From 12a404fcb0023abbc2990cc3afe832dd20d78dc3 Mon Sep 17 00:00:00 2001
From: Thomas <thomas.musset@pasteur.fr>
Date: Tue, 10 Dec 2024 15:33:54 +0100
Subject: [PATCH] updated to v2.0.0-a.2, updated to Java 23, fix some errors
---
pom.xml | 11 +----
.../java/plugins/fab/trackmanager/Link.java | 2 +-
.../PluginTrackManagerProcessor.java | 10 +----
.../fab/trackmanager/TrackDetection.java | 5 ---
.../plugins/fab/trackmanager/TrackGroup.java | 1 -
.../fab/trackmanager/TrackManager.java | 42 +++++-------------
.../fab/trackmanager/TrackManagerPainter.java | 16 ++-----
.../plugins/fab/trackmanager/TrackPool.java | 16 +++----
.../blocks/LoadTracksFromXML.java | 3 +-
.../trackmanager/blocks/SaveTracksToXML.java | 2 +-
.../fab/trackmanager}/track-manager.png | Bin
11 files changed, 27 insertions(+), 81 deletions(-)
rename src/main/resources/{ => plugins/fab/trackmanager}/track-manager.png (100%)
diff --git a/pom.xml b/pom.xml
index 582587f..974c0c6 100644
--- a/pom.xml
+++ b/pom.xml
@@ -8,11 +8,11 @@
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
- <version>3.0.0-a.1</version>
+ <version>3.0.0-a.3</version>
</parent>
<artifactId>track-manager</artifactId>
- <version>2.0.0-a.1</version>
+ <version>2.0.0-a.2</version>
<name>Track Manager</name>
<description>
@@ -34,11 +34,4 @@
<artifactId>spot-detection-utilities</artifactId>
</dependency>
</dependencies>
-
- <repositories>
- <repository>
- <id>icy</id>
- <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
- </repository>
- </repositories>
</project>
\ No newline at end of file
diff --git a/src/main/java/plugins/fab/trackmanager/Link.java b/src/main/java/plugins/fab/trackmanager/Link.java
index a2fc342..ca6271f 100644
--- a/src/main/java/plugins/fab/trackmanager/Link.java
+++ b/src/main/java/plugins/fab/trackmanager/Link.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
diff --git a/src/main/java/plugins/fab/trackmanager/PluginTrackManagerProcessor.java b/src/main/java/plugins/fab/trackmanager/PluginTrackManagerProcessor.java
index 3468c73..bdd7cd3 100644
--- a/src/main/java/plugins/fab/trackmanager/PluginTrackManagerProcessor.java
+++ b/src/main/java/plugins/fab/trackmanager/PluginTrackManagerProcessor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -130,18 +130,10 @@ public abstract class PluginTrackManagerProcessor extends Plugin {
return mainPanel;
}
- /*@Override
- protected void finalize() throws Throwable {
- trackPool = null;
- super.finalize();
- }*/
-
- @SuppressWarnings("UnstableApiUsage")
@Contract(mutates = "this")
public final void setTrackPool(final TrackPool trackPool) {
this.trackPool = trackPool;
}
abstract public void displaySequenceChanged();
-
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackDetection.java b/src/main/java/plugins/fab/trackmanager/TrackDetection.java
index 2fb2b13..cd5b439 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackDetection.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackDetection.java
@@ -37,11 +37,6 @@ public class TrackDetection extends JPanel {
public TrackDetection(final Detection detection) {
super();
this.detection = detection;
- // if ( detection.getDetectionType() == Detection.DETECTIONTYPE_REAL_DETECTION ) color =
- // Color.blue;
- // if ( detection.getDetectionType() == Detection.DETECTIONTYPE_VIRTUAL_DETECTION ) color =
- // Color.orange;
-
}
public Detection getDetection() {
diff --git a/src/main/java/plugins/fab/trackmanager/TrackGroup.java b/src/main/java/plugins/fab/trackmanager/TrackGroup.java
index 597e931..2d686fa 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackGroup.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackGroup.java
@@ -63,7 +63,6 @@ public class TrackGroup {
}
public TrackSegment getTrackSegmentWithDetection(final Detection detection) {
-
final ArrayList<TrackSegment> trackSegmentList = getTrackSegmentList();
for (final TrackSegment ts : trackSegmentList) {
diff --git a/src/main/java/plugins/fab/trackmanager/TrackManager.java b/src/main/java/plugins/fab/trackmanager/TrackManager.java
index 9adf815..e2664d0 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackManager.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackManager.java
@@ -67,13 +67,8 @@ import java.util.prefs.Preferences;
* @author Fabrice de Chaumont
*/
@IcyPluginName("Track Manager")
-@IcyPluginIcon(path = "/track-manager.png")
+@IcyPluginIcon(path = "/plugins/fab/trackmanager/track-manager.png")
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.)
*/
@@ -124,9 +119,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
trackPool.addTrackProcessor(ptep);
// rebuild trackList
-
rebuildTrackProcessorDisplay();
-
}
public TrackPool getTrackPool() {
@@ -134,7 +127,6 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
}
void rebuildTrackProcessorDisplay() {
-
rightContentPanel.removeAll();
for (final PluginTrackManagerProcessor trackProcessor : trackPool.getTrackManagerProcessorList()) {
@@ -407,7 +399,6 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
// add the trackColor Processor
final PluginDescriptor pd = PluginLoader.getPlugin("plugins.fab.trackmanager.processors.TrackProcessorColorTrack");
loadTrackProcessor(pd);
-
}
/**
@@ -466,11 +457,9 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
}
// trackGroupSourceInnerPanel.updateUI();
-
}
private void initTrackPoolInnerPanel() {
-
// trackingGroupSourceMenu.removeAll();
// trackGroupSourceInnerPanel.removeAll();
@@ -503,7 +492,6 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
}
}
-
}
// /**
@@ -538,7 +526,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
// }
// }
- ///** 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>();
/**
@@ -567,7 +555,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
// System.out.println("Synchro sequence");
// for (Sequence sequence : sequenceToKeepSynchronizeInT)
// {
- //// System.out.println("synchro on sequence : " + sequence );
+ // System.out.println("synchro on sequence : " + sequence );
// sequence.setT(currentT);
// }
@@ -582,7 +570,6 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
}
class CheckBoxResultSource extends JCheckBoxMenuItem implements ActionListener {
-
// JCheckBox checkBox = new JCheckBox();
// JToggleButton trackTimeOnSequenceButton = new JToggleButton("T");
SwimmingObject result;
@@ -630,7 +617,6 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
// }
// }
// ----------
-
}
// public void setSelected(boolean b) {
@@ -642,7 +628,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
// remove the sequence tracked
// if (trackTimeOnSequenceButton.isSelected())
// {
- //// sequenceToKeepSynchronizeInT.remove(sequence);
+ // sequenceToKeepSynchronizeInT.remove(sequence);
// }
trackingGroupSourceMenu.remove(this);
// trackGroupSourceInnerPanel.remove(this);
@@ -657,12 +643,12 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
// {
// if (trackTimeOnSequenceButton.isSelected())
// {
- //// if (sequence != null)
- //// sequenceToKeepSynchronizeInT.add(sequence);
+ // if (sequence != null)
+ // sequenceToKeepSynchronizeInT.add(sequence);
// }
// else
// {
- //// sequenceToKeepSynchronizeInT.remove(sequence);
+ // sequenceToKeepSynchronizeInT.remove(sequence);
// }
// reSynchroTSequence();
// }
@@ -678,7 +664,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
// if (trackEditor != TrackManager.this)
// {
// // System.out.println("call ok");
- //// trackEditor.setEnableCheckBoxResultSource(result, false);
+ // trackEditor.setEnableCheckBoxResultSource(result, false);
// }
// }
@@ -688,8 +674,8 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
// trackPool.getDisplaySequence().painterChanged( null );
// for (TrackManager trackEditor : trackManagerList)
// {
- //// if (trackEditor != TrackManager.this)
- //// trackEditor.setEnableCheckBoxResultSource(result, true);
+ // if (trackEditor != TrackManager.this)
+ // trackEditor.setEnableCheckBoxResultSource(result, true);
// }
}
@@ -1129,7 +1115,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
int newX = (int) trackPanel.getDetectDim().getWidth() - 5;
if (newX <= 0)
newX = 5;
- trackPanel.setDetectDim(new Dimension(newX, newX));
+ trackPanel.setDetectDim(new Dimension(newX, newX)); // TODO check if 'newX' should be used as 'Y' argument
trackPool.fireTrackEditorProcessorChange();
}
if (e.getSource() == zoomMoreButton) {
@@ -1151,7 +1137,6 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
// .getDetectDim().getHeight() + 5));
// trackPool.fireTrackEditorProcessorChange();
// }
-
}
@Override
@@ -1179,7 +1164,6 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
menuItem.addActionListener(new MenuItemActionListener(plugin, PluginTrackManagerProcessor.class));
}
}
-
}
public void moveTrackProcessor(final PluginTrackManagerProcessor trackEditorProcessor, final int i) {
@@ -1201,7 +1185,6 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
trackPool.fireTrackEditorProcessorChange();
// System.out.println("Demande changement de place.");
-
}
@Override
@@ -1291,11 +1274,10 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
public void setDisplaySequence(final Sequence sequence) {
sequenceSelector.setSelectedSequence(sequence);
-
}
@Override
public void run() {
-
+ //
}
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackManagerPainter.java b/src/main/java/plugins/fab/trackmanager/TrackManagerPainter.java
index 6a6687b..422a88e 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackManagerPainter.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackManagerPainter.java
@@ -496,7 +496,8 @@ public class TrackManagerPainter extends Overlay {
//
// if ( StringUtil.equals(metadataName, Sequence.ID_PIXEL_SIZE_Z ))
// {
- //// adjustZScaling( getSequence().getPixelSizeZ() );
+
+ // adjustZScaling( getSequence().getPixelSizeZ() );
// }
//
// break;
@@ -508,18 +509,7 @@ public class TrackManagerPainter extends Overlay {
// {
// }
- private static class TrackLineSection {
- final Detection start;
- final Detection end;
-
- @Contract(pure = true)
- public TrackLineSection(final Detection start, final Detection end) {
- super();
-
- this.start = start;
- this.end = end;
- }
-
+ private record TrackLineSection(Detection start, Detection end) {
@Contract("_ -> param1")
public @NotNull Line2D getLine2D(final @NotNull Line2D line) {
line.setLine(start.getX(), start.getY(), end.getX(), end.getY());
diff --git a/src/main/java/plugins/fab/trackmanager/TrackPool.java b/src/main/java/plugins/fab/trackmanager/TrackPool.java
index 6771976..5d4a648 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackPool.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackPool.java
@@ -116,19 +116,17 @@ public class TrackPool {
* Creates a virtual track
*/
public void createVirtualTrackWith2Detection(Detection detectionStart, Detection detectionEnd) {
-
TrackSegment segmentStart = getTrackSegmentWithDetection(detectionStart);
TrackSegment segmentEnd = getTrackSegmentWithDetection(detectionEnd);
if (segmentStart == segmentEnd) {
- MessageDialog.showDialog("Can't link 2 detections belonging to the same track.",
- MessageDialog.INFORMATION_MESSAGE);
+ MessageDialog.showDialog("Can't link 2 detections belonging to the same track.", MessageDialog.INFORMATION_MESSAGE);
return;
}
- if (segmentStart.getOwnerTrackGroup() != segmentStart.getOwnerTrackGroup()) {
- MessageDialog.showDialog("The two tracks should be from the same track group.",
- MessageDialog.INFORMATION_MESSAGE);
+ //if (segmentStart.getOwnerTrackGroup() != segmentStart.getOwnerTrackGroup()) { // TODO I think it's an error
+ if (segmentStart.getOwnerTrackGroup() != segmentEnd.getOwnerTrackGroup()) {
+ MessageDialog.showDialog("The two tracks should be from the same track group.", MessageDialog.INFORMATION_MESSAGE);
return;
}
@@ -143,8 +141,7 @@ public class TrackPool {
// The detection is not the last of the track.
// Must split the start track.
- final ArrayList<TrackSegment> returnList = splitTrackSegment(segmentStart,
- segmentStart.getDetectionIndex(detectionStart), true);
+ final ArrayList<TrackSegment> returnList = splitTrackSegment(segmentStart, segmentStart.getDetectionIndex(detectionStart), true);
// should render 2 segments. The first is the one we want. We take the last detection of the first tracksegment.
detectionStart = returnList.getFirst().getLastDetection();
segmentStart = getTrackSegmentWithDetection(detectionStart);
@@ -154,8 +151,7 @@ public class TrackPool {
// The detection is not the first of the track.
// Must split the end track.
- final ArrayList<TrackSegment> returnList = splitTrackSegment(segmentEnd,
- segmentEnd.getDetectionIndex(detectionEnd) - 1, true);
+ final ArrayList<TrackSegment> returnList = splitTrackSegment(segmentEnd, segmentEnd.getDetectionIndex(detectionEnd) - 1, true);
// should render 2 segments. The second is the one we want. We take the first detection of the second tracksegment.
detectionEnd = returnList.get(1).getFirstDetection();
segmentEnd = getTrackSegmentWithDetection(detectionEnd);
diff --git a/src/main/java/plugins/fab/trackmanager/blocks/LoadTracksFromXML.java b/src/main/java/plugins/fab/trackmanager/blocks/LoadTracksFromXML.java
index e0b91c2..6776f16 100644
--- a/src/main/java/plugins/fab/trackmanager/blocks/LoadTracksFromXML.java
+++ b/src/main/java/plugins/fab/trackmanager/blocks/LoadTracksFromXML.java
@@ -39,7 +39,7 @@ import java.util.List;
* @author Stephane Dallongeville
*/
@IcyPluginName("Load Tracks From XML")
-@IcyPluginIcon(path = "/track-manager.png")
+@IcyPluginIcon(path = "/plugins/fab/trackmanager/track-manager.png")
public class LoadTracksFromXML extends Plugin implements ROIBlock {
final VarMutable file = new VarMutable("XML file", null) {
@Override
@@ -78,6 +78,5 @@ public class LoadTracksFromXML extends Plugin implements ROIBlock {
@Override
public void declareOutput(final @NotNull VarList outputMap) {
outputMap.add("tracks", tracks);
-
}
}
diff --git a/src/main/java/plugins/fab/trackmanager/blocks/SaveTracksToXML.java b/src/main/java/plugins/fab/trackmanager/blocks/SaveTracksToXML.java
index e8c88a1..a0da90b 100644
--- a/src/main/java/plugins/fab/trackmanager/blocks/SaveTracksToXML.java
+++ b/src/main/java/plugins/fab/trackmanager/blocks/SaveTracksToXML.java
@@ -38,7 +38,7 @@ import java.io.File;
* @author Stephane Dallongeville
*/
@IcyPluginName("Save Tracks To XML")
-@IcyPluginIcon(path = "/track-manager.png")
+@IcyPluginIcon(path = "/plugins/fab/trackmanager/track-manager.png")
public class SaveTracksToXML extends Plugin implements ROIBlock {
final Var<TrackGroup> tracks = new Var<>("Track group", new TrackGroup(null));
final VarMutable file = new VarMutable("XML file", null) {
diff --git a/src/main/resources/track-manager.png b/src/main/resources/plugins/fab/trackmanager/track-manager.png
similarity index 100%
rename from src/main/resources/track-manager.png
rename to src/main/resources/plugins/fab/trackmanager/track-manager.png
--
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