Updated the tif reader to match the new writer (3D support).

src/MATLAB/+MicroscopeData/ReaderTIF.m

@@ -65,15 +65,17 @@ if (isempty(args.normalize))
         args.normalize = false;
     end
 
-if (~exist(fullfile(imPath,sprintf('%s_c%02d_t%04d_z%04d.tif',imD.DatasetName,1,1,1)),'file'))
+    dList = dir(fullfile(imPath,[imD.DatasetName,'_c*_t*.tif']));
+    if (isempty(dList))
         warning('No image to read!');
         return
     end
 
     useROI = (nnz(args.roi_xyz(:,1:2) ~= [1 1;imD.Dimensions(1:2)]) > 0);
     
-chkFilename = fullfile(imPath,sprintf('%s_c%02d_t%04d_z%04d.tif',imD.DatasetName,1,1,1));
-inType = MicroscopeData.Helper.GetPixelTypeTIF(chkFilename);
+    filePerZ = ~isempty(regexpi(dList(1).name,'.*_z\d+.tif'));
+
+    inType = MicroscopeData.Helper.GetPixelTypeTIF(fullfile(imPath,dList(1).name));
     inIdx = find(strcmp(inType,dataTypeLookup));
     if ( ~isempty(inIdx) )
         inBytes = dataTypeSize(inIdx);
@@ -117,16 +119,13 @@ if ( args.verbose )
             (prod(imSize)*outBytes)/(1024*1024));
     end
 
-if ( args.verbose )
     iter = imSize(5)*length(args.chanList)*imSize(3);
-    cp = Utils.CmdlnProgress(iter,true,sprintf('Reading %s...',imD.DatasetName));
-    i=1;
-end
+    prgs = Utils.CmdlnProgress(iter,true,sprintf('Reading %s...',imD.DatasetName));
 
-tic
     for t=1:imSize(5)
         timeVal = t+args.timeRange(1)-1;
         for c=1:length(args.chanList)
+            if (filePerZ)
                 for z=1:imSize(3)
                     zVal = z+args.roi_xyz(1,3)-1;
 
@@ -136,10 +135,16 @@ for t=1:imSize(5)
                     else
                         im(:,:,z,c,t) = imread(tifName,'TIF');
                     end
-
-            if ( args.verbose )
-                cp.PrintProgress(i);
-                i = i+1;
+                end
+            else
+                tifName = fullfile(imPath,sprintf('%s_c%02d_t%04d.tif',imD.DatasetName,args.chanList(c),timeVal));
+                for z=1:imSize(3)
+                    zVal = z+args.roi_xyz(1,3)-1;
+                    if (convert || useROI)
+                        tempIm(:,:,z) = imread(tifName,'TIF','index',zVal);
+                    else
+                        im(:,:,z,c,t) = imread(tifName,'TIF','index',zVal);
+                    end
                 end
             end
 
@@ -150,12 +155,14 @@ for t=1:imSize(5)
             elseif (useROI)
                 im(:,:,:,c,t) = tempIm(args.roi_xyz(1,2):args.roi_xyz(2,2),args.roi_xyz(1,1):args.roi_xyz(2,1),:);
             end
+            if ( args.verbose )
+                prgs.PrintProgress(c+(t-1)*length(args.chanList));
+            end
         end
     end
 
     if ( args.verbose )
-    cp.ClearProgress(true);
-    fprintf(' took:%s\n',Utils.PrintTime(toc));
+        prgs.ClearProgress(true);
     end
 
     imD.Dimensions = Utils.SwapXY_RC(imSize(1:3));