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

Example 1 with ShortProcessor

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

the class CreateData method updateArea.

private void updateArea(int[] mask, int w, int h) {
    // Note: The apparent area will be bigger due to the PSF width blurring the edges.
    // Assume the entire max intensity mask is in focus and the PSF is Gaussian in the focal plane.
    // Blur the mask
    float[] pixels = new float[mask.length];
    for (int i = 0; i < pixels.length; i++) pixels[i] = mask[i];
    GaussianFilter blur = new GaussianFilter();
    final double scaleX = (double) settings.size / w;
    final double scaleY = (double) settings.size / h;
    // Allow extra?
    double extra = 1;
    double sd = getPsfSD() * extra;
    blur.convolve(pixels, w, h, sd / scaleX, sd / scaleY);
    // Count pixels in blurred mask. Ignore those that are very faint (at the edge of the region)
    int c = 0;
    //		// By fraction of max value
    //		float limit = 0.1f;
    //		//float min = (float) (Maths.max(pixels) * limit);
    //		float min = limit;
    //		for (float f : pixels)
    //			if (f > min)
    //				c++;
    //		// Rank in order and get fraction of sum
    //		Arrays.sort(pixels);
    //		double sum = 0;
    //		double stop = Maths.sum(pixels) * 0.95;
    //		float after = Maths.max(pixels) + 1;
    //		for (float f : pixels)
    //		{
    //			sum += f;
    //			if (sum > stop)
    //			{
    //				break;
    //				//after = f;
    //				//stop = Float.POSITIVE_INFINITY;
    //			}
    //			if (f > after)
    //				break;
    //			c++;
    //		}
    // Threshold to a mask
    FloatProcessor fp = new FloatProcessor(w, h, pixels);
    ShortProcessor sp = (ShortProcessor) fp.convertToShort(true);
    final int t = AutoThreshold.getThreshold(AutoThreshold.Method.OTSU, sp.getHistogram());
    //Utils.display("Blurred", fp);
    for (int i = 0; i < mask.length; i++) if (sp.get(i) >= t)
        c++;
    // Convert 
    final double scale = ((double) c) / mask.length;
    //System.out.printf("Scale = %f\n", scale);
    areaInUm = scale * settings.size * settings.pixelPitch * settings.size * settings.pixelPitch / 1e6;
}

Example 2 with ShortProcessor

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

the class PCPALMMolecules method drawImage.

static ImageProcessor drawImage(ArrayList<Molecule> molecules, double minx, double miny, double maxx, double maxy, double nmPerPixel, boolean checkBounds, boolean binary) {
    double scalex = maxx - minx;
    double scaley = maxy - miny;
    int width = (int) Math.round(scalex / nmPerPixel) + 1;
    int height = (int) Math.round(scaley / nmPerPixel) + 1;
    // ***
    if (binary) {
        byte[] data = new byte[width * height];
        for (Molecule m : molecules) {
            if (checkBounds) {
                if (m.x < minx || m.x >= maxx || m.y < miny || m.y >= maxy)
                    continue;
            }
            // Shift to the origin. This makes the image more memory efficient.
            int x = (int) Math.round((m.x - minx) / nmPerPixel);
            int y = (int) Math.round((m.y - miny) / nmPerPixel);
            int index = y * width + x;
            // Construct a binary image
            data[index] = (byte) 1;
        }
        ByteProcessor ip = new ByteProcessor(width, height, data, null);
        ip.setMinAndMax(0, 1);
        return ip;
    } else {
        short[] data = new short[width * height];
        for (Molecule m : molecules) {
            if (checkBounds) {
                if (m.x < minx || m.x >= maxx || m.y < miny || m.y >= maxy)
                    continue;
            }
            // Shift to the origin. This makes the image more memory efficient.
            int x = (int) Math.round((m.x - minx) / nmPerPixel);
            int y = (int) Math.round((m.y - miny) / nmPerPixel);
            int index = y * width + x;
            // Construct a count image
            data[index]++;
        }
        ShortProcessor ip = new ShortProcessor(width, height, data, null);
        ip.setMinAndMax(0, Maths.max(data));
        return ip;
    }
}

Example 3 with ShortProcessor

use of ij.process.ShortProcessor in project imagingbook-common by imagingbook.

the class RegionLabeling method makeLabelImageGray.

private ShortProcessor makeLabelImageGray() {
    ShortProcessor sp = new ShortProcessor(width, height);
    for (int v = 0; v < height; v++) {
        for (int u = 0; u < width; u++) {
            int lb = getLabel(u, v);
            sp.set(u, v, (lb >= 0) ? lb : 0);
        }
    }
    sp.resetMinAndMax();
    return sp;
}

Example 4 with ShortProcessor

use of ij.process.ShortProcessor in project bioformats by openmicroscopy.

the class ImageProcessorReader method openProcessors.

/**
 * Returns an array of ImageProcessors that represent the given slice.
 * There is one ImageProcessor per RGB channel;
 * i.e., length of returned array == getRGBChannelCount().
 *
 * @param no Position of image plane.
 */
public ImageProcessor[] openProcessors(int no, int x, int y, int w, int h) throws FormatException, IOException {
    // read byte array
    byte[] b = openBytes(no, x, y, w, h);
    int c = getRGBChannelCount();
    int type = getPixelType();
    int bpp = FormatTools.getBytesPerPixel(type);
    boolean interleave = isInterleaved();
    if (b.length != w * h * c * bpp && b.length != w * h * bpp) {
        throw new FormatException("Invalid byte array length: " + b.length + " (expected w=" + w + ", h=" + h + ", c=" + c + ", bpp=" + bpp + ")");
    }
    // create a color model for this plane (null means default)
    final LUT cm = createColorModel();
    // convert byte array to appropriate primitive array type
    boolean isFloat = FormatTools.isFloatingPoint(type);
    boolean isLittle = isLittleEndian();
    boolean isSigned = FormatTools.isSigned(type);
    // construct image processors
    ImageProcessor[] ip = new ImageProcessor[c];
    for (int i = 0; i < c; i++) {
        byte[] channel = ImageTools.splitChannels(b, i, c, bpp, false, interleave);
        Object pixels = DataTools.makeDataArray(channel, bpp, isFloat, isLittle);
        if (pixels instanceof byte[]) {
            byte[] q = (byte[]) pixels;
            if (q.length != w * h) {
                byte[] tmp = q;
                q = new byte[w * h];
                System.arraycopy(tmp, 0, q, 0, Math.min(q.length, tmp.length));
            }
            if (isSigned)
                q = DataTools.makeSigned(q);
            ip[i] = new ByteProcessor(w, h, q, null);
            if (cm != null)
                ip[i].setColorModel(cm);
        } else if (pixels instanceof short[]) {
            short[] q = (short[]) pixels;
            if (q.length != w * h) {
                short[] tmp = q;
                q = new short[w * h];
                System.arraycopy(tmp, 0, q, 0, Math.min(q.length, tmp.length));
            }
            if (isSigned)
                q = DataTools.makeSigned(q);
            ip[i] = new ShortProcessor(w, h, q, cm);
        } else if (pixels instanceof int[]) {
            int[] q = (int[]) pixels;
            if (q.length != w * h) {
                int[] tmp = q;
                q = new int[w * h];
                System.arraycopy(tmp, 0, q, 0, Math.min(q.length, tmp.length));
            }
            ip[i] = new FloatProcessor(w, h, q);
        } else if (pixels instanceof float[]) {
            float[] q = (float[]) pixels;
            if (q.length != w * h) {
                float[] tmp = q;
                q = new float[w * h];
                System.arraycopy(tmp, 0, q, 0, Math.min(q.length, tmp.length));
            }
            ip[i] = new FloatProcessor(w, h, q, null);
        } else if (pixels instanceof double[]) {
            double[] q = (double[]) pixels;
            if (q.length != w * h) {
                double[] tmp = q;
                q = new double[w * h];
                System.arraycopy(tmp, 0, q, 0, Math.min(q.length, tmp.length));
            }
            ip[i] = new FloatProcessor(w, h, q);
        }
    }
    return ip;
}

Example 5 with ShortProcessor

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

the class DownsamplerMipMaps method create.

public static final ImageBytes[] create(final Patch patch, final int type, final int n_levels, final ImageProcessor ip, final ByteProcessor alpha, final ByteProcessor outside) {
    // Create pyramid
    final ImageBytes[] p = new ImageBytes[n_levels];
    if (null == alpha && null == outside) {
        int i = 1;
        switch(type) {
            case ImagePlus.GRAY8:
                ByteProcessor bp = (ByteProcessor) ip;
                p[0] = asBytes(bp);
                while (i < p.length) {
                    bp = Downsampler.downsampleByteProcessor(bp);
                    p[i++] = asBytes(bp);
                }
                break;
            case ImagePlus.GRAY16:
                ShortProcessor sp = (ShortProcessor) ip;
                p[0] = asBytes(sp);
                Pair<ShortProcessor, byte[]> rs;
                while (i < p.length) {
                    rs = Downsampler.downsampleShort(sp);
                    sp = rs.a;
                    p[i++] = new ImageBytes(new byte[][] { rs.b }, sp.getWidth(), sp.getHeight());
                }
                break;
            case ImagePlus.GRAY32:
                FloatProcessor fp = (FloatProcessor) ip;
                p[0] = asBytes(fp);
                Pair<FloatProcessor, byte[]> rf;
                while (i < p.length) {
                    rf = Downsampler.downsampleFloat(fp);
                    fp = rf.a;
                    p[i++] = new ImageBytes(new byte[][] { rf.b }, fp.getWidth(), fp.getHeight());
                }
                break;
            case ImagePlus.COLOR_RGB:
                ColorProcessor cp = (ColorProcessor) ip;
                // TODO the int[] could be reused
                p[0] = asBytes(cp);
                Pair<ColorProcessor, byte[][]> rc;
                while (i < p.length) {
                    rc = Downsampler.downsampleColor(cp);
                    cp = rc.a;
                    p[i++] = new ImageBytes(rc.b, cp.getWidth(), cp.getHeight());
                }
                break;
        }
    } else {
        // Alpha channel
        final ByteProcessor[] masks = new ByteProcessor[p.length];
        if (null != alpha && null != outside) {
            // Use both alpha and outside:
            final byte[] b1 = (byte[]) alpha.getPixels(), b2 = (byte[]) outside.getPixels();
            for (int i = 0; i < b1.length; ++i) {
                // 'outside' is a binary mask, qualitative. -1 means 255
                b1[i] = b2[i] != -1 ? 0 : b1[i];
            }
            masks[0] = alpha;
            // 
            int i = 1;
            Pair<ByteProcessor, ByteProcessor> pair;
            ByteProcessor a = alpha, o = outside;
            while (i < p.length) {
                pair = Downsampler.downsampleAlphaAndOutside(a, o);
                a = pair.a;
                o = pair.b;
                // o is already combined into it
                masks[i] = a;
                ++i;
            }
        } else {
            // Only one of the two is not null:
            if (null == alpha) {
                masks[0] = outside;
                int i = 1;
                while (i < p.length) {
                    masks[i] = Downsampler.downsampleOutside(masks[i - 1]);
                    ++i;
                }
            } else {
                masks[0] = alpha;
                int i = 1;
                while (i < p.length) {
                    masks[i] = Downsampler.downsampleByteProcessor(masks[i - 1]);
                    ++i;
                }
            }
        }
        // Image channels
        int i = 1;
        switch(type) {
            case ImagePlus.GRAY8:
                ByteProcessor bp = (ByteProcessor) ip;
                p[0] = asBytes(bp, masks[0]);
                while (i < p.length) {
                    bp = Downsampler.downsampleByteProcessor(bp);
                    p[i] = asBytes(bp, masks[i]);
                    ++i;
                }
                break;
            case ImagePlus.GRAY16:
                ShortProcessor sp = (ShortProcessor) ip;
                p[0] = asBytes(sp, masks[0]);
                while (i < p.length) {
                    final Pair<ShortProcessor, byte[]> rs = Downsampler.downsampleShort(sp);
                    sp = rs.a;
                    p[i] = new ImageBytes(new byte[][] { rs.b, (byte[]) masks[i].getPixels() }, sp.getWidth(), sp.getHeight());
                    ++i;
                }
                break;
            case ImagePlus.GRAY32:
                FloatProcessor fp = (FloatProcessor) ip;
                p[0] = asBytes(fp, masks[0]);
                while (i < p.length) {
                    final Pair<FloatProcessor, byte[]> rs = Downsampler.downsampleFloat(fp);
                    fp = rs.a;
                    p[i] = new ImageBytes(new byte[][] { rs.b, (byte[]) masks[i].getPixels() }, fp.getWidth(), fp.getHeight());
                    ++i;
                }
                break;
            case ImagePlus.COLOR_RGB:
                ColorProcessor cp = (ColorProcessor) ip;
                // TODO the int[] could be reused
                p[0] = asBytes(cp, masks[0]);
                while (i < p.length) {
                    final Pair<ColorProcessor, byte[][]> rs = Downsampler.downsampleColor(cp);
                    cp = rs.a;
                    final byte[][] rgb = rs.b;
                    p[i] = new ImageBytes(new byte[][] { rgb[0], rgb[1], rgb[2], (byte[]) masks[i].getPixels() }, cp.getWidth(), cp.getHeight());
                    ++i;
                }
                break;
        }
    }
    return p;
}