updated to v2.0.0-a.2, updated to Java 23

pom.xml

@@ -7,18 +7,11 @@
     <parent>
         <groupId>org.bioimageanalysis.icy</groupId>
 		<artifactId>pom-icy</artifactId>
-        <version>3.0.0-a.1</version>
+        <version>3.0.0-a.3</version>
     </parent>
 
     <artifactId>spot-detection-utilities</artifactId>
-    <version>2.0.0-a.1</version>
+    <version>2.0.0-a.2</version>
 
     <name>Detection Utilities</name>
-	
-    <repositories>
-        <repository>
-            <id>icy</id>
-            <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
-        </repository>
-    </repositories>
 </project>
\ No newline at end of file

src/main/java/plugins/nchenouard/spot/Detection.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
@@ -22,7 +22,7 @@ import org.bioimageanalysis.icy.common.reflect.ClassUtil;
 import org.bioimageanalysis.icy.io.xml.XMLPersistent;
 import org.bioimageanalysis.icy.io.xml.XMLUtil;
 import org.bioimageanalysis.icy.model.overlay.Overlay;
-import org.bioimageanalysis.icy.system.IcyExceptionHandler;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
 import org.w3c.dom.Element;
 import org.w3c.dom.Node;
 
@@ -36,10 +36,8 @@ import java.lang.reflect.Constructor;
  */
 
 public class Detection extends Overlay implements Cloneable, XMLPersistent {
-
     @Override
     public Object clone() throws CloneNotSupportedException {
-
         final Detection clone = (Detection) super.clone();
 
         clone.x = x;
@@ -53,7 +51,6 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
         clone.originalColor = new Color(originalColor.getRGB());
 
         return clone;
-
     }
 
     /**
@@ -209,7 +206,6 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
      */
     @Override
     public boolean loadFromXML(final Node node) {
-
         final Element detectionElement = (Element) node;
 
         x = XMLUtil.getAttributeDoubleValue(detectionElement, "x", 0);
@@ -228,7 +224,6 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
      */
     @Override
     public boolean saveToXML(final Node node) {
-
         final Element detectionElement = (Element) node;
 
         XMLUtil.setAttributeDoubleValue(detectionElement, "x", x);
@@ -263,27 +258,18 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
             }
         }
         catch (final Exception e) {
-            System.err.println("********* TrackManager.createDetection('" + className + "', ...) error :");
-            IcyExceptionHandler.showErrorMessage(e, false);
-            System.err.println("The object is maybe not compatible (should have a default constructor with no arguments and extends Detection)");
-            System.err.println("Loading as a the default Detection object.");
-
+            IcyLogger.error(
+                    Detection.class,
+                    e,
+                    "TrackManager.createDetection('" + className + "', ...)",
+                    "The object is maybe not compatible (should have a default constructor with no arguments and extends Detection)"
+            );
+
+            IcyLogger.warn(Detection.class, "Loading as the default Detection object.");
             // Load as a default detection.
-
             result = new Detection();
-
         }
 
         return result;
     }
-
 }
-
-
-
-
-
-
-
-
-

src/main/java/plugins/nchenouard/spot/DetectionResult.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
@@ -25,7 +25,6 @@ import org.bioimageanalysis.icy.model.sequence.Sequence;
 import java.util.TreeMap;
 import java.util.Vector;
 
-
 /**
  * A class to manage detection results
  *
@@ -76,11 +75,11 @@ public class DetectionResult extends Plugin {
         this.sourceSequence = seq;
     }
 
-    @Override
+    /*@Override
     protected void finalize() throws Throwable {
         results.clear();
         super.finalize();
-    }
+    }*/
 
     public DetectionResult() {
         results = new TreeMap<>();

src/main/java/plugins/nchenouard/spot/Point3D.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
@@ -18,10 +18,12 @@
 
 package plugins.nchenouard.spot;
 
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
+
 import java.awt.geom.Point2D;
 
 public class Point3D {
-
     @Override
     public String toString() {
         return "Point3D[" + x + "," + y + "," + z + "]";
@@ -29,7 +31,9 @@ public class Point3D {
 
     public double x, y, z;
 
+    @Contract(pure = true)
     public Point3D() {
+        //
     }
 
     public Point3D(final double x, final double y, final double z) {
@@ -44,7 +48,7 @@ public class Point3D {
         this.z = 0;
     }
 
-    public Point3D(final double[] coord) {
+    public Point3D(final double @NotNull [] coord) {
         this.x = coord[0];
         this.y = coord[1];
         if (coord.length > 2)

src/main/java/plugins/nchenouard/spot/Spot.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
@@ -18,7 +18,9 @@
 
 package plugins.nchenouard.spot;
 
-import org.bioimageanalysis.icy.system.IcyExceptionHandler;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.io.PrintStream;
 import java.text.NumberFormat;
@@ -26,7 +28,6 @@ import java.text.ParseException;
 import java.util.ArrayList;
 
 public class Spot {
-
     public Point3D mass_center;
     public double minIntensity;
     public double maxIntensity;
@@ -60,7 +61,7 @@ public class Spot {
         this.point3DList = new ArrayList<>(point3DList);
     }
 
-    public static Spot load(String line) {
+    public static @Nullable Spot load(@NotNull String line) {
         if (line.startsWith("detection")) {
             String[] tmpTab = line.split("\\[");
             tmpTab = tmpTab[1].split("]");
@@ -75,7 +76,7 @@ public class Spot {
                     s.mass_center.z = nf.parse(coordinates[2]).intValue();
                 }
                 catch (final ParseException e) {
-                    IcyExceptionHandler.showErrorMessage(e, true);
+                    IcyLogger.error(Spot.class, e);
                     return null;
                 }
                 return s;
@@ -84,7 +85,7 @@ public class Spot {
         return null;
     }
 
-    public void save(final PrintStream printOut, final int num) {
+    public void save(final @NotNull PrintStream printOut, final int num) {
         printOut.print("detection{" + num + "} = [");
         printOut.print(mass_center.x + ",");
         printOut.print(mass_center.y + ",");