Java Code Examples for ij.process.ColorProcessor#getHeight()

private static void processColor(final ColorProcessor ip,
                                 final int value,
                                 final int min,
                                 final int max) {
    final int scale = max - min + 1;
    final Random rnd = new Random();
    final int n = ip.getWidth() * ip.getHeight();
    for (int i = 0; i < n; ++i) {
        final int v = ip.get(i) & 0x00ffffff;
        if (v == value) {
            final int r = rnd.nextInt(scale) + min;
            final int g = rnd.nextInt(scale) + min;
            final int b = rnd.nextInt(scale) + min;

            ip.set(i, (((((0xff << 8) | r) << 8) | g) << 8) | b);
        }
    }
}
 

/**
 * Prints the content of the input color image on the console. This can be
 * used for debugging (small) images.
 * 
 * @param image
 *            the color image to display on the console
 */
public static final void print(ColorProcessor image) 
{
	for (int y = 0; y < image.getHeight(); y++)
	{
		for (int x = 0; x < image.getWidth(); x++)
		{
			int intCode = image.get(x, y);
			int r = (intCode & 0xFF0000) >> 16;
			int g = (intCode & 0xFF00) >> 8;
			int b = (intCode & 0xFF);
			System.out.print(String.format("(%3d,%3d,%3d) ", r, g, b));
		}
		System.out.println("");
	}
}
 

/**
 * Tests closing can be run on an RGB image.
 */
@Test
public void testClosing_Square_RGB() {
	String fileName = getClass().getResource("/files/peppers-crop.png").getFile();
	ImagePlus imagePlus = IJ.openImage(fileName);
	assertNotNull(imagePlus);
	ColorProcessor image = (ColorProcessor) imagePlus.getProcessor();
	
	Strel strel = SquareStrel.fromDiameter(5);
	ColorProcessor result = (ColorProcessor) Morphology.closing(image, strel);
	assertNotNull(result);
	
	// Check that result is greater than or equal to the original image
	int width = image.getWidth();
	int height = image.getHeight();
	int[] rgb0 = new int[3];
	int[] rgb = new int[3];
	for (int y = 0; y < height; y++) {
		for (int x = 0; x < width; x++) {
			image.getPixel(x, y, rgb0);
			result.getPixel(x, y, rgb);
			for (int c = 0; c < 3; c++)
				assertTrue(rgb[c] >= rgb0[c]);
		}
	}
}
 

/**
 * Tests closing can be run on an RGB image.
 */
@Test
public void testOpening_Square_RGB() {
	String fileName = getClass().getResource("/files/peppers-crop.png").getFile();
	ImagePlus imagePlus = IJ.openImage(fileName);
	assertNotNull(imagePlus);
	ColorProcessor image = (ColorProcessor) imagePlus.getProcessor();
	
	Strel strel = SquareStrel.fromDiameter(5);
	ColorProcessor result = (ColorProcessor) Morphology.opening(image, strel);
	assertNotNull(result);
	
	// Check that result is lower than or equal to the original image
	int width = image.getWidth();
	int height = image.getHeight();
	int[] rgb0 = new int[3];
	int[] rgb = new int[3];
	for (int y = 0; y < height; y++) {
		for (int x = 0; x < width; x++) {
			image.getPixel(x, y, rgb0);
			result.getPixel(x, y, rgb);
			for (int c = 0; c < 3; c++)
				assertTrue(rgb[c] <= rgb0[c]);
		}
	}
}
 

final static private void processColor(final ColorProcessor ip, final int value, final int min, final int max) {
	final int scale = max - min + 1;
	final Random rnd = new Random();
	final int n = ip.getWidth() * ip.getHeight();
	for (int i =0; i < n; ++i) {
		final int v = ip.get(i);
		if (v == value)
		{
			final int r = rnd.nextInt(scale) + min;
			final int g = rnd.nextInt(scale) + min;
			final int b = rnd.nextInt(scale) + min;

			ip.set(i, (((((0xff << 8) | r) << 8) | g) << 8) | b);
		}
	}
}
 

public Pair<ColorProcessor, ByteProcessor> makeFlatColorImage()
{
	if ( canUseAWTImage() ) { // less than 0.5 GB array size
		final ColorProcessor cp = new ColorProcessor( createAWTImage( ImagePlus.COLOR_RGB ) );
		final ByteProcessor alpha = new ByteProcessor( cp.getWidth(), cp.getHeight(), cp.getChannel( 4 ) );
		return new Pair<ColorProcessor, ByteProcessor>( cp, alpha );
	}

	if ( !isSmallerThan2GB() ) {
		Utils.log("Cannot create an image larger than 2 GB.");
		return null;
	}

	if ( loader.isMipMapsRegenerationEnabled() )
	{
		return ExportARGB.makeFlatImageARGBFromMipMaps( patches, finalBox, 0, scale );
	}

	// No mipmaps: create an image as large as possible, then downsample it
	final Pair<ColorProcessor, ByteProcessor> pair = ExportARGB.makeFlatImageARGBFromOriginals( patches, finalBox, 0, scaleUP );

	final double sigma = computeSigma( pair.a.getWidth(), pair.a.getHeight());
	new GaussianBlur().blurGaussian( pair.a, sigma, sigma, 0.0002 );
	new GaussianBlur().blurGaussian( pair.b, sigma, sigma, 0.0002 );
	return pair;
}
 

/**
 * Duplicates {@link ColorProcessor} to the corresponding OpenCV image of
 * type {@link Mat}.
 *
 * @param cp The {@link ColorProcessor} to be converted
 * @return The OpenCV image (of type {@link Mat})
 */
public static Mat toMat(ColorProcessor cp) {
    final int w = cp.getWidth();
    final int h = cp.getHeight();
    final int[] pixels = (int[]) cp.getPixels();
    byte[] bData = new byte[w * h * 3];

    // convert int-encoded RGB values to byte array
    for (int i = 0; i < pixels.length; i++) {
        bData[i * 3 + 0] = (byte) ((pixels[i] >> 16) & 0xFF);	// red
        bData[i * 3 + 1] = (byte) ((pixels[i] >> 8) & 0xFF);	// grn
        bData[i * 3 + 2] = (byte) ((pixels[i]) & 0xFF);	// blu
    }
    return new Mat(h, w, opencv_core.CV_8UC3, new BytePointer(bData));
}
 

public FloatProcessorT2(final ColorProcessor cp, final int channel) {
	this(cp.getWidth(), cp.getHeight(), 0, 255);
	final int[] c = (int[])cp.getPixels();
	int bitmask = 0;
	int shift = 0;
	switch (channel) {
		case 0: bitmask = 0x00ff0000; shift = 16; break; // red
		case 1: bitmask = 0x0000ff00; shift =  8; break; // green
		case 2: bitmask = 0x000000ff; break; // blue
	}
	final float[] pixels = (float[])this.getPixels(); // I luv pointlessly private fields
	for (int i=0; i<pixels.length; i++) pixels[i] = ((c[i] & bitmask)>>shift);
	super.setMinAndMax(0, 255); // we know them
}
 

/**
 * Converts the processor to an ARGB image.
 *
 * @param  renderedImageProcessorWithMasks  processor to convert.
 * @param  binaryMask                       indicates whether a binary mask should be applied.
 *
 * @return the converted image.
 */
public static BufferedImage targetToARGBImage(final ImageProcessorWithMasks renderedImageProcessorWithMasks,
                                              final boolean binaryMask) {

    // convert to 24bit RGB
    final ColorProcessor cp = renderedImageProcessorWithMasks.ip.convertToColorProcessor();

    // set alpha channel
    final int[] cpPixels = (int[]) cp.getPixels();
    final byte[] alphaPixels;

    if (renderedImageProcessorWithMasks.mask != null) {
        alphaPixels = (byte[]) renderedImageProcessorWithMasks.mask.getPixels();
    } else if (renderedImageProcessorWithMasks.outside != null) {
        alphaPixels = (byte[]) renderedImageProcessorWithMasks.outside.getPixels();
    } else {
        alphaPixels = null;
    }

    if (alphaPixels == null) {
        for (int i = 0; i < cpPixels.length; ++i) {
            cpPixels[i] &= 0xffffffff;
        }
    } else if (binaryMask) {
        for (int i = 0; i < cpPixels.length; ++i) {
            if (alphaPixels[i] == -1)
                cpPixels[i] &= 0xffffffff;
            else
                cpPixels[i] &= 0x00ffffff;
        }
    } else {
        for (int i = 0; i < cpPixels.length; ++i) {
            cpPixels[i] &= 0x00ffffff | (alphaPixels[i] << 24);
        }
    }

    final BufferedImage image = new BufferedImage(cp.getWidth(), cp.getHeight(), BufferedImage.TYPE_INT_ARGB);
    final WritableRaster raster = image.getRaster();
    raster.setDataElements(0, 0, cp.getWidth(), cp.getHeight(), cpPixels);

    return image;
}
 

@SuppressWarnings({ "unused", "unchecked", "null" })
private static final BufferedImage[] createRGB(
		final Patch patch,
		final ColorProcessor ip,
		final ByteProcessor mask) {
	final int w = ip.getWidth();
	final int h = ip.getHeight();
	final int[] dims = new int[]{w, h};
	final ScaleAreaAveraging2d<LongType, UnsignedByteType> saar, saag, saab, saam;
	{
		// Split color channels
		final int[] p = (int[]) ip.getPixels();
		final byte[] r = new byte[p.length],
		             g = new byte[p.length],
		             b = new byte[p.length];
		for (int i=0; i<p.length; ++i) {
			final int a = p[i];
			r[i] = (byte)((a >> 16)&0xff);
			g[i] = (byte)((a >> 8)&0xff);
			b[i] = (byte)(a&0xff);
		}
		//
		saar = saa(r, dims);
		saag = saa(g, dims);
		saab = saa(b, dims);
		saam = null == mask? null : saa((byte[])mask.getPixels(), dims);
	}
	
	// Generate images
	final BufferedImage[] bis = new BufferedImage[Loader.getHighestMipMapLevel(patch) + 1];
	//
	if (null == saam) { // mask is null
		bis[0] = ImageSaver.createARGBImage((int[])ip.getPixels(), w, h); // sharing the int[] pixels
		for (int i=1; i<bis.length; i++) {
			final int K = (int) Math.pow(2, i),
		          wk = w / K,
		          hk = h / K;
			// An image of the scaled size
			saar.setOutputDimensions(wk, hk);
			saar.process();
			saag.setOutputDimensions(wk, hk);
			saag.process();
			saab.setOutputDimensions(wk, hk);
			saab.process();
			bis[i] = ImageSaver.createARGBImage(
				blend(((Array<UnsignedByteType,ByteArray>) saar.getResult().getContainer()).update(null).getCurrentStorageArray(),
					  ((Array<UnsignedByteType,ByteArray>) saag.getResult().getContainer()).update(null).getCurrentStorageArray(),
					  ((Array<UnsignedByteType,ByteArray>) saab.getResult().getContainer()).update(null).getCurrentStorageArray()),
				wk, hk);
		}
	} else {
		// With alpha channel
		bis[0] = ImageSaver.createARGBImage(blend((int[])ip.getPixels(), (byte[])mask.getPixels()), w, h); // sharing the int[] pixels
		for (int i=1; i<bis.length; i++) {
			final int K = (int) Math.pow(2, i),
		          wk = w / K,
		          hk = h / K;
			// An image of the scaled size
			saar.setOutputDimensions(wk, hk);
			saar.process();
			saag.setOutputDimensions(wk, hk);
			saag.process();
			saab.setOutputDimensions(wk, hk);
			saab.process();
			saam.setOutputDimensions(wk, hk);
			saam.process();
			bis[i] = ImageSaver.createARGBImage(
				blend(((Array<UnsignedByteType,ByteArray>) saar.getResult().getContainer()).update(null).getCurrentStorageArray(),
					  ((Array<UnsignedByteType,ByteArray>) saag.getResult().getContainer()).update(null).getCurrentStorageArray(),
					  ((Array<UnsignedByteType,ByteArray>) saab.getResult().getContainer()).update(null).getCurrentStorageArray(),
					  ((Array<UnsignedByteType,ByteArray>) saam.getResult().getContainer()).update(null).getCurrentStorageArray()),
				wk, hk);
		}
	}
	
	return bis;
}
 

private static final ImageBytes[] fastCreateRGB(
		final Patch patch,
		final ColorProcessor ip,
		final ByteProcessor mask) {
	final int w = ip.getWidth();
	final int h = ip.getHeight();
	
	final long[] ir, ig, ib, im;
	{
		// Split color channels
		final int[] p = (int[]) ip.getPixels();
		final byte[] r = new byte[p.length],
		             g = new byte[p.length],
		             b = new byte[p.length];
		for (int i=0; i<p.length; ++i) {
			final int a = p[i];
			r[i] = (byte)((a >> 16)&0xff);
			g[i] = (byte)((a >> 8)&0xff);
			b[i] = (byte)(a&0xff);
		}
		//
		ir = FastIntegralImage.longIntegralImage(r, w, h);
		ig = FastIntegralImage.longIntegralImage(g, w, h);
		ib = FastIntegralImage.longIntegralImage(b, w, h);
		im = null == mask ? null : FastIntegralImage.longIntegralImage((byte[])mask.getPixels(), w, h);
	}
	
	// Generate images
	final ImageBytes[] bis = new ImageBytes[Loader.getHighestMipMapLevel(patch) + 1];
	//
	if (null == mask) {
		bis[0] = new ImageBytes(P.asRGBBytes((int[])ip.getPixels()), ip.getWidth(), ip.getHeight());
		for (int i=1; i<bis.length; i++) {
			final int K = (int) Math.pow(2, i),
		          wk = w / K,
		          hk = h / K;
			// An image of the scaled size
			bis[i] = new ImageBytes(new byte[][]{FastIntegralImage.scaleAreaAverage(ir, w+1, h+1, wk, hk),
			                                     FastIntegralImage.scaleAreaAverage(ig, w+1, h+1, wk, hk),
			                                     FastIntegralImage.scaleAreaAverage(ib, w+1, h+1, wk, hk)},
			                        wk, hk);
		}
	} else {
		// With alpha channel
		bis[0] = new ImageBytes(P.asRGBABytes((int[])ip.getPixels(), (byte[])mask.getPixels(), null), ip.getWidth(), ip.getHeight());
		for (int i=1; i<bis.length; i++) {
			final int K = (int) Math.pow(2, i),
		          wk = w / K,
		          hk = h / K;
			// An image of the scaled size
			bis[i] = new ImageBytes(new byte[][]{FastIntegralImage.scaleAreaAverage(ir, w+1, h+1, wk, hk),
			                                     FastIntegralImage.scaleAreaAverage(ig, w+1, h+1, wk, hk),
			                                     FastIntegralImage.scaleAreaAverage(ib, w+1, h+1, wk, hk),
			                                     FastIntegralImage.scaleAreaAverage(im, w+1, h+1, wk, hk)},
			                        wk, hk);
		}
	}

	return bis;
}
 

static private final ImageBytes asBytes(final ColorProcessor cp) {
	return new ImageBytes(P.asRGBBytes((int[])cp.getPixels()), cp.getWidth(), cp.getHeight());
}
 

static private final ImageBytes asBytes(final ColorProcessor cp, final ByteProcessor mask) {
	return new ImageBytes(P.asRGBABytes((int[])cp.getPixels(), (byte[])mask.getPixels(), null), cp.getWidth(), cp.getHeight());
}