Fixes/Updates to SegAndTrackFolders for new initialization order/name parsing.

src/MATLAB/+Segmentation/SegAndTrackDataset.m

@@ -46,7 +46,10 @@ function [status tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, imag
         system('mkdir .\segmentationData');
     end
     
-    dirName = fileparts(CONSTANTS.rootImageFolder);
+    [dirName chkFile] = fileparts(CONSTANTS.rootImageFolder);
+    if ( ~isempty(chkFile) )
+        dirName = fullfile(dirName, chkFile);
+    end
     for i=1:numProcessors
          system(['start Segmentor ' num2str(i) ' ' num2str(numProcessors) ' ' ...
             num2str(numberOfImages) ' ' CONSTANTS.cellType ' ' ...
@@ -80,7 +83,7 @@ function [status tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, imag
         % Collect segmentation error logs into one place
         errlog = fopen([datasetName '_seg_error.log'], 'w');
         for i=1:length(bSegFileExists)
-            if ( bSegFileExists )
+            if ( bSegFileExists(i) )
                 continue;
             end
             fprintf(errlog, '----------------------------------\n');

src/MATLAB/LEVER_SegAndTrackFolders.m

@@ -11,10 +11,10 @@ global CONSTANTS softwareVersion;
 
 CONSTANTS=[];
 
-softwareVersion = '6.1 Adult';
+softwareVersion = '7.1 Multi-Cell';
 
-Load.InitializeConstants();
-Load.AddConstant('version',softwareVersion,1);
+cellType = Load.QueryCellType();
+Load.AddConstant('cellType',cellType,1);
 
 directory_name = uigetdir('','Select Root Folder for Seg and Track');
 if(~directory_name),return,end
@@ -51,13 +51,23 @@ for dd=1:length(dlist)
     end
         
     CONSTANTS.rootImageFolder = [directory_name filesep dlist(dd).name];
-    CONSTANTS.datasetName = dlist(dd).name;
+    CONSTANTS.datasetName = [dlist(dd).name '_'];
     CONSTANTS.matFullFile = fullfile(outputDir, [CONSTANTS.datasetName '_LEVer.mat']);
     
+    flist = dir(fullfile(CONSTANTS.rootImageFolder,'*.tif'));
+    if ( isempty(flist) )
+        continue;
+    end
+    
+    Helper.ParseImageName(flist(1).name);
+    
     if exist(CONSTANTS.matFullFile,'file')
         continue
     end
     
+    Load.InitializeConstants();
+    Load.AddConstant('version',softwareVersion,1);
+    
     fprintf('seg&track file : %s\n',CONSTANTS.datasetName);
     tic
     CONSTANTS.imageAlpha=1.5;
@@ -69,7 +79,7 @@ for dd=1:length(dlist)
         continue;
     end
     
-    if ( ~strcmpi(firstimfile, Helper.GetFullImagePath(1)) )
+    if ( ~strcmpi(firstimfile, Helper.GetImageName(1)) )
         fprintf('\n**** Image list does not begin with frame 1 for %s.  Skipping\n\n',CONSTANTS.datasetName);
         continue;
     end
@@ -80,7 +90,7 @@ for dd=1:length(dlist)
         continue;
     end
     
-    UI.SaveData(1);
+    Helper.SaveLEVerState([CONSTANTS.matFullFile]);
 
     Error.LogAction('Segmentation time - Tracking time',tSeg,tTrack);
 end %dd