- Added new Bragg peak determination functionality to combat new datasets with sub-optimal signal-to-noise ratio. Further added Brillouin zone determination based on Bragg peak locations (#42).
- Fixed an issue where masks needed to be provided in bragg_peaks (#41).
- Updated bounds on pyqtgraph.
- Added explicit testing with python 3.10.
- Cleaned up unused imports.
- Updated some modules which were using deprecated code.
- This release brings no changes, and only fixes the conda-forge package.
- Fixed an issue where :func:`gaussian` would trip on a full-width at half-maximum of 0.
- Fixed an issue where the first stage of the dual-tree complex wavelet transform was not shifted properly (#36).
- Releases are now automatically performed using Github Actions
- It is now possible to install all the dependencies required to use :func:`diffshow` using the following installation option:
pip install scikit-ued[diffshow].
- Increased the reliability of :func:`bragg_peaks` to distinguish between noise and Bragg peaks.
- Added the function :func:`bragg_peaks` to determine the location of single-crystal diffraction peaks in an image.
- Fixed deprecation warnings regarding NumPy's dtypes.
- Improved :func:`autocenter` for diffraction patterns with large Ewald sphere walkoff.
- :func:`diffread` now supports NumPy's
*.npyformat. - Speedup of all routines that use the Fast Fourier transform (:func:`autocenter`, :func:`align`, :func:`ialign`, :func:`itrack_peak`, and :func:`kinematicsim`) by 50%.
- Added the :func:`autocenter` routine, to automatically find the center of diffraction patterns. This works for both single-crystal and polycrystalline patterns.
- Support for Python 3.6 and NumPy<1.17 has been dropped
This release brings major infrastructure improvements, which in turn have allowed to squash some bugs.
- Migration of continuous integration testing to GitHub Actions.
- Migration of test infrastructure to pytest.
- Tests are now included in source distributions.
- Code snippets in documentation are now tested for correctness.
User-facing changes:
- Fixed an issue where the detected shift in skued.align and skued.ialign might be partial (i.e. only shift in one direction).
- Fixed an issue with packaging data on Linux.
- The fast argument to skued.align and skued.ialign has been removed. It was previously-marked as deprecated.
- Added pre-emptive support for Python 3.10+ by removing deprecations.
- Increased the precision of the pseudo-voigt approximation in skued.pseudo_voigt.
- Fixed many issues regarding documentation being out-of-date.
- scikit-ued is being re-licensed from the MIT license to the GPLv3 license.
- The fast argument to skued.align and skued.ialign has been deprecated. Its value has no effect anymore.
- Official support for Python 3.9.
- Removed explicit requirement for the tifffile package.
- Added skued.kinematicsim, a simple function to compute electron diffraction patterns from crystals structures in the kinematic approximation (i.e. thin samples).
- Added the skued.RingArcSelection area.
- Various documentation improvements and fixes.
- Added support for crystals.ElectronicStructure. This requires crystals version 1.1.0 and up.
- Added the function with_irf, which allows to modify fitting functions to include the effects of instrument response.
- Various documentation fixes.
- Added the Selection.mpatch method to draw patches on Matplotlib plots.
- Added the spectrum_cmap Matplotlib colormap, available under the name "spectrum".
- Fixed an issue where diffracted intensities were not correctly scaled in potential_map.
- Added the :class:`Selection` class and :class:`RectSelection`, :class:`DiskSelection`, :class:`RingSelection`, and :class:`ArbitrarySelection` to assemble time-series. This is a generalization of iris-ued's time-series rects.
- Added real-time pixel value and cursor position to
skued.diffshow. - Added indices_to_text, a plotting utility function to render Miller indices to Mathjax/LaTeX-style text (Matplotlib-compatible).
skued.diffshowwill temporarily switch PyQtGraph's image axis order to the row-major, which is a saner default.- Added skued command-line utilities. Images can be shown (with interactive viewer) using
skued diffshow [path]. Crystal information can be determined usingskued crystinfo [path]. - Fixed an issue where a typo in
electron_velocitywould raise an exception.
Due to a conflict between scikit-image and scikit-ued conventions, some breaking changes are required. Image conventions will now follow that of scikit-image. Most importantly:
- Changed the convention on image masks to align with the scikit-image convention. Masks will be
Truefor valid pixels, andFalseon invalid pixels.
We took the opportunity to make other breaking changes:
- Broke off the
skued.structurepackage into its own library,crystals. - Removed masked_register_translation in favour of the new scikit-image implementation ported from scikit-ued.
- Removed xcorr and mnxc as these were the backbone of masked_register_translation and are no longer needed.
- Added aspherical electron form factor parametrization from Zheng et al. 2009.
- Removed
diff_registerin favor of an analog of scikit-image's register_translation and masked_register_translation. - Removed powder_center due to unpredictable performance.
- Removed calibrate_scattvector, which was deprecated.
- Removed time_shift and time_shifts, which were deprecated.
- Removed shift_image in favor of scipy.ndimage.shift.
- bounded_reflections has been removed in favor of
Crystal.bounded_reflectionsin the crystals library (version >= 0.6.4)
We have also added some features:
- Added the patterson function to calculate Patterson pair-pair distribution functions from polycrystalline diffraction patterns.
- Added the detector_scattvectors function to determine the wavevectors visible on a detector, in transmission, based on experimental geometry.
- Added time-series fitting.
- Added support for Gatan Digital Micrograph image formats DM3 and DM4
available_dt_filtersandavailable_first_stage_filtershave been added to list available baseline-removal filters.