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

Example 11 with ShortProcessor

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

the class ImageArrayConverter method ImageToDoubleArray1DZeroPadding.

public static double[] ImageToDoubleArray1DZeroPadding(ImageProcessor ip, int width, int height) {
    double[] image;
    Object pixelArray = ip.getPixels();
    int count = 0;
    int offsetX = (width - ip.getWidth()) / 2;
    int offsetY = (height - ip.getHeight()) / 2;
    if (offsetX < 0) {
        System.err.println("mpi.fruitfly.general.ImageArrayConverter.ImageToDoubleArray1DZeroPadding(): Zero-Padding size in X smaller than image! " + width + " < " + ip.getWidth());
        return null;
    }
    if (offsetY < 0) {
        System.err.println("mpi.fruitfly.general.ImageArrayConverter.ImageToDoubleArray1DZeroPadding(): Zero-Padding size in Y smaller than image! " + height + " < " + ip.getHeight());
        return null;
    }
    if (ip instanceof ByteProcessor) {
        image = new double[width * height];
        byte[] pixels = (byte[]) pixelArray;
        for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[(y + offsetY) * width + x + offsetX] = pixels[count++] & 0xff;
    } else if (ip instanceof ShortProcessor) {
        image = new double[width * height];
        short[] pixels = (short[]) pixelArray;
        for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[(y + offsetY) * width + x + offsetX] = pixels[count++] & 0xffff;
    } else if (ip instanceof FloatProcessor) {
        image = new double[width * height];
        float[] pixels = (float[]) pixelArray;
        for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image[(y + offsetY) * width + x + offsetX] = pixels[count++];
    } else // RGB
    {
        image = new double[width * height];
        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 12 with ShortProcessor

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

the class ImageArrayConverter method ImageToIntArray.

public static int[][] ImageToIntArray(ImageProcessor ip) {
    int[][] image;
    Object pixelArray = ip.getPixels();
    int count = 0;
    if (ip instanceof ByteProcessor) {
        image = new int[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 int[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 int[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] = (int) pixels[count++];
    } else // RGB
    {
        image = new int[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 13 with ShortProcessor

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

the class ImageArrayConverter method ImageToFloatArray2DZeroPadding.

public static FloatArray2D ImageToFloatArray2DZeroPadding(ImageProcessor ip, int width, int height) {
    FloatArray2D image = new FloatArray2D(width, height);
    Object pixelArray = ip.getPixels();
    int count = 0;
    int offsetX = (width - ip.getWidth()) / 2;
    int offsetY = (height - ip.getHeight()) / 2;
    if (offsetX < 0) {
        System.err.println("mpi.fruitfly.general.ImageArrayConverter.ImageToFloatArray2DZeroPadding(): Zero-Padding size in X smaller than image! " + width + " < " + ip.getWidth());
        return null;
    }
    if (offsetY < 0) {
        System.err.println("mpi.fruitfly.general.ImageArrayConverter.ImageToFloatArray2DZeroPadding(): Zero-Padding size in Y smaller than image! " + height + " < " + ip.getHeight());
        return null;
    }
    if (ip instanceof ByteProcessor) {
        byte[] pixels = (byte[]) pixelArray;
        for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image.set(pixels[count++] & 0xff, x + offsetX, y + offsetY);
    } else if (ip instanceof ShortProcessor) {
        short[] pixels = (short[]) pixelArray;
        for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image.set(pixels[count++] & 0xffff, x + offsetX, y + offsetY);
    } else if (ip instanceof FloatProcessor) {
        float[] pixels = (float[]) pixelArray;
        for (int y = 0; y < ip.getHeight(); y++) for (int x = 0; x < ip.getWidth(); x++) image.set(pixels[count++], x + offsetX, y + offsetY);
    } else // RGB
    {
        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 14 with ShortProcessor

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

the class ImageArrayConverter method ImageToDoubleArray1D.

public static double[] ImageToDoubleArray1D(ImageProcessor ip) {
    double[] image;
    Object pixelArray = ip.getPixels();
    int count = 0;
    if (ip instanceof ByteProcessor) {
        image = new double[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[count] = pixels[count++] & 0xff;
    } else if (ip instanceof ShortProcessor) {
        image = new double[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[count] = pixels[count++] & 0xffff;
    } else if (ip instanceof FloatProcessor) {
        image = new double[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[count] = pixels[count++];
    } else // RGB
    {
        image = new double[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 15 with ShortProcessor

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

the class CreateData method updateArea.

private void updateArea(int[] mask, int width, int height) {
    // 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
    final float[] pixels = new float[mask.length];
    for (int i = 0; i < pixels.length; i++) {
        pixels[i] = mask[i];
    }
    final GaussianFilter blur = new GaussianFilter();
    final double scaleX = (double) settings.getSize() / width;
    final double scaleY = (double) settings.getSize() / height;
    // Allow extra?
    final double extra = 1;
    final double sd = getPsfSd() * extra;
    blur.convolve(pixels, width, height, sd / scaleX, sd / scaleY);
    // Count pixels in blurred mask. Ignore those that are very faint (at the edge of the region)
    int count = 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
    final FloatProcessor fp = new FloatProcessor(width, height, pixels);
    final 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) {
            count++;
        }
    }
    // Convert
    final double scale = ((double) count) / mask.length;
    // System.out.printf("Scale = %f\n", scale);
    areaInUm = scale * settings.getSize() * settings.getPixelPitch() * settings.getSize() * settings.getPixelPitch() / 1e6;
}