What’s New in PypeIt

Version 1.15.1dev

Installation Changes

Dependency Changes

Functionality/Performance Improvements and Additions

Instrument-specific Updates

Script Changes

Datamodel Changes

Under-the-hood Improvements

Bug Fixes

  • The subpixel algorithm used to resample datacubes that are generated by pypeit_coadd_datacube produced error cubes that were not properly propagating the noise. The error cubes of the NGP algorithm were unaffected. The error cubes are now regularly inspected with vet tests to ensure the error cubes are reliable.

Version 1.15.0

Installation Changes

  • PypeIt will no longer be available through conda-forge and must be installed via pip from PyPI. Users may still use conda for management of PypeIt’s virtual environment.

Dependency Changes

  • Removes use of deprecated pkg_resources.

  • Require version >=1.12 for specutils.

  • Add psutil as a dependency for [dev] installs.

  • Add pytest-qt as a dependency for [dev] installs.

  • Require version >=0.3.1 for linetools

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.

  • 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' to overscan_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 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

  • Add support for the R4K detector for MDM OSMOS

  • Updated archival sensitivity 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 of pypeit_chk_wavecalib changed to SpatOrderID 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 new GUI for creating and editing PypeIt input files: pypeit_setup_gui

  • Added a -G option to pypeit_setup and pypeit_obslog that will start the new Setup GUI.

  • Improvements and bug fixes for how the mask is displayed by pypeit_show_2dspec, and added pypeit_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 SlitTraceSet 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 deprecated numpy.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 and chk_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 for overscan_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 file

    • Added possibility to specify more than one Science folder in pypeit_setup_coadd2d

    • Now only_slits parameter in pypeit_coadd_2dspec includes the detector number (similar to slitspatnum)

    • Added exclude_slits parameter in pypeit_coadd_2dspec to exclude specific slits

    • Fix 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 prevent run_pypeit to crash)

    • Added a function check_spectrograph() (currently only defined for LRIS), that checks (during pypeit_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 and spec1d 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 setup

    • support 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 of slitspatnum 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* to Arc*.

  • 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 of pathlib

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 by pypeit_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 generated

  • Hotfix 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.