diff --git a/pom.xml b/pom.xml
index cfb970d2d52ef68ac54521fcc1b219cde62ea64d..fb4a752df21d4e5148ad61de4c2b074f92b88da0 100644
--- a/pom.xml
+++ b/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
diff --git a/src/main/java/plugins/nchenouard/spot/Detection.java b/src/main/java/plugins/nchenouard/spot/Detection.java
index f28d23dc5ddc7dacef28f026b9a47ec42da1b9c6..5c88f29696100b88f6f54ea831582f4205278002 100644
--- a/src/main/java/plugins/nchenouard/spot/Detection.java
+++ b/src/main/java/plugins/nchenouard/spot/Detection.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
@@ -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;
}
-
}
-
-
-
-
-
-
-
-
-
diff --git a/src/main/java/plugins/nchenouard/spot/DetectionResult.java b/src/main/java/plugins/nchenouard/spot/DetectionResult.java
index fa7e09e11519743ae6e438ea775e40940fe94e6e..ffaff2bd40607072f7b8907a4ad8842c3ddc16f0 100644
--- a/src/main/java/plugins/nchenouard/spot/DetectionResult.java
+++ b/src/main/java/plugins/nchenouard/spot/DetectionResult.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
@@ -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<>();
diff --git a/src/main/java/plugins/nchenouard/spot/Point3D.java b/src/main/java/plugins/nchenouard/spot/Point3D.java
index aeb4b1f654c4571c720446f763640446422a43c3..c11965208b9aa3435494c0aa86c569a8d910ca73 100644
--- a/src/main/java/plugins/nchenouard/spot/Point3D.java
+++ b/src/main/java/plugins/nchenouard/spot/Point3D.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
@@ -18,10 +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)
diff --git a/src/main/java/plugins/nchenouard/spot/Spot.java b/src/main/java/plugins/nchenouard/spot/Spot.java
index 604e12c1e7594332c371cfd34d31066aa885e9cb..16034413576aca3a07b73a1ee92d25f1c62a35ea 100644
--- a/src/main/java/plugins/nchenouard/spot/Spot.java
+++ b/src/main/java/plugins/nchenouard/spot/Spot.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
@@ -18,7 +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 + ",");