diff --git a/.gitignore b/.gitignore
index 5fe16ebb8b4e949b1d5f2b3189fcef93a07f070c..57f16fb67c1b1589981416b323d7a9debc728665 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,9 +1,41 @@
-/ROIToDistanceMap/bin/
-*.jar
+/build*
+/workspace
+setting.xml
+release/
+target/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
.idea/
+*.iws
*.iml
-.settings/
-.project
+*.ipr
+
+### Eclipse ###
+.apt_generated
.classpath
-target/
+.factorypath
+.project
+.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 fb3ae4ddc30b36b199d0244852143d54046ea86d..5cea3293f698f951a26cb46f3c41d42936205dbc 100644
--- a/pom.xml
+++ b/pom.xml
@@ -8,12 +8,12 @@
<parent>
<artifactId>pom-icy</artifactId>
<groupId>org.bioimageanalysis.icy</groupId>
- <version>2.2.0</version>
+ <version>3.0.0-a.1</version>
</parent>
<!-- Project Information -->
<artifactId>roi-to-distance-map</artifactId>
- <version>4.0.0</version>
+ <version>4.0.0-a.1</version>
<name>ROI to Distance Map</name>
<description>Convert ROI to a Distance Map</description>
@@ -62,23 +62,19 @@
<dependencies>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>protocols</artifactId>
+ <artifactId>ezplug</artifactId>
</dependency>
-
- <!-- The EzPlug library, simplifies writing UI for Icy plugins. -->
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>ezplug</artifactId>
+ <artifactId>protocols</artifactId>
</dependency>
-
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>3d-mesh-roi</artifactId>
+ <artifactId>kernel-extensions</artifactId>
</dependency>
-
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>icy-bioformats</artifactId>
+ <artifactId>3d-mesh-roi</artifactId>
</dependency>
</dependencies>
@@ -86,8 +82,7 @@
<repositories>
<repository>
<id>icy</id>
- <name>Icy's Nexus</name>
- <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+ <url>https://nexus.pasteur.cloud/repository/icy/</url>
</repository>
</repositories>
</project>
diff --git a/src/main/java/plugins/adufour/distancetransforms/Chamfer3.java b/src/main/java/plugins/adufour/distancetransforms/Chamfer3.java
index 0ca266af963fc9764efc93265410bffa8bbc58cb..4087f44f964b6da3d0ac2b9e9275368c5eb830dc 100644
--- a/src/main/java/plugins/adufour/distancetransforms/Chamfer3.java
+++ b/src/main/java/plugins/adufour/distancetransforms/Chamfer3.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
@@ -18,6 +18,10 @@
package plugins.adufour.distancetransforms;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.jetbrains.annotations.NotNull;
+
/**
* Pseudo-Euclidean distance transform based on a two-pass sweeping algorithm using a 3x3 (in 2D) or
* 3x3x3 (in 3D) chamfer mask. <br>
@@ -35,9 +39,11 @@ package plugins.adufour.distancetransforms;
*
* @author Alexandre Dufour
*/
+@IcyPluginName("Chamfer 3")
+@IcyPluginIcon(path = "/distance-transforms.png")
public class Chamfer3 extends ChamferDistanceTransform {
@Override
- public void updateUnsignedChamferDistance2D(final float[] map, final int width, final float planarLateralDistance) {
+ public void updateUnsignedChamferDistance2D(final float @NotNull [] map, final int width, final float planarLateralDistance) {
final double xy2 = planarLateralDistance * planarLateralDistance;
final float planarDiagonalDistance = (float) Math.sqrt(xy2 + xy2);
@@ -95,7 +101,7 @@ public class Chamfer3 extends ChamferDistanceTransform {
}
@Override
- public void updateUnsignedChamferDistance3D(final float[][] map, final int width, final float planoLateralDistance, final float axioLateralDistance) {
+ public void updateUnsignedChamferDistance3D(final float @NotNull [] @NotNull [] map, final int width, final float planoLateralDistance, final float axioLateralDistance) {
final double xy2 = planoLateralDistance * planoLateralDistance;
final double xz2 = axioLateralDistance * axioLateralDistance;
final float planoDiagonalDistance = (float) Math.sqrt(xy2 + xy2);
diff --git a/src/main/java/plugins/adufour/distancetransforms/Chamfer5.java b/src/main/java/plugins/adufour/distancetransforms/Chamfer5.java
index 7682d7403d7be3ecf41b47ec3596703b7765a443..0696d08953e6d7fe823b4239106451a6f556585a 100644
--- a/src/main/java/plugins/adufour/distancetransforms/Chamfer5.java
+++ b/src/main/java/plugins/adufour/distancetransforms/Chamfer5.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
@@ -18,6 +18,10 @@
package plugins.adufour.distancetransforms;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.jetbrains.annotations.NotNull;
+
/**
* Pseudo-Euclidean distance transform based on a two-pass sweeping algorithm using a 5x5 (in 2D) or
* 5x5x5 (in 3D) chamfer mask. <br>
@@ -40,9 +44,11 @@ package plugins.adufour.distancetransforms;
*
* @author Alexandre Dufour
*/
+@IcyPluginName("Chamfer 5")
+@IcyPluginIcon(path = "/distance-transforms.png")
public class Chamfer5 extends ChamferDistanceTransform {
@Override
- public void updateUnsignedChamferDistance2D(final float[] map, final int width, final float lateralDistance) {
+ public void updateUnsignedChamferDistance2D(final float @NotNull [] map, final int width, final float lateralDistance) {
// pre-calculate distances
final float a = lateralDistance;
final float b = (float) Math.sqrt(a * a + a * a);
@@ -121,8 +127,9 @@ public class Chamfer5 extends ChamferDistanceTransform {
}
}
+ // TODO: Make this method more simple
@Override
- public void updateUnsignedChamferDistance3D(final float[][] map, final int width, final float planarLateralDistance, final float axialLateralDistance) {
+ public void updateUnsignedChamferDistance3D(final float @NotNull [] @NotNull [] map, final int width, final float planarLateralDistance, final float axialLateralDistance) {
// 2D distances
final float xySq = planarLateralDistance * planarLateralDistance;
final float b = (float) Math.sqrt(xySq + xySq);
diff --git a/src/main/java/plugins/adufour/distancetransforms/ChamferDistanceTransform.java b/src/main/java/plugins/adufour/distancetransforms/ChamferDistanceTransform.java
index 1ee632d68092046ab2ccccd3c0a54a1396a19fa6..bbe2ed78f43148538c680887e07d9b2ef187b08c 100644
--- a/src/main/java/plugins/adufour/distancetransforms/ChamferDistanceTransform.java
+++ b/src/main/java/plugins/adufour/distancetransforms/ChamferDistanceTransform.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 +18,18 @@
package plugins.adufour.distancetransforms;
-import icy.common.Version;
-import icy.image.IcyBufferedImage;
-import icy.main.Icy;
-import icy.roi.ROI;
-import icy.roi.ROI2D;
-import icy.roi.ROI3D;
-import icy.sequence.Sequence;
-import icy.sequence.SequenceDataIterator;
-import icy.type.DataIteratorUtil;
-import icy.type.DataType;
-import icy.type.collection.array.Array1DUtil;
-import icy.util.OMEUtil;
+import org.bioimageanalysis.extension.kernel.roi.roi3d.ROI3DArea;
+import org.bioimageanalysis.icy.common.collection.array.Array1DUtil;
+import org.bioimageanalysis.icy.common.type.DataIteratorUtil;
+import org.bioimageanalysis.icy.common.type.DataType;
+import org.bioimageanalysis.icy.model.OMEUtil;
+import org.bioimageanalysis.icy.model.image.IcyBufferedImage;
+import org.bioimageanalysis.icy.model.roi.ROI;
+import org.bioimageanalysis.icy.model.roi.ROI3D;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.bioimageanalysis.icy.model.sequence.SequenceDataIterator;
+import org.jetbrains.annotations.NotNull;
import plugins.adufour.roi.mesh.ROI3DMesh;
-import plugins.kernel.roi.roi3d.ROI3DArea;
-import plugins.kernel.roi.roi3d.ROI3DStack;
import java.util.ArrayList;
import java.util.Arrays;
@@ -41,12 +38,12 @@ import java.util.concurrent.Future;
public abstract class ChamferDistanceTransform extends DistanceTransform {
@Override
- public Sequence createDistanceMap(final Sequence input, final int channel, final double threshold, final boolean invertMap, final boolean useRealUnits) {
+ public Sequence createDistanceMap(final @NotNull Sequence input, final int channel, final double threshold, final boolean invertMap, final boolean useRealUnits) {
final int width = input.getSizeX();
final int height = input.getSizeY();
final int depth = input.getSizeZ();
final int time = input.getSizeT();
- final DataType type = input.getDataType_();
+ final DataType type = input.getDataType();
final int maxDistance = width * height * depth;
@@ -92,7 +89,7 @@ public abstract class ChamferDistanceTransform extends DistanceTransform {
* @return sequence
*/
@Override
- public Sequence createDistanceMap(final Sequence sequence, final boolean mapOnlySelectedROI, final boolean invertMap, final boolean useRealUnits) throws InterruptedException {
+ public Sequence createDistanceMap(final @NotNull Sequence sequence, final boolean mapOnlySelectedROI, final boolean invertMap, final boolean useRealUnits) throws InterruptedException {
final List<ROI> rois = mapOnlySelectedROI ? sequence.getSelectedROIs() : sequence.getROIs();
String title = "Distance map ";
@@ -121,17 +118,17 @@ public abstract class ChamferDistanceTransform extends DistanceTransform {
// Fill the ROI with the default distance
// Warning: Icy <= 1.8.6 have an issue with the data iterator
- final Version patch = new Version(1, 8, 6);
+ //final Version patch = new Version(1, 8, 6);
for (final ROI r : rois) {
- if (Icy.version.isLowerOrEqual(patch) && r instanceof ROI3DStack) {
- final ROI3DStack<?> stack = (ROI3DStack<?>) r;
+ /*if (Icy.VERSION.isLowerOrEqual(patch) && r instanceof final ROI3DStack<?> stack) {
for (final ROI2D slice : stack) {
final SequenceDataIterator iterator = new SequenceDataIterator(output, slice, true);
DataIteratorUtil.set(iterator, maxDistance);
}
}
- else if (r instanceof ROI3DMesh) {
+ else*/
+ if (r instanceof ROI3DMesh) {
final ROI3D rea = new ROI3DArea(((ROI3D) r).getBooleanMask(true));
rea.setC(((ROI3D) r).getC());
rea.setT(((ROI3D) r).getT());
@@ -150,7 +147,7 @@ public abstract class ChamferDistanceTransform extends DistanceTransform {
return output;
}
- private void updateUnsignedChamferDistance(final Sequence output, final boolean useRealUnits) {
+ private void updateUnsignedChamferDistance(final @NotNull Sequence output, final boolean useRealUnits) {
final int width = output.getSizeX();
final int length = output.getSizeT();
diff --git a/src/main/java/plugins/adufour/distancetransforms/DistanceTransform.java b/src/main/java/plugins/adufour/distancetransforms/DistanceTransform.java
index 8a7868db9a884a270fdae97760d843ae4eb5caef..1cb708004be60b545a8ca4b26a18e05159e1af3b 100644
--- a/src/main/java/plugins/adufour/distancetransforms/DistanceTransform.java
+++ b/src/main/java/plugins/adufour/distancetransforms/DistanceTransform.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
@@ -18,14 +18,13 @@
package plugins.adufour.distancetransforms;
-import icy.plugin.abstract_.Plugin;
-import icy.plugin.interface_.PluginLibrary;
-import icy.sequence.Sequence;
+import org.bioimageanalysis.icy.extension.plugin.abstract_.Plugin;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
-public abstract class DistanceTransform extends Plugin implements PluginLibrary {
+public abstract class DistanceTransform extends Plugin {
protected static ExecutorService multiThreadService = Executors.newCachedThreadPool();
/**
diff --git a/src/main/java/plugins/adufour/distancetransforms/ROIToDistanceMap.java b/src/main/java/plugins/adufour/distancetransforms/ROIToDistanceMap.java
index 358fe29febf1400c38c376fd096ff0262471b77b..172cf7b2929e04750cd30f78fcdd6fcb3da3b7de 100644
--- a/src/main/java/plugins/adufour/distancetransforms/ROIToDistanceMap.java
+++ b/src/main/java/plugins/adufour/distancetransforms/ROIToDistanceMap.java
@@ -18,7 +18,10 @@
package plugins.adufour.distancetransforms;
-import icy.sequence.Sequence;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginIcon;
+import org.bioimageanalysis.icy.extension.plugin.annotation_.IcyPluginName;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
+import org.jetbrains.annotations.NotNull;
import plugins.adufour.blocks.lang.Block;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.ezplug.EzPlug;
@@ -27,6 +30,8 @@ import plugins.adufour.ezplug.EzVarPlugin;
import plugins.adufour.ezplug.EzVarSequence;
import plugins.adufour.vars.lang.VarSequence;
+@IcyPluginName("ROI to Distance Map")
+@IcyPluginIcon(path = "/distance-transforms.png")
public class ROIToDistanceMap extends EzPlug implements Block {
EzVarSequence sequence = new EzVarSequence("Sequence");
@@ -41,7 +46,7 @@ public class ROIToDistanceMap extends EzPlug implements Block {
VarSequence map = new VarSequence("Distance map", null);
@Override
- public void declareInput(final VarList inputMap) {
+ public void declareInput(final @NotNull VarList inputMap) {
inputMap.add("Use ROI from", sequence.getVariable());
inputMap.add("Algorithm", transform.getVariable());
inputMap.add("Invert map", invert.getVariable());
@@ -49,7 +54,7 @@ public class ROIToDistanceMap extends EzPlug implements Block {
}
@Override
- public void declareOutput(final VarList outputMap) {
+ public void declareOutput(final @NotNull VarList outputMap) {
outputMap.add("Distance map", map);
}
@@ -64,6 +69,7 @@ public class ROIToDistanceMap extends EzPlug implements Block {
setTimeDisplay(true);
}
+ @SuppressWarnings("resource")
@Override
protected void execute() {
try {
diff --git a/src/main/resources/distance-transforms.png b/src/main/resources/distance-transforms.png
new file mode 100644
index 0000000000000000000000000000000000000000..0a94830619320fe2524441b7180769d3196dc1c8
Binary files /dev/null and b/src/main/resources/distance-transforms.png differ