/*
 * Cumulative_Z-Project.bsh
 * IJ BAR: https://github.com/tferr/Scripts#scripts
 *
 * BeanShell script that produces cumulative projections using ImageJ's built-in projector
 * ("Image>Stacks>Z Project.."). An immediate application of these progressive projections is
 * the display of trailing paths of moving particles in timelapse experiments. For a demo, run
 * it on Trackmate's sample image ("File>Open Samples>Tracks for TrackMate", in  Fiji/IJ2)
 */

import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.WindowManager;
import ij.gui.GenericDialog;
import ij.plugin.RGBStackConverter;
import ij.plugin.ZProjector;
import ij.process.ImageProcessor;


int startSlice, stopSlice;
int method = ZProjector.MAX_METHOD;
ImagePlus imp;

void run(String arg) {
	imp = WindowManager.getCurrentImage();
	if (invalidImage(imp)) {
		String sample = "http://fiji.sc/samples/FakeTracks.tif";
		if (IJ.showMessageWithCancel("Invalid image",
				"A stack is required but none was found.\nOpen sample image from fiji.sc?")) {
			imp = new ImagePlus(sample);
			if (invalidImage(imp)) {
				IJ.error("Error:\n\"" + sample + "\" could not be retrieved.");
				return;
			}
			imp.show();
		} else
			return;
	}
	if (imp.isComposite()) {
		if (IJ.showMessageWithCancel("Convert to RGB?",
				"Multichannel images must be first converted to RGB.\nConvert?")) {
			(new RGBStackConverter()).convertToRGB(imp);
		} else
			return;
	}
	startSlice = 1;
	stopSlice = (imp.isHyperStack()) ? imp.getNSlices() : imp.getStackSize();
	if (!showDialog(imp))
		return;
	ImagePlus imp2 = cumulativeZProject(imp, method);
	if (imp2 != null) {
		imp2.setCalibration(imp.getCalibration());
		imp2.show();
	}
}

ImagePlus cumulativeZProject(ImagePlus imp, int method) {
	if (method<0 || method>=ZProjector.METHODS.length)
		return null;
	
	if (imp.isHyperStack() && imp.getNFrames() > 1) {
		ZProjector zp = new ZProjector(imp);
		zp.setMethod(method);
		zp.setStartSlice(startSlice);
		zp.setStopSlice(stopSlice);
		zp.doHyperStackProjection(true);
		imp = zp.getProjection();
		startSlice = 1;
		stopSlice = imp.getStackSize();
	}

	ZProjector zp = new ZProjector(imp);
	zp.setMethod(method);
	zp.setStartSlice(startSlice);
	ImageStack stack = new ImageStack(imp.getWidth(), imp.getHeight());
	for (int z = startSlice; z <= stopSlice; z++) {
		zp.setStopSlice(z);
		if (imp.getBitDepth() == 24)
			zp.doRGBProjection(true);
		else
			zp.doProjection(true);
		ImageProcessor ip = zp.getProjection().getProcessor();
		stack.addSlice("Proj " + startSlice + "-" + z, ip);
   }
   return new ImagePlus(WindowManager.makeUniqueName("CumulativeProj_" + imp.getTitle()), stack);
}

boolean invalidImage(ImagePlus imp) {
	return imp == null || (imp != null && imp.getStackSize() == imp.getNChannels());
}

boolean showDialog(ImagePlus imp) {
	GenericDialog gd = new GenericDialog("Cumulative Z-Project");
	gd.addSlider("Start slice:", startSlice, stopSlice, startSlice);
	gd.addSlider("Stop slice:", startSlice, stopSlice, stopSlice);
	gd.addChoice("Projection type:", ZProjector.METHODS, ZProjector.METHODS[method]);
	gd.addHelp("https://github.com/tferr/Scripts/tree/master/Annotation#cumulative-z-project");
	gd.showDialog();
	if (gd.wasCanceled())
		return false;
	startSlice = (int)Math.min(1, gd.getNextNumber());
	stopSlice = (int)Math.max(stopSlice, gd.getNextNumber());
	method = gd.getNextChoiceIndex();
	return true;
}

run("");