OpenComet_.java

/**
* OpenComet_.java
* Created in 2012 by Benjamin Gyori
* National University of Singapore
* e-mail: ben.gyori@gmail.com
*
* OpenComet_.java is the outside wrapper for the OpenComet plug-in.
* It displays the GUI and manages all input-output functions
* by the plug-in.
*
* This plugin is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License version 3 
* as published by the Free Software Foundation.
*
* This work is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* When you use this plugin for your work, please cite
* Gyori BM, Venkatachalam G, et al. OpenComet: An automated tool for 
* comet assay image analysis

* You should have received a copy of the GNU General Public License
* along with this plugin; if not, write to the Free Software
* Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
*/

import ij.*;
import ij.process.*;
import ij.gui.*;
import ij.plugin.*;

import java.io.*;
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
import java.util.Date;
import java.text.DateFormat;
import java.text.SimpleDateFormat;

//import CometStatistics.CometAnalyzer;
import java.util.HashMap;
import java.util.Map;


public class OpenComet_ implements PlugIn, MouseListener {
    //private JLabel inFilesLabel, outDirLabel;
    private JLabel inFilesStatusLabel, outDirStatusLabel;
    private JButton inFilesButton, outDirButton, runButton;
    private JButton updateOutputButton;
    private JButton liveButton;
    private ActionListener inFilesButtonLis, outDirButtonLis, runButtonLis;
    private ActionListener updateOutputButtonLis;
    private ActionListener liveButtonLis;
    private JFileChooser inFileChooser, outDirChooser;
    private JTextField outFileNameField;
    private JCheckBox bgCorrectCheck;
    private JRadioButton headFindingAuto, headFindingProfile;
    private JRadioButton headFindingBrightest;
    private int cometOptions;

    private static Color labelInvalidColor = new Color(200,0,0);
    private static Color labelValidColor = new Color(0,150,0);

    File[] inFiles;
    File outDir;
    String outDirPath;
    String outFileName;

    private static Color cometValidColor = Color.red;
    private static Color cometInvalidColor = Color.gray;
    private static Color cometOutlierColor = Color.orange;
    private static Color cometColor = Color.yellow;
    private static Color headColor = Color.green;
    private static Color tailColor = Color.blue;

    private HashMap<ImagePlus,Comet[]> Comets;

    public OpenComet_(){}

    public void run(String arg) {
        IJ.log("Welcome to OpenComet v1.3.1!");
        makeLayout();
        updateOutputButton.setEnabled(false);
        }

    private void runOnInput(int type){
        // Make an instance of the comet analyzer class
        CometAnalyzer cometAnalyzer = new CometAnalyzer();
        Comets = new HashMap<ImagePlus,Comet[]>();
        cometOptions = 0;
        // Setup comet analysis options
        if(bgCorrectCheck.isSelected())
            cometOptions |= CometAnalyzer.COMETFIND_BGCORRECT;
        if(headFindingAuto.isSelected())
            cometOptions |= CometAnalyzer.HEADFIND_AUTO;
        if(headFindingProfile.isSelected())
            cometOptions |= CometAnalyzer.HEADFIND_PROFILE;
        if(headFindingBrightest.isSelected())
            cometOptions |= CometAnalyzer.HEADFIND_BRIGHTEST;

        String tmpText = outFileNameField.getText();
        if((tmpText!=null) && (tmpText.length()>1)){
            outFileName = tmpText;
        }

        IJ.log(cometOptions+"");

        if(type==0) {
        // Open each input image and run comet analysis
            // Iterate over each input file
            for(int i=0;i<inFiles.length;i++){
                // Try to open file as image
                ImagePlus imp = IJ.openImage(inFiles[i].getPath());

                // If image could be opened, run comet analysis
                if(imp!=null){
                    String imageKey =  inFiles[i].getName();

                    IJ.log("Run started, image key: "+ imageKey);

                    Comet[] cometsOut =
                        cometAnalyzer.cometAnalyzerRun(imp, cometOptions);
                    IJ.log("Run complete, image key: "+ imageKey);
                    storeComets(cometsOut,imp,imageKey);
                    // if(cometsOut!=null && cometsOut.length>0){
                        // ImageProcessor ip = imp.getProcessor();
                        // int imgType = imp.getType();
                        // ColorProcessor ip_out = null;
                        // if(imgType == 0){
                            // TypeConverter t = new TypeConverter(ip,false);
                            // ip_out = (ColorProcessor)t.convertToRGB();
                            // }
                        //RGB
                        // else if(imgType == 4){
                            // ip_out = (ColorProcessor)(ip.duplicate());
                            // }

                        // String imgOutFileName = imageKey +"_out.tif";
                        // ImagePlus img_out = new ImagePlus(imgOutFileName,ip_out);
                        // Comets.put(img_out, cometsOut);
                        // for(int j=0;j<cometsOut.length;j++){
                            // if(cometsOut[j].status==Comet.VALID)
                                // printArray(cometsOut[j].cometProfile);
                        // }
                        // Overlay cometOverlay = new Overlay();
                        // drawComets(ip_out, cometOverlay, cometsOut);
                        // img_out.setOverlay(cometOverlay);
                        // img_out.show();
                        // img_out.getCanvas().addMouseListener(this);
                        // ImagePlus img_out_save = img_out.flatten();
                        // IJ.save(img_out_save, outDirPath + imgOutFileName);
                        // }
                    // else {
                        // IJ.log("No comets stored");
                    // }
                 }
                else {
                    IJ.log("Could not open " + inFiles[i].getName() +
                           ", unsupported format");
                    }
                }
            }
            else {
                ImageWindow imw = WindowManager.getCurrentWindow();
                if(imw!=null){
                    ImagePlus img = imw.getImagePlus();
                    ImagePlus img2 = imw.getImagePlus().duplicate();
                    if(img!=null){
                        Comet[] cometsOut = 
                            cometAnalyzer.cometAnalyzerRun(img,cometOptions);
                        if(cometsOut==null || cometsOut.length==0){
                            IJ.log("No comets found.");
                        }
                        else {
                            IJ.log("Number of comets found: "+cometsOut.length);
                        }
                        storeComets(cometsOut,img2,outFileName+"_image");
                        }
                    }
                }

            printComets(outFileName);
            updateOutputButton.setEnabled(true);
            runButton.setEnabled(false);
            }

        private void storeComets(Comet[] cometsOut, ImagePlus imp,
                                 String imageKey){
            ImageProcessor ip = imp.getProcessor();
            int imgType = imp.getType();
            ColorProcessor ip_out = null;
            if(imgType == ImagePlus.GRAY8){
                TypeConverter t = new TypeConverter(ip,false);
                ip_out = (ColorProcessor)t.convertToRGB();
            }
            else if (imgType == ImagePlus.GRAY16 || imgType == ImagePlus.GRAY32){
                ImageProcessor ip_temp = ip.convertToByte(true); 
                TypeConverter t = new TypeConverter(ip_temp,false);
                ip_out = (ColorProcessor)t.convertToRGB();
            }
            else if(imgType == ImagePlus.COLOR_RGB){
                ip_out = (ColorProcessor)(ip.duplicate());
            }
            else {
                IJ.log("Unhandled image type: "+imgType);
            }

            String imgOutFileName = imageKey +"_out.tif";
            ImagePlus img_out = new ImagePlus(imgOutFileName,ip_out);

            if(cometsOut!=null && cometsOut.length>0){
                Comets.put(img_out, cometsOut);

                for(int j=0;j<cometsOut.length;j++){
                    if(cometsOut[j].status==Comet.VALID)
                        printArray(cometsOut[j].cometProfile);
                }

                Overlay cometOverlay = new Overlay();
                drawComets(ip_out, cometOverlay, cometsOut);
                img_out.setOverlay(cometOverlay);
            } else {
                IJ.log("No comets in image stored.");
            }

            img_out.show();
            img_out.getCanvas().addMouseListener(this);

            ImagePlus img_out_save = img_out.flatten();
            IJ.save(img_out_save, outDirPath + imgOutFileName);
        }

    private void drawComets(ImageProcessor ip, Overlay overlay, Comet[] comets){
        for(int i=0;i<comets.length;i++){
            if(comets[i].status == Comet.INVALID){
                comets[i].cometRoi.setStrokeColor(cometInvalidColor);
                overlay.add(comets[i].cometRoi);
            }
            else if (comets[i].status == Comet.OUTLIER){
                comets[i].cometRoi.setStrokeColor(cometOutlierColor);
                comets[i].headRoi.setStrokeColor(cometOutlierColor);
                //overlay.add(comets[i].cometRoi);
                overlay.add(comets[i].oldRoi);
                overlay.add(comets[i].headRoi);

                ip.setColor(Color.red);
                TextRoi textRoi = new TextRoi(comets[i].x+comets[i].width,
                                              comets[i].y, "" + comets[i].id,
                                              new Font("Arial", Font.BOLD, 22));
                textRoi.drawPixels(ip);
            }
            else if(comets[i].status == Comet.VALID){
                comets[i].cometRoi.setStrokeColor(cometValidColor);
                comets[i].headRoi.setStrokeColor(cometValidColor);
                overlay.add(comets[i].cometRoi);
                overlay.add(comets[i].headRoi);

                ip.setColor(Color.red);
                TextRoi textRoi = new TextRoi(comets[i].x+comets[i].width,
                                              comets[i].y, ""+comets[i].id,
                                              new Font("Arial", Font.BOLD, 22));
                textRoi.drawPixels(ip);
                ImageProcessor ipProfile = getCometProfilePlot(comets[i]);
                ip.copyBits(ipProfile, comets[i].x,
                            comets[i].y,Blitter.COPY_TRANSPARENT);
            }

        }
    }

    private ImageProcessor getCometProfilePlot(Comet comet){
        ImageProcessor ip = new ColorProcessor(comet.width, comet.height);
        ip.invert();

        double heightStep = comet.height / comet.profileMax;
        drawProfilePlot(ip, comet.cometProfile, cometColor, heightStep);
        drawProfilePlot(ip, comet.headProfile, headColor, heightStep);
        drawProfilePlot(ip, comet.tailProfile, tailColor, heightStep);

        return ip;
        }

    private void drawProfilePlot(ImageProcessor ip, double[] profile,
                                 Color col, double heightStep){
        int height = ip.getHeight();
        int width = ip.getWidth();
        int x1,x2,y1,y2;
        ip.setColor(col);
        for(int x=0;x<width-1;x++){
            x1 = x; x2 = x+1;
            y1 = (int)((height - 1) - profile[x]*heightStep);
            y2 = (int)((height - 1) - profile[x+1]*heightStep);
            ip.drawLine(x1,y1,x2,y2);
            }
        }

    private void printComets(String fileName){
        // Setup output data file
        try {
            String outFileName = outDirPath + fileName + ".xls";
            FileOutputStream fos = new FileOutputStream(outFileName);
            BufferedOutputStream bos = new BufferedOutputStream(fos);
            PrintWriter outPrintWriter = new PrintWriter(bos);

            IJ.log("Out filename: " + outFileName);

            String sep = "\t";
            String headerstr = "FileName" + sep + "Num" + sep + 
                    "Flag" + sep + "CometArea" + sep + 
                    "CometIntensity" + sep + 
                    "CometLength" + sep + "CometDNA" + sep +
                    "HeadArea" + sep + "HeadIntensity" + sep +
                    "HeadLength" + sep + "HeadDNA"+ sep +
                    "HeadDNAPercent" + sep + 
                    "TailArea" + sep + "TailIntensity" + sep +
                    "TailLength" + sep + "TailDNA"+ sep + 
                    "TailDNAPercent" + sep + "TailMoment"
                    + sep + "OliveMoment";
            outPrintWriter.println(headerstr);

            for (Map.Entry<ImagePlus,Comet[]> element : Comets.entrySet()) {
                    ImagePlus imp = element.getKey();
                    String imgTitle = imp.getTitle();
                    IJ.log("Image title: "+imgTitle);
                    int endIdx = imgTitle.lastIndexOf('_');
                    if(endIdx > 0){
                        String imageKey = imgTitle.substring(0,endIdx);
                        Comet[] imageComets = element.getValue();
                        for(int i=0;i<imageComets.length;i++){
                            if(imageComets[i].status != Comet.INVALID){
                                String outstr = imageKey + sep;
                                outstr += imageComets[i].getMeasurementString(sep);
                                outPrintWriter.println(outstr);
                            }
                        }
                    }
                }

            CometStatistics cometStats = new CometStatistics(Comets,Comet.VALID);
            String outstr = cometStats.getStatisticsString(sep,"normal");
            outPrintWriter.print(outstr);

            cometStats = new CometStatistics(Comets,Comet.VALID|Comet.OUTLIER);
            outstr = cometStats.getStatisticsString(sep,"normal+outlier");
            outPrintWriter.print(outstr);

            outPrintWriter.close();
        }
        catch (Exception ex) {
            IJ.log(ex.toString());
            }
    }

    private void makeLayout(){
        ij.util.Java2.setSystemLookAndFeel();
        JDialog mainDialog = new JDialog(ij.IJ.getInstance(),"OpenComet",false);
        mainDialog.setLocationRelativeTo(ij.IJ.getInstance());
        mainDialog.setLayout(new BorderLayout(0,10));

        //ImagePlus imlogo = IJ.openImage("opencometlogo.gif");
        //if (imlogo != null) {
        //      mainDialog.setIconImage(imlogo.getImage());
        //    }

        inFileChooser = new JFileChooser();
        outDirChooser = new JFileChooser();

        runButtonLis = new ActionListener(){
            public void actionPerformed(ActionEvent e){
                if((inFiles == null) || (inFiles.length == 0)){
                    IJ.log("Select input files");
                    }
                else if((outDir == null)){
                    IJ.log("Select output directory");
                    }
                else {
                    runOnInput(0);
                    }
                }
            };

        liveButtonLis = new ActionListener(){
            public void actionPerformed(ActionEvent e){
                if((outDir == null)){
                    IJ.log("Select output directory");
                    }
                else {
                    runOnInput(1);
                }
            }
        };

        inFilesButtonLis = new ActionListener(){
            public void actionPerformed(ActionEvent e) {
                inFileChooser.setDialogTitle("Input Files");
                inFileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
                inFileChooser.setMultiSelectionEnabled(true);

                inFileChooser.showOpenDialog(null);

                inFiles = inFileChooser.getSelectedFiles();
                if(inFiles.length == 0){
                    inFilesStatusLabel.setText("Choose input files");
                    inFilesStatusLabel.setForeground(labelInvalidColor);
                    }
                else if(inFiles.length == 1){
                    inFilesStatusLabel.setText("1 file selected");
                    inFilesStatusLabel.setForeground(labelValidColor);
                    }
                else {
                    inFilesStatusLabel.setText(inFiles.length+" files selected");
                    inFilesStatusLabel.setForeground(labelValidColor);
                    }

                inFilesStatusLabel.repaint(); 
                    }
            };

        outDirButtonLis = new ActionListener(){
            public void actionPerformed(ActionEvent e){
                outDirChooser.setDialogTitle("Output Directory");
                outDirChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
                outDirChooser.setMultiSelectionEnabled(false);

                int result = outDirChooser.showOpenDialog(null);
                outDir = outDirChooser.getSelectedFile();  
                if(result==0){
                    outDirPath = outDir+"";
                    int len = outDirPath.length();

                    if(outDirPath.charAt(len-1) != File.separatorChar){
                        outDirPath = outDirPath + File.separatorChar;
                        }


                    String outDirStatusLabelText = outDirPath ;

                    if(len > 25){
                        outDirStatusLabelText = outDirPath.substring(0,12) +
                            "..." + outDirPath.substring(len-12,len);
                        }

                    boolean canWrite = checkWriteAccess(outDirPath);

                    if(canWrite) {
                          outDirStatusLabel.setText(outDirStatusLabelText);
                        outDirStatusLabel.setForeground(labelValidColor);
                        } else {
                          outDirStatusLabel.setText(outDirStatusLabelText);
                        outDirStatusLabel.setForeground(labelInvalidColor);
                        }
                    }
                else {
                    outDirStatusLabel.setText("Choose output directory");
                    outDirStatusLabel.setForeground(labelInvalidColor);
                    }
                    outDirStatusLabel.repaint(); 
                }
            };

        updateOutputButtonLis = new ActionListener(){
            public void actionPerformed(ActionEvent e){
                printComets(outFileName + "_update");

                for (Map.Entry<ImagePlus,Comet[]> element : Comets.entrySet()) {
                    ImagePlus imp = element.getKey();
                    if(imp.getCanvas()==null) continue;
                    ImagePlus impSave = imp.flatten();
                    IJ.save(impSave, outDirPath + imp.getTitle());
                }
            }
        }; 

        // liveButtonLis = new ActionListener(){
            // public void actionPerformed(ActionEvent e){
                // ImageWindow imw = WindowManager.getCurrentWindow();
                // if(imw!=null){
                    // ImagePlus img = imw.getImagePlus();
                    // if(img!=null){
                        // CometAnalyzer cometAnalyzer = new CometAnalyzer();
                        // Comet[] cometsOut = cometAnalyzer.cometAnalyzerRun(img,3);
                        // IJ.log("Number of comets found: "+cometsOut.length);
                    // }
                // }
            // }
        // }; 

        // Set up main dialog layout
        Panel mainPanel = new Panel();
        mainPanel.setLayout(new GridBagLayout());
        GridBagConstraints c = new GridBagConstraints();
        c.insets = new Insets(2,2,8,8);

        // Input files label 
        JLabel inFilesLabel = new JLabel("Input files");
        c.fill = GridBagConstraints.NONE; c.gridx = 0; c.gridy = 0;
        c.anchor = GridBagConstraints.LINE_START;
        mainPanel.add(inFilesLabel, c);
        // Input files browse button
        inFilesButton = new JButton("Browse");
        c.fill = GridBagConstraints.NONE; c.gridx = 1; c.gridy = 0;
        c.anchor = GridBagConstraints.LINE_START;
        mainPanel.add(inFilesButton, c);
        inFilesButton.addActionListener(inFilesButtonLis);
        // Input files status label
        inFilesStatusLabel = new JLabel("Choose input files");
        inFilesStatusLabel.setForeground(labelInvalidColor);
        c.fill = GridBagConstraints.NONE; c.gridx = 0; c.gridy = 1;
        c.gridwidth = 2;
        c.anchor = GridBagConstraints.LINE_START;

        mainPanel.add(inFilesStatusLabel, c);

        // Output directory label
        JLabel outDirLabel = new JLabel("Output directory");
        c.fill = GridBagConstraints.NONE; c.gridx = 0; c.gridy = 2;
        c.gridwidth = 1;
        c.anchor = GridBagConstraints.LINE_START;
        mainPanel.add(outDirLabel, c);
        // Output directory browse button
        outDirButton = new JButton("Browse");
        c.fill = GridBagConstraints.NONE; c.gridx = 1; c.gridy = 2;
        c.gridwidth = 1;
        c.anchor = GridBagConstraints.LINE_START;
        mainPanel.add(outDirButton, c);
        outDirButton.addActionListener(outDirButtonLis);
        // Output directory status label
        outDirStatusLabel = new JLabel("Choose output directory");
        outDirStatusLabel.setForeground(labelInvalidColor);
        c.fill = GridBagConstraints.NONE; c.gridx = 0; c.gridy = 3;
        c.gridwidth = 2;
        c.anchor = GridBagConstraints.LINE_START;
        mainPanel.add(outDirStatusLabel, c);
        JLabel outFileNameLabel = new JLabel("Output file name");

        c.fill = GridBagConstraints.NONE; c.gridx = 0; c.gridy = 4;
        c.gridwidth = 1;
        c.anchor = GridBagConstraints.LINE_START;
        mainPanel.add(outFileNameLabel, c);

        Date dateNow = new Date();
        DateFormat dateFormat = new SimpleDateFormat("yyyy_MMdd_HHmmss");
        outFileName = "comets_" + dateFormat.format(dateNow);

        outFileNameField = new JTextField(20);
        outFileNameField.setText(outFileName);
        c.fill = GridBagConstraints.NONE; c.gridx = 0; c.gridy = 5;
        c.gridwidth = 2;
        c.anchor = GridBagConstraints.LINE_START;
        mainPanel.add(outFileNameField, c);

        // Comet finding options
        JSeparator cometFindingSep = new JSeparator(SwingConstants.HORIZONTAL);
        cometFindingSep.setPreferredSize(new Dimension(1,1));
        c.fill = GridBagConstraints.HORIZONTAL;
        c.gridy = 6;
        mainPanel.add(cometFindingSep,c);

        JLabel cometFindingLabel = new JLabel("Comet finding");
        bgCorrectCheck = new JCheckBox("Background correction",true);

        c.fill = GridBagConstraints.NONE; c.gridx = 0; c.gridy = 7;
        c.gridwidth = 2;
        c.anchor = GridBagConstraints.LINE_START;
        mainPanel.add(cometFindingLabel, c);
        c.gridy = 8;
        mainPanel.add(bgCorrectCheck, c);

        // Head finding options
        JSeparator headFindingSep = new JSeparator(SwingConstants.HORIZONTAL);
        headFindingSep.setPreferredSize(new Dimension(1,1));
        c.fill = GridBagConstraints.HORIZONTAL;
        c.gridy = 9;
        mainPanel.add(headFindingSep,c);

        JLabel headFindingLabel = new JLabel("Head finding");

        Panel headFindingGroupPanel = new Panel();
        headFindingGroupPanel.setLayout(new BoxLayout(headFindingGroupPanel,
                                                      BoxLayout.Y_AXIS));
        headFindingAuto = new JRadioButton("Auto",true);
        headFindingProfile = new JRadioButton("Profile analysis");
        headFindingBrightest = new JRadioButton("Brigthest region");

        ButtonGroup headFindingGroup = new ButtonGroup();
        headFindingGroup.add(headFindingAuto);
        headFindingGroup.add(headFindingProfile);
        headFindingGroup.add(headFindingBrightest);
        headFindingGroupPanel.add(headFindingAuto);
        headFindingGroupPanel.add(headFindingProfile);
        headFindingGroupPanel.add(headFindingBrightest);

        c.fill = GridBagConstraints.NONE; c.gridx = 0; c.gridy = 10;
        c.gridwidth = 2;
        c.anchor = GridBagConstraints.LINE_START;
        mainPanel.add(headFindingLabel, c);

        c.fill = GridBagConstraints.NONE; c.gridx = 0; c.gridy = 11;
        c.gridwidth = 2;
        c.anchor = GridBagConstraints.LINE_START;
        mainPanel.add(headFindingGroupPanel, c);
        //mainPanel.add(headFindingAuto, c);
        //c.gridy = 10;
        //mainPanel.add(headFindingProfile, c);
        //c.gridy = 11;
        //mainPanel.add(headFindingBrightest, c);

        // Run button panel
        Panel runPanel = new Panel();
        runButton = new JButton("Run");
        updateOutputButton = new JButton("Update");
        liveButton = new JButton("Live");
        runPanel.add(runButton);
        runPanel.add(updateOutputButton);
        runPanel.add(liveButton);
        runButton.addActionListener(runButtonLis);
        updateOutputButton.addActionListener(updateOutputButtonLis);
        liveButton.addActionListener(liveButtonLis);

        // Add panels to main dialog
        Box mainBox = Box.createVerticalBox();
        mainBox.add(mainPanel);
        mainBox.add(Box.createVerticalStrut(3) );
        mainDialog.add(mainBox, BorderLayout.CENTER);
        mainDialog.add(runPanel, BorderLayout.SOUTH);
        mainDialog.pack();
        mainDialog.setResizable(false);
        mainDialog.setVisible(true);
        }

    public void mousePressed (MouseEvent e) {
        int x = e.getX();
        int y = e.getY();
        ImageCanvas canvas = (ImageCanvas)e.getSource();
        ImagePlus imp = canvas.getImage();
        x = canvas.offScreenX(x);
        y = canvas.offScreenY(y);
        IJ.log(x+","+y);
        Comet comet = findClickedComet(imp, x, y);
        if(comet!=null){
            IJ.log("Comet found");
            comet.status = Comet.DELETED;
            comet.cometRoi.setStrokeColor(Color.gray);
            comet.oldRoi.setStrokeColor(Color.gray);
            if(comet.headRoi!=null){
                comet.headRoi.setStrokeColor(Color.gray);
                }
            }
        }


    private Comet findClickedComet(ImagePlus imp, int x,int y){
        Comet[] comets = (Comet[])Comets.get(imp);
        if(comets!=null){
            for(int i=0;i<comets.length;i++){
                if(comets[i].cometRoi.contains(x, y)){
                    return comets[i];
                }
            }
        }
        return null;
    }

    public void mouseReleased (MouseEvent e) {}
    public void mouseClicked (MouseEvent e) {}
    public void mouseEntered (MouseEvent e) {}
    public void mouseExited (MouseEvent e) {}

    private boolean checkWriteAccess(String path){
        File tmpFile = new File(path+"tmp");
        try {
            tmpFile.createNewFile();
            tmpFile.delete();
            }
        catch(IOException e) {
            return false;
            }
        return true;
        }

    private void printArray(double[] arr){
        String s = "";
        for(int i=0;i<arr.length;i++){
            s += arr[i];
            if(i<arr.length-1) s+=",";
            }
        IJ.log(s);
        }
}