diff --git a/pom.xml b/pom.xml
index 1be905bb3178056b842ca267fcaa88dc2747cf96..ffb9c4edbc7019d9d5e9ec70735433afd19981f3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -11,7 +11,7 @@
</parent>
<artifactId>spot-detection-utilities</artifactId>
- <version>1.1.7</version>
+ <version>2.0.0</version>
<packaging>jar</packaging>
diff --git a/src/main/java/plugins/nchenouard/spot/Detection.java b/src/main/java/plugins/nchenouard/spot/Detection.java
index dfbfbdca018220da2d715ee8629f680ec70d8dc6..79c94bd86dc865543a0df9af4f67298161fa3f1d 100644
--- a/src/main/java/plugins/nchenouard/spot/Detection.java
+++ b/src/main/java/plugins/nchenouard/spot/Detection.java
@@ -1,21 +1,21 @@
/*
- * Copyright 2010-2023 Institut Pasteur.
+ * Copyright (c) 2010-2023. Institut Pasteur.
*
- * This file is part of ICY.
- *
- * ICY is free software: you can redistribute it and/or modify
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
- * ICY is distributed in the hope that it will be useful,
+ * Icy is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with ICY. If not, see <https://www.gnu.org/licenses/>.
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
+
package plugins.nchenouard.spot;
import icy.file.xml.XMLPersistent;
@@ -23,13 +23,12 @@ import icy.painter.Overlay;
import icy.system.IcyExceptionHandler;
import icy.util.ClassUtil;
import icy.util.XMLUtil;
-
-import java.awt.Color;
-import java.lang.reflect.Constructor;
-
import org.w3c.dom.Element;
import org.w3c.dom.Node;
+import java.awt.*;
+import java.lang.reflect.Constructor;
+
/**
* Detection is the basic detection class. Extends Detection to create more complete Detection.
*
@@ -41,7 +40,7 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
@Override
public Object clone() throws CloneNotSupportedException {
- Detection clone = (Detection) super.clone();
+ final Detection clone = (Detection) super.clone();
clone.x = x;
clone.y = y;
@@ -49,7 +48,6 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
clone.t = t;
clone.detectionType = detectionType;
clone.selected = selected;
- clone.detectionEditor = detectionEditor;
clone.enabled = enabled;
clone.color = new Color(color.getRed(), color.getGreen(), color.getBlue());
clone.originalColor = new Color(originalColor.getRGB());
@@ -84,22 +82,23 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
protected boolean selected = false;
/**
* Detection enabled/disable is the internal mechanism to filter track with TrackProcessor. At
- * the start of TrackProcessor process, the enable track are all set to true. any TSP can then
+ * the start of the TrackProcessor process, the enable tracks are all set to true. Any TSP can then
* disable it.
*/
protected boolean enabled = true;
/**
- * This color is used each time the TrackProcessor start, as it call the detection.reset() function.
+ * This color is used each time the TrackProcessor start, as it calls the detection.reset() function.
* This color is loaded when using an XML file.
- * While saving, the current color of the track ( color property ) is used. So at load it will become the new originalColor.
+ * While saving, the current color of the track (color property) is used.
+ * So at loading, it will become the new originalColor.
*/
protected Color originalColor = Color.blue;
public final static int DETECTIONTYPE_REAL_DETECTION = 1;
public final static int DETECTIONTYPE_VIRTUAL_DETECTION = 2;
- public Detection(double x, double y, double z, int t) {
+ public Detection(final double x, final double y, final double z, final int t) {
super("Detection", OverlayPriority.SHAPE_NORMAL);
this.x = x;
this.y = y;
@@ -117,7 +116,7 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
return t;
}
- public void setT(int t) {
+ public void setT(final int t) {
this.t = t;
}
@@ -125,7 +124,7 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
return x;
}
- public void setX(double x) {
+ public void setX(final double x) {
this.x = x;
}
@@ -133,7 +132,7 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
return y;
}
- public void setY(double y) {
+ public void setY(final double y) {
this.y = y;
}
@@ -141,7 +140,7 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
return z;
}
- public void setZ(double z) {
+ public void setZ(final double z) {
this.z = z;
}
@@ -156,7 +155,7 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
return detectionType;
}
- public void setDetectionType(int detectionType) {
+ public void setDetectionType(final int detectionType) {
this.detectionType = detectionType;
}
@@ -164,7 +163,7 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
return selected;
}
- public void setSelected(boolean selected) {
+ public void setSelected(final boolean selected) {
this.selected = selected;
}
@@ -172,7 +171,7 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
return color;
}
- public void setColor(Color color) {
+ public void setColor(final Color color) {
this.color = color;
}
@@ -180,33 +179,15 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
return enabled;
}
- public void setEnabled(boolean enabled) {
+ public void setEnabled(final boolean enabled) {
this.enabled = enabled;
}
- @Deprecated
- private DetectionEditor detectionEditor = null;
-
- @Deprecated
- public void setExternalDetectionTools(DetectionEditor detectionEditor) {
- this.detectionEditor = detectionEditor;
- }
-
public void reset() {
this.color = originalColor;
this.setEnabled(true);
}
- @Deprecated
- public DetectionEditor getDetectionEditor() {
- return detectionEditor;
- }
-
- @Deprecated
- public void setDeet(DetectionEditor detectionEditor) {
- this.detectionEditor = detectionEditor;
- }
-
// @Override
// public void paint(Graphics2D g, Sequence sequence, IcyCanvas canvas) {
// if (enabled)
@@ -227,9 +208,9 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
* @return true if load is successful.
*/
@Override
- public boolean loadFromXML(Node node) {
+ public boolean loadFromXML(final Node node) {
- Element detectionElement = (Element) node;
+ final Element detectionElement = (Element) node;
x = XMLUtil.getAttributeDoubleValue(detectionElement, "x", 0);
y = XMLUtil.getAttributeDoubleValue(detectionElement, "y", 0);
@@ -246,9 +227,9 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
* @return true if save is successful.
*/
@Override
- public boolean saveToXML(Node node) {
+ public boolean saveToXML(final Node node) {
- Element detectionElement = (Element) node;
+ final Element detectionElement = (Element) node;
XMLUtil.setAttributeDoubleValue(detectionElement, "x", x);
XMLUtil.setAttributeDoubleValue(detectionElement, "y", y);
@@ -265,7 +246,7 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
}
// Inspired from the ROI Persistance mechanism
- public static Detection createDetection(String className) {
+ public static Detection createDetection(final String className) {
Detection result = null;
try {
@@ -280,7 +261,8 @@ public class Detection extends Overlay implements Cloneable, XMLPersistent {
result = constructor.newInstance();
}
- } catch (Exception e) {
+ }
+ 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)");
diff --git a/src/main/java/plugins/nchenouard/spot/DetectionEditor.java b/src/main/java/plugins/nchenouard/spot/DetectionEditor.java
deleted file mode 100644
index 2d3f82bd0f0b15887027704578a11c2f1e3a0935..0000000000000000000000000000000000000000
--- a/src/main/java/plugins/nchenouard/spot/DetectionEditor.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- * Copyright 2010-2023 Institut Pasteur.
- *
- * This file is part of ICY.
- *
- * ICY is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * ICY is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with ICY. If not, see <https://www.gnu.org/licenses/>.
- */
-package plugins.nchenouard.spot;
-
-import javax.swing.JPanel;
-
-/**
- * @author Fabrice de Chaumont
- * @deprecated detection editor not ready yet
- */
-@Deprecated
-public abstract class DetectionEditor {
-
- private final JPanel panel;
- //protected TrackPool trackPool = null;
- protected Detection currentDetection = null;
-
- public DetectionEditor() {
- panel = new JPanel();
- }
-
- public JPanel getPanel() {
- return panel;
- }
-
- public abstract Detection createDetection(double x, double y, double z, int t);
-
- /**
- * called by the trackManager to set a new detection when the user select a detection
- */
- public final void setDetection(Detection detection) {
- currentDetection = detection;
- currentDetectionAsChanged();
- }
-
- /**
- * Send the detection to the inheriting class. Should display data about it. Then use
- * trackPool.<br>
- * Fire to update TrackEditor Interface.
- */
- protected abstract void currentDetectionAsChanged();
-
- /* The trackPool is set by the trackEditor constructor */
-// public final void setTrackPool(TrackPool trackPool)
-// {
-// this.trackPool = trackPool;
-// }
-
-}
diff --git a/src/main/java/plugins/nchenouard/spot/DetectionResult.java b/src/main/java/plugins/nchenouard/spot/DetectionResult.java
index 75ebf84ee1b8ec8ab000ab8a0f1c416fb55ea0a7..c599990396de852a73c121c6d9ffd64ec16822e8 100644
--- a/src/main/java/plugins/nchenouard/spot/DetectionResult.java
+++ b/src/main/java/plugins/nchenouard/spot/DetectionResult.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.nchenouard.spot;
import icy.plugin.abstract_.Plugin;
@@ -42,7 +60,7 @@ public class DetectionResult extends Plugin {
private void computeNumberOfDetection() {
detectionNumber = 0;
- for (int index : results.keySet()) {
+ for (final int index : results.keySet()) {
detectionNumber += results.get(index).size();
}
numberOfDetectionShouldBeRecomputed = false;
@@ -53,10 +71,11 @@ public class DetectionResult extends Plugin {
return sourceSequence;
}
- public void setSequence(Sequence seq) {
+ public void setSequence(final Sequence seq) {
this.sourceSequence = seq;
}
+ @Override
protected void finalize() throws Throwable {
results.clear();
super.finalize();
@@ -67,38 +86,33 @@ public class DetectionResult extends Plugin {
numberOfDetectionShouldBeRecomputed = true;
}
- public DetectionResult(TreeMap<Integer, Vector<Spot>> results) {
+ public DetectionResult(final TreeMap<Integer, Vector<Spot>> results) {
this.results = results;
numberOfDetectionShouldBeRecomputed = true;
}
- public void addDetection(int t, Spot s) {
- Vector<Spot> spots;
- if (results.containsKey(Integer.valueOf(t)))
- spots = results.get(Integer.valueOf(t));
+ public void addDetection(final int t, final Spot s) {
+ final Vector<Spot> spots;
+ if (results.containsKey(t))
+ spots = results.get(t);
else {
spots = new Vector<>(1);
- results.put(Integer.valueOf(t), spots);
+ results.put(t, spots);
}
spots.add(s);
numberOfDetectionShouldBeRecomputed = true;
}
- public void setResult(int t, Vector<Spot> detections) {
- results.put(Integer.valueOf(t), new Vector<>(detections));
+ public void setResult(final int t, final Vector<Spot> detections) {
+ results.put(t, new Vector<>(detections));
numberOfDetectionShouldBeRecomputed = true;
}
/**
* @return a COPY of the detection vector at time t
*/
- public Vector<Spot> getDetectionsAtT(int t) {
- Vector<Spot> spots = results.get(t);
- if (spots == null) {
- spots = new Vector<>();
- results.put(Integer.valueOf(t), spots);
- }
- return spots;
+ public Vector<Spot> getDetectionsAtT(final int t) {
+ return results.computeIfAbsent(t, k -> new Vector<>());
}
/**
@@ -109,22 +123,22 @@ public class DetectionResult extends Plugin {
}
public DetectionResult copy() {
- TreeMap<Integer, Vector<Spot>> copy = new TreeMap<>();
- for (int key : results.keySet()) {
- @SuppressWarnings("unchecked")
- Vector<Spot> spotVectorClone = (Vector<Spot>) results.get(key).clone();
+ final TreeMap<Integer, Vector<Spot>> copy = new TreeMap<>();
+ for (final int key : results.keySet()) {
+ @SuppressWarnings("unchecked") final Vector<Spot> spotVectorClone = (Vector<Spot>) results.get(key).clone();
copy.put(key, spotVectorClone);
}
- DetectionResult dr = new DetectionResult(copy);
+ final DetectionResult dr = new DetectionResult(copy);
dr.setName(name);
return dr;
}
+ @Override
public String getName() {
return name;
}
- public void setName(String name) {
+ public void setName(final String name) {
this.name = name;
}
diff --git a/src/main/java/plugins/nchenouard/spot/Point3D.java b/src/main/java/plugins/nchenouard/spot/Point3D.java
index c34b27b9b9ec81ed945d56b263ff96e7ab4364eb..aeb4b1f654c4571c720446f763640446422a43c3 100644
--- a/src/main/java/plugins/nchenouard/spot/Point3D.java
+++ b/src/main/java/plugins/nchenouard/spot/Point3D.java
@@ -1,13 +1,29 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.nchenouard.spot;
import java.awt.geom.Point2D;
-
public class Point3D {
@Override
public String toString() {
-
return "Point3D[" + x + "," + y + "," + z + "]";
}
@@ -16,19 +32,19 @@ public class Point3D {
public Point3D() {
}
- public Point3D(double x, double y, double z) {
+ public Point3D(final double x, final double y, final double z) {
this.x = x;
this.y = y;
this.z = z;
}
- public Point3D(double x, double y) {
+ public Point3D(final double x, final double y) {
this.x = x;
this.y = y;
this.z = 0;
}
- public Point3D(double[] coord) {
+ public Point3D(final double[] 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 f807fdd179d1a76a43b10e251c03a50bd78a5235..3ba66ba75769c905851536afa8d2acf440ccb81a 100644
--- a/src/main/java/plugins/nchenouard/spot/Spot.java
+++ b/src/main/java/plugins/nchenouard/spot/Spot.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
+
package plugins.nchenouard.spot;
import java.io.PrintStream;
@@ -13,7 +31,7 @@ public class Spot {
public double meanIntensity;
/**
- * List of point of the detection
+ * List of detection points
*/
public ArrayList<Point3D> point3DList = new ArrayList<>();
@@ -21,18 +39,18 @@ public class Spot {
mass_center = new Point3D();
}
- public Spot(double x, double y, double z) {
+ public Spot(final double x, final double y, final double z) {
mass_center = new Point3D(x, y, z);
}
- public Spot(double x, double y, double z, double minIntensity, double maxIntensity, double meanIntensity) {
+ public Spot(final double x, final double y, final double z, final double minIntensity, final double maxIntensity, final double meanIntensity) {
mass_center = new Point3D(x, y, z);
this.minIntensity = minIntensity;
this.maxIntensity = maxIntensity;
this.meanIntensity = meanIntensity;
}
- public Spot(double x, double y, double z, double minIntensity, double maxIntensity, double meanIntensity, ArrayList<Point3D> point3DList) {
+ public Spot(final double x, final double y, final double z, final double minIntensity, final double maxIntensity, final double meanIntensity, final ArrayList<Point3D> point3DList) {
mass_center = new Point3D(x, y, z);
this.minIntensity = minIntensity;
this.maxIntensity = maxIntensity;
@@ -45,15 +63,16 @@ public class Spot {
String[] tmpTab = line.split("\\[");
tmpTab = tmpTab[1].split("]");
line = tmpTab[0];
- String[] coordinates = line.split(",", 3);
+ final String[] coordinates = line.split(",", 3);
if (coordinates.length > 2) {
- NumberFormat nf = NumberFormat.getInstance();
- Spot s = new Spot();
+ final NumberFormat nf = NumberFormat.getInstance();
+ final Spot s = new Spot();
try {
s.mass_center.x = nf.parse(coordinates[0]).intValue();
s.mass_center.y = nf.parse(coordinates[1]).intValue();
s.mass_center.z = nf.parse(coordinates[2]).intValue();
- } catch (ParseException e) {
+ }
+ catch (final ParseException e) {
e.printStackTrace();
return null;
}
@@ -63,7 +82,7 @@ public class Spot {
return null;
}
- public void save(PrintStream printOut, int num) {
+ public void save(final PrintStream printOut, final int num) {
printOut.print("detection{" + num + "} = [");
printOut.print(mass_center.x + ",");
printOut.print(mass_center.y + ",");