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Update to Java 3D 1.7.2
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And account for backwards-incompatible API changes.

And bump the major version from 4 to 5, because the Java 3D package
prefix changed from org.scijava to org.jogamp, meaning any API
signatures involving Java 3D classes will be binary-incompatible.
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@ctrueden
ctrueden committed Sep 28, 2024
1 parent 5696ce5 commit 903bb6b
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Showing 89 changed files with 557 additions and 521 deletions.
2 changes: 1 addition & 1 deletion customnode/TestDynamicLineMesh.py
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from customnode import *;

from java.util import ArrayList;
from org.scijava.vecmath import *;
from org.jogamp.vecmath import *;

univ = Image3DUniverse();
univ.show();
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20 changes: 14 additions & 6 deletions pom.xml
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<groupId>sc.fiji</groupId>
<artifactId>3D_Viewer</artifactId>
<version>4.0.6-SNAPSHOT</version>
<version>5.0.0-SNAPSHOT</version>

<name>3D Viewer</name>
<description>3D Viewer for visualizing image stacks three-dimensionally.</description>
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<!-- NB: Deploy releases to the SciJava Maven repository. -->
<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>

<jogamp-java3d.version>1.7.2</jogamp-java3d.version>
<org.jogamp.java3d.java3d-core.version>${jogamp-java3d.version}</org.jogamp.java3d.java3d-core.version>
<org.jogamp.java3d.java3d-utils.version>${jogamp-java3d.version}</org.jogamp.java3d.java3d-utils.version>
<org.jogamp.java3d.vecmath.version>${jogamp-java3d.version}</org.jogamp.java3d.vecmath.version>
</properties>

<repositories>
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<!-- Java 3D dependencies -->
<dependency>
<groupId>org.scijava</groupId>
<artifactId>j3dcore</artifactId>
<groupId>org.jogamp.java3d</groupId>
<artifactId>java3d-core</artifactId>
<version>${org.jogamp.java3d.java3d-core.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>j3dutils</artifactId>
<groupId>org.jogamp.java3d</groupId>
<artifactId>java3d-utils</artifactId>
<version>${org.jogamp.java3d.java3d-utils.version}</version>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<groupId>org.jogamp.java3d</groupId>
<artifactId>vecmath</artifactId>
<version>${org.jogamp.java3d.vecmath.version}</version>
</dependency>
</dependencies>
</project>
2 changes: 1 addition & 1 deletion src/main/java/customnode/Box.java
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package customnode;

import org.scijava.vecmath.Point3f;
import org.jogamp.vecmath.Point3f;

public class Box extends Primitive {

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4 changes: 2 additions & 2 deletions src/main/java/customnode/Cone.java
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package customnode;

import org.scijava.vecmath.Matrix4f;
import org.scijava.vecmath.Point3f;
import org.jogamp.vecmath.Matrix4f;
import org.jogamp.vecmath.Point3f;

public class Cone extends Primitive {

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22 changes: 11 additions & 11 deletions src/main/java/customnode/CustomIndexedTriangleMesh.java
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import java.util.List;

import org.scijava.java3d.Appearance;
import org.scijava.java3d.ColoringAttributes;
import org.scijava.java3d.Geometry;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.IndexedTriangleArray;
import org.scijava.java3d.Material;
import org.scijava.java3d.PolygonAttributes;
import org.scijava.java3d.TransparencyAttributes;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Vector3f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.ColoringAttributes;
import org.jogamp.java3d.Geometry;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.IndexedTriangleArray;
import org.jogamp.java3d.Material;
import org.jogamp.java3d.PolygonAttributes;
import org.jogamp.java3d.TransparencyAttributes;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;
import org.jogamp.vecmath.Vector3f;

import ij.ImagePlus;
import ij.measure.Calibration;
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24 changes: 12 additions & 12 deletions src/main/java/customnode/CustomLineMesh.java
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import java.util.Arrays;
import java.util.List;

import org.scijava.java3d.Appearance;
import org.scijava.java3d.ColoringAttributes;
import org.scijava.java3d.Geometry;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.LineArray;
import org.scijava.java3d.LineAttributes;
import org.scijava.java3d.LineStripArray;
import org.scijava.java3d.Material;
import org.scijava.java3d.PolygonAttributes;
import org.scijava.java3d.TransparencyAttributes;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.ColoringAttributes;
import org.jogamp.java3d.Geometry;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.LineArray;
import org.jogamp.java3d.LineAttributes;
import org.jogamp.java3d.LineStripArray;
import org.jogamp.java3d.Material;
import org.jogamp.java3d.PolygonAttributes;
import org.jogamp.java3d.TransparencyAttributes;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;

public class CustomLineMesh extends CustomMesh {

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24 changes: 12 additions & 12 deletions src/main/java/customnode/CustomMesh.java
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import java.util.HashMap;
import java.util.List;

import org.scijava.java3d.Appearance;
import org.scijava.java3d.ColoringAttributes;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.GeometryStripArray;
import org.scijava.java3d.Material;
import org.scijava.java3d.PolygonAttributes;
import org.scijava.java3d.Shape3D;
import org.scijava.java3d.TransparencyAttributes;
import org.scijava.java3d.utils.geometry.GeometryInfo;
import org.scijava.java3d.utils.geometry.NormalGenerator;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.ColoringAttributes;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.GeometryStripArray;
import org.jogamp.java3d.Material;
import org.jogamp.java3d.PolygonAttributes;
import org.jogamp.java3d.Shape3D;
import org.jogamp.java3d.TransparencyAttributes;
import org.jogamp.java3d.utils.geometry.GeometryInfo;
import org.jogamp.java3d.utils.geometry.NormalGenerator;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;

import ij.ImagePlus;
import ij.measure.Calibration;
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8 changes: 4 additions & 4 deletions src/main/java/customnode/CustomMeshNode.java
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package customnode;

import org.scijava.java3d.View;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Tuple3d;
import org.jogamp.java3d.View;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;
import org.jogamp.vecmath.Tuple3d;

import ij3d.ContentNode;

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12 changes: 6 additions & 6 deletions src/main/java/customnode/CustomMultiMesh.java
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import java.util.HashMap;
import java.util.List;

import org.scijava.java3d.BranchGroup;
import org.scijava.java3d.Group;
import org.scijava.java3d.View;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Tuple3d;
import org.jogamp.java3d.BranchGroup;
import org.jogamp.java3d.Group;
import org.jogamp.java3d.View;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;
import org.jogamp.vecmath.Tuple3d;

public class CustomMultiMesh extends CustomMeshNode {

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22 changes: 11 additions & 11 deletions src/main/java/customnode/CustomPointMesh.java
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import java.util.Arrays;
import java.util.List;

import org.scijava.java3d.Appearance;
import org.scijava.java3d.ColoringAttributes;
import org.scijava.java3d.Geometry;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.Material;
import org.scijava.java3d.PointArray;
import org.scijava.java3d.PointAttributes;
import org.scijava.java3d.PolygonAttributes;
import org.scijava.java3d.TransparencyAttributes;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.ColoringAttributes;
import org.jogamp.java3d.Geometry;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.Material;
import org.jogamp.java3d.PointArray;
import org.jogamp.java3d.PointAttributes;
import org.jogamp.java3d.PolygonAttributes;
import org.jogamp.java3d.TransparencyAttributes;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;

public class CustomPointMesh extends CustomMesh {

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14 changes: 7 additions & 7 deletions src/main/java/customnode/CustomQuadMesh.java
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import java.util.Arrays;
import java.util.List;

import org.scijava.java3d.Geometry;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.QuadArray;
import org.scijava.java3d.utils.geometry.GeometryInfo;
import org.scijava.java3d.utils.geometry.NormalGenerator;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.jogamp.java3d.Geometry;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.QuadArray;
import org.jogamp.java3d.utils.geometry.GeometryInfo;
import org.jogamp.java3d.utils.geometry.NormalGenerator;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;

public class CustomQuadMesh extends CustomTriangleMesh {

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26 changes: 13 additions & 13 deletions src/main/java/customnode/CustomTransparentTriangleMesh.java
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import java.util.Arrays;
import java.util.List;

import org.scijava.java3d.Appearance;
import org.scijava.java3d.ColoringAttributes;
import org.scijava.java3d.Geometry;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.Material;
import org.scijava.java3d.PolygonAttributes;
import org.scijava.java3d.TransparencyAttributes;
import org.scijava.java3d.TriangleArray;
import org.scijava.java3d.utils.geometry.GeometryInfo;
import org.scijava.java3d.utils.geometry.NormalGenerator;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Color4f;
import org.scijava.vecmath.Point3f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.ColoringAttributes;
import org.jogamp.java3d.Geometry;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.Material;
import org.jogamp.java3d.PolygonAttributes;
import org.jogamp.java3d.TransparencyAttributes;
import org.jogamp.java3d.TriangleArray;
import org.jogamp.java3d.utils.geometry.GeometryInfo;
import org.jogamp.java3d.utils.geometry.NormalGenerator;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Color4f;
import org.jogamp.vecmath.Point3f;

public class CustomTransparentTriangleMesh extends CustomTriangleMesh {

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22 changes: 11 additions & 11 deletions src/main/java/customnode/CustomTriangleMesh.java
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import java.util.Arrays;
import java.util.List;

import org.scijava.java3d.Canvas3D;
import org.scijava.java3d.Geometry;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.Transform3D;
import org.scijava.java3d.TriangleArray;
import org.scijava.java3d.utils.geometry.GeometryInfo;
import org.scijava.java3d.utils.geometry.NormalGenerator;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point2d;
import org.scijava.vecmath.Point3d;
import org.scijava.vecmath.Point3f;
import org.jogamp.java3d.Canvas3D;
import org.jogamp.java3d.Geometry;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.Transform3D;
import org.jogamp.java3d.TriangleArray;
import org.jogamp.java3d.utils.geometry.GeometryInfo;
import org.jogamp.java3d.utils.geometry.NormalGenerator;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point2d;
import org.jogamp.vecmath.Point3d;
import org.jogamp.vecmath.Point3f;

import isosurface.MeshProperties;

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4 changes: 2 additions & 2 deletions src/main/java/customnode/EdgeContraction.java
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import java.util.SortedSet;
import java.util.TreeSet;

import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Vector3f;
import org.jogamp.vecmath.Point3f;
import org.jogamp.vecmath.Vector3f;

import customnode.FullInfoMesh.Edge;
import customnode.FullInfoMesh.Vertex;
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4 changes: 2 additions & 2 deletions src/main/java/customnode/FullInfoMesh.java
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Expand Up @@ -29,8 +29,8 @@
import java.util.List;
import java.util.Set;

import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Vector3f;
import org.jogamp.vecmath.Point3f;
import org.jogamp.vecmath.Vector3f;

public class FullInfoMesh {

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4 changes: 2 additions & 2 deletions src/main/java/customnode/MeshMaker.java
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import java.util.HashMap;
import java.util.List;

import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Vector3f;
import org.jogamp.vecmath.Point3f;
import org.jogamp.vecmath.Vector3f;

import ij.IJ;
import ij3d.Pipe;
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17 changes: 9 additions & 8 deletions src/main/java/customnode/Mesh_Maker.java
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import java.awt.Color;

import org.scijava.java3d.Transform3D;
import org.scijava.vecmath.Color3f;
import ij3d.Utils;
import org.jogamp.java3d.Transform3D;
import org.jogamp.vecmath.Color3f;

import ij.plugin.PlugIn;
import ij3d.Content;
Expand All @@ -47,24 +48,24 @@ public void run(final String arg) {

// define two spheres: an X,Y,Z point with a radius
final double x1 = 10, y1 = 100, z1 = 150, r1 = 20;
final Color3f color1 = new Color3f(Color.pink);
final Color3f color1 = Utils.toColor3f(Color.pink);

final double x2 = 50, y2 = 200, z2 = 40, r2 = 35;
final Color3f color2 = new Color3f(Color.white);
final Color3f color2 = Utils.toColor3f(Color.white);

// define a tube as a polyline in space
final double[] px = new double[] { 100, 230, 320, 400 };
final double[] py = new double[] { 100, 120, 230, 400 };
final double[] pz = new double[] { 100, 200, 300, 400 };
final double[] pr = new double[] { 10, 15, 40, 110 };
final Color3f colort = new Color3f(Color.yellow);
final Color3f colort = Utils.toColor3f(Color.yellow);

// define a second tube as a curving spiral in space
final double[] px2 = new double[200];
final double[] py2 = new double[200];
final double[] pz2 = new double[200];
final double[] pr2 = new double[200];
final Color3f color_t2 = new Color3f(Color.magenta);
final Color3f color_t2 = Utils.toColor3f(Color.magenta);
for (int i = 0; i < px2.length; i++) {
final double angle = Math.toRadians(10 * i);
final double radius = 50 + i * 5;
Expand All @@ -87,8 +88,8 @@ public void run(final String arg) {
univ.addMesh(createTube(px2, py2, pz2, pr2, 12, false), color_t2,
"Tube spiral", 1);
final Content disc1 =
univ.addMesh(createDisc(100, 100, 50, 3, 3, 3, 50, 12), new Color3f(
Color.blue), "Disc 1", 1);
univ.addMesh(createDisc(100, 100, 50, 3, 3, 3, 50, 12),
Utils.toColor3f(Color.blue), "Disc 1", 1);

// Extra:
// Now modify some attributes:
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This commit has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/j3dcore-dependency-in-scijava-39-0-0/106239/3

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