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.

2024-06-10 - version 0.19.1#

Fixed#

  • Fixed bugs releated to orientation mapping with multiple phases and the plotting of the vector annotations. (#1090)

2024-06-08 - version 0.19.0#

Restructuring of DPC processing#

  • Total restructure of data processing of DPC data. This has now all been moved to the pyxem.signals.BeamShift class.

  • DPCBaseSignal, DPCSignal1D, DPCSignal2D, LazyDPCBaseSignal, LazyDPCSignal1D, LazyDPCSignal2D has been deprecated.

  • Diffraction2D.center_of_mass has been deprecated. The functionality now resides in pyxem.signals.Diffraction2D.get_center_beam_position(). Use get_center_beam_position(method=”center_of_mass”)

  • Several dummy_data functions has been renamed to reflect this change: dpc_signal to beam_shift_signal

  • get_color_image_with_indicator has been renamed and moved, pyxem.utils.plotting.plot_beam_shift_color()

  • correct_ramp has been deprecated, with the functionality now residing in pyxem.signals.BeamShift.get_linear_plane(). You can use s_bs_lp = s_bs.get_linear_plane(fit_corners=0.05), then s_bs -= s_bs_lp to correct for the dscan shifts

  • :meth:`pyxem.signals.BeamShift.make_linear_plane is being deprecated, and replaced with :meth:`pyxem.signals.BeamShift.get_linear_plane. It now returns a new signal, instead of altering the old one.

  • gaussian_blur and flip_axis_90_degrees has been deprecated, as this can easily be done using s.map

Fixed#

Added#

  • Added Examples for doing a Circular Hough Transform and Increased Documentation for Filtering Data (#1082)

  • Added circular_background to template_match_disk() to account for an amorphous circular background when template matching (#1084)

  • Added new datasets of in situ crystalization, Ag SPED, Organic Semiconductor Orientation mapping, Orientation Mapping, and DPC (#1081)

  • Added Vectors to mask in to_mask() (#1087)

  • Add pyxem.signals.PolarDiffraction2D.get_orientation() to get the phase orientation (#1073)

  • Add pyxem.signals.OrientationMap to organize and visualize orientation results (#1073)

2024-05-08 - version 0.18.0#

Fixed#

  • Fixed pytest failure. Changed setup –> setup_method (#997)

  • pyxem.signals.Diffraction2D.center_of_mass() now uses the hyperspy.api.BaseSignal.map() function. (#1005)

  • Replace matplotlib.cm.get_cmap (removed in matplotlib 3.9) with matplotlib.colormaps. (#1023)

  • Documentation fixes and improvement. (#1028)

  • Fixed bug with flattening diffraction Vectors when there are different scales (#1024)

  • Fixed intersphinx links and improved api documentation (#1056)

  • Fix an off-by-one error in the pyxem.signals.Diffraction2D.get_azimuthal_integral2d() (#1058)

  • Fix handling of azimuthal range in pyxem.signals.Diffraction2D.get_azimuthal_integral2d() (#1060)

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 pyxem.utils.calibration.Calibration class (#1000)

  • Detector module as we move away from pyfai

  • Deprecated pyxem.generators.virtual_image_generator.VirtualImageGenerator in favor of 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#

  • LazyDiffractionVectors are now supported(#969)

  • DiffractionVectors now support intensity(#969)

  • Add Examples for vector_finding and determining_ellipticity(#969)

  • Add slicing methods to DiffractionVectors using ivec (#972)

  • DiffractionVectors now explicitly handles lazy signals (#972)

  • Added html representation for non-lazy DiffractionVectors (#972)

  • Added pyxem.signals.PolarVectors for polar vectors (#981)

  • Added clustering methods using pyxem.signals.DiffractionVectors.cluster() (#981)

  • Added pyxem.signals.LabeledDiffractionVectors for labeled diffraction vectors after clustering (#981)

Changed#

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

Fixed#

  • Update pyxem to work with hyperspy 2.0.0 (#969)

  • Fixed slow markers (#969)

  • Removed parallel and max_workers keywords in favor of using dask (#969)

  • DiffractionVectors2D now extends DiffractionVectors for a more consistent API (#972)

  • Fix zrnb_precipitate() dataset to point to proper dataset

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#

  • Remove ipywidgets from requirements as it is not a dependency

  • Set skimage != to version 0.21.0 because of regression

  • Do not reverse the y-axis of diffraction patterns when template matching (#925)

  • Fixed bug in pyxem.generators.indexation_generator.AcceleratedIndexationGenerator when passing orientations as tuples.

  • Fix bug in calculating strain (#958)

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

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