tomcat-fiji-plugins/docs/source/FijiInstallationInstructions.rst

Fiji Installation Instructions including TOMCAT plugins

This page explains step by step the instructions for the installation of a new Fiji version from scratch with all relevant TOMCAT plugins.

1. Download and unpack the relevant Fiji.zip file
2. Copy the following files to the TOMCAT folder (to be created) in the existing Fiji plugins folder
   1. Reco_Manager.py
   2. DMP_Reader.class
   3. centering_overlay.py
   4. multiscale_coords.txt
   5. ZeroMQ_Viewer-0.5.0.jar
3. DMP viewer (https://git.psi.ch/tomcat/TOMCAT-DMP-Files/tree/master/ImageJ)
   1. Copy DMP_Reader.class to the plugins/TOMCAT folder
   2. Copy HandleExtraFileTypes.class to the plugins folder
   3. If necessary run
      1. cd location/of/Fiji/plugins
      2. jar -uf IO_-2.1.0.jar HandleExtraFileTypes.class
4. HDF5 Viewer (https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5)

   1. Download and unzip plugin

   2. Decompile HandleExtraFileTypes.class to HandleExtraFileTypes.java (previously done with Jad v1.5.8g, but not tried now)

   3. Add the following line to HandleExtraFileTypes.java:

      if (s1.endsWith(".h5") || s1.endsWith(".hdf5")) {
         return tryPlugIn("ch.psi.imagej.hdf5.HDF5Reader", s2);
      }

   4. Recompile using: javac -classpath ../jars/ij-1.51s.jar HandleExtraFileTypes.java

   5. Run jar -uf IO_-2.1.0.jar HandleExtraFileTypes.class

5. Jython
   1. Jython 2.7 has some problems:
      1. The os module is missing some attributes (e.g. getuid)
      2. os.path.realpath has a strange behavior
   2. Jython 2.5 should be used instead
   3. Therefore remove jython-shaded-2.7.0.jar from the Fiji jars folder
   4. Substitute it with jython-shaded-2.5.3.jar from an older Fiji distribution (if available) or from here.
6. Permissions
   1. Group for the personal account is different from the group of the e-account
   2. Therefore, others need to have read permissions for files and directories
   3. For this purpose, run /net/gfa-fs-3/export/tomcat/x86_64/bin/x02da_copy_permissions_fijiInstallation.py