package ij.plugin;
import ij.*;
import ij.gui.*;
import ij.process.*;
import ij.measure.Calibration;
import ij.macro.Interpreter;
import ij.io.FileInfo;
import ij.plugin.frame.Recorder;
import java.awt.image.ColorModel;


/** Implements the "Stack to HyperStack", "RGB to HyperStack" 
    and "HyperStack to Stack" commands. */
public class HyperStackConverter implements PlugIn {
    public static final int CZT=0, CTZ=1, ZCT=2, ZTC=3, TCZ=4, TZC=5;
    static final int C=0, Z=1, T=2;
    static final String[] orders = {"xyczt(default)", "xyctz", "xyzct", "xyztc", "xytcz", "xytzc"};
    static int ordering = CZT;
    static boolean splitRGB = true;

    public void run(String arg) {
        if (arg.equals("new"))
            {newHyperStack(); return;}
        ImagePlus imp = IJ.getImage();
        if (arg.equals("stacktohs"))
            convertStackToHS(imp);
        else if (arg.equals("hstostack"))
            convertHSToStack(imp);
    }
    
    /** Converts the specified stack into a hyperstack with 'c' channels, 'z' slices and
         't' frames using the default ordering ("xyczt") and display mode ("Composite"). */
    public static ImagePlus toHyperStack(ImagePlus imp, int c, int z, int t) {
        return toHyperStack(imp, c, z, t, null, null);
    }

    /** Converts the specified stack into a hyperstack with 'c' channels,
     *  'z' slices and 't' frames. The default "xyczt" order is used if
     * 'order' is null. The default "composite" display mode is used
     * if 'mode' is null.
     * @param imp the stack to be converted
     * @param c channels
     * @param z slices
     * @param t frames
     * @param order hyperstack order ("default", "xyctz", "xyzct", "xyztc", "xytcz" or "xytzc")
     * @param mode display mode ("composite", "color" or "grayscale")
     * @return the resulting hyperstack
    */
    public static ImagePlus toHyperStack(ImagePlus imp, int c, int z, int t, String order, String mode) {
        int n = imp.getStackSize();
        if (n==1 || imp.getBitDepth()==24)
            throw new IllegalArgumentException("Non-RGB stack required");
        if (c*z*t!=n)
            throw new IllegalArgumentException("C*Z*T not equal stack size");
        imp.setDimensions(c, z, t);
        if (order==null || order.equals("default") || order.equals("xyczt"))
            order = orders[0];
        int intOrder = CZT;
        for (int i=0; i<orders.length; i++) {
            if (order.equals(orders[i])) {
                intOrder = i;
                break;
            }
        }
        if (intOrder!=CZT && imp.getStack().isVirtual())
            throw new IllegalArgumentException("Virtual stacks must by in XYCZT order");
        (new HyperStackConverter()).shuffle(imp, intOrder);
        ImagePlus imp2 = imp;
        int intMode = IJ.COMPOSITE;
        if (mode!=null) {
            if (mode.equalsIgnoreCase("color"))
                intMode = IJ.COLOR;
            else if (mode.equalsIgnoreCase("grayscale"))
                intMode = IJ.GRAYSCALE;
        }
        if (c>1) {
            LUT[] luts = imp.getLuts();
            if (luts!=null && luts.length<c)
                luts = null;
            imp2 = new CompositeImage(imp, intMode);
            if (luts!=null)
                ((CompositeImage)imp2).setLuts(luts);
        }
        imp2.setOpenAsHyperStack(true);
        imp2.setOverlay(imp.getOverlay());
        return imp2;
    }
        
    /** Displays the specified stack in a HyperStack window. Based on the 
        Stack_to_Image5D class in Joachim Walter's Image5D plugin. */
    void convertStackToHS(ImagePlus imp) {
        int nChannels = imp.getNChannels();
        int nSlices = imp.getNSlices();
        int nFrames = imp.getNFrames();
        int stackSize = imp.getImageStackSize();
        if (stackSize==1) {
            IJ.error("Stack to HyperStack", "Stack required");
            return;
        }
        boolean rgb = imp.getBitDepth()==24;
        String[] modes = {"Composite", "Color", "Grayscale"};
        GenericDialog gd = new GenericDialog("Convert to HyperStack");
        gd.addChoice("Order:", orders, orders[ordering]);
        gd.addNumericField("Channels (c):", nChannels, 0);
        gd.addNumericField("Slices (z):", nSlices, 0);
        gd.addNumericField("Frames (t):", nFrames, 0);
        gd.addChoice("Display Mode:", modes, modes[1]);
        if (rgb) {
            gd.setInsets(15, 0, 0);
            gd.addCheckbox("Convert RGB to 3 Channel Hyperstack", splitRGB);
        }
        gd.showDialog();
        if (gd.wasCanceled()) return;
        ordering = gd.getNextChoiceIndex();
        nChannels = (int) gd.getNextNumber();
        nSlices = (int) gd.getNextNumber();
        nFrames = (int) gd.getNextNumber();
        int mode = gd.getNextChoiceIndex();
        if (rgb)
            splitRGB = gd.getNextBoolean();
        if (rgb && splitRGB==true) {
            new CompositeConverter().run(mode==0?"composite":"color");
            return;
        }
        if (rgb && nChannels>1) {
            IJ.error("HyperStack Converter", "RGB stacks are limited to one channel");
            return;
        }
        if (nChannels*nSlices*nFrames!=stackSize) {
            IJ.error("HyperStack Converter", "channels x slices x frames <> stack size");
            return;
        }
        imp.setDimensions(nChannels, nSlices, nFrames);
        if (ordering!=CZT && imp.getStack().isVirtual())
            IJ.error("HyperStack Converter", "Virtual stacks must by in XYCZT order.");
        else {
            shuffle(imp, ordering);
            ImagePlus imp2 = imp;
            if (nChannels>1 && imp.getBitDepth()!=24) {
                LUT[] luts = imp.getLuts();
                if (luts!=null && luts.length<nChannels) luts = null;
                imp2 = new CompositeImage(imp, mode+1);
                if (luts!=null)
                    ((CompositeImage)imp2).setLuts(luts);
            } else if (imp.getClass().getName().indexOf("Image5D")!=-1) {
                imp2 = imp.createImagePlus();
                imp2.setStack(imp.getTitle(), imp.getImageStack());
                imp2.setDimensions(imp.getNChannels(), imp.getNSlices(), imp.getNFrames());
                imp2.getProcessor().resetMinAndMax();
            }
            imp2.setOpenAsHyperStack(true);
            if (imp.getWindow()!=null || imp!=imp2)
                new StackWindow(imp2);
            if (imp!=imp2) {
                imp2.setOverlay(imp.getOverlay());
                imp.hide();
                WindowManager.setCurrentWindow(imp2.getWindow());
            }
        }
        if (Recorder.record && Recorder.scriptMode()) {
            String order = orders[ordering];
            if (order.equals(orders[0]))
                order = "default";
            Recorder.recordCall("imp2 = HyperStackConverter.toHyperStack(imp, "+nChannels+", "+
                nSlices+", "+nFrames+", \""+order+"\", \""+modes[mode]+"\");");
        }

    }

    /** Changes the dimension order of a 4D or 5D stack from 
        the specified order (CTZ, ZCT, ZTC, TCZ or TZC) to 
        the XYCZT order used by ImageJ. */
    public void shuffle(ImagePlus imp, int order) {
        int nChannels = imp.getNChannels();
        int nSlices = imp.getNSlices();
        int nFrames = imp.getNFrames();
        int first=C, middle=Z, last=T;
        int nFirst=nChannels, nMiddle=nSlices, nLast=nFrames;
        switch (order) {
            case CTZ: first=C; middle=T; last=Z;
                nFirst=nChannels; nMiddle=nFrames; nLast=nSlices;
                break;
            case ZCT: first=Z; middle=C; last=T;
                nFirst=nSlices; nMiddle=nChannels; nLast=nFrames;
                break;
            case ZTC: first=Z; middle=T; last=C;
                nFirst=nSlices; nMiddle=nFrames; nLast=nChannels;
                break;
            case TCZ: first=T; middle=C; last=Z;
                nFirst=nFrames; nMiddle=nChannels; nLast=nSlices;
                break;
            case TZC: first=T; middle=Z; last=C;
                nFirst=nFrames; nMiddle=nSlices; nLast=nChannels;
                break;
        }
        if (order!=CZT) {
            ImageStack stack = imp.getImageStack();
            Object[] images1 = stack.getImageArray();
            Object[] images2 = new Object[images1.length];
            System.arraycopy(images1, 0, images2, 0, images1.length);
            String[] labels1 = stack.getSliceLabels();
            String[] labels2 = new String[labels1.length];
            System.arraycopy(labels1, 0, labels2, 0, labels1.length);
            int[] index = new int[3];
            for (index[2]=0; index[2]<nFrames; ++index[2]) {
                for (index[1]=0; index[1]<nSlices; ++index[1]) {
                    for (index[0]=0; index[0]<nChannels; ++index[0]) {
                        int dstIndex = index[0] + index[1]*nChannels + index[2]*nChannels*nSlices;
                        int srcIndex = index[first] + index[middle]*nFirst + index[last]*nFirst*nMiddle;
                        images1[dstIndex] = images2[srcIndex];
                        labels1[dstIndex] = labels2[srcIndex];
                    }
                }
            }
        }
    }

    void convertHSToStack(ImagePlus imp) {
        if (!(imp.isHyperStack()||imp.isComposite()))
            return;
        ImagePlus imp2 = imp;
        if (imp.isComposite()) {
            ImageStack stack = imp.getStack();
            imp2 = imp.createImagePlus();
            imp2.setStack(imp.getTitle(), stack);
            int[] dim = imp.getDimensions();
            imp2.setDimensions(dim[2], dim[3], dim[4]);
            ImageProcessor ip2 = imp2.getProcessor();
            ip2.setColorModel(ip2.getDefaultColorModel());
        }
        imp2.setOpenAsHyperStack(false);
        if (imp.getWindow()!=null || imp!=imp2)
            new StackWindow(imp2);
        if (imp!=imp2) {
            imp2.setOverlay(imp.getOverlay());
            imp.hide();
        }
    }
    
    void newHyperStack() {
        IJ.runMacroFile("ij.jar:HyperStackMaker", "");
    }
    
}