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

/**
 * Apply the current filter settings to process the given image.
 */
public void run(ImageProcessor image)
{
	synchronized (this){
		if (floatProcessing)
			result = processFloat(image, weights.getFloatWeights(), normalize );
		else
			result = processShort(image, weights.getShortWeights(), normalize);
	}
	if (previewing)
	{
		// Fill up the values of original image with values of the result
		double valMax = result.getMax();
		for (int i = 0; i < image.getPixelCount(); i++)
		{
			image.set(i, (int) (255 * result.getf(i) / valMax));
		}
		image.resetMinAndMax();
		if (image.isInvertedLut())
			image.invertLut();
	}
}
 

/**
   * Apply the current filter settings to process the given image. 
   */
  public void run(ImageProcessor image) 
  {
  	if (floatProcessing)
  	{
  		result = processFloat(image, weights.getFloatWeights(), normalize);
} else 
{
	result = processShort(image, weights.getShortWeights(), normalize);
}
  	
  	if (previewing)
  	{
  		// Fill up the values of original image with values of the result
  		double valMax = result.getMax();
  		for (int i = 0; i < image.getPixelCount(); i++)
  		{
  			image.set(i, (int) (255 * result.getf(i) / valMax));
  		}
  		image.resetMinAndMax();
  		if (image.isInvertedLut())
  			image.invertLut();
      }
  }
 

/**
 * Displays the current structuring element in a new ImagePlus. 
 * @param strel the structuring element to display
 */
private void showStrelImage(Strel3D strel) {
	// Size of the strel image (little bit larger than strel)
	int[] dim = strel.getSize();
	int width = dim[0] + 20; 
	int height = dim[1] + 20;
	
	// Creates strel image by dilating a point
	ImageProcessor maskProcessor = new ByteProcessor(width, height);
	maskProcessor.set(width / 2, height / 2, 255);
	ImageStack stack = new ImageStack();
	stack.addSlice(maskProcessor);
	stack = Morphology.dilation(stack, strel);
	maskProcessor = stack.getProcessor(1);
	
	// Forces the display to inverted LUT (display a black over white)
	if (!maskProcessor.isInvertedLut())
		maskProcessor.invertLut();
	
	// Display strel image
	ImagePlus maskImage = new ImagePlus("Element", maskProcessor);
	maskImage.show();
}
 

void setInvertedLut(ImagePlus imp) {
	ImageProcessor ip = imp.getProcessor();
	ip.invertLut();
	int nImages = imp.getStackSize();
	if (nImages==1)
		ip.invert();
	else {
		ImageStack stack = imp.getStack();
		for (int slice=1; slice<=nImages; slice++)
			stack.getProcessor(slice).invert();
		stack.setColorModel(ip.getColorModel());
	}
}
 

/**
 * Displays the current structuring element in a new ImagePlus. 
 * @param strel the structuring element to display
 */
private void showStrelImage(Strel strel)
{
	// Size of the strel image (little bit larger than strel)
	int[] dim = strel.getSize();
	int width = dim[0] + 20; 
	int height = dim[1] + 20;
	
	// Creates strel image by dilating a point
	ImageProcessor strelImage = new ByteProcessor(width, height);
	strelImage.set(width / 2, height / 2, 255);
	strelImage = Morphology.dilation(strelImage, strel);
	
	// Forces the display to inverted LUT (display a black over white)
	if (!strelImage.isInvertedLut())
		strelImage.invertLut();
	
	// Display strel image
	if (strelDisplay == null)
	{
		strelDisplay = new ImagePlus("Structuring Element", strelImage);
	} 
	else 
	{
		strelDisplay.setProcessor(strelImage);
	}
	strelDisplay.show();
}
 

/**
 * Apply the current filter settings to process the given image.
 */
public void run( ImageProcessor image )
{
	if( null == image )
		return;
	long t0 = System.currentTimeMillis();

	// Compute geodesic reconstruction
	result = process( image, imagePlus.getRoi() );

	if ( null == result )
	{
		// force preview to be unchecked when processing fails
		gd.getPreviewCheckbox().setState( false );
		pfr.dialogItemChanged( gd,
				new ActionEvent( gd.getPreviewCheckbox(),
						ActionEvent.ACTION_PERFORMED, "Preview" ) );
		return;
	}
	if( previewing )
	{
		// Fill up the values of original image with values of the result
		image.setPixels( result.getPixels() );

		image.resetMinAndMax();

		if (image.isInvertedLut())
			image.invertLut();
	}

	long t1 = System.currentTimeMillis();
	IJUtils.showElapsedTime(operation.toString(), t1 - t0, imagePlus);
}
 

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();
}
 

/**
 * Make binary.
 */
public void makeBinary() {
	ImagePlus binary = IJ.createHyperStack(imp.getTitle() + " Detected segments", imp.getWidth(), imp.getHeight(),
			imp.getNChannels(), imp.getStackSize() / imp.getNChannels(), 1, 8);
	binary.copyScale(imp);

	ImageProcessor binaryProcessor = binary.getProcessor();
	binaryProcessor.invertLut();
	if (imp.getCompositeMode() > 0) {
		((CompositeImage) binary).setLuts(imp.getLuts());
	}

	ImageStack is = binary.getImageStack();
	ImageProcessor ip = binary.getProcessor();

	for (Lines contours : result) {
		for (Line c : contours) {

			float[] x = c.getXCoordinates();
			float[] y = c.getYCoordinates();

			int[] x_poly_r = new int[x.length];
			int[] y_poly_r = new int[x.length];

			Polygon LineSurface = new Polygon();

			ip = is.getProcessor(c.getFrame());

			ip.setLineWidth(1);
			ip.setColor(255);

			for (int j = 0; j < x.length; j++) {
				// this draws the identified line
				if (j > 0) {
					ip.drawLine((int) Math.round(x[j - 1]), (int) Math.round(y[j - 1]), (int) Math.round(x[j]),
							(int) Math.round(y[j]));
				}

				// If Estimate Width is ticked, we also draw the line surface in the binary
				if (doEstimateWidth) {

					double nx = Math.sin(c.angle[j]);
					double ny = Math.cos(c.angle[j]);

					// left point coordinates are directly added to the polygon. right coordinates
					// are saved to be added at the end of the coordinates list
					LineSurface.addPoint((int) Math.round(x[j] - c.width_l[j] * nx),
							(int) Math.round(y[j] - c.width_l[j] * ny));

					x_poly_r[j] = (int) Math.round(x[j] + c.width_r[j] * nx);
					y_poly_r[j] = (int) Math.round(y[j] + c.width_r[j] * ny);
				}
			}

			if (doEstimateWidth) {
				// loop to add the right coordinates to the end of the polygon, reversed
				for (int j = 0; j < x.length; j++) {
					if (j < x.length) {
						LineSurface.addPoint(x_poly_r[x.length - 1 - j], y_poly_r[x.length - 1 - j]);
					}
				}
				// draw surfaces.
				ip.fillPolygon(LineSurface);
			}
		}
	}
	binary.show();
	binary.updateAndDraw();
}
 

/**
 * Apply the current filter settings to process the given image.
 */
public void run( ImageProcessor image )
{
	if( null == image )
		return;
	long t0 = System.currentTimeMillis();

	// Execute core of the plugin
	if (resultAsFloat)
		result = process( image, imagePlus.getRoi(),
				weights.getFloatWeights(), normalize );
	else
		result = process( image, imagePlus.getRoi(),
				weights.getShortWeights(), normalize );

	if ( null == result )
	{
		// force preview to be unchecked when processing fails
		gd.getPreviewCheckbox().setState( false );
		pfr.dialogItemChanged( gd,
				new ActionEvent( gd.getPreviewCheckbox(),
						ActionEvent.ACTION_PERFORMED, "Preview" ) );
		return;
	}

	if( previewing )
	{
		// Fill up the values of original image with values of the result
		double valMax = result.getMax();
		// values need to be adjusted to the input image type
		for (int i = 0; i < image.getPixelCount(); i++)
		{
			image.set(i, (int) (255 * result.getf(i) / valMax));
		}
		// Copy LUT
		image.setLut( result.getLut() );
		image.resetMinAndMax();
		if (image.isInvertedLut())
			image.invertLut();
	}

	long t1 = System.currentTimeMillis();
	IJUtils.showElapsedTime( "Interactive Geodesic Distance Map",
			t1 - t0, imagePlus );
}