ilastik import script

ctc/reImportIlastik.m

+% function importFolder(infolder,outfolder,expname)
+
+ilastikFolder='/z/Raw/Shipper';
+outfolder='/z/leverjs/ctc2020/2d';
+expname='DIC-C2DH-HeLa_training_01_ix';
+infolder='/z/Raw/2d_DIC-C2DH-HeLa_training/DIC-C2DH-HeLa/01';
+flist=dir(fullfile(infolder,'*.tif'));
+im=[];
+
+imd1=[];
+if exist(fullfile(infolder,'t000.tif'),'file')
+    tFormat='%03d';
+else
+    if exist(fullfile(infolder,'t0000.tif'),'file')
+        tFormat='%04d';
+    else
+        fprintf(2,'importFolder : %s : could not read tif format! no t000 or t0000\n',infolder);
+        return;
+    end
+end
+ 
+for t=1:length(flist)
+    fname=['t' num2str(t-1,tFormat) '.tif'];
+    info=imfinfo(fullfile(infolder,fname));
+    if 1==t
+        try
+            imd1=MicroscopeData.Original.ReadMetadata(infolder,fname);
+        catch
+            imd1.PixelPhysicalSize=[1,1,1];
+        end
+        imd1.NumberOfChannels=2;
+    end
+    im(:,:,1,1,t)=imread(fullfile(infolder,fname));
+    % now let's get the ilastik image
+    fnameIlastik=['t' num2str(t,tFormat) '_Probabilities Stage 2.tiff'];
+    fnameIlastik=fullfile(ilastikFolder,fnameIlastik);
+    if exist(fnameIlastik,'file')
+        imIlastik=imread(fnameIlastik);
+        im(:,:,1,2,t)=imIlastik(:,:,2);
+    end
+end
+im=mat2gray(im);
+imd1.DatasetName=expname;
+writeH5(im,imd1,expname,outfolder);

ctc/writeH5.m

+
+function writeH5(im,imd1,expName,outfolder)
+% make sure leverjsUtilities project is on your path!
+% e.g. path(path,'pathTo\git\utilities\src\MATLAB')
+imd=MicroscopeData.MakeMetadataFromImage(im);
+imd.DatasetName=expName;
+imd.PixelPhysicalSize=imd1.PixelPhysicalSize;
+if (size(imd.Dimensions,2)~=3)
+    imd.Dimensions=[imd.Dimensions 1];
+end
+
+MicroscopeData.WriterH5(im,'imageData',imd,'path',outfolder);