preparing release version. Bug fix in furrow interception code.

README.md

@@ -1,6 +1,15 @@
 [![Build Status](https://github.com/PaluchLabUCL/DeformingMesh3D/actions/workflows/build.yml/badge.svg)](https://github.com/PaluchLabUCL/DeformingMesh3D/actions/workflows/build.yml)
 
 # DM3D
+
+##
+**This is being moved. This is the original version that was published. I've moved it to 
+a version 1.0.x to signify feature complete release. Development will continue at 
+[Living Technologies](https://github.com/Living-Technologies)**
+
+This one will remain at the update site and might receive bug fixes. Future features
+will be found at a new update site.
+
 ThreeD image segmentation algorithm, for roundish cells.
 
 The latest documentation can be found at:
@@ -35,6 +44,13 @@ which can be found in "plugins"->"PL_Mesh3D"->"Deforming Mesh 3D", and JFilament
 This includes guides for using the plugin, and javadoc for using the plugin via scripting.
 
 # Changes
+
+1.0.0
+- Furrow controls in the 3D Canvas window.
+- Tracking controls in 3D canvas window
+- guessMesh api has more options
+- BUG FIX: there was a condition error in the spit mesh algorithm
+
 0.9.8
 - Changed volume calculation technique.
 - Added a way to create training labels from a labelled image.

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>paluchlab</groupId>
 	<artifactId>Deformable_Mesh</artifactId>
-	<version>0.9.11-SNAPSHOT</version>
+	<version>1.0.0</version>
 
 	<name>Deforming Mesh</name>
 	<description>Triangulated surface for deforming in 3D.</description>

src/main/java/deformablemesh/Deforming3DMesh_Plugin.java

@@ -43,7 +43,7 @@
  * Created by msmith on 12/1/15.
  */
 public class Deforming3DMesh_Plugin implements PlugInFilter {
-    public static final String version = "0.9.7";
+    public static final String version = "1.0.0 Last One Targeting Eight";
     public static SegmentationController createDeformingMeshApplication(){
 
         MeshFrame3D mf3d = new MeshFrame3D();

src/main/java/deformablemesh/geometry/Box3D.java

@@ -28,6 +28,7 @@
 import deformablemesh.util.Vector3DOps;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
@@ -185,6 +186,11 @@ public double getVolume() {
     public double[] getCenter() {
         return Vector3DOps.average(high, low);
     }
+
+    @Override
+    public String toString(){
+        return "Box3D: " + Arrays.toString(low) + " :: " + Arrays.toString(high);
+    }
 }
 
 class AxisPlane implements Interceptable{
@@ -220,4 +226,5 @@ public List<Intersection> getIntersections(double[] origin, double[] direction)
 
         return Collections.unmodifiableList(sections);
     }
+
 }

src/main/java/deformablemesh/geometry/Furrow3D.java

@@ -492,8 +492,10 @@ public List<Intersection> getIntersections(double[] origin, double[] direction)
         double toPlane = Vector3DOps.dot(r, normal);
 
         double dot = Vector3DOps.dot(direction, normal);
-        double t = dot<0 ? 1 + dot : 1 - dot;
-        if(t < 1e-6 ){
+        //Line has to be going towards the plan and against the normal.
+
+        final double tolerance = 1e-6;
+        if(dot < 0 ? dot > - tolerance : dot < tolerance ){
             //parallel to normal.
             return new ArrayList<>();
         }

src/test/java/deformablemesh/geometry/SplittingSpheres.java

@@ -0,0 +1,75 @@
+package deformablemesh.geometry;
+
+import deformablemesh.meshview.MeshFrame3D;
+import deformablemesh.util.Vector3DOps;
+
+import java.awt.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+public class SplittingSpheres {
+    public static void main(String[] args){
+        MeshFrame3D mesh = new MeshFrame3D();
+        mesh.showFrame(true);
+        mesh.addLights();
+        //create a spherical mesh
+        double[] center = new double[]{0, 0, 0};
+        DeformableMesh3D m = RayCastMesh.sphereRayCastMesh(2);
+        m.translate(center);
+        m.scale(0.025, center);
+        //place the furrow at the center
+        Furrow3D f = new Furrow3D(center, Vector3DOps.nzhat);
+        List<DeformableMesh3D> meshes = f.sliceMesh(m);
+        Furrow3D reversed = new Furrow3D(f.cm,
+                new double[]{-f.normal[0], -f.normal[1], -f.normal[2]}
+        );
+        List<DeformableMesh3D> splits = new ArrayList<>();
+        Color[] colors = {new Color(255, 0, 0, 79), new Color(0,0, 255, 79)};
+        int ci = 0;
+
+        InterceptingMesh3D im = new InterceptingMesh3D(m);
+
+
+        List<List<Node3D>> nodes = f.splitNodes(m.nodes);
+
+        for(List<Node3D> side: nodes){
+            List<Interceptable> interceptables = Arrays.asList(reversed, f, im);
+            if(side.size()==0){
+                continue;
+            }
+            double[] c = new double[3];
+            for(Node3D n: side){
+                double[] xyz = n.getCoordinates();
+                c[0] += xyz[0];
+                c[1] += xyz[1];
+                c[2] += xyz[2];
+            }
+            c[0] = c[0]/side.size();
+            c[1] = c[1]/side.size();
+            c[2] = c[2]/side.size();
+            DeformableMesh3D a = RayCastMesh.rayCastMesh(interceptables, c, 2);
+            splits.add(a);
+        }
+
+        //split it
+        //BUG the split mesh has a point across the midline.
+        DeformableMesh3D a = splits.get(0);
+        DeformableMesh3D b = splits.get(1);
+        System.out.println(a.getBoundingBox());
+        System.out.println(b.getBoundingBox());
+
+        a.setColor(Color.RED);
+        a.setShowSurface(true);
+        a.create3DObject();
+        b.setColor(Color.BLUE);
+        b.setShowSurface(true);
+        b.create3DObject();
+        mesh.addDataObject(b.data_object);
+        mesh.addDataObject(a.data_object);
+        f.create3DObject();
+        mesh.addDataObject(f.getDataObject());
+
+
+    }
+}