This document describes how PypeIt performs object extraction. The standard run will perform both boxcar and optimal extractions of every object discovered with the Object Finding algorithm.
The boxcar extraction is based on the
boxcar_radius set in
The optimal extraction is the standard Horne algorithm.
The following are some tips for customizing extractions.
If you are extracting a source with bright emission lines which differ spatially from the continuum (e.g. a galaxy), the code may reject a set of the related pixels. These will, by default, not be extracted.
You can, however, turn off the rejection of these pixels
based on their different spatial profile
by setting the
use_2dmodel_mask parameter in
ExtractionPar Keywords to False, e.g. add
the following to your PypeIt Reduction File:
use_2dmodel_mask = False
This may lead to a few additional cosmic rays entering your extraction.
And when viewing the 2D spectrum using the
you should use the
For very extended, bright emission lines you may need
no_local_sky to avoid poor local sky subtraction.
See Sky Subtraction for further details.
Custom FWHM for optimal extraction
If you want to perform an optimal extraction using a defined FWHM
(i.e., not letting PypeIt to compute it from the flux profile), you can
set the parameter
use_user_fwhm in ExtractionPar Keywords
True. In this case, PypeIt will assume for the object a Gaussian profile
with a FWMH equal to
find_fwhm (see FindObjPar Keywords).
It may be occasionally necessary to set
no_local_sky = True
in SkySubPar Keywords to avoid a bad local sky subtraction.
Here are additional docs on somewhat common edits that PypeIt users make: