diff --git a/pom.xml b/pom.xml
index 107ccb9feff3336eba517ca04d328fd3cec64b6a..d7827329d567dc7eee839ff9cea5f39b754e5b37 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,11 +7,11 @@
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
- <version>3.0.0-a.1</version>
+ <version>3.0.0-a.3</version>
</parent>
<artifactId>connected-components</artifactId>
- <version>5.0.0-a.1</version>
+ <version>5.0.0-a.2</version>
<name>ConnectedComponents</name>
<description>
@@ -47,12 +47,4 @@
<artifactId>jama</artifactId>
</dependency>
</dependencies>
-
- <repositories>
- <repository>
- <id>icy</id>
- <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/connectedcomponents/ConnectedComponent.java b/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponent.java
index fa8fa12154b7508e4079ba0d7f4cee12fcd6db53..9187727616c3debf5ee26b87ca72c40c4228793b 100644
--- a/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponent.java
+++ b/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponent.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2024. Institut Pasteur.
+ * Copyright (c) 2010-2025. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -18,7 +18,6 @@
package plugins.adufour.connectedcomponents;
-
import org.bioimageanalysis.extension.kernel.roi.roi2d.ROI2DArea;
import org.bioimageanalysis.extension.kernel.roi.roi3d.ROI3DArea;
import org.bioimageanalysis.icy.common.collection.array.Array1DUtil;
@@ -174,7 +173,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @param t int
* @return an array containing the average intensity of the component in each band
*/
- public double[] computeMeanIntensity(final Sequence sequence, final int t) {
+ public double[] computeMeanIntensity(final @NotNull Sequence sequence, final int t) {
final double[] intensitySum = new double[sequence.getSizeC()];
for (final Point3i point : points) {
@@ -249,7 +248,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @param t int
* @return an array containing the average intensity of the component in each band
*/
- public double[] computeMaxIntensity(final Sequence sequence, final int t) {
+ public double[] computeMaxIntensity(final @NotNull Sequence sequence, final int t) {
final double[] maxIntensity = new double[sequence.getSizeC()];
for (final Point3i point : points) {
@@ -529,7 +528,7 @@ public class ConnectedComponent extends Detection implements Iterable<Point3i> {
* @return true if this component intersects (e.g. has at least one voxel overlapping with) the
* specified component
*/
- public boolean intersects(final ConnectedComponent component) {
+ public boolean intersects(final @NotNull ConnectedComponent component) {
final int thisSize = getSize();
final int componentSize = component.getSize();
diff --git a/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponentDescriptor.java b/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponentDescriptor.java
index abe0eeb05d47329ff0d3a403bada3671896933b6..b681d04c55ef603d023e3292de01c414b3ee88ce 100644
--- a/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponentDescriptor.java
+++ b/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponentDescriptor.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2024. Institut Pasteur.
+ * Copyright (c) 2010-2025. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -22,9 +22,12 @@ import Jama.EigenvalueDecomposition;
import Jama.Matrix;
import org.bioimageanalysis.icy.common.type.DataType;
import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
-import org.bioimageanalysis.icy.extension.plugin.interface_.PluginBundled;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import plugins.adufour.blocks.lang.Block;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.quickhull.QuickHull2D;
@@ -38,7 +41,9 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
-public class ConnectedComponentDescriptor extends Plugin implements PluginBundled, Block {
+@IcyPluginName("Connected Components Block")
+@IcyPluginIcon(path = "/plugins/adufour/connectedcomponents/Connected_Components.png")
+public class ConnectedComponentDescriptor extends Plugin implements Block {
Var<ConnectedComponent> varCC = new Var<>("Connected component", ConnectedComponent.class);
VarDouble perimeter = new VarDouble("perimeter", 0.0);
@@ -54,17 +59,12 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
VarDouble shortAxisZ = new VarDouble("short diameter (Z)", 0.0);
@Override
- public String getMainPluginClassName() {
- return ConnectedComponents.class.getName();
- }
-
- @Override
- public void declareInput(final VarList inputMap) {
+ public void declareInput(final @NotNull VarList inputMap) {
inputMap.add("component", varCC);
}
@Override
- public void declareOutput(final VarList outputMap) {
+ public void declareOutput(final @NotNull VarList outputMap) {
outputMap.add("perimeter", perimeter);
outputMap.add("long diameter", longAxis);
outputMap.add("short diameter", shortAxis);
@@ -168,7 +168,11 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* @param bsCenter the computed center of the bounding sphere
* @param bsRadius the computed radius of the bounding sphere
*/
- public void computeBoundingSphere(final ConnectedComponent cc, final Point3d bsCenter, final VarDouble bsRadius) {
+ public void computeBoundingSphere(
+ final @NotNull ConnectedComponent cc,
+ final @NotNull Point3d bsCenter,
+ final @NotNull VarDouble bsRadius
+ ) {
bsCenter.set(cc.getMassCenter());
bsRadius.setValue(cc.getMaxDistanceTo(bsCenter));
}
@@ -181,7 +185,11 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* extracted contour
* @return The 3D perimeter (or 3D surface) of this component
*/
- public double computePerimeter(final ConnectedComponent cc, final ArrayList<Point3i> contourPoints, final Sequence outputSequence) {
+ public double computePerimeter(
+ final ConnectedComponent cc,
+ final ArrayList<Point3i> contourPoints,
+ final Sequence outputSequence
+ ) {
double perimeter = 0;
if (contourPoints != null)
@@ -368,7 +376,7 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* object. The 2 values are returned together because their computation is simultaneous
* (in the 3D case only)
*/
- public double[] computeConvexAreaAndVolume(final ConnectedComponent cc) {
+ public double[] computeConvexAreaAndVolume(final @NotNull ConnectedComponent cc) {
int i = 0;
final int n = cc.getSize();
if (n == 1)
@@ -447,7 +455,7 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* @param r the moment order along Z (set to 0 if the object is 2D)
* @return the geometric moment
*/
- public double computeGeometricMoment(final ConnectedComponent cc, final int p, final int q, final int r) {
+ public double computeGeometricMoment(final @NotNull ConnectedComponent cc, final int p, final int q, final int r) {
double moment = 0;
final Point3d center = cc.getMassCenter();
@@ -478,8 +486,13 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* @throws IllegalArgumentException if the number of points in the component is too low (minimum is 9)
* @throws SingularMatrixException if the component is flat (i.e., lies in a 2D plane)
*/
- public void computeEllipse(final ConnectedComponent cc, final Point3d center, final Point3d radii, final Vector3d[] eigenVectors,
- final double[] equation) throws IllegalArgumentException {
+ public void computeEllipse(
+ final @NotNull ConnectedComponent cc,
+ final Point3d center,
+ final Point3d radii,
+ final Vector3d[] eigenVectors,
+ final double[] equation
+ ) throws IllegalArgumentException {
final int nPoints = cc.getSize();
if (nPoints < 9) {
throw new IllegalArgumentException("Too few points; need at least 9 to calculate a unique ellipsoid");
@@ -560,8 +573,13 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
* vector <b>A</b> represented in the array is normed, so that ||<b>A</b>||=1.
* @throws RuntimeException if the ellipse calculation fails (e.g., if a singular matrix is detected)
*/
- public void computeEllipse(final ConnectedComponent cc, final Point2d center, final Point2d radii, final VarDouble angle, final double[] equation)
- throws RuntimeException {
+ public void computeEllipse(
+ final @NotNull ConnectedComponent cc,
+ final Point2d center,
+ final Point2d radii,
+ final VarDouble angle,
+ final double[] equation
+ ) throws RuntimeException {
final Point3i[] points = cc.getPoints();
final Point3d ccenter = cc.getMassCenter();
@@ -595,8 +613,11 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
final Matrix M = S1.plus(S2.times(T));
final double[][] m = M.getArray();
- final double[][] n = {{m[2][0] / 2, m[2][1] / 2, m[2][2] / 2}, {-m[1][0], -m[1][1], -m[1][2]},
- {m[0][0] / 2, m[0][1] / 2, m[0][2] / 2}};
+ final double[][] n = {
+ {m[2][0] / 2, m[2][1] / 2, m[2][2] / 2},
+ {-m[1][0], -m[1][1], -m[1][2]},
+ {m[0][0] / 2, m[0][1] / 2, m[0][2] / 2}
+ };
final Matrix N = new Matrix(n);
@@ -692,7 +713,8 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
return minBB.z == maxBB.z;
}
- private Matrix diag(final Matrix matrix) {
+ @Contract("_ -> new")
+ private @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++) {
@@ -701,7 +723,8 @@ public class ConnectedComponentDescriptor extends Plugin implements PluginBundle
return new Matrix(diag);
}
- private Matrix ones(final int m, final int n) {
+ @Contract("_, _ -> new")
+ private @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);
diff --git a/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponents.java b/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponents.java
index f8113aab490c93a7ff99014e453cf3371815f2e1..2d6690ea376171c8ffc2530ac411438654dae07c 100644
--- a/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponents.java
+++ b/src/main/java/plugins/adufour/connectedcomponents/ConnectedComponents.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2010-2024. Institut Pasteur.
+ * Copyright (c) 2010-2025. Institut Pasteur.
*
* This file is part of Icy.
* Icy is free software: you can redistribute it and/or modify
@@ -40,6 +40,8 @@ import org.bioimageanalysis.icy.model.sequence.SequenceDataIterator;
import org.bioimageanalysis.icy.model.sequence.VolumetricImage;
import org.bioimageanalysis.icy.model.swimmingPool.SwimmingObject;
import org.bioimageanalysis.icy.system.IcyHandledException;
+import org.jetbrains.annotations.Contract;
+import org.jetbrains.annotations.NotNull;
import plugins.adufour.blocks.lang.Block;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.ezplug.*;
@@ -58,7 +60,7 @@ import java.io.IOException;
import java.util.*;
@IcyPluginName("Connected Components")
-@IcyPluginIcon(path = "/icon/Connected_Components.png")
+@IcyPluginIcon(path = "/plugins/adufour/connectedcomponents/Connected_Components.png")
public class ConnectedComponents extends EzPlug implements Block {
/**
* List of extraction methods suitable for the Connected Components plugin
@@ -517,6 +519,7 @@ public class ConnectedComponents extends EzPlug implements Block {
* @param value the pixel value
* @param label the label value
*/
+ @Contract(pure = true)
Label(final double value, final int label) {
this.imageValue = value;
this.targetLabelValue = label;
@@ -525,6 +528,7 @@ public class ConnectedComponents extends EzPlug implements Block {
/**
* Retrieves the final object label (recursively)
*/
+ @Contract(pure = true)
int getFinalLabelValue() {
return targetLabel == null ? targetLabelValue : targetLabel.getFinalLabelValue();
}
@@ -542,7 +546,11 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ExtractionType
* @see ConnectedComponent
*/
- public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(final Sequence inputSequence, final Sequence labeledSequence) {
+ @Contract("null, _ -> fail")
+ public static @NotNull Map<Integer, List<ConnectedComponent>> extractConnectedComponents(
+ final Sequence inputSequence,
+ final Sequence labeledSequence
+ ) {
return extractConnectedComponents(inputSequence, false, 0, Integer.MAX_VALUE, labeledSequence);
}
@@ -560,7 +568,13 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ExtractionType
* @see ConnectedComponent
*/
- public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(final Sequence inputSequence, final int minSize, final int maxSize, final Sequence labeledSequence) {
+ @Contract("null, _, _, _ -> fail")
+ public static @NotNull Map<Integer, List<ConnectedComponent>> extractConnectedComponents(
+ final Sequence inputSequence,
+ final int minSize,
+ final int maxSize,
+ final Sequence labeledSequence
+ ) {
return extractConnectedComponents(inputSequence, false, minSize, maxSize, labeledSequence);
}
@@ -579,10 +593,22 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ExtractionType
* @see ConnectedComponent
*/
- public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(final Sequence inputSequence, final boolean isInputLabeled, final int minSize, final int maxSize, final Sequence labeledSequence) {
- return extractConnectedComponents(inputSequence, 0,
- isInputLabeled ? ExtractionType.BACKGROUND_LABELED : ExtractionType.BACKGROUND, minSize, maxSize,
- labeledSequence);
+ @Contract("null, _, _, _, _ -> fail")
+ public static @NotNull Map<Integer, List<ConnectedComponent>> extractConnectedComponents(
+ final Sequence inputSequence,
+ final boolean isInputLabeled,
+ final int minSize,
+ final int maxSize,
+ final Sequence labeledSequence
+ ) {
+ return extractConnectedComponents(
+ inputSequence,
+ 0,
+ isInputLabeled ? ExtractionType.BACKGROUND_LABELED : ExtractionType.BACKGROUND,
+ minSize,
+ maxSize,
+ labeledSequence
+ );
}
/**
@@ -601,8 +627,26 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ExtractionType
* @see ConnectedComponent
*/
- public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(final Sequence inputSequence, final double value, final ExtractionType type, final int minSize, final int maxSize, final Sequence labeledSequence) {
- return extractConnectedComponents(inputSequence, value, type, false, false, false, minSize, maxSize, labeledSequence);
+ @Contract("null, _, _, _, _, _ -> fail")
+ public static @NotNull Map<Integer, List<ConnectedComponent>> extractConnectedComponents(
+ final Sequence inputSequence,
+ final double value,
+ final ExtractionType type,
+ final int minSize,
+ final int maxSize,
+ final Sequence labeledSequence
+ ) {
+ return extractConnectedComponents(
+ inputSequence,
+ value,
+ type,
+ false,
+ false,
+ false,
+ minSize,
+ maxSize,
+ labeledSequence
+ );
}
/**
@@ -627,8 +671,17 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ExtractionType
* @see ConnectedComponent
*/
- public static Map<Integer, List<ConnectedComponent>> extractConnectedComponents(
- final Sequence inputSequence, final double value, final ExtractionType type, final boolean noEdgeX, final boolean noEdgeY, final boolean noEdgeZ, final int minSize, final int maxSize, Sequence labeledSequence
+ @Contract("null, _, _, _, _, _, _, _, _ -> fail")
+ public static @NotNull Map<Integer, List<ConnectedComponent>> extractConnectedComponents(
+ final Sequence inputSequence,
+ final double value,
+ final ExtractionType type,
+ final boolean noEdgeX,
+ final boolean noEdgeY,
+ final boolean noEdgeZ,
+ final int minSize,
+ final int maxSize,
+ Sequence labeledSequence
) {
if (inputSequence == null || inputSequence.getSizeT() == 0)
throw new IllegalArgumentException("Cannot extract connected components from an empty sequence !");
@@ -688,10 +741,28 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ExtractionType
* @see ConnectedComponent
*/
- public static List<ConnectedComponent> extractConnectedComponents(
- final VolumetricImage stack, final double value, final ExtractionType type, final boolean noEdgeX, final boolean noEdgeY, final boolean noEdgeZ, final int minSize, final int maxSize
+ @Contract("_, _, _, _, _, _, _, _ -> new")
+ public static @NotNull List<ConnectedComponent> extractConnectedComponents(
+ final VolumetricImage stack,
+ final double value,
+ final ExtractionType type,
+ final boolean noEdgeX,
+ final boolean noEdgeY,
+ final boolean noEdgeZ,
+ final int minSize,
+ final int maxSize
) {
- return extractConnectedComponents(stack, value, type, noEdgeX, noEdgeY, noEdgeZ, minSize, maxSize, new VolumetricImage());
+ return extractConnectedComponents(
+ stack,
+ value,
+ type,
+ noEdgeX,
+ noEdgeY,
+ noEdgeZ,
+ minSize,
+ maxSize,
+ new VolumetricImage()
+ );
}
/**
@@ -719,8 +790,17 @@ public class ConnectedComponents extends EzPlug implements Block {
* @see ExtractionType
* @see ConnectedComponent
*/
- public static List<ConnectedComponent> extractConnectedComponents(
- final VolumetricImage stack, final double value, final ExtractionType type, final boolean noEdgeX, final boolean noEdgeY, final boolean noEdgeZ, final int minSize, final int maxSize, final VolumetricImage labeledStack
+ @Contract("_, _, _, _, _, _, _, _, _ -> new")
+ public static @NotNull List<ConnectedComponent> extractConnectedComponents(
+ final @NotNull VolumetricImage stack,
+ final double value,
+ final ExtractionType type,
+ final boolean noEdgeX,
+ final boolean noEdgeY,
+ final boolean noEdgeZ,
+ final int minSize,
+ final int maxSize,
+ final VolumetricImage labeledStack
) throws NullPointerException {
final int width = stack.getFirstImage().getSizeX();
final int height = stack.getFirstImage().getSizeY();
@@ -1181,8 +1261,10 @@ public class ConnectedComponents extends EzPlug implements Block {
return new ArrayList<>(componentsMap.values());
}
- public static DetectionResult convertToDetectionResult(final Map<Integer, List<ConnectedComponent>> detections, final Sequence sequence) {
-
+ public static @NotNull DetectionResult convertToDetectionResult(
+ final @NotNull Map<Integer, List<ConnectedComponent>> detections,
+ final Sequence sequence
+ ) {
final DetectionResult detectionResult = new DetectionResult();
for (final Integer t : detections.keySet())
for (final ConnectedComponent cc : detections.get(t)) {
@@ -1204,7 +1286,11 @@ public class ConnectedComponents extends EzPlug implements Block {
* @param components Map of List of ConnectedComponent
* @param comparator Comparator of ConnectedComponents
*/
- public static void createLabeledSequence(final Sequence output, final Map<Integer, List<ConnectedComponent>> components, final Comparator<ConnectedComponent> comparator) {
+ public static void createLabeledSequence(
+ final Sequence output,
+ final Map<Integer, List<ConnectedComponent>> components,
+ final Comparator<ConnectedComponent> comparator
+ ) {
if (comparator == null)
return;
diff --git a/src/main/resources/icon/Connected_Components.png b/src/main/resources/plugins/adufour/connectedcomponents/Connected_Components.png
similarity index 100%
rename from src/main/resources/icon/Connected_Components.png
rename to src/main/resources/plugins/adufour/connectedcomponents/Connected_Components.png