refactor! everything moves

src/+ImportExport/ctc2lever.m

+%  ctc2lever
+% import ctc format tiff folder into .LEVER
+function h5File=ctc2lever(filename,outpath,expName)
+
+h5File=[];
+if ~exist('gtFile','var')
+    gtFile=[];
+end
+if ~exist('expName','var')
+    expName=[];
+end
+
+[~,~,ext]=fileparts(filename);
+
+h5File=importFolder(filename,outpath,expName);
+
+Import.leverImport([],outpath,h5File);
+4;
+
+function h5File=importFolder(folder,outfolder,expName)
+
+h5File=[];
+parts=strsplit(folder,filesep);
+if isempty(expName)
+    expName=[parts{end-1} '_challenge_' parts{end}];
+end
+h5File=fullfile(outfolder,[expName '.h5']);
+if exist(h5File,'file')
+    return
+end
+
+fprintf(1,'importing folder %s -> %s\n',folder, h5File);
+
+flist=dir(fullfile(folder,'*.tif'));
+im=[];
+
+imd1=[];
+
+for t=1:length(flist)
+    fname=['t' num2str(t-1,'%03d') '.tif'];
+    if ~exist(fullfile(folder,fname),'file')
+        fname=['t' num2str(t-1,'%04d') '.tif'];
+    end
+    info=imfinfo(fullfile(folder,fname));
+    if 1==t
+        try
+            imd1=MicroscopeData.Original.ReadMetadata(folder,fname);
+        catch
+            imd1.PixelPhysicalSize=[1,1,1];
+        end
+        
+    end    
+    
+    for z=1:length(info)
+        im(:,:,z)=imread(fullfile(folder,fname),z);
+    end
+    if 1==t        
+        imd=MicroscopeData.MakeMetadataFromImage(im);
+        imd.DatasetName=expName;
+        imd.NumberOfFrames = length(flist);
+        imd.PixelPhysicalSize=imd1.PixelPhysicalSize;
+        if (size(imd.Dimensions,2)~=3)
+            imd.Dimensions=[imd.Dimensions 1];
+        end
+        Import.prepareH5(h5File,imd);
+    end
+    % ACK - mat2gray here??!?
+    im=mat2gray(im);
+    Import.appendH5Frame(h5File,im,t);
+end
+

src/importExport.m → src/+ImportExport/lever2ctc.m

 % importExport.m
 % mcc -m importExport.m -a D:\Andy\git\leverjs\matlab\sqlite-jdbc-3.21.0.jar -a ./assignment
-function bExport=importExport(filename,outpath,config, gtFile)
+function [bExport,h5File]=importExport(filename,outpath,config, gtFile,expName)
 tic
 
+h5File=[];
 if ~exist('gtFile','var')
     gtFile=[];
 end
+if ~exist('expName','var')
+    expName=[];
+end
 
 [~,~,ext]=fileparts(filename);
 
@@ -13,7 +17,7 @@ if strcmp(ext,'.LEVER')
     bExport=export(filename,outpath,config,gtFile);
 elseif exist(filename,'dir')
     bExport=false;
-    importFolder(filename,outpath);
+    h5File=importFolder(filename,outpath,expName);
 else
     fprintf(2,'error - argument unknown (tif or .lever): %s\n',filename);
 end
@@ -26,14 +30,18 @@ else
 end
 4;
 
-function importFolder(folder,outfolder)
+function h5File=importFolder(folder,outfolder,expName)
 
+h5File=[];
 parts=strsplit(folder,filesep);
-expname=[parts{end-1} '_challenge_' parts{end}];
-if exist(fullfile(outfolder,[expname '.h5']),'file')
+if isempty(expName)
+    expName=[parts{end-1} '_challenge_' parts{end}];
+end
+h5File=fullfile(outfolder,[expName '.h5']);
+if exist(h5File,'file')
     return
 end
-h5File=fullfile(outfolder,[expname '.h5']);
+
 fprintf(1,'importing folder %s -> %s\n',folder, h5File);
 
 flist=dir(fullfile(folder,'*.tif'));
@@ -61,7 +69,8 @@ for t=1:length(flist)
     end
     if 1==t        
         imd=MicroscopeData.MakeMetadataFromImage(im);
-        imd.DatasetName=expname;
+        imd.DatasetName=expName;
+        imd.NumberOfFrames = length(flist);
         imd.PixelPhysicalSize=imd1.PixelPhysicalSize;
         if (size(imd.Dimensions,2)~=3)
             imd.Dimensions=[imd.Dimensions 1];