What’s New in PypeIt
Version 1.14.1dev
Installation Changes
PypeIt will no longer be available through
conda-forge
and must be installed viapip
from PyPI. Users may still useconda
for management of PypeIt’s virtual environment.
Dependency Changes
Removes use of deprecated
pkg_resources
.Require version
>=1.12
forspecutils
.Add
psutil
as a dependency for [dev] installs.Add
pytest-qt
as a dependency for [dev] installs.Require version
>=0.3.1
forlinetools
Functionality/Performance Improvements and Additions
Started the development of instrument-specific scattered light removal. In this release, we only model KCWI/KCRM scattered light.
Turned on usage of the use_2dmodel_mask parameter for echelle spectrographs
Added support for Keck/KCRM RL data reduction.
Allow one to turn off reinit of reduce_bpm in global_skysub and made this the default for the final pass
Allow pypeit Spectrum1D loaders to circumvent the requirement that reduced spectrum have monotonically increasing wavelength data. Non-monotonic wavelength data usually indicate a problem with the data reduction, but this at least lets users ingest the spectrum.
Add a sensible error message to the pypeit Spectrum1D loaders in the event a user inadvertently tries to use Spectrum1D instead of SpectrumList for a
spec1d
file.Add support for the R4K detector for MDM OSMOS
Enabled interpolation and extrapolation of missing echelle orders. This is currently only used for Keck/HIRES, but the code is general.
Allow the specification of wavelength limits on the flexure cross-correlation against a sky template to limit the effect of unconstrained wavelength solutions at the ends of the spectrum.
Change
overscan_method = 'polynomial'
tooverscan_method = 'chebyshev'
to reflect the type of polynomial being fit. Both names point to the same code, but the name'polynomial'
is deprecated and will be removed in the future.Introduced PCA method for telluric corrections
Added a new GUI for creating and editing PypeIt input files:
pypeit_setup_gui
Added slicer subpixel sampling for DataCube generation
Added
trace_rms_tol
parameter for edge tracing, which helps guard against poorly constrained traces for spectrally truncated slits/orders.
Instrument-specific Updates
Updated archival sensivity functions for DEIMOS 1200G, 800G, and 600ZD gratings.
Keck/KCWI and Keck/KCRM: Turned on polynomial correction for sky subtraction.
We now support the reduction of VLT/FORS2 data taken in MOS mode.
Fixed fluxing file format in the
Keck-DEIMOS HOWTO
documentation.LDT/DeVeny: default parameter & wavelength template updates, add instrument- specific line lists, use SCITARG for target name if none entered in the LOUI.
Added support for NTT/EFOSC2 Gr#4
Keck/KCWI: FeAr are used for wavelength calibration, while the ThAr lamp is used to determine the wavelength tilt.
Improvement to the wavelength calibration for Keck/HIRES. New arxiv templates added. Templates available for orders 35-117.
Various updates to default parameters for Keck/HIRES.
Added
Keck-LRIS HOWTO
documentation.
Script Changes
When making datacubes, the user can select a separate frame to use for the sky subtraction. In this case, it is the processed data that will be used for sky subtraction (akin to nodding).
Allow a list of files to be passed to
pypeit_chk_wavecalib
.A new script has been written (
chk_scattlight
) to check the generation of the scattered light calibration frame model.Added the
pypeit_edge_inspector
script, which allows users to edit the edge traces by-hand.pypeit_parse_slits
now prints also the echelle order number, if applicable.Column
SpatID
in the output ofpypeit_chk_wavecalib
changed toSpatOrderID
and now show the echelle order number, if applicable, otherwise the slit number.pypeit_chk_edges
now load SlitTraceSet (if available) to be able to overlay the echelle order numbers.Added a -G option to
pypeit_setup
andpypeit_obslog
that will start the new Setup GUI.Improvements and bug fixes for how the mask is displayed by
pypeit_show_2dspec
, and addedpypeit_print_bpm
to allow for a quick report on the flags associated with a given bit value.
Datamodel Changes
A wavelength array is now stored for DataCube()
Wavecalib and Wavefit datacontainers now store information about echelle order number, if applicable.
Change to how Slit datamodel stores and checks bit flag values.
Under-the-hood Improvements
The CoAdd3D code has been refactored into a series of core modules and PypeIt-specific routines.
Polynomial overscan fitting now uses the
numpy.polynomial.Chebyshev
class instead of the deprecatednumpy.polyfit()
function.Improvements to echelle wavelength calibration. Code changes in:
pypeit/core/wavecal/wvutils.py
,pypeit/core/wavecal/echelle.py
,pypeit/core/wavecal/autoid.py
,pypeit/wavecalib.py
.Fixed some failure modes when matching measured order positions to expected positions for fixed-format echelle spectrographs.
More extensive propagation of turning off datamodel version checking (using
try_old
andchk_version
) throughout the code.
Bug Fixes
Fixed bug associated with finding more than one file with the same name (but presumably different extensions).
Fixed differential atmospheric refraction (DAR) correction bug. This bug affected datacubes combined using CoAdd3D(). Previously, the DAR was being computed, applied, and then later overwritten. The new routine is faster and more accurate.
Fixed a bug associated with an incorrect date for the transition to the Mark4 detector for Keck/LRIS RED.
Fixed a bug with the
pypeit_identify
script when using echelle data. Previously, the sigdetect parameter was a list of all orders, instead of a single value.Fixed a bug with the GUI
pypeit_skysub_regions
. Previously, the calib header information was not included, and this led to a calibration error.Corrected the binning scaling for BOXCAR_RADIUS in the object-finding algorithm. Previously, the platescale was multiplied by the spectral binning and not the spatial binning.
Aligned the documentation and parameters with the code for polynomial overscan subtraction. Docs/params specified 3 values to be passed in
overscan_par
foroverscan_method = 'polynomial'
, but the code only uses one (poly order).Fixed duplicate object bug reported in Issue #1690.
Version 1.14.0
Dependency Changes
Main dependency bumps: numpy>=1.22, matplotlib>=3.7, ginga>=4.1.1, qtpy>=2.0.1
Functionality/Performance Improvements and Additions
Improvements to wavelength grids and masking in coadd routines.
Refactored coadding routines to work with lists to support coadding data from different setups.
Sensitivity function models can now be computed relative to the flat-field spectrum.
Improvements in 2D coaddition
Fix a bug in
pypeit_setup_coadd2d
for the output file name of the.coadd2d
fileAdded possibility to specify more than one Science folder in
pypeit_setup_coadd2d
Now
only_slits
parameter inpypeit_coadd_2dspec
includes the detector number (similar toslitspatnum
)Added
exclude_slits
parameter inpypeit_coadd_2dspec
to exclude specific slitsFix wrong RA and Dec for 2D coadded serendips
Allow wavelength calibrations for specific slits/orders to be redone (instead of adopting the value from a processed calibration frame); see new
redo_slits
parameter.
Instrument-specific Updates
Adds/Improves support for Gemini/GNIRS (IFU), Keck/KCRM, Keck/ESI, MDM/Modspec, Keck/HIRES, JWST
HIRES wavelength solution improvements galore
Improvements for Keck/LRIS
Generated wavelength templates for all the LRIS grism & grating
Added FeAr line list
Improved calibration association and frame typing
Improved and added documentation
Changes to
metadata.py
including commenting out, in the pypeit file, files that have frametype None (this preventrun_pypeit
to crash)Added a function
check_spectrograph()
(currently only defined for LRIS), that checks (duringpypeit_setup
) if the selected spectrograph is the corrected one for the data used.
Script Changes
Added a script to convert a wavelength solution into something that can be placed in the reid archive.
Store user-generated wavelength solution in pypeit cache
Datamodel Changes
Changed calibration frame naming as an attempt to avoid very long names for files with many calibration groups. Sequential numbers are reduced to a range; e.g.,
'0-1-2-3-4'
becomes'0+4'
and'3-5-6-10-11-12-15-18-19'
becomes'3-5+6-10+12-15-18+19'
Instrumental FWHM map is calculated and output in
Calibrations
andspec1d
files.
Under-the-hood Improvements
Change how masking is dealt with in extraction to fix a bug in how masks were being treated for echelle data
Refactored function that loads wavelength calibration line lists
Bug Fixes
Hotfix for GTC/OSIRIS lamp list
Hotfix for Arc1D stats annotations on the QA
Hotfix for metadata:
correctly set
config_independent_frames
when multiple configurations are being setupsupport lists in
config_independent_frames
Hotfix for rebin (speed-up and conserves flux)
Hotfix for skysub regions GUI that used
np.bool
Hotfix to stop pypeit_setup from crashing on data from lbt_luci1, lbt_luci2, magellan_fire, magellan_fire_long, p200_tspec, or vlt_sinfoni.
Hotfix to set BPM for each type of calibration file.
Fixed a bug in echelle coadding where the wrong coadded spectra were being used in final stacks.
Fix a bug in
spectrograph.select_detectors
, where a list ofslitspatnum
could not be used.
Version 1.13.0
Functionality/Performance Improvements and Additions
Allow user control of the local sky subtraction window
Implemented a resample algorithm when generating datacubes
Sensitivity function masking and output updates
Improve speed in ginga visualization of traces and added pypeit_chk_tilts. Note that this script uses an update of the tilts datamodel, so it will not work on older reductions.
Fixed a bug in the variance_model calculation for combined images.
Datamodel Changes
Removed use of the term “master”, renamed to calibration frames/files. Default output directory for calibration frames is now
Calibrations
. Calibration frames renamed from, e.g.,MasterArc*
toArc*
.Names of associated calibration frames now written to
spec2d
file headers.
Dependency Changes
Deprecate support for python 3.8 with PypeIt, allow python 3.11
Make pypeit_show_2dspec (somewhat) backwards compatible.
Added the option to disable strict version checking for 1d coadds.
Start to deprecate use of
os.path
in favor ofpathlib
Script Changes
In PypeIt files, the
'calib'
column is now always added to the pypeit file, regardless of whether or not you also request the'comb_id'
and'bkg_id'
columns.In PypeIt files, the calibration group numbers can now be anything, as long as there are no more than 63 unique integers.
Deprecated
pypeit_parse_calib_id
script, but improved the.calib
file provided bypypeit_setup
. The.calib
file is now always written, and provides a direct association between input raw files and output calibration files. Discussed in new docs.Added coadd2d setup script
Added the possibility to use dither offsets saved in the header of the science frames for coadding 2D spectra (
dithoff
must be part of the spectrograph metadata).Major quicklook updates; see documentation. ql_multislit.py deprecated.
Instrument-specific Updates
Updates to reduction parameters for LDT/DeVeny
Hotfixes
Hotfix to docs to ensure
pypeit_loaders
api doc is generatedHotfix for KCWI when using alignment (aka ContBars) frames for the astrometric correction.
Version 1.12.2
Instrument-specific Updates
Include Gemini/GMOS mask design slurping and usage documentation
New Gemini/GMOS wavelength solution
Added NIRES tutorial doc
reid_arxiv templates for all MMTO Blue Channel gratings and for MMTO Binospec G600 and G1000
Usage Updates
Added new specutils interface
Datamodel Updates
Include the S/N of extracted spectra in the SpecObj datamodel
Hotfixes
Various bug fixes and enhancements to mmt_bluechannel and mmt_binospec support
Fixed bugs when only performing calibrations and (1) calib groups are all set to ‘all’ or (2) anything other than ‘0’.
Version 1.12.1
Instrument-specific Updates
Implemented the upgraded GTC/OSIRIS+
Added support for more NOT/ALFOSC grisms as well as NOT recommended standards
Implemented the SOAR/Goodman (blue) M1 only
Minor Updates
Modify install notes to allow python 3.10; python3.8 not longer explicitly supported
Allow for bad orders during extraction without crashing
Hotfixes
Specify sphinx versions to correctly work with sphinx_rtd_theme
Fixed bug that caused crash of sensfunc routines using telluric grids in offline processing
Fixed error when showing flats in Ginga when the fine correction is not performed
Fixed keymap error when displaying GUIs
New docs on OneSpec
Version 1.12.0
Functionality Improvements / User-level Updates
Refactor quicklook scripts
Added spectral flexure and reference frame corrections for IFU data
Allow separate sky frame to be used for sky subtraction with IFU data
Limit the images written to the Edges file to only the trace image, mask, and detector.
Instrument-specific Updates
Limit LRISr header crashes
Parse Keck/NIRES dither patterns, similar to MOSFIRE
Started modifications and support for JWST NIRSpec
Minor / Under-the-hood Updates and Bug Fixes
Fixed bug that allowed science frames to be assigned to multiple instrument configurations
Fixed typo related to GitHub download for offline processing
OpenMP link fix
Enable boxcar_radius for manual extraction
Prevent flexure crash
Fixed error with deprecated numpy types
Improved optimization of bspline c code
Introduce BitMaskArray class to ease use of bitmasks
Fixed memory hogging by matplotlib when using version >= 3.6.1
Version 1.11.0
Significant Updates
Add ability for users to specify custom arc line lists for wavelength calibration, saved in the user’s PypeIt cache
Allow for the specification of a specific UVIS extinction file for sensitivity function computation and flux calibration.
Now more than one setup can be assigned to the same calibration frame, allowing to associate the same calibration frames to different science/standard frames, if desired.
Refactor and general update of documentation
Instrument-specific Updates
Correctly associate calibrations with science data for MOSFIRE longslit and long2pos masks.
Automatically assign comb_id and bkg_id to MOSFIRE science data, using the information on the dither pattern.
Minor
Added Keck/NIRES frame-typing development doc.
Allow verbosity specification for various post-processing command-line scripts.
Version 1.10.0
Major Changes
Refactor PypeIt input files. Main pypeit file remains the same, except that inclusion of leading and trailing | characters in the data table (required in previous versions) will now result in DeprecationWarnings. All post-processing scripts (coadding, fluxing, etc) must use the new format. See the main documentation pages.
Minor Changes/Improvements
Apply find_min_max when clipping the image for object finding
Mask bad detector regions for global sky flexure calculation
Added wavelength diagnostics to the spec2d output
Instrument-specific Changes/Improvements
Modify tweak_standard for Keck-MOSFIRE/J2
Detector structure correction included in flatfield calibration (Keck-KCWI only)
Version 1.9.1
Addresses bug related to downloading from the reid_arxiv when using the reidentify wavelength calibration method.
Version 1.9.0
Major Changes
Reduction of Keck/DEIMOS now defaults to mosaics of red and blue detector pairs
Package data is no longer distributed via PyPI. Instead, we use astropy’s downloading/caching system as needed by the user
Significant refactor of object finding and 2D extraction algorithms
Added support for: - VLT FORS2 600z grism - VLT XShooter UVB arm
Minor Changes/Improvements
Default comb_id ordering matches the sorted file name in pypeit_setup
Save output wavelength calibration from pypeit_identify to the cache for direct reuse in data reduction.
The pypeit_identify GUI can now toggle between linear and log scaling of the arc spectrum flux.
Dark subtraction now ignores any difference in exposure time, by default
Added more flexible quicklook that can handle dithering.
Bug fixes in local sky subtraction and extraction
Fixed pypeit_setup issues due to bad LRIS headers.
Fixed a bug in 2d coadding when objects were not being identified.
Refactored 2d extraction.
Minor enhancements to pypeit_identify GUI
Refactoring of pypeit_show_wvcalib GUI
Instrument-specific Changes/Improvements
Improve Keck/KCWI automatic frame typing.
Added wavelength templates for - Keck/MOSFIRE (OH and arc lines) - bok_bc 300 grating template
Improved wavelength solution for Gemini-Nort E2V detector
Keck/DEIMOS now uses gain/RN values measured periodically by WMKO
Added enhancements and fixes for Keck lris red Mark4.
Added code to better parse Gemini/GNIRS dither sequences
Version 1.8.1
Various hotfixes
Include preliminary support for fluxing with archived SensFunc files for DEIMOS.
Version 1.8.0
Significant changes
Code to allow for mosaicing multiple detectors into a single reduction. This is now the default for Gemini GMOS and improves stability of wavelength calibration.
Introduces pypeit_parse_calib_id script
Refactored manual extraction
Update for LDT/DeVeny including support for binned data, use_header for reading arc lamps used from frames, and reid_arxiv templates for three additional gratings.
Slurps in and uses slitmask design for Keck/LRIS (limited usage)
Significant improvements in 2D coadding.
Scripts to explore the noise residuals in PypeIt
Datamodel changes and algorithmic improvements
Improved performance of L.A. Cosmic implementation
Now uses stars in alignment boxes for default calculation of slitmask offsets in DEIMOS reductions.
2D wavelength calibration image now added to Flat output
Improved treatment of saturation.
Dark counts used for calculating the shot noise now includes measured dark images if provided.
Include sky model in 2nd pass of global sky subtraction (not for IR redux).
Skymask is now computed also for the maskdef_extract objects.
Added dedicated fwhm and boxcar_radius for maskdef_extract objects.
Added pypeit_version to the pypeit file header.
Set DEIMOS find_fwhm default to 0.8” in binned pixels.
Added row-dependent pattern-noise calculation for KCWI
Bug fixes
Fixed a bug about how maskdef_offset is assigned to each detector
Fixed 2Dcoadd spec bugs for central wavelength dithers.
Version 1.7.0
Major Changes
MOSFIRE improvements: - improved frame typing
ingestion of slitmask metadata for MOSFIRE with association of extracted spectra to object name and coordinates
extraction of undetected objects
incorporates dither pattern from file headers
Implements new Mark4 detector for Keck/LRISr; selected as the keck_lris_red_mark4 “spectrograph”
Minor Changes
Introduces pypeit_parse_calib_id script
Throw a warning if the chosen spectrograph has a header which does not match expectation
Pypeit can now read (currently for Keck DEIMOS only) the list of arc lamps from the header and use it for wavelength calibration.
Allow one to restrict the wavelength range of the arxiv template
Set DEIMOS FWHM default to 10 pixels
Fixed a bug in HolyGrail that did not allow for sigdetect and rms_wavelength to be slit dependent lists
Version 1.6.0
Improved basic image processing, particularly error propagation and documentation
Minor changes to Bias, Dark, and spec1d datamodel.
Version 1.5.0
Improvement to installation docs and scripts to ease installation of telluric and quick-look files.
Support dithered observations for DEIMOS.
Starting after version 1.14.0, the logged changes are now only recorded by these release docs. Before that, a detailed log of code edits (including releases earlier than version 1.5.0) was kept in a single location; see the CHANGELOG.