Revisions of python-photutils

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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