/** Returns the base image stack. */ public ImageStack getImageStack() { if (stack==null) return getStack(); else { stack.update(ip); return stack; } }
/** Returns the base image stack. */ public ImageStack getImageStack() { if (stack==null) return getStack(); else { stack.update(ip); return stack; } }
private static ImageStack sortStack(ImageStack stack, String[] strings) { ImageProcessor ip = stack.getProcessor(1); ImageStack stack2 = new ImageStack(ip.getWidth(), ip.getHeight(), ip.getColorModel()); for (int i=0; i<stack.getSize(); i++) { int slice = (int)Tools.parseDouble(strings[i].substring(strings[i].length()-MAX_DIGITS), 0.0); if (slice==0) return null; stack2.addSlice(sliceLabels[slice-1], stack.getPixels(slice)); } stack2.update(stack.getProcessor(1)); return stack2; }
private static ImageStack sortStack(ImageStack stack, String[] strings) { ImageProcessor ip = stack.getProcessor(1); ImageStack stack2 = new ImageStack(ip.getWidth(), ip.getHeight(), ip.getColorModel()); for (int i=0; i<stack.getSize(); i++) { int slice = (int)Tools.parseDouble(strings[i].substring(strings[i].length()-MAX_DIGITS), 0.0); if (slice==0) return null; stack2.addSlice(sliceLabels[slice-1], stack.getPixels(slice)); } stack2.update(stack.getProcessor(1)); return stack2; }
/** * Process the image. * * @see ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor) */ public void run(ImageProcessor ip) { this.width = this.imRef.getWidth(); this.height = this.imRef.getHeight(); this.depth = this.imRef.getStackSize(); this.inputImage = this.imRef.getStack(); // Prepare data prepareData(this.inputImage); // Compute Thinning computeThinImage(this.inputImage); // Convert image to binary 0-255 for(int i = 1; i <= this.inputImage.getSize(); i++) this.inputImage.getProcessor(i).multiply(255); this.inputImage.update(ip); } /* end run */
public ImagePlus imageplus() { final ImageStack imagestack = new ImageStack(dims.x,dims.y); for (int t=0; t<dims.t; ++t) for (int z=0; z<dims.z; ++z) for (int c=0; c<dims.c; ++c) imagestack.addSlice("",elements[c][t][z]); final FloatProcessor minmax = new FloatProcessor(2,1); final double[] evals = extrema(); minmax.putPixelValue(0,0,evals[0]); minmax.putPixelValue(1,0,evals[1]); minmax.resetMinAndMax(); imagestack.update(minmax); final Calibration cal = new Calibration(); cal.pixelWidth = aspects.x; cal.pixelHeight = aspects.y; cal.pixelDepth = aspects.z; cal.frameInterval = aspects.t; ImagePlus imageplus = new ImagePlus(name,imagestack); imageplus.setDimensions(dims.c,dims.z,dims.t); imageplus.setCalibration(cal); return imageplus; }
public ImagePlus imageplus() { final ImageStack imagestack = new ImageStack(dims.x,dims.y); for (int t=0; t<dims.t; ++t) for (int z=0; z<dims.z; ++z) for (int c=0; c<dims.c; ++c) imagestack.addSlice("",elements[c][t][z]); final FloatProcessor minmax = new FloatProcessor(2,1); final double[] evals = extrema(); minmax.putPixelValue(0,0,evals[0]); minmax.putPixelValue(1,0,evals[1]); minmax.resetMinAndMax(); imagestack.update(minmax); final Calibration cal = new Calibration(); cal.pixelWidth = aspects.x; cal.pixelHeight = aspects.y; cal.pixelDepth = aspects.z; cal.frameInterval = aspects.t; ImagePlus imageplus = new ImagePlus(name,imagestack); imageplus.setDimensions(dims.c,dims.z,dims.t); imageplus.setCalibration(cal); return imageplus; }
ImageProcessor ip = stack.getProcessor(1); ip.resetMinAndMax(); stack.update(ip);
ImageProcessor ip = stack.getProcessor(1); ip.resetMinAndMax(); stack.update(ip);
else prefix = "Drawing of "; outlines.update(drawIP); outputImage = new ImagePlus(prefix+title, outlines); outputImage.setCalibration(imp.getCalibration());
else prefix = "Drawing of "; outlines.update(drawIP); outputImage = new ImagePlus(prefix+title, outlines); outputImage.setCalibration(imp.getCalibration());