<commit_before>What's new
==========

.. _changes_0_9:

Current
-----------

Changelog
~~~~~~~~~

   - Add support for mayavi figures in `add_section` method in Report by `<NAME>`_

   - 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.export_volume` method by `Alan Leggitt`_

   - Automatically compute proper box sizes when generating layouts on the fly by `<NAME>`_

   - 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 `<NAME>`_

   - Add support for montage files by `<NAME>`_, `<NAME>`_, `<NAME>`_, `<NAME>`_ and `Teon Brooks`_

   - Add support for spatiotemporal permutation clustering on sensors by `Denis Engemann`_

   - Add support for multitaper time-frequency analysis by `<NAME>`_

   - 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 methods `get_channel_positions`, `set_channel_positions` for setting channel positions,
     and `plot_projs_topomap` to `Raw`, `Epochs` and `Evoked` objects by `Teon Brooks`_

   - Add EEG bad channel interpolation method (based on spherical splines) to `Raw`, `Epochs` and `Evoked` objects
     by `<NAME>`_

   - Add parameter to `whiten_evoked`, `compute_whitener` and `prepare_noise_cov` to set the exact rank by `<NAME>`_ and `Denis Engemann`_

   - Add fiff I/O for processing history and MaxFilter info by `<NAME>`_ and `<NAME>`_

   - Add automated regularization with support for multiple sensor types to mne.cov.compute_covariance by `<NAME>`_ and `<NAME>`_

   - Add ``mne.viz.plot_evoked_white`` function and `Evoked.plot_white` method to diagnose the quality of the estimated noise covariance and its impact on spatial whitening by `<NAME>`_ and `<NAME>`_

   - Add ``mne.evoked.grand_average`` function to compute grand average of Evoked data while interpolating bad EEG channels if necessary by `<NAME>`_ and `<NAME>`_

   - Improve EEG referencing support and add support for bipolar referencing by `<NAME>`_ and `<NAME>`_

   - Enable TFR calculation on Evoked objects by `<NAME>`_

   - Add support for combining Evoked datasets with arbitrary weights (e.g., for oddball paradigms) by `<NAME>`_ and `<NAME>`_

   - Add support for concatenating a list of Epochs objects by `<NAME>gemann`_

   - Labels support subtraction (``label_1 - label_2``) by `<NAME>`_

   - Add GeneralizationAcrossTime object with support for cross-condition generalization by `<NAME>`_ and `Denis Engemann`_

   - Add support for single dipole fitting by `<NAME>`_

   - Add support for spherical models in forward calculations by `Eric Larson`_

   - Add support for SNR estimation by `<NAME>`_

   - Add support for Savitsky-Golay filtering of Evoked and Epochs by `<NAME>`_

   - Add `render_bem`, `add_htmls_to_section` methods to `mne.Report` by `<NAME>oks`_

   - Add support for adding an empty reference channel to data by `Teon Brooks`_

BUG
~~~

   - Fix energy conservation for STFT with tight frames by `<NAME>`_

   - Fix incorrect data matrix when tfr was plotted with parameters `tmin`, `tmax`, `fmin` and `fmax` by `<NAME>`_

   - Fix channel names in topomaps by `<NAME>`_

   - 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 `<NAME>`_

   - Fix repeated samples in client to FieldTrip buffer by `Main<NAME>`_ and `<NAME>`_

   - Fix highpass and lowpass units read from Brainvision vhdr files by `<NAME>`_

   - 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 `<NAME>`_

   - Generating EEG layouts no longer requires digitization points by `<NAME>`_

   - Add missing attributes to BTI, KIT, and BrainVision by `<NAME>`_

   - 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 `<NAME>gemann`_

   - Average reference projections will no longer by automatically added after applying a custom EEG reference by `<NAME>`_

   - 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 `<NAME>`_ and `<NAME>`_

   - Fix scalings for bad EEG channels in `mne.viz.plot_topo` by `<NAME>et`_

   - Fix EGI reading when no events are present by `Federico Raimondo`_

   - Add functionality to determine plot limits automatically or by data percentiles by `<NAME>`_

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 `<NAME>`_

   - `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 `<NAME>`_ and `<NAME>`_

   - 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 `<NAME>`_ and `<NAME>`_ and `<NAME>`_

   - 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 `<NAME>`_

   - Add `transform`, `unit` parameters to `read_montage` by `Teon Brooks`_

   - Deprecated `fmin, fmid, fmax` in stc.plot and added clim by `<NAME>`_

.. _changes_0_8:

Version 0.8
-----------

Changelog
~~~~~~~~~

   - Add Python3 support by `<NAME>`_, `<NAME>`_, `<NAME>`_, and `<NAME>`_

   - Add `get_peak` method for evoked and stc objects by  `Denis Engemann`_

   - Add `iter_topography` function for radically simplified custom sensor topography plotting by `Denis Engemann`_

   - Add field line interpolation by `Eric Larson`_

   - Add full provenance tacking for epochs and improve `drop_log` by `<NAME>`_, `<NAME>`_ and `Denis Engemann`_

   - Add systematic contains method to Raw, Epochs and Evoked for channel type membership testing by `Denis Engemann`_

   - Add fiff unicode writing and reading support by `Denis Engemann`_

   - Add 3D MEG/EEG field plotting function and evoked method by `Denis Engemann`_ and  `<NAME>`_

   - Add consistent channel-dropping methods to Raw, Epochs and Evoked by `Denis Engemann`_ and  `Alex Gramfort`_

   - Add `equalize_channnels` function to set common channels for a list of Raw, Epochs, or Evoked objects by `Denis Engemann`_
<commit_msg>Fix markdown<commit_after>What's new
==========

.. _changes_0_9:

Current
-----------

Changelog
~~~~~~~~~

   - Add support for mayavi figures in `add_section` method in Report by `<NAME>`_

   - 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.export_volume` method by `Alan Leggitt`_

   - Automatically compute proper box sizes when generating layouts on the fly by `<NAME>`_

   - 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 `<NAME>`_

   - Add support for montage files by `<NAME>`_, `<NAME>`_, `<NAME>`_, `<NAME>`_ and `Teon Brooks`_

   - Add support for spatiotemporal permutation clustering on sensors by `<NAME>ann`_

   - Add support for multitaper time-frequency analysis by `<NAME>`_

   - Add Stockwell (S) transform for time-frequency representations by `<NAME>`_ and `<NAME>`_

   - Add reading and writing support for time frequency data (AverageTFR objects) by  `<NAME>`_

   - Add reading and writing support for digitizer data, and function for adding dig points to info by `Teon Brooks`_

   - Add methods `get_channel_positions`, `set_channel_positions` for setting channel positions,
     and `plot_projs_topomap` to `Raw`, `Epochs` and `Evoked` objects by `Teon Brooks`_

   - Add EEG bad channel interpolation method (based on spherical splines) to `Raw`, `Epochs` and `Evoked` objects
     by `<NAME>gemann`_

   - Add parameter to `whiten_evoked`, `compute_whitener` and `prepare_noise_cov` to set the exact rank by `<NAME>`_ and `Denis Engemann`_

   - Add fiff I/O for processing history and MaxFilter info by `<NAME>`_ and `<NAME>`_

   - Add automated regularization with support for multiple sensor types to mne.cov.compute_covariance by `<NAME>`_ and `<NAME>`_

   - Add ``mne.viz.plot_evoked_white`` function and `Evoked.plot_white` method to diagnose the quality of the estimated noise covariance and its impact on spatial whitening by `<NAME>`_ and `<NAME>`_

   - Add ``mne.evoked.grand_average`` function to compute grand average of Evoked data while interpolating bad EEG channels if necessary by `<NAME>`_ and `<NAME>`_

   - Improve EEG referencing support and add support for bipolar referencing by `<NAME>`_ and `<NAME>`_

   - Enable TFR calculation on Evoked objects by `Eric Larson`_

   - Add support for combining Evoked datasets with arbitrary weights (e.g., for oddball paradigms) by `<NAME>`_ and `<NAME>`_

   - Add support for concatenating a list of Epochs objects by `<NAME>`_

   - Labels support subtraction (``label_1 - label_2``) by `<NAME>`_

   - Add GeneralizationAcrossTime object with support for cross-condition generalization by `<NAME>`_ and `<NAME>`_

   - Add support for single dipole fitting by `<NAME>`_

   - Add support for spherical models in forward calculations by `<NAME>`_

   - Add support for SNR estimation by `<NAME>`_

   - Add support for Savitsky-Golay filtering of Evoked and Epochs by `<NAME>`_

   - Add `render_bem`, `add_htmls_to_section` methods to `mne.Report` by `Teon Brooks`_

   - Add support for adding an empty reference channel to data by `Teon Brooks`_

BUG
~~~

   - Fix energy conservation for STFT with tight frames by `<NAME>`_

   - Fix incorrect data matrix when tfr was plotted with parameters `tmin`, `tmax`, `fmin` and `fmax` by `<NAME>`_

   - Fix channel names in topomaps by `<NAME>`_

   - Fix mapping of `l_trans_bandwidth` (to low frequency) and
    `h_trans_bandwidth` (to high frequency) in `_BaseRaw.filter` by `<NAME>`_

   - Fix scaling source spaces when distances have to be recomputed by `Christian Brodbeck`_

   - Fix repeated samples in client to FieldTrip buffer by `<NAME>`_ and `<NAME>`_

   - Fix highpass and lowpass units read from Brainvision vhdr files by `<NAME>`_

   - 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 `<NAME>`_

   - Generating EEG layouts no longer requires digitization points by `<NAME>`_

   - Add missing attributes to BTI, KIT, and BrainVision by `<NAME>`_

   - 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 `<NAME>`_

   - Average reference projections will no longer by automatically added after applying a custom EEG reference by `<NAME>`_

   - Fix picks argument to filter in n dimensions (affects FilterEstimator), and highpass filter in FilterEstimator by `<NAME>`_

   - Fix beamformer code LCMV/DICS for CTF data with reference channels by `<NAME>`_ and `<NAME>`_

   - Fix scalings for bad EEG channels in `mne.viz.plot_topo` by `<NAME>`_

   - Fix EGI reading when no events are present by `<NAME>`_

   - Add functionality to determine plot limits automatically or by data percentiles by `<NAME>`_

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 `<NAME>`_

   - `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 `<NAME>`_ and `<NAME>`_

   - 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 `<NAME>`_ and `<NAME>`_ and `<NAME>`_

   - 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 `<NAME>`_

   - Add `transform`, `unit` parameters to `read_montage` by `Teon Brooks`_

   - Deprecated `fmin, fmid, fmax` in stc.plot and added `clim` by `<NAME>`_

.. _changes_0_8:

Version 0.8
-----------

Changelog
~~~~~~~~~

   - Add Python3 support by `<NAME>`_, `<NAME>`_, `<NAME>`_, and `<NAME>`_

   - Add `get_peak` method for evoked and stc objects by  `Denis Engemann`_

   - Add `iter_topography` function for radically simplified custom sensor topography plotting by `Denis Engemann`_

   - Add field line interpolation by `<NAME>`_

   - Add full provenance tacking for epochs and improve `drop_log` by `<NAME>`_, `<NAME>`_ and `<NAME>`_

   - Add systematic contains method to Raw, Epochs and Evoked for channel type membership testing by `<NAME>`_

   - Add fiff unicode writing and reading support by `<NAME>`_

   - Add 3D MEG/EEG field plotting function and evoked method by `<NAME>`_ and  `<NAME>`_

   - Add consistent channel-dropping methods to Raw, Epochs and Evoked by `<NAME>`_ and  `<NAME>`_

   - Add `equalize_channnels` function to set common channels for a list of Raw, Epochs, or Evoked objects by `<NAME>ann`_

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