diff --git a/.gitignore b/.gitignore
index 159dee38dba1df3c6af2c3793586d29a79dfa29e..57f16fb67c1b1589981416b323d7a9debc728665 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,11 +1,41 @@
-.idea/
-.settings/
-build/
+/build*
+/workspace
+setting.xml
+release/
target/
-bin/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
*.iml
-*.jar
+*.ipr
+
+### Eclipse ###
+.apt_generated
.classpath
+.factorypath
.project
-export.jardesc
+.settings
+.springBeans
+.sts4-cache
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+
+### Mac OS ###
**/.DS_Store
+Icon?
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 99e28706964b287f0d9b4d1af0e0f10bdf5ca574..176698256dd00ef9e08d785ef7eeb59e16c58631 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,11 +7,11 @@
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
- <version>2.2.0</version>
+ <version>3.0.0-a.1</version>
</parent>
<artifactId>color-picker-threshold</artifactId>
- <version>2.0.0</version>
+ <version>2.0.0-a.1</version>
<name>Color Picker Threshold</name>
<description>
@@ -21,16 +21,24 @@
</description>
<dependencies>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>kernel-extensions</artifactId>
+ </dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>nherve-toolbox</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>vecmath</artifactId>
+ </dependency>
</dependencies>
<repositories>
<repository>
<id>icy</id>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
</repository>
</repositories>
</project>
\ No newline at end of file
diff --git a/src/main/java/plugins/nherve/colorpickerthreshold/ColorPickerThreshold.java b/src/main/java/plugins/nherve/colorpickerthreshold/ColorPickerThreshold.java
index 5f0a92d8a944a697a41e4eaa081e92adcbe472f9..dfea999443ea705563d565358415d8adf759bd12 100644
--- a/src/main/java/plugins/nherve/colorpickerthreshold/ColorPickerThreshold.java
+++ b/src/main/java/plugins/nherve/colorpickerthreshold/ColorPickerThreshold.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,17 +18,21 @@
package plugins.nherve.colorpickerthreshold;
-import icy.canvas.IcyCanvas;
-import icy.gui.util.ComponentUtil;
-import icy.gui.util.GuiUtil;
-import icy.image.IcyBufferedImage;
-import icy.main.Icy;
-import icy.painter.Overlay;
-import icy.sequence.Sequence;
-import icy.swimmingPool.SwimmingObject;
-import icy.type.TypeUtil;
-import icy.type.point.Point5D;
-import plugins.kernel.roi.roi2d.ROI2DArea;
+import org.bioimageanalysis.extension.kernel.roi.roi2d.ROI2DArea;
+import org.bioimageanalysis.icy.Icy;
+import org.bioimageanalysis.icy.common.geom.point.Point5D;
+import org.bioimageanalysis.icy.common.type.TypeUtil;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.gui.GuiUtil;
+import org.bioimageanalysis.icy.gui.canvas.IcyCanvas;
+import org.bioimageanalysis.icy.gui.component.ComponentUtil;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
+import org.bioimageanalysis.icy.model.overlay.Overlay;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.swimmingPool.SwimmingObject;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import plugins.nherve.toolbox.Algorithm;
import plugins.nherve.toolbox.NherveToolbox;
import plugins.nherve.toolbox.image.BinaryIcyBufferedImage;
@@ -62,10 +66,10 @@ import java.util.ArrayList;
*
* @author Nicolas HERVE - nicolas.herve@pasteur.fr
*/
+@IcyPluginName("Color Picker Threshold")
+@IcyPluginIcon(path = "/ColorPickerThreshold_icon.png")
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.
@@ -73,7 +77,6 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* @author Nicolas HERVE - nicolas.herve@pasteur.fr
*/
private class ColorSelector extends JPanel implements MouseListener {
-
private final ColorBox box;
/**
@@ -86,6 +89,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
setOpaque(true);
}
+ @Contract(pure = true)
@Override
public Dimension getPreferredSize() {
return COL_DIM;
@@ -99,7 +103,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* )
*/
@Override
- public void mouseClicked(final MouseEvent me) {
+ public void mouseClicked(final @NotNull 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);
@@ -114,6 +118,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* java.awt.event.MouseListener#mouseEntered(java.awt.event.MouseEvent
* )
*/
+ @Contract(pure = true)
@Override
public void mouseEntered(final MouseEvent e) {
// Nothing to do here
@@ -126,6 +131,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* java.awt.event.MouseListener#mouseExited(java.awt.event.MouseEvent
* )
*/
+ @Contract(pure = true)
@Override
public void mouseExited(final MouseEvent e) {
// Nothing to do here
@@ -138,6 +144,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* java.awt.event.MouseListener#mousePressed(java.awt.event.MouseEvent
* )
*/
+ @Contract(pure = true)
@Override
public void mousePressed(final MouseEvent e) {
// Nothing to do here
@@ -150,6 +157,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* java.awt.event.MouseListener#mouseReleased(java.awt.event.MouseEvent
* )
*/
+ @Contract(pure = true)
@Override
public void mouseReleased(final MouseEvent e) {
// Nothing to do here
@@ -161,7 +169,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* @see javax.swing.JComponent#paintComponent(java.awt.Graphics)
*/
@Override
- public void paintComponent(final Graphics g) {
+ public void paintComponent(final @NotNull Graphics g) {
g.setColor(getBackground());
g.fillRect(0, 0, getWidth(), getHeight());
@@ -354,7 +362,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
}
@Override
- public void actionPerformed(final ActionEvent e) {
+ public void actionPerformed(final @NotNull ActionEvent e) {
final Object o = e.getSource();
if (o == null) {
@@ -373,7 +381,6 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
}
}
}
-
}
/**
@@ -382,7 +389,6 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* @author Nicolas HERVE - nicolas.herve@pasteur.fr
*/
interface ColorBoxListener {
-
/**
* Cancel filter.
*/
@@ -405,7 +411,6 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* @author Nicolas HERVE - nicolas.herve@pasteur.fr
*/
public class ColorPickerThresholdPainter extends Overlay implements ColorBoxListener {
-
/**
* The mask.
*/
@@ -577,13 +582,10 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
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;
/**
@@ -788,7 +790,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
*/
@Override
- public void actionPerformed(final ActionEvent e) {
+ public void actionPerformed(final @NotNull ActionEvent e) {
final Object o = e.getSource();
if (o == null) {
@@ -877,7 +879,6 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
}
if (o instanceof JRadioButton) {
-
final JRadioButton b = (JRadioButton) e.getSource();
if (b == rbRGB) {
choosenCS = ColorSpaceTools.RGB;
@@ -945,7 +946,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* @return the mask
* @throws SignatureException the signature exception
*/
- private Mask doFilter(final ColorPickerThresholdPainter painter) throws SignatureException {
+ private Mask doFilter(final @NotNull ColorPickerThresholdPainter painter) throws SignatureException {
final Sequence currentSequence = painter.getSequence();
final IcyBufferedImage currentImage = currentSequence.getFirstImage();
Mask m = null;
@@ -976,7 +977,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* @return the mask
* @throws MaskException the mask exception
*/
- private Mask filter1(final ColorBox box, final IcyBufferedImage image) throws MaskException {
+ private @NotNull Mask filter1(final @NotNull ColorBox box, final IcyBufferedImage image) throws MaskException {
if (box.nbColors == 0) {
throw new MaskException("No color selected, filtering aborted");
}
@@ -1035,7 +1036,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* @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 {
+ private @NotNull Mask filter2(final @NotNull ColorBox boxP, final ColorBox boxN, final IcyBufferedImage image) throws MaskException, SignatureException {
if (boxP.nbColors == 0) {
throw new MaskException("No positive color selected, filtering aborted");
}
@@ -1130,7 +1131,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* java.awt.event.ItemListener#itemStateChanged(java.awt.event.ItemEvent)
*/
@Override
- public void itemStateChanged(final ItemEvent e) {
+ public void itemStateChanged(final @NotNull ItemEvent e) {
final Object o = e.getSource();
if (o == null) {
@@ -1214,7 +1215,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
*
* @param distance the new distance
*/
- public void setDistance(final ColorDistance distance) {
+ public void setDistance(final @NotNull ColorDistance distance) {
this.distance = distance;
colMaxDist = (int) Math.floor(distance.getMaxDistance());
@@ -1230,7 +1231,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
}
@Override
- public void fillInterface(final JPanel mainPanel) {
+ public void fillInterface(final @NotNull JPanel mainPanel) {
// KNN
final ButtonGroup bgd = new ButtonGroup();
rbL1 = new JRadioButton("L1");
@@ -1369,7 +1370,7 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
* )
*/
@Override
- public void stateChanged(final ChangeEvent e) {
+ public void stateChanged(final @NotNull ChangeEvent e) {
final JSlider s = (JSlider) e.getSource();
if (s == null) {
return;
@@ -1399,5 +1400,4 @@ public class ColorPickerThreshold extends PainterManagerSingletonPlugin<ColorPic
@Override
public void stopInterface() {
}
-
}