v0.9.rst

Version 0.9 (2015-05-22)

Changelog

• Add support for mayavi figures in add_section method in Report by `Mainak Jas`_
• Add extract volumes of interest from freesurfer segmentation and setup as volume source space by `Alan Leggitt`_
• Add support to combine source spaces of different types by `Alan Leggitt`_
• Add support for source estimate for mixed source spaces by `Alan Leggitt`_
• Add SourceSpaces.save_as_volume method by `Alan Leggitt`_
• Automatically compute proper box sizes when generating layouts on the fly by `Marijn van Vliet`_
• Average evoked topographies across time points by `Denis Engemann`_
• Add option to Report class to save images as vector graphics (SVG) by `Denis Engemann`_
• Add events count to mne.viz.plot_events by `Denis Engemann`_
• Add support for stereotactic EEG (sEEG) channel type by `Marmaduke Woodman`_
• Add support for montage files by `Denis Engemann`_, `Marijn van Vliet`_, `Jona Sassenhagen`_, `Alex Gramfort`_ and `Teon Brooks`_
• Add support for spatiotemporal permutation clustering on sensors by `Denis Engemann`_
• Add support for multitaper time-frequency analysis by `Hari Bharadwaj`_
• Add Stockwell (S) transform for time-frequency representations by `Denis Engemann`_ and `Alex Gramfort`_
• Add reading and writing support for time frequency data (AverageTFR objects) by `Denis Engemann`_
• Add reading and writing support for digitizer data, and function for adding dig points to info by `Teon Brooks`_
• Add plot_projs_topomap method to Raw, Epochs and Evoked objects by `Teon Brooks`_
• Add EEG (based on spherical splines) and MEG (based on field interpolation) bad channel interpolation method to Raw, Epochs and Evoked objects by `Denis Engemann`_ and `Mainak Jas`_
• Add parameter to whiten_evoked, compute_whitener and prepare_noise_cov to set the exact rank by `Martin Luessi`_ and `Denis Engemann`_
• Add fiff I/O for processing history and MaxFilter info by `Denis Engemann`_ and `Eric Larson`_
• Add automated regularization with support for multiple sensor types to compute_covariance by `Denis Engemann`_ and `Alex Gramfort`_
• Add Evoked.plot_white method to diagnose the quality of the estimated noise covariance and its impact on spatial whitening by `Denis Engemann`_ and `Alex Gramfort`_
• Add mne.evoked.grand_average function to compute grand average of Evoked data while interpolating bad EEG channels if necessary by `Mads Jensen`_ and `Alex Gramfort`_
• Improve EEG referencing support and add support for bipolar referencing by `Marijn van Vliet`_ and `Alex Gramfort`_
• Enable TFR calculation on Evoked objects by `Eric Larson`_
• Add support for combining Evoked datasets with arbitrary weights (e.g., for oddball paradigms) by `Eric Larson`_ and `Alex Gramfort`_
• Add support for concatenating a list of Epochs objects by `Denis Engemann`_
• Labels support subtraction (label_1 - label_2) by `Christian Brodbeck`_
• Add GeneralizationAcrossTime object with support for cross-condition generalization by `Jean-Rémi King`_ and `Denis Engemann`_
• Add support for single dipole fitting by `Eric Larson`_
• Add support for spherical models in forward calculations by `Eric Larson`_
• Add support for SNR estimation by `Eric Larson`_
• Add support for Savitsky-Golay filtering of Evoked and Epochs by `Eric Larson`_
• Add support for adding an empty reference channel to data by `Teon Brooks`_
• Add reader function mne.io.read_raw_fif for Raw FIF files by `Teon Brooks`_
• Add example of creating MNE objects from arbitrary data and NEO files by `Jaakko Leppakangas`_
• Add plot_psd and plot_psd_topomap methods to epochs by `Yousra Bekhti`_, `Eric Larson`_ and `Denis Engemann`_
• evoked.pick_types, epochs.pick_types, and tfr.pick_types added by `Eric Larson`_
• rename_channels and set_channel_types added as methods to Raw, Epochs and Evoked objects by `Teon Brooks`_
• Add RAP-MUSIC inverse method by `Yousra Bekhti`_ and `Alex Gramfort`_
• Add evoked.as_type to allow remapping data in MEG channels to virtual magnetometer or gradiometer channels by `Mainak Jas`_
• Add mne.Report.add_bem_to_section, mne.Report.add_htmls_to_section methods to :class:`mne.Report` by `Teon Brooks`_
• Add support for KIT epochs files with read_epochs_kit by `Teon Brooks`_
• Add whitening plots for evokeds to mne.Report by `Mainak Jas`_
• Add DigMontage class and reader to interface with digitization info by `Teon Brooks`_ and `Christian Brodbeck`_
• Add set_montage method to the Raw, Epochs, and Evoked objects by `Teon Brooks`_ and `Denis Engemann`_
• Add support for capturing sensor positions when clicking on an image by `Chris Holdgraf`_
• Add support for custom sensor positions when creating Layout objects by `Chris Holdgraf`_

BUG

• Fix energy conservation for STFT with tight frames by `Daniel Strohmeier`_
• Fix incorrect data matrix when tfr was plotted with parameters tmin, tmax, fmin and fmax by `Mainak Jas`_
• Fix channel names in topomaps by `Alex Gramfort`_
• Fix mapping of l_trans_bandwidth (to low frequency) and h_trans_bandwidth (to high frequency) in _BaseRaw.filter by `Denis Engemann`_
• Fix scaling source spaces when distances have to be recomputed by `Christian Brodbeck`_
• Fix repeated samples in client to FieldTrip buffer by `Mainak Jas`_ and `Federico Raimondo`_
• Fix highpass and lowpass units read from Brainvision vhdr files by `Alex Gramfort`_
• Add missing attributes for BrainVision and KIT systems needed for resample by `Teon Brooks`_
• Fix file extensions of SSP projection files written by mne commands (from _proj.fif to -prof.fif) by `Alex Gramfort`_
• Generating EEG layouts no longer requires digitization points by `Marijn van Vliet`_
• Add missing attributes to BTI, KIT, and BrainVision by `Eric Larson`_
• The API change to the edf, brainvision, and egi break backwards compatibility for when importing eeg data by `Teon Brooks`_
• Fix bug in mne.viz.plot_topo if ylim was passed for single sensor layouts by `Denis Engemann`_
• Average reference projections will no longer by automatically added after applying a custom EEG reference by `Marijn van Vliet`_
• Fix picks argument to filter in n dimensions (affects FilterEstimator), and highpass filter in FilterEstimator by `Mainak Jas`_
• Fix beamformer code LCMV/DICS for CTF data with reference channels by `Denis Engemann`_ and `Alex Gramfort`_
• Fix scalings for bad EEG channels in mne.viz.plot_topo by `Marijn van Vliet`_
• Fix EGI reading when no events are present by `Federico Raimondo`_
• Add functionality to determine plot limits automatically or by data percentiles by `Mark Wronkiewicz`_
• Fix bug in mne.io.edf where the channel offsets were omitted in the voltage calculations by `Teon Brooks`_
• Decouple section ordering in command-line from python interface for mne-report by `Mainak Jas`_
• Fix bug with ICA resetting by `Denis Engemann`_

API

• apply_inverse functions have a new boolean parameter prepared which saves computation time by calling prepare_inverse_operator only if it is False
• find_events and read_events functions have a new parameter mask to set some bits to a don't care state by `Teon Brooks`_
• New channels module including layouts, electrode montages, and neighbor definitions of sensors which deprecates mne.layouts by `Denis Engemann`_
• read_raw_brainvision, read_raw_edf, read_raw_egi all use a standard montage import by `Teon Brooks`_
• Fix missing calibration factors for mne.io.egi.read_raw_egi by `Denis Engemann`_ and `Federico Raimondo`_
• Allow multiple filename patterns as a list (e.g., *raw.fif and *-eve.fif) to be parsed by mne report in Report.parse_folder() by `Mainak Jas`_
• read_hsp, read_elp, and write_hsp, write_mrk were removed and made private by `Teon Brooks`_
• When computing the noise covariance or MNE inverse solutions, the rank is estimated empirically using more sensitive thresholds, which stabilizes results by `Denis Engemann`_ and `Eric Larson`_ and `Alex Gramfort`_
• Raw FIFF files can be preloaded after class instantiation using raw.preload_data()
• Add label parameter to apply_inverse by `Teon Brooks`_
• Deprecated label_time_courses for in_label method in SourceEstimate by `Teon Brooks`_
• Deprecated as_data_frame for to_data_frame by `Chris Holdgraf`_
• Add transform, unit parameters to read_montage by `Teon Brooks`_
• Deprecated fmin, fmid, fmax in stc.plot and added clim by `Mark Wronkiewicz`_
• Use scipy.signal.welch instead of matplotlib.psd inside compute_raw_psd and compute_epochs_psd by `Yousra Bekhti`_ `Eric Larson`_ and `Denis Engemann`_. As a consequence, Raw.plot_raw_psds has been deprecated.
• Raw instances returned by mne.forward.apply_forward_raw now always have times starting from zero to be consistent with all other Raw instances. To get the former start and stop times, use raw.first_samp / raw.info['sfreq'] and raw.last_samp / raw.info['sfreq'].
• pick_types_evoked has been deprecated in favor of evoked.pick_types.
• Deprecated changing the sensor type of channels in rename_channels by `Teon Brooks`_
• CUDA is no longer initialized at module import, but only when first used.
• add_figs_to_section and add_images_to_section now have a textbox parameter to add comments to the image by `Teon Brooks`_
• Deprecated iir_filter_raw for fit_iir_model_raw.
• Add montage parameter to the create_info function to create the info using montages by `Teon Brooks`_

Authors

The committer list for this release is the following (preceded by number of commits):

• 515 Eric Larson
• 343 Denis A. Engemann
• 304 Alexandre Gramfort
• 300 Teon Brooks
• 142 Mainak Jas
• 119 Jean-Rémi King
• 77 Alan Leggitt
• 75 Marijn van Vliet
• 63 Chris Holdgraf
• 57 Yousra Bekhti
• 49 Mark Wronkiewicz
• 44 Christian Brodbeck
• 30 Jona Sassenhagen
• 29 Hari Bharadwaj
• 27 Clément Moutard
• 24 Ingoo Lee
• 18 Marmaduke Woodman
• 16 Martin Luessi
• 10 Jaakko Leppakangas
• 9 Andrew Dykstra
• 9 Daniel Strohmeier
• 7 kjs
• 6 Dan G. Wakeman
• 5 Federico Raimondo
• 3 Basile Pinsard
• 3 Christoph Dinh
• 3 Hafeza Anevar
• 2 Martin Billinger
• 2 Roan LaPlante
• 1 Manoj Kumar
• 1 Matt Tucker
• 1 Romain Trachel
• 1 mads jensen
• 1 sviter