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add EuclideanDistanceMapPlugin (for both 2D and 3D images)
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‎src/main/java/inra/ijpb/plugins/EuclideanDistanceMapPlugin.java‎

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/*-
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* #%L
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* Mathematical morphology library and plugins for ImageJ/Fiji.
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* %%
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* Copyright (C) 2014 - 2024 INRA.
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* %%
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* This program is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Lesser General Public License as
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* published by the Free Software Foundation, either version 3 of the
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* License, or (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Lesser Public License for more details.
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*
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* You should have received a copy of the GNU General Lesser Public
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* License along with this program. If not, see
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* <http://www.gnu.org/licenses/lgpl-3.0.html>.
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* #L%
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*/
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package inra.ijpb.plugins;
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import java.awt.AWTEvent;
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import ij.ImagePlus;
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import ij.ImageStack;
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import ij.gui.DialogListener;
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import ij.gui.GenericDialog;
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import ij.measure.Calibration;
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import ij.plugin.filter.ExtendedPlugInFilter;
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import ij.plugin.filter.PlugInFilterRunner;
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import ij.process.ImageProcessor;
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import inra.ijpb.algo.DefaultAlgoListener;
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import inra.ijpb.data.image.Images3D;
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import inra.ijpb.label.distmap.SaitoToriwakiDistanceTransform2DFloat;
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import inra.ijpb.label.distmap.SaitoToriwakiDistanceTransform3DFloat;
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import inra.ijpb.util.IJUtils;
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/**
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* Compute distance map, with possibility to choose the chamfer mask, the result
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* type (integer or floating point), and to normalize result or not.
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*
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* Can process either binary images, or label images (that can be coded with 8,
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* 16 or 32 bits).
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*
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* @see inra.ijpb.label.distmap.DistanceTransform2D
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* @see inra.ijpb.binary.distmap.ChamferMask2D
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* @see inra.ijpb.label.distmap.ChamferDistanceTransform2DShort
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* @see inra.ijpb.label.distmap.ChamferDistanceTransform2DFloat
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*
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* @author dlegland
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*/
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public class EuclideanDistanceMapPlugin
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implements ExtendedPlugInFilter, DialogListener
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{
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/** Apparently, it's better to store flags in plugin */
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private int flags = DOES_8G | DOES_16 | DOES_32 | KEEP_PREVIEW | FINAL_PROCESSING;
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PlugInFilterRunner pfr;
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int nPasses;
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boolean previewing = false;
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/** need to keep the instance of ImagePlus */
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private ImagePlus imagePlus;
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/** keep the original image, to restore it after the preview */
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private ImageProcessor baseImage;
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// private boolean floatProcessing = false;
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private boolean normalize = false;
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/** Keep instance of result image */
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private ImageProcessor result;
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/**
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* Called at the beginning of the process to know if the plugin can be run
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* with current image, and at the end to finalize.
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*/
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public int setup(String arg, ImagePlus imp)
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{
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// Special case of plugin called to finalize the process
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if (arg.equals("final"))
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{
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// replace the preview image by the original image
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imagePlus.setProcessor(baseImage);
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imagePlus.draw();
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// Create a new ImagePlus with the filter result
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ImagePlus resPlus = process(imagePlus, normalize);
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resPlus.show();
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if (imagePlus.getStackSize() > 1)
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{
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resPlus.setSlice(imagePlus.getCurrentSlice());
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}
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return DONE;
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}
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return flags;
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}
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public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr)
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{
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// Store user data
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this.imagePlus = imp;
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this.baseImage = imp.getProcessor().duplicate();
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this.pfr = pfr;
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// Create a new generic dialog with appropriate options
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GenericDialog gd = new GenericDialog("Euclidean Distance Transform");
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gd.addCheckbox("Normalize", true);
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gd.addPreviewCheckbox(pfr);
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gd.addDialogListener(this);
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previewing = true;
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gd.addHelp("https://imagej.net/MorphoLibJ");
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gd.showDialog();
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previewing = false;
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// test cancel
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if (gd.wasCanceled())
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return DONE;
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// set up current parameters
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normalize = gd.getNextBoolean();
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return flags;
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}
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/**
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* Called when a dialog widget has been modified: recomputes option values
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* from dialog content.
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*/
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public boolean dialogItemChanged(GenericDialog gd, AWTEvent evt)
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{
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// set up current parameters
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normalize = gd.getNextBoolean();
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return true;
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}
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public void setNPasses(int nPasses)
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{
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this.nPasses = nPasses;
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}
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/**
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* Uses the current settings of the algorithm to process the current (2D)
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* image.
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*
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* This method is used to compute the "preview" image.
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*/
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public void run(ImageProcessor image)
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{
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result = process(image, normalize);
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if (previewing)
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{
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// Fill up the values of original image with values of the result
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double valMax = result.getMax();
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for (int i = 0; i < image.getPixelCount(); i++)
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{
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image.set(i, (int) (255 * result.getf(i) / valMax));
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}
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image.resetMinAndMax();
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if (image.isInvertedLut())
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image.invertLut();
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}
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}
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/**
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* Computes the result of Euclidean distance map algorithm on the specified
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* image.
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*
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* @param imagePlus
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* the image to use as a binary mask
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* @param normalize
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* the option to compute Euclidean distance (true) or squared
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* Euclidean distance (false)
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* @return the Eucldiean distance map, in a 32-bits floating point 2D or 3D
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* image.
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*/
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private ImagePlus process(ImagePlus imagePlus, boolean normalize)
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{
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String newName = createResultImageName(imagePlus);
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long t0 = System.currentTimeMillis();
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ImagePlus resultPlus;
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if (imagePlus.getStackSize() == 1)
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{
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// compute array of pixel dimensions
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Calibration calib = imagePlus.getCalibration();
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double[] spacings = new double[] { calib.pixelWidth, calib.pixelHeight };
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// Initialize calculator
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SaitoToriwakiDistanceTransform2DFloat algo = new SaitoToriwakiDistanceTransform2DFloat(normalize);
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DefaultAlgoListener.monitor(algo);
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// Compute distance on specified images
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ImageProcessor res = algo.distanceMap(imagePlus.getProcessor(), spacings);
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res.resetMinAndMax();
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if (res.isInvertedLut())
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res.invertLut();
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// Create a new ImagePlus with the filter result
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resultPlus = new ImagePlus(newName, res);
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}
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else
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{
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// compute array of pixel dimensions
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Calibration calib = imagePlus.getCalibration();
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double[] spacings = new double[] { calib.pixelWidth, calib.pixelHeight, calib.pixelDepth };
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// Initialize calculator
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SaitoToriwakiDistanceTransform3DFloat algo = new SaitoToriwakiDistanceTransform3DFloat(normalize);
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DefaultAlgoListener.monitor(algo);
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// Compute distance on specified images
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ImageStack res = algo.distanceMap(imagePlus.getStack(), spacings);
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// Create a new ImagePlus with the filter result
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resultPlus = new ImagePlus(newName, res);
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// calibrate display range of distances
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double[] distExtent = Images3D.findMinAndMax(resultPlus);
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resultPlus.setDisplayRange(0, distExtent[1]);
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}
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// Display elapsed time
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long t1 = System.currentTimeMillis();
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IJUtils.showElapsedTime("Euclidean distance map", t1 - t0, imagePlus);
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resultPlus.copyScale(imagePlus);
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return resultPlus;
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}
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private ImageProcessor process(ImageProcessor image, boolean normalize)
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{
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// Initialize calculator
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SaitoToriwakiDistanceTransform2DFloat algo = new SaitoToriwakiDistanceTransform2DFloat(normalize);
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// compute array of pixel dimensions
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Calibration calib = imagePlus.getCalibration();
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double[] spacings = new double[] { calib.pixelWidth, calib.pixelHeight };
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// add monitoring
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DefaultAlgoListener.monitor(algo);
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// Compute distance on specified images
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return algo.distanceMap(image, spacings);
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}
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private static String createResultImageName(ImagePlus baseImage)
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{
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return baseImage.getShortTitle() + "-dist";
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}
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}

‎src/main/resources/plugins.config‎

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# List of entries for binary images sub-menu
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Plugins>MorphoLibJ>Binary Images, "Connected Components Labeling", inra.ijpb.plugins.LabelingPlugin
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Plugins>MorphoLibJ>Binary Images, "-"
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Plugins>MorphoLibJ>Binary Images, "Euclidean Distance Map", inra.ijpb.plugins.EuclideanDistanceMapPlugin
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Plugins>MorphoLibJ>Binary Images, "Chamfer Distance Map", inra.ijpb.plugins.ChamferDistanceMapPlugin
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Plugins>MorphoLibJ>Binary Images, "Chamfer Distance Map 3D", inra.ijpb.plugins.ChamferDistanceMap3DPlugin
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Plugins>MorphoLibJ>Binary Images, "Geodesic Distance Map", inra.ijpb.plugins.GeodesicDistanceMapPlugin

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