-
Notifications
You must be signed in to change notification settings - Fork 5
/
AnalyzeMovie.m
222 lines (158 loc) · 5.24 KB
/
AnalyzeMovie.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
function AnalyzeMovie
% AnalyzeMovie - Save analyze images to a kine-loop AVI
%
% Options are the size of the movie and the views.
%
% NOTE ON UNIX THERE IS NO OPTION TO COMPRESS, SO THE
% FILES GET REALLY BIG!!!
%
% I'll work on compression for a windows version - maybe.
%
% $Revision: 1.1 $ $Date: 2004/11/12 01:30:23 $
% Licence: GNU GPL, no express or implied warranties
% 10/2002, Robert C. Welsh <[email protected]>
% University of Michigan, Radiology
% 02/2003, [email protected]
% - attempt to adapt for mri_toolbox, rather than
% depend on spm
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
SCCSid = '0.5';
global BCH; %- used as a flag to know if we are in batch mode or not.
%-GUI setup
%-----------------------------------------------------------------------
SPMid = spm('FnBanner',mfilename,SCCSid);
[Finter,Fgraph,CmdLine] = spm('FnUIsetup','Analyze Movie Maker',0);
fprintf('AnalyzeMovie Toolbox 0.5\n');
spm('FigName','Analyze Image Movie Maker',Finter,CmdLine);
% get the name of the rois file.
movieSize = spm_input_ui('Movie size?','+1','m',...
['Small (200x200)|', ...
'Medium (300x300)|', ...
'Large (400x400)|'],[1 2 3],1);
imageView = spm_input_ui('Image View?','+1','m',...
['Axial|', ...
'Coronal|', ...
'Sagitall|All'],[1 2 3 4],1);
pixSize = [200 300 400];
movieType= ['a' 'c' 's' 'o'];
% smoothing parameters
nMovies = spm_input('Number of movies','+1','i','1',1,[0,Inf]);
if nMovies < 1
spm('alert','Exiting as you requested.','AnalyzeMovie',[],0);
return
end
% change this...
spmImgFiles = {};
for iMovie = 1:nMovies,
% change this...
spmImgFiles{iMovie} = spm_get([0,Inf],'*.img',sprintf(['Pick' ...
' Image files for movie %d'],iMovie),'./',0);
if (length(spmImgFiles{iMovie})< 2)
spm('alert','Exiting as you requested.','AnalyzeMovie',[],0);
return
end
end
% Now extract the files.
figMovie=figure;
close(figMovie);
figMovie=figure(figMovie);
set(figMovie,'visible','off');
set(figMovie,'DoubleBuffer','on');
set(figMovie,'color',[0 0 0]);
curPos = get(figMovie,'Position');
set(figMovie,'Position',[curPos(1) curPos(2) pixSize(movieSize) pixSize(movieSize)]);
for iMovie = 1:nMovies,
[movieDir movieName] = fileparts(spmImgFiles{iMovie}(1,:));
newMovieName = fullfile(movieDir,['kine-loop-' ...
movieType(imageView:imageView) '.avi']);
theMovie = avifile(newMovieName);
% change this...
spm_progress_bar('Init',size(spmImgFiles{iMovie},1),sprintf(['Movie #' ...
' %d of %d'],iMovie,nMovies),'Extracting data');
% change spmImgFiles...
for iFile = 1:size(spmImgFiles{iMovie},1),
spm_progress_bar('Set',iFile);
% change this...
volHdr = spm_vol(spmImgFiles{iMovie}(iFile,:));
slices = movieView(volHdr);
%aVol = spm_read_vols(spm_vol(spmImgFiles{iMovie}(iFile,:)));
%[nX nY nZ] = size(aVol);
%midX = floor(nX/2);
%midY = floor(nY/2);
%midZ = floor(nZ/2);
switch imageView
case 1
aSlice = slices.aS;
%aSlice = squeeze(aVol(:,:,midZ));
case 2
aSlice = rot90(slices.cS,1);
%aSlice = squeeze(aVol(:,midY,:));
case 3
aSlice = rot90(slices.sS,1);
%aSlice = squeeze(aVol(midX,:,:));
case 4
aSlice = slices.ortho;
end
aSlice = aSlice/max(max(max(aSlice)));
aSlice = aSlice*256;
image(aSlice);
axis image;
colormap(gray(256));
curFrame = getframe(gca);
theMovie = addframe(theMovie,curFrame);
end
theMovie=close(theMovie);
end
% Change this...
spm_progress_bar('Clear');
spm_clf(Finter);
spm('FigName','Finished',Finter,CmdLine);
spm('Pointer','Arrow');
close(figMovie);
fprintf('\nFinished making movie : %s\n',newMovieName);
return
%-----------------------------------------------------------
function results = movieView(vHdr)
% A macro to build the views (based on spm_orthoviews)
%
% Robert C. Welsh <[email protected]>
% Radiology, University of Michigan
%
% 2002.10.29, Version 0.1
bb = [-78 -112 -50; 78 76 85];
Dims = diff(bb)'+1;
TM0 = [ 1 0 0 -bb(1,1)+1;...
0 1 0 -bb(1,2)+1;...
0 0 1 0;...
0 0 0 1];
CM0 = [ 1 0 0 -bb(1,1)+1;...
0 0 1 -bb(1,3)+1;...
0 1 1 0;...
0 0 0 1];
SM0 = [ 0 -1 0 -bb(1,2)+1;...
0 0 1 -bb(1,3)+1;...
1 0 0 0;...
0 0 0 1];
TD = [Dims(1) Dims(2)];
CD = [Dims(1) Dims(3)];
SD = [Dims(2) Dims(3)];
notSure = [1 0 0 0; 0 1 0 0 ; 0 0 1 0; 0 0 0 1];
TM = inv(TM0*(notSure\vHdr.mat));
CM = inv(CM0*(notSure\vHdr.mat));
SM = inv(SM0*(notSure\vHdr.mat));
%
% Change this...
axialSlice = spm_slice_vol(vHdr,TM,TD,0);
coronalSlice = spm_slice_vol(vHdr,CM,CD,0);
sagittalSlice = spm_slice_vol(vHdr,SM,SD,0);
results.aS = axialSlice;
results.cS = coronalSlice;
results.sS = sagittalSlice;
bigPix = zeros(Dims(2)+Dims(3),Dims(1)+Dims(2));
bigPix(1:Dims(2),1:Dims(1)) = rot90(axialSlice,1);
bigPix(Dims(2)+1:Dims(2)+Dims(3),1:Dims(1)) = rot90(coronalSlice);
bigPix(Dims(2)+1:Dims(2)+Dims(3),Dims(1)+1:Dims(1)+Dims(2)) = ...
rot90(sagittalSlice);
results.ortho=bigPix;
return