Re-Arranged lots of stuff

.classpath

@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="src/main/resources"/>
+	<classpathentry kind="src" path="src/test/resources"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="hdf-java/jhdf.jar"/>
+	<classpathentry kind="lib" path="hdf-java/jhdf5.jar"/>
+	<classpathentry kind="lib" path="hdf-java/jhdf5obj.jar"/>
+	<classpathentry kind="lib" path="hdf-java/jhdfobj.jar"/>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

.gitignore

@@ -0,0 +1 @@
+/target

.project

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ImageJHDF5</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,5 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5
+org.eclipse.jdt.core.compiler.compliance=1.5
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.5

.settings/org.eclipse.m2e.core.prefs

@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

LICENSE

@@ -1,202 +0,0 @@
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NOTICE

@@ -1,14 +0,0 @@
-   =========================================================================
-   ==  NOTICE file corresponding to the section 4 d of                    ==
-   ==  the Apache License, Version 2.0,                                   ==
-   ==  in this case for the ImageJ HDF Plugin distribution.               ==
-   =========================================================================
-
-   ImageJ HDF Plugin
-   Copyright 2011 Matthias Schlachter
-
-   This product includes software developed by Matthias Schlachter.
-
-   The initial release of this software was developed by Matthias Schlachter
-   at the Chair of Pattern Recognition and Image Processing, University of 
-   Freiburg, Germany.

README

@@ -1,33 +0,0 @@
-####################################################################
-#                          INSTALL NOTES                           #
-####################################################################
-- For linux 32bit:
- Edit the "run" file in your ImageJ installation directory that it 
- looks like the following
- ./jre/bin/java -Djava.library.path=./lib/linux32 
-                -Xmx512m -jar ij.jar
-
-- For linux 64bit:
-Edit the "run" file in your ImageJ installation directory that it 
-looks like the following
-java -Djava.library.path=./lib/linux64
-     -Xmx512m -jar ij.jar
-
-Note: You must have 64bit JRE installed!
-
-- For windows 32bit:
- Edit the "ImageJ.cfg" file in your ImageJ installation directory
- that it looks like the following
- C:\Programme\Java\jdk1.5.0_14\bin\javaw.exe
-        -Djava.library.path=lib\win32 -Xmx640m -cp ij.jar ij.ImageJ
-
-- For Mac 32bit (tested on Snow Leopard):
-Edit the "run" file in your ImageJ installation directory that it 
-looks like the following
-java -Djava.library.path=./lib/mac32
-     -Xmx512m -jar ij.jar
-
-Note: You must have 32bit JRE installed or force the JVM to use a 
-      32bit data model (-d32)!
-
-####################################################################

Readme.md

@@ -0,0 +1,23 @@
+# Installation
+
+Drop jar into plugins directory of the ImageJ installation.
+
+## Linux 32Bit
+Edit the `run` file of your ImageJ installation
+`./jre/bin/java -Djava.library.path=./lib/linux32 -Xmx512m -jar ij.jar`
+
+## Linux 64Bit
+Edit the `run` file of your ImageJ installation
+`java -Djava.library.path=./lib/linux64 -Xmx512m -jar ij.jar`
+
+## Windows 32Bit
+Edit the "ImageJ.cfg" of your ImageJ installation
+`C:\Programme\Java\jdk1.5.0_14\bin\javaw.exe -Djava.library.path=lib\win32 -Xmx640m -cp ij.jar ij.ImageJ`
+
+## Mac 32Bit
+Edit the `run` file of your ImageJ installation
+`java -Djava.library.path=./lib/mac32 -Xmx512m -jar ij.jar`
+
+# References 
+Inspired by: ImageJ HDF Plugin of Matthias Schlachter Chair of Pattern Recognition and Image Processing, University of Freiburg, Germany.
+https://code.google.com/p/imagej-hdf/

pom.xml

@@ -0,0 +1,16 @@
+<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>ch.psi</groupId>
+	<artifactId>imagej.h5</artifactId>
+	<version>0.0.1</version>
+
+	<dependencies>
+		<dependency>
+			<groupId>gov.nih.imagej</groupId>
+			<artifactId>imagej</artifactId>
+			<version>1.46</version>
+			<scope>provided</scope>
+		</dependency>
+	</dependencies>
+</project>

src/main/java/HDF5_Batch_.java

@@ -16,29 +16,6 @@
  *
  *=========================================================================*/
 
-
-import ij.*;
-import ij.io.*;
-import ij.plugin.*;
-import ij.plugin.filter.PlugInFilter;
-import ij.process.*;
-import ij.gui.*;
-import java.awt.*;
-import java.lang.Math;
-
-import java.io.IOException;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-
-import javax.swing.tree.DefaultMutableTreeNode;
-
-import ncsa.hdf.object.*; // the common object package
-import ncsa.hdf.object.h5.*; // the HDF5 implementation
-import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
-import ncsa.hdf.hdflib.HDFException;
-
 public class HDF5_Batch_ 
 {
   public static void run(String arg)

src/main/java/HDF5_Config.java

@@ -17,14 +17,10 @@
  *=========================================================================*/
 
 
-import ij.IJ;
 import ij.Prefs;
 import ij.gui.GenericDialog;
 import ij.plugin.PlugIn;
 import java.util.regex.*;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
 import java.lang.String;
 
 

src/main/java/HDF5_GroupedVarnames.java

@@ -16,9 +16,6 @@
  *
  *=========================================================================*/
 
-import ij.IJ;
-import ij.Prefs;
-import ij.plugin.PlugIn;
 import java.util.regex.*;
 import java.util.ArrayList;
 import java.util.Arrays;

src/main/java/HDF5_Reader_.java

@@ -32,10 +32,7 @@ import java.io.File;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
-// for scrollbar
 import java.awt.*;
-import java.awt.image.*;
-import java.io.*;
 
 import ncsa.hdf.object.*; // the common object package
 import ncsa.hdf.object.h5.*; // the HDF5 implementation

src/main/java/HDF5_Writer_.java

@@ -19,15 +19,9 @@
 
 import ij.*;
 import ij.io.*;
-import ij.plugin.*;
 import ij.plugin.filter.PlugInFilter;
 import ij.process.*;
 import ij.gui.*;
-import java.awt.*;
-import java.lang.Math;
-
-import java.io.IOException;
-import java.io.File;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
@@ -37,7 +31,6 @@ import javax.swing.tree.DefaultMutableTreeNode;
 import ncsa.hdf.object.*; // the common object package
 import ncsa.hdf.object.h5.*; // the HDF5 implementation
 import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
-import ncsa.hdf.hdflib.HDFException;
 
 public class HDF5_Writer_ implements PlugInFilter
 {

src/main/java/TimeFrame.java

@@ -18,9 +18,6 @@
 
 import java.util.ArrayList;
 import java.util.Arrays;
-//import java.util.Iterator;
-//import java.util.List;
-
 
 public class TimeFrame implements Comparable
 {