package ij.process;

import java.util.*;
import java.awt.*;
import java.awt.image.*;
import ij.gui.*;

/** ShortProcessors contain a 16-bit unsigned image
    and methods that operate on that image. */
public class ShortProcessor extends ImageProcessor {

    private int min, max, snapshotMin, snapshotMax;
    private short[] pixels;
    private byte[] pixels8;
    private short[] snapshotPixels;
    private byte[] LUT;
    private boolean fixedScale;


    /** Creates a new ShortProcessor using the specified pixel array and ColorModel.
        Set 'cm' to null to use the default grayscale LUT. */
    public ShortProcessor(int width, int height, short[] pixels, ColorModel cm) {
        if (pixels!=null && width*height!=pixels.length)
            throw new IllegalArgumentException(WRONG_LENGTH);
        init(width, height, pixels, cm);
    }

    /** Creates a blank ShortProcessor using the default grayscale LUT that
        displays zero as black. Call invertLut() to display zero as white. */
    public ShortProcessor(int width, int height) {
        this(width, height, new short[width*height], null);
    }
    
    /** Creates a ShortProcessor from a TYPE_USHORT_GRAY BufferedImage. */
    public ShortProcessor(BufferedImage bi) {
        if (bi.getType()!=BufferedImage.TYPE_USHORT_GRAY)
            throw new IllegalArgumentException("Type!=TYPE_USHORT_GRAY");
        WritableRaster raster = bi.getRaster();
        DataBuffer buffer = raster.getDataBuffer();
        short[] data = ((DataBufferUShort) buffer).getData();
        //short[] data2 = new short[data.length];
        //System.arraycopy(data, 0, data2, 0, data.length);
        init(raster.getWidth(), raster.getHeight(), data, null);
    }

    void init(int width, int height, short[] pixels, ColorModel cm) {
        this.width = width;
        this.height = height;
        this.pixels = pixels;
        this.cm = cm;
        resetRoi();
    }

    /**
    * @deprecated
    * 16 bit images are normally unsigned but signed images can be simulated by
    * subtracting 32768 and using a calibration function to restore the original values.
    */
    public ShortProcessor(int width, int height, short[] pixels, ColorModel cm, boolean unsigned) {
        this(width, height, pixels, cm);
    }

    /** Obsolete. 16 bit images are normally unsigned but signed images can be used by
        subtracting 32768 and using a calibration function to restore the original values. */
    public ShortProcessor(int width, int height,  boolean unsigned) {
        this(width, height);
    }
    
    public void findMinAndMax() {
        if (fixedScale || pixels==null)
            return;
        int size = width*height;
        int value;
        min = 65535;
        max = 0;
        for (int i=0; i<size; i++) {
            value = pixels[i]&0xffff;
            if (value<min)
                min = value;
            if (value>max)
                max = value;
        }
        minMaxSet = true;
    }

    /** Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255. */
    public Image createImage() {
        boolean firstTime = pixels8==null;
        if (firstTime || !lutAnimation)
            create8BitImage();
        if (cm==null)
            makeDefaultColorModel();
        if (ij.IJ.isJava16())
            return createBufferedImage();
        if (source==null) {
            source = new MemoryImageSource(width, height, cm, pixels8, 0, width);
            source.setAnimated(true);
            source.setFullBufferUpdates(true);
            img = Toolkit.getDefaultToolkit().createImage(source);
        } else if (newPixels) {
            source.newPixels(pixels8, cm, 0, width);
            newPixels = false;
        } else
            source.newPixels();
        lutAnimation = false;
        return img;
    }
    
    // create 8-bit image by linearly scaling from 16-bits to 8-bits
    byte[] create8BitImage() {
        int size = width*height;
        if (pixels8==null)
            pixels8 = new byte[size];
        int value;
        int min2=(int)getMin(), max2=(int)getMax(); 
        double scale = 256.0/(max2-min2+1);
        for (int i=0; i<size; i++) {
            value = (pixels[i]&0xffff)-min2;
            if (value<0) value = 0;
            value = (int)(value*scale+0.5);
            if (value>255) value = 255;
            pixels8[i] = (byte)value;
        }
        return pixels8;
    }

    Image createBufferedImage() {
        if (raster==null) {
            SampleModel sm = getIndexSampleModel();
            DataBuffer db = new DataBufferByte(pixels8, width*height, 0);
            raster = Raster.createWritableRaster(sm, db, null);
        }
        if (image==null || cm!=cm2) {
            if (cm==null) cm = getDefaultColorModel();
            image = new BufferedImage(cm, raster, false, null);
            cm2 = cm;
        }
        lutAnimation = false;
        return image;
    }

    /** Returns this image as an 8-bit BufferedImage . */
    public BufferedImage getBufferedImage() {
        return convertToByte(true).getBufferedImage();
    }

    /** Returns a copy of this image as a TYPE_USHORT_GRAY BufferedImage. */
    public BufferedImage get16BitBufferedImage() {
        BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_USHORT_GRAY);
        Raster raster = bi.getData();
        DataBufferUShort db = (DataBufferUShort)raster.getDataBuffer();
        System.arraycopy(getPixels(), 0, db.getData(), 0, db.getData().length);
        bi.setData(raster);
        return bi;
    }

    /** Returns a new, blank ShortProcessor with the specified width and height. */
    public ImageProcessor createProcessor(int width, int height) {
        ImageProcessor ip2 = new ShortProcessor(width, height, new short[width*height], getColorModel());
        ip2.setMinAndMax(getMin(), getMax());
        ip2.setInterpolationMethod(interpolationMethod);
        return ip2;
    }

    public void snapshot() {
        snapshotWidth=width;
        snapshotHeight=height;
        snapshotMin=(int)getMin();
        snapshotMax=(int)getMax();
        if (snapshotPixels==null || (snapshotPixels!=null && snapshotPixels.length!=pixels.length))
            snapshotPixels = new short[width * height];
        System.arraycopy(pixels, 0, snapshotPixels, 0, width*height);
    }
    
    public void reset() {
        if (snapshotPixels==null)
            return;
        min=snapshotMin;
        max=snapshotMax;
        minMaxSet = true;
        System.arraycopy(snapshotPixels, 0, pixels, 0, width*height);
    }
    
    public void reset(ImageProcessor mask) {
        if (mask==null || snapshotPixels==null)
            return; 
        if (mask.getWidth()!=roiWidth||mask.getHeight()!=roiHeight)
            throw new IllegalArgumentException(maskSizeError(mask));
        byte[] mpixels = (byte[])mask.getPixels();
        for (int y=roiY, my=0; y<(roiY+roiHeight); y++, my++) {
            int i = y * width + roiX;
            int mi = my * roiWidth;
            for (int x=roiX; x<(roiX+roiWidth); x++) {
                if (mpixels[mi++]==0)
                    pixels[i] = snapshotPixels[i];
                i++;
            }
        }
    }

    /** Swaps the pixel and snapshot (undo) arrays. */
    public void swapPixelArrays() {
        if (snapshotPixels==null) return;   
        short pixel;
        for (int i=0; i<pixels.length; i++) {
            pixel = pixels[i];
            pixels[i] = snapshotPixels[i];
            snapshotPixels[i] = pixel;
        }
    }

    public void setSnapshotPixels(Object pixels) {
        snapshotPixels = (short[])pixels;
        snapshotWidth=width;
        snapshotHeight=height;
    }

    public Object getSnapshotPixels() {
        return snapshotPixels;
    }

    /** Returns the smallest displayed pixel value. */
    public double getMin() {
        if (!minMaxSet) findMinAndMax();
        return min;
    }

    /** Returns the largest displayed pixel value. */
    public double getMax() {
        if (!minMaxSet) findMinAndMax();
        return max;
    }

    /**
    Sets the min and max variables that control how real
    pixel values are mapped to 0-255 screen values.
    @see #resetMinAndMax
    @see ij.plugin.frame.ContrastAdjuster 
    */
    public void setMinAndMax(double minimum, double maximum) {
        if (minimum==0.0 && maximum==0.0)
            {resetMinAndMax(); return;}
        if (minimum<0.0)
            minimum = 0.0;
        if (maximum>65535.0)
            maximum = 65535.0;
        min = (int)minimum;
        max = (int)maximum;
        fixedScale = true;
        minMaxSet = true;
        resetThreshold();
    }
    
    /** Recalculates the min and max values used to scale pixel
        values to 0-255 for display. This ensures that this 
        ShortProcessor is set up to correctly display the image. */
    public void resetMinAndMax() {
        fixedScale = false;
        findMinAndMax();
        resetThreshold();
    }

    public int getPixel(int x, int y) {
        if (x>=0 && x<width && y>=0 && y<height)
            return pixels[y*width+x]&0xffff;
        else
            return 0;
    }

    public final int get(int x, int y) {
        return pixels[y*width+x]&0xffff;
    }

    public final void set(int x, int y, int value) {
        pixels[y*width+x] = (short)value;
    }

    public final int get(int index) {
        return pixels[index]&0xffff;
    }

    public final void set(int index, int value) {
        pixels[index] = (short)value;
    }

    public final float getf(int x, int y) {
        return pixels[y*width+x]&0xffff;
    }

    public final void setf(int x, int y, float value) {
        pixels[y*width + x] = (short)(value+0.5f);
    }

    public final float getf(int index) {
        return pixels[index]&0xffff;
    }

    public final void setf(int index, float value) {
        pixels[index] = (short)value;
    }

    /** Uses the current interpolation method (BILINEAR or BICUBIC)
        to calculate the pixel value at real coordinates (x,y). */
    public double getInterpolatedPixel(double x, double y) {
        if (interpolationMethod==BICUBIC)
            return getBicubicInterpolatedPixel(x, y, this);
        else {
            if (x<0.0) x = 0.0;
            if (x>=width-1.0) x = width-1.001;
            if (y<0.0) y = 0.0;
            if (y>=height-1.0) y = height-1.001;
            return getInterpolatedPixel(x, y, pixels);
        }
    }

    final public int getPixelInterpolated(double x, double y) {
        if (interpolationMethod==BILINEAR) {
            if (x<0.0 || y<0.0 || x>=width-1 || y>=height-1)
                return 0;
            else
                return (int)Math.round(getInterpolatedPixel(x, y, pixels));
        } else if (interpolationMethod==BICUBIC) {
            int value = (int)(getBicubicInterpolatedPixel(x, y, this)+0.5);
            if (value<0) value = 0;
            if (value>65535) value = 65535;
            return value;
        } else
            return getPixel((int)(x+0.5), (int)(y+0.5));
    }

    /** Stores the specified value at (x,y). Does
        nothing if (x,y) is outside the image boundary.
        Values outside the range 0-65535 are clipped.
    */
    public final void putPixel(int x, int y, int value) {
        if (x>=0 && x<width && y>=0 && y<height) {
            if (value>65535) value = 65535;
            if (value<0) value = 0;
            pixels[y*width + x] = (short)value;
        }
    }

    /** Stores the specified real value at (x,y). Does nothing
        if (x,y) is outside the image boundary. Values outside 
        the range 0-65535 (-32768-32767 for signed images)
        are clipped. Support for signed values requires a calibration
        table, which is set up automatically with PlugInFilters.
    */
    public void putPixelValue(int x, int y, double value) {
        if (x>=0 && x<width && y>=0 && y<height) {
            if (cTable!=null&&cTable[0]==-32768f) // signed image
                value += 32768.0;
            if (value>65535.0)
                value = 65535.0;
            else if (value<0.0)
                value = 0.0;
            pixels[y*width + x] = (short)(value+0.5);
        }
    }

    /** Draws a pixel in the current foreground color. */
    public void drawPixel(int x, int y) {
        if (x>=clipXMin && x<=clipXMax && y>=clipYMin && y<=clipYMax)
            putPixel(x, y, fgColor);
    }

    /** Returns the value of the pixel at (x,y) as a float. For signed
        images, returns a signed value if a calibration table has
        been set using setCalibrationTable() (this is done automatically 
        in PlugInFilters). */
    public float getPixelValue(int x, int y) {
        if (x>=0 && x<width && y>=0 && y<height) {
            if (cTable==null)
                return pixels[y*width + x]&0xffff;
            else
                return cTable[pixels[y*width + x]&0xffff];
        } else
            return 0f;
    }

    /** Returns a reference to the short array containing this image's
        pixel data. To avoid sign extension, the pixel values must be
        accessed using a mask (e.g. int i = pixels[j]&0xffff). */
    public Object getPixels() {
        return (Object)pixels;
    }

    /** Returns a copy of the pixel data. Or returns a reference to the
        snapshot buffer if it is not null and 'snapshotCopyMode' is true.
        @see ImageProcessor#snapshot
        @see ImageProcessor#setSnapshotCopyMode
    */
    public Object getPixelsCopy() {
        if (snapshotPixels!=null && snapshotCopyMode) {
            snapshotCopyMode = false;
            return snapshotPixels;
        } else {
            short[] pixels2 = new short[width*height];
            System.arraycopy(pixels, 0, pixels2, 0, width*height);
            return pixels2;
        }
    }

    public void setPixels(Object pixels) {
        this.pixels = (short[])pixels;
        resetPixels(pixels);
        if (pixels==null) snapshotPixels = null;
        if (pixels==null) pixels8 = null;
        raster = null;
    }

    void getRow2(int x, int y, int[] data, int length) {
        int value;
        for (int i=0; i<length; i++)
            data[i] = pixels[y*width+x+i]&0xffff;
    }
    
    void putColumn2(int x, int y, int[] data, int length) {
        int value;
        for (int i=0; i<length; i++)
            pixels[(y+i)*width+x] = (short)data[i];
    }
    
    /** Copies the image contained in 'ip' to (xloc, yloc) using one of
        the transfer modes defined in the Blitter interface. */
    public void copyBits(ImageProcessor ip, int xloc, int yloc, int mode) {
        ip = ip.convertToShort(false);
        new ShortBlitter(this).copyBits(ip, xloc, yloc, mode);
    }

    /** Transforms the pixel data using a 65536 entry lookup table. */
    public void applyTable(int[] lut) {
        if (lut.length!=65536)
            throw new IllegalArgumentException("lut.length!=65536");
        int lineStart, lineEnd, v;
        for (int y=roiY; y<(roiY+roiHeight); y++) {
            lineStart = y * width + roiX;
            lineEnd = lineStart + roiWidth;
            for (int i=lineEnd; --i>=lineStart;) {
                v = lut[pixels[i]&0xffff];
                pixels[i] = (short)v;
            }
        }
        findMinAndMax();
    }

    private void process(int op, double value) {
        int v1, v2;
        double range = getMax()-getMin();
        //boolean resetMinMax = roiWidth==width && roiHeight==height && !(op==FILL);
        int offset = isSigned16Bit()?32768:0;
        int min2 = (int)getMin() - offset;
        int max2 = (int)getMax() - offset;
        int fgColor2 = fgColor - offset;
        int intValue = (int)value;
        
        for (int y=roiY; y<(roiY+roiHeight); y++) {
            int i = y * width + roiX;
            for (int x=roiX; x<(roiX+roiWidth); x++) {
                v1 = (pixels[i]&0xffff) - offset;
                switch(op) {
                    case INVERT:
                        v2 = max2 - (v1 - min2);
                        //v2 = 65535 - (v1+offset);
                        break;
                    case FILL:
                        v2 = fgColor2;
                        break;
                    case SET:
                        v2 = intValue;
                        break;
                    case ADD:
                        v2 = v1 + intValue;
                        break;
                    case MULT:
                        v2 = (int)Math.round(v1*value);
                        break;
                    case AND:
                        v2 = v1 & intValue;
                        break;
                    case OR:
                        v2 = v1 | intValue;
                        break;
                    case XOR:
                        v2 = v1 ^ intValue;
                        break;
                    case GAMMA:
                        if (range<=0.0 || v1==min2)
                            v2 = v1;
                        else                    
                            v2 = (int)(Math.exp(value*Math.log((v1-min2)/range))*range+min2);
                        break;
                    case LOG:
                        if (v1<=0)
                            v2 = 0;
                        else 
                            v2 = (int)(Math.log(v1)*(max2/Math.log(max2)));
                        break;
                    case EXP:
                        v2 = (int)(Math.exp(v1*(Math.log(max2)/max2)));
                        break;
                    case SQR:
                        double d1 = v1;
                        v2 = (int)(d1*d1);
                        break;
                    case SQRT:
                        v2 = (int)Math.sqrt(v1);
                        break;
                    case ABS:
                        v2 = (int)Math.abs(v1);
                        break;
                    case MINIMUM:
                        if (v1<value)
                            v2 = intValue;
                        else
                            v2 = v1;
                        break;
                    case MAXIMUM:
                        if (v1>value)
                            v2 = intValue;
                        else
                            v2 = v1;
                        break;
                     default:
                        v2 = v1;
                }
                v2 += offset;
                if (v2 < 0)
                    v2 = 0;
                if (v2 > 65535)
                    v2 = 65535;
                pixels[i++] = (short)v2;
            }
        }
    }

    public void invert() {
        resetMinAndMax();
        process(INVERT, 0.0);
    }
    
    public void add(int value) {process(ADD, value);}
    public void add(double value) {process(ADD, value);}
    public void set(double value) {process(SET, value);}
    public void multiply(double value) {process(MULT, value);}
    public void and(int value) {process(AND, value);}
    public void or(int value) {process(OR, value);}
    public void xor(int value) {process(XOR, value);}
    public void gamma(double value) {process(GAMMA, value);}
    public void log() {process(LOG, 0.0);}
    public void exp() {process(EXP, 0.0);}
    public void sqr() {process(SQR, 0.0);}
    public void sqrt() {process(SQRT, 0.0);}
    public void abs() {process(ABS, 0.0);}
    public void min(double value) {process(MINIMUM, value);}
    public void max(double value) {process(MAXIMUM, value);}

    /** Fills the current rectangular ROI. */
    public void fill() {
        process(FILL, 0.0);
    }

    /** Fills pixels that are within roi and part of the mask.
        Does nothing if the mask is not the same as the ROI. */
    public void fill(ImageProcessor mask) {
        if (mask==null)
            {fill(); return;}
        int roiWidth=this.roiWidth, roiHeight=this.roiHeight;
        int roiX=this.roiX, roiY=this.roiY;
        if (mask.getWidth()!=roiWidth||mask.getHeight()!=roiHeight)
            return;
        byte[] mpixels = (byte[])mask.getPixels();
        for (int y=roiY, my=0; y<(roiY+roiHeight); y++, my++) {
            int i = y * width + roiX;
            int mi = my * roiWidth;
            for (int x=roiX; x<(roiX+roiWidth); x++) {
                if (mpixels[mi++]!=0)
                    pixels[i] = (short)fgColor;
                i++;
            }
        }
    }

    /** Does 3x3 convolution. */
    public void convolve3x3(int[] kernel) {
        filter3x3(CONVOLVE, kernel);
    }

    /** Filters using a 3x3 neighborhood. */
    public void filter(int type) {
        filter3x3(type, null);
    }

    /** 3x3 filter operations, code partly based on 3x3 convolution code
     *  contributed by Glynne Casteel. */
    void filter3x3(int type, int[] kernel) {
        int v1, v2, v3;           //input pixel values around the current pixel
        int v4, v5, v6;
        int v7, v8, v9;
        int k1=0, k2=0, k3=0;  //kernel values (used for CONVOLVE only)
        int k4=0, k5=0, k6=0;
        int k7=0, k8=0, k9=0;
        int scale = 0;
        if (type==CONVOLVE) {
            k1=kernel[0]; k2=kernel[1]; k3=kernel[2];
            k4=kernel[3]; k5=kernel[4]; k6=kernel[5];
            k7=kernel[6]; k8=kernel[7]; k9=kernel[8];
            for (int i=0; i<kernel.length; i++)
                scale += kernel[i];
            if (scale==0) scale = 1;
        }

        short[] pixels2 = (short[])getPixelsCopy();
        int xEnd = roiX + roiWidth;
        int yEnd = roiY + roiHeight;
        for (int y=roiY; y<yEnd; y++) {
            int p  = roiX + y*width;            //points to current pixel
            int p6 = p - (roiX>0 ? 1 : 0);      //will point to v6, currently lower
            int p3 = p6 - (y>0 ? width : 0);    //will point to v3, currently lower
            int p9 = p6 + (y<height-1 ? width : 0); // ...  to v9, currently lower
            v2 = pixels2[p3]&0xffff;
            v5 = pixels2[p6]&0xffff;
            v8 = pixels2[p9]&0xffff;
            if (roiX>0) { p3++; p6++; p9++; }
            v3 = pixels2[p3]&0xffff;
            v6 = pixels2[p6]&0xffff;
            v9 = pixels2[p9]&0xffff;

            switch (type) {
                case BLUR_MORE:
                for (int x=roiX; x<xEnd; x++,p++) {
                    if (x<width-1) { p3++; p6++; p9++; }
                    v1 = v2; v2 = v3;
                    v3 = pixels2[p3]&0xffff;
                    v4 = v5; v5 = v6;
                    v6 = pixels2[p6]&0xffff;
                    v7 = v8; v8 = v9;
                    v9 = pixels2[p9]&0xffff;
                    pixels[p] = (short)((v1+v2+v3+v4+v5+v6+v7+v8+v9+4)/9);
                }
                break;
                case FIND_EDGES:
                for (int x=roiX; x<xEnd; x++,p++) {
                    if (x<width-1) { p3++; p6++; p9++; }
                    v1 = v2; v2 = v3;
                    v3 = pixels2[p3]&0xffff;
                    v4 = v5; v5 = v6;
                    v6 = pixels2[p6]&0xffff;
                    v7 = v8; v8 = v9;
                    v9 = pixels2[p9]&0xffff;
                    double sum1 = v1 + 2*v2 + v3 - v7 - 2*v8 - v9;
                    double sum2 = v1  + 2*v4 + v7 - v3 - 2*v6 - v9;
                    double result = Math.sqrt(sum1*sum1 + sum2*sum2);
                    if (result>65535.0) result = 65535.0;
                    pixels[p] = (short)result;
                }
                break;
                case CONVOLVE:
                for (int x=roiX; x<xEnd; x++,p++) {
                    if (x<width-1) { p3++; p6++; p9++; }
                    v1 = v2; v2 = v3;
                    v3 = pixels2[p3]&0xffff;
                    v4 = v5; v5 = v6;
                    v6 = pixels2[p6]&0xffff;
                    v7 = v8; v8 = v9;
                    v9 = pixels2[p9]&0xffff;
                    int sum = k1*v1 + k2*v2 + k3*v3
                            + k4*v4 + k5*v5 + k6*v6
                            + k7*v7 + k8*v8 + k9*v9;
                    sum = (sum+scale/2)/scale;   //scale/2 for rounding
                    if(sum>65535) sum = 65535;
                    if(sum<0) sum = 0;
                    pixels[p] = (short)sum;
                }
                break;
            }
        }
    }

    /** Rotates the image or ROI 'angle' degrees clockwise.
        @see ImageProcessor#setInterpolate
    */
    public void rotate(double angle) {
        short[] pixels2 = (short[])getPixelsCopy();
        ImageProcessor ip2 = null;
        if (interpolationMethod==BICUBIC)
            ip2 = new ShortProcessor(getWidth(), getHeight(), pixels2, null);
        double centerX = roiX + (roiWidth-1)/2.0;
        double centerY = roiY + (roiHeight-1)/2.0;
        int xMax = roiX + this.roiWidth - 1;
        
        double angleRadians = -angle/(180.0/Math.PI);
        double ca = Math.cos(angleRadians);
        double sa = Math.sin(angleRadians);
        double tmp1 = centerY*sa-centerX*ca;
        double tmp2 = -centerX*sa-centerY*ca;
        double tmp3, tmp4, xs, ys;
        int index, ixs, iys;
        double dwidth=width,dheight=height;
        double xlimit = width-1.0, xlimit2 = width-1.001;
        double ylimit = height-1.0, ylimit2 = height-1.001;
        // zero is 32768 for signed images
        int background = isSigned16Bit()?32768:0; 
        
        if (interpolationMethod==BICUBIC) {
            for (int y=roiY; y<(roiY + roiHeight); y++) {
                index = y*width + roiX;
                tmp3 = tmp1 - y*sa + centerX;
                tmp4 = tmp2 + y*ca + centerY;
                for (int x=roiX; x<=xMax; x++) {
                    xs = x*ca + tmp3;
                    ys = x*sa + tmp4;
                    int value = (int)(getBicubicInterpolatedPixel(xs, ys, ip2)+0.5);
                    if (value<0) value = 0;
                    if (value>65535) value = 65535;
                    pixels[index++] = (short)value;
                }
            }
        } else {
            for (int y=roiY; y<(roiY + roiHeight); y++) {
                index = y*width + roiX;
                tmp3 = tmp1 - y*sa + centerX;
                tmp4 = tmp2 + y*ca + centerY;
                for (int x=roiX; x<=xMax; x++) {
                    xs = x*ca + tmp3;
                    ys = x*sa + tmp4;
                    if ((xs>=-0.01) && (xs<dwidth) && (ys>=-0.01) && (ys<dheight)) {
                        if (interpolationMethod==BILINEAR) {
                            if (xs<0.0) xs = 0.0;
                            if (xs>=xlimit) xs = xlimit2;
                            if (ys<0.0) ys = 0.0;           
                            if (ys>=ylimit) ys = ylimit2;
                            pixels[index++] = (short)(getInterpolatedPixel(xs, ys, pixels2)+0.5);
                        } else {
                            ixs = (int)(xs+0.5);
                            iys = (int)(ys+0.5);
                            if (ixs>=width) ixs = width - 1;
                            if (iys>=height) iys = height -1;
                            pixels[index++] = pixels2[width*iys+ixs];
                        }
                    } else
                        pixels[index++] = (short)background;
                }
            }
        }
    }

    public void flipVertical() {
        int index1,index2;
        short tmp;
        for (int y=0; y<roiHeight/2; y++) {
            index1 = (roiY+y)*width+roiX;
            index2 = (roiY+roiHeight-1-y)*width+roiX;
            for (int i=0; i<roiWidth; i++) {
                tmp = pixels[index1];
                pixels[index1++] = pixels[index2];
                pixels[index2++] = tmp;
            }
        }
    }
    
    /** Scales the image or selection using the specified scale factors.
        @see ImageProcessor#setInterpolationMethod
    */
    public void scale(double xScale, double yScale) {
        double xCenter = roiX + roiWidth/2.0;
        double yCenter = roiY + roiHeight/2.0;
        int xmin, xmax, ymin, ymax;
        if ((xScale>1.0) && (yScale>1.0)) {
            //expand roi
            xmin = (int)(xCenter-(xCenter-roiX)*xScale);
            if (xmin<0) xmin = 0;
            xmax = xmin + (int)(roiWidth*xScale) - 1;
            if (xmax>=width) xmax = width - 1;
            ymin = (int)(yCenter-(yCenter-roiY)*yScale);
            if (ymin<0) ymin = 0;
            ymax = ymin + (int)(roiHeight*yScale) - 1;
            if (ymax>=height) ymax = height - 1;
        } else {
            xmin = roiX;
            xmax = roiX + roiWidth - 1;
            ymin = roiY;
            ymax = roiY + roiHeight - 1;
        }
        short[] pixels2 = (short[])getPixelsCopy();
        ImageProcessor ip2 = null;
        if (interpolationMethod==BICUBIC)
            ip2 = new ShortProcessor(getWidth(), getHeight(), pixels2, null);
        boolean checkCoordinates = (xScale < 1.0) || (yScale < 1.0);
        short min2 = (short)getMin();
        int index1, index2, xsi, ysi;
        double ys, xs;
        if (interpolationMethod==BICUBIC) {
            for (int y=ymin; y<=ymax; y++) {
                ys = (y-yCenter)/yScale + yCenter;
                int index = y*width + xmin;
                for (int x=xmin; x<=xmax; x++) {
                    xs = (x-xCenter)/xScale + xCenter;
                    int value = (int)(getBicubicInterpolatedPixel(xs, ys, ip2)+0.5);
                    if (value<0) value=0; if (value>65535) value=65535;
                    pixels[index++] = (short)value;
                }
            }
        } else {
            double xlimit = width-1.0, xlimit2 = width-1.001;
            double ylimit = height-1.0, ylimit2 = height-1.001;
            for (int y=ymin; y<=ymax; y++) {
                ys = (y-yCenter)/yScale + yCenter;
                ysi = (int)ys;
                if (ys<0.0) ys = 0.0;           
                if (ys>=ylimit) ys = ylimit2;
                index1 = y*width + xmin;
                index2 = width*(int)ys;
                for (int x=xmin; x<=xmax; x++) {
                    xs = (x-xCenter)/xScale + xCenter;
                    xsi = (int)xs;
                    if (checkCoordinates && ((xsi<xmin) || (xsi>xmax) || (ysi<ymin) || (ysi>ymax)))
                        pixels[index1++] = min2;
                    else {
                        if (interpolationMethod==BILINEAR) {
                            if (xs<0.0) xs = 0.0;
                            if (xs>=xlimit) xs = xlimit2;
                            pixels[index1++] = (short)(getInterpolatedPixel(xs, ys, pixels2)+0.5);
                        } else
                            pixels[index1++] = pixels2[index2+xsi];
                    }
                }
            }
        }
    }

    /** Uses bilinear interpolation to find the pixel value at real coordinates (x,y). */
    private final double getInterpolatedPixel(double x, double y, short[] pixels) {
        int xbase = (int)x;
        int ybase = (int)y;
        double xFraction = x - xbase;
        double yFraction = y - ybase;
        int offset = ybase * width + xbase;
        int lowerLeft = pixels[offset]&0xffff;
        int lowerRight = pixels[offset + 1]&0xffff;
        int upperRight = pixels[offset + width + 1]&0xffff;
        int upperLeft = pixels[offset + width]&0xffff;
        double upperAverage = upperLeft + xFraction * (upperRight - upperLeft);
        double lowerAverage = lowerLeft + xFraction * (lowerRight - lowerLeft);
        return lowerAverage + yFraction * (upperAverage - lowerAverage);
    }

    /** Creates a new ShortProcessor containing a scaled copy of this image or selection. */
    public ImageProcessor resize(int dstWidth, int dstHeight) {
        if (roiWidth==dstWidth && roiHeight==dstHeight)
            return crop();
        if ((width==1||height==1) && interpolationMethod!=NONE)
            return resizeLinearly(dstWidth, dstHeight);
        double srcCenterX = roiX + roiWidth/2.0;
        double srcCenterY = roiY + roiHeight/2.0;
        double dstCenterX = dstWidth/2.0;
        double dstCenterY = dstHeight/2.0;
        double xScale = (double)dstWidth/roiWidth;
        double yScale = (double)dstHeight/roiHeight;
        if (interpolationMethod!=NONE) {
            if (dstWidth!=width) dstCenterX+=xScale/4.0;
            if (dstHeight!=height) dstCenterY+=yScale/4.0;
        }
        int inc = getProgressIncrement(dstWidth,dstHeight);
        ImageProcessor ip2 = createProcessor(dstWidth, dstHeight);
        short[] pixels2 = (short[])ip2.getPixels();
        double xs, ys;
        if (interpolationMethod==BICUBIC) {
            for (int y=0; y<=dstHeight-1; y++) {
                if (inc>0&&y%inc==0) showProgress((double)y/dstHeight);
                ys = (y-dstCenterY)/yScale + srcCenterY;
                int index2 = y*dstWidth;
                for (int x=0; x<=dstWidth-1; x++) {
                    xs = (x-dstCenterX)/xScale + srcCenterX;
                    int value = (int)(getBicubicInterpolatedPixel(xs, ys, this)+0.5);
                    if (value<0) value=0; if (value>65535) value=65535;
                    pixels2[index2++] = (short)value;
                }
            }
        } else {
            double xlimit = width-1.0, xlimit2 = width-1.001;
            double ylimit = height-1.0, ylimit2 = height-1.001;
            int index1, index2;
            for (int y=0; y<=dstHeight-1; y++) {
                if (inc>0&&y%inc==0) showProgress((double)y/dstHeight);
                ys = (y-dstCenterY)/yScale + srcCenterY;
                if (interpolationMethod==BILINEAR) {
                    if (ys<0.0) ys = 0.0;
                    if (ys>=ylimit) ys = ylimit2;
                }
                index1 = width*(int)ys;
                index2 = y*dstWidth;
                for (int x=0; x<=dstWidth-1; x++) {
                    xs = (x-dstCenterX)/xScale + srcCenterX;
                    if (interpolationMethod==BILINEAR) {
                        if (xs<0.0) xs = 0.0;
                        if (xs>=xlimit) xs = xlimit2;
                        pixels2[index2++] = (short)(getInterpolatedPixel(xs, ys, pixels)+0.5);
                    } else
                        pixels2[index2++] = pixels[index1+(int)xs];
                }
            }
        }
        if (inc>0) showProgress(1.0);
        return ip2;
    }

    public ImageProcessor crop() {
        ImageProcessor ip2 = createProcessor(roiWidth, roiHeight);
        short[] pixels2 = (short[])ip2.getPixels();
        for (int ys=roiY; ys<roiY+roiHeight; ys++) {
            int offset1 = (ys-roiY)*roiWidth;
            int offset2 = ys*width+roiX;
            for (int xs=0; xs<roiWidth; xs++)
                pixels2[offset1++] = pixels[offset2++];
        }
        return ip2;
    }
    
    /** Returns a duplicate of this image. */ 
    public ImageProcessor duplicate() { 
        ImageProcessor ip2 = createProcessor(width, height); 
        short[] pixels2 = (short[])ip2.getPixels(); 
        System.arraycopy(pixels, 0, pixels2, 0, width*height); 
        return ip2; 
    } 

    /** Sets the foreground fill/draw color. */
    public void setColor(Color color) {
        drawingColor = color;
        int bestIndex = getBestIndex(color);
        if (bestIndex>0 && getMin()==0.0 && getMax()==0.0) {
            setValue(bestIndex);
            setMinAndMax(0.0,255.0);
        } else if (bestIndex==0 && getMin()>0.0 && (color.getRGB()&0xffffff)==0) {
            if (isSigned16Bit())
                setValue(32768);
            else
                setValue(0.0);
        } else
            fgColor = (int)(getMin() + (getMax()-getMin())*(bestIndex/255.0));
    }
    
    /** Sets the default fill/draw value, where 0<=value<=65535). */
    public void setValue(double value) {
            fgColor = (int)value;
            if (fgColor<0) fgColor = 0;
            if (fgColor>65535) fgColor = 65535;
    }

    /** Does nothing. The rotate() and scale() methods always zero fill. */
    public void setBackgroundValue(double value) {
    }

    /** Always returns 0. */
    public double getBackgroundValue() {
        return 0.0;
    }

    /** Returns 65536 bin histogram of the current ROI, which
        can be non-rectangular. */
    public int[] getHistogram() {
        if (mask!=null)
            return getHistogram(mask);
        int[] histogram = new int[65536];
        for (int y=roiY; y<(roiY+roiHeight); y++) {
            int i = y*width + roiX;
            for (int x=roiX; x<(roiX+roiWidth); x++)
                    histogram[pixels[i++]&0xffff]++;
        }
        return histogram;
    }

    int[] getHistogram(ImageProcessor mask) {
        if (mask.getWidth()!=roiWidth||mask.getHeight()!=roiHeight)
            throw new IllegalArgumentException(maskSizeError(mask));
        byte[] mpixels = (byte[])mask.getPixels();
        int[] histogram = new int[65536];
        for (int y=roiY, my=0; y<(roiY+roiHeight); y++, my++) {
            int i = y * width + roiX;
            int mi = my * roiWidth;
            for (int x=roiX; x<(roiX+roiWidth); x++) {
                if (mpixels[mi++]!=0)
                    histogram[pixels[i]&0xffff]++;
                i++;
            }
        }
        return histogram;
    }

    int[] getHistogram2() {
        if (mask!=null)
            return getHistogram2(mask);
        int[] histogram = makeHistogramArray();
        for (int y=roiY; y<(roiY+roiHeight); y++) {
            int index = y*width + roiX;
            for (int i=0; i<roiWidth; i++)
                    histogram[pixels[index++]&0xffff]++;
        }
        return histogram;
    }

    private int[] getHistogram2(ImageProcessor mask) {
        if (mask.getWidth()!=roiWidth||mask.getHeight()!=roiHeight)
            throw new IllegalArgumentException(maskSizeError(mask));
        byte[] mpixels = (byte[])mask.getPixels();
        int[] histogram = makeHistogramArray();
        for (int y=roiY, my=0; y<(roiY+roiHeight); y++, my++) {
            int index = y * width + roiX;
            int mi = my * roiWidth;
            for (int i=0; i<roiWidth; i++) {
                if (mpixels[mi++]!=0)
                    histogram[pixels[index]&0xffff]++;
                index++;
            }
        }
        return histogram;
    }

    private int[] makeHistogramArray() {
        int max = 0;
        int value;
        for (int y=roiY; y<(roiY+roiHeight); y++) {
            int index = y*width + roiX;
            for (int i=0; i<roiWidth; i++) {
                value = pixels[index++]&0xffff;
                if (value>max)
                    max = value;
            }
        }
        int size = max + 1;
        if (size<256)
            size = 256;
        return new int[size];
    }

    public void setThreshold(double minThreshold, double maxThreshold, int lutUpdate) {
        if (minThreshold==NO_THRESHOLD)
            {resetThreshold(); return;}
        if (minThreshold<0.0) minThreshold = 0.0;
        if (maxThreshold>65535.0) maxThreshold = 65535.0;
        int min2=(int)getMin(), max2=(int)getMax();
        if (max2>min2) {
            // scale to 0-255 using same method as create8BitImage()
            double scale = 256.0/(max2-min2+1);
            double minT = minThreshold-min2;
            if (minT<0) minT = 0;
            minT = (int)(minT*scale+0.5);
            if (minT>255) minT = 255;
            //ij.IJ.log("setThreshold: "+minT+" "+Math.round(((minThreshold-min2)/(max2-min2))*255.0));
            double maxT = maxThreshold-min2;
            if (maxT<0) maxT = 0;
            maxT = (int)(maxT*scale+0.5);
            if (maxT>255) maxT = 255;
            super.setThreshold(minT, maxT, lutUpdate); // update LUT
        } else
            super.resetThreshold();
        this.minThreshold = Math.round(minThreshold);
        this.maxThreshold = Math.round(maxThreshold);
    }
    
    /** Performs a convolution operation using the specified kernel. */
    public void convolve(float[] kernel, int kernelWidth, int kernelHeight) {
        ImageProcessor ip2 = convertToFloat();
        ip2.setRoi(getRoi());
        new ij.plugin.filter.Convolver().convolve(ip2, kernel, kernelWidth, kernelHeight);
        ip2 = ip2.convertToShort(false);
        short[] pixels2 = (short[])ip2.getPixels();
        System.arraycopy(pixels2, 0, pixels, 0, pixels.length);
    }

    /** Adds pseudorandom, Gaussian ("normally") distributed values, with
        mean 0.0 and the specified standard deviation, to this image or ROI. */
    public void noise(double standardDeviation) {
        Random rnd=new Random();
        int v, ran;
        boolean inRange;
        for (int y=roiY; y<(roiY+roiHeight); y++) {
            int i = y * width + roiX;
            for (int x=roiX; x<(roiX+roiWidth); x++) {
                inRange = false;
                do {
                    ran = (int)Math.round(rnd.nextGaussian()*standardDeviation);
                    v = (pixels[i] & 0xffff) + ran;
                    inRange = v>=0 && v<=65535;
                    if (inRange) pixels[i] = (short)v;
                } while (!inRange);
                i++;
            }
        }
        resetMinAndMax();
    }
    
    public void threshold(int level) {
        for (int i=0; i<width*height; i++) {
            if ((pixels[i]&0xffff)<=level)
                pixels[i] = 0;
            else
                pixels[i] = (short)255;
        }
        findMinAndMax();
    }

    /** Returns a FloatProcessor with the same image, no scaling or calibration
    *  (pixel values 0 to 65535).
    *  The roi, mask, lut (ColorModel), threshold, min&max are
    *  also set for the FloatProcessor
    *  @param channelNumber   Ignored (needed for compatibility with ColorProcessor.toFloat)
    *  @param fp              Here a FloatProcessor can be supplied, or null. The FloatProcessor
    *                         is overwritten by this method (re-using its pixels array 
    *                         improves performance).
    *  @return A FloatProcessor with the converted image data
    */
    public FloatProcessor toFloat(int channelNumber, FloatProcessor fp) {
        int size = width*height;
        if (fp == null || fp.getWidth()!=width || fp.getHeight()!=height)
            fp = new FloatProcessor(width, height, new float[size], cm);
        float[] fPixels = (float[])fp.getPixels();
        for (int i=0; i<size; i++)
            fPixels[i] = pixels[i]&0xffff;
        fp.setRoi(getRoi());
        fp.setMask(mask);
        fp.setMinAndMax(getMin(), getMax());
        fp.setThreshold(minThreshold, maxThreshold, ImageProcessor.NO_LUT_UPDATE);
        return fp;
    }
    
    /** Sets the pixels from a FloatProcessor, no scaling.
    *  Also the min&max values are taken from the FloatProcessor.
    *  @param channelNumber   Ignored (needed for compatibility with ColorProcessor.toFloat)
    *  @param fp              The FloatProcessor where the image data are read from.
    */
    public void setPixels(int channelNumber, FloatProcessor fp) {
        float[] fPixels = (float[])fp.getPixels();
        float value;
        int size = width*height;
        for (int i=0; i<size; i++) {
            value = fPixels[i] + 0.5f;
            if (value<0f) value = 0f;
            if (value>65535f) value = 65535f;
            pixels[i] = (short)value;
        }
        setMinAndMax(fp.getMin(), fp.getMax());
    }
        
    /** Returns the maximum possible pixel value. */
    public double maxValue() {
        return 65535.0;
    }

    public int getBitDepth() {
        return 16;
    }

    /** Returns 'true' if this is a signed 16-bit image. */
    public boolean isSigned16Bit() {
        return cTable!=null && cTable[0]==-32768f && cTable[1]==-32767f;
    }

    /** Not implemented. */
    public void medianFilter() {}
    /** Not implemented. */
    public void erode() {}
    /** Not implemented. */
    public void dilate() {}

}