import ij.*;
import ij.plugin.filter.PlugInFilter;
import ij.process.*;
import ij.gui.*;
import ij.measure.Calibration;
import java.awt.*;
import java.util.*;

public class Radial_Profile implements PlugInFilter {

	ImagePlus imp;
	boolean canceled=false;
	double X0;
	double Y0;
	double mR;
	Rectangle rct;
	int nBins=100;
	//static boolean doNormalize = true;
	static boolean useCalibration = false;

	public int setup(String arg, ImagePlus imp) {
		this.imp = imp;
		return DOES_ALL+NO_UNDO+ROI_REQUIRED;
	}

	public void run(ImageProcessor ip) {
		setXYcenter();
		IJ.makeOval((int)(X0-mR), (int)(Y0-mR), (int)(2*mR), (int)(2*mR));
		doDialog();
		IJ.makeOval((int)(X0-mR), (int)(Y0-mR), (int)(2*mR), (int)(2*mR));
		imp.startTiming();
		if (canceled) return;
		doRadialDistribution(ip);
	}
	
	private void setXYcenter() {
		rct = imp.getRoi().getBoundingRect();
		X0 = (double)rct.x+(double)rct.width/2;
		Y0 =  (double)rct.y+(double)rct.height/2;
		mR =  (rct.width+rct.height)/4.0;
	}

	private void doRadialDistribution(ImageProcessor ip) {
		nBins = (int) (3*mR/4);
		int thisBin;
		float[][] Accumulator = new float[2][nBins];
		double R;
		double xmin=X0-mR, xmax=X0+mR, ymin=Y0-mR, ymax=Y0+mR;
		for (double i=xmin; i<xmax; i++) {
			for (double j=ymin; j<ymax; j++) {
				R = Math.sqrt((i-X0)*(i-X0)+(j-Y0)*(j-Y0));
				thisBin = (int) Math.floor((R/mR)*(double)nBins);
				if (thisBin==0) thisBin=1;
				thisBin=thisBin-1;
				if (thisBin>nBins-1) thisBin=nBins-1;
				Accumulator[0][thisBin]=Accumulator[0][thisBin]+1;
				Accumulator[1][thisBin]=Accumulator[1][thisBin]+ip.getPixelValue((int)i,(int)j);
			}
		}
		Calibration cal = imp.getCalibration();
		if (cal.getUnit() == "pixel") useCalibration=false;
		Plot plot = null;
		if (useCalibration) {
			for (int i=0; i<nBins;i++) {
				Accumulator[1][i] =  Accumulator[1][i] / Accumulator[0][i];
				Accumulator[0][i] = (float)(cal.pixelWidth*mR*((double)(i+1)/nBins));
			}
			plot = new Plot("Radial Profile Plot", "Radius ["+cal.getUnits()+"]", "Normalized Integrated Intensity",  Accumulator[0], Accumulator[1]);
		} else {
			for (int i=0; i<nBins;i++) {
				Accumulator[1][i] = Accumulator[1][i] / Accumulator[0][i];
				Accumulator[0][i] = (float)(mR*((double)(i+1)/nBins));
			}
			plot = new Plot("Radial Profile Plot", "Radius [pixels]", "Normalized Integrated Intensity",  Accumulator[0], Accumulator[1]);
		}
		plot.show();
	}

	private void doDialog() {
		canceled=false;
		GenericDialog gd = new GenericDialog("Radial Distribution...", IJ.getInstance());
		gd.addNumericField("X center (pixels):",X0,2);
		gd.addNumericField("Y center (pixels):", Y0,2);
		gd.addNumericField("Radius (pixels):", mR,2);
		//gd.addCheckbox("Normalize", doNormalize);
		gd.addCheckbox("Use Spatial Calibration", useCalibration);
		gd.showDialog();
		if (gd.wasCanceled()) {
			canceled = true;
			return;
		}
		X0=gd.getNextNumber();
		Y0=gd.getNextNumber();
		mR=gd.getNextNumber();
		//doNormalize = gd.getNextBoolean();
		useCalibration = gd.getNextBoolean();
		if(gd.invalidNumber()) {
			IJ.showMessage("Error", "Invalid input Number");
			canceled=true;
			return;
		}
	}
}