import java.awt.*;
import java.awt.event.*;
import java.awt.Container.*;
import java.io.*;
import ij.io.*;
import java.awt.GridLayout.*;
import ij.plugin.frame.*;
import ij.*;
import java.util.*;
import ij.process.*;
import ij.gui.*;
import java.lang.Math;
import ij.measure.*;
import ij.plugin.*;
import ij.plugin.frame.RoiManager;
import ij.measure.Calibration; 
import ij.measure.ResultsTable; 
import javax.swing.*; 
import javax.swing.filechooser.*;

/**
	FRET ROI - designed to calculate FRET from acceptor bleaching within regions of interest
	Written by Ben Corry July 2008
*/
public class FRET_ROI extends PlugInFrame implements ActionListener {

	Panel panel;
	int previousID;
	static Frame instance;
	boolean useThreshold = true;
	double donorThreshold=0.0;
	double acceptorThreshold=0.0;

	public FRET_ROI() {
		super("FRET ROI");
		if (instance!=null) {
			instance.toFront();
			return;
		}
		instance = this;
		addKeyListener(IJ.getInstance());

		setLayout(new FlowLayout());
		panel = new Panel();
		panel.setLayout(new GridLayout(0, 1, 5, 5));
		panel.setBackground(new Color(240,240,220)); 


		panel.add(new Label("FRET ROI ")); 
		addButton("Open Files");
		addButton("Build Stack");
		addButton("LUT Fire");
		addButton("Start ROI Manager");
//		addButton("Settings");
		addButton("FRET Calculation");
		addButton("Mini Calculation");
		addButton("Single ROI Calculation");
		addButton("Help");
		panel.add(new Label(" ")); 

		add(panel);
		
		pack();
		GUI.center(this);
		setVisible(true);
	}
	
	void addButton(String label) {
		Button b = new Button(label);
		b.addActionListener(this);
		b.addKeyListener(IJ.getInstance());
		panel.add(b);
	}


	public void actionPerformed(ActionEvent e) {
		String label = e.getActionCommand();
		if (label==null)
			return;
		new FRETRunner(label);
	}

	public void processWindowEvent(WindowEvent e) {
		super.processWindowEvent(e);
		if (e.getID()==WindowEvent.WINDOW_CLOSING) {
			instance = null;	
		}
	}

}

class FRETRunner extends Thread {
	private String command;

	FRETRunner(String command) {
		super(command);
		this.command = command;
		setPriority(Math.max(getPriority()-2, MIN_PRIORITY));
		start();
	}

	public void run() {
		try {runCommand(command);}
		catch(OutOfMemoryError e) {
			IJ.outOfMemory(command);
		} catch(Exception e) {
			CharArrayWriter caw = new CharArrayWriter();
			PrintWriter pw = new PrintWriter(caw);
			e.printStackTrace(pw);
			IJ.write(caw.toString());
			IJ.showStatus("");
		}
	}

	void runCommand(String command) {

		double donorThreshold=0.0;

		IJ.showStatus(command + "...");

		if (command.equals("Open Files"))
			macroOpen(); 
		else if (command.equals("Build Stack"))
			macroStack();
		else if (command.equals("LUT Fire"))
			IJ.run("Fire");
		else if (command.equals("Start ROI Manager"))
			IJ.run("ROI Manager...");
//		else if (command.equals("Settings")){
//			GenericDialog gd = new GenericDialog("Settings");
//			gd.addCheckbox("Use Donor Threshold values", false);
//			gd.addNumericField("Donor Threshold",0,0 );
//		 	gd.addNumericField("Acceptor Threshold",10,0 );
//		 	gd.showDialog();
//		 	useThreshold = gd.getNextBoolean();
//			donorThreshold =  gd.getNextNumber();
//		 	acceptorThreshold =  (int)gd.getNextNumber();
//			}
		else if (command.equals("FRET Calculation")){
			int previousID=0;

			ImagePlus imp = WindowManager.getCurrentImage();
			imp.unlock();
			if (imp==null) {
				IJ.beep();
				IJ.showStatus("No image");
				IJ.showMessage("Open an image to use buttons");
				previousID = 0;
				return;
			}
			if (!imp.lock())
				{previousID = 0; return;}
			ImageProcessor ip = imp.getProcessor();
			int id = imp.getID();
			if (id!=previousID)
				ip.snapshot();
			previousID = id;

			ResultsTable rt = ResultsTable.getResultsTable();
			rt.reset();
			rt.incrementCounter();
	
		 	RoiManager roim;
		 	roim=RoiManager.getInstance();
			if (roim==null) {
				IJ.showMessage("Must have the ROI Manager open");
			}
             	int nr=roim.getCount();

		 	ImageStack stack = imp.getStack();
			if (stack==null) {
				IJ.showMessage("Must have an image stack");
			}
		 	int ns = stack.getSize();

			GenericDialog gd = new GenericDialog("Settings");
			gd.addNumericField("Donor Threshold",0,0 );
  		 	gd.showDialog();
			donorThreshold =  gd.getNextNumber();

		 	int count[][] = new int[ns][nr];
		 	double m[][] = new double[ns][nr];
		 	double sum[][] = new double[ns][nr];
		 	double normd[] = new double[3];
		 	double norma[] = new double[3];

        	 	for(int j=0; j<ns; j++){

		 		ImageProcessor ipnow= stack.getProcessor(j+1);

        	 		for(int i=0; i<nr; i++){

					count[j][i] = 0;
					sum[j][i] = 0.0;

					roim.select(i);

		   			Roi roi = imp.getRoi();
		   			if (roi!=null && !roi.isArea()) roi = null;
		   			ImageProcessor mask = roi!=null?roi.getMask():null;
		   			Rectangle r = roi!=null?roi.getBounds():new Rectangle(0,0,ipnow.getWidth(),ipnow.getHeight());
					for (int y=0; y<r.height; y++) {
						for (int x=0; x<r.width; x++) {
							if (mask==null||mask.getPixel(x,y)!=0) {
								if (j>2 && i==0) {
									if (ipnow.getPixelValue(x+r.x, y+r.y)>donorThreshold) {
										count[j][i]++;
										sum[j][i] += ipnow.getPixelValue(x+r.x, y+r.y);
									}
								}
								else {
									count[j][i]++;
									sum[j][i] += ipnow.getPixelValue(x+r.x, y+r.y);
								}
							}	
						}
		   			}
					m[j][i]=sum[j][i]/count[j][i];					
				}
			}

			for (int j=0; j<3; j++){
				norma[j] = Math.max((m[j][1]-m[j][2])/(m[0][1]-m[0][2]),0);
				normd[j] = (m[j+3][0]-m[j+3][2])/(m[3][0]-m[3][2]);
			}

			double chbleach = Math.max(1 - (normd[2]/normd[1]),0.0);
			double corrD1 = normd[1]*(1.0+chbleach);
			double corrD2 = corrD1 + ((corrD1-1)*(norma[1]/(1-norma[1])));
			double fret = Math.max(1-(1/corrD2),0.0);

			for (int j=0; j<3; j++){				
				rt.addValue("Donor:",m[j+3][0]);
				rt.addValue("Acceptor:",m[j][1]);
				rt.addValue("Donor bg:",m[j+3][2]);
				rt.addValue("Acceptor bg:",m[j][2]);
				rt.addValue("Norm Donor:",normd[j]);
				rt.addValue("Norm Acceptor:",norma[j]);
				rt.addValue("chbleach:",chbleach);
				rt.addValue("corrD1:",corrD1);
				rt.addValue("corrD2:",corrD2);
				rt.addValue("fret:",fret);
				if (j<2) rt.incrementCounter();
			}
	     	 rt.show("Results");
		}
		else if (command.equals("Mini Calculation")){
			int previousID=0;

			ImagePlus imp = WindowManager.getCurrentImage();
			imp.unlock();
			if (imp==null) {
				IJ.beep();
				IJ.showStatus("No image");
				IJ.showMessage("Open an image to use buttons");
				previousID = 0;
				return;
			}
			if (!imp.lock())
				{previousID = 0; return;}
			ImageProcessor ip = imp.getProcessor();
			int id = imp.getID();
			if (id!=previousID)
				ip.snapshot();
			previousID = id;

			ResultsTable rt = ResultsTable.getResultsTable();
			rt.reset();
			rt.incrementCounter();
	
		 	RoiManager roim;
		 	roim=RoiManager.getInstance();
			if (roim==null) {
				IJ.showMessage("Must have the ROI Manager open");
			}
             	int nr=roim.getCount();

		 	ImageStack stack = imp.getStack();
			if (stack==null) {
				IJ.showMessage("Must have an image stack");
			}
		 	int ns = stack.getSize();

			GenericDialog gd = new GenericDialog("Settings");
			gd.addNumericField("Donor Threshold",0,0 );
  		 	gd.showDialog();
			donorThreshold =  gd.getNextNumber();

		 	int count[][] = new int[ns][nr];
		 	double m[][] = new double[ns][nr];
		 	double sum[][] = new double[ns][nr];

        	 	for(int j=0; j<ns; j++){

		 		ImageProcessor ipnow= stack.getProcessor(j+1);

        	 		for(int i=0; i<nr; i++){

					count[j][i] = 0;
					sum[j][i] = 0.0;

					roim.select(i);

		   			Roi roi = imp.getRoi();
		   			if (roi!=null && !roi.isArea()) roi = null;
		   			ImageProcessor mask = roi!=null?roi.getMask():null;
		   			Rectangle r = roi!=null?roi.getBounds():new Rectangle(0,0,ipnow.getWidth(),ipnow.getHeight());
					for (int y=0; y<r.height; y++) {
						for (int x=0; x<r.width; x++) {
							if (mask==null||mask.getPixel(x,y)!=0) {
								if (j>2 &&i==0) {
									if (ipnow.getPixelValue(x+r.x, y+r.y)>donorThreshold) {
										count[j][i]++;
										sum[j][i] += ipnow.getPixelValue(x+r.x, y+r.y);
									}
								}
								else {
									count[j][i]++;
									sum[j][i] += ipnow.getPixelValue(x+r.x, y+r.y);
								}
							}	
						}
		   			}
					m[j][i]=sum[j][i]/count[j][i];					
				}
			}
			for (int j=0; j<3; j++){				
				rt.addValue("Donor:",m[j+3][0]);
				rt.addValue("Acceptor:",m[j][1]);
				rt.addValue("Donor bg:",m[j+3][2]);
				rt.addValue("Acceptor bg:",m[j][2]);
				if (j<2) rt.incrementCounter();
			}
	     	 rt.show("Results");
		}
		else if (command.equals("Single ROI Calculation")){
			int previousID=0;

			ImagePlus imp = WindowManager.getCurrentImage();
			imp.unlock();
			if (imp==null) {
				IJ.beep();
				IJ.showStatus("No image");
				IJ.showMessage("Open an image to use buttons");
				previousID = 0;
				return;
			}
			if (!imp.lock())
				{previousID = 0; return;}
			ImageProcessor ip = imp.getProcessor();
			int id = imp.getID();
			if (id!=previousID)
				ip.snapshot();
			previousID = id;

			ResultsTable rt = ResultsTable.getResultsTable();
			rt.reset();
			rt.incrementCounter();
	
             	int nr=1;

		 	ImageStack stack = imp.getStack();
			if (stack==null) {
				IJ.showMessage("Must have an image stack");
			}
		 	int ns = stack.getSize();

			GenericDialog gd = new GenericDialog("Settings");
			gd.addNumericField("Donor Threshold",0,0 );
  		 	gd.showDialog();
			donorThreshold =  gd.getNextNumber();

		 	int count[][] = new int[ns][nr];
		 	double m[][] = new double[ns][nr];
		 	double sum[][] = new double[ns][nr];

        	 	for(int j=0; j<ns; j++){

		 		ImageProcessor ipnow= stack.getProcessor(j+1);

        	 		for(int i=0; i<nr; i++){

					count[j][i] = 0;
					sum[j][i] = 0.0;

		   			Roi roi = imp.getRoi();
		   			if (roi!=null && !roi.isArea()) roi = null;
		   			ImageProcessor mask = roi!=null?roi.getMask():null;
		   			Rectangle r = roi!=null?roi.getBounds():new Rectangle(0,0,ipnow.getWidth(),ipnow.getHeight());
					for (int y=0; y<r.height; y++) {
						for (int x=0; x<r.width; x++) {
							if (mask==null||mask.getPixel(x,y)!=0) {
								if (j>2 &&i==0) {
									if (ipnow.getPixelValue(x+r.x, y+r.y)>donorThreshold) {
										count[j][i]++;
										sum[j][i] += ipnow.getPixelValue(x+r.x, y+r.y);
									}
								}
								else {
									count[j][i]++;
									sum[j][i] += ipnow.getPixelValue(x+r.x, y+r.y);
								}
							}	
						}
		   			}
					m[j][i]=sum[j][i]/count[j][i];					
				}
			}
			for (int j=0; j<6; j++){				
				rt.addValue("Mean:",m[j][0]);
				if (j<5) rt.incrementCounter();
			}
	     	 rt.show("Results");
}
		else if (command.equals("Help"))
			macroHelp();
		IJ.showStatus("");
	}


	void macroStack() {

                  ImagePlus imp;
        		ImageProcessor ip;
		      int nbrFenetre;
        		int[] listFenetre;
       		Rectangle[] listRoi;
        		int maxWidth, maxHeight;
        		boolean rgbStack = false;

        		nbrFenetre = WindowManager.getWindowCount();
        		listFenetre = new int[nbrFenetre];
        		listRoi = new Rectangle[nbrFenetre];
        		listFenetre = WindowManager.getIDList();
        		maxWidth=0;
        		maxHeight=0;
        		if (listFenetre==null)
            	{IJ.noImage(); return;}

        		// Create an array with ROIs attributes, search the biggest width and height
        		// and check image types
        		boolean allSameType =true;
        		boolean is16or32BitImage = false;
        		int typeOfFirstImage = WindowManager.getImage(listFenetre[0]).getType();
        		for(int i=0; i<nbrFenetre; i++){
            	imp=WindowManager.getImage(listFenetre[i]);
              	int type = imp.getType();
            	if (type!=typeOfFirstImage)
                		allSameType = false;
            	switch (type) {
                	case ImagePlus.GRAY16: case ImagePlus.GRAY32:
                  	is16or32BitImage=true; break;
                	case ImagePlus.COLOR_RGB:
                    	rgbStack = true;
                	default:
            	}
            	ip=imp.getProcessor();
            	listRoi[i]= ip.getRoi();
            	if (listRoi[i].width>maxWidth) {maxWidth=listRoi[i].width;};
            	if (listRoi[i].height>maxHeight) {maxHeight=listRoi[i].height;};
            	//if (maxWidth>ip.getWidth()) {maxWidth=ip.getWidth();};
            	//if (maxHeight>ip.getHeight()) {maxHeight=ip.getHeight();};
        		}

        		if (!allSameType && is16or32BitImage) {
            	if (!IJ.showMessageWithCancel("Stack Builder", "Images are not all the same type and some are\n"+
            	"16 or 32 bits. All the images will be converted\n"+
            	"to 8-bits or RGB to create the stack."))
               	return;
        		}
         
        		// Resizes the ROIs according to the biggest size found 
        		for(int i=0; i<nbrFenetre; i++){
            	listRoi[i].x-=(int)Math.ceil((maxWidth-listRoi[i].width)/2);
            	if (listRoi[i].x<0)
                		listRoi[i].x =0;
            	listRoi[i].y-=(int)Math.ceil((maxHeight-listRoi[i].height)/2);
            	if (listRoi[i].y<0) {
                	listRoi[i].y=0;
            	};
            	listRoi[i].width=maxWidth;
            	listRoi[i].height=maxHeight;
        		}
        
        		// set the ROIs and make a stack from the selections
        		ImageStack newStack= new ImageStack(maxWidth, maxHeight);
        		for(int i=0; i<nbrFenetre; i++){
            		imp=WindowManager.getImage(listFenetre[i]);
            		ip=imp.getProcessor();

            		if (listRoi[i].x+listRoi[i].width>=ip.getWidth())
                			listRoi[i].x =ip.getWidth()-listRoi[i].width;
            		if (listRoi[i].y+listRoi[i].height>=ip.getHeight())
                			listRoi[i].y =ip.getHeight()-listRoi[i].height;
            		ip.setRoi(listRoi[i]);
            		ip=ip.crop();
            		if (ip.getWidth()!=maxWidth || ip.getHeight()!=maxHeight) {
               			ImageProcessor ip2 = ip.createProcessor(maxWidth, maxHeight);
               			ip2.setColor(Toolbar.getForegroundColor());
               			ip2.fill();
               			ip2.insert(ip, (maxWidth-ip.getWidth())/2, (maxHeight-ip.getHeight())/2);
               			ip = ip2;
            		}
            		if (rgbStack)
                		ip = ip.convertToRGB();
            		else if (!allSameType)
                		ip = ip.convertToByte(true);
            		//Rectangle r = ip.getRoi();
            		//IJ.write(i+" "+r.width+" "+r.height);
            		newStack.addSlice(imp.getTitle(),ip);
				imp.close();
        		}
        		ImagePlus newImage = new ImagePlus("the stack", newStack);
        		newImage.show();

    			} // end of run

	void macroOpen() {
			File dir=null;
			JFileChooser fc = null;
			try {fc = new JFileChooser();}
			catch (Throwable e) {IJ.error("This plugin requires Java 2 or Swing."); return;}
			fc.setMultiSelectionEnabled(true);
			if (dir==null) {
				String sdir = OpenDialog.getDefaultDirectory();
				if (sdir!=null)
					dir = new File(sdir);
			}
			if (dir!=null)
				fc.setCurrentDirectory(dir);
			int returnVal = fc.showOpenDialog(IJ.getInstance());
			if (returnVal!=JFileChooser.APPROVE_OPTION)
				return;
			File[] files = fc.getSelectedFiles();
			if (files.length==0) { // getSelectedFiles does not work on some JVMs
				files = new File[1];
				files[0] = fc.getSelectedFile();
			}
			String path = fc.getCurrentDirectory().getPath()+Prefs.getFileSeparator();
			dir = fc.getCurrentDirectory();
			Opener opener = new Opener();
			for (int i=0; i<files.length; i++) {
				ImagePlus img = opener.openImage(path, files[i].getName());
				if (img!=null)
					img.show();
			}        
		}


	void macroHelp() {

			IJ.showMessage("Help",
			"FRET ROI\n"+
			" \n"+
			"This is a plugin designed to expediate the process of analysing FRET\n"+
		 	"in regions of interestest from acceptor bleacing experiments\n"+
			" \n"+
			"Written by Ben Corry July 2008\n"+
			" \n"+
			"Expects you to open 6 images to form into a stack\n"+ 
			"in the order A1, A2, A3, D1, D2, D3\n"+
			" \n"+
			"Also you should specify 3 regions of interst using the ROI mangaer \n"+ 
			"in the order Donor region, Acceptor region and background region\n"+ 
			" \n"+
			"Remove slice information before running FRET calculation\n"+ 
			"(ROI manager -> More -> Remove slice info)\n"+ 
			" \n");
		}

}