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|---|---|---|---|---|---|---|---|---|
github
|
jacksky64/imageProcessing-master
|
upBlur.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/upBlur.m
| 1,213 |
utf_8
|
7b07d26940520537edb6e8dc25b72242
|
% RES = upBlur(IM, LEVELS, FILT)
%
% Upsample and blur an image. The blurring is done with filter
% kernel specified by FILT (default = 'binom5'), which can be a string
% (to be passed to namedFilter), a vector (applied separably as a 1D
% convolution kernel in X and Y), or a matrix (applied as a 2D
% convolution kernel). The downsampling is always by 2 in each
% direction.
%
% The procedure is applied recursively LEVELS times (default=1).
% Eero Simoncelli, 4/97.
function res = upBlur(im, nlevs, filt)
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('nlevs') ~= 1)
nlevs = 1;
end
if (exist('filt') ~= 1)
filt = 'binom5';
end
%------------------------------------------------------------
if isstr(filt)
filt = namedFilter(filt);
end
if nlevs > 1
im = upBlur(im,nlevs-1,filt);
end
if (nlevs >= 1)
if (any(size(im)==1))
if (size(im,1)==1)
filt = filt';
end
res = upConv(im,filt,'reflect1',(size(im)~=1)+1);
elseif (any(size(filt)==1))
filt = filt(:);
res = upConv(im,filt,'reflect1',[2 1]);
res = upConv(res,filt','reflect1',[1 2]);
else
res = upConv(im,filt,'reflect1',[2 2]);
end
else
res = im;
end
|
github
|
jacksky64/imageProcessing-master
|
nextFig.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/nextFig.m
| 363 |
utf_8
|
94a66b00983cd3840ff1cc88f118a022
|
% nextFig (MAXFIGS, SKIP)
%
% Make figure number mod((GCF+SKIP), MAXFIGS) the current figure.
% MAXFIGS is optional, and defaults to 2.
% SKIP is optional, and defaults to 1.
% Eero Simoncelli, 2/97.
function nextFig(maxfigs, skip)
if (exist('maxfigs') ~= 1)
maxfigs = 2;
end
if (exist('skip') ~= 1)
skip = 1;
end
figure(1+mod(gcf-1+skip,maxfigs));
|
github
|
jacksky64/imageProcessing-master
|
zconv2.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/zconv2.m
| 1,164 |
utf_8
|
cd266795530db4cb146c1038383316f3
|
% RES = ZCONV2(MTX1, MTX2, CTR)
%
% Convolution of two matrices, with boundaries handled as if the larger mtx
% lies in a sea of zeros. Result will be of size of LARGER vector.
%
% The origin of the smaller matrix is assumed to be its center.
% For even dimensions, the origin is determined by the CTR (optional)
% argument:
% CTR origin
% 0 DIM/2 (default)
% 1 (DIM/2)+1 (behaves like conv2(mtx1,mtx2,'same'))
% Eero Simoncelli, 2/97.
function c = zconv2(a,b,ctr)
if (exist('ctr') ~= 1)
ctr = 0;
end
if (( size(a,1) >= size(b,1) ) & ( size(a,2) >= size(b,2) ))
large = a; small = b;
elseif (( size(a,1) <= size(b,1) ) & ( size(a,2) <= size(b,2) ))
large = b; small = a;
else
error('one arg must be larger than the other in both dimensions!');
end
ly = size(large,1);
lx = size(large,2);
sy = size(small,1);
sx = size(small,2);
%% These values are the index of the small mtx that falls on the
%% border pixel of the large matrix when computing the first
%% convolution response sample:
sy2 = floor((sy+ctr+1)/2);
sx2 = floor((sx+ctr+1)/2);
clarge = conv2(large,small);
c = clarge(sy2:ly+sy2-1, sx2:lx+sx2-1);
|
github
|
jacksky64/imageProcessing-master
|
mkZonePlate.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/mkZonePlate.m
| 633 |
utf_8
|
d88329c8d374e54e124222c825679768
|
% IM = mkZonePlate(SIZE, AMPL, PHASE)
%
% Make a "zone plate" image:
% AMPL * cos( r^2 + PHASE)
% SIZE specifies the matrix size, as for zeros().
% AMPL (default = 1) and PHASE (default = 0) are optional.
% Eero Simoncelli, 6/96.
function [res] = mkZonePlate(sz, ampl, ph)
sz = sz(:);
if (size(sz,1) == 1)
sz = [sz,sz];
end
mxsz = max(sz(1),sz(2));
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('ampl') ~= 1)
ampl = 1;
end
if (exist('ph') ~= 1)
ph = 0;
end
%------------------------------------------------------------
res = ampl * cos( (pi/mxsz) * mkR(sz,2) + ph );
|
github
|
jacksky64/imageProcessing-master
|
steer2HarmMtx.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/steer2HarmMtx.m
| 1,803 |
utf_8
|
35816be985c308717168260dc97419d8
|
% MTX = steer2HarmMtx(HARMONICS, ANGLES, REL_PHASES)
%
% Compute a steering matrix (maps a directional basis set onto the
% angular Fourier harmonics). HARMONICS is a vector specifying the
% angular harmonics contained in the steerable basis/filters. ANGLES
% (optional) is a vector specifying the angular position of each filter.
% REL_PHASES (optional, default = 'even') specifies whether the harmonics
% are cosine or sine phase aligned about those positions.
% The result matrix is suitable for passing to the function STEER.
% Eero Simoncelli, 7/96.
function mtx = steer2HarmMtx(harmonics, angles, evenorodd)
%%=================================================================
%%% Optional Parameters:
if (exist('evenorodd') ~= 1)
evenorodd = 'even';
end
% Make HARMONICS a row vector
harmonics = harmonics(:)';
numh = 2*size(harmonics,2) - any(harmonics == 0);
if (exist('angles') ~= 1)
angles = pi * [0:numh-1]'/numh;
else
angles = angles(:);
end
%%=================================================================
if isstr(evenorodd)
if strcmp(evenorodd,'even')
evenorodd = 0;
elseif strcmp(evenorodd,'odd')
evenorodd = 1;
else
error('EVEN_OR_ODD should be the string EVEN or ODD');
end
end
%% Compute inverse matrix, which maps Fourier components onto
%% steerable basis.
imtx = zeros(size(angles,1),numh);
col = 1;
for h=harmonics
args = h*angles;
if (h == 0)
imtx(:,col) = ones(size(angles));
col = col+1;
elseif evenorodd
imtx(:,col) = sin(args);
imtx(:,col+1) = -cos(args);
col = col+2;
else
imtx(:,col) = cos(args);
imtx(:,col+1) = sin(args);
col = col+2;
end
end
r = rank(imtx);
if (( r ~= numh ) & ( r ~= size(angles,1) ))
fprintf(2,'WARNING: matrix is not full rank');
end
mtx = pinv(imtx);
|
github
|
jacksky64/imageProcessing-master
|
mkAngularSine.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/mkAngularSine.m
| 845 |
utf_8
|
78a5e0afe3fef5c42804516e2ea1ccc8
|
% IM = mkAngularSine(SIZE, HARMONIC, AMPL, PHASE, ORIGIN)
%
% Make an angular sinusoidal image:
% AMPL * sin( HARMONIC*theta + PHASE),
% where theta is the angle about the origin.
% SIZE specifies the matrix size, as for zeros().
% AMPL (default = 1) and PHASE (default = 0) are optional.
% Eero Simoncelli, 2/97.
function [res] = mkAngularSine(sz, harmonic, ampl, ph, origin)
sz = sz(:);
if (size(sz,1) == 1)
sz = [sz,sz];
end
mxsz = max(sz(1),sz(2));
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('harmonic') ~= 1)
harmonic = 1;
end
if (exist('ampl') ~= 1)
ampl = 1;
end
if (exist('ph') ~= 1)
ph = 0;
end
if (exist('origin') ~= 1)
origin = (sz+1)/2;
end
%------------------------------------------------------------
res = ampl * sin(harmonic*mkAngle(sz,ph,origin) + ph);
|
github
|
jacksky64/imageProcessing-master
|
mkRamp.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/mkRamp.m
| 1,110 |
utf_8
|
28989822e19c604a816a287a4bee873d
|
% IM = mkRamp(SIZE, DIRECTION, SLOPE, INTERCEPT, ORIGIN)
%
% Compute a matrix of dimension SIZE (a [Y X] 2-vector, or a scalar)
% containing samples of a ramp function, with given gradient DIRECTION
% (radians, CW from X-axis, default = 0), SLOPE (per pixel, default =
% 1), and a value of INTERCEPT (default = 0) at the ORIGIN (default =
% (size+1)/2, [1 1] = upper left). All but the first argument are
% optional.
% Eero Simoncelli, 6/96. 2/97: adjusted coordinate system.
function [res] = mkRamp(sz, dir, slope, intercept, origin)
sz = sz(:);
if (size(sz,1) == 1)
sz = [sz,sz];
end
% -----------------------------------------------------------------
% OPTIONAL args:
if (exist('dir') ~= 1)
dir = 0;
end
if (exist('slope') ~= 1)
slope = 1;
end
if (exist('intercept') ~= 1)
intercept = 0;
end
if (exist('origin') ~= 1)
origin = (sz+1)/2;
end
% -----------------------------------------------------------------
xinc = slope*cos(dir);
yinc = slope*sin(dir);
[xramp,yramp] = meshgrid( xinc*([1:sz(2)]-origin(2)), ...
yinc*([1:sz(1)]-origin(1)) );
res = intercept + xramp + yramp;
|
github
|
jacksky64/imageProcessing-master
|
histoMatch.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/histoMatch.m
| 858 |
utf_8
|
8936fc2eadacc591ecdffe5967726780
|
% RES = histoMatch(MTX, N, X)
%
% Modify elements of MTX so that normalized histogram matches that
% specified by vectors X and N, where N contains the histogram counts
% and X the histogram bin positions (see histo).
% Eero Simoncelli, 7/96.
function res = histoMatch(mtx, N, X)
if ( exist('histo') == 3 )
[oN, oX] = histo(mtx(:), size(X(:),1));
else
[oN, oX] = hist(mtx(:), size(X(:),1));
end
oStep = oX(2) - oX(1);
oC = [0, cumsum(oN)]/sum(oN);
oX = [oX(1)-oStep/2, oX+oStep/2];
N = N(:)';
X = X(:)';
N = N + mean(N)/(1e8); %% HACK: no empty bins ensures nC strictly monotonic
nStep = X(2) - X(1);
nC = [0, cumsum(N)]/sum(N);
nX = [X(1)-nStep/2, X+nStep/2];
nnX = interp1(nC, nX, oC, 'linear');
if ( exist('pointOp') == 3 )
res = pointOp(mtx, nnX, oX(1), oStep);
else
res = reshape(interp1(oX, nnX, mtx(:)),size(mtx,1),size(mtx,2));
end
|
github
|
jacksky64/imageProcessing-master
|
subMtx.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/subMtx.m
| 420 |
utf_8
|
c660029ce728dcb8c540c9cf419fa7bc
|
% MTX = subMtx(VEC, DIMENSIONS, START_INDEX)
%
% Reshape a portion of VEC starting from START_INDEX (optional,
% default=1) to the given dimensions.
% Eero Simoncelli, 6/96.
function mtx = subMtx(vec, sz, offset)
if (exist('offset') ~= 1)
offset = 1;
end
vec = vec(:);
sz = sz(:);
if (size(sz,1) ~= 2)
error('DIMENSIONS must be a 2-vector.');
end
mtx = reshape( vec(offset:offset+prod(sz)-1), sz(1), sz(2) );
|
github
|
jacksky64/imageProcessing-master
|
showLpyr.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/showLpyr.m
| 5,421 |
utf_8
|
0646b94ae144cf6160a44f50e67f8dd5
|
% RANGE = showLpyr (PYR, INDICES, RANGE, GAP, LEVEL_SCALE_FACTOR)
%
% Display a Laplacian (or Gaussian) pyramid, specified by PYR and
% INDICES (see buildLpyr), in the current figure.
%
% RANGE is a 2-vector specifying the values that map to black and
% white, respectively. These values are scaled by
% LEVEL_SCALE_FACTOR^(lev-1) for bands at each level. Passing a value
% of 'auto1' sets RANGE to the min and max values of MATRIX. 'auto2'
% sets RANGE to 3 standard deviations below and above 0.0. In both of
% these cases, the lowpass band is independently scaled. A value of
% 'indep1' sets the range of each subband independently, as in a call
% to showIm(subband,'auto1'). Similarly, 'indep2' causes each subband
% to be scaled independently as if by showIm(subband,'indep2').
% The default value for RANGE is 'auto1' for 1D images, and 'auto2' for
% 2D images.
%
% GAP (optional, default=1) specifies the gap in pixels to leave
% between subbands (2D images only).
%
% LEVEL_SCALE_FACTOR indicates the relative scaling between pyramid
% levels. This should be set to the sum of the kernel taps of the
% lowpass filter used to construct the pyramid (default assumes
% L2-normalalized filters, using a value of 2 for 2D images, sqrt(2) for
% 1D images).
% Eero Simoncelli, 2/97.
function [range] = showLpyr(pyr, pind, range, gap, scale);
% Determine 1D or 2D pyramid:
if ((pind(1,1) == 1) | (pind(1,2) ==1))
oned = 1;
else
oned = 0;
end
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('range') ~= 1)
if (oned==1)
range = 'auto1';
else
range = 'auto2';
end
end
if (exist('gap') ~= 1)
gap = 1;
end
if (exist('scale') ~= 1)
if (oned == 1)
scale = sqrt(2);
else
scale = 2;
end
end
%------------------------------------------------------------
nind = size(pind,1);
%% Auto range calculations:
if strcmp(range,'auto1')
range = zeros(nind,1);
mn = 0.0; mx = 0.0;
for bnum = 1:(nind-1)
band = pyrBand(pyr,pind,bnum)/(scale^(bnum-1));
range(bnum) = scale^(bnum-1);
[bmn,bmx] = range2(band);
mn = min(mn, bmn); mx = max(mx, bmx);
end
if (oned == 1)
pad = (mx-mn)/12; % *** MAGIC NUMBER!!
mn = mn-pad; mx = mx+pad;
end
range = range * [mn mx]; % outer product
band = pyrLow(pyr,pind);
[mn,mx] = range2(band);
if (oned == 1)
pad = (mx-mn)/12; % *** MAGIC NUMBER!!
mn = mn-pad; mx = mx+pad;
end
range(nind,:) = [mn, mx];
elseif strcmp(range,'indep1')
range = zeros(nind,2);
for bnum = 1:nind
band = pyrBand(pyr,pind,bnum);
[mn,mx] = range2(band);
if (oned == 1)
pad = (mx-mn)/12; % *** MAGIC NUMBER!!
mn = mn-pad; mx = mx+pad;
end
range(bnum,:) = [mn mx];
end
elseif strcmp(range,'auto2')
range = zeros(nind,1);
sqsum = 0; numpixels = 0;
for bnum = 1:(nind-1)
band = pyrBand(pyr,pind,bnum)/(scale^(bnum-1));
sqsum = sqsum + sum(sum(band.^2));
numpixels = numpixels + prod(size(band));
range(bnum) = scale^(bnum-1);
end
stdev = sqrt(sqsum/(numpixels-1));
range = range * [ -3*stdev 3*stdev ]; % outer product
band = pyrLow(pyr,pind);
av = mean2(band); stdev = sqrt(var2(band));
range(nind,:) = [av-2*stdev,av+2*stdev];
elseif strcmp(range,'indep2')
range = zeros(nind,2);
for bnum = 1:(nind-1)
band = pyrBand(pyr,pind,bnum);
stdev = sqrt(var2(band));
range(bnum,:) = [ -3*stdev 3*stdev ];
end
band = pyrLow(pyr,pind);
av = mean2(band); stdev = sqrt(var2(band));
range(nind,:) = [av-2*stdev,av+2*stdev];
elseif isstr(range)
error(sprintf('Bad RANGE argument: %s',range))
elseif ((size(range,1) == 1) & (size(range,2) == 2))
scales = scale.^[0:nind-1];
range = scales(:) * range; % outer product
band = pyrLow(pyr,pind);
range(nind,:) = range(nind,:) + mean2(band) - mean(range(nind,:));
end
%% Clear Figure
clf;
if (oned == 1)
%%%%% 1D signal:
for bnum=1:nind
band = pyrBand(pyr,pind,bnum);
subplot(nind,1,nind-bnum+1);
plot(band);
axis([1, prod(size(band)), range(bnum,:)]);
end
else
%%%%% 2D signal:
colormap(gray);
cmap = get(gcf,'Colormap');
nshades = size(cmap,1);
% Find background color index:
clr = get(gcf,'Color');
bg = 1;
dist = norm(cmap(bg,:)-clr);
for n = 1:nshades
ndist = norm(cmap(n,:)-clr);
if (ndist < dist)
dist = ndist;
bg = n;
end
end
%% Compute positions of subbands:
llpos = ones(nind,2);
dir = [-1 -1];
ctr = [pind(1,1)+1+gap 1];
sz = [0 0];
for bnum = 1:nind
prevsz = sz;
sz = pind(bnum,:);
% Determine center position of new band:
ctr = ctr + gap*dir/2 + dir.* floor((prevsz+(dir>0))/2);
dir = dir * [0 -1; 1 0]; % ccw rotation
ctr = ctr + gap*dir/2 + dir.* floor((sz+(dir<0))/2);
llpos(bnum,:) = ctr - floor(sz./2);
end
%% Make position list positive, and allocate appropriate image:
llpos = llpos - ones(nind,1)*min(llpos) + 1;
urpos = llpos + pind - 1;
d_im = bg + zeros(max(urpos));
%% Paste bands into image, (im-r1)*(nshades-1)/(r2-r1) + 1.5
for bnum=1:nind
mult = (nshades-1) / (range(bnum,2)-range(bnum,1));
d_im(llpos(bnum,1):urpos(bnum,1), llpos(bnum,2):urpos(bnum,2)) = ...
mult*pyrBand(pyr,pind,bnum) + (1.5-mult*range(bnum,1));
end
hh = image(d_im);
axis('off');
pixelAxes(size(d_im),'full');
set(hh,'UserData',range);
end
|
github
|
jacksky64/imageProcessing-master
|
sp1Filters.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/sp1Filters.m
| 9,435 |
utf_8
|
81cfbf726744492bee2374b9b564ebdf
|
% Steerable pyramid filters. Transform described in:
%
% @INPROCEEDINGS{Simoncelli95b,
% TITLE = "The Steerable Pyramid: A Flexible Architecture for
% Multi-Scale Derivative Computation",
% AUTHOR = "E P Simoncelli and W T Freeman",
% BOOKTITLE = "Second Int'l Conf on Image Processing",
% ADDRESS = "Washington, DC", MONTH = "October", YEAR = 1995 }
%
% Filter kernel design described in:
%
%@INPROCEEDINGS{Karasaridis96,
% TITLE = "A Filter Design Technique for
% Steerable Pyramid Image Transforms",
% AUTHOR = "A Karasaridis and E P Simoncelli",
% BOOKTITLE = "ICASSP", ADDRESS = "Atlanta, GA",
% MONTH = "May", YEAR = 1996 }
% Eero Simoncelli, 6/96.
function [lo0filt,hi0filt,lofilt,bfilts,mtx,harmonics] = sp1Filters();
harmonics = [ 1 ];
%% filters only contain first harmonic.
mtx = eye(2);
lo0filt = [ ...
-8.701000e-05 -1.354280e-03 -1.601260e-03 -5.033700e-04 2.524010e-03 -5.033700e-04 -1.601260e-03 -1.354280e-03 -8.701000e-05
-1.354280e-03 2.921580e-03 7.522720e-03 8.224420e-03 1.107620e-03 8.224420e-03 7.522720e-03 2.921580e-03 -1.354280e-03
-1.601260e-03 7.522720e-03 -7.061290e-03 -3.769487e-02 -3.297137e-02 -3.769487e-02 -7.061290e-03 7.522720e-03 -1.601260e-03
-5.033700e-04 8.224420e-03 -3.769487e-02 4.381320e-02 1.811603e-01 4.381320e-02 -3.769487e-02 8.224420e-03 -5.033700e-04
2.524010e-03 1.107620e-03 -3.297137e-02 1.811603e-01 4.376250e-01 1.811603e-01 -3.297137e-02 1.107620e-03 2.524010e-03
-5.033700e-04 8.224420e-03 -3.769487e-02 4.381320e-02 1.811603e-01 4.381320e-02 -3.769487e-02 8.224420e-03 -5.033700e-04
-1.601260e-03 7.522720e-03 -7.061290e-03 -3.769487e-02 -3.297137e-02 -3.769487e-02 -7.061290e-03 7.522720e-03 -1.601260e-03
-1.354280e-03 2.921580e-03 7.522720e-03 8.224420e-03 1.107620e-03 8.224420e-03 7.522720e-03 2.921580e-03 -1.354280e-03
-8.701000e-05 -1.354280e-03 -1.601260e-03 -5.033700e-04 2.524010e-03 -5.033700e-04 -1.601260e-03 -1.354280e-03 -8.701000e-05
];
lofilt = [ ...
-4.350000e-05 1.207800e-04 -6.771400e-04 -1.243400e-04 -8.006400e-04 -1.597040e-03 -2.516800e-04 -4.202000e-04 1.262000e-03 -4.202000e-04 -2.516800e-04 -1.597040e-03 -8.006400e-04 -1.243400e-04 -6.771400e-04 1.207800e-04 -4.350000e-05 ; ...
1.207800e-04 4.460600e-04 -5.814600e-04 5.621600e-04 -1.368800e-04 2.325540e-03 2.889860e-03 4.287280e-03 5.589400e-03 4.287280e-03 2.889860e-03 2.325540e-03 -1.368800e-04 5.621600e-04 -5.814600e-04 4.460600e-04 1.207800e-04 ; ...
-6.771400e-04 -5.814600e-04 1.460780e-03 2.160540e-03 3.761360e-03 3.080980e-03 4.112200e-03 2.221220e-03 5.538200e-04 2.221220e-03 4.112200e-03 3.080980e-03 3.761360e-03 2.160540e-03 1.460780e-03 -5.814600e-04 -6.771400e-04 ; ...
-1.243400e-04 5.621600e-04 2.160540e-03 3.175780e-03 3.184680e-03 -1.777480e-03 -7.431700e-03 -9.056920e-03 -9.637220e-03 -9.056920e-03 -7.431700e-03 -1.777480e-03 3.184680e-03 3.175780e-03 2.160540e-03 5.621600e-04 -1.243400e-04 ; ...
-8.006400e-04 -1.368800e-04 3.761360e-03 3.184680e-03 -3.530640e-03 -1.260420e-02 -1.884744e-02 -1.750818e-02 -1.648568e-02 -1.750818e-02 -1.884744e-02 -1.260420e-02 -3.530640e-03 3.184680e-03 3.761360e-03 -1.368800e-04 -8.006400e-04 ; ...
-1.597040e-03 2.325540e-03 3.080980e-03 -1.777480e-03 -1.260420e-02 -2.022938e-02 -1.109170e-02 3.955660e-03 1.438512e-02 3.955660e-03 -1.109170e-02 -2.022938e-02 -1.260420e-02 -1.777480e-03 3.080980e-03 2.325540e-03 -1.597040e-03 ; ...
-2.516800e-04 2.889860e-03 4.112200e-03 -7.431700e-03 -1.884744e-02 -1.109170e-02 2.190660e-02 6.806584e-02 9.058014e-02 6.806584e-02 2.190660e-02 -1.109170e-02 -1.884744e-02 -7.431700e-03 4.112200e-03 2.889860e-03 -2.516800e-04 ; ...
-4.202000e-04 4.287280e-03 2.221220e-03 -9.056920e-03 -1.750818e-02 3.955660e-03 6.806584e-02 1.445500e-01 1.773651e-01 1.445500e-01 6.806584e-02 3.955660e-03 -1.750818e-02 -9.056920e-03 2.221220e-03 4.287280e-03 -4.202000e-04 ; ...
1.262000e-03 5.589400e-03 5.538200e-04 -9.637220e-03 -1.648568e-02 1.438512e-02 9.058014e-02 1.773651e-01 2.120374e-01 1.773651e-01 9.058014e-02 1.438512e-02 -1.648568e-02 -9.637220e-03 5.538200e-04 5.589400e-03 1.262000e-03 ; ...
-4.202000e-04 4.287280e-03 2.221220e-03 -9.056920e-03 -1.750818e-02 3.955660e-03 6.806584e-02 1.445500e-01 1.773651e-01 1.445500e-01 6.806584e-02 3.955660e-03 -1.750818e-02 -9.056920e-03 2.221220e-03 4.287280e-03 -4.202000e-04 ; ...
-2.516800e-04 2.889860e-03 4.112200e-03 -7.431700e-03 -1.884744e-02 -1.109170e-02 2.190660e-02 6.806584e-02 9.058014e-02 6.806584e-02 2.190660e-02 -1.109170e-02 -1.884744e-02 -7.431700e-03 4.112200e-03 2.889860e-03 -2.516800e-04 ; ...
-1.597040e-03 2.325540e-03 3.080980e-03 -1.777480e-03 -1.260420e-02 -2.022938e-02 -1.109170e-02 3.955660e-03 1.438512e-02 3.955660e-03 -1.109170e-02 -2.022938e-02 -1.260420e-02 -1.777480e-03 3.080980e-03 2.325540e-03 -1.597040e-03 ; ...
-8.006400e-04 -1.368800e-04 3.761360e-03 3.184680e-03 -3.530640e-03 -1.260420e-02 -1.884744e-02 -1.750818e-02 -1.648568e-02 -1.750818e-02 -1.884744e-02 -1.260420e-02 -3.530640e-03 3.184680e-03 3.761360e-03 -1.368800e-04 -8.006400e-04 ; ...
-1.243400e-04 5.621600e-04 2.160540e-03 3.175780e-03 3.184680e-03 -1.777480e-03 -7.431700e-03 -9.056920e-03 -9.637220e-03 -9.056920e-03 -7.431700e-03 -1.777480e-03 3.184680e-03 3.175780e-03 2.160540e-03 5.621600e-04 -1.243400e-04 ; ...
-6.771400e-04 -5.814600e-04 1.460780e-03 2.160540e-03 3.761360e-03 3.080980e-03 4.112200e-03 2.221220e-03 5.538200e-04 2.221220e-03 4.112200e-03 3.080980e-03 3.761360e-03 2.160540e-03 1.460780e-03 -5.814600e-04 -6.771400e-04 ; ...
1.207800e-04 4.460600e-04 -5.814600e-04 5.621600e-04 -1.368800e-04 2.325540e-03 2.889860e-03 4.287280e-03 5.589400e-03 4.287280e-03 2.889860e-03 2.325540e-03 -1.368800e-04 5.621600e-04 -5.814600e-04 4.460600e-04 1.207800e-04 ; ...
-4.350000e-05 1.207800e-04 -6.771400e-04 -1.243400e-04 -8.006400e-04 -1.597040e-03 -2.516800e-04 -4.202000e-04 1.262000e-03 -4.202000e-04 -2.516800e-04 -1.597040e-03 -8.006400e-04 -1.243400e-04 -6.771400e-04 1.207800e-04 -4.350000e-05 ];
hi0filt = [...
-9.570000e-04 -2.424100e-04 -1.424720e-03 -8.742600e-04 -1.166810e-03 -8.742600e-04 -1.424720e-03 -2.424100e-04 -9.570000e-04 ; ...
-2.424100e-04 -4.317530e-03 8.998600e-04 9.156420e-03 1.098012e-02 9.156420e-03 8.998600e-04 -4.317530e-03 -2.424100e-04 ; ...
-1.424720e-03 8.998600e-04 1.706347e-02 1.094866e-02 -5.897780e-03 1.094866e-02 1.706347e-02 8.998600e-04 -1.424720e-03 ; ...
-8.742600e-04 9.156420e-03 1.094866e-02 -7.841370e-02 -1.562827e-01 -7.841370e-02 1.094866e-02 9.156420e-03 -8.742600e-04 ; ...
-1.166810e-03 1.098012e-02 -5.897780e-03 -1.562827e-01 7.282593e-01 -1.562827e-01 -5.897780e-03 1.098012e-02 -1.166810e-03 ; ...
-8.742600e-04 9.156420e-03 1.094866e-02 -7.841370e-02 -1.562827e-01 -7.841370e-02 1.094866e-02 9.156420e-03 -8.742600e-04 ; ...
-1.424720e-03 8.998600e-04 1.706347e-02 1.094866e-02 -5.897780e-03 1.094866e-02 1.706347e-02 8.998600e-04 -1.424720e-03 ; ...
-2.424100e-04 -4.317530e-03 8.998600e-04 9.156420e-03 1.098012e-02 9.156420e-03 8.998600e-04 -4.317530e-03 -2.424100e-04 ; ...
-9.570000e-04 -2.424100e-04 -1.424720e-03 -8.742600e-04 -1.166810e-03 -8.742600e-04 -1.424720e-03 -2.424100e-04 -9.570000e-04 ];
bfilts = -[ ...
6.125880e-03 -8.052600e-03 -2.103714e-02 -1.536890e-02 -1.851466e-02 -1.536890e-02 -2.103714e-02 -8.052600e-03 6.125880e-03 ...
-1.287416e-02 -9.611520e-03 1.023569e-02 6.009450e-03 1.872620e-03 6.009450e-03 1.023569e-02 -9.611520e-03 -1.287416e-02 ...
-5.641530e-03 4.168400e-03 -2.382180e-02 -5.375324e-02 -2.076086e-02 -5.375324e-02 -2.382180e-02 4.168400e-03 -5.641530e-03 ...
-8.957260e-03 -1.751170e-03 -1.836909e-02 1.265655e-01 2.996168e-01 1.265655e-01 -1.836909e-02 -1.751170e-03 -8.957260e-03 ...
0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 ...
8.957260e-03 1.751170e-03 1.836909e-02 -1.265655e-01 -2.996168e-01 -1.265655e-01 1.836909e-02 1.751170e-03 8.957260e-03 ...
5.641530e-03 -4.168400e-03 2.382180e-02 5.375324e-02 2.076086e-02 5.375324e-02 2.382180e-02 -4.168400e-03 5.641530e-03 ...
1.287416e-02 9.611520e-03 -1.023569e-02 -6.009450e-03 -1.872620e-03 -6.009450e-03 -1.023569e-02 9.611520e-03 1.287416e-02 ...
-6.125880e-03 8.052600e-03 2.103714e-02 1.536890e-02 1.851466e-02 1.536890e-02 2.103714e-02 8.052600e-03 -6.125880e-03; ...
...
-6.125880e-03 1.287416e-02 5.641530e-03 8.957260e-03 0.000000e+00 -8.957260e-03 -5.641530e-03 -1.287416e-02 6.125880e-03 ...
8.052600e-03 9.611520e-03 -4.168400e-03 1.751170e-03 0.000000e+00 -1.751170e-03 4.168400e-03 -9.611520e-03 -8.052600e-03 ...
2.103714e-02 -1.023569e-02 2.382180e-02 1.836909e-02 0.000000e+00 -1.836909e-02 -2.382180e-02 1.023569e-02 -2.103714e-02 ...
1.536890e-02 -6.009450e-03 5.375324e-02 -1.265655e-01 0.000000e+00 1.265655e-01 -5.375324e-02 6.009450e-03 -1.536890e-02 ...
1.851466e-02 -1.872620e-03 2.076086e-02 -2.996168e-01 0.000000e+00 2.996168e-01 -2.076086e-02 1.872620e-03 -1.851466e-02 ...
1.536890e-02 -6.009450e-03 5.375324e-02 -1.265655e-01 0.000000e+00 1.265655e-01 -5.375324e-02 6.009450e-03 -1.536890e-02 ...
2.103714e-02 -1.023569e-02 2.382180e-02 1.836909e-02 0.000000e+00 -1.836909e-02 -2.382180e-02 1.023569e-02 -2.103714e-02 ...
8.052600e-03 9.611520e-03 -4.168400e-03 1.751170e-03 0.000000e+00 -1.751170e-03 4.168400e-03 -9.611520e-03 -8.052600e-03 ...
-6.125880e-03 1.287416e-02 5.641530e-03 8.957260e-03 0.000000e+00 -8.957260e-03 -5.641530e-03 -1.287416e-02 6.125880e-03 ...
]';
|
github
|
jacksky64/imageProcessing-master
|
spyrHt.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/spyrHt.m
| 305 |
utf_8
|
06e83c1f45c1a99e242fa7ea37093a11
|
% [HEIGHT] = spyrHt(INDICES)
%
% Compute height of steerable pyramid with given index matrix.
% Eero Simoncelli, 6/96.
function [ht] = spyrHt(pind)
nbands = spyrNumBands(pind);
% Don't count lowpass, or highpass residual bands
if (size(pind,1) > 2)
ht = (size(pind,1)-2)/nbands;
else
ht = 0;
end
|
github
|
jacksky64/imageProcessing-master
|
spyrBand.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/spyrBand.m
| 819 |
utf_8
|
7d15b24244e521c9e85c68b3037f569b
|
% [LEV,IND] = spyrBand(PYR,INDICES,LEVEL,BAND)
%
% Access a band from a steerable pyramid.
%
% LEVEL indicates the scale (finest = 1, coarsest = spyrHt(INDICES)).
%
% BAND (optional, default=1) indicates which subband
% (1 = vertical, rest proceeding anti-clockwise).
% Eero Simoncelli, 6/96.
function res = spyrBand(pyr,pind,level,band)
if (exist('level') ~= 1)
level = 1;
end
if (exist('band') ~= 1)
band = 1;
end
nbands = spyrNumBands(pind);
if ((band > nbands) | (band < 1))
error(sprintf('Bad band number (%d) should be in range [1,%d].', band, nbands));
end
maxLev = spyrHt(pind);
if ((level > maxLev) | (level < 1))
error(sprintf('Bad level number (%d), should be in range [1,%d].', level, maxLev));
end
firstband = 1 + band + nbands*(level-1);
res = pyrBand(pyr, pind, firstband);
|
github
|
jacksky64/imageProcessing-master
|
wpyrBand.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/wpyrBand.m
| 873 |
utf_8
|
12e08d90ccd6261b737e2d3c5ac5b1e7
|
% RES = wpyrBand(PYR, INDICES, LEVEL, BAND)
%
% Access a subband from a separable QMF/wavelet pyramid.
%
% LEVEL (optional, default=1) indicates the scale (finest = 1,
% coarsest = wpyrHt(INDICES)).
%
% BAND (optional, default=1) indicates which subband (1=horizontal,
% 2=vertical, 3=diagonal).
% Eero Simoncelli, 6/96.
function im = wpyrBand(pyr,pind,level,band)
if (exist('level') ~= 1)
level = 1;
end
if (exist('band') ~= 1)
band = 1;
end
if ((pind(1,1) == 1) | (pind(1,2) ==1))
nbands = 1;
else
nbands = 3;
end
if ((band > nbands) | (band < 1))
error(sprintf('Bad band number (%d) should be in range [1,%d].', band, nbands));
end
maxLev = wpyrHt(pind);
if ((level > maxLev) | (level < 1))
error(sprintf('Bad level number (%d), should be in range [1,%d].', level, maxLev));
end
band = band + nbands*(level-1);
im = pyrBand(pyr,pind,band);
|
github
|
jacksky64/imageProcessing-master
|
skew2.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/skew2.m
| 478 |
utf_8
|
b304767117ab43e408c5757ab9e3402d
|
% S = SKEW2(MTX,MEAN,VAR)
%
% Sample skew (third moment divided by variance^3/2) of a matrix.
% MEAN (optional) and VAR (optional) make the computation faster.
function res = skew2(mtx, mn, v)
if (exist('mn') ~= 1)
mn = mean2(mtx);
end
if (exist('v') ~= 1)
v = var2(mtx,mn);
end
if (isreal(mtx))
res = mean(mean((mtx-mn).^3)) / (v^(3/2));
else
res = mean(mean(real(mtx-mn).^3)) / (real(v)^(3/2)) + ...
i * mean(mean(imag(mtx-mn).^3)) / (imag(v)^(3/2));
end
|
github
|
jacksky64/imageProcessing-master
|
imStats.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/imStats.m
| 1,217 |
utf_8
|
aab8c3264c5939806bbca5657c925734
|
% imStats(IM1,IM2)
%
% Report image (matrix) statistics.
% When called on a single image IM1, report min, max, mean, stdev, skew,
% and kurtosis (4th moment about the mean, divided by squared variance)
%
% When called on two images (IM1 and IM2), report min, max, mean,
% stdev of the difference, and also SNR (relative to IM1).
% Eero Simoncelli, 6/96.
function [] = imStats(im1,im2)
if (~isreal(im1))
error('Args must be real-valued matrices');
end
if (exist('im2') == 1)
difference = im1 - im2;
[mn,mx] = range2(difference);
mean = mean2(difference);
v = var2(difference,mean);
if (v < realmin)
snr = Inf;
else
snr = 10 * log10(var2(im1)/v);
end
fprintf(1, 'Difference statistics:\n');
fprintf(1, ' Range: [%c, %c]\n',mn,mx);
fprintf(1, ' Mean: %f, Stdev (rmse): %f, SNR (dB): %f\n',...
mean,sqrt(v),snr);
else
[mn,mx] = range2(im1);
mean = mean2(im1);
var = var2(im1,mean);
stdev = sqrt(real(var))+sqrt(imag(var));
sk = skew2(im1, mean, stdev^2);
kurt = kurt2(im1, mean, stdev^2);
fprintf(1, 'Image statistics:\n');
fprintf(1, ' Range: [%f, %f]\n',mn,mx);
fprintf(1, ' Mean: %f, Stdev: %f, Skew: %f, Kurt: %f\n',mean,stdev,sk,kurt);
end
|
github
|
jacksky64/imageProcessing-master
|
innerProd.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/innerProd.m
| 314 |
utf_8
|
e2ea166f9b3ddbc08cb54ef697343d06
|
% RES = innerProd(MTX)
%
% Compute (MTX' * MTX) efficiently (i.e., without copying the matrix)
%
% NOTE: This function used to call a MEX function (C code) to avoid copying, but
% newer versions of matlab have eliminated the overhead of the
% simpler form below.
function res = innerProd(mtx)
res = mtx' * mtx;
|
github
|
jacksky64/imageProcessing-master
|
reconSFpyr.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/reconSFpyr.m
| 3,114 |
utf_8
|
ebb08817efc597692b9026a84e2a6906
|
% RES = reconSFpyr(PYR, INDICES, LEVS, BANDS, TWIDTH)
%
% Reconstruct image from its steerable pyramid representation, in the Fourier
% domain, as created by buildSFpyr.
%
% PYR is a vector containing the N pyramid subbands, ordered from fine
% to coarse. INDICES is an Nx2 matrix containing the sizes of
% each subband. This is compatible with the MatLab Wavelet toolbox.
%
% LEVS (optional) should be a list of levels to include, or the string
% 'all' (default). 0 corresonds to the residual highpass subband.
% 1 corresponds to the finest oriented scale. The lowpass band
% corresponds to number spyrHt(INDICES)+1.
%
% BANDS (optional) should be a list of bands to include, or the string
% 'all' (default). 1 = vertical, rest proceeding anti-clockwise.
%
% TWIDTH is the width of the transition region of the radial lowpass
% function, in octaves (default = 1, which gives a raised cosine for
% the bandpass filters).
%%% MODIFIED VERSION, 7/04, uses different lookup table for radial frequency!
% Eero Simoncelli, 5/97.
function res = reconSFpyr(pyr, pind, levs, bands, twidth)
%%------------------------------------------------------------
%% DEFAULTS:
if (exist('levs') ~= 1)
levs = 'all';
end
if (exist('bands') ~= 1)
bands = 'all';
end
if (exist('twidth') ~= 1)
twidth = 1;
elseif (twidth <= 0)
fprintf(1,'Warning: TWIDTH must be positive. Setting to 1.\n');
twidth = 1;
end
%%------------------------------------------------------------
nbands = spyrNumBands(pind);
maxLev = 1+spyrHt(pind);
if strcmp(levs,'all')
levs = [0:maxLev]';
else
if (any(levs > maxLev) | any(levs < 0))
error(sprintf('Level numbers must be in the range [0, %d].', maxLev));
end
levs = levs(:);
end
if strcmp(bands,'all')
bands = [1:nbands]';
else
if (any(bands < 1) | any(bands > nbands))
error(sprintf('Band numbers must be in the range [1,3].', nbands));
end
bands = bands(:);
end
%----------------------------------------------------------------------
dims = pind(1,:);
ctr = ceil((dims+0.5)/2);
[xramp,yramp] = meshgrid( ([1:dims(2)]-ctr(2))./(dims(2)/2), ...
([1:dims(1)]-ctr(1))./(dims(1)/2) );
angle = atan2(yramp,xramp);
log_rad = sqrt(xramp.^2 + yramp.^2);
log_rad(ctr(1),ctr(2)) = log_rad(ctr(1),ctr(2)-1);
log_rad = log2(log_rad);
%% Radial transition function (a raised cosine in log-frequency):
[Xrcos,Yrcos] = rcosFn(twidth,(-twidth/2),[0 1]);
Yrcos = sqrt(Yrcos);
YIrcos = sqrt(abs(1.0 - Yrcos.^2));
if (size(pind,1) == 2)
if (any(levs==1))
resdft = fftshift(fft2(pyrBand(pyr,pind,2)));
else
resdft = zeros(pind(2,:));
end
else
resdft = reconSFpyrLevs(pyr(1+prod(pind(1,:)):size(pyr,1)), ...
pind(2:size(pind,1),:), ...
log_rad, Xrcos, Yrcos, angle, nbands, levs, bands);
end
lo0mask = pointOp(log_rad, YIrcos, Xrcos(1), Xrcos(2)-Xrcos(1), 0);
resdft = resdft .* lo0mask;
%% residual highpass subband
if any(levs == 0)
hi0mask = pointOp(log_rad, Yrcos, Xrcos(1), Xrcos(2)-Xrcos(1), 0);
hidft = fftshift(fft2(subMtx(pyr, pind(1,:))));
resdft = resdft + hidft .* hi0mask;
end
res = real(ifft2(ifftshift(resdft)));
|
github
|
jacksky64/imageProcessing-master
|
corrDn.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/corrDn.m
| 2,272 |
utf_8
|
cce615994bded51a721560b782ea9eef
|
% RES = corrDn(IM, FILT, EDGES, STEP, START, STOP)
%
% Compute correlation of matrices IM with FILT, followed by
% downsampling. These arguments should be 1D or 2D matrices, and IM
% must be larger (in both dimensions) than FILT. The origin of filt
% is assumed to be floor(size(filt)/2)+1.
%
% EDGES is a string determining boundary handling:
% 'circular' - Circular convolution
% 'reflect1' - Reflect about the edge pixels
% 'reflect2' - Reflect, doubling the edge pixels
% 'repeat' - Repeat the edge pixels
% 'zero' - Assume values of zero outside image boundary
% 'extend' - Reflect and invert (continuous values and derivs)
% 'dont-compute' - Zero output when filter overhangs input boundaries
%
% Downsampling factors are determined by STEP (optional, default=[1 1]),
% which should be a 2-vector [y,x].
%
% The window over which the convolution occurs is specfied by START
% (optional, default=[1,1], and STOP (optional, default=size(IM)).
%
% NOTE: this operation corresponds to multiplication of a signal
% vector by a matrix whose rows contain copies of the FILT shifted by
% multiples of STEP. See upConv.m for the operation corresponding to
% the transpose of this matrix.
% Eero Simoncelli, 6/96, revised 2/97.
function res = corrDn(im, filt, edges, step, start, stop)
%% NOTE: THIS CODE IS NOT ACTUALLY USED! (MEX FILE IS CALLED INSTEAD)
fprintf(1,'WARNING: You should compile the MEX version of "corrDn.c",\n found in the MEX subdirectory of matlabPyrTools, and put it in your matlab path. It is MUCH faster, and provides more boundary-handling options.\n');
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('edges') == 1)
if (strcmp(edges,'reflect1') ~= 1)
warning('Using REFLECT1 edge-handling (use MEX code for other options).');
end
end
if (exist('step') ~= 1)
step = [1,1];
end
if (exist('start') ~= 1)
start = [1,1];
end
if (exist('stop') ~= 1)
stop = size(im);
end
%------------------------------------------------------------
% Reverse order of taps in filt, to do correlation instead of convolution
filt = filt(size(filt,1):-1:1,size(filt,2):-1:1);
tmp = rconv2(im,filt);
res = tmp(start(1):step(1):stop(1),start(2):step(2):stop(2));
|
github
|
jacksky64/imageProcessing-master
|
vectify.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/vectify.m
| 186 |
utf_8
|
1da0e519af06d6baaff1decc40dc3702
|
% [VEC] = columnize(MTX)
%
% Pack elements of MTX into a column vector. Just provides a
% function-call notatoin for the operation MTX(:)
function vec = columnize(mtx)
vec = mtx(:);
|
github
|
jacksky64/imageProcessing-master
|
maxPyrHt.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/maxPyrHt.m
| 603 |
utf_8
|
019e5ce9d036a893ec979c63f51ff54a
|
% HEIGHT = maxPyrHt(IMSIZE, FILTSIZE)
%
% Compute maximum pyramid height for given image and filter sizes.
% Specifically: the number of corrDn operations that can be sequentially
% performed when subsampling by a factor of 2.
% Eero Simoncelli, 6/96.
function height = maxPyrHt(imsz, filtsz)
imsz = imsz(:);
filtsz = filtsz(:);
if any(imsz == 1) % 1D image
imsz = prod(imsz);
filtsz = prod(filtsz);
elseif any(filtsz == 1) % 2D image, 1D filter
filtsz = [filtsz(1); filtsz(1)];
end
if any(imsz < filtsz)
height = 0;
else
height = 1 + maxPyrHt( floor(imsz/2), filtsz );
end
|
github
|
jacksky64/imageProcessing-master
|
buildSpyrLevs.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/buildSpyrLevs.m
| 861 |
utf_8
|
a5fa1e98161a8137e666c1406c28a748
|
% [PYR, INDICES] = buildSpyrLevs(LOIM, HEIGHT, LOFILT, BFILTS, EDGES)
%
% Recursive function for constructing levels of a steerable pyramid. This
% is called by buildSpyr, and is not usually called directly.
% Eero Simoncelli, 6/96.
function [pyr,pind] = buildSpyrLevs(lo0,ht,lofilt,bfilts,edges);
if (ht <= 0)
pyr = lo0(:);
pind = size(lo0);
else
% Assume square filters:
bfiltsz = round(sqrt(size(bfilts,1)));
bands = zeros(prod(size(lo0)),size(bfilts,2));
bind = zeros(size(bfilts,2),2);
for b = 1:size(bfilts,2)
filt = reshape(bfilts(:,b),bfiltsz,bfiltsz);
band = corrDn(lo0, filt, edges);
bands(:,b) = band(:);
bind(b,:) = size(band);
end
lo = corrDn(lo0, lofilt, edges, [2 2], [1 1]);
[npyr,nind] = buildSpyrLevs(lo, ht-1, lofilt, bfilts, edges);
pyr = [bands(:); npyr];
pind = [bind; nind];
end
|
github
|
jacksky64/imageProcessing-master
|
showSpyr.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/showSpyr.m
| 5,213 |
utf_8
|
bc643d88c491a55c0a0abb5e86c91757
|
% RANGE = showSpyr (PYR, INDICES, RANGE, GAP, LEVEL_SCALE_FACTOR)
%
% Display a steerable pyramid, specified by PYR and INDICES
% (see buildSpyr), in the current figure. The highpass band is not shown.
%
% RANGE is a 2-vector specifying the values that map to black and
% white, respectively. These values are scaled by
% LEVEL_SCALE_FACTOR^(lev-1) for bands at each level. Passing a value
% of 'auto1' sets RANGE to the min and max values of MATRIX. 'auto2'
% sets RANGE to 3 standard deviations below and above 0.0. In both of
% these cases, the lowpass band is independently scaled. A value of
% 'indep1' sets the range of each subband independently, as in a call
% to showIm(subband,'auto1'). Similarly, 'indep2' causes each subband
% to be scaled independently as if by showIm(subband,'indep2').
% The default value for RANGE is 'auto2'.
%
% GAP (optional, default=1) specifies the gap in pixels to leave
% between subbands.
%
% LEVEL_SCALE_FACTOR indicates the relative scaling between pyramid
% levels. This should be set to the sum of the kernel taps of the
% lowpass filter used to construct the pyramid (default is 2, which is
% correct for L2-normalized filters.
% Eero Simoncelli, 2/97.
function [range] = showSpyr(pyr, pind, range, gap, scale);
nbands = spyrNumBands(pind);
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('range') ~= 1)
range = 'auto2';
end
if (exist('gap') ~= 1)
gap = 1;
end
if (exist('scale') ~= 1)
scale = 2;
end
%------------------------------------------------------------
ht = spyrHt(pind);
nind = size(pind,1);
%% Auto range calculations:
if strcmp(range,'auto1')
range = ones(nind,1);
band = spyrHigh(pyr,pind);
[mn,mx] = range2(band);
for lnum = 1:ht
for bnum = 1:nbands
band = spyrBand(pyr,pind,lnum,bnum)/(scale^(lnum-1));
range((lnum-1)*nbands+bnum+1) = scale^(lnum-1);
[bmn,bmx] = range2(band);
mn = min(mn, bmn);
mx = max(mx, bmx);
end
end
range = range * [mn mx]; % outer product
band = pyrLow(pyr,pind);
[mn,mx] = range2(band);
range(nind,:) = [mn, mx];
elseif strcmp(range,'indep1')
range = zeros(nind,2);
for bnum = 1:nind
band = pyrBand(pyr,pind,bnum);
[mn,mx] = range2(band);
range(bnum,:) = [mn mx];
end
elseif strcmp(range,'auto2')
range = ones(nind,1);
band = spyrHigh(pyr,pind);
sqsum = sum(sum(band.^2)); numpixels = prod(size(band));
for lnum = 1:ht
for bnum = 1:nbands
band = spyrBand(pyr,pind,lnum,bnum)/(scale^(lnum-1));
sqsum = sqsum + sum(sum(band.^2));
numpixels = numpixels + prod(size(band));
range((lnum-1)*nbands+bnum+1) = scale^(lnum-1);
end
end
stdev = sqrt(sqsum/(numpixels-1));
range = range * [ -3*stdev 3*stdev ]; % outer product
band = pyrLow(pyr,pind);
av = mean2(band); stdev = sqrt(var2(band));
range(nind,:) = [av-2*stdev,av+2*stdev];
elseif strcmp(range,'indep2')
range = zeros(nind,2);
for bnum = 1:(nind-1)
band = pyrBand(pyr,pind,bnum);
stdev = sqrt(var2(band));
range(bnum,:) = [ -3*stdev 3*stdev ];
end
band = pyrLow(pyr,pind);
av = mean2(band); stdev = sqrt(var2(band));
range(nind,:) = [av-2*stdev,av+2*stdev];
elseif isstr(range)
error(sprintf('Bad RANGE argument: %s',range))
elseif ((size(range,1) == 1) & (size(range,2) == 2))
scales = scale.^[0:(ht-1)];
scales = ones(nbands,1) * scales; %outer product
scales = [1; scales(:); scale^ht]; %tack on highpass and lowpass
range = scales * range; % outer product
band = pyrLow(pyr,pind);
range(nind,:) = range(nind,:) + mean2(band) - mean(range(nind,:));
end
% CLEAR FIGURE:
clf;
colormap(gray);
cmap = get(gcf,'Colormap');
nshades = size(cmap,1);
% Find background color index:
clr = get(gcf,'Color');
bg = 1;
dist = norm(cmap(bg,:)-clr);
for n = 1:nshades
ndist = norm(cmap(n,:)-clr);
if (ndist < dist)
dist = ndist;
bg = n;
end
end
%% Compute positions of subbands:
llpos = ones(nind,2);
if (nbands == 2)
ncols = 1; nrows = 2;
else
ncols = ceil((nbands+1)/2); nrows = ceil(nbands/2);
end
relpos = [ (1-nrows):0, zeros(1,(ncols-1)); ...
zeros(1,nrows), -1:-1:(1-ncols) ]';
if (nbands > 1)
mvpos = [-1 -1];
else
mvpos = [0 -1];
end
basepos = [0 0];
for lnum = 1:ht
ind1 = (lnum-1)*nbands + 2;
sz = pind(ind1,:)+gap;
basepos = basepos + mvpos .* sz;
if (nbands < 5) % to align edges...
sz = sz + gap*(ht-lnum+1);
end
llpos(ind1:ind1+nbands-1,:) = relpos * diag(sz) + ones(nbands,1)*basepos;
end
% lowpass band
sz = pind(nind-1,:)+gap;
basepos = basepos + mvpos .* sz;
llpos(nind,:) = basepos;
%% Make position list positive, and allocate appropriate image:
llpos = llpos - ones(nind,1)*min(llpos) + 1;
llpos(1,:) = [1 1];
urpos = llpos + pind - 1;
d_im = bg + zeros(max(urpos));
%% Paste bands into image, (im-r1)*(nshades-1)/(r2-r1) + 1.5
for bnum=2:nind
mult = (nshades-1) / (range(bnum,2)-range(bnum,1));
d_im(llpos(bnum,1):urpos(bnum,1), llpos(bnum,2):urpos(bnum,2)) = ...
mult*pyrBand(pyr,pind,bnum) + (1.5-mult*range(bnum,1));
end
hh = image(d_im);
axis('off');
pixelAxes(size(d_im),'full');
set(hh,'UserData',range);
|
github
|
jacksky64/imageProcessing-master
|
histo.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/histo.m
| 1,835 |
utf_8
|
e76d8956cd1d59f518a8146dc5145f9b
|
% [N,X] = histo(MTX, nbinsOrBinsize, binCenter);
%
% Compute a histogram of (all) elements of MTX. N contains the histogram
% counts, X is a vector containg the centers of the histogram bins.
%
% nbinsOrBinsize (optional, default = 101) specifies either
% the number of histogram bins, or the negative of the binsize.
%
% binCenter (optional, default = mean2(MTX)) specifies a center position
% for (any one of) the histogram bins.
%
% How does this differ from MatLab's HIST function? This function:
% - allows uniformly spaced bins only.
% +/- operates on all elements of MTX, instead of columnwise.
% + is much faster (approximately a factor of 80 on my machine).
% + allows specification of number of bins OR binsize. Default=101 bins.
% + allows (optional) specification of binCenter.
% Eero Simoncelli, 3/97.
function [N, X] = histo(mtx, nbins, binCtr)
%% NOTE: THIS CODE IS NOT ACTUALLY USED! (MEX FILE IS CALLED INSTEAD)
fprintf(1,'WARNING: You should compile the MEX version of "histo.c",\n found in the MEX subdirectory of matlabPyrTools, and put it in your matlab path. It is MUCH faster.\n');
mtx = mtx(:);
%------------------------------------------------------------
%% OPTIONAL ARGS:
[mn,mx] = range2(mtx);
if (exist('binCtr') ~= 1)
binCtr = mean(mtx);
end
if (exist('nbins') == 1)
if (nbins < 0)
binSize = -nbins;
else
binSize = ((mx-mn)/nbins);
tmpNbins = round((mx-binCtr)/binSize) - round((mn-binCtr)/binSize);
if (tmpNbins ~= nbins)
warning('Using %d bins instead of requested number (%d)',tmpNbins,nbins);
end
end
else
binSize = ((mx-mn)/101);
end
firstBin = binCtr + binSize*round( (mn-binCtr)/binSize );
tmpNbins = round((mx-binCtr)/binSize) - round((mn-binCtr)/binSize);
bins = firstBin + binSize*[0:tmpNbins];
[N, X] = hist(mtx, bins);
|
github
|
jacksky64/imageProcessing-master
|
lplot.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/lplot.m
| 1,009 |
utf_8
|
87c83936af0b318d55077862065b56df
|
% lplot(VEC, XRANGE)
%
% Plot VEC, a vector, in "lollipop" format.
% XRANGE (optional, default = [1,length(VEC)]), should be a 2-vector
% specifying the X positions (for labeling purposes) of the first and
% last sample of VEC.
% Mark Liberman, Linguistics Dept, UPenn, 1994.
function lplot(x,xrange)
if (exist('xrange') ~= 1)
xrange = [1,length(x)];
end
msize = size(x);
if ( msize(2) == 1)
x = x';
elseif (msize(1) ~= 1)
error('First arg must be a vector');
end
if (~isreal(x))
fprintf(1,'Warning: Imaginary part of signal ignored\n');
x = abs(x);
end
N = length(x);
index = xrange(1) + (xrange(2)-xrange(1))*[0:(N-1)]/(N-1);
xinc = index(2)-index(1);
xx = [zeros(1,N);x;zeros(1,N)];
indexis = [index;index;index];
xdiscrete = [0 xx(:)' 0];
idiscrete = [index(1)-xinc indexis(:)' index(N)+xinc];
[mn,mx] = range2(xdiscrete);
ypad = (mx-mn)/12; % MAGIC NUMBER: graph padding
plot(idiscrete, xdiscrete, index, x, 'o');
axis([index(1)-xinc, index(N)+xinc, mn-ypad, mx+ypad]);
return
|
github
|
jacksky64/imageProcessing-master
|
blurDn.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/blurDn.m
| 1,364 |
utf_8
|
d528010bfd2b4c50e7dbb2aede757214
|
% RES = blurDn(IM, LEVELS, FILT)
%
% Blur and downsample an image. The blurring is done with filter
% kernel specified by FILT (default = 'binom5'), which can be a string
% (to be passed to namedFilter), a vector (applied separably as a 1D
% convolution kernel in X and Y), or a matrix (applied as a 2D
% convolution kernel). The downsampling is always by 2 in each
% direction.
%
% The procedure is applied recursively LEVELS times (default=1).
% Eero Simoncelli, 3/97.
function res = blurDn(im, nlevs, filt)
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('nlevs') ~= 1)
nlevs = 1;
end
if (exist('filt') ~= 1)
filt = 'binom5';
end
%------------------------------------------------------------
if isstr(filt)
filt = namedFilter(filt);
end
filt = filt/sum(filt(:));
if nlevs > 1
im = blurDn(im,nlevs-1,filt);
end
if (nlevs >= 1)
if (any(size(im)==1))
if (~any(size(filt)==1))
error('Cant apply 2D filter to 1D signal');
end
if (size(im,2)==1)
filt = filt(:);
else
filt = filt(:)';
end
res = corrDn(im,filt,'reflect1',(size(im)~=1)+1);
elseif (any(size(filt)==1))
filt = filt(:);
res = corrDn(im,filt,'reflect1',[2 1]);
res = corrDn(res,filt','reflect1',[1 2]);
else
res = corrDn(im,filt,'reflect1',[2 2]);
end
else
res = im;
end
|
github
|
jacksky64/imageProcessing-master
|
reconSpyrLevs.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/reconSpyrLevs.m
| 1,126 |
utf_8
|
1f10e3cea5d79a4f4a30d979f3bb1298
|
% RES = reconSpyrLevs(PYR,INDICES,LOFILT,BFILTS,EDGES,LEVS,BANDS)
%
% Recursive function for reconstructing levels of a steerable pyramid
% representation. This is called by reconSpyr, and is not usually
% called directly.
% Eero Simoncelli, 6/96.
function res = reconSpyrLevs(pyr,pind,lofilt,bfilts,edges,levs,bands);
nbands = size(bfilts,2);
lo_ind = nbands+1;
res_sz = pind(1,:);
% Assume square filters:
bfiltsz = round(sqrt(size(bfilts,1)));
if any(levs > 1)
if (size(pind,1) > lo_ind)
nres = reconSpyrLevs( pyr(1+sum(prod(pind(1:lo_ind-1,:)')):size(pyr,1)), ...
pind(lo_ind:size(pind,1),:), ...
lofilt, bfilts, edges, levs-1, bands);
else
nres = pyrBand(pyr,pind,lo_ind); % lowpass subband
end
res = upConv(nres, lofilt, edges, [2 2], [1 1], res_sz);
else
res = zeros(res_sz);
end
if any(levs == 1)
ind = 1;
for b = 1:nbands
if any(bands == b)
bfilt = reshape(bfilts(:,b), bfiltsz, bfiltsz);
res = upConv(reshape(pyr(ind:ind+prod(res_sz)-1), res_sz(1), res_sz(2)), ...
bfilt, edges, [1 1], [1 1], res_sz, res);
end
ind = ind + prod(res_sz);
end
end
|
github
|
jacksky64/imageProcessing-master
|
mkSine.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/mkSine.m
| 1,725 |
utf_8
|
35c6d83f70860ab6defcbdcf7366d89e
|
% IM = mkSine(SIZE, PERIOD, DIRECTION, AMPLITUDE, PHASE, ORIGIN)
% or
% IM = mkSine(SIZE, FREQ, AMPLITUDE, PHASE, ORIGIN)
%
% Compute a matrix of dimension SIZE (a [Y X] 2-vector, or a scalar)
% containing samples of a 2D sinusoid, with given PERIOD (in pixels),
% DIRECTION (radians, CW from X-axis, default = 0), AMPLITUDE (default
% = 1), and PHASE (radians, relative to ORIGIN, default = 0). ORIGIN
% defaults to the center of the image.
%
% In the second form, FREQ is a 2-vector of frequencies (radians/pixel).
% Eero Simoncelli, 6/96.
function [res] = mkSine(sz, per_freq, dir_amp, amp_phase, phase_orig, orig)
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (prod(size(per_freq)) == 2)
frequency = norm(per_freq);
direction = atan2(per_freq(1),per_freq(2));
if (exist('dir_amp') == 1)
amplitude = dir_amp;
else
amplitude = 1;
end
if (exist('amp_phase') == 1)
phase = amp_phase;
else
phase = 0;
end
if (exist('phase_orig') == 1)
origin = phase_orig;
end
if (exist('orig') == 1)
error('Too many arguments for (second form) of mkSine');
end
else
frequency = 2*pi/per_freq;
if (exist('dir_amp') == 1)
direction = dir_amp;
else
direction = 0;
end
if (exist('amp_phase') == 1)
amplitude = amp_phase;
else
amplitude = 1;
end
if (exist('phase_orig') == 1)
phase = phase_orig;
else
phase = 0;
end
if (exist('orig') == 1)
origin = orig;
end
end
%------------------------------------------------------------
if (exist('origin') == 1)
res = amplitude*sin(mkRamp(sz, direction, frequency, phase, origin));
else
res = amplitude*sin(mkRamp(sz, direction, frequency, phase));
end
|
github
|
jacksky64/imageProcessing-master
|
buildSFpyrLevs.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/buildSFpyrLevs.m
| 1,891 |
utf_8
|
52ab858761411b2a5a75e7de641259cf
|
% [PYR, INDICES] = buildSFpyrLevs(LODFT, LOGRAD, XRCOS, YRCOS, ANGLE, HEIGHT, NBANDS)
%
% Recursive function for constructing levels of a steerable pyramid. This
% is called by buildSFpyr, and is not usually called directly.
% Eero Simoncelli, 5/97.
function [pyr,pind] = buildSFpyrLevs(lodft,log_rad,Xrcos,Yrcos,angle,ht,nbands);
if (ht <= 0)
lo0 = ifft2(ifftshift(lodft));
pyr = real(lo0(:));
pind = size(lo0);
else
bands = zeros(prod(size(lodft)), nbands);
bind = zeros(nbands,2);
% log_rad = log_rad + 1;
Xrcos = Xrcos - log2(2); % shift origin of lut by 1 octave.
lutsize = 1024;
Xcosn = pi*[-(2*lutsize+1):(lutsize+1)]/lutsize; % [-2*pi:pi]
order = nbands-1;
%% divide by sqrt(sum_(n=0)^(N-1) cos(pi*n/N)^(2(N-1)) )
%% Thanks to Patrick Teo for writing this out :)
const = (2^(2*order))*(factorial(order)^2)/(nbands*factorial(2*order));
Ycosn = sqrt(const) * (cos(Xcosn)).^order;
himask = pointOp(log_rad, Yrcos, Xrcos(1), Xrcos(2)-Xrcos(1), 0);
for b = 1:nbands
anglemask = pointOp(angle, Ycosn, Xcosn(1)+pi*(b-1)/nbands, Xcosn(2)-Xcosn(1));
banddft = ((-sqrt(-1))^order) .* lodft .* anglemask .* himask;
band = ifft2(ifftshift(banddft));
bands(:,b) = real(band(:));
bind(b,:) = size(band);
end
dims = size(lodft);
ctr = ceil((dims+0.5)/2);
lodims = ceil((dims-0.5)/2);
loctr = ceil((lodims+0.5)/2);
lostart = ctr-loctr+1;
loend = lostart+lodims-1;
log_rad = log_rad(lostart(1):loend(1),lostart(2):loend(2));
angle = angle(lostart(1):loend(1),lostart(2):loend(2));
lodft = lodft(lostart(1):loend(1),lostart(2):loend(2));
YIrcos = abs(sqrt(1.0 - Yrcos.^2));
lomask = pointOp(log_rad, YIrcos, Xrcos(1), Xrcos(2)-Xrcos(1), 0);
lodft = lomask .* lodft;
[npyr,nind] = buildSFpyrLevs(lodft, log_rad, Xrcos, Yrcos, angle, ht-1, nbands);
pyr = [bands(:); npyr];
pind = [bind; nind];
end
|
github
|
jacksky64/imageProcessing-master
|
pixelAxes.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/pixelAxes.m
| 1,983 |
utf_8
|
1b2a2bfddd425fee2ccd276f3948cec7
|
% [ZOOM] = pixelAxes(DIMS, ZOOM)
%
% Set the axes of the current plot to cover a multiple of DIMS pixels,
% thereby eliminating screen aliasing artifacts when displaying an
% image of size DIMS.
%
% ZOOM (optional, default='same') expresses the desired number of
% samples displayed per screen pixel. It should be a scalar, which
% will be rounded to the nearest integer, or 1 over an integer. It
% may also be the string 'same' or 'auto', in which case the value is chosen so
% as to produce an image closest in size to the currently displayed
% image. It may also be the string 'full', in which case the image is
% made as large as possible while still fitting in the window.
% Eero Simoncelli, 2/97.
function [zoom] = pixelAxes(dims, zoom)
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('zoom') ~= 1)
zoom = 'same';
end
%% Reverse dimension order, since Figure Positions reported as (x,y).
dims = dims(2:-1:1);
%% Use MatLab's axis function to force square pixels, etc:
axis('image');
ax = gca;
oldunits = get(ax,'Units');
if strcmp(zoom,'full');
set(ax,'Units','normalized');
set(ax,'Position',[0 0 1 1]);
zoom = 'same';
end
set(ax,'Units','pixels');
pos = get(ax,'Position');
ctr = pos(1:2)+pos(3:4)/2;
if (strcmp(zoom,'same') | strcmp(zoom,'auto'))
%% HACK: enlarge slightly so that floor doesn't round down
zoom = min( pos(3:4) ./ (dims - 1) );
elseif isstr(zoom)
error(sprintf('Bad ZOOM argument: %s',zoom));
end
%% Force zoom value to be an integer, or inverse integer.
if (zoom < 0.75)
zoom = 1/ceil(1/zoom);
%% Round upward, subtracting 0.5 to avoid floating point errors.
newsz = ceil(zoom*(dims-0.5));
else
zoom = floor(zoom + 0.001); % Avoid floating pt errors
if (zoom < 1.5) % zoom=1
zoom = 1;
newsz = dims + 0.5;
else
newsz = zoom*(dims-1) + mod(zoom,2);
end
end
set(ax,'Position', [floor(ctr-newsz/2)+0.5, newsz] )
% Restore units
set(ax,'Units',oldunits);
|
github
|
jacksky64/imageProcessing-master
|
pyrBandIndices.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/pyrBandIndices.m
| 589 |
utf_8
|
28f90484526c294bdb24bdbf8014012d
|
% RES = pyrBandIndices(INDICES, BAND_NUM)
%
% Return indices for accessing a subband from a pyramid
% (gaussian, laplacian, QMF/wavelet, steerable).
% Eero Simoncelli, 6/96.
function indices = pyrBandIndices(pind,band)
if ((band > size(pind,1)) | (band < 1))
error(sprintf('BAND_NUM must be between 1 and number of pyramid bands (%d).', ...
size(pind,1)));
end
if (size(pind,2) ~= 2)
error('INDICES must be an Nx2 matrix indicating the size of the pyramid subbands');
end
ind = 1;
for l=1:band-1
ind = ind + prod(pind(l,:));
end
indices = ind:ind+prod(pind(band,:))-1;
|
github
|
jacksky64/imageProcessing-master
|
pointOp.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/pointOp.m
| 1,207 |
utf_8
|
f3b4f566bebca0b7f56477785bb89fc5
|
% RES = pointOp(IM, LUT, ORIGIN, INCREMENT, WARNINGS)
%
% Apply a point operation, specified by lookup table LUT, to image IM.
% LUT must be a row or column vector, and is assumed to contain
% (equi-spaced) samples of the function. ORIGIN specifies the
% abscissa associated with the first sample, and INCREMENT specifies the
% spacing between samples. Between-sample values are estimated via
% linear interpolation. If WARNINGS is non-zero, the function prints
% a warning whenever the lookup table is extrapolated.
%
% This function is much faster than MatLab's interp1, and allows
% extrapolation beyond the lookup table domain. The drawbacks are
% that the lookup table must be equi-spaced, and the interpolation is
% linear.
% Eero Simoncelli, 8/96.
function res = pointOp(im, lut, origin, increment, warnings)
%% NOTE: THIS CODE IS NOT ACTUALLY USED! (MEX FILE IS CALLED INSTEAD)
fprintf(1,'WARNING: You should compile the MEX version of "pointOp.c",\n found in the MEX subdirectory of matlabPyrTools, and put it in your matlab path. It is MUCH faster.\n');
X = origin + increment*[0:size(lut(:),1)-1];
Y = lut(:);
res = reshape(interp1(X, Y, im(:), 'linear', 'extrap'),size(im));
|
github
|
jacksky64/imageProcessing-master
|
reconWpyr.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/reconWpyr.m
| 3,992 |
utf_8
|
859a606f214bce204ce3c9ea18c0fc87
|
% RES = reconWpyr(PYR, INDICES, FILT, EDGES, LEVS, BANDS)
%
% Reconstruct image from its separable orthonormal QMF/wavelet pyramid
% representation, as created by buildWpyr.
%
% PYR is a vector containing the N pyramid subbands, ordered from fine
% to coarse. INDICES is an Nx2 matrix containing the sizes of
% each subband. This is compatible with the MatLab Wavelet toolbox.
%
% FILT (optional) can be a string naming a standard filter (see
% namedFilter), or a vector which will be used for (separable)
% convolution. Default = 'qmf9'. EDGES specifies edge-handling,
% and defaults to 'reflect1' (see corrDn).
%
% LEVS (optional) should be a vector of levels to include, or the string
% 'all' (default). 1 corresponds to the finest scale. The lowpass band
% corresponds to wpyrHt(INDICES)+1.
%
% BANDS (optional) should be a vector of bands to include, or the string
% 'all' (default). 1=horizontal, 2=vertical, 3=diagonal. This is only used
% for pyramids of 2D images.
% Eero Simoncelli, 6/96.
function res = reconWpyr(pyr, ind, filt, edges, levs, bands)
if (nargin < 2)
error('First two arguments (PYR INDICES) are required');
end
%%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('filt') ~= 1)
filt = 'qmf9';
end
if (exist('edges') ~= 1)
edges= 'reflect1';
end
if (exist('levs') ~= 1)
levs = 'all';
end
if (exist('bands') ~= 1)
bands = 'all';
end
%%------------------------------------------------------------
maxLev = 1+wpyrHt(ind);
if strcmp(levs,'all')
levs = [1:maxLev]';
else
if (any(levs > maxLev))
error(sprintf('Level numbers must be in the range [1, %d].', maxLev));
end
levs = levs(:);
end
if strcmp(bands,'all')
bands = [1:3]';
else
if (any(bands < 1) | any(bands > 3))
error('Band numbers must be in the range [1,3].');
end
bands = bands(:);
end
if isstr(filt)
filt = namedFilter(filt);
end
filt = filt(:);
hfilt = modulateFlip(filt);
%% For odd-length filters, stagger the sampling lattices:
if (mod(size(filt,1),2) == 0)
stag = 2;
else
stag = 1;
end
%% Compute size of result image: assumes critical sampling (boundaries correct)
res_sz = ind(1,:);
if (res_sz(1) == 1)
loind = 2;
res_sz(2) = sum(ind(:,2));
elseif (res_sz(2) == 1)
loind = 2;
res_sz(1) = sum(ind(:,1));
else
loind = 4;
res_sz = ind(1,:) + ind(2,:); %%horizontal + vertical bands.
hres_sz = [ind(1,1), res_sz(2)];
lres_sz = [ind(2,1), res_sz(2)];
end
%% First, recursively collapse coarser scales:
if any(levs > 1)
if (size(ind,1) > loind)
nres = reconWpyr( pyr(1+sum(prod(ind(1:loind-1,:)')):size(pyr,1)), ...
ind(loind:size(ind,1),:), filt, edges, levs-1, bands);
else
nres = pyrBand(pyr, ind, loind); % lowpass subband
end
if (res_sz(1) == 1)
res = upConv(nres, filt', edges, [1 2], [1 stag], res_sz);
elseif (res_sz(2) == 1)
res = upConv(nres, filt, edges, [2 1], [stag 1], res_sz);
else
ires = upConv(nres, filt', edges, [1 2], [1 stag], lres_sz);
res = upConv(ires, filt, edges, [2 1], [stag 1], res_sz);
end
else
res = zeros(res_sz);
end
%% Add in reconstructed bands from this level:
if any(levs == 1)
if (res_sz(1) == 1)
upConv(pyrBand(pyr,ind,1), hfilt', edges, [1 2], [1 2], res_sz, res);
elseif (res_sz(2) == 1)
upConv(pyrBand(pyr,ind,1), hfilt, edges, [2 1], [2 1], res_sz, res);
else
if any(bands == 1) % horizontal
ires = upConv(pyrBand(pyr,ind,1),filt',edges,[1 2],[1 stag],hres_sz);
upConv(ires,hfilt,edges,[2 1],[2 1],res_sz,res); %destructively modify res
end
if any(bands == 2) % vertical
ires = upConv(pyrBand(pyr,ind,2),hfilt',edges,[1 2],[1 2],lres_sz);
upConv(ires,filt,edges,[2 1],[stag 1],res_sz,res); %destructively modify res
end
if any(bands == 3) % diagonal
ires = upConv(pyrBand(pyr,ind,3),hfilt',edges,[1 2],[1 2],hres_sz);
upConv(ires,hfilt,edges,[2 1],[2 1],res_sz,res); %destructively modify res
end
end
end
|
github
|
jacksky64/imageProcessing-master
|
showWpyr.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/showWpyr.m
| 5,491 |
utf_8
|
4bc0b260425f553810ae04afced17fda
|
% RANGE = showWpyr (PYR, INDICES, RANGE, GAP, LEVEL_SCALE_FACTOR)
%
% Display a separable QMF/wavelet pyramid, specified by PYR and INDICES
% (see buildWpyr), in the current figure.
%
% RANGE is a 2-vector specifying the values that map to black and
% white, respectively. These values are scaled by
% LEVEL_SCALE_FACTOR^(lev-1) for bands at each level. Passing a value
% of 'auto1' sets RANGE to the min and max values of MATRIX. 'auto2'
% sets RANGE to 3 standard deviations below and above 0.0. In both of
% these cases, the lowpass band is independently scaled. A value of
% 'indep1' sets the range of each subband independently, as in a call
% to showIm(subband,'auto1'). Similarly, 'indep2' causes each subband
% to be scaled independently as if by showIm(subband,'indep2').
% The default value for RANGE is 'auto1' for 1D images, and 'auto2' for
% 2D images.
%
% GAP (optional, default=1) specifies the gap in pixels to leave
% between subbands (2D images only).
%
% LEVEL_SCALE_FACTOR indicates the relative scaling between pyramid
% levels. This should be set to the sum of the kernel taps of the
% lowpass filter used to construct the pyramid (default assumes
% L2-normalized filters, using a value of 2 for 2D images, sqrt(2) for
% 1D images).
% Eero Simoncelli, 2/97.
function [range] = showWpyr(pyr, pind, range, gap, scale);
% Determine 1D or 2D pyramid:
if ((pind(1,1) == 1) | (pind(1,2) ==1))
nbands = 1;
else
nbands = 3;
end
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('range') ~= 1)
if (nbands==1)
range = 'auto1';
else
range = 'auto2';
end
end
if (exist('gap') ~= 1)
gap = 1;
end
if (exist('scale') ~= 1)
if (nbands == 1)
scale = sqrt(2);
else
scale = 2;
end
end
%------------------------------------------------------------
ht = wpyrHt(pind);
nind = size(pind,1);
%% Auto range calculations:
if strcmp(range,'auto1')
range = zeros(nind,1);
mn = 0.0; mx = 0.0;
for lnum = 1:ht
for bnum = 1:nbands
band = wpyrBand(pyr,pind,lnum,bnum)/(scale^(lnum-1));
range((lnum-1)*nbands+bnum) = scale^(lnum-1);
[bmn,bmx] = range2(band);
mn = min(mn, bmn); mx = max(mx, bmx);
end
end
if (nbands == 1)
pad = (mx-mn)/12; % *** MAGIC NUMBER!!
mn = mn-pad; mx = mx+pad;
end
range = range * [mn mx]; % outer product
band = pyrLow(pyr,pind);
[mn,mx] = range2(band);
if (nbands == 1)
pad = (mx-mn)/12; % *** MAGIC NUMBER!!
mn = mn-pad; mx = mx+pad;
end
range(nind,:) = [mn, mx];
elseif strcmp(range,'indep1')
range = zeros(nind,2);
for bnum = 1:nind
band = pyrBand(pyr,pind,bnum);
[mn,mx] = range2(band);
if (nbands == 1)
pad = (mx-mn)/12; % *** MAGIC NUMBER!!
mn = mn-pad; mx = mx+pad;
end
range(bnum,:) = [mn mx];
end
elseif strcmp(range,'auto2')
range = zeros(nind,1);
sqsum = 0; numpixels = 0;
for lnum = 1:ht
for bnum = 1:nbands
band = wpyrBand(pyr,pind,lnum,bnum)/(scale^(lnum-1));
sqsum = sqsum + sum(sum(band.^2));
numpixels = numpixels + prod(size(band));
range((lnum-1)*nbands+bnum) = scale^(lnum-1);
end
end
stdev = sqrt(sqsum/(numpixels-1));
range = range * [ -3*stdev 3*stdev ]; % outer product
band = pyrLow(pyr,pind);
av = mean2(band); stdev = sqrt(var2(band));
range(nind,:) = [av-2*stdev,av+2*stdev];
elseif strcmp(range,'indep2')
range = zeros(nind,2);
for bnum = 1:(nind-1)
band = pyrBand(pyr,pind,bnum);
stdev = sqrt(var2(band));
range(bnum,:) = [ -3*stdev 3*stdev ];
end
band = pyrLow(pyr,pind);
av = mean2(band); stdev = sqrt(var2(band));
range(nind,:) = [av-2*stdev,av+2*stdev];
elseif isstr(range)
error(sprintf('Bad RANGE argument: %s',range))
elseif ((size(range,1) == 1) & (size(range,2) == 2))
scales = scale.^[0:ht];
if (nbands ~= 1)
scales = [scales; scales; scales];
end
range = scales(:) * range; % outer product
band = pyrLow(pyr,pind);
range(nind,:) = range(nind,:) + mean2(band) - mean(range(nind,:));
end
% CLEAR FIGURE:
clf;
if (nbands == 1)
%%%%% 1D signal:
for bnum=1:nind
band = pyrBand(pyr,pind,bnum);
subplot(nind,1,nind-bnum+1);
plot(band);
axis([1, prod(size(band)), range(bnum,:)]);
end
else
%%%%% 2D signal:
colormap(gray);
cmap = get(gcf,'Colormap');
nshades = size(cmap,1);
% Find background color index:
clr = get(gcf,'Color');
bg = 1;
dist = norm(cmap(bg,:)-clr);
for n = 1:nshades
ndist = norm(cmap(n,:)-clr);
if (ndist < dist)
dist = ndist;
bg = n;
end
end
%% Compute positions of subbands:
llpos = ones(nind,2);
for lnum = 1:ht
ind1 = nbands*(lnum-1) + 1;
xpos = pind(ind1,2) + 1 + gap*(ht-lnum+1);
ypos = pind(ind1+1,1) + 1 + gap*(ht-lnum+1);
llpos(ind1:ind1+2,:) = [ypos 1; 1 xpos; ypos xpos];
end
llpos(nind,:) = [1 1]; %lowpass
%% Make position list positive, and allocate appropriate image:
llpos = llpos - ones(nind,1)*min(llpos) + 1;
urpos = llpos + pind - 1;
d_im = bg + zeros(max(urpos));
%% Paste bands into image, (im-r1)*(nshades-1)/(r2-r1) + 1.5
for bnum=1:nind
mult = (nshades-1) / (range(bnum,2)-range(bnum,1));
d_im(llpos(bnum,1):urpos(bnum,1), llpos(bnum,2):urpos(bnum,2)) = ...
mult*pyrBand(pyr,pind,bnum) + (1.5-mult*range(bnum,1));
end
hh = image(d_im);
axis('off');
pixelAxes(size(d_im),'full');
set(hh,'UserData',range);
end
|
github
|
jacksky64/imageProcessing-master
|
imGradient.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/imGradient.m
| 1,547 |
utf_8
|
b13a85bea09c3f4e0c1e6140c9a31f7a
|
% [dx, dy] = imGradient(im, edges)
%
% Compute the gradient of the image using smooth derivative filters
% optimized for accurate direction estimation. Coordinate system
% corresponds to standard pixel indexing: X axis points rightward. Y
% axis points downward. EDGES specify boundary handling (see corrDn
% for options).
%
% Unlike matlab's new gradient function, which is based on local
% differences, this function computes derivatives using 5x5 filters
% designed to accurately reflect the local orientation content.
% EPS, 1997.
% original filters from Int'l Conf Image Processing, 1994.
% updated filters 10/2003: see Farid & Simoncelli, IEEE Trans Image Processing, 13(4):496-508, April 2004.
% Incorporated into matlabPyrTools 10/2004.
function [dx, dy] = imGradient(im, edges)
if (exist('edges') ~= 1)
edges = 'dont-compute';
end
%% kernels from Farid & Simoncelli, IEEE Trans Image Processing, 13(4):496-508, April 2004.
gp = [0.037659 0.249153 0.426375 0.249153 0.037659]';
gd = [-0.109604 -0.276691 0.000000 0.276691 0.109604]';
dx = corrDn(corrDn(im, gp, edges), gd', edges);
dy = corrDn(corrDn(im, gd, edges), gp', edges);
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% TEST:
%%Make a ramp with random slope and direction
dir = 2*pi*rand - pi;
slope = 10*rand;
sz = 32
im = mkRamp(sz, dir, slope);
[dx,dy] = imGradient(im);
showIm(dx + sqrt(-1)*dy);
ctr = (sz*sz/2)+sz/2;
slopeEst = sqrt(dx(ctr).^2 + dy(ctr).^2);
dirEst = atan2(dy(ctr), dx(ctr));
[slope, slopeEst]
[dir, dirEst]
|
github
|
jacksky64/imageProcessing-master
|
lpyrHt.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/lpyrHt.m
| 233 |
utf_8
|
dd0b45926abda2b3fe9aaec0a4f4d214
|
% [HEIGHT] = lpyrHt(INDICES)
%
% Compute height of Laplacian pyramid with given its INDICES matrix.
% See buildLpyr.m
% Eero Simoncelli, 6/96.
function [ht] = lpyrHt(pind)
% Don't count lowpass residual band
ht = size(pind,1)-1;
|
github
|
jacksky64/imageProcessing-master
|
buildGpyr.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/buildGpyr.m
| 1,931 |
utf_8
|
3f1cfe5507fe34b51d71a87d955abbf5
|
% [PYR, INDICES] = buildGpyr(IM, HEIGHT, FILT, EDGES)
%
% Construct a Gaussian pyramid on matrix IM.
%
% HEIGHT (optional) specifies the number of pyramid levels to build. Default
% is 1+maxPyrHt(size(IM),size(FILT)).
% You can also specify 'auto' to use this value.
%
% FILT (optional) can be a string naming a standard filter (see
% namedFilter), or a vector which will be used for (separable)
% convolution. Default = 'binom5'. EDGES specifies edge-handling, and
% defaults to 'reflect1' (see corrDn).
%
% PYR is a vector containing the N pyramid subbands, ordered from fine
% to coarse. INDICES is an Nx2 matrix containing the sizes of
% each subband. This is compatible with the MatLab Wavelet toolbox.
% Eero Simoncelli, 6/96.
function [pyr,pind] = buildGpyr(im, ht, filt, edges)
if (nargin < 1)
error('First argument (IM) is required');
end
im_sz = size(im);
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('filt') ~= 1)
filt = 'binom5';
end
if isstr(filt)
filt = namedFilter(filt);
end
if ( (size(filt,1) > 1) & (size(filt,2) > 1) )
error('FILT should be a 1D filter (i.e., a vector)');
else
filt = filt(:);
end
max_ht = 1 + maxPyrHt(im_sz, size(filt,1));
if ( (exist('ht') ~= 1) | (ht == 'auto') )
ht = max_ht;
else
if (ht > max_ht)
error(sprintf('Cannot build pyramid higher than %d levels.',max_ht));
end
end
if (exist('edges') ~= 1)
edges= 'reflect1';
end
%------------------------------------------------------------
if (ht <= 1)
pyr = im(:);
pind = im_sz;
else
if (im_sz(2) == 1)
lo2 = corrDn(im, filt, edges, [2 1], [1 1]);
elseif (im_sz(1) == 1)
lo2 = corrDn(im, filt', edges, [1 2], [1 1]);
else
lo = corrDn(im, filt', edges, [1 2], [1 1]);
lo2 = corrDn(lo, filt, edges, [2 1], [1 1]);
end
[npyr,nind] = buildGpyr(lo2, ht-1, filt, edges);
pyr = [im(:); npyr];
pind = [im_sz; nind];
end
|
github
|
jacksky64/imageProcessing-master
|
shift.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/shift.m
| 438 |
utf_8
|
2ac42b171e4ca683ef1d361eaf331870
|
% [RES] = shift(MTX, OFFSET)
%
% Circular shift 2D matrix samples by OFFSET (a [Y,X] 2-vector),
% such that RES(POS) = MTX(POS-OFFSET).
function res = shift(mtx, offset)
dims = size(mtx);
offset = mod(-offset,dims);
res = [ mtx(offset(1)+1:dims(1), offset(2)+1:dims(2)), ...
mtx(offset(1)+1:dims(1), 1:offset(2)); ...
mtx(1:offset(1), offset(2)+1:dims(2)), ...
mtx(1:offset(1), 1:offset(2)) ];
|
github
|
jacksky64/imageProcessing-master
|
namedFilter.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/namedFilter.m
| 3,207 |
utf_8
|
8f45ef65fca60f53e0f734c4f1ae01bf
|
% KERNEL = NAMED_FILTER(NAME)
%
% Some standard 1D filter kernels. These are scaled such that
% their L2-norm is 1.0.
%
% binomN - binomial coefficient filter of order N-1
% haar: - Haar wavelet.
% qmf8, qmf12, qmf16 - Symmetric Quadrature Mirror Filters [Johnston80]
% daub2,daub3,daub4 - Daubechies wavelet [Daubechies88].
% qmf5, qmf9, qmf13: - Symmetric Quadrature Mirror Filters [Simoncelli88,Simoncelli90]
%
% See bottom of file for full citations.
% Eero Simoncelli, 6/96.
function [kernel] = named_filter(name)
if strcmp(name(1:min(5,size(name,2))), 'binom')
kernel = sqrt(2) * binomialFilter(str2num(name(6:size(name,2))));
elseif strcmp(name,'qmf5')
kernel = [-0.076103 0.3535534 0.8593118 0.3535534 -0.076103]';
elseif strcmp(name,'qmf9')
kernel = [0.02807382 -0.060944743 -0.073386624 0.41472545 0.7973934 ...
0.41472545 -0.073386624 -0.060944743 0.02807382]';
elseif strcmp(name,'qmf13')
kernel = [-0.014556438 0.021651438 0.039045125 -0.09800052 ...
-0.057827797 0.42995453 0.7737113 0.42995453 -0.057827797 ...
-0.09800052 0.039045125 0.021651438 -0.014556438]';
elseif strcmp(name,'qmf8')
kernel = sqrt(2) * [0.00938715 -0.07065183 0.06942827 0.4899808 ...
0.4899808 0.06942827 -0.07065183 0.00938715 ]';
elseif strcmp(name,'qmf12')
kernel = sqrt(2) * [-0.003809699 0.01885659 -0.002710326 -0.08469594 ...
0.08846992 0.4843894 0.4843894 0.08846992 -0.08469594 -0.002710326 ...
0.01885659 -0.003809699 ]';
elseif strcmp(name,'qmf16')
kernel = sqrt(2) * [0.001050167 -0.005054526 -0.002589756 0.0276414 -0.009666376 ...
-0.09039223 0.09779817 0.4810284 0.4810284 0.09779817 -0.09039223 -0.009666376 ...
0.0276414 -0.002589756 -0.005054526 0.001050167 ]';
elseif strcmp(name,'haar')
kernel = [1 1]' / sqrt(2);
elseif strcmp(name,'daub2')
kernel = [0.482962913145 0.836516303738 0.224143868042 -0.129409522551]';
elseif strcmp(name,'daub3')
kernel = [0.332670552950 0.806891509311 0.459877502118 -0.135011020010 ...
-0.085441273882 0.035226291882]';
elseif strcmp(name,'daub4')
kernel = [0.230377813309 0.714846570553 0.630880767930 -0.027983769417 ...
-0.187034811719 0.030841381836 0.032883011667 -0.010597401785]';
elseif strcmp(name,'gauss5') % for backward-compatibility
kernel = sqrt(2) * [0.0625 0.25 0.375 0.25 0.0625]';
elseif strcmp(name,'gauss3') % for backward-compatibility
kernel = sqrt(2) * [0.25 0.5 0.25]';
else
error(sprintf('Bad filter name: %s\n',name));
end
% [Johnston80] - J D Johnston, "A filter family designed for use in quadrature
% mirror filter banks", Proc. ICASSP, pp 291-294, 1980.
%
% [Daubechies88] - I Daubechies, "Orthonormal bases of compactly supported wavelets",
% Commun. Pure Appl. Math, vol. 42, pp 909-996, 1988.
%
% [Simoncelli88] - E P Simoncelli, "Orthogonal sub-band image transforms",
% PhD Thesis, MIT Dept. of Elec. Eng. and Comp. Sci. May 1988.
% Also available as: MIT Media Laboratory Vision and Modeling Technical
% Report #100.
%
% [Simoncelli90] - E P Simoncelli and E H Adelson, "Subband image coding",
% Subband Transforms, chapter 4, ed. John W Woods, Kluwer Academic
% Publishers, Norwell, MA, 1990, pp 143--192.
|
github
|
jacksky64/imageProcessing-master
|
buildLpyr.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/buildLpyr.m
| 2,632 |
utf_8
|
b62aad457634fd598b373448741860cd
|
% [PYR, INDICES] = buildLpyr(IM, HEIGHT, FILT1, FILT2, EDGES)
%
% Construct a Laplacian pyramid on matrix (or vector) IM.
%
% HEIGHT (optional) specifies the number of pyramid levels to build. Default
% is 1+maxPyrHt(size(IM),size(FILT)). You can also specify 'auto' to
% use this value.
%
% FILT1 (optional) can be a string naming a standard filter (see
% namedFilter), or a vector which will be used for (separable)
% convolution. Default = 'binom5'. FILT2 specifies the "expansion"
% filter (default = filt1). EDGES specifies edge-handling, and
% defaults to 'reflect1' (see corrDn).
%
% PYR is a vector containing the N pyramid subbands, ordered from fine
% to coarse. INDICES is an Nx2 matrix containing the sizes of
% each subband. This is compatible with the MatLab Wavelet toolbox.
% Eero Simoncelli, 6/96.
function [pyr,pind] = buildLpyr(im, ht, filt1, filt2, edges)
if (nargin < 1)
error('First argument (IM) is required');
end
im_sz = size(im);
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('filt1') ~= 1)
filt1 = 'binom5';
end
if isstr(filt1)
filt1 = namedFilter(filt1);
end
if ( (size(filt1,1) > 1) & (size(filt1,2) > 1) )
error('FILT1 should be a 1D filter (i.e., a vector)');
else
filt1 = filt1(:);
end
if (exist('filt2') ~= 1)
filt2 = filt1;
end
if isstr(filt2)
filt2 = namedFilter(filt2);
end
if ( (size(filt2,1) > 1) & (size(filt2,2) > 1) )
error('FILT2 should be a 1D filter (i.e., a vector)');
else
filt2 = filt2(:);
end
max_ht = 1 + maxPyrHt(im_sz, max(size(filt1,1), size(filt2,1)));
if ( (exist('ht') ~= 1) | (ht == 'auto') )
ht = max_ht;
else
if (ht > max_ht)
error(sprintf('Cannot build pyramid higher than %d levels.',max_ht));
end
end
if (exist('edges') ~= 1)
edges= 'reflect1';
end
%------------------------------------------------------------
if (ht <= 1)
pyr = im(:);
pind = im_sz;
else
if (im_sz(2) == 1)
lo2 = corrDn(im, filt1, edges, [2 1], [1 1]);
elseif (im_sz(1) == 1)
lo2 = corrDn(im, filt1', edges, [1 2], [1 1]);
else
lo = corrDn(im, filt1', edges, [1 2], [1 1]);
int_sz = size(lo);
lo2 = corrDn(lo, filt1, edges, [2 1], [1 1]);
end
[npyr,nind] = buildLpyr(lo2, ht-1, filt1, filt2, edges);
if (im_sz(1) == 1)
hi2 = upConv(lo2, filt2', edges, [1 2], [1 1], im_sz);
elseif (im_sz(2) == 1)
hi2 = upConv(lo2, filt2, edges, [2 1], [1 1], im_sz);
else
hi = upConv(lo2, filt2, edges, [2 1], [1 1], int_sz);
hi2 = upConv(hi, filt2', edges, [1 2], [1 1], im_sz);
end
hi2 = im - hi2;
pyr = [hi2(:); npyr];
pind = [im_sz; nind];
end
|
github
|
jacksky64/imageProcessing-master
|
mkAngle.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/mkAngle.m
| 788 |
utf_8
|
126297224256c6e9077dc58f4094c39a
|
% IM = mkAngle(SIZE, PHASE, ORIGIN)
%
% Compute a matrix of dimension SIZE (a [Y X] 2-vector, or a scalar)
% containing samples of the polar angle (in radians, CW from the
% X-axis, ranging from -pi to pi), relative to angle PHASE (default =
% 0), about ORIGIN pixel (default = (size+1)/2).
% Eero Simoncelli, 6/96.
function [res] = mkAngle(sz, phase, origin)
sz = sz(:);
if (size(sz,1) == 1)
sz = [sz,sz];
end
% -----------------------------------------------------------------
% OPTIONAL args:
if (exist('origin') ~= 1)
origin = (sz+1)/2;
end
% -----------------------------------------------------------------
[xramp,yramp] = meshgrid( [1:sz(2)]-origin(2), [1:sz(1)]-origin(1) );
res = atan2(yramp,xramp);
if (exist('phase') == 1)
res = mod(res+(pi-phase),2*pi)-pi;
end
|
github
|
jacksky64/imageProcessing-master
|
wpyrHt.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/wpyrHt.m
| 270 |
utf_8
|
18e1a724afee99389db70484333eb05a
|
% [HEIGHT] = wpyrHt(INDICES)
%
% Compute height of separable QMF/wavelet pyramid with given index matrix.
% Eero Simoncelli, 6/96.
function [ht] = wpyrHt(pind)
if ((pind(1,1) == 1) | (pind(1,2) ==1))
nbands = 1;
else
nbands = 3;
end
ht = (size(pind,1)-1)/nbands;
|
github
|
jacksky64/imageProcessing-master
|
sp0Filters.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/sp0Filters.m
| 6,140 |
utf_8
|
0c5cd7bafff21efacd2a8ec71af90f49
|
% Steerable pyramid filters. Transform described in:
%
% @INPROCEEDINGS{Simoncelli95b,
% TITLE = "The Steerable Pyramid: A Flexible Architecture for
% Multi-Scale Derivative Computation",
% AUTHOR = "E P Simoncelli and W T Freeman",
% BOOKTITLE = "Second Int'l Conf on Image Processing",
% ADDRESS = "Washington, DC", MONTH = "October", YEAR = 1995 }
%
% Filter kernel design described in:
%
%@INPROCEEDINGS{Karasaridis96,
% TITLE = "A Filter Design Technique for
% Steerable Pyramid Image Transforms",
% AUTHOR = "A Karasaridis and E P Simoncelli",
% BOOKTITLE = "ICASSP", ADDRESS = "Atlanta, GA",
% MONTH = "May", YEAR = 1996 }
% Eero Simoncelli, 6/96.
function [lo0filt,hi0filt,lofilt,bfilts,mtx,harmonics] = sp0Filters();
harmonics = [ 0 ];
lo0filt = [ ...
-4.514000e-04 -1.137100e-04 -3.725800e-04 -3.743860e-03 -3.725800e-04 -1.137100e-04 -4.514000e-04
-1.137100e-04 -6.119520e-03 -1.344160e-02 -7.563200e-03 -1.344160e-02 -6.119520e-03 -1.137100e-04
-3.725800e-04 -1.344160e-02 6.441488e-02 1.524935e-01 6.441488e-02 -1.344160e-02 -3.725800e-04
-3.743860e-03 -7.563200e-03 1.524935e-01 3.153017e-01 1.524935e-01 -7.563200e-03 -3.743860e-03
-3.725800e-04 -1.344160e-02 6.441488e-02 1.524935e-01 6.441488e-02 -1.344160e-02 -3.725800e-04
-1.137100e-04 -6.119520e-03 -1.344160e-02 -7.563200e-03 -1.344160e-02 -6.119520e-03 -1.137100e-04
-4.514000e-04 -1.137100e-04 -3.725800e-04 -3.743860e-03 -3.725800e-04 -1.137100e-04 -4.514000e-04];
lofilt = [ ...
-2.257000e-04 -8.064400e-04 -5.686000e-05 8.741400e-04 -1.862800e-04 -1.031640e-03 -1.871920e-03 -1.031640e-03 -1.862800e-04 8.741400e-04 -5.686000e-05 -8.064400e-04 -2.257000e-04
-8.064400e-04 1.417620e-03 -1.903800e-04 -2.449060e-03 -4.596420e-03 -7.006740e-03 -6.948900e-03 -7.006740e-03 -4.596420e-03 -2.449060e-03 -1.903800e-04 1.417620e-03 -8.064400e-04
-5.686000e-05 -1.903800e-04 -3.059760e-03 -6.401000e-03 -6.720800e-03 -5.236180e-03 -3.781600e-03 -5.236180e-03 -6.720800e-03 -6.401000e-03 -3.059760e-03 -1.903800e-04 -5.686000e-05
8.741400e-04 -2.449060e-03 -6.401000e-03 -5.260020e-03 3.938620e-03 1.722078e-02 2.449600e-02 1.722078e-02 3.938620e-03 -5.260020e-03 -6.401000e-03 -2.449060e-03 8.741400e-04
-1.862800e-04 -4.596420e-03 -6.720800e-03 3.938620e-03 3.220744e-02 6.306262e-02 7.624674e-02 6.306262e-02 3.220744e-02 3.938620e-03 -6.720800e-03 -4.596420e-03 -1.862800e-04
-1.031640e-03 -7.006740e-03 -5.236180e-03 1.722078e-02 6.306262e-02 1.116388e-01 1.348999e-01 1.116388e-01 6.306262e-02 1.722078e-02 -5.236180e-03 -7.006740e-03 -1.031640e-03
-1.871920e-03 -6.948900e-03 -3.781600e-03 2.449600e-02 7.624674e-02 1.348999e-01 1.576508e-01 1.348999e-01 7.624674e-02 2.449600e-02 -3.781600e-03 -6.948900e-03 -1.871920e-03
-1.031640e-03 -7.006740e-03 -5.236180e-03 1.722078e-02 6.306262e-02 1.116388e-01 1.348999e-01 1.116388e-01 6.306262e-02 1.722078e-02 -5.236180e-03 -7.006740e-03 -1.031640e-03
-1.862800e-04 -4.596420e-03 -6.720800e-03 3.938620e-03 3.220744e-02 6.306262e-02 7.624674e-02 6.306262e-02 3.220744e-02 3.938620e-03 -6.720800e-03 -4.596420e-03 -1.862800e-04
8.741400e-04 -2.449060e-03 -6.401000e-03 -5.260020e-03 3.938620e-03 1.722078e-02 2.449600e-02 1.722078e-02 3.938620e-03 -5.260020e-03 -6.401000e-03 -2.449060e-03 8.741400e-04
-5.686000e-05 -1.903800e-04 -3.059760e-03 -6.401000e-03 -6.720800e-03 -5.236180e-03 -3.781600e-03 -5.236180e-03 -6.720800e-03 -6.401000e-03 -3.059760e-03 -1.903800e-04 -5.686000e-05
-8.064400e-04 1.417620e-03 -1.903800e-04 -2.449060e-03 -4.596420e-03 -7.006740e-03 -6.948900e-03 -7.006740e-03 -4.596420e-03 -2.449060e-03 -1.903800e-04 1.417620e-03 -8.064400e-04
-2.257000e-04 -8.064400e-04 -5.686000e-05 8.741400e-04 -1.862800e-04 -1.031640e-03 -1.871920e-03 -1.031640e-03 -1.862800e-04 8.741400e-04 -5.686000e-05 -8.064400e-04 -2.257000e-04];
mtx = [ 1.000000 ];
hi0filt = [...
5.997200e-04 -6.068000e-05 -3.324900e-04 -3.325600e-04 -2.406600e-04 -3.325600e-04 -3.324900e-04 -6.068000e-05 5.997200e-04
-6.068000e-05 1.263100e-04 4.927100e-04 1.459700e-04 -3.732100e-04 1.459700e-04 4.927100e-04 1.263100e-04 -6.068000e-05
-3.324900e-04 4.927100e-04 -1.616650e-03 -1.437358e-02 -2.420138e-02 -1.437358e-02 -1.616650e-03 4.927100e-04 -3.324900e-04
-3.325600e-04 1.459700e-04 -1.437358e-02 -6.300923e-02 -9.623594e-02 -6.300923e-02 -1.437358e-02 1.459700e-04 -3.325600e-04
-2.406600e-04 -3.732100e-04 -2.420138e-02 -9.623594e-02 8.554893e-01 -9.623594e-02 -2.420138e-02 -3.732100e-04 -2.406600e-04
-3.325600e-04 1.459700e-04 -1.437358e-02 -6.300923e-02 -9.623594e-02 -6.300923e-02 -1.437358e-02 1.459700e-04 -3.325600e-04
-3.324900e-04 4.927100e-04 -1.616650e-03 -1.437358e-02 -2.420138e-02 -1.437358e-02 -1.616650e-03 4.927100e-04 -3.324900e-04
-6.068000e-05 1.263100e-04 4.927100e-04 1.459700e-04 -3.732100e-04 1.459700e-04 4.927100e-04 1.263100e-04 -6.068000e-05
5.997200e-04 -6.068000e-05 -3.324900e-04 -3.325600e-04 -2.406600e-04 -3.325600e-04 -3.324900e-04 -6.068000e-05 5.997200e-04 ];
bfilts = [ ...
-9.066000e-05 -1.738640e-03 -4.942500e-03 -7.889390e-03 -1.009473e-02 -7.889390e-03 -4.942500e-03 -1.738640e-03 -9.066000e-05 ...
-1.738640e-03 -4.625150e-03 -7.272540e-03 -7.623410e-03 -9.091950e-03 -7.623410e-03 -7.272540e-03 -4.625150e-03 -1.738640e-03 ...
-4.942500e-03 -7.272540e-03 -2.129540e-02 -2.435662e-02 -3.487008e-02 -2.435662e-02 -2.129540e-02 -7.272540e-03 -4.942500e-03 ...
-7.889390e-03 -7.623410e-03 -2.435662e-02 -1.730466e-02 -3.158605e-02 -1.730466e-02 -2.435662e-02 -7.623410e-03 -7.889390e-03 ...
-1.009473e-02 -9.091950e-03 -3.487008e-02 -3.158605e-02 9.464195e-01 -3.158605e-02 -3.487008e-02 -9.091950e-03 -1.009473e-02 ...
-7.889390e-03 -7.623410e-03 -2.435662e-02 -1.730466e-02 -3.158605e-02 -1.730466e-02 -2.435662e-02 -7.623410e-03 -7.889390e-03 ...
-4.942500e-03 -7.272540e-03 -2.129540e-02 -2.435662e-02 -3.487008e-02 -2.435662e-02 -2.129540e-02 -7.272540e-03 -4.942500e-03 ...
-1.738640e-03 -4.625150e-03 -7.272540e-03 -7.623410e-03 -9.091950e-03 -7.623410e-03 -7.272540e-03 -4.625150e-03 -1.738640e-03 ...
-9.066000e-05 -1.738640e-03 -4.942500e-03 -7.889390e-03 -1.009473e-02 -7.889390e-03 -4.942500e-03 -1.738640e-03 -9.066000e-05 ]';
|
github
|
jacksky64/imageProcessing-master
|
sp5Filters.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/sp5Filters.m
| 6,949 |
utf_8
|
305fb0c0ca0709fc34ca6c5b4bb91712
|
% Steerable pyramid filters. Transform described in:
%
% @INPROCEEDINGS{Simoncelli95b,
% TITLE = "The Steerable Pyramid: A Flexible Architecture for
% Multi-Scale Derivative Computation",
% AUTHOR = "E P Simoncelli and W T Freeman",
% BOOKTITLE = "Second Int'l Conf on Image Processing",
% ADDRESS = "Washington, DC", MONTH = "October", YEAR = 1995 }
%
% Filter kernel design described in:
%
%@INPROCEEDINGS{Karasaridis96,
% TITLE = "A Filter Design Technique for
% Steerable Pyramid Image Transforms",
% AUTHOR = "A Karasaridis and E P Simoncelli",
% BOOKTITLE = "ICASSP", ADDRESS = "Atlanta, GA",
% MONTH = "May", YEAR = 1996 }
% Eero Simoncelli, 6/96.
function [lo0filt,hi0filt,lofilt,bfilts,mtx,harmonics] = sp5Filters();
harmonics = [1 3 5];
mtx = [ ...
0.3333 0.2887 0.1667 0.0000 -0.1667 -0.2887
0.0000 0.1667 0.2887 0.3333 0.2887 0.1667
0.3333 -0.0000 -0.3333 -0.0000 0.3333 -0.0000
0.0000 0.3333 0.0000 -0.3333 0.0000 0.3333
0.3333 -0.2887 0.1667 -0.0000 -0.1667 0.2887
-0.0000 0.1667 -0.2887 0.3333 -0.2887 0.1667];
hi0filt = [
-0.00033429 -0.00113093 -0.00171484 -0.00133542 -0.00080639 -0.00133542 -0.00171484 -0.00113093 -0.00033429
-0.00113093 -0.00350017 -0.00243812 0.00631653 0.01261227 0.00631653 -0.00243812 -0.00350017 -0.00113093
-0.00171484 -0.00243812 -0.00290081 -0.00673482 -0.00981051 -0.00673482 -0.00290081 -0.00243812 -0.00171484
-0.00133542 0.00631653 -0.00673482 -0.07027679 -0.11435863 -0.07027679 -0.00673482 0.00631653 -0.00133542
-0.00080639 0.01261227 -0.00981051 -0.11435863 0.81380200 -0.11435863 -0.00981051 0.01261227 -0.00080639
-0.00133542 0.00631653 -0.00673482 -0.07027679 -0.11435863 -0.07027679 -0.00673482 0.00631653 -0.00133542
-0.00171484 -0.00243812 -0.00290081 -0.00673482 -0.00981051 -0.00673482 -0.00290081 -0.00243812 -0.00171484
-0.00113093 -0.00350017 -0.00243812 0.00631653 0.01261227 0.00631653 -0.00243812 -0.00350017 -0.00113093
-0.00033429 -0.00113093 -0.00171484 -0.00133542 -0.00080639 -0.00133542 -0.00171484 -0.00113093 -0.00033429];
lo0filt = [
0.00341614 -0.01551246 -0.03848215 -0.01551246 0.00341614
-0.01551246 0.05586982 0.15925570 0.05586982 -0.01551246
-0.03848215 0.15925570 0.40304148 0.15925570 -0.03848215
-0.01551246 0.05586982 0.15925570 0.05586982 -0.01551246
0.00341614 -0.01551246 -0.03848215 -0.01551246 0.00341614];
lofilt = 2*[
0.00085404 -0.00244917 -0.00387812 -0.00944432 -0.00962054 -0.00944432 -0.00387812 -0.00244917 0.00085404
-0.00244917 -0.00523281 -0.00661117 0.00410600 0.01002988 0.00410600 -0.00661117 -0.00523281 -0.00244917
-0.00387812 -0.00661117 0.01396746 0.03277038 0.03981393 0.03277038 0.01396746 -0.00661117 -0.00387812
-0.00944432 0.00410600 0.03277038 0.06426333 0.08169618 0.06426333 0.03277038 0.00410600 -0.00944432
-0.00962054 0.01002988 0.03981393 0.08169618 0.10096540 0.08169618 0.03981393 0.01002988 -0.00962054
-0.00944432 0.00410600 0.03277038 0.06426333 0.08169618 0.06426333 0.03277038 0.00410600 -0.00944432
-0.00387812 -0.00661117 0.01396746 0.03277038 0.03981393 0.03277038 0.01396746 -0.00661117 -0.00387812
-0.00244917 -0.00523281 -0.00661117 0.00410600 0.01002988 0.00410600 -0.00661117 -0.00523281 -0.00244917
0.00085404 -0.00244917 -0.00387812 -0.00944432 -0.00962054 -0.00944432 -0.00387812 -0.00244917 0.00085404];
bfilts = [...
0.00277643 0.00496194 0.01026699 0.01455399 0.01026699 0.00496194 0.00277643 ...
-0.00986904 -0.00893064 0.01189859 0.02755155 0.01189859 -0.00893064 -0.00986904 ...
-0.01021852 -0.03075356 -0.08226445 -0.11732297 -0.08226445 -0.03075356 -0.01021852 ...
0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 ...
0.01021852 0.03075356 0.08226445 0.11732297 0.08226445 0.03075356 0.01021852 ...
0.00986904 0.00893064 -0.01189859 -0.02755155 -0.01189859 0.00893064 0.00986904 ...
-0.00277643 -0.00496194 -0.01026699 -0.01455399 -0.01026699 -0.00496194 -0.00277643;
...
-0.00343249 -0.00640815 -0.00073141 0.01124321 0.00182078 0.00285723 0.01166982 ...
-0.00358461 -0.01977507 -0.04084211 -0.00228219 0.03930573 0.01161195 0.00128000 ...
0.01047717 0.01486305 -0.04819057 -0.12227230 -0.05394139 0.00853965 -0.00459034 ...
0.00790407 0.04435647 0.09454202 -0.00000000 -0.09454202 -0.04435647 -0.00790407 ...
0.00459034 -0.00853965 0.05394139 0.12227230 0.04819057 -0.01486305 -0.01047717 ...
-0.00128000 -0.01161195 -0.03930573 0.00228219 0.04084211 0.01977507 0.00358461 ...
-0.01166982 -0.00285723 -0.00182078 -0.01124321 0.00073141 0.00640815 0.00343249;
...
0.00343249 0.00358461 -0.01047717 -0.00790407 -0.00459034 0.00128000 0.01166982 ...
0.00640815 0.01977507 -0.01486305 -0.04435647 0.00853965 0.01161195 0.00285723 ...
0.00073141 0.04084211 0.04819057 -0.09454202 -0.05394139 0.03930573 0.00182078 ...
-0.01124321 0.00228219 0.12227230 -0.00000000 -0.12227230 -0.00228219 0.01124321 ...
-0.00182078 -0.03930573 0.05394139 0.09454202 -0.04819057 -0.04084211 -0.00073141 ...
-0.00285723 -0.01161195 -0.00853965 0.04435647 0.01486305 -0.01977507 -0.00640815 ...
-0.01166982 -0.00128000 0.00459034 0.00790407 0.01047717 -0.00358461 -0.00343249;
...
-0.00277643 0.00986904 0.01021852 -0.00000000 -0.01021852 -0.00986904 0.00277643 ...
-0.00496194 0.00893064 0.03075356 -0.00000000 -0.03075356 -0.00893064 0.00496194 ...
-0.01026699 -0.01189859 0.08226445 -0.00000000 -0.08226445 0.01189859 0.01026699 ...
-0.01455399 -0.02755155 0.11732297 -0.00000000 -0.11732297 0.02755155 0.01455399 ...
-0.01026699 -0.01189859 0.08226445 -0.00000000 -0.08226445 0.01189859 0.01026699 ...
-0.00496194 0.00893064 0.03075356 -0.00000000 -0.03075356 -0.00893064 0.00496194 ...
-0.00277643 0.00986904 0.01021852 -0.00000000 -0.01021852 -0.00986904 0.00277643;
...
-0.01166982 -0.00128000 0.00459034 0.00790407 0.01047717 -0.00358461 -0.00343249 ...
-0.00285723 -0.01161195 -0.00853965 0.04435647 0.01486305 -0.01977507 -0.00640815 ...
-0.00182078 -0.03930573 0.05394139 0.09454202 -0.04819057 -0.04084211 -0.00073141 ...
-0.01124321 0.00228219 0.12227230 -0.00000000 -0.12227230 -0.00228219 0.01124321 ...
0.00073141 0.04084211 0.04819057 -0.09454202 -0.05394139 0.03930573 0.00182078 ...
0.00640815 0.01977507 -0.01486305 -0.04435647 0.00853965 0.01161195 0.00285723 ...
0.00343249 0.00358461 -0.01047717 -0.00790407 -0.00459034 0.00128000 0.01166982;
...
-0.01166982 -0.00285723 -0.00182078 -0.01124321 0.00073141 0.00640815 0.00343249 ...
-0.00128000 -0.01161195 -0.03930573 0.00228219 0.04084211 0.01977507 0.00358461 ...
0.00459034 -0.00853965 0.05394139 0.12227230 0.04819057 -0.01486305 -0.01047717 ...
0.00790407 0.04435647 0.09454202 -0.00000000 -0.09454202 -0.04435647 -0.00790407 ...
0.01047717 0.01486305 -0.04819057 -0.12227230 -0.05394139 0.00853965 -0.00459034 ...
-0.00358461 -0.01977507 -0.04084211 -0.00228219 0.03930573 0.01161195 0.00128000 ...
-0.00343249 -0.00640815 -0.00073141 0.01124321 0.00182078 0.00285723 0.01166982]';
|
github
|
jacksky64/imageProcessing-master
|
steer.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/steer.m
| 1,990 |
utf_8
|
3db4dd948e0ece7c7237330b7d4f191e
|
% RES = STEER(BASIS, ANGLE, HARMONICS, STEERMTX)
%
% Steer BASIS to the specfied ANGLE.
%
% BASIS should be a matrix whose columns are vectorized rotated copies of a
% steerable function, or the responses of a set of steerable filters.
%
% ANGLE can be a scalar, or a column vector the size of the basis.
%
% HARMONICS (optional, default is N even or odd low frequencies, as for
% derivative filters) should be a list of harmonic numbers indicating
% the angular harmonic content of the basis.
%
% STEERMTX (optional, default assumes cosine phase harmonic components,
% and filter positions at 2pi*n/N) should be a matrix which maps
% the filters onto Fourier series components (ordered [cos0 cos1 sin1
% cos2 sin2 ... sinN]). See steer2HarmMtx.m
% Eero Simoncelli, 7/96.
function res = steer(basis,angle,harmonics,steermtx)
num = size(basis,2);
if ( any(size(angle) ~= [size(basis,1) 1]) & any(size(angle) ~= [1 1]) )
error('ANGLE must be a scalar, or a column vector the size of the basis elements');
end
%% If HARMONICS are not passed, assume derivatives.
if (exist('harmonics') ~= 1)
if (mod(num,2) == 0)
harmonics = [0:(num/2)-1]'*2 + 1;
else
harmonics = [0:(num-1)/2]'*2;
end
else
harmonics = harmonics(:);
if ((2*size(harmonics,1)-any(harmonics == 0)) ~= num)
error('harmonics list is incompatible with basis size');
end
end
%% If STEERMTX not passed, assume evenly distributed cosine-phase filters:
if (exist('steermtx') ~= 1)
steermtx = steer2HarmMtx(harmonics, pi*[0:num-1]/num, 'even');
end
steervect = zeros(size(angle,1),num);
arg = angle * harmonics(find(harmonics~=0))';
if (all(harmonics))
steervect(:, 1:2:num) = cos(arg);
steervect(:, 2:2:num) = sin(arg);
else
steervect(:, 1) = ones(size(arg,1),1);
steervect(:, 2:2:num) = cos(arg);
steervect(:, 3:2:num) = sin(arg);
end
steervect = steervect * steermtx;
if (size(steervect,1) > 1)
tmp = basis' .* steervect';
res = sum(tmp)';
else
res = basis * steervect';
end
|
github
|
jacksky64/imageProcessing-master
|
mkGaussian.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/mkGaussian.m
| 1,565 |
utf_8
|
1f55e73fbc9155a38607b0667da2d7f3
|
% IM = mkGaussian(SIZE, COVARIANCE, MEAN, AMPLITUDE)
%
% Compute a matrix with dimensions SIZE (a [Y X] 2-vector, or a
% scalar) containing a Gaussian function, centered at pixel position
% specified by MEAN (default = (size+1)/2), with given COVARIANCE (can
% be a scalar, 2-vector, or 2x2 matrix. Default = (min(size)/6)^2),
% and AMPLITUDE. AMPLITUDE='norm' (default) will produce a
% probability-normalized function. All but the first argument are
% optional.
% Eero Simoncelli, 6/96.
function [res] = mkGaussian(sz, cov, mn, ampl)
sz = sz(:);
if (size(sz,1) == 1)
sz = [sz,sz];
end
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (exist('cov') ~= 1)
cov = (min(sz(1),sz(2))/6)^2;
end
if ( (exist('mn') ~= 1) | isempty(mn) )
mn = (sz+1)/2;
else
mn = mn(:);
if (size(mn,1) == 1)
mn = [mn, mn];
end
end
if (exist('ampl') ~= 1)
ampl = 'norm';
end
%------------------------------------------------------------
[xramp,yramp] = meshgrid([1:sz(2)]-mn(2),[1:sz(1)]-mn(1));
if (sum(size(cov)) == 2) % scalar
if (strcmp(ampl,'norm'))
ampl = 1/(2*pi*cov(1));
end
e = (xramp.^2 + yramp.^2)/(-2 * cov);
elseif (sum(size(cov)) == 3) % a 2-vector
if (strcmp(ampl,'norm'))
ampl = 1/(2*pi*sqrt(cov(1)*cov(2)));
end
e = xramp.^2/(-2 * cov(2)) + yramp.^2/(-2 * cov(1));
else
if (strcmp(ampl,'norm'))
ampl = 1/(2*pi*sqrt(det(cov)));
end
cov = -inv(cov)/2;
e = cov(2,2)*xramp.^2 + (cov(1,2)+cov(2,1))*(xramp.*yramp) ...
+ cov(1,1)*yramp.^2;
end
res = ampl .* exp(e);
|
github
|
jacksky64/imageProcessing-master
|
factorial.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/factorial.m
| 273 |
utf_8
|
370971eae7a2351704973c452848d194
|
%% RES = factorial(NUM)
%
% Factorial function that works on matrices (matlab's does not).
% EPS, 11/02
function res = factorial(num)
res = ones(size(num));
ind = find(num > 0);
if ( ~isempty(ind) )
subNum = num(ind);
res(ind) = subNum .* factorial(subNum-1);
end
|
github
|
jacksky64/imageProcessing-master
|
entropy2.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/entropy2.m
| 693 |
utf_8
|
c637630f7ac8912e5cb30f67551aece7
|
% E = ENTROPY2(MTX,BINSIZE)
%
% Compute the first-order sample entropy of MTX. Samples of VEC are
% first discretized. Optional argument BINSIZE controls the
% discretization, and defaults to 256/(max(VEC)-min(VEC)).
%
% NOTE: This is a heavily biased estimate of entropy (it is too
% small) when you don't have much data!
% Eero Simoncelli, 6/96.
function res = entropy2(mtx,binsize)
%% Ensure it's a vector, not a matrix.
vec = mtx(:);
[mn,mx] = range2(vec);
if (exist('binsize') == 1)
nbins = max((mx-mn)/binsize, 1);
else
nbins = 256;
end
[bincount,bins] = histo(vec,nbins);
%% Collect non-zero bins:
H = bincount(find(bincount));
H = H/sum(H);
res = -sum(H .* log2(H));
|
github
|
jacksky64/imageProcessing-master
|
buildSFpyr.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/buildSFpyr.m
| 3,256 |
utf_8
|
84c0a17ac90df74f317c29833c54ffa3
|
% [PYR, INDICES, STEERMTX, HARMONICS] = buildSFpyr(IM, HEIGHT, ORDER, TWIDTH)
%
% Construct a steerable pyramid on matrix IM, in the Fourier domain.
% This is similar to buildSpyr, except that:
%
% + Reconstruction is exact (within floating point errors)
% + It can produce any number of orientation bands.
% - Typically slower, especially for non-power-of-two sizes.
% - Boundary-handling is circular.
%
% HEIGHT (optional) specifies the number of pyramid levels to build. Default
% is maxPyrHt(size(IM),size(FILT));
%
% The squared radial functions tile the Fourier plane, with a raised-cosine
% falloff. Angular functions are cos(theta-k\pi/(K+1))^K, where K is
% the ORDER (one less than the number of orientation bands, default= 3).
%
% TWIDTH is the width of the transition region of the radial lowpass
% function, in octaves (default = 1, which gives a raised cosine for
% the bandpass filters).
%
% PYR is a vector containing the N pyramid subbands, ordered from fine
% to coarse. INDICES is an Nx2 matrix containing the sizes of
% each subband. This is compatible with the MatLab Wavelet toolbox.
% See the function STEER for a description of STEERMTX and HARMONICS.
% Eero Simoncelli, 5/97.
% See http://www.cns.nyu.edu/~eero/STEERPYR/ for more
% information about the Steerable Pyramid image decomposition.
function [pyr,pind,steermtx,harmonics] = buildSFpyr(im, ht, order, twidth)
%-----------------------------------------------------------------
%% DEFAULTS:
max_ht = floor(log2(min(size(im)))) - 2;
if (exist('ht') ~= 1)
ht = max_ht;
else
if (ht > max_ht)
error(sprintf('Cannot build pyramid higher than %d levels.',max_ht));
end
end
if (exist('order') ~= 1)
order = 3;
elseif ((order > 15) | (order < 0))
fprintf(1,'Warning: ORDER must be an integer in the range [0,15]. Truncating.\n');
order = min(max(order,0),15);
else
order = round(order);
end
nbands = order+1;
if (exist('twidth') ~= 1)
twidth = 1;
elseif (twidth <= 0)
fprintf(1,'Warning: TWIDTH must be positive. Setting to 1.\n');
twidth = 1;
end
%-----------------------------------------------------------------
%% Steering stuff:
if (mod((nbands),2) == 0)
harmonics = [0:(nbands/2)-1]'*2 + 1;
else
harmonics = [0:(nbands-1)/2]'*2;
end
steermtx = steer2HarmMtx(harmonics, pi*[0:nbands-1]/nbands, 'even');
%-----------------------------------------------------------------
dims = size(im);
ctr = ceil((dims+0.5)/2);
[xramp,yramp] = meshgrid( ([1:dims(2)]-ctr(2))./(dims(2)/2), ...
([1:dims(1)]-ctr(1))./(dims(1)/2) );
angle = atan2(yramp,xramp);
log_rad = sqrt(xramp.^2 + yramp.^2);
log_rad(ctr(1),ctr(2)) = log_rad(ctr(1),ctr(2)-1);
log_rad = log2(log_rad);
%% Radial transition function (a raised cosine in log-frequency):
[Xrcos,Yrcos] = rcosFn(twidth,(-twidth/2),[0 1]);
Yrcos = sqrt(Yrcos);
YIrcos = sqrt(1.0 - Yrcos.^2);
lo0mask = pointOp(log_rad, YIrcos, Xrcos(1), Xrcos(2)-Xrcos(1), 0);
imdft = fftshift(fft2(im));
lo0dft = imdft .* lo0mask;
[pyr,pind] = buildSFpyrLevs(lo0dft, log_rad, Xrcos, Yrcos, angle, ht, nbands);
hi0mask = pointOp(log_rad, Yrcos, Xrcos(1), Xrcos(2)-Xrcos(1), 0);
hi0dft = imdft .* hi0mask;
hi0 = ifft2(ifftshift(hi0dft));
pyr = [real(hi0(:)) ; pyr];
pind = [size(hi0); pind];
|
github
|
jacksky64/imageProcessing-master
|
spyrLev.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/spyrLev.m
| 668 |
utf_8
|
8d25ccc2790a62ab21a20cc3d0772706
|
% [LEV,IND] = spyrLev(PYR,INDICES,LEVEL)
%
% Access a level from a steerable pyramid.
% Return as an SxB matrix, B = number of bands, S = total size of a band.
% Also returns an Bx2 matrix containing dimensions of the subbands.
% Eero Simoncelli, 6/96.
function [lev,ind] = spyrLev(pyr,pind,level)
nbands = spyrNumBands(pind);
if ((level > spyrHt(pind)) | (level < 1))
error(sprintf('Level number must be in the range [1, %d].', spyrHt(pind)));
end
firstband = 2 + nbands*(level-1);
firstind = 1;
for l=1:firstband-1
firstind = firstind + prod(pind(l,:));
end
ind = pind(firstband:firstband+nbands-1,:);
lev = pyr(firstind:firstind+sum(prod(ind'))-1);
|
github
|
jacksky64/imageProcessing-master
|
pgmWrite.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/pgmWrite.m
| 3,119 |
utf_8
|
6425008296069df51c5c30ee1c011850
|
% RANGE = pgmWrite(MTX, FILENAME, RANGE, TYPE, COMMENT)
%
% Write a MatLab matrix to a pgm (graylevel image) file.
% This format is accessible from the XV image browsing utility.
%
% RANGE (optional) is a 2-vector specifying the values that map to
% black and white, respectively. Passing a value of 'auto' (default)
% sets RANGE=[min,max] (as in MatLab's imagesc). 'auto2' sets
% RANGE=[mean-2*stdev, mean+2*stdev]. 'auto3' sets
% RANGE=[p1-(p2-p1)/8, p2+(p2-p1)/8], where p1 is the 10th percentile
% value of the sorted MATRIX samples, and p2 is the 90th percentile
% value.
%
% TYPE (optional) should be 'raw' or 'ascii'. Defaults to 'raw'.
% Hany Farid, Spring '96. Modified by Eero Simoncelli, 6/96.
function range = pgmWrite(mtx, fname, range, type, comment );
[fid,msg] = fopen( fname, 'w' );
if (fid == -1)
error(msg);
end
%------------------------------------------------------------
%% optional ARGS:
if (exist('range') ~= 1)
range = 'auto';
end
if (exist('type') ~= 1)
type = 'raw';
end
%------------------------------------------------------------
%% Automatic range calculation:
if (strcmp(range,'auto1') | strcmp(range,'auto'))
[mn,mx] = range2(mtx);
range = [mn,mx];
elseif strcmp(range,'auto2')
stdev = sqrt(var2(mtx));
av = mean2(mtx);
range = [av-2*stdev,av+2*stdev]; % MAGIC NUMBER: 2 stdevs
elseif strcmp(range, 'auto3')
percentile = 0.1; % MAGIC NUMBER: 0<p<0.5
[N,X] = histo(mtx);
binsz = X(2)-X(1);
N = N+1e-10; % Ensure cumsum will be monotonic for call to interp1
cumN = [0, cumsum(N)]/sum(N);
cumX = [X(1)-binsz, X] + (binsz/2);
ctrRange = interp1(cumN,cumX, [percentile, 1-percentile]);
range = mean(ctrRange) + (ctrRange-mean(ctrRange))/(1-2*percentile);
elseif isstr(range)
error(sprintf('Bad RANGE argument: %s',range))
end
if ((range(2) - range(1)) <= eps)
range(1) = range(1) - 0.5;
range(2) = range(2) + 0.5;
end
%%% First line contains ID string:
%%% "P1" = ascii bitmap, "P2" = ascii greymap,
%%% "P3" = ascii pixmap, "P4" = raw bitmap,
%%% "P5" = raw greymap, "P6" = raw pixmap
if strcmp(type,'raw')
fprintf(fid,'P5\n');
format = 5;
elseif strcmp(type,'ascii')
fprintf(fid,'P2\n');
format = 2;
else
error(sprintf('PGMWRITE: Bad type argument: %s',type));
end
fprintf(fid,'# MatLab PGMWRITE file, saved %s\n',date);
if (exist('comment') == 1)
fprintf(fid,'# %s\n', comment);
end
%%% dimensions
fprintf(fid,'%d %d\n',size(mtx,2),size(mtx,1));
%%% Maximum pixel value
fprintf(fid,'255\n');
%% MatLab's "fprintf" floors when writing floats, so we compute
%% (mtx-r1)*255/(r2-r1)+0.5
mult = (255 / (range(2)-range(1)));
mtx = (mult * mtx) + (0.5 - mult * range(1));
mtx = max(-0.5+eps,min(255.5-eps,mtx));
if (format == 2)
count = fprintf(fid,'%d ',mtx');
elseif (format == 5)
count = fwrite(fid,mtx','uchar');
end
fclose(fid);
if (count ~= size(mtx,1)*size(mtx,2))
fprintf(1,'Warning: File output terminated early!');
end
%%% TEST:
% foo = 257*rand(100)-1;
% pgmWrite(foo,'foo.pgm',[0 255]);
% foo2=pgmRead('foo.pgm');
% size(find((foo2-round(foo))~=0))
% foo(find((foo2-round(foo))~=0))
|
github
|
jacksky64/imageProcessing-master
|
modulateFlip.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/modulateFlip.m
| 461 |
utf_8
|
92f12f8068fcf49b9863851f106a5aa3
|
% [HFILT] = modulateFlipShift(LFILT)
%
% QMF/Wavelet highpass filter construction: modulate by (-1)^n,
% reverse order (and shift by one, which is handled by the convolution
% routines). This is an extension of the original definition of QMF's
% (e.g., see Simoncelli90).
% Eero Simoncelli, 7/96.
function [hfilt] = modulateFlipShift(lfilt)
lfilt = lfilt(:);
sz = size(lfilt,1);
sz2 = ceil(sz/2);
ind = [sz:-1:1]';
hfilt = lfilt(ind) .* (-1).^(ind-sz2);
|
github
|
jacksky64/imageProcessing-master
|
mkFract.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/mkFract.m
| 843 |
utf_8
|
f0d97e35133978ade3a5fe34dea5d08a
|
% IM = mkFract(SIZE, FRACT_DIM)
%
% Make a matrix of dimensions SIZE (a [Y X] 2-vector, or a scalar)
% containing fractal (pink) noise with power spectral density of the
% form: 1/f^(5-2*FRACT_DIM). Image variance is normalized to 1.0.
% FRACT_DIM defaults to 1.0
% Eero Simoncelli, 6/96.
%% TODO: Verify that this matches Mandelbrot defn of fractal dimension.
%% Make this more efficient!
function res = mkFract(dims, fract_dim)
if (exist('fract_dim') ~= 1)
fract_dim = 1.0;
end
res = randn(dims);
fres = fft2(res);
sz = size(res);
ctr = ceil((sz+1)./2);
shape = ifftshift(mkR(sz, -(2.5-fract_dim), ctr));
shape(1,1) = 1; %%DC term
fres = shape .* fres;
fres = ifft2(fres);
if (max(max(abs(imag(fres)))) > 1e-10)
error('Symmetry error in creating fractal');
else
res = real(fres);
res = res / sqrt(var2(res));
end
|
github
|
jacksky64/imageProcessing-master
|
mkSquare.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/mkSquare.m
| 2,344 |
utf_8
|
7d9553e391552cd91cdd6d81348404e2
|
% IM = mkSquare(SIZE, PERIOD, DIRECTION, AMPLITUDE, PHASE, ORIGIN, TWIDTH)
% or
% IM = mkSine(SIZE, FREQ, AMPLITUDE, PHASE, ORIGIN, TWIDTH)
%
% Compute a matrix of dimension SIZE (a [Y X] 2-vector, or a scalar)
% containing samples of a 2D square wave, with given PERIOD (in
% pixels), DIRECTION (radians, CW from X-axis, default = 0), AMPLITUDE
% (default = 1), and PHASE (radians, relative to ORIGIN, default = 0).
% ORIGIN defaults to the center of the image. TWIDTH specifies width
% of raised-cosine edges on the bars of the grating (default =
% min(2,period/3)).
%
% In the second form, FREQ is a 2-vector of frequencies (radians/pixel).
% Eero Simoncelli, 6/96.
% TODO: Add duty cycle.
function [res] = mkSquare(sz, per_freq, dir_amp, amp_phase, phase_orig, orig_twidth, twidth)
%------------------------------------------------------------
%% OPTIONAL ARGS:
if (prod(size(per_freq)) == 2)
frequency = norm(per_freq);
direction = atan2(per_freq(1),per_freq(2));
if (exist('dir_amp') == 1)
amplitude = dir_amp;
else
amplitude = 1;
end
if (exist('amp_phase') == 1)
phase = amp_phase;
else
phase = 0;
end
if (exist('phase_orig') == 1)
origin = phase_orig;
end
if (exist('orig_twidth') == 1)
transition = orig_twidth;
else
transition = min(2,2*pi/(3*frequency));
end
if (exist('twidth') == 1)
error('Too many arguments for (second form) of mkSine');
end
else
frequency = 2*pi/per_freq;
if (exist('dir_amp') == 1)
direction = dir_amp;
else
direction = 0;
end
if (exist('amp_phase') == 1)
amplitude = amp_phase;
else
amplitude = 1;
end
if (exist('phase_orig') == 1)
phase = phase_orig;
else
phase = 0;
end
if (exist('orig_twidth') == 1)
origin = orig_twidth;
end
if (exist('twidth') == 1)
transition = twidth;
else
transition = min(2,2*pi/(3*frequency));
end
end
%------------------------------------------------------------
if (exist('origin') == 1)
res = mkRamp(sz, direction, frequency, phase, origin) - pi/2;
else
res = mkRamp(sz, direction, frequency, phase) - pi/2;
end
[Xtbl,Ytbl] = rcosFn(transition*frequency,pi/2,[-amplitude amplitude]);
res = pointOp(abs(mod(res+pi, 2*pi)-pi),Ytbl,Xtbl(1),Xtbl(2)-Xtbl(1),0);
% OLD threshold version:
%res = amplitude * (mod(res,2*pi) < pi);
|
github
|
jacksky64/imageProcessing-master
|
spyrNumBands.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/spyrNumBands.m
| 480 |
utf_8
|
4a10cb68438c7dfc197ec00066f48fd4
|
% [NBANDS] = spyrNumBands(INDICES)
%
% Compute number of orientation bands in a steerable pyramid with
% given index matrix. If the pyramid contains only the highpass and
% lowpass bands (i.e., zero levels), returns 0.
% Eero Simoncelli, 2/97.
function [nbands] = spyrNumBands(pind)
if (size(pind,1) == 2)
nbands = 0;
else
% Count number of orientation bands:
b = 3;
while ((b <= size(pind,1)) & all( pind(b,:) == pind(2,:)) )
b = b+1;
end
nbands = b-2;
end
|
github
|
jacksky64/imageProcessing-master
|
reconSpyr.m
|
.m
|
imageProcessing-master/Matlab imaging/matlabPyrTools/reconSpyr.m
| 2,671 |
utf_8
|
ea9e71a5f8a76eadbe8c1a2472d89344
|
% RES = reconSpyr(PYR, INDICES, FILTFILE, EDGES, LEVS, BANDS)
%
% Reconstruct image from its steerable pyramid representation, as created
% by buildSpyr.
%
% PYR is a vector containing the N pyramid subbands, ordered from fine
% to coarse. INDICES is an Nx2 matrix containing the sizes of
% each subband. This is compatible with the MatLab Wavelet toolbox.
%
% FILTFILE (optional) should be a string referring to an m-file that returns
% the rfilters. examples: sp0Filters, sp1Filters, sp3Filters
% (default = 'sp1Filters').
% EDGES specifies edge-handling, and defaults to 'reflect1' (see
% corrDn).
%
% LEVS (optional) should be a list of levels to include, or the string
% 'all' (default). 0 corresonds to the residual highpass subband.
% 1 corresponds to the finest oriented scale. The lowpass band
% corresponds to number spyrHt(INDICES)+1.
%
% BANDS (optional) should be a list of bands to include, or the string
% 'all' (default). 1 = vertical, rest proceeding anti-clockwise.
% Eero Simoncelli, 6/96.
function res = reconSpyr(pyr, pind, filtfile, edges, levs, bands)
%%------------------------------------------------------------
%% DEFAULTS:
if (exist('filtfile') ~= 1)
filtfile = 'sp1Filters';
end
if (exist('edges') ~= 1)
edges= 'reflect1';
end
if (exist('levs') ~= 1)
levs = 'all';
end
if (exist('bands') ~= 1)
bands = 'all';
end
%%------------------------------------------------------------
if (isstr(filtfile) & (exist(filtfile) == 2))
[lo0filt,hi0filt,lofilt,bfilts,steermtx,harmonics] = eval(filtfile);
nbands = spyrNumBands(pind);
if ((nbands > 0) & (size(bfilts,2) ~= nbands))
error('Number of pyramid bands is inconsistent with filter file');
end
else
error('filtfile argument must be the name of an M-file containing SPYR filters.');
end
maxLev = 1+spyrHt(pind);
if strcmp(levs,'all')
levs = [0:maxLev]';
else
if (any(levs > maxLev) | any(levs < 0))
error(sprintf('Level numbers must be in the range [0, %d].', maxLev));
end
levs = levs(:);
end
if strcmp(bands,'all')
bands = [1:nbands]';
else
if (any(bands < 1) | any(bands > nbands))
error(sprintf('Band numbers must be in the range [1,3].', nbands));
end
bands = bands(:);
end
if (spyrHt(pind) == 0)
if (any(levs==1))
res1 = pyrBand(pyr,pind,2);
else
res1 = zeros(pind(2,:));
end
else
res1 = reconSpyrLevs(pyr(1+prod(pind(1,:)):size(pyr,1)), ...
pind(2:size(pind,1),:), ...
lofilt, bfilts, edges, levs, bands);
end
res = upConv(res1, lo0filt, edges);
%% residual highpass subband
if any(levs == 0)
res = upConv( subMtx(pyr, pind(1,:)), hi0filt, edges, [1 1], [1 1], size(res), res);
end
|
github
|
jacksky64/imageProcessing-master
|
PSMF.m
|
.m
|
imageProcessing-master/Matlab imaging/Nonlinear Image filter Matlab/Total variation/PSMF.m
| 1,729 |
utf_8
|
475d67192dff5927c8e02dd0c73206fe
|
%% Implementation of Progressive Switching Median Filter
%% Base Paper : Zhou Wang and David Zhang, "Progressive Switching Median
%% Filter for the Removal of Impulse Noise from Highly Corrupted Images",
%% IEEE Trans. on Cir. and Sys., vol. 46, no. 1, Jan. 1999.
%% Function Y = PSMF(x)
%% input x = Image is corrupted by Salt & Pepper Noise
%%
%% Example: Y = PSMF(x);
%% Posted date : 16 - 10 - 2008
%% Modified date :
%%
%% Developed By : K.Kannan ([email protected])
%% & Jeny Rajan ([email protected])
%% Medical Imaging Research Group (MIRG), NeST,
%% Trivandrum.
%% Progressive Switching Median Filter
function Y = PSMF(x)
x = double(x);
WF = 3; ND = 3;T = 40;a = 65;b = -50;
M = medfilt2(x,[3 3]);
N = abs(x - M);
N(N>T)=0;
N = N ~= 0;
N = double(N);
R = sum(N(:))/(size(x,1) * size(x,2));
if R <= 0.25
WD = 3;
else
WD = 5;
end
TD = a + (b * R);
z = IMPDET(x,ND,WD,TD);
Y = NF(x,z,WF);
%% Impulse Detection
function F1 = IMPDET(x,ND,WD,TD)
X = x;
M = medfilt2(X,[WD WD]);
D = abs(X - M);
F = zeros(size(x));
F(D>=TD)=1;
F1 = F;
X(F1==F)=X(F1==F);
X(F1~=F)=M(F1~=F);
for i = 1:ND-1
M = medfilt2(X,[WD WD]);
F1(abs(X - M)<TD)=F(abs(X - M)<TD);
F1((X - M)>=TD)=1;
X(F1==F)=X(F1==F);
X(F1~=F)=M(F1~=F);
F = F1;
end
return;
%% Noise Filtering
function Y = NF(x,f,WF)
g = f;
Y = x;
Y1 = Y;
g1 = g;
s = sum(g(:));
while s ~= 0
M = medfilt2(Y,[WF WF]);
Y1(g==1)=M(g==1);
g1(Y~=Y1)=0;
Y = Y1;
g = g1;
s1 = sum(g(:));
if s1 ~= s
s = s1;
else
s = 0;
end
end
return;
|
github
|
jacksky64/imageProcessing-master
|
Hessian3D.m
|
.m
|
imageProcessing-master/frangifilter/Hessian3D.m
| 1,938 |
utf_8
|
9204648b80240369948918e5b591d037
|
function [Dxx, Dyy, Dzz, Dxy, Dxz, Dyz] = Hessian3D(Volume,Sigma)
% This function Hessian3D filters the image with an Gaussian kernel
% followed by calculation of 2nd order gradients, which aprroximates the
% 2nd order derivatives of the image.
%
% [Dxx, Dyy, Dzz, Dxy, Dxz, Dyz] = Hessian3D(I,Sigma)
%
% inputs,
% I : The image volume, class preferable double or single
% Sigma : The sigma of the gaussian kernel used. If sigma is zero
% no gaussian filtering.
%
% outputs,
% Dxx, Dyy, Dzz, Dxy, Dxz, Dyz: The 2nd derivatives
%
% Function is written by D.Kroon University of Twente (June 2009)
% defaults
if nargin < 2, Sigma = 1; end
if(Sigma>0)
F=imgaussian(Volume,Sigma);
else
F=Volume;
end
% Create first and second order diferentiations
Dz=gradient3(F,'z');
Dzz=(gradient3(Dz,'z'));
clear Dz;
Dy=gradient3(F,'y');
Dyy=(gradient3(Dy,'y'));
Dyz=(gradient3(Dy,'z'));
clear Dy;
Dx=gradient3(F,'x');
Dxx=(gradient3(Dx,'x'));
Dxy=(gradient3(Dx,'y'));
Dxz=(gradient3(Dx,'z'));
clear Dx;
function D = gradient3(F,option)
% This function does the same as the default matlab "gradient" function
% but with one direction at the time, less cpu and less memory usage.
%
% Example:
%
% Fx = gradient3(F,'x');
[k,l,m] = size(F);
D = zeros(size(F),class(F));
switch lower(option)
case 'x'
% Take forward differences on left and right edges
D(1,:,:) = (F(2,:,:) - F(1,:,:));
D(k,:,:) = (F(k,:,:) - F(k-1,:,:));
% Take centered differences on interior points
D(2:k-1,:,:) = (F(3:k,:,:)-F(1:k-2,:,:))/2;
case 'y'
D(:,1,:) = (F(:,2,:) - F(:,1,:));
D(:,l,:) = (F(:,l,:) - F(:,l-1,:));
D(:,2:l-1,:) = (F(:,3:l,:)-F(:,1:l-2,:))/2;
case 'z'
D(:,:,1) = (F(:,:,2) - F(:,:,1));
D(:,:,m) = (F(:,:,m) - F(:,:,m-1));
D(:,:,2:m-1) = (F(:,:,3:m)-F(:,:,1:m-2))/2;
otherwise
disp('Unknown option')
end
|
github
|
jacksky64/imageProcessing-master
|
gkdeb.m
|
.m
|
imageProcessing-master/gkde/gkdeb.m
| 4,605 |
utf_8
|
9d82eb477f61ff42700f0fa30bf20f71
|
function p=gkdeb(x,p)
% GKDEB Gaussian Kernel Density Estimation with Bounded Support
%
% Usage:
% p = gkdeb(d) returns an estmate of pdf of the given random data d in p,
% where p.pdf and p.cdf are the pdf and cdf vectors estimated at
% p.x locations, respectively and p.h is the bandwidth used for
% the estimation.
% p = gkdeb(d,p) specifies optional parameters for the estimation:
% p.h - bandwidth
% p.x - locations to make estimation
% p.uB - upper bound
% p.lB - lower bound.
% p.alpha - to calculate inverse cdfs at p.alpha locations
%
% Without output, gkdeb(d) and gkdeb(d,p) will disply the pdf and cdf
% (cumulative distribution function) plot.
%
% See also: hist, histc, ksdensity, ecdf, cdfplot, ecdfhist
% Example 1: Normal distribution
%{
gkdeb(randn(1e4,1));
%}
% Example 2: Uniform distribution
%{
clear p
p.uB=1;
p.lB=0;
gkdeb(rand(1e3,1),p);
%}
% Example 3: Exponential distribution
%{
clear p
p.lB=0;
gkdeb(-log(1-rand(1,1000)),p);
%}
% Example 4: Rayleigh distribution
%{
clear p
p.lB=0;
gkdeb(sqrt(randn(1,1000).^2 + randn(1,1000).^2),p);
%}
% V3.2 by Yi Cao at Cranfield University on 7th April 2010
%
% Check input and output
error(nargchk(1,2,nargin));
error(nargoutchk(0,1,nargout));
n=length(x);
% Default parameters
if nargin<2
N=100;
h=median(abs(x-median(x)))/0.6745*(4/3/n)^0.2;
xmax=max(x);
xmin=min(x);
xmax=xmax+3*h;
xmin=xmin-3*h;
dx=(xmax-xmin)/(N-1);
p.x=xmin+(0:N-1)*dx;
p.pdf=zeros(1,N);
p.cdf=zeros(1,N);
p.h=h;
dxdz=ones(size(p.x));
z=p.x;
else
[p,x,dxdz,z]=checkp(x,p);
N=numel(p.x);
h=p.h;
end
% Gaussian kernel function
kerf=@(z)exp(-z.*z/2);
ckerf=@(z)(1+erf(z/sqrt(2)))/2;
nh=n*h*sqrt(2*pi);
for k=1:N
p.pdf(k)=sum(kerf((p.x(k)-x)/h));
p.cdf(k)=sum(ckerf((p.x(k)-x)/h));
end
p.x=z;
p.pdf=p.pdf.*dxdz/nh;
dx=[0 diff(p.x)];
p.cdf=p.cdf/n;
% p.cdf=cumsum(p.pdf.*dx);
if isfield(p,'alpha')
n=numel(p.alpha);
p.icdf=p.alpha;
for k=1:n
alpha=p.alpha(k);
ix=find(p.cdf>alpha,1)-1;
x1=p.x(ix);
x2=p.x(ix+1);
F1=p.cdf(ix);
F2=p.cdf(ix+1);
p.icdf(k)=x1+(alpha-F1)*(x2-x1)/(F2-F1);
end
end
% Plot
if ~nargout
subplot(211)
plot(p.x,p.pdf,'linewidth',2)
grid
% set(gca,'ylim',[0 max(p.pdf)*1.1])
ylabel('f(x)')
title('Estimated Probability Density Function');
subplot(212)
plot(p.x,p.cdf,'linewidth',2)
ylabel('F(x)')
title('Cumulative Distribution Function')
xlabel('x')
grid
meanx = sum(p.x.*p.pdf.*dx);
varx = sum((p.x-meanx).^2.*p.pdf.*dx);
text(min(p.x),0.6,sprintf('mean(x) = %g\n var(x) = %g\n',meanx,varx));
if isfield(p,'alpha') && numel(p.alpha)==1
text(min(p.x),0.85,sprintf('icdf at %g = %g',p.alpha,p.icdf));
end
end
function [p,x,dxdz,z]=checkp(x,p)
n=numel(x);
%check structure p
if ~isstruct(p)
error('p is not a structure.');
end
if ~isfield(p,'uB')
p.uB=Inf;
end
if ~isfield(p,'lB')
p.lB=-Inf;
end
if p.lB>-Inf || p.uB<Inf
[p,x,dxdz,z]=bounded(x,p);
else
if ~isfield(p,'h')
p.h=median(abs(x-median(x)))/0.6745*(4/3/n)^0.2;
end
error(varchk(eps, inf, p.h, 'Bandwidth, p.h is not positive.'));
if ~isfield(p,'x')
N=100;
xmax=max(x);
xmin=min(x);
xmax=xmax+3*p.h;
xmin=xmin-3*p.h;
dx=(xmax-xmin)/(N-1);
p.x=xmin+(0:N-1)*dx;
end
dxdz=ones(N,1);
z=p.x;
end
p.pdf=zeros(size(p.x));
p.cdf=zeros(size(p.x));
function [p,x,dxdz,z]=bounded(x,p)
if p.lB==-Inf
dx=@(t)1./(p.uB-t);
y=@(t)-log(p.uB-t);
zf=@(t)(p.uB-exp(-t));
elseif p.uB==Inf
dx=@(t)1./(t-p.lB);
y=@(t)log(t-p.lB);
zf=@(t)exp(t)+p.lB;
else
dx=@(t)(p.uB-p.lB)./(t-p.lB)./(p.uB-t);
y=@(t)log((t-p.lB)./(p.uB-t));
zf=@(t)(exp(t)*p.uB+p.lB)./(exp(t)+1);
end
x=y(x);
n=numel(x);
if ~isfield(p,'h')
p.h=median(abs(x-median(x)))/0.6745*(4/3/n)^0.2;
end
h=p.h;
if ~isfield(p,'x')
N=100;
xmax=max(x);
xmin=min(x);
xmax=xmax+3*h;
xmin=xmin-3*h;
p.x=xmin+(0:N-1)*(xmax-xmin)/(N-1);
z=zf(p.x);
else
z=p.x;
p.x=y(p.x);
end
dxdz=dx(z);
function msg=varchk(low,high,n,msg)
% check if variable n is not between low and high, returns msg, otherwise
% empty matrix
if n>=low && n<=high
msg=[];
end
|
github
|
jacksky64/imageProcessing-master
|
filter_function.m
|
.m
|
imageProcessing-master/ImageDiffusionFiltering/ImageDenoising/filter_function.m
| 398 |
utf_8
|
503e499f9e7a72b3417c25f62aa6fb32
|
% CAP 6516 Medical Image Processing Programming Assignment 1
% Author: Ritwik K Kumar, Dept. of CISE, UFL
% (c) 2006 Ritwik K Kumar
% this function is called by other m files
function [smth] = filter_function(image, sigma);
% This function smooths the image with a Gaussian filter of width sigma
smask = fspecial('gaussian', ceil(3*sigma), sigma);
smth = filter2(smask, image, 'same');
|
github
|
jacksky64/imageProcessing-master
|
imagine.m
|
.m
|
imageProcessing-master/matlab imagine/imagine_2016/imagine.m
| 167,700 |
utf_8
|
30fbbb9031cf1ff3577fe03ddd20e8ad
|
function argout = imagine2(varargin)
% IMAGINE IMAGe visualization, analysis and evaluation engINE
%
% IMAGINE starts the IMAGINE user interface without initial data
%
% IMAGINE(DATA) Starts the IMAGINE user interface with one (DATA is 3D)
% or multiple panels (DATA is 4D).
%
% IMAGINE(DATA, PROPERTY1, VALUE1, ...)) Starts the IMAGINE user
% interface with data DATA plus supplying some additional information
% about the dataset in the usual property/value pair format. Possible
% combinations are:
% PROPERTY VALUE
% 'Name' String: A name for the dataset
% 'Voxelsize' [3x1] or [1x3] double: The voxel size of the first
% three dimensions of DATA.
% 'Units' String: The physical unit of the pixels (e.g. 'mm')
%
% IMAGINE(DATA1, DATA2, ...) Starts the IMAGINE user interface with
% multiple panels, where each input can be either a 3D- or 4D-array. Each
% dataset can be defined more detailedly with the properties above.
%
%
% Examples:
%
% 1. >> load mri % Gives variable D
% >> imagine(squeeze(D)); % squeeze because D is in rgb format
%
% 2. >> load mri % Gives variable D
% >> imagine(squeeze(D), 'Name', 'Head T1', 'Voxelsize', [1 1 2.7]);
% This syntax gives a more realistic aspect ration if you rotate the data.
%
% For more information about the IMAGINE functions refer to the user's
% guide file in the documentation folder supplied with the code.
%
% Copyright 2012-2015 Christian Wuerslin, Stanford University
% Contact: [email protected]
% =========================================================================
% Warp Zone! (using Cntl + D)
% -------------------------------------------------------------------------
% *** The callbacks ***
% fCloseGUI % On figure close
% fResizeFigure % On figure resize
% fIconClick % On clicking menubar or tool icons
% fWindowMouseHoverFcn % Standard figure mouse move callback
% fWindowButtonDownFcn % Figure mouse button down function
% fWindowMouseMoveFcn % Figure mouse move function when button is pressed or ROI drawing active
% fWindowButtonUpFcn % Figure mouse button up function: Starts most actions
% fKeyPressFcn % Keyboard callback
% fContextFcn % Context menu callback
% fSetWindow % Callback of the colorbars
%
% -------------------------------------------------------------------------
% *** IMAGINE Core ***
% fFillPanels
% fUpdateActivation
% fZoom
% fWindow
% fChangeImage
% fEval
%
% -------------------------------------------------------------------------
% *** Lengthy subfunction ***
% fLoadFiles
% fParseInputs
% fAddImageToData
% fSaveToFiles
%
% -------------------------------------------------------------------------
% *** Helpers ***
% fCreatePanels
% fGetPanel
% fServesSizeCriterion
% fIsOn
% fGetNActiveVisibleSeries
% fGetNVisibleSeries
% fGetImg
% fGetData
% fPrintNumber
% fBackgroundImg
% fReplicate
%
% -------------------------------------------------------------------------
% *** GUIS ***
% fGridSelect
% fColormapSelect
% fSelectEvalFcns
% =========================================================================
% =========================================================================
% *** FUNCTION imagine
% ***
% *** Main GUI function. Creates the figure and all its contents and
% *** registers the callbacks.
% ***
% =========================================================================
% -------------------------------------------------------------------------
% Control the figure's appearance
SAp.sVERSION = '2.2 - Belly Jeans';
SAp.sTITLE = ['IMAGINE ',SAp.sVERSION];% Title of the figure
SAp.iICONSIZE = 24; % Size if the icons
SAp.iICONPADDING = SAp.iICONSIZE/2; % Padding between icons
SAp.iMENUBARHEIGHT = SAp.iICONSIZE*2; % Height of the menubar (top)
SAp.iTOOLBARWIDTH = SAp.iICONSIZE*2; % Width of the toolbar (left)
SAp.iTITLEBARHEIGHT = 24; % Height of the titles (above each image)
SAp.iCOLORBARHEIGHT = 12; % Height of the colorbar
SAp.iCOLORBARPADDING = 60; % The space on the left and right of the colorbar for the min/max values
SAp.iEVALBARHEIGHT = 16; % Height of the evaluation bar
SAp.iDISABLED_SCALE = 0.3; % Brightness of disabled buttons (decrease to make darker)
SAp.iINACTIVE_SCALE = 0.6; % Brightness of inactive buttons (toggle buttons and radio groups)
SAp.dBGCOLOR = [0.2 0.3 0.4]; % Color scheme
SAp.dEmptyImg = 0; % The background image (is calculated in fResizeFigure);
SAp.iCOLORMAPLENGTH = 2.^12;
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Set some paths.
SPref.sMFILEPATH = fileparts(mfilename('fullpath')); % This is the path of this m-file
SPref.sICONPATH = [SPref.sMFILEPATH, filesep, 'icons', filesep]; % That's where the icons are
SPref.sSaveFilename = [SPref.sMFILEPATH, filesep, 'imagineSave.mat']; % A .mat-file to save the GUI settings
addpath([SPref.sMFILEPATH, filesep, 'EvalFunctions'], ...
[SPref.sMFILEPATH, filesep, 'colormaps'], ...
[SPref.sMFILEPATH, filesep, 'import'], ...
[SPref.sMFILEPATH, filesep, 'tools']);
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Define some preferences
S = load('mylines.mat');
SPref.dCOLORMAP = S.mylines;% The color scheme of the overlays and lines
SPref.dWINDOWSENSITIVITY = 0.02; % Defines mouse sensitivity for windowing operation
SPref.dZOOMSENSITIVITY = 0.02; % Defines mouse sensitivity for zooming operation
SPref.dROTATION_THRESHOLD = 50; % Defines the number of pixels the cursor has to move to rotate an image
SPref.dLWRADIUS = 200; % The radius in which the path maps are calculated in the livewire algorithm
SPref.lGERMANEXPORT = false; % Not a beer! Determines whether the data is exported with a period or a comma as decimal point
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% This is the definition of the menubar. If a radiobutton-like
% functionality is to implemented, the GroupIndex parameter of all
% icons within the group has to be set to the same positive integer
% value. Normal Buttons have group index -1, toggel switches have group
% index 0. The toolbar has the GroupIndex 255.
SIcons = struct( ...
'Name', {'folder_open', 'doc_import', 'save', 'doc_delete', 'exchange', 'grid', 'colormap', 'link', 'link1', 'reset', 'phase', 'max', 'min', 'record', 'stop', 'rewind', 'clock', 'line1', 'cursor_arrow', 'rotate', 'line', 'roi', 'lw', 'rg', 'ic', 'tag'}, ...
'Spacer', { 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}, ...
'GroupIndex', { -1, -1, -1, -1, -1, -1, -1, 0, 0, -1, 1, 1, 1, -1, -1, -1, 0, 0, 255, 255, 255, 255, 255, 255, 255, 255}, ...
'Enabled', { 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}, ...
'Active', { 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0}, ...
'Accelerator', { 'o', 'i', 's', 'delete', 'x', '', '', 'l', '', '0', '', '', '', 'r', 'r', 'z', 't', 'w', 'm', 'r', 'l', 'o', 'w', 'g', 'i', 'p'}, ...
'Modifier', { 'Cntl', 'Cntl', 'Cntl', '', 'Cntl', '', '', 'Cntl', '', 'Cntl', '', '', '', 'Cntl', 'Alt', 'Cntl', 'Cntl', 'Cntl', '', '', '', '', '', '', '', ''}, ...
'Tooltip', {'Open Files' , 'Import Workspace Variables', 'Save To Files', 'Delete', 'Exchange', 'Change Layout', 'Colormap', 'Link Actions', 'Link Windowing','Reset View', 'Phase Image', 'Maximum Intensity Projection', 'Minimum Intensity Projection', 'Log Evaluation', 'Stop Logging Evaluation', 'Undo Last Evaluation', 'Eval Timeseries', 'Show Line Plots', 'Move/Zoom/Window', 'Rotate', 'Profile Evaluation', 'ROI Evaluation', 'Livewire ROI Evaluation', 'Region Growing Volume Evaluation', 'Isocontour Evaluation', 'Properties'});
% -------------------------------------------------------------------------
% ------------------------------------------------------------------------
% Reset the GUI's state variable
SState.iLastSeries = 0;
SState.iStartSeries = 1;
SState.sTool = 'cursor_arrow';
SState.sPath = [SPref.sMFILEPATH, filesep];
SState.csEvalLineFcns = {};
SState.csEvalROIFcns = {};
SState.csEvalVolFcns = {};
SState.sEvalFilename = [];
SState.iROIState = 0; % The ROI state machine
SState.dROILineX = [];
SState.dROILineY = [];
SState.iPanels = [0, 0];
SState.lShowColorbar = true;
SState.lShowEvalbar = true;
SState.dColormapBack = gray(SAp.iCOLORMAPLENGTH);
SState.dColormapMask = S.mylines;
SState.dMaskOpacity = 0.3;
SState.sDrawMode = 'mag';
SState.dTolerance = 1.0;
SState.hEvalFigure = 0.1;
% ------------------------------------------------------------------------
% ------------------------------------------------------------------------
% Create some globals
SData = []; % A struct for hoding the data (image data + visualization parameters)
SImg = []; % A struct for the image component handles
SLines = []; % A struct for the line component handles
SMouse = []; % A Struct to hold parameters of the mouse operations
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Read the preferences from the save file
iPosition = [100 100 1000 600];
if exist(SPref.sSaveFilename, 'file')
load(SPref.sSaveFilename);
SState.sPath = SSaveVar.sPath;
SState.csEvalLineFcns = SSaveVar.csEvalLineFcns;
SState.csEvalROIFcns = SSaveVar.csEvalROIFcns;
SState.csEvalVolFcns = SSaveVar.csEvalVolFcns;
iPosition = SSaveVar.iPosition;
SPref.lGERMANEXPORT = SSaveVar.lGermanExport;
clear SSaveVar; % <- no one needs you anymore! :((
else
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% First-time call: Do some setup
sAns = questdlg('Do you want to use periods (anglo-american) or commas (german) as decimal separator in the exported .csv spreadsheet files? This is important for a smooth Excel import.', 'IMAGINE First-Time Setup', 'Stick to the point', 'Use se commas', 'Stick to the point');
SPref.lGERMANEXPORT = strcmp(sAns, 'Use se commas');
fCompileMex;
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Make sure the figure fits on the screen
iScreenSize = get(0, 'ScreenSize');
if (iPosition(1) + iPosition(3) > iScreenSize(3)) || ...
(iPosition(2) + iPosition(4) > iScreenSize(4))
iPosition(1:2) = 50;
iPosition(3:4) = iScreenSize(3:4) - 100;
end
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Create the figure. Mouse scroll wheel is supported since Version 7.4 (I think).
hF = figure(...
'BusyAction' , 'cancel', ...
'Interruptible' , 'off', ...
'Position' , iPosition, ...
'Units' , 'pixels', ...
'Color' , SAp.dBGCOLOR/2, ...
'ResizeFcn' , @fResizeFigure, ...
'DockControls' , 'on', ...
'MenuBar' , 'none', ...
'Name' , SAp.sTITLE, ...
'NumberTitle' , 'off', ...
'KeyPressFcn' , @fKeyPressFcn, ...
'CloseRequestFcn' , @fCloseGUI, ...
'WindowButtonDownFcn' , @fWindowButtonDownFcn, ...
'WindowButtonMotionFcn' , @fWindowMouseHoverFcn, ...
'Visible' , 'off');
try
set(hF, 'WindowScrollWheelFcn' , @fChangeImage);
catch
warning('IMAGINE: No scroll wheel functionality!');
end
colormap(gray(256));
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Crate context menu for the region growing
hContextMenu = uicontextmenu;
uimenu(hContextMenu, 'Label', 'Tolerance +50%', 'Callback', @fContextFcn);
uimenu(hContextMenu, 'Label', 'Tolerance +10%', 'Callback', @fContextFcn);
uimenu(hContextMenu, 'Label', 'Tolerance -10%', 'Callback', @fContextFcn);
uimenu(hContextMenu, 'Label', 'Tolerance -50%', 'Callback', @fContextFcn);
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Create the menubar and the toolbar including their components
SAxes.hMenu = axes('Parent', hF, 'Color', 'k', 'Units', 'pixels', 'YDir', 'reverse', 'XTick', [], 'YTick', []);
SAxes.hTools = axes('Parent', hF, 'Color', 'k', 'Units', 'pixels', 'YDir', 'reverse', 'XTick', [], 'YTick', []);
SImg .hIcons = zeros(length(SIcons), 1);
iXStart = SAp.iTOOLBARWIDTH - SAp.iICONSIZE;
iYStart = SAp.iICONPADDING;
for iI = 1:length(SIcons)
if SIcons(iI).GroupIndex ~= 255, iXStart = iXStart + SAp.iICONPADDING + SAp.iICONSIZE; end
dImage = double(imread([SPref.sICONPATH, SIcons(iI).Name, '.png'])); % icon file name (.png) has to be equal to icon name
if size(dImage, 3) == 1, dImage = repmat(dImage, [1 1 3]); end
dImage = imresize(dImage, [SAp.iICONSIZE SAp.iICONSIZE]);
dImage(dImage < 0) = 0;
dImage(dImage > 255) = 255;
SIcons(iI).dImg = dImage./255;
if SIcons(iI).GroupIndex == 255
hParent = SAxes.hTools;
iX = SAp.iICONPADDING;
iY = iYStart;
else
hParent = SAxes.hMenu;
iX = iXStart;
iY = SAp.iICONPADDING;
end
SImg.hIcons(iI) = image(...
'CData' , SIcons(iI).dImg, ...
'XData' , iX, ...
'YData' , iY, ...
'Parent' , hParent, ...
'ButtonDownFcn' , @fIconClick);
if SIcons(iI).Spacer && SIcons(iI).GroupIndex ~= 255, iXStart = iXStart + SAp.iICONSIZE; end
if SIcons(iI).GroupIndex == 255, iYStart = iYStart + SAp.iICONSIZE + SAp.iICONPADDING; end
end
SState.dIconEnd = iXStart + SAp.iICONPADDING + SAp.iICONSIZE;
STexts.hStatus = uicontrol(... % Create the text element
'Style' ,'Text', ...
'FontName' , 'Helvetica Neue', ...
'FontWeight' , 'light', ...
'Parent' , hF, ...
'FontUnits' , 'normalized', ...
'FontSize' , 0.7, ...
'BackgroundColor' , 'k', ...
'ForegroundColor' , 'w', ...
'HorizontalAlignment' , 'right', ...
'Units' , 'pixels');
clear iStartPos hParent iI dImage
% -------------------------------------------------------------------------
dLogo = [0 0 0 1 1 0 0 0; ...
0 0 0 1 1 0 0 0; ...
0 0 0 0 0 0 0 0; ...
0 0 1 1 1 0 0 0; ...
0 0 0 1 1 0 0 0; ...
0 0 0 1 1 0 0 0; ...
0 0 1 1 1 1 0 0; ...
0 0 0 0 0 0 0 0;];
% dPattern = max(cat(3, rand(12), padarray(dLogo, [2 2], 0, 'both')), [], 3);
dPattern = 0.2*rand(16) + 0.3*padarray(dLogo, [4 4], 0, 'both');
dPattern = dPattern.*repmat(linspace(1, 0, 16)', [1, 16]);
SAp.dBGImg = fBlend(SAp.dBGCOLOR, dPattern, 'multiply', 0.5);
% -------------------------------------------------------------------------
% Parse Inputs and determine and create the initial amount of panels
if ~isempty(varargin), fParseInputs(varargin); end
if ~prod(SState.iPanels), SState.iPanels = [1 1]; end
fCreatePanels;
clear varargin; % <- no one needs you anymore! :((
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Update the figure components
fUpdateActivation(); % Acitvate/deactivate some buttons according to the gui state
set(hF, 'Visible', 'on', 'UserData', @fGetData);
fDraw; % Resize only calls fPosition
argout = hF;
% -------------------------------------------------------------------------
% The 'end' of the IMAGINE main function. The real end is, of course, after
% all the nested functions. Using the nested functions, shared varaiables
% (the variables of the IMAGINE function) can be used which makes the usage
% of the 'guidata' commands obsolete.
% =========================================================================
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fCloseGUI (nested in imagine)
% * *
% * * Figure callback
% * *
% * * Closes the figure and saves the settings
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fCloseGUI(hObject, eventdata) %#ok<*INUSD> eventdata is repeatedly unused
% -----------------------------------------------------------------
% Save the settings
SSaveVar.sPath = SState.sPath;
SSaveVar.csEvalLineFcns = SState.csEvalLineFcns;
SSaveVar.csEvalROIFcns = SState.csEvalROIFcns;
SSaveVar.csEvalVolFcns = SState.csEvalVolFcns;
SSaveVar.iPosition = get(hObject, 'Position');
SSaveVar.lGermanExport = SPref.lGERMANEXPORT;
try
save(SPref.sSaveFilename, 'SSaveVar');
catch
warning('Could not save the settings! Is the IMAGINE folder protected?');
end
% -----------------------------------------------------------------
delete(hObject); % Bye-bye figure
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fCloseGUI
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fCreatePanels (nested in imagine)
% * *
% * * Create the panels and its child object.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fCreatePanels
% -----------------------------------------------------------------
% Delete panels and their handles if necessary
if isfield(SAxes, 'hImg')
delete(SAxes.hImg); % Deletes hImgFrame and its children
delete(SAxes.hColorbar);
STexts = rmfield(STexts, {'hImg1', 'hImg2', 'hColorbarMin', 'hColorbarMax','hEval', 'hVal'});
SAxes = rmfield(SAxes, {'hImg', 'hColorbar'});
SImg = rmfield(SImg, {'hImg', 'hColorbar'});
end
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% For each panel create panels, axis, image and text objects
for i = 1:prod(SState.iPanels)
SAxes.hImg(i) = axes(...
'Parent' , hF, ...
'Units' , 'pixels', ...
'Color' , 'k', ...
'XTick' , [], ...
'YTick' , [], ...
'YDir' , 'reverse', ...
'XColor' , SAp.dBGCOLOR, ...
'YColor' , SAp.dBGCOLOR, ...
'Box' , 'on');
SImg.hImg(i) = image(...
'CData' , 0, ...
'Parent' , SAxes.hImg(i), ...
'HitTest' , 'off');
STexts.hImg1(i) = text('Units', 'pixels', 'FontSize', 14, 'Color', 'w', 'HorizontalAlignment', 'left', 'VerticalAlignment', 'top', 'Interpreter', 'none');
STexts.hImg2(i) = text('Units', 'pixels', 'FontSize', 14, 'Color', 'w', 'HorizontalAlignment', 'right', 'VerticalAlignment', 'top');
STexts.hColorbarMin(i) = text('Units', 'pixels', 'FontSize', 12, 'Color', 'w', 'HorizontalAlignment', 'right', 'VerticalAlignment', 'middle');
STexts.hColorbarMax(i) = text('Units', 'pixels', 'FontSize', 12, 'Color', 'w', 'HorizontalAlignment', 'left', 'VerticalAlignment', 'middle');
STexts.hEval(i) = text('Units', 'pixels', 'FontSize', 12, 'Color', 'w', 'HorizontalAlignment', 'left', 'VerticalAlignment', 'bottom');
STexts.hVal(i) = text('Units', 'pixels', 'FontSize', 12, 'Color', 'w', 'HorizontalAlignment', 'right', 'VerticalAlignment', 'bottom');
SAxes.hColorbar(i) = axes(...
'Parent' , hF, ...
'XTick' , [], ...
'YTick' , [], ...
'Units' , 'pixels', ...
'XLim' , [0 256] + 0.5, ...
'YLim' , [0.5 1.5], ...
'Visible' , 'off');
SImg.hColorbar(i) = image(...
'CData' , uint8(0:255), ...
'Parent' , SAxes.hColorbar(i), ...
'ButtonDownFcn' , @fSetWindow);
iDataInd = i + SState.iStartSeries - 1;
if (iDataInd > 0) && (iDataInd <= length(SData))
set(STexts.hColorbarMin(i), 'String', sprintf('%s', fPrintNumber(SData(iDataInd).dWindowCenter - SData(iDataInd).dWindowWidth./2)));
set(STexts.hColorbarMax(i), 'String', sprintf('%s', fPrintNumber(SData(iDataInd).dWindowCenter + SData(iDataInd).dWindowWidth./2)));
end
end % of loop over pannels
% -----------------------------------------------------------------
if strcmp(SState.sTool, 'rg'), set(SAxes.hImg, 'uicontextmenu', hContextMenu); end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fCreatePanels
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fResizeFigure (nested in imagine)
% * *
% * * Figure callback
% * *
% * * Re-arranges all the GUI elements after a figure resize
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fResizeFigure(hObject, eventdata)
% -----------------------------------------------------------------
% Get figure dimensions
iFigureSize = get(hF, 'Position');
iViewWidth = round((iFigureSize(3) - SAp.iTOOLBARWIDTH ) / SState.iPanels(2));
iViewHeight = round((iFigureSize(4) - SAp.iMENUBARHEIGHT) / SState.iPanels(1));
% -----------------------------------------------------------------
% Arrange the panels and all their contents
iYStart = 2;
for iY = SState.iPanels(1):-1:1 % Start from the bottom
if iY > 1
iHeight = iViewHeight;
else
iHeight = iFigureSize(4) - iYStart - SAp.iMENUBARHEIGHT;
end
iXStart = SAp.iTOOLBARWIDTH + 2;
for iX = 1:SState.iPanels(2)
iLinInd = (iY - 1).*SState.iPanels(2) + iX;
if iX == SState.iPanels(2)
iWidth = iFigureSize(3) - iXStart;
else
iWidth = iViewWidth;
end
set(STexts.hEval(iLinInd), 'Position', [5, 5]);
set(STexts.hVal(iLinInd), 'Position', [iWidth - 5, 5]);
set(SAxes.hImg(iLinInd), 'Position', [iXStart, iYStart, iWidth, iHeight]);
set(STexts.hImg1(iLinInd), 'Position', [5, iHeight - 5]);
set(STexts.hImg2(iLinInd), 'Position', [iWidth - 5, iHeight - 5]);
set(SAxes.hColorbar(iLinInd), 'Position', [iXStart + SAp.iCOLORBARPADDING, iYStart + iHeight - SAp.iCOLORBARHEIGHT - SAp.iTITLEBARHEIGHT + 4, max([iWidth - 2*SAp.iCOLORBARPADDING, 1]), SAp.iCOLORBARHEIGHT - 3]);
set(STexts.hColorbarMin(iLinInd), 'Position', [SAp.iCOLORBARPADDING - 5, iHeight - SAp.iTITLEBARHEIGHT - SAp.iCOLORBARHEIGHT + 6]);
set(STexts.hColorbarMax(iLinInd), 'Position', [iWidth - SAp.iCOLORBARPADDING + 5, iHeight - SAp.iTITLEBARHEIGHT - SAp.iCOLORBARHEIGHT + 6]);
iXStart = iXStart + iWidth;
end
iYStart = iYStart + iHeight;
end
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Arrange the menubar
dTextWidth = max([iFigureSize(3) - SState.dIconEnd - 48, 1]);
set(SAxes.hMenu, 'Position', [1, iFigureSize(4) - SAp.iMENUBARHEIGHT + 1, iFigureSize(3), SAp.iMENUBARHEIGHT], ...
'XLim', [0 iFigureSize(3)] + 0.5, 'YLim', [0 SAp.iMENUBARHEIGHT] + 0.5);
set(STexts.hStatus, 'Position', [SState.dIconEnd + 5, iFigureSize(4) - SAp.iMENUBARHEIGHT + 1 + 10, dTextWidth, 28]);
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Arrange the toolbar
set(SAxes.hTools, 'Position', [1, 1, SAp.iTOOLBARWIDTH, iFigureSize(4) - SAp.iMENUBARHEIGHT], ...
'XLim', [0 SAp.iTOOLBARWIDTH] + 0.5, 'YLim', [0 iFigureSize(4) - SAp.iMENUBARHEIGHT] + 0.5);
% -----------------------------------------------------------------
fPosition;
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fResizeFigure
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fFillPanels (nested in imagine)
% * *
% * * Display the current data in all panels.
% * * The holy grail of Imagine!
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fFillPanels
fDraw;
fPosition;
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fFillPanels
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fDraw
for i = 1:length(SAxes.hImg)
iSeriesInd = SState.iStartSeries + i - 1;
if iSeriesInd <= length(SData) % Panel not empty
if strcmp(SState.sDrawMode, 'phase')
dMin = -pi; dMax = pi;
else
dMin = SData(SState.iStartSeries).dWindowCenter - 0.5.*SData(SState.iStartSeries).dWindowWidth;
dMax = SData(SState.iStartSeries).dWindowCenter + 0.5.*SData(SState.iStartSeries).dWindowWidth;
end
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Get the image data, do windowing and apply colormap
if ~fIsOn('link1') && ~strcmp(SState.sDrawMode, 'phase')
dMin = SData(iSeriesInd).dWindowCenter - 0.5.*SData(iSeriesInd).dWindowWidth;
dMax = SData(iSeriesInd).dWindowCenter + 0.5.*SData(iSeriesInd).dWindowWidth;
end
dImg = fGetImg(iSeriesInd);
dImg = dImg - dMin;
iImg = round(dImg./(dMax - dMin).*(SAp.iCOLORMAPLENGTH - 1)) + 1;
iImg(iImg < 1) = 1;
iImg(iImg > SAp.iCOLORMAPLENGTH) = SAp.iCOLORMAPLENGTH;
dImg = reshape(SState.dColormapBack(iImg, :), [size(iImg, 1) ,size(iImg, 2), 3]);
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Apply mask if any
if ~isempty(SData(iSeriesInd).lMask)
% dColormap = [0 0 0; SPref.dCOLORMAP(i, :)]
dColormap = [0 0 0; lines(max(SData(iSeriesInd).lMask(:)))];
switch SState.sDrawMode
case {'mag', 'phase'}, iMask = uint8(SData(iSeriesInd).lMask(:,:,SData(iSeriesInd).iActiveImage)) + 1;
case {'max', 'min'} , iMask = uint8(max(SData(iSeriesInd).lMask, [], 3)) + 1;
end
dMask = reshape(dColormap(iMask, :), [size(iMask, 1) ,size(iMask, 2), 3]);
dImg = 1 - (1 - dImg).*(1 - SState.dMaskOpacity.*dMask); % The 'screen' overlay mode
end
set(SImg.hImg(i), 'CData', dImg, 'Visible', 'on');
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Update the text elements
set(STexts.hColorbarMin(i), 'String', sprintf('%s', fPrintNumber(dMin)));
set(STexts.hColorbarMax(i), 'String', sprintf('%s', fPrintNumber(dMax)));
set(STexts.hImg1(i), 'String', ['[', int2str(iSeriesInd), ']: ', SData(iSeriesInd).sName]);
if strcmp(SState.sDrawMode, 'max') || strcmp(SState.sDrawMode, 'min')
iMin = max(1, SData(iSeriesInd).iActiveImage - 3);
iMax = min(size(SData(iSeriesInd).dImg, 3), SData(iSeriesInd).iActiveImage + 3);
set(STexts.hImg2(i), 'String', sprintf('[%u - %u]/%u', iMin, iMax, size(SData(iSeriesInd).dImg, 3)));
else
set(STexts.hImg2(i), 'String', sprintf('%u/%u', SData(iSeriesInd).iActiveImage, size(SData(iSeriesInd).dImg, 3)));
end
set(STexts.hEval(i), 'String', SData(iSeriesInd).sEvalText);
set(SImg.hColorbar(i), 'Visible', 'on');
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
else % Panel is empty
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Set image to the background image (RGB)
set(SImg.hImg(i), 'CData', SAp.dBGImg, 'Visible', 'on');
set([STexts.hImg1(i), STexts.hEval(i), STexts.hVal(i), STexts.hImg2(i), STexts.hColorbarMin(i), STexts.hColorbarMax(i)], 'String', '');
set(SImg.hColorbar(i), 'Visible', 'off');
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
end
end
function fPosition
for i = 1:length(SAxes.hImg)
iSeriesInd = SState.iStartSeries + i - 1;
dAxesPos = get(SAxes.hImg(i), 'Position');
if iSeriesInd <= length(SData) % Panel not empty
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Handle zoom and shift
dScale = SData(iSeriesInd).dPixelSpacing;
dScale = dScale(1, 1:2)./min(dScale); % Smallest Entry scaled to 1
dDelta_mm = dAxesPos([4, 3])./SData(iSeriesInd).dZoomFactor./dScale;
set(SAxes.hImg(i), ...
'XLim', SData(iSeriesInd).dDrawCenter(2) + 0.5 * [-dDelta_mm(2) dDelta_mm(2)], ...
'YLim', SData(iSeriesInd).dDrawCenter(1) + 0.5 * [-dDelta_mm(1) dDelta_mm(1)]);
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
else
dSize = dAxesPos(4:-1:3);
dLim = size(SAp.dBGImg(:,:,1))./max(dSize).*dSize;
set(SAxes.hImg(i), 'XLim', size(SAp.dBGImg, 2)/2 + 0.5*[-dLim(2) dLim(2)] + 0.5, ...
'YLim', size(SAp.dBGImg, 1)/2 + 0.5*[-dLim(1) dLim(1)] + 0.5);
end
end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fIconClick (nested in imagine)
% * *
% * * Common callback for all buttons in the menubar
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fIconClick(hObject, eventdata)
% -----------------------------------------------------------------
% Get the source's (pressed buttton) data and exit if disabled
iInd = find(SImg.hIcons == hObject);
if ~SIcons(iInd).Enabled, return, end;
% -----------------------------------------------------------------
sActivate = [];
% -----------------------------------------------------------------
% Distinguish the idfferent button types (normal, toggle, radio)
switch SIcons(iInd).GroupIndex
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% NORMAL pushbuttons
case -1
switch(SIcons(iInd).Name)
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% LOAD new FILES using file dialog
case 'folder_open'
if strcmp(get(hF, 'SelectionType'), 'normal')
% Load Files
[csFilenames, sPath] = uigetfile( ...
{'*.*', 'All Files'; ...
'*.dcm; *.DCM; *.mat; *.MAT; *.jpg; *.jpeg; *.JPG; *.JPEG; *.tif; *.tiff; *.TIF; *.TIFF; *.gif; *.GIF; *.bmp; *.BMP; *.png; *.PNG; *.nii; *.NII; *.gipl; *.GIPL', 'All images'; ...
'*.mat; *.MAT', 'Matlab File (*.mat)'; ...
'*.jpg; *.jpeg; *.JPG; *.JPEG', 'JPEG-Image (*.jpg)'; ...
'*.tif; *.tiff; *.TIF; *.TIFF;', 'TIFF-Image (*.tif)'; ...
'*.gif; *.GIF', 'Gif-Image (*.gif)'; ...
'*.bmp; *.BMP', 'Bitmaps (*.bmp)'; ...
'*.png; *.PNG', 'Portable Network Graphics (*.png)'; ...
'*.dcm; *.DCM', 'DICOM Files (*.dcm)'; ...
'*.nii; *.NII', 'NifTy Files (*.nii)'; ...
'*.gipl; *.GIPL', 'Guys Image Processing Lab Files (*.gipl)'}, ...
'OpenLocation' , SState.sPath, ...
'Multiselect' , 'on');
if isnumeric(sPath), return, end; % Dialog aborted
else
% Load a folder
sPath = uigetdir(SState.sPath);
if isnumeric(sPath), return, end;
sPath = [sPath, filesep];
SFiles = dir(sPath);
SFiles = SFiles(~[SFiles.isdir]);
csFilenames = cell(length(SFiles), 1);
for i = 1:length(SFiles), csFilenames{i} = SFiles(i).name; end
end
SState.sPath = sPath;
fLoadFiles(csFilenames);
fFillPanels();
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% IMPORT workspace (base) VARIABLE(S)
case 'doc_import'
csVars = fWSImport();
if isempty(csVars), return, end % Dialog aborted
for i = 1:length(csVars)
dVar = evalin('base', csVars{i});
fAddImageToData(dVar, csVars{i}, 'workspace');
end
fFillPanels();
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% SAVE panel data to file(s)
case 'save'
if strcmp(get(hF, 'SelectionType'), 'normal')
[sFilename, sPath] = uiputfile( ...
{'*.jpg', 'JPEG-Image (*.jpg)'; ...
'*.tif', 'TIFF-Image (*.tif)'; ...
'*.gif', 'Gif-Image (*.gif)'; ...
'*.bmp', 'Bitmaps (*.bmp)'; ...
'*.png', 'Portable Network Graphics (*.png)'}, ...
'Save selected series to files', ...
[SState.sPath, filesep, '%SeriesName%_%ImageNumber%']);
if isnumeric(sPath), return, end; % Dialog aborted
SState.sPath = sPath;
fSaveToFiles(sFilename, sPath);
else
[sFilename, sPath] = uiputfile( ...
{'*.jpg', 'JPEG-Image (*.jpg)'; ...
'*.tif', 'TIFF-Image (*.tif)'; ...
'*.gif', 'Gif-Image (*.gif)'; ...
'*.bmp', 'Bitmaps (*.bmp)'; ...
'*.png', 'Portable Network Graphics (*.png)'}, ...
'Save MASK of selected series to files', ...
[SState.sPath, filesep, '%SeriesName%_%ImageNumber%_Mask']);
if isnumeric(sPath), return, end; % Dialog aborted
SState.sPath = sPath;
fSaveMaskToFiles(sFilename, sPath);
end
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% DELETE DATA from structure
case 'doc_delete'
iSeriesInd = find([SData.lActive]); % Get indices of selected axes
iSeriesInd = iSeriesInd(iSeriesInd >= SState.iStartSeries);
SData(iSeriesInd) = []; % Delete the visible active data
fFillPanels();
fUpdateActivation(); % To make sure panels without data are not selected
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% EXCHANGE SERIES
case 'exchange'
iSeriesInd = find([SData.lActive]); % Get indices of selected axes
SData1 = SData(iSeriesInd(1));
SData(iSeriesInd(1)) = SData(iSeriesInd(2)); % Exchange the data
SData(iSeriesInd(2)) = SData1;
fFillPanels();
fUpdateActivation(); % To make sure panels without data are not selected
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Determine the NUMBER OF PANELS and their LAYOUT
case 'grid'
iPanels = fGridSelect(4, 4);
if ~sum(iPanels), return, end % Dialog aborted
SState.iPanels = iPanels;
fCreatePanels; % also updates the SState.iPanels
fFillPanels;
fUpdateActivation;
fResizeFigure(hF, []);
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Select the COLORMAP
case 'colormap'
sColormap = fColormapSelect(STexts.hStatus);
if ~isempty(sColormap)
eval(sprintf('dColormap = %s(SAp.iCOLORMAPLENGTH);', sColormap));
SState.dColormapBack = dColormap;
fFillPanels;
eval(sprintf('colormap(%s(256));', sColormap));
set(SAxes.hImg, 'Color', dColormap(1,:));
end
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% RESET the view (zoom/window/center)
case 'reset' % Reset the view properties of all data
for i = 1:length(SData)
SData(i).dZoomFactor = 1;
SData(i).dWindowCenter = mean(SData(i).dDynamicRange);
SData(i).dWindowWidth = SData(i).dDynamicRange(2) - SData(i).dDynamicRange(1);
SData(i).dDrawCenter = [0.5 0.5];
end
fFillPanels();
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% RECORD Start recording data
case 'record'
[sName, sPath] = uiputfile( ...
{'*.csv', 'Comma-separated File (*.csv)'}, ...
'Chose Logfile', SState.sPath);
if isnumeric(sPath)
SState.sEvalFilename = '';
else
SState.sEvalFilename = [sPath, sName];
end
SState.sPath = sPath;
fUpdateActivation;
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% STOP logging data
case 'stop'
SState.sEvalFilename = '';
fUpdateActivation;
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% REWIND last measurement
case 'rewind'
iPosDel = fGetEvalFilePos;
if iPosDel < 0
fprintf('File ''%s''does not exist yet or is write-protexted!\n', SState.sEvalFilename);
return
end
if iPosDel == 0
fprintf('Log file ''%s'' is empty!\n', SState.sEvalFilename);
return
end
fid = fopen(SState.sEvalFilename, 'r');
sLine = fgets(fid);
i = 1;
lLast = false;
while ischar(sLine)
csText{i} = sLine;
i = i + 1;
sLine = fgets(fid);
csPos = textscan(sLine, '"%d"');
if isempty(csPos{1})
iPos = 0;
else
iPos = csPos{1};
end
if iPos == iPosDel - 1, lLast = true; end
if iPos ~= iPosDel - 1 && lLast, break, end
end
fclose(fid);
iEnd = length(csText);
if iPosDel == 1, iEnd = 3; end
fid = fopen(SState.sEvalFilename, 'w');
for i = 1:iEnd
fprintf(fid, '%s', csText{i});
end
fprintf('Removed entry %d from ''%s''!\n', iPosDel, SState.sEvalFilename);
fclose(fid);
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
otherwise
end
% End of NORMAL buttons
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% TOGGLE buttons: Invert the state
case 0
SIcons(iInd).Active = ~SIcons(iInd).Active;
fUpdateActivation();
fFillPanels; % Because of link button
% End of TOGGLE buttons
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The render-mode group
case 1 % The render-mode group
if ~strcmp(SState.sDrawMode, SIcons(iInd).Name)
SState.sDrawMode = SIcons(iInd).Name;
sActivate = SIcons(iInd).Name;
else
SState.sDrawMode = 'mag';
end
fFillPanels;
case 255 % The toolbar
% - - - - - - - - - - - - -
% Right-click setup menus
if strcmp(get(hF, 'SelectionType'), 'alt') && ~isfield(eventdata, 'Character')% Right click, open tool settings in neccessary
switch SIcons(iInd).Name
case 'line',
csFcns = fSelectEvalFcns(SState.csEvalLineFcns, [SPref.sMFILEPATH, filesep, 'EvalFunctions']);
if iscell(csFcns), SState.csEvalLineFcns = csFcns; end
case {'roi', 'lw'},
csFcns = fSelectEvalFcns(SState.csEvalROIFcns, [SPref.sMFILEPATH, filesep, 'EvalFunctions']);
if iscell(csFcns), SState.csEvalROIFcns = csFcns; end
case 'rg'
csFcns = fSelectEvalFcns(SState.csEvalVolFcns, [SPref.sMFILEPATH, filesep, 'EvalFunctions']);
if iscell(csFcns), SState.csEvalVolFcns = csFcns; end
end
end
% - - - - - - - - - - - - -
% - - - - - - - - - - - - -
if ~strcmp(SState.sTool, SIcons(iInd).Name) % Tool change
% Try to delete the lines of the ROI and line eval tools
if isfield(SLines, 'hEval')
try delete(SLines.hEval); end %#ok<TRYNC>
SLines = rmfield(SLines, 'hEval');
end
% Set tool-specific context menus
switch SIcons(iInd).Name
case 'rg', set(SAxes.hImg, 'uicontextmenu', hContextMenu);
otherwise, set(SAxes.hImg, 'uicontextmenu', []);
end
% Remove the masks, if a new eval tool is selected
switch SIcons(iInd).Name
case {'line', 'roi', 'lw', 'rg', 'ic'}
for i = 1:length(SData), SData(i).lMask = []; end
fFillPanels;
end
% -----------------------------------------------------------------
% Reset the ROI painting state machine and Mouse callbacks
SState.iROIState = 0;
set(gcf, 'WindowButtonDownFcn' , @fWindowButtonDownFcn);
set(gcf, 'WindowButtonMotionFcn', @fWindowMouseHoverFcn);
set(gcf, 'WindowButtonUpFcn' , '');
% -----------------------------------------------------------------
end
SState.sTool = SIcons(iInd).Name;
sActivate = SIcons(iInd).Name;
% - - - - - - - - - - - - -
end
% - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - -
% Common code for all radio groups
if SIcons(iInd).GroupIndex > 0
for i = 1:length(SIcons)
if SIcons(i).GroupIndex == SIcons(iInd).GroupIndex
SIcons(i).Active = strcmp(SIcons(i).Name, sActivate);
end
end
end
fUpdateActivation();
% - - - - - - - - - - - - - - - - - - -
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fIconClick
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fWindowMouseHoverFcn (nested in imagine)
% * *
% * * Figure callback
% * *
% * * The standard mouse move callback. Displays cursor coordinates and
% * * intensity value of corresponding pixel.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fWindowMouseHoverFcn(hObject, eventdata)
iAxisInd = fGetPanel();
if iAxisInd
% -------------------------------------------------------------
% Cursor is over a panel -> show coordinates and intensity
iPos = uint16(get(SAxes.hImg(iAxisInd), 'CurrentPoint')); % Get cursor poition in axis coordinate system
for i = 1:length(SAxes.hImg)
iSeriesInd = SState.iStartSeries + i - 1;
if iSeriesInd > length(SData), continue, end
if iPos(1, 1) > 0 && iPos(1, 2) > 0 && iPos(1, 1) <= size(SData(iSeriesInd).dImg, 2) && iPos(1, 2) <= size(SData(iSeriesInd).dImg, 1)
switch SState.sDrawMode
case {'mag', 'phase'}
dImg = fGetImg(iSeriesInd);
dVal = dImg(iPos(1, 2), iPos(1, 1));
case 'max'
if isreal(SData(iSeriesInd).dImg)
dVal = max(SData(iSeriesInd).dImg(iPos(1, 2), iPos(1, 1), :), [], 3);
else
dVal = max(abs(SData(iSeriesInd).dImg(iPos(1, 2), iPos(1, 1), :)), [], 3);
end
case 'min'
if isreal(SData(iSeriesInd).dImg)
dVal = min(SData(iSeriesInd).dImg(iPos(1, 2), iPos(1, 1), :), [], 3);
else
dVal = min(abs(SData(iSeriesInd).dImg(iPos(1, 2), iPos(1, 1), :)), [], 3);
end
end
if i == iAxisInd, set(STexts.hStatus, 'String', sprintf('I(%u,%u) = %s', iPos(1, 1), iPos(1, 2), fPrintNumber(dVal))); end
set(STexts.hVal(i), 'String', sprintf('%s', fPrintNumber(dVal)));
else
if i == iAxisInd, set(STexts.hStatus, 'String', ''); end
set(STexts.hVal(i), 'String', '');
end
end
% -------------------------------------------------------------
else
% -------------------------------------------------------------
% Cursor is not over a panel -> Check if tooltip has to be shown
hOver = hittest;
iInd = find([SImg.hIcons] == hOver);
if iInd
sText = SIcons(iInd).Tooltip;
sAccelerator = SIcons(iInd).Accelerator;
if ~isempty(SIcons(iInd).Modifier), sAccelerator = sprintf('%s+%s', SIcons(iInd).Modifier, SIcons(iInd).Accelerator); end
if ~isempty(SIcons(iInd).Accelerator), sText = sprintf('%s [%s]', sText, sAccelerator); end
set(STexts.hStatus, 'String', sText);
else
set(STexts.hStatus, 'String', '');
end
% -------------------------------------------------------------
end
drawnow update
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fWindowMouseHoverFcn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fWindowButtonDownFcn (nested in imagine)
% * *
% * * Figure callback
% * *
% * * Starting callback for mouse button actions.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fWindowButtonDownFcn(hObject, eventdata)
iAxisInd = fGetPanel();
if ~iAxisInd, return, end % Exit if event didn't occurr in a panel
% -----------------------------------------------------------------
% Save starting parameters
dPos = get(SAxes.hImg(iAxisInd), 'CurrentPoint');
SMouse.iStartAxis = iAxisInd;
SMouse.iStartPos = get(hObject, 'CurrentPoint');
SMouse.dAxesStartPos = [dPos(1, 1), dPos(1, 2)];
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Backup the display settings of all data
SMouse.dDrawCenter = reshape([SData.dDrawCenter], [2, length(SData)]);
SMouse.dZoomFactor = [SData.dZoomFactor];
SMouse.dWindowCenter = [SData.dWindowCenter];
SMouse.dWindowWidth = [SData.dWindowWidth];
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Delete existing line objects, clear masks
if isfield(SLines, 'hEval')
try delete(SLines.hEval); end %#ok<TRYNC>
SLines = rmfield(SLines, 'hEval');
end
switch SState.sTool
case {'line', 'roi', 'lw', 'rg', 'ic'}
for i = 1:length(SData), SData(i).lMask = []; end
fFillPanels;
end
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Activate the callbacks for drag operations
set(hObject, 'WindowButtonUpFcn', @fWindowButtonUpFcn);
set(hObject, 'WindowButtonMotionFcn', @fWindowMouseMoveFcn);
% -----------------------------------------------------------------
drawnow update
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fWindowButtonDownFcn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fWindowMouseMoveFcn (nested in imagine)
% * *
% * * Figure callback
% * *
% * * Callback for mouse movement while button is pressed.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fWindowMouseMoveFcn(hObject, eventdata)
iAxesInd = fGetPanel();
% -----------------------------------------------------------------
% Get some frequently used values
lLinked = fIsOn('link'); % Determines whether axes are linked
iD = get(hF, 'CurrentPoint') - SMouse.iStartPos; % Mouse distance travelled since button down
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Tool-specific code
switch SState.sTool
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The NORMAL CURSOR: select, move, zoom, window
case 'cursor_arrow'
switch get(hF, 'SelectionType')
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Normal, left mouse button -> MOVE operation
case 'normal'
dD = double(iD); % Scale mouse movement to panel size (since DrawCenter is a relative value)
dD(2) = -dD(2);
for i = 1:length(SData)
iAxisInd = i - SState.iStartSeries + 1;
if ~((lLinked) || (iAxisInd == SMouse.iStartAxis)), continue, end % Skip if axes not linked and current figure not active
dScale = SData(i).dPixelSpacing(1:2)./min(SData(i).dPixelSpacing);
dNewPos = SMouse.dDrawCenter(:, i)' - flip(dD)./dScale./SData(i).dZoomFactor; % Calculate new draw center relative to saved one
SData(i).dDrawCenter = dNewPos; % Save DrawCenter data
end
fPosition;
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Shift key or right mouse button -> ZOOM operation
case 'alt'
for i = 1:length(SData)
if (~fIsOn('link')) && i ~= (SMouse.iStartAxis + SState.iStartSeries - 1), continue, end % Skip if axes not linked and current figure not active
dZoom = min(100, max(0.25, SMouse.dZoomFactor(i).*exp(SPref.dZOOMSENSITIVITY.*iD(2))));
dOldDrawCenter = SMouse.dDrawCenter(:, i)';
dMouseStart = flip(SMouse.dAxesStartPos, 2);
dD = dOldDrawCenter - dMouseStart;
SData(i).dDrawCenter = dMouseStart + SMouse.dZoomFactor(i)./dZoom.*dD;
SData(i).dZoomFactor = dZoom; % Save ZoomFactor data
end
fPosition;
case 'extend' % Control key or middle mouse button -> WINDOW operation
for i = 1:length(SData)
if (~fIsOn('link')) && (i ~= SMouse.iStartAxis + SState.iStartSeries - 1), continue, end % Skip if axes not linked and current figure not active
SData(i).dWindowWidth = SMouse.dWindowWidth(i) .*exp(SPref.dWINDOWSENSITIVITY*(-iD(2)));
SData(i).dWindowCenter = SMouse.dWindowCenter(i).*exp(SPref.dWINDOWSENSITIVITY* iD(1));
iAxisInd = i - SState.iStartSeries + 1;
if iAxisInd < 1 || iAxisInd > length(SAxes.hImg), continue, end % Do not update images outside the figure's scope (will be done with next call of fFillPanels)
if iAxisInd == SMouse.iStartAxis % Show windowing information for the starting axes
set(STexts.hStatus, 'String', sprintf('C: %s, W: %s', fPrintNumber(SData(i).dWindowCenter), fPrintNumber(SData(i).dWindowWidth)));
end
end
fFillPanels;
end
% end of the NORMAL CURSOR
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The ROTATION tool
case 'rotate'
if ~any(abs(iD) > SPref.dROTATION_THRESHOLD), return, end % Only proceed if action required
iStartSeries = SMouse.iStartAxis + SState.iStartSeries - 1;
for i = 1:length(SData)
if ~(lLinked || i == iStartSeries || SData(i).iGroupIndex == SData(iStartSeries).iGroupIndex), continue, end % Skip if axes not linked and current figure not active
switch get(hObject, 'SelectionType')
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Normal, left mouse button -> volume rotation operation
case 'normal'
if iD(1) > SPref.dROTATION_THRESHOLD % Moved mouse to left
SData(i).iActiveImage = uint16(SMouse.dAxesStartPos(1, 1));
iPermutation = [1 3 2]; iFlipdim = 2;
end
if iD(1) < -SPref.dROTATION_THRESHOLD % Moved mouse to right
SData(i).iActiveImage = uint16(size(SData(i).dImg, 2) - SMouse.dAxesStartPos(1, 1) + 1);
iPermutation = [1 3 2]; iFlipdim = 3;
end
if iD(2) > SPref.dROTATION_THRESHOLD
SData(i).iActiveImage = uint16(size(SData(i).dImg, 1) - SMouse.dAxesStartPos(1, 2) + 1);
iPermutation = [3 2 1]; iFlipdim = 3;
end
if iD(2) < -SPref.dROTATION_THRESHOLD
SData(i).iActiveImage = uint16(SMouse.dAxesStartPos(1, 2));
iPermutation = [3 2 1]; iFlipdim = 1;
end
% - - - - - - - - - - - - - - - - - - - - - - - - -
% Shift key or right mouse button -> rotate in-plane
case 'alt'
if any(iD > SPref.dROTATION_THRESHOLD)
iPermutation = [2 1 3]; iFlipdim = 2;
end
if any(iD < -SPref.dROTATION_THRESHOLD)
iPermutation = [2 1 3]; iFlipdim = 1;
end
% - - - - - - - - - - - - - - - - - - - - - - - - -
case 'extend'
return
end
% Switch statement
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Apply the transformation
SData(i).dImg = flipdim(permute(SData(i).dImg, iPermutation), iFlipdim);
SData(i).lMask = flipdim(permute(SData(i).lMask, iPermutation), iFlipdim);
SData(i).dPixelSpacing = SData(i).dPixelSpacing(iPermutation);
set(hObject, 'WindowButtonMotionFcn', @fWindowMouseHoverFcn);
% - - - - - - - - - - - - - - - - - - - - - - -
% Limit active image range to image dimensions
if SData(i).iActiveImage < 1, SData(i).iActiveImage = 1; end
if SData(i).iActiveImage > size(SData(i).dImg, 3), SData(i).iActiveImage = size(SData(i).dImg, 3); end
end
% Loop over the data
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
fFillPanels();
% END of the rotate tool
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The LINE EVALUATION tool
case 'line'
if ~iAxesInd, return, end % Exit if event didn't occurr in a panel
dPos = get(SAxes.hImg(iAxesInd), 'CurrentPoint');
if ~isfield(SLines, 'hEval') % Make sure line object exists
for i = 1:length(SAxes.hImg)
if i + SState.iStartSeries - 1 > length(SData), continue, end
SLines.hEval(i) = line([SMouse.dAxesStartPos(1, 1), dPos(1, 1)], [SMouse.dAxesStartPos(1, 2), dPos(1, 2)], ...
'Parent' , SAxes.hImg(i), ...
'Color' , SPref.dCOLORMAP(i,:), ...
'LineStyle' , '-');
end
else
set(SLines.hEval, 'XData', [SMouse.dAxesStartPos(1, 1), dPos(1, 1)], 'YData', [SMouse.dAxesStartPos(1, 2), dPos(1, 2)]);
end
fWindowMouseHoverFcn(hF, []); % Update the position display by triggering the mouse hover callback
% end of the LINE EVALUATION tool
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Handle special case of ROI drawing (update the lines), ellipse
case 'roi'
if ~iAxesInd || iAxesInd + SState.iStartSeries - 1 > length(SData), return, end
switch SState.iROIState
case 0 % No drawing -> Check if one should start an elliplse or rectangle
dPos = get(SAxes.hImg(SMouse.iStartAxis), 'CurrentPoint');
if sum((dPos(1, 1:2) - SMouse.dAxesStartPos).^2) > 4
for i = 1:length(SAxes.hImg)
if i + SState.iStartSeries - 1 > length(SData), continue, end
SLines.hEval(i) = line(dPos(1, 1), dPos(1, 2), ...
'Parent' , SAxes.hImg(i), ...
'Color' , SPref.dCOLORMAP(i,:),...
'LineStyle' , '-');
end
switch(get(hF, 'SelectionType'))
case 'normal', SState.iROIState = 2; % -> Rectangle
case {'alt', 'extend'}, SState.iROIState = 3; % -> Ellipse
end
end
case 1 % Polygon mode
dPos = get(SAxes.hImg(iAxesInd), 'CurrentPoint');
dROILineX = [SState.dROILineX; dPos(1, 1)]; % Draw a line to the cursor position
dROILineY = [SState.dROILineY; dPos(1, 2)];
set(SLines.hEval, 'XData', dROILineX, 'YData', dROILineY);
case 2 % Rectangle mode
dPos = get(SAxes.hImg(iAxesInd), 'CurrentPoint');
SState.dROILineX = [SMouse.dAxesStartPos(1); SMouse.dAxesStartPos(1); dPos(1, 1); dPos(1, 1); SMouse.dAxesStartPos(1)];
SState.dROILineY = [SMouse.dAxesStartPos(2); dPos(1, 2); dPos(1, 2); SMouse.dAxesStartPos(2); SMouse.dAxesStartPos(2)];
set(SLines.hEval, 'XData', SState.dROILineX, 'YData', SState.dROILineY);
case 3 % Ellipse mode
dPos = get(SAxes.hImg(iAxesInd), 'CurrentPoint');
dDX = dPos(1, 1) - SMouse.dAxesStartPos(1);
dDY = dPos(1, 2) - SMouse.dAxesStartPos(2);
if strcmp(get(hF, 'SelectionType'), 'extend')
dD = max(abs([dDX, dDY]));
dDX = sign(dDX).*dD;
dDY = sign(dDY).*dD;
end
dT = linspace(-pi, pi, 100)';
SState.dROILineX = SMouse.dAxesStartPos(1) + dDX./2.*(1 + cos(dT));
SState.dROILineY = SMouse.dAxesStartPos(2) + dDY./2.*(1 + sin(dT));
set(SLines.hEval, 'XData', SState.dROILineX, 'YData', SState.dROILineY);
end
fWindowMouseHoverFcn(hF, []); % Update the position display by triggering the mouse hover callback
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Handle special case of LW drawing (update the lines)
case 'lw'
if iAxesInd == SMouse.iStartAxis
if SState.iROIState == 1 && sum(abs(SState.iPX(:))) > 0 % ROI drawing in progress
dPos = get(SAxes.hImg(SMouse.iStartAxis), 'CurrentPoint');
[iXPath, iYPath] = fLiveWireGetPath(SState.iPX, SState.iPY, dPos(1, 1), dPos(1, 2));
if isempty(iXPath)
iXPath = dPos(1, 1);
iYPath = dPos(1, 2);
end
set(SLines.hEval, 'XData', [SState.dROILineX; double(iXPath(:))], ...
'YData', [SState.dROILineY; double(iYPath(:))]);
drawnow update
end
end
fWindowMouseHoverFcn(hF, []); % Update the position display by triggering the mouse hover callback
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
otherwise
end
% end of the TOOL switch statement
% -----------------------------------------------------------------
drawnow update
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fWindowMouseMoveFcn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fWindowButtonUpFcn (nested in imagine)
% * *
% * * Figure callback
% * *
% * * End of mouse operations.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fWindowButtonUpFcn(hObject, eventdata)
iAxisInd = fGetPanel();
iCursorPos = get(hF, 'CurrentPoint');
% -----------------------------------------------------------------
% Stop the operation by disabling the corresponding callbacks
set(hF, 'WindowButtonMotionFcn' ,@fWindowMouseHoverFcn);
set(hF, 'WindowButtonUpFcn' ,'');
set(STexts.hStatus, 'String', '');
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Tool-specific code
switch SState.sTool
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The NORMAL CURSOR: select, move, zoom, window
% In this function, only the select case has to be handled
case 'cursor_arrow'
if ~sum(abs(iCursorPos - SMouse.iStartPos)) % Proceed only if mouse was moved
switch get(hF, 'SelectionType')
% - - - - - - - - - - - - - - - - - - - - - - - - -
% NORMAL selection: Select only current series
case 'normal'
iN = fGetNActiveVisibleSeries();
for iSeries = 1:length(SData)
if SMouse.iStartAxis + SState.iStartSeries - 1 == iSeries
SData(iSeries).lActive = ~SData(iSeries).lActive || iN > 1;
else
SData(iSeries).lActive = false;
end
end
SState.iLastSeries = SMouse.iStartAxis + SState.iStartSeries - 1; % The lastAxis is needed for the shift-click operation
% end of normal selection
% - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - -
% Shift key or right mouse button: Select ALL axes
% between last selected axis and current axis
case 'extend'
iSeriesInd = SMouse.iStartAxis + SState.iStartSeries - 1;
if sum([SData.lActive] == true) == 0
% If no panel active, only select the current axis
SData(iSeriesInd).lActive = true;
SState.iLastSeries = iSeriesInd;
else
if SState.iLastSeries ~= iSeriesInd
iSortedInd = sort([SState.iLastSeries, iSeriesInd], 'ascend');
for i = 1:length(SData)
SData(i).lActive = (i >= iSortedInd(1)) && (i <= iSortedInd(2));
end
end
end
% end of shift key/right mouse button
% - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - -
% Cntl key or middle mouse button: ADD/REMOVE axis
% from selection
case 'alt'
iSeriesInd = SMouse.iStartAxis + SState.iStartSeries - 1;
SData(iSeriesInd).lActive = ~SData(iSeriesInd).lActive;
SState.iLastSeries = iSeriesInd;
% end of alt/middle mouse buttton
% - - - - - - - - - - - - - - - - - - - - - - - - -
end
end
% end of the NORMAL CURSOR
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The LINE EVALUATION tool
case 'line'
fEval(SState.csEvalLineFcns);
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% End of the LINE EVALUATION tool
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The ROI EVALUATION tool
case 'roi'
set(hF, 'WindowButtonMotionFcn', @fWindowMouseMoveFcn);
set(hF, 'WindowButtonDownFcn', '');
set(hF, 'WindowButtonUpFcn', @fWindowButtonUpFcn); % But keep the button up function
if iAxisInd && iAxisInd + SState.iStartSeries - 1 <= length(SData) % ROI drawing in progress
dPos = get(SAxes.hImg(iAxisInd), 'CurrentPoint');
if SState.iROIState > 1 || any(strcmp({'extend', 'open'}, get(hF, 'SelectionType')))
SState.dROILineX = [SState.dROILineX; SState.dROILineX(1)]; % Close line
SState.dROILineY = [SState.dROILineY; SState.dROILineY(1)];
delete(SLines.hEval);
SState.iROIState = 0;
set(hF, 'WindowButtonMotionFcn',@fWindowMouseHoverFcn);
set(hF, 'WindowButtonDownFcn', @fWindowButtonDownFcn);
set(hF, 'WindowButtonUpFcn', '');
fEval(SState.csEvalROIFcns);
return
end
switch get(hF, 'SelectionType')
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% NORMAL selection: Add point to roi
case 'normal'
if ~SState.iROIState % This is the first polygon point
SState.dROILineX = dPos(1, 1);
SState.dROILineY = dPos(1, 2);
for i = 1:length(SAxes.hImg)
if i + SState.iStartSeries - 1 > length(SData), continue, end
SLines.hEval(i) = line(SState.dROILineX, SState.dROILineY, ...
'Parent' , SAxes.hImg(i), ...
'Color' , SPref.dCOLORMAP(i,:),...
'LineStyle' , '-');
end
SState.iROIState = 1;
else % Add point to existing polygone
SState.dROILineX = [SState.dROILineX; dPos(1, 1)];
SState.dROILineY = [SState.dROILineY; dPos(1, 2)];
set(SLines.hEval, 'XData', SState.dROILineX, 'YData', SState.dROILineY);
end
% End of NORMAL selection
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Right mouse button/shift key: UNDO last point, quit
% if is no point remains
case 'alt'
if ~SState.iROIState, return, end % Only perform action if painting in progress
if length(SState.dROILineX) > 1
SState.dROILineX = SState.dROILineX(1:end-1); % Delete last point
SState.dROILineY = SState.dROILineY(1:end-1);
dROILineX = [SState.dROILineX; dPos(1, 1)]; % But draw line to current cursor position
dROILineY = [SState.dROILineY; dPos(1, 2)];
set(SLines.hEval, 'XData', dROILineX, 'YData', dROILineY);
else % Abort drawing ROI
SState.iROIState = 0;
delete(SLines.hEval);
SLines = rmfield(SLines, 'hEval');
set(hF, 'WindowButtonMotionFcn',@fWindowMouseHoverFcn);
set(hF, 'WindowButtonDownFcn', @fWindowButtonDownFcn); % Disable the button down function
end
% End of right click/shift-click
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
end
% End of the ROI EVALUATION tool
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The LIVEWIRE EVALUATION tool
case 'lw'
set(hF, 'WindowButtonMotionFcn', @fWindowMouseMoveFcn);
set(hF, 'WindowButtonDownFcn', '');
set(hF, 'WindowButtonUpFcn', @fWindowButtonUpFcn); % But keep the button up function
if iAxisInd ~= SMouse.iStartAxis, return, end
dPos = get(SAxes.hImg(SMouse.iStartAxis), 'CurrentPoint');
switch get(hF, 'SelectionType')
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% NORMAL selection: Add point to roi
case 'normal'
if ~SState.iROIState % This is the first polygon point
dImg = SData(SMouse.iStartAxis + SState.iStartSeries - 1).dImg(:,:,SData(SMouse.iStartAxis + SState.iStartSeries - 1).iActiveImage);
SState.dLWCostFcn = fLiveWireGetCostFcn(dImg);
SState.dROILineX = dPos(1, 1);
SState.dROILineY = dPos(1, 2);
for i = 1:length(SAxes.hImg)
if i + SState.iStartSeries - 1 > length(SData), continue, end
SLines.hEval(i) = line(SState.dROILineX, SState.dROILineY, ...
'Parent' , SAxes.hImg(i), ...
'Color' , SPref.dCOLORMAP(i,:),...
'LineStyle' , '-');
end
SState.iROIState = 1;
SState.iLWAnchorList = zeros(200, 1);
SState.iLWAnchorInd = 0;
else % Add point to existing polygone
[iXPath, iYPath] = fLiveWireGetPath(SState.iPX, SState.iPY, dPos(1, 1), dPos(1, 2));
if isempty(iXPath)
iXPath = dPos(1, 1);
iYPath = dPos(1, 2);
end
SState.dROILineX = [SState.dROILineX; double(iXPath(:))];
SState.dROILineY = [SState.dROILineY; double(iYPath(:))];
set(SLines.hEval, 'XData', SState.dROILineX, 'YData', SState.dROILineY);
end
SState.iLWAnchorInd = SState.iLWAnchorInd + 1;
SState.iLWAnchorList(SState.iLWAnchorInd) = length(SState.dROILineX); % Save the previous path length for the undo operation
[SState.iPX, SState.iPY] = fLiveWireCalcP(SState.dLWCostFcn, dPos(1, 1), dPos(1, 2), SPref.dLWRADIUS);
% End of NORMAL selection
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Right mouse button/shift key: UNDO last point, quit
% if is no point remains
case 'alt'
if SState.iROIState
SState.iLWAnchorInd = SState.iLWAnchorInd - 1;
if SState.iLWAnchorInd
SState.dROILineX = SState.dROILineX(1:SState.iLWAnchorList(SState.iLWAnchorInd)); % Delete last point
SState.dROILineY = SState.dROILineY(1:SState.iLWAnchorList(SState.iLWAnchorInd));
set(SLines.hEval, 'XData', SState.dROILineX, 'YData', SState.dROILineY);
drawnow;
[SState.iPX, SState.iPY] = fLiveWireCalcP(SState.dLWCostFcn, SState.dROILineX(end), SState.dROILineY(end), SPref.dLWRADIUS);
fWindowMouseMoveFcn(hObject, []);
else % Abort drawing ROI
SState.iROIState = 0;
delete(SLines.hEval);
SLines = rmfield(SLines, 'hEval');
set(hF, 'WindowButtonMotionFcn',@fWindowMouseHoverFcn);
set(hF, 'WindowButtonDownFcn', @fWindowButtonDownFcn);
end
end
% End of right click/shift-click
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Middle mouse button/double-click/cntl-click: CLOSE
% POLYGONE and quit roi action
case {'extend', 'open'} % Middle mouse button or double-click ->
if ~SState.iROIState, return, end % Only perform action if painting in progress
[iXPath, iYPath] = fLiveWireGetPath(SState.iPX, SState.iPY, dPos(1, 1), dPos(1, 2));
if isempty(iXPath)
iXPath = dPos(1, 1);
iYPath = dPos(1, 2);
end
SState.dROILineX = [SState.dROILineX; double(iXPath(:))];
SState.dROILineY = [SState.dROILineY; double(iYPath(:))];
[SState.iPX, SState.iPY] = fLiveWireCalcP(SState.dLWCostFcn, dPos(1, 1), dPos(1, 2), SPref.dLWRADIUS);
[iXPath, iYPath] = fLiveWireGetPath(SState.iPX, SState.iPY, SState.dROILineX(1), SState.dROILineY(1));
if isempty(iXPath)
iXPath = SState.dROILineX(1);
iYPath = SState.dROILineX(2);
end
SState.dROILineX = [SState.dROILineX; double(iXPath(:))];
SState.dROILineY = [SState.dROILineY; double(iYPath(:))];
set(SLines.hEval, 'XData', SState.dROILineX, 'YData', SState.dROILineY);
delete(SLines.hEval);
SState.iROIState = 0;
set(hF, 'WindowButtonMotionFcn',@fWindowMouseHoverFcn);
set(hF, 'WindowButtonDownFcn', @fWindowButtonDownFcn);
set(hF, 'WindowButtonUpFcn', '');
fEval(SState.csEvalROIFcns);
% End of middle mouse button/double-click/cntl-click
% - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
% End of the LIVEWIRE EVALUATION tool
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The REGION GROWING tool
case 'rg'
if ~strcmp(get(hF, 'SelectionType'), 'normal'), return, end; % Otherwise calling the context menu starts a rg
if ~iAxisInd || iAxisInd > length(SData), return, end;
iSeriesInd = iAxisInd + SState.iStartSeries - 1;
iSize = size(SData(iSeriesInd).dImg);
dPos = get(SAxes.hImg(iAxisInd), 'CurrentPoint');
if dPos(1, 1) < 1 || dPos(1, 2) < 1 || dPos(1, 1) > iSize(2) || dPos(1, 2) > iSize(1), return, end
fEval(SState.csEvalVolFcns);
% End of the REGION GROWING tool
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The ISOCONTOUR tool
case 'ic'
if ~iAxisInd || iAxisInd > length(SData), return, end;
iSeriesInd = iAxisInd + SState.iStartSeries - 1;
iSize = size(SData(iSeriesInd).dImg);
dPos = get(SAxes.hImg(iAxisInd), 'CurrentPoint');
if dPos(1, 1) < 1 || dPos(1, 2) < 1 || dPos(1, 1) > iSize(2) || dPos(1, 2) > iSize(1), return, end
fEval(SState.csEvalVolFcns);
% End of the ISOCONTOUR tool
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% The PROPERTIES tool: Rename the data
case 'tag'
if ~iAxisInd || iAxisInd > length(SData), return, end;
iSeriesInd = SState.iStartSeries + iAxisInd - 1;
csPrompt = {'Name', 'Voxel Size', 'Units'};
dDim = SData(iSeriesInd).dPixelSpacing;
sDim = sprintf('%4.2f x ', dDim([2, 1, 3]));
csVal = {SData(iSeriesInd).sName, sDim(1:end-3), SData(iSeriesInd).sUnits};
csAns = inputdlg(csPrompt, sprintf('Change %s', SData(iSeriesInd).sName), 1, csVal);
if isempty(csAns), return, end
sName = csAns{1};
iInd = find([SData.iGroupIndex] == SData(iSeriesInd).iGroupIndex);
if length(iInd) > 1
if ~isnan(str2double(sName(end - 1:end))), sName = sName(1:end - 2); end % Crop the number
end
dDim = cell2mat(textscan(csAns{2}, '%fx%fx%f'));
iCnt = 1;
for i = iInd
if length(iInd) > 1
SData(i).sName = sprintf('%s%02d', sName, iCnt);
else
SData(i).sName = sName;
end
SData(i).dPixelSpacing = dDim([2, 1, 3]);
SData(i).sUnits = csAns{3};
iCnt = iCnt + 1;
end
fFillPanels;
% End of the TAG tool
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
% end of the tool switch-statement
% -----------------------------------------------------------------
fUpdateActivation();
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fWindowButtonUpFcn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fKeyPressFcn (nested in imagine)
% * *
% * * Figure callback
% * *
% * * Callback for keyboard actions.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fKeyPressFcn(hObject, eventdata)
% -----------------------------------------------------------------
% Bail if only a modifier has been pressed
switch eventdata.Key
case {'shift', 'control', 'alt'}, return
end
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Get the modifier (shift, cntl, alt) keys and determine whether
% the control key was pressed
csModifier = eventdata.Modifier;
sModifier = '';
for i = 1:length(csModifier)
if strcmp(csModifier{i}, 'shift' ), sModifier = 'Shift'; end
if strcmp(csModifier{i}, 'control'), sModifier = 'Cntl'; end
if strcmp(csModifier{i}, 'alt' ), sModifier = 'Alt'; end
end
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Look for buttons with corresponding accelerators/modifiers
for i = 1:length(SIcons)
if strcmp(SIcons(i).Accelerator, eventdata.Key) && ...
strcmp(SIcons(i).Modifier, sModifier)
fIconClick(SImg.hIcons(i), eventdata);
end
end
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Functions not implemented by buttons
switch eventdata.Key
case {'numpad1', 'leftarrow'} % Image up
fChangeImage(hObject, -1);
case {'numpad2', 'rightarrow'} % Image down
fChangeImage(hObject, 1);
case {'numpad4', 'uparrow'} % Series up
SState.iStartSeries = max([1 SState.iStartSeries - 1]);
fFillPanels();
fUpdateActivation();
fWindowMouseHoverFcn(hObject, eventdata); % Update the cursor value
case {'numpad5', 'downarrow'} % Series down
SState.iStartSeries = min([SState.iStartSeries + 1 length(SData)]);
SState.iStartSeries = max([SState.iStartSeries 1]);
fFillPanels();
fUpdateActivation();
fWindowMouseHoverFcn(hObject, eventdata); % Update the cursor value
case 'period'
SState.iStartSeries = SState.iStartSeries + 1;
if SState.iStartSeries > length(SData), SState.iStartSeries = 1; end
fFillPanels();
fUpdateActivation();
fWindowMouseHoverFcn(hObject, eventdata); % Update the cursor value
case 'space' % Cycle Tools
iTools = find([SIcons.GroupIndex] == 255 & [SIcons.Enabled]);
iToolInd = find(strcmp({SIcons.Name}, SState.sTool));
iToolIndInd = find(iTools == iToolInd);
iTools = [iTools(end), iTools, iTools(1)];
if ~strcmp(sModifier, 'Shift'), iToolIndInd = iToolIndInd + 2; end
iToolInd = iTools(iToolIndInd);
fIconClick(SImg.hIcons(iToolInd), eventdata);
end
% -----------------------------------------------------------------
set(hF, 'SelectionType', 'normal');
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fKeyPressFcn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fContextFcn (nested in imagine)
% * *
% * * Menu callback
% * *
% * * Callback for context menu clicks
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fContextFcn(hObject, eventdata)
switch get(hObject, 'Label')
case 'Tolerance +50%', SState.dTolerance = SState.dTolerance.*1.5;
case 'Tolerance +10%', SState.dTolerance = SState.dTolerance.*1.1;
case 'Tolerance -10%', SState.dTolerance = SState.dTolerance./1.1;
case 'Tolerance -50%', SState.dTolerance = SState.dTolerance./1.5;
end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fContextFcn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fEval (nested in imagine)
% * *
% * * Do the evaluation of line/ROIs
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fEval(csFcns)
dPos = get(SAxes.hImg(fGetPanel), 'CurrentPoint');
% -----------------------------------------------------------------
% Depending on the time series setting, eval only visible or all data
if fIsOn('clock')
iSeries = 1:length(SData); % Eval all series
else
iSeries = 1:length(SData);
iSeries = iSeries(iSeries >= SState.iStartSeries & iSeries < SState.iStartSeries + length(SAxes.hImg));
end
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Get the rawdata for evaluation and the distance/area/volume
csSeriesName = cell(length(iSeries), 1);
cData = cell(length(iSeries), 1);
dMeasures = zeros(length(iSeries), length(csFcns) + 1);
csName = cell(1, length(csFcns) + 1);
csUnitString = cell(1, length(csFcns) + 1);
% -----------------------------------------------------------------
% Series Loop
for i = 1:length(iSeries)
iSeriesInd = iSeries(i);
csSeriesName{i} = SData(i).sName;
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Tool dependent code
switch SState.sTool
case 'line'
dXStart = SMouse.dAxesStartPos(1,1); dYStart = SMouse.dAxesStartPos(1,2);
dXEnd = dPos(1,1); dYEnd = dPos(1,2);
dDist = sqrt(((dXStart - dXEnd).*SData(iSeriesInd).dPixelSpacing(2)).^2 + ((dYStart - dYEnd).*SData(iSeriesInd).dPixelSpacing(1)).^2);
if dDist < 1.0, return, end % In case of a misclick
csName{1} = 'Length';
csUnitString{1} = sprintf('%s', SData(iSeriesInd).sUnits);
dMeasures(i, 1) = dDist;
cData{i} = improfile(fGetImg(iSeriesInd), [dXStart dXEnd], [dYStart, dYEnd], round(dDist), 'bilinear');
case {'roi', 'lw'}
csName{1} = 'Area';
csUnitString{1} = sprintf('%s^2', SData(iSeriesInd).sUnits);
dImg = fGetImg(iSeriesInd);
lMask = poly2mask(SState.dROILineX, SState.dROILineY, size(dImg, 1), size(dImg, 2));
dMeasures(i, 1) = nnz(lMask).*SData(iSeriesInd).dPixelSpacing(2).*SData(iSeriesInd).dPixelSpacing(1);
cData{i} = dImg(lMask);
SData(iSeriesInd).lMask = false(size(SData(iSeriesInd).dImg));
SData(iSeriesInd).lMask(:,:,SData(iSeriesInd).iActiveImage) = lMask;
fFillPanels;
case 'rg'
csName{1} = 'Volume';
csUnitString{1} = sprintf('%s^3', SData(iSeriesInd).sUnits);
if strcmp(SState.sDrawMode, 'phase')
dImg = angle(SData(iSeriesInd).dImg);
else
dImg = SData(iSeriesInd).dImg;
if ~isreal(dImg), dImg = abs(dImg); end
end
if i == 1 % In the first series detrmine the tolerance and use the same tolerance in the other series
[lMask, dTol] = fRegionGrowingAuto_mex(dImg, int16([dPos(1, 2); dPos(1, 1); SData(iSeriesInd).iActiveImage]), -1, SState.dTolerance);
else
lMask = fRegionGrowingAuto_mex(dImg, int16([dPos(1, 2); dPos(1, 1); SData(iSeriesInd).iActiveImage]), dTol);
end
dMeasures(i, 1) = nnz(lMask).*prod(SData(iSeriesInd).dPixelSpacing);
cData{i} = dImg(lMask);
SData(iSeriesInd).lMask = lMask;
fFillPanels;
case 'ic'
csName{1} = 'Volume';
csUnitString{1} = sprintf('%s^3', SData(iSeriesInd).sUnits);
if strcmp(SState.sDrawMode, 'phase')
dImg = angle(SData(iSeriesInd).dImg);
else
dImg = SData(iSeriesInd).dImg;
if ~isreal(dImg), dImg = abs(dImg); end
end
lMask = fIsoContour_mex(dImg, int16([dPos(1, 2); dPos(1, 1); SData(iSeriesInd).iActiveImage]), 0.5);
dMeasures(i, 1) = nnz(lMask).*prod(SData(iSeriesInd).dPixelSpacing);
cData{i} = dImg(lMask);
SData(iSeriesInd).lMask = lMask;
fFillPanels;
end
% End of switch SState.sTool
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Do the evaluation
sEvalString = sprintf('%s = %s %s\n', csName{1}, num2str(dMeasures(i, 1)), csUnitString{1});
for iJ = 2:length(csFcns) + 1
[dMeasures(i, iJ), csName{iJ}, sUnitFormat] = eval([csFcns{iJ - 1}, '(cData{i});']);
csUnitString{iJ} = sprintf(sUnitFormat, SData(iSeriesInd).sUnits);
if isempty(csUnitString{iJ}), csUnitString{iJ} = ''; end
sEvalString = sprintf('%s%s = %s %s\n', sEvalString, csName{iJ}, num2str(dMeasures(i, iJ)), csUnitString{iJ});
end
SData(iSeriesInd).sEvalText = sEvalString(1:end-1);
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
% End of series loop
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Plot the line profile and add name to legend
% Check for presence of plot figure and create if necessary.
if (fIsOn('line1') && fIsOn('clock')) || (fIsOn('line1') && ~fIsOn('clock') && strcmp(SState.sTool, 'line'))
if ~ishandle(SState.hEvalFigure)
SState.hEvalFigure = figure('Units', 'pixels', 'Position', [100 100 600, 400], 'NumberTitle', 'off');
axes('Parent', SState.hEvalFigure);
hold on;
end
figure(SState.hEvalFigure);
hL = findobj(SState.hEvalFigure, 'Type', 'line');
hAEval = gca;
delete(hL);
if fIsOn('clock')
for i = 2:size(dMeasures, 2)
plot(dMeasures(:,i), 'Color', SPref.dCOLORMAP(i - 1,:));
end
legend(csName{2:end}); % Show legend
set(SState.hEvalFigure, 'Name', 'Time Series');
set(get(hAEval, 'XLabel'), 'String', 'Time Point');
set(get(hAEval, 'YLabel'), 'String', 'Value');
else
for i = 1:length(cData);
plot(cData{i}, 'Color', SPref.dCOLORMAP(i,:));
end
legend(csSeriesName); % Show legend
set(SState.hEvalFigure, 'Name', 'Line Profile');
set(get(hAEval, 'XLabel'), 'String', sprintf('x [%s]', SData(SState.iStartSeries).sUnits));
set(get(hAEval, 'YLabel'), 'String', 'Intensity');
end
end
fFillPanels;
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Export to file if enabled
if isempty(SState.sEvalFilename), return, end
iPos = fGetEvalFilePos;
if iPos < 0
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% File does not exist -> Write header
fid = fopen(SState.sEvalFilename, 'w');
if fid < 0, warning('IMAGINE: Cannot write to file ''%s''!', SState.sEvalFilename); return, end
if fIsOn('clock')
fprintf(fid, '\n'); % First line (series names) empty
fprintf(fid, ['"";"";', fPrintCell('"%s";', csName), '\n']); % The eval function names
fprintf(fid, ['"";"";', fPrintCell('"%s";', csUnitString), '\n']); % The eval function names
else
sFormatString = ['"%s";', repmat('"";', [1, length(csName) - 1])];
fprintf(fid, ['"";"";', fPrintCell(sFormatString, csSeriesName), '\n']);
fprintf(fid, ['"";"";', fPrintCell('"%s";', repmat(csName, [1, length(csSeriesName)])), '\n']); % The eval function names
fprintf(fid, ['"";"";', fPrintCell('"%s";', repmat(csUnitString, [1, length(csSeriesName)])), '\n']); % The eval function names
end
fclose(fid);
fprintf('Created file ''%s''!\n', SState.sEvalFilename);
iPos = 0;
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
% ----------------------------------------------------------------
% Write the measurements to file
fid = fopen(SState.sEvalFilename, 'a');
if fid < 0, warning('IMAGINE: Cannot write to file ''%s''!', SState.sEvalFilename); return, end
iPos = iPos + 1;
if fIsOn('clock')
fprintf(fid, '\n');
for i = 1:length(csSeriesName)
fprintf(fid, '"%d";"%s";', iPos, csSeriesName{i});
if SPref.lGERMANEXPORT
for iJ = 1:size(dMeasures, 2), fprintf(fid, '"%s";', strrep(num2str(dMeasures(i, iJ)), '.', ',')); end
else
for iJ = 1:size(dMeasures, 2), fprintf(fid, '"%s";', num2str(dMeasures(i, iJ))); end
end
fprintf(fid, '\n');
end
else
fprintf(fid, '"%d";"";', iPos);
dMeasures = dMeasures';
dMeasures = dMeasures(:);
if SPref.lGERMANEXPORT
for i = 1:length(dMeasures), fprintf(fid, '"%s";', strrep(num2str(dMeasures(i)), '.', ',')); end
else
for i = 1:length(dMeasures), fprintf(fid, '"%s";', num2str(dMeasures(i))); end
end
fprintf(fid, '\n');
end
fclose(fid);
fprintf('Written to position %d in file ''%s''!\n', iPos, SState.sEvalFilename);
% -----------------------------------------------------------------
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fEval
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function sString = fPrintCell(sFormatString, csCell)
sString = '';
for i = 1:length(csCell);
sString = sprintf(['%s', sFormatString], sString, csCell{i});
end
end
function iPos = fGetEvalFilePos
iPos = -1;
if ~exist(SState.sEvalFilename, 'file'), return, end
fid = fopen(SState.sEvalFilename, 'r');
if fid < 0, return, end
iPos = 0; i = 1;
sLine = fgets(fid);
while ischar(sLine)
csText{i} = sLine;
sLine = fgets(fid);
i = 1 + 1;
end
fclose(fid);
csPos = textscan(csText{end}, '"%d"');
if ~isempty(csPos{1}), iPos = csPos{1}; end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fChangeImage (nested in imagine)
% * *
% * * Change image index of all series (if linked) or all selected
% * * series.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fChangeImage(hObject, iCnt)
% -----------------------------------------------------------------
% Return if projection image selected or ROI drawing in progress
% if strcmp(SState.sDrawMode, 'max') || strcmp(SState.sDrawMode, 'min') || SState.iROIState, return, end
if SState.iROIState, return, end
% -----------------------------------------------------------------
if isstruct(iCnt), iCnt = iCnt.VerticalScrollCount; end % Origin is mouse wheel
if isobject(iCnt), iCnt = iCnt.VerticalScrollCount; end % Origin is mouse wheel, R2014b
% -----------------------------------------------------------------
% Loop over all data (visible or not)
for iSeriesInd = 1:length(SData)
if (~fIsOn('link')) && (~SData(iSeriesInd).lActive), continue, end % Skip if axes not linked and current figure not active
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Calculate new image index and make sure it's not out of bounds
iNewImgInd = SData(iSeriesInd).iActiveImage + iCnt;
iNewImgInd = max([iNewImgInd, 1]);
iNewImgInd = min([iNewImgInd, size(SData(iSeriesInd).dImg, 3)]);
SData(iSeriesInd).iActiveImage = iNewImgInd;
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Update corresponding axes if necessary (visible)
iAxisInd = iSeriesInd - SState.iStartSeries + 1;
if (iAxisInd) > 0 && (iAxisInd <= length(SAxes.hImg)) % Update Corresponding Axis
set(STexts.hImg2(iAxisInd), 'String', sprintf('%u/%u', iNewImgInd, size(SData(iSeriesInd).dImg, 3)));
end
end
fFillPanels;
% fWindowMouseHoverFcn(hObject, []); % Update the cursor value
% -----------------------------------------------------------------
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fChangeImage
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fSaveToFiles (nested in imagine)
% * *
% * * Save image data of selected panels to file(s)
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fSaveToFiles(sFilename, sPath)
set(hF, 'Pointer', 'watch'); drawnow
[~, ~, sExt] = fileparts(sFilename);
if strcmp(sExt, '.gif')
iImg = zeros([size(SData(1).dImg(:,:,1)), 1, length(SData)], 'uint8');
for i = 1:length(SData)
if strcmp(SState.sDrawMode, 'phase')
dMin = -pi; dMax = pi;
else
dMin = SData(1).dWindowCenter - 0.5.*SData(1).dWindowWidth;
dMax = SData(1).dWindowCenter + 0.5.*SData(1).dWindowWidth;
end
if ~fIsOn('link1') && ~strcmp(SState.sDrawMode, 'phase')
dMin = SData(i).dWindowCenter - 0.5.*SData(i).dWindowWidth;
dMax = SData(i).dWindowCenter + 0.5.*SData(i).dWindowWidth;
end
dImg = fGetImg(i);
dImg = dImg - dMin;
dImg = round(dImg./(dMax - dMin).*(SAp.iCOLORMAPLENGTH - 1)) + 1;
dImg(dImg < 1) = 1;
dImg(dImg > SAp.iCOLORMAPLENGTH) = SAp.iCOLORMAPLENGTH;
dImg = reshape(SState.dColormapBack(dImg, :), [size(iImg, 1) ,size(iImg, 2), 3]);
iImg(:,:,1,i) = uint8(dImg(:,:,1).*255);
end
imwrite(iImg, [sPath, sFilename], 'LoopCount', Inf, 'DelayTime', 0.05);
else
iNSeries = fGetNVisibleSeries;
dMin = SData(SState.iStartSeries).dWindowCenter - 0.5.*SData(SState.iStartSeries).dWindowWidth;
dMax = SData(SState.iStartSeries).dWindowCenter + 0.5.*SData(SState.iStartSeries).dWindowWidth;
for i = 1:iNSeries
iSeriesInd = i + SState.iStartSeries - 1;
if ~fIsOn('link1')
dMin = SData(iSeriesInd).dWindowCenter - 0.5.*SData(iSeriesInd).dWindowWidth;
dMax = SData(iSeriesInd).dWindowCenter + 0.5.*SData(iSeriesInd).dWindowWidth;
end
if strcmp(SState.sDrawMode, 'phase')
dMin = -pi;
dMax = pi;
end
switch SState.sDrawMode
case {'mag', 'phase'}
dImg = zeros(size(SData(iSeriesInd).dImg));
for iJ = 1:size(SData(iSeriesInd).dImg, 3);
dImg(:,:,iJ) = fGetImg(iSeriesInd, iJ);
end
case {'min', 'max'}
dImg = fGetImg(iSeriesInd);
end
dImg = dImg - dMin;
iImg = round(dImg./(dMax - dMin).*(SAp.iCOLORMAPLENGTH - 1)) + 1;
iImg(iImg < 1) = 1;
iImg(iImg > SAp.iCOLORMAPLENGTH) = SAp.iCOLORMAPLENGTH;
dImg = reshape(SState.dColormapBack(iImg, :), [size(iImg, 1), size(iImg, 2), size(iImg, 3), 3]);
dImg = permute(dImg, [1 2 4 3]); % rgb mode
dImg = dImg.*255;
dImg(dImg < 0) = 0;
dImg(dImg > 255) = 255;
sSeriesFilename = strrep(sFilename, '%SeriesName%', SData(iSeriesInd).sName);
switch SState.sDrawMode
case {'mag', 'phase'}
hW = waitbar(0, sprintf('Saving Stack ''%s''', SData(iSeriesInd).sName));
for iImgInd = 1:size(dImg, 4)
sImgFilename = strrep(sSeriesFilename, '%ImageNumber%', sprintf('%03u', iImgInd));
imwrite(uint8(dImg(:,:,:,iImgInd)), [sPath, filesep, sImgFilename]);
waitbar(iImgInd./size(dImg, 4), hW); drawnow;
end
close(hW);
case {'max', 'min'}
sImgFilename = strrep(sSeriesFilename, '%ImageNumber%', sprintf('%sProjection', SState.sDrawMode));
imwrite(uint8(dImg), [sPath, filesep, sImgFilename]);
end
end
end
set(hF, 'Pointer', 'arrow');
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fSaveToFiles
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fSaveToFiles (nested in imagine)
% * *
% * * Save image data of selected panels to file(s)
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fSaveMaskToFiles(sFilename, sPath)
set(hF, 'Pointer', 'watch'); drawnow expose
iNSeries = fGetNVisibleSeries;
for i = 1:iNSeries
iSeriesInd = i + SState.iStartSeries - 1;
lImg = SData(iSeriesInd).lMask;
if isempty(lImg), continue, end
lMask = max(max(lImg, [], 1), [], 2);
dImg = double(lImg);
switch nnz(lMask)
case 0, continue % no mask
case 1 % its a 2D mask
iInd = find(lMask);
sSeriesFilename = strrep(sFilename, '%SeriesName%', SData(iSeriesInd).sName);
sImgFilename = strrep(sSeriesFilename, '%ImageNumber%', sprintf('%03d', iInd));
imwrite(dImg(:,:,iInd), [sPath, filesep, sImgFilename]);
otherwise
sSeriesFilename = strrep(sFilename, '%SeriesName%', SData(iSeriesInd).sName);
for iInd = 1:size(dImg, 3)
sImgFilename = strrep(sSeriesFilename, '%ImageNumber%', sprintf('%03d', iInd));
imwrite(dImg(:,:,iInd), [sPath, filesep, sImgFilename]);
end
end
end
set(hF, 'Pointer', 'arrow');
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fSaveToFiles
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fGetImg (nested in imagine)
% * *
% * * Return data for view according to drawmode
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function dImg = fGetImg(iInd, iImgInd)
if nargin < 2, iImgInd = SData(iInd).iActiveImage; end
if strcmp(SState.sDrawMode, 'phase')
dImg = angle(SData(iInd).dImg(:,:,iImgInd));
return
end
dImg = SData(iInd).dImg;
if ~isreal(dImg), dImg = abs(dImg); end
switch SState.sDrawMode
case 'mag', dImg = dImg(:,:,iImgInd);
case 'max'
iMin = max(1, iImgInd - 3);
iMax = min(size(dImg, 3), iImgInd + 3);
dImg = max(dImg(:,:,iMin:iMax), [], 3);
case 'min', dImg = min(dImg, [], 3);
end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fGetImg
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fSetWindow(hObject, eventdata)
iAxisInd = find(SImg.hColorbar == hObject);
iSeriesInd = iAxisInd + SState.iStartSeries - 1;
if iSeriesInd > length(SData), return, end
dMin = SData(iSeriesInd).dWindowCenter - 0.5.*SData(iSeriesInd).dWindowWidth;
dMax = SData(iSeriesInd).dWindowCenter + 0.5.*SData(iSeriesInd).dWindowWidth;
csVal{1} = fPrintNumber(dMin);
csVal{2} = fPrintNumber(dMax);
csAns = inputdlg({'Min', 'Max'}, sprintf('Change %s windowing', SData(iSeriesInd).sName), 1, csVal);
if isempty(csAns), return, end
csVal = textscan([csAns{1}, ' ', csAns{2}], '%f %f');
if ~isempty(csVal{1}), dMin = csVal{1}; end
if ~isempty(csVal{2}), dMax = csVal{2}; end
SData(iSeriesInd).dWindowCenter = (dMin + dMax)./2;
SData(iSeriesInd).dWindowWidth = (dMax - dMin);
fFillPanels;
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fUpdateActivation (nested in imagine)
% * *
% * * Set the activation and availability of some switches according to
% * * the GUI state.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fUpdateActivation
% -----------------------------------------------------------------
% Update states of some menubar buttons according to panel selection
csLabels = {SIcons.Name};
SIcons(strcmp(csLabels, 'save')) .Enabled = fGetNActiveVisibleSeries() > 0;
SIcons(strcmp(csLabels, 'doc_delete')).Enabled = fGetNActiveVisibleSeries() > 0;
SIcons(strcmp(csLabels, 'exchange')) .Enabled = fGetNActiveVisibleSeries() == 2;
SIcons(strcmp(csLabels, 'record')) .Enabled = isempty(SState.sEvalFilename);
SIcons(strcmp(csLabels, 'stop')) .Enabled = ~isempty(SState.sEvalFilename);
SIcons(strcmp(csLabels, 'rewind')) .Enabled = ~isempty(SState.sEvalFilename);
% -----------------------------------------------------------------
SIcons(strcmp(csLabels, 'lw')).Enabled = exist('fLiveWireCalcP') == 3; % Compiled mex file
SIcons(strcmp(csLabels, 'rg')).Enabled = exist('fRegionGrowingAuto_mex') == 3; % Compiled mex file
SIcons(strcmp(csLabels, 'ic')).Enabled = exist('fIsoContour_mex') == 3; % Compiled mex file
% -----------------------------------------------------------------
% Treat the menubar items
dScale = ones(length(SIcons));
dScale(~[SIcons.Enabled]) = SAp.iDISABLED_SCALE;
dScale( [SIcons.Enabled] & ~[SIcons.Active]) = SAp.iINACTIVE_SCALE;
for i = 1:length(SIcons), set(SImg.hIcons(i), 'CData', SIcons(i).dImg.*dScale(i)); end
% -----------------------------------------------------------------
% -----------------------------------------------------------------
% Treat the panels
for i = 1:length(SAxes.hImg)
iSeriesInd = i + SState.iStartSeries - 1;
if iSeriesInd > length(SData) || ~SData(iSeriesInd).lActive
set(STexts.hImg1(i), 'FontWeight', 'normal');
else
set(STexts.hImg1(i), 'FontWeight', 'bold');
end
end
% -----------------------------------------------------------------
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fUpdateActivation
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fGetNActiveVisibleSeries (nested in imagine)
% * *
% * * Returns the number of visible active series.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function iNActiveSeries = fGetNActiveVisibleSeries()
iNActiveSeries = 0;
if isempty(SData), return, end
iStartInd = SState.iStartSeries;
iEndInd = min([iStartInd + length(SAxes.hImg) - 1, length(SData)]);
iNActiveSeries = nnz([SData(iStartInd:iEndInd).lActive]);
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fGetNActiveVisibleSeries
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fGetNVisibleSeries (nested in imagine)
% * *
% * * Returns the number of visible active series.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function iNVisibleSeries = fGetNVisibleSeries()
if isempty(SData)
iNVisibleSeries = 0;
else
iNVisibleSeries = min([length(SAxes.hImgFrame), length(SData) - SState.iStartSeries + 1]);
end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fGetNVisibleSeries
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fParseInputs (nested in imagine)
% * *
% * * Parse the varargin input variable. It can be either pairs of
% * * data/captions or just data. Data can be either 2D, 3D or 4D.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fParseInputs(cInput)
iInd = 1;
iDataInd = 0;
% xInput = cInput{iInd};
% if ~(isnumeric(xInput) || islogical(xInput)), error('First input must be image data of some kind!'); end
% iDataInd = iDataInd + 1;
% dImg = xInput;
% sName = sprintf('Input_%02d', iDataInd);
% dDim = [1 1 1];
% sUnits = 'px';
% dWindow = [];
% lMask = [];
% iInd = iInd + 1;
while iInd <= length(cInput);
xInput = cInput{iInd};
if ~(isnumeric(xInput) || islogical(xInput) || iscell(xInput) || ischar(xInput)), error('Argument %d expected to be either property or data!', iInd); end
if isnumeric(xInput) || islogical(xInput) || iscell(xInput)% New image data
if iDataInd, fAddImageToData(dImg, sName, 'startup', dDim, sUnits, dWindow, lMask, dZoom); end% Add the last Dataset
iDataInd = iDataInd + 1;
sName = sprintf('Input_%02d', iDataInd);
dDim = [1 1 1];
dZoom = 1;
sUnits = 'px';
dWindow = [];
lMask = [];
if iscell(xInput)
iNDims = ndims(xInput{1});
xInput = xInput(:);
xInput = shiftdim(xInput, -iNDims);
dImg = cell2mat(xInput);
else
dImg = xInput;
end
end
if ischar(xInput)
iInd = iInd + 1;
if iInd > length(cInput), error('Argument %d (property) must be followed by a value!', iInd - 1); end
xVal = cInput{iInd};
switch lower(xInput)
case {'n', 'name'}
if ~ischar(xVal), error('Name property must be a string!'); end
sName = xVal;
case {'v', 'voxelsize'}
if ~isnumeric(xVal) || numel(xVal) ~= 3, error('Voxelsize property must be a [3x1] or [1x3] numeric vector!'); end
dDim = xVal;
case {'z', 'zoom'}
if ~isnumeric(xVal), error('Zoom property must be a numeric scalar!'); end
dZoom = xVal;
case {'u', 'units'}
if ~ischar(xVal), error('Units property must be a string!'); end
sUnits = xVal;
case {'w', 'window'}
if ~isnumeric(xVal) || numel(xVal) ~= 2, error('Window limits property must be a [2x1] or [1x2] numeric vector!'); end
dWindow = xVal;
case {'m', 'mask'}
if ndims(xVal) ~= ndims(dImg), error('Mask must have same number of dimensions as the image!'); end
if any(size(dImg) ~= size(xVal)), error('Mask must have same size as image'); end
lMask = xVal;
case {'p', 'panels'}
if ~isnumeric(xVal) || numel(xVal) ~= 2, error('Panel size must be a [2x1] or [1x2] numeric vector!'); end
SState.iPanels = xVal(:)';
otherwise, error('Unknown property ''%s''!', xInput);
end
end
iInd = iInd + 1;
end
if iDataInd, fAddImageToData(dImg, sName, 'startup', dDim, sUnits, dWindow, lMask, dZoom); end
if sum(SState.iPanels) == 0
iNumImages = length(SData);
dRoot = sqrt(iNumImages);
iPanelsN = ceil(dRoot);
iPanelsM = ceil(dRoot);
while iPanelsN*iPanelsM >= iNumImages
iPanelsN = iPanelsN - 1;
end
iPanelsN = iPanelsN + 1;
iPanelsN = min([4, iPanelsN]);
iPanelsM = min([4, iPanelsM]);
SState.iPanels = [iPanelsN, iPanelsM];
end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fParseInputs
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fLoadFiles (nested in imagine)
% * *
% * * Load image files from disk and sort into series.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fLoadFiles(csFilenames)
if ~iscell(csFilenames), csFilenames = {csFilenames}; end % If only one file
lLoaded = false(length(csFilenames), 1);
SImageData = [];
hW = waitbar(0, 'Loading files');
for i = 1:length(csFilenames)
[sPath, sName, sExt] = fileparts(csFilenames{i}); %#ok<ASGLU>
switch lower(sExt)
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Standard image data: Try to group according to size
case {'.jpg', '.jpeg', '.tif', '.tiff', '.gif', '.bmp', '.png'}
try
dImg = double(imread([SState.sPath, csFilenames{i}]))./255;
lLoaded(i) = true;
catch %#ok<CTCH>
disp(['Error when loading "', SState.sPath, csFilenames{i}, '": File extenstion and type do not match']);
continue;
end
dImg = mean(dImg, 3);
iInd = fServesSizeCriterion(size(dImg), SImageData);
if iInd
dImg = cat(3, SImageData(iInd).dImg, dImg);
SImageData(iInd).dImg = dImg;
else
iLength = length(SImageData) + 1;
SImageData(iLength).dImg = dImg;
SImageData(iLength).sOrigin = 'Image File';
SImageData(iLength).sName = csFilenames{i};
SImageData(iLength).dPixelSpacing = [1 1 1];
end
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% NifTy Data
case '.nii'
set(hF, 'Pointer', 'watch'); drawnow;
[dImg, dDim] = fNifTyRead([SState.sPath, csFilenames{i}]);
if ndims(dImg) > 4, error('Only 4D data supported'); end
lLoaded(i) = true;
fAddImageToData(dImg, csFilenames{i}, 'NifTy File', dDim, 'mm');
set(hF, 'Pointer', 'arrow');
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
case '.gipl'
set(hF, 'Pointer', 'watch'); drawnow;
[dImg, dDim] = fGIPLRead([SState.sPath, csFilenames{i}]);
lLoaded(i) = true;
fAddImageToData(dImg, csFilenames{i}, 'GIPL File', dDim, 'mm');
set(hF, 'Pointer', 'arrow');
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
case '.mat'
csVars = fMatRead([SState.sPath, csFilenames{i}]);
lLoaded(i) = true;
if isempty(csVars), continue, end % Dialog aborted
set(hF, 'Pointer', 'watch'); drawnow;
for iJ = 1:length(csVars)
S = load([SState.sPath, csFilenames{i}], csVars{iJ});
eval(['dImg = S.', csVars{iJ}, ';']);
fAddImageToData(dImg, sprintf('%s in %s', csVars{iJ}, csFilenames{i}), 'MAT File');
end
set(hF, 'Pointer', 'arrow');
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
waitbar(i/length(csFilenames), hW);
end
close(hW);
for i = 1:length(SImageData)
fAddImageToData(SImageData(i).dImg, SImageData.sName, 'Image File', [1 1 1]);
end
set(hF, 'Pointer', 'watch'); drawnow;
SDicomData = fDICOMRead(csFilenames(~lLoaded), SState.sPath);
for i = 1:length(SDicomData)
fAddImageToData(SDicomData(i).dImg, SDicomData(i).SeriesDescriptions, 'DICOM', SDicomData(i).Aspect, 'mm');
end
set(hF, 'Pointer', 'arrow');
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fLoadFiles
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fAddImageToData (nested in imagine)
% * *
% * * Add image data to the global SDATA variable. Can handle 2D, 3D or
% * * 4D data.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fAddImageToData(dImage, sName, sOrigin, dDim, sUnits, dWindow, lMask, dZoom)
if nargin < 8, dZoom = 1; end
if nargin < 7, lMask = []; end
if nargin < 6, dWindow = []; end
if nargin < 5, sUnits = 'px'; end
if nargin < 4, dDim = [1 1 1]; end
if islogical(dImage), dImage = ones(size(dImage)).*dImage; end
dImage = double(dImage);
dImage(isnan(dImage)) = 0;
iInd = length(SData) + 1;
iGroupIndex = 1;
if ~isempty(SData)
iExistingGroups = unique([SData.iGroupIndex]);
if ~isempty(iExistingGroups)
while nnz(iExistingGroups == iGroupIndex), iGroupIndex = iGroupIndex + 1; end
end
end
if size(dImage, 3) == 3
SData(iInd).dImg = dImage;
if ~isempty(dWindow)
dMin = dWindow(1);
dMax = dWindow(2);
else
if isreal(SData(iInd).dImg)
if numel(SData(iInd).dImg) > 1E6
dMin = min(SData(iInd).dImg(1:100:end));
dMax = max(SData(iInd).dImg(1:100:end));
else
dMin = min(SData(iInd).dImg(:));
dMax = max(SData(iInd).dImg(:));
end
else
if numel(SData(iInd).dImg) > 1E6
dMin = min(abs(SData(iInd).dImg(1:100:end)));
dMax = max(abs(SData(iInd).dImg(1:100:end)));
else
dMin = min(abs(SData(iInd).dImg(:)));
dMax = max(abs(SData(iInd).dImg(:)));
end
end
end
if dMax == dMin, dMax = dMin + 1; end
SData(iInd).dDynamicRange = [dMin, dMax];
SData(iInd).sOrigin = sOrigin;
SData(iInd).dWindowCenter = (dMax + dMin)./2;
SData(iInd).dWindowWidth = dMax - dMin;
SData(iInd).dZoomFactor = dZoom;
SData(iInd).dDrawCenter = [size(SData(iInd).dImg, 1), size(SData(iInd).dImg, 2)]/2;
SData(iInd).iActiveImage = max(1, round(size(SData(iInd).dImg, 3)/2));
SData(iInd).lActive = false;
if dDim(end) == 0, dDim(end) = min(dDim(1:2)); end
SData(iInd).dPixelSpacing = dDim(:)';
SData(iInd).sUnits = sUnits;
SData(iInd).lMask = [];
SData(iInd).iGroupIndex = iGroupIndex;
SData(iInd).sEvalText = '';
SData(iInd).sName = sName;
iInd = iInd + 1;
else
for i = 1:size(dImage, 4)
SData(iInd).dImg = dImage(:,:,:,i);
if ~isempty(dWindow)
dMin = dWindow(1);
dMax = dWindow(2);
else
if isreal(SData(iInd).dImg)
if numel(SData(iInd).dImg) > 1E6
dMin = min(SData(iInd).dImg(1:100:end));
dMax = max(SData(iInd).dImg(1:100:end));
else
dMin = min(SData(iInd).dImg(:));
dMax = max(SData(iInd).dImg(:));
end
else
if numel(SData(iInd).dImg) > 1E6
dMin = min(abs(SData(iInd).dImg(1:100:end)));
dMax = max(abs(SData(iInd).dImg(1:100:end)));
else
dMin = min(abs(SData(iInd).dImg(:)));
dMax = max(abs(SData(iInd).dImg(:)));
end
end
end
if dMax == dMin, dMax = dMin + 1; end
SData(iInd).dDynamicRange = [dMin, dMax];
SData(iInd).sOrigin = sOrigin;
SData(iInd).dWindowCenter = (dMax + dMin)./2;
SData(iInd).dWindowWidth = dMax - dMin;
SData(iInd).dZoomFactor = dZoom;
SData(iInd).dDrawCenter = [size(SData(iInd).dImg, 1), size(SData(iInd).dImg, 2)]/2;
SData(iInd).iActiveImage = max(1, round(size(SData(iInd).dImg, 3)/2));
SData(iInd).lActive = false;
if dDim(end) == 0, dDim(end) = min(dDim(1:2)); end
SData(iInd).dPixelSpacing = dDim(:)';
SData(iInd).sUnits = sUnits;
if isempty(lMask)
SData(iInd).lMask = [];
else
SData(iInd).lMask = lMask(:,:,:,i);
end
SData(iInd).iGroupIndex = iGroupIndex;
SData(iInd).sEvalText = '';
if ndims(dImage) > 3
SData(iInd).sName = sprintf('%s_%02u', sName, i);
else
SData(iInd).sName = sName;
end
iInd = iInd + 1;
end
end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fAddImageToData
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fGetPanel (nested in imagine)
% * *
% * * Determine the panelnumber under the mouse cursor. Returns 0 if
% * * not over a panel at all.
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function iPanelInd = fGetPanel()
iCursorPos = get(hF, 'CurrentPoint');
iPanelInd = uint8(0);
for i = 1:min([length(SAxes.hImg), length(SData) - SState.iStartSeries + 1])
dPos = get(SAxes.hImg(i), 'Position');
if ((iCursorPos(1) >= dPos(1)) && (iCursorPos(1) < dPos(1) + dPos(3)) && ...
(iCursorPos(2) >= dPos(2) + SAp.iEVALBARHEIGHT) && (iCursorPos(2) < dPos(2) + dPos(4) - SAp.iTITLEBARHEIGHT - SAp.iCOLORBARHEIGHT))
iPanelInd = uint8(i);
end
end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fGetPanel
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fServesSizeCriterion (nested in imagine)
% * *
% * * Determines, whether the data structure contains an image series
% * * with the same x- and y-dimensions as iSize
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function iInd = fServesSizeCriterion(iSize, SNewData)
iInd = 0;
for i = 1:length(SNewData)
if (iSize(1) == size(SNewData(i).dImg, 1)) && ...
(iSize(2) == size(SNewData(i).dImg, 2))
iInd = i;
return;
end
end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fServesSizeCriterion
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fIsOn (nested in imagine)
% * *
% * * Determine whether togglebutton is active
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function lOn = fIsOn(sTag)
lOn = SIcons(strcmp({SIcons.Name}, sTag)).Active;
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fIsOn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION SDataOut (nested in imagine)
% * *
% * * Thomas' hack function to get the data structure
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function SDataOut = fGetData
SDataOut = SData;
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION SDataOut
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fPrintNumber (nested in imagine3D)
% * *
% * * Display a value in adequate format
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function sString = fPrintNumber(xNumber)
if ((abs(xNumber) < 0.01) && (xNumber ~= 0)) || (abs(xNumber) > 1E4)
sString = sprintf('%2.1E', xNumber);
else
sString = sprintf('%4.2f', xNumber);
end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fPrintNumber
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fReplicate (nested in imagine)
% * *
% * * Scale image by power of 2 by nearest neighbour interpolation
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function dImgOut = fReplicate(dImg, iIter)
dImgOut = zeros(2.*size(dImg));
dImgOut(1:2:end, 1:2:end) = dImg;
dImgOut(2:2:end, 1:2:end) = dImg;
dImgOut(1:2:end, 2:2:end) = dImg;
dImgOut(2:2:end, 2:2:end) = dImg;
iIter = iIter - 1;
if iIter > 0, dImgOut = fReplicate(dImgOut, iIter); end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fReplicate
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * NESTED FUNCTION fCompileMex (nested in imagine)
% * *
% * * Scale image by power of 2 by nearest neighbour interpolation
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fCompileMex
fprintf('Imagine will try to compile some mex files!\n');
sToolsPath = [SPref.sMFILEPATH, filesep, 'tools'];
S = dir([sToolsPath, filesep, '*.cpp']);
sPath = cd;
cd(sToolsPath);
lSucc = true;
for i = 1:length(S)
[temp, sName] = fileparts(S(i).name); %#ok<ASGLU>
if exist(sName, 'file') == 3, continue, end
try
eval(['mex ', S(i).name]);
catch
warning('Could nor compile ''%s''!', S(i).name);
lSucc = false;
end
end
cd(sPath);
if ~lSucc
warndlg(sprintf('Not all mex files could be compiled, thus some tools will not be available. Try to setup the mex-compiler using ''mex -setup'' and compile the *.cpp files in the ''tools'' folder manually.'), 'IMAGINE');
else
fprintf('Hey, it worked!\n');
end
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fCompileMex
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function dOut = fBlend(dBot, dTop, sMode, dAlpha)
% -------------------------------------------------------------------------
% Parse the inputs
if nargin < 4, dAlpha = 1.0; end % Top is fully opaque
if nargin < 3, sMode = 'overlay'; end
if nargin < 2, error('At least 2 input arguments required!'); end
if isa(dBot, 'uint8')
dBot = double(dBot);
dBot = dBot./255;
end
if isa(dTop, 'uint8')
dTop = double(dTop);
dTop = dTop./255;
end
% -------------------------------------------------------------------------
% Check Inputs
if numel(dTop) == 3
% if isscalar(dAlpha), error('If top layer is given as a color, alpha map must be supplied!'); end
dTop = repmat(permute(dTop(:), [3 2 1]), [size(dAlpha) 1]);
end
dTopSize = [size(dTop, 1), size(dTop, 2), size(dTop, 3), size(dTop, 4)];
% Check if background is monochrome
if numel(dBot) == 1 % grayscale background
dBot = dBot.*ones(dTopSize);
end
if numel(dBot) == 3 % rgb background color
dBot = repmat(permute(dBot(:), [2 3 1]), [dTopSize(1), dTopSize(2), 1, dTopSize(4)]);
end
dBotSize = [size(dBot, 1), size(dBot, 2), size(dBot, 3), size(dBot, 4)];
if dBotSize(3) ~= 1 && dBotSize(3) ~= 3, error('Bottom layer must be either grayscale or RGB!'); end
if dTopSize(3) > 4, error('Size of 3rd top layer dimension must not exceed 4!'); end
if any(dBotSize(1, 2) ~= dTopSize(1, 2)), error('Size of image data does not match'); end
if dBotSize(4) ~= dTopSize(4)
if dBotSize(4) > 1 && dTopSize(4) > 1, error('4th dimension of image data mismatch!'); end
if dBotSize(4) == 1, dBot = repmat(dBot, [1, 1, 1, dTopSize(4)]); end
if dTopSize(4) == 1, dTop = repmat(dTop, [1, 1, 1, dBotSize(4)]); end
end
%% Handle the alpha map
if dTopSize(3) == 2 || dTopSize(3) == 4 % Alpha channel included
dAlpha = dTop(:,:,end, :);
dTop = dTop(:,:,1:end-1,:);
else
if isscalar(dAlpha)
dAlpha = dAlpha.*ones(dTopSize(1), dTopSize(2), 1, dTopSize(4));
else
dAlphaSize = [size(dAlpha, 1), size(dAlpha, 2), size(dAlpha, 3), size(dAlpha, 4)];
if any(dAlphaSize(1:2) ~= dTopSize(1:2)), error('Top layer alpha map dimension mismatch!'); end
if dAlphaSize(3) > 1, error('3rd dimension of alpha map must have size 1!'); end
if dAlphaSize(4) > 1
if dAlphaSize(4) ~= dTopSize(4), error('Alpha map dimension mismatch!'); end
else
dAlpha = repmat(dAlpha, [1, 1, 1, dTopSize(4)]);
end
end
end
% Bring data into the right format
dMaxDim = max([size(dBot, 3), size(dTop, 3)]);
if dMaxDim > 2, lRGB = true; else lRGB = false; end
if lRGB && dBotSize(3) == 1, dBot = repmat(dBot, [1, 1, 3, 1]); end
if lRGB && dTopSize(3) == 1, dTop = repmat(dTop, [1, 1, 3, 1]); end
if lRGB, dAlpha = repmat(dAlpha, [1, 1, 3, 1]); end
% Check Range
dBot = fCheckRange(dBot);
dTop = fCheckRange(dTop);
dAlpha = fCheckRange(dAlpha);
% Do the blending
switch lower(sMode)
case 'normal', dOut = dTop;
case 'multiply', dOut = dBot.*dTop;
case 'screen', dOut = 1 - (1 - dBot).*(1 - dTop);
case 'overlay'
lMask = dBot < 0.5;
dOut = 1 - 2.*(1 - dBot).*(1 - dTop);
dOut(lMask) = 2.*dBot(lMask).*dTop(lMask);
case 'hard_light'
lMask = dTop < 0.5;
dOut = 1 - 2.*(1 - dBot).*(1 - dTop);
dOut(lMask) = 2.*dBot(lMask).*dTop(lMask);
case 'soft_light', dOut = (1 - 2.*dTop).*dBot.^2 + 2.*dTop.*dBot; % pegtop
case 'darken', dOut = min(cat(4, dTop, dBot), [], 4);
case 'lighten', dOut = max(cat(4, dTop, dBot), [], 4);
otherwise, error('Unknown blend mode ''%s''!', sMode);
end
dOut = dAlpha.*dOut + (1 - dAlpha).*dBot;
dOut(dOut > 1) = 1;
dOut(dOut < 0) = 0;
end
function dData = fCheckRange(dData)
dData(dData < 0) = 0;
dData(dData > 1) = 1;
end
end
% =========================================================================
% *** END FUNCTION imagine (and its nested functions)
% =========================================================================
% #########################################################################
% ***
% *** Helper GUIS and their callbacks
% ***
% #########################################################################
% =========================================================================
% *** FUNCTION fGridSelect
% ***
% *** Creates a tiny GUI to select the GUI layout, i.e. the number of
% *** panels and the grid dimensions.
% ***
% =========================================================================
function iSizeOut = fGridSelect(iM, iN)
iGRIDSIZE = 30;
iSizeOut = [0 0];
% -------------------------------------------------------------------------
% Create a new figure at the current mouse pointer position
iPos = get(0, 'PointerLocation');
hGridFig = figure(...
'Position' , [iPos(1), iPos(2) - iGRIDSIZE*iM, iGRIDSIZE*iN, iGRIDSIZE*iM], ...
'Units' , 'pixels', ...
'DockControls' , 'off', ...
'WindowStyle' , 'modal', ...
'Name' , '', ...
'WindowButtonMotionFcn' , @fGridMouseMoveFcn, ...
'WindowButtonDownFcn' , 'uiresume(gcbf)', ... % continues the execution of this function after the uiwait when the mousebutton is pressed
'NumberTitle' , 'off', ...
'Resize' , 'off', ...
'Colormap' , [0.2 0.3 0.4; ...
0.3 0.4 0.5], ...
'Visible' , 'off');
hA = axes(...
'Units' , 'normalized', ...
'Position' , [0 0 1 1], ...
'Parent' , hGridFig, ...
'XLim' , [0 iM] + 0.5, ...
'YLim' , [0 iN] + 0.5, ...
'YDir' , 'reverse', ...
'XGrid' , 'on', ...
'YGrid' , 'on', ...
'Layer' , 'top', ...
'XTick' , (1:iN) + 0.5, ...
'YTick' , (1:iM) + 0.5, ...
'TickLength', [0 0]);
hI = image(...
'CData' , zeros(iM, iN, 'uint8'), ...
'CDataMapping' , 'direct');
set(hGridFig, 'Visible', 'on');
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Handle GUI interaction
uiwait(hGridFig); % Wait until the uiresume function is called (happens when mouse button is pressed, see creation of the figure above)
try % Button was pressed, return the amount of selected panels
delete(hGridFig); % close the figure
catch %#ok<CTCH> % if figure could not be deleted (dialog aborted), return [0 0]
iSizeOut = [0 0];
end
% -------------------------------------------------------------------------
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fGridMouseMoveFcn (nested in fGridSelect)
% * *
% * * Determine whether axes are linked
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fGridMouseMoveFcn(hObject, eventdata)
dCursorPos = get(hA, 'CurrentPoint');
iSizeOut = round(dCursorPos(1, 2:-1:1));
dCData = zeros(iM, iN, 'uint8');
dCData(1:iSizeOut(1), 1:iSizeOut(2)) = 1;
set(hI, 'CData', dCData);
drawnow update
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fGridMouseMoveFcn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
end
% =========================================================================
% *** END FUNCTION fGridSelect (and its nested functions)
% =========================================================================
% =========================================================================
% *** FUNCTION fColormapSelect
% ***
% *** Creates a tiny GUI to select the colormap.
% ***
% =========================================================================
function sColormap = fColormapSelect(hText)
iWIDTH = 128;
iBARHEIGHT = 32;
% -------------------------------------------------------------------------
% List the MATLAB built-in colormaps
csColormaps = {'gray', 'bone', 'copper', 'pink', 'hot', 'jet', 'hsv', 'cool'};
iNColormaps = length(csColormaps);
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Add custom colormaps (if any)
sColormapPath = [fileparts(mfilename('fullpath')), filesep, 'colormaps'];
SDir = dir([sColormapPath, filesep, '*.m']);
for iI = 1:length(SDir)
iNColormaps = iNColormaps + 1;
[sPath, sName] = fileparts(SDir(iI).name); %#ok<ASGLU>
csColormaps{iNColormaps} = sName;
end
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Create a new figure at the current mouse pointer position
iPos = get(0, 'PointerLocation');
iHeight = iNColormaps.*iBARHEIGHT;
hColormapFig = figure(...
'Position' , [iPos(1), iPos(2) - iHeight, iWIDTH, iHeight], ...
'WindowStyle' , 'modal', ...
'Name' , '', ...
'WindowButtonMotionFcn', @fColormapMouseMoveFcn, ...
'WindowButtonDownFcn' , 'uiresume(gcbf)', ... % continues the execution of this function after the uiwait when the mousebutton is pressed
'NumberTitle' , 'off', ...
'Resize' , 'off');
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Make the true-color image with the colormaps
dImg = zeros(iNColormaps, iWIDTH, 3);
dLine = zeros(iWIDTH, 3);
for iI = 1:iNColormaps
eval(['dLine = ', csColormaps{iI}, '(iWIDTH);']);
dImg(iI, :, :) = permute(dLine, [3, 1, 2]);
end
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Create axes and image for selection
hA = axes(...
'Units' , 'pixels', ...
'Position' , [1, 1, iWIDTH, iHeight], ...
'Parent' , hColormapFig, ...
'Color' , 'w', ...
'XLim' , [0.5 128.5], ...
'YLim' , [0.5 length(csColormaps) + 0.5]);
image(dImg, 'Parent', hA);
axis(hA, 'off');
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Handle GUI interaction
iLastInd = 0;
uiwait(hColormapFig); % Wait until the uiresume function is called (happens when mouse button is pressed, see creation of the figure above)
try % Button was pressed, return the amount of selected panels
dPos = get(hA, 'CurrentPoint');
iInd = round(dPos(1, 2));
sColormap = csColormaps{iInd};
delete(hColormapFig); % close the figure
catch %#ok<CTCH> % if figure could not be deleted (dialog aborted), return [0 0]
sColormap = 'gray';
end
% -------------------------------------------------------------------------
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fColormapMouseMoveFcn (nested in fColormapSelect)
% * *
% * * Determine whether axes are linked
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fColormapMouseMoveFcn(hObject, eventdata)
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Determine over which colormap the mouse pointer is located
dPos = get(hA, 'CurrentPoint');
iInd = round(dPos(1, 2));
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Update the figure's colormap if desired
if iInd ~= iLastInd
set(hText, 'String', csColormaps{iInd});
iLastInd = iInd;
end
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fColormapMouseMoveFcn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
end
% =========================================================================
% *** END FUNCTION fColormapSelect (and its nested functions)
% =========================================================================
% =========================================================================
% *** FUNCTION fSelectEvalFcns
% ***
% *** Lets the user select the eval functions for evaluation
% ***
% =========================================================================
function csFcns = fSelectEvalFcns(csActive, sPath)
iFIGUREWIDTH = 300;
iFIGUREHEIGHT = 400;
iBUTTONHEIGHT = 24;
csFcns = 0;
iPos = get(0, 'ScreenSize');
SDir = dir([sPath, filesep, '*.m']);
lActive = false(length(SDir), 1);
csNames = cell(length(SDir), 1);
for iI = 1:length(SDir)
csNames{iI} = SDir(iI).name(1:end-2);
for iJ = 1:length(csActive);
if strcmp(csNames{iI}, csActive{iJ}), lActive(iI) = true; end
end
end
% -------------------------------------------------------------------------
% Create figure and GUI elements
hF = figure( ...
'Position' , [(iPos(3) - iFIGUREWIDTH)/2, (iPos(4) - iFIGUREHEIGHT)/2, iFIGUREWIDTH, iFIGUREHEIGHT], ...
'WindowStyle' , 'modal', ...
'Name' , 'Select Eval Functions...', ...
'NumberTitle' , 'off', ...
'KeyPressFcn' , @SelectEvalCallback, ...
'Resize' , 'off');
hList = uicontrol(hF, ...
'Style' , 'listbox', ...
'Position' , [1 iBUTTONHEIGHT + 1 iFIGUREWIDTH iFIGUREHEIGHT - iBUTTONHEIGHT], ...
'String' , csNames, ...
'Min' , 0, ...
'Max' , 2, ...
'Value' , find(lActive), ...
'KeyPressFcn' , @SelectEvalCallback, ...
'Callback' , @SelectEvalCallback);
hButOK = uicontrol(hF, ...
'Style' , 'pushbutton', ...
'Position' , [1 1 iFIGUREWIDTH/2 iBUTTONHEIGHT], ...
'Callback' , @SelectEvalCallback, ...
'String' , 'OK');
uicontrol(hF, ...
'Style' , 'pushbutton', ...
'Position' , [iFIGUREWIDTH/2 + 1 1 iFIGUREWIDTH/2 iBUTTONHEIGHT], ...
'Callback' , 'uiresume(gcf);', ...
'String' , 'Cancel');
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Set default action and enable gui interaction
sAction = 'Cancel';
uiwait(hF);
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% uiresume was triggered (in fMouseActionFcn) -> return
if strcmp(sAction, 'OK')
iList = get(hList, 'Value');
csFcns = cell(length(iList), 1);
for iI = 1:length(iList)
csFcns(iI) = csNames(iList(iI));
end
end
try %#ok<TRYNC>
close(hF);
end
% -------------------------------------------------------------------------
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION SelectEvalCallback (nested in fSelectEvalFcns)
% * *
% * * Determine whether axes are linked
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function SelectEvalCallback(hObject, eventdata)
if isfield(eventdata, 'Key')
switch eventdata.Key
case 'escape', uiresume(hF);
case 'return'
sAction = 'OK';
uiresume(hF);
end
end
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% React on action depending on its source component
switch(hObject)
case hList
if strcmp(get(hF, 'SelectionType'), 'open')
sAction = 'OK';
uiresume(hF);
end
case hButOK
sAction = 'OK';
uiresume(hF);
otherwise
end
% End of switch statement
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION SelectEvalCallback
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
end
% =========================================================================
% *** END FUNCTION fSelectEvalFcns (and its nested functions)
% =========================================================================
|
github
|
jacksky64/imageProcessing-master
|
fMatRead.m
|
.m
|
imageProcessing-master/matlab imagine/imagine_2016/import/fMatRead.m
| 5,941 |
utf_8
|
2813566ac29fd2282b28bc24f561112e
|
% =========================================================================
% *** FUNCTION fMatRead
% ***
% *** Lets the user select one or multiple variables from the base
% *** workspace for import into imagine
% ***
% =========================================================================
function csVarOut = fMatRead(sFilename)
iFIGUREWIDTH = 300;
iFIGUREHEIGHT = 400;
iBUTTONHEIGHT = 24;
csVarOut = {};
iPos = get(0, 'ScreenSize');
% -------------------------------------------------------------------------
% Get variables in the mat file
set(gcf, 'Pointer', 'watch'); drawnow
SInfo = whos('-file', sFilename);
set(gcf, 'Pointer', 'arrow');
csNames = {};
csNamesDims = {};
for iI = 1:length(SInfo)
if length(SInfo(iI).size) < 2 || length(SInfo(iI).size) > 4, continue, end
if strcmp(SInfo(iI).class, 'struct') || ...
strcmp(SInfo(iI).class, 'cell')
continue
end
csNames{iI} = SInfo(iI).name;
sString = sprintf('%s (%s', SInfo(iI).name, sprintf('%ux', SInfo(iI).size));
sString = [sString(1:end-1), ')'];
csNamesDims{iI} = sString;
end
% -------------------------------------------------------------------------
if isempty(csNames)
fprintf('fMatRead: No matching variables stored in ''%s''\n!', sFilename);
return
end
if length(csNames) == 1
csVarOut(1) = csNames(1);
return
end
% -------------------------------------------------------------------------
% Create figure and GUI elements
hF = figure( ...
'Position' , [(iPos(3) - iFIGUREWIDTH)/2, (iPos(4) - iFIGUREHEIGHT)/2, iFIGUREWIDTH, iFIGUREHEIGHT], ...
'Units' , 'pixels', ...
'DockControls' , 'off', ...
'WindowStyle' , 'modal', ...
'Name' , 'Load variables from mat-File...', ...
'NumberTitle' , 'off', ...
'KeyPressFcn' , @fMatMouseActionFcn, ...
'Resize' , 'off');
hList = uicontrol(hF, ...
'Style' , 'listbox', ...
'Units' , 'pixels', ...
'Position' , [1 iBUTTONHEIGHT + 1 iFIGUREWIDTH iFIGUREHEIGHT - iBUTTONHEIGHT], ...
'HitTest' , 'on', ...
'Min' , 0, ...
'Max' , 2, ...
'String' , csNamesDims, ...
'KeyPressFcn' , @fMatMouseActionFcn, ...
'Callback' , @fMatMouseActionFcn);
hButOK = uicontrol(hF, ...
'Style' , 'pushbutton', ...
'Units' , 'pixels', ...
'Position' , [1 1 iFIGUREWIDTH/2 iBUTTONHEIGHT], ...
'Callback' , @fMatMouseActionFcn, ...
'HitTest' , 'on', ...
'String' , 'OK');
hButCancel = uicontrol(hF, ...
'Style' , 'pushbutton', ...
'Units' , 'pixels', ...
'Position' , [iFIGUREWIDTH/2 + 1 1 iFIGUREWIDTH/2 iBUTTONHEIGHT], ...
'Callback' , 'uiresume(gcf);', ...
'HitTest' , 'on', ...
'String' , 'Cancel');
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Set default action and enable gui interaction
sAction = 'Cancel';
uiwait(hF);
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% uiresume was triggered (in fMouseActionFcn) -> return
if strcmp(sAction, 'OK')
iList = get(hList, 'Value');
csVarOut = cell(length(iList), 1);
for iI = 1:length(iList)
csVarOut(iI) = csNames(iList(iI));
end
end
close(hF);
% -------------------------------------------------------------------------
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fMatMouseActionFcn (nested in fGetMatFileVar)
% * *
% * * Determine whether axes are linked
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fMatMouseActionFcn(hObject, eventdata)
if isfield(eventdata, 'Key')
switch eventdata.Key
case 'escape', uiresume(hF);
case 'return'
sAction = 'OK';
uiresume(hF);
end
end
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% React on action depending on its source component
switch(hObject)
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Click in LISBOX: return if double-clicked
case hList
if strcmp(get(hF, 'SelectionType'), 'open')
sAction = 'OK';
uiresume(hF);
end
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% OK button
case hButOK
sAction = 'OK';
uiresume(hF);
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
otherwise
end
% End of switch statement
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fMatMouseActionFcn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
end
% =========================================================================
% *** END FUNCTION fMatRead (and its nested functions)
% =========================================================================
|
github
|
jacksky64/imageProcessing-master
|
fWSImport.m
|
.m
|
imageProcessing-master/matlab imagine/imagine_2016/import/fWSImport.m
| 5,071 |
utf_8
|
1a1a9b39e2ced78065ea7a3ae96d8df3
|
% =========================================================================
% *** FUNCTION fWSImport
% ***
% *** Lets the user select one or multiple variables from the base
% *** workspace for import into imagine
% ***
% =========================================================================
function csVarOut = fWSImport()
iFIGUREWIDTH = 300;
iFIGUREHEIGHT = 400;
iBUTTONHEIGHT = 24;
csVarOut = {};
iPos = get(0, 'ScreenSize');
% -------------------------------------------------------------------------
% Create figure and GUI elements
hF = figure( ...
'Position' , [(iPos(3) - iFIGUREWIDTH)/2, (iPos(4) - iFIGUREHEIGHT)/2, iFIGUREWIDTH, iFIGUREHEIGHT], ...
'Units' , 'pixels', ...
'DockControls' , 'off', ...
'WindowStyle' , 'modal', ...
'Name' , 'Load workspace variable...', ...
'NumberTitle' , 'off', ...
'KeyPressFcn' , @fMouseActionFcn, ...
'Resize' , 'off');
csVars = evalin('base', 'who');
hList = uicontrol(hF, ...
'Style' , 'listbox', ...
'Units' , 'pixels', ...
'Position' , [1 iBUTTONHEIGHT + 1 iFIGUREWIDTH iFIGUREHEIGHT - iBUTTONHEIGHT], ...
'HitTest' , 'on', ...
'String' , csVars, ...
'Min' , 0, ...
'Max' , 2, ...
'KeyPressFcn' , @fMouseActionFcn, ...
'Callback' , @fMouseActionFcn);
hButOK = uicontrol(hF, ...
'Style' , 'pushbutton', ...
'Units' , 'pixels', ...
'Position' , [1 1 iFIGUREWIDTH/2 iBUTTONHEIGHT], ...
'Callback' , @fMouseActionFcn, ...
'HitTest' , 'on', ...
'String' , 'OK');
hButCancel = uicontrol(hF, ...
'Style' , 'pushbutton', ...
'Units' , 'pixels', ...
'Position' , [iFIGUREWIDTH/2 + 1 1 iFIGUREWIDTH/2 iBUTTONHEIGHT], ...
'Callback' , 'uiresume(gcf);', ...
'HitTest' , 'on', ...
'String' , 'Cancel');
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% Set default action and enable gui interaction
sAction = 'Cancel';
uiwait(hF);
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% uiresume was triggered (in fMouseActionFcn) -> return
if strcmp(sAction, 'OK')
iList = get(hList, 'Value');
csVarOut = cell(length(iList), 1);
for iI = 1:length(iList)
csVarOut(iI) = csVars(iList(iI));
end
end
try
close(hF);
catch %#ok<CTCH>
csVarOut = {};
end
% -------------------------------------------------------------------------
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * *
% * * NESTED FUNCTION fMouseActionFcn (nested in fGetWorkspaceVar)
% * *
% * * Determine whether axes are linked
% * *
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
function fMouseActionFcn(hObject, eventdata)
if isfield(eventdata, 'Key')
switch eventdata.Key
case 'escape', uiresume(hF);
case 'return'
sAction = 'OK';
uiresume(hF);
end
end
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% React on action depending on its source component
switch(hObject)
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% Click in LISBOX: return if double-clicked
case hList
if strcmp(get(hF, 'SelectionType'), 'open')
sAction = 'OK';
uiresume(hF);
end
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% OK button
case hButOK
sAction = 'OK';
uiresume(hF);
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
otherwise
end
% End of switch statement
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
end
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
% * * END NESTED FUNCTION fGridMouseMoveFcn
% = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
end
% =========================================================================
% *** END FUNCTION fWSImport (and its nested functions)
% =========================================================================
|
github
|
jacksky64/imageProcessing-master
|
viewer3d.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/viewer3d.m
| 242,127 |
utf_8
|
54313e095ad9115e782e9c7c86fd600b
|
function varargout = viewer3d(varargin)
% VIEWER3D is a Matlab GUI for fast shearwarp volume rendering. It also
% allows segmentation and measurements in the imagedata.
%
%
% Just start with
% VIEWER3D
%
% Or to display one or more matlab volumes
%
% VIEWER3D(V); VIEWER3D(V1,V2,V3 ....);
%
%
% inputs,
% V : 2D, 3D or 4D Input image, of type double, single, uint8,
% uint16, uint32, int8, int16 or int32
% (the render process uses only double calculations)
%
% example,
% % Load data
% load('ExampleData\CommandlineData.mat');
% viewer3d(V);
%
% See also: render
%
% Function is written by D.Kroon University of Twente (January 2008 - January 2011)
% Edit the above text to modify the response to help viewer3ds
% Last Modified by GUIDE v2.5 12-Jan-2011 14:34:37
% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d is made visible.
function viewer3d_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d (see VARARGIN)
% Choose default command line output for viewer3d
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% addpath mexcode and help
functiondir=getFunctionFolder();
addpath(functiondir);
addpath([functiondir '/Help']);
addpath([functiondir '/ReadData3D']);
addpath(genpath([functiondir '/SubFunctions']));
data.Menu=showmenu(hObject);
% Store handles to the figure menu
for i=1:length(data.Menu)
z2=data.Menu(i);
data.handles.(z2.Tag)=z2.Handle;
if(isfield(z2,'Children')&&~isempty(z2.Children))
for j=1:length(z2.Children)
z3=z2.Children(j);
data.handles.(z3.Tag)=z3.Handle;
end
end
end
data.handles.figure1=hObject;
% Disable warning
warning('off', 'MATLAB:maxNumCompThreads:Deprecated')
data.mouse.pressed=false;
data.mouse.button='arrow';
data.mouse.action='';
% Save the default config
filename_config=[functiondir '/default_config.mat'];
if(exist(filename_config,'file'))
load(filename_config,'config')
data.config=config;
else
data.config.VolumeScaling=100;
data.config.VolumeSize=32;
data.config.ImageSizeRender=400;
data.config.PreviewVolumeSize=32;
data.config.ShearInterpolation= 'bilinear';
data.config.WarpInterpolation= 'bilinear';
data.config.PreRender= 0;
data.config.StoreXYZ=0;
end
% Check if history information is present from a previous time
historyfile=[functiondir '/lastfiles.mat'];
if(exist(historyfile,'file')),
load(historyfile);
data.history=history;
else
for i=1:5, data.history.filenames{i}=''; end
end
data.history.historyfile=historyfile;
data.rendertypes(1).label='None';
data.rendertypes(1).type='black';
data.rendertypes(2).label='View X slice';
data.rendertypes(2).type='slicex';
data.rendertypes(3).label='View Y slice';
data.rendertypes(3).type='slicey';
data.rendertypes(4).label='View Z slice';
data.rendertypes(4).type='slicez';
data.rendertypes(5).label='MIP';
data.rendertypes(5).type='mip';
data.rendertypes(6).label='Greyscale';
data.rendertypes(6).type='vr';
data.rendertypes(7).label='Color';
data.rendertypes(7).type='vrc';
data.rendertypes(8).label='Shaded';
data.rendertypes(8).type='vrs';
data.figurehandles.viewer3d=gcf;
data.figurehandles.histogram=[];
data.figurehandles.console=[];
data.figurehandles.voxelsize=[];
data.figurehandles.lightvector=[];
data.figurehandles.contrast=[];
data.figurehandles.qualityspeed=[];
data.volumes=[];
data.substorage=[];
data.axes_select=[];
data.volume_select=[];
data.subwindow=[];
data.NumberWindows=0;
data.MenuVolume=[];
data=loadmousepointershapes(data);
data.NumberWindows=1;
data=addWindows(data);
setMyData(data);
showhistory(data);
allshow3d(false,true);
% Get input voxel volume and convert to double
if (~isempty(varargin)),
if(ndims(varargin{1})>=2)
for i=1:length(varargin);
V=varargin{i};
volumemax=double(max(V(:))); volumemin=double(min(V(:)));
info=struct;
info.WindowWidth=volumemax-volumemin;
info.WindowLevel=0.5*(volumemax+volumemin);
if(isnumeric(V)), addVolume(V,[1 1 1],info); end
end
else
error('viewer3d:inputs', 'Input image not 3 dimensional');
end
end
function addVolume(V,Scales,Info,Editable)
if(nargin<2), Scales=[1 1 1]; end
if(nargin<3), Info=[]; end
if(nargin<4), Editable=false; end
data=getMyData(); if(isempty(data)), return, end
for i=1:size(V,4)
data=addOneVolume(data,V(:,:,:,i),Scales,Info,Editable);
end
data=addWindowsMenus(data);
setMyData(data);
addMenuVolume();
function data=addOneVolume(data,V,Scales,Info,Editable)
nv=length(data.volumes)+1;
data.volumes(nv).Editable=Editable;
data.volumes(nv).WindowWidth=1;
data.volumes(nv).WindowLevel=0.5;
data.volumes(nv).volume_original=V;
data.volumes(nv).volume_scales=[1 1 1];
data.volumes(nv).info=Info;
data.volumes(nv).id=rand;
data.volumes(nv).Scales=Scales;
if(ndims(V)==2)
data.volumes(nv).Size_original=[size(V) 1];
else
data.volumes(nv).Size_original=size(V);
end
name=['Volume ' num2str(nv)];
while(~isempty(structfind(data.volumes,'name',name)))
name=['Volume ' num2str(round(rand*10000))];
end
data.volumes(nv).name=name;
data.volumes(nv).MeasureList=[];
data.volumes(nv).histogram_pointselected=[];
data=checkvolumetype(data,nv);
data=makeVolumeXY(data,nv);
data=computeNormals(data,nv);
data=makePreviewVolume(data,nv);
data=makeRenderVolume(data,nv);
if(~isempty(Info)),
if(isfield(Info,'WindowWidth'));
data.volumes(nv).WindowWidth=Info.WindowWidth;
end
if (isfield(Info,'WindowCenter'));
data.volumes(nv).WindowLevel=Info.WindowCenter;
end
if (isfield(Info,'WindowLevel'));
data.volumes(nv).WindowLevel=Info.WindowLevel;
end
end
data.volumes(nv).histogram_positions = [0 0.2 0.4 0.6 1];
data.volumes(nv).histogram_positions= data.volumes(nv).histogram_positions*(data.volumes(nv).volumemax-data.volumes(nv).volumemin)+data.volumes(nv).volumemin;
data.volumes(nv).histogram_alpha = [0 0.03 0.1 0.35 1];
data.volumes(nv).histogram_colors= [0 0 0; 0.7 0 0; 1 0 0; 1 1 0; 1 1 1];
data=createAlphaColorTable(nv,data);
function data=makePreviewVolume(data,dvs)
if(data.config.PreviewVolumeSize==100)
data.volumes(dvs).volume_preview=data.volumes(dvs).volume_original;
else
t=data.config.PreviewVolumeSize;
data.volumes(dvs).volume_preview=imresize3d(data.volumes(dvs).volume_original,[],[t t t],'linear');
end
if(ndims(data.volumes(dvs).volume_preview)==2)
data.volumes(dvs).Size_preview=[size(data.volumes(dvs).volume_preview) 1];
else
data.volumes(dvs).Size_preview=size(data.volumes(dvs).volume_preview);
end
function functiondir=getFunctionFolder()
functionname='viewer3d.m';
functiondir=which(functionname);
functiondir=functiondir(1:end-length(functionname));
function data=makeRenderVolume(data,dvs)
if(data.config.VolumeScaling==100)
data.volumes(dvs).volume=data.volumes(dvs).volume_original;
else
data.volumes(dvs).volume=imresize3d(data.volumes(dvs).volume_original,data.config.VolumeScaling/100,[],'linear');
end
if(ndims(data.volumes(dvs).volume)==2)
data.volumes(dvs).Size=[size(data.volumes(dvs).volume) 1];
else
data.volumes(dvs).Size=size(data.volumes(dvs).volume);
end
function data=createAlphaColorTable(i,data)
% This function creates a Matlab colormap and alphamap from the markers
if(nargin<2)
data=getMyData(); if(isempty(data)), return, end
end
if(nargin>0),
dvs=i;
else
dvs=data.volume_select;
end
check=~isfield(data.volumes(dvs),'histogram_positions');
if(~check), check=isempty(data.volumes(dvs).histogram_positions); end
if(check)
data.volumes(dvs).histogram_positions = [0 0.2 0.4 0.6 1];
data.volumes(dvs).histogram_positions= data.volumes(dvs).histogram_positions*(data.volumes(dvs).volumemax-data.volumes(dvs).volumemin)+data.volumes(dvs).volumemin;
data.volumes(dvs).histogram_alpha = [0 0.03 0.1 0.35 1];
data.volumes(dvs).histogram_colors= [0 0 0; 0.7 0 0; 1 0 0; 1 1 0; 1 1 1];
setMyData(data);
end
histogram_positions=data.volumes(dvs).histogram_positions;
data.volumes(dvs).colortable=zeros(1000,3);
data.volumes(dvs).alphatable=zeros(1000,1);
% Loop through all 256 color/alpha indexes
i=linspace(data.volumes(dvs).volumemin,data.volumes(dvs).volumemax,1000);
for j=1:1000
if (i(j)< histogram_positions(1)), alpha=0; color=data.volumes(dvs).histogram_colors(1,:);
elseif(i(j)> histogram_positions(end)), alpha=0; color=data.volumes(dvs).histogram_colors(end,:);
elseif(i(j)==histogram_positions(1)), alpha=data.volumes(dvs).histogram_alpha(1); color=data.volumes(dvs).histogram_colors(1,:);
elseif(i(j)==histogram_positions(end)), alpha=data.volumes(dvs).histogram_alpha(end); color=data.volumes(dvs).histogram_colors(end,:);
else
% Linear interpolate the color and alpha between markers
index_down=find(histogram_positions<=i(j)); index_down=index_down(end);
index_up =find(histogram_positions>i(j) ); index_up=index_up(1);
perc= (i(j)-histogram_positions(index_down)) / (histogram_positions(index_up) - histogram_positions(index_down));
color=(1-perc)*data.volumes(dvs).histogram_colors(index_down,:)+perc*data.volumes(dvs).histogram_colors(index_up,:);
alpha=(1-perc)*data.volumes(dvs).histogram_alpha(index_down)+perc*data.volumes(dvs).histogram_alpha(index_up);
end
data.volumes(dvs).colortable(j,:)=color;
data.volumes(dvs).alphatable(j)=alpha;
end
if(nargin<2)
setMyData(data);
end
function data=loadmousepointershapes(data)
I=[0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0; 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0;
0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0; 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0;
0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0; 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0;
0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0; 0 0 1 0 0 0 1 1 1 1 0 0 0 0 0 0;
0 1 1 1 1 1 0 1 0 0 1 1 1 1 1 1; 1 1 1 1 0 0 0 1 0 0 0 0 0 0 1 1;
1 1 1 1 0 0 0 1 0 0 0 0 0 1 1 1; 1 0 0 0 0 0 0 0 1 0 1 0 0 0 1 1;
0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 1; 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0;
0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0; 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0];
I(I==0)=NaN; data.icons.icon_mouse_rotate1=I;
I=[1 0 0 0 0 1 1 1 1 1 1 0 0 0 0 0; 1 1 0 1 1 1 1 1 1 1 1 1 1 0 0 0;
1 1 1 1 1 1 0 0 0 0 0 1 1 1 0 0; 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0;
1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0; 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0;
1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0; 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0;
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0; 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1;
0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 1; 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 1;
0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 1; 0 0 1 1 1 0 0 0 0 0 1 1 1 1 1 1;
0 0 0 1 1 1 1 1 1 1 1 1 1 0 1 1; 0 0 0 0 0 1 1 1 1 1 1 0 0 0 0 1];
I(I==0)=NaN; data.icons.icon_mouse_rotate2=I;
I=[0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0; 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0;
0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0; 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0;
1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0; 1 0 0 1 1 1 1 1 0 0 1 0 0 0 0 0;
1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0; 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0;
0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0; 0 0 1 0 0 0 0 1 1 1 1 0 0 0 0 0;
0 0 0 1 1 1 1 0 0 1 1 1 0 0 0 0; 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0;
0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0; 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0;
0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1; 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1];
I(I==0)=NaN; data.icons.icon_mouse_zoom=I;
I=[0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0; 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0;
0 0 0 0 0 1 1 0 1 1 0 0 0 0 0 0; 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0;
0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0; 0 0 1 1 0 0 0 1 0 0 0 1 1 0 0 0;
0 1 1 0 0 0 0 1 0 0 0 0 1 1 0 0; 1 0 0 1 1 1 1 1 1 1 1 1 0 0 1 0;
0 1 1 0 0 0 0 1 0 0 0 0 1 1 0 0; 0 0 1 1 0 0 0 1 0 0 0 1 1 0 0 0;
0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0; 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0;
0 0 0 0 0 1 1 0 1 1 0 0 0 0 0 0; 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0;
0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0; 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0];
I(I==0)=NaN; data.icons.icon_mouse_pan=I;
function allshow3d(preview,render_new_image)
data=getMyData(); if(isempty(data)), return, end
for i=1:data.NumberWindows
show3d(preview,render_new_image,i);
end
function show3d(preview,render_new_image,wsel)
data=getMyData(); if(isempty(data)), return, end
tic;
if(nargin<3)
wsel=data.axes_select;
else
data.axes_select=wsel;
end
dvss=structfind(data.volumes,'id',data.subwindow(wsel).volume_id_select(1));
nvolumes=length(data.subwindow(wsel).volume_id_select);
if(isempty(dvss)),
data.subwindow(wsel).render_type='black';
datarender.RenderType='black';
datarender.ImageSize=[data.config.ImageSizeRender data.config.ImageSizeRender];
datarender.imin=0; datarender.imax=1;
renderimage = render(zeros(3,3,3),datarender);
data.subwindow(wsel).render_image(1).image=renderimage;
else
if(render_new_image)
for i=1:nvolumes
dvss=structfind(data.volumes,'id',data.subwindow(wsel).volume_id_select(i));
data.subwindow(wsel).render_image(i).image=MakeRenderImage(data,dvss,wsel,preview);
end
end
if(nvolumes==1), combine='trans'; else combine=data.subwindow(wsel).combine; end
for i=1:nvolumes
dvss=structfind(data.volumes,'id',data.subwindow(wsel).volume_id_select(i));
renderimage1=LevelRenderImage(data.subwindow(wsel).render_image(i).image,data,dvss,wsel);
if(i==1)
switch(combine)
case 'trans'
renderimage=renderimage1;
case 'rgb'
renderimage=zeros([size(renderimage1,1) size(renderimage1,2) 3]);
renderimage(:,:,i)=mean(renderimage1,3);
end
else
switch(combine)
case 'trans'
renderimage=renderimage+renderimage1;
case 'rgb'
renderimage(:,:,i)=mean(renderimage1,3);
end
end
end
switch(combine)
case 'trans'
if(nvolumes>1), renderimage=renderimage*(1/nvolumes); end
end
end
data.subwindow(wsel).total_image=renderimage;
% Add position information etc. to the rendered image
data=InfoOnScreen(data);
data=showMeasureList(data);
% To range
data.subwindow(wsel).total_image(data.subwindow(wsel).total_image<0)=0;
data.subwindow(wsel).total_image(data.subwindow(wsel).total_image>1)=1;
if(data.subwindow(wsel).first_render)
data.subwindow(wsel).imshow_handle=imshow(data.subwindow(wsel).total_image,'Parent',data.subwindow(wsel).handles.axes); drawnow('expose')
data.subwindow(wsel).first_render=false;
else
set(data.subwindow(wsel).imshow_handle,'Cdata',data.subwindow(wsel).total_image);
end
data.subwindow(wsel).axes_size=get(data.subwindow(wsel).handles.axes,'PlotBoxAspectRatio');
set(get(data.subwindow(wsel).handles.axes,'Children'),'ButtonDownFcn','viewer3d(''axes_ButtonDownFcn'',gcbo,[],guidata(gcbo))');
data=console_addline(data,['Render Time : ' num2str(toc)]);
setMyData(data);
function renderimage=MakeRenderImage(data,dvss,wsel,preview)
datarender=struct();
datarender.ImageSize=[data.config.ImageSizeRender data.config.ImageSizeRender];
datarender.imin=data.volumes(dvss).volumemin;
datarender.imax=data.volumes(dvss).volumemax;
switch data.subwindow(wsel).render_type
case 'mip'
datarender.RenderType='mip';
datarender.ShearInterp=data.config.ShearInterpolation;
datarender.WarpInterp=data.config.WarpInterpolation;
case 'vr'
datarender.RenderType='bw';
datarender.AlphaTable=data.volumes(dvss).alphatable;
datarender.ShearInterp=data.config.ShearInterpolation;
datarender.WarpInterp=data.config.WarpInterpolation;
case 'vrc'
datarender.RenderType='color';
datarender.AlphaTable=data.volumes(dvss).alphatable;
datarender.ColorTable=data.volumes(dvss).colortable;
datarender.ShearInterp=data.config.ShearInterpolation;
datarender.WarpInterp=data.config.WarpInterpolation;
case 'vrs'
datarender.RenderType='shaded';
datarender.AlphaTable=data.volumes(dvss).alphatable; datarender.ColorTable=data.volumes(dvss).colortable;
datarender.LightVector=data.subwindow(wsel).LightVector; datarender.ViewerVector=data.subwindow(wsel).ViewerVector;
datarender.ShadingMaterial=data.subwindow(wsel).shading_material;
datarender.ShearInterp=data.config.ShearInterpolation;
datarender.WarpInterp=data.config.WarpInterpolation;
case 'slicex'
datarender.RenderType='slicex';
datarender.ColorTable=data.volumes(dvss).colortable;
datarender.SliceSelected=data.subwindow(wsel).SliceSelected(1);
datarender.WarpInterp='bicubic';
datarender.ColorSlice=data.subwindow(data.axes_select).ColorSlice;
case 'slicey'
datarender.RenderType='slicey';
datarender.ColorTable=data.volumes(dvss).colortable;
datarender.SliceSelected=data.subwindow(wsel).SliceSelected(2);
datarender.WarpInterp='bicubic';
datarender.ColorSlice=data.subwindow(data.axes_select).ColorSlice;
case 'slicez'
datarender.RenderType='slicez';
datarender.ColorTable=data.volumes(dvss).colortable;
datarender.SliceSelected=data.subwindow(wsel).SliceSelected(3);
datarender.WarpInterp='bicubic';
datarender.ColorSlice=data.subwindow(data.axes_select).ColorSlice;
case 'black'
datarender.RenderType='black';
end
if(preview)
switch data.subwindow(wsel).render_type
case {'slicex','slicey','slicez'}
datarender.WarpInterp='nearest';
datarender.Mview=data.subwindow(wsel).viewer_matrix;
renderimage = render(data.volumes(dvss).volume_original, datarender);
otherwise
R=ResizeMatrix(data.volumes(dvss).Size_preview./data.volumes(dvss).Size_original);
datarender.Mview=data.subwindow(wsel).viewer_matrix*R;
renderimage = render(data.volumes(dvss).volume_preview,datarender);
end
else
mouse_button_old=data.mouse.button;
set_mouse_shape('watch',data); drawnow('expose');
switch data.subwindow(wsel).render_type
case {'slicex','slicey','slicez'}
datarender.Mview=data.subwindow(wsel).viewer_matrix;
renderimage = render(data.volumes(dvss).volume_original, datarender);
case 'black'
renderimage = render(data.volumes(dvss).volume, datarender);
otherwise
datarender.Mview=data.subwindow(wsel).viewer_matrix*ResizeMatrix(data.volumes(dvss).Size./data.volumes(dvss).Size_original);
datarender.VolumeX=data.volumes(dvss).volumex;
datarender.VolumeY=data.volumes(dvss).volumey;
datarender.Normals=data.volumes(dvss).normals;
renderimage = render(data.volumes(dvss).volume, datarender);
end
set_mouse_shape(mouse_button_old,data); drawnow('expose');
end
function renderimage=LevelRenderImage(renderimage,data,dvss,wsel)
if(~isempty(dvss))
switch data.subwindow(wsel).render_type
case {'mip','slicex', 'slicey', 'slicez'}
% The render image is scaled to fit to [0..1], perform both back scaling
% and Window level and Window width
if ((ndims(renderimage)==2)&&(data.volumes(dvss).WindowWidth~=0||data.volumes(dvss).WindowLevel~=0))
m=(data.volumes(dvss).volumemax-data.volumes(dvss).volumemin)*(1/data.volumes(dvss).WindowWidth);
o=(data.volumes(dvss).volumemin-data.volumes(dvss).WindowLevel)*(1/data.volumes(dvss).WindowWidth)+0.5;
renderimage=renderimage*m+o;
end
end
end
function data=set_initial_view_matrix(data)
dvss=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
switch data.subwindow(data.axes_select).render_type
case 'slicex'
data.subwindow(data.axes_select).viewer_matrix=[data.volumes(dvss).Scales(1)*data.subwindow(data.axes_select).Zoom 0 0 0; 0 data.volumes(dvss).Scales(2)*data.subwindow(data.axes_select).Zoom 0 0; 0 0 data.volumes(dvss).Scales(3)*data.subwindow(data.axes_select).Zoom 0; 0 0 0 1];
data.subwindow(data.axes_select).viewer_matrix=[0 0 1 0;0 1 0 0; -1 0 0 0;0 0 0 1]*data.subwindow(data.axes_select).viewer_matrix;
case 'slicey'
data.subwindow(data.axes_select).viewer_matrix=[data.volumes(dvss).Scales(1)*data.subwindow(data.axes_select).Zoom 0 0 0; 0 data.volumes(dvss).Scales(2)*data.subwindow(data.axes_select).Zoom 0 0; 0 0 data.volumes(dvss).Scales(3)*data.subwindow(data.axes_select).Zoom 0; 0 0 0 1];
data.subwindow(data.axes_select).viewer_matrix=[1 0 0 0;0 0 -1 0; 0 1 0 0;0 0 0 1]*data.subwindow(data.axes_select).viewer_matrix;
case 'slicez'
data.subwindow(data.axes_select).viewer_matrix=[data.volumes(dvss).Scales(1)*data.subwindow(data.axes_select).Zoom 0 0 0; 0 data.volumes(dvss).Scales(2)*data.subwindow(data.axes_select).Zoom 0 0; 0 0 data.volumes(dvss).Scales(3)*data.subwindow(data.axes_select).Zoom 0; 0 0 0 1];
data.subwindow(data.axes_select).viewer_matrix=data.subwindow(data.axes_select).viewer_matrix*[1 0 0 0;0 1 0 0; 0 0 1 0;0 0 0 1];
otherwise
data.subwindow(data.axes_select).viewer_matrix=[data.volumes(dvss).Scales(1)*data.subwindow(data.axes_select).Zoom 0 0 0; 0 data.volumes(dvss).Scales(2)*data.subwindow(data.axes_select).Zoom 0 0; 0 0 data.volumes(dvss).Scales(3)*data.subwindow(data.axes_select).Zoom 0; 0 0 0 1];
end
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
function set_menu_checks(data)
for i=1:data.NumberWindows
C=data.subwindow(i).menu.Children(2).Children;
for j=1:length(C)
set(C(j).Handle,'Checked','off');
end
D=data.subwindow(i).menu.Children(3).Children;
s=structfind(D,'Tag','menu_config_slicescolor');
set(D(s).Handle,'Checked','off');
if(data.subwindow(i).ColorSlice)
set(D(s).Handle,'Checked','on');
end
s1=structfind(D,'Tag','menu_metal');
s2=structfind(D,'Tag','menu_shiny');
s3=structfind(D,'Tag','menu_dull');
set(D(s1).Handle,'Checked','off');
set(D(s2).Handle,'Checked','off');
set(D(s3).Handle,'Checked','off');
switch(data.subwindow(i).shading_material)
case 'metal'
set(D(s1).Handle,'Checked','on');
case 'shiny'
set(D(s2).Handle,'Checked','on');
case 'dull'
set(D(s3).Handle,'Checked','on');
end
s1=structfind(D,'Tag','menu_combine_trans');
s2=structfind(D,'Tag','menu_combine_rgb');
set(D(s1).Handle,'Checked','off');
set(D(s2).Handle,'Checked','off');
switch(data.subwindow(i).combine)
case 'trans'
set(D(s1).Handle,'Checked','on');
case 'rgb'
set(D(s2).Handle,'Checked','on');
end
if(data.subwindow(i).volume_id_select(1)>0)
n=length(data.subwindow(i).volume_id_select);
st=['wmenu-' num2str(i)];
for j=1:n
dvss=structfind(data.volumes,'id',data.subwindow(i).volume_id_select(j));
st=[st '-' num2str(dvss)];
end
Ci=structfind(C,'Tag',st);
else
Ci=1;
end
if(~isempty(Ci))
set(C(Ci).Handle,'Checked','on');
end
d=get(data.subwindow(i).menu.Children(1).Handle,'Children');
e=zeros(size(d));
for j=1:length(d), set(d(j),'Checked','off'); e(j)=get(d(j),'Position'); end
[t,in]=sort(e); d=d(in);
dv=structfind(data.rendertypes,'type',data.subwindow(i).render_type);
set(d(dv),'Checked','on');
sl=strcmp(data.subwindow(i).render_type(1:min(5,end)),'slice');
if(sl)
set(data.subwindow(i).menu.Children(4).Handle,'Enable','on')
id=data.subwindow(i).volume_id_select;
editable=false(1,length(id));
for k=1:length(id)
editable(k)=data.volumes(structfind(data.volumes,'id',data.subwindow(i).volume_id_select(k))).Editable;
end
if(any(editable))
set(data.subwindow(i).menu.Children(5).Handle,'Enable','on')
else
set(data.subwindow(i).menu.Children(5).Handle,'Enable','off')
end
else
set(data.subwindow(i).menu.Children(4).Handle,'Enable','off')
set(data.subwindow(i).menu.Children(5).Handle,'Enable','off')
end
end
menubar;
% --- Executes on mouse motion over figure - except title and menu.
function figure1_WindowButtonMotionFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
menubar('MotionFcn',gcf);
cursor_position_in_axes(hObject,handles);
data=getMyData(); if(isempty(data)), return, end
if(isempty(data.axes_select)), return, end
if(strcmp(data.subwindow(data.axes_select).render_type,'black')), return; end
if((length(data.subwindow(data.axes_select).render_type)>5)&&strcmp(data.subwindow(data.axes_select).render_type(1:5),'slice'))
data=mouseposition_to_voxelposition(data);
setMyData(data);
end
if(data.mouse.pressed)
switch(data.mouse.button)
case 'rotate1'
r1=-360*(data.subwindow(data.axes_select).mouse_position_last(1)-data.subwindow(data.axes_select).mouse_position(1));
r2=360*(data.subwindow(data.axes_select).mouse_position_last(2)-data.subwindow(data.axes_select).mouse_position(2));
R=RotationMatrix([r1 r2 0]);
data.subwindow(data.axes_select).viewer_matrix=R*data.subwindow(data.axes_select).viewer_matrix;
setMyData(data);
show3d(true,true)
case 'rotate2'
r1=100*(data.subwindow(data.axes_select).mouse_position_last(1)-data.subwindow(data.axes_select).mouse_position(1));
r2=100*(data.subwindow(data.axes_select).mouse_position_last(2)-data.subwindow(data.axes_select).mouse_position(2));
if(data.subwindow(data.axes_select).mouse_position(2)>0.5), r1=-r1; end
if(data.subwindow(data.axes_select).mouse_position(1)<0.5), r2=-r2; end
r3=r1+r2;
R=RotationMatrix([0 0 r3]);
data.subwindow(data.axes_select).viewer_matrix=R*data.subwindow(data.axes_select).viewer_matrix;
setMyData(data);
show3d(true,true)
case 'pan'
t2=200*(data.subwindow(data.axes_select).mouse_position_last(1)-data.subwindow(data.axes_select).mouse_position(1));
t1=200*(data.subwindow(data.axes_select).mouse_position_last(2)-data.subwindow(data.axes_select).mouse_position(2));
M=TranslateMatrix([t1 t2 0]);
data.subwindow(data.axes_select).viewer_matrix=M*data.subwindow(data.axes_select).viewer_matrix;
setMyData(data);
show3d(true,true)
case 'zoom'
z1=1+2*(data.subwindow(data.axes_select).mouse_position_last(1)-data.subwindow(data.axes_select).mouse_position(1));
z2=1+2*(data.subwindow(data.axes_select).mouse_position_last(2)-data.subwindow(data.axes_select).mouse_position(2));
z=0.5*(z1+z2);
R=ResizeMatrix([z z z]);
data.subwindow(data.axes_select).Zoom=data.subwindow(data.axes_select).Zoom*(1/z);
data.subwindow(data.axes_select).viewer_matrix=R*data.subwindow(data.axes_select).viewer_matrix;
setMyData(data);
show3d(true,true)
case 'drag'
id=data.subwindow(data.axes_select).object_id_select;
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
n=structfind(data.volumes(dvs).MeasureList,'id',id(1));
object=data.volumes(dvs).MeasureList(n);
s=round(id(3)*length(object.x));
if(s==0)
object.x=object.x-mean(object.x(:))+ data.subwindow(data.axes_select).VoxelLocation(1);
object.y=object.y-mean(object.y(:))+ data.subwindow(data.axes_select).VoxelLocation(2);
object.z=object.z-mean(object.z(:))+ data.subwindow(data.axes_select).VoxelLocation(3);
else
object.x(s)=data.subwindow(data.axes_select).VoxelLocation(1);
object.y(s)=data.subwindow(data.axes_select).VoxelLocation(2);
object.z(s)=data.subwindow(data.axes_select).VoxelLocation(3);
end
switch object.type
case 'd'
dx=data.volumes(dvs).Scales(1)*(object.x(1)-object.x(2));
dy=data.volumes(dvs).Scales(2)*(object.y(1)-object.y(2));
dz=data.volumes(dvs).Scales(3)*(object.z(1)-object.z(2));
distance=sqrt(dx.^2+dy.^2+dz.^2);
object.varmm=distance;
otherwise
end
data.volumes(dvs).MeasureList(n)=object;
setMyData(data);
show3d(false,false)
otherwise
end
end
function R=RotationMatrix(r)
% Determine the rotation matrix (View matrix) for rotation angles xyz ...
Rx=[1 0 0 0; 0 cosd(r(1)) -sind(r(1)) 0; 0 sind(r(1)) cosd(r(1)) 0; 0 0 0 1];
Ry=[cosd(r(2)) 0 sind(r(2)) 0; 0 1 0 0; -sind(r(2)) 0 cosd(r(2)) 0; 0 0 0 1];
Rz=[cosd(r(3)) -sind(r(3)) 0 0; sind(r(3)) cosd(r(3)) 0 0; 0 0 1 0; 0 0 0 1];
R=Rx*Ry*Rz;
function M=ResizeMatrix(s)
M=[1/s(1) 0 0 0;
0 1/s(2) 0 0;
0 0 1/s(3) 0;
0 0 0 1];
function M=TranslateMatrix(t)
M=[1 0 0 -t(1);
0 1 0 -t(2);
0 0 1 -t(3);
0 0 0 1];
function cursor_position_in_axes(hObject,handles)
data=getMyData(); if(isempty(data)), return, end;
if(isempty(data.axes_select)), return, end
data.subwindow(data.axes_select).mouse_position_last=data.subwindow(data.axes_select).mouse_position;
% Get position of the mouse in the large axes
% p = get(0, 'PointerLocation');
% pf = get(hObject, 'pos');
% p(1:2) = p(1:2)-pf(1:2);
% set(gcf, 'CurrentPoint', p(1:2));
h=data.subwindow(data.axes_select).handles.axes;
if(~ishandle(h)), return; end
p = get(h, 'CurrentPoint');
if (~isempty(p))
data.subwindow(data.axes_select).mouse_position=[p(1, 1) p(1, 2)]./data.subwindow(data.axes_select).axes_size(1:2);
end
setMyData(data);
function setMyData(data,handle)
% Store data struct in figure
if(nargin<2), handle=gcf; end
setappdata(handle,'data3d',data);
function data=getMyData(handle)
% Get data struct stored in figure
if(nargin<1), handle=gcf; end
data=getappdata(handle,'data3d');
% --- Executes on mouse press over axes background.
function axes_ButtonDownFcn(hObject, eventdata, handles)
% hObject handle to axes1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
ha=zeros(1,data.NumberWindows);
for i=1:data.NumberWindows, ha(i)=data.subwindow(i).handles.axes; end
data.axes_select=find(ha==gca);
data.mouse.pressed=true;
data.mouse.button=get(handles.figure1,'SelectionType');
data.subwindow(data.axes_select).mouse_position_pressed=data.subwindow(data.axes_select).mouse_position;
if(strcmp(data.mouse.button,'normal'))
sr=strcmp(data.subwindow(data.axes_select).render_type(1:min(end,5)),'slice');
if(sr)
switch(data.mouse.action)
case 'measure_distance'
if(getnumberofpoints(data)==0)
% Do measurement
data=addMeasureList('p',data.subwindow(data.axes_select).VoxelLocation(1),data.subwindow(data.axes_select).VoxelLocation(2),data.subwindow(data.axes_select).VoxelLocation(3),0,data);
data.mouse.button='select_distance';
data.mouse.pressed=false;
setMyData(data);
show3d(false,false);
return
elseif(getnumberofpoints(data)>0)
VoxelLocation1=[data.volumes(dvs).MeasureList(end).x data.volumes(dvs).MeasureList(end).y data.volumes(dvs).MeasureList(end).z];
VoxelLocation2=data.subwindow(data.axes_select).VoxelLocation;
% First remove the point (will be replaced by distance)
data=rmvMeasureList(data.volumes(dvs).MeasureList(end).id,data);
% Do measurement
x=[VoxelLocation1(1) VoxelLocation2(1)];
y=[VoxelLocation1(2) VoxelLocation2(2)];
z=[VoxelLocation1(3) VoxelLocation2(3)];
dx=data.volumes(dvs).Scales(1)*(x(1)-x(2));
dy=data.volumes(dvs).Scales(2)*(y(1)-y(2));
dz=data.volumes(dvs).Scales(3)*(z(1)-z(2));
distance=sqrt(dx.^2+dy.^2+dz.^2);
data=addMeasureList('d',x,y,z,distance,data);
data.mouse.action='';
data.mouse.pressed=false;
setMyData(data);
show3d(false,false);
return
end
case 'measure_landmark'
data=addMeasureList('l',data.subwindow(data.axes_select).VoxelLocation(1),data.subwindow(data.axes_select).VoxelLocation(2),data.subwindow(data.axes_select).VoxelLocation(3),0,data);
data.mouse.button='select_landmark';
data.mouse.action='';
data.mouse.pressed=false;
setMyData(data);
show3d(false,false);
return
case 'segment_click_roi'
% Do measurement
[vx,vy,vz]=getClickRoi(data);
for i=1:length(vx), data=addMeasureList('p',vx(i),vy(i),vz(i),0,data); end
data=points2roi(data,false);
data.mouse.button='click_roi';
data.subwindow(data.axes_select).click_roi=false;
data.mouse.pressed=false;
setMyData(data);
show3d(false,false);
return
case 'measure_roi'
% Do measurement
data=addMeasureList('p',data.subwindow(data.axes_select).VoxelLocation(1),data.subwindow(data.axes_select).VoxelLocation(2),data.subwindow(data.axes_select).VoxelLocation(3),0,data);
data.mouse.button='select_roi';
data.mouse.pressed=false;
setMyData(data);
show3d(false,false);
return
case 'segment_roi'
% Do measurement
data=addMeasureList('p',data.subwindow(data.axes_select).VoxelLocation(1),data.subwindow(data.axes_select).VoxelLocation(2),data.subwindow(data.axes_select).VoxelLocation(3),0,data);
data.mouse.button='select_roi';
data.mouse.pressed=false;
setMyData(data);
show3d(true,false);
return
otherwise
id_detect=getHitMapClick(data);
if(id_detect(1)>0)
data.subwindow(data.axes_select).object_id_select=id_detect;
data.mouse.button='drag';
setMyData(data);
return;
end
end
end
distance_center=sum((data.subwindow(data.axes_select).mouse_position-[0.5 0.5]).^2);
if((distance_center<0.15)&&data.subwindow(data.axes_select).render_type(1)~='s')
data.mouse.button='rotate1';
set_mouse_shape('rotate1',data)
else
data.mouse.button='rotate2';
set_mouse_shape('rotate2',data)
end
end
if(strcmp(data.mouse.button,'open'))
switch(data.mouse.action)
case 'measure_roi'
data=addMeasureList('p',data.subwindow(data.axes_select).VoxelLocation(1),data.subwindow(data.axes_select).VoxelLocation(2),data.subwindow(data.axes_select).VoxelLocation(3),0,data);
data=points2roi(data,false);
data.mouse.action='';
data.mouse.pressed=false;
setMyData(data);
show3d(false,false);
return
case 'segment_roi'
data=addMeasureList('p',data.subwindow(data.axes_select).VoxelLocation(1),data.subwindow(data.axes_select).VoxelLocation(2),data.subwindow(data.axes_select).VoxelLocation(3),0,data);
data=points2roi(data,true);
data.mouse.action='';
data.mouse.pressed=false;
setMyData(data);
show3d(false,true);
return
otherwise
end
end
if(strcmp(data.mouse.button,'extend'))
data.mouse.button='pan';
set_mouse_shape('pan',data)
end
if(strcmp(data.mouse.button,'alt'))
if(data.subwindow(data.axes_select).render_type(1)=='s')
id_detect=getHitMapClick(data);
if(id_detect(1)>0)
data=rmvMeasureList(id_detect(1),data);
setMyData(data);
show3d(false,false);
return;
end
end
data.mouse.button='zoom';
set_mouse_shape('zoom',data);
end
setMyData(data);
function id_detect=getHitMapClick(data)
% Get the mouse position
x_2d=data.subwindow(data.axes_select).mouse_position(2);
y_2d=data.subwindow(data.axes_select).mouse_position(1);
% To rendered image position
x_2d=round(x_2d*data.config.ImageSizeRender);
y_2d=round(y_2d*data.config.ImageSizeRender);
m=3;
x_2d_start=x_2d-m; x_2d_start(x_2d_start<1)=1;
x_2d_end=x_2d+m; x_2d_end(x_2d_end>size(data.subwindow(data.axes_select).hitmap,1))=size(data.subwindow(data.axes_select).hitmap,1);
y_2d_start=y_2d-m; y_2d_start(y_2d_start<1)=1;
y_2d_end=y_2d+m; y_2d_end(y_2d_end>size(data.subwindow(data.axes_select).hitmap,2))=size(data.subwindow(data.axes_select).hitmap,2);
hitmap_part=data.subwindow(data.axes_select).hitmap(x_2d_start:x_2d_end,y_2d_start:y_2d_end,:);
h1=hitmap_part(:,:,1); h2=hitmap_part(:,:,2); h3=hitmap_part(:,:,3);
id_detect=[max(h1(:)) max(h2(:)) max(h3(:))];
if(isempty(id_detect)), id_detect=[0 0 0]; end
function data=points2roi(data,segment)
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
np=getnumberofpoints(data);
x=zeros(1,np); y=zeros(1,np); z=zeros(1,np);
for i=1:np;
x(i)=data.volumes(dvs).MeasureList(end).x;
y(i)=data.volumes(dvs).MeasureList(end).y;
z(i)=data.volumes(dvs).MeasureList(end).z;
data=rmvMeasureList(data.volumes(dvs).MeasureList(end).id,data);
end
[x,y,z]=interpcontour(x,y,z,2);
switch (data.subwindow(data.axes_select).render_type)
case {'slicex'}
x_2d=y; y_2d=z;
sizeI=[size(data.volumes(dvs).volume_original,2) size(data.volumes(dvs).volume_original,3)];
case {'slicey'}
x_2d=x; y_2d=z;
sizeI=[size(data.volumes(dvs).volume_original,1) size(data.volumes(dvs).volume_original,3)];
case {'slicez'}
x_2d=x; y_2d=y;
sizeI=[size(data.volumes(dvs).volume_original,1) size(data.volumes(dvs).volume_original,2)];
end
I=bitmapplot(x_2d,y_2d,zeros(sizeI),struct('FillColor',[1 1 1 1],'Color',[1 1 1 1]))>0;
if(segment)
data=addMeasureList('s',x,y,z,0,data);
data.volumes(dvs).MeasureList(length(data.volumes(dvs).MeasureList)).SliceSelected=0;
else
volume=sum(I(:))*prod(data.volumes(dvs).Scales);
data=addMeasureList('r',x,y,z,volume,data);
end
function [vx,vy,vz]=getClickRoi(data)
switch(data.subwindow(data.axes_select).render_type)
case 'slicex'
B=squeeze(data.volumes(dvs).volume_original(data.subwindow(data.axes_select).SliceSelected(1),:,:));
Bx=data.subwindow(data.axes_select).VoxelLocation(2); By=data.subwindow(data.axes_select).VoxelLocation(3);
case 'slicey'
B=squeeze(data.volumes(dvs).volume_original(:,data.subwindow(data.axes_select).SliceSelected(2),:));
Bx=data.subwindow(data.axes_select).VoxelLocation(1); By=data.subwindow(data.axes_select).VoxelLocation(3);
case 'slicez'
B=squeeze(data.volumes(dvs).volume_original(:,:,data.subwindow(data.axes_select).SliceSelected(3)));
Bx=data.subwindow(data.axes_select).VoxelLocation(1); By=data.subwindow(data.axes_select).VoxelLocation(2);
end
B=(B-data.volumes(dvs).WindowLevel)./data.volumes(dvs).WindowWidth;
Bx=round(max(min(Bx,size(B,1)-1),2));
By=round(max(min(By,size(B,2)-1),2));
val=mean(mean(B(Bx-1:Bx+1,By-1:By+1)));
B=B-val; B=abs(B)<0.15;
L=bwlabel(B);
B=L==L(Bx,By);
B=bwmorph(bwmorph(bwmorph(imfill(B,'holes'),'remove'),'skel'),'spur',inf);
[x,y]=find(B);
for i=2:length(x)
dist=(x(i:end)-x(i-1)).^2+(y(i:end)-y(i-1)).^2;
[t,j]=min(dist); j=j+i-1;
t=x(i); x(i)=x(j); x(j)=t;
t=y(i); y(i)=y(j); y(j)=t;
dist=(x(1)-x(i)).^2+(y(1)-y(i)).^2;
if((i>4)&&dist<2), break; end
end
x=x(1:3:i); y=y(1:3:i);
switch(data.subwindow(data.axes_select).render_type)
case 'slicex'
vx=repmat(data.subwindow(data.axes_select).SliceSelected(1),size(x));
vy=x; vz=y;
case 'slicey'
vy=repmat(data.subwindow(data.axes_select).SliceSelected(2),size(x));
vx=x; vz=y;
case 'slicez'
vz=repmat(data.subwindow(data.axes_select).SliceSelected(3),size(x));
vx=x; vy=y;
end
function p=getnumberofpoints(data)
p=0;
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
for i=length(data.volumes(dvs).MeasureList):-1:1,
if(data.volumes(dvs).MeasureList(i).type=='p'), p=p+1; else return; end
end
function data=showMeasureList(data)
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
data.subwindow(data.axes_select).hitmap=zeros([size(data.subwindow(data.axes_select).total_image,1) size(data.subwindow(data.axes_select).total_image,2) 3]);
if(~isfield(data.volumes(dvs),'MeasureList')), return; end
if(length(data.subwindow(data.axes_select).render_type)<6), return; end
SliceSelected=data.subwindow(data.axes_select).SliceSelected(uint8(data.subwindow(data.axes_select).render_type(6))-119);
for i=1:length(data.volumes(dvs).MeasureList)
S=data.volumes(dvs).MeasureList(i).SliceSelected;
if(data.subwindow(data.axes_select).render_type(6)==data.volumes(dvs).MeasureList(i).RenderSelected&&(SliceSelected==S||S==0))
id=data.volumes(dvs).MeasureList(i).id;
x=data.volumes(dvs).MeasureList(i).x;
y=data.volumes(dvs).MeasureList(i).y;
z=data.volumes(dvs).MeasureList(i).z;
[x,y]=voxelposition_to_imageposition(x,y,z,data);
switch data.volumes(dvs).MeasureList(i).type
case 'd'
distancemm=data.volumes(dvs).MeasureList(i).varmm;
data=plotDistance(x,y,distancemm,id,data);
case 'r'
volumemm=data.volumes(dvs).MeasureList(i).varmm;
data=plotRoi(x,y,volumemm,id,data);
case 's'
data=plotSegRoi(x,y,id,data);
case 'p'
data=plotPoint(x,y,id,data);
case 'l'
data=plotPointBlue(x,y,id,data);
end
end
end
function data=plotPoint(x,y,id,data)
I=data.subwindow(data.axes_select).total_image;
I=bitmapplot(x,y,I,struct('Marker','*','MarkerColor',[1 0 0 1],'Color',[0 0 1 1]));
data.subwindow(data.axes_select).hitmap=bitmapplot(x,y,data.subwindow(data.axes_select).hitmap,struct('Marker','*','MarkerColor',[id id 0 1],'Color',[id id 0 1]));
data.subwindow(data.axes_select).total_image=I;
function data=plotPointBlue(x,y,id,data)
I=data.subwindow(data.axes_select).total_image;
I=bitmapplot(x,y,I,struct('Marker','*','MarkerColor',[0 0 1 1],'Color',[1 0 0 1]));
data.subwindow(data.axes_select).hitmap=bitmapplot(x,y,data.subwindow(data.axes_select).hitmap,struct('Marker','*','MarkerColor',[id id 0 1],'Color',[id id 0 1]));
data.subwindow(data.axes_select).total_image=I;
function data=plotDistance(x,y,distancemm,id,data)
I=data.subwindow(data.axes_select).total_image;
I=bitmapplot(x,y,I,struct('Marker','*','MarkerColor',[1 0 0 1],'Color',[0 0 1 1]));
MC=zeros(length(x),4); MC(:,1)=id; MC(:,2)=id; MC(:,3)=(1:length(x))/length(x); MC(:,4)=1;
data.subwindow(data.axes_select).hitmap=bitmapplot(x,y,data.subwindow(data.axes_select).hitmap,struct('Marker','*','MarkerColor',MC,'Color',[id id 0 1]));
info=[num3str(distancemm,0,2) ' mm'];
I=bitmaptext(info,I,[mean(x)-5 mean(y)-5],struct('Color',[0 1 0 1]));
data.subwindow(data.axes_select).total_image=I;
function data=plotRoi(x,y,volumemm,id,data)
I=data.subwindow(data.axes_select).total_image;
I=bitmapplot(x,y,I,struct('FillColor',[0 0 1 0.1],'Color',[1 0 0 1]));
data.subwindow(data.axes_select).hitmap=bitmapplot(x,y,data.subwindow(data.axes_select).hitmap,struct('Color',[id id 0 1]));
info=[num3str(volumemm,0,2) ' mm^3'];
I=bitmaptext(info,I,[mean(x)-5 mean(y)-5],struct('Color',[0 1 0 1]));
data.subwindow(data.axes_select).total_image=I;
function data=plotSegRoi(x,y,id,data)
I=data.subwindow(data.axes_select).total_image;
I=bitmapplot(x,y,I,struct('FillColor',[0 1 1 0.3],'Color',[0 1 1 1],'Marker','+'));
MC=zeros(length(x),4); MC(:,1)=id; MC(:,2)=id; MC(:,3)=(1:length(x))/length(x); MC(:,4)=1;
data.subwindow(data.axes_select).hitmap=bitmapplot(x,y,data.subwindow(data.axes_select).hitmap,struct('Marker','+','MarkerColor',MC,'Color',[id id 0 1]));
data.subwindow(data.axes_select).total_image=I;
function numstr=num3str(num,bef,aft)
numstr=num2str(num,['%.' num2str(aft) 'f']);
if(aft>0), maxlen = bef + aft +1; else maxlen = bef; end
while (length(numstr)<maxlen), numstr=['0' numstr]; end
function data=addMeasureList(type,x,y,z,varmm,data)
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
if(isempty(data.volumes(dvs).MeasureList)), p=1; else p=length(data.volumes(dvs).MeasureList)+1; end
data.volumes(dvs).MeasureList(p).id=(rand+sum(clock)-floor(sum(clock)))/2;
data.volumes(dvs).MeasureList(p).type=type;
data.volumes(dvs).MeasureList(p).RenderSelected=data.subwindow(data.axes_select).render_type(6);
SliceSelected=data.subwindow(data.axes_select).SliceSelected(uint8(data.subwindow(data.axes_select).render_type(6))-119);
data.volumes(dvs).MeasureList(p).SliceSelected=SliceSelected;
data.volumes(dvs).MeasureList(p).x=x;
data.volumes(dvs).MeasureList(p).y=y;
data.volumes(dvs).MeasureList(p).z=z;
data.volumes(dvs).MeasureList(p).varmm=varmm;
data=calcTotalVolume(data);
function data=rmvMeasureList(id,data)
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
index=-1;
for i=1:length(data.volumes(dvs).MeasureList)
if(data.volumes(dvs).MeasureList(i).id==id), index=i;end
end
if(index>-1)
data.volumes(dvs).MeasureList(index)=[];
end
data=calcTotalVolume(data);
function data=calcTotalVolume(data)
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
data.subwindow(data.axes_select).tVolumemm=0;
for i=1:length(data.volumes(dvs).MeasureList)
if(data.volumes(dvs).MeasureList(i).type=='r')
data.subwindow(data.axes_select).tVolumemm=data.subwindow(data.axes_select).tVolumemm+data.volumes(dvs).MeasureList(i).varmm;
end
end
function set_mouse_shape(type,data)
if(isempty(type)), type='normal'; end
switch(type)
case 'rotate1'
set(gcf,'Pointer','custom','PointerShapeCData',data.icons.icon_mouse_rotate1,'PointerShapeHotSpot',round(size(data.icons.icon_mouse_rotate1)/2))
set(data.handles.figure1,'Pointer','custom');
case 'rotate2'
set(gcf,'Pointer','custom','PointerShapeCData',data.icons.icon_mouse_rotate2,'PointerShapeHotSpot',round(size(data.icons.icon_mouse_rotate2)/2))
set(data.handles.figure1,'Pointer','custom');
case 'select_distance'
set(data.handles.figure1,'Pointer','crosshair')
case 'select_landmark'
set(data.handles.figure1,'Pointer','crosshair')
case 'select_roi'
set(data.handles.figure1,'Pointer','crosshair')
case 'click_roi'
set(data.handles.figure1,'Pointer','crosshair')
case 'normal'
set(data.handles.figure1,'Pointer','arrow')
case 'alt'
set(data.handles.figure1,'Pointer','arrow')
case 'open'
set(data.handles.figure1,'Pointer','arrow')
case 'zoom'
set(gcf,'Pointer','custom','PointerShapeCData',data.icons.icon_mouse_zoom,'PointerShapeHotSpot',round(size(data.icons.icon_mouse_zoom)/2))
set(data.handles.figure1,'Pointer','custom');
case 'pan'
set(gcf,'Pointer','custom','PointerShapeCData',data.icons.icon_mouse_pan,'PointerShapeHotSpot',round(size(data.icons.icon_mouse_pan)/2))
set(data.handles.figure1,'Pointer','custom');
otherwise
set(data.handles.figure1,'Pointer','arrow')
end
% --- Executes on mouse press over figure background, over a disabled or
% --- inactive control, or over an axes background.
function figure1_WindowButtonUpFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
if(isempty(data.axes_select)), return, end
if(data.mouse.pressed)
data.mouse.pressed=false;
setMyData(data);
show3d(false,true)
end
switch(data.mouse.action)
case 'measure_distance',
set_mouse_shape('select_distance',data)
case 'measure_roi',
set_mouse_shape('select_roi',data)
otherwise
set_mouse_shape('arrow',data)
end
function A=imresize3d(V,scale,tsize,ntype,npad)
% This function resizes a 3D image volume to new dimensions
% Vnew = imresize3d(V,scale,nsize,ntype,npad);
%
% inputs,
% V: The input image volume
% scale: scaling factor, when used set tsize to [];
% nsize: new dimensions, when used set scale to [];
% ntype: Type of interpolation ('nearest', 'linear', or 'cubic')
% npad: Boundary condition ('replicate', 'symmetric', 'circular', 'fill', or 'bound')
%
% outputs,
% Vnew: The resized image volume
%
% example,
% load('mri','D'); D=squeeze(D);
% Dnew = imresize3d(D,[],[80 80 40],'nearest','bound');
%
% This function is written by D.Kroon University of Twente (July 2008)
% Check the inputs
if(exist('ntype', 'var') == 0), ntype='nearest'; end
if(exist('npad', 'var') == 0), npad='bound'; end
if(exist('scale', 'var')&&~isempty(scale)), tsize=round(size(V)*scale); end
if(ndims(V)>2)
if(exist('tsize', 'var')&&~isempty(tsize)), scale=(tsize./size(V)); end
vmin=min(V(:));
vmax=max(V(:));
% Make transformation structure
T = makehgtform('scale',scale);
tform = maketform('affine', T);
% Specify resampler
R = makeresampler(ntype, npad);
% Resize the image volueme
A = tformarray(V, tform, R, [1 2 3], [1 2 3], tsize, [], 0);
% Limit to range
A(A<vmin)=vmin; A(A>vmax)=vmax;
else
if(exist('tsize', 'var')&&~isempty(tsize)),
tsize=tsize(1:2);
scale=(tsize./size(V));
end
vmin=min(V(:));
vmax=max(V(:));
switch(ntype(1))
case 'n'
ntype2='nearest';
case 'l'
ntype2='bilinear';
otherwise
ntype2='bicubic';
end
% Transform the image
A=imresize(V,scale.*size(V),ntype2);
% Limit to range
A(A<vmin)=vmin; A(A>vmax)=vmax;
end
% --------------------------------------------------------------------
function menu_file_Callback(hObject, eventdata, handles)
% hObject handle to menu_file (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_config_Callback(hObject, eventdata, handles)
% hObject handle to menu_config (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_change_alpha_colors_Callback(hObject, eventdata, handles)
% hObject handle to menu_change_alpha_colors (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.volume_select=eventdata;
data.figurehandles.histogram=viewer3d_histogram(data.figurehandles.viewer3d);
handles_histogram=guidata(data.figurehandles.histogram);
data.figurehandles.histogram_axes=handles_histogram.axes_histogram;
setMyData(data);
createHistogram();
drawHistogramPoints();
% --------------------------------------------------------------------
function menu_load_view_Callback(hObject, eventdata, handles)
% hObject handle to menu_load_view (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData();
if(ishandle(data.figurehandles.histogram)), close(data.figurehandles.histogram); end
[filename, dirname] = uigetfile('*.mat', 'Select a Viewer3D Matlab file',fileparts(data.history.filenames{1}));
if(ischar(filename))
filename=[dirname filename];
load_view(filename);
else
viewer3d_error({'No File selected'}); return
end
function load_view(filename)
dataold=getMyData();
if(exist(filename,'file'))
load(filename);
else
viewer3d_error({'File Not Found'}); return
end
if(exist('data','var'))
% Remove current Windows and VolumeMenu's
dataold.NumberWindows=0;
dataold=deleteWindows(dataold);
for i=1:length(dataold.volumes)
delete(dataold.MenuVolume(i).Handle);
end
% Temporary store the loaded data in a new variable
datanew=data;
% Make an empty data-structure
data=struct;
% Add the current figure handles and other information about the
% current render figure.
data.Menu=dataold.Menu;
data.handles=dataold.handles;
data.mouse=dataold.mouse;
data.config=dataold.config;
data.history=dataold.history;
data.rendertypes=dataold.rendertypes;
data.figurehandles=dataold.figurehandles;
data.volumes=[];
data.axes_select=[];
data.volume_select=[];
data.subwindow=[];
data.NumberWindows=0;
data.MenuVolume=[];
data.icons=dataold.icons;
% Add the loaded volumes
data.volumes=datanew.volumes;
for nv=1:length(data.volumes)
data=makeVolumeXY(data,nv);
data=computeNormals(data,nv);
data=makePreviewVolume(data,nv);
data=makeRenderVolume(data,nv);
data=createAlphaColorTable(nv,data);
end
data.NumberWindows=datanew.NumberWindows;
data=addWindows(data);
cfield={'tVolumemm', ...
'VoxelLocation','mouse_position_pressed','mouse_position','mouse_position_last','shading_material', ...
'ColorSlice','render_type','ViewerVector','LightVector','volume_id_select','object_id_select' ...
'render_image','total_image','hitmap','axes_size','Zoom','viewer_matrix','SliceSelected','Mview','combine'};
for i=1:data.NumberWindows
for j=1:length(cfield);
if(isfield(datanew.subwindow(i),cfield{j}))
data.subwindow(i).(cfield{j})=datanew.subwindow(i).(cfield{j});
else
data.subwindow(i).(cfield{j})=dataold.subwindow(1).(cfield{j});
end
end
end
data.substorage=datanew.substorage;
data.axes_select=datanew.axes_select;
data.volume_select=datanew.volume_select;
setMyData(data);
addMenuVolume();
set_menu_checks(data);
allshow3d(false,true);
% Menu: [1x5 struct]
% handles: [1x1 struct]
% mouse: [1x1 struct]
% config: [1x1 struct]
% history: [1x1 struct]
% rendertypes: [1x8 struct]
% figurehandles: [1x1 struct]
% volumes: [1x2 struct]
% axes_select: 1
% volume_select: 2
% subwindow: [1x2 struct]
% NumberWindows: 2
% MenuVolume: [1x2 struct]
% icons: [1x1 struct]
% substorage:
else
viewer3d_error({'Matlab File does not contain','data from "Save View"'})
end
function data=add_filename_to_history(data,filename)
% Add curent filename to history
for i=1:5
if(strcmpi(data.history.filenames{i},filename));
data.history.filenames{i}='';
end
end
for i=5:-1:1
if(i==1)
data.history.filenames{i}=filename;
else
data.history.filenames{i}=data.history.filenames{i-1};
end
end
% Save filename history
history=data.history;
save(data.history.historyfile,'history');
showhistory(data);
function load_variable_Callback(hObject, eventdata, handles)
% hObject handle to menu_load_view (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
V=eventdata;
volumemax=double(max(V(:))); volumemin=double(min(V(:)));
info=struct;
info.WindowWidth=volumemax-volumemin;
info.WindowLevel=0.5*(volumemax+volumemin);
addVolume(V,[1 1 1],info);
% --------------------------------------------------------------------
function menu_load_data_Callback(hObject, eventdata, handles)
% hObject handle to menu_load_data (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
if(ishandle(data.figurehandles.histogram)), close(data.figurehandles.histogram); end
[volume,info]=ReadData3D;
% Make the volume nD -> 4D
V=reshape(volume,size(volume,1),size(volume,2),size(volume,3),[]);
if(isempty(info)),return; end
scales=info.PixelDimensions;
if(nnz(scales)<3)
viewer3d_error({'Pixel Scaling Unknown using [1, 1, 1]'})
scales=[1 1 1];
end
if(exist('volume','var'))
addVolume(V,scales,info)
else
viewer3d_error({'Matlab Data Load Error'})
end
% --------------------------------------------------------------------
function menu_save_view_Callback(hObject, eventdata, handles)
% hObject handle to menu_save_view (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
for dvs=1:length(data.volumes)
data.volumes(dvs).volume_preview=[];
data.volumes(dvs).volume=[];
data.volumes(dvs).volumex=[];
data.volumes(dvs).volumey=[];
data.volumes(dvs).normals=[];
end
[filename, dirname] = uiputfile('*.mat', 'Store a Viewer3D file',fileparts(data.history.filenames{1}));
if(ischar(filename))
filename=[dirname filename];
h = waitbar(0,'Please wait...'); drawnow('expose')
save(filename,'data');
close(h);
else
viewer3d_error({'No File selected'}); return
end
% Add curent filename to history
data=getMyData(); if(isempty(data)), return, end
data=add_filename_to_history(data,filename);
setMyData(data);
function menu_load_histogram_Callback(hObject, eventdata, handles)
% hObject handle to menu_load_view (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
alpha=0;
uiload;
if(exist('positions','var'))
data.volumes(dvs).histogram_positions=positions;
data.volumes(dvs).histogram_colors=colors;
data.volumes(dvs).histogram_alpha=alpha;
setMyData(data);
drawHistogramPoints();
createAlphaColorTable();
show3d(false,true);
else
viewer3d_error({'Matlab File does not contain','data from "Save AlphaColors"'})
end
% --------------------------------------------------------------------
function menu_save_histogram_Callback(hObject, eventdata, handles)
% hObject handle to menu_save_view (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
positions=data.volumes(dvs).histogram_positions;
colors=data.volumes(dvs).histogram_colors;
alpha=data.volumes(dvs).histogram_alpha;
uisave({'positions','colors','alpha'});
% --------------------------------------------------------------------
function menu_render_Callback(hObject, eventdata, handles)
% hObject handle to menu_render (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_info_Callback(hObject, eventdata, handles)
% hObject handle to menu_info (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_save_picture_Callback(hObject, eventdata, handles)
% hObject handle to menu_save_picture (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
[filename, pathname] = uiputfile({'*.png';'*.jpg'}, 'Save Rendered Image as');
data=getMyData(); if(isempty(data)), return, end
imwrite(data.subwindow(data.axes_select).total_image,[pathname filename]);
% --------------------------------------------------------------------
function menu_about_Callback(hObject, eventdata, handles)
% hObject handle to menu_about (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
viewer3d_about
function createHistogram()
% This function creates and show the (log) histogram of the data
data=getMyData(); if(isempty(data)), return, end
dvs=data.volume_select;
% Get histogram
volumepart=single(data.volumes(dvs).volume(1:8:end));
data.volumes(dvs).histogram_countsx=linspace(data.volumes(dvs).volumemin,data.volumes(dvs).volumemax,1000);
data.volumes(dvs).histogram_countsy=hist(volumepart,data.volumes(dvs).histogram_countsx);
% Log the histogram data
data.volumes(dvs).histogram_countsy=log(data.volumes(dvs).histogram_countsy+100);
data.volumes(dvs).histogram_countsy=data.volumes(dvs).histogram_countsy-min(data.volumes(dvs).histogram_countsy);
data.volumes(dvs).histogram_countsy=data.volumes(dvs).histogram_countsy./max(data.volumes(dvs).histogram_countsy(:));
% Focus on histogram axes
figure(data.figurehandles.histogram)
% Display the histogram
stem(data.figurehandles.histogram_axes,data.volumes(dvs).histogram_countsx,data.volumes(dvs).histogram_countsy,'Marker', 'none');
hold(data.figurehandles.histogram_axes,'on');
% Set the axis of the histogram axes
data.volumes(dvs).histogram_maxy=max(data.volumes(dvs).histogram_countsy(:));
data.volumes(dvs).histogram_maxx=max(data.volumes(dvs).histogram_countsx(:));
set(data.figurehandles.histogram_axes,'yLim', [0 1]);
set(data.figurehandles.histogram_axes,'xLim', [data.volumes(dvs).volumemin data.volumes(dvs).volumemax]);
setMyData(data);
% --- Executes on selection change in popupmenu_colors.
function popupmenu_colors_Callback(hObject, eventdata, handles)
% hObject handle to popupmenu_colors (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = get(hObject,'String') returns popupmenu_colors contents as cell array
% contents{get(hObject,'Value')} returns selected item from popupmenu_colors
data=getMyData(); if(isempty(data)), return, end
dvs=data.volume_select;
% Generate the new color markers
c_choice=get(handles.popupmenu_colors,'Value');
ncolors=length(data.volumes(dvs).histogram_positions);
switch c_choice,
case 1,new_colormap=jet(1000);
case 2, new_colormap=hsv(1000);
case 3, new_colormap=hot(1000);
case 4, new_colormap=cool(1000);
case 5, new_colormap=spring(1000);
case 6, new_colormap=summer(1000);
case 7, new_colormap=autumn(1000);
case 8, new_colormap=winter(1000);
case 9, new_colormap=gray(1000);
case 10, new_colormap=bone(1000);
case 11, new_colormap=copper(1000);
case 12, new_colormap=pink(1000);
otherwise, new_colormap=hot(1000);
end
new_colormap=new_colormap(round(1:(end-1)/(ncolors-1):end),:);
data.volumes(dvs).histogram_colors=new_colormap;
% Draw the new color markers and make the color and alpha map
setMyData(data);
drawHistogramPoints();
createAlphaColorTable();
show3d(false,true);
function drawHistogramPoints()
data=getMyData(); if(isempty(data)), return, end
dvs=data.volume_select;
% Delete old points and line
try
delete(data.volumes(dvs).histogram_linehandle),
for i=1:length(data.volumes(dvs).histogram_pointhandle),
delete(data.volumes(dvs).histogram_pointhandle(i)),
end,
catch
end
stem(data.figurehandles.histogram_axes,data.volumes(dvs).histogram_countsx,data.volumes(dvs).histogram_countsy,'Marker', 'none');
hold(data.figurehandles.histogram_axes,'on');
% Display the markers and line through the markers.
data.volumes(dvs).histogram_linehandle=plot(data.figurehandles.histogram_axes,data.volumes(dvs).histogram_positions,data.volumes(dvs).histogram_alpha*data.volumes(dvs).histogram_maxy,'m');
set(data.volumes(dvs).histogram_linehandle,'ButtonDownFcn','viewer3d(''lineHistogramButtonDownFcn'',gcbo,[],guidata(gcbo))');
for i=1:length(data.volumes(dvs).histogram_positions)
data.volumes(dvs).histogram_pointhandle(i)=plot(data.figurehandles.histogram_axes,data.volumes(dvs).histogram_positions(i),data.volumes(dvs).histogram_alpha(i)*data.volumes(dvs).histogram_maxy,'bo','MarkerFaceColor',data.volumes(dvs).histogram_colors(i,:));
set(data.volumes(dvs).histogram_pointhandle(i),'ButtonDownFcn','viewer3d(''pointHistogramButtonDownFcn'',gcbo,[],guidata(gcbo))');
end
% For detection of mouse up, down and in histogram figure.
set(data.figurehandles.histogram, 'WindowButtonDownFcn','viewer3d(''HistogramButtonDownFcn'',gcbo,[],guidata(gcbo))');
set(data.figurehandles.histogram, 'WindowButtonMotionFcn','viewer3d(''HistogramButtonMotionFcn'',gcbo,[],guidata(gcbo))');
set(data.figurehandles.histogram, 'WindowButtonUpFcn','viewer3d(''HistogramButtonUpFcn'',gcbo,[],guidata(gcbo))');
setMyData(data);
function pointHistogramButtonDownFcn(hObject, eventdata, handles)
data=getMyData(); if(isempty(data)), return, end
dvs=data.volume_select;
data.mouse.button=get(data.figurehandles.histogram,'SelectionType');
if(strcmp(data.mouse.button,'normal'))
data.volumes(dvs).histogram_pointselected=find(data.volumes(dvs).histogram_pointhandle==gcbo);
data.volumes(dvs).histogram_pointselectedhandle=gcbo;
set(data.volumes(dvs).histogram_pointselectedhandle, 'MarkerSize',8);
setMyData(data);
elseif(strcmp(data.mouse.button,'extend'))
data.volumes(dvs).histogram_pointselected=find(data.volumes(dvs).histogram_pointhandle==gcbo);
data.volumes(dvs).histogram_colors(data.volumes(dvs).histogram_pointselected,:)=rand(1,3);
data.volumes(dvs).histogram_pointselected=[];
setMyData(data);
drawHistogramPoints();
createAlphaColorTable();
% Show the data
histogram_handles=guidata(data.figurehandles.histogram);
if(get(histogram_handles.checkbox_auto_update,'value'))
show3d(false,true);
else
show3d(true,true);
end
elseif(strcmp(data.mouse.button,'alt'))
data.volumes(dvs).histogram_pointselected=find(data.volumes(dvs).histogram_pointhandle==gcbo);
data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected)=[];
data.volumes(dvs).histogram_colors(data.volumes(dvs).histogram_pointselected,:)=[];
data.volumes(dvs).histogram_alpha(data.volumes(dvs).histogram_pointselected)=[];
data.volumes(dvs).histogram_pointselected=[];
setMyData(data);
drawHistogramPoints();
createAlphaColorTable();
% Show the data
histogram_handles=guidata(data.figurehandles.histogram);
if(get(histogram_handles.checkbox_auto_update,'value'))
show3d(false,true);
else
show3d(true,true);
end
end
function HistogramButtonDownFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
function HistogramButtonUpFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
dvs=data.volume_select;
if(~isempty(data.volumes(dvs).histogram_pointselected))
set(data.volumes(dvs).histogram_pointselectedhandle, 'MarkerSize',6);
data.volumes(dvs).histogram_pointselected=[];
setMyData(data);
createAlphaColorTable();
% Show the data
histogram_handles=guidata(data.figurehandles.histogram);
if(get(histogram_handles.checkbox_auto_update,'value'))
allshow3d(false,true);
else
allshow3d(true,true);
end
end
function Histogram_pushbutton_update_view_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton_update_view (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
allshow3d(false,true)
function HistogramButtonMotionFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
cursor_position_in_histogram_axes(hObject,handles);
data=getMyData(); if(isempty(data)), return, end
dvs=data.volume_select;
if(~isempty(data.volumes(dvs).histogram_pointselected))
% Set point to location mouse
data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected)=data.volumes(dvs).histogram_mouse_position(1,1);
data.volumes(dvs).histogram_alpha(data.volumes(dvs).histogram_pointselected)=data.volumes(dvs).histogram_mouse_position(1,2);
% Correct new location
if(data.volumes(dvs).histogram_alpha(data.volumes(dvs).histogram_pointselected)<0), data.volumes(dvs).histogram_alpha(data.volumes(dvs).histogram_pointselected)=0; end
if(data.volumes(dvs).histogram_alpha(data.volumes(dvs).histogram_pointselected)>1), data.volumes(dvs).histogram_alpha(data.volumes(dvs).histogram_pointselected)=1; end
if(data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected)<data.volumes(dvs).volumemin), data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected)=data.volumes(dvs).volumemin; end
if(data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected)>data.volumes(dvs).volumemax), data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected)=data.volumes(dvs).volumemax; end
if((data.volumes(dvs).histogram_pointselected>1)&&(data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected-1)>data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected)))
data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected)=data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected-1);
end
if((data.volumes(dvs).histogram_pointselected<length(data.volumes(dvs).histogram_positions))&&(data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected+1)<data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected)))
data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected)=data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected+1);
end
% Move point
set(data.volumes(dvs).histogram_pointselectedhandle, 'xdata', data.volumes(dvs).histogram_positions(data.volumes(dvs).histogram_pointselected));
set(data.volumes(dvs).histogram_pointselectedhandle, 'ydata', data.volumes(dvs).histogram_alpha(data.volumes(dvs).histogram_pointselected));
% Move line
set(data.volumes(dvs).histogram_linehandle, 'xdata',data.volumes(dvs).histogram_positions);
set(data.volumes(dvs).histogram_linehandle, 'ydata',data.volumes(dvs).histogram_alpha);
end
setMyData(data);
function lineHistogramButtonDownFcn(hObject, eventdata, handles)
data=getMyData(); if(isempty(data)), return, end
dvs=data.volume_select;
% New point on mouse location
newposition=data.volumes(dvs).histogram_mouse_position(1,1);
% List for the new markers
newpositions=zeros(1,length(data.volumes(dvs).histogram_positions)+1);
newalphas=zeros(1,length(data.volumes(dvs).histogram_alpha)+1);
newcolors=zeros(size(data.volumes(dvs).histogram_colors,1)+1,3);
% Check if the new point is between old points
index_down=find(data.volumes(dvs).histogram_positions<=newposition);
if(isempty(index_down))
else
index_down=index_down(end);
index_up=find(data.volumes(dvs).histogram_positions>newposition);
if(isempty(index_up))
else
index_up=index_up(1);
% Copy the (first) old markers to the new lists
newpositions(1:index_down)=data.volumes(dvs).histogram_positions(1:index_down);
newalphas(1:index_down)=data.volumes(dvs).histogram_alpha(1:index_down);
newcolors(1:index_down,:)=data.volumes(dvs).histogram_colors(1:index_down,:);
% Add the new interpolated marker
perc=(newposition-data.volumes(dvs).histogram_positions(index_down)) / (data.volumes(dvs).histogram_positions(index_up) - data.volumes(dvs).histogram_positions(index_down));
color=(1-perc)*data.volumes(dvs).histogram_colors(index_down,:)+perc*data.volumes(dvs).histogram_colors(index_up,:);
alpha=(1-perc)*data.volumes(dvs).histogram_alpha(index_down)+perc*data.volumes(dvs).histogram_alpha(index_up);
newpositions(index_up)=newposition;
newalphas(index_up)=alpha;
newcolors(index_up,:)=color;
% Copy the (last) old markers to the new lists
newpositions(index_up+1:end)=data.volumes(dvs).histogram_positions(index_up:end);
newalphas(index_up+1:end)=data.volumes(dvs).histogram_alpha(index_up:end);
newcolors(index_up+1:end,:)=data.volumes(dvs).histogram_colors(index_up:end,:);
% Make the new lists the used marker lists
data.volumes(dvs).histogram_positions=newpositions;
data.volumes(dvs).histogram_alpha=newalphas;
data.volumes(dvs).histogram_colors=newcolors;
end
end
% Update the histogram window
cla(data.figurehandles.histogram_axes);
setMyData(data);
drawHistogramPoints();
createAlphaColorTable();
% Show the data
histogram_handles=guidata(data.figurehandles.histogram);
if(get(histogram_handles.checkbox_auto_update,'value'))
show3d(false,true);
else
show3d(true,true);
end
function cursor_position_in_histogram_axes(hObject,handles)
data=getMyData(); if(isempty(data)), return, end
dvs=data.volume_select;
% % Get position of the mouse in the large axes
% p = get(0, 'PointerLocation');
% pf = get(hObject, 'pos');
% p(1:2) = p(1:2)-pf(1:2);
% set(data.figurehandles.histogram, 'CurrentPoint', p(1:2));
p = get(data.figurehandles.histogram_axes, 'CurrentPoint');
data.volumes(dvs).histogram_mouse_position=[p(1, 1) p(1, 2)];
setMyData(data);
% --------------------------------------------------------------------
function menu_help_Callback(hObject, eventdata, handles)
% hObject handle to menu_help (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
web('info.html');
% --- Executes when user attempts to close figure1.
function figure1_CloseRequestFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: delete(hObject) closes the figure
data=getMyData(); if(isempty(data)), delete(hObject); return, end
try
if(ishandle(data.figurehandles.histogram)), delete(data.figurehandles.histogram); end
if(ishandle(data.figurehandles.qualityspeed)), delete(data.figurehandles.qualityspeed); end
if(ishandle(data.figurehandles.console)), delete(data.figurehandles.console); end
if(ishandle(data.figurehandles.contrast)), delete(data.figurehandles.contrast); end
if(ishandle(data.figurehandles.voxelsize)), delete(data.figurehandles.voxelsize); end
if(ishandle(data.figurehandles.lightvector)), delete(data.figurehandles.lightvector); end
catch me
disp(me.message);
end
% Remove the data of this figure
try rmappdata(gcf,'data3d'); catch end
delete(hObject);
% --------------------------------------------------------------------
function menu_shiny_Callback(hObject, eventdata, handles)
% hObject handle to menu_shiny (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.axes_select=eventdata;
data.subwindow(data.axes_select).shading_material='shiny';
set_menu_checks(data);
setMyData(data);
show3d(false,true);
% --------------------------------------------------------------------
function menu_dull_Callback(hObject, eventdata, handles)
% hObject handle to menu_dull (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.axes_select=eventdata;
data.subwindow(data.axes_select).shading_material='dull';
set_menu_checks(data);
setMyData(data);
show3d(false,true);
% --------------------------------------------------------------------
function menu_metal_Callback(hObject, eventdata, handles)
% hObject handle to menu_metal (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.axes_select=eventdata;
data.subwindow(data.axes_select).shading_material='metal';
set_menu_checks(data);
setMyData(data);
show3d(false,true);
function menu_combine_Callback(hObject, eventdata, handles)
% hObject handle to menu_metal (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.axes_select=eventdata(1);
switch(eventdata(2))
case 1
data.subwindow(data.axes_select).combine='trans';
case 2
data.subwindow(data.axes_select).combine='rgb';
end
setMyData(data);
set_menu_checks(data);
show3d(false,true);
function button_voxelsize_apply_Callback(hObject, eventdata, handles)
data=getMyData(); if(isempty(data)), return, end
dvs=data.volume_select;
handles_voxelsize=guidata(data.figurehandles.voxelsize);
Scales_old=data.volumes(dvs).Scales;
data.volumes(dvs).Scales(1)=str2double(get(handles_voxelsize.edit_scax,'String'));
data.volumes(dvs).Scales(2)=str2double(get(handles_voxelsize.edit_scay,'String'));
data.volumes(dvs).Scales(3)=str2double(get(handles_voxelsize.edit_scaz,'String'));
for i=1:data.NumberWindows
if(data.volumes(dvs).id==data.subwindow(i).volume_id_select(1))
Zoom_old=data.subwindow(i).Zoom;
data.subwindow(i).first_render=true;
data.subwindow(i).Zoom=(sqrt(3)./sqrt(sum(data.volumes(dvs).Scales.^2)));
data.subwindow(i).viewer_matrix=data.subwindow(i).viewer_matrix*ResizeMatrix((Scales_old.*Zoom_old)./(data.volumes(dvs).Scales.*data.subwindow(i).Zoom));
end
end
%data=set_initial_view_matrix(data);
setMyData(data);
show3d(false,true);
% --------------------------------------------------------------------
function show3d_Callback(hObject, eventdata, handles)
% hObject handle to menu_file (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if(~isempty(eventdata))
show3d(eventdata(1),eventdata(2));
else
show3d(false,false);
end
% --------------------------------------------------------------------
function UpdatedVolume_Callback(hObject, eventdata, handles)
% hObject handle to menu_file (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
dvs=eventdata(1);
data=getMyData(); if(isempty(data)), return, end
data=makePreviewVolume(data,dvs);
data=makeRenderVolume(data,dvs);
setMyData(data);
allshow3d(true,true);
% --------------------------------------------------------------------
function menu_voxelsize_Callback(hObject, eventdata, handles)
% hObject handle to menu_voxelsize (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
dvs=eventdata;
data.volume_select=dvs;
data.figurehandles.voxelsize=viewer3d_voxelsize;
setMyData(data);
handles_voxelsize=guidata(data.figurehandles.voxelsize);
set(handles_voxelsize.edit_volx,'String',num2str(size(data.volumes(dvs).volume,1)));
set(handles_voxelsize.edit_voly,'String',num2str(size(data.volumes(dvs).volume,2)));
set(handles_voxelsize.edit_volz,'String',num2str(size(data.volumes(dvs).volume,3)));
set(handles_voxelsize.edit_scax,'String',num2str(data.volumes(dvs).Scales(1)));
set(handles_voxelsize.edit_scay,'String',num2str(data.volumes(dvs).Scales(2)));
set(handles_voxelsize.edit_scaz,'String',num2str(data.volumes(dvs).Scales(3)));
function button_lightvector_apply_Callback(hObject, eventdata, handles)
data=getMyData(); if(isempty(data)), return, end
handles_lightvector=guidata(data.figurehandles.lightvector);
data.subwindow(data.axes_select).LightVector(1)=str2double(get(handles_lightvector.edit_lightx,'String'));
data.subwindow(data.axes_select).LightVector(2)=str2double(get(handles_lightvector.edit_lighty,'String'));
data.subwindow(data.axes_select).LightVector(3)=str2double(get(handles_lightvector.edit_lightz,'String'));
setMyData(data);
show3d(false,true);
% --------------------------------------------------------------------
function menu_lightvector_Callback(hObject, eventdata, handles)
% hObject handle to menu_voxelsize (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.axes_select=eventdata;
data.figurehandles.lightvector=viewer3d_lightvector;
setMyData(data);
handles_lightvector=guidata(data.figurehandles.lightvector);
set(handles_lightvector.edit_lightx,'String',num2str(data.subwindow(data.axes_select).LightVector(1)));
set(handles_lightvector.edit_lighty,'String',num2str(data.subwindow(data.axes_select).LightVector(2)));
set(handles_lightvector.edit_lightz,'String',num2str(data.subwindow(data.axes_select).LightVector(3)));
% --------------------------------------------------------------------
function menu_load_worksp_Callback(hObject, eventdata, handles)
% hObject handle to menu_load_worksp (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.figurehandles.workspacevars=viewer3d_workspacevars;
setMyData(data)
% Get variables in the workspace
vars = evalin('base','who');
% Select only variables with 3 dimensions
vars3d=[];
for i=1:length(vars),
if(evalin('base',['ndims(' vars{i} ')'])>1), vars3d{length(vars3d)+1}=vars{i}; end
end
% Show the 3D variables in the workspace
handles_workspacevars=guidata(data.figurehandles.workspacevars);
set(handles_workspacevars.listbox_vars,'String',vars3d);
% --- Executes on button press in pushbutton1.
function workspacevars_button_load_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
handles_workspacevars=guidata(data.figurehandles.workspacevars);
list_entries = get(handles_workspacevars.listbox_vars,'String');
index_selected = get(handles_workspacevars.listbox_vars,'Value');
if length(index_selected) ~= 1
errordlg('You must select one variable')
return;
else
var1 = list_entries{index_selected(1)};
evalin('base',['viewer3d(''load_variable_Callback'',gcf,' var1 ',guidata(gcf))']);
end
if(ishandle(data.figurehandles.workspacevars)), close(data.figurehandles.workspacevars); end
function console_button_clear_Callback(hObject, eventdata, handles)
data=getMyData(); if(isempty(data)), return, end
data.subwindow(data.axes_select).consoletext=[];
data.subwindow(data.axes_select).consolelines=0;
set(data.figurehandles.console_edit,'String','');
setMyData(data);
function data=console_addline(data,newline)
if(ishandle(data.figurehandles.console)),
data.subwindow(data.axes_select).consolelines=data.subwindow(data.axes_select).consolelines+1;
data.subwindow(data.axes_select).consoletext{data.subwindow(data.axes_select).consolelines}=newline;
if(data.subwindow(data.axes_select).consolelines>14),
data.subwindow(data.axes_select).consolelines=14;
data.subwindow(data.axes_select).consoletext={data.subwindow(data.axes_select).consoletext{2:end}};
end
set(data.figurehandles.console_edit,'String',data.subwindow(data.axes_select).consoletext);
end
% --------------------------------------------------------------------
function menu_console_Callback(hObject, eventdata, handles)
% hObject handle to menu_console (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
keyboard
data.figurehandles.console=viewer3d_console;
handles_console=guidata(data.figurehandles.console);
data.figurehandles.console_edit=handles_console.edit_console;
data.subwindow(data.axes_select).consoletext=[];
data.subwindow(data.axes_select).consolelines=0;
setMyData(data)
set(data.figurehandles.console_edit,'String','');
function menu_compile_files_Callback(hObject, eventdata, handles)
% This script will compile all the C files
cd('SubFunctions');
clear affine_transform_2d_double;
mex affine_transform_2d_double.c image_interpolation.c -v
cd('..');
% --------------------------------------------------------------------
function menu_quality_speed_Callback(hObject, eventdata, handles)
% hObject handle to menu_quality_speed (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.figurehandles.qualityspeed=viewer3d_qualityspeed;
setMyData(data);
handles_qualityspeed=guidata(data.figurehandles.qualityspeed);
switch(data.config.VolumeScaling)
case{25}
set(handles_qualityspeed.uipanel_VolumeScaling,'SelectedObject',handles_qualityspeed.radiobutton_scaling25);
case{50}
set(handles_qualityspeed.uipanel_VolumeScaling,'SelectedObject',handles_qualityspeed.radiobutton_scaling50);
case{100}
set(handles_qualityspeed.uipanel_VolumeScaling,'SelectedObject',handles_qualityspeed.radiobutton_scaling100);
case{200}
set(handles_qualityspeed.uipanel_VolumeScaling,'SelectedObject',handles_qualityspeed.radiobutton_scaling200);
end
switch(data.config.PreviewVolumeSize)
case{32}
set(handles_qualityspeed.uipanel_PreviewVolumeSize,'SelectedObject',handles_qualityspeed.radiobutton_preview_32);
case{64}
set(handles_qualityspeed.uipanel_PreviewVolumeSize,'SelectedObject',handles_qualityspeed.radiobutton_preview_64);
case{100}
set(handles_qualityspeed.uipanel_PreviewVolumeSize,'SelectedObject',handles_qualityspeed.radiobutton_preview_100);
end
switch(data.config.ImageSizeRender)
case{150}
set(handles_qualityspeed.uipanel_ImageSizeRender,'SelectedObject',handles_qualityspeed.radiobutton_rendersize150);
case{250}
set(handles_qualityspeed.uipanel_ImageSizeRender,'SelectedObject',handles_qualityspeed.radiobutton_rendersize250);
case{400}
set(handles_qualityspeed.uipanel_ImageSizeRender,'SelectedObject',handles_qualityspeed.radiobutton_rendersize400);
case{600}
set(handles_qualityspeed.uipanel_ImageSizeRender,'SelectedObject',handles_qualityspeed.radiobutton_rendersize600);
case{800}
set(handles_qualityspeed.uipanel_ImageSizeRender,'SelectedObject',handles_qualityspeed.radiobutton_rendersize800);
case{1400}
set(handles_qualityspeed.uipanel_ImageSizeRender,'SelectedObject',handles_qualityspeed.radiobutton_rendersize1400);
case{2500}
set(handles_qualityspeed.uipanel_ImageSizeRender,'SelectedObject',handles_qualityspeed.radiobutton_rendersize2500);
end
switch(data.config.ShearInterpolation)
case{'bilinear'}
set(handles_qualityspeed.uipanel_ShearInterpolation,'SelectedObject',handles_qualityspeed.radiobutton_shear_int_bilinear);
case{'nearest'}
set(handles_qualityspeed.uipanel_ShearInterpolation,'SelectedObject',handles_qualityspeed.radiobutton_shear_int_nearest);
end
switch(data.config.WarpInterpolation)
case{'bicubic'}
set(handles_qualityspeed.uipanel_WarpInterpolation,'SelectedObject',handles_qualityspeed.radiobutton_warp_int_bicubic);
case{'bilinear'}
set(handles_qualityspeed.uipanel_WarpInterpolation,'SelectedObject',handles_qualityspeed.radiobutton_warp_int_bilinear);
case{'nearest'}
set(handles_qualityspeed.uipanel_WarpInterpolation,'SelectedObject',handles_qualityspeed.radiobutton_warp_int_nearest);
end
set(handles_qualityspeed.checkbox_prerender,'Value',data.config.PreRender);
set(handles_qualityspeed.checkbox_storexyz,'Value',data.config.StoreXYZ);
% --- Executes on button press in pushbutton_applyconfig.
function qualityspeed_pushbutton_applyconfig_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton_applyconfig (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
handles_qualityspeed=guidata(data.figurehandles.qualityspeed);
VolumeScaling=get(get(handles_qualityspeed.uipanel_VolumeScaling,'SelectedObject'),'Tag');
PreviewVolumeSize=get(get(handles_qualityspeed.uipanel_PreviewVolumeSize,'SelectedObject'),'Tag');
ShearInterpolation=get(get(handles_qualityspeed.uipanel_ShearInterpolation,'SelectedObject'),'Tag');
WarpInterpolation=get(get(handles_qualityspeed.uipanel_WarpInterpolation,'SelectedObject'),'Tag');
ImageSizeRender=get(get(handles_qualityspeed.uipanel_ImageSizeRender,'SelectedObject'),'Tag');
VolumeScaling=str2double(VolumeScaling(20:end));
ImageSizeRender=str2double(ImageSizeRender(23:end));
PreviewVolumeSize=str2double(PreviewVolumeSize(21:end));
data.config.ShearInterpolation=ShearInterpolation(23:end);
data.config.WarpInterpolation=WarpInterpolation(22:end);
data.config.PreRender=get(handles_qualityspeed.checkbox_prerender,'Value');
data.config.StoreXYZ=get(handles_qualityspeed.checkbox_storexyz,'Value');
if(ImageSizeRender~=data.config.ImageSizeRender)
s=data.config.ImageSizeRender/ImageSizeRender;
data.subwindow(data.axes_select).viewer_matrix=data.subwindow(data.axes_select).viewer_matrix*ResizeMatrix([s s s]);
data.config.ImageSizeRender=ImageSizeRender;
end
scale_change=data.config.VolumeScaling~=VolumeScaling;
if(scale_change)
data.config.VolumeScaling=VolumeScaling;
for dvs=1:length(data.volumes)
data=makeRenderVolume(data,dvs);
end
end
if(data.config.PreviewVolumeSize~=PreviewVolumeSize)
data.config.PreviewVolumeSize=PreviewVolumeSize;
for dvs=1:length(data.volumes)
data=makePreviewVolume(data,dvs);
end
end
for dvs=1:length(data.volumes)
data.volume_id_select(1)=data.volumes(dvs).id;
if((isempty(data.volumes(dvs).volumey)||scale_change)&&data.config.StoreXYZ)
data=makeVolumeXY(data);
end
if(~data.config.StoreXYZ)
data.volumes(dvs).volumex=[]; data.volumes(dvs).volumey=[];
end
end
if((isempty(data.volumes(dvs).normals)||scale_change)&&data.config.PreRender)
% Make normals
for dvs=1:length(data.volumes)
data=computeNormals(data,dvs);
end
end
if(~data.config.PreRender)
data.volumes(dvs).normals=[];
end
data.subwindow(data.axes_select).first_render=true;
setMyData(data);
show3d(false,true);
function data=makeVolumeXY(data,dvs)
if(data.config.StoreXYZ)
data.volumes(dvs).volumex=shiftdim(data.volumes(dvs).volume,1);
data.volumes(dvs).volumey=shiftdim(data.volumes(dvs).volume,2);
else
data.volumes(dvs).volumex=[];
data.volumes(dvs).volumey=[];
end
function data=computeNormals(data,dvs)
if(data.config.PreRender)
% Pre computer Normals for faster shading rendering.
[fy,fx,fz]=gradient(imgaussian(double(data.volumes(dvs).volume),1/2));
flength=sqrt(fx.^2+fy.^2+fz.^2)+1e-6;
data.volumes(dvs).normals=zeros([size(fx) 3]);
data.volumes(dvs).normals(:,:,:,1)=fx./flength;
data.volumes(dvs).normals(:,:,:,2)=fy./flength;
data.volumes(dvs).normals(:,:,:,3)=fz./flength;
else
data.volumes(dvs).normals=[];
end
function I=imgaussian(I,sigma,siz)
% IMGAUSSIAN filters an 1D, 2D or 3D image with an gaussian filter.
% This function uses IMFILTER, for the filtering but instead of using
% a multidimensional gaussian kernel, it uses the fact that a gaussian
% filter can be separated in 1D gaussian kernels.
%
% J=IMGAUSSIAN(I,SIGMA,SIZE)
%
% inputs,
% I: The 1D, 2D, or 3D input image
% SIGMA: The sigma used for the gaussian
% SIZE: Kernel size (single value) (default: sigma*6)
%
% outputs,
% J: The gaussian filterd image
%
% example,
% I = im2double(rgb2gray(imread('peppers.png')));
% figure, imshow(imgaussian(I,3));
%
% Function is written by D.Kroon University of Twente (October 2008)
if(~exist('siz','var')), siz=sigma*6; end
% Make 1D gaussian kernel
x=-(siz/2)+0.5:siz/2;
H = exp(-(x.^2/(2*sigma^2)));
H = H/sum(H(:));
% Filter each dimension with the 1D gaussian kernels
if(ndims(I)==1)
I=imfilter(I,H);
elseif(ndims(I)==2)
Hx=reshape(H,[length(H) 1]);
Hy=reshape(H,[1 length(H)]);
I=imfilter(imfilter(I,Hx),Hy);
elseif(ndims(I)==3)
Hx=reshape(H,[length(H) 1 1]);
Hy=reshape(H,[1 length(H) 1]);
Hz=reshape(H,[1 1 length(H)]);
I=imfilter(imfilter(imfilter(I,Hx),Hy),Hz);
else
error('imgaussian:input','unsupported input dimension');
end
% --- Executes on button press in pushbutton_saveconfig.
function qualityspeed_pushbutton_saveconfig_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton_saveconfig (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
handles_qualityspeed=guidata(data.figurehandles.qualityspeed);
VolumeScaling=get(get(handles_qualityspeed.uipanel_VolumeScaling,'SelectedObject'),'Tag');
PreviewVolumeSize=get(get(handles_qualityspeed.uipanel_PreviewVolumeSize,'SelectedObject'),'Tag');
ShearInterpolation=get(get(handles_qualityspeed.uipanel_ShearInterpolation,'SelectedObject'),'Tag');
WarpInterpolation=get(get(handles_qualityspeed.uipanel_WarpInterpolation,'SelectedObject'),'Tag');
ImageSizeRender=get(get(handles_qualityspeed.uipanel_ImageSizeRender,'SelectedObject'),'Tag');
VolumeScaling=str2double(VolumeScaling(20:end));
PreviewVolumeSize=str2double(PreviewVolumeSize(21:end));
data.config.ImageSizeRender=str2double(ImageSizeRender(23:end));
data.config.ShearInterpolation=ShearInterpolation(23:end);
data.config.WarpInterpolation=WarpInterpolation(22:end);
data.config.PreRender=get(handles_qualityspeed.checkbox_prerender,'Value');
data.config.StoreXYZ=get(handles_qualityspeed.checkbox_storexyz,'Value');
data.config.VolumeScaling=VolumeScaling;
data.config.PreviewVolumeSize=PreviewVolumeSize;
% Save the default config
config=data.config;
functiondir=which('viewer3d.m'); functiondir=functiondir(1:end-length('viewer3d.m'));
save([functiondir '/default_config.mat'],'config')
% --------------------------------------------------------------------
function menu_measure_Callback(hObject, eventdata, handles)
% hObject handle to menu_measure (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_config_contrast_Callback(hObject, eventdata, handles)
% hObject handle to menu_config_contrast (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.figurehandles.contrast=viewer3d_contrast(data.figurehandles.viewer3d);
handles_contrast=guidata(data.figurehandles.contrast);
dvs=eventdata;
data.volume_select=dvs;
c=(data.volumes(dvs).volumemin+data.volumes(dvs).volumemax)/2;
dmin=c-data.volumes(dvs).volumemin;
dmax=data.volumes(dvs).volumemax-c;
amin=c-dmin*4; amax=c+dmax*4;
set(handles_contrast.slider_window_width,'Min',0);
set(handles_contrast.slider_window_width,'Max',amax);
set(handles_contrast.slider_window_level,'Min',amin);
set(handles_contrast.slider_window_level,'Max',amax);
data.volumes(dvs).WindowWidth=min(max(data.volumes(dvs).WindowWidth,0),amax);
data.volumes(dvs).WindowLevel=min(max(data.volumes(dvs).WindowLevel,amin),amax);
set(handles_contrast.slider_window_width,'value',data.volumes(dvs).WindowWidth);
set(handles_contrast.slider_window_level,'value',data.volumes(dvs).WindowLevel);
set(handles_contrast.edit_window_width,'String',num2str(data.volumes(dvs).WindowWidth));
set(handles_contrast.edit_window_level,'String',num2str(data.volumes(dvs).WindowLevel));
setMyData(data);
% --------------------------------------------------------------------
function menu_measure_distance_Callback(hObject, eventdata, handles)
% hObject handle to menu_measure_distance (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.mouse.button='select_distance';
data.mouse.action='measure_distance';
setMyData(data);
set_mouse_shape('select_distance',data)
% --------------------------------------------------------------------
function menu_measure_roi_Callback(hObject, eventdata, handles)
% hObject handle to menu_measure_roi (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.mouse.button='select_roi';
data.mouse.action='measure_roi';
setMyData(data);
set_mouse_shape('select_roi',data)
% --------------------------------------------------------------------
function menu_segment_roi_Callback(hObject, eventdata, handles)
% hObject handle to menu_measure_roi (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.mouse.button='select_roi';
data.mouse.action='segment_roi';
setMyData(data);
viewer3d_segment;
set_mouse_shape('select_roi',data)
function data=checkvolumetype(data,nv)
if(nargin<2), s=1; e=length(data.volumes); else s=nv; e=nv; end
for i=s:e
data.volumes(i).volumemin=double(min(data.volumes(i).volume_original(:)));
data.volumes(i).volumemax=double(max(data.volumes(i).volume_original(:)));
if( data.volumes(i).volumemax==0), data.volumes(i).volumemax=1; end
switch(class(data.volumes(i).volume_original))
case {'uint8','uint16','uint32','int8','int16','int32','single','double'}
otherwise
viewer3d_error({'Unsupported input datatype converted to double'});
data.volumes(i).volume_original=double(data.volumes(i).volume_original);
end
data.volumes(i).WindowWidth=data.volumes(i).volumemax-data.volumes(i).volumemin;
data.volumes(i).WindowLevel=0.5*(data.volumes(i).volumemax+data.volumes(i).volumemin);
end
% --- Executes on scroll wheel click while the figure is in focus.
function figure1_WindowScrollWheelFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata structure with the following fields (see FIGURE)
% VerticalScrollCount: signed integer indicating direction and number of clicks
% VerticalScrollAmount: number of lines scrolled for each click
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
if(isempty(data.axes_select)), return, end
switch data.subwindow(data.axes_select).render_type
case {'slicex','slicey','slicez'}
handles=guidata(hObject);
data=changeslice(eventdata.VerticalScrollCount,handles,data);
setMyData(data);
show3d(false,true);
end
% --- Executes on key press with focus on figure1 and none of its controls.
function figure1_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata structure with the following fields (see FIGURE)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
if(strcmp(eventdata.Key,'uparrow')), eventdata.Character='+'; end
if(strcmp(eventdata.Key,'downarrow')), eventdata.Character='-'; end
switch data.subwindow(data.axes_select).render_type
case {'slicex','slicey','slicez'}
handles=guidata(hObject);
switch(eventdata.Character)
case '+'
data=changeslice(1,handles,data);
setMyData(data); show3d(true,true);
case '-'
data=changeslice(-1,handles,data);
setMyData(data); show3d(true,true);
case 'r'
menu_measure_roi_Callback(hObject, eventdata, handles);
case 'd'
menu_measure_distance_Callback(hObject, eventdata, handles);
case 'l'
menu_measure_landmark_Callback(hObject, eventdata, handles);
case 'c'
menu_segment_roi_Callback(hObject, eventdata, handles);
otherwise
end
otherwise
end
function data=changeslice(updown,handles,data)
dvss=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
switch data.subwindow(data.axes_select).render_type
case 'slicex'
data.subwindow(data.axes_select).SliceSelected(1)=data.subwindow(data.axes_select).SliceSelected(1)+updown;
if(data.subwindow(data.axes_select).SliceSelected(1)>size(data.volumes(dvss).volume_original,1)), data.subwindow(data.axes_select).SliceSelected(1)=size(data.volumes(dvss).volume_original,1); end
case 'slicey'
data.subwindow(data.axes_select).SliceSelected(2)=data.subwindow(data.axes_select).SliceSelected(2)+updown;
if(data.subwindow(data.axes_select).SliceSelected(2)>size(data.volumes(dvss).volume_original,2)), data.subwindow(data.axes_select).SliceSelected(2)=size(data.volumes(dvss).volume_original,2); end
case 'slicez'
data.subwindow(data.axes_select).SliceSelected(3)=data.subwindow(data.axes_select).SliceSelected(3)+updown;
if(data.subwindow(data.axes_select).SliceSelected(3)>size(data.volumes(dvss).volume_original,3)), data.subwindow(data.axes_select).SliceSelected(3)=size(data.volumes(dvss).volume_original,3); end
end
% Boundary limit
data.subwindow(data.axes_select).SliceSelected(data.subwindow(data.axes_select).SliceSelected<1)=1;
% Stop measurement
data.mouse.action='';
% --- Executes on key release with focus on figure1 and none of its controls.
function figure1_KeyReleaseFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata structure with the following fields (see FIGURE)
% Key: name of the key that was released, in lower case
% Character: character interpretation of the key(s) that was released
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) released
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
switch data.subwindow(data.axes_select).render_type
case {'slicex','slicey','slicez'}
show3d(false,true);
end
function data=InfoOnScreen(data)
if (size(data.subwindow(data.axes_select).total_image,3)==3)
I=data.subwindow(data.axes_select).total_image;
else
% Greyscale to color
I(:,:,1)=data.subwindow(data.axes_select).total_image;
I(:,:,2)=data.subwindow(data.axes_select).total_image;
I(:,:,3)=data.subwindow(data.axes_select).total_image;
end
if(data.subwindow(data.axes_select).render_type(1)=='s')
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
info=cell(1,5);
switch data.subwindow(data.axes_select).render_type
case 'slicex'
info{1}=['Slice X : ' num2str(data.subwindow(data.axes_select).SliceSelected(1))];
case 'slicey'
info{1}=['Slice y : ' num2str(data.subwindow(data.axes_select).SliceSelected(2))];
case 'slicez'
info{1}=['Slice Z : ' num2str(data.subwindow(data.axes_select).SliceSelected(3))];
end
VL=data.subwindow(data.axes_select).VoxelLocation;
VL(1)=min(max(VL(1),1),data.volumes(dvs).Size_original(1));
VL(2)=min(max(VL(2),1),data.volumes(dvs).Size_original(2));
VL(3)=min(max(VL(3),1),data.volumes(dvs).Size_original(3));
info{2}=['ROIs mm^3: ' num2str(data.subwindow(data.axes_select).tVolumemm)];
info{3}=['x,y,z px: ' num2str(VL(1)) ' - ' num2str(VL(2)) ' - ' num2str(VL(3))];
info{4}=['x,y,z mm: ' num2str(VL(1)*data.volumes(dvs).Scales(1)) ' - ' num2str(VL(2)*data.volumes(dvs).Scales(2)) ' - ' num2str(VL(3)*data.volumes(dvs).Scales(3))];
info{5}=['Val: ' num2str(data.volumes(dvs).volume_original(VL(1),VL(2),VL(3)))];
I=bitmaptext(info,I,[1 1],struct('Color',[0 1 0 1]));
end
data.subwindow(data.axes_select).total_image=I;
function I=bitmaptext(lines,I,pos,options)
% The function BITMAPTEXT will insert textline(s) on the specified position
% in the image.
%
% I=bitmaptext(Text,Ibackground,Position,options)
%
% inputs,
% Text : Cell array with text lines
% Ibackground: the bitmap used as background when a m x n x 3 matrix
% color plots are made, when m x n a greyscale plot. If empty []
% autosize to fit text.
% Position: x,y position of the text
% options: struct with options such as color
%
% outputs,
% Iplot: The bitmap containing the plotted text
%
% note,
% Colors are always [r(ed) g(reen) b(lue) a(pha)], with range 0..1.
% when Ibackground is grayscale, the mean of r,g,b is used as grey value.
%
% options,
% options.Color: The color of the text.
% options.FontSize: The size of the font, 1,2 or 3 (small,medium,large).
%
% example,
%
% % The text consisting of 2 lines
% lines={'a_A_j_J?,','ImageText version 1.1'};
% % Background image
% I=ones([256 256 3]);
% % Plot text into background image
% I=bitmaptext(lines,I,[1 1],struct('FontSize',3));
% % Show the result
% figure, imshow(I),
%
% Function is written by D.Kroon University of Twente (March 2009)
global character_images;
% Process inputs
defaultoptions=struct('Color',[0 0 1 1],'FontSize',1);
if(~exist('options','var')),
options=defaultoptions;
else
tags = fieldnames(defaultoptions);
for i=1:length(tags)
if(~isfield(options,tags{i})), options.(tags{i})=defaultoptions.(tags{i}); end
end
if(length(tags)~=length(fieldnames(options))),
warning('register_images:unknownoption','unknown options found');
end
end
% If single line make it a cell array
if(~iscell(lines)), lines={lines}; end
if(~exist('I','var')), I=[]; end
if(exist('pos','var')),
if(length(pos)~=2)
error('imagtext:inputs','position must have x,y coordinates');
end
else
pos=[1 1];
end
% Round the position
pos=round(pos);
% Set the size of the font
fsize=options.FontSize;
% The character bitmap and character set;
character_set='abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890!@#$%^&*()_+-=[]\;'''',./{}|:"<>?';
if(isempty(character_images)), character_images=load_font(); end
% Font parameters
Font_sizes_x=[8 10 11];
Font_sizes_y=[13 15 18];
Font_startx=[1 1 1];
Font_starty=[1 14 29];
% Get maximum sentence length
lengths=zeros(1,length(lines));
for i=1:length(lines), lengths(i)=length(lines{i}); end
max_line_length=max(lengths);
% Make text image from the lines
lines_image=zeros([(Font_sizes_y(fsize)+4)*length(lines),max_line_length*Font_sizes_x(fsize)],'double');
for j=1:length(lines)
line=lines{j};
for i=1:length(line),
[t,p]=find(character_set==line(i));
if(~isempty(p))
p=p(1)-1;
character_bitmap=character_images(Font_starty(fsize):(Font_starty(fsize)+Font_sizes_y(fsize)-1),Font_startx(fsize)+(1+p*Font_sizes_x(fsize)):Font_startx(fsize)+((p+1)*Font_sizes_x(fsize)));
posx=Font_sizes_x(fsize)*(i-1);
posy=(Font_sizes_y(fsize)+4)*(j-1);
lines_image((1:Font_sizes_y(fsize))+posy,(1:Font_sizes_x(fsize))+posx)=character_bitmap;
end
end
end
if(isempty(I)), I=zeros([size(lines_image) 3]); end
% Remove part of textimage which will be outside of the output image
if(pos(1)<1), lines_image=lines_image(2-pos(1):end,:); pos(1)=1; end
if(pos(2)<2), lines_image=lines_image(:,2-pos(2):end); pos(2)=1; end
if((pos(1)+size(lines_image,1))>size(I,1)), dif=size(I,1)-(pos(1)+size(lines_image,1)); lines_image=lines_image(1:end+dif,:); end
if((pos(2)+size(lines_image,2))>size(I,2)), dif=size(I,2)-(pos(2)+size(lines_image,2)); lines_image=lines_image(:,1:end+dif); end
% Make text image the same size as background image
I_line=zeros([size(I,1) size(I,2)]);
I_line(pos(1):(pos(1)+size(lines_image,1)-1),pos(2):(pos(2)+size(lines_image,2)-1))=lines_image;
I_line=I_line*options.Color(4);
% Insert the text image into the output image
if(~isempty(lines_image))
if(size(I,3)==3)
for i=1:3
I(:,:,i)=I(:,:,i).*(1-I_line)+options.Color(i)*(I_line);
end
else
I=I.*(1-I_line)+mean(options.Color(1:3))*(I_line);
end
end
function character_images=load_font()
character_images=uint8([0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 9 9 6 0 0 0 0 1 4 2 3 0 0 0 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0;
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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 9 9 9 9 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 9 9 9 9 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 9 9 9 9 1 0 0 0 0 0 0 0 0 0 0 1 8 9 9 9 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 8 9 9 9 9 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0;
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 8 9 9 9 9 9 9 9 9 9 9 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]);
character_images=double(character_images)/9;
function [x_2d,y_2d]=voxelposition_to_imageposition(x,y,z,data)
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
data.subwindow(data.axes_select).Mview=data.subwindow(data.axes_select).viewer_matrix;
switch (data.subwindow(data.axes_select).render_type)
case {'slicex'}
sizeIin=[size(data.volumes(dvs).volume_original,2) size(data.volumes(dvs).volume_original,3)];
M=[data.subwindow(data.axes_select).Mview(1,2) data.subwindow(data.axes_select).Mview(1,3) data.subwindow(data.axes_select).Mview(1,4); data.subwindow(data.axes_select).Mview(2,2) data.subwindow(data.axes_select).Mview(2,3) data.subwindow(data.axes_select).Mview(2,4); 0 0 1];
case {'slicey'}
sizeIin=[size(data.volumes(dvs).volume_original,1) size(data.volumes(dvs).volume_original,3)];
M=[data.subwindow(data.axes_select).Mview(1,1) data.subwindow(data.axes_select).Mview(1,3) data.subwindow(data.axes_select).Mview(1,4); data.subwindow(data.axes_select).Mview(2,1) data.subwindow(data.axes_select).Mview(2,3) data.subwindow(data.axes_select).Mview(2,4); 0 0 1]; % Rotate 90
case {'slicez'}
sizeIin=[size(data.volumes(dvs).volume_original,1) size(data.volumes(dvs).volume_original,2)];
M=[data.subwindow(data.axes_select).Mview(1,1) data.subwindow(data.axes_select).Mview(1,2) data.subwindow(data.axes_select).Mview(1,4); data.subwindow(data.axes_select).Mview(2,1) data.subwindow(data.axes_select).Mview(2,2) data.subwindow(data.axes_select).Mview(2,4); 0 0 1];
end
switch (data.subwindow(data.axes_select).render_type)
case {'slicex'}
Tlocalx=y; Tlocaly=z;
case {'slicey'}
Tlocalx=x; Tlocaly=z;
case {'slicez'}
Tlocalx=x; Tlocaly=y;
end
% Calculate center of the input image
mean_in=sizeIin/2;
x_2d=zeros(1,length(Tlocalx)); y_2d=zeros(1,length(Tlocalx));
Tlocalx=Tlocalx-mean_in(1);
Tlocaly=Tlocaly-mean_in(2);
for i=1:length(x)
vector=M*[Tlocalx(i);Tlocaly(i);1];
x_2d(i)=vector(1);
y_2d(i)=vector(2);
end
% Calculate center of the output image
mean_out=[data.config.ImageSizeRender data.config.ImageSizeRender]/2;
% Make center of the image coordinates 0,0
x_2d=x_2d+mean_out(1);
y_2d=y_2d+mean_out(2);
function data=mouseposition_to_voxelposition(data)
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
if(isempty(dvs)), return; end
data.subwindow(data.axes_select).Mview=data.subwindow(data.axes_select).viewer_matrix;
switch (data.subwindow(data.axes_select).render_type)
case {'slicex'}
sizeIin=[size(data.volumes(dvs).volume_original,2) size(data.volumes(dvs).volume_original,3)];
M=[data.subwindow(data.axes_select).Mview(1,2) data.subwindow(data.axes_select).Mview(1,3) data.subwindow(data.axes_select).Mview(1,4); data.subwindow(data.axes_select).Mview(2,2) data.subwindow(data.axes_select).Mview(2,3) data.subwindow(data.axes_select).Mview(2,4); 0 0 1];
case {'slicey'}
sizeIin=[size(data.volumes(dvs).volume_original,1) size(data.volumes(dvs).volume_original,3)];
M=[data.subwindow(data.axes_select).Mview(1,1) data.subwindow(data.axes_select).Mview(1,3) data.subwindow(data.axes_select).Mview(1,4); data.subwindow(data.axes_select).Mview(2,1) data.subwindow(data.axes_select).Mview(2,3) data.subwindow(data.axes_select).Mview(2,4); 0 0 1]; % Rotate 90
case {'slicez'}
sizeIin=[size(data.volumes(dvs).volume_original,1) size(data.volumes(dvs).volume_original,2)];
M=[data.subwindow(data.axes_select).Mview(1,1) data.subwindow(data.axes_select).Mview(1,2) data.subwindow(data.axes_select).Mview(1,4); data.subwindow(data.axes_select).Mview(2,1) data.subwindow(data.axes_select).Mview(2,2) data.subwindow(data.axes_select).Mview(2,4); 0 0 1];
end
M=inv(M);
% Get the mouse position
x_2d=data.subwindow(data.axes_select).mouse_position(2);
y_2d=data.subwindow(data.axes_select).mouse_position(1);
% To rendered image position
x_2d=x_2d*data.config.ImageSizeRender; y_2d=y_2d*data.config.ImageSizeRender;
% Calculate center of the input image
mean_in=sizeIin/2;
% Calculate center of the output image
mean_out=[data.config.ImageSizeRender data.config.ImageSizeRender]/2;
% Calculate the Transformed coordinates
x_2d=x_2d - mean_out(1);
y_2d=y_2d - mean_out(2);
location(1)= mean_in(1) + M(1,1) * x_2d + M(1,2) *y_2d + M(1,3) * 1;
location(2)= mean_in(2) + M(2,1) * x_2d + M(2,2) *y_2d + M(2,3) * 1;
switch (data.subwindow(data.axes_select).render_type)
case {'slicex'}
data.subwindow(data.axes_select).VoxelLocation=[data.subwindow(data.axes_select).SliceSelected(1) location(1) location(2)];
case {'slicey'}
data.subwindow(data.axes_select).VoxelLocation=[location(1) data.subwindow(data.axes_select).SliceSelected(2) location(2)];
case {'slicez'}
data.subwindow(data.axes_select).VoxelLocation=[location(1) location(2) data.subwindow(data.axes_select).SliceSelected(3)];
end
data.subwindow(data.axes_select).VoxelLocation=round(data.subwindow(data.axes_select).VoxelLocation);
data.subwindow(data.axes_select).VoxelLocation(data.subwindow(data.axes_select).VoxelLocation<1)=1;
if(data.subwindow(data.axes_select).VoxelLocation(1)>size(data.volumes(dvs).volume_original,1)), data.subwindow(data.axes_select).VoxelLocation(1)=size(data.volumes(dvs).volume_original,1); end
if(data.subwindow(data.axes_select).VoxelLocation(2)>size(data.volumes(dvs).volume_original,2)), data.subwindow(data.axes_select).VoxelLocation(2)=size(data.volumes(dvs).volume_original,2); end
if(data.subwindow(data.axes_select).VoxelLocation(3)>size(data.volumes(dvs).volume_original,3)), data.subwindow(data.axes_select).VoxelLocation(3)=size(data.volumes(dvs).volume_original,3); end
% --- Executes on mouse motion over figure - except title and menu.
function brightness_contrast_WindowButtonMotionFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
dvs=data.volume_select;
if(~isempty(data.figurehandles.contrast)&&ishandle(data.figurehandles.contrast))
handles_contrast=guidata(data.figurehandles.contrast);
level=get(handles_contrast.slider_window_level,'value');
width=get(handles_contrast.slider_window_width,'value');
if((width~=data.volumes(dvs).WindowWidth)||(level~=data.volumes(dvs).WindowLevel))
data.volumes(dvs).WindowWidth=width;
data.volumes(dvs).WindowLevel=level;
set(handles_contrast.edit_window_width,'String',num2str(data.volumes(dvs).WindowWidth));
set(handles_contrast.edit_window_level,'String',num2str(data.volumes(dvs).WindowLevel));
setMyData(data);
allshow3d(false,false);
end
end
function brightness_contrast_pushbutton_auto_Callback(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
dvs=data.volume_select;
handles_contrast=guidata(data.figurehandles.contrast);
data.volumes(dvs).WindowWidth=data.volumes(dvs).volumemax-data.volumes(dvs).volumemin;
data.volumes(dvs).WindowLevel=0.5*(data.volumes(dvs).volumemax+data.volumes(dvs).volumemin);
set(handles_contrast.slider_window_level,'value',data.volumes(dvs).WindowLevel);
set(handles_contrast.slider_window_width,'value',data.volumes(dvs).WindowWidth);
setMyData(data);
allshow3d(false,false);
% --------------------------------------------------------------------
function menu_config_slicescolor_Callback(hObject, eventdata, handles)
% hObject handle to menu_config_slicescolor (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData();
data.axes_select=eventdata;
if(data.subwindow(data.axes_select).ColorSlice)
data.subwindow(data.axes_select).ColorSlice=false;
else
data.subwindow(data.axes_select).ColorSlice=true;
end
setMyData(data);
set_menu_checks(data);
show3d(false,true);
% --------------------------------------------------------------------
function menu_measure_landmark_Callback(hObject, eventdata, handles)
% hObject handle to menu_measure_landmark (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.mouse.button='select_landmark';
data.mouse.action='measure_landmark';
setMyData(data);
set_mouse_shape('select_landmark',data)
% --------------------------------------------------------------------
function menu_data_info_Callback(hObject, eventdata, handles)
% hObject handle to menu_data_info (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
dvs=eventdata;
viewer3d_dicominfo(data.volumes(dvs).info);
% --------------------------------------------------------------------
function menu_addseg_Callback(hObject, eventdata, handles)
% hObject handle to menu_data_info (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
dvs=eventdata;
volumedata=data.volumes(dvs);
Info=[];
Scales=volumedata.Scales;
V=zeros(size(volumedata.volume_original),'uint8');
Editable=true;
addVolume(V,Scales,Info,Editable);
%viewer3d_dicominfo(data.volumes(dvs).info);
% --------------------------------------------------------------------
function menu_click_roi_Callback(hObject, eventdata, handles)
% hObject handle to menu_click_roi (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.mouse.button='click_roi';
data.mouse.action='click_roi';
setMyData(data);
set_mouse_shape('click_roi',data)
% --------------------------------------------------------------------
function load_filename1_Callback(hObject, eventdata, handles)
% hObject handle to load_filename1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
load_view(data.history.filenames{1})
% --------------------------------------------------------------------
function load_filename2_Callback(hObject, eventdata, handles)
% hObject handle to load_filename2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
load_view(data.history.filenames{2})
% --------------------------------------------------------------------
function load_filename3_Callback(hObject, eventdata, handles)
% hObject handle to load_filename3 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
load_view(data.history.filenames{3})
% --------------------------------------------------------------------
function load_filename4_Callback(hObject, eventdata, handles)
% hObject handle to load_filename4 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
load_view(data.history.filenames{4})
% --------------------------------------------------------------------
function load_filename5_Callback(hObject, eventdata, handles)
% hObject handle to load_filename5 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
load_view(data.history.filenames{5})
function showhistory(data)
for i=1:5
filename=data.history.filenames{i};
switch(i)
case 1, h=data.handles.load_filename1;
case 2, h=data.handles.load_filename2;
case 3, h=data.handles.load_filename3;
case 4, h=data.handles.load_filename4;
case 5, h=data.handles.load_filename5;
end
if(~isempty(filename))
set(h,'Visible','on');
set(h,'Label',['...' filename(max(end-40,1):end)]);
else
set(h,'Visible','off');
end
end
% --------------------------------------------------------------------
function menu_windows1_Callback(hObject, eventdata, handles)
% hObject handle to menu_windows1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.NumberWindows=1;
data=deleteWindows(data);
data=addWindows(data);
setMyData(data);
allshow3d(false,true);
% --------------------------------------------------------------------
function menu_windows2_Callback(hObject, eventdata, handles)
% hObject handle to menu_windows2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.NumberWindows=2;
data=deleteWindows(data);
data=addWindows(data);
setMyData(data);
allshow3d(false,true);
% --------------------------------------------------------------------
function menu_windows3_Callback(hObject, eventdata, handles)
% hObject handle to menu_windows3 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.NumberWindows=3;
data=deleteWindows(data);
data=addWindows(data);
setMyData(data);
allshow3d(false,true);
% --------------------------------------------------------------------
function menu_windows4_Callback(hObject, eventdata, handles)
% hObject handle to menu_windows4 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.NumberWindows=4;
data=deleteWindows(data);
data=addWindows(data);
setMyData(data);
allshow3d(false,true);
function menu_ChangeVolume_Callback(hObject, eventdata, handles)
data=getMyData(); if(isempty(data)), return, end
s=eventdata(2);
if(s>0);
switch length(eventdata)
case 2
data.subwindow(eventdata(1)).volume_id_select=data.volumes(eventdata(2)).id;
case 3
data.subwindow(eventdata(1)).volume_id_select=[data.volumes(eventdata(2)).id; data.volumes(eventdata(3)).id];
case 4
data.subwindow(eventdata(1)).volume_id_select=[data.volumes(eventdata(2)).id; data.volumes(eventdata(3)).id; data.volumes(eventdata(4)).id];
end
else
data.subwindow(eventdata(1)).volume_id_select=0;
data.subwindow(eventdata(1)).render_type='black';
end
data.axes_select=eventdata(1);
if(s>0)
data.subwindow(eventdata(1)).Zoom=(sqrt(3)./sqrt(sum(data.volumes(s).Scales.^2)));
data=set_initial_view_matrix(data);
data.subwindow(data.axes_select).SliceSelected=round(data.volumes(s).Size/2);
end
setMyData(data);
show3d(false,true);
set_menu_checks(data);
function menu_ChangeRender_Callback(hObject, eventdata, handles) %#ok<*INUSD,*INUSL>
data=getMyData(); if(isempty(data)), return, end
if(data.subwindow(eventdata(1)).volume_id_select(1)>0)
data.axes_select=eventdata(1);
data.subwindow(data.axes_select).render_type=data.rendertypes(eventdata(2)).type;
switch data.rendertypes(eventdata(2)).type
case {'slicex','slicey','slicez'}
data=set_initial_view_matrix(data);
end
set_menu_checks(data);
data.subwindow(data.axes_select).first_render=true;
setMyData(data);
show3d(false,true);
end
function data=deleteWindows(data)
for i=(data.NumberWindows+1):length(data.subwindow)
h=data.subwindow(i).handles.axes;
if(~isempty(h)),
delete(data.subwindow(i).handles.axes),
set(data.subwindow(i).handles.uipanelmenu,'UIContextMenu',uicontextmenu);
menubar
delete(data.subwindow(i).handles.uipanelmenu),
end
data.subwindow(i).handles.axes=[];
end
function data=addWindows(data)
for i=1:data.NumberWindows
if(length(data.subwindow)>=i), h=data.subwindow(i).handles.axes; else h=[]; end
if(isempty(h)),
data.subwindow(i).click_roi=false;
data.subwindow(i).tVolumemm=0;
data.subwindow(i).VoxelLocation=[1 1 1];
data.subwindow(i).first_render=true;
data.subwindow(i).mouse_position_pressed=[0 0];
data.subwindow(i).mouse_position=[0 0];
data.subwindow(i).mouse_position_last=[0 0];
data.subwindow(i).shading_material='shiny';
data.subwindow(i).combine='rgb';
data.subwindow(i).volume_id_select=0;
data.subwindow(i).object_id_select=0;
data.subwindow(i).first_render=true;
data.subwindow(i).ColorSlice=false;
data.subwindow(i).render_type='black';
data.subwindow(i).ViewerVector = [0 0 1];
data.subwindow(i).LightVector = [0.5 -0.5 -0.67];
data.subwindow(i).handles.uipanelmenu=uipanel('units','normalized');
data.subwindow(i).handles.axes=axes;
set(data.subwindow(i).handles.axes,'units','normalized');
data.subwindow(i).menu.Handle=[];
end
end
data=addWindowsMenus(data);
% Units Normalized Margin
switch(data.NumberWindows)
case 1
w=1; h=1;
makeWindow(data,1,0,0,w,h);
case 2
w=0.5; h=1;
makeWindow(data,1,0,0,w,h);
makeWindow(data,2,0.5,0,w,h);
case 3
w=1/3; h=1;
makeWindow(data,1,0,0,w,h);
makeWindow(data,2,1/3,0,w,h);
makeWindow(data,3,2/3,0,w,h);
case 4
w=0.5; h=0.5;
makeWindow(data,1,0.5,0 ,w,h);
makeWindow(data,2,0.5,0.5,w,h);
makeWindow(data,3,0 ,0.5,w,h);
makeWindow(data,4,0 ,0 ,w,h);
end
menubar
function data=makeWindow(data,id,x,y,w,h)
a=0.01;
set(data.subwindow(id).handles.axes, 'position', [(x+a/2) (y+a/2) (w-a) (h-0.07-a) ]);
set(data.subwindow(id).handles.uipanelmenu, 'position', [x y w h]);
function data=addWindowsMenus(data)
for i=1:data.NumberWindows
% Attach a contextmenu (right-mouse button menu)
if(ishandle(data.subwindow(i).menu.Handle))
delete(data.subwindow(i).menu.Handle);
data.subwindow(i).menu=[];
end
Menu(1).Label='Render';
Menu(1).Tag='menu_render';
Menu(1).Callback='';
for f=1:length(data.rendertypes)
Menu(1).Children(f).Label=data.rendertypes(f).label;
Menu(1).Children(f).Callback=['viewer3d(''menu_ChangeRender_Callback'',gcbo,[' num2str(i) ' ' num2str(f) '],guidata(gcbo))'];
end
Menu(2).Label='Volume';
hn=0;
for f=0:length(data.volumes)
if(f==0),
name='None';
g=[];
else
name=data.volumes(f).name;
g=structfind(data.volumes(f+1:end),'Size_original',data.volumes(f).Size_original);
if(~isempty(g)); g=g+f; g=g(1:min(end,2)); end
end
hn=hn+1;
Menu(2).Children(hn).Callback=['viewer3d(''menu_ChangeVolume_Callback'',gcbo,[' num2str(i) ' ' num2str(f) '],guidata(gcbo))'];
Menu(2).Children(hn).Label=name;
Menu(2).Children(hn).Tag=['wmenu-' num2str(i) '-' num2str(f)];
if(~isempty(g))
hn=hn+1;
Menu(2).Children(hn).Callback=['viewer3d(''menu_ChangeVolume_Callback'',gcbo,[' num2str(i) ' ' num2str(f) ' ' num2str(g(1)) '],guidata(gcbo))'];
Menu(2).Children(hn).Label=[name ' & ' data.volumes(g(1)).name];
Menu(2).Children(hn).Tag=['wmenu-' num2str(i) '-' num2str(f) '-' num2str(g(1))];
if(length(g)>1)
hn=hn+1;
Menu(2).Children(hn).Callback=['viewer3d(''menu_ChangeVolume_Callback'',gcbo,[' num2str(i) ' ' num2str(f) ' ' num2str(g(1)) ' ' num2str(g(2)) '],guidata(gcbo))'];
Menu(2).Children(hn).Label=[name ' & ' data.volumes(g(1)).name ' & ' data.volumes(g(2)).name];
Menu(2).Children(hn).Tag=['wmenu-' num2str(i) '-' num2str(f) '-' num2str(g(1)) '-' num2str(g(2)) ];
end
end
end
Menu(3).Label='Config';
Menu(3).Tag='menu_config';
Menu(3).Callback='viewer3d(''menu_measure_Callback'',gcbo,[],guidata(gcbo))';
Menu(3).Children(1).Label='Light Vector';
Menu(3).Children(1).Tag='menu_lightvector';
Menu(3).Children(1).Callback=['viewer3d(''menu_lightvector_Callback'',gcbo,' num2str(i) ',guidata(gcbo))'];
Menu(3).Children(2).Label='Shading Shiny';
Menu(3).Children(2).Tag='menu_shiny';
Menu(3).Children(2).Callback=['viewer3d(''menu_shiny_Callback'',gcbo,' num2str(i) ',guidata(gcbo))'];
Menu(3).Children(3).Label='Shading Dull';
Menu(3).Children(3).Tag='menu_dull';
Menu(3).Children(3).Callback=['viewer3d(''menu_dull_Callback'',gcbo,' num2str(i) ',guidata(gcbo))'];
Menu(3).Children(4).Label='Shading Metal';
Menu(3).Children(4).Tag='menu_metal';
Menu(3).Children(4).Callback=['viewer3d(''menu_metal_Callback'',gcbo,' num2str(i) ',guidata(gcbo))'];
Menu(3).Children(5).Label='Slices Color';
Menu(3).Children(5).Tag='menu_config_slicescolor';
Menu(3).Children(5).Callback=['viewer3d(''menu_config_slicescolor_Callback'',gcbo,' num2str(i) ',guidata(gcbo))'];
Menu(3).Children(6).Label='Combine Transparent';
Menu(3).Children(6).Tag='menu_combine_trans';
Menu(3).Children(6).Callback=['viewer3d(''menu_combine_Callback'',gcbo,[' num2str(i) ' 1],guidata(gcbo))'];
Menu(3).Children(7).Label='Combine RGB';
Menu(3).Children(7).Tag='menu_combine_rgb';
Menu(3).Children(7).Callback=['viewer3d(''menu_combine_Callback'',gcbo,[' num2str(i) ' 2],guidata(gcbo))'];
Menu(4).Label='Measure';
Menu(4).Tag='menu_measure';
Menu(4).Callback='viewer3d(''menu_measure_Callback'',gcbo,[],guidata(gcbo))';
Menu(4).Children(1).Label='Distance (key D)';
Menu(4).Children(1).Tag='menu_measure_distance';
Menu(4).Children(1).Callback='viewer3d(''menu_measure_distance_Callback'',gcbo,[],guidata(gcbo))';
Menu(4).Children(2).Label='Roi Selection (key R)';
Menu(4).Children(2).Tag='menu_measure_roi';
Menu(4).Children(2).Callback='viewer3d(''menu_measure_roi_Callback'',gcbo,[],guidata(gcbo))';
Menu(4).Children(3).Label='LandMark (key L)';
Menu(4).Children(3).Tag='menu_measure_landmark';
Menu(4).Children(3).Callback='viewer3d(''menu_measure_landmark_Callback'',gcbo,[],guidata(gcbo))';
Menu(5).Label='Segment';
Menu(5).Tag='menu_segment';
Menu(5).Callback='viewer3d(''menu_measure_Callback'',gcbo,[],guidata(gcbo))';
Menu(5).Children(1).Label='Roi Selection (key C)';
Menu(5).Children(1).Tag='menu_segment_roi';
Menu(5).Children(1).Callback='viewer3d(''menu_segment_roi_Callback'',gcbo,[],guidata(gcbo))';
handle_menu=uicontextmenu;
Menu=addMenu(handle_menu,Menu);
data.subwindow(i).menu.Handle=handle_menu;
data.subwindow(i).menu.Children=Menu;
set(data.subwindow(i).handles.uipanelmenu,'UIContextMenu',data.subwindow(i).menu.Handle);
end
menubar
set_menu_checks(data);
% --------------------------------------------------------------------
function menu_window_Callback(hObject, eventdata, handles)
% hObject handle to menu_window (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_volume_ws_Callback(hObject, eventdata, handles)
% hObject handle to menu_window (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
volume_select=eventdata;
% Get variables in the workspace
assignin('base','VolumeData',data.volumes(volume_select).volume_original);
assignin('base','VolumeInfo',data.volumes(volume_select).info);
assignin('base','VolumeScales',data.volumes(volume_select).Scales);
% --------------------------------------------------------------------
function menu_volume_close_Callback(hObject, eventdata, handles)
% hObject handle to menu_window (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
volume_select=eventdata;
data.volume_id_select(1)=data.volumes(volume_select).id;
for i=1:data.NumberWindows
if(any(data.subwindow(i).volume_id_select==data.volume_id_select))
data.subwindow(i).volume_id_select=0;
data.subwindow(i).render_type='black';
end
end
delete(data.MenuVolume(volume_select).Handle);
data.MenuVolume(volume_select)=[];
data.volumes(volume_select)=[];
data=addWindowsMenus(data);
setMyData(data);
addMenuVolume();
set_menu_checks(data);
allshow3d(false,true);
function Menu=showmenu(handle_figure)
Menu(1).Label='File';
Menu(1).Tag='menu_file';
Menu(1).Callback='viewer3d(''menu_file_Callback'',gcbo,[],guidata(gcbo))';
Menu(1).Children(1).Label='Load View';
Menu(1).Children(1).Tag='menu_load_view';
Menu(1).Children(1).Callback='viewer3d(''menu_load_view_Callback'',gcbo,[],guidata(gcbo))';
Menu(1).Children(2).Label='Load Workspace Variable';
Menu(1).Children(2).Tag='menu_load_worksp';
Menu(1).Children(2).Callback='viewer3d(''menu_load_worksp_Callback'',gcbo,[],guidata(gcbo))';
Menu(1).Children(3).Label='Open Medical 3D File';
Menu(1).Children(3).Tag='menu_load_data';
Menu(1).Children(3).Callback='viewer3d(''menu_load_data_Callback'',gcbo,[],guidata(gcbo))';
Menu(1).Children(4).Label='Save View';
Menu(1).Children(4).Tag='menu_save_view';
Menu(1).Children(4).Callback='viewer3d(''menu_save_view_Callback'',gcbo,[],guidata(gcbo))';
Menu(1).Children(5).Label='Save Picture';
Menu(1).Children(5).Tag='menu_save_picture';
Menu(1).Children(5).Callback='viewer3d(''menu_save_picture_Callback'',gcbo,[],guidata(gcbo))';
Menu(1).Children(6).Label='filename1';
Menu(1).Children(6).Tag='load_filename1';
Menu(1).Children(6).Callback='viewer3d(''load_filename1_Callback'',gcbo,[],guidata(gcbo))';
Menu(1).Children(7).Label='filename2';
Menu(1).Children(7).Tag='load_filename2';
Menu(1).Children(7).Callback='viewer3d(''load_filename2_Callback'',gcbo,[],guidata(gcbo))';
Menu(1).Children(8).Label='filename3';
Menu(1).Children(8).Tag='load_filename3';
Menu(1).Children(8).Callback='viewer3d(''load_filename3_Callback'',gcbo,[],guidata(gcbo))';
Menu(1).Children(9).Label='filename4';
Menu(1).Children(9).Tag='load_filename4';
Menu(1).Children(9).Callback='viewer3d(''load_filename4_Callback'',gcbo,[],guidata(gcbo))';
Menu(1).Children(10).Label='filename5';
Menu(1).Children(10).Tag='load_filename5';
Menu(1).Children(10).Callback='viewer3d(''load_filename5_Callback'',gcbo,[],guidata(gcbo))';
Menu(2).Label='Window';
Menu(2).Tag='menu_window';
Menu(2).Callback='viewer3d(''menu_window_Callback'',gcbo,[],guidata(gcbo))';
Menu(2).Children(1).Label='One Window';
Menu(2).Children(1).Tag='menu_windows1';
Menu(2).Children(1).Callback='viewer3d(''menu_windows1_Callback'',gcbo,[],guidata(gcbo))';
Menu(2).Children(2).Label='Two Windows';
Menu(2).Children(2).Tag='menu_windows2';
Menu(2).Children(2).Callback='viewer3d(''menu_windows2_Callback'',gcbo,[],guidata(gcbo))';
Menu(2).Children(3).Label='Three Windows';
Menu(2).Children(3).Tag='menu_windows3';
Menu(2).Children(3).Callback='viewer3d(''menu_windows3_Callback'',gcbo,[],guidata(gcbo))';
Menu(2).Children(4).Label='Four Windows';
Menu(2).Children(4).Tag='menu_windows4';
Menu(2).Children(4).Callback='viewer3d(''menu_windows4_Callback'',gcbo,[],guidata(gcbo))';
Menu(3).Label='Config';
Menu(3).Tag='menu_config';
Menu(3).Callback='viewer3d(''menu_config_Callback'',gcbo,[],guidata(gcbo))';
Menu(3).Children(1).Label='Quality v. Speed';
Menu(3).Children(1).Tag='menu_quality_speed';
Menu(3).Children(1).Callback='viewer3d(''menu_quality_speed_Callback'',gcbo,[],guidata(gcbo))';
Menu(3).Children(2).Label='Compile C Files';
Menu(3).Children(2).Tag='menu_compile_files';
Menu(3).Children(2).Callback='viewer3d(''menu_compile_files_Callback'',gcbo,[],guidata(gcbo))';
Menu(4).Label='Help';
Menu(4).Tag='menu_info';
Menu(4).Callback='viewer3d(''menu_info_Callback'',gcbo,[],guidata(gcbo))';
Menu(4).Children(1).Label='Help';
Menu(4).Children(1).Tag='menu_help';
Menu(4).Children(1).Callback='viewer3d(''menu_help_Callback'',gcbo,[],guidata(gcbo))';
Menu(4).Children(2).Label='About';
Menu(4).Children(2).Tag='menu_about';
Menu(4).Children(2).Callback='viewer3d(''menu_about_Callback'',gcbo,[],guidata(gcbo))';
Menu(4).Children(3).Label='Console';
Menu(4).Children(3).Tag='menu_console';
Menu(4).Children(3).Callback='viewer3d(''menu_console_Callback'',gcbo,[],guidata(gcbo))';
%set(figurehandles.figure,'Toolbar','none')
%set(figurehandles.figure,'MenuBar','none')
Menu=addMenu(handle_figure,Menu);
function addMenuVolume()
%data.MenuVolume=addMenuVolume(data.figurehandles.viewer3d,data.volumes);
data=getMyData(); if(isempty(data)), return, end
if(isempty(data.volumes)), return, end
% Delete existing volume menus
for i=1:length(data.MenuVolume)
delete(data.MenuVolume(i).Handle);
end
MenuVolume=struct;
for i=1:length(data.volumes)
MenuVolume(i).Label=data.volumes(i).name;
MenuVolume(i).Tag='menu_volume';
if(data.volumes(i).Editable)
MenuVolume(i).ForegroundColor=[0 0.5 0];
else
MenuVolume(i).ForegroundColor=[0 0 1];
end
MenuVolume(i).Callback='';
MenuVolume(i).Children(1).Label='WindowLevel&Width';
MenuVolume(i).Children(1).Tag='menu_config_contrast';
MenuVolume(i).Children(1).Callback=['viewer3d(''menu_config_contrast_Callback'',gcbo,' num2str(i) ',guidata(gcbo))'];
MenuVolume(i).Children(2).Label='Change Alpha&Colors';
MenuVolume(i).Children(2).Tag='menu_change_alpha_colors';
MenuVolume(i).Children(2).Callback=['viewer3d(''menu_change_alpha_colors_Callback'',gcbo,' num2str(i) ',guidata(gcbo))'];
MenuVolume(i).Children(3).Label='Voxel Size';
MenuVolume(i).Children(3).Tag='menu_voxelsize';
MenuVolume(i).Children(3).Callback=['viewer3d(''menu_voxelsize_Callback'',gcbo,' num2str(i) ',guidata(gcbo))'];
MenuVolume(i).Children(4).Label='Data Info';
MenuVolume(i).Children(4).Tag='menu_data_info';
MenuVolume(i).Children(4).Callback=['viewer3d(''menu_data_info_Callback'',gcbo,' num2str(i) ',guidata(gcbo))'];
MenuVolume(i).Children(5).Label='Add Empty(Segment)Volume';
MenuVolume(i).Children(5).Tag='menu_add_segvol';
MenuVolume(i).Children(5).Callback=['viewer3d(''menu_addseg_Callback'',gcbo,' num2str(i) ',guidata(gcbo))'];
MenuVolume(i).Children(6).Label='Volume to Workspace';
MenuVolume(i).Children(6).Tag='menu_volume_ws';
MenuVolume(i).Children(6).Callback=['viewer3d(''menu_volume_ws_Callback'',gcbo,' num2str(i) ',guidata(gcbo))'];
MenuVolume(i).Children(7).Label='Close';
MenuVolume(i).Children(7).Tag='menu_volume_close';
MenuVolume(i).Children(7).Callback=['viewer3d(''menu_volume_close_Callback'',gcbo,' num2str(i) ',guidata(gcbo))'];
end
data.MenuVolume=addMenu(data.figurehandles.viewer3d,MenuVolume);
setMyData(data);
function Menu=addMenu(handle_figure,Menu)
Properties={'Label','Callback','Separator','Checked','Enable','ForegroundColor','Position','ButtonDownFcn','Selected','SelectionHighlight','Visible','UserData'};
for i=1:length(Menu)
z2=Menu(i);
z2.Handle=uimenu(handle_figure, 'Label',z2.Label);
for j=1:length(Properties)
Pr=Properties{j};
if(isfield(z2,Pr))
val=z2.(Pr);
if(~isempty(val)), set(z2.Handle ,Pr,val); end
end
end
if(isfield(z2,'Children')&&~isempty(z2.Children))
Menu(i).Children=addMenu(z2.Handle,z2.Children);
end
Menu(i).Handle=z2.Handle;
end
% --- Executes when figure1 is resized.
function figure1_ResizeFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
menubar('ResizeFcn',gcf);
|
github
|
jacksky64/imageProcessing-master
|
render.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/render.m
| 40,381 |
utf_8
|
c1baff4ae87d57f8f014f914f1b14c19
|
function render_image = render(volume,options)
% Function RENDER will volume render a image of a 3D volume,
% with transperancy, shading and ColorTable.
%
% I = RENDER(VOLUME,OPTIONS);
%
% outputs,
% I: The rendered image
%
% inputs,
% VOLUME : Input image volume (Data of type double has short render
% times uint16 the longest)
% OPTIONS: A struct with all the render options and parameters:
% OPTIONS.RenderType : Maximum intensitity projections (default) 'mip',
% greyscale volume rendering 'bw', color volume rendering
% 'color' and volume rendering with shading 'shaded'
% OPTIONS.ShearInterp : Interpolation method used in the Shear steps
% of the shearwarp algoritm, nearest or (default) bilinear
% OPTIONS.WarpInterp : Interpolation method used in the warp step
% of the shearwarp algoritm, nearest or (default)
% bilinear
% OPTIONS.ImageSize : Size of the rendered image, defaults to [400 400]
% OPTIONS.Mview : This 4x4 matrix is the viewing matrix
% defaults to [1 0 0 0;0 1 0 0;0 0 1 0;0 0 0 1]
% OPTIONS.AlphaTable : This Nx1 table is linear interpolated such that
% every
% voxel intensity gets a specific alpha (transparency)
% [0 0.01 0.05 0.1 0.2 1 1 1 1 1]
% OPTIONS.ColorTable : This Nx3 table is linear interpolated such that
% every voxel intensity gets a specific color.
% defaults to [1 0 0;1 0 0;1 0 0;1 0 0;1 0 0;1 0 0;1 0 0]
% OPTIONS.LightVector : Light Direction defaults to [0.67 0.33 -0.67]
% OPTIONS.ViewerVector : View vector X,Y,Z defaults to [0 0 1]
% OPTIONS.ShadingMaterial : The type of material shading : dull,
% shiny(default) or metal.
%
% Optional parameters to speed up rendering:
% OPTIONS.VolumeX, OPTIONS.VolumeY : Dimensions shifted Voxel volumes,
% Must be used like:
% OPTIONS.VolumeX=shiftdim(OPTIONS.Volume,1);
% OPTIONS.VolumeY=shiftdim(OPTIONS.Volume,2);
% OPTIONS.Normals : The normalized gradient of the voxel volume
% Must be used like:
% [fy,fx,fz]=gradient(OPTIONS.Volume);
% flength=sqrt(fx.^2+fy.^2+fz.^2)+1e-6;
% OPTIONS.Normals=zeros([size(fx) 3]);
% OPTIONS.Normals(:,:,:,1)=fx./flength;
% OPTIONS.Normals(:,:,:,2)=fy./flength;
% OPTIONS.Normals(:,:,:,3)=fz./flength;
%
% example,
% %Add paths
% functionname='render.m';
% functiondir=which(functionname);
% functiondir=functiondir(1:end-length(functionname));
% addpath(functiondir);
% addpath([functiondir '/SubFunctions']);
% % Load data
% load('ExampleData/TestVolume.mat'); V=data.volumes(1).volume_original;
% % Type of rendering
% options.RenderType = 'shaded';
% % color and alpha table
% options.AlphaTable=[0 0 0 0 0 1 1 1 1 1];
% options.ColorTable=[1 0 0;1 0 0;1 0 0;1 0 0;1 0 0;1 0 0;1 0 0];
% % Viewer Matrix
% options.Mview=makeViewMatrix([0 0 0],[0.25 0.25 0.25],[0 0 0]);
% % Render and show image
% figure,
% I = render(V,options);
% imshow(I);
%
% Function is written by D.Kroon University of Twente (April 2009)
%% Set the default options
defaultoptions=struct( ...
'RenderType','mip', ...
'Volume', zeros(3,3,3), ...
'VolumeX', [], ...
'VolumeY', [], ...
'Normals', [], ...
'imax',[], ...
'imin',[], ...
'ShearInterp', 'bilinear', ...
'WarpInterp', 'bilinear', ...
'ImageSize', [400 400], ...
'Mview', [1 0 0 0;0 1 0 0;0 0 1 0;0 0 0 1], ...
'AlphaTable', [0 0.01 0.05 0.1 0.2 1 1 1 1 1], ...
'ColorTable', [1 0 0;1 0 0;1 0 0;1 0 0;1 0 0;1 0 0;1 0 0], ...
'LightVector',[0.67 0.33 -0.67], ...
'ViewerVector',[0 0 1], ...
'SliceSelected', 1, ...
'ColorSlice', false, ...
'ShadingMaterial','shiny');
%% Check the input options
if(~exist('options','var')),
options=defaultoptions;
else
tags = fieldnames(defaultoptions);
for i=1:length(tags)
if(~isfield(options,tags{i})), options.(tags{i})=defaultoptions.(tags{i}); end
end
if(length(tags)~=length(fieldnames(options))),
warning('Render:unknownoption','unknown options found');
end
end
% Make the data structure from the options structure
data=options;
if(exist('volume','var')); data.Volume=volume; end
%% If black
if(strcmp(data.RenderType,'black'))
render_image = zeros(data.ImageSize);
return
end
%% Needed to convert intensities to range [0 1]
if(isempty(data.imax))
switch class(data.Volume)
case 'uint8',
data.imax=2^8-1; data.imin=0;
case 'uint16',
data.imax=2^16-1; data.imin=0;
case 'uint32',
data.imax=2^32-1; data.imin=0;
case 'int8',
data.imax=2^7-1; data.imin=-2^7;
case 'int16',
data.imax=2^15-1; data.imin=-2^15;
case 'int32',
data.imax=2^31-1; data.imin=-2^31;
otherwise,
data.imax=max(data.Volume(:));
data.imin=min(data.Volume(:));
end
end
data.imaxmin=data.imax-data.imin;
%% Split ColorTable in R,G,B
if(~isempty(data.ColorTable))
if(size(data.ColorTable,2)>size(data.ColorTable,1)), data.ColorTable=data.ColorTable'; end
data.ColorTable_r=data.ColorTable(:,1); data.ColorTable_g=data.ColorTable(:,2); data.ColorTable_b=data.ColorTable(:,3);
end
%% If no 3D but slice render do slicerender
if((length(data.RenderType)>5)&&strcmp(data.RenderType(1:5),'slice'))
render_image = render_slice(data);
return
end
%% Calculate the Shear and Warp Matrices
if(ndims(data.Volume)==2)
sizes=[size(data.Volume) 1];
else
sizes=size(data.Volume);
end
[data.Mshear,data.Mwarp2D,data.c]=makeShearWarpMatrix(data.Mview,sizes);
data.Mwarp2Dinv=inv(double(data.Mwarp2D));
data.Mshearinv=inv(data.Mshear);
%% Store Volume sizes
data.Iin_sizex=size(data.Volume,1); data.Iin_sizey=size(data.Volume,2); data.Iin_sizez=size(data.Volume,3);
%% Create Shear (intimidate) buffer
data.Ibuffer_sizex=ceil(1.7321*max(size(data.Volume))+1);
data.Ibuffer_sizey=data.Ibuffer_sizex;
switch data.RenderType
case {'mip'}
data.Ibuffer=zeros([data.Ibuffer_sizex data.Ibuffer_sizey])+data.imin;
case {'bw'}
data.Ibuffer=zeros([data.Ibuffer_sizex data.Ibuffer_sizey]);
otherwise
data.Ibuffer=zeros([data.Ibuffer_sizex data.Ibuffer_sizey 3]);
end
%% Adjust alpha table by voxel length because of rotation and volume size
lengthcor=sqrt(1+data.Mshearinv(1,3)^2+data.Mshearinv(2,3)^2)*mean(size(data.Volume))/100;
data.AlphaTable=1 - (1-data.AlphaTable).^(1/lengthcor);
data.AlphaTable(data.AlphaTable<0)=0; data.AlphaTable(data.AlphaTable>1)=1;
%% Shading type -> Phong values
switch lower(data.ShadingMaterial)
case {'shiny'}
data.material=[0.7, 0.6, 0.9, 15];
case {'dull'}
data.material=[0.7, 0.8, 0.0, 10];
case {'metal'}
data.material=[0.7, 0.3, 1.0, 20];
otherwise
data.material=[0.7, 0.6, 0.9, 20];
end
%% Normalize Light and Viewer vectors
data.LightVector=[data.LightVector(:);0]; data.LightVector=data.LightVector./sqrt(sum(data.LightVector(1:3).^2));
data.ViewerVector=[data.ViewerVector(:);0]; data.ViewerVector=data.ViewerVector./sqrt(sum(data.ViewerVector(1:3).^2));
%% Shear Rendering
data = shear(data);
data = warp(data);
render_image = data.Iout;
%% Slice rendering
function Iout=render_slice(data)
switch (data.RenderType)
case {'slicex'}
Iin=(double(squeeze(data.Volume(data.SliceSelected,:,:,:)))-data.imin)/data.imaxmin;
M=[data.Mview(1,2) data.Mview(1,3) data.Mview(1,4); data.Mview(2,2) data.Mview(2,3) data.Mview(2,4); 0 0 1];
% Rotate 90
case {'slicey'}
Iin=(double(squeeze(data.Volume(:,data.SliceSelected,:,:)))-data.imin)/data.imaxmin;
M=[data.Mview(1,1) data.Mview(1,3) data.Mview(1,4); data.Mview(2,1) data.Mview(2,3) data.Mview(2,4); 0 0 1]; % Rotate 90
case {'slicez'}
Iin=(double(squeeze(data.Volume(:,:,data.SliceSelected,:)))-data.imin)/data.imaxmin;
M=[data.Mview(1,1) data.Mview(1,2) data.Mview(1,4); data.Mview(2,1) data.Mview(2,2) data.Mview(2,4); 0 0 1];
end
M=inv(M);
% Perform the affine transformation
switch(data.WarpInterp)
case 'nearest', wi=5;
case 'bicubic', wi=3;
case 'bilinear', wi=1;
otherwise, wi=1;
end
Ibuffer=affine_transform_2d_double(Iin,M,wi,data.ImageSize);
if(data.ColorSlice)
Ibuffer(Ibuffer<0)=0; Ibuffer(Ibuffer>1)=1;
betaC=(length(data.ColorTable_r)-1);
indexColor=round(Ibuffer*betaC)+1;
% Greyscale to Color
Ibuffer=zeros([size(Ibuffer) 3]);
Ibuffer(:,:,1)=data.ColorTable_r(indexColor);
Ibuffer(:,:,2)=data.ColorTable_g(indexColor);
Ibuffer(:,:,3)=data.ColorTable_b(indexColor);
Iout=Ibuffer;
else
Iout=Ibuffer;
end
%% Shearwarp functions
function data=shear(data)
switch (data.c)
case 1
for z=0:(data.Iin_sizex-1);
% Offset calculation
xd=(-data.Ibuffer_sizex/2)+data.Mshearinv(1,3)*(z-data.Iin_sizex/2)+data.Iin_sizey/2;
yd=(-data.Ibuffer_sizey/2)+data.Mshearinv(2,3)*(z-data.Iin_sizex/2)+data.Iin_sizez/2;
xdfloor=floor(xd); ydfloor=floor(yd);
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=data.Iin_sizez-ydfloor;
if(pyend>data.Ibuffer_sizey), pyend=data.Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=data.Iin_sizey-xdfloor;
if(pxend>data.Ibuffer_sizex), pxend=data.Ibuffer_sizex; end
data.py=(pystart+1:pyend-1); data.px=(pxstart+1:pxend-1);
if(isempty(data.px)), data.px=pxstart+1; end
if(isempty(data.py)), data.py=pystart+1; end
% Determine x and y coordinates of pixel(s) which will be come current pixel
yBas=data.py+ydfloor; xBas=data.px+xdfloor;
switch (data.ShearInterp)
case {'bilinear'}
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc=[(1-xCom)*(1-yCom) (1-xCom)*yCom xCom*(1-yCom) xCom*yCom];
if(isempty(data.VolumeX))
% Get the intensities
if(data.Iin_sizez>1)
slice=double(squeeze(data.Volume(z+1,:,:)));
else
slice=double(data.Volume(z+1,:))';
end
intensity_xyz1=slice(xBas, yBas);
intensity_xyz2=slice(xBas, yBas1);
intensity_xyz3=slice(xBas1, yBas);
intensity_xyz4=slice(xBas1, yBas1);
else
slice=double(data.VolumeX(:, :,z+1));
intensity_xyz1=slice(xBas, yBas);
intensity_xyz2=slice(xBas, yBas1);
intensity_xyz3=slice(xBas1, yBas);
intensity_xyz4=slice(xBas1, yBas1);
end
% Calculate the interpolated intensity
data.intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4));
otherwise
if(isempty(data.VolumeX))
data.intensity_loc=double(squeeze(data.Volume(z+1,xBas, yBas)));
else
data.intensity_loc=double(data.VolumeX(xBas, yBas,z+1));
end
end
% Update the shear image buffer
switch (data.RenderType)
case {'mip'}
data=updatebuffer_MIP(data);
case {'color'}
data=updatebuffer_COLOR(data);
case {'bw'}
data=updatebuffer_BW(data);
case {'shaded'}
data=returnnormal(z+1,xBas, yBas,data);
data=updatebuffer_SHADED(data);
end
end
case 2
for z=0:(data.Iin_sizey-1),
% Offset calculation
xd=(-data.Ibuffer_sizex/2)+data.Mshearinv(1,3)*(z-data.Iin_sizey/2)+data.Iin_sizez/2;
yd=(-data.Ibuffer_sizey/2)+data.Mshearinv(2,3)*(z-data.Iin_sizey/2)+data.Iin_sizex/2;
xdfloor=floor(xd); ydfloor=floor(yd);
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=data.Iin_sizex-ydfloor;
if(pyend>data.Ibuffer_sizey), pyend=data.Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=data.Iin_sizez-xdfloor;
if(pxend>data.Ibuffer_sizex), pxend=data.Ibuffer_sizex; end
data.py=(pystart+1:pyend-1); data.px=(pxstart+1:pxend-1);
if(isempty(data.px)), data.px=pxstart+1; end
if(isempty(data.py)), data.py=pystart+1; end
%Determine x,y coordinates of pixel(s) which will be come current pixel
yBas=data.py+ydfloor; xBas=data.px+xdfloor;
switch (data.ShearInterp)
case {'bilinear'}
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
if(isempty(data.VolumeY))
% Get the intensities
slice=double(squeeze(data.Volume(:,z+1,:)));
intensity_xyz1=slice(yBas, xBas);
intensity_xyz2=slice(yBas1,xBas);
intensity_xyz3=slice(yBas, xBas1);
intensity_xyz4=slice(yBas1, xBas1);
else
% Get the intensities
slice=double(data.VolumeY(:,:,z+1));
intensity_xyz1=slice(xBas,yBas);
intensity_xyz2=slice(xBas,yBas1);
intensity_xyz3=slice(xBas1,yBas);
intensity_xyz4=slice(xBas1,yBas1);
end
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc=[(1-xCom)*(1-yCom) (1-xCom)*yCom xCom*(1-yCom) xCom*yCom];
% Calculate the interpolated intensity
data.intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4));
otherwise
if(isempty(data.VolumeY))
data.intensity_loc=double(squeeze(data.Volume(yBas, z+1,xBas)));
else
data.intensity_loc=double(data.VolumeY(xBas,yBas,z+1));
end
end
% Rotate image
if (isempty(data.VolumeY)), data.intensity_loc=data.intensity_loc'; end
% Update the shear image buffer
switch (data.RenderType)
case {'mip'}
data=updatebuffer_MIP(data);
case {'color'}
data=updatebuffer_COLOR(data);
case {'bw'}
data=updatebuffer_BW(data);
case {'shaded'}
data=returnnormal(yBas, z+1,xBas,data);
data=updatebuffer_SHADED(data);
end
end
case 3
for z=0:(data.Iin_sizez-1),
% Offset calculation
xd=(-data.Ibuffer_sizex/2)+data.Mshearinv(1,3)*(z-data.Iin_sizez/2)+data.Iin_sizex/2;
yd=(-data.Ibuffer_sizey/2)+data.Mshearinv(2,3)*(z-data.Iin_sizez/2)+data.Iin_sizey/2;
xdfloor=floor(xd); ydfloor=floor(yd);
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=data.Iin_sizey-ydfloor;
if(pyend>data.Ibuffer_sizey), pyend=data.Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=data.Iin_sizex-xdfloor;
if(pxend>data.Ibuffer_sizex), pxend=data.Ibuffer_sizex; end
data.py=(pystart+1:pyend-1); data.px=(pxstart+1:pxend-1);
if(isempty(data.px)), data.px=pxstart+1; end
if(isempty(data.py)), data.py=pystart+1; end
%Determine x,y coordinates of pixel(s) which will be come current pixel
yBas=data.py+ydfloor; xBas=data.px+xdfloor;
switch (data.ShearInterp)
case {'bilinear'}
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
slice=double(data.Volume(:,:,z+1));
intensity_xyz1=slice(xBas, yBas);
intensity_xyz2=slice(xBas, yBas1);
intensity_xyz3=slice(xBas1, yBas);
intensity_xyz4=slice(xBas1, yBas1);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc=[(1-xCom)*(1-yCom) (1-xCom)*yCom xCom*(1-yCom) xCom*yCom];
% Calculate the interpolated intensity
data.intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4));
otherwise
data.intensity_loc=double(data.Volume(xBas, yBas, z+1));
end
% Update the shear image buffer
switch (data.RenderType)
case {'mip'}
data=updatebuffer_MIP(data);
case {'color'}
data=updatebuffer_COLOR(data);
case {'bw'}
data=updatebuffer_BW(data);
case {'shaded'}
data=returnnormal(xBas,yBas,z+1,data);
data=updatebuffer_SHADED(data);
end
end
case 4
for z=(data.Iin_sizex-1):-1:0,
% Offset calculation
xd=(-data.Ibuffer_sizex/2)+data.Mshearinv(1,3)*(z-data.Iin_sizex/2)+data.Iin_sizey/2;
yd=(-data.Ibuffer_sizey/2)+data.Mshearinv(2,3)*(z-data.Iin_sizex/2)+data.Iin_sizez/2;
xdfloor=floor(xd); ydfloor=floor(yd);
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=data.Iin_sizez-ydfloor;
if(pyend>data.Ibuffer_sizey), pyend=data.Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=data.Iin_sizey-xdfloor;
if(pxend>data.Ibuffer_sizex), pxend=data.Ibuffer_sizex; end
data.py=(pystart+1:pyend-1); data.px=(pxstart+1:pxend-1);
if(isempty(data.px)), data.px=pxstart+1; end
if(isempty(data.py)), data.py=pystart+1; end
% Determine x,y coordinates of pixel(s) which will be come current pixel
yBas=data.py+ydfloor; xBas=data.px+xdfloor;
switch (data.ShearInterp)
case {'bilinear'}
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
if(isempty(data.VolumeX))
% Get the intensities
if(data.Iin_sizez>1)
slice=double(squeeze(data.Volume(z+1,:,:)));
else
slice=double(data.Volume(z+1,:))';
end
intensity_xyz1=slice(xBas, yBas);
intensity_xyz2=slice(xBas, yBas1);
intensity_xyz3=slice(xBas1, yBas);
intensity_xyz4=slice(xBas1, yBas1);
else
slice=double(data.VolumeX(:, :,z+1));
intensity_xyz1=slice(xBas,yBas);
intensity_xyz2=slice(xBas,yBas1);
intensity_xyz3=slice(xBas1,yBas);
intensity_xyz4=slice(xBas1,yBas1);
end
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc=[(1-xCom)*(1-yCom) (1-xCom)*yCom xCom*(1-yCom) xCom*yCom];
% Calculate the interpolated intensity
data.intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4));
otherwise
if(isempty(data.VolumeX))
data.intensity_loc=double(squeeze(data.Volume(z+1,xBas, yBas)));
else
data.intensity_loc=double(data.VolumeX(xBas, yBas,z+1));
end
end
% Update the shear image buffer
switch (data.RenderType)
case {'mip'}
data=updatebuffer_MIP(data);
case {'color'}
data=updatebuffer_COLOR(data);
case {'bw'}
data=updatebuffer_BW(data);
case {'shaded'}
data=returnnormal(z+1,xBas,yBas,data);
data=updatebuffer_SHADED(data);
end
end
case 5
for z=(data.Iin_sizey-1):-1:0,
% Offset calculation
xd=(-data.Ibuffer_sizex/2)+data.Mshearinv(1,3)*(z-data.Iin_sizey/2)+data.Iin_sizez/2;
yd=(-data.Ibuffer_sizey/2)+data.Mshearinv(2,3)*(z-data.Iin_sizey/2)+data.Iin_sizex/2;
xdfloor=floor(xd); ydfloor=floor(yd);
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=data.Iin_sizex-ydfloor;
if(pyend>data.Ibuffer_sizey), pyend=data.Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=data.Iin_sizez-xdfloor;
if(pxend>data.Ibuffer_sizex), pxend=data.Ibuffer_sizex; end
data.py=(pystart+1:pyend-1); data.px=(pxstart+1:pxend-1);
if(isempty(data.px)), data.px=pxstart+1; end
if(isempty(data.py)), data.py=pystart+1; end
%Determine x,y coordinates of pixel(s) which will be come current pixel
xBas=data.px+xdfloor; yBas=data.py+ydfloor;
switch (data.ShearInterp)
case {'bilinear'}
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
if(isempty(data.VolumeY))
% Get the intensities
slice=double(squeeze(data.Volume(:, z+1,:)));
intensity_xyz1=slice(yBas, xBas);
intensity_xyz2=slice(yBas1,xBas);
intensity_xyz3=slice(yBas, xBas1);
intensity_xyz4=slice(yBas1, xBas1);
else
% Get the intensities
slice=double(data.VolumeY(:,:,z+1));
intensity_xyz1=slice(xBas,yBas);
intensity_xyz2=slice(xBas,yBas1);
intensity_xyz3=slice(xBas1,yBas);
intensity_xyz4=slice(xBas1,yBas1);
end
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc=[(1-xCom)*(1-yCom) (1-xCom)*yCom xCom*(1-yCom) xCom*yCom];
% Calculate the interpolated intensity
data.intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4));
otherwise
if(isempty(data.VolumeY))
data.intensity_loc=double(squeeze(data.Volume(yBas, z+1,xBas)));
else
data.intensity_loc=double(data.VolumeY(xBas,yBas,z+1));
end
end
% Rotate image
if (isempty(data.VolumeY)), data.intensity_loc=data.intensity_loc'; end
% Update the shear image buffer
switch (data.RenderType)
case {'mip'}
data=updatebuffer_MIP(data);
case {'color'}
data=updatebuffer_COLOR(data);
case {'bw'}
data=updatebuffer_BW(data);
case {'shaded'}
data=returnnormal(yBas,z+1,xBas,data);
data=updatebuffer_SHADED(data);
end
end
case 6
for z=(data.Iin_sizez-1):-1:0,
% Offset calculation
xd=(-data.Ibuffer_sizex/2)+data.Mshearinv(1,3)*(z-data.Iin_sizez/2)+data.Iin_sizex/2;
yd=(-data.Ibuffer_sizey/2)+data.Mshearinv(2,3)*(z-data.Iin_sizez/2)+data.Iin_sizey/2;
xdfloor=floor(xd); ydfloor=floor(yd);
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=data.Iin_sizey-ydfloor;
if(pyend>data.Ibuffer_sizey), pyend=data.Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=data.Iin_sizex-xdfloor;
if(pxend>data.Ibuffer_sizex), pxend=data.Ibuffer_sizex; end
data.py=(pystart+1:pyend-1); data.px=(pxstart+1:pxend-1);
if(isempty(data.px)), data.px=pxstart+1; end
if(isempty(data.py)), data.py=pystart+1; end
% Determine x,y coordinates of pixel(s) which will be come current pixel
xBas=data.px+xdfloor; yBas=data.py+ydfloor;
switch (data.ShearInterp)
case {'bilinear'}
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
slice=double(data.Volume(:, :, z+1));
intensity_xyz1=slice(xBas, yBas);
intensity_xyz2=slice(xBas, yBas1);
intensity_xyz3=slice(xBas1, yBas );
intensity_xyz4=slice(xBas1, yBas1 );
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc=[(1-xCom)*(1-yCom) (1-xCom)*yCom xCom*(1-yCom) xCom*yCom];
% Calculate the interpolated intensity
data.intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4));
otherwise
data.intensity_loc=double(data.Volume(xBas, yBas, z+1));
end
% Update the shear image buffer
switch (data.RenderType)
case {'mip'}
data=updatebuffer_MIP(data);
case {'color'}
data=updatebuffer_COLOR(data);
case {'bw'}
data=updatebuffer_BW(data);
case {'shaded'}
data=returnnormal(xBas,yBas,z+1,data);
data=updatebuffer_SHADED(data);
end
end
end
switch (data.RenderType)
case {'mip'}
if(data.imin~=0), data.Ibuffer=data.Ibuffer-data.imin; end
data.Ibuffer=data.Ibuffer/data.imaxmin;
end
function data=returnnormal(x,y,z,data)
% Calculate the normals for a certain pixel / slice or volume.
% The Normals are calculated by normalizing the voxel volume gradient.
% The central pixel positions
x1=x; y1=y; z1=z;
% Check if the gradients is delivered by the user
if(isempty(data.Normals))
% The forward pixel positions
x2=x1+1; y2=y1+1; z2=z1+1;
% Everything inside the boundaries
checkx=x2>size(data.Volume,1); checky=y2>size(data.Volume,2); checkz=z2>size(data.Volume,3);
if(nnz(checkx)>0), x1(checkx)=x1-1; x2(checkx)=size(data.Volume,1); end
if(nnz(checky)>0), y1(checky)=y1-1; y2(checky)=size(data.Volume,2); end
if(nnz(checkz)>0), z1(checkz)=z1-1; z2(checkz)=size(data.Volume,3); end
% Calculate the forward gradient
S(:,:,1)=double(squeeze(data.Volume(x2,y1,z1)-data.Volume(x1,y1,z1)));
S(:,:,2)=double(squeeze(data.Volume(x1,y2,z1)-data.Volume(x1,y1,z1)));
S(:,:,3)=double(squeeze(data.Volume(x1,y1,z2)-data.Volume(x1,y1,z1)));
% Normalize the gradient data
nlength=sqrt(S(:,:,1).^2+S(:,:,2).^2+S(:,:,3).^2)+0.000001;
N=zeros(size(S));
N(:,:,1)=S(:,:,1)./nlength;
N(:,:,2)=S(:,:,2)./nlength;
N(:,:,3)=S(:,:,3)./nlength;
else
% Get the user inputed normal information
N(:,:,1)=squeeze(data.Normals(x1,y1,z1,1));
N(:,:,2)=squeeze(data.Normals(x1,y1,z1,2));
N(:,:,3)=squeeze(data.Normals(x1,y1,z1,3));
end
% Rotate the data in case of certain views
if(data.c==2||data.c==5),
N2=zeros([size(N,2) size(N,1) 3]);
N2(:,:,1)=N(:,:,1)'; N2(:,:,2)=N(:,:,2)'; N2(:,:,3)=N(:,:,3)'; N=N2;
end
% "Return" the Normals
data.N=N;
function data=updatebuffer_MIP(data)
% Update the current pixel in the shear image buffer
check=double(data.intensity_loc>data.Ibuffer(data.px,data.py));
data.Ibuffer(data.px,data.py)=(check).*data.intensity_loc+(1-check).*data.Ibuffer(data.px,data.py);
function data=updatebuffer_BW(data)
% Calculate index in alpha transparency look up table
if(data.imin~=0), data.intensity_loc=data.intensity_loc-data.imin; end
if(data.imaxmin~=1), data.intensity_loc=data.intensity_loc./data.imaxmin; end
betaA=(length(data.AlphaTable)-1);
indexAlpha=round(data.intensity_loc*betaA)+1;
% calculate current alphaimage
alphaimage=data.AlphaTable(indexAlpha);
% 2D volume fix because alphaimage becomes a row instead of column
if(data.Iin_sizez==1), alphaimage=reshape(alphaimage,size(data.Ibuffer(data.px,data.py))); end
alphaimage_inv=(1-alphaimage);
% Update the current pixel in the shear image buffer
data.Ibuffer(data.px,data.py)=alphaimage_inv.*data.Ibuffer(data.px,data.py)+alphaimage.*data.intensity_loc;
function data=updatebuffer_COLOR(data)
% Calculate index in alpha transparency look up table
if(data.imin~=0), data.intensity_loc=data.intensity_loc-data.imin; end
betaA=(length(data.AlphaTable)-1)/data.imaxmin;
betaC=(length(data.ColorTable_r)-1)/data.imaxmin;
indexAlpha=round(data.intensity_loc*betaA)+1;
% Calculate index in color look up table
if(betaA~=betaC)
indexColor=round(data.intensity_loc*betaC)+1;
else
indexColor=indexAlpha;
end
r=data.ColorTable_r(indexColor);
g=data.ColorTable_g(indexColor);
b=data.ColorTable_b(indexColor);
% calculate current alphaimage
alphaimage=data.AlphaTable(indexAlpha);
% Update the current pixel in the shear image buffer
if(data.Iin_sizez==1),
alphaimage=reshape(alphaimage,size(data.Ibuffer(data.px,data.py,1)));
r=reshape(r,size(data.Ibuffer(data.px,data.py,1)));
g=reshape(g,size(data.Ibuffer(data.px,data.py,1)));
b=reshape(b,size(data.Ibuffer(data.px,data.py,1)));
end
% 2D volume fix because alphaimage becomes a row instead of column
alphaimage_inv=(1-alphaimage);
data.Ibuffer(data.px,data.py,1)=alphaimage_inv.*data.Ibuffer(data.px,data.py,1)+alphaimage.*r;
data.Ibuffer(data.px,data.py,2)=alphaimage_inv.*data.Ibuffer(data.px,data.py,2)+alphaimage.*g;
data.Ibuffer(data.px,data.py,3)=alphaimage_inv.*data.Ibuffer(data.px,data.py,3)+alphaimage.*b;
function data=updatebuffer_SHADED(data)
if(data.imin~=0), data.intensity_loc=data.intensity_loc-data.imin; end
betaA=(length(data.AlphaTable)-1)/data.imaxmin;
betaC=(length(data.ColorTable_r)-1)/data.imaxmin;
% Calculate index in alpha transparency look up table
indexAlpha=round(data.intensity_loc*betaA)+1;
% Calculate index in color look up table
if(betaA~=betaC)
indexColor=round(data.intensity_loc*betaC)+1;
else
indexColor=indexAlpha;
end
% Rotate the light and view vector
data.LightVector2=data.Mview\data.LightVector;
data.LightVector2=data.LightVector2./sqrt(sum(data.LightVector2(1:3).^2));
data.ViewerVector2=data.Mview\data.ViewerVector;
data.ViewerVector2=data.ViewerVector2./sqrt(sum(data.ViewerVector2(1:3).^2));
Ia=1;
Id=data.N(:,:,1)*data.LightVector2(1)+data.N(:,:,2)*data.LightVector2(2)+data.N(:,:,3)*data.LightVector2(3);
% R = 2.0*dot(N,L)*N - L;
R(:,:,1)=2*Id.*data.N(:,:,1)-data.LightVector2(1);
R(:,:,2)=2*Id.*data.N(:,:,2)-data.LightVector2(2);
R(:,:,3)=2*Id.*data.N(:,:,3)-data.LightVector2(3);
%Is = max(pow(dot(R,V),3),0);
Is=-(R(:,:,1)*data.ViewerVector2(1)+R(:,:,2)*data.ViewerVector2(2)+R(:,:,3)*data.ViewerVector2(3));
% No spectacular highlights on "shadow" part
Is(Id<0)=0;
% Specular exponent
Is=Is.^data.material(4);
% Phong shading values
Ipar=zeros([size(Id) 2]);
Ipar(:,:,1)=data.material(1)*Ia+data.material(2)*Id;
Ipar(:,:,2)=data.material(3)*Is;
% calculate current alphaimage
alphaimage=data.AlphaTable(indexAlpha);
alphaimage_inv=(1-alphaimage);
% Update the current pixel in the shear image buffer
data.Ibuffer(data.px,data.py,1)=alphaimage_inv.*data.Ibuffer(data.px,data.py,1)+alphaimage.*(data.ColorTable_r(indexColor).*Ipar(:,:,1)+Ipar(:,:,2));
data.Ibuffer(data.px,data.py,2)=alphaimage_inv.*data.Ibuffer(data.px,data.py,2)+alphaimage.*(data.ColorTable_g(indexColor).*Ipar(:,:,1)+Ipar(:,:,2));
data.Ibuffer(data.px,data.py,3)=alphaimage_inv.*data.Ibuffer(data.px,data.py,3)+alphaimage.*(data.ColorTable_b(indexColor).*Ipar(:,:,1)+Ipar(:,:,2));
function data=warp(data)
% This function warp, will warp the shear rendered buffer image
% Make Affine matrix
M=zeros(3,3);
M(1,1)=data.Mwarp2Dinv(1,1);
M(2,1)=data.Mwarp2Dinv(2,1);
M(1,2)=data.Mwarp2Dinv(1,2);
M(2,2)=data.Mwarp2Dinv(2,2);
M(1,3)=data.Mwarp2Dinv(1,3)+data.Mshearinv(1,4);
M(2,3)=data.Mwarp2Dinv(2,3)+data.Mshearinv(2,4);
% Perform the affine transformation
switch(data.WarpInterp)
case 'nearest', wi=5;
case 'bicubic', wi=3;
case 'bilinear', wi=1;
otherwise, wi=1;
end
data.Iout=affine_transform_2d_double(data.Ibuffer,M,wi,data.ImageSize);
function [Mshear,Mwarp2D,c]=makeShearWarpMatrix(Mview,sizes)
% Function MAKESHEARWARPMATRIX splits a View Matrix in to
% a shear matrix and warp matrix, for efficient 3D volume rendering.
%
% [Mshear,Mwarp2D,c]=makeShearWarpMatrix(Mview,sizes)
%
% inputs,
% Mview: The 4x4 viewing matrix
% sizes: The sizes of the volume which will be rendered
%
% outputs,
% Mshear: The shear matrix
% Mwarp2D: The warp matrix
% c: The principal viewing axis 1..6
%
% example,
%
% Mview=makeViewMatrix([45 45 0],[0.5 0.5 0.5],[0 0 0]);
% sizes=[512 512];
% [Mshear,Mwarp2D,c]=makeShearWarpMatrix(Mview,sizes)
%
% Function is written by D.Kroon University of Twente (October 2008)
% Find the principal viewing axis
Vo=[Mview(1,2)*Mview(2,3) - Mview(2,2)*Mview(1,3);
Mview(2,1)*Mview(1,3) - Mview(1,1)*Mview(2,3);
Mview(1,1)*Mview(2,2) - Mview(2,1)*Mview(1,2)];
[maxv,c]=max(abs(Vo));
% Choose the corresponding Permutation matrix P
switch(c)
case 1, %yzx
P=[0 1 0 0; 0 0 1 0; 1 0 0 0; 0 0 0 1;];
case 2, % zxy
P=[0 0 1 0; 1 0 0 0; 0 1 0 0; 0 0 0 1;];
case 3, % xyz
P=[1 0 0 0; 0 1 0 0; 0 0 1 0; 0 0 0 1;];
end
% Compute the permuted view matrix from Mview and P
Mview_p=Mview/P;
% 180 degrees rotate detection
if(Mview_p(3,3)<0), c=c+3; end
% Compute the shear coeficients from the permuted view matrix
Si = (Mview_p(2,2)* Mview_p(1,3) - Mview_p(1,2)* Mview_p(2,3)) / (Mview_p(1,1)* Mview_p(2,2) - Mview_p(2,1)* Mview_p(1,2));
Sj = (Mview_p(1,1)* Mview_p(2,3) - Mview_p(2,1)* Mview_p(1,3)) / (Mview_p(1,1)* Mview_p(2,2) - Mview_p(2,1)* Mview_p(1,2));
% Compute the translation between the orgins of standard object coordinates
% and intermdiate image coordinates
if((c==1)||(c==4)), kmax=sizes(1)-1; end
if((c==2)||(c==5)), kmax=sizes(2)-1; end
if((c==3)||(c==6)), kmax=sizes(3)-1; end
if ((Si>=0)&&(Sj>=0)), Ti = 0; Tj = 0; end
if ((Si>=0)&&(Sj<0)), Ti = 0; Tj = -Sj*kmax; end
if ((Si<0)&&(Sj>=0)), Ti = -Si*kmax; Tj = 0; end
if ((Si<0)&&(Sj<0)), Ti = -Si*kmax; Tj = -Sj*kmax; end
% Compute the shear matrix
Mshear=[1 0 Si Ti;
0 1 Sj Tj;
0 0 1 0;
0 0 0 1];
% Compute the 2Dwarp matrix
Mwarp2D=[Mview_p(1,1) Mview_p(1,2) (Mview_p(1,4)-Ti*Mview_p(1,1)-Tj*Mview_p(1,2));
Mview_p(2,1) Mview_p(2,2) (Mview_p(2,4)-Ti*Mview_p(2,1)-Tj*Mview_p(2,2));
0 0 1 ];
% Compute the 3Dwarp matrix
% Mwarp3Da=[Mview_p(1,1) Mview_p(1,2) (Mview_p(1,3)-Si*Mview_p(1,1)-Sj*Mview_p(1,2)) Mview_p(1,4);
% Mview_p(2,1) Mview_p(2,2) (Mview_p(2,3)-Si*Mview_p(2,1)-Sj*Mview_p(2,2)) Mview_p(2,4);
% Mview_p(3,1) Mview_p(3,2) (Mview_p(3,3)-Si*Mview_p(3,1)-Sj*Mview_p(3,2)) Mview_p(3,4);
% 0 0 0 1 ];
% Mwarp3Db=[1 0 0 -Ti;
% 0 1 0 -Tj;
% 0 0 1 0;
% 0 0 0 1];
% Mwarp3D=Mwarp3Da*Mwarp3Db;
% % Control matrix Mview
% Mview_control = Mwarp3D*Mshear*P;
% disp(Mview)
% disp(Mview_control)
|
github
|
jacksky64/imageProcessing-master
|
ReadData3D.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/ReadData3D/ReadData3D.m
| 14,704 |
utf_8
|
0cf98e0452dcfacfd88336aba55fe9aa
|
function varargout = ReadData3D(varargin)
% This function ReadData3D allows the user to open medical 3D files. It
% supports the following formats :
%
% Dicom Files ( .dcm , .dicom )
% V3D Philips Scanner ( .v3d )
% GIPL Guys Image Processing Lab ( .gipl )
% HDR/IMG Analyze ( .hdr )
% ISI Files ( .isi )
% NifTi ( .nii )
% RAW files ( .raw , .* )
% VMP BrainVoyager ( .vmp )
% XIF HDllab/ATL ultrasound ( .xif )
% VTK Visualization Toolkit ( .vtk )
% Insight Meta-Image ( .mha, .mhd )
% Micro CT ( .vff )
% PAR/REC Philips ( .par, .rec)
%
% usage:
%
% [V,info]=ReadData3D;
%
% or,
%
% [V,info]=ReadData3D(filename)
%
% or,
%
% [V,info]=ReadData3D(filename,real);
%
%
% outputs,
% V : The 3D Volume
% info : Struct with info about the data
% Always the following fields are present
% info.Filename : Name of file
% info.Dimensions : Dimensions of Volume
% info.PixelDimensions : Size of one pixel / voxel
% real : If set to true (default), convert the raw data to
% type Single-precision and rescale data to real units
% (in CT Hounsfield). When false, it returns the raw-data.
%
% Warning!
% The read functions are not fully implemented as defined in
% the file-format standards. thus do not use this function for
% critical applications.
%
%
% Function is written by D.Kroon University of Twente (July 2010)
% Edit the above text to modify the response to help ReadData3D
% Last Modified by GUIDE v2.5 09-Nov-2010 14:12:50
% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @ReadData3D_OpeningFcn, ...
'gui_OutputFcn', @ReadData3D_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if (nargin>2) && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before ReadData3D is made visible.
function ReadData3D_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to ReadData3D (see VARARGIN)
% Choose default command line output for ReadData3D
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes ReadData3D wait for user response (see UIRESUME)
% uiwait(handles.figure1);
%---- Start supported file formats ----%
data.fileformat(1).ext='*.dcm';
data.fileformat(1).type='Dicom Files';
data.fileformat(1).folder='dicom';
data.fileformat(1).functioninfo='dicom_read_header';
data.fileformat(1).functionread='dicom_read_volume';
data.fileformat(2).ext='*.gipl';
data.fileformat(2).type='GIPL Guys Image Processing Lab';
data.fileformat(2).folder='gipl';
data.fileformat(2).functioninfo='gipl_read_header';
data.fileformat(2).functionread='gipl_read_volume';
data.fileformat(3).ext='*.hdr';
data.fileformat(3).type='HDR/IMG Analyze';
data.fileformat(3).folder='hdr';
data.fileformat(3).functioninfo='hdr_read_header';
data.fileformat(3).functionread='hdr_read_volume';
data.fileformat(4).ext='*.isi';
data.fileformat(4).type='ISI Files';
data.fileformat(4).folder='isi';
data.fileformat(4).functioninfo='isi_read_header';
data.fileformat(4).functionread='isi_read_volume';
data.fileformat(5).ext='*.nii';
data.fileformat(5).type='NifTi';
data.fileformat(5).folder='nii';
data.fileformat(5).functioninfo='nii_read_header';
data.fileformat(5).functionread='nii_read_volume';
data.fileformat(6).ext='*.raw';
data.fileformat(6).type='RAW files';
data.fileformat(6).folder='raw';
data.fileformat(6).functioninfo='raw_read_header';
data.fileformat(6).functionread='raw_read_volume';
data.fileformat(7).ext='*.v3d';
data.fileformat(7).type='V3D Philips Scanner';
data.fileformat(7).folder='v3d';
data.fileformat(7).functioninfo='v3d_read_header';
data.fileformat(7).functionread='v3d_read_volume';
data.fileformat(8).ext='*.vmp';
data.fileformat(8).type='VMP BrainVoyager';
data.fileformat(8).folder='vmp';
data.fileformat(8).functioninfo='vmp_read_header';
data.fileformat(8).functionread='vmp_read_volume';
data.fileformat(9).ext='*.xif';
data.fileformat(9).type='XIF HDllab/ATL ultrasound';
data.fileformat(9).folder='xif';
data.fileformat(9).functioninfo='xif_read_header';
data.fileformat(9).functionread='xif_read_volume';
data.fileformat(10).ext='*.vtk';
data.fileformat(10).type='VTK Visualization Toolkit';
data.fileformat(10).folder='vtk';
data.fileformat(10).functioninfo='vtk_read_header';
data.fileformat(10).functionread='vtk_read_volume';
data.fileformat(11).ext='*.mha';
data.fileformat(11).type='Insight Meta-Image';
data.fileformat(11).folder='mha';
data.fileformat(11).functioninfo='mha_read_header';
data.fileformat(11).functionread='mha_read_volume';
data.fileformat(12).ext='*.vff';
data.fileformat(12).type='Micro CT';
data.fileformat(12).folder='vff';
data.fileformat(12).functioninfo='vff_read_header';
data.fileformat(12).functionread='vff_read_volume';
data.fileformat(13).ext='*.par';
data.fileformat(13).type='Philips PAR/REC';
data.fileformat(13).folder='par';
data.fileformat(13).functioninfo='par_read_header';
data.fileformat(13).functionread='par_read_volume';
%---- End supported file formats ----%
% Get path of ReadData3D
functionname='ReadData3D.m';
functiondir=which(functionname);
functiondir=functiondir(1:end-length(functionname));
% Add the file-reader functions also to the matlab path
addpath([functiondir '/subfunctions']);
for i=1:length(data.fileformat), addpath([functiondir '/' data.fileformat(i).folder]); end
% Make popuplist file formats
fileformatcell=cell(1,length(data.fileformat));
for i=1:length(data.fileformat), fileformatcell{i}=[data.fileformat(i).type ' (' data.fileformat(i).ext ')']; end
set(handles.popupmenu_format,'String',fileformatcell);
% Check if last filename is present from a previous time
data.configfile=[functiondir '/lastfile.mat'];
filename='';
fileformatid=1;
if(exist(data.configfile,'file')), load(data.configfile); end
data.handles=handles;
data.lastfilename=[];
data.volume=[];
data.info=[];
% If filename is selected, look if the extention is known
found=0;
if(~isempty(varargin))
filename=varargin{1}; [pathstr,name,ext]=fileparts(filename);
for i=1:length(data.fileformat)
if(strcmp(data.fileformat(i).ext(2:end),ext)), found=1; fileformatid=i; end
end
end
% Rescale the databack to original units.
if(length(varargin)>1), real=varargin{2}; else real=true; end
data.real=real;
data.filename=filename;
data.fileformatid=fileformatid;
set(handles.checkbox_real,'Value',data.real);
set(handles.edit_filename,'String',data.filename)
set(handles.popupmenu_format,'Value',data.fileformatid);
% Store all data
setMyData(data);
if(found==0)
% Show Dialog File selection
uiwait(handles.figure1);
else
% Load the File directly
loaddata();
end
% --- Outputs from this function are returned to the command line.
function varargout = ReadData3D_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
if(ishandle(hObject))
data=getMyData();
else
data=[];
end
if(~isempty(data))
varargout{1} = data.volume;
varargout{2} = data.info;
else
varargout{1}=[];
varargout{2}=[];
end
if(ishandle(hObject))
close(hObject)
end
function edit_filename_Callback(hObject, eventdata, handles)
% hObject handle to edit_filename (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_filename as text
% str2double(get(hObject,'String')) returns contents of edit_filename as a double
% --- Executes during object creation, after setting all properties.
function edit_filename_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_filename (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in pushbutton_browse.
function pushbutton_browse_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton_browse (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData();
[extlist extlistid]=FileDialogExtentionList(data);
[filename, dirname,filterindex] = uigetfile(extlist, 'Select a dicom file',fileparts(data.filename));
if(filterindex>0)
if(extlistid(filterindex)~=0)
data.fileformatid=extlistid(filterindex);
set( handles.popupmenu_format,'Value',data.fileformatid);
end
if(filename==0), return; end
filename=[dirname filename];
data.filename=filename;
setMyData(data);
set(handles.edit_filename,'String',data.filename)
end
function [extlist extlistid]=FileDialogExtentionList(data)
extlist=cell(length(data.fileformat)+1,2);
extlistid=zeros(length(data.fileformat)+1,1);
ext=data.fileformat(data.fileformatid).ext;
type=data.fileformat(data.fileformatid).type;
extlistid(1)=data.fileformatid;
extlist{1,1}=ext; extlist{1,2}=[type ' (' ext ')'];
j=1;
for i=1:length(data.fileformat);
if(i~=data.fileformatid)
j=j+1;
ext=data.fileformat(i).ext;
type=data.fileformat(i).type;
extlistid(j)=i;
extlist{j,1}=ext; extlist{j,2}=[type ' (' ext ')'];
end
end
extlist{end,1}='*.*';
extlist{end,2}='All Files (*.*)';
function setMyData(data)
% Store data struct in figure
setappdata(gcf,'dataload3d',data);
function data=getMyData()
% Get data struct stored in figure
data=getappdata(gcf,'dataload3d');
% --- Executes on button press in pushbutton_cancel.
function pushbutton_cancel_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton_cancel (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
setMyData([]);
uiresume;
% --- Executes on selection change in popupmenu_format.
function popupmenu_format_Callback(hObject, eventdata, handles)
% hObject handle to popupmenu_format (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = cellstr(get(hObject,'String')) returns popupmenu_format contents as cell array
% contents{get(hObject,'Value')} returns selected item from popupmenu_format
data=getMyData();
data.fileformatid=get( handles.popupmenu_format,'Value');
setMyData(data);
% --- Executes during object creation, after setting all properties.
function popupmenu_format_CreateFcn(hObject, eventdata, handles)
% hObject handle to popupmenu_format (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: popupmenu controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in pushbutton_load.
function pushbutton_load_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton_load (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData();
data.filename=get(handles.edit_filename,'string');
loaddata();
pause(0.1);
uiresume
function loaddata()
data=getMyData();
set(data.handles.figure1,'Pointer','watch'); drawnow('expose');
if(~strcmp(data.lastfilename,data.filename))
% Get info
fhandle = str2func( data.fileformat(data.fileformatid).functioninfo);
data.info=feval(fhandle,data.filename);
data.lastfilename=data.filename;
end
fhandle = str2func( data.fileformat(data.fileformatid).functionread);
data.volume=feval(fhandle,data.info);
if(data.real)
data.volume=single(data.volume);
if(isfield(data.info,'RescaleSlope')),
data.volume=data.volume*data.info.RescaleSlope;
else
disp('RescaleSlope not available, assuming 1')
end
if(isfield(data.info,'RescaleIntercept')),
data.volume=data.volume+data.info.RescaleIntercept;
else
disp('RescaleIntercept not available, assuming 0')
end
end
setMyData(data);
set(data.handles.figure1,'Pointer','arrow')
% Save the filename, for the next time this function is used
filename=data.filename; fileformatid=data.fileformatid;
try save(data.configfile,'filename','fileformatid'); catch ME; disp(ME.message); end
% --- Executes on button press in pushbutton_info.
function pushbutton_info_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton_info (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData();
data.filename=get(handles.edit_filename,'string');
if(~strcmp(data.lastfilename,data.filename))
% Get info
set(data.handles.figure1,'Pointer','watch'); drawnow('expose');
fhandle = str2func( data.fileformat(data.fileformatid).functioninfo);
data.info=feval(fhandle,data.filename);
data.lastfilename=data.filename;
set(data.handles.figure1,'Pointer','arrow')
end
setMyData(data);
% Show info
InfoData3D(data.info);
% --- Executes on button press in checkbox_real.
function checkbox_real_Callback(hObject, eventdata, handles)
% hObject handle to checkbox_real (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of checkbox_real
data=getMyData();
data.real=get(handles.checkbox_real,'Value');
setMyData(data);
|
github
|
jacksky64/imageProcessing-master
|
dicom_folder_info.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/ReadData3D/dicom/dicom_folder_info.m
| 8,444 |
utf_8
|
0c58b3656654e208a0c51854cd32d2e6
|
function datasets=dicom_folder_info(link,subfolders)
% Function DICOM_FOLDER_INFO gives information about all Dicom files
% in a certain folder (and subfolders), or of a certain dataset
%
% datasets=dicom_folder_info(link,subfolders)
%
% inputs,
% link : A link to a folder like "C:\temp" or a link to the first
% file of a dicom volume "C:\temp\01.dcm"
% subfolders : Boolean if true (default) also look in sub-folders for
% dicom files
%
% ouputs,
% datasets : A struct with information about all dicom datasets in a
% folder or of the selected dicom-dataset.
% (Filenames are already sorted by InstanceNumber)
%
%
% Example output:
% datasets=dicom_folder_info('D:\MedicalVolumeData',true);
%
% datasets = 1x7 struct array with fields
%
% datasets(1) =
% Filenames: {24x1 cell}
% Sizes: [512 512 24]
% Scales: [0.3320 0.3320 4.4992]
% DicomInfo: [1x1 struct]
% SeriesInstanceUID: '1.2.840.113619.2.176.2025'
% SeriesDescription: 'AX. FSE PD'
% SeriesDate: '20070101'
% SeriesTime: '120000.000000'
% Modality: 'MR'
%
% datasets(1).Filenames =
% 'D:\MedicalVolumeData\IM-0001-0001.dcm'
% 'D:\MedicalVolumeData\IM-0001-0002.dcm'
% 'D:\MedicalVolumeData\IM-0001-0003.dcm'
%
% Function is written by D.Kroon University of Twente (June 2010)
% If no Folder given, give folder selection dialog
if(nargin<1), link = uigetdir(); end
% If no subfolders option defined set it to true
if(nargin<2), subfolders=true; end
% Check if the input is a file or a folder
if(isdir(link))
dirname=link; filehash=[];
else
dirname = fileparts(link);
info=dicominfo(link);
SeriesInstanceUID=0;
if(isfield(info,'SeriesInstanceUID')), SeriesInstanceUID=info.SeriesInstanceUID; end
filehash=string2hash([dirname SeriesInstanceUID]);
subfolders=false;
end
% Make a structure to store all files and folders
dicomfilelist.Filename=cell(1,100000);
dicomfilelist.InstanceNumber=zeros(1,100000);
dicomfilelist.ImagePositionPatient=zeros(100000,3);
dicomfilelist.hash=zeros(1,100000);
nfiles=0;
% Get all dicomfiles in the current folder (and sub-folders)
[dicomfilelist,nfiles]=getdicomfilelist(dirname,dicomfilelist,nfiles,filehash,subfolders);
if(nfiles==0), datasets=[]; return; end
% Sort all dicom files based on a hash from dicom-series number and folder name
datasets=sortdicomfilelist(dicomfilelist,nfiles);
% Add Dicom information like scaling and size
datasets=AddDicomInformation(datasets);
function datasets=AddDicomInformation(datasets)
for i=1:length(datasets)
Scales=[0 0 0];
Sizes=[0 0 0];
SeriesInstanceUID=0;
SeriesDescription='';
SeriesDate='';
SeriesTime='';
Modality='';
info=dicominfo(datasets(i).Filenames{1});
nf=length(datasets(i).Filenames);
if(isfield(info,'SpacingBetweenSlices')), Scales(3)=info.SpacingBetweenSlices; end
if(isfield(info,'PixelSpacing')), Scales(1:2)=info.PixelSpacing(1:2); end
if(isfield(info,'ImagerPixelSpacing ')), Scales(1:2)=info.PixelSpacing(1:2); end
if(isfield(info,'Rows')), Sizes(1)=info.Rows; end
if(isfield(info,'Columns')), Sizes(2)=info.Columns; end
if(isfield(info,'NumberOfFrames')), Sizes(3)=info.NumberOfFrames; end
if(isfield(info,'SeriesInstanceUID')), SeriesInstanceUID=info.SeriesInstanceUID; end
if(isfield(info,'SeriesDescription')), SeriesDescription=info.SeriesDescription; end
if(isfield(info,'SeriesDate')),SeriesDate=info.SeriesDate; end
if(isfield(info,'SeriesTime')),SeriesTime=info.SeriesTime; end
if(isfield(info,'Modality')), Modality=info. Modality; end
if(nf>1), Sizes(3)=nf; end
if(nf>1)
info1=dicominfo(datasets(i).Filenames{2});
if(isfield(info1,'ImagePositionPatient'))
dis=abs(info1.ImagePositionPatient(3)-info.ImagePositionPatient(3));
if(dis>0), Scales(3)=dis; end
end
end
datasets(i).Sizes=Sizes;
datasets(i).Scales=Scales;
datasets(i).DicomInfo=info;
datasets(i).SeriesInstanceUID=SeriesInstanceUID;
datasets(i).SeriesDescription=SeriesDescription;
datasets(i).SeriesDate=SeriesDate;
datasets(i).SeriesTime=SeriesTime;
datasets(i).Modality= Modality;
end
function datasets=sortdicomfilelist(dicomfilelist,nfiles)
datasetids=unique(dicomfilelist.hash(1:nfiles));
ndatasets=length(datasetids);
for i=1:ndatasets
h=find(dicomfilelist.hash(1:nfiles)==datasetids(i));
InstanceNumbers=dicomfilelist.InstanceNumber(h);
ImagePositionPatient=dicomfilelist.ImagePositionPatient(h,:);
if(length(unique(InstanceNumbers))==length(InstanceNumbers))
[temp ind]=sort(InstanceNumbers);
else
[temp ind]=sort(ImagePositionPatient(:,3));
end
h=h(ind);
datasets(i).Filenames=cell(length(h),1);
for j=1:length(h)
datasets(i).Filenames{j}=dicomfilelist.Filename{h(j)};
end
end
function [dicomfilelist nfiles]=getdicomfilelist(dirname,dicomfilelist,nfiles,filehash,subfolders)
dirn=fullfile(dirname,'');
if(~isempty(dirn)), filelist = dir(dirn); else filelist = dir; end
for i=1:length(filelist)
fullfilename=fullfile(dirname,filelist(i).name);
if((filelist(i).isdir))
if((filelist(i).name(1)~='.')&&(subfolders))
[dicomfilelist nfiles]=getdicomfilelist(fullfilename ,dicomfilelist,nfiles,filehash,subfolders);
end
else
if(file_is_dicom(fullfilename))
try info=dicominfo(fullfilename); catch me, info=[]; end
if(~isempty(info))
InstanceNumber=0;
ImagePositionPatient=[0 0 0];
SeriesInstanceUID=0;
Filename=info.Filename;
if(isfield(info,'InstanceNumber')), InstanceNumber=info.InstanceNumber; end
if(isfield(info,'ImagePositionPatient')),ImagePositionPatient=info.ImagePositionPatient; end
if(isfield(info,'SeriesInstanceUID')), SeriesInstanceUID=info.SeriesInstanceUID; end
hash=string2hash([dirname SeriesInstanceUID]);
if(isempty(filehash)||(filehash==hash))
nfiles=nfiles+1;
dicomfilelist.Filename{ nfiles}=Filename;
dicomfilelist.InstanceNumber( nfiles)=InstanceNumber;
dicomfilelist.ImagePositionPatient(nfiles,:)=ImagePositionPatient(:)';
dicomfilelist.hash( nfiles)=hash;
end
end
end
end
end
function isdicom=file_is_dicom(filename)
isdicom=false;
try
fid = fopen(filename, 'r');
status=fseek(fid,128,-1);
if(status==0)
tag = fread(fid, 4, 'uint8=>char')';
isdicom=strcmpi(tag,'DICM');
end
fclose(fid);
catch me
end
function hash=string2hash(str,type)
% This function generates a hash value from a text string
%
% hash=string2hash(str,type);
%
% inputs,
% str : The text string, or array with text strings.
% outputs,
% hash : The hash value, integer value between 0 and 2^32-1
% type : Type of has 'djb2' (default) or 'sdbm'
%
% From c-code on : http://www.cse.yorku.ca/~oz/hash.html
%
% djb2
% this algorithm was first reported by dan bernstein many years ago
% in comp.lang.c
%
% sdbm
% this algorithm was created for sdbm (a public-domain reimplementation of
% ndbm) database library. it was found to do well in scrambling bits,
% causing better distribution of the keys and fewer splits. it also happens
% to be a good general hashing function with good distribution.
%
% example,
%
% hash=string2hash('hello world');
% disp(hash);
%
% Function is written by D.Kroon University of Twente (June 2010)
% From string to double array
str=double(str);
if(nargin<2), type='djb2'; end
switch(type)
case 'djb2'
hash = 5381*ones(size(str,1),1);
for i=1:size(str,2),
hash = mod(hash * 33 + str(:,i), 2^32-1);
end
case 'sdbm'
hash = zeros(size(str,1),1);
for i=1:size(str,2),
hash = mod(hash * 65599 + str(:,i), 2^32-1);
end
otherwise
error('string_hash:inputs','unknown type');
end
|
github
|
jacksky64/imageProcessing-master
|
dicom_write_volume.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/ReadData3D/dicom/dicom_write_volume.m
| 2,219 |
utf_8
|
a3f41a386dcd02f121e040857f26b55a
|
function dicom_write_volume(Volume,filename,volscale,info)
% This function DICOM_WRITE_VOLUME will write a Matlab 3D volume as
% a stack of 2D slices in separate dicom files.
%
% dicom_write_volume(Volume,Filename,Scales,Info)
%
% inputs,
% Volume: The 3D Matlab volume
% Filename: The name of the dicom files
% Scales: The dimensions of every voxel/pixel
% Info: A struct with dicom tags and values
%
% Function is written by D.Kroon University of Twente (May 2009)
% Check inputs
if(exist('filename','var')==0), filename=[]; end
if(exist('info','var')==0), info=[]; end
if(exist('volscale','var')==0), volscale=[1 1 1]; end
% Show file dialog if no file name specified
if(isempty(filename))
[filename, pathname] = uiputfile('*.dcm', 'Save to Dicom');
filename= [pathname filename];
end
% Add dicom tags to info structure
if(~isstruct(info))
info=struct;
% Make random series number
SN=round(rand(1)*1000);
% Get date of today
today=[datestr(now,'yyyy') datestr(now,'mm') datestr(now,'dd')];
info.SeriesNumber=SN;
info.AcquisitionNumber=SN;
info.StudyDate=today;
info.StudyID=num2str(SN);
info.PatientID=num2str(SN);
info.PatientPosition='HFS';
info.AccessionNumber=num2str(SN);
info.StudyDescription=['StudyMAT' num2str(SN)];
info.SeriesDescription=['StudyMAT' num2str(SN)];
info.Manufacturer='Matlab Convert';
info.SliceThickness=volscale(3);
info.PixelSpacing=volscale(1:2);
info.SliceLocation=0;
end
% Remove filename extention
pl=find(filename=='.'); if(~isempty(pl)), filename=filename(1:pl-1); end
% Read Volume data
disp('Writing Dicom Files...');
for slicenum=1:size(Volume,3)
filenamedicom=[filename number2string(slicenum) '.dcm'];
% Add slice specific dicom info
info.InstanceNumber = slicenum;
info.SliceLocation = info.SliceLocation+volscale(3);
% Write the dicom file
disp(['Writing : ' filenamedicom]);
dicomwrite(Volume(:,:,slicenum), filenamedicom, info)
end
function numstr=number2string(num)
num=num2str(num);
numzeros='000000';
numstr=[numzeros(length(num):end) num];
|
github
|
jacksky64/imageProcessing-master
|
choose_from_list.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/ReadData3D/dicom/choose_from_list.m
| 1,062 |
utf_8
|
9a5736ab8c4022c2092521054615df27
|
function [id,name] = choose_from_list(varargin)
%
% example :
%
% c{1}='apple'
% c{2}='orange'
% c{3}='berries'
% [id,name]=choose_from_list(c,'Select a Fruit');
%
if(strcmp(varargin{1},'press'))
handles=guihandles;
id=get(handles.listbox1,'Value');
setMyData(id);
uiresume
return
end
% listbox1 Position [12, 36 , 319, 226]
% pushbutton [16,12,69,22]
% figure position 520 528 348 273
handles.figure1=figure;
c=varargin{1};
set(handles.figure1,'tag','figure1','Position',[520 528 348 273],'MenuBar','none','name',varargin{2});
handles.listbox1=uicontrol('tag','listbox1','Style','listbox','Position',[12 36 319 226],'String', c);
handles.pushbutton1=uicontrol('tag','pushbutton1','Style','pushbutton','Position',[16 12 69 22],'String','Select','Callback','choose_from_list(''press'');');
uiwait(handles.figure1);
id=getMyData();
name=c{id};
close(handles.figure1);
function setMyData(data)
% Store data struct in figure
setappdata(gcf,'data3d',data);
function data=getMyData()
% Get data struct stored in figure
data=getappdata(gcf,'data3d');
|
github
|
jacksky64/imageProcessing-master
|
mha_read_volume.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/ReadData3D/mha/mha_read_volume.m
| 2,646 |
utf_8
|
21298fee32e8afb8010bca7385a11d6e
|
function V = mha_read_volume(info)
% Function for reading the volume of a Insight Meta-Image (.mha, .mhd) file
%
% volume = tk_read_volume(file-header)
%
% examples:
% 1: info = mha_read_header()
% V = mha_read_volume(info);
% imshow(squeeze(V(:,:,round(end/2))),[]);
%
% 2: V = mha_read_volume('test.mha');
if(~isstruct(info)), info=mha_read_header(info); end
switch(lower(info.DataFile))
case 'local'
otherwise
% Seperate file
info.Filename=fullfile(fileparts(info.Filename),info.DataFile);
end
% Open file
switch(info.ByteOrder(1))
case ('true')
fid=fopen(info.Filename','rb','ieee-be');
otherwise
fid=fopen(info.Filename','rb','ieee-le');
end
switch(lower(info.DataFile))
case 'local'
% Skip header
fseek(fid,info.HeaderSize,'bof');
otherwise
fseek(fid,0,'bof');
end
datasize=prod(info.Dimensions)*info.BitDepth/8;
switch(info.CompressedData(1))
case 'f'
% Read the Data
switch(info.DataType)
case 'char'
V = int8(fread(fid,datasize,'char'));
case 'uchar'
V = uint8(fread(fid,datasize,'uchar'));
case 'short'
V = int16(fread(fid,datasize,'short'));
case 'ushort'
V = uint16(fread(fid,datasize,'ushort'));
case 'int'
V = int32(fread(fid,datasize,'int'));
case 'uint'
V = uint32(fread(fid,datasize,'uint'));
case 'float'
V = single(fread(fid,datasize,'float'));
case 'double'
V = double(fread(fid,datasize,'double'));
end
case 't'
switch(info.DataType)
case 'char', DataType='int8';
case 'uchar', DataType='uint8';
case 'short', DataType='int16';
case 'ushort', DataType='uint16';
case 'int', DataType='int32';
case 'uint', DataType='uint32';
case 'float', DataType='single';
case 'double', DataType='double';
end
Z = fread(fid,inf,'uchar=>uint8');
V = zlib_decompress(Z,DataType);
end
fclose(fid);
V = reshape(V,info.Dimensions);
function M = zlib_decompress(Z,DataType)
import com.mathworks.mlwidgets.io.InterruptibleStreamCopier
a=java.io.ByteArrayInputStream(Z);
b=java.util.zip.InflaterInputStream(a);
isc = InterruptibleStreamCopier.getInterruptibleStreamCopier;
c = java.io.ByteArrayOutputStream;
isc.copyStream(b,c);
M=typecast(c.toByteArray,DataType);
|
github
|
jacksky64/imageProcessing-master
|
raw_read_header.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/ReadData3D/raw/raw_read_header.m
| 19,605 |
utf_8
|
4012e947c5ae87248c1a2034fb83864e
|
function varargout = raw_read_header(varargin)
% function for reading header of raw volume file
%
% info = raw_read_header(filename);
%
% examples:
% 1, info=raw_read_header()
% 2, info=raw_read_header('volume.raw');
% Edit the above text to modify the response to help raw_read_header
% Last Modified by GUIDE v2.5 06-Jul-2010 14:01:48
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @raw_read_header_OpeningFcn, ...
'gui_OutputFcn', @raw_read_header_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if (nargin>1) && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before raw_read_header is made visible.
function raw_read_header_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to raw_read_header (see VARARGIN)
% Choose default command line output for raw_read_header
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes raw_read_header wait for user response (see UIRESUME)
if(isempty(varargin))
[filename, pathname] = uigetfile({'*.raw', 'Read Raw file (*.raw) ';'*.*', 'All Files (*.*)'});
filename = [pathname filename];
else
filename=varargin{1};
end
fileInfo = dir(filename);
info.Filesize= fileInfo.bytes;
info.Filename=filename;
setMyData(info);
updateGUIvalues(handles);
uiwait(handles.figure1);
function updateGUIvalues(handles)
info=getMyData();
set(handles.text_filesize,'string',['File Size (Bytes) : ' num2str(info.Filesize)]);
info.Headersize=str2double(get(handles.edit_header_size,'String'));
info.Dimensions(1)=str2double(get(handles.edit_dimx,'String'));
info.Dimensions(2)=str2double(get(handles.edit_dimy,'String'));
info.Dimensions(3)=str2double(get(handles.edit_dimz,'String'));
info.PixelDimensions(1)=str2double(get(handles.edit_scalex,'String'));
info.PixelDimensions(2)=str2double(get(handles.edit_scaley,'String'));
info.PixelDimensions(3)=str2double(get(handles.edit_scalez,'String'));
switch(get(handles.popupmenu_dataclass,'Value'))
case 1
info.Nbits=8;
info.DataType='uchar';
case 2
info.Nbits=8;
info.DataType='char';
case 3
info.Nbits=16;
info.DataType='ushort';
case 4
info.Nbits=16;
info.DataType='short';
case 5
info.Nbits=32;
info.DataType='uint';
case 6
info.Nbits=32;
info.DataType='int';
case 7
info.Nbits=32;
info.DataType='float';
case 8
info.Nbits=64;
info.DataType='double';
end
switch(get(handles.popupmenu_data_alligment,'Value'))
case 1
info.Alignment='LittleEndian';
case 2
info.Alignment='BigEndian';
end
currentbytes=(info.Nbits/8)*info.Dimensions(1)*info.Dimensions(2)*info.Dimensions(3)+info.Headersize;
set(handles.text_setbytes,'string',['Current (Bytes) : ' num2str(currentbytes)]);
if(currentbytes==info.Filesize)
set(handles.pushbutton1,'enable','on');
else
set(handles.pushbutton1,'enable','off');
end
drawnow
setMyData(info);
% --- Outputs from this function are returned to the command line.
function varargout = raw_read_header_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
info=getMyData();
if(~isempty(info))
varargout{1} = info;
end
if(ishandle(hObject))
close(hObject)
end
function edit_header_size_Callback(hObject, eventdata, handles)
% hObject handle to edit_header_size (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_header_size as text
% str2double(get(hObject,'String')) returns contents of edit_header_size as a double
updateGUIvalues(handles);
% --- Executes during object creation, after setting all properties.
function edit_header_size_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_header_size (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in popupmenu_data_alligment.
function popupmenu_data_alligment_Callback(hObject, eventdata, handles)
% hObject handle to popupmenu_data_alligment (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = cellstr(get(hObject,'String')) returns popupmenu_data_alligment contents as cell array
% contents{get(hObject,'Value')} returns selected item from popupmenu_data_alligment
updateGUIvalues(handles);
% --- Executes during object creation, after setting all properties.
function popupmenu_data_alligment_CreateFcn(hObject, eventdata, handles)
% hObject handle to popupmenu_data_alligment (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: popupmenu controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in popupmenu_dataclass.
function popupmenu_dataclass_Callback(hObject, eventdata, handles)
% hObject handle to popupmenu_dataclass (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = cellstr(get(hObject,'String')) returns popupmenu_dataclass contents as cell array
% contents{get(hObject,'Value')} returns selected item from popupmenu_dataclass
updateGUIvalues(handles);
% --- Executes during object creation, after setting all properties.
function popupmenu_dataclass_CreateFcn(hObject, eventdata, handles)
% hObject handle to popupmenu_dataclass (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: popupmenu controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_dimx_Callback(hObject, eventdata, handles)
% hObject handle to edit_dimx (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_dimx as text
% str2double(get(hObject,'String')) returns contents of edit_dimx as a double
updateGUIvalues(handles);
% --- Executes during object creation, after setting all properties.
function edit_dimx_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_dimx (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_dimy_Callback(hObject, eventdata, handles)
% hObject handle to edit_dimy (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_dimy as text
% str2double(get(hObject,'String')) returns contents of edit_dimy as a double
updateGUIvalues(handles);
% --- Executes during object creation, after setting all properties.
function edit_dimy_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_dimy (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_dimz_Callback(hObject, eventdata, handles)
% hObject handle to edit_dimz (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_dimz as text
% str2double(get(hObject,'String')) returns contents of edit_dimz as a double
updateGUIvalues(handles);
% --- Executes during object creation, after setting all properties.
function edit_dimz_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_dimz (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_scalex_Callback(hObject, eventdata, handles)
% hObject handle to edit_scalex (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_scalex as text
% str2double(get(hObject,'String')) returns contents of edit_scalex as a double
updateGUIvalues(handles);
% --- Executes during object creation, after setting all properties.
function edit_scalex_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_scalex (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_scaley_Callback(hObject, eventdata, handles)
% hObject handle to edit_scaley (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_scaley as text
% str2double(get(hObject,'String')) returns contents of edit_scaley as a double
updateGUIvalues(handles);
% --- Executes during object creation, after setting all properties.
function edit_scaley_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_scaley (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_scalez_Callback(hObject, eventdata, handles)
% hObject handle to edit_scalez (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_scalez as text
% str2double(get(hObject,'String')) returns contents of edit_scalez as a double
updateGUIvalues(handles);
% --- Executes during object creation, after setting all properties.
function edit_scalez_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_scalez (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in pushbutton1.
function pushbutton1_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
updateGUIvalues(handles);
uiresume
% --- Executes on button press in pushbutton2.
function pushbutton2_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
setMyData(0);
uiresume
function setMyData(data)
% Store data struct in figure
setappdata(gcf,'rawinfo',data);
function data=getMyData()
% Get data struct stored in figure
data=getappdata(gcf,'rawinfo');
% --- Executes on key press with focus on edit_header_size and none of its controls.
function edit_header_size_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to edit_header_size (see GCBO)
% eventdata structure with the following fields (see UICONTROL)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
updateGUIvalues(handles);
% --- Executes on key press with focus on edit_dimx and none of its controls.
function edit_dimx_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to edit_dimx (see GCBO)
% eventdata structure with the following fields (see UICONTROL)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
updateGUIvalues(handles);
% --- Executes on key press with focus on edit_dimy and none of its controls.
function edit_dimy_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to edit_dimy (see GCBO)
% eventdata structure with the following fields (see UICONTROL)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
updateGUIvalues(handles);
% --- Executes on key press with focus on edit_dimz and none of its controls.
function edit_dimz_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to edit_dimz (see GCBO)
% eventdata structure with the following fields (see UICONTROL)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
updateGUIvalues(handles);
% --- Executes on key press with focus on edit_scalex and none of its controls.
function edit_scalex_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to edit_scalex (see GCBO)
% eventdata structure with the following fields (see UICONTROL)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
updateGUIvalues(handles);
% --- Executes on key press with focus on edit_scaley and none of its controls.
function edit_scaley_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to edit_scaley (see GCBO)
% eventdata structure with the following fields (see UICONTROL)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
updateGUIvalues(handles);
% --- Executes on key press with focus on edit_scalez and none of its controls.
function edit_scalez_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to edit_scalez (see GCBO)
% eventdata structure with the following fields (see UICONTROL)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
updateGUIvalues(handles);
% --- Executes on key press with focus on popupmenu_dataclass and none of its controls.
function popupmenu_dataclass_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to popupmenu_dataclass (see GCBO)
% eventdata structure with the following fields (see UICONTROL)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
updateGUIvalues(handles);
% --- Executes on key press with focus on popupmenu_data_alligment and none of its controls.
function popupmenu_data_alligment_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to popupmenu_data_alligment (see GCBO)
% eventdata structure with the following fields (see UICONTROL)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
updateGUIvalues(handles);
% --- Executes on button press in pushbutton3.
function pushbutton3_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton3 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
info=getMyData();
currentbytes=(info.Nbits/8)*info.Dimensions(1)*info.Dimensions(2)*info.Dimensions(3);
info.Headersize=info.Filesize-currentbytes;
set(handles.edit_header_size,'String',num2str(info.Headersize));
updateGUIvalues(handles);
|
github
|
jacksky64/imageProcessing-master
|
par_read_header.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/ReadData3D/par/par_read_header.m
| 9,281 |
utf_8
|
d35b414f478ff294a6ca3ab889e04551
|
function info =par_read_header(filename)
% Function for reading the header of a Philips Par / Rec MR V4.* file
%
% info = par_read_header(filename);
%
% examples:
% 1, info=par_read_header()
% 2, info=par_read_header('volume.par');
if(exist('filename','var')==0)
[filename, pathname] = uigetfile('*.par', 'Read par-file');
filename = [pathname filename];
end
fid=fopen(filename,'rb');
if(fid<0)
fprintf('could not open file %s\n',filename);
return
end
info.Filename=filename;
mode = -1; nHC=0; nIC=0; nSC=0;
while(true)
str=fgetl(fid);
if ~ischar(str), break, end
if(isempty(str)), continue, end
if(strfind(str,'= DATA DESCRIPTION FILE =')), mode=0; end
if(strfind(str,'= GENERAL INFORMATION =')), mode=1; end
if(strfind(str,'= PIXEL VALUES =')), mode=2; end
if(strfind(str,'= IMAGE INFORMATION DEFINITION =')),
mode=3; fgetl(fid); str=fgetl(fid);
% Skip a line
end
if(strfind(str,'= IMAGE INFORMATION =')), mode=4; end
if(strfind(str,'= END OF DATA DESCRIPTION FILE =')), mode=5; end
switch(mode)
case -1;
case 0
nHC=nHC+1; HeaderComment{nHC}=str;
case 1
if(str(1)=='.')
[type data]=General_Information_Line(str);
switch(type)
case 'PatientName'
info.(type)=data;
case 'ProtocolName'
info.(type)=data;
case 'ExaminationName'
info.(type)=data;
case 'ExaminationDateTime'
info.(type)=data;
case 'SeriesType'
info.(type)=data;
case 'AcquisitionNr'
info.(type)=sscanf(data, '%d')';
case 'ReconstructionNr'
info.(type)=sscanf(data, '%d')';
case 'ScanDuration'
info.(type)=sscanf(data, '%lf')';
case 'MaxNumberOfCardiacPhases'
info.(type)=sscanf(data, '%d')';
case 'MaxNumberOfEchoes'
info.(type)=sscanf(data, '%d')';
case 'MaxNumberOfSlicesLocations'
info.(type)=sscanf(data, '%d')';
case 'MaxNumberOfDynamics'
info.(type)=sscanf(data, '%d')';
case 'MaxNumberOfMixes'
info.(type)=sscanf(data, '%d')';
case 'PatientPosition'
info.(type)=data;
case 'PreparationDirection'
info.(type)=data;
case 'Technique'
info.(type)=data;
case 'ScanResolution'
info.(type)=sscanf(data, '%d')';
case 'ScanMode'
info.(type)=data;
case 'RepetitionTime'
info.(type)=sscanf(data, '%lf')';
case 'Fov'
info.(type)=sscanf(data, '%lf')';
case 'WaterFatShift'
info.(type)=sscanf(data, '%lf')';
case 'Angulation'
info.(type)=sscanf(data, '%lf')';
case 'OffCentre'
info.(type)=sscanf(data, '%lf')';
case 'FlowCompensation'
info.(type)=sscanf(data, '%d')';
case 'Presaturation'
info.(type)=sscanf(data, '%d')';
case 'PhaseEncodingVelocity'
info.(type)=sscanf(data, '%lf')';
case 'Mtc'
info.(type)=sscanf(data, '%lf')';
case 'Spir'
info.(type)=sscanf(data, '%lf')';
case 'EpiFactor'
info.(type)=sscanf(data, '%lf')';
case 'DynamicScan'
info.(type)=sscanf(data, '%lf')';
case 'Diffusion'
info.(type)=sscanf(data, '%lf')';
case 'DiffusionEchoTime'
info.(type)=sscanf(data, '%lf')';
case 'MaxNumberOfDiffusionValues'
info.(type)=sscanf(data, '%d')';
case 'MaxNumberOfGradientOrients'
info.(type)=sscanf(data, '%d')';
case 'NumberOfLabelTypes'
info.(type)=sscanf(data, '%d')';
case 'HeaderComment'
otherwise
info.(type)=data;
end
end
case 2
case 3
if(str(1)=='#');
[type datatype datalength]=Image_Information_Line(str);
if(~isempty(type))
nIC=nIC+1;
ImageInformationTags(nIC).Name=type;
ImageInformationTags(nIC).DataType=datatype;
ImageInformationTags(nIC).NumberOfValues=datalength;
end
end
case 4
if(str(1)~='#');
nSC=nSC+1;
vals=regexp(str, '\s+','split');
vald=sscanf(str, '%lf')';
current_loc=0;
for i=1:length(ImageInformationTags)
IIT=ImageInformationTags(i);
if(strcmp(IIT.DataType,'string'))
SliceInformation(nSC).(IIT.Name)=vals{current_loc+1};
else
SliceInformation(nSC).(IIT.Name)=vald(current_loc+1:current_loc+IIT.NumberOfValues);
end
current_loc=current_loc+IIT.NumberOfValues;
end
end
case 5
otherwise
%disp(str);
end
end
fclose(fid);
info.HeaderComment=HeaderComment;
info.SliceInformation=SliceInformation;
info.ImageInformationTags=ImageInformationTags;
% Add Dimensions and Voxel Spacing. Warning, based on only 1 slice!
infof=info.SliceInformation(1);
if(isfield(infof,'ReconResolution'))
if(isfield(info,'MaxNumberOfSlicesLocations'))
zs(1)=info.MaxNumberOfSlicesLocations;
zs(2)=length(SliceInformation)/zs(1);
if((mod(zs(2),1)>0)||zs(2)==1)
zs=length(SliceInformation);
end
else
zs=length(SliceInformation);
end
info.Dimensions=[infof.ReconResolution zs];
else
info.Dimensions=[info.ScanResolution length(SliceInformation)];
end
if(isfield(infof,'PixelSpacing'))
if(isfield(infof,'SliceThickness')&&isfield(infof,'SliceGap'))
zs=infof.SliceThickness+infof.SliceGap;
else
zs=0;
end
info.Scales=[infof.PixelSpacing zs];
else
info.Scales=[0 0 0];
end
[folder,filen]=fileparts(info.Filename);
info.FilenameREC=fullfile(folder,[filen '.rec']);
% Add bith depth
if(infof.ImagePixelSize)
info.BitDepth=infof.ImagePixelSize;
else
if(exist(info.FilenameREC,'file'))
file_info=dir(info.FilenameREC);
bytes=file_info.bytes;
info.BitDepth=(bytes/prod(info.Dimensions))*8;
end
end
function [type datatype datalength]=Image_Information_Line(str)
s=find(str=='(',1,'last');
if(isempty(s)), s=length(str); end
type=str(1:s-1); data=str(s+1:end);
type=regexp(type, '\s+|/|_', 'split');
type_clean='';
for i=1:length(type)
part=type{i};
part(part=='#')=[]; part(part==' ')=[]; partu=uint8(part);
if(~isempty(part))
check=((partu>=97)&(partu<=122))|((partu>=65)&(partu<=90));
if(check)
part=lower(part); part(1)=upper(part(1));
type_clean=[type_clean part];
else
break;
end
end
end
type=type_clean;
while(~isempty(data)&&data(1)==' '), data=data(2:end); end
while(~isempty(data)&&data(end)==' '), data=data(1:end-1); end
if(~isempty(data))
data=data(1:end-1);
s=find(data=='*',1,'first');
if(isempty(s)),
datalength=1; datatype=data;
else
datalength=str2double(data(1:s-1)); datatype=data(s+1:end);
end
else
datalength=0; datatype=''; type='';
end
function [type data]=General_Information_Line(str)
s=find(str==':',1,'first');
if(isempty(s)), s=length(str); end
type=str(1:s-1); data=str(s+1:end);
type=regexp(type, '\s+|/', 'split');
type_clean='';
for i=1:length(type)
part=type{i};
part(part=='.')=[]; part(part==' ')=[]; partu=uint8(part);
if(~isempty(part))
check=((partu>=97)&(partu<=122))|((partu>=65)&(partu<=90));
if(check)
part=lower(part); part(1)=upper(part(1));
type_clean=[type_clean part];
else
break;
end
end
end
type=type_clean;
while(~isempty(data)&&data(1)==' '), data=data(2:end); end
while(~isempty(data)&&data(end)==' '), data=data(1:end-1); end
|
github
|
jacksky64/imageProcessing-master
|
hdr_read_volume.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/ReadData3D/hdr/hdr_read_volume.m
| 1,429 |
utf_8
|
ddbf082bf0adb5cc48c5ad55a65a4f07
|
function V=hdr_read_volume(info)
% function for reading volume of HDR/IMG Analyze ( .hdr ) volume file
%
% volume = hdr_read_volume(file-header)
%
% examples:
% 1: info = hdr_read_volume(()
% V = hdr_read_volume(info);
% imshow(squeeze(V(:,:,round(end/2))),[]);
%
% 2: V = hdr_read_volume(('test.hdr');
%
if(~isstruct(info)), info=hdr_read_header(info); end
if(exist('analyze75read','file')>0)
V = analyze75read(info);
else
V = get_analyze_volume(info);
end
function V = get_analyze_volume(info)
% Open img file
[folder filename] = fileparts(info.Filename);
Filename = fullfile(folder, [filename '.img']);
fid=fopen(Filename,'rb',info.ByteOrder);
datasize=prod(info.Dimensions)*(info.BitDepth/8);
fseek(fid,0,'bof');
switch(info.ImgDataType)
case 'DT_BINARY'
V = logical(fread(fid,datasize,'bit1'));
case 'DT_UNSIGNED_CHAR'
V = uint8(fread(fid,datasize,'uchar'));
case 'DT_SIGNED_SHORT'
V = int16(fread(fid,datasize,'short'));
case 'DT_SIGNED_INT'
V = int32(fread(fid,datasize,'int'));
case 'DT_FLOAT'
V = single(fread(fid,datasize,'float'));
case 'DT_DOUBLE'
V = double(fread(fid,datasize,'double'));
case 'DT_COMPLEX'
case 'DT_RGB'
case 'DT_ALL'
end
fclose(fid);
% Reshape the volume data to the right dimensions
V = reshape(V,info.Dimensions);
|
github
|
jacksky64/imageProcessing-master
|
hdr_read_header.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/ReadData3D/hdr/hdr_read_header.m
| 4,707 |
utf_8
|
a2dc54e78b103557c78fd2f7652f1bfe
|
function info=hdr_read_header(filename)
% function for reading header of HDR/IMG Analyze ( .hdr ) volume file
%
% info = hdr_read_header(filename);
%
% examples:
% 1, info=hdr_read_header()
% 2, info=hdr_read_header('volume.hdr');
if(exist('filename','var')==0)
[filename, pathname] = uigetfile('*.hdr', 'Read hdr-file');
filename = [pathname filename];
end
if(exist('analyze75info','file')>0)
info=analyze75info(filename);
else
info=get_info_analyze_hdr(filename);
end
function info=get_info_analyze_hdr(filename)
% Strings for data type (compatible names with analyze75info)
strImgData{1}.ImgDataType = 'DT_UNKNOWN';
strImgData{1}.ColorType = 'unknown';
strImgData{2}.ImgDataType = 'DT_BINARY';
strImgData{2}.ColorType = 'grayscale';
strImgData{3}.ImgDataType = 'DT_UNSIGNED_CHAR';
strImgData{3}.ColorType = 'grayscale';
strImgData{5}.ImgDataType = 'DT_SIGNED_SHORT';
strImgData{5}.ColorType = 'grayscale';
strImgData{9}.ImgDataType = 'DT_SIGNED_INT';
strImgData{9}.ColorType = 'grayscale';
strImgData{17}.ImgDataType = 'DT_FLOAT';
strImgData{17}.ColorType = 'grayscale';
strImgData{33}.ImgDataType = 'DT_COMPLEX';
strImgData{33}.ColorType = 'grayscale';
strImgData{65}.ImgDataType = 'DT_DOUBLE';
strImgData{65}.ColorType = 'grayscale';
strImgData{129}.ImgDataType = 'DT_RGB';
strImgData{129}.ColorType = 'truecolor';
strImgData{256}.ImgDataType = 'DT_ALL';
strImgData{256}.ColorType = 'unknown';
strOriData{1} = 'Transverse unflipped';
strOriData{2} = 'Coronal unflipped';
strOriData{3} = 'Sagittal unflipped';
strOriData{4} = 'Transverse flipped';
strOriData{5} = 'Coronal flipped';
strOriData{6} = 'Sagittal flipped';
strOriData{7} = 'Orientation unavailable';
% Open the HDR-file, change MachineFormat if not the right
% header size
info.Filename=filename;
fid = fopen(filename,'rb','l'); fseek(fid,0,'bof');
info.ByteOrder='ieee-le';
info.HdrFileSize = fread(fid, 1,'int32');
if(info.HdrFileSize>2000);
fclose(fid);
fid = fopen(filename,'rb','b'); fseek(fid,0,'bof');
info.ByteOrder='ieee-be';
info.HdrFileSize = fread(fid, 1,'int32');
end
% Read the Whole Analyze Header
info.Format='Analyze';
info.HdrDataType = fread(fid,10,'char=>char')';
info.DatabaseName = fread(fid,18,'char=>char')';
info.Extents = fread(fid, 1,'int32');
info.SessionError = fread(fid, 1,'int16');
info.Regular = fread(fid, 1,'char=>char')';
unused= fread(fid, 1,'uint8')';
dim = fread(fid,8,'int16')';
if (dim(1) < 3), dim(1) = 4; end
info.Dimensions=dim(2:dim(1)+1);
info.Width=info.Dimensions(1);
info.Height=info.Dimensions(2);
info.VoxelUnits = fread(fid,4,'char=>char')';
info.CalibrationUnits = fread(fid,8,'char=>char')';
unused = fread(fid,1,'int16');
ImgDataType = fread(fid,1,'int16');
info.ImgDataType=strImgData{ImgDataType+1}.ImgDataType;
info.ColorType=strImgData{ImgDataType+1}.ColorType;
info.BitDepth = fread(fid,1,'int16');
unused = fread(fid,1,'int16');
PixelDimensions = fread(fid,8,'float')';
info.PixelDimensions=PixelDimensions(2:length(info.Dimensions)+1);
info.VoxelOffset = fread(fid,1,'float');
info.RoiScale = fread(fid,1,'float');
unused = fread(fid,1,'float');
unused = fread(fid,1,'float');
info.CalibrationMax = fread(fid,1,'float');
info.CalibrationMin = fread(fid,1,'float');
info.Compressed = fread(fid,1,'int32');
info.Verified = fread(fid,1,'int32');
info.GlobalMax = fread(fid,1,'int32');
info.GlobalMin = fread(fid,1,'int32');
info.Descriptor = fread(fid,80,'char=>char')';
info.AuxFile = fread(fid,24,'char=>char')';
Orientationt = fread(fid, 1,'uint8');
if((Orientationt>=48)&&(Orientationt<=53)), Orientationt = Orientationt -48; end
info.Orientationt=strOriData{min(Orientationt,5)+1};
info.Originator = fread(fid,10,'char=>char')';
info.Generated = fread(fid,10,'char=>char')';
info.Scannumber = fread(fid,10,'char=>char')';
info.PatientID = fread(fid,10,'char=>char')';
info.ExposureDate = fread(fid,10,'char=>char')';
info.ExposureTime = fread(fid,10,'char=>char')';
unused = fread(fid, 3,'char=>char')';
info.Views = fread(fid, 1,'int32');
info.VolumesAdded = fread(fid, 1,'int32');
info.StartField = fread(fid, 1,'int32');
info.FieldSkip = fread(fid, 1,'int32');
info.Omax = fread(fid, 1,'int32');
info.Omin = fread(fid, 1,'int32');
info.Smax = fread(fid, 1,'int32');
info.Smin = fread(fid, 1,'int32');
fclose(fid);
% Remove empty string parts from the info struct
names = fieldnames(info);
for i=1:length(names)
value=info.(names{i});
if(ischar(value))
value(uint8(value)==0)=[];
if(isempty(value)), info.(names{i})=''; else info.(names{i})=value; end
end
end
|
github
|
jacksky64/imageProcessing-master
|
ErrorData3D.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/ReadData3D/subfunctions/ErrorData3D.m
| 3,246 |
utf_8
|
66924055ba5a507e5363c6d4666bdac8
|
function varargout = ErrorData3D(varargin)
% ERRORDATA3D M-file for ErrorData3D.fig
% ERRORDATA3D, by itself, creates a new ERRORDATA3D or raises the existing
% singleton*.
%
% H = ERRORDATA3D returns the handle to a new ERRORDATA3D or the handle to
% the existing singleton*.
%
% ERRORDATA3D('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in ERRORDATA3D.M with the given input arguments.
%
% ERRORDATA3D('Property','Value',...) creates a new ERRORDATA3D or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before ErrorData3D_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to ErrorData3D_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help ErrorData3D
% Last Modified by GUIDE v2.5 05-Jul-2010 15:17:44
% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @ErrorData3D_OpeningFcn, ...
'gui_OutputFcn', @ErrorData3D_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before ErrorData3D is made visible.
function ErrorData3D_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to ErrorData3D (see VARARGIN)
% Choose default command line output for ErrorData3D
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
if (~isempty(varargin))
set(handles.text1,'string',varargin{1})
end
% UIWAIT makes ErrorData3D wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = ErrorData3D_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on button press in pushbutton1.
function pushbutton1_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
delete(handles.figure1);
|
github
|
jacksky64/imageProcessing-master
|
InfoData3D.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/ReadData3D/subfunctions/InfoData3D.m
| 3,553 |
utf_8
|
da6f4f6491166d601be56e443974a131
|
function varargout = InfoData3D(varargin)
% INFODATA3D M-file for InfoData3D.fig
% INFODATA3D, by itself, creates a new INFODATA3D or raises the existing
% singleton*.
%
% H = INFODATA3D returns the handle to a new INFODATA3D or the handle to
% the existing singleton*.
%
% INFODATA3D('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in INFODATA3D.M with the given input arguments.
%
% INFODATA3D('Property','Value',...) creates a new INFODATA3D or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before InfoData3D_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to InfoData3D_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help InfoData3D
% Last Modified by GUIDE v2.5 05-Jul-2010 15:13:54
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @InfoData3D_OpeningFcn, ...
'gui_OutputFcn', @InfoData3D_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before InfoData3D is made visible.
function InfoData3D_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to InfoData3D (see VARARGIN)
% Choose default command line output for InfoData3D
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes InfoData3D wait for user response (see UIRESUME)
% uiwait(handles.figure1);
info=varargin{1};
infocell=cell(100000,2);
[infocell,poscell]=showinfo(info,infocell,0,'');
infocell(poscell+1:end,:)=[];
set(handles.uitable1,'Data',infocell)
function [infocell,poscell] = showinfo(info,infocell,poscell,s)
fnames=fieldnames(info);
for i=1:length(fnames)
type=fnames{i};
data=info.(type);
if(isnumeric(data))
poscell=poscell+1;
infocell{poscell,1}=[s type];
infocell{poscell,2}=num2str(data(:)');
elseif(ischar(data))
poscell=poscell+1;
infocell{poscell,1}=[s type];
infocell{poscell,2}=data;
elseif(iscell(data))
elseif(isstruct(data))
[infocell,poscell]=showinfo(data,infocell,poscell,[type '.']);
end
end
% --- Outputs from this function are returned to the command line.
function varargout = InfoData3D_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
|
github
|
jacksky64/imageProcessing-master
|
render_color.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/Old_Viewer3D_with_c_code/render_color.m
| 15,776 |
utf_8
|
87aefba963f0a02cb4434837aed8651d
|
function render_image = render_color(V, image_size, Mview,alphatable,colortable)
% Function RENDER_COLOR will volume render a Image of a 3D volume with
% transperancy and colortable.
%
% I = RENDER_COLOR(V, SIZE, Mview, ALPHATABLE, COLORTABLE);
%
% inputs,
% V: Input image volume
% SIZE: Sizes (height and length) of output image
% Mview: Viewer (Transformation) matrix 4x4
% ALPHATABLE: Mapping from intensities to transperancy
% range [0 1], dimensions Nx1
% COLORTALBE: Mapping form intensities to color
% range [0 1], dimensions Nx3
%
% outputs,
% I: The maximum intensity output image
%
% Volume Data,
% Range of V must be [0 1] in case of double or single otherwise
% mex function will crash. Data of type double has short render times,
% uint16 the longest.
%
% example,
% % Load data
% load TestVolume;
% % Parameters
% sizes=[400 400];
% Mview=makeViewMatrix([45 45 0],[0.5 0.5 0.5],[0 0 0]);
% alphatable=(0:999)/999;
% colortable=hsv(1000);
% % Render and show image
% I = render_color(V, sizes, Mview,alphatable,colortable);
% imshow(I);
%
% Function is written by D.Kroon University of Twente (October 2008)
% Needed to convert intensities to range [0 1]
imax=1;
if(isa(V,'uint8')), imax=2^8-1; end
if(isa(V,'uint16')), imax=2^16-1; end
if(isa(V,'uint32')), imax=2^32-1; end
% Calculate the Shear and Warp Matrices
[Mshear,Mwarp2D,c]=makeShearWarpMatrix(Mview,size(V));
Mwarp2Dinv=inv(double(Mwarp2D)); Mshearinv=inv(Mshear);
% Store Volume sizes
Iin_sizex=size(V,1); Iin_sizey=size(V,2); Iin_sizez=size(V,3);
% Create Shear (intimidate) buffer
Ibuffer_sizex=ceil(1.7321*max(size(V))+1);
Ibuffer_sizey=Ibuffer_sizex;
Ibuffer=zeros([Ibuffer_sizex Ibuffer_sizey 3]);
% Split Colortable in R,G,B
if(size(colortable,2)>size(colortable,1)), colortable=colortable'; end
colortable_r=colortable(:,1); colortable_g=colortable(:,2); colortable_b=colortable(:,3);
switch (c)
case 1
for z=0:(Iin_sizex-1);
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizex/2)+Iin_sizey/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizex/2)+Iin_sizez/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizez-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizey-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(z+1,xBas, yBas)));
intensity_xyz2=double(squeeze(V(z+1,xBas, yBas1)));
intensity_xyz3=double(squeeze(V(z+1,xBas1, yBas)));
intensity_xyz4=double(squeeze(V(z+1,xBas1, yBas1)));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b);
end
case 2
for z=0:(Iin_sizey-1),
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizey/2)+Iin_sizez/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizey/2)+Iin_sizex/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizex-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizez-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(yBas, z+1,xBas)));
intensity_xyz2=double(squeeze(V(yBas1, z+1,xBas)));
intensity_xyz3=double(squeeze(V(yBas, z+1,xBas1)));
intensity_xyz4=double(squeeze(V(yBas1, z+1,xBas1)));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b);
end
case 3
for z=0:(Iin_sizez-1),
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizez/2)+Iin_sizex/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizez/2)+Iin_sizey/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizey-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizex-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(V(xBas, yBas, z+1));
intensity_xyz2=double(V(xBas, yBas1, z+1));
intensity_xyz3=double(V(xBas1, yBas, z+1));
intensity_xyz4=double(V(xBas1, yBas1, z+1));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b);
end
case 4
for z=(Iin_sizex-1):-1:0,
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizex/2)+Iin_sizey/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizex/2)+Iin_sizez/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizez-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizey-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(z+1,xBas, yBas)));
intensity_xyz2=double(squeeze(V(z+1,xBas, yBas1)));
intensity_xyz3=double(squeeze(V(z+1,xBas1, yBas)));
intensity_xyz4=double(squeeze(V(z+1,xBas1, yBas1)));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b);
end
case 5
for z=(Iin_sizey-1):-1:0,
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizey/2)+Iin_sizez/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizey/2)+Iin_sizex/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizex-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizez-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(yBas, z+1,xBas)));
intensity_xyz2=double(squeeze(V(yBas1, z+1,xBas)));
intensity_xyz3=double(squeeze(V(yBas, z+1,xBas1)));
intensity_xyz4=double(squeeze(V(yBas1, z+1,xBas1)));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b);
end
case 6
for z=(Iin_sizez-1):-1:0,
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizez/2)+Iin_sizex/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizez/2)+Iin_sizey/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizey-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizex-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(V(xBas, yBas, z+1));
intensity_xyz2=double(V(xBas, yBas1, z+1));
intensity_xyz3=double(V(xBas1, yBas, z+1));
intensity_xyz4=double(V(xBas1, yBas1, z+1));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b);
end
end
render_image = warp(Ibuffer, image_size(1:2),Mshearinv,Mwarp2Dinv,c);
function Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b)
% Rotate image for two main view directions
if(c==2||c==5), intensity_loc=intensity_loc'; end
% Calculate index in alpha transparency look up table
indexAlpha=round(intensity_loc*(length(alphatable)-1))+1;
% Calculate index in color look up table
indexColor=round(intensity_loc*(length(colortable_r)-1))+1;
% calculate current alphaimage
alphaimage=alphatable(indexAlpha);
% Update the current pixel in the shear image buffer
Ibuffer(px,py,1)=(1-alphaimage).*Ibuffer(px,py,1)+alphaimage.*colortable_r(indexColor);
Ibuffer(px,py,2)=(1-alphaimage).*Ibuffer(px,py,2)+alphaimage.*colortable_g(indexColor);
Ibuffer(px,py,3)=(1-alphaimage).*Ibuffer(px,py,3)+alphaimage.*colortable_b(indexColor);
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_histogram.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/Old_Viewer3D_with_c_code/viewer3d_histogram.m
| 4,424 |
utf_8
|
04cc06c842af8e3042d6ea77f91aedfb
|
function varargout = viewer3d_histogram(varargin)
% This function is part of VIEWER3D
%
% color and alpha maps can be changed on the fly by dragging and creating
% new color/alpha markers with the left mouse button.
%
% Function is written by D.Kroon University of Twente (October 2008)
% Edit the above text to modify the response to help viewer3d_histogram
% Last Modified by GUIDE v2.5 01-Nov-2008 21:04:04
% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_histogram_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_histogram_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_histogram is made visible.
function viewer3d_histogram_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_histogram (see VARARGIN)
% Choose default command line output for viewer3d_histogram
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
function figure1_WindowButtonMotionFcn(hObject, eventdata, handles)
function varargout = viewer3d_histogram_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes during object creation, after setting all properties.
function popupmenu_colors_CreateFcn(hObject, eventdata, handles)
% hObject handle to popupmenu_colors (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: popupmenu controls usually have a white background on Windows.
% See ISPC and COMPUTER.
set(hObject,'String',{'jet','hsv','hot','cool','spring','summer','autumn','winter','gray','bone','copper','pink'});
set(hObject,'Value',3);
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function setMyData(data)
% Store data struct in figure
setappdata(gcf,'data3d',data);
function data=getMyData()
% Get data struct stored in figure
data=getappdata(gcf,'data3d');
% --------------------------------------------------------------------
function menu_file_Callback(hObject, eventdata, handles)
% hObject handle to menu_file (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_load_Callback(hObject, eventdata, handles)
% hObject handle to menu_load (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_save_Callback(hObject, eventdata, handles)
% hObject handle to menu_save (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --- Executes on selection change in popupmenu_colors.
function popupmenu_colors_Callback(hObject, eventdata, handles)
% hObject handle to popupmenu_colors (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = get(hObject,'String') returns popupmenu_colors contents as cell array
% contents{get(hObject,'Value')} returns selected item from popupmenu_colors
|
github
|
jacksky64/imageProcessing-master
|
makeViewMatrix.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/Old_Viewer3D_with_c_code/makeViewMatrix.m
| 1,190 |
utf_8
|
49d443a4402c434f497d4b2dba34f211
|
function Mview=makeViewMatrix(r,s,t)
% function makeViewMatrix construct a 4x4 transformation matrix from
% rotation, resize and translation variables.
%
% Mview=makeViewMatrix(R,S,T)
%
% inputs,
% R: Rotation vector [Rx, Ry, Rz];
% S: Resize vector [Sx, Sy, Sz];
% T: Translation vector [Tx, Ty, Tz];
%
% outputs,
% Mview: 4x4 transformation matrix
%
% Example,
% Mview=makeViewMatrix([45 45 0],[1 1 1],[0 0 0]);
% disp(Mview);
%
% Function is written by D.Kroon University of Twente (October 2008)
R=RotationMatrix(r);
S=ResizeMatrix(s);
T=TranslateMatrix(t);
Mview=R*S*T;
function R=RotationMatrix(r)
% Determine the rotation matrix (View matrix) for rotation angles xyz ...
Rx=[1 0 0 0; 0 cosd(r(1)) -sind(r(1)) 0; 0 sind(r(1)) cosd(r(1)) 0; 0 0 0 1];
Ry=[cosd(r(2)) 0 sind(r(2)) 0; 0 1 0 0; -sind(r(2)) 0 cosd(r(2)) 0; 0 0 0 1];
Rz=[cosd(r(3)) -sind(r(3)) 0 0; sind(r(3)) cosd(r(3)) 0 0; 0 0 1 0; 0 0 0 1];
R=Rx*Ry*Rz;
function S=ResizeMatrix(s)
S=[1/s(1) 0 0 0;
0 1/s(2) 0 0;
0 0 1/s(3) 0;
0 0 0 1];
function T=TranslateMatrix(t)
T=[1 0 0 -t(1);
0 1 0 -t(2);
0 0 1 -t(3);
0 0 0 1];
|
github
|
jacksky64/imageProcessing-master
|
render_shaded.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/Old_Viewer3D_with_c_code/render_shaded.m
| 19,351 |
utf_8
|
8c97f4730b447f5fb0c7ee9ac5424e62
|
function render_image = render_shaded(V, image_size, Mview,alphatable,colortable,LVector,VVector,shadingtype)
% Function RENDER_SHADED will volume render a shaded Image of a 3D volume,
% with transperancy and colortable.
%
% I = RENDER_SHADED(V, SIZE, Mview, ALPHATABLE, COLORTABLE,LightVector,ViewerVector,SHADINGMATERIAL);
%
% inputs,
% V: Input image volume
% SIZE: Sizes (height and length) of output image
% Mview: Viewer (Transformation) matrix 4x4
% ALPHATABLE: Mapping from intensities to transperancy
% range [0 1], dimensions Nx1
% COLORTALBE: Mapping form intensities to color
% range [0 1], dimensions Nx3
% LightVector: Light direction
% ViewerVector: Viewer direction
% SHADINGMATERIAL: 'shiny' or 'dull' or 'metal', set the
% object shading look
%
% outputs,
% I: The maximum intensity output image
%
% Volume Data,
% Range of V must be [0 1] in case of double or single otherwise
% mex function will crash. Data of type double has short render times,
% uint16 the longest.
%
% example,
% % Load data
% load TestVolume2;
% % Output image size
% sizes=[400 400];
% % color and alpha table
% alphatable=[0 0 0 0 0 1 1 1 1 1];
% colortable=[1 0 0;1 0 0;1 0 0;1 0 0;1 0 0;1 0 0;1 0 0];
% % Viewer and Light direction
% Vd = [0 0 1];
% Ld = [0.67 0.33 0.67];
% % Viewer Matrix
% Mview=makeViewMatrix([0 0 0],[0.5 0.5 0.5],[0 0 0]);
% % Render and show image
% figure,
% I = render_shaded(V, sizes, Mview,alphatable,colortable,Ld,Vd,'shiny');
% imshow(I);
%
% Function is written by D.Kroon University of Twente (November 2008)
% Needed to convert intensities to range [0 1]
imax=1;
if(isa(V,'uint8')), imax=2^8-1; end
if(isa(V,'uint16')), imax=2^16-1; end
if(isa(V,'uint32')), imax=2^32-1; end
% Calculate the Shear and Warp Matrices
[Mshear,Mwarp2D,c]=makeShearWarpMatrix(Mview,size(V));
Mwarp2Dinv=inv(double(Mwarp2D)); Mshearinv=inv(Mshear);
% Store Volume sizes
Iin_sizex=size(V,1); Iin_sizey=size(V,2); Iin_sizez=size(V,3);
% Create Shear (intimidate) buffer
Ibuffer_sizex=ceil(1.7321*max(size(V))+1);
Ibuffer_sizey=Ibuffer_sizex;
Ibuffer=zeros([Ibuffer_sizex Ibuffer_sizey 3]);
% Adjust alpha table by voxel length change because of rotation
lengthcor=sqrt(1+(Mshearinv(1,3)^2+Mshearinv(2,3)^2));
alphatable= alphatable*lengthcor;
% Split Colortable in R,G,B
if(size(colortable,2)>size(colortable,1)), colortable=colortable'; end
colortable_r=colortable(:,1); colortable_g=colortable(:,2); colortable_b=colortable(:,3);
% Shading type -> Phong values
switch lower(shadingtype)
case {'shiny'}
materialc=[0.7, 0.6, 0.9, 20];
case {'dull'}
materialc=[0.7, 0.8, 0.0, 10];
case {'metal'}
materialc=[0.7, 0.3, 1.0, 25];
otherwise
materialc=[0.7, 0.6, 0.9, 20];
end
% Normalize Light and Viewer vectors
LightVector=[LVector(:);0]; LightVector=LightVector./sqrt(sum(LightVector(1:3).^2));
ViewerVector=[VVector(:);0]; ViewerVector=ViewerVector./sqrt(sum(ViewerVector(1:3).^2));
switch (c)
case 1
for z=0:(Iin_sizex-1);
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizex/2)+Iin_sizey/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizex/2)+Iin_sizez/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizez-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizey-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(z+1,xBas, yBas)));
intensity_xyz2=double(squeeze(V(z+1,xBas, yBas1)));
intensity_xyz3=double(squeeze(V(z+1,xBas1, yBas)));
intensity_xyz4=double(squeeze(V(z+1,xBas1, yBas1)));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
N=returnnormal(z+1,xBas, yBas,V,Mview,c);
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b,LightVector,ViewerVector,materialc,N);
end
case 2
for z=0:(Iin_sizey-1),
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizey/2)+Iin_sizez/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizey/2)+Iin_sizex/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizex-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizez-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(yBas, z+1,xBas)));
intensity_xyz2=double(squeeze(V(yBas1, z+1,xBas)));
intensity_xyz3=double(squeeze(V(yBas, z+1,xBas1)));
intensity_xyz4=double(squeeze(V(yBas1, z+1,xBas1)));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
N=returnnormal(yBas, z+1,xBas,V,Mview,c);
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b,LightVector,ViewerVector,materialc,N);
end
case 3
for z=0:(Iin_sizez-1),
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizez/2)+Iin_sizex/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizez/2)+Iin_sizey/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizey-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizex-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(V(xBas, yBas, z+1));
intensity_xyz2=double(V(xBas, yBas1, z+1));
intensity_xyz3=double(V(xBas1, yBas, z+1));
intensity_xyz4=double(V(xBas1, yBas1, z+1));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
N=returnnormal(xBas,yBas,z+1,V,Mview,c);
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b,LightVector,ViewerVector,materialc,N);
end
case 4
for z=(Iin_sizex-1):-1:0,
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizex/2)+Iin_sizey/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizex/2)+Iin_sizez/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizez-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizey-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(z+1,xBas, yBas)));
intensity_xyz2=double(squeeze(V(z+1,xBas, yBas1)));
intensity_xyz3=double(squeeze(V(z+1,xBas1, yBas)));
intensity_xyz4=double(squeeze(V(z+1,xBas1, yBas1)));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
N=returnnormal(z+1,xBas,yBas,V,Mview,c);
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b,LightVector,ViewerVector,materialc,N);
end
case 5
for z=(Iin_sizey-1):-1:0,
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizey/2)+Iin_sizez/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizey/2)+Iin_sizex/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizex-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizez-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(yBas, z+1,xBas)));
intensity_xyz2=double(squeeze(V(yBas1, z+1,xBas)));
intensity_xyz3=double(squeeze(V(yBas, z+1,xBas1)));
intensity_xyz4=double(squeeze(V(yBas1, z+1,xBas1)));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
N=returnnormal(yBas,z+1,xBas,V,Mview,c);
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b,LightVector,ViewerVector,materialc,N);
end
case 6
for z=(Iin_sizez-1):-1:0,
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizez/2)+Iin_sizex/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizez/2)+Iin_sizey/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizey-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizex-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(V(xBas, yBas, z+1));
intensity_xyz2=double(V(xBas, yBas1, z+1));
intensity_xyz3=double(V(xBas1, yBas, z+1));
intensity_xyz4=double(V(xBas1, yBas1, z+1));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
N=returnnormal(xBas,yBas,z+1,V,Mview,c);
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b,LightVector,ViewerVector,materialc,N);
end
end
render_image = warp(Ibuffer, image_size(1:2),Mshearinv,Mwarp2Dinv,c);
function N=returnnormal(x,y,z,V,Mview,c)
x1=x; y1=y; z1=z;
x2=x1+1;
check=x2>size(V,1);
if(nnz(check)>0)
x1(check)=x1-1;
x2(x2>size(V,1))=size(V,1);
end
y2=y1+1;
check=y2>size(V,2);
if(nnz(check)>0)
y1(check)=y1-1;
y2(check)=size(V,2);
end
z2=z1+1;
check=z2>size(V,3);
if(nnz(check)>0)
z1(check)=z1-1;
z2(check)=size(V,3);
end
S(:,:,1)=squeeze(V(x2,y1,z1)-V(x1,y1,z1));
S(:,:,2)=squeeze(V(x1,y2,z1)-V(x1,y1,z1));
S(:,:,3)=squeeze(V(x1,y1,z2)-V(x1,y1,z1));
if(c==2||c==5),
S2=zeros([size(S,2) size(S,1) 3]);
S2(:,:,1)=S(:,:,1)'; S2(:,:,2)=S(:,:,2)'; S2(:,:,3)=S(:,:,3)'; S=S2;
end
N=zeros(size(S));
% Rotate the gradient and normalize to get the surface normal in direction of the viewer
N(:,:,1)=Mview(1,1)*S(:,:,1)+Mview(1,2)*S(:,:,2)+Mview(1,3)*S(:,:,3);
N(:,:,2)=Mview(2,1)*S(:,:,1)+Mview(2,2)*S(:,:,2)+Mview(2,3)*S(:,:,3);
N(:,:,3)=Mview(3,1)*S(:,:,1)+Mview(3,2)*S(:,:,2)+Mview(3,3)*S(:,:,3);
nlength=sqrt(N(:,:,1).^2+N(:,:,2).^2+N(:,:,3).^2)+0.000001;
N(:,:,1)=N(:,:,1)./nlength;
N(:,:,2)=N(:,:,2)./nlength;
N(:,:,3)=N(:,:,3)./nlength;
function Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable,colortable_r,colortable_g,colortable_b,L,V,material,N)
% Rotate image for two main view directions
if(c==2||c==5), intensity_loc=intensity_loc'; end
% Calculate index in alpha transparency look up table
indexAlpha=round(intensity_loc*(length(alphatable)-1))+1;
% Calculate index in color look up table
indexColor=round(intensity_loc*(length(colortable_r)-1))+1;
Ia=1;
% Id = dot(N,L);
Id=N(:,:,1)*L(1)+N(:,:,2)*L(2)+N(:,:,3)*L(3);
% R = 2.0*dot(N,L)*N - L;
R(:,:,1)=2*Id.*N(:,:,1)-L(1);
R(:,:,2)=2*Id.*N(:,:,2)-L(2);
R(:,:,3)=2*Id.*N(:,:,3)-L(3);
%Is = max(pow(dot(R,V),3),0);
Is=R(:,:,1)*V(1)+R(:,:,2)*V(2)+R(:,:,3)*V(3);
Is(Is<0)=0;
% Specular exponent
Is=Is.^material(4);
% Phong shading values
Ipar=zeros([size(Id) 3]);
Ipar(:,:,1)=material(1)*Ia;
Ipar(:,:,2)=material(2)*Id;
Ipar(:,:,3)=material(3)*Is;
% calculate current alphaimage
alphaimage=alphatable(indexAlpha);
% Update the current pixel in the shear image buffer
Ibuffer(px,py,1)=(1-alphaimage).*Ibuffer(px,py,1)+alphaimage.*(colortable_r(indexColor).*(Ipar(:,:,1)+Ipar(:,:,2))+Ipar(:,:,3));
Ibuffer(px,py,2)=(1-alphaimage).*Ibuffer(px,py,2)+alphaimage.*(colortable_g(indexColor).*(Ipar(:,:,1)+Ipar(:,:,2))+Ipar(:,:,3));
Ibuffer(px,py,3)=(1-alphaimage).*Ibuffer(px,py,3)+alphaimage.*(colortable_b(indexColor).*(Ipar(:,:,1)+Ipar(:,:,2))+Ipar(:,:,3));
|
github
|
jacksky64/imageProcessing-master
|
viewer3d.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/Old_Viewer3D_with_c_code/viewer3d.m
| 39,153 |
utf_8
|
9fa9fa60946c257acdeb09c113487637
|
function varargout = viewer3d(varargin)
% VIEWER3D a Matlab 3D volume renderer using the fast shearwarp algorithm.
%
% VIEWER3D(V, RENDERTYPE, SCALES);
%
% inputs,
% V : 3D Input image volume, of type double, single, uint8, uint16 or
% uint32
% (the render process uses only double calculations)
% RENDERTYPE: 'MIP' Maximum Intensity Render (default)
% 'VR' Volume Rendering
% 'VRC' Volume Rendering Color
% 'VRS' Volume Rendering with Shading
% SCALES: The sizes(height, width, depth) of one voxel. (default [1 1 1])
%
% Volume Data,
% Range of V must be [0 1] in case of double or single. Volume Data of
% type double has shorter render times than data of uint8 or uint16.
%
% example,
% % Load data
% load TestVolume;
% viewer3d(V);
%
% See also: render_mip, render_bw, render_color, render_shaded
%
% Function is written by D.Kroon University of Twente (November 2008)
% Edit the above text to modify the response to help viewer3d
% Last Modified by GUIDE v2.5 04-Nov-2008 14:16:11
% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d is made visible.
function viewer3d_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d (see VARARGIN)
% Choose default command line output for viewer3d
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
%matlabpool(3);
% addpath mexcode and help
try
functionname='viewer3d.m';
functiondir=which(functionname);
functiondir=functiondir(1:end-length(functionname));
addpath([functiondir '/help'])
catch end
% Initialized data storage structure
data.mouse_pressed=false;
data.mouse_button='';
% Get input voxel volume and convert to double
if (isempty(varargin)),
data.volume=zeros(3,3,3);
data.volume_preview=zeros(3,3,3);
else
if(ndims(varargin{1})==3)
data.volume=varargin{1};
switch(class(data.volume))
case {'uint8','uint16'}
case 'single'
data.volume(data.volume<0)=0; data.volume(data.volume>1)=1;
case 'double'
data.volume(data.volume<0)=0; data.volume(data.volume>1)=1;
otherwise
warning('viewer3d:inputs', 'Unsupported input datatype converted to double');
data.volume=im2double(data.volume);
data.volume(data.volume<0)=0; data.volume(data.volume>1)=1;
end
data.volume_preview=imresize3d(data.volume,[],[32 32 32],'linear');
else
error('viewer3d:inputs', 'Input image not 3 dimensional');
end
end
% Get input render type
if(length(varargin)>1)
switch lower(varargin{2})
case 'mip'
data.render_type='mip';
case 'vr'
data.render_type='vr';
case 'vrc'
data.render_type='vrc';
case 'vrs'
data.render_type='vrs';
otherwise
error('viewer3d:inputs', 'Render type unknown');
end
else
data.render_type='mip';
end
% Get input voxelvolume scaling
if(length(varargin)>2)
Scales=varargin{3}; Scales=sqrt(3)*Scales./sqrt(sum(Scales.^2));
data.viewer_matrix=[Scales(1) 0 0 0; 0 Scales(2) 0 0; 0 0 Scales(3) 0; 0 0 0 1];
else
data.viewer_matrix=[1 0 0 0; 0 1 0 0; 0 0 1 0; 0 0 0 1];
end
data.handle_viewer3d=gcf;
data.handle_histogram=[];
data.histogram_positions = [0.2 0.4 0.6 0.9];
data.histogram_alpha = [0 0.5 0.35 1];
data.histogram_colors= [0 0 0; 1 0 0; 1 1 0; 1 1 1];
data.first_render=true;
data.axes_size=[400 400];
data.histogram_pointselected=[];
data.mouse_position_pressed=[0 0];
data.mouse_position=[0 0];
data.mouse_position_last=[0 0];
data.shading_material='shiny';
data=loadmousepointershapes(data);
data.handles=handles;
setMyData(data);
createAlphaColorTable();
% Show the data
show3d(false)
% UIWAIT makes viewer3d wait for user response (see UIRESUME)
% uiwait(handles.figure1);
function createAlphaColorTable()
% This function creates a Matlab colormap and alphamap from the markers
data=getMyData(); if(isempty(data)), return, end
data.colortable=zeros(1000,3);
data.alphatable=zeros(1000,1);
% Loop through all 256 color/alpha indexes
for j=0:999
i=j/999;
if (i<data.histogram_positions(1)), alpha=0; color=data.histogram_colors(1,:);
elseif(i>data.histogram_positions(end)), alpha=0; color=data.histogram_colors(end,:);
elseif(i==data.histogram_positions(1)), alpha=data.histogram_alpha(1); color=data.histogram_colors(1,:);
elseif(i==data.histogram_positions(end)), alpha=data.histogram_alpha(end); color=data.histogram_colors(end,:);
else
% Linear interpolate the color and alpha between markers
index_down=find(data.histogram_positions<=i); index_down=index_down(end);
index_up=find(data.histogram_positions>i); index_up=index_up(1);
perc=(i-data.histogram_positions(index_down)) / (data.histogram_positions(index_up) - data.histogram_positions(index_down));
color=(1-perc)*data.histogram_colors(index_down,:)+perc*data.histogram_colors(index_up,:);
alpha=(1-perc)*data.histogram_alpha(index_down)+perc*data.histogram_alpha(index_up);
end
data.colortable(j+1,:)=color;
data.alphatable(j+1)=alpha;
end
setMyData(data);
function data=loadmousepointershapes(data)
I=1-(imread('icon_mouse_rotate1.png')>0); I(I==0)=NaN;
data.icon_mouse_rotate1=I;
I=1-(imread('icon_mouse_rotate2.png')>0); I(I==0)=NaN;
data.icon_mouse_rotate2=I;
I=1-(imread('icon_mouse_zoom.png')>0); I(I==0)=NaN;
data.icon_mouse_zoom=I;
I=1-(imread('icon_mouse_pan.png')>0); I(I==0)=NaN;
data.icon_mouse_pan=I;
function show3d(preview)
data=getMyData(); if(isempty(data)), return, end
% Calculate light and viewer vectors
data.ViewerVector = [0 0 1];
data.LightVector = [0.67 0.33 0.67];
if(preview)
viewer_matrix=data.viewer_matrix*ResizeMatrix(size(data.volume_preview)./size(data.volume));
switch data.render_type
case 'mip'
data.render_image = render_mip(data.volume_preview, data.axes_size(1:2), viewer_matrix);
case 'vr'
data.render_image = render_bw(data.volume_preview, data.axes_size(1:2), viewer_matrix, data.alphatable);
case 'vrc'
data.render_image = render_color(data.volume_preview, data.axes_size(1:2), viewer_matrix, data.alphatable, data.colortable);
case 'vrs'
data.render_image = render_shaded(data.volume_preview, data.axes_size(1:2), viewer_matrix, data.alphatable, data.colortable, data.LightVector, data.ViewerVector,data.shading_material);
end
else
set_mouse_shape('watch',data); pause(0.001);
switch data.render_type
case 'mip'
data.render_image = render_mip(data.volume, data.axes_size(1:2), data.viewer_matrix);
case 'vr'
data.render_image = render_bw(data.volume, data.axes_size(1:2), data.viewer_matrix, data.alphatable);
case 'vrc'
data.render_image = render_color(data.volume, data.axes_size(1:2), data.viewer_matrix, data.alphatable, data.colortable);
case 'vrs'
data.render_image = render_shaded(data.volume, data.axes_size(1:2), data.viewer_matrix, data.alphatable, data.colortable, data.LightVector, data.ViewerVector,data.shading_material);
end
set_mouse_shape('arrow',data); pause(0.001);
end
if(data.first_render)
data.imshow_handle=imshow(data.render_image);
data.first_render=false;
else
set(data.imshow_handle,'Cdata',data.render_image);
end
data.axes_size=get(data.handles.axes3d,'PlotBoxAspectRatio');
set(get(data.handles.axes3d,'Children'),'ButtonDownFcn','viewer3d(''axes3d_ButtonDownFcn'',gcbo,[],guidata(gcbo))');
setMyData(data);
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on mouse motion over figure - except title and menu.
function figure1_WindowButtonMotionFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
cursor_position_in_axes(hObject,handles);
data=getMyData(); if(isempty(data)), return, end
if(isempty(data)), return, end;
if(data.mouse_pressed)
switch(data.mouse_button)
case 'rotate1'
r1=-360*(data.mouse_position_last(1)-data.mouse_position(1));
r2=360*(data.mouse_position_last(2)-data.mouse_position(2));
R=RotationMatrix([r1 r2 0]);
data.viewer_matrix=R*data.viewer_matrix;
setMyData(data);
show3d(true)
case 'rotate2'
r1=100*(data.mouse_position_last(1)-data.mouse_position(1));
r2=100*(data.mouse_position_last(2)-data.mouse_position(2));
if(data.mouse_position(2)>0.5), r1=-r1; end
if(data.mouse_position(1)<0.5), r2=-r2; end
r3=r1+r2;
R=RotationMatrix([0 0 r3]);
data.viewer_matrix=R*data.viewer_matrix;
setMyData(data);
show3d(true)
case 'pan'
t2=200*(data.mouse_position_last(1)-data.mouse_position(1));
t1=200*(data.mouse_position_last(2)-data.mouse_position(2));
M=TranslateMatrix([t1 t2 0]);
data.viewer_matrix=M*data.viewer_matrix;
setMyData(data);
show3d(true)
case 'zoom'
z1=1+2*(data.mouse_position_last(1)-data.mouse_position(1));
z2=1+2*(data.mouse_position_last(2)-data.mouse_position(2));
z=0.5*(z1+z2); %sqrt(z1.^2+z2.^2);
R=ResizeMatrix([z z z]);
data.viewer_matrix=R*data.viewer_matrix;
setMyData(data);
show3d(true)
otherwise
end
end
function R=RotationMatrix(r)
% Determine the rotation matrix (View matrix) for rotation angles xyz ...
Rx=[1 0 0 0; 0 cosd(r(1)) -sind(r(1)) 0; 0 sind(r(1)) cosd(r(1)) 0; 0 0 0 1];
Ry=[cosd(r(2)) 0 sind(r(2)) 0; 0 1 0 0; -sind(r(2)) 0 cosd(r(2)) 0; 0 0 0 1];
Rz=[cosd(r(3)) -sind(r(3)) 0 0; sind(r(3)) cosd(r(3)) 0 0; 0 0 1 0; 0 0 0 1];
R=Rx*Ry*Rz;
function M=ResizeMatrix(s)
M=[1/s(1) 0 0 0;
0 1/s(2) 0 0;
0 0 1/s(3) 0;
0 0 0 1];
function M=TranslateMatrix(t)
M=[1 0 0 -t(1);
0 1 0 -t(2);
0 0 1 -t(3);
0 0 0 1];
function cursor_position_in_axes(hObject,handles)
data=getMyData();
if(isempty(data)), return, end;
data.mouse_position_last=data.mouse_position;
% Get position of the mouse in the large axes
p = get(0, 'PointerLocation');
pf = get(hObject, 'pos');
p(1:2) = p(1:2)-pf(1:2);
set(gcf, 'CurrentPoint', p(1:2));
p = get(handles.axes3d, 'CurrentPoint');
data.mouse_position=[p(1, 1) p(1, 2)]./data.axes_size(1:2);
setMyData(data);
function setMyData(data)
% Store data struct in figure
setappdata(gcf,'data3d',data);
function data=getMyData()
% Get data struct stored in figure
data=getappdata(gcf,'data3d');
% --- Executes on mouse press over axes background.
function axes3d_ButtonDownFcn(hObject, eventdata, handles)
% hObject handle to axes3d (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.mouse_pressed=true;
data.mouse_button=get(handles.figure1,'SelectionType');
if(strcmp(data.mouse_button,'normal'))
if(sum((data.mouse_position-[0.5 0.5]).^2)<0.15)
data.mouse_button='rotate1';
set_mouse_shape('rotate1',data)
else
data.mouse_button='rotate2';
set_mouse_shape('rotate2',data)
end
end
if(strcmp(data.mouse_button,'extend'))
data.mouse_button='pan';
set_mouse_shape('pan',data)
end
if(strcmp(data.mouse_button,'alt'))
data.mouse_button='zoom';
set_mouse_shape('zoom',data)
end
data.mouse_position_pressed=data.mouse_position;
setMyData(data);
function set_mouse_shape(type,data)
switch(type)
case 'rotate1'
set(gcf,'Pointer','custom','PointerShapeCData',data.icon_mouse_rotate1,'PointerShapeHotSpot',round(size(data.icon_mouse_rotate1)/2))
set(data.handles.figure1,'Pointer','custom');
case 'rotate2'
set(gcf,'Pointer','custom','PointerShapeCData',data.icon_mouse_rotate2,'PointerShapeHotSpot',round(size(data.icon_mouse_rotate2)/2))
set(data.handles.figure1,'Pointer','custom');
case 'zoom'
set(gcf,'Pointer','custom','PointerShapeCData',data.icon_mouse_zoom,'PointerShapeHotSpot',round(size(data.icon_mouse_zoom)/2))
set(data.handles.figure1,'Pointer','custom');
case 'pan'
set(gcf,'Pointer','custom','PointerShapeCData',data.icon_mouse_pan,'PointerShapeHotSpot',round(size(data.icon_mouse_pan)/2))
set(data.handles.figure1,'Pointer','custom');
otherwise
set(data.handles.figure1,'Pointer',type);
end
% --- Executes on mouse press over figure background, over a disabled or
% --- inactive control, or over an axes background.
function figure1_WindowButtonUpFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.mouse_pressed=false;
setMyData(data);
show3d(false)
set(handles.figure1,'Pointer','arrow');
function A=imresize3d(V,scale,tsize,ntype,npad)
% This function resizes a 3D image volume to new dimensions
% Vnew = imresize3d(V,scale,nsize,ntype,npad);
%
% inputs,
% V: The input image volume
% scale: scaling factor, when used set tsize to [];
% nsize: new dimensions, when used set scale to [];
% ntype: Type of interpolation ('nearest', 'linear', or 'cubic')
% npad: Boundary condition ('replicate', 'symmetric', 'circular', 'fill', or 'bound')
%
% outputs,
% Vnew: The resized image volume
%
% example,
% load('mri','D'); D=squeeze(D);
% Dnew = imresize3d(D,[],[80 80 40],'nearest','bound');
%
% This function is written by D.Kroon University of Twente (July 2008)
% Check the inputs
if(exist('ntype', 'var') == 0), ntype='nearest'; end
if(exist('npad', 'var') == 0), npad='bound'; end
if(exist('scale', 'var')&&~isempty(scale)), tsize=round(size(V)*scale); end
if(exist('tsize', 'var')&&~isempty(tsize)), scale=(tsize./size(V)); end
% Make transformation structure
T = makehgtform('scale',scale);
tform = maketform('affine', T);
% Specify resampler
R = makeresampler(ntype, npad);
% Resize the image volueme
A = tformarray(V, tform, R, [1 2 3], [1 2 3], tsize, [], 0);
function [Mshear,Mwarp2D,c]=matrixshearwarp(Mview,sizes)
% Find the principal viewing axis
Vo=[Mview(1,2)*Mview(2,3) - Mview(2,2)*Mview(1,3);
Mview(2,1)*Mview(1,3) - Mview(1,1)*Mview(2,3);
Mview(1,1)*Mview(2,2) - Mview(2,1)*Mview(1,2)];
[maxv,c]=max(abs(Vo));
% Choose the corresponding Permutation matrix P
switch(c)
case 1, %yzx
P=[0 1 0 0;
0 0 1 0;
1 0 0 0;
0 0 0 1;];
case 2, % zxy
P=[0 0 1 0;
1 0 0 0;
0 1 0 0;
0 0 0 1;];
case 3, % xyz
P=[1 0 0 0;
0 1 0 0;
0 0 1 0;
0 0 0 1;];
end
% Compute the permuted view matrix from Mview and P
Mview_p=Mview*inv(P);
% 180 degrees rotate detection
if(Mview_p(3,3)<0), c=c+3; end
% Compute the shear coeficients from the permuted view matrix
Si = (Mview_p(2,2)* Mview_p(1,3) - Mview_p(1,2)* Mview_p(2,3)) / (Mview_p(1,1)* Mview_p(2,2) - Mview_p(2,1)* Mview_p(1,2));
Sj = (Mview_p(1,1)* Mview_p(2,3) - Mview_p(2,1)* Mview_p(1,3)) / (Mview_p(1,1)* Mview_p(2,2) - Mview_p(2,1)* Mview_p(1,2));
% Compute the translation between the orgins of standard object coordinates
% and intermdiate image coordinates
if((c==1)||(c==4)), kmax=sizes(1)-1; end
if((c==2)||(c==5)), kmax=sizes(2)-1; end
if((c==3)||(c==6)), kmax=sizes(3)-1; end
if ((Si>=0)&&(Sj>=0)), Ti = 0; Tj = 0; end
if ((Si>=0)&&(Sj<0)), Ti = 0; Tj = -Sj*kmax; end
if ((Si<0)&&(Sj>=0)), Ti = -Si*kmax; Tj = 0; end
if ((Si<0)&&(Sj<0)), Ti = -Si*kmax; Tj = -Sj*kmax; end
% Compute the shear matrix
Mshear=[1 0 Si Ti;
0 1 Sj Tj;
0 0 1 0;
0 0 0 1];
% Compute the 2Dwarp matrix
Mwarp2D=[Mview_p(1,1) Mview_p(1,2) (Mview_p(1,4)-Ti*Mview_p(1,1)-Tj*Mview_p(1,2));
Mview_p(2,1) Mview_p(2,2) (Mview_p(2,4)-Ti*Mview_p(2,1)-Tj*Mview_p(2,2));
0 0 1 ];
% Compute the 3Dwarp matrix
% Mwarp3Da=[Mview_p(1,1) Mview_p(1,2) (Mview_p(1,3)-Si*Mview_p(1,1)-Sj*Mview_p(1,2)) Mview_p(1,4);
% Mview_p(2,1) Mview_p(2,2) (Mview_p(2,3)-Si*Mview_p(2,1)-Sj*Mview_p(2,2)) Mview_p(2,4);
% Mview_p(3,1) Mview_p(3,2) (Mview_p(3,3)-Si*Mview_p(3,1)-Sj*Mview_p(3,2)) Mview_p(3,4);
% 0 0 0 1 ];
% Mwarp3Db=[1 0 0 -Ti;
% 0 1 0 -Tj;
% 0 0 1 0;
% 0 0 0 1];
% Mwarp3D=Mwarp3Da*Mwarp3Db;
% % Control matrix Mview
% Mview_control = Mwarp3D*Mshear*P;
% disp(Mview)
% disp(Mview_control)
% --------------------------------------------------------------------
function menu_file_Callback(hObject, eventdata, handles)
% hObject handle to menu_file (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_config_Callback(hObject, eventdata, handles)
% hObject handle to menu_config (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_change_alpha_colors_Callback(hObject, eventdata, handles)
% hObject handle to menu_change_alpha_colors (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.handle_histogram=viewer3d_histogram(data.handle_viewer3d);
handles_histogram=guidata(data.handle_histogram);
data.handle_histogram_axes=handles_histogram.axes_histogram;
setMyData(data);
createHistogram();
drawHistogramPoints();
% --------------------------------------------------------------------
function menu_load_view_Callback(hObject, eventdata, handles)
% hObject handle to menu_load_view (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
dataold=getMyData();
dataold.volume=[];
if(ishandle(dataold.handle_histogram)), close(dataold.handle_histogram); end
uiload();
if(exist('data','var'))
data.first_render=true;
data.handle_viewer3d=dataold.handle_viewer3d;
data.handles.axes3d=dataold.handles.axes3d;
data.handles.figure1=dataold.handles.figure1;
setMyData(data);
createAlphaColorTable();
show3d(false);
else
viewer3d_error({'Matlab File does not contain','data from "Save Render"'})
end
% --------------------------------------------------------------------
function menu_save_view_Callback(hObject, eventdata, handles)
% hObject handle to menu_save_view (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
uisave('data');
function menu_load_histogram_Callback(hObject, eventdata, handles)
% hObject handle to menu_load_view (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
alpha=0;
uiload;
if(exist('positions','var'))
data.histogram_positions=positions;
data.histogram_colors=colors;
data.histogram_alpha=alpha;
setMyData(data);
drawHistogramPoints();
createAlphaColorTable();
show3d(false);
else
viewer3d_error({'Matlab File does not contain','data from "Save AlphaColors"'})
end
% --------------------------------------------------------------------
function menu_save_histogram_Callback(hObject, eventdata, handles)
% hObject handle to menu_save_view (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
positions=data.histogram_positions;
colors=data.histogram_colors;
alpha=data.histogram_alpha;
uisave({'positions','colors','alpha'});
% --------------------------------------------------------------------
function menu_render_Callback(hObject, eventdata, handles)
% hObject handle to menu_render (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_render_Mip_Callback(hObject, eventdata, handles)
% hObject handle to menu_render_Mip (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.render_type='mip';
data.first_render=true;
setMyData(data);
show3d(false);
% --------------------------------------------------------------------
function menu_render_vr_Callback(hObject, eventdata, handles)
% hObject handle to menu_render_vr (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.render_type='vr';
data.first_render=true;
setMyData(data);
show3d(false);
% --------------------------------------------------------------------
function menu_render_vrc_Callback(hObject, eventdata, handles)
% hObject handle to menu_render_vrc (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.render_type='vrc';
data.first_render=true;
setMyData(data);
show3d(false);
% --------------------------------------------------------------------
function menu_render_vrs_Callback(hObject, eventdata, handles)
% hObject handle to menu_render_vrs (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.render_type='vrs';
data.first_render=true;
setMyData(data);
show3d(false);
% --------------------------------------------------------------------
function menu_info_Callback(hObject, eventdata, handles)
% hObject handle to menu_info (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_save_picture_Callback(hObject, eventdata, handles)
% hObject handle to menu_save_picture (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
[filename, pathname] = uiputfile({'*.png';'*.jpg'}, 'Save Rendered Image as');
data=getMyData(); if(isempty(data)), return, end
imwrite(data.render_image,[pathname filename]);
% --------------------------------------------------------------------
function menu_about_Callback(hObject, eventdata, handles)
% hObject handle to menu_about (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
viewer3d_about
function createHistogram()
% This function creates and show the (log) histogram of the data
data=getMyData(); if(isempty(data)), return, end
% Get histogram
[data.histogram_countsy, data.histogram_countsx]=imhist(data.volume(:));
% Log the histogram data
data.histogram_countsy=log(data.histogram_countsy+100); data.histogram_countsy=data.histogram_countsy-min(data.histogram_countsy);
data.histogram_countsx=data.histogram_countsx./max(data.histogram_countsx(:));
data.histogram_countsy=data.histogram_countsy./max(data.histogram_countsy(:));
% Focus on histogram axes
figure(data.handle_histogram)
% Display the histogram
stem(data.handle_histogram_axes,data.histogram_countsx,data.histogram_countsy,'Marker', 'none');
hold(data.handle_histogram_axes,'on');
% Set the axis of the histogram axes
data.histogram_maxy=max(data.histogram_countsy(:));
data.histogram_maxx=max(data.histogram_countsx(:));
set(data.handle_histogram_axes,'yLim', [0 1]);
set(data.handle_histogram_axes,'xLim', [0 1]);
setMyData(data);
% --- Executes on selection change in popupmenu_colors.
function popupmenu_colors_Callback(hObject, eventdata, handles)
% hObject handle to popupmenu_colors (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = get(hObject,'String') returns popupmenu_colors contents as cell array
% contents{get(hObject,'Value')} returns selected item from popupmenu_colors
data=getMyData(); if(isempty(data)), return, end
% Generate the new color markers
c_choice=get(handles.popupmenu_colors,'Value');
ncolors=length(data.histogram_positions);
switch c_choice,
case 1,new_colormap=jet(1000);
case 2, new_colormap=hsv(1000);
case 3, new_colormap=hot(1000);
case 4, new_colormap=cool(1000);
case 5, new_colormap=spring(1000);
case 6, new_colormap=summer(1000);
case 7, new_colormap=autumn(1000);
case 8, new_colormap=winter(1000);
case 9, new_colormap=gray(1000);
case 10, new_colormap=bone(1000);
case 11, new_colormap=copper(1000);
case 12, new_colormap=pink(1000);
otherwise, new_colormap=hot(1000);
end
new_colormap=new_colormap(round(1:(end-1)/(ncolors-1):end),:);
data.histogram_colors=new_colormap;
% Draw the new color markers and make the color and alpha map
setMyData(data);
drawHistogramPoints();
createAlphaColorTable();
show3d(false);
function drawHistogramPoints()
data=getMyData(); if(isempty(data)), return, end
% Delete old points and line
try
delete(data.histogram_linehandle),
for i=1:length(data.histogram_pointhandle),
delete(data.histogram_pointhandle(i)),
end,
catch
end
stem(data.handle_histogram_axes,data.histogram_countsx,data.histogram_countsy,'Marker', 'none');
hold(data.handle_histogram_axes,'on');
% Display the markers and line through the markers.
data.histogram_linehandle=plot(data.handle_histogram_axes,data.histogram_positions,data.histogram_alpha*data.histogram_maxy,'m');
set(data.histogram_linehandle,'ButtonDownFcn','viewer3d(''lineHistogramButtonDownFcn'',gcbo,[],guidata(gcbo))');
for i=1:length(data.histogram_positions)
data.histogram_pointhandle(i)=plot(data.handle_histogram_axes,data.histogram_positions(i),data.histogram_alpha(i)*data.histogram_maxy,'bo','MarkerFaceColor',data.histogram_colors(i,:));
set(data.histogram_pointhandle(i),'ButtonDownFcn','viewer3d(''pointHistogramButtonDownFcn'',gcbo,[],guidata(gcbo))');
end
% For detection of mouse up, down and motion in histogram figure.
set(data.handle_histogram, 'WindowButtonDownFcn','viewer3d(''HistogramButtonDownFcn'',gcbo,[],guidata(gcbo))');
set(data.handle_histogram, 'WindowButtonMotionFcn','viewer3d(''HistogramButtonMotionFcn'',gcbo,[],guidata(gcbo))');
set(data.handle_histogram, 'WindowButtonUpFcn','viewer3d(''HistogramButtonUpFcn'',gcbo,[],guidata(gcbo))');
setMyData(data);
function pointHistogramButtonDownFcn(hObject, eventdata, handles)
data=getMyData(); if(isempty(data)), return, end
data.mouse_button=get(data.handle_histogram,'SelectionType');
if(strcmp(data.mouse_button,'normal'))
data.histogram_pointselected=find(data.histogram_pointhandle==gcbo);
data.histogram_pointselectedhandle=gcbo;
set(data.histogram_pointselectedhandle, 'MarkerSize',8);
setMyData(data);
elseif(strcmp(data.mouse_button,'extend'))
data.histogram_pointselected=find(data.histogram_pointhandle==gcbo);
data.histogram_colors(data.histogram_pointselected,:)=rand(1,3);
data.histogram_pointselected=[];
setMyData(data);
drawHistogramPoints();
createAlphaColorTable();
show3d(false);
elseif(strcmp(data.mouse_button,'alt'))
data.histogram_pointselected=find(data.histogram_pointhandle==gcbo);
data.histogram_positions(data.histogram_pointselected)=[];
data.histogram_colors(data.histogram_pointselected,:)=[];
data.histogram_alpha(data.histogram_pointselected)=[];
data.histogram_pointselected=[];
setMyData(data);
drawHistogramPoints();
createAlphaColorTable();
show3d(false);
end
function HistogramButtonDownFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
function HistogramButtonUpFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
if(~isempty(data.histogram_pointselected))
set(data.histogram_pointselectedhandle, 'MarkerSize',6);
data.histogram_pointselected=[];
setMyData(data);
createAlphaColorTable();
% Show the data
show3d(false)
end
function HistogramButtonMotionFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
cursor_position_in_histogram_axes(hObject,handles);
data=getMyData(); if(isempty(data)), return, end
if(~isempty(data.histogram_pointselected))
% Set point to location mouse
data.histogram_positions(data.histogram_pointselected)=data.histogram_mouse_position(1,1);
data.histogram_alpha(data.histogram_pointselected)=data.histogram_mouse_position(1,2);
% Correct new location
if(data.histogram_alpha(data.histogram_pointselected)<0), data.histogram_alpha(data.histogram_pointselected)=0; end
if(data.histogram_alpha(data.histogram_pointselected)>1), data.histogram_alpha(data.histogram_pointselected)=1; end
if(data.histogram_positions(data.histogram_pointselected)<0), data.histogram_positions(data.histogram_pointselected)=0; end
if(data.histogram_positions(data.histogram_pointselected)>1), data.histogram_positions(data.histogram_pointselected)=1; end
if((data.histogram_pointselected>1)&&(data.histogram_positions(data.histogram_pointselected-1)>data.histogram_positions(data.histogram_pointselected)))
data.histogram_positions(data.histogram_pointselected)=data.histogram_positions(data.histogram_pointselected-1);
end
if((data.histogram_pointselected<length(data.histogram_positions))&&(data.histogram_positions(data.histogram_pointselected+1)<data.histogram_positions(data.histogram_pointselected)))
data.histogram_positions(data.histogram_pointselected)=data.histogram_positions(data.histogram_pointselected+1);
end
% Move point
set(data.histogram_pointselectedhandle, 'xdata', data.histogram_positions(data.histogram_pointselected));
set(data.histogram_pointselectedhandle, 'ydata', data.histogram_alpha(data.histogram_pointselected));
% Move line
set(data.histogram_linehandle, 'xdata',data.histogram_positions);
set(data.histogram_linehandle, 'ydata',data.histogram_alpha);
end
setMyData(data);
function lineHistogramButtonDownFcn(hObject, eventdata, handles)
data=getMyData(); if(isempty(data)), return, end
% New point on mouse location
newposition=data.histogram_mouse_position(1,1);
% List for the new markers
newpositions=zeros(1,length(data.histogram_positions)+1);
newalphas=zeros(1,length(data.histogram_alpha)+1);
newcolors=zeros(size(data.histogram_colors,1)+1,3);
% Check if the new point is between old points
index_down=find(data.histogram_positions<=newposition);
if(isempty(index_down))
else
index_down=index_down(end);
index_up=find(data.histogram_positions>newposition);
if(isempty(index_up))
else
index_up=index_up(1);
% Copy the (first) old markers to the new lists
newpositions(1:index_down)=data.histogram_positions(1:index_down);
newalphas(1:index_down)=data.histogram_alpha(1:index_down);
newcolors(1:index_down,:)=data.histogram_colors(1:index_down,:);
% Add the new interpolated marker
perc=(newposition-data.histogram_positions(index_down)) / (data.histogram_positions(index_up) - data.histogram_positions(index_down));
color=(1-perc)*data.histogram_colors(index_down,:)+perc*data.histogram_colors(index_up,:);
alpha=(1-perc)*data.histogram_alpha(index_down)+perc*data.histogram_alpha(index_up);
newpositions(index_up)=newposition;
newalphas(index_up)=alpha;
newcolors(index_up,:)=color;
% Copy the (last) old markers to the new lists
newpositions(index_up+1:end)=data.histogram_positions(index_up:end);
newalphas(index_up+1:end)=data.histogram_alpha(index_up:end);
newcolors(index_up+1:end,:)=data.histogram_colors(index_up:end,:);
% Make the new lists the used marker lists
data.histogram_positions=newpositions;
data.histogram_alpha=newalphas;
data.histogram_colors=newcolors;
end
end
% Update the histogram window
cla(data.handle_histogram_axes);
setMyData(data);
drawHistogramPoints();
createAlphaColorTable();
show3d(false);
function cursor_position_in_histogram_axes(hObject,handles)
data=getMyData(); if(isempty(data)), return, end
% Get position of the mouse in the large axes
p = get(0, 'PointerLocation');
pf = get(hObject, 'pos');
p(1:2) = p(1:2)-pf(1:2);
set(data.handle_histogram, 'CurrentPoint', p(1:2));
p = get(data.handle_histogram_axes, 'CurrentPoint');
data.histogram_mouse_position=[p(1, 1) p(1, 2)];
setMyData(data);
% --------------------------------------------------------------------
function menu_help_Callback(hObject, eventdata, handles)
% hObject handle to menu_help (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
web('info.html');
% --- Executes when user attempts to close figure1.
function figure1_CloseRequestFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: delete(hObject) closes the figure
data=getMyData(); if(isempty(data)), return, end
try
delete(data.handle_histogram);
catch end
try
rmappdata(gcf,'data3d');
catch end
delete(hObject);
% parallel
% matlabpool close;
% --------------------------------------------------------------------
function menu_shiny_Callback(hObject, eventdata, handles)
% hObject handle to menu_shiny (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.shading_material='shiny';
setMyData(data);
show3d(false);
% --------------------------------------------------------------------
function menu_dull_Callback(hObject, eventdata, handles)
% hObject handle to menu_dull (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.shading_material='dull';
setMyData(data);
show3d(false);
% --------------------------------------------------------------------
function menu_metal_Callback(hObject, eventdata, handles)
% hObject handle to menu_metal (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.shading_material='metal';
setMyData(data);
show3d(false);
% --------------------------------------------------------------------
function menu_rendersize400_Callback(hObject, eventdata, handles)
% hObject handle to menu_rendersize400 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.axes_size=[400 400];
data.first_render=true;
setMyData(data);
show3d(false);
% --------------------------------------------------------------------
function menu_rendersize800_Callback(hObject, eventdata, handles)
% hObject handle to menu_rendersize800 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.axes_size=[800 800];
data.first_render=true;
setMyData(data);
show3d(false);
|
github
|
jacksky64/imageProcessing-master
|
render_bw.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/Old_Viewer3D_with_c_code/render_bw.m
| 14,821 |
utf_8
|
2cb5030bd45ce542008cf0137d46a44a
|
function render_image = render_bw(V, image_size, Mview,alphatable)
% Function RENDER_BW will volume render a Image of a 3D volume with
% a transperancy table.
%
% I = RENDER_MIP(V, SIZE, Mview, ALPHAtable);
%
% inputs,
% V: Input image volume
% SIZE: Sizes (height and length) of output image
% Mview: Viewer (Transformation) matrix 4x4
% ALPHATABLE: Mapping from intensities to transperancy
% range [0 1], dimensions Nx1
% outputs,
% I: The maximum intensity output image
%
% Volume Data,
% Range of V must be [0 1] in case of double or single otherwise
% mex function will crash. Data of type double has short render times,
% uint16 the longest.
%
% example,
% % Load data
% load TestVolume;
% % Parameters
% sizes=[400 400];
% Mview=makeViewMatrix([45 45 0],[0.5 0.5 0.5],[0 0 0]);
% alphatable=(0:999)/999;
% % Render and show image
% I = render_bw(V, sizes, Mview,alphatable);
% imshow(I);
%
% Function is written by D.Kroon University of Twente (November 2008)
% Needed to convert intensities to range [0 1]
imax=1;
if(isa(V,'uint8')), imax=2^8-1; end
if(isa(V,'uint16')), imax=2^16-1; end
if(isa(V,'uint32')), imax=2^32-1; end
% Calculate the Shear and Warp Matrices
[Mshear,Mwarp2D,c]=makeShearWarpMatrix(Mview,size(V));
Mwarp2Dinv=inv(double(Mwarp2D)); Mshearinv=inv(Mshear);
% Store Volume sizes
Iin_sizex=size(V,1); Iin_sizey=size(V,2); Iin_sizez=size(V,3);
% Create Shear (intimidate) buffer
Ibuffer_sizex=ceil(1.7321*max(size(V))+1);
Ibuffer_sizey=Ibuffer_sizex;
Ibuffer=zeros([Ibuffer_sizex Ibuffer_sizey]);
switch (c)
case 1
for z=0:(Iin_sizex-1);
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizex/2)+Iin_sizey/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizex/2)+Iin_sizez/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizez-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizey-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(z+1,xBas, yBas)));
intensity_xyz2=double(squeeze(V(z+1,xBas, yBas1)));
intensity_xyz3=double(squeeze(V(z+1,xBas1, yBas)));
intensity_xyz4=double(squeeze(V(z+1,xBas1, yBas1)));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable);
end
case 2
for z=0:(Iin_sizey-1),
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizey/2)+Iin_sizez/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizey/2)+Iin_sizex/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizex-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizez-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(yBas, z+1,xBas)));
intensity_xyz2=double(squeeze(V(yBas1, z+1,xBas)));
intensity_xyz3=double(squeeze(V(yBas, z+1,xBas1)));
intensity_xyz4=double(squeeze(V(yBas1, z+1,xBas1)));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable);
end
case 3
for z=0:(Iin_sizez-1),
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizez/2)+Iin_sizex/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizez/2)+Iin_sizey/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizey-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizex-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(V(xBas, yBas, z+1));
intensity_xyz2=double(V(xBas, yBas1, z+1));
intensity_xyz3=double(V(xBas1, yBas, z+1));
intensity_xyz4=double(V(xBas1, yBas1, z+1));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable);
end
case 4
for z=(Iin_sizex-1):-1:0,
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizex/2)+Iin_sizey/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizex/2)+Iin_sizez/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizez-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizey-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(z+1,xBas, yBas)));
intensity_xyz2=double(squeeze(V(z+1,xBas, yBas1)));
intensity_xyz3=double(squeeze(V(z+1,xBas1, yBas)));
intensity_xyz4=double(squeeze(V(z+1,xBas1, yBas1)));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable);
end
case 5
for z=(Iin_sizey-1):-1:0,
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizey/2)+Iin_sizez/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizey/2)+Iin_sizex/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizex-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizez-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(yBas, z+1,xBas)));
intensity_xyz2=double(squeeze(V(yBas1, z+1,xBas)));
intensity_xyz3=double(squeeze(V(yBas, z+1,xBas1)));
intensity_xyz4=double(squeeze(V(yBas1, z+1,xBas1)));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable);
end
case 6
for z=(Iin_sizez-1):-1:0,
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizez/2)+Iin_sizex/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizez/2)+Iin_sizey/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizey-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizex-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(V(xBas, yBas, z+1));
intensity_xyz2=double(V(xBas, yBas1, z+1));
intensity_xyz3=double(V(xBas1, yBas, z+1));
intensity_xyz4=double(V(xBas1, yBas1, z+1));
% Calculate the interpolated intensity
intensity_loc=(intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4))/imax;
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable);
end
end
render_image = warp(Ibuffer, image_size(1:2),Mshearinv,Mwarp2Dinv,c);
function Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c,alphatable)
% Rotate image for two main view directions
if(c==2||c==5), intensity_loc=intensity_loc'; end
% Calculate index in alpha transparency look up table
indexAlpha=round(intensity_loc*(length(alphatable)-1))+1;
% calculate current alphaimage
alphaimage=alphatable(indexAlpha);
% Update the current pixel in the shear image buffer
Ibuffer(px,py)=(1-alphaimage).*Ibuffer(px,py)+alphaimage.*intensity_loc;
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_error.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/Old_Viewer3D_with_c_code/viewer3d_error.m
| 3,313 |
utf_8
|
abc306910c64efef252c1762e396a06b
|
function varargout = viewer3d_error(varargin)
% VIEWER3D_ERROR M-file for viewer3d_error.fig
% VIEWER3D_ERROR, by itself, creates a new VIEWER3D_ERROR or raises the existing
% singleton*.
%
% H = VIEWER3D_ERROR returns the handle to a new VIEWER3D_ERROR or the handle to
% the existing singleton*.
%
% VIEWER3D_ERROR('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VIEWER3D_ERROR.M with the given input arguments.
%
% VIEWER3D_ERROR('Property','Value',...) creates a new VIEWER3D_ERROR or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before viewer3d_error_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to viewer3d_error_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help viewer3d_error
% Last Modified by GUIDE v2.5 05-Nov-2008 14:39:24
% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_error_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_error_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_error is made visible.
function viewer3d_error_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_error (see VARARGIN)
% Choose default command line output for viewer3d_error
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
if (~isempty(varargin))
set(handles.text1,'string',varargin{1})
end
% UIWAIT makes viewer3d_error wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_error_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on button press in pushbutton1.
function pushbutton1_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
delete(handles.figure1);
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_about.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/Old_Viewer3D_with_c_code/viewer3d_about.m
| 2,927 |
utf_8
|
9e977443451bfd53ee2b650fe96f2246
|
function varargout = viewer3d_about(varargin)
% VIEWER3D_ABOUT M-file for viewer3d_about.fig
% VIEWER3D_ABOUT, by itself, creates a new VIEWER3D_ABOUT or raises the existing
% singleton*.
%
% H = VIEWER3D_ABOUT returns the handle to a new VIEWER3D_ABOUT or the handle to
% the existing singleton*.
%
% VIEWER3D_ABOUT('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VIEWER3D_ABOUT.M with the given input arguments.
%
% VIEWER3D_ABOUT('Property','Value',...) creates a new VIEWER3D_ABOUT or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before viewer3d_about_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to viewer3d_about_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help viewer3d_about
% Last Modified by GUIDE v2.5 30-Oct-2008 19:58:12
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_about_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_about_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_about is made visible.
function viewer3d_about_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_about (see VARARGIN)
% Choose default command line output for viewer3d_about
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes viewer3d_about wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_about_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
|
github
|
jacksky64/imageProcessing-master
|
render_mip.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/Old_Viewer3D_with_c_code/render_mip.m
| 14,111 |
utf_8
|
c8a9c3c0b5d6a93f349bfba6f1cbc48b
|
function render_image = render_mip(V, image_size, Mview)
% Function RENDER_MIP will render a Maximum Intensity Image of a 3D volume
%
% I = RENDER_MIP(V, SIZE, Mview);
%
% inputs,
% V: Input image volume
% SIZE: Sizes (height and length) of output image
% Mview: Transformation matrix
%
% outputs,
% I: The maximum intensity output image
%
% example,
% % Load data
% load TestVolume;
% % Parameters
% sizes=[400 400];
% Mview=makeViewMatrix([45 45 0],[0.5 0.5 0.5],[0 0 0]);
% % Render and show image
% I = render_mip(V, sizes, Mview);
% imshow(I);
%
% Function is written by D.Kroon University of Twente (November 2008)
% Needed to convert intensities to range [0 1]
imax=1;
if(isa(V,'uint8')), imax=2^8-1; end
if(isa(V,'uint16')), imax=2^16-1; end
if(isa(V,'uint32')), imax=2^32-1; end
% Calculate the Shear and Warp Matrices
[Mshear,Mwarp2D,c]=makeShearWarpMatrix(Mview,size(V));
Mwarp2Dinv=inv(double(Mwarp2D)); Mshearinv=inv(Mshear);
% Store Volume sizes
Iin_sizex=size(V,1); Iin_sizey=size(V,2); Iin_sizez=size(V,3);
% Create Shear (intimidate) buffer
Ibuffer_sizex=ceil(1.7321*max(size(V))+1);
Ibuffer_sizey=Ibuffer_sizex;
Ibuffer=zeros([Ibuffer_sizex Ibuffer_sizey]);
switch (c)
case 1
for z=0:(Iin_sizex-1);
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizex/2)+Iin_sizey/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizex/2)+Iin_sizez/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizez-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizey-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(z+1,xBas, yBas)));
intensity_xyz2=double(squeeze(V(z+1,xBas, yBas1)));
intensity_xyz3=double(squeeze(V(z+1,xBas1, yBas)));
intensity_xyz4=double(squeeze(V(z+1,xBas1, yBas1)));
% Calculate the interpolated intensity
intensity_loc=intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4);
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c);
end
case 2
for z=0:(Iin_sizey-1),
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizey/2)+Iin_sizez/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizey/2)+Iin_sizex/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizex-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizez-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(yBas, z+1,xBas)));
intensity_xyz2=double(squeeze(V(yBas1, z+1,xBas)));
intensity_xyz3=double(squeeze(V(yBas, z+1,xBas1)));
intensity_xyz4=double(squeeze(V(yBas1, z+1,xBas1)));
% Calculate the interpolated intensity
intensity_loc=intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4);
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c);
end
case 3
for z=0:(Iin_sizez-1),
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizez/2)+Iin_sizex/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizez/2)+Iin_sizey/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizey-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizex-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(V(xBas, yBas, z+1));
intensity_xyz2=double(V(xBas, yBas1, z+1));
intensity_xyz3=double(V(xBas1, yBas, z+1));
intensity_xyz4=double(V(xBas1, yBas1, z+1));
% Calculate the interpolated intensity
intensity_loc=intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4);
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c);
end
case 4
for z=(Iin_sizex-1):-1:0,
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizex/2)+Iin_sizey/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizex/2)+Iin_sizez/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizez-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizey-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(z+1,xBas, yBas)));
intensity_xyz2=double(squeeze(V(z+1,xBas, yBas1)));
intensity_xyz3=double(squeeze(V(z+1,xBas1, yBas)));
intensity_xyz4=double(squeeze(V(z+1,xBas1, yBas1)));
% Calculate the interpolated intensity
intensity_loc=intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4);
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c);
end
case 5
for z=(Iin_sizey-1):-1:0,
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizey/2)+Iin_sizez/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizey/2)+Iin_sizex/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizex-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizez-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(squeeze(V(yBas, z+1,xBas)));
intensity_xyz2=double(squeeze(V(yBas1, z+1,xBas)));
intensity_xyz3=double(squeeze(V(yBas, z+1,xBas1)));
intensity_xyz4=double(squeeze(V(yBas1, z+1,xBas1)));
% Calculate the interpolated intensity
intensity_loc=intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4);
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c);
end
case 6
for z=(Iin_sizez-1):-1:0,
% Offset calculation
xd=(-Ibuffer_sizex/2)+Mshearinv(1,3)*(z-Iin_sizez/2)+Iin_sizex/2;
yd=(-Ibuffer_sizey/2)+Mshearinv(2,3)*(z-Iin_sizez/2)+Iin_sizey/2;
xdfloor=floor(xd); ydfloor=floor(yd);
% Linear interpolation constants (percentages)
xCom=xd-floor(xd); yCom=yd-floor(yd);
perc(1)=(1-xCom) * (1-yCom);
perc(2)=(1-xCom) * yCom;
perc(3)=xCom * (1-yCom);
perc(4)=xCom * yCom;
%Calculate the coordinates on which a image slice starts and
%ends in the temporary shear image (buffer)
pystart=-ydfloor;
if(pystart<0), pystart=0; end
pyend=Iin_sizey-ydfloor;
if(pyend>Ibuffer_sizey), pyend=Ibuffer_sizey; end
pxstart=-xdfloor;
if(pxstart<0), pxstart=0; end
pxend=Iin_sizex-xdfloor;
if(pxend>Ibuffer_sizex), pxend=Ibuffer_sizex; end
py=(pystart+1:pyend-1);
% Determine y coordinates of pixel(s) which will be come current pixel
yBas=py+ydfloor;
px=(pxstart+1:pxend-1);
%Determine x coordinates of pixel(s) which will be come current pixel
xBas=px+xdfloor;
xBas1=xBas+1; xBas1(end)=xBas1(end)-1;
yBas1=yBas+1; yBas1(end)=yBas1(end)-1;
% Get the intensities
intensity_xyz1=double(V(xBas, yBas, z+1));
intensity_xyz2=double(V(xBas, yBas1, z+1));
intensity_xyz3=double(V(xBas1, yBas, z+1));
intensity_xyz4=double(V(xBas1, yBas1, z+1));
% Calculate the interpolated intensity
intensity_loc=intensity_xyz1*perc(1)+intensity_xyz2*perc(2)+intensity_xyz3*perc(3)+intensity_xyz4*perc(4);
% Update the shear image buffer
Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c);
end
end
Ibuffer=Ibuffer/imax;
render_image = warp(Ibuffer, image_size(1:2),Mshearinv,Mwarp2Dinv,c);
function Ibuffer=updatebuffer(intensity_loc,Ibuffer,px,py,c)
if(c==2||c==5), intensity_loc=intensity_loc'; end
% Update the current pixel in the shear image buffer
check=double(intensity_loc>Ibuffer(px,py));
Ibuffer(px,py)=(check).*intensity_loc+(1-check).*Ibuffer(px,py);
|
github
|
jacksky64/imageProcessing-master
|
bitmaptext.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/bitmaptext.m
| 100,462 |
utf_8
|
6a905a18b93a3d3e263a7630face0e68
|
function I=bitmaptext(lines,I,pos,options)
% The function BITMAPTEXT will insert textline(s) on the specified position
% in the image.
%
% I=bitmaptext(Text,Ibackground,Position,options)
%
% inputs,
% Text : Cell array with text lines
% Ibackground: the bitmap used as background when a m x n x 3 matrix
% color plots are made, when m x n a greyscale plot. If empty []
% autosize to fit text.
% Position: x,y position of the text
% options: struct with options such as color
%
% outputs,
% Iplot: The bitmap containing the plotted text
%
% note,
% Colors are always [r(ed) g(reen) b(lue) a(pha)], with range 0..1.
% when Ibackground is grayscale, the mean of r,g,b is used as grey value.
%
% options,
% options.Color: The color of the text.
% options.FontSize: The size of the font, 1,2 or 3 (small,medium,large).
%
% example,
%
% % The text consisting of 2 lines
% lines={'a_A_j_J?,','ImageText version 1.1'};
% % Background image
% I=ones([256 256 3]);
% % Plot text into background image
% I=bitmaptext(lines,I,[1 1],struct('FontSize',3));
% % Show the result
% figure, imshow(I),
%
% Function is written by D.Kroon University of Twente (March 2009)
global character_images;
% Process inputs
defaultoptions=struct('Color',[0 0 1 1],'FontSize',1);
if(~exist('options','var')),
options=defaultoptions;
else
tags = fieldnames(defaultoptions);
for i=1:length(tags)
if(~isfield(options,tags{i})), options.(tags{i})=defaultoptions.(tags{i}); end
end
if(length(tags)~=length(fieldnames(options))),
warning('register_images:unknownoption','unknown options found');
end
end
% If single line make it a cell array
if(~iscell(lines)), lines={lines}; end
if(~exist('I','var')), I=[]; end
if(exist('pos','var')),
if(length(pos)~=2)
error('imagtext:inputs','position must have x,y coordinates');
end
else
pos=[1 1];
end
% Set the size of the font
fsize=options.FontSize;
% The character bitmap and character set;
character_set='abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890!@#$%^&*()_+-=[]\;'''',./{}|:"<>?';
if(isempty(character_images)), character_images=load_font(); end
% Font parameters
Font_sizes_x=[8 10 11];
Font_sizes_y=[13 15 18];
Font_startx=[1 1 1];
Font_starty=[1 14 29];
% Get maximum sentence length
lengths=zeros(1,length(lines));
for i=1:length(lines), lengths(i)=length(lines{i}); end
max_line_length=max(lengths);
% Make text image from the lines
lines_image=zeros([(Font_sizes_y(fsize)+4)*length(lines),max_line_length*Font_sizes_x(fsize)],'double');
for j=1:length(lines)
line=lines{j};
for i=1:length(line),
[t,p]=find(character_set==line(i));
if(~isempty(p))
p=p(1)-1;
character_bitmap=character_images(Font_starty(fsize):(Font_starty(fsize)+Font_sizes_y(fsize)-1),Font_startx(fsize)+(1+p*Font_sizes_x(fsize)):Font_startx(fsize)+((p+1)*Font_sizes_x(fsize)));
posx=Font_sizes_x(fsize)*(i-1);
posy=(Font_sizes_y(fsize)+4)*(j-1);
lines_image((1:Font_sizes_y(fsize))+posy,(1:Font_sizes_x(fsize))+posx)=character_bitmap;
end
end
end
if(isempty(I)), I=zeros([size(lines_image) 3]); end
% Remove part of textimage which will be outside of the output image
if(pos(1)<1), lines_image=lines_image(2-pos(1):end,:); pos(1)=1; end
if(pos(2)<2), lines_image=lines_image(:,2-pos(2):end); pos(2)=1; end
if((pos(1)+size(lines_image,1))>size(I,1)), dif=size(I,1)-(pos(1)+size(lines_image,1)); lines_image=lines_image(1:end+dif,:); end
if((pos(2)+size(lines_image,2))>size(I,2)), dif=size(I,2)-(pos(2)+size(lines_image,2)); lines_image=lines_image(:,1:end+dif); end
% Make text image the same size as background image
I_line=zeros([size(I,1) size(I,2)]);
I_line(pos(1):(pos(1)+size(lines_image,1)-1),pos(2):(pos(2)+size(lines_image,2)-1))=lines_image;
I_line=I_line*options.Color(4);
% Insert the text image into the output image
if(~isempty(lines_image))
if(size(I,3)==3)
for i=1:3
I(:,:,i)=I(:,:,i).*(1-I_line)+options.Color(i)*(I_line);
end
else
I=I.*(1-I_line)+mean(options.Color(1:3))*(I_line);
end
end
function character_images=load_font()
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character_images=double(character_images)/9;
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_qualityspeed.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/viewer3d_qualityspeed.m
| 6,060 |
utf_8
|
b56938bc38cf2f4eccdd0ba38ff93d0a
|
function varargout = viewer3d_qualityspeed(varargin)
% VIEWER3D_QUALITYSPEED M-file for viewer3d_qualityspeed.fig
% VIEWER3D_QUALITYSPEED, by itself, creates a new VIEWER3D_QUALITYSPEED or raises the existing
% singleton*.
%
% H = VIEWER3D_QUALITYSPEED returns the handle to a new VIEWER3D_QUALITYSPEED or the handle to
% the existing singleton*.
%
% VIEWER3D_QUALITYSPEED('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VIEWER3D_QUALITYSPEED.M with the given input arguments.
%
% VIEWER3D_QUALITYSPEED('Property','Value',...) creates a new VIEWER3D_QUALITYSPEED or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before viewer3d_qualityspeed_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to viewer3d_qualityspeed_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help viewer3d_qualityspeed
% Last Modified by GUIDE v2.5 10-Nov-2010 13:55:49
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_qualityspeed_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_qualityspeed_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_qualityspeed is made visible.
function viewer3d_qualityspeed_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_qualityspeed (see VARARGIN)
% Choose default command line output for viewer3d_qualityspeed
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes viewer3d_qualityspeed wait for user response (see UIRESUME)
% uiwait(handles.figurequalityspeed);
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_qualityspeed_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on button press in checkbox_prerender.
function checkbox_prerender_Callback(hObject, eventdata, handles)
% hObject handle to checkbox_prerender (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of checkbox_prerender
% --- Executes on button press in radiobutton_scaling25.
function radiobutton_scaling25_Callback(hObject, eventdata, handles)
% hObject handle to radiobutton_scaling25 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of radiobutton_scaling25
% --- Executes on button press in radiobutton_scaling50.
function radiobutton_scaling50_Callback(hObject, eventdata, handles)
% hObject handle to radiobutton_scaling50 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of radiobutton_scaling50
% --- Executes on button press in radiobutton_scaling100.
function radiobutton_scaling100_Callback(hObject, eventdata, handles)
% hObject handle to radiobutton_scaling100 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of radiobutton_scaling100
% --- Executes on button press in radiobutton_scaling200.
function radiobutton_scaling200_Callback(hObject, eventdata, handles)
% hObject handle to radiobutton_scaling200 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of radiobutton_scaling200
% --- Executes on button press in checkbox_storexyz.
function checkbox_storexyz_Callback(hObject, eventdata, handles)
% hObject handle to checkbox_storexyz (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of checkbox_storexyz
% --- Executes on button press in pushbutton_applyconfig.
function pushbutton_applyconfig_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton_applyconfig (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --- Executes on button press in pushbutton_saveconfig.
function pushbutton_saveconfig_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton_saveconfig (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_voxelsize.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/viewer3d_voxelsize.m
| 8,989 |
utf_8
|
05035f45cf682370f5de14ad000e1ffa
|
function varargout = viewer3d_voxelsize(varargin)
% VIEWER3D_VOXELSIZE M-file for viewer3d_voxelsize.fig
% VIEWER3D_VOXELSIZE, by itself, creates a new VIEWER3D_VOXELSIZE or raises the existing
% singleton*.
%
% H = VIEWER3D_VOXELSIZE returns the handle to a new VIEWER3D_VOXELSIZE or the handle to
% the existing singleton*.
%
% VIEWER3D_VOXELSIZE('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VIEWER3D_VOXELSIZE.M with the given input arguments.
%
% VIEWER3D_VOXELSIZE('Property','Value',...) creates a new VIEWER3D_VOXELSIZE or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before viewer3d_voxelsize_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to viewer3d_voxelsize_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help viewer3d_voxelsize
% Last Modified by GUIDE v2.5 10-Nov-2010 13:54:19
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_voxelsize_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_voxelsize_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_voxelsize is made visible.
function viewer3d_voxelsize_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_voxelsize (see VARARGIN)
% Choose default command line output for viewer3d_voxelsize
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes viewer3d_voxelsize wait for user response (see UIRESUME)
% uiwait(handles.figurevoxelsize);
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_voxelsize_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
function edit_scax_Callback(hObject, eventdata, handles)
% hObject handle to edit_scax (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_scax as text
% str2double(get(hObject,'String')) returns contents of edit_scax as a double
% --- Executes during object creation, after setting all properties.
function edit_scax_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_scax (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_scay_Callback(hObject, eventdata, handles)
% hObject handle to edit_scay (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_scay as text
% str2double(get(hObject,'String')) returns contents of edit_scay as a double
% --- Executes during object creation, after setting all properties.
function edit_scay_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_scay (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_scaz_Callback(hObject, eventdata, handles)
% hObject handle to edit_scaz (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_scaz as text
% str2double(get(hObject,'String')) returns contents of edit_scaz as a double
% --- Executes during object creation, after setting all properties.
function edit_scaz_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_scaz (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_volx_Callback(hObject, eventdata, handles)
% hObject handle to edit_volx (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_volx as text
% str2double(get(hObject,'String')) returns contents of edit_volx as a double
% --- Executes during object creation, after setting all properties.
function edit_volx_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_volx (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_voly_Callback(hObject, eventdata, handles)
% hObject handle to edit_voly (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_voly as text
% str2double(get(hObject,'String')) returns contents of edit_voly as a double
% --- Executes during object creation, after setting all properties.
function edit_voly_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_voly (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_volz_Callback(hObject, eventdata, handles)
% hObject handle to edit_volz (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_volz as text
% str2double(get(hObject,'String')) returns contents of edit_volz as a double
% --- Executes during object creation, after setting all properties.
function edit_volz_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_volz (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in button_apply.
function button_apply_Callback(hObject, eventdata, handles)
% hObject handle to button_apply (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_lightvector.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/viewer3d_lightvector.m
| 6,223 |
utf_8
|
15bbf1983818b61fcb3e2747adea2fe1
|
function varargout = viewer3d_lightvector(varargin)
% VIEWER3D_LIGHTVECTOR M-file for viewer3d_lightvector.fig
% VIEWER3D_LIGHTVECTOR, by itself, creates a new VIEWER3D_LIGHTVECTOR or raises the existing
% singleton*.
%
% H = VIEWER3D_LIGHTVECTOR returns the handle to a new VIEWER3D_LIGHTVECTOR or the handle to
% the existing singleton*.
%
% VIEWER3D_LIGHTVECTOR('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VIEWER3D_LIGHTVECTOR.M with the given input arguments.
%
% VIEWER3D_LIGHTVECTOR('Property','Value',...) creates a new VIEWER3D_LIGHTVECTOR or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before viewer3d_lightvector_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to viewer3d_lightvector_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help viewer3d_lightvector
% Last Modified by GUIDE v2.5 25-Feb-2009 14:27:43
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_lightvector_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_lightvector_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_lightvector is made visible.
function viewer3d_lightvector_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_lightvector (see VARARGIN)
% Choose default command line output for viewer3d_lightvector
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes viewer3d_lightvector wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_lightvector_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
function edit_lightx_Callback(hObject, eventdata, handles)
% hObject handle to edit_lightx (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_lightx as text
% str2double(get(hObject,'String')) returns contents of edit_lightx as a double
% --- Executes during object creation, after setting all properties.
function edit_lightx_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_lightx (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_lighty_Callback(hObject, eventdata, handles)
% hObject handle to edit_lighty (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_lighty as text
% str2double(get(hObject,'String')) returns contents of edit_lighty as a double
% --- Executes during object creation, after setting all properties.
function edit_lighty_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_lighty (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit_lightz_Callback(hObject, eventdata, handles)
% hObject handle to edit_lightz (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_lightz as text
% str2double(get(hObject,'String')) returns contents of edit_lightz as a double
% --- Executes during object creation, after setting all properties.
function edit_lightz_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_lightz (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in button_apply.
function button_apply_Callback(hObject, eventdata, handles)
% hObject handle to button_apply (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_histogram.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/viewer3d_histogram.m
| 4,955 |
utf_8
|
707fcbdb2a3d383b3de6cfbb144169d0
|
function varargout = viewer3d_histogram(varargin)
% This function is part of VIEWER3D
%
% color and alpha maps can be changed on the fly by dragging and creating
% new color/alpha markers with the left mouse button.
%
% Function is written by D.Kroon University of Twente (October 2008)
% Edit the above text to modify the response to help viewer3d_histogram
% Last Modified by GUIDE v2.5 10-Nov-2010 13:53:41
% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_histogram_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_histogram_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_histogram is made visible.
function viewer3d_histogram_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_histogram (see VARARGIN)
% Choose default command line output for viewer3d_histogram
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
function figurehistogram_WindowButtonMotionFcn(hObject, eventdata, handles)
function varargout = viewer3d_histogram_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes during object creation, after setting all properties.
function popupmenu_colors_CreateFcn(hObject, eventdata, handles)
% hObject handle to popupmenu_colors (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: popupmenu controls usually have a white background on Windows.
% See ISPC and COMPUTER.
set(hObject,'String',{'jet','hsv','hot','cool','spring','summer','autumn','winter','gray','bone','copper','pink'});
set(hObject,'Value',3);
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --------------------------------------------------------------------
function menu_file_Callback(hObject, eventdata, handles)
% hObject handle to menu_file (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_load_Callback(hObject, eventdata, handles)
% hObject handle to menu_load (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function menu_save_Callback(hObject, eventdata, handles)
% hObject handle to menu_save (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --- Executes on selection change in popupmenu_colors.
function popupmenu_colors_Callback(hObject, eventdata, handles)
% hObject handle to popupmenu_colors (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = get(hObject,'String') returns popupmenu_colors contents as cell array
% contents{get(hObject,'Value')} returns selected item from popupmenu_colors
% --- Executes on button press in pushbutton_update_view.
function pushbutton_update_view_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton_update_view (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --- Executes on button press in checkbox_auto_update.
function checkbox_auto_update_Callback(hObject, eventdata, handles)
% hObject handle to checkbox_auto_update (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of checkbox_auto_update
|
github
|
jacksky64/imageProcessing-master
|
makeViewMatrix.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/makeViewMatrix.m
| 1,190 |
utf_8
|
49d443a4402c434f497d4b2dba34f211
|
function Mview=makeViewMatrix(r,s,t)
% function makeViewMatrix construct a 4x4 transformation matrix from
% rotation, resize and translation variables.
%
% Mview=makeViewMatrix(R,S,T)
%
% inputs,
% R: Rotation vector [Rx, Ry, Rz];
% S: Resize vector [Sx, Sy, Sz];
% T: Translation vector [Tx, Ty, Tz];
%
% outputs,
% Mview: 4x4 transformation matrix
%
% Example,
% Mview=makeViewMatrix([45 45 0],[1 1 1],[0 0 0]);
% disp(Mview);
%
% Function is written by D.Kroon University of Twente (October 2008)
R=RotationMatrix(r);
S=ResizeMatrix(s);
T=TranslateMatrix(t);
Mview=R*S*T;
function R=RotationMatrix(r)
% Determine the rotation matrix (View matrix) for rotation angles xyz ...
Rx=[1 0 0 0; 0 cosd(r(1)) -sind(r(1)) 0; 0 sind(r(1)) cosd(r(1)) 0; 0 0 0 1];
Ry=[cosd(r(2)) 0 sind(r(2)) 0; 0 1 0 0; -sind(r(2)) 0 cosd(r(2)) 0; 0 0 0 1];
Rz=[cosd(r(3)) -sind(r(3)) 0 0; sind(r(3)) cosd(r(3)) 0 0; 0 0 1 0; 0 0 0 1];
R=Rx*Ry*Rz;
function S=ResizeMatrix(s)
S=[1/s(1) 0 0 0;
0 1/s(2) 0 0;
0 0 1/s(3) 0;
0 0 0 1];
function T=TranslateMatrix(t)
T=[1 0 0 -t(1);
0 1 0 -t(2);
0 0 1 -t(3);
0 0 0 1];
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_console.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/viewer3d_console.m
| 4,231 |
utf_8
|
c358c82f26d26886a33ea68845e6cfb0
|
function varargout = viewer3d_console(varargin)
% VIEWER3D_CONSOLE M-file for viewer3d_console.fig
% VIEWER3D_CONSOLE, by itself, creates a new VIEWER3D_CONSOLE or raises the existing
% singleton*.
%
% H = VIEWER3D_CONSOLE returns the handle to a new VIEWER3D_CONSOLE or the handle to
% the existing singleton*.
%
% VIEWER3D_CONSOLE('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VIEWER3D_CONSOLE.M with the given input arguments.
%
% VIEWER3D_CONSOLE('Property','Value',...) creates a new VIEWER3D_CONSOLE or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before viewer3d_console_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to viewer3d_console_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help viewer3d_console
% Last Modified by GUIDE v2.5 10-Nov-2010 13:56:33
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_console_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_console_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_console is made visible.
function viewer3d_console_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_console (see VARARGIN)
% Choose default command line output for viewer3d_console
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes viewer3d_console wait for user response (see UIRESUME)
% uiwait(handles.figureconsole);
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_console_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
function edit_console_Callback(hObject, eventdata, handles)
% hObject handle to edit_console (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_console as text
% str2double(get(hObject,'String')) returns contents of edit_console as a double
% --- Executes during object creation, after setting all properties.
function edit_console_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_console (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in button_clear.
function button_clear_Callback(hObject, eventdata, handles)
% hObject handle to button_clear (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_error.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/viewer3d_error.m
| 3,313 |
utf_8
|
abc306910c64efef252c1762e396a06b
|
function varargout = viewer3d_error(varargin)
% VIEWER3D_ERROR M-file for viewer3d_error.fig
% VIEWER3D_ERROR, by itself, creates a new VIEWER3D_ERROR or raises the existing
% singleton*.
%
% H = VIEWER3D_ERROR returns the handle to a new VIEWER3D_ERROR or the handle to
% the existing singleton*.
%
% VIEWER3D_ERROR('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VIEWER3D_ERROR.M with the given input arguments.
%
% VIEWER3D_ERROR('Property','Value',...) creates a new VIEWER3D_ERROR or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before viewer3d_error_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to viewer3d_error_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help viewer3d_error
% Last Modified by GUIDE v2.5 05-Nov-2008 14:39:24
% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_error_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_error_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_error is made visible.
function viewer3d_error_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_error (see VARARGIN)
% Choose default command line output for viewer3d_error
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
if (~isempty(varargin))
set(handles.text1,'string',varargin{1})
end
% UIWAIT makes viewer3d_error wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_error_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on button press in pushbutton1.
function pushbutton1_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
delete(handles.figure1);
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_about.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/viewer3d_about.m
| 2,931 |
utf_8
|
b00f2eccc530dd07ac25d2285ef08012
|
function varargout = viewer3d_about(varargin)
% VIEWER3D_ABOUT M-file for viewer3d_about.fig
% VIEWER3D_ABOUT, by itself, creates a new VIEWER3D_ABOUT or raises the existing
% singleton*.
%
% H = VIEWER3D_ABOUT returns the handle to a new VIEWER3D_ABOUT or the handle to
% the existing singleton*.
%
% VIEWER3D_ABOUT('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VIEWER3D_ABOUT.M with the given input arguments.
%
% VIEWER3D_ABOUT('Property','Value',...) creates a new VIEWER3D_ABOUT or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before viewer3d_about_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to viewer3d_about_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help viewer3d_about
% Last Modified by GUIDE v2.5 10-Nov-2010 13:57:15
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_about_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_about_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_about is made visible.
function viewer3d_about_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_about (see VARARGIN)
% Choose default command line output for viewer3d_about
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes viewer3d_about wait for user response (see UIRESUME)
% uiwait(handles.figureabout);
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_about_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_workspacevars.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/viewer3d_workspacevars.m
| 4,426 |
utf_8
|
7a77a2a3833854c6146fc182b03521b8
|
function varargout = viewer3d_workspacevars(varargin)
% VIEWER3D_WORKSPACEVARS M-file for viewer3d_workspacevars.fig
% VIEWER3D_WORKSPACEVARS, by itself, creates a new VIEWER3D_WORKSPACEVARS or raises the existing
% singleton*.
%
% H = VIEWER3D_WORKSPACEVARS returns the handle to a new VIEWER3D_WORKSPACEVARS or the handle to
% the existing singleton*.
%
% VIEWER3D_WORKSPACEVARS('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VIEWER3D_WORKSPACEVARS.M with the given input arguments.
%
% VIEWER3D_WORKSPACEVARS('Property','Value',...) creates a new VIEWER3D_WORKSPACEVARS or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before viewer3d_workspacevars_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to viewer3d_workspacevars_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help viewer3d_workspacevars
% Last Modified by GUIDE v2.5 10-Nov-2010 13:55:11
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_workspacevars_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_workspacevars_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_workspacevars is made visible.
function viewer3d_workspacevars_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_workspacevars (see VARARGIN)
% Choose default command line output for viewer3d_workspacevars
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes viewer3d_workspacevars wait for user response (see UIRESUME)
% uiwait(handles.figureworkspacevars);
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_workspacevars_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on selection change in listbox_vars.
function listbox_vars_Callback(hObject, eventdata, handles)
% hObject handle to listbox_vars (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = get(hObject,'String') returns listbox_vars contents as cell array
% contents{get(hObject,'Value')} returns selected item from listbox_vars
% --- Executes during object creation, after setting all properties.
function listbox_vars_CreateFcn(hObject, eventdata, handles)
% hObject handle to listbox_vars (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: listbox controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in button_load.
function button_load_Callback(hObject, eventdata, handles)
% hObject handle to button_load (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_dicominfo.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/viewer3d_dicominfo.m
| 3,768 |
utf_8
|
799dc4c250afac440206ca300c785cf9
|
function varargout = viewer3d_dicominfo(varargin)
% VIEWER3D_DICOMINFO M-file for viewer3d_dicominfo.fig
% VIEWER3D_DICOMINFO, by itself, creates a new VIEWER3D_DICOMINFO or raises the existing
% singleton*.
%
% H = VIEWER3D_DICOMINFO returns the handle to a new VIEWER3D_DICOMINFO or the handle to
% the existing singleton*.
%
% VIEWER3D_DICOMINFO('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VIEWER3D_DICOMINFO.M with the given input arguments.
%
% VIEWER3D_DICOMINFO('Property','Value',...) creates a new VIEWER3D_DICOMINFO or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before viewer3d_dicominfo_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to viewer3d_dicominfo_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help viewer3d_dicominfo
% Last Modified by GUIDE v2.5 10-Nov-2010 13:56:13
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_dicominfo_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_dicominfo_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_dicominfo is made visible.
function viewer3d_dicominfo_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_dicominfo (see VARARGIN)
% Choose default command line output for viewer3d_dicominfo
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes viewer3d_dicominfo wait for user response (see UIRESUME)
% uiwait(handles.figuredicominfo);
info=varargin{1};
if(isempty(info)), return; end
infocell=cell(100000,2);
[infocell,poscell]=showinfo(info,infocell,0,'');
infocell(poscell+1:end,:)=[];
set(handles.uitable1,'Data',infocell)
function [infocell,poscell] = showinfo(info,infocell,poscell,s)
fnames=fieldnames(info);
for i=1:length(fnames)
type=fnames{i};
data=info.(type);
if(isnumeric(data))
poscell=poscell+1;
infocell{poscell,1}=[s type];
infocell{poscell,2}=num2str(data(:)');
elseif(ischar(data))
poscell=poscell+1;
infocell{poscell,1}=[s type];
infocell{poscell,2}=data;
elseif(iscell(data))
elseif(isstruct(data))
[infocell,poscell]=showinfo(data,infocell,poscell,[type '.']);
end
end
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_dicominfo_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
|
github
|
jacksky64/imageProcessing-master
|
interpcontour.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/interpcontour.m
| 698 |
utf_8
|
693643a87f9f2e5d508ebbbaef519f29
|
function [x,y,z]=interpcontour(x,y,z,s)
% [x,y,z]=interpcontour(x,y,z,s)
%
pos=[x(:) y(:) z(:)];
[t,ind]=unique(pos,'rows');
pos=pos(sort(ind),:);
x=pos(:,1); y=pos(:,2); z=pos(:,3);
[x,y,z]=interpcontour1(x,y,z,1);
[x,y,z]=interpcontour1(x,y,z,s);
function [x,y,z]=interpcontour1(x,y,z,s)
i1=(length(x)+1);
i2=(length(x)*2)+1;
x=[x(:);x(:);x(:)];
y=[y(:);y(:);y(:)];
z=[z(:);z(:);z(:)];
dx=x(2:end)-x(1:end-1);
dy=y(2:end)-y(1:end-1);
dz=z(2:end)-z(1:end-1);
d=cumsum([0;sqrt(dx.^2+dy.^2+dz.^2)]);
n=ceil((d(i2)-d(i1))/s);
di=linspace(d(i1),d(i2),n+1); di=di(1:end-1);
x = interp1(d,x,di,'spline');
y = interp1(d,y,di,'spline');
z = interp1(d,z,di,'spline');
|
github
|
jacksky64/imageProcessing-master
|
menubar.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/menubar.m
| 22,307 |
utf_8
|
7934250b43bec6ecb3cd05f58e364c50
|
function menubar(varargin)
% This function MenuBar, allows the user to create menu's anywhere in a figure
% it replaces UIcontextmenu of UIpanels by real menu bars.
%
% menubar(figure_handle) or menubar
%
% Mouse hover, and window-resize updates can be enabled by
%
% menubar('start',figure_handle) or menubar('start')
%
% Or alternatively by:
%
% set(figure_handle,'ResizeFcn','menubar(''ResizeFcn'',gcf)');
% set(figure_handle,'WindowButtonMotionFcn','menubar(''MotionFcn'',gcf)');
%
% Example,
%
% % Creat figure with uipanel
% figure,
% uipanel1 = uipanel('Units','Pixels','Position',[10 200 400 200]);
%
% % Attach a contextmenu (right-mouse button menu)
% menu_panel1=uicontextmenu;
% set(uipanel1,'UIContextMenu',menu_panel1);
%
% % Add menu-items to the context menu
% hchild=uimenu(menu_panel1, 'Label', 'Random Pixels');
% uimenu(hchild, 'Label', 'Red','Callback','disp(''Red callback'')');
% uimenu(hchild, 'Label', 'Blue','Callback','disp(''Blue callback'')');
%
% % Make form the context menu a real menubar
% menubar
%
% % Add some other menu-buttons
% hchild=uimenu(menu_panel1, 'Label', 'Clear','Callback','disp(''Clear'')');
% hchild=uimenu(menu_panel1, 'Label', 'Help');
% uimenu(hchild, 'Label', 'Info','Callback','disp(''Info callback'')');
%
% % Update the menubar
% menubar
%
% % Enable the mouse over and resize effects
% menubar('start');
%
% Function is written by D.Kroon University of Twente (December 2010)
% Get Figure Handle
figure_handle=gcf;
if(nargin>0)
if(isnumeric(varargin{1})), figure_handle=varargin{1}; end
if(nargin==2), figure_handle=varargin{2}; end
if(ischar(varargin{1}))
switch lower(varargin{1})
case 'resizefcn'
menubar_ResizeFcn(figure_handle);
case 'motionfcn'
menubar_MotionFcn(figure_handle);
case 'start'
renewtimer(figure_handle);
end
return
end
end
% There must be Motion Function otherwise the cursorpostion
% in the axis is not updated.
if(isempty(get(figure_handle,'WindowButtonMotionFcn')))
set(figure_handle,'WindowButtonMotionFcn',@menubar_DummyFcn);
end
% Get the Children of the Figure which are UIpanels
C=get(figure_handle,'Children');
D=false(size(C));
for i=1:length(C), D(i)=strcmpi(get(C(i),'Type'),'uipanel'); end
C=C(D);
% Copy UIContextMenu of uipanels to real menubars
for i=1:length(C)
% If the panel has a UIContextMenu it is processed
uimenuhandle=get(C(i),'UIContextMenu');
if(isempty(uimenuhandle)||(~ishandle(uimenuhandle))), continue; end
datahandle=C(i);
UpdateMenu(datahandle,figure_handle);
end
figuredata.uipanels=C;
setMyData(figuredata,figure_handle)
function renewtimer(figure_handle)
figuredata=getMyData(figure_handle); if(isempty(figuredata)),return; end
if(isfield(figuredata,'timer'))
stop(figuredata.timer); delete(figuredata.timer);
end
figuredata.timer = timer('TimerFcn',@(x,y)menubar_Timer(x,y,figure_handle), 'Period', 0.2,'ExecutionMode','fixedSpacing');
% Start the event-timer
start(figuredata.timer);
setMyData(figuredata,figure_handle);
function m=AddChildren(h,Properties)
% This function will create a Matlab Structure from the UICContextMenu
%
% The structure looks like :
% m(1).Label='File';
% m(1).Children(1).Label='New';
% m(1).Children(1).Children(1).Label='Script';
% m(1).Children(1).Children(2).Label='Function';
% m(1).Children(1).Children(2).Separator='on';
% m(1).Children(1).Children(3).Label='Class';
% m(1).Children(1).Children(3).Callback='disp(''callback'')';
% m(1).Children(2).Label='Open';
% m(1).Children(3).Label='Close';
% m(2).Label='Edit';
% m(2).Callback='disp(''callback'')';
% m(3).Label='View';
% m(4).Label='Insert';
%
m=struct;
% Get all children (menu-items) of the handle
hc=get(h,'Children');
% Sort the children by their tag position (menu-items)
p=zeros(1,length(hc));
for i=1:length(hc), p(i)=get(hc(i),'Position'); end;
[t,i]=sort(p);
% Add the menu-item to the structure
hc=hc(i);
for i=1:length(hc)
for j=1:length(Properties)
m(i).(Properties{j})=get(hc(i),Properties{j});
end
% If the menu-item has also children (sub-menus), then use the current
% function recursivly to get all sub-(sub)-(sub)-menus.
C=get(hc(i),'Children');
if(~isempty(C)), m(i).Children=AddChildren(hc(i),Properties); end
end
function CreatMenuBar(uimenuhandle,datahandle,Pos,figure_handle)
% Properties (Writeable) of a menu-item
Properties={'Label','Callback','Separator','Checked','Enable','ForegroundColor','Position','ButtonDownFcn','Selected','SelectionHighlight','Visible','UserData'};
% This will create a Matlab Structure from the UICContextMenu
data.menuitems=AddChildren(uimenuhandle,Properties);
% This variable will store the selected-menu button
data.sel=[];
% Store the handle to the current figure
data.figure_handle=figure_handle;
% This variable will store the menu button beneath the mouse
% used for hover-animation
data.hov=[];
% Store position of uipanel
data.Pos=Pos;
% This Calculates the length and position of each menu-button
% related to the string-lenght of the label
tstr=zeros(length(data.menuitems),1);
for i=1:length(data.menuitems)
tstr(i)=length(data.menuitems(i).Label)*7+16;
end
% Pos(1) and Pos(2), are the location of the UIpanel in the figure
xpositions=[0;cumsum(tstr)]+Pos(1)+1;
data.xpositions=xpositions;
data.yposition=Pos(2)+Pos(4)-26;
% Instead of .png files with the images, we store the pixels to make
% menubuttons inside the function loadbarimages
[data.IN,data.IS,data.IH]=loadbarimages();
% This function will paint all menu-buttons in the figure
for i=1:length(data.menuitems);
w=tstr(i);
h=25;
x=xpositions(i);
[barimage,barimagehover,barimageselect]=getbarimage(w,data);
data.menuitems(i).Handle=axes('Units','Pixels','Position',[x data.yposition w h],'Parent',figure_handle);
data.menuitems(i).HandleImshow=imshow(barimage,'Parent',data.menuitems(i).Handle);
set(data.menuitems(i).HandleImshow,'ButtonDownFcn',@(x,y)menubar_ButtonDownFcn(x,y,datahandle));
if(strcmpi(data.menuitems(i).Enable,'on'))
hc=text(8,25/2,data.menuitems(i).Label,'Parent',data.menuitems(i).Handle);
set(hc,'ButtonDownFcn',@(x,y)menubar_ButtonDownFcn(x,y,datahandle));
else
hc=text(8,25/2,data.menuitems(i).Label,'Parent',data.menuitems(i).Handle);
data.menuitems(i).Children=[];
set(hc,'Color',[0.5 0.5 0.5]);
end
data.menuitems(i).barimage=barimage;
data.menuitems(i).barimagehover=barimagehover;
data.menuitems(i).barimageselect=barimageselect;
end
i=length(data.menuitems)+1;
w=round(Pos(3))-sum(tstr(1:end))-3; w(w<1)=1;
x=xpositions(i);
barimage=getbarimage(w,data);
data.menuitems(i).Handle=axes('Units','Pixels','Position',[x data.yposition w h],'Parent',figure_handle);
data.menuitems(i).HandleImshow=imshow(barimage,'Parent',data.menuitems(i).Handle);
% This function builds the sub-menus which will appear beneath the menubar
% in the figure
z=data.menuitems;
for i=1:length(z)
data.cMenu(i) = uicontextmenu('Parent',figure_handle);
addMenuChilds(z(i),data.cMenu(i),Properties)
end
% Store all data (this structure is attached to the uipanel-handle
setMyData(data,datahandle);
function addMenuChilds(z,h,Properties)
% This function builds the sub-menus of the menubar
% (adding sub-sub-menus recursively)
if(isfield(z,'Children')&&~isempty(z.Children))
for i=1:length(z.Children)
z2=z.Children(i);
hchild=uimenu(h, 'Label', z2.Label);
for j=1:length(Properties)
Pr=Properties{j};
if(isfield(z2,Pr))
val=z2.(Pr);
if(~isempty(val)), set(hchild ,Pr,val); end
end
end
addMenuChilds(z2,hchild,Properties)
end
end
function [barimage,barimagehover,barimageselect]=getbarimage(w,data)
% This function builds the whole menu-buttons from the few pixel-lines stored
% in loadbarimages
barimage=zeros(size(data.IN,1),w,'uint8');
barimage(:,:,1)=repmat(data.IN(:,1),1,w);
barimage(:,:,2)=repmat(data.IN(:,2),1,w);
barimage(:,:,3)=repmat(data.IN(:,3),1,w);
barimagehover=zeros(size(data.IN,1),w,'uint8');
barimagehover(:,:,1)=repmat(data.IH(:,4,1),1,w);
barimagehover(:,:,2)=repmat(data.IH(:,4,2),1,w);
barimagehover(:,:,3)=repmat(data.IH(:,4,3),1,w);
barimagehover(:,1:3,1)=data.IH(:,1:3,1);
barimagehover(:,1:3,2)=data.IH(:,1:3,2);
barimagehover(:,1:3,3)=data.IH(:,1:3,3);
barimagehover(:,end-2:end,1)=data.IH(:,5:7,1);
barimagehover(:,end-2:end,2)=data.IH(:,5:7,2);
barimagehover(:,end-2:end,3)=data.IH(:,5:7,3);
barimageselect=zeros(size(data.IN,1),w,'uint8');
barimageselect(:,:,1)=repmat(data.IS(:,4,1),1,w);
barimageselect(:,:,2)=repmat(data.IS(:,4,2),1,w);
barimageselect(:,:,3)=repmat(data.IS(:,4,3),1,w);
barimageselect(:,1:3,1)=data.IS(:,1:3,1);
barimageselect(:,1:3,2)=data.IS(:,1:3,2);
barimageselect(:,1:3,3)=data.IS(:,1:3,3);
barimageselect(:,end-2:end,1)=data.IS(:,5:7,1);
barimageselect(:,end-2:end,2)=data.IS(:,5:7,2);
barimageselect(:,end-2:end,3)=data.IS(:,5:7,3);
function menubar_ButtonDownFcn(hObject, eventdata,datahandle)
data=getMyData(datahandle); if(isempty(data)), return; end
% Get the handle of the axes, (which is a parant of the clicked image or text).
hp=hObject;
switch get(hp,'Type');
case 'text', hp=get(hObject,'Parent');
case 'image', hp=get(hObject,'Parent');
end
% Detect the number of the clicked button
sel=find([data.menuitems.Handle]==hp);
% If another button was selected, reset the image to normal
if(~isempty(data.sel))
I=data.menuitems(data.sel).barimage;
set(data.menuitems(data.sel).HandleImshow,'CData',I);
end
% Set the selected-button image to selected, and display menu if present
data.sel=sel;
setSelect(data);
% If this main menu-item has a callback executes it.
dm=data.menuitems(data.sel);
if(isfield(dm,'Callback')&&(~isempty(dm.Callback)))
if(isa(dm.Callback,'function_handle'))
feval(dm.Callback);
else
eval(dm.Callback);
end
end
% Store the Data
setMyData(data,datahandle);
function setSelect(data)
% Set the selected-button image to selected, and display menu if present
cMenu=data.cMenu(data.sel);
I=data.menuitems(data.sel).barimageselect;
set(data.menuitems(data.sel).HandleImshow,'CData',I);
set(cMenu,'Visible','off');
u=get(data.menuitems(data.sel).Handle,'Units');
set(data.menuitems(data.sel).Handle,'Units','pixels');
pos=get(data.menuitems(data.sel).Handle,'Position');
set(data.menuitems(data.sel).Handle,'Units',u);
set(cMenu,'Position',[pos(1) pos(2)])
set(cMenu,'Visible','on'); drawnow
function menubar_DummyFcn(hObject, eventdata)
function menubar_MotionFcn(figurehandle)
figuredata=getMyData(figurehandle); if(isempty(figuredata)), return; end
arrayfun(@(x)ProcessMotion(x),figuredata.uipanels)
function menubar_ResizeFcn(figurehandle)
figuredata=getMyData(figurehandle); if(isempty(figuredata)), return; end
arrayfun(@(x)ProcessResize(x),figuredata.uipanels)
function menubar_Timer(hObject, eventdata,figurehandle)
% This function acts like a MotionFcn, (Used to animated hover effect
% on menu buttons)
if(ishandle(figurehandle))
figuredata=getMyData(figurehandle); if(isempty(figuredata)), return; end
arrayfun(@(x)ProcessResize(x),figuredata.uipanels)
arrayfun(@(x)ProcessMotion(x),figuredata.uipanels)
else
stop(hObject); delete(hObject);
end
function ProcessResize(datahandle)
% This function is responsible for the hover-effect of the menu-buttons.
data=getMyData(datahandle); if(isempty(data)), return; end
% Get Position of Panel in Pixels
U=get(datahandle,'Units'); set(datahandle,'Units','Pixels'); Pos=get(datahandle,'Position'); set(datahandle,'Units',U);
% Replace the menu-bar by a new one, if window resized.
if(any(abs(Pos-data.Pos)>1e-3))
UpdateMenu(datahandle,data.figure_handle)
end
function UpdateMenu(datahandle,figure_handle)
% Get Position of Panel in Pixels
U=get(datahandle,'Units'); set(datahandle,'Units','Pixels'); Pos=get(datahandle,'Position'); set(datahandle,'Units',U);
% Remove old existing menubars of the panel
removeOldMenuBar(datahandle);
uimenuhandle=get(datahandle,'UIContextMenu');
% Create a real-menubar from the panel UICContextMenu
if(~isempty( get(uimenuhandle,'Children')))
CreatMenuBar(uimenuhandle,datahandle,Pos,figure_handle)
end
drawnow('expose');
function ProcessMotion(datahandle)
% This function is responsible for the hover-effect of the menu-buttons.
data=getMyData(datahandle); if(isempty(data)), return; end
hover=false;
for i=1:length(data.menuitems),
if(~ishandle(data.menuitems(i).Handle)), return; end
% Detect mouseposition relative to axis coordinates
p = get(data.menuitems(i).Handle, 'CurrentPoint');
y= p(1,2); x= p(1,1);
% The position must be inside the axis it self
if(y<0||y>25||x<0), break; end
if(x>0&&x<size( data.menuitems(i).barimage,2))
% The Mouse is hovering over a menu-button
hover=true;
if(~isempty(data.hov)&&(data.hov~=i))
% If another button is already in hover-modes, set
% that button to normal-look
I=data.menuitems( data.hov).barimage;
set(data.menuitems( data.hov).HandleImshow,'CData',I);
end
data.hov=i;
if(isempty(data.sel))
% Set current button to hover look
I=data.menuitems( data.hov).barimagehover;
set(data.menuitems( data.hov).HandleImshow,'CData',I);
else
% If another button is selected, set that button
% to normal look
if(data.hov~=data.sel)
I=data.menuitems( data.hov).barimagehover;
set(data.menuitems( data.hov).HandleImshow,'CData',I);
end
end
% If another button was already selected, disable the menu
% beneath the button, enable the menu of the hover-button,
% and set it to selected modus.
if(~isempty(data.sel)&&(data.sel~=data.hov))
cMenu=data.cMenu(data.sel);
set(cMenu,'Visible','off');
data.sel=data.hov;
setSelect(data)
end
drawnow('expose');
break;
end
end
if(hover)
setMyData(data,datahandle);
else
% If the mouse isn't above a button reset any past hover-button to
% normal
if(~isempty(data.hov))
I=data.menuitems( data.hov).barimage;
set(data.menuitems( data.hov).HandleImshow,'CData',I);
data.hov=[];
setMyData(data,datahandle);
drawnow('expose');
end
end
% If there is an menubar in selected modus, but his sub-menu already
% disappeared, because the user clicked elsewhere in the figure
% reset also the button in the menubar.
if(~isempty(data.sel))
cMenu=data.cMenu(data.sel);
p=get(cMenu,'Visible');
if(strcmpi(p,'off'))
I=data.menuitems(data.sel).barimage;
set(data.menuitems(data.sel).HandleImshow,'CData',I);
data.sel=[];
setMyData(data,datahandle);
drawnow('expose');
end
end
function [IN,IS,IH]=loadbarimages()
IN(:,:,1) = [254 252 249 246 242 239 235 232 229 211 211 211 212 212 213 214 215 217 218 219 220 222 223 224 225;
254 253 250 248 245 242 239 236 234 218 218 218 219 219 220 221 222 223 224 225 226 227 228 229 230;
255 254 253 252 250 249 248 246 245 237 237 237 237 238 238 239 240 240 241 242 243 243 244 245 245]';
IS(:,:,1) = [254 252 175 106 84 83 82 81 80 74 74 74 74 74 74 75 75 76 76 76 77 77 96 157 225;
254 179 92 145 202 200 206 207 205 193 196 196 200 197 198 199 200 202 202 204 204 207 213 109 156;
254 111 146 187 206 203 206 207 205 193 196 196 200 197 198 199 200 202 202 204 204 207 213 196 96;
254 88 161 185 202 200 205 207 205 193 196 196 200 196 197 199 202 203 206 209 210 212 213 212 79;
254 111 146 169 186 183 191 194 191 181 184 184 188 184 185 187 189 191 193 195 196 198 200 181 96;
254 179 102 147 163 161 166 168 166 158 160 160 163 161 162 162 165 166 167 170 171 172 162 100 156;
254 252 175 106 84 83 82 81 80 74 74 74 74 74 74 75 75 76 76 76 77 77 96 157 225]';
IS(:,:,2) = [254 253 175 107 86 84 83 82 82 76 76 76 76 76 77 77 77 78 78 79 79 79 98 161 230;
254 180 92 146 205 202 209 211 209 199 203 203 206 204 204 205 206 207 207 209 210 212 217 111 160;
254 111 147 189 208 206 210 211 209 199 203 203 206 204 204 205 206 207 207 209 210 212 217 200 98;
254 88 161 186 205 202 208 211 209 199 203 203 206 203 204 205 208 209 212 214 215 216 218 217 80;
254 111 147 171 188 186 195 197 195 187 190 190 194 190 191 193 195 196 198 200 201 202 204 185 98;
254 180 102 148 164 163 168 170 169 162 165 165 167 166 166 167 169 170 171 174 175 175 165 102 160;
254 253 175 107 86 84 83 82 82 76 76 76 76 76 77 77 77 78 78 79 79 79 98 161 230]';
IS(:,:,3) = [255 254 178 109 87 87 87 86 86 83 83 83 83 83 83 83 84 84 84 84 85 85 105 172 245;
255 180 93 148 209 208 217 220 219 217 220 220 223 221 221 222 223 223 223 225 226 227 233 119 170;
255 112 148 192 213 212 218 220 219 217 220 220 223 221 221 222 223 223 223 225 226 227 233 214 105;
255 89 163 189 209 208 216 220 219 217 220 220 223 220 220 222 225 225 228 231 232 232 233 232 86;
255 112 148 173 191 191 202 205 204 202 206 206 209 206 206 208 210 210 212 215 216 216 218 197 105;
255 180 103 150 167 167 174 176 176 174 177 177 179 178 178 179 181 181 183 185 186 186 175 109 170;
255 254 178 109 87 87 87 86 86 83 83 83 83 83 83 83 84 84 84 84 85 85 105 172 245]';
IH(:,:,1) = [254 252 215 181 169 167 164 162 160 147 147 147 148 148 149 149 150 151 152 153 154 155 164 193 225;
254 218 192 242 251 250 248 246 244 235 234 234 233 210 211 214 218 219 223 229 229 233 226 176 193;
254 187 242 252 244 242 237 231 229 214 211 211 209 193 194 197 201 203 208 213 214 219 233 228 165;
254 176 252 248 244 242 237 231 229 214 211 211 209 193 194 197 201 203 208 213 214 219 223 238 157;
254 187 242 252 244 242 237 231 229 214 211 211 209 193 194 197 201 203 208 213 214 219 233 228 165;
254 218 192 242 251 250 248 246 244 235 234 234 233 210 211 214 218 219 223 229 229 233 226 176 193;
254 252 215 181 169 167 164 162 160 147 147 147 148 148 149 149 150 151 152 153 154 155 164 193 225]';
IH(:,:,2) = [254 253 216 183 171 169 167 165 163 152 152 152 153 153 154 154 155 156 156 157 158 158 168 198 230;
254 219 193 243 252 251 249 247 246 238 237 237 237 214 214 217 222 222 226 232 232 235 229 179 198;
254 188 242 253 245 244 239 234 233 219 216 216 215 199 200 203 207 208 213 219 220 224 236 231 169;
254 177 253 249 245 244 239 234 233 219 216 216 215 199 200 203 207 208 213 219 220 224 227 241 161;
254 188 242 253 245 244 239 234 233 219 216 216 215 199 200 203 207 208 213 219 220 224 236 231 169;
254 219 193 243 252 251 249 247 246 238 237 237 237 214 214 217 222 222 226 232 232 235 229 179 198;
254 253 216 183 171 169 167 165 163 152 152 152 153 153 154 154 155 156 156 157 158 158 168 198 230]';
IH(:,:,3) = [255 254 218 186 175 174 173 172 171 165 165 165 165 166 166 167 168 168 168 169 170 170 180 211 245;
255 220 195 244 253 253 252 251 251 247 246 246 246 222 222 226 230 230 234 240 240 243 237 189 210;
255 188 243 254 248 248 245 241 240 233 231 231 229 215 215 218 222 222 228 234 234 238 246 240 180;
255 177 253 251 248 248 245 241 240 233 231 231 229 215 215 218 222 222 228 234 234 238 242 249 171;
255 188 243 254 248 248 245 241 240 233 231 231 229 215 215 218 222 222 228 234 234 238 246 240 180;
255 220 195 244 253 253 252 251 251 247 246 246 246 222 222 226 230 230 234 240 240 243 237 189 210;
255 254 218 186 175 174 173 172 171 165 165 165 165 166 166 167 168 168 168 169 170 170 180 211 245]';
IN=uint8(IN);
IH=uint8(IH);
IS=uint8(IS);
function w=removeOldMenuBar(datahandle)
% This function detects if the uipanel is replaced in the past by
% a menubar, and removes the menubar in the figure, and the stored-data.
data=getMyData(datahandle); if(isempty(data)),return; end
for i=1:length(data.menuitems)
if(ishandle(data.menuitems(i).Handle))
delete(data.menuitems(i).Handle);
end
if(ishandle(data.cMenu(i)))
delete(data.cMenu(i));
end
end
remMyData(datahandle);
w=true;
function remMyData(datahandle)
% Get data struct stored in figure
rmappdata(datahandle,'menubar');
function setMyData(data,datahandle)
% Store data struct in figure
setappdata(datahandle,'menubar',data);
function data=getMyData(datahandle)
% Get data struct stored in figure
data=getappdata(datahandle,'menubar');
|
github
|
jacksky64/imageProcessing-master
|
bitmapplot.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/bitmapplot.m
| 9,087 |
utf_8
|
375759d6ed5becf085537d9f29bcb6c2
|
function I=bitmapplot(x,y,Ibackground,options)
% BITMAPPLOT, Linear plot in bitmap.
%
% Iplot=bitmapplot(x,y,Ibackground,options)
%
% inputs,
% x : a vector with x values
% y : a vector with y values, with same length as x
% Ibackground: the bitmap used as background when a m x n x 3 matrix
% color plots are made, when m x n a greyscale plot.
% options: struct with options such as color
%
% outputs,
% Iplot: The bitmap containing the plotted lines
%
% note,
% Colors are always [r(ed) g(reen) b(lue) a(pha)], with range 0..1.
% when Ibackground is grayscale, the mean of r,g,b is used as grey value.
%
% options,
% options.Color: The color of the line.
% options.FillColor: If this color is set, the region between
% the x and y coordnates will be filled with this color.
% options.LineWidth: Thickness of the line in pixels 1,2,3..n
% options.Marker: The marker type: 'o', '+' or '*'.
% options.MarkerColor: The color of the markers used.
% options.MarkerSize: The size of the markers used
%
% example,
% % Make empty bitmap
% I = zeros([320 256 3]);
%
% % Add a line
% x=rand(1,10)*50+50; y=linspace(1,512,10);
% I=bitmapplot(x,y,I);
%
% % Add a thick red line
% x=rand(1,10)*50+100; y=linspace(1,256,10);
% I=bitmapplot(x,y,I,struct('LineWidth',5,'Color',[1 0 0 1]));
%
% % Add a line with markers
% x=rand(1,10)*50+150; y=linspace(1,256,10);
% I=bitmapplot(x,y,I,struct('Marker','*','MarkerColor',[1 0 1 1],'Color',[1 1 0 1]));
%
% % Add a filled polygon
% x=[1 100 30 100]+200; y=[30 1 250 200];
% I=bitmapplot(x,y,I,struct('FillColor',[0 1 0 0.5],'Color',[1 1 0 1]));
%
% % Add a filled polygon on top
% x=[30 80 70 120]+200; y=[30 1 250 200];
% I=bitmapplot(x,y,I,struct('FillColor',[1 0 0 0.5],'Color',[1 0 0 1]));
%
% lines={'Plot Test,','BitmapPlot version 1.2'};
% % Plot text into background image
% I=bitmaptext(lines,I,[1 1],struct('Color',[1 1 1 1]));
%
% % Show the bitmap
% figure, imshow(I);
%
% Function is written by D.Kroon University of Twente (April 2009)
% Process inputs
defaultoptions=struct('Color',[0 0 1 1],'FillColor',[],'LineWidth',1,'Grid',[],'MarkerColor',[1 0 0 1],'Marker',[],'MarkerSize',6);
if(~exist('options','var')),
options=defaultoptions;
else
tags = fieldnames(defaultoptions);
for i=1:length(tags)
if(~isfield(options,tags{i})), options.(tags{i})=defaultoptions.(tags{i}); end
end
if(length(tags)~=length(fieldnames(options))),
warning('register_images:unknownoption','unknown options found');
end
end
% The function works with double values (store class for ouput)
Classb=class(Ibackground);
Ibackground=im2double(Ibackground);
% Detect if RGB mode
isRGB=size(Ibackground,3)==3;
% x and y to row vectors
x=round(x(:))'; y=round(y(:))';
% Make line, marker an fill bitmap
I_line=zeros([size(Ibackground,1) size(Ibackground,2)]);
I_marker=zeros([size(Ibackground,1)*size(Ibackground,2) 4]);
I_fill = zeros([size(Ibackground,1)+2 size(Ibackground,2)+2]);
% Close the line if, fill color is set
if(~isempty(options.FillColor)), x=[x x(1)]; y=[y y(1)]; end
% Get all Pixels of the line
pline = arrayfun(@(i)(LinePixels(x,y,i)), 1:(length(x)-1), 'UniformOutput', false);
pline=[pline{:}];
if(~isempty(pline))
xline=pline(1,:);
yline=pline(2,:);
else
xline=x; yline=y;
end
% Make closed line structure for fill if FillColor specified.
if(~isempty(options.FillColor))
xline_fill=xline; yline_fill=yline;
% Limit to boundaries
xline_fill(xline_fill<1)=1; yline_fill(yline_fill<1)=1;
xline_fill(xline_fill>size(I_line,1))=size(I_line,1);
yline_fill(yline_fill>size(I_line,2))=size(I_line,2);
% I_fill is one pixel larger than I_line to allow background fill
xline_fill=xline_fill+1; yline_fill=yline_fill+1;
% Insert all pixels in the fill image
I_fill(round(xline_fill)+(round(yline_fill)-1)*size(I_fill,1))=1;
% Fill the line image I_fill
I_fill=bwfill(I_fill,1,1); I_fill=1-I_fill(2:end-1,2:end-1);
% Adjust the fill with alpha value
I_fill=I_fill*options.FillColor(4);
end
if(options.LineWidth==1)
% Remove pixels outside image
xline1=xline; yline1=yline;
check=(xline1<1)|(yline1<1)|(xline1>size(I_line,1))|(yline1>size(I_line,2));
xline1(check)=[]; yline1(check)=[];
% Insert all pixels in the line image
I_line(round(xline1)+round(yline1-1)*size(I_line,1))=1;
elseif(options.LineWidth>1) % Add more pixel is line-width is larger than 1...
% Calculate normal on line
ang=[yline(end)-yline(1) xline(end)-xline(1)]; ang=ang./(0.00001+sqrt(sum(ang.^2)));
for j=-((options.LineWidth-1)/2):((options.LineWidth-1)/2);
% Make lines close to the other lines
xline1=xline+(ang(1)*j); yline1=yline-(ang(2)*j);
% Remove pixels outside image
check=(xline1<1)|(yline1<1)|(xline1>size(I_line,1))|(yline1>size(I_line,2));
xline1(check)=[]; yline1(check)=[];
% Insert all pixels in the line image
I_line(ceil(xline1)+floor(yline1-1)*size(I_line,1))=1;
I_line(floor(xline1)+floor(yline1-1)*size(I_line,1))=1;
I_line(ceil(xline1)+ceil(yline1-1)*size(I_line,1))=1;
I_line(floor(xline1)+ceil(yline1-1)*size(I_line,1))=1;
end
end
% Adjust the lines with alpha value
I_line=I_line*options.Color(4);
% Make marker image
if(~isempty(options.Marker))
% Make marker pixels (center 0,0)
switch(options.Marker)
case '+'
markerx=[-(options.MarkerSize/2):(options.MarkerSize/2) zeros(1,options.MarkerSize+1)];
markery=[zeros(1,options.MarkerSize+1) -(options.MarkerSize/2):(options.MarkerSize/2)];
case '*'
markerx=[-(options.MarkerSize/2):(options.MarkerSize/2) zeros(1,options.MarkerSize+1)];
markery=[zeros(1,options.MarkerSize+1) -(options.MarkerSize/2):(options.MarkerSize/2)];
markerx=[markerx -(options.MarkerSize/2):(options.MarkerSize/2) -(options.MarkerSize/2):(options.MarkerSize/2)];
markery=[markery -(options.MarkerSize/2):(options.MarkerSize/2) (options.MarkerSize/2):-1:-(options.MarkerSize/2)];
case 'o'
step=360/(2*pi*options.MarkerSize);
markerx=options.MarkerSize/2*sind(0:step:90);
markery=options.MarkerSize/2*cosd(0:step:90);
markerx=[markerx -markerx markerx -markerx];
markery=[markery markery -markery -markery];
end
% Add all line markers to the marker image
isColorTable=size(options.MarkerColor,1)==length(x);
for i=1:length(x);
% Move marker to line coordinate
xp=round(markerx)+round(x(i)); yp=round(markery)+round(y(i));
% Remove outside marker pixels
check=(xp<1)|(yp<1)|(xp>size(I_line,1))|(yp>size(I_line,2));
xp(check)=[]; yp(check)=[];
ind=xp+(yp-1)*size(I_line,1);
if(isColorTable), k=i; else k=1; end
I_marker(ind,1)=options.MarkerColor(k,1);
I_marker(ind,2)=options.MarkerColor(k,2);
I_marker(ind,3)=options.MarkerColor(k,3);
I_marker(ind,4)=options.MarkerColor(k,4);
end
I_marker=reshape(I_marker,[size(Ibackground,1) size(Ibackground,2) 4]);
end
% Add lines, markers and fill in the right colors in the image
I=Ibackground;
if(isRGB)
% Color image
for i=1:3
if(~isempty(options.FillColor)),
I(:,:,i)=I(:,:,i).*(1-I_fill)+options.FillColor(i)*(I_fill);
end
I(:,:,i)=I(:,:,i).*(1-I_line)+options.Color(i)*(I_line);
if(~isempty(options.Marker)),
I(:,:,i)=I(:,:,i).*(1-I_marker(:,:,4))+I_marker(:,:,4).*I_marker(:,:,i);
end
end
else
% Grey scale
if(~isempty(options.FillColor)),
I=I.*(1-I_fill)+mean(options.FillColor(1:3))*(I_fill);
end
I=I.*(1-I_line)+mean(options.Color(1:3))*(I_line);
if(~isempty(options.Marker)),
I=I.*(1-I_marker(:,:,4))+mean(I_marker(:,:,1:3),3).*(I_marker(:,:,4));
end
end
% Set to range 0..1
I(I>1)=1; I(I<0)=0;
% Back to class background
switch (Classb)
case 'single', I=im2single(I);
case 'int16', I=im2int16(I);
case 'uint8', I=im2uint8(I);
case 'uint16', I=im2uint16(I);
end
function pline=LinePixels(x,y,i)
% Calculate the pixels needed to construct a line of 1 pixel thickness
% between two coordinates.
xp=[x(i) x(i+1)]; yp=[y(i) y(i+1)];
dx=abs(xp(2)-xp(1)); dy=abs(yp(2)-yp(1));
if(dx==dy)
if(xp(2)>xp(1)), xline=xp(1):xp(2); else xline=xp(1):-1:xp(2); end
if(yp(2)>yp(1)), yline=yp(1):yp(2); else yline=yp(1):-1:yp(2); end
elseif(dx>dy)
if(xp(2)>xp(1)), xline=xp(1):xp(2); else xline=xp(1):-1:xp(2); end
yline=linspace(yp(1),yp(2),length(xline));
else
if(yp(2)>yp(1)), yline=yp(1):yp(2); else yline=yp(1):-1:yp(2); end
xline=linspace(xp(1),xp(2),length(yline));
end
pline(1,:)=xline;
pline(2,:)=yline;
|
github
|
jacksky64/imageProcessing-master
|
viewer3d_segment.m
|
.m
|
imageProcessing-master/Matlab Viewer3D/SubFunctions/viewer3d_segment.m
| 10,723 |
utf_8
|
7b38f76dbd5d9b62bc3cdb6a3b682bc5
|
function varargout = viewer3d_segment(varargin)
% VIEWER3D_SEGMENT MATLAB code for viewer3d_segment.fig
% VIEWER3D_SEGMENT, by itself, creates a new VIEWER3D_SEGMENT or raises the existing
% singleton*.
%
% H = VIEWER3D_SEGMENT returns the handle to a new VIEWER3D_SEGMENT or the handle to
% the existing singleton*.
%
% VIEWER3D_SEGMENT('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VIEWER3D_SEGMENT.M with the given input arguments.
%
% VIEWER3D_SEGMENT('Property','Value',...) creates a new VIEWER3D_SEGMENT or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before viewer3d_segment_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to viewer3d_segment_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help viewer3d_segment
% Last Modified by GUIDE v2.5 25-Jan-2011 16:41:31
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @viewer3d_segment_OpeningFcn, ...
'gui_OutputFcn', @viewer3d_segment_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before viewer3d_segment is made visible.
function viewer3d_segment_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to viewer3d_segment (see VARARGIN)
% Choose default command line output for viewer3d_segment
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes viewer3d_segment wait for user response (see UIRESUME)
% uiwait(handles.figure1);
data=getMyData(); if(isempty(data)), return, end
Options=struct('Verbose',false,'nPoints',100,'Wline',0.04,'Wedge',2,'Wterm',0.01,'Sigma1',1,'Sigma2',1,'Alpha',0.2,'Beta',0.2,'Delta',0.1,'Gamma',1,'Kappa',2,'Iterations',100,'GIterations',0,'Mu',0.2,'Sigma3',1);
% Initalize Snake Parameters
n=structfind(data.substorage,'name','viewer3d_segment');
if(isempty(n))
n=length(data.substorage)+1;
data.substorage(n).name='viewer3d_segment';
data.substorage(n).data.Options=Options;
end
setMyData(data);
fn=fields(data.substorage(n).data.Options);
set(handles.listbox2,'String',fn);
listbox2_Callback(hObject, eventdata, handles);
% --- Outputs from this function are returned to the command line.
function varargout = viewer3d_segment_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on button press in pushbutton1.
function pushbutton1_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
% ID's to volume struct location
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
id=data.subwindow(data.axes_select).volume_id_select;
editable=false(1,length(id));
dv2=zeros(1,length(id));
for i=1:length(id)
dv2(i)=structfind(data.volumes,'id',id(i));
editable(i)=data.volumes(dv2(i)).Editable;
end
[editable,i]=sort(editable);
dv2=dv2(i);
dvs2=dv2(1);
n=structfind(data.volumes(dvs).MeasureList,'type','s');
if(isempty(n)), return; end
n=n(end);
vm=data.volumes(dvs).MeasureList(n);
SliceSelected=data.subwindow(data.axes_select).SliceSelected(uint8(data.subwindow(data.axes_select).render_type(6))-119);
switch(vm.RenderSelected)
case {'x'}
I=data.volumes(dvs2).volume_original(SliceSelected,:,:);
y=vm.z; x=vm.y;
case {'y'}
I=data.volumes(dvs2).volume_original(:,SliceSelected,:);
y=vm.z; x=vm.x;
case {'z'}
I=data.volumes(dvs2).volume_original(:,:,SliceSelected);
y=vm.y; x=vm.x;
end
I=double(I);
I=I-min(I(:));
I=I./max(I(:));
% Make an array with the clicked coordinates
P=[x(:) y(:)];
% Start Snake Process
n=structfind(data.substorage,'name','viewer3d_segment');
Options=data.substorage(n).data.Options;
O=Snake2D(I,P,Options);
figure(data.handles.figure1);
x=O(:,1); y=O(:,2);
[x,y]=interpcontour(x,y,zeros(size(x)),2);
switch(vm.RenderSelected)
case {'x'}
vm.z=y; vm.y=x;
case {'y'}
vm.z=y; vm.x=x;
case {'z'}
vm.y=y; vm.x=x;
end
data.volumes(dvs).MeasureList(n)=vm;
setMyData(data);
viewer3d('show3d_Callback',gcf,[false false],guidata(gcf));
% --- Executes on button press in pushbutton2.
function pushbutton2_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
% ID's to volume struct location
dvs=structfind(data.volumes,'id',data.subwindow(data.axes_select).volume_id_select(1));
id=data.subwindow(data.axes_select).volume_id_select;
editable=false(1,length(id));
dv2=zeros(1,length(id));
for i=1:length(id)
dv2(i)=structfind(data.volumes,'id',id(i));
editable(i)=data.volumes(dv2(i)).Editable;
end
[editable,i]=sort(editable);
dv2=dv2(i);
dvs2=dv2(end);
n=structfind(data.volumes(dvs).MeasureList,'type','s');
if(isempty(n)), return; end
n=n(end);
x=data.volumes(dvs).MeasureList(n).x;
y=data.volumes(dvs).MeasureList(n).y;
z=data.volumes(dvs).MeasureList(n).z;
S=data.subwindow(data.axes_select).SliceSelected;
switch (data.volumes(dvs).MeasureList(n).RenderSelected)
case {'x'}
J=squeeze(data.volumes(dvs2).volume_original(S(1),:,:,:));
J=bitmapplot(y,z,J,struct('FillColor',[1 1 1 1],'Color',[1 1 1 1]))>0;
data.volumes(dvs2).volume_original(S(1),:,:,:)=J;
case {'y'}
J=squeeze(data.volumes(dvs2).volume_original(:,S(2),:,:));
J=bitmapplot(x,z,J,struct('FillColor',[1 1 1 1],'Color',[1 1 1 1]))>0;
data.volumes(dvs2).volume_original(:,S(2),:,:)=J;
case {'z'}
J=squeeze(data.volumes(dvs2).volume_original(:,:,S(3),:));
J=bitmapplot(x,y,J,struct('FillColor',[1 1 1 1],'Color',[1 1 1 1]))>0;
data.volumes(dvs2).volume_original(:,:,S(3),:)=J;
end
setMyData(data);
viewer3d('UpdatedVolume_Callback',gcf,dvs2,guidata(gcf));
% --- Executes on selection change in listbox2.
function listbox2_Callback(hObject, eventdata, handles)
% hObject handle to listbox2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = cellstr(get(hObject,'String')) returns listbox2 contents as cell array
% contents{get(hObject,'Value')} returns selected item from listbox2
data=getMyData(); if(isempty(data)), return, end
n=structfind(data.substorage,'name','viewer3d_segment');
fn=fields(data.substorage(n).data.Options);
sel=get(handles.listbox2,'Value');
val=data.substorage(n).data.Options.(fn{sel});
set(handles.edit1,'String',num2str(val));
% --- Executes during object creation, after setting all properties.
function listbox2_CreateFcn(hObject, eventdata, handles)
% hObject handle to listbox2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: listbox controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edit1_Callback(hObject, eventdata, handles)
% hObject handle to edit1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit1 as text
% str2double(get(hObject,'String')) returns contents of edit1 as a double
data=getMyData(); if(isempty(data)), return, end
n=structfind(data.substorage,'name','viewer3d_segment');
fn=fields(data.substorage(n).data.Options);
sel=get(handles.listbox2,'Value');
data.substorage(n).data.Options.(fn{sel})=str2double(get(handles.edit1,'String'));
setMyData(data);
% --- Executes during object creation, after setting all properties.
function edit1_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on key press with focus on edit1 and none of its controls.
function edit1_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to edit1 (see GCBO)
% eventdata structure with the following fields (see UICONTROL)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
% --- Executes on button press in pushbutton3.
function pushbutton3_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton3 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
data=getMyData(); if(isempty(data)), return, end
data.mouse.button='select_roi';
data.mouse.action='segment_roi';
setMyData(data);
|
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