diff --git a/.gitignore b/.gitignore
index 5abffee43749afc5d07d2735617b71e4130a8b93..b2f15ce895696fd311b35bd9ebb831c094d75ac0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,4 +7,5 @@ bin/
*.jar
.classpath
.project
-export.jardesc
\ No newline at end of file
+export.jardesc
+**/.DS_Store
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index bc0cfd355a6a01328796c83529a6505ca5f661c7..3c8ae15a3d8fd31a78ccd09ee0ab247463756965 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,17 +1,17 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>parent-pom-plugin</artifactId>
- <version>1.0.8</version>
+ <artifactId>pom-icy</artifactId>
+ <version>2.2.0</version>
</parent>
<artifactId>convexify</artifactId>
- <version>2.0.7</version>
+ <version>3.0.0</version>
<packaging>jar</packaging>
@@ -28,12 +28,10 @@
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>quickhull</artifactId>
- <version>${quickhull.version}</version>
</dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>3d-mesh-roi</artifactId>
- <version>${three-d-mesh-roi.version}</version>
</dependency>
</dependencies>
diff --git a/src/main/java/plugins/adufour/roi/Convexify.java b/src/main/java/plugins/adufour/roi/Convexify.java
index cdecc0da65e02e330d32f7e764bb2634b8005b5c..ef15db7f09951d41c34c7c66e99a226d02d04bc9 100644
--- a/src/main/java/plugins/adufour/roi/Convexify.java
+++ b/src/main/java/plugins/adufour/roi/Convexify.java
@@ -1,3 +1,21 @@
+/*
+ * Copyright (c) 2010-2023. Institut Pasteur.
+ *
+ * This file is part of Icy.
+ * Icy is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Icy is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * 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.roi;
import icy.roi.ROI;
@@ -6,13 +24,6 @@ import icy.roi.ROI3D;
import icy.roi.ROIUtil;
import icy.sequence.Sequence;
import icy.type.point.Point3D;
-
-import java.awt.geom.Point2D;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.vecmath.Point3d;
-
import plugins.adufour.blocks.tools.roi.ROIBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.ezplug.EzPlug;
@@ -27,52 +38,50 @@ import plugins.kernel.roi.roi2d.ROI2DPolygon;
import plugins.kernel.roi.roi2d.ROI2DShape;
import plugins.kernel.roi.roi3d.ROI3DArea;
-public class Convexify extends EzPlug implements ROIBlock
-{
- private EzVarSequence input = new EzVarSequence("Input sequence");
+import javax.vecmath.Point3d;
+import java.awt.geom.Point2D;
+import java.util.Arrays;
+import java.util.List;
+
+public class Convexify extends EzPlug implements ROIBlock {
+ private final EzVarSequence input = new EzVarSequence("Input sequence");
- private EzVarBoolean replace = new EzVarBoolean("Replace existing ROI", false);
+ private final EzVarBoolean replace = new EzVarBoolean("Replace existing ROI", false);
- private VarROIArray roiIN = new VarROIArray("List of ROI");
+ private final VarROIArray roiIN = new VarROIArray("List of ROI");
- private VarROIArray roiOUT = new VarROIArray("List of ROI");
+ private final VarROIArray roiOUT = new VarROIArray("List of ROI");
@Override
- protected void initialize()
- {
+ protected void initialize() {
addEzComponent(input);
addEzComponent(replace);
}
@Override
- public void clean()
- {
+ public void clean() {
}
@Override
- public void execute()
- {
- if (!isHeadLess())
- {
+ public void execute() {
+ if (!isHeadLess()) {
roiIN.setValue(new ROI[0]);
- Sequence s = input.getValue(true);
+ final Sequence s = input.getValue(true);
roiIN.add(s.getROIs().toArray(new ROI[0]));
}
roiOUT.setValue(new ROI[0]);
- for (ROI roi : roiIN)
+ for (final ROI roi : roiIN)
roiOUT.add(createConvexROI(roi));
- if (!isHeadLess())
- {
- Sequence s = input.getValue(true);
+ if (!isHeadLess()) {
+ final Sequence s = input.getValue(true);
if (replace.getValue())
s.removeAllROI();
- for (ROI roi : roiOUT)
- {
+ for (final ROI roi : roiOUT) {
s.addROI(roi);
}
}
@@ -80,36 +89,28 @@ public class Convexify extends EzPlug implements ROIBlock
/**
* Creates a convex ROI from the specified ROI.
- *
- * @param roi
- * the ROI to be converted into a convex version
+ *
+ * @param roi the ROI to be converted into a convex version
* @return a convex version of the ROI. This ROI is currently of type {@link ROI2DPolygon} in
- * 2D, and of type {@link ROI3DArea} in 3D, although the return types may change in the
- * future.
- * @throws IllegalArgumentException
- * if the specified ROI is not supported
+ * 2D, and of type {@link ROI3DArea} in 3D, although the return types may change in the
+ * future.
+ * @throws IllegalArgumentException if the specified ROI is not supported
*/
- public static ROI createConvexROI(ROI roi) throws IllegalArgumentException
- {
+ public static ROI createConvexROI(final ROI roi) throws IllegalArgumentException {
ROI output = null;
- try
- {
- if (roi instanceof ROI2D)
- {
+ try {
+ if (roi instanceof ROI2D) {
final List<Point2D> envelope;
- if (roi instanceof ROI2DShape)
- {
+ if (roi instanceof ROI2DShape) {
envelope = QuickHull2D.computeConvexEnvelope(((ROI2DShape) roi).getPoints());
}
- else if (roi instanceof ROI2DArea)
- {
- Point2D[] points = ((ROI2DArea) roi).getBooleanMask(true).getContourPoints();
+ else if (roi instanceof ROI2DArea) {
+ final Point2D[] points = ((ROI2DArea) roi).getBooleanMask(true).getContourPoints();
envelope = QuickHull2D.computeConvexEnvelope(Arrays.asList(points));
}
- else
- {
+ else {
throw new IllegalArgumentException("Cannot compute convex hull for ROI " + roi.getName()
+ " of type " + roi.getClassName() + ".");
}
@@ -122,19 +123,17 @@ public class Convexify extends EzPlug implements ROIBlock
((ROI2D) output).setZ(roi2d.getZ());
((ROI2D) output).setC(roi2d.getC());
}
- else if (roi instanceof ROI3D)
- {
- Point3D[] points = ((ROI3D) roi).getBooleanMask(true).getContourPoints();
+ else if (roi instanceof ROI3D) {
+ final Point3D[] points = ((ROI3D) roi).getBooleanMask(true).getContourPoints();
// convert to vecmath's Point3d
- Point3d[] pt3d = new Point3d[points.length];
- for (int i = 0; i < points.length; i++)
- {
- Point3D p = points[i];
+ final Point3d[] pt3d = new Point3d[points.length];
+ for (int i = 0; i < points.length; i++) {
+ final Point3D p = points[i];
pt3d[i] = new Point3d(p.getX(), p.getY(), p.getZ());
}
- QuickHull3D qhull = new QuickHull3D();
+ final QuickHull3D qhull = new QuickHull3D();
qhull.build(pt3d, pt3d.length);
// Use a 3D mesh to prepare the final ROI
@@ -142,12 +141,11 @@ public class Convexify extends EzPlug implements ROIBlock
// copy position info
final ROI3D roi3d = (ROI3D) roi;
- ((ROI3D)output).setT(roi3d.getT());
- ((ROI3D)output).setC(roi3d.getC());
+ ((ROI3D) output).setT(roi3d.getT());
+ ((ROI3D) output).setC(roi3d.getC());
}
}
- catch (Throwable t)
- {
+ catch (final Throwable t) {
// can happen with QuickHull3D / ROI3DPolygonalMesh...
throw new IllegalArgumentException(
"Cannot compute convex hull for ROI " + roi.getName() + " of type " + roi.getClassName() + ".", t);
@@ -164,14 +162,12 @@ public class Convexify extends EzPlug implements ROIBlock
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(final VarList inputMap) {
inputMap.add("Regions of interest", roiIN);
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(final VarList outputMap) {
outputMap.add("Regions of interest", roiOUT);
}
}