v0.18.rst

Version 0.18 (2019-05-19)

Changelog

• Add event_id='auto' in :func:`mne.events_from_annotations` to accommodate Brainvision markers by `Jona Sassenhagen`_, `Joan Massich`_ and `Eric Larson`_
• Add example on how to simulate raw data using subject anatomy, by `Ivana Kojcic`_, `Eric Larson`_, `Samuel Deslauriers-Gauthier`_ and `Kostiantyn Maksymenko`_
• :func:`mne.beamformer.apply_lcmv_cov` returns static source power after supplying a data covariance matrix to the beamformer filter by `Britta Westner`_ and `Marijn van Vliet`_
• Add butterfly and order arguments to :func:`mne.viz.plot_epochs` and offer separated traces for non-meg data (seeg, eeg, ecog) in butterfly view by `Stefan Repplinger`_ and `Eric Larson`_
• :meth:`mne.Epochs.get_data` now takes a picks parameter by `Jona Sassenhagen`_
• :func:`~mne.viz.plot_compare_evokeds` will generate topo plots if axes='topo' by `Jona Sassenhagen`_
• mne.viz.iter_topography can yield an additional axis, e.g., for plotting legends by `Jona Sassenhagen`_ and `Daniel McCloy`_
• Default plot title reflects channel type when picks is a channel type in :func:`~mne.viz.plot_compare_evokeds` by `Daniel McCloy`_
• Color scale limits in :func:`~mne.viz.plot_topo_image_epochs` are now computed separately per channel type in combined mag/grad plots, by `Daniel McCloy`_
• :func:`mne.simulation.simulate_stc` now allows for label overlaps by `Nathalie Gayraud`_, and `Ivana Kojcic`_
• Add long_format option to the pandas dataframe exporters, e.g :meth:`mne.Epochs.to_data_frame` by `Denis Engemann`_
• Add example on how to load standard montage :ref:`plot_montage` by `Joan Massich`_
• Add new tutorial on :ref:`tut-eeg-fsaverage-source-modeling` by `Alex Gramfort`_, and `Joan Massich`_
• Add :meth:`mne.Epochs.apply_hilbert` and :meth:`mne.Evoked.apply_hilbert` by `Eric Larson`_
• Add convenience fsaverage subject dataset fetcher / updater :func:`mne.datasets.fetch_fsaverage` by `Eric Larson`_
• Add fmin and fmax argument to :meth:`mne.time_frequency.AverageTFR.crop` and to :meth:`mne.time_frequency.EpochsTFR.crop` to crop TFR objects along frequency axis by `Dirk Gütlin`_
• Add support to :func:`mne.read_annotations` to read CNT formats by `Joan Massich`_
• Add reject parameter to :meth:`mne.preprocessing.ICA.plot_properties` to visualize rejected epochs by `Antoine Gauthier`_
• Add support for picking channels using channel name and type strings to functions with picks arguments, along with a convenience :meth:`mne.io.Raw.pick`, :meth:`mne.Epochs.pick`, and :meth:`mne.Evoked.pick` method, by `Eric Larson`_
• Add new tutorial on :ref:`tut-sleep-stage-classif` by `Alex Gramfort`_, `Stanislas Chambon`_ and `Joan Massich`_
• Add data fetchers for polysomnography (PSG) recordings from Physionet (:func:`mne.datasets.sleep_physionet.age.fetch_data` and :func:`mne.datasets.sleep_physionet.temazepam.fetch_data`) by `Alex Gramfort`_ and `Joan Massich`_
• Add envelope correlation code in mne.connectivity.envelope_correlation by `Denis Engemann`_, `Sheraz Khan`_, and `Eric Larson`_
• Add option to toggle all projectors in :meth:`mne.io.Raw.plot` and related functions by `Eric Larson`_
• Add support for indexing, slicing, and iterating :class:`mne.Annotations` by `Joan Massich`_
• :meth:`mne.io.Raw.plot` now uses the lesser of n_channels and raw.ch_names, by `Joan Massich`_
• Add support for FIR filtering in :meth:`mne.io.Raw.plot` and :ref:`mne browse_raw` by passing filtorder=0 or --filtorder 0, respectively, by `Eric Larson`_
• Add chunk_duration parameter to :func:`mne.events_from_annotations` to allow multiple events from a single annotation by `Joan Massich`_
• Add :class:`mne.simulation.SourceSimulator` class to simplify simulating SourceEstimates, by `Samuel Deslauriers-Gauthier`_, `Kostiantyn Maksymenko`_, `Nathalie Gayraud`_, `Ivana Kojcic`_, `Alex Gramfort`_, and `Eric Larson`_
• :func:`mne.io.read_raw_edf` now detects analog stim channels labeled 'STATUS' and sets them as stim channel. :func:`mne.io.read_raw_edf` no longer synthesize TAL annotations into stim channel but stores them in raw.annotations when reading by `Joan Massich`_
• Add mne.simulation.add_noise for ad-hoc noise addition to io.Raw, Epochs, and Evoked instances, by `Eric Larson`_
• Add drop_refs=True parameter to :func:`set_bipolar_reference` to drop/keep anode and cathode channels after applying the reference by `Cristóbal Moënne-Loccoz`_.
• Add processing of reference MEG channels to :class:`mne.preprocessing.ICA` by `Jevri Hanna`_
• Add use of :func:`scipy.signal.windows.dpss` for faster multitaper window computations in PSD functions by `Eric Larson`_
• Add :func:`mne.morph_labels` to facilitate morphing label sets obtained from parcellations, by `Eric Larson`_
• Add :func:`mne.labels_to_stc` to facilitate working with label data, by `Eric Larson`_
• Add :func:`mne.label.select_sources` to simplify the selection of sources within a label, by `Samuel Deslauriers-Gauthier`_
• Add support for using :class:`mne.Info` in :func:`mne.simulation.simulate_raw` instead of :class:`mne.io.Raw` by `Eric Larson`_
• Add support for passing an iterable and stim channel values using stc parameter of :func:`mne.simulation.simulate_raw` by `Eric Larson`_
• Add overlap argument to :func:`mne.make_fixed_length_events` by `Eric Larson`_
• Add approximate distance-based spacing source space decimation algorithm to :func:`mne.setup_source_space` by `Eric Larson`_
• Add 448-labels subdivided aparc cortical parcellation by `Denis Engemann`_ and `Sheraz Khan`_
• Add option to improve rendering in :ref:`mne coreg` for modern graphics cards by `Eric Larson`_
• Add mne.preprocessing.mark_flat to automate marking of flat channels and segments of raw data by `Eric Larson`_
• Add support for CUDA-based correlation computations and progress bars in :class:`mne.decoding.ReceptiveField` by `Eric Larson`_
• Add support for file-like objects in :func:`mne.io.read_raw_fif` as long as preloading is used by `Eric Larson`_
• Add keyboard shortcuts to nativate volume source estimates in time using (shift+)left/right arrow keys by `Mainak Jas`_
• Add option to SSP preprocessing functions (e.g., :func:`mne.preprocessing.compute_proj_eog` and :func:`mne.compute_proj_epochs`) to process MEG channels jointly with meg='combined' by `Eric Larson`_
• Add Epoch selection and metadata functionality to :class:`mne.time_frequency.EpochsTFR` using new mixin class by `Keith Doelling`_
• Add reject_by_annotation argument to :func:`mne.preprocessing.find_ecg_events` by `Eric Larson`_
• Add pca argument to return the rank-reduced whitener in :func:`mne.cov.compute_whitener` by `Eric Larson`_
• Add extrapolate argument to :func:`mne.viz.plot_topomap` for better control of extrapolation points placement by `Mikołaj Magnuski`_
• Add channel_wise argument to :func:`mne.io.Raw.apply_function` to allow applying a function on multiple channels at once by `Hubert Banville`_
• Add option copy='auto' to control data copying in :class:`mne.io.RawArray` by `Eric Larson`_
• The mri parameter in :func:`mne.setup_volume_source_space` is now automatically set to T1.mgz if subject is provided. This allows to get a :class:`mne.SourceSpaces` of kind volume more automatically. By `Alex Gramfort`_
• Add better __repr__ for constants, and :class:`info['dig'] <mne.Info>` entries via DigPoint by `Eric Larson`_
• Allow string argument in :meth:`mne.io.Raw.drop_channels` to remove a single channel by `Clemens Brunner`_
• Add additional depth weighting options for inverse solvers (e.g., :func:`mne.inverse_sparse.gamma_map` and :func:`mne.inverse_sparse.mixed_norm`) by `Eric Larson`_
• Add depth weighting to LCMV beamformers via depth argument in :func:`mne.beamformer.make_lcmv` by `Eric Larson`_
• Allow toggling of DC removal in :meth:`mne.io.Raw.plot` by pressing the 'd' key by `Clemens Brunner`_
• Improved clicking in :meth:`mne.io.Raw.plot` (left click on trace toggles bad, left click on background sets green line, right click anywhere removes green line) by `Clemens Brunner`_
• Add mne.realtime.LSLClient for realtime data acquisition with LSL streams of data by `Teon Brooks`_ and `Mainak Jas`_
• Add partial support for PyVista as a 3D backend using :func:`mne.viz.use_3d_backend` by `Guillaume Favelier`_
• Add option ids = None in :func:`mne.event.shift_time_events` for considering all events by `Nikolas Chalas`_ and `Joan Massich`_
• Add mne.realtime.MockLSLStream to simulate an LSL stream for testing and examples by `Teon Brooks`_
• Add support for file-like objects in :func:`mne.read_epochs` as long as preloading is used by `Paul Roujansky`_

Bug

• Fix annotations in split fif files :func:`mne.io.read_raw_fif` by `Joan Massich`_
• Fix :meth:`mne.Epochs.plot` with scalings='auto' to properly compute channel-wise scalings by `Stefan Repplinger`_
• Fix :func:`mne.gui.coregistration` and :ref:`mne coreg` crashing with segmentation fault when switching subjects by `Eric Larson`_
• Fix :func:`mne.io.read_raw_brainvision` to accommodate vmrk files which do not have any annotations by Alexander Kovrig
• Fix :meth:`mne.io.Raw.plot` and :meth:`mne.Epochs.plot` to auto-scale misc channel types by default by `Eric Larson`_
• Fix filtering functions (e.g., :meth:`mne.io.Raw.filter`) to properly take into account the two elements in n_pad parameter by `Bruno Nicenboim`_
• Fix feature_names parameter change after fitting in :class:`mne.decoding.ReceptiveField` by `Jean-Rémi King`_
• Fix index error in :func:`mne.io.read_raw_cnt` when creating stim_channel manually by `Joan Massich`_
• Fix bug with weight_norm='unit-gain' in :func:`mne.beamformer.make_lcmv` and :func:`mne.beamformer.make_dics` by `Britta Westner`_
• Fix 32bits annotations in :func:`mne.io.read_raw_cnt` by `Joan Massich`_
• Fix :func:`mne.events_from_annotations` to ignore 'BAD_' and 'EDGE_' annotations by default using a new default regexp by `Eric Larson`_
• Fix bug in mne.preprocessing.mark_flat where raw.first_samp was not taken into account by `Evgenii Kalenkovich`_
• Fix date parsing in :func:`mne.io.read_raw_cnt` by `Joan Massich`_
• Fix topological checks and error messages for BEM surfaces in :func:`mne.make_bem_model` by `Eric Larson`_
• Fix default HTML language of :class:`mne.Report` to be "en-us" instead of "fr" and allow setting via report.lang property by `Eric Larson`_
• Fix bug where loading epochs with preload=True and subsequently using :meth:`mne.Epochs.drop_bad` with new reject or flat entries leads to improper data (and epochs.selection) since v0.16.0 by `Eric Larson`_. If your code uses Epochs(..., preload=True).drop_bad(reject=..., flat=...), we recommend regenerating these data.
• Fix :ref:`mne flash_bem` to properly utilize flash30 images when conversion from DICOM images is used, and to properly deal with non-standard acquisition affines by `Eric Larson`_
• Fix :meth:`mne.io.Raw.set_annotations` with annotations=None to create an empty annotations object with orig_time that matches the :class:`mne.io.Raw` instance by `Eric Larson`_
• Fix :func:`mne.io.read_raw_edf` returning all the annotations with the same name in GDF files by `Joan Massich`_
• Fix boundaries during plotting of raw data with :func:`mne.io.Raw.plot` and :ref:`mne browse_raw` on scaled displays (e.g., macOS with HiDPI/Retina screens) by `Clemens Brunner`_
• Fix bug where filtering was not performed with lowpass or highpass in :meth:`mne.io.Raw.plot` and :ref:`mne browse_raw` by `Eric Larson`_
• Fix :func:`mne.simulation.simulate_evoked` that was failing to simulate the noise with heterogeneous sensor types due to poor conditioning of the noise covariance and make sure the projections from the noise covariance are taken into account `Alex Gramfort`_
• Fix checking of data dimensionality in :class:`mne.SourceEstimate` and related constructors by `Eric Larson`_
• Fix :meth:`mne.io.Raw.append` annotations miss-alignment by `Joan Massich`_
• Fix hash bug in the mne.io.edf module when installing on Windows by `Eric Larson`_
• Fix :func:`mne.io.read_raw_edf` reading duplicate channel names by `Larry Eisenman`_
• Fix :func:`set_bipolar_reference` in the case of generating all bipolar combinations and also in the case of repeated channels in both lists (anode and cathode) by `Cristóbal Moënne-Loccoz`_
• Fix missing code for computing the median when method='median' in :meth:`mne.Epochs.average` by `Cristóbal Moënne-Loccoz`_
• Fix CTF helmet plotting in :func:`mne.viz.plot_evoked_field` by `Eric Larson`_
• Fix saving of rejection parameters in :meth:`mne.Epochs.save` by `Eric Larson`_
• Fix orientations returned by :func:`mne.dipole.get_phantom_dipoles` (half were flipped 180 degrees) by `Eric Larson`_
• Fix bug in :func:`mne.viz.plot_compare_evokeds` when evoked.times[0] >= 0 would cause a problem with vlines='auto' mode by `Eric Larson`_
• Fix path bugs in :func:`mne.bem.make_flash_bem` and :ref:`mne flash_bem` by `Eric Larson`_
• Fix :meth:`mne.time_frequency.AverageTFR.plot_joint` mishandling bad channels, by `David Haslacher`_ and `Jona Sassenhagen`_
• Fix :func:`mne.beamformer.make_lcmv` failing when full rank data is used (i.e., when no projection is done) with reg=0., by `Eric Larson`_
• Fix issue with bad channels ignored in :func:`mne.beamformer.make_lcmv` and :func:`mne.beamformer.make_dics` by `Alex Gramfort`_
• Fix :func:`mne.compute_proj_raw` when duration != None not to apply existing proj and to avoid using duplicate raw data samples by `Eric Larson`_
• Fix reject_by_annotation not being passed internally by :func:`mne.preprocessing.create_ecg_epochs` and :ref:`mne clean_eog_ecg` to :func:`mne.preprocessing.find_ecg_events` by `Eric Larson`_
• Fix :func:`mne.io.read_raw_edf` failing when EDF header fields (such as patient name) contained special characters, by `Clemens Brunner`_
• Fix :func:`mne.io.read_raw_eeglab` incorrectly parsing event durations by `Clemens Brunner`_
• Fix :func:`mne.io.read_raw_egi` when cropping non-preloaded EGI MFF data by `Alex Gramfort`_
• Fix :meth:`mne.io.Raw.interpolate_bads` for interpolating CTF MEG channels when reference sensors are present by `jeythekey`_
• Fix a bug in :meth:`mne.io.Raw.resample`, where resampling events could result in indices > n_times-1, by `jeythekey`_
• Fix :meth:`mne.preprocessing.ICA.score_sources` to use the sfreq of the raw data to filter rather than the sfreq when the ICA was fit, by `jeythekey`_
• Fix a bug in :class:`mne.preprocessing.ICA`, where manually setting the attribute ICA.exclude to an np.array resulted in the removal of random components when later also providing the exclude argument to any apply...-method, by `jeythekey`_
• Ascending changed to descending sorting of scores for integer ..._criterion arguments in mne.preprocessing.ICA.detect_artifacts and mne.preprocessing.run_ica, as it used to be documented; the docstring in these functions was corrected for float ..._criterion arguments, by `jeythekey`_

API

• Deprecate cov, iir_params, blink, ecg, chpi, random_state and support for :class:`mne.io.Raw` instance inputs in :func:`mne.simulation.simulate_raw`; use :func:`mne.simulation.add_noise`, :func:`mne.simulation.add_ecg`, :func:`mne.simulation.add_eog`, and :func:`mne.simulation.add_chpi` by `Eric Larson`_
• Add overwrite parameter in :func:`mne.Epochs.save` by `Katarina Slama`_
• Add stim_channel parameter in :func:`mne.io.read_raw_cnt` to toggle stim channel synthesis by `Joan Massich`_
• Python 2 is no longer supported; MNE-Python now requires Python 3.5+, by `Eric Larson`_
• A new class :class:`mne.VolVectorSourceEstimate` is returned by :func:`mne.minimum_norm.apply_inverse` (and related functions) when a volume source space and pick_ori='vector' is used, by `Eric Larson`_
• Converting a forward solution with a volume source space to fixed orientation using :func:`mne.convert_forward_solution` now raises an error, by `Eric Larson`_
• raw.estimate_rank has been deprecated and will be removed in 0.19 in favor of :func:`mne.compute_rank` by `Eric Larson`_
• :class:`Annotations` are now kept sorted (by onset time) during instantiation and :meth:`~Annotations.append` operations, by `Eric Larson`_
• Deprecate mne.io.find_edf_events by `Joan Massich`_
• Deprecate limit_depth_chs in :func:`mne.minimum_norm.make_inverse_operator` in favor of depth=dict(limit_depth_chs=...) by `Eric Larson`_
• Reading BDF and GDF files with :func:`mne.io.read_raw_edf` is deprecated and replaced by :func:`mne.io.read_raw_bdf` and :func:`mne.io.read_raw_gdf`, by `Clemens Brunner`_
• :func:`mne.forward.compute_depth_prior` has been reworked to operate directly on :class:`Forward` instance as forward rather than a representation scattered across the parameters G, is_fixed_ori, patch_info, by `Eric Larson`_
• Deprecate method='extended-infomax' in :class:`mne.preprocessing.ICA`; Extended Infomax can now be computed with method='infomax' and fit_params=dict(extended=True) by `Clemens Brunner`_
• Fix support for supplying extrapolate via :meth:`ica.plot_properties(..., topomap_args=dict(extrapolate=...)) <mne.preprocessing.ICA.plot_properties>` by `Sebastian Castano`_
• The peak finder that was formerly accessible via from mne.preprocessing.peak_finder import peak_finder should now be imported directly from the enclosing namespace as from mne.preprocessing import peak_finder by `Eric Larson`_
• Deprecate mne.realtime module to make a standalone module mne-realtime that will live outside of this package by `Teon Brooks`_