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1.5.inc
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.. NOTE: we use cross-references to highlight new functions and classes.
Please follow the examples below like :func:`mne.stats.f_mway_rm`, so the
whats_new page will have a link to the function/class documentation.
.. NOTE: there are 3 separate sections for changes, based on type:
- "Enhancements" for new features
- "Bugs" for bug fixes
- "API changes" for backward-incompatible changes
.. NOTE: changes from first-time contributors should be added to the TOP of
the relevant section (Enhancements / Bugs / API changes), and should look
like this (where xxxx is the pull request number):
- description of enhancement/bugfix/API change (:gh:`xxxx` by
:newcontrib:`Firstname Lastname`)
Also add a corresponding entry for yourself in doc/changes/names.inc
.. _changes_1_5_1:
Version 1.5.1 (2023-09-06)
--------------------------
Bugs
~~~~
- Fix bug with multi-plot 3D rendering where only one plot was updated (:gh:`11896` by `Eric Larson`_)
- Fix bug with :func:`mne.chpi.compute_head_pos` for CTF data where digitization points were modified in-place, producing an incorrect result during a save-load round-trip (:gh:`11934` by `Eric Larson`_)
- Fix bug with notebooks when using PyVista 0.42 by implementing ``trame`` backend support (:gh:`11956` by `Eric Larson`_)
- Fix bug with ``subject_info`` when loading data from and exporting to EDF file (:gh:`11952` by `Paul Roujansky`_)
- Fix handling of channel information in annotations when loading data from and exporting to EDF file (:gh:`11960` by `Paul Roujansky`_)
.. _changes_1_5_0:
Version 1.5.0 (2023-08-14)
--------------------------
Enhancements
~~~~~~~~~~~~
- Add reader for NSx files (Blackrock Microsystems Data Acquisition Systems) (:gh:`11432` by :newcontrib:`Proloy Das`)
- Add ``cmap`` argument for the :func:`mne.viz.plot_sensors` (:gh:`11720` by :newcontrib:`Gennadiy Belonosov`)
- Return unmodified instance if new sampling frequency is identical to the original in :meth:`mne.io.Raw.resample`, :meth:`mne.Epochs.resample`, :meth:`mne.Evoked.resample` and :meth:`mne.SourceEstimate.resample` (:gh:`11736` by :newcontrib:`Gennadiy Belonosov`)
- When failing to locate a file, we now print the full path in quotation marks to help spot accidentally added trailing spaces (:gh:`11718` by `Richard Höchenberger`_)
- Add standard montage lookup table for ``easycap-M43`` (:gh:`11744` by :newcontrib:`Diptyajit Das`)
- Added :class:`mne.preprocessing.eyetracking.Calibration` to store eye-tracking calibration info, and :func:`mne.preprocessing.eyetracking.read_eyelink_calibration` to read calibration data from EyeLink systems (:gh:`11719` by `Scott Huberty`_)
- Ocular :class:`mne.Annotations` read in by :func:`mne.io.read_raw_eyelink` are now channel aware. This means if the left eye blinked, the associated annotation will store this in the ``'ch_names'`` key. (:gh:`11746` by `Scott Huberty`_)
- Added :func:`mne.preprocessing.eyetracking.interpolate_blinks` to linear interpolate eyetrack signals during blink periods. (:gh:`11740` by `Scott Huberty`_)
- Added a section for combining eye-tracking and EEG data to the preprocessing tutorial "working with eye tracker data in MNE-Python" (:gh:`11770` by `Scott Huberty`_)
- Added a ``show_bytes`` option to :ref:`mne show_fiff` to show byte offsets (:gh:`11800` by `Eric Larson`_)
- Add :meth:`mne.Annotations.count` and :func:`mne.count_annotations` to count unique annotations (:gh:`11796` by `Clemens Brunner`_)
- Split the display of :meth:`mne.preprocessing.ICA.plot_overlay` between sensor types and display the RMS for MEG sensors and the :term:`GFP` for EEG sensors in the second panel instead of the channel average (:gh:`11830` by `Mathieu Scheltienne`_)
- Add :meth:`mne.Info.set_channel_types`, :meth:`mne.Info.rename_channels`, :meth:`mne.Info.plot_sensors`, :meth:`mne.Info.anonymize`, :meth:`mne.Info.set_meas_date` (:gh:`11839` by `Alex Rockhill`_)
- Curry and NEDF raw files can now also be read with the generic :func:`mne.io.read_raw` function (:gh:`11841` by `Richard Höchenberger`_)
Bugs
~~~~
- Fix bug in :func:`mne.bem.convert_flash_mris` to handle missing "flash5_reg.mgz" when processing "flash30" data. (:gh:`11842` by :newcontrib:`Hamza Abdelhedi`)
- Fix bug where epochs ``event_id`` was not kept by :func:`mne.channels.combine_channels` (:gh:`11786` by :newcontrib:`Samuel Louviot`)
- Fix bug where user-provided codec was not used to read annotations when loading EEGLAB ``.set`` files (:gh:`11773` by :newcontrib:`Yiping Zuo`)
- Fix bug that required curv.*h files to create Brain object (:gh:`11704` by :newcontrib:`Aaron Earle-Richardson`)
- Extended test to highlight bug in :func:`mne.stats.permutation_t_test` (:gh:`11575` by :newcontrib:`Joshua Calder-Travis`)
- Fix bug that used wrong indices for line/label styles (sometimes causing an ``IndexError``) in :meth:`mne.preprocessing.ICA.plot_sources` under certain conditions (:gh:`11808` by :newcontrib:`Joshua Calder-Travis`)
- Fix bug with :func:`~mne.io.read_raw_snirf` to handle files with measurement time containing milliseconds (:gh:`11804` by :newcontrib:`Daniel Tse`)
- Fix loading of EDF with mixed sampling frequencies with :func:`mne.io.read_raw_edf`: Upsampling is now applied to the entire signal and no longer block based, significantly reducing edge artifacts (:gh:`11549` by `Simon Kern`_)
- Fix bug where :func:`mne.io.read_raw_cnt` imports unnecessary durations (:gh:`11828` by `Jacob Woessner`_)
- Fix bug where :meth:`mne.viz.Brain.add_volume_labels` used an incorrect orientation (:gh:`11730` by `Alex Rockhill`_)
- Fix bug with :func:`mne.forward.restrict_forward_to_label` where cortical patch information was not adjusted (:gh:`11694` by `Eric Larson`_)
- Fix bug with PySide6 compatibility (:gh:`11721` by `Eric Larson`_)
- Fix bug with :class:`mne.io.Raw`, :class:`mne.SourceEstimate`, and related classes where the ``decimate`` and ``shift_time`` methods were errantly added (:gh:`11853` by `Eric Larson`_)
- Fix hanging interpreter with matplotlib figures using ``mne/viz/_mpl_figure.py`` in spyder console and jupyter notebooks (:gh:`11696` by `Mathieu Scheltienne`_)
- Fix bug with overlapping text for :meth:`mne.Evoked.plot` (:gh:`11698` by `Alex Rockhill`_)
- Fix bug with :func:`mne.preprocessing.corrmap` where the template iteration had non-standard map averaging (:gh:`11857` by `Eric Larson`_)
- For :func:`mne.io.read_raw_eyelink`, the default value of the ``gap_description`` parameter is now ``'BAD_ACQ_SKIP'``, following MNE convention (:gh:`11719` by `Scott Huberty`_)
- Fix bug with :func:`mne.io.read_raw_fil` where datasets without sensor positions would not import (:gh:`11733` by `George O'Neill`_)
- Fix bug with :func:`mne.chpi.compute_chpi_snr` where cHPI being off for part of the recording or bad channels being defined led to an error or incorrect behavior (:gh:`11754`, :gh:`11755` by `Eric Larson`_)
- Allow int-like for the argument ``id`` of `~mne.make_fixed_length_events` (:gh:`11748` by `Mathieu Scheltienne`_)
- Fix bugs with :mod:`mne.decoding` classes (:gh:`11846` by `Eric Larson`_):
- :class:`mne.decoding.ReceptiveField` now sets ``rf.fit_intercept_`` during ``fit()`` rather than overwriting ``rf.fit_intercept``
- :class:`mne.decoding.SlidingEstimator` now returns the same ``dtype`` as ``X`` (usually ``float64``) in ``sl.transform(X)`` rather than always returning ``int``
- Fix bug with :func:`mne.beamformer.make_lcmv` where the source space was not checked properly when the ``label`` argument was provided (:gh:`11852` by `Eric Larson`_)
- Fix bug where :func:`mne.io.read_raw_egi` did not properly set the EEG reference location for the reference channel itself (:gh:`11822` by `Eric Larson`_)
- Fix bug with legacy :meth:`~mne.io.Raw.plot_psd` method where passed axes were not used (:gh:`11778` by `Daniel McCloy`_)
- blink :class:`mne.Annotations` read in by :func:`mne.io.read_raw_eyelink` now begin with ``'BAD_'``, i.e. ``'BAD_blink'``, because ocular data are missing during blinks. (:gh:`11746` by `Scott Huberty`_)
- Fix bug where :ref:`mne show_fiff` could fail with an ambiguous error if the file is corrupt (:gh:`11800` by `Eric Larson`_)
- Fix bug where annotation FIF files lacked an end block tag (:gh:`11800` by `Eric Larson`_)
- Fix display of :class:`~mne.Annotations` in `mne.preprocessing.ICA.plot_sources` when the ``raw`` has ``raw.first_samp != 0`` and doesn't have a measurement date (:gh:`11766` by `Mathieu Scheltienne`_)
- Fix bug in read_raw_eyelink, where STATUS information of samples was always assumed to be in the file. Performance and memory improvements were also made. (:gh:`11823` by `Scott Huberty`_)
- Fix closing of a topographic map created from an interactive drag on an Evoked or PSD plot (:gh:`11862` by `Mathieu Scheltienne`_)
API changes
~~~~~~~~~~~
- The ``baseline`` argument can now be array-like (e.g. ``list``, ``tuple``, ``np.ndarray``, ...) instead of only a ``tuple`` (:gh:`11713` by `Clemens Brunner`_)
- The ``events`` and ``event_id`` parameters of `:meth:`Epochs.plot() <mne.Epochs.plot>` now accept boolean values; see docstring for details (:gh:`11445` by `Daniel McCloy`_ and `Clemens Brunner`_)
- Deprecated ``gap_description`` keyword argument of :func:`mne.io.read_raw_eyelink`, which will be removed in mne version 1.6, in favor of using :meth:`mne.Annotations.rename` (:gh:`11719` by `Scott Huberty`_)
Authors
~~~~~~~
* Aaron Earle-Richardson+
* Alex Rockhill
* Alexandre Gramfort
* Britta Westner
* Clemens Brunner
* Daniel McCloy
* Daniel Tse+
* Diptyajit Das+
* Eric Larson
* Gennadiy Belonosov+
* George O'Neill
* Hamza Abdelhedi+
* Jacob Woessner
* Joshua Calder-Travis+
* Mathieu Scheltienne
* Proloy Das
* Richard Höchenberger
* Rob Luke
* Samuel Louviot+
* Scott Huberty
* Simon Kern
* Stefan Appelhoff
* Thomas Moreau
* Yiping Zuo+