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Update to 3D_Viewer 5.0.0
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@tferr
tferr committed Sep 30, 2024
1 parent 9c6d4a0 commit 1d4badb
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Showing 5 changed files with 29 additions and 33 deletions.
12 changes: 6 additions & 6 deletions pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>38.0.1</version>
<version>39.0.0-SNAPSHOT</version>
<relativePath />
</parent>

Expand Down Expand Up @@ -242,6 +242,10 @@
</dependency>

<!-- ImageJ dependencies -->
<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej-legacy</artifactId>
</dependency>
<dependency>
<groupId>net.imagej</groupId>
<artifactId>ij</artifactId>
Expand Down Expand Up @@ -274,10 +278,6 @@
<groupId>org.scijava</groupId>
<artifactId>batch-processor</artifactId>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>j3dcore</artifactId>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-common</artifactId>
Expand All @@ -295,7 +295,7 @@
<artifactId>script-editor</artifactId>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<groupId>org.jogamp.java3d</groupId>
<artifactId>vecmath</artifactId>
</dependency>
<dependency>
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13 changes: 7 additions & 6 deletions src/main/java/sc/fiji/snt/Path.java
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Expand Up @@ -27,6 +27,7 @@
import ij3d.Content;
import ij3d.Image3DUniverse;
import ij3d.Pipe;
import ij3d.Utils;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.math3.analysis.interpolation.LinearInterpolator;
import org.apache.commons.math3.analysis.polynomials.PolynomialFunction;
Expand All @@ -36,9 +37,9 @@
import org.apache.commons.math3.util.MathUtils;
import org.scijava.util.ColorRGB;
import org.scijava.util.ColorRGBA;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Vector3d;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;
import org.jogamp.vecmath.Vector3d;
import sc.fiji.snt.analysis.PathProfiler;
import sc.fiji.snt.annotation.BrainAnnotation;
import sc.fiji.snt.gui.GuiUtils;
Expand Down Expand Up @@ -2476,7 +2477,7 @@ private boolean is3DViewInvalid() {
public Content addAsLinesTo3DViewer(final Image3DUniverse univ, final Color c,
final ImagePlus colorImage)
{
return addAsLinesTo3DViewer(univ, new Color3f(c), colorImage);
return addAsLinesTo3DViewer(univ, Utils.toColor3f(c), colorImage);
}

@Deprecated
Expand All @@ -2491,7 +2492,7 @@ protected Content addAsLinesTo3DViewer(final Image3DUniverse univ,
public Content addDiscsTo3DViewer(final Image3DUniverse univ, final Color c,
final ImagePlus colorImage)
{
return addDiscsTo3DViewer(univ, new Color3f(c), colorImage);
return addDiscsTo3DViewer(univ, Utils.toColor3f(c), colorImage);
}

@Deprecated
Expand Down Expand Up @@ -2526,7 +2527,7 @@ synchronized public void addTo3DViewer(final Image3DUniverse univ,
{
if (c == null) throw new IllegalArgumentException(
"In addTo3DViewer, Color can no longer be null");
addTo3DViewer(univ, new Color3f(c), colorImage);
addTo3DViewer(univ, Utils.toColor3f(c), colorImage);
}

@Deprecated
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7 changes: 4 additions & 3 deletions src/main/java/sc/fiji/snt/PathAndFillManager.java
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Expand Up @@ -27,6 +27,7 @@
import ij.measure.Calibration;
import ij3d.Content;
import ij3d.UniverseListener;
import ij3d.Utils;
import net.imagej.Dataset;
import net.imagej.axis.Axes;
import net.imglib2.RandomAccessibleInterval;
Expand All @@ -35,9 +36,9 @@
import org.jgrapht.Graphs;
import org.jgrapht.traverse.DepthFirstIterator;
import org.json.JSONException;
import org.scijava.java3d.View;
import org.jogamp.java3d.View;
import org.scijava.util.ColorRGB;
import org.scijava.vecmath.Color3f;
import org.jogamp.vecmath.Color3f;
import org.xml.sax.Attributes;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
Expand Down Expand Up @@ -3637,7 +3638,7 @@ protected void update3DViewerContents() {
final boolean selected = p.isSelected();
final boolean customColor = plugin.displayCustomPathColors && p.hasCustomColor();
Color3f color3f;
if (customColor) color3f = new Color3f(p.getColor());
if (customColor) color3f = Utils.toColor3f(p.getColor());
else if (selected) color3f = plugin.selectedColor3f;
else color3f = plugin.deselectedColor3f;

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2 changes: 1 addition & 1 deletion src/main/java/sc/fiji/snt/QueueJumpingKeyListener.java
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Expand Up @@ -32,7 +32,7 @@

import javax.swing.SwingUtilities;

import org.scijava.vecmath.Point3d;
import org.jogamp.vecmath.Point3d;

import ij.gui.Toolbar;
import ij3d.Content;
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28 changes: 11 additions & 17 deletions src/main/java/sc/fiji/snt/SNT.java
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Expand Up @@ -31,10 +31,7 @@
import ij.process.ColorProcessor;
import ij.process.ImageStatistics;
import ij.process.ShortProcessor;
import ij3d.Content;
import ij3d.ContentConstants;
import ij3d.ContentCreator;
import ij3d.Image3DUniverse;
import ij3d.*;
import io.scif.services.DatasetIOService;
import net.imagej.Dataset;
import net.imagej.display.ColorTables;
Expand Down Expand Up @@ -67,9 +64,9 @@
import org.scijava.convert.ConvertService;
import org.scijava.plugin.Parameter;
import org.scijava.util.ColorRGB;
import org.scijava.vecmath.Color3f;
import org.scijava.vecmath.Point3d;
import org.scijava.vecmath.Point3f;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3d;
import org.jogamp.vecmath.Point3f;
import sc.fiji.snt.event.SNTEvent;
import sc.fiji.snt.event.SNTListener;
import sc.fiji.snt.filter.Frangi;
Expand Down Expand Up @@ -321,10 +318,8 @@ public String toString() {
/* Colors */
private static final Color DEFAULT_SELECTED_COLOR = Color.GREEN;
protected static final Color DEFAULT_DESELECTED_COLOR = Color.MAGENTA;
protected static final Color3f DEFAULT_SELECTED_COLOR3F = new Color3f(
Color.GREEN);
protected static final Color3f DEFAULT_DESELECTED_COLOR3F = new Color3f(
Color.MAGENTA);
protected static final Color3f DEFAULT_SELECTED_COLOR3F = Utils.toColor3f(Color.GREEN);
protected static final Color3f DEFAULT_DESELECTED_COLOR3F = Utils.toColor3f(Color.MAGENTA);
protected Color3f selectedColor3f = DEFAULT_SELECTED_COLOR3F;
protected Color3f deselectedColor3f = DEFAULT_DESELECTED_COLOR3F;
protected Color selectedColor = DEFAULT_SELECTED_COLOR;
Expand Down Expand Up @@ -2387,7 +2382,7 @@ protected void addSphere(final String name, final double x, final double y,
if (use3DViewer) {
final List<Point3f> sphere = customnode.MeshMaker.createSphere(x, y, z,
radius);
univ.addTriangleMesh(sphere, new Color3f(color), name);
univ.addTriangleMesh(sphere, Utils.toColor3f(color), name);
}
}

Expand Down Expand Up @@ -2916,12 +2911,11 @@ public void showCorrespondencesTo(final File tracesFile, final Color c,
final String ballName = univ.getSafeContentName("ball " + done);
final List<Point3f> sphere = customnode.MeshMaker.createSphere(
np.near.x, np.near.y, np.near.z, Math.abs(x_spacing / 2));
univ.addTriangleMesh(sphere, new Color3f(c), ballName);
univ.addTriangleMesh(sphere, Utils.toColor3f(c), ballName);
}
++done;
}
univ.addLineMesh(linePoints, new Color3f(Color.RED), "correspondences",
false);
univ.addLineMesh(linePoints, Utils.toColor3f(Color.RED), "correspondences", false);

for (int pi = 0; pi < pafmTraces.size(); ++pi) {
final Path p = pafmTraces.getPath(pi);
Expand Down Expand Up @@ -3116,13 +3110,13 @@ protected void updateImageContent(final int resamplingFactor) {

protected void setSelectedColor(final Color newColor) {
selectedColor = newColor;
selectedColor3f = new Color3f(newColor);
selectedColor3f = Utils.toColor3f(newColor);
updateTracingViewers(true);
}

protected void setDeselectedColor(final Color newColor) {
deselectedColor = newColor;
deselectedColor3f = new Color3f(newColor);
deselectedColor3f = Utils.toColor3f(newColor);
if (getUI() != null && getUI().recViewer != null) {
getUI().recViewer.setDefaultColor(new ColorRGB(newColor.getRed(), newColor
.getGreen(), newColor.getBlue()));
Expand Down

1 comment on commit 1d4badb

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This commit has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/jaunch-a-new-java-launcher-test-fiji-with-java-21/92058/89

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