Revisions of python-photutils

Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 1222854 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 26)
- Update to 2.0.2
  ## Bug Fixes
  * Due to an upstream bug in bottleneck with float32 arrays,
    bottleneck nan-functions are now used internally only for
    float64 arrays. Performance may be impacted for computations
    involving arrays with dtype other than float64. Affected
    functions are used in the aperture, background, detection,
    profiles, psf, and segmentation subpackages. This change has no
    impact if bottleneck is not installed.
  ### photutils.background
  * Fixed a bug in Background2D where an error would be raised when
    using the BkgIDWInterpolator interpolator when any mesh was
    excluded, e.g., due to an input mask. [#1940]
  ### photutils.detection
  * Fixed a bug in the star finders (DAOStarFinder, IRAFStarFinder,
    and StarFinder) when exclude_border=True. Also, fixed an issue
    with exclude_border=True where if all sources were in the
    border region then an error would be raised. [#1943]
- Release 2.0.1
  ## Bug Fixes
  ### photutils.background
  * Fixed a bug in SExtractorBackground where the dimensionality of
    the returned value would not be preserved if the output was a
    single value. [#1934]
  * Fixed an issue in Background2D where if the box_size equals the
    input array shape the input data array could be modified.
    [#1935]
- Release 2.0.0
  ## General
  * The regions package is now an optional dependency. [#1813]
Ana Guerrero's avatar Ana Guerrero (anag+factory) accepted request 1186836 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 25)
- Update to 1.13.0
  ## General
  * scikit-learn has been removed as an optional dependency.
    [#1774]
  ## New Features
  ### photutils.datasets
  * Added a make_model_image function for generating simulated
    images with model sources. This function has more options and
    is significantly faster than the now-deprecated
    make_model_sources_image function. [#1759, #1790]
  * Added a make_model_params function to make a table of randomly
    generated model positions and fluxes for simulated sources.
    [#1766, #1796]
  ### photutils.detection
  * The find_peaks function now supports input arrays with units.
    [#1743]
  * The Table returned from find_peaks now has an id column that
    contains unique integer IDs for each peak. [#1743]
  * The DAOStarFinder, IRAFStarFinder, and StarFinder classes now
    support input arrays with units. [#1746]
  ### photutils.profiles
  * Added an unnormalize method to RadialProfile and CurveOfGrowth
    to return the profile to the state before any normalize calls
    were run. [#1732]
  * Added calc_ee_from_radius and calc_radius_from_ee methods to
    CurveOfGrowth. [#1733]
  ### photutils.psf
  * Added an include_localbkg keyword to the IterativePSFPhotometry
    make_model_image and make_residual_image methods. [#1756]
  * Added “x_fit”, “xfit”, “y_fit”, “yfit”, “flux_fit”, and (forwarded request 1186835 from bnavigator)
Ana Guerrero's avatar Ana Guerrero (anag+factory) accepted request 1171971 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 24)
- Update to 1.12
  ## General
  * The minimum required Python is now 3.10. [#1719]
  * The minimum required NumPy is now 1.23. [#1719]
  * The minimum required SciPy is now 1.8. [#1719]
  * The minimum required scikit-image is now 0.20. [#1719]
  * The minimum required scikit-learn is now 1.1. [#1719]
  * The minimum required pytest-astropy is now 0.11. [#1719]
  * The minimum required sphinx-astropy is now 1.9. [#1719]
  * NumPy 2.0 is supported.
  ## Bug Fixes
  ### photutils.background
  * No longer warn about NaNs in the data if those NaNs are masked
    in mask passed to Background2D. [#1712]
  ## API Changes
  ### photutils.utils
  * The default value for the ImageDepth mask_pad keyword is now
    set to 0. [#1714] (forwarded request 1171970 from bnavigator)
Ana Guerrero's avatar Ana Guerrero (anag+factory) accepted request 1147437 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 23)
- Update to 1.11.0
  ## New Features
  ### photutils.psf
  * An init_params table is now included in the PSFPhotometry
    fit_results dictionary. [#1681]
  * Added an include_localbkg keyword to the PSF photometry
    make_model_image and make_residual_image methods. [#1691]
  * Significantly reduced the memory usage of PSF photometry when
    using a GriddedPSFModel PSF model. [#1679]
  * Added a mode keyword to IterativePSFPhotometry for controlling
    the fitting mode. [#1708]
  ### photutils.datasets
  * Improved the performance of make_test_psf_data when generating
    random coordinates with a minimum separation. [#1668]
  ### photutils.segmentation
  * The SourceFinder npixels keyword can now be a tuple
    corresponding to the values used for the source finder and
    source deblender, respectively. [#1688]
  ### photutils.utils
  * Improved the performance of ImageDepth when generating random
    coordinates with a minimum separation. [#1668]
  ## Bug Fixes
  ### photutils.psf
  * Fixed an issue where PSF models produced by make_psf_model
    would raise an error with PSFPhotometry if the fit did not
    converge. [#1672]
  * Fixed an issue where GriddedPSFModel fixed model parameters
    were not respected when copying the model or fitting with the
    PSF photometry classes. [#1679]
  ## API Changes
Ana Guerrero's avatar Ana Guerrero (anag+factory) accepted request 1128558 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 22)
- Update to 1.10.0
  ## General
  * The minimum required Astropy is now 5.1. [#1627]
  ## New Features
  ### photutils.datasets
  * Added a border_size keyword to make_test_psf_data. [#1665]
  * Improved the generation of random PSF positions in
    make_test_psf_data. [#1665]
  ### photutils.detection
  * Added a min_separation keyword to DAOStarFinder and
    IRAFStarFinder. [#1663]
  ### photutils.morphology
  * Added a wcs keyword to data_properties. [#1648]
  ### photutils.psf
  * The GriddedPSFModel plot_grid method now returns a
    matplotlib.figure.Figure object. [#1653]
  * Added the ability for the GriddedPSFModel read method to read
    FITS files generated by WebbPSF. [#1654]
  * Added “flux_0” and “flux0” as allowed flux column names in the
    init_params table input to the PSF photometry objects. [#1656]
  * PSF models output from prepare_psf_model can now be input into
    the PSF photometry classes. [#1657]
  * Added make_psf_model function for making a PSF model from a 2D
    Astropy model. Compound models are also supported. [#1658]
  * The GriddedPSFModel oversampling can now be different in the x
    and y directions. The oversampling attribute is now stored as a
    1D numpy.ndarray with two elements. [#1664]
  ### photutils.segmentation
  * The SegmentationImage make_source_mask method now uses a much
    faster implementation of binary dilation. [#1638]
Ana Guerrero's avatar Ana Guerrero (anag+factory) accepted request 1105925 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 21)
- Update to 1.9.0
  ## General
  * The minimum required Python is now 3.9. [#1569]
  * The minimum required NumPy is now 1.22. [#1572]
  ## New Features
  ### photutils.background
  * Added LocalBackground class for computing local backgrounds in
    a circular annulus aperture. [#1556]
  ### photutils.datasets
  * Added new make_test_psf_data function. [#1558, #1582, #1585]
  ### photutils.psf
  * Propagate measurement uncertainties in PSF fitting. [#1543]
  * Added new PSFPhotometry and IterativePSFPhotometry classes for
    performing PSF-fitting photometry. [#1558, #1559, #1563, #1566,
    #1567, #1581, #1586, #1590, #1594, #1603, #1604]
  * Added a new SourceGrouper class. [#1558, #1605]
  * Added a GriddedPSFModel fill_value attribute. [#1583]
  * Added a grid_from_epsfs function to make a GriddedPSFModel from
    ePSFs. [#1596]
  * Added a read method to GriddedPSFModel for reading “STDPSF”
    FITS files containing grids of ePSF models. [#1557]
  * Added a plot_grid method to GriddedPSFModel for plotting ePSF
    grids. [#1557]
  * Added a STDPSFGrid class for reading “STDPSF” FITS files
    containing grids of ePSF models and plotting the ePSF grids.
    [#1557]
  ## Bug Fixes
  ### photutils.aperture
  * Fixed a bug in the validation of PixelAperture positions.
    [#1553]
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 1087845 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 20)
- Update to 1.8.0
  ## New Features
  ### photutils.profiles
  * The RadialProfile and CurveOfGrowth radial bins can now be
    directly input, which also allows for non-uniform radial
    spacing. [#1540]
  ## Bug Fixes
  ### photutils.psf
  * Fixed an issue with the local model cache in GriddedPSFModel,
    significantly improving performance. [#1536]
  ## API Changes
  * Removed the deprecated axes keyword in favor of ax for
    consistency with other packages. [#1523]
  ## photutils.aperture
  * Removed the ApertureStats unpack_nddata method. [#1537]
  ## photutils.profiles
  * The API for defining the radial bins for the RadialProfile and
    CurveOfGrowth classes was changed. While the new API allows for
    more flexibility, unfortunately, it is not
    backwards-compatible. [#1540]
  ## photutils.segmentation
  * Removed the deprecated kernel keyword from detect_sources and
    deblend_sources. [#1524]
  * Deprecated the kernel keyword in SourceCatalog. [#1525]
  * Removed the deprecated outline_segments method from
    SegmentationImage. [#1526]
  * The SourceCatalog kron_params attribute is no longer returned
    as a ndarray. It is returned as a tuple. [#1531] (forwarded request 1087844 from bnavigator)
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 1044300 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 18)
- Update to 1.6.0
  ## General
  * Following NEP 29, the minimum required Numpy is now 1.20.
    [#1442]
  * The minimum required Matplotlib is now 3.3.0. [#1442]
  * The minimum required scikit-image is now 0.18.0. [#1442]
  * The minimum required scikit-learn is now 1.0. [#1442]
  ## New Features
  ### photutils.aperture
  * The ApertureStats class now accepts astropy NDData objects as
    input. [#1409]
  * Improved the performance of aperture photometry by 10-25%
    (depending on the number of aperture positions). [#1438]
  ### photutils.psf
  * Added a progress bar for fitting PSF photometry [#1426]
  * Added a subshape keyword to the PSF-fitting classes to define
    the shape over which the PSF is subtracted. [#1477]
  ### photutils.segmentation
  * Added the ability to slice SegmentationImage objects. [#1413]
  * Added mode and fill_value keywords to SourceCatalog
    make_cutouts method. [#1420]
  * Added segment_area source property and wcs, localbkg_width,
    apermask_method, and kron_params attributes to SourceCatalog.
    [#1425]
  * Added the ability to use Quantity arrays with detect_threshold,
    detect_sources, deblend_sources, and SourceFinder. [#1436]
  * The progress bar used when deblending sources now is prepended
    with “Deblending”. [#1439]
  * Added “windowed” centroids to SourceCatalog. [#1447, #1468]
  * Added quadratic centroids to SourceCatalog. [#1467, #1469] (forwarded request 1044299 from bnavigator)
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 992078 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 17)
- Update to 1.5.0
  General
  * Added tqdm as an optional dependency. [#1364]
  New Features
  * photutils.psf
    - Added a mask keyword when calling the PSF-fitting classes.
      [#1350, #1351]
    - The EPSFBuilder progress bar will use tqdm if the optional
      package is installed. [#1367]
  * photutils.segmentation
    - Added SourceFinder class, which is a convenience class
      combining detect_sources and deblend_sources. [#1344]
    - Added a sigma_clip keyword to detect_threshold. [#1354]
    - Added a make_source_mask method to SegmentationImage. [#1355]
    - Added a make_2dgaussian_kernel convenience function. [#1356]
    - Allow SegmentationImage.make_cmap background_color to be in
      any matplotlib color format. [#1361]
    - Added an imshow convenience method to SegmentationImage.
      [#1362]
    - Improved performance of deblend_sources. [#1364]
    - Added a progress_bar keyword to deblend_sources. [#1364]
    - Added a 'sinh' mode to deblend_sources. [#1368]
    - Improved the resetting of cached SegmentationImage properties
      so that custom (non-cached) attributes can be kept. [#1368]
    - Added a nproc keyword to enable multiprocessing in
      deblend_sources and SourceFinder. [#1372]
    - Added a make_cutouts method to SourceCatalog for making
      custom-shaped cutout images. [#1376]
    - Added the ability to set a minimum unscaled Kron radius in
      SourceCatalog. [#1381]
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 965460 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 16)
- Update to 1.4.0 
  New Features
  * photutils.aperture
    * Added a copy method to Aperture objects. [#1304]
    * Added the ability to compare Aperture objects for equality.
      [#1304]
    * The theta keyword for EllipticalAperture, EllipticalAnnulus,
      RectangularAperture, and RectangularEllipse can now be an
      Astropy Angle or Quantity in angular units. [#1308]
    * Added an ApertureStats class for computing statistics of
      unmasked pixels within an aperture. [#1309, #1314, #1315,
      #1318]
    * Added a dtype keyword to the ApertureMask to_image method.
      [#1320]
  * photutils.background
    * Added an alpha keyword to the Background2D.plot_meshes
      method. [#1286]
    * Added a clip keyword to the BkgZoomInterpolator class.
      [#1324]
  * photutils.segmentation
    * Added SegmentationImage cmap attribute containing a default
      colormap. [#1319]
    * Improved the performance of SegmentationImage and
      SourceCatalog, especially for large data arrays. [#1320]
    * Added a convolved_data keyword to SourceCatalog. This is
      recommended instead of using the kernel keyword. [#1321]
  Bug Fixes
  * photutils.aperture
    * Fixed a bug in aperture_photometry where an error was not
      raised if the data and error arrays have different units.
      [#1285].
  * photutils.background
    * Fixed a bug in Background2D where using the pad edge method
      would result in incorrect image padding if only one of the
      axes needed padding. [#1292]
  * photutils.centroid
    * Fixed a bug in centroid_sources where setting error, xpeak,
      or ypeak to None would result in an error. [#1297]
    * Fixed a bug in centroid_quadratic where inputting a mask
      would alter the input data array. [#1317]
  * photutils.segmentation
    * Fixed a bug in SourceCatalog where a UFuncTypeError would be
      raised if the input data had an integer dtype [#1312].
  API Changes
  * photutils.aperture
    * A ValueError is now raised if non-positive sizes are input to
      sky-based apertures. [#1295]
    * The BoundingBox.plot() method now returns a
      matplotlib.patches.Patch object. [#1305]
    * Inputting PixelAperture positions as an Astropy Quantity in
      pixel units is deprecated. [#1310]
    * Inputting SkyAperture shape parameters as an Astropy Quantity
      in pixel units is deprecated. [#1310]
  * photutils.background
    * Removed the deprecated background_mesh_ma and
      background_rms_mesh_ma Background2D properties. [#1280]
    * By default, BkgZoomInterpolator uses clip=True to prevent the
      interpolation from producing values outside the given input
      range. If backwards-compatiblity is needed with older
      Photutils versions, set clip=False. [#1324]
  * photutils.centroid
    * Removed the deprecated centroid_epsf and gaussian1d_moments
      functions. [#1280]
    * Importing tools from the centroids subpackage now requires
      including the subpackage name. [#1280]
  * photutils.morphology
    * Importing tools from the morphology subpackage now requires
      including the subpackage name. [#1280]
  * photutils.segmentation
    * Removed the deprecated source_properties function and the
      SourceProperties and LegacySourceCatalog classes. [#1280]
    * Removed the deprecated the filter_kernel keyword in the
      detect_sources, deblend_sources, and make_source_mask
      functions. [#1280]
    * A TypeError is raised if the input array to SegmentationImage
      does not have integer type. [#1319]
    * A SegmentationImage may contain an array of all zeros.
      [#1319]
    * Deprecated the mask_value keyword in detect_threshold. Use
      the mask keyword instead. [#1322]
    * Deprecated the filter_fwhm and filter_size keywords in
      make_source_mask. Use the kernel keyword instead. [#1322]
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 942354 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 15)
- Update to 1.3.0
  General
  * The metadata in output tables now contains version information
    for all dependencies. [#1274]
  New Features
  * photutils.centroid
    * Extra keyword arguments can be input to centroid_sources that
      are then passed on to the centroid_func if supported.
      [#1276,#1278]
  * photutils.segmentation
    * Added copy method to SourceCatalog. [#1264]
    * Added kron_photometry method to SourceCatalog. [#1264]
    * Added add_extra_property, remove_extra_property,
      remove_extra_properties, and rename_extra_property methods
      and extra_properties attribute to SourceCatalog. [#1264,
      #1268]
    * Added name and overwrite keywords to SourceCatalog
      circular_photometry and fluxfrac_radius methods. [#1264]
    * SourceCatalog fluxfrac_radius was improved for cases where
      the source flux doesn't monotonically increase with
      increasing radius. [#1264]
    * Added meta and properties attributes to SourceCatalog.
      [#1268]
    * The SourceCatalog output table (using to_table) meta
      dictionary now includes a field for the date/time. [#1268]
    * Added SourceCatalog make_kron_apertures method. [#1268]
    * Added SourceCatalog plot_circular_apertures and
      plot_kron_apertures methods. [#1268]
  Bug fixes
  * photutils.segmentation
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 837400 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 10)
- Update to Version 1.0.1
  Bug Fixes
  * photutils.psf
    Fixed checks on oversampling factors. [#1086]
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 836282 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 9)
- Update to Version 1.0.0
  General
  * The minimum required python version is 3.6. [#952]
  * The minimum required astropy version is 4.0. [#1081]
  * The minimum required numpy version is 1.17. [#1079]
  * Removed astropy-helpers and updated the package 
    infrastructure as described in Astropy APE 17. [#915]
  New Features
  * photutils.aperture
  * Added b_in as an optional ellipse annulus keyword. [#1070]
  * Added h_in as an optional rectangle annulus keyword. 
    [#1070]
  * photutils.background
  * Added coverage_mask and fill_value keyword options to 
    Background2D. [#1061]
  * photutils.centroids
  * Added quadratic centroid estimator function 
    (centroid_quadratic). [#1067]
  * photutils.psf
  * Added the ability to use odd oversampling factors in 
    EPSFBuilder. [#1076]
  * photutils.segmentation
  * Added Kron radius, flux, flux error, and aperture to 
    SourceProperties. [#1068]
  * Added local background to SourceProperties. [#1075]
  Bug Fixes
  * photutils.isophote
  * Fixed a typo in the calculation of the b4 higher-order 
    harmonic coefficient in build_ellipse_model. [#1052]
  * Fixed a bug where build_ellipse_model falls into an 
    infinite loop when the pixel to fit is outside of the 
    image. [#1039]
  * Fixed a bug where build_ellipse_model falls into an 
    infinite loop under certain image/parameters input 
    combinations. [#1056]
  * photutils.psf
  * Fixed a bug in subtract_psf caused by using a fill_value of 
    np.nan with an integer input array. [#1062]
  * photutils.segmentation
  * Fixed a bug where source_properties would fail with 
    unitless gwcs.wcs.WCS objects. [#1020]
  * photutils.utils
  * The effective_gain parameter in calc_total_error can now be 
    zero (or contain zero values). [#1019]
  API changes
  * photutils.aperture
  * Aperture pixel positions can no longer be shaped as 2xN. 
    [#953]
  * Removed the deprecated units keyword in aperture_photometry 
    and PixelAperture.do_photometry. [#953]
  * PrimaryHDU, ImageHDU, and HDUList can no longer be input to 
    aperture_photometry. [#953]
  * Removed the deprecated the Aperture mask_area method. 
    [#953]
  * Removed the deprecated Aperture plot keywords ax and 
    indices. [#953]
  * photutils.background
  * Removed the deprecated ax keyword in 
    Background2D.plot_meshes. [#953]
  * Background2D keyword options can not be input as positional 
    arguments. [#1061]
  * photutils.centroids
  * centroid_1dg, centroid_2dg, gaussian1d_moments, 
    fit_2dgaussian, and GaussianConst2D have been moved to a 
    new photutils.centroids.gaussian module. [#1064]
  * Deprecated fit_2dgaussian and GaussianConst2D. [#1064]
  * photutils.datasets
  * Removed the deprecated type keyword in make_noise_image. 
    [#953]
  * Renamed the random_state keyword (deprecated) to seed in 
    apply_poisson_noise, make_noise_image, 
    make_random_models_table, and make_random_gaussians_table 
    functions. [#1080]
  * photutils.detection
  * Removed the deprecated snr keyword in detect_threshold. 
    [#953]
  * photutils.psf
  * Added flux_residual_sigclip as an input parameter, allowing 
    for custom sigma clipping options in EPSFBuilder. [#984]
  * Added extra_output_cols as a parameter to 
    BasicPSFPhotometry, IterativelySubtractedPSFPhotometry and 
    DAOPhotPSFPhotometry. [#745]
  * photutils.segmentation
  * Removed the deprecated SegmentationImage methods cmap and 
    relabel. [#953]
  * Removed the deprecated SourceProperties values and coords 
    attributes. [#953]
  * Removed the deprecated xmin/ymin and xmax/ymax properties. 
    [#953]
  * Removed the deprecated snr and mask_value keywords in 
    make_source_mask. [#953]
  * Renamed the random_state keyword (deprecated) to seed in 
    the make_cmap method. [#1080]
  * photutils.utils
  * Removed the deprecated random_cmap, mask_to_mirrored_num, 
    get_version_info, filter_data, and std_blocksum functions. 
    [#953]
  * Removed the deprecated wcs_helpers functions 
    pixel_scale_angle_at_skycoord, assert_angle_or_pixel, 
    assert_angle, and pixel_to_icrs_coords. [#953]
  * Deprecated the check_random_state function. [#1080]
  * Renamed the random_state keyword (deprecated) to seed in 
    the make_random_cmap function. [#1080] 
- Drop patches merged upstream
  * 0001-aperture-mask-test-assert-almost-equal.patch
  * photutils-pr1041-update-watershed-import.patch
  
Dominique Leuenberger's avatar Dominique Leuenberger (dimstar_suse) accepted request 826649 from Benjamin Greiner's avatar Benjamin Greiner (bnavigator) (revision 8)
- add photutils-pr1041-update-watershed-import.patch to fix failing
  test gh#astropy/photutils#1041
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