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kbwestfall committed Sep 6, 2024
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10 changes: 0 additions & 10 deletions doc/help/pypeit_coadd_2dspec.rst
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$ pypeit_coadd_2dspec -h
usage: pypeit_coadd_2dspec [-h] [--show] [--debug_offsets] [--peaks]
[--basename BASENAME] [--debug] [-v VERBOSITY]
[--spec_samp_fact SPEC_SAMP_FACT]
[--spat_samp_fact SPAT_SAMP_FACT]
coadd2d_file
Coadd 2D spectra produced by PypeIt
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Verbosity level between 0 [none] and 2 [all]. Default:
1. Level 2 writes a log with filename
coadd_2dspec_YYYYMMDD-HHMM.log (default: 1)
--spec_samp_fact SPEC_SAMP_FACT
Make the wavelength grid finer (spec_samp_fact < 1.0) or
coarser (spec_samp_fact > 1.0) by this sampling factor,
i.e. units of spec_samp_fact are pixels. (default: 1.0)
--spat_samp_fact SPAT_SAMP_FACT
Make the spatial grid finer (spat_samp_fact < 1.0) or
coarser (spat_samp_fact > 1.0) by this sampling factor,
i.e. units of spat_samp_fact are pixels. (default: 1.0)
40 changes: 22 additions & 18 deletions doc/help/pypeit_ql.rst
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[--calibs_only] [--overwrite_calibs] [--det DET [DET ...]]
[--slitspatnum SLITSPATNUM] [--maskID MASKID]
[--boxcar_radius BOXCAR_RADIUS] [--snr_thresh SNR_THRESH]
[--ignore_std] [--skip_display] [--coadd2d]
[--only_slits ONLY_SLITS [ONLY_SLITS ...]] [--offsets OFFSETS]
[--weights WEIGHTS] [--spec_samp_fact SPEC_SAMP_FACT]
[--spat_samp_fact SPAT_SAMP_FACT] [--try_old]
[--ignore_std] [--skip_display] [--removetrace] [--coadd2d]
[--spec_samp_fact SPEC_SAMP_FACT]
[--spat_samp_fact SPAT_SAMP_FACT] [--offsets OFFSETS]
[--weights WEIGHTS] [--only_slits ONLY_SLITS [ONLY_SLITS ...]]
[--try_old]
spectrograph
Script to produce quick-look PypeIt reductions
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detected, ignore those frames. Otherwise, they are
included with the reduction of the science frames.
(default: False)
--skip_display Run the quicklook without displaying any results.
(default: True)
--skip_display Run the quicklook without displaying any results. The
default skip_display=False will show the results.
(default: False)
--removetrace When the image is shown, do not overplot traces in the
skysub, sky_resid, and resid channels (default: False)
--coadd2d Perform default 2D coadding. (default: False)
--only_slits ONLY_SLITS [ONLY_SLITS ...]
If coadding, only coadd this space-separated set of
slits. If not provided, all slits are coadded. (default:
None)
--spec_samp_fact SPEC_SAMP_FACT
If coadding, adjust the wavelength grid sampling by this
factor. For a finer grid, set value to <1.0; for coarser
sampling, set value to >1.0). (default: 1.0)
--spat_samp_fact SPAT_SAMP_FACT
If coadding, adjust the spatial grid sampling by this
factor. For a finer grid, set value to <1.0; for coarser
sampling, set value to >1.0). (default: 1.0)
--offsets OFFSETS If coadding, spatial offsets to apply to each image; see
the [coadd2d][offsets] parameter. Options are restricted
here to either maskdef_offsets or auto. If not
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[coadd2d][weights] parameter. Options are restricted
here to either uniform or auto. If not specified, the
(spectrograph-specific) default is used. (default: None)
--spec_samp_fact SPEC_SAMP_FACT
If coadding, adjust the wavelength grid sampling by this
factor. For a finer grid, set value to <1.0; for coarser
sampling, set value to >1.0). (default: 1.0)
--spat_samp_fact SPAT_SAMP_FACT
If coadding, adjust the spatial grid sampling by this
factor. For a finer grid, set value to <1.0; for coarser
sampling, set value to >1.0). (default: 1.0)
--only_slits ONLY_SLITS [ONLY_SLITS ...]
If coadding, only coadd this space-separated set of
slits. If not provided, all slits are coadded. (default:
None)
--try_old Attempt to load old datamodel versions. A crash may
ensue.. (default: False)
10 changes: 10 additions & 0 deletions doc/help/pypeit_setup_coadd2d.rst
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[--exclude_slits EXCLUDE_SLITS [EXCLUDE_SLITS ...]]
[--spat_toler SPAT_TOLER] [--offsets OFFSETS]
[--weights WEIGHTS]
[--spec_samp_fact SPEC_SAMP_FACT]
[--spat_samp_fact SPAT_SAMP_FACT]
Prepare a configuration file for performing 2D coadds
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or auto. If not specified, the (spectrograph-specific)
default is used. Other options exist but must be entered
by directly editing the coadd2d file. (default: None)
--spec_samp_fact SPEC_SAMP_FACT
Make the wavelength grid finer (spec_samp_fact < 1.0) or
coarser (spec_samp_fact > 1.0) by this sampling factor,
i.e. units of spec_samp_fact are pixels. (default: 1.0)
--spat_samp_fact SPAT_SAMP_FACT
Make the spatial grid finer (spat_samp_fact < 1.0) or
coarser (spat_samp_fact > 1.0) by this sampling factor,
i.e. units of spat_samp_fact are pixels. (default: 1.0)
3 changes: 2 additions & 1 deletion doc/help/pypeit_show_2dspec.rst
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constructed assuming the reduction is for a single
detector. If a string, it must match the name of the
detector object (e.g., DET01 for a detector, MSC01 for a
mosaic). (default: 1)
mosaic). If not set, the first available detectorin the
spec2d file will be shown (default: None)
--spat_id SPAT_ID Restrict plotting to this slit (PypeIt ID notation)
(default: None)
--maskID MASKID Restrict plotting to this maskID (default: None)
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2 changes: 1 addition & 1 deletion doc/help/run_pypeit.rst
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usage: run_pypeit [-h] [-v VERBOSITY] [-r REDUX_PATH] [-m] [-s] [-o] [-c]
pypeit_file
## [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.16.1.dev336+gdf3013372.d20240827[0m
## [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.16.1.dev468+g832ee84e4[0m
##
## Available spectrographs include:
## aat_uhrf, bok_bc, gemini_flamingos1, gemini_flamingos2,
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2 changes: 2 additions & 0 deletions doc/pypeit_par.rst
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Expand Up @@ -570,7 +570,9 @@ Key Type Options Default Description
``manual`` str .. .. Manual extraction parameters. det:spat:spec:fwhm:boxcar_radius. Multiple manual extractions are semi-colon separated, and spat,spec are in the pseudo-image generated by COADD2D.boxcar_radius is optional and in pixels (not arcsec!).
``offsets`` str, list .. ``auto`` Offsets for the images being combined (spat pixels). Options are: ``maskdef_offsets``, ``header``, ``auto``, and a list of offsets. Use ``maskdef_offsets`` to use the offsets computed during the slitmask design matching (currently available for these :ref:`slitmask_info_instruments` only). If equal to ``header``, the dither offsets recorded in the header, when available, will be used. If ``auto`` is chosen, PypeIt will try to compute the offsets using a reference object with the highest S/N, or an object selected by the user (see ``user_obj``). If a list of offsets is provided, PypeIt will use it.
``only_slits`` str, list .. .. Restrict coaddition to one or more of slits. Example syntax -- DET01:175,DET02:205 or MSC02:2234. This and ``exclude_slits`` are mutually exclusive. If both are provided, ``only_slits`` takes precedence.
``spat_samp_fact`` float .. 1.0 Make the spatial sampling finer (``spat_samp_fact`` lessthan 1.0) or coarser (``spat_samp_fact`` greather than 1.0) bythis sampling factor. This basically multiples the 'native'spatial pixel size by ``spat_samp_fact``, i.e. the units of``spat_samp_fact`` are pixels.
``spat_toler`` int .. 5 This parameter provides the desired tolerance in spatial pixel used to identify slits in different exposures
``spec_samp_fact`` float .. 1.0 Make the wavelength grid sampling finer (``spec_samp_fact`` less than 1.0)or coarser (``spec_samp_fact`` greater than 1.0) by this sampling factor.This multiples the 'native' spectral pixel size by ``spec_samp_fact``,i.e. the units of ``spec_samp_fact`` are pixels.
``use_slits4wvgrid`` bool .. False If True, use the slits to set the trace down the center
``user_obj`` int, list .. .. Object that the user wants to use to compute the weights and/or the offsets for coadding images. For longslit/multislit spectroscopy, provide the ``SLITID`` and the ``OBJID``, separated by comma, of the selected object. For echelle spectroscopy, provide the ``ECH_OBJID`` of the selected object. See :doc:`out_spec1D` for more info about ``SLITID``, ``OBJID`` and ``ECH_OBJID``. If this parameter is not ``None``, it will be used to compute the offsets only if ``offsets = auto``, and it will used to compute the weights only if ``weights = auto``.
``wave_method`` str .. .. Argument to :func:`~pypeit.core.wavecal.wvutils.get_wave_grid` method, which determines how the 2d coadd wavelength grid is constructed. The default is None, which will use a linear gridfor longslit/multislit coadds and a log10 grid for echelle coadds. Currently supported options with 2d coadding are:* 'iref' -- Use one of the exposures (the first) as the reference for the wavelength grid * 'velocity' -- Grid is uniform in velocity* 'log10' -- Grid is uniform in log10(wave). This is the same as velocity.* 'linear' -- Grid is uniform in wavelength
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