diff --git a/.gitignore b/.gitignore
index e457b00fe9212931d0bfaea3a80a1f7a91bcfaff..159dee38dba1df3c6af2c3793586d29a79dfa29e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,4 @@ bin/
.classpath
.project
export.jardesc
+**/.DS_Store
diff --git a/pom.xml b/pom.xml
index 8db483e9fdecaea0a70e4688660704ac6569da16..99e28706964b287f0d9b4d1af0e0f10bdf5ca574 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,19 +1,17 @@
<?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">
+ 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>
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
- <version>2.1.5</version>
+ <version>2.2.0</version>
</parent>
<artifactId>color-picker-threshold</artifactId>
- <version>1.2.3</version>
-
- <packaging>jar</packaging>
+ <version>2.0.0</version>
<name>Color Picker Threshold</name>
<description>
diff --git a/src/main/java/plugins/nherve/colorpickerthreshold/ColorPickerThreshold.java b/src/main/java/plugins/nherve/colorpickerthreshold/ColorPickerThreshold.java
index 19f5a2b2349526b89803a40b7e71614baac4f549..5f0a92d8a944a697a41e4eaa081e92adcbe472f9 100644
--- a/src/main/java/plugins/nherve/colorpickerthreshold/ColorPickerThreshold.java
+++ b/src/main/java/plugins/nherve/colorpickerthreshold/ColorPickerThreshold.java
@@ -1,64 +1,34 @@
/*
- * Copyright 2010, 2011 Institut Pasteur.
- * Copyright 2012, 2013 Nicolas Hervé.
- *
- * This file is part of Color Picker Threshold, which is an ICY plugin.
- *
- * Color Picker Threshold 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.
- *
- * Color Picker Threshold 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 Color Picker Threshold. If not, see <http://www.gnu.org/licenses/>.
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
+
package plugins.nherve.colorpickerthreshold;
import icy.canvas.IcyCanvas;
-import icy.gui.component.ComponentUtil;
+import icy.gui.util.ComponentUtil;
import icy.gui.util.GuiUtil;
import icy.image.IcyBufferedImage;
import icy.main.Icy;
-import icy.painter.Painter;
-import icy.roi.ROI2DArea;
+import icy.painter.Overlay;
import icy.sequence.Sequence;
import icy.swimmingPool.SwimmingObject;
import icy.type.TypeUtil;
-
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Graphics;
-import java.awt.Graphics2D;
-import java.awt.Point;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-
-import javax.swing.Box;
-import javax.swing.ButtonGroup;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JRadioButton;
-import javax.swing.JSlider;
-import javax.swing.JTabbedPane;
-import javax.swing.border.TitledBorder;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
-
+import icy.type.point.Point5D;
+import plugins.kernel.roi.roi2d.ROI2DArea;
import plugins.nherve.toolbox.Algorithm;
import plugins.nherve.toolbox.NherveToolbox;
import plugins.nherve.toolbox.image.BinaryIcyBufferedImage;
@@ -79,1334 +49,1355 @@ import plugins.nherve.toolbox.libsvm.svm;
import plugins.nherve.toolbox.libsvm.svm_parameter;
import plugins.nherve.toolbox.plugin.PainterManagerSingletonPlugin;
+import javax.swing.*;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import java.awt.*;
+import java.awt.event.*;
+import java.util.ArrayList;
+
/**
* The Class ColorPickerThreshold.
- *
+ *
* @author Nicolas HERVE - nicolas.herve@pasteur.fr
*/
public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPickerThreshold.ColorPickerThresholdPainter> implements ActionListener, ChangeListener, ItemListener {
- class ColorBox extends JPanel implements ActionListener {
-
- /**
- * The color selector manages and displays the colors picked by the
- * user.
- *
- * @author Nicolas HERVE - nicolas.herve@pasteur.fr
- */
- private class ColorSelector extends JPanel implements MouseListener {
- /** The Constant serialVersionUID. */
- private static final long serialVersionUID = 5232546251526771415L;
-
- private ColorBox box;
-
- /**
- * Instantiates a new color box.
- */
- public ColorSelector(ColorBox box) {
- super();
- this.box = box;
- addMouseListener(this);
- setOpaque(true);
- }
-
- public Dimension getPreferredSize() {
- return COL_DIM;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * java.awt.event.MouseListener#mouseClicked(java.awt.event.MouseEvent
- * )
- */
- @Override
- public void mouseClicked(MouseEvent me) {
- if (me.getButton() == MouseEvent.BUTTON1) {
- int row = (int) Math.floor((double) me.getY() / (double) COL_FULL_BLOCK_SIZE);
- int col = (int) Math.floor((double) me.getX() / (double) COL_FULL_BLOCK_SIZE);
- box.removeColor(row, col);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * java.awt.event.MouseListener#mouseEntered(java.awt.event.MouseEvent
- * )
- */
- @Override
- public void mouseEntered(MouseEvent e) {
- // Nothing to do here
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * java.awt.event.MouseListener#mouseExited(java.awt.event.MouseEvent
- * )
- */
- @Override
- public void mouseExited(MouseEvent e) {
- // Nothing to do here
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * java.awt.event.MouseListener#mousePressed(java.awt.event.MouseEvent
- * )
- */
- @Override
- public void mousePressed(MouseEvent e) {
- // Nothing to do here
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * java.awt.event.MouseListener#mouseReleased(java.awt.event.MouseEvent
- * )
- */
- @Override
- public void mouseReleased(MouseEvent e) {
- // Nothing to do here
- }
-
- /*
- * (non-Javadoc)
- *
- * @see javax.swing.JComponent#paintComponent(java.awt.Graphics)
- */
- public void paintComponent(Graphics g) {
- g.setColor(getBackground());
- g.fillRect(0, 0, getWidth(), getHeight());
-
- for (int row = 0; row < COL_GRID_HEIGHT; row++) {
- int y = row * (COL_FULL_BLOCK_SIZE + COL_BLOCK_SPACER);
- for (int column = 0; column < COL_GRID_WIDTH; column++) {
- int x = column * (COL_FULL_BLOCK_SIZE + COL_BLOCK_SPACER);
- g.setColor(box.getColor(row, column));
- g.fillRect(x, y, COL_BLOCK_SIZE, COL_BLOCK_SIZE);
- g.setColor(Color.black);
- g.drawRect(x, y, COL_BLOCK_SIZE, COL_BLOCK_SIZE);
- }
- }
- }
- }
-
- private static final long serialVersionUID = -2779071071132708790L;
-
- /** The colors. */
- private Color[] colors;
- /** The nb colors. */
- private int nbColors;
- /** The threshold. */
- private int threshold;
-
- /** The listeners. */
- private ArrayList<ColorBoxListener> listeners;
-
- private ColorSelector selector;
-
- private JButton btInitColors;
-
- public ColorBox(String label) {
- super();
-
- colors = new Color[COL_GRID_MAXCOLORS];
- listeners = new ArrayList<ColorBoxListener>();
-
- selector = new ColorSelector(this);
- btInitColors = new JButton("Clear");
- btInitColors.setEnabled(false);
- btInitColors.addActionListener(this);
-
- JPanel p1 = GuiUtil.createLineBoxPanel(new JLabel(label), Box.createHorizontalGlue(), btInitColors);
- JPanel p2 = GuiUtil.createPageBoxPanel(selector, Box.createVerticalGlue(), p1);
- add(p2);
-
- initColors();
- }
-
- /**
- * Adds the color.
- *
- * @param c
- * the c
- */
- public void addColor(int[] c) {
- if (nbColors < COL_GRID_MAXCOLORS) {
- colors[nbColors] = new Color(c[0], c[1], c[2]);
- nbColors++;
- btFilter.setEnabled(true);
- btKeepMask.setEnabled(true);
- btAsROI.setEnabled(true);
- btInitColors.setEnabled(true);
- repaint();
- fireFilterParametersChangeEvent();
- }
- }
-
- public Color getColor(int row, int col) {
- return colors[row * COL_GRID_WIDTH + col];
- }
-
- /**
- * Fire cancel filter event.
- */
- public void fireCancelFilterEvent() {
- for (ColorBoxListener l : listeners) {
- l.cancelFilter();
- }
- }
-
- /**
- * Fire display parameters change event.
- */
- public void fireDisplayParametersChangeEvent() {
- for (ColorBoxListener l : listeners) {
- l.displayParametersHaveChanged();
- }
- }
-
- /**
- * Fire filter parameters change event.
- */
- public void fireFilterParametersChangeEvent() {
- for (ColorBoxListener l : listeners) {
- l.filterParametersHaveChanged();
- }
- }
-
- /**
- * Gets the average color.
- *
- * @return the average color
- */
- public Color getAverageColor() {
- int r = 0;
- int g = 0;
- int b = 0;
- for (int k = 0; k < nbColors; k++) {
- r += colors[k].getRed();
- g += colors[k].getGreen();
- b += colors[k].getBlue();
- }
- r /= nbColors;
- g /= nbColors;
- b /= nbColors;
-
- return new Color(r, g, b);
- }
-
- /**
- * Gets the threshold.
- *
- * @return the threshold
- */
- public int getThreshold() {
- return threshold;
- }
-
- /**
- * Inits the colors.
- */
- public void initColors() {
- nbColors = 0;
- for (int i = 0; i < COL_GRID_MAXCOLORS; i++) {
- colors[i] = getBackground();
- }
- repaint();
- fireFilterParametersChangeEvent();
- }
-
- /**
- * Register.
- *
- * @param l
- * the l
- */
- public void register(ColorBoxListener l) {
- listeners.add(l);
- }
-
- /**
- * Removes the.
- *
- * @param l
- * the l
- */
- public void remove(ColorBoxListener l) {
- listeners.remove(l);
- }
-
- public void removeColor(int row, int col) {
- if ((row < COL_GRID_HEIGHT) && (col < COL_GRID_WIDTH)) {
- int idx = row * COL_GRID_WIDTH + col;
- if (idx < nbColors) {
- for (int c = idx; (c < nbColors) && (c < COL_GRID_MAXCOLORS - 1); c++) {
- colors[c] = colors[c + 1];
- }
- colors[nbColors - 1] = getBackground();
- nbColors--;
- if (nbColors == 0) {
- btInitColors.setEnabled(false);
- }
- repaint();
- fireFilterParametersChangeEvent();
- }
- }
- }
-
- /**
- * Sets the threshold.
- *
- * @param threshold
- * the new threshold
- */
- public void setThreshold(int threshold) {
- this.threshold = threshold;
- fireFilterParametersChangeEvent();
- }
-
- @Override
- public void actionPerformed(ActionEvent e) {
- Object o = e.getSource();
-
- if (o == null) {
- return;
- }
-
- if (o instanceof JButton) {
- JButton b = (JButton) e.getSource();
- if (b == null) {
- return;
- }
-
- if (b == btInitColors) {
- initColors();
- btInitColors.setEnabled(false);
- }
- }
- }
-
- }
-
- /**
- * The Interface ColorBoxListener.
- *
- * @author Nicolas HERVE - nicolas.herve@pasteur.fr
- */
- interface ColorBoxListener {
-
- /**
- * Cancel filter.
- */
- void cancelFilter();
-
- /**
- * Display parameters have changed.
- */
- void displayParametersHaveChanged();
-
- /**
- * Filter parameters have changed.
- */
- void filterParametersHaveChanged();
- }
-
- /**
- * This Painter is needed to access the colors picked in the image.
- *
- * @author Nicolas HERVE - nicolas.herve@pasteur.fr
- */
- class ColorPickerThresholdPainter implements Painter, ColorBoxListener {
-
- /** The mask. */
- private Mask mask;
-
- /** The sequence. */
- private Sequence sequence;
-
- /**
- * Instantiates a new color picker threshold painter.
- */
- public ColorPickerThresholdPainter() {
- super();
-
- setMask(null);
- setSequence(null);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * plugins.nherve.colorpickerthreshold.ColorPickerThreshold.ColorBoxListener
- * #cancelFilter()
- */
- @Override
- public void cancelFilter() {
- setMask(null);
- displayParametersHaveChanged();
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * plugins.nherve.colorpickerthreshold.ColorPickerThreshold.ColorBoxListener
- * #displayParametersHaveChanged()
- */
- @Override
- public void displayParametersHaveChanged() {
- getSequence().painterChanged(null);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * plugins.nherve.colorpickerthreshold.ColorPickerThreshold.ColorBoxListener
- * #filterParametersHaveChanged()
- */
- @Override
- public void filterParametersHaveChanged() {
- if (cbAuto.isSelected()) {
- try {
- doFilter(this);
- } catch (SignatureException e1) {
- Algorithm.err(e1);
- }
- }
- }
-
- /**
- * Gets the clicked color.
- *
- * @param pt
- * the pt
- * @return the clicked color
- * @throws SignatureException
- * the signature exception
- */
- private int[] getClickedColor(Point pt) throws SignatureException {
- IcyBufferedImage image = getCurrentSequence().getFirstImage();
- int[] c = null;
- if ((image != null) && image.isInside(pt)) {
- int x = (int) pt.getX();
- int y = (int) pt.getY();
- c = ColorSpaceTools.getColorComponentsI_0_255(image, ColorSpaceTools.RGB, x, y);
- }
-
- return c;
- }
-
- /**
- * Gets the mask.
- *
- * @return the mask
- */
- public Mask getMask() {
- return mask;
- }
-
- /**
- * Gets the sequence.
- *
- * @return the sequence
- */
- public Sequence getSequence() {
- return sequence;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see icy.painter.Painter#keyPressed(java.awt.event.KeyEvent,
- * java.awt.geom.Point2D, icy.canvas.IcyCanvas)
- */
- @Override
- public void keyPressed(KeyEvent e, Point2D imagePoint, IcyCanvas canvas) {
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see icy.painter.Painter#keyReleased(java.awt.event.KeyEvent,
- * java.awt.geom.Point2D, icy.canvas.IcyCanvas)
- */
- @Override
- public void keyReleased(KeyEvent e, Point2D imagePoint, IcyCanvas canvas) {
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see icy.painter.Painter#mouseClick(java.awt.event.MouseEvent,
- * java.awt.geom.Point2D, icy.canvas.IcyCanvas)
- */
- @Override
- public void mouseClick(MouseEvent e, Point2D imagePoint, IcyCanvas canvas) {
- int comp = tabbedPane.getSelectedIndex();
- try {
- if (comp == 0) {
- if (e.getButton() == MouseEvent.BUTTON1) {
- int[] c = getClickedColor(TypeUtil.toPoint(imagePoint));
- if (c != null) {
- m1ColorBox.addColor(c);
- }
- }
- } else if (comp == 1) {
- if (e.getButton() == MouseEvent.BUTTON1) {
- int[] c = getClickedColor(TypeUtil.toPoint(imagePoint));
- if (c != null) {
- m2PosColorBox.addColor(c);
- }
- } else if ((e.getButton() == MouseEvent.BUTTON2) || (e.getButton() == MouseEvent.BUTTON3)) {
- int[] c = getClickedColor(TypeUtil.toPoint(imagePoint));
- if (c != null) {
- m2NegColorBox.addColor(c);
- }
- }
- }
-
- } catch (SignatureException ex) {
- Algorithm.err(ex);
- }
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see icy.painter.Painter#mouseDrag(java.awt.event.MouseEvent,
- * java.awt.geom.Point2D, icy.canvas.IcyCanvas)
- */
- @Override
- public void mouseDrag(MouseEvent e, Point2D imagePoint, IcyCanvas canvas) {
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see icy.painter.Painter#mouseMove(java.awt.event.MouseEvent,
- * java.awt.geom.Point2D, icy.canvas.IcyCanvas)
- */
- @Override
- public void mouseMove(MouseEvent e, Point2D imagePoint, IcyCanvas canvas) {
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see icy.painter.Painter#mousePressed(java.awt.event.MouseEvent,
- * java.awt.geom.Point2D, icy.canvas.IcyCanvas)
- */
- @Override
- public void mousePressed(MouseEvent e, Point2D imagePoint, IcyCanvas canvas) {
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see icy.painter.Painter#mouseReleased(java.awt.event.MouseEvent,
- * java.awt.geom.Point2D, icy.canvas.IcyCanvas)
- */
- @Override
- public void mouseReleased(MouseEvent e, Point2D imagePoint, IcyCanvas canvas) {
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see icy.painter.Painter#paint(java.awt.Graphics2D,
- * icy.sequence.Sequence, icy.canvas.IcyCanvas)
- */
- @Override
- public void paint(Graphics2D g, Sequence sequence, IcyCanvas canvas) {
- if ((getMask() != null) && (cbShow.isSelected())) {
- getMask().paint(g);
- }
- }
-
- /**
- * Sets the mask.
- *
- * @param mask
- * the new mask
- */
- public void setMask(Mask mask) {
- this.mask = mask;
- }
-
- /**
- * Sets the sequence.
- *
- * @param sequence
- * the new sequence
- */
- public void setSequence(Sequence sequence) {
- this.sequence = sequence;
- }
-
- }
-
- private final static int COL_BLOCK_BORDER = 1;
-
- private final static int COL_BLOCK_SPACER = 1;
-
- private final static int COL_BLOCK_SIZE = 25;
-
- /** The Constant COL_GRID_HEIGHT. */
- private final static int COL_GRID_HEIGHT = 3;
-
- /** The Constant COL_GRID_WIDTH. */
- private final static int COL_GRID_WIDTH = 8;
-
- private final static int COL_FULL_BLOCK_SIZE = COL_BLOCK_SIZE + 2 * COL_BLOCK_BORDER;
- private final static Dimension COL_DIM = new Dimension(COL_GRID_WIDTH * (COL_FULL_BLOCK_SIZE + COL_BLOCK_SPACER) - 1, COL_GRID_HEIGHT * (COL_FULL_BLOCK_SIZE + COL_BLOCK_SPACER) - 1);
-
- /** The Constant COL_GRID_MAXCOLORS. */
- private final static int COL_GRID_MAXCOLORS = COL_GRID_HEIGHT * COL_GRID_WIDTH;
-
- /** The Constant METHOD_1. */
- private final static String METHOD_1 = "KNN";
-
- /** The Constant METHOD_2. */
- private final static String METHOD_2 = "SVM";
-
- /** The bt cancel filter. */
- private JButton btCancelFilter;
-
- /** The bt filter. */
- private JButton btFilter;
-
- /** The bt keep mask. */
- private JButton btKeepMask;
-
- /** The bt as roi. */
- private JButton btAsROI;
-
- /** The bt minus. */
- private JButton btMinus;
-
- /** The bt plus. */
- private JButton btPlus;
-
- /** The col default dist. */
- private int colDefaultDist;
-
- /** The col max dist. */
- private int colMaxDist;
-
- /** The m1 color box. */
- private ColorBox m1ColorBox;
-
- /** The m2 pos color box. */
- private ColorBox m2PosColorBox;
-
- /** The m2 neg color box. */
- private ColorBox m2NegColorBox;
-
- /** The lb current. */
- private JLabel lbCurrent;
-
- /** The rb rgb. */
- private JRadioButton rbRGB;
-
- /** The rb hsv. */
- private JRadioButton rbHSV;
-
- /** The rb h1 h2 h3. */
- private JRadioButton rbH1H2H3;
-
- /** The rb l1. */
- private JRadioButton rbL1;
-
- /** The rb l2. */
- private JRadioButton rbL2;
-
- /** The rb kernel lin. */
- private JRadioButton rbKernelLin;
-
- /** The rb kernel rbf. */
- private JRadioButton rbKernelRBF;
-
- /** The rb kernel tri. */
- private JRadioButton rbKernelTri;
-
- /** The sl c. */
- private JSlider slC;
-
- /** The sl gamma. */
- private JSlider slGamma;
-
- /** The val c. */
- private JLabel valC;
-
- /** The val gamma. */
- private JLabel valGamma;
-
- /** The distance. */
- private ColorDistance distance;
-
- /** The choosen cs. */
- private int choosenCS;
-
- /** The sl dist threshold. */
- private JSlider slDistThreshold;
-
- /** The sl maj tick. */
- private int slMajTick;
-
- /** The sl min tick. */
- private int slMinTick;
-
- /** The cb show. */
- private JCheckBox cbShow;
-
- /** The cb auto. */
- private JCheckBox cbAuto;
-
- /** The tabbed pane. */
- private JTabbedPane tabbedPane;
-
- /**
- * Instantiates a new color picker threshold.
- */
- public ColorPickerThreshold() {
- super();
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
- */
- @Override
- public void actionPerformed(ActionEvent e) {
- Object o = e.getSource();
-
- if (o == null) {
- return;
- }
-
- if (o instanceof JButton) {
- JButton b = (JButton) e.getSource();
- if (b == null) {
- return;
- }
-
- if (b == btFilter) {
- if (hasCurrentSequence()) {
- try {
- doFilter(getCurrentSequencePainter());
- } catch (SignatureException e1) {
- Algorithm.err(e1);
- }
- }
-
- return;
- }
-
- if (b == btCancelFilter) {
- if (cbAuto.isSelected()) {
- m1ColorBox.fireCancelFilterEvent();
- } else if (hasCurrentSequence()) {
- getCurrentSequencePainter().setMask(null);
- getCurrentSequence().painterChanged(null);
- }
- return;
- }
-
- if (b == btPlus) {
- if (slDistThreshold.getValue() < slDistThreshold.getMaximum()) {
- slDistThreshold.setValue(slDistThreshold.getValue() + 1);
- }
- return;
- }
-
- if (b == btMinus) {
- if (slDistThreshold.getValue() > slDistThreshold.getMinimum()) {
- slDistThreshold.setValue(slDistThreshold.getValue() - 1);
- }
- return;
- }
-
- if (b == btKeepMask) {
- if (hasCurrentSequence()) {
- Sequence currentSequence = getCurrentSequence();
- try {
- Mask m = doFilter(getCurrentSequencePainter());
- if (m != null) {
- SwimmingObject result = new SwimmingObject(m);
- Icy.getMainInterface().getSwimmingPool().add(result);
- }
- } catch (SignatureException e1) {
- Algorithm.err(e1);
- }
- currentSequence.dataChanged();
- }
- return;
- }
-
- if (b == btAsROI) {
- if (hasCurrentSequence()) {
- Sequence currentSequence = getCurrentSequence();
- try {
- Mask m = doFilter(getCurrentSequencePainter());
- if (m != null) {
- ROI2DArea a = m.asROI2DArea(currentSequence);
- a.setName("From " + getName());
- }
- } catch (SignatureException e1) {
- Algorithm.err(e1);
- }
- currentSequence.dataChanged();
- }
- return;
- }
- }
-
- if (o instanceof JRadioButton) {
-
- JRadioButton b = (JRadioButton) e.getSource();
- if (b == rbRGB) {
- choosenCS = ColorSpaceTools.RGB;
- }
- if (b == rbHSV) {
- choosenCS = ColorSpaceTools.RGB_TO_HSV;
- }
- if (b == rbH1H2H3) {
- choosenCS = ColorSpaceTools.RGB_TO_H1H2H3;
- }
- if ((b == rbL1) || (b == rbL2)) {
- double currentPct = (double) slDistThreshold.getValue() / (double) slDistThreshold.getMaximum();
-
- if (b == rbL1) {
- setDistance(new L1ColorDistance());
- }
- if (b == rbL2) {
- setDistance(new L2ColorDistance());
- }
-
- slDistThreshold.setMaximum(colMaxDist);
- int currentValue = (int) (currentPct * slDistThreshold.getMaximum());
- slDistThreshold.setValue(currentValue);
- m1ColorBox.setThreshold(currentValue);
- slDistThreshold.setMajorTickSpacing(slMajTick);
- slDistThreshold.setMinorTickSpacing(slMinTick);
- }
- if (hasCurrentSequence() && cbAuto.isSelected()) {
- try {
- doFilter(getCurrentSequencePainter());
- } catch (SignatureException e1) {
- Algorithm.err(e1);
- }
- }
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see plugins.nherve.toolbox.plugin.PainterFactory#createNewPainter()
- */
- @Override
- public ColorPickerThresholdPainter createNewPainter() {
- ColorPickerThresholdPainter painter = new ColorPickerThresholdPainter();
- Sequence currentSequence = getCurrentSequence();
- painter.setSequence(currentSequence);
- m1ColorBox.register(painter);
- m2PosColorBox.register(painter);
- m2NegColorBox.register(painter);
- try {
- doFilter(painter);
- } catch (SignatureException e1) {
- Algorithm.err(e1);
- }
- return painter;
- }
-
- /**
- * Do filter.
- *
- * @param painter
- * the painter
- * @return the mask
- * @throws SignatureException
- * the signature exception
- */
- private Mask doFilter(ColorPickerThresholdPainter painter) throws SignatureException {
- Sequence currentSequence = painter.getSequence();
- IcyBufferedImage currentImage = currentSequence.getFirstImage();
- Mask m = null;
- int comp = tabbedPane.getSelectedIndex();
- try {
- if (comp == 0) {
- m = filter1(m1ColorBox, currentImage);
- m.setLabel(getName() + " " + METHOD_1);
- } else if (comp == 1) {
- m = filter2(m2PosColorBox, m2NegColorBox, currentImage);
- m.setLabel(getName() + " " + METHOD_2);
- }
- } catch (MaskException e) {
- // ignore
- }
- painter.setMask(m);
- currentSequence.painterChanged(null);
- return m;
- }
-
- /**
- * Filter1.
- *
- * @param box
- * the box
- * @param image
- * the image
- * @return the mask
- * @throws MaskException
- * the mask exception
- * @throws SignatureException
- * the signature exception
- */
- private Mask filter1(ColorBox box, IcyBufferedImage image) throws MaskException, SignatureException {
- if (box.nbColors == 0) {
- throw new MaskException("No color selected, filtering aborted");
- }
-
- // CPUMonitor moni = new CPUMonitor();
- // moni.start();
-
- // System.out.println("starting filtering");
- // Raster raster = image.getRaster();
- Mask m = new Mask(image.getWidth(), image.getHeight(), false);
- BinaryIcyBufferedImage bin = m.getBinaryData();
-
- ArrayList<double[]> csColors = new ArrayList<double[]>();
- for (int k = 0; k < box.nbColors; k++) {
- csColors.add(ColorSpaceTools.getColorComponentsD_0_255(choosenCS, box.colors[k].getRed(), box.colors[k].getGreen(), box.colors[k].getBlue()));
- }
-
- byte[] raw = bin.getRawData();
- int idx = 0;
- for (int j = 0; j < image.getHeight(); j++) {
- for (int i = 0; i < image.getWidth(); i++) {
- double[] cc = ColorSpaceTools.getColorComponentsD_0_255(image, choosenCS, i, j);
- boolean keep = false;
- for (int k = 0; k < box.nbColors; k++) {
- if (distance.computeDistance(cc, csColors.get(k)) < box.getThreshold()) {
- keep = true;
- break;
- }
- }
- if (keep) {
- raw[idx] = BinaryIcyBufferedImage.TRUE;
- }
- idx++;
- }
- }
- Color c = box.getAverageColor();
- int ir = 255 - c.getRed();
- int ig = 255 - c.getGreen();
- int ib = 255 - c.getBlue();
- m.setColor(new Color(ir, ig, ib));
- m.setOpacity(1f);
-
- // moni.stop();
- // System.out.println("Filtering done (" + getThreshold() + ") : " +
- // moni.getUserElapsedTimeMilli() + " ms");
- return m;
- }
-
- /**
- * Filter2.
- *
- * @param boxP
- * the box p
- * @param boxN
- * the box n
- * @param image
- * the image
- * @return the mask
- * @throws MaskException
- * the mask exception
- * @throws SignatureException
- * the signature exception
- */
- private Mask filter2(ColorBox boxP, ColorBox boxN, IcyBufferedImage image) throws MaskException, SignatureException {
- if (boxP.nbColors == 0) {
- throw new MaskException("No positive color selected, filtering aborted");
- }
- if (boxN.nbColors == 0) {
- throw new MaskException("No negative color selected, filtering aborted");
- }
-
- // Raster raster = image.getRaster();
-
- VectorSignature[] pos = new VectorSignature[boxP.nbColors];
- VectorSignature[] neg = new VectorSignature[boxN.nbColors];
-
- for (int i = 0; i < boxP.nbColors; i++) {
- double[] ddd = ColorSpaceTools.getColorComponentsD_0_1(choosenCS, boxP.colors[i].getRed(), boxP.colors[i].getGreen(), boxP.colors[i].getBlue());
- DenseVectorSignature s = new DenseVectorSignature(ColorSpaceTools.NB_COLOR_CHANNELS);
- for (int d = 0; d < ColorSpaceTools.NB_COLOR_CHANNELS; d++) {
- s.set(d, ddd[d]);
- }
- pos[i] = s;
- }
- for (int i = 0; i < boxN.nbColors; i++) {
- double[] ddd = ColorSpaceTools.getColorComponentsD_0_1(choosenCS, boxN.colors[i].getRed(), boxN.colors[i].getGreen(), boxN.colors[i].getBlue());
- DenseVectorSignature s = new DenseVectorSignature(ColorSpaceTools.NB_COLOR_CHANNELS);
- for (int d = 0; d < ColorSpaceTools.NB_COLOR_CHANNELS; d++) {
- s.set(d, ddd[d]);
- }
- neg[i] = s;
- }
-
- SVMClassifier svm = new SVMClassifier();
- svm.createProblem(pos, neg);
-
- svm.setC(Math.pow(2, slC.getValue()));
- svm.setGamma(Math.pow(2, slGamma.getValue()));
-
- if (rbKernelLin.isSelected()) {
- svm.setKernel(svm_parameter.LINEAR);
- } else if (rbKernelTri.isSelected()) {
- svm.setKernel(svm_parameter.TRIANGULAR);
- } else if (rbKernelRBF.isSelected()) {
- svm.setKernel(svm_parameter.RBF);
- }
-
- svm.learnModel();
-
- Mask m = new Mask(image.getWidth(), image.getHeight(), false);
- BinaryIcyBufferedImage bin = m.getBinaryData();
- SegmentableIcyBufferedImage simg = new SegmentableIcyBufferedImage(image);
-
- ColorPixel col = new ColorPixel(false);
- col.setColorSpace(choosenCS);
-
- byte[] raw = bin.getRawData();
- int idx = 0;
- for (int y = 0; y < image.getHeight(); y++) {
- for (int x = 0; x < image.getWidth(); x++) {
- IcyPixel pix = new IcyPixel(x, y);
- VectorSignature vs = (VectorSignature) col.extractLocalSignature(simg, pix);
- if (svm.predict(vs) > 0) {
- raw[idx] = BinaryIcyBufferedImage.TRUE;
- }
- idx++;
- }
- }
-
- Color c = m.getAverageColor(image);
- int ir = 255 - c.getRed();
- int ig = 255 - c.getGreen();
- int ib = 255 - c.getBlue();
- m.setColor(new Color(ir, ig, ib));
- m.setOpacity(1f);
-
- return m;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see plugins.nherve.toolbox.plugin.PainterManager#getPainterName()
- */
- @Override
- public String getPainterName() {
- return ColorPickerThresholdPainter.class.getName();
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * java.awt.event.ItemListener#itemStateChanged(java.awt.event.ItemEvent)
- */
- @Override
- public void itemStateChanged(ItemEvent e) {
- Object o = e.getSource();
-
- if (o == null) {
- return;
- }
-
- if (o instanceof JCheckBox) {
- JCheckBox c = (JCheckBox) e.getSource();
-
- int comp = tabbedPane.getSelectedIndex();
- ColorBox bx = null;
- if (comp == 0) {
- bx = m1ColorBox;
- } else if (comp == 1) {
- bx = m2PosColorBox;
- }
-
- if (c == cbShow) {
- bx.fireDisplayParametersChangeEvent();
- }
-
- if (c == cbAuto) {
- if (cbAuto.isSelected()) {
- bx.fireFilterParametersChangeEvent();
- }
- }
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see plugins.nherve.toolbox.plugin.PainterManagerSingletonPlugin#
- * sequenceHasChangedAfterSettingPainter()
- */
- @Override
- public void sequenceHasChangedAfterSettingPainter() {
- if (hasCurrentSequence()) {
- Sequence currentSequence = getCurrentSequence();
- setTitle(getName() + " - " + currentSequence.getName());
- btFilter.setEnabled(true);
- btKeepMask.setEnabled(true);
- btAsROI.setEnabled(true);
- btCancelFilter.setEnabled(true);
- } else {
- setTitle(getName());
- btFilter.setEnabled(false);
- btKeepMask.setEnabled(false);
- btAsROI.setEnabled(false);
- btCancelFilter.setEnabled(false);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see plugins.nherve.toolbox.plugin.PainterManagerSingletonPlugin#
- * sequenceHasChangedBeforeSettingPainter()
- */
- @Override
- public void sequenceHasChangedBeforeSettingPainter() {
- // Nothing to do here
- }
-
- /*
- * (non-Javadoc)
- *
- * @see plugins.nherve.toolbox.plugin.SingletonPlugin#sequenceWillChange()
- */
- @Override
- public void sequenceWillChange() {
- // Nothing to do here
- }
-
- /**
- * Sets the distance.
- *
- * @param distance
- * the new distance
- */
- public void setDistance(ColorDistance distance) {
- this.distance = distance;
-
- colMaxDist = (int) Math.floor(distance.getMaxDistance());
- slMajTick = (int) Math.ceil((double) colMaxDist / 100.0) * 20;
- slMinTick = (int) Math.ceil((double) slMajTick / 5.0);
- colMaxDist = (int) Math.ceil((double) colMaxDist / (double) slMajTick) * slMajTick;
- colDefaultDist = (int) Math.ceil((double) colMaxDist / 10.0);
- }
-
- @Override
- public Dimension getDefaultFrameDimension() {
- return null;
- }
-
- @Override
- public void fillInterface(JPanel mainPanel) {
- // KNN
- ButtonGroup bgd = new ButtonGroup();
- rbL1 = new JRadioButton("L1");
- rbL1.addActionListener(this);
- bgd.add(rbL1);
- rbL2 = new JRadioButton("L2");
- rbL2.addActionListener(this);
- bgd.add(rbL2);
- rbL1.setSelected(true);
- setDistance(new L1ColorDistance());
-
- slDistThreshold = new JSlider(JSlider.HORIZONTAL, 0, colMaxDist, colDefaultDist);
- slDistThreshold.addChangeListener(this);
- slDistThreshold.setMajorTickSpacing(slMajTick);
- slDistThreshold.setMinorTickSpacing(slMinTick);
- slDistThreshold.setPaintTicks(true);
- slDistThreshold.setPaintLabels(true);
-
- btPlus = new JButton(NherveToolbox.plusIcon);
- btPlus.addActionListener(this);
- btMinus = new JButton(NherveToolbox.minusIcon);
- btMinus.addActionListener(this);
- JPanel pmbt = GuiUtil.createPageBoxPanel(btPlus, btMinus);
-
- lbCurrent = new JLabel(Integer.toString(slDistThreshold.getValue()));
-
- JPanel boxDist = GuiUtil.createPageBoxPanel(GuiUtil.createLineBoxPanel(Box.createHorizontalGlue(), new JLabel("Distance"), Box.createHorizontalGlue()), GuiUtil.createLineBoxPanel(new Component[] { Box.createHorizontalGlue(), rbL1, Box.createHorizontalGlue(), rbL2, Box.createHorizontalGlue() }));
-
- JPanel thresh = GuiUtil.createLineBoxPanel(new Component[] { Box.createHorizontalGlue(), boxDist, Box.createHorizontalGlue(), slDistThreshold, Box.createHorizontalGlue(), pmbt, Box.createHorizontalGlue(), lbCurrent, Box.createHorizontalGlue() });
- thresh.setBorder(new TitledBorder("Threshold"));
-
- m1ColorBox = new ColorBox("Choosen colors");
- m1ColorBox.setThreshold(colDefaultDist);
- JPanel box1 = GuiUtil.createLineBoxPanel(new Component[] { Box.createHorizontalGlue(), m1ColorBox, Box.createHorizontalGlue() });
-
- // SVM
-
- m2PosColorBox = new ColorBox("Positive");
- m2NegColorBox = new ColorBox("Negative");
- JPanel box2 = GuiUtil.createLineBoxPanel(new Component[] { Box.createHorizontalGlue(), m2PosColorBox, Box.createHorizontalGlue(), m2NegColorBox, Box.createHorizontalGlue() });
-
- ButtonGroup kern = new ButtonGroup();
- rbKernelLin = new JRadioButton(svm.kernel_type_table[svm_parameter.LINEAR]);
- kern.add(rbKernelLin);
- rbKernelTri = new JRadioButton(svm.kernel_type_table[svm_parameter.TRIANGULAR]);
- kern.add(rbKernelTri);
- rbKernelRBF = new JRadioButton(svm.kernel_type_table[svm_parameter.RBF]);
- kern.add(rbKernelRBF);
- rbKernelTri.setSelected(true);
- JPanel box3 = GuiUtil.createLineBoxPanel(new Component[] { Box.createHorizontalGlue(), rbKernelTri, rbKernelLin, rbKernelRBF, Box.createHorizontalGlue() });
-
- slC = new JSlider(JSlider.HORIZONTAL, -10, 10, 0);
- slC.setMajorTickSpacing(5);
- slC.setMinorTickSpacing(1);
- slC.setSnapToTicks(true);
- slC.setPaintTicks(true);
- slC.setPaintLabels(true);
- slC.addChangeListener(this);
- ComponentUtil.setFixedSize(slC, new Dimension(275, 50));
- valC = new JLabel("C = " + Math.pow(2, slC.getValue()));
- JPanel box4 = GuiUtil.createLineBoxPanel(new Component[] { valC, Box.createHorizontalGlue(), slC });
-
- slGamma = new JSlider(JSlider.HORIZONTAL, -10, 10, 0);
- slGamma.setMajorTickSpacing(5);
- slGamma.setMinorTickSpacing(1);
- slGamma.setSnapToTicks(true);
- slGamma.setPaintTicks(true);
- slGamma.setPaintLabels(true);
- slGamma.addChangeListener(this);
- ComponentUtil.setFixedSize(slGamma, new Dimension(275, 50));
- valGamma = new JLabel("gamma = " + Math.pow(2, slGamma.getValue()));
- JPanel box5 = GuiUtil.createLineBoxPanel(new Component[] { valGamma, Box.createHorizontalGlue(), slGamma });
-
- JPanel box6 = GuiUtil.createPageBoxPanel(new Component[] { box3, box4, box5 });
- box6.setBorder(new TitledBorder("Kernel"));
-
- // TABBED
-
- JPanel tabbed1 = GuiUtil.createPageBoxPanel(new Component[] { Box.createVerticalGlue(), box1, Box.createVerticalGlue(), thresh, Box.createVerticalGlue() });
- JPanel tabbed2 = GuiUtil.createPageBoxPanel(box2, box6);
-
- tabbedPane = new JTabbedPane();
- tabbedPane.addTab(METHOD_1, tabbed1);
- tabbedPane.addTab(METHOD_2, tabbed2);
-
- // BOTTOM
-
- ButtonGroup bgcs = new ButtonGroup();
- rbRGB = new JRadioButton("RGB");
- rbRGB.addActionListener(this);
- bgcs.add(rbRGB);
-
- rbRGB.setSelected(true);
- choosenCS = ColorSpaceTools.RGB;
- rbHSV = new JRadioButton("HSV");
- rbHSV.addActionListener(this);
- bgcs.add(rbHSV);
- rbH1H2H3 = new JRadioButton("H1H2H3");
- rbH1H2H3.addActionListener(this);
- bgcs.add(rbH1H2H3);
-
- cbShow = new JCheckBox("Show");
- cbShow.setSelected(true);
- cbShow.addItemListener(this);
-
- cbAuto = new JCheckBox("Auto");
- cbAuto.addItemListener(this);
-
- btFilter = new JButton("Launch filtering");
- btFilter.addActionListener(this);
- btFilter.setEnabled(false);
- btCancelFilter = new JButton("Cancel filtering");
- btCancelFilter.addActionListener(this);
- btCancelFilter.setEnabled(false);
- btKeepMask = new JButton("As mask");
- btKeepMask.setEnabled(false);
- btKeepMask.addActionListener(this);
- btAsROI = new JButton("As ROI");
- btAsROI.setEnabled(false);
- btAsROI.addActionListener(this);
-
- JPanel buttons1 = GuiUtil.createLineBoxPanel(new Component[] { Box.createHorizontalGlue(), btFilter, btCancelFilter, btKeepMask, btAsROI, Box.createHorizontalGlue() });
- JPanel csp = GuiUtil.createLineBoxPanel(new Component[] { Box.createHorizontalGlue(), rbRGB, rbHSV, rbH1H2H3, cbShow, cbAuto, Box.createHorizontalGlue() });
-
- JPanel notTabbed = GuiUtil.createPageBoxPanel(csp, buttons1);
-
- mainPanel.add(tabbedPane);
- mainPanel.add(notTabbed);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * javax.swing.event.ChangeListener#stateChanged(javax.swing.event.ChangeEvent
- * )
- */
- @Override
- public void stateChanged(ChangeEvent e) {
- JSlider s = (JSlider) e.getSource();
- if (s == null) {
- return;
- }
-
- if (s == slDistThreshold) {
- lbCurrent.setText(Integer.toString(slDistThreshold.getValue()));
- m1ColorBox.setThreshold(slDistThreshold.getValue());
- }
-
- if (s == slC) {
- valC.setText("C = " + Math.pow(2, slC.getValue()));
- m2PosColorBox.fireFilterParametersChangeEvent();
- }
-
- if (s == slGamma) {
- valGamma.setText("gamma = " + Math.pow(2, slGamma.getValue()));
- m2PosColorBox.fireFilterParametersChangeEvent();
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see plugins.nherve.toolbox.plugin.SingletonPlugin#stopInterface()
- */
- @Override
- public void stopInterface() {
- }
+ class ColorBox extends JPanel implements ActionListener {
+
+ /**
+ * The color selector manages and displays the colors picked by the
+ * user.
+ *
+ * @author Nicolas HERVE - nicolas.herve@pasteur.fr
+ */
+ private class ColorSelector extends JPanel implements MouseListener {
+
+ private final ColorBox box;
+
+ /**
+ * Instantiates a new color box.
+ */
+ public ColorSelector(final ColorBox box) {
+ super();
+ this.box = box;
+ addMouseListener(this);
+ setOpaque(true);
+ }
+
+ @Override
+ public Dimension getPreferredSize() {
+ return COL_DIM;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.MouseListener#mouseClicked(java.awt.event.MouseEvent
+ * )
+ */
+ @Override
+ public void mouseClicked(final MouseEvent me) {
+ if (me.getButton() == MouseEvent.BUTTON1) {
+ final int row = (int) Math.floor((double) me.getY() / (double) COL_FULL_BLOCK_SIZE);
+ final int col = (int) Math.floor((double) me.getX() / (double) COL_FULL_BLOCK_SIZE);
+ box.removeColor(row, col);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.MouseListener#mouseEntered(java.awt.event.MouseEvent
+ * )
+ */
+ @Override
+ public void mouseEntered(final MouseEvent e) {
+ // Nothing to do here
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.MouseListener#mouseExited(java.awt.event.MouseEvent
+ * )
+ */
+ @Override
+ public void mouseExited(final MouseEvent e) {
+ // Nothing to do here
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.MouseListener#mousePressed(java.awt.event.MouseEvent
+ * )
+ */
+ @Override
+ public void mousePressed(final MouseEvent e) {
+ // Nothing to do here
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.MouseListener#mouseReleased(java.awt.event.MouseEvent
+ * )
+ */
+ @Override
+ public void mouseReleased(final MouseEvent e) {
+ // Nothing to do here
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.JComponent#paintComponent(java.awt.Graphics)
+ */
+ @Override
+ public void paintComponent(final Graphics g) {
+ g.setColor(getBackground());
+ g.fillRect(0, 0, getWidth(), getHeight());
+
+ for (int row = 0; row < COL_GRID_HEIGHT; row++) {
+ final int y = row * (COL_FULL_BLOCK_SIZE + COL_BLOCK_SPACER);
+ for (int column = 0; column < COL_GRID_WIDTH; column++) {
+ final int x = column * (COL_FULL_BLOCK_SIZE + COL_BLOCK_SPACER);
+ g.setColor(box.getColor(row, column));
+ g.fillRect(x, y, COL_BLOCK_SIZE, COL_BLOCK_SIZE);
+ g.setColor(Color.black);
+ g.drawRect(x, y, COL_BLOCK_SIZE, COL_BLOCK_SIZE);
+ }
+ }
+ }
+ }
+
+ /**
+ * The colors.
+ */
+ private final Color[] colors;
+ /**
+ * The nb colors.
+ */
+ private int nbColors;
+ /**
+ * The threshold.
+ */
+ private int threshold;
+
+ /**
+ * The listeners.
+ */
+ private final ArrayList<ColorBoxListener> listeners;
+
+ private final JButton btInitColors;
+
+ public ColorBox(final String label) {
+ super();
+
+ colors = new Color[COL_GRID_MAXCOLORS];
+ listeners = new ArrayList<>();
+
+ final ColorSelector selector = new ColorSelector(this);
+ btInitColors = new JButton("Clear");
+ btInitColors.setEnabled(false);
+ btInitColors.addActionListener(this);
+
+ final JPanel p1 = GuiUtil.createLineBoxPanel(new JLabel(label), Box.createHorizontalGlue(), btInitColors);
+ final JPanel p2 = GuiUtil.createPageBoxPanel(selector, Box.createVerticalGlue(), p1);
+ add(p2);
+
+ initColors();
+ }
+
+ /**
+ * Adds the color.
+ *
+ * @param c the c
+ */
+ public void addColor(final int[] c) {
+ if (nbColors < COL_GRID_MAXCOLORS) {
+ colors[nbColors] = new Color(c[0], c[1], c[2]);
+ nbColors++;
+ btFilter.setEnabled(true);
+ btKeepMask.setEnabled(true);
+ btAsROI.setEnabled(true);
+ btInitColors.setEnabled(true);
+ repaint();
+ fireFilterParametersChangeEvent();
+ }
+ }
+
+ public Color getColor(final int row, final int col) {
+ return colors[row * COL_GRID_WIDTH + col];
+ }
+
+ /**
+ * Fire cancel filter event.
+ */
+ public void fireCancelFilterEvent() {
+ for (final ColorBoxListener l : listeners) {
+ l.cancelFilter();
+ }
+ }
+
+ /**
+ * Fire display parameters change event.
+ */
+ public void fireDisplayParametersChangeEvent() {
+ for (final ColorBoxListener l : listeners) {
+ l.displayParametersHaveChanged();
+ }
+ }
+
+ /**
+ * Fire filter parameters change event.
+ */
+ public void fireFilterParametersChangeEvent() {
+ for (final ColorBoxListener l : listeners) {
+ l.filterParametersHaveChanged();
+ }
+ }
+
+ /**
+ * Gets the average color.
+ *
+ * @return the average color
+ */
+ public Color getAverageColor() {
+ int r = 0;
+ int g = 0;
+ int b = 0;
+ for (int k = 0; k < nbColors; k++) {
+ r += colors[k].getRed();
+ g += colors[k].getGreen();
+ b += colors[k].getBlue();
+ }
+ r /= nbColors;
+ g /= nbColors;
+ b /= nbColors;
+
+ return new Color(r, g, b);
+ }
+
+ /**
+ * Gets the threshold.
+ *
+ * @return the threshold
+ */
+ public int getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Inits the colors.
+ */
+ public void initColors() {
+ nbColors = 0;
+ for (int i = 0; i < COL_GRID_MAXCOLORS; i++) {
+ colors[i] = getBackground();
+ }
+ repaint();
+ fireFilterParametersChangeEvent();
+ }
+
+ /**
+ * Register.
+ *
+ * @param l the l
+ */
+ public void register(final ColorBoxListener l) {
+ listeners.add(l);
+ }
+
+ /**
+ * Removes the.
+ *
+ * @param l the l
+ */
+ public void remove(final ColorBoxListener l) {
+ listeners.remove(l);
+ }
+
+ public void removeColor(final int row, final int col) {
+ if ((row < COL_GRID_HEIGHT) && (col < COL_GRID_WIDTH)) {
+ final int idx = row * COL_GRID_WIDTH + col;
+ if (idx < nbColors) {
+ for (int c = idx; (c < nbColors) && (c < COL_GRID_MAXCOLORS - 1); c++) {
+ colors[c] = colors[c + 1];
+ }
+ colors[nbColors - 1] = getBackground();
+ nbColors--;
+ if (nbColors == 0) {
+ btInitColors.setEnabled(false);
+ }
+ repaint();
+ fireFilterParametersChangeEvent();
+ }
+ }
+ }
+
+ /**
+ * Sets the threshold.
+ *
+ * @param threshold the new threshold
+ */
+ public void setThreshold(final int threshold) {
+ this.threshold = threshold;
+ fireFilterParametersChangeEvent();
+ }
+
+ @Override
+ public void actionPerformed(final ActionEvent e) {
+ final Object o = e.getSource();
+
+ if (o == null) {
+ return;
+ }
+
+ if (o instanceof JButton) {
+ final JButton b = (JButton) e.getSource();
+ if (b == null) {
+ return;
+ }
+
+ if (b == btInitColors) {
+ initColors();
+ btInitColors.setEnabled(false);
+ }
+ }
+ }
+
+ }
+
+ /**
+ * The Interface ColorBoxListener.
+ *
+ * @author Nicolas HERVE - nicolas.herve@pasteur.fr
+ */
+ interface ColorBoxListener {
+
+ /**
+ * Cancel filter.
+ */
+ void cancelFilter();
+
+ /**
+ * Display parameters have changed.
+ */
+ void displayParametersHaveChanged();
+
+ /**
+ * Filter parameters have changed.
+ */
+ void filterParametersHaveChanged();
+ }
+
+ /**
+ * This Painter is needed to access the colors picked in the image.
+ *
+ * @author Nicolas HERVE - nicolas.herve@pasteur.fr
+ */
+ public class ColorPickerThresholdPainter extends Overlay implements ColorBoxListener {
+
+ /**
+ * The mask.
+ */
+ private Mask mask;
+
+ /**
+ * The sequence.
+ */
+ private Sequence sequence;
+
+ /**
+ * Instantiates a new color picker threshold painter.
+ */
+ public ColorPickerThresholdPainter() {
+ super("ColorPickerThreshold");
+
+ setMask(null);
+ setSequence(null);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * plugins.nherve.colorpickerthreshold.ColorPickerThreshold.ColorBoxListener
+ * #cancelFilter()
+ */
+ @Override
+ public void cancelFilter() {
+ setMask(null);
+ displayParametersHaveChanged();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * plugins.nherve.colorpickerthreshold.ColorPickerThreshold.ColorBoxListener
+ * #displayParametersHaveChanged()
+ */
+ @Override
+ public void displayParametersHaveChanged() {
+ getSequence().overlayChanged((Overlay) null);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * plugins.nherve.colorpickerthreshold.ColorPickerThreshold.ColorBoxListener
+ * #filterParametersHaveChanged()
+ */
+ @Override
+ public void filterParametersHaveChanged() {
+ if (cbAuto.isSelected()) {
+ try {
+ doFilter(this);
+ }
+ catch (final SignatureException e1) {
+ Algorithm.err(e1);
+ }
+ }
+ }
+
+ /**
+ * Gets the clicked color.
+ *
+ * @param pt the pt
+ * @return the clicked color
+ * @throws SignatureException the signature exception
+ */
+ private int[] getClickedColor(final Point pt) throws SignatureException {
+ final IcyBufferedImage image = getCurrentSequence().getFirstImage();
+ int[] c = null;
+ if ((image != null) && image.isInside(pt)) {
+ final int x = (int) pt.getX();
+ final int y = (int) pt.getY();
+ c = ColorSpaceTools.getColorComponentsI_0_255(image, ColorSpaceTools.RGB, x, y);
+ }
+
+ return c;
+ }
+
+ /**
+ * Gets the mask.
+ *
+ * @return the mask
+ */
+ public Mask getMask() {
+ return mask;
+ }
+
+ /**
+ * Gets the sequence.
+ *
+ * @return the sequence
+ */
+ public Sequence getSequence() {
+ return sequence;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see icy.painter.Painter#mouseClick(java.awt.event.MouseEvent,
+ * java.awt.geom.Point2D, icy.canvas.IcyCanvas)
+ */
+ @Override
+ public void mouseClick(final MouseEvent e, final Point5D.Double imagePoint, final IcyCanvas canvas) {
+ final int comp = tabbedPane.getSelectedIndex();
+ try {
+ if (comp == 0) {
+ if (e.getButton() == MouseEvent.BUTTON1) {
+ final int[] c = getClickedColor(TypeUtil.toPoint(imagePoint.toPoint2D()));
+ if (c != null) {
+ m1ColorBox.addColor(c);
+ }
+ }
+ }
+ else if (comp == 1) {
+ if (e.getButton() == MouseEvent.BUTTON1) {
+ final int[] c = getClickedColor(TypeUtil.toPoint(imagePoint.toPoint2D()));
+ if (c != null) {
+ m2PosColorBox.addColor(c);
+ }
+ }
+ else if ((e.getButton() == MouseEvent.BUTTON2) || (e.getButton() == MouseEvent.BUTTON3)) {
+ final int[] c = getClickedColor(TypeUtil.toPoint(imagePoint.toPoint2D()));
+ if (c != null) {
+ m2NegColorBox.addColor(c);
+ }
+ }
+ }
+
+ }
+ catch (final SignatureException ex) {
+ Algorithm.err(ex);
+ }
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see icy.painter.Painter#paint(java.awt.Graphics2D,
+ * icy.sequence.Sequence, icy.canvas.IcyCanvas)
+ */
+ @Override
+ public void paint(final Graphics2D g, final Sequence sequence, final IcyCanvas canvas) {
+ if ((getMask() != null) && (cbShow.isSelected())) {
+ getMask().paint(g);
+ }
+ }
+
+ /**
+ * Sets the mask.
+ *
+ * @param mask the new mask
+ */
+ public void setMask(final Mask mask) {
+ this.mask = mask;
+ }
+
+ /**
+ * Sets the sequence.
+ *
+ * @param sequence the new sequence
+ */
+ public void setSequence(final Sequence sequence) {
+ this.sequence = sequence;
+ }
+
+ }
+
+ private final static int COL_BLOCK_BORDER = 1;
+
+ private final static int COL_BLOCK_SPACER = 1;
+
+ private final static int COL_BLOCK_SIZE = 25;
+
+ /**
+ * The Constant COL_GRID_HEIGHT.
+ */
+ private final static int COL_GRID_HEIGHT = 3;
+
+ /**
+ * The Constant COL_GRID_WIDTH.
+ */
+ private final static int COL_GRID_WIDTH = 8;
+
+ private final static int COL_FULL_BLOCK_SIZE = COL_BLOCK_SIZE + 2 * COL_BLOCK_BORDER;
+ private final static Dimension COL_DIM = new Dimension(COL_GRID_WIDTH * (COL_FULL_BLOCK_SIZE + COL_BLOCK_SPACER) - 1, COL_GRID_HEIGHT * (COL_FULL_BLOCK_SIZE + COL_BLOCK_SPACER) - 1);
+
+ /**
+ * The Constant COL_GRID_MAXCOLORS.
+ */
+ private final static int COL_GRID_MAXCOLORS = COL_GRID_HEIGHT * COL_GRID_WIDTH;
+
+ /**
+ * The Constant METHOD_1.
+ */
+ private final static String METHOD_1 = "KNN";
+
+ /**
+ * The Constant METHOD_2.
+ */
+ private final static String METHOD_2 = "SVM";
+
+ /**
+ * The bt cancel filter.
+ */
+ private JButton btCancelFilter;
+
+ /**
+ * The bt filter.
+ */
+ private JButton btFilter;
+
+ /**
+ * The bt keep mask.
+ */
+ private JButton btKeepMask;
+
+ /**
+ * The bt as roi.
+ */
+ private JButton btAsROI;
+
+ /**
+ * The bt minus.
+ */
+ private JButton btMinus;
+
+ /**
+ * The bt plus.
+ */
+ private JButton btPlus;
+
+ /**
+ * The col default dist.
+ */
+ private int colDefaultDist;
+
+ /**
+ * The col max dist.
+ */
+ private int colMaxDist;
+
+ /**
+ * The m1 color box.
+ */
+ private ColorBox m1ColorBox;
+
+ /**
+ * The m2 pos color box.
+ */
+ private ColorBox m2PosColorBox;
+
+ /**
+ * The m2 neg color box.
+ */
+ private ColorBox m2NegColorBox;
+
+ /**
+ * The lb current.
+ */
+ private JLabel lbCurrent;
+
+ /**
+ * The rb rgb.
+ */
+ private JRadioButton rbRGB;
+
+ /**
+ * The rb hsv.
+ */
+ private JRadioButton rbHSV;
+
+ /**
+ * The rb h1 h2 h3.
+ */
+ private JRadioButton rbH1H2H3;
+
+ /**
+ * The rb l1.
+ */
+ private JRadioButton rbL1;
+
+ /**
+ * The rb l2.
+ */
+ private JRadioButton rbL2;
+
+ /**
+ * The rb kernel lin.
+ */
+ private JRadioButton rbKernelLin;
+
+ /**
+ * The rb kernel rbf.
+ */
+ private JRadioButton rbKernelRBF;
+
+ /**
+ * The rb kernel tri.
+ */
+ private JRadioButton rbKernelTri;
+
+ /**
+ * The sl c.
+ */
+ private JSlider slC;
+
+ /**
+ * The sl gamma.
+ */
+ private JSlider slGamma;
+
+ /**
+ * The val c.
+ */
+ private JLabel valC;
+
+ /**
+ * The val gamma.
+ */
+ private JLabel valGamma;
+
+ /**
+ * The distance.
+ */
+ private ColorDistance distance;
+
+ /**
+ * The choosen cs.
+ */
+ private int choosenCS;
+
+ /**
+ * The sl dist threshold.
+ */
+ private JSlider slDistThreshold;
+
+ /**
+ * The sl maj tick.
+ */
+ private int slMajTick;
+
+ /**
+ * The sl min tick.
+ */
+ private int slMinTick;
+
+ /**
+ * The cb show.
+ */
+ private JCheckBox cbShow;
+
+ /**
+ * The cb auto.
+ */
+ private JCheckBox cbAuto;
+
+ /**
+ * The tabbed pane.
+ */
+ private JTabbedPane tabbedPane;
+
+ /**
+ * Instantiates a new color picker threshold.
+ */
+ public ColorPickerThreshold() {
+ super();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
+ */
+ @Override
+ public void actionPerformed(final ActionEvent e) {
+ final Object o = e.getSource();
+
+ if (o == null) {
+ return;
+ }
+
+ if (o instanceof JButton) {
+ final JButton b = (JButton) e.getSource();
+ if (b == null) {
+ return;
+ }
+
+ if (b == btFilter) {
+ if (hasCurrentSequence()) {
+ try {
+ doFilter(getCurrentSequencePainter());
+ }
+ catch (final SignatureException e1) {
+ Algorithm.err(e1);
+ }
+ }
+
+ return;
+ }
+
+ if (b == btCancelFilter) {
+ if (cbAuto.isSelected()) {
+ m1ColorBox.fireCancelFilterEvent();
+ }
+ else if (hasCurrentSequence()) {
+ getCurrentSequencePainter().setMask(null);
+ getCurrentSequence().overlayChanged((Overlay) null);
+ }
+ return;
+ }
+
+ if (b == btPlus) {
+ if (slDistThreshold.getValue() < slDistThreshold.getMaximum()) {
+ slDistThreshold.setValue(slDistThreshold.getValue() + 1);
+ }
+ return;
+ }
+
+ if (b == btMinus) {
+ if (slDistThreshold.getValue() > slDistThreshold.getMinimum()) {
+ slDistThreshold.setValue(slDistThreshold.getValue() - 1);
+ }
+ return;
+ }
+
+ if (b == btKeepMask) {
+ if (hasCurrentSequence()) {
+ final Sequence currentSequence = getCurrentSequence();
+ try {
+ final Mask m = doFilter(getCurrentSequencePainter());
+ if (m != null) {
+ final SwimmingObject result = new SwimmingObject(m);
+ Icy.getMainInterface().getSwimmingPool().add(result);
+ }
+ }
+ catch (final SignatureException e1) {
+ Algorithm.err(e1);
+ }
+ currentSequence.dataChanged();
+ }
+ return;
+ }
+
+ if (b == btAsROI) {
+ if (hasCurrentSequence()) {
+ final Sequence currentSequence = getCurrentSequence();
+ try {
+ final Mask m = doFilter(getCurrentSequencePainter());
+ if (m != null) {
+ final ROI2DArea a = m.asROI2DArea(currentSequence);
+ a.setName("From " + getName());
+ }
+ }
+ catch (final SignatureException e1) {
+ Algorithm.err(e1);
+ }
+ currentSequence.dataChanged();
+ }
+ return;
+ }
+ }
+
+ if (o instanceof JRadioButton) {
+
+ final JRadioButton b = (JRadioButton) e.getSource();
+ if (b == rbRGB) {
+ choosenCS = ColorSpaceTools.RGB;
+ }
+ if (b == rbHSV) {
+ choosenCS = ColorSpaceTools.RGB_TO_HSV;
+ }
+ if (b == rbH1H2H3) {
+ choosenCS = ColorSpaceTools.RGB_TO_H1H2H3;
+ }
+ if ((b == rbL1) || (b == rbL2)) {
+ final double currentPct = (double) slDistThreshold.getValue() / (double) slDistThreshold.getMaximum();
+
+ if (b == rbL1) {
+ setDistance(new L1ColorDistance());
+ }
+ if (b == rbL2) {
+ setDistance(new L2ColorDistance());
+ }
+
+ slDistThreshold.setMaximum(colMaxDist);
+ final int currentValue = (int) (currentPct * slDistThreshold.getMaximum());
+ slDistThreshold.setValue(currentValue);
+ m1ColorBox.setThreshold(currentValue);
+ slDistThreshold.setMajorTickSpacing(slMajTick);
+ slDistThreshold.setMinorTickSpacing(slMinTick);
+ }
+ if (hasCurrentSequence() && cbAuto.isSelected()) {
+ try {
+ doFilter(getCurrentSequencePainter());
+ }
+ catch (final SignatureException e1) {
+ Algorithm.err(e1);
+ }
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see plugins.nherve.toolbox.plugin.PainterFactory#createNewPainter()
+ */
+ @Override
+ public ColorPickerThresholdPainter createNewPainter() {
+ final ColorPickerThresholdPainter painter = new ColorPickerThresholdPainter();
+ final Sequence currentSequence = getCurrentSequence();
+ painter.setSequence(currentSequence);
+ m1ColorBox.register(painter);
+ m2PosColorBox.register(painter);
+ m2NegColorBox.register(painter);
+ try {
+ doFilter(painter);
+ }
+ catch (final SignatureException e1) {
+ Algorithm.err(e1);
+ }
+ return painter;
+ }
+
+ /**
+ * Do filter.
+ *
+ * @param painter the painter
+ * @return the mask
+ * @throws SignatureException the signature exception
+ */
+ private Mask doFilter(final ColorPickerThresholdPainter painter) throws SignatureException {
+ final Sequence currentSequence = painter.getSequence();
+ final IcyBufferedImage currentImage = currentSequence.getFirstImage();
+ Mask m = null;
+ final int comp = tabbedPane.getSelectedIndex();
+ try {
+ if (comp == 0) {
+ m = filter1(m1ColorBox, currentImage);
+ m.setLabel(getName() + " " + METHOD_1);
+ }
+ else if (comp == 1) {
+ m = filter2(m2PosColorBox, m2NegColorBox, currentImage);
+ m.setLabel(getName() + " " + METHOD_2);
+ }
+ }
+ catch (final MaskException e) {
+ // ignore
+ }
+ painter.setMask(m);
+ currentSequence.overlayChanged((Overlay) null);
+ return m;
+ }
+
+ /**
+ * Filter1.
+ *
+ * @param box the box
+ * @param image the image
+ * @return the mask
+ * @throws MaskException the mask exception
+ */
+ private Mask filter1(final ColorBox box, final IcyBufferedImage image) throws MaskException {
+ if (box.nbColors == 0) {
+ throw new MaskException("No color selected, filtering aborted");
+ }
+
+ // CPUMonitor moni = new CPUMonitor();
+ // moni.start();
+
+ // System.out.println("starting filtering");
+ // Raster raster = image.getRaster();
+ final Mask m = new Mask(image.getWidth(), image.getHeight(), false);
+ final BinaryIcyBufferedImage bin = m.getBinaryData();
+
+ final ArrayList<double[]> csColors = new ArrayList<>();
+ for (int k = 0; k < box.nbColors; k++) {
+ csColors.add(ColorSpaceTools.getColorComponentsD_0_255(choosenCS, box.colors[k].getRed(), box.colors[k].getGreen(), box.colors[k].getBlue()));
+ }
+
+ final byte[] raw = bin.getRawData();
+ int idx = 0;
+ for (int j = 0; j < image.getHeight(); j++) {
+ for (int i = 0; i < image.getWidth(); i++) {
+ final double[] cc = ColorSpaceTools.getColorComponentsD_0_255(image, choosenCS, i, j);
+ boolean keep = false;
+ for (int k = 0; k < box.nbColors; k++) {
+ if (distance.computeDistance(cc, csColors.get(k)) < box.getThreshold()) {
+ keep = true;
+ break;
+ }
+ }
+ if (keep) {
+ raw[idx] = BinaryIcyBufferedImage.TRUE;
+ }
+ idx++;
+ }
+ }
+ final Color c = box.getAverageColor();
+ final int ir = 255 - c.getRed();
+ final int ig = 255 - c.getGreen();
+ final int ib = 255 - c.getBlue();
+ m.setColor(new Color(ir, ig, ib));
+ m.setOpacity(1f);
+
+ // moni.stop();
+ // System.out.println("Filtering done (" + getThreshold() + ") : " +
+ // moni.getUserElapsedTimeMilli() + " ms");
+ return m;
+ }
+
+ /**
+ * Filter2.
+ *
+ * @param boxP the box p
+ * @param boxN the box n
+ * @param image the image
+ * @return the mask
+ * @throws MaskException the mask exception
+ * @throws SignatureException the signature exception
+ */
+ private Mask filter2(final ColorBox boxP, final ColorBox boxN, final IcyBufferedImage image) throws MaskException, SignatureException {
+ if (boxP.nbColors == 0) {
+ throw new MaskException("No positive color selected, filtering aborted");
+ }
+ if (boxN.nbColors == 0) {
+ throw new MaskException("No negative color selected, filtering aborted");
+ }
+
+ // Raster raster = image.getRaster();
+
+ final VectorSignature[] pos = new VectorSignature[boxP.nbColors];
+ final VectorSignature[] neg = new VectorSignature[boxN.nbColors];
+
+ for (int i = 0; i < boxP.nbColors; i++) {
+ final double[] ddd = ColorSpaceTools.getColorComponentsD_0_1(choosenCS, boxP.colors[i].getRed(), boxP.colors[i].getGreen(), boxP.colors[i].getBlue());
+ final DenseVectorSignature s = new DenseVectorSignature(ColorSpaceTools.NB_COLOR_CHANNELS);
+ for (int d = 0; d < ColorSpaceTools.NB_COLOR_CHANNELS; d++) {
+ s.set(d, ddd[d]);
+ }
+ pos[i] = s;
+ }
+ for (int i = 0; i < boxN.nbColors; i++) {
+ final double[] ddd = ColorSpaceTools.getColorComponentsD_0_1(choosenCS, boxN.colors[i].getRed(), boxN.colors[i].getGreen(), boxN.colors[i].getBlue());
+ final DenseVectorSignature s = new DenseVectorSignature(ColorSpaceTools.NB_COLOR_CHANNELS);
+ for (int d = 0; d < ColorSpaceTools.NB_COLOR_CHANNELS; d++) {
+ s.set(d, ddd[d]);
+ }
+ neg[i] = s;
+ }
+
+ final SVMClassifier svm = new SVMClassifier();
+ svm.createProblem(pos, neg);
+
+ svm.setC(Math.pow(2, slC.getValue()));
+ svm.setGamma(Math.pow(2, slGamma.getValue()));
+
+ if (rbKernelLin.isSelected()) {
+ svm.setKernel(svm_parameter.LINEAR);
+ }
+ else if (rbKernelTri.isSelected()) {
+ svm.setKernel(svm_parameter.TRIANGULAR);
+ }
+ else if (rbKernelRBF.isSelected()) {
+ svm.setKernel(svm_parameter.RBF);
+ }
+
+ svm.learnModel();
+
+ final Mask m = new Mask(image.getWidth(), image.getHeight(), false);
+ final BinaryIcyBufferedImage bin = m.getBinaryData();
+ final SegmentableIcyBufferedImage simg = new SegmentableIcyBufferedImage(image);
+
+ final ColorPixel col = new ColorPixel(false);
+ col.setColorSpace(choosenCS);
+
+ final byte[] raw = bin.getRawData();
+ int idx = 0;
+ for (int y = 0; y < image.getHeight(); y++) {
+ for (int x = 0; x < image.getWidth(); x++) {
+ final IcyPixel pix = new IcyPixel(x, y);
+ final VectorSignature vs = (VectorSignature) col.extractLocalSignature(simg, pix);
+ if (svm.predict(vs) > 0) {
+ raw[idx] = BinaryIcyBufferedImage.TRUE;
+ }
+ idx++;
+ }
+ }
+
+ final Color c = m.getAverageColor(image);
+ final int ir = 255 - c.getRed();
+ final int ig = 255 - c.getGreen();
+ final int ib = 255 - c.getBlue();
+ m.setColor(new Color(ir, ig, ib));
+ m.setOpacity(1f);
+
+ return m;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see plugins.nherve.toolbox.plugin.PainterManager#getPainterName()
+ */
+ @Override
+ public String getPainterName() {
+ return ColorPickerThresholdPainter.class.getName();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.ItemListener#itemStateChanged(java.awt.event.ItemEvent)
+ */
+ @Override
+ public void itemStateChanged(final ItemEvent e) {
+ final Object o = e.getSource();
+
+ if (o == null) {
+ return;
+ }
+
+ if (o instanceof JCheckBox) {
+ final JCheckBox c = (JCheckBox) e.getSource();
+
+ final int comp = tabbedPane.getSelectedIndex();
+ ColorBox bx = null;
+ if (comp == 0) {
+ bx = m1ColorBox;
+ }
+ else if (comp == 1) {
+ bx = m2PosColorBox;
+ }
+
+ if (c == cbShow) {
+ assert bx != null;
+ bx.fireDisplayParametersChangeEvent();
+ }
+
+ if (c == cbAuto) {
+ if (cbAuto.isSelected()) {
+ assert bx != null;
+ bx.fireFilterParametersChangeEvent();
+ }
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see plugins.nherve.toolbox.plugin.PainterManagerSingletonPlugin#
+ * sequenceHasChangedAfterSettingPainter()
+ */
+ @Override
+ public void sequenceHasChangedAfterSettingPainter() {
+ if (hasCurrentSequence()) {
+ final Sequence currentSequence = getCurrentSequence();
+ setTitle(getName() + " - " + currentSequence.getName());
+ btFilter.setEnabled(true);
+ btKeepMask.setEnabled(true);
+ btAsROI.setEnabled(true);
+ btCancelFilter.setEnabled(true);
+ }
+ else {
+ setTitle(getName());
+ btFilter.setEnabled(false);
+ btKeepMask.setEnabled(false);
+ btAsROI.setEnabled(false);
+ btCancelFilter.setEnabled(false);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see plugins.nherve.toolbox.plugin.PainterManagerSingletonPlugin#
+ * sequenceHasChangedBeforeSettingPainter()
+ */
+ @Override
+ public void sequenceHasChangedBeforeSettingPainter() {
+ // Nothing to do here
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see plugins.nherve.toolbox.plugin.SingletonPlugin#sequenceWillChange()
+ */
+ @Override
+ public void sequenceWillChange() {
+ // Nothing to do here
+ }
+
+ /**
+ * Sets the distance.
+ *
+ * @param distance the new distance
+ */
+ public void setDistance(final ColorDistance distance) {
+ this.distance = distance;
+
+ colMaxDist = (int) Math.floor(distance.getMaxDistance());
+ slMajTick = (int) Math.ceil((double) colMaxDist / 100.0) * 20;
+ slMinTick = (int) Math.ceil((double) slMajTick / 5.0);
+ colMaxDist = (int) Math.ceil((double) colMaxDist / (double) slMajTick) * slMajTick;
+ colDefaultDist = (int) Math.ceil((double) colMaxDist / 10.0);
+ }
+
+ @Override
+ public Dimension getDefaultFrameDimension() {
+ return null;
+ }
+
+ @Override
+ public void fillInterface(final JPanel mainPanel) {
+ // KNN
+ final ButtonGroup bgd = new ButtonGroup();
+ rbL1 = new JRadioButton("L1");
+ rbL1.addActionListener(this);
+ bgd.add(rbL1);
+ rbL2 = new JRadioButton("L2");
+ rbL2.addActionListener(this);
+ bgd.add(rbL2);
+ rbL1.setSelected(true);
+ setDistance(new L1ColorDistance());
+
+ slDistThreshold = new JSlider(JSlider.HORIZONTAL, 0, colMaxDist, colDefaultDist);
+ slDistThreshold.addChangeListener(this);
+ slDistThreshold.setMajorTickSpacing(slMajTick);
+ slDistThreshold.setMinorTickSpacing(slMinTick);
+ slDistThreshold.setPaintTicks(true);
+ slDistThreshold.setPaintLabels(true);
+
+ btPlus = new JButton(NherveToolbox.plusIcon);
+ btPlus.addActionListener(this);
+ btMinus = new JButton(NherveToolbox.minusIcon);
+ btMinus.addActionListener(this);
+ final JPanel pmbt = GuiUtil.createPageBoxPanel(btPlus, btMinus);
+
+ lbCurrent = new JLabel(Integer.toString(slDistThreshold.getValue()));
+
+ final JPanel boxDist = GuiUtil.createPageBoxPanel(GuiUtil.createLineBoxPanel(Box.createHorizontalGlue(), new JLabel("Distance"), Box.createHorizontalGlue()), GuiUtil.createLineBoxPanel(Box.createHorizontalGlue(), rbL1, Box.createHorizontalGlue(), rbL2, Box.createHorizontalGlue()));
+
+ final JPanel thresh = GuiUtil.createLineBoxPanel(Box.createHorizontalGlue(), boxDist, Box.createHorizontalGlue(), slDistThreshold, Box.createHorizontalGlue(), pmbt, Box.createHorizontalGlue(), lbCurrent, Box.createHorizontalGlue());
+ thresh.setBorder(new TitledBorder("Threshold"));
+
+ m1ColorBox = new ColorBox("Choosen colors");
+ m1ColorBox.setThreshold(colDefaultDist);
+ final JPanel box1 = GuiUtil.createLineBoxPanel(Box.createHorizontalGlue(), m1ColorBox, Box.createHorizontalGlue());
+
+ // SVM
+
+ m2PosColorBox = new ColorBox("Positive");
+ m2NegColorBox = new ColorBox("Negative");
+ final JPanel box2 = GuiUtil.createLineBoxPanel(Box.createHorizontalGlue(), m2PosColorBox, Box.createHorizontalGlue(), m2NegColorBox, Box.createHorizontalGlue());
+
+ final ButtonGroup kern = new ButtonGroup();
+ rbKernelLin = new JRadioButton(svm.kernel_type_table[svm_parameter.LINEAR]);
+ kern.add(rbKernelLin);
+ rbKernelTri = new JRadioButton(svm.kernel_type_table[svm_parameter.TRIANGULAR]);
+ kern.add(rbKernelTri);
+ rbKernelRBF = new JRadioButton(svm.kernel_type_table[svm_parameter.RBF]);
+ kern.add(rbKernelRBF);
+ rbKernelTri.setSelected(true);
+ final JPanel box3 = GuiUtil.createLineBoxPanel(Box.createHorizontalGlue(), rbKernelTri, rbKernelLin, rbKernelRBF, Box.createHorizontalGlue());
+
+ slC = new JSlider(JSlider.HORIZONTAL, -10, 10, 0);
+ slC.setMajorTickSpacing(5);
+ slC.setMinorTickSpacing(1);
+ slC.setSnapToTicks(true);
+ slC.setPaintTicks(true);
+ slC.setPaintLabels(true);
+ slC.addChangeListener(this);
+ ComponentUtil.setFixedSize(slC, new Dimension(275, 50));
+ valC = new JLabel("C = " + Math.pow(2, slC.getValue()));
+ final JPanel box4 = GuiUtil.createLineBoxPanel(valC, Box.createHorizontalGlue(), slC);
+
+ slGamma = new JSlider(JSlider.HORIZONTAL, -10, 10, 0);
+ slGamma.setMajorTickSpacing(5);
+ slGamma.setMinorTickSpacing(1);
+ slGamma.setSnapToTicks(true);
+ slGamma.setPaintTicks(true);
+ slGamma.setPaintLabels(true);
+ slGamma.addChangeListener(this);
+ ComponentUtil.setFixedSize(slGamma, new Dimension(275, 50));
+ valGamma = new JLabel("gamma = " + Math.pow(2, slGamma.getValue()));
+ final JPanel box5 = GuiUtil.createLineBoxPanel(valGamma, Box.createHorizontalGlue(), slGamma);
+
+ final JPanel box6 = GuiUtil.createPageBoxPanel(box3, box4, box5);
+ box6.setBorder(new TitledBorder("Kernel"));
+
+ // TABBED
+
+ final JPanel tabbed1 = GuiUtil.createPageBoxPanel(Box.createVerticalGlue(), box1, Box.createVerticalGlue(), thresh, Box.createVerticalGlue());
+ final JPanel tabbed2 = GuiUtil.createPageBoxPanel(box2, box6);
+
+ tabbedPane = new JTabbedPane();
+ tabbedPane.addTab(METHOD_1, tabbed1);
+ tabbedPane.addTab(METHOD_2, tabbed2);
+
+ // BOTTOM
+
+ final ButtonGroup bgcs = new ButtonGroup();
+ rbRGB = new JRadioButton("RGB");
+ rbRGB.addActionListener(this);
+ bgcs.add(rbRGB);
+
+ rbRGB.setSelected(true);
+ choosenCS = ColorSpaceTools.RGB;
+ rbHSV = new JRadioButton("HSV");
+ rbHSV.addActionListener(this);
+ bgcs.add(rbHSV);
+ rbH1H2H3 = new JRadioButton("H1H2H3");
+ rbH1H2H3.addActionListener(this);
+ bgcs.add(rbH1H2H3);
+
+ cbShow = new JCheckBox("Show");
+ cbShow.setSelected(true);
+ cbShow.addItemListener(this);
+
+ cbAuto = new JCheckBox("Auto");
+ cbAuto.addItemListener(this);
+
+ btFilter = new JButton("Launch filtering");
+ btFilter.addActionListener(this);
+ btFilter.setEnabled(false);
+ btCancelFilter = new JButton("Cancel filtering");
+ btCancelFilter.addActionListener(this);
+ btCancelFilter.setEnabled(false);
+ btKeepMask = new JButton("As mask");
+ btKeepMask.setEnabled(false);
+ btKeepMask.addActionListener(this);
+ btAsROI = new JButton("As ROI");
+ btAsROI.setEnabled(false);
+ btAsROI.addActionListener(this);
+
+ final JPanel buttons1 = GuiUtil.createLineBoxPanel(Box.createHorizontalGlue(), btFilter, btCancelFilter, btKeepMask, btAsROI, Box.createHorizontalGlue());
+ final JPanel csp = GuiUtil.createLineBoxPanel(Box.createHorizontalGlue(), rbRGB, rbHSV, rbH1H2H3, cbShow, cbAuto, Box.createHorizontalGlue());
+
+ final JPanel notTabbed = GuiUtil.createPageBoxPanel(csp, buttons1);
+
+ mainPanel.add(tabbedPane);
+ mainPanel.add(notTabbed);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * javax.swing.event.ChangeListener#stateChanged(javax.swing.event.ChangeEvent
+ * )
+ */
+ @Override
+ public void stateChanged(final ChangeEvent e) {
+ final JSlider s = (JSlider) e.getSource();
+ if (s == null) {
+ return;
+ }
+
+ if (s == slDistThreshold) {
+ lbCurrent.setText(Integer.toString(slDistThreshold.getValue()));
+ m1ColorBox.setThreshold(slDistThreshold.getValue());
+ }
+
+ if (s == slC) {
+ valC.setText("C = " + Math.pow(2, slC.getValue()));
+ m2PosColorBox.fireFilterParametersChangeEvent();
+ }
+
+ if (s == slGamma) {
+ valGamma.setText("gamma = " + Math.pow(2, slGamma.getValue()));
+ m2PosColorBox.fireFilterParametersChangeEvent();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see plugins.nherve.toolbox.plugin.SingletonPlugin#stopInterface()
+ */
+ @Override
+ public void stopInterface() {
+ }
}