snapshot, working on fbs
Christoph Budziszewski commited on 2009-03-27 14:57:26
Zeige 5 geänderte Dateien mit 195 Einfügungen und 12 Löschungen.
git-svn-id: https://svn.discofish.de/MATLAB/spmtoolbox/SVMCrossVal@166 83ab2cfd-5345-466c-8aeb-2b2739fb922d
- private/fbs_calculateDecodePerformance.m 0000000..3e6a66f
- private/fbs_load_mask.m 0000000..5cf0037
- private/main.m d967c52..e85da0c
- private/runFBSImageMaskMode.m 0000000..3842e46
- private/ui_main.m 1f2cbd2..64e0840
| ... | ... |
@@ -0,0 +1,40 @@ |
| 1 |
+function decode = fbs_calculateDecodePerformance(header,psth,svmopts) |
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| 2 |
+ |
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| 3 |
+RANDOMIZE_DATAPOINTS = header.svmrnd; |
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+ |
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| 5 |
+timeline = header.timeline; |
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| 6 |
+timeline.frameShiftStart = header.frameShift.frameShiftStart; |
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+timeline.frameShiftEnd = header.frameShift.frameShiftEnd; |
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+timeline.decodeDuration = header.frameShift.decodeDuration; |
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+ |
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+timeLineStart = timeline.frameShiftStart; |
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| 11 |
+timeLineEnd = timeline.frameShiftEnd; |
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+ |
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+timePointArgs.pst = psth; |
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+timePointArgs.labelMap = LabelMap(header.classDef.labelCells,header.classDef.conditionCells); |
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+timePointArgs.eventList = header.classDef.eventMatrix; |
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+ |
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+timePointMatrix = buildTimePointMatrix(timeline,timePointArgs); |
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+ |
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+decodePerformance = []; |
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+for index = 1:timeLineEnd-timeLineStart+1 |
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+ |
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+ svmdata = timePointMatrix{index}(:,2:size(timePointMatrix{index},2));
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+ svmlabel = timePointMatrix{index}(:,1);
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+ |
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+ if RANDOMIZE_DATAPOINTS |
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+ rndindex = randperm(length(svmlabel)); |
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+ svmdata = svmdata(rndindex,:); |
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+ svmlabel = svmlabel(rndindex); |
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+ end |
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+ |
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+ decodePerformance = [decodePerformance; svm_single_crossval(svmlabel,svmdata,svmopts)]; |
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+ |
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+ |
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+end |
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+ |
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+decode = decodePerformance; |
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+end |
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+ |
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+ |
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+ |
| ... | ... |
@@ -0,0 +1,18 @@ |
| 1 |
+function subjectStruct = fbs_load_mask(basedir,subjects) |
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+nSubjects = numel(subjects); |
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+ |
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+for s = 1:nSubjects |
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+ |
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+ subjectName = cell2mat(subjects(s)); |
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+ |
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+ subjectStruct{s}.dir = fullfile(basedir,cell2mat(subjects(s)));
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+ d = load(fullfile(subjectStruct{s}.dir,'results','SPM.mat'));
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+ subjectStruct{s}.des = d.SPM;
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+ subjectStruct{s}.name = subjectName;
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+ subjectStruct{s}.roiFile = ui_selectRoiImage(...
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+ sprintf('Select MASK File for %s',subjectName),...
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+ fullfile(subjectStruct{s}.dir,'results'));
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+ |
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+end |
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+ |
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+end |
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| 0 | 19 |
\ No newline at end of file |
| ... | ... |
@@ -49,8 +49,6 @@ switch task |
| 49 | 49 |
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| 50 | 50 |
out.subjectdata = runCoordTable(coordargs); |
| 51 | 51 |
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- assignin('base','preprocessedData',out);
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- |
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| 54 | 52 |
case 'ROI' |
| 55 | 53 |
disp('ROI');
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| 56 | 54 |
out = struct; |
| ... | ... |
@@ -71,8 +69,6 @@ switch task |
| 71 | 69 |
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| 72 | 70 |
out.subjectdata = runROIImageMaskMode(roiargs); |
| 73 | 71 |
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- assignin('base','preprocessedData',out);
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- |
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| 76 | 72 |
case 'FBS' |
| 77 | 73 |
disp('FSB');
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| 78 | 74 |
out = struct; |
| ... | ... |
@@ -81,14 +77,15 @@ switch task |
| 81 | 77 |
out.header.timeline = timeLine; |
| 82 | 78 |
out.header.classDef = classDef; |
| 83 | 79 |
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- fbsargs = struct; |
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- fbsargs.subject = subjects; |
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+ |
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+ out.subjectdata = fbs_load_mask(model.baseDir,subjects); |
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| 86 | 82 |
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| 87 | 83 |
if(size(subjects,2)>1) |
| 88 | 84 |
display(sprintf('No BATCH Support for Searchlight!'));
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| 89 | 85 |
return |
| 90 | 86 |
end |
| 91 | 87 |
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| 88 |
+ fbsargs = struct; |
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| 92 | 89 |
fbsargs.timeline = timeLine; |
| 93 | 90 |
fbsargs.classes = classDef; |
| 94 | 91 |
fbsargs.mask = mask; |
| ... | ... |
@@ -97,9 +94,15 @@ switch task |
| 97 | 94 |
fbsargs.eventList = classDef.eventMatrix; |
| 98 | 95 |
fbsargs.psthOpts = psthOpts; |
| 99 | 96 |
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- out.subjectdata = runFBSImageMaskMode(fbsargs); |
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+ out.header.args = fbsargs; |
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+ |
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+ % no more preprocessing in this step! |
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| 101 | 100 |
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| 102 | 101 |
end |
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+ |
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+assignin('base','preprocessedData',out);
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+ |
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+ |
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| 103 | 106 |
end |
| 104 | 107 |
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| 105 | 108 |
function decode(model,task) |
| ... | ... |
@@ -137,8 +140,9 @@ switch task |
| 137 | 140 |
case 'X-SOM' |
| 138 | 141 |
disp('not implemented')
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| 139 | 142 |
case 'FBS' |
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- disp('not implemented')
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- fbs.radius = getSearchlightRadius(model); |
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+ disp('this method is under high development.')
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+ fbsargs.radius = getSearchlightRadius(model); |
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+ runFBSImageMaskMode(header,data,fbsargs); |
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| 142 | 146 |
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| 143 | 147 |
end |
| 144 | 148 |
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| ... | ... |
@@ -0,0 +1,121 @@ |
| 1 |
+function output = runFBSImageMaskMode(header,subjectdata,fbsargs) |
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+args = header.args; |
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+ |
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+subjects = subjectdata; |
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+nSubjects = numel(subjects); |
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+sessionlist = args.sessionList; |
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+pstopts = args.psthOpts; |
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+pstopts.eventList = args.eventList; |
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+pstopts.sessionList = sessionlist; |
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+ |
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+radius = fbsargs.radius; |
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+ |
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+timeline = header.timeline; |
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+timeline.frameShiftStart = header.frameShift.frameShiftStart; |
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+timeline.frameShiftEnd = header.frameShift.frameShiftEnd; |
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+timeline.decodeDuration = header.frameShift.decodeDuration; |
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+ |
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+timePointArgs.labelMap = LabelMap(header.classDef.labelCells,header.classDef.conditionCells); |
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+timePointArgs.eventList = header.classDef.eventMatrix; |
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+ |
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+timeLineStart = timeline.frameShiftStart; |
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+timeLineEnd = timeline.frameShiftEnd; |
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+ |
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+disp(sprintf('batch processing %g subjects.',nSubjects));
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+ |
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+for s = 1:nSubjects |
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+ |
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+ disp(sprintf('processing subject %s.',subjects{s}.name));
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+ % load image data |
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+ |
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+ disp('fetching volume definitions, please wait');
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+ volumes = spm_vol(getImageFileList(subjects{s}.dir,sessionlist,args.mask));
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+ |
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+ disp('computing volume values, please wait');
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+ |
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+ [extr x y z] = calculateRoiImageData(volumes,subjects{s}.roiFile);
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+ |
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+clear volumes; %save memory ?? |
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+disp('cleared volumes');
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+ |
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+ |
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+ nVoxel = size(extr(1).dat,1); |
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+ |
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+ indexToCoordMap = java.util.HashMap; |
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+ coordToIndexMap = java.util.HashMap; |
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+ for iVoxel = 1:nVoxel |
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+ coord = [x(iVoxel),y(iVoxel),z(iVoxel)]; |
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+ indexToCoordMap.put(iVoxel,coord); |
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+ coordToIndexMap.put(coord,iVoxel); |
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+ end |
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+ |
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+ subjects{s}.indexToCoordMap = indexToCoordMap;
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+ subjects{s}.coordToIndexMap = coordToIndexMap;
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+ |
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+ % calculate psth |
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+ |
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+ warn = warning('off','all');
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+ pstopts.des = subjects{s}.des;
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+ |
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+ disp(sprintf('computing psth for %g voxel.',nVoxel));
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+ |
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+ for iVoxel = 1:nVoxel |
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+ rawdata = []; |
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+ for iImage = 1:length(extr); |
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+ tmp = extr(iImage); |
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+ rawdata = [rawdata tmp.dat(iVoxel)]; |
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+ end |
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+% coordNameHelper = strcat('v',num2str(iVoxel));
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+ pst{iVoxel} = calculatePST(args.timeline,pstopts,rawdata); % do not store in subjectStruct, so we can clear it later.
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+ |
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+ p = iVoxel/nVoxel*100; |
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+ if(mod(iVoxel,nVoxel/100)==0) |
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+ sprintf(' %g%%\t complete',p);
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+ end |
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+ end |
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+ disp('psth done');
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+ warning(warn); |
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+ %run searchlight |
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+ |
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+ |
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+ |
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+ display(sprintf('rastering %g coordinates with approx. %g mm radius',nVoxel,radius));
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+ % for each timeslice |
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+ |
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+ for index = 1:timeLineEnd-timeLineStart+1 |
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+ timeShift = index; |
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+ % center timepoint && relative shift |
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+ frameStart = floor(-globalStart+1+timeShift - 0.5*decodeDuration); |
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+ frameEnd = min(ceil(frameStart+decodeDuration + 0.5*decodeDuration),-globalStart+globalEnd); |
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+ |
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+ |
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+ |
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+ for iVoxel = 1:nVoxel % linear structure avoids 3D-Loop. |
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+ % get coordinate for iVoxel |
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+% coord = |
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+ |
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+ % get surrounding coordinates within radius |
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+% sphere = |
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+ |
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+ % calculate decode performance on these coordinates |
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+ svmdata = timePointMatrix{index}(:,2:size(timePointMatrix{index},2));
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+ svmlabel = timePointMatrix{index}(:,1);
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+ |
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+ if RANDOMIZE_DATAPOINTS |
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+ rndindex = randperm(length(svmlabel)); |
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+ svmdata = svmdata(rndindex,:); |
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+ svmlabel = svmlabel(rndindex); |
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+ end |
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+ decode = svm_single_crossval(svmlabel,svmdata,svmopts); |
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+ % save the decode value to the corresponding coordinate |
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+ end |
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+ |
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+ display('rastering done');
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+ % save data for timeslice |
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+ |
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+ end %for each timeslice |
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+ |
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+ clear pst; %save memory! |
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+end |
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+ |
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| 121 |
+end |
| ... | ... |
@@ -266,10 +266,10 @@ function model = createFirstStepPanel(model,parent,DEFAULT) |
| 266 | 266 |
set(btnRunButton1,'Callback',{@cbRunPreprocessing,model,'COORD'}); % set here, because of model.
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| 267 | 267 |
set(btnRunButton1,'Enable','on'); |
| 268 | 268 |
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| 269 |
- btnRunButton2 = uicontrol(pButtons,'String','run full-brain Searchlight',... |
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| 269 |
+ btnRunButton2 = uicontrol(pButtons,'String',sprintf('use this settings for FBS'),...
|
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| 270 | 270 |
'Units','normalized','Position',[0.33 0 0.33 1]); |
| 271 | 271 |
set(btnRunButton2,'Callback',{@cbRunPreprocessing,model,'FBS'}); % set here, because of model.
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| 272 |
- set(btnRunButton2,'Enable','off'); |
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| 272 |
+ set(btnRunButton2,'Enable','on'); |
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| 273 | 273 |
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| 274 | 274 |
btnRunButton3 = uicontrol(pButtons,'String','run ROI-Image processing',... |
| 275 | 275 |
'Units','normalized','Position',[0.66 0 0.33 1]); |
| ... | ... |
@@ -363,7 +363,7 @@ pSearchlight = uipanel(parent,'Units','normalized','Position',[0.0 0.1 1 0.3]); |
| 363 | 363 |
btnRunFBS = uicontrol(pSearchlight,'String','run Spatiotemporal FB classification',... |
| 364 | 364 |
'Units','normalized',... |
| 365 | 365 |
'Position',[0.0 0.0 1 0.3]); |
| 366 |
- set(btnRunFBS,'Enable','off'); |
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| 366 |
+ set(btnRunFBS,'Enable','on'); |
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| 367 | 367 |
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| 368 | 368 |
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| 369 | 369 |
% button callbacks set here, because of model. |
| 370 | 370 |