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update readme / cleanup

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ebner 2020-10-13 08:32:39 +02:00
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Readme.md
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@ -43,8 +43,12 @@ stack = reader.open("",False, "/Users/ebner/Desktop/A8_d_400N030_.h5", "/exchang
# Installation # Installation
## Prerequisites 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.
To be able to install this plugin, ImageJ needs to be run with a Java 7 or
# Troubleshooting
### Prerequisites
To be able to run this plugin, ImageJ needs to be run with a Java 8 or
greater JVM. greater JVM.
At the time of writing, the latest Fiji distribution of ImageJ comes bundled At the time of writing, the latest Fiji distribution of ImageJ comes bundled
@ -62,7 +66,7 @@ In the following, the installation procedure is detailed for a Fiji
installation with Java 8 included and also for older installations based on installation with Java 8 included and also for older installations based on
Java 6. Java 6.
## Checking the Java version ### Checking the Java version
You can check whether Java-8 is included with Fiji as follows: You can check whether Java-8 is included with Fiji as follows:
@ -76,15 +80,10 @@ You can check whether Java-8 is included with Fiji as follows:
![ImageJ Updater Advanced Mode](ImageJ_Updater_AdvancedMode.png) ![ImageJ Updater Advanced Mode](ImageJ_Updater_AdvancedMode.png)
![ImageJ Updater Search Java 8](ImageJ_Updater_search_java8.png) ![ImageJ Updater Search Java 8](ImageJ_Updater_search_java8.png)
## Downloading the source
Download latest HDF5 ImageJ plugin from ### Installation for Fiji with Java 8
[releases](https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5/releases).
#### Deactivate the distributed hdf5 plugin
## Installation for Fiji with Java 8
### Deactivate the distributed hdf5 plugin
As mentioned previously, unfortunately the standard hdf5 plugin (HDF5_Vibez) of As mentioned previously, unfortunately the standard hdf5 plugin (HDF5_Vibez) of
Fiji interferes with the PSI plugin. You will be able to tell which plugin is Fiji interferes with the PSI plugin. You will be able to tell which plugin is
@ -109,16 +108,11 @@ To disable the standard hdf5 plugin, follow these steps.
### Install the PSI hdf5 plugin ### Install the PSI hdf5 plugin
The installation of the plugin essentially only requires one to add the The installation of the plugin essentially only requires one to add the downloaded jar into the `plugins`
contents of the downloaded source archive into the `plugins` and `lib` directory inside the Fiji installation directory. Follow these steps:
directories inside the Fiji installation directory. Follow these steps:
* Locate the installation directory of the Fiji application (`FIJI_DIR`). * Locate the installation directory of the Fiji application (`FIJI_DIR`).
* Unpack the contents of the downloaded source file into `FIJI_DIR`: * Copy the downloaded jar file file into `FIJI_DIR/plugins`
* Windows: Right-click the zip file with the source and select "Extract
to...", then navigate to `FIJI_DIR`.
* Linux: `unzip <Source.zip> <FIJI_DIR>`
* macOS: `unzip <Source.zip> <FIJI_DIR>`
* Close any running instances of the Fiji applications, then reopen Fiji. * Close any running instances of the Fiji applications, then reopen Fiji.
* Try to import an hdf5 file: `Fiji > File > Import > HDF5...`. * Try to import an hdf5 file: `Fiji > File > Import > HDF5...`.
* If the installation of the pluging was sucessful, the file import dialog * If the installation of the pluging was sucessful, the file import dialog
@ -174,63 +168,36 @@ done as follows:
``` ```
cd <FIJI_HOME> cd <FIJI_HOME>
<fiji> --java-home /usr/lib/jvm/jre-1.7.0-openjdk.x86_64 -Djava.library.path=lib/linux64 <fiji> --java-home /usr/lib/jvm/jre-1.8.0-openjdk.x86_64
``` ```
Starting with Java 8 just the LD_LIBRARY_PATH variable need to be set. For
MacOSX it is `export DYLD_LIBRARY_PATH=lib/mac64/:$DYLD_LIBRARY_PATH`.
# Usage # Usage
For normal usage, you should just be able to open Fiji/ImageJ as usual and For normal usage, you should just be able to open Fiji/ImageJ as usual and
start using the hdf5 plugin. Below are some hints for advanved usage, start using the hdf5 plugin. Below are some hints for advanced usage,
specifying the amount of memory to be used, etc. specifying the amount of memory to be used, etc.
## Mac OS X
``` ```
java -Djava.library.path=./lib/mac64 -Xmx3048m -jar ImageJ64.app/Contents/Resources/Java/ij.jar java -Xmx3048m -jar ij.jar
``` ```
## Linux The `Xmx` setting is quite "random" it depends on how big hdf5 files you are
```
java -Djava.library.path=./lib/linux64 -Xmx3048m -jar ij.jar
```
The `Xmx` setting is quite random it depends on how big hdf5 files you are
planning to open. planning to open.
## Windows
As the provided zip currently does not provide the Windows binaries for HDF5, the simplest way
to get things working is to install HDFView (https://www.hdfgroup.org/downloads/hdfview/) and
then opening ImageJ.
# Development # Development
To be able to run the tests and plugin from within the following arguments need
to be passed:
![RunSettings](RunSettings.png) To create an all in one jar file for installation in a ImageJ installation use:
`./gradlew clean fatJar`
To create an all in one zip file for installation in a ImageJ installation use: The jar file is an all in one jar including all required native libraries for Windows, Linux and Mac OS X.
`mvn clean compile assembly:assembly`
The zip file contains an all in one jar as well as the required native
libraries for Windows, Linux and Mac OS X.
Note: to be able to build the package you need to have access to the PSI
artifact server. Therefore this only works within the PSI networks and if you
have a certain maven configuration. An example Maven settings.xml that you can
copy to `~/.m2/settings.xml` is located [here](settings.xml).
## Dependencies ## Dependencies
The java HDF5 libary as well as the precompiled code we downloaded and copied from: The java HDF5 libary as well as the precompiled code we downloaded and copied from: https://wiki-bsse.ethz.ch/display/JHDF5/Download+Page
https://wiki-bsse.ethz.ch/display/JHDF5/Download+Page All the necessary jars where copied from there into the `/lib` directory.
All the necessary jars where copied from there into the /lib directory.
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. 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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src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java
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@ -29,7 +29,7 @@ public class HDF5Reader implements PlugIn {
public static void main(String[] args){ public static void main(String[] args){
HDF5Reader r = new HDF5Reader(); HDF5Reader r = new HDF5Reader();
// r.run(""); // r.run("");
r.open("",false, "/Users/ebner/Desktop/pollen.h5", "/t0/channel0", true); r.open("",false, "pollen.h5", "/t0/channel0", true);
} }
public void run(String arg) { public void run(String arg) {