Changed how image names are handled

src/MATLAB/+Helper/GetFullImagePath.m

+function pathString = GetFullImagePath(frame)
+global CONSTANTS
+
+image = Helper.GetImageName(frame);
+
+pathString = [CONSTANTS.rootImageFolder image];
+end
+

src/MATLAB/+Helper/GetImageName.m

+function imageName = GetImageName(frame)
+global CONSTANTS
+
+imageName = sprintf(CONSTANTS.imageNamePattern,frame);
+end
+

src/MATLAB/+Helper/ParseImageName.m

 % [sigDigits imageDataset] = ParseImageName(imageName)
 
-function [sigDigits imageDataset] = ParseImageName(imageName)
-    sigDigits = 0;
+function [sigDigits imageDataset] = ParseImageName(imageName)    
+    tIndex = strfind(imageName,'t');
     
-    index = strfind(imageName,'_t');
-    if ( ~isempty(index) )
-        indexEnd = strfind(imageName,'.');
-        sigDigits = indexEnd - index - 2;
-        
-        imageDataset = imageName(1:(index(length(index))-1));
+    if (isempty(tIndex))
+        error('File name does not have time component: %s',imageName);
     end
+    
+    endIndex = strfind(imageName,'.');
+    tIndex = tIndex(find(tIndex<endIndex,1,'last'));
+    
+    if (tIndex+1==endIndex)
+        %TODO the t comes after the number
+        error('File name pattern is not yet supported: %s',imageName);
+    end
+    
+    nanIndex = tIndex;
+    for i=1:endIndex-tIndex
+        if(isnan(str2double(imageName(tIndex+i))))
+            nanIndex = tIndex+i;
+            break;
+        end
+    end
+    
+    if (nanIndex~=tIndex)
+        endIndex = nanIndex;
+    end
+    
+    sigDigits = endIndex - tIndex - 1;
+    imageDataset = imageName(1:(tIndex)-1);
+    
+    imageNamePattern = [imageDataset 't%0' num2str(sigDigits) 'd' imageName(endIndex:end)];
+    Load.AddConstant('imageNamePattern',imageNamePattern,1);
 end
\ No newline at end of file

src/MATLAB/+Load/AddImagePixelsField.m

@@ -43,7 +43,7 @@ function AddImagePixelsField()
     for t=1:length(HashedCells)
         progress = progress+1;
         UI.Progressbar(progress/iterations);
-        imgfname = [CONSTANTS.rootImageFolder CONSTANTS.datasetName '_t' Helper.GetDigitString(t) '.TIF'];
+        imgfname = Helper.GetFullImagePath(t);
         curimg = Helper.LoadIntensityImage(imgfname);
 
         hullIdx = [HashedCells{t}.hullID];

src/MATLAB/+Load/FindSegLevels.m

@@ -14,7 +14,7 @@ function FindSegLevels(bShowProgress)
             UI.Progressbar((t-1)/length(HashedCells));
         end
         
-        fileName = [CONSTANTS.rootImageFolder CONSTANTS.datasetName '_t' Helper.GetDigitString(t) '.TIF'];
+        fileName = Helper.GetFullImagePath(t);
         if exist(fileName,'file')
             im = Helper.LoadIntensityImage(fileName);
         else

src/MATLAB/+Load/OpenData.m

@@ -44,16 +44,14 @@ else
     save('ColorScheme','colors');
 end
     
-if (~exist('settings','var') || isempty(settings))
-    if (exist('LEVerSettings.mat','file'))
-        load('LEVerSettings.mat');
-    else
-        settings.imagePath = '.\';
-        settings.matFilePath = '.\';
-    end
+
+if (exist('LEVerSettings.mat','file'))
+    load('LEVerSettings.mat');
+else
+    settings.imagePath = '.\';
+    settings.matFilePath = '.\';
 end
 
-filterIndexImage = 0;
 goodLoad = 0;
 opened = 0;
 
@@ -111,7 +109,7 @@ while ( (sigDigits == 0) || ~exist(fileName,'file') )
     CONSTANTS.imageDatasetName = imageDataset;
     CONSTANTS.datasetName = imageDataset;
     CONSTANTS.imageSignificantDigits = sigDigits;
-    fileName = [CONSTANTS.rootImageFolder imageDataset '_t' Helper.GetDigitString(1) '.TIF'];
+    fileName = Helper.GetFullImagePath(1);
 
     tryidx = tryidx + 1;
 end

src/MATLAB/+Segmentation/AddNewSegmentHull.m

@@ -27,7 +27,7 @@
 function newTrackID = AddNewSegmentHull(clickPt, time)
     global CONSTANTS
 
-    filename = [CONSTANTS.rootImageFolder CONSTANTS.datasetName '_t' Helper.GetDigitString(time) '.TIF'];
+    filename = Helper.GetFullImagePath(time);
     img = Helper.LoadIntensityImage(filename);
     
     [newObj newFeat] = Segmentation.PartialImageSegment(img, clickPt, 200, 1.0);

src/MATLAB/+Segmentation/HematoSegmentation.m

@@ -20,7 +20,7 @@ CellHulls = struct(...
     'userEdited',       {});
 
 for i=1:length(dir([CONSTANTS.rootImageFolder '\*.tif']))
-    filename = ['.\segmentationData\' CONSTANTS.datasetName '_t' Helper.GetDigitString(i) '.TIF_seg.txt'];
+    filename = ['.\segmentationData\' Helper.GetImageName(i) '_seg.txt'];
     while (isempty(dir(filename)))
         pause(5);
     end
@@ -46,7 +46,7 @@ for i=1:length(dir([CONSTANTS.rootImageFolder '\*.tif']))
     
 end
 
-im = imread([CONSTANTS.rootImageFolder '\' CONSTANTS.datasetName '_t' Helper.GetDigitString(1) '.TIF']);
+im = imread(Helper.GetFullImagePath(1));
 CONSTANTS.imageSize = size(im);
 
 for i=1:length(CellHulls)

src/MATLAB/+Segmentation/PartialSegDarkCenters.m

 function [bwDark bwig bwHalo xlims ylims] = PartialSegDarkCenters(centerPt, t, imageAlpha)
     global CONSTANTS SegLevels
     
-    fileName = [CONSTANTS.rootImageFolder CONSTANTS.datasetName '_t' Helper.GetDigitString(t) '.TIF'];
+    fileName = Helper.GetFullImagePath(t);
     if exist(fileName,'file')
         im = Helper.LoadIntensityImage(fileName);
     else

src/MATLAB/+Segmentation/ResegmentFromTree.m

@@ -155,7 +155,7 @@ function newHullID = tryAddSegmentation(prevHull)
     global CONSTANTS CellHulls CellFeatures HashedCells Figures
 
     newHullID = [];
-    fileName = [CONSTANTS.rootImageFolder CONSTANTS.datasetName '_t' Helper.GetDigitString(Figures.time) '.TIF'];
+    fileName = Helper.GetFullImagePath(Figures.time);
     img = Helper.LoadIntensityImage(fileName);
     
     clickPt = [CellHulls(prevHull).centerOfMass(2) CellHulls(prevHull).centerOfMass(1)];

src/MATLAB/+UI/DrawCells.m

@@ -37,7 +37,7 @@ if(isempty(CellFamilies(Figures.tree.familyID).tracks)),return,end
 % figure(Figures.cells.handle);
 set(Figures.cells.timeLabel,'String',['Time: ' num2str(Figures.time)]);
 %read in image
-filename = [CONSTANTS.rootImageFolder CONSTANTS.datasetName '_t' Helper.GetDigitString(Figures.time) '.TIF'];
+filename = Helper.GetFullImagePath(Figures.time);
 if exist(filename,'file')
     img = Helper.LoadIntensityImage(filename);
 else