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66 lines
1.6 KiB
Markdown
66 lines
1.6 KiB
Markdown
# Overview
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ImageJ plugin for reading and writing HDF5 files.
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This project originated from and is inspired by: ImageJ HDF Plugin of Matthias Schlachter Chair of Pattern Recognition and Image Processing, University of Freiburg, Germany.
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https://code.google.com/p/imagej-hdf/
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# Usage
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To open a HDF5 file use:
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```
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File > Import > HDF5...
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```
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To save to an HDF5 file use:
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```
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File > SaveAs > HDF5
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```
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# Installation
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* Download latest HDF5 ImageJ plugin from [here](http://slsyoke4.psi.ch:8081/artifactory/releases/HDF5_Viewer-0.2.0.zip).
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* Go into the ImageJ installation folder and extract the downloaded zip.
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```
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cd <IMAGEJ_HOME>
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unzip <path of downloaded zip>
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```
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## Prerequisites
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This plugin requires ImageJ to be run with a Java 7 or greater JVM.
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# Usage
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## Mac OS X
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```
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java -Djava.library.path=./lib/mac64 -Xmx3048m -jar ImageJ64.app/Contents/Resources/Java/ij.jar
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```
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## Linux
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```
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java -Djava.library.path=./lib/linux64 -Xmx3048m -jar ij.jar
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```
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The `Xmx` setting is quite random it depends on how big hdf5 files you are planning to open.
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# Fiji
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Fiji currently comes with Java 6 bundled. As the HDF5 Plugin requires Java 7 or higher we have to instruct Fiji to use an alternative Java.
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This can be done as follows:
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```
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cd <FIJI_HOME>
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<fiji> --java-home /usr/lib/jvm/jre-1.7.0-openjdk.x86_64 -Djava.library.path=lib/linux64
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```
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# Development
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To create an all in one zip file for installation in a ImageJ installation use:
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`mvn clean compile assembly:assembly`
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The zip file contains an all in one jar as well as the required native libraries for Windows, Linux and Mac OS X.
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