import java.lang.Math;
import ij.gui.NewImage;
import java.awt.Point;
import java.util.Set;
import java.util.HashSet;
import java.util.ArrayList;
import ij.gui.GenericDialog;
import ij.IJ;

helpURL = "https://github.com/MontpellierRessourcesImagerie/imagej_macros_and_scripts/wiki/MRI_Spiral_Mosaic_Tool";
options = ij.Macro.getOptions();

IJ.log(options);

east = new Point(1, 0);
north = new Point(0, -1);
west = new Point(-1, 0);
south = new Point(0, 1);

TURNLEFT = false;
START_DIRECTION = north;

int[] quaterSquares = {0,0,1,2,4,6,9,12,16,20,25,30,36,42,49,56,64,72,81,90,100,110,121,132,144,156,169,182,196,210,225,240,256,272,289,306,324,342,361,380,400,420,441,462,484,506,529,552,576,600,625,650,676,702,729,756,784,812};

 nextQuarterSquareFor(n) {
 	for (qs : quaterSquares) {
 		if (qs >= n) return qs;
 	}
 	return -1;
 }

 indexOfNextQuarterSquareFor(n) {
 	index=0;
 	for (qs : quaterSquares) {
 		if (qs >= n) return index;
 		index++;
 	}
 	return -1;
 }

Point turnLeft(Point direction) {
	result = south;
	if (direction.equals(south)) result = east;
	if (direction.equals(east)) result = north;
	if (direction.equals(north)) result = west;  
	return result;
}


Point turnRight(Point direction) {
	result = north;
	if (direction.equals(south)) result = west;
	if (direction.equals(east)) result = south;
	if (direction.equals(north)) result = east;  
	return result;
}

relativePositions(n) {
	Set burnedPoints = new HashSet();
	positions = new ArrayList();
	direction = START_DIRECTION; 
	currentPosition = new Point(0,0);
	for (i=0; i<n; i++) {
		burnedPoints.add(currentPosition);
		positions.add(currentPosition);
		if (i==n-1) break;
		oldDirection = direction;
		if (TURNLEFT) newDirection = turnLeft(direction);
		else newDirection = turnRight(direction);
		newPosition = new Point(currentPosition.x + newDirection.x, currentPosition.y + newDirection.y);
		if (burnedPoints.contains(newPosition)) {
			newPosition = new Point(currentPosition.x + direction.x, currentPosition.y + direction.y);
		} else direction = newDirection;
		currentPosition = newPosition;
	}
	return positions;
}

clockwise = !TURNLEFT;
startEast = true;
step = false;

if (options==null) {
	GenericDialog gd = new GenericDialog("MRI - Spiral Image Reconstruction");
	gd.addCheckbox("clockwise", !TURNLEFT);
	startEast = true;
	if (START_DIRECTION.equals(north)&&TURNLEFT) startEast=false; 
	if (START_DIRECTION.equals(south)&&!TURNLEFT) startEast=false;
	gd.addCheckbox("start to the east", startEast); 
	gd.addCheckbox("step", false);
	gd.addHelp(helpURL);
	gd.pack();
	gd.showDialog();

	if (gd.wasCanceled()) return;

	clockwise = gd.getNextBoolean();
	startEast = gd.getNextBoolean();
	step = gd.getNextBoolean();
} else {
	options = options.split(" ");
    IJ.log("options[0]:" + options[0]);	
	comps = options[0].split("=");
	val = comps[1];
	IJ.log("val:" + val);	
	clockwise = val.equals("true");
	startEast = options[1].split("=")[1].equals("true");
	step = options[2].split("=")[1].equals("true");
}

START_DIRECTION = north;

IJ.log("clockwise:" + clockwise);
IJ.log("startEast:" + startEast);

if ((!clockwise && startEast) || (clockwise && !startEast)) START_DIRECTION = south;
TURNLEFT = true;
if (clockwise) TURNLEFT = false;

image = ij.IJ.getImage();
numberOfImages = image.getNSlices();
n = indexOfNextQuarterSquareFor(numberOfImages);
imageWidth = image.getWidth();
imageHeight = image.getHeight();
width = (int)Math.ceil(n/2.0) * imageWidth;
height = (int)Math.floor(n/2.0) * imageHeight;

mosaic = NewImage.createImage(image.getTitle() + "- reconstructed", width, height, 1, image.getBitDepth(), NewImage.FILL_BLACK);
mosaic.show();

relativePositions = relativePositions(numberOfImages);
slice = 1;
mip = mosaic.getProcessor();
for (pos : relativePositions) {
	offsetX =  imageWidth;
	if (!startEast) offsetX = 0;
	if ((int)Math.ceil(n/2.0)%2!=0) offsetX = imageWidth / 2;
	offsetY = 0;
	if (startEast && !TURNLEFT) offsetY = imageHeight;
	if (!startEast && TURNLEFT) offsetY = imageHeight;
	if ((int)Math.floor(n/2.0)%2!=0) offsetY = imageHeight / 2;
	positionX = (width / 2) - offsetX + (pos.x * imageWidth);
	positionY = (height / 2) - offsetY + (pos.y * imageHeight);
	image.setSlice(slice);
	ip = image.getProcessor();
	mip.insert(ip, positionX, positionY);
	ij.IJ.run("Enhance Contrast", "saturated=0.35");
	mosaic.updateAndDraw();
	if (step) new ij.gui.WaitForUserDialog("Cont...").show();
 	slice++;
}