diff --git a/doc/help/pypeit_chk_for_calibs.rst b/doc/help/pypeit_chk_for_calibs.rst index 4341e6ef53..49f6126ff6 100644 --- a/doc/help/pypeit_chk_for_calibs.rst +++ b/doc/help/pypeit_chk_for_calibs.rst @@ -19,13 +19,13 @@ 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, diff --git a/doc/help/pypeit_collate_1d.rst b/doc/help/pypeit_collate_1d.rst index 09ab80a066..0256bf7940 100644 --- a/doc/help/pypeit_collate_1d.rst +++ b/doc/help/pypeit_collate_1d.rst @@ -1,11 +1,11 @@ .. 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] @@ -36,7 +36,7 @@ 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 @@ -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. diff --git a/doc/help/pypeit_install_ql_masters.rst b/doc/help/pypeit_install_ql_masters.rst index 45f68b1c8a..360fef26b3 100644 --- a/doc/help/pypeit_install_ql_masters.rst +++ b/doc/help/pypeit_install_ql_masters.rst @@ -14,6 +14,6 @@ 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) \ No newline at end of file diff --git a/doc/help/pypeit_install_telluric.rst b/doc/help/pypeit_install_telluric.rst index 11f4240492..a1e99b16bc 100644 --- a/doc/help/pypeit_install_telluric.rst +++ b/doc/help/pypeit_install_telluric.rst @@ -9,5 +9,5 @@ -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) \ No newline at end of file diff --git a/doc/help/pypeit_obslog.rst b/doc/help/pypeit_obslog.rst index eb27c1165c..bb08a4bbb8 100644 --- a/doc/help/pypeit_obslog.rst +++ b/doc/help/pypeit_obslog.rst @@ -16,13 +16,13 @@ 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, @@ -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 @@ -76,7 +76,7 @@ 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 diff --git a/doc/help/pypeit_ql_keck_mosfire.rst b/doc/help/pypeit_ql_keck_mosfire.rst index 651e496fee..d887cb6a38 100644 --- a/doc/help/pypeit_ql_keck_mosfire.rst +++ b/doc/help/pypeit_ql_keck_mosfire.rst @@ -40,11 +40,10 @@ (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) diff --git a/doc/help/pypeit_setup.rst b/doc/help/pypeit_setup.rst index 68c8dc2b11..046e90e6ee 100644 --- a/doc/help/pypeit_setup.rst +++ b/doc/help/pypeit_setup.rst @@ -16,13 +16,13 @@ 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, @@ -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 diff --git a/doc/help/pypeit_trace_edges.rst b/doc/help/pypeit_trace_edges.rst index c3df753ef2..648fb775a2 100644 --- a/doc/help/pypeit_trace_edges.rst +++ b/doc/help/pypeit_trace_edges.rst @@ -29,17 +29,18 @@ 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. diff --git a/doc/help/pypeit_view_fits.rst b/doc/help/pypeit_view_fits.rst index 34d2d05595..69ab2998f4 100644 --- a/doc/help/pypeit_view_fits.rst +++ b/doc/help/pypeit_view_fits.rst @@ -13,10 +13,11 @@ 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, diff --git a/doc/help/run_pypeit.rst b/doc/help/run_pypeit.rst index 3ff367481f..f37f7ee175 100644 --- a/doc/help/run_pypeit.rst +++ b/doc/help/run_pypeit.rst @@ -5,22 +5,22 @@ [-d DETECTOR] [-c] pypeit_file - ## PypeIt : The Python Spectroscopic Data Reduction Pipeline v1.6.1.dev74+gb978c26d6 + ## PypeIt : The Python Spectroscopic Data Reduction Pipeline v1.6.1.dev77+gd460d041b.d20211118 ## ## 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) diff --git a/doc/include/inst_detector_table.rst b/doc/include/inst_detector_table.rst index fe66e47cc6..dc339da141 100644 --- a/doc/include/inst_detector_table.rst +++ b/doc/include/inst_detector_table.rst @@ -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 diff --git a/doc/include/keck_deimos.sorted.rst b/doc/include/keck_deimos.sorted.rst index dcb09ae414..b51077bbb2 100644 --- a/doc/include/keck_deimos.sorted.rst +++ b/doc/include/keck_deimos.sorted.rst @@ -10,8 +10,8 @@ filter1: OG550 #--------------------------------------------------------- | filename | frametype | ra | dec | target | dispname | decker | binning | mjd | airmass | exptime | dispangle | amp | filter1 | dateobs | utc | frameno | - | d0527_0030.fits.gz | arc,tilt | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.077631 | 1.41291034 | 1.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 01:51:53.87 | 30 | | DE.20170527.06713.fits | arc,tilt | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.077631 | 1.41291034 | 1.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 01:51:53.87 | 30 | + | d0527_0030.fits.gz | arc,tilt | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.077631 | 1.41291034 | 1.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 01:51:53.87 | 30 | | d0527_0031.fits.gz | pixelflat,illumflat,trace | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.07851 | 1.41291034 | 4.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 01:53:10.93 | 31 | | DE.20170527.06790.fits | pixelflat,illumflat,trace | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.07851 | 1.41291034 | 4.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 01:53:10.93 | 31 | | d0527_0032.fits.gz | pixelflat,illumflat,trace | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.079356 | 1.41291034 | 4.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 01:54:24.03 | 32 | @@ -21,8 +21,8 @@ | DE.20170527.37601.fits | science | 261.0363749999999 | 19.028166666666667 | P261_OFF | 830G | LongMirr | 1,1 | 57900.435131 | 1.03078874 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 10:26:41.61 | 80 | | d0527_0081.fits.gz | science | 261.0363749999999 | 19.028166666666667 | P261_OFF | 830G | LongMirr | 1,1 | 57900.449842 | 1.01267696 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 10:47:52.92 | 81 | | DE.20170527.38872.fits | science | 261.0363749999999 | 19.028166666666667 | P261_OFF | 830G | LongMirr | 1,1 | 57900.449842 | 1.01267696 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 10:47:52.92 | 81 | - | d0527_0083.fits.gz | science | 261.0362916666666 | 19.028888888888886 | P261_OFF | 830G | LongMirr | 1,1 | 57900.483427 | 1.00093023 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 11:36:15.35 | 83 | | DE.20170527.41775.fits | science | 261.0362916666666 | 19.028888888888886 | P261_OFF | 830G | LongMirr | 1,1 | 57900.483427 | 1.00093023 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 11:36:15.35 | 83 | + | d0527_0083.fits.gz | science | 261.0362916666666 | 19.028888888888886 | P261_OFF | 830G | LongMirr | 1,1 | 57900.483427 | 1.00093023 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 11:36:15.35 | 83 | | DE.20170527.43045.fits | science | 261.0362916666666 | 19.028888888888886 | P261_OFF | 830G | LongMirr | 1,1 | 57900.498135 | 1.00838805 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 11:57:25.35 | 84 | | DE.20170527.44316.fits | science | 261.0362916666666 | 19.028888888888886 | P261_OFF | 830G | LongMirr | 1,1 | 57900.512854 | 1.02377681 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 12:18:36.71 | 85 | | DE.20170527.53184.fits | science | 349.99316666666664 | -5.16575 | Feige 110 | 830G | LongMirr | 1,1 | 57900.615484 | 1.42505162 | 45.0 | 8099.98291016 | SINGLE:B | OG550 | 2017-05-27 | 14:46:24.88 | 93 | diff --git a/doc/include/shane_kast_blue_A.pypeit.rst b/doc/include/shane_kast_blue_A.pypeit.rst index 2fc44ac35e..45ed84fc06 100644 --- a/doc/include/shane_kast_blue_A.pypeit.rst +++ b/doc/include/shane_kast_blue_A.pypeit.rst @@ -1,7 +1,7 @@ .. code-block:: console # Auto-generated PypeIt file - # 2021-11-16 + # 2021-11-19 # User-defined execution parameters [rdx] @@ -16,7 +16,7 @@ # Read in the data data read - path /Users/dpelliccia/Pypeit/PypeIt-development-suite/RAW_DATA/shane_kast_blue/600_4310_d55 + path /Users/westfall/Work/packages/PypeIt-development-suite/RAW_DATA/shane_kast_blue/600_4310_d55 | filename | frametype | ra | dec | target | dispname | decker | binning | mjd | airmass | exptime | dichroic | | b1.fits.gz | arc,tilt | 140.44166666666663 | 37.43222222222222 | Arcs | 600/4310 | 0.5 arcsec | 1,1 | 57162.06664467593 | 1.0 | 30.0 | d55 | | b14.fits.gz | bias | 172.34291666666664 | 36.86833333333333 | Bias | 600/4310 | 2.0 arcsec | 1,1 | 57162.15420034722 | 1.0 | 0.0 | d55 | diff --git a/doc/include/spectrographs_table.rst b/doc/include/spectrographs_table.rst index 313ef4fbbb..938fb9ed31 100644 --- a/doc/include/spectrographs_table.rst +++ b/doc/include/spectrographs_table.rst @@ -15,8 +15,9 @@ keck_hires_red :class:`~pypeit.spectrographs.keck_hires.KECKHIRESRSpe keck_kcwi :class:`~pypeit.spectrographs.keck_kcwi.KeckKCWISpectrograph` KECK KCWI IFU True Supported setups: BM, BH2; see :doc:`keck_kcwi` keck_lris_blue :class:`~pypeit.spectrographs.keck_lris.KeckLRISBSpectrograph` KECK LRISb MultiSlit True Blue camera; see :doc:`lris` keck_lris_blue_orig :class:`~pypeit.spectrographs.keck_lris.KeckLRISBOrigSpectrograph` KECK LRISb MultiSlit True Original detector; replaced in 20??; see :doc:`lris` -keck_lris_red :class:`~pypeit.spectrographs.keck_lris.KeckLRISRSpectrograph` KECK LRISr MultiSlit True Red camera; see :doc:`lris` -keck_lris_red_orig :class:`~pypeit.spectrographs.keck_lris.KeckLRISROrigSpectrograph` KECK LRISr MultiSlit True Original detector; replaced in 20??; see :doc:`lris` +keck_lris_red :class:`~pypeit.spectrographs.keck_lris.KeckLRISRSpectrograph` KECK LRISr MultiSlit True Red camera; LBNL detector, 2kx4k; see :doc:`lris` +keck_lris_red_mark4 :class:`~pypeit.spectrographs.keck_lris.KeckLRISRMark4Spectrograph` KECK LRISr MultiSlit True New Mark4 detector, circa Spring 2021; Supported setups = R400 +keck_lris_red_orig :class:`~pypeit.spectrographs.keck_lris.KeckLRISROrigSpectrograph` KECK LRISr MultiSlit True Original detector; replaced in 2009; see :doc:`lris` keck_mosfire :class:`~pypeit.spectrographs.keck_mosfire.KeckMOSFIRESpectrograph` KECK MOSFIRE MultiSlit True Gratings tested: Y, J, K; see :doc:`mosfire` keck_nires :class:`~pypeit.spectrographs.keck_nires.KeckNIRESSpectrograph` KECK NIRES Echelle True keck_nirspec_low :class:`~pypeit.spectrographs.keck_nirspec.KeckNIRSPECLowSpectrograph` KECK NIRSPEC MultiSlit True Low-dispersion grating diff --git a/doc/pypeit_par.rst b/doc/pypeit_par.rst index 2462800d2b..ac5f94ba44 100644 --- a/doc/pypeit_par.rst +++ b/doc/pypeit_par.rst @@ -501,18 +501,18 @@ Collate1DPar Keywords Class Instantiation: :class:`pypeit.par.pypeitpar.Collate1DPar` -========================= ========== ======= ======================================= ============================================================================================================================================================================================================================================================================================================================================================================================================== -Key Type Options Default Description -========================= ========== ======= ======================================= ============================================================================================================================================================================================================================================================================================================================================================================================================== -``archive_root`` str .. .. The path where files and metadata will be archived. -``dry_run`` bool .. False If set, the script will display the matching File and Object Ids but will not flux, coadd or archive. -``exclude_serendip`` bool .. False Whether to exclude SERENDIP objects from collating. -``exclude_slit_trace_bm`` list, str .. [] A list of slit trace bitmask bits that should be excluded. -``match_using`` str .. ``ra/dec`` Determines how 1D spectra are matched as being the same object. Must be either 'pixel' or 'ra/dec'. -``outdir`` str .. ``/Users/dpelliccia/PypeIt/PypeIt/doc`` The path where all coadded output files and report files will be placed. -``pypeit_file`` str .. .. 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. -``tolerance`` str, float .. ``3.0`` 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. -========================= ========== ======= ======================================= ============================================================================================================================================================================================================================================================================================================================================================================================================== +========================= ========== ======= ============================================ ============================================================================================================================================================================================================================================================================================================================================================================================================== +Key Type Options Default Description +========================= ========== ======= ============================================ ============================================================================================================================================================================================================================================================================================================================================================================================================== +``archive_root`` str .. .. The path where files and metadata will be archived. +``dry_run`` bool .. False If set, the script will display the matching File and Object Ids but will not flux, coadd or archive. +``exclude_serendip`` bool .. False Whether to exclude SERENDIP objects from collating. +``exclude_slit_trace_bm`` list, str .. [] A list of slit trace bitmask bits that should be excluded. +``match_using`` str .. ``ra/dec`` Determines how 1D spectra are matched as being the same object. Must be either 'pixel' or 'ra/dec'. +``outdir`` str .. ``/Users/westfall/Work/packages/pypeit/doc`` The path where all coadded output files and report files will be placed. +``pypeit_file`` str .. .. 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. +``tolerance`` str, float .. ``3.0`` 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. +========================= ========== ======= ============================================ ============================================================================================================================================================================================================================================================================================================================================================================================================== ---- @@ -522,14 +522,14 @@ FlexurePar Keywords Class Instantiation: :class:`pypeit.par.pypeitpar.FlexurePar` -================= ========== ================================= ========================================================================= ====================================================================================================================================================================================================================== -Key Type Options Default Description -================= ========== ================================= ========================================================================= ====================================================================================================================================================================================================================== -``multi_min_SN`` int, float .. 1 Minimum S/N for analyzing sky spectrum for flexure -``spec_maxshift`` int, float .. 20 Maximum allowed spectral flexure shift in pixels. -``spec_method`` str ``boxcar``, ``slitcen``, ``skip`` ``skip`` Method used to correct for flexure. Use skip for no correction. If slitcen is used, the flexure correction is performed before the extraction of objects (not recommended). Options are: None, boxcar, slitcen, skip -``spectrum`` str .. ``/Users/dpelliccia/PypeIt/PypeIt/pypeit/data/sky_spec/paranal_sky.fits`` Archive sky spectrum to be used for the flexure correction. -================= ========== ================================= ========================================================================= ====================================================================================================================================================================================================================== +================= ========== ================================= ============================================================================== ====================================================================================================================================================================================================================== +Key Type Options Default Description +================= ========== ================================= ============================================================================== ====================================================================================================================================================================================================================== +``multi_min_SN`` int, float .. 1 Minimum S/N for analyzing sky spectrum for flexure +``spec_maxshift`` int, float .. 20 Maximum allowed spectral flexure shift in pixels. +``spec_method`` str ``boxcar``, ``slitcen``, ``skip`` ``skip`` Method used to correct for flexure. Use skip for no correction. If slitcen is used, the flexure correction is performed before the extraction of objects (not recommended). Options are: None, boxcar, slitcen, skip +``spectrum`` str .. ``/Users/westfall/Work/packages/pypeit/pypeit/data/sky_spec/paranal_sky.fits`` Archive sky spectrum to be used for the flexure correction. +================= ========== ================================= ============================================================================== ====================================================================================================================================================================================================================== ---- @@ -554,19 +554,19 @@ ReduxPar Keywords Class Instantiation: :class:`pypeit.par.pypeitpar.ReduxPar` -====================== ========== ======= ======================================= ============================================================================================================================================================================================================================================================================== -Key Type Options Default Description -====================== ========== ======= ======================================= ============================================================================================================================================================================================================================================================================== -``calwin`` int, float .. 0 The window of time in hours to search for calibration frames for a science frame -``detnum`` int, list .. .. Restrict reduction to a list of detector indices.This cannot (and should not) be used with slitspatnum. -``ignore_bad_headers`` bool .. False Ignore bad headers (NOT recommended unless you know it is safe). -``qadir`` str .. ``QA`` Directory relative to calling directory to write quality assessment files. -``redux_path`` str .. ``/Users/dpelliccia/PypeIt/PypeIt/doc`` Path to folder for performing reductions. Default is the current working directory. -``scidir`` str .. ``Science`` Directory relative to calling directory to write science files. -``slitspatnum`` str, list .. .. Restrict reduction to a set of slit DET:SPAT values (closest slit is used). Example syntax -- slitspatnum = 1:175,1:205 If you are re-running the code, (i.e. modifying one slit) you *must* have the precise SPAT_ID index.This cannot (and should not) be used with detnum -``sortroot`` str .. .. A filename given to output the details of the sorted files. If None, the default is the root name of the pypeit file. If off, no output is produced. -``spectrograph`` str .. .. Spectrograph that provided the data to be reduced. See :ref:`instruments` for valid options. -====================== ========== ======= ======================================= ============================================================================================================================================================================================================================================================================== +====================== ========== ======= ============================================ ============================================================================================================================================================================================================================================================================== +Key Type Options Default Description +====================== ========== ======= ============================================ ============================================================================================================================================================================================================================================================================== +``calwin`` int, float .. 0 The window of time in hours to search for calibration frames for a science frame +``detnum`` int, list .. .. Restrict reduction to a list of detector indices.This cannot (and should not) be used with slitspatnum. +``ignore_bad_headers`` bool .. False Ignore bad headers (NOT recommended unless you know it is safe). +``qadir`` str .. ``QA`` Directory relative to calling directory to write quality assessment files. +``redux_path`` str .. ``/Users/westfall/Work/packages/pypeit/doc`` Path to folder for performing reductions. Default is the current working directory. +``scidir`` str .. ``Science`` Directory relative to calling directory to write science files. +``slitspatnum`` str, list .. .. Restrict reduction to a set of slit DET:SPAT values (closest slit is used). Example syntax -- slitspatnum = 1:175,1:205 If you are re-running the code, (i.e. modifying one slit) you *must* have the precise SPAT_ID index.This cannot (and should not) be used with detnum +``sortroot`` str .. .. A filename given to output the details of the sorted files. If None, the default is the root name of the pypeit file. If off, no output is produced. +``spectrograph`` str .. .. Spectrograph that provided the data to be reduced. See :ref:`instruments` for valid options. +====================== ========== ======= ============================================ ============================================================================================================================================================================================================================================================================== ---- @@ -844,48 +844,48 @@ TelluricPar Keywords Class Instantiation: :class:`pypeit.par.pypeitpar.TelluricPar` -======================= ================== ======= ====================================================================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= -Key Type Options Default Description -======================= ================== ======= ====================================================================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= -``bal_wv_min_max`` list, ndarray .. .. Min/max wavelength of broad absorption features. If there are several BAL features, the format for this mask is [wave_min_bal1, wave_max_bal1,wave_min_bal2, wave_max_bal2,...]. These masked pixels will be ignored during the fitting. -``bounds_norm`` tuple .. 0.1, 3.0 Normalization bounds for scaling the initial object model. -``delta_coeff_bounds`` tuple .. -20.0, 20.0 Parameters setting the polynomial coefficient bounds for sensfunc optimization. -``delta_redshift`` float .. 0.1 Range within the redshift can be varied for telluric fitting, i.e. the code performs a bounded optimization withinthe redshift +- delta_redshift -``disp`` bool .. False Argument for scipy.optimize.differential_evolution which will display status messages to the screen indicating the status of the optimization. See documentation for telluric.Telluric for a description of the output and how to know if things are working well. -``fit_wv_min_max`` list .. .. Pixels within this mask will be used during the fitting. The formatis the same with bal_wv_min_max, but this mask is good pixel masks. -``func`` str .. ``legendre`` Polynomial model function -``lower`` int, float .. 3.0 Lower rejection threshold in units of sigma_corr*sigma, where sigma is the formal noise of the spectrum, and sigma_corr is an empirically determined correction to the formal error. The distribution of input chi (defined by chi = (data - model)/sigma) values is analyzed, and a correction factor to the formal error sigma_corr is returned which is multiplied into the formal errors. In this way, a rejection threshold of i.e. 3-sigma, will always correspond to roughly the same percentile. This renormalization is performed with coadd1d.renormalize_errors function, and guarantees that rejection is not too agressive in cases where the empirical errors determined from the chi-distribution differ significantly from the formal noise which is used to determine chi. -``mask_abs_lines`` bool .. True Mask stellar absorption line? -``mask_lyman_a`` bool .. True Mask the blueward of Lyman-alpha line during the fitting? -``maxiter`` int .. 2 Maximum number of iterations for the telluric + object model fitting. The code performs multiple iterations rejecting outliers at each step. The fit is then performed anew to the remaining good pixels. For this reason if you run with the disp=True option, you will see that the f(x) loss function gets progressively better during the iterations. -``minmax_coeff_bounds`` tuple .. -5.0, 5.0 Parameters setting the polynomial coefficient bounds for sensfunc optimization.Bounds are currently determined as follows. We compute an initial fit to the sensfunc in the pypeit.core.telluric.init_sensfunc_model function. That deterines a set of coefficients. The bounds are then determined according to: [(np.fmin(np.abs(this_coeff)*obj_params['delta_coeff_bounds'][0], obj_params['minmax_coeff_bounds'][0]), np.fmax(np.abs(this_coeff)*obj_params['delta_coeff_bounds'][1],obj_params['minmax_coeff_bounds'][1]))] -``model`` str .. ``exp`` Types of polynomial model. Options are poly, square, exp corresponding to normal polynomial,squared polynomial, or exponentiated polynomial -``npca`` int .. 8 Number of pca for the objmodel=qso qso PCA fit -``objmodel`` str .. .. The object model to be used for telluric fitting. Currently the options are: qso, star, and poly -``only_orders`` int, list, ndarray .. .. Order number, or list of order numbers if you only want to fit specific orders -``pca_file`` str .. ``/Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/models/qso_pca_1200_3100.fits`` Fits file containing quasar PCA model. Needed for objmodel=qso -``pca_lower`` int, float .. 1220.0 Minimum wavelength for the qso pca model -``pca_upper`` int, float .. 3100.0 Maximum wavelength for the qso pca model -``pix_shift_bounds`` tuple .. -5.0, 5.0 Bounds for the pixel shift optimization in telluric model fit in units of pixels. The atmosphere will be allowed to shift within this range during the fit. -``polish`` bool .. True If True then differential evolution will perform an additional optimizatino at the end to polish the best fit at the end, which can improve the optimization slightly. See scipy.optimize.differential_evolution for details. -``polyorder`` int .. 3 Order of the polynomial model fit -``popsize`` int .. 30 A multiplier for setting the total population size for the differential evolution optimization. See scipy.optimize.differential_evolution for details. -``recombination`` int, float .. 0.7 The recombination constant for the differential evolution optimization. This should be in the range [0, 1]. See scipy.optimize.differential_evolution for details. -``redshift`` int, float .. 0.0 The redshift for the object model. This is currently only used by objmodel=qso -``resln_frac_bounds`` tuple .. 0.5, 1.5 Bounds for the resolution fit optimization which is part of the telluric model. This range is in units of the resln_guess, so the (0.5, 1.5) would bound the spectral resolution fit to be within the range bounds_resln = (0.5*resln_guess, 1.5*resln_guess) -``resln_guess`` int, float .. .. A guess for the resolution of your spectrum expressed as lambda/dlambda. The resolution is fit explicitly as part of the telluric model fitting, but this guess helps determine the bounds for the optimization (see next). If not provided, the wavelength sampling of your spectrum will be used and the resolution calculated using a typical sampling of 3 spectral pixels per resolution element. -``seed`` int .. 777 An initial seed for the differential evolution optimization, which is a random process. The default is a seed = 777 which will be used to generate a unique seed for every order. A specific seed is used because otherwise the random number generator will use the time for the seed, and the results will not be reproducible. -``sn_clip`` int, float .. 30.0 This adds an error floor to the ivar, preventing too much rejection at high-S/N (i.e. standard stars, bright objects) using the function utils.clip_ivar. A small erorr is added to the input ivar so that the output ivar_out will never give S/N greater than sn_clip. This prevents overly aggressive rejection in high S/N ratio spectra which neverthless differ at a level greater than the formal S/N due to the fact that our telluric models are only good to about 3%. -``star_dec`` float .. .. Object declination in decimal deg -``star_mag`` float, int .. .. AB magnitude in V band -``star_ra`` float .. .. Object right-ascension in decimal deg -``star_type`` str .. .. stellar type -``sticky`` bool .. True Sticky parameter for the utils.djs_reject algorithm for iterative model fit rejection. If set to True then points rejected from a previous iteration are kept rejected, in other words the bad pixel mask is the OR of all previous iterations and rejected pixels accumulate. If set to False, the bad pixel mask is the mask from the previous iteration, and if the model fit changes between iterations, points can alternate from being rejected to not rejected. At present this code only performs optimizations with differential evolution and experience shows that sticky needs to be True in order for these to converge. This is because the outliers can be so large that they dominate the loss function, and one never iteratively converges to a good model fit. In other words, the deformations in the model between iterations with sticky=False are too small to approach a reasonable fit. -``telgridfile`` str .. .. File containing the telluric grid for the observatory in question. These grids are generated from HITRAN models for each observatory using nominal site parameters. They must be downloaded from the GoogleDrive and stored in PypeIt/pypeit/data/telluric/ -``tell_norm_thresh`` int, float .. 0.9 Threshold of telluric absorption region -``tol`` float .. 0.001 Relative tolerance for converage of the differential evolution optimization. See scipy.optimize.differential_evolution for details. -``upper`` int, float .. 3.0 Upper rejection threshold in units of sigma_corr*sigma, where sigma is the formal noise of the spectrum, and sigma_corr is an empirically determined correction to the formal error. See above for description. -======================= ================== ======= ====================================================================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +======================= ================== ======= =========================================================================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +Key Type Options Default Description +======================= ================== ======= =========================================================================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +``bal_wv_min_max`` list, ndarray .. .. Min/max wavelength of broad absorption features. If there are several BAL features, the format for this mask is [wave_min_bal1, wave_max_bal1,wave_min_bal2, wave_max_bal2,...]. These masked pixels will be ignored during the fitting. +``bounds_norm`` tuple .. 0.1, 3.0 Normalization bounds for scaling the initial object model. +``delta_coeff_bounds`` tuple .. -20.0, 20.0 Parameters setting the polynomial coefficient bounds for sensfunc optimization. +``delta_redshift`` float .. 0.1 Range within the redshift can be varied for telluric fitting, i.e. the code performs a bounded optimization withinthe redshift +- delta_redshift +``disp`` bool .. False Argument for scipy.optimize.differential_evolution which will display status messages to the screen indicating the status of the optimization. See documentation for telluric.Telluric for a description of the output and how to know if things are working well. +``fit_wv_min_max`` list .. .. Pixels within this mask will be used during the fitting. The formatis the same with bal_wv_min_max, but this mask is good pixel masks. +``func`` str .. ``legendre`` Polynomial model function +``lower`` int, float .. 3.0 Lower rejection threshold in units of sigma_corr*sigma, where sigma is the formal noise of the spectrum, and sigma_corr is an empirically determined correction to the formal error. The distribution of input chi (defined by chi = (data - model)/sigma) values is analyzed, and a correction factor to the formal error sigma_corr is returned which is multiplied into the formal errors. In this way, a rejection threshold of i.e. 3-sigma, will always correspond to roughly the same percentile. This renormalization is performed with coadd1d.renormalize_errors function, and guarantees that rejection is not too agressive in cases where the empirical errors determined from the chi-distribution differ significantly from the formal noise which is used to determine chi. +``mask_abs_lines`` bool .. True Mask stellar absorption line? +``mask_lyman_a`` bool .. True Mask the blueward of Lyman-alpha line during the fitting? +``maxiter`` int .. 2 Maximum number of iterations for the telluric + object model fitting. The code performs multiple iterations rejecting outliers at each step. The fit is then performed anew to the remaining good pixels. For this reason if you run with the disp=True option, you will see that the f(x) loss function gets progressively better during the iterations. +``minmax_coeff_bounds`` tuple .. -5.0, 5.0 Parameters setting the polynomial coefficient bounds for sensfunc optimization.Bounds are currently determined as follows. We compute an initial fit to the sensfunc in the pypeit.core.telluric.init_sensfunc_model function. That deterines a set of coefficients. The bounds are then determined according to: [(np.fmin(np.abs(this_coeff)*obj_params['delta_coeff_bounds'][0], obj_params['minmax_coeff_bounds'][0]), np.fmax(np.abs(this_coeff)*obj_params['delta_coeff_bounds'][1],obj_params['minmax_coeff_bounds'][1]))] +``model`` str .. ``exp`` Types of polynomial model. Options are poly, square, exp corresponding to normal polynomial,squared polynomial, or exponentiated polynomial +``npca`` int .. 8 Number of pca for the objmodel=qso qso PCA fit +``objmodel`` str .. .. The object model to be used for telluric fitting. Currently the options are: qso, star, and poly +``only_orders`` int, list, ndarray .. .. Order number, or list of order numbers if you only want to fit specific orders +``pca_file`` str .. ``/Users/westfall/Work/packages/pypeit/pypeit/data/telluric/models/qso_pca_1200_3100.fits`` Fits file containing quasar PCA model. Needed for objmodel=qso +``pca_lower`` int, float .. 1220.0 Minimum wavelength for the qso pca model +``pca_upper`` int, float .. 3100.0 Maximum wavelength for the qso pca model +``pix_shift_bounds`` tuple .. -5.0, 5.0 Bounds for the pixel shift optimization in telluric model fit in units of pixels. The atmosphere will be allowed to shift within this range during the fit. +``polish`` bool .. True If True then differential evolution will perform an additional optimizatino at the end to polish the best fit at the end, which can improve the optimization slightly. See scipy.optimize.differential_evolution for details. +``polyorder`` int .. 3 Order of the polynomial model fit +``popsize`` int .. 30 A multiplier for setting the total population size for the differential evolution optimization. See scipy.optimize.differential_evolution for details. +``recombination`` int, float .. 0.7 The recombination constant for the differential evolution optimization. This should be in the range [0, 1]. See scipy.optimize.differential_evolution for details. +``redshift`` int, float .. 0.0 The redshift for the object model. This is currently only used by objmodel=qso +``resln_frac_bounds`` tuple .. 0.5, 1.5 Bounds for the resolution fit optimization which is part of the telluric model. This range is in units of the resln_guess, so the (0.5, 1.5) would bound the spectral resolution fit to be within the range bounds_resln = (0.5*resln_guess, 1.5*resln_guess) +``resln_guess`` int, float .. .. A guess for the resolution of your spectrum expressed as lambda/dlambda. The resolution is fit explicitly as part of the telluric model fitting, but this guess helps determine the bounds for the optimization (see next). If not provided, the wavelength sampling of your spectrum will be used and the resolution calculated using a typical sampling of 3 spectral pixels per resolution element. +``seed`` int .. 777 An initial seed for the differential evolution optimization, which is a random process. The default is a seed = 777 which will be used to generate a unique seed for every order. A specific seed is used because otherwise the random number generator will use the time for the seed, and the results will not be reproducible. +``sn_clip`` int, float .. 30.0 This adds an error floor to the ivar, preventing too much rejection at high-S/N (i.e. standard stars, bright objects) using the function utils.clip_ivar. A small erorr is added to the input ivar so that the output ivar_out will never give S/N greater than sn_clip. This prevents overly aggressive rejection in high S/N ratio spectra which neverthless differ at a level greater than the formal S/N due to the fact that our telluric models are only good to about 3%. +``star_dec`` float .. .. Object declination in decimal deg +``star_mag`` float, int .. .. AB magnitude in V band +``star_ra`` float .. .. Object right-ascension in decimal deg +``star_type`` str .. .. stellar type +``sticky`` bool .. True Sticky parameter for the utils.djs_reject algorithm for iterative model fit rejection. If set to True then points rejected from a previous iteration are kept rejected, in other words the bad pixel mask is the OR of all previous iterations and rejected pixels accumulate. If set to False, the bad pixel mask is the mask from the previous iteration, and if the model fit changes between iterations, points can alternate from being rejected to not rejected. At present this code only performs optimizations with differential evolution and experience shows that sticky needs to be True in order for these to converge. This is because the outliers can be so large that they dominate the loss function, and one never iteratively converges to a good model fit. In other words, the deformations in the model between iterations with sticky=False are too small to approach a reasonable fit. +``telgridfile`` str .. .. File containing the telluric grid for the observatory in question. These grids are generated from HITRAN models for each observatory using nominal site parameters. They must be downloaded from the GoogleDrive and stored in PypeIt/pypeit/data/telluric/ +``tell_norm_thresh`` int, float .. 0.9 Threshold of telluric absorption region +``tol`` float .. 0.001 Relative tolerance for converage of the differential evolution optimization. See scipy.optimize.differential_evolution for details. +``upper`` int, float .. 3.0 Upper rejection threshold in units of sigma_corr*sigma, where sigma is the formal noise of the spectrum, and sigma_corr is an empirically determined correction to the formal error. See above for description. +======================= ================== ======= =========================================================================================== ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= @@ -1236,7 +1236,7 @@ Alterations to the default parameters are:: algorithm = IR polyorder = 8 [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_LasCampanas_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_LasCampanas_3100_26100_R20000.fits GEMINI-N GMOS-N (``gemini_gmos_north_e2v``) ------------------------------------------- @@ -1532,7 +1532,7 @@ Alterations to the default parameters are:: multi_spec_det = 1, 2, 3 algorithm = IR [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_LasCampanas_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_LasCampanas_3100_26100_R20000.fits GEMINI-N GNIRS (``gemini_gnirs``) --------------------------------- @@ -1643,7 +1643,7 @@ Alterations to the default parameters are:: algorithm = IR polyorder = 6 [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits GTC OSIRIS (``gtc_osiris``) --------------------------- @@ -1826,7 +1826,7 @@ Alterations to the default parameters are:: spec_method = boxcar [sensfunc] [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits KECK HIRES_R (``keck_hires_red``) --------------------------------- @@ -2259,6 +2259,98 @@ Alterations to the default parameters are:: [flexure] spec_method = boxcar +KECK LRISr (``keck_lris_red_mark4``) +------------------------------------ +Alterations to the default parameters are:: + + [rdx] + spectrograph = keck_lris_red_mark4 + [calibrations] + [[biasframe]] + exprng = None, 1 + [[[process]]] + combine = median + use_biasimage = False + shot_noise = False + use_pixelflat = False + use_illumflat = False + [[darkframe]] + exprng = 999999, None + [[[process]]] + mask_cr = True + use_pixelflat = False + use_illumflat = False + [[arcframe]] + [[[process]]] + use_pixelflat = False + use_illumflat = False + [[tiltframe]] + [[[process]]] + use_pixelflat = False + use_illumflat = False + [[pixelflatframe]] + exprng = None, 60 + [[[process]]] + satpix = nothing + use_pixelflat = False + use_illumflat = False + [[pinholeframe]] + exprng = 999999, None + [[alignframe]] + [[[process]]] + satpix = nothing + use_pixelflat = False + use_illumflat = False + [[traceframe]] + exprng = None, 60 + [[[process]]] + use_pixelflat = False + use_illumflat = False + [[illumflatframe]] + [[[process]]] + satpix = nothing + use_pixelflat = False + use_illumflat = False + [[skyframe]] + [[[process]]] + mask_cr = True + noise_floor = 0.01 + [[standardframe]] + exprng = None, 30 + [[[process]]] + mask_cr = True + noise_floor = 0.01 + spat_flexure_correct = True + [[wavelengths]] + lamps = NeI, ArI, CdI, KrI, XeI, ZnI, HgI + sigdetect = 10.0 + rms_threshold = 0.2 + [[slitedges]] + fit_order = 3 + sync_center = gap + minimum_slit_length = 4.0 + minimum_slit_length_sci = 6 + [[tilts]] + tracethresh = 25 + maxdev_tracefit = 1.0 + spat_order = 4 + spec_order = 7 + maxdev2d = 1.0 + sigrej2d = 5.0 + [scienceframe] + exprng = 60, None + [[process]] + mask_cr = True + sigclip = 5.0 + objlim = 5.0 + noise_floor = 0.01 + spat_flexure_correct = True + [reduce] + [[skysub]] + bspline_spacing = 0.8 + [flexure] + spec_method = boxcar + KECK LRISr (``keck_lris_red_orig``) ----------------------------------- Alterations to the default parameters are:: @@ -2458,7 +2550,7 @@ Alterations to the default parameters are:: algorithm = IR polyorder = 13 [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits KECK NIRES (``keck_nires``) --------------------------- @@ -2580,7 +2672,7 @@ Alterations to the default parameters are:: algorithm = IR polyorder = 8 [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits KECK NIRSPEC (``keck_nirspec_low``) ----------------------------------- @@ -2691,7 +2783,7 @@ Alterations to the default parameters are:: algorithm = IR polyorder = 8 [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits LBT LUCI1 (``lbt_luci1``) ------------------------- @@ -3435,7 +3527,7 @@ Alterations to the default parameters are:: [sensfunc] algorithm = IR [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_LasCampanas_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_LasCampanas_3100_26100_R20000.fits MAGELLAN FIRE (``magellan_fire_long``) -------------------------------------- @@ -3547,7 +3639,7 @@ Alterations to the default parameters are:: find_trim_edge = 50, 50 [sensfunc] [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/TelFit_LasCampanas_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/TelFit_LasCampanas_3100_26100_R20000.fits MAGELLAN MagE (``magellan_mage``) --------------------------------- @@ -3802,7 +3894,7 @@ Alterations to the default parameters are:: [sensfunc] polyorder = 7 [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits MMT Blue_Channel (``mmt_bluechannel``) -------------------------------------- @@ -4015,7 +4107,7 @@ Alterations to the default parameters are:: algorithm = IR polyorder = 8 [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits NOT ALFOSC (``not_alfosc``) --------------------------- @@ -4340,7 +4432,7 @@ Alterations to the default parameters are:: [[UVIS]] polycorrect = False [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_Lick_3100_11100_R10000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_Lick_3100_11100_R10000.fits P200 TSPEC (``p200_tspec``) --------------------------- @@ -4462,7 +4554,7 @@ Alterations to the default parameters are:: algorithm = IR polyorder = 8 [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_MaunaKea_3100_26100_R20000.fits SHANE KASTb (``shane_kast_blue``) --------------------------------- @@ -4546,7 +4638,7 @@ Alterations to the default parameters are:: noise_floor = 0.01 [flexure] spec_method = boxcar - spectrum = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/sky_spec/sky_kastb_600.fits + spectrum = /Users/westfall/Work/packages/pypeit/pypeit/data/sky_spec/sky_kastb_600.fits SHANE KASTr (``shane_kast_red``) -------------------------------- @@ -4624,7 +4716,7 @@ Alterations to the default parameters are:: spec_method = boxcar [sensfunc] [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_Lick_3100_11100_R10000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_Lick_3100_11100_R10000.fits SHANE KASTr (``shane_kast_red_ret``) ------------------------------------ @@ -4786,7 +4878,7 @@ Alterations to the default parameters are:: noise_floor = 0.01 [sensfunc] [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_LasCampanas_3100_26100_R20000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_LasCampanas_3100_26100_R20000.fits TNG DOLORES (``tng_dolores``) ----------------------------- @@ -5062,7 +5154,7 @@ Alterations to the default parameters are:: algorithm = IR polyorder = 7 [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_Paranal_NIR_9800_25000_R25000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_Paranal_NIR_9800_25000_R25000.fits VLT XShooter_NIR (``vlt_xshooter_nir``) --------------------------------------- @@ -5198,7 +5290,7 @@ Alterations to the default parameters are:: algorithm = IR polyorder = 8 [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_Paranal_NIR_9800_25000_R25000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_Paranal_NIR_9800_25000_R25000.fits VLT XShooter_UVB (``vlt_xshooter_uvb``) --------------------------------------- @@ -5401,7 +5493,7 @@ Alterations to the default parameters are:: algorithm = IR polyorder = 9, 11, 11, 9, 9, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7 [[IR]] - telgridfile = /Users/dpelliccia/PypeIt/PypeIt/pypeit/data/telluric/atm_grids/TelFit_Paranal_VIS_4900_11100_R25000.fits + telgridfile = /Users/westfall/Work/packages/pypeit/pypeit/data/telluric/atm_grids/TelFit_Paranal_VIS_4900_11100_R25000.fits WHT ISISb (``wht_isis_blue``) -----------------------------