Segmentation Call Fixes

src/MATLAB/+Segmentation/HematoSegmentation.m

@@ -7,7 +7,10 @@ minVol = 175;
 % catch errorMessage
 %     %fprintf(errorMessage);
 % end
-system(['start HematoSeg.exe ' CONSTANTS.rootImageFolder '* ' num2str(imageAlpha) ' ' num2str(minVol) ' ' num2str(eccentricity) ' 1.0 && exit']);
+
+fprintf(1,'Segmentation...');
+
+system(['start HematoSeg.exe ' CONSTANTS.rootImageFolder '* ' num2str(imageAlpha) ' ' num2str(minVol) ' ' num2str(eccentricity) ' .75 && exit']);
 
 pause(5);
 CellHulls = struct(...
@@ -47,7 +50,7 @@ for i=1:length(dir([CONSTANTS.rootImageFolder '\*.tif']))
 end
 
 im = imread(Helper.GetFullImagePath(1));
-CONSTANTS.imageSize = size(im);
+Load.AddConstant('imageSize',size(im),1);
 
 for i=1:length(CellHulls)
     [r c] = ind2sub(CONSTANTS.imageSize,CellHulls(i).indexPixels);
@@ -55,5 +58,6 @@ for i=1:length(CellHulls)
     CellHulls(i).points = [c(ch) r(ch)];
 end
 
+fprintf(1,'Done\n');
 end
 

src/MATLAB/+Segmentation/SegAndTrackDataset.m

 function [status tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, imageAlpha, sigDigits, numProcessors)
-    global SegLevels CONSTANTS
+    global CONSTANTS
     
     status = 1;
     tSeg = 0;
@@ -22,11 +22,15 @@ function [status tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, imag
     fprintf('Segmenting (using %s processors)...\n',num2str(numProcessors));
 
     if(~isempty(dir('.\segmentationData')))
-        system('rmdir /S /Q .\segmentationData');
+        errFile = '.\segmentationData\err_*.log';
+        fileName = '.\segmentationData\objs_*.mat';
+        semFile = '.\segmentationData\done_*.txt';
+        system(['del /Q' errFile ' ' fileName ' ' semFile]);
+%         system('rmdir /S /Q .\segmentationData');
     end
     
     % Set CONSTANTS.imageSize as soon as possible
-    firstImg = fullfile(rootFolder, [datasetName '_t' Helper.GetDigitString(1,sigDigits) '.TIF']);
+    firstImg = Helper.GetFullImagePath(1);
     chkIm = Helper.LoadIntensityImage(firstImg);
     CONSTANTS.imageSize = size(chkIm);
     
@@ -38,12 +42,17 @@ function [status tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, imag
         return;
     end
     
+    if(isempty(dir('.\segmentationData')))
+        system('mkdir .\segmentationData');
+    end
+    
+    dirName = fileparts(CONSTANTS.rootImageFolder);
     for i=1:numProcessors
-        system(['start Segmentor ' num2str(i) ' ' num2str(numProcessors) ' ' ...
-            num2str(numberOfImages) ' "' rootFolder '" "' datasetName '" ' ...
-            num2str(imageAlpha) ' ' num2str(sigDigits) ' && exit']);
+         system(['start Segmentor ' num2str(i) ' ' num2str(numProcessors) ' ' ...
+            num2str(numberOfImages) ' ' ...
+            num2str(imageAlpha) ' "' dirName '" ' CONSTANTS.imageNamePattern ' && exit']);
         %use line below instead of the 3 lines above for non-parallel or to debug
-        % Segmentor(i,numProcessors,numberOfImages,rootFolder,datasetName,imageAlpha,sigDigits);
+%         Segmentor(i,numProcessors,numberOfImages,imageAlpha,dir,CONSTANTS.imageNamePattern);
     end
 
     bSegFileExists = false(1,numProcessors);
@@ -146,12 +155,10 @@ function [status tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, imag
 
     %% Inport into LEVer's data sturcture
     [objHulls gConnect HashedHulls] = Tracker.ReadTrackData(CONSTANTS.imageSize, cellSegments, datasetName);
-    
-    SegLevels = cellSegLevels;
 
     fprintf('Finalizing Data...');
     try
-        Tracker.ConvertTrackingData(objHulls,gConnect,cellFeat);
+        Tracker.ConvertTrackingData(objHulls,gConnect);
     catch excp
         
         cltime = clock();
@@ -164,10 +171,6 @@ function [status tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, imag
         return;
     end
     
-    % Adds the special origin action, to indicate that this is initial
-    % segmentation data from which edit actions are built.
-    Editor.ReplayableEditAction(@Editor.OriginAction, 1);
-    
     fprintf('Done\n');
     
     clear cellSegments;

src/MATLAB/+Tracker/HematoTracker.m

 function HematoTracker()
-    global CONSTANTS CellHulls HashedCells CellFeatures ConnectedDist
+    global CONSTANTS CellHulls HashedCells ConnectedDist
     
     bKeep = (~[CellHulls.deleted]);
     CellHulls = CellHulls(bKeep);
     
-    segtimes = [CellHulls.time];
-    
-    [srtseg srtidx] = sort(segtimes);
-    [dump idxmap] = sort(srtidx);
-    
-    CellHulls = CellHulls(srtidx);
-    if (~isempty(CellFeatures))
-        CellFeatures = CellFeatures(srtidx);
-    end
-    
-%     newConnectedDist = ConnectedDist(srtidx);
-%     for i=1:length(newConnectedDist)
-%         if ( isempty(newConnectedDist{i}) )
-%             continue;
-%         end
-%         
-%         newConnectedDist{i}(:,1) = idxmap(newConnectedDist{i}(:,1))';
-%     end
-    
     tmax = max([CellHulls.time]);
     HashedCells = cell(1,tmax);
     for t=1:tmax
@@ -48,13 +29,14 @@ function HematoTracker()
     
     fnameIn=['.\segmentationData\SegObjs_' CONSTANTS.datasetName '.txt'];
     fnameOut=['.\segmentationData\Tracked_' CONSTANTS.datasetName '.txt'];
-    tic
+    
     fprintf(1,'Tracking...');
     system(['.\MTC.exe ' num2str(CONSTANTS.dMaxCenterOfMass) ' ' num2str(CONSTANTS.dMaxConnectComponentTracker) ' "' fnameIn '" "' fnameOut '" > out.txt']);
     fprintf('Done\n');
-    tTrack=toc;
     
-    [objTracks gConnect oldHashedHulls] = Tracker.RereadTrackData('segmentationData', CONSTANTS.datasetName);
+    fprintf(1,'Importing Tracking Results...');
+    [objTracks gConnect] = Tracker.RereadTrackData('segmentationData', CONSTANTS.datasetName);
+    fprintf('Done\n');
     
     fprintf('Finalizing Data...');
     Tracker.RebuildTrackingData(objTracks, gConnect);