updated pom to v3.0.0-a.1, fix classes accordingly to new architecture, added...

updated pom to v3.0.0-a.1, fix classes accordingly to new architecture, added icon, updated .gitignore

.gitignore

-.idea/
+/build*
+/workspace
+setting.xml
+release/
 target/
-.settings/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+icy.log
+
+### IntelliJ IDEA ###
+.idea/
+*.iws
 *.iml
-.project
+*.ipr
+
+### Eclipse ###
+.apt_generated
 .classpath
-**/.DS_Store
+.factorypath
\ No newline at end of file
+.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

pom.xml

@@ -8,12 +8,12 @@
     <parent>
         <groupId>org.bioimageanalysis.icy</groupId>
         <artifactId>pom-icy</artifactId>
-        <version>2.2.0</version>
+        <version>3.0.0-a.1</version>
     </parent>
 
     <!-- Project Information -->
     <artifactId>invert</artifactId>
-    <version>3.0.0</version>
+    <version>3.0.0-a.1</version>
 
     <name>Invert</name>
     <description>Invert the image</description>
@@ -57,7 +57,6 @@
             <groupId>org.bioimageanalysis.icy</groupId>
             <artifactId>ezplug</artifactId>
         </dependency>
-
         <dependency>
             <groupId>org.bioimageanalysis.icy</groupId>
             <artifactId>protocols</artifactId>
@@ -69,7 +68,7 @@
         <repository>
             <id>icy</id>
             <name>Icy's Nexus</name>
-            <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+            <url>https://nexus-icy.pasteur.cloud/repository/icy/</url>
         </repository>
     </repositories>
 </project>

src/main/java/plugins/fab/invert/Invert.java

 /*
- * 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 +18,16 @@
 
 package plugins.fab.invert;
 
-import icy.common.listener.ProgressListener;
-import icy.image.IcyBufferedImage;
-import icy.sequence.Sequence;
-import icy.type.DataType;
-import icy.type.collection.array.Array1DUtil;
-import icy.util.OMEUtil;
+import org.bioimageanalysis.icy.common.collection.array.Array1DUtil;
+import org.bioimageanalysis.icy.common.listener.ProgressListener;
+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.OMEUtil;
+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.ezplug.EzGUI;
@@ -39,6 +43,8 @@ import java.util.ArrayList;
  * @author Fabrice de Chaumont
  * @author Stephane Dallongeville
  */
+@IcyPluginName("Invert")
+@IcyPluginIcon(path = "/invert.png")
 public class Invert extends EzPlug implements Block, EzStoppable {
     private final EzVarSequence input = new EzVarSequence("Sequence");
     private final EzVarSequence output = new EzVarSequence("Result");
@@ -85,15 +91,16 @@ public class Invert extends EzPlug implements Block, EzStoppable {
     }
 
     @Override
-    public void declareInput(final VarList inputMap) {
+    public void declareInput(final @NotNull VarList inputMap) {
         inputMap.add("Sequence", input.getVariable());
     }
 
     @Override
-    public void declareOutput(final VarList outputMap) {
+    public void declareOutput(final @NotNull VarList outputMap) {
         outputMap.add("Result", output.getVariable());
     }
 
+    @Contract("null, _ -> null")
     public static Sequence createInvert(final Sequence sequence, final ProgressListener listener) {
         if (sequence == null)
             return null;
@@ -103,7 +110,7 @@ public class Invert extends EzPlug implements Block, EzStoppable {
         final int sizeC = sequence.getSizeC();
         final int sizeZ = sequence.getSizeZ();
         final int sizeT = sequence.getSizeT();
-        final DataType dataType = sequence.getDataType_();
+        final DataType dataType = sequence.getDataType();
 
         final double[] minAndMax = sequence.getChannelsGlobalTypeBounds();
         final double min = minAndMax[0];
@@ -177,7 +184,7 @@ public class Invert extends EzPlug implements Block, EzStoppable {
         final ArrayList<IcyBufferedImage> images = sequence.getAllImage();
 
         for (final IcyBufferedImage image : images) {
-            for (int channel = 0; channel < images.get(0).getSizeC(); channel++) {
+            for (int channel = 0; channel < images.getFirst().getSizeC(); channel++) {
 
                 final double[] resultDataBuffer = Array1DUtil.arrayToDoubleArray(image.getDataXY(channel), image.isSignedDataType());
                 for (int i = 0; i < resultDataBuffer.length; i++) {