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WIP: draft pull request #1

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14 changes: 14 additions & 0 deletions .classpath
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<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
<attributes>
<attribute name="module" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="src" path=""/>
<classpathentry kind="lib" path="./jars/vecmath-1.6.0-scijava-2.jar"/>
<classpathentry kind="lib" path="./jars/3D_Viewer-4.0.5.jar"/>
<classpathentry kind="lib" path="./jars/ij-1.54f.jar"/>
<classpathentry kind="lib" path="./jars/SNT-4.2.2-45764a7.jar"/>
<classpathentry kind="output" path=""/>
</classpath>
17 changes: 17 additions & 0 deletions .project
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<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>tubularity</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>
5 changes: 0 additions & 5 deletions FijiITKInterface/OOFTubularityMeasure_Plugin.java
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Expand Up @@ -12,16 +12,11 @@
import ij.gui.ImageCanvas;

import javax.swing.*;
import javax.swing.event.*;
import java.awt.*;
import java.awt.event.*;
import java.util.*;
import java.io.*;


import ij.measure.Calibration;

import ij3d.*;

public class OOFTubularityMeasure_Plugin implements MouseListener, MouseMotionListener, PlugIn {

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4 changes: 2 additions & 2 deletions FijiITKInterface/TubularGeodesics.java
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@@ -1,8 +1,8 @@
package FijiITKInterface;

import fiji.jni.LibraryLoader;
import tracing.PathResult;
import tracing.TubularGeodesicsTracer;
import sc.fiji.snt.tracing.PathResult;
import sc.fiji.snt.tracing.TubularGeodesicsTracer;

public class TubularGeodesics extends LibraryLoader {

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45 changes: 20 additions & 25 deletions FijiITKInterface/TubularGeodesics_Plugin.java
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@@ -1,35 +1,30 @@
package FijiITKInterface;

import java.awt.Color;
import java.awt.Point;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.util.ArrayList;

import javax.swing.JPanel;

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

import ij.IJ;
import ij.plugin.PlugIn;
import ij.ImagePlus;
import ij.ImageStack;
import ij.process.ByteProcessor;
import ij.process.FloatProcessor;
import ij.io.FileInfo;
import ij.gui.GenericDialog;
import ij.gui.ImageCanvas;

import javax.swing.*;
import javax.swing.event.*;
import java.awt.*;
import java.awt.geom.Point2D;
import java.awt.event.*;
import java.util.*;
import java.io.*;

import java.lang.Math;

import com.sun.j3d.utils.applet.MainFrame;
import com.sun.j3d.utils.universe.*;
import com.sun.j3d.utils.geometry.*;
import javax.media.j3d.*;
import javax.vecmath.*;
import javax.media.j3d.ColoringAttributes;

import ij.io.FileInfo;
import ij.measure.Calibration;

import ij3d.*;
import ij.plugin.PlugIn;
import ij.process.ByteProcessor;
import ij.process.FloatProcessor;
import ij3d.Content;
import ij3d.Image3DUniverse;
import ij3d.Pipe;

public class TubularGeodesics_Plugin implements MouseListener, MouseMotionListener, PlugIn {

Expand Down Expand Up @@ -146,7 +141,7 @@ public void run( String ignored ) {

// Create a universe and show it
univ = new Image3DUniverse();
univ.getViewingPlatform().setNominalViewingTransform();
//univ.getViewingPlatform().setNominalViewingTransform();
univ.show();

// Add the image as an isosurface
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2 changes: 1 addition & 1 deletion OOFTubularityMeasure.config
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Plugins, "MultiScale Oriented-Flux Tubularity Measure", FijiITKInterface.OOFTubularityMeasure_Plugin
Plugins>Segmentation, "MultiScale Oriented-Flux Tubularity Measure", FijiITKInterface.OOFTubularityMeasure_Plugin
Binary file added jars/3D_Viewer-4.0.5.jar
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Binary file added jars/vecmath-1.6.0-scijava-2.jar
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