diff --git a/.gitignore b/.gitignore
index 2ea4565051a4733129b9c415dd6583e7ded50d4d..7f5de7386c755a464525cef7566010bd05abae0d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,4 +7,5 @@ target/
*.jar
.classpath
.project
-export.jardesc
\ No newline at end of file
+export.jardesc
+**/.DS_Store
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index b9a25e94c4734bf657cf362fb6cf40a41600aa5f..76b47f7511a4b315fd8808f635d9ca157340403b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,13 +6,13 @@
<!-- Inherited Icy Parent POM -->
<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>track-manager</artifactId>
- <version>1.5.0</version>
+ <version>1.5.1</version>
<packaging>jar</packaging>
@@ -21,26 +21,15 @@
he track manager enables the use of DSP-like trackProcessors.
This can affect the display of tracks, selection in time or by ROIs, and also compute some views like the overlaid and animated local flow graph, polar graph.
</description>
-
- <profiles>
- <profile>
- <id>icy-plugin</id>
- <activation>
- <activeByDefault>true</activeByDefault>
- </activation>
- </profile>
- </profiles>
<dependencies>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-kernel</artifactId>
- <version>${icy-kernel.version}</version>
+ <artifactId>protocols</artifactId>
</dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>connected-components</artifactId>
- <version>${connected-components.version}</version>
+ <artifactId>spot-detection-utilities</artifactId>
</dependency>
</dependencies>
diff --git a/src/main/java/plugins/fab/trackmanager/Link.java b/src/main/java/plugins/fab/trackmanager/Link.java
index a4a6d9489e71e311312866bc57040f679302518f..64fbda80423f068011265c59606562565579ec2f 100644
--- a/src/main/java/plugins/fab/trackmanager/Link.java
+++ b/src/main/java/plugins/fab/trackmanager/Link.java
@@ -1,60 +1,54 @@
/*
- * 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.fab.trackmanager;
import plugins.nchenouard.spot.Detection;
-public class Link
-{
+public class Link {
TrackSegment start;
TrackSegment end;
- public Link(TrackSegment start, TrackSegment end)
- {
+ public Link(TrackSegment start, TrackSegment end) {
this.start = start;
this.end = end;
}
- public Detection getEndDetection()
- {
+ public Detection getEndDetection() {
return end.getFirstDetection();
}
- public TrackSegment getEndSegment()
- {
+ public TrackSegment getEndSegment() {
return end;
}
- public Detection getStartDetection()
- {
+ public Detection getStartDetection() {
return start.getLastDetection();
}
- public TrackSegment getStartSegment()
- {
+ public TrackSegment getStartSegment() {
return start;
}
-
+
@Override
public String toString() {
- return "link start:" + getStartDetection() + " end:" + getEndDetection();
+ return "link start:" + getStartDetection() + " end:" + getEndDetection();
}
}
diff --git a/src/main/java/plugins/fab/trackmanager/PluginTrackManagerProcessor.java b/src/main/java/plugins/fab/trackmanager/PluginTrackManagerProcessor.java
index 5bf053eb134fc2537345c9685238198155cee52f..49913762220cf3fd6076fa8d0b7fe48ada4e40fd 100644
--- a/src/main/java/plugins/fab/trackmanager/PluginTrackManagerProcessor.java
+++ b/src/main/java/plugins/fab/trackmanager/PluginTrackManagerProcessor.java
@@ -1,20 +1,20 @@
/*
- * 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.fab.trackmanager;
@@ -32,12 +32,13 @@ import icy.gui.component.PopupPanel;
import icy.gui.util.GuiUtil;
import icy.plugin.abstract_.Plugin;
-public abstract class PluginTrackManagerProcessor extends Plugin
-{
+public abstract class PluginTrackManagerProcessor extends Plugin {
- /** Panel to used by herited class to display data */
+ /**
+ * Panel to used by inherited class to display data
+ */
protected JPanel panel = new JPanel();
- private PopupPanel mainpanel = new PopupPanel("no name");
+ private final PopupPanel mainPanel = new PopupPanel("no name");
protected TrackPool trackPool;
protected JCheckBox enabledCheckBox = new JCheckBox("Enable");
@@ -47,9 +48,8 @@ public abstract class PluginTrackManagerProcessor extends Plugin
protected JLabel performanceLabel = new JLabel("----");
ActionButton actionButton = new ActionButton();
- public PluginTrackManagerProcessor()
- {
- mainpanel.expand();
+ public PluginTrackManagerProcessor() {
+ mainPanel.expand();
enabledCheckBox.setSelected(true);
enabledCheckBox.addActionListener(actionButton);
@@ -66,82 +66,75 @@ public abstract class PluginTrackManagerProcessor extends Plugin
moveUpButton.addActionListener(actionButton);
moveDownButton.addActionListener(actionButton);
- mainpanel.getMainPanel().setLayout(new BoxLayout(mainpanel.getMainPanel(), BoxLayout.PAGE_AXIS));
+ mainPanel.getMainPanel().setLayout(new BoxLayout(mainPanel.getMainPanel(), BoxLayout.PAGE_AXIS));
- mainpanel.getMainPanel().add(GuiUtil.createLineBoxPanel(commandPanel));
- mainpanel.getMainPanel().add(GuiUtil.createLineBoxPanel(panel));
+ mainPanel.getMainPanel().add(GuiUtil.createLineBoxPanel(commandPanel));
+ mainPanel.getMainPanel().add(GuiUtil.createLineBoxPanel(panel));
}
- protected void setName(String name)
- {
- mainpanel.setTitle(name);
+ protected void setName(String name) {
+ mainPanel.setTitle(name);
}
- protected boolean isEnabled()
- {
+ protected boolean isEnabled() {
return enabledCheckBox.isSelected();
}
- class ActionButton implements ActionListener
- {
- public void actionPerformed(ActionEvent e)
- {
+ class ActionButton implements ActionListener {
+ public void actionPerformed(ActionEvent e) {
- if (e.getSource() == closeButton)
- {
+ if (e.getSource() == closeButton) {
Close();
removeTrackProcessor();
trackPool.fireTrackEditorProcessorChange();
}
- if (e.getSource() == enabledCheckBox)
- {
+ if (e.getSource() == enabledCheckBox) {
trackPool.fireTrackEditorProcessorChange();
}
- if (e.getSource() == moveUpButton)
- {
+ if (e.getSource() == moveUpButton) {
trackPool.getTrackManager().moveTrackProcessor(PluginTrackManagerProcessor.this, -1);
}
- if (e.getSource() == moveDownButton)
- {
+ if (e.getSource() == moveDownButton) {
trackPool.getTrackManager().moveTrackProcessor(PluginTrackManagerProcessor.this, +1);
}
}
}
- /** Override this function to perform special action before destroying the TrackProcessor. */
+ /**
+ * Override this function to perform special action before destroying the TrackProcessor.
+ */
public abstract void Close();
- /** Override this to affect data on detection (color (...) ) */
+ /**
+ * Override this to affect data on detection (color (...) )
+ */
public abstract void Compute();
- public void setPerformance(int ms)
- {
+ public void setPerformance(int ms) {
performanceLabel.setText(ms + " ms ");
}
- private void removeTrackProcessor()
- {
+ private void removeTrackProcessor() {
trackPool.removeTrackProcessor(this);
- JPanel parent = (JPanel) mainpanel.getParent();
- parent.remove(mainpanel);
+ JPanel parent = (JPanel) mainPanel.getParent();
+ parent.remove(mainPanel);
parent.revalidate();
}
- /** Return the Panel Control of this TrackProcessor */
- public JPanel getPanel()
- {
- return mainpanel;
+ /**
+ * Return the Panel Control of this TrackProcessor
+ */
+ public JPanel getPanel() {
+ return mainPanel;
}
@Override
- protected void finalize() throws Throwable
- {
+ protected void finalize() throws Throwable {
trackPool = null;
super.finalize();
}
- public final void setTrackPool(TrackPool trackPool)
- {
+ public final void setTrackPool(TrackPool trackPool) {
this.trackPool = trackPool;
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackDetection.java b/src/main/java/plugins/fab/trackmanager/TrackDetection.java
index 1bcbe80b91680f8bd31886a540666ef9570f7b48..580167802db7b6f2f79ee0e30d9a94869ff48588 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackDetection.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackDetection.java
@@ -1,20 +1,20 @@
/*
- * 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.fab.trackmanager;
@@ -34,19 +34,14 @@ import plugins.nchenouard.spot.Detection;
/**
* Display a single detection of a track. Used by TrackPanel / TrackEditor
- *
+ *
* @author fab
- * @deprecated not anymore a panel or an objet to speed up the rendering process.
*/
-public class TrackDetection extends JPanel
-{
-
- private static final long serialVersionUID = 7254806428248130683L;
+public class TrackDetection extends JPanel {
private boolean Selected = false;
- private Detection detection;
+ private final Detection detection;
- public TrackDetection(Detection detection)
- {
+ public TrackDetection(Detection detection) {
super();
this.detection = detection;
// if ( detection.getDetectionType() == Detection.DETECTIONTYPE_REAL_DETECTION ) color =
@@ -56,25 +51,21 @@ public class TrackDetection extends JPanel
}
- public Detection getDetection()
- {
+ public Detection getDetection() {
return detection;
}
- public void setSelected(boolean Selected)
- {
+ public void setSelected(boolean Selected) {
this.Selected = Selected;
this.updateUI();
}
- public boolean isSelected(boolean Selected)
- {
+ public boolean isSelected(boolean Selected) {
return Selected;
}
@Override
- protected void paintComponent(Graphics g)
- {
+ protected void paintComponent(Graphics g) {
super.paintComponent(g);
Graphics2D g2 = (Graphics2D) g;
@@ -90,29 +81,30 @@ public class TrackDetection extends JPanel
// Draw plot
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
g2.setColor(Color.black);
- Shape shape = new Rectangle2D.Float(getWidth() / 3f, getHeight() / 3f, getWidth() - 2 * getWidth() / 3f,
- getHeight() - 2 * getHeight() / 3f);
+ Shape shape = new Rectangle2D.Float(
+ getWidth() / 3f,
+ getHeight() / 3f,
+ getWidth() - 2 * getWidth() / 3f,
+ getHeight() - 2 * getHeight() / 3f
+ );
g2.fill(shape);
// Draw red square if selected for drag and drop
- if (Selected)
- {
+ if (Selected) {
g2.setColor(Color.red);
g2.drawRect(1, 1, getWidth() - 3, getHeight() - 3);
}
// Draw square if depending detection is selected.
- if (detection.isSelected())
- {
+ if (detection.isSelected()) {
g2.setStroke(new BasicStroke(4));
g2.setColor(Color.black);
g2.drawRect(0, 0, getWidth(), getHeight());
g2.setStroke(new BasicStroke(1));
}
- if (detection.getDetectionType() == Detection.DETECTIONTYPE_VIRTUAL_DETECTION)
- {
+ if (detection.getDetectionType() == Detection.DETECTIONTYPE_VIRTUAL_DETECTION) {
g2.setStroke(new BasicStroke(2));
g2.setColor(Color.white);
g2.drawLine(0, 0, getWidth(), getHeight());
diff --git a/src/main/java/plugins/fab/trackmanager/TrackGroup.java b/src/main/java/plugins/fab/trackmanager/TrackGroup.java
index 34f4a11ea4d79a97e70af90d0c34821e98187bc0..635eaf92ba99e5aa73e94039114630f4b5517c4a 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackGroup.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackGroup.java
@@ -1,20 +1,20 @@
/*
- * 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.fab.trackmanager;
@@ -24,93 +24,79 @@ import java.util.ArrayList;
import plugins.nchenouard.spot.Detection;
-public class TrackGroup
-{
+public class TrackGroup {
private final Sequence sequence;
- /**
+ /**
* DO NOT DIRECTLY ADD OR REMOVE tracks from this trackSegmentList. Always use getters and adder/setters
- * */
- private ArrayList<TrackSegment> trackSegmentList;
+ */
+ private final ArrayList<TrackSegment> trackSegmentList;
- public TrackGroup(Sequence sequence)
- {
+ public TrackGroup(Sequence sequence) {
this.sequence = sequence;
- trackSegmentList = new ArrayList<TrackSegment>();
+ trackSegmentList = new ArrayList<>();
}
/**
* @return the sequence
*/
- public Sequence getSequence()
- {
+ public Sequence getSequence() {
return sequence;
}
- public ArrayList<TrackSegment> getTrackSegmentList()
- {
+ public ArrayList<TrackSegment> getTrackSegmentList() {
return trackSegmentList;
}
- public void addTrackSegment(TrackSegment ts)
- {
- if (ts.getOwnerTrackGroup() != null)
- {
+ public void addTrackSegment(TrackSegment ts) {
+ if (ts.getOwnerTrackGroup() != null) {
System.err.println("The trackSegment is already owned by another TrackGroup.");
return;
}
-
+
//System.out.println("Track segment added to group. TS: " +ts.toString() );
-
+
ts.setOwnerTrackGroup(this);
trackSegmentList.add(ts);
}
- public TrackSegment getTrackSegmentWithDetection(Detection detection)
- {
+ public TrackSegment getTrackSegmentWithDetection(Detection detection) {
- ArrayList<TrackSegment> trackSegmentList = getTrackSegmentList();
+ ArrayList<TrackSegment> trackSegmentList = getTrackSegmentList();
- for ( TrackSegment ts : trackSegmentList )
- {
- if ( ts.containsDetection( detection ) ) return ts;
- }
+ for (TrackSegment ts : trackSegmentList) {
+ if (ts.containsDetection(detection)) return ts;
+ }
- return null;
+ return null;
}
-
- public void clearAllTrackSegment()
- {
- ArrayList<TrackSegment> trackSegmentListCopy = new ArrayList<TrackSegment>( trackSegmentList );
-
- for ( TrackSegment ts: trackSegmentListCopy )
- {
- removeTrackSegment( ts );
- }
+
+ public void clearAllTrackSegment() {
+ ArrayList<TrackSegment> trackSegmentListCopy = new ArrayList<>(trackSegmentList);
+
+ for (TrackSegment ts : trackSegmentListCopy) {
+ removeTrackSegment(ts);
+ }
}
-
- public void removeTrackSegment(TrackSegment ts)
- {
- // should remove links
+
+ public void removeTrackSegment(TrackSegment ts) {
+ // should remove links
ts.setOwnerTrackGroup(null);
ts.removeAllLinks();
- trackSegmentList.remove(ts);
+ trackSegmentList.remove(ts);
}
private String description;
- public String getDescription()
- {
+ public String getDescription() {
return description;
}
- public void setDescription(String description)
- {
+ public void setDescription(String description) {
this.description = description;
}
@Override
- public String toString()
- {
+ public String toString() {
return description;
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackLengthDialog.java b/src/main/java/plugins/fab/trackmanager/TrackLengthDialog.java
index a26c90200b94a9748bf1019572ea5c32f87cb0ba..bd8df0345e77a81924f3c0d750724db128b8fc8e 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackLengthDialog.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackLengthDialog.java
@@ -12,56 +12,54 @@ import javax.swing.JTextField;
public class TrackLengthDialog implements ActionListener {
- JTextField textField= new JTextField("3-10");
- TrackPool trackPool;
-
- public TrackLengthDialog( TrackPool trackPool ) {
-
- this.trackPool = trackPool;
- ActionDialog actionDialog = new ActionDialog("Select by length");
- actionDialog.getContentPane().setLayout(
- new BoxLayout( actionDialog.getContentPane(), BoxLayout.PAGE_AXIS ) );
-
- actionDialog.getContentPane().add( GuiUtil.createLineBoxPanel( new JLabel("Use the syntax: from-to (in number of frame):" ) ) );
- actionDialog.getContentPane().add( GuiUtil.createLineBoxPanel( textField ) );
-
- actionDialog.pack();
- actionDialog.setLocationRelativeTo( null );
-
- actionDialog.setOkAction( this );
- actionDialog.setVisible( true );
-
-
- }
-
- @Override
- public void actionPerformed(ActionEvent e) {
-
- String text = textField.getText();
-
- String[] values = text.split("-");
- int lowVal = 0;
- int highVal = Integer.MAX_VALUE;
- try
- {
- lowVal = Integer.parseInt( values[0] );
- } catch ( Exception e1 )
- {
- lowVal = 0;
- }
- try
- {
- highVal = Integer.parseInt( values[1] );
- } catch ( Exception e1 )
- {
- highVal = Integer.MAX_VALUE;
- }
-
- System.out.println( "low val : " +lowVal );
- System.out.println( "high val : " +highVal );
-
- trackPool.selectTracksByLength( lowVal , highVal );
-
-
- }
+ JTextField textField = new JTextField("3-10");
+ TrackPool trackPool;
+
+ public TrackLengthDialog(TrackPool trackPool) {
+
+ this.trackPool = trackPool;
+ ActionDialog actionDialog = new ActionDialog("Select by length");
+ actionDialog.getContentPane().setLayout(
+ new BoxLayout(actionDialog.getContentPane(), BoxLayout.PAGE_AXIS));
+
+ actionDialog.getContentPane().add(GuiUtil.createLineBoxPanel(new JLabel("Use the syntax: from-to (in number of frame):")));
+ actionDialog.getContentPane().add(GuiUtil.createLineBoxPanel(textField));
+
+ actionDialog.pack();
+ actionDialog.setLocationRelativeTo(null);
+
+ actionDialog.setOkAction(this);
+ actionDialog.setVisible(true);
+
+
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+
+ String text = textField.getText();
+
+ String[] values = text.split("-");
+ int lowVal;
+ int highVal;
+ try {
+ lowVal = Integer.parseInt(values[0]);
+ }
+ catch (Exception e1) {
+ lowVal = 0;
+ }
+ try {
+ highVal = Integer.parseInt(values[1]);
+ }
+ catch (Exception e1) {
+ highVal = Integer.MAX_VALUE;
+ }
+
+ System.out.println("low val : " + lowVal);
+ System.out.println("high val : " + highVal);
+
+ trackPool.selectTracksByLength(lowVal, highVal);
+
+
+ }
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackManager.java b/src/main/java/plugins/fab/trackmanager/TrackManager.java
index c4b7814350a38f72eaefd6b1fb3125003d634114..923e38968682158e5937cbbccec6854ecf1ea4f3 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackManager.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackManager.java
@@ -1,20 +1,20 @@
/*
- * 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.fab.trackmanager;
@@ -78,58 +78,50 @@ import plugins.nchenouard.spot.Detection;
/**
* @author Fabrice de Chaumont
*/
-public class TrackManager extends PluginActionable
- implements AdjustmentListener, ActionListener, SwimmingPoolListener, IcyFrameListener
-{
+public class TrackManager extends PluginActionable implements AdjustmentListener, ActionListener, SwimmingPoolListener, IcyFrameListener {
- /**
+ /*
* List of active trackEditor shared between trackeditors (not used anymore)
*/
// private static ArrayList<TrackManager> trackManagerList = new ArrayList<TrackManager>();
- /** is this track manager not used anymore (TODO:Should change to a listener structure.) */
+ /**
+ * is this track manager not used anymore (TODO:Should change to a listener structure.)
+ */
boolean trackManagerDestroyed = false;
- public boolean isTrackManagerDestroyed()
- {
+ public boolean isTrackManagerDestroyed() {
return trackManagerDestroyed;
}
- private class MenuItemActionListener implements ActionListener
- {
+ private class MenuItemActionListener implements ActionListener {
Class<? extends PluginTrackManagerProcessor> pluginTrackManagerProcessor;
PluginDescriptor pluginDescriptor;
public MenuItemActionListener(PluginDescriptor pluginDescriptor,
- Class<? extends PluginTrackManagerProcessor> pluginTrackEditorProcessor)
- {
+ Class<? extends PluginTrackManagerProcessor> pluginTrackEditorProcessor) {
this.pluginTrackManagerProcessor = pluginTrackEditorProcessor;
this.pluginDescriptor = pluginDescriptor;
}
@Override
- public void actionPerformed(ActionEvent event)
- {
+ public void actionPerformed(ActionEvent event) {
loadTrackProcessor(pluginDescriptor);
}
}
- void loadTrackProcessor(PluginDescriptor pluginDescriptor)
- {
+ void loadTrackProcessor(PluginDescriptor pluginDescriptor) {
PluginTrackManagerProcessor ptep = null;
- try
- {
- ptep = (PluginTrackManagerProcessor) pluginDescriptor.getPluginClass().newInstance();
+ try {
+ ptep = (PluginTrackManagerProcessor) pluginDescriptor.getPluginClass().getDeclaredConstructor().newInstance();
}
- catch (Exception e)
- {
+ catch (Exception e) {
e.printStackTrace();
}
- if (ptep == null)
- {
+ if (ptep == null) {
System.out.println("Can't load processor.");
return;
}
@@ -143,24 +135,21 @@ public class TrackManager extends PluginActionable
}
- public TrackPool getTrackPool()
- {
+ public TrackPool getTrackPool() {
return trackPool;
}
- void rebuildTrackProcessorDisplay()
- {
+ void rebuildTrackProcessorDisplay() {
rightContentPanel.removeAll();
- for (PluginTrackManagerProcessor trackProcessor : trackPool.getTrackManagerProcessorList())
- {
+ for (PluginTrackManagerProcessor trackProcessor : trackPool.getTrackManagerProcessorList()) {
rightContentPanel.add(trackProcessor.getPanel());
}
rightContentPanel.revalidate();
- ((JPanel) rightContentPanel.getParent()).revalidate();
+ rightContentPanel.getParent().revalidate();
}
JButton addTrackProcessorButton = new JButton("add Track Processor...");
@@ -184,14 +173,14 @@ public class TrackManager extends PluginActionable
* void
* {
* String node = "plugins/fab/trackmanager/browser";
- *
+ *
* Preferences preferences = Preferences.userRoot().node( node );
* String path = preferences.get( "path" , "" );
* chooser.setCurrentDirectory( new File(path) );
- *
+ *
* int returnVal = chooser.showOpenDialog(null);
* if(returnVal != JFileChooser.APPROVE_OPTION) return;
- *
+ *
* preferences.put( "path", chooser.getCurrentDirectory().getAbsolutePath() );
* }
*/
@@ -207,8 +196,7 @@ public class TrackManager extends PluginActionable
JPanel mainPanel = GuiUtil.generatePanel();
- IcyFrame mainFrame = GuiUtil.generateTitleFrame("TrackManager", mainPanel, new Dimension(400, 0), true, true, true,
- true);
+ IcyFrame mainFrame = GuiUtil.generateTitleFrame("TrackManager", mainPanel, new Dimension(400, 0), true, true, true, true);
JMenuBar menuBar = new JMenuBar();
JPopupMenu pluginPopupMenu = new JPopupMenu("Add plugin to queue");
@@ -243,8 +231,7 @@ public class TrackManager extends PluginActionable
JMenuItem onlineHelpMenuItem;
- public TrackManager()
- {
+ public TrackManager() {
mainFrame.addFrameListener(this);
@@ -315,8 +302,7 @@ public class TrackManager extends PluginActionable
trackingGroupSourceMenu = new JMenu("Tracking groups");
- trackingGroupSourceHelpMenuItem = new JMenuItem(
- "No track group available: use either file/load, a tracker or a benchmark generator to generate tracks.");
+ trackingGroupSourceHelpMenuItem = new JMenuItem("No track group available: use either file/load, a tracker or a benchmark generator to generate tracks.");
trackingGroupSourceMenu.add(trackingGroupSourceHelpMenuItem);
trackingGroupSourceHelpMenuItem.setEnabled(false);
@@ -388,8 +374,7 @@ public class TrackManager extends PluginActionable
intermediatePanel.add(rightContentPanel, BorderLayout.NORTH);
intermediatePanel.add(Box.createGlue(), BorderLayout.CENTER);
- JScrollPane rightScrollPanel = new JScrollPane(intermediatePanel, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,
- JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
+ JScrollPane rightScrollPanel = new JScrollPane(intermediatePanel, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
// JScrollPane rightScrollPanel = new JScrollPane(rightContentPanel,
// JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,
// JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
@@ -434,20 +419,17 @@ public class TrackManager extends PluginActionable
}
/**
- * Monitor swimming pool change event and change the track view. If a trackgroup is used in an
- * other trackeditor, the trackgroup checkbox is disabled.
+ * Monitor swimming pool change event and change the track view. If a trackgroup is used in
+ * another trackeditor, the trackgroup checkbox is disabled.
*/
@Override
- public void swimmingPoolChangeEvent(SwimmingPoolEvent swimmingPoolEvent)
- {
- if (swimmingPoolEvent.getType() == SwimmingPoolEventType.ELEMENT_ADDED)
- {
+ public void swimmingPoolChangeEvent(SwimmingPoolEvent swimmingPoolEvent) {
+ if (swimmingPoolEvent.getType() == SwimmingPoolEventType.ELEMENT_ADDED) {
// System.out.println("TrackManager : swimming pool element added.");
// System.out.println("object: " +
// swimmingPoolEvent.getResult().getObject().getClass());
- if (swimmingPoolEvent.getResult().getObject() instanceof TrackGroup)
- {
+ if (swimmingPoolEvent.getResult().getObject() instanceof TrackGroup) {
CheckBoxResultSource checkBoxResultSource = new CheckBoxResultSource(swimmingPoolEvent.getResult(),
true);
trackingGroupSourceMenu.add(checkBoxResultSource);
@@ -455,26 +437,21 @@ public class TrackManager extends PluginActionable
trackingGroupSourceHelpMenuItem.setVisible(false);
}
}
- if (swimmingPoolEvent.getType() == SwimmingPoolEventType.ELEMENT_REMOVED)
- {
+ if (swimmingPoolEvent.getType() == SwimmingPoolEventType.ELEMENT_REMOVED) {
trackPool.removeResult(swimmingPoolEvent.getResult());
// resultList.remove( swimmingPoolEvent.getResult() );
// If there is only one item to remove, no item will be left, then display help message.
- if (trackingGroupSourceMenu.getItemCount() == 2)
- {
+ if (trackingGroupSourceMenu.getItemCount() == 2) {
trackingGroupSourceHelpMenuItem.setVisible(true);
}
- for (int i = 0; i < trackingGroupSourceMenu.getItemCount(); i++)
- {
+ for (int i = 0; i < trackingGroupSourceMenu.getItemCount(); i++) {
JMenuItem mi = trackingGroupSourceMenu.getItem(i);
- if (mi instanceof CheckBoxResultSource)
- {
+ if (mi instanceof CheckBoxResultSource) {
CheckBoxResultSource cbrs = (CheckBoxResultSource) mi;
- if (cbrs.result == swimmingPoolEvent.getResult())
- {
+ if (cbrs.result == swimmingPoolEvent.getResult()) {
cbrs.destroy();
return;
}
@@ -502,8 +479,7 @@ public class TrackManager extends PluginActionable
}
- private void initTrackPoolInnerPanel()
- {
+ private void initTrackPoolInnerPanel() {
// trackingGroupSourceMenu.removeAll();
@@ -511,10 +487,8 @@ public class TrackManager extends PluginActionable
ArrayList<SwimmingObject> swimmingPoolArrayList = Icy.getMainInterface().getSwimmingPool().getObjects();
- for (SwimmingObject result : swimmingPoolArrayList)
- {
- if (result.getObject() instanceof TrackGroup)
- {
+ for (SwimmingObject result : swimmingPoolArrayList) {
+ if (result.getObject() instanceof TrackGroup) {
boolean enabled = true;
// for (TrackManager trackEditor : trackManagerList)
// {
@@ -526,7 +500,7 @@ public class TrackManager extends PluginActionable
// }
CheckBoxResultSource checkBoxResultResource = new CheckBoxResultSource( // "" +
- // result.getObject().toString(),
+ // result.getObject().toString(),
result, enabled);
trackingGroupSourceMenu.add(checkBoxResultResource);
@@ -542,15 +516,12 @@ public class TrackManager extends PluginActionable
}
- /**
- * Called from other trackeditor to check wich results are already used.
- *
- * @return
- */
- private ArrayList<SwimmingObject> getResultList()
- {
- return trackPool.resultList;
- }
+// /**
+// * Called from other trackeditor to check witch results are already used.
+// */
+// private ArrayList<SwimmingObject> getResultList() {
+// return trackPool.resultList;
+// }
// /**
// * Called from other TrackEditor to avoid having the same track used
@@ -577,32 +548,32 @@ public class TrackManager extends PluginActionable
// }
// }
- /** List of sequences which will be kept synchronize while the t cursor are moving. */
+ ///** List of sequences which will be kept synchronize while the t cursor are moving. */
// private ArrayList<Sequence> sequenceToKeepSynchronizeInT = new ArrayList<Sequence>();
- /** current time in track window */
+ /**
+ * current time in track window
+ */
int currentT = 0;
- public int getCurrentPositionT()
- {
+ public int getCurrentPositionT() {
return currentT;
}
- public void setCurrentPositionT(int t)
- {
+ public void setCurrentPositionT(int t) {
currentT = t;
reSynchroTSequence();
trackPool.fireTrackEditorProcessorChange();
}
- void timeCursorChanged(int t)
- {
+ void timeCursorChanged(int t) {
setCurrentPositionT(t);
}
- /** set the sequence with the current time set in trackEditor */
- private void reSynchroTSequence()
- {
+ /**
+ * set the sequence with the current time set in trackEditor
+ */
+ private void reSynchroTSequence() {
// System.out.println("Synchro sequence");
// for (Sequence sequence : sequenceToKeepSynchronizeInT)
// {
@@ -611,10 +582,8 @@ public class TrackManager extends PluginActionable
// }
Sequence sequence = sequenceSelector.getSelectedSequence();
- if (sequence != null)
- {
- for (Viewer viewer : Icy.getMainInterface().getViewers(sequence))
- {
+ if (sequence != null) {
+ for (Viewer viewer : Icy.getMainInterface().getViewers(sequence)) {
viewer.setPositionT(currentT);
}
// sequence.setT( currentT );
@@ -622,18 +591,14 @@ public class TrackManager extends PluginActionable
}
- class CheckBoxResultSource extends JCheckBoxMenuItem implements ActionListener
- {
- private static final long serialVersionUID = -2021713434786505514L;
+ class CheckBoxResultSource extends JCheckBoxMenuItem implements ActionListener {
// JCheckBox checkBox = new JCheckBox();
// JToggleButton trackTimeOnSequenceButton = new JToggleButton("T");
SwimmingObject result;
- public CheckBoxResultSource(SwimmingObject result, boolean enabled)
- {
- if (!(result.getObject() instanceof TrackGroup))
- {
+ public CheckBoxResultSource(SwimmingObject result, boolean enabled) {
+ if (!(result.getObject() instanceof TrackGroup)) {
System.out.println("Result object type not supported.");
return;
}
@@ -641,7 +606,7 @@ public class TrackManager extends PluginActionable
TrackGroup trackGroup = (TrackGroup) result.getObject();
int nbTracks = trackGroup.getTrackSegmentList().size();
- String label = "" + result.getObject().toString() + " (" + nbTracks + " Tracks)";
+ String label = result.getObject().toString() + " (" + nbTracks + " Tracks)";
// trackTimeOnSequenceButton.setToolTipText("Keep Time synchro with sequence");
// trackTimeOnSequenceButton.setSelected( true ) ;
@@ -684,8 +649,7 @@ public class TrackManager extends PluginActionable
// checkBox.setSelected( b );
// }
- public void destroy()
- {
+ public void destroy() {
// remove the sequence tracked
// if (trackTimeOnSequenceButton.isSelected())
// {
@@ -698,8 +662,7 @@ public class TrackManager extends PluginActionable
}
@Override
- public void actionPerformed(ActionEvent e)
- {
+ public void actionPerformed(ActionEvent e) {
// if (e.getSource() == trackTimeOnSequenceButton)
// {
@@ -715,10 +678,8 @@ public class TrackManager extends PluginActionable
// reSynchroTSequence();
// }
- if (e.getSource() == this)
- {
- if (this.isSelected())
- {
+ if (e.getSource() == this) {
+ if (this.isSelected()) {
// resultList.add( result );
trackPool.addResult(result);
// trackPool.getDisplaySequence().painterChanged( null );
@@ -733,8 +694,7 @@ public class TrackManager extends PluginActionable
// }
}
- else
- {
+ else {
trackPool.removeResult(result);
// trackPool.getDisplaySequence().painterChanged( null );
// for (TrackManager trackEditor : trackManagerList)
@@ -764,8 +724,7 @@ public class TrackManager extends PluginActionable
}
- private void loadTracks()
- {
+ private void loadTracks() {
JFileChooser chooser = new JFileChooser();
chooser.setDialogTitle("Select track.xml file.");
@@ -783,34 +742,28 @@ public class TrackManager extends PluginActionable
preferences.put("path", chooser.getCurrentDirectory().getAbsolutePath());
- try
- {
+ try {
final List<TrackGroup> groups = loadTracks(chooser.getSelectedFile().getAbsolutePath());
// add group to swimming pool
- for (TrackGroup group : groups)
- {
+ for (TrackGroup group : groups) {
SwimmingObject so = new SwimmingObject(group);
Icy.getMainInterface().getSwimmingPool().add(so);
}
trackPool.fireTrackEditorProcessorChange();
}
- catch (IllegalArgumentException ex)
- {
+ catch (IllegalArgumentException ex) {
MessageDialog.showDialog(ex.getMessage(), MessageDialog.ERROR_MESSAGE);
- return;
}
}
- public static List<TrackGroup> loadTracks(String path) throws IllegalArgumentException
- {
+ public static List<TrackGroup> loadTracks(String path) throws IllegalArgumentException {
final Document document = XMLUtil.loadDocument(path, false);
return loadTracks(document);
}
- public static List<TrackGroup> loadTracks(Document document) throws IllegalArgumentException
- {
+ public static List<TrackGroup> loadTracks(Document document) throws IllegalArgumentException {
if (document == null)
throw new IllegalArgumentException("Invalid track file !");
@@ -821,14 +774,12 @@ public class TrackManager extends PluginActionable
final List<TrackGroup> result = new ArrayList<>();
- for (Element trackGroupElement : XMLUtil.getElements(rootElement, "trackgroup"))
- {
+ for (Element trackGroupElement : XMLUtil.getElements(rootElement, "trackgroup")) {
// create track group
final TrackGroup trackGroup = new TrackGroup(null);
trackGroup.setDescription(XMLUtil.getAttributeValue(trackGroupElement, "description", "no description"));
- for (Element trackSegmentElement : XMLUtil.getElements(trackGroupElement))
- {
+ for (Element trackSegmentElement : XMLUtil.getElements(trackGroupElement)) {
// create track segment
final TrackSegment trackSegment = new TrackSegment();
final int id = XMLUtil.getAttributeIntValue(trackSegmentElement, "id", -1);
@@ -838,8 +789,7 @@ public class TrackManager extends PluginActionable
else
trackSegment.setId(id);
- for (Element detectionElement : XMLUtil.getElements(trackSegmentElement))
- {
+ for (Element detectionElement : XMLUtil.getElements(trackSegmentElement)) {
// create detection
final Detection detection = Detection.createDetection(XMLUtil.getAttributeValue(detectionElement,
"classname", "plugins.nchenouard.spot.Detection"));
@@ -853,16 +803,14 @@ public class TrackManager extends PluginActionable
// add track segment to track group
trackGroup.addTrackSegment(trackSegment);
}
-
+
// add track group to result
result.add(trackGroup);
}
// get links
- for (Element linkListElement : XMLUtil.getElements(rootElement, "linklist"))
- {
- for (Element link : XMLUtil.getElements(linkListElement))
- {
+ for (Element linkListElement : XMLUtil.getElements(rootElement, "linklist")) {
+ for (Element link : XMLUtil.getElements(linkListElement)) {
final int idFrom = XMLUtil.getAttributeIntValue(link, "from", -1);
final int idTo = XMLUtil.getAttributeIntValue(link, "to", -1);
@@ -877,8 +825,7 @@ public class TrackManager extends PluginActionable
return result;
}
- private void loadTracksFromTrackMate()
- {
+ private void loadTracksFromTrackMate() {
JFileChooser chooser = new JFileChooser();
chooser.setDialogTitle("Import TrackMate xml track file.");
@@ -896,57 +843,48 @@ public class TrackManager extends PluginActionable
preferences.put("path", chooser.getCurrentDirectory().getAbsolutePath());
- try
- {
+ try {
final List<TrackGroup> groups = loadTracksFromTrackMate(chooser.getSelectedFile().getAbsolutePath());
// add group to swimming pool
- for (TrackGroup group : groups)
- {
+ for (TrackGroup group : groups) {
SwimmingObject so = new SwimmingObject(group);
Icy.getMainInterface().getSwimmingPool().add(so);
}
trackPool.fireTrackEditorProcessorChange();
}
- catch (IllegalArgumentException ex)
- {
+ catch (IllegalArgumentException ex) {
MessageDialog.showDialog(ex.getMessage(), MessageDialog.ERROR_MESSAGE);
- return;
}
}
- public static List<TrackGroup> loadTracksFromTrackMate(String path)
- {
+ public static List<TrackGroup> loadTracksFromTrackMate(String path) {
final Document document = XMLUtil.loadDocument(path, false);
return loadTracksFromTrackMate(document);
}
- public static List<TrackGroup> loadTracksFromTrackMate(Document document) throws IllegalArgumentException
- {
+ public static List<TrackGroup> loadTracksFromTrackMate(Document document) throws IllegalArgumentException {
if (document == null)
throw new IllegalArgumentException("Invalid track file !");
final Element trackNode = XMLUtil.getElement(document.getDocumentElement().getParentNode(), "Tracks");
if (trackNode == null)
- throw new IllegalArgumentException(
- "Unsupported version of TrackMate XML file !\nTry to use the Icy XML export in TrackMate instead and directly load it with 'TrackManager-->File->Load...' command.");
+ throw new IllegalArgumentException("Unsupported version of TrackMate XML file !\nTry to use the Icy XML export in TrackMate instead and directly load it with 'TrackManager-->File->Load...' command.");
final List<TrackGroup> result = new ArrayList<>();
- final String unit = XMLUtil.getAttributeValue(trackNode, "spaceUnits", "pixel");
+ //final String unit = XMLUtil.getAttributeValue(trackNode, "spaceUnits", "pixel");
- double unitMultiplicator = 1;
- if (unit == "micron")
- unitMultiplicator = 0.000001d;
+ //double unitMultiplicator = 1;
+ //if (unit.equals("micron"))
+ // unitMultiplicator = 0.000001d;
- for (Element trackElement : XMLUtil.getElements(document.getDocumentElement().getParentNode(), "Tracks"))
- {
+ for (Element trackElement : XMLUtil.getElements(document.getDocumentElement().getParentNode(), "Tracks")) {
// create track group
final TrackGroup trackGroup = new TrackGroup(null);
trackGroup.setDescription(XMLUtil.getAttributeValue(trackElement, "description", "no description"));
- for (Element trackSegmentElement : XMLUtil.getElements(trackElement))
- {
+ for (Element trackSegmentElement : XMLUtil.getElements(trackElement)) {
// create track segment
final TrackSegment trackSegment = new TrackSegment();
@@ -956,8 +894,7 @@ public class TrackManager extends PluginActionable
else
trackSegment.setId(id);
- for (Element detectionElement : XMLUtil.getElements(trackSegmentElement))
- {
+ for (Element detectionElement : XMLUtil.getElements(trackSegmentElement)) {
// create detection
final Detection detection = Detection.createDetection("plugins.nchenouard.spot.Detection");
@@ -970,7 +907,7 @@ public class TrackManager extends PluginActionable
// add track segment to group
trackGroup.addTrackSegment(trackSegment);
}
-
+
// add track group to result
result.add(trackGroup);
}
@@ -978,8 +915,7 @@ public class TrackManager extends PluginActionable
return result;
}
- private void debug()
- {
+ private void debug() {
System.out.println("--- debug");
// for ( Link link : trackPool.getLinks() )
@@ -993,8 +929,7 @@ public class TrackManager extends PluginActionable
}
- private void saveTracks()
- {
+ private void saveTracks() {
JFileChooser chooser = new JFileChooser();
chooser.setDialogTitle("Select track.xml file.");
chooser.setFileFilter(new FileNameExtensionFilter("XML track file", "xml"));
@@ -1014,8 +949,7 @@ public class TrackManager extends PluginActionable
saveTracks(chooser.getSelectedFile().getAbsolutePath(), trackPool.getTrackGroupList());
}
- public static void saveTracks(String path, List<TrackGroup> groups)
- {
+ public static void saveTracks(String path, List<TrackGroup> groups) {
// get file
final File file = new File(FileUtil.setExtension(path, ".xml"));
// generate document
@@ -1024,26 +958,22 @@ public class TrackManager extends PluginActionable
XMLUtil.saveDocument(document, file);
}
- public static Document saveTracks(List<TrackGroup> groups)
- {
+ public static Document saveTracks(List<TrackGroup> groups) {
final Document result = XMLUtil.createDocument(true);
final Element rootElement = result.getDocumentElement();
final Element versionElement = XMLUtil.addElement(rootElement, "trackfile");
versionElement.setAttribute("version", "1");
- for (TrackGroup trackGroup : groups)
- {
+ for (TrackGroup trackGroup : groups) {
final Element trackGroupElement = XMLUtil.addElement(rootElement, "trackgroup");
trackGroupElement.setAttribute("description", trackGroup.getDescription());
- for (TrackSegment trackSegment : trackGroup.getTrackSegmentList())
- {
+ for (TrackSegment trackSegment : trackGroup.getTrackSegmentList()) {
final Element trackElement = XMLUtil.addElement(trackGroupElement, "track");
- trackElement.setAttribute("id", "" + trackSegment.getId());
+ trackElement.setAttribute("id", String.valueOf(trackSegment.getId()));
- for (Detection detection : trackSegment.getDetectionList())
- {
+ for (Detection detection : trackSegment.getDetectionList()) {
final Element detectionElement = XMLUtil.addElement(trackElement, "detection");
detectionElement.setAttribute("classname", detection.getClass().getName());
@@ -1058,12 +988,11 @@ public class TrackManager extends PluginActionable
// save links
final Element linklistElement = XMLUtil.addElement(rootElement, "linklist");
- for (Link link : TrackPool.getLinks(groups))
- {
+ for (Link link : TrackPool.getLinks(groups)) {
final Element trackElement = XMLUtil.addElement(linklistElement, "link");
- trackElement.setAttribute("from", "" + link.getStartSegment().getId());
- trackElement.setAttribute("to", "" + link.getEndSegment().getId());
+ trackElement.setAttribute("from", String.valueOf(link.getStartSegment().getId()));
+ trackElement.setAttribute("to", String.valueOf(link.getEndSegment().getId()));
}
return result;
@@ -1072,23 +1001,19 @@ public class TrackManager extends PluginActionable
/**
* Attempt to re-classify / re-organize the track order to improve track understandment.
*/
- public void reOrganize()
- {
- for (TrackGroup trackGroup : trackPool.getTrackGroupList())
- {
+ public void reOrganize() {
+ for (TrackGroup trackGroup : trackPool.getTrackGroupList()) {
+ @SuppressWarnings("unchecked")
List<TrackSegment> trackSegmentList = (ArrayList<TrackSegment>) trackGroup.getTrackSegmentList().clone();
- List<TrackSegment> trackSegmentListOrganized = (ArrayList<TrackSegment>) trackGroup.getTrackSegmentList()
- .clone();
+ @SuppressWarnings("unchecked")
+ List<TrackSegment> trackSegmentListOrganized = (ArrayList<TrackSegment>) trackGroup.getTrackSegmentList().clone();
int tMax = trackPool.getLastDetectionTimePoint();
for (int t = 0; t < tMax; t++)
- for (TrackSegment ts : trackSegmentList)
- {
- if (ts.getFirstDetection().getT() == t)
- {
- for (int index = 0; index < ts.nextList.size(); index++)
- {
+ for (TrackSegment ts : trackSegmentList) {
+ if (ts.getFirstDetection().getT() == t) {
+ for (int index = 0; index < ts.nextList.size(); index++) {
TrackSegment ts2 = ts.nextList.get(index);
trackSegmentListOrganized.remove(ts2);
int targetIndex = trackSegmentListOrganized.indexOf(ts) - ts.nextList.size() / 2 + index
@@ -1111,40 +1036,32 @@ public class TrackManager extends PluginActionable
}
@Override
- public void actionPerformed(ActionEvent e)
- {
- if (e.getSource() == onlineHelpMenuItem)
- {
- NetworkUtil.openBrowser("http://icy.bioimageanalysis.org/index.php?display=detailPlugin&pluginId=88");
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource() == onlineHelpMenuItem) {
+ NetworkUtil.openBrowser("https://icy.bioimageanalysis.org/plugin/track-manager/");
}
- if (e.getSource() == loadMenuItem)
- {
+ if (e.getSource() == loadMenuItem) {
loadTracks();
}
- if (e.getSource() == loadFromTrackMateMenuItem)
- {
+ if (e.getSource() == loadFromTrackMateMenuItem) {
loadTracksFromTrackMate();
}
- if (e.getSource() == saveMenuItem)
- {
+ if (e.getSource() == saveMenuItem) {
saveTracks();
}
- if (e.getSource() == sequenceSelector)
- {
+ if (e.getSource() == sequenceSelector) {
trackPool.setDisplaySequence(sequenceSelector.getSelectedSequence());
}
- if (e.getSource() == reOrganizeMenuItem)
- {
+ if (e.getSource() == reOrganizeMenuItem) {
reOrganize();
}
- if (e.getSource() == displayTrackPanelCheckBoxMenuItem)
- {
+ if (e.getSource() == displayTrackPanelCheckBoxMenuItem) {
trackPanel.setEnableLeftPanelTrackDisplay(displayTrackPanelCheckBoxMenuItem.isSelected());
String node = "plugins/fab/trackmanager/displaytrackpanel";
@@ -1159,41 +1076,33 @@ public class TrackManager extends PluginActionable
// trackPool.fireTrackEditorProcessorChange();
}
- if (e.getSource() == externaliseCheckBoxMenuItem)
- {
- if (externaliseCheckBoxMenuItem.isSelected())
- {
+ if (e.getSource() == externaliseCheckBoxMenuItem) {
+ if (externaliseCheckBoxMenuItem.isSelected()) {
mainFrame.externalize();
}
- else
- {
+ else {
mainFrame.internalize();
}
}
- if (e.getSource() == addTrackProcessorButton)
- {
+ if (e.getSource() == addTrackProcessorButton) {
pluginPopupMenu.show(addTrackProcessorButton, 0, 0);
}
- if (e.getSource() == showHideTrackPoolSourcesPanel)
- {
+ if (e.getSource() == showHideTrackPoolSourcesPanel) {
trackGroupSourceInnerPanel.setVisible(showHideTrackPoolSourcesPanel.isSelected());
}
- if (e.getSource() == selectAllMenuItem)
- {
+ if (e.getSource() == selectAllMenuItem) {
trackPool.selectAllTracks();
}
- if (e.getSource() == unselectAllMenuItem)
- {
+ if (e.getSource() == unselectAllMenuItem) {
trackPool.unselectAllTracks();
}
- if (e.getSource() == selectTrackByLengthMenuItem)
- {
- TrackLengthDialog tld = new TrackLengthDialog(trackPool);
+ //if (e.getSource() == selectTrackByLengthMenuItem) {
+ //TrackLengthDialog tld = new TrackLengthDialog(trackPool);
// TrackLengthDialog tld = new TrackLengthDialog();
// JDialog dialog = new JDialog();
@@ -1207,43 +1116,36 @@ public class TrackManager extends PluginActionable
// dialog.setSize(200, 100);
// dialog.setLocationRelativeTo(null);
// dialog.setVisible(true);
- }
+ //}
- if (e.getSource() == invertSelectionMenuItem)
- {
+ if (e.getSource() == invertSelectionMenuItem) {
trackPool.invertSelection();
}
- if (e.getSource() == deleteLinkMenuItem)
- {
+ if (e.getSource() == deleteLinkMenuItem) {
trackPool.deleteSelectedLink();
}
- if (e.getSource() == deleteSelectionMenuItem)
- {
+ if (e.getSource() == deleteSelectionMenuItem) {
trackPool.deleteSelectedTracks();
}
- if (e.getSource() == debugMenuItem)
- {
+ if (e.getSource() == debugMenuItem) {
debug();
}
- if (e.getSource() == fuseTracksMenuItem)
- {
+ if (e.getSource() == fuseTracksMenuItem) {
trackPool.fuseAllTracks();
}
- if (e.getSource() == zoomLessButton)
- {
+ if (e.getSource() == zoomLessButton) {
int newX = (int) trackPanel.getDetectDim().getWidth() - 5;
if (newX <= 0)
newX = 5;
trackPanel.setDetectDim(new Dimension(newX, newX));
trackPool.fireTrackEditorProcessorChange();
}
- if (e.getSource() == zoomMoreButton)
- {
+ if (e.getSource() == zoomMoreButton) {
trackPanel.setDetectDim(new Dimension((int) trackPanel.getDetectDim().getWidth() + 5,
(int) trackPanel.getDetectDim().getHeight() + 5));
trackPool.fireTrackEditorProcessorChange();
@@ -1267,13 +1169,11 @@ public class TrackManager extends PluginActionable
}
@Override
- public void adjustmentValueChanged(AdjustmentEvent arg0)
- {
+ public void adjustmentValueChanged(AdjustmentEvent arg0) {
}
- private void buildPluginMenu()
- {
+ private void buildPluginMenu() {
pluginPopupMenu.removeAll();
@@ -1284,11 +1184,9 @@ public class TrackManager extends PluginActionable
pluginPopupMenu.addSeparator();
}
- for (PluginDescriptor plugin : PluginLoader.getPlugins())
- {
+ for (PluginDescriptor plugin : PluginLoader.getPlugins()) {
if (plugin.isInstanceOf(PluginTrackManagerProcessor.class))
- if (!plugin.isAbstract())
- {
+ if (!plugin.isAbstract()) {
JMenuItem menuItem = new JMenuItem(plugin.getName(), ResourceUtil.scaleIcon(plugin.getIcon(), 24));
pluginPopupMenu.add(menuItem);
@@ -1300,8 +1198,7 @@ public class TrackManager extends PluginActionable
}
- public void moveTrackProcessor(PluginTrackManagerProcessor trackEditorProcessor, int i)
- {
+ public void moveTrackProcessor(PluginTrackManagerProcessor trackEditorProcessor, int i) {
int newIndex = trackPool.getTrackManagerProcessorList().indexOf(trackEditorProcessor);
// System.out.println("previous index: " + newIndex );
newIndex += i;
@@ -1324,14 +1221,12 @@ public class TrackManager extends PluginActionable
}
@Override
- public void icyFrameActivated(IcyFrameEvent e)
- {
+ public void icyFrameActivated(IcyFrameEvent e) {
}
@Override
- public void icyFrameClosed(IcyFrameEvent e)
- {
+ public void icyFrameClosed(IcyFrameEvent e) {
// release T synchro with sequences.
// sequenceToKeepSynchronizeInT.clear();
@@ -1349,10 +1244,9 @@ public class TrackManager extends PluginActionable
// close all track processors.
- ArrayList<PluginTrackManagerProcessor> processorList = (ArrayList<PluginTrackManagerProcessor>) trackPool
- .getTrackManagerProcessorList().clone();
- for (PluginTrackManagerProcessor tep : processorList)
- {
+ @SuppressWarnings("unchecked")
+ ArrayList<PluginTrackManagerProcessor> processorList = (ArrayList<PluginTrackManagerProcessor>) trackPool.getTrackManagerProcessorList().clone();
+ for (PluginTrackManagerProcessor tep : processorList) {
tep.Close();
}
@@ -1368,80 +1262,57 @@ public class TrackManager extends PluginActionable
}
@Override
- public void icyFrameClosing(IcyFrameEvent e)
- {
+ public void icyFrameClosing(IcyFrameEvent e) {
}
@Override
- public void icyFrameDeactivated(IcyFrameEvent e)
- {
+ public void icyFrameDeactivated(IcyFrameEvent e) {
}
@Override
- public void icyFrameDeiconified(IcyFrameEvent e)
- {
+ public void icyFrameDeiconified(IcyFrameEvent e) {
}
@Override
- public void icyFrameIconified(IcyFrameEvent e)
- {
+ public void icyFrameIconified(IcyFrameEvent e) {
}
@Override
- public void icyFrameOpened(IcyFrameEvent e)
- {
+ public void icyFrameOpened(IcyFrameEvent e) {
}
@Override
- public void icyFrameExternalized(IcyFrameEvent e)
- {
+ public void icyFrameExternalized(IcyFrameEvent e) {
}
@Override
- public void icyFrameInternalized(IcyFrameEvent e)
- {
+ public void icyFrameInternalized(IcyFrameEvent e) {
}
- @Override
- public void compute()
- {
- // TODO Auto-generated method stub
-
- }
- //
- // public void unSelectAllTrackGroup() {
- // // TODO Auto-generated method stub
- //
- // }
-
// public void setDisplaySequence(Sequence sequence) {
//
// sequenceSelector.setSequenceSelected( sequence );
//
// }
- public Sequence getDisplaySequence()
- {
+ public Sequence getDisplaySequence() {
return sequenceSelector.getSelectedSequence();
}
- public void setDisplaySequence(Sequence sequence)
- {
+ public void setDisplaySequence(Sequence sequence) {
sequenceSelector.setSelectedSequence(sequence);
}
@Override
- public void run()
- {
+ public void run() {
}
-
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackManagerPainter.java b/src/main/java/plugins/fab/trackmanager/TrackManagerPainter.java
index b303c455b0b34ee9066db1c0e2f73914d0f73860..5c21ad206a2a56412056380622317199644057d6 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackManagerPainter.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackManagerPainter.java
@@ -1,20 +1,20 @@
/*
- * 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.fab.trackmanager;
@@ -35,44 +35,43 @@ import icy.canvas.IcyCanvas;
import icy.painter.Overlay;
import icy.sequence.Sequence;
import icy.swimmingPool.SwimmingObject;
+import icy.type.point.Point5D;
import icy.util.GraphicsUtil;
import icy.util.ShapeUtil;
import plugins.nchenouard.spot.Detection;
/**
* Painter used to display tracks on sequence (as overlay)
- *
+ *
* @author Fabrice de Chaumont
*/
-public class TrackManagerPainter extends Overlay
-{
- private TrackPool trackPool = null;
+public class TrackManagerPainter extends Overlay {
+ private final TrackPool trackPool;
- /** List of Listeners */
- private List<TrackPainterListener> trackPainterListener = new ArrayList<TrackPainterListener>();
+ /**
+ * List of Listeners
+ */
+ private final List<TrackPainterListener> trackPainterListener = new ArrayList<>();
private boolean drawTracksOnSequence = true;
private boolean subPixelicDisplay = true;
- public TrackManagerPainter(TrackPool trackPool)
- {
+ public TrackManagerPainter(TrackPool trackPool) {
super("Track painter");
this.trackPool = trackPool;
}
- public boolean isSubPixelicDisplay()
- {
+ public boolean isSubPixelicDisplay() {
return subPixelicDisplay;
}
- public void setSubPixelicDisplay(boolean subPixelicDisplay)
- {
+ public void setSubPixelicDisplay(boolean subPixelicDisplay) {
this.subPixelicDisplay = subPixelicDisplay;
}
- public void mouseClick(MouseEvent e, Point2D p, IcyCanvas icyCanvas)
- {
+ @Override
+ public void mouseClick(MouseEvent e, /*Point2D p*/ Point5D.Double imagePoint, IcyCanvas icyCanvas) {
if (e.isConsumed())
return;
@@ -80,22 +79,51 @@ public class TrackManagerPainter extends Overlay
distanceThresholdSqr *= distanceThresholdSqr;
// Check if a detection is around.
- for (TrackGroup tg : trackPool.getTrackGroupList())
- {
- for (TrackSegment ts : tg.getTrackSegmentList())
- {
- for (Detection d : ts.getDetectionList())
- {
- if (d.isEnabled())
- {
+ for (TrackGroup tg : trackPool.getTrackGroupList()) {
+ for (TrackSegment ts : tg.getTrackSegmentList()) {
+ for (Detection d : ts.getDetectionList()) {
+ if (d.isEnabled()) {
+ //final double dist = new Point2D.Double(p.getX(), p.getY()).distanceSq(new Point2D.Double(d.getX(), d.getY()));
+ final Point2D p2d = imagePoint.toPoint2D();
+ final double dist = new Point2D.Double(p2d.getX(), p2d.getY())
+ .distanceSq(new Point2D.Double(d.getX(), d.getY()));
+
+ if (dist < distanceThresholdSqr) {
+ TrackSegment ts1 = trackPool.getTrackSegmentWithDetection(d);
+ if (ts1 != null) {
+ ts1.setAllDetectionSelected(!ts1.isAllDetectionSelected());
+ trackPool.getDisplaySequence().overlayChanged(this);
+ // so tracks in left panel will be refreshed
+ fireTrackPainterEvent();
+ e.consume();
+ }
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /*@Override
+ public void mouseClick(MouseEvent e, Point2D p, IcyCanvas icyCanvas) {
+ if (e.isConsumed())
+ return;
+
+ float distanceThresholdSqr = (float) icyCanvas.canvasToImageDeltaX(3);
+ distanceThresholdSqr *= distanceThresholdSqr;
+
+ // Check if a detection is around.
+ for (TrackGroup tg : trackPool.getTrackGroupList()) {
+ for (TrackSegment ts : tg.getTrackSegmentList()) {
+ for (Detection d : ts.getDetectionList()) {
+ if (d.isEnabled()) {
final double dist = new Point2D.Double(p.getX(), p.getY())
.distanceSq(new Point2D.Double(d.getX(), d.getY()));
- if (dist < distanceThresholdSqr)
- {
+ if (dist < distanceThresholdSqr) {
TrackSegment ts1 = trackPool.getTrackSegmentWithDetection(d);
- if (ts1 != null)
- {
+ if (ts1 != null) {
ts1.setAllDetectionSelected(!ts1.isAllDetectionSelected());
trackPool.getDisplaySequence().overlayChanged(this);
// so tracks in left panel will be refreshed
@@ -109,7 +137,7 @@ public class TrackManagerPainter extends Overlay
}
}
- }
+ }*/
// // should switch to an hashmap to manage several 3D viewers.
// ArrayList<vtkActor> actorList = new ArrayList<vtkActor>();
@@ -283,19 +311,14 @@ public class TrackManagerPainter extends Overlay
// }
@Override
- public void paint(Graphics2D g, Sequence sequence, IcyCanvas canvas)
- {
+ public void paint(Graphics2D g, Sequence sequence, IcyCanvas canvas) {
// System.out.println("TP");
- if (trackPool != null)
- {
- if (trackPool.getTrackManager() != null)
- {
- if (canvas != null)
- {
- if (trackPool.getTrackManager().currentT != canvas.getPositionT())
- {
+ if (trackPool != null) {
+ if (trackPool.getTrackManager() != null) {
+ if (canvas != null) {
+ if (trackPool.getTrackManager().currentT != canvas.getPositionT()) {
// synchronize processors now so repaint is ok
trackPool.getTrackManager().currentT = canvas.getPositionT();
trackPool.getTrackManager().trackPanel.recomputeProcessors();
@@ -312,7 +335,7 @@ public class TrackManagerPainter extends Overlay
// System.out.println("TP: now painting frame " + trackPool.getTrackManager().currentT );
- if (isDrawTracksOnSequence() == false)
+ if (!isDrawTracksOnSequence())
return;
// if (canvas instanceof VtkCanvas)
@@ -320,8 +343,7 @@ public class TrackManagerPainter extends Overlay
// draw3D(sequence, (VtkCanvas) canvas);
// }
- if (canvas instanceof Canvas2D)
- {
+ if (canvas instanceof Canvas2D) {
final Graphics2D g2 = (Graphics2D) g.create();
final Rectangle2D bounds = new Rectangle2D.Double();
final Line2D line = new Line2D.Double();
@@ -338,27 +360,23 @@ public class TrackManagerPainter extends Overlay
g2.setStroke(new BasicStroke(trackWidth));
// build the list of line section
- final List<Detection> allDetections = new ArrayList<Detection>();
- final List<TrackLineSection> lineSections = new ArrayList<TrackLineSection>();
- final List<TrackLineSection> connectorSections = new ArrayList<TrackLineSection>();
-
- for (SwimmingObject result : trackPool.resultList)
- {
- final TrackGroup tg = (TrackGroup) result.getObject();
- {
- for (TrackSegment ts : tg.getTrackSegmentList())
- {
+ final List<Detection> allDetections = new ArrayList<>();
+ final List<TrackLineSection> lineSections = new ArrayList<>();
+ final List<TrackLineSection> connectorSections = new ArrayList<>();
+
+ if (trackPool != null) {
+ for (SwimmingObject result : trackPool.resultList) {
+ final TrackGroup tg = (TrackGroup) result.getObject();
+ for (TrackSegment ts : tg.getTrackSegmentList()) {
final List<Detection> detectionList = ts.getDetectionList();
allDetections.addAll(detectionList);
// line sections
- if (detectionList.size() > 1)
- {
+ if (detectionList.size() > 1) {
Detection startDetection = detectionList.get(0);
- for (int i = 1; i < ts.getDetectionList().size(); i++)
- {
+ for (int i = 1; i < ts.getDetectionList().size(); i++) {
final Detection endDetection = detectionList.get(i);
lineSections.add(new TrackLineSection(startDetection, endDetection));
@@ -368,10 +386,8 @@ public class TrackManagerPainter extends Overlay
}
// connector between 2 tracks
- if (ts.getLastDetection().isEnabled())
- {
- for (TrackSegment tsNext : ts.nextList)
- {
+ if (ts.getLastDetection().isEnabled()) {
+ for (TrackSegment tsNext : ts.nextList) {
final Detection endDetection = tsNext.getFirstDetection();
if (endDetection.isEnabled())
@@ -386,20 +402,16 @@ public class TrackManagerPainter extends Overlay
g2.setStroke(new BasicStroke(trackWidth * 3));
g2.setColor(Color.white);
- for (TrackLineSection lineSection : lineSections)
- {
- if (lineSection.isEnabled() && lineSection.isSelected()
- && GraphicsUtil.isVisible(g2, lineSection.getBounds(bounds, trackWidth * 2)))
+ for (TrackLineSection lineSection : lineSections) {
+ if (lineSection.isEnabled() && lineSection.isSelected() && GraphicsUtil.isVisible(g2, lineSection.getBounds(bounds, trackWidth * 2)))
g2.draw(lineSection.getLine2D(line));
}
// display tracks
g2.setStroke(new BasicStroke(trackWidth));
- for (TrackLineSection lineSection : lineSections)
- {
- if (lineSection.isEnabled() && GraphicsUtil.isVisible(g2, lineSection.getBounds(bounds, trackWidth)))
- {
+ for (TrackLineSection lineSection : lineSections) {
+ if (lineSection.isEnabled() && GraphicsUtil.isVisible(g2, lineSection.getBounds(bounds, trackWidth))) {
g2.setColor(lineSection.getColor());
g2.draw(lineSection.getLine2D(line));
}
@@ -408,15 +420,13 @@ public class TrackManagerPainter extends Overlay
// display link between tracks
g2.setColor(Color.green);
- for (TrackLineSection lineSection : connectorSections)
- {
+ for (TrackLineSection lineSection : connectorSections) {
if (GraphicsUtil.isVisible(g2, lineSection.getBounds(bounds, trackWidth)))
g2.draw(lineSection.getLine2D(line));
}
// display detections
- for (Detection detection : allDetections)
- {
+ for (Detection detection : allDetections) {
// current detection is visible
if (detection.isEnabled() && (detection.getT() == canvas.getPositionT()))
// && (Math.round(detection.getZ()) == canvas.getPositionZ()))
@@ -425,8 +435,7 @@ public class TrackManagerPainter extends Overlay
final double y = detection.getY();
bounds.setFrame(x - (trackWidth * 1.5d), y - (trackWidth * 1.5d), trackWidth * 3, trackWidth * 3);
- if (GraphicsUtil.isVisible(g2, bounds))
- {
+ if (GraphicsUtil.isVisible(g2, bounds)) {
ellipse.setFrame(bounds);
g2.setColor(detection.getColor());
@@ -439,15 +448,17 @@ public class TrackManagerPainter extends Overlay
}
}
- /** add a listener */
- public void addTrackPainterListener(TrackPainterListener trackPainterListener)
- {
+ /**
+ * add a listener
+ */
+ public void addTrackPainterListener(TrackPainterListener trackPainterListener) {
this.trackPainterListener.add(trackPainterListener);
}
- /** remove a listener */
- public void removeTrackPainterListener(TrackPainterListener trackPainterListener)
- {
+ /**
+ * remove a listener
+ */
+ public void removeTrackPainterListener(TrackPainterListener trackPainterListener) {
this.trackPainterListener.remove(trackPainterListener);
}
@@ -460,22 +471,20 @@ public class TrackManagerPainter extends Overlay
// }
// }
- /** fire event with a non-specific TrackPainterChangeEvent */
- private void fireTrackPainterEvent()
- {
- for (TrackPainterListener tpl : trackPainterListener)
- {
+ /**
+ * fire event with a non-specific TrackPainterChangeEvent
+ */
+ private void fireTrackPainterEvent() {
+ for (TrackPainterListener tpl : trackPainterListener) {
tpl.trackPainterChanged(new TrackPainterChangeEvent(this));
}
}
- public boolean isDrawTracksOnSequence()
- {
+ public boolean isDrawTracksOnSequence() {
return drawTracksOnSequence;
}
- public void setDrawTracksOnSequence(boolean drawTracksOnSequence)
- {
+ public void setDrawTracksOnSequence(boolean drawTracksOnSequence) {
this.drawTracksOnSequence = drawTracksOnSequence;
}
@@ -501,44 +510,37 @@ public class TrackManagerPainter extends Overlay
// {
// }
- private class TrackLineSection
- {
+ private static class TrackLineSection {
final Detection start;
final Detection end;
- public TrackLineSection(Detection start, Detection end)
- {
+ public TrackLineSection(Detection start, Detection end) {
super();
this.start = start;
this.end = end;
}
- public Line2D getLine2D(Line2D line)
- {
+ public Line2D getLine2D(Line2D line) {
line.setLine(start.getX(), start.getY(), end.getX(), end.getY());
return line;
}
- public Color getColor()
- {
+ public Color getColor() {
return start.getColor();
}
- public Rectangle2D getBounds(Rectangle2D bounds, float stroke)
- {
+ public Rectangle2D getBounds(Rectangle2D bounds, float stroke) {
bounds.setFrameFromDiagonal(start.getX(), start.getY(), end.getX(), end.getY());
ShapeUtil.enlarge(bounds, stroke, stroke, true);
return bounds;
}
- public boolean isSelected()
- {
+ public boolean isSelected() {
return start.isSelected() && end.isSelected();
}
- public boolean isEnabled()
- {
+ public boolean isEnabled() {
return start.isEnabled() && end.isEnabled();
}
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackManagerProcessorListener.java b/src/main/java/plugins/fab/trackmanager/TrackManagerProcessorListener.java
index 9edffeff0d3f872f48a65cbc4f3db121e3f6552d..47e660431885d30b6fcd9473dbc514921949d3c4 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackManagerProcessorListener.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackManagerProcessorListener.java
@@ -1,26 +1,25 @@
/*
- * 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.fab.trackmanager;
import javax.swing.event.ChangeEvent;
-public interface TrackManagerProcessorListener
-{
- public void TrackEditorProcessorChange(ChangeEvent e);
+public interface TrackManagerProcessorListener {
+ void TrackEditorProcessorChange(ChangeEvent e);
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackPainterChangeEvent.java b/src/main/java/plugins/fab/trackmanager/TrackPainterChangeEvent.java
index b96286b550a074685101bdaa1438528fa099246a..2a87eb8508dd45eea2fa8b910d2079a498d5bbf5 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackPainterChangeEvent.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackPainterChangeEvent.java
@@ -1,31 +1,27 @@
/*
- * 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.fab.trackmanager;
import java.util.EventObject;
-public class TrackPainterChangeEvent extends EventObject
-{
- private static final long serialVersionUID = 7586741803753458072L;
-
- public TrackPainterChangeEvent(Object source)
- {
+public class TrackPainterChangeEvent extends EventObject {
+ public TrackPainterChangeEvent(Object source) {
super(source);
}
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackPainterListener.java b/src/main/java/plugins/fab/trackmanager/TrackPainterListener.java
index 78df5823070678a66ca985e5ffe17c6d3c5600ec..1f691019c815ca0582c783f80bfe6c242e0c36a5 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackPainterListener.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackPainterListener.java
@@ -1,24 +1,23 @@
/*
- * 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.fab.trackmanager;
-public interface TrackPainterListener
-{
- public void trackPainterChanged(TrackPainterChangeEvent e);
+public interface TrackPainterListener {
+ void trackPainterChanged(TrackPainterChangeEvent e);
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackPanel.java b/src/main/java/plugins/fab/trackmanager/TrackPanel.java
index 1132c5c1bba30007182d5cc85990b0d9320da8bc..08355e2f77e5f83c28e1178616297292ef7f9215 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackPanel.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackPanel.java
@@ -1,20 +1,20 @@
/*
- * 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.fab.trackmanager;
@@ -46,6 +46,7 @@ import icy.gui.viewer.Viewer;
import icy.gui.viewer.ViewerEvent;
import icy.gui.viewer.ViewerListener;
import icy.main.Icy;
+import icy.painter.Overlay;
import icy.sequence.DimensionId;
import icy.sequence.Sequence;
import icy.system.thread.ThreadUtil;
@@ -53,27 +54,22 @@ import plugins.nchenouard.spot.Detection;
/**
* Panel managing Tracks and users interactions.
- *
+ *
* @author Fabrice de Chaumont
*/
public class TrackPanel extends JPanel implements MouseListener, MouseMotionListener, TrackPainterListener,
- TrackManagerProcessorListener, ViewerListener, GlobalSequenceListener, GlobalViewerListener, Runnable
-{
-
- /**
- *
- */
- private static final long serialVersionUID = 938480382468773601L;
+ TrackManagerProcessorListener, ViewerListener, GlobalSequenceListener, GlobalViewerListener, Runnable {
TimeCursor timeCursor = new TimeCursor();
- /** Dimension of a single detection */
+ /**
+ * Dimension of a single detection
+ */
private Dimension detectDim = new Dimension(10, 10);
private TrackPool trackPool;
- public TrackPanel(TrackPool trackPool, boolean enableLeftPanelTrackDisplay)
- {
+ public TrackPanel(TrackPool trackPool, boolean enableLeftPanelTrackDisplay) {
super();
this.enableLeftPanelTrackDisplay = enableLeftPanelTrackDisplay;
@@ -90,16 +86,14 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
Icy.getMainInterface().addGlobalSequenceListener(this);
Icy.getMainInterface().addGlobalViewerListener(this);
- // System.out.println("TEST tackpanel");
+ // System.out.println("TEST trackpanel");
}
- void setupViewerListener()
- {
+ void setupViewerListener() {
// remove all listener
- for (Viewer viewer : Icy.getMainInterface().getViewers())
- {
+ for (Viewer viewer : Icy.getMainInterface().getViewers()) {
viewer.removeListener(this);
}
@@ -109,27 +103,23 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
if (sequence == null)
return;
- for (Viewer viewer : Icy.getMainInterface().getViewers(sequence))
- {
+ for (Viewer viewer : Icy.getMainInterface().getViewers(sequence)) {
viewer.addListener(this);
}
}
- public void mouseClicked(MouseEvent e)
- {
+ public void mouseClicked(MouseEvent e) {
if (!enableLeftPanelTrackDisplay)
return;
MouseLink.clear();
// Watch if a detection exists for selection.
- {
- TrackSegment ts = getTrackSegmentAt(e.getY());
- if (ts == null)
- return;
- ts.setAllDetectionSelected(!ts.isAllDetectionSelected());
- redrawDetection3();
- }
+ TrackSegment ts = getTrackSegmentAt(e.getY());
+ if (ts == null)
+ return;
+ ts.setAllDetectionSelected(!ts.isAllDetectionSelected());
+ redrawDetection3();
// Feature: add the detection panel
@@ -146,8 +136,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
}
- private TrackSegment getTrackSegmentAt(int y)
- {
+ private TrackSegment getTrackSegmentAt(int y) {
TrackSegment tsResult = null;
@@ -155,11 +144,10 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
int currentLine = 0;
- loop: for (TrackGroup trackGroup : trackPool.getTrackGroupList())
- for (TrackSegment ts : trackGroup.getTrackSegmentList())
- {
- if (currentLine == y)
- {
+ loop:
+ for (TrackGroup trackGroup : trackPool.getTrackGroupList())
+ for (TrackSegment ts : trackGroup.getTrackSegmentList()) {
+ if (currentLine == y) {
tsResult = ts;
break loop;
}
@@ -169,10 +157,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
return tsResult;
}
- private Detection getDetectionAt(int x, int y)
- {
- Detection detection = null;
-
+ private Detection getDetectionAt(int x, int y) {
TrackSegment ts = getTrackSegmentAt(y);
if (ts == null)
@@ -180,37 +165,32 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
int t = x / getDetectDim().width;
- detection = ts.getDetectionAtTime(t);
-
- return detection;
+ return ts.getDetectionAtTime(t);
}
- public void mouseEntered(MouseEvent e)
- {
+ public void mouseEntered(MouseEvent e) {
}
- public void mouseExited(MouseEvent e)
- {
+ public void mouseExited(MouseEvent e) {
}
- public void mousePressed(MouseEvent e)
- {
+ public void mousePressed(MouseEvent e) {
if (!enableLeftPanelTrackDisplay)
return;
MouseLink.clear();
- MouseLink.xstart = e.getX();
- MouseLink.ystart = e.getY();
+ MouseLink.xStart = e.getX();
+ MouseLink.yStart = e.getY();
- MouseLink.xend = e.getX();
- MouseLink.yend = e.getY();
+ MouseLink.xEnd = e.getX();
+ MouseLink.yEnd = e.getY();
// System.out.println( "debug info: mouse pressed.");
- Component component = getComponentAt(MouseLink.xstart, MouseLink.ystart);
+ Component component = getComponentAt(MouseLink.xStart, MouseLink.yStart);
// System.out.println("Mouse pressed component: " + component );
@@ -233,33 +213,27 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// System.out.println( "detection at click : " + detection );
- if (detection != null)
- {
- MouseLink.xstart = e.getX();
- MouseLink.ystart = e.getY();
+ if (detection != null) {
+ MouseLink.xStart = e.getX();
+ MouseLink.yStart = e.getY();
MouseLink.detectionStart = detection;
- MouseLink.ispressed = true;
+ MouseLink.isPressed = true;
// System.out.println("Debug detection mouse link start : " + detection );
}
// System.out.println("debug Track selected : " + track );
// manage track and time drag. Time has priority.
- if (component == this)
- {
- if (timeCursor.contains(e.getX(), e.getY()))
- {
+ if (component == this) {
+ if (timeCursor.contains(e.getX(), e.getY())) {
// enables time drag.
timeCursor.dragging = true;
}
- else
- {
+ else {
// look if at least one track exists.
boolean oneAtLeast = false;
- for (TrackGroup trackGroup : trackPool.getTrackGroupList())
- {
- if (trackGroup.getTrackSegmentList().size() != 0)
- {
+ for (TrackGroup trackGroup : trackPool.getTrackGroupList()) {
+ if (trackGroup.getTrackSegmentList().size() != 0) {
oneAtLeast = true;
break;
}
@@ -267,8 +241,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// enables trackDrag.
// if ( trackPool.getTrackSegmentList().size() != 0 )
- if (oneAtLeast)
- {
+ if (oneAtLeast) {
TrackDrag.dragging = true;
TrackDrag.ts = getCurrentTrackSegmentWithY(e.getY());
repaint();
@@ -278,14 +251,14 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
}
- /** Manage time cursor. */
- private class TimeCursor
- {
+ /**
+ * Manage time cursor.
+ */
+ private class TimeCursor {
int currentT = 0;
boolean dragging = false;
- boolean contains(int x, int y)
- {
+ boolean contains(int x, int y) {
Rectangle r = new Rectangle(currentT * (int) detectDim.getWidth(), 0, (int) detectDim.getWidth(),
Integer.MAX_VALUE);
return r.contains(x, y);
@@ -295,20 +268,16 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
/**
* Returns the track at Y //FIXME !
*/
- private TrackSegment getCurrentTrackSegmentWithY(int Y)
- {
+ private TrackSegment getCurrentTrackSegmentWithY(int Y) {
// System.out.println("drag a refaire.");
// return null;
- TrackSegment ts = null;
- ts = trackPool.getTrackSegmentList().get(getCurrentTrackSegmentIndexWithY(Y));
- return ts;
+ return trackPool.getTrackSegmentList().get(getCurrentTrackSegmentIndexWithY(Y));
}
/**
* Returns the number of the track with Y //FIXME !
*/
- private int getCurrentTrackSegmentIndexWithY(int Y)
- {
+ private int getCurrentTrackSegmentIndexWithY(int Y) {
// System.out.println("drag a refaire.");
// return 0;
int index = (int) (Y / detectDim.getHeight());
@@ -319,31 +288,29 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
return index;
}
- /** class use to record Track Drag states. */
- private static class TrackDrag
- {
+ /**
+ * class use to record Track Drag states.
+ */
+ private static class TrackDrag {
static boolean dragging = false;
static TrackSegment ts = null;
}
- public void mouseReleased(MouseEvent e)
- {
- MouseLink.xend = e.getX();
- MouseLink.yend = e.getY();
+ public void mouseReleased(MouseEvent e) {
+ MouseLink.xEnd = e.getX();
+ MouseLink.yEnd = e.getY();
// System.out.println("mouse released");
- if (MouseLink.ispressed)
- {
+ if (MouseLink.isPressed) {
// System.out.println("Mouse link is pressed");
Detection detection = getDetectionAt(e.getX(), e.getY());
- if (detection != null)
- {
- MouseLink.xend = e.getX();
- MouseLink.yend = e.getY();
+ if (detection != null) {
+ MouseLink.xEnd = e.getX();
+ MouseLink.yEnd = e.getY();
MouseLink.detectionEnd = detection;
// System.out.println("Debug detection mouse link end : " + detection );
}
@@ -374,26 +341,22 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
}
MouseLink.clear();
- if (TrackDrag.dragging)
- {
+ if (TrackDrag.dragging) {
TrackDrag.dragging = false;
repaint();
}
- if (timeCursor.dragging)
- {
+ if (timeCursor.dragging) {
timeCursor.dragging = false;
repaint();
}
}
- public void mouseDragged(MouseEvent e)
- {
- if (MouseLink.ispressed)
- {
- MouseLink.xend = e.getX();
- MouseLink.yend = e.getY();
+ public void mouseDragged(MouseEvent e) {
+ if (MouseLink.isPressed) {
+ MouseLink.xEnd = e.getX();
+ MouseLink.yEnd = e.getY();
// Component component = getComponentAt(MouseLink.xend, MouseLink.yend);
//
@@ -427,21 +390,19 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
}
// if track dragging , moves track.
- if (TrackDrag.dragging)
- {
+ if (TrackDrag.dragging) {
trackPool.moveTrackToIndex(TrackDrag.ts, getCurrentTrackSegmentIndexWithY(e.getY()));
clearDetectionsAndReDisplay();
}
// if time dragging , moves times.
- if (timeCursor.dragging)
- {
+ if (timeCursor.dragging) {
timeCursor.currentT = (int) (e.getX() / detectDim.getWidth());
// System.out.println( TimeCursor.currentT );
// System.out.println( "track editor : " + trackPool.getTrackEditor() );
- // FIXME : remettre ces securites.
+ // FIXME : remettre ces sécurités.
if (timeCursor.currentT < 0)
timeCursor.currentT = 0;
// if ( TimeCursor.currentT > trackPool.getSequence().getLength() -1 )
@@ -452,24 +413,24 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
}
}
- public void mouseMoved(MouseEvent e)
- {
+ public void mouseMoved(MouseEvent e) {
}
+
/*
* @Override
* protected void paintComponent(Graphics g)
* {
* super.paintComponent(g);
- *
+ *
* Graphics2D g2 = (Graphics2D) g;
- *
+ *
* // affichage des fond de tracks.
* // boolean swapcolor = false;
* // Color c1 = new Color( 0.8f ,0.8f , 0.8f );
* // Color c2 = new Color( 0.9f ,0.9f , 0.9f );
* //
- *
+ *
* // VERSION AVEC CLIPPER.
* // int startTrackSegmentToDisplay = getVisibleRect().y / getDetectDim().height ;
* // int lastTrackSegmentToDisplay = ( getVisibleRect().y+getVisibleRect().height ) /
@@ -483,7 +444,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
* // for ( int tracknb = startTrackSegmentToDisplay ; tracknb < lastTrackSegmentToDisplay ;
* // tracknb++ )
* // for ( int tracknb = 0 ; tracknb < trackPool.getTrackSegmentList().size() ; tracknb++ )
- *
+ *
* // TODO : remettre la peinture au fond ( les bandes horizontales. )
* // boolean switchBackground = false;
* //
@@ -509,7 +470,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
* // g2.drawString("#"+tracknb , 10 , detectDim.height*tracknb -2 );
* //
* // }
- *
+ *
* // draw current Time Cursor.
* {
* g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .5f));
@@ -518,7 +479,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
* getVisibleRect().height);
* g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 1.0f));
* }
- *
+ *
* // draw current MouseLink user operation.
* // FIXME : re-introduce mouse link user operations
* // if (MouseLink.ispressed)
@@ -529,7 +490,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
* // g2.drawLine(MouseLink.xstart, MouseLink.ystart, MouseLink.xend, MouseLink.yend);
* // g2.setStroke(new BasicStroke(1));
* // }
- *
+ *
* // emphasis track selection.
* // if ( TrackDrag.dragging )
* // {
@@ -539,9 +500,9 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
* // getWidth() , getDetectDim().height );
* // g2.setComposite( AlphaComposite.getInstance( AlphaComposite.SRC_OVER, 1.0f) );
* // }
- *
+ *
* // TODO : affiche les liens entre tracks.
- *
+ *
* // {
* // // Graphics2D g2 = (Graphics2D) this.getGraphics();
* // // if ( g2 !=null )
@@ -600,9 +561,9 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
* // g2.setStroke( new BasicStroke( 1 ) );
* // }
* // }
- *
+ *
* // if ( true ) return; // FIXME a enlever
- *
+ *
* // draw links.
* // {
* // ArrayList<Link> links = trackPool.getLinks();
@@ -661,22 +622,19 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
* //
* // }
* // }
- *
+ *
* }
*/
- public Dimension getDetectDim()
- {
+ public Dimension getDetectDim() {
return detectDim;
}
- public void setDetectDim(Dimension detectDim)
- {
+ public void setDetectDim(Dimension detectDim) {
this.detectDim = detectDim;
}
- public void setTrackPool(TrackPool trackPool)
- {
+ public void setTrackPool(TrackPool trackPool) {
this.trackPool = trackPool;
clearDetectionsAndReDisplay();
@@ -685,8 +643,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
/**
* Clear Detections and redisplay them.
*/
- private void clearDetectionsAndReDisplay()
- {
+ private void clearDetectionsAndReDisplay() {
// do it in background
ThreadUtil.bgRunSingle(this);
}
@@ -694,26 +651,19 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
/**
* Recompute all processors
*/
- public void recomputeProcessors()
- {
+ public void recomputeProcessors() {
// important to do it on EDT (otherwise we can get death lock)
- ThreadUtil.invokeNow(new Runnable()
- {
- @Override
- public void run()
- {
- // reset color of detection
- for (Detection d : trackPool.getAllDetection())
- d.reset();
- // then execute processors (important to do the whole in EDT so painting always happen after all processes)
- trackPool.computeTrackProcessor();
- }
+ ThreadUtil.invokeNow(() -> {
+ // reset color of detection
+ for (Detection d : trackPool.getAllDetection())
+ d.reset();
+ // then execute processors (important to do the whole in EDT so painting always happen after all processes)
+ trackPool.computeTrackProcessor();
});
}
@Override
- public void run()
- {
+ public void run() {
// refresh processors
recomputeProcessors();
// redraw left panel
@@ -722,15 +672,16 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// update painters
Sequence sequence = trackPool.getDisplaySequence();
if (sequence != null)
- sequence.painterChanged(null);
+ //sequence.painterChanged(null);
+ sequence.overlayChanged((Overlay) null);
}
// boolean disableLeftPanel= false;
+
/**
* Re-create the tracking image.
*/
- public void redrawDetection3()
- {
+ public void redrawDetection3() {
if (!enableLeftPanelTrackDisplay)
return;
@@ -746,8 +697,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
int width = getDetectDim().width * (maxSizeT + 1);
int height = getDetectDim().height * totalNumberOfTrack;
- if (width * height > maxSize)
- {
+ if (width * height > maxSize) {
height = maxSize / width;
System.out.println(
"too much track to display them all in trackManager left panel. Still, they all appear on the sequence.");
@@ -765,23 +715,18 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// drop image if dimensions have changed.
if (bufferedImage != null)
if ((bufferedImage.getWidth() != trackingPanelSize.width)
- || (bufferedImage.getHeight() != trackingPanelSize.height))
- {
+ || (bufferedImage.getHeight() != trackingPanelSize.height)) {
bufferedImage = null;
}
- // create cache image if it does not exists.
- if (bufferedImage == null)
- {
- if (!(trackingPanelSize.width == 0 || trackingPanelSize.height == 0))
- {
- try
- {
+ // create cache image if it does not exist.
+ if (bufferedImage == null) {
+ if (!(trackingPanelSize.width == 0 || trackingPanelSize.height == 0)) {
+ try {
bufferedImage = new BufferedImage(trackingPanelSize.width, trackingPanelSize.height,
BufferedImage.TYPE_INT_RGB);
}
- catch (OutOfMemoryError e)
- {
+ catch (OutOfMemoryError e) {
System.out.println("can't create " + trackingPanelSize.width + "x" + trackingPanelSize.height
+ " bitmap for track representation in trackPanel");
System.out.println("left panel disabled");
@@ -789,8 +734,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
return;
}
}
- else
- {
+ else {
// no track to display.
return;
}
@@ -800,39 +744,33 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
// fill background
+ Color c1 = new Color(0.8f, 0.8f, 0.8f);
+ Color c2 = new Color(0.9f, 0.9f, 0.9f);
+ int offsetY = 0;
+ boolean switchBackground = true;
+ g.setFont(new Font("Arial", Font.BOLD, detectDim.height - 2));
+ for (TrackGroup trackGroup : trackPool.getTrackGroupList())
+ for (int tracknb = 0; tracknb < trackGroup.getTrackSegmentList().size(); tracknb++) {
+ // display consecutive horizontal bars.
- {
- Color c1 = new Color(0.8f, 0.8f, 0.8f);
- Color c2 = new Color(0.9f, 0.9f, 0.9f);
- int offsetY = 0;
- boolean switchBackground = true;
- g.setFont(new Font("Arial", Font.BOLD, detectDim.height - 2));
- for (TrackGroup trackGroup : trackPool.getTrackGroupList())
- for (int tracknb = 0; tracknb < trackGroup.getTrackSegmentList().size(); tracknb++)
- {
- // display consecutive horizontal bars.
-
- switchBackground = !switchBackground;
- if (switchBackground)
- {
- g.setColor(c1);
- }
- else
- {
- g.setColor(c2);
- }
+ switchBackground = !switchBackground;
+ if (switchBackground) {
+ g.setColor(c1);
+ }
+ else {
+ g.setColor(c2);
+ }
- g.fillRect(0, detectDim.height * offsetY, detectDim.width * (maxSizeT + 1), detectDim.height);
- offsetY++;
+ g.fillRect(0, detectDim.height * offsetY, detectDim.width * (maxSizeT + 1), detectDim.height);
+ offsetY++;
- }
- }
+ }
// draw detections
int currentLine = 0; // current track line ( y offset )
- HashMap<Detection, Point2D> detectionHashMap = new HashMap<Detection, Point2D>();
+ HashMap<Detection, Point2D> detectionHashMap = new HashMap<>();
for (TrackGroup trackGroup : trackPool.getTrackGroupList())
for (TrackSegment ts : trackGroup.getTrackSegmentList())
@@ -845,8 +783,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// ts.detectionList.size() );
// TrackSegment ts = trackPool.getTrackSegmentList().get( trackSegmentIndex );
- for (int detectionIndex = 0; detectionIndex < ts.getDetectionList().size(); detectionIndex++)
- {
+ for (int detectionIndex = 0; detectionIndex < ts.getDetectionList().size(); detectionIndex++) {
final Detection d = ts.getDetectionList().get(detectionIndex);
// TrackDetection td = new TrackDetection(d);
@@ -856,9 +793,16 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// + getDetectDim().width, -0 + getDetectDim().height);
// add(td);
- Rectangle2D bounds = new Rectangle2D.Double(0 + getDetectDim().width * d.getT(),
- 0 + getDetectDim().height * currentLine, -0 + getDetectDim().width,
- -0 + getDetectDim().height);
+ Rectangle2D bounds = new Rectangle2D.Double(
+ //0 + getDetectDim().width * d.getT(),
+ getDetectDim().width * d.getT(),
+ //0 + getDetectDim().height * currentLine,
+ getDetectDim().height * currentLine,
+ //-0 + getDetectDim().width,
+ getDetectDim().width,
+ //-0 + getDetectDim().height
+ getDetectDim().height
+ );
drawDetection(g, d, bounds);
detectionHashMap.put(d,
@@ -878,16 +822,14 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
int detectHeight = getDetectDim().height / 2;
int detectWidth = getDetectDim().width / 2;
- for (Link link : links)
- {
+ for (Link link : links) {
Detection startDetection = link.getStartDetection();
Detection endDetection = link.getEndDetection();
Point2D startDetectionPoint2D = detectionHashMap.get(startDetection);
Point2D endDetectionPoint2D = detectionHashMap.get(endDetection);
- if (startDetectionPoint2D != null && endDetectionPoint2D != null)
- {
+ if (startDetectionPoint2D != null && endDetectionPoint2D != null) {
g2.drawLine((int) startDetectionPoint2D.getX() + detectHeight,
(int) startDetectionPoint2D.getY() + detectWidth,
(int) endDetectionPoint2D.getX() + detectHeight,
@@ -896,7 +838,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
}
/*
- *
+ *
* // previous version
* for (TrackGroup trackGroup : trackPool.getTrackGroupList())
* for (TrackSegment ts : trackGroup.getTrackSegmentList())
@@ -905,7 +847,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
* if ( lastDetection !=null )
* {
* Point2D lastDetectionPoint2D = detectionHashMap.get( lastDetection );
- *
+ *
* for ( TrackSegment tsNext : ts.nextList )
* {
* Detection nextDetection = tsNext.getFirstDetection();
@@ -927,45 +869,39 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
* }
* }
* }
- *
+ *
* }
*/
// display track number
- {
- int offsetY = 1;
- g.setColor(Color.white);
- for (TrackGroup trackGroup : trackPool.getTrackGroupList())
- {
- for (int tracknb = 0; tracknb < trackGroup.getTrackSegmentList().size(); tracknb++)
- {
- g.drawString(trackGroup.getDescription() + " # " + tracknb, 10, detectDim.height * offsetY - 2);
- offsetY++;
- }
+ //int offsetY = 1;
+ offsetY = 1;
+ g.setColor(Color.white);
+ for (TrackGroup trackGroup : trackPool.getTrackGroupList()) {
+ for (int tracknb = 0; tracknb < trackGroup.getTrackSegmentList().size(); tracknb++) {
+ g.drawString(trackGroup.getDescription() + " # " + tracknb, 10, detectDim.height * offsetY - 2);
+ offsetY++;
}
}
repaint();
}
- private void drawDetection(Graphics2D g, Detection d, Rectangle2D bounds)
- {
+ private void drawDetection(Graphics2D g, Detection d, Rectangle2D bounds) {
g.setColor(d.getColor());
g.fill(bounds);
g.setColor(d.getColor().darker());
g.draw(bounds);
- if (d.isSelected())
- {
+ if (d.isSelected()) {
g.setStroke(new BasicStroke(3));
g.setColor(Color.white);
g.draw(bounds);
g.setStroke(new BasicStroke(1));
}
- if (d.getDetectionType() == Detection.DETECTIONTYPE_VIRTUAL_DETECTION)
- {
+ if (d.getDetectionType() == Detection.DETECTIONTYPE_VIRTUAL_DETECTION) {
g.setStroke(new BasicStroke(2));
g.setColor(Color.white);
g.drawLine((int) bounds.getMinX(), (int) bounds.getMinY(), (int) bounds.getMaxX(), (int) bounds.getMaxY());
@@ -976,28 +912,25 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
BufferedImage bufferedImage;
- boolean enableLeftPanelTrackDisplay = true;
+ boolean enableLeftPanelTrackDisplay;
/**
* Paint the tracking Panel
*/
@Override
- protected void paintComponent(Graphics g1)
- {
+ protected void paintComponent(Graphics g1) {
super.paintComponent(g1);
Graphics2D g = (Graphics2D) g1;
g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
- if (!enableLeftPanelTrackDisplay)
- {
+ if (!enableLeftPanelTrackDisplay) {
g.clearRect(0, 0, this.getWidth(), this.getHeight());
g.drawString("Display disabled. Enable selecting Display > Enable Track Panel", 20, 20);
return;
}
int totalNumberOfTrack = trackPool.getTotalNumberOfTrack();
- if (totalNumberOfTrack == 0)
- {
+ if (totalNumberOfTrack == 0) {
g.drawString("No track to display", 20, 20);
}
@@ -1007,31 +940,27 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
g.drawImage(bufferedImage, null, 0, 0);
// draw MouseLink
- if (MouseLink.ispressed)
- {
+ if (MouseLink.isPressed) {
g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
g.setStroke(new BasicStroke(2));
g.setColor(Color.red);
- g.drawLine(MouseLink.xstart, MouseLink.ystart, MouseLink.xend, MouseLink.yend);
+ g.drawLine(MouseLink.xStart, MouseLink.yStart, MouseLink.xEnd, MouseLink.yEnd);
g.setStroke(new BasicStroke(1));
}
// draw current Time Cursor.
- {
- g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .5f));
- g.setColor(Color.red);
- g.fillRect(getDetectDim().width * timeCursor.currentT, getVisibleRect().y, getDetectDim().width,
- getVisibleRect().height);
- g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 1.0f));
- }
+ g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .5f));
+ g.setColor(Color.red);
+ g.fillRect(getDetectDim().width * timeCursor.currentT, getVisibleRect().y, getDetectDim().width,
+ getVisibleRect().height);
+ g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 1.0f));
}
/**
* @deprecated replaced by redrawDetection3()
*/
- public void redrawDetection2()
- {
+ public void redrawDetection2() {
// FIXME: dimension should update ( le 400 est fixe ici... )
// old code:
@@ -1068,8 +997,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// ts.detectionList.size() );
// TrackSegment ts = trackPool.getTrackSegmentList().get( trackSegmentIndex );
- for (int detectionIndex = 0; detectionIndex < ts.getDetectionList().size(); detectionIndex++)
- {
+ for (int detectionIndex = 0; detectionIndex < ts.getDetectionList().size(); detectionIndex++) {
final Detection d = ts.getDetectionList().get(detectionIndex);
// final TrackDetection td ;
// ThreadUtil.invokeLater( new Runnable() {
@@ -1083,9 +1011,17 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// System.out.println( "detec : " + getDetectDim().height* ligne );
- // specification de la taille des panels representant les detections ici.
- td.setBounds(0 + getDetectDim().width * d.getT(), 0 + getDetectDim().height * ligne,
- -0 + getDetectDim().width, -0 + getDetectDim().height);
+ // specification de la taille des panels représentant les detections ici.
+ td.setBounds(
+ //0 + getDetectDim().width * d.getT(),
+ getDetectDim().width * d.getT(),
+ //0 + getDetectDim().height * ligne,
+ getDetectDim().height * ligne,
+ //-0 + getDetectDim().width,
+ getDetectDim().width,
+ //-0 + getDetectDim().height
+ getDetectDim().height
+ );
add(td);
}
ligne++;
@@ -1176,9 +1112,10 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
}
- /** Should be called when a mouse-link operation has been finished */
- public void finishMouseConnexion()
- {
+ /**
+ * Should be called when a mouse-link operation has been finished
+ */
+ public void finishMouseConnexion() {
// Look for particular case where the detection belongs to the same TrackSegment, and are
// joined
// --> cut tracksegment.
@@ -1187,20 +1124,17 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// System.out.println("MouseLink start : " + MouseLink.detectionStart );
// System.out.println("MouseLink end : " + MouseLink.detectionEnd );
- if (MouseLink.detectionStart != null && MouseLink.detectionEnd != null)
- {
+ if (MouseLink.detectionStart != null && MouseLink.detectionEnd != null) {
// System.out.println("Enter detect start & end valid.");
Detection d1 = MouseLink.detectionStart;
Detection d2 = MouseLink.detectionEnd;
- if (d1.getT() + 1 == d2.getT())
- {
- if (trackPool.getTrackSegmentWithDetection(d1) == trackPool.getTrackSegmentWithDetection(d2))
- {
+ if (d1.getT() + 1 == d2.getT()) {
+ if (trackPool.getTrackSegmentWithDetection(d1) == trackPool.getTrackSegmentWithDetection(d2)) {
trackPool.cutTrackAfterDetection(d1);
- if (trackPool.getDisplaySequence() != null)
- {
- trackPool.getDisplaySequence().painterChanged(null);
+ if (trackPool.getDisplaySequence() != null) {
+ //trackPool.getDisplaySequence().painterChanged(null);
+ trackPool.getDisplaySequence().overlayChanged((Overlay) null);
}
clearDetectionsAndReDisplay();
updateUI();
@@ -1215,29 +1149,29 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// updates GUI
// trackPool.getSequence().painterChanged(null);
- if (trackPool.getDisplaySequence() != null)
- {
- trackPool.getDisplaySequence().painterChanged(null);
+ if (trackPool.getDisplaySequence() != null) {
+ //trackPool.getDisplaySequence().painterChanged(null);
+ trackPool.getDisplaySequence().overlayChanged((Overlay) null);
}
clearDetectionsAndReDisplay();
updateUI();
}
- /** This Internal class is used to create the mouseLink */
- static class MouseLink
- {
+ /**
+ * This Internal class is used to create the mouseLink
+ */
+ static class MouseLink {
static Detection detectionEnd;
static Detection detectionStart;
- static int xstart, ystart;
- static int xend, yend;
- static boolean ispressed = false;
+ static int xStart, yStart;
+ static int xEnd, yEnd;
+ static boolean isPressed = false;
// static TrackDetection TrackDetectionStart = null;
// static TrackDetection TrackDetectionEnd = null;
- public static void clear()
- {
- ispressed = false;
+ public static void clear() {
+ isPressed = false;
detectionStart = null;
detectionEnd = null;
@@ -1246,23 +1180,21 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
}
}
- public void trackPainterChanged(TrackPainterChangeEvent e)
- {
+ public void trackPainterChanged(TrackPainterChangeEvent e) {
// that means we may have selected / unselected a track --> repaint the tracks panel
redrawDetection3();
}
- /** Called when TSP List change */
- public void TrackEditorProcessorChange(ChangeEvent e)
- {
+ /**
+ * Called when TSP List change
+ */
+ public void TrackEditorProcessorChange(ChangeEvent e) {
clearDetectionsAndReDisplay();
}
@Override
- public void viewerChanged(ViewerEvent event)
- {
- if (event.getDim() == DimensionId.T)
- {
+ public void viewerChanged(ViewerEvent event) {
+ if (event.getDim() == DimensionId.T) {
timeCursor.currentT = event.getSource().getPositionT();
// trackPool.fireTrackEditorProcessorChange();
// clearDetectionsAndReDisplay();
@@ -1272,42 +1204,36 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// main listener
- public void displaySequenceChanged()
- {
+ public void displaySequenceChanged() {
setupViewerListener();
}
- public void setEnableLeftPanelTrackDisplay(boolean selected)
- {
+ public void setEnableLeftPanelTrackDisplay(boolean selected) {
this.enableLeftPanelTrackDisplay = selected;
redrawDetection3();
}
@Override
- public void viewerClosed(Viewer viewer)
- {
+ public void viewerClosed(Viewer viewer) {
setupViewerListener();
}
@Override
- public void viewerOpened(Viewer viewer)
- {
+ public void viewerOpened(Viewer viewer) {
setupViewerListener();
}
@Override
- public void sequenceOpened(Sequence sequence)
- {
+ public void sequenceOpened(Sequence sequence) {
setupViewerListener();
}
@Override
- public void sequenceClosed(Sequence sequence)
- {
+ public void sequenceClosed(Sequence sequence) {
setupViewerListener();
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackPool.java b/src/main/java/plugins/fab/trackmanager/TrackPool.java
index 5df0025e7412a8d36c90a22c0e9d8e908b1dd8ae..280a9fb7e6c5a567d6bfe52a7a84d76f0255cfd6 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackPool.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackPool.java
@@ -1,20 +1,20 @@
/*
- * 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.fab.trackmanager;
@@ -33,61 +33,54 @@ import plugins.nchenouard.spot.Detection;
/**
* TrackPool object used for TrackEditor. A trackPool is as a pool of TrackSegment.
- *
+ *
* @author Fabrice de Chaumont
*/
-public class TrackPool
-{
+public class TrackPool {
- private TrackManagerPainter tePainter;
+ private final TrackManagerPainter tePainter;
- private ArrayList<PluginTrackManagerProcessor> trackManagerProcessorList = new ArrayList<PluginTrackManagerProcessor>();
+ private final ArrayList<PluginTrackManagerProcessor> trackManagerProcessorList = new ArrayList<>();
- private ArrayList<TrackManagerProcessorListener> trackEditorProcessorListener = new ArrayList<TrackManagerProcessorListener>();
+ private final ArrayList<TrackManagerProcessorListener> trackEditorProcessorListener = new ArrayList<>();
- public TrackPool()
- {
+ public TrackPool() {
tePainter = new TrackManagerPainter(this);
}
- public ArrayList<PluginTrackManagerProcessor> getTrackManagerProcessorList()
- {
+ public ArrayList<PluginTrackManagerProcessor> getTrackManagerProcessorList() {
return trackManagerProcessorList;
}
- public void addTrackProcessor(PluginTrackManagerProcessor tep)
- {
+ public void addTrackProcessor(PluginTrackManagerProcessor tep) {
trackManagerProcessorList.add(tep);
fireTrackEditorProcessorChange();
}
- /** Add a listener that will send changes on TrackEditorProcessor's ArrayList */
- public void addTrackProcessorListener(TrackManagerProcessorListener tepl)
- {
- trackEditorProcessorListener.add(tepl);
+ /**
+ * Add a listener that will send changes on TrackEditorProcessor's ArrayList
+ */
+ public void addTrackProcessorListener(TrackManagerProcessorListener tmpl) {
+ trackEditorProcessorListener.add(tmpl);
}
- public void computeTrackProcessor()
- {
- for (PluginTrackManagerProcessor tep : trackManagerProcessorList)
- {
+ public void computeTrackProcessor() {
+ for (PluginTrackManagerProcessor tep : trackManagerProcessorList) {
long startTimeInNs = System.nanoTime();
tep.Compute();
tep.setPerformance((int) ((System.nanoTime() - startTimeInNs) / 1000000f));
}
}
- public void clearTracks()
- {
+ public void clearTracks() {
for (TrackGroup trackGroup : getTrackGroupList())
trackGroup.getTrackSegmentList().clear();
fireTrackEditorProcessorChange();
}
- public static boolean linkExists(List<Link> links, TrackSegment start, TrackSegment end)
- {
+ public static boolean linkExists(List<Link> links, TrackSegment start, TrackSegment end) {
// check if the link already exists
for (Link link : links)
if ((link.start == start) && (link.end == end))
@@ -96,65 +89,56 @@ public class TrackPool
return false;
}
- public static boolean isLinkExists(List<TrackGroup> groups, TrackSegment start, TrackSegment end)
- {
+ public static boolean isLinkExists(List<TrackGroup> groups, TrackSegment start, TrackSegment end) {
return linkExists(getLinks(groups), start, end);
}
- public boolean isLinkExists(TrackSegment start, TrackSegment end)
- {
+ public boolean isLinkExists(TrackSegment start, TrackSegment end) {
return linkExists(getLinks(), start, end);
}
- public static void createLink(List<TrackGroup> groups, TrackSegment start, TrackSegment end)
- {
- if (!isLinkExists(groups, start, end))
- {
+ public static void createLink(List<TrackGroup> groups, TrackSegment start, TrackSegment end) {
+ if (!isLinkExists(groups, start, end)) {
start.nextList.add(end);
end.previousList.add(start);
}
}
- public void createLink(TrackSegment start, TrackSegment end)
- {
- if (!isLinkExists(start, end))
- {
+ public void createLink(TrackSegment start, TrackSegment end) {
+ if (!isLinkExists(start, end)) {
start.nextList.add(end);
end.previousList.add(start);
}
}
- /** Creates a virtual track */
- public void createVirtualTrackWith2Detection(Detection detectionStart, Detection detectionEnd)
- {
+ /**
+ * Creates a virtual track
+ */
+ public void createVirtualTrackWith2Detection(Detection detectionStart, Detection detectionEnd) {
TrackSegment segmentStart = getTrackSegmentWithDetection(detectionStart);
TrackSegment segmentEnd = getTrackSegmentWithDetection(detectionEnd);
- if (segmentStart == segmentEnd)
- {
+ if (segmentStart == segmentEnd) {
MessageDialog.showDialog("Can't link 2 detections belonging to the same track.",
MessageDialog.INFORMATION_MESSAGE);
return;
}
- if (segmentStart.getOwnerTrackGroup() != segmentStart.getOwnerTrackGroup())
- {
+ if (segmentStart.getOwnerTrackGroup() != segmentStart.getOwnerTrackGroup()) {
MessageDialog.showDialog("The two tracks should be from the same track group.",
MessageDialog.INFORMATION_MESSAGE);
return;
}
- if (detectionStart.getT() >= detectionEnd.getT())
- {
+ if (detectionStart.getT() >= detectionEnd.getT()) {
MessageDialog.showDialog("Can't create a backward link.", MessageDialog.INFORMATION_MESSAGE);
return;
}
// check if detection are at start and end of their tracksegment.
{
- if (detectionStart != segmentStart.getLastDetection())
- {
+ if (detectionStart != segmentStart.getLastDetection()) {
// The detection is not the last of the track.
// Must split the start track.
@@ -165,8 +149,7 @@ public class TrackPool
segmentStart = getTrackSegmentWithDetection(detectionStart);
}
- if (detectionEnd != segmentEnd.getFirstDetection())
- {
+ if (detectionEnd != segmentEnd.getFirstDetection()) {
// The detection is not the first of the track.
// Must split the end track.
@@ -184,12 +167,10 @@ public class TrackPool
// check if start detection is t-1 end detection.
// if not, creates a bridge with a tracksegment of virtual detections.
- if (detectionEnd.getT() - detectionStart.getT() != 1)
- {
+ if (detectionEnd.getT() - detectionStart.getT() != 1) {
TrackSegment vts = new TrackSegment();
- for (int t = detectionStart.getT() + 1; t < detectionEnd.getT(); t++)
- {
+ for (int t = detectionStart.getT() + 1; t < detectionEnd.getT(); t++) {
// linear interpolation.
double xstart = detectionStart.getX();
@@ -236,17 +217,14 @@ public class TrackPool
createLink(vts, segmentEnd);
new AnnounceFrame("Link(s) created", 2);
}
- else
- {
+ else {
// segmentEnd.setTrackGroup( segmentStart.getTrackGroup() );
- if (isLinkExists(segmentStart, segmentEnd))
- {
+ if (isLinkExists(segmentStart, segmentEnd)) {
removeLink(segmentStart, segmentEnd);
new AnnounceFrame("Link deleted", 2);
}
- else
- {
+ else {
createLink(segmentStart, segmentEnd);
new AnnounceFrame("Link created", 2);
}
@@ -257,14 +235,11 @@ public class TrackPool
// ****** check and remove identical links
// int nbIdenticalLink = 0;
ArrayList<Link> linkList = getLinks();
- for (Link l1 : linkList)
- {
- for (Link l2 : linkList)
- {
+ for (Link l1 : linkList) {
+ for (Link l2 : linkList) {
if (l1.getStartDetection() == l2.getStartDetection())
if (l1.getEndDetection() == l2.getEndDetection())
- if (l1 != l2)
- {
+ if (l1 != l2) {
// nbIdenticalLink++;
removeLink(l1.getStartSegment(), l2.getEndSegment());
// System.err.println( "REMOVING DUPLICATED LINK");
@@ -279,9 +254,10 @@ public class TrackPool
// }
}
- /** Creates a virtual track */
- public void createVirtualTrackWith2TrackDetection(Detection detectionStart, Detection detectionEnd)
- {
+ /**
+ * Creates a virtual track
+ */
+ public void createVirtualTrackWith2TrackDetection(Detection detectionStart, Detection detectionEnd) {
// check if both sides of the link are TrackDetectionComponents.
if (detectionStart == null)
@@ -296,24 +272,23 @@ public class TrackPool
createVirtualTrackWith2Detection(detectionStart, detectionEnd);
}
- /** cuts track after detection */
- public void cutTrackAfterDetection(Detection d)
- {
+ /**
+ * cuts track after detection
+ */
+ public void cutTrackAfterDetection(Detection d) {
TrackSegment ts = getTrackSegmentWithDetection(d);
splitTrackSegment(ts, ts.getDetectionList().indexOf(d), false);
new AnnounceFrame("Track split", 2);
}
- public void deleteSelectedLink()
- {
+ public void deleteSelectedLink() {
// System.out.println("debug delete selected link");
ArrayList<Link> links = getLinks();
- ArrayList<Link> linksClone = new ArrayList<Link>(links);
+ ArrayList<Link> linksClone = new ArrayList<>(links);
- for (Link link : linksClone)
- {
+ for (Link link : linksClone) {
// System.out.println( "link: " + link );
// TrackSegment tsEndtest = getTrackSegmentWithDetection(link.getEndDetection());
@@ -321,8 +296,7 @@ public class TrackPool
// System.out.println( "end ts all selected: " + tsEndtest.isAllDetectionSelected() );
// System.out.println( "start ts all selected: " + tsStarttest.isAllDetectionSelected() );
- if (link.getStartDetection().isSelected() && link.getEndDetection().isSelected())
- {
+ if (link.getStartDetection().isSelected() && link.getEndDetection().isSelected()) {
// System.out.println("Link selected " + link );
// System.out.println( "debug found link with selection");
links.remove(link);
@@ -345,14 +319,11 @@ public class TrackPool
fireTrackEditorProcessorChange();
}
- public void deleteSelectedTracks()
- {
+ public void deleteSelectedTracks() {
beginUpdate();
- ArrayList<TrackSegment> tsListClone = new ArrayList<TrackSegment>(getTrackSegmentList());
- for (TrackSegment ts : tsListClone)
- {
- if (ts.isAllDetectionSelected())
- {
+ ArrayList<TrackSegment> tsListClone = new ArrayList<>(getTrackSegmentList());
+ for (TrackSegment ts : tsListClone) {
+ if (ts.isAllDetectionSelected()) {
deleteTrack(ts);
}
}
@@ -361,43 +332,36 @@ public class TrackPool
}
/**
- * @param ts
* @return null if no trackgroup contains the tracksegment
*/
- public TrackGroup getTrackGroupContainingSegment(TrackSegment ts)
- {
+ public TrackGroup getTrackGroupContainingSegment(TrackSegment ts) {
return ts.getOwnerTrackGroup();
}
- public void deleteTrack(TrackSegment ts)
- {
+ public void deleteTrack(TrackSegment ts) {
// System.out.println("----");
// System.out.println("Track segment id: " + ts.toString() );
TrackGroup trackGroup = getTrackGroupContainingSegment(ts);
- if (trackGroup == null)
- {
+ if (trackGroup == null) {
System.out.println(
- "Can't delete The track segment " + ts.toString() + " Reason: it is not in any trackGroup");
+ "Can't delete The track segment " + ts + " Reason: it is not in any trackGroup");
return;
}
trackGroup.getTrackSegmentList().remove(ts);
ArrayList<Link> links = getLinks();
- ArrayList<Link> linksClone = new ArrayList<Link>(links);
+ ArrayList<Link> linksClone = new ArrayList<>(links);
- for (Link link : linksClone)
- {
- if (ts.containsDetection(link.getStartDetection()))
- {
+ for (Link link : linksClone) {
+ if (ts.containsDetection(link.getStartDetection())) {
links.remove(link);
TrackSegment tsEnd = getTrackSegmentWithDetection(link.getEndDetection());
tsEnd.removePrevious(ts);
}
- if (ts.containsDetection(link.getEndDetection()))
- {
+ if (ts.containsDetection(link.getEndDetection())) {
links.remove(link);
TrackSegment tsStart = getTrackSegmentWithDetection(link.getStartDetection());
tsStart.removeNext(ts);
@@ -410,51 +374,38 @@ public class TrackPool
}
- @Override
- protected void finalize() throws Throwable
- {
-
- tePainter = null;
- super.finalize();
- }
-
boolean isUpdating = false;
- public void beginUpdate()
- {
+ public void beginUpdate() {
isUpdating = true;
}
- public void endUpdate()
- {
+ public void endUpdate() {
isUpdating = false;
}
- public void fireTrackEditorProcessorChange()
- {
- if (!isUpdating)
- {
- for (TrackManagerProcessorListener tepl : trackEditorProcessorListener)
- tepl.TrackEditorProcessorChange(new ChangeEvent(this));
+ public void fireTrackEditorProcessorChange() {
+ if (!isUpdating) {
+ for (TrackManagerProcessorListener tmpl : trackEditorProcessorListener)
+ tmpl.TrackEditorProcessorChange(new ChangeEvent(this));
}
}
- /** If only one link is linking 2 tracks, it means they could be the same track */
- public void fuseAllTracks()
- {
+ /**
+ * If only one link is linking 2 tracks, it means they could be the same track
+ */
+ public void fuseAllTracks() {
// System.out.println("Start Fusion.");
boolean fuseOperationPerformed = true; // flag to restart fuse operation from zero each time a fuse has been performed.
- while (fuseOperationPerformed)
- {
+ while (fuseOperationPerformed) {
fuseOperationPerformed = false;
// System.out.println("****** re-Start Fusion.");
- ArrayList<TrackSegment> trackSegmentListClone = new ArrayList<TrackSegment>(getTrackSegmentList());
- for (TrackSegment ts : trackSegmentListClone)
- {
+ ArrayList<TrackSegment> trackSegmentListClone = new ArrayList<>(getTrackSegmentList());
+ for (TrackSegment ts : trackSegmentListClone) {
// System.out.println("Computing trackSegment # " + trackSegmentListClone.indexOf( ts ) );
if (ts.nextList.size() == 1) // if the track has only one successor.
if (ts.nextList.get(0).previousList.size() == 1) // If successor has only one predecessor.
@@ -473,25 +424,22 @@ public class TrackPool
/**
* Fusing 2 tracks ts1 is one step before ts2.
*/
- public void fuseTrack(TrackSegment ts1, TrackSegment ts2)
- {
+ public void fuseTrack(TrackSegment ts1, TrackSegment ts2) {
// System.out.println("debug fuse track: fusing ");
// System.out.println("ts1 = " + ts1);
// System.out.println("ts2 = " + ts2);
- for (Detection detection : ts2.getDetectionList())
- {
+ for (Detection detection : ts2.getDetectionList()) {
ts1.addDetection(detection);
// System.out.println("Adding 1 detection to ts1. t=" + detection.getT() );
}
// System.out.println("Copy next List");
- ts1.nextList = new ArrayList<TrackSegment>(new ArrayList<TrackSegment>(ts2.nextList));
+ ts1.nextList = new ArrayList<>(new ArrayList<>(ts2.nextList));
// ts1.getDetectionList().addAll(ts2.getDetectionList());
- while (ts2.getDetectionList().size() > 0)
- {
+ while (ts2.getDetectionList().size() > 0) {
Detection detection = ts2.getFirstDetection();
ts2.removeDetection(detection);
// System.out.println("Remove 1 detection to ts2. t=" + detection.getT() );
@@ -503,47 +451,41 @@ public class TrackPool
fireTrackEditorProcessorChange();
}
- public ArrayList<Detection> getAllDetection()
- {
- ArrayList<Detection> detectionList = new ArrayList<Detection>();
+ public ArrayList<Detection> getAllDetection() {
+ ArrayList<Detection> detectionList = new ArrayList<>();
for (TrackGroup trackGroup : getTrackGroupList())
for (TrackSegment tracksegment : trackGroup.getTrackSegmentList())
- for (Detection detection : tracksegment.getDetectionList())
- {
- detectionList.add(detection);
- }
+ detectionList.addAll(tracksegment.getDetectionList());
return detectionList;
}
- /** return distance between 2 detections */
- public double getDistance(Detection d1, Detection d2)
- {
+ /**
+ * return distance between 2 detections
+ */
+ public double getDistance(Detection d1, Detection d2) {
return getDistance(d1.getX(), d1.getY(), d1.getZ(), d2.getX(), d2.getY(), d2.getZ());
}
- /** return distance between 2 pos */
- public double getDistance(double x1, double y1, double z1, double x2, double y2, double z2)
- {
- double distance = Math.sqrt((x1 - x2) * (x1 - x2) + (y1 - y2) * (y1 - y2) + (z1 - z2) * (z1 - z2));
- return distance;
+ /**
+ * return distance between 2 pos
+ */
+ public double getDistance(double x1, double y1, double z1, double x2, double y2, double z2) {
+ return Math.sqrt((x1 - x2) * (x1 - x2) + (y1 - y2) * (y1 - y2) + (z1 - z2) * (z1 - z2));
}
- public ArrayList<Link> getLinks()
- {
- ArrayList<Link> linkarray = new ArrayList<Link>();
+ public ArrayList<Link> getLinks() {
+ ArrayList<Link> linkarray = new ArrayList<>();
// System.out.println("debug : getLinks");
- for (int trackSegmentIndex = 0; trackSegmentIndex < getTrackSegmentList().size(); trackSegmentIndex++)
- {
+ for (int trackSegmentIndex = 0; trackSegmentIndex < getTrackSegmentList().size(); trackSegmentIndex++) {
TrackSegment ts = getTrackSegmentList().get(trackSegmentIndex);
// for ( int i = 0 ; i < ts.previousList.size() ; i++ )
// {
// linkarray.add( new Link( ts.previousList.get( i ) , ts ) );
// }
- for (int i = 0; i < ts.nextList.size(); i++)
- {
+ for (int i = 0; i < ts.nextList.size(); i++) {
linkarray.add(new Link(ts, ts.nextList.get(i)));
}
@@ -552,9 +494,8 @@ public class TrackPool
return linkarray;
}
- public static List<Link> getLinks(List<TrackGroup> groups)
- {
- final List<Link> result = new ArrayList<Link>();
+ public static List<Link> getLinks(List<TrackGroup> groups) {
+ final List<Link> result = new ArrayList<>();
final List<TrackSegment> segments = getTrackSegmentList(groups);
for (TrackSegment segment : segments)
@@ -567,8 +508,7 @@ public class TrackPool
// FIXME: put a WeakReference in here
private Sequence displaySequence = null;
- public void setDisplaySequence(Sequence displaySequence)
- {
+ public void setDisplaySequence(Sequence displaySequence) {
this.displaySequence = displaySequence;
@@ -578,56 +518,49 @@ public class TrackPool
removePainter();
// add the painter to the selected display sequence.
- if (displaySequence != null)
- {
+ if (displaySequence != null) {
// System.out.println("adding the painter");
displaySequence.addOverlay(tePainter);
}
// fire a sequenceChanged to all trackManagerProcessor
- for (PluginTrackManagerProcessor ptmp : trackManagerProcessorList)
- {
+ for (PluginTrackManagerProcessor ptmp : trackManagerProcessorList) {
ptmp.displaySequenceChanged();
}
// tell to trackPanel the display sequence has changed.
- if (trackManager != null)
- {
- if (trackManager.trackPanel != null)
- {
+ if (trackManager != null) {
+ if (trackManager.trackPanel != null) {
trackManager.trackPanel.displaySequenceChanged();
}
}
}
- public Sequence getDisplaySequence()
- {
+ public Sequence getDisplaySequence() {
return displaySequence;
}
TrackManager trackManager;
- /** @deprecated Use getTrackManager instead */
- public TrackManager getTrackEditor()
- {
+ /**
+ * @deprecated Use getTrackManager instead
+ */
+ public TrackManager getTrackEditor() {
return trackManager;
}
- public TrackManager getTrackManager()
- {
+ public TrackManager getTrackManager() {
return trackManager;
}
- public TrackManagerPainter getTrackPainter()
- {
+ public TrackManagerPainter getTrackPainter() {
return tePainter;
}
/**
* @return the pool of tracksegment of all the trackgroup
*/
- public static List<TrackSegment> getTrackSegmentList(List<TrackGroup> groups)
- {
- final List<TrackSegment> result = new ArrayList<TrackSegment>();
+ public static List<TrackSegment> getTrackSegmentList(List<TrackGroup> groups) {
+ final List<TrackSegment> result = new ArrayList<>();
for (TrackGroup group : groups)
result.addAll(group.getTrackSegmentList());
@@ -638,26 +571,24 @@ public class TrackPool
/**
* @return the pool of tracksegment of all the trackgroup
*/
- public ArrayList<TrackSegment> getTrackSegmentList()
- {
+ public ArrayList<TrackSegment> getTrackSegmentList() {
- ArrayList<TrackSegment> trackSegmentList = new ArrayList<TrackSegment>();
- for (TrackGroup group : getTrackGroupList())
- {
+ ArrayList<TrackSegment> trackSegmentList = new ArrayList<>();
+ for (TrackGroup group : getTrackGroupList()) {
trackSegmentList.addAll(group.getTrackSegmentList());
}
return trackSegmentList;
}
- /** find the tracksegment containing the given detection */
- public TrackSegment getTrackSegmentWithDetection(Detection detection)
- {
+ /**
+ * find the tracksegment containing the given detection
+ */
+ public TrackSegment getTrackSegmentWithDetection(Detection detection) {
ArrayList<TrackSegment> trackSegmentList = getTrackSegmentList();
- for (TrackSegment ts : trackSegmentList)
- {
+ for (TrackSegment ts : trackSegmentList) {
if (ts.containsDetection(detection))
return ts;
}
@@ -665,33 +596,28 @@ public class TrackPool
return null;
}
- public static ArrayList<TrackSegment> loadTracks(File f) throws Exception
- {
+ // FIXME: 05/04/2023 does nothing
+ public static ArrayList<TrackSegment> loadTracks(File f) {
- ArrayList<TrackSegment> inputTrackSegmentList = new ArrayList<TrackSegment>();
- ArrayList<TrackSegment> targetTrackSegmentList = new ArrayList<TrackSegment>();
+ ArrayList<TrackSegment> inputTrackSegmentList = new ArrayList<>();
+ ArrayList<TrackSegment> targetTrackSegmentList = new ArrayList<>();
- for (TrackSegment ts : inputTrackSegmentList)
- {
- if (ts.getFirstDetection() == null || ts.getLastDetection() == null)
- {
+ for (TrackSegment ts : inputTrackSegmentList) {
+ if (ts.getFirstDetection() == null || ts.getLastDetection() == null) {
System.out.println("Warning, found and removed empty track segment");
continue;
}
boolean skipTrackSegment = false;
- for (TrackSegment ts2 : ts.nextList)
- {
- if (ts2.getFirstDetection() == null || ts2.getLastDetection() == null)
- {
+ for (TrackSegment ts2 : ts.nextList) {
+ if (ts2.getFirstDetection() == null || ts2.getLastDetection() == null) {
skipTrackSegment = true;
break;
}
}
- if (skipTrackSegment)
- {
+ if (skipTrackSegment) {
System.out.println("Warning, found and removed empty track segment");
continue;
}
@@ -701,16 +627,16 @@ public class TrackPool
return targetTrackSegmentList;
}
- public void moveTrackToIndex(TrackSegment ts, int index)
- {
+ public void moveTrackToIndex(TrackSegment ts, int index) {
// trackSegmentList.remove( ts );
// if ( index > trackSegmentList.size() ) index = trackSegmentList.size();
// trackSegmentList.add( index , ts );
}
- /** remove a link between 2 track segment. */
- public void removeLink(TrackSegment start, TrackSegment end)
- {
+ /**
+ * remove a link between 2 track segment.
+ */
+ public void removeLink(TrackSegment start, TrackSegment end) {
// int nb = 0;
// while ( start.nextList.contains( end ) )
// {
@@ -730,34 +656,29 @@ public class TrackPool
// }
}
- public void removeTrackProcessor(PluginTrackManagerProcessor tep)
- {
+ public void removeTrackProcessor(PluginTrackManagerProcessor tep) {
trackManagerProcessorList.remove(tep);
fireTrackEditorProcessorChange();
}
- /** remove a listener that will send changes on TrackEditorProcessor's ArrayList */
- public void removeTrackProcessorListener(TrackManagerProcessorListener tepl)
- {
- trackEditorProcessorListener.remove(tepl);
+ /**
+ * remove a listener that will send changes on TrackEditorProcessor's ArrayList
+ */
+ public void removeTrackProcessorListener(TrackManagerProcessorListener tmpl) {
+ trackEditorProcessorListener.remove(tmpl);
}
- public void selectAllTracks()
- {
- for (TrackSegment ts : getTrackSegmentList())
- {
+ public void selectAllTracks() {
+ for (TrackSegment ts : getTrackSegmentList()) {
ts.setAllDetectionSelected(true);
}
fireTrackEditorProcessorChange();
}
- public void selectTracksByLength(int lowVal, int highVal)
- {
+ public void selectTracksByLength(int lowVal, int highVal) {
- for (TrackSegment ts : getTrackSegmentList())
- {
- if (ts.getDetectionList().size() >= lowVal && ts.getDetectionList().size() <= highVal)
- {
+ for (TrackSegment ts : getTrackSegmentList()) {
+ if (ts.getDetectionList().size() >= lowVal && ts.getDetectionList().size() <= highVal) {
ts.setAllDetectionSelected(true);
}
}
@@ -765,17 +686,14 @@ public class TrackPool
}
- public void unselectAllTracks()
- {
- for (TrackSegment ts : getTrackSegmentList())
- {
+ public void unselectAllTracks() {
+ for (TrackSegment ts : getTrackSegmentList()) {
ts.setAllDetectionSelected(false);
}
fireTrackEditorProcessorChange();
}
- public void invertSelection()
- {
+ public void invertSelection() {
for (TrackSegment ts : getTrackSegmentList())
for (Detection d : ts.getDetectionList())
d.setSelected(!d.isSelected());
@@ -784,24 +702,17 @@ public class TrackPool
/**
* Splits a track into 2 tracks.
- *
- * @param ts
- * The track to split - Important NOTE: This track will be destructed after call.
- * @param lastIndexOfFirstTrack
- * Index of where the track should be splited.
- *
- * <pre>
- * @param CreateLinkBetweenSplittedTrack if true, creates a link between splitted tracks.
- * @return an ArrayList with the 2 new track created.
- * Track : TTTTTT
- * Split Index : S
- * Result : 111
- * 222
- * </pre>
+ *
+ * @param ts The track to split - Important NOTE: This track will be destructed after call.
+ * @param lastIndexOfFirstTrack Index of where the track should be split.
+ * @param createLinkBetweenSplitTrack if true, creates a link between split tracks.
+ * @return an ArrayList with the 2 new track created.
+ * Track : TTTTTT
+ * Split Index : S
+ * Result : 111
+ * 222
*/
- public ArrayList<TrackSegment> splitTrackSegment(TrackSegment ts, int lastIndexOfFirstTrack,
- boolean CreateLinkBetweenSplittedTrack)
- {
+ public ArrayList<TrackSegment> splitTrackSegment(TrackSegment ts, int lastIndexOfFirstTrack, boolean createLinkBetweenSplitTrack) {
// System.out.println("Entering split track segment.");
// last version, but still need to consider the track group
@@ -809,8 +720,7 @@ public class TrackPool
TrackSegment ts2 = new TrackSegment();
// copy first segment detections.
- for (int i = 0; i < lastIndexOfFirstTrack + 1; i++)
- {
+ for (int i = 0; i < lastIndexOfFirstTrack + 1; i++) {
// old: ts1.detectionList.add( ts.detectionList.get( i ) );
ts1.addDetection(ts.getDetectionAt(i));
}
@@ -819,8 +729,7 @@ public class TrackPool
ts1.previousList.addAll(ts.previousList);
// copy second segment detections.
- for (int i = lastIndexOfFirstTrack + 1; i < ts.getDetectionList().size(); i++)
- {
+ for (int i = lastIndexOfFirstTrack + 1; i < ts.getDetectionList().size(); i++) {
// old: ts2.detectionList.add( ts.detectionList.get( i ) );
ts2.addDetection(ts.getDetectionAt(i));
}
@@ -828,24 +737,20 @@ public class TrackPool
// copy second segment next list.
ts2.nextList.addAll(ts.nextList);
- for (TrackSegment tracksegment : getTrackSegmentList())
- {
+ for (TrackSegment tracksegment : getTrackSegmentList()) {
// change pointer of others previouslisttracks to point here.
- for (TrackSegment tracksegmentprevious : tracksegment.previousList)
- {
+ for (TrackSegment tracksegmentprevious : tracksegment.previousList) {
if (tracksegmentprevious == ts)
tracksegmentprevious = ts2;
}
// change pointer of others nextlisttracks to point here.
- for (TrackSegment tracksegmentnext : tracksegment.nextList)
- {
+ for (TrackSegment tracksegmentnext : tracksegment.nextList) {
if (tracksegmentnext == ts)
tracksegmentnext = ts1;
}
}
- if (CreateLinkBetweenSplittedTrack)
- {
+ if (createLinkBetweenSplitTrack) {
createLink(ts1, ts2);
}
@@ -872,17 +777,16 @@ public class TrackPool
// System.out.println("ts1 trackGroup = " + ts1.getOwnerTrackGroup() );
// System.out.println("ts2 trackGroup = " + ts1.getOwnerTrackGroup() );
- ArrayList<TrackSegment> trackSegmentReturnList = new ArrayList<TrackSegment>();
+ ArrayList<TrackSegment> trackSegmentReturnList = new ArrayList<>();
trackSegmentReturnList.add(ts1);
trackSegmentReturnList.add(ts2);
return trackSegmentReturnList;
}
- public ArrayList<TrackGroup> getTrackGroupList()
- {
+ public ArrayList<TrackGroup> getTrackGroupList() {
- ArrayList<TrackGroup> trackGroupList = new ArrayList<TrackGroup>();
+ ArrayList<TrackGroup> trackGroupList = new ArrayList<>();
for (SwimmingObject result : resultList)
trackGroupList.add((TrackGroup) result.getObject());
@@ -890,13 +794,13 @@ public class TrackPool
return trackGroupList;
}
- /** List of results where trackGroup has been found to process. */
- ArrayList<SwimmingObject> resultList = new ArrayList<SwimmingObject>();
+ /**
+ * List of results where trackGroup has been found to process.
+ */
+ ArrayList<SwimmingObject> resultList = new ArrayList<>();
- public void addResult(SwimmingObject result)
- {
- if (!(result.getObject() instanceof TrackGroup))
- {
+ public void addResult(SwimmingObject result) {
+ if (!(result.getObject() instanceof TrackGroup)) {
// System.out.println("Object " + result + " is not recognized as a TrackGroup.");
return;
}
@@ -905,15 +809,13 @@ public class TrackPool
}
- public void removeResult(SwimmingObject result)
- {
+ public void removeResult(SwimmingObject result) {
if (result == null)
return;
resultList.remove(result);
- if (result.getObject() instanceof TrackGroup)
- {
+ if (result.getObject() instanceof TrackGroup) {
final TrackGroup tg = (TrackGroup) result.getObject();
// remove track segment from hash map
@@ -925,21 +827,18 @@ public class TrackPool
/**
* removes the painter from all sequences.
*/
- public void removePainter()
- {
+ public void removePainter() {
// System.out.println("remove painter");
List<Sequence> sequenceList = Icy.getMainInterface().getSequencesContaining(tePainter);
- for (Sequence sequence : sequenceList)
- {
+ for (Sequence sequence : sequenceList) {
sequence.removeOverlay(tePainter);
}
}
- public int getTrackIndex(TrackSegment ts)
- {
+ public int getTrackIndex(TrackSegment ts) {
return getTrackSegmentList().indexOf(ts);
@@ -948,17 +847,13 @@ public class TrackPool
/**
* @return the timepoint corresponding to the last detection of all the trackgroup.
*/
- public int getLastDetectionTimePoint()
- {
+ public int getLastDetectionTimePoint() {
int maxT = 0;
- for (TrackGroup tg : getTrackGroupList())
- {
- for (TrackSegment ts : tg.getTrackSegmentList())
- {
+ for (TrackGroup tg : getTrackGroupList()) {
+ for (TrackSegment ts : tg.getTrackSegmentList()) {
Detection d = ts.getLastDetection();
- if (d != null)
- {
+ if (d != null) {
if (d.getT() > maxT)
maxT = d.getT();
}
@@ -970,14 +865,11 @@ public class TrackPool
/**
* @return the number of track considering all the track groups.
*/
- public int getTotalNumberOfTrack()
- {
+ public int getTotalNumberOfTrack() {
int total = 0;
- for (TrackGroup tg : getTrackGroupList())
- {
+ for (TrackGroup tg : getTrackGroupList()) {
total += tg.getTrackSegmentList().size();
}
return total;
}
-
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackSegment.java b/src/main/java/plugins/fab/trackmanager/TrackSegment.java
index 72ca4e2c13c1c332ba32a0998b8db43a6cc84af3..5dd71b628811dd9c403823d52752a33c32be205d 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackSegment.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackSegment.java
@@ -1,20 +1,20 @@
/*
- * 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.fab.trackmanager;
@@ -30,33 +30,29 @@ import plugins.nchenouard.spot.Detection;
/**
* TrackSegment is a pool of consecutive detection.
- *
+ *
* @author Fabrice de Chaumont
* @author Stephane
*/
-public class TrackSegment implements Cloneable
-{
+public class TrackSegment implements Cloneable {
// better to use weak reference in the map
- protected static Map<Integer, Reference<TrackSegment>> idKeyHashMapList = new HashMap<Integer, Reference<TrackSegment>>(); // 1-1 hashmap.
+ protected final static Map<Integer, Reference<TrackSegment>> idKeyHashMapList = new HashMap<>(); // 1-1 hashmap.
- List<Detection> detectionList = new ArrayList<Detection>();
- List<TrackSegment> previousList = new ArrayList<TrackSegment>();
- List<TrackSegment> nextList = new ArrayList<TrackSegment>();
+ List<Detection> detectionList = new ArrayList<>();
+ List<TrackSegment> previousList = new ArrayList<>();
+ List<TrackSegment> nextList = new ArrayList<>();
private TrackGroup ownerTrackGroup = null;
private int id = 0;
- public static TrackSegment getTrackSegmentById(int id)
- {
+ public static TrackSegment getTrackSegmentById(int id) {
final Integer iid = Integer.valueOf(id);
- synchronized (idKeyHashMapList)
- {
+ synchronized (idKeyHashMapList) {
final Reference<TrackSegment> ref = idKeyHashMapList.get(iid);
// null ? --> can remove it from the hashmap
- if (ref.get() == null)
- {
+ if (ref.get() == null) {
idKeyHashMapList.remove(iid);
}
@@ -64,16 +60,16 @@ public class TrackSegment implements Cloneable
}
}
- public TrackSegment()
- {
+ public TrackSegment() {
super();
generateId();
}
- /** Constructor with a list of detection */
- public TrackSegment(ArrayList<Detection> detectionList)
- {
+ /**
+ * Constructor with a list of detection
+ */
+ public TrackSegment(ArrayList<Detection> detectionList) {
super();
this.detectionList = detectionList;
@@ -92,19 +88,17 @@ public class TrackSegment implements Cloneable
}
@Override
- protected Object clone() throws CloneNotSupportedException
- {
+ protected Object clone() throws CloneNotSupportedException {
TrackSegment cloneSegment = (TrackSegment) super.clone();
- for (Detection detection : detectionList)
- {
+ for (Detection detection : detectionList) {
Detection cloneDetection = (Detection) detection.clone();
// cloneDetection.setOwnerTrackSegment(cloneSegment);
cloneSegment.detectionList.add(cloneDetection);
}
- previousList = new ArrayList<TrackSegment>(previousList);
- nextList = new ArrayList<TrackSegment>(nextList);
+ previousList = new ArrayList<>(previousList);
+ nextList = new ArrayList<>(nextList);
generateId();
@@ -112,34 +106,27 @@ public class TrackSegment implements Cloneable
}
- public void removeId()
- {
- synchronized (idKeyHashMapList)
- {
+ public void removeId() {
+ synchronized (idKeyHashMapList) {
idKeyHashMapList.remove(Integer.valueOf(id));
}
}
- public int getId()
- {
+ public int getId() {
return id;
}
- public void generateId()
- {
+ public void generateId() {
// just for safety
removeId();
- synchronized (idKeyHashMapList)
- {
- while (true)
- {
+ synchronized (idKeyHashMapList) {
+ while (true) {
final Integer key = Integer.valueOf(Random.nextInt());
// available ?
- if (idKeyHashMapList.get(key) == null)
- {
- idKeyHashMapList.put(key, new WeakReference<TrackSegment>(this));
+ if (idKeyHashMapList.get(key) == null) {
+ idKeyHashMapList.put(key, new WeakReference<>(this));
id = key.intValue();
return;
@@ -148,16 +135,13 @@ public class TrackSegment implements Cloneable
}
}
- public void setId(int id)
- {
+ public void setId(int id) {
final Integer key = Integer.valueOf(id);
- synchronized (idKeyHashMapList)
- {
+ synchronized (idKeyHashMapList) {
// available ?
- if (idKeyHashMapList.get(key) == null)
- {
- idKeyHashMapList.put(key, new WeakReference<TrackSegment>(this));
+ if (idKeyHashMapList.get(key) == null) {
+ idKeyHashMapList.put(key, new WeakReference<>(this));
this.id = key.intValue();
}
else
@@ -165,22 +149,25 @@ public class TrackSegment implements Cloneable
}
}
- /** */
- public boolean containsDetection(Detection detection)
- {
+ /**
+ *
+ */
+ public boolean containsDetection(Detection detection) {
return detectionList.contains(detection);
}
- /** set all dependent selection */
- public void setAllDetectionEnabled(boolean selected)
- {
+ /**
+ * set all dependent selection
+ */
+ public void setAllDetectionEnabled(boolean selected) {
for (Detection d : detectionList)
d.setEnabled(selected);
}
- /** is all dependent selection are enabled */
- public boolean isAllDetectionEnabled()
- {
+ /**
+ * is all dependent selection are enabled
+ */
+ public boolean isAllDetectionEnabled() {
if (detectionList.isEmpty())
return false;
@@ -192,16 +179,18 @@ public class TrackSegment implements Cloneable
return result;
}
- /** set all dependent selection */
- public void setAllDetectionSelected(boolean selected)
- {
+ /**
+ * set all dependent selection
+ */
+ public void setAllDetectionSelected(boolean selected) {
for (Detection d : detectionList)
d.setSelected(selected);
}
- /** check if all dependent selection are selected */
- public boolean isAllDetectionSelected()
- {
+ /**
+ * check if all dependent selection are selected
+ */
+ public boolean isAllDetectionSelected() {
if (detectionList.isEmpty())
return false;
@@ -213,14 +202,13 @@ public class TrackSegment implements Cloneable
return result;
}
- /** Add a detection in the segmentTrack */
- public void addDetection(Detection detection)
- {
- if (detectionList.size() > 0)
- {
+ /**
+ * Add a detection in the segmentTrack
+ */
+ public void addDetection(Detection detection) {
+ if (detectionList.size() > 0) {
Detection detectionPrevious = getLastDetection();
- if (detection.getT() != detectionPrevious.getT() + 1)
- {
+ if (detection.getT() != detectionPrevious.getT() + 1) {
System.err.println(
"TrackSegment : The detection must be added with consecutive T value. Detection was not added");
// throw new IllegalArgumentException();
@@ -238,67 +226,73 @@ public class TrackSegment implements Cloneable
detectionList.add(detection);
}
- public void removeDetection(Detection detection)
- {
+ public void removeDetection(Detection detection) {
// detection.setOwnerTrackSegment(null);
detectionList.remove(detection);
}
- /** Remove a detection in the segmentTrack */
- public void removeLastDetection()
- {
+ /**
+ * Remove a detection in the segmentTrack
+ */
+ public void removeLastDetection() {
// getLastDetection().ownerTrackSegment = null;
detectionList.remove(getLastDetection());
}
- /** Add a TrackSegment before this trackSegment */
- public void addPrevious(TrackSegment trackSegment)
- {
+ /**
+ * Add a TrackSegment before this trackSegment
+ */
+ public void addPrevious(TrackSegment trackSegment) {
previousList.add(trackSegment);
trackSegment.nextList.add(this);
}
- /** Remove a TrackSegment before this trackSegment */
- public void removePrevious(TrackSegment trackSegment)
- {
+ /**
+ * Remove a TrackSegment before this trackSegment
+ */
+ public void removePrevious(TrackSegment trackSegment) {
previousList.remove(trackSegment);
trackSegment.nextList.remove(this);
}
- /** Add a TrackSegment after this trackSegment */
- public void addNext(TrackSegment trackSegment)
- {
+ /**
+ * Add a TrackSegment after this trackSegment
+ */
+ public void addNext(TrackSegment trackSegment) {
nextList.add(trackSegment);
trackSegment.previousList.add(this);
}
- /** Remove a TrackSegment after this trackSegment */
- public void removeNext(TrackSegment trackSegment)
- {
+ /**
+ * Remove a TrackSegment after this trackSegment
+ */
+ public void removeNext(TrackSegment trackSegment) {
nextList.remove(trackSegment);
trackSegment.previousList.remove(this);
}
- /** return first detection ( should be first in time too ) */
- public Detection getFirstDetection()
- {
+ /**
+ * return first detection ( should be first in time too )
+ */
+ public Detection getFirstDetection() {
if (detectionList.size() == 0)
return null;
return detectionList.get(0);
}
- /** return detection at index i */
- public Detection getDetectionAt(int i)
- {
+ /**
+ * return detection at index i
+ */
+ public Detection getDetectionAt(int i) {
return detectionList.get(i);
}
- /** return detection at time t */
- public Detection getDetectionAtTime(int t)
- {
- for (Detection detection : detectionList)
- {
+ /**
+ * return detection at time t
+ */
+ public Detection getDetectionAtTime(int t) {
+ for (Detection detection : detectionList) {
if (detection.getT() == t)
return detection;
}
@@ -314,43 +308,41 @@ public class TrackSegment implements Cloneable
* Detection
* to be correctly updated.
*/
- public ArrayList<Detection> getDetectionList()
- {
+ public ArrayList<Detection> getDetectionList() {
return (ArrayList<Detection>) detectionList;
}
- /** return last detection ( should be last in time too ) */
- public Detection getLastDetection()
- {
+ /**
+ * return last detection ( should be last in time too )
+ */
+ public Detection getLastDetection() {
if (detectionList.size() == 0)
return null;
return detectionList.get(detectionList.size() - 1);
}
- /** return detection index */
- public int getDetectionIndex(Detection detection)
- {
+ /**
+ * return detection index
+ */
+ public int getDetectionIndex(Detection detection) {
return detectionList.indexOf(detection);
}
- public void setOwnerTrackGroup(TrackGroup tg)
- {
+ public void setOwnerTrackGroup(TrackGroup tg) {
ownerTrackGroup = tg;
}
- public TrackGroup getOwnerTrackGroup()
- {
+ public TrackGroup getOwnerTrackGroup() {
return ownerTrackGroup;
}
- public void removeAllLinks()
- {
- List<TrackSegment> previousListCopy = new ArrayList<TrackSegment>(previousList);
+ public void removeAllLinks() {
+ List<TrackSegment> previousListCopy = new ArrayList<>(previousList);
for (TrackSegment previousTrackSegment : previousListCopy)
removePrevious(previousTrackSegment);
- List<TrackSegment> nextListCopy = new ArrayList<TrackSegment>(nextList);
+ List<TrackSegment> nextListCopy = new ArrayList<>(nextList);
for (TrackSegment nextTrackSegment : nextListCopy)
removeNext(nextTrackSegment);
}
diff --git a/src/main/java/plugins/fab/trackmanager/blocks/LoadTracksFromXML.java b/src/main/java/plugins/fab/trackmanager/blocks/LoadTracksFromXML.java
index 0b30ee1078540ec2ddf43618c8f945e0e8dd3e46..c9e44b5974340d0f14f6f0899f98c4ce58bcfa71 100644
--- a/src/main/java/plugins/fab/trackmanager/blocks/LoadTracksFromXML.java
+++ b/src/main/java/plugins/fab/trackmanager/blocks/LoadTracksFromXML.java
@@ -16,25 +16,21 @@ import plugins.fab.trackmanager.TrackManager;
/**
* Block to load a set of ROI from a file
- *
+ *
* @author Stephane
*/
-public class LoadTracksFromXML extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
-{
- final VarMutable file = new VarMutable("XML file", null)
- {
+public class LoadTracksFromXML extends Plugin implements ROIBlock, PluginLibrary, PluginBundled {
+ final VarMutable file = new VarMutable("XML file", null) {
@Override
- public boolean isAssignableFrom(@SuppressWarnings("rawtypes") Var source)
- {
+ public boolean isAssignableFrom(Var source) {
return (String.class == source.getType()) || (File.class == source.getType());
}
};
final VarInteger groupIndex = new VarInteger("Group index", 0);
- final Var<TrackGroup> tracks = new Var<TrackGroup>("Track group", new TrackGroup(null));
+ final Var<TrackGroup> tracks = new Var<>("Track group", new TrackGroup(null));
@Override
- public void run()
- {
+ public void run() {
final Object obj = file.getValue();
if (obj == null)
return;
@@ -53,22 +49,19 @@ public class LoadTracksFromXML extends Plugin implements ROIBlock, PluginLibrary
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(VarList inputMap) {
inputMap.add("file", file);
inputMap.add("groupIndex", groupIndex);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(VarList outputMap) {
outputMap.add("tracks", tracks);
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return TrackManager.class.getName();
}
}
diff --git a/src/main/java/plugins/fab/trackmanager/blocks/SaveTracksToXML.java b/src/main/java/plugins/fab/trackmanager/blocks/SaveTracksToXML.java
index c35bb0a76544a344c43633fd59db856824af7d7e..27229b293397695766273fef432f296daa79a0a7 100644
--- a/src/main/java/plugins/fab/trackmanager/blocks/SaveTracksToXML.java
+++ b/src/main/java/plugins/fab/trackmanager/blocks/SaveTracksToXML.java
@@ -15,24 +15,20 @@ import plugins.fab.trackmanager.TrackManager;
/**
* Block to save a set of ROI to a file
- *
+ *
* @author Stephane
*/
-public class SaveTracksToXML extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
-{
- final Var<TrackGroup> tracks = new Var<TrackGroup>("Track group", new TrackGroup(null));
- final VarMutable file = new VarMutable("XML file", null)
- {
+public class SaveTracksToXML extends Plugin implements ROIBlock, PluginLibrary, PluginBundled {
+ final Var<TrackGroup> tracks = new Var<>("Track group", new TrackGroup(null));
+ final VarMutable file = new VarMutable("XML file", null) {
@Override
- public boolean isAssignableFrom(@SuppressWarnings("rawtypes") Var source)
- {
+ public boolean isAssignableFrom(Var source) {
return (String.class == source.getType()) || (File.class == source.getType());
}
};
@Override
- public void run()
- {
+ public void run() {
final TrackGroup group = tracks.getValue();
// nothing to do
if (group == null)
@@ -54,21 +50,18 @@ public class SaveTracksToXML extends Plugin implements ROIBlock, PluginLibrary,
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(VarList inputMap) {
inputMap.add("tracks", tracks);
inputMap.add("file", file);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(VarList outputMap) {
//
}
@Override
- public String getMainPluginClassName()
- {
+ public String getMainPluginClassName() {
return TrackManager.class.getName();
}
}