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add Binary morphological filters plugins (2D and 3D)
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‎src/main/java/inra/ijpb/plugins/BinaryMorphologicalFilter3DPlugin.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 - 2017 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 ij.IJ;
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import ij.ImagePlus;
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import ij.ImageStack;
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import ij.WindowManager;
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import ij.gui.GenericDialog;
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import ij.plugin.PlugIn;
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import inra.ijpb.algo.DefaultAlgoListener;
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import inra.ijpb.morphology.BinaryMorphology;
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import inra.ijpb.morphology.binary.DistanceMapBinaryClosing3D;
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import inra.ijpb.morphology.binary.DistanceMapBinaryDilation3D;
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import inra.ijpb.morphology.binary.DistanceMapBinaryErosion3D;
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import inra.ijpb.morphology.binary.DistanceMapBinaryOpening3D;
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import inra.ijpb.util.IJUtils;
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/**
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* Morphological filtering for 3D binary images, using ball-shaped structuring
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* element with user-specified radius.
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*
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* Morphological operations are computed using thresholding distance maps.
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*
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* @see net.ijt.BinaryMorphology
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*
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* @author David Legland
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*
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*/
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public class BinaryMorphologicalFilter3DPlugin implements PlugIn
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{
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enum Operation
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{
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EROSION("Erosion"),
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DILATION("Dilation"),
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OPENING("Opening"),
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CLOSING("Closing");
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String label;
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Operation(String label)
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{
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this.label = label;
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}
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public ImageStack process(ImageStack image, double radius)
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{
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switch(this)
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{
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case EROSION:
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{
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DistanceMapBinaryErosion3D algo = new DistanceMapBinaryErosion3D(radius);
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DefaultAlgoListener.monitor(algo);
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return algo.processBinary(image);
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}
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case DILATION:
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{
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DistanceMapBinaryDilation3D algo = new DistanceMapBinaryDilation3D(radius);
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DefaultAlgoListener.monitor(algo);
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return algo.processBinary(image);
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}
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case OPENING:
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{
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DistanceMapBinaryOpening3D algo = new DistanceMapBinaryOpening3D(radius);
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DefaultAlgoListener.monitor(algo);
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return algo.processBinary(image);
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}
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case CLOSING:
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{
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DistanceMapBinaryClosing3D algo = new DistanceMapBinaryClosing3D(radius);
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DefaultAlgoListener.monitor(algo);
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return algo.processBinary(image);
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}
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default:
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{
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throw new RuntimeException("Can not manange this Operation: " + label);
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}
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}
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}
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public String toString()
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{
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return this.label;
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}
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public static String[] getAllLabels()
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{
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int n = Operation.values().length;
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String[] result = new String[n];
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int i = 0;
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for (Operation op : Operation.values())
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result[i++] = op.label;
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return result;
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}
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/**
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* Determines the operation type from its label.
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*
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* @param opLabel
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* the label of the operation
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* @return the parsed Operation
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* @throws IllegalArgumentException
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* if label is not recognized.
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*/
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public static Operation fromLabel(String opLabel)
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{
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if (opLabel != null)
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opLabel = opLabel.toLowerCase();
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for (Operation op : Operation.values())
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{
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String cmp = op.label.toLowerCase();
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if (cmp.equals(opLabel))
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return op;
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}
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throw new IllegalArgumentException("Unable to parse Operation with label: " + opLabel);
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}
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}
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/* (non-Javadoc)
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* @see ij.plugin.PlugIn#run(java.lang.String)
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*/
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@Override
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public void run(String arg)
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{
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if ( IJ.getVersion().compareTo("1.48a") < 0 )
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{
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IJ.error( "Morphological Filter 3D", "ERROR: detected ImageJ version " + IJ.getVersion()
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+ ".\nThis plugin requires version 1.48a or superior, please update ImageJ!" );
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return;
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}
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ImagePlus imagePlus = WindowManager.getCurrentImage();
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if (imagePlus == null)
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{
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IJ.error("No image", "Need at least one image to work");
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return;
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}
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// create the dialog
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GenericDialog gd = new GenericDialog("Morphological Filters (3D)");
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gd.addChoice("Operation", Operation.getAllLabels(), Operation.DILATION.toString());
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gd.addNumericField("Radius (in voxels)", 2, 1);
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gd.addCheckbox("Show Element", false);
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// Could also add an option for the type of operation
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gd.showDialog();
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if (gd.wasCanceled())
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return;
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long t0 = System.currentTimeMillis();
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// extract chosen parameters
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Operation op = Operation.fromLabel(gd.getNextChoice());
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double radius = gd.getNextNumber();
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boolean showStrel = gd.getNextBoolean();
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// Eventually display the structuring element used for processing
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if (showStrel)
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{
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showStrelImage(radius);
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}
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// Execute core of the plugin
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ImagePlus resPlus = process(imagePlus, op, radius);
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if (resPlus == null)
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return;
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// Display the result image
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resPlus.show();
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resPlus.setSlice(imagePlus.getCurrentSlice());
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// Display elapsed time
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long t1 = System.currentTimeMillis();
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IJUtils.showElapsedTime(op.toString(), t1 - t0, imagePlus);
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}
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/**
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* Displays the current structuring element in a new ImagePlus.
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* @param strel the 3D structuring element to display
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*/
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private void showStrelImage(double radius)
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{
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// Size of the strel image (little bit larger than strel)
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int intRadius = (int) Math.ceil(radius);
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int sizeX = 2 * intRadius + 20;
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int sizeY = 2 * intRadius + 20;
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int sizeZ = 2 * intRadius + 20;
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// Creates strel image by dilating a point
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ImageStack stack = ImageStack.create(sizeX, sizeY, sizeZ, 8);
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stack.setVoxel(sizeX / 2, sizeY / 2, sizeZ / 2, 255);
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stack = BinaryMorphology.dilationBall(stack, radius);
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// Display strel image
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ImagePlus strelImage = new ImagePlus("Structuring Element", stack);
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strelImage.setSlice(((sizeZ - 1) / 2) + 1);
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strelImage.show();
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}
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public ImagePlus process(ImagePlus image, Operation op, double radius)
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{
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// Check validity of parameters
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if (image == null)
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return null;
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// extract the input stack
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ImageStack inputStack = image.getStack();
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// apply morphological operation
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ImageStack resultStack = op.process(inputStack, radius);
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// create the new image plus from the processor
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String newName = image.getShortTitle() + "-" + op.toString();
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ImagePlus resultPlus = new ImagePlus(newName, resultStack);
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resultPlus.copyScale(image);
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// return the created array
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return resultPlus;
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}
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}

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