File python-hyperspy.changes of Package python-hyperspy

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File python-hyperspy.changes of Package python-hyperspy

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Fri Jan 20 17:18:20 UTC 2023 - Ben Greiner <code@bnavigator.de>

- Update to 1.7.3
  ## Bug Fixes
  * Fix error when reading Velox containing FFT with odd number of
    pixels (#3040)
  * Fix pint Unit for pint>=0.20 (#3052)
  ## Maintenance
  * Fix deprecated import of scipy ascent in docstrings and the
    test suite (#3032)
  * Fix error handling when trying to convert a ragged signal to
    non-ragged for numpy >=1.24 (#3033)
  * Fix getting random state dask for dask>=2022.10.0 (#3049)
- Release Hyperspy 1.7.2
  ## Bug Fixes
  * Fix some errors and remove unnecessary code identified by LGTM.
    (#2977)
  * Fix error which occurs when guessing output size in the map()
    function and using dask newer than 2022.7.1 (#2981)
  * Fix display of x-ray lines when using log norm and the
    intensity at the line is 0 (#2995)
  * Fix handling constant derivative in spikes_removal_tool()
    (#3005)
  * Fix removing horizontal or vertical line widget; regression
    introduced in hyperspy 1.7.0 (#3008)
  ## Maintenance
  * Fix extension test suite CI workflow. Enable workflow manual
    trigger (#2982)
  * Fix deprecation warning and time zone test failing on windows
    (locale dependent) (#2984)
  * Fix external links in the documentation and add CI build to
    check external links (#3001)
  * Fix hyperlink in bibliography (#3015)
  * Fix matplotlib SpanSelector import for matplotlib 3.6 (#3016)
- Release Hyperspy 1.7.1
  ## Bug Fixes
  * Fixes invalid file chunks when saving some signals to hspy/zspy
    formats. (#2940)
  * Fix issue where a TIFF image from an FEI FIB/SEM navigation
    camera image would not be read due to missing metadata (#2941)
  * Respect show_progressbar parameter in map() (#2946)
  * Fix regression in set_signal_range() which was raising an error
    when used interactively (#2948)
  * Fix SpanROI regression: the output of interactive() was not
    updated when the ROI was changed. Fix errors with updating
    limits when plotting empty slice of data. Improve docstrings
    and test coverage. (#2952)
  * Fix stacking signals that contain their variance in metadata.
    Previously it was raising an error when specifying the stacking
    axis. (#2954)
  * Fix missing API documentation of several signal classes.
    (#2957)
  * Fix two bugs in decomposition():
  * The poisson noise normalization was not applied when giving a
    signal_mask
  * An error was raised when applying a signal_mask on a signal
    with signal dimension larger than 1. (#2964)
  ## Maintenance
  * Minor refactor of the EELS subshells in the elements
    dictionary. (#2868)
  * Fix packaging of test suite and tweak tests to pass on
    different platform of blas implementation (#2933)
- Release Hyperspy 1.7.0
  ## New Features
  * Add filter_zero_loss_peak argument to the spikes_removal_tool()
    method (#1412)
  * Add calibrate() method to Signal2D signal, which allows for
    interactive calibration (#1791)
  * Add vacuum_mask() method to EELSSpectrum signal (#2183)
  * Support for relative slicing (#2386)
  * Implement non-uniform axes, not all hyperspy functionalities
    support non-uniform axes, see this tracking issue for progress.
    (#2399)
  * Add (weighted) linear least square fitting. Close #488 and
    #574. (#2422)
  * Support for reading JEOL EDS data (#2488)
  * Plot overlayed images - see plotting several images (#2599)
  * Add initial support for GPU computation using cupy (#2670)
  * Add height property to the Gaussian2D component (#2688)
  * Support for reading and writing TVIPS image stream data (#2780)
  * Add in zspy format: hspy specification with the zarr format.
    Particularly useful to speed up loading and saving large
    datasets by using concurrency. (#2825)
  * Support for reading DENSsolutions Impulse data (#2828)
  * Add lazy loading for JEOL EDS data (#2846)
  * Add html representation for lazy signals and the
    get_chunk_size() method to get the chunk size of given axes
    (#2855)
  * Add support for Hamamatsu HPD-TA Streak Camera tiff files, with
    axes and metadata parsing. (#2908)
  ## Bug Fixes
  * Signals with 1 value in the signal dimension will now be
    BaseSignal (#2773)
  * density_of_mixture() now throws a Value error when the density
    of an element is unknown (#2775)
  * Improve error message when performing Cliff-Lorimer
    quantification with a single line intensity (#2822)
  * Fix bug for the hydrogenic gdos k edge (#2859)
  * Fix bug in axes.UnitConversion: the offset value was
    initialized by units. (#2864)
  * Fix bug where the map() function wasn’t operating properly when
    an iterating signal was larger than the input signal. (#2878)
  * In case the Bruker defined XML element node at SpectrumRegion
    contains no information on the specific selected X-ray line (if
    there is only single line available), suppose it is ‘Ka’ line.
    (#2881)
  * When loading Bruker Bcf, cutoff_at_kV=None does no cutoff
    (#2898)
  * Fix bug where the map() function wasn’t operating properly when
    an iterating signal was not an array. (#2903)
  * Fix bug for not saving ragged arrays with dimensions larger
    than 2 in the ragged dimension. (#2906)
  * Fix bug with importing some spectra from eelsdb and add
    progress bar (#2916)
  * Fix bug when the spikes_removal_tool would not work
    interactively for signal with 0-dimension navigation space.
    (#2918)
  ## Deprecations
  * Deprecate set_signal_dimension() in favour of using
    as_signal1D(), as_signal2D() or transpose() of the signal
    instance instead. (#2830)
  ## Enhancements
  * Region of Interest (ROI) can now be created without specifying
    values (#2341)
  * mpfit cleanup (#2494)
  * Document reading Attolight data with the sur/pro format reader
    (#2559)
  * Lazy signals now caches the current data chunk when using
    multifit and when plotting, improving performance. (#2568)
  * Read cathodoluminescence metadata from digital micrograph
    files, amended in PR #2894 (#2590)
  * Add possibility to search/access nested items in
    DictionaryTreeBrowser (metadata) without providing full path to
    item. (#2633)
  * Improve map() function in BaseSignal by utilizing dask for both
    lazy and non-lazy signals. This includes adding a lazy_output
    parameter, meaning non-lazy signals now can output lazy
    results. See the user guide for more information. (#2703)
  * NeXus file with more options when reading and writing (#2725)
  * Add dtype argument to rebin() (#2764)
  * Add option to set output size when exporting images (#2791)
  * Add switch_iterpath() context manager to switch iterpath
    (#2795)
  * Add options not to close file (lazy signal only) and not to
    write dataset for hspy file format, see HSpy - HyperSpy’s HDF5
    Specification for details (#2797)
  * Add Github workflow to run test suite of extension from a pull
    request. (#2824)
  * Add ragged attribute to BaseSignal to clarify when a signal
    contains a ragged array. Fix inconsistency caused by ragged
    array and add a ragged array section to the user guide (#2842)
  * Import hyperspy submodules lazily to speed up importing
    hyperspy. Fix autocompletion signals submodule (#2850)
  * Add support for JEOL SightX tiff file (#2862)
  * Add new markers arrow, ellipse and filled rectangle. (#2871)
  * Add metadata about the file-reading and saving operations to
    the Signals produced by load() and save() (see the metadata
    structure section of the user guide) (#2873)
  * expose Stage coordinates and rotation angle in metada for sem
    images in bcf reader. (#2911)
  ## API changes
  * metadata.Signal.binned is replaced by an axis parameter, e. g.
    axes_manager[-1].is_binned (#2652)
  * when loading Bruker bcf, cutoff_at_kV=None (default) applies no
    more automatic cutoff.
  * New acceptable values "zealous" and "auto" do automatic cutoff.
    (#2910)
  * Deprecate the ability to directly set metadata and
    original_metadata Signal attributes in favor of using
    set_item() and add_dictionary() methods or specifying metadata
    when creating signals (#2913)
  ## Maintenance
  * Drop support for python 3.6 (#2839)
  * Continuous integration fixes and improvements; Bump minimal
    version requirement of dask to 2.11.0 and matplotlib to 3.1.3
    (#2866)
  * Tweak tests tolerance to fix tests failure on aarch64 platform;
    Add python 3.10 build. (#2914)
  * Add support for matplotlib 3.5, simplify maintenance of
    RangeWidget and some signal tools. (#2922)
  * Compress some tiff tests files to reduce package size (#2926)
- Release v1.6.5
  ## Bug Fixes
  * Suspend plotting during smart_fit() call (#2796)
  * make add_marker() also check if the plot is not active before
    plotting signal (#2799)
  * Fix irresponsive ROI added to a signal plot with a right hand
    side axis (#2809)
  * Fix plot_histograms() drawstyle following matplotlib API change
    (#2810)
  * Fix incorrect map() output size of lazy signal when input and
    output axes do not match (#2837)
  * Add support for latest h5py release (3.5) (#2843)
  ## Deprecations
  * Rename line_style to linestyle in plot_spectra() to match
    matplotlib argument name (#2810)
  ## Enhancements
  * add_widget() can now take a string or integer instead of tuple
    of string or integer (#2809)
- Release v1.6.4
  ## Bug Fixes
  * Fix parsing EELS aperture label with unexpected value, for
    example ‘Imaging’ instead of ‘5 mm’ (#2772)
  * Lazy datasets can now be saved out as blockfiles (blo) (#2774)
  * ComplexSignals can now be rebinned without error (#2789)
  * Method estimate_parameters() of the Polynomial component now
    supports order greater than 10 (#2790)
  * Update minimal requirement of dependency importlib_metadata
    from >= 1.6.0 to >= 3.6 (#2793)
  ## Enhancements
  * When saving a dataset with a dtype other than uint8 to a
    blockfile (blo) it is now possible to provide the argument
    intensity_scaling to map the intensity values to the reduced
    range (#2774)
  ## Maintenance
  * Fix image comparison failure with numpy 1.21.0 (#2774)
- Release v1.6.3
  ## Bug Fixes
  * Fix ROI snapping regression (#2720)
  * Fix shift1D(), align1D() and align_zero_loss_peak() regression
    with navigation dimension larger than one (#2729)
  * Fix disconnecting events when closing figure and
    remove_background() is active (#2734)
  * Fix map() regression of lazy signal with navigation chunks of
    size of 1 (#2748)
  * Fix unclear error message when reading a hspy file saved using
    blosc compression and hdf5plugin hasn’t been imported
    previously (#2760)
  * Fix saving navigator of lazy signal (#2763)
  ## Enhancements
  * Use importlib_metadata instead of pkg_resources for extensions
    registration to speed up the import process and making it
    possible to install extensions and use them without restarting
    the python session (#2709)
  * Don’t import hyperspy extensions when registering extensions
    (#2711)
  * Improve docstrings of various fitting methods (#2724)
  * Improve speed of shift1D() (#2750)
  * Add support for recent EMPAD file; scanning size wasn’t parsed.
    (#2757)
- Add scipy-datasets.tar.gz for testing
  * hyperspy-e2d6483-scipy-datasets-fix.patch for typo fix
    gh#hyperspy/hyperspy/commit/e2d6483

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Wed Apr 14 10:26:35 UTC 2021 - andy great <andythe_great@pm.me>

- Update to version 1.6.2.
  * Widgets plotting improvement and add ``pick_tolerance`` to plot 
    preferences 
  * Update external links in the loading data section of the user 
    guide
  * Pass keyword argument to the image IO plugins
  * Drop support for numpy<1.16, in line with NEP 29 and fix 
    protochip reader for numpy 1.20 
  * Run test suite against upstream dependencies 
    (numpy, scipy, scikit-learn and scikit-image) 
  * Improve error message when file not found 
  * Add update instructions to user guide 
  * Fix disconnect event when closing navigator only plot
  * Improve plotting navigator of lazy signals, add ``navigator`` 
    setter to lazy signals 
  * Use 'dask_auto' when rechunk=True in ``change_dtype`` for lazy
    signal 
  * Use dask chunking when saving lazy signal instead of rechunking
    and leave the user to decide what is the suitable chunking 
  * Fix incorrect chunksize when saving EMD NCEM file and 
    specifying chunks 
  * Fix ``find_peaks`` GUIs call with laplacian/difference of 
    gaussian methods 
  * Added lazy reading support for FFT and DPC datasets in FEI 
    emd datasets
  * Fix various future and deprecation warnings from numpy 
    and scikit-learn 
  * Improve error message when initialising SpanROI with 
    left >= right
  * Fix ``iterpath`` VisibleDeprecationWarning when using 
    ``fit_component`` 
  * Fix various bugs with ``CircleWidget`` and ``Line2DWidget``
  * Allow running the test suite without the pytest-mpl plugin 
  * Fix warnings when building documentation 
  * Add Releasing guide
  * Fix setting signal range of model with negative axis scales
  * Fix and improve mask handling in lazy decomposition
  * Plot scalebar when the axis scales have different sign
  * Fix align1D returning zeros shifts 
  * Fix finding dataset path for EMD NCEM file containing more 
    than one dataset in a group
  * Add support for python 3.9, fix deprecation warning with 
    matplotlib 3.4.0 and bump minimum requirement to numpy 1.17.1
    and dask 2.1.0. 
  * Add integration test suite documentation in the developer guide.
  * Fix squeeze function for multiple zero-dimensional entries, 
    improved docstring, added to user guide.
  * Use native endianess in numba jitted functions.
  * Fix error in Cliff-Lorimer quantification using absorption
    correction
  * Fix ``navigation_mask`` bug in decomposition when provided as 
    numpy array 
  * Fix closing image contrast tool and setting vmin/vmax values
  * Fix range widget with matplotlib 3.4
  * Fix bug in `hs.interactive` with function returning `None`. 
    Improve user guide example. 
  * Add option not to snap ROI when calling the `interactive` 
    method of a ROI
  * Fix broken events when changing signal type
  * Make DictionaryTreeBrowser lazy by default
  * Fix setting offset in rebin: the offset was changed in the 
    wrong axis
  * Fix reading XRF bruker file
  * Speed up setting CI on azure pipeline
  * Fix performance issue with the lazy map method of lazy
  * Add option to copy/load original metadata in ``hs.stack`` 
    and ``hs.load`` to avoid large ``original_metadata`` which can
    slowdown processing.
  * Fix SkewNormal component compatibility with sympy 1.8

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Tue Apr 14 00:10:55 UTC 2020 - andy great <andythe_great@pm.me>

- Initial package release, version 1.6.1.

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