Changelog#

Changelog entries for the development version are available at https://hyperspy.readthedocs.io/en/latest/changes.html

2.1.1.dev58+g95c194c [UNRELEASED] (2024-06-06)#

Enhancements#

  • Only import gui widget when the toolkit is enabled. (#3366)

  • Tweak documention on dask scheduler. (#3380)

Bug Fixes#

2.1.0 (2024-05-08)#

Enhancements#

  • Add a dynamic navigator which updates when the number of navigation dimensions is greater than 3 (#3199)

  • Add an example to the gallery to show how to extract a line profile from an image using a Line2DROI (#3227)

  • Add an example showing how to handle RGB images. (#3346)

  • Use pint.get_application_registry() to get pint.UnitRegistry and facilitate interoperability of pint quantity operation with other modules. (#3357)

  • plot_roi_map() improvement:

    • Add ROIs on signal plot instead of adding them on a sum signal.

    • Add support for more than 3 ROIs.

    • Add color and cmap parameters to specify color and colormap.

    • Add single_figure parameter to enable plotting on a single figure using plot_images() or plot_spectra().

    • Improve performance of updating ROI maps by a factor 2-4 when moving ROI.

    • Update images in plot_images() on data change event.

    • Remove ROI widgets and disconnect interactive function when closing ROI map figures. (#3364)

  • Documentation improvement. (#3365)

Bug Fixes#

API changes#

Maintenance#

  • Ruff update:

    • Set the RELEASE_next_patch branch as target for the pre-commit.ci update to keep all branches in synchronisation.

    • Update ruff to version 0.3.3 and run ruff check/format on source code. (#3335)

  • Replace deprecated np.string_ by np.bytes_. (#3338)

  • Enable ruff isort and all pyflakes/Pycodestyle rules, except E501 to avoid confict with black formatting. (#3348)

  • Merge hyperspy.api.no and hyperspy.api.no_gui modules since the latter is not necessary anymore. (#3349)

  • Convert projet readme to markdown, fixes badges on github (#3351)

  • Simplify Azure Pipeline CI by removing build and uploading wheels, since this is now done on GitHub CI. (#3356)

  • Fix duplicated test and occasional test failure. (#3365)

  • Use lower case when checking matplotlib backend in the test suite. (#3367)

  • Add percentile_range traitsui attribute to ImageContrastEditor necessary for hyperspy/hyperspy_gui_traitsui#76. (#3368)

2.0.1 (2024-02-26)#

Bug Fixes#

  • Fix bug with side by side plotting of signal containing navigation dimension only. (#3304)

  • Fix getting release on some linux system wide install, e.g. Debian or Google colab (#3318)

  • Fix incorrect position of Texts marker when using mathtext. (#3319)

Maintenance#

  • Update version switcher. (#3291)

  • Fix readme badges and fix broken web links. (#3298)

  • Use ruff to lint code. (#3299)

  • Use ruff to format code. (#3300)

  • Run test suite on osx arm64 on GitHub CI and speed running test suite using all available CPUs (3 or 4) instead of only 2. (#3305)

  • Fix API changes in scipy (scipy.signal.windows.tukey()) and scikit-image (skimage.restoration.unwrap_phase()). (#3306)

  • Fix deprecation warnings and warnings in the test suite (#3320)

  • Add documentation on how the documentation is updated and the required manual changes for minor and major releases. (#3321)

  • Add Google Analytics ID to learn more about documentation usage. (#3322)

  • Setup workflow to push development documentation automatically. (#3297)

2.0 (2023-12-20)#

Release Highlights#

  • Hyperspy has split off some of the file reading/writing and domain specific functionalities into separate libraries!

  • The markers API has been refactored

    • Lazy markers are now supported

    • Plotting many markers is now much faster

    • Added Polygons marker

  • The documentation has been restructured and improved!

    • Short example scripts are now included in the documentation

    • Improved guides for lazy computing as well as an improved developer guide

  • Plotting is easier and more consistent:

    • Added horizontal figure layout choice when using the ipympl backend

    • Changing navigation coordinates using the keyboard arrow-keys has been removed. Use Crtl + Arrow instead.

    • Jump to navigation position using shift + click in the navigator figure.

  • HyperSpy now works with Pyodide/Jupyterlite, checkout hyperspy.org/jupyterlite-hyperspy!

  • The deprecated API has removed: see the list of API changes and removal in the sections below.

New features#

  • compute() will now pass keyword arguments to the dask dask.array.Array.compute() method. This enables setting the scheduler and the number of computational workers. (#2971)

  • Changes to plot():

    • Added horizontal figure layout choice when using the ipympl backend. The default layour can be set in the plot section of the preferences GUI. (#3140)

  • Changes to find_peaks():

    • Lazy signals return lazy peak signals

    • get_intensity argument added to get the intensity of the peaks

    • The signal axes are now stored in the metadata.Peaks.signal_axes attribute of the peaks’ signal. (#3142)

  • Change the logging output so that logging messages are not displayed in red, to avoid confusion with errors. (#3173)

  • Added hyperspy.decorators.deprecated and hyperspy.decorators.deprecated_argument:

    • Provide consistent and clean deprecation

    • Added a guide for deprecating code (#3174)

  • Add functionality to select navigation position using shift + click in the navigator. (#3175)

  • Added a plot_residual to plot(). When True, a residual line (Signal - Model) appears in the model figure. (#3186)

  • Switch to matplotlib.axes.Axes.pcolormesh() for image plots involving non-uniform axes. The following cases are covered: 2D-signal with arbitrary navigation-dimension, 1D-navigation and 1D-signal (linescan). Not covered are 2D-navigation images (still uses sliders). (#3192)

  • New interpolate_on_axis() method to switch one axis of a signal. The data is interpolated in the process. (#3214)

  • Added plot_roi_map(). Allows interactively using a set of ROIs to select regions of the signal axes of a signal and visualise how the signal varies in this range spatially. (#3224)

Bug Fixes#

  • Improve syntax in the io module. (#3091)

  • Fix behaviour of DictionaryTreeBrowser setter with value of dictionary type (#3094)

  • Avoid slowing down fitting by optimising attribute access of model. (#3155)

  • Fix harmless error message when using multiple RectangularROI: check if resizer patches are drawn before removing them. Don’t display resizers when adding the widget to the figure (widget in unselected state) for consistency with unselected state (#3222)

  • Fix keeping dtype in rebin() when the endianess is specified in the dtype (#3237)

  • Fix serialization error due to traits.api.Property not being serializable if a dtype is specified. See #3261 for more details. (#3262)

  • Fix setting bounds for "trf", "dogbox" optimizer (#3244)

  • Fix bugs in new marker implementation:

    • Markers str representation fails if the marker isn’t added to a signal

    • make from_signal() to work with all markers - it was only working with Points (#3270)

  • Documentation fixes:

    • Fix cross-references in documentation and enable sphinx “nitpicky” when building documentation to check for broken links.

    • Fix using mutable objects as default argument.

    • Change some Component attributes to properties in order to include their docstrings in the API reference. (#3273)

Improved Documentation#

  • Restructure documentation:

    • Improve structure of the API reference

    • Improve introduction and overall structure of documentation

    • Add gallery of examples (#3050)

  • Add examples to the gallery to show how to use SpanROI and slice signal interactively (#3221)

  • Add a section on keeping a clean and sensible commit history to the developer guide. (#3064)

  • Replace sphinx.ext.imgmath by sphinx.ext.mathjax to fix the math rendering in the ReadTheDocs build (#3084)

  • Fix docstring examples in BaseSignal class. Describe how to test docstring examples in developer guide. (#3095)

  • Update intersphinx_mapping links of matplotlib, numpy and scipy. (#3218)

  • Add examples on creating signal from tabular data or reading from a simple text file (#3246)

  • Activate checking of example code in docstring and user guide using doctest and fix errors in the code. (#3281)

  • Update warning of “beta” state in big data section to be more specific. (#3282)

Enhancements#

  • Add support for passing **kwargs to plot() when using heatmap style in plot_spectra() . (#3219)

  • Add support for pep 660 on editable installs for pyproject.toml based builds of extension (#3252)

  • Make HyperSpy compatible with pyodide (hence JupyterLite):

    • Set numba and numexpr as optional dependencies.

    • Replace dill by cloudpickle.

    • Fallback to dask synchronous scheduler when running on pyodide.

    • Reduce packaging size to less than 1MB.

    • Add packaging test on GitHub CI. (#3255)

API changes#

  • RosettaSciIO was split out of the HyperSpy repository on July 23, 2022. The IO-plugins and related functions so far developed in HyperSpy were moved to the RosettaSciIO repository. (#2972)

  • Extend the IO functions to accept alias names for format name as defined in RosettaSciIO. (#3009)

  • Fix behaviour of print_current_values(), print_current_values() and print_known_signal_types(), which were not printing when running from a script - they were only printing when running in notebook or qtconsole. Now all print_* functions behave consistently: they all print the output instead of returning an object (string or html). The IPython.display.display() will pick a suitable rendering when running in an “ipython” context, for example notebook, qtconsole. (#3145)

  • The markers have been refactored - see the new markers API and the gallery of examples for usage. The new Markers uses matplotlib.collections.Collection, is faster and more generic than the previous implementation and also supports lazy markers. Markers saved in HyperSpy files (hspy, zspy) with HyperSpy < 2.0 are converted automatically when loading the file. (#3148)

  • For all functions with the rechunk parameter, the default has been changed from True to False. This means HyperSpy will not automatically try to change the chunking for lazy signals. The old behaviour could lead to a reduction in performance when working with large lazy datasets, for example 4D-STEM data. (#3166)

  • Renamed Signal2D.crop_image to crop_signal() (#3197)

  • Changes and improvement of the map function:

    • Removes the parallel argument

    • Replace the max_workers with the num_workers argument to be consistent with dask

    • Adds more documentation on setting the dask backend and how to use multiple cores

    • Adds navigation_chunk argument for setting the chunks with a non-lazy signal

    • Fix axes handling when the function to be mapped can be applied to the whole dataset - typically when it has the axis or axes keyword argument. (#3198)

  • Remove physics_tools since it is not used and doesn’t fit in the scope of HyperSpy. (#3235)

  • Improve the readability of the code by replacing the __call__ method of some objects with the more explicit _get_current_data.

  • Rename hyperspy.api.datasets to hyperspy.api.data and simplify submodule structure:

API Removal#

As the HyperSpy API evolves, some of its parts are occasionally reorganized or removed. When APIs evolve, the old API is deprecated and eventually removed in a major release. The functions and methods removed in HyperSpy 2.0 are listed below along with migration advises:

Axes#

Components#

  • The API of the Polynomial has changed (it was deprecated in HyperSpy 1.5). The old API had a single parameters coefficients, which has been replaced by a0, a1, etc.

  • The legacy option (introduced in HyperSpy 1.6) for Arctan has been removed, use exspy.components.EELSArctan to use the old API.

  • The legacy option (introduced in HyperSpy 1.6) for Voigt has been removed, use exspy.components.PESVoigt to use the old API.

Data Visualization#

  • The saturated_pixels keyword argument of plot() has been removed, use vmin and/or vmax instead.

  • The get_complex property of hyperspy.drawing.signal1d.Signal1DLine has been removed.

  • The keyword argument line_style of plot_spectra() has been renamed to linestyle.

  • Changing navigation coordinates using keyboard Arrow has been removed, use Crtl + Arrow instead.

  • The markers submodules can not be imported from the api anymore, use hyperspy.api.plot.markers directly, i.e. hyperspy.api.plot.markers.Arrows, instead.

  • The creation of markers has changed to use their class name instead of aliases, for example, use m = hs.plot.markers.Lines instead of m = hs.plot.markers.line_segment.

Loading and Saving data#

The following deprecated keyword arguments have been removed during the migration of the IO plugins to the RosettaSciIO library:

  • The arguments mmap_dir and load_to_memory of the load() function have been removed, use the lazy argument instead.

  • Bruker composite file (BCF): The 'spectrum' option for the select_type parameter was removed. Use 'spectrum_image' instead.

  • Electron Microscopy Dataset (EMD) NCEM: Using the keyword dataset_name was removed, use dataset_path instead.

  • NeXus data format: The dataset_keys, dataset_paths and metadata_keys keywords were removed. Use dataset_key, dataset_path and metadata_key instead.

Machine Learning#

  • The polyfit keyword argument has been removed. Use var_func instead.

  • The list of possible values for the algorithm argument of the decomposition() method has been changed according to the following table:

    Change of the algorithm argument#

    hyperspy < 2.0

    hyperspy >= 2.0

    fast_svd

    SVD along with the argument svd_solver=”randomized”

    svd

    SVD

    fast_mlpca

    MLPCA along with the argument svd_solver=”randomized

    mlpca

    MLPCA

    nmf

    NMF

    RPCA_GoDec

    RPCA

  • The argument learning_rate of the ORPCA algorithm has been renamed to subspace_learning_rate.

  • The argument momentum of the ORPCA algorithm has been renamed to subspace_momentum.

  • The list of possible values for the centre keyword argument of the decomposition() method when using the SVD algorithm has been changed according to the following table:

    Change of the centre argument#

    hyperspy < 2.0

    hyperspy >= 2.0

    trials

    navigation

    variables

    signal

  • For lazy signals, a possible value of the algorithm keyword argument of the decomposition() method has been changed from "ONMF" to "ORNMF".

  • Setting the metadata and original_metadata attribute of signals is removed, use the set_item() and add_dictionary() methods of the metadata and original_metadata attribute instead.

Model fitting#

  • The iterpath default value has changed from 'flyback' to 'serpentine'.

  • Changes in the arguments of the fit() and multifit() methods:

    • The fitter argument has been renamed to optimizer.

    • The list of possible values for the optimizer argument has been renamed according to the following table:

      Renaming of the optimizer argument#

      hyperspy < 2.0

      hyperspy >= 2.0

      fmin

      Nelder-Mead

      fmin_cg

      CG

      fmin_ncg

      Newton-CG

      fmin_bfgs

      Newton-BFGS

      fmin_l_bfgs_b

      L-BFGS-B

      fmin_tnc

      TNC

      fmin_powell

      Powell

      mpfit

      lm

      leastsq

      lm

      • loss_function="ml" has been renamed to loss_function="ML-poisson".

      • grad=True has been changed to grad="analytical".

      • The ext_bounding argument has been renamed to bounded.

      • The min_function argument has been removed, use the loss_function argument instead.

      • The min_function_grad argument has been removed, use the grad argument instead.

  • The following BaseModel methods have been removed:

    • hyperspy.model.BaseModel.set_boundaries

    • hyperspy.model.BaseModel.set_mpfit_parameters_info

  • The arguments parallel and max_workers have been removed from the as_signal() methods.

  • Setting the metadata attribute of a Samfire has been removed, use the set_item() and add_dictionary() methods of the metadata attribute instead.

  • The deprecated twin_function and twin_inverse_function have been privatized.

  • Remove fancy argument of print_current_values() and print_current_values(), which wasn’t changing the output rendering.

  • The attribute channel_switches of BaseModel have been privatized, instead use the set_signal_range_from_mask() or any other methods to set the signal range, such as set_signal_range(), add_signal_range() or remove_signal_range() and their Model2D counterparts.

Signal#

  • metadata.Signal.binned is removed, use the is_binned axis attribute instead, e. g. s.axes_manager[-1].is_binned.

  • Some possible values for the bins argument of the get_histogram() method have been changed according to the following table:

    Change of the bins argument#

    hyperspy < 2.0

    hyperspy >= 2.0

    scotts

    scott

    freedman

    fd

  • The integrate_in_range method has been removed, use SpanROI followed by integrate1D() instead.

  • The progressbar keyword argument of the compute() method has been removed, use show_progressbar instead.

  • The deprecated comp_label argument of the methods plot_decomposition_loadings(), plot_decomposition_factors(), plot_bss_loadings(), plot_bss_factors(), plot_cluster_distances(), plot_cluster_labels() has been removed, use the title argument instead.

  • The set_signal_type() now raises an error when passing None to the signal_type argument. Use signal_type="" instead.

  • Passing an “iterating over navigation argument” to the map() method is removed, pass a HyperSpy signal with suitable navigation and signal shape instead.

Signal2D#

  • find_peaks() now returns lazy signals in case of lazy input signal.

Preferences#

  • The warn_if_guis_are_missing HyperSpy preferences setting has been removed, as it is not necessary anymore.

Maintenance#

  • Pin third party GitHub actions and add maintenance guidelines on how to update them (#3027)

  • Drop support for python 3.7, update oldest supported dependencies and simplify code accordingly (#3144)

  • IPython and IParallel are now optional dependencies (#3145)

  • Fix Numpy 1.25 deprecation: implicit array to scalar conversion in align2D() (#3189)

  • Replace deprecated scipy.misc by scipy.datasets in documentation (#3225)

  • Fix documentation version switcher (#3228)

  • Replace deprecated scipy.interpolate.interp1d with scipy.interpolate.make_interp_spline() (#3233)

  • Add support for python 3.12 (#3256)

  • Consolidate package metadata:

    • use pyproject.toml only

    • clean up unmaintained packaging files

    • use setuptools_scm to define version

    • add python 3.12 to test matrix (#3268)

  • Pin pytest-xdist to 3.5 as a workaround for test suite failure on Azure Pipeline (#3274)

1.7.6 (2023-11-17)#

Bug Fixes#

  • Allows for loading of .hspy files saved with version 2.0.0 and greater and no unit or name set for some axis. (#3241)

Maintenance#

  • Backport of 3189: fix Numpy1.25 deprecation: implicite array to scalar conversion in align2D() (#3243)

  • Pin pillow to <10.1 to avoid imageio error. (#3251)

1.7.5 (2023-05-04)#

Bug Fixes#

  • Fix plotting boolean array with plot_images() (#3118)

  • Fix test with scipy1.11 and update deprecated scipy.interpolate.interp2d in the test suite (#3124)

  • Use intersphinx links to fix links to scikit-image documentation (#3125)

Enhancements#

  • Improve performance of model.multifit by avoiding axes.is_binned repeated evaluation (#3126)

Maintenance#

  • Simplify release workflow and replace deprecated actions/create-release action with softprops/action-gh-release. (#3117)

  • Add support for python 3.11 (#3134)

  • Pin imageio to <2.28 (#3138)

1.7.4 (2023-03-16)#

Bug Fixes#

  • Fixes an array indexing bug when loading a .sur file format spectra series. (#3060)

  • Speed up to_numpy function to avoid slow down when used repeatedly, typically during fitting (#3109)

Improved Documentation#

  • Replace sphinx.ext.imgmath by sphinx.ext.mathjax to fix the math rendering in the ReadTheDocs build (#3084)

Enhancements#

  • Add support for Phenom .elid revision 3 and 4 formats (#3073)

Maintenance#

  • Add pooch as test dependency, as it is required to use scipy.dataset in latest scipy (1.10) and update plotting test. Fix warning when plotting non-uniform axis (#3079)

  • Fix matplotlib 3.7 and scikit-learn 1.4 deprecations (#3102)

  • Add support for new pattern to generate random numbers introduced in dask 2023.2.1. Deprecate usage of numpy.random.RandomState in favour of numpy.random.default_rng(). Bump scipy minimum requirement to 1.4.0. (#3103)

  • Fix checking links in documentation for domain, which aren’t compatible with sphinx linkcheck (#3108)

1.7.3 (2022-10-29)#

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)

1.7.2 (2022-09-17)#

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)

Improved Documentation#

  • Add a note in the user guide to explain that when a file contains several datasets, load() returns a list of signals instead of a single signal and that list indexation can be used to access a single signal. (#2975)

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)

1.7.1 (2022-06-18)#

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)

Improved Documentation#

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)

1.7.0 (2022-04-26)#

New features#

Bug Fixes#

  • Signals with 1 value in the signal dimension will now be BaseSignal (#2773)

  • exspy.material.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#

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 hyperspy.drawing._markers.arrow, hyperspy.drawing._markers.ellipse and filled hyperspy.drawing._markers.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#

  • Fix warning when build doc and formatting user guide (#2762)

  • 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)

1.6.5 (2021-10-28)#

Bug Fixes#

Deprecations#

Enhancements#

  • add_widget() can now take a string or integer instead of tuple of string or integer (#2809)

1.6.4 (2021-07-08)#

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)

1.6.3 (2021-06-10)#

Bug Fixes#

  • Fix ROI snapping regression (#2720)

  • Fix shift1D(), align1D() and hyperspy._signals.eels.EELSSpectrum.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)

Maintenance#

  • Add drone CI to test arm64 platform (#2713)

  • Fix latex doc build on github actions (#2714)

  • Use towncrier to generate changelog automatically (#2717)

  • Fix test suite to support dask 2021.4.1 (#2722)

  • Generate changelog when building doc to keep the changelog of the development doc up to date on https://hyperspy.readthedocs.io/en/latest (#2758)

  • Use mamba and conda-forge channel on azure pipeline (#2759)

1.6.2 (2021-04-13)#

This is a maintenance release that adds support for python 3.9 and includes numerous bug fixes and enhancements. See the issue tracker for details.

Bug Fixes#

  • Fix disconnect event when closing navigator only plot (fixes #996), (#2631)

  • Fix incorrect chunksize when saving EMD NCEM file and specifying chunks (#2629)

  • Fix find_peaks() GUIs call with laplacian/difference of gaussian methods (#2622 and #2647)

  • Fix various bugs with CircleWidget and Line2DWidget (#2625)

  • Fix setting signal range of model with negative axis scales (#2656)

  • Fix and improve mask handling in lazy decomposition; Close #2605 (#2657)

  • Plot scalebar when the axis scales have different sign, fixes #2557 (#2657)

  • Fix align1D() returning zeros shifts (#2675)

  • Fix finding dataset path for EMD NCEM file containing more than one dataset in a group (#2673)

  • Fix squeeze function for multiple zero-dimensional entries, improved docstring, added to user guide. (#2676)

  • Fix error in Cliff-Lorimer quantification using absorption correction (#2681)

  • Fix navigation_mask bug in decomposition when provided as numpy array (#2679)

  • Fix closing image contrast tool and setting vmin/vmax values (#2684)

  • Fix range widget with matplotlib 3.4 (#2684)

  • Fix bug in interactive() with function returning None. Improve user guide example. (#2686)

  • Fix broken events when changing signal type #2683

  • Fix setting offset in rebin: the offset was changed in the wrong axis (#2690)

  • Fix reading XRF bruker file, close #2689 (#2694)

Enhancements#

  • Widgets plotting improvement and add pick_tolerance to plot preferences (#2615)

  • Pass keyword argument to the image IO plugins (#2627)

  • Improve error message when file not found (#2597)

  • Add update instructions to user guide (#2621)

  • Improve plotting navigator of lazy signals, add navigator setter to lazy signals (#2631)

  • Use 'dask_auto' when rechunk=True in change_dtype() for lazy signal (#2645)

  • Use dask chunking when saving lazy signal instead of rechunking and leave the user to decide what is the suitable chunking (#2629)

  • Added lazy reading support for FFT and DPC datasets in FEI emd datasets (#2651).

  • Improve error message when initialising SpanROI with left >= right (#2604)

  • Allow running the test suite without the pytest-mpl plugin (#2624)

  • Add Releasing guide (#2595)

  • 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. (#2663)

  • Use native endianess in numba jitted functions. (#2678)

  • Add option not to snap ROI when calling the interactive() method of a ROI (#2686)

  • Make DictionaryTreeBrowser lazy by default - see #368 (#2623)

  • Speed up setting CI on azure pipeline (#2694)

  • Improve performance issue with the map method of lazy signal (#2617)

  • Add option to copy/load original metadata in hs.stack and hs.load to avoid large original_metadata which can slowdown processing. Close #1398, #2045, #2536 and #1568. (#2691)

Maintenance#

  • Fix warnings when building documentation (#2596)

  • Drop support for numpy<1.16, in line with NEP 29 and fix protochip reader for numpy 1.20 (#2616)

  • Run test suite against upstream dependencies (numpy, scipy, scikit-learn and scikit-image) (#2616)

  • Update external links in the loading data section of the user guide (#2627)

  • Fix various future and deprecation warnings from numpy and scikit-learn (#2646)

  • Fix iterpath VisibleDeprecationWarning when using fit_component() (#2654)

  • Add integration test suite documentation in the developer guide. (#2663)

  • Fix SkewNormal component compatibility with sympy 1.8 (#2701)

1.6.1 (2020-11-28)#

This is a maintenance release that adds compatibility with h5py 3.0 and includes numerous bug fixes and enhancements. See the issue tracker for details.

1.6.0 (2020-08-05)#

NEW#

Enhancements#

  • The get_histogram() now uses numpy’s np.histogram_bin_edges() and supports all of its bins keyword values.

  • Further improvements to the contrast adjustment tool. Test it by pressing the h key on any image.

  • The following components have been rewritten using Expression, boosting their speeds among other benefits.

  • The model fitting fit() and multifit() methods have been vastly improved. See Fitting the model to the data and the API changes section below.

  • New serpentine iteration path for multi-dimensional fitting. See Fitting multidimensional datasets.

  • The plot_spectra() function now listens to events to update the figure automatically. See this example.

  • Improve thread-based parallelism. Add max_workers argument to the map() method, such that the user can directly control how many threads they launch.

  • Many improvements to the decomposition() and blind_source_separation() methods, including support for scikit-learn like algorithms, better API and much improved documentation. See Machine learning and the API changes section below.

  • Add option to calculate the absolute thickness to the EELS hyperspy._signals.eels.EELSSpectrum.estimate_thickness method. See Thickness estimation.

  • Vastly improved performance and memory footprint of the estimate_shift2D() method.

  • The remove_background() method can now remove Doniach, exponential, Lorentzian, skew normal, split Voigt and Voigt functions. Furthermore, it can return the background model that includes an estimation of the reduced chi-squared.

  • The performance of the maximum-likelihood PCA method was greatly improved.

  • All ROIs now have a __getitem__ method, enabling e.g. using them with the unpack * operator. See Slicing using ROIs for an example.

  • New syntax to set the contrast when plotting images. In particular, the vmin and vmax keywords now take values like vmin="30th" to clip the minimum value to the 30th percentile. See Fast Fourier Transform (FFT) for an example.

  • The plot() and plot() methods take a new keyword argument autoscale. See Customising image plot for details.

  • The contrast editor and the decomposition methods can now operate on complex signals.

  • The default colormap can now be set in preferences.

API changes#

  • The plot() keyword argument saturated_pixels is deprecated. Please use vmin and/or vmax instead.

  • The load() keyword argument dataset_name has been renamed to dataset_path.

  • The set_signal_type() method no longer takes None. Use the empty string "" instead.

  • The get_histogram() bins keyword values have been renamed as follows for consistency with numpy:

    • "scotts" -> "scott",

    • "freedman" -> "fd"

  • Multiple changes to the syntax of the fit() and multifit() methods:

    • The fitter keyword has been renamed to optimizer.

    • The values that the optimizer keyword take have been renamed for consistency with scipy:

      • "fmin" -> "Nelder-Mead",

      • "fmin_cg" -> "CG",

      • "fmin_ncg" -> "Newton-CG",

      • "fmin_bfgs" -> "BFGS",

      • "fmin_l_bfgs_b" -> "L-BFGS-B",

      • "fmin_tnc" -> "TNC",

      • "fmin_powell" -> "Powell",

      • "mpfit" -> "lm" (in combination with "bounded=True"),

      • "leastsq" -> "lm",

    • Passing integer arguments to parallel to select the number of workers is now deprecated. Use parallel=True, max_workers={value} instead.

    • The method keyword has been renamed to loss_function.

    • The loss_function value "ml" has been renamed to "ML-poisson".

    • The grad keyword no longer takes boolean values. It takes the following values instead: "fd", "analytical", callable or None.

    • The ext_bounding keyword has been deprecated and will be removed. Use bounded=True instead.

    • The min_function keyword argument has been deprecated and will be removed. Use loss_function instead.,

    • The min_function_grad keyword arguments has been deprecated and will be removed. Use grad instead.

    • The iterpath default will change from 'flyback' to 'serpentine' in HyperSpy version 2.0.

  • The following BaseModel methods are now private:

    • hyperspy.model.BaseModel.set_boundaries

    • hyperspy.model.BaseModel.set_mpfit_parameters_info

  • The comp_label keyword of the machine learning plotting functions has been renamed to title.

  • The orpca constructor’s learning_rate keyword has been renamed to subspace_learning_rate

  • The orpca constructor’s momentum keyword has been renamed to subspace_momentum

  • The svd_pca constructor’s centre keyword values have been renamed as follows:

    • "trials" -> "navigation"

    • "variables" -> "signal"

  • The bounds keyword argument of the decomposition() is deprecated and will be removed.

  • Several syntax changes in the decomposition() method:

    • Several algorithm keyword values have been renamed as follows:

      • "svd": "SVD",

      • "fast_svd": "SVD",

      • "nmf": "NMF",

      • "fast_mlpca": "MLPCA",

      • "mlpca": "MLPCA",

      • "RPCA_GoDec": "RPCA",

    • The polyfit argument has been deprecated and will be removed. Use var_func instead.

1.5.2 (2019-09-06)#

This is a maintenance release that adds compatibility with Numpy 1.17 and Dask 2.3.0 and fixes a bug in the Bruker reader. See the issue tracker for details.

1.5.1 (2019-07-28)#

This is a maintenance release that fixes some regressions introduced in v1.5. Follow the following links for details on all the bugs fixed.

1.5.0 (2019-07-27)#

NEW#

Enhancements#

For developers#

1.4.2 (2019-06-19)#

This is a maintenance release. Among many other fixes and enhancements, this release fixes compatibility issues with Matplotlib v 3.1. Follow the following links for details on all the bugs fixed and enhancements.

1.4.1 (2018-10-23)#

This is a maintenance release. Follow the following links for details on all the bugs fixed and enhancements.

This release fixes compatibility issues with Python 3.7.

1.4.0 (2018-09-02)#

This is a minor release. Follow the following links for details on all the bugs fixed, enhancements and new features.

NEW#

Enhancements#

  • plot_images() improvements (see Plotting several images for details):

    • The cmap option of plot_images() supports iterable types, allowing the user to specify different colormaps for the different images that are plotted by providing a list or other generator.

    • Clicking on an individual image updates it.

  • New customizable keyboard shortcuts to navigate multi-dimensional datasets. See Data visualization.

  • The remove_background() method now operates much faster in multi-dimensional datasets and adds the options to interatively plot the remainder of the operation and to set the removed background to zero. See Background removal for details.

  • The plot() method now takes a norm keyword that can be “linear”, “log”, “auto” or a matplotlib norm. See Customising image plot for details. Moreover, there are three new extra keyword arguments, fft_shift and power_spectrum, that are useful when plotting fourier transforms. See Fast Fourier Transform (FFT).

  • The align2D() and estimate_shift2D() can operate with sub-pixel accuracy using skimage’s upsampled matrix-multiplication DFT. See Signal registration and alignment.

1.3.2 (2018-07-03)#

This is a maintenance release. Follow the following links for details on all the bugs fixed and enhancements.

1.3.1 (2018-04-19)#

This is a maintenance release. Follow the following links for details on all the bugs fixed and enhancements.

Starting with this version, the HyperSpy WinPython Bundle distribution is no longer released in sync with HyperSpy. For HyperSpy WinPython Bundle releases see hyperspy/hyperspy-bundle

1.3.0 (2017-05-27)#

This is a minor release. Follow the following links for details on all the bugs fixed, feature and documentation enhancements, and new features.

NEW#

Enhancements#

  • Creating many markers is now much faster.

  • New “Stage” metadata node. See Metadata structure for details.

  • The Brucker file reader now supports the new version of the format. See Bruker.

  • HyperSpy is now compatible with all matplotlib backends, including the nbagg which is particularly convenient for interactive data analysis in the Jupyter Notebook in combination with the new hyperspy_gui_ipywidgets package. See Starting Python in Windows.

  • The vmin and vmax arguments of the plot_images() function now accept lists to enable setting these parameters for each plot individually.

  • The plot_decomposition_results() and plot_bss_results() methods now makes a better guess of the number of navigators (if any) required to visualise the components. (Previously they were always plotting four figures by default.)

  • All functions that take a signal range can now take a SpanROI.

  • The following ROIs can now be used for indexing or slicing (see here for details):

API changes#

  • Permanent markers (if any) are now displayed when plotting by default.

  • HyperSpy no longer depends on traitsui (fixing many installation issues) and ipywidgets as the GUI elements based on these packages have now been splitted into separate packages and are not installed by default.

  • The following methods now raise a ValueError when not providing the number of components if output_dimension was not specified when performing a decomposition. (Previously they would plot as many figures as available components, usually resulting in memory saturation):

  • The default extension when saving to HDF5 following HyperSpy’s specification is now hspy instead of hdf5. See HSpy - HyperSpy’s HDF5 Specification.

  • The following methods are deprecated and will be removed in HyperSpy 2.0

    • .axes.AxesManager.show. Use gui() instead.

    • All notebook_interaction method. Use the equivalent gui method instead.

    • hyperspy.api.signals.Signal1D.integrate_in_range. Use integrate1D() instead.

  • The following items have been removed from preferences:

    • General.default_export_format

    • General.lazy

    • Model.default_fitter

    • Machine_learning.multiple_files

    • Machine_learning.same_window

    • Plot.default_style_to_compare_spectra

    • Plot.plot_on_load

    • Plot.pylab_inline

    • EELS.fine_structure_width

    • EELS.fine_structure_active

    • EELS.fine_structure_smoothing

    • EELS.synchronize_cl_with_ll

    • EELS.preedge_safe_window_width

    • EELS.min_distance_between_edges_for_fine_structure

  • New Preferences.GUIs section to enable/disable the installed GUI toolkits.

For developers#

  • In addition to adding ipywidgets GUI elements, the traitsui GUI elements have been splitted into a separate package. See the new hyperspy_gui_traitsui package.

  • The new hyperspy.ui_registry enables easy connection of external GUI elements to HyperSpy. This is the mechanism used to split the traitsui and ipywidgets GUI elements.

1.2.0 (2017-02-02)#

This is a minor release. Follow the following links for details on all the bugs fixed, enhancements and new features.

NEW#

Enhancements#

For developers#

1.1.2 (2079-01-12)#

This is a maintenance release. Follow the following links for details on all the bugs fixed and enhancements.

1.1.1 (2016-08-24)#

This is a maintenance release. Follow the following link for details on all the bugs fixed.

Enhancements#

  • Prettier X-ray lines labels.

  • New metadata added to the HyperSpy metadata specifications: magnification, frame_number, camera_length, authors, doi, notes and quantity. See Metadata structure for details.

  • The y-axis label (for 1D signals) and colorbar label (for 2D signals) are now taken from the new metadata.Signal.quantity.

  • The time and date metadata are now stored in the ISO 8601 format.

  • All metadata in the HyperSpy metadata specification is now read from all supported file formats when available.

1.1.0 (2016-08-03)#

This is a minor release. Follow the following links for details on all the bugs fixed.

NEW#

Enhancements#

  • fit() takes a new algorithm, the global optimizer differential evolution.

  • fit() algorithm, leastsq, inherits SciPy’s bound constraints support (requires SciPy >= 0.17).

  • fit() algorithm names changed to be consistent scipy.optimze.minimize() notation.

1.0.1 (2016-07-27)#

This is a maintenance release. Follow the following links for details on all the bugs fixed.

1.0.0 (2016-07-14)#

This is a major release. Here we only list the highlist. A detailed list of changes is available in github.

NEW#

Model#

EDS#

IO#

Enhancements#

Documentation#

API changes#

  • Split components into components1D and components2D.

  • Remove record_by from metadata.

  • Remove simulation classes.

  • The Signal1D, hyperspy._signals.image.Signal2D and BaseSignal classes deprecated the old Spectrum Image and Signal classes.

0.8.5 (2016-07-02)#

This is a maintenance release. Follow the following links for details on all the bugs fixed, feature and documentation enhancements.

It also includes a new feature and introduces an important API change that will be fully enforced in Hyperspy 1.0.

New feature#

  • Widgets to interact with the model components in the Jupyter Notebook. See here and #1007 .

API changes#

The new BaseSignal, Signal1D and Signal2D deprecate hyperspy.signal.Signal, Signal1D and Signal2D respectively. Also as_signal1D, as_signal2D`, to_signal1D and to_signal2D deprecate as_signal1D, as_signal2D, to_spectrum and to_image. See #963 and #943 for details.

0.8.4 (2016-03-04)#

This release adds support for Python 3 and drops support for Python 2. In all other respects it is identical to 0.8.3.

0.8.3 (2016-03-04)#

This is a maintenance release that includes fixes for multiple bugs, some enhancements, new features and API changes. This is set to be the last HyperSpy release for Python 2. The release (HyperSpy 0.8.4) will support only Python 3.

Importantly, the way to start HyperSpy changes (again) in this release. Please read carefully Starting Python in Windows for details.

The broadcasting rules have also changed. See Signal operations for details.

Follow the following links for details on all the bugs fixed, documentation enhancements, enhancements, new features and API changes

0.8.2 (2015-08-13)#

This is a maintenance release that fixes an issue with the Python installers. Those who have successfully installed 0.8.1 do not need to upgrade.

0.8.1 (2015-08-12)#

This is a maintenance release. Follow the following links for details on all the bugs fixed, feature and documentation enhancements.

Importantly, the way to start HyperSpy changes in this release. Read Starting Python in Windows for details.

It also includes some new features and introduces important API changes that will be fully enforced in Hyperspy 1.0.

New features#

  • Support for IPython 3.0.

  • %hyperspy IPython magic to easily and transparently import HyperSpy, matplotlib and numpy when using IPython.

  • Expression model component to easily create analytical function components. More details here.

  • hyperspy.signal.Signal.unfolded context manager.

  • hyperspy.signal.Signal.derivative method.

  • syntax to access the components in the model that includes pretty printing of the components.

API changes#

  • hyperspy.hspy is now deprecated in favour of the new hyperspy.api. The new API renames and/or move several modules as folows:

    • hspy.components -> hyperspy.api.model.components

    • hspy.utils-> hyperspy.api

    • hspy.utils.markers hyperspy.api.plot.markers

    • hspy.utils.example_signals -> hyperspy.api.datasets.example_signals

    In HyperSpy 0.8.1 the full content of hyperspy.hspy is still imported in the user namespace, but this can now be disabled in hs.preferences.General.import_hspy. In Hyperspy 1.0 it will be disabled by default and the hyperspy.hspy module will be fully removed in HyperSpy 0.10. We encourage all users to migrate to the new syntax. For more details see Starting Python in Windows.

  • Indexing the hyperspy.signal.Signal class is now deprecated. We encourage all users to use isig and inav instead for indexing.

  • hyperspy.hspy.create_model is now deprecated in favour of the new equivalent hyperspy.signal.Signal.create_model Signal method.

  • hyperspy.signal.Signal.unfold_if_multidim is deprecated.

0.8.0 (2015-04-07)#

New features#

Core#

  • spikes_removal_tool() displays derivative max value when used with GUI.

  • Progress-bar can now be suppressed by passing show_progressbar argument to all functions that generate it.

IO#

  • HDF5 file format now supports saving lists, tuples, binary strings and signals in metadata.

Plotting#

  • New class, hyperspy.drawing.marker.MarkerBase, to plot markers with hspy.utils.plot.markers module. See Markers.

  • New method to plot images with the plot_images() function in hspy.utils.plot.plot_images. See Plotting several images.

  • Improved hyperspy._signals.image.Signal2D.plot method to customize the image. See Customising image plot.

EDS#

  • New method for quantifying EDS TEM spectra using Cliff-Lorimer method, hyperspy._signals.eds_tem.EDSTEMSpectrum.quantification. See EDS Quantification.

  • New method to estimate for background subtraction, hyperspy._signals.eds.EDSSpectrum.estimate_background_windows. See Background subtraction.

  • New method to estimate the windows of integration, hyperspy._signals.eds.EDSSpectrum.estimate_integration_windows.

  • New specific hyperspy._signals.eds.EDSSpectrum.plot method, with markers to indicate the X-ray lines, the window of integration or/and the windows for background subtraction. See Plotting X-ray lines.

  • New examples of signal in the hspy.utils.example_signals module.

    • hyperspy.misc.example_signals_loading.load_1D_EDS_SEM_spectrum

    • hyperspy.misc.example_signals_loading.load_1D_EDS_TEM_spectrum

  • New method to mask the vaccum, hyperspy._signals.eds_tem.EDSTEMSpectrum.vacuum_mask and a specific hyperspy._signals.eds_tem.EDSTEMSpectrum.decomposition method that incoroporate the vacuum mask

API changes#

  • Component and Parameter now inherit traits.api.HasTraits that enable traitsui to modify these objects.

  • hyperspy.misc.utils.attrsetter is added, behaving as the default python setattr with nested attributes.

  • Several widget functions were made internal and/or renamed:
    • add_patch_to -> _add_patch_to

    • set_patch -> _set_patch

    • onmove -> _onmousemove

    • update_patch_position -> _update_patch_position

    • update_patch_size -> _update_patch_size

    • add_axes -> set_mpl_ax

0.7.3 (2015-08-22)#

This is a maintenance release. A list of fixed issues is available in the 0.7.3 milestone in the github repository.

0.7.2 (2015-08-22)#

This is a maintenance release. A list of fixed issues is available in the 0.7.2 milestone in the github repository.

0.7.1 (2015-06-17)#

This is a maintenance release. A list of fixed issues is available in the 0.7.1 milestone in the github repository.

New features#

0.7.0 (2014-04-03)#

New features#

Core#

  • New syntax to index the AxesManager.

  • New Signal methods to transform between Signal subclasses. More information here.

    • hyperspy.signal.Signal.set_signal_type

    • hyperspy.signal.Signal.set_signal_origin

    • hyperspy.signal.Signal.as_signal2D

    • hyperspy.signal.Signal.as_signal1D

  • The string representation of the Signal class now prints the shape of the data and includes a separator between the navigation and the signal axes e.g (100, 10| 5) for a signal with two navigation axes of size 100 and 10 and one signal axis of size 5.

  • Add support for RGBA data. See Changing the data type.

  • The default toolkit can now be saved in the preferences.

  • Added full compatibility with the Qt toolkit that is now the default.

  • Added compatibility witn the the GTK and TK toolkits, although with no GUI features.

  • It is now possible to run HyperSpy in a headless system.

  • Added a CLI to hyperspy.signal.Signal1DTools.remove_background.

  • New hyperspy.signal.Signal1DTools.estimate_peak_width method to estimate peak width.

  • New methods to integrate over one axis: hyperspy.signal.Signal.integrate1D and hyperspy.signal.Signal1DTools.integrate_in_range.

  • New hyperspy.signal.Signal.metadata attribute, Signal.binned. Several methods behave differently on binned and unbinned signals. See Binned and unbinned signals.

  • New hyperspy.signal.Signal.map method to easily transform the data using a function that operates on individual signals. See Iterating over the navigation axes.

  • New hyperspy.signal.Signal.get_histogram and hyperspy.signal.Signal.print_summary_statistics methods.

  • The spikes removal tool has been moved to the Signal1D class so that it is available for all its subclasses.

  • The hyperspy.signal.Signal.split` method now can automatically split back stacked signals into its original part. See Splitting and stacking.

IO#

  • Improved support for FEI’s emi and ser files.

  • Improved support for Gatan’s dm3 files.

  • Add support for reading Gatan’s dm4 files.

Plotting#

Curve fitting#

Machine learning#

  • The PCA scree plot can now be easily obtained as a Signal. See Scree plots.

  • The decomposition and blind source separation components can now be obtained as hyperspy.signal.Signal instances. See Clustering plots.

  • New methods to plot the decomposition and blind source separation results that support n-dimensional loadings. See Visualizing results.

Dielectric function#

  • New hyperspy.signal.Signal subclass, hyperspy._signals.dielectric_function.DielectricFunction.

EELS#

  • New method, hyperspy._signals.eels.EELSSpectrum.kramers_kronig_analysis to calculate the dielectric function from low-loss electron energy-loss spectra based on the Kramers-Kronig relations. See Kramers-Kronig Analysis.

  • New method to align the zero-loss peak, hyperspy._signals.eels.EELSSpectrum.align_zero_loss_peak.

EDS#

  • New signal, EDSSpectrum especialized in EDS data analysis, with subsignal for EDS with SEM and with TEM: EDSSEMSpectrum and EDSTEMSpectrum. See Energy-Dispersive X-ray Spectrometry (EDS).

  • New database of EDS lines available in the elements attribute of the hspy.utils.material module.

  • Adapted methods to calibrate the spectrum, the detector and the microscope. See Microscope and detector parameters.

  • Specific methods to describe the sample, hyperspy._signals.eds.EDSSpectrum.add_elements and hyperspy._signals.eds.EDSSpectrum.add_lines. See Describing the sample

  • New method to get the intensity of specific X-ray lines: hyperspy._signals.eds.EDSSpectrum.get_lines_intensity. See Describing the sample

API changes#

  • hyperspy.misc has been reorganized. Most of the functions in misc.utils has been rellocated to specialized modules. misc.utils is no longer imported in hyperspy.hspy. A new hyperspy.utils module is imported instead.

  • Objects that have been renamed

    • hspy.elements -> utils.material.elements.

    • Signal.navigation_indexer -> inav.

    • Signal.signal_indexer -> isig.

    • Signal.mapped_parameters -> Signal.metadata.

    • Signal.original_parameters -> Signal.original_metadata.

  • The metadata has been reorganized. See Metadata structure.

  • The following signal methods now operate out-of-place:

    • hyperspy.signal.Signal.swap_axes

    • hyperspy.signal.Signal.rebin

0.6.0 (2013-05-25)#

New features#

  • Signal now supports indexing and slicing. See Indexing.

  • Most arithmetic and rich arithmetic operators work with signal. See Signal operations.

  • Much improved EELSSpectrum methods: hyperspy._signals.eels.EELSSpectrum.estimate_zero_loss_peak_centre, hyperspy._signals.eels.EELSSpectrum.estimate_elastic_scattering_intensity and hyperspy._signals.eels.EELSSpectrum.estimate_elastic_scattering_threshold.

  • The axes can now be given using their name e.g. s.crop("x", 1,10)

  • New syntax to specify position over axes: an integer specifies the indexes over the axis and a floating number specifies the position in the axis units e.g. s.crop("x", 1, 10.) crops over the axis x (in meters) from index 1 to value 10 meters. Note that this may make your old scripts behave in unexpected ways as just renaming the old *_in_units and *_in_values methods won’t work in most cases.

  • Most methods now use the natural order i.e. X,Y,Z.. to index the axes.

  • Add padding to fourier-log and fourier-ratio deconvolution to fix the wrap-around problem and increase its performance.

  • New hyperspy.components.eels_cl_edge.EELSCLEdge.get_fine_structure_as_spectrum EELSCLEdge method.

  • New hyperspy.components.arctan.Arctan model component.

  • New hyperspy.model.Model.enable_adjust_position and hyperspy.model.Model.disable_adjust_position to easily change the position of components using the mouse on the plot.

  • New Model methods hyperspy.model.Model.set_parameters_value, hyperspy.model.Model.set_parameters_free and hyperspy.model.Model.set_parameters_not_free to easily set several important component attributes of a list of components at once.

  • New stack() function to stack signals.

  • New Signal methods: hyperspy.signal.Signal.integrate_simpson, hyperspy.signal.Signal.max, hyperspy.signal.Signal.min, hyperspy.signal.Signal.var, and hyperspy.signal.Signal.std.

  • New sliders window to easily navigate signals with navigation_dimension > 2.

  • The Ripple (rpl) reader can now read rpl files produced by INCA.

API changes#

  • The following functions has been renamed or removed:

    • components.EELSCLEdge

      • knots_factor -> fine_structure_smoothing

      • edge_position -> onset_energy

      • energy_shift removed

    • components.Voigt.origin -> centre

    • signals.Signal1D

      • find_peaks_1D -> Signal.find_peaks1D_ohaver

      • align_1D -> Signal.align1D

      • shift_1D -> Signal.shift1D

      • interpolate_1D -> Signal.interpolate1D

    • signals.Signal2D.estimate_2D_translation -> Signal.estimate_shift2D

    • Signal

      • split_in -> split

      • crop_in_units -> crop

      • crop_in_pixels -> crop

  • Change syntax to create Signal objects. Instead of a dictionary Signal.__init__ takes keywords e.g with a new syntax . >>> s = signals.Signal1D(np.arange(10)) instead of >>> s = signals.Signal1D({'data' : np.arange(10)})

0.5.1 (2012-09-28)#

New features#

  • New Signal method get_current_signal proposed by magnunor.

  • New Signal save method keyword extension to easily change the saving format while keeping the same file name.

  • New EELSSpectrum methods: estimate_elastic_scattering_intensity, fourier_ratio_deconvolution, richardson_lucy_deconvolution, power_law_extrapolation.

  • New Signal1D method: hanning_taper.

Major bugs fixed#

  • The print_current_values Model method was raising errors when fine structure was enabled or when only_free = False.

  • The load function signal_type keyword was not passed to the readers.

  • The spikes removal tool was unable to find the next spikes when the spike was detected close to the limits of the spectrum.

  • load was raising an UnicodeError when the title contained non-ASCII characters.

  • In Windows HyperSpy Here was opening in the current folder, not in the selected folder.

  • The fine structure coefficients were overwritten with their std when charging values from the model.

  • Storing the parameters in the maps and all the related functionality was broken for 1D spectrum.

  • Remove_background was broken for 1D spectrum.

API changes#

  • EELSSpectrum.find_low_loss_centre was renamed to estimate_zero_loss_peak_centre.

  • EELSSpectrum.calculate_FWHM was renamed to estimate_FWHM.

0.5.0 (2012-09-07)#

New features#

  • The documentation was thoroughly revised, courtesy of M. Walls.

  • New user interface to remove spikes from EELS spectra.

  • New align2D signals.Signal2D method to align image stacks.

  • When loading image files, the data are now automatically converted to grayscale when all the color channels are equal.

  • Add the possibility to load a stack memory mapped (similar to ImageJ virtual stack).

  • Improved hyperspy starter script that now includes the possibility to start HyperSpy in the new IPython notebook.

  • Add “HyperSpy notebook here” to the Windows context menu.

  • The information displayed in the plots produced by Signal.plot have been enhanced.

  • Added Egerton’s sigmak3 and sigmal3 GOS calculations (translated from matlab by I. Iyengar) to the EELS core loss component.

  • A browsable dictionary containing the chemical elements and their onset energies is now available in the user namespace under the variable name elements.

  • The ripple file format now supports storing the beam energy, the collection and the convergence angle.

Major bugs fixed#

  • The EELS core loss component had a bug in the calculation of the relativistic gamma that produced a gamma that was always approximately zero. As a consequence the GOS calculation was wrong, especially for high beam energies.

  • Loading msa files was broken when running on Python 2.7.2 and newer.

  • Saving images to rpl format was broken.

  • Performing BSS on data decomposed with poissonian noise normalization was failing when some columns or rows of the unfolded data were zero, what occurs often in EDX data for example.

  • Importing some versions of scikits learn was broken

  • The progress bar was not working properly in the new IPython notebook.

  • The constrast of the image was not automatically updated.

API changes#

  • spatial_mask was renamed to navigation_mask.

  • Signal1D and Signal2D are not loaded into the user namespace by default. The signals module is loaded instead.

  • Change the default BSS algorithm to sklearn fastica, that is now distributed with HyperSpy and used in case that sklearn is not installed e.g. when using EPDFree.

  • _slicing_axes was renamed to signal_axes.

  • _non_slicing_axes to navigation_axes.

  • All the Model *_in_pixels methods were renamed to to _*_in_pixel.

  • EELSCLEdge.fs_state was renamed to fine_structure_active.

  • EELSCLEdge.fslist was renamed to fine_structure_coeff.

  • EELSCLEdge.fs_emax was renamed to fine_structure_width.

  • EELSCLEdge.freedelta was renamed to free_energy_shift.

  • EELSCLEdge.delta was renamed to energy_shift.

  • A value of True in a mask now means that the item is masked all over HyperSpy.

0.4.1 (2012-04-16)#

New features#

  • Added TIFF 16, 32 and 64 bits support by using (and distributing) Christoph Gohlke’s tifffile library.

  • Improved UTF8 support.

  • Reduce the number of required libraries by making mdp and hdf5 not mandatory.

  • Improve the information returned by __repr__ of several objects.

  • DictionaryBrowser now has an export method, i.e. mapped parameters and original_parameters can be exported.

  • New _id_name attribute for Components and Parameters. Improvements in their __repr__ methods.

  • Component.name can now be overwriten by the user.

  • New Signal.__str__ method.

  • Include HyperSpy in The Python Package Index.

Bugs fixed#

  • Non-ascii characters breaking IO and print features fixed.

  • Loading of multiple files at once using wildcards fixed.

  • Remove broken hyperspy-gui script.

  • Remove unmantained and broken 2D peak finding and analysis features.

Syntax changes#

  • In EELS automatic background feature creates a PowerLaw component, adds it to the model an add it to a variable in the user namespace. The variable has been renamed from bg to background.

  • pes_gaussian Component renamed to pes_core_line_shape.

0.4.0 (2012-02-29)#

New features#

  • Add a slider to the filter ui.

  • Add auto_replot to sum.

  • Add butterworth filter.

  • Added centring and auto_transpose to the svd_pca algorithm.

  • Keep the mva_results information when changing the signal type.

  • Added sparse_pca and mini_batch_sparse_pca to decomposition algorithms.

  • Added TV to the smoothing algorithms available in BSS.

  • Added whitening to the mdp ICA preprocessing.

  • Add explained_variance_ratio.

  • Improvements in saving/loading mva data.

  • Add option to perform ICA on the scores.

  • Add orthomax FA algorithm.

  • Add plot methods to Component and Parameter.

  • Add plot_results to Model.

  • Add possibility to export the decomposition and bss results to a folder.

  • Add Signal method change_dtype.

  • Add the possibility to pass extra parameters to the ICA algorithm.

  • Add the possibility to reproject the data after a decomposition.

  • Add warning when decomposing a non-float signal.

  • adds a method to get the PCs as a Signal1D object and adds smoothing to the ICA preprocessing.

  • Add the possibility to select the energy range in which to perform spike removal operations.

  • the smoothings guis now offer differentiation and line color option. Smoothing now does not require a gui.

  • Fix reverse_ic which was not reversing the scores and improve the autoreversing method.

  • Avoid cropping when is not needed.

  • Changed criteria to reverse the ICs.

  • Changed nonans default to False for plotting.

  • Change the whitening algorithm to a svd based one and add sklearn fastica algorithm.

  • Clean the ummixing info after a new decomposition.

  • Increase the chances that similar independent components will have the same indexes.

  • Make savitzky-golay smoothing work without raising figures.

  • Make plot_decomposition* plot only the number of factors/scores determined by output_dimension.

  • make the Parameter __repr__ method print its name.

  • New contrast adjustment tool.

  • New export method for Model, Component and Parameter.

  • New Model method: print_current_values.

  • New signal, spectrum_simulation.

  • New smoothing algorithm: total variance denoising.

  • Plotting the components in the same or separate windows is now configurable in the preferences.

  • Plotting the spikes is now optional.

  • Return an error message when the decomposition algorithm is not recognised.

  • Store the masks in mva_results.

  • The free parameters are now automically updated on chaning the free attribute.

Bugs fixed#

  • Added missing keywords to plot_pca_factors and plot_ica_factors.

  • renamed incorrectly named exportPca and exportIca functions.

  • an error was raised when calling generate_data_from_model.

  • a signal with containing nans was failing to plot.

  • attempting to use any decomposition plotting method after loading with mva_results.load was raising an error.

  • a typo was causing in error in pca when normalize_variance = True.

  • a typo was raising an error when cropping the decomposition dimension.

  • commit 5ff3798105d6 made decomposition and other methods raise an error.

  • BUG-FIXED: the decomposition centering index was wrong.

  • ensure_directory was failing for the current directory.

  • model data forced to be 3D unnecessarily.

  • non declared variable was raising an error.

  • plot naming for peak char factor plots were messed up.

  • plot_RGB was broken.

  • plot_scores_2D was using the transpose of the shape to reshape the scores.

  • remove background was raising an error when the navigation dimension was 0.

  • saving the scores was sometimes transposing the shape.

  • selecting indexes while using the learning export functions was raising an error.

  • the calibrate ui was calculating wrongly the calibration the first time that Apply was pressed.

  • the offset estimation was summing instead of averaging.

  • the plot_explained_variance_ratio was actually plotting the cumulative, renamed.

  • the signal mask in decomposition and ica was not being raveled.

  • the slice attribute was not correctly set at init in some scenarios.

  • the smoothing and calibrabrion UIs were freezing when the plots where closed before closing the UI window.

  • to_spectrum was transposing the navigation dimension.

  • variance2one was operating in the wrong axis.

  • when closing the plots of a model, the UI object was not being destroyed.

  • when plotting an image the title was not displayed.

  • when the axis size was changed (e.g. after cropping) the set_signal_dimension method was not being called.

  • when using transform the data was being centered and the resulting scores were wrong.

Syntax changes#

  • in decomposition V rename to explained_variance.

  • In FixedPattern, default interpolation changed to linear.

  • Line and parabole components deleted + improvements in the docstrings.

  • pca_V = variance.

  • mva_result renamed to learning_results.

  • pca renamed to decomposition.

  • pca_v and mva_results.v renamed to scores pc renamed to factors . pca_build_SI renamed to get_pca_model ica_build_SI renamed to get_ica_model.

  • plot_explained_variance renamed to plot_explained_variance_ratio.

  • principal_components_analysis renamed to decomposition.

  • rename eels_simulation to eels_spectrum_simulation.

  • Rename the output parameter of svd_pca and add scores.

  • Replace plot_lev by plot_explained_variance_ratio.

  • Scores renamed to loadings.

  • slice_bool renamed to navigate to make its function more explicit.

  • smoothing renamed to pretreatment and butter added.

  • variance2one renamed to normalize_variance.

  • w renamed to unmixing matrix and fixes a bug when loading a mva_result in which output_dimension = None.

  • ubshells are again availabe in the interactive session.

  • Several changes to the interface.

  • The documentation was updated to reflex the last changes.

  • The microscopes.csv file was updated so it no longer contains the Orsay VG parameters.