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.. _changes_0_9:
Version 0.9
-----------
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-Remi 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 :meth:`mne.Report.add_bem_to_section`, :meth:`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 consquence, ``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-Remi 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
|
