v0.22.rst

Version 0.22.0 (2020-12-17)

Enhancements

• Add :func:`mne.read_evokeds_mff` to read averaged MFFs (requires mffpy >= 0.5.7) by new contributor |Evan Hathaway|_ (:gh:`8354`)
• Add :class:`mne.decoding.SSD` for spatial filtering with spatio-spectral-decomposition (:gh:`7070` by new contributor |Victoria Peterson|_ and `Denis Engemann`_)
• Add reader for optical imaging data recorded using ISS Imgagent I/II hardware and BOXY recording software in :func:`mne.io.read_raw_boxy` (:gh:`7717` by new contributor |Jonathan Kuziek|_ and `Kyle Mathewson`_)
• Add options to use labels in :func:`mne.minimum_norm.get_point_spread` and :func:`mne.minimum_norm.get_cross_talk` (:gh:`8275` by `Olaf Hauk`_)
• Update surfaces argument in :func:`mne.viz.plot_alignment` to allow dict for transparency values, and set default for sEEG data to have transparency (:gh:`8445` by `Keith Doelling`_)
• Add support for mri_fiducials='estimated' in :func:`mne.viz.plot_alignment` to allow estimating MRI fiducial locations using :func:`mne.coreg.get_mni_fiducials` (:gh:`8553` by `Eric Larson`_)
• Update default values in :ref:`mne coreg` and :func:`mne.viz.plot_alignment` for clearer representation of MRI and digitized fiducial points (:gh:`8553` by `Alex Gramfort`_ and `Eric Larson`_)
• Add n_pca_components argument to :func:`mne.viz.plot_ica_overlay` (:gh:`8351` by `Eric Larson`_)
• Add :func:`mne.stc_near_sensors` to facilitate plotting ECoG data (:gh:`8190` by `Eric Larson`_)
• Add proj argument to :func:`mne.make_fixed_length_epochs` (:gh:`8351` by `Eric Larson`_)
• Add :func:`mne.preprocessing.realign_raw` to realign simultaneous raw recordings in the presence of clock drift (:gh:`8539` by `Eric Larson`_)
• Reduce memory usage of volume source spaces (:gh:`8379` by `Eric Larson`_)
• Speed up heavy use of :meth:`mne.SourceMorph.apply` for volumetric source spaces by use of the method :meth:`mne.SourceMorph.compute_vol_morph_mat` (:gh:`8366` by `Eric Larson`_)
• Add support for non-uniform zooms (e.g., when using a surrogate MRI via :func:`mne.scale_mri`) in volumetric morphing (:gh:`8642` by `Eric Larson`_)
• In :func:`mne.compute_source_morph` zooms are no longer required to match the spacing of src_to, which is useful to ensure the morphing is accurate when the src_to spacing is large (e.g., 1 cm) (:gh:`8642` by `Eric Larson`_)
• Add volumetric source space support to :func:`mne.labels_to_stc` (:gh:`8447` by `Eric Larson`_)
• Speed up :class:`mne.decoding.TimeDelayingRidge` with edge correction using Numba (:gh:`8323` by `Eric Larson`_)
• Add :meth:`mne.Epochs.reset_drop_log_selection` to facilitate writing epochs with many ignored entries in their drop log (:gh:`8449` by `Eric Larson`_)
• Add sEEG source visualization using :func:`mne.stc_near_sensors` and sEEG working tutorial (:gh:`8402` by `Eric Larson`_ and `Adam Li`_)
• Add :meth:`mne.channels.DigMontage.get_positions`, which will return a dictionary of channel positions, coordinate frame and fiducial locations (:gh:`8460` by `Adam Li`_)
• Add support for writing digitization points in a coordinate frame other than head in :meth:`mne.channels.DigMontage.save` (:gh:`8532` by `Eric Larson`_)
• Add picks parameter to :func:`mne.preprocessing.fix_stim_artifact` to specify which channel needs to be fixed (:gh:`8482` by `Alex Gramfort`_)
• Add progress bar support to :func:`mne.time_frequency.csd_morlet` (:gh:`8608` by `Eric Larson`_)
• Further improved documentation building instructions and execution on Windows (:gh:`8502` by `Evgenii Kalenkovich`_ and `Eric Larson`_)
• Add option to disable TQDM entirely with MNE_TQDM='off' (:gh:`8515` by `Eric Larson`_)
• Add option on_header_missing to :func:`mne.channels.read_polhemus_fastscan` (:gh:`8622` by `Eric Larson`_)
• Add option window to mne.time_frequency.psd_welch and related functions (:gh:`8862` by `Eric Larson`_)
• mne.preprocessing.ICA.plot_sources now displays an mne.preprocessing.ICA.plot_properties window when right-clicking on component names on the y-axis (:gh:`8381` by `Daniel McCloy`_)
• :func:`mne.io.read_raw_edf`, :func:`mne.io.read_raw_bdf`, and :func:`mne.io.read_raw_gdf` now detect and handle invalid highpass/lowpass filter settings (:gh:`8584` by `Clemens Brunner`_)
• If a baseline tuple containing one or two None values – e.g. (None, 0), (0, None), or (None, None) – is passed to ~mne.Epochs or ~mne.Epochs.apply_baseline, the None value(s) will be replaced with the actual time (i.e., :attr:`~mne.Epochs.tmin` and :attr:`~mne.Epochs.tmax`, respectively) when populating Epochs.baseline (:gh:`8442` by `Richard Höchenberger`_)
• ~mne.Epochs will now retain the information about an applied baseline correction, even if the baseline period is partially or completely removed through cropping later on (:gh:`8442` by `Richard Höchenberger`_)
• Add :func:`mne.source_space.compute_distance_to_sensors` to compute distances between vertices and sensors (:gh:`8534` by `Olaf Hauk`_ and `Marijn van Vliet`_)
• Annotations can now be shown/hidden interactively in raw plots (:gh:`8624` by `Daniel McCloy`_)
• Added argument colors to mne.grow_labels (:gh:`8519` by `Olaf Hauk`_)
• Added mne.SourceEstimate.apply_baseline method for baseline-correction of source estimates (:gh:`8452` by `Olaf Hauk`_)
• New mne.viz.Brain.set_time method to set the displayed time in seconds (:gh:`8415` by `Daniel McCloy`_)
• Update the backend parameter of :func:`mne.viz.plot_source_estimates` to integrate pyvista (:gh:`8395` by `Guillaume Favelier`_)
• Add group_by parameter to mne.viz.plot_epochs and mne.Epochs.plot to allow displaying channel data by sensor position (:gh:`8381` by `Daniel McCloy`_)

Bugs

• Fix orthogonalization of power envelopes in mne.connectivity.envelope_correlation (:gh:`8658` by new contributor |Qianliang Li|_ and `Eric Larson`_)
• Fix data overwrite of cascading simulation operations :mne.simulation.simulate_raw (:gh:`8633` by new contributor |Jeff Stout|_)
• Fix a transpose issue of :func:`mne.decoding.CSP.plot_filters` (:gh:`8580` by new contributor |Hongjiang Ye|_)
• Fix :func:`mne.io.read_raw_curry` to deal with Curry datasets that have channels that are listed in the labels file, but which are absent from the saved data file (e.g. 'Ref' channel). Also now populates info['meas_date'] if possible (:gh:`8400` by new contributor |Tod Flak|_)
• Fix bug with mne.io.egi.tests/test_egi.py where it mandatorily downloaded testing data when it was not necessary (:gh:`8474` by new contributor |Aniket Pradhan|_)
• Fix bug with reading split files that have dashes in the filename (:gh:`8339` by new contributor |Eduard Ort|_)
• Fix bug with parsing EDF dates and date integers (:gh:`8558` by new contributor |Austin Hurst|_ and `Eric Larson`_)
• Fix bug with reading EDF and KIT files on big endian architectures such as s390x (:gh:`8618` by `Eric Larson`_)
• Fix bug with :func:`mne.beamformer.make_dics` where the rank parameter was not properly handled (:gh:`8594` by `Marijn van Vliet`_ and `Eric Larson`_)
• Fix bug with :func:`mne.beamformer.apply_dics` where the whitener was not properly applied (:gh:`8610` by `Eric Larson`_)
• Fix bug with ~mne.viz.plot_epochs_image when order is supplied and multiple conditions are plotted (:gh:`8377` by `Daniel McCloy`_ )
• Fix bug with :func:`mne.viz.plot_source_estimates` when using the PyVista backend where singleton time points were not handled properly (:gh:`8285` by `Eric Larson`_)
• Fix bug when passing axes to plotting functions, :func:`matplotlib.pyplot.tight_layout` will not be called when the figure was created using a constrained layout (:gh:`8344` by `Eric Larson`_)
• Fix bug with compensated CTF data when picking channels without preload (:gh:`8318` by `Eric Larson`_)
• Fix bug with plotting MEG topographies where the wrong extrapolation made was used in ICA (:gh:`8637` by `Eric Larson`_)
• Fix bug when merging fNIRS channels in :func:`mne.viz.plot_evoked_topomap` and related functions (:gh:`8306` by `Robert Luke`_)
• Fix bug where events could overflow when writing to FIF (:gh:`8448` by `Eric Larson`_)
• :func:`mne.io.read_raw_edf` now supports EDF files with invalid recording dates (:gh:`8283` by `Clemens Brunner`_)
• Fix bug with :func:`mne.io.Raw.save` when using split_naming='bids' where non-split files would still be named name_split-01_meg.fif instead of the requested name_meg.fif (:gh:`8464` by `Alex Gramfort`_ and `Eric Larson`_)
• Fix bug with :class:`mne.preprocessing.ICA` where n_pca_components as a :class:`python:float` would give the number of components that explained less than or equal to the given variance. It now gives greater than the given number for better usability and consistency with :class:`sklearn.decomposition.PCA`. Generally this will mean that one more component will be included (:gh:`8326` by `Eric Larson`_)
• Fix bug with :class:`mne.preprocessing.ICA` where projections were not tracked properly (:gh:`8343` by `Eric Larson`_)
• Fix bug where extrapolation points created artifacts in :func:`mne.viz.plot_evoked_topomap` and related functions (:gh:`8425` by `Mikołaj Magnuski`_)
• Fix bug with :func:`mne.preprocessing.read_ica_eeglab` where full-rank data were not handled properly (:gh:`8326` by `Eric Larson`_)
• Fix bug with :ref:`somato-dataset` where the BEM was not included (:gh:`8317` by `Eric Larson`_)
• Fix bug with coordinate frames when performing volumetric morphs via :func:`mne.compute_source_morph` and :meth:`mne.SourceMorph.apply` that could lead to ~5 mm bias (:gh:`8642` by `Eric Larson`_)
• Fix bug with volumetric rendering alpha in :meth:`mne.VolSourceEstimate.plot_3d` and related functions (:gh:`8663` by `Eric Larson`_)
• Fix missing documentation of :func:`mne.io.read_raw_nihon` in :ref:`tut-imorting-eeg-data` (:gh:`8320` by `Adam Li`_)
• Fix bug with :func:`mne.add_reference_channels` when :func:`mne.io.Raw.reorder_channels` or related methods are used afterward (:gh:`8303`, :gh:`#8484` by `Eric Larson`_)
• Fix bug where the verbose arguments to :meth:`mne.Evoked.apply_baseline` and :meth:`mne.Epochs.apply_baseline` were not keyword-only (:gh:`8349` by `Eric Larson`_)
• ICA.max_pca_components will not be altered by calling ~mne.preprocessing.ICA.fit anymore. Instead, the new attribute ICA.max_pca_components_ will be set (:gh:`8321` by `Richard Höchenberger`_)
• Fix bug that ~mne.viz.plot_ica_overlay would sometimes not create red traces (:gh:`8341` by `Richard Höchenberger`_)
• Fix bug with :class:`~mne.preprocessing.ICA` where n_components=None, n_pca_components=None could lead to unstable unmixing matrix inversion by making n_components=None also use the lesser of n_components=0.999999 and n_components=n_pca_components (:gh:`8351` by `Eric Larson`_)
• The ica.n_pca_components property is no longer be updated during :meth:`mne.preprocessing.ICA.fit`, instead ica.n_components_ will be added to the instance (:gh:`8351` by `Eric Larson`_)
• Pass rank everyhwere in forward preparation for source imaging. This bug affected sparse solvers when using maxfilter data (:gh:`8368` by `Alex Gramfort`_)
• Fix bug in :func:`mne.viz.plot_alignment` where ECoG and sEEG channels were not plotted and fNIRS channels were always plotted in the head coordinate frame (:gh:`8393` by `Eric Larson`_)
• Fix bug in :func:`mne.set_bipolar_reference` where ch_info could contain invalid channel information keys (:gh:`8416` by `Eric Larson`_)
• When reading BrainVision raw data, the channel units and types were sometimes not inferred correctly (:gh:`8434` by `Richard Höchenberger`_)
• Attempting to remove baseline correction from preloaded ~mne.Epochs will now raise an exception (:gh:`8435` by `Richard Höchenberger`_)
• :meth:`mne.Report.parse_folder` will now correctly handle split FIFF files (:gh:`8486`, :gh:`8491` by `Richard Höchenberger`_)
• Fix bug where BrainVision channel names, event types, and event descriptions containing commas were incorrectly parsed (:gh:`8492` by `Stefan Appelhoff`_)
• Fix bug in :func:`mne.preprocessing.compute_fine_calibration` where the magnetometer calibration coefficients were computed incorrectly (:gh:`8522` by `Eric Larson`_)
• Fix bug in :func:`mne.io.read_raw_eeglab` where empty event durations led to an error (:gh:`8384` by `Mikołaj Magnuski`_)
• Fix inset sensor plots to always use equal aspect (:gh:`8545` by `Daniel McCloy`_)
• Fix bug in mne.viz.plot_compare_evokeds where evokeds with identical comment attributes would not plot properly if passed as a list (:gh:`8590` by `Daniel McCloy`_)
• Fix bug in mne.time_frequency.psd_welch and related functions where the window default errantly changed from 'hamming' to ('tukey', 0.25) (:gh:`8862` by `Eric Larson`_)
• Fix bug in :func:`mne.io.read_raw_kit` where scale factors for EEG channels could be set to zero (:gh:`8542` by `Eric Larson`_)
• Fix reading GDF files with excluded channels in :func:`mne.io.read_raw_gdf` (:gh:`8520` by `Clemens Brunner`_)
• Fix automatic selection of extrapolation mask type from channel type when plotting field maps (:gh:`8589` by `Daniel McCloy`_)
• Fix bug in :func:`mne.viz.set_3d_title` where 3D plot could have multiple titles that overlap (:gh:`8564` by `Guillaume Favelier`_)
• Fix bug in :func:`mne.viz.set_3d_view` where plotter is not updated properly causing camera issues in the doc (:gh:`8564` by `Guillaume Favelier`_)
• :func:`mne.preprocessing.find_ecg_events` didn't take the tstart parameter value into account when calculating the average heart rate (:gh:`8605` by `Richard Höchenberger`_)

API changes

• Minimum required versions were increased for core dependencies NumPy (1.15.4), SciPy (1.1.0), and Matplotlib (3.0) and for the optional dependencies scikit-learn (0.20.2) and pandas (0.23.4) (:gh:`8374` by `Eric Larson`_)
• The parameter on_split_missing has been added to :func:`mne.io.read_raw_fif` and its default will change from 'warn' to 'raise' in 0.23, by (:gh:`8357` `Eric Larson`_)
• The max_pca_components argument of :class:`~mne.preprocessing.ICA` has been deprecated, use n_components during initialization and n_pca_components in :meth:`~mne.preprocessing.ICA.apply` instead (:gh:`8351` by `Eric Larson`_)
• The n_pca_components argument of :class:`~mne.preprocessing.ICA` has been deprecated, use n_pca_components in :meth:`~mne.preprocessing.ICA.apply` (:gh:`8356` by `Eric Larson`_)
• The trans argument of :func:`mne.extract_label_time_course` is deprecated and will be removed in 0.23 as it is no longer necessary (:gh:`8389` by `Eric Larson`_)
• Parameter event_colors in mne.viz.plot_epochs and mne.Epochs.plot is deprecated, replaced by event_color which is consistent with mne.viz.plot_raw and provides greater flexibility (:gh:`8381` by `Daniel McCloy`_)

Authors

People who contributed to this release in alphabetical order (people with a + are first time contributors):

• Adam Li
• Alexandre Gramfort
• Aniket Pradhan +
• Austin Hurst +
• Christian Brodbeck
• Clemens Brunner
• Daniel McCloy
• Denis A. Engemann
• Eduard Ort +
• Eric Larson
• Evan Hathaway +
• Evgenii Kalenkovich
• Fede Raimondo
• Guillaume Favelier
• Hongjiang Ye +
• Jean-Rémi King
• Jeff Stout +
• Jonathan Kuziek +
• Jussi Nurminen
• Justus Schwabedal
• Keith Doelling
• Kyle Mathewson
• Mads Jensen
• Mainak Jas
• Marijn van Vliet
• Mikolaj Magnuski
• Olaf Hauk
• Qianliang Li +
• Richard Höchenberger
• Robert Luke
• Stefan Appelhoff
• Thomas Hartmann
• Tod Flak +
• Victoria Peterson +