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CHANGELOG.rst

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Changelog

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.

Unreleased

Fixed

Added

Deprecated

  • The module & all functions within utils.reduced_intensity1d are deprecated in favour of using the methods of ReducedIntensity1D (#994).
  • Deprecated CalibrationGenerator and CalibrationLibrary in favour of :class:`pyxem.utils.calibration.Calibration` class (#1000)
  • Detector module as we move away from pyfai
  • Deprecated pyxem.generators.virtual_image_generator.VirtualImageGenerator in favor of :meth:`pyxem.signals.CommonDiffraction.get_virtual_image` (#1014)
  • Several utility modules have been deprecated: utils.{pyfai,segement,virtual_images,background_utils,cluster_tools,signals, radial_utils} (#1030 & #1060, #1055).
  • The following utils: insitu_utils, correlations_utils and pixelated_stem_tools, dask_tools are now private.
  • utils.vector_utils, prefer utils.vectors
  • utils.symmetric_vector_utils, prefer utils.vectors
  • utils.labeled_vector_utils, prefer utils.vectors
  • utils.expt_utils, prefer utils.diffraction

Deleted

Changed

2024-01-05 - version 0.17.0

Added

Changed

  • Revised the pyxem logo banner and favicon (#988)

Fixed

Removed

  • Removed MIB reader (#979) in favor of hyperspy/rosettasciio#174
  • Support for Hyperspy 1.x.x is not supported. Use pyxem 0.16.0 instead if using Hyperspy 1.x.x (#969)

2023-11-14 - version 0.16.0

Added

Fixed

2023-05-08 - version 0.15.1

Fixed

  • Fixed type error in separate_watershed with scikit-image 0.21 (#921)
  • Fixed VDF creation from peaks using generators.VirtualDarkFieldGenerator.get_virtual_dark_field_images (#926)
  • Updating and correcting Zenodo (#924)
  • Bug fix for center_direct_beam and half_square_width (#928 Thanks to @PVacek )

2023-04-06 - version 0.15.0

Added

  • Added damp_extrapolate_to_zero to ReducedIntensity1D
  • Added in deprecation wrapper class to wrap deprecated functions in pyxem.
  • Center-of-mass algorithm added to get_direct_beam_position (#845)
  • Added VectorSignal1D class to handle 1 dimensional signals
  • Added kwargs to find_beam_offset_cross_correlation allowing for parameters to be passed to phase_cross_correlation (#907)
  • Added LazyVirtualDarkField signal

Changed

  • Sklearn is now required to be on the 1.0 series.
  • Changed set_signal_dimension to Hyperspy.signals.BaseSignal.transpose
  • Moved code from VectorSignal to VectorSignal2D. Change is more inline with stated dimensions
  • VectorSignal pixel_calibration deprecated and replaced with scales.
  • Fixed bugs resulting from API change in hyperspy/hyperspy#3045. Markers explicitly initialized
  • DiffractionVectors.get_diffraction_pixels_map returns a ragged signal
  • VirtualDarkFieldImage.get_vdf_segment changed to properly handle setting of axes
  • Increased minimal version of scikit-image to >= 0.19.0
  • Increased minimal version of Matplotlib to >= 3.3

Fixed

  • Fixed a factor of 1/2 missing in ScatteringFitComponentXTables
  • Fixed error related to DiffractionSignal2D.apply_affine_transformation when multiple affine transformations are given. (#870)
  • Bugfix related to Numpy 1.24.0. Strict array creation with dtype=object is needed for ragged arrays. (#880 & #881)
  • Bug fix for doubling of inplane rotation in template matching. (#905 & #853)
  • Bug fix for filtering vectors using a basis and DBSCAN
  • Bug fix for passing vector attributes when signal is copied or changed.

2022-06-15 - version 0.14.2

Changed

  • Increase minimal version of orix to >= 0.9.
  • Increase minimal version of diffsims to >= 0.5.

Fixed

  • Fix bug in get_DisplacementGradientMap (#852)
  • Fix template matching bugs (originally fixed in #771 but omitted from 0.14 series by accident)

2022-04-29 - version 0.14.1

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

2022-04-29 - version 0.14.0

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

2021-04-14 - version 0.13.2

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

2021-03-21 - version 0.13.1

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

2021-01-13 - version 0.13.0

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

2020-12-02 - version 0.12.3

Changed

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

2020-10-04 - version 0.12.2

Added

  • This project now keeps a Changelog

Changed

  • Slow tests now don't run by default
  • Depend only on hyperspy-base and pyfai-base