2023-07-21
2023-05-02
run_odrp and osirisDropDRF scripts to run better on more modern Linux environments.2022-04-12
2021-02-22
2020-09-22
Previous Release Notes
For older release notes see: RELEASE_NOTES.md
Cosmic Ray Module
Bad pixel mask A preliminary bad pixel mask is available for data taken after 2016 (new spectrograph detector). The mask was computed from a series of darks. There is both a bad pixel mask of hot pixels (pixels with permanently elevated value) as well as a dead pixel mask (pixels with permanently low values). This mask meant to be used as extension 2 in the raw fits files. Currently, the mask is not automatically applied by Keck. To apply it, use the following command in the raw spectra directory once the pipeline is installed:
apply_mask.py *.fitsNOTE: this requires python installed with numpy and astropy packages. Tests show that using the bad pixel mask improves the SNR by about 10%.
Old Modules
Current Important OSIRIS Issues
Please cite Lyke et al. (2017) and Lockhart et al. (2019) if you use this pipeline in a publication.
To install and run the OSIRIS DRP, you will need the following:
gcc)apt)sudo apt get csh. PATH environment variable)Either clone or download the source from github, choose either the master branch or the develop branch.
Set up the following environment variables to compile the code (you can remove these variables after compiling). 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. On linux, this might be IDL_INCLUDE=/usr/local/harris/idl/external/includeCFITSIOLIBDIR: 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. On Ubuntu Linux, you can install libcfitsio-dev from apt. The library is then located at CFITSIOLIBDR=/usr/lib/x86_64-linux-gnuRun the makefile from the top level of the OSIRIS DRP source code:
make allYou should see that the pipeline has been built correctly by seeing that the file modules/source/libosiris_drp_ext_null.so.0.0 exists.
The OSIRIS DRP requires various environment variables 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 can add the environment variable,
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.
You can add these lines to your .bashrc file or other startup profile if you want to set up the osiris environment variables for all of your shell sessions. Add these lines to your profile:
OSIRIS_VERBOSE=0
source /my/path/to/osiris/drp/scripts/osirisSetup.sh
osirisSetup /my/path/to/osiris/drpRemember if your IDL binary is not in your path, you should also add it to your .bashrc file, for example:
export PATH=$PATH:/Applications/exelis/idl/binYou 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 these lines to your profile:
set OSIRIS_VERBOSE=0
setenv OSIRIS_ROOT=/my/path/to/osiris/drp/
source ${OSIRIS_ROOT}/scripts/osirisSetup.csh
setenv PATH ${PATH}:${OSIRIS_ROOT}/scriptsRemember if your IDL binary is not in your path, you should also add it to your .cshrc file, for example:
setenv PATH ${PATH}:/Applications/exelis/idl/binTo 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: OSIRIS_Manual_v5.pdf in this directory.
You can run the xml file in tests/test_emission_line/emission_obj.xml by downloading the following files:
tests/test_emission_line/tests/test_emission_line/tests/calib/To set the default directories for the guis, you can edit the following two files:
odrfgui/odrfgui_cfg.xmloopgui/oopgui_cfg.xmlIf you run into problems, please re-read this README.md, then read INSTALLPROBLEMS.md for some common installation problems. Please post an issue on the issue page if you have problems not addressed in the above documents or in the manual.
(If you have contributed to the OSIRIS pipeline and your name is missing, please send an email to the coordinators, or If you have contributed to the OSIRIS pipeline and your name is missing, please send an email to the coordinators, or open a pull request for this page in the OsirisDRP repository