Browse code

moved things

git-svn-id: https://svn.discofish.de/MATLAB/spmtoolbox/SVMCrossVal@127 83ab2cfd-5345-466c-8aeb-2b2739fb922d

Christoph Budziszewski authored on 09/02/2009 16:44:50
Showing 10 changed files
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similarity index 100%
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rename from computeCoordinates.m
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rename to private/computeCoordinates.m
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similarity index 100%
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rename from getProjectBasePath.m
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rename to private/getProjectBasePath.m
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similarity index 100%
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rename from getStudyBasePath.m
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rename to private/getStudyBasePath.m
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new file mode 100644
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@@ -0,0 +1,15 @@
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+function dirs = listDirs(wd)
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+% d = listDirs(dir) returns all directories below dir as a cell array. 
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+% the Structure is the same as from the 'dir' command (because this
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+% function relies on 'dir'
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+% . and .. are filterd. no intetion to include an option switch for those
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+% special dirs.
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+allfiles = dir(wd);
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+nDirs = 1;
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+for i = 1:size(allfiles)
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+    file = allfiles(i);
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+    if file.isdir && file.name(1)~='.'
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+        dirs{nDirs}=file;
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+        nDirs = nDirs +1;
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+    end
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+end
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similarity index 71%
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rename from loadImageFileNamesData.m
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rename to private/loadImageFileNamesData.m
... ...
@@ -15,9 +15,13 @@ for subjectCell = loadParams.subjectCellArray
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     datastruct.(subjectString).images      = getImageFileList(des,loadParams.use_smoothed_image_hack);
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+    subjectPath = fullfile(getStudyBasePath(loadParams.StudyID),SubjectID);
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+    
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     ROIIMAGE = 1;
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     if ROIIMAGE
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         %load ROI Image Header
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-        datastruct.(subjectString).roiImages = readRoiImage(sprintf('Select ROI Images for Subject %s',SubjectID));
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+%         wd = 'C:\Dokumente und Einstellungen\Christoph\Eigene Dateien\Diplomarbeit\data';
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+        wd = subjectPath;
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+        datastruct.(subjectString).roiImages = readRoiImage(sprintf('Select ROI Images for Subject %s',SubjectID),wd);
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     end
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 end
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similarity index 79%
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rename from main.m
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rename to private/main.m
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@@ -4,7 +4,8 @@ switch action
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     case 'COORD-LOOKUP-TABLE'
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         runCoordTable(timeline,parameterModel);
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     case 'ROI-IMAGE-MASK'
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-        runROIImageMaskMode(parameterModel)
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+        runROIImageMaskMode(parameterModel);
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+        disp('DONE');
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     case 'FULL-BRAIN'
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         error('SVMCrossVal:main:notImplemented','Feature not yet implemented');
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     otherwise 
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@@ -12,17 +13,7 @@ switch action
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 end
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 end
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-function runROIImageMaskMode(parameterModel)
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-        loadParams.StudyID = 'CHOICE24';
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-        loadParams.use_smoothed_image_hack = 1;
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-        loadParams.subjectCellArray = getSubjectIDString(parameterModel);
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-        imageStruct = loadImageFileNamesData(loadParams);
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-        assignin('base','imageStruct',imageStruct);
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-        
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-%         coordinateStruct = computeCoordinates(imageStruct);
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-%         assignin('base','coordinateStruct',coordinateStruct);
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-end
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 % generate parameter structs for subroutines
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 function timelineParams = getTimeLineParams(paramModel)
... ...
@@ -139,7 +139,7 @@ DEFAULT.svmoptstring    = '-s 0 -t 0 -v 6 -c 1';
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     set(btnRunButton1,'Callback',{@cbRunCoordTable,model}); % set here, because of model.    
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     set(btnRunButton2,'Callback',{@cbRunROIImage,model}); % set here, because of model.    
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-    set(btnRunButton2,'Enable','off');
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+%     set(btnRunButton2,'Enable','off');
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     uimenu(savemenu,'Label','Save','Callback',{@mcb_save,model});
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     uimenu(savemenu,'Label','Load','Callback',{@mcb_load,model});
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similarity index 100%
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rename from plotDecodePerformance.m
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rename to private/plotDecodePerformance.m
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@@ -1,4 +1,3 @@
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-function imageList = readRoiImage(formatstring)
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-wd = 'C:\Dokumente und Einstellungen\Christoph\Eigene Dateien\Diplomarbeit\data';
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+function imageList = readRoiImage(formatstring,wd)
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 imageList = spm_vol(spm_select([1 Inf],'image',formatstring,[],wd));
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 end
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@@ -0,0 +1,40 @@
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+function runROIImageMaskMode(parameterModel)
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+        loadParams.StudyID = 'CHOICE24';
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+        loadParams.use_smoothed_image_hack = 1;
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+        loadParams.subjectCellArray = getSubjectIDString(parameterModel);
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+
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+        imageStruct = loadImageFileNamesData(loadParams);
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+        assignin('base','imageStruct',imageStruct);
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+        
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+%         coordinateStruct = computeCoordinates(imageStruct);
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+%         assignin('base','coordinateStruct',coordinateStruct);
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+end
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+
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+function extr = claculateRoiImageData(filenameList,roiImageList)
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+
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+V = filenameList;
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+nImage = numel(V);
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+Vm = roiImageList;
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+nRoi = numel(Vm);
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+for kImage=1:nImage
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+    x = []; y = []; z = [];
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+    for iRoiFile = 1:nRoi
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+        [x1 y1] = ndgrid(1:V(k).dim(1),1:V(k).dim(2));
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+        for p = 1:V(k).dim(3) % resample mask Vm(i) in space of V(k)
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+            B = spm_matrix([0 0 -p 0 0 0 1 1 1]);
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+            M = inv(B*inv(V(k).mat)*Vm(iRoiFile).mat);
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+            msk = find(spm_slice_vol(Vm(iRoiFile),M,V(k).dim(1:2),0));
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+            if ~isempty(msk)
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+                z1 = p*ones(size(msk(:)));
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+                x = [x; x1(msk(:))];
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+                y = [y; y1(msk(:))];
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+                z = [z; z1];
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+            end
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+        end
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+        dat = spm_sample_vol(V(k), x, y, z,0);
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+
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+        extr(kImage).dat(iRoiFile) = dat;
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+    end
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+end
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+
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+end
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