File python-hyperspy.changes of Package python-hyperspy
-------------------------------------------------------------------
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.
