import ij.process.*;

import ij.IJ;
import org.micromanager.utils.ImageUtils;
import ij.plugin.FFTMath;
import java.awt.Point;
import ij.process.ImageProcessor;
import ij.ImagePlus;
import ij.process.FHT;
import java.awt.geom.Point2D;
import ij.process.ShortProcessor;

// Performs a 2D cross-correlation between two images)

ImageProcessor crossCorrelate(ImageProcessor proc1, ImageProcessor proc2) {
	h1 = new FHT(proc1);
	h2 = new FHT(proc2);
	h1.transform();
	h2.transform();
	result = h1.conjugateMultiply(h2);
	result.inverseTransform();
	result.swapQuadrants();
	result.resetMinAndMax();
	return result;
}

// Measures the displacement between two images by cross-correlating, and then finding the maximum value.
// Accurate to one pixel only.

Point measureDisplacement(ImageProcessor proc1, ImageProcessor proc2) {
	result = crossCorrelate(proc1,proc2);
	img = new ImagePlus("",result);
	p = ImageUtils.findMaxPixel(img);
	d = new Point(p.x - img.getWidth()/2, p.y - img.getHeight()/2);
	img.show();
	img.setRoi(p.x-5,p.y-5,11,11);
	return d;
}

moveRelative(dx, dy) {
	xystage = mmc.getXYStageDevice();
	mmc.waitForDevice(xystage);
	startPos = gui.getXYStagePosition();
	mmc.waitForDevice(xystage);
	gui.setXYStagePosition(startPos.x + dx, startPos.y + dy);
	mmc.waitForDevice(xystage);
	curPos = gui.getXYStagePosition();
	return new Point2D.Double(curPos.x - startPos.x, curPos.y - startPos.y);
}

update();
/*
stageDelta = 20;
mmc.snapImage();
pix1 = mmc.getImage();
gui.displayImage(pix1);
stageMove = moveRelative(0,stageDelta);
mmc.snapImage();
pix2 = mmc.getImage();
gui.displayImage(pix2);
proc1 = new ShortProcessor(512,512);
proc1.setPixels(pix1);
proc2 = new ShortProcessor(512,512);
proc2.setPixels(pix2);
pixelDelta = measureDisplacement(proc1,proc2);
print("Stage: " + stageMove.y + " um.");
print("Pixels: " + pixelDelta.x);
print("Pixel size: " + (stageMove.y / (float) pixelDelta.x) + " um/pixel");
*/