-
Notifications
You must be signed in to change notification settings - Fork 49
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
add plugin "Label Morphological Filter"
- Loading branch information
Showing
2 changed files
with
262 additions
and
1 deletion.
There are no files selected for viewing
260 changes: 260 additions & 0 deletions
260
src/main/java/inra/ijpb/plugins/LabelMapMorphologicalFilteringPlugin.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,260 @@ | ||
| /*- | ||
| * #%L | ||
| * Mathematical morphology library and plugins for ImageJ/Fiji. | ||
| * %% | ||
| * Copyright (C) 2014 - 2017 INRA. | ||
| * %% | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Lesser General Public License as | ||
| * published by the Free Software Foundation, either version 3 of the | ||
| * License, or (at your option) any later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU General Lesser Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU General Lesser Public | ||
| * License along with this program. If not, see | ||
| * <http://www.gnu.org/licenses/lgpl-3.0.html>. | ||
| * #L% | ||
| */ | ||
| package inra.ijpb.plugins; | ||
|
|
||
| import ij.IJ; | ||
| import ij.ImagePlus; | ||
| import ij.ImageStack; | ||
| import ij.gui.GenericDialog; | ||
| import ij.plugin.PlugIn; | ||
| import ij.process.ImageProcessor; | ||
| import inra.ijpb.binary.distmap.ChamferMask2D; | ||
| import inra.ijpb.binary.distmap.ChamferMask3D; | ||
| import inra.ijpb.label.filter.ChamferLabelDilation2DShort; | ||
| import inra.ijpb.label.filter.ChamferLabelDilation3DShort; | ||
| import inra.ijpb.label.filter.ChamferLabelErosion2DShort; | ||
| import inra.ijpb.label.filter.ChamferLabelErosion3DShort; | ||
| import inra.ijpb.util.IJUtils; | ||
|
|
||
| /** | ||
| * Dilate all labels within a label image. | ||
| */ | ||
| public class LabelMapMorphologicalFilteringPlugin implements PlugIn | ||
| { | ||
| public enum Operation | ||
| { | ||
| /** Morphological erosion (local minima)*/ | ||
| EROSION("Erosion"), | ||
| /** Morphological dilation (local maxima)*/ | ||
| DILATION("Dilation"), | ||
| /** Morphological opening (erosion followed by dilation)*/ | ||
| OPENING("Opening"), | ||
| /** Morphological closing (dilation followed by erosion)*/ | ||
| CLOSING("Closing"); | ||
|
|
||
| private final String label; | ||
|
|
||
| private Operation(String label) | ||
| { | ||
| this.label = label; | ||
| } | ||
|
|
||
| /** | ||
| * Applies the current operator to the input image. | ||
| * | ||
| * @param image | ||
| * the image to process | ||
| * @param mask | ||
| * the chamfer mask used for propagating distances | ||
| * @param radius | ||
| * the radius used to threshold the distance map | ||
| * @return the result of morphological operation applied to image | ||
| */ | ||
| public ImageProcessor process(ImageProcessor image, ChamferMask2D mask, double radius) | ||
| { | ||
| if (this == DILATION) | ||
| { | ||
| ChamferLabelDilation2DShort dilation = new ChamferLabelDilation2DShort(mask, radius); | ||
| return dilation.process(image); | ||
| } | ||
| if (this == EROSION) | ||
| { | ||
| ChamferLabelErosion2DShort erosion = new ChamferLabelErosion2DShort(mask, radius); | ||
| return erosion.process(image); | ||
| } | ||
| if (this == CLOSING) | ||
| { | ||
| ChamferLabelDilation2DShort dilation = new ChamferLabelDilation2DShort(mask, radius); | ||
| ChamferLabelErosion2DShort erosion = new ChamferLabelErosion2DShort(mask, radius); | ||
| return erosion.process(dilation.process(image)); | ||
| } | ||
| if (this == OPENING) | ||
| { | ||
| ChamferLabelErosion2DShort erosion = new ChamferLabelErosion2DShort(mask, radius); | ||
| ChamferLabelDilation2DShort dilation = new ChamferLabelDilation2DShort(mask, radius); | ||
| return dilation.process(erosion.process(image)); | ||
| } | ||
|
|
||
| throw new RuntimeException( | ||
| "Unable to process the " + this + " morphological operation"); | ||
| } | ||
|
|
||
| /** | ||
| * Applies the current operator to the input 3D image. | ||
| * | ||
| * @param image | ||
| * the image to process | ||
| * @param mask | ||
| * the chamfer mask used for propagating distances | ||
| * @param radius | ||
| * the radius used to threshold the distance map | ||
| * @return the result of morphological operation applied to image | ||
| */ | ||
| public ImageStack process(ImageStack image, ChamferMask3D mask, double radius) | ||
| { | ||
| if (this == DILATION) | ||
| { | ||
| ChamferLabelDilation3DShort dilation = new ChamferLabelDilation3DShort(mask, radius); | ||
| return dilation.process(image); | ||
| } | ||
| if (this == EROSION) | ||
| { | ||
| ChamferLabelErosion3DShort erosion = new ChamferLabelErosion3DShort(mask, radius); | ||
| return erosion.process(image); | ||
| } | ||
| if (this == CLOSING) | ||
| { | ||
| ChamferLabelDilation3DShort dilation = new ChamferLabelDilation3DShort(mask, radius); | ||
| ChamferLabelErosion3DShort erosion = new ChamferLabelErosion3DShort(mask, radius); | ||
| return erosion.process(dilation.process(image)); | ||
| } | ||
| if (this == OPENING) | ||
| { | ||
| ChamferLabelDilation3DShort dilation = new ChamferLabelDilation3DShort(mask, radius); | ||
| ChamferLabelErosion3DShort erosion = new ChamferLabelErosion3DShort(mask, radius); | ||
| return dilation.process(erosion.process(image)); | ||
| } | ||
|
|
||
| throw new RuntimeException( | ||
| "Unable to process the " + this + " morphological operation"); | ||
| } | ||
|
|
||
| public String toString() | ||
| { | ||
| return this.label; | ||
| } | ||
|
|
||
| /** | ||
| * Returns the list of labels for this enumeration. | ||
| * | ||
| * @return the list of labels for this enumeration. | ||
| */ | ||
| public static String[] getAllLabels() | ||
| { | ||
| int n = Operation.values().length; | ||
| String[] result = new String[n]; | ||
|
|
||
| int i = 0; | ||
| for (Operation op : Operation.values()) | ||
| result[i++] = op.label; | ||
|
|
||
| return result; | ||
| } | ||
|
|
||
| /** | ||
| * Determines the operation type from its label. | ||
| * | ||
| * @param opLabel | ||
| * the label of the operation | ||
| * @return the parsed Operation | ||
| * @throws IllegalArgumentException | ||
| * if label is not recognized. | ||
| */ | ||
| public static Operation fromLabel(String opLabel) | ||
| { | ||
| if (opLabel != null) | ||
| opLabel = opLabel.toLowerCase(); | ||
| for (Operation op : Operation.values()) | ||
| { | ||
| String cmp = op.label.toLowerCase(); | ||
| if (cmp.equals(opLabel)) | ||
| return op; | ||
| } | ||
| throw new IllegalArgumentException("Unable to parse Operation with label: " + opLabel); | ||
| } | ||
| }; | ||
|
|
||
| Operation op = Operation.DILATION; | ||
| double radius = 2.0; | ||
|
|
||
| @Override | ||
| public void run(String arg0) | ||
| { | ||
| ImagePlus imagePlus = IJ.getImage(); | ||
|
|
||
| // open a dialog to choose options | ||
| GenericDialog gd = new GenericDialog("Dilate Labels"); | ||
| gd.addChoice("Operation", Operation.getAllLabels(), this.op.toString()); | ||
| gd.addNumericField("Radius", this.radius, 1); | ||
|
|
||
| // If cancel was clicked, do nothing | ||
| gd.showDialog(); | ||
| if (gd.wasCanceled()) | ||
| return; | ||
|
|
||
| // parse user options | ||
| Operation op = Operation.fromLabel(gd.getNextChoice()); | ||
| double radius = gd.getNextNumber(); | ||
| this.op = op; | ||
| this.radius = radius; | ||
|
|
||
| String newName = imagePlus.getShortTitle() + "-" + op.toString(); | ||
| ImagePlus resultPlus; | ||
|
|
||
| // apply operator on current image | ||
| long t0 = System.currentTimeMillis(); | ||
| if (imagePlus.getStackSize() == 1) | ||
| { | ||
| // Process 2D image | ||
| ImageProcessor image = imagePlus.getProcessor(); | ||
|
|
||
| ChamferMask2D mask = ChamferMask2D.CHESSKNIGHT; | ||
| ImageProcessor result = op.process(image, mask, radius); | ||
|
|
||
| result.setMinAndMax(image.getMin(), image.getMax()); | ||
| result.setColorModel(image.getColorModel()); | ||
| resultPlus = new ImagePlus(newName, result); | ||
| } | ||
| else | ||
| { | ||
| // Process 3D image | ||
| ImageStack image = imagePlus.getStack(); | ||
| ChamferMask3D mask = ChamferMask3D.SVENSSON_3_4_5_7; | ||
|
|
||
| // ChamferLabelDilation3DShort algo = new ChamferLabelDilation3DShort(ChamferMask3D.SVENSSON_3_4_5_7, radius); | ||
| // DefaultAlgoListener.monitor(algo); | ||
| // ImageProcessor result = op.process(image, mask, radius); | ||
| ImageStack result = op.process(image, mask, radius); | ||
|
|
||
| result.setColorModel(image.getColorModel()); | ||
| resultPlus = new ImagePlus(newName, result); | ||
|
|
||
| // update display range | ||
| double min = imagePlus.getDisplayRangeMin(); | ||
| double max = imagePlus.getDisplayRangeMax(); | ||
| resultPlus.setDisplayRange(min, max); | ||
| } | ||
| long elapsedTime = System.currentTimeMillis() - t0; | ||
|
|
||
| // display result | ||
| resultPlus.show(); | ||
| resultPlus.copyScale(imagePlus); | ||
|
|
||
| if (imagePlus.getStackSize() > 1) | ||
| { | ||
| resultPlus.setSlice(imagePlus.getCurrentSlice()); | ||
| } | ||
|
|
||
| // display elapsed time | ||
| IJUtils.showElapsedTime("Dilate Labels", elapsedTime, imagePlus); | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters