From 7897422d15a84737970ed8838e6483ade79f900d Mon Sep 17 00:00:00 2001
From: Thomas <thomas.musset@pasteur.fr>
Date: Mon, 3 Feb 2025 15:35:57 +0100
Subject: [PATCH] updated to v2.0.0-a.2, updated to Java 23, clean some classes
---
pom.xml | 11 +---
.../java/plugins/adufour/quickhull/Face.java | 7 ++-
.../plugins/adufour/quickhull/FaceList.java | 2 +-
.../plugins/adufour/quickhull/HalfEdge.java | 2 +-
.../plugins/adufour/quickhull/QuickHull.java | 9 ++-
.../adufour/quickhull/QuickHull2D.java | 4 +-
.../adufour/quickhull/QuickHull3D.java | 58 +++++++++++-------
.../plugins/adufour/quickhull/Vertex.java | 3 +-
.../plugins/adufour/quickhull/VertexList.java | 2 +-
.../adufour/quickhull}/quickhull.png | Bin
10 files changed, 52 insertions(+), 46 deletions(-)
rename src/main/resources/{ => plugins/adufour/quickhull}/quickhull.png (100%)
diff --git a/pom.xml b/pom.xml
index b3cfb94..0834e88 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,11 +7,11 @@
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
- <version>3.0.0-a.1</version>
+ <version>3.0.0-a.3</version>
</parent>
<artifactId>quickhull</artifactId>
- <version>2.0.0-a.1</version>
+ <version>2.0.0-a.2</version>
<name>QuickHull</name>
<description>
@@ -24,11 +24,4 @@
<artifactId>vecmath</artifactId>
</dependency>
</dependencies>
-
- <repositories>
- <repository>
- <id>icy</id>
- <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 2afe11a..91d9b5a 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) 2010-2024. Institut Pasteur.
+ * Copyright (c) 2010-2025. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,6 +18,7 @@
package plugins.adufour.quickhull;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import org.jetbrains.annotations.NotNull;
import javax.vecmath.Vector3d;
@@ -65,7 +66,7 @@ public class Face {
computeNormal(normal);
if (area < minArea) {
- System.out.println("area=" + area);
+ IcyLogger.debug(this.getClass(), "area=" + area);
// make the normal more robust by removing
// components parallel to the longest edge
@@ -288,7 +289,7 @@ public class Face {
final StringBuilder s = new StringBuilder();
HalfEdge he = he0;
do {
- if (s.length() == 0) {
+ if (s.isEmpty()) {
s.append(he.head().index);
}
else {
diff --git a/src/main/java/plugins/adufour/quickhull/FaceList.java b/src/main/java/plugins/adufour/quickhull/FaceList.java
index be6d7b2..fac5a90 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) 2010-2024. Institut Pasteur.
+ * Copyright (c) 2010-2025. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
diff --git a/src/main/java/plugins/adufour/quickhull/HalfEdge.java b/src/main/java/plugins/adufour/quickhull/HalfEdge.java
index e31d21e..1d4c128 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) 2010-2024. Institut Pasteur.
+ * Copyright (c) 2010-2025. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
diff --git a/src/main/java/plugins/adufour/quickhull/QuickHull.java b/src/main/java/plugins/adufour/quickhull/QuickHull.java
index 5277b47..a15438b 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) 2010-2024. Institut Pasteur.
+ * Copyright (c) 2010-2025. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -21,7 +21,6 @@ package plugins.adufour.quickhull;
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
@@ -32,7 +31,7 @@ import org.bioimageanalysis.icy.extension.plugin.interface_.PluginLibrary;
* @author Alexandre Dufour
*/
@IcyPluginName("QuickHull")
-@IcyPluginIcon(path = "/quickhull.png")
-public class QuickHull extends Plugin implements PluginLibrary {
-
+@IcyPluginIcon(path = "/plugins/adufour/quickhull/quickhull.png")
+public class QuickHull extends Plugin {
+ //
}
diff --git a/src/main/java/plugins/adufour/quickhull/QuickHull2D.java b/src/main/java/plugins/adufour/quickhull/QuickHull2D.java
index df97cf9..290935a 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) 2010-2024. Institut Pasteur.
+ * Copyright (c) 2010-2025. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -19,6 +19,7 @@
package plugins.adufour.quickhull;
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.jetbrains.annotations.NotNull;
@@ -28,6 +29,7 @@ import java.util.ArrayList;
import java.util.List;
@IcyPluginName("QuickHull 2D")
+@IcyPluginIcon(path = "/plugins/adufour/quickhull/quickhull.png")
public class QuickHull2D extends Plugin {
public static @NotNull List<Point2D> computeConvexEnvelope(final @NotNull List<Point2D> points) {
final ArrayList<Point2D> envelope = new ArrayList<>();
diff --git a/src/main/java/plugins/adufour/quickhull/QuickHull3D.java b/src/main/java/plugins/adufour/quickhull/QuickHull3D.java
index d370f79..8ede2f6 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) 2010-2024. Institut Pasteur.
+ * Copyright (c) 2010-2025. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -15,6 +15,7 @@
* You should have received a copy of the GNU General Public License
* along with Icy. If not, see <https://www.gnu.org/licenses/>.
*/
+
package plugins.adufour.quickhull;
import org.bioimageanalysis.icy.system.logging.IcyLogger;
@@ -339,12 +340,14 @@ public class QuickHull3D {
}
protected void setFromQhull(final double[] coords, final int nump, final boolean triangulate) {
- String commandStr = "./qhull i";
- if (triangulate) {
- commandStr += " -Qt";
- }
+ final String[] commandStr;
+ if (triangulate)
+ commandStr = new String[]{"./qhull", "i", "-Qt"};
+ else
+ commandStr = new String[]{"./qhull", "i"};
+
try {
- final Process proc = Runtime.getRuntime().exec(commandStr); // FIXME change command from String to String[]
+ final Process proc = Runtime.getRuntime().exec(commandStr);
final PrintStream ps = new PrintStream(proc.getOutputStream());
final StreamTokenizer stok = new StreamTokenizer(new InputStreamReader(proc.getInputStream()));
@@ -365,8 +368,8 @@ public class QuickHull3D {
stok.nextToken();
}
if (stok.ttype != StreamTokenizer.TT_NUMBER) {
- System.out.println("Expecting number of faces");
- System.exit(1);
+ IcyLogger.fatal(this.getClass(), "Expecting number of faces");
+ System.exit(1); // TODO replace with runtime exception ?
}
final int numf = (int) stok.nval;
stok.nextToken(); // clear EOL
@@ -375,8 +378,8 @@ public class QuickHull3D {
indexList.clear();
while (stok.nextToken() != StreamTokenizer.TT_EOL) {
if (stok.ttype != StreamTokenizer.TT_NUMBER) {
- System.out.println("Expecting face index");
- System.exit(1);
+ IcyLogger.fatal(this.getClass(), "Expecting face index");
+ System.exit(1); // TODO replace with runtime exception ?
}
indexList.addFirst((int) stok.nval);
}
@@ -655,11 +658,19 @@ public class QuickHull3D {
}
if (debug) {
- System.out.println("initial vertices:");
+ IcyLogger.debug(
+ this.getClass(),
+ "initial vertices:",
+ vtx[0].index + ": " + vtx[0].pnt,
+ vtx[1].index + ": " + vtx[1].pnt,
+ vtx[2].index + ": " + vtx[2].pnt,
+ vtx[3].index + ": " + vtx[3].pnt
+ );
+ /*System.out.println("initial vertices:");
System.out.println(vtx[0].index + ": " + vtx[0].pnt);
System.out.println(vtx[1].index + ": " + vtx[1].pnt);
System.out.println(vtx[2].index + ": " + vtx[2].pnt);
- System.out.println(vtx[3].index + ": " + vtx[3].pnt);
+ System.out.println(vtx[3].index + ": " + vtx[3].pnt);*/
}
final Face[] tris = new Face[4];
@@ -925,12 +936,12 @@ public class QuickHull3D {
if (maxFace != null) {
addPointToFace(vtx, maxFace);
if (debug && vtx.index == findIndex) {
- System.out.println(findIndex + " CLAIMED BY " + maxFace.getVertexString());
+ IcyLogger.debug(this.getClass(), findIndex + " CLAIMED BY " + maxFace.getVertexString());
}
}
else {
if (debug && vtx.index == findIndex) {
- System.out.println(findIndex + " DISCARDED");
+ IcyLogger.debug(this.getClass(), findIndex + " DISCARDED");
}
}
}
@@ -1003,7 +1014,7 @@ public class QuickHull3D {
if (merge) {
if (debug) {
- System.out.println(" merging " + face.getVertexString() + " and " + oppFace.getVertexString());
+ IcyLogger.debug(this.getClass(), " merging " + face.getVertexString() + " and " + oppFace.getVertexString());
}
final int numd = face.mergeAdjacentFace(hedge, discardedFaces);
@@ -1011,7 +1022,7 @@ public class QuickHull3D {
deleteFacePoints(discardedFaces[i], face);
}
if (debug) {
- System.out.println(" result: " + face.getVertexString());
+ IcyLogger.debug(this.getClass(), " result: " + face.getVertexString());
}
return true;
}
@@ -1028,7 +1039,7 @@ public class QuickHull3D {
deleteFacePoints(face, null);
face.mark = Face.DELETED;
if (debug) {
- System.out.println(" visiting face " + face.getVertexString());
+ IcyLogger.debug(this.getClass(), " visiting face " + face.getVertexString());
}
HalfEdge edge;
if (edge0 == null) {
@@ -1047,7 +1058,7 @@ public class QuickHull3D {
else {
horizon.add(edge);
if (debug) {
- System.out.println(" adding horizon edge " + edge.getVertexString());
+ IcyLogger.debug(this.getClass(), " adding horizon edge " + edge.getVertexString());
}
}
}
@@ -1071,7 +1082,7 @@ public class QuickHull3D {
for (final HalfEdge horizonHe : horizon) {
final HalfEdge hedgeSide = addAdjoiningFace(eyeVtx, horizonHe);
if (debug) {
- System.out.println("new face: " + hedgeSide.face.getVertexString());
+ IcyLogger.debug(this.getClass(), "new face: " + hedgeSide.face.getVertexString());
}
if (hedgeSidePrev != null) {
hedgeSide.next.setOpposite(hedgeSidePrev);
@@ -1105,13 +1116,14 @@ public class QuickHull3D {
}
}
+ @SuppressWarnings("StatementWithEmptyBody")
protected void addPointToHull(final Vertex eyeVtx) {
horizon.clear();
unclaimed.clear();
if (debug) {
- System.out.println("Adding point: " + eyeVtx.index);
- System.out.println(" which is " + eyeVtx.face.distanceToPlane(eyeVtx.pnt) + " above face " + eyeVtx.face.getVertexString());
+ IcyLogger.debug(this.getClass(), "Adding point: " + eyeVtx.index);
+ IcyLogger.debug(this.getClass(), " which is " + eyeVtx.face.distanceToPlane(eyeVtx.pnt) + " above face " + eyeVtx.face.getVertexString());
}
removePointFromFace(eyeVtx, eyeVtx.face);
calculateHorizon(eyeVtx.pnt, null, eyeVtx.face, horizon);
@@ -1149,12 +1161,12 @@ public class QuickHull3D {
addPointToHull(eyeVtx);
cnt++;
if (debug) {
- System.out.println("iteration " + cnt + " done");
+ IcyLogger.debug(this.getClass(), "iteration " + cnt + " done");
}
}
reindexFacesAndVertices();
if (debug) {
- System.out.println("hull done");
+ IcyLogger.debug(this.getClass(), "hull done");
}
}
diff --git a/src/main/java/plugins/adufour/quickhull/Vertex.java b/src/main/java/plugins/adufour/quickhull/Vertex.java
index cdbbfc3..d49d98c 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) 2010-2024. Institut Pasteur.
+ * Copyright (c) 2010-2025. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -71,5 +71,4 @@ public class Vertex {
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 2b6816f..5237c56 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) 2010-2024. Institut Pasteur.
+ * Copyright (c) 2010-2025. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
diff --git a/src/main/resources/quickhull.png b/src/main/resources/plugins/adufour/quickhull/quickhull.png
similarity index 100%
rename from src/main/resources/quickhull.png
rename to src/main/resources/plugins/adufour/quickhull/quickhull.png
--
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