Added gain and readnoise to get_metadata() in imaging_pipeline.py. For Ticket#115.
Header information now passed to get_cosmicx_params(). If the readnoise and gain are given in the header, they should override manually specified files in the cosmicx_cfg yaml files.
Fixed get_metadata trying to find CCDGAIN in SBC data. This version of the pipeline appears to successfully run up to the astrodrizzle step on images from all six detectors.
Changed list comprehension in run_imaging_pipeline to accept _flt.fits input. Made the symlink function in run_cosmicx only run for _c0m.fits input.
Corrected syntax errors and other mistakes. This version of the pipeline appears to be running correctly.
Merge pull request #126 from STScI-Citizen-Science/filename_handling

Merging add_metadata and filename_handling. Ticket #117 can be closed.
Corrected issue in run_cosmicx for ACS/WFC files, which have a variable number of extensions depending on the chips used. Previously, we only try/excepted for the case where extensions were empty. This version of the pipeline appears to run successfully for inputs from all six detectors, up to astrodrizzle.
Modified parameters for cosmicx. Stopped using gain information from WFPC2, as it produced bad CR rejection results. See Ticket #111.
Set all pixels more negative than -10 to 0, for better cr rejection. For Ticket #111.
Made changes to UVIS cosmicx parameters. For Ticket #111.
Changed run_cosmicx.py such that cr rejection does not run on SBC and IR images. A copy of the input, with the output name, is produced instead.
Changed run_cosmicx.py such that cr rejection does not run on SBC and IR images. A copy of the input, with the output name, is produced instead.
Set num_cores to 4 so I can get the pipeline running. For Ticket #128.
Merge pull request #127 from STScI-Citizen-Science/add_metadata

add_metadata adds the remaining logic for the master branch to be able to run CR rejection on inputs from all six detectors. The pipeline now accepts _flt.fits files, in addition to _c0m.fits files.

CR rejection is run on WFPC2, HRC, WFC, and UVIS using parameters acquired from files unique to each detector in MTPipeline/cosmicx_cfg. For HRC, WFC, and UVIS, the readnoise and gain are read from the image header files and supplant the readnoise and gain set in the configuration files. CR rejection is not run on IR or SBC images. We are confident that no CR rejection is needed for our IR data, and the same likely holds true for SBC (though not for the same reason). At the moment, the cosmicx parameter files for IR and SBC remain, but can in the future be removed (although this will require changes into get_cosmicx_params).