diff --git a/pom.xml b/pom.xml
index 3a93736c9e08f7cf4f137c5b1ff124c35e6cadc0..61a58cf8dc9130da00dfc48ee6daa3b8c9243ea7 100644
--- a/pom.xml
+++ b/pom.xml
@@ -13,7 +13,7 @@
<!-- Project Information -->
<artifactId>3d-spheres-vtk</artifactId>
- <version>1.0.1</version>
+ <version>2.0.0</version>
<packaging>jar</packaging>
diff --git a/src/main/java/plugins/lagache/spherevtk/DrawSpheresVTK.java b/src/main/java/plugins/lagache/spherevtk/DrawSpheresVTK.java
index 5347509d4b748190c25b60c880b1528ce03c7b1d..b20e0efcd68fc541e42f8f2b3d4080da1f241cc9 100644
--- a/src/main/java/plugins/lagache/spherevtk/DrawSpheresVTK.java
+++ b/src/main/java/plugins/lagache/spherevtk/DrawSpheresVTK.java
@@ -1,59 +1,67 @@
-package plugins.lagache.spherevtk;
+/*
+ * 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/>.
+ */
-import java.awt.Color;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
+package plugins.lagache.spherevtk;
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;
+import plugins.adufour.vars.lang.*;
-// Colocalisation with Ripley function K
-// Significant
+import java.awt.*;
+/**
+ * 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()));
- }
-
- }
+ 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(final 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(final 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()));
+ }
+
+}
diff --git a/src/main/java/plugins/lagache/spherevtk/SphereVTK.java b/src/main/java/plugins/lagache/spherevtk/SphereVTK.java
index 1f038980d4c36d1dfedd41268da1da62b3f7ed60..639a95a20ace5baf1465b644629e705a798596ab 100644
--- a/src/main/java/plugins/lagache/spherevtk/SphereVTK.java
+++ b/src/main/java/plugins/lagache/spherevtk/SphereVTK.java
@@ -1,59 +1,43 @@
/*
- * Copyright 2010, 2011 Institut Pasteur.
- *
- * This file is part of ICY.
- *
- * ICY is free software: you can redistribute it and/or modify
+ * 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,
+ *
+ * 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/>.
+ * along with Icy. If not, see <https://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;
+import vtk.*;
+
+import java.awt.*;
/**
* @author stephane
*/
-public class SphereVTK extends Overlay implements VtkPainter
-{
+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)
- {
+ public SphereVTK(final double[] x, final double[] y, final double[] z, final double size, final Color color, final String name) {
super(name);
this.x = x;
@@ -65,8 +49,7 @@ public class SphereVTK extends Overlay implements VtkPainter
init();
}
- private void init()
- {
+ private void init() {
// create points
final vtkPoints points = new vtkPoints();
// setup scales
@@ -82,8 +65,7 @@ public class SphereVTK extends Overlay implements VtkPainter
// 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++)
- {
+ for (int i = 0; i < x.length; i++) {
points.InsertNextPoint(x[i], y[i], z[i]);
scales.InsertNextValue(1);
col.InsertNextValue(0); // first color
@@ -91,12 +73,12 @@ public class SphereVTK extends Overlay implements VtkPainter
// 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();
@@ -109,8 +91,8 @@ public class SphereVTK extends Overlay implements VtkPainter
sphere.SetPhiResolution(6);
// object to group sphere and grid and keep smooth interaction
- final vtkGlyph3D glyph3D = new vtkGlyph3D();
-
+ final vtkGlyph3D glyph3D = new vtkGlyph3D();
+
glyph3D.SetInputData(grid);
glyph3D.SetSourceConnection(sphere.GetOutputPort());
@@ -130,95 +112,18 @@ public class SphereVTK extends Overlay implements VtkPainter
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)
- {
+ public void paint(final Graphics2D g, final Sequence sequence, final IcyCanvas canvas) {
super.paint(g, sequence, canvas);
- if (canvas instanceof VtkCanvas)
- {
+ if (canvas instanceof VtkCanvas) {
// disable picking by using this property
((VtkCanvas) canvas).getPicker().PickFromListOn();
}
}
@Override
- public vtkProp[] getProps()
- {
+ public vtkProp[] getProps() {
return sphere_ens;
}
}
\ No newline at end of file