CHANGELOG.md

Changelog

[Unreleased]

Added

• Ability to read in instrumental fluxes and stokes beam amplitudes from FHD catalogs into extra_columns.

Changed

• Promote RA/Dec values from FHD catalogs to float32.
• If no extended models remain after a select, the extended_model_group parameter is set to None after the select.
• Updated minimum optional dependency versions: lunarsky>=1.0 (to drop spiceypy requirement)

Fixed

• A bug where the frame for FHD catalogs was set to ICRS when it should have been FK5.
• A bug where the extended_model_group was set to an array of empty strings when reading in FHD catalogs with no extended models.

Removed

• Spiceypy error catching in tests

[1.1.1] - 2026-06-01

Added

• New option when reading FHD catalogs to include available columns in extra_columns.
• New SkyModel.remove_extra_columns method to allow for removal of extra columns.

Changed

• Improved logic for duplicate source IDs in FHD catalogs.
• Updated minimum dependency versions: pyuvdata>=3.2.3
• Use pyuvdata.UVBase._select_along_param_axis rather than custom logic in SkyModel.select.

Fixed

• Entry point scripts are now properly installed.

[1.1.0] - 2025-06-26

Added

• New option to SkyModel.select to select components that do not have NaN values in the stokes parameter at either any or all frequencies.
• New option to SkyModel.select to select components with no negative Stokes I values.
• New check warnings about NaN stokes and spectral index values and negative Stokes I values.
• An option to skip optional parameters when reading in skyh5 files.

Changed

• Updated minimum dependency versions: h5py>=3.7, python>=3.11, scipy>=1.9
• Converted scripts to entry points to be better aligned with the pyproject.toml approach.
• Only import lunarsky if needed.
• Use the new pyuvdata analytic short dipole beam for polarized source testing.
• Updated minimum dependency versions: pyuvdata>=3.1.0
• Updated minimum optional dependency versions: lunarsky>=0.2.5

Fixed

• A bug where running check on read was impossible to turn off.

[1.0.1] - 2024-07-01

Changed

• Updated minimum dependency versions: setuptools_scm>=8.1, scipy>=1.8
• pyuvdata utils imports to ensure compatibility with version 3.0.
• numpy.string_ calls to numpy.bytes_, np.in1d to np.isin and a few other changes for numpy 2.0 compatibility.

Fixed

• An error when Skymodel.concat was called serially.

[1.0.0] - 2024-05-09

Changed

• Updated minimum dependency versions: astropy>=6.0, h5py>=3.4, numpy>=1.23, pyuvdata>=2.4.3, scipy>=1.7.3, python>=3.10
• Updated minimum optional dependency versions: astropy-healpix>=1.0.2, lunarsky>=0.2.2

[0.3.1] - 2024-02-22

Added

• A memo describing the SkyH5 format in docs/references.

Changed

• Added support for more types of FHD catalog files and better error messages.
• Added support (and testing) for python 3.12, dropped support for python 3.8
• Moved the optional data-sized arrays (stokes_error and beam_amp) from the Header datagroup to the Data datagroup in SkyH5 files.
• Added an extra_columns attribute to SkyModel, a recarray to store other catalog information with a value per component.
• Updated the pyuvdata requirement to >= 2.4.1
• Updated the scipy requirement to >= 1.5

Fixed

• A bug where FHD frequencies were interpreted as being in Hz rather than MHz.

[0.3.0] - 2023-04-10

Added

• A freq_edge_array parameter to store the top and bottom of the sub-bands with shape (2, Nfreqs). This will become required for objects with "subband" spectral types in version 0.5. A freq_edge_array parameter was also added to the read_votable_file, read and from_file methods.

Changed

• When writing to text files, "subband" spectral types are represented in the same way as "full" spectral types (losing the frequency edge array information).
• Increase the minimum compatible version for lunarsky to 0.2.1 to fix astropy deprecation warnings.

Deprecated

• Not setting the freq_edge_array parameter for subband spectral types.

Removed

• Defaulting for the coordinate frame, frame is now required to be passed to the __init__ method for Healpix maps and point-like components when passing individual components rather than a SkyCoord object. It is also required to be passed to the read_votable_file method.
• Handling for accessing the deprecated ra_dec_coherency, lon, lat attributes.
• Handling for accessing galactic l and b coordinates as gl and gb.
• The point_to_healpix method, use the assign_to_healpix instead.
• The frame parameter to the assign_to_healpix method. The frame from the object's skycoord parameter is now always used for the Healpix frame, use transform_to to convert to the desired frame before calling assign_to_healpix.
• The source_cuts method and the associated source_select_keywords parameters from the various read methods.
• The to_recarray and from_recarray methods.
• Support for reading old healvis style Healpix hdf5 files (via the associated read_healpix_hdf5, from_healpix_hdf5 and write_healpix_hdf5 methods). skyh5 files are now the only supported hdf5 file format.
• The ra_column and dec_column parameters to the read and from_file methods. Use the more generic lon_column and lat_column parameters instead.

[0.2.0] - 2023-02-01

Added

• Add support for all astropy coordinate frames with the new skycoord attribute (which contains an astropy SkyCoord object) on point objects and the new hpx_frame attribute on healpix objects. Users can interact with the SkyCoord object directly or use convenience methods on SkyModel as appropriate. References to older SkyModel attributes are handled for backwards compatibility.
• Read/write methods for text and votable files now support more astropy frames (not just icrs).
• New lon_column, lat_column and frame parameters to the read and from_file methods which apply when reading votable files.
• Added calc_frame_coherency method to calculate and optionally store the frame_coherency on the object.

Changed

• Updated the astropy requirement to >= 5.2
• No longer calculate frame_coherency (previously ra_dec_coherency) on SkyModel initialization to save memory.
• J2000 in ra and dec columns names of text files are now properly identified as indicating that the coordinates are in the FK5 frame rather than ICRS.
• Added handling for the new skycoord and hpx_frame parameters in skyh5 read/write methods.
• Updated the pyuvdata requirement to >= 2.2.10
• Added support for allowed_failures keyword in SkyModel.__eq__ to match pyuvdata.UVBase, update pyuvdata minimum version to 2.2.1 when that keyword was introduced.
• Updated the astropy requirement to >= 5.0.4
• Dropped support for python 3.7

Deprecated

• The ra_dec_coherency attribute in favor of frame_coherency because SkyModel objects can be in frames that do not use ra/dec coordinates.
• The lon, lat and frame attributes, in favor of the skycoord attribute for point objects and the hpx_inds and hpx_frame attributes for healpix objects.
• The ra_column and dec_column parameters in the read and from_file methods in favor of the lon_column and lat_column as a part of supporting more frames in votable files.
• The to_recarray and from_recarray methods.

Removed

• Removed support for the older input parameter order to SkyModel.__init__.
• Removed support for passing freq_array, reference_freq or stokes to SkyModel.__init__ as anything other than appropriate Quantities.
• set_spectral_type_params and read_idl_catalog methods have been removed from SkyModel
• Removed the read_healpix_hdf5, healpix_to_sky, write_healpix_hdf5, skymodel_to_array, array_to_skymodel, source_cuts, read_votable_catalog, read_gleam_catalog, read_text_catalog, read_idl_catalog, write_catalog_to_file functions (many similar methods on SkyModel remain).
• Removed support for passing telescope_location directly to the SkyModel.coherency_calc method.
• Removed support for votable_files with tables with no name or ID.
• Removed frequency column and alias like flux_density_I for flux columns in output of SkyModel.to_recarray,

[0.1.3] - 2022-02-22

Added

• Generic read and from_file methods to SkyModel objects that accept any file type supported by SkyModel.

Added

• A filename attribute to SkyModel objects.
• The nan_handling keyword to the at_frequencies method to control how NaNs in the stokes array on subband objects are handled during interpolation.
• The lat_range and lon_range keywords to the select method to support selecting on fields.
• The min_brightness, max_brightness and brightness_freq_range keywords to the select method to support selecting on brightness.
• The cut_nonrising method to remove sources that never rise given a telescope location, replacing functionality that was in the source_cuts method.
• The calculate_rise_set_lsts method to calculate and set the _rise_lst and _set_lst attributes on the object, replacing functionality that was in the source_cuts method.
• The get_lon_lat method which computes the values from hpx_inds on healpix objects and just returns the parameter values on point objects.
• The assign_to_healpix method to assign point component objects to a healpix grid (using the nearest neighbor approach).

Fixed

• A bug that caused the stokes array to be all NaNs after using the at_frequencies method on a subband spectral_type object if any NaNs appeared in the input stokes.

Changed

• ra and dec are no longer required parameters on healpix objects (since that information is encoded in the hpx_inds parameter). When objects are initialized as healpix objects the ra and dec parameters are no longer populated.
• point_to_healpix has been renamed to _point_to_healpix because it's only intended to be used internally to undo the healpix_to_point method.

Fixed

• A bug in concat when optional spectral paramters are not None on one of the objects.

Deprecated

• The source_cuts method and the source_select_kwds keywords to the reading methods.
• The point_to_healpix method.

[0.1.2] - 2021-07-06

Added

• Ability to overwrite default ra/dec when importing a healpix map
• clobber keyword to allow overwriting of skyh5 files
• Support for ring / nested healpix ordering.
• New SkyModel.concat method to support concatenating catalogs.
• A new optional parameters stokes_error to track errors on the fluxes reported by catalogs.

Fixed

• Fix bug in writing skyh5 files with composite stokes units (e.g. Jy/sr)
• Fix bugs causing healpix ordering to not be round tripped properly.
• Some bugs related to writing & reading skyh5 files after converting object using healpix_to_point method.

[0.1.1] - 2021-02-17

Added

• Read and write methods for skyh5 -- our newly defined hdf5 file format that fully supports all SkyModel types.
• Classmethods from_recarray, from_healpix_hdf5, from_votable_catalog, from_text_catalog, from_gleam_catalog and from_idl_catalog to enable instantiation from different formats directly.

Changed

• Changed default spectral_type for read_gleam_catalog to subband rather than flat.
• Changed extended_model_group in read_fhd_catalog to match the parent source name.

Fixed

• Improved handling of lists passed to SkyModel.__init__.
• A bug in the download_gleam utility method that caused missing columns for the subband spectral type
• Enabled subselecting to a given tolerance in at_frequencies (for full spectral type).
• A bug in Skymodel.__init__ that caused extended_model_group and beam_amps to not be added to the object.
• Enabled proper handling of duplicated source IDs in read_fhd_catalog.
• A bug in read_fhd_catalog did not order the name and beam_amp attributes correctly for extended sources.

[0.1.0] - 2020-6-29

Added

• The methods jansky_to_kelvin and 'kelvin_to_jansky' to convert between Jy and K based units.
• The methods healpix_to_point and point_to_healpix to convert between component types.

Changed

• Renamed the read_idl_catalog method to read_fhd_catalog.
• The stokes and coherency_radec parameters are now Quantity objects and must have units of 'Jy' or 'K sr' if component_type is 'point' and 'Jy/sr' or 'K' if the component_type is 'healpix'.
• The inputs to the utility functions stokes_to_coherency and coherency_to_stokes must now be Quantity objects.
• The utility function jy_to_ksr now uses astropy's built in conversion methods.

Deprecated

• The read_idl_catalog method.
• Initializing a SkyModel object with a float array rather than a Quantity for stokes is deprecated and support will be removed in a future version.
• Passing floats rather than Quantity objects as inputs to the stokes_to_coherency and coherency_to_stokes utility functions.

[0.0.2] - 2020-6-4

Added

• Documentation is now hosted on ReadTheDocs at https://pyradiosky.readthedocs.io/en/latest/
• A utility function and a script to download the GLEAM catalog.
• An at_frequencies function that will return a new SkyModel at requested frequencies.
• A new component_type parameter that can be set to "healpix" or "point".
• Better support for HEALPix maps, with new nside and hpx_inds parameters.
• Added the following methods to the SkyModel class: select, source_cuts, to_recarray, from_recarray, read_healpix_hdf5, read_votable_catalog, read_gleam_catalog, read_text_catalog, read_idl_catalog, write_healpix_hdf5 write_text_catalog.

Fixed

• A bug in spherical_coords_transforms.rotate_points_3d where an arccos calculation failed for a value larger than one by ~1e-12.

Deprecated

• The following functions in the skymodel module were deprecated: read_healpix_hdf5, write_healpix_hdf5, healpix_to_sky, skymodel_to_array, array_to_skymodel, source_cuts, read_votable_catalog, read_gleam_catalog, read_text_catalog, read_idl_catalog, write_catalog_to_file.

[0.0.1] - 2020-4-6

Added

• SkyModel object inherits from UVBase.
• Moved existing code from pyuvsim, got package set up.