Skip to content

Latest commit

 

History

History
2269 lines (1754 loc) · 116 KB

CHANGES.rst

File metadata and controls

2269 lines (1754 loc) · 116 KB
Raw

Changelog

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

.. towncrier-draft-entries:: |release| [UNRELEASED]

2.1.0 (2024-05-08)

Enhancements

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 (:func:`scipy.signal.windows.tukey`) and scikit-image (:func:`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 :py:mod:`~.api.plot.markers` API has been refactored
  • 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 :ref:`sections below <hyperspy_2.0_api_changes>`.

New features

Bug Fixes

  • Improve syntax in the io module. (#3091)
  • Fix behaviour of :py:class:`~.misc.utils.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 :class:`~.api.roi.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 :py:meth:`~.api.signals.BaseSignal.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:
  • 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 :class:`~.component.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 :class:`~.api.signals.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 :py:meth:`~.api.signals.Signal2D.plot` when using heatmap style in :py:func:`~.api.plot.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

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

Data Visualization

Loading and Saving data

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

Machine Learning

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

  • The list of possible values for the algorithm argument of the :py:meth:`~.api.signals.BaseSignal.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 :py:meth:`~.api.signals.BaseSignal.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 :py:meth:`~._signals.lazy.LazySignal.decomposition` method has been changed from "ONMF" to "ORNMF".

  • Setting the metadata and original_metadata attribute of signals is removed, use the :py:meth:`~.misc.utils.DictionaryTreeBrowser.set_item` and :py:meth:`~.misc.utils.DictionaryTreeBrowser.add_dictionary` methods of the metadata and original_metadata attribute instead.

Model fitting

Signal

Signal2D

Preferences

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

Maintenance

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

1.7.5 (2023-05-04)

Bug Fixes

  • Fix plotting boolean array with :py:func:`~.api.plot.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 :py:class:`numpy.random.RandomState` in favour of :py:func:`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

Improved Documentation

  • Add a note in the user guide to explain that when a file contains several datasets, :py:func:`~.api.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

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 :py:class:`~.api.signals.BaseSignal` (#2773)
  • :py:func:`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 :py:meth:`~.api.signals.BaseSignal.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 :py:meth:`~.api.signals.BaseSignal.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

API changes

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

1.6.4 (2021-07-08)

Bug Fixes

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

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 :py:meth:`~.api.signals.Signal1D.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 :py:meth:`~.api.signals.Signal2D.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 :py:meth:`~.api.signals.Signal1D.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 :py:func:`~.api.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 :py:meth:`~._signals.lazy.LazySignal.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 :py:meth:`~.roi.BaseInteractiveROI.interactive` method of a ROI (#2686)
  • Make :py:class:`~.misc.utils.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 :py:meth:`~.models.model1d.Model1D.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

API changes

  • The :py:meth:`~.api.signals.Signal2D.plot` keyword argument saturated_pixels is deprecated. Please use vmin and/or vmax instead.
  • The :py:func:`~.api.load` keyword argument dataset_name has been renamed to dataset_path.
  • The :py:meth:`~.api.signals.BaseSignal.set_signal_type` method no longer takes None. Use the empty string "" instead.
  • The :py:meth:`~.api.signals.BaseSignal.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 :py:meth:`~hyperspy.model.BaseModel.fit` and :py:meth:`~hyperspy.model.BaseModel.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 :py:class:`~hyperspy.model.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 :py:class:`~hyperspy.learn.rpca.orpca` constructor's learning_rate keyword has been renamed to subspace_learning_rate
  • The :py:class:`~hyperspy.learn.rpca.orpca` constructor's momentum keyword has been renamed to subspace_momentum
  • The :py:class:`~hyperspy.learn.svd_pca.svd_pca` constructor's centre keyword values have been renamed as follows:
    • "trials" -> "navigation"
    • "variables" -> "signal"
  • The bounds keyword argument of the :py:meth:`~._signals.lazy.LazySignal.decomposition` is deprecated and will be removed.
  • Several syntax changes in the :py:meth:`~.api.signals.BaseSignal.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

  • Drop support for python 3.5
  • New extension mechanism that enables external packages to register HyperSpy objects. See :ref:`writing_extensions-label` for details.

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

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 https://github.com/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

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 :external+rsciio:ref:`hspy-format`.
  • The following methods are deprecated and will be removed in HyperSpy 2.0
  • The following items have been removed from :ref:`preferences <configuring-hyperspy-label>`:
    • 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 :ref:`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

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

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

API changes

The new :py:class:`~.api.signals.BaseSignal`, :py:class:`~.api.signals.Signal1D` and :py:class:`~.api.signals.Signal2D` deprecate hyperspy.signal.Signal, :py:class:`~.api.signals.Signal1D` and :py:class:`~.api.signals.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 :ref:`importing_hyperspy-label` for details.

The broadcasting rules have also changed. See :ref:`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 :ref:`importing_hyperspy-label` for details.

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

New features

API changes

  • hyperspy.hspy is now deprecated in favour of the new :py:mod:`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 :ref:`importing_hyperspy-label`.

  • 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

IO

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

Plotting

EDS

  • New method for quantifying EDS TEM spectra using Cliff-Lorimer method, hyperspy._signals.eds_tem.EDSTEMSpectrum.quantification. See :external+exspy:ref:`eds_quantification-label`.
  • New method to estimate for background subtraction, hyperspy._signals.eds.EDSSpectrum.estimate_background_windows. See :external+exspy:ref:`eds_background_subtraction-label`.
  • 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 :external+exspy:ref:`eds_plot_markers-label`.
  • 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

  • :py:class:`~hyperspy.component.Component` and :py:class:`~hyperspy.component.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 :py:class:`~.axes.AxesManager`.
  • New Signal methods to transform between Signal subclasses. More information :ref:`here <transforming_signal-label>`.
    • 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 :ref:`signal.change_dtype`.
  • 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 :ref:`signal.binned`.
  • New hyperspy.signal.Signal.map method to easily transform the data using a function that operates on individual signals. See :ref:`signal.iterator`.
  • New hyperspy.signal.Signal.get_histogram and hyperspy.signal.Signal.print_summary_statistics methods.
  • The spikes removal tool has been moved to the :class:`~.api.signals.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 :ref:`signal.stack_split`.

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

  • The chi-squared, reduced chi-squared and the degrees of freedom are computed automatically when fitting. See :ref:`model.fitting`.
  • New functionality to plot the individual components of a model. See :ref:`model.visualization`.
  • New method, hyperspy.model.Model.fit_component, to help setting the starting parameters. See :ref:`model.starting`.

Machine learning

  • The PCA scree plot can now be easily obtained as a Signal. See :ref:`mva.scree_plot`.
  • The decomposition and blind source separation components can now be obtained as hyperspy.signal.Signal instances. See :ref:`mva.get_results`.
  • New methods to plot the decomposition and blind source separation results that support n-dimensional loadings. See :ref:`mva.visualization`.

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 :external+exspy:ref:`eels.kk`.
  • New method to align the zero-loss peak, hyperspy._signals.eels.EELSSpectrum.align_zero_loss_peak.

EDS

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 :ref:`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 :ref:`signal.indexing`.
  • Most arithmetic and rich arithmetic operators work with signal. See :ref:`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 :py:func:`~.api.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.