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Commit 2e0d7476 authored by Thomas MUSSET's avatar Thomas MUSSET
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updated pom, optimized code for java 11

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.gitignore
+ 2
− 1
View file @ 2e0d7476
......@@ -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
pom.xml
+ 5
− 7
View file @ 2e0d7476
<?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>
......
src/main/java/plugins/adufour/roi/Convexify.java
+ 60
− 64
View file @ 2e0d7476
/*
* 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);
}
}
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