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update readme / cleanup
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Readme.md
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Readme.md
@ -43,8 +43,12 @@ stack = reader.open("",False, "/Users/ebner/Desktop/A8_d_400N030_.h5", "/exchang
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# Installation
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## Prerequisites
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To be able to install this plugin, ImageJ needs to be run with a Java 7 or
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All you need is to download the latest HDF5 ImageJ plugin from [releases](https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5/releases) and copy the jar into the `plugins` directory of ImageJ. After this you should be able to simply start ImageJ and use the Plugin.
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# Troubleshooting
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### Prerequisites
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To be able to run this plugin, ImageJ needs to be run with a Java 8 or
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greater JVM.
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At the time of writing, the latest Fiji distribution of ImageJ comes bundled
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@ -62,7 +66,7 @@ In the following, the installation procedure is detailed for a Fiji
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installation with Java 8 included and also for older installations based on
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Java 6.
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## Checking the Java version
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### Checking the Java version
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You can check whether Java-8 is included with Fiji as follows:
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@ -76,15 +80,10 @@ You can check whether Java-8 is included with Fiji as follows:
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## Downloading the source
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Download latest HDF5 ImageJ plugin from
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[releases](https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5/releases).
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### Installation for Fiji with Java 8
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## Installation for Fiji with Java 8
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### Deactivate the distributed hdf5 plugin
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#### Deactivate the distributed hdf5 plugin
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As mentioned previously, unfortunately the standard hdf5 plugin (HDF5_Vibez) of
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Fiji interferes with the PSI plugin. You will be able to tell which plugin is
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@ -109,16 +108,11 @@ To disable the standard hdf5 plugin, follow these steps.
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### Install the PSI hdf5 plugin
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The installation of the plugin essentially only requires one to add the
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contents of the downloaded source archive into the `plugins` and `lib`
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directories inside the Fiji installation directory. Follow these steps:
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The installation of the plugin essentially only requires one to add the downloaded jar into the `plugins`
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directory inside the Fiji installation directory. Follow these steps:
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* Locate the installation directory of the Fiji application (`FIJI_DIR`).
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* Unpack the contents of the downloaded source file into `FIJI_DIR`:
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* Windows: Right-click the zip file with the source and select "Extract
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to...", then navigate to `FIJI_DIR`.
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* Linux: `unzip <Source.zip> <FIJI_DIR>`
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* macOS: `unzip <Source.zip> <FIJI_DIR>`
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* Copy the downloaded jar file file into `FIJI_DIR/plugins`
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* Close any running instances of the Fiji applications, then reopen Fiji.
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* Try to import an hdf5 file: `Fiji > File > Import > HDF5...`.
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* If the installation of the pluging was sucessful, the file import dialog
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@ -174,63 +168,36 @@ 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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<fiji> --java-home /usr/lib/jvm/jre-1.8.0-openjdk.x86_64
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```
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Starting with Java 8 just the LD_LIBRARY_PATH variable need to be set. For
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MacOSX it is `export DYLD_LIBRARY_PATH=lib/mac64/:$DYLD_LIBRARY_PATH`.
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# Usage
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For normal usage, you should just be able to open Fiji/ImageJ as usual and
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start using the hdf5 plugin. Below are some hints for advanved usage,
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start using the hdf5 plugin. Below are some hints for advanced usage,
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specifying the amount of memory to be used, etc.
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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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java -Xmx3048m -jar 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
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The `Xmx` setting is quite "random" it depends on how big hdf5 files you are
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planning to open.
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## Windows
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As the provided zip currently does not provide the Windows binaries for HDF5, the simplest way
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to get things working is to install HDFView (https://www.hdfgroup.org/downloads/hdfview/) and
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then opening ImageJ.
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# Development
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To be able to run the tests and plugin from within the following arguments need
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to be passed:
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To create an all in one jar file for installation in a ImageJ installation use:
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`./gradlew clean fatJar`
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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 jar file is an all in one jar including all required native libraries for Windows, Linux and Mac OS X.
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The zip file contains an all in one jar as well as the required native
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libraries for Windows, Linux and Mac OS X.
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Note: to be able to build the package you need to have access to the PSI
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artifact server. Therefore this only works within the PSI networks and if you
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have a certain maven configuration. An example Maven settings.xml that you can
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copy to `~/.m2/settings.xml` is located [here](settings.xml).
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## Dependencies
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The java HDF5 libary as well as the precompiled code we downloaded and copied from:
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https://wiki-bsse.ethz.ch/display/JHDF5/Download+Page
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All the necessary jars where copied from there into the /lib directory.
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The java HDF5 libary as well as the precompiled code we downloaded and copied from: https://wiki-bsse.ethz.ch/display/JHDF5/Download+Page
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All the necessary jars where copied from there into the `/lib` directory.
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The files in the package hdf.objects in this repository were copied from the hdfviewer source code. We were not able to find a jar that contained them.
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@ -29,7 +29,7 @@ public class HDF5Reader implements PlugIn {
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public static void main(String[] args){
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HDF5Reader r = new HDF5Reader();
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// r.run("");
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r.open("",false, "/Users/ebner/Desktop/pollen.h5", "/t0/channel0", true);
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r.open("",false, "pollen.h5", "/t0/channel0", true);
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}
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public void run(String arg) {
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