Releases | Open Source Science

New Features

Add new flux_col keyword argument to JWST x1d reader to override flux column auto-detected from source type column (point vs surface brightness). [#1244]
The readers can now read IRAF MULTISPEC files with linear and log-linear wavelength solutions; at the same time the IRAF equispec format gains the ability to read log-linear wavelength solutions. [#1254]

Bug Fixes

Fixed/updated SDSS-V mwm data loader to account for a subset of targets with bad datasums. [#1253]

Other Changes and Additions

Updated the JWST data readers to accomodate new WFSS file formats with SpectrumList.read(). [#1252]

- Python
Published by rosteen 7 months ago

specutils - v1.20.3

Minor doc fix to make 1.20.x docs available long-term.

- Python
Published by rosteen 8 months ago

specutils - v2.0.0

See https://specutils.readthedocs.io/en/latest/#changes-in-version-2 for more details about major changes between version 1.x and 2.x.

New Features

Spectral axis can now be any axis, rather than being forced to be last. See docs for more details. [#1033, #1226]
specutils.Spectrum now properly handles GWCS input for wcs attribute. [#1074]
JWST reader no longer transposes the input data cube for 3D data and retains full GWCS information (including spatial). [#1074]
Spectrum1D renamed to Spectrum. [#1126]

Other Changes and Additions

Initializing a Spectrum with only a spectral axis (not full WCS) will now result in a GWCS matching the dimensionality of the flux array, rather than a 1D spectral GWCS in all cases. [#1211, #1222]
Spectrum arithmetic now checks whether the spectral axes of the two operand Spectrum objects are equal, and fails if they are not. [#1211]
Added documentation about transitioning from 1.x to 2.x. [#1226]

- Python
Published by rosteen 9 months ago

Bug Fixes

Fixed loaders for HST/STIS. Added an "HST/STIS multi" reader for use with SpectrumCollection to read multi-extension and/or multi-order echelle datasets. [#1233]

Other Changes and Additions

Warn about use of spectral_axis_index (new Spectrum1D kwarg for 2.0) in 1.x. [#1238]

- Python
Published by rosteen 9 months ago

Bug Fixes

Switch to using an alias rather than a subclass for the temporary 1.x access to the new 2.x class name (Spectrum). [#1236]

- Python
Published by rosteen 10 months ago

1.20.0 (2025-05-01)

Bug Fixes

Fixed loaders for IRAF-encoded non-linear Chebychev + Legendre wavelength solutions that were imposing integer-valued domain limits. [#1199]
Fixed loaders for SDSS APOGEE not correctly identifying the format [#1217]
Fixed template comparison returning empty list of chi2 values in some cases. [#1228]

Other Changes and Additions

Added Spectrum class wrapper around Spectrum1D to ease transition to new class name in 2.0. [#1229, #1230]
Removed redshift and radial velocity setters in Spectrum1D that have been deprecated since 1.8. [#1229]
Added documentation about upcoming changes in specutils 2.0. [#1231]

- Python
Published by rosteen 10 months ago

1.19.0 (2024-11-05)

Bug Fixes

Fixed mwmVisit SDSS-V Spectrum1D and SpectrumList default loader being unable to load files containing only BOSS instrument spectra. [#1185]
Fixed automatic format detection for SDSS-V SpectrumList default loaders. [#1185]
Fixed SplineInterpolatedResampler when input and output spectral axes are different physical types, e.g. wavelength and velocity. [#1190]

Other Changes and Additions

"Multi" loaders have been removed from SDSS-V SpectrumList default loaders. [#1185]

- Python
Published by rosteen over 1 year ago

New Features

New Spectrum1D.with_spectral_axis_and_flux_units method to convert both spectral axis and flux units at the same time. [#1184]

Bug Fixes

Fixed Spectrum1D.with_flux_unit() not converting uncertainty along with flux unit. [#1181]
Fixed extracting a spectral region when one of spectrum/region is in wavelength and the other is in frequency units. [#1187]

Other Changes and Additions

Replaced LevMarLSQFitter with TRFLSQFitter as the former is no longer recommended by astropy. [#1180]

- Python
Published by rosteen over 1 year ago

v1.17.0

New Features

Fitting and excision functions can now use inclusive upper bounds for input regions if specified. [#1171]

Bug Fixes

Fixed specifying a single value for window in analysis.fit_lines. [#1164]

Other Changes and Additions

Dropped support for python 3.9. [#1176]
utils.wcs_utils.refraction_index (and thus air_to_vac and vac_to_air) now defaults to Morton2000 as the method instead of Griesen2006. [#1169]

- Python
Published by rosteen over 1 year ago

1.16.0 (2024-08-08)

Bug Fixes

Arithmetic operations on Spectrum1D objects now preserve spectral axis values that were updated by setting redshift or radial velocity. [#1158]
Ensure supported dtype is passed to medfilt during smoothing. [#1156]
Adjusted copy semantics for numpy 2 compatibility. [#1145]
Fixed moment 0 calculation to sum flux*dx (rather than flux) to match line_flux. [#1141]

Other Changes and Additions

Changed the tabular-fits reader/writer to round-trip the header, by default in the primary HDU. The reader now reads the primary header into meta['header']; the old behaviour of reading the header from the data extension can be restored by setting the option store_data_header=True. The writer is taking a corresponding option for saving meta['header'] to either primary or data extension headers. [#1113]
Improved documentation for readers/writers. [#1152, #1157]

** Note: re-released on Github 2024-09-23 to re-trigger Zenodo hook

- Python
Published by rosteen over 1 year ago

1.16.0 (2024-08-08)

Bug Fixes

Arithmetic operations on Spectrum1D objects now preserve spectral axis values that were updated by setting redshift or radial velocity. [#1158]
Ensure supported dtype is passed to medfilt during smoothing. [#1156]
Adjusted copy semantics for numpy 2 compatibility. [#1145]
Fixed moment 0 calculation to sum flux*dx (rather than flux) to match line_flux. [#1141]

Other Changes and Additions

Changed the tabular-fits reader/writer to round-trip the header, by default in the primary HDU. The reader now reads the primary header into meta['header']; the old behaviour of reading the header from the data extension can be restored by setting the option store_data_header=True. The writer is taking a corresponding option for saving meta['header'] to either primary or data extension headers. [#1113]
Improved documentation for readers/writers. [#1152, #1157]

- Python
Published by rosteen over 1 year ago

New Features

Implemented SpectralRegion.write() and SpectralRegion.read() to round-trip spectral regions to/from ECSV files via astropy.table.QTable. [#1133]

- Python
Published by rosteen almost 2 years ago

Changes

new_flux_unit changed to with_flux_unit to match spectral version, updated docstring to reflect actual behavior. [#1124]
Compatibility with numpy 2.0 and astropy 6.1. [#1130]

- Python
Published by rosteen almost 2 years ago

New Features

Added SDSS-V file format readers. [#1107]
Switched from using numpy.correlate to scipy.signal.correlate in template_correlate and enabled passing through the method argument. [#1114]
Added DESI file format readers. [#1116]
Added truncate option for resampler and template correlation extrapolation treatment. [#1121]

Bug Fixes

SDSS reader now properly exposes the spPlate_identify and spPlate_loader functions. [#1097]
Masks now round-trip through tabular-fits reader/write. [#1104]
template_correlate no longer errors when used on a Spectrum1D that lacks an uncertainty array. [#1118]
with_spectral_unit has been changed to with_spectral_axis_unit and actually works now. [#1119]
Template correlation functions now truncate to overlapping region to avoid NaNs in normalization when spectrum and template have non-overlapping regions. [#1121]
Fixed numpy error when printing a Spectrum1D object. [#1123]

Other Changes and Additions

Made a couple small updates to developer docs. [#1110, #1112]
Updated the format of Spectrum1D.__str__ and Spectrum1D.__repr__. [#1123]

- Python
Published by rosteen about 2 years ago

specutils - v1.12.0

New Features

Registering a SpectrumList reader for a data loader is now optional. [#1068]

Bug Fixes

Fixed SDSS-I/II spSpec units. [#1066]
Addressed compatibility with ASDF 3.0 for JWST data. [#1079]

Other Changes and Additions

Corrected velocity_convention options in Spectrum1D docstring. [#1088]

- Python
Published by rosteen over 2 years ago

specutils - v1.11.0

New Features

wcs1d-fits loader now reads and writes boolean masks. [#1051]

Bug Fixes

Reimplementation of FluxConservingResampler. It is now faster and yields more accurate results. [#1060]
Fixed uncertainty calculations in centroid and gaussian width functions, also added an option to use an astropy.uncertainty distribution instead of the analytic solution. [#1057]

Other Changes and Additions

Drastically improved performance of region extraction. [#1048]
When creating a Spectrum1D object, it is enforced that the spectral axis is sorted and either strictly increasing or decreasing. [#1061]

- Python
Published by rosteen over 2 years ago

New Features

wcs1d-fits loader now reads and writes celestial components of of multi-dimensional WCS, and handles mask and uncertainty attributes. [#1009]
Added support for reading from files with flux in counts. [#1018]

Bug Fixes

Fixed SpectralAxis.with_observer_stationary_relative_to to actually return the updated spectral axis. [#992]
Fixed region extraction for axes/regions in units of u.pix. [#1001]
tabular-fits writer now properly converts uncertainties to StdDevUncertainty if needed. [#1027]
Fix bug in fit_lines which gave unexpected outputs from the get_fit_info and ignore_units keyword arguments. [#1030]
Fix SNR calculations with both masks and regions. [#1044]

Other Changes and Additions

Added some basic documentation for Spectrum1D.write. [#1017]
JWST s2d and s3d readers now requires the optional dependency, stdatamodels, which user has to install separately. [#1038]
ASDF tag for Spectrum1D is now compatible with ASDF v3. As a result, minversion of asdf has been bumped to 2.14. Redundant ASDF schema for SpectralCoord is removed. It also now supports mask serialization. [#1042, #1053]
JWST X1D reader will no longer raise a UnitWarning for surface brightness error. [#1050]

- Python
Published by rosteen almost 3 years ago

specutils - v1.9.1

Bug Fixes

Add and subtract operations on Spectrum1D now allow for other operand's class to handle the arithmetic if that class has special handling. [#988]

- Python
Published by rosteen over 3 years ago

Bug Fixes

Fix bug in fitting with weights if weights argument is set to 'unc'. [#979]
Fix bug in JWST reader which caused multi-extension files to load only the primary HDU [#982]
Implemented conversion to expected uncertainty type in a few functions that were still just assuming the uncertainty was the correct type. [#984]

Other Changes and Additions

Bumped astropy minimum version to 5.1. [#984]

- Python
Published by rosteen over 3 years ago

Bug Fixes

Arithmetic with constants and Spectrum1D now works in either order. [#964]
Fixed uncertainty propagation in FluxConservingResampler. [#976]

- Python
Published by rosteen over 3 years ago

specutils - V1.8.0

New Features

Implemented uncertainty propagation for analysis functions. [#938, #939, #961, #968]
Model fitting with fit_lines now returns uncertainties from the underlying scipy fitter by default. [#962]

Bug Fixes

Fixed a bug with moment map orders greater than 1 not being able to handle cubes with non-square spatial dimensions. [#970]
Added a workaround for reading JWST IFUs with incorrect GWCS. [#973]

Other Changes and Additions

The Spectrum1D redshift and radialvelocity attribute setters were deprecated in favor of the more explicit ``setredshiftto,shiftspectrumto, andsetradialvelocityto`` methods. [#946, #943]
estimate_line_parameters now calculates estimates based on the selected region, rather than the entire spectrum. [#962]

- Python
Published by rosteen over 3 years ago

specutils - V1.7.0

Bug Fixes

Fixed spectral_slab crashing when spectral_axis has unit of pixels and the bounds are also defined in the unit of pixels. [#926]
Fixed resulting spectral_axis containing NaN when a cube is passed into Spectrum1D without WCS nor spectral axis and the spatial-spatial dimension is smaller than spectral dimension. [#926]
Fixed WCS not accurately reflecting the updated spectral axis after slicing a Spectrum1D. [#918]

Other Changes and Additions

Logger usage is removed. Warnings now issued using Python warnings module. This enables more granular warning control for downstream packages. [#922]

- Python
Published by rosteen about 4 years ago

New Features

Added collapse methods to Spectrum1D (mean, median, max, min, sum). [#904, #906]
SpectralRegion and Spectrum1D now allow descending (in wavelength space) as well as ascending spectral values. [#911]

- Python
Published by rosteen about 4 years ago

specutils - V1.5.0

New Features ^^^^^^^^^^^^

Convolution-based smoothing will now apply a 1D kernel to multi-dimensional fluxes by convolving along the spectral axis only, rather than raising an error. [#885]
template_comparison now handles astropy.nddata.Variance and astropy.nddata.InverseVariance uncertainties instead of assuming the uncertainty is standard deviation. [#899]

Bug Fixes ^^^^^^^^^

Speed up JWST s3d loader and reduce memory usage. [#874]
SpectralRegion can now handle pixels. [#886]
Fix bug where template_comparison would return the wrong chi2 value. [#872]

Other Changes and Additions ^^^^^^^^^^^^^^^^^^^^^^^^^^^

fit_lines now makes use of unit support in astropy.modeling. [#891]
Spectrum1D.with_spectral_units now attempts to fall back on the spectral_axis units if units could not be retrieved from the WCS. [#892]
ndcube package pin updated to released version (2.0). [#897]
Minor changes for astropy 5.0 compatibility. [#895]

- Python
Published by rosteen over 4 years ago