/*
 * Multichannel_Plot_Profile.bsh
 * IJ BAR: https://github.com/tferr/Scripts#scripts
 *
 * BeanShell script that extends the Analyze>Plot Profile to multichannel (composite) images. It
 * features a "live" option, guesses displayed lookup tables and ignores disabled channels (i.e.,
 * those deselected in the "Channels" widget (which can be called by pressing "Z", the shortcut for
 * "Image>Color>Channels Tool"). Similarly to the built-in Analyze>Plot Profile, Y-axis limits are
 * always set by the active channel.
 *
 * This builds upon Jerome Mutterer's take on a remarkably succinct script using bit-twiddling to
 * detect displayed LUTs (discussed here: https://github.com/tferr/Scripts/issues/6).
 *
 */

import ij.CompositeImage;
import ij.IJ;
import ij.ImagePlus;
import ij.Prefs;
import ij.gui.Plot;
import ij.gui.ProfilePlot;
import ij.gui.Roi;
import ij.measure.Calibration;
import java.util.Arrays;


pixelUnits = false; // Set to true to ignore the image's spatial calibration

/* Returns the ProfilePlot for the active c,z,t position */
ProfilePlot getProfilePlot() {
	roi = imp.getRoi();
	if (roi==null || invalidRoi(roi)) return null;
	averageHorizontally = Prefs.verticalProfile || IJ.altKeyDown();
	return new ProfilePlot(imp, averageHorizontally);
}

/* Returns the multichannel Plot for the active z,t position */
Plot getPlot() {
	p = getProfilePlot();
	n = (p==null) ? 0 : p.getProfile().length;
	if (p==null || n==0) return null;
	xvalues = assignXvalues(n);

	Plot plot = new Plot("Plot of "+ imp.getTitle(), "Distance ("+ cal.getUnits() +")", "Value");
	plot.setLimits(xvalues[0], xvalues[n-1], p.getMin(), p.getMax());

	states = ci.getActiveChannels();
	c = imp.getC(); z = imp.getZ(); t = imp.getT();
	for (ch=1; ch<=imp.getNChannels(); ch++) {
		if (states[ch-1]) {
			imp.setPositionWithoutUpdate(ch, z, t);
			plot.setColor(ci.getChannelColor());
			yvalues = getProfilePlot().getProfile();
			n = Math.min(xvalues.length, yvalues.length);
			plot.addPoints(Arrays.copyOf(xvalues,n), Arrays.copyOf(yvalues,n), Plot.LINE);
		}
	}
	imp.setPositionWithoutUpdate(c, z, t);

	return plot;
}

/* Returns positions in calibrated increments */
double[] assignXvalues(size) {
	xvalues = new double[size];
	for (i=0; i<size; i++)
		xvalues[i] = i * (cal.pixelWidth + cal.pixelHeight)/2;
	return xvalues;
}

/* Checks if roi is of the right type */
boolean invalidRoi(roi) {
	return (roi==null || !(roi.isLine()||roi.getType()==Roi.RECTANGLE));
}

/* Checks if all requirements are met */
boolean invalidRequirements() {
	errorMsg = "";
	if (!imp.isComposite())
		errorMsg += "\nError: Multichannel image required.";
	if (invalidRoi(imp.getRoi()))
		errorMsg += "\nError: Line or rectangular ROI required.";
	invalid = !errorMsg.equals("");
	if (invalid) IJ.error("Multichannel Profiler", errorMsg);
	return invalid;
}

/* Returns the spatial calibration of the profile */
Calibration getSpatialCalibration() {
	if (super.pixelUnits) {
		cal = new Calibration();
		cal.pixelWidth = 1.0;
		cal.pixelHeight = 1.0;
		cal.setUnit("pixel");
	} else
		cal = imp.getCalibration();
	return cal;
}

/* PlotMaker interface */
ImagePlus getSourceImage() {
	return imp;
}


imp = IJ.getImage();
if (invalidRequirements()) return;
ci = (CompositeImage)imp;
cal = getSpatialCalibration();
plot = getPlot();
if (plot==null) return;
plot.setPlotMaker(this);
plot.show();