PypeIt scripts¶

PypeIt is packaged with several scripts that should have been installed directly into your path (e.g. ~/anaconda/bin).

Pipeline Scripts¶

pypeit_setup¶

This setups files for data reduction. See Setups for details

run_pypeit¶

This is the main executable for PypeIt. See Running PypeIt for details.

Inspecting Data¶

The following scripts are inspecting the data products produced by PypeIt.

pypeit_show_1dspec¶

Wrapper around the linetools XSpecGUI. Grabs a single 1D spectrum from the PypeIt spec1d output and runs:

unix> pypeit_show_1dspec -h
 usage: pypeit_show_1dspec [-h] [--list] [--exten EXTEN] [--extract EXTRACT] [--obj OBJ] file

 Parse

 positional arguments:
   file           Spectral file

 optional arguments:
   -h, --help         show this help message and exit
   --list             List the extensions only?
   --exten EXTEN      FITS extension
   --obj OBJ          Object name in lieu of extension, e.g. O424-S1466-D02-I0013
   --extract EXTRACT  Extraction method. Default is boxcar. ['box', 'opt']

pypeit_show_2dspec¶

This script displays the sky-subtracted 2D image for a single detector in a Ginga RC viewer. It also overlays the slits and any objects extracted. It should be called from the reduction directory, i.e. above the Science folder where the spec2d image is located. Here is the usage:

unix> pypeit_show_2dspec -h
usage: pypeit_show_2dspec [-h] [--list] [--det DET] file

Display spec2d image in a Ginga viewer

positional arguments:
  file        PypeIt spec2d file

optional arguments:
  -h, --help  show this help message and exit
  --list      List the extensions only? (default: False)
  --det DET   Detector (default: 1)

The script can be called multiple times to load multiple detectors into one Ginga viewer.

pypeit_view_fits¶

This is a wrapper to the Ginga image viewer. It is a bit of a kludge in that it writes a dummy tmp.fits file to the harddrive and sends that into Ginga. The dummy file is deleted afterwards.:

unix> pyp_view_fits -h
usage: pyp_view_fits [-h] [--list] [--raw_lris] [--exten EXTEN] file

positional arguments:
  file           FITS file

optional arguments:
  -h, --help     show this help message and exit
  --list         List the extensions only? (default: False)
  --raw_lris
  --exten EXTEN  FITS extension (default: None)

Data Processing Scripts¶

pypeit_coadd_1dspec¶

See Coadd 1D Spectra for further details.

Calibration Scripts¶

pypeit_arcid_plot¶

Generate a PDF plot from a MasterFrame_WaveCalib.json file. This may be useful to ID lines in other data.:

unix> pypeit_arcid_plot -h
usage: pypeit_arcid_plot [-h] wave_soln title outfile

positional arguments:
  wave_soln   MasterWaveSoln file [JSON]
  title       Title for the plot
  outfile     Output PDF file

optional arguments:
  -h, --help  show this help message and exit

pypeit_lowrdx_pixflat¶

Convert a LowRedux pixel flat into a PypeIt ready file:

unix> pypeit_lowrdx_pixflat -h
usage: pypeit_lowrdx_pixflat [-h] lowrdx_file new_file

positional arguments:
  lowrdx_file  LowRedux Pixel Flat FITS file
  new_file     PypeIt FITS file

optional arguments:
  -h, --help   show this help message and exit

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