ext = {'.*\.gii$','.*\.GII$','.*\.mat$','.*\.MAT$'};
case {'nifti'}, code = 0; ext = {'.*\.nii$','.*\.img$','.*\.NII$','.*\.IMG$'};
case {'gifti'}, code = 0; ext = {'.*\.gii$','.*\.GII$'};
case {'extimage'}, code = 1; ext = {'.*\.nii(,[0-9]*){0,2}$',...
'.*\.img(,[0-9]*){0,2}$',...
'.*\.NII(,[0-9]*){0,2}$',...
'.*\.IMG(,[0-9]*){0,2}$'};
case {'xml'}, code = 0; ext = {'.*\.xml$','.*\.XML$'};
case {'mat'}, code = 0; ext = {'.*\.mat$','.*\.MAT$','.*\.txt','.*\.TXT'};
case {'batch'}, code = 0; ext = {'.*\.mat$','.*\.MAT$','.*\.m$','.*\.M$','.*\.xml$','.*\.XML$'};
case {'dir'}, code =-1; ext = {'.*'};
case {'extdir'}, code =-1; ext = {['.*' filesep '$']};
otherwise, code = 0; ext = {typ};
end;
sfilt = struct('code',code,'frames',frames,'ext',{ext},...
'filt',{{filt}});
%=======================================================================
%=======================================================================
function drivestr = listdrives(reread)
persistent mydrivestr;
if isempty(mydrivestr) || reread
driveLett = strcat(cellstr(char(('C':'Z')')), ':');
dsel = false(size(driveLett));
for i=1:numel(driveLett)
dsel(i) = exist([driveLett{i} '\'],'dir')~=0;
end
mydrivestr = driveLett(dsel);
end;
drivestr = mydrivestr;
%=======================================================================
%=======================================================================
|
github
|
lcnbeapp/beapp-master
|
coor2D.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@meeg/coor2D.m
| 4,007 |
utf_8
|
f94070275bb14e35788e110abf929115
|
function [res, plotind] = coor2D(this, ind, val, mindist)
% returns x and y coordinates of channels in 2D plane
% FORMAT coor2D(this)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Vladimir Litvak, Laurence Hunt
% $Id: coor2D.m 4372 2011-06-21 21:26:46Z vladimir $
megind = strmatch('MEG', chantype(this));
eegind = strmatch('EEG', chantype(this), 'exact');
otherind = setdiff(1:nchannels(this), [megind; eegind]);
if nargin==1 || isempty(ind)
if nargin<3 || (size(val, 2)<nchannels(this))
if ~isempty(megind)
ind = megind;
elseif ~isempty(eegind)
ind = eegind;
else
ind = 1:nchannels(this);
end
else
ind = 1:nchannels(this);
end
elseif ischar(ind)
switch upper(ind)
case 'MEG'
ind = megind;
case 'EEG'
ind = eegind;
otherwise
ind = otherind;
end
end
if nargin < 3 || isempty(val)
if ~isempty(intersect(ind, megind))
if ~any(cellfun('isempty', {this.channels(megind).X_plot2D}))
meg_xy = [this.channels(megind).X_plot2D; this.channels(megind).Y_plot2D];
elseif all(cellfun('isempty', {this.channels(megind).X_plot2D}))
meg_xy = grid(length(megind));
else
error('Either all or none of MEG channels should have 2D coordinates defined.');
end
end
if ~isempty(intersect(ind, eegind))
if ~any(cellfun('isempty', {this.channels(eegind).X_plot2D}))
eeg_xy = [this.channels(eegind).X_plot2D; this.channels(eegind).Y_plot2D];
elseif all(cellfun('isempty', {this.channels(eegind).X_plot2D}))
eeg_xy = grid(length(eegind));
else
error('Either all or none of EEG channels should have 2D coordinates defined.');
end
end
if ~isempty(intersect(ind, otherind))
other_xy = grid(length(otherind));
end
xy = zeros(2, length(ind));
plotind = zeros(1, length(ind));
for i = 1:length(ind)
[found, loc] = ismember(ind(i), megind);
if found
xy(:, i) = meg_xy(:, loc);
plotind(i) = 1;
else
[found, loc] = ismember(ind(i), eegind);
if found
xy(:, i) = eeg_xy(:, loc);
plotind(i) = 2;
else
[found, loc] = ismember(ind(i), otherind);
if found
xy(:, i) = other_xy(:, loc);
plotind(i) = 3;
end
end
end
end
if nargin > 3 && ~isempty(mindist)
xy = shiftxy(xy,mindist);
end
res = xy;
else
this = getset(this, 'channels', 'X_plot2D', ind, val(1, :));
this = getset(this, 'channels', 'Y_plot2D', ind, val(2, :));
res = this;
end
function xy = grid(n)
ncol = ceil(sqrt(n));
x = 0:(1/(ncol+1)):1;
x = 0.9*x+0.05;
x = x(2:(end-1));
y = fliplr(x);
[X, Y] = meshgrid(x, y);
xy = [X(1:n); Y(1:n)];
function xy = shiftxy(xy,mindist)
x = xy(1,:);
y = xy(2,:);
l=1;
i=1; %filler
mindist = mindist/0.999; % limits the number of loops
while (~isempty(i) && l<50)
xdiff = repmat(x,length(x),1) - repmat(x',1,length(x));
ydiff = repmat(y,length(y),1) - repmat(y',1,length(y));
xydist= sqrt(xdiff.^2 + ydiff.^2); %euclidean distance between all sensor pairs
[i,j] = find(xydist<mindist*0.999);
rm=(i<=j); i(rm)=[]; j(rm)=[]; %only look at i>j
for m = 1:length(i);
if (xydist(i(m),j(m)) == 0)
diffvec = [mindist./sqrt(2) mindist./sqrt(2)];
else
xydiff = [xdiff(i(m),j(m)) ydiff(i(m),j(m))];
diffvec = xydiff.*mindist./xydist(i(m),j(m)) - xydiff;
end
x(i(m)) = x(i(m)) - diffvec(1)/2;
y(i(m)) = y(i(m)) - diffvec(2)/2;
x(j(m)) = x(j(m)) + diffvec(1)/2;
y(j(m)) = y(j(m)) + diffvec(2)/2;
end
l = l+1;
end
xy = [x; y];
|
github
|
lcnbeapp/beapp-master
|
cache.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@meeg/cache.m
| 754 |
utf_8
|
327310c88f9e84a225af302977c46fe6
|
function res = cache(this, stuff)
% Method for retrieving/putting stuff from/into the temporary cache
% FORMAT res = cache(obj, name)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Stefan Kiebel
% $Id: cache.m 1373 2008-04-11 14:24:03Z spm $
if ischar(stuff)
% assume this is a retrieval
res = getcache(this, stuff);
else
% assume this is a put
name = inputname(2);
res = setcache(this, name, stuff);
end
function res = getcache(this, stuff)
if isfield(this.cache, stuff)
eval(['res = this.cache.' stuff ';']);
else
res = [];
end
function this = setcache(this, name, stuff)
eval(['this.cache(1).' name ' = stuff;']);
|
github
|
lcnbeapp/beapp-master
|
path.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@meeg/path.m
| 558 |
utf_8
|
7149045fd0a2ac178f0e2dcaf166b5e0
|
function res = path(this, name)
% Method for getting/setting path
% FORMAT res = path(this, name)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Stefan Kiebel
% $Id: path.m 1373 2008-04-11 14:24:03Z spm $
switch nargin
case 1
res = getpath(this);
case 2
res = setpath(this, name);
otherwise
end
function res = getpath(this)
try
res = this.path;
catch
res = '';
end
function this = setpath(this, name)
this.path = name;
|
github
|
lcnbeapp/beapp-master
|
fname.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@meeg/fname.m
| 538 |
utf_8
|
00404808a43026efada0ed0cb853d259
|
function res = fname(this, name)
% Method for getting/setting file name
% FORMAT res = fname(this, name)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Stefan Kiebel
% $Id: fname.m 1373 2008-04-11 14:24:03Z spm $
switch nargin
case 1
res = getfname(this);
case 2
res = setfname(this, name);
otherwise
end
function res = getfname(this)
res = this.fname;
function this = setfname(this, name)
this.fname = name;
|
github
|
lcnbeapp/beapp-master
|
fnamedat.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@meeg/fnamedat.m
| 589 |
utf_8
|
39857f5d9ecf819f3bc1581bde7009cf
|
function res = fnamedat(this, name)
% Method for getting/setting file name of data file
% FORMAT res = fnamedat(this, name)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Stefan Kiebel
% $Id: fnamedat.m 1373 2008-04-11 14:24:03Z spm $
switch nargin
case 1
res = getfnamedat(this);
case 2
res = setfnamedat(this, name);
otherwise
end
function res = getfnamedat(this)
res = this.data.fnamedat;
function this = setfnamedat(this, name)
this.data.fnamedat = name;
|
github
|
lcnbeapp/beapp-master
|
privatepermission.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/privatepermission.m
| 827 |
utf_8
|
be8d85c3b8ab99ec9cf086139103335f
|
function varargout = permission(varargin)
% Format
% For getting the value
% dat = permission(obj)
%
% For setting the value
% obj = permission(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wrong number of arguments.');
end;
return;
function dat = ref(obj)
dat = obj.permission;
return;
function obj = asgn(obj,dat)
if ischar(dat)
tmp = lower(deblank(dat(:)'));
switch tmp,
case 'ro',
case 'rw',
otherwise,
error('Permission must be either "ro" or "rw"');
end
obj.permission = tmp;
else
error('"permission" must be a character string.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
privatescl_slope.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/privatescl_slope.m
| 680 |
utf_8
|
4f91ac10412885a1654d520cdaf4c008
|
function varargout = scl_slope(varargin)
% Format
% For getting the value
% dat = scl_slope(obj)
%
% For setting the value
% obj = scl_slope(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wrong number of arguments.');
end;
return;
function dat = ref(obj)
dat = obj.scl_slope;
return;
function obj = asgn(obj,dat)
if isnumeric(dat), % && numel(dat)<=1,
obj.scl_slope = double(dat);
else
error('"scl_slope" must be numeric.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
subsasgn.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/subsasgn.m
| 4,553 |
utf_8
|
8649bb5b2b003aef0a04f01504128d47
|
function obj = subsasgn(obj,subs,dat)
% Overloaded subsasgn function for file_array objects.
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if isempty(subs)
return;
end;
if ~strcmp(subs(1).type,'()'),
if strcmp(subs(1).type,'.'),
%error('Attempt to reference field of non-structure array.');
if numel(struct(obj))~=1,
error('Can only change the fields of simple file_array objects.');
end;
switch(subs(1).subs)
case 'fname', obj = asgn(obj,@fname, subs(2:end),dat); %fname(obj,dat);
case 'dtype', obj = asgn(obj,@dtype, subs(2:end),dat); %dtype(obj,dat);
case 'offset', obj = asgn(obj,@offset, subs(2:end),dat); %offset(obj,dat);
case 'dim', obj = asgn(obj,@dim, subs(2:end),dat); %obj = dim(obj,dat);
case 'scl_slope', obj = asgn(obj,@scl_slope, subs(2:end),dat); %scl_slope(obj,dat);
case 'scl_inter', obj = asgn(obj,@scl_inter, subs(2:end),dat); %scl_inter(obj,dat);
case 'permission', obj = asgn(obj,@permission,subs(2:end),dat); %permission(obj,dat);
otherwise, error(['Reference to non-existent field "' subs.subs '".']);
end;
return;
end;
if strcmp(subs(1).type,'{}'), error('Cell contents reference from a non-cell array object.'); end;
end;
if numel(subs)~=1, error('Expression too complicated');end;
dm = size(obj);
sobj = struct(obj);
if length(subs.subs) < length(dm),
l = length(subs.subs);
dm = [dm(1:(l-1)) prod(dm(l:end))];
if numel(sobj) ~= 1,
error('Can only reshape simple file_array objects.');
end;
if numel(sobj.scl_slope)>1 || numel(sobj.scl_inter)>1,
error('Can not reshape file_array objects with multiple slopes and intercepts.');
end;
end;
dm = [dm ones(1,16)];
do = ones(1,16);
args = {};
for i=1:length(subs.subs),
if ischar(subs.subs{i}),
if ~strcmp(subs.subs{i},':'), error('This shouldn''t happen....'); end;
args{i} = int32(1:dm(i));
else
args{i} = int32(subs.subs{i});
end;
do(i) = length(args{i});
end;
for j=1:length(sobj),
if strcmp(sobj(j).permission,'ro'),
error('Array is read-only.');
end
end
if length(sobj)==1
sobj.dim = dm;
if numel(dat)~=1,
subfun(sobj,double(dat),args{:});
else
dat1 = double(dat) + zeros(do);
subfun(sobj,dat1,args{:});
end;
else
for j=1:length(sobj),
ps = [sobj(j).pos ones(1,length(args))];
dm = [sobj(j).dim ones(1,length(args))];
siz = ones(1,16);
for i=1:length(args),
msk = args{i}>=ps(i) & args{i}<(ps(i)+dm(i));
args2{i} = find(msk);
args3{i} = int32(double(args{i}(msk))-ps(i)+1);
siz(i) = numel(args2{i});
end;
if numel(dat)~=1,
dat1 = double(subsref(dat,struct('type','()','subs',{args2})));
else
dat1 = double(dat) + zeros(siz);
end;
subfun(sobj(j),dat1,args3{:});
end
end
return
function sobj = subfun(sobj,dat,varargin)
va = varargin;
dt = datatypes;
ind = find(cat(1,dt.code)==sobj.dtype);
if isempty(ind), error('Unknown datatype'); end;
if dt(ind).isint, dat(~isfinite(dat)) = 0; end;
if ~isempty(sobj.scl_inter),
inter = sobj.scl_inter;
if numel(inter)>1,
inter = resize_scales(inter,sobj.dim,varargin);
end;
dat = double(dat) - inter;
end;
if ~isempty(sobj.scl_slope),
slope = sobj.scl_slope;
if numel(slope)>1,
slope = resize_scales(slope,sobj.dim,varargin);
dat = double(dat)./slope;
else
dat = double(dat)/slope;
end;
end;
if dt(ind).isint, dat = round(dat); end;
% Avoid warning messages in R14 SP3
wrn = warning;
warning('off');
dat = feval(dt(ind).conv,dat);
warning(wrn);
nelem = dt(ind).nelem;
if nelem==1,
mat2file(sobj,dat,va{:});
elseif nelem==2,
sobj1 = sobj;
sobj1.dim = [2 sobj.dim];
sobj1.dtype = dt(find(strcmp(dt(ind).prec,{dt.prec}) & (cat(2,dt.nelem)==1))).code;
dat = reshape(dat,[1 size(dat)]);
dat = [real(dat) ; imag(dat)];
mat2file(sobj1,dat,int32([1 2]),va{:});
else
error('Inappropriate number of elements per voxel.');
end;
return
function obj = asgn(obj,fun,subs,dat)
if ~isempty(subs),
tmp = feval(fun,obj);
tmp = subsasgn(tmp,subs,dat);
obj = feval(fun,obj,tmp);
else
obj = feval(fun,obj,dat);
end;
|
github
|
lcnbeapp/beapp-master
|
privatedim.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/privatedim.m
| 762 |
utf_8
|
0ad58f05456fccb279755b25289027c4
|
function varargout = dim(varargin)
% Format
% For getting the value
% dat = dim(obj)
%
% For setting the value
% obj = dim(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wrong number of arguments.');
end;
return;
function dat = ref(obj)
dat = obj.dim;
return;
function obj = asgn(obj,dat)
if isnumeric(dat) && all(dat>=0) && all(rem(dat,1)==0),
dat = [double(dat(:)') 1 1];
lim = max([2 find(dat~=1)]);
dat = dat(1:lim);
obj.dim = dat;
else
error('"dim" must be a vector of positive integers.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
privatescl_inter.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/privatescl_inter.m
| 681 |
utf_8
|
341f747372c0465de4be134d3595e133
|
function varargout = scl_inter(varargin)
% Format
% For getting the value
% dat = scl_inter(obj)
%
% For setting the value
% obj = scl_inter(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wrong number of arguments.');
end;
return;
function dat = ref(obj)
dat = obj.scl_inter;
return;
function obj = asgn(obj,dat)
if isnumeric(dat), % && numel(dat)<=1,
obj.scl_inter = double(dat);
else
error('"scl_inter" must be numeric.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
privatefname.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/privatefname.m
| 648 |
utf_8
|
87ba48423085238dda8deb873c3a5a24
|
function varargout = fname(varargin)
% Format
% For getting the value
% dat = fname(obj)
%
% For setting the value
% obj = fname(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wrong number of arguments.');
end;
return;
function dat = ref(obj)
dat = obj.fname;
return;
function obj = asgn(obj,dat)
if ischar(dat)
obj.fname = deblank(dat(:)');
else
error('"fname" must be a character string.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
privateoffset.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/privateoffset.m
| 697 |
utf_8
|
5b5493cb277651ae207a6e094e50f16f
|
function varargout = offset(varargin)
% Format
% For getting the value
% dat = offset(obj)
%
% For setting the value
% obj = offset(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wrong number of arguments.');
end;
return;
function dat = ref(obj)
dat = obj.offset;
return;
function obj = asgn(obj,dat)
if isnumeric(dat) && numel(dat)==1 && dat>=0 && rem(dat,1)==0,
obj.offset = double(dat);
else
error('"offset" must be a positive integer.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
privatedtype.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/privatedtype.m
| 2,225 |
utf_8
|
4e4a2cfe6a4a9d295f1b9f3eb3fd3eb1
|
function varargout = dtype(varargin)
% Format
% For getting the value
% dat = dtype(obj)
%
% For setting the value
% obj = dtype(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wring number of arguments.');
end;
return;
function t = ref(obj)
d = datatypes;
mch = find(cat(1,d.code)==obj.dtype);
if isempty(mch), t = 'UNKNOWN'; else t = d(mch).label; end;
if obj.be, t = [t '-BE']; else t = [t '-LE']; end;
return;
function obj = asgn(obj,dat)
d = datatypes;
if isnumeric(dat)
if numel(dat)>=1,
mch = find(cat(1,d.code)==dat(1));
if isempty(mch) || mch==0,
fprintf('Invalid datatype (%d).', dat(1));
disp('First part of datatype should be of one of the following');
disp(sortrows([num2str(cat(1,d.code)) ...
repmat(' ',numel(d),2) strvcat(d.label)]));
%error(['Invalid datatype (' num2str(dat(1)) ').']);
return;
end;
obj.dtype = double(dat(1));
end;
if numel(dat)>=2,
obj.be = double(dat(2)~=0);
end;
if numel(dat)>2,
error('Too many elements in numeric datatype.');
end;
elseif ischar(dat),
dat1 = lower(dat);
sep = find(dat1=='-' | dat1=='/');
sep = sep(sep~=1);
if ~isempty(sep),
c1 = dat1(1:(sep(1)-1));
c2 = dat1((sep(1)+1):end);
else
c1 = dat1;
c2 = '';
end;
mch = find(strcmpi(c1,lower({d.label})));
if isempty(mch),
disp('First part of datatype should be of one of the following');
disp(sortrows([num2str(cat(1,d.code)) ...
repmat(' ',numel(d),2) strvcat(d.label)]));
%error(['Invalid datatype (' c1 ').']);
return;
else
obj.dtype = double(d(mch(1)).code);
end;
if any(c2=='b'),
if any(c2=='l'),
error('Cannot be both big and little endian.');
end;
obj.be = 1;
elseif any(c2=='l'),
obj.be = 0;
end;
else
error('Invalid datatype.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
subsref.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/subsref.m
| 5,222 |
utf_8
|
80f9298dd645012f0fe42fcb32d6beef
|
function varargout=subsref(obj,subs)
% SUBSREF Subscripted reference
% An overloaded function...
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if isempty(subs), return; end
switch subs(1).type
case '{}'
error('Cell contents reference from a non-cell array object.');
case '.'
varargout = access_fields(obj,subs);
return;
end
if numel(subs)~=1, error('Expression too complicated'); end;
dim = [size(obj) ones(1,16)];
nd = find(dim>1,1,'last')-1;
sobj = struct(obj);
if ~numel(subs.subs)
[subs.subs{1:nd+1}] = deal(':');
elseif length(subs.subs) < nd
l = length(subs.subs);
dim = [dim(1:(l-1)) prod(dim(l:end))];
if numel(sobj) ~= 1
error('Can only reshape simple file_array objects.');
else
if numel(sobj.scl_slope)>1 || numel(sobj.scl_inter)>1
error('Can not reshape file_array objects with multiple slopes and intercepts.');
end
sobj.dim = dim;
end
end
do = ones(16,1);
args = cell(1,length(subs.subs));
for i=1:length(subs.subs)
if ischar(subs.subs{i})
if ~strcmp(subs.subs{i},':'), error('This shouldn''t happen....'); end
if length(subs.subs) == 1
args{i} = 1:prod(dim); % possible overflow when int32()
k = 0;
for j=1:length(sobj)
sobj(j).dim = [prod(sobj(j).dim) 1];
sobj(j).pos = [k+1 1];
k = k + sobj(j).dim(1);
end
else
args{i} = 1:dim(i);
end
else
args{i} = subs.subs{i};
end
do(i) = length(args{i});
end
if length(sobj)==1
t = subfun(sobj,args{:});
else
dt = datatypes;
dt = dt([dt.code]==sobj(1).dtype); % assuming identical datatypes
t = zeros(do',func2str(dt.conv));
for j=1:length(sobj)
ps = [sobj(j).pos ones(1,length(args))];
dm = [sobj(j).dim ones(1,length(args))];
for i=1:length(args)
msk = find(args{i}>=ps(i) & args{i}<(ps(i)+dm(i)));
args2{i} = msk;
args3{i} = double(args{i}(msk))-ps(i)+1;
end
t = subsasgn(t,struct('type','()','subs',{args2}),subfun(sobj(j),args3{:}));
end
end
varargout = {t};
%==========================================================================
% function t = subfun(sobj,varargin)
%==========================================================================
function t = subfun(sobj,varargin)
%sobj.dim = [sobj.dim ones(1,16)];
try
args = cell(size(varargin));
for i=1:length(varargin)
args{i} = int32(varargin{i});
end
t = file2mat(sobj,args{:});
catch
t = multifile2mat(sobj,varargin{:});
end
if ~isempty(sobj.scl_slope) || ~isempty(sobj.scl_inter)
slope = 1;
inter = 0;
if ~isempty(sobj.scl_slope), slope = sobj.scl_slope; end
if ~isempty(sobj.scl_inter), inter = sobj.scl_inter; end
if numel(slope)>1
slope = resize_scales(slope,sobj.dim,varargin);
t = double(t).*slope;
else
t = double(t)*slope;
end
if numel(inter)>1
inter = resize_scales(inter,sobj.dim,varargin);
end;
t = t + inter;
end
%==========================================================================
% function c = access_fields(obj,subs)
%==========================================================================
function c = access_fields(obj,subs)
sobj = struct(obj);
c = cell(1,numel(sobj));
for i=1:numel(sobj)
%obj = class(sobj(i),'file_array');
obj = sobj(i);
switch(subs(1).subs)
case 'fname', t = fname(obj);
case 'dtype', t = dtype(obj);
case 'offset', t = offset(obj);
case 'dim', t = dim(obj);
case 'scl_slope', t = scl_slope(obj);
case 'scl_inter', t = scl_inter(obj);
case 'permission', t = permission(obj);
otherwise
error(['Reference to non-existent field "' subs(1).subs '".']);
end
if numel(subs)>1
t = subsref(t,subs(2:end));
end
c{i} = t;
end
%==========================================================================
% function val = multifile2mat(sobj,varargin)
%==========================================================================
function val = multifile2mat(sobj,varargin)
% Convert subscripts into linear index
[indx2{1:length(varargin)}] = ndgrid(varargin{:},1);
ind = sub2ind(sobj.dim,indx2{:});
% Work out the partition
dt = datatypes;
dt = dt([dt.code]==sobj.dtype);
sz = dt.size;
mem = spm('memory'); % in bytes, has to be a multiple of 16 (max([dt.size]))
s = ceil(prod(sobj.dim) * sz / mem);
% Assign indices to partitions
[x,y] = ind2sub([mem/sz s],ind(:));
c = histc(y,1:s);
cc = [0 reshape(cumsum(c),1,[])];
% Read data in relevant partitions
obj = sobj;
val = zeros(length(x),1,func2str(dt.conv));
for i=reshape(find(c),1,[])
obj.offset = sobj.offset + mem*(i-1);
obj.dim = [1 min(mem/sz, prod(sobj.dim)-(i-1)*mem/sz)];
val(cc(i)+1:cc(i+1)) = file2mat(obj,int32(1),int32(x(y==i)));
end
r = cellfun('length',varargin);
if numel(r) == 1, r = [r 1]; end
val = reshape(val,r);
|
github
|
lcnbeapp/beapp-master
|
disp.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/disp.m
| 887 |
utf_8
|
64720ef6ff6e10ebb67d01f5d3a04f7f
|
function disp(obj)
% Display a file_array object
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if numel(struct(obj))>1,
fprintf(' %s object: ', class(obj));
sz = size(obj);
if length(sz)>4,
fprintf('%d-D\n',length(sz));
else
for i=1:(length(sz)-1),
fprintf('%d-by-',sz(i));
end;
fprintf('%d\n',sz(end));
end;
else
display(mystruct(obj))
end;
return;
%=======================================================================
%=======================================================================
function t = mystruct(obj)
fn = fieldnames(obj);
for i=1:length(fn)
t.(fn{i}) = subsref(obj,struct('type','.','subs',fn{i}));
end;
return;
%=======================================================================
|
github
|
lcnbeapp/beapp-master
|
offset.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/private/offset.m
| 697 |
utf_8
|
5b5493cb277651ae207a6e094e50f16f
|
function varargout = offset(varargin)
% Format
% For getting the value
% dat = offset(obj)
%
% For setting the value
% obj = offset(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wrong number of arguments.');
end;
return;
function dat = ref(obj)
dat = obj.offset;
return;
function obj = asgn(obj,dat)
if isnumeric(dat) && numel(dat)==1 && dat>=0 && rem(dat,1)==0,
obj.offset = double(dat);
else
error('"offset" must be a positive integer.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
scl_slope.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/private/scl_slope.m
| 680 |
utf_8
|
4f91ac10412885a1654d520cdaf4c008
|
function varargout = scl_slope(varargin)
% Format
% For getting the value
% dat = scl_slope(obj)
%
% For setting the value
% obj = scl_slope(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wrong number of arguments.');
end;
return;
function dat = ref(obj)
dat = obj.scl_slope;
return;
function obj = asgn(obj,dat)
if isnumeric(dat), % && numel(dat)<=1,
obj.scl_slope = double(dat);
else
error('"scl_slope" must be numeric.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
scl_inter.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/private/scl_inter.m
| 681 |
utf_8
|
341f747372c0465de4be134d3595e133
|
function varargout = scl_inter(varargin)
% Format
% For getting the value
% dat = scl_inter(obj)
%
% For setting the value
% obj = scl_inter(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wrong number of arguments.');
end;
return;
function dat = ref(obj)
dat = obj.scl_inter;
return;
function obj = asgn(obj,dat)
if isnumeric(dat), % && numel(dat)<=1,
obj.scl_inter = double(dat);
else
error('"scl_inter" must be numeric.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
fname.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/private/fname.m
| 648 |
utf_8
|
87ba48423085238dda8deb873c3a5a24
|
function varargout = fname(varargin)
% Format
% For getting the value
% dat = fname(obj)
%
% For setting the value
% obj = fname(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wrong number of arguments.');
end;
return;
function dat = ref(obj)
dat = obj.fname;
return;
function obj = asgn(obj,dat)
if ischar(dat)
obj.fname = deblank(dat(:)');
else
error('"fname" must be a character string.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
dim.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/private/dim.m
| 762 |
utf_8
|
0ad58f05456fccb279755b25289027c4
|
function varargout = dim(varargin)
% Format
% For getting the value
% dat = dim(obj)
%
% For setting the value
% obj = dim(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wrong number of arguments.');
end;
return;
function dat = ref(obj)
dat = obj.dim;
return;
function obj = asgn(obj,dat)
if isnumeric(dat) && all(dat>=0) && all(rem(dat,1)==0),
dat = [double(dat(:)') 1 1];
lim = max([2 find(dat~=1)]);
dat = dat(1:lim);
obj.dim = dat;
else
error('"dim" must be a vector of positive integers.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
permission.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/private/permission.m
| 827 |
utf_8
|
be8d85c3b8ab99ec9cf086139103335f
|
function varargout = permission(varargin)
% Format
% For getting the value
% dat = permission(obj)
%
% For setting the value
% obj = permission(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wrong number of arguments.');
end;
return;
function dat = ref(obj)
dat = obj.permission;
return;
function obj = asgn(obj,dat)
if ischar(dat)
tmp = lower(deblank(dat(:)'));
switch tmp,
case 'ro',
case 'rw',
otherwise,
error('Permission must be either "ro" or "rw"');
end
obj.permission = tmp;
else
error('"permission" must be a character string.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
dtype.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@file_array/private/dtype.m
| 2,225 |
utf_8
|
4e4a2cfe6a4a9d295f1b9f3eb3fd3eb1
|
function varargout = dtype(varargin)
% Format
% For getting the value
% dat = dtype(obj)
%
% For setting the value
% obj = dtype(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
if nargin==2,
varargout{1} = asgn(varargin{:});
elseif nargin==1,
varargout{1} = ref(varargin{:});
else
error('Wring number of arguments.');
end;
return;
function t = ref(obj)
d = datatypes;
mch = find(cat(1,d.code)==obj.dtype);
if isempty(mch), t = 'UNKNOWN'; else t = d(mch).label; end;
if obj.be, t = [t '-BE']; else t = [t '-LE']; end;
return;
function obj = asgn(obj,dat)
d = datatypes;
if isnumeric(dat)
if numel(dat)>=1,
mch = find(cat(1,d.code)==dat(1));
if isempty(mch) || mch==0,
fprintf('Invalid datatype (%d).', dat(1));
disp('First part of datatype should be of one of the following');
disp(sortrows([num2str(cat(1,d.code)) ...
repmat(' ',numel(d),2) strvcat(d.label)]));
%error(['Invalid datatype (' num2str(dat(1)) ').']);
return;
end;
obj.dtype = double(dat(1));
end;
if numel(dat)>=2,
obj.be = double(dat(2)~=0);
end;
if numel(dat)>2,
error('Too many elements in numeric datatype.');
end;
elseif ischar(dat),
dat1 = lower(dat);
sep = find(dat1=='-' | dat1=='/');
sep = sep(sep~=1);
if ~isempty(sep),
c1 = dat1(1:(sep(1)-1));
c2 = dat1((sep(1)+1):end);
else
c1 = dat1;
c2 = '';
end;
mch = find(strcmpi(c1,lower({d.label})));
if isempty(mch),
disp('First part of datatype should be of one of the following');
disp(sortrows([num2str(cat(1,d.code)) ...
repmat(' ',numel(d),2) strvcat(d.label)]));
%error(['Invalid datatype (' c1 ').']);
return;
else
obj.dtype = double(d(mch(1)).code);
end;
if any(c2=='b'),
if any(c2=='l'),
error('Cannot be both big and little endian.');
end;
obj.be = 1;
elseif any(c2=='l'),
obj.be = 0;
end;
else
error('Invalid datatype.');
end;
return;
|
github
|
lcnbeapp/beapp-master
|
subsasgn.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@nifti/subsasgn.m
| 14,522 |
utf_8
|
86db451a023fd9a4a9252278adcab3ab
|
function obj = subsasgn(obj,subs,varargin)
% Subscript assignment
% See subsref for meaning of fields.
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
switch subs(1).type,
case {'.'},
if numel(obj)~=nargin-2,
error('The number of outputs should match the number of inputs.');
end;
objs = struct(obj);
for i=1:length(varargin),
val = varargin{i};
obji = class(objs(i),'nifti');
obji = fun(obji,subs,val);
objs(i) = struct(obji);
end;
obj = class(objs,'nifti');
case {'()'},
objs = struct(obj);
if length(subs)>1,
t = subsref(objs,subs(1));
% A lot of this stuff is a little flakey, and may cause Matlab to bomb.
%
%if numel(t) ~= nargin-2,
% error('The number of outputs should match the number of inputs.');
%end;
for i=1:numel(t),
val = varargin{1};
obji = class(t(i),'nifti');
obji = subsasgn(obji,subs(2:end),val);
t(i) = struct(obji);
end;
objs = subsasgn(objs,subs(1),t);
else
if numel(varargin)>1,
error('Illegal right hand side in assignment. Too many elements.');
end;
val = varargin{1};
if isa(val,'nifti'),
objs = subsasgn(objs,subs,struct(val));
elseif isempty(val),
objs = subsasgn(objs,subs,[]);
else
error('Assignment between unlike types is not allowed.');
end;
end;
obj = class(objs,'nifti');
otherwise
error('Cell contents reference from a non-cell array object.');
end;
return;
%=======================================================================
%=======================================================================
function obj = fun(obj,subs,val)
% Subscript referencing
switch subs(1).type,
case {'.'},
objs = struct(obj);
for ii=1:numel(objs)
obj = objs(ii);
if any(strcmpi(subs(1).subs,{'dat'})),
if length(subs)>1,
val = subsasgn(obj.dat,subs(2:end),val);
end;
obj = assigndat(obj,val);
objs(ii) = obj;
continue;
end;
if isempty(obj.hdr), obj.hdr = empty_hdr; end;
if ~isfield(obj.hdr,'magic'), error('Not a NIFTI-1 header'); end;
if length(subs)>1, % && ~strcmpi(subs(1).subs,{'raw','dat'}),
val0 = subsref(class(obj,'nifti'),subs(1));
val1 = subsasgn(val0,subs(2:end),val);
else
val1 = val;
end;
switch(subs(1).subs)
case {'extras'}
if length(subs)>1,
obj.extras = subsasgn(obj.extras,subs(2:end),val);
else
obj.extras = val;
end;
case {'mat0'}
if ~isnumeric(val1) || ndims(val1)~=2 || any(size(val1)~=[4 4]) || sum((val1(4,:)-[0 0 0 1]).^2)>1e-8,
error('"mat0" should be a 4x4 matrix, with a last row of 0,0,0,1.');
end;
if obj.hdr.qform_code==0, obj.hdr.qform_code=2; end;
s = double(bitand(obj.hdr.xyzt_units,7));
if s
d = findindict(s,'units');
val1 = diag([[1 1 1]/d.rescale 1])*val1;
end;
obj.hdr = encode_qform0(double(val1), obj.hdr);
case {'mat0_intent'}
if isempty(val1),
obj.hdr.qform_code = 0;
else
if ~ischar(val1) && ~(isnumeric(val1) && numel(val1)==1),
error('"mat0_intent" should be a string or a scalar.');
end;
d = findindict(val1,'xform');
if ~isempty(d)
obj.hdr.qform_code = d.code;
end;
end;
case {'mat'}
if ~isnumeric(val1) || ndims(val1)~=2 || any(size(val1)~=[4 4]) || sum((val1(4,:)-[0 0 0 1]).^2)>1e-8
error('"mat" should be a 4x4 matrix, with a last row of 0,0,0,1.');
end;
if obj.hdr.sform_code==0, obj.hdr.sform_code=2; end;
s = double(bitand(obj.hdr.xyzt_units,7));
if s
d = findindict(s,'units');
val1 = diag([[1 1 1]/d.rescale 1])*val1;
end;
val1 = val1 * [eye(4,3) [1 1 1 1]'];
obj.hdr.srow_x = val1(1,:);
obj.hdr.srow_y = val1(2,:);
obj.hdr.srow_z = val1(3,:);
case {'mat_intent'}
if isempty(val1),
obj.hdr.sform_code = 0;
else
if ~ischar(val1) && ~(isnumeric(val1) && numel(val1)==1),
error('"mat_intent" should be a string or a scalar.');
end;
d = findindict(val1,'xform');
if ~isempty(d),
obj.hdr.sform_code = d.code;
end;
end;
case {'intent'}
if ~valid_fields(val1,{'code','param','name'})
obj.hdr.intent_code = 0;
obj.hdr.intent_p1 = 0;
obj.hdr.intent_p2 = 0;
obj.hdr.intent_p3 = 0;
obj.hdr.intent_name = '';
else
if ~isfield(val1,'code'),
val1.code = obj.hdr.intent_code;
end;
d = findindict(val1.code,'intent');
if ~isempty(d),
obj.hdr.intent_code = d.code;
if isfield(val1,'param'),
prm = [double(val1.param(:)) ; 0 ; 0; 0];
prm = [prm(1:length(d.param)) ; 0 ; 0; 0];
obj.hdr.intent_p1 = prm(1);
obj.hdr.intent_p2 = prm(2);
obj.hdr.intent_p3 = prm(3);
end;
if isfield(val1,'name'),
obj.hdr.intent_name = val1.name;
end;
end;
end;
case {'diminfo'}
if ~valid_fields(val1,{'frequency','phase','slice','slice_time'})
tmp = obj.hdr.dim_info;
for bit=1:6,
tmp = bitset(tmp,bit,0);
end;
obj.hdr.dim_info = tmp;
obj.hdr.slice_start = 0;
obj.hdr.slice_end = 0;
obj.hdr.slice_duration = 0;
obj.hdr.slice_code = 0;
else
if isfield(val1,'frequency'),
tmp = val1.frequency;
if ~isnumeric(tmp) || numel(tmp)~=1 || tmp<0 || tmp>3,
error('Invalid frequency direction');
end;
obj.hdr.dim_info = bitset(obj.hdr.dim_info,1,bitget(tmp,1));
obj.hdr.dim_info = bitset(obj.hdr.dim_info,2,bitget(tmp,2));
end;
if isfield(val1,'phase'),
tmp = val1.phase;
if ~isnumeric(tmp) || numel(tmp)~=1 || tmp<0 || tmp>3,
error('Invalid phase direction');
end;
obj.hdr.dim_info = bitset(obj.hdr.dim_info,3,bitget(tmp,1));
obj.hdr.dim_info = bitset(obj.hdr.dim_info,4,bitget(tmp,2));
end;
if isfield(val1,'slice'),
tmp = val1.slice;
if ~isnumeric(tmp) || numel(tmp)~=1 || tmp<0 || tmp>3,
error('Invalid slice direction');
end;
obj.hdr.dim_info = bitset(obj.hdr.dim_info,5,bitget(tmp,1));
obj.hdr.dim_info = bitset(obj.hdr.dim_info,6,bitget(tmp,2));
end;
if isfield(val1,'slice_time')
tim = val1.slice_time;
if ~valid_fields(tim,{'start','end','duration','code'}),
obj.hdr.slice_code = 0;
obj.hdr.slice_start = 0;
obj.hdr.end_slice = 0;
obj.hdr.slice_duration = 0;
else
% sld = double(bitget(obj.hdr.dim_info,5)) + 2*double(bitget(obj.hdr.dim_info,6));
if isfield(tim,'start'),
ss = double(tim.start);
if isnumeric(ss) && numel(ss)==1 && ~rem(ss,1), % && ss>=1 && ss<=obj.hdr.dim(sld+1)
obj.hdr.slice_start = ss-1;
else
error('Inappropriate "slice_time.start".');
end;
end;
if isfield(tim,'end'),
ss = double(tim.end);
if isnumeric(ss) && numel(ss)==1 && ~rem(ss,1), % && ss>=1 && ss<=obj.hdr.dim(sld+1)
obj.hdr.slice_end = ss-1;
else
error('Inappropriate "slice_time.end".');
end;
end;
if isfield(tim,'duration')
sd = double(tim.duration);
if isnumeric(sd) && numel(sd)==1,
s = double(bitand(obj.hdr.xyzt_units,24));
d = findindict(s,'units');
if ~isempty(d) && d.rescale, sd = sd/d.rescale; end;
obj.hdr.slice_duration = sd;
else
error('Inappropriate "slice_time.duration".');
end;
end;
if isfield(tim,'code'),
d = findindict(tim.code,'sliceorder');
if ~isempty(d),
obj.hdr.slice_code = d.code;
end;
end;
end;
end;
end;
case {'timing'}
if ~valid_fields(val1,{'toffset','tspace'}),
obj.hdr.pixdim(5) = 0;
obj.hdr.toffset = 0;
else
s = double(bitand(obj.hdr.xyzt_units,24));
d = findindict(s,'units');
if isfield(val1,'toffset'),
if isnumeric(val1.toffset) && numel(val1.toffset)==1,
if d.rescale,
val1.toffset = val1.toffset/d.rescale;
end;
obj.hdr.toffset = val1.toffset;
else
error('"timing.toffset" needs to be numeric with 1 element');
end;
end;
if isfield(val1,'tspace'),
if isnumeric(val1.tspace) && numel(val1.tspace)==1,
if d.rescale,
val1.tspace = val1.tspace/d.rescale;
end;
obj.hdr.pixdim(5) = val1.tspace;
else
error('"timing.tspace" needs to be numeric with 1 element');
end;
end;
end;
case {'descrip'}
if isempty(val1), val1 = char(val1); end;
if ischar(val1),
obj.hdr.descrip = val1;
else
error('"descrip" must be a string.');
end;
case {'cal'}
if isempty(val1),
obj.hdr.cal_min = 0;
obj.hdr.cal_max = 0;
else
if isnumeric(val1) && numel(val1)==2,
obj.hdr.cal_min = val1(1);
obj.hdr.cal_max = val1(2);
else
error('"cal" should contain two elements.');
end;
end;
case {'aux_file'}
if isempty(val1), val1 = char(val1); end;
if ischar(val1),
obj.hdr.aux_file = val1;
else
error('"aux_file" must be a string.');
end;
case {'hdr'}
error('hdr is a read-only field.');
obj.hdr = val1;
otherwise
error(['Reference to non-existent field ''' subs(1).subs '''.']);
end;
objs(ii) = obj;
end
obj = class(objs,'nifti');
otherwise
error('This should not happen.');
end;
return;
%=======================================================================
%=======================================================================
function obj = assigndat(obj,val)
if isa(val,'file_array'),
sz = size(val);
if numel(sz)>8,
error('Too many dimensions in data.');
end;
sz = [sz 1 1 1 1 1 1 1 1];
sz = sz(1:8);
sval = struct(val);
d = findindict(sval.dtype,'dtype');
if isempty(d)
error(['Unknown datatype (' num2str(double(sval.datatype)) ').']);
end;
[pth,nam,suf] = fileparts(sval.fname);
if any(strcmp(suf,{'.img','.IMG'}))
val.offset = max(sval.offset,0);
obj.hdr.magic = 'ni1';
elseif any(strcmp(suf,{'.nii','.NII'}))
val.offset = max(sval.offset,352);
obj.hdr.magic = 'n+1';
else
error(['Unknown filename extension (' suf ').']);
end;
val.offset = (ceil(val.offset/16))*16;
obj.hdr.vox_offset = val.offset;
obj.hdr.dim(2:(numel(sz)+1)) = sz;
nd = max(find(obj.hdr.dim(2:end)>1));
if isempty(nd), nd = 3; end;
obj.hdr.dim(1) = nd;
obj.hdr.datatype = sval.dtype;
obj.hdr.bitpix = d.size*8;
if ~isempty(sval.scl_slope), obj.hdr.scl_slope = sval.scl_slope; end;
if ~isempty(sval.scl_inter), obj.hdr.scl_inter = sval.scl_inter; end;
obj.dat = val;
else
error('"raw" must be of class "file_array"');
end;
return;
function ok = valid_fields(val,allowed)
if isempty(val), ok = false; return; end;
if ~isstruct(val),
error(['Expecting a structure, not a ' class(val) '.']);
end;
fn = fieldnames(val);
for ii=1:length(fn),
if ~any(strcmpi(fn{ii},allowed)),
fprintf('Allowed fieldnames are:\n');
for i=1:length(allowed), fprintf(' %s\n', allowed{i}); end;
error(['"' fn{ii} '" is not a valid fieldname.']);
end
end
ok = true;
return;
|
github
|
lcnbeapp/beapp-master
|
subsref.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@nifti/subsref.m
| 8,717 |
utf_8
|
3e5580b77072a8d2a98deb98231f6bab
|
function varargout = subsref(opt,subs)
% Subscript referencing
%
% Fields are:
% dat - a file-array representing the image data
% mat0 - a 9-parameter affine transform (from qform0)
% Note that the mapping is from voxels (where the first
% is considered to be at [1,1,1], to millimetres. See
% mat0_interp for the meaning of the transform.
% mat - a 12-parameter affine transform (from sform0)
% Note that the mapping is from voxels (where the first
% is considered to be at [1,1,1], to millimetres. See
% mat1_interp for the meaning of the transform.
% mat_intent - intention of mat. This field may be missing/empty.
% mat0_intent - intention of mat0. This field may be missing/empty.
% intent - interpretation of image. When present, this structure
% contains the fields
% code - name of interpretation
% params - parameters needed to interpret the image
% diminfo - MR encoding of different dimensions. This structure may
% contain some or all of the following fields
% frequency - a value of 1-3 indicating frequency direction
% phase - a value of 1-3 indicating phase direction
% slice - a value of 1-3 indicating slice direction
% slice_time - only present when "slice" field is present.
% Contains the following fields
% code - ascending/descending etc
% start - starting slice number
% end - ending slice number
% duration - duration of each slice acquisition
% Setting frequency, phase or slice to 0 will remove it.
% timing - timing information. When present, contains the fields
% toffset - acquisition time of first volume (seconds)
% tspace - time between sucessive volumes (seconds)
% descrip - a brief description of the image
% cal - a two-element vector containing cal_min and cal_max
% aux_file - name of an auxiliary file
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
varargout = rec(opt,subs);
return;
function c = rec(opt,subs)
switch subs(1).type,
case {'.'},
c = {};
opts = struct(opt);
for ii=1:numel(opts)
opt = class(opts(ii),'nifti');
%if ~isstruct(opt)
% error('Attempt to reference field of non-structure array.');
%end;
h = opt.hdr;
if isempty(h),
%error('No header.');
h = empty_hdr;
end;
% NIFTI-1 FORMAT
switch(subs(1).subs)
case 'extras',
t = opt.extras;
case 'raw', % A hidden field
if isa(opt.dat,'file_array'),
tmp = struct(opt.dat);
tmp.scl_slope = [];
tmp.scl_inter = [];
t = file_array(tmp);
else
t = opt.dat;
end;
case 'dat',
t = opt.dat;
case 'mat0',
t = decode_qform0(h);
s = double(bitand(h.xyzt_units,7));
if s
d = findindict(s,'units');
if ~isempty(d)
t = diag([d.rescale*[1 1 1] 1])*t;
end;
end;
case 'mat0_intent',
d = findindict(h.qform_code,'xform');
if isempty(d) || d.code==0,
t = '';
else
t = d.label;
end;
case 'mat',
if h.sform_code > 0
t = double([h.srow_x ; h.srow_y ; h.srow_z ; 0 0 0 1]);
t = t * [eye(4,3) [-1 -1 -1 1]'];
else
t = decode_qform0(h);
end
s = double(bitand(h.xyzt_units,7));
if s
d = findindict(s,'units');
t = diag([d.rescale*[1 1 1] 1])*t;
end;
case 'mat_intent',
if h.sform_code>0,
t = h.sform_code;
else
t = h.qform_code;
end;
d = findindict(t,'xform');
if isempty(d) || d.code==0,
t = '';
else
t = d.label;
end;
case 'intent',
d = findindict(h.intent_code,'intent');
if isempty(d) || d.code == 0,
%t = struct('code','UNKNOWN','param',[]);
t = [];
else
t = struct('code',d.label,'param',...
double([h.intent_p1 h.intent_p2 h.intent_p3]), 'name',deblank(h.intent_name));
t.param = t.param(1:length(d.param));
end
case 'diminfo',
t = [];
tmp = bitand( h.dim_info ,3); if tmp, t.frequency = double(tmp); end;
tmp = bitand(bitshift(h.dim_info,-2),3); if tmp, t.phase = double(tmp); end;
tmp = bitand(bitshift(h.dim_info,-4),3); if tmp, t.slice = double(tmp); end;
% t = struct('frequency',bitand( h.dim_info ,3),...
% 'phase',bitand(bitshift(h.dim_info,-2),3),...
% 'slice',bitand(bitshift(h.dim_info,-4),3))
if isfield(t,'slice')
sc = double(h.slice_code);
ss = double(h.slice_start)+1;
se = double(h.slice_end)+1;
ss = max(ss,1);
se = min(se,double(h.dim(t.slice+1)));
sd = double(h.slice_duration);
s = double(bitand(h.xyzt_units,24));
d = findindict(s,'units');
if d.rescale, sd = sd*d.rescale; end;
ns = (se-ss+1);
d = findindict(sc,'sliceorder');
if isempty(d)
label = 'UNKNOWN';
else
label = d.label;
end;
t.slice_time = struct('code',label,'start',ss,'end',se,'duration',sd);
if 0, % Never
t.times = zeros(1,double(h.dim(t.slice+1)))+NaN;
switch sc,
case 0, % Unknown
t.times(ss:se) = zeros(1,ns);
case 1, % sequential increasing
t.times(ss:se) = (0:(ns-1))*sd;
case 2, % sequential decreasing
t.times(ss:se) = ((ns-1):-1:0)*sd;
case 3, % alternating increasing
t.times(ss:2:se) = (0:floor((ns+1)/2-1))*sd;
t.times((ss+1):2:se) = (floor((ns+1)/2):(ns-1))*sd;
case 4, % alternating decreasing
t.times(se:-2:ss) = (0:floor((ns+1)/2-1))*sd;
t.times(se:-2:(ss+1)) = (floor((ns+1)/2):(ns-1))*sd;
end;
end;
end;
case 'timing',
to = double(h.toffset);
dt = double(h.pixdim(5));
if to==0 && dt==0,
t = [];
else
s = double(bitand(h.xyzt_units,24));
d = findindict(s,'units');
if d.rescale,
to = to*d.rescale;
dt = dt*d.rescale;
end;
t = struct('toffset',to,'tspace',dt);
end;
case 'descrip',
t = deblank(h.descrip);
msk = find(t==0);
if any(msk), t=t(1:(msk(1)-1)); end;
case 'cal',
t = [double(h.cal_min) double(h.cal_max)];
if all(t==0), t = []; end;
case 'aux_file',
t = deblank(h.aux_file);
case 'hdr', % Hidden field
t = h;
otherwise
error(['Reference to non-existent field ''' subs(1).subs '''.']);
end;
if numel(subs)>1,
t = subsref(t,subs(2:end));
end;
c{ii} = t;
end;
case {'{}'},
error('Cell contents reference from a non-cell array object.');
case {'()'},
opt = struct(opt);
t = subsref(opt,subs(1));
if length(subs)>1
c = {};
for i=1:numel(t),
ti = class(t(i),'nifti');
ti = rec(ti,subs(2:end));
c = {c{:}, ti{:}};
end;
else
c = {class(t,'nifti')};
end;
otherwise
error('This should not happen.');
end;
|
github
|
lcnbeapp/beapp-master
|
create.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@nifti/create.m
| 1,922 |
utf_8
|
3d0a267602ecbe433be656c175acb2a2
|
function create(obj,wrt)
% Create a NIFTI-1 file
% FORMAT create(obj)
% This writes out the header information for the nifti object
%
% create(obj,wrt)
% This also writes out an empty image volume if wrt==1
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
for i=1:numel(obj)
create_each(obj(i));
end;
function create_each(obj)
if ~isa(obj.dat,'file_array'),
error('Data must be a file-array');
end;
fname = obj.dat.fname;
if isempty(fname),
error('No filename to write to.');
end;
dt = obj.dat.dtype;
ok = write_hdr_raw(fname,obj.hdr,dt(end-1)=='B');
if ~ok,
error(['Unable to write header for "' fname '".']);
end;
write_extras(fname,obj.extras);
if nargin>2 && any(wrt==1),
% Create an empty image file if necessary
d = findindict(obj.hdr.datatype, 'dtype');
dim = double(obj.hdr.dim(2:end));
dim((double(obj.hdr.dim(1))+1):end) = 1;
nbytes = ceil(d.size*d.nelem*prod(dim(1:2)))*prod(dim(3:end))+double(obj.hdr.vox_offset);
[pth,nam,ext] = fileparts(obj.dat.fname);
if any(strcmp(deblank(obj.hdr.magic),{'n+1','nx1'})),
ext = '.nii';
else
ext = '.img';
end;
iname = fullfile(pth,[nam ext]);
fp = fopen(iname,'a+');
if fp==-1,
error(['Unable to create image for "' fname '".']);
end;
fseek(fp,0,'eof');
pos = ftell(fp);
if pos<nbytes,
bs = 2048; % Buffer-size
nbytes = nbytes - pos;
buf = uint8(0);
buf(bs) = 0;
while(nbytes>0)
if nbytes<bs, buf = buf(1:nbytes); end;
nw = fwrite(fp,buf,'uint8');
if nw<min(bs,nbytes),
fclose(fp);
error(['Problem while creating image for "' fname '".']);
end;
nbytes = nbytes - nw;
end;
end;
fclose(fp);
end;
return;
|
github
|
lcnbeapp/beapp-master
|
getdict.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@nifti/private/getdict.m
| 5,184 |
utf_8
|
eebe7d552eb3613897e82d860005c90e
|
function d = getdict
% Dictionary of NIFTI stuff
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
persistent dict;
if ~isempty(dict),
d = dict;
return;
end;
% Datatype
t = true;
f = false;
table = {...
0 ,'UNKNOWN' ,'uint8' ,@uint8 ,1,1 ,t,t,f
1 ,'BINARY' ,'uint1' ,@logical,1,1/8,t,t,f
256 ,'INT8' ,'int8' ,@int8 ,1,1 ,t,f,t
2 ,'UINT8' ,'uint8' ,@uint8 ,1,1 ,t,t,t
4 ,'INT16' ,'int16' ,@int16 ,1,2 ,t,f,t
512 ,'UINT16' ,'uint16' ,@uint16 ,1,2 ,t,t,t
8 ,'INT32' ,'int32' ,@int32 ,1,4 ,t,f,t
768 ,'UINT32' ,'uint32' ,@uint32 ,1,4 ,t,t,t
1024,'INT64' ,'int64' ,@int64 ,1,8 ,t,f,f
1280,'UINT64' ,'uint64' ,@uint64 ,1,8 ,t,t,f
16 ,'FLOAT32' ,'float32' ,@single ,1,4 ,f,f,t
64 ,'FLOAT64' ,'double' ,@double ,1,8 ,f,f,t
1536,'FLOAT128' ,'float128',@crash ,1,16 ,f,f,f
32 ,'COMPLEX64' ,'float32' ,@single ,2,4 ,f,f,f
1792,'COMPLEX128','double' ,@double ,2,8 ,f,f,f
2048,'COMPLEX256','float128',@crash ,2,16 ,f,f,f
128 ,'RGB24' ,'uint8' ,@uint8 ,3,1 ,t,t,f};
dtype = struct(...
'code' ,table(:,1),...
'label' ,table(:,2),...
'prec' ,table(:,3),...
'conv' ,table(:,4),...
'nelem' ,table(:,5),...
'size' ,table(:,6),...
'isint' ,table(:,7),...
'unsigned' ,table(:,8),...
'min',-Inf,'max',Inf',...
'supported',table(:,9));
for i=1:length(dtype),
if dtype(i).isint
if dtype(i).unsigned
dtype(i).min = 0;
dtype(i).max = 2^(8*dtype(i).size)-1;
else
dtype(i).min = -2^(8*dtype(i).size-1);
dtype(i).max = 2^(8*dtype(i).size-1)-1;
end;
end;
end;
% Intent
table = {...
0 ,'NONE' ,'None',{}
2 ,'CORREL' ,'Correlation statistic',{'DOF'}
3 ,'TTEST' ,'T-statistic',{'DOF'}
4 ,'FTEST' ,'F-statistic',{'numerator DOF','denominator DOF'}
5 ,'ZSCORE' ,'Z-score',{}
6 ,'CHISQ' ,'Chi-squared distribution',{'DOF'}
7 ,'BETA' ,'Beta distribution',{'a','b'}
8 ,'BINOM' ,'Binomial distribution',...
{'number of trials','probability per trial'}
9 ,'GAMMA' ,'Gamma distribution',{'shape','scale'}
10 ,'POISSON' ,'Poisson distribution',{'mean'}
11 ,'NORMAL' ,'Normal distribution',{'mean','standard deviation'}
12 ,'FTEST_NONC' ,'F-statistic noncentral',...
{'numerator DOF','denominator DOF','numerator noncentrality parameter'}
13 ,'CHISQ_NONC' ,'Chi-squared noncentral',{'DOF','noncentrality parameter'}
14 ,'LOGISTIC' ,'Logistic distribution',{'location','scale'}
15 ,'LAPLACE' ,'Laplace distribution',{'location','scale'}
16 ,'UNIFORM' ,'Uniform distribition',{'lower end','upper end'}
17 ,'TTEST_NONC' ,'T-statistic noncentral',{'DOF','noncentrality parameter'}
18 ,'WEIBULL' ,'Weibull distribution',{'location','scale','power'}
19 ,'CHI' ,'Chi distribution',{'DOF'}
20 ,'INVGAUSS' ,'Inverse Gaussian distribution',{'mu','lambda'}
21 ,'EXTVAL' ,'Extreme Value distribution',{'location','scale'}
22 ,'PVAL' ,'P-value',{}
23 ,'LOGPVAL' ,'Log P-value',{}
24 ,'LOG10PVAL' ,'Log_10 P-value',{}
1001,'ESTIMATE' ,'Estimate',{}
1002,'LABEL' ,'Label index',{}
1003,'NEURONAMES' ,'NeuroNames index',{}
1004,'MATRIX' ,'General matrix',{'M','N'}
1005,'MATRIX_SYM' ,'Symmetric matrix',{}
1006,'DISPLACEMENT' ,'Displacement vector',{}
1007,'VECTOR' ,'Vector',{}
1008,'POINTS' ,'Pointset',{}
1009,'TRIANGLE' ,'Triangle',{}
1010,'QUATERNION' ,'Quaternion',{}
1011,'DIMLESS' ,'Dimensionless',{}
};
intent = struct('code',table(:,1),'label',table(:,2),...
'fullname',table(:,3),'param',table(:,4));
% Units
table = {...
0, 1,'UNKNOWN'
1,1000,'m'
2, 1,'mm'
3,1e-3,'um'
8, 1,'s'
16,1e-3,'ms'
24,1e-6,'us'
32, 1,'Hz'
40, 1,'ppm'
48, 1,'rads'};
units = struct('code',table(:,1),'label',table(:,3),'rescale',table(:,2));
% Reference space
% code = {0,1,2,3,4};
table = {...
0,'UNKNOWN'
1,'Scanner Anat'
2,'Aligned Anat'
3,'Talairach'
4,'MNI_152'};
anat = struct('code',table(:,1),'label',table(:,2));
% Slice Ordering
table = {...
0,'UNKNOWN'
1,'sequential_increasing'
2,'sequential_decreasing'
3,'alternating_increasing'
4,'alternating_decreasing'};
sliceorder = struct('code',table(:,1),'label',table(:,2));
% Q/S Form Interpretation
table = {...
0,'UNKNOWN'
1,'Scanner'
2,'Aligned'
3,'Talairach'
4,'MNI152'};
xform = struct('code',table(:,1),'label',table(:,2));
dict = struct('dtype',dtype,'intent',intent,'units',units,...
'space',anat,'sliceorder',sliceorder,'xform',xform);
d = dict;
return;
function varargout = crash(varargin)
error('There is a NIFTI-1 data format problem (an invalid datatype).');
|
github
|
lcnbeapp/beapp-master
|
write_extras.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/spm8/@nifti/private/write_extras.m
| 829 |
utf_8
|
598b84950ce613b42919ce1f50a59132
|
function extras = write_extras(fname,extras)
% Write extra bits of information
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id$
[pth,nam,ext] = fileparts(fname);
switch ext
case {'.hdr','.img','.nii'}
mname = fullfile(pth,[nam '.mat']);
case {'.HDR','.IMG','.NII'}
mname = fullfile(pth,[nam '.MAT']);
otherwise
mname = fullfile(pth,[nam '.mat']);
end
if isstruct(extras) && ~isempty(fieldnames(extras)),
savefields(mname,extras);
end;
function savefields(fnam,p)
if length(p)>1, error('Can''t save fields.'); end;
fn = fieldnames(p);
for i_=1:length(fn),
eval([fn{i_} '= p.' fn{i_} ';']);
end;
if str2num(version('-release'))>=14,
fn = {'-V6',fn{:}};
end;
if numel(fn)>0,
save(fnam,fn{:});
end;
return;
|
github
|
lcnbeapp/beapp-master
|
delete.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@xmltree/delete.m
| 1,189 |
utf_8
|
9ca7b2db1b9fc84848585e118ac9d026
|
function tree = delete(tree,uid)
% XMLTREE/DELETE Delete (delete a subtree given its UID)
%
% tree - XMLTree object
% uid - array of UID's of subtrees to be deleted
%__________________________________________________________________________
%
% Delete a subtree given its UID
% The tree parameter must be in input AND in output
%__________________________________________________________________________
% Copyright (C) 2002-2011 http://www.artefact.tk/
% Guillaume Flandin
% $Id: delete.m 4460 2011-09-05 14:52:16Z guillaume $
%error(nargchk(2,2,nargin));
uid = uid(:);
for i=1:length(uid)
if uid(i)==1
warning('[XMLTree] Cannot delete root element.');
else
p = tree.tree{uid(i)}.parent;
tree = sub_delete(tree,uid(i));
tree.tree{p}.contents(find(tree.tree{p}.contents==uid(i))) = [];
end
end
%==========================================================================
function tree = sub_delete(tree,uid)
if isfield(tree.tree{uid},'contents')
for i=1:length(tree.tree{uid}.contents)
tree = sub_delete(tree,tree.tree{uid}.contents(i));
end
end
tree.tree{uid} = struct('type','deleted');
|
github
|
lcnbeapp/beapp-master
|
save.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@xmltree/save.m
| 5,114 |
utf_8
|
1c7adbb3f79946f51f25d9031fcb515c
|
function varargout = save(tree, filename)
% XMLTREE/SAVE Save an XML tree in an XML file
% FORMAT varargout = save(tree,filename)
%
% tree - XMLTree
% filename - XML output filename
% varargout - XML string
%__________________________________________________________________________
%
% Convert an XML tree into a well-formed XML string and write it into
% a file or return it as a string if no filename is provided.
%__________________________________________________________________________
% Copyright (C) 2002-2011 http://www.artefact.tk/
% Guillaume Flandin
% $Id: save.m 4460 2011-09-05 14:52:16Z guillaume $
%error(nargchk(1,2,nargin));
prolog = '<?xml version="1.0" ?>\n';
%- Return the XML tree as a string
if nargin == 1
varargout{1} = [sprintf(prolog) ...
print_subtree(tree,'',root(tree))];
%- Output specified
else
%- Filename provided
if ischar(filename)
[fid, msg] = fopen(filename,'w');
if fid==-1, error(msg); end
if isempty(tree.filename), tree.filename = filename; end
%- File identifier provided
elseif isnumeric(filename) && numel(filename) == 1
fid = filename;
prolog = ''; %- With this option, do not write any prolog
else
error('[XMLTree] Invalid argument.');
end
fprintf(fid,prolog);
save_subtree(tree,fid,root(tree));
if ischar(filename), fclose(fid); end
if nargout == 1
varargout{1} = print_subtree(tree,'',root(tree));
end
end
%==========================================================================
function xmlstr = print_subtree(tree,xmlstr,uid,order)
if nargin < 4, order = 0; end
xmlstr = [xmlstr blanks(3*order)];
switch tree.tree{uid}.type
case 'element'
xmlstr = sprintf('%s<%s',xmlstr,tree.tree{uid}.name);
for i=1:length(tree.tree{uid}.attributes)
xmlstr = sprintf('%s %s="%s"', xmlstr, ...
tree.tree{uid}.attributes{i}.key,...
tree.tree{uid}.attributes{i}.val);
end
if isempty(tree.tree{uid}.contents)
xmlstr = sprintf('%s/>\n',xmlstr);
else
xmlstr = sprintf('%s>\n',xmlstr);
for i=1:length(tree.tree{uid}.contents)
xmlstr = print_subtree(tree,xmlstr, ...
tree.tree{uid}.contents(i),order+1);
end
xmlstr = [xmlstr blanks(3*order)];
xmlstr = sprintf('%s</%s>\n',xmlstr,...
tree.tree{uid}.name);
end
case 'chardata'
xmlstr = sprintf('%s%s\n',xmlstr, ...
entity(tree.tree{uid}.value));
case 'cdata'
xmlstr = sprintf('%s<![CDATA[%s]]>\n',xmlstr, ...
tree.tree{uid}.value);
case 'pi'
xmlstr = sprintf('%s<?%s %s?>\n',xmlstr, ...
tree.tree{uid}.target, tree.tree{uid}.value);
case 'comment'
xmlstr = sprintf('%s<!-- %s -->\n',xmlstr,...
tree.tree{uid}.value);
otherwise
warning(sprintf('Type %s unknown: not saved', ...
tree.tree{uid}.type));
end
%==========================================================================
function save_subtree(tree,fid,uid,order)
if nargin < 4, order = 0; end
fprintf(fid,blanks(3*order));
switch tree.tree{uid}.type
case 'element'
fprintf(fid,'<%s',tree.tree{uid}.name);
for i=1:length(tree.tree{uid}.attributes)
fprintf(fid,' %s="%s"',...
tree.tree{uid}.attributes{i}.key, ...
tree.tree{uid}.attributes{i}.val);
end
if isempty(tree.tree{uid}.contents)
fprintf(fid,'/>\n');
else
fprintf(fid,'>\n');
for i=1:length(tree.tree{uid}.contents)
save_subtree(tree,fid,...
tree.tree{uid}.contents(i),order+1)
end
fprintf(fid,blanks(3*order));
fprintf(fid,'</%s>\n',tree.tree{uid}.name);
end
case 'chardata'
fprintf(fid,'%s\n',entity(tree.tree{uid}.value));
case 'cdata'
fprintf(fid,'<![CDATA[%s]]>\n',tree.tree{uid}.value);
case 'pi'
fprintf(fid,'<?%s %s?>\n',tree.tree{uid}.target, ...
tree.tree{uid}.value);
case 'comment'
fprintf(fid,'<!-- %s -->\n',tree.tree{uid}.value);
otherwise
warning(sprintf('[XMLTree] Type %s unknown: not saved', ...
tree.tree{uid}.type));
end
%==========================================================================
function str = entity(str)
% This has the side effect of strtrim'ming the char array.
str = char(strrep(cellstr(str), '&', '&' ));
str = char(strrep(cellstr(str), '<', '<' ));
str = char(strrep(cellstr(str), '>', '>' ));
str = char(strrep(cellstr(str), '"', '"'));
str = char(strrep(cellstr(str), '''', '''));
|
github
|
lcnbeapp/beapp-master
|
branch.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@xmltree/branch.m
| 1,750 |
utf_8
|
407ff520e9de6dc9150a5b4f44d75c90
|
function subtree = branch(tree,uid)
% XMLTREE/BRANCH Branch Method
% FORMAT uid = parent(tree,uid)
%
% tree - XMLTree object
% uid - UID of the root element of the subtree
% subtree - XMLTree object (a subtree from tree)
%__________________________________________________________________________
%
% Return a subtree from a tree.
%__________________________________________________________________________
% Copyright (C) 2002-2011 http://www.artefact.tk/
% Guillaume Flandin
% $Id: branch.m 4460 2011-09-05 14:52:16Z guillaume $
%error(nargchk(2,2,nargin));
if uid > length(tree) || ...
numel(uid)~=1 || ...
~strcmp(tree.tree{uid}.type,'element')
error('[XMLTree] Invalid UID.');
end
subtree = xmltree;
subtree = set(subtree,root(subtree),'name',tree.tree{uid}.name);
%- fix by Piotr Dollar to copy attributes for the root node:
subtree = set(subtree,root(subtree),'attributes',tree.tree{uid}.attributes);
child = children(tree,uid);
for i=1:length(child)
l = length(subtree);
subtree = sub_branch(tree,subtree,child(i),root(subtree));
subtree.tree{root(subtree)}.contents = [subtree.tree{root(subtree)}.contents l+1];
end
%==========================================================================
function tree = sub_branch(t,tree,uid,p)
l = length(tree);
tree.tree{l+1} = t.tree{uid};
tree.tree{l+1}.uid = l + 1;
tree.tree{l+1}.parent = p;
tree.tree{l+1}.contents = [];
if isfield(t.tree{uid},'contents')
contents = get(t,uid,'contents');
m = length(tree);
for i=1:length(contents)
tree.tree{l+1}.contents = [tree.tree{l+1}.contents m+1];
tree = sub_branch(t,tree,contents(i),l+1);
m = length(tree);
end
end
|
github
|
lcnbeapp/beapp-master
|
flush.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@xmltree/flush.m
| 1,413 |
utf_8
|
64502185e2efb9de8f36e36751a39517
|
function tree = flush(tree,uid)
% XMLTREE/FLUSH Flush (Clear a subtree given its UID)
%
% tree - XMLTree object
% uid - array of UID's of subtrees to be cleared
% Default is root
%__________________________________________________________________________
%
% Clear a subtree given its UID (remove all the leaves of the tree)
% The tree parameter must be in input AND in output
%__________________________________________________________________________
% Copyright (C) 2002-2011 http://www.artefact.tk/
% Guillaume Flandin
% $Id: flush.m 4460 2011-09-05 14:52:16Z guillaume $
%error(nargchk(1,2,nargin));
if nargin == 1,
uid = root(tree);
end
uid = uid(:);
for i=1:length(uid)
tree = sub_flush(tree,uid(i));
end
%==========================================================================
function tree = sub_flush(tree,uid)
if isfield(tree.tree{uid},'contents')
% contents is parsed in reverse order because each child is
% deleted and the contents vector is then eventually reduced
for i=length(tree.tree{uid}.contents):-1:1
tree = sub_flush(tree,tree.tree{uid}.contents(i));
end
end
if strcmp(tree.tree{uid}.type,'chardata') ||...
strcmp(tree.tree{uid}.type,'pi') ||...
strcmp(tree.tree{uid}.type,'cdata') ||...
strcmp(tree.tree{uid}.type,'comment')
tree = delete(tree,uid);
end
|
github
|
lcnbeapp/beapp-master
|
copy.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@xmltree/copy.m
| 1,634 |
utf_8
|
e6df62a4f41243b78ed8c517b15e493b
|
function tree = copy(tree,subuid,uid)
% XMLTREE/COPY Copy Method (copy a subtree in another branch)
% FORMAT tree = copy(tree,subuid,uid)
%
% tree - XMLTree object
% subuid - UID of the subtree to copy
% uid - UID of the element where the subtree must be duplicated
%__________________________________________________________________________
%
% Copy a subtree to another branch.
% The tree parameter must be in input AND in output.
%__________________________________________________________________________
% Copyright (C) 2002-2015 http://www.artefact.tk/
% Guillaume Flandin
% $Id: copy.m 6480 2015-06-13 01:08:30Z guillaume $
%error(nargchk(2,3,nargin));
if nargin == 2
uid = parent(tree,subuid);
end
l = length(tree);
tree = sub_copy(tree,subuid,uid);
tree.tree{uid}.contents = [tree.tree{uid}.contents l+1];
% to have the copy next to the original and not at the end?
% contents = get(tree,parent,'contents');
% i = find(contents==uid);
% tree = set(tree,parent,'contents',[contents(1:i) l+1 contents(i+1:end)]);
%==========================================================================
function tree = sub_copy(tree,uid,p)
l = length(tree);
tree.tree{l+1} = tree.tree{uid};
tree.tree{l+1}.uid = l+1;
tree.tree{l+1}.parent = p;
tree.tree{l+1}.contents = [];
if isfield(tree.tree{uid},'contents')
contents = get(tree,uid,'contents');
m = length(tree);
for i=1:length(contents)
tree.tree{l+1}.contents = [tree.tree{l+1}.contents m+1];
tree = sub_copy(tree,contents(i),l+1);
m = length(tree);
end
end
|
github
|
lcnbeapp/beapp-master
|
convert.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@xmltree/convert.m
| 5,573 |
utf_8
|
05b85174fb85e5d62de81654b76ef7ab
|
function s = convert(tree,uid)
% XMLTREE/CONVERT Converter an XML tree in a structure
%
% tree - XMLTree object
% uid - uid of the root of the subtree, if provided.
% Default is root
% s - converted structure
%__________________________________________________________________________
%
% Convert an XMLTree into a structure, when possible.
% When several identical tags are present, a cell array is used.
% The root tag is not saved in the structure.
% If provided, only the structure corresponding to the subtree defined
% by the uid UID is returned.
%__________________________________________________________________________
% Copyright (C) 2002-2015 http://www.artefact.tk/
% Guillaume Flandin
% $Id: convert.m 6480 2015-06-13 01:08:30Z guillaume $
% Exemple:
% tree = '<a><b>field1</b><c>field2</c><b>field3</b></a>';
% toto = convert(xmltree(tree));
% <=> toto = struct('b',{{'field1', 'field3'}},'c','field2')
%error(nargchk(1,2,nargin));
% Get the root uid of the output structure
if nargin == 1
% Get the root uid of the XML tree
root_uid = root(tree);
else
% Uid provided by user
root_uid = uid;
end
% Initialize the output structure
% struct([]) should be used but this only works with Matlab 6
% So we create a field that we delete at the end
%s = struct(get(tree,root_uid,'name'),''); % struct([])
s = struct('deletedummy','');
%s = sub_convert(tree,s,root_uid,{get(tree,root_uid,'name')});
s = sub_convert(tree,s,root_uid,{});
s = rmfield(s,'deletedummy');
%==========================================================================
function s = sub_convert(tree,s,uid,arg)
type = get(tree,uid,'type');
switch type
case 'element'
child = children(tree,uid);
l = {};
ll = {};
for i=1:length(child)
if isfield(tree,child(i),'name')
ll = { ll{:}, get(tree,child(i),'name') };
end
end
for i=1:length(child)
if isfield(tree,child(i),'name')
name = get(tree,child(i),'name');
nboccur = sum(ismember(l,name));
nboccur2 = sum(ismember(ll,name));
l = { l{:}, name };
if nboccur || (nboccur2>1)
arg2 = { arg{:}, name, {nboccur+1} };
else
arg2 = { arg{:}, name};
end
else
arg2 = arg;
end
s = sub_convert(tree,s,child(i),arg2);
end
if isempty(child)
s = sub_setfield(s,arg{:},'');
end
%- saving attributes : does not work with <a t='q'>b</a>
%- but ok with <a t='q'><c>b</c></a>
% attrb = attributes(tree,'get',uid); %-
% if ~isempty(attrb) %-
% arg2 = {arg{:} 'attributes'}; %-
% s = sub_setfield(s,arg2{:},attrb); %-
% end %-
case 'chardata'
s = sub_setfield(s,arg{:},get(tree,uid,'value'));
%- convert strings into their numerical equivalent when possible
%- e.g. string '3.14159' becomes double scalar 3.14159
% v = get(tree,uid,'value'); %-
% cv = str2num(v); %-
% if isempty(cv) %-
% s = sub_setfield(s,arg{:},v); %-
% else %-
% s = sub_setfield(s,arg{:},cv); %-
% end %-
case 'cdata'
s = sub_setfield(s,arg{:},get(tree,uid,'value'));
case 'pi'
% Processing instructions are evaluated if possible
app = get(tree,uid,'target');
switch app
case {'matlab',''}
s = sub_setfield(s,arg{:},eval(get(tree,uid,'value')));
case 'unix'
s = sub_setfield(s,arg{:},unix(get(tree,uid,'value')));
case 'dos'
s = sub_setfield(s,arg{:},dos(get(tree,uid,'value')));
case 'system'
s = sub_setfield(s,arg{:},system(get(tree,uid,'value')));
otherwise
try
s = sub_setfield(s,arg{:},feval(app,get(tree,uid,'value')));
catch
warning('[XMLTree] Unknown target application');
end
end
case 'comment'
% Comments are forgotten
otherwise
warning(sprintf('Type %s unknown : not saved',get(tree,uid,'type')));
end
%==========================================================================
function s = sub_setfield(s,varargin)
% Same as setfield but using '{}' rather than '()'
%if (isempty(varargin) | length(varargin) < 2)
% error('Not enough input arguments.');
%end
subs = varargin(1:end-1);
for i = 1:length(varargin)-1
if (isa(varargin{i}, 'cell'))
types{i} = '{}';
elseif ischar(varargin{i})
types{i} = '.';
subs{i} = varargin{i}; %strrep(varargin{i},' ',''); % deblank field name
else
error('Inputs must be either cell arrays or strings.');
end
end
% Perform assignment
try
s = builtin('subsasgn', s, struct('type',types,'subs',subs), varargin{end});
catch
error(lasterr)
end
|
github
|
lcnbeapp/beapp-master
|
editor.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@xmltree/editor.m
| 12,418 |
utf_8
|
80850644600bde45b47898d068ef0978
|
function editor(tree)
%XMLTREE/EDITOR A Graphical User Interface for an XML tree
% EDITOR(TREE) opens a new figure displaying the xmltree object TREE.
% H = EDITOR(TREE) also returns the figure handle H.
%
% This is a beta version of <xmltree/view> successor
%
% See also XMLTREE
%__________________________________________________________________________
% Copyright (C) 2002-2015 http://www.artefact.tk/
% Guillaume Flandin
% $Id: editor.m 6480 2015-06-13 01:08:30Z guillaume $
%error(nargchk(1,1,nargin));
if ~isempty(getfilename(tree))
title = getfilename(tree);
elseif ~isempty(inputname(1))
title = ['Variable ''' inputname(1) ''''];
else
title = 'Untitled';
end
h = initWindow(title);
setappdata(h,'handles',guihandles(h));
setappdata(h,'save',0);
tree = set(tree,root(tree),'show',1);
setappdata(h,'tree',tree);
doUpdate([],[],h);
set(h,'HandleVisibility','callback');
%==========================================================================
function h = initWindow(title)
wincolor = struct('bg', [0.8 0.8 0.8], ...
'fg', [1.0 1.0 1.0], ...
'title', [0.9 0.9 0.9]);
title = [':: XMLTree Editor :: ' title];
h = figure('Name', title, ...
'Units', 'Points', ...
'NumberTitle', 'off', ...
'Resize', 'on', ...
'Color', wincolor.bg,...
'Position', [200 200 440 330], ...
'MenuBar', 'none', ...
'Tag', mfilename);
set(h, 'CloseRequestFcn', {@doClose,h});
%- Left box
uicontrol('Style', 'listbox', ...
'HorizontalAlignment','left', ...
'Units','Normalized', ...
'Visible','on',...
'BackgroundColor', wincolor.fg, ...
'Max', 1, ...
'Value', 1 , ...
'Enable', 'on', ...
'Position', [0.04 0.12 0.3 0.84], ...
'Callback', {@doList,h}, ...
'String', ' ', ...
'Tag', 'xmllistbox');
%- Right box
uicontrol('Style', 'listbox', ...
'HorizontalAlignment','left', ...
'Units','Normalized', ...
'Visible','on',...
'BackgroundColor', wincolor.bg, ...
'Min', 0, ...
'Max', 2, ...
'Value', [], ...
'Enable', 'inactive', ...
'Position', [0.38 0.50 0.58 0.46], ...
'Callback', '', ...
'String', ' ', ...
'Tag', 'xmllist');
%- The Add button
uicontrol('Style', 'pushbutton', ...
'Units', 'Normalized', ...
'Position', [0.04 0.03 0.11 0.06], ...
'String', 'Add', ...
'Enable','on',...
'Tag', 'addbutton', ...
'Callback', {@doAdd,h});
%- The Modify button
uicontrol('Style', 'pushbutton', ...
'Units', 'Normalized', ...
'Position', [0.175 0.03 0.11 0.06], ...
'String', 'Modify', ...
'Enable','on',...
'Tag', 'modifybutton', ...
'Callback', {@doModify,h});
%- The Copy button
uicontrol('Style', 'pushbutton', ...
'Units', 'Normalized', ...
'Position', [0.310 0.03 0.11 0.06], ...
'String', 'Copy', ...
'Enable','on',...
'Tag', 'copybutton', ...
'Callback', {@doCopy,h});
%- The Delete button
uicontrol('Style', 'pushbutton', ...
'Units', 'Normalized', ...
'Position', [0.445 0.03 0.11 0.06], ...
'String', 'Delete', ...
'Enable','on',...
'Tag', 'delbutton', ...
'Callback', {@doDelete,h});
%- The Save button
uicontrol('Style', 'pushbutton', ...
'Units', 'Normalized', ...
'Position', [0.580 0.03 0.11 0.06], ...
'String', 'Save', ...
'Tag', 'savebutton', ...
'Callback', {@doSave,h});
%- The Run button
%uicontrol('Style', 'pushbutton', ...
% 'Units', 'Normalized', ...
% 'Position', [0.715 0.03 0.11 0.06], ...
% 'String', 'Run', ...
% 'Enable', 'off', ...
% 'Tag', 'runbutton', ...
% 'Callback', {@doRun,h});
%- The Attributes button
uicontrol('Style', 'pushbutton', ...
'Units', 'Normalized', ...
'Position', [0.715 0.03 0.11 0.06], ...
'String', 'Attr.', ...
'Enable', 'on', ...
'Tag', 'runbutton', ...
'Callback', {@doAttributes,h});
%- The Close button
uicontrol('Style', 'pushbutton', ...
'Units', 'Normalized', ...
'Position', [0.850 0.03 0.11 0.06], ...
'String', 'Close', ...
'Tag', 'closebutton', ...
'Callback', {@doClose,h});
%==========================================================================
function doClose(fig,evd,h)
s = getappdata(h, 'save');
status = 1;
if s
button = questdlg(sprintf('Save changes to the XML tree?'),...
'XMLTree Editor','Yes','No','Cancel','Yes');
if strcmp(button,'Yes')
status = doSave([],[],h);
elseif strcmp(button,'Cancel')
status = 0;
end
end
if status
delete(h);
end
function doAdd(fig,evd,h)
tree = getappdata(h, 'tree');
uidList = getappdata(h, 'uidlist');
handles = getappdata(h, 'handles');
pos = get(handles.xmllistbox,'value');
uid = uidList(pos);
answer = questdlg('Which kind of item to add?', ...
'XMLTree Editor :: Add','Node','Leaf','Node');
switch answer
case 'Node'
tree = add(tree,uid,'element','New_Node');
case 'Leaf'
tree = add(tree,uid,'element','New_Leaf');
l = length(tree);
tree = add(tree,l,'chardata','default');
end
tree = set(tree,uid,'show',1);
setappdata(h, 'tree', tree);
setappdata(h, 'save', 1);
doUpdate([],[],h);
doList([],[],h);
function doModify(fig,evd,h)
tree = getappdata(h, 'tree');
uidList = getappdata(h, 'uidlist');
handles = getappdata(h, 'handles');
pos = get(handles.xmllistbox,'value');
uid = uidList(pos);
contents = children(tree,uid);
if length(contents) > 0 && ...
strcmp(get(tree,contents(1),'type'),'chardata')
str = get(tree,contents(1),'value');
prompt = {'Name :','New value:'};
def = {get(tree,uid,'name'),str};
title = sprintf('Modify %s',get(tree,uid,'name'));
lineNo = 1;
answer = inputdlg(prompt,title,lineNo,def);
if ~isempty(answer)
tree = set(tree,uid,'name',answer{1});
str = answer{2};
tree = set(tree,contents(1),'value',str);
setappdata(h, 'tree', tree);
setappdata(h, 'save', 1);
end
else
str = ['Tag ' get(tree,uid,'name')];
prompt = {'Name :'};
def = {get(tree,uid,'name'),str};
title = sprintf('Modify %s tag',get(tree,uid,'name'));
lineNo = 1;
answer = inputdlg(prompt,title,lineNo,def);
if ~isempty(answer)
tree = set(tree,uid,'name',answer{1});
str = ['Tag ' get(tree,uid,'name')];
setappdata(h, 'tree', tree);
setappdata(h, 'save', 1);
end
end
%- Trying to keep the slider active
set(handles.xmllist, 'Enable', 'on');
set(handles.xmllist, 'String', ' ');
set(handles.xmllist, 'Enable', 'Inactive');
set(handles.xmllist, 'String', str);
doUpdate([],[],h);
doList([],[],h);
function doCopy(fig,evd,h)
tree = getappdata(h, 'tree');
uidList = getappdata(h, 'uidlist');
handles = getappdata(h, 'handles');
pos = get(handles.xmllistbox,'value');
uid = uidList(pos);
if pos ~= 1
tree = copy(tree,uid);
setappdata(h, 'tree', tree);
setappdata(h, 'save', 1);
doUpdate([],[],h);
doList([],[],h);
end
function doDelete(fig,evd,h)
tree = getappdata(h, 'tree');
uidList = getappdata(h, 'uidlist');
handles = getappdata(h, 'handles');
pos = get(handles.xmllistbox,'value');
uid = uidList(pos);
if pos > 1
tree = delete(tree,uid);
set(handles.xmllistbox,'value',pos-1);
setappdata(h, 'save', 1);
end
setappdata(h, 'tree', tree);
doUpdate([],[],h);
doList([],[],h);
function status = doSave(fig,evd,h)
tree = getappdata(h, 'tree');
[filename, pathname] = uiputfile({'*.xml' 'XML file (*.xml)'}, ...
'Save XML file as');
status = ~(isequal(filename,0) | isequal(pathname,0));
if status
save(tree,fullfile(pathname, filename));
set(h,'Name',[':: XMLTree Editor :: ' filename]);
setappdata(h, 'save', 0);
end
function doRun(fig,evd,h)
warndlg('Not implemented','XMLTree :: Run');
function doAttributes(fig,evd,h)
tree = getappdata(h, 'tree');
uidList = getappdata(h, 'uidlist');
handles = getappdata(h, 'handles');
pos = get(handles.xmllistbox,'value');
uid = uidList(pos);
attr = attributes(tree,'get',uid);
if ~isempty(attr)
fprintf('This element has %d attributes.\n',length(attr));
%%%
%%% Do what you want with 'attr'
%%% to modify them, use:
%%% tree = attributes(tree,'set',uid,n,key,val)
%%% to add one, use:
%%% tree = attributes(tree,'add',uid,key,val)
%%% to delete one, use:
%%% tree = attributes(tree,'del',uid[,n]);
%%%
setappdata(h, 'tree', tree);
setappdata(h, 'save', 1); %- only if attributes have been modified
end
%==========================================================================
function doList(fig,evd,h)
tree = getappdata(h, 'tree');
uidList = getappdata(h, 'uidlist');
handles = getappdata(h, 'handles');
uid = uidList(get(handles.xmllistbox, 'value'));
%- Single mouse click
if strcmp(get(h,'SelectionType'),'normal')
contents = children(tree, uid);
if length(contents) > 0 && ...
strcmp(get(tree,contents(1),'type'),'chardata')
str = get(tree,contents(1),'value');
set(handles.addbutton,'Enable','off');
elseif length(contents) == 0
str = '';
tree = add(tree,uid,'chardata',str);
setappdata(h, 'tree', tree);
set(handles.addbutton,'Enable','off');
else
str = ['Tag ' get(tree,uid,'name')];
set(handles.addbutton,'Enable','on');
end
if get(handles.xmllistbox,'value') == 1
set(handles.copybutton,'Enable','off');
set(handles.delbutton,'Enable','off');
else
set(handles.copybutton,'Enable','on');
set(handles.delbutton,'Enable','on');
end
%- Trying to keep the slider active
set(handles.xmllist, 'Enable', 'on');
set(handles.xmllist, 'String', ' ');
set(handles.xmllist, 'Enable', 'Inactive');
set(handles.xmllist, 'String', str);
%- Double mouse click
else
tree = doFlip(tree, uid);
setappdata(h, 'tree', tree);
doUpdate([],[],h);
end
function doUpdate(fig,evd,h)
tree = getappdata(h, 'tree');
handles = getappdata(h, 'handles');
[batchString, uidList] = doUpdateR(tree);
set(handles.xmllistbox, 'String', batchString);
setappdata(h, 'uidlist', uidList);
%==========================================================================
function [batchString, uidList] = doUpdateR(tree, uid, o)
if nargin < 2, uid = root(tree); end
if nargin < 3 || o == 0
o = 0;
sep = ' ';
else
sep = blanks(4*o);
end
if attributes(tree,'length',uid) > 0
batchString = {[sep, get(tree, uid, 'name') ' *']};
else
batchString = {[sep, get(tree, uid, 'name')]};
end
uidList = [get(tree,uid,'uid')];
haselementchild = 0;
contents = get(tree, uid, 'contents');
if isfield(tree, uid, 'show') && get(tree, uid, 'show') == 1
for i=1:length(contents)
if strcmp(get(tree,contents(i),'type'),'element')
[subbatchString, subuidList] = doUpdateR(tree,contents(i),o+1);
batchString = {batchString{:} subbatchString{:}};
uidList = [uidList subuidList];
haselementchild = 1;
end
end
if haselementchild == 1, batchString{1}(length(sep)) = '-'; end
else
for i=1:length(contents)
if strcmp(get(tree,contents(i),'type'),'element')
haselementchild = 1;
end
end
if haselementchild == 1, batchString{1}(length(sep)) = '+'; end
end
function tree = doFlip(tree, uid)
if isfield(tree,uid,'show')
show = get(tree,uid,'show');
else
show = 0;
end
tree = set(tree,uid,'show',~show);
|
github
|
lcnbeapp/beapp-master
|
find.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@xmltree/find.m
| 5,901 |
utf_8
|
b241bfaac569f137b8b809b7b66765f3
|
function list = find(varargin)
% XMLTREE/FIND Find elements in a tree with specified characteristics
% FORMAT list = find(varargin)
%
% tree - XMLTree object
% xpath - string path with specific grammar (XPath)
% uid - lists of root uid's
% parameter/value - pair of pattern
% list - list of uid's of matched elements
%
% list = find(tree,xpath)
% list = find(tree,parameter,value[,parameter,value])
% list = find(tree,uid,parameter,value[,parameter,value])
%
% Grammar for addressing parts of an XML document:
% XML Path Language XPath (http://www.w3.org/TR/xpath)
% Example: /element1//element2[1]/element3[5]/element4
%__________________________________________________________________________
%
% Find elements in an XML tree with specified characteristics or given
% a path (using a subset of XPath language).
%__________________________________________________________________________
% Copyright (C) 2002-2011 http://www.artefact.tk/
% Guillaume Flandin
% $Id: find.m 4460 2011-09-05 14:52:16Z guillaume $
% TODO:
% - clean up subroutines
% - find should only be documented using XPath (other use is internal)
% - handle '*', 'last()' in [] and '@'
% - if a key is invalid, should rather return [] than error ?
if nargin==0
error('[XMLTree] A tree must be provided');
elseif nargin==1
list = 1:length(tree.tree);
return
elseif mod(nargin,2)
list = sub_find_subtree1(varargin{1}.tree,root(varargin{1}),varargin{2:end});
elseif isa(varargin{2},'double') && ...
ndims(varargin{2}) == 2 && ...
min(size(varargin{2})) == 1
list = unique(sub_find_subtree1(varargin{1}.tree,varargin{2:end}));
elseif nargin==2 && ischar(varargin{2})
list = sub_pathfinder(varargin{:});
else
error('[XMLTree] Arguments must be parameter/value pairs.');
end
%==========================================================================
function list = sub_find_subtree1(varargin)
list = [];
for i=1:length(varargin{2})
res = sub_find_subtree2(varargin{1},...
varargin{2}(i),varargin{3:end});
list = [list res];
end
%==========================================================================
function list = sub_find_subtree2(varargin)
uid = varargin{2};
list = [];
if sub_comp_element(varargin{1}{uid},varargin{3:end})
list = [list varargin{1}{uid}.uid];
end
if isfield(varargin{1}{uid},'contents')
list = [list sub_find_subtree1(varargin{1},...
varargin{1}{uid}.contents,varargin{3:end})];
end
%==========================================================================
function match = sub_comp_element(varargin)
match = 0;
try
% v = getfield(varargin{1}, varargin{2}); % slow...
for i=1:floor(nargin/2)
v = subsref(varargin{1}, struct('type','.','subs',varargin{i+1}));
if strcmp(v,varargin{i+2})
match = 1;
end
end
catch
end
% More powerful but much slower
%match = 0;
%for i=1:length(floor(nargin/2)) % bug: remove length !!!
% if isfield(varargin{1},varargin{i+1})
% if ischar(getfield(varargin{1},varargin{i+1})) & ischar(varargin{i+2})
% if strcmp(getfield(varargin{1},varargin{i+1}),char(varargin{i+2}))
% match = 1;
% end
% elseif isa(getfield(varargin{1},varargin{i+1}),'double') & ...
% isa(varargin{i+2},'double')
% if getfield(varargin{1},varargin{i+1}) == varargin{i+2}
% match = 1;
% end
% else
% warning('Cannot compare different objects');
% end
% end
%end
%==========================================================================
function list = sub_pathfinder(tree,pth)
%- Search for the delimiter '/' in the path
i = strfind(pth,'/');
%- Begin search by root
list = root(tree);
%- Walk through the tree
j = 1;
while j <= length(i)
%- Look for recursion '//'
if j<length(i) && i(j+1)==i(j)+1
recursive = 1;
j = j + 1;
else
recursive = 0;
end
%- Catch the current tag 'element[x]'
if j ~= length(i)
element = pth(i(j)+1:i(j+1)-1);
else
element = pth(i(j)+1:end);
end
%- Search for [] brackets
k = xml_findstr(element,'[',1,1);
%- If brackets are present in current element
if ~isempty(k)
l = xml_findstr(element,']',1,1);
val = str2num(element(k+1:l-1));
element = element(1:k-1);
end
%- Use recursivity
if recursive
list = find(tree,list,'name',element);
%- Just look at children
else
if i(j)==1 % if '/root/...' (list = root(tree) in that case)
if sub_comp_element(tree.tree{list},'name',element)
% list = 1; % list still contains root(tree)
else
list = [];
return;
end
else
list = sub_findchild(tree,list,element);
end
end
% If an element is specified using a key
if ~isempty(k)
if val < 1 || val > length(list)+1
error('[XMLTree] Bad key in the path.');
elseif val == length(list)+1
list = [];
return;
end
list = list(val);
end
if isempty(list), return; end
j = j + 1;
end
%==========================================================================
function list = sub_findchild(tree,listt,elmt)
list = [];
for a=1:length(listt)
for b=1:length(tree.tree{listt(a)}.contents)
if sub_comp_element(tree.tree{tree.tree{listt(a)}.contents(b)},'name',elmt)
list = [list tree.tree{tree.tree{listt(a)}.contents(b)}.uid];
end
end
end
|
github
|
lcnbeapp/beapp-master
|
xml_parser.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@xmltree/private/xml_parser.m
| 16,192 |
utf_8
|
7e44abd21a10863623b455d03e0651bb
|
function tree = xml_parser(xmlstr)
% XML (eXtensible Markup Language) Processor
% FORMAT tree = xml_parser(xmlstr)
%
% xmlstr - XML string to parse
% tree - tree structure corresponding to the XML file
%__________________________________________________________________________
%
% xml_parser.m is an XML 1.0 (http://www.w3.org/TR/REC-xml) parser.
% It aims to be fully conforming. It is currently not a validating
% XML processor.
%
% A description of the tree structure provided in output is detailed in
% the header of this m-file.
%__________________________________________________________________________
% Copyright (C) 2002-2015 http://www.artefact.tk/
% Guillaume Flandin
% $Id: xml_parser.m 6480 2015-06-13 01:08:30Z guillaume $
% XML Processor for GNU Octave and MATLAB (The Mathworks, Inc.)
% Copyright (C) 2002-2015 Guillaume Flandin <[email protected]>
%
% 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]>
% Check also the latest developments on the following webpage:
% <http://www.artefact.tk/software/matlab/xml/>
%--------------------------------------------------------------------------
% The implementation of this XML parser is much inspired from a
% Javascript parser that used to be available at <http://www.jeremie.com/>
% A C-MEX file xml_findstr.c is also required, to encompass some
% limitations of the built-in FINDSTR function.
% Compile it on your architecture using 'mex -O xml_findstr.c' command
% if the compiled version for your system is not provided.
% If this function does not behave as expected, comment the line
% '#define __HACK_MXCHAR__' in xml_findstr.c and compile it again.
%--------------------------------------------------------------------------
% Structure of the output tree:
% There are 5 types of nodes in an XML file: element, chardata, cdata,
% pi and comment.
% Each of them contains an UID (Unique Identifier): an integer between
% 1 and the number of nodes of the XML file.
%
% element (a tag <name key="value"> [contents] </name>
% |_ type: 'element'
% |_ name: string
% |_ attributes: cell array of struct 'key' and 'value' or []
% |_ contents: double array of uid's or [] if empty
% |_ parent: uid of the parent ([] if root)
% |_ uid: double
%
% chardata (a character array)
% |_ type: 'chardata'
% |_ value: string
% |_ parent: uid of the parent
% |_ uid: double
%
% cdata (a litteral string <![CDATA[value]]>)
% |_ type: 'cdata'
% |_ value: string
% |_ parent: uid of the parent
% |_ uid: double
%
% pi (a processing instruction <?target value ?>)
% |_ type: 'pi'
% |_ target: string (may be empty)
% |_ value: string
% |_ parent: uid of the parent
% |_ uid: double
%
% comment (a comment <!-- value -->)
% |_ type: 'comment'
% |_ value: string
% |_ parent: uid of the parent
% |_ uid: double
%
%--------------------------------------------------------------------------
% TODO/BUG/FEATURES:
% - [compile] only a warning if TagStart is empty ?
% - [attribution] should look for " and ' rather than only "
% - [main] with normalize as a preprocessing, CDATA are modified
% - [prolog] look for a DOCTYPE in the whole string even if it occurs
% only in a far CDATA tag, bug even if the doctype is inside a comment
% - [tag_element] erode should replace normalize here
% - remove globals? uppercase globals rather persistent (clear mfile)?
% - xml_findstr is indeed xml_strfind according to Mathworks vocabulary
% - problem with entities: do we need to convert them here? (é)
%--------------------------------------------------------------------------
%- XML string to parse and number of tags read
global xmlstring Xparse_count xtree;
%- Check input arguments
%error(nargchk(1,1,nargin));
if isempty(xmlstr)
error('[XML] Not enough parameters.')
elseif ~ischar(xmlstr) || sum(size(xmlstr)>1)>1
error('[XML] Input must be a string.')
end
%- Initialize number of tags (<=> uid)
Xparse_count = 0;
%- Remove prolog and white space characters from the XML string
xmlstring = normalize(prolog(xmlstr));
%- Initialize the XML tree
xtree = {};
tree = fragment;
tree.str = 1;
tree.parent = 0;
%- Parse the XML string
tree = compile(tree);
%- Return the XML tree
tree = xtree;
%- Remove global variables from the workspace
clear global xmlstring Xparse_count xtree;
%==========================================================================
% SUBFUNCTIONS
%--------------------------------------------------------------------------
function frag = compile(frag)
global xmlstring xtree Xparse_count;
while 1,
if length(xmlstring)<=frag.str || ...
(frag.str == length(xmlstring)-1 && strcmp(xmlstring(frag.str:end),' '))
return
end
TagStart = xml_findstr(xmlstring,'<',frag.str,1);
if isempty(TagStart)
%- Character data
error('[XML] Unknown data at the end of the XML file.');
Xparse_count = Xparse_count + 1;
xtree{Xparse_count} = chardata;
xtree{Xparse_count}.value = erode(entity(xmlstring(frag.str:end)));
xtree{Xparse_count}.parent = frag.parent;
xtree{frag.parent}.contents = [xtree{frag.parent}.contents Xparse_count];
frag.str = '';
elseif TagStart > frag.str
if strcmp(xmlstring(frag.str:TagStart-1),' ')
%- A single white space before a tag (ignore)
frag.str = TagStart;
else
%- Character data
Xparse_count = Xparse_count + 1;
xtree{Xparse_count} = chardata;
xtree{Xparse_count}.value = erode(entity(xmlstring(frag.str:TagStart-1)));
xtree{Xparse_count}.parent = frag.parent;
xtree{frag.parent}.contents = [xtree{frag.parent}.contents Xparse_count];
frag.str = TagStart;
end
else
if strcmp(xmlstring(frag.str+1),'?')
%- Processing instruction
frag = tag_pi(frag);
else
if length(xmlstring)-frag.str>4 && strcmp(xmlstring(frag.str+1:frag.str+3),'!--')
%- Comment
frag = tag_comment(frag);
else
if length(xmlstring)-frag.str>9 && strcmp(xmlstring(frag.str+1:frag.str+8),'![CDATA[')
%- Litteral data
frag = tag_cdata(frag);
else
%- A tag element (empty (<.../>) or not)
if ~isempty(frag.end)
endmk = ['/' frag.end '>'];
else
endmk = '/>';
end
if strcmp(xmlstring(frag.str+1:frag.str+length(frag.end)+2),endmk) || ...
strcmp(strip(xmlstring(frag.str+1:frag.str+length(frag.end)+2)),endmk)
frag.str = frag.str + length(frag.end)+3;
return
else
frag = tag_element(frag);
end
end
end
end
end
end
%--------------------------------------------------------------------------
function frag = tag_element(frag)
global xmlstring xtree Xparse_count;
close = xml_findstr(xmlstring,'>',frag.str,1);
if isempty(close)
error('[XML] Tag < opened but not closed.');
else
empty = strcmp(xmlstring(close-1:close),'/>');
if empty
close = close - 1;
end
starttag = normalize(xmlstring(frag.str+1:close-1));
nextspace = xml_findstr(starttag,' ',1,1);
attribs = '';
if isempty(nextspace)
name = starttag;
else
name = starttag(1:nextspace-1);
attribs = starttag(nextspace+1:end);
end
Xparse_count = Xparse_count + 1;
xtree{Xparse_count} = element;
xtree{Xparse_count}.name = strip(name);
if frag.parent
xtree{Xparse_count}.parent = frag.parent;
xtree{frag.parent}.contents = [xtree{frag.parent}.contents Xparse_count];
end
if ~isempty(attribs)
xtree{Xparse_count}.attributes = attribution(attribs);
end
if ~empty
contents = fragment;
contents.str = close+1;
contents.end = name;
contents.parent = Xparse_count;
contents = compile(contents);
frag.str = contents.str;
else
frag.str = close+2;
end
end
%--------------------------------------------------------------------------
function frag = tag_pi(frag)
global xmlstring xtree Xparse_count;
close = xml_findstr(xmlstring,'?>',frag.str,1);
if isempty(close)
warning('[XML] Tag <? opened but not closed.')
else
nextspace = xml_findstr(xmlstring,' ',frag.str,1);
Xparse_count = Xparse_count + 1;
xtree{Xparse_count} = pri;
if nextspace > close || nextspace == frag.str+2
xtree{Xparse_count}.value = erode(xmlstring(frag.str+2:close-1));
else
xtree{Xparse_count}.value = erode(xmlstring(nextspace+1:close-1));
xtree{Xparse_count}.target = erode(xmlstring(frag.str+2:nextspace));
end
if frag.parent
xtree{frag.parent}.contents = [xtree{frag.parent}.contents Xparse_count];
xtree{Xparse_count}.parent = frag.parent;
end
frag.str = close+2;
end
%--------------------------------------------------------------------------
function frag = tag_comment(frag)
global xmlstring xtree Xparse_count;
close = xml_findstr(xmlstring,'-->',frag.str,1);
if isempty(close)
warning('[XML] Tag <!-- opened but not closed.')
else
Xparse_count = Xparse_count + 1;
xtree{Xparse_count} = comment;
xtree{Xparse_count}.value = erode(xmlstring(frag.str+4:close-1));
if frag.parent
xtree{frag.parent}.contents = [xtree{frag.parent}.contents Xparse_count];
xtree{Xparse_count}.parent = frag.parent;
end
frag.str = close+3;
end
%--------------------------------------------------------------------------
function frag = tag_cdata(frag)
global xmlstring xtree Xparse_count;
close = xml_findstr(xmlstring,']]>',frag.str,1);
if isempty(close)
warning('[XML] Tag <![CDATA[ opened but not closed.')
else
Xparse_count = Xparse_count + 1;
xtree{Xparse_count} = cdata;
xtree{Xparse_count}.value = xmlstring(frag.str+9:close-1);
if frag.parent
xtree{frag.parent}.contents = [xtree{frag.parent}.contents Xparse_count];
xtree{Xparse_count}.parent = frag.parent;
end
frag.str = close+3;
end
%--------------------------------------------------------------------------
function all = attribution(str)
%- Initialize attributs
nbattr = 0;
all = cell(nbattr);
%- Look for 'key="value"' substrings
while 1,
eq = xml_findstr(str,'=',1,1);
if isempty(str) || isempty(eq), return; end
id = sort([xml_findstr(str,'"',1,1),xml_findstr(str,'''',1,1)]); id=id(1);
nextid = sort([xml_findstr(str,'"',id+1,1),xml_findstr(str,'''',id+1,1)]);nextid=nextid(1);
nbattr = nbattr + 1;
all{nbattr}.key = strip(str(1:(eq-1)));
all{nbattr}.val = entity(str((id+1):(nextid-1)));
str = str((nextid+1):end);
end
%--------------------------------------------------------------------------
function elm = element
global Xparse_count;
elm = struct('type','element','name','','attributes',[],'contents',[],'parent',[],'uid',Xparse_count);
%--------------------------------------------------------------------------
function cdat = chardata
global Xparse_count;
cdat = struct('type','chardata','value','','parent',[],'uid',Xparse_count);
%--------------------------------------------------------------------------
function cdat = cdata
global Xparse_count;
cdat = struct('type','cdata','value','','parent',[],'uid',Xparse_count);
%--------------------------------------------------------------------------
function proce = pri
global Xparse_count;
proce = struct('type','pi','value','','target','','parent',[],'uid',Xparse_count);
%--------------------------------------------------------------------------
function commt = comment
global Xparse_count;
commt = struct('type','comment','value','','parent',[],'uid',Xparse_count);
%--------------------------------------------------------------------------
function frg = fragment
frg = struct('str','','parent','','end','');
%--------------------------------------------------------------------------
function str = prolog(str)
%- Initialize beginning index of elements tree
b = 1;
%- Initial tag
start = xml_findstr(str,'<',1,1);
if isempty(start)
error('[XML] No tag found.')
end
%- Header (<?xml version="1.0" ... ?>)
if strcmpi(str(start:start+2),'<?x')
close = xml_findstr(str,'?>',1,1);
if ~isempty(close)
b = close + 2;
else
warning('[XML] Header tag incomplete.')
end
end
%- Doctype (<!DOCTYPE type ... [ declarations ]>)
start = xml_findstr(str,'<!DOCTYPE',b,1); % length('<!DOCTYPE') = 9
if ~isempty(start)
close = xml_findstr(str,'>',start+9,1);
if ~isempty(close)
b = close + 1;
dp = xml_findstr(str,'[',start+9,1);
if (~isempty(dp) && dp < b)
k = xml_findstr(str,']>',start+9,1);
if ~isempty(k)
b = k + 2;
else
warning('[XML] Tag [ in DOCTYPE opened but not closed.')
end
end
else
warning('[XML] Tag DOCTYPE opened but not closed.')
end
end
%- Skip prolog from the xml string
str = str(b:end);
%--------------------------------------------------------------------------
function str = strip(str)
str(isspace(str)) = '';
%--------------------------------------------------------------------------
function str = normalize(str)
% Find white characters (space, newline, carriage return, tabs, ...)
i = isspace(str);
i = find(i == 1);
str(i) = ' ';
% replace several white characters by only one
if ~isempty(i)
j = i - [i(2:end) i(end)];
str(i(j == -1)) = [];
end
%--------------------------------------------------------------------------
function str = entity(str)
str = strrep(str,'<','<');
str = strrep(str,'>','>');
str = strrep(str,'"','"');
str = strrep(str,''','''');
str = strrep(str,'&','&');
%--------------------------------------------------------------------------
function str = erode(str)
if ~isempty(str) && str(1)==' ', str(1)=''; end;
if ~isempty(str) && str(end)==' ', str(end)=''; end;
|
github
|
lcnbeapp/beapp-master
|
save.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@gifti/save.m
| 21,043 |
utf_8
|
747d3d8c45fa4a27160c0c333450a4dc
|
function save(this,filename,encoding)
% Save GIfTI object in a GIfTI format file
% FORMAT save(this,filename)
% this - GIfTI object
% filename - name of GIfTI file to be created [Default: 'untitled.gii']
% encoding - optional argument to specify encoding format, among
% ASCII, Base64Binary, GZipBase64Binary, ExternalFileBinary,
% Collada (.dae), IDTF (.idtf). [Default: 'GZipBase64Binary']
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id$
% Check filename and file format
%--------------------------------------------------------------------------
ext = '.gii';
if nargin == 1
filename = 'untitled.gii';
else
if nargin == 3 && strcmpi(encoding,'collada')
ext = '.dae';
end
if nargin == 3 && strcmpi(encoding,'idtf')
ext = '.idtf';
end
[p,f,e] = fileparts(filename);
if ~ismember(lower(e),{ext})
e = ext;
end
filename = fullfile(p,[f e]);
end
% Open file for writing
%--------------------------------------------------------------------------
fid = fopen(filename,'wt');
if fid == -1
error('Unable to write file %s: permission denied.',filename);
end
% Write file
%--------------------------------------------------------------------------
switch ext
case '.gii'
if nargin < 3, encoding = 'GZipBase64Binary'; end
fid = save_gii(fid,this,encoding);
case '.dae'
fid = save_dae(fid,this);
case '.idtf'
fid = save_idtf(fid,this);
otherwise
error('Unknown file format.');
end
% Close file
%--------------------------------------------------------------------------
fclose(fid);
%==========================================================================
% function fid = save_gii(fid,this,encoding)
%==========================================================================
function fid = save_gii(fid,this,encoding)
% Defaults for DataArray's attributes
%--------------------------------------------------------------------------
[unused,unused,mach] = fopen(fid);
if strncmp('ieee-be',mach,7)
def.Endian = 'BigEndian';
elseif strncmp('ieee-le',mach,7)
def.Endian = 'LittleEndian';
else
error('[GIFTI] Unknown byte order "%s".',mach);
end
def.Encoding = encoding;
def.Intent = 'NIFTI_INTENT_NONE';
def.DataType = 'NIFTI_TYPE_FLOAT32';
def.ExternalFileName = '';
def.ExternalFileOffset = '';
def.offset = 0;
if strcmp(def.Encoding,'GZipBase64Binary') && ~usejava('jvm')
warning(['Cannot save GIfTI in ''GZipBase64Binary'' encoding. ' ...
'Revert to ''Base64Binary''.']);
def.Encoding = 'Base64Binary';
end
% Edit object DataArray attributes
%--------------------------------------------------------------------------
for i=1:length(this.data)
% Revert the dimension storage
d = this.data{i}.attributes.Dim;
this.data{i}.attributes = rmfield(this.data{i}.attributes,'Dim');
this.data{i}.attributes.Dimensionality = num2str(length(d));
for j=1:length(d)
this.data{i}.attributes.(sprintf('Dim%d',j-1)) = num2str(d(j));
end
% Enforce some conventions
this.data{i}.attributes.ArrayIndexingOrder = 'ColumnMajorOrder';
if ~isfield(this.data{i}.attributes,'DataType') || ...
isempty(this.data{i}.attributes.DataType)
warning('DataType set to default: %s', def.DataType);
this.data{i}.attributes.DataType = def.DataType;
end
if ~isfield(this.data{i}.attributes,'Intent') || ...
isempty(this.data{i}.attributes.Intent)
warning('Intent code set to default: %s', def.Intent);
this.data{i}.attributes.Intent = def.Intent;
end
this.data{i}.attributes.Encoding = def.Encoding;
this.data{i}.attributes.Endian = def.Endian;
this.data{i}.attributes.ExternalFileName = def.ExternalFileName;
this.data{i}.attributes.ExternalFileOffset = def.ExternalFileOffset;
switch this.data{i}.attributes.Encoding
case {'ASCII', 'Base64Binary','GZipBase64Binary' }
case 'ExternalFileBinary'
extfilename = this.data{i}.attributes.ExternalFileName;
if isempty(extfilename)
[p,f] = fileparts(fopen(fid));
extfilename = [f '.dat'];
end
[p,f,e] = fileparts(extfilename);
this.data{i}.attributes.ExternalFileName = fullfile(fileparts(fopen(fid)),[f e]);
this.data{i}.attributes.ExternalFileOffset = num2str(def.offset);
otherwise
error('[GIFTI] Unknown data encoding: %s.',this.data{i}.attributes.Encoding);
end
end
% Prolog
%--------------------------------------------------------------------------
fprintf(fid,'<?xml version="1.0" encoding="UTF-8"?>\n');
fprintf(fid,'<!DOCTYPE GIFTI SYSTEM "http://www.nitrc.org/frs/download.php/115/gifti.dtd">\n');
fprintf(fid,'<GIFTI Version="1.0" NumberOfDataArrays="%d">\n',numel(this.data));
o = @(x) blanks(x*3);
% MetaData
%--------------------------------------------------------------------------
fprintf(fid,'%s<MetaData',o(1));
if isempty(this.metadata)
fprintf(fid,'/>\n');
else
fprintf(fid,'>\n');
for i=1:length(this.metadata)
fprintf(fid,'%s<MD>\n',o(2));
fprintf(fid,'%s<Name><![CDATA[%s]]></Name>\n',o(3),...
this.metadata(i).name);
fprintf(fid,'%s<Value><![CDATA[%s]]></Value>\n',o(3),...
this.metadata(i).value);
fprintf(fid,'%s</MD>\n',o(2));
end
fprintf(fid,'%s</MetaData>\n',o(1));
end
% LabelTable
%--------------------------------------------------------------------------
fprintf(fid,'%s<LabelTable',o(1));
if isempty(this.label)
fprintf(fid,'/>\n');
else
fprintf(fid,'>\n');
for i=1:length(this.label.name)
if ~all(isnan(this.label.rgba(i,:)))
label_rgba = sprintf(' Red="%f" Green="%f" Blue="%f" Alpha="%f"',...
this.label.rgba(i,:));
else
label_rgba = '';
end
fprintf(fid,'%s<Label Key="%d"%s><![CDATA[%s]]></Label>\n',o(2),...
this.label.key(i), label_rgba, this.label.name{i});
end
fprintf(fid,'%s</LabelTable>\n',o(1));
end
% DataArray
%--------------------------------------------------------------------------
for i=1:length(this.data)
fprintf(fid,'%s<DataArray',o(1));
if def.offset
this.data{i}.attributes.ExternalFileOffset = num2str(def.offset);
end
fn = sort(fieldnames(this.data{i}.attributes));
oo = repmat({o(5) '\n'},length(fn),1); oo{1} = ' '; oo{end} = '';
for j=1:length(fn)
if strcmp(fn{j},'ExternalFileName')
[p,f,e] = fileparts(this.data{i}.attributes.(fn{j}));
attval = [f e];
else
attval = this.data{i}.attributes.(fn{j});
end
fprintf(fid,'%s%s="%s"%s',oo{j,1},...
fn{j},attval,sprintf(oo{j,2}));
end
fprintf(fid,'>\n');
% MetaData
%----------------------------------------------------------------------
fprintf(fid,'%s<MetaData>\n',o(2));
for j=1:length(this.data{i}.metadata)
fprintf(fid,'%s<MD>\n',o(3));
fprintf(fid,'%s<Name><![CDATA[%s]]></Name>\n',o(4),...
this.data{i}.metadata(j).name);
fprintf(fid,'%s<Value><![CDATA[%s]]></Value>\n',o(4),...
this.data{i}.metadata(j).value);
fprintf(fid,'%s</MD>\n',o(3));
end
fprintf(fid,'%s</MetaData>\n',o(2));
% CoordinateSystemTransformMatrix
%----------------------------------------------------------------------
for j=1:length(this.data{i}.space)
fprintf(fid,'%s<CoordinateSystemTransformMatrix>\n',o(2));
fprintf(fid,'%s<DataSpace><![CDATA[%s]]></DataSpace>\n',o(3),...
this.data{i}.space(j).DataSpace);
fprintf(fid,'%s<TransformedSpace><![CDATA[%s]]></TransformedSpace>\n',o(3),...
this.data{i}.space(j).TransformedSpace);
fprintf(fid,'%s<MatrixData>%s</MatrixData>\n',o(3),...
sprintf('%f ',this.data{i}.space(j).MatrixData));
fprintf(fid,'%s</CoordinateSystemTransformMatrix>\n',o(2));
end
% Data (saved using MATLAB's ColumnMajorOrder)
%----------------------------------------------------------------------
fprintf(fid,'%s<Data>',o(2));
tp = getdict;
try
tp = tp.(this.data{i}.attributes.DataType);
catch
error('[GIFTI] Unknown DataType.');
end
switch this.data{i}.attributes.Encoding
case 'ASCII'
fprintf(fid, [tp.format ' '], this.data{i}.data);
case 'Base64Binary'
fprintf(fid,base64encode(typecast(this.data{i}.data(:),'uint8')));
% uses native machine format
case 'GZipBase64Binary'
fprintf(fid,base64encode(dzip(typecast(this.data{i}.data(:),'uint8'))));
% uses native machine format
case 'ExternalFileBinary'
extfilename = this.data{i}.attributes.ExternalFileName;
dat = this.data{i}.data;
if isa(dat,'file_array')
dat = subsref(dat,substruct('()',repmat({':'},1,numel(dat.dim))));
end
if ~def.offset
fide = fopen(extfilename,'w'); % uses native machine format
else
fide = fopen(extfilename,'a'); % uses native machine format
end
if fide == -1
error('Unable to write file %s: permission denied.',extfilename);
end
fseek(fide,0,1);
fwrite(fide,dat,tp.class);
def.offset = ftell(fide);
fclose(fide);
otherwise
error('[GIFTI] Unknown data encoding.');
end
fprintf(fid,'</Data>\n');
fprintf(fid,'%s</DataArray>\n',o(1));
end
fprintf(fid,'</GIFTI>\n');
%==========================================================================
% function fid = save_dae(fid,this)
%==========================================================================
function fid = save_dae(fid,this)
o = @(x) blanks(x*3);
% Split the mesh into connected components
%--------------------------------------------------------------------------
s = struct(this);
try
C = spm_mesh_label(s.faces);
d = [];
for i=1:numel(unique(C))
d(i).faces = s.faces(C==i,:);
u = unique(d(i).faces);
d(i).vertices = s.vertices(u,:);
a = 1:max(d(i).faces(:));
a(u) = 1:size(d(i).vertices,1);
%a = sparse(1,double(u),1:1:size(d(i).vertices,1));
d(i).faces = a(d(i).faces);
end
s = d;
end
% Prolog & root of the Collada XML file
%--------------------------------------------------------------------------
fprintf(fid,'<?xml version="1.0"?>\n');
fprintf(fid,'<COLLADA xmlns="http://www.collada.org/2008/03/COLLADASchema" version="1.5.0">\n');
% Assets
%--------------------------------------------------------------------------
fprintf(fid,'%s<asset>\n',o(1));
fprintf(fid,'%s<contributor>\n',o(2));
fprintf(fid,'%s<author_website>%s</author_website>\n',o(3),...
'http://www.fil.ion.ucl.ac.uk/spm/');
fprintf(fid,'%s<authoring_tool>%s</authoring_tool>\n',o(3),spm('Ver'));
fprintf(fid,'%s</contributor>\n',o(2));
fprintf(fid,'%s<created>%s</created>\n',o(2),datestr(now,'yyyy-mm-ddTHH:MM:SSZ'));
fprintf(fid,'%s<modified>%s</modified>\n',o(2),datestr(now,'yyyy-mm-ddTHH:MM:SSZ'));
fprintf(fid,'%s<unit name="millimeter" meter="0.001"/>\n',o(2));
fprintf(fid,'%s<up_axis>Z_UP</up_axis>\n',o(2));
fprintf(fid,'%s</asset>\n',o(1));
% Image, Materials, Effects
%--------------------------------------------------------------------------
%fprintf(fid,'%s<library_images/>\n',o(1));
fprintf(fid,'%s<library_materials>\n',o(1));
for i=1:numel(s)
fprintf(fid,'%s<material id="material%d" name="material%d">\n',o(2),i,i);
fprintf(fid,'%s<instance_effect url="#material%d-effect"/>\n',o(3),i);
fprintf(fid,'%s</material>\n',o(2));
end
fprintf(fid,'%s</library_materials>\n',o(1));
fprintf(fid,'%s<library_effects>\n',o(1));
for i=1:numel(s)
fprintf(fid,'%s<effect id="material%d-effect" name="material%d-effect">\n',o(2),i,i);
fprintf(fid,'%s<profile_COMMON>\n',o(3));
fprintf(fid,'%s<technique sid="COMMON">\n',o(4));
fprintf(fid,'%s<lambert>\n',o(5));
fprintf(fid,'%s<emission>\n',o(6));
fprintf(fid,'%s<color>%f %f %f %d</color>\n',o(7),[0 0 0 1]);
fprintf(fid,'%s</emission>\n',o(6));
fprintf(fid,'%s<ambient>\n',o(6));
fprintf(fid,'%s<color>%f %f %f %d</color>\n',o(7),[0 0 0 1]);
fprintf(fid,'%s</ambient>\n',o(6));
fprintf(fid,'%s<diffuse>\n',o(6));
fprintf(fid,'%s<color>%f %f %f %d</color>\n',o(7),[0.5 0.5 0.5 1]);
fprintf(fid,'%s</diffuse>\n',o(6));
fprintf(fid,'%s<transparent>\n',o(6));
fprintf(fid,'%s<color>%d %d %d %d</color>\n',o(7),[1 1 1 1]);
fprintf(fid,'%s</transparent>\n',o(6));
fprintf(fid,'%s<transparency>\n',o(6));
fprintf(fid,'%s<float>%f</float>\n',o(7),0);
fprintf(fid,'%s</transparency>\n',o(6));
fprintf(fid,'%s</lambert>\n',o(5));
fprintf(fid,'%s</technique>\n',o(4));
fprintf(fid,'%s</profile_COMMON>\n',o(3));
fprintf(fid,'%s</effect>\n',o(2));
end
fprintf(fid,'%s</library_effects>\n',o(1));
% Geometry
%--------------------------------------------------------------------------
fprintf(fid,'%s<library_geometries>\n',o(1));
for i=1:numel(s)
fprintf(fid,'%s<geometry id="shape%d" name="shape%d">\n',o(2),i,i);
fprintf(fid,'%s<mesh>\n',o(3));
fprintf(fid,'%s<source id="shape%d-positions">\n',o(4),i);
fprintf(fid,'%s<float_array id="shape%d-positions-array" count="%d">',o(5),i,numel(s(i).vertices));
fprintf(fid,'%f ',repmat(s(i).vertices',1,[]));
fprintf(fid,'</float_array>\n');
fprintf(fid,'%s<technique_common>\n',o(5));
fprintf(fid,'%s<accessor count="%d" offset="0" source="#shape%d-positions-array" stride="3">\n',o(6),size(s(i).vertices,1),i);
fprintf(fid,'%s<param name="X" type="float" />\n',o(7));
fprintf(fid,'%s<param name="Y" type="float" />\n',o(7));
fprintf(fid,'%s<param name="Z" type="float" />\n',o(7));
fprintf(fid,'%s</accessor>\n',o(6));
fprintf(fid,'%s</technique_common>\n',o(5));
fprintf(fid,'%s</source>\n',o(4));
fprintf(fid,'%s<vertices id="shape%d-vertices">\n',o(4),i);
fprintf(fid,'%s<input semantic="POSITION" source="#shape%d-positions"/>\n',o(5),i);
fprintf(fid,'%s</vertices>\n',o(4));
fprintf(fid,'%s<triangles material="material%d" count="%d">\n',o(4),i,size(s(i).faces,1));
fprintf(fid,'%s<input semantic="VERTEX" source="#shape%d-vertices" offset="0"/>\n',o(5),i);
fprintf(fid,'%s<p>',o(5));
fprintf(fid,'%d ',repmat(s(i).faces',1,[])-1);
fprintf(fid,'</p>\n');
fprintf(fid,'%s</triangles>\n',o(4));
fprintf(fid,'%s</mesh>\n',o(3));
fprintf(fid,'%s</geometry>\n',o(2));
end
fprintf(fid,'%s</library_geometries>\n',o(1));
% Scene
%--------------------------------------------------------------------------
fprintf(fid,'%s<library_visual_scenes>\n',o(1));
fprintf(fid,'%s<visual_scene id="VisualSceneNode" name="SceneNode">\n',o(2));
for i=1:numel(s)
fprintf(fid,'%s<node id="node%d">\n',o(3),i);
fprintf(fid,'%s<instance_geometry url="#shape%d">\n',o(4),i);
fprintf(fid,'%s<bind_material>\n',o(5));
fprintf(fid,'%s<technique_common>\n',o(6));
fprintf(fid,'%s<instance_material symbol="material%d" target="#material%d"/>\n',o(7),i,i);
fprintf(fid,'%s</technique_common>\n',o(6));
fprintf(fid,'%s</bind_material>\n',o(5));
fprintf(fid,'%s</instance_geometry>\n',o(4));
fprintf(fid,'%s</node>\n',o(3));
end
fprintf(fid,'%s</visual_scene>\n',o(2));
fprintf(fid,'%s</library_visual_scenes>\n',o(1));
fprintf(fid,'%s<scene>\n',o(1));
fprintf(fid,'%s<instance_visual_scene url="#VisualSceneNode" />\n',o(2));
fprintf(fid,'%s</scene>\n',o(1));
% End of XML
%--------------------------------------------------------------------------
fprintf(fid,'</COLLADA>\n');
%==========================================================================
% function fid = save_idtf(fid,this)
%==========================================================================
function fid = save_idtf(fid,this)
o = inline('blanks(x*3)');
s = struct(this);
% Compute normals
%--------------------------------------------------------------------------
if ~isfield(s,'normals')
try
s.normals = spm_mesh_normals(...
struct('vertices',s.vertices,'faces',s.faces),true);
catch
s.normals = [];
end
end
% Split the mesh into connected components
%--------------------------------------------------------------------------
try
C = spm_mesh_label(s.faces);
d = [];
try
if size(s.cdata,2) == 1 && (any(s.cdata>1) || any(s.cdata<0))
mi = min(s.cdata); ma = max(s.cdata);
s.cdata = (s.cdata-mi)/ (ma-mi);
else
end
end
for i=1:numel(unique(C))
d(i).faces = s.faces(C==i,:);
u = unique(d(i).faces);
d(i).vertices = s.vertices(u,:);
d(i).normals = s.normals(u,:);
a = 1:max(d(i).faces(:));
a(u) = 1:size(d(i).vertices,1);
%a = sparse(1,double(u),1:1:size(d(i).vertices,1));
d(i).faces = a(d(i).faces);
d(i).mat = s.mat;
try
d(i).cdata = s.cdata(u,:);
if size(d(i).cdata,2) == 1
d(i).cdata = repmat(d(i).cdata,1,3);
end
end
end
s = d;
end
% FILE_HEADER
%--------------------------------------------------------------------------
fprintf(fid,'FILE_FORMAT "IDTF"\n');
fprintf(fid,'FORMAT_VERSION 100\n\n');
% NODES
%--------------------------------------------------------------------------
for i=1:numel(s)
fprintf(fid,'NODE "MODEL" {\n');
fprintf(fid,'%sNODE_NAME "%s"\n',o(1),sprintf('Mesh%04d',i));
fprintf(fid,'%sPARENT_LIST {\n',o(1));
fprintf(fid,'%sPARENT_COUNT %d\n',o(2),1);
fprintf(fid,'%sPARENT %d {\n',o(2),0);
fprintf(fid,'%sPARENT_NAME "%s"\n',o(3),'<NULL>');
fprintf(fid,'%sPARENT_TM {\n',o(3));
I = s(i).mat; % eye(4);
for j=1:size(I,2)
fprintf(fid,'%s',o(4)); fprintf(fid,'%f ',I(:,j)'); fprintf(fid,'\n');
end
fprintf(fid,'%s}\n',o(3));
fprintf(fid,'%s}\n',o(2));
fprintf(fid,'%s}\n',o(1));
fprintf(fid,'%sRESOURCE_NAME "%s"\n',o(1),sprintf('Mesh%04d',i));
%fprintf(fid,'%sMODEL_VISIBILITY "BOTH"\n',o(1));
fprintf(fid,'}\n\n');
end
% NODE_RESOURCES
%--------------------------------------------------------------------------
for i=1:numel(s)
fprintf(fid,'RESOURCE_LIST "MODEL" {\n');
fprintf(fid,'%sRESOURCE_COUNT %d\n',o(1),1);
fprintf(fid,'%sRESOURCE %d {\n',o(1),0);
fprintf(fid,'%sRESOURCE_NAME "%s"\n',o(2),sprintf('Mesh%04d',i));
fprintf(fid,'%sMODEL_TYPE "MESH"\n',o(2));
fprintf(fid,'%sMESH {\n',o(2));
fprintf(fid,'%sFACE_COUNT %d\n',o(3),size(s(i).faces,1));
fprintf(fid,'%sMODEL_POSITION_COUNT %d\n',o(3),size(s(i).vertices,1));
fprintf(fid,'%sMODEL_NORMAL_COUNT %d\n',o(3),size(s(i).normals,1));
if ~isfield(s(i),'cdata') || isempty(s(i).cdata)
c = 0;
else
c = size(s(i).cdata,1);
end
fprintf(fid,'%sMODEL_DIFFUSE_COLOR_COUNT %d\n',o(3),c);
fprintf(fid,'%sMODEL_SPECULAR_COLOR_COUNT %d\n',o(3),0);
fprintf(fid,'%sMODEL_TEXTURE_COORD_COUNT %d\n',o(3),0);
fprintf(fid,'%sMODEL_BONE_COUNT %d\n',o(3),0);
fprintf(fid,'%sMODEL_SHADING_COUNT %d\n',o(3),1);
fprintf(fid,'%sMODEL_SHADING_DESCRIPTION_LIST {\n',o(3));
fprintf(fid,'%sSHADING_DESCRIPTION %d {\n',o(4),0);
fprintf(fid,'%sTEXTURE_LAYER_COUNT %d\n',o(5),0);
fprintf(fid,'%sSHADER_ID %d\n',o(5),0);
fprintf(fid,'%s}\n',o(4));
fprintf(fid,'%s}\n',o(3));
fprintf(fid,'%sMESH_FACE_POSITION_LIST {\n',o(3));
fprintf(fid,'%d %d %d\n',s(i).faces'-1);
fprintf(fid,'%s}\n',o(3));
fprintf(fid,'%sMESH_FACE_NORMAL_LIST {\n',o(3));
fprintf(fid,'%d %d %d\n',s(i).faces'-1);
fprintf(fid,'%s}\n',o(3));
fprintf(fid,'%sMESH_FACE_SHADING_LIST {\n',o(3));
fprintf(fid,'%d\n',zeros(size(s(i).faces,1),1));
fprintf(fid,'%s}\n',o(3));
if c
fprintf(fid,'%sMESH_FACE_DIFFUSE_COLOR_LIST {\n',o(3));
fprintf(fid,'%d %d %d\n',s(i).faces'-1);
fprintf(fid,'%s}\n',o(3));
end
fprintf(fid,'%sMODEL_POSITION_LIST {\n',o(3));
fprintf(fid,'%f %f %f\n',s(i).vertices');
fprintf(fid,'%s}\n',o(3));
fprintf(fid,'%sMODEL_NORMAL_LIST {\n',o(3));
fprintf(fid,'%f %f %f\n',s(i).normals');
fprintf(fid,'%s}\n',o(3));
if c
fprintf(fid,'%sMODEL_DIFFUSE_COLOR_LIST {\n',o(3));
fprintf(fid,'%f %f %f\n',s(i).cdata');
fprintf(fid,'%s}\n',o(3));
end
fprintf(fid,'%s}\n',o(2));
fprintf(fid,'%s}\n',o(1));
fprintf(fid,'}\n');
end
|
github
|
lcnbeapp/beapp-master
|
gifti.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@gifti/gifti.m
| 3,728 |
utf_8
|
37f5d9e67cb8f5e79f2ac46e1486ffd0
|
function this = gifti(varargin)
% GIfTI Geometry file format class
% Geometry format under the Neuroimaging Informatics Technology Initiative
% (NIfTI):
% http://www.nitrc.org/projects/gifti/
% http://nifti.nimh.nih.gov/
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id$
switch nargin
case 0
this = giftistruct;
this = class(this,'gifti');
case 1
if isa(varargin{1},'gifti')
this = varargin{1};
elseif isstruct(varargin{1})
f = {'faces', 'face', 'tri' 'vertices', 'vert', 'pnt', 'cdata'};
ff = {'faces', 'faces', 'faces', 'vertices', 'vertices', 'vertices', 'cdata'};
[c, ia] = intersect(f,fieldnames(varargin{1}));
if ~isempty(c)
this = gifti;
for i=1:length(c)
this = subsasgn(this,...
struct('type','.','subs',ff{ia(i)}),...
varargin{1}.(c{i}));
end
elseif isempty(setxor(fieldnames(varargin{1}),...
{'metadata','label','data'}))
this = class(varargin{1},'gifti');
else
error('[GIFTI] Invalid structure.');
end
elseif ishandle(varargin{1})
this = struct('vertices',get(varargin{1},'Vertices'), ...
'faces', get(varargin{1},'Faces'));
if ~isempty(get(varargin{1},'FaceVertexCData'));
this.cdata = get(varargin{1},'FaceVertexCData');
end
this = gifti(this);
elseif isnumeric(varargin{1})
this = gifti;
this = subsasgn(this,...
struct('type','.','subs','cdata'),...
varargin{1});
elseif ischar(varargin{1})
if size(varargin{1},1)>1
this = gifti(cellstr(varargin{1}));
return;
end
[p,n,e] = fileparts(varargin{1});
if strcmpi(e,'.mat')
try
this = gifti(load(varargin{1}));
catch
error('[GIFTI] Loading of file %s failed.', varargin{1});
end
elseif strcmpi(e,'.asc') || strcmpi(e,'.srf')
this = read_freesurfer_file(varargin{1});
this = gifti(this);
else
this = read_gifti_file(varargin{1},giftistruct);
this = class(this,'gifti');
end
elseif iscellstr(varargin{1})
fnames = varargin{1};
this(numel(fnames)) = giftistruct;
this = class(this,'gifti');
for i=1:numel(fnames)
this(i) = gifti(fnames{i});
end
else
error('[GIFTI] Invalid object construction.');
end
otherwise
error('[GIFTI] Invalid object construction.');
end
%==========================================================================
function s = giftistruct
s = struct(...
'metadata', ...
struct(...
'name', {}, ...
'value', {} ...
), ...
'label', ...
struct(...
'name', {}, ...
'index', {} ...
), ...
'data', ...
struct(...
'attributes', {}, ...
'metadata', struct('name',{}, 'value',{}), ...
'space', {}, ...
'data', {} ...
) ...
);
|
github
|
lcnbeapp/beapp-master
|
read_gifti_file.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@gifti/private/read_gifti_file.m
| 6,604 |
utf_8
|
3e691fdd0839d8cfad3929e4e181a5c1
|
function this = read_gifti_file(filename, this)
% Low level reader of GIfTI 1.0 files
% FORMAT this = read_gifti_file(filename, this)
% filename - XML GIfTI filename
% this - structure with fields 'metaData', 'label' and 'data'.
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id$
% Import XML-based GIfTI file
%--------------------------------------------------------------------------
try
t = xmltree(filename);
catch
error('[GIFTI] Loading of XML file %s failed.', filename);
end
% Root element of a GIFTI file
%--------------------------------------------------------------------------
if ~strcmp(get(t,root(t),'name'),'GIFTI')
error('[GIFTI] %s is not a GIFTI 1.0 file.', filename);
end
attr = cell2mat(attributes(t,'get',root(t)));
attr = cell2struct({attr.val},strrep({attr.key},':','___'),2);
if ~all(ismember({'Version','NumberOfDataArrays'},fieldnames(attr)))
error('[GIFTI] Missing mandatory attributes for GIFTI root element.');
end
if str2double(attr.Version) ~= 1
warning('[GIFTI] Unknown specification version of GIFTI file (%s).',attr.Version);
end
nbData = str2double(attr.NumberOfDataArrays);
% Read children elements
%--------------------------------------------------------------------------
uid = children(t,root(t));
for i=1:length(uid)
switch get(t,uid(i),'name')
case 'MetaData'
this.metadata = gifti_MetaData(t,uid(i));
case 'LabelTable'
this.label = gifti_LabelTable(t,uid(i));
case 'DataArray'
this.data{end+1} = gifti_DataArray(t,uid(i),filename);
otherwise
warning('[GIFTI] Unknown element "%s": ignored.',get(t,uid(i),'name'));
end
end
if nbData ~= length(this.data)
warning('[GIFTI] Mismatch between expected and effective number of datasets.');
end
%==========================================================================
function s = gifti_MetaData(t,uid)
s = struct('name',{}, 'value',{});
c = children(t,uid);
for i=1:length(c)
for j=children(t,c(i))
s(i).(lower(get(t,j,'name'))) = get(t,children(t,j),'value');
end
end
%==========================================================================
function s = gifti_LabelTable(t,uid)
s = struct('name',{}, 'key',[], 'rgba',[]);
c = children(t,uid);
for i=1:length(c)
a = attributes(t,'get',c(i));
s(1).rgba(i,1:4) = NaN;
for j=1:numel(a)
switch lower(a{j}.key)
case {'key','index'}
s(1).key(i) = str2double(a{j}.val);
case 'red'
s(1).rgba(i,1) = str2double(a{j}.val);
case 'green'
s(1).rgba(i,2) = str2double(a{j}.val);
case 'blue'
s(1).rgba(i,3) = str2double(a{j}.val);
case 'alpha'
s(1).rgba(i,4) = str2double(a{j}.val);
otherwise
end
end
s(1).name{i} = get(t,children(t,c(i)),'value');
end
%==========================================================================
function s = gifti_DataArray(t,uid,filename)
s = struct(...
'attributes', {}, ...
'data', {}, ...
'metadata', struct([]), ...
'space', {} ...
);
attr = cell2mat(attributes(t,'get',uid));
s(1).attributes = cell2struct({attr.val},{attr.key},2);
s(1).attributes.Dim = [];
for i=1:str2double(s(1).attributes.Dimensionality)
f = sprintf('Dim%d',i-1);
s(1).attributes.Dim(i) = str2double(s(1).attributes.(f));
s(1).attributes = rmfield(s(1).attributes,f);
end
s(1).attributes = rmfield(s(1).attributes,'Dimensionality');
if isfield(s(1).attributes,'ExternalFileName') && ...
~isempty(s(1).attributes.ExternalFileName)
s(1).attributes.ExternalFileName = fullfile(fileparts(filename),...
s(1).attributes.ExternalFileName);
end
c = children(t,uid);
for i=1:length(c)
switch get(t,c(i),'name')
case 'MetaData'
s(1).metadata = gifti_MetaData(t,c(i));
case 'CoordinateSystemTransformMatrix'
s(1).space(end+1) = gifti_Space(t,c(i));
case 'Data'
s(1).data = gifti_Data(t,c(i),s(1).attributes);
otherwise
error('[GIFTI] Unknown DataArray element "%s".',get(t,c(i),'name'));
end
end
%==========================================================================
function s = gifti_Space(t,uid)
s = struct('DataSpace','', 'TransformedSpace','', 'MatrixData',[]);
for i=children(t,uid)
s.(get(t,i,'name')) = get(t,children(t,i),'value');
end
s.MatrixData = reshape(str2num(s.MatrixData),4,4)';
%==========================================================================
function d = gifti_Data(t,uid,s)
tp = getdict;
try
tp = tp.(s.DataType);
catch
error('[GIFTI] Unknown DataType.');
end
[unused,unused,mach] = fopen(1);
sb = @(x) x;
try
if (strcmp(s.Endian,'LittleEndian') && ~isempty(strmatch('ieee-be',mach))) ...
|| (strcmp(s.Endian,'BigEndian') && ~isempty(strmatch('ieee-le',mach)))
sb = @swapbyte;
end
catch
% Byte Order can be absent if encoding is ASCII, assume native otherwise
end
switch s.Encoding
case 'ASCII'
d = sscanf(get(t,children(t,uid),'value'),tp.format);
case 'Base64Binary'
d = typecast(sb(base64decode(get(t,children(t,uid),'value'))), tp.cast);
case 'GZipBase64Binary'
d = typecast(dunzip(sb(base64decode(get(t,children(t,uid),'value')))), tp.cast);
case 'ExternalFileBinary'
[p,f,e] = fileparts(s.ExternalFileName);
if isempty(p)
s.ExternalFileName = fullfile(pwd,[f e]);
end
if false
fid = fopen(s.ExternalFileName,'r');
if fid == -1
error('[GIFTI] Unable to read binary file %s.',s.ExternalFileName);
end
fseek(fid,str2double(s.ExternalFileOffset),0);
d = sb(fread(fid,prod(s.Dim),['*' tp.class]));
fclose(fid);
else
d = file_array(s.ExternalFileName, s.Dim, tp.class, ...
str2double(s.ExternalFileOffset),1,0,'rw');
end
otherwise
error('[GIFTI] Unknown data encoding: %s.',s.Encoding);
end
if length(s.Dim) == 1, s.Dim(end+1) = 1; end
switch s.ArrayIndexingOrder
case 'RowMajorOrder'
d = permute(reshape(d,fliplr(s.Dim)),length(s.Dim):-1:1);
case 'ColumnMajorOrder'
d = reshape(d,s.Dim);
otherwise
error('[GIFTI] Unknown array indexing order.');
end
|
github
|
lcnbeapp/beapp-master
|
isintent.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/gifti/@gifti/private/isintent.m
| 2,477 |
utf_8
|
611bd4b3bf09d89f88da3652cc8e6320
|
function [a, b] = isintent(this,intent)
% Correspondance between fieldnames and NIfTI intent codes
% FORMAT ind = isintent(this,intent)
% this - GIfTI object
% intent - fieldnames
% a - indices of found intent(s)
% b - indices of dataarrays of found intent(s)
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id$
a = [];
b = [];
if ischar(intent), intent = cellstr(intent); end
for i=1:length(this(1).data)
switch this(1).data{i}.attributes.Intent(14:end)
case 'POINTSET'
[tf, loc] = ismember('vertices',intent);
if tf
a(end+1) = loc;
b(end+1) = i;
end
[tf, loc] = ismember('mat',intent);
if tf
a(end+1) = loc;
b(end+1) = i;
end
case 'TRIANGLE'
[tf, loc] = ismember('faces',intent);
if tf
a(end+1) = loc;
b(end+1) = i;
end
case 'VECTOR'
[tf, loc] = ismember('normals',intent);
if tf
a(end+1) = loc;
b(end+1) = i;
end
case cdata
[tf, loc] = ismember('cdata',intent);
if tf
a(end+1) = loc;
b(end+1) = i;
end
if strcmp(this(1).data{i}.attributes.Intent(14:end),'LABEL')
[tf, loc] = ismember('labels',intent);
if tf
a(end+1) = loc;
b(end+1) = i;
end
end
otherwise
fprintf('Intent %s is ignored.\n',this.data{i}.attributes.Intent);
end
end
%[d,i] = unique(a);
%if length(d) < length(a)
% warning('Several fields match intent type. Using first.');
% a = a(i);
% b = b(i);
%end
function c = cdata
c = {
'NONE'
'CORREL'
'TTEST'
'FTEST'
'ZSCORE'
'CHISQ'
'BETA'
'BINOM'
'GAMMA'
'POISSON'
'NORMAL'
'FTEST_NONC'
'CHISQ_NONC'
'LOGISTIC'
'LAPLACE'
'UNIFORM'
'TTEST_NONC'
'WEIBULL'
'CHI'
'INVGAUSS'
'EXTVAL'
'PVAL'
'LOGPVAL'
'LOG10PVAL'
'ESTIMATE'
'LABEL'
'NEURONAMES'
'GENMATRIX'
'SYMMATRIX'
'DISPVECT'
'QUATERNION'
'DIMLESS'
'TIME_SERIES'
'RGB_VECTOR'
'RGBA_VECTOR'
'NODE_INDEX'
'SHAPE'
'CONNECTIVITY_DENSE'
'CONNECTIVITY_DENSE_TIME'
'CONNECTIVITY_PARCELLATED'
'CONNECTIVITY_PARCELLATED_TIME'
'CONNECTIVITY_CONNECTIVITY_TRAJECTORY'
};
|
github
|
lcnbeapp/beapp-master
|
sb_rhs_venant.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/simbio/sb_rhs_venant.m
| 1,317 |
utf_8
|
2a6743d0e11f6cd5ca8bc3f2a5bab884
|
function rhs = sb_rhs_venant(pos,dir,vol);
% SB_RHS_VENANT
%
% $Id$
%find node closest to source position
next_nd = sb_get_next_nd(pos,vol.pos);
%find nodes neighbouring closest node
if isfield(vol,'tet')
ven_nd = sb_get_ven_nd(next_nd,vol.tet);
elseif isfield(vol,'hex')
ven_nd = sb_get_ven_nd(next_nd,vol.hex);
else
error('No connectivity information given!');
end
%calculate rhs matrix
loads = sb_calc_ven_loads(pos,dir,ven_nd,vol.pos);
%assign values in sparse matrix
i = reshape(ven_nd',[],1);
j = reshape(repmat([1:size(ven_nd,1)],size(ven_nd,2),1),[],1);
loads = reshape(loads',[],1);
j = j(i~=0);
loads = loads(i~=0);
i = i(i~=0);
rhs = sparse(i,j,loads,size(vol.pos,1),size(pos,1));
end
function next_nd = sb_get_next_nd(pos,node);
next_nd = zeros(size(pos,1),1);
for i=1:size(pos,1)
[dist, next_nd(i)] = min(sum(bsxfun(@minus,node,pos(i,:)).^2,2));
end
end
function ven_nd = sb_get_ven_nd(next_nd,elem);
ven_nd = zeros(size(next_nd,1),1);
for i=1:size(next_nd,1)
[tmp1,tmp2] = find(elem == next_nd(i));
tmp = unique(elem(tmp1,:));
%tmp = tmp(tmp~=next_nd(i)); seems like this is not done in the
%original.
if(length(tmp) > size(ven_nd,2))
ven_nd = [ven_nd, zeros(size(ven_nd,1),length(tmp)-size(ven_nd,2))];
end
ven_nd(i,1:length(tmp)) = tmp;
end
end
|
github
|
lcnbeapp/beapp-master
|
netcdf.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/netcdf/netcdf.m
| 5,097 |
utf_8
|
3cc73e65d1ed73e0a6836af118228033
|
function S = netcdf(File,varargin)
% Function to read NetCDF files
% S = netcdf(File)
% Input Arguments
% File = NetCDF file to read
% Optional Input Arguments:
% 'Var',Var - Read data for VarArray(Var), default [1:length(S.VarArray)]
% 'Rec',Rec - Read data for Record(Rec), default [1:S.NumRecs]
% Output Arguments:
% S = Structure of NetCDF data organised as per NetCDF definition
% Notes:
% Only version 1, classic 32bit, NetCDF files are supported. By default
% data are extracted into the S.VarArray().Data field for all variables.
% To read the header only call S = netcdf(File,'Var',[]);
%
% SEE ALSO
% ---------------------------------------------------------------------------
S = [];
try
if exist(File,'file') fp = fopen(File,'r','b');
else fp = []; error('File not found'); end
if fp == -1 error('Unable to open file'); end
% Read header
Magic = fread(fp,4,'uint8=>char');
if strcmp(Magic(1:3),'CDF') error('Not a NetCDF file'); end
if uint8(Magic(4))~=1 error('Version not supported'); end
S.NumRecs = fread(fp,1,'uint32=>uint32');
S.DimArray = DimArray(fp);
S.AttArray = AttArray(fp);
S.VarArray = VarArray(fp);
% Setup indexing to arrays and records
Var = ones(1,length(S.VarArray));
Rec = ones(1,S.NumRecs);
for i = 1:2:length(varargin)
if strcmp(upper(varargin{i}),'VAR') Var=Var*0; Var(varargin{i+1})=1;
elseif strcmp(upper(varargin{i}),'REC') Rec=Rec*0; Rec(varargin{i+1})=1;
else error('Optional input argument not recognised'); end
end
if sum(Var)==0 fclose(fp); return; end
% Read non-record variables
Dim = double(cat(2,S.DimArray.Dim));
ID = double(cat(2,S.VarArray.Type));
for i = 1:length(S.VarArray)
D = Dim(S.VarArray(i).DimID+1); N = prod(D); RecID{i}=find(D==0);
if isempty(RecID{i})
if length(D)==0 D = [1,1]; N = 1; elseif length(D)==1 D=[D,1]; end
if Var(i)
S.VarArray(i).Data = ReOrder(fread(fp,N,[Type(ID(i)),'=>',Type(ID(i))]),D);
fread(fp,(Pad(N,ID(i))-N)*Size(ID(i)),'uint8=>uint8');
else fseek(fp,Pad(N,ID(i))*Size(ID(i)),'cof'); end
else S.VarArray(i).Data = []; end
end
% Read record variables
for k = 1:S.NumRecs
for i = 1:length(S.VarArray)
if ~isempty(RecID{i})
D = Dim(S.VarArray(i).DimID+1); D(RecID{i}) = 1; N = prod(D);
if length(D)==1 D=[D,1]; end
if Var(i) & Rec(k)
S.VarArray(i).Data = cat(RecID{i},S.VarArray(i).Data,...
ReOrder(fread(fp,N,[Type(ID(i)),'=>',Type(ID(i))]),D));
if N > 1 fread(fp,(Pad(N,ID(i))-N)*Size(ID(i)),'uint8=>uint8'); end
else fseek(fp,Pad(N,ID(i))*Size(ID(i)),'cof'); end
end
end
end
fclose(fp);
catch
Err = lasterror; fprintf('%s\n',Err.message);
if ~isempty(fp) && fp ~= -1 fclose(fp); end
end
% ---------------------------------------------------------------------------------------
% Utility functions
function S = Size(ID)
% Size of NetCDF data type, ID, in bytes
S = subsref([1,1,2,4,4,8],struct('type','()','subs',{{ID}}));
function T = Type(ID)
% Matlab string for CDF data type, ID
T = subsref({'int8','char','int16','int32','single','double'},...
struct('type','{}','subs',{{ID}}));
function N = Pad(Num,ID)
% Number of elements to read after padding to 4 bytes for type ID
N = (double(Num) + mod(4-double(Num)*Size(ID),4)/Size(ID)).*(Num~=0);
function S = String(fp)
% Read a CDF string; Size,[String,[Padding]]
S = fread(fp,Pad(fread(fp,1,'uint32=>uint32'),1),'uint8=>char').';
function A = ReOrder(A,S)
% Rearrange CDF array A to size S with matlab ordering
A = permute(reshape(A,fliplr(S)),fliplr(1:length(S)));
function S = DimArray(fp)
% Read DimArray into structure
if fread(fp,1,'uint32=>uint32') == 10 % NC_DIMENSION
for i = 1:fread(fp,1,'uint32=>uint32')
S(i).Str = String(fp);
S(i).Dim = fread(fp,1,'uint32=>uint32');
end
else fread(fp,1,'uint32=>uint32'); S = []; end
function S = AttArray(fp)
% Read AttArray into structure
if fread(fp,1,'uint32=>uint32') == 12 % NC_ATTRIBUTE
for i = 1:fread(fp,1,'uint32=>uint32')
S(i).Str = String(fp);
ID = fread(fp,1,'uint32=>uint32');
Num = fread(fp,1,'uint32=>uint32');
S(i).Val = fread(fp,Pad(Num,ID),[Type(ID),'=>',Type(ID)]).';
end
else fread(fp,1,'uint32=>uint32'); S = []; end
function S = VarArray(fp)
% Read VarArray into structure
if fread(fp,1,'uint32=>uint32') == 11 % NC_VARIABLE
for i = 1:fread(fp,1,'uint32=>uint32')
S(i).Str = String(fp);
Num = double(fread(fp,1,'uint32=>uint32'));
S(i).DimID = double(fread(fp,Num,'uint32=>uint32'));
S(i).AttArray = AttArray(fp);
S(i).Type = fread(fp,1,'uint32=>uint32');
S(i).VSize = fread(fp,1,'uint32=>uint32');
S(i).Begin = fread(fp,1,'uint32=>uint32'); % Classic 32 bit format only
end
else fread(fp,1,'uint32=>uint32'); S = []; end
|
github
|
lcnbeapp/beapp-master
|
writeCPersist.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/ctf/writeCPersist.m
| 5,086 |
utf_8
|
0c56dc571aa56100f050678e5fe815ff
|
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%% Function writeCPersist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function writeCPersist(filename,Tag)
% Version 1.2 24 April 2007. Removed terminating null characters from charatcer strings
% types 10,11)
% Version 1.1 13 April 2007
% Write a CTF CPersist file. See document CTF MEG File Format, PN900-0066
% Inputs : filename : Name of the output file name including path
% Tag: Structure array containing all of the tags, types, and data.
% 31 Aug 2006: Recognizes type=1,...,17. If other data types are specified,
% writeCPersist will print an error message.
% Delete existing file so the new file has the correct creation data/time.
if nargin==0
fprintf(['writeCPersist: Version 1.2 24 April 2007 Writes a CTF CPersist file.\n'...
'\twriteCPersist(filename,Tag) writes a CPersist file from the contents of\n',...
'\tstructure array Tag. Tag is in the format prepared by readCPersist.\n\n']);
Tag=[];
return
end
if exist(filename)==2
delete(filename);
end
startString='WS1_';
EOFstring='EndOfParameters';
startVal=256.^[3:-1:0]*double(startString)'; % Integer version of startString
fid=fopen(filename,'w','ieee-be');
EOFcount=0; % Make sure that the startString's and EOFstring's balance
count=0;
while count<length(Tag)
count=count+1;
if strcmp(Tag(count).name,startString) % start of Cpersist object
fwrite(fid,startVal,'int32');
EOFcount=EOFcount-1;
continue
end
fwrite(fid,length(Tag(count).name),'int32'); % end of CPersist object
fwrite(fid,Tag(count).name,'char');
if strcmp(Tag(count).name,EOFstring);
EOFcount=EOFcount+1;
continue;
end
fwrite(fid,Tag(count).type,'int32');
if Tag(count).type==1
fwrite(fid,Tag(count).data,'int32');
elseif Tag(count).type==2 % Start embedded CPersist object
elseif Tag(count).type==3 % binary list
fwrite(fid,2*length(Tag(count).data),'int32');
fwrite(fid,Tag(count).data,'int16');
elseif Tag(count).type==4 % double
fwrite(fid,Tag(count).data,'float64');
elseif Tag(count).type==5 % integer
fwrite(fid,Tag(count).data,'int32');
elseif Tag(count).type==6 % short integer
fwrite(fid,Tag(count).data,'int16');
elseif Tag(count).type==7 % unsigned short integer
fwrite(fid,Tag(count).data,'uint16');
elseif Tag(count).type==8 % Boolean byte
fwrite(fid,Tag(count).data,'uint8');
elseif Tag(count).type==9; % CStr32
nChar=min(32,length(Tag(count).data));
fwrite(fid,[double(Tag(count).data(1:nChar)) zeros(1,32-nChar)],'uint8');
elseif Tag(count).type==10; % CString
fwrite(fid,length(Tag(count).data),'int32');
fwrite(fid,double(Tag(count).data),'uint8');
elseif Tag(count).type==11; % Cstring list.
nList=size(Tag(count).data,1);
fwrite(fid,nList,'int32');
for k=1:nList
% Do not force termination of strings with nulls (char(0))
Cstring=[deblank(Tag(count).data(k,:))];
fwrite(fid,length(Cstring),'int32');
fwrite(fid,double(Cstring),'uint8');
end
clear k CString nList;
elseif Tag(count).type==12; % CStr32 list.
nList=size(Tag(count).data,1); %size(data)=[nList 32]
fwrite(fid,nList,'int32');
% Do not force termination of strings with nulls (char(0))
for k=1:nList
strng=deblank(Tag(count).data(k,:));
nChar=min(32,length(strng));
Tag(count).data(k,:)=[strng(1:nChar) char(zeros(1,32-nChar))];
end
fwrite(fid,double(Tag(count).data)','uint8');
clear k strng nChar nList;
elseif Tag(count).type==13; % SensorClass list.
fwrite(fid,length(Tag(count).data),'int32');
fwrite(fid,Tag(count).data,'int32')
elseif Tag(count).type==14 % long integer
fwrite(fid,Tag(count).data,'int32');
elseif Tag(count).type==15 % unsigned longinteger
fwrite(fid,Tag(count).data,'uint32');
elseif Tag(count).type==16 % unsigned integer
fwrite(fid,Tag(count).data,'uint32');
elseif Tag(count).type==17 % Boolean
if ~any(Tag(count).data==[0 1])
fprintf('writeCPersist: tagname=%s type=%d value=%d? (Must =0 or 1)\n',...
tagname,type,Tag(count).data);
Tag(count).data=(Tag(count).data~=0);
fprintf(' Set value=%d.\n',Tag(count).data);
end
fwrite(fid,Tag(count).data,'int32');
else
fprintf('writeCPersist: Tag(%d) name=%s type=%d\n',count,Tag(count).name,Tag(count).type);
fprintf('\t\t UNRECOGNIZED type.\n');
fclose(fid);
break;
end
end % Loop over tags
fclose(fid);
% EOF_count should be zero at the end of the file
if EOFcount~=0;
fprintf('write_CPerist: EOFcount=%d Stop strings do not balance start strings.\n',...
EOFcount);
fprintf(' Start string=%s Stop string=%s\n',startString,EOFstring);
end
return
%%%%%%%% End of writeCPersist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
github
|
lcnbeapp/beapp-master
|
getCTFBalanceCoefs.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/ctf/getCTFBalanceCoefs.m
| 20,490 |
utf_8
|
2c434fcbdb53fbc50ee3fbda72e98883
|
function [alphaMEG,MEGindex,MEGbalanceindex,alphaGref,Grefindex,Gbalanceindex]=...
getCTFBalanceCoefs(ds,balanceType,unit);
% Reads balance coefficients for SQUID data in phi0's, and converts to coefficients
% for data in physical units.
% Input : ds : (1) ds structure from readCTFds
% balanceType : 'NONE' : No balancing
% 'G1BR' : 1st order balancing
% 'G2BR' : 2nd order balancing
% 'G3BR' : 3rd order balancing
% 'G3AR' : 3rd order balancing + adaptive
% If only MEG balance table is requested, size(balanceType)=[1 5]
% If Gref balance table is requested also, size(balanceType)=[2 4]
% unit: Type of units. Option: 'fT','T','phi0','int'.
% If unit is not entered, of unit=[], the default is unit='fT'.
% Outputs :
% alphaMEG,MEGindex,MEGbalanceindex : MEG balancing coefficients for data in fT or T.
% Suppose data array returned by getTrial2 has size(data)=[npt nchan].
% nMEG = number of MEG channels in the data set.
% MEG channels have sensorTypeIndex==5.
%
% MEGindex = list of MEG channels referred to the channel numbering in
% the complete dataset (i.e. it is not referred to only the list of
% SQUID sensors).
% by looking for sensors with ds.res4.senres.sensorTypeIndex==5
% size(MEGindex)=[1 nMEG]
% MEG data = data(:,MEGindex)
% MEGbalanceindex = list of reference channels for MEG balancing.
% size(MEGbalanceindex)=[1 nRef]
% Reference data for MEG balancing = data(:,MEGbalanceindex)
% alphaMEG = balance coefficients. size(alphaMEG)=[nRef nMEG]
%
% Balancing MEG data :
% - Start with data AFTER converting to physical units.
% (I.e. SQUID data must be in fT or T.)
% - balanced_data(:,MEGindex)=data(:,MEGindex)-data(:,MEGbalanceindex)*alphaMEG
% If user specifies balanceType=[], ' ' or 'none', then getCTFBalanceCoefs returns
% alphaMEG=zeros(0,nMEG), MEGindex=list of MEG sensor channels,
% MEGbalanceindex=[], alphaGref=zeros(0,nGef), Grefindex=list of Gref channels
% and Gbalanceindex=[];
% alphaGref,Grefindex,Gbalanceindex : Reference-gradiometer balancing coeficients.
% These output arrays are optional. If the calling statement includes
% them, then this program extracts a table of balance coefficients for
% the reference gradiometers from the G1BR table in the coefficient files.
% nGref = no. of reference gradiometers channels in the data set
% (sensorTypeIndex=1)
% Grefindex = list of reference channels. size(Grefindex)=[1 nGref]
% Gradient reference data = data(:,Grefindex)
% Gbalanceindex = list of channels for balancing reference
% gradiometers. size(Gbalanceindex)=[1 nGbalcoef]
% Balancing reference data = data(:,Gbalanceindex)
% alphaGref = balance coefficients for ref. grads.
% size(alphaGref)=[nGbalcoef nGref]
%
% Balancing ref. gradiometer data :
% - Use data AFTER converting to physical units. (I.e. data in fT or T.)
% balanced_data(:,Grefindex)=data(:,Grefindex)-data(:,Gbalanceindex)*alphaGref
% Calls function getRawCTFBalanceCoefs (included in this listing).
if nargout==0 & nargin==0
fprintf(['\ngetCTFBalanceCoefs: Version 1.1 17 April 2007 ',...
'Reads balance coefficients from ds.res4.scrr.\n\n',...
'\tMEG balancing : [alphaMEG,MEGindex,MEGbalanceindex]=',...
'getCTFBalanceCoefs(ds,balanceType,unit);\n\n',...
'\tMEG & Gref balancing : [alphaMEG,MEGindex,MEGbalanceindex,',...
'alphaGref,Grefindex,Gbalanceindex]=\n',...
'\t ',...
'getCTFBalanceCoefs(ds,balanceType,unit);\n\n']);
return
end
balanceOptions=strvcat('NONE','G1BR','G2BR','G3BR', 'G3AR');
balanceOptionsEnds = [size(balanceOptions, 1), 2]; % Which options are available for MEGs and Grefs.
physical_options=strvcat('fT','T');
raw_options=strvcat('phi0','int');
unit_options=strvcat(physical_options,raw_options);
default_unit='fT';
% Specify outputs in case of an early return due to an error.
MEGindex=[];
Grefindex=[];
alphaMEG=[];
MEGbalanceindex=[];
alphaGref=[];
Gbalanceindex=[];
% Check that the inputs are sensible.
if nargin<2
fprintf(['\ngetCTFBalanceCoefs: Only %d input arguments? ',...
'Must specify at least ds and balanceType.\n\n'],nargin);
return
elseif ~isstruct(ds) | isempty(ds) | ~ischar(balanceType) | isempty(balanceType)
fprintf('\ngetCTFBalanceCoefs: Wrong argument types or sizes.\n\n');
whos ds balanceType
return
elseif ~isfield(ds,'res4')
fprintf('\ngetCTFBalanceCoefs: Field res4 is missing from structure ds.\n\n');
ds
return
elseif size(balanceType,1)>2
fprintf('\ngetCTFBalanceCoefs: size(balanceType)=[');fprintf(' %d',size(balanceType));...
fprintf('] Must be[1 4] or [2 4].\n\n');
return
end
% Must have 3 or 6 output arguments. Set balanceType(2,:)='NONE' if necessary.
if ~any(nargout==[3 6]);
fprintf(['\ngetCTFBalanceCoefs: Called with %d output arguments. ',...
'Must be 3 or 6.\n\n'],nargout);
return
elseif (nargout==3 & size(balanceType,1)>1) | (nargout==6 & size(balanceType,1)==1)
balanceType=strvcat(deblank(balanceType(1,:)),'NONE');
end
% At this point, size(balanceType,1)=2.
% Check that balanceType has allowed values
for k=1:size(balanceType,1) % k=1:MEGs, k=2:Grefs
if isempty(strmatch(balanceType(k,:),balanceOptions(1:balanceOptionsEnds(k),:)))
fprintf('\ngetCTFBalanceCoefs: balanceType(%d,:)=%s Not an allowed option.\n\n',...
k,balanceType(k,:));
return
end
end
% Check the data units, convert to lower case and flag incorrect unit specification
if ~exist('unit');
unit=default_unit;
elseif isempty(unit);
unit=default_unit;
elseif ~ischar(unit)
fprintf('\ngetCTFBalanceCoefs: Input unit has the wrong type: class(unit)=%s\n\n',...
class(unit));
return
end
unit=lower(unit);
if isempty(strmatch(unit,lower(strvcat(physical_options,raw_options))))
fprintf('\ngetCTFBalanceCoefs: unit=%s. Must be one of ',unit);
for k=1:size(unit_options,1);fprintf(' %s,',deblank(unit_options(k,:)));end;
fprintf('\n\n');
return
end
physical=~isempty(strmatch(unit,lower(physical_options)));
balanceType=upper(deblank(balanceType));
[betaMEG,MEGindex,MEGbalanceindex,betaGref,Grefindex,Gbalanceindex]=...
getRawCTFBalanceCoefs(ds,balanceType);
% No balancing is requested, just return lists of MEGindex and Grefindex.
if isempty(MEGbalanceindex)
alphaMEG=zeros(0,length(MEGindex));
MEGbalanceindex=[]; % force size=[0 0]
end
if isempty(Gbalanceindex)
alphaGref=zeros(0,length(Grefindex));
Gbalanceindex=[]; % force size=[0 0]
end
if isempty(MEGbalanceindex) & isempty(Gbalanceindex)
return
end
% betaMEG and betaGref are the balance coefficients when signals are in phi0's.
% Convert to balance coefficients when signals are in physical units (T or fT).
% invproperGain is introduced to take care of situations where bad channels
% are labelled by setting their gain to zero.
if physical
properGain=zeros(1,ds.res4.no_channels);
invproperGain=zeros(1,ds.res4.no_channels);
for k=1:ds.res4.no_channels
if any(ds.res4.senres(k).sensorTypeIndex==[0 1 5:7]) % SQUIDs only
properGain(k)=ds.res4.senres(k).properGain; % properGain = phi0/T
if properGain(k)~=0
invproperGain(k)=1/properGain(k);
end
end
end
end
if ~isempty(MEGbalanceindex)
if physical
alphaMEG=betaMEG.*(properGain(MEGbalanceindex)'*invproperGain(MEGindex));
else
alphaMEG=betaMEG;
end
end
if ~isempty(Gbalanceindex)
if physical
alphaGref=betaGref.*(properGain(Gbalanceindex)'*invproperGain(Grefindex));
else
alphaGref=betaGref;
end
end
return
%%%%%%%%%%% End of getBalanceCoef %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%% Function getRawCTFBalanceCoefs %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [betaMEG,MEGindex,Refindex,betaGref,Grefindex,Gbalanceindex]=...
getRawCTFBalanceCoefs(ds,balanceType);
% getRawCTFBalanceCoefs. Extracts raw-data (i.e. integer data) gradiometer balancing
% coefficients from structure array ds.res4.scrr (ds is produced
% by readCTFds).
% Date : 24 OCt 2006
% Author : Harold Wilson
% Inputs : ds : Structure returned by readCTFds.
% balanceType : 'NONE' : No balancing
% 'G1BR' : 1st order balancing
% 'G2BR' : 2nd order balancing
% 'G3BR' : 3rd order balancing
% 'G3AR' : 3rd order balancing + adaptive
% If only MEG balance table is requested, size(balanceType)=[1 4]
% If Gref balance table is requested also, size(balanceType)=[2 4]
% If balancing 'NONE' is specified, getRawCTFBalanceCoefs returns lists MEGindex and
% Grefindex, and sets Refindex=[], Gbalanceindex=[].
% The reference gradiometers have only G1BR balancing coefficients.
% Outputs :
% betaMEG,MEGindex,Refindex : MEG balancing coefficients.
% Suppose data array returned by getCTFdata has size(data)=[npt nchan].
% nMEG = number of MEG channels in the data set.
% MEG channels have sensorTypeIndex==5.
%
% MEGindex = list of MEG channels in the data set. It is assembled
% by looking for sensors with ds.res4.senres.sensorTypeIndex==5
% size(MEGindex)=[1 nMEG]
% MEG data = data(:,MEGindex)
% Refindex = list of reference channels for MEG balancing.
% size(Refindex)=[1 nRef]
% Reference data = data(:,Refindex)
% betaMEG = balance coefficients. size(betaMEG)=[nRef nMEG]
%
% Balancing MEG data :
% - Start with data BEFORE converting to physical units.
% (I.e. SQUID data must be in phi0's or raw integers.)
% - balanced_data(:,MEGindex)=data(:,MEGindex)-data(:,Refindex)*betaMEG
% If user specifies balanceType=[] or ' ', then getRawCTFBalanceCoefs returns
% betaMEG=zeros(1,nMEG),Refindex=3 and nRef=1;
% betaGref,Grefindex,Gbalanceindex : Reference-gradiometer balancing coeficients.
% These output arrays are optional. If the calling statement includes
% them, then this program extracts a table of balance coefficients for
% the reference gradiometers from the G1BR table in the coefficient files.
% nGref = no. of reference gradiometers channels in the data set
% (sensorTypeIndex=1)
% Grefindex = list of reference channels. size(Grefindex)=[1 nGref]
% Gradient reference data = data(:,Grefindex)
% Gbalanceindex = list of channels for balancing reference
% gradiometers. size(Gbalanceindex)=[1 nGbalcoef]
% Balancing reference data = data(:,Gbalanceindex)
% betaGref = balance coefficients for ref. grads.
% size(betaGref)=[nGbalcoef nGref]
%
% Balancing ref. gradiometer data :
% balanced_data(:,Grefindex)=data(:,Grefindex)-data(:,Gbalanceindex)*betaGref
% No function calls.
missingMEGMessage=0;
missingGrefMessage=0;
balanceOptions=strvcat('NONE','G1BR','G2BR','G3BR', 'G3AR');
balanceOptionsEnds = [size(balanceOptions, 1), 2]; % Which options are available for MEGs and Grefs.
common_mode_only=0;
Brefindex=[]; % Index list of reference magnetometers in the data arrays
Grefindex=[]; % Index list of reference gradiometers in the data arrays
MEGindex=[]; % Index list of MEG sensors in the data arrays
Gbalanceindex=[]; % Index list of sensors used as references to balance the reference
% gradiometers
Refindex=[]; % Index list of sensors used to balance the MEG sensors
betaMEG=[];
betaGref=[];
% Check that the inputs are sensible.
if nargin<2
fprintf(['\ngetRawCTFBalanceCoefs: Only %d input arguments? ',...
'Must specify at least ds and balance.\n\n'],nargin);
return
elseif ~isstruct(ds) | isempty(ds) | ~ischar(balanceType) | isempty(balanceType)
fprintf('\ngetRawCTFBalanceCoefs: Wrong argument types or sizes.\n\n');
whos ds balanceType
return
elseif ~isfield(ds,'res4')
fprintf('\ngetRawCTFBalanceCoefs: Field res4 is missing from structure ds.\n\n');
ds
return
end
% Check that the output list is OK.
if nargout~=3 & nargout~=6
fprintf('\ngetRawCTFBalanceCoefs : Call specifies %d output arguments.\n',nargout);
fprintf('\t\tMust have 3 output arguments (MEG balance coefficients)\n');
fprintf('\t\tor 6 output arguments (reference gradiometer balancing also).\n\n');
return
elseif nargout==3
if size(balanceType,1)>1;balanceType=balanceType(1,:);end
else
if size(balanceType,1)==1;balanceType=strvcat(balanceType,'NONE');end
end
% Check that balanceType has allowed values
for k=1:size(balanceType,1) % k=1:MEGs, k=2:Grefs
if isempty(strmatch(balanceType(k,:),balanceOptions(1:balanceOptionsEnds(k),:)))
fprintf('\ngetRawCTFBalanceCoefs: balance(%d,:)=%s Not an allowed option.\n\n',...
k,balanceType(k,:));
return
end
end
% Make lists of reference magnetometers, reference gradiometers and MEG sensors.
for q=1:length(ds.res4.senres)
if ds.res4.senres(q).sensorTypeIndex==0
Brefindex=[Brefindex q];
elseif ds.res4.senres(q).sensorTypeIndex==1
Grefindex=[Grefindex q];
elseif ds.res4.senres(q).sensorTypeIndex==5 % Allow other MEG sensors?
MEGindex=[MEGindex q];
end
end
nBref=length(Brefindex); % Don't currently use Brefindex or nBref
nGref=length(Grefindex);
nMEG=length(MEGindex);
nGbalcoef=0; % Set to zero until we know the number by examining ds.res4.scrr
if nargout==6 & strcmp(balanceType(2,:),'NONE')
Gbalanceindex=[];
betaGref=zeros(0,nGref);
elseif nargout==6 & ~strcmp(balanceType(2,:),'NONE')
m1=1; % Get coefficients for balancing the reference gradiometers.
mtot=size(ds.res4.scrr,2);
for n=1:nGref
Gname=strtok(ds.res4.chanNames(Grefindex(n),:),['- ',char(0)]);
nGchar=length(Gname);
for m=[m1:mtot 1:(m1-1)]
if strncmp(Gname,char(ds.res4.scrr(m).sensorName),nGchar) & ...
strcmp('G1BR',char(ds.res4.scrr(m).coefType));
if nGbalcoef<=0 % 1st match. Initialize table and get list of references
nGbalcoef=ds.res4.scrr(m).numcoefs;
betaGref=zeros(nGbalcoef,nGref);
% Assemble index array for balancing the reference gradiometers
for q=1:nGbalcoef
Refname=strtok(char(ds.res4.scrr(m).sensor(:,q))',['- ',char(0)]);
pRef=strmatch(Refname,ds.res4.chanNames);
if isempty(pRef)
fprintf(['getRawCTFBalanceCoefs : Sensor %s appears in ',...
'ds.res4.scrr, but not in ds.res4.chanNames\n'],Refname);
return
end
Gbalanceindex=[Gbalanceindex pRef];
end
end % end setup of balancing table for Ref. gradiometers
if ds.res4.scrr(m).numcoefs~=nGbalcoef
fprintf('\ngetRawCTFBalanceCoefs : %s has %d coefficients\n',...
ds.res4.chanNames(Grefindex(1),1:nGchar),nGbalcoef);
fprintf(' %s " %d " ????\n\n',...
ds.res4.chanNames(Grefindex(n),1:nGchar),ds.res4.scrr(m).numcoefs);
betaGref=[]; % Force useless output.
return
end
betaGref(:,n)=reshape(ds.res4.scrr(m).coefs(1:nGbalcoef),nGbalcoef,1);
m1=m+1;
break; % Break out of m-loop. Go to nect n value.
end
if (m==m1-1 & m1>1) | (m==mtot & m1==1)
if missingGrefMessage==0
if strncmp(balanceType(2,:), balanceOptions(5,:), 4)
% Avoid warning for all sensors for adaptive coefficients.
fprintf('\ngetRawCTFBalanceCoefs: Failed to find %s balance coefficients for reference sensors.\n',...
balanceType(2,:));
else
fprintf(['\ngetRawCTFBalanceCoefs: Failed to find %s balance coefficients',...
' for sensor(s)'],balanceType(2,:));
fprintf('\n\t\t\t\t');
end
end
missingGrefMessage=missingGrefMessage+1;
if ~strncmp(balanceType(2,:), balanceOptions(5,:), 4)
if missingGrefMessage==10*round(missingGrefMessage/10)
fprintf('\n\t\t\t\t');
end
fprintf(' %s',Gname);
end
betaGRef(:,n)=zeros(nGbalcoef,1);
return
end
end % End loop over m (searching for scrr(m).sensorName)
end % End loop over n (list of reference gradiometers)
end % End of section getting coefficients to balance the reference gradiometers.
if missingGrefMessage>0;fprintf('\n');end
if strcmp(balanceType(1,:),'NONE')
Refindex=[];
betaMEG=zeros(0,nMEG);
return
end
% Get balance coefficients for the MEG sensors
nRef=0;
% Pointers for search through ds.res4.scrr structure array.
m1=1;
mtot=size(ds.res4.scrr,2);
for n=1:nMEG
MEGname=strtok(ds.res4.chanNames(MEGindex(n),:),['- ',char(0)]);
nChar=length(MEGname);
for m=[m1:mtot 1:(m1-1)]
if strncmp(MEGname,char(ds.res4.scrr(m).sensorName),nChar) & ...
strcmp(balanceType(1,:),char(ds.res4.scrr(m).coefType));
if nRef<=0
nRef=ds.res4.scrr(m).numcoefs;
betaMEG=zeros(nRef,nMEG);
for q=1:nRef % Assemble index array for balancing the MEG sensors
Refname=strtok(char(ds.res4.scrr(m).sensor(:,q))',['- ',char(0)]);
pRef=strmatch(Refname,ds.res4.chanNames);
if isempty(pRef)
fprintf(['\ngetRawCTFBalanceCoefs : Sensor %s appears in ',...
'ds.res4.scrr, but not in ds.res4.chanNames\n\n'],Refname);
return
end
Refindex=[Refindex pRef];
end
end % end setup of balancing table for MEG sensors
if ds.res4.scrr(m).numcoefs~=nRef
fprintf('\ngetRawCTFBalanceCoefs : %s - %s has %d coefficients\n',...
ds.res4.chanNames(MEGindex(1),1:nChar),balanceType,nRef);
fprintf(' %s - %s " %d " ????\n\n',...
ds.res4.chanNames(MEGindex(n),1:nChar),balanceType,...
ds.res4.scrr(m).numcoefs);
betaMEG=[]; % An output that will force an error in the calling program.
return
end
betaMEG(:,n)=reshape(ds.res4.scrr(m).coefs(1:nRef),nRef,1);
m1=m+1;
break;
end
if (m==m1-1 & m1>1) | (m==mtot & m1==1)
if missingMEGMessage==0
if strncmp(balanceType(2,:), balanceOptions(5,:), 4)
% Avoid warning for all sensors for adaptive coefficients.
fprintf('\ngetRawCTFBalanceCoefs: Failed to find %s balance coefficients for sensors.\n',...
balanceType(2,:));
else
fprintf(['\ngetRawCTFBalanceCoefs: Failed to find %s balance coefficients',...
' for sensor(s)'],balanceType(1,:));
fprintf('\n\t\t\t\t');
end
end
missingMEGMessage=missingMEGMessage+1;
if ~strncmp(balanceType(2,:), balanceOptions(5,:), 4)
if missingMEGMessage==10*round(missingMEGMessage/10)
fprintf('\n\t\t\t\t');
end
fprintf(' %s',MEGname);
end
betaMEG(:,n)=zeros(nRef,1);
end
end % End of loop over m (ds.res4.scrr table)
end % End of loop over MEG sensors
if missingMEGMessage>0;fprintf('\n');end
if common_mode_only
if size(betaMEG,1)>3 & nMEG>0
betaMEG=betaMEG(1:3,:);
Refindex=Refindex(1:3);
end
if size(betaGref,1)>3 & nGref>0
betaGref=betaGref(1:3,:);
Gbalanceindex=Gbalanceindex(1:3);
end
end
return
|
github
|
lcnbeapp/beapp-master
|
writeCTFds.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/plugins/fieldtrip-20160917/external/ctf/writeCTFds.m
| 68,946 |
utf_8
|
96615f4833d69490d5b3e47f6f86c538
|
function ds=writeCTFds(datasetname,ds,data,unit);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %
% This program creates datasets that can be analyzed by CTF software. %
% %
% Datasets created by this program MUST NOT BE USED FOR CLINICAL APPLICATIONS. %
% %
% Please do not redistribute it without permission from VSM MedTech Ltd. %
% %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Author : Harold Wilson
% Version 1.3 5 October 2007 Spelling errors in some variables corrected.
% Version 1.2 24 April 2007 Modified to write both MEG and fMEG .hc files.
% writeCTFds.m Version 1.1 Prepares a CTF-format data set. MATLAB to CTF conversion.
% Adds record of filter changes to hist and newds files.
% Adds no-clinical-use messages.
% Creates multiple meg4 files when the total size of the data array
% >536870910 elements.
% Operation :
% 1. User reads a data set using readCTFds and getTrial2.
% size(data)= [SAMPLES, CHANNELS, TRIALS].
% 2. After working on data in MATLAB, user adjusts ds structure to reflect changes.
% (writeCTFds will adjust the number of channels, channel names and trial structure.)
% 3. This program then creates a new CTF data set.
% datasetname must include the complete path description.
% If a data set with name datasetname already exists, writeCTFds will issue an error message.
% The new directory contains files for each field of structure ds. If the field is
% missing no file is created. If the field is empty, an empty file is created.
% Files default.* are not created by writeCTFds.
% 4. The following fields of structure ds.res4 are modified based on the size of array data :
% no_samples
% no_channels
% no_trials.
% If size(ds.res4.chanNames,1)<no_channels, additional channel names are created
% as required. The additional channels are called MXT%%%. It is assumed that
% there will be <1000 new channels.
% Inputs : datasetname : Output dataset including path. Extension '.ds' is optional.
% ds : Structure produced by readCTFds.
% data : MEG data array. size(data)=[no_samples no_channels no_trials]
% Array data may be single or double.
% unit : Determines the unit of the SQUID and EEG signals:
% If unit is missing or unit==[], the unit is set to 'fT'.
% 'ft' or 'fT' : Convert to fT (MEG), uV (EEG)
% 't' or 'T' : Convert to T (MEG), V (EEG)
% 'phi0' : Convert to phi0 (MEG), uV (EEG)
% 'int': Read plain integers from *.meg4-file
% Outputs : - ds : The ds structure of the output data set.
% - datasetout : the name of the output data set.
% - A data set. The .hz and .hz2 subdirectories are not included.
% Function calls
% Included in this listing:
% - check_senres: Does simple checks on the fields of the senres table.
% - writeHc: Creates the new .hc file
% - checkMrk: Checks structure ds.mrk to see if it is valid marker set.
% - writeEEG: Creates the new .EEG file.
% - writeBadSegments: Creates the new bad.segments file.
% - writeClassFile: Creates the new ClassFile.cls file.
% - writeVirtualChannels: Creates the new VirtualChannels file.
% - updateDescriptors: Adds non-clinical-use and creation software messages to
% infods, res4, newds and hist fields of ds.
% - updateHLC: Adds head-coil movement information to infods.
% - updateDateTime : Resets dattime fields of res4 and infods.
% - updateBandwidth: Resets bandwidth of newds and infods. Adds res4 filter
% description to ds.hist.
% - getArrayField : Extracts one field of a structure array to make it easier to
% manipulate.
% - writeMarkerFile: Creates the new MarkerFile.mrk file.
% - writeCPersist: Creates the new .acq and .infods files.
% Other calls:
% - writeRes4: Writes the new .res4 file.
% Output files are opened with 'w' permission and 'ieee-be' machine format in order
% to be compatible with the Linux acquisition and analysis software. Do not open files
% with 'wt' permission because this will add an extra char(13) byte at the end of each
% line of text.
persistent printWarning bandwidthMessage
delim=filesep;
if nargin==0 & nargout==0 % Print a version number
fprintf(['\twriteCTFds: Version 1.3 5 October 2007 ',...
'Creates v4.1 and v4.2 CTF data sets.\n',...
'\tCall: ds=writeCTFds(datasetname,ds,data,unit);\n',...
'\t\tdatasetname = Name of the new dataset including the path.\n',...
'\t\tds = Structure describing the new dataset (ds.hc must be v1.2 format).\n',...
'\t\tdata = data that will be written to the new dataset .meg4 file.\n',...
'\t\tunit = physical units of the data.\n\n']);
return
end
% Allowed 8-byte headers for res4 and meg4 files.
res4_headers=strvcat(['MEG41RS',char(0)],['MEG42RS',char(0)]);
meg4_headers=strvcat(['MEG41CP',char(0)],['MEG42CP',char(0)]);
maxMEG4Size=2^31; % Maximum MEG$ file in bytes. (Limit set by Linux software)
MAX_COILS=8; % Parameter that determines the size of the ds.res.senres structure.
lenSensorName=32; % Channel names must be 32 characters
printDefaultBandwidthMessage=0; % Print a message about default bandwidth?
default_flp=0.25; % Default is flp=0.25*ds.res4.sample_rate
clinicalUseMessage='NOT FOR CLINICAL USE';
creatorSoftware='writeCTFds'; % Added to .infods file
meg4ChunkSize=2^20; % Write new .meg4 file in chunks of 4*meg4ChunkSize bytes.
DATASET_HZ_UNKNOWN=round(2^31-1); % Peculiar requirement of DataEditor as of 23 Oct. 2006
if ~exist('clinicalUseMessage');
clinicalUseMessage=char([]);
end
% Check inputs
if nargin<3
fprintf(['\nwriteCTFds: Must supply inputs datasetname,ds,data. ',...
'Only %d input arguments are present.\n\n'],nargin);
ds=-1; % Force an error in the calling program.
return
end
% Check input argument unit. Convert unit to lower case.
if exist('unit')~=1
unit='ft'; % default
elseif isempty(unit)
unit='ft'; % default
elseif ischar(unit)
unit=lower(unit);
if ~strcmp(unit,'int') & ~strcmp(unit,'ft') & ~strcmp(unit,'t') & ~strcmp(unit,'phi0')
fprintf(['\nwriteCTFds : unit=%s Not a valid option. Must be ',...
'''fT'', ''T'', ''phi0'' or ''int''\n\n'],unit);
ds=-1; % Force an error in the calling program.
return
end
end
% Check argument type
if ~isstruct(ds) | ~isnumeric(data) | ~ischar(unit) | ~ischar(datasetname)
fprintf('\nwriteCTFds: Some of the inputs are the wrong type.\n');
whos datasetname ds data unit;
ds=-1;
return
elseif ~isfield(ds,'res4') | ~isfield(ds,'meg4')
fprintf('\nwriteCTFds: Fields res4 and meg4 must be present in structure ds.\n\n');
ds % List the fields of structure ds.
ds=-1; % Force an error in the calling program.
return
end
% Refuse to write a data set with balanced reference gradiometers.
balancedGref=0;
for k=1:ds.res4.no_channels
balancedGref=(ds.res4.senres(k).sensorTypeIndex==1 & ds.res4.senres(k).grad_order_no~=0);
end
if balancedGref
fprintf('\nwriteCTFds: ds.res4.senres indicates balanced reference gradiometers.\n\n');
ds=-1; % Force an error in the calling program.
return
end
clear k balancedGref;
% Separate datasetname into a path and the baseName
datasetname=deblank(datasetname);
ksep=max([0 findstr(datasetname,delim)]);
baseName=datasetname((ksep+1):length(datasetname));
path=datasetname(1:ksep); % String path is terminated by the file delimiter (or path=[]).
% Remove the last .ds from baseName.
kdot=max(findstr(baseName,'.ds'));
if kdot==(length(baseName)-2)
baseName=baseName(1:(max(kdot)-1));
else
datasetname=[datasetname,'.ds'];
end
clear ksep kdot;
% Save the name already in structure ds, and change to the new datset name.
if isfield(ds,'baseName')
olddatasetname=[ds.baseName,'.ds'];
if isfield(ds, 'path')
olddatasetname=[ds.path,olddatasetname];
end
else
olddatasetname=' None ';
end
ds.path=path;
ds.baseName=baseName;
% Does the dataset already exist?
if exist(datasetname)==7
fprintf('\nwriteCTFds: Dataset %s already exists. Use a different name.\n\n',...
datasetname);
ds=-1; % Force an error in the calling program.
return
end
if size(ds.res4.chanNames,2)~=lenSensorName
fprintf(['\nwriteCTFds : size(ds.res4.chanNames)=[%d %d] ? Must ',...
'have %d-character channel names.\n\n'],size(ds.res4.chanNames),lenSensorName);
ds=-1;
return
end
% Check that the channel names have a sensor-file identification extensions.
% If it is missing, print a warning message.
% Sensor type indices : SQUIDs (0:7), ADCs (10), DACs(14), Clock (17), HLC (13,28,29)
% See Document CTF MEG File Formats (PN 900-0088), RES4 File Format/
for index=[0:7 10 13 14 17 28 29]
for k=find([ds.res4.senres.sensorTypeIndex]==index);
if isempty(strfind(ds.res4.chanNames(k,:),'-'))
fprintf(['writeCTFds: Channel %3d %s No sensor-file identification.',...
' (''-xxxx'' appended to channel name).\n',...
'\t\tSome CTF software may not work with these channel names.\n'],...
k,deblank(ds.res4.chanNames(k,:)));
break;
end
end
if isempty(strfind(ds.res4.chanNames(k,:),'-'));break;end
end
clear index k chanName;
% Update the data description in the ds.res4 structure.
[nSample, nChan, trials]=size(data);
% Update ds.res4 fields to match the size of array data.
ds.res4.no_trials=trials;
ds.res4.no_channels=nChan;
ds.res4.no_samples=nSample;
ds.res4.epoch_time=nSample*trials/ds.res4.sample_rate;
% Check if channels have been added or removed from array data.
[no_chanNames len_chanNames]=size(ds.res4.chanNames);
if no_chanNames<nChan
% Assume that new channel are at the end of the data set. Add a fake extension.
for kx=1:(nChan-no_chanNames)
ds.res4.chanNames=...
strvcat(ds.res4.chanNames,['MXT' num2str(kx,'%3.3d') '-0001' char(0)]);
end
fprintf('\tAdded %d SQUID channels to the end of ds.res4.chanNames table.\n',...
nChan-no_chanNames);
elseif no_chanNames>nChan
fprintf(['\nlength(chanNames)=%d, but only %d channels of data. ',...
'writeCTFds cannot tell which channel names to remove.\n\n'],no_chanNames,nChan);
ds=-1;
return
end
clear no_chanNames len_chanNames;
% The senres table may have been changed, especially if channels are added or removed.
% Check structure senres, print error messages, and possibly fix the errors.
[ds.res4.senres,status]=check_senres(ds.res4.senres,ds.res4.no_channels);
if status<0;ds=-1;return;end
clear status;
% Check that ds.res4.numcoef is the size of structure array ds.res4.scrr.
if isfield(ds.res4,'scrr')
if ~isequal(size(ds.res4.scrr,2),ds.res4.numcoef)
fprintf('Error in ds.res4: ds.res4.numcoef=%d, but size(ds.res4.scrr)=[',...
ds.res4.numcoef);
fprintf(' %d',size(ds.res4.scrr));fprintf('] ?\n');
return
end
elseif ds.res4.numcoef~=0
fprintf(['Error in ds.res4: ds.res4.numcoef=%d,',...
' but scrr is not a field of ds.res4\n'],ds.res4.numcoef);
return
end
% Before converting data to integers, save HLC channels for motion analysis in function
% make_new_infods. Pass HLCdata to function make_new_infods
if isempty(strmatch('HLC',ds.res4.chanNames))
HLCdata=[];
else
% Make a list of head-coil channels
coil=0;
HLClist=[];
while ~isempty(strmatch(['HLC00',int2str(coil+1)],ds.res4.chanNames))
coil=coil+1;
for k=1:3
HLClist=[HLClist strmatch(['HLC00',int2str(coil),int2str(k)],ds.res4.chanNames)];
end
end
HLCdata=reshape(double(data(:,HLClist,:)),ds.res4.no_samples,3,coil,ds.res4.no_trials);
clear coil k HLClist;
end
% Convert data to integers because CTF data sets are stored as raw numbers and
% not as physical qunatities. The res4 file contains the calibrations for
% converting back to physical units. Array data may be single precision, so
% convert to double before doing any adjustments to the data.
% Already checked that unit is valid.
if strcmp(unit,'int')
data=reshape(data,nSample,nChan*trials);
for k=1:nChan*trials
if strcmp(class(data),'single')
data(:,k)=single(round(double(data(:,k))));
else
data(:,k)=round(double(data(:,k)));
end
end
data=reshape(data,nSample,nChan,trials);
clear k;
else
for chan=1:nChan % Convert EEGs from uV to V, SQUIDs from fT to T
SQUIDtype=any(ds.res4.senres(chan).sensorTypeIndex==[0:7]);
EEGtype=any(ds.res4.senres(chan).sensorTypeIndex==[8 9]);
if EEGtype & (strcmp(unit,'ft') | strtcmp(unit,'phi0'))
alphaG=1e-6;
elseif SQUIDtype & strcmp(unit,'ft')
alphaG=1e-15;
elseif SQUIDtype & strcmp(unit,'phi0')
alphaG=1./(ds.res4.senres(chan).properGain*ds.res4.senres(chan).ioGain);
else
alphaG=1;
end
% Convert from physical units to integers using the gains in the senres table.
for kt=1:trials
buff=round(double(data(:,chan,kt))*(alphaG*...
(ds.res4.senres(chan).properGain*ds.res4.senres(chan).qGain*ds.res4.senres(chan).ioGain)));
if strcmp(class(data),'single')
data(:,chan,kt)=single(buff);
else
data(:,chan,kt)=buff;
end
end
end
clear chan alphaG SQUIDtype EEGtype buff kt;
end
% Create the output dataset
[status,msg]=mkdir(path,[baseName '.ds']);
if status==0 | ~isempty(msg)
fprintf('\nwriteCTFds: Failed to create directory.\n');
fprintf(' [status,msg]=mkdir(%s)\n',datasetname);
fprintf(' returns status=%d, msg=%s',status,msg);fprintf('\n\n');
ds=-1;
return
end
clear msg status;
% Write the data file (meg4 file). Check ds.meg4.header and make sure that
% the output .meg4 file has an acceptable header.
headerMessage=1;
if ~isfield(ds.meg4,'header'); % If ds.meg4.header is missing, add it.
nChar=length(deblank(meg4_headers(1,:)));
ds.meg4.header=[meg4_headers(1,1:min(7,nChar)) char(zeros(1,7-nChar))];
elseif isempty(strmatch(ds.meg4.header(1:7),meg4_headers(:,1:7),'exact'))
ds.meg4.header=meg4_headers(1,1:7);
else
headerMessage=0;
end
if headerMessage;
fprintf('writeCTFds: Set ds.meg4.header=%s\n',ds.meg4.header);
end
clear headerMessage;
if isempty(printWarning)
fprintf(['\nwriteCTFds: The data you are writing have been processed by software not\n',...
'\tmanufactured by VSM MedTech Ltd. and that has not received marketing clearance\n',...
'\tfor clinical applications. These data should not be later employed for clinical\n',...
'\tand/or diagnostic purposes.\n\n']);
printWarning=1;
end
% Write the meg4 file(s). If there are more than maxMEG4Size-8 bytes, then additional meg4
% files will be created.
% Convert data to a 1-D array
ndata=prod(size(data));
data=reshape(data,ndata,1);
ptsPerTrial=nSample*nChan;
maxPtsPerFile=ptsPerTrial*floor((maxMEG4Size-8)/(4*ptsPerTrial));
pt=0; % Last point written to the output file(s).
while pt<ndata
endPt=pt+min(ndata-pt,maxPtsPerFile);
if pt==0
meg4Ext='.meg4';
else
meg4Ext=['.',int2str(floor(pt/maxPtsPerFile)),'_meg4'];
end
fidMeg4=fopen([path,baseName,'.ds',delim,baseName,meg4Ext],'w','ieee-be');
fwrite(fidMeg4,[ds.meg4.header(1:7),char(0)],'uint8');
while pt<endPt
pt1=min(pt+meg4ChunkSize,endPt); % Convert to double in case data is
fwrite(fidMeg4,double(data((pt+1):pt1)),'int32'); % is single and write in short
pt=pt1; % pieces.
end
fclose(fidMeg4);
end
% Update the .meg4 part of structure ds.
ds.meg4.fileSize=4*ndata+8*(1+floor(ndata/maxPtsPerFile));
clear data pt pt1 ndata fidMeg4 ptsPerTrial maxPtsPerFile meg4Ext;
% Add dataset names to .hist
if ~isfield(ds,'hist');ds.hist=char([]);end
ds.hist=[ds.hist char(10) char(10) datestr(now) ' :' char(10) ...
' Read into MATLAB as data set ' olddatasetname char(10) ...
' Rewritten by writeCTFds as data set ' datasetname char(10)];
% If infods doesn't exist or is empty create it.
if ~isfield(ds,'infods');ds.infods=[];end
if isempty(ds.infods)
ds.infods=make_dummy_infods(isfield(ds,'hc'),~isempty(HLCdata),ds.res4.sample_rate);
end
% Update text fields of res4,infods, newds and hist.
ds=updateDescriptors(ds,clinicalUseMessage,creatorSoftware);
% Add HLC data to infods
ds.infods=updateHLC(ds.infods,HLCdata);
% Analyze structure array ds.res4.filters to make text info for .hist file and
% bandwidth parameters for .newds file.
fhp=0; % High-pass cutoff assuming no filters
flp=default_flp*ds.res4.sample_rate; % Assumed lowpass cutoff. SHOULD THIS BE CHANGED?
if isempty(bandwidthMessage) & printDefaultBandwidthMessage
fprintf('writeCTFds: Lowpass filter set to flp=%0.2f*sample_rate\n',default_flp);
bandwidthMessage=1;
end
ds=updateBandwidth(ds,fhp,flp);
% Update date/time fields of infods and res4
ds=updateDateTime(ds);
% Create the .res4 file in the output dataset.
ds.res4=writeRes4([path,baseName,'.ds',delim,baseName,'.res4'],ds.res4,MAX_COILS);
if ds.res4.numcoef<0
fprintf('\nwriteCTFds: writeRes4 returned ds.res4.numcoef=%d (<0??)\n\n',...
ds.res4.numcoef);
% Kill the output dataset.
rmdir([path,baseName,'.ds'],'s');
ds=-1;
return
end
% Create .hist file
histfile=[path,baseName,'.ds',delim,baseName,'.hist'];
fid=fopen(histfile,'w');
fwrite(fid,ds.hist,'uint8');
fclose(fid);
% New .newds file
if isfield(ds,'newds')
fid=fopen([path,baseName,'.ds',delim,baseName,'.newds'],'w');
fwrite(fid,ds.newds,'uint8');
fclose(fid);
end
% New infods file.
if isfield(ds,'infods')
writeCPersist([path,baseName,'.ds',delim,baseName,'.infods'],ds.infods);
end
% new hc file
if isfield(ds,'hc')
ds.hc=writeHc([path,baseName,'.ds',delim,baseName,'.hc'],ds.hc,HLCdata(:,:,1));
end
clear HLCdata;
% MarkerFile.mrk
if checkMrk(ds)
writeMarkerFile([path,baseName,'.ds',delim,'MarkerFile.mrk'],ds.mrk);
end
% .EEG
if isfield(ds,'EEG')
writeEEG([path,baseName,'.ds',delim,baseName,'.EEG'],ds.EEG);
end
% .acq
if isfield(ds,'acq');
% Check that ds.acq has the correct fields
if isfield(ds.acq,'name') & isfield(ds.acq,'type') & isfield(ds.acq,'data')
acqFilename=[path,baseName,'.ds',delim,baseName,'.acq'];
writeCPersist(acqFilename,ds.acq);
end
end
% bad.segments file
if isfield(ds,'badSegments')
writeBadSegments([path,baseName,'.ds',delim,'bad.segments'],ds.badSegments,...
ds.res4.no_trials,ds.res4.no_samples/ds.res4.sample_rate);
end
% BadChannels
if isfield(ds,'BadChannels');
if ischar(ds.BadChannels) & ~isempty(ds.BadChannels)
fid=fopen([path,baseName,'.ds',delim,'BadChannels'],'w','ieee-be');
for k=1:size(ds.BadChannels,1)
fprintf(fid,'%s\n',deblank(ds.BadChannels(k,:)));
end
fclose(fid);
end
end
% ClassFile
if check_cls(ds)
writeClassFile([path,baseName,'.ds',delim,'ClassFile.cls'],ds.TrialClass);
end
% VirtualChannels
if isfield(ds,'Virtual')
writeVirtualChannels([path,baseName,'.ds',delim,'VirtualChannels'],ds.Virtual);
end
% processing.cfg
if isfield(ds,'processing');
if ischar(ds.processing)
fid=fopen([datasetname,delim,'processing.cfg'],'w','ieee-be');
fwrite(fid,ds.processing,'uint8');
fclose(fid);
end
end
% Update the data set path and name
ds.path=path;
ds.baseName=baseName;
return
% *************** End of function writeCTFds ********************************************
% **************************************************************************************
% **************************************************************************************
% *************** Function check_senres **************************
function [senres,status]=check_senres(senres,numChan);
% A user may have augmented the senres table, so check that all the fields have the
% correct size. This will cause errors in programs that try to compute
% sensor response using the geometry in the senres table.
% Does "sanity" checks on the senres table. If there are obviously incorrect entries, it
% tries to fix them, and prints a message. If the senres table does not specify coil
% positions, orientations or areas, set them to zero, but give them the correct array
% size.
newChannelType=4; % Create the fake sensors as MEG magnetometers. This way offsets can be removed.
status=-1;
% Does the senres table have the correct no. of channels?
no_senres=length(senres);
if no_senres<numChan
% Add channels. Assume that they are gradiometers.
ioGain=1;
qGain=2^20;
gain=0.3;
properGain=1e15/(qGain*ioGain*gain); % sensor gain in phi0/fT
for kx=(no_senres+1):numChan
senres(kx)=struct(...
'sensorTypeIndex',newChannelType,'originalRunNum',0,'coilShape',0,...
'properGain',properGain,'qGain',qGain,'ioGain',ioGain,...
'ioOffset',0,'numCoils',1,...
'grad_order_no',0,...
'gain',gain,...
'pos0',zeros(3,1),'ori0',zeros(3,1),...
'area',0.1,'numturns',1,...
'pos',[0 0 21]','ori',zeros(3,1));
end
fprintf(['\tAdded %d SQUID channels to senres table. Nominal gain of each = ',...
'%8.4f fT/step\n'],numChan-no_senres,gain);
clear kx gain qGain ioGain properGain;
elseif no_senres>numChan
% Channels have been removed from the data set, but can't tell which elements of the
% senres table to remove.
fprintf(['length(senres)=%d, but only %d channels of data. writeCTFds can''t',...
' tell which channels to remove from senres table.\n'],no_senres,numChan);
return
end
no_senres=length(senres);
% Previous version of check_senres ensures that several fields had size [1 1].
% Seems unnecessary, so removed it.
for k=1:no_senres
% Check the fields that define pickup loops. Force the field defining the pickup
% loops to have the correct size. It is not clear why the EEG channels and
% the type=13,28,29 HLC channels need numCoils=1, and area>0.
if any(senres(k).sensorTypeIndex==[0:7]) % SQUID channels
correct_numCoils=rem(senres(k).sensorTypeIndex,4)+1;
elseif any(senres(k).sensorTypeIndex==[13 28 29]) % HLC channels
correct_numCoils=1;
elseif any(senres(k).sensorTypeIndex==[8 9]) % EEG channels
correct_numCoils=1;
else
correct_numCoils=0;
end
if senres(k).numCoils~=correct_numCoils & any(senres(k).sensorTypeIndex==[0:7])
fprintf('writeCTFds_test: senres(%d).sensorTypeIndex=%d but numCoils=%d??\n',...
k,senres(k).sensorTypeIndex,senres(k).numCoils);
fprintf(' Set numCoils=%d\n',correct_numCoils);
senres(k).numCoils=correct_numCoils;
end
numCoils=senres(k).numCoils;
if size(senres(k).pos0)~=[3 numCoils];pos0=zeros(3,numCoils);end
if size(senres(k).ori0)~=[3 numCoils];ori0=zeros(3,numCoils);end
if size(senres(k).pos)~=[3 numCoils];pos=zeros(3,numCoils);end
if size(senres(k).ori)~=[3 numCoils];ori=zeros(3,numCoils);end
if size(senres(k).numturns)~=[1 numCoils];numturns=zeros(1,numCoils);end
if size(senres(k).area)~=[1 numCoils];area=zeros(3,numCoils);end
end
status=1;
return
% ************* End of function check_senres*********************************************
% **************************************************************************************
% **************************************************************************************
% ************* function make_dummy_infods*********************************************
function Tag=make_dummy_infods(exist_hc,exist_HLC,sample_rate);
% If the user does not supply ds.infos, this code makes a dummy version. It has all of
% the tags that Acq created in file Richard_SEF_20060606_04.infods.
% ***********************************************************************************
% ***********************************************************************************
DATASET_HZ_UNKNOWN=round(2^31-1); % Peculiar requirement of DataEditor as of 23 Oct. 2006
fprintf('writeCTDds (make_dummy_infods): Creating a dummy infods file with all the tags.\n');
Tag(1)=struct('name','WS1_','type',0,'data',[]);
Tag(length(Tag)+1)=struct('name','_PATIENT_INFO','type',2,'data',[]);
Tag(length(Tag)+1)=struct('name','WS1_','type',0,'data',[]);
Tag(length(Tag)+1)=struct('name','_PATIENT_UID','type',10,...
'data','2.16.124.113000.000000.00000000000000.000000000.00000000.0011');
Tag(length(Tag)+1)=struct('name','_PATIENT_NAME_FIRST','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_PATIENT_NAME_MIDDLE','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_PATIENT_NAME_LAST','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_PATIENT_ID','type',10,'data','x');
Tag(length(Tag)+1)=struct('name','_PATIENT_BIRTHDATE','type',10,'data','19500101000000');
Tag(length(Tag)+1)=struct('name','_PATIENT_SEX','type',5,'data',2);
Tag(length(Tag)+1)=struct('name','_PATIENT_PACS_NAME','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_PATIENT_PACS_UID','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_PATIENT_INSTITUTE','type',10,'data','');
Tag(length(Tag)+1)=struct('name','EndOfParameters','type',-1,'data',[]);
Tag(length(Tag)+1)=struct('name','_PROCEDURE_INFO','type',2,'data',[]);
Tag(length(Tag)+1)=struct('name','WS1_','type',0,'data',[]);
Tag(length(Tag)+1)=struct('name','_PROCEDURE_VERSION','type',5,'data',1);
Tag(length(Tag)+1)=struct('name','_PROCEDURE_UID','type',10,...
'data','2.16.124.113000.000000.00000000000000.000000000.00000000.0041');
Tag(length(Tag)+1)=struct('name','_PROCEDURE_ACCESSIONNUMBER','type',10,'data','0');
Tag(length(Tag)+1)=struct('name','_PROCEDURE_TITLE','type',10,'data','0');
Tag(length(Tag)+1)=struct('name','_PROCEDURE_SITE','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_PROCEDURE_STATUS','type',5,'data',1);
Tag(length(Tag)+1)=struct('name','_PROCEDURE_TYPE','type',5,'data',2); % Research type
Tag(length(Tag)+1)=struct('name','_PROCEDURE_STARTEDDATETIME','type',10,...
'data','20060606164306');
Tag(length(Tag)+1)=struct('name','_PROCEDURE_CLOSEDDATETIME','type',10,...
'data','19000100000000');
Tag(length(Tag)+1)=struct('name','_PROCEDURE_COMMENTS','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_PROCEDURE_LOCATION','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_PROCEDURE_ISINDB','type',5,'data',0);
Tag(length(Tag)+1)=struct('name','EndOfParameters','type',-1,'data',[]);
Tag(length(Tag)+1)=struct('name','_DATASET_INFO','type',2,'data',[]);
Tag(length(Tag)+1)=struct('name','WS1_','type',0,'data',[]);
Tag(length(Tag)+1)=struct('name','_DATASET_VERSION','type',5,'data',2);
Tag(length(Tag)+1)=struct('name','_DATASET_UID','type',10,...
'data','2.16.124.113000.000000.00000000000000.000000000.00000000.0042');
Tag(length(Tag)+1)=struct('name','_DATASET_PATIENTUID','type',10,...
'data','2.16.124.113000.000000.00000000000000.000000000.00000000.0011');
Tag(length(Tag)+1)=struct('name','_DATASET_PROCEDUREUID','type',10,...
'data','2.16.124.113000.000000.00000000000000.000000000.00000000.0041');
Tag(length(Tag)+1)=struct('name','_DATASET_STATUS','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_DATASET_RPFILE','type',10,'data','default.rp');
Tag(length(Tag)+1)=struct('name','_DATASET_PROCSTEPTITLE','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_DATASET_PROCSTEPPROTOCOL','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_DATASET_PROCSTEPDESCRIPTION','type',10,...
'data','');
Tag(length(Tag)+1)=struct('name','_DATASET_COLLECTIONDATETIME','type',10,...
'data','Unknown');
Tag(length(Tag)+1)=struct('name','_DATASET_COLLECTIONSOFTWARE','type',10,...
'data','Acq ');
Tag(length(Tag)+1)=struct('name','_DATASET_CREATORDATETIME','type',10,...
'data',sprintf('%d',floor(clock)));
Tag(length(Tag)+1)=struct('name','_DATASET_CREATORSOFTWARE','type',10,...
'data','Acq ');
Tag(length(Tag)+1)=struct('name','_DATASET_KEYWORDS','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_DATASET_COMMENTS','type',10,...
'data','Dummy infods.');
Tag(length(Tag)+1)=struct('name','_DATASET_OPERATORNAME','type',10,'data','');
Tag(length(Tag)+1)=struct('name','_DATASET_LASTMODIFIEDDATETIME','type',10,...
'data',sprintf('%d',floor(clock)));
if exist_hc
nominalPositions=0; % Measured
else
nominalPositions=1; % Nominal
end
Tag(length(Tag)+1)=struct('name','_DATASET_NOMINALHCPOSITIONS','type',5,...
'data',nominalPositions);
Tag(length(Tag)+1)=struct('name','_DATASET_COEFSFILENAME','type',10,...
'data','ds.res4.scrr');
Tag(length(Tag)+1)=struct('name','_DATASET_SENSORSFILENAME','type',10,...
'data','ds.res4.senres');
%Tag(length(Tag)+1)=struct('name','_DATASET_COEFSFILENAME','type',10,...
% 'data','/opt/ctf-5.1/hardware/M015/M015_1609.coef');
%Tag(length(Tag)+1)=struct('name','_DATASET_SENSORSFILENAME','type',10,...
% 'data','/opt/ctf-5.1/hardware/M015/M015_1609.sens');
Tag(length(Tag)+1)=struct('name','_DATASET_SYSTEM','type',10,'data','DSQ-2010');
Tag(length(Tag)+1)=struct('name','_DATASET_SYSTEMTYPE','type',10,'data','Untitled');
Tag(length(Tag)+1)=struct('name','_DATASET_LOWERBANDWIDTH','type',4,'data',0);
Tag(length(Tag)+1)=struct('name','_DATASET_UPPERBANDWIDTH','type',4,'data',...
round(0.25*sample_rate));
Tag(length(Tag)+1)=struct('name','_DATASET_ISINDB','type',5,'data',0);
if exist_HLC
HZ_MODE=5;
elseif exist_hc
HZ_MODE=1;
else
HZ_MODE=DATASET_HZ_UNKNOWN;
end
Tag(length(Tag)+1)=struct('name','_DATASET_HZ_MODE','type',5,'data',HZ_MODE);
Tag(length(Tag)+1)=struct('name','_DATASET_MOTIONTOLERANCE','type',4,'data',0.005);
Tag(length(Tag)+1)=struct('name','_DATASET_MAXHEADMOTION','type',4,'data',0.005);
Tag(length(Tag)+1)=struct('name','_DATASET_MAXHEADMOTIONTRIAL','type',7,'data',0);
Tag(length(Tag)+1)=struct('name','_DATASET_MAXHEADMOTIONCOIL','type',10,'data','1');
Tag(length(Tag)+1)=struct('name','EndOfParameters','type',-1,'data',[]);
Tag(length(Tag)+1)=struct('name','EndOfParameters','type',-1,'data',[]);
return
% ************* End of function make_dummy_infods*********************************************
% **************************************************************************************
% **************************************************************************************
% ************* Function writeHc*********************************************
function hc=writeHc(hcFileName,hc,HLCdata);
% Modified for v1.2 ds.hc structures. ds.hc.names has the exact, complete names of the
% head coils. The coordinates relative to the subject may be ds.hc.head(MEG) OR
% ds.hc.abdomen (fMEG).
% Creates a .hc file in a CTF dataset
% Inputs: hcFileName : Complete name of .hc file including path, basename and .hc ext.
% hc : structure with nasion, left, right head coil positions in dewar and
% CTF head coordinates.
% HLCdata : head coil locations at the start of 1st trial. unit=m
% coordinates=dewar. Used only if structure hc is empty and it is MEG
% data (not fMEG data).
% Output : hc : hc structure. hc=struct([]) on failure. hc is set to the coil positions
% in array HLCdata if hc=[] on entry.
% Check inputs
if exist('hc')~=1
hc=struct([]);
elseif ~isstruct(hc)
hc=struct([]);
end
hcfields=fieldnames(hc);
if exist('HLCdata')~=1
HLCdata=[];
elseif ~isnumeric(HLCdata) | size(HLCdata,1)~=3 | size(HLCdata,2)<3
HLCdata=[];
end
% Check hc Filename
if exist('hcFileName')~=1;hcFileName=char([]);end
if ~ischar(hcFileName) | isempty(hcFileName)
fprintf('writeCTFds (writeHc): Called writeHc with bad file name.\n');
hcFileName
return
end
% Both hc and HLCdata bad?
if length(hcfields)~=4 & isempty(HLCdata)
fprintf('writeCTFds (writeHc): Called writeHc with bad hc and bad HLCdata.\n');
hc=struct([])
return
elseif length(hcfields)~=4
rstandard=8/sqrt(2)*[1 1 0;-1 1 0;1 -1 0]';
rstandard(3,:)=-27;
rdewar=100*HLCdata(:,1:3);
% Convert from dewar coordinates to CTF head coordinates.
originCTF=0.5*(hc.dewar(:,2)+hc.dewar(:,3));
% Unit vectors for the CTF coordinates
uCTF(:,1)=hc.dewar(:,1)-originCTF;
uCTF(:,3)=cross(uxCTF,hc.dewar(:,2)-hc.dewar(:,3));
uCTF(:,2)=cross(uCTF(:,3),uCTF(:,1));
uCTF=uCTF./(ones(3,1)*sqrt(sum(uCTF.^2,1)));
rCTF=uCTF'*(rdewar-originCTF*ones(1,3))
hc=struct('names',strvcat('nasion','left ear','right ear'),...
'standard',rstandard,'dewar',rdewar,'head',rCTF);
clear originCTF uCTF rstandard rdewar rCTF;
end
% Character strings for generating the .hc text file
% Should never have both 'head' and 'abdomen' fields.
labelword=strvcat('standard','measured','measured');
printField=[strmatch('standard',hcfields) strmatch('dewar',hcfields) ...
strmatch('head',hcfields) strmatch('abdomen',hcfields)];
if ~strmatch('names',hcfields) | length(printField)~=3
fprintf(['writeCTFds (writeHc): Structure hc does not have all of the required fields.\n',...
' No .hc file will appear in the output dataset.\n']);
hc;
hc=struct([]);
return
end
relative=strvcat('dewar','dewar',hcfields{printField(3)});
coilcoord=strvcat('standard','dewar',hcfields{printField(3)});
comp='xyz';
coilname=hc.names;
fid=fopen(hcFileName,'w','ieee-be');
for k=1:size(coilcoord,1)
rcoil=getfield(hc,coilcoord(k,:));
for coil=1:size(hc.names,1)
clName=deblank(hc.names(coil,:));
fwrite(fid,[labelword(k,:) ' ' clName ' coil position relative to ',...
deblank(relative(k,:)) ' (cm):' char(10)],'uint8');
for m=1:3
fwrite(fid,[char(9) comp(m) ' = ' num2str(rcoil(m,coil),'%7.5f') char(10)],'uint8');
end
end
end
fclose(fid);
status=0;
return
% ************* End of function writeHc*********************************************
% **************************************************************************************
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%Function checkMrk %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function MarkerFileOK=checkMrk(ds);
% Examines structure ds to see if a sensible MarkerFile can be created from ds.mrk.
% Output: MarkerFileOK=1 : ds.mrk looks OK
% MarkerFileOK=0 : ds.mrk cannot be a set of valid markers for these data.
MarkerFileOK=isfield(ds,'mrk');
if MarkerFileOK
MarkerFileOK=~isempty(ds.mrk);
end
if MarkerFileOK
% Are the markers appropriate?
minMarkerTrial=[];
minMarkerTime=[];
maxMarkerTrial=[];
maxMarkerTime=[];
for k=1:length(ds.mrk)
maxMarkerTrial=max([maxMarkerTrial max(ds.mrk(k).trial)]);
maxMarkerTime=max([maxMarkerTime max(ds.mrk(k).time)]);
minMarkerTrial=min([minMarkerTrial min(ds.mrk(k).trial)]);
minMarkerTime=min([minMarkerTime min(ds.mrk(k).time)]);
end
if isempty(maxMarkerTrial) | isempty(maxMarkerTime)
MarkerFileOK=0; % Do not create MarkerFile.mrk if all of the marker classes are empty.
else
MarkerFileOK=(maxMarkerTrial<=ds.res4.no_trials & minMarkerTrial>=1 & ...
maxMarkerTime<=(ds.res4.no_samples/ds.res4.sample_rate) & ...
minMarkerTime>=(-ds.res4.preTrigPts/ds.res4.sample_rate));
if ~MarkerFileOK
fprintf(['\nwriteCTFds (checkMrk): ds.mrk cannot possibly be a set of markers ',...
'for array(data).\n']);
fprintf([' minMarkerTrial=%d (must be >=1) ',...
'maxMarkerTrial=%d (must be <=%d)\n'],...
minMarkerTrial,maxMarkerTrial,ds.res4.no_trials);
fprintf([' minMarkerTime=%7.4f (must be >=%7.4f) ',...
'maxMarkerTrial=%7.4f (must be <=%7.4f )\n'],...
minMarkerTime,-ds.res4.preTrigPts/ds.res4.sample_rate,...
maxMarkerTime,ds.res4.no_samples/ds.res4.sample_rate);
fprintf(' MarkerFile.mrk will not be created.\n\n');
end
end
end
return
%%%%%%%%%%%%%% end of checkMrk %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%% Function writeEEG %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function writeEEG(eegFileName,EEG);
% Reads the EEG file of a dtaset and stores the infoemation in strucure array EEG.
% EEG(k).chanName = channel name in the dataset (EEGmmm where mmm=channel number)
% EEG(k).name = channel name given by the user (e.g. Fp4)
% EEG(k).pos = electrode position in cm in CTF head coordinates
% Check inputs
if exist('eegFileName')~=1;eegFileName=char([]);end
if ~ischar(eegFileName) | isempty(eegFileName)
fprintf('writeCTFds (writeEEG): Called writeEEG with bad file name.\n');
eegFileName
EEG=struct([]);
end
if exist('EEG')~=1
EEG=struct([]);
elseif ~isstruct(EEG)
EEG=struct([]);
end
if isempty(EEG);return;end
fid=fopen(eegFileName,'w','ieee-be');
if fid<0
fprintf('writeCTFds (writeEEG): Could not open file %s\n',eegFileName);
return
end
nEEG=length(EEG);
for k=1:nEEG
fprintf(fid,'%d\t%s\t%7.5f\t%7.5f\t%7.5f\n',EEG(k).chanNum,EEG(k).name,EEG(k).pos);
end
fclose(fid);
return
%%%%%%%%% End of writeEEG %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%% Function writeBadSegments %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function writeBadSegments(badSegmentsFile,badSegments,nTrial,tTrial);
% Creates a bad.segements file in a CTF data set from the information in structure
% badSegments which is created by read_badSegments, or by the user.
% If structure badSegments is empty, then the file is not created.
% badSegments structure:
% badSegments.trial = List of trial numbers
% badSegments.StartTime = List of bad segment start times (relative to trial).
% badSegments.EndTime = List of bad segment end times.
% Check badSegmentsFile
if exist('badSegmentsFile')~=1;badSegmentsFile=char([]);end
if isempty(badSegmentsFile) | ~ischar(badSegmentsFile)
fprintf('writeCTFds(writeBadSegments): Bad file name.\n');
badSegmentsFile
return
end
% Check that structure badSegments is defined correctly
if exist('badSegments')~=1 | exist('nTrial')~=1
return
elseif ~isstruct(badSegments) | isempty(badSegments)
return
elseif ~isfield(badSegments,'trial') | ~isfield(badSegments,'StartTime') | ...
~isfield(badSegments,'EndTime')
return
elseif isempty(badSegments.trial) | isempty(badSegments.StartTime) | ...
isempty(badSegments.EndTime)
return
elseif ~isequal(size(badSegments.trial),size(badSegments.StartTime),...
size(badSegments.EndTime))
fprintf(['\nwriteCTFds (writeBadSegments): ',...
'The fields of structure badSegments do not all have the same size.\n']);
return
elseif any(badSegments.trial>nTrial) | any(badSegments.trial<1) | ...
any(badSegments.EndTime>tTrial)
fprintf(['\nwriteCTFds (writeBadSegments): ds.badSegments cannot possibly describe ',...
'bad segments for these data.\n',...
'\tmin(badSegments.trial)=%d max(badSegments.trial)=%d ',...
'max(badSegments.EndTime)=%0.4f s\n\t\tDataset: nTrial=%d tTrial=%0.4f s\n'],...
min(badSegments.trial),max(badSegments.trial),max(badSegments.EndTime),...
nTrial,tTrial);
fprintf('\t\tbad.segments file will not be created.\n\n');
return
end
% Convert all fields to simple vectors
nSeg=prod(size(badSegments.trial));
trial=reshape(badSegments.trial,1,nSeg);
StartTime=reshape(badSegments.StartTime,1,nSeg);
EndTime=reshape(badSegments.EndTime,1,nSeg);
fid=fopen(badSegmentsFile,'w','ieee-be');
if fid<0
fprintf('writeCTFds (writeBadSegments): Could not open file %s\n',badSegmentsFile);
return
end
% Extra tabs are inserted to reproduce the format of bad.segments files produced by
% DataEditor (5.3.0-experimental-linux-20060918).
fprintf(fid,'%0.6g\t\t%0.6g\t\t%0.6g\t\t\n',[trial;StartTime;EndTime]);
fclose(fid);
return
%%%%%%%%% End of writeBadSegments %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%Function check_cls %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function ClassFileOK=check_cls(ds);
% Examines structure ds to see if a sensible ClassFile can be created from ds.TrialClass.
ClassFileOK=isfield(ds,'TrialClass');
if ClassFileOK
ClassFileOK=~isempty(ds.TrialClass);
end
if ClassFileOK
% Are the class trials appropriate?
minClassTrial=[];
maxClassTrial=[];
for k=1:length(ds.TrialClass)
maxClassTrial=max([maxClassTrial max(ds.TrialClass(k).trial)]);
minClassTrial=min([minClassTrial min(ds.TrialClass(k).trial)]);
end
% Create ClassFile.cls even when the trail classes are empty.
if ~isempty(maxClassTrial)
ClassFileOK=(maxClassTrial<=ds.res4.no_trials & minClassTrial>=1);
if ~ClassFileOK
fprintf(['\nwriteCTFds (check_cls): ds.TrialClass cannot possibly be a set of ',...
'trial classes for array(data).\n minClassTrial=%d (must be >=1) ',...
'maxClassTrial=%d (must be <=%d)\n'],...
minClassTrial,maxClassTrial,ds.res4.no_trials);
fprintf(' ClassFile.cls will not be created.\n');
end
end
end
return
%%%%%%%%%%%%%% end of check_cls %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%% Function writeClassFile %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function writeClassFile(ClassFile,TrialClass);
% Write the ClassFile of a CTF data set.
% The CLassFile allows a user to store a list of trial classifications in a data set.
% The ClassFile format is defined in document CTF MEG File Formats, PN900-0088.
% This format is rigid.
% Inputs :
% ClassFile : marker file including the full path and extension .mrk.
% TrialClass : Structure creted by read_ClassFile.
% Output : ClassFile.cls.
% Check input TrialClass.
if exist('TrialClass')~=1;TrialClass=[];end
if isempty(TrialClass) | ~isstruct(TrialClass)
fprintf('writeCTFds (writeClassFile): TrialClass is empty or is not a structure.\n');
TrialClass
return
end
% Check ClassFile
if exist('ClassFile')~=1;ClassFile=char([]);end
if isempty(ClassFile) | ~ischar(ClassFile)
fprintf('writeCTFds (writeClassFile): Bad file name.\n');
ClassFile
end
fid=fopen(ClassFile,'w','ieee-be');
if fid<0
fprintf('writeCTFds (writeClassFile): Could not open file %s\n',ClassFile);
return
end
nClass=length(TrialClass);
% Generate datasetname from ClassFIle.
ksep=max([0 strfind(ClassFile,filesep)]);
datasetname=ClassFile(1:ksep-1);
if isempty(datasetname);datasetname=cd;end
fprintf(fid,'PATH OF DATASET:\n%s\n\n\n',datasetname);
fprintf(fid,'NUMBER OF CLASSES:\n%d\n\n\n',nClass);
for k=1:nClass
if k==1 % Add sign character to make output match the output of Acq.
sgn=char([]); % There should be no real significance to this.
else % Why does DataEditor places the + sign only on ClassID 2,3,...?
sgn='+';
end
No_of_Trials=prod(size(TrialClass(k).trial));
fprintf(fid,'CLASSGROUPID:\n%s%d\nNAME:\n%s\nCOMMENT:\n%s\n',...
sgn,TrialClass(k).ClassGroupId,TrialClass(k).Name,TrialClass(k).Comment);
fprintf(fid,'COLOR:\n%s\nEDITABLE:\n%s\nCLASSID:\n%s%d\nNUMBER OF TRIALS:\n%d\n',...
TrialClass(k).Color,TrialClass(k).Editable,sgn,TrialClass(k).ClassId,No_of_Trials);
fprintf(fid,'LIST OF TRIALS:\nTRIAL NUMBER\n');
% Subtract one so trial numbering starts at 0 in ClassFile.cls
fprintf(fid,'%20d\n',reshape(TrialClass(k).trial,1,No_of_Trials)-1);
fprintf(fid,'\n\n');
end
fclose(fid);
return
%%%%%%%%%%%%%% end of writeClassFile %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%% Function writeVirtualChannels %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function writeVirtualChannels(VirtualChannelsFile,Virtual);
% Writes a VirtualChannels file using the information in structure Virtual.
% S\tructure Virtual is prepared by read_VirtualChannels
% Check VirtualChannelsFile
if exist('VirtualChannelsFile')~=1;VirtualChannelsFile=char([]);end
if isempty(VirtualChannelsFile) | ~ischar(VirtualChannelsFile)
fprintf('write_VirtualChannelsFile: Bad file name.\n');
VirtualChannelsFile
return
end
% Check structure array Virtual
if exist('Virtual')~=1
fprintf('writeVirtualChannels: Must specify structure Virtual.\n');
return
elseif isempty(Virtual) | ~isstruct(Virtual)
return
elseif ~isfield(Virtual,'Name') | ~isfield(Virtual,'wt');
return
elseif isempty(Virtual(1).Name)
return
end
fid=fopen(VirtualChannelsFile,'w','ieee-be');
if fid<0
fprintf('writeCTFds (writeVirtualChannels): Could not open file %s\n',VirtualChannelsFile);
return
end
fprintf(fid,'//Virtual channel configuration\n\n');
for k=1:length(Virtual)
fprintf(fid,'VirtualChannel\n{\n\tName:\t%s\n\tUnit:\t%s\n',...
Virtual(k).Name,Virtual(k).Unit);
for q=1:size(Virtual(k).wt)
% Floating format chosen to match VirtualChanels file creatd by
% DataEditor (5.3.0-experimental-linux-20060918).
fprintf(fid,'\tRef:\t%s,%0.6g\n',deblank(Virtual(k).chan(q,:)),Virtual(k).wt(q));
end
fprintf(fid,'}\n\n');
end
fclose(fid);
return
%%%%%%%%%%%%%% end of writeVirtualChannels %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%% Function updateDescriptors %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function ds=updateDescriptors(ds,comment,creatorSoftware,HLCcntrl);
% Makes sure that certain tags are in structure infods, and makes sure that information
% is transfered to infods and newds from res4. Updates several fields of res4 with
% clinical use message (=comment) and name of creator program.
% Inputs: ds : ds structure produced by readCTFds.
% comment : Character string that is added to infods tags listed in addCommentTag
% and res4 fields listed in addCommentField
% creatorSoftware : Character string indicating that the data set was
% created by writeCTFds. Added to infods tags listed in addCreatorTag and
% appName field of res4.
% HLCcntrl: If ds.infods is missing or empty, HLCcntrl determines the
% _DATA_HZ_MODE tage of infods. if noit present or empty, HLCcntrl=0.
% Creates a dummy infods structure if necessary using function make_dummy_infods.
% Changes infods and newds to match information in
% ds.res4.nf_run_title
% ds.res4.collect_descriptor
% ds.res4.nf_subject_id
% ds.res4.nf_operator
% Adds comment (clinical use message) and creator software name to infods, newds and hist files.
if ~isfield(ds,'infods');ds.infods=[];end
% infods tags that will display the comment.
addCommentTag=strvcat('_PATIENT_ID','_PATIENT_INSTITUTE','_PROCEDURE_COMMENTS',...
'_DATASET_COMMENTS','_DATASET_STATUS','_DATASET_PROCSTEPTITLE');
% res4 text fields that will display the comment
addCommentField=strvcat('appName','dataOrigin','dataDescription',...
'nf_run_title','nf_subject_id','run_description');
% res4 text string lengths (from document "CTF MEG File Formats", PN900-0088)
addCommentLength=[256 256 256 256 32 -1]'; % -1 indicates variable length
% infods tags that will display the creator software.
addCreatorTag=strvcat('_PROCEDURE_COMMENTS','_DATASET_STATUS',...
'_DATASET_COLLECTIONSOFTWARE','_DATASET_CREATORSOFTWARE');
% res4 text fields that will display the creator software.
addCreatorField=strvcat('appName','run_description');
addCreatorLength=[256 -1]';
% List of infods tags that will be set to ds.res4.fields (not necessarily fields listed in
% addCommentField or addCreatorField
addRes4Tag=strvcat('_PATIENT_ID','_DATASET_PROCSTEPTITLE',...
'_DATASET_PROCSTEPDESCRIPTION','_DATASET_OPERATORNAME');
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Add the Tags to infods. In most cases they will already be there, but just to be sure.
addTag=strvcat(addRes4Tag,addCommentTag,addCreatorTag);
tagClass=strvcat('_PATIENT','_PROCEDURE','_DATASET');
% List of all the tag names as a character array
tagName=getArrayField(ds.infods,'name')';
if length(ds.infods)==1;tagName=tagName';end
tagType=getArrayField(ds.infods,'type');
tagPtr=1; % If a class is missing, inject the class starting at tagPtr+1.
for k=1:size(tagClass,1)
addIndex=strmatch(deblank(tagClass(k,:)),addTag)';
% Are there any tags to be added in this class?
if isempty(addIndex);continue;end
% List of infods tags in the tagClass, but excluding the CPerist type (which marks the
% start of a class.
infodsIndex=strmatch(deblank(tagClass(k,:)),tagName);
if isempty(infodsIndex) % Create a new class of tags.
if strcmp(deblank(tagName(tagPtr+1,:)),'EndOfParameters') & k>1;
tagPtr=tagPtr+1;
end
nTag=length(ds.infods);
tagName((tagPtr+4):(nTag+3),:)=tagName((tagPtr+1):nTag,:);
ds.infods((tagPtr+4):(nTag+3))=ds.infods((tagPtr+1):nTag);
ds.infods(tagPtr+1)=struct('name',[deblank(tagClass(k,:)),'_INFO'],'type',2,'data',[]);
ds.infods(tagPtr+2)=struct('name','WS1_','type',0,'data',[]);
ds.infods(tagPtr+3)=struct('name','EndOfParameters','type',-1,'data',[]);
tagName=strvcat(tagName(1:tagPtr,:),...
strvcat([deblank(tagClass(k,:)),'_INFO'],'WS1_','EndOfParameters'),...
tagName(tagPtr+1:nTag,:));
nTag=nTag+3;
tagPtr=tagPtr+2;
else
if ds.infods(max(infodsIndex)).type==2
tagPtr=max(infodsIndex)+1; % Class consists of no tags beyond the CPersist definition
else
tagPtr=max(infodsIndex); % Class contains at least one real tag.
end
clear infodsIndex;
end
for q=addIndex
if isempty(strmatch(deblank(addTag(q,:)),tagName))
tagName=strvcat(tagName(1:tagPtr,:),deblank(addTag(q,:)),tagName(tagPtr+1:nTag,:));
ds.infods((tagPtr+2):(nTag+1))=ds.infods((tagPtr+1):nTag);
ds.infods(tagPtr+1)=struct('name',deblank(addTag(q,:)),'type',10,'data',char([]));
tagPtr=tagPtr+1;
nTag=nTag+1;
end
end
end
clear k q nTag tagPtr infodsIndex addIndex;
% All of the tags in addTag have been added to ds.infods.
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if exist('creatorSoftware')~=1;
creatorSoftware=char([]);
elseif ~ischar(creatorSoftware)
creatorSoftware=char([]);
else
creatorSoftware=deblank(creatorSoftware);
end
if exist('comment')~=1;
comment=char([]);
elseif ~ischar(comment)
comment=char([]);
else
comment=deblank(comment);
end
tagName=getArrayField(ds.infods,'name')';
% Update the res4 fields : add creator message.
% Don't check field length, but truncate later.
for q=1:size(addCreatorField,1);
strng=deblank(getfield(ds.res4,deblank(addCreatorField(q,:))));
if isempty(strfind(strng,creatorSoftware))
newStrng=creatorSoftware;
if ~isempty(strng);newStrng=[strng ' ' newStrng];end
ds.res4=setfield(ds.res4,deblank(addCreatorField(q,:)),newStrng);
end
end
clear q strng nChar strng0 ns;
% Update the res4 fields : add comment (= clinical use message)
% Don't check field length, but truncate later.
for q=1:size(addCommentField,1);
strng=deblank(getfield(ds.res4,deblank(addCommentField(q,:))));
if isempty(strfind(strng,comment))
newStrng=comment;
if ~isempty(strng);newStrng=[strng ' ' newStrng];end
ds.res4=setfield(ds.res4,deblank(addCommentField(q,:)),newStrng);
end
end
clear strng newStrng q;
% Update res4.run_description
ds.res4.run_description=[ds.res4.run_description,char(0)];
ds.res4.rdlen=length(ds.res4.run_description);
% Update infods entries from .res4 fields
ds.infods(strmatch('_PATIENT_ID',tagName)).data=deblank(ds.res4.nf_subject_id);
ds.infods(strmatch('_DATASET_PROCSTEPTITLE',tagName)).data=deblank(ds.res4.nf_run_title);
ds.infods(strmatch('_DATASET_PROCSTEPDESCRIPTION',tagName)).data=...
deblank(ds.res4.nf_collect_descriptor);
ds.infods(strmatch('_DATASET_OPERATORNAME',tagName)).data=deblank(ds.res4.nf_operator);
% Truncate the .res4. fields. Leave room for a final char(0).
for q=1:size(addCreatorField,1);
strng=deblank(getfield(ds.res4,deblank(addCreatorField(q,:))));
if length(strng)>addCreatorLength(q)-1 & addCreatorLength(q)>0
ds.res4=setfield(ds.res4,deblank(addCreatorField(q,:)),...
strng(length(strng)+[-addCreatorLength(q)+2:0]));
end
end
for q=1:size(addCommentField,1);
strng=deblank(getfield(ds.res4,deblank(addCommentField(q,:))));
if length(strng)>addCommentLength(q)-1 & addCommentLength(q)>0
ds.res4=setfield(ds.res4,deblank(addCommentField(q,:)),...
strng(length(strng)+[-addCommentLength(q)+2:0]));
end
end
clear q strng;
% Add creator software to infods tags. Have already cheked that the tags are there.
for q=1:size(addCreatorTag,1)
if isempty(strmatch(deblank(addCreatorTag(q,:)),addRes4Tag))
k=strmatch(deblank(addCreatorTag(q,:)),tagName);
if length(k)==1
if isempty(strfind(ds.infods(k).data,creatorSoftware))
newStrng=creatorSoftware;
if ~isempty(deblank(ds.infods(k).data));
newStrng=[deblank(ds.infods(k).data) ' ' newStrng];
end
ds.infods(k).data=newStrng;
end
else
fprintf('writeCTFds: Tag %s appears %d times in ds.infods ??\n',...
deblank(addCreatorTag(q,:)),length(k));
end
end
end
clear q k;
% Add comment (clinical use statement) to ds.infods
for q=1:size(addCommentTag,1)
if isempty(strmatch(deblank(addCommentTag(q,:)),addRes4Tag))
k=strmatch(deblank(addCommentTag(q,:)),tagName);
if length(k)==1
if isempty(strfind(ds.infods(k).data,comment))
newStrng=comment;
if ~isempty(deblank(ds.infods(k).data));
newStrng=[deblank(ds.infods(k).data) ' ' newStrng];
end
ds.infods(k).data=newStrng;
end
else
fprintf(['writeCTFds (updateDescriptors): Tag %s appears %d times in ',...
'ds.infods ??\n'],deblank(addCommentTag(q,:)),length(k));
end
end
end
clear q k;
% Add the creator and comment information to the newds file
if isfield(ds,'newds');
nChar=length(ds.newds);
% Keyword positions
aNpos=max(strfind(ds.newds,[char(9) 'appName:' char(9)]));
if isempty(aNpos)
fprintf(['writeCTFds (update_decsriptors): Keyword ''appName'' ',...
'does not appear in ds.newds.\n',...
' set ds.newds=[].\n']);
ds.newds=char([]);
else
eol=max([11 min(strfind(ds.newds(aNpos+1:length(ds.newds)),char(10)))]);
ds.newds=[ds.newds(1:(aNpos+eol-1)) ' ' creatorSoftware ' ' comment ...
ds.newds((aNpos+eol):length(ds.newds))];
end
clear nChar aNpos eol;
end
% Add clinical use message to hist file.
if isfield(ds,'hist') & ~isempty(comment)
ds.hist=[ds.hist char(10) comment char(10)];
end
return
%%%%%%%%%%%%%% End of updateDescriptors %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%% Function updateHLC %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [infods,status]=updateHLC(infods,HLCdata);
% Adds notes and continuous-head-localization tags to .infods file
% Inputs : infods : Structure of tags to be written to output infods file.
% HLCdata : 0 or [] or not defined - There are no HLC channels
% (head-coil position) in the data. Just pass the existing tags to
% the output dataset.
% HLCdata : real array : size(HLCdata)=[samplesPerTrial 3 Ncoil nTrial]
% Calculate the head motion tags.
% Outputs : status : 0: Everything looks OK
% 1: Couldn't find _DATASET tags.
% <0: There is a problem with the new infods file.
% Calls:
% - getArrayField: Extracts field names from structure array S.
% Defaults for the head localization tags.
% Might do this better with a structure.
HZ_MODE_UNKNOWN=2^31-1; % Bug in DataEditor and acquisition software, Oct. 2006
% Should be -1.
% New dataset tags for HLC specification.
addTag=strvcat('_DATASET_HZ_MODE',...
'_DATASET_MOTIONTOLERANCE',...
'_DATASET_MAXHEADMOTION',...
'_DATASET_MAXHEADMOTIONTRIAL',...
'_DATASET_MAXHEADMOTIONCOIL');
addTagType=[5 4 4 7 10]';
% Check HLCdata array. HLCdata=[] indicates no continuous head localization.
if ~exist('HLCdata')==1
HLCdata=[];
elseif ~isempty(HLCdata)
[samplesPerTrial nDim Ncoil nTrial]=size(HLCdata);
if nDim~=3;
fprintf('writeCTFds (updateHLC): size(HLCdata)=[');fprintf(' %d',size(HLCdata));
fprintf(']\n');
fprintf(' nDim=%d?? Setting HLCdata=[].\n',nDim);
HLCdata=[];
end
end
% Assume that all the tag names are different. There is no checking when a tag listed in
% addTag matches more than one entry in array name.
name=getArrayField(infods,'name')'; %size(name)=[nTag lengthTag]
DATASET_tags=strmatch('_DATASET',name)'; % size(DATASET_tags)=[1 nTag]
if isempty(DATASET_tags)
status=1; % No _DATASET tags. Don't add anything.
else
status=0;
if isempty(HLCdata)
TagValue(1)=HZ_MODE_UNKNOWN;
TextTagValue=char(0);
addTag=addTag(1,:); % Remove the other HLC tags
addTagType=addTagType(1);
else % ~isempty(HLCdata)
% Remove HLC offsets.
HLCoffset=squeeze(HLCdata(1,:,:,1));
for q=1:Ncoil
for k=1:3
HLCdata(:,k,q,:)=HLCdata(:,k,q,:)-HLCoffset(k,q);
end
end
% Calculate motions as displacement from the start of the dataset.
absMotion=squeeze(sqrt(sum(HLCdata.^2,2))); %size(absMotion)=[samplesPerTrial Ncoil nTrial]
maxCoilMotion=squeeze(max(absMotion,[],1)); % size(maxCoilMovement)=[Ncoil nTrial]
maxHeadMotion=max(max(maxCoilMotion));
[mx maxHeadMotionCoil]=max(max(maxCoilMotion,[],2));
[mx maxHeadMotionTrial]=max(max(maxCoilMotion,[],1));
% Create a list of head motion tag values
TagValue(1)=5; % Indicates continuous head localization
TagValue(2)=max(2*maxHeadMotion,0.02); % _DATASET_MOTIONTOLERANCE
TagValue(3)=maxHeadMotion; % _DATASET_MAXHEADMOTION
% Subtract 1 from the trial so trial numbering starts at 0.
TagValue(4)=maxHeadMotionTrial-1; % _DATASET_MAXHEADMOTIONTRIAL
TextTagValue=char(zeros(4,1)); % Placeholder since tags1:4 are numerical
% _MAXHEADMOTIONCOIL value
TextTagValue=strvcat(TextTagValue,sprintf('%d',maxHeadMotionCoil));
TagValue=[TagValue 0]; % Placeholder only since the 5th tag is a text string.
end
% Add or insert tags.
for q=1:size(addTag,1)
nTag=length(infods);
tagName=deblank(addTag(q,:));
TagNo=strmatch(tagName,name,'exact')';
if isempty(TagNo) % Insert a tag at the end of the _DATASET tags.
TagNo=max(DATASET_tags)+1;
infods((TagNo+1):(nTag+1))=infods(TagNo:nTag);
name=strvcat(name(1:TagNo-1,:),tagName,name(TagNo:nTag,:));
DATASET_tags=[DATASET_tags TagNo];
end
if addTagType(q)~=10
infods(TagNo)=struct('name',tagName,'type',addTagType(q),'data',TagValue(q));
else
infods(TagNo)=struct('name',tagName,'type',addTagType(q),...
'data',deblank(TextTagValue(q,:)));
end
end % End loop over head position and head motion tags.
clear q TagNo TextTagValue TagValue;
end % End section add _DATASET tags
return
%%%%%%%%%%%%%% End of updateHLC %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%% Function updateBandwidth %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function ds=updateBandwidth(ds,fhp,flp);
% Updates the bandwidth fields of infods and newds.
% 3 possible dources of bandwidth:
% 1. fhp,flp inputs (default)
% 2. newds fiels
% 3. res4.filter
% 4. infods field
% Almost always, fhp,flp will have the default values, but it could be defined in the
% fields of ds, so check. Result: lots of code to achieve a simple result.
% read fhp,flp from newds (if it exists)
if isfield(ds,'newds')
BWpos=max(strfind(ds.newds,[char(9) 'bandwidth:' char(9)])); % Keyword position
if isempty(BWpos)
fprintf(['writeCTFds (updateBandwidth): Keyword ''bandwidth:''',...
'does not appear in ds.newds.\n',...
' Field newds removed from structure ds.\n']);
ds=rmfield(ds,'newds');
else
% Get the bandwidth parameters from ds.newds.
eol=max([13 min(strfind(ds.newds(BWpos+1:length(ds.newds)),char(10)))]);
buff=sscanf(ds.newds((BWpos+13):(BWpos+eol)),'%f%c%f');
fhp=max(fhp,buff(1));
flp=min(flp,buff(3));
end
clear eol buff BWpos;
end
% Get fhp, flp from res4.
if ~isempty(ds.res4.filters)
for kq=1:ds.res4.num_filters
freq=ds.res4.filters(kq).freq;
if ds.res4.filters(kq).fType==1;
flp=min(flp,freq);
elseif ds.res4.filters(kq).fType==2;
fhp=max(fhp,freq);
end
end
clear kq freq;
end
% Get fhp, flp from ds.infods
if isfield(ds,'infods')
name=getArrayField(ds.infods,'name')';
TagNo=strmatch('_DATASET_LOWERBANDWIDTH',name,'exact');
if ~isempty(TagNo);fhp=max(fhp,ds.infods(TagNo).data);end
TagNo=strmatch('_DATASET_UPPERBANDWIDTH',name,'exact');
if ~isempty(TagNo);flp=min(flp,ds.infods(TagNo).data);end
end
% Now have fhp,flp. Update hist. Add all the res4 filters.
if ~isempty(ds.res4.filters)
if ~isfield(ds,'hist');hist=char([]);end
ds.hist=[ds.hist 'Filters specified in res4 file :' char(10)];
for kq=1:ds.res4.num_filters
freq=ds.res4.filters(kq).freq;
if ds.res4.filters(kq).fType==1;
ds.hist=[ds.hist ...
num2str(kq,'%8d') ' Lowpass ' num2str(freq,'%6.2f') ' Hz' char(10)];
elseif ds.res4.filters(kq).fType==2;
ds.hist=[ds.hist ...
num2str(kq,'%8d') ' Highpass ' num2str(freq,'%6.2f') ' Hz' char(10)];
elseif ds.res4.filters(kq).fType==3;
ds.hist=[ds.hist num2str(kq,'%8d') ' Notch ' num2str(freq,'%6.2f') ...
' Hz width=' num2str(ds.res4.filters(kq).Param,'%6.2f') ' Hz' char(10)];
else
ds.hist=[ds.hist ' fType=',num2str(ds.res4.filters(kq).fType,'%d') char(10)];
end
end
ds.hist=[ds.hist ,...
'Bandwidth: ',num2str(fhp,'%0.3g'),' - ',num2str(flp,'%0.3g'),' Hz',char(10)];
clear kq freq;
end
% Update newds bandwidth
if isfield(ds,'newds')
BWpos=max(strfind(ds.newds,[char(9) 'bandwidth:' char(9)]));
eol=max([12 min(strfind(ds.newds(BWpos+1:length(ds.newds)),char(10)))]);
ds.newds=[ds.newds(1:BWpos+11) num2str(fhp,'%0.6f') ', ' num2str(flp,'%0.6f') ...
ds.newds((BWpos+eol):length(ds.newds))];
clear BWpos eol;
end
% Update infods bandwidth tags. Lots of coding becasue it's possible that infods does
% not already have bandwidth tags.
name=getArrayField(ds.infods,'name')';
DATASET_tags=strmatch('_DATASET_',name);
if ~isempty(DATASET_tags)
addTag=strvcat('_DATASET_LOWERBANDWIDTH','_DATASET_UPPERBANDWIDTH');
TagValue=[fhp flp];
% Add or update tags.
for q=1:size(addTag,1)
nTag=length(ds.infods);
TagNo=strmatch(deblank(addTag(q,:)),name,'exact')';
if isempty(TagNo) % Insert a tag at the end of the _DATASET tags.
TagNo=max(DATASET_tags)+1;
ds.infods((TagNo+1):(nTag+1))=ds.infods(TagNo:nTag);
ds.infods(TagNo)=struct('name',deblank(addTag(q,:)),'type',4,'data',TagValue(q));
name=strvcat(name(1:TagNo-1,:),deblank(addTag(q,:)),name(TagNo:nTag,:));
DATASET_tags=[DATASET_tags TagNo];
else
ds.infods(TagNo).data=TagValue(q); % Tag exists. Just update the value.
end
end % End loop over head position and head motion tags.
clear q nTag DATASET_tags;
else
fprintf(['writeCTFds (updateBandwidth): Found no _DATASET tags in infods.\n'...
'\t\t\tDid not add bandwidth tags.\n']);
end
return
%%%%%%%%%%%%%% End of updateBandwidth %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%% Function updateDateTime %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function ds=updateDateTime(ds);
% Update the dat/time fields of res4 and and infods
datetime=floor(clock);
if isfield(ds,'infods');
name=getArrayField(ds.infods,'name')';
DATASET_tags=strmatch('_DATASET_',name);
if ~isempty(DATASET_tags)
addTag=strvcat('_DATASET_CREATORDATETIME','_DATASET_LASTMODIFIEDDATETIME');
tagData=sprintf('%d%2.2d%2.2d%2.2d%2.2d%2.2d',datetime);
tagType=10;
for q=1:size(addTag,1)
nTag=length(ds.infods);
TagNo=strmatch(deblank(addTag(q,:)),name,'exact')';
if isempty(TagNo) % Insert a tag at the end of the _DATASET tags.
TagNo=max(DATASET_tags)+1;
ds.infods((TagNo+1):(nTag+1))=ds.infods(TagNo:nTag);
name=strvcat(name(1:TagNo-1,:),deblank(addTag(q,:)),name(TagNo:nTag,:));
DATASET_tags=[DATASET_tags TagNo];
end
ds.infods(TagNo)=struct('name',deblank(addTag(q,:)),'type',tagType,'data',tagData);
end
clear nTag TagNo name DATASET_tags addTag tagData tagType;
else
fprintf('writeCTFds (updateDateTime): Cannot find any _DATASET tags in ds.infods.\n');
end % End loop over head position and head motion tags.
else
fprintf('writeCTFds (updateDateTime): Cannot find ds.infods.\n');
end
ds.res4.data_date=sprintf('%4d/%2.2d/%2.2d',datetime(1:3));
ds.res4.data_time=sprintf('%2.2d:%2.2d:%2.2d',datetime(4:6));
return
%%%%%%%%%%%%%% End of updateDateTime %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%% Function getArrayField %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function x=getArrayField(S,yfield)
% Extracts one field of a structure array.
% Inputs: S : structure array.
% yfield: name of field of S (string)
% Output: x. x(:,n)=S(n).yfield; size(x)=[size(yfield) length(S)]
% Field sizes: Two options:
% 1. size(S(n).yfield) is the same for all n. Any size allowed.
% 2. S(n).yfield is a 2-D array for all structure elements S(n).
% Then yfield of different array elements S(n) can have different sizes.
% The array returned will be large enough to accomodate all of the data.
sizeS=size(S);
nS=prod(sizeS);
S=reshape(S,1,nS);
% Determine which array-size option to use.
sizey=size(getfield(S,{1},yfield));
option1=1;
option2=(length(sizey)==2);
for n=2:nS
sizeyn=size(getfield(S,{n},yfield));
option1=option1 & isequal(sizey,sizeyn);
option2=option2 & length(sizeyn)==2;
if option2
sizey=max([sizey;sizeyn],[],1);
end
end
if option1 % All fields have the same size
nY=prod(sizey);
if isnumeric(getfield(S,{1},yfield))
x=zeros(nY,nS);
elseif ischar(getfield(S,{1},yfield))
x=char(zeros(nY,nS));
end
for n=1:nS
x(:,n)=reshape(getfield(S,{n},yfield),nY,1);
end
x=reshape(x,[sizey nS]);
elseif option2 % All fields have only two dimensions
if isnumeric(getfield(S,{1},yfield))
x=zeros([sizey nS]);
elseif ischar(getfield(S,{1},yfield))
x=char(zeros([sizey nS]));
end
for n=1:nS
y=getfield(S,{n},yfield);
sizeyn=size(y);
x(1:sizeyn(1),1:sizeyn(2),n)=y;
end
else
fprintf(['getArrayField: Field %s of the structure array has >2 dimensions ',...
'and not all field have the same size.\n'],yfield);
x=[];
end
x=squeeze(x);
return
%%%%%%%% End of getArrayField %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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