updated pom to v2.0.0-a.1, fix classes accordingly to new architecture, added...

updated pom to v2.0.0-a.1, fix classes accordingly to new architecture, added icon, updated .gitignore

.gitignore

-.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

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

src/main/java/plugins/nherve/colorpickerthreshold/ColorPickerThreshold.java

 /*
- * 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() {
     }
-
 }