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kbwestfall committed Nov 19, 2021
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14 changes: 7 additions & 7 deletions doc/help/pypeit_chk_for_calibs.rst
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gemini_gmos_north_ham_ns, gemini_gmos_south_ham,
gemini_gnirs, gtc_osiris, keck_deimos, keck_hires_red,
keck_kcwi, keck_lris_blue, keck_lris_blue_orig,
keck_lris_red, keck_lris_red_orig, keck_mosfire,
keck_nires, 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_osmos_mdm4k, mmt_binospec,
mmt_bluechannel, mmt_mmirs, not_alfosc, ntt_efosc2,
p200_dbsp_blue, p200_dbsp_red, p200_tspec,
keck_lris_red, keck_lris_red_mark4, keck_lris_red_orig,
keck_mosfire, keck_nires, 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_osmos_mdm4k,
mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
ntt_efosc2, p200_dbsp_blue, p200_dbsp_red, p200_tspec,
shane_kast_blue, shane_kast_red, shane_kast_red_ret,
soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,
vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis,
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8 changes: 4 additions & 4 deletions doc/help/pypeit_collate_1d.rst
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.. code-block:: console
$ pypeit_collate_1d -h
usage: pypeit_collate_1d [-h] [--spec1d_files [SPEC1D_FILES [SPEC1D_FILES ...]]]
usage: pypeit_collate_1d [-h] [--spec1d_files [SPEC1D_FILES ...]]
[--par_outfile PAR_OUTFILE] [--outdir OUTDIR]
[--tolerance TOLERANCE] [--match MATCH] [--dry_run]
[--archive_dir ARCHIVE_DIR] [--pypeit_file PYPEIT_FILE]
[--exclude_slit_bm [EXCLUDE_SLIT_BM [EXCLUDE_SLIT_BM ...]]]
[--exclude_slit_bm [EXCLUDE_SLIT_BM ...]]
[--exclude_serendip]
[input_file]
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optional arguments:
-h, --help show this help message and exit
--spec1d_files [SPEC1D_FILES [SPEC1D_FILES ...]]
--spec1d_files [SPEC1D_FILES ...]
One or more spec1d files to flux/coadd/archive. Can
contain wildcards
--par_outfile PAR_OUTFILE
Expand All @@ -62,7 +62,7 @@
A .pypeit file to place into the archive. Only used if
archive_root is specified. Defaults to looking in the
parent directory of the spec1d files.
--exclude_slit_bm [EXCLUDE_SLIT_BM [EXCLUDE_SLIT_BM ...]]
--exclude_slit_bm [EXCLUDE_SLIT_BM ...]
A list of slit trace bitmask bits that should be
excluded.
--exclude_serendip Whether to exclude SERENDIP objects from collating.
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2 changes: 1 addition & 1 deletion doc/help/pypeit_install_ql_masters.rst
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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:
/Users/dpelliccia/PypeIt/PypeIt/doc)
/Users/westfall/Work/packages/pypeit/doc)
--rmzip Remove the downloaded zip file (default: False)
2 changes: 1 addition & 1 deletion doc/help/pypeit_install_telluric.rst
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-h, --help show this help message and exit
--path PATH Path to directory with TelFit files downloaded from the PypeIt
Google Drive Telluric/ folder (default:
/Users/dpelliccia/PypeIt/PypeIt/doc)
/Users/westfall/Work/packages/pypeit/doc)
18 changes: 9 additions & 9 deletions doc/help/pypeit_obslog.rst
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gemini_gmos_north_ham_ns, gemini_gmos_south_ham,
gemini_gnirs, gtc_osiris, keck_deimos, keck_hires_red,
keck_kcwi, keck_lris_blue, keck_lris_blue_orig,
keck_lris_red, keck_lris_red_orig, keck_mosfire,
keck_nires, 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_osmos_mdm4k, mmt_binospec,
mmt_bluechannel, mmt_mmirs, not_alfosc, ntt_efosc2,
p200_dbsp_blue, p200_dbsp_red, p200_tspec,
keck_lris_red, keck_lris_red_mark4, keck_lris_red_orig,
keck_mosfire, keck_nires, 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_osmos_mdm4k,
mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
ntt_efosc2, p200_dbsp_blue, p200_dbsp_red, p200_tspec,
shane_kast_blue, shane_kast_red, shane_kast_red_ret,
soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,
vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis,
Expand All @@ -35,7 +35,7 @@
up through the wildcard (.e.g, /data/Kast/b). Use the
--extension option to set the types of files to search
for. Default is the current working directory. (default:
/Users/dpelliccia/PypeIt/PypeIt/doc)
/Users/westfall/Work/packages/pypeit/doc)
-k, --keys Do not produce the log; simply list the pypeit-specific
metadata keys available for this spectrograph and their
associated header cards. Metadata keys with header cards
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required. (default: .fits)
-d OUTPUT_PATH, --output_path OUTPUT_PATH
Path to top-level output directory. (default:
/Users/dpelliccia/PypeIt/PypeIt/doc)
/Users/westfall/Work/packages/pypeit/doc)
-o, --overwrite Overwrite any existing files/directories (default:
False)
-f FILE, --file FILE Name for the ascii output file. Any leading directory
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5 changes: 2 additions & 3 deletions doc/help/pypeit_ql_keck_mosfire.rst
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(negative) B image to the left. (default: None)
--redux_path REDUX_PATH
Location where reduction outputs should be stored.
(default: /Users/dpelliccia/PypeIt/PypeIt/doc)
(default: /Users/westfall/Work/packages/pypeit/doc)
--master_dir MASTER_DIR
Location of PypeIt Master files used for the reduction.
(default: /Users/dpelliccia/Pypeit/PypeIt-development-
suite/QL_MASTERS)
(default: None)
--embed Upon completion embed in ipython shell (default: False)
--show Show the reduction steps. Equivalent to the -s option
when running pypeit. (default: False)
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18 changes: 9 additions & 9 deletions doc/help/pypeit_setup.rst
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gemini_gmos_north_ham_ns, gemini_gmos_south_ham,
gemini_gnirs, gtc_osiris, keck_deimos, keck_hires_red,
keck_kcwi, keck_lris_blue, keck_lris_blue_orig,
keck_lris_red, keck_lris_red_orig, keck_mosfire,
keck_nires, 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_osmos_mdm4k, mmt_binospec,
mmt_bluechannel, mmt_mmirs, not_alfosc, ntt_efosc2,
p200_dbsp_blue, p200_dbsp_red, p200_tspec,
keck_lris_red, keck_lris_red_mark4, keck_lris_red_orig,
keck_mosfire, keck_nires, 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_osmos_mdm4k,
mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
ntt_efosc2, p200_dbsp_blue, p200_dbsp_red, p200_tspec,
shane_kast_blue, shane_kast_red, shane_kast_red_ret,
soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,
vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis,
Expand All @@ -32,13 +32,13 @@
up through the wildcard (.e.g, /data/Kast/b). Use the
--extension option to set the types of files to search
for. Default is the current working directory. (default:
/Users/dpelliccia/PypeIt/PypeIt/doc)
/Users/westfall/Work/packages/pypeit/doc)
-e EXTENSION, --extension EXTENSION
File extension; compression indicators (e.g. .gz) not
required. (default: .fits)
-d OUTPUT_PATH, --output_path OUTPUT_PATH
Path to top-level output directory. (default:
/Users/dpelliccia/PypeIt/PypeIt/doc)
/Users/westfall/Work/packages/pypeit/doc)
-o, --overwrite Overwrite any existing files/directories (default:
False)
-c CFG_SPLIT, --cfg_split CFG_SPLIT
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23 changes: 12 additions & 11 deletions doc/help/pypeit_trace_edges.rst
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gemini_gmos_north_ham, gemini_gmos_north_ham_ns,
gemini_gmos_south_ham, gemini_gnirs, gtc_osiris,
keck_deimos, keck_hires_red, keck_kcwi, keck_lris_blue,
keck_lris_blue_orig, keck_lris_red, keck_lris_red_orig,
keck_mosfire, keck_nires, 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_osmos_mdm4k,
mmt_binospec, mmt_bluechannel, mmt_mmirs, not_alfosc,
ntt_efosc2, p200_dbsp_blue, p200_dbsp_red, p200_tspec,
shane_kast_blue, shane_kast_red, shane_kast_red_ret,
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)
keck_lris_blue_orig, keck_lris_red, keck_lris_red_mark4,
keck_lris_red_orig, keck_mosfire, keck_nires,
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_osmos_mdm4k, mmt_binospec, mmt_bluechannel,
mmt_mmirs, not_alfosc, ntt_efosc2, p200_dbsp_blue,
p200_dbsp_red, p200_tspec, shane_kast_blue,
shane_kast_red, shane_kast_red_ret, 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)
-b BINNING, --binning BINNING
Image binning in spectral and spatial directions. Only
used if providing files directly; default is 1,1.
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9 changes: 5 additions & 4 deletions doc/help/pypeit_view_fits.rst
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gemini_gmos_north_ham, gemini_gmos_north_ham_ns,
gemini_gmos_south_ham, gemini_gnirs, gtc_osiris, keck_deimos,
keck_hires_red, keck_kcwi, keck_lris_blue,
keck_lris_blue_orig, keck_lris_red, keck_lris_red_orig,
keck_mosfire, keck_nires, keck_nirspec_low, lbt_luci1,
lbt_luci2, lbt_mods1b, lbt_mods1r, lbt_mods2b, lbt_mods2r,
ldt_deveny, magellan_fire, magellan_fire_long, magellan_mage,
keck_lris_blue_orig, keck_lris_red, keck_lris_red_mark4,
keck_lris_red_orig, keck_mosfire, keck_nires,
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_osmos_mdm4k, mmt_binospec, mmt_bluechannel, mmt_mmirs,
not_alfosc, ntt_efosc2, p200_dbsp_blue, p200_dbsp_red,
p200_tspec, shane_kast_blue, shane_kast_red,
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20 changes: 10 additions & 10 deletions doc/help/run_pypeit.rst
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[-d DETECTOR] [-c]
pypeit_file
## [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.6.1.dev74+gb978c26d6[0m
## [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.6.1.dev77+gd460d041b.d20211118[0m
##
## Available spectrographs include:
## 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, gtc_osiris, keck_deimos,
## keck_hires_red, keck_kcwi, keck_lris_blue, keck_lris_blue_orig,
## keck_lris_red, keck_lris_red_orig, keck_mosfire, keck_nires,
## 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_osmos_mdm4k, mmt_binospec, mmt_bluechannel,
## mmt_mmirs, not_alfosc, ntt_efosc2, p200_dbsp_blue, p200_dbsp_red,
## p200_tspec, shane_kast_blue, shane_kast_red, shane_kast_red_ret,
## soar_goodman_red, tng_dolores, vlt_fors2, vlt_sinfoni,
## vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis, wht_isis_blue,
## wht_isis_red
## keck_lris_red, keck_lris_red_mark4, keck_lris_red_orig, keck_mosfire,
## keck_nires, 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_osmos_mdm4k, mmt_binospec,
## mmt_bluechannel, mmt_mmirs, not_alfosc, ntt_efosc2, p200_dbsp_blue,
## p200_dbsp_red, p200_tspec, shane_kast_blue, shane_kast_red,
## shane_kast_red_ret, soar_goodman_red, tng_dolores, vlt_fors2,
## vlt_sinfoni, vlt_xshooter_nir, vlt_xshooter_uvb, vlt_xshooter_vis,
## wht_isis_blue, wht_isis_red
positional arguments:
pypeit_file PypeIt reduction file (must have .pypeit extension)
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1 change: 1 addition & 0 deletions doc/include/inst_detector_table.rst
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Expand Up @@ -34,6 +34,7 @@ Instrument Det specaxis specflip spatflip namp gain
... 2 0 True False 2 1.63, 1.7 3.6, 3.6 0.0 -1.0e+10 65535.0 0.8600 0.1350
``keck_lris_red`` 1 0 False False 2 1.255, 1.18 4.64, 4.76 0.0 -1.0e+10 65535.0 0.7600 0.1350
... 2 0 False False 2 1.191, 1.162 4.54, 4.62 0.0 -1.0e+10 65535.0 0.7600 0.1350
``keck_lris_red_mark4`` 1 0 True False 2 1.61, 1.60153 3.65, 3.52 0.0 -1.0e+10 65535.0 0.7600 0.1230
``keck_lris_red_orig`` 1 1 False False 2 1.98, 2.17 6.1, 6.3 0.0 -1.0e+10 65535.0 0.7600 0.2100
``keck_mosfire`` 1 1 False False 1 2.15 5.8 0.8 -1.0e+10 1000000000.0 1.0000 0.1798
``keck_nires`` 1 1 True False 1 3.8 5.0 0.01 -1.0e+10 1000000.0 0.7600 0.1500
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