Image File Name Fixed

src/MATLAB/+Helper/GetFullImagePath.m

@@ -3,6 +3,6 @@ global CONSTANTS
 
 image = Helper.GetImageName(frame);
 
-pathString = [CONSTANTS.rootImageFolder image];
+pathString = fullfile(CONSTANTS.rootImageFolder,image);
 end
 

src/MATLAB/+Helper/ImageFileDialog.m

+function ImageFileDialog()
+global CONSTANTS
+
+oldCONSTANTS = CONSTANTS;
+
+load('LEVerSettings.mat');
+
+%find the first image
+imageFilter = [settings.imagePath '*.TIF'];
+
+sigDigits = 0;
+fileName = [];
+tryidx = 0;
+
+while ( (sigDigits == 0) || ~exist(fileName,'file') )
+    if ( tryidx > 0 )
+        fprintf('Image file name not in correct format:%s_t%s.TIF\nPlease choose another...\n',CONSTANTS.datasetName,frameT);
+    else
+        fprintf('\nSelect first .TIF image...\n\n');
+    end
+    
+    [settings.imageFile,settings.imagePath,filterIndexImage] = uigetfile(imageFilter,'Open First Image in dataset: ');
+    if (filterIndexImage==0)
+        CONSTANTS = oldCONSTANTS;
+        return
+    end
+    
+    [sigDigits imageDataset] = Helper.ParseImageName(settings.imageFile);
+    
+    CONSTANTS.rootImageFolder = settings.imagePath;
+    CONSTANTS.datasetName = imageDataset;
+    CONSTANTS.imageSignificantDigits = sigDigits;
+    CONSTANTS.matFullFile = [settings.matFilePath settings.matFile];
+    fileName = Helper.GetFullImagePath(1);
+    
+    tryidx = tryidx + 1;
+end
+
+save('LEVerSettings.mat','settings');
+end
\ No newline at end of file

src/MATLAB/+Segmentation/RewriteSegData.m

 function RewriteSegData(DatasetDir, DatasetName)
 global CONSTANTS CellHulls ConnectedDist
 
-% fname=[CONSTANTS.rootImageFolder '\' CONSTANTS.datasetName '_t' Helper.GetDigitString(1) '.TIF'];
+% fname=Helper.GetFullImagePath(1);
 % im = Helper.LoadIntensityImage(fname);
 % if isempty(im)
 %     fprintf('error - unable to extract image size - tracking will fail\n');

src/MATLAB/+Segmentation/WriteSegData.m

@@ -26,9 +26,7 @@
 
 function WriteSegData(objsSegment,DatasetName)
 
-global CONSTANTS;
-
-fname=[CONSTANTS.rootImageFolder '\' CONSTANTS.datasetName '_t' Helper.GetDigitString(1) '.TIF'];
+fname=Helper.GetFullImagePath(1);
 im = Helper.LoadIntensityImage(fname);
 if isempty(im)
     fprintf('error - unable to extract image size - tracking will fail\n');

src/MATLAB/+Tracker/GetDarkConnectedHulls.m

@@ -31,7 +31,7 @@ global CONSTANTS
 
 th=max([objsSegment.t]);
 
-fname=[CONSTANTS.rootImageFolder '\' CONSTANTS.datasetName '_t' Helper.GetDigitString(1) '.TIF'];
+fname=Helper.GetFullImagePath(1);
 im = Helper.LoadIntensityImage(fname);
 HashedHulls=cell(th,1);
 
@@ -111,7 +111,7 @@ end
 
     function bwHalo=GetHalo(t)
         
-        fname=[CONSTANTS.rootImageFolder '\' CONSTANTS.datasetName '_t' Helper.GetDigitString(t) '.TIF'];
+        fname=Helper.GetFullImagePath(t);
         im = Helper.LoadIntensityImage(fname);
         
         

src/MATLAB/LEVER_SegAndTrackFolders.m

@@ -14,7 +14,7 @@ CONSTANTS=[];
 softwareVersion = '6.1 Adult';
 
 Load.InitializeConstants();
-Load.UpdateFileVersionString(softwareVersion);
+Load.AddConstant('version',softwareVersion,1);
 
 directory_name = uigetdir('','Select Root Folder for Seg and Track');
 if(~directory_name),return,end
@@ -69,7 +69,7 @@ for dd=1:length(dlist)
         continue;
     end
     
-    if ( ~strcmpi(firstimfile, [CONSTANTS.datasetName '_t' Helper.GetDigitString(1) '.TIF']) )
+    if ( ~strcmpi(firstimfile, Helper.GetFullImagePath(1)) )
         fprintf('\n**** Image list does not begin with frame 1 for %s.  Skipping\n\n',CONSTANTS.datasetName);
         continue;
     end

src/MATLAB/Segmentor.m

@@ -28,28 +28,29 @@
 %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-function [objs features levels] = Segmentor(tStart,tStep,tEnd,rootImageFolder,datasetName,imageAlpha,imageSignificantDigits)
-    
+function [objs features levels] = Segmentor(tStart,tStep,tEnd,imageAlpha,rootImageFolder,imageNamePattern)
+global CONSTANTS
+
 objs=[];
 features = [];
 levels = struct('haloLevel',{}, 'igLevel',{});
 
 try
-    if(isempty(dir('.\segmentationData')))
-        system('mkdir .\segmentationData');
-    end
-
     if(ischar(tStart)),tStart = str2double(tStart);end
     if(ischar(tStep)),tStep = str2double(tStep);end
     if(ischar(tEnd)),tEnd = str2double(tEnd);end
     if(ischar(imageAlpha)),imageAlpha = str2double(imageAlpha);end
-    if(ischar(imageSignificantDigits)),imageSignificantDigits = str2double(imageSignificantDigits);end
-
+    
+    fprintf(1,'%s\n',rootImageFolder);
+    fprintf(1,'%s\n',imageNamePattern);
+    
+    CONSTANTS.rootImageFolder = rootImageFolder;
+    CONSTANTS.imageNamePattern = imageNamePattern;
+    
     numImages = tEnd/tStep;
 
     for t = tStart:tStep:tEnd
-        frameT = Helper.GetDigitString(t,imageSignificantDigits);
-        fname=fullfile(rootImageFolder, [datasetName '_t' frameT '.TIF']);
+        fname=Helper.GetFullImagePath(t);
         if(isempty(dir(fname)))
             continue;
         end
@@ -68,7 +69,7 @@ catch excp
     cltime = clock();
     errFilename = ['.\segmentationData\err_' num2str(tStart) '.log'];
     fid = fopen(errFilename, 'w');
-    fprintf(fid, '%02d:%02d:%02.1f - Problem segmenting frame %d\n',cltime(4),cltime(5),cltime(6), t);
+    fprintf(fid, '%02d:%02d:%02.1f - Problem segmenting frame \n',cltime(4),cltime(5),cltime(6));%, t);
     Error.PrintException(fid, excp);
     fclose(fid);
     return;