TrackMate v9

.github/workflows/build.yml

@@ -28,6 +28,7 @@ jobs:
       - name: Execute the build
         run: .github/build.sh
         env:
+          MAVEN_OPTS: -Djava.awt.headless=true
           GPG_KEY_NAME: ${{ secrets.GPG_KEY_NAME }}
           GPG_PASSPHRASE: ${{ secrets.GPG_PASSPHRASE }}
           MAVEN_USER: ${{ secrets.MAVEN_USER }}

pom.xml

@@ -1,17 +1,19 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>43.0.0</version>
+		<version>45.0.0</version>
 		<relativePath />
 	</parent>
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>TrackMate</artifactId>
-	<version>8.1.7-SNAPSHOT</version>
+	<version>9.0.0-SNAPSHOT</version>
 
 	<name>TrackMate</name>
 	<description>TrackMate plugin for Fiji.</description>
@@ -164,6 +166,7 @@
 	</ciManagement>
 
 	<properties>
+		<enforcer.skip>true</enforcer.skip>
 		<package-name>fiji.plugin.trackmate</package-name>
 		<license.licenseName>gpl_v3</license.licenseName>
 		<license.copyrightOwners>TrackMate developers.</license.copyrightOwners>
@@ -176,28 +179,42 @@
 		(https://github.com/scijava/scijava-coding-style) -->
 		<scijava.coding-style>imglib2</scijava.coding-style>
 
-		<fontchooser.version>2.5.2</fontchooser.version>
 		<javaGeom.version>0.11.1</javaGeom.version>
-		<imglib2.version>8.0.0</imglib2.version>
-		<bigdataviewer-core.version>10.6.7</bigdataviewer-core.version>
+		<imglib2-mesh.version>1.2.0</imglib2-mesh.version>
 
-	    <!-- TrackMate >=8 requires Java 21 -->			
-	    <scijava.jvm.version>21</scijava.jvm.version>
-	    <scijava.jvm.build.version>[21,)</scijava.jvm.build.version>
-   	    <scijava.javadoc.url.java>https://docs.oracle.com/en/java/javase/21/docs/api/</scijava.javadoc.url.java>
-   	    <!-- If we don't do this, mvn javadoc:javadoc fails because of 
+		<!-- TrackMate >=8 requires Java 21 -->
+		<scijava.jvm.version>21</scijava.jvm.version>
+		<scijava.jvm.build.version>[21,)</scijava.jvm.build.version>
+		<scijava.javadoc.url.java>
+			https://docs.oracle.com/en/java/javase/21/docs/api/</scijava.javadoc.url.java>
+		<!-- If we don't do this, mvn javadoc:javadoc fails because of 
    	    Anisotropic_Diffusion_2D (bad naming, does not like the '2D' at the end), 
-   	    which is a depdency of Labkit.' -->			
-   	    <maven.javadoc.failOnError>false</maven.javadoc.failOnError>
+   	    which is a depdency of Labkit.' -->
+		<maven.javadoc.failOnError>false</maven.javadoc.failOnError>
 	</properties>
 
 	<dependencies>
 
+		<!-- Config UI -->
+		<dependency>
+			<groupId>org.scijava</groupId>
+			<artifactId>config-ui</artifactId>
+			<version>0.0.6</version>
+		</dependency>
+
+		<!-- Logging dependencies -->
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-simple</artifactId>
 		</dependency>
 
+		<!-- Geff dependency for IO -->
+		<dependency>
+			<groupId>org.litt</groupId>
+			<artifactId>geff</artifactId>
+			<version>1.1.1-SNAPSHOT</version>
+		</dependency>
+
 		<!-- Fiji dependencies -->
 		<dependency>
 			<groupId>sc.fiji</groupId>
@@ -231,6 +248,32 @@
 			<groupId>net.imagej</groupId>
 			<artifactId>imagej-common</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>net.imglib2</groupId>
+			<artifactId>imglib2-mesh</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>sc.fiji</groupId>
+			<artifactId>bigvolumeviewer</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.jogamp.jogl</groupId>
+			<artifactId>jogl-all</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.jogamp.gluegen</groupId>
+			<artifactId>gluegen-rt</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.jogamp.gluegen</groupId>
+			<artifactId>gluegen-rt</artifactId>
+			<classifier>${scijava.natives.classifier.gluegen}</classifier>
+		</dependency>
+		<dependency>
+			<groupId>org.jogamp.jogl</groupId>
+			<artifactId>jogl-all</artifactId>
+			<classifier>${scijava.natives.classifier.jogl}</classifier>
+		</dependency>
 
 		<!-- ImgLib2 dependencies -->
 		<dependency>
@@ -271,16 +314,16 @@
 			<groupId>org.scijava</groupId>
 			<artifactId>scijava-listeners</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.scijava</groupId>
+			<artifactId>ui-behaviour</artifactId>
+		</dependency>
 
 		<!-- Other dependencies -->
 		<dependency>
 			<groupId>com.github.vlsi.mxgraph</groupId>
 			<artifactId>jgraphx</artifactId>
 		</dependency>
-		<!--<dependency>
-			<groupId>com.google.code.gson</groupId>
-			<artifactId>gson</artifactId>
-		</dependency> -->
 		<dependency>
 			<groupId>com.itextpdf</groupId>
 			<artifactId>itextpdf</artifactId>
@@ -346,18 +389,19 @@
 			<artifactId>javaGeom</artifactId>
 			<version>${javaGeom.version}</version>
 		</dependency>
-		<dependency>
-			<groupId>org.drjekyll</groupId>
-			<artifactId>fontchooser</artifactId>
-			<version>${fontchooser.version}</version>
-		</dependency>
 
 		<!-- Test dependencies -->
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.assertj</groupId>
+			<artifactId>assertj-core</artifactId>
+			<version>3.27.7</version>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 
 	<repositories>

src/main/java/fiji/plugin/trackmate/Dimension.java

@@ -31,11 +31,64 @@ public enum Dimension
 	POSITION,
 	VELOCITY,
 	LENGTH,
-	AREA, TIME, ANGLE, RATE, // count per frames
-	ANGLE_RATE, STRING; // for non-numeric features
+	AREA,
+	VOLUME,
+	TIME,
+	ANGLE,
+	RATE, // count per frames
+	ANGLE_RATE,
+	STRING; // for non-numeric features
 
 	/*
 	 * We separated length and position so that x,y,z are plotted on a different
 	 * graph from spot sizes.
 	 */
+
+	/**
+	 * Returns a String unit for the given dimension. When suitable, the unit is
+	 * taken from the settings field, which contains the spatial and time units.
+	 * Otherwise, default units are used.
+	 *
+	 * @param spaceUnits
+	 *            the space units.
+	 * @param timeUnits
+	 *            the time units.
+	 * @return the units for the specified dimension.
+	 */
+	public String units( final String spaceUnits, final String timeUnits )
+	{
+		switch ( this )
+		{
+		case ANGLE:
+			return "radians";
+		case INTENSITY:
+			return "counts";
+		case INTENSITY_SQUARED:
+			return "counts^2";
+		case NONE:
+			return "";
+		case POSITION:
+		case LENGTH:
+			return spaceUnits;
+		case AREA:
+			return spaceUnits + "^2";
+		case VOLUME:
+			return spaceUnits + "^3";
+		case QUALITY:
+			return "quality";
+		case COST:
+			return "cost";
+		case TIME:
+			return timeUnits;
+		case VELOCITY:
+			return spaceUnits + "/" + timeUnits;
+		case RATE:
+			return "/" + timeUnits;
+		case ANGLE_RATE:
+			return "rad/" + timeUnits;
+		default:
+		case STRING:
+			return null;
+		}
+	}
 }

src/main/java/fiji/plugin/trackmate/LoadTrackMatePlugIn.java

@@ -34,6 +34,7 @@
 import fiji.plugin.trackmate.features.edges.EdgeAnalyzer;
 import fiji.plugin.trackmate.features.spot.SpotAnalyzerFactoryBase;
 import fiji.plugin.trackmate.features.track.TrackAnalyzer;
+import fiji.plugin.trackmate.gui.GuiModel;
 import fiji.plugin.trackmate.gui.GuiUtils;
 import fiji.plugin.trackmate.gui.components.LogPanel;
 import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
@@ -45,9 +46,7 @@
 import fiji.plugin.trackmate.io.SettingsPersistence;
 import fiji.plugin.trackmate.io.TmXmlReader;
 import fiji.plugin.trackmate.util.TMUtils;
-import fiji.plugin.trackmate.visualization.TrackMateModelView;
 import fiji.plugin.trackmate.visualization.ViewUtils;
-import fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer;
 import ij.IJ;
 import ij.ImageJ;
 import ij.ImagePlus;
@@ -135,7 +134,7 @@ public void run( final String filePath )
 
 		ImagePlus imp = reader.readImage();
 		if ( null == imp )
-			imp = ViewUtils.makeEmpytImagePlus( model );
+			imp = ViewUtils.makeEmptyImagePlus( model );
 
 		/*
 		 * Read settings.
@@ -180,20 +179,17 @@ public void run( final String filePath )
 					analyzer.getFeatureDimensions(),
 					analyzer.getIsIntFeature() );
 
+		// Display settings.
+		final DisplaySettings displaySettings = reader.getDisplaySettings();
+
 		/*
-		 * Create TrackMate.
+		 * Create GuiModel.
 		 */
 
-		final TrackMate trackmate = createTrackMate( model, settings );
+		final GuiModel guiModel = new GuiModel( model, settings, displaySettings );
 
 		// Hook actions
-		postRead( trackmate );
-
-		// Display settings.
-		final DisplaySettings displaySettings = reader.getDisplaySettings();
-
-		// Selection model.
-		final SelectionModel selectionModel = new SelectionModel( model );
+		postRead( guiModel );
 
 		if ( !reader.isReadingOk() )
 		{
@@ -202,8 +198,7 @@ public void run( final String filePath )
 		}
 
 		// Main view.
-		final TrackMateModelView displayer = new HyperStackDisplayer( model, selectionModel, settings.imp, displaySettings );
-		displayer.render();
+		guiModel.getWindowManager().createHyperStackDisplayer();
 
 		// GUI state
 		String panelIdentifier = reader.getGUIState();
@@ -212,7 +207,7 @@ public void run( final String filePath )
 			panelIdentifier = ConfigureViewsDescriptor.KEY;
 
 		// Wizard.
-		final WizardSequence sequence = createSequence( trackmate, selectionModel, displaySettings );
+		final WizardSequence sequence = createSequence( guiModel );
 		sequence.setCurrent( panelIdentifier );
 		final JFrame frame = sequence.run( "TrackMate on " + settings.imp.getShortTitle() );
 		frame.setIconImage( TRACKMATE_ICON.getImage() );
@@ -268,13 +263,13 @@ public void run( final String filePath )
 
 	/**
 	 * Hook for subclassers:<br>
-	 * The {@link TrackMate} object is loaded and properly configured. This
+	 * The {@link guiModel} object is loaded and properly configured. This
 	 * method is called just before the controller and GUI are launched.
 	 *
 	 * @param trackmate
-	 *            the {@link TrackMate} instance that was fledged after loading.
+	 *            the {@link guiModel} instance that was fledged after loading.
 	 */
-	protected void postRead( final TrackMate trackmate )
+	protected void postRead( final GuiModel guiModel )
 	{}
 
 	/**
@@ -297,13 +292,20 @@ protected TmXmlReader createReader( final File lFile )
 
 	public static void main( final String[] args )
 	{
-		GuiUtils.setSystemLookAndFeel();
-		ImageJ.main( args );
-		final LoadTrackMatePlugIn plugIn = new LoadTrackMatePlugIn();
+		try
+		{
+			GuiUtils.setSystemLookAndFeel();
+			ImageJ.main( args );
+			final LoadTrackMatePlugIn plugIn = new LoadTrackMatePlugIn();
 //		plugIn.run( null );
 //		plugIn.run( "samples/FakeTracks.xml" );
-		plugIn.run( "samples/MAX_Merged.xml" );
+			plugIn.run( "samples/MAX_Merged.xml" );
 //		plugIn.run( "c:/Users/tinevez/Development/TrackMateWS/TrackMate-Cellpose/samples/R2_multiC.xml" );
 //		plugIn.run( "/Users/tinevez/Desktop/230901_DeltaRcsB-ZipA-mCh_timestep5min_Stage9_reg/230901_DeltaRcsB-ZipA-mCh_timestep5min_Stage9_reg_merge65.xml" );
+		}
+		catch ( final Throwable t )
+		{
+			t.printStackTrace();
+		}
 	}
 }