Java Code Examples for javax.media.jai.PlanarImage#getWidth()

public PlanarImage process(final PlanarImage image) {
    if (image == null || (image.getWidth() * image.getHeight() > 6000 * 6000L))
        throw new IllegalArgumentException("this implementation can only handle images where width*height<=6000*6000. (And image cannot be null)");

    TMAPointsResult res = findCircles(image);
    this.radius = res.getRadius();
    List<Point> pList = res.getSpotList();

    HashMap<Point, Point> pMap = clusterLines(pList);
    pMap = discardDuplicatePoints(pMap);

    BufferedImage buffImg = res.getSpotImage();
    Graphics g = buffImg.createGraphics();
    g.setColor(Color.blue);
    g.setFont(new Font("System", Font.PLAIN, 9));
    for (Point p : pMap.keySet()) {
        Point pos = pMap.get(p);
        g.drawString(pos.x + "/" + pos.y, p.x, p.y);
    }

    spotMap = pMap;

    return PlanarImage.wrapRenderedImage(buffImg);
}
 

/**
 * returns all UEP with a threshold > min in a pointlist.
 * The UEP process has to be applied before!
 *
 * @param img
 * @param min
 * @return
 */
private List<Point> reportPoints(PlanarImage img, int min) {
    Raster r = img.getData();
    int[] rgb = new int[3];
    double d;
    List<Point> pList = new ArrayList<Point>();
    for (int x = 0; x < img.getWidth(); x++)
        for (int y = 0; y < img.getHeight(); y++) {
            rgb = r.getPixel(x, y, rgb);
            d = (rgb[0]);
            if (d > min) {
                Point p = new Point(x, y);
                pList.add(p);
                if (logger.isTraceEnabled()) {
                    logger.trace(x + "," + y + ": " + d);
                }
            }
        }
    return pList;
}
 

/**
 * Creats a binary ImagePlus based on a planar image. If a pixel is fg it is set to white, otherwise to black.
 *
 * @param image
 * @param fg
 * @return
 */
public static ImagePlus toBinaryImagePlus(PlanarImage image, Color fg) {
    if (image == null || (image.getWidth() * image.getHeight() > 6000 * 6000L))
        throw new IllegalArgumentException("this implementation can only handle images where width*height<=6000*6000. (And image cannot be null)");
    int width = image.getWidth();
    int height = image.getHeight();
    Raster raster = image.getData();
    int[] arr = new int[4];

    // set background to black and foreground to white for imageJ watershed
    BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
    int b = 0;
    for (int y = b; y < height - b; y++) {
        for (int x = b; x < width - b; x++) {
            arr = raster.getPixel(x, y, arr);
            if (arr[0] == fg.getRed() && arr[1] == fg.getGreen() && arr[2] == fg.getBlue()) {
                bi.setRGB(x, y, Color.WHITE.getRGB());
            } else {
                bi.setRGB(x, y, Color.BLACK.getRGB());
            }

        }
    }
    ImagePlus ip = new ImagePlus("watershed", bi);
    return ip;
}
 

/**
 * Creats a planar image based on an ImagePlus. The originalImage is just used for dimensions and tileSize (could be replaced by its int values).
 *
 * @param ip
 * @param originalImage
 * @param fg
 * @param bg
 * @return
 */
public static PlanarImage toPlanarImage(ImagePlus ip, PlanarImage originalImage, Color fg, Color bg) {
    TiledImageWriter imageWriter = new TiledImageWriter(originalImage.getWidth(), originalImage.getHeight(), originalImage.getTileWidth(), originalImage.getTileHeight());

    // resImg
    Point[] tileArr = imageWriter.getImage().getTileIndices(null);
    int[] p = new int[4];
    int[] bgArr = new int[]{bg.getRed(), bg.getGreen(), bg.getBlue(), 255};
    int[] fgArr = new int[]{fg.getRed(), fg.getGreen(), fg.getBlue(), 255};
    for (Point tileNum : tileArr) {
        WritableRaster writeRaster = imageWriter.getImage().getWritableTile(tileNum.x, tileNum.y);
        for (int x = imageWriter.getImage().tileXToX(tileNum.x); x < Math.min(imageWriter.getImage().tileXToX(tileNum.x) + imageWriter.getImage().getTileWidth(), imageWriter.getImage().getWidth()); x++)
            for (int y = imageWriter.getImage().tileYToY(tileNum.y); y < Math.min(imageWriter.getImage().tileYToY(tileNum.y) + imageWriter.getImage().getTileHeight(), imageWriter.getImage().getHeight()); y++) {
                p = ip.getPixel(x, y);
                if (p[0] != 0) p = fgArr;
                else p = bgArr;
                writeRaster.setPixel(x, y, p);  // since it is not a gray-scale image, we just use the red channel
            } // x,y
        imageWriter.getImage().releaseWritableTile(tileNum.x, tileNum.y);
    } // tileNum

    return imageWriter.getImage();
}
 

public TiledImageWriter(PlanarImage inputImage, int xOffs, int yOffs) {
    this.width = inputImage.getWidth();
    this.height = inputImage.getHeight();
    this.tileWidth = inputImage.getTileWidth();
    this.tileHeight = inputImage.getTileHeight();
    colorModel = new ComponentColorModel(
            ColorSpace.getInstance(ColorSpace.CS_sRGB),
            new int[]{8, 8, 8, 8}, true, false,
            Transparency.TRANSLUCENT,
            DataBuffer.TYPE_BYTE);
    sampleModel = colorModel.createCompatibleSampleModel(tileWidth, tileHeight);
    image = new DiskMemImageOrbit(xOffs, yOffs, width, height, 0, 0, sampleModel, colorModel);
    ((DiskMemImageOrbit) image).setUseCommonCache(true);

    TiledImagePainter painter = new TiledImagePainter(inputImage, "");
    Graphics2D g2d = image.createGraphics();
    try { // 03.05.2010 Manuel (exception with JRE 1.5, with JRE 1.6 fine)
        painter.drawImage(g2d, xOffs, yOffs, width, height, 100d, -1);
    } catch (Throwable e) {
        //System.out.println("TiledImageWriter Error",e);
        //e.printStackTrace();
    }
}
 

/** Displays information about an image.

      @param image image to display information about */

  public static void printImageInfo(PlanarImage image) {
    String result;

    SampleModel sm = image.getSampleModel();
    ColorModel cm = image.getColorModel();
    ColorSpace cs = cm.getColorSpace();

    result  = "Width:           " + image.getWidth() + "\n";
    result += "Height:          " + image.getHeight() + "\n";
    result += "SampleModel:     " + sm.getClass().getName() + "\n";
    result += "DataType:        " + getDataType(sm.getDataType()) + "\n";
    result += "Bands:           " + sm.getNumBands() + "\n";
    result += "SampleSizes:     ";
    for (int i = 0; i < sm.getNumBands(); i++) {
      result += sm.getSampleSize(i) + " ";
    }
    result += "\n";
    result += "ColorModel:      " + cm.getClass().getName() + "\n";
    result += "ColorComponents: " + cm.getNumComponents() + "\n";
    result += "HasAlpha:        " + ((cm.hasAlpha()) ? "yes" : "no") + "\n";
    result += "ColorSpace:      " + cs.getClass().getName() + "\n";
    result += "TileSize:        " + image.getTileWidth() + "/" + image.getTileHeight() + "\n";

    System.out.print(result);
  }
 

public List<Shape> detectSegmentations(int minSegmentationSize, PlanarImage sourceImage) {
    logger.trace("getSegmentations (minSegmentation=" + minSegmentationSize + ")");
    rf.initializeClassColors();
    //if (rf.getNegativeChannel() != null) rf.getNegativeChannel().initializeClassColors();
    if (sourceImage == null) return new ArrayList<Shape>(0);
    short[][] smap = new short[sourceImage.getWidth()][sourceImage.getHeight()];

    for (int x = 0; x < sourceImage.getWidth(); x++)
        for (int y = 0; y < sourceImage.getHeight(); y++)
            smap[x][y] = Short.MAX_VALUE;

    // init
    Point[] tileArr = sourceImage.getTileIndices(null);
    int c;
    for (Point tileNum : tileArr) {
        if (isCancelled()) break;
        final int b = 2;

        Raster raster = sourceImage.getTile(tileNum.x, tileNum.y);
        for (int x = sourceImage.tileXToX(tileNum.x) + b; x < Math.min(sourceImage.tileXToX(tileNum.x) + sourceImage.getTileWidth() - b, sourceImage.getWidth()); x++) {
            for (int y = sourceImage.tileYToY(tileNum.y) + b; y < Math.min(sourceImage.tileYToY(tileNum.y) + sourceImage.getTileHeight() - b, sourceImage.getHeight()); y++) {
                if (fullRoi != null && !(fullRoi.contains(x + roi.getBounds().x, y + roi.getBounds().y))) {
                    continue;
                }

                c = raster.getSample(x, y, 0) < 200 ? 0 : 1; // dark=foreground, white=background (only red channel is taken into account)
                if (c == 0) {  // not background, not assigned
                    smap[x][y] = 1; // 1
                } else {
                    smap[x][y] = 0; // 0
                }
            } //y
        } // x
    } // tileNum


    if (isCancelled()) return null;
    return findPolygons(smap, minSegmentationSize);
}
 

public void run() {
    try {
        ClassShape classShape = annotation.getShape();
        if (classShape != null && classShape.getShapeList() != null) {
            if (classShape.getShapeList() != null && classShape.getShapeList().size() > 0) {
                IScaleableShape p = (IScaleableShape) classShape.getShapeList().get(0); // only the first shape

                ImageFrame iFrame = OrbitImageAnalysis.getInstance().getIFrame();
                if (iFrame != null) {
                    final long maxW = 2000;
                    Rectangle rect = p.getScaledInstance(100d, new Point(0, 0)).getBounds();
                    PlanarImage img = iFrame.recognitionFrame.bimg.getImage();
                    if ((long) rect.getWidth() * rect.getHeight() > (maxW * maxW)) {
                        if (iFrame.recognitionFrame.bimg.getMipMaps() != null && iFrame.recognitionFrame.bimg.getMipMaps().length > 0) {
                            img = iFrame.recognitionFrame.bimg.getMipMaps()[iFrame.recognitionFrame.bimg.getMipMaps().length - 1].getImage();
                            double scale = (double) img.getWidth() / (double) iFrame.recognitionFrame.bimg.getImage().getWidth();
                            rect = p.getScaledInstance(scale * 100d, new Point(0, 0)).getBounds();
                        }
                    }
                    BufferedImage bi = img.getAsBufferedImage(rect, iFrame.recognitionFrame.bimg.getImage().getColorModel());
                    bi = TiffConverter.makeScaledImage(bi, thumbnailWidth, thumbnailHeight);
                    ImageIcon icon = new ImageIcon(bi);
                    if ((cellCache != null) && (icon != null)) {
                        cellCache.put(hash, icon);
                        list.revalidate();
                        list.repaint();
                    }
                }
            }
        }

    } catch (Throwable t) {
        // can happen (e.g, outofmemory), but no problem
    }

}
 

private PlanarImage makeTiledImage(PlanarImage img, int tileWidth, int tileHeight) {
    ImageLayout tileLayout = new ImageLayout(img);
    tileLayout.setTileWidth(tileWidth);
    tileLayout.setTileHeight(tileHeight);
    tileLayout.setSampleModel(img.getColorModel().createCompatibleSampleModel(tileWidth,tileHeight));
    tileLayout.setColorModel(img.getColorModel());
    RenderingHints tileHints = new RenderingHints(JAI.KEY_IMAGE_LAYOUT, tileLayout);
    ParameterBlock pb = new ParameterBlock();
    pb.addSource(img);
    PlanarImage pi = JAI.create("format", pb, tileHints);
    pi.getWidth();
    return pi;
}
 

public OrbitTiledImagePlanarImage(PlanarImage image) throws Exception {
        super("");
        this.image = image;
        this.width = image.getWidth();
        this.height = image.getHeight();
        this.tileWidth = image.getTileWidth();
        this.tileHeight = image.getTileHeight();
        this.tileGridXOffset = image.getTileGridXOffset();
        this.tileGridYOffset = image.getTileGridYOffset();
        this.minX = image.getMinX();
        this.minY = image.getMinY();
        this.numBands = image.getNumBands();

        this.colorModel = image.getColorModel();
        this.sampleModel = image.getSampleModel();

//		if (numBands==1) this.colorModel = grayColorModel; else
//		{
//			this.colorModel = rgbColorModel;
//		}

//		this.colorModel = rgbColorModel; // an OrbitTiledImage is always a RGB image
//		this.sampleModel = colorModel.createCompatibleSampleModel(tileWidth, tileHeight);

        // bugfix 20.04.2012 Manuel: colorModel is now always defined by input image (overview image problem)
        this.colorModel = image.getColorModel();
        this.sampleModel = image.getSampleModel();
        this.filename = "PlanarImage " + image.hashCode();
        // better set useCache always to false here???
    }
 

public TiledImageWriter(PlanarImage inputImage, SampleModel sampleModel, ColorModel colorModel, int xOffs, int yOffs) {
    this.width = inputImage.getWidth();
    this.height = inputImage.getHeight();
    this.tileWidth = inputImage.getTileWidth();
    this.tileHeight = inputImage.getTileHeight();
    image = new DiskMemImageOrbit(xOffs, yOffs, width, height, 0, 0, sampleModel, colorModel);
    ((DiskMemImageOrbit) image).setUseCommonCache(true);

    TiledImagePainter painter = new TiledImagePainter(inputImage, "");
    Graphics2D g2d = image.createGraphics();
    painter.drawImage(g2d, xOffs, yOffs, width, height, 100d, -1);
}
 

public static PlanarImage adjustBlur(PlanarImage srcImg, final int b) {
    final int width = srcImg.getWidth();
    final int height = srcImg.getHeight();
    final int[] src = srcImg.getData().getPixels(0, 0, width, height, new int[width * height * 3]);
    final int[] dest = new int[width * height * 3];

    for (int l = 0; l < b; l++) {
        if (l == 0) {
            int dum;
            for (int i = 0; i < src.length - 3; i += 3) {
                dum = src[i + 0];
                src[i + 0] = src[i + 2];
                src[i + 2] = dum;
            }
        } else {
            for (int i = 0; i < src.length - 3; i += 3) {
                src[i + 0] = dest[i + 0];
                src[i + 1] = dest[i + 1];
                src[i + 2] = dest[i + 2];
            }
        }
        for (int i = width * 3 + 3; i < src.length - 3 - width * 3; i += 3) {
            dest[i + 0] = (src[i + 0] + src[i + 0 + 3] + src[i + 0 - 3] + src[i + 0 - width * 3] + src[i + 0 + 3 - width * 3] + src[i + 0 - 3 - width * 3] + src[i + 0 + width * 3] + src[i + 0 + 3 + width * 3] + src[i + 0 - 3 + width * 3]) / 9;
            dest[i + 1] = (src[i + 1] + src[i + 1 + 3] + src[i + 1 - 3] + src[i + 1 - width * 3] + src[i + 1 + 3 - width * 3] + src[i + 1 - 3 - width * 3] + src[i + 1 + width * 3] + src[i + 1 + 3 + width * 3] + src[i + 1 - 3 + width * 3]) / 9;
            dest[i + 2] = (src[i + 2] + src[i + 2 + 3] + src[i + 2 - 3] + src[i + 2 - width * 3] + src[i + 2 + 3 - width * 3] + src[i + 2 - 3 - width * 3] + src[i + 2 + width * 3] + src[i + 2 + 3 + width * 3] + src[i + 2 - 3 + width * 3]) / 9;
        }
    }

    DataBufferByte db = new DataBufferByte(dest.length);
    for (int i = 0; i < dest.length; i++) {
        db.setElem(i, dest[i]);
    }
    WritableRaster raster = WritableRaster.createWritableRaster(srcImg.getSampleModel(), db, new Point(0, 0));
    BufferedImage bi = new BufferedImage(srcImg.getColorModel(), raster, srcImg.getColorModel().isAlphaPremultiplied(), null);
    return PlanarImage.wrapRenderedImage(bi);
}
 

public void run() {
    try {
        ClassShape classShape = annotation.getShape();
        if (classShape != null && classShape.getShapeList() != null) {
            if (classShape.getShapeList() != null && classShape.getShapeList().size() > 0) {
                IScaleableShape p = (IScaleableShape) classShape.getShapeList().get(0); // only the first shape
                ImageFrame iFrame = OrbitImageAnalysis.getInstance().getIFrame();
                if (iFrame != null) {
                    final long maxW = 2000;
                    Rectangle rect = p.getScaledInstance(100d, new Point(0, 0)).getBounds();
                    extendBB(rect, bbExtend);
                    PlanarImage img = iFrame.recognitionFrame.bimg.getImage();
                    if ((long) rect.getWidth() * rect.getHeight() > (maxW * maxW)) {
                        if (iFrame.recognitionFrame.bimg.getMipMaps() != null && iFrame.recognitionFrame.bimg.getMipMaps().length > 0) {
                            img = iFrame.recognitionFrame.bimg.getMipMaps()[iFrame.recognitionFrame.bimg.getMipMaps().length - 1].getImage();
                            double scale = (double) img.getWidth() / (double) iFrame.recognitionFrame.bimg.getImage().getWidth();
                            rect = p.getScaledInstance(scale * 100d, new Point(0, 0)).getBounds();
                        }
                    }
                    BufferedImage bi = img.getAsBufferedImage(rect, iFrame.recognitionFrame.bimg.getImage().getColorModel());
                    bi = TiffConverter.makeScaledImage(bi, thumbnailWidth, thumbnailHeight);
                    ImageIcon icon = new ImageIcon(bi);
                    if ((cellCache != null) && (icon != null)) {
                        cellCache.put(hash, icon);
                        list.revalidate();
                        list.repaint();
                    }
                }
            }
        }

    } catch (Throwable t) {
        // can happen (e.g, outofmemory), but no problem
    }

}
 

public List<Shape> detectSegmentations(int minSegmentationSize, PlanarImage sourceImage, Shape roi) {
    logger.trace("getSegmentations (minSegmentation=" + minSegmentationSize + ")");
    if (sourceImage == null) return new ArrayList<Shape>(0);
    short[][] smap = new short[sourceImage.getWidth()][sourceImage.getHeight()];

    for (int x = 0; x < sourceImage.getWidth(); x++)
        for (int y = 0; y < sourceImage.getHeight(); y++)
            smap[x][y] = Short.MAX_VALUE;

    // init
    Point[] tileArr = sourceImage.getTileIndices(null);
    int c;
    for (Point tileNum : tileArr) {
        if (isCancelled()) break;
        final int b = 2;

        Raster raster = sourceImage.getTile(tileNum.x, tileNum.y);
        for (int x = sourceImage.tileXToX(tileNum.x) + b; x < Math.min(sourceImage.tileXToX(tileNum.x) + sourceImage.getTileWidth() - b, sourceImage.getWidth()); x++) {
            for (int y = sourceImage.tileYToY(tileNum.y) + b; y < Math.min(sourceImage.tileYToY(tileNum.y) + sourceImage.getTileHeight() - b, sourceImage.getHeight()); y++) {
                if (fullRoi != null && !(fullRoi.contains(x + roi.getBounds().x, y + roi.getBounds().y))) {
                    continue;
                }

                c = raster.getSample(x, y, 0) < 200 ? 0 : 1; // dark=foreground, white=background (only red channel is taken into account)
                if (c == 0) {  // not background, not assigned
                    smap[x][y] = 1; // 1
                } else {
                    smap[x][y] = 0; // 0
                }
            } //y
        } // x
    } // tileNum


    if (isCancelled()) return null;
    return findPolygons(smap, orderPoints, minSegmentationSize, roi);
}
 

private TMAPointsResult findCircles(PlanarImage img) {
    double r = 6d;
    double d;
    Color classCol = OrbitImageAnalysis.getInstance().getModel().getClassShapes().get(1).getColor();
    int red = classCol.getRed();
    int green = classCol.getGreen();
    int blue = classCol.getBlue();
    int[] c = new int[4];
    logger.trace("class color: " + classCol.toString());
    final Raster raster = img.getData();
    short[][] buf = new short[img.getWidth()][img.getHeight()]; // num tissue pixels buffer
    for (int x = 0; x < img.getWidth(); x++)
        for (int y = 0; y < img.getHeight(); y++) {
            // x,y is center. Now count #tissue pixel in radius around center
            for (int bx = x - (int) r; bx <= x + r; bx++) {
                if (bx < 0 || bx >= img.getWidth()) continue;
                for (int by = y - (int) r; by <= y + r; by++) {
                    if (by < 0 || by >= img.getHeight()) continue;
                    d = Point.distance(bx, by, x, y);
                    if (d <= r) {
                        c = raster.getPixel(bx, by, c);
                        if (c[0] == red && c[1] == green && c[2] == blue) {
                            buf[x][y]++;
                        }
                    }
                }
            }
        }


    BufferedImage resImg = new BufferedImage(img.getWidth(), img.getHeight(), BufferedImage.TYPE_INT_RGB);
    WritableRaster raster2 = resImg.getRaster();
    for (int x = 0; x < resImg.getWidth(); x++)
        for (int y = 0; y < resImg.getHeight(); y++) {
            raster2.setPixel(x, y, new int[]{buf[x][y], buf[x][y], buf[x][y]});
            //System.out.println(buf[x][y]);
        }

    // TODO: instead of UEP create TMPSpot lost, order (by score) and take highest scored spots
    // and check for intersection (maybe with min threshold)
    ImagePlus ip = new ImagePlus("TMAPoints", resImg);
    thresholder.applyThreshold(ip);
    edm.setup("points", null); // "points" for Ultimate points
    edm.run(ip.getProcessor());
    PlanarImage img1 = PlanarImage.wrapRenderedImage(ip.getBufferedImage());
    List<Point> pList = reportPoints(img1, 1);
    double radius = guessRadius(pList);
    return new TMAPointsResult(pList, radius, resImg);
}
 

private static PlanarImage RGBToGray (PlanarImage image)
{
    logger.info("Converting RGB image to gray ...");

    if (constants.useMaxChannelInColorToGray.isSet()) {
        // We use the max value among the RGB channels
        int width = image.getWidth();
        int height = image.getHeight();
        BufferedImage im = new BufferedImage(
                width,
                height,
                BufferedImage.TYPE_BYTE_GRAY);
        WritableRaster raster = im.getRaster();
        Raster source = image.getData();
        int[] levels = new int[3];
        int maxLevel;

        for (int y = 0; y < height; y++) {
            for (int x = 0; x < width; x++) {
                source.getPixel(x, y, levels);
                maxLevel = 0;

                for (int level : levels) {
                    if (maxLevel < level) {
                        maxLevel = level;
                    }
                }

                raster.setSample(x, y, 0, maxLevel);
            }
        }

        return PlanarImage.wrapRenderedImage(im);
    } else {
        // We use luminance value based on standard RGB combination
        double[][] matrix = {
            {0.114d, 0.587d, 0.299d, 0.0d}
        };

        return JAI.create(
                "bandcombine",
                new ParameterBlock().addSource(image).add(matrix),
                null);
    }
}
 

/**
 * Defines RenderingHints for JAI create operations (otherwise JAI will use defaultTileSize tiling)
 *
 * @param image
 * @return
 */
public static RenderingHints getRenderingHints(PlanarImage image) {
    ImageLayout layout = new ImageLayout(image.getMinX(), image.getMinY(), image.getWidth(), image.getHeight(), image.getTileGridXOffset(), image.getTileGridYOffset(), image.getTileWidth(), image.getTileHeight(), image.getSampleModel(), image.getColorModel());
    RenderingHints renderingHints = new RenderingHints(JAI.KEY_IMAGE_LAYOUT, layout);
    return renderingHints;
}