diff --git a/.gitignore b/.gitignore
index 3d47f986c41db29ec6dc0d5036bf760b3a1cf366..8d47cace3a5bd898da9fb12bed716d60838191a4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,5 @@ target/
.settings/
*.iml
.project
-.classpath
\ No newline at end of file
+.classpath
+**/.DS_Store
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index d4f3419bee216abb2d3c4f3a4d3f23827e0f0de3..82a4ff738b8bfe382d4ea39ab5ab9001f564ec6c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,19 +7,17 @@
<!-- Inherited Icy Parent POM -->
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>parent-pom-plugin</artifactId>
- <version>1.0.3</version>
+ <artifactId>pom-icy</artifactId>
+ <version>2.2.0</version>
</parent>
<!-- Project Information -->
<artifactId>kmeans-color-quantization</artifactId>
- <version>1.2.1</version>
-
- <packaging>jar</packaging>
+ <version>2.0.0</version>
<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>
+ <url>https://icy.bioimageanalysis.org/plugin/kmeans-color-quantization/</url>
<inceptionYear>2020</inceptionYear>
<organization>
@@ -53,34 +51,16 @@
</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>
diff --git a/src/main/java/plugins/nherve/colorquantization/KMeansColorQuantization.java b/src/main/java/plugins/nherve/colorquantization/KMeansColorQuantization.java
index 286fac3fad353ee0fe8df52ca1d5c9cf75e1fecf..767e55a549d61777b9378f478772d1aba1198f9f 100644
--- a/src/main/java/plugins/nherve/colorquantization/KMeansColorQuantization.java
+++ b/src/main/java/plugins/nherve/colorquantization/KMeansColorQuantization.java
@@ -1,59 +1,37 @@
/*
- * 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
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy 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,
+ *
+ * Icy 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/>.
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
+
package plugins.nherve.colorquantization;
-import icy.gui.component.ComponentUtil;
+import icy.gui.util.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 icy.system.IcyExceptionHandler;
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.IcySupportRegion;
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;
@@ -70,354 +48,343 @@ import plugins.nherve.toolbox.image.toolboxes.ColorSpaceTools;
import plugins.nherve.toolbox.plugin.HelpWindow;
import plugins.nherve.toolbox.plugin.SingletonPlugin;
+import javax.swing.*;
+import javax.swing.border.TitledBorder;
+import java.awt.*;
+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;
+
/**
* The Class KMeansColorQuantization.
- *
+ * <p>
* 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);
- }
+ private static final 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<String> 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(final JPanel mainPanel) {
+ currentlyRunning = null;
+
+ final XMLPreferences preferences = getPreferences();
+ final int nbc2 = preferences.getInt("nbc2", 10);
+ final int nbi2 = preferences.getInt("nbi2", 100);
+ final double stab2 = preferences.getDouble("stab2", 0.001);
+
+ final boolean dsp = preferences.getBoolean("dsp", false);
+
+ indexToColorspace = new HashMap<>();
+ 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));
+
+ final 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));
+ final JPanel p1 = GuiUtil.createLineBoxPanel(new JLabel("Nb. clusters"), Box.createHorizontalGlue(), tfNbCluster2);
+
+ tfNbIteration2 = new JTextField(Integer.toString(nbi2));
+ ComponentUtil.setFixedSize(tfNbIteration2, new Dimension(100, 25));
+ final 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));
+ final JPanel p3 = GuiUtil.createLineBoxPanel(new JLabel("Stabilization criterion"), Box.createHorizontalGlue(), tfStabCrit2);
+
+ final 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());
+
+ final JPanel bottom = GuiUtil.createLineBoxPanel(
+ 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 {
+ final 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 (final NumberFormatException e) {
+ IcyExceptionHandler.showErrorMessage(e, true);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(final ActionEvent e) {
+ final 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(() -> {
+ try {
+ final Sequence cs = getCurrentSequence();
+ final Segmentation seg = doClustering(cs);
+ if (cbSendMaskDirectly.isSelected()) {
+ final MaskEditor me = MaskEditor.getRunningInstance(true);
+ currentlyRunning = null;
+ final Runnable r = () -> {
+ me.setSegmentationForSequence(cs, seg);
+ me.switchOpacityOn();
+ btStart.setEnabled(true);
+ };
+ SwingUtilities.invokeAndWait(r);
+ }
+ else {
+ final SwimmingObject result = new SwimmingObject(seg);
+ Icy.getMainInterface().getSwimmingPool().add(result);
+ currentlyRunning = null;
+ final Runnable r = () -> btStart.setEnabled(true);
+ SwingUtilities.invokeAndWait(r);
+ }
+ }
+ catch (final SupportRegionException | SegmentationException | InterruptedException | InvocationTargetException | MaskException | NumberFormatException | SignatureException e1) {
+ logError(e1.getClass().getName() + " : " + e1.getMessage());
+ }
+ });
+ currentlyRunning.start();
+ }
+ }
+
+ }
+
+ /**
+ * Do single clustering.
+ *
+ * @param img the img
+ * @param regions the regions
+ * @param descriptor the descriptor
+ * @param algo the algo
+ * @return the segmentation
+ * @throws SegmentationException the segmentation exception
+ */
+ private Segmentation doSingleClustering(final SegmentableIcyBufferedImage img, final IcySupportRegion[] regions, final DefaultDescriptorImpl<SegmentableIcyBufferedImage, ? extends Signature> descriptor, final DefaultClusteringAlgorithmImpl<VectorSignature> algo) throws SegmentationException {
+ final DefaultSegmentationAlgorithm<SegmentableIcyBufferedImage> segAlgo = new DefaultSegmentationAlgorithm<>(descriptor, algo);
+ segAlgo.setLogEnabled(isLogEnabled());
+
+ return segAlgo.segment(img, regions);
+ }
+
+ /**
+ * Gets the some stats.
+ *
+ * @param seg the seg
+ * @return the some stats
+ */
+ private void getSomeStats(final Segmentation seg) {
+ final DecimalFormat df = new DecimalFormat("0");
+ Algorithm.out("id;label;h1;h2;h3");
+ for (final Mask m : seg) {
+ final Color rgb = m.getColor();
+ final 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(final Sequence currentSequence) throws SupportRegionException, SegmentationException, MaskException, NumberFormatException, SignatureException {
+ final Segmentation seg;
+
+ 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 NumberFormatException the number format exception
+ */
+ private Segmentation doClusteringKM(final Sequence currentSequence) throws SupportRegionException, SegmentationException, NumberFormatException {
+ final int nbc2 = Integer.parseInt(tfNbCluster2.getText());
+ final int nbi2 = Integer.parseInt(tfNbIteration2.getText());
+ final double stab2 = Double.parseDouble(tfStabCrit2.getText());
+ final int cs = indexToColorspace.get(cbColorSpace.getSelectedIndex());
+
+ log("Working on " + ColorSpaceTools.COLOR_SPACES[cs]);
+
+ final SegmentableIcyBufferedImage img = new SegmentableIcyBufferedImage(currentSequence.getFirstImage());
+
+ final KMeans km2 = new KMeans(nbc2, nbi2, stab2);
+ km2.setLogEnabled(isLogEnabled());
+
+ final Segmentation seg;
+
+ final DefaultDescriptorImpl<SegmentableIcyBufferedImage, ? extends Signature> col;
+
+ final ColorPixel cd = new ColorPixel(isLogEnabled());
+ cd.setColorSpace(cs);
+ col = cd;
+
+ col.setLogEnabled(isLogEnabled());
+
+ final GridFactory factory = new GridFactory(GridFactory.ALGO_ONLY_PIXELS);
+ factory.setLogEnabled(isLogEnabled());
+ final List<IcySupportRegion> lRegions = factory.extractRegions(img);
+ final IcySupportRegion[] regions = new IcySupportRegion[lRegions.size()];
+ int r = 0;
+ for (final IcySupportRegion sr : lRegions) {
+ regions[r++] = sr;
+ }
+
+ seg = doSingleClustering(img, regions, col, km2);
+
+ return seg;
+ }
+
+ @Override
+ public Dimension getDefaultFrameDimension() {
+ return new Dimension(550, 300);
+ }
}