diff --git a/doc/_includes/channel_interpolation.rst b/doc/_includes/channel_interpolation.rst index 4639604af58..e90a763d214 100644 --- a/doc/_includes/channel_interpolation.rst +++ b/doc/_includes/channel_interpolation.rst @@ -59,7 +59,7 @@ where :math:`G_{ds} \in R^{M \times N}` computes :math:`g_{m}(\boldsymbol{r_i}, To interpolate bad channels, one can simply do: - >>> evoked.interpolate_bads(reset_bads=False) # doctest: +SKIP + >>> evoked.interpolate_bads(reset_bads=False) # doctest: +SKIP and the bad channel will be fixed. @@ -67,4 +67,4 @@ and the bad channel will be fixed. .. topic:: Examples: - * :ref:`ex-interpolate-bad-channels` + * :ref:`ex-interpolate-bad-channels` diff --git a/doc/_includes/forward.rst b/doc/_includes/forward.rst index f92632f8220..d04eeba7b5b 100644 --- a/doc/_includes/forward.rst +++ b/doc/_includes/forward.rst @@ -130,26 +130,26 @@ transformation symbols (:math:`T_x`) indicate the transformations actually present in the FreeSurfer files. Generally, .. math:: \begin{bmatrix} - x_2 \\ - y_2 \\ - z_2 \\ - 1 - \end{bmatrix} = T_{12} \begin{bmatrix} - x_1 \\ - y_1 \\ - z_1 \\ - 1 - \end{bmatrix} = \begin{bmatrix} - R_{11} & R_{12} & R_{13} & x_0 \\ - R_{21} & R_{22} & R_{23} & y_0 \\ - R_{31} & R_{32} & R_{33} & z_0 \\ - 0 & 0 & 0 & 1 - \end{bmatrix} \begin{bmatrix} - x_1 \\ - y_1 \\ - z_1 \\ - 1 - \end{bmatrix}\ , + x_2 \\ + y_2 \\ + z_2 \\ + 1 + \end{bmatrix} = T_{12} \begin{bmatrix} + x_1 \\ + y_1 \\ + z_1 \\ + 1 + \end{bmatrix} = \begin{bmatrix} + R_{11} & R_{12} & R_{13} & x_0 \\ + R_{21} & R_{22} & R_{23} & y_0 \\ + R_{31} & R_{32} & R_{33} & z_0 \\ + 0 & 0 & 0 & 1 + \end{bmatrix} \begin{bmatrix} + x_1 \\ + y_1 \\ + z_1 \\ + 1 + \end{bmatrix}\ , where :math:`x_k`, :math:`y_k`,and :math:`z_k` are the location coordinates in two coordinate systems, :math:`T_{12}` is the coordinate transformation from @@ -161,20 +161,20 @@ files produced by FreeSurfer and MNE. The fixed transformations :math:`T_-` and :math:`T_+` are: .. math:: T_{-} = \begin{bmatrix} - 0.99 & 0 & 0 & 0 \\ - 0 & 0.9688 & 0.042 & 0 \\ - 0 & -0.0485 & 0.839 & 0 \\ - 0 & 0 & 0 & 1 - \end{bmatrix} + 0.99 & 0 & 0 & 0 \\ + 0 & 0.9688 & 0.042 & 0 \\ + 0 & -0.0485 & 0.839 & 0 \\ + 0 & 0 & 0 & 1 + \end{bmatrix} and .. math:: T_{+} = \begin{bmatrix} - 0.99 & 0 & 0 & 0 \\ - 0 & 0.9688 & 0.046 & 0 \\ - 0 & -0.0485 & 0.9189 & 0 \\ - 0 & 0 & 0 & 1 - \end{bmatrix} + 0.99 & 0 & 0 & 0 \\ + 0 & 0.9688 & 0.046 & 0 \\ + 0 & -0.0485 & 0.9189 & 0 \\ + 0 & 0 & 0 & 1 + \end{bmatrix} .. note:: This section does not discuss the transformation between the MRI voxel @@ -352,11 +352,11 @@ coordinates (:math:`r_D`) by where .. math:: T = \begin{bmatrix} - e_x & 0 \\ - e_y & 0 \\ - e_z & 0 \\ - r_{0D} & 1 - \end{bmatrix}\ . + e_x & 0 \\ + e_y & 0 \\ + e_z & 0 \\ + r_{0D} & 1 + \end{bmatrix}\ . Calculation of the magnetic field --------------------------------- diff --git a/doc/_includes/ssp.rst b/doc/_includes/ssp.rst index 1bc860d15db..40b25a237db 100644 --- a/doc/_includes/ssp.rst +++ b/doc/_includes/ssp.rst @@ -101,12 +101,12 @@ The EEG average reference is the mean signal over all the sensors. It is typical in EEG analysis to subtract the average reference from all the sensor signals :math:`b^{1}(t), ..., b^{n}(t)`. That is: -.. math:: {b}^{j}_{s}(t) = b^{j}(t) - \frac{1}{n}\sum_{k}{b^k(t)} +.. math:: {b}^{j}_{s}(t) = b^{j}(t) - \frac{1}{n}\sum_{k}{b^k(t)} :name: eeg_proj where the noise term :math:`b_{n}^{j}(t)` is given by -.. math:: b_{n}^{j}(t) = \frac{1}{n}\sum_{k}{b^k(t)} +.. math:: b_{n}^{j}(t) = \frac{1}{n}\sum_{k}{b^k(t)} :name: noise_term Thus, the projector vector :math:`P_{\perp}` will be given by diff --git a/doc/api/events.rst b/doc/api/events.rst index f9447741a09..3f7159a22d5 100644 --- a/doc/api/events.rst +++ b/doc/api/events.rst @@ -55,4 +55,4 @@ Events average_movements combine_event_ids equalize_epoch_counts - make_metadata \ No newline at end of file + make_metadata diff --git a/doc/api/file_io.rst b/doc/api/file_io.rst index 3b43de6ce64..2da9059deb3 100644 --- a/doc/api/file_io.rst +++ b/doc/api/file_io.rst @@ -63,4 +63,4 @@ Base class: :toctree: ../generated/ :template: autosummary/class_no_members.rst - BaseEpochs \ No newline at end of file + BaseEpochs diff --git a/doc/changes/v0.10.rst b/doc/changes/v0.10.rst index 6a0c3322e88..ac4f2e42857 100644 --- a/doc/changes/v0.10.rst +++ b/doc/changes/v0.10.rst @@ -91,7 +91,7 @@ BUG - Fix dropping of events after downsampling stim channels by `Marijn van Vliet`_ -- Fix scaling in :func:``mne.viz.utils._setup_vmin_vmax`` by `Jaakko Leppakangas`_ +- Fix scaling in ``mne.viz.utils._setup_vmin_vmax`` by `Jaakko Leppakangas`_ - Fix order of component selection in :class:`mne.decoding.CSP` by `Clemens Brunner`_ diff --git a/doc/changes/v0.12.rst b/doc/changes/v0.12.rst index cf01f8ff62c..b3b7aba1a39 100644 --- a/doc/changes/v0.12.rst +++ b/doc/changes/v0.12.rst @@ -129,7 +129,7 @@ BUG - Fix bug in :func:`mne.io.Raw.save` where, in rare cases, automatically split files could end up writing an extra empty file that wouldn't be read properly by `Eric Larson`_ -- Fix :class:``mne.realtime.StimServer`` by removing superfluous argument ``ip`` used while initializing the object by `Mainak Jas`_. +- Fix ``mne.realtime.StimServer`` by removing superfluous argument ``ip`` used while initializing the object by `Mainak Jas`_. - Fix removal of projectors in :func:`mne.preprocessing.maxwell_filter` in ``st_only=True`` mode by `Eric Larson`_ @@ -175,37 +175,37 @@ Authors The committer list for this release is the following (preceded by number of commits): -* 348 Eric Larson -* 347 Jaakko Leppakangas -* 157 Alexandre Gramfort -* 139 Jona Sassenhagen -* 67 Jean-Remi King -* 32 Chris Holdgraf -* 31 Denis A. Engemann -* 30 Mainak Jas -* 16 Christopher J. Bailey -* 13 Marijn van Vliet -* 10 Mark Wronkiewicz -* 9 Teon Brooks -* 9 kaichogami -* 8 Clément Moutard -* 5 Camilo Lamus -* 5 mmagnuski -* 4 Christian Brodbeck -* 4 Daniel McCloy -* 4 Yousra Bekhti -* 3 Fede Raimondo -* 1 Jussi Nurminen -* 1 MartinBaBer -* 1 Mikolaj Magnuski -* 1 Natalie Klein -* 1 Niklas Wilming -* 1 Richard Höchenberger -* 1 Sagun Pai -* 1 Sourav Singh -* 1 Tom Dupré la Tour -* 1 jona-sassenhagen@ -* 1 kambysese -* 1 pbnsilva -* 1 sviter -* 1 zuxfoucault +* 348 Eric Larson +* 347 Jaakko Leppakangas +* 157 Alexandre Gramfort +* 139 Jona Sassenhagen +* 67 Jean-Remi King +* 32 Chris Holdgraf +* 31 Denis A. Engemann +* 30 Mainak Jas +* 16 Christopher J. Bailey +* 13 Marijn van Vliet +* 10 Mark Wronkiewicz +* 9 Teon Brooks +* 9 kaichogami +* 8 Clément Moutard +* 5 Camilo Lamus +* 5 mmagnuski +* 4 Christian Brodbeck +* 4 Daniel McCloy +* 4 Yousra Bekhti +* 3 Fede Raimondo +* 1 Jussi Nurminen +* 1 MartinBaBer +* 1 Mikolaj Magnuski +* 1 Natalie Klein +* 1 Niklas Wilming +* 1 Richard Höchenberger +* 1 Sagun Pai +* 1 Sourav Singh +* 1 Tom Dupré la Tour +* 1 jona-sassenhagen@ +* 1 kambysese +* 1 pbnsilva +* 1 sviter +* 1 zuxfoucault diff --git a/doc/changes/v0.13.rst b/doc/changes/v0.13.rst index 425ba4c76a1..aee297d9d2d 100644 --- a/doc/changes/v0.13.rst +++ b/doc/changes/v0.13.rst @@ -198,7 +198,7 @@ API - Deprecated ``mne.time_frequency.cwt_morlet`` and ``mne.time_frequency.single_trial_power`` in favour of :func:`mne.time_frequency.tfr_morlet` with parameter average=False, by `Jean-Remi King`_ and `Alex Gramfort`_ -- Add argument ``mask_type`` to func:`mne.read_events` and func:`mne.find_events` to support MNE-C style of trigger masking by `Teon Brooks`_ and `Eric Larson`_ +- Add argument ``mask_type`` to :func:`mne.read_events` and :func:`mne.find_events` to support MNE-C style of trigger masking by `Teon Brooks`_ and `Eric Larson`_ - Extended Infomax is now the new default in :func:`mne.preprocessing.infomax` (``extended=True``), by `Clemens Brunner`_ diff --git a/doc/changes/v0.15.rst b/doc/changes/v0.15.rst index ada8180d4ac..e2de7301973 100644 --- a/doc/changes/v0.15.rst +++ b/doc/changes/v0.15.rst @@ -226,7 +226,7 @@ API - ``mne.viz.decoding.plot_gat_times``, ``mne.viz.decoding.plot_gat_matrix`` are now deprecated. Use matplotlib instead as shown in the examples, by `Jean-Remi King`_ and `Alex Gramfort`_ -- Add ``norm_trace`` parameter to control single-epoch covariance normalization in :class:mne.decoding.CSP, by `Jean-Remi King`_ +- Add ``norm_trace`` parameter to control single-epoch covariance normalization in :class:`mne.decoding.CSP`, by `Jean-Remi King`_ - Allow passing a list of channel names as ``show_names`` in function :func:`mne.viz.plot_sensors` and methods :meth:`mne.Evoked.plot_sensors`, :meth:`mne.Epochs.plot_sensors` and :meth:`mne.io.Raw.plot_sensors` to show only a subset of channel names by `Jaakko Leppakangas`_ diff --git a/doc/changes/v0.17.rst b/doc/changes/v0.17.rst index 40896b6f383..49e722c584d 100644 --- a/doc/changes/v0.17.rst +++ b/doc/changes/v0.17.rst @@ -234,7 +234,7 @@ API In 0.19 The ``stim_channel`` keyword arguments will be removed from ``read_raw_...`` functions. -- Calling :meth:``mne.io.pick.pick_info`` removing channels that are needed by compensation matrices (``info['comps']``) no longer raises ``RuntimeException`` but instead logs an info level message. By `Luke Bloy`_ +- Calling ``mne.io.pick.pick_info`` removing channels that are needed by compensation matrices (``info['comps']``) no longer raises ``RuntimeException`` but instead logs an info level message. By `Luke Bloy`_ - :meth:`mne.Epochs.save` now has the parameter ``fmt`` to specify the desired format (precision) saving epoched data, by `Stefan Repplinger`_, `Eric Larson`_ and `Alex Gramfort`_ @@ -274,44 +274,44 @@ Authors People who contributed to this release (in alphabetical order): -* Alexandre Gramfort -* Antoine Gauthier -* Britta Westner -* Christian Brodbeck -* Clemens Brunner -* Daniel McCloy -* David Sabbagh -* Denis A. Engemann -* Eric Larson -* Ezequiel Mikulan -* Henrich Kolkhorst -* Hubert Banville -* Jasper J.F. van den Bosch -* Jen Evans -* Joan Massich -* Johan van der Meer -* Jona Sassenhagen -* Kambiz Tavabi -* Lorenz Esch -* Luke Bloy -* Mainak Jas -* Manu Sutela -* Marcin Koculak -* Marijn van Vliet -* Mikolaj Magnuski -* Peter J. Molfese -* Sam Perry -* Sara Sommariva -* Sergey Antopolskiy -* Sheraz Khan -* Stefan Appelhoff -* Stefan Repplinger -* Steven Bethard -* Teekuningas -* Teon Brooks -* Thomas Hartmann -* Thomas Jochmann -* Tom Dupré la Tour -* Tristan Stenner -* buildqa -* jeythekey +* Alexandre Gramfort +* Antoine Gauthier +* Britta Westner +* Christian Brodbeck +* Clemens Brunner +* Daniel McCloy +* David Sabbagh +* Denis A. Engemann +* Eric Larson +* Ezequiel Mikulan +* Henrich Kolkhorst +* Hubert Banville +* Jasper J.F. van den Bosch +* Jen Evans +* Joan Massich +* Johan van der Meer +* Jona Sassenhagen +* Kambiz Tavabi +* Lorenz Esch +* Luke Bloy +* Mainak Jas +* Manu Sutela +* Marcin Koculak +* Marijn van Vliet +* Mikolaj Magnuski +* Peter J. Molfese +* Sam Perry +* Sara Sommariva +* Sergey Antopolskiy +* Sheraz Khan +* Stefan Appelhoff +* Stefan Repplinger +* Steven Bethard +* Teekuningas +* Teon Brooks +* Thomas Hartmann +* Thomas Jochmann +* Tom Dupré la Tour +* Tristan Stenner +* buildqa +* jeythekey diff --git a/doc/changes/v1.2.rst b/doc/changes/v1.2.rst index b6a8b5a8edf..e292b472b03 100644 --- a/doc/changes/v1.2.rst +++ b/doc/changes/v1.2.rst @@ -63,7 +63,7 @@ Bugs API changes ~~~~~~~~~~~ -- In meth:`mne.Evoked.plot`, the default value of the ``spatial_colors`` parameter has been changed to ``'auto'``, which will use spatial colors if channel locations are available (:gh:`11201` by :newcontrib:`Hüseyin Orkun Elmas` and `Daniel McCloy`_) +- In :meth:`mne.Evoked.plot`, the default value of the ``spatial_colors`` parameter has been changed to ``'auto'``, which will use spatial colors if channel locations are available (:gh:`11201` by :newcontrib:`Hüseyin Orkun Elmas` and `Daniel McCloy`_) - Starting with this release we now follow the Python convention of using ``FutureWarning`` instead of ``DeprecationWarning`` to signal user-facing changes to our API (:gh:`11120` by `Daniel McCloy`_) - The ``names`` parameter of :func:`mne.viz.plot_arrowmap` and :func:`mne.viz.plot_regression_weights` has been deprecated; sensor names will be automatically drawn from the ``info_from`` or ``model`` parameter (respectively), and can be hidden, shown, or altered via the ``show_names`` parameter (:gh:`11123` by `Daniel McCloy`_) - The ``bands`` parameter of :meth:`mne.Epochs.plot_psd_topomap` now accepts :class:`dict` input; legacy :class:`tuple` input is supported, but discouraged for new code (:gh:`11050` by `Daniel McCloy`_) diff --git a/doc/documentation/datasets.rst b/doc/documentation/datasets.rst index 063d06da363..70da39cccd8 100644 --- a/doc/documentation/datasets.rst +++ b/doc/documentation/datasets.rst @@ -516,7 +516,7 @@ Contains both EEG (EGI) and eye-tracking (ASCII format) data recorded from a pupillary light reflex experiment, stored in separate files. 1 participant fixated on the screen while short light flashes appeared. Event onsets were recorded by a photodiode attached to the screen and were sent to both the EEG and eye-tracking -systems. +systems. .. topic:: Examples