/** Produce a binary image based on the current confidence matrix */ private void createBinaryMask() { if (null != confMatrix) { final ByteProcessor result = (ByteProcessor) confMatrix.convertToByte(false); result.multiply(255); // Set background color based on the Process > Binary > Options if (!Prefs.blackBackground) result.invert(); new ImagePlus("Mask", result).show(); } }
/** Called by the PlugInFilterRunner to process the image or one frame of a stack */ public void run(ImageProcessor ip) { if (interrupted) return; int width = ip.getWidth(); int height = ip.getHeight(); int backgroundValue = (processType == VORONOI) ? (background255 ? 0 : (byte) 255) : // Voronoi needs EDM of the background (background255 ? (byte) 255 : 0); // all others do EDM of the foreground if (USES_WATERSHED[processType]) nPasses = 0; // watershed has its own progress bar FloatProcessor floatEdm = makeFloatEDM(ip, backgroundValue, false); ByteProcessor maxIp = null; if (USES_MAX_FINDER[processType]) { if (processType == VORONOI) floatEdm.multiply(-1); // Voronoi starts from minima of EDM int maxOutputType = USES_WATERSHED[processType] ? MaximumFinder.SEGMENTED : MaximumFinder.SINGLE_POINTS; boolean isEDM = processType != VORONOI; maxIp = maxFinder.findMaxima( floatEdm, MAXFINDER_TOLERANCE, ImageProcessor.NO_THRESHOLD, maxOutputType, false, isEDM); if (maxIp == null) { // segmentation cancelled by user? interrupted = true; return; } else if (processType != WATERSHED) { if (processType == VORONOI) floatEdm.multiply(-1); resetMasked(floatEdm, maxIp, processType == VORONOI ? -1 : 0); } } ImageProcessor outIp = null; if (processType == WATERSHED) { if (background255) maxIp.invert(); ip.copyBits(maxIp, 0, 0, Blitter.COPY); ip.setBinaryThreshold(); } else switch (outImageType) { // for all these, output contains the values of the EDM case FLOAT: outIp = floatEdm; break; case SHORT: floatEdm.setMinAndMax(0., 65535.); outIp = floatEdm.convertToShort(true); break; case BYTE: floatEdm.setMinAndMax(0., 255.); outIp = floatEdm.convertToByte(true); break; case BYTE_OVERWRITE: ip.setPixels(0, floatEdm); if (floatEdm.getMax() > 255.) ip.resetMinAndMax(); // otherwise we have max of floatEdm } if (outImageType != BYTE_OVERWRITE) { // new output image if (outStack == null) { outImp = new ImagePlus(TITLE_PREFIX[processType] + imp.getShortTitle(), outIp); } else outStack.setPixels(outIp.getPixels(), pfr.getSliceNumber()); } } // public void run