Photutils

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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]

1.4.0

------------------

General
^^^^^^^

- The minimum required Python is now 3.8. [1279]

- The minimum required Numpy is now 1.18. [1279]

- The minimum required Astropy is now 5.0. [1279]

- The minimum required Matplotlib is now 3.1. [1279]

- The minimum required scikit-image is now 0.15.0 [1279]

- The minimum required gwcs is now 0.16.0 [1279]

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.centroids``

- 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-compatibility is needed with older Photutils
versions, set ``clip=False``. [1324]

- ``photutils.centroids``

- 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]

1.3.0

------------------

General
^^^^^^^

- The metadata in output tables now contains version information for all
dependencies. [1274]

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

- ``photutils.centroids``

- 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]

1.2.0

------------------

General
^^^^^^^

- The minimum required scipy version is 1.6.0 [1239]

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

- ``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]

Bug Fixes
^^^^^^^^^

- ``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-compatibility is needed with
older Photutils versions, set ``grid_mode=False``. [1239]

- ``photutils.centroids``

- 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]

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_photometry`` 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.centroids``

- Removed the deprecated ``fit_2dgaussian`` function and
``GaussianConst2D`` class. [1147]

- Importing tools from the centroids subpackage without including the
subpackage name is deprecated. [1190]

- ``photutils.detection``

- Importing the ``DAOStarFinder``, ``IRAFStarFinder``, and
``StarFinderBase`` classes from the deprecated ``findstars.py``
module is now deprecated. These classes can be imported using ``from
photutils.detection import <class>``. [1173]

- Importing the ``find_peaks`` function from the deprecated
``core.py`` module is now deprecated. This function can be imported
using ``from photutils.detection import find_peaks``. [1173]

- ``photutils.morphology``

- Importing tools from the morphology subpackage 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]

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]

- Changed the default ``recentering_func`` in ``EPSFBuilder``, to
avoid convergence issues. [1144]

- ``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]

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