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

Example 26 with ShortProcessor

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

the class DownsamplerTest method main.

/**
 * @param args
 */
public static void main(final String[] args) {
    new ImageJ();
    final Timer timer = new Timer();
    final ImagePlus imp = new ImagePlus("/home/saalfeld/tmp/fetter-example.tif");
    // final ImagePlus imp = new ImagePlus( "/home/albert/Desktop/t2/fetter-example.tif" );
    // final ImagePlus imp = new ImagePlus( "/home/saalfeld/Desktop/norway.jpg" );
    imp.show();
    final ImageProcessor ip = imp.getProcessor().duplicate();
    System.out.println("short");
    final ShortProcessor ipShort = (ShortProcessor) ip.convertToShort(false);
    for (int i = 0; i < n; ++i) {
        timer.start();
        testShort(ipShort);
        final long t = timer.stop();
        System.out.println(i + ": " + t + "ms");
    }
    System.out.println("downsampleShort() + downsampleByteProcessor() (independent short with byte mapping + alpha)");
    for (int i = 0; i < n; ++i) {
        final Pair<ShortProcessor, byte[]> ba = new Pair<ShortProcessor, byte[]>(ipShort, (byte[]) ipShort.convertToByte(true).getPixels());
        final ByteProcessor alpha = new ByteProcessor(ipShort.getWidth(), ipShort.getHeight(), (byte[]) ipShort.convertToByte(true).getPixels(), null);
        timer.start();
        testShortAlphaIndependently(ba, alpha);
        final long t = timer.stop();
        System.out.println(i + ": " + t + "ms");
    }
    System.out.println("downsampleShortProcessor() + convertToByte() + downsampleByteProcessor() (independent short + byte mapping + alpha)");
    for (int i = 0; i < n; ++i) {
        final ByteProcessor alpha = new ByteProcessor(ipShort.getWidth(), ipShort.getHeight(), (byte[]) ipShort.convertToByte(true).getPixels(), null);
        timer.start();
        testShortAlphaByteMappingIndependently(ipShort, alpha);
        final long t = timer.stop();
        System.out.println(i + ": " + t + "ms");
    }
    System.out.println("float");
    final FloatProcessor ipFloat = (FloatProcessor) ip.convertToFloat();
    for (int i = 0; i < n; ++i) {
        timer.start();
        testFloat(ipFloat);
        final long t = timer.stop();
        System.out.println(i + ": " + t + "ms");
    }
    System.out.println("independent float with byte mapping + alpha");
    for (int i = 0; i < n; ++i) {
        final Pair<FloatProcessor, byte[]> ba = new Pair<FloatProcessor, byte[]>(ipFloat, (byte[]) ipShort.convertToByte(true).getPixels());
        final ByteProcessor alpha = new ByteProcessor(ipShort.getWidth(), ipShort.getHeight(), (byte[]) ipShort.convertToByte(true).getPixels(), null);
        timer.start();
        testFloatAlphaIndependently(ba, alpha);
        final long t = timer.stop();
        System.out.println(i + ": " + t + "ms");
    }
    System.out.println("byte");
    final ByteProcessor ipByte = (ByteProcessor) ip.convertToByte(true);
    for (int i = 0; i < n; ++i) {
        timer.start();
        testByte(ipByte);
        final long t = timer.stop();
        System.out.println(i + ": " + t + "ms");
    }
    System.out.println("2 x byte");
    final ByteProcessor ipByte2 = (ByteProcessor) ipByte.duplicate();
    for (int i = 0; i < n; ++i) {
        timer.start();
        testByte(ipByte);
        testByte(ipByte2);
        final long t = timer.stop();
        System.out.println(i + ": " + t + "ms");
    }
    System.out.println("color");
    final ColorProcessor ipColor = (ColorProcessor) ip.convertToRGB();
    for (int i = 0; i < n; ++i) {
        timer.start();
        testColor(ipColor);
        final long t = timer.stop();
        System.out.println(i + ": " + t + "ms");
    }
    System.out.println("independent color with byte mapping + alpha");
    for (int i = 0; i < n; ++i) {
        final byte[][] rgb = new byte[4][ipColor.getWidth() * ipColor.getHeight()];
        ipColor.getRGB(rgb[0], rgb[1], rgb[2]);
        final Pair<ColorProcessor, byte[][]> ba = new Pair<ColorProcessor, byte[][]>(ipColor, rgb);
        final ByteProcessor alpha = new ByteProcessor(ipShort.getWidth(), ipShort.getHeight(), (byte[]) ipShort.convertToByte(true).getPixels(), null);
        timer.start();
        testColorAlphaIndependently(ba, alpha);
        final long t = timer.stop();
        System.out.println(i + ": " + t + "ms");
    }
    System.out.println("alpha + outside");
    for (int i = 0; i < n; ++i) {
        ByteProcessor outside = new ByteProcessor(ipByte.getWidth(), ipByte.getHeight());
        outside.setRoi(new OvalRoi(100, 100, ipByte.getWidth() - 200, ipByte.getHeight() - 200));
        outside.setValue(255);
        outside.fill(outside.getMask());
        final Pair<ByteProcessor, ByteProcessor> ba = new Pair<ByteProcessor, ByteProcessor>(ipByte, outside);
        timer.start();
        testAlphaOutside(ba);
        final long t = timer.stop();
        System.out.println(i + ": " + t + "ms");
    }
    System.out.println("outside");
    for (int i = 0; i < n; ++i) {
        ByteProcessor outside = new ByteProcessor(ipByte.getWidth(), ipByte.getHeight());
        outside.setRoi(new OvalRoi(100, 100, ipByte.getWidth() - 200, ipByte.getHeight() - 200));
        outside.setValue(255);
        outside.fill(outside.getMask());
        timer.start();
        testOutside(outside);
        final long t = timer.stop();
        System.out.println(i + ": " + t + "ms");
    }
// System.out.println( "byte integral" );
// final ByteProcessor ipByteI = ( ByteProcessor )ipShort.convertToByte( true );
// 
// for ( int i = 0; i < 10; ++i )
// {
// timer.start();
// testByteIntegral( ipByteI );
// final long t = timer.stop();
// System.out.println( i + ": " + t  + "ms" );
// }
}

Example 27 with ShortProcessor

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

the class CorrectBackground method process.

@Override
public ImageProcessor process(final ImageProcessor ip) {
    final ShortProcessor sp;
    try {
        sp = (ShortProcessor) ip;
    } catch (ClassCastException cce) {
        System.out.println("CorrectBackground supports 16-bit images only!");
        return ip;
    }
    final double min = ip.getMin(), max = ip.getMax();
    final long[] hist = IntegralHistogram2d.integralHistogram2d((short[]) sp.getPixels(), sp.getWidth(), sp.getHeight(), nBins, min, max);
    final short[] median = IntegralHistogram2d.median(sp.getWidth(), sp.getHeight(), hist, nBins, min, max, this.medianRadius);
    if (this.postGaussian) {
        ij.plugin.filter.GaussianBlur g = new ij.plugin.filter.GaussianBlur();
        g.blurGaussian(new ShortProcessor(sp.getWidth(), sp.getHeight(), median, null), this.sigma, this.sigma, 0.02);
    }
    // Approximate mean image value (within min-max range) from the histogram present in the last set of nBins in the integral histogram
    final double binInc = (max - min + 1) / nBins;
    double sum = 0;
    long count = 0;
    for (int i = hist.length - nBins, j = 0; j < nBins; ++i, ++j) {
        sum += hist[i] * (min + (j * binInc));
        count += hist[i];
    }
    // TODO error the sum of hist[-16] to hist[-1] doesn't add up to width*height !!!
    // can't use median.length or p.length, there is an erroneous mismatch
    final double mean = sum / count;
    final short[] p = (short[]) sp.getPixels();
    // The pixels of the provided image
    for (int i = 0; i < p.length; ++i) {
        final double m = median[i] & 0xffff;
        p[i] = (short) (((p[i] & 0xffff) / m) * mean);
    }
    return ip;
}

Example 28 with ShortProcessor

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

the class IntegralHistogram2d method main.

@SuppressWarnings("unused")
public static final void main(String[] args) {
    final ShortProcessor sp = (ShortProcessor) IJ.openImage("/home/albert/Desktop/t2/bridge-16bit.tif").getProcessor();
    final ShortProcessor filtered = median(sp, 64, 0, 65535, 100);
    new ImageJ();
    new ImagePlus("median", filtered).show();
}

Example 29 with ShortProcessor

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

the class ExportUnsignedShort method mapIntensities.

protected static final ShortProcessor mapIntensities(final PatchIntensityRange pir, final double min, final double max) {
    final double a = 65535.0 / (max - min);
    final ImageProcessor source = pir.patch.getImageProcessor();
    final short[] targetPixels = new short[source.getWidth() * source.getHeight()];
    for (int i = 0; i < targetPixels.length; ++i) {
        targetPixels[i] = (short) Math.max(0, Math.min(65535, Math.round(((source.getf(i) - pir.patch.getMin()) / pir.a - min) * a)));
    }
    final ShortProcessor target = new ShortProcessor(source.getWidth(), source.getHeight(), targetPixels, null);
    target.setMinAndMax(-min * a, (1.0 - min) * a);
    return target;
}

Example 30 with ShortProcessor

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

the class ExportUnsignedShort method makeFlatImage.

public static final Pair<ShortProcessor, ByteProcessor> makeFlatImage(final List<Patch> patches, final Rectangle roi, final double backgroundValue, final double scale, final boolean makeAlphaMask) {
    final ArrayList<PatchIntensityRange> patchIntensityRanges = new ArrayList<PatchIntensityRange>();
    double min = Double.MAX_VALUE;
    double max = -Double.MAX_VALUE;
    for (final Displayable d : patches) {
        final Patch patch = (Patch) d;
        final PatchIntensityRange pir = new PatchIntensityRange(patch);
        if (pir.min < min)
            min = pir.min;
        if (pir.max > max)
            max = pir.max;
        patchIntensityRanges.add(pir);
    }
    final double minI = -min * 65535.0 / (max - min);
    final double maxI = (1.0 - min) * 65535.0 / (max - min);
    final ShortProcessor sp;
    if (Double.isNaN(scale)) {
        sp = new ShortProcessor(roi.width, roi.height);
    } else {
        sp = new ShortProcessor((int) (roi.width * scale + 0.5), (int) (roi.height * scale + 0.5));
    }
    sp.setMinAndMax(minI, maxI);
    if (0 != backgroundValue) {
        sp.setValue(backgroundValue);
        sp.setRoi(0, 0, roi.width, roi.height);
        sp.fill();
    }
    final ByteProcessor alphaTarget = makeAlphaMask ? new ByteProcessor(sp.getWidth(), sp.getHeight()) : null;
    for (final PatchIntensityRange pir : patchIntensityRanges) {
        map(new PatchTransform(pir), roi.x, roi.y, scale, mapIntensities(pir, min, max), sp, alphaTarget);
    }
    return new Pair<ShortProcessor, ByteProcessor>(sp, alphaTarget);
}