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Update for pom-scijava 39.0.0 compatibility
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Update to the pom to avoid duplicate attache sources goal.

Package change for java3d.

Package change for EJML. Update to new class names.

Update to Protobufs API usage.
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@aherbert
aherbert committed Nov 20, 2024
1 parent 2c01a46 commit 550892a
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Showing 38 changed files with 3,748 additions and 414 deletions.
4 changes: 2 additions & 2 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/ArrayColorUpdater.java
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Expand Up @@ -24,8 +24,8 @@

package uk.ac.sussex.gdsc.smlm.ij.ij3d;

import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Color4f;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Color4f;

/**
* Class to create the colour array for a set of vertex coordinates with the same colour.
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4 changes: 2 additions & 2 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/CustomContentHelper.java
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import it.unimi.dsi.fastutil.objects.Object2IntOpenHashMap;
import java.util.List;
import org.apache.commons.lang3.tuple.Pair;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;
import uk.ac.sussex.gdsc.core.utils.LocalList;
import vib.InterpolatedImage;

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30 changes: 15 additions & 15 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/CustomContentInstant.java
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Expand Up @@ -44,21 +44,21 @@
import java.io.PrintStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Enumeration;
import java.util.Iterator;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.scijava.java3d.BranchGroup;
import org.scijava.java3d.Group;
import org.scijava.java3d.Node;
import org.scijava.java3d.OrderedGroup;
import org.scijava.java3d.Switch;
import org.scijava.java3d.Transform3D;
import org.scijava.java3d.TransformGroup;
import org.scijava.java3d.View;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Matrix3f;
import org.scijava.vecmath.Point3d;
import org.scijava.vecmath.Vector3d;
import org.jogamp.java3d.BranchGroup;
import org.jogamp.java3d.Group;
import org.jogamp.java3d.Node;
import org.jogamp.java3d.OrderedGroup;
import org.jogamp.java3d.Switch;
import org.jogamp.java3d.Transform3D;
import org.jogamp.java3d.TransformGroup;
import org.jogamp.java3d.View;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Matrix3f;
import org.jogamp.vecmath.Point3d;
import org.jogamp.vecmath.Vector3d;
import orthoslice.MultiOrthoGroup;
import orthoslice.OrthoGroup;
import surfaceplot.SurfacePlotGroup;
Expand Down Expand Up @@ -192,8 +192,8 @@ public void displayAs(final int type) {
@Override
public void display(final ContentNode node) {
// Remove everything if possible
for (final Enumeration<Node> e = ordered.getAllChildren(); e.hasMoreElements();) {
final Switch s = (Switch) e.nextElement();
for (final Iterator<Node> e = ordered.getAllChildren(); e.hasNext();) {
final Switch s = (Switch) e.next();
s.removeAllChildren();
}
// Remove custom switch objects
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36 changes: 18 additions & 18 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/ItemGeometryGroup.java
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Expand Up @@ -25,24 +25,24 @@
package uk.ac.sussex.gdsc.smlm.ij.ij3d;

import java.util.Arrays;
import org.scijava.java3d.Appearance;
import org.scijava.java3d.Bounds;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.Group;
import org.scijava.java3d.Material;
import org.scijava.java3d.PointArray;
import org.scijava.java3d.PointAttributes;
import org.scijava.java3d.PolygonAttributes;
import org.scijava.java3d.Shape3D;
import org.scijava.java3d.Transform3D;
import org.scijava.java3d.TransparencyAttributes;
import org.scijava.java3d.utils.geometry.Primitive;
import org.scijava.java3d.utils.geometry.Sphere;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Color4f;
import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Vector3d;
import org.scijava.vecmath.Vector3f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.Bounds;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.Group;
import org.jogamp.java3d.Material;
import org.jogamp.java3d.PointArray;
import org.jogamp.java3d.PointAttributes;
import org.jogamp.java3d.PolygonAttributes;
import org.jogamp.java3d.Shape3D;
import org.jogamp.java3d.Transform3D;
import org.jogamp.java3d.TransparencyAttributes;
import org.jogamp.java3d.utils.geometry.Primitive;
import org.jogamp.java3d.utils.geometry.Sphere;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Color4f;
import org.jogamp.vecmath.Point3f;
import org.jogamp.vecmath.Vector3d;
import org.jogamp.vecmath.Vector3f;

/**
* This class represents a list as a number of repeated shapes in the universe. Each item has its
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12 changes: 6 additions & 6 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/ItemGroup.java
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Expand Up @@ -26,12 +26,12 @@

import java.util.Arrays;
import java.util.Objects;
import org.scijava.java3d.Group;
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.Group;
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;

/**
* This class represents a list of repeated shapes in the universe that can be added to a scene. It
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8 changes: 4 additions & 4 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/ItemGroupNode.java
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Expand Up @@ -25,10 +25,10 @@
package uk.ac.sussex.gdsc.smlm.ij.ij3d;

import ij3d.ContentNode;
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;

/**
* Node to allow display of ItemGroup content.
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12 changes: 6 additions & 6 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/ItemIndexedTriangleMesh.java
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Expand Up @@ -26,12 +26,12 @@

import customnode.CustomIndexedTriangleMesh;
import java.util.Objects;
import org.scijava.java3d.Geometry;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.IndexedTriangleArray;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Vector3f;
import org.jogamp.java3d.Geometry;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.IndexedTriangleArray;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;
import org.jogamp.vecmath.Vector3f;
import uk.ac.sussex.gdsc.core.utils.SimpleArrayUtils;

/**
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34 changes: 17 additions & 17 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/ItemMesh.java
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Expand Up @@ -29,23 +29,23 @@
import java.util.Arrays;
import java.util.Objects;
import java.util.logging.Level;
import org.scijava.java3d.Appearance;
import org.scijava.java3d.ColoringAttributes;
import org.scijava.java3d.Geometry;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.GeometryStripArray;
import org.scijava.java3d.GeometryUpdater;
import org.scijava.java3d.IndexedGeometryArray;
import org.scijava.java3d.IndexedGeometryStripArray;
import org.scijava.java3d.IndexedPointArray;
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.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.GeometryStripArray;
import org.jogamp.java3d.GeometryUpdater;
import org.jogamp.java3d.IndexedGeometryArray;
import org.jogamp.java3d.IndexedGeometryStripArray;
import org.jogamp.java3d.IndexedPointArray;
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.Color4f;
import org.jogamp.vecmath.Point3f;
import uk.ac.sussex.gdsc.core.data.NotImplementedException;
import uk.ac.sussex.gdsc.core.ij.ImageJPluginLoggerHelper;
import uk.ac.sussex.gdsc.core.utils.BitFlagUtils;
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16 changes: 8 additions & 8 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/ItemPointMesh.java
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Expand Up @@ -27,14 +27,14 @@
import customnode.CustomPointMesh;
import java.util.Arrays;
import java.util.List;
import org.scijava.java3d.Appearance;
import org.scijava.java3d.Geometry;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.GeometryUpdater;
import org.scijava.java3d.PointArray;
import org.scijava.java3d.PointAttributes;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.Geometry;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.GeometryUpdater;
import org.jogamp.java3d.PointArray;
import org.jogamp.java3d.PointAttributes;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;

/**
* Create an object to represent a set of points.
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4 changes: 2 additions & 2 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/ItemShape.java
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Expand Up @@ -24,8 +24,8 @@

package uk.ac.sussex.gdsc.smlm.ij.ij3d;

import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;

/**
* Interface for shape objects that represent a set of items.
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20 changes: 10 additions & 10 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/ItemTriangleMesh.java
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Expand Up @@ -27,16 +27,16 @@
import customnode.CustomTriangleMesh;
import java.util.Arrays;
import java.util.Objects;
import org.scijava.java3d.Appearance;
import org.scijava.java3d.Geometry;
import org.scijava.java3d.GeometryArray;
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.Point3f;
import org.scijava.vecmath.Vector3f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.Geometry;
import org.jogamp.java3d.GeometryArray;
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.Point3f;
import org.jogamp.vecmath.Vector3f;
import uk.ac.sussex.gdsc.core.logging.NullTrackProgress;
import uk.ac.sussex.gdsc.core.logging.Ticker;
import uk.ac.sussex.gdsc.core.logging.TrackProgress;
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12 changes: 6 additions & 6 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/OrderedItemGeometryGroup.java
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Expand Up @@ -24,12 +24,12 @@

package uk.ac.sussex.gdsc.smlm.ij.ij3d;

import org.scijava.java3d.Appearance;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.Group;
import org.scijava.java3d.OrderedGroup;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.Group;
import org.jogamp.java3d.OrderedGroup;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;

/**
* This class represents a list as a number of repeated shapes in the universe. The shape is defined
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16 changes: 8 additions & 8 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/ReferenceItemMesh.java
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Expand Up @@ -25,14 +25,14 @@
package uk.ac.sussex.gdsc.smlm.ij.ij3d;

import java.util.Arrays;
import org.scijava.java3d.Appearance;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.GeometryStripArray;
import org.scijava.java3d.IndexedGeometryArray;
import org.scijava.java3d.IndexedGeometryStripArray;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Color4f;
import org.scijava.vecmath.Point3f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.GeometryStripArray;
import org.jogamp.java3d.IndexedGeometryArray;
import org.jogamp.java3d.IndexedGeometryStripArray;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Color4f;
import org.jogamp.vecmath.Point3f;

/**
* Use a mesh object to represent a set of points. The object is duplicated, scaled and translated
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28 changes: 14 additions & 14 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/Shape3DHelper.java
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Expand Up @@ -29,20 +29,20 @@
import java.util.Arrays;
import java.util.List;
import org.apache.commons.lang3.tuple.Pair;
import org.scijava.java3d.Appearance;
import org.scijava.java3d.ColoringAttributes;
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.Shape3D;
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.Point3f;
import org.scijava.vecmath.Vector3f;
import org.jogamp.java3d.Appearance;
import org.jogamp.java3d.ColoringAttributes;
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.Shape3D;
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.Point3f;
import org.jogamp.vecmath.Vector3f;
import uk.ac.sussex.gdsc.core.utils.LocalList;
import uk.ac.sussex.gdsc.smlm.data.NamedObject;

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12 changes: 6 additions & 6 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/TransparentItemPointMesh.java
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Expand Up @@ -26,12 +26,12 @@

import java.util.Arrays;
import java.util.List;
import org.scijava.java3d.Geometry;
import org.scijava.java3d.GeometryArray;
import org.scijava.java3d.PointArray;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Color4f;
import org.scijava.vecmath.Point3f;
import org.jogamp.java3d.Geometry;
import org.jogamp.java3d.GeometryArray;
import org.jogamp.java3d.PointArray;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Color4f;
import org.jogamp.vecmath.Point3f;

/**
* Create an object to represent a set of points.
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2 changes: 1 addition & 1 deletion gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/TransparentItemShape.java
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Expand Up @@ -24,7 +24,7 @@

package uk.ac.sussex.gdsc.smlm.ij.ij3d;

import org.scijava.vecmath.Color4f;
import org.jogamp.vecmath.Color4f;

/**
* Interface for shape objects that represent a set of items to have transparent colours.
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18 changes: 9 additions & 9 deletions gdsc-smlm-ij/src/main/java/uk/ac/sussex/gdsc/smlm/ij/ij3d/TransparentItemTriangleMesh.java
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Expand Up @@ -25,15 +25,15 @@
package uk.ac.sussex.gdsc.smlm.ij.ij3d;

import java.util.Arrays;
import org.scijava.java3d.Geometry;
import org.scijava.java3d.GeometryArray;
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.scijava.vecmath.Vector3f;
import org.jogamp.java3d.Geometry;
import org.jogamp.java3d.GeometryArray;
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;
import org.jogamp.vecmath.Vector3f;
import uk.ac.sussex.gdsc.core.logging.TrackProgress;

/**
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