Merge pull request #279 from trackmate-sc/v8-bvv-imglib2-mesh

Base the 3D mesh on the prototype imglib2-mesh library.
trackmate-sc · Sep 12, 2023 · 3b57316 · 3b57316
2 parents 110941e + 25d244e
commit 3b57316
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Showing 26 changed files with 115 additions and 508 deletions.
diff --git a/pom.xml b/pom.xml
@@ -167,14 +167,9 @@
 			<artifactId>imagej-common</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>net.imagej</groupId>
-			<artifactId>imagej-mesh</artifactId>
-			<version>0.8.2-SNAPSHOT</version>
-		</dependency>
-		<dependency>
-			<groupId>net.imagej</groupId>
-			<artifactId>imagej-mesh-io</artifactId>
-			<version>0.1.3-SNAPSHOT</version>
+			<groupId>net.imglib2</groupId>
+			<artifactId>imglib2-mesh</artifactId>
+			<version>1.0.0-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.imagej</groupId>
@@ -237,6 +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/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;
 
@@ -50,7 +49,7 @@ public SpotMesh(
 	 * 
 	 * @param quality
 	 * @param name
-	 * @param mesh
+	 * @param m
 	 */
 	public SpotMesh(
 			final Mesh m,
@@ -207,7 +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++ )
@@ -311,7 +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/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
@@ -412,11 +412,11 @@ public static < T extends RealType< T >, R extends RealType< R > > List< Spot >
 	 * @return a list of spots, with ROI.
 	 */
 	public static < T extends RealType< T >, S extends RealType< S > > List< Spot > fromMaskWithROI(
-			final RandomAccessible< T > input,
-			final Interval interval,
-			final double[] calibration,
-			final boolean simplify,
-			final int numThreads,
+			final RandomAccessible< T > input, 
+			final Interval interval, 
+			final double[] calibration, 
+			final boolean simplify, 
+			final int numThreads, 
 			final RandomAccessibleInterval< S > qualityImage )
 	{
 		final ImgLabeling< Integer, IntType > labeling = toLabeling(

diff --git a/src/main/java/fiji/plugin/trackmate/detection/Process2DZ.java b/src/main/java/fiji/plugin/trackmate/detection/Process2DZ.java
@@ -14,14 +14,14 @@
 import fiji.plugin.trackmate.util.TMUtils;
 import ij.ImagePlus;
 import net.imagej.ImgPlus;
-import net.imagej.mesh.alg.TaubinSmoothing;
-import net.imagej.mesh.nio.BufferMesh;
-import net.imagej.mesh.obj.transform.TranslateMesh;
 import net.imglib2.Interval;
 import net.imglib2.RandomAccess;
 import net.imglib2.RandomAccessible;
 import net.imglib2.algorithm.MultiThreadedBenchmarkAlgorithm;
 import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.mesh.alg.TaubinSmoothing;
+import net.imglib2.mesh.obj.nio.BufferMesh;
+import net.imglib2.mesh.obj.transform.TranslateMesh;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
 import net.imglib2.view.IntervalView;

diff --git a/src/main/java/fiji/plugin/trackmate/detection/SpotMeshUtils.java b/src/main/java/fiji/plugin/trackmate/detection/SpotMeshUtils.java
@@ -7,16 +7,16 @@
 
 import fiji.plugin.trackmate.Spot;
 import fiji.plugin.trackmate.SpotMesh;
-import net.imagej.mesh.Mesh;
-import net.imagej.mesh.MeshConnectedComponents;
-import net.imagej.mesh.Meshes;
-import net.imagej.mesh.Vertices;
-import net.imagej.mesh.nio.BufferMesh;
 import net.imglib2.Interval;
 import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccessible;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.RealInterval;
+import net.imglib2.mesh.Meshes;
+import net.imglib2.mesh.alg.MeshConnectedComponents;
+import net.imglib2.mesh.obj.Mesh;
+import net.imglib2.mesh.obj.Vertices;
+import net.imglib2.mesh.obj.nio.BufferMesh;
 import net.imglib2.roi.labeling.ImgLabeling;
 import net.imglib2.roi.labeling.LabelRegion;
 import net.imglib2.roi.labeling.LabelRegions;

diff --git a/src/main/java/fiji/plugin/trackmate/features/spot/Spot3DFitEllipsoidAnalyzer.java b/src/main/java/fiji/plugin/trackmate/features/spot/Spot3DFitEllipsoidAnalyzer.java
@@ -22,9 +22,9 @@
 
 import fiji.plugin.trackmate.Spot;
 import fiji.plugin.trackmate.SpotMesh;
-import fiji.plugin.trackmate.util.mesh.EllipsoidFitter;
-import fiji.plugin.trackmate.util.mesh.EllipsoidFitter.EllipsoidFit;
 import net.imglib2.RealLocalizable;
+import net.imglib2.mesh.alg.EllipsoidFitter;
+import net.imglib2.mesh.alg.EllipsoidFitter.EllipsoidFit;
 import net.imglib2.type.numeric.RealType;
 
 public class Spot3DFitEllipsoidAnalyzer< T extends RealType< T > > extends AbstractSpotFeatureAnalyzer< T >

diff --git a/src/main/java/fiji/plugin/trackmate/features/spot/Spot3DShapeAnalyzer.java b/src/main/java/fiji/plugin/trackmate/features/spot/Spot3DShapeAnalyzer.java
@@ -23,26 +23,19 @@
 
 import fiji.plugin.trackmate.Spot;
 import fiji.plugin.trackmate.SpotMesh;
-import net.imagej.mesh.Mesh;
-import net.imagej.mesh.Meshes;
-import net.imagej.ops.geom.geom3d.DefaultConvexHull3D;
-import net.imagej.ops.geom.geom3d.DefaultSurfaceArea;
+import net.imglib2.mesh.MeshShapeDescriptors;
+import net.imglib2.mesh.alg.hull.ConvexHull;
+import net.imglib2.mesh.obj.naive.NaiveDoubleMesh;
 import net.imglib2.type.numeric.RealType;
 
 public class Spot3DShapeAnalyzer< T extends RealType< T > > extends AbstractSpotFeatureAnalyzer< T >
 {
 
 	private final boolean is3D;
 
-	private final DefaultConvexHull3D convexHull;
-
-	private final DefaultSurfaceArea surfaceArea;
-
 	public Spot3DShapeAnalyzer( final boolean is3D )
 	{
 		this.is3D = is3D;
-		this.convexHull = new DefaultConvexHull3D();
-		this.surfaceArea = new DefaultSurfaceArea();
 	}
 
 	@Override
@@ -58,13 +51,13 @@ public void process( final Spot spot )
 			if ( spot instanceof SpotMesh )
 			{
 				final SpotMesh sm = ( SpotMesh ) spot;
-				final Mesh ch = convexHull.calculate( sm.getMesh() );
+				final NaiveDoubleMesh ch = ConvexHull.calculate( sm.getMesh() );
 				volume = sm.volume();
-				final double volumeCH = Meshes.volume( ch );
+				final double volumeCH = MeshShapeDescriptors.volume( ch );
 				solidity = volume / volumeCH;
 
-				sa = surfaceArea.calculate( sm.getMesh() ).get();
-				final double saCH = surfaceArea.calculate( ch ).get();
+				sa = MeshShapeDescriptors.surfaceArea( sm.getMesh() );
+				final double saCH = MeshShapeDescriptors.surfaceArea( ch );
 				convexity = sa / saCH;
 
 				final double sphereArea = Math.pow( Math.PI, 1. / 3. )

diff --git a/src/main/java/fiji/plugin/trackmate/gui/wizard/TrackMateWizardSequence.java b/src/main/java/fiji/plugin/trackmate/gui/wizard/TrackMateWizardSequence.java
@@ -485,6 +485,10 @@ public void run()
 							GuiUtils.positionWindow( SwingUtilities.getWindowAncestor( bvvHandle.getViewerPanel() ), c );
 						}
 					}
+					catch ( final Exception e )
+					{
+						e.printStackTrace();
+					}
 					finally
 					{
 						enabler.reenable();

diff --git a/src/main/java/fiji/plugin/trackmate/io/TmXmlReader.java b/src/main/java/fiji/plugin/trackmate/io/TmXmlReader.java
@@ -92,7 +92,6 @@
 import static fiji.plugin.trackmate.io.TmXmlKeys.TRACK_ID_ELEMENT_KEY;
 import static fiji.plugin.trackmate.io.TmXmlKeys.TRACK_NAME_ATTRIBUTE_NAME;
 import static fiji.plugin.trackmate.io.TmXmlWriter.MESH_FILE_EXTENSION;
-import static fiji.plugin.trackmate.io.TmXmlWriter.PLY_MESH_IO;
 import static fiji.plugin.trackmate.tracking.TrackerKeys.XML_ATTRIBUTE_TRACKER_NAME;
 
 import java.io.File;
@@ -156,9 +155,10 @@
 import fiji.plugin.trackmate.visualization.trackscheme.TrackScheme;
 import ij.IJ;
 import ij.ImagePlus;
-import net.imagej.mesh.Mesh;
-import net.imagej.mesh.Meshes;
-import net.imagej.mesh.nio.BufferMesh;
+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;
 
 public class TmXmlReader
 {
@@ -960,7 +960,7 @@ private SpotCollection getSpots( final Element modelElement )
 						// Deserialize mesh.
 						try
 						{
-							final Mesh m = PLY_MESH_IO.open( zipFile.getInputStream( entry ) );
+							final Mesh m = PLYMeshIO.open( zipFile.getInputStream( entry ) );
 							final BufferMesh mesh = new BufferMesh( ( int ) m.vertices().size(), ( int ) m.triangles().size() );
 							Meshes.calculateNormals( m, mesh );
 

diff --git a/src/main/java/fiji/plugin/trackmate/io/TmXmlWriter.java b/src/main/java/fiji/plugin/trackmate/io/TmXmlWriter.java
@@ -133,15 +133,13 @@
 import fiji.plugin.trackmate.gui.displaysettings.DisplaySettingsIO;
 import gnu.trove.map.hash.TIntIntHashMap;
 import gnu.trove.procedure.TIntIntProcedure;
-import net.imagej.mesh.Mesh;
-import net.imagej.mesh.io.ply.PLYMeshIO;
-import net.imagej.mesh.obj.transform.TranslateMesh;
+import net.imglib2.mesh.io.ply.PLYMeshIO;
+import net.imglib2.mesh.obj.Mesh;
+import net.imglib2.mesh.obj.transform.TranslateMesh;
 
 public class TmXmlWriter
 {
 
-	static final PLYMeshIO PLY_MESH_IO = new PLYMeshIO();
-
 	static final String MESH_FILE_EXTENSION = ".meshes";
 
 	/** Zip compression level (0-9) */
@@ -791,7 +789,7 @@ protected void writeSpotMeshes( final Iterable< Spot > spots )
 					final SpotMesh sm = ( SpotMesh ) spot;
 					final Mesh mesh = sm.getMesh();
 					final Mesh translated = TranslateMesh.translate( mesh, spot );
-					final byte[] bs = PLY_MESH_IO.writeBinary( translated );
+					final byte[] bs = PLYMeshIO.writeBinary( translated );
 
 					final String entryName = spot.ID() + ".ply";
 					zos.putNextEntry( new ZipEntry( entryName ) );