Examples with ShortProcessor ij.process.ShortProcessor used on opensource projects

Example 31 with ShortProcessor

use of ij.process.ShortProcessor in project TrakEM2 by trakem2.

the class ImageArrayConverter method ImageToFloatArray2DDeprecated.

public static float[][] ImageToFloatArray2DDeprecated(ImageProcessor ip) {
    float[][] image;
    Object pixelArray = ip.getPixels();
    int count = 0;
    if (ip instanceof ByteProcessor) {
        image = new float[ip.getWidth()][ip.getHeight()];
        byte[] pixels = (byte[]) pixelArray;
        for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[x][y] = pixels[count++] & 0xff;
    } else if (ip instanceof ShortProcessor) {
        image = new float[ip.getWidth()][ip.getHeight()];
        short[] pixels = (short[]) pixelArray;
        for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[x][y] = pixels[count++] & 0xffff;
    } else if (ip instanceof FloatProcessor) {
        image = new float[ip.getWidth()][ip.getHeight()];
        float[] pixels = (float[]) pixelArray;
        for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[x][y] = pixels[count++];
    } else // RGB
    {
        image = new float[ip.getWidth()][ip.getHeight()];
        int[] pixels = (int[]) pixelArray;
    // still unknown how to do...
    /*
            for (int y = 0; y < ip.getHeight(); y++)
                for (int x = 0; x < ip.getWidth(); x++)
                        image[x][y] = pixels[count++];// & 0xffffff;
            */
    }
    return image;
}

Example 32 with ShortProcessor

use of ij.process.ShortProcessor in project TrakEM2 by trakem2.

the class ImageArrayConverter method ImageToFloatArray2D.

public static FloatArray2D ImageToFloatArray2D(ImageProcessor ip) {
    FloatArray2D image;
    Object pixelArray = ip.getPixels();
    int count = 0;
    if (ip instanceof ByteProcessor) {
        image = new FloatArray2D(ip.getWidth(), ip.getHeight());
        byte[] pixels = (byte[]) pixelArray;
        for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image.data[count] = pixels[count++] & 0xff;
    } else if (ip instanceof ShortProcessor) {
        image = new FloatArray2D(ip.getWidth(), ip.getHeight());
        short[] pixels = (short[]) pixelArray;
        for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image.data[count] = pixels[count++] & 0xffff;
    } else if (ip instanceof FloatProcessor) {
        image = new FloatArray2D(ip.getWidth(), ip.getHeight());
        float[] pixels = (float[]) pixelArray;
        for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image.data[count] = pixels[count++];
    } else // RGB
    {
        image = new FloatArray2D(ip.getWidth(), ip.getHeight());
        int[] pixels = (int[]) pixelArray;
    // still unknown how to do...
    /*
            for (int y = 0; y < ip.getHeight(); y++)
                for (int x = 0; x < ip.getWidth(); x++)
                        image[x][y] = pixels[count++];// & 0xffffff;
            */
    }
    return image;
}

Example 33 with ShortProcessor

use of ij.process.ShortProcessor in project GDSC-SMLM by aherbert.

the class SplitResults method splitResults.

private void splitResults(MemoryPeakResults results, ImageProcessor ip) {
    IJ.showStatus("Splitting " + TextUtils.pleural(results.size(), "result"));
    // Create an object mask
    final ObjectAnalyzer objectAnalyzer = new ObjectAnalyzer(ip, false);
    final int maxx = ip.getWidth();
    final int maxy = ip.getHeight();
    final Rectangle bounds = results.getBounds();
    final double ox = bounds.getX();
    final double oy = bounds.getY();
    final double scaleX = bounds.getWidth() / maxx;
    final double scaleY = bounds.getHeight() / maxy;
    // Create a results set for each object
    final int maxObject = objectAnalyzer.getMaxObject();
    final MemoryPeakResults[] resultsSet = new MemoryPeakResults[maxObject + 1];
    for (int object = 0; object <= maxObject; object++) {
        final MemoryPeakResults newResults = new MemoryPeakResults();
        newResults.copySettings(results);
        newResults.setName(results.getName() + " " + object);
        resultsSet[object] = newResults;
    }
    final int[] mask = objectAnalyzer.getObjectMask();
    if (settings.showObjectMask) {
        final ImageProcessor objectIp = (maxObject <= 255) ? new ByteProcessor(maxx, maxy) : new ShortProcessor(maxx, maxy);
        for (int i = 0; i < mask.length; i++) {
            objectIp.set(i, mask[i]);
        }
        final ImagePlus imp = ImageJUtils.display(settings.objectMask + " Objects", objectIp);
        imp.setDisplayRange(0, maxObject);
        imp.updateAndDraw();
    }
    // Process the results mapping them to their objects
    final Counter i = new Counter();
    final int size = results.size();
    final int step = ImageJUtils.getProgressInterval(size);
    results.forEach(DistanceUnit.PIXEL, (XyrResultProcedure) (xx, yy, result) -> {
        if (i.incrementAndGet() % step == 0) {
            IJ.showProgress(i.getCount(), size);
        }
        // Map to the mask objects
        final int object;
        final int x = (int) ((xx - ox) / scaleX);
        final int y = (int) ((yy - oy) / scaleY);
        if (x < 0 || x >= maxx || y < 0 || y >= maxy) {
            object = 0;
        } else {
            final int index = y * maxx + x;
            // is within the bounds of the image processor?
            if (index < 0 || index >= mask.length) {
                object = 0;
            } else {
                object = mask[index];
            }
        }
        resultsSet[object].add(result);
    });
    IJ.showProgress(1);
    // Add the new results sets to memory
    i.reset();
    for (int object = (settings.nonMaskDataset) ? 0 : 1; object <= maxObject; object++) {
        if (resultsSet[object].isNotEmpty()) {
            MemoryPeakResults.addResults(resultsSet[object]);
            i.increment();
        }
    }
    IJ.showStatus("Split " + TextUtils.pleural(results.size(), "result") + " into " + TextUtils.pleural(i.getCount(), "set"));
}

Example 34 with ShortProcessor

use of ij.process.ShortProcessor in project GDSC-SMLM by aherbert.

the class ImageJImagePeakResults method createNewProcessor.

private ImageProcessor createNewProcessor(int imageWidth, int imageHeight) {
    // Equalised display requires a 16-bit image to allow fast processing of the histogram
    if ((displayFlags & DISPLAY_EQUALIZED) != 0) {
        pixels = new short[data.length];
        return new ShortProcessor(imageWidth, imageHeight, (short[]) pixels, null);
    }
    pixels = new float[data.length];
    // Zero is mapped to 0 in the LUT.
    if ((displayFlags & DISPLAY_MAPPED) != 0) {
        final MappedFloatProcessor fp = new MappedFloatProcessor(imageWidth, imageHeight, (float[]) pixels, null);
        fp.setMapZero((displayFlags & DISPLAY_MAP_ZERO) != 0);
        return fp;
    }
    // -Infinity is mapped to 0 in the LUT.
    if ((displayFlags & DISPLAY_NEGATIVES) != 0) {
        return new InfinityMappedFloatProcessor(imageWidth, imageHeight, (float[]) pixels, null);
    }
    return new FloatProcessor(imageWidth, imageHeight, (float[]) pixels, null);
}