/**
 * root_tools
 * 
 * The root tools help to efficiently measure the following characteristics of plant roots:
 * - the angle of the opening of the whole root 
 * - the depth to which it goes down
 * - the number of roots at 30 cm depth
 * - the diameters of the roots at depth
 *
 * written 2013 by Volker Baecker (INSERM) at Montpellier RIO Imaging (www.mri.cnrs.fr)
*/

var helpURL = "http://dev.mri.cnrs.fr/wiki/imagej-macros/Root_Tools";

var KNOWN_DISTANCE = 40;		// known distance for spatial calibration (there are 20mm between two nails)
var RADIUS=75;		// radius of the circle drawn around the root point
var ROOT_POINT_LINE_WIDTH = 15; 	// line width of the circle drawn around the root point
var COLOR_ROOT_POINT = "red";	// color of the circle drawn around the root point
var COUNT_ROOT_DEPTH = 30;	// depth from the root point at which the horizontal line is drawn. The number of roots will be counted at that depth
var HALF_LINE_WIDTH = 10;		// half of the width of the line drawn at count root depth
var WIDTH_DEPTH = 8;		// line width of the line drawn at count root depth
var COLOR_DEPTH = "cyan";		// color of the line drawn at count root depth
var DX_ANGLE = 300;		// delta x for the angle tool that is added to the image
var DY_ANGLE = 600;		// delta y for the angle tool that is added to the image
var ANGLE_COLOR = "red";		// the color for marking the measured angle
var ANGLE_LINE_WIDTH = 8;		// the line width for marking the measured angle
var MEASURE_DEPTH_COLOR = "magenta";	// the color of the line indicating the max. depth to which the root goes down
var MEASURE_DEPTH_WIDTH = 8;	// the line width of the line indicating the max. depth to which the root goes down
var ZOOM_RADIUS = 20;		// radius of the region around the click that is copied and zoomed
var DIAMETER_COLOR = "yellow";	// color of the line indicating the measured root diameters
var DIAMETER_WIDTH = 2;		// width of the line indicating the measured root diameters
var ON_IMAGE_OPEN_ON = false;	// if true commands are run when an image is opened
var ON_IMAGE_OPEN_COMMANDS = newArray("Rotate 90 Degrees Left", "Enhance Contrast, saturated=0.35");
var ON_IMAGE_OPEN_COMMANDS_CHECKED = newArray(true, true);
var USE_GLOBAL_SCALE = true;
var rootX;
var rootY;
var deepX;
var deepY;
var UNIT = "mm";
var X1;
var X2;
var Y;
var MAX_ROOTS = 20;
var DIAMETERS = newArray(MAX_ROOTS);
var numberOfRootsAtThirty = 0;
var DEPTH = 0;
var ID = 0;
var ANGLE = 0;
var TITLE;
var NUMBER = 0;
var FOLDER;

macro "AutoRun" {
	script = getJSRemoveAllImageListeners();
	runJS(script);
	ON_IMAGE_OPEN_ON = call("ij.Prefs.get", "roots.on_image_open_on", false);
	if (ON_IMAGE_OPEN_ON) {
		 script = getJSAddListeners();
		 runJS(script);
	}
}

macro "zoomIn [f1]" {
    run("In [+]");
}

macro "zoomOut [f2]" {
    run("Out [-]");
}

macro "Root Tools Help Action Tool- 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" {
	run('URL...', 'url='+helpURL);
}  

macro "Root Tools Help Action Tool Options" {
	ON_IMAGE_OPEN_ON = call("ij.Prefs.get", "roots.on_image_open_on", false);
	Dialog.create("Root Tools - Options");
	Dialog.addCheckbox("auto run commands when image opened", ON_IMAGE_OPEN_ON);
	for (i=0; i<lengthOf(ON_IMAGE_OPEN_COMMANDS_CHECKED); i++) {
		Dialog.setInsets(0, 40, 0);
		Dialog.addCheckbox(ON_IMAGE_OPEN_COMMANDS[i], ON_IMAGE_OPEN_COMMANDS_CHECKED[i]);
	}
	Dialog.show();
	ON_IMAGE_OPEN_ON = Dialog.getCheckbox();
	for (i=0; i<lengthOf(ON_IMAGE_OPEN_COMMANDS_CHECKED); i++) {
		ON_IMAGE_OPEN_COMMANDS_CHECKED[i] = Dialog.getCheckbox();
	}
	script = getJSRemoveAllImageListeners();
	runJS(script);
	if (ON_IMAGE_OPEN_ON) {
		call("ij.Prefs.set", "roots.on_image_open_on", true);
		 script = getJSAddListeners();
		 runJS(script);
	} else {
		call("ij.Prefs.set", "roots.on_image_open_on", false);
	}
}  

macro "Set Scale [f5]" {
	setScale();
}

macro "Define Root Point [f6]" {
	 setTool("Define Root Point Tool");
}

macro "Angle [f7]" {
	measureAngle();
}

macro "Measure Depth [f8]" {
	setTool("Measure Depth Tool");
}

macro "Zoom Region [f9]" {
	setTool("Zoom region Tool");
}

macro "Measure Diameter [f10]" {
	measureDiameter();
}

macro "Write Report [f11]" {
	writeReport();
}

macro "Set Scale Action Tool- C000T4b12s"{
	setScale();
}

macro "Set Scale Action Tool Options" {
	Dialog.create("Root Tools - Set Scale - Options");
	Dialog.addNumber("known distance [cm]: ", KNOWN_DISTANCE);	
	Dialog.addCheckbox("use global scale", USE_GLOBAL_SCALE);
	Dialog.show();
	KNOWN_DISTANCE = Dialog.getNumber();
	USE_GLOBAL_SCALE =  Dialog.getCheckbox();
}

macro "Define Root Point Tool- C000T4b12r" {
	getCursorLoc(x, y, z, flags);
	ID = getImageID();
	TITLE = getTitle();
	FOLDER = getDirectory("image");
	run("Remove Overlay");
	rootX = x;
	rootY = y;
	setColor(COLOR_ROOT_POINT);
	setLineWidth(ROOT_POINT_LINE_WIDTH);
	Overlay.drawEllipse(rootX-RADIUS, rootY-RADIUS, 2*RADIUS+1, 2*RADIUS+1);
	Overlay.show();
	run("Select None");
	lineAtThirtyCM();
	angleSelection();
	setTool("Angle tool");	
}

macro "Define Root Point Tool Options" {
	Dialog.create("Root Tools - Define Root Point - Options");
	Dialog.addNumber("radius: ", RADIUS);
	Dialog.addNumber("line width: ", ROOT_POINT_LINE_WIDTH);
	Dialog.addString("root point color: ", COLOR_ROOT_POINT);
	Dialog.addNumber("depth [cm]: ", COUNT_ROOT_DEPTH);
	Dialog.addNumber("half of length [cm]: ", HALF_LINE_WIDTH); 
	Dialog.addNumber("line width for depth: ", WIDTH_DEPTH);
	Dialog.addString("depth line color: ", COLOR_DEPTH);
	Dialog.addNumber("dx angle: ", DX_ANGLE); 
	Dialog.addNumber("dy angle: ", DY_ANGLE); 
	Dialog.show();
	RADIUS = Dialog.getNumber();
	ROOT_POINT_LINE_WIDTH = Dialog.getNumber();
	COLOR_ROOT_POINT = Dialog.getString();
	COUNT_ROOT_DEPTH = Dialog.getNumber();
	HALF_LINE_WIDTH = Dialog.getNumber();
	WIDTH_DEPTH = Dialog.getNumber();
	COLOR_DEPTH = Dialog.getString();
	DX_ANGLE = Dialog.getNumber();
	DY_ANGLE = Dialog.getNumber();
}

macro "Angle Action Tool- C000T4b12a" {
	measureAngle();
}

macro "Angle Action Tool Options" {
	Dialog.create("Root Tools - Angle - Options");
	Dialog.addString("angle color: ", ANGLE_COLOR);
	Dialog.addNumber("line width: ", ANGLE_LINE_WIDTH);
	Dialog.show();
	ANGLE_COLOR = Dialog.getString();
	ANGLE_LINE_WIDTH = Dialog.getNumber();
}

macro "Measure Depth Tool- C000T4b12d" {
	getCursorLoc(x, y, z, flags);
	deepX = x;
	deepY =  y;
	DEPTH = deepY - rootY;
	toScaled(DEPTH);
	setColor(MEASURE_DEPTH_COLOR);
	setLineWidth(MEASURE_DEPTH_WIDTH);
	Overlay.drawLine(rootX, rootY, rootX, deepY);
	Overlay.drawLine(rootX, deepY, deepX, deepY);
	Overlay.show();
	run("Select None");
	setTool("Zoom region Tool");
}

macro "Measure Depth Tool Options" {
	Dialog.create("Root Tools - Measure Depth - Options");
	Dialog.addString("line color: ", MEASURE_DEPTH_COLOR);
	Dialog.addNumber("line width: ", MEASURE_DEPTH_WIDTH);
	Dialog.show();
	MEASURE_DEPTH_COLOR = Dialog.getString();
	MEASURE_DEPTH_WIDTH = Dialog.getNumber();
}

macro "Zoom region Tool- C000T4b12z" {
	  title = getTitle();
	  getCursorLoc(x, y, z, flags);
	  makeRectangle(x-ZOOM_RADIUS, y-ZOOM_RADIUS, 2*ZOOM_RADIUS+1, 2*ZOOM_RADIUS+1);
	  run("Duplicate...", "title="+title+"box");
	  run("Remove Overlay");
  	  run("In [+]");
   	  run("In [+]");
                          run("In [+]");
	  run("In [+]");
	  run("In [+]");
	  run("In [+]");
	  setTool("line");
}

macro "Zoom region Tool Options" {
	Dialog.create("Root Tools - Zoom region - Options");
	Dialog.addNumber("radius ", ZOOM_RADIUS);
	Dialog.show();
	ZOOM_RADIUS = Dialog.getNumber();
}

macro "Measure diameter Action Tool- C000T4b12m" {
	measureDiameter();
}

macro "Measure diameter Action Tool Options" {
	Dialog.create("Root Tools - Measure diameter - Options");
	Dialog.addString("line color: ", DIAMETER_COLOR);
	Dialog.addNumber("line width", DIAMETER_WIDTH);
	Dialog.show();
	DIAMETER_COLOR = Dialog.getString();
	DIAMETER_WIDTH = Dialog.getNumber();
}

macro "Write report Action Tool- C000T4b12w" {
	writeReport();
}

function lineAtThirtyCM() {
	setColor(COLOR_DEPTH);
	setLineWidth(WIDTH_DEPTH);
	tenUnscaled = HALF_LINE_WIDTH;
	toUnscaled(tenUnscaled);
	thirtyUnscaled = COUNT_ROOT_DEPTH;
	toUnscaled(thirtyUnscaled);
	X1 = rootX - tenUnscaled;
	X2 = rootX + tenUnscaled;
	Y = rootY + thirtyUnscaled;
	Overlay.drawLine(X1, Y, X2, Y);
	Overlay.show();
}

function angleSelection() {
	xCoords = newArray(3);
	yCoords = newArray(3);
	xCoords[0] = rootX - DX_ANGLE;
	xCoords[1] = rootX;
	xCoords[2] = rootX + DX_ANGLE;
	yCoords[0] = rootY + DY_ANGLE;
	yCoords[1] = rootY;
	yCoords[2] = rootY + DY_ANGLE;
	makeSelection("angle", xCoords, yCoords);
}

function setScale() {
   getLine(x1, y1, x2, y2, lineWidth);
   dx = x2-x1; 
   dy = y2-y1;
   length = sqrt(dx*dx+dy*dy);
   options = "distance=" + length+" known="+KNOWN_DISTANCE+" pixel=1 unit="+UNIT;
   if (USE_GLOBAL_SCALE) options = options + " global";
   run("Set Scale...", options);
   run("Select None");
   setTool("Define Root Point Tool");
}

function measureAngle() {
	run("Measure");
	ANGLE = getResult("Angle", nResults-1);
	selectWindow("Results");
	run("Close");
	getSelectionCoordinates(xCoordinates, yCoordinates);
	run("Select None");
	setColor(ANGLE_COLOR);
	setLineWidth(ANGLE_LINE_WIDTH);
	Overlay.drawLine(xCoordinates[0], yCoordinates[0], xCoordinates[1], yCoordinates[1]);
	Overlay.drawLine(xCoordinates[1], yCoordinates[1], xCoordinates[2], yCoordinates[2]);
	Overlay.show();
	setTool("Measure Depth Tool");
}

function measureDiameter() {
	getLine(x1, y1, x2, y2, lineWidth);
	dx = x2-x1;
	dy = y2-y1;
	length = sqrt(dx*dx+dy*dy);
	toScaled(length);
	DIAMETERS[numberOfRootsAtThirty++] = length;
	close();
	selectImage(ID);
	getSelectionBounds(x, y, width, height);
	run("Select None");
	setColor(DIAMETER_COLOR);
	setLineWidth(DIAMETER_WIDTH);
	Overlay.drawLine(x+x1, y+y1, x+x2, y+y2);
	Overlay.show();
	setTool("Zoom region Tool");
}

function writeReport() {
	NUMBER++;
	getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
	title = "root measurements - " + year + "-" + month + "-" + dayOfMonth + ".txt";
	ref = "[" + title + "]";
	if (!isOpen(title)) {
		run("Table...", "name="+ref+" width=250 height=600");
		header = "\\Headings:" + "nr." + "\t" + "image" + "\t" + "root x" + "\t" + "root y" + "\t" + "angle" + "\t" + "depth" + "\t" + "nr at 30cm";
		for (i=0; i<MAX_ROOTS; i++) {
			header = header + "\t" + "d" + (i+1);
		}
		print(ref, header);
	}
	row = "" + NUMBER + "\t" + TITLE + "\t" + rootX + "\t" + rootY + "\t" + ANGLE + "\t" + DEPTH + "\t" + numberOfRootsAtThirty;
	for (i=0; i<numberOfRootsAtThirty; i++) {
		row = row + "\t" + DIAMETERS[i];
	}
	print(ref, row);
	resetMeasurements();
	if (!File.exists(FOLDER + "/" + "control/")) File.makeDirectory(FOLDER + "/" + "control/");
	path = FOLDER + "/" + "control/" + TITLE;
	saveAs("tiff", path);
	Overlay.remove;
	setTool("line");
}

function resetMeasurements() {
	numberOfRootsAtThirty = 0;
	 DIAMETERS = newArray(MAX_ROOTS);
}

function getJSAddListeners() {
	events = newArray("imageOpened", "imageUpdated", "imageClosed");
	event = "imageOpened";
	commands = ON_IMAGE_OPEN_COMMANDS;
	commandFlags = ON_IMAGE_OPEN_COMMANDS_CHECKED;
	script = "listenerImpl = {";
	 for (i=0; i<lengthOf(events); i++) {
	     script = script + events[i] + ": function(imp){";
	     if (events[i]==event) {
	          for (j=0; j<lengthOf(commands); j++) {
		if (commandFlags[j]) {
			components = split(commands[j],",");
			if (lengthOf(components)==1) 
				script = script + "IJ.run(\"" + commands[j] + "\");";
			else
				script = script + "IJ.run(\"" + components[0] + "\",\""+components[1]  +"\");";
		}
	          }
                             }
	     script = script + "}";
	     if (i<lengthOf(events)-1) script = script + ",";
	 }
	script = script + "}; listener = new ImageListener(listenerImpl); ImagePlus.addImageListener(listener);";
	return script;
}

function runJS(script) {
	 eval("script", script);
}

function getJSRemoveAllImageListeners() {
	script = "cl = new ImagePlus().getClass(); df = cl.getDeclaredField(\"listeners\"); df.setAccessible(true); df.get(null).removeAllElements();";
	return script;
}