Change Log

Release 0.2.5 (11 May 2022)

• updated for compatibility with latest scikit-image (issue 53).
• HyperSpy is now an optional dependency. It can be installed with pip by specifying fpd[HS] instead fpd, or separately by any other means.

Release 0.2.4 (2 May 2022)

• virtual_images() now pads input data with pixels of fill_value in cases where image shifts are larger than the ‘spare’ space allowed by the aperture(s).
• new radial_profiles() for calculating radial profiles of 4-D datasets with variable centre coordinates. (The older radial_profile() function may still be used on single images or a small number of them.)
• internal (hidden) utility functions for finding integer factors are now public: int_factors() and nearest_int_factor().
• rotate_vector() now also accepts an iterable as the yx_array input.
• SegmentedDPC (fpd.segmented_dpc_class.SegmentedDPC) is deprecated and will be removed in a future version.
• new segmented_dpc module containing new (and improved) functions for segmented DPC analysis: SegmentedDPC (fpd.segmented_dpc.SegmentedDPC); and experimental dataset parsing: load_gla_dpc().

Release 0.2.3 (26 February 2022)

• improve speed of the method='linear' mode of shift_im() by 4.6x.
• synthetic_aperture() and synthetic_images() are deprecated in favour of the new functions: virtual_apertures() and virtual_images().
• virtual_images() includes new features (described below) and is around 2x faster than synthetic_images().
• virtual_apertures() removes singular output axes in cases of a single aperture.
• virtual_images() accepts singular apertures and returns output without aperture axis in those cases.
• sum_dif(), virtual_images(), and VirtualAnnularImages can now shift images during the calculations through the dyx and dyx_method parameters.
• shift_im() has a new method=pixel setting for pixel-resolution image shifts.
• fill_value is now applied to all methods in shift_im().
• new cmap_nfold parameter in dpc_explorer_class, allowing the colormap to be repeated for improved angular contrast and use with data with symmetry axes.
• the colormap index is now included in the command output of dpc_explorer_class.

Release 0.2.2 (29 November 2021)

• strain() now handles LinAlgError exceptions.
• the return of blob_log_detect() now includes estimates of the error in the fitted coordinates.
• optimise_lattice() now also returns a measure of the error in the lattice fit.
• improved filtering of correlation peaks in blob_log_detect().
• setting negative sigma values in blob_log_detect() and phase_correlation() now generates a reference image by subtracting a smoothed version of it from itself.
• setting sigma=0 in blob_log_detect() now passes the images through unmodified, matching the longstanding behaviour in phase_correlation().
• blob_log_detect() now uses fftcorrelate() internally, allowing normalisation of the correlation to be set with the phase_exponent parameter.
• new fftcorrelate() function for correlation of images through cross- (default), phase- and hybrid-correlations.

Release 0.2.1 (19 October 2021)

• improve size of centre rectangle GUI element in dpc_explorer_class for very small data ranges.
• the save_data() method now returns the full filename of the output file.
• new signal_from and per_pixel parameters in snr_single_image() for specifying the origin of the signal and whether the returns are per pixel, respectively, mirroring the parameters in the new snr_single_image_wl() function. The equivalent precision for the snr is also now included in the output.
• new snr_single_image_wl() function for calculating the snr ratio of a single image using wavelet analysis for the noise component.
• new decibel() function for calculating decibels from power ratios.
• new strain() function for infinitesimal strain tensor calculations.
• the DataBrowser class can now handle non-fpd hdf5 datasets, and the diffraction plot normalisation can be set through the new norm parameter.
• removal of deprecated functions: radial_average() and disc_edge_sigma() (use radial_profile() and disc_edge_properties() instead).
• the map_image_function() function now allows the function parameters to be spatially varying by specifying them through the mapped_params parameter, for issue 46.
• new compression parameter in write_hdf5(), allowing use of the LZ4 algorithm for around 2x faster data reading and writing. See Compression for details. The LZ4 algorithm is provided by the hdf5plugin package, a new dependency. The default compression method remains gzip for maximum file portability.
• update MerlinBinary class for Merlin file format version 0.77.0.16.
• greatly improved Medipix colour handling and file conversion without header files in the MerlinBinary class. See merge request and Detector Axis and Colour Mode for details.
• improve metadata compatibility for Hyperspy version > 1.6. See merge request for details.
• improve test coverage (from around 81% to 88%).

Release 0.2.0 (25 March 2021)

• automatic runtime configuration of BLAS libraries with the threadpoolctl package. This additional control has allowed speed increases of several functions.
• parallel execution may be by multithreading or multiprocessing. Threading is the default, which should improve performance on across different OSs.
• new Timer class for simple timing.
• new update_calibration() for updating file calibrations.
• more efficient data handling and OS warning messaging in make_updated_fpd_file(). The changes also fix issue #39.

Release 0.1.13 (23 January 2021)

• Several internal changes to maintain support for newer versions of dependences.
• The minimum version of h5py is now 2.10.0 for new indexing style.
• add warning to fpd_to_hyperspy() for issues with specific HyperSpy versions.
• center_of_mass() and phase_correlation() now print useful stats and a warning when nans are preset.
• center_of_mass() now gracefully handles exceptions with Otsu thresholds.
• make_updated_fpd_file() prints info and reopens file before processing to avoid issues on Windows.

Release 0.1.12 (21 December 2020)

• fpd_to_tuple() now has a field with the file object.
• new determine_read_chunks() function for calculating chunk sizes.
• new make_updated_fpd_file() function for creating modified files.
• more robust conversion of app5 files with multiple datasets in topspin_app5_to_hdf5().
• improved version tags in hdf5 files made with topspin_app5_to_hdf5(), with PED_version incremented to 0.4.1.
• update MerlinBinary for Merlin file format version 0.75.4.84.
• Python2 legacy support has been dropped.
• The AlignNR is now public and imported at the top level.
• update phase_correlation() for register_translation deprecation in newer skimage.

Release 0.1.11 (1 November 2020)

synthetic_data module:

• method and fill_value are now exposed in shift_images().
• new array_image() function to make it easier to generate synthetic lattice (and other ‘arrayed’) images.

mag_tools module:

• new exchange_length() function.
• new vortex() and cross_tie() functions for generating magnetic textures.
• new fresnel() and tie() functions for calculation of Fresnel images and performing transport of intensity analysis.
• new tem_dpc() function for performing TEM-DPC analysis.

fft_tools module:

• new fft_diff() and fft2_diff() functions for performing Fourier space differentiation and integration of 1-D arrays and images.
• new fft2_laplacian() and fft2_ilaplacian() functions for performing Fourier space Laplacian and inverse Laplacian calculations.
• new im2fftrdf() function for calculating the azimuthally averaged profile of the spectral components of an image.
• sub-pixel calculations are now possible in fft2rdf() through the new sp parameter.
• new pad_image() function for convenient padding of images to a given size and shape.
• new cepstrum() and cepstrum2() functions for performing 1-D and 2-D cepstrum calculations.
• new fft2_igrad() function for inverse 2-D gradient calculations.

tem_tools module:

• new defocus_from_image() function to automate extraction of defocus in TEM images.
• the radius and angle of the mouse position are now displayed in the plot in synthetic_lattice(), allowing the coordinates to be more easily seen (e.g. for specifying in lattice_resolver()).
• the search angle range is now exposed in lattice_resolver() through the search_dangle parameter.
• the optimise_lattice() function now performs a weighted fit if the weights are specified in the weights parameter.
• blob_log_detect() now extracts a signal metric and returns it in an additional column, which may be used for weighting the lattice fit, or for other purposes.
• new background_erosion() function to perform background estimation and removal in diffraction images.
• new multithreaded non-rigid image alignment class AlignNR.

fpd_processing module:

• nrmse() can now handle nans by setting the parameter allow_nans to True.

fpd_file module:

• chunking for sum image calculations in write_hdf5() is now automated, with control set by the new MiB_max parameter.

Others:

• new progress_bar option in many functions and classes (write_hdf5(), to_array(), topspin_app5_to_hdf5(), sum_im(), sum_dif(), synthetic_images(), center_of_mass(), find_matching_images(), map_image_function(), VirtualAnnularImages).
• reading GSF files with readGSF() is much faster for large files.
• new gaussian_fwhm() function for calculating Gaussian FWHM.

Plus many minor improvements.

Release 0.1.10 (7 April 2020)

• find_circ_centre() now returns subpixel centre coordinates by peak fitting in Hough space.
• fix typo in function name fpd_to_hyperspy().
• y-axes are now shared in plots from lattice_magnitudes().
• polar plots have been improved in disc_edge_properties() and erf fits now use a free minimum value.

Release 0.1.9 (1 March 2020)

• reverse angle direction in disc_edge_sigma() for consistency.
• new sum_ax() function for summing over an axis.
• fix bug in reshaping phase_correlation() with pre_func and post_func.
• add rebin option to downscaling in synthetic_aperture() (now the default method).
• add rebin option to downscaling in disk_image().
• improve normalisation of live radius plotting in dpc_explorer_class.
• new tem_tools/airy_fwhm() function in tem_tools module.
• radial_average() is marked as deprecated in favour of the new and currently identical radial_profile() function.
• drop hyperspy option from disc_edge_sigma() function.
• fix edge-case bug center_of_mass() when using pre_func but not rebinning.
• phase_correlation() can now be set to not perform derivatives with sigma=0.
• sum_ax() progress bar can now be disabled with progress_bar=False.
• shift_im() now has multiple methods for image shifting (default is now linear).
• new disc_edge_properties() to replace the simpler disc_edge_sigma() function. The latter is deprecated and will be removed in a future release. The former performs more analysis and returns a namedtuple with many additional properties extracted.
• the array interface of MerlinBinary progress bar is now suppressed (re-enable with array_interface_progress_bar=True).
• write_hdf5() now uses functions in fpd_processing for sum images.
• some optimisation of file conversion with write_hdf5().
• write_hdf5() now accepts a function to manipulate images during conversion (doc: Data Manipulation).
• new fpd_to_tuple() function for accessing our HDF5 files (doc: Updating Files).

Release 0.1.8 (4 November 2019)

• updates for compatibility with most recent skimage and numpy.

Release 0.1.7 (1 September 2019)

• new Airy disc diameter airy_d()
• new 7-smooth number smooth7()
• new module for io fpd_io featuring a NanoMegas Topspin app5 file converter for SPED data topspin_app5_to_hdf5() (documentation: Converting Topspin app5 Files).

Release 0.1.6 (24 March 2019)

• improvements to MerlinBinary class
• speed optimisations in synthetic_images()
• ‘Uniform’ colourmap renamed to ‘MLP’
• additional conversion functions in mag_tools
• improvements to the single image SNR function, snr_single_image()

Release 0.1.5 (18 February 2019)

• improvements to or new lattice functions: lattice_from_inliers(), blob_log_detect(), lattice_resolver()
• new SNR and gun noise correction tools in a new utils module
• many other small improvements.

Release 0.1.4 (27 October 2018)

• new CubicImageInterpolator and VirtualAnnularImages classes
• several lattice finding tools: blob_log_detect(), friedel_filter(), synthetic_lattice(), vector_combinations(), lattice_angles(), lattice_magnitudes(), lattice_inlier(), optimise_lattice()
• ctf tools: ctf(), scherzer_defocus(), defocus_from_ctf_crossing()
• image alignment tools: orb_trans(), optimise_trans(), apply_image_trans()
• many other small improvements.

Release 0.1.3 (31 July 2018)

• new MerlinBinary class
• many other small improvements.

25 Mar 2018

• Notebook demos are now available at https://gitlab.com/fpdpy/fpd-demos