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.. _changes_1_8_0:
Version 1.8.0 (2024-08-18)
==========================
Dependencies
------------
- Minimum versions for dependencies were bumped to those ~2 years old at the time of release (by `Eric Larson`_), including:
- NumPy ≥ 1.23
- SciPy ≥ 1.9
- Matplotlib ≥ 3.6
- scikit-learn ≥ 1.1 (`#12554 <https://github.com/mne-tools/mne-python/pull/12554>`__)
- Official support for PySide2 has been dropped in this release (though it might continue
to work), by `Eric Larson`_. (`#12742 <https://github.com/mne-tools/mne-python/pull/12742>`__)
Bugfixes
--------
- Fix bug where an event that occurred only once was excluded in :func:`mne.io.read_raw_egi`, by :newcontrib:`Ping-Keng Jao`. (`#12300 <https://github.com/mne-tools/mne-python/pull/12300>`__)
- Fix bug where :func:`mne.stats.permutation_cluster_test` (and related functions) uses excessive amount of memory for large 2D data when TFCE method is selected, by :newcontrib:`Nicolas Fourcaud-Trocmé`. (`#12609 <https://github.com/mne-tools/mne-python/pull/12609>`__)
- Assure that blink times are handled correctly :func:`mne.preprocessing.eyetracking.interpolate_blinks`, even when the raw object is cropped by `Scott Huberty`_ and :newcontrib:`Sammi Chekroud`. (`#12759 <https://github.com/mne-tools/mne-python/pull/12759>`__)
- Fix check for dropping all channels in :meth:`mne.io.Raw.drop_channels` and related methods, by :newcontrib:`Farzin Negahbani`. (`#12763 <https://github.com/mne-tools/mne-python/pull/12763>`__)
- Fix scrolling behavior in :class:`~mne.Report` when clicking on a TOC entry multiple times, by `Richard Höchenberger`_. (`#12561 <https://github.com/mne-tools/mne-python/pull/12561>`__)
- Fix bug where :func:`mne.decoding.get_coef` did not work properly with :class:`mne.decoding.CSP`, by `Eric Larson`_. (`#12562 <https://github.com/mne-tools/mne-python/pull/12562>`__)
- The color scaling of Evoked topomaps added to reports via :meth:`mne.Report.add_evokeds`
was sometimes sub-optimal if bad channels were present in the data. This has now been fixed
and should be more consistent with the topomaps shown in the joint plots, by `Richard Höchenberger`_. (`#12578 <https://github.com/mne-tools/mne-python/pull/12578>`__)
- Fix error causing :meth:`mne.Epochs.interpolate_bads` not to work for ``seeg`` channels and fix a single contact on neighboring shafts sometimes being included in interpolation, by `Alex Rockhill`_ (`#12593 <https://github.com/mne-tools/mne-python/pull/12593>`__)
- Fix bug where :func:`mne.io.read_raw_fil` could not assign bad channels on import, by `George O'Neill`_. (`#12597 <https://github.com/mne-tools/mne-python/pull/12597>`__)
- Fixed a bug where :meth:`mne.Evoked.animate_topomap` did not work with :func:`mne.preprocessing.compute_current_source_density` - modified data, by `Michal Žák`_. (`#12605 <https://github.com/mne-tools/mne-python/pull/12605>`__)
- Fix overflow when plotting source estimates where data is all zero (or close to zero), and fix the range of allowed values for the colorbar sliders, by `Marijn van Vliet`_. (`#12612 <https://github.com/mne-tools/mne-python/pull/12612>`__)
- Fix adding channels to :class:`~mne.time_frequency.EpochsTFR` objects, by `Clemens Brunner`_. (`#12616 <https://github.com/mne-tools/mne-python/pull/12616>`__)
- Fix for new sklearn metadata routing protocol in decoding search_light, by `Alex Gramfort`_ (`#12620 <https://github.com/mne-tools/mne-python/pull/12620>`__)
- Fix bug where :func:`mne.time_frequency.csd_multitaper`, :func:`mne.time_frequency.csd_fourier`, :func:`mne.time_frequency.csd_array_multitaper`, and :func:`mne.time_frequency.csd_array_fourier` would return cross-spectral densities with the ``fmin`` and ``fmax`` frequencies missing, by `Thomas Binns`_ (`#12633 <https://github.com/mne-tools/mne-python/pull/12633>`__)
- Output types of sparse arrays were changed from ``matrix`` to ``array`` in
:func:`~mne.channels.read_ch_adjacency`, :func:`~mne.channels.find_ch_adjacency`,
:func:`~mne.stats.combine_adjacency`, :func:`~mne.spatio_temporal_src_adjacency`,
and related functions to comply with the pending deprecation of ``np.matrix``.
The returned objects now behave like standard :class:`~numpy.ndarray` objects, and
in particular ``*`` now operates element-wise instead of performing matrix
multiplication. You can use ``@`` as a backward compatible matrix multiplication
for both ``np.matrix`` and ``np.ndarray`` objects, and if a matrix is desired
the outputs can be cast directly, for example as ``scipy.sparse.csr_matrix(out)``.
Changed by `Eric Larson`_. (`#12646 <https://github.com/mne-tools/mne-python/pull/12646>`__)
- Fix incorrect RuntimeWarning (different channel filter settings) in EDF/BDF import, by `Clemens Brunner`_. (`#12661 <https://github.com/mne-tools/mne-python/pull/12661>`__)
- In :func:`mne.export.export_raw` (``fmt='edf'``), when padding data to create equal-length data blocks,
edge-padding is favored over zero-padding in order to avoid accidentally enlarging physical range, by `Qian Chu`_. (`#12676 <https://github.com/mne-tools/mne-python/pull/12676>`__)
- In :func:`mne.io.read_raw_eyelink`, gracefully handle missing datetime in file by `Scott Huberty`_. (`#12687 <https://github.com/mne-tools/mne-python/pull/12687>`__)
- Fix regression with :class:`mne.decoding.CSP` where using ``rank="full"`` errantly
raised an error, by `Eric Larson`_. (`#12694 <https://github.com/mne-tools/mne-python/pull/12694>`__)
- Fix in-memory anonymization of data read with :func:`mne.io.read_raw_edf` by `Eric Larson`_. (`#12720 <https://github.com/mne-tools/mne-python/pull/12720>`__)
- Fix bug with overplotting of butterfly labels in :func:`mne.viz.plot_raw` and related
functions and methods, by `Eric Larson`_. (`#12721 <https://github.com/mne-tools/mne-python/pull/12721>`__)
- Fix a bug where the ``ylim`` parameter would sometimes apply to the wrong channel types in :func:`mne.viz.plot_evoked_topo`, by `Marijn van Vliet`_. (`#12724 <https://github.com/mne-tools/mne-python/pull/12724>`__)
- Fix bug where ad-hoc regularization of a covariance with
:func:`mne.cov.regularize` did not properly account for bad channels
in rank calculations, by `Eric Larson`_. (`#12727 <https://github.com/mne-tools/mne-python/pull/12727>`__)
- Fix bug when reading NIRX files saved in a non-western encoding, by `Daniel McCloy`_. (`#12730 <https://github.com/mne-tools/mne-python/pull/12730>`__)
- :func:`~mne.set_log_file` and :func:`~mne.set_log_level` can now be correctly detected by
static analysis tools like Pylance, by `Richard Höchenberger`_. (`#12735 <https://github.com/mne-tools/mne-python/pull/12735>`__)
- Safeguard loading of ``meas_date`` in :func:`mne.io.read_raw_edf`, by `Mathieu Scheltienne`_. (`#12754 <https://github.com/mne-tools/mne-python/pull/12754>`__)
- Fix bug in :func:`~mne.preprocessing.maxwell_filter_prepare_emptyroom` where a difference in sampling frequencies between data and emptyroom files was ignored, by `Daniel McCloy`_. (`#12760 <https://github.com/mne-tools/mne-python/pull/12760>`__)
API changes by deprecation
--------------------------
- A new argument ``events_as_annotations`` has been added to :func:`mne.io.read_raw_egi`
with a default value of ``False`` that will change to ``True`` in version 1.9, by
`Scott Huberty`_ and `Eric Larson`_. (`#12300 <https://github.com/mne-tools/mne-python/pull/12300>`__)
- ``mne.Info.ch_names`` will now return an empty list instead of raising a ``KeyError`` if no channels
are present, by `Richard Höchenberger`_. (`#12583 <https://github.com/mne-tools/mne-python/pull/12583>`__)
- Documented that :func:`~mne.match_channel_orders` can also work on Epochs, and Evoked objects. Reflecting this, deprecated the ``raws`` parameter in favor of an ``insts`` parameter, by `Stefan Appelhoff`_. (`#12699 <https://github.com/mne-tools/mne-python/pull/12699>`__)
- The ``block`` argument to :class:`mne.viz.Brain` is deprecated and will be removed in
1.9, use :func:`matplotlib.pyplot.show` with ``block=True`` instead, by `Eric Larson`_. (`#12719 <https://github.com/mne-tools/mne-python/pull/12719>`__)
- :func:`mne.datasets.fetch_fsaverage` now returns a :class:`python:pathlib.Path` object
rather than a string. Support for string concatenation with plus (``+``) is thus
deprecated and will be removed in 1.9, use the forward-slash ``/`` operator instead,
by `Eric Larson`_. (`#12771 <https://github.com/mne-tools/mne-python/pull/12771>`__)
New features
------------
- Added internals to allow modifying single-channel annotations in the Qt
raw browser, by :newcontrib:`Noah Markowitz`. (`#12669 <https://github.com/mne-tools/mne-python/pull/12669>`__)
- Adding :meth:`mne.channels.Layout.copy` and :meth:`mne.channels.Layout.pick` to copy and select channels from a :class:`mne.channels.Layout` object. Plotting 2D topographies of evoked responses with :func:`mne.viz.plot_evoked_topo` with both arguments ``layout`` and ``exclude`` now ignores excluded channels from the :class:`mne.channels.Layout`. By `Mathieu Scheltienne`_. (`#12338 <https://github.com/mne-tools/mne-python/pull/12338>`__)
- In :class:`~mne.Report` you can now easily navigate through images and figures connected to a slider with the left and right arrow keys. Clicking on the slider or respective image will focus the slider, enabling keyboard navigation, by `Richard Höchenberger`_ (`#12556 <https://github.com/mne-tools/mne-python/pull/12556>`__)
- When plotting EOG and ECG artifact scores for ICA in :meth:`mne.Report.add_ica`,
the channel names used for artifact detection are now displayed in the titles of
each respective subplot, by `Richard Höchenberger`_. (`#12573 <https://github.com/mne-tools/mne-python/pull/12573>`__)
- Use ``aseg='auto'`` for :meth:`mne.viz.Brain.add_volume_labels` and :func:`mne.get_montage_volume_labels` to use ``aparc+aseg`` by default or if not present use ``wmparc`` because freesurfer uses ``wmparc`` in the latest version, by `Alex Rockhill`_. (`#12576 <https://github.com/mne-tools/mne-python/pull/12576>`__)
- The HTML representations of :class:`~mne.io.Raw`, :class:`~mne.Epochs`,
and :class:`~mne.Evoked` (which you will see e.g. when working with Jupyter Notebooks or
:class:`~mne.Report`) have been updated to be more consistent and contain
slightly more information, by `Richard Höchenberger`_. (:gh:`12624`) (`#12583 <https://github.com/mne-tools/mne-python/pull/12583>`__)
- When adding :class:`~mne.Evoked` data to a :class:`~mne.Report` via
:meth:`~mne.Report.add_evokeds`, we now also include an "Info" section
with some basic summary info, as has already been the case for raw and
epochs data, by `Richard Höchenberger`_. (`#12584 <https://github.com/mne-tools/mne-python/pull/12584>`__)
- We added new installation variants for a full installation with the PySide6 Qt binding
(``"mne[full-pyside6]"``), with the PyQt6 binding (``"mne[full-pyqt6]"``, equivalent to
``"mne[full]"``), and without any Qt binding (``"mne[full-no-qt]"``), which may be useful
in certain situations by `Richard Höchenberger`_. (`#12628 <https://github.com/mne-tools/mne-python/pull/12628>`__)
- Adding argument ``'random'`` to :func:`~mne.epochs.equalize_epoch_counts` and to :meth:`~mne.Epochs.equalize_event_counts` to randomly select epochs or events. By `Mathieu Scheltienne`_. (`#12649 <https://github.com/mne-tools/mne-python/pull/12649>`__)
- Add new parameter ``ignore_marker_types`` to :func:`~mne.io.read_raw_brainvision` to ignore marker types (and only use marker descriptions) when reading BrainVision files, by `Clemens Brunner`_. (`#12652 <https://github.com/mne-tools/mne-python/pull/12652>`__)
- Added support for passing ``axes`` to :func:`mne.viz.plot_head_positions` when
``mode='field'``, by `Eric Larson`_. (`#12655 <https://github.com/mne-tools/mne-python/pull/12655>`__)
- The HTML representation of :class:`~mne.Epochs` (visible e.g. in Jupyter or in :class:`~mne.Report`) now
indicates whether metadata is attached to the epochs, by `Richard Höchenberger`_. (`#12686 <https://github.com/mne-tools/mne-python/pull/12686>`__)
- Montage plots created with :meth:`~mne.channels.DigMontage.plot` now scale both the channel dots *and* channel names with the new ``scale`` parameter. The default is ``scale=1`` (factors less than 1 will scale down, whereas factors greater than 1 will scale up). The previous ``scale_factor`` parameter only affected marker size, and this parameter is now deprecated. By `Clemens Brunner`_. (`#12703 <https://github.com/mne-tools/mne-python/pull/12703>`__)
- Add :func:`~mne.stats.erp.compute_sme` to compute the analytical standardized measurement error (SME) as a data quality measure for ERP studies, by `Clemens Brunner`_. (`#12707 <https://github.com/mne-tools/mne-python/pull/12707>`__)
- Use :class:`python:datetime.date` for ``info["subject_info"]["birthday"]`` rather than
a tuple of ``(year, month, day)`` by `Eric Larson`_. (`#12720 <https://github.com/mne-tools/mne-python/pull/12720>`__)
- Add default ``spatial_colors="auto"`` to :func:`mne.viz.plot_evoked_white` and
:meth:`mne.Evoked.plot_white` to enable spatial colors by default, by `Eric Larson`_. (`#12725 <https://github.com/mne-tools/mne-python/pull/12725>`__)
- :func:`mne.minimum_norm.make_inverse_operator` and related functions now more robustly
warn if the whitener computed from the noise covariance has an incorrect rank,
by `Eric Larson`_. (`#12727 <https://github.com/mne-tools/mne-python/pull/12727>`__)
- When indexing :class:`~mne.Epochs` (e.g. by doing ``epochs[0]``), static code analysis tools like Pylance
should now be able to infer that the returned object is an epoch, too, and provide editor support
like automated code completions, by `Richard Höchenberger`_. (`#12733 <https://github.com/mne-tools/mne-python/pull/12733>`__)
- When using the ``data_path()`` in any dataset included in :py:mod:`mne.datasets`,
static analysis tools like Pylance will now correctly infer that a `pathlib.Path` will
be returned and provide editor support like automated code completions, by `Richard Höchenberger`_. (`#12734 <https://github.com/mne-tools/mne-python/pull/12734>`__)
- Add support for storing Fourier coefficients in :class:`mne.time_frequency.Spectrum`,
:class:`mne.time_frequency.EpochsSpectrum`, :class:`mne.time_frequency.SpectrumArray`,
and :class:`mne.time_frequency.EpochsSpectrumArray` objects, by `Thomas Binns`_. (`#12747 <https://github.com/mne-tools/mne-python/pull/12747>`__)
Other changes
-------------
- Fixed issue template links by :newcontrib:`Michal Žák` (`#12600 <https://github.com/mne-tools/mne-python/pull/12600>`__)
- Enhance documentation on decimation filtering to prevent aliasing, by :newcontrib:`Xabier de Zuazo`. (`#12650 <https://github.com/mne-tools/mne-python/pull/12650>`__)
- Added `vulture <https://github.com/jendrikseipp/vulture>`__ as a pre-commit hook and removed related dead code, by `Eric Larson`_. (`#12569 <https://github.com/mne-tools/mne-python/pull/12569>`__)
- Add link to BEst-Python in the list of related software. by `Ilian Azz`_. (`#12659 <https://github.com/mne-tools/mne-python/pull/12659>`__)
- Improved clarity of parameter documentation for `mne.decoding.SSD.fit`, by `Thomas Binns`_. (`#12664 <https://github.com/mne-tools/mne-python/pull/12664>`__)
- Disable the "Back to top" button in the documentation, by `Richard Höchenberger`_. (`#12688 <https://github.com/mne-tools/mne-python/pull/12688>`__)
- Improve argument ``ylim`` documentation through :class:`~mne.Evoked` plotting function and validate type to :class:`dict` or ``None`` to prevent misuage, by `Mathieu Scheltienne`_. (`#12697 <https://github.com/mne-tools/mne-python/pull/12697>`__)
- Code contributions are now measured using PRs and reported on the :ref:`contributors`
page, by `Eric Larson`_. (`#12774 <https://github.com/mne-tools/mne-python/pull/12774>`__)
- Authorship headers in MNE-Python code have been standardized, by `Eric Larson`_. (`#12781 <https://github.com/mne-tools/mne-python/pull/12781>`__)
Authors
-------
* Alex Rockhill
* Alexandre Gramfort
* Clemens Brunner
* Daniel McCloy
* Dimitri Papadopoulos Orfanos
* Eric Larson
* Farzin Negahbani+
* George O'Neill
* Ilian AZZ
* Marijn van Vliet
* Mathieu Scheltienne
* Michal Žák+
* Nabil Alibou
* Nicolas Fourcaud-Trocmé+
* Noah Markowitz+
* Ping-Keng Jao+
* Qian Chu
* Richard Höchenberger
* Sammi Chekroud+
* Scott Huberty
* Stefan Appelhoff
* Thomas S. Binns
* Xabier de Zuazo+
|
