From 0b2ea33e6b1c0fc18f45b78ac0afd543c4e357f8 Mon Sep 17 00:00:00 2001
From: Thomas <thomas.musset@pasteur.fr>
Date: Wed, 3 Jul 2024 16:28:54 +0200
Subject: [PATCH] updated pom to v6.0.0-a.1, fix classes accordingly to new
architecture, added icon, updated .gitignore
---
.gitignore | 46 +++++--
pom.xml | 46 ++++++-
.../adufour/roi/ROIConvexHullDescriptor.java | 46 +++----
.../roi/ROIEllipsoidFittingDescriptor.java | 62 ++++-----
.../roi/ROIFeretDiameterDescriptor.java | 37 +++---
.../roi/ROIHaralickTextureDescriptor.java | 43 +++---
.../java/plugins/adufour/roi/ROIMeasures.java | 123 ++++++++++--------
.../adufour/roi/ROIRoundnessDescriptor.java | 36 +++--
.../adufour/roi/ROISphericityDescriptor.java | 31 +++--
.../roi/ROIStatisticsTrackProcessor.java | 39 +++---
.../adufour/roi/ROITrackStatistics.java | 52 ++++----
.../ROIIntensityCenterDescriptorsPlugin.java | 32 +++--
.../ROIIntensityCenterXDescriptor.java | 18 +--
.../ROIIntensityCenterYDescriptor.java | 18 +--
.../ROIIntensityCenterZDescriptor.java | 18 +--
src/main/resources/roi-stat.png | Bin 0 -> 19128 bytes
16 files changed, 363 insertions(+), 284 deletions(-)
create mode 100644 src/main/resources/roi-stat.png
diff --git a/.gitignore b/.gitignore
index 0f33221..57f16fb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,13 +1,41 @@
-.idea/
-.settings/
-bin/
-build/
+/build*
+/workspace
+setting.xml
+release/
target/
-workspace/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
*.iml
-*.jar
+*.ipr
+
+### Eclipse ###
+.apt_generated
.classpath
+.factorypath
.project
-export.jardesc
-setting.xml
-**/.DS_Store
\ No newline at end of file
+.settings
+.springBeans
+.sts4-cache
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+
+### Mac OS ###
+**/.DS_Store
+Icon?
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index ead22e3..02ef00b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,11 +5,11 @@
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
- <version>2.2.0</version>
+ <version>3.0.0-a.1</version>
</parent>
<artifactId>roi-statistics</artifactId>
- <version>6.0.0</version>
+ <version>6.0.0-a.1</version>
<name>ROI Statistics</name>
<description>
@@ -18,36 +18,68 @@
</description>
<dependencies>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>kernel-extensions</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>quickhull</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>3d-mesh-roi</artifactId>
+ </dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>vecmath</artifactId>
</dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>active-contours</artifactId>
+ <artifactId>jama</artifactId>
</dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>convexify</artifactId>
+ <artifactId>ezplug</artifactId>
</dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>sequence-blocks</artifactId>
+ <artifactId>convexify</artifactId>
</dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>spot-tracking</artifactId>
+ <artifactId>protocols</artifactId>
</dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>workbooks</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>icy-jmath</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>track-manager</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>active-contours</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>spot-detection-utilities</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>spot-tracking</artifactId>
+ </dependency>
</dependencies>
<repositories>
<repository>
<id>icy</id>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
</repository>
</repositories>
</project>
\ No newline at end of file
diff --git a/src/main/java/plugins/adufour/roi/ROIConvexHullDescriptor.java b/src/main/java/plugins/adufour/roi/ROIConvexHullDescriptor.java
index cae4e71..13791ba 100644
--- a/src/main/java/plugins/adufour/roi/ROIConvexHullDescriptor.java
+++ b/src/main/java/plugins/adufour/roi/ROIConvexHullDescriptor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,20 +18,22 @@
package plugins.adufour.roi;
-import icy.plugin.abstract_.Plugin;
-import icy.plugin.interface_.PluginBundled;
-import icy.plugin.interface_.PluginROIDescriptor;
-import icy.roi.ROI;
-import icy.roi.ROI2D;
-import icy.roi.ROI3D;
-import icy.roi.ROIDescriptor;
-import icy.sequence.Sequence;
-import icy.type.point.Point3D;
+import org.bioimageanalysis.extension.kernel.roi.roi2d.ROI2DRectShape;
+import org.bioimageanalysis.icy.common.geom.point.Point3D;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.extension.plugin.interface_.PluginROIDescriptor;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.roi.ROI2D;
+import org.bioimageanalysis.icy.model.roi.ROI3D;
+import org.bioimageanalysis.icy.model.roi.ROIDescriptor;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import plugins.adufour.quickhull.QuickHull2D;
import plugins.adufour.quickhull.QuickHull3D;
import plugins.adufour.roi.mesh.Vertex3D;
import plugins.adufour.roi.mesh.polygon.ROI3DPolygonalMesh;
-import plugins.kernel.roi.roi2d.ROI2DRectShape;
import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;
@@ -42,7 +44,9 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
-public class ROIConvexHullDescriptor extends Plugin implements PluginROIDescriptor, PluginBundled {
+@IcyPluginName("ROI Convex Hull Descriptor")
+@IcyPluginIcon(path = "/roi-stat.png")
+public class ROIConvexHullDescriptor extends Plugin implements PluginROIDescriptor {
public static class ROIConvexity extends ROIDescriptor {
protected ROIConvexity() {
super("Convexity", Double.class);
@@ -85,9 +89,7 @@ public class ROIConvexHullDescriptor extends Plugin implements PluginROIDescript
if (roi.getNumberOfPoints() < 4)
return 100;
- if (roi instanceof ROI2D) {
- final ROI2D r2 = (ROI2D) roi;
-
+ if (roi instanceof final ROI2D r2) {
final Point[] pts = r2.getBooleanMask(true).getContourPoints();
if (pts.length < 4)
@@ -105,7 +107,7 @@ public class ROIConvexHullDescriptor extends Plugin implements PluginROIDescript
// contour = sum( sqrt[ (x[i] - x[i-1])^2 + (y[i] - y[i-1])^2 ] )
// area = 0.5 * sum( (x[i-1] * y[i]) - (y[i-1] * x[i]) )
- Point2D p1 = points.get(points.size() - 1), p2;
+ Point2D p1 = points.getLast(), p2;
for (final Point2D point : points) {
p2 = point;
@@ -118,8 +120,7 @@ public class ROIConvexHullDescriptor extends Plugin implements PluginROIDescript
else if (roi instanceof ROI3D) {
final Point3d[] points;
- if (roi instanceof ROI3DPolygonalMesh) {
- final ROI3DPolygonalMesh mesh = (ROI3DPolygonalMesh) roi;
+ if (roi instanceof final ROI3DPolygonalMesh mesh) {
// Tuple3d res = mesh.getPixelSize();
points = new Point3d[mesh.getNumberOfVertices(true)];
@@ -174,11 +175,11 @@ public class ROIConvexHullDescriptor extends Plugin implements PluginROIDescript
}
}
catch (final RuntimeException e) {
- System.err.println("Warning while computing the convexity of " + roi.getName() + ": " + e.getMessage());
+ IcyLogger.warn(ROIConvexity.class, e, "Warning while computing the convexity of " + roi.getName());
}
}
else {
- System.err.println("WARNING: cannot compute the convexity of a " + roi.getClassName());
+ IcyLogger.warn(ROIConvexity.class, "WARNING: cannot compute the convexity of a " + roi.getClassName());
return Double.NaN;
}
@@ -202,9 +203,4 @@ public class ROIConvexHullDescriptor extends Plugin implements PluginROIDescript
map.put(convexity, convexity.compute(roi, sequence));
return map;
}
-
- @Override
- public String getMainPluginClassName() {
- return ROIMeasures.class.getName();
- }
}
diff --git a/src/main/java/plugins/adufour/roi/ROIEllipsoidFittingDescriptor.java b/src/main/java/plugins/adufour/roi/ROIEllipsoidFittingDescriptor.java
index 7a0b1b9..0bc83ab 100644
--- a/src/main/java/plugins/adufour/roi/ROIEllipsoidFittingDescriptor.java
+++ b/src/main/java/plugins/adufour/roi/ROIEllipsoidFittingDescriptor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -20,19 +20,19 @@ package plugins.adufour.roi;
import Jama.EigenvalueDecomposition;
import Jama.Matrix;
-import icy.math.MathUtil;
-import icy.math.UnitUtil;
-import icy.plugin.abstract_.Plugin;
-import icy.plugin.interface_.PluginBundled;
-import icy.plugin.interface_.PluginROIDescriptor;
-import icy.roi.ROI;
-import icy.roi.ROI2D;
-import icy.roi.ROI3D;
-import icy.roi.ROIDescriptor;
-import icy.sequence.Sequence;
-import icy.type.point.Point3D;
+import org.bioimageanalysis.icy.common.geom.point.Point3D;
+import org.bioimageanalysis.icy.common.math.MathUtil;
+import org.bioimageanalysis.icy.common.math.UnitUtil;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.extension.plugin.interface_.PluginROIDescriptor;
+import org.bioimageanalysis.icy.model.roi.*;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import plugins.adufour.vars.lang.VarDouble;
-import plugins.kernel.roi.descriptor.measure.ROIMassCenterDescriptorsPlugin;
import javax.vecmath.*;
import java.awt.*;
@@ -40,7 +40,9 @@ import java.awt.geom.Point2D;
import java.util.List;
import java.util.*;
-public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDescriptor, PluginBundled {
+@IcyPluginName("ROI Ellipsoid Fitting Descriptor")
+@IcyPluginIcon(path = "/roi-stat.png")
+public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDescriptor {
public static class ROIFirstDiameter extends ROIDescriptor {
protected ROIFirstDiameter() {
super("1st Diameter", Double.class);
@@ -175,7 +177,7 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
* @return The first (or major) principle axis of the best fitting ellipse
* @throws InterruptedException if thread was interrupted
*/
- public static Vector3d computeFirstAxis(final ROI roi, final Sequence sequence) throws InterruptedException {
+ public static @NotNull Vector3d computeFirstAxis(final ROI roi, final Sequence sequence) throws InterruptedException {
final double[] ellipse = computeOrientation(roi, sequence);
return new Vector3d(ellipse[3], ellipse[4], ellipse[5]);
}
@@ -210,7 +212,7 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
* @return The second principle axis of the best fitting ellipse
* @throws InterruptedException if thread was interrupted
*/
- public static Vector3d computeSecondAxis(final ROI roi, final Sequence sequence) throws InterruptedException {
+ public static @NotNull Vector3d computeSecondAxis(final ROI roi, final Sequence sequence) throws InterruptedException {
final double[] ellipse = computeOrientation(roi, sequence);
return new Vector3d(ellipse[6], ellipse[7], ellipse[8]);
}
@@ -245,7 +247,7 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
* @return The third principle axis of the best fitting ellipse
* @throws InterruptedException if thread was interrupted
*/
- public static Vector3d computeThirdAxis(final ROI roi, final Sequence sequence) throws InterruptedException {
+ public static @NotNull Vector3d computeThirdAxis(final ROI roi, final Sequence sequence) throws InterruptedException {
if (roi instanceof ROI2D)
return new Vector3d();
@@ -457,6 +459,7 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
* @param ellipse ellipse orientation
* @return The elongation ratio of the X-Y plane
*/
+ @Contract(pure = true)
public static double computeElongation(final double[] ellipse) {
if (ellipse == null)
return Double.NaN;
@@ -503,6 +506,7 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
* @param ellipse ellipse orientation
* @return The 3D flatness ratio of the Y-Z plane
*/
+ @Contract(pure = true)
public static double computeFlatness3D(final double[] ellipse) {
if (ellipse == null)
return Double.NaN;
@@ -567,7 +571,8 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
return map;
}
- private static String getUnit(final Sequence sequence) {
+ @Contract(pure = true)
+ private static @NotNull String getUnit(final Sequence sequence) {
if (sequence == null)
return "px";
@@ -596,7 +601,7 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
* </ul>
* @throws InterruptedException if thread was interrupted
*/
- public static double[] computeOrientation(final ROI roi, final Sequence sequence) throws InterruptedException {
+ public static double @NotNull [] computeOrientation(final ROI roi, final Sequence sequence) throws InterruptedException {
final double[] ellipse = new double[12];
if (roi instanceof ROI2D) {
@@ -661,7 +666,7 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
}
}
else {
- System.err.println("Cannot compute ellipse dimensions for ROI of type: " + roi.getClassName());
+ IcyLogger.error(ROIEllipsoidFittingDescriptor.class, "Cannot compute ellipse dimensions for ROI of type: " + roi.getClassName());
Arrays.fill(ellipse, Double.NaN);
}
@@ -695,7 +700,7 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
* @throws InterruptedException
* @throws SingularMatrixException if the component is flat (i.e. lies in a 2D plane)
*/
- private static void fitEllipse(final ROI3D cc, final Point3d radii, final Vector3d[] eigenVectors, final double[] equation) throws IllegalArgumentException, InterruptedException {
+ private static void fitEllipse(final @NotNull ROI3D cc, final Point3d radii, final Vector3d[] eigenVectors, final double[] equation) throws IllegalArgumentException, InterruptedException {
final Point3D.Integer[] points = cc.getBooleanMask(true).getContourPoints();
if (points.length < 9) {
@@ -789,7 +794,7 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
* @throws InterruptedException
*/
private static void fitEllipse(
- final ROI2D roi,
+ final @NotNull ROI2D roi,
final Point2d center,
final Point2d radii,
final VarDouble angle,
@@ -801,7 +806,7 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
if (points.length < 4)
return;
- final Point2D ccenter = ROIMassCenterDescriptorsPlugin.computeMassCenter(roi).toPoint2D();
+ final Point2D ccenter = ROIUtil.computeMassCenter(roi).toPoint2D();
final double cx = ccenter.getX();
final double cy = ccenter.getY();
@@ -924,7 +929,8 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
}
}
- private static Matrix diag(final Matrix matrix) {
+ @Contract("_ -> new")
+ private static @NotNull Matrix diag(final @NotNull Matrix matrix) {
final int min = Math.min(matrix.getRowDimension(), matrix.getColumnDimension());
final double[][] diag = new double[min][1];
for (int i = 0; i < min; i++) {
@@ -933,15 +939,11 @@ public class ROIEllipsoidFittingDescriptor extends Plugin implements PluginROIDe
return new Matrix(diag);
}
- private static Matrix ones(final int m, final int n) {
+ @Contract("_, _ -> new")
+ private static @NotNull Matrix ones(final int m, final int n) {
final double[][] array = new double[m][n];
for (final double[] row : array)
Arrays.fill(row, 1.0);
return new Matrix(array, m, n);
}
-
- @Override
- public String getMainPluginClassName() {
- return ROIMeasures.class.getName();
- }
}
diff --git a/src/main/java/plugins/adufour/roi/ROIFeretDiameterDescriptor.java b/src/main/java/plugins/adufour/roi/ROIFeretDiameterDescriptor.java
index 859adbb..49960e3 100644
--- a/src/main/java/plugins/adufour/roi/ROIFeretDiameterDescriptor.java
+++ b/src/main/java/plugins/adufour/roi/ROIFeretDiameterDescriptor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,19 +18,21 @@
package plugins.adufour.roi;
-import icy.math.UnitUtil;
-import icy.plugin.abstract_.Plugin;
-import icy.plugin.interface_.PluginBundled;
-import icy.plugin.interface_.PluginROIDescriptor;
-import icy.roi.ROI;
-import icy.roi.ROI2D;
-import icy.roi.ROI3D;
-import icy.roi.ROIDescriptor;
-import icy.sequence.Sequence;
-import icy.type.point.Point3D;
+import org.bioimageanalysis.extension.kernel.roi.roi2d.ROI2DRectShape;
+import org.bioimageanalysis.icy.common.geom.point.Point3D;
+import org.bioimageanalysis.icy.common.math.UnitUtil;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.extension.plugin.interface_.PluginROIDescriptor;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.roi.ROI2D;
+import org.bioimageanalysis.icy.model.roi.ROI3D;
+import org.bioimageanalysis.icy.model.roi.ROIDescriptor;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import plugins.adufour.roi.mesh.Vertex3D;
import plugins.adufour.roi.mesh.polygon.ROI3DPolygonalMesh;
-import plugins.kernel.roi.roi2d.ROI2DRectShape;
import javax.vecmath.Point3d;
import java.awt.*;
@@ -41,7 +43,9 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
-public class ROIFeretDiameterDescriptor extends Plugin implements PluginROIDescriptor, PluginBundled {
+@IcyPluginName("ROI Feret Diameter Descriptor")
+@IcyPluginIcon(path = "/roi-stat.png")
+public class ROIFeretDiameterDescriptor extends Plugin implements PluginROIDescriptor {
public static class ROIFeretDiameter extends ROIDescriptor {
protected ROIFeretDiameter() {
super("Max Feret diameter", Double.class);
@@ -153,7 +157,7 @@ public class ROIFeretDiameterDescriptor extends Plugin implements PluginROIDescr
maxDistance = Math.sqrt(maxDistance);
}
else {
- System.err.println("Cannot compute Max. Feret diameter for ROI of type: " + roi.getClassName());
+ IcyLogger.error(ROIFeretDiameter.class, "Cannot compute Max. Feret diameter for ROI of type: " + roi.getClassName());
maxDistance = 0.0d;
}
@@ -176,9 +180,4 @@ public class ROIFeretDiameterDescriptor extends Plugin implements PluginROIDescr
map.put(feretDiameter, feretDiameter.compute(roi, sequence));
return map;
}
-
- @Override
- public String getMainPluginClassName() {
- return ROIMeasures.class.getName();
- }
}
diff --git a/src/main/java/plugins/adufour/roi/ROIHaralickTextureDescriptor.java b/src/main/java/plugins/adufour/roi/ROIHaralickTextureDescriptor.java
index cb2273e..514218d 100644
--- a/src/main/java/plugins/adufour/roi/ROIHaralickTextureDescriptor.java
+++ b/src/main/java/plugins/adufour/roi/ROIHaralickTextureDescriptor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,25 +18,29 @@
package plugins.adufour.roi;
-import icy.image.IcyBufferedImage;
-import icy.image.IcyBufferedImageUtil;
-import icy.math.ArrayMath;
-import icy.plugin.abstract_.Plugin;
-import icy.plugin.interface_.PluginBundled;
-import icy.plugin.interface_.PluginROIDescriptor;
-import icy.roi.BooleanMask2D;
-import icy.roi.ROI;
-import icy.roi.ROI2D;
-import icy.roi.ROIDescriptor;
-import icy.sequence.Sequence;
-import icy.type.DataType;
+import org.bioimageanalysis.icy.common.math.ArrayMath;
+import org.bioimageanalysis.icy.common.type.DataType;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.extension.plugin.interface_.PluginROIDescriptor;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImageUtil;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.roi.ROI2D;
+import org.bioimageanalysis.icy.model.roi.ROIDescriptor;
+import org.bioimageanalysis.icy.model.roi.mask.BooleanMask2D;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.jetbrains.annotations.NotNull;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-public class ROIHaralickTextureDescriptor extends Plugin implements PluginROIDescriptor, PluginBundled {
+@IcyPluginName("ROI Haralick Texture Descriptor")
+@IcyPluginIcon(path = "/roi-stat.png")
+public class ROIHaralickTextureDescriptor extends Plugin implements PluginROIDescriptor {
private static abstract class ROIHaralickDescriptor extends ROIDescriptor {
protected final int step;
@@ -211,7 +215,7 @@ public class ROIHaralickTextureDescriptor extends Plugin implements PluginROIDes
* (see {@link #getDescriptors()}) for a full list
* @throws InterruptedException
*/
- public static Map<ROIDescriptor, Object> computeHaralickFeatures(final Sequence sequence, final ROI2D roi, final int step) throws InterruptedException {
+ public static @NotNull Map<ROIDescriptor, Object> computeHaralickFeatures(final Sequence sequence, final @NotNull ROI2D roi, final int step) throws InterruptedException {
final int c = roi.getC();
if (c == -1)
throw new UnsupportedOperationException("Texture can only be calculated on a single channel");
@@ -295,10 +299,10 @@ public class ROIHaralickTextureDescriptor extends Plugin implements PluginROIDes
* input region of interest (ROI)
* @throws InterruptedException
*/
- private static IcyBufferedImage buildGLCM(final IcyBufferedImage image, final ROI2D roi, final int step) throws InterruptedException {
+ private static @NotNull IcyBufferedImage buildGLCM(final @NotNull IcyBufferedImage image, final ROI2D roi, final int step) throws InterruptedException {
// Rescale to [0-255] if necessary
IcyBufferedImage imByte = null;
- if (image.getDataType_() == DataType.UBYTE) {
+ if (image.getDataType() == DataType.UBYTE) {
imByte = image;
}
else {
@@ -372,9 +376,4 @@ public class ROIHaralickTextureDescriptor extends Plugin implements PluginROIDes
return coocImage;
}
-
- @Override
- public String getMainPluginClassName() {
- return ROIMeasures.class.getName();
- }
}
diff --git a/src/main/java/plugins/adufour/roi/ROIMeasures.java b/src/main/java/plugins/adufour/roi/ROIMeasures.java
index 15a2b8d..aeb14a0 100644
--- a/src/main/java/plugins/adufour/roi/ROIMeasures.java
+++ b/src/main/java/plugins/adufour/roi/ROIMeasures.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,31 +18,35 @@
package plugins.adufour.roi;
-import icy.file.FileUtil;
-import icy.gui.main.GlobalSequenceListener;
-import icy.main.Icy;
-import icy.plugin.PluginLauncher;
-import icy.plugin.PluginLoader;
-import icy.preferences.XMLPreferences;
-import icy.roi.*;
-import icy.roi.ROIEvent.ROIEventType;
-import icy.sequence.Sequence;
-import icy.sequence.SequenceDataIterator;
-import icy.sequence.SequenceEvent;
-import icy.sequence.SequenceEvent.SequenceEventSourceType;
-import icy.sequence.SequenceListener;
-import icy.system.IcyExceptionHandler;
-import icy.system.SystemUtil;
-import icy.system.thread.Processor;
-import icy.system.thread.ThreadUtil;
-import icy.type.point.Point3D;
-import icy.type.point.Point5D;
-import icy.type.rectangle.Rectangle5D;
-import icy.util.StringUtil;
import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.ss.usermodel.Workbook;
import org.apache.poi.ss.util.WorkbookUtil;
+import org.bioimageanalysis.extension.kernel.roi.descriptor.measure.ROIContourDescriptor;
+import org.bioimageanalysis.extension.kernel.roi.descriptor.measure.ROIInteriorDescriptor;
+import org.bioimageanalysis.icy.Icy;
+import org.bioimageanalysis.icy.common.geom.point.Point5D;
+import org.bioimageanalysis.icy.common.geom.point.Point3D;
+import org.bioimageanalysis.icy.common.geom.rectangle.Rectangle5D;
+import org.bioimageanalysis.icy.common.string.StringUtil;
+import org.bioimageanalysis.icy.extension.plugin.PluginLauncher;
+import org.bioimageanalysis.icy.extension.plugin.PluginLoader;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.gui.listener.GlobalSequenceListener;
+import org.bioimageanalysis.icy.io.FileUtil;
+import org.bioimageanalysis.icy.model.roi.*;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.SequenceDataIterator;
+import org.bioimageanalysis.icy.model.sequence.SequenceEvent;
+import org.bioimageanalysis.icy.model.sequence.SequenceListener;
+import org.bioimageanalysis.icy.system.SystemUtil;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
+import org.bioimageanalysis.icy.system.preferences.XMLPreferences;
+import org.bioimageanalysis.icy.system.thread.Processor;
+import org.bioimageanalysis.icy.system.thread.ThreadUtil;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import plugins.adufour.blocks.tools.roi.ROIBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.ezplug.EzDialog;
@@ -65,8 +69,6 @@ import plugins.adufour.vars.util.VarReferencingPolicy;
import plugins.adufour.workbooks.IcySpreadSheet;
import plugins.adufour.workbooks.Workbooks;
import plugins.kernel.roi.descriptor.measure.ROIBasicMeasureDescriptorsPlugin;
-import plugins.kernel.roi.descriptor.measure.ROIContourDescriptor;
-import plugins.kernel.roi.descriptor.measure.ROIInteriorDescriptor;
import plugins.kernel.roi.descriptor.measure.ROIMassCenterDescriptorsPlugin;
import javax.swing.*;
@@ -85,8 +87,9 @@ import java.util.concurrent.Future;
* @author Alexandre Dufour
* @author Daniel Gonzalez
*/
+@IcyPluginName("ROI Measures")
+@IcyPluginIcon(path = "/roi-stat.png")
public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListener, SequenceListener, ROIListener {
-
/**
* Measures available for this plugin.
* <b>Note:</b> The id is used when loading and saving parameters.
@@ -121,6 +124,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
final int id;
final String unit;
+ @Contract(pure = true)
Measures(final String name, final int id, final String unit) {
this.name = name;
this.id = id;
@@ -129,31 +133,39 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
boolean selected = true;
+ @SuppressWarnings("UnstableApiUsage")
+ @Contract(mutates = "this")
public void toggleSelection() {
selected = !selected;
}
+ @SuppressWarnings("UnstableApiUsage")
+ @Contract(mutates = "this")
public void setSelected(final boolean value) {
selected = value;
}
+ @Contract(pure = true)
@Override
public String toString() {
return name;
}
- public String toHeader() {
+ public @NotNull String toHeader() {
return name + (hasUnit() ? " (" + getUnit() + ")" : "");
}
+ @Contract(pure = true)
public boolean hasUnit() {
return unit != null && !unit.isEmpty();
}
+ @Contract(pure = true)
public String getUnit() {
return unit;
}
+ @Contract(pure = true)
public boolean isSelected() {
return selected;
}
@@ -226,7 +238,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
}
@Override
- public void declareInput(final VarList inputMap) {
+ public void declareInput(final @NotNull VarList inputMap) {
measureSelector.setReferencingPolicy(VarReferencingPolicy.NONE);
inputMap.add("measures", measureSelector);
inputMap.add("Regions of interest", rois);
@@ -234,7 +246,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
}
@Override
- public void declareOutput(final VarList outputMap) {
+ public void declareOutput(final @NotNull VarList outputMap) {
outputMap.add("Workbook", book);
}
@@ -271,7 +283,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
book.setValue(wbs);
}
catch (final IOException e) {
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(this.getClass(), e);
}
//book.setValue(wb = Workbooks.createEmptyWorkbook());
}
@@ -293,7 +305,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
// try retrieving the sequence attached to the first ROI
final List<Sequence> sequences = rois.getValue()[0].getSequences();
if (!sequences.isEmpty())
- sequenceOfInterest = sequences.get(0);
+ sequenceOfInterest = sequences.getFirst();
}
if (sequenceOfInterest == null) {
@@ -418,7 +430,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
return;
}
catch (final Exception e) {
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(this.getClass(), e);
return;
}
@@ -433,7 +445,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
}
}
- private void updateStatistics(final ROI roi) {
+ private void updateStatistics(final @NotNull ROI roi) {
final Workbook wb = book.getValue();
for (final Sequence sequenceOfInterest : roi.getSequences())
@@ -452,13 +464,13 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
}
}
- private static String colorToString(final Color color) {
+ private static @NotNull String colorToString(final @NotNull Color color) {
return (StringUtil.toHexaString(color.getAlpha(), 2) + StringUtil.toHexaString(color.getRed(), 2)
+ StringUtil.toHexaString(color.getGreen(), 2) + StringUtil.toHexaString(color.getBlue(), 2))
.toUpperCase();
}
- private void updateWorkbook(final Workbook wb, final IcySpreadSheet sheet, final int rowID, final List<Object> measures, final boolean updateInterface) {
+ private void updateWorkbook(final Workbook wb, final IcySpreadSheet sheet, final int rowID, final @NotNull List<Object> measures, final boolean updateInterface) {
for (int colID = 0; colID < measures.size(); colID++) {
final Object value = measures.get(colID);
@@ -474,7 +486,9 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
book.valueChanged(book, null, book.getValue());
}
- private Callable<List<Object>> createUpdater(final Sequence sequenceOfInterest, final ROI roi2Update) {
+ @SuppressWarnings("resource")
+ @Contract(pure = true)
+ private @NotNull Callable<List<Object>> createUpdater(final Sequence sequenceOfInterest, final ROI roi2Update) {
return () -> {
final List<Object> measures = new ArrayList<>();
final List<Measures> measuresToCalculate = new ArrayList<>();
@@ -493,7 +507,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
|| Measures.T_CENTER.isSelected() || Measures.C_CENTER.isSelected()
|| Measures.X_GLOBAL_CENTER.isSelected() || Measures.Y_GLOBAL_CENTER.isSelected()
|| Measures.Z_GLOBAL_CENTER.isSelected()) {
- center = ROIMassCenterDescriptorsPlugin.computeMassCenter(roi);
+ center = ROIUtil.computeMassCenter(roi);
globalCenter = center.toPoint3D();
if (sequenceOfInterest != null) {
globalCenter.setX(sequenceOfInterest.getPositionX()
@@ -596,7 +610,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
// we don't want to spam output with these errors
if (!haralickErrors.contains(mess)) {
haralickErrors.add(mess);
- System.err.println(mess);
+ IcyLogger.error(this.getClass(), ex);
}
}
}
@@ -866,8 +880,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
if (sequenceOfInterest == null)
measures.add("NA");
else {
- final double mul = ROIBasicMeasureDescriptorsPlugin
- .getMultiplierFactor(sequenceOfInterest, roi, 2);
+ final double mul = ROIUtil.getMultiplierFactor(sequenceOfInterest, roi, 2);
// 0 means the operation is not supported for this ROI
if (mul == 0d)
@@ -888,8 +901,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
if (sequenceOfInterest == null)
measures.add("NA");
else {
- final double mul1 = ROIBasicMeasureDescriptorsPlugin
- .getMultiplierFactor(sequenceOfInterest, roi, 3);
+ final double mul1 = ROIUtil.getMultiplierFactor(sequenceOfInterest, roi, 3);
// 0 means the operation is not supported for this ROI
if (mul1 == 0d)
@@ -902,16 +914,19 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
}
break;
case INTENSITY_X:
+ Objects.requireNonNull(intensityCenters);
for (int c = 0; c < sizeC; c++) {
measures.add(intensityCenters[c].getX());
}
break;
case INTENSITY_Y:
+ Objects.requireNonNull(intensityCenters);
for (int c = 0; c < sizeC; c++) {
measures.add(intensityCenters[c].getY());
}
break;
case INTENSITY_Z:
+ Objects.requireNonNull(intensityCenters);
for (int c = 0; c < sizeC; c++) {
measures.add(intensityCenters[c].getZ());
}
@@ -931,7 +946,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
// MAIN LISTENER //
@Override
- public void sequenceOpened(final Sequence openedSequence) {
+ public void sequenceOpened(final @NotNull Sequence openedSequence) {
openedSequence.addListener(this);
for (final ROI roi : openedSequence.getROIs())
roi.addListener(this);
@@ -944,7 +959,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
}
@Override
- public void sequenceClosed(final Sequence closedSequence) {
+ public void sequenceClosed(final @NotNull Sequence closedSequence) {
closedSequence.removeListener(this);
for (final ROI roi : closedSequence.getROIs())
roi.removeListener(this);
@@ -963,12 +978,12 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
// SEQUENCE LISTENER //
@Override
- public void sequenceChanged(final SequenceEvent sequenceEvent) {
- if (sequenceEvent.getSourceType() == SequenceEventSourceType.SEQUENCE_DATA) {
+ public void sequenceChanged(final @NotNull SequenceEvent sequenceEvent) {
+ if (sequenceEvent.getSourceType() == SequenceEvent.SequenceEventSourceType.SEQUENCE_DATA) {
updateStatistics(sequenceEvent.getSequence());
}
- else if (sequenceEvent.getSourceType() == SequenceEventSourceType.SEQUENCE_ROI) {
+ else if (sequenceEvent.getSourceType() == SequenceEvent.SequenceEventSourceType.SEQUENCE_ROI) {
final ROI roi = (ROI) sequenceEvent.getSource();
switch (sequenceEvent.getType()) {
@@ -991,7 +1006,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
if (roi == null) {
// multiple ROIs have been removed
- System.err.println("[ROI Statistics] Warning: potential memory leak");
+ IcyLogger.warn(this.getClass(), "Warning: potential memory leak");
}
else {
roi.removeListener(this);
@@ -1021,9 +1036,9 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
}
@Override
- public void roiChanged(final ROIEvent event) {
- if (event.getType() == ROIEventType.ROI_CHANGED
- || event.getType() == ROIEventType.PROPERTY_CHANGED && (event.getPropertyName().equalsIgnoreCase("name")
+ public void roiChanged(final @NotNull ROIEvent event) {
+ if (event.getType() == ROIEvent.ROIEventType.ROI_CHANGED
+ || event.getType() == ROIEvent.ROIEventType.PROPERTY_CHANGED && (event.getPropertyName().equalsIgnoreCase("name")
|| event.getPropertyName().equalsIgnoreCase("color"))) {
updateStatistics(event.getSource());
// this is mandatory since sheet modification cannot be detected
@@ -1049,8 +1064,9 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
setNameVisible(false);
}
+ @Contract(" -> new")
@Override
- protected JButton createEditorComponent() {
+ protected @NotNull JButton createEditorComponent() {
if (getEditorComponent() != null)
deactivateListeners();
@@ -1074,6 +1090,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
getEditorComponent().removeActionListener(listener);
}
+ @Contract(pure = true)
@Override
protected void updateInterfaceValue() {
// nothing to do (it's just a button with a name)
@@ -1103,8 +1120,9 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
addListener(gui);
}
+ @Contract(" -> new")
@Override
- public VarEditor<Long> createVarEditor() {
+ public @NotNull VarEditor<Long> createVarEditor() {
return new ButtonVarEditor(this);
}
@@ -1241,6 +1259,7 @@ public class ROIMeasures extends EzPlug implements ROIBlock, GlobalSequenceListe
}
}
+ @SuppressWarnings("resource")
public static void main(final String[] args) {
Icy.main(args);
diff --git a/src/main/java/plugins/adufour/roi/ROIRoundnessDescriptor.java b/src/main/java/plugins/adufour/roi/ROIRoundnessDescriptor.java
index 2da0b4c..ab3da3b 100644
--- a/src/main/java/plugins/adufour/roi/ROIRoundnessDescriptor.java
+++ b/src/main/java/plugins/adufour/roi/ROIRoundnessDescriptor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,19 +18,18 @@
package plugins.adufour.roi;
-import icy.plugin.abstract_.Plugin;
-import icy.plugin.interface_.PluginBundled;
-import icy.plugin.interface_.PluginROIDescriptor;
-import icy.roi.ROI;
-import icy.roi.ROI2D;
-import icy.roi.ROI3D;
-import icy.roi.ROIDescriptor;
-import icy.sequence.Sequence;
-import icy.type.point.Point3D;
-import icy.type.point.Point5D;
+import org.bioimageanalysis.extension.kernel.roi.roi2d.ROI2DEllipse;
+import org.bioimageanalysis.icy.common.geom.point.Point3D;
+import org.bioimageanalysis.icy.common.geom.point.Point5D;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.extension.plugin.interface_.PluginROIDescriptor;
+import org.bioimageanalysis.icy.model.roi.*;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import plugins.adufour.roi.ROISphericityDescriptor.ROISphericity;
import plugins.kernel.roi.descriptor.measure.ROIMassCenterDescriptorsPlugin;
-import plugins.kernel.roi.roi2d.ROI2DEllipse;
import javax.vecmath.Point3d;
import java.awt.*;
@@ -41,7 +40,9 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
-public class ROIRoundnessDescriptor extends Plugin implements PluginROIDescriptor, PluginBundled {
+@IcyPluginName("ROI Roundness Descriptor")
+@IcyPluginIcon(path = "/roi-stat.png")
+public class ROIRoundnessDescriptor extends Plugin implements PluginROIDescriptor {
public static class ROIRoundness extends ROIDescriptor {
public ROIRoundness() {
super("Roundness", Double.class);
@@ -111,7 +112,7 @@ public class ROIRoundnessDescriptor extends Plugin implements PluginROIDescripto
public static double computeRoundness(final ROI roi) throws InterruptedException {
double minDistance = Double.MAX_VALUE, maxDistance = 0.0d;
- final Point5D center = ROIMassCenterDescriptorsPlugin.computeMassCenter(roi);
+ final Point5D center = ROIUtil.computeMassCenter(roi);
if (roi instanceof ROI2D) {
if (roi instanceof ROI2DEllipse) {
@@ -146,7 +147,7 @@ public class ROIRoundnessDescriptor extends Plugin implements PluginROIDescripto
}
}
else {
- System.err.println("Cannot compute roundness for ROI of type: " + roi.getClassName());
+ IcyLogger.error(ROIRoundness.class, "Cannot compute roundness for ROI of type: " + roi.getClassName());
return Double.NaN;
}
@@ -171,9 +172,4 @@ public class ROIRoundnessDescriptor extends Plugin implements PluginROIDescripto
map.put(roundness, roundness.compute(roi, sequence));
return map;
}
-
- @Override
- public String getMainPluginClassName() {
- return ROIMeasures.class.getName();
- }
}
diff --git a/src/main/java/plugins/adufour/roi/ROISphericityDescriptor.java b/src/main/java/plugins/adufour/roi/ROISphericityDescriptor.java
index ce81dae..a3edb22 100644
--- a/src/main/java/plugins/adufour/roi/ROISphericityDescriptor.java
+++ b/src/main/java/plugins/adufour/roi/ROISphericityDescriptor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,21 +18,25 @@
package plugins.adufour.roi;
-import icy.plugin.abstract_.Plugin;
-import icy.plugin.interface_.PluginBundled;
-import icy.plugin.interface_.PluginROIDescriptor;
-import icy.roi.ROI;
-import icy.roi.ROI2D;
-import icy.roi.ROI3D;
-import icy.roi.ROIDescriptor;
-import icy.sequence.Sequence;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.extension.plugin.interface_.PluginROIDescriptor;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.roi.ROI2D;
+import org.bioimageanalysis.icy.model.roi.ROI3D;
+import org.bioimageanalysis.icy.model.roi.ROIDescriptor;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-public class ROISphericityDescriptor extends Plugin implements PluginROIDescriptor, PluginBundled {
+@IcyPluginName("ROI Sphericity Descriptor")
+@IcyPluginIcon(path = "/roi-stat.png")
+public class ROISphericityDescriptor extends Plugin implements PluginROIDescriptor {
public static class ROISphericity extends ROIDescriptor {
public ROISphericity() {
super("Sphericity", Double.class);
@@ -101,7 +105,7 @@ public class ROISphericityDescriptor extends Plugin implements PluginROIDescript
dim = 3.0d;
}
else {
- System.err.println("Cannot compute sphericity for ROI of type: " + roi.getClassName());
+ IcyLogger.error(ROISphericity.class, "Cannot compute sphericity for ROI of type: " + roi.getClassName());
return Double.NaN;
}
@@ -147,9 +151,4 @@ public class ROISphericityDescriptor extends Plugin implements PluginROIDescript
map.put(sphericity, sphericity.compute(roi, sequence));
return map;
}
-
- @Override
- public String getMainPluginClassName() {
- return ROIMeasures.class.getName();
- }
}
diff --git a/src/main/java/plugins/adufour/roi/ROIStatisticsTrackProcessor.java b/src/main/java/plugins/adufour/roi/ROIStatisticsTrackProcessor.java
index 67bab6d..0b79970 100644
--- a/src/main/java/plugins/adufour/roi/ROIStatisticsTrackProcessor.java
+++ b/src/main/java/plugins/adufour/roi/ROIStatisticsTrackProcessor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,15 +18,14 @@
package plugins.adufour.roi;
-import icy.file.FileUtil;
-import icy.gui.dialog.SaveDialog;
-import icy.gui.frame.progress.AnnounceFrame;
-import icy.gui.util.GuiUtil;
-import icy.plugin.interface_.PluginBundled;
-import icy.roi.ROIDescriptor;
-import icy.sequence.Sequence;
-import icy.system.IcyExceptionHandler;
import org.apache.poi.ss.usermodel.Workbook;
+import org.bioimageanalysis.icy.gui.GuiUtil;
+import org.bioimageanalysis.icy.gui.dialog.SaveDialog;
+import org.bioimageanalysis.icy.gui.frame.progress.AnnounceFrame;
+import org.bioimageanalysis.icy.io.FileUtil;
+import org.bioimageanalysis.icy.model.roi.ROIDescriptor;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.system.logging.IcyLogger;
import org.math.plot.Plot2DPanel;
import plugins.adufour.blocks.tools.io.WorkbookToFile;
import plugins.adufour.blocks.tools.io.WorkbookToFile.MergePolicy;
@@ -42,12 +41,7 @@ import javax.swing.*;
import java.awt.*;
import java.io.IOException;
-public class ROIStatisticsTrackProcessor extends PluginTrackManagerProcessor implements PluginBundled {
- @Override
- public String getMainPluginClassName() {
- return ROIMeasures.class.getName();
- }
-
+public class ROIStatisticsTrackProcessor extends PluginTrackManagerProcessor {
private final JButton exportButton = new JButton("Export to XLS...");
private final VarSequence sequence = new VarSequence("Sequence", null);
@@ -134,8 +128,13 @@ public class ROIStatisticsTrackProcessor extends PluginTrackManagerProcessor imp
final Sequence seq = trackPool.getDisplaySequence();
try {
- ROITrackStatistics.buildPlot(trackPool.getTrackGroupList(), seq, channel.getValue(),
- ROIDescriptor.getDescriptor(roiDescriptor.getValue()), plotPanel);
+ ROITrackStatistics.buildPlot(
+ trackPool.getTrackGroupList(),
+ seq,
+ channel.getValue(),
+ ROIDescriptor.getDescriptor(roiDescriptor.getValue()),
+ plotPanel
+ );
if (!plotPanel.getPlots().isEmpty()) {
chartPanel.add(plotPanel);
@@ -148,7 +147,7 @@ public class ROIStatisticsTrackProcessor extends PluginTrackManagerProcessor imp
}
}
catch (final Exception e) {
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(this.getClass(), e, "Cannot compute descriptor.");
chartPanel.add(new JLabel("Cannot compute descriptor: " + e.getMessage()));
exportButton.setEnabled(false);
}
@@ -172,7 +171,7 @@ public class ROIStatisticsTrackProcessor extends PluginTrackManagerProcessor imp
// Restore last used folder
final String xlsFolder = getPreferencesRoot().get("xlsFolder", null);
- final String path = SaveDialog.chooseFile("Export statistics", xlsFolder, name, ".xls");
+ final String path = SaveDialog.chooseFile("Export statistics", xlsFolder, name, ".xlsx");
// canceled
if (path == null)
@@ -191,7 +190,7 @@ public class ROIStatisticsTrackProcessor extends PluginTrackManagerProcessor imp
}
}
catch (final IOException e) {
- IcyExceptionHandler.showErrorMessage(e, true);
+ IcyLogger.error(this.getClass(), e, "Cannot export statistics.");
}
finally {
message.close();
diff --git a/src/main/java/plugins/adufour/roi/ROITrackStatistics.java b/src/main/java/plugins/adufour/roi/ROITrackStatistics.java
index 6cf4613..0e49661 100644
--- a/src/main/java/plugins/adufour/roi/ROITrackStatistics.java
+++ b/src/main/java/plugins/adufour/roi/ROITrackStatistics.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,15 +18,21 @@
package plugins.adufour.roi;
-import icy.plugin.abstract_.Plugin;
-import icy.plugin.interface_.PluginBundled;
-import icy.roi.ROI;
-import icy.roi.ROI2D;
-import icy.roi.ROI3D;
-import icy.roi.ROIDescriptor;
-import icy.sequence.Sequence;
-import icy.type.collection.CollectionUtil;
import org.apache.poi.ss.usermodel.Workbook;
+import org.bioimageanalysis.extension.kernel.roi.roi2d.ROI2DArea;
+import org.bioimageanalysis.extension.kernel.roi.roi2d.ROI2DPoint;
+import org.bioimageanalysis.extension.kernel.roi.roi3d.ROI3DArea;
+import org.bioimageanalysis.extension.kernel.roi.roi3d.ROI3DPoint;
+import org.bioimageanalysis.icy.common.collection.CollectionUtil;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.roi.ROI2D;
+import org.bioimageanalysis.icy.model.roi.ROI3D;
+import org.bioimageanalysis.icy.model.roi.ROIDescriptor;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.jetbrains.annotations.NotNull;
import org.math.plot.Plot2DPanel;
import org.math.plot.plots.Plot;
import plugins.adufour.activecontours.ActiveContour;
@@ -39,10 +45,6 @@ import plugins.adufour.workbooks.IcySpreadSheet;
import plugins.adufour.workbooks.Workbooks;
import plugins.fab.trackmanager.TrackGroup;
import plugins.fab.trackmanager.TrackSegment;
-import plugins.kernel.roi.roi2d.ROI2DArea;
-import plugins.kernel.roi.roi2d.ROI2DPoint;
-import plugins.kernel.roi.roi3d.ROI3DArea;
-import plugins.kernel.roi.roi3d.ROI3DPoint;
import plugins.nchenouard.particletracking.DetectionSpotTrack;
import plugins.nchenouard.particletracking.legacytracker.SpotTrack;
import plugins.nchenouard.spot.Detection;
@@ -55,15 +57,22 @@ import java.util.List;
*
* @author Stephane Dallongeville
*/
-public class ROITrackStatistics extends Plugin implements ROIBlock, PluginBundled {
+@IcyPluginName("ROI Track Statistics")
+@IcyPluginIcon(path = "/roi-stat.png")
+public class ROITrackStatistics extends Plugin implements ROIBlock {
/**
* Build the plot describing the {@link ROIDescriptor} evolution along given input tracks
*
* @throws InterruptedException
* @throws UnsupportedOperationException
*/
- public static void buildPlot(final List<TrackGroup> trackGroups, final Sequence sequence, final int channel, final ROIDescriptor descriptor, final Plot2DPanel plotPanel)
- throws UnsupportedOperationException, InterruptedException {
+ public static void buildPlot(
+ final @NotNull List<TrackGroup> trackGroups,
+ final Sequence sequence,
+ final int channel,
+ final @NotNull ROIDescriptor descriptor,
+ final @NotNull Plot2DPanel plotPanel
+ ) throws UnsupportedOperationException, InterruptedException {
final int sizeZ = (sequence != null) ? sequence.getSizeZ() : 1;
final double timeInterval = (sequence != null) ? sequence.getTimeInterval() : 1d;
@@ -178,7 +187,7 @@ public class ROITrackStatistics extends Plugin implements ROIBlock, PluginBundle
/**
* Build and return the workbook describing the {@link ROIDescriptor} evolution along given input tracks
*/
- public static Workbook getWorkBook(final Sequence sequence, final String name, final Plot2DPanel plotPanel) {
+ public static @NotNull Workbook getWorkBook(final Sequence sequence, final String name, final Plot2DPanel plotPanel) {
final Workbook wb = Workbooks.createEmptyWorkbook();
final IcySpreadSheet sheet = Workbooks.getSheet(wb, name);
@@ -225,7 +234,7 @@ public class ROITrackStatistics extends Plugin implements ROIBlock, PluginBundle
}
@Override
- public void declareInput(final VarList inputMap) {
+ public void declareInput(final @NotNull VarList inputMap) {
inputMap.add("trackgroup", tracks);
inputMap.add("sequence", sequence);
inputMap.add("channel", channel);
@@ -233,7 +242,7 @@ public class ROITrackStatistics extends Plugin implements ROIBlock, PluginBundle
}
@Override
- public void declareOutput(final VarList outputMap) {
+ public void declareOutput(final @NotNull VarList outputMap) {
outputMap.add("workbook", workbook);
}
@@ -268,9 +277,4 @@ public class ROITrackStatistics extends Plugin implements ROIBlock, PluginBundle
Thread.currentThread().interrupt();
}
}
-
- @Override
- public String getMainPluginClassName() {
- return ROIMeasures.class.getName();
- }
}
diff --git a/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterDescriptorsPlugin.java b/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterDescriptorsPlugin.java
index ea06b98..b60eb67 100644
--- a/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterDescriptorsPlugin.java
+++ b/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterDescriptorsPlugin.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,16 +18,20 @@
package plugins.adufour.roi.intensitycenter;
-import icy.plugin.abstract_.Plugin;
-import icy.plugin.interface_.PluginROIDescriptor;
-import icy.roi.ROI;
-import icy.roi.ROIDescriptor;
-import icy.sequence.Sequence;
-import icy.sequence.SequenceDataIterator;
-import icy.type.point.Point3D;
-import icy.type.rectangle.Rectangle5D;
-import plugins.kernel.roi.roi2d.ROI2DPoint;
-import plugins.kernel.roi.roi3d.ROI3DPoint;
+import org.bioimageanalysis.extension.kernel.roi.roi2d.ROI2DPoint;
+import org.bioimageanalysis.extension.kernel.roi.roi3d.ROI3DPoint;
+import org.bioimageanalysis.icy.common.geom.point.Point3D;
+import org.bioimageanalysis.icy.common.geom.rectangle.Rectangle5D;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.extension.plugin.interface_.PluginROIDescriptor;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.roi.ROIDescriptor;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.SequenceDataIterator;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import java.util.ArrayList;
import java.util.HashMap;
@@ -41,6 +45,8 @@ import java.util.Map;
*
* @author Daniel Felipe Gonzalez Obando
*/
+@IcyPluginName("ROI Intensity Center Descriptor")
+@IcyPluginIcon(path = "/roi-stat.png")
public class ROIIntensityCenterDescriptorsPlugin extends Plugin implements PluginROIDescriptor {
public static final String ID_MASS_CENTER_X = ROIIntensityCenterXDescriptor.ID;
public static final String ID_MASS_CENTER_Y = ROIIntensityCenterYDescriptor.ID;
@@ -58,7 +64,8 @@ public class ROIIntensityCenterDescriptorsPlugin extends Plugin implements Plugi
* @return Position of the intensity center.
* @throws InterruptedException If the thread is interrupted during the descriptors computation.
*/
- public static Point3D computeIntensityCenter(final ROI roi, final Sequence sequence) throws InterruptedException {
+ @Contract("_, _ -> new")
+ public static @NotNull Point3D computeIntensityCenter(final @NotNull ROI roi, final Sequence sequence) throws InterruptedException {
final Rectangle5D bounds = roi.getBounds5D();
// special case of empty bounds ? --> return position
@@ -142,5 +149,4 @@ public class ROIIntensityCenterDescriptorsPlugin extends Plugin implements Plugi
return result;
}
-
}
diff --git a/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterXDescriptor.java b/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterXDescriptor.java
index f97178f..fd462e2 100644
--- a/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterXDescriptor.java
+++ b/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterXDescriptor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,12 +18,12 @@
package plugins.adufour.roi.intensitycenter;
-import icy.roi.ROI;
-import icy.roi.ROIDescriptor;
-import icy.sequence.Sequence;
-import icy.sequence.SequenceEvent;
-import icy.sequence.SequenceEvent.SequenceEventSourceType;
-import icy.type.point.Point3D;
+import org.bioimageanalysis.icy.common.geom.point.Point3D;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.roi.ROIDescriptor;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.SequenceEvent;
+import org.jetbrains.annotations.NotNull;
public class ROIIntensityCenterXDescriptor extends ROIDescriptor {
public static final String ID = "Intensity center X";
@@ -48,8 +48,8 @@ public class ROIIntensityCenterXDescriptor extends ROIDescriptor {
}
@Override
- public boolean needRecompute(final SequenceEvent change) {
- return (change.getSourceType() == SequenceEventSourceType.SEQUENCE_DATA);
+ public boolean needRecompute(final @NotNull SequenceEvent change) {
+ return (change.getSourceType() == SequenceEvent.SequenceEventSourceType.SEQUENCE_DATA);
}
@Override
diff --git a/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterYDescriptor.java b/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterYDescriptor.java
index 8e55be6..b6eab03 100644
--- a/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterYDescriptor.java
+++ b/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterYDescriptor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,12 +18,12 @@
package plugins.adufour.roi.intensitycenter;
-import icy.roi.ROI;
-import icy.roi.ROIDescriptor;
-import icy.sequence.Sequence;
-import icy.sequence.SequenceEvent;
-import icy.sequence.SequenceEvent.SequenceEventSourceType;
-import icy.type.point.Point3D;
+import org.bioimageanalysis.icy.common.geom.point.Point3D;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.roi.ROIDescriptor;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.SequenceEvent;
+import org.jetbrains.annotations.NotNull;
public class ROIIntensityCenterYDescriptor extends ROIDescriptor {
public static final String ID = "Intensity center Y";
@@ -48,8 +48,8 @@ public class ROIIntensityCenterYDescriptor extends ROIDescriptor {
}
@Override
- public boolean needRecompute(final SequenceEvent change) {
- return (change.getSourceType() == SequenceEventSourceType.SEQUENCE_DATA);
+ public boolean needRecompute(final @NotNull SequenceEvent change) {
+ return (change.getSourceType() == SequenceEvent.SequenceEventSourceType.SEQUENCE_DATA);
}
@Override
diff --git a/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterZDescriptor.java b/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterZDescriptor.java
index 55ad853..ecae5f7 100644
--- a/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterZDescriptor.java
+++ b/src/main/java/plugins/adufour/roi/intensitycenter/ROIIntensityCenterZDescriptor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2023. Institut Pasteur.
+ * Copyright (c) 2010-2024. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,12 +18,12 @@
package plugins.adufour.roi.intensitycenter;
-import icy.roi.ROI;
-import icy.roi.ROIDescriptor;
-import icy.sequence.Sequence;
-import icy.sequence.SequenceEvent;
-import icy.sequence.SequenceEvent.SequenceEventSourceType;
-import icy.type.point.Point3D;
+import org.bioimageanalysis.icy.common.geom.point.Point3D;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.roi.ROIDescriptor;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.SequenceEvent;
+import org.jetbrains.annotations.NotNull;
public class ROIIntensityCenterZDescriptor extends ROIDescriptor {
public static final String ID = "Intensity center Z";
@@ -48,8 +48,8 @@ public class ROIIntensityCenterZDescriptor extends ROIDescriptor {
}
@Override
- public boolean needRecompute(final SequenceEvent change) {
- return (change.getSourceType() == SequenceEventSourceType.SEQUENCE_DATA);
+ public boolean needRecompute(final @NotNull SequenceEvent change) {
+ return (change.getSourceType() == SequenceEvent.SequenceEventSourceType.SEQUENCE_DATA);
}
@Override
diff --git a/src/main/resources/roi-stat.png b/src/main/resources/roi-stat.png
new file mode 100644
index 0000000000000000000000000000000000000000..cefa2397373f100d897d68f81231284f3e2aaccc
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--
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