Update to 3D Viewer 5.0.0 + Java 3D 1.7.2

And adjust for backwards-incompatible API changes. And bump the major version from 2 to 3 due to API signature breakages in this component -- e.g. Tree#getOriginPoint(boolean) returns Point3f, which changed package prefix.
trakem2 · Sep 28, 2024 · d88145f · d88145f
1 parent 1941776
commit d88145f
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diff --git a/pom.xml b/pom.xml
@@ -5,13 +5,13 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>37.0.0</version>
+		<version>38.0.1</version>
 		<relativePath />
 	</parent>
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>TrakEM2_</artifactId>
-	<version>1.3.11-SNAPSHOT</version>
+	<version>2.0.0-SNAPSHOT</version>
 
 	<name>TrakEM2</name>
 	<description>TrakEM2 plugin for ImageJ.</description>
@@ -147,6 +147,9 @@
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
+
+		<_3D_Viewer.version>5.0.0</_3D_Viewer.version>
+		<VectorString.version>3.0.0</VectorString.version>
 	</properties>
 
 	<repositories>
@@ -214,15 +217,15 @@
 			<artifactId>postgresql</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.scijava</groupId>
-			<artifactId>j3dcore</artifactId>
+			<groupId>org.jogamp.java3d</groupId>
+			<artifactId>java3d-core</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.scijava</groupId>
-			<artifactId>j3dutils</artifactId>
+			<groupId>org.jogamp.java3d</groupId>
+			<artifactId>java3d-utils</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>org.scijava</groupId>
+			<groupId>org.jogamp.java3d</groupId>
 			<artifactId>vecmath</artifactId>
 		</dependency>
 		<dependency>

diff --git a/src/main/java/ini/trakem2/analysis/Compare.java b/src/main/java/ini/trakem2/analysis/Compare.java
@@ -54,13 +54,13 @@
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.regex.Pattern;
 
-import org.scijava.java3d.Transform3D;
-import org.scijava.vecmath.Color3f;
-import org.scijava.vecmath.Matrix3d;
-import org.scijava.vecmath.Matrix4d;
-import org.scijava.vecmath.Point3d;
-import org.scijava.vecmath.Tuple3d;
-import org.scijava.vecmath.Vector3d;
+import org.jogamp.java3d.Transform3D;
+import org.jogamp.vecmath.Color3f;
+import org.jogamp.vecmath.Matrix3d;
+import org.jogamp.vecmath.Matrix4d;
+import org.jogamp.vecmath.Point3d;
+import org.jogamp.vecmath.Tuple3d;
+import org.jogamp.vecmath.Vector3d;
 
 import ij.IJ;
 import ij.ImagePlus;
@@ -1883,7 +1883,7 @@ public void run() {
 						continue;
 					}
 
-					final Content sphere = d3d.getUniverse().addMesh(ij3d.Mesh_Maker.createSphere(x, y, z, r), new Color3f(heat_table.get(name)), name + "-sphere", 1);
+					final Content sphere = d3d.getUniverse().addMesh(ij3d.Mesh_Maker.createSphere(x, y, z, r), ij3d.Utils.toColor3f(heat_table.get(name)), name + "-sphere", 1);
 				}
 			}
 

diff --git a/src/main/java/ini/trakem2/display/AreaList.java b/src/main/java/ini/trakem2/display/AreaList.java
@@ -56,7 +56,7 @@
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Future;
 
-import org.scijava.vecmath.Point3f;
+import org.jogamp.vecmath.Point3f;
 
 import amira.AmiraMeshEncoder;
 import fiji.geom.AreaCalculations;

diff --git a/src/main/java/ini/trakem2/display/AreaTree.java b/src/main/java/ini/trakem2/display/AreaTree.java
@@ -50,8 +50,8 @@
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Future;
 
-import org.scijava.vecmath.Color3f;
-import org.scijava.vecmath.Point3f;
+import org.jogamp.vecmath.Color3f;
+import org.jogamp.vecmath.Point3f;
 
 import customnode.CustomTriangleMesh;
 import fiji.geom.AreaCalculations;
@@ -592,7 +592,7 @@ public MeshData generateMesh(final double scale, final int resample) {
 		// Determine colors by proximity to a node, since there isn't any other way.
 		// TODO
 		Utils.log("WARNING: AreaTree multicolor 3D mesh is not yet implemented.");
-		final Color3f cf = new Color3f(color);
+		final Color3f cf = ij3d.Utils.toColor3f(color);
 		for (int i=0; i<ps.size(); i++) colors.add(cf);
 
 		return new MeshData(ps, colors);

diff --git a/src/main/java/ini/trakem2/display/Ball.java b/src/main/java/ini/trakem2/display/Ball.java
@@ -45,7 +45,7 @@
 import java.util.List;
 import java.util.Map;
 
-import org.scijava.vecmath.Point3f;
+import org.jogamp.vecmath.Point3f;
 
 import ij.gui.GenericDialog;
 import ij.measure.Calibration;
@@ -931,7 +931,7 @@ static public double[][][] generateGlobe(int meridians, int parallels) {
 	/** Put all balls as a single 'mesh'; the returned list contains all faces as three consecutive Point3f. The mesh is also translated by x,y,z of this Displayable.*/
 	public List<Point3f> generateTriangles(final double scale, final double[][][] globe) {
 		try {
-			Class.forName("org.scijava.vecmath.Point3f");
+			Class.forName("org.jogamp.vecmath.Point3f");
 		} catch (final ClassNotFoundException cnfe) {
 			Utils.log("Java3D is not installed.");
 			return null;

diff --git a/src/main/java/ini/trakem2/display/Connector.java b/src/main/java/ini/trakem2/display/Connector.java
@@ -39,7 +39,7 @@
 import java.util.Map;
 import java.util.Set;
 
-import org.scijava.vecmath.Point3f;
+import org.jogamp.vecmath.Point3f;
 
 import ij.measure.Calibration;
 import ij.measure.ResultsTable;

diff --git a/src/main/java/ini/trakem2/display/Display3D.java b/src/main/java/ini/trakem2/display/Display3D.java
@@ -46,11 +46,11 @@
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.atomic.AtomicInteger;
 
-import org.scijava.java3d.PolygonAttributes;
-import org.scijava.java3d.Transform3D;
-import org.scijava.java3d.View;
-import org.scijava.vecmath.Color3f;
-import org.scijava.vecmath.Point3f;
+import org.jogamp.java3d.PolygonAttributes;
+import org.jogamp.java3d.Transform3D;
+import org.jogamp.java3d.View;
+import org.jogamp.vecmath.Color3f;
+import org.jogamp.vecmath.Point3f;
 
 import customnode.CustomLineMesh;
 import customnode.CustomMesh;
@@ -310,7 +310,7 @@ static private boolean hasLibs() {
 		if (check_j3d) {
 			check_j3d = false;
 			try {
-				Class.forName("org.scijava.vecmath.Point3f");
+				Class.forName("org.jogamp.vecmath.Point3f");
 				has_j3d_3dviewer = true;
 			} catch (final ClassNotFoundException cnfe) {
 				Utils.log("Java 3D not installed.");
@@ -895,7 +895,7 @@ public Content call() {
 		Content ct = null;
 
 		try {
-			final Color3f c3 = new Color3f(color);
+			final Color3f c3 = ij3d.Utils.toColor3f(color);
 
 			// If it exists, remove and add as new:
 			universe.removeContent(title);
@@ -996,7 +996,7 @@ public Content asContent(final Display3D d3d) {
 				Utils.log("WARNING: adding a 3D object fully transparent.");
 			}
 			final List<Point3f> triangles = Pipe.generateTriangles(Pipe.makeTube(vs.getPoints(0), vs.getPoints(1), vs.getPoints(2), wi, 1, 12, null), d3d.scale);
-			final Content ct = d3d.universe.createContent(new CustomTriangleMesh(triangles, new Color3f(color), 0), title);
+			final Content ct = d3d.universe.createContent(new CustomTriangleMesh(triangles, ij3d.Utils.toColor3f(color), 0), title);
 			ct.setTransparency(transp);
 			ct.setLocked(true);
 			return ct;
@@ -1125,7 +1125,7 @@ public Boolean call() {
 			Content content = d3d.universe.getContent(makeTitle(d));
 			if (null == content) content = getProfileContent(d);
 			if (null != content) {
-				content.setColor(new Color3f(color));
+				content.setColor(ij3d.Utils.toColor3f(color));
 				return true;
 			}
 			return false;
@@ -1237,7 +1237,7 @@ public List<Point3f> createFatPoint(final double wx, final double wy, final doub
 	static public final Future<Content> addFatPoint(final String title, final LayerSet ls, final double wx, final double wy, final double wz, final double wr, final Color color) {
 		final Display3D d3d = Display3D.get(ls);
 		d3d.universe.removeContent(title);
-		final Content ct = d3d.universe.createContent(new CustomTriangleMesh(d3d.createFatPoint(wx, wy, wz, wr, ls.getCalibrationCopy()), new Color3f(color), 0), title);
+		final Content ct = d3d.universe.createContent(new CustomTriangleMesh(d3d.createFatPoint(wx, wy, wz, wr, ls.getCalibrationCopy()), ij3d.Utils.toColor3f(color), 0), title);
 		ct.setLocked(true);
 		return d3d.addContent(ct);
 	}

diff --git a/src/main/java/ini/trakem2/display/DisplayCanvas.java b/src/main/java/ini/trakem2/display/DisplayCanvas.java
@@ -71,9 +71,9 @@
 import java.util.concurrent.ScheduledFuture;
 import java.util.concurrent.TimeUnit;
 
-import org.scijava.vecmath.Point2f;
-import org.scijava.vecmath.Vector2f;
-import org.scijava.vecmath.Vector3d;
+import org.jogamp.vecmath.Point2f;
+import org.jogamp.vecmath.Vector2f;
+import org.jogamp.vecmath.Vector3d;
 
 import ij.IJ;
 import ij.ImagePlus;

diff --git a/src/main/java/ini/trakem2/display/Line3D.java b/src/main/java/ini/trakem2/display/Line3D.java
@@ -26,7 +26,7 @@
 import java.awt.Color;
 import java.util.List;
 
-import org.scijava.vecmath.Point3f;
+import org.jogamp.vecmath.Point3f;
 
 import ini.trakem2.Project;
 import ini.trakem2.vector.VectorString3D;

diff --git a/src/main/java/ini/trakem2/display/Node.java b/src/main/java/ini/trakem2/display/Node.java
@@ -46,7 +46,7 @@
 import java.util.Set;
 import java.util.TreeSet;
 
-import org.scijava.vecmath.Point3f;
+import org.jogamp.vecmath.Point3f;
 
 import ini.trakem2.Project;
 import ini.trakem2.utils.IJError;

diff --git a/src/main/java/ini/trakem2/display/Pipe.java b/src/main/java/ini/trakem2/display/Pipe.java
@@ -41,7 +41,7 @@
 import java.util.Iterator;
 import java.util.List;
 
-import org.scijava.vecmath.Point3f;
+import org.jogamp.vecmath.Point3f;
 
 import ij.measure.Calibration;
 import ij.measure.ResultsTable;

diff --git a/src/main/java/ini/trakem2/display/Polyline.java b/src/main/java/ini/trakem2/display/Polyline.java
@@ -44,8 +44,8 @@
 import java.util.Map;
 import java.util.Random;
 
-import org.scijava.vecmath.Point3f;
-import org.scijava.vecmath.Vector3d;
+import org.jogamp.vecmath.Point3f;
+import org.jogamp.vecmath.Vector3d;
 
 import features.ComputeCurvatures;
 import ij.IJ;

diff --git a/src/main/java/ini/trakem2/display/Profile.java b/src/main/java/ini/trakem2/display/Profile.java
@@ -42,7 +42,7 @@
 import java.util.List;
 import java.util.Map;
 
-import org.scijava.vecmath.Point3f;
+import org.jogamp.vecmath.Point3f;
 
 import ij.measure.Calibration;
 import ij.measure.ResultsTable;

diff --git a/src/main/java/ini/trakem2/display/Tree.java b/src/main/java/ini/trakem2/display/Tree.java
@@ -87,8 +87,8 @@
 import javax.swing.table.AbstractTableModel;
 import javax.swing.table.DefaultTableCellRenderer;
 
-import org.scijava.vecmath.Color3f;
-import org.scijava.vecmath.Point3f;
+import org.jogamp.vecmath.Color3f;
+import org.jogamp.vecmath.Point3f;
 
 import fiji.geom.AreaCalculations;
 import ij.ImagePlus;
@@ -630,7 +630,7 @@ public MeshData generateSkeleton(final double scale_, final int parallels, final
 		// The method, by the way, is very parallelizable: each is independent.
 
 		final HashMap<Color,Color3f> cached_colors = new HashMap<Color, Color3f>();
-		final Color3f cf = new Color3f(this.color);
+		final Color3f cf = ij3d.Utils.toColor3f(this.color);
 		cached_colors.put(this.color, cf);
 
 		boolean go = true;
@@ -662,7 +662,7 @@ public MeshData generateSkeleton(final double scale_, final int parallels, final
 				} else {
 					Color3f c = cached_colors.get(node.color);
 					if (null == c) {
-						c = new Color3f(node.color);
+						c = ij3d.Utils.toColor3f(node.color);
 						cached_colors.put(node.color, c);
 					}
 					colors.add(c);

diff --git a/src/main/java/ini/trakem2/display/Treeline.java b/src/main/java/ini/trakem2/display/Treeline.java
@@ -48,11 +48,11 @@
 import java.util.List;
 import java.util.Set;
 
-import org.scijava.java3d.Transform3D;
-import org.scijava.vecmath.AxisAngle4f;
-import org.scijava.vecmath.Color3f;
-import org.scijava.vecmath.Point3f;
-import org.scijava.vecmath.Vector3f;
+import org.jogamp.java3d.Transform3D;
+import org.jogamp.vecmath.AxisAngle4f;
+import org.jogamp.vecmath.Color3f;
+import org.jogamp.vecmath.Point3f;
+import org.jogamp.vecmath.Vector3f;
 
 import ij.gui.GenericDialog;
 import ij.measure.Calibration;
@@ -665,7 +665,7 @@ public MeshData generateMesh(final double scale_, int parallels) {
 		final AxisAngle4f aa = new AxisAngle4f();
 
 		final List<Color3f> colors = new ArrayList<Color3f>();
-		final Color3f cf = new Color3f(this.color);
+		final Color3f cf = ij3d.Utils.toColor3f(this.color);
 		final HashMap<Color,Color3f> cached_colors = new HashMap<Color,Color3f>();
 		cached_colors.put(this.color, cf);
 
@@ -733,7 +733,7 @@ public MeshData generateMesh(final double scale_, int parallels) {
 				} else {
 					c = cached_colors.get(nd.color);
 					if (null == c) {
-						c = new Color3f(nd.color);
+						c = ij3d.Utils.toColor3f(nd.color);
 						cached_colors.put(nd.color, c);
 					}
 				}

diff --git a/src/main/java/ini/trakem2/display/d3d/ControlClickBehavior.java b/src/main/java/ini/trakem2/display/d3d/ControlClickBehavior.java
@@ -23,7 +23,7 @@
 
 import java.awt.event.MouseEvent;
 
-import org.scijava.vecmath.Point3d;
+import org.jogamp.vecmath.Point3d;
 
 import ij.measure.Calibration;
 import ij3d.Content;

diff --git a/src/main/java/ini/trakem2/display/d3d/Display3DGUI.java b/src/main/java/ini/trakem2/display/d3d/Display3DGUI.java
@@ -36,8 +36,8 @@
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.util.ArrayList;
-import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.TreeMap;
@@ -58,10 +58,10 @@
 import javax.swing.table.AbstractTableModel;
 import javax.swing.table.TableColumn;
 
-import org.scijava.java3d.BranchGroup;
-import org.scijava.java3d.Canvas3D;
-import org.scijava.java3d.View;
-import org.scijava.vecmath.Color3f;
+import org.jogamp.java3d.BranchGroup;
+import org.jogamp.java3d.Canvas3D;
+import org.jogamp.java3d.View;
+import org.jogamp.vecmath.Color3f;
 
 import ij3d.Content;
 import ij3d.Image3DUniverse;
@@ -149,9 +149,9 @@ public ImageWindow3D init() {
 	 */
 	static private final List<Content> getOrderedContents(final Image3DUniverse univ) {
 		final ArrayList<Content> cs = new ArrayList<Content>();
-		final Enumeration<?> seq = univ.getScene().getAllChildren();
-		while (seq.hasMoreElements()) {
-			final Object o = seq.nextElement();
+		final Iterator<?> seq = univ.getScene().getAllChildren();
+		while (seq.hasNext()) {
+			final Object o = seq.next();
 			if (o instanceof Content) cs.add((Content)o);
 		}
 		return cs;

diff --git a/src/main/java/ini/trakem2/utils/AreaUtils.java b/src/main/java/ini/trakem2/utils/AreaUtils.java
@@ -37,7 +37,7 @@
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
 
-import org.scijava.vecmath.Point3f;
+import org.jogamp.vecmath.Point3f;
 
 import ij.ImagePlus;
 import ij.gui.Roi;

diff --git a/src/main/java/ini/trakem2/utils/M.java b/src/main/java/ini/trakem2/utils/M.java
@@ -39,10 +39,10 @@
 import java.util.Collection;
 import java.util.List;
 
-import org.scijava.vecmath.Point3f;
-import org.scijava.vecmath.Tuple3d;
-import org.scijava.vecmath.Vector3d;
-import org.scijava.vecmath.Vector3f;
+import org.jogamp.vecmath.Point3f;
+import org.jogamp.vecmath.Tuple3d;
+import org.jogamp.vecmath.Vector3d;
+import org.jogamp.vecmath.Vector3f;
 
 import ij.gui.PolygonRoi;
 import ij.gui.Roi;

diff --git a/src/main/java/ini/trakem2/utils/MCCube.java b/src/main/java/ini/trakem2/utils/MCCube.java
@@ -30,7 +30,7 @@
 import java.util.HashMap;
 import java.util.List;
 
-import org.scijava.vecmath.Point3f;
+import org.jogamp.vecmath.Point3f;
 
 import ij.IJ;
 import ij3d.Volume;