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Changelog

kikuchipy is an open-source Python library for processing and analysis of electron backscatter diffraction patterns: https://kikuchipy.org.

All notable changes to this project will be documented in this file. The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Contributors to each release are listed in alphabetical order by first name. List entries are sorted in descending chronological order.

0.4.0 (2021-07-08)

Contributors

  • Håkon Wiik Ånes

Added

  • Sample tilt about RD can be passed as part of an EBSDDetector. This can be used when projecting parts of master patterns onto a detector. (#381)
  • Reader for uncompressed EBSD patterns stored in Oxford Instrument's binary .ebsp file format. (#371, #391)
  • Unit testing of docstring examples. (#350)
  • Support for Python 3.9. (#348)
  • Projection/pattern center calibration via the moving screen technique in a kikuchipy.detectors.calibration module. (#322)
  • Three single crystal Si EBSD patterns, from the same sample position but with varying detector distances, to the data module (via external repo). (#320)
  • Reading of NORDIF calibration patterns specified in a setting file into an EBSD signal. (#317)

Changed

  • Only return figure from kikuchipy.filters.Window.plot() if desired, also add a colorbar only if desired. (#375)

Deprecated

  • The kikuchipy.pattern.correlate module will be removed in v0.5. Use kikuchipy.indexing.similarity_metrics instead. (#377)
  • Rename the EBSD.match_patterns() method to EBSD.dictionary_indexing(). match_patterns() will be removed in v0.5. (#376)

Fixed

  • Set minimal requirement of importlib_metadata to v3.6 so Binder can run user guide notebooks with HyperSpy 1.6.3. (#395)
  • Row (y) coordinate array returned with the crystal map from dictionary indexing is correctly sorted. (#392)
  • Deep copying EBSD and EBSDMasterPattern signals carry over, respectively, xmap and detector, and phase, hemisphere and projection properties (#356).
  • Scaling of region of interest coordinates used in virtual backscatter electron imaging to physical coordinates. (#349)

0.3.4 (2021-05-26)

Contributors

  • Håkon Wiik Ånes

Added

  • Restricted newest version of dask<=2021.03.1 and pinned orix==0.6.0. (#360)

0.3.3 (2021-04-18)

Contributors

  • Håkon Wiik Ånes
  • Ole Natlandsmyr

Fixed

  • Reading of EBSD patterns from Bruker h5ebsd with a region of interest. (#339)
  • Merging of (typically refined) crystal maps, where either a simulation indices array is not present or the array contains more indices per point than scores. (#335)
  • Bugs in getting plot markers from geometrical EBSD simulation. (#334)
  • Passing a static background pattern to EBSD.remove_static_background() for a non-square detector dataset works. (#331)

0.3.2 (2021-02-01)

Contributors

  • Håkon Wiik Ånes

Fixed

  • Deletion of temporary files saved to temporary directories in user guide. (#312)
  • Pattern matching sometimes failing to generate a crystal map due to incorrect creation of spatial arrays. (#307)

0.3.1 (2021-01-22)

Contributors

  • Håkon Wiik Ånes

Fixed

  • Version link Binder uses to make the Jupyter Notebooks run in the browser. (#301)

0.3.0 (2021-01-22)

Details of all development associated with this release is listed below and in this GitHub milestone.

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)
  • A nice gallery to the documentation with links to each user guide page. (#285)
  • Support for writing/reading an EBSD signal with 1 or 0 navigation axes to/from a kikuchipy h5ebsd file. (#276)
  • Better control over dask array chunking when processing patterns. (#275)
  • User guide notebook showing basic pattern matching. (#263)
  • EBSD.detector property storing an EBSDDetector. (#262)
  • Link to Binder in README and in the notebooks for running them in the browser. (#257)
  • Creation of dictionary of dynamically simulated EBSD patterns from a master pattern in the square Lambert projection. (#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, #237, #243)
  • Pattern matching of EBSD patterns with a dictionary of pre-computed simulated patterns with known crystal orientations, and related useful tools (#231, #233, #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)
  • Dependency on the diffsims package for handling of electron scattering and diffraction. (#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)
  • 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, #219, #232)
  • EBSD detector class to handle detector parameters, including detector pixels' gnomonic coordinates. EBSD reference frame documentation. (#204, #215)
  • Reader for EMsoft's simulated EBSD patterns returned by their EMEBSD.f90 program. (#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)
  • Averaging EBSD patterns with nearest neighbours now rescales to input data type range, thus loosing relative intensities, to avoid clipping intensities. (#280)
  • Dependency requirement of diffsims from >= 0.3 to >= 0.4 (#282)
  • Name of hemisphere axis in EBSDMasterPattern from "y" to "hemisphere". (#275)
  • Replace Travis CI with GitHub Actions. (#250)
  • The EBSDMasterPattern gets phase, hemisphere and projection properties. (#246)
  • EMsoft EBSD master pattern plugin can read a single energy pattern. Parameter energy_range changed to energy. (240)
  • Migrate user guide from reST files to Jupyter Notebooks converted to HTML with the nbsphinx package. (#236, #237, #244, #245, #279, #245, #279, #281)
  • Move GitHub repository to the pyxem organization. Update relevant URLs. (#198)
  • Allow scikit-image >= 0.16. (#196)
  • Remove language_version in pre-commit config file. (#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)

Fixed

  • IndexError in neighbour pattern averaging (#280)
  • Reading of square Lambert projections from EMsoft's master pattern file now sums contributions from asymmetric positions correctly. (#255)
  • NumPy array creation when calculating window pixel's distance to the origin is not ragged anymore. (#221)

0.2.2 (2020-05-24)

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)

0.2.1 (2020-05-20)

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)

Fixed

  • With the change above, kikuchipy 0.2 should be installable from Anaconda and not just PyPI. (#180)

0.2.0 (2020-05-19)

Details of all development associated with this release are available here.

Contributors

  • Håkon Wiik Ånes
  • Tina Bergh

Added

  • Jupyter Notebooks with tutorials and example workflows available via https://github.com/pyxem/kikuchipy-demos.
  • 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)
  • EBSD master pattern class and reader of master patterns from EMsoft's EBSD master pattern file. (#159)
  • Python 3.8 support. (#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)
  • Intensity normalization of scan or single patterns. (#157)
  • Fast Fourier Transform (FFT) filtering of scan or single patterns using SciPy's fft routines and Connelly Barnes' filterfft. (#157)
  • Numba dependency to improve pattern rescaling and normalization. (#157)
  • Computing of the dynamic background in the spatial or frequency domain for scan or single patterns. (#157)
  • Image quality (IQ) computation for scan or single patterns based on N. C. K. Lassen's definition. (#157)
  • Averaging of patterns with nearest neighbours with an arbitrary kernel, e.g. rectangular or Gaussian. (#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, #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, #170)
  • Renamed kikuchipy_metadata to ebsd_metadata. (#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)
  • Read the Docs CSS style. (#157)
  • New logo with a gradient from experimental to simulated pattern (with EMsoft), with a color gradient from the plasma color maps. (#157)
  • Dynamic background correction can be done faster due to Gaussian blurring in the frequency domain to get the dynamic background to remove. (#157)

Removed

  • Explicit dependency on scikit-learn (it is imported via HyperSpy). (#168)
  • Dependency on pyxem. Parts of their virtual imaging methods are adapted here---a big thank you to the pyxem/HyperSpy team! (#168)

Fixed

  • RtD builds documentation with Python 3.8 (fixed problem of missing .egg leading build to fail). (#158)

0.1.3 (2020-05-11)

kikuchipy is an open-source Python library for processing and analysis of electron backscatter diffraction patterns: https://kikuchipy.org.

This is a patch release. It is anticipated to be the final release in the 0.1.x series.

Added

Fixed

  • Static and dynamic background corrections are done at float 32-bit precision, and not integer 16-bit.
  • Chunking of static background pattern.
  • Chunking of patterns in the h5ebsd reader.

0.1.2 (2020-01-09)

kikuchipy is an open-source Python library for processing and analysis of electron backscatter diffraction patterns: https://kikuchipy.org.

This is a bug-fix release that ensures, unlike the previous bug-fix release, that necessary files are downloaded when installing from PyPI.

0.1.1 (2020-01-04)

This is a bug fix release that ensures that necessary files are uploaded to PyPI.

0.1.0 (2020-01-04)

We're happy to announce the release of kikuchipy v0.1.0!

kikuchipy is an open-source Python library for processing and analysis of electron backscatter diffraction (EBSD) patterns. The library builds upon the tools for multi-dimensional data analysis provided by the HyperSpy library.

For more information, a user guide, and the full reference API documentation, please visit: https://kikuchipy.org.

This is the initial pre-release, where things start to get serious... seriously fun!

Features

  • Load EBSD patterns and metadata from the NORDIF binary format (.dat), or Bruker Nano's or EDAX TSL's h5ebsd formats (.h5) into an EBSD object, e.g. s, based upon HyperSpy's Signal2D class, using s = kp.load(). This ensures easy access to patterns and metadata in the attributes s.data and s.metadata, respectively.
  • Save EBSD patterns to the NORDIF binary format (.dat) and our own h5ebsd format (.h5), using s.save(). Both formats are readable by EMsoft's NORDIF and EMEBSD readers, respectively.
  • All functionality in kikuchipy can be performed both directly and lazily (except some multivariate analysis algorithms). The latter means that all operations on a scan, including plotting, can be done by loading only necessary parts of the scan into memory at a time. Ultimately, this lets us operate on scans larger than memory using all of our cores.
  • Visualize patterns easily with HyperSpy's powerful and versatile s.plot(). Any image of the same navigation size, e.g. a virtual backscatter electron image, quality map, phase map, or orientation map, can be used to navigate in. Multiple scans of the same size, e.g. a scan of experimental patterns and the best matching simulated patterns to that scan, can be plotted simultaneously with HyperSpy's plot_signals().
  • Virtual backscatter electron (VBSE) imaging is easily performed with s.virtual_backscatter_electron_imaging() based upon similar functionality in pyXem. Arbitrary regions of interests can be used, and the corresponding VBSE image can be inspected interactively. Finally, the VBSE image can be obtained in a new EBSD object with vbse = s.get_virtual_image(), before writing the data to an image file in your desired format with matplotlib's imsave('filename.png', vbse.data).
  • Change scan and pattern size, e.g. by cropping on the detector or extracting a region of interest, by using s.isig or s.inav, respectively. Patterns can be binned (upscaled or downscaled) using s.rebin. These methods are provided by HyperSpy.
  • Perform static and dynamic background correction by subtraction or division with s.static_background_correction() and s.dynamic_background_correction(). For the former correction, relative intensities between patterns can be kept if desired.
  • Perform adaptive histogram equalization by setting an appropriate contextual region (kernel size) with s.adaptive_histogram_equalization().
  • Rescale pattern intensities to desired data type and range using s.rescale_intensities().
  • Multivariate statistical analysis, like principal component analysis and many other decomposition algorithms, can be easily performed with s.decomposition(), provided by HyperSpy.
  • Since the EBSD class is based upon HyperSpy's Signal2D class, which itself is based upon their BaseSignal class, all functionality available to Signal2D is also available to the EBSD class. See HyperSpy's user guide (http://hyperspy.org/hyperspy-doc/current/user_guide) for details.

Contributors

  • Håkon Wiik Ånes
  • Tina Bergh