diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..3d47f986c41db29ec6dc0d5036bf760b3a1cf366 --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +.idea/ +target/ +.settings/ +*.iml +.project +.classpath \ No newline at end of file diff --git a/pom.xml b/pom.xml new file mode 100644 index 0000000000000000000000000000000000000000..d4f3419bee216abb2d3c4f3a4d3f23827e0f0de3 --- /dev/null +++ b/pom.xml @@ -0,0 +1,95 @@ +<?xml version="1.0" encoding="UTF-8"?> +<project xmlns="http://maven.apache.org/POM/4.0.0" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> + <modelVersion>4.0.0</modelVersion> + + <!-- Inherited Icy Parent POM --> + <parent> + <groupId>org.bioimageanalysis.icy</groupId> + <artifactId>parent-pom-plugin</artifactId> + <version>1.0.3</version> + </parent> + + <!-- Project Information --> + <artifactId>kmeans-color-quantization</artifactId> + <version>1.2.1</version> + + <packaging>jar</packaging> + + <name>KMeans Color Quantization</name> + <description>Quantize a color image in any given number of colors.</description> + <url>http://icy.bioimageanalysis.org/plugin/kmeans-color-quantization/</url> + <inceptionYear>2020</inceptionYear> + + <organization> + <name>Institut Pasteur</name> + <url>https://pasteur.fr</url> + </organization> + + <licenses> + <license> + <name>GNU GPLv3</name> + <url>https://www.gnu.org/licenses/gpl-3.0.en.html</url> + <distribution>repo</distribution> + </license> + </licenses> + + <developers> + <developer> + <id>sdallongeville</id> + <name>Stéphane Dallongeville</name> + <url>https://research.pasteur.fr/fr/member/stephane-dallongeville/</url> + <roles> + <role>founder</role> + <role>lead</role> + <role>architect</role> + <role>developer</role> + <role>debugger</role> + <role>tester</role> + <role>maintainer</role> + <role>support</role> + </roles> + </developer> + </developers> + + <!-- Project properties --> + <properties> + + </properties> + + <!-- Project build configuration --> + <build> + + </build> + + <!-- List of project's dependencies --> + <dependencies> + <!-- The core of Icy --> + <dependency> + <groupId>org.bioimageanalysis.icy</groupId> + <artifactId>icy-kernel</artifactId> + </dependency> + + <dependency> + <groupId>org.bioimageanalysis.icy</groupId> + <artifactId>nherve-toolbox</artifactId> + <version>1.3.2</version> + </dependency> + + <dependency> + <groupId>org.bioimageanalysis.icy</groupId> + <artifactId>mask-editor</artifactId> + <version>1.2.1</version> + </dependency> + </dependencies> + + <!-- Icy Maven repository (to find parent POM) --> + <repositories> + <repository> + <id>icy</id> + <name>Icy's Nexus</name> + <url>https://icy-nexus.pasteur.fr/repository/Icy/</url> + </repository> + </repositories> +</project> \ No newline at end of file diff --git a/src/main/java/plugins/nherve/colorquantization/KMeansColorQuantization.java b/src/main/java/plugins/nherve/colorquantization/KMeansColorQuantization.java new file mode 100644 index 0000000000000000000000000000000000000000..286fac3fad353ee0fe8df52ca1d5c9cf75e1fecf --- /dev/null +++ b/src/main/java/plugins/nherve/colorquantization/KMeansColorQuantization.java @@ -0,0 +1,423 @@ +/* + * Copyright 2010, 2011 Institut Pasteur. + * + * This file is part of ${CurrentProject}, which is an ICY plugin. + * + * ${CurrentProject} is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * ${CurrentProject} 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 Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with ${CurrentProject}. If not, see <http://www.gnu.org/licenses/>. + */ +package plugins.nherve.colorquantization; + +import icy.gui.component.ComponentUtil; +import icy.gui.util.GuiUtil; +import icy.main.Icy; +import icy.preferences.XMLPreferences; +import icy.sequence.Sequence; +import icy.swimmingPool.SwimmingObject; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Component; +import java.awt.Dimension; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.lang.reflect.InvocationTargetException; +import java.text.DecimalFormat; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import javax.swing.Box; +import javax.swing.JButton; +import javax.swing.JCheckBox; +import javax.swing.JComboBox; +import javax.swing.JLabel; +import javax.swing.JPanel; +import javax.swing.JTextField; +import javax.swing.SwingUtilities; +import javax.swing.border.TitledBorder; + +import plugins.nherve.maskeditor.MaskEditor; +import plugins.nherve.toolbox.Algorithm; +import plugins.nherve.toolbox.NherveToolbox; +import plugins.nherve.toolbox.image.feature.DefaultClusteringAlgorithmImpl; +import plugins.nherve.toolbox.image.feature.SegmentableIcyBufferedImage; +import plugins.nherve.toolbox.image.feature.Signature; +import plugins.nherve.toolbox.image.feature.IcySupportRegion; +import plugins.nherve.toolbox.image.feature.clustering.KMeans; +import plugins.nherve.toolbox.image.feature.descriptor.ColorPixel; +import plugins.nherve.toolbox.image.feature.descriptor.DefaultDescriptorImpl; +import plugins.nherve.toolbox.image.feature.region.GridFactory; +import plugins.nherve.toolbox.image.feature.region.SupportRegionException; +import plugins.nherve.toolbox.image.feature.signature.SignatureException; +import plugins.nherve.toolbox.image.feature.signature.VectorSignature; +import plugins.nherve.toolbox.image.mask.Mask; +import plugins.nherve.toolbox.image.mask.MaskException; +import plugins.nherve.toolbox.image.segmentation.DefaultSegmentationAlgorithm; +import plugins.nherve.toolbox.image.segmentation.Segmentation; +import plugins.nherve.toolbox.image.segmentation.SegmentationException; +import plugins.nherve.toolbox.image.toolboxes.ColorSpaceTools; +import plugins.nherve.toolbox.plugin.HelpWindow; +import plugins.nherve.toolbox.plugin.SingletonPlugin; + +/** + * The Class KMeansColorQuantization. + * + * The pixel colors extraction is not optimized as it uses a more generic + * framework. If you need a quicker version, you'll have to change this part. + * However, the KMeans implementation is optimized and multithreaded. + * + * @author Nicolas HERVE - nicolas.herve@pasteur.fr + */ +public class KMeansColorQuantization extends SingletonPlugin implements ActionListener { + private static String HELP = "<html>" + "<p align=\"center\"><b>" + HelpWindow.getTagFullPluginName() + "</b></p>" + "<p align=\"center\"><b>" + NherveToolbox.getDevNameHtml() + "</b></p>" + "<p align=\"center\"><b>" + NherveToolbox.getCopyrightHtml() + "</b></p>" + "<hr/>" + "<p>" + HelpWindow.getTagPluginName() + NherveToolbox.getLicenceHtml() + "</p>" + "<p>" + NherveToolbox.getLicenceHtmllink() + "</p>" + "</html>"; + + private Map<Integer, Integer> indexToColorspace; + + /** The cb color space. */ + private JComboBox cbColorSpace; + + /** The bt start. */ + private JButton btStart; + + /** The tf nb cluster2. */ + private JTextField tfNbCluster2; + + /** The tf nb iteration2. */ + private JTextField tfNbIteration2; + + /** The tf stab crit2. */ + private JTextField tfStabCrit2; + + /** The cb display. */ + private JCheckBox cbDisplay; + + /** The cb send mask directly. */ + private JCheckBox cbSendMaskDirectly; + + private JButton btHelp; + + /** The currently running. */ + private Thread currentlyRunning; + + /* + * (non-Javadoc) + * + * @see plugins.nherve.toolbox.AbleToLogMessages#isDisplayEnabled() + */ + @Override + public boolean isLogEnabled() { + return cbDisplay.isSelected(); + } + + /* + * (non-Javadoc) + * + * @see plugins.nherve.toolbox.plugin.SingletonPlugin#sequenceHasChanged() + */ + @Override + public void sequenceHasChanged() { + btStart.setEnabled(hasCurrentSequence()); + } + + /* + * (non-Javadoc) + * + * @see plugins.nherve.toolbox.plugin.SingletonPlugin#sequenceWillChange() + */ + @Override + public void sequenceWillChange() { + } + + @Override + public void fillInterface(JPanel mainPanel) { + currentlyRunning = null; + + XMLPreferences preferences = getPreferences(); + int nbc2 = preferences.getInt("nbc2", 10); + int nbi2 = preferences.getInt("nbi2", 100); + double stab2 = preferences.getDouble("stab2", 0.001); + + boolean dsp = preferences.getBoolean("dsp", false); + + indexToColorspace = new HashMap<Integer, Integer>(); + cbColorSpace = new JComboBox(); + cbColorSpace.addItem(ColorSpaceTools.COLOR_SPACES[ColorSpaceTools.RGB]); + indexToColorspace.put(0, ColorSpaceTools.RGB); + cbColorSpace.addItem(ColorSpaceTools.COLOR_SPACES[ColorSpaceTools.RGB_TO_HSV]); + indexToColorspace.put(1, ColorSpaceTools.RGB_TO_HSV); + cbColorSpace.addItem(ColorSpaceTools.COLOR_SPACES[ColorSpaceTools.RGB_TO_H1H2H3]); + indexToColorspace.put(2, ColorSpaceTools.RGB_TO_H1H2H3); + ComponentUtil.setFixedSize(cbColorSpace, new Dimension(100, 25)); + + JPanel cs = GuiUtil.createLineBoxPanel(new JLabel("Color space"), Box.createHorizontalGlue(), cbColorSpace); + cs.setBorder(new TitledBorder("Color description")); + mainPanel.add(cs, BorderLayout.NORTH); + + tfNbCluster2 = new JTextField(Integer.toString(nbc2)); + ComponentUtil.setFixedSize(tfNbCluster2, new Dimension(100, 25)); + JPanel p1 = GuiUtil.createLineBoxPanel(new JLabel("Nb. clusters"), Box.createHorizontalGlue(), tfNbCluster2); + + tfNbIteration2 = new JTextField(Integer.toString(nbi2)); + ComponentUtil.setFixedSize(tfNbIteration2, new Dimension(100, 25)); + JPanel p2 = GuiUtil.createLineBoxPanel(new JLabel("Nb. max iterations"), Box.createHorizontalGlue(), tfNbIteration2); + + tfStabCrit2 = new JTextField(Double.toString(stab2)); + ComponentUtil.setFixedSize(tfStabCrit2, new Dimension(100, 25)); + JPanel p3 = GuiUtil.createLineBoxPanel(new JLabel("Stabilization criterion"), Box.createHorizontalGlue(), tfStabCrit2); + + JPanel algo = GuiUtil.createPageBoxPanel(p1, p2, p3); + algo.setBorder(new TitledBorder("KMeans clustering algorithm")); + mainPanel.add(algo, BorderLayout.CENTER); + + btHelp = new JButton(NherveToolbox.questionIcon); + btHelp.setToolTipText("Get some basic informations"); + btHelp.addActionListener(this); + cbDisplay = new JCheckBox("Log"); + cbDisplay.setSelected(dsp); + cbSendMaskDirectly = new JCheckBox("Send to editor"); + cbSendMaskDirectly.setSelected(true); + btStart = new JButton("Start"); + btStart.addActionListener(this); + btStart.setEnabled(hasCurrentSequence()); + + JPanel bottom = GuiUtil.createLineBoxPanel(new Component[] { btHelp, Box.createHorizontalGlue(), cbDisplay, cbSendMaskDirectly, Box.createHorizontalGlue(), btStart }); + mainPanel.add(bottom, BorderLayout.SOUTH); + } + + /* + * (non-Javadoc) + * + * @see plugins.nherve.toolbox.plugin.SingletonPlugin#stopInterface() + */ + @Override + public void stopInterface() { + try { + XMLPreferences preferences = getPreferences(); + + preferences.putInt("nbc2", Integer.parseInt(tfNbCluster2.getText())); + preferences.putInt("nbi2", Integer.parseInt(tfNbIteration2.getText())); + preferences.putDouble("stab2", Double.parseDouble(tfStabCrit2.getText())); + preferences.putInt("cs", cbColorSpace.getSelectedIndex()); + preferences.putBoolean("dsp", cbDisplay.isSelected()); + } catch (NumberFormatException e) { + e.printStackTrace(); + } + } + + /* + * (non-Javadoc) + * + * @see + * java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent) + */ + @Override + public void actionPerformed(ActionEvent e) { + JButton b = (JButton) e.getSource(); + if (b == null) { + return; + } + + if (b == btHelp) { + openHelpWindow(HELP, 400, 300); + return; + } + + if (b == btStart) { + if (hasCurrentSequence() && (currentlyRunning == null)) { + btStart.setEnabled(false); + currentlyRunning = new Thread() { + @Override + public void run() { + try { + final Sequence cs = getCurrentSequence(); + final Segmentation seg = doClustering(cs); + if (cbSendMaskDirectly.isSelected()) { + final MaskEditor me = MaskEditor.getRunningInstance(true); + currentlyRunning = null; + Runnable r = new Runnable() { + @Override + public void run() { + me.setSegmentationForSequence(cs, seg); + me.switchOpacityOn(); + btStart.setEnabled(true); + } + }; + SwingUtilities.invokeAndWait(r); + } else { + SwimmingObject result = new SwimmingObject(seg); + Icy.getMainInterface().getSwimmingPool().add(result); + currentlyRunning = null; + Runnable r = new Runnable() { + @Override + public void run() { + btStart.setEnabled(true); + } + }; + SwingUtilities.invokeAndWait(r); + } + } catch (SupportRegionException e1) { + logError(e1.getClass().getName() + " : " + e1.getMessage()); + } catch (SegmentationException e1) { + logError(e1.getClass().getName() + " : " + e1.getMessage()); + } catch (InterruptedException e1) { + logError(e1.getClass().getName() + " : " + e1.getMessage()); + } catch (InvocationTargetException e1) { + logError(e1.getClass().getName() + " : " + e1.getMessage()); + } catch (MaskException e1) { + logError(e1.getClass().getName() + " : " + e1.getMessage()); + } catch (NumberFormatException e) { + logError(e.getClass().getName() + " : " + e.getMessage()); + } catch (SignatureException e) { + logError(e.getClass().getName() + " : " + e.getMessage()); + } + } + }; + currentlyRunning.start(); + } + return; + } + + } + + /** + * Do single clustering. + * + * @param img + * the img + * @param regions + * the regions + * @param descriptor + * the descriptor + * @param algo + * the algo + * @return the segmentation + * @throws SupportRegionException + * the support region exception + * @throws SegmentationException + * the segmentation exception + */ + private Segmentation doSingleClustering(SegmentableIcyBufferedImage img, IcySupportRegion[] regions, DefaultDescriptorImpl<SegmentableIcyBufferedImage, ? extends Signature> descriptor, DefaultClusteringAlgorithmImpl<VectorSignature> algo) throws SupportRegionException, SegmentationException { + DefaultSegmentationAlgorithm<SegmentableIcyBufferedImage> segAlgo = new DefaultSegmentationAlgorithm<SegmentableIcyBufferedImage>(descriptor, algo); + segAlgo.setLogEnabled(isLogEnabled()); + + Segmentation seg = segAlgo.segment(img, regions); + + return seg; + } + + /** + * Gets the some stats. + * + * @param seg + * the seg + * @return the some stats + */ + private void getSomeStats(Segmentation seg) { + DecimalFormat df = new DecimalFormat("0"); + Algorithm.out("id;label;h1;h2;h3"); + for (Mask m : seg) { + Color rgb = m.getColor(); + double[] h1h2h3 = ColorSpaceTools.getColorComponentsD_0_255(ColorSpaceTools.RGB_TO_I1H2H3, rgb.getRed(), rgb.getGreen(), rgb.getBlue()); + log(m.getId() + ";" + m.getLabel() + ";" + df.format(h1h2h3[0]) + ";" + df.format(h1h2h3[1]) + ";" + df.format(h1h2h3[2])); + } + } + + /** + * Do clustering. + * + * @param currentSequence + * the current sequence + * @return the segmentation + * @throws SupportRegionException + * the support region exception + * @throws SegmentationException + * the segmentation exception + * @throws MaskException + * the mask exception + * @throws NumberFormatException + * the number format exception + * @throws SignatureException + * the signature exception + */ + private Segmentation doClustering(Sequence currentSequence) throws SupportRegionException, SegmentationException, MaskException, NumberFormatException, SignatureException { + Segmentation seg = null; + + seg = doClusteringKM(currentSequence); + seg.reInitColors(currentSequence.getImage(0, 0)); + if (isLogEnabled()) { + getSomeStats(seg); + } + + return seg; + } + + /** + * Do clustering km. + * + * @param currentSequence + * the current sequence + * @return the segmentation + * @throws SupportRegionException + * the support region exception + * @throws SegmentationException + * the segmentation exception + * @throws MaskException + * the mask exception + * @throws NumberFormatException + * the number format exception + * @throws SignatureException + * the signature exception + */ + private Segmentation doClusteringKM(Sequence currentSequence) throws SupportRegionException, SegmentationException, MaskException, NumberFormatException, SignatureException { + int nbc2 = Integer.parseInt(tfNbCluster2.getText()); + int nbi2 = Integer.parseInt(tfNbIteration2.getText()); + double stab2 = Double.parseDouble(tfStabCrit2.getText()); + int cs = indexToColorspace.get(cbColorSpace.getSelectedIndex()); + + log("Working on " + ColorSpaceTools.COLOR_SPACES[cs]); + + SegmentableIcyBufferedImage img = new SegmentableIcyBufferedImage(currentSequence.getFirstImage()); + + KMeans km2 = new KMeans(nbc2, nbi2, stab2); + km2.setLogEnabled(isLogEnabled()); + + Segmentation seg = null; + + DefaultDescriptorImpl<SegmentableIcyBufferedImage, ? extends Signature> col = null; + + ColorPixel cd = new ColorPixel(isLogEnabled()); + cd.setColorSpace(cs); + col = cd; + + col.setLogEnabled(isLogEnabled()); + + GridFactory factory = new GridFactory(GridFactory.ALGO_ONLY_PIXELS); + factory.setLogEnabled(isLogEnabled()); + List<IcySupportRegion> lRegions = factory.extractRegions(img); + IcySupportRegion[] regions = new IcySupportRegion[lRegions.size()]; + int r = 0; + for (IcySupportRegion sr : lRegions) { + regions[r++] = sr; + } + + seg = doSingleClustering(img, regions, col, km2); + + return seg; + } + + @Override + public Dimension getDefaultFrameDimension() { + return new Dimension(550, 300); + } +} diff --git a/src/main/resources/COPYING b/src/main/resources/COPYING new file mode 100644 index 0000000000000000000000000000000000000000..94a9ed024d3859793618152ea559a168bbcbb5e2 --- /dev/null +++ b/src/main/resources/COPYING @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + <one line to give the program's name and a brief idea of what it does.> + Copyright (C) <year> <name of author> + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU 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 Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + <program> Copyright (C) <year> <name of author> + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +<http://www.gnu.org/licenses/>. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +<http://www.gnu.org/philosophy/why-not-lgpl.html>. diff --git a/src/main/resources/KMeansColorQuantization.png b/src/main/resources/KMeansColorQuantization.png new file mode 100644 index 0000000000000000000000000000000000000000..497ac05c586f10b0c4911a6a04a9371545194d47 Binary files /dev/null and b/src/main/resources/KMeansColorQuantization.png differ diff --git a/src/main/resources/KMeansColorQuantization_icon.png b/src/main/resources/KMeansColorQuantization_icon.png new file mode 100644 index 0000000000000000000000000000000000000000..925a08bd9f8a49b448220caa618befd91be5d711 Binary files /dev/null and b/src/main/resources/KMeansColorQuantization_icon.png differ diff --git a/src/main/resources/KMeansColorQuantization_miniscreen.png b/src/main/resources/KMeansColorQuantization_miniscreen.png new file mode 100644 index 0000000000000000000000000000000000000000..f66d54965591bada2003568f4c37dc9a5c46f856 Binary files /dev/null and b/src/main/resources/KMeansColorQuantization_miniscreen.png differ