/*
 * Smoothed_Plot_Profile.bsh
 * IJ BAR: https://github.com/tferr/Scripts#scripts
 *
 * BeanShell script that extends the Analyze>Plot Profile by plotting a simple moving average of
 * profiled data. It also exemplifies how to use BAR libs[1]: The simple moving average calculation
 * is performed by getSimpleMovingAverage(), loaded from BARlib.bsh.
 *
 * NB: In 'Live' mode and with profiled image as the frontmost window, press 'Control' to readjust
 * the number of data points to be used in the moving average calculation.
 *
 * [1] https://github.com/tferr/Scripts/tree/master/lib#lib
 */

import ij.IJ;
import ij.ImagePlus;
import ij.Prefs;
import ij.WindowManager;
import ij.gui.Plot;
import ij.gui.ProfilePlot;
import ij.gui.Roi;
import ij.measure.Calibration;

import java.awt.event.KeyEvent;

/* Ignore the image's spatial calibration? */
boolean pixelUnits = false;

/* Default size for moving average (SMA) window */
int window = 4;

/* Allow interactive refinement of SMA window? */
boolean interactive = true;

ImagePlus imp;		// The image being analyzed
Calibration cal;	// The image's calibration
Roi roi;			// The ROI being profiled
Plot plot;			// The analysis plot
boolean firstRun;	// Flag monitoring first run


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

/* Returns the Plot for the active image/slice */
Plot getPlot() {
	p = getProfilePlot();
	if (p==null) return null;

	//Define sampled data
	rawYvalues = getProfilePlot().getProfile();
	xvalues = assignXvalues(rawYvalues.length);

	// Get new window and generate smoothed data
	if (!firstRun && super.interactive && IJ.controlKeyDown()) {
		IJ.setKeyUp(KeyEvent.VK_CONTROL);
		newWindow = getWindow();
		if (newWindow!=IJ.CANCELED) window = newWindow;
	}
	avgYvalues = super.lib.getSimpleMovingAverage(rawYvalues, window);
	//avgYvalues = super.lib.getGaussian(xvalues, rawYvalues);

	// Prepare plot
	Plot plot = new Plot("Plot of "+ imp.getTitle(), "Distance ("+ cal.getUnits() +")", "Value");
	plot.setLimits(xvalues[0], xvalues[xvalues.length-1], p.getMin(), p.getMax());
	label = (super.interactive) ? "In live mode, press 'Ctrl' to adjust " : "";
	plot.addLabel(0, 0, label + "moving avg. window:  "+ window);

	// Plot data
	plot.setColor(Color.BLUE);
	plot.addPoints(xvalues, rawYvalues, Plot.LINE);
	plot.setColor(Color.RED);
	plot.addPoints(xvalues, avgYvalues, Plot.LINE);

	return plot;
}

/* Returns X 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;
}

/* Returns the moving average window */
int getWindow() {
	return (int)IJ.getNumber("Moving average window:", window);
}

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

/* Returns the spatial calibration of the image */
Calibration getSpatialCalibration() {
	if (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;
}


// Get image to be profiled. Do not proceed if active ROI cannot be profiled
imp = WindowManager.getCurrentImage();
if (imp==void || imp==null) {
	IJ.noImage();
	return;
}
if (invalidRoi(imp.getRoi())) {
	IJ.error("Smoothed Profiler", "Line or rectangular ROI required.");
	return;
}

// Ask user for moving avg. window
if (super.interactive) {
	window = getWindow();
	if (window==IJ.CANCELED) return;
}

// Load BAR/lib/BARlib.bsh
addClassPath(bar.Utils.getBARDir());
importCommands("lib/");
BARlib();
lib = new BARlib();

firstRun = true;
cal = getSpatialCalibration();
plot = getPlot();
if (plot==null) return;
plot.setPlotMaker(this);
plot.show();
firstRun = false;
return;