diff --git a/.gitignore b/.gitignore
index b0a9905575783f18d92dd5f505a52d187802980d..57f16fb67c1b1589981416b323d7a9debc728665 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,8 +1,41 @@
-.idea/
-.settings/
-build/
+/build*
+/workspace
+setting.xml
+release/
target/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
*.iml
+*.ipr
+
+### Eclipse ###
+.apt_generated
.classpath
+.factorypath
.project
-**/.DS_Store
\ No newline at end of file
+.settings
+.springBeans
+.sts4-cache
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+
+### Mac OS ###
+**/.DS_Store
+Icon?
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index b5454c536209a709a3ea1bebe7dd073fa0cb9d6e..b3cfb94422f755cb869fe48c57a7dd7fbbeba45c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,13 +7,11 @@
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
- <version>2.2.0</version>
+ <version>3.0.0-a.1</version>
</parent>
<artifactId>quickhull</artifactId>
- <version>2.0.0</version>
-
- <packaging>jar</packaging>
+ <version>2.0.0-a.1</version>
<name>QuickHull</name>
<description>
@@ -30,8 +28,7 @@
<repositories>
<repository>
<id>icy</id>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
</repository>
</repositories>
-
</project>
\ No newline at end of file
diff --git a/src/main/java/plugins/adufour/quickhull/Face.java b/src/main/java/plugins/adufour/quickhull/Face.java
index 042eea7dd17d6ed255403726a30c6fbff8f6c7e2..2afe11a2eb3e0d862f81a5f8308aa640a39e9a39 100644
--- a/src/main/java/plugins/adufour/quickhull/Face.java
+++ b/src/main/java/plugins/adufour/quickhull/Face.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,6 +18,8 @@
package plugins.adufour.quickhull;
+import org.jetbrains.annotations.NotNull;
+
import javax.vecmath.Vector3d;
/**
@@ -30,7 +32,7 @@ import javax.vecmath.Vector3d;
*
* @author John E. Lloyd, Fall 2004
*/
-class Face {
+public class Face {
HalfEdge he0;
private final Vector3d normal;
double area;
@@ -49,7 +51,7 @@ class Face {
Vertex outside;
- public void computeCentroid(final Vector3d centroid) {
+ public void computeCentroid(final @NotNull Vector3d centroid) {
centroid.set(0, 0, 0);
HalfEdge he = he0;
do {
@@ -95,7 +97,7 @@ class Face {
}
}
- public void computeNormal(final Vector3d normal) {
+ public void computeNormal(final @NotNull Vector3d normal) {
HalfEdge he1 = he0.next;
HalfEdge he2 = he1.next;
@@ -153,7 +155,7 @@ class Face {
planeOffset = normal.dot(centroid);
}
- public static Face createTriangle(final Vertex v0, final Vertex v1, final Vertex v2) {
+ public static @NotNull Face createTriangle(final Vertex v0, final Vertex v1, final Vertex v2) {
return createTriangle(v0, v1, v2, 0);
}
@@ -164,7 +166,7 @@ class Face {
* @param v1 second vertex
* @param v2 third vertex
*/
- public static Face createTriangle(final Vertex v0, final Vertex v1, final Vertex v2, final double minArea) {
+ public static @NotNull Face createTriangle(final Vertex v0, final Vertex v1, final Vertex v2, final double minArea) {
final Face face = new Face();
final HalfEdge he0 = new HalfEdge(v0, face);
final HalfEdge he1 = new HalfEdge(v1, face);
@@ -184,7 +186,7 @@ class Face {
return face;
}
- public static Face create(final Vertex[] vtxArray, final int[] indices) {
+ public static @NotNull Face create(final Vertex[] vtxArray, final int @NotNull [] indices) {
final Face face = new Face();
HalfEdge hePrev = null;
for (final int j : indices) {
@@ -261,7 +263,7 @@ class Face {
* @param p the point
* @return distance from the point to the plane
*/
- public double distanceToPlane(final Vector3d p) {
+ public double distanceToPlane(final @NotNull Vector3d p) {
return normal.x * p.x + normal.y * p.y + normal.z * p.z - planeOffset;
}
@@ -297,7 +299,7 @@ class Face {
return s.toString();
}
- public void getVertexIndices(final int[] idxs) {
+ public void getVertexIndices(final int @NotNull [] idxs) {
HalfEdge he = he0;
int i = 0;
do {
@@ -306,7 +308,7 @@ class Face {
} while (he != he0);
}
- private Face connectHalfEdges(final HalfEdge hedgePrev, final HalfEdge hedge) {
+ private Face connectHalfEdges(final @NotNull HalfEdge hedgePrev, final @NotNull HalfEdge hedge) {
Face discardedFace = null;
if (hedgePrev.oppositeFace() == hedge.oppositeFace()) { // then there is a redundant edge that we can get rid off
@@ -389,7 +391,7 @@ class Face {
}
- public int mergeAdjacentFace(final HalfEdge hedgeAdj, final Face[] discarded) {
+ public int mergeAdjacentFace(final @NotNull HalfEdge hedgeAdj, final Face @NotNull [] discarded) {
final Face oppFace = hedgeAdj.oppositeFace();
int numDiscarded = 0;
@@ -481,6 +483,5 @@ class Face {
for (Face face = face0; face != null; face = face.next) {
face.checkConsistency();
}
-
}
}
diff --git a/src/main/java/plugins/adufour/quickhull/FaceList.java b/src/main/java/plugins/adufour/quickhull/FaceList.java
index 1713a1210f3e7f2a95204e28ae8d411044df3dac..be6d7b2bd91077ffbd2675d079c2af26a152256b 100644
--- a/src/main/java/plugins/adufour/quickhull/FaceList.java
+++ b/src/main/java/plugins/adufour/quickhull/FaceList.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -21,7 +21,7 @@ package plugins.adufour.quickhull;
/**
* Maintains a single-linked list of faces for use by QuickHull3D
*/
-class FaceList {
+public class FaceList {
private Face head;
private Face tail;
diff --git a/src/main/java/plugins/adufour/quickhull/HalfEdge.java b/src/main/java/plugins/adufour/quickhull/HalfEdge.java
index 1290f57b48b741c00bddc7dfb2856f9357f303a8..e31d21e232f13a407a5bb9027cccf15c320cf6e9 100644
--- a/src/main/java/plugins/adufour/quickhull/HalfEdge.java
+++ b/src/main/java/plugins/adufour/quickhull/HalfEdge.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,6 +18,9 @@
package plugins.adufour.quickhull;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
+
import javax.vecmath.Vector3d;
/**
@@ -25,7 +28,7 @@ import javax.vecmath.Vector3d;
*
* @author John E. Lloyd, Fall 2004
*/
-class HalfEdge {
+public class HalfEdge {
/**
* The vertex associated with the head of this half-edge.
*/
@@ -58,11 +61,13 @@ class HalfEdge {
* @param v head vertex
* @param f left-hand triangular face
*/
+ @Contract(pure = true)
public HalfEdge(final Vertex v, final Face f) {
vertex = v;
face = f;
}
+ @Contract(pure = true)
public HalfEdge() {
}
@@ -125,7 +130,7 @@ class HalfEdge {
*
* @param edge opposite half-edge
*/
- public void setOpposite(final HalfEdge edge) {
+ public void setOpposite(final @NotNull HalfEdge edge) {
opposite = edge;
edge.opposite = this;
}
diff --git a/src/main/java/plugins/adufour/quickhull/QuickHull.java b/src/main/java/plugins/adufour/quickhull/QuickHull.java
index 1be8ced11f2604d7018236dd257eade51d8375f9..5277b47d54fe474a364af75cb1d45163c1c0ec1f 100644
--- a/src/main/java/plugins/adufour/quickhull/QuickHull.java
+++ b/src/main/java/plugins/adufour/quickhull/QuickHull.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,8 +18,10 @@
package plugins.adufour.quickhull;
-import icy.plugin.abstract_.Plugin;
-import icy.plugin.interface_.PluginLibrary;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.extension.plugin.interface_.PluginLibrary;
/**
* Main class of the QuickHull library for Icy
@@ -29,6 +31,8 @@ import icy.plugin.interface_.PluginLibrary;
*
* @author Alexandre Dufour
*/
+@IcyPluginName("QuickHull")
+@IcyPluginIcon(path = "/quickhull.png")
public class QuickHull extends Plugin implements PluginLibrary {
}
diff --git a/src/main/java/plugins/adufour/quickhull/QuickHull2D.java b/src/main/java/plugins/adufour/quickhull/QuickHull2D.java
index 2f2542b8f2f76c693bed3e76cf24335e41fe4866..df97cf9c6e539cf00dfbe39ac59f780eb4ef22b4 100644
--- a/src/main/java/plugins/adufour/quickhull/QuickHull2D.java
+++ b/src/main/java/plugins/adufour/quickhull/QuickHull2D.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,21 +18,24 @@
package plugins.adufour.quickhull;
-import icy.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.jetbrains.annotations.NotNull;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.List;
+@IcyPluginName("QuickHull 2D")
public class QuickHull2D extends Plugin {
- public static List<Point2D> computeConvexEnvelope(final List<Point2D> points) {
+ public static @NotNull List<Point2D> computeConvexEnvelope(final @NotNull List<Point2D> points) {
final ArrayList<Point2D> envelope = new ArrayList<>();
// find two points: right (bottom) and left (top)
- Point2D l = points.get(0);
- Point2D r = points.get(0);
+ Point2D l = points.getFirst();
+ Point2D r = points.getFirst();
for (int i = 1; i < points.size(); i++) {
final Point2D p = points.get(i);
@@ -69,8 +72,8 @@ public class QuickHull2D extends Plugin {
return envelope;
}
- private static void quickhull(final ArrayList<Point2D> envelope, final Point2D a, final Point2D b, final ArrayList<Point2D> neighbors) {
- if (neighbors.size() == 0) return;
+ private static void quickhull(final ArrayList<Point2D> envelope, final Point2D a, final Point2D b, final @NotNull ArrayList<Point2D> neighbors) {
+ if (neighbors.isEmpty()) return;
final Point2D c = farthestpoint(a, b, neighbors);
@@ -95,7 +98,7 @@ public class QuickHull2D extends Plugin {
quickhull(envelope, c, b, al2);
}
- private static Point2D farthestpoint(final Point2D a, final Point2D b, final ArrayList<Point2D> points) {
+ private static Point2D farthestpoint(final Point2D a, final Point2D b, final @NotNull ArrayList<Point2D> points) {
double maxD = -1;
Point2D maxP = null;
diff --git a/src/main/java/plugins/adufour/quickhull/QuickHull3D.java b/src/main/java/plugins/adufour/quickhull/QuickHull3D.java
index dac0a2f64c73c3a27a01d3b946d9216b37939689..d370f7991c9cbf7d0e0fdb9a732d8dbdb80b6bcd 100644
--- a/src/main/java/plugins/adufour/quickhull/QuickHull3D.java
+++ b/src/main/java/plugins/adufour/quickhull/QuickHull3D.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -17,6 +17,10 @@
*/
package plugins.adufour.quickhull;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+
import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;
import java.io.*;
@@ -224,7 +228,7 @@ public class QuickHull3D {
return explicitTolerance;
}
- private void addPointToFace(final Vertex vtx, final Face face) {
+ private void addPointToFace(final @NotNull Vertex vtx, final @NotNull Face face) {
vtx.face = face;
if (face.outside == null) {
@@ -236,7 +240,7 @@ public class QuickHull3D {
face.outside = vtx;
}
- private void removePointFromFace(final Vertex vtx, final Face face) {
+ private void removePointFromFace(final Vertex vtx, final @NotNull Face face) {
if (vtx == face.outside) {
if (vtx.next != null && vtx.next.face == face) {
face.outside = vtx.next;
@@ -248,7 +252,7 @@ public class QuickHull3D {
claimed.delete(vtx);
}
- private Vertex removeAllPointsFromFace(final Face face) {
+ private @Nullable Vertex removeAllPointsFromFace(final @NotNull Face face) {
if (face.outside != null) {
Vertex end = face.outside;
while (end.next != null && end.next.face == face) {
@@ -293,7 +297,7 @@ public class QuickHull3D {
build(points, points.length);
}
- private HalfEdge findHalfEdge(final Vertex tail, final Vertex head) {
+ private @Nullable HalfEdge findHalfEdge(final Vertex tail, final Vertex head) {
// brute force ... OK, since setHull is not used much
for (final Face face : faces) {
final HalfEdge he = face.findEdge(tail, head);
@@ -322,7 +326,7 @@ public class QuickHull3D {
}
}
- private void printQhullErrors(final Process proc) throws IOException {
+ private void printQhullErrors(final @NotNull Process proc) throws IOException {
boolean wrote = false;
final InputStream es = proc.getErrorStream();
while (es.available() > 0) {
@@ -340,7 +344,7 @@ public class QuickHull3D {
commandStr += " -Qt";
}
try {
- final Process proc = Runtime.getRuntime().exec(commandStr);
+ final Process proc = Runtime.getRuntime().exec(commandStr); // FIXME change command from String to String[]
final PrintStream ps = new PrintStream(proc.getOutputStream());
final StreamTokenizer stok = new StreamTokenizer(new InputStreamReader(proc.getInputStream()));
@@ -374,7 +378,7 @@ public class QuickHull3D {
System.out.println("Expecting face index");
System.exit(1);
}
- indexList.add(0, (int) stok.nval);
+ indexList.addFirst((int) stok.nval);
}
faceIndices[i] = new int[indexList.size()];
int k = 0;
@@ -385,8 +389,9 @@ public class QuickHull3D {
setHull(coords, nump, faceIndices, numf);
}
catch (final Exception e) {
- e.printStackTrace();
- System.exit(1);
+ IcyLogger.fatal(this.getClass(), e, e.getLocalizedMessage());
+ //System.exit(1);
+ throw new RuntimeException(e);
}
}
@@ -878,7 +883,7 @@ public class QuickHull3D {
}
}
- private void getFaceIndices(final int[] indices, final Face face, final int flags) {
+ private void getFaceIndices(final int[] indices, final @NotNull Face face, final int flags) {
final boolean ccw = ((flags & CLOCKWISE) == 0);
final boolean indexedFromOne = ((flags & INDEXED_FROM_ONE) != 0);
final boolean pointRelative = ((flags & POINT_RELATIVE) != 0);
@@ -956,11 +961,11 @@ public class QuickHull3D {
private static final int NONCONVEX_WRT_LARGER_FACE = 1;
private static final int NONCONVEX = 2;
- protected double oppFaceDistance(final HalfEdge he) {
+ protected double oppFaceDistance(final @NotNull HalfEdge he) {
return he.face.distanceToPlane(he.opposite.face.getCentroid());
}
- private boolean doAdjacentMerge(final Face face, final int mergeType) {
+ private boolean doAdjacentMerge(final @NotNull Face face, final int mergeType) {
HalfEdge hedge = face.he0;
boolean convex = true;
@@ -1050,14 +1055,14 @@ public class QuickHull3D {
} while (edge != edge0);
}
- private HalfEdge addAdjoiningFace(final Vertex eyeVtx, final HalfEdge he) {
+ private HalfEdge addAdjoiningFace(final Vertex eyeVtx, final @NotNull HalfEdge he) {
final Face face = Face.createTriangle(eyeVtx, he.tail(), he.head());
faces.add(face);
face.getEdge(-1).setOpposite(he.getOpposite());
return face.getEdge(0);
}
- protected void addNewFaces(final FaceList newFaces, final Vertex eyeVtx, final Vector<HalfEdge> horizon) {
+ protected void addNewFaces(final @NotNull FaceList newFaces, final Vertex eyeVtx, final @NotNull Vector<HalfEdge> horizon) {
newFaces.clear();
HalfEdge hedgeSidePrev = null;
@@ -1153,7 +1158,7 @@ public class QuickHull3D {
}
}
- private void markFaceVertices(final Face face, final int mark) {
+ private void markFaceVertices(final @NotNull Face face, final int mark) {
final HalfEdge he0 = face.getFirstEdge();
HalfEdge he = he0;
do {
@@ -1189,7 +1194,7 @@ public class QuickHull3D {
}
}
- protected boolean checkFaceConvexity(final Face face, final double tol, final PrintStream ps) {
+ protected boolean checkFaceConvexity(final @NotNull Face face, final double tol, final PrintStream ps) {
double dist;
HalfEdge he = face.he0;
do {
diff --git a/src/main/java/plugins/adufour/quickhull/Vertex.java b/src/main/java/plugins/adufour/quickhull/Vertex.java
index b652810c483efa49a5b10f856204856ba50a1697..cdbbfc37cc0db3dfc798171e122f98726bf6c73d 100644
--- a/src/main/java/plugins/adufour/quickhull/Vertex.java
+++ b/src/main/java/plugins/adufour/quickhull/Vertex.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,6 +18,8 @@
package plugins.adufour.quickhull;
+import org.jetbrains.annotations.Contract;
+
import javax.vecmath.Vector3d;
/**
@@ -26,7 +28,7 @@ import javax.vecmath.Vector3d;
*
* @author John E. Lloyd, Fall 2004
*/
-class Vertex {
+public class Vertex {
/**
* Spatial point associated with this vertex.
*/
@@ -55,6 +57,7 @@ class Vertex {
/**
* Constructs a vertex and sets its coordinates to 0.
*/
+ @Contract(pure = true)
public Vertex() {
pnt = new Vector3d();
}
@@ -63,6 +66,7 @@ class Vertex {
* Constructs a vertex with the specified coordinates
* and index.
*/
+ @Contract(pure = true)
public Vertex(final double x, final double y, final double z, final int idx) {
pnt = new Vector3d(x, y, z);
index = idx;
diff --git a/src/main/java/plugins/adufour/quickhull/VertexList.java b/src/main/java/plugins/adufour/quickhull/VertexList.java
index f6d6247b1b9a65228fc201e3635a1461b67ce9e9..2b6816f191a0f48ec14b3dad4bbaf261066dad27 100644
--- a/src/main/java/plugins/adufour/quickhull/VertexList.java
+++ b/src/main/java/plugins/adufour/quickhull/VertexList.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,10 +18,12 @@
package plugins.adufour.quickhull;
+import org.jetbrains.annotations.NotNull;
+
/**
* Maintains a double-linked list of vertices for use by QuickHull3D
*/
-class VertexList {
+public class VertexList {
private Vertex head;
private Vertex tail;
@@ -67,7 +69,7 @@ class VertexList {
/**
* Deletes a vertex from this list.
*/
- public void delete(final Vertex vtx) {
+ public void delete(final @NotNull Vertex vtx) {
if (vtx.prev == null) {
head = vtx.next;
}
@@ -85,7 +87,7 @@ class VertexList {
/**
* Deletes a chain of vertices from this list.
*/
- public void delete(final Vertex vtx1, final Vertex vtx2) {
+ public void delete(final @NotNull Vertex vtx1, final Vertex vtx2) {
if (vtx1.prev == null) {
head = vtx2.next;
}
@@ -103,7 +105,7 @@ class VertexList {
/**
* Inserts a vertex into this list before another specificed vertex.
*/
- public void insertBefore(final Vertex vtx, final Vertex next) {
+ public void insertBefore(final @NotNull Vertex vtx, final @NotNull Vertex next) {
vtx.prev = next.prev;
if (next.prev == null) {
head = vtx;
diff --git a/src/main/resources/quickhull.png b/src/main/resources/quickhull.png
new file mode 100644
index 0000000000000000000000000000000000000000..9c8c783a833888f37d0123b8de62ecbe8cdd7ea6
Binary files /dev/null and b/src/main/resources/quickhull.png differ