OSIRIS Data Reduction Pipeline

v4.0beta Release Notes (2016-05-30)

• Updates to the code in order to run the pipeline for the new detector.
• For data taken in 2016 onward, it is no longer necessary to run the following modules: Remove Cross Talk, Glitch Identification. It is fine to keep them in the DRF XML, these modules will automatically not run on the new data.
• Installation has now been simplified (see below for install directions). Bash scripts have been included for those who would like to use bash shell.
• Test framework is now available to run tests of the pipeline (requires pytest module in python, see README in ''tests'' directory)
• WCS bugs have been fixed.

Prerequisites

To install and run the OSIRIS DRP, you will need the following:

• A working C compiler (e.g. gcc)
• A copy of the compiled library cfitsio
• A working installation of IDL

Compiling a Local version of the DRP

Set up the following environment variables if the defaults won't work for your installation. The defaults should work for installations of IDL on Mac OS X and CFITSIO installed using MacPorts:

• IDL_INCLUDE: The IDL include directory. If you don't set IDL_INCLUDE, it defaults to IDL_INCLUDE=/Applications/exelis/idl/external/include
• CFITSIOLIBDIR: The directory containing your installation of CFITSIO. If you don't set CFITSIOLIBDIR, it will default to CFITSIOLIBDIR=/opt/local/lib, which is correct for MacPorts.

Then you can run the makefile from the top level of the OSIRIS DRP source code:

make all

and you should see that the pipeline has been built correctly. Be sure you are using gmake (which on OS X is the only make, so using make works.)

OSIRIS Environment

The OSIRIS DRP requires that you set various environment variables to that it knows how to find and run the pipeline. Instructions are below for bash (should work for other POSIX compliant shells) and c-shell. If you want to set up your environment every time you start your shell (e.g. via .cshrc or .bashrc), you should set OSIRIS_VERBOSE=0 to silence the output of the setup scripts. Otherwise, they will print useful messages about the setup of your OSIRIS pipeline environment.

Environment Setup in Bash

To setup the OSIRIS environment, source the file scripts/osirisSetup.sh, then run osirisSetup with the root directory of your OSIRIS DRF installation. If your OSIRIS pipeline is installed in /usr/local/osiris/drs/, then you would do:

$ source scripts/osirisSetup.sh
To use the OSIRIS DRP, run osirisSetup /path/to/my/drp
$ osirisSetup /my/path/to/osiris/drp/
Setting OSIRIS_ROOT=/my/path/to/osiris/drp/
Adding /my/path/to/osiris/drp/scripts to your path.
Successfully setup OSIRIS DRP environment.
The DRP is in /my/path/to/osiris/drp/

You can change all of the relevant OSIRIS variables later by running osirisSetup again. osirisSetup will by default add $OSIRIS_ROOT/scripts to your environment's PATH variable. To skip this step, run osirisSetup with -n:

$ osirisSetup -n /my/path/to/osiris/drp/
Setting OSIRIS_ROOT=/my/path/to/osiris/drp/
Successfully setup OSIRIS DRP environment.
The DRP is in /my/path/to/osiris/drp/

You can add these lines to your .bashrc file or other startup profile if you want to set up the osiris environment variables for each of your shell sessions. Add lines like this to your profile:

OSIRIS_VERBOSE=0
source scripts/osirisSetup.sh
osirisSetup /my/path/to/osiris/drp/

Environment Setup in CSH

To setup the OSIRIS environment, set the environment variable OSIRIS_ROOT to the root directory for the OSIRIS data reduction pipeline. Then source the file scripts/osirisSetup.csh.

$ setenv OSIRIS_ROOT /my/path/to/osiris/drp/
$ source scripts/osirisSetup.csh
Using OSIRIS_ROOT=/my/path/to/osiris/drp/
Successfully setup OSIRIS DRP environment.
The DRP is in /my/path/to/osiris/drp/
You might want to add /my/path/to/osiris/drp/scripts to your PATH.

You can add these lines to your .cshrc file or other startup profile if you want to set up the osiris environment variables for each of your shell sessions. Add lines like this to your profile:

set OSIRIS_VERBOSE=0
setenv OSIRIS_ROOT=/my/path/to/osiris/drp/
source scripts/osirisSetup.csh

Running the Pipeline

To run the pipeline, use run_odrp. If you don't want the pipeline to open a new xterm window, call run_odrp -n.

Please check out the OSIRIS pipeline manual: http://www2.keck.hawaii.edu/inst/osiris/OSIRIS_Manual_v2.3.pdf

Troubleshooting

If you run into problems, please re-read this README.md, then read INSTALLPROBLEMS.md for some common installation problems.