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Update to 3D Viewer 5.0.0 + Java 3D 1.7.2
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And adjust for backwards-incompatible API changes.

And bump the major version from 3 to 4 due to API signature breakages
in this component -- e.g. Test_Java3D#createSceneGraph() now returns
org.jogamp.java3d.BranchGroup, not org.scijava.java3d.BranchGroup.
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@ctrueden
ctrueden committed Sep 28, 2024
1 parent dca31af commit 3c1c86e
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Showing 7 changed files with 79 additions and 80 deletions.
16 changes: 9 additions & 7 deletions pom.xml
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Expand Up @@ -5,13 +5,13 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>33.2.0</version>
<version>38.0.1</version>
<relativePath />
</parent>

<groupId>sc.fiji</groupId>
<artifactId>VIB_</artifactId>
<version>3.0.5-SNAPSHOT</version>
<version>4.0.0-SNAPSHOT</version>

<name>VIB</name>
<description>VIB plugin for Fiji.</description>
Expand Down Expand Up @@ -108,6 +108,8 @@

<!-- NB: Deploy releases to the SciJava Maven repository. -->
<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>

<_3D_Viewer.version>5.0.0</_3D_Viewer.version>
</properties>

<repositories>
Expand Down Expand Up @@ -144,15 +146,15 @@

<!-- Java 3D dependencies -->
<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>

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26 changes: 13 additions & 13 deletions src/main/java/MC_Test.java
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Expand Up @@ -19,7 +19,6 @@
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
import org.scijava.java3d.utils.geometry.Sphere;

import ij.ImagePlus;
import ij.ImageStack;
Expand All @@ -35,17 +34,18 @@
import java.awt.event.AdjustmentListener;
import java.util.List;

import org.scijava.java3d.Appearance;
import org.scijava.java3d.BranchGroup;
import org.scijava.java3d.ColoringAttributes;
import org.scijava.java3d.PolygonAttributes;
import org.scijava.java3d.QuadArray;
import org.scijava.java3d.Shape3D;
import org.scijava.java3d.Transform3D;
import org.scijava.java3d.TransformGroup;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Vector3f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.BranchGroup;
import org.jogamp.java3d.ColoringAttributes;
import org.jogamp.java3d.PolygonAttributes;
import org.jogamp.java3d.QuadArray;
import org.jogamp.java3d.Shape3D;
import org.jogamp.java3d.Transform3D;
import org.jogamp.java3d.TransformGroup;
import org.jogamp.java3d.utils.geometry.Sphere;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;
import org.jogamp.vecmath.Vector3f;

import marchingcubes.MCCube;

Expand All @@ -55,7 +55,7 @@ public class MC_Test implements PlugIn {
private ImagePlus image;
private byte[][] data;

private static final Color3f GREY = new Color3f(Color.LIGHT_GRAY);
private static final Color3f GREY = new Color3f(0.753f, 0.753f, 0.753f);
private static final Color3f RED = new Color3f(1f, 0, 0);

@Override
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19 changes: 9 additions & 10 deletions src/main/java/Test_Java3D.java
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Expand Up @@ -19,8 +19,6 @@
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
import org.scijava.java3d.utils.geometry.ColorCube;
import org.scijava.java3d.utils.universe.SimpleUniverse;

import ij.gui.GenericDialog;
import ij.plugin.PlugIn;
Expand All @@ -29,14 +27,15 @@
import java.awt.Dimension;
import java.awt.Panel;

import org.scijava.java3d.Alpha;
import org.scijava.java3d.BoundingSphere;
import org.scijava.java3d.BranchGroup;
import org.scijava.java3d.Canvas3D;
import org.scijava.java3d.RotationInterpolator;
import org.scijava.java3d.Transform3D;
import org.scijava.java3d.TransformGroup;

import org.jogamp.java3d.Alpha;
import org.jogamp.java3d.BoundingSphere;
import org.jogamp.java3d.BranchGroup;
import org.jogamp.java3d.Canvas3D;
import org.jogamp.java3d.RotationInterpolator;
import org.jogamp.java3d.Transform3D;
import org.jogamp.java3d.TransformGroup;
import org.jogamp.java3d.utils.geometry.ColorCube;
import org.jogamp.java3d.utils.universe.SimpleUniverse;

public class Test_Java3D implements PlugIn {

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4 changes: 2 additions & 2 deletions src/main/java/marchingcubes/ExportMesh_.java
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Expand Up @@ -45,8 +45,8 @@
import java.util.Iterator;
import java.util.List;

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

public class ExportMesh_ implements PlugIn {

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45 changes: 22 additions & 23 deletions src/main/java/textureByRef/Texture_By_Ref.java
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Expand Up @@ -21,8 +21,6 @@
*/
package textureByRef;

import org.scijava.java3d.utils.pickfast.PickCanvas;

import ij.IJ;
import ij.ImageListener;
import ij.ImagePlus;
Expand All @@ -44,27 +42,28 @@
import java.awt.image.SampleModel;
import java.awt.image.WritableRaster;

import org.scijava.java3d.Appearance;
import org.scijava.java3d.BranchGroup;
import org.scijava.java3d.ColoringAttributes;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.ImageComponent;
import org.scijava.java3d.ImageComponent2D;
import org.scijava.java3d.Material;
import org.scijava.java3d.PickInfo;
import org.scijava.java3d.PolygonAttributes;
import org.scijava.java3d.QuadArray;
import org.scijava.java3d.RenderingAttributes;
import org.scijava.java3d.Shape3D;
import org.scijava.java3d.TexCoordGeneration;
import org.scijava.java3d.Texture;
import org.scijava.java3d.Texture2D;
import org.scijava.java3d.TextureAttributes;
import org.scijava.java3d.TransparencyAttributes;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3d;
import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Vector4f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.BranchGroup;
import org.jogamp.java3d.ColoringAttributes;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.ImageComponent;
import org.jogamp.java3d.ImageComponent2D;
import org.jogamp.java3d.Material;
import org.jogamp.java3d.PickInfo;
import org.jogamp.java3d.PolygonAttributes;
import org.jogamp.java3d.QuadArray;
import org.jogamp.java3d.RenderingAttributes;
import org.jogamp.java3d.Shape3D;
import org.jogamp.java3d.TexCoordGeneration;
import org.jogamp.java3d.Texture;
import org.jogamp.java3d.Texture2D;
import org.jogamp.java3d.TextureAttributes;
import org.jogamp.java3d.TransparencyAttributes;
import org.jogamp.java3d.utils.pickfast.PickCanvas;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3d;
import org.jogamp.vecmath.Point3f;
import org.jogamp.vecmath.Vector4f;

public class Texture_By_Ref implements PlugInFilter,
ImageListener,
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45 changes: 22 additions & 23 deletions src/main/java/textureByRef/Texture_By_Ref_col.java
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Expand Up @@ -21,8 +21,6 @@
*/
package textureByRef;

import org.scijava.java3d.utils.pickfast.PickCanvas;

import ij.IJ;
import ij.ImageListener;
import ij.ImagePlus;
Expand All @@ -46,27 +44,28 @@
import java.awt.image.Raster;
import java.awt.image.WritableRaster;

import org.scijava.java3d.Appearance;
import org.scijava.java3d.BranchGroup;
import org.scijava.java3d.ColoringAttributes;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.ImageComponent;
import org.scijava.java3d.ImageComponent2D;
import org.scijava.java3d.Material;
import org.scijava.java3d.PickInfo;
import org.scijava.java3d.PolygonAttributes;
import org.scijava.java3d.QuadArray;
import org.scijava.java3d.RenderingAttributes;
import org.scijava.java3d.Shape3D;
import org.scijava.java3d.TexCoordGeneration;
import org.scijava.java3d.Texture;
import org.scijava.java3d.Texture2D;
import org.scijava.java3d.TextureAttributes;
import org.scijava.java3d.TransparencyAttributes;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3d;
import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Vector4f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.BranchGroup;
import org.jogamp.java3d.ColoringAttributes;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.ImageComponent;
import org.jogamp.java3d.ImageComponent2D;
import org.jogamp.java3d.Material;
import org.jogamp.java3d.PickInfo;
import org.jogamp.java3d.PolygonAttributes;
import org.jogamp.java3d.QuadArray;
import org.jogamp.java3d.RenderingAttributes;
import org.jogamp.java3d.Shape3D;
import org.jogamp.java3d.TexCoordGeneration;
import org.jogamp.java3d.Texture;
import org.jogamp.java3d.Texture2D;
import org.jogamp.java3d.TextureAttributes;
import org.jogamp.java3d.TransparencyAttributes;
import org.jogamp.java3d.utils.pickfast.PickCanvas;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3d;
import org.jogamp.vecmath.Point3f;
import org.jogamp.vecmath.Vector4f;

public class Texture_By_Ref_col implements PlugInFilter,
ImageListener,
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4 changes: 2 additions & 2 deletions src/main/java/vib/Extract_Surface.java
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Expand Up @@ -38,10 +38,10 @@
import math3d.NormalEstimator;
import math3d.Point3d;

import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;
import org.scijava.util.DoubleArray;
import org.scijava.util.IntArray;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;

import ij.IJ;
import ij.ImagePlus;
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