==================
Added
-----
- ``kikuchipy.imaging.VirtualBSEImager`` replaces the
``kikuchipy.generators.VirtualBSEGenerator`` class.
(`608 <https://github.com/pyxem/kikuchipy/pull/608>`_)
- Adaptive histogram equalization is available to all signals.
(`606 <https://github.com/pyxem/kikuchipy/pull/606>`_)
- Option to return a new signal (lazy or not) instead of operating inplace is added to
many methods in all classes via ``inplace`` and ``lazy_output`` boolean parameters.
(`605 <https://github.com/pyxem/kikuchipy/pull/605>`_)
- Lazy version of the ``VirtualBSEImage`` class.
(`605 <https://github.com/pyxem/kikuchipy/pull/605>`_)
- Allow providing a color for simulator reflections when plotting with Matplotlib.
(`599 <https://github.com/pyxem/kikuchipy/pull/599>`_)
- Passing pseudo-symmetry operators to orientation and orientation/PC EBSD refinement
methods in order to find the best match among pseudo-symmetric variants.
(`598 <https://github.com/pyxem/kikuchipy/pull/598>`_)
- Saving and loading of an ``EBSDDetector``.
(`595 <https://github.com/pyxem/kikuchipy/pull/595>`_)
- EBSD refinement methods now return the number of function evaluations.
(`593 <https://github.com/pyxem/kikuchipy/pull/593>`_)
- Which points in a crystal map to refine can be controlled by passing a navigation
mask. (`593 <https://github.com/pyxem/kikuchipy/pull/593>`_)
- Which points to consider when merging crystal maps can be controlled by passing
navigation masks. (`593 <https://github.com/pyxem/kikuchipy/pull/593>`_)
- Which patterns to do dictionary indexing of can be controlled by passing a navigation
mask. (`593 <https://github.com/pyxem/kikuchipy/pull/593>`_)
- Downsampling of EBSD patterns which maintain the data type by also rescaling to the
data type range. (`592 <https://github.com/pyxem/kikuchipy/pull/592>`_)
- Method to get a PyEBSDIndex ``EBSDIndexer`` instance from an ``EBSDDetector``,
convenient for either indexing with PyEBSDIndex or for use with kikuchipy.
(`590 <https://github.com/pyxem/kikuchipy/pull/590>`_)
- Convenience function to get a ``CrystalMap`` from a PyEBSDIndex Hough indexing result
array. (`590 <https://github.com/pyxem/kikuchipy/pull/590>`_)
- PyEBSDIndex as an optional dependency.
(`590 <https://github.com/pyxem/kikuchipy/pull/590>`_)
- Two tutorials showing projection center (PC) fitting and extrapolation to obtain a
plane of PCs to index a full dataset.
(`588 <https://github.com/pyxem/kikuchipy/pull/588>`_)
- Tutorial showing sloppy projection center (PC)/orientation optimization landscape of
the Ni dataset from Jackson et al. (2019), replicating the results from Pang et al.
(2020). (`588 <https://github.com/pyxem/kikuchipy/pull/588>`_)
- Method ``EBSDDetector.fit_pc()`` to fit a plane using a projective or affine
transformation to projection centers following work by Winkelmann and co-workers
(2020). (`587 <https://github.com/pyxem/kikuchipy/pull/587>`_)
- Method ``EBSDDetector.extrapolate_pc()`` to return a new detector with a plane of
projection centers (PCs) extrapolated from a mean PC calculated from one or more PCs
following work by Singh et al. (2017).
(`587 <https://github.com/pyxem/kikuchipy/pull/587>`_)
- Methods ``EBSDDetector.estimate_xtilt()`` and ``EBSDDetector.estimate_xtilt_ztilt()``
to estimate the tilts about the detector X and Z axes which bring the detector plane
normal parallel to the sample plane normal, following work by Winkelmann and
co-workers (2020). (`587 <https://github.com/pyxem/kikuchipy/pull/587>`_)
- Method ``EBSDDetector.plot_pc()`` to plot projection centers (PCs) in maps, scatter
plots or in 3D. (`587 <https://github.com/pyxem/kikuchipy/pull/587>`_)
- Convenience function ``kikuchipy.draw.plot_pattern_positions_in_map()`` to plot
positions of selected patterns (typically calibration patterns) in a 2D map.
(`587 <https://github.com/pyxem/kikuchipy/pull/587>`_)
- EBSD signal returned from NORDIF calibration pattern reader tries to add the following
new info to the original metadata: Shapes of area and region of interest (ROI), offset
of ROI, calibration pattern indices and area overview image. All shapes and
coordinates are given both in units of area overview image pixels and scaled according
to the pixels in the ROI (actual navigation shape).
(`586 <https://github.com/pyxem/kikuchipy/pull/586>`_)
- Method ``EBSD.extract_grid()`` to get a new signal from grid positions evenly spaced
in navigation space. (`585 <https://github.com/pyxem/kikuchipy/pull/585>`_)
- Utility function ``grid_indices()`` to extract a smaller 1D or 2D grid of indices from
a larger grid. (`585 <https://github.com/pyxem/kikuchipy/pull/585>`_)
- Seven EBSD master pattern files simulated with EMsoft are available from
``ebsd_master_pattern()`` via the data module for download to the local cache:
aluminium, nickel, silicon, austenite, ferrite, a chi-phase in steel and a sigma-phase
in steel. (`584 <https://github.com/pyxem/kikuchipy/pull/584>`_,
`607 <https://github.com/pyxem/kikuchipy/pull/607>`_)
- Some experimental EBSD datasets are available for download to the local cache via the
data module: (50, 50) patterns of (480, 480) pixels from an Si wafer via
``si_wafer()``, ten full Ni datasets of (149, 200) patterns of (60, 60) pixels via
``ni_gain(number)`` (number 1-10) (parts of number 1 are used in
``nickel_ebsd_small()/large()``) and the calibration patterns of the ten Ni datasets,
``ni_gain_calibration(number)``.
(`584 <https://github.com/pyxem/kikuchipy/pull/584>`_,
`593 <https://github.com/pyxem/kikuchipy/pull/593>`_,
`607 <https://github.com/pyxem/kikuchipy/pull/607>`_)
- When using the following HyperSpy ``Signal2D`` methods via the ``EBSD`` class, the
class attributes ``xmap``, ``static_background`` and ``detector`` are handled
correctly, which they were not before: ``inav``, ``isig``, ``crop()``,
``crop_image()``. If handling fails, the old behavior is retained. This handling is
experimental. (`578 <https://github.com/pyxem/kikuchipy/pull/578>`_)
- ``EBSDDetector.crop()`` method to get a new detector with its shape cropped, also
updating the PC values accordingly.
(`578 <https://github.com/pyxem/kikuchipy/pull/578>`_)
Changed
-------
- Minimal version of orix set to >= 0.11 and of Numba set to >= 0.55.
(`608 <https://github.com/pyxem/kikuchipy/pull/608>`_)
- Added warnings when trying to perform adaptive histogram equalization on a signal with
data in floating type or when some of the data is NaN.
(`606 <https://github.com/pyxem/kikuchipy/pull/606>`_)
- Dask arrays returned from EBSD refinement methods has the number of function
evaluations as the second element after the score.
(`593 <https://github.com/pyxem/kikuchipy/pull/593>`_)
- Stricter phase comparison in EBSD refinement. The phase in the crystal map points to
refine must have the same name, space group, point group and structure (atoms and
lattice) as the master pattern phase.
(`593 <https://github.com/pyxem/kikuchipy/pull/593>`_)
- Passing two crystal maps with identical phases when merging returns a map with one
phase instead of two and does not raise a warning, as before.
(`593 <https://github.com/pyxem/kikuchipy/pull/593>`_)
- Exclude documentation and tests from source distribution.
(`588 <https://github.com/pyxem/kikuchipy/pull/588>`_)
- Minimal version of HyperSpy increased to >= 1.7.3.
(`585 <https://github.com/pyxem/kikuchipy/pull/585>`_)
- When binning the navigation dimension(s) with ``EBSD.rebin()``, the class attributes
``xmap`` and ``static_background`` are set to ``None`` and ``detector.pc`` is set to
``[0.5, 0.5, 0.5]`` in the appropriate navigation shape. If the signal dimension(s)
are binned, the ``static_background`` is binned similarly while the ``detector.shape``
and ``detector.binning`` are updated. If this handling of attributes fails, the old
behavior is retained. This handling is experimental.
(`578 <https://github.com/pyxem/kikuchipy/pull/578>`_)
- EBSD signal loaded with ``nickel_ebsd_small()`` and ``nickel_ebsd_large()`` now
contain crystal maps with orientations and detectors with PC values found from Hough
indexing with PyEBSDIndex followed by orientation and PC refinement.
(`578 <https://github.com/pyxem/kikuchipy/pull/578>`_,
`584 <https://github.com/pyxem/kikuchipy/pull/584>`_)
- Minimal version of Matplotlib is 3.5.0 when installing optional dependencies with
``pip install kikuchipy[viz]`` since PyVista requires this.
(`578 <https://github.com/pyxem/kikuchipy/pull/578>`_)
Deprecated
----------
- ``kikuchipy.generators.VirtualBSEGenerator`` class is deprecated and will be removed
in version 0.9. Use ``kikuchipy.imaging.VirtualBSEImager`` instead.
(`608 <https://github.com/pyxem/kikuchipy/pull/608>`_)
- The data module functions ``silicon_ebsd_moving_screen_x()``, where "x" is "in",
"out5mm" or "out10mm", are deprecated and will be removed in v0.9. Use
``si_ebsd_moving_screen(distance)`` instead, where ``distance`` is ``0`` (in), ``5``
or ``10``. (`607 <https://github.com/pyxem/kikuchipy/pull/607>`_)
- The PyPI selector ``viz`` is replaced by ``all``, which installs all optional
dependencies. ``viz`` will be removed in version 0.9. Install optional dependencies
manually or via ``pip install kikuchipy[all]``.
(`590 <https://github.com/pyxem/kikuchipy/pull/590>`_)
- ``projections`` module with classes ``GnomonicProjection``, ``HesseNormalForm``,
``LambertProjection`` and ``SphericalProjection``. These will be removed in version
0.9.0, as they are unused internally. If you depend on this module, please open an
issue at https://github.com/pyxem/kikuchipy/issues.
(`577 <https://github.com/pyxem/kikuchipy/pull/577>`_)
Removed
-------
- ``mask`` parameter in EBSD refinement methods; use ``signal_mask`` instead.
(`577 <https://github.com/pyxem/kikuchipy/pull/577>`_)
- ``ebsd_projections`` module. (`577 <https://github.com/pyxem/kikuchipy/pull/577>`_)
Fixed
-----
- Default ``EBSD.detector.shape`` is now correct when a detector is not passed upon
initialization. (`603 <https://github.com/pyxem/kikuchipy/pull/603>`_)
- Oxford Instruments .ebsp files of version 4 can now be read.
(`602 <https://github.com/pyxem/kikuchipy/pull/602>`_)
- When loading EBSD patterns from H5OINA files, the detector tilt and binning are
available in the returned signal's ``detector`` attribute.
(`600 <https://github.com/pyxem/kikuchipy/pull/600>`_)
- Range of (kinematical) intensities in ``KikuchiPatternSimulator.plot()`` maximizes the
strongest reflectors (make black) instead of minimizing the weakest reflectors (make
white), which was the previous behavior.
(`599 <https://github.com/pyxem/kikuchipy/pull/599>`_)
- Inversion of ``signal_mask`` in the normalized cross-correlation and normalized dot
product metrics is now done internally, to be in line with the docstrings (does not
affect the use of this parameter and ``metric="ncc"`` or ``metric="ndp"`` in
``EBSD.dictionary_indexing()``).
(`593 <https://github.com/pyxem/kikuchipy/pull/593>`_)
- ``EBSDDetector.pc_average`` no longer rounds the PC to three decimals.
(`586 <https://github.com/pyxem/kikuchipy/pull/586>`_)
- Microscope magnification is now read correctly from EDAX h5ebsd files.
(`586 <https://github.com/pyxem/kikuchipy/pull/586>`_)
- kikuchipy h5ebsd reader can read a signal with an EBSD detector with a PC array of
different navigation shape than determined from the HDF5 file's navigation shape
(e.g. ``Scan 1/EBSD/Header/n_columns`` and ``n_rows``).
(`578 <https://github.com/pyxem/kikuchipy/pull/578>`_)