mijwrite_stack.m
3e35ee179701cluster_pipeline

mijwrite_stack.m
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			function mijwrite_stack(img,filename,color)

			if nargin<3
			color=0;
			end

			%iProc=ij.process.ImageProcessor();
			stack=ij.ImageStack(size(img,2),size(img,1));
			if color==0
			for i=1:size(img,3)
			%slice=iProc.setFloatArray(img(:,:,i));
			slice=ij.process.FloatProcessor(img(:,:,i)');
			stack.addSlice('metadata',slice);
			end
			else
			for i=1:size(img,4)
			sliceR=ij.process.FloatProcessor(img(:,:,1,i)');
			sliceR=ij.process.ByteProcessor(sliceR,false);
			sliceG=ij.process.FloatProcessor(img(:,:,2,i)');
			sliceG=ij.process.ByteProcessor(sliceG,false);
			sliceB=ij.process.FloatProcessor(img(:,:,3,i)');
			sliceB=ij.process.ByteProcessor(sliceB,false);

			slice=ij.process.ColorProcessor(size(img,2),size(img,1));
			slice.setChannel(1,sliceR);
			slice.setChannel(2,sliceG);
			slice.setChannel(3,sliceB);

			stack.addSlice('metadata',slice);
			end
			end

			iPlus=ij.ImagePlus();
			iPlus.setStack(stack);

			f=ij.io.FileSaver(iPlus);

			f.saveAsTiff(filename);