Pyxem

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

Added
-----
- Getting and plot integrated intensity now support signals containing nan (722)
- Add Symmetry1D signal class and symmetry analysis methods (724)
- BeamShift class, which includes the `make_linear_plane` method for better correction of the beam shift when scanning large regions in STEM (746)
- Add unit testing of docstring examples (766)
- Add function for optimizing calibration of SPED data (785)
- Add function for creating a orix CrystalMap from indexation results (794)
- Speed optimizations for the fast template matching on CPU and GPU, improving speeds by 200% and 40% respectively (796)
- Added the ability to determine the center and ellipticity using the `determine_ellipse` function.

Removed
-------
- lazy_* virtual imaging has been removed, use get_integrated_intensity (722)
- `big_data_utils` has been removed as this is not the modern way of attacking this problem
- similarly, `TemplateIndexationGenerator` has been removed as the Accelerated approach is far better (823)

Fixed
^^^^^
- Symmetry STEM Class updated to allow for better interpolation and lazy operation. (809)
- Generalized plotting diffraction vectors on ND stacks of images (783)
- Small bugfix with dask/cuda scheduler to prevent running out of VRAM (779)
- Bugfix:AzimuthalIntegral1D accepts masks and uses updated `map` function (826)

Deprecated
^^^^^^^^^^
- The `lazy_result` keyword, which has been changed to `lazy_output` to conform to similar keyword in HyperSpy

Changed
^^^^^^^
- For developers: HyperSpy's `.map` function will now be used to process big datasets, instead of pyXem's `process_dask_array`

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

The code contained in this version is identical to 0.14.1, the release was
recreated to fix an error with the Zenodo files.

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

Added
-----
- Code now support python 3.9
- Code now runs on hyperspy 1.6.2

Fixed
-----
- np.bool replaced by bool
- np.object replaced by object

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

Fixed
-----
- load_mib (734)
- correct_bad_pixels now returns the same result when lazy/not-lazy (bug 723, fix 735)
- mirrored templates now correctly dealt with in radial template matching (740)
- further bugfixes for AcceleratedIndexationGenerator (744)
- a k-space error effecting azimuthal integration (738)
- bug in .to_crystal_map()

Deprecated
----------
- lazy_virtual_bright_field, use get_integrated_intensity instead
- lazy_virtual_dark_field, use get_integrated_intensity instead

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

Added
-----
- Faster rotation indexing, using in plane speeds up, added as AcceleratedIndexationGenerator (673)
- get_direct_beam_position now supports lazy processing (648)
- center_direct_beam now supports lazy processing (658)
- Several functions for processing large datasets using dask (648, 658)
- Methods to retrieve phase from DPC signal are added (662)
- Add VirtualImageGenerator.set_ROI_mesh method to set mesh of CircleROI (700)
- Added a setup.cfg

Changed
-------
- The importing of pyxem objects has been standardized (704)
- get_direct_beam_position now has reversed order of the shifts [y, x] to [x, y] (653)
- .apply_affine_transform now uses a default order of 1 (changed from 3)
- find_peaks is now provided by hyperspy, method 'xc' now called 'template_matching'
- virtual_annular_dark_field and virtual_bright_field renamed; now have a `lazy\_` prefixing (698)
- Plotting large, lazy, datasets will be much faster now (655)
- Calibration workflow has been altered (see PR 640 for details)
- Azimuthal integration has been refactored (see PRs 625,676 for details)

Removed
-------
- Diffraction2D.remove_dead_pixels has been removed, use .correct_bad_pixels (681)
- Diffraction2D.remove_background, has been moved to .subtract_diffraction_background (697)
- The diffraction_component and scalable_reference_pattern modules have been removed (674)
- local_gaussian_method for subpixel refinement has been removed
- utils.plot removed, functionality now in signals.diffraction_vectors
- utils.subpixelrefinement_utils removed, functionality in subpxielrefinement_generator
- utils.dpc_tools removed, either downstreamed to diffsims or up to differential_phase_contrast.py
- utils.diffraction_tools removed, downstreamed to diffsims
- utils.sim_utils removed, instead use the relevant diffsims functionality
- utils.calibration_utils removed, downstreamed to diffsims

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

Changed
-------
- CI is now provided by github actions
- Code now depends on hyperspy==1.6.1 and skimage>=0.17.0