Initial commit

.gitignore

+.idea/
+.settings/
+build/
+target/
+*.iml
+.classpath
+.project
\ No newline at end of file

pom.xml

+<?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">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>org.bioimageanalysis.icy</groupId>
+    <artifactId>icy-convexify</artifactId>
+    <version>2.0.4</version>
+
+    <packaging>jar</packaging>
+
+    <name>Convexify</name>
+    <description>
+        Creates convex versions of regions of interests in 2D or 3D using the QuickHull library.
+    </description>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <jdk.version>1.8</jdk.version>
+
+        <maven.compiler.source>1.8</maven.compiler.source>
+        <maven.compiler.target>1.8</maven.compiler.target>
+
+        <outputJar>${project.build.outputDirectory}/../plugin</outputJar>
+    </properties>
+
+    <build>
+        <finalName>${project.artifactId}</finalName>
+
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <version>3.1.2</version>
+                <configuration>
+                    <outputDirectory>${outputJar}</outputDirectory>
+                    <archive>
+                        <manifest>
+                            <addClasspath>true</addClasspath>
+                            <mainClass>plugins.adufour.roi.Convexify</mainClass>
+                        </manifest>
+                    </archive>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.bioimageanalysis.icy</groupId>
+            <artifactId>icy-kernel</artifactId>
+            <version>2.1.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.bioimageanalysis.icy</groupId>
+            <artifactId>icy-protocols</artifactId>
+            <version>3.0.9</version>
+        </dependency>
+        <dependency>
+            <groupId>org.bioimageanalysis.icy</groupId>
+            <artifactId>icy-quickhull</artifactId>
+            <version>1.0.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.bioimageanalysis.icy</groupId>
+            <artifactId>icy-3d-mesh-roi</artifactId>
+            <version>1.4.7</version>
+        </dependency>
+    </dependencies>
+
+    <repositories>
+        <repository>
+            <id>icy</id>
+            <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+        </repository>
+    </repositories>
+
+    <distributionManagement>
+        <snapshotRepository>
+            <id>icy-dev</id>
+            <name>icy-dev</name>
+            <url>https://icy-nexus-dev.pasteur.cloud/repository/icy-core/</url>
+        </snapshotRepository>
+        <repository>
+            <id>icy-prod</id>
+            <name>icy-prod</name>
+            <url>https://icy-nexus.pasteur.fr/repository/icy-core/</url>
+        </repository>
+    </distributionManagement>
+</project>
\ No newline at end of file

src/main/java/plugins/adufour/roi/Convexify.java

+package plugins.adufour.roi;
+
+import icy.roi.ROI;
+import icy.roi.ROI2D;
+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;
+import plugins.adufour.ezplug.EzVarBoolean;
+import plugins.adufour.ezplug.EzVarSequence;
+import plugins.adufour.quickhull.QuickHull2D;
+import plugins.adufour.quickhull.QuickHull3D;
+import plugins.adufour.roi.mesh.polygon.ROI3DPolygonalMesh;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.kernel.roi.roi2d.ROI2DArea;
+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");
+
+    private EzVarBoolean replace = new EzVarBoolean("Replace existing ROI", false);
+
+    private VarROIArray roiIN = new VarROIArray("List of ROI");
+
+    private VarROIArray roiOUT = new VarROIArray("List of ROI");
+
+    @Override
+    protected void initialize()
+    {
+        addEzComponent(input);
+        addEzComponent(replace);
+    }
+
+    @Override
+    public void clean()
+    {
+
+    }
+
+    @Override
+    public void execute()
+    {
+        if (!isHeadLess())
+        {
+            roiIN.setValue(new ROI[0]);
+            Sequence s = input.getValue(true);
+            roiIN.add(s.getROIs().toArray(new ROI[0]));
+        }
+
+        roiOUT.setValue(new ROI[0]);
+        for (ROI roi : roiIN)
+            roiOUT.add(createConvexROI(roi));
+
+        if (!isHeadLess())
+        {
+            Sequence s = input.getValue(true);
+
+            if (replace.getValue())
+                s.removeAllROI();
+
+            for (ROI roi : roiOUT)
+            {
+                s.addROI(roi);
+            }
+        }
+    }
+
+    /**
+     * Creates a convex ROI from the specified ROI.
+     * 
+     * @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
+     */
+    public static ROI createConvexROI(ROI roi) throws IllegalArgumentException
+    {
+        ROI output = null;
+
+        try
+        {
+            if (roi instanceof ROI2D)
+            {
+                final List<Point2D> envelope;
+
+                if (roi instanceof ROI2DShape)
+                {
+                    envelope = QuickHull2D.computeConvexEnvelope(((ROI2DShape) roi).getPoints());
+                }
+                else if (roi instanceof ROI2DArea)
+                {
+                    Point2D[] points = ((ROI2DArea) roi).getBooleanMask(true).getContourPoints();
+                    envelope = QuickHull2D.computeConvexEnvelope(Arrays.asList(points));
+                }
+                else
+                {
+                    throw new IllegalArgumentException("Cannot compute convex hull for ROI " + roi.getName()
+                            + " of type " + roi.getClassName() + ".");
+                }
+
+                output = new ROI2DPolygon(envelope);
+
+                // copy position info
+                final ROI2D roi2d = (ROI2D) roi;
+                ((ROI2D) output).setT(roi2d.getT());
+                ((ROI2D) output).setZ(roi2d.getZ());
+                ((ROI2D) output).setC(roi2d.getC());
+            }
+            else if (roi instanceof ROI3D)
+            {
+                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];
+                    pt3d[i] = new Point3d(p.getX(), p.getY(), p.getZ());
+                }
+
+                QuickHull3D qhull = new QuickHull3D();
+                qhull.build(pt3d, pt3d.length);
+
+                // Use a 3D mesh to prepare the final ROI
+                output = new ROI3DPolygonalMesh(qhull);
+
+                // copy position info
+                final ROI3D roi2d = (ROI3D) roi;
+                ((ROI3D) output).setT(roi2d.getT());
+                ((ROI2D) output).setC(roi2d.getC());
+            }
+        }
+        catch (Throwable t)
+        {
+            // can happen with QuickHull3D / ROI3DPolygonalMesh...
+        }
+
+        if (output == null)
+            throw new IllegalArgumentException(
+                    "Cannot compute convex hull for ROI " + roi.getName() + " of type " + roi.getClassName() + ".");
+
+        ROIUtil.copyROIProperties(roi, output, false);
+        output.setName(roi.getName() + " (convex)");
+
+        return output;
+    }
+
+    @Override
+    public void declareInput(VarList inputMap)
+    {
+        inputMap.add("Regions of interest", roiIN);
+    }
+
+    @Override
+    public void declareOutput(VarList outputMap)
+    {
+        outputMap.add("Regions of interest", roiOUT);
+    }
+}