OpenImagesInImage5D.txt

requires("1.42k"); 
argument = getArgument;

tmpDir=getDirectory("temp")+"OpenImagesInImage5D"

if(argument=="") {
	print("Wrong number of arguments");
	exit();
} else {

// Make a tmp dir
	if(File.exists(getDirectory("temp")+"OpenImagesInImage5D")==1){
		cmd="rm -r -f "+tmpDir;
		exec(cmd);
	}
	File.makeDirectory(tmpDir)
	
	argument = split(argument,",");	
	
// Make soft links for the brains
	noImages=0;
	for( i=1; i<argument.length; i++){
//		print(argument[i]);
		if(File.exists(argument[i])==1){
			cmd="ln -s "+ argument[i] + " " + tmpDir + "/tmpFile" + i;
			exec(cmd);
//			print(argument[i]+" exists!");
			noImages=noImages+1;
			
		} else {
			print(argument[i]+" doesn't exist!");
		}
	}
	cmd="open="+tmpDir+"/tmpFile1.nrrd number="+noImages+" starting=1 increment=1 scale=100 file=tmpFile 3rd=z 4th=ch 3rd_dimension_size="+argument[0]+" 4th_dimension_size="+noImages+" assign";
	run("Open Series As Image5D", cmd);
}
	
for( i=1; i<argument.length; i++){
	run("Set Position", "x-position=1 y-position=1 channel="+(i+1)+" slice=100 frame=1 display=overlay");
	resetMinAndMax();
	run("Set Channel Labels", i+"="+File.getName(argument[i]));
}
run("Set Position", "x-position=1 y-position=1 channel=1 slice=1 frame=1 display=overlay");