Pyxem

===========================
Fixed
-----
- Fixed bugs releated to orientation mapping with multiple phases and the plotting of the
vector annotations. (1090)

===========================

Restructuring of DPC processing
-------------------------------
- Total restructure of data processing of DPC data. This has now all been moved to the :class:`pyxem.signals.BeamShift` class.
- `DPCBaseSignal`, `DPCSignal1D`, `DPCSignal2D`, `LazyDPCBaseSignal`, `LazyDPCSignal1D`, `LazyDPCSignal2D` has been deprecated.
- `Diffraction2D.center_of_mass` has been deprecated. The functionality now resides in :meth:`pyxem.signals.Diffraction2D.get_center_beam_position`. Use `get_center_beam_position(method="center_of_mass")`
- Several `dummy_data` functions has been renamed to reflect this change: `dpc_signal` to `beam_shift_signal`
- `get_color_image_with_indicator` has been renamed and moved, :func:`pyxem.utils.plotting.plot_beam_shift_color`
- `correct_ramp` has been deprecated, with the functionality now residing in :meth:`pyxem.signals.BeamShift.get_linear_plane`. You can use `s_bs_lp = s_bs.get_linear_plane(fit_corners=0.05)`, then `s_bs -= s_bs_lp` to correct for the dscan shifts
- `:meth:`pyxem.signals.BeamShift.make_linear_plane` is being deprecated, and replaced with `:meth:`pyxem.signals.BeamShift.get_linear_plane`. It now returns a new signal, instead of altering the old one.
- `gaussian_blur` and `flip_axis_90_degrees` has been deprecated, as this can easily be done using `s.map`

Fixed
-----
- Fixed indexing error in :meth:`~pyxem.signals.Diffraction2D.get_direct_beam_position` (1080)

Added
-----
- Added Examples for doing a Circular Hough Transform and Increased Documentation for Filtering Data (1082)
- Added `circular_background` to :meth:`~pyxem.signals.Diffraction2D.template_match_disk` to account for
an amorphous circular background when template matching (1084)
- Added new datasets of in situ crystalization, Ag SPED,
Organic Semiconductor Orientation mapping, Orientation Mapping, and DPC (1081)
- Added Vectors to mask in :meth:`~pyxem.signals.DiffractionVectors.to_mask` (1087)
- Add :meth:`pyxem.signals.PolarDiffraction2D.get_orientation` to get the phase orientation (1073)
- Add :class:`pyxem.signals.OrientationMap` to organize and visualize orientation results (1073)

===========================
Fixed
-----
- Fixed pytest failure. Changed ``setup`` --> ``setup_method`` (997)
- :meth:`pyxem.signals.Diffraction2D.center_of_mass` now uses the :meth:`hyperspy.api.BaseSignal.map` function. (1005)
- Replace ``matplotlib.cm.get_cmap`` (removed in matplotlib 3.9) with ``matplotlib.colormaps``. (1023)
- Documentation fixes and improvement. (1028)
- Fixed bug with flattening diffraction Vectors when there are different scales (1024)
- Fixed intersphinx links and improved api documentation (1056)
- Fix an off-by-one error in the :meth:`pyxem.signals.Diffraction2D.get_azimuthal_integral2d` (1058)
- Fix handling of azimuthal range in :meth:`pyxem.signals.Diffraction2D.get_azimuthal_integral2d` (1060)

Added
-----
- Added :class:`pyxem.utils.calibration_utils.Calibration` class for calibrating the signal axes of a 4-D STEM dataset(993)
- Added :meth:`pyxem.signals.Diffraction2D.get_azimuthal_integral1D` method to calculate the azimuthal integral of a 2D diffraction pattern (1008)
- Added example for doing azimuthal integration of a 2d diffraction pattern (1009)
- Added :meth:`pyxem.signals.CommonDiffraction.get_virtual_image` method to calculate multiple virtual images
from a 4D STEM dataset (1014)
- Added GPU support for lazy signals. (1012)
- Added GPU processing for :meth:`pyxem.signals.Diffraction2D.get_azimuthal_integral2d` (1012)
- Added :meth:`pyxem.signals.Diffraction2D.get_diffraction_vectors` to directly return the diffraction vectors (1053)
- Added method for calibrating the detector gain (1046)
- Added :meth:`pyxem.signals.PolarDiffraction2D.subtract_diffraction_background` for polar-specific background subtraction (1062)

Deprecated
----------
- The module & all functions within ``utils.reduced_intensity1d`` are deprecated in favour of using the methods of `ReducedIntensity1D` (994).
- Deprecated ``CalibrationGenerator`` and ``CalibrationLibrary`` in favour of :class:`pyxem.utils.calibration.Calibration` class (1000)
- Detector module as we move away from pyfai
- Deprecated ``pyxem.generators.virtual_image_generator.VirtualImageGenerator`` in
favor of :meth:`pyxem.signals.CommonDiffraction.get_virtual_image` (1014)
- Several utility modules have been deprecated: utils.{pyfai,segement,virtual_images,background_utils,cluster_tools,signals, radial_utils} (1030 & 1060, 1055).
- The following utils: ``insitu_utils``, ``correlations_utils`` and ``pixelated_stem_tools``, ``dask_tools`` are now private.
- ``utils.vector_utils``, prefer ``utils.vectors``
- ``utils.symmetric_vector_utils``, prefer ``utils.vectors``
- ``utils.labeled_vector_utils``, prefer ``utils.vectors``
- ``utils.expt_utils``, prefer ``utils.diffraction``

Deleted
-------
- Several expired methods of :class:`pyxem.signals.Diffraction2D` associated with radial integration (998)
- The ``peak_find_lazy`` method of :class:`pyxem.signals.Diffraction2D` (1040)
- ``dummy_data`` that content is now available under ``data.dummy_data``

Changed
-------
- Subpixel refinement now a function of the :py:class:`~pyxem.signals.DiffractionVectors` class (980)
- The :py:class:`~pyxem.generators.SubpixelrefinementGenerator` class has been deprecated (980)

===========================
Added
-----
- LazyDiffractionVectors are now supported(969)
- DiffractionVectors now support intensity(969)
- Add Examples for vector_finding and determining_ellipticity(969)
- Add slicing methods to DiffractionVectors using ``ivec`` (972)
- :class:`~pyxem.signals.DiffractionVectors` now explicitly handles lazy signals (972)
- Added html representation for non-lazy :class:`~pyxem.signals.DiffractionVectors` (972)
- Added :class:`pyxem.signals.PolarVectors` for polar vectors (981)
- Added clustering methods using :func:`pyxem.signals.DiffractionVectors.cluster` (981)
- Added :class:`pyxem.signals.LabeledDiffractionVectors` for labeled diffraction vectors after clustering (981)

Changed
-------
- Revised the pyxem logo banner and favicon (988)

Fixed
-----
- Update pyxem to work with hyperspy 2.0.0 (969)
- Fixed slow markers (969)
- Removed parallel and max_workers keywords in favor of using dask (969)
- :class:`~pyxem.signals.DiffractionVectors2D` now extends :class:`~pyxem.signals.DiffractionVectors`
for a more consistent API (972)
- Fix :meth:`~pyxem.data.zrnb_precipitate` dataset to point to proper dataset

Removed
-------
- Removed MIB reader (979) in favor of https://github.com/hyperspy/rosettasciio/pull/174
- Support for Hyperspy 1.x.x is not supported. Use pyxem 0.16.0 instead if using Hyperspy 1.x.x (969)

===========================

Added
-----
- Added `magnitude_limits` to `DPCSignal2D` methods (949)
- Added :py:class:`~pyxem.signals.LazyCorrelation1D` for lazy Correlation1D signals
- Improved the documentation and added Examples
- Add N-D filtering using :py:meth:`~pyxem.signals.Diffraction2D.filter`
- Add new :py:class:`pyxem.signals.InSituDiffraction2D` class for in-situ diffraction data

Fixed
-----
- Remove ``ipywidgets`` from requirements as it is not a dependency
- Set skimage != to version 0.21.0 because of regression
- Do not reverse the y-axis of diffraction patterns when template matching (925)
- Fixed bug in :py:class:`pyxem.generators.indexation_generator.AcceleratedIndexationGenerator` when
passing orientations as tuples.
- Fix bug in calculating strain (958)

===========================

Fixed
-----
- Fixed type error in ``separate_watershed`` with scikit-image 0.21 (921)
- Fixed VDF creation from peaks using generators.VirtualDarkFieldGenerator.get_virtual_dark_field_images (926)
- Updating and correcting Zenodo (924)
- Bug fix for center_direct_beam and `half_square_width` (928 Thanks to PVacek )