From c8e9733ce369d8891bdac75b98d419b74696e60d Mon Sep 17 00:00:00 2001
From: Thomas <thomas.musset@pasteur.fr>
Date: Thu, 27 Jun 2024 17:32:53 +0200
Subject: [PATCH] updated pom to v2.0.0-a.1, fix classes accordingly to new
architecture, added icon, updated .gitignore
---
.gitignore | 44 +++++++++++++++---
pom.xml | 12 +++--
.../plugins/adufour/roi/LabelExtractor.java | 22 +++++----
src/main/resources/label-extractor.png | Bin 0 -> 3354 bytes
4 files changed, 57 insertions(+), 21 deletions(-)
create mode 100644 src/main/resources/label-extractor.png
diff --git a/.gitignore b/.gitignore
index b2f15ce..57f16fb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,11 +1,41 @@
-.idea/
-.settings/
-build/
+/build*
+/workspace
+setting.xml
+release/
target/
-bin/
+!.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
-**/.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 158ce2e..8475dd0 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,13 +7,11 @@
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>pom-icy</artifactId>
- <version>2.2.0</version>
+ <version>3.0.0-a.1</version>
</parent>
<artifactId>label-extractor</artifactId>
- <version>2.0.0</version>
-
- <packaging>jar</packaging>
+ <version>2.0.0-a.1</version>
<name>Label extractor</name>
<description>
@@ -21,6 +19,10 @@
</description>
<dependencies>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>kernel-extensions</artifactId>
+ </dependency>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
<artifactId>ezplug</artifactId>
@@ -34,7 +36,7 @@
<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/LabelExtractor.java b/src/main/java/plugins/adufour/roi/LabelExtractor.java
index 4b8ad5c..f6cda00 100644
--- a/src/main/java/plugins/adufour/roi/LabelExtractor.java
+++ b/src/main/java/plugins/adufour/roi/LabelExtractor.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
@@ -18,17 +18,19 @@
package plugins.adufour.roi;
-import icy.image.IcyBufferedImage;
-import icy.roi.ROI;
-import icy.sequence.Sequence;
-import icy.type.DataType;
-import icy.type.collection.array.Array1DUtil;
+import org.bioimageanalysis.extension.kernel.roi.roi2d.ROI2DArea;
+import org.bioimageanalysis.extension.kernel.roi.roi3d.ROI3DArea;
+import org.bioimageanalysis.icy.common.collection.array.Array1DUtil;
+import org.bioimageanalysis.icy.common.type.DataType;
+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.roi.ROI;
+import org.bioimageanalysis.icy.model.sequence.Sequence;
import plugins.adufour.blocks.lang.Block;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.ezplug.*;
import plugins.adufour.vars.lang.VarROIArray;
-import plugins.kernel.roi.roi2d.ROI2DArea;
-import plugins.kernel.roi.roi3d.ROI3DArea;
import java.util.ArrayList;
import java.util.HashMap;
@@ -42,6 +44,8 @@ import java.util.Map;
*
* @author Alexandre Dufour
*/
+@IcyPluginName("Label Extractor")
+@IcyPluginIcon(path = "/label-extractor.png")
public class LabelExtractor extends EzPlug implements Block, EzStoppable {
EzVarSequence inSeq = new EzVarSequence("Labeled sequence");
@@ -231,7 +235,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable {
final int slice = width * height;
final int depth = sequence.getSizeZ();
final boolean is3D = depth > 1;
- final DataType dataType = sequence.getDataType_();
+ final DataType dataType = sequence.getDataType();
final Map<Integer, ConnectedComponent> ccs = new HashMap<>();
final Map<Integer, ROI> roiMap = new HashMap<>();
diff --git a/src/main/resources/label-extractor.png b/src/main/resources/label-extractor.png
new file mode 100644
index 0000000000000000000000000000000000000000..d171741d0b9a24535c02f56e8cdbcd6b1411bff0
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--
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