diff --git a/CHANGES.rst b/CHANGES.rst index 40070378f3..0a6e3277f4 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,5 +1,5 @@ -1.9.2dev --------- +1.10.0 (11 July 2022) +--------------------- - Modify tweak_standard for Mosfire/J2 - Apply find_min_max when clipping the image for object finding diff --git a/doc/api/pypeit.rst b/doc/api/pypeit.rst index 16cfe44ff2..64bef31496 100644 --- a/doc/api/pypeit.rst +++ b/doc/api/pypeit.rst @@ -31,7 +31,6 @@ Submodules pypeit.coadd1d pypeit.coadd2d pypeit.compiler_version - pypeit.compiler_version pypeit.datamodel pypeit.edgetrace pypeit.extraction 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_obslog.rst b/doc/help/pypeit_obslog.rst index d50f28c60d..bb08a4bbb8 100644 --- a/doc/help/pypeit_obslog.rst +++ b/doc/help/pypeit_obslog.rst @@ -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_deimos.rst b/doc/help/pypeit_ql_keck_deimos.rst index 1a4356a98e..2013712493 100644 --- a/doc/help/pypeit_ql_keck_deimos.rst +++ b/doc/help/pypeit_ql_keck_deimos.rst @@ -1,8 +1,11 @@ .. code-block:: console $ pypeit_ql_keck_deimos -h - usage: pypeit_ql_keck_deimos [-h] [--redux_path REDUX_PATH] [--root ROOT] [--calibs_only] [--science SCIENCE] [-b BOX_RADIUS] [-d DET] [--ignore_headers] [--user_pixflat USER_PIXFLAT] - [--maskID MASKID] [--slit_spat SLIT_SPAT] + usage: pypeit_ql_keck_deimos [-h] [--redux_path REDUX_PATH] [--root ROOT] + [--calibs_only] [--science SCIENCE] + [-b BOX_RADIUS] [-d DET] [--ignore_headers] + [--user_pixflat USER_PIXFLAT] [--maskID MASKID] + [--slit_spat SLIT_SPAT] full_rawpath Script to run PypeIt in QuickLook on a set of Keck/DEIMOS files @@ -18,12 +21,17 @@ --calibs_only Run on calibs only (default: False) --science SCIENCE Science frame filename (default: None) -b BOX_RADIUS, --box_radius BOX_RADIUS - Set the radius for the boxcar extraction (arcsec) (default: None) - -d DET, --det DET Detector number. Cannot use with --slit_spat (default: 0) + Set the radius for the boxcar extraction (arcsec) + (default: None) + -d DET, --det DET Detector number. Cannot use with --slit_spat (default: + 0) --ignore_headers Ignore bad headers? (default: False) --user_pixflat USER_PIXFLAT - Use a user-supplied pixel flat (e.g. keck_lris_blue) (default: None) - --maskID MASKID Reduce this slit as specified by the maskID value (default: None) + Use a user-supplied pixel flat (e.g. keck_lris_blue) + (default: None) + --maskID MASKID Reduce this slit as specified by the maskID value + (default: None) --slit_spat SLIT_SPAT - Reduce only this slit on this detector DET:SPAT_ID, e.g. 0:175 (default: None) + Reduce only this slit on this detector DET:SPAT_ID, + e.g. 0:175 (default: None) \ No newline at end of file diff --git a/doc/help/pypeit_setup.rst b/doc/help/pypeit_setup.rst index 5d9f982533..e78d99d9e4 100644 --- a/doc/help/pypeit_setup.rst +++ b/doc/help/pypeit_setup.rst @@ -33,13 +33,13 @@ 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/run_pypeit.rst b/doc/help/run_pypeit.rst index 13c549221c..8ab8a96b17 100644 --- a/doc/help/run_pypeit.rst +++ b/doc/help/run_pypeit.rst @@ -5,7 +5,7 @@ [-d DETECTOR] [-c] pypeit_file - ## PypeIt : The Python Spectroscopic Data Reduction Pipeline v1.9.2.dev322+gbe682ddb1 + ## PypeIt : The Python Spectroscopic Data Reduction Pipeline v1.8.2.dev482+gf1da42021.d20220523 ## ## Available spectrographs include: ## bok_bc, gemini_flamingos1, gemini_flamingos2, gemini_gmos_north_e2v, diff --git a/doc/include/keck_deimos.sorted.rst b/doc/include/keck_deimos.sorted.rst index 8dec85b69f..7e3689617a 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 | lampstat01 | 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 | Kr Xe Ar Ne | 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 | Kr Xe Ar Ne | 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 | Kr Xe Ar Ne | 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 | Qz | 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 | Qz | 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 | Qz | 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 | Off | 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 | Off | 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 | Off | 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 | Off | 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 | Off | 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 | Off | 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 | Off | 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 | Off | 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 | Off | 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 a1af81e759..3511fa07c3 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 input file using PypeIt version: 1.9.2.dev322+gbe682ddb1 - # UTC 2022-07-09T01:15:05.545 + # Auto-generated PypeIt input file using PypeIt version: 1.8.2.dev482+gf1da42021.d20220523 + # UTC 2022-07-11T17:05:23.772 # User-defined execution parameters [rdx] @@ -16,7 +16,7 @@ # Data block 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/pypeit_par.rst b/doc/pypeit_par.rst index 29250ea208..ee0971f519 100644 --- a/doc/pypeit_par.rst +++ b/doc/pypeit_par.rst @@ -513,19 +513,19 @@ Collate1DPar Keywords Class Instantiation: :class:`pypeit.par.pypeitpar.Collate1DPar` -========================= ========== ======= ======================================= ============================================================================================================================================================================================================================================================================================================================================================================================================== -Key Type Options Default Description -========================= ========== ======= ======================================= ============================================================================================================================================================================================================================================================================================================================================================================================================== -``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. -``flux`` bool .. False If set, the script will flux calibrate using archived sensfuncs before coadding. -``ignore_flux`` bool .. False 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. -``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. -``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. -``wv_rms_thresh`` float .. .. If set, any objects with a wavelength RMS > this value are skipped, else all wavelength RMS values are accepted. -========================= ========== ======= ======================================= ============================================================================================================================================================================================================================================================================================================================================================================================================== +========================= ========== ======= ============================================ ============================================================================================================================================================================================================================================================================================================================================================================================================== +Key Type Options Default Description +========================= ========== ======= ============================================ ============================================================================================================================================================================================================================================================================================================================================================================================================== +``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. +``flux`` bool .. False If set, the script will flux calibrate using archived sensfuncs before coadding. +``ignore_flux`` bool .. False 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. +``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. +``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. +``wv_rms_thresh`` float .. .. If set, any objects with a wavelength RMS > this value are skipped, else all wavelength RMS values are accepted. +========================= ========== ======= ============================================ ============================================================================================================================================================================================================================================================================================================================================================================================================== ---- @@ -568,20 +568,20 @@ 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. In case of mosaic reduction (currently only available for Gemini/GMOS and Keck/DEIMOS) ``detnum`` should be a list of tuples of the detector indices that are mosaiced together. E.g., for Gemini/GMOS ``detnum`` would be ``[(1,2,3)]`` and for KEck/DEIMOS it would be ``[(1, 5), (2, 6), (3, 7), (4, 8)]`` 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). -``maskIDs`` str, int, list .. .. Restrict reduction to a set of slitmask IDsExample syntax -- maskIDs = 818006,818015 This must be used with detnum (for now). -``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. In case of mosaic reduction (currently only available for Gemini/GMOS and Keck/DEIMOS) ``detnum`` should be a list of tuples of the detector indices that are mosaiced together. E.g., for Gemini/GMOS ``detnum`` would be ``[(1,2,3)]`` and for KEck/DEIMOS it would be ``[(1, 5), (2, 6), (3, 7), (4, 8)]`` 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). +``maskIDs`` str, int, list .. .. Restrict reduction to a set of slitmask IDsExample syntax -- maskIDs = 818006,818015 This must be used with detnum (for now). +``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. +====================== ============== ======= ============================================ ======================================================================================================================================================================================================================================================================================================================================================================================================================= ----