Using the pipeline

The 3 main parts to this pipeline are pre-reduction, extraction, and flux calibration. Each of the files specified below need to be made executable:

Pre-reduction

(pre_reduction_dev.py)

  • Starts with folder containing raw arcs, flats, and science frames.

  • Overscan correction, trimming, master arcs, master flats, and object folder organizing

  • A “pre_reduced” directory is created containing these new calibration files and folders for individual targets.

Recommended procedure:

  1. run pre_reduction_dev.py, this will create a configuration file and attempt to organize files by category

  2. edit the custom_config.json file manually (rsubl custom_config.json), correct any mistakes that the pipeline makes in file classification

  3. run pre_reduction_dev.py -c custom_config.json –make-arc –make-flat (or to use archival cals, pre_reduction_dev.py -c custom_config.json -q) include –red-amp-bad if LRIS bottom amplifier broken when prompted to edit the response file, enter “p” to fit and replace preset regions of the response

Extraction

(QUICKLOOK.py -i -a -c)

  • Move to a target folder created in step 1 and run this script.

  • Cosmic ray removal (-c), using the python implementation of LACOS

  • Define the wavelength solution using iraf identify (can use predefined master solution if it exists)

  • Extract a spectrum using the apall task from IRAF

  • Map the extracted spectrum with the calculated wavelength solution

  • The same for the red arm

  • If more than one red exposures are provided (normal), the images are combined prior to reduction Creates “target_ex” directory containing the d*_ex.fits file used in flux calibration

Flux Calibration

(cal.py)

  • Run cal.py in the same directory.

  • Flux calibrates and telluric corrects the extracted spectrum from part 2.

  • If you specified to use an archival flux calibration in part 2, then the relevant files have been moved into this directory. Simply choose “n” when prompted to fit a flux or bstar.