Command-line Scripts
PypeIt is packaged with several scripts that should have been installed directly
into your path (e.g. ~/anaconda/bin). This document provides brief
summaries of each script and points to other pages with more information.
If you are developing a new script, see Developing New PypeIt Scripts.
Warning
Whenever you upgrade PypeIt, beware that this may include changes to the
output file data models. These changes are not required to be
backwards-compatible, meaning that, e.g., pypeit_show_2dspec may fault
when trying to view spec2d* files produced with your existing PypeIt
version after upgrading to a new version. The best approach is to always
re-reduce data you’re still working with anytime you update PypeIt.
Installation Scripts
To install PypeIt, see Installation. The following scripts are used to install ancillary data not included in the baseline package distribution; see Additional Data and the PypeIt Cache.
pypeit_cache_github_data
Because a fresh install of PypeIt does not contain all of the ancillary data
that might be required for data reduction, users planning to run the pipeline
without an internet connection will need to cache the necessary data files ahead
of time. The pypeit_cache_github_data script eases this process. For
example, to download the needed files for the keck_deimos spectrograph, you
would execute:
$ pypeit_cache_github_data keck_deimos
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_cache_github_data -h
usage: pypeit_cache_github_data [-h] [--exclude EXCLUDE [EXCLUDE ...] |
--include INCLUDE [INCLUDE ...]]
[--spec_dependent_only] [--force_update]
spectrograph [spectrograph ...]
Script to download/cache PypeIt github data
positional arguments:
spectrograph A valid spectrograph identifier: aat_uhrf, bok_bc,
gemini_flamingos1, gemini_flamingos2,
gemini_gmos_north_e2v, gemini_gmos_north_ham,
gemini_gmos_north_ham_ns, gemini_gmos_south_ham,
gemini_gnirs_echelle, gemini_gnirs_ifu, gtc_maat,
gtc_osiris, gtc_osiris_plus, jwst_nircam, jwst_nirspec,
keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire,
keck_nires, keck_nirspec_high, keck_nirspec_high_old,
keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b,
lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
magellan_fire, magellan_fire_long, magellan_mage,
mdm_modspec, mdm_osmos_mdm4k, mdm_osmos_r4k,
mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
p200_dbsp_red, p200_tspec, shane_kast_blue,
shane_kast_red, shane_kast_red_ret, soar_goodman_blue,
soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,
vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis,
wht_isis_blue, wht_isis_red
options:
-h, --help show this help message and exit
--exclude EXCLUDE [EXCLUDE ...]
A subset of the directories to *exclude* from the list
of files to download. Options are: tests, reid_arxiv,
nist, standards, skisim, sensfunc, pixelflat. This
option is mutually exclusive with --include. (default:
['tests'])
--include INCLUDE [INCLUDE ...]
The directories to *include* in the list of files to
download. Use "--include all" to include all
directories. Options are: all, tests, reid_arxiv, nist,
standards, skisim, sensfunc, pixelflat. This option is
mutually exclusive with --exclude. (default: None)
--spec_dependent_only
Only include files that are specific to the provided
list of spectrographs. By default, the script also
includes any files in the selected directories that are
*not* specific to a given spectrograph (e.g.,
atmospheric extinction curves). (default: False)
--force_update Force re-download of existing files (default: False)
pypeit_clean_cache
View/Remove files from the PypeIt data cache. The script usage can be displayed
by calling the script with the -h option:
$ pypeit_clean_cache -h
usage: pypeit_clean_cache [-h] [-p PATTERN [PATTERN ...]]
[-v VERSION [VERSION ...]] [--remove_all] [-l]
View/Remove fils in the PypeIt data cache
options:
-h, --help show this help message and exit
-p PATTERN [PATTERN ...], --pattern PATTERN [PATTERN ...]
Remove any files matching the provided pattern. If
combined with --version, this selects only files
downloaded from the identified GitHub versoin. If the
version is not specified, any file matching the provided
pattern(s) are removed. (default: None)
-v VERSION [VERSION ...], --version VERSION [VERSION ...]
Remove files associated one or more provided tags,
branches, or commit references on GitHub. These must be
an exact match to the relevant GitHub reference. If
combined with --pattern, this selects the GitHub
reference for the files found. If no files are
specified, all files associated with the given reference
are removed. Note this is only relevant for the files on
GitHub, not s3. For files on s3, do not specify the
version. (default: None)
--remove_all BEWARE: Removes all data from the pypeit cache. Use of
this option ignores the --pattern and --version options.
(default: False)
-l, --list Only list the contents of the cache. (default: False)
pypeit_install_telluric
When needed, atmospheric model grids will be download automatically, but given
the size of these files and your downlink speed, this may take some time. To
install the grid independent of a reduction, run the pypeit_install_telluric
script, calling the filename of the grid required. For example, if you needed
the file TelFit_MaunaKea_3100_26100_R200000.fits, you would execute:
$ pypeit_install_telluric TelFit_MaunaKea_3100_26100_R200000.fits
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_install_telluric -h
usage: pypeit_install_telluric [-h] [--force_update] [--local_file]
files [files ...]
Script to download/install PypeIt telluric files
positional arguments:
files Exact paths to TelFits files to be downloaded from the Cloud
and installed in the PypeIt cache
options:
-h, --help show this help message and exit
--force_update Force download of latest version of the telluric grid
(default: False)
--local_file This is a local file to be installed in the cache (default:
False)
pypeit_install_ql_calibs
After downloading the QL_CALIB directory for use with the quick-look
scripts, this script “installs” the files by creating a symlink to it within the
PypeIt code base.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_install_ql_calibs -h
usage: pypeit_install_ql_calibs [-h] [--zip ZIP | --ql_path QL_PATH]
[--odir ODIR] [--rmzip]
Script to install PypeIt QL calibration files
options:
-h, --help show this help message and exit
--zip ZIP Zip file of the full QL_CALIB directory downloaded from the
PypeIt Google Drive (default: None)
--ql_path QL_PATH An existing directory to symlink as the QL_CALIB directory.
(default: None)
--odir ODIR The directory in which to extract the zip file. Ignored if
a direct path is provided using --ql_path. (default:
current working directory)
--rmzip Remove the downloaded zip file (default: False)
pypeit_install_linelist
If an instrument-specific arc line list that is not already included in the PypeIt repository is needed for a particular reduction, this script may be used to install a user-generated line list file in the user’s PypeIt cache. See User-Supplied Line Lists.
The script usage can be displayed by calling the script with the -h option:
$ pypeit_install_linelist -h
usage: pypeit_install_linelist [-h] files [files ...]
Script to install user-created arc line lists
positional arguments:
files Filename(s) of the line list files to be installed in the PypeIt
cache
options:
-h, --help show this help message and exit
pypeit_install_extinctfile
In the event of doing flux calibration for data from an observatory without an included extinction file in the PypeIt repository, this script may be used to install a user-supplied extinction file in the user’s PypeIt cache. See Extinction Correction.
The script usage can be displayed by calling the script with the -h option:
$ pypeit_install_extinctfile -h
usage: pypeit_install_extinctfile [-h] files [files ...]
Script to install user-created extinction file
positional arguments:
files One or more files with extinction curve data to be installed in
the PypeIt cache. May include wildcards for multiple files with
the same root.
options:
-h, --help show this help message and exit
pypeit_c_enabled
This is a simple script to check of the compiled C code used by PypeIt was successfully installed. The script takes no arguments and reports success if the C libraries were successfully imported.
pypeit_chk_plugins
This is a simple script to check if all ginga plugins are successfully installed. The script takes no arguments.
pypeit_version
This simply prints the PypeIt version you have installed.
Core Processing Scripts
The core data processing scripts provided by PypeIt perform the standard data reductions expected for all spectrographs. These include basic image processing, slit identification, wavelength calibration, flat-fielding, sky-subtraction, and 1D object extraction.
pypeit_chk_for_calibs
This script, which is similar to pypeit_setup, examines a set of files for an input spectrograph and scans for the standard calibrations. It raises warnings when these are not found.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_chk_for_calibs -h
usage: pypeit_chk_for_calibs [-h] [-s SPECTROGRAPH] [-e EXTENSION]
[--save_setups]
root
Script to check for calibrations
positional arguments:
root File path+root, e.g. /data/Kast/b
options:
-h, --help show this help message and exit
-s SPECTROGRAPH, --spectrograph SPECTROGRAPH
A valid spectrograph identifier: aat_uhrf, bok_bc,
gemini_flamingos1, gemini_flamingos2,
gemini_gmos_north_e2v, gemini_gmos_north_ham,
gemini_gmos_north_ham_ns, gemini_gmos_south_ham,
gemini_gnirs_echelle, gemini_gnirs_ifu, gtc_maat,
gtc_osiris, gtc_osiris_plus, jwst_nircam, jwst_nirspec,
keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire,
keck_nires, keck_nirspec_high, keck_nirspec_high_old,
keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b,
lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
magellan_fire, magellan_fire_long, magellan_mage,
mdm_modspec, mdm_osmos_mdm4k, mdm_osmos_r4k,
mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
p200_dbsp_red, p200_tspec, shane_kast_blue,
shane_kast_red, shane_kast_red_ret, soar_goodman_blue,
soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,
vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis,
wht_isis_blue, wht_isis_red (default: None)
-e EXTENSION, --extension EXTENSION
File extension to use. Must include the period (e.g.,
".fits") and it must be one of the allowed extensions
for this spectrograph. If None, root directory will be
searched for all files with any of the allowed
extensions. (default: None)
--save_setups If not toggled, remove setup_files/ folder and its
files. (default: False)
A typical call is:
pypeit_chk_calibs /PypeIt-development-suite/RAW_DATA/not_alfosc/grism4/ALDc2 -s not_alfosc
After a running stream of detailed notes, it prints a table of results to the screen; e.g.:
setups pass scifiles
------ -------- ---------------
A False ALDc200205.fits
None True
pypeit_obslog
The pypeit_obslog script allows you to see a simple listing of the data
files in a given directory (or directories) and the metadata that PypeIt
will pull from their headers. See pypeit_obslog for details.
pypeit_setup
This is used to setup PypeIt for data reduction, including writing the
automatically generated pypeit file that you will likely need to edit by
hand. See pypeit_setup for details.
run_pypeit
This is the main executable for PypeIt for its core end-to-end data processing. See run_pypeit for details.
pypeit_trace_edges
This isolates the slit-edge tracing to a stand-alone script that can be used to troubleshoot issues before executing run_pypeit. See pypeit_trace_edges.
pypeit_compare_sky
You may find that the default sky models used for your spectrograph are not the best suited for your data. If so, this script allows you to plot a sky spectrum extracted from your data against any of the sky models in the PypeIt archive; see Alternate sky models.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_compare_sky -h
usage: pypeit_compare_sky [-h] [--exten EXTEN] [--optimal]
[--scale_user SCALE_USER]
file skyfile
Compare the extracted sky spectrum against an archived sky model maintained by
PypeIt.
positional arguments:
file spec1d Spectral file
skyfile Archived PypeIt sky file (e.g. paranal_sky.fits)
options:
-h, --help show this help message and exit
--exten EXTEN FITS extension (default: None)
--optimal Show Optimal? Default is boxcar (default: False)
--scale_user SCALE_USER
Scale user spectrum by a factor (default: 1.0)
pypeit_qa_html
Deprecated?
This script constructs the QA html files. This should be done by default at the end of the run_pypeit execution.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_qa_html -h
usage: pypeit_qa_html [-h] [--qapath QAPATH] pypeit_file type
Script to build HTML files for PYPIT QA.
positional arguments:
pypeit_file PYPIT file
type QA Type (MF, exp, all)
options:
-h, --help show this help message and exit
--qapath QAPATH Path the QA folder including QA/) (default: QA/)
Quick-look Scripts
PypeIt provides a script for faster, less robust data reductions for quick-look assessments of the data.
pypeit_ql
This script performs a boxcar (only) extraction of a long- or multi-slit observation taken with one of PypeIt’s spectrographs; see Quick-Look Reductions for full details.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_ql -h
usage: pypeit_ql [-h] [--raw_files RAW_FILES [RAW_FILES ...]]
[--raw_path RAW_PATH] [--sci_files SCI_FILES [SCI_FILES ...]]
[--redux_path REDUX_PATH] [--parent_calib_dir PARENT_CALIB_DIR]
[--setup_calib_dir SETUP_CALIB_DIR] [--clear_science]
[--calibs_only] [--overwrite_calibs] [--det DET [DET ...]]
[--slitspatnum SLITSPATNUM] [--maskID MASKID]
[--boxcar_radius BOXCAR_RADIUS] [--snr_thresh SNR_THRESH]
[--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
positional arguments:
spectrograph A valid spectrograph identifier: aat_uhrf, bok_bc,
gemini_flamingos1, gemini_flamingos2,
gemini_gmos_north_e2v, gemini_gmos_north_ham,
gemini_gmos_north_ham_ns, gemini_gmos_south_ham,
gemini_gnirs_echelle, gemini_gnirs_ifu, gtc_maat,
gtc_osiris, gtc_osiris_plus, jwst_nircam, jwst_nirspec,
keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire,
keck_nires, keck_nirspec_high, keck_nirspec_high_old,
keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b,
lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
magellan_fire, magellan_fire_long, magellan_mage,
mdm_modspec, mdm_osmos_mdm4k, mdm_osmos_r4k,
mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
p200_dbsp_red, p200_tspec, shane_kast_blue,
shane_kast_red, shane_kast_red_ret, soar_goodman_blue,
soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,
vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis,
wht_isis_blue, wht_isis_red
options:
-h, --help show this help message and exit
--raw_files RAW_FILES [RAW_FILES ...]
Either a PypeIt-formatted input file with the list of
raw images to process and the relevant path, or a space-
separated list of the filenames (e.g., "img1.fits
img2.fits"). For the latter entry mode, the path
containing the files is set using --raw_path. (default:
None)
--raw_path RAW_PATH Directory with the raw files to process. Ignored if a
PypeIt-formatted file is provided using the --rawfiles
option. (default: current working directory)
--sci_files SCI_FILES [SCI_FILES ...]
A space-separated list of raw file names that are
science exposures. These files must *also* be in the
list of raw files. Use of this option overrides the
automated PypeIt frame typing. Should only be used of
automatic frame typing fails or is undesirable.
(default: None)
--redux_path REDUX_PATH
Path for the QL reduction outputs. (default: current
working directory)
--parent_calib_dir PARENT_CALIB_DIR
Directory with/for calibrations for *all* instrument
configurations/setups. If provided, the data for your
instrument configuration will be placed or pulled from a
relevant sub-directory. If None, the redux_path is used.
(default: None)
--setup_calib_dir SETUP_CALIB_DIR
Directory with/for calibrations specific to your
instrument configuration/setup. Use of this option
circumvents the automated naming system for the
configuration/setup sub-directories. If None, the code
will try to find relevant calibrations in the
parent_calib_dir. If no calibrations exist in that
directory that match the instrument setup/configuration
of the provided data, the code will construct new
calibrations (assuming relevant raw files are provided).
(default: None)
--clear_science Remove the existing output science directories to force
a fresh reduction. If False, any existing directory
structure will remain, and any alterations to existing
science files will follow the normal behavior of
run_pypeit. (default: False)
--calibs_only Reduce only the calibrations? (default: False)
--overwrite_calibs Re-process and overwrite any existing calibration files.
(default: False)
--det DET [DET ...] A space-separated set of detectors or detector mosaics
to reduce. By default, *all* detectors or default
mosaics for this instrument will be reduced. Detectors
in a mosaic must be a mosaic "allowed" by PypeIt and
should be provided as comma-separated integers (with no
spaces). For example, to separately reduce detectors 1
and 5 for Keck/DEIMOS, you would use --det 1 5; to
reduce mosaics made up of detectors 1,5 and 3,7, you
would use --det 1,5 3,7 (default: None)
--slitspatnum SLITSPATNUM
Reduce the slit(s) as specified by the slitspatnum
value(s) (default: None)
--maskID MASKID Reduce the slit(s) as specified by the maskID value(s)
(default: None)
--boxcar_radius BOXCAR_RADIUS
Set the radius for the boxcar extraction in arcseconds
(default: None)
--snr_thresh SNR_THRESH
Change the default S/N threshold used during source
detection (default: None)
--ignore_std If standard star observations are automatically
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. 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)
--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
specified, the (spectrograph-specific) default is used.
(default: None)
--weights WEIGHTS If coadding, weights used to coadd images; see the
[coadd2d][weights] parameter. Options are restricted
here to either uniform or auto. If not specified, the
(spectrograph-specific) default is used. (default: None)
--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)
Further Processing Scripts
PypeIt separates its Core Processing Scripts from subsequent processing steps, like flux calibration and coadding. The scripts that focus on the latter are as follows.
pypeit_sensfunc
Provided observations of a standard star, this script is used to create a sensitivity function of your observations given the known fluxes of the observed standard. See Fluxing and, specifically, pypeit_sensfunc.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_sensfunc -h
usage: pypeit_sensfunc [-h] [--extr {OPT,BOX}] [--algorithm {UVIS,IR}]
[--multi MULTI] [-o OUTFILE] [-s SENS_FILE] [-f]
[--debug] [--par_outfile PAR_OUTFILE] [-v VERBOSITY]
spec1dfile
Compute a sensitivity function
positional arguments:
spec1dfile spec1d file for the standard that will be used to
compute the sensitivity function
options:
-h, --help show this help message and exit
--extr {OPT,BOX} Override the default extraction method used for
computing the sensitivity function. Note that it is not
possible to set --extr and simultaneously use a .sens
file with the --sens_file option. If you are using a
.sens file, set the algorithm there via:
[sensfunc]
extr = BOX
The extraction options are: OPT or BOX
--algorithm {UVIS,IR}
Override the default algorithm for computing the
sensitivity function. Note that it is not possible to
set --algorithm and simultaneously use a .sens file with
the --sens_file option. If you are using a .sens file,
set the algorithm there via:
[sensfunc]
algorithm = IR
The algorithm options are:
UVIS = Should be used for data with lambda < 7000A. No
detailed model of telluric absorption but corrects for
atmospheric extinction.
IR = Should be used for data with lambbda > 7000A.
Performs joint fit for sensitivity function and telluric
absorption using HITRAN models.
--multi MULTI List of detector numbers to splice together for
instruments with multiple detectors arranged in the
spectral direction, e.g. --multi = '3,7'. Note that it
is not possible to set --multi and simultaneously use a
.sens file with the --sens_file option. If you are
using a .sens file, set the multi_spec_det param there
via:
[sensfunc]
multi_spec_det = 3,7
-o OUTFILE, --outfile OUTFILE
Output file for sensitivity function. If not specified,
the sensitivity function will be written out to a
standard filename in the current working directory, i.e.
if the standard spec1d file is named
spec1d_b24-Feige66_KASTb_foo.fits the sensfunc will be
written to sens_b24-Feige66_KASTb_foo.fits. A QA file
will also be written as
sens_spec1d_b24-Feige66_KASTb_foo_QA.pdf and a file
showing throughput plots to
sens_spec1d_b24-Feige66_KASTb_foo_throughput.pdf. The
same extensions for QA and throughput will be used if
outfile is provided but with .fits trimmed off if it is
in the filename.
-s SENS_FILE, --sens_file SENS_FILE
Configuration file with sensitivity function parameters
-f, --use_flat Use the extracted spectrum of the flatfield calibration
to estimate the blaze function when generating the
sensitivity function. This is helpful to account for
small scale undulations in the sensitivity function. The
spec1dfile must contain the extracted flatfield response
in order to use this option. This spectrum is extracted
by default, unless you did not compute a pixelflat
frame. Note that it is not possible to set --use_flat
and simultaneously use a .sens file with the --sens_file
option. If you are using a .sens file, set the use_flat
flag with the argument:
[sensfunc]
use_flat = True
--debug show debug plots?
--par_outfile PAR_OUTFILE
Name of output file to save the parameters used by the
fit
-v VERBOSITY, --verbosity VERBOSITY
Verbosity level between 0 [none] and 2 [all]. Default:
1. Level 2 writes a log with filename sensfunc_YYYYMMDD-
HHMM.log
pypeit_flux_setup
Once you have a set of 1D object spectra and a sensitivity function, this script helps you create the necessary input file to perform the flux calibration, 1d coadding, and telluric correction. See Fluxing (specifically, Applying the PypeIt Sensitivity Function), Coadd 1D Spectra, and Telluric correction for details.
Note you will need to hand edit the files generated by this script:
Double check the fluxing pypeit file (ending in
.flux) to make sure that the correct sensitivity function files were found by the script, and were matched with the right spec1d files. This is in the section betweenflux readandflux end.Remove unwanted spec1d files from the fluxing file.
The coadding pypeit file (ending in
.coadd1d) includes all objects extracted from your main reduction, so you need to pick the ones you are interested in and remove all others in the coadding pypeit file (betweencoadd1d readandcoadd1d end).For echelle spectrographs, double check that the coadding pypeit file has the sensitivity function files matched to the correct spec1d files, and that the files have been correctly separated into different setups.
Add any additional configuration parameters if needed; see User-level Parameters.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_flux_setup -h
usage: pypeit_flux_setup [-h] [--name NAME] [--objmodel {qso,star,poly}]
paths [paths ...]
Setup configuration files to perform flux calibration, 1D coadding, and telluric
correction.
positional arguments:
paths One or more paths for Science folders or sensitivity
functions. Sensitivity functions must start with 'sens_'
to be detected.
options:
-h, --help show this help message and exit
--name NAME The base name to use for the output files. Defaults to
the instrument name is used.
--objmodel {qso,star,poly}
science object model used in the telluric fitting. The
options are:
qso = For quasars. You might need to set redshift,
bal_wv_min_max in the tell file.
star = For stars. You need to set star_type, star_ra,
star_dec, and star_mag in the tell_file.
poly = For other type object, You might need to set
fit_wv_min_max, and norder in the tell_file.
pypeit_flux_calib
Once you have a set of 1D object spectra and a sensitivity function, this script applies the flux calibration to your object spectra provided the necessary input file. See Fluxing and, specifically, Applying the PypeIt Sensitivity Function.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_flux_calib -h
usage: pypeit_flux_calib [-h] [--par_outfile] [-v VERBOSITY] [--try_old]
flux_file
Flux calibrate 1D spectra produced by PypeIt
positional arguments:
flux_file File to guide fluxing process. This file must have the
following format:
flux read
filename | sensfile
spec1dfile1 | sensfile1
spec1dfile2 |
...
flux end
OR
flux read
filename | sensfile
spec1dfile1 | sensfile1
spec1dfile2 | sensfile2
spec1dfile3 | sensfile3
...
flux end
OR
[fluxcalib]
use_archived_sens = True
flux read
filename
spec1dfile1
spec1dfile2
spec1dfile3
...
flux end
That is, you must specify either a sensfile for all
spec1dfiles on the first line, specify one sensfile for
each spec1dfile, or specify no sensfiles and use an
archived one.
Archived sensfiles are available for the following
spectrographs: keck_deimos
options:
-h, --help show this help message and exit
--par_outfile Output to save the parameters
-v VERBOSITY, --verbosity VERBOSITY
Verbosity level between 0 [none] and 2 [all]. Default:
1. Level 2 writes a log with filename
flux_calib_YYYYMMDD-HHMM.log
--try_old Attempt to load old datamodel versions. A crash may
ensue..
pypeit_coadd_1dspec
This script coadds flux-calibrated 1D spectra; see Coadd 1D Spectra.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_coadd_1dspec -h
usage: pypeit_coadd_1dspec [-h] [--debug] [--show] [--par_outfile PAR_OUTFILE]
[-v VERBOSITY]
coadd1d_file
Coadd 1D spectra produced by PypeIt
positional arguments:
coadd1d_file File to guide coadding process.
------------------------
MultiSlit
------------------------
For coadding Multislit spectra the file must have the
following format (see docs for further details including
the use of paths):
[coadd1d]
coaddfile='output_filename.fits' # Optional
coadd1d read
filename | obj_id
spec1dfile1 | objid1
spec1dfile2 | objid2
spec1dfile3 | objid3
...
coadd1d end
OR the coadd1d read/end block can look like
coadd1d read
filename | obj_id
spec1dfile1 | objid
spec1dfile2 |
spec1dfile3 |
...
coadd1d end
That is the coadd1d block must be a two column list of
spec1dfiles and objids, but you can specify only a
single objid for all spec1dfiles on the first line
Where:
spec1dfile: full path to a PypeIt spec1dfile
objid: the object identifier. To determine the objids
inspect the spec1d_*.txt files or run pypeit_show_1dspec
spec1dfile --list
------------------------
Echelle
------------------------
For coadding Echelle spectra the file must have the
following format (see docs for further details):
[coadd1d]
coaddfile='output_filename.fits' # Optional
coadd1d read
filename | obj_id | sensfile | setup_id
spec1dfile1 | objid1 | sensfile1 | setup_id1
spec1dfile2 | objid2 | sensfile2 | setup_id2
spec1dfile3 | objid3 | sensfile3 | setup_id3
...
coadd1d end
OR the coadd1d read/end block can look like
coadd1d read
filename | obj_id | sensfile | setup_id
spec1dfile1 | objid1 | sensfile | setup_id
spec1dfile2 | | |
spec1dfile3 | | |
...
coadd1d end
That is the coadd1d block is a four column list of
spec1dfiles, objids, sensitivity function files, and
setup_ids, but you can specify only a single objid,
sensfile, and setup_id for all spec1dfiles on the first
line
Here:
spec1dfile: full path to a PypeIt spec1dfile
objid: the object identifier (see details above)
sensfile: full path to a PypeIt sensitivity function
file for the echelle setup in question
setup_id: string identifier for the echelle setup in
question, i.e. 'VIS', 'NIR', or 'UVB'
If the coaddfile is not given the output file will be
placed in the same directory as the first spec1d file.
options:
-h, --help show this help message and exit
--debug show debug plots?
--show show QA during coadding process
--par_outfile PAR_OUTFILE
Output to save the parameters
-v VERBOSITY, --verbosity VERBOSITY
Verbosity level between 0 [none] and 2 [all]. Default:
1. Level 2 writes a log with filename
coadd_1dspec_YYYYMMDD-HHMM.log
pypeit_tellfit
This script performs telluric corrections for flux-calibrated, coadded 1D spectra; see Telluric correction.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_tellfit -h
usage: pypeit_tellfit [-h] [--objmodel {qso,star,poly}] [-r REDSHIFT]
[-g TELL_GRID] [-p PCA_FILE] [-t TELL_FILE] [--debug]
[--plot] [--par_outfile PAR_OUTFILE] [-v VERBOSITY]
[--chk_version]
spec1dfile
Telluric correct a spectrum
positional arguments:
spec1dfile spec1d or coadd file that will be used for telluric
correction.
options:
-h, --help show this help message and exit
--objmodel {qso,star,poly}
science object model used in the fitting. The options
are:
qso = For quasars. You might need to set redshift,
bal_wv_min_max in the tell file.
star = For stars. You need to set star_type, star_ra,
star_dec, and star_mag in the tell_file.
poly = For other type object, You might need to set
fit_wv_min_max, and norder in the tell_file.
-r REDSHIFT, --redshift REDSHIFT
Specify redshift. Used with the --objmodel qso option
above.
-g TELL_GRID, --tell_grid TELL_GRID
Telluric grid. You should download the giant grid file
to the pypeit/data/telluric folder. It should only be
passed if you want to overwrite the default tell_grid
that is set via each spectrograph file.
-p PCA_FILE, --pca_file PCA_FILE
Quasar PCA fits file with full path. The default file
(qso_pca_1200_3100.fits) is stored in the
pypeit/data/telluric folder. If you change the fits
file, make sure to set the pca_lower and pca_upper in
the tell_file to specify the wavelength coverage of your
model. The defaults are pca_lower=1220. and
pca_upper=3100.
-t TELL_FILE, --tell_file TELL_FILE
Configuration file to change default telluric
parameters. Note that the parameters in this file will
be overwritten if you set argument in your terminal.
The --tell_file option requires a .tell file with the
following format:
[telluric]
objmodel = qso
redshift = 7.6
bal_wv_min_max = 10825,12060
OR
[telluric]
objmodel = star
star_type = A0
star_mag = 8.
OR
[telluric]
objmodel = poly
polyorder = 3
fit_wv_min_max = 9000.,9500.
--debug show debug plots?
--plot Show the telluric corrected spectrum
--par_outfile PAR_OUTFILE
Name of output file to save the parameters used by the
fit
-v VERBOSITY, --verbosity VERBOSITY
Verbosity level between 0 [none] and 2 [all]. Default:
1. Level 2 writes a log with filename tellfit_YYYYMMDD-
HHMM.log
--chk_version Ensure the datamodels are from the current PypeIt
version. By default (consistent with previous
functionality) this is not enforced and crashes may
ensue ...
pypeit_collate_1d
This is a tool to help organize spectra in multiple spec1d files, group them by source, and flux/coadd them. See Collating 1D Spectra.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_collate_1d -h
usage: pypeit_collate_1d [-h] [--spec1d_files [SPEC1D_FILES ...]]
[--par_outfile PAR_OUTFILE] [--outdir OUTDIR]
[--spec1d_outdir SPEC1D_OUTDIR] [--tolerance TOLERANCE]
[--match_using MATCH_USING] [--dry_run] [--ignore_flux]
[--flux] [--exclude_slit_bm EXCLUDE_SLIT_BM]
[--exclude_serendip] [--wv_rms_thresh WV_RMS_THRESH]
[--refframe {observed,heliocentric,barycentric}]
[--chk_version] [-v VERBOSITY]
[input_file]
Flux/Coadd multiple 1d spectra from multiple nights and prepare a directory for
the KOA.
positional arguments:
input_file (Optional) File for guiding the collate process.
Parameters in this file are overidden by the command
line. The file must have the following format:
[collate1d]
tolerance <tolerance>
outdir <directory to place output files>
spec1d_outdir <directory to place modified spec1ds, if any>
exclude_slit_trace_bm <slit types to exclude>
exclude_serendip If set serendipitous objects are skipped.
match_using Whether to match using "pixel" or
"ra/dec"
dry_run If set the matches are displayed
without any processing
flux Flux calibrate using archived sensfuncs.
ignore_flux Ignore any flux calibration information in
spec1d files.
wv_rms_thresh If set, any objects with a wavelength rms > than the input
value are skipped, else all wavelength rms values are accepted.
refframe Perform reference frame correction prior to coadding.
Options are ['observed', 'heliocentric', 'barycentric']. Defaults to None.
spec1d read
<path to spec1d files, wildcards allowed>
...
end
options:
-h, --help show this help message and exit
--spec1d_files [SPEC1D_FILES ...]
One or more spec1d files to flux/coadd/archive. Can
contain wildcards
--par_outfile PAR_OUTFILE
Output to save the parameters
--outdir OUTDIR The path where all coadded output files and report files
will be placed. Defaults to the current directory.
--spec1d_outdir SPEC1D_OUTDIR
The path where all modified spec1d files are placed.
These are only created if flux calibration or refframe
correction are asked for. Defaults to overwriting
existing spec1ds.
--tolerance TOLERANCE
The tolerance used when comparing the coordinates of
objects. If two objects are within this distance from
each other, they are considered the same object. If
match_using is 'ra/dec' (the default) this is an angular
distance. The defaults units are arcseconds but other
units supported by astropy.coordinates.Angle can be used
(`e.g.`, '0.003d' or '0h1m30s'). If match_using is
'pixel' this is a float.
--match_using MATCH_USING
Determines how 1D spectra are matched as being the same
object. Must be either 'pixel' or 'ra/dec'.
--dry_run If set, the script will display the matching File and
Object Ids but will not flux, coadd or archive.
--ignore_flux If set, the script will only coadd non-fluxed spectra
even if flux data is present. Otherwise fluxed spectra
are coadded if all spec1ds have been fluxed calibrated.
--flux If set, the script will flux calibrate using archived
sensfuncs before coadding.
--exclude_slit_bm EXCLUDE_SLIT_BM
A list of slit trace bitmask bits that should be
excluded. Comma separated.
--exclude_serendip Whether to exclude SERENDIP objects from collating.
--wv_rms_thresh WV_RMS_THRESH
If set, any objects with a wavelength RMS > this value
are skipped, else all wavelength RMS values are
accepted.
--refframe {observed,heliocentric,barycentric}
Perform reference frame correction prior to coadding.
Options are: observed, heliocentric, barycentric
--chk_version If True enforce strict PypeIt version checking to ensure
that all files were created with the current version of
PypeIt. If set to False, the code will attempt to read
out-of-date files and keep going. Beware (!!) that this
can lead to unforeseen bugs that either cause the code
to crash or lead to erroneous results. I.e., you really
need to know what you are doing if you set this to
False!
-v VERBOSITY, --verbosity VERBOSITY
Verbosity level between 0 [none] and 2 [all]. Default:
1. Level 2 writes a log with filename
collate_1d_YYYYMMDD-HHMM.log
pypeit_multislit_flexure
This script calculates a flexure correction across multiple detectors, i.e. with an expanded wavelength coverage. Thus far, it has only been developed and fine-tuned for the 1200 line grating of Keck/DEIMOS. See Flexure Correction and, specifically, pypeit_multislit_flexure.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_multislit_flexure -h
usage: pypeit_multislit_flexure [-h] [--clobber] [--debug] flex_file outroot
Calculate and apply flexure corrections for 1D spectra produced by PypeIt.
positional arguments:
flex_file File to guide flexure corrections for this multi-slit mode. This
file must have the following format:
flexure read
filename
spec1dfile1
spec1dfile2
...
flexure end
outroot Output fileroot for the flexure fits saved as FITS.
options:
-h, --help show this help message and exit
--clobber Clobber output files
--debug show debug plots?
pypeit_setup_coadd2d
This is used to setup a coadd2d file for performing 2D coadds; see Coadd 2D Spectra.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_setup_coadd2d -h
usage: pypeit_setup_coadd2d [-h]
(-f PYPEIT_FILE | -d SCIENCE_DIR [SCIENCE_DIR ...])
[--keep_par] [--obj OBJ [OBJ ...]]
[--det DET [DET ...]]
[--only_slits ONLY_SLITS [ONLY_SLITS ...]]
[--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
options:
-h, --help show this help message and exit
-f PYPEIT_FILE, --pypeit_file PYPEIT_FILE
PypeIt reduction file (default: None)
-d SCIENCE_DIR [SCIENCE_DIR ...], --science_dir SCIENCE_DIR [SCIENCE_DIR ...]
One or more directories with spec2d files to stack (use
wildcard to specify multiple directories). (default:
None)
--keep_par Propagate all parameters from the pypeit file to the
coadd2d file(s). If not set, only the required
parameters and their default values are included in the
output file(s). (default: True)
--obj OBJ [OBJ ...] Limit the coadd2d files created to observations of the
specified target. If not provided, a coadd2D file is
written for each target found in the science directory.
The target names are included in the PypeIt spec2d file
names.For example, the target for spec2d file "spec2d_cN
20170331S0216-pisco_GNIRS_20170331T085412.181.fits" is
"pisco". (default: None)
--det DET [DET ...] A space-separated set of detectors or detector mosaics
to coadd. By default, *all* detectors or default mosaics
for this instrument will be coadded. Detectors in a
mosaic must be a mosaic "allowed" by PypeIt and should
be provided as comma-separated integers (with no
spaces). For example, to separately coadd detectors 1
and 5 for Keck/DEIMOS, you would use --det 1 5; to coadd
mosaics made up of detectors 1,5 and 3,7, you would use
--det 1,5 3,7 (default: None)
--only_slits ONLY_SLITS [ONLY_SLITS ...]
A space-separated set of slits to coadd. Example syntax
for argument is DET01:175,DET02:205 or MSC02:2234. If
not provided, all slits are coadded. If both --det and
--only_slits are provided, --det will be ignored. This
and --exclude_slits are mutually exclusive. If both are
provided, --only_slits takes precedence. (default: None)
--exclude_slits EXCLUDE_SLITS [EXCLUDE_SLITS ...]
A space-separated set of slits to exclude in the
coaddition. This and --only_slits are mutually
exclusive. If both are provided, --only_slits takes
precedence. (default: None)
--spat_toler SPAT_TOLER
Desired tolerance in spatial pixel used to identify
slits in different exposures. If not provided, the
default value for the specific instrument/configuration
is used. (default: None)
--offsets OFFSETS Spatial offsets to apply to each image; see the
[coadd2d][offsets] parameter. Options are restricted
here to either maskdef_offsets 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)
--weights WEIGHTS Weights used to coadd images; see the [coadd2d][weights]
parameter. Options are restricted here to either uniform
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)
pypeit_coadd_2dspec
This script combines 2D spectral output from run_pypeit for multiple observations of the same (set of) target(s). See Coadd 2D Spectra.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_coadd_2dspec -h
usage: pypeit_coadd_2dspec [-h] [--show] [--debug_offsets] [--peaks]
[--basename BASENAME] [--debug] [-v VERBOSITY]
coadd2d_file
Coadd 2D spectra produced by PypeIt
positional arguments:
coadd2d_file File to guide 2d coadds
options:
-h, --help show this help message and exit
--show Show the reduction steps. Equivalent to the -s option
when running pypeit. (default: False)
--debug_offsets Show QA plots useful for debugging automatic offset
determination (default: False)
--peaks Show the peaks found by the object finding algorithm.
(default: False)
--basename BASENAME Basename of files to save the parameters, spec1d, and
spec2d (default: None)
--debug show debug plots? (default: False)
-v VERBOSITY, --verbosity VERBOSITY
Verbosity level between 0 [none] and 2 [all]. Default:
1. Level 2 writes a log with filename
coadd_2dspec_YYYYMMDD-HHMM.log (default: 1)
pypeit_coadd_datacube
This script combines 2D spectral output from run_pypeit for multiple IFU observations of the same (set of) target(s) into a 3D datacube. See Coadd 3D Spectra.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_coadd_datacube -h
usage: pypeit_coadd_datacube [-h] [--det DET] [-o] [-v VERBOSITY] file
Read in an array of spec2D files and convert them into a datacube
positional arguments:
file filename.coadd3d file
options:
-h, --help show this help message and exit
--det DET Detector (default: 1)
-o, --overwrite Overwrite any existing files/directories (default:
False)
-v VERBOSITY, --verbosity VERBOSITY
Verbosity level between 0 [none] and 2 [all]. Default:
1. Level 2 writes a log with filename
coadd_datacube_YYYYMMDD-HHMM.log (default: 1)
Inspection Scripts
PypeIt provides numerous scripts for helping you inspect its outputs, mostly by loading and displaying the data in a ginga viewer. The provided scripts are as follows.
pypeit_view_fits
This is a simple, general-purpose wrapper to the ginga image viewer that allows you to open and view both raw and processed files.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_view_fits -h
usage: pypeit_view_fits [-h] [--list] [--proc] [--bkg_file BKG_FILE]
[--exten EXTEN] [--det [DET ...]] [--chname CHNAME]
[--showmask] [--embed]
spectrograph file
View FITS files with ginga
positional arguments:
spectrograph A valid spectrograph identifier: aat_uhrf, bok_bc,
gemini_flamingos1, gemini_flamingos2,
gemini_gmos_north_e2v, gemini_gmos_north_ham,
gemini_gmos_north_ham_ns, gemini_gmos_south_ham,
gemini_gnirs_echelle, gemini_gnirs_ifu, gtc_maat,
gtc_osiris, gtc_osiris_plus, jwst_nircam, jwst_nirspec,
keck_deimos, keck_esi, keck_hires, keck_kcrm, keck_kcwi,
keck_lris_blue, keck_lris_blue_orig, keck_lris_red,
keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire,
keck_nires, keck_nirspec_high, keck_nirspec_high_old,
keck_nirspec_low, lbt_luci1, lbt_luci2, lbt_mods1b,
lbt_mods1r, lbt_mods2b, lbt_mods2r, ldt_deveny,
magellan_fire, magellan_fire_long, magellan_mage,
mdm_modspec, mdm_osmos_mdm4k, mdm_osmos_r4k,
mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
not_alfosc_vert, ntt_efosc2, p200_dbsp_blue,
p200_dbsp_red, p200_tspec, shane_kast_blue,
shane_kast_red, shane_kast_red_ret, soar_goodman_blue,
soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,
vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis,
wht_isis_blue, wht_isis_red
file FITS file
options:
-h, --help show this help message and exit
--list List the extensions only? (default: False)
--proc Process the image (i.e. orient, overscan subtract,
multiply by gain) using pypeit.images.buildimage.
(default: False)
--bkg_file BKG_FILE FITS file to be subtracted from the image in file.--proc
must be set in order for this option to work. (default:
None)
--exten EXTEN Show a FITS extension in the raw file. Note --proc and
--mosaic will not work with this option. (default: None)
--det [DET ...] Detector(s) to show. If more than one, the list of
detectors, i.e. --det 4 8 to show detectors 4 and 8. This
combination must be one of the allowed mosaics hard-coded
for the selected spectrograph. Using "mosaic" for
gemini_gmos, keck_deimos, or keck_lris will show the
mosaic of all detectors. (default: 1)
--chname CHNAME Name of Ginga tab (default: Image)
--showmask Overplot masked pixels (default: False)
--embed Upon completion embed in ipython shell (default: False)
pypeit_chk_alignments
This script simply shows the Alignments file for visual inspection;
see Alignment.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_chk_alignments -h
usage: pypeit_chk_alignments [-h] [--chname CHNAME] [--try_old] file
Display Alignment image and the trace data
positional arguments:
file PypeIt Alignment file [e.g. Alignment_A_1_DET01.fits]
options:
-h, --help show this help message and exit
--chname CHNAME Channel name for image in Ginga (default: Alignments)
--try_old Attempt to load old datamodel versions. A crash may ensue..
(default: False)
pypeit_chk_edges
Inspect the slit/order edges identified by PypeIt in a ginga window. See Slit Tracing.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_chk_edges -h
usage: pypeit_chk_edges [-h] [--slits_file SLITS_FILE] [--mpl] [--try_old]
trace_file
Display trace image and edge traces
positional arguments:
trace_file PypeIt Edges file [e.g. Edges_A_0_DET01.fits.gz]
options:
-h, --help show this help message and exit
--slits_file SLITS_FILE
PypeIt Slits file [e.g. Slits_A_1_01.fits]. If this file
does not exist or is not provided, PypeIt will attempt
to read the default file name (in the Calibrations
directory). Ignored if plotting using a matplotlib
window instead of ginga. (default: None)
--mpl Use a matplotlib window instead of ginga to show the
trace (default: False)
--try_old Attempt to load old datamodel versions. A crash may
ensue.. (default: False)
pypeit_parse_slits
This script prints a simple summary of the state of the reduction for all of the slits in a given Spec2D Output or Slits file. Here is a standard call:
pypeit_parse_slits spec2d_d0315_45929-agsmsk_DEIMOS_2018Mar15T124523.587.fits
And the output to screen will look like:
================ DET 04 ======================
SpatID MaskID Flags
0021 958445 None
0073 958470 None
0143 958434 None
0212 958458 None
0278 958410 None
0479 958400 None
1257 958466 None
1352 958392 BOXSLIT
1413 958396 None
1492 958403 None
1568 958457 None
1640 958405 None
1725 958435 None
1818 958422 None
1880 958390 BOXSLIT
1984 958393 BOXSLIT
The MaskID will be populated only if the instrument includes mask design (e.g. Keck/DEIMOS). The Flags column describes failure modes or reasons why the slit was not reduced. None is the preferred state for a science slit.
pypeit_chk_wavecalib
This script prints a set of simple wavelength calibration diagnostics for all of the slits in a given Spec2D Output or WaveCalib file. See pypeit_chk_wavecalib for more details. Standard command-line calls are:
pypeit_chk_wavecalib Science/spec2d_DE.20100913.22358-CFHQS1_DEIMOS_20100913T061231.334.fits
or:
pypeit_chk_wavecalib Calibrations/WaveCalib_A_1_DET07.fits
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_chk_wavecalib -h
usage: pypeit_chk_wavecalib [-h] [--try_old] input_file [input_file ...]
Print QA on Wavelength Calib to the screen
positional arguments:
input_file One or more PypeIt WaveCalib file [e.g. WaveCalib_A_1_DET01.fits]
or spec2d file
options:
-h, --help show this help message and exit
--try_old Attempt to load old datamodel versions. A crash may ensue..
(default: False)
pypeit_show_wvcalib
Allows the user to plot the calibrated arc spectrum for a given slit/order. This is primarily useful for generating new wavelength solutions. Here is a standard call:
pypeit_show_wvcalib WaveCalib_A_1_DET01.fits 17 --is_order # for magellan_mage
This launches a matplotlib GUI plot of Order=17 for the magellan_mage spectrograph.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_show_wvcalib -h
usage: pypeit_show_wvcalib [-h] [--slit_file SLIT_FILE] [--is_order] [--try_old]
file slit_order
Show the result of wavelength calibration
positional arguments:
file WaveCalib file
slit_order Slit or Order number
options:
-h, --help show this help message and exit
--slit_file SLIT_FILE
Slit file (default: None)
--is_order Input slit/order is an order (default: False)
--try_old Attempt to load old datamodel versions. A crash may
ensue.. (default: False)
pypeit_show_arxiv
This script simply plots the selected archive arc spectrum from PypeIt’s
pypeit/data/arc_liens/reid_arxiv directory.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_show_arxiv -h
usage: pypeit_show_arxiv [-h] [--det DET] file
Show an archived arc spectrum located in pypeit/data/arc_liens/reid_arxiv
positional arguments:
file Arxiv filename, e.g. gemini_gmos_r831_ham.fits
options:
-h, --help show this help message and exit
--det DET Detector number (default: 1)
pypeit_chk_tilts
This script displays Tiltimg and 2D fitted tilts in a ginga viewer or matplotlib window, allowing to assess the quality of the tilts calibration. See pypeit_chk_tilts for more details.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_chk_tilts -h
usage: pypeit_chk_tilts [-h] [--mpl] [--show_traces] [--try_old] file
Display Tiltimg image and 2D fitted tilts in Ginga viewer or Matplotlib window.
Tiltimg file must be in the same directory as Tilts.
positional arguments:
file PypeIt Tilts file [e.g. Tilt_A_1_01.fits]
options:
-h, --help show this help message and exit
--mpl Use a matplotlib window instead of ginga to show the tilts.
Faster plotting. (default: False)
--show_traces Show the traced tilts. This slows down the plotting (mostly in
Ginga). If not set, only the fitted, masked and rejected in the
fit tilts are shown. (default: False)
--try_old Attempt to load old datamodel versions. A crash may ensue..
(default: False)
pypeit_chk_flats
Inspect the flat field images produced by PypeIt in a RC Ginga window. This includes the stacked ‘raw’ image, the pixel flat, the illumination flat, and the flat model.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_chk_flats -h
usage: pypeit_chk_flats [-h] [--type TYPE] [--try_old] file
Display flat images in Ginga viewer
positional arguments:
file PypeIt Flat file [e.g. Flat_A_1_DET01.fits]
options:
-h, --help show this help message and exit
--type TYPE Which flats to display. Must be one of: pixel, illum, all
(default: all)
--try_old Attempt to load old datamodel versions. A crash may ensue..
(default: False)
pypeit_show_pixflat
Inspect in a Ginga window the (slitless) pixel flat produced by PypeIt and stored in the PypeIt cache (see ref:data_installation). It displays each detector separately in different channels. The script is useful for assessing the quality of the pixel-to-pixel response of the detector. Typical call is:
pypeit_show_pixflat PYPEIT_LRISb_pixflat_B600_2x2_17sep2009_specflip.fits.gz
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_show_pixflat -h
usage: pypeit_show_pixflat [-h] [--det DET [DET ...]] file
Show an archived Pixel Flat image in a ginga window.
positional arguments:
file Pixel Flat filename, e.g.
pixelflat_keck_lris_blue.fits.gz
options:
-h, --help show this help message and exit
--det DET [DET ...] Detector(s) to show. If more than one, list the detectors
as, e.g. --det 1 2 to show detectors 1 and 2. If not
provided, all detectors will be shown. (default: None)
pypeit_show_2dspec
This script displays the sky-subtracted 2D image for a single detector in a ginga RC viewer. See pypeit_show_2dspec.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_show_2dspec -h
usage: pypeit_show_2dspec [-h] [--list] [--det DET] [--spat_id SPAT_ID]
[--maskID MASKID] [--showmask [SHOWMASK ...]]
[--removetrace] [--embed] [--ignore_extract_mask]
[--channels CHANNELS] [--prefix PREFIX] [--no_clear]
[-v VERBOSITY] [--try_old]
file
Display sky subtracted, spec2d image in a ginga viewer.
positional arguments:
file Path to a PypeIt spec2d file
options:
-h, --help show this help message and exit
--list List the extensions only? (default: False)
--det DET Detector name or number. If a number, the name is
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). 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)
--showmask [SHOWMASK ...]
Include a channel showing the mask. If no arguments are
provided, the mask bit values are provided directly. You
can also specify one or more mask flags used to
construct an image identifying which pixels are flagged
by any of these issues. E.g., to show pixels flagged by
the instrument specific bad-pixel mask or cosmic arrays,
use --showmask BPM CR . See
https://pypeit.readthedocs.io/en/release/out_masks.html
for the list of flags. (default: None)
--removetrace Do not overplot traces in the skysub, sky_resid, and
resid channels (default: False)
--embed Upon completion embed in ipython shell (default: False)
--ignore_extract_mask
Ignore the extraction mask (default: False)
--channels CHANNELS Only show a subset of the channels (0-indexed), e.g. 1,3
(default: None)
--prefix PREFIX Channel name prefix [lets you display more than one set]
(default: )
--no_clear Do *not* clear all existing tabs (default: True)
-v VERBOSITY, --verbosity VERBOSITY
Verbosity level between 0 [none] and 2 [all] (default:
1)
--try_old Attempt to load old datamodel versions. A crash may
ensue.. (default: False)
pypeit_chk_noise_2dspec
Script to view the \(chi\) distribution of the residuals for a processed slit (or order) of the 2D image. Both the sky and object model are subtracted.
Ideally, one sees an image without structure and that the chi values are unit Gaussian distributed.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_chk_noise_2dspec -h
usage: pypeit_chk_noise_2dspec [-h] [--det DET] [--z [Z ...]]
[--maskdef_id MASKDEF_ID] [--pypeit_id PYPEIT_ID]
[--pad PAD] [--aspect_ratio ASPECT_RATIO]
[--wavemin WAVEMIN] [--wavemax WAVEMAX]
[--mode MODE] [--list] [--try_old]
[files ...]
Examine the noise in a PypeIt slit/order
positional arguments:
files PypeIt spec2d file(s) (default: None)
options:
-h, --help show this help message and exit
--det DET Detector name or number. If a number, the name is
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)
--z [Z ...] Object redshift (default: None)
--maskdef_id MASKDEF_ID
MASKDEF_ID of the slit that you want to plot. If
maskdef_id is not provided, nor a pypeit_id, all the 2D
spectra in the file(s) will be plotted. (default: None)
--pypeit_id PYPEIT_ID
PypeIt ID of the slit that you want to plot. If
pypeit_id is not provided, nor a maskdef_id, all the 2D
spectra in the file(s) will be plotted. (default: None)
--pad PAD Padding for the selected slit. Negative value will trim.
(default: -5)
--aspect_ratio ASPECT_RATIO
Aspect ratio when plotting the spec2d (default: 3)
--wavemin WAVEMIN Wavelength min. This is for selecting a region of the
spectrum to analyze. (default: None)
--wavemax WAVEMAX Wavelength max. This is for selecting a region of the
spectrum to analyze. (default: None)
--mode MODE Options are: [plot, save, print]. "plot" will open a
plot in a mpl window. "save" will create a folder called
spec2d*_noisecheck where all the relevant plots will be
placed. "print" will cause the check noise values to be
printed in the terminal. (default: plot)
--list List the extensions only? (default: False)
--try_old Attempt to load old datamodel versions. A crash may
ensue.. (default: False)
Here is an example from the Dev Suite:
pypeit_chk_noise_2dspec spec2d_s190519_0067-J1450+3302_NIRES_20190519T095152.165.fits --pypeit_id 6
pypeit_show_1dspec
This script loads a 1D spectrum file from PypeIt and launches a GUI from the linetools package for inspection; see pypeit_show_1dspec.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_show_1dspec -h
usage: pypeit_show_1dspec [-h] [--list] [--exten EXTEN] [--obj OBJ]
[--extract EXTRACT] [--flux] [-m]
file
Show a 1D spectrum
positional arguments:
file Spectral file
options:
-h, --help show this help message and exit
--list List the extensions only? (default: False)
--exten EXTEN FITS extension (default: 1)
--obj OBJ Object name in lieu of extension, e.g.
SPAT0424-SLIT0000-DET01 (default: None)
--extract EXTRACT Extraction method. Default is OPT. ['BOX', 'OPT'] (default:
OPT)
--flux Show fluxed spectrum? (default: False)
-m, --unmasked Only show unmasked data. (default: True)
pypeit_chk_noise_1dspec
Script to view the \(\chi\) distribution of the residuals for a processed spectrum. This makes most sense if restricted to a region of the spectrum without signal.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_chk_noise_1dspec -h
usage: pypeit_chk_noise_1dspec [-h] [--fileformat FILEFORMAT]
[--extraction EXTRACTION] [--ploterr] [--step]
[--z [Z ...]] [--maskdef_objname MASKDEF_OBJNAME]
[--pypeit_name PYPEIT_NAME] [--wavemin WAVEMIN]
[--wavemax WAVEMAX] [--plot_or_save PLOT_OR_SAVE]
[--try_old]
[files ...]
Examine the noise in a PypeIt spectrum
positional arguments:
files PypeIt spec1d file(s) (default: None)
options:
-h, --help show this help message and exit
--fileformat FILEFORMAT
Is this coadd1d or spec1d? (default: spec1d)
--extraction EXTRACTION
If spec1d, which extraction? opt or box (default: opt)
--ploterr Plot noise spectrum (default: False)
--step Use `steps-mid` as linestyle (default: False)
--z [Z ...] Object redshift (default: None)
--maskdef_objname MASKDEF_OBJNAME
MASKDEF_OBJNAME of the target that you want to plot. If
maskdef_objname is not provided, nor a pypeit_name, all
the 1D spectra in the file(s) will be plotted. (default:
None)
--pypeit_name PYPEIT_NAME
PypeIt name of the target that you want to plot. If
pypeit_name is not provided, nor a maskdef_objname, all
the 1D spectra in the file(s) will be plotted. (default:
None)
--wavemin WAVEMIN Wavelength min. This is for selecting a region of the
spectrum to analyze. (default: None)
--wavemax WAVEMAX Wavelength max.This is for selecting a region of the
spectrum to analyze. (default: None)
--plot_or_save PLOT_OR_SAVE
Do you want to save to disk or open a plot in a mpl
window. If you choose save, a folder called
spec1d*_noisecheck will be created and all the relevant
plot will be placed there. (default: plot)
--try_old Attempt to load old datamodel versions. A crash may
ensue.. (default: False)
Here is an example from the Dev Suite:
pypeit_chk_noise_1dspec Science/spec1d_d0225_0054-16045h_DEIMOS_20190225T145727.158.fits
Interactive Scripts
PypeIt provides a few interactive GUI scripts for specific parts of the data reduction. These are never run as a part of an execution of run_pypeit. Instead, they produce files or parameters that ensure run_pypeit is successful.
pypeit_identify
This script provides an interactive GUI used for hands-on wavelength calibration. See Wavelength Calibration and, specifically, the By-Hand Approach.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_identify -h
usage: pypeit_identify [-h] [--lamps LAMPS] [-s] [--wmin WMIN] [--wmax WMAX]
[--slits SLITS] [-m] [-n] [--det DET] [--rmstol RMSTOL]
[--fwhm FWHM] [--sigdetect SIGDETECT] [--pixtol PIXTOL]
[--linear] [--force_save] [--rescale_resid]
[-v VERBOSITY] [--try_old]
arc_file slits_file
Launch PypeIt pypeit_identify tool, display extracted Arc, and load linelist.
positional arguments:
arc_file PypeIt Arc file
slits_file PypeIt Slits file
options:
-h, --help show this help message and exit
--lamps LAMPS Comma separated list of calibration lamps (no spaces)
(default: None)
-s, --solution Load a wavelength solution from the arc_file (if it
exists) (default: False)
--wmin WMIN Minimum wavelength range (default: 3000.0)
--wmax WMAX Maximum wavelength range (default: 50000.0)
--slits SLITS Which slit to load for wavelength calibration. Format
should be [0,1,...] for multiple slits, 0 for only one
slit. If creating a new WaveCalib with the -n flag, this
is not necessary. (default: 0)
-m, --multi Set this flag to create wavelength solutions for muliple
slits (default: False)
-n, --new_sol Set this flag to construct a new WaveCalib file, rather
than using the exising one (default: False)
--det DET Detector index (default: 1)
--rmstol RMSTOL RMS tolerance (default: 0.1)
--fwhm FWHM FWHM for line finding (default: 4.0)
--sigdetect SIGDETECT
sigma detection for line finding (default: None)
--pixtol PIXTOL Pixel tolerance for Auto IDs (default: 0.1)
--linear Show the spectrum in linear (rather than log) scale
(default: False)
--force_save Save the solutions, despite the RMS (default: False)
--rescale_resid Rescale the residual plot to include all points?
(default: False)
-v VERBOSITY, --verbosity VERBOSITY
Verbosity level between 0 [none] and 2 [all]. Default:
1. Level 2 writes a log with filename identify_YYYYMMDD-
HHMM.log (default: 1)
--try_old Attempt to load old datamodel versions. A crash may
ensue.. (default: False)
pypeit_skysub_regions
This script provides an interactive GUI used to define bespoke sky regions for each slit. See Sky Subtraction and, specifically, Interactively defining the sky regions.
The script usage can be displayed by calling the script with the
-h option:
$ pypeit_skysub_regions -h
usage: pypeit_skysub_regions [-h] [--det DET] [-o] [-i] [-f] [-s] [-v VERBOSITY]
[--try_old]
file
Display a spec2d frame and interactively define the sky regions using a GUI. Run
in the same folder as your .pypeit file
positional arguments:
file spec2d file
options:
-h, --help show this help message and exit
--det DET Detector (default: 1)
-o, --overwrite Overwrite any existing files/directories (default:
False)
-i, --initial Use initial slit edges? (default: False)
-f, --flexure Use flexure corrected slit edges? (default: False)
-s, --standard List standard stars as well? (default: False)
-v VERBOSITY, --verbosity VERBOSITY
Verbosity level between 0 [none] and 2 [all]. Default:
1. Level 2 writes a log with filename
skysub_regions_YYYYMMDD-HHMM.log (default: 1)
--try_old Attempt to load old datamodel versions. A crash may
ensue.. (default: False)
Developer Scripts
The following are developer-only scripts and can safely be ignored:
pypeit_lowrdx_skyspec
pypeit_clean
pypeit_cp_spec1d