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.. _whatsnew-2.0:

****************************
What's New in Photutils 2.0?
****************************

Photutils 2.0 is a major release that adds significant new functionality
and improvements to the package. Here we highlight some of the new
functionality of the 2.0 release. In addition to these changes,
Photutils 2.0 includes a large number of smaller improvements and bug
fixes, which are described in the full :ref:`changelog`.

.. contents::
   :local:
   :depth: 2


Imports
=======

Importing tools from all subpackages now requires including the
subpackage name. These deprecations were introduced in version 1.6.0
(2022-12-09). Also, PSF matching tools must now be imported from
``photutils.psf.matching`` instead of ``photutils.psf``

For example, this is no longer allowed: ``from photutils import
CircularAperture``. Instead use this: ``from photutils.aperture import
CircularAperture``.


SciPy is now a required dependency
==================================

`SciPy <https://scipy.org/>`_ is now a required dependency for
Photutils, instead of an optional dependency. This change was made
because most of the subpackages in Photutils require SciPy for
functionality.


Aperture photometry tools now accept Region objects
===================================================

The `~photutils.aperture.aperture_photometry` and
`~photutils.aperture.ApertureStats` tools now accept supported
``regions.Region`` objects from the `Astropy regions package
<https://astropy-regions.readthedocs.io/en/latest/>`_, i.e., those
corresponding to circular, elliptical, and rectangular apertures.

A new `~photutils.aperture.region_to_aperture` convenience function
also has been added to convert supported ``regions.Region`` objects to
``Aperture`` objects.

With these changes, the `Astropy regions package
<https://astropy-regions.readthedocs.io/en/latest/>`_ is now an optional
dependency for Photutils. It will need to be installed to use the above
functionality.


Background2D improved performance and changes
=============================================

The `~photutils.background.Background2D` class has been refactored
to significantly reduce its memory usage. In some cases, it is also
significantly faster.

To reduce memory usage, ``Background2D`` no longer keeps a cached copy
of the returned ``background`` and ``background_rms`` properties. Assign
these properties to variables if you need to use them multiple times,
otherwise they will need to be recomputed.

The ``background``, ``background_rms``, ``background_mesh``, and
``background_rms_mesh`` properties now have the same ``dtype`` as the
input data.

Two new properties were also added to the ``Background2D`` class,
``npixels_mesh`` and ``npixels_map``, that give a 2D array of the number
of pixels used to compute the statistics in the low-resolution grid and
the resized image, respectively.

Additionally, the ``background_mesh`` and ``background_rms_mesh``
properties will have units if the input data has units.

As part of these changes, the ``edge_method`` keyword is now
deprecated and will be removed in a future version. When removed, the
``edge_method`` will always be ``'pad'``. The ``'crop'`` option has been
strongly discouraged for some time now. Its usage creates a undesirable
scaling of the low-resolution maps that leads to incorrect results.

The ``background_mesh_masked``, ``background_rms_mesh_masked``, and
``mesh_nmasked`` properties are now deprecated and will be removed in
a future version. The ``data``, ``mask``, ``total_mask``, ``nboxes``,
``box_npixels``, and ``nboxes_tot`` class attributes have been removed.

Finally, the `~photutils.background.BkgZoomInterpolator` ``grid_mode``
keyword is now deprecated. When ``grid_mode`` is eventually removed, the
`True` option will always be used. For zooming 2D images, this keyword
should be set to `True`, which makes zoom's behavior consistent with
`scipy.ndimage.map_coordinates` and `skimage.transform.resize`. The
`False` option was provided only for backwards-compatibility.


GriddedPSFModel improved performance
====================================

The `~photutils.psf.GriddedPSFModel` class has been refactored to
significantly improve its performance. In typical PSF photometry use
cases, it is now about 4 times faster than previous versions.


New PSF Model classes
======================

New models were added to the ``photutils.psf`` module. These include:

- `~photutils.psf.ImagePSF`: a general class for image-based PSF models
  that allows for intensity scaling and translations.

- `~photutils.psf.GaussianPSF`: a general 2D Gaussian PSF model
  parameterized in terms of the position, total flux, and full width
  at half maximum (FWHM) along the x and y axes. Rotation can also be
  included.

- `~photutils.psf.CircularGaussianPSF`: a circular 2D Gaussian PSF model
  parameterized in terms of the position, total flux, and FWHM.

- `~photutils.psf.GaussianPRF`: a general 2D Gaussian PSF model
  parameterized in terms of the position, total flux, and FWHM
  along the x and y axes. Rotation can also be included.

- `~photutils.psf.CircularGaussianPRF`: a circular 2D Gaussian PRF model
  parameterized in terms of the position, total flux, and FWHM.

- `~photutils.psf.CircularGaussianSigmaPRF`: a circular 2D Gaussian PRF
  model parameterized in terms of the position, total flux, and sigma
  (standard deviation).

- `~photutils.psf.MoffatPSF`: a 2D Moffat PSF model parameterized in
  terms of the position, total flux, :math:`\alpha`, and :math:`\beta`
  parameters.

- `~photutils.psf.AiryDiskPSF`: a 2D Airy disk PSF model parameterized
  in terms of the position, total flux, and radius of the first dark
  ring.

Note there are two types of defined models, PSF and PRF models. The PSF
models are evaluated by sampling the analytic function at the input (x,
y) coordinates. The PRF models are evaluated by integrating the analytic
function over the pixel areas.

The existing ``IntegratedGaussianPRF`` model is now deprecated and
will be removed in a future version. It has been replaced by the
`~photutils.psf.CircularGaussianSigmaPRF` model.

The existing ``FittableImageModel`` and ``EPSFModel`` classes are now
deprecated and will be removed in a future version. They have been
replaced by the new `~photutils.psf.ImagePSF` class.


Legacy ``LevMarLSQFitter`` no longer used
=========================================

The default Astropy fitter for ``PSFPhotometry``,
``IterativePSFPhotometry``, and ``EPSFFitter`` was changed from
``LevMarLSQFitter`` to ``TRFLSQFitter``.

``LevMarLSQFitter`` uses the Levenberg-Marquardt algorithm via
the SciPy legacy function ``scipy.optimize.leastsq``, which is no
longer recommended. This fitter supports parameter bounds using an
unsophisticated min/max condition where parameters that are out of
bounds are simply reset to the min or max of the bounds during each
step. This can cause parameters to stick to one of the bounds during the
fitting process if the parameter gets close to the bound. If needed,
this fitter can still be used by explicitly setting the fitter in the
``PSFPhotometry``, ``IterativePSFPhotometry``, and ``EPSFFitter``
classes.

The fitter used in ``RadialProfile`` to fit the profile with a Gaussian
was also changed from ``LevMarLSQFitter`` to ``TRFLSQFitter``.

The fitter used in ``centroid_1dg`` and ``centroid_2dg`` was also
changed from ``LevMarLSQFitter`` to ``TRFLSQFitter``.

For more information about Astropy's non-linear fitters, see
:ref:`astropy:modeling-getting-started-nonlinear-notes`.


Breaking API Change for PSF Photometry residual/model images
============================================================

The ``sub_shape`` keyword in `~photutils.psf.IterativePSFPhotometry`
now defaults to using the model bounding box to define the shape. This
is a change from the previous behavior where the default shape was set
to ``fit_shape``. In general, one should want the subtraction shape to
cover a large portion of the model image, which the bounding box does.
If one wants to use a different shape, then the ``sub_shape`` keyword
can be explicitly set. If the PSF model does not have a bounding box
attribute, then the ``sub_shape`` keyword must be set to define the
subtraction shape.

Similarly, ``psf_shape`` is now an optional keyword in
the ``make_model_image`` and ``make_residual_image``
methods of `~photutils.psf.PSFPhotometry` and
`~photutils.psf.IterativePSFPhotometry`. The value defaults to using the
model bounding box to define the shape and is required only if the PSF
model does not have a bounding box attribute. In general, one should
want the model and residual images to be constructed using a large
portion of model image, which the bounding box does. If one wants to use
a different shape, then the ``psf_shape`` keyword can be explicitly set.


Bounding model fits in PSF Photometry
=====================================

A new ``xy_bounds`` keyword was added to `~photutils.psf.PSFPhotometry`
and `~photutils.psf.IterativePSFPhotometry` to allow one to bound
the x and y model parameters during the fitting. This can be used to
prevent the fit values from wandering too far from the initial parameter
guesses.


New FWHM estimation tool
========================

A new `~photutils.psf.fit_fwhm` convenience function was added to
estimate the FWHM of one or more sources in an image by fitting a
circular 2D Gaussian PRF model using the PSF photometry tools.

Similarly, a new `~photutils.psf.fit_2dgaussian` convenience function
was added to fit a circular 2D Gaussian PRF to one or more sources in an
image.


Segmentation Image data type
============================

The `~photutils.segmentation.detect_sources` and
`~photutils.segmentation.deblend_sources` functions and
`~photutils.segmentation.SourceFinder` class now return a
``SegmentationImage`` instance whose data dtype is ``np.int32`` instead
of ``int`` (``int64``) unless more than (2**32 - 1) labels are needed.

Also, the ``relabel_consecutive``, ``resassign_label(s)``,
``keep_label(s)``, ``remove_label(s)``, ``remove_border_labels``, and
``remove_masked_labels`` methods now keep the original dtype of the
segmentation image instead of always changing it to ``int`` (``int64``).


Improved performance for source deblending
==========================================

Performance improvements and significant reductions in memory usage
were made for source deblending, especially for large sources
and/or large ``nlevels`` values. The memory usage is now mostly
independent of the number of ``nlevels``, and the memory usage
will be significantly reduced for large sources. This affects
the `~photutils.segmentation.deblend_sources` function and the
`~photutils.segmentation.SourceFinder` class.

Additionally, the accuracy of the deblending progress bar is now
improved when using multiprocessing. The progress bar now also displays
the ID label number of either the current source being deblended
(serial) or the last source that was deblended (multiprocessing).


DAOStarFinder flux and mag changes
==================================

The `~photutils.detection.DAOStarFinder` ``flux`` and ``mag`` columns
were changed to give sensible values. Previously, the ``flux`` value was
defined by the original DAOFIND algorithm as a measure of the intensity
ratio of the amplitude of the best fitting Gaussian function at the
object position to the detection threshold. Over the years, this has
led to a lot of (understandable) confusion. The new ``flux`` column now
gives the sum of data values within the kernel footprint.

A ``daofind_mag`` column was added for comparison to the original IRAF
DAOFIND algorithm.


DAOStarFinder and IRAFStarFinder sky keyword removed
====================================================

The deprecated ``sky`` keyword in `~photutils.detection.DAOStarFinder`
and `~photutils.detection.IRAFStarFinder` has been removed.
Also, there will no longer be a ``sky`` column in the
`~photutils.detection.DAOStarFinder` output table. As documented, the
input data is assumed to be background-subtracted.


Quantity arrays in Centroids
============================

``Quantity`` arrays can now be input to
`~photutils.centroids.centroid_1dg` and
`~photutils.centroids.centroid_2dg`.


New Sphinx Theme
================

The documentation now uses the `PyData Sphinx
<https://pydata-sphinx-theme.readthedocs.io/>`_ theme, which is a
modern, responsive theme that is easy to read and navigate.


Other changes
=============

Please see the :ref:`changelog` for the complete list of changes.
