ENH: Efficient read

Author: larsoner

doc/changes/latest.inc

@@ -20,11 +20,15 @@ Current (0.22.dev0)
 
 .. |Victoria Peterson| replace:: **Victoria Peterson**
 
+.. |Jonathan Kuziek| replace:: **Jonathan Kuziek**
+
 
 Enhancements
 ~~~~~~~~~~~~
 - Add :class:`mne.decoding.SSD` for spatial filtering with spatio-spectral-decomposition (:gh:`7070` **by new contributor** |Victoria Peterson|_ and `Denis Engemann`_)
 
+- Add reader for optical imaging data recorded using ISS Imgagent I/II hardware and BOXY recording software in :func:`mne.io.read_raw_boxy` (:gh:`7717` **by new contributor** |Jonathan Kuziek|_ and `Kyle Mathewson`_)
+
 - Add options to use labels in :func:`mne.minimum_norm.get_point_spread` and :func:`mne.minimum_norm.get_cross_talk` (:gh:`8275` by `Olaf Hauk`_)
 
 - Update ``surfaces`` argument in :func:`mne.viz.plot_alignment` to allow dict for transparency values, and set default for sEEG data to have transparency (:gh:`8445` by `Keith Doelling`_)
@@ -157,206 +161,4 @@ API changes
 
 - Add ``group_by`` parameter to `mne.viz.plot_epochs` and `mne.Epochs.plot` to allow displaying channel data by sensor position (:gh:`8381` by `Daniel McCloy`_)
 
-- Add ``proj='reconstruct'`` to :meth:`mne.Evoked.plot` and related functions to apply projectors and then undo the signal bias using field mapping by `Eric Larson`_
-
-- When picking a subset of channels, or when dropping channels from `~mne.io.Raw`, `~mne.Epochs`, or `~mne.Evoked`, projectors that can only be applied to the removed channels will now be dropped automatically by `Richard Höchenberger`_
-
-- :class:`mne.Report` now can add topomaps of SSP projectors to the generated report. This behavior can be toggled via the new ``projs`` argument by `Richard Höchenberger`_
-
-- Add function :func:`mne.channels.combine_channels` to combine channels from Raw, Epochs, or Evoked according to ROIs (combinations including mean, median, or standard deviation; can also use a callable) by `Johann Benerradi`_
-
-- Improved documentation building instructions and execution on Windows by `Eric Larson`_, `kalenkovich`_ and `Martin Schulz`_
-
-- When passing a list of `~mne.Evoked` objects to `~mne.viz.plot_compare_evokeds`, each evoked's ``.comment`` attribute will be used to label the trace. If ``.comment`` is empty, a 1-based index is assigned as the label by  `Richard Höchenberger`_
-
-- Speed up :func:`mne.stats.summarize_clusters_stc` using Numba by `Yu-Han Luo`_
-
-- Add ``reject_by_annotation=True`` to :func:`mne.make_fixed_length_epochs` and :meth:`mne.preprocessing.ICA.plot_properties` to reject bad data segments based on annotation by `Yu-Han Luo`_
-
-- Add reader for optical imaging data recorded using ISS Imgagent I/II hardware and BOXY recording software in :func:`mne.io.read_raw_boxy` by `Kyle Mathewson`_ and `Jonathan Kuziek`_
-
-- `~mne.Report.parse_folder` now accepts a path-like folder name (it used to work with strings only) by `Alex Gramfort`_
-
-Bug
-~~~
-
-- Fix bug for writing and reading complex evoked data modifying :func:`mne.write_evokeds` and :func:`mne.read_evokeds` by `Lau Møller Andersen`_
-
-- Fix bug by adding error message when trying to save complex stc data in a non.-h5 format :meth:`mne.VolSourceEstimate.save` by `Lau Møller Andersen`_
-
-- Fix bug with :func:`mne.preprocessing.ICA.find_bads_eog` when more than one EOG components are present by `Christian O'Reilly`_
-
-- Fix bug to permit :meth:`stc.project('nn', src) <mne.VectorSourceEstimate.project>` to be applied after ``stc`` was restricted to an :class:`mne.Label` by `Luke Bloy`_
-
-- Fix bug with :func:`mne.io.Raw.set_meas_date` to support setting ``meas_date`` to ``None``, by `Luke Bloy`_
-
-- Fix bug with :func:`mne.setup_volume_source_space` when ``volume_label`` was supplied where voxels slightly (in a worst case, about 37% times ``pos`` in distance) outside the voxel-grid-based bounds of regions were errantly included, by `Eric Larson`_
-
-- Fix bug with :func:`mne.io.read_raw_ctf` when reference magnetometers have the compensation grade marked by `Eric Larson`_
-
-- Fix bug with `mne.SourceSpaces.export_volume` with ``use_lut=False`` where no values were written by `Eric Larson`_
-
-- Fix bug with :func:`mne.preprocessing.annotate_movement` where bad data segments, specified in ``raw.annotations``, would be handled incorrectly by `Luke Bloy`_
-
-- Fix bug with :func:`mne.compute_source_morph` when more than one volume source space was present (e.g., when using labels) where only the first label would be interpolated when ``mri_resolution=True`` by `Eric Larson`_
-
-- Fix bug with :func:`mne.compute_source_morph` when morphing to a volume source space when ``src_to`` is used and the destination subject is not ``fsaverage`` by `Eric Larson`_
-
-- Fix bug with :func:`mne.compute_source_morph` where outermost voxels in the destination source space could be errantly omitted by `Eric Larson`_
-
-- Fix bug with :func:`mne.compute_source_morph` where complex data was cast to real when doing a volumetric morph by `Eric Larson`_
-
-- Fix bug with :func:`mne.minimum_norm.compute_source_psd_epochs` and :func:`mne.minimum_norm.source_band_induced_power` raised errors when ``method='eLORETA'`` by `Eric Larson`_
-
-- Fix bug with :func:`mne.minimum_norm.apply_inverse` where the explained variance did not work for complex data by `Eric Larson`_
-
-- Fix bug with :func:`mne.preprocessing.compute_current_source_density` where values were not properly computed; maps should now be more focal, by `Alex Rockhill`_ and `Eric Larson`_
-
-- Fix bug with :func:`mne.combine_evoked` where equal-weighted averages were wrongly computed as equal-weighted sums, by `Daniel McCloy`_
-
-- Fix bug with setting HTML classes when using :meth:`mne.Report.add_bem_to_section` by `Eric Larson`_
-
-- Fix bug with convex-hull based MEG helmet creation where the face area could be covered up, by `Eric Larson`_
-
-- Fix to enable interactive plotting with no colorbar with :func:`mne.viz.plot_evoked_topomap` by `Daniel McCloy`_
-
-- Fix plotting with :func:`mne.viz.plot_evoked_topomap` to pre-existing axes by `Daniel McCloy`_
-
-- Fix bug with :func:`mne.viz.plot_vector_source_estimates` using the PyVista backend with ``time_viewer=True`` when updating the arrow colormaps by `Eric Larson`_
-
-- The default plotting mode for :func:`mne.io.Raw.plot` and :ref:`mne browse_raw` has been changed to ``clipping=3.`` to facilitate data analysis with large deflections, by `Eric Larson`_
-
-- PSD plots will now show non-data channels (e.g., ``misc``) if those channels are explicitly passed to ``picks``, by `Daniel McCloy`_.
-
-- Fix bug with :func:`mne.time_frequency.read_tfrs` where ``info['meas_date']`` was not parsed correctly, by `Eric Larson`_
-
-- Fix bug with :func:`mne.time_frequency.tfr_array_stockwell` where inputs were not properly validated by `Eric Larson`_
-
-- Fix handling of NaN when using TFCE in clustering functions such as :func:`mne.stats.spatio_temporal_cluster_1samp_test` by `Eric Larson`_
-
-- Fix handling of signs when using TFCE by `Eric Larson`_
-
-- The :class:`mne.MixedSourceEstimate` class has been clarified to contain two cortical surface source spaces, plus at least one other source space. Creating source estimates in other orderings is not supported, by `Eric Larson`_
-
-- Fix bug where :class:`VolSourceEstimate.vertices <mne.VolSourceEstimate>` was an instance of :class:`~numpy.ndarray` instead of :class:`python:list` of one :class:`~numpy.ndarray`, by `Eric Larson`_
-
-- Fix default to be ``foreground=None`` in :func:`mne.viz.plot_source_estimates` to use white or black text based on the background color by `Eric Larson`_
-
-- Fix bug with writing EGI and CTF `mne.Info` to H5 format, e.g., with `mne.time_frequency.AverageTFR.save` by `Eric Larson`_
-
-- Fix bug with :func:`mne.io.Raw.plot` where toggling all projectors did not actually take effect by `Eric Larson`_
-
-- Fix bug with :func:`mne.read_epochs` when loading data in complex format with ``preload=False`` by `Eric Larson`_
-
-- Fix bug with :meth:`mne.Epochs.save` where the file splitting calculations did not account for the sizes of non-data writes by `Eric Larson`_
-
-- Fix bug with :class:`mne.Epochs` when metadata was not subselected properly when ``event_repeated='drop'`` by `Eric Larson`_
-
-- Fix bug with :class:`mne.Epochs` where ``epochs.drop_log`` was a list of list of str rather than an immutable tuple of tuple of str (not meant to be changed by the user) by `Eric Larson`_
-
-- Fix bug with :class:`mne.Report` where the BEM section could not be toggled by `Eric Larson`_
-
-- Fix bug when using :meth:`mne.Epochs.crop` to exclude the baseline period would break :func:`mne.Epochs.save` / :func:`mne.read_epochs` round-trip by `Eric Larson`_
-
-- Fix bug with `mne.Epochs.subtract_evoked` where using decimated epochs would lead to an error by `Eric Larson`_
-
-- Fix bug with :func:`mne.viz.plot_bem` and :class:`mne.Report` when plotting BEM contours when MRIs are not in standard FreeSurfer orientation by `Eric Larson`_
-
-- Fix bug with :func:`mne.minimum_norm.make_inverse_operator` where it would warn even when an explicit ``rank`` was used by `Eric Larson`_
-
-- Fix bugs with :func:`mne.beamformer.make_lcmv` and :func:`mne.beamformer.make_dics` where:
-
-  - Noise normalization factors ``weight_norm='unit-noise-gain'`` and ``weight_norm='nai'`` were computed incorrectly
-  - ``pick_ori='max-power'`` computed the max-power orientation incorrectly
-  - ``pick_ori='normal'`` did not compute power or noise normalization factors correctly
-  - :func:`mne.beamformer.apply_lcmv_cov` did not apply whitening and projections properly
-
-- Fix :ref:`mne setup_forward_model` to have it actually compute the BEM solution in addition to creating the BEM model by `Eric Larson`_
-
-- Fix bug with :func:`mne.io.read_raw_edf` where null bytes were not properly handled, causing an error when opening a file by `Eric Larson`_
-
-- Fix bug with :func:`mne.Report` where unicode characters were not rendered properly (encoding for HTML was not set) by `Eric Larson`_
-
-- Fix bug with :func:`mne.preprocessing.nirs.scalp_coupling_index` where filter transition was incorrectly assigned by `Robert Luke`_
-
-- Fix bug with :func:`mne.make_forward_dipole` where :func:`mne.write_forward_solution` could not be used by `Eric Larson`_
-
-- Fix bug with :meth:`mne.io.Raw.plot` when ``scalings='auto'`` where bad data would prevent channel plotting by `Eric Larson`_
-
-- Default ``border`` and ``extrapolate`` arguments for :func:`mne.Evoked.plot_topomap` and related functions were changed from ``0.`` to ``'mean'`` and ``'box'`` to ``'auto'``, respectively, to help more accurately reflect sensor geometries and boundary conditions. ``extrapolate='auto'`` uses ``extrapolate='local'`` for MEG data and ``extrapolate='head'`` otherwise, by `Eric Larson`_
-
-- Fix bug that prevents ``n_jobs`` from being a NumPy integer type, by `Daniel McCloy`_.
-
-- Fix bug with :func:`mne.epochs.average_movements` where epoch weights were computed using all basis vectors instead of the internal basis only by `Eric Larson`_
-
-- Fix bug with :func:`mne.io.read_raw_gdf` where birthdays were not parsed properly, leading to an error by `Svea Marie Meyer`_
-
-- Fix bug with :func:`mne.io.read_raw_edf` where recording ID was not read properly for non-ASCII characters by `Lx37`_
-
-- Fix bug with :func:`mne.get_volume_labels_from_aseg` where the returned labels were alphabetical instead of reflecting their volumetric ID-based order by `Eric Larson`_
-
-- Fix bug with :func:`mne.preprocessing.find_bad_channels_maxwell` where good data of exactly ``step`` duration would lead to an error by `Eric Larson`_
-
-- Fix bug with :func:`mne.preprocessing.find_bad_channels_maxwell` where indices were not handled properly when MEG channels were not first in the raw instance, and logging messages incorrectly reported the interval used by `Eric Larson`_
-
-- Make :func:`mne.set_config` accept path-like input values by `Richard Höchenberger`_
-
-- Fix bug with :func:`mne.write_labels_to_annot` and :func:`mne.datasets.fetch_hcp_mmp_parcellation` where label name strings were not properly terminated, leading to problems loading in FreeSurfer by `Eric Larson`_
-
-- Fix bug with :func:`mne.beamformer.make_dics` where complex conjugates were not applied properly by `Britta Westner`_ and `Eric Larson`_
-
-- Fix bug with :func:`mne.bem.make_watershed_bem` where the RAS coordinates of watershed bem surfaces were not updated correctly from the volume file by `Yu-Han Luo`_
-
-- Fix bug with :meth:`mne.io.Raw.get_channel_types` and related methods where the ordering of ``picks`` was not preserved, by `Eric Larson`_
-
-- Fix bug with :meth:`mne.io.Raw.plot_psd` with ``average=False`` and multiple channel types where channel locations were not shown properly by `Eric Larson`_
-
-- Fix bug in FieldTrip reader functions when channels are missing in the ``info`` object by `Thomas Hartmann`_
-
-- Throw proper error when trying to import FieldTrip Epochs data with non-uniform time for trials by `Thomas Hartmann`_
-
-- Throw proper error when trying to import FieldTrip data saved by an old, incompatible version by `Thomas Hartmann`_
-
-- Fix bug in :func:`mne.read_epochs_fieldtrip` when importing data without a ``trialinfo`` field by `Thomas Hartmann`_
-
-- Fix bug in :meth:`mne.preprocessing.ICA.plot_properties` where time series plot doesn't start at the proper tmin by `Teon Brooks`_
-
-- Fix bug with :meth:`mne.preprocessing.ICA.plot_properties` where a :class:`mne.io.Raw` object with annotations would lead to an error by `Yu-Han Luo`_
-
-API
-~~~
-
-- Python 3.5 is no longer supported, Python 3.6+ is required, by `Eric Larson`_
-
-- ``adjacency`` has replaced ``connectivity`` in the names of:
-
-  1. Arguments to clustering functions, such as `mne.stats.permutation_cluster_test`, and
-  2. Function names for defining adjacency, such as `mne.spatio_temporal_src_adjacency` replacing ``mne.spatio_temporal_src_connectivity``.
-
-  "connectivity" is now reserved for discussions of functional and effective connectivity of the brain, and "adjacency" for source or sensor neighbor definitions for cluster-based analyses, by `Eric Larson`_.
-
-- The default for the ``standardize_names`` argument of :func:`mne.io.read_raw_kit` will change from ``True`` to ``False`` in 0.22, by `Eric Larson`_
-
-- The ``normalize_fwd`` argument of :func:`mne.beamformer.make_dics` has been deprecated in favor of ``depth``, by `Eric Larson`_
-
-- Add ``n_cols`` parameter to :meth:`mne.preprocessing.ICA.plot_scores` to allow plotting scores in multiple columns, by `Luke Bloy`_
-
-- In :func:`mne.stats.permutation_cluster_test` and :func:`mne.stats.permutation_cluster_1samp_test` the default parameter value ``out_type='mask'`` has changed to ``None``, which in 0.21 means ``'mask'`` but will change to mean ``'indices'`` in the next version, by `Daniel McCloy`_
-
-- The default window size set by ``filter_length`` when ``method='spectrum_fit'`` in :meth:`mne.io.Raw.notch_filter` will change from ``None`` (use whole file) to ``'10s'`` in 0.22, by `Eric Larson`_
-
-- ``vmin`` and ``vmax`` parameters are deprecated in :meth:`mne.Epochs.plot_psd_topomap` and :func:`mne.viz.plot_epochs_psd_topomap`; use new ``vlim`` parameter instead, by `Daniel McCloy`_.
-
-- The method ``stc_mixed.plot_surface`` for a :class:`mne.MixedSourceEstimate` has been deprecated in favor of :meth:`stc.surface().plot(...) <mne.MixedSourceEstimate.surface>` by `Eric Larson`_
-
-- The method ``stc.normal`` for :class:`mne.VectorSourceEstimate` has been deprecated in favor of :meth:`stc.project('nn', src) <mne.VectorSourceEstimate.project>` by `Eric Larson`_
-
-- Add ``use_dev_head_trans`` parameter to :func:`mne.preprocessing.annotate_movement` to allow choosing the device to head transform is used to define the fixed cHPI coordinates by `Luke Bloy`_
-
-- The function ``mne.channels.read_dig_captrack`` will be deprecated in version 0.22 in favor of :func:`mne.channels.read_dig_captrak` to correct the spelling error: "captraCK" -> "captraK", by `Stefan Appelhoff`_
-
-- The ``threshold`` argument in :meth:`mne.preprocessing.ICA.find_bads_ecg` defaults to ``None`` in version 0.21 but will change to ``'auto'`` in 0.22 by `Yu-Han Luo`_
-
-- The default argument ``meg=True`` in :func:`mne.pick_types` will change to ``meg=False`` in version 0.22 by `Clemens Brunner`_
-
 - Parameter ``event_colors`` in `mne.viz.plot_epochs` and `mne.Epochs.plot` is deprecated, replaced by ``event_color`` which is consistent with `mne.viz.plot_raw` and provides greater flexibility (:gh:`8381` by `Daniel McCloy`_)