This is the 0.1 version of a quicklook spectral reduction pipeline. For now, it works on KAST spectral images, the plan is to include every longslit spectral instrument.

The pipeline is a python script called QUICKLOOK.py, utilising an implementation of IRAF called, not surprisingly, pyRAF. It is heavily influenced from Stefano Valenti's work on similar pipelines for NNT (EFOSC) and LCO (FLOYDS) pipelines. For a small description, type:

QUICKLOOK.py -h

In order for the pipeline to work, collect in a folder the science files (for KAST, these are b****.fits and r****.fits for the blue and red arm, respectively), plus a set of arcs (for KAST, these are again on the form of b****.fits and r****.fits. It works for 2 arcsec slit arcs, which, if everything during the night went well, they are probably b1003.fits and r1003.fits)

The recommended syntax is

QUICKLOOK.py -i -a -c

Installation of the pipeline.

• Via anaconda, install astroconda. More info on https://astroconda.readthedocs.io/en/latest/

• Make sure you include the iraf environment, https://astroconda.readthedocs.io/en/latest/installation.html

• After that, just in case, check if you have pyraf, numpy, astropy and pylab.

• Clone the repository

  git clone https://github.com/msiebert1/UCSC_spectral_pipeline.git

• In your ~/.bashrc file (or your ~/.bash_profile for Mac people), add the following lines:

  export UCSC_SPECPIPE=<the new directory just created by git>

  export PATH=$UCSC_SPECPIPE/spectral_reduction:$PATH

• Copy the disp.cl file (located in the extra_files folder) into your iraf folder (this was hopefully created when you installed astroconda). If you cannot find it, copy the disp.cl file into ~/iraf and run mkiraf in that directory.

• At the end of your iraf login.cl file, add the following line with the appropriate path:

  task disp='<your_iraf_directory>/disp.cl'

• For the flux calibration portion of the pipline make sure you have a python 3 environment. This can be created with a command like:

  conda create -n py36 python=3.6 anaconda

The pipeline includes 3 folders with the relevant scripts, and this readme file:

• Spectral_reduction. This includes the scripts + functions, used in the pipeline. There may be some left-over functions from other codes, or functions that are not called at all. In time, this will be corrected. Moreover, there is a folder called trunk, where the archival files, used in the pipeline are included.
• Extra_files. This includes 2 plots with emission arc lines for KAST, for your convenience, and the disp.cl file, for which we will mention later on.
• Test_data. Contains arcs (b1003, r1003), flats (b1020-b1030, r1020-r1030), and science frames (b1064, r1073-r1075).

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:

1. Pre-reduction (pre_reduction.py)

• IMPORTANT: requires the iraf27 env
• 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.

2. Extraction (QUICKLOOK.py -i -a -c)

• IMPORTANT: requires the iraf27 env
• Move to a target folder created in step 1 and run this script.
• Cosmic ray removal (-c), using the python implementation of LACOS
• Compares the night's arcs with a set of already wavelength identified arcs calculating a new set of wavelength solutions
• 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

3. Flux Calibration (headerfix.py, cal.py, wombat.py)

• IMPORTANT: requires a python3 env
• Run headerfix.py inside of the "target_ex" directory.
• 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.