diff --git a/.gitignore b/.gitignore
index 3d47f986c41db29ec6dc0d5036bf760b3a1cf366..57f16fb67c1b1589981416b323d7a9debc728665 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,41 @@
-.idea/
+/build*
+/workspace
+setting.xml
+release/
target/
-.settings/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
*.iml
+*.ipr
+
+### Eclipse ###
+.apt_generated
+.classpath
+.factorypath
.project
-.classpath
\ No newline at end of file
+.settings
+.springBeans
+.sts4-cache
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+
+### Mac OS ###
+**/.DS_Store
+Icon?
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index b2ac9bb9ab412940e18222b5c0b6d2155c1eef41..68dd4b727d41c21cb3019e6c8a508ebaba688b96 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,23 +6,21 @@
<!-- Inherited Icy Parent POM -->
<parent>
- <artifactId>pom-icy</artifactId>
+ <artifactId>pom-icy</artifactId>
<groupId>org.bioimageanalysis.icy</groupId>
- <version>2.0.0</version>
- </parent>
+ <version>3.0.0-a.1</version>
+ </parent>
<!-- Project Information -->
<artifactId>track-painter</artifactId>
- <version>2.2.1</version>
-
- <packaging>jar</packaging>
+ <version>3.0.0-a.1</version>
<name>Track Painter</name>
<description>
Track Manager plugin that displays available tracks on the selected sequence, in both 2D and 3D viewers, with various visualisation
options. Tracks never looked so good!
</description>
- <url>http://icy.bioimageanalysis.org/plugin/track-painter/</url>
+ <url>https://icy.bioimageanalysis.org/plugin/track-painter/</url>
<inceptionYear>2020</inceptionYear>
<organization>
@@ -56,39 +54,23 @@
</developer>
</developers>
- <!-- Project properties -->
- <properties>
-
- </properties>
-
- <profiles>
- <profile>
- <id>icy-plugin</id>
- <activation>
- <activeByDefault>true</activeByDefault>
- </activation>
- </profile>
- </profiles>
-
- <!-- List of project's dependencies -->
<dependencies>
- <!-- The core of Icy -->
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-kernel</artifactId>
- <version>${icy-kernel.version}</version>
+ <artifactId>ezplug</artifactId>
</dependency>
-
- <dependency>
+
+ <dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-vtk</artifactId>
- <version>${icy-vtk.version}</version>
+ <artifactId>spot-detection-utilities</artifactId>
</dependency>
-
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>track-manager</artifactId>
- <version>${track-manager.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>vecmath</artifactId>
</dependency>
</dependencies>
@@ -96,8 +78,7 @@
<repositories>
<repository>
<id>icy</id>
- <name>Icy's Nexus</name>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
</repository>
</repositories>
</project>
diff --git a/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$1.class b/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$1.class
deleted file mode 100644
index eb6281a50c89ae7fad5d7bd157e72eaca215bf47..0000000000000000000000000000000000000000
Binary files a/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$1.class and /dev/null differ
diff --git a/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$2.class b/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$2.class
deleted file mode 100644
index 12df67be3bdcbd8aea76960581666b999dd539e7..0000000000000000000000000000000000000000
Binary files a/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$2.class and /dev/null differ
diff --git a/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$3.class b/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$3.class
deleted file mode 100644
index 64de8e96805093b8f6d8f660db86941cb3ef52e8..0000000000000000000000000000000000000000
Binary files a/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$3.class and /dev/null differ
diff --git a/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$4.class b/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$4.class
deleted file mode 100644
index 7b1497261f426535cfe5942d43016f37fc73a535..0000000000000000000000000000000000000000
Binary files a/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$4.class and /dev/null differ
diff --git a/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$5.class b/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$5.class
deleted file mode 100644
index 8e4a2a969e26241a7c08063ed838303688d3c275..0000000000000000000000000000000000000000
Binary files a/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay$5.class and /dev/null differ
diff --git a/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay.class b/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay.class
deleted file mode 100644
index 7fbca38c9758049c2a618310ecf5ef7642844dde..0000000000000000000000000000000000000000
Binary files a/src/main/java/plugins/adufour/trackprocessors/TrackPainter$TrackOverlay.class and /dev/null differ
diff --git a/src/main/java/plugins/adufour/trackprocessors/TrackPainter.class b/src/main/java/plugins/adufour/trackprocessors/TrackPainter.class
deleted file mode 100644
index bdd3ca266783068259e3fa5acca8cb930244d83f..0000000000000000000000000000000000000000
Binary files a/src/main/java/plugins/adufour/trackprocessors/TrackPainter.class and /dev/null differ
diff --git a/src/main/java/plugins/adufour/trackprocessors/TrackPainter.java b/src/main/java/plugins/adufour/trackprocessors/TrackPainter.java
index 1d432ee11f158157e6c0f271e492c2924b0babea..8fd7a828a78f9c778a00655bbce876c9fbd04f2e 100644
--- a/src/main/java/plugins/adufour/trackprocessors/TrackPainter.java
+++ b/src/main/java/plugins/adufour/trackprocessors/TrackPainter.java
@@ -1,34 +1,34 @@
-package plugins.adufour.trackprocessors;
-
-import java.awt.BasicStroke;
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseWheelEvent;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.Line2D;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.TreeMap;
+/*
+ * Copyright (c) 2010-2024. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Icy. If not, see <https://www.gnu.org/licenses/>.
+ */
-import javax.swing.BoxLayout;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.border.TitledBorder;
-import javax.vecmath.Point2d;
-import javax.vecmath.Point3d;
+package plugins.adufour.trackprocessors;
-import icy.canvas.IcyCanvas;
-import icy.canvas.IcyCanvas2D;
-import icy.painter.Overlay;
-import icy.painter.OverlayWrapper;
-import icy.painter.VtkPainter;
-import icy.sequence.Sequence;
-import icy.type.point.Point5D;
+import org.bioimageanalysis.icy.common.geom.point.Point5D;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.gui.canvas.IcyCanvas;
+import org.bioimageanalysis.icy.gui.canvas.IcyCanvas2D;
+import org.bioimageanalysis.icy.gui.canvas.VtkCanvas;
+import org.bioimageanalysis.icy.model.overlay.Overlay;
+import org.bioimageanalysis.icy.model.overlay.VtkPainter;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.NotNull;
import plugins.adufour.vars.gui.swing.SwingVarEditor;
import plugins.adufour.vars.lang.Var;
import plugins.adufour.vars.lang.VarBoolean;
@@ -36,50 +36,47 @@ import plugins.fab.trackmanager.PluginTrackManagerProcessor;
import plugins.fab.trackmanager.TrackManagerPainter;
import plugins.fab.trackmanager.TrackPool;
import plugins.fab.trackmanager.TrackSegment;
-import plugins.kernel.canvas.VtkCanvas;
import plugins.nchenouard.spot.Detection;
-import vtk.vtkActor;
-import vtk.vtkAppendPolyData;
-import vtk.vtkGlyph3D;
-import vtk.vtkLODActor;
-import vtk.vtkParametricFunctionSource;
-import vtk.vtkParametricSpline;
-import vtk.vtkPoints;
-import vtk.vtkPolyData;
-import vtk.vtkPolyDataMapper;
-import vtk.vtkProp;
-import vtk.vtkRenderer;
-import vtk.vtkSphereSource;
-import vtk.vtkTubeFilter;
-import vtk.vtkUnsignedCharArray;
-
-public class TrackPainter extends PluginTrackManagerProcessor
-{
+import vtk.*;
+
+import javax.swing.*;
+import javax.swing.border.TitledBorder;
+import javax.vecmath.Point2d;
+import javax.vecmath.Point3d;
+import java.awt.*;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseWheelEvent;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.Line2D;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.TreeMap;
+
+@IcyPluginName("Track Painter")
+@IcyPluginIcon(path = "/track-painter.png")
+public class TrackPainter extends PluginTrackManagerProcessor {
private static final String filterName = "Display tracks on sequence";
private TrackOverlay overlay;
- private boolean keepLegacyOverlay = true;
+ private final boolean keepLegacyOverlay = true;
private Overlay legacyOverlay;
private List<TrackSegment> tracks;
- public TrackPainter()
- {
+ public TrackPainter() {
super();
setName(filterName);
- tracks = new ArrayList<TrackSegment>();
+ tracks = new ArrayList<>();
}
@Override
- public void Close()
- {
+ public void Close() {
if (overlay != null)
overlay.remove();
// put the legacy overlay back in place
- if (keepLegacyOverlay && legacyOverlay != null)
- {
+ if (keepLegacyOverlay && legacyOverlay != null) {
if (trackPool.getDisplaySequence() != null)
trackPool.getDisplaySequence().addOverlay(legacyOverlay);
@@ -88,11 +85,9 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
@Override
- public void displaySequenceChanged()
- {
- System.out.println("display sequence changed");
- if (overlay != null)
- {
+ public void displaySequenceChanged() {
+ IcyLogger.info(this.getClass(), "Display sequence changed.");
+ if (overlay != null) {
overlay.remove();
overlay = null;
}
@@ -100,22 +95,21 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
@Override
- public void Compute()
- {
- if (overlay == null)
- {
- Sequence s = trackPool.getDisplaySequence();
- if (s != null)
- {
+ public void Compute() {
+ if (overlay == null) {
+ final Sequence s = trackPool.getDisplaySequence();
+ if (s != null) {
// remove the current legacy painter and store it here
- for (Overlay layer : s.getOverlays(OverlayWrapper.class))
- {
- OverlayWrapper wrapper = (OverlayWrapper) layer;
- if (wrapper.getPainter() instanceof TrackManagerPainter)
- {
+ /*for (final Overlay layer : s.getOverlays(OverlayWrapper.class)) {
+ final OverlayWrapper wrapper = (OverlayWrapper) layer;
+ if (wrapper.getPainter() instanceof TrackManagerPainter) {
legacyOverlay = layer;
s.removeOverlay(legacyOverlay);
}
+ }*/
+
+ for (final Overlay layer : s.getOverlays(TrackManagerPainter.class)) {
+ s.removeOverlay(layer);
}
s.addOverlay(overlay = new TrackOverlay(trackPool));
@@ -126,26 +120,22 @@ public class TrackPainter extends PluginTrackManagerProcessor
panel.invalidate();
}
}
- else
- {
- // overlay.upToDate = false;
- }
+ //else {
+ // overlay.upToDate = false;
+ //}
- // store current state of tracks (so we display it correctly depending the order of the processor)
- final List<TrackSegment> newTracks = new ArrayList<TrackSegment>();
- for (TrackSegment track : trackPool.getTrackSegmentList())
- {
- final ArrayList<Detection> detections = new ArrayList<Detection>();
+ // store current state of tracks (so we display it correctly depending on the order of the processor)
+ final List<TrackSegment> newTracks = new ArrayList<>();
+ for (final TrackSegment track : trackPool.getTrackSegmentList()) {
+ final ArrayList<Detection> detections = new ArrayList<>();
- try
- {
- for (Detection detection : track.getDetectionList())
+ try {
+ for (final Detection detection : track.getDetectionList())
detections.add((Detection) detection.clone());
}
- catch (CloneNotSupportedException e)
- {
+ catch (final CloneNotSupportedException e) {
// should never happen
- e.printStackTrace();
+ IcyLogger.error(this.getClass(), e, "Clone not supported.");
}
newTracks.add(new TrackSegment(detections));
@@ -158,8 +148,7 @@ public class TrackPainter extends PluginTrackManagerProcessor
overlay.upToDate = false;
}
- public class TrackOverlay extends Overlay implements VtkPainter
- {
+ public class TrackOverlay extends Overlay implements VtkPainter {
private final TrackPool trackPool;
private double xScale, yScale, zScale;
@@ -175,7 +164,7 @@ public class TrackPainter extends PluginTrackManagerProcessor
private final vtkPolyDataMapper lineMapper = new vtkPolyDataMapper();
private final vtkActor lineActor = new vtkActor();
- private final List<vtkActor> visibleActors = new ArrayList<vtkActor>(2);
+ private final List<vtkActor> visibleActors = new ArrayList<>(2);
private IcyCanvas canvas;
private vtkRenderer renderer = null;
@@ -183,29 +172,26 @@ public class TrackPainter extends PluginTrackManagerProcessor
private boolean upToDate = false;
// user settings (detections)
- private final VarBoolean detectionDisplay = new VarBoolean("Show detections", true)
- {
- protected void fireVariableChanged(Boolean oldValue, Boolean newValue)
- {
+ private final VarBoolean detectionDisplay = new VarBoolean("Show detections", true) {
+ @Override
+ protected void fireVariableChanged(final Boolean oldValue, final Boolean newValue) {
setDetectionDisplay(newValue);
super.fireVariableChanged(oldValue, newValue);
}
};
// user settings (tracks)
- private final VarBoolean trackDisplay = new VarBoolean("Show tracks", true)
- {
- protected void fireVariableChanged(Boolean oldValue, Boolean newValue)
- {
+ private final VarBoolean trackDisplay = new VarBoolean("Show tracks", true) {
+ @Override
+ protected void fireVariableChanged(final Boolean oldValue, final Boolean newValue) {
setTrackDisplay(newValue);
super.fireVariableChanged(oldValue, newValue);
}
};
- private final VarBoolean displaySelectionOnly = new VarBoolean("Show selected tracks", false)
- {
- protected void fireVariableChanged(Boolean oldValue, Boolean newValue)
- {
+ private final VarBoolean displaySelectionOnly = new VarBoolean("Show selected tracks", false) {
+ @Override
+ protected void fireVariableChanged(final Boolean oldValue, final Boolean newValue) {
super.fireVariableChanged(oldValue, newValue);
upToDate = false;
painterChanged();
@@ -214,12 +200,10 @@ public class TrackPainter extends PluginTrackManagerProcessor
// 3D settings
- private final VarBoolean autoScale3D = new VarBoolean("Auto-scale with zoom", true)
- {
- protected void fireVariableChanged(Boolean oldValue, Boolean newValue)
- {
- if (newValue)
- {
+ private final VarBoolean autoScale3D = new VarBoolean("Auto-scale with zoom", true) {
+ @Override
+ protected void fireVariableChanged(final Boolean oldValue, final @NotNull Boolean newValue) {
+ if (newValue) {
upToDate = false;
painterChanged();
}
@@ -227,31 +211,27 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
};
- private final VarBoolean trackTubes = new VarBoolean("Show tracks as tubes", true)
- {
- protected void fireVariableChanged(Boolean oldValue, Boolean newValue)
- {
+ private final VarBoolean trackTubes = new VarBoolean("Show tracks as tubes", true) {
+ @Override
+ protected void fireVariableChanged(final Boolean oldValue, final Boolean newValue) {
setTrackDisplayAsTubes(newValue);
super.fireVariableChanged(oldValue, newValue);
}
};
- public TrackOverlay(TrackPool trackPool)
- {
+ public TrackOverlay(final @NotNull TrackPool trackPool) {
super(filterName);
this.trackPool = trackPool;
final Sequence seq = trackPool.getDisplaySequence();
- if (seq == null)
- {
+ if (seq == null) {
xScale = 1d;
yScale = 1d;
zScale = 1d;
}
- else
- {
+ else {
xScale = seq.getPixelSizeX();
yScale = seq.getPixelSizeY();
zScale = seq.getPixelSizeZ();
@@ -265,21 +245,20 @@ public class TrackPainter extends PluginTrackManagerProcessor
// createGUI(getOptionsPanel());
}
- public JPanel getOptionsPanel()
- {
- JPanel container = new JPanel();
+ @Override
+ public JPanel getOptionsPanel() {
+ final JPanel container = new JPanel();
container.setBorder(null);
container.setLayout(new BoxLayout(container, BoxLayout.X_AXIS));
// Create a panel for the detections
- JPanel detectionPanel = new JPanel(new GridBagLayout());
+ final JPanel detectionPanel = new JPanel(new GridBagLayout());
detectionPanel.setBorder(new TitledBorder("Common settings"));
container.add(detectionPanel);
- for (Var<?> var : new Var<?>[] {detectionDisplay, trackDisplay, displaySelectionOnly})
- {
- GridBagConstraints gbc = new GridBagConstraints();
+ for (final Var<?> var : new Var<?>[]{detectionDisplay, trackDisplay, displaySelectionOnly}) {
+ final GridBagConstraints gbc = new GridBagConstraints();
gbc.insets = new Insets(2, 10, 2, 5);
gbc.fill = GridBagConstraints.HORIZONTAL;
@@ -287,7 +266,7 @@ public class TrackPainter extends PluginTrackManagerProcessor
gbc.weightx = 1;
gbc.gridwidth = GridBagConstraints.REMAINDER;
- SwingVarEditor<?> editor = (SwingVarEditor<?>) var.createVarEditor();
+ final SwingVarEditor<?> editor = (SwingVarEditor<?>) var.createVarEditor();
editor.setEnabled(true);
editor.getEditorComponent().setFocusable(false);
detectionPanel.add(editor.getEditorComponent(), gbc);
@@ -295,13 +274,12 @@ public class TrackPainter extends PluginTrackManagerProcessor
// Create a panel for the tracks
- JPanel trackPanel = new JPanel(new GridBagLayout());
+ final JPanel trackPanel = new JPanel(new GridBagLayout());
trackPanel.setBorder(new TitledBorder("3D settings"));
container.add(trackPanel);
- for (Var<?> var : new Var<?>[] {autoScale3D, trackTubes})
- {
- GridBagConstraints gbc = new GridBagConstraints();
+ for (final Var<?> var : new Var<?>[]{autoScale3D, trackTubes}) {
+ final GridBagConstraints gbc = new GridBagConstraints();
gbc.insets = new Insets(2, 10, 2, 5);
gbc.fill = GridBagConstraints.HORIZONTAL;
@@ -309,7 +287,7 @@ public class TrackPainter extends PluginTrackManagerProcessor
gbc.weightx = 1;
gbc.gridwidth = GridBagConstraints.REMAINDER;
- SwingVarEditor<?> editor = (SwingVarEditor<?>) var.createVarEditor();
+ final SwingVarEditor<?> editor = (SwingVarEditor<?>) var.createVarEditor();
editor.setEnabled(true);
editor.getEditorComponent().setFocusable(false);
trackPanel.add(editor.getEditorComponent(), gbc);
@@ -320,11 +298,10 @@ public class TrackPainter extends PluginTrackManagerProcessor
/**
* Initializes (immutable) rendering components and default user settings
- *
+ *
* @param vtkCanvas
*/
- private void initRenderer(VtkCanvas vtkCanvas)
- {
+ private void initRenderer(final @NotNull VtkCanvas vtkCanvas) {
// 1) initialize immutable items
renderer = vtkCanvas.getRenderer();
@@ -357,14 +334,12 @@ public class TrackPainter extends PluginTrackManagerProcessor
/**
* Enables/Disables detection display. See below for further display options
- *
- * @param display
- * <code>true</code> if detections should be displayed, <code>false</code>
- * otherwise
- * see #setDetectionRadius(double)
+ *
+ * @param display <code>true</code> if detections should be displayed, <code>false</code>
+ * otherwise
+ * see #setDetectionRadius(double)
*/
- public void setDetectionDisplay(boolean display)
- {
+ public void setDetectionDisplay(final boolean display) {
this.detectionDisplay.setValue(display);
// VTK uses integers...
@@ -378,14 +353,12 @@ public class TrackPainter extends PluginTrackManagerProcessor
/**
* Enables/Disables track display. See below for further display options
- *
- * @param display
- * <code>true</code> if tracks should be displayed, <code>false</code> otherwise
+ *
+ * @param display <code>true</code> if tracks should be displayed, <code>false</code> otherwise
* @see #setTrackDisplayAsTubes(boolean)
* see #setTrackTubeRadius(double)
*/
- public void setTrackDisplay(boolean display)
- {
+ public void setTrackDisplay(final boolean display) {
this.trackDisplay.setValue(display);
// VTK uses integers...
@@ -398,14 +371,12 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
/**
- * @param displayAsTubes
- * <code>true</code> if the tracks should be displayed as 3D tubes, or
- * <code>false</code> to display tracks as lines (no thickness). Note that
- * displaying tracks as 3D tubes can be considerably slower on some systems
- * see #setTrackTubeRadius(double)
+ * @param displayAsTubes <code>true</code> if the tracks should be displayed as 3D tubes, or
+ * <code>false</code> to display tracks as lines (no thickness). Note that
+ * displaying tracks as 3D tubes can be considerably slower on some systems
+ * see #setTrackTubeRadius(double)
*/
- public void setTrackDisplayAsTubes(boolean displayAsTubes)
- {
+ public void setTrackDisplayAsTubes(final boolean displayAsTubes) {
this.trackTubes.setValue(displayAsTubes);
upToDate = false;
@@ -413,29 +384,22 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
@Override
- public void paint(Graphics2D g, Sequence sequence, IcyCanvas theCanvas)
- {
- if (theCanvas instanceof VtkCanvas)
- {
- VtkCanvas vtk = (VtkCanvas) theCanvas;
-
- if (renderer != vtk.getRenderer())
- {
+ public void paint(final Graphics2D g, final Sequence sequence, final IcyCanvas theCanvas) {
+ if (theCanvas instanceof final VtkCanvas vtk) {
+ if (renderer != vtk.getRenderer()) {
initRenderer(vtk);
upToDate = false;
}
if ((sequence.getPixelSizeX() != xScale) || (sequence.getPixelSizeY() != yScale)
- || (sequence.getPixelSizeZ() != zScale))
- {
+ || (sequence.getPixelSizeZ() != zScale)) {
xScale = sequence.getPixelSizeX();
yScale = sequence.getPixelSizeY();
zScale = sequence.getPixelSizeZ();
upToDate = false;
}
- if (theCanvas.getPositionT() != positionT)
- {
+ if (theCanvas.getPositionT() != positionT) {
positionT = theCanvas.getPositionT();
// need to check that because of the screenshot rendering which doesn't send position change event
if (trackPool.getTrackManager().getCurrentPositionT() != positionT)
@@ -454,61 +418,56 @@ public class TrackPainter extends PluginTrackManagerProcessor
upToDate = true;
}
- else if (theCanvas instanceof IcyCanvas2D)
- {
+ else if (theCanvas instanceof IcyCanvas2D) {
drawTracks2D((Graphics2D) g.create(), (IcyCanvas2D) theCanvas);
}
}
- private void drawTracks2D(Graphics2D g, IcyCanvas2D theCanvas)
- {
+ private void drawTracks2D(final Graphics2D g, final @NotNull IcyCanvas2D theCanvas) {
// need to check that because of the screenshot rendering which doesn't send position change event
if (trackPool.getTrackManager().getCurrentPositionT() != theCanvas.getPositionT())
trackPool.getTrackManager().setCurrentPositionT(theCanvas.getPositionT());
- Graphics2D g2 = (Graphics2D) g.create();
- double zoom = theCanvas.getScaleX();
+ final Graphics2D g2 = (Graphics2D) g.create();
+ final double zoom = theCanvas.getScaleX();
- double lodThreshold = 2.0 / zoom;
+ final double lodThreshold = 2.0 / zoom;
- float strokeWidth = (float) theCanvas.canvasToImageLogDeltaX(2);
+ final float strokeWidth = (float) theCanvas.canvasToImageLogDeltaX(2);
g.setStroke(new BasicStroke(strokeWidth));
- Point2d p1 = new Point2d(), p2 = new Point2d();
- Line2D.Double l = new Line2D.Double();
+ final Point2d p1 = new Point2d();
+ final Point2d p2 = new Point2d();
+ final Line2D.Double l = new Line2D.Double();
- double shapeFactor = 5.0;
- Ellipse2D.Double detectionShape = new Ellipse2D.Double(0, 0, strokeWidth * shapeFactor,
+ final double shapeFactor = 5.0;
+ final Ellipse2D.Double detectionShape = new Ellipse2D.Double(0, 0, strokeWidth * shapeFactor,
strokeWidth * shapeFactor);
- double shapeCenter = strokeWidth * shapeFactor / 2;
+ final double shapeCenter = strokeWidth * shapeFactor / 2;
g.translate(0.5, 0.5);
- for (TrackSegment ts : tracks)
- {
- ArrayList<Detection> detections = ts.getDetectionList();
+ for (final TrackSegment ts : tracks) {
+ final ArrayList<Detection> detections = ts.getDetectionList();
- int nDet = detections.size();
+ final int nDet = detections.size();
- for (int t = 0; t < nDet; t++)
- {
- Detection d1 = detections.get(t);
+ for (int t = 0; t < nDet; t++) {
+ final Detection d1 = detections.get(t);
if (d1 == null || !d1.isEnabled())
continue;
p1.set(d1.getX(), d1.getY());
g.setColor(d1.getColor());
- if (displaySelectionOnly.getValue())
- {
+ if (displaySelectionOnly.getValue()) {
if (!d1.isSelected())
continue;
}
else if (d1.isSelected())
g.setColor(Color.white);
- if (d1.getT() == theCanvas.getPositionT() && d1 != null && detectionDisplay.getValue())
- {
+ if (d1.getT() == theCanvas.getPositionT() && d1 != null && detectionDisplay.getValue()) {
// draw current detection
// if selected, switch color to white
detectionShape.x = p1.x - shapeCenter;
@@ -518,21 +477,17 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
// LOD find the shortest segment above the drawing threshold
- for (; t < nDet - 1; t++)
- {
- Detection d2 = detections.get(t + 1);
+ for (; t < nDet - 1; t++) {
+ final Detection d2 = detections.get(t + 1);
if (d2 == null || !d2.isEnabled())
break;
- if (trackDisplay.getValue())
- {
+ if (trackDisplay.getValue()) {
p2.set(d2.getX(), d2.getY());
- if (p1.distanceSquared(p2) < lodThreshold)
- {
+ if (p1.distanceSquared(p2) < lodThreshold) {
// draw the detection in case it was skipped due to the LOD
- if (d2.getT() == theCanvas.getPositionT() && d2 != null && detectionDisplay.getValue())
- {
+ if (d2.getT() == theCanvas.getPositionT() && d2 != null && detectionDisplay.getValue()) {
// draw current detection
// if selected, switch color to white
detectionShape.x = p2.x - shapeCenter;
@@ -556,40 +511,37 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
}
- private void drawTracks3D()
- {
- double viewScale = Math.sqrt(((VtkCanvas) canvas).getCamera().GetDistance()) * (xScale + yScale + zScale)
+ private void drawTracks3D() {
+ final double viewScale = Math.sqrt(((VtkCanvas) canvas).getCamera().GetDistance()) * (xScale + yScale + zScale)
/ 3;
- double tubeRadius = viewScale / 15.0;
+ final double tubeRadius = viewScale / 15.0;
- int tubeSection = (int) Math.min(8, 100.0 / viewScale);
- int tubeSmoothness = Math.max(1, tubeSection - 1);
+ final int tubeSection = (int) Math.min(8, 100.0 / viewScale);
+ final int tubeSmoothness = Math.max(1, tubeSection - 1);
lines.RemoveAllInputs();
- for (TrackSegment ts : tracks)
- {
- List<Detection> detections = ts.getDetectionList();
+ for (final TrackSegment ts : tracks) {
+ final List<Detection> detections = ts.getDetectionList();
- vtkPoints points = new vtkPoints();
- vtkUnsignedCharArray colors = new vtkUnsignedCharArray();
+ final vtkPoints points = new vtkPoints();
+ final vtkUnsignedCharArray colors = new vtkUnsignedCharArray();
colors.SetName("colors");
colors.SetNumberOfComponents(3);
- for (int t = 0; t < detections.size(); t++)
- {
- Detection detection = detections.get(t);
-
+ for (final Detection detection : detections) {
if (detection == null)
continue;
if (displaySelectionOnly.getValue() && !detection.isSelected())
continue;
- if (detection.isEnabled())
- {
- Point3d position = new Point3d(detection.getX() * xScale, detection.getY() * yScale,
- detection.getZ() * zScale);
- Color color = (displaySelectionOnly.getValue() == detection.isSelected()) ? detection.getColor()
+ if (detection.isEnabled()) {
+ final Point3d position = new Point3d(
+ detection.getX() * xScale,
+ detection.getY() * yScale,
+ detection.getZ() * zScale
+ );
+ final Color color = (displaySelectionOnly.getValue() == detection.isSelected()) ? detection.getColor()
: Color.white;
points.InsertNextPoint(position.x, position.y, position.z);
@@ -599,20 +551,19 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
}
- vtkParametricSpline spline = new vtkParametricSpline();
+ final vtkParametricSpline spline = new vtkParametricSpline();
spline.SetPoints(points);
- vtkParametricFunctionSource function = new vtkParametricFunctionSource();
+ final vtkParametricFunctionSource function = new vtkParametricFunctionSource();
function.SetParametricFunction(spline);
- function.SetUResolution(points.GetNumberOfPoints() * tubeSmoothness);
+ function.SetUResolution((int) (points.GetNumberOfPoints() * tubeSmoothness));
function.Update();
- vtkPolyData lineData = function.GetOutput();
+ final vtkPolyData lineData = function.GetOutput();
lineData.GetPointData().SetScalars(colors);
- if (trackTubes.getValue())
- {
+ if (trackTubes.getValue()) {
// draw the splines as thick 3D tubes
- vtkTubeFilter tuber = new vtkTubeFilter();
+ final vtkTubeFilter tuber = new vtkTubeFilter();
tuber.SetInputData(lineData);
tuber.SetRadius(tubeRadius);
tuber.CappingOn();
@@ -627,8 +578,7 @@ public class TrackPainter extends PluginTrackManagerProcessor
// cleanup
tuber.Delete();
}
- else
- {
+ else {
// just draw the spline itself (no thickness)
lines.AddInputData(lineData);
}
@@ -645,19 +595,17 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
}
- private void drawDetections3D(int positionT)
- {
- double viewScale = (xScale + yScale + zScale) / 3;
- double sphereRadius = Math.sqrt(((VtkCanvas) canvas).getCamera().GetDistance()) * viewScale / 5.0;
+ private void drawDetections3D(final int positionT) {
+ final double viewScale = (xScale + yScale + zScale) / 3;
+ final double sphereRadius = Math.sqrt(((VtkCanvas) canvas).getCamera().GetDistance()) * viewScale / 5.0;
sphere.SetRadius(sphereRadius);
- vtkPoints spherePositions = new vtkPoints();
- vtkUnsignedCharArray sphereColors = new vtkUnsignedCharArray();
+ final vtkPoints spherePositions = new vtkPoints();
+ final vtkUnsignedCharArray sphereColors = new vtkUnsignedCharArray();
sphereColors.SetName("colors");
sphereColors.SetNumberOfComponents(3);
- for (Detection detection : trackPool.getAllDetection())
- {
+ for (final Detection detection : trackPool.getAllDetection()) {
if (detection == null || !detection.isEnabled())
continue;
@@ -667,9 +615,9 @@ public class TrackPainter extends PluginTrackManagerProcessor
if (displaySelectionOnly.getValue() && !detection.isSelected())
continue;
- Point3d position = new Point3d(detection.getX() * xScale, detection.getY() * yScale,
+ final Point3d position = new Point3d(detection.getX() * xScale, detection.getY() * yScale,
detection.getZ() * zScale);
- Color color = (displaySelectionOnly.getValue() == detection.isSelected()) ? detection.getColor()
+ final Color color = (displaySelectionOnly.getValue() == detection.isSelected()) ? detection.getColor()
: Color.white;
spherePositions.InsertNextPoint(position.x, position.y, position.z);
@@ -686,8 +634,7 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
@Override
- public void remove()
- {
+ public void remove() {
if (renderer != null)
renderer = null;
@@ -695,8 +642,7 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
@Override
- public void mouseClick(MouseEvent e, Point5D.Double imagePoint, IcyCanvas theCanvas)
- {
+ public void mouseClick(final MouseEvent e, final Point5D.Double imagePoint, final IcyCanvas theCanvas) {
super.mouseClick(e, imagePoint, theCanvas);
if (!(theCanvas instanceof IcyCanvas2D))
@@ -705,33 +651,37 @@ public class TrackPainter extends PluginTrackManagerProcessor
imagePoint.x -= 0.5;
imagePoint.y -= 0.5;
- double selectThreshold = Math.min(10.0, Math.max(0.25, 10.0 / theCanvas.getScaleX()));
+ final double selectThreshold = Math.min(10.0, Math.max(0.25, 10.0 / theCanvas.getScaleX()));
// List all candidate tracks close to the click
// => store this in a map of [distance <=> track]
- TreeMap<Double, TrackSegment> candidates = new TreeMap<Double, TrackSegment>();
+ final TreeMap<Double, TrackSegment> candidates = new TreeMap<>();
- for (TrackSegment ts : trackPool.getTrackSegmentList())
- {
- ArrayList<Detection> detections = ts.getDetectionList();
+ for (final TrackSegment ts : trackPool.getTrackSegmentList()) {
+ final ArrayList<Detection> detections = ts.getDetectionList();
- int nDet = detections.size() - 1;
+ final int nDet = detections.size() - 1;
- detectionLoop: for (int t = 0; t < nDet; t++)
- {
+ detectionLoop:
+ for (int t = 0; t < nDet; t++) {
// Retrieve the "d1-d2" segment
- Detection d1 = detections.get(t);
- Detection d2 = detections.get(t + 1);
+ final Detection d1 = detections.get(t);
+ final Detection d2 = detections.get(t + 1);
if (d1 == null || d2 == null || !d1.isEnabled() || !d2.isEnabled())
continue;
// Check if the click is close to the segment
- double distSq = Line2D.ptSegDistSq(d1.getX(), d1.getY(), d2.getX(), d2.getY(), imagePoint.x,
- imagePoint.y);
-
- if (distSq < selectThreshold)
- {
+ final double distSq = Line2D.ptSegDistSq(
+ d1.getX(),
+ d1.getY(),
+ d2.getX(),
+ d2.getY(),
+ imagePoint.x,
+ imagePoint.y
+ );
+
+ if (distSq < selectThreshold) {
candidates.put(distSq, ts);
// move to the next track segment
break detectionLoop;
@@ -739,10 +689,9 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
}
- if (candidates.size() > 0)
- {
+ if (!candidates.isEmpty()) {
// highlight the closest candidate
- for (Detection d : candidates.firstEntry().getValue().getDetectionList())
+ for (final Detection d : candidates.firstEntry().getValue().getDetectionList())
d.setSelected(!d.isSelected());
trackPool.fireTrackEditorProcessorChange();
@@ -750,8 +699,7 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
@Override
- public void mouseWheelMoved(MouseWheelEvent e, icy.type.point.Point5D.Double imagePoint, IcyCanvas theCanvas)
- {
+ public void mouseWheelMoved(final MouseWheelEvent e, final Point5D.Double imagePoint, final IcyCanvas theCanvas) {
if (autoScale3D.getValue())
upToDate = false;
@@ -759,9 +707,8 @@ public class TrackPainter extends PluginTrackManagerProcessor
}
@Override
- public vtkProp[] getProps()
- {
- return new vtkProp[] {lineActor, sphereActor};
+ public vtkProp[] getProps() {
+ return new vtkProp[]{lineActor, sphereActor};
}
}
}
diff --git a/src/main/resources/track-painter.png b/src/main/resources/track-painter.png
new file mode 100644
index 0000000000000000000000000000000000000000..33283de571a12bdc0a1a87c395ede199ff040035
Binary files /dev/null and b/src/main/resources/track-painter.png differ