openStackorRGBinImage5d.txt

// Expects a Stack or an RGB.
// The macro comes with a shortcup key 6.
// You can get this to start up with Fiji
// by going to Plugins->Macros->StartUp Macros...
// and pasting everything in the macro block into the file.

// Made by Aaron Ostrovsky for use because I'm lazy.
// Liberal use of code stolen from OpenImagesInImage5D.txt
// and http://rsb.info.nih.gov/ij/macros/Image5dMacros.txt.
// Code to be used as is or modified, I don't take responsibility,
// blah blah blah...

macro "openStackOrRGBinImage5d... [6]" {
	// Get image ID
	workingImage=getImageID();
	selectImage(workingImage);
	// Get image dimensions
	getDimensions(width, height, channels, slices, frames);
	// check if image is a composite
	if(is("composite")){ 
		run("Stack to Image5D", "3rd=ch 4th=z 3rd_dimension_size="+ channels +" 4th_dimension_size="+ slices +" assign");

	} else {
		run("RGB to Image5D", "3rd=z 3rd_dimension_size="+slices);
	}

	// reset the min/max of each channel at a slice halfway through the stack
	run("Image5D Extensions");
	getDimensions(nw,nh,nch,nsl,nfr);
	for( i=1; i<nch; i++){
		// print("i: " + i);
		// print("channels: "+nch);
		run("Set Position", "x-position=1 y-position=1 channel="+(i+1)+" slice=" + nsl/2 + " frame=1 display=overlay");
		resetMinAndMax();
		//run("Set Channel Labels", i+"="+File.getName(argument[i]));
	}
	// reset position at first slice and force overlay display
	run("Set Position", "x-position=1 y-position=1 channel=1 slice=1 frame=1 display=overlay");
}