diff --git a/.classpath b/.classpath new file mode 100644 index 0000000..ce86f24 --- /dev/null +++ b/.classpath @@ -0,0 +1,32 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..ea8c4bf --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +/target diff --git a/.project b/.project new file mode 100644 index 0000000..442dae8 --- /dev/null +++ b/.project @@ -0,0 +1,23 @@ + + + ImageJHDF5 + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.jdt.core.javanature + org.eclipse.m2e.core.maven2Nature + + diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs new file mode 100644 index 0000000..abec6ca --- /dev/null +++ b/.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 diff --git a/.settings/org.eclipse.m2e.core.prefs b/.settings/org.eclipse.m2e.core.prefs new file mode 100644 index 0000000..f897a7f --- /dev/null +++ b/.settings/org.eclipse.m2e.core.prefs @@ -0,0 +1,4 @@ +activeProfiles= +eclipse.preferences.version=1 +resolveWorkspaceProjects=true +version=1 diff --git a/LICENSE b/LICENSE deleted file mode 100644 index d645695..0000000 --- a/LICENSE +++ /dev/null @@ -1,202 +0,0 @@ - - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff --git a/NOTICE b/NOTICE deleted file mode 100644 index 09d60de..0000000 --- a/NOTICE +++ /dev/null @@ -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. diff --git a/README b/README deleted file mode 100644 index a300ee7..0000000 --- a/README +++ /dev/null @@ -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)! - -#################################################################### diff --git a/Readme.md b/Readme.md new file mode 100644 index 0000000..6b3aa9a --- /dev/null +++ b/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/ diff --git a/pom.xml b/pom.xml new file mode 100644 index 0000000..0097125 --- /dev/null +++ b/pom.xml @@ -0,0 +1,16 @@ + + 4.0.0 + ch.psi + imagej.h5 + 0.0.1 + + + + gov.nih.imagej + imagej + 1.46 + provided + + + \ No newline at end of file diff --git a/src/HDF5_Batch_.java b/src/main/java/HDF5_Batch_.java similarity index 74% rename from src/HDF5_Batch_.java rename to src/main/java/HDF5_Batch_.java index 95d3279..83492ef 100644 --- a/src/HDF5_Batch_.java +++ b/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) diff --git a/src/HDF5_Config.java b/src/main/java/HDF5_Config.java similarity index 98% rename from src/HDF5_Config.java rename to src/main/java/HDF5_Config.java index 89d8d74..28a4715 100644 --- a/src/HDF5_Config.java +++ b/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; diff --git a/src/HDF5_GroupedVarnames.java b/src/main/java/HDF5_GroupedVarnames.java similarity index 99% rename from src/HDF5_GroupedVarnames.java rename to src/main/java/HDF5_GroupedVarnames.java index 421c2b1..01fc4f4 100644 --- a/src/HDF5_GroupedVarnames.java +++ b/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; diff --git a/src/HDF5_Reader_.java b/src/main/java/HDF5_Reader_.java similarity index 99% rename from src/HDF5_Reader_.java rename to src/main/java/HDF5_Reader_.java index 4572b8b..e32ffd1 100644 --- a/src/HDF5_Reader_.java +++ b/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 diff --git a/src/HDF5_Writer_.java b/src/main/java/HDF5_Writer_.java similarity index 99% rename from src/HDF5_Writer_.java rename to src/main/java/HDF5_Writer_.java index 1f530c5..943df5a 100644 --- a/src/HDF5_Writer_.java +++ b/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 { diff --git a/src/TimeFrame.java b/src/main/java/TimeFrame.java similarity index 98% rename from src/TimeFrame.java rename to src/main/java/TimeFrame.java index 9e6da3e..5aeb922 100644 --- a/src/TimeFrame.java +++ b/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 { diff --git a/plugins.config b/src/main/resources/plugins.config similarity index 100% rename from plugins.config rename to src/main/resources/plugins.config