Kikuchipy

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

Contributors
------------
- Håkon Wiik Ånes

Fixed
-----
- Deletion of temporary files saved to temporary directories in user guide.
(`312 <https://github.com/pyxem/kikuchipy/pull/312>`_)
- Pattern matching sometimes failing to generate a crystal map due to incorrect creation
of spatial arrays. (`307 <https://github.com/pyxem/kikuchipy/pull/307>`_)

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

Contributors
------------
- Håkon Wiik Ånes

Fixed
-----
- Version link Binder uses to make the Jupyter Notebooks run in the browser.
(`301 <https://github.com/pyxem/kikuchipy/pull/301>`_)

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

Details of all development associated with this release is listed below and in `this
GitHub milestone <https://github.com/pyxem/kikuchipy/milestone/3?closed=1>`_.

Contributors
------------
- Håkon Wiik Ånes
- Lars Andreas Hastad Lervik
- Ole Natlandsmyr

Added
-----
- Calculation of an average dot product map, or just the dot product matrices.
(`280 <https://github.com/pyxem/kikuchipy/pull/280>`_)
- A nice gallery to the documentation with links to each user guide page.
(`285 <https://github.com/pyxem/kikuchipy/pull/285>`_)
- Support for writing/reading an EBSD signal with 1 or 0 navigation axes to/from a
kikuchipy h5ebsd file.
(`276 <https://github.com/pyxem/kikuchipy/pull/276>`_)
- Better control over dask array chunking when processing patterns.
(`275 <https://github.com/pyxem/kikuchipy/pull/275>`_)
- User guide notebook showing basic pattern matching.
(`263 <https://github.com/pyxem/kikuchipy/pull/263>`_)
- EBSD.detector property storing an EBSDDetector.
(`262 <https://github.com/pyxem/kikuchipy/pull/262>`_)
- Link to Binder in README and in the notebooks for running them in the browser.
(`257 <https://github.com/pyxem/kikuchipy/pull/257>`_)
- Creation of dictionary of dynamically simulated EBSD patterns from a master pattern in
the square Lambert projection. (`239 <https://github.com/pyxem/kikuchipy/pull/239>`_)
- A data module with a small Nickel EBSD data set and master pattern, and a larger EBSD
data set downloadable via the module. Two dependencies, pooch and tqdm, are added
along with this module.
(`236 <https://github.com/pyxem/kikuchipy/pull/236>`_,
`237 <https://github.com/pyxem/kikuchipy/pull/237>`_,
`243 <https://github.com/pyxem/kikuchipy/pull/243>`_)
- Pattern matching of EBSD patterns with a dictionary of pre-computed simulated patterns
with known crystal orientations, and related useful tools
(`231 <https://github.com/pyxem/kikuchipy/pull/231>`_,
`233 <https://github.com/pyxem/kikuchipy/pull/233>`_,
`234 <https://github.com/pyxem/kikuchipy/pull/234>`_): (1) A framework for creation
of similarity metrics used in pattern matching, (2) computation of an orientation
similarity map from indexing results, and (3) creation of a multi phase crystal map
from single phase maps from pattern matching.
- EBSD.xmap property storing an orix CrystalMap.
(`226 <https://github.com/pyxem/kikuchipy/pull/226>`_)
- Dependency on the diffsims package for handling of electron scattering and
diffraction. (`220 <https://github.com/pyxem/kikuchipy/pull/220>`_)
- Square Lambert mapping, and its inverse, from points on the unit sphere to a 2D square
grid, as implemented in Callahan and De Graef (2013).
(`214 <https://github.com/pyxem/kikuchipy/pull/214>`_)
- Geometrical EBSD simulations, projecting a set of Kikuchi bands and zone axes onto a
detector, which can be added to an EBSD signal as markers.
(`204 <https://github.com/pyxem/kikuchipy/pull/204>`_,
`219 <https://github.com/pyxem/kikuchipy/pull/219>`_,
`232 <https://github.com/pyxem/kikuchipy/pull/232>`_)
- EBSD detector class to handle detector parameters, including detector pixels' gnomonic
coordinates. EBSD reference frame documentation.
(`204 <https://github.com/pyxem/kikuchipy/pull/204>`_,
`215 <https://github.com/pyxem/kikuchipy/pull/215>`_)
- Reader for EMsoft's simulated EBSD patterns returned by their EMEBSD.f90 program.
(`202 <https://github.com/pyxem/kikuchipy/pull/202>`_)

Changed
-------
- The feature maps notebook to include how to obtain an average dot product map and dot
product matrices for an EBSD signal.
(`280 <https://github.com/pyxem/kikuchipy/pull/280>`_)
- Averaging EBSD patterns with nearest neighbours now rescales to input data type range,
thus loosing relative intensities, to avoid clipping intensities.
(`280 <https://github.com/pyxem/kikuchipy/pull/280>`_)
- Dependency requirement of diffsims from >= 0.3 to >= 0.4
(`282 <https://github.com/pyxem/kikuchipy/pull/282>`_)
- Name of hemisphere axis in EBSDMasterPattern from "y" to "hemisphere".
(`275 <https://github.com/pyxem/kikuchipy/pull/275>`_)
- Replace Travis CI with GitHub Actions.
(`250 <https://github.com/pyxem/kikuchipy/pull/250>`_)
- The EBSDMasterPattern gets phase, hemisphere and projection properties.
(`246 <https://github.com/pyxem/kikuchipy/pull/246>`_)
- EMsoft EBSD master pattern plugin can read a single energy pattern. Parameter
`energy_range` changed to `energy`.
(`240 <https://github.com/pyxem/kikuchipy/pull/240>`_)
- Migrate user guide from reST files to Jupyter Notebooks converted to HTML with the
`nbsphinx` package.
(`236 <https://github.com/pyxem/kikuchipy/pull/236>`_,
`237 <https://github.com/pyxem/kikuchipy/pull/237>`_,
`244 <https://github.com/pyxem/kikuchipy/pull/244>`_,
`245 <https://github.com/pyxem/kikuchipy/pull/245>`_,
`279 <https://github.com/pyxem/kikuchipy/pull/279>`_,
`245 <https://github.com/pyxem/kikuchipy/pull/245>`_,
`279 <https://github.com/pyxem/kikuchipy/pull/279>`_,
`281 <https://github.com/pyxem/kikuchipy/pull/281>`_)
- Move GitHub repository to the pyxem organization. Update relevant URLs.
(`198 <https://github.com/pyxem/kikuchipy/pull/198>`_)
- Allow scikit-image >= 0.16. (`196 <https://github.com/pyxem/kikuchipy/pull/196>`_)
- Remove language_version in pre-commit config file.
(`195 <https://github.com/pyxem/kikuchipy/pull/195>`_)

Removed
-------
- The EBSDMasterPattern and EBSD metadata node Sample.Phases, to be replaced
by class attributes. The set_phase_parameters() method is removed from both
classes, and the set_simulation_parameters() is removed from the former class.
(`246 <https://github.com/pyxem/kikuchipy/pull/246>`_)

Fixed
-----
- IndexError in neighbour pattern averaging
(`280 <https://github.com/pyxem/kikuchipy/pull/280>`_)
- Reading of square Lambert projections from EMsoft's master pattern file now sums
contributions from asymmetric positions correctly.
(`255 <https://github.com/pyxem/kikuchipy/pull/255>`_)
- NumPy array creation when calculating window pixel's distance to the origin is not
ragged anymore. (`221 <https://github.com/pyxem/kikuchipy/pull/221>`_)

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

This is a patch release that fixes reading of EBSD data sets from h5ebsd files with
arbitrary scan group names.

Contributors
------------
- Håkon Wiik Ånes

Fixed
-------
- Allow reading of EBSD patterns from h5ebsd files with arbitrary scan group names, not
just "Scan 1", "Scan 2", etc., like was the case before.
(`188 <https://github.com/pyxem/kikuchipy/pull/188>`_)

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

This is a patch release that enables installing kikuchipy 0.2 from Anaconda and not just
PyPI.

Contributors
------------
- Håkon Wiik Ånes

Changed
-------
- Use numpy.fft instead of scipy.fft because HyperSpy requires scipy < 1.4 on
conda-forge, while scipy.fft was introduced in scipy 1.4.
(`180 <https://github.com/pyxem/kikuchipy/pull/180>`_)

Fixed
-----
- With the change above, kikuchipy 0.2 should be installable from Anaconda and not just
PyPI. (`180 <https://github.com/pyxem/kikuchipy/pull/180>`_)

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

Details of all development associated with this release are available `here
<https://github.com/pyxem/kikuchipy/milestone/2?closed=1>`_.

Contributors
------------
- Håkon Wiik Ånes
- Tina Bergh

Added
-----
- Jupyter Notebooks with tutorials and example workflows available.
- Grey scale and RGB virtual backscatter electron (BSE) images can be easily generated
with the VirtualBSEGenerator class. The generator return objects of the new signal
class VirtualBSEImage, which inherit functionality from HyperSpy's Signal2D class.
(`170 <https://github.com/pyxem/kikuchipy/pull/170>`_)
- EBSD master pattern class and reader of master patterns from EMsoft's EBSD master
pattern file. (`159 <https://github.com/pyxem/kikuchipy/pull/159>`_)
- Python 3.8 support. (`157 <https://github.com/pyxem/kikuchipy/pull/157>`_)
- The public API has been restructured. The pattern processing used by the EBSD class is
available in the kikuchipy.pattern subpackage, and filters/kernels used in frequency
domain filtering and pattern averaging are available in the kikuchipy.filters
subpackage.
(`169 <https://github.com/pyxem/kikuchipy/pull/169>`_)
- Intensity normalization of scan or single patterns.
(`157 <https://github.com/pyxem/kikuchipy/pull/157>`_)
- Fast Fourier Transform (FFT) filtering of scan or single patterns using SciPy's fft
routines and `Connelly Barnes' filterfft
<https://www.connellybarnes.com/code/python/filterfft>`_.
(`157 <https://github.com/pyxem/kikuchipy/pull/157>`_)
- Numba dependency to improve pattern rescaling and normalization.
(`157 <https://github.com/pyxem/kikuchipy/pull/157>`_)
- Computing of the dynamic background in the spatial or frequency domain for scan or
single patterns. (`157 <https://github.com/pyxem/kikuchipy/pull/157>`_)
- Image quality (IQ) computation for scan or single patterns based on N. C. K. Lassen's
definition. (`157 <https://github.com/pyxem/kikuchipy/pull/157>`_)
- Averaging of patterns with nearest neighbours with an arbitrary kernel, e.g.
rectangular or Gaussian. (`134 <https://github.com/pyxem/kikuchipy/pull/134>`_)
- Window/kernel/filter/mask class to handle such things, e.g. for pattern averaging or
filtering in the frequency or spatial domain. Available in the kikuchipy.filters
module.
(`134 <https://github.com/pyxem/kikuchipy/pull/134>`_,
`157 <https://github.com/pyxem/kikuchipy/pull/157>`_)

Changed
-------
- Renamed five EBSD methods: static_background_correction to remove_static_background,
dynamic_background_correction to remove_dynamic_background, rescale_intensities to
rescale_intensity, virtual_backscatter_electron_imaging to plot_virtual_bse_intensity,
and get_virtual_image to get_virtual_bse_intensity.
(`157 <https://github.com/pyxem/kikuchipy/pull/157>`_,
`170 <https://github.com/pyxem/kikuchipy/pull/170>`_)
- Renamed kikuchipy_metadata to ebsd_metadata.
(`169 <https://github.com/pyxem/kikuchipy/pull/169>`_)
- Source code link in the documentation should point to proper GitHub line. This
`linkcode_resolve` in the `conf.py` file is taken from SciPy.
(`157 <https://github.com/pyxem/kikuchipy/pull/157>`_)
- Read the Docs CSS style. (`157 <https://github.com/pyxem/kikuchipy/pull/157>`_)
- New logo with a gradient from experimental to simulated pattern (with EMsoft), with a
color gradient from the plasma color maps.
(`157 <https://github.com/pyxem/kikuchipy/pull/157>`_)
- Dynamic background correction can be done faster due to Gaussian blurring in the
frequency domain to get the dynamic background to remove.
(`157 <https://github.com/pyxem/kikuchipy/pull/157>`_)

Removed
-------
- Explicit dependency on scikit-learn (it is imported via HyperSpy).
(`168 <https://github.com/pyxem/kikuchipy/pull/168>`_)
- Dependency on pyxem. Parts of their virtual imaging methods are adapted here---a big
thank you to the pyxem/HyperSpy team!
(`168 <https://github.com/pyxem/kikuchipy/pull/168>`_)

Fixed
-----
- RtD builds documentation with Python 3.8 (fixed problem of missing .egg leading build
to fail). (`158 <https://github.com/pyxem/kikuchipy/pull/158>`_)