Java Code Examples for ij.process.ImageProcessor#setColorModel()

/**
 * Applies the specified morphological operation with specified structuring
 * element to the input image.
 * 
 * @param image
 *            the input image (grayscale or color)
 * @param op
 *            the operation to apply
 * @param strel
 *            the structuring element to use for the operation
 * @return the result of morphological operation applied to the input image
 * @deprecated use the process method instead
 */
@Deprecated
public ImagePlus exec(ImagePlus image, Operation op, Strel strel)
{
	// Check validity of parameters
	if (image == null)
		return null;
	
	// extract the input processor
	ImageProcessor inputProcessor = image.getProcessor();
	
	// apply morphological operation
	ImageProcessor resultProcessor = op.apply(inputProcessor, strel);
	
	// Keep same color model
	resultProcessor.setColorModel(inputProcessor.getColorModel());
	
	// create the new image plus from the processor
	ImagePlus resultImage = new ImagePlus(op.toString(), resultProcessor);
	resultImage.copyScale(image);
				
	// return the created array
	return resultImage;
}
 

/**
 * Applies the specified morphological operation with specified structuring
 * element to the input image.
 * 
 * @param image
 *            the input image (grayscale or color)
 * @param op
 *            the operation to apply
 * @param strel
 *            the structuring element to use for the operation
 * @return the result of morphological operation applied to the input image
 */
public ImagePlus process(ImagePlus image, Operation op, Strel strel)
{
	// Check validity of parameters
	if (image == null)
		return null;
	
	// extract the input processor
	ImageProcessor inputProcessor = image.getProcessor();
	
	// apply morphological operation
	ImageProcessor resultProcessor = op.apply(inputProcessor, strel);
	
	// Keep same color model
	resultProcessor.setColorModel(inputProcessor.getColorModel());
	
	// create the new image plus from the processor
	ImagePlus resultImage = new ImagePlus(op.toString(), resultProcessor);
	resultImage.copyScale(image);
				
	// return the created array
	return resultImage;
}
 

@Override
public ImageProcessor process(ImageProcessor ip) {
	if (ip instanceof ColorProcessor) {
		Utils.log("Ignoring " + getClass().getSimpleName() + " filter for RGB image");
		return ip;
	}
	byte[] s1 = new byte[256];
	byte[] s2 = new byte[256];
	byte[] s3 = new byte[256];
	for (int i=0; i<256; ++i) {
		s1[i] = (byte)(int)(i * r);
		s2[i] = (byte)(int)(i * g);
		s3[i] = (byte)(int)(i * b);
		Utils.log2(i + ": r, g, b " + s1[i] + ", " + s2[i] + ", " + s3[i]);
	}
	ip.setColorModel(new IndexColorModel(8, 256, s1, s2, s3));
	return ip;
}
 

private void setColorModel(ColorModel cm)
{
	ImageProcessor baseImage = imagePlus.getProcessor();
	baseImage.setColorModel(cm);
	if (imagePlus.getStackSize() > 1)
	{
		ImageStack stack = imagePlus.getStack();
		stack.setColorModel(cm);
	}
}
 

/** Returns a PatchImage object containing the bottom-of-transformation-stack image and alpha mask, if any (except the AffineTransform, which is used for direct hw-accel screen rendering). */
public Patch.PatchImage createTransformedImage() {
	final Patch.PatchImage pi = createCoordinateTransformedImage();
	if (null != pi) return pi;
	// else, a new one with the untransformed, original image (a duplicate):
	final ImageProcessor ip = getImageProcessor();
	if (null == ip) return null;
	project.getLoader().releaseToFit(o_width, o_height, type, 3);
	final ImageProcessor copy = ip.duplicate();
	copy.setColorModel(ip.getColorModel()); // one would expect "duplicate" to do this but it doesn't!
	return new PatchImage(copy, getAlphaMask(), null, new Rectangle(0, 0, o_width, o_height), false);
}
 

@Override
public ImageProcessor process(ImageProcessor ip) {
	if (ip instanceof ColorProcessor) {
		Utils.log("Ignoring " + getClass().getSimpleName() + " filter for RGB image");
		return ip;
	}
	byte[] s = new byte[256];
	for (int i=0; i<256; ++i) s[i] = (byte)i;
	ip.setColorModel(new IndexColorModel(8, 256, s, new byte[256], s));
	return ip;
}
 

@Override
public ImageProcessor process(ImageProcessor ip) {
	if (ip instanceof ColorProcessor) {
		Utils.log("Ignoring " + getClass().getSimpleName() + " filter for RGB image");
		return ip;
	}
	byte[] s = new byte[256];
	for (int i=0; i<256; ++i) s[i] = (byte)i;
	ip.setColorModel(new IndexColorModel(8, 256, s, s, new byte[256]));
	return ip;
}
 

@Override
public ImageProcessor process(ImageProcessor ip) {
	if (ip instanceof ColorProcessor) {
		Utils.log("Ignoring " + getClass().getSimpleName() + " filter for RGB image");
		return ip;
	}
	byte[] s = new byte[256];
	for (int i=0; i<256; ++i) s[i] = (byte)i;
	ip.setColorModel(new IndexColorModel(8, 256, new byte[256], s, new byte[256]));
	return ip;
}
 

@Override
public ImageProcessor process(ImageProcessor ip) {
	if (ip instanceof ColorProcessor) {
		Utils.log("Ignoring " + getClass().getSimpleName() + " filter for RGB image");
		return ip;
	}
	byte[] s = new byte[256];
	for (int i=0; i<256; ++i) s[i] = (byte)i;
	ip.setColorModel(new IndexColorModel(8, 256, s, new byte[256], new byte[256]));
	return ip;
}
 

@Override
public ImageProcessor process(ImageProcessor ip) {
	if (ip instanceof ColorProcessor) {
		Utils.log("Ignoring " + getClass().getSimpleName() + " filter for RGB image");
		return ip;
	}
	byte[] s = new byte[256];
	for (int i=0; i<256; ++i) s[i] = (byte)i;
	ip.setColorModel(new IndexColorModel(8, 256, new byte[256], new byte[256], s));
	return ip;
}
 

@Override
public ImageProcessor process(ImageProcessor ip) {
	if (ip instanceof ColorProcessor) {
		Utils.log("Ignoring " + getClass().getSimpleName() + " filter for RGB image");
		return ip;
	}
	byte[] s = new byte[256];
	for (int i=0; i<256; ++i) s[i] = (byte)i;
	ip.setColorModel(new IndexColorModel(8, 256, new byte[256], s, s));
	return ip;
}
 

public void applyThreshold(ImagePlus imp) {
	imp.deleteRoi();
	ImageProcessor ip = imp.getProcessor();
	ip.resetBinaryThreshold();
	int type = imp.getType();
	if (type==ImagePlus.GRAY16 || type==ImagePlus.GRAY32) {
		applyShortOrFloatThreshold(imp);
		return;
	}
	if (!imp.lock()) return;
	double saveMinThreshold = ip.getMinThreshold();
	double saveMaxThreshold = ip.getMaxThreshold();
	autoThreshold = saveMinThreshold==ImageProcessor.NO_THRESHOLD;

	boolean useBlackAndWhite = true;
	boolean noArgMacro =IJ.macroRunning() && Macro.getOptions()==null;
	if (skipDialog)
		fill1 = fill2 = useBlackAndWhite = true;
	else if (!(autoThreshold||noArgMacro)) {
		GenericDialog gd = new GenericDialog("Make Binary");
		gd.addCheckbox("Thresholded pixels to foreground color", fill1);
		gd.addCheckbox("Remaining pixels to background color", fill2);
		gd.addMessage("");
		gd.addCheckbox("Black foreground, white background", useBW);
		gd.showDialog();
		if (gd.wasCanceled())
		{imp.unlock(); return;}
		fill1 = gd.getNextBoolean();
		fill2 = gd.getNextBoolean();
		useBW = useBlackAndWhite = gd.getNextBoolean();
	} else {
		fill1 = fill2 = true;
		convertToMask = true;
	}

	if (type!=ImagePlus.GRAY8)
		convertToByte(imp);
	ip = imp.getProcessor();

	if (autoThreshold)
		autoThreshold(ip);
	else {
		if (Recorder.record && !Recorder.scriptMode() && (!IJ.isMacro()||Recorder.recordInMacros))
			Recorder.record("setThreshold", (int)saveMinThreshold, (int)saveMaxThreshold);
		minThreshold = saveMinThreshold;
		maxThreshold = saveMaxThreshold;
	}

	if (convertToMask && ip.isColorLut())
		ip.setColorModel(ip.getDefaultColorModel());
	int fcolor, bcolor;
	ip.resetThreshold();
	int savePixel = ip.getPixel(0,0);
	if (useBlackAndWhite)
		ip.setColor(Color.black);
	else
		ip.setColor(Toolbar.getForegroundColor());
	ip.drawPixel(0,0);
	fcolor = ip.getPixel(0,0);
	if (useBlackAndWhite)
		ip.setColor(Color.white);
	else
		ip.setColor(Toolbar.getBackgroundColor());
	ip.drawPixel(0,0);
	bcolor = ip.getPixel(0,0);
	ip.setColor(Toolbar.getForegroundColor());
	ip.putPixel(0,0,savePixel);

	int[] lut = new int[256];
	for (int i=0; i<256; i++) {
		if (i>=minThreshold && i<=maxThreshold)
			lut[i] = fill1?fcolor:(byte)i;
		else {
			lut[i] = fill2?bcolor:(byte)i;
		}
	}
	if (imp.getStackSize()>1)
		new StackProcessor(imp.getStack(), ip).applyTable(lut);
	else
		ip.applyTable(lut);
	if (convertToMask) {
		if (!imp.isInvertedLut()) {
			setInvertedLut(imp);
			fcolor = 255 - fcolor;
			bcolor = 255 - bcolor;
		}
		if (Prefs.blackBackground)
			ip.invertLut();
	}
	if (fill1 && fill2 && ((fcolor==0&&bcolor==255)||(fcolor==255&&bcolor==0)))
		imp.getProcessor().setThreshold(fcolor, fcolor, ImageProcessor.NO_LUT_UPDATE);
	imp.updateAndRepaintWindow();
	imp.unlock();
}
 

public ImagePlus makeShollCrossingsImagePlus(final ImagePlus original) {
	final int width = original.getWidth();
	final int height = original.getHeight();
	final int depth = original.getStackSize();
	final Calibration c = original.getCalibration();
	double x_spacing = 1;
	double y_spacing = 1;
	double z_spacing = 1;
	if (c != null) {
		x_spacing = c.pixelWidth;
		y_spacing = c.pixelHeight;
		z_spacing = c.pixelDepth;
	}
	final ImageStack stack = new ImageStack(width, height);
	for (int z = 0; z < depth; ++z) {
		final short[] pixels = new short[width * height];
		for (int y = 0; y < height; ++y) {
			for (int x = 0; x < width; ++x) {
				final double xdiff = x_spacing * x - x_start;
				final double ydiff = y_spacing * y - y_start;
				final double zdiff = z_spacing * z - z_start;
				final double distanceSquared = xdiff * xdiff + ydiff * ydiff + zdiff * zdiff;
				pixels[y * width + x] = (short) crossingsAtDistanceSquared(distanceSquared);
			}
		}
		final ShortProcessor sp = new ShortProcessor(width, height);
		sp.setPixels(pixels);
		stack.addSlice("", sp);
	}
	final ImagePlus result = new ImagePlus(description, stack);
	result.show();
	final IndexColorModel icm = FindConnectedRegions.backgroundAndSpectrum(255);
	stack.setColorModel(icm);
	final ImageProcessor ip = result.getProcessor();
	if (ip != null) {
		ip.setColorModel(icm);
		ip.setMinAndMax(0, maxCrossings);
	}
	result.updateAndDraw();

	if (c != null)
		result.setCalibration(c);
	return result;
}
 

@Override
public void run(String arg) {
	// Open a dialog to choose:
	// - mask image
	// - marker image
	int[] indices = WindowManager.getIDList();
	if (indices == null) {
		IJ.error("No image", "Need at least one image to work");
		return;
	}

	// create the list of image names
	String[] imageNames = new String[indices.length];
	for (int i = 0; i < indices.length; i++) {
		imageNames[i] = WindowManager.getImage(indices[i]).getTitle();
	}
	
	// create the dialog
	GenericDialog gd = new GenericDialog("Impose Min & Max");
	
	gd.addChoice("Original Image", imageNames, IJ.getImage().getTitle());
	gd.addChoice("Marker Image", imageNames, IJ.getImage().getTitle());
	gd.addChoice("Operation", 
			Operation.getAllLabels(), 
			Operation.IMPOSE_MINIMA.label);
	gd.addChoice("Connectivity", connectivityLabels, connectivityLabels[0]);
	gd.showDialog();
	
	if (gd.wasCanceled())
		return;

	// set up current parameters
	int refImageIndex = gd.getNextChoiceIndex();
	ImagePlus refImage = WindowManager.getImage(refImageIndex + 1);
	int markerImageIndex = gd.getNextChoiceIndex();
	ImagePlus markerImage = WindowManager.getImage(markerImageIndex + 1);
	Operation op = Operation.fromLabel(gd.getNextChoice());
	int conn = connectivityValues[gd.getNextChoiceIndex()];
	
	// Extract image procesors
	ImageProcessor refProc = refImage.getProcessor();
	ImageProcessor markerProc = markerImage.getProcessor();
	
	long t0 = System.currentTimeMillis();
	
	// Compute geodesic reconstruction
	ImageProcessor recProc = op.applyTo(refProc, markerProc, conn);
	
	// Keep same color model as 
	recProc.setColorModel(refProc.getColorModel());

	// create resulting image
	String newName = createResultImageName(refImage);
	ImagePlus resultImage = new ImagePlus(newName, recProc);
	resultImage.copyScale(markerImage);
	resultImage.show();
	
	long t1 = System.currentTimeMillis();
	IJ.showStatus("Elapsed time: " + (t1 - t0) / 1000. + "s");
	IJUtils.showElapsedTime(op.toString(), t1 - t0, refImage);
}
 

@Override
public void run(String arg) 
{
	// Open a dialog to choose:
	// - mask image
	// - marker image
	int[] indices = WindowManager.getIDList();
	if (indices == null) 
	{
		IJ.error("No image", "Need at least one image to work");
		return;
	}

	// create the list of image names
	String[] imageNames = new String[indices.length];
	for (int i = 0; i < indices.length; i++) 
	{
		imageNames[i] = WindowManager.getImage(indices[i]).getTitle();
	}
	
	// create the dialog
	GenericDialog gd = new GenericDialog("Morphological Reconstruction");
	
	gd.addChoice("Marker Image", imageNames, IJ.getImage().getTitle());
	gd.addChoice("Mask Image", imageNames, IJ.getImage().getTitle());
	gd.addChoice("Type of Reconstruction", 
			Operation.getAllLabels(),
			Operation.BY_DILATION.label);
	gd.addChoice("Connectivity", 
			Conn2D.getAllLabels(), 
			Conn2D.C4.label);
	gd.showDialog();
	
	if (gd.wasCanceled())
		return;

	// set up current parameters
	int markerImageIndex = gd.getNextChoiceIndex();
	ImagePlus markerImage = WindowManager.getImage(markerImageIndex + 1);
	int maskImageIndex = gd.getNextChoiceIndex();
	ImagePlus maskImage = WindowManager.getImage(maskImageIndex + 1);
	Operation op = Operation.fromLabel(gd.getNextChoice());
	int conn = Conn2D.fromLabel(gd.getNextChoice()).getValue();
	
	// Extract image procesors
	ImageProcessor markerProc = markerImage.getProcessor();
	ImageProcessor maskProc = maskImage.getProcessor();
	
	long t0 = System.currentTimeMillis();
	
	// Compute geodesic reconstruction
	ImageProcessor recProc = op.applyTo(markerProc, maskProc, conn);
	
	// Keep same color model
	recProc.setColorModel(maskProc.getColorModel());

	// create resulting image
	String newName = createResultImageName(markerImage);
	ImagePlus resultImage = new ImagePlus(newName, recProc);
	resultImage.copyScale(maskImage);
	resultImage.show();
	
	long t1 = System.currentTimeMillis();
	IJUtils.showElapsedTime(op.toString(), t1 - t0, markerImage);
}