diff --git a/.gitignore b/.gitignore
index 4d6d26eb5c996073a0b63007cf16faee399b26cd..22af9746b07a854159ce190cf70f35b692fe6fdc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,4 +5,5 @@ target/
*.iml
*.eml
.classpath
-.project
\ No newline at end of file
+.project
+**/.DS_Store
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index e90eddbff19a9c94c1dad306f05b5f5a52e8db6b..1be905bb3178056b842ca267fcaa88dc2747cf96 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,54 +5,18 @@
<modelVersion>4.0.0</modelVersion>
<parent>
- <artifactId>pom-icy</artifactId>
<groupId>org.bioimageanalysis.icy</groupId>
- <version>2.0.0</version>
+ <artifactId>pom-icy</artifactId>
+ <version>2.2.0</version>
</parent>
<artifactId>spot-detection-utilities</artifactId>
- <version>1.1.6</version>
+ <version>1.1.7</version>
<packaging>jar</packaging>
<name>Detection Utilities</name>
- <profiles>
- <profile>
- <id>icy-plugin</id>
- <activation>
- <activeByDefault>true</activeByDefault>
- </activation>
- </profile>
- </profiles>
-
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-javadoc-plugin</artifactId>
- <configuration>
- <overview>${basedir}/src/main/javadoc/overview.html</overview>
- <stylesheetfile>${basedir}/src/main/javadoc/java7doc.css</stylesheetfile>
- <!-- disable javadoc errors for substance library (too many, and we don't care really) -->
- <additionalOptions>
- <additionalOption>-Xdoclint:none</additionalOption>
- </additionalOptions>
- </configuration>
- </plugin>
- </plugins>
- </build>
-
- <!-- List of project's dependencies -->
- <dependencies>
- <!-- The core of Icy -->
- <dependency>
- <groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-kernel</artifactId>
- <version>${icy-kernel.version}</version>
- </dependency>
- </dependencies>
-
<repositories>
<repository>
<id>icy</id>
diff --git a/src/main/java/plugins/nchenouard/spot/Detection.java b/src/main/java/plugins/nchenouard/spot/Detection.java
index df6a1853b69f3947a1427baf72d1bda8f205b6e6..dfbfbdca018220da2d715ee8629f680ec70d8dc6 100644
--- a/src/main/java/plugins/nchenouard/spot/Detection.java
+++ b/src/main/java/plugins/nchenouard/spot/Detection.java
@@ -1,39 +1,30 @@
/*
- * Copyright 2010, 2011 Institut Pasteur.
- *
+ * 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 <http://www.gnu.org/licenses/>.
+ * along with ICY. If not, see <https://www.gnu.org/licenses/>.
*/
package plugins.nchenouard.spot;
-import icy.canvas.Canvas2D;
-import icy.canvas.IcyCanvas;
import icy.file.xml.XMLPersistent;
-import icy.painter.Painter;
-import icy.sequence.Sequence;
+import icy.painter.Overlay;
import icy.system.IcyExceptionHandler;
import icy.util.ClassUtil;
import icy.util.XMLUtil;
-import java.awt.BasicStroke;
import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
import java.lang.reflect.Constructor;
import org.w3c.dom.Element;
@@ -41,16 +32,14 @@ import org.w3c.dom.Node;
/**
* Detection is the basic detection class. Extends Detection to create more complete Detection.
- *
+ *
* @author Fabrice de Chaumont
*/
-public class Detection implements Painter, Cloneable , XMLPersistent
-{
+public class Detection extends Overlay implements Cloneable, XMLPersistent {
@Override
- public Object clone() throws CloneNotSupportedException
- {
+ public Object clone() throws CloneNotSupportedException {
Detection clone = (Detection) super.clone();
@@ -63,23 +52,35 @@ public class Detection implements Painter, Cloneable , XMLPersistent
clone.detectionEditor = detectionEditor;
clone.enabled = enabled;
clone.color = new Color(color.getRed(), color.getGreen(), color.getBlue());
- clone.originalColor = new Color( originalColor.getRGB() );
+ clone.originalColor = new Color(originalColor.getRGB());
return clone;
}
- /** x position of detection. */
+ /**
+ * x position of detection.
+ */
protected double x;
- /** y position of detection. */
+ /**
+ * y position of detection.
+ */
protected double y;
- /** z position of detection. */
+ /**
+ * z position of detection.
+ */
protected double z;
- /** t position of detection. */
+ /**
+ * t position of detection.
+ */
protected int t;
- /** default detection type */
+ /**
+ * Default detection type
+ */
protected int detectionType = DETECTIONTYPE_REAL_DETECTION;
- /** Selected */
+ /**
+ * Selected
+ */
protected boolean selected = false;
/**
* Detection enabled/disable is the internal mechanism to filter track with TrackProcessor. At
@@ -91,183 +92,123 @@ public class Detection implements Painter, Cloneable , XMLPersistent
/**
* This color is used each time the TrackProcessor start, as it call the detection.reset() function.
* This color is loaded when using an XML file.
- * While saving, the current color of the track ( color propertie ) 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 load 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(double x, double y, double z, int t) {
+ super("Detection", OverlayPriority.SHAPE_NORMAL);
this.x = x;
this.y = y;
this.z = z;
this.t = t;
reset();
}
-
- public Detection()
- {
- reset();
+
+ public Detection() {
+ super("Detection", OverlayPriority.SHAPE_NORMAL);
+ reset();
}
-
- public int getT()
- {
+
+ public int getT() {
return t;
}
- public void setT(int t)
- {
+ public void setT(int t) {
this.t = t;
}
- public double getX()
- {
+ public double getX() {
return x;
}
- public void setX(double x)
- {
+ public void setX(double x) {
this.x = x;
}
- public double getY()
- {
+ public double getY() {
return y;
}
- public void setY(double y)
- {
+ public void setY(double y) {
this.y = y;
}
- public double getZ()
- {
+ public double getZ() {
return z;
}
- public void setZ(double z)
- {
+ public void setZ(double z) {
this.z = z;
}
@Override
- public String toString()
- {
+ public String toString() {
return "Detection [x:" + x + " y:" + y + " z:" + z + " t:" + t + "]";
}
Color color;
- public int getDetectionType()
- {
+ public int getDetectionType() {
return detectionType;
}
- public void setDetectionType(int detectionType)
- {
+ public void setDetectionType(int detectionType) {
this.detectionType = detectionType;
}
- public boolean isSelected()
- {
+ public boolean isSelected() {
return selected;
}
- public void setSelected(boolean selected)
- {
+ public void setSelected(boolean selected) {
this.selected = selected;
}
- public Color getColor()
- {
+ public Color getColor() {
return color;
}
- public void setColor(Color color)
- {
+ public void setColor(Color color) {
this.color = color;
}
- public boolean isEnabled()
- {
+ public boolean isEnabled() {
return enabled;
}
- public void setEnabled(boolean enabled)
- {
+ public void setEnabled(boolean enabled) {
this.enabled = enabled;
}
+ @Deprecated
private DetectionEditor detectionEditor = null;
- public void setExternalDetectionTools(DetectionEditor detectionEditor)
- {
+ @Deprecated
+ public void setExternalDetectionTools(DetectionEditor detectionEditor) {
this.detectionEditor = detectionEditor;
}
- public void reset()
- {
- this.color = originalColor;
+ public void reset() {
+ this.color = originalColor;
this.setEnabled(true);
}
- public DetectionEditor getDetectionEditor()
- {
+ @Deprecated
+ public DetectionEditor getDetectionEditor() {
return detectionEditor;
}
- public void setDeet(DetectionEditor detectionEditor)
- {
+ @Deprecated
+ public void setDeet(DetectionEditor detectionEditor) {
this.detectionEditor = detectionEditor;
}
- @Override
- public void keyPressed(KeyEvent e, Point2D imagePoint, IcyCanvas icyCanvas)
- {
-
- }
-
- @Override
- public void mouseClick(MouseEvent e, Point2D p, IcyCanvas icyCanvas)
- {
-
- }
-
- @Override
- public void mouseDrag(MouseEvent e, Point2D p, IcyCanvas icyCanvas)
- {
-
- }
-
- @Override
- public void mouseMove(MouseEvent e, Point2D p, IcyCanvas icyCanvas)
- {
-
- }
-
- @Override
- public void keyReleased(KeyEvent e, Point2D imagePoint, IcyCanvas canvas)
- {
-
- }
-
- @Override
- public void mousePressed(MouseEvent e, Point2D imagePoint, IcyCanvas canvas)
- {
-
- }
-
- @Override
- public void mouseReleased(MouseEvent e, Point2D imagePoint, IcyCanvas canvas)
- {
-
- }
-
- @Override
- public void paint(Graphics2D g, Sequence sequence, IcyCanvas canvas)
- {
+// @Override
+// public void paint(Graphics2D g, Sequence sequence, IcyCanvas canvas) {
// if (enabled)
// {
// if (canvas instanceof Canvas2D)
@@ -280,83 +221,77 @@ public class Detection implements Painter, Cloneable , XMLPersistent
// g.setStroke(new BasicStroke(1f));
// }
// }
+// }
+
+ /**
+ * @return true if load is successful.
+ */
+ @Override
+ public boolean loadFromXML(Node node) {
+
+ Element detectionElement = (Element) node;
+
+ x = XMLUtil.getAttributeDoubleValue(detectionElement, "x", 0);
+ y = XMLUtil.getAttributeDoubleValue(detectionElement, "y", 0);
+ z = XMLUtil.getAttributeDoubleValue(detectionElement, "z", 0);
+ t = XMLUtil.getAttributeIntValue(detectionElement, "t", 0);
+ detectionType = XMLUtil.getAttributeIntValue(detectionElement, "type", DETECTIONTYPE_REAL_DETECTION);
+ selected = XMLUtil.getAttributeBooleanValue(detectionElement, "selected", false);
+ originalColor = new Color(XMLUtil.getAttributeIntValue(detectionElement, "color", Color.blue.getRGB()));
+
+ return true;
}
/**
- * return true if load is successful.
+ * @return true if save is successful.
*/
- @Override
- public boolean loadFromXML(Node node) {
-
- Element detectionElement = (Element) node;
-
- x = XMLUtil.getAttributeDoubleValue( detectionElement , "x" , 0 );
- y = XMLUtil.getAttributeDoubleValue( detectionElement , "y" , 0 );
- z = XMLUtil.getAttributeDoubleValue( detectionElement , "z" , 0 );
- t = XMLUtil.getAttributeIntValue( detectionElement , "t" , 0 );
- detectionType = XMLUtil.getAttributeIntValue( detectionElement , "type" , DETECTIONTYPE_REAL_DETECTION );
- selected = XMLUtil.getAttributeBooleanValue( detectionElement , "selected" , false );
- originalColor = new Color ( XMLUtil.getAttributeIntValue( detectionElement , "color" , Color.blue.getRGB() ) );
-
- return true;
- }
-
- /**
- * return true if save is successful.
- */
- @Override
- public boolean saveToXML(Node node) {
-
- Element detectionElement = (Element) node;
-
- XMLUtil.setAttributeDoubleValue(detectionElement, "x", x );
- XMLUtil.setAttributeDoubleValue(detectionElement, "y", y );
- XMLUtil.setAttributeDoubleValue(detectionElement, "z", z );
- XMLUtil.setAttributeIntValue(detectionElement, "t", t );
- XMLUtil.setAttributeIntValue(detectionElement, "type", detectionType );
- XMLUtil.setAttributeIntValue(detectionElement, "color", color.getRGB() );
-
- if ( selected )
- {
- XMLUtil.setAttributeBooleanValue(detectionElement, "selected", true );
- }
-
- return true;
- }
-
- // Inpired form the ROI Persistance mechanism
- public static Detection createDetection( String className )
- {
+ @Override
+ public boolean saveToXML(Node node) {
+
+ Element detectionElement = (Element) node;
+
+ XMLUtil.setAttributeDoubleValue(detectionElement, "x", x);
+ XMLUtil.setAttributeDoubleValue(detectionElement, "y", y);
+ XMLUtil.setAttributeDoubleValue(detectionElement, "z", z);
+ XMLUtil.setAttributeIntValue(detectionElement, "t", t);
+ XMLUtil.setAttributeIntValue(detectionElement, "type", detectionType);
+ XMLUtil.setAttributeIntValue(detectionElement, "color", color.getRGB());
+
+ if (selected) {
+ XMLUtil.setAttributeBooleanValue(detectionElement, "selected", true);
+ }
+
+ return true;
+ }
+
+ // Inspired from the ROI Persistance mechanism
+ public static Detection createDetection(String className) {
Detection result = null;
- try
- {
+ try {
// search for the specified className
final Class<?> clazz = ClassUtil.findClass(className);
-
+
// class found
- if (clazz != null)
- {
- final Class<? extends Detection> detectionClazz = clazz.asSubclass(Detection.class);
-
- final Constructor<? extends Detection> constructor = detectionClazz.getConstructor(new Class[] {});
- result = constructor.newInstance(new Object[] {});
-
+ if (clazz != null) {
+ final Class<? extends Detection> detectionClazz = clazz.asSubclass(Detection.class);
+
+ final Constructor<? extends Detection> constructor = detectionClazz.getConstructor();
+ result = constructor.newInstance();
+
}
- }
- catch (Exception e)
- {
+ } catch (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.");
// Load as a default detection.
-
- result = new Detection();
-
- }
-
+
+ result = new Detection();
+
+ }
+
return result;
}
diff --git a/src/main/java/plugins/nchenouard/spot/DetectionEditor.java b/src/main/java/plugins/nchenouard/spot/DetectionEditor.java
index 08e94d70724ed1a1450205d86bd4fa82e8080b7c..2d3f82bd0f0b15887027704578a11c2f1e3a0935 100644
--- a/src/main/java/plugins/nchenouard/spot/DetectionEditor.java
+++ b/src/main/java/plugins/nchenouard/spot/DetectionEditor.java
@@ -1,44 +1,41 @@
/*
- * Copyright 2010, 2011 Institut Pasteur.
- *
+ * 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 <http://www.gnu.org/licenses/>.
+ * along with ICY. If not, see <https://www.gnu.org/licenses/>.
*/
package plugins.nchenouard.spot;
import javax.swing.JPanel;
/**
- * @deprecated detection editor not ready yet
* @author Fabrice de Chaumont
- *
+ * @deprecated detection editor not ready yet
*/
-public abstract class DetectionEditor
-{
+@Deprecated
+public abstract class DetectionEditor {
- private JPanel panel;
+ private final JPanel panel;
//protected TrackPool trackPool = null;
protected Detection currentDetection = null;
- public DetectionEditor()
- {
+ public DetectionEditor() {
panel = new JPanel();
}
- public JPanel getPanel()
- {
+ public JPanel getPanel() {
return panel;
}
@@ -46,22 +43,20 @@ public abstract class DetectionEditor
/**
* called by the trackManager to set a new detection when the user select a detection
- *
- * @param detection
*/
- public final void setDetection(Detection detection)
- {
+ public final void setDetection(Detection detection) {
currentDetection = detection;
currentDetectionAsChanged();
}
/**
- * Send the detection to the heriting class. Should display data about it. Then use
- * trackPool.fire to update TrackEditor Interface.
+ * 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 */
+ /* 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 b5ff1b14d176e566e1ba5d72fbf8584cdcce15a9..75ebf84ee1b8ec8ab000ab8a0f1c416fb55ea0a7 100644
--- a/src/main/java/plugins/nchenouard/spot/DetectionResult.java
+++ b/src/main/java/plugins/nchenouard/spot/DetectionResult.java
@@ -7,154 +7,132 @@ import java.util.TreeMap;
import java.util.Vector;
-/** A class to manage detection results
- *
- * @author nicolas chenouard and Fabrice de Chaumont
+/**
+ * A class to manage detection results
*
- * */
-
-public class DetectionResult extends Plugin
-{
- private TreeMap<Integer, Vector<Spot>> results;
- private Sequence sourceSequence;
- private boolean numberOfDetectionShouldBeRecomputed = true;
- private int detectionNumber = 0;
- private String name = null;
-
- @Override
- public String toString() {
- if (name == null)
- {
- if (!results.isEmpty())
- return "Detection set from t:" + getFirstFrameTime() + " to t:" + getLastFrameTime() + " #detection(s): " + getNumberOfDetection();
- else
- return "Detection set (empty)";
- }
- else
- return name;
- }
-
- public int getNumberOfDetection()
- {
- if ( numberOfDetectionShouldBeRecomputed )
- {
- computeNumberOfDetection();
- }
- return detectionNumber;
- }
-
- private void computeNumberOfDetection() {
-
- detectionNumber = 0;
- for ( int index : results.keySet() )
- {
- detectionNumber+=results.get( index ).size();
- }
- numberOfDetectionShouldBeRecomputed = false;
-
- }
-
- public Sequence getSequence()
- {
- return sourceSequence;
- }
-
- public void setSequence(Sequence seq)
- {
- this.sourceSequence = seq;
- }
-
- protected void finalize() throws Throwable {
- results.clear();
- super.finalize();
- }
-
- public DetectionResult()
- {
- results = new TreeMap<Integer, Vector<Spot>>();
- numberOfDetectionShouldBeRecomputed = true;
- }
-
- public DetectionResult(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));
- else
- {
- spots = new Vector<Spot>(1);
- results.put(Integer.valueOf(t), spots);
- }
- spots.add(s);
- numberOfDetectionShouldBeRecomputed = true;
- }
-
- public void setResult(int t, Vector<Spot> detections)
- {
- results.put(Integer.valueOf(t), new Vector<Spot>(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<Spot>();
- results.put(Integer.valueOf(t), spots);
- }
- return spots;
- }
-
- /**
- *
- * @return a Copy of the TreeMap.
- */
- public TreeMap<Integer, Vector<Spot>> getResults()
- {
- return new TreeMap<Integer, Vector<Spot>>(results);
- }
-
- public DetectionResult copy()
- {
- TreeMap<Integer, Vector<Spot>> copy = new TreeMap<Integer, Vector<Spot>>();
- for ( int key : results.keySet() )
- {
- Vector<Spot> spotVectorClone = (Vector<Spot>) results.get( key ).clone();
- copy.put( key , spotVectorClone );
- }
- DetectionResult dr = new DetectionResult(copy);
- dr.setName(name);
- return dr;
- }
-
- public String getName()
- {
- return name;
- }
-
- public void setName(String name)
- {
- this.name = name;
- }
-
- public int getFirstFrameTime()
- {
- return results.firstKey();
- }
-
- public int getLastFrameTime()
- {
- return results.lastKey();
-
- }
+ * @author nicolas chenouard and Fabrice de Chaumont
+ */
+
+public class DetectionResult extends Plugin {
+ private final TreeMap<Integer, Vector<Spot>> results;
+ private Sequence sourceSequence;
+ private boolean numberOfDetectionShouldBeRecomputed;
+ private int detectionNumber = 0;
+ private String name = null;
+
+ @Override
+ public String toString() {
+ if (name == null) {
+ if (!results.isEmpty())
+ return "Detection set from t:" + getFirstFrameTime() + " to t:" + getLastFrameTime() + " #detection(s): " + getNumberOfDetection();
+ else
+ return "Detection set (empty)";
+ }
+ else
+ return name;
+ }
+
+ public int getNumberOfDetection() {
+ if (numberOfDetectionShouldBeRecomputed) {
+ computeNumberOfDetection();
+ }
+ return detectionNumber;
+ }
+
+ private void computeNumberOfDetection() {
+
+ detectionNumber = 0;
+ for (int index : results.keySet()) {
+ detectionNumber += results.get(index).size();
+ }
+ numberOfDetectionShouldBeRecomputed = false;
+
+ }
+
+ public Sequence getSequence() {
+ return sourceSequence;
+ }
+
+ public void setSequence(Sequence seq) {
+ this.sourceSequence = seq;
+ }
+
+ protected void finalize() throws Throwable {
+ results.clear();
+ super.finalize();
+ }
+
+ public DetectionResult() {
+ results = new TreeMap<>();
+ numberOfDetectionShouldBeRecomputed = true;
+ }
+
+ public DetectionResult(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));
+ else {
+ spots = new Vector<>(1);
+ results.put(Integer.valueOf(t), spots);
+ }
+ spots.add(s);
+ numberOfDetectionShouldBeRecomputed = true;
+ }
+
+ public void setResult(int t, Vector<Spot> detections) {
+ results.put(Integer.valueOf(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;
+ }
+
+ /**
+ * @return a Copy of the TreeMap.
+ */
+ public TreeMap<Integer, Vector<Spot>> getResults() {
+ return new TreeMap<>(results);
+ }
+
+ 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();
+ copy.put(key, spotVectorClone);
+ }
+ DetectionResult dr = new DetectionResult(copy);
+ dr.setName(name);
+ return dr;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ public int getFirstFrameTime() {
+ return results.firstKey();
+ }
+
+ public int getLastFrameTime() {
+ return results.lastKey();
+ }
}
diff --git a/src/main/java/plugins/nchenouard/spot/Point3D.java b/src/main/java/plugins/nchenouard/spot/Point3D.java
index 96582224807ec8bca519de418e1bc345038ebaed..c34b27b9b9ec81ed945d56b263ff96e7ab4364eb 100644
--- a/src/main/java/plugins/nchenouard/spot/Point3D.java
+++ b/src/main/java/plugins/nchenouard/spot/Point3D.java
@@ -5,43 +5,38 @@ import java.awt.geom.Point2D;
public class Point3D {
- @Override
- public String toString() {
-
- return "Point3D["+x+","+y+","+z+"]";
- }
-
- public double x,y,z;
-
- public Point3D(){}
-
- public Point3D( double x, double y , double z )
- {
- this.x = x;
- this.y = y;
- this.z = z;
- }
-
- public Point3D( double x, double y)
- {
- this.x = x;
- this.y = y;
- this.z = 0;
- }
-
- public Point3D( double[] coord)
- {
- this.x = coord[0];
- this.y = coord[1];
- if (coord.length>2)
- this.z = coord[2];
- else this.z = 0;
- }
-
- public Point2D asPoint2D()
- {
- return new Point2D.Double( x , y );
- }
-
+ @Override
+ public String toString() {
+ return "Point3D[" + x + "," + y + "," + z + "]";
+ }
+
+ public double x, y, z;
+
+ public Point3D() {
+ }
+
+ public Point3D(double x, double y, double z) {
+ this.x = x;
+ this.y = y;
+ this.z = z;
+ }
+
+ public Point3D(double x, double y) {
+ this.x = x;
+ this.y = y;
+ this.z = 0;
+ }
+
+ public Point3D(double[] coord) {
+ this.x = coord[0];
+ this.y = coord[1];
+ if (coord.length > 2)
+ this.z = coord[2];
+ else this.z = 0;
+ }
+
+ public Point2D asPoint2D() {
+ return new Point2D.Double(x, y);
+ }
}
diff --git a/src/main/java/plugins/nchenouard/spot/Spot.java b/src/main/java/plugins/nchenouard/spot/Spot.java
index 3fc34317d16335db8dc1f4b132ca3b2078558153..f807fdd179d1a76a43b10e251c03a50bd78a5235 100644
--- a/src/main/java/plugins/nchenouard/spot/Spot.java
+++ b/src/main/java/plugins/nchenouard/spot/Spot.java
@@ -6,81 +6,67 @@ import java.text.ParseException;
import java.util.ArrayList;
public class Spot {
-
- public Point3D mass_center;
- public double minIntensity;
- public double maxIntensity;
- public double meanIntensity;
-
- /** List of point of the detection */
- public ArrayList<Point3D> point3DList = new ArrayList<Point3D>();
-
- public Spot()
- {
- mass_center = new Point3D();
- }
- public Spot( double x , double y , double z )
- {
- mass_center = new Point3D( x , y , z );
- }
+ public Point3D mass_center;
+ public double minIntensity;
+ public double maxIntensity;
+ public double meanIntensity;
- public Spot( double x , double y , double z , double minIntensity , double maxIntensity, double meanIntensity )
- {
- mass_center = new Point3D( x , y , z );
- this.minIntensity = minIntensity;
- this.maxIntensity = maxIntensity;
- this.meanIntensity = meanIntensity;
- }
+ /**
+ * List of point of the detection
+ */
+ public ArrayList<Point3D> point3DList = new ArrayList<>();
- public Spot( double x , double y , double z , double minIntensity , double maxIntensity, double meanIntensity , ArrayList<Point3D> point3DList )
- {
- mass_center = new Point3D( x , y , z );
- this.minIntensity = minIntensity;
- this.maxIntensity = maxIntensity;
- this.meanIntensity = meanIntensity;
- this.point3DList = new ArrayList<Point3D>( point3DList );
- }
-
- @Override
- protected void finalize() throws Throwable
- {
- mass_center = null;
- super.finalize();
- }
-
- public static Spot load(String line)
- {
- if (line.startsWith("detection"))
- {
- String[] tmpTab = line.split("\\[");
- tmpTab = tmpTab[1].split("]");
- line = tmpTab[0];
- String[] coordinates = line.split(",",3);
- if (coordinates.length>2)
- {
- NumberFormat nf = NumberFormat.getInstance();
- 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) {
- e.printStackTrace();
- return null;
- }
- return s;
- }
- return null;
- }
- else return null;
- }
-
- public void save(PrintStream printOut, int num)
- {
- printOut.print("detection{"+num+"} = [");
- printOut.print ( mass_center.x +"," );
- printOut.print ( mass_center.y +"," );
- printOut.print ( mass_center.z +"];" );
- }
+ public Spot() {
+ mass_center = new Point3D();
+ }
+
+ public Spot(double x, double y, double z) {
+ mass_center = new Point3D(x, y, z);
+ }
+
+ public Spot(double x, double y, double z, double minIntensity, double maxIntensity, 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) {
+ mass_center = new Point3D(x, y, z);
+ this.minIntensity = minIntensity;
+ this.maxIntensity = maxIntensity;
+ this.meanIntensity = meanIntensity;
+ this.point3DList = new ArrayList<>(point3DList);
+ }
+
+ public static Spot load(String line) {
+ if (line.startsWith("detection")) {
+ String[] tmpTab = line.split("\\[");
+ tmpTab = tmpTab[1].split("]");
+ line = tmpTab[0];
+ String[] coordinates = line.split(",", 3);
+ if (coordinates.length > 2) {
+ NumberFormat nf = NumberFormat.getInstance();
+ 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) {
+ e.printStackTrace();
+ return null;
+ }
+ return s;
+ }
+ }
+ return null;
+ }
+
+ public void save(PrintStream printOut, int num) {
+ printOut.print("detection{" + num + "} = [");
+ printOut.print(mass_center.x + ",");
+ printOut.print(mass_center.y + ",");
+ printOut.print(mass_center.z + "];");
+ }
}