Version 1.4.0 (2023-05-10)

Enhancements

Add functionality for reading CNT spans/annotations marked bad to :func:`mne.io.read_raw_cnt` (:gh:`11631` by :newcontrib:`Jacob Woessner`)
Add :unit: Sphinx directive to enable use of uniform non-breaking spaces throughout the documentation (:gh:`11469` by :newcontrib:`Sawradip Saha`)
Adjusted the algorithm used in :class:`mne.decoding.SSD` to support non-full rank data (:gh:`11458` by :newcontrib:`Thomas Binns`)
Changed suggested type for ch_groups in mne.viz.plot_sensors from array to list of list(s) (arrays are still supported). (:gh:`11465` by `Hyonyoung Shin`_)
Add support for UCL/FIL OPM data using :func:`mne.io.read_raw_fil` (:gh:`11366` by :newcontrib:`George O'Neill` and `Robert Seymour`_)
Add harmonic field correction (HFC) for OPM sensors in :func:`mne.preprocessing.compute_proj_hfc` (:gh:`11536` by :newcontrib:`George O'Neill` and `Eric Larson`_)
Forward argument axes from mne.viz.plot_sensors to mne.channels.DigMontage.plot (:gh:`11470` by :newcontrib:`Jan Ebert` and `Mathieu Scheltienne`_)
Add forward IIR filtering, using parameters method='iir', phase='forward' (:gh:`11078` by :newcontrib:`Quentin Barthélemy`)
Added ability to read stimulus durations from SNIRF files when using :func:`mne.io.read_raw_snirf` (:gh:`11397` by `Robert Luke`_)
Add :meth:`mne.Info.save` to save an :class:`mne.Info` object to a fif file (:gh:`11401` by `Alex Rockhill`_)
Improved error message when downloads are corrupted for :func:`mne.datasets.sample.data_path` and related functions (:gh:`11407` by `Eric Larson`_)
Improved :func:`mne.get_config("") <mne.get_config>` behavior to return a dict of key-value pairs (config key and its description) rather than just a tuple of config keys (:gh:`11166` by `Clemens Brunner`_, `Daniel McCloy`_, and `Eric Larson`_)
Add support for skip_by_annotation in :func:`mne.io.Raw.notch_filter` (:gh:`11388` by `Mainak Jas`_)
Add support for output='complex' to :func:`mne.time_frequency.psd_array_welch` and when using method='welch' with :meth:`mne.Epochs.compute_psd` (:gh:`11556` by `Eric Larson`_)
Slightly adjusted the window title for :func:`mne.Epochs.plot` (:gh:`11419` by `Richard Höchenberger`_ and `Daniel McCloy`_)
Add :func:`mne.count_events` to count unique event types in a given event array (:gh:`11430` by `Clemens Brunner`_)
Add a video to :ref:`tut-freesurfer-mne` of a brain inflating from the pial surface to aid in understanding the inflated brain (:gh:`11440` by `Alex Rockhill`_)
Add automatic projection of sEEG contact onto the inflated surface for :meth:`mne.viz.Brain.add_sensors` (:gh:`11436` by `Alex Rockhill`_)
Allow an image with intracranial electrode contacts (e.g. computed tomography) to be used without the freesurfer recon-all surfaces to locate contacts so that it doesn't have to be downsampled to freesurfer dimensions (for microelectrodes) and show an example :ref:`ex-ieeg-micro` with :func:`mne.transforms.apply_volume_registration_points` added to aid this transform (:gh:`11567` by `Alex Rockhill`_)
Use new :meth:`dipy.align.imwarp.DiffeomorphicMap.transform_points` to transform a montage of intracranial contacts more efficiently (:gh:`11572` by `Alex Rockhill`_)
Improve performance of raw data browsing with many annotations (:gh:`11614` by `Eric Larson`_)
Add support for :func:`mne.preprocessing.maxwell_filter` with gradient-compensated CTF data, e.g., for tSSS-only mode (:gh:`10554` by `Eric Larson`_)
Add support for eyetracking data using :func:`mne.io.read_raw_eyelink` (:gh:`11152` by `Dominik Welke`_ and `Scott Huberty`_)
:func:`mne.channels.make_1020_channel_selections` gained a new parameter, return_ch_names, to allow for easy retrieval of EEG channel names corresponding to the left, right, and midline portions of the montage (:gh:`11632` by `Richard Höchenberger`_)
Methods for setting the sensor types of channels (e.g., for raw data, :meth:`mne.io.Raw.set_channel_types`) gained a new parameter, on_unit_change, to control behavior (raise an exception, emit a warning, or do nothing) in case the measurement unit is adjusted automatically (:gh:`11668` by `Richard Höchenberger`_)
:func:`mne.beamformer.trap_music` implements the TRAP-MUSIC localisation algorithm with the same signature as :func:`mne.beamformer.rap_music` (:gh:`11679` by `Théodore Papadopoulo`_)

Bugs

Improving compatibility with Qt6 by removing the use of deprecated AA_UseHighDpiPixmaps attribute for this Qt version (:gh:`11662` by :newcontrib:`Florin Pop`)
Fix :func:`mne.time_frequency.psd_array_multitaper` docstring where argument bandwidth incorrectly reported argument as half-bandwidth and gave wrong explanation of default value (:gh:`11479` by :newcontrib:`Tom Stone`)
Fix bug where installation of a package depending on mne will error when done in an environment where setuptools is not present (:gh:`11454` by :newcontrib:`Arne Pelzer`)
Fix bug in :meth:`mne.Annotations.rename` where replacements were not done correctly (:gh:`11666` by :newcontrib:`Timur Sokhin` and `Eric Larson`_)
Fix :meth:`mne.time_frequency.Spectrum.to_data_frame`'s docstring to reflect the correct name for the appended frequencies column (:gh:`11457` by :newcontrib:`Zvi Baratz`)
Fix bug with :func:`mne.io.read_raw_egi` where events outside the recording window could break data reading (:gh:`11505` by :newcontrib:`Niels Focke`)
Fix bug where :func:`mne.preprocessing.regress_artifact` and :class:`mne.preprocessing.EOGRegression` incorrectly tracked picks (:gh:`11366` by `Eric Larson`_)
Fix bug where channel names were not properly sanitized in :func:`mne.write_evokeds` and related functions (:gh:`11399` by `Eric Larson`_)
Fix bug where splash screen would not always disappear (:gh:`11398` by `Eric Larson`_)
Fix bug where having a different combination of volumes loaded into freeview caused different affines to be returned by :func:`mne.read_lta` for the same Linear Transform Array (LTA) (:gh:`11402` by `Alex Rockhill`_)
Fix how :class:`mne.channels.DigMontage` is set when using mne.gui.locate_ieeg so that :func:`mne.Info.get_montage` works and does not return None (:gh:`11421` by `Alex Rockhill`_)
Fix :func:`mne.io.read_raw_edf` when reading EDF data with different sampling rates and a mix of data channels when using infer_types=True (:gh:`11427` by `Alex Gramfort`_)
Fix how :class:`mne.channels.DigMontage` is set when using :func:`mne.preprocessing.ieeg.project_sensors_onto_brain` so that :func:`mne.Info.get_montage` works and does not return None (:gh:`11436` by `Alex Rockhill`_)
Fix configuration folder discovery on Windows, which would fail in certain edge cases; and produce a helpful error message if discovery still fails (:gh:`11441` by `Richard Höchenberger`_)
Make :class:`~mne.decoding.SlidingEstimator` and :class:`~mne.decoding.GeneralizingEstimator` respect the verbose argument. Now with verbose=False, the progress bar is not shown during fitting, scoring, etc. (:gh:`11450` by `Mikołaj Magnuski`_)
Fix bug with mne.gui.locate_ieeg where Freesurfer ?h.pial.T1 was not recognized and suppress excess logging (:gh:`11489` by `Alex Rockhill`_)
All functions accepting paths can now correctly handle :class:`~pathlib.Path` as input. Historically, we expected strings (instead of "proper" path objects), and only added :class:`~pathlib.Path` support in a few select places, leading to inconsistent behavior. (:gh:`11473` and :gh:`11499` by `Mathieu Scheltienne`_)
Fix visualization dialog compatibility with matplotlib 3.7 (:gh:`11409` by `Daniel McCloy`_ and `Eric Larson`_)
Expand tilde (user directory) in config keys (:gh:`11537` by `Clemens Brunner`_)
Fix bug in :func:`mne.preprocessing.compute_maxwell_basis` where using int_order=0 would raise an error (:gh:`11562` by `Eric Larson`_)
In the legacy function :func:`mne.viz.plot_epochs_psd_topomap`, the parameter names now works again (:gh:`11563` by `Daniel McCloy`_)
Fix :func:`mne.io.read_raw` for file names containing multiple dots (:gh:`11521` by `Clemens Brunner`_)
Fix bug in :func:`mne.export.export_raw` when exporting to EDF with a physical range set smaller than the data range (:gh:`11569` by `Mathieu Scheltienne`_)
Fix bug in :func:`mne.concatenate_raws` where two raws could not be merged if the order of the bad channel lists did not match (:gh:`11502` by `Moritz Gerster`_)
Fix bug where :meth:`mne.Evoked.plot_topomap` opened an extra figure (:gh:`11607` by `Alex Rockhill`_)
Fix bug where :func:`mne.transforms.apply_volume_registration_points` modified info in place (:gh:`11612` by `Alex Rockhill`_)
Fix bug where Maxwell-filtered data rank was not handled properly in :func:`mne.beamformer.make_lcmv` (:gh:`11664` by `Eric Larson`_)
In :class:`~mne.Report`, custom figures now show up correctly when image_format='svg' is requested (:gh:`11623` by `Richard Höchenberger`_)
Fix bug where providing axes in mne.preprocessing.ICA.plot_components would fail (:gh:`11654` by `Mathieu Scheltienne`_)
Fix deprecation of title, vmin and vmax in ~mne.viz.plot_tfr_topomap called from interactive mne.time_frequency.AverageTFR.plot_topo (:gh:`11683` by `Mathieu Scheltienne`_)

API changes

Deprecate mne.gui.locate_ieeg in favor of :func:`mne-gui-addons:mne_gui_addons.locate_ieeg` (:gh:`11616` by `Alex Rockhill`_)
Deprecate arguments kind and path from :func:`mne.channels.read_layout` in favor of a common argument fname (:gh:`11500` by `Mathieu Scheltienne`_)
Change aligned_ct positional argument in mne.gui.locate_ieeg to base_image to reflect that this can now be used with unaligned images (:gh:`11567` by `Alex Rockhill`_)
mne.warp_montage_volume was deprecated in favor of :func:`mne.preprocessing.ieeg.warp_montage` (acts directly on points instead of using an intermediate volume) and :func:`mne.preprocessing.ieeg.make_montage_volume` (which makes a volume of ieeg contact locations which can still be useful) (:gh:`11572` by `Alex Rockhill`_)
Deprecate mne.pick_channels_evoked in favor of evoked.copy().pick(...) (:gh:`11665` by `Eric Larson`_)
Set instance methods inst.pick_types and inst.pick_channels as legacy in favor of inst.pick(...) (:gh:`11665` by `Eric Larson`_)
The default of inst.pick_channels(..., ordered=False) will change to ordered=True in 1.5 to avoid silent bugs (:gh:`11665` by `Eric Larson`_)

Authors

Alex Rockhill
Alexandre Gramfort
Arne Pelzer+
Britta Westner
Carlos de la Torre
Clemens Brunner
Daniel Hasegan
Daniel McCloy
Denis A. Engemann
Dimitri Papadopoulos Orfanos
Dinara Issagaliyeva
Dominik Welke
Enzo Altamiranda
Eric Brayet
Eric Larson
Erkka Heinila
Felix Klotzsche
Florin Pop+
George O'Neill+
Giulio
Hakimeh Aslsardroud
Hyonyoung Shin+
Jacob Woessner+
Jan Ebert+
Jennifer Behnke
Jevri Hanna
Lukas Hecker
Mainak Jas
Mark Alexander Henney
Mathieu Scheltienne
Mauricio Cespedes
Michiru Kaneda
Mikołaj Magnuski
Moritz Gerster
Niels Focke+
Omer Shubi
Pavel Navratil
Quentin Barthélemy+
Richard Höchenberger
Rob Luke
Robert Seymour+
Santeri Ruuskanen
Sawradip Saha+
Scott Huberty
Stefan Appelhoff
Theodore Papadopoulo
Thomas Samuel Binns+
Timon Merk
Timur Sokhin+
Tom Ma
Tom Stone+
Toomas Erik Anijärv
Zvi Baratz+