From cc4dea9b291f32af42e8588ff705bec2b8ca1686 Mon Sep 17 00:00:00 2001
From: Thomas <thomas.musset@pasteur.fr>
Date: Thu, 4 Jul 2024 16:06:10 +0200
Subject: [PATCH] added annotations, fixed NullPointerException on MenuItem
generation
---
.../java/plugins/fab/trackmanager/Link.java | 3 +-
.../PluginTrackManagerProcessor.java | 16 ++++-
.../fab/trackmanager/TrackDetection.java | 4 +-
.../plugins/fab/trackmanager/TrackGroup.java | 11 ++--
.../fab/trackmanager/TrackLengthDialog.java | 13 +---
.../fab/trackmanager/TrackManager.java | 59 +++++++++----------
.../fab/trackmanager/TrackManagerPainter.java | 12 ++--
.../plugins/fab/trackmanager/TrackPanel.java | 46 ++++++---------
.../plugins/fab/trackmanager/TrackPool.java | 56 +++++++-----------
.../fab/trackmanager/TrackSegment.java | 13 ++--
.../blocks/LoadTracksFromXML.java | 18 ++----
.../trackmanager/blocks/SaveTracksToXML.java | 16 ++---
12 files changed, 116 insertions(+), 151 deletions(-)
diff --git a/src/main/java/plugins/fab/trackmanager/Link.java b/src/main/java/plugins/fab/trackmanager/Link.java
index 8145eb3..a2fc342 100644
--- a/src/main/java/plugins/fab/trackmanager/Link.java
+++ b/src/main/java/plugins/fab/trackmanager/Link.java
@@ -18,12 +18,14 @@
package plugins.fab.trackmanager;
+import org.jetbrains.annotations.Contract;
import plugins.nchenouard.spot.Detection;
public class Link {
TrackSegment start;
TrackSegment end;
+ @Contract(pure = true)
public Link(final TrackSegment start, final TrackSegment end) {
this.start = start;
this.end = end;
@@ -49,5 +51,4 @@ public class Link {
public String toString() {
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 1276a8b..3468c73 100644
--- a/src/main/java/plugins/fab/trackmanager/PluginTrackManagerProcessor.java
+++ b/src/main/java/plugins/fab/trackmanager/PluginTrackManagerProcessor.java
@@ -21,6 +21,8 @@ package plugins.fab.trackmanager;
import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
import org.bioimageanalysis.icy.gui.GuiUtil;
import org.bioimageanalysis.icy.gui.component.panel.PopupPanel;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import javax.swing.*;
import java.awt.event.ActionEvent;
@@ -47,8 +49,14 @@ public abstract class PluginTrackManagerProcessor extends Plugin {
enabledCheckBox.setSelected(true);
enabledCheckBox.addActionListener(actionButton);
- final JPanel commandPanel = GuiUtil.createLineBoxPanel(enabledCheckBox, Box.createHorizontalGlue(), performanceLabel,
- moveUpButton, moveDownButton, closeButton);
+ final JPanel commandPanel = GuiUtil.createLineBoxPanel(
+ enabledCheckBox,
+ Box.createHorizontalGlue(),
+ performanceLabel,
+ moveUpButton,
+ moveDownButton,
+ closeButton
+ );
closeButton.addActionListener(actionButton);
closeButton.setToolTipText("Close processor");
@@ -75,7 +83,7 @@ public abstract class PluginTrackManagerProcessor extends Plugin {
class ActionButton implements ActionListener {
@Override
- public void actionPerformed(final ActionEvent e) {
+ public void actionPerformed(final @NotNull ActionEvent e) {
if (e.getSource() == closeButton) {
Close();
@@ -128,6 +136,8 @@ public abstract class PluginTrackManagerProcessor extends Plugin {
super.finalize();
}*/
+ @SuppressWarnings("UnstableApiUsage")
+ @Contract(mutates = "this")
public final void setTrackPool(final 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 0876f46..2fb2b13 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackDetection.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackDetection.java
@@ -28,7 +28,7 @@ import java.awt.geom.Rectangle2D;
/**
* Display a single detection of a track. Used by TrackPanel / TrackEditor
*
- * @author fab
+ * @author Fabrice de Chaumont
*/
public class TrackDetection extends JPanel {
private boolean Selected = false;
@@ -103,7 +103,5 @@ public class TrackDetection extends JPanel {
g2.drawLine(0, 0, getWidth(), getHeight());
g2.setStroke(new BasicStroke(1));
}
-
}
-
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackGroup.java b/src/main/java/plugins/fab/trackmanager/TrackGroup.java
index e600bab..597e931 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackGroup.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackGroup.java
@@ -19,6 +19,9 @@
package plugins.fab.trackmanager;
import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import plugins.nchenouard.spot.Detection;
import java.util.ArrayList;
@@ -30,6 +33,7 @@ public class TrackGroup {
*/
private final ArrayList<TrackSegment> trackSegmentList;
+ @Contract(pure = true)
public TrackGroup(final Sequence sequence) {
this.sequence = sequence;
trackSegmentList = new ArrayList<>();
@@ -46,9 +50,9 @@ public class TrackGroup {
return trackSegmentList;
}
- public void addTrackSegment(final TrackSegment ts) {
+ public void addTrackSegment(final @NotNull TrackSegment ts) {
if (ts.getOwnerTrackGroup() != null) {
- System.err.println("The trackSegment is already owned by another TrackGroup.");
+ IcyLogger.warn(this.getClass(), "The trackSegment is already owned by another TrackGroup.");
return;
}
@@ -77,7 +81,7 @@ public class TrackGroup {
}
}
- public void removeTrackSegment(final TrackSegment ts) {
+ public void removeTrackSegment(final @NotNull TrackSegment ts) {
// should remove links
ts.setOwnerTrackGroup(null);
ts.removeAllLinks();
@@ -98,5 +102,4 @@ public class TrackGroup {
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 aeb940e..702fe65 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackLengthDialog.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackLengthDialog.java
@@ -20,21 +20,20 @@ package plugins.fab.trackmanager;
import org.bioimageanalysis.icy.gui.GuiUtil;
import org.bioimageanalysis.icy.gui.dialog.ActionDialog;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import javax.swing.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
public class TrackLengthDialog implements ActionListener {
-
JTextField textField = new JTextField("3-10");
TrackPool trackPool;
public TrackLengthDialog(final TrackPool trackPool) {
this.trackPool = trackPool;
final ActionDialog actionDialog = new ActionDialog("Select by length");
- actionDialog.getContentPane().setLayout(
- new BoxLayout(actionDialog.getContentPane(), BoxLayout.PAGE_AXIS));
+ 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));
@@ -44,13 +43,10 @@ public class TrackLengthDialog implements ActionListener {
actionDialog.setOkAction(this);
actionDialog.setVisible(true);
-
-
}
@Override
public void actionPerformed(final ActionEvent e) {
-
final String text = textField.getText();
final String[] values = text.split("-");
@@ -69,11 +65,8 @@ public class TrackLengthDialog implements ActionListener {
highVal = Integer.MAX_VALUE;
}
- System.out.println("low val : " + lowVal);
- System.out.println("high val : " + highVal);
+ IcyLogger.debug(this.getClass(), "low val : " + lowVal, "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 29e10d7..9adf815 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackManager.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackManager.java
@@ -26,6 +26,7 @@ import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
import org.bioimageanalysis.icy.gui.GuiUtil;
import org.bioimageanalysis.icy.gui.component.ComponentUtil;
+import org.bioimageanalysis.icy.gui.component.menu.IcyPluginMenuItem;
import org.bioimageanalysis.icy.gui.component.panel.PopupPanel;
import org.bioimageanalysis.icy.gui.dialog.MessageDialog;
import org.bioimageanalysis.icy.gui.frame.IcyFrame;
@@ -42,7 +43,9 @@ import org.bioimageanalysis.icy.model.swimmingPool.SwimmingPoolEvent;
import org.bioimageanalysis.icy.model.swimmingPool.SwimmingPoolEventType;
import org.bioimageanalysis.icy.model.swimmingPool.SwimmingPoolListener;
import org.bioimageanalysis.icy.network.NetworkUtil;
-import org.bioimageanalysis.icy.system.IcyExceptionHandler;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import plugins.nchenouard.spot.Detection;
@@ -84,6 +87,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
Class<? extends PluginTrackManagerProcessor> pluginTrackManagerProcessor;
PluginDescriptor pluginDescriptor;
+ @Contract(pure = true)
public MenuItemActionListener(final PluginDescriptor pluginDescriptor,
final Class<? extends PluginTrackManagerProcessor> pluginTrackEditorProcessor) {
this.pluginTrackManagerProcessor = pluginTrackEditorProcessor;
@@ -98,9 +102,8 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
}
void loadTrackProcessor(final PluginDescriptor pluginDescriptor) {
-
if (pluginDescriptor == null || pluginDescriptor.getPluginClass() == null) {
- System.err.println("Can't load processor (plugin not found)");
+ IcyLogger.error(this.getClass(), "Can't load processor (plugin not found)");
return;
}
@@ -109,11 +112,11 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
ptep = (PluginTrackManagerProcessor) pluginDescriptor.getPluginClass().getDeclaredConstructor().newInstance();
}
catch (final Exception e) {
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(this.getClass(), e, "Can't instantiate plugin class " + pluginDescriptor.getPluginClass());
}
if (ptep == null) {
- System.err.println("Can't load processor.");
+ IcyLogger.error(this.getClass(), "Can't load processor.");
return;
}
@@ -157,8 +160,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
* Preferences preferences = Preferences.userRoot().node( node );
* preferences.put( "path", chooser.getCurrentDirectory().getAbsolutePath() );
*/
- JCheckBoxMenuItem displayTrackPanelCheckBoxMenuItem = new JCheckBoxMenuItem("Display Track Panel",
- displayTrackManagerBoolean);
+ JCheckBoxMenuItem displayTrackPanelCheckBoxMenuItem = new JCheckBoxMenuItem("Display Track Panel", displayTrackManagerBoolean);
/*
* void
@@ -223,7 +225,6 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
JMenuItem onlineHelpMenuItem;
public TrackManager() {
-
mainFrame.addFrameListener(this);
trackPool = new TrackPool();
@@ -414,7 +415,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
* another trackeditor, the trackgroup checkbox is disabled.
*/
@Override
- public void swimmingPoolChangeEvent(final SwimmingPoolEvent swimmingPoolEvent) {
+ public void swimmingPoolChangeEvent(final @NotNull SwimmingPoolEvent swimmingPoolEvent) {
if (swimmingPoolEvent.getType() == SwimmingPoolEventType.ELEMENT_ADDED) {
// System.out.println("TrackManager : swimming pool element added.");
// System.out.println("object: " +
@@ -439,9 +440,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
for (int i = 0; i < trackingGroupSourceMenu.getItemCount(); i++) {
final JMenuItem mi = trackingGroupSourceMenu.getItem(i);
- if (mi instanceof CheckBoxResultSource) {
- final CheckBoxResultSource cbrs = (CheckBoxResultSource) mi;
-
+ if (mi instanceof final CheckBoxResultSource cbrs) {
if (cbrs.result == swimmingPoolEvent.getResult()) {
cbrs.destroy();
return;
@@ -588,13 +587,12 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
// JToggleButton trackTimeOnSequenceButton = new JToggleButton("T");
SwimmingObject result;
- public CheckBoxResultSource(final SwimmingObject result, final boolean enabled) {
- if (!(result.getObject() instanceof TrackGroup)) {
- System.out.println("Result object type not supported.");
+ public CheckBoxResultSource(final @NotNull SwimmingObject result, final boolean enabled) {
+ if (!(result.getObject() instanceof final TrackGroup trackGroup)) {
+ IcyLogger.error(this.getClass(), "Result object type not supported.");
return;
}
- final TrackGroup trackGroup = (TrackGroup) result.getObject();
final int nbTracks = trackGroup.getTrackSegmentList().size();
final String label = result.getObject().toString() + " (" + nbTracks + " Tracks)";
@@ -653,7 +651,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
}
@Override
- public void actionPerformed(final ActionEvent e) {
+ public void actionPerformed(final @NotNull ActionEvent e) {
// if (e.getSource() == trackTimeOnSequenceButton)
// {
@@ -749,12 +747,13 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
}
}
- public static List<TrackGroup> loadTracks(final String path) throws IllegalArgumentException {
+ public static @NotNull List<TrackGroup> loadTracks(final String path) throws IllegalArgumentException {
final Document document = XMLUtil.loadDocument(path, false);
return loadTracks(document);
}
- public static List<TrackGroup> loadTracks(final Document document) throws IllegalArgumentException {
+ @Contract("null -> fail")
+ public static @NotNull List<TrackGroup> loadTracks(final Document document) throws IllegalArgumentException {
if (document == null)
throw new IllegalArgumentException("Invalid track file !");
@@ -850,12 +849,13 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
}
}
- public static List<TrackGroup> loadTracksFromTrackMate(final String path) {
+ public static @NotNull List<TrackGroup> loadTracksFromTrackMate(final String path) {
final Document document = XMLUtil.loadDocument(path, false);
return loadTracksFromTrackMate(document);
}
- public static List<TrackGroup> loadTracksFromTrackMate(final Document document) throws IllegalArgumentException {
+ @Contract("null -> fail")
+ public static @NotNull List<TrackGroup> loadTracksFromTrackMate(final Document document) throws IllegalArgumentException {
if (document == null)
throw new IllegalArgumentException("Invalid track file !");
@@ -907,8 +907,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
}
private void debug() {
-
- System.out.println("--- debug");
+ IcyLogger.debug(this.getClass(), "--- debug");
// for ( Link link : trackPool.getLinks() )
// {
// System.out.println( link );
@@ -917,7 +916,6 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
// System.out.println( "Track segment idHashMapSize = " + TrackSegment.idHashMapList.size()
// );
// TrackSegment.idHashMapList.clear();
-
}
private void saveTracks() {
@@ -949,7 +947,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
XMLUtil.saveDocument(document, file);
}
- public static Document saveTracks(final List<TrackGroup> groups) {
+ public static @NotNull Document saveTracks(final @NotNull List<TrackGroup> groups) {
final Document result = XMLUtil.createDocument(true);
final Element rootElement = result.getDocumentElement();
@@ -1025,7 +1023,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
}
@Override
- public void actionPerformed(final ActionEvent e) {
+ public void actionPerformed(final @NotNull ActionEvent e) {
if (e.getSource() == onlineHelpMenuItem) {
NetworkUtil.openBrowser("https://icy.bioimageanalysis.org/plugin/track-manager/");
}
@@ -1135,8 +1133,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
trackPool.fireTrackEditorProcessorChange();
}
if (e.getSource() == zoomMoreButton) {
- trackPanel.setDetectDim(new Dimension((int) trackPanel.getDetectDim().getWidth() + 5,
- (int) trackPanel.getDetectDim().getHeight() + 5));
+ trackPanel.setDetectDim(new Dimension((int) trackPanel.getDetectDim().getWidth() + 5, (int) trackPanel.getDetectDim().getHeight() + 5));
trackPool.fireTrackEditorProcessorChange();
}
// if (e.getSource() == zoomYLessButton)
@@ -1163,9 +1160,7 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
}
private void buildPluginMenu() {
-
pluginPopupMenu.removeAll();
-
{
final JMenuItem menuItem = new JMenuItem("Add Track Processor Plugin...");
menuItem.setEnabled(false);
@@ -1176,12 +1171,12 @@ public class TrackManager extends PluginActionable implements AdjustmentListener
for (final PluginDescriptor plugin : PluginLoader.getPlugins()) {
if (plugin.isInstanceOf(PluginTrackManagerProcessor.class))
if (!plugin.isAbstract()) {
- final JMenuItem menuItem = new JMenuItem(plugin.getName(), new ImageIcon(plugin.getIcon().getImage().getScaledInstance(24, 24, Image.SCALE_SMOOTH)));
+ //final JMenuItem menuItem = new JMenuItem(plugin.getName(), new ImageIcon(plugin.getIcon().getImage().getScaledInstance(24, 24, Image.SCALE_SMOOTH)));
+ final IcyPluginMenuItem menuItem = new IcyPluginMenuItem(plugin);
pluginPopupMenu.add(menuItem);
menuItem.addActionListener(new MenuItemActionListener(plugin, PluginTrackManagerProcessor.class));
-
}
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackManagerPainter.java b/src/main/java/plugins/fab/trackmanager/TrackManagerPainter.java
index 16e38f3..6a6687b 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackManagerPainter.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackManagerPainter.java
@@ -26,6 +26,8 @@ import org.bioimageanalysis.icy.gui.canvas.IcyCanvas;
import org.bioimageanalysis.icy.model.overlay.Overlay;
import org.bioimageanalysis.icy.model.sequence.Sequence;
import org.bioimageanalysis.icy.model.swimmingPool.SwimmingObject;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import plugins.nchenouard.spot.Detection;
import java.awt.*;
@@ -68,7 +70,7 @@ public class TrackManagerPainter extends Overlay {
}
@Override
- public void mouseClick(final MouseEvent e, /*Point2D p*/ final Point5D.Double imagePoint, final IcyCanvas icyCanvas) {
+ public void mouseClick(final @NotNull MouseEvent e, final Point5D.Double imagePoint, final IcyCanvas icyCanvas) {
if (e.isConsumed())
return;
@@ -309,7 +311,6 @@ public class TrackManagerPainter extends Overlay {
@Override
public void paint(final Graphics2D g, final Sequence sequence, final IcyCanvas canvas) {
-
// System.out.println("TP");
if (trackPool != null) {
@@ -511,6 +512,7 @@ public class TrackManagerPainter extends Overlay {
final Detection start;
final Detection end;
+ @Contract(pure = true)
public TrackLineSection(final Detection start, final Detection end) {
super();
@@ -518,7 +520,8 @@ public class TrackManagerPainter extends Overlay {
this.end = end;
}
- public Line2D getLine2D(final Line2D line) {
+ @Contract("_ -> param1")
+ public @NotNull Line2D getLine2D(final @NotNull Line2D line) {
line.setLine(start.getX(), start.getY(), end.getX(), end.getY());
return line;
}
@@ -527,7 +530,8 @@ public class TrackManagerPainter extends Overlay {
return start.getColor();
}
- public Rectangle2D getBounds(final Rectangle2D bounds, final float stroke) {
+ @Contract("_, _ -> param1")
+ public @NotNull Rectangle2D getBounds(final @NotNull Rectangle2D bounds, final float stroke) {
bounds.setFrameFromDiagonal(start.getX(), start.getY(), end.getX(), end.getY());
ShapeUtil.enlarge(bounds, stroke, stroke, true);
return bounds;
diff --git a/src/main/java/plugins/fab/trackmanager/TrackPanel.java b/src/main/java/plugins/fab/trackmanager/TrackPanel.java
index 40c0702..9a3436b 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackPanel.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackPanel.java
@@ -27,7 +27,10 @@ import org.bioimageanalysis.icy.gui.viewer.ViewerListener;
import org.bioimageanalysis.icy.model.overlay.Overlay;
import org.bioimageanalysis.icy.model.sequence.DimensionId;
import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import org.bioimageanalysis.icy.system.thread.ThreadUtil;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
import plugins.nchenouard.spot.Detection;
import javax.swing.*;
@@ -48,7 +51,6 @@ import java.util.HashMap;
* @author Fabrice de Chaumont
*/
public class TrackPanel extends JPanel implements MouseListener, MouseMotionListener, TrackPainterListener, TrackManagerProcessorListener, ViewerListener, GlobalSequenceListener, GlobalViewerListener, Runnable {
-
TimeCursor timeCursor = new TimeCursor();
/**
@@ -58,8 +60,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
private TrackPool trackPool;
- public TrackPanel(final TrackPool trackPool, final boolean enableLeftPanelTrackDisplay) {
-
+ public TrackPanel(final @NotNull TrackPool trackPool, final boolean enableLeftPanelTrackDisplay) {
super();
this.enableLeftPanelTrackDisplay = enableLeftPanelTrackDisplay;
this.trackPool = trackPool;
@@ -76,7 +77,6 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
Icy.getMainInterface().addGlobalViewerListener(this);
// System.out.println("TEST trackpanel");
-
}
void setupViewerListener() {
@@ -127,7 +127,6 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
}
private TrackSegment getTrackSegmentAt(int y) {
-
TrackSegment tsResult = null;
y = y / getDetectDim().height;
@@ -147,7 +146,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
return tsResult;
}
- private Detection getDetectionAt(final int x, final int y) {
+ private @Nullable Detection getDetectionAt(final int x, final int y) {
final TrackSegment ts = getTrackSegmentAt(y);
if (ts == null)
@@ -226,7 +225,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// look if at least one track exists.
boolean oneAtLeast = false;
for (final TrackGroup trackGroup : trackPool.getTrackGroupList()) {
- if (trackGroup.getTrackSegmentList().size() != 0) {
+ if (!trackGroup.getTrackSegmentList().isEmpty()) {
oneAtLeast = true;
break;
}
@@ -285,13 +284,12 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
* class use to record Track Drag states.
*/
private static class TrackDrag {
-
static boolean dragging = false;
static TrackSegment ts = null;
}
@Override
- public void mouseReleased(final MouseEvent e) {
+ public void mouseReleased(final @NotNull MouseEvent e) {
MouseLink.xEnd = e.getX();
MouseLink.yEnd = e.getY();
@@ -344,7 +342,6 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
timeCursor.dragging = false;
repaint();
}
-
}
@Override
@@ -633,7 +630,6 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
public void setTrackPool(final TrackPool trackPool) {
this.trackPool = trackPool;
clearDetectionsAndReDisplay();
-
}
/**
@@ -695,8 +691,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
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.");
+ IcyLogger.warn(this.getClass(), "too much track to display them all in trackManager left panel.", "Still, they all appear on the sequence.");
}
// if ( trackingPanelSize.width * trackingPanelSize.height > maxSize )
@@ -723,9 +718,12 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
BufferedImage.TYPE_INT_RGB);
}
catch (final 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");
+ IcyLogger.error(
+ this.getClass(),
+ e,
+ "can't create " + trackingPanelSize.width + "x" + trackingPanelSize.height + " bitmap for track representation in trackPanel.",
+ "left panel disabled"
+ );
enableLeftPanelTrackDisplay = false;
return;
}
@@ -883,8 +881,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
repaint();
}
- private void drawDetection(final Graphics2D g, final Detection d, final Rectangle2D bounds) {
-
+ private void drawDetection(final @NotNull Graphics2D g, final @NotNull Detection d, final Rectangle2D bounds) {
g.setColor(d.getColor());
g.fill(bounds);
g.setColor(d.getColor().darker());
@@ -903,7 +900,6 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
g.drawLine((int) bounds.getMinX(), (int) bounds.getMinY(), (int) bounds.getMaxX(), (int) bounds.getMaxY());
g.setStroke(new BasicStroke(1));
}
-
}
BufferedImage bufferedImage;
@@ -947,10 +943,8 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
// 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.fillRect(getDetectDim().width * timeCursor.currentT, getVisibleRect().y, getDetectDim().width, getVisibleRect().height);
g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 1.0f));
-
}
/**
@@ -996,7 +990,6 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
}
clearDetectionsAndReDisplay();
updateUI();
-
}
/**
@@ -1036,7 +1029,7 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
}
@Override
- public void viewerChanged(final ViewerEvent event) {
+ public void viewerChanged(final @NotNull ViewerEvent event) {
if (event.getDim() == DimensionId.T) {
timeCursor.currentT = event.getSource().getPositionT();
// trackPool.fireTrackEditorProcessorChange();
@@ -1049,13 +1042,11 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
public void displaySequenceChanged() {
setupViewerListener();
-
}
public void setEnableLeftPanelTrackDisplay(final boolean selected) {
this.enableLeftPanelTrackDisplay = selected;
redrawDetection3();
-
}
@Override
@@ -1066,18 +1057,15 @@ public class TrackPanel extends JPanel implements MouseListener, MouseMotionList
@Override
public void viewerOpened(final Viewer viewer) {
setupViewerListener();
-
}
@Override
public void sequenceOpened(final Sequence sequence) {
setupViewerListener();
-
}
@Override
public void sequenceClosed(final Sequence sequence) {
setupViewerListener();
}
-
}
diff --git a/src/main/java/plugins/fab/trackmanager/TrackPool.java b/src/main/java/plugins/fab/trackmanager/TrackPool.java
index 879d3fd..6771976 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackPool.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackPool.java
@@ -23,6 +23,9 @@ import org.bioimageanalysis.icy.gui.dialog.MessageDialog;
import org.bioimageanalysis.icy.gui.frame.progress.AnnounceFrame;
import org.bioimageanalysis.icy.model.sequence.Sequence;
import org.bioimageanalysis.icy.model.swimmingPool.SwimmingObject;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import plugins.nchenouard.spot.Detection;
import javax.swing.event.ChangeEvent;
@@ -35,9 +38,7 @@ import java.util.List;
*
* @author Fabrice de Chaumont
*/
-
public class TrackPool {
-
private final TrackManagerPainter tePainter;
private final ArrayList<PluginTrackManagerProcessor> trackManagerProcessorList = new ArrayList<>();
@@ -79,7 +80,8 @@ public class TrackPool {
fireTrackEditorProcessorChange();
}
- public static boolean linkExists(final List<Link> links, final TrackSegment start, final TrackSegment end) {
+ @Contract(pure = true)
+ public static boolean linkExists(final @NotNull List<Link> links, final TrackSegment start, final TrackSegment end) {
// check if the link already exists
for (final Link link : links)
if ((link.start == start) && (link.end == end))
@@ -144,7 +146,7 @@ public class TrackPool {
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.get(0).getLastDetection();
+ detectionStart = returnList.getFirst().getLastDetection();
segmentStart = getTrackSegmentWithDetection(detectionStart);
}
@@ -257,7 +259,6 @@ public class TrackPool {
* Creates a virtual track
*/
public void createVirtualTrackWith2TrackDetection(final Detection detectionStart, final Detection detectionEnd) {
-
// check if both sides of the link are TrackDetectionComponents.
if (detectionStart == null)
return;
@@ -333,7 +334,7 @@ public class TrackPool {
/**
* @return null if no trackgroup contains the tracksegment
*/
- public TrackGroup getTrackGroupContainingSegment(final TrackSegment ts) {
+ public TrackGroup getTrackGroupContainingSegment(final @NotNull TrackSegment ts) {
return ts.getOwnerTrackGroup();
}
@@ -345,8 +346,7 @@ public class TrackPool {
final TrackGroup trackGroup = getTrackGroupContainingSegment(ts);
if (trackGroup == null) {
- System.out.println(
- "Can't delete The track segment " + ts + " Reason: it is not in any trackGroup");
+ IcyLogger.warn(this.getClass(), "Can't delete The track segment " + ts + " Reason: it is not in any trackGroup.");
return;
}
trackGroup.getTrackSegmentList().remove(ts);
@@ -407,10 +407,10 @@ public class TrackPool {
for (final 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.
+ if (ts.nextList.getFirst().previousList.size() == 1) // If successor has only one predecessor.
{
// System.out.println("Fusing...");
- fuseTrack(ts, ts.nextList.get(0)); // fuse tracks.
+ fuseTrack(ts, ts.nextList.getFirst()); // fuse tracks.
fuseOperationPerformed = true;
break;
}
@@ -423,7 +423,7 @@ public class TrackPool {
/**
* Fusing 2 tracks ts1 is one step before ts2.
*/
- public void fuseTrack(final TrackSegment ts1, final TrackSegment ts2) {
+ public void fuseTrack(final TrackSegment ts1, final @NotNull TrackSegment ts2) {
// System.out.println("debug fuse track: fusing ");
// System.out.println("ts1 = " + ts1);
// System.out.println("ts2 = " + ts2);
@@ -438,7 +438,7 @@ public class TrackPool {
// ts1.getDetectionList().addAll(ts2.getDetectionList());
- while (ts2.getDetectionList().size() > 0) {
+ while (!ts2.getDetectionList().isEmpty()) {
final Detection detection = ts2.getFirstDetection();
ts2.removeDetection(detection);
// System.out.println("Remove 1 detection to ts2. t=" + detection.getT() );
@@ -461,7 +461,7 @@ public class TrackPool {
/**
* return distance between 2 detections
*/
- public double getDistance(final Detection d1, final Detection d2) {
+ public double getDistance(final @NotNull Detection d1, final @NotNull Detection d2) {
return getDistance(d1.getX(), d1.getY(), d1.getZ(), d2.getX(), d2.getY(), d2.getZ());
}
@@ -493,7 +493,7 @@ public class TrackPool {
return linkarray;
}
- public static List<Link> getLinks(final List<TrackGroup> groups) {
+ public static @NotNull List<Link> getLinks(final List<TrackGroup> groups) {
final List<Link> result = new ArrayList<>();
final List<TrackSegment> segments = getTrackSegmentList(groups);
@@ -551,7 +551,7 @@ public class TrackPool {
/**
* @return the pool of tracksegment of all the trackgroup
*/
- public static List<TrackSegment> getTrackSegmentList(final List<TrackGroup> groups) {
+ public static @NotNull List<TrackSegment> getTrackSegmentList(final @NotNull List<TrackGroup> groups) {
final List<TrackSegment> result = new ArrayList<>();
for (final TrackGroup group : groups)
@@ -564,7 +564,6 @@ public class TrackPool {
* @return the pool of tracksegment of all the trackgroup
*/
public ArrayList<TrackSegment> getTrackSegmentList() {
-
final ArrayList<TrackSegment> trackSegmentList = new ArrayList<>();
for (final TrackGroup group : getTrackGroupList()) {
trackSegmentList.addAll(group.getTrackSegmentList());
@@ -577,7 +576,6 @@ public class TrackPool {
* find the tracksegment containing the given detection
*/
public TrackSegment getTrackSegmentWithDetection(final Detection detection) {
-
final ArrayList<TrackSegment> trackSegmentList = getTrackSegmentList();
for (final TrackSegment ts : trackSegmentList) {
@@ -589,14 +587,13 @@ public class TrackPool {
}
// FIXME: 05/04/2023 does nothing
- public static ArrayList<TrackSegment> loadTracks(final File f) {
-
+ public static @NotNull ArrayList<TrackSegment> loadTracks(final File f) {
final ArrayList<TrackSegment> inputTrackSegmentList = new ArrayList<>();
final ArrayList<TrackSegment> targetTrackSegmentList = new ArrayList<>();
for (final TrackSegment ts : inputTrackSegmentList) {
if (ts.getFirstDetection() == null || ts.getLastDetection() == null) {
- System.out.println("Warning, found and removed empty track segment");
+ IcyLogger.warn(TrackPool.class, "Warning, found and removed empty track segment");
continue;
}
@@ -610,7 +607,7 @@ public class TrackPool {
}
if (skipTrackSegment) {
- System.out.println("Warning, found and removed empty track segment");
+ IcyLogger.warn(TrackPool.class, "Warning, found and removed empty track segment");
continue;
}
@@ -628,7 +625,7 @@ public class TrackPool {
/**
* remove a link between 2 track segment.
*/
- public void removeLink(final TrackSegment start, final TrackSegment end) {
+ public void removeLink(final @NotNull TrackSegment start, final TrackSegment end) {
// int nb = 0;
// while ( start.nextList.contains( end ) )
// {
@@ -668,14 +665,12 @@ public class TrackPool {
}
public void selectTracksByLength(final int lowVal, final int highVal) {
-
for (final TrackSegment ts : getTrackSegmentList()) {
if (ts.getDetectionList().size() >= lowVal && ts.getDetectionList().size() <= highVal) {
ts.setAllDetectionSelected(true);
}
}
fireTrackEditorProcessorChange();
-
}
public void unselectAllTracks() {
@@ -773,11 +768,9 @@ public class TrackPool {
trackSegmentReturnList.add(ts1);
trackSegmentReturnList.add(ts2);
return trackSegmentReturnList;
-
}
public ArrayList<TrackGroup> getTrackGroupList() {
-
final ArrayList<TrackGroup> trackGroupList = new ArrayList<>();
for (final SwimmingObject result : resultList)
@@ -791,7 +784,7 @@ public class TrackPool {
*/
ArrayList<SwimmingObject> resultList = new ArrayList<>();
- public void addResult(final SwimmingObject result) {
+ public void addResult(final @NotNull SwimmingObject result) {
if (!(result.getObject() instanceof TrackGroup)) {
// System.out.println("Object " + result + " is not recognized as a TrackGroup.");
return;
@@ -807,9 +800,7 @@ public class TrackPool {
resultList.remove(result);
- if (result.getObject() instanceof TrackGroup) {
- final TrackGroup tg = (TrackGroup) result.getObject();
-
+ if (result.getObject() instanceof final TrackGroup tg) {
// remove track segment from hash map
for (final TrackSegment ts : tg.getTrackSegmentList())
ts.removeId();
@@ -820,27 +811,22 @@ public class TrackPool {
* removes the painter from all sequences.
*/
public void removePainter() {
-
// System.out.println("remove painter");
final List<Sequence> sequenceList = Icy.getMainInterface().getSequencesContaining(tePainter);
for (final Sequence sequence : sequenceList) {
sequence.removeOverlay(tePainter);
}
-
}
public int getTrackIndex(final TrackSegment ts) {
-
return getTrackSegmentList().indexOf(ts);
-
}
/**
* @return the timepoint corresponding to the last detection of all the trackgroup.
*/
public int getLastDetectionTimePoint() {
-
int maxT = 0;
for (final TrackGroup tg : getTrackGroupList()) {
for (final TrackSegment ts : tg.getTrackSegmentList()) {
diff --git a/src/main/java/plugins/fab/trackmanager/TrackSegment.java b/src/main/java/plugins/fab/trackmanager/TrackSegment.java
index 4afa588..7a76dc6 100644
--- a/src/main/java/plugins/fab/trackmanager/TrackSegment.java
+++ b/src/main/java/plugins/fab/trackmanager/TrackSegment.java
@@ -19,6 +19,7 @@
package plugins.fab.trackmanager;
import org.bioimageanalysis.icy.common.math.Random;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import plugins.nchenouard.spot.Detection;
import java.lang.ref.Reference;
@@ -32,9 +33,8 @@ import java.util.Map;
* TrackSegment is a pool of consecutive detection.
*
* @author Fabrice de Chaumont
- * @author Stephane
+ * @author Stephane Dallongeville
*/
-
public class TrackSegment implements Cloneable {
// better to use weak reference in the map
protected final static Map<Integer, Reference<TrackSegment>> idKeyHashMapList = new HashMap<>(); // 1-1 hashmap.
@@ -145,7 +145,7 @@ public class TrackSegment implements Cloneable {
this.id = key;
}
else
- System.out.println("track id already loaded");
+ IcyLogger.warn(this.getClass(), "Track ID already loaded.");
}
}
@@ -209,8 +209,7 @@ public class TrackSegment implements Cloneable {
if (!detectionList.isEmpty()) {
final Detection detectionPrevious = getLastDetection();
if (detection.getT() != detectionPrevious.getT() + 1) {
- System.err.println(
- "TrackSegment : The detection must be added with consecutive T value. Detection was not added");
+ IcyLogger.warn(this.getClass(), "TrackSegment : The detection must be added with consecutive T value. Detection was not added.");
// throw new IllegalArgumentException();
return;
}
@@ -275,10 +274,10 @@ public class TrackSegment implements Cloneable {
* return first detection ( should be first in time too )
*/
public Detection getFirstDetection() {
- if (detectionList.size() == 0)
+ if (detectionList.isEmpty())
return null;
- return detectionList.get(0);
+ return detectionList.getFirst();
}
/**
diff --git a/src/main/java/plugins/fab/trackmanager/blocks/LoadTracksFromXML.java b/src/main/java/plugins/fab/trackmanager/blocks/LoadTracksFromXML.java
index 9487a08..e0b91c2 100644
--- a/src/main/java/plugins/fab/trackmanager/blocks/LoadTracksFromXML.java
+++ b/src/main/java/plugins/fab/trackmanager/blocks/LoadTracksFromXML.java
@@ -21,8 +21,7 @@ package plugins.fab.trackmanager.blocks;
import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
-import org.bioimageanalysis.icy.extension.plugin.interface_.PluginBundled;
-import org.bioimageanalysis.icy.extension.plugin.interface_.PluginLibrary;
+import org.jetbrains.annotations.NotNull;
import plugins.adufour.blocks.tools.roi.ROIBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.Var;
@@ -37,14 +36,14 @@ import java.util.List;
/**
* Block to load a set of ROI from a file
*
- * @author Stephane
+ * @author Stephane Dallongeville
*/
@IcyPluginName("Load Tracks From XML")
@IcyPluginIcon(path = "/track-manager.png")
-public class LoadTracksFromXML extends Plugin implements ROIBlock, PluginLibrary, PluginBundled {
+public class LoadTracksFromXML extends Plugin implements ROIBlock {
final VarMutable file = new VarMutable("XML file", null) {
@Override
- public boolean isAssignableFrom(final Var source) {
+ public boolean isAssignableFrom(final @NotNull Var source) {
return (String.class == source.getType()) || (File.class == source.getType());
}
};
@@ -71,19 +70,14 @@ public class LoadTracksFromXML extends Plugin implements ROIBlock, PluginLibrary
}
@Override
- public void declareInput(final VarList inputMap) {
+ public void declareInput(final @NotNull VarList inputMap) {
inputMap.add("file", file);
inputMap.add("groupIndex", groupIndex);
}
@Override
- public void declareOutput(final VarList outputMap) {
+ public void declareOutput(final @NotNull VarList outputMap) {
outputMap.add("tracks", tracks);
}
-
- @Override
- 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 72cffb4..e8c88a1 100644
--- a/src/main/java/plugins/fab/trackmanager/blocks/SaveTracksToXML.java
+++ b/src/main/java/plugins/fab/trackmanager/blocks/SaveTracksToXML.java
@@ -22,8 +22,7 @@ import org.bioimageanalysis.icy.common.collection.CollectionUtil;
import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
-import org.bioimageanalysis.icy.extension.plugin.interface_.PluginBundled;
-import org.bioimageanalysis.icy.extension.plugin.interface_.PluginLibrary;
+import org.jetbrains.annotations.NotNull;
import plugins.adufour.blocks.tools.roi.ROIBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.Var;
@@ -36,15 +35,15 @@ import java.io.File;
/**
* Block to save a set of ROI to a file
*
- * @author Stephane
+ * @author Stephane Dallongeville
*/
@IcyPluginName("Save Tracks To XML")
@IcyPluginIcon(path = "/track-manager.png")
-public class SaveTracksToXML extends Plugin implements ROIBlock, PluginLibrary, PluginBundled {
+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) {
@Override
- public boolean isAssignableFrom(final Var source) {
+ public boolean isAssignableFrom(final @NotNull Var source) {
return (String.class == source.getType()) || (File.class == source.getType());
}
};
@@ -72,7 +71,7 @@ public class SaveTracksToXML extends Plugin implements ROIBlock, PluginLibrary,
}
@Override
- public void declareInput(final VarList inputMap) {
+ public void declareInput(final @NotNull VarList inputMap) {
inputMap.add("tracks", tracks);
inputMap.add("file", file);
}
@@ -81,9 +80,4 @@ public class SaveTracksToXML extends Plugin implements ROIBlock, PluginLibrary,
public void declareOutput(final VarList outputMap) {
//
}
-
- @Override
- public String getMainPluginClassName() {
- return TrackManager.class.getName();
- }
}
--
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