v0.16.rst

Version 0.16 (2018-05-01)

Changelog

• Add possibility to pass dict of floats as argument to :func:`mne.make_ad_hoc_cov` by `Nathalie Gayraud`_
• Add support for metadata in :class:`mne.Epochs` by `Chris Holdgraf`_, `Alex Gramfort`_, `Jona Sassenhagen`_, and `Eric Larson`_
• Add support for plotting a dense head in :func:`mne.viz.plot_alignment` by `Eric Larson`_
• Allow plotting in user-created mayavi Scene in :func:`mne.viz.plot_alignment` by `Daniel McCloy`_
• Reduce memory consumption and do not require data to be loaded in :meth:`mne.Epochs.apply_baseline` by `Eric Larson`_
• Add option render_bem to :meth:`mne.Report.parse_folder` by `Eric Larson`_
• Add to :func:`mne.viz.plot_alignment` plotting of coordinate frame axes via show_axes and terrain-style interaction via interaction, by `Eric Larson`_
• Add option initial_event to :func:`mne.find_events` by `Clemens Brunner`_
• Left and right arrow keys now scroll by 25% of the visible data, whereas Shift+left/right scroll by a whole page in :meth:`mne.io.Raw.plot` by `Clemens Brunner`_
• Add support for gantry tilt angle determination from Elekta FIF file header by `Chris Bailey`_
• Add possibility to concatenate :class:`mne.Annotations` objects with + or += operators by `Clemens Brunner`_
• Add support for MaxShield raw files in :class:`mne.Report` by `Eric Larson`_
• Add ability to plot whitened data in :meth:`mne.io.Raw.plot`, :meth:`mne.Epochs.plot`, :meth:`mne.Evoked.plot`, and :meth:`mne.Evoked.plot_topo` by `Eric Larson`_
• Workaround for reading EGI MFF files with physiological signals that also present a bug from the EGI system in :func:`mne.io.read_raw_egi` by `Federico Raimondo`_
• Add support for reading subject height and weight in info['subject_info'] by `Eric Larson`_
• Improve online filtering of raw data when plotting with :meth:`mne.io.Raw.plot` to filter in segments in accordance with the default skip_by_annotation=('edge', 'bad_acq_skip') of :meth:`mne.io.Raw.filter` to avoid edge ringing by `Eric Larson`_
• Add support for multiple head position files, plotting of sensors, and control of plotting color and axes in :func:`mne.viz.plot_head_positions` by `Eric Larson`_
• Add ability to read and write :class:`Annotations` separate from :class:`mne.io.Raw` instances via :meth:`Annotations.save` and :func:`read_annotations` by `Eric Larson`_
• Add option to unset a montage by passing None to :meth:`mne.io.Raw.set_montage` by `Clemens Brunner`_
• Add sensor denoising via :func:`mne.preprocessing.oversampled_temporal_projection` by `Eric Larson`_
• Add mne.io.pick.get_channel_types which returns all available channel types in MNE by `Clemens Brunner`_
• Use standard PCA instead of randomized PCA whitening prior to ICA to increase reproducibility by `Clemens Brunner`_
• Plot sEEG electrodes in :func:`mne.viz.plot_alignment` by `Alex Gramfort`_
• Add support for any data type like sEEG or ECoG in covariance related functions (estimation, whitening and plotting) by `Alex Gramfort`_ and `Eric Larson`_
• Add function mne.io.read_annotations_eeglab to allow loading annotations from EEGLAB files, by `Alex Gramfort`_
• :meth:`mne.io.Raw.set_montage` now accepts a string as its montage argument; this will set a builtin montage, by `Clemens Brunner`_
• Add 4D BTi phantom dataset :func:`mne.datasets.phantom_4dbti.data_path`, by `Alex Gramfort`_
• Changed the background color to grey in :func:`mne.viz.plot_alignment` to make helmet more visible, by `Alex Gramfort`_
• Add :meth:`mne.io.Raw.reorder_channels`, :meth:`mne.Evoked.reorder_channels`, etc. to reorder channels, by `Eric Larson`_
• Add to mne coreg and :func:`mne.gui.coregistration` by `Eric Larson`_:
  • Improved visibility of points inside the head
  • Projection of EEG electrodes
  • Orientation of extra points toward the surface
  • Scaling points by distance to the head surface
  • Display of HPI points
  • ICP fitting with convergence criteria
  • Faster display updates
  • Scaling of mri/*.mgz files
  • Scaling of mri/trainsforms/talairach.xfm files for conversion to MNI space
• Add ability to exclude components interactively by clicking on their labels in :meth:`mne.preprocessing.ICA.plot_components` by `Mikołaj Magnuski`_
• Add reader for manual annotations of raw data produced by Brainstorm by `Anne-Sophie Dubarry`_
• Add eLORETA noise normalization for minimum-norm solvers by `Eric Larson`_
• Tighter duality gap computation in mne.inverse_sparse.tf_mxne_optim and new parametrization with alpha and l1_ratio instead of alpha_space and alpha_time by `Mathurin Massias`_ and `Daniel Strohmeier`_
• Add dgap_freq parameter in mne.inverse_sparse.mxne_optim solvers to control the frequency of duality gap computation by `Mathurin Massias`_ and `Daniel Strohmeier`_
• Add support for reading Eximia files by `Eric Larson`_ and `Federico Raimondo`_
• Add the Picard algorithm to perform ICA for :class:`mne.preprocessing.ICA`, by `Pierre Ablin`_ and `Alex Gramfort`_
• Add ability to supply a mask to the plot in :func:`mne.viz.plot_evoked_image` by `Jona Sassenhagen`_
• Add connectivity=False to cluster-based statistical functions to perform non-clustering stats by `Eric Larson`_
• Add :func:`mne.time_frequency.csd_morlet` and :func:`mne.time_frequency.csd_array_morlet` to estimate cross-spectral density using Morlet wavelets, by `Marijn van Vliet`_
• Add multidictionary time-frequency support to :func:`mne.inverse_sparse.tf_mixed_norm` by `Mathurin Massias`_ and `Daniel Strohmeier`_
• Add new DICS implementation as :func:`mne.beamformer.make_dics`, :func:`mne.beamformer.apply_dics`, :func:`mne.beamformer.apply_dics_csd` and :func:`mne.beamformer.apply_dics_epochs`, by `Marijn van Vliet`_ and `Susanna Aro`_

Bug

• Fix bug in EEG interpolation code to do nothing if there is no channel to interpolate by `Mainak Jas`_
• Fix bug in mne.preprocessing.peak_finder to output datatype consistently and added input check for empty vectors by `Tommy Clausner`_
• Fix bug in :func:`mne.io.read_raw_brainvision` to use the correct conversion for filters from time constant to frequency by `Stefan Appelhoff`_
• Fix bug with events when saving split files using :meth:`mne.Epochs.save` by `Eric Larson`_
• Fix bug in :class:`mne.decoding.SlidingEstimator` and :class:`mne.decoding.GeneralizingEstimator` to allow :func:`mne.decoding.cross_val_multiscore` to automatically detect whether the base_estimator is a classifier and use a StratifiedKFold instead of a KFold when cv is not specified, by `Jean-Rémi King`_
• Fix bug in :func:`mne.set_eeg_reference` to remove an average reference projector when setting the reference to [] (i.e. do not change the existing reference) by `Clemens Brunner`_
• Fix bug in threshold-free cluster enhancement parameter validation (:func:`mne.stats.permutation_cluster_1samp_test` and :func:`mne.stats.permutation_cluster_test`) by `Clemens Brunner`_
• Fix bug in :meth:`mne.io.Raw.plot` to correctly display event types when annotations are present by `Clemens Brunner`_
• Fix bug in :func:`mne.stats.spatio_temporal_cluster_test` default value for threshold is now calculated based on the array sizes in X, by `Eric Larson`_
• Fix bug in :func:`mne.simulation.simulate_raw` with use_cps=True where CPS was not actually used by `Eric Larson`_
• Fix bug in :func:`mne.simulation.simulate_raw` where 1- and 3-layer BEMs were not properly transformed using trans by `Eric Larson`_
• Fix bug in :func:`mne.viz.plot_alignment` where the head surface file -head.fif was not used even though present by `Chris Bailey`_
• Fix bug when writing compressed sparse column matrices (e.g., Maxwell filtering cross-talk matrices) by `Marijn van Vliet`_ and `Eric Larson`_
• Fix bug in :meth:`mne.io.Raw.plot_psd` to correctly deal with reject_by_annotation=False by `Clemens Brunner`_
• Fix bug in :func:`mne.make_fixed_length_events` when hitting corner case problems rounding to sample numbers by `Eric Larson`_
• Fix bug in :class:`mne.Epochs` when passing events as list with event_id=None by `Alex Gramfort`_
• Fix bug in mne.Report.add_figs_to_section when passing :class:`numpy.ndarray` by `Eric Larson`_
• Fix bug in CSS class setting in mne.Report BEM section by `Eric Larson`_
• Fix bug in :class:`Annotations` where annotations that extend to the end of a recording were not extended properly by `Eric Larson`_
• Fix bug in :meth:`mne.io.Raw.filter` to properly raw data with acquisition skips in separate segments by `Eric Larson`_
• Fix bug in :func:`mne.preprocessing.maxwell_filter` where homogeneous fields were not removed for CTF systems by `Eric Larson`_
• Fix computation of average quaternions in :func:`mne.preprocessing.maxwell_filter` by `Eric Larson`_
• Fix bug in writing raw.annotations where empty annotations could not be written to disk, by `Eric Larson`_
• Fix support for writing FIF files with acquisition skips by using empty buffers rather than writing zeros by `Eric Larson`_
• Fix bug in the mne make_scalp_surfaces command where --force (to bypass topology check failures) was ignored by `Eric Larson`_
• Fix bug in :func:`mne.preprocessing.maxwell_filter` when providing origin in 'meg' coordinate frame for recordings with a MEG to head transform (i.e., non empty-room recordings) by `Eric Larson`_
• Fix bug in :func:`mne.viz.plot_cov` that ignored colorbar argument by `Nathalie Gayraud`_
• Fix bug when picking CTF channels that could cause data saved to disk to be unreadable by `Eric Larson`_
• Fix bug when reading event latencies (in samples) from eeglab files didn't translate indices to 0-based python indexing by `Mikołaj Magnuski`_
• Fix consistency between :class:`mne.Epochs` and :func:`mne.stats.linear_regression_raw` in converting between samples and times (:func:`mne.stats.linear_regression_raw` now rounds, instead of truncating) by `Phillip Alday`_
• Fix bug in mne coreg where sphere surfaces were scaled by `Eric Larson`_
• Fix bug in :meth:`mne.Evoked.plot_topomap` when using proj='interactive' mode by `Eric Larson`_
• Fix bug when passing show_sensors=1 to :func:`mne.viz.plot_compare_evokeds` resulted in sensors legend placed in lower right of the figure (position 4 in matplotlib), not upper right by `Mikołaj Magnuski`_
• Fix handling of annotations when cropping and concatenating raw data by `Alex Gramfort`_ and `Eric Larson`_
• Fix bug in :func:`mne.preprocessing.create_ecg_epochs` where keep_ecg=False was ignored by `Eric Larson`_
• Fix bug in :meth:`mne.io.Raw.plot_psd` when picks is not None and picks spans more than one channel type by `Eric Larson`_
• Fix bug in :class:`mne.make_forward_solution` when passing data with compensation channels (e.g. CTF) that contain bad channels by `Alex Gramfort`_
• Fix bug in :meth:`mne.SourceEstimate.get_peak` and :meth:`mne.VolSourceEstimate.get_peak` when there is only a single time point by `Marijn van Vliet`_
• Fix bug in :func:`mne.io.read_raw_edf` when reading BDF files stimulus channels are now not scaled anymore by `Clemens Brunner`_

API

• Channels with unknown locations are now assigned position [np.nan, np.nan, np.nan] instead of [0., 0., 0.], by `Eric Larson`_
• Removed unused image_mask argument from :func:`mne.viz.plot_topomap` by `Eric Larson`_
• Unknown measurement dates are now stored as info['meas_date'] = None rather than using the current date. None is also now used when anonymizing data and when determining the machine ID for writing files, by `Mainak Jas`_ and `Eric Larson`_
• :meth:`mne.Evoked.plot` will now append the number of epochs averaged for the evoked data in the first plot title, by `Eric Larson`_
• Changed the line width in :func:`mne.viz.plot_bem` from 2.0 to 1.0 for better visibility of underlying structures, by `Eric Larson`_
• Changed the behavior of :meth:`mne.io.Raw.pick_channels` and similar methods to be consistent with :func:`mne.pick_channels` to treat channel list as a set (ignoring order) -- if reordering is necessary use inst.reorder_channels, by `Eric Larson`_
• Changed the labeling of some plotting functions to use more standard capitalization and units, e.g. "Time (s)" instead of "time [sec]" by `Eric Larson`_
• mne.time_frequency.csd_epochs has been refactored into :func:`mne.time_frequency.csd_fourier` and :func:`mne.time_frequency.csd_multitaper`, by `Marijn van Vliet`_
• mne.time_frequency.csd_array has been refactored into :func:`mne.time_frequency.csd_array_fourier` and :func:`mne.time_frequency.csd_array_multitaper`, by `Marijn van Vliet`_
• Added clean_names=False parameter to :func:`mne.io.read_raw_ctf` for control over cleaning of main channel names and compensation channel names from CTF suffixes by `Oleh Kozynets`_
• The functions lcmv, lcmv_epochs, and lcmv_raw are now deprecated in favor of :func:`mne.beamformer.make_lcmv` and :func:`mne.beamformer.apply_lcmv`, :func:`mne.beamformer.apply_lcmv_epochs`, and :func:`mne.beamformer.apply_lcmv_raw`, by `Britta Westner`_
• The functions mne.beamformer.dics, mne.beamformer.dics_epochs and mne.beamformer.dics_source_power are now deprecated in favor of :func:`mne.beamformer.make_dics`, :func:`mne.beamformer.apply_dics`, and :func:`mne.beamformer.apply_dics_csd`, by `Marijn van Vliet`_

Authors

People who contributed to this release (in alphabetical order):

• Alejandro Weinstein
• Alexandre Gramfort
• Annalisa Pascarella
• Anne-Sophie Dubarry
• Britta Westner
• Chris Bailey
• Chris Holdgraf
• Christian Brodbeck
• Claire Braboszcz
• Clemens Brunner
• Daniel McCloy
• Denis A. Engemann
• Desislava Petkova
• Dominik Krzemiński
• Eric Larson
• Erik Hornberger
• Fede Raimondo
• Henrich Kolkhorst
• Jean-Rémi King
• Jen Evans
• Joan Massich
• Jon Houck
• Jona Sassenhagen
• Juergen Dammers
• Jussi Nurminen
• Kambiz Tavabi
• Katrin Leinweber
• Kostiantyn Maksymenko
• Larry Eisenman
• Luke Bloy
• Mainak Jas
• Marijn van Vliet
• Mathurin Massias
• Mikolaj Magnuski
• Nathalie Gayraud
• Oleh Kozynets
• Phillip Alday
• Pierre Ablin
• Stefan Appelhoff
• Stefan Repplinger
• Tommy Clausner
• Yaroslav Halchenko