package ij.plugin;
import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import ij.plugin.ChannelSplitter;
import java.awt.image.BufferedImage;
import java.awt.event.*;
import java.util.Vector;

/**
 * This plugin implements the Image/Colors/Arrange Channels command,
 *  which allows the user to change the order of channels.
 *
 * @author Norbert Vischer <vischer@science.uva.nl> 23-sep-2012
 */
public class ChannelArranger implements PlugIn, TextListener {
    private ThumbnailsCanvas thumbNails;
    private String patternString;
    private String allowedDigits;
    private TextField orderField;
    private int nChannels;

    public void run(String arg) {
        ImagePlus imp = IJ.getImage();
        nChannels = imp.getNChannels();
        if (nChannels==1) {
            IJ.error("Channel Arranger", "Image must have more than one channel");
            return;
        }
        if (nChannels>9) {
            IJ.error("Channel Arranger", "This command does not work with more than 9 channels.");
            return;
        }
        patternString = "1234567890".substring(0, nChannels);
        allowedDigits = patternString;
        GenericDialog gd = new GenericDialog("Arrange Channels");
        thumbNails = new ThumbnailsCanvas(imp);
        Panel panel = new Panel();
        panel.add(thumbNails);
        gd.addPanel(panel);
        //gd.setInsets(20, 20, 5);
        gd.addStringField("New channel order:", allowedDigits);
        Vector v = gd.getStringFields();
        orderField = (TextField)v.elementAt(0);
        orderField.addTextListener(this);
        gd.addHelp(IJ.URL+"/docs/menus/image.html#arrange");
        gd.showDialog();
        if (gd.wasCanceled())
            return;
        String newOrder = gd.getNextString();
        int nChannels2 = newOrder.length();
        if (nChannels2==0)
            return;
        for (int i=0; i<nChannels2; i++) {
            if (!Character.isDigit(newOrder.charAt(i))) {
                IJ.error("Channel Arranger", "Non-digit in new order string: \""+newOrder+"\"");
                return;
            }
        }
        if (nChannels2<nChannels) {
            String msg = "The number of channels will be reduced from "+nChannels+" to "+nChannels2+".";
            if (!IJ.showMessageWithCancel("Reduce Number of Channels?", msg))
                return;
        }
        Point location = imp.getWindow()!=null?imp.getWindow().getLocation():null;
        int[] newOrder2 = new int[nChannels2];
        for (int i=0; i<nChannels2; i++)
            newOrder2[i] = newOrder.charAt(i)-48;
        ImagePlus imp2 = run(imp, newOrder2);
        imp2.copyAttributes(imp);
        if (location!=null)
            ImageWindow.setNextLocation(location);
        imp2.changes = true;
        imp2.show();
    }
    
    /** Changes the order of the channels in a hyperstack.
        @param img source hyperstack
        @param newOrder the new channel order
        @return a hyperstack with channels in the specified order
        <p>
        The following example opens the FluorescentCells sample  
        image and reverses the order of the channels.
        <pre>
        ImagePlus img = IJ.openImage("http://imagej.nih.gov/ij/images/FluorescentCells.zip");
        int[] order = {3,2,1};
        ImagePlus img2 = ChannelArranger.run(img, order);
        img2.setDisplayMode(IJ.COLOR);
        img2.show();
        </pre>
    */
    public static ImagePlus run(ImagePlus img, int[] newOrder) {
        int channel = img.getChannel();
        int slice = img.getSlice();
        int frame = img.getFrame();
        ImagePlus[] channels = ChannelSplitter.split(img);
        int nChannels2 = newOrder.length;
        if (nChannels2>channels.length)
            nChannels2 = channels.length;
        ImagePlus[] channels2 = new ImagePlus[nChannels2];
        for (int i=0; i<nChannels2; i++) {
            int index = newOrder[i]-1;
            if (index<0 || index>=channels.length)
                throw new IllegalArgumentException("value out of range:"+newOrder[i]);
            channels2[i] = channels[index];
        }
        ImagePlus img2 = null;
        if (nChannels2==1)
            img2 = channels2[0];
        else
            img2 = RGBStackMerge.mergeChannels(channels2, false);
        int mode2 = IJ.COLOR;
        if (img.isComposite())
            mode2 = ((CompositeImage)img).getMode();
        if (img2.isComposite())
            ((CompositeImage)img2).setMode(mode2);
        if (channel<=nChannels2) {
            int channel2 = newOrder[channel-1];
            img2.setPosition(channel2, slice, frame);
        }
        Overlay overlay = img.getOverlay();
        if (overlay!=null) {
            for (int i=0; i<overlay.size(); i++) {
                Roi roi = overlay.get(i);
                int c = roi.getCPosition();
                int z = roi.getZPosition();
                int t = roi.getTPosition();
                if (c>=1 && c<=nChannels2)
                    roi.setPosition(newOrder[c-1], z, t);
            }
            img2.setOverlay(overlay);
        }
        img.changes = false;
        img.close();
        return img2;
    }

    public void textValueChanged(TextEvent e) {
        TextField tf = (TextField) e.getSource();
        String typed = tf.getText();
        if (typed.length()>nChannels) {
            orderField.setText(patternString);
            return;
        }
        for (int jj=0; jj<typed.length(); jj++) {
            String digit = typed.substring(jj, jj + 1);
            int found = typed.indexOf(digit, jj + 1);
            if (found != -1) {
                orderField.setText(patternString);
                return;
            }
            if (allowedDigits.indexOf(digit)==-1) {
                orderField.setText(patternString);
                return;
            }
        }
        patternString = typed;
        thumbNails.setSequence(patternString);
        thumbNails.repaint();
        //orderField.setText(patternString);
    }

}

class ThumbnailsCanvas extends Canvas implements MouseListener, MouseMotionListener, ActionListener {

    protected static Cursor handCursor = new Cursor(Cursor.HAND_CURSOR);
    protected static Cursor defaultCursor = new Cursor(Cursor.DEFAULT_CURSOR);
    Image os;
    Graphics osg;
    CompositeImage cImp;
    int iconSize = 100;
    int iconWidth = iconSize, iconHeight = iconSize;
    int dx = 0, dy = 0;
    int separatorY = 6;
    int marginY = 10;
    int marginX = 44;
    int nChannels;
    int channelUnderCursor = 0;
    String seq = "1234567890";
    int currentChannel, currentSlice, currentFrame;

    public ThumbnailsCanvas(ImagePlus imp) {
        if (!imp.isComposite()) {
            return;
        }
        cImp = (CompositeImage) imp;
        addMouseListener(this);
        addMouseMotionListener(this);
        currentChannel = cImp.getChannel();
        currentSlice = cImp.getSlice();
        currentFrame = cImp.getFrame();
        channelUnderCursor = currentChannel;
        int ww = cImp.getWidth();
        int hh = cImp.getHeight();
        if (ww > hh) {
            iconHeight = iconWidth * hh / ww;
            dy = (iconWidth - iconHeight) / 2;
        }
        if (ww < hh) {
            iconWidth = iconHeight * ww / hh;
            dx = (iconHeight - iconWidth) / 2;
        }
        nChannels = cImp.getNChannels();
        seq = seq.substring(0, nChannels);
        setSize((nChannels + 1) * iconSize, 2 * iconSize + 30);
    }

    public void update(Graphics g) {
        paint(g);
    }

    public void setSequence(String seq) {
        this.seq = seq;
    }

    public int[] getStackPos() {
        return new int[]{currentChannel, currentSlice, currentFrame};
    }

    public void paint(Graphics g) {
        if (g == null) {
            return;
        }
        int savedMode = cImp.getMode();
        if (savedMode==IJ.COMPOSITE)
            cImp.setMode(IJ.COLOR);
        BufferedImage bImg;
        ImageProcessor ipSmall;

        os = createImage((nChannels + 1) * iconSize, 2 * iconSize + 30);
        osg = os.getGraphics();
        osg.setFont(ImageJ.SansSerif12);
        int y1;
        for (int chn = 1; chn <= nChannels; chn++) {
            cImp.setPositionWithoutUpdate(chn, currentSlice, currentFrame);
            cImp.updateImage();
            ipSmall = cImp.getProcessor().resize(iconWidth, iconHeight, true);
            bImg = ipSmall.getBufferedImage();
            int index = chn - 1;
            y1 = marginY;
            for (int row = 0; row < 2; row++) {
                if (index >= 0) {
                    int xx = index * iconSize + marginX;
                    osg.drawImage(bImg, xx + dx, y1 + dy, null);
                    osg.setColor(Color.LIGHT_GRAY);
                    osg.drawRect(xx, y1, iconSize, iconSize);
                    osg.fillRoundRect(xx + iconSize / 2 - 4, y1 + iconSize - 22, 18, 18, 6, 6);
                    osg.setColor(Color.BLACK);
                    osg.drawRoundRect(xx + iconSize / 2 - 4, y1 + iconSize - 22, 18, 18, 6, 6);
                    osg.drawString("" + chn, xx + 52, y1 + iconSize - 7);
                    index = seq.indexOf("" + chn, 0);
                    if (seq.indexOf("" + chn, index) == -1) {//char must not occur twice
                        index = -1;
                    }
                }
                y1 += (iconSize + separatorY);
            }
        }
        y1 = marginY + iconSize - 7;
        osg.drawString("Old:", 6, y1);
        y1 += (iconSize + separatorY);
        osg.drawString("New:", 6, y1);
        osg.dispose();
        if (os == null) {
            return;
        }
        g.drawImage(os, 0, 0, this);
        if (savedMode==IJ.COMPOSITE)
            cImp.setMode(savedMode);
        cImp.setPosition(currentChannel, currentSlice, currentFrame);
        cImp.updateImage();
    }

    protected void handlePopupMenu(MouseEvent e) {
        int x = e.getX();
        int y = e.getY();
        PopupMenu popup = new PopupMenu();
        String[] colors = "Grays,-,Red,Green,Blue,Yellow,Magenta,Cyan,-,Fire,Ice,Spectrum,3-3-2 RGB,Red/Green".split(",");
        for (int jj = 0; jj < colors.length; jj++) {
            if (colors[jj].equals("-")) {
                popup.addSeparator();
            } else {
                MenuItem mi = new MenuItem(colors[jj]);
                popup.add(mi);
                mi.addActionListener(this);
            }
        }
        add(popup);
        if (IJ.isMacOSX()) {
            IJ.wait(10);
        }
        popup.show(this, x, y);
        setCursor(defaultCursor);
    }

    public void actionPerformed(ActionEvent e) {
        String cmd = e.getActionCommand();
        cImp.setPosition(currentChannel, currentSlice, currentFrame);
        CompositeImage cImp = (CompositeImage) this.cImp;

        IJ.run(cmd);

        repaint();
        setCursor(defaultCursor);
    }

    public void mouseMoved(MouseEvent e) {
        int x = e.getX() - marginX;
        int y = e.getY() - marginY;
        if (x < 0 || x > nChannels * iconSize || y < 0 || y > iconSize * 2 + separatorY) {
            setCursor(defaultCursor);
            channelUnderCursor = 0;
        } else {
            int chn = x / iconSize + 1;
            if (y > iconSize) {
                if (chn <= seq.length()) {
                    String digit = seq.substring(chn - 1, chn);
                    chn = "1234567890".indexOf(digit) + 1;
                } else {
                    chn = 0;
                }
            }
            if (y > 2 * iconSize + separatorY) {
                chn = 0;
            }
            channelUnderCursor = chn;
        }

        if (channelUnderCursor > 0) {
            setCursor(handCursor);
        } else {
            setCursor(defaultCursor);
        }

    }

    public void mouseEntered(MouseEvent e) {
    }

    public void mousePressed(MouseEvent e) {
        if (channelUnderCursor > 0) {
            currentChannel = channelUnderCursor;
            handlePopupMenu(e);
            repaint();
        }
    }

    public void mouseReleased(MouseEvent e) {
        mouseMoved(e);
    }

    public void mouseExited(MouseEvent e) {
    }

    public void mouseDragged(MouseEvent e) {
    }

    public void mouseClicked(MouseEvent e) {
    }
}