Mavenized Micro-Manager Blocks + exclusion of MicroscopeSnapChannels,...

Mavenized Micro-Manager Blocks + exclusion of MicroscopeSnapChannels, VarChannels, VarChannelsEditor and MicroscopeChannels until an EzPlug fix

.classpath

 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry excluding="plugins/stef/micromanager/block/lang/VarChannels.java|plugins/stef/micromanager/block/lang/VarChannelsEditor.java|plugins/stef/micromanager/block/capture/MicroscopeSnapChannels.java|plugins/stef/micromanager/block/setting/MicroscopeChannels.java" kind="src" path="src"/>
+	<classpathentry kind="src" path="src/main/java"/>
+	<classpathentry kind="src" path="src/main/resources"/>
+	<classpathentry kind="src" path="src/test/java"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jdk6"/>
-	<classpathentry kind="var" path="ICY_HOME/icy.jar"/>
-	<classpathentry kind="var" path="MM_HOME/plugins/Micro-Manager/MMCoreJ.jar"/>
-	<classpathentry kind="var" path="MM_HOME/plugins/Micro-Manager/MMJ_.jar" sourcepath="/GIT/micro-manager"/>
-	<classpathentry kind="var" path="ICY_PLUGINS/adufour/blocks/Blocks.jar"/>
-	<classpathentry kind="var" path="ICY_PLUGINS/adufour/ezplug/EzPlug.jar"/>
-	<classpathentry kind="var" path="ICY_PLUGINS/tprovoost/Microscopy/MicroManagerForIcy/MicromanagerPlugin.jar"/>
-	<classpathentry kind="var" path="ICY_PLUGINS/adufour/protocols/Protocols.jar"/>
-	<classpathentry kind="output" path="bin"/>
+	<classpathentry kind="var" path="USER_HOME/SDKs/Java/jdk1.8.0_251/lib/tools.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-kernel:2.1.0"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: net.sf.ehcache:ehcache:2.10.6"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.slf4j:slf4j-api:1.7.25"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-bioformats:6.3.1"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-insubstantial:7.3.7"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-vtk:6.3.0.1"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: net.imagej:ij:1.52q"/>
+	<classpathentry kind="var" path="USER_HOME/SDKs/Java/jdk1.8.0_251/lib/tools.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: javax.media:jai-core:1.1.3"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: javax.media:jai-codec:1.1.3"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all:2.1.5-01"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-linux-amd64:2.1.5"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-linux-i586:2.1.5"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-macosx-universal:2.1.5"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-windows-amd64:2.1.5"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.jogl:jogl-all-natives-windows-i586:2.1.5"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt:2.1.5-01"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-linux-amd64:2.1.5"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-linux-i586:2.1.5"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-macosx-universal:2.1.5"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-windows-amd64:2.1.5"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.jogamp.gluegen:gluegen-rt-natives-windows-i586:2.1.5"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.javassist:javassist:3.22.0-GA"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: net.sourceforge.jexcelapi:jxl:2.6.12"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: log4j:log4j:1.2.14"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.swinglabs.swingx:swingx-all:1.6.5-1"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-micromanager:1.0.3"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: joda-time:joda-time:2.10.5"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.micromanager:MMCoreJ:1.4.22"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.micromanager:MMJ_:1.4.22"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-blocks:1.0.1"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-protocols:1.0.0"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-javadocparser:1.0.0"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: com.nativelibs4java:ochafik-util:0.12"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Maven: org.bioimageanalysis.icy:icy-ezplug:1.0.0"/>
+	<classpathentry kind="output" path="target/classes"/>
 </classpath>

.gitignore

+.idea/
+target/
+build/
+*.iml
+*.eml
+*.classpath
+*.project
\ No newline at end of file

pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>org.bioimageanalysis.icy</groupId>
+    <artifactId>icy-micromanager-block</artifactId>
+    <version>1.0.3</version>
+
+    <name>Micro-Manager Block</name>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <jdk.version>1.8</jdk.version>
+
+        <maven.compiler.source>1.8</maven.compiler.source>
+        <maven.compiler.target>1.8</maven.compiler.target>
+
+        <outputJar>${project.build.outputDirectory}/../plugin</outputJar>
+    </properties>
+
+    <build>
+        <finalName>${project.artifactId}</finalName>
+
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.8.1</version>
+                <configuration>
+                    <excludes>
+                        <exclude>**/plugins/stef/micromanager/block/capture/MicroscopeSnapChannels.java</exclude>
+                        <exclude>**/plugins/stef/micromanager/block/lang/VarChannels.java</exclude>
+                        <exclude>**/plugins/stef/micromanager/block/lang/VarChannelsEditor.java</exclude>
+                        <exclude>**/plugins/stef/micromanager/block/setting/MicroscopeChannels.java</exclude>
+                    </excludes>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <version>3.1.2</version>
+                <configuration>
+                    <outputDirectory>${outputJar}</outputDirectory>
+                    <archive>
+                        <manifest>
+                            <addClasspath>true</addClasspath>
+                            <mainClass>plugins.stef.micromanager.block.MicroscopyBlocks</mainClass>
+                        </manifest>
+                    </archive>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.bioimageanalysis.icy</groupId>
+            <artifactId>icy-kernel</artifactId>
+            <version>2.1.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.bioimageanalysis.icy</groupId>
+            <artifactId>icy-micromanager</artifactId>
+            <version>1.0.3</version>
+        </dependency>
+        <dependency>
+            <groupId>org.bioimageanalysis.icy</groupId>
+            <artifactId>icy-blocks</artifactId>
+            <version>1.0.1</version>
+        </dependency>
+    </dependencies>
+
+    <repositories>
+        <repository>
+            <id>icy</id>
+            <url>https://icy-nexus.pasteur.fr/repository/Icy/</url>
+        </repository>
+    </repositories>
+
+    <distributionManagement>
+        <snapshotRepository>
+            <id>icy-dev</id>
+            <name>icy-dev</name>
+            <url>https://icy-nexus-dev.pasteur.cloud/repository/icy-core/</url>
+        </snapshotRepository>
+        <repository>
+            <id>icy-prod</id>
+            <name>icy-prod</name>
+            <url>https://icy-nexus.pasteur.fr/repository/icy-core/</url>
+        </repository>
+    </distributionManagement>
+</project>
\ No newline at end of file

src/plugins/stef/micromanager/block/capture/MicroscopeSnapChannels.java → src/main/java/plugins/stef/micromanager/block/capture/MicroscopeSnapChannels.java

@@ -23,7 +23,8 @@ import plugins.tprovoost.Microscopy.MicroManager.tools.StageMover;
 
 /**
  * Snap multi channel image (Micro-Manager)
- * 
+ * Class in standby until an EzPlug fix
+ *
  * @author Stephane
  */
 public class MicroscopeSnapChannels extends AbstractMicroscopeBlock

src/plugins/stef/micromanager/block/lang/VarChannels.java → src/main/java/plugins/stef/micromanager/block/lang/VarChannels.java

@@ -9,6 +9,9 @@ import plugins.adufour.vars.lang.Var;
 import plugins.adufour.vars.lang.VarArray;
 import plugins.adufour.vars.util.VarListener;
 
+/**
+ * Class in standby until an EzPlug fix
+ */
 public class VarChannels extends VarArray<ChannelSpec>
 {
     VarChannelsEditor editor;

src/plugins/stef/micromanager/block/lang/VarChannelsEditor.java → src/main/java/plugins/stef/micromanager/block/lang/VarChannelsEditor.java

@@ -19,6 +19,9 @@ import plugins.adufour.vars.gui.VarEditor;
 import plugins.adufour.vars.lang.Var;
 import plugins.tprovoost.Microscopy.MicroManager.gui.ChannelTable;
 
+/**
+ * Class in standby until an EzPlug fix
+ */
 public class VarChannelsEditor extends VarEditor<ChannelSpec[]>
 {
     protected JPanel mainPanel;

src/plugins/stef/micromanager/block/setting/MicroscopeChannels.java → src/main/java/plugins/stef/micromanager/block/setting/MicroscopeChannels.java

@@ -8,6 +8,7 @@ import plugins.stef.micromanager.block.lang.VarChannels;
 
 /**
  * Define a list of channel (Micro-Manager)
+ * Class in standby until an EzPlug fix
  * 
  * @author Stephane Dallongeville
  */