Merge pull request #280 from trackmate-sc/v8-bvv

A 3D viewer for TrackMate based on the BVV.
trackmate-sc · Sep 12, 2023 · 89c9faf · 89c9faf
2 parents ca5c5e1 + 3b57316
commit 89c9faf
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Showing 36 changed files with 1,133 additions and 464 deletions.
diff --git a/pom.xml b/pom.xml
@@ -167,19 +167,29 @@
 			<artifactId>imagej-common</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>net.imagej</groupId>
-			<artifactId>imagej-mesh</artifactId>
-			<version>0.8.2-SNAPSHOT</version>
+			<groupId>net.imglib2</groupId>
+			<artifactId>imglib2-mesh</artifactId>
+			<version>1.0.0-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.imagej</groupId>
-			<artifactId>imagej-mesh-io</artifactId>
-			<version>0.1.3-SNAPSHOT</version>
+			<artifactId>imagej-ops</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>net.imagej</groupId>
-			<artifactId>imagej-ops</artifactId>
+			<groupId>sc.fiji</groupId>
+			<artifactId>bigvolumeviewer</artifactId>
+			<version>0.3.1</version>
 		</dependency>
+		<dependency>
+	        <groupId>org.jogamp.jogl</groupId>
+	        <artifactId>jogl-all-main</artifactId>
+	        <version>2.3.2</version>
+	    </dependency>
+	    <dependency>
+	        <groupId>org.jogamp.gluegen</groupId>
+	        <artifactId>gluegen-rt-main</artifactId>
+	        <version>2.3.2</version>
+	    </dependency>			
 
 		<!-- ImgLib2 dependencies -->
 		<dependency>
@@ -222,6 +232,10 @@
 		</dependency>
 
 		<!-- Other dependencies -->
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+		</dependency>		
 		<dependency>
 			<groupId>com.github.vlsi.mxgraph</groupId>
 			<artifactId>jgraphx</artifactId>

diff --git a/src/main/java/fiji/plugin/trackmate/Spot.java b/src/main/java/fiji/plugin/trackmate/Spot.java
@@ -422,34 +422,34 @@ default int numDimensions()
 	@Override
 	public default void move( final float distance, final int d )
 	{
-		putFeature( POSITION_FEATURES[d], getFeature( POSITION_FEATURES[d] + distance ) );
+		putFeature( POSITION_FEATURES[ d ], getFeature( POSITION_FEATURES[ d ] ) + distance );
 	}
 
 	@Override
 	public default void move( final double distance, final int d )
 	{
-		putFeature( POSITION_FEATURES[d], getFeature( POSITION_FEATURES[d] + distance ) );
+		putFeature( POSITION_FEATURES[ d ], getFeature( POSITION_FEATURES[ d ] ) + distance );
 	}
 
 	@Override
 	public default void move( final RealLocalizable distance )
 	{
 		for ( int d = 0; d < 3; d++ )
-			putFeature( POSITION_FEATURES[ d ], getFeature( POSITION_FEATURES[ d ] + distance ) );
+			putFeature( POSITION_FEATURES[ d ], getFeature( POSITION_FEATURES[ d ] ) + distance.getDoublePosition( d ) );
 	}
 
 	@Override
 	public default void move( final float[] distance )
 	{
 		for ( int d = 0; d < 3; d++ )
-			putFeature( POSITION_FEATURES[ d ], getFeature( POSITION_FEATURES[ d ] + distance[ d ] ) );
+			putFeature( POSITION_FEATURES[ d ], getFeature( POSITION_FEATURES[ d ] ) + distance[ d ] );
 	}
 
 	@Override
 	public default void move( final double[] distance )
 	{
 		for ( int d = 0; d < 3; d++ )
-			putFeature( POSITION_FEATURES[ d ], getFeature( POSITION_FEATURES[ d ] + distance[ d ] ) );
+			putFeature( POSITION_FEATURES[ d ], getFeature( POSITION_FEATURES[ d ] ) + distance[ d ] );
 	}
 
 	@Override

diff --git a/src/main/java/fiji/plugin/trackmate/SpotMesh.java b/src/main/java/fiji/plugin/trackmate/SpotMesh.java
@@ -6,19 +6,18 @@
 import java.util.stream.Collectors;
 
 import fiji.plugin.trackmate.util.mesh.SpotMeshIterable;
-import net.imagej.mesh.Mesh;
-import net.imagej.mesh.Meshes;
-import net.imagej.mesh.Triangles;
-import net.imagej.mesh.Vertices;
-import net.imagej.mesh.alg.zslicer.RamerDouglasPeucker;
-import net.imagej.mesh.alg.zslicer.Slice;
-import net.imagej.mesh.alg.zslicer.ZSlicer;
-import net.imagej.mesh.nio.BufferMesh;
 import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccessible;
 import net.imglib2.RealInterval;
 import net.imglib2.RealLocalizable;
 import net.imglib2.RealPoint;
+import net.imglib2.mesh.Meshes;
+import net.imglib2.mesh.alg.zslicer.RamerDouglasPeucker;
+import net.imglib2.mesh.alg.zslicer.Slice;
+import net.imglib2.mesh.alg.zslicer.ZSlicer;
+import net.imglib2.mesh.obj.Mesh;
+import net.imglib2.mesh.obj.Vertices;
+import net.imglib2.mesh.obj.nio.BufferMesh;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.util.Intervals;
 
@@ -50,15 +49,20 @@ public SpotMesh(
 	 * 
 	 * @param quality
 	 * @param name
-	 * @param mesh
+	 * @param m
 	 */
 	public SpotMesh(
-			final Mesh mesh,
+			final Mesh m,
 			final double quality,
 			final String name )
 	{
 		// Dummy coordinates and radius.
 		super( 0., 0., 0., 0., quality, name );
+
+		// Compute triangles and vertices normals.
+		final BufferMesh mesh = new BufferMesh( ( int ) m.vertices().size(), ( int ) m.triangles().size() );
+		Meshes.calculateNormals( m, mesh );
+
 		this.mesh = mesh;
 		final RealPoint center = Meshes.center( mesh );
 
@@ -202,7 +206,7 @@ public static double volume( final Mesh mesh )
 	{
 
 		final Vertices vertices = mesh.vertices();
-		final Triangles triangles = mesh.triangles();
+		final net.imglib2.mesh.obj.Triangles triangles = mesh.triangles();
 		final long nTriangles = triangles.size();
 		double sum = 0.;
 		for ( long t = 0; t < nTriangles; t++ )
@@ -306,7 +310,7 @@ public String toString()
 			str.append( String.format( "\n%5d: %7.2f %7.2f %7.2f",
 					i, vertices.x( i ), vertices.y( i ), vertices.z( i ) ) );
 
-		final Triangles triangles = mesh.triangles();
+		final net.imglib2.mesh.obj.Triangles triangles = mesh.triangles();
 		final long nTriangles = triangles.size();
 		str.append( "\nF (" + nTriangles + "):" );
 		for ( long i = 0; i < nTriangles; i++ )

diff --git a/src/main/java/fiji/plugin/trackmate/SpotRoi.java b/src/main/java/fiji/plugin/trackmate/SpotRoi.java
@@ -75,7 +75,7 @@ public SpotRoi(
 			final double[] x,
 			final double[] y )
 	{
-		super( ID );
+		super( ID ); 
 		this.x = x;
 		this.y = y;
 	}

diff --git a/src/main/java/fiji/plugin/trackmate/action/MeshSeriesExporter.java b/src/main/java/fiji/plugin/trackmate/action/MeshSeriesExporter.java
@@ -43,11 +43,11 @@
 import fiji.plugin.trackmate.TrackMate;
 import fiji.plugin.trackmate.gui.displaysettings.DisplaySettings;
 import fiji.plugin.trackmate.io.IOUtils;
-import net.imagej.mesh.Mesh;
-import net.imagej.mesh.Meshes;
-import net.imagej.mesh.io.ply.PLYMeshIO;
-import net.imagej.mesh.nio.BufferMesh;
-import net.imagej.mesh.obj.transform.TranslateMesh;
+import net.imglib2.mesh.Meshes;
+import net.imglib2.mesh.io.ply.PLYMeshIO;
+import net.imglib2.mesh.obj.Mesh;
+import net.imglib2.mesh.obj.nio.BufferMesh;
+import net.imglib2.mesh.obj.transform.TranslateMesh;
 
 public class MeshSeriesExporter extends AbstractTMAction
 {
@@ -106,8 +106,6 @@ public static void exportMeshesToFileSeries( final SpotCollection spots, final F
 		final File folder = new File( folderName );
 		folder.mkdirs();
 
-		final PLYMeshIO io = new PLYMeshIO();
-
 		final NavigableSet< Integer > frames = spots.keySet();
 		for ( final Integer frame : frames )
 		{
@@ -128,7 +126,7 @@ public static void exportMeshesToFileSeries( final SpotCollection spots, final F
 			Meshes.calculateNormals( merged, mesh );
 			try
 			{
-				io.save( mesh, targetFile.getAbsolutePath() );
+				PLYMeshIO.save( mesh, targetFile.getAbsolutePath() );
 			}
 			catch ( final IOException e )
 			{

diff --git a/src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java b/src/main/java/fiji/plugin/trackmate/detection/MaskUtils.java
@@ -516,7 +516,6 @@ else if ( input.numDimensions() == 3 )
 					threshold,
 					simplify,
 					qualityImage );
-
 		}
 		else
 		{