Added project

.gitignore

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

export.jardesc

+<?xml version="1.0" encoding="WINDOWS-1252" standalone="no"?>
+<jardesc>
+    <jar path="sphereVTK/drawSphereVTK.jar"/>
+    <options buildIfNeeded="true" compress="true" descriptionLocation="/sphereVTK/export.jardesc" exportErrors="false" exportWarnings="true" includeDirectoryEntries="true" overwrite="true" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
+    <storedRefactorings deprecationInfo="true" structuralOnly="false"/>
+    <selectedProjects/>
+    <manifest generateManifest="true" manifestLocation="/Icy-Kernel/META-INF/MANIFEST.MF" manifestVersion="1.0" reuseManifest="false" saveManifest="false" usesManifest="true">
+        <sealing sealJar="false">
+            <packagesToSeal/>
+            <packagesToUnSeal/>
+        </sealing>
+    </manifest>
+    <selectedElements exportClassFiles="true" exportJavaFiles="true" exportOutputFolder="false">
+        <javaElement handleIdentifier="=sphereVTK/src"/>
+    </selectedElements>
+</jardesc>

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>
+
+    <!-- Inherited Icy Parent POM -->
+    <parent>
+        <groupId>org.bioimageanalysis.icy</groupId>
+        <artifactId>parent-pom-plugin</artifactId>
+        <version>1.0.3</version>
+    </parent>
+
+    <!-- Project Information -->
+    <artifactId>3d-spheres-vtk</artifactId>
+    <version>1.0.0</version>
+
+    <packaging>jar</packaging>
+
+    <name>Draw 3D Spheres with VTK.</name>
+    <description>
+        This protocol’s block draws 3D spheres with VTK from a list of cartesian coordinates (x,y,z). It is used by SODA-STORM protocol to
+        visualize SODA results obtained with single localizations microscopy (STORM).
+        Mapping molecular assemblies with fluorescence microscopy and object-based spatial statistics:
+        https://www.nature.com/articles/s41467-018-03053-x
+    </description>
+    <url>http://icy.bioimageanalysis.org/plugin/draw-3d-spheres-with-vtk/</url>
+    <inceptionYear>2020</inceptionYear>
+
+    <organization>
+        <name>Institut Pasteur</name>
+        <url>https://pasteur.fr</url>
+    </organization>
+
+    <licenses>
+        <license>
+            <name>GNU GPLv3</name>
+            <url>https://www.gnu.org/licenses/gpl-3.0.en.html</url>
+            <distribution>repo</distribution>
+        </license>
+    </licenses>
+
+    <developers>
+        <developer>
+            <id>lagache</id>
+            <name>Thibault Lagache</name>
+            <url>https://research.pasteur.fr/fr/member/thibault-lagache/</url>
+            <roles>
+                <role>founder</role>
+                <role>developer</role>
+            </roles>
+        </developer>
+        <developer>
+            <id>sdallongeville</id>
+            <name>Stéphane Dallongeville</name>
+            <url>https://research.pasteur.fr/fr/member/stephane-dallongeville/</url>
+            <roles>
+                <role>founder</role>
+                <role>lead</role>
+                <role>architect</role>
+                <role>developer</role>
+                <role>debugger</role>
+                <role>tester</role>
+                <role>maintainer</role>
+                <role>support</role>
+            </roles>
+        </developer>
+    </developers>
+
+    <!-- Project properties -->
+    <properties>
+
+    </properties>
+
+    <!-- Project build configuration -->
+    <build>
+
+    </build>
+
+    <!-- List of project's dependencies -->
+    <dependencies>
+        <!-- The core of Icy -->
+        <dependency>
+            <groupId>org.bioimageanalysis.icy</groupId>
+            <artifactId>icy-kernel</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.bioimageanalysis.icy</groupId>
+            <artifactId>protocols</artifactId>
+        </dependency>
+    </dependencies>
+
+    <!-- Icy Maven repository (to find parent POM) -->
+    <repositories>
+        <repository>
+            <id>icy</id>
+            <name>Icy's Nexus</name>
+            <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+        </repository>
+    </repositories>
+</project>

src/main/java/plugins/lagache/spherevtk/DrawSpheresVTK.java

+package plugins.lagache.spherevtk;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+
+import icy.plugin.abstract_.Plugin;
+import icy.roi.BooleanMask2D;
+import icy.roi.ROI;
+import icy.roi.ROI2D;
+import plugins.adufour.blocks.lang.Block;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarColor;
+import plugins.adufour.vars.lang.VarDouble;
+import plugins.adufour.vars.lang.VarDoubleArrayNative;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.lang.VarString;
+import plugins.kernel.roi.roi2d.ROI2DPoint;
+
+// Colocalisation with Ripley function K
+// Significant 
+
+public class DrawSpheresVTK extends Plugin implements Block {
+
+	VarSequence input_sequence = new VarSequence("Input sequence", null);
+	VarDoubleArrayNative x= new VarDoubleArrayNative("x", null);
+	VarDoubleArrayNative y= new VarDoubleArrayNative("y", null);
+	VarDoubleArrayNative z= new VarDoubleArrayNative("z", null);
+	VarString name = new VarString("Name of the overlay", "detections");
+	VarColor color = new VarColor("Color",  Color.blue);
+	VarDouble size = new VarDouble("Size", 1.0);	
+		@Override
+	public void declareInput(VarList inputMap) {
+
+		inputMap.add("Input Sequence", input_sequence);
+		inputMap.add("x",x);
+		inputMap.add("y",y);
+		inputMap.add("z",z);
+		inputMap.add("Size",size);		
+		inputMap.add("Color",color);		
+		inputMap.add("Name of the overlay",name);
+	}
+
+	@Override
+	public void declareOutput(VarList outputMap) {		
+	}
+
+		@Override
+	public void run() {
+			
+		 // Add the cross overlay, it becomes active after being added.				
+        input_sequence.getValue().addOverlay(new SphereVTK(x.getValue(),y.getValue(),z.getValue(),size.getValue(),color.getValue(),name.getValue()));
+		}
+		
+		}
+		
+	
+
+	
\ No newline at end of file

src/main/java/plugins/lagache/spherevtk/SphereVTK.java

+/*
+ * Copyright 2010, 2011 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 <http://www.gnu.org/licenses/>.
+ */
+package plugins.lagache.spherevtk;
+
+import icy.canvas.IcyCanvas;
+import icy.painter.Overlay;
+import icy.painter.VtkPainter;
+import icy.sequence.Sequence;
+import icy.vtk.VtkUtil;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+
+import plugins.kernel.canvas.VtkCanvas;
+import vtk.vtkActor;
+import vtk.vtkFloatArray;
+import vtk.vtkGlyph3D;
+import vtk.vtkLookupTable;
+import vtk.vtkMolecule;
+import vtk.vtkMoleculeMapper;
+import vtk.vtkPoints;
+import vtk.vtkPolyDataMapper;
+import vtk.vtkProp;
+import vtk.vtkSphereSource;
+import vtk.vtkUnsignedShortArray;
+import vtk.vtkUnstructuredGrid;
+
+/**
+ * @author stephane
+ */
+public class SphereVTK extends Overlay implements VtkPainter
+{
+    double[] x, y, z;
+    double size;
+    Color color;
+
+    private vtkActor[] sphere_ens;
+
+    public SphereVTK(double[] x, double[] y, double[] z, double size, Color color, String name)
+    {
+        super(name);
+
+        this.x = x;
+        this.y = y;
+        this.z = z;
+        this.size = size;
+        this.color = color;
+
+        init();
+    }
+
+    private void init()
+    {
+        // create points
+        final vtkPoints points = new vtkPoints();
+        // setup scales
+        final vtkFloatArray scales = new vtkFloatArray();
+        scales.SetName("scales");
+        // setup color label
+        final vtkFloatArray col = new vtkFloatArray();
+        col.SetName("col");
+
+        // setup lookupTable and add some colors
+        final vtkLookupTable colors = new vtkLookupTable();
+        colors.SetNumberOfTableValues(1);
+        // index, R, G, B, A
+        colors.SetTableValue(0, color.getRed() / 255f, color.getGreen() / 255f, color.getBlue() / 255f, 1.0);
+
+        for (int i = 0; i < x.length; i++)
+        {
+            points.InsertNextPoint(x[i], y[i], z[i]);
+            scales.InsertNextValue(1);
+            col.InsertNextValue(0); // first color
+        }
+
+        // grid structured to append center, radius and color label
+        final vtkUnstructuredGrid grid = new vtkUnstructuredGrid();
+        
+        grid.SetPoints(points);
+        grid.GetPointData().AddArray(scales);
+        grid.GetPointData().SetActiveScalars("scales"); // !!!to set radius first
+        grid.GetPointData().AddArray(col);
+        
+        points.Delete();
+        scales.Delete();
+        col.Delete();
+
+        // create anything you want here, we will use a sphere for the demo
+        final vtkSphereSource sphere = new vtkSphereSource();
+
+        sphere.SetRadius(size);
+        sphere.SetThetaResolution(6);
+        sphere.SetPhiResolution(6);
+
+        // object to group sphere and grid and keep smooth interaction
+        final  vtkGlyph3D glyph3D = new vtkGlyph3D();
+        
+        glyph3D.SetInputData(grid);
+        glyph3D.SetSourceConnection(sphere.GetOutputPort());
+
+        // create a mapper and actor
+        final vtkPolyDataMapper mapper = new vtkPolyDataMapper();
+        mapper.SetInputConnection(glyph3D.GetOutputPort());
+
+        mapper.SetScalarModeToUsePointFieldData(); // without, color are displayed regarding radius and not color label
+        // mapper.SetScalarRange(0, 3); // to scale color label (without, col should be between 0 and 1)
+        mapper.SelectColorArray("col"); // !!!to set color (nevertheless you will have nothing)
+        mapper.SetLookupTable(colors);
+
+        final vtkActor actor = new vtkActor();
+        actor.SetMapper(mapper);
+
+        sphere_ens = new vtkActor[1];
+        sphere_ens[0] = actor;
+    }
+
+    // init vtk objects
+    private void init_2()
+    {
+        final double[] pts = new double[x.length * 3];
+
+        // convert to single array
+        for (int i = 0; i < x.length; i++)
+        {
+            pts[(i * 3) + 0] = x[i];
+            pts[(i * 3) + 1] = y[i];
+            pts[(i * 3) + 2] = z[i];
+        }
+
+        final vtkPoints vtkPts = VtkUtil.getPoints(pts);
+
+        sphere_ens = new vtkActor[1];
+        final vtkMolecule mol = new vtkMolecule();
+
+        mol.SetPoints(vtkPts);
+        vtkPts.Delete();
+
+        final vtkUnsignedShortArray atomicNums = (vtkUnsignedShortArray) mol.GetVertexData().GetScalars();
+
+        // set atomic num
+        for (int i = 0; i < x.length; i++)
+            atomicNums.InsertValue(i, 0);
+
+        // mapper
+        final vtkMoleculeMapper molMapper = new vtkMoleculeMapper();
+
+        molMapper.SetInputData(mol);
+        molMapper.UseFastSettings();
+
+        // molMapper.SetRenderAtoms(true);
+        // molMapper.SetRenderBonds(false);
+
+        // actor
+        final vtkActor molActor = new vtkActor();
+        molActor.SetMapper(molMapper);
+
+        sphere_ens[0] = molActor;
+    }
+
+    // init vtk objects
+    private void init_old()
+    {
+        sphere_ens = new vtkActor[x.length];
+        for (int i = 0; i < x.length; i++)
+        {
+            // source
+            final vtkSphereSource sphere = new vtkSphereSource();
+            sphere.SetRadius(size);
+            sphere.SetThetaResolution(6);
+            sphere.SetPhiResolution(6);
+
+            sphere.SetCenter(x[i], y[i], z[i]);
+
+            // mapper
+            final vtkPolyDataMapper map = new vtkPolyDataMapper();
+            map.SetInputConnection(sphere.GetOutputPort());
+
+            // actor
+            vtkActor aSphere = new vtkActor();
+            aSphere.SetMapper(map);
+            // double total = color.getRed()+ color.getGreen()+ color.getBlue();
+            double red = color.getRed() / 255.;
+            double green = color.getGreen() / 255.;
+            double blue = color.getBlue() / 255.;
+
+            aSphere.GetProperty().SetColor(red, green, blue);
+            sphere_ens[i] = aSphere;
+        }
+    }
+    
+    @Override
+    public void paint(Graphics2D g, Sequence sequence, IcyCanvas canvas)
+    {
+        super.paint(g, sequence, canvas);
+
+        if (canvas instanceof VtkCanvas)
+        {
+            // disable picking by using this property
+            ((VtkCanvas) canvas).getPicker().PickFromListOn();
+        }
+    }
+
+    @Override
+    public vtkProp[] getProps()
+    {
+        return sphere_ens;
+    }
+}
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