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

updated pom to v2.0.0-a.1, fix classes accordingly to new architecture, added...
6824c117 · Thomas MUSSET · 232f36c7 · 6824c117 · 6824c117 · 6824c117
Commit 6824c117 authored 9 months ago by Thomas MUSSET
--- a/.gitignore
+++ b/.gitignore
-.idea/
+/build*
+/workspace
+setting.xml
+release/
 target/
-.settings/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+### IntelliJ IDEA ###
+.idea/
+*.iws
 *.iml
-.project
+*.ipr
+### Eclipse ###
+.apt_generated
 .classpath
-**/.DS_Store
+.factorypath
\ No newline at end of file
+.project
+.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
--- a/pom.xml
+++ b/pom.xml
@@ -8,12 +8,12 @@
    <parent>
        <groupId>org.bioimageanalysis.icy</groupId>
        <artifactId>pom-icy</artifactId>
-        <version>2.2.0</version>
+        <version>3.0.0-a.1</version>
    </parent>
    <!-- Project Information -->
    <artifactId>kmeans-color-quantization</artifactId>
-    <version>2.0.0</version>
+    <version>2.0.0-a.1</version>
    <name>KMeans Color Quantization</name>
    <description>Quantize a color image in any given number of colors.</description>
@@ -68,8 +68,7 @@
    <repositories>
        <repository>
            <id>icy</id>
-            <name>Icy's Nexus</name>
+            <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
-            <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
        </repository>
    </repositories>
 </project>
\ No newline at end of file
--- a/src/main/java/plugins/nherve/colorquantization/KMeansColorQuantization.java
+++ b/src/main/java/plugins/nherve/colorquantization/KMeansColorQuantization.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
@@ -18,13 +18,16 @@
 package plugins.nherve.colorquantization;
-import icy.gui.util.ComponentUtil;
+import org.bioimageanalysis.icy.Icy;
-import icy.gui.util.GuiUtil;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
-import icy.main.Icy;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
-import icy.preferences.XMLPreferences;
+import org.bioimageanalysis.icy.gui.GuiUtil;
-import icy.sequence.Sequence;
+import org.bioimageanalysis.icy.gui.component.ComponentUtil;
-import icy.swimmingPool.SwimmingObject;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
-import icy.system.IcyExceptionHandler;
+import org.bioimageanalysis.icy.model.swimmingPool.SwimmingObject;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.bioimageanalysis.icy.system.preferences.XMLPreferences;
+import org.jetbrains.annotations.NotNull;
 import plugins.nherve.maskeditor.MaskEditor;
 import plugins.nherve.toolbox.Algorithm;
 import plugins.nherve.toolbox.NherveToolbox;
@@ -68,6 +71,8 @@ import java.util.Map;
 *
 * @author Nicolas HERVE - nicolas.herve@pasteur.fr
 */
+@IcyPluginName("KMeans Color Quantization")
+@IcyPluginIcon(path = "/KMeansColorQuantization_icon.png")
 public class KMeansColorQuantization extends SingletonPlugin implements ActionListener {
    private static final String HELP = "<html>" + "<p align=\"center\"><b>" + HelpWindow.getTagFullPluginName() + "</b></p>" + "<p align=\"center\"><b>" + NherveToolbox.getDevNameHtml() + "</b></p>" + "<p align=\"center\"><b>" + NherveToolbox.getCopyrightHtml() + "</b></p>" + "<hr/>" + "<p>" + HelpWindow.getTagPluginName() + NherveToolbox.getLicenceHtml() + "</p>" + "<p>" + NherveToolbox.getLicenceHtmllink() + "</p>" + "</html>";
@@ -145,7 +150,7 @@ public class KMeansColorQuantization extends SingletonPlugin implements ActionLi
    }
    @Override
-    public void fillInterface(final JPanel mainPanel) {
+    public void fillInterface(final @NotNull JPanel mainPanel) {
        currentlyRunning = null;
        final XMLPreferences preferences = getPreferences();
@@ -224,7 +229,7 @@ public class KMeansColorQuantization extends SingletonPlugin implements ActionLi
            preferences.putBoolean("dsp", cbDisplay.isSelected());
        }
        catch (final NumberFormatException e) {
-            IcyExceptionHandler.showErrorMessage(e, true);
+            IcyLogger.error(this.getClass(), e, "Error parsing color space.");
        }
    }
@@ -235,7 +240,7 @@ public class KMeansColorQuantization extends SingletonPlugin implements ActionLi
     * java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
     */
    @Override
-    public void actionPerformed(final ActionEvent e) {
+    public void actionPerformed(final @NotNull ActionEvent e) {
        final JButton b = (JButton) e.getSource();
        if (b == null) {
            return;
@@ -272,7 +277,7 @@ public class KMeansColorQuantization extends SingletonPlugin implements ActionLi
                        }
                    }
                    catch (final SupportRegionException | SegmentationException | InterruptedException | InvocationTargetException | MaskException | NumberFormatException | SignatureException e1) {
-                        logError(e1.getClass().getName() + " : " + e1.getMessage());
+                        IcyLogger.error(this.getClass(), e1, "Error while clustering.");
                    }
                });
                currentlyRunning.start();
@@ -304,7 +309,7 @@ public class KMeansColorQuantization extends SingletonPlugin implements ActionLi
     * @param seg the seg
     * @return the some stats
     */
-    private void getSomeStats(final Segmentation seg) {
+    private void getSomeStats(final @NotNull Segmentation seg) {
        final DecimalFormat df = new DecimalFormat("0");
        Algorithm.out("id;label;h1;h2;h3");
        for (final Mask m : seg) {
@@ -325,7 +330,7 @@ public class KMeansColorQuantization extends SingletonPlugin implements ActionLi
     * @throws NumberFormatException  the number format exception
     * @throws SignatureException     the signature exception
     */
-    private Segmentation doClustering(final Sequence currentSequence) throws SupportRegionException, SegmentationException, MaskException, NumberFormatException, SignatureException {
+    private @NotNull Segmentation doClustering(final Sequence currentSequence) throws SupportRegionException, SegmentationException, MaskException, NumberFormatException, SignatureException {
        final Segmentation seg;
        seg = doClusteringKM(currentSequence);
@@ -346,7 +351,7 @@ public class KMeansColorQuantization extends SingletonPlugin implements ActionLi
     * @throws SegmentationException  the segmentation exception
     * @throws NumberFormatException  the number format exception
     */
-    private Segmentation doClusteringKM(final Sequence currentSequence) throws SupportRegionException, SegmentationException, NumberFormatException {
+    private Segmentation doClusteringKM(final @NotNull Sequence currentSequence) throws SupportRegionException, SegmentationException, NumberFormatException {
        final int nbc2 = Integer.parseInt(tfNbCluster2.getText());
        final int nbi2 = Integer.parseInt(tfNbIteration2.getText());
        final double stab2 = Double.parseDouble(tfStabCrit2.getText());