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dependencies.txt
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dependencies.txt
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Up until now I haven't set the dependency installation correctly. Majorly, as the final package shall be a conda-package rather than a pip package
If you have anaconda already installed (and I highly recommend to do so) you only have to install 2 dependency packages:
tifffile
napari (for the napari viewer)
javabridge (for using VIEW5D)
If you are not using anaconda you have to install a lot of extra packages IN ADDITION such as:
numpy
scipy
re
inspect
... (you will get error messages when running the NanoImagingPack and then install those)
tifffile
========
Install the tiff handler tifffile via
conda install -c conda-forge tifffile
pyjnius for VIEW5D
==================
Rainers cool viewer requires the Java Virtual machine and javabridge. That has to be set up.
!!! Note you should use anaconda for successfully running this package!!!
1.) Windows:
a. install javabridge (type in cmd):
conda install -c conda-forge javabridge
b. set up Java
- Download JRE from
https://java.com/en/download/
- set up environment variables:
* at the system PATH variable add the java\bin folder (should contain java.exe):
C:\Program Files\Java\jre1.8.0_201\bin (in my case!)
* if you installed Python only for your account:
- add new Variable (at user variables):
Name = JAVA_HOME
Value = java\bin folder (should contain java.exe; C:\Program Files\Java\jre1.8.0_201\bin in my case!)
- add the folder that contains jvm.dll to user variable PATH (should be C:\Program Files\Java\jre1.8.0_201\bin\server)
* if you installed Python only for your account:
- do the same as above but for the system variables instead of the user variable
2.) Linux:
a. install pyjnius (type in cmd):
conda install -c conda-forge javabridge
b. install java runtime environment (if not yet done, acutally linux should have that)
- note openJDK7 or 6 (as in my Ubuntu V14 only availible) will not work
- however an openJDK11 will be installed automatically, once you install javabridge via conda
- it is found in the site packages folder of your Anaconda installation (e.g. /home/christian/anaconda3/pkgs/openjdk-11.0.1-h14c3975_1014/
c. set up JAVA_HOME:
- Check if set via
echo $JAVA_HOME
- If nothing appears its not set (or points towards an opendJDK6 or 7 version), set it:
- edit the file /etc/environment
- add the line JAVA_HOME="/home/christian/anaconda3/pkgs/openjdk-11.0.1-h14c3975_1014/" (or the your JAVA HOME folder)
- reboot
- if you have an open JDK8 or 11 version installed you should be able to use its path for the JAVA_HOME-dir as well
- NOTE: Editing of /etc/environment will permanently add the JAVA_HOME, some people consider this to be not nice. You can also add it at every session new via:
export JAVA_HOME="/home/christian/anaconda3/pkgs/openjdk-11.0.1-h14c3975_1014/"
Christian, 22.02.2019