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File python-photutils.changes of Package python-photutils
------------------------------------------------------------------- Sun Feb 18 15:10:59 UTC 2024 - Ben Greiner <code@bnavigator.de> - 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 ### photutils.aperture * PixelAperture instances now raise an informative error message when positions is input as a zip object containing Astropy Quantity objects. [#1682] ### photutils.psf * The GridddedPSFModel string representations now include the model flux, x_0, and y_0 parameters. [#1680] * The PSF photometry make_model_image and make_residual_image methods no longer include the local background by default. This is a backwards-incompatible change. If the previous behavior is desired, set include_localbkg=True. [#1703] * The PSF photometry finder_results attribute is now returned as a QTable instead of a list of QTable. [#1704] * Deprecated the NonNormalizable custom warning class in favor of AstropyUserWarning. [#1710] ### photutils.segmentation * The SourceCatalog get_label and get_labels methods now raise a ValueError if any of the input labels are invalid. [#1694] ------------------------------------------------------------------- Fri Nov 24 12:38:58 UTC 2023 - Ben Greiner <code@bnavigator.de> - 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] * Added a scale keyword to the SegmentationImage.to_patches() method to scale the sizes of the polygon patches. [#1641, #1646] * Improved the SegmentationImage imshow method to ensure that labels are plotted with unique colors. [#1649] * Added a imshow_map method to SegmentationImage for plotting segmentation images with a small number of non-consecutive labels. [#1649] * Added a reset_cmap method to SegmentationImage for resetting the colormap to a new random colormap. [#1649] ### photutils.utils * Improved the generation of random aperture positions in ImageDepth. [#1666] ## Bug Fixes ### photutils.aperture * Fixed an issue where the aperture plot method **kwargs were not reset to the default values when called multiple times. [#1655] ### photutils.psf * Fixed a bug where SourceGrouper would fail if only one source was input. [#1617] * Fixed a bug in GriddedPSFModel plot_grid where the grid could be plotted incorrectly if the input xygrid was not sorted in y then x order. [#1661] ### photutils.segmentation * Fixed an issue where deblend_sources and SourceFinder would raise an error if the contrast keyword was set to 1 (meaning no deblending). [#1636] * Fixed an issue where the vertices of the SegmentationImage polygons were shifted by 0.5 pixels in both x and y. [#1646] * API Changes * The metadata in output tables now contains a timestamp. [#1640] * Package versions in table metadata are now stored in the “versions” key. [#1640] * The order of the metadata in a table is now preserved when writing to a file. [#1640] ### photutils.psf * Deprecated the prepare_psf_model function. Use the new make_psf_model function instead. [#1658] * The GriddedPSFModel now stores the ePSF grid such that it is first sorted by y then by x. As a result, the order of the data and xygrid attributes may be different. [#1661] * The oversampling attribute is now stored as a 1D numpy.ndarray with two elements. [#1664] * A ValueError is raised if GriddedPSFModel is called with x and y arrays that have more than 2 dimensions. [#1662] ### photutils.segmentation * Removed the deprecated kernel keyword from SourceCatalog. [#1613] ------------------------------------------------------------------- Fri Aug 25 14:57:13 UTC 2023 - Ben Greiner <code@bnavigator.de> - 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] ## API Changes ### photutils.psf * Deprecated the PSF photometry classes BasicPSFPhotometry, IterativelySubtractedPSFPhotometry, and DAOPhotPSFPhotometry. Use the new PSFPhotometry or IterativePSFPhotometry class instead. [#1578] * Deprecated the DAOGroup, DBSCANGroup, and GroupStarsBase classes. Use the new SourceGrouper class instead. [#1578] * Deprecated the get_grouped_psf_model and subtract_psf function. [#1578] ------------------------------------------------------------------- Thu May 18 18:27:21 UTC 2023 - Ben Greiner <code@bnavigator.de> - 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] ------------------------------------------------------------------- Wed Apr 26 10:01:15 UTC 2023 - Ben Greiner <code@bnavigator.de> - Update to 1.7.0 ## General * The rasterio and shapely packages are now optional dependencies. [#1509] ## New Features ### photutils.aperture * Significantly improved the performance of aperture_photometry and the PixelAperture do_photometry method for large arrays. [#1485] * Significantly improved the performance of the PixelAperture area_overlap method, especially for large arrays. [#1490] ### photutils.profiles * Added a new profiles subpackage containing RadialProfile and CurveOfGrowth classes. [#1494, #1496, #1498, #1499] ### photutils.psf * Significantly improved the performance of evaluating and fitting GriddedPSFModel instances. [#1503] ### photutils.segmentation * Added a size keyword to the SegmentationImage make_source_mask method. [#1506] * Significantly improved the performance of SegmentationImage make_source_mask when using square footprints for source dilation. [#1506] * Added the polygons property and to_patches and plot_patches methods to SegmentationImage. [#1509] * Added polygon keyword to the Segment class. [#1509] ## Bug Fixes ### photutils.centroids * Fixed an issue where centroid_quadratic would sometimes fail if the input data contained NaNs. [#1495] ### photutils.detection * Fixed an issue with the starfinders (DAOStarFinder, IRAFStarFinder, and StarFinder) where an exception was raised if exclude_border=True and there were no detections. [#1512]. ### photutils.isophote * Fixed a bug where the upper harmonics (a3, a4, b3, and b4) had the incorrect sign. [#1501] * Fixed a bug in the calculation of the upper harmonic errors (a3_err, a4_err, b3_err, and b4_err). [#1501]. ### photutils.psf * Fixed an issue where the PSF-photometry progress bar was not shown. [#1517] * Fixed an issue where all PSF uncertainties were excluded if the last star group had no covariance matrix. [#1519] ### photutils.utils * Fixed a bug in the calculation of ImageCutout xyorigin when using the 'partial' mode when the cutout extended beyond the right or top edge. [#1508] ## API Changes ### photutils.aperture * The ApertureStats local_bkg keyword can now be broadcast for apertures with multiple positions. [#1504] ### photutils.centroids * The centroid_sources function will now raise an error if the cutout mask contains all True values. [#1516] ### photutils.datasets * Removed the deprecated load_fermi_image function. [#1479] ### photutils.psf * Removed the deprecated sandbox classes DiscretePRF and Reproject. [#1479] ### photutils.segmentation * Removed the deprecated make_source_mask function in favor of the SegmentationImage.make_source_mask method. [#1479] * The SegmentationImage imshow method now uses "nearest" interpolation instead of "none" to avoid rendering issues with some backends. [#1507] * The repr() notebook output for the Segment class now includes a SVG polygon representation of the segment if the rasterio and shapely packages are installed. [#1509] * Deprecated the SegmentationImage outline_segments method. Use the plot_patches method instead. [#1509] - Drop photutils-pr1484-no-setuptools.patch ------------------------------------------------------------------- Thu Dec 22 15:05:47 UTC 2022 - Ben Greiner <code@bnavigator.de> - 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] * Added a progress_bar option to SourceCatalog for displaying progress bars when calculating some source properties. [#1471] ### photutils.utils * Added xyorigin attribute to CutoutImage. [#1419] * Added ImageDepth class. [#1434] ## Bug Fixes ### photutils.aperture * Fixed a bug in the PixelAperture area_overlap method so that the returned value does not inherit the data units. [#1408] * Fixed an issue in ApertureStats get_ids for the case when the ID numbers are not sorted (due to slicing). [#1423] ### photutils.datasets * Fixed a bug in the various load functions where FITS files were not closed. [#1455] ### photutils.segmentation * Fixed an issue in the SourceCatalog kron_photometry, make_kron_apertures, and plot_kron_apertures methods where the input minimum Kron and circular radii would not be applied. Instead the instance-level minima would always be used. [#1421] * Fixed an issue where the SourceCatalog plot_kron_apertures method would raise an error for a scalar SourceCatalog. [#1421] * Fixed an issue in SourceCatalog get_labels for the case when the labels are not sorted (due to slicing). [#1423] ## API Changes * Deprecated axes keyword in favor of ax for consistency with other packages. [#1432] * Importing tools from all subpackages now requires including the subpackage name. ### photutils.aperture * Inputting PixelAperture positions as an Astropy Quantity in pixel units is no longer allowed. [#1398] * Inputting SkyAperture shape parameters as an Astropy Quantity in pixel units is no longer allowed. [#1398] * Removed the deprecated BoundingBox as_patch method. [#1462] ### photutils.centroids * Removed the deprecated oversampling keyword in centroid_com. [#1398] ### photutils.datasets * Deprecated the load_fermi_image function. [#1455] ### photutils.psf * Removed the deprecated flux_residual_sigclip keyword in EPSFBuilder. Use sigma_clip instead. [#1398] * PSF photometry classes will no longer emit a RuntimeWarning if the fitted parameter variance is negative. [#1458] ### photutils.segmentation * Removed the deprecated sigclip_sigma and sigclip_iters keywords in detect_threshold. Use the sigma_clip keyword instead. [#1398] * Removed the mask_value, sigclip_sigma, and sigclip_iters keywords in detect_threshold. Use the mask or sigma_clip keywords instead. [#1398] * Removed the deprecated the filter_fwhm and filter_size keywords in make_source_mask. Use the kernel keyword instead. [#1398] * If detection_cat is input to SourceCatalog, then the detection catalog source centroids and morphological/shape properties will be returned instead of calculating them from the input data. Also, if detection_cat is input, then the input wcs, apermask_method, and kron_params keywords will be ignored. [#1425] - Add photutils-pr1484-no-setuptools.patch gh#astropy/photutils#1484 ------------------------------------------------------------------- Mon Aug 1 17:22:10 UTC 2022 - Ben Greiner <code@bnavigator.de> - 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] * photutils.utils - Added a circular_footprint convenience function. [#1355] - Added a CutoutImage class. [#1376] Bug Fixes * photutils.psf - Fixed a warning message in EPSFFitter. [#1382] * photutils.segmentation - Fixed an issue in generating watershed markers used for source deblending. [#1383] API Changes * photutils.centroids - Changed the axes order of oversampling keyword in centroid_com when input as a tuple. [#1358] - Deprecated the oversampling keyword in centroid_com. [#1377] * photutils.psf - Invalid data values (i.e., NaN or inf) are now automatically masked when performing PSF fitting. [#1350] - Deprecated the sandbox classes DiscretePRF and Reproject. [#1357] - Changed the axes order of oversampling keywords when input as a tuple. [#1358] - Removed the unused shift_val keyword in EPSFBuilder and EPSFModel. [#1377] - Renamed the flux_residual_sigclip keyword (now deprecated) to sigma_clip in EPSFBuilder. [#1378] - The EPSFBuilder progress bar now requires that the optional tqdm package be installed. [#1379] - The tools in the PSF package now require keyword-only arguments. [#1386] * photutils.segmentation - Removed the deprecated circular_aperture method from SourceCatalog. [#1329] - The SourceCatalog plot_kron_apertures method now sets a default kron_apers value. [#1346] - deblend_sources no longer allows an array to be input as a segmentation image. It must be a SegmentationImage object. [#1347] - SegmentationImage no longer allows array-like input. It must be a numpy ndarray. [#1347] - Deprecated the sigclip_sigma and sigclip_iters keywords in detect_threshold. Use the sigma_clip keyword instead. [#1354] - Deprecated the make_source_mask function in favor of the SegmentationImage.make_source_mask method. [#1355] - Deprecated the kernel keyword in detect_sources and deblend_sources. Instead, if filtering is desired, input a convolved image directly into the data parameter. [#1365] - Sources with a data minimum of zero are now treated the same as negative minima (i.e., the mode is changed to “linear”) for the “exponential” deblending mode. [#1368] - A single warning (as opposed to 1 per source) is now raised about negative/zero minimum data values using the ‘exponential’ deblending mode. The affected labels is available in a new “info” attribute. [#1368] - If the mode in deblend_sources is “exponential” or “sinh” and there are too many potential deblended sources within a given source (watershed markers), a warning will be raised and the mode will be changed to “linear”. [#1369] - The SourceCatalog make_circular_apertures and make_kron_apertures methods now return a single aperture (instead of a list with one item) for a scalar SourceCatalog. [#1376] - The SourceCatalog kron_params keyword now has an optional third item representing the minimum circular radius. [#1381] - The SourceCatalog kron_radius is now set to the minimum Kron radius (the second element of kron_params) if the data or radially weighted data sum to zero. [#1381] * photutils.utils - The colormap returned from make_random_cmap now has colors in RGBA format. [#1361] ------------------------------------------------------------------- Mon Mar 28 17:36:19 UTC 2022 - Ben Greiner <code@bnavigator.de> - 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] ------------------------------------------------------------------- Fri Dec 24 14:06:32 UTC 2021 - Ben Greiner <code@bnavigator.de> - 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 * If detection_catalog is input to SourceCatalog then the detection centroids are used to calculate the circular_aperture, circular_photometry, and fluxfrac_radius. [#1264] * Units are applied to SourceCatalog circular_photometry output if the input data has units. [#1264] * SourceCatalog circular_photometry returns scalar values if catalog is scalar. [#1264] * SourceCatalog fluxfrac_radius returns a Quantity with pixel units. [#1264] * Fixed a bug where the SourceCatalog detection_catalog was not indexed/sliced when SourceCatalog was indexed/sliced. [#1268] * SourceCatalog circular_photometry now returns NaN for completely-masked sources. [#1268] * SourceCatalog kron_flux is always NaN for sources where kron_radius is NaN. [#1268] * SourceCatalog fluxfrac_radius now returns NaN if kron_flux is zero. [#1268] API changes * photutils.centroids * A ValueError is now raised in centroid_sources if the input xpos or ypos is outside of the input data. [#1276] * A ValueError is now raised in centroid_quadratic if the input xpeak or ypeak is outside of the input data. [#1276] * NaNs are now returned from centroid_sources where the centroid failed. This is usually due to a box_size that is too small when using a fitting-based centroid function. [#1276] * photutils.segmentation * Renamed the SourceCatalog circular_aperture method to make_circular_apertures. The old name is deprecated. [#1268] * The SourceCatalog kron_params keyword must have a minimum circular radius that is greater than zero. The default value is now 1.0. [#1268] * detect_sources now uses astropy.convolution.convolve, which allows for masking pixels. [#1269] ------------------------------------------------------------------- Sun Sep 26 14:11:48 UTC 2021 - Ben Greiner <code@bnavigator.de> - Update to 1.2.0 * The minimum required scipy version is 1.6.0 [#1239] photutils.aperture * Added a mask keyword to the area_overlap method. [#1241] photutils.background * Improved the performance of Background2D by up to 10-50% when the optional bottleneck package is installed. [#1232] * Added a masked keyword to the background classes MeanBackground, MedianBackground, ModeEstimatorBackground, MMMBackground, SExtractorBackground, BiweightLocationBackground, StdBackgroundRMS, MADStdBackgroundRMS, and BiweightScaleBackgroundRMS. [#1232] * Enable all background classes to work with Quantity inputs. [#1233] * Added a markersize keyword to the Background2D method plot_meshes. [#1234] * Added __repr__ methods to all background classes. [#1236] * Added a grid_mode keyword to BkgZoomInterpolator. [#1239] photutils.detection * Added a xycoords keyword to DAOStarFinder and IRAFStarFinder. [#1248] photutils.psf * Enabled the reuse of an output table from BasicPSFPhotometry and its subclasses as an initial guess for another photometry run. [#1251] * Added the ability to skip the group_maker step by inputing an initial guess table with a group_id column. [#1251] photutils.aperture * Fixed a bug when converting between pixel and sky apertures with a gwcs object. [#1221] photutils.background * Fixed an issue where Background2D could fail when using the 'pad' edge method. [#1227] photutils.detection * Fixed the DAOStarFinder import deprecation message. [#1195] photutils.morphology * Fixed an issue in data_properties where a scalar background input would raise an error. [#1198] photutils.psf * Fixed an issue in prepare_psf_model when xname or yname was None where the model offsets were applied in the wrong direction, resulting in the initial photometry guesses not being improved by the fit. [#1199] photutils.segmentation * Fixed an issue in SourceCatalog where the user-input mask was ignored when apermask_method='correct' for Kron-related calculations. [#1210] * Fixed an issue in SourceCatalog where the segment array could incorrectly have units. [#1220] photutils.utils * Fixed an issue in ShepardIDWInterpolator to allow its initialization with scalar data values and coordinate arrays having more than one dimension. [#1226] API changes photutils.aperture * The ApertureMask.get_values() function now returns an empty array if there is no overlap with the data. [#1212] * Removed the deprecated BoundingBox.slices and PixelAperture. bounding_boxes attributes. [#1215] photutils.background * Invalid data values (i.e., NaN or inf) are now automatically masked in Background2D. [#1232] * The background classes MeanBackground, MedianBackground, ModeEstimatorBackground, MMMBackground, SExtractorBackground, BiweightLocationBackground, StdBackgroundRMS, MADStdBackgroundRMS, and BiweightScaleBackgroundRMS now return by default a numpy.ndarray with np.nan values representing masked pixels instead of a masked array. A masked array can be returned by setting masked=True. [#1232] * Deprecated the Background2D attributes background_mesh_ma and background_rms_mesh_ma. They have been renamed to background_mesh_masked and background_rms_mesh_masked. [#1232] * By default, BkgZoomInterpolator now uses grid_mode=True. For zooming 2D images, this keyword should be set to True, which makes the interpolator’s behavior consistent with scipy. ndimage.map_coordinates, skimage.transform.resize, and OpenCV (cv2.resize). If backwards-compatiblity is needed with older Photutils’ versions, set grid_mode=False. [#1239] photutils.centroid * Deprecated the gaussian1d_moments and centroid_epsf functions. [#1240] photutils.datasets * Removed the deprecated random_state keyword in the apply_poisson_noise, make_noise_image, make_random_models_table, and make_random_gaussians_table functions. [#1244] * make_random_models_table and make_random_gaussians_table now return an astropy QTable with version metadata. [#1247] photutils.detection * DAOStarFinder, IRAFStarFinder, and find_peaks now return an astropy QTable with version metadata. [#1247] * The StarFinder label column was renamed to id for consistency with the other star finder classes. [#1254] photutils.isophote * The Isophote to_table method nows return an astropy QTable with version metadata. [#1247] photutils.psf * BasicPSFPhotometry, IterativelySubtractedPSFPhotometry, and DAOPhotPSFPhotometry now return an astropy QTable with version metadata. [#1247] photutils.segmentation * Deprecated the filter_kernel keyword in the detect_sources, deblend_sources, and make_source_mask functions. It has been renamed to simply kernel for consistency with SourceCatalog. [#1242] * Removed the deprecated random_state keyword in the make_cmap method. [#1244] * The SourceCatalog to_table method nows return an astropy QTable with version metadata. [#1247] photutils.utils * Removed the deprecated check_random_state function. [#1244] * Removed the deprecated random_state keyword in the make_random_cmap function. [#1244] ------------------------------------------------------------------- Sat Mar 20 18:02:02 UTC 2021 - Ben Greiner <code@bnavigator.de> - Update ot Version 1.1.0 General ------- * The minimum required python version is 3.7. [#1120] New Features ------------ photutils.aperture * The PixelAperture.plot() method now returns a list of matplotlib.patches.Patch objects. [#923] * Added an area_overlap method for PixelAperture objects that gives the overlapping area of the aperture on the data. [#874] * Added a get_overlap_slices method and a center attribute to BoundingBox. [#1157] * Added a get_values method to ApertureMask that returns a 1D array of mask-weighted values. [#1158, #1161] * Added get_overlap_slices method to ApertureMask. [#1165] photutils.background * The Background2D class now accepts astropy NDData, CCDData, and Quantity objects as data inputs. [#1140] photutils.detection * Added a StarFinder class to detect stars with a user-defined kernel. [#1182] photutils.isophote * Added the ability to specify the output columns in the IsophoteList to_table method. [#1117] photutils.psf * The EPSFStars class is now usable with multiprocessing. [#1152] * Slicing EPSFStars now returns an EPSFStars instance. [#1185] photutils.segmentation * Added a modified, significantly faster, SourceCatalog class. [#1170, #1188, #1191] * Added circular_aperture and circular_phometry methods to the SourceCatalog class. [#1188] * Added fwhm property to the SourceCatalog class. [#1191] * Added fluxfrac_radius method to the SourceCatalog class. [#1192] * Added a bbox attribute to SegmentationImage. [#1187] Bug Fixes --------- photutils.aperture * Slicing a scalar Aperture object now raises an informative error message. [#1154] * Fixed an issue where ApertureMask.multiply fill_value was not applied to pixels outside of the aperture mask, but within the aperture bounding box. [#1158] * Fixed an issue where ApertureMask.cutout would raise an error if fill_value was non-finite and the input array was integer type. [#1158] * Fixed an issue where RectangularAnnulus with a non-default h_in would give an incorrect ApertureMask. [#1160] photutils.isophote * Fix computation of gradient relative error when gradient=0. [#1180] photutils.psf * Fixed a bug in EPSFBuild where a warning was raised if the input smoothing_kernel was an numpy.ndarray. [#1146] * Fixed a bug that caused photometry to fail on an EPSFmodel with multiple stars in a group. [#1135] * Added a fallback aperture_radius for PSF models without a FWHM or sigma attribute, raising a warning. [#740] photutils.segmentation * Fixed SourceProperties local_background to work with Quantity data inputs. [#1162] * Fixed SourceProperties local_background for sources near the image edges. [#1162] * Fixed SourceProperties kron_radius for sources that are completely masked. [#1164] * Fixed SourceProperties Kron properties for sources near the image edges. [#1167] * Fixed SourceProperties Kron mask correction. [#1167] API changes ----------- photutils.aperture * Deprecated the BoundingBox slices attribute. Use the get_overlap_slices method instead. [#1157] photutils.centroid * Removed the deprecated fit_2dgaussian function and GaussianConst2D class. [#1147] * Importing tools from the centroids subpackge without including the subpackage name is deprecated. [#1190] photutils.morphology * Importing tools from the morphology subpackge without including the subpackage name is deprecated. [#1190] photutils.segmentation * Deprecated the "mask_all" option in the SourceProperties kron_params keyword. [#1167] * Deprecated source_properties, SourceProperties, and LegacySourceCatalog. Use the new SourceCatalog function instead. [#1170] * The detect_threshold function was moved to the segmentation subpackage. [#1171] * Removed the ability to slice SegmentationImage. Instead slice the segments attribute. [#1187] ------------------------------------------------------------------- Wed Jan 20 23:50:38 UTC 2021 - Benjamin Greiner <code@bnavigator.de> - Update to Version 1.0.2 General ------ photutils.background * Improved the performance of Background2D (e.g., by a factor of ~4 with 2048x2048 input arrays when using the default interpolator). [#1103, #1108] Bug Fixes -------- photutils.background * Fixed a bug with Background2D where using BkgIDWInterpolator would give incorrect results. [#1104] photutils.isophote * Corrected calculations of upper harmonics and their errors [#1089] * Fixed bug that caused an infinite loop when the sample extracted from an image has zero length. [#1129] * Fixed a bug where the default fixed_parameters in EllipseSample.update() were not defined. [#1139] photutils.psf * Fixed a bug where very incorrect PSF-fitting uncertainties could be returned when the astropy fitter did not return fit uncertainties. [#1143] photutils.segmentation * Fixed an issue where negative Kron radius values could be returned, which would cause an error when calculating Kron fluxes. [#1132] * Fixed an issue where an error was raised with SegmentationImage.remove_border_labels() with relabel=True when no segments remain. [#1133] photutils.psf * Changed the default recentering_func in EPSFBuilder, to avoid convergence issues. [#1144] - Drop photutils-ease-background2d-tests.patch fixed upstream gh#astropy/photutils#1145 ------------------------------------------------------------------- Fri Jan 15 14:57:42 UTC 2021 - Benjamin Greiner <code@bnavigator.de> - Add photutils-ease-background2d-tests.patch -- ease precision tolerance in background 2D tests gh#astropy/photutils#1145 ------------------------------------------------------------------- Fri Sep 25 11:41:40 UTC 2020 - Benjamin Greiner <code@bnavigator.de> - Update to Version 1.0.1 Bug Fixes * photutils.psf Fixed checks on oversampling factors. [#1086] ------------------------------------------------------------------- Wed Sep 23 09:24:36 UTC 2020 - Benjamin Greiner <code@bnavigator.de> - 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 ------------------------------------------------------------------- Fri Aug 14 09:13:48 UTC 2020 - Benjamin Greiner <code@bnavigator.de> - add photutils-pr1041-update-watershed-import.patch to fix failing test gh#astropy/photutils#1041 ------------------------------------------------------------------- Fri Jul 17 11:35:55 UTC 2020 - Benjamin Greiner <code@bnavigator.de> - actually detect failures with sys.exit(photutils.test()) ------------------------------------------------------------------- Mon Jul 13 18:40:46 UTC 2020 - Benjamin Greiner <code@bnavigator.de> - fix failing tests: use astropy's test suite logic to call pytest - add URL for 0001-aperture-mask-test-assert-almost-equal.patch gh#astropy/photutils#1014 ------------------------------------------------------------------- Fri Jan 24 17:09:13 UTC 2020 - Benjamin Greiner <code@bnavigator.de> - 0001-aperture-mask-test-assert-almost-equal.patch: upstream PR#1014 to avoid occasionally failing builds ------------------------------------------------------------------- Wed Dec 11 14:44:27 UTC 2019 - Benjamin Greiner <code@bnavigator.de> - update to version 0.7.2: photutils.isophote * Fixed computation of upper harmonics a3, b3, a4, and b4 in the ellipse fitting algorithm. [#1008] photutils.psf * Fix to algorithm in EPSFBuilder, addressing issues where ePSFs failed to build (yielding striped ePSFs). [#974] * Fix to IterativelySubtractedPSFPhotometry where an error could be thrown when a Finder was passed which did not return None if no sources were found. [#986] * Fix to centroid_epsf where the wrong oversampling factor was used along the y axis. [#1002] - needs new python-pytest-astropy 0.7 because of -header package - fix clean c source files ------------------------------------------------------------------- Thu Oct 10 09:48:35 UTC 2019 - Benjamin Greiner <code@bnavigator.de> - update to version 0.7.1 ------------------------------------------------------------------- Sat Sep 14 12:17:38 UTC 2019 - Benjamin Greiner <code@bnavigator.de> - remove generated c source files ------------------------------------------------------------------- Sat Sep 14 09:49:39 UTC 2019 - Benjamin Greiner <code@bnavigator.de> - new version 0.7 ------------------------------------------------------------------- Wed Apr 24 14:34:08 UTC 2019 - Benjamin Greiner <code@bnavigator.de> - add astropy helpers ------------------------------------------------------------------- Wed Apr 24 14:23:15 UTC 2019 - Benjamin Greiner <code@bnavigator.de> - add dmb and scikit-* modules to build deps for module tests ------------------------------------------------------------------- Wed Apr 24 14:13:37 UTC 2019 - Benjamin Greiner <code@bnavigator.de> - add numpy-devel as dep ------------------------------------------------------------------- Wed Apr 24 14:09:05 UTC 2019 - Benjamin Greiner <code@bnavigator.de> - fix deps typos ------------------------------------------------------------------- Wed Apr 24 14:07:25 UTC 2019 - Benjamin Greiner <code@bnavigator.de> - initial spec
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