From 46b02ed0557b999cf523509934f5c0dbb1d0eed2 Mon Sep 17 00:00:00 2001 From: John Griffiths Date: Fri, 21 Jun 2024 05:54:19 -0400 Subject: [PATCH] removed lots of things --- doc/changes/devel/12338.newfeature.rst | 1 - doc/changes/devel/12554.dependency.rst | 6 - doc/changes/devel/12556.newfeature.rst | 1 - doc/changes/devel/12561.bugfix.rst | 1 - doc/changes/devel/12562.bugfix.rst | 1 - doc/changes/devel/12569.other.rst | 1 - doc/changes/devel/12573.newfeature.rst | 3 - doc/changes/devel/12576.newfeature.rst | 1 - doc/changes/devel/12578.bugfix.rst | 3 - doc/changes/devel/12583.apichange.rst | 2 - doc/changes/devel/12583.newfeature.rst | 4 - doc/changes/devel/12584.newfeature.rst | 4 - doc/changes/devel/12593.bugfix.rst | 1 - doc/changes/devel/12597.bugfix.rst | 1 - doc/changes/devel/12600.other.rst | 1 - doc/changes/devel/12605.bugfix.rst | 1 - doc/changes/devel/12609.bugfix.rst | 1 - doc/changes/devel/12612.bugfix.rst | 1 - doc/changes/devel/12616.bugfix.rst | 1 - doc/changes/devel/12620.bugfix.rst | 1 - doc/changes/devel/12628.newfeature.rst | 4 - doc/changes/devel/12633.bugfix.rst | 1 - doc/changes/devel/12646.bugfix.rst | 10 - doc/changes/devel/12649.newfeature.rst | 1 - doc/changes/devel/12650.other.rst | 1 - doc/changes/devel/12652.newfeature.rst | 1 - doc/changes/devel/12655.newfeature.rst | 2 - doc/changes/devel/12659.other.rst | 1 - doc/changes/devel/12661.bugfix.rst | 1 - doc/changes/devel/12664.other.rst | 1 - doc/changes/v0.10.rst | 148 -------- doc/changes/v0.11.rst | 92 ----- doc/changes/v0.12.rst | 211 ----------- doc/changes/v0.13.rst | 248 ------------- doc/changes/v0.14.rst | 250 ------------- doc/changes/v0.15.rst | 329 ----------------- doc/changes/v0.16.rst | 258 ------------- doc/changes/v0.17.rst | 317 ---------------- doc/changes/v0.18.rst | 268 -------------- doc/changes/v0.19.rst | 232 ------------ doc/changes/v0.20.rst | 407 --------------------- doc/changes/v0.21.rst | 486 ------------------------- doc/changes/v0.22.rst | 263 ------------- doc/changes/v0.23.rst | 388 -------------------- doc/changes/v0.24.rst | 411 --------------------- doc/changes/v0.3.rst | 40 -- doc/changes/v0.4.rst | 52 --- doc/changes/v0.5.rst | 125 ------- doc/changes/v0.6.rst | 156 -------- doc/changes/v0.7.rst | 136 ------- doc/changes/v0.8.rst | 194 ---------- doc/changes/v0.9.rst | 239 ------------ doc/changes/v1.1.rst | 271 -------------- doc/changes/v1.2.rst | 116 ------ doc/changes/v1.3.rst | 89 ----- doc/changes/v1.4.rst | 133 ------- doc/changes/v1.5.rst | 107 ------ doc/changes/v1.6.rst | 132 ------- 58 files changed, 6157 deletions(-) delete mode 100644 doc/changes/devel/12338.newfeature.rst delete mode 100644 doc/changes/devel/12554.dependency.rst delete mode 100644 doc/changes/devel/12556.newfeature.rst delete mode 100644 doc/changes/devel/12561.bugfix.rst delete mode 100644 doc/changes/devel/12562.bugfix.rst delete mode 100644 doc/changes/devel/12569.other.rst delete mode 100644 doc/changes/devel/12573.newfeature.rst delete mode 100644 doc/changes/devel/12576.newfeature.rst delete mode 100644 doc/changes/devel/12578.bugfix.rst delete mode 100644 doc/changes/devel/12583.apichange.rst delete mode 100644 doc/changes/devel/12583.newfeature.rst delete mode 100644 doc/changes/devel/12584.newfeature.rst delete mode 100644 doc/changes/devel/12593.bugfix.rst delete mode 100644 doc/changes/devel/12597.bugfix.rst delete mode 100644 doc/changes/devel/12600.other.rst delete mode 100644 doc/changes/devel/12605.bugfix.rst delete mode 100644 doc/changes/devel/12609.bugfix.rst delete mode 100644 doc/changes/devel/12612.bugfix.rst delete mode 100644 doc/changes/devel/12616.bugfix.rst delete mode 100644 doc/changes/devel/12620.bugfix.rst delete mode 100644 doc/changes/devel/12628.newfeature.rst delete mode 100644 doc/changes/devel/12633.bugfix.rst delete mode 100644 doc/changes/devel/12646.bugfix.rst delete mode 100644 doc/changes/devel/12649.newfeature.rst delete mode 100644 doc/changes/devel/12650.other.rst delete mode 100644 doc/changes/devel/12652.newfeature.rst delete mode 100644 doc/changes/devel/12655.newfeature.rst delete mode 100644 doc/changes/devel/12659.other.rst delete mode 100644 doc/changes/devel/12661.bugfix.rst delete mode 100644 doc/changes/devel/12664.other.rst delete mode 100644 doc/changes/v0.10.rst delete mode 100644 doc/changes/v0.11.rst delete mode 100644 doc/changes/v0.12.rst delete mode 100644 doc/changes/v0.13.rst delete mode 100644 doc/changes/v0.14.rst delete mode 100644 doc/changes/v0.15.rst delete mode 100644 doc/changes/v0.16.rst delete mode 100644 doc/changes/v0.17.rst delete mode 100644 doc/changes/v0.18.rst delete mode 100644 doc/changes/v0.19.rst delete mode 100644 doc/changes/v0.20.rst delete mode 100644 doc/changes/v0.21.rst delete mode 100644 doc/changes/v0.22.rst delete mode 100644 doc/changes/v0.23.rst delete mode 100644 doc/changes/v0.24.rst delete mode 100644 doc/changes/v0.3.rst delete mode 100644 doc/changes/v0.4.rst delete mode 100644 doc/changes/v0.5.rst delete mode 100644 doc/changes/v0.6.rst delete mode 100644 doc/changes/v0.7.rst delete mode 100644 doc/changes/v0.8.rst delete mode 100644 doc/changes/v0.9.rst delete mode 100644 doc/changes/v1.1.rst delete mode 100644 doc/changes/v1.2.rst delete mode 100644 doc/changes/v1.3.rst delete mode 100644 doc/changes/v1.4.rst delete mode 100644 doc/changes/v1.5.rst delete mode 100644 doc/changes/v1.6.rst diff --git a/doc/changes/devel/12338.newfeature.rst b/doc/changes/devel/12338.newfeature.rst deleted file mode 100644 index 899884d8b61..00000000000 --- a/doc/changes/devel/12338.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Adding :meth:`mne.channels.Layout.copy` and :meth:`mne.channels.Layout.pick` to copy and select channels from a :class:`mne.channels.Layout` object. Plotting 2D topographies of evoked responses with :func:`mne.viz.plot_evoked_topo` with both arguments ``layout`` and ``exclude`` now ignores excluded channels from the :class:`mne.channels.Layout`. By `Mathieu Scheltienne`_. diff --git a/doc/changes/devel/12554.dependency.rst b/doc/changes/devel/12554.dependency.rst deleted file mode 100644 index 5c77efd325f..00000000000 --- a/doc/changes/devel/12554.dependency.rst +++ /dev/null @@ -1,6 +0,0 @@ -Minimum versions for dependencies were bumped to those ~2 years old at the time of release (by `Eric Larson`_), including: - -- NumPy ≥ 1.23 -- SciPy ≥ 1.9 -- Matplotlib ≥ 3.6 -- scikit-learn ≥ 1.1 \ No newline at end of file diff --git a/doc/changes/devel/12556.newfeature.rst b/doc/changes/devel/12556.newfeature.rst deleted file mode 100644 index cbd86d984e7..00000000000 --- a/doc/changes/devel/12556.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -In :class:`~mne.Report` you can now easily navigate through images and figures connected to a slider with the left and right arrow keys. Clicking on the slider or respective image will focus the slider, enabling keyboard navigation, by `Richard Höchenberger`_ diff --git a/doc/changes/devel/12561.bugfix.rst b/doc/changes/devel/12561.bugfix.rst deleted file mode 100644 index e647b2770e1..00000000000 --- a/doc/changes/devel/12561.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix scrolling behavior in :class:`~mne.Report` when clicking on a TOC entry multiple times, by `Richard Höchenberger`_. diff --git a/doc/changes/devel/12562.bugfix.rst b/doc/changes/devel/12562.bugfix.rst deleted file mode 100644 index 8b58e1bc109..00000000000 --- a/doc/changes/devel/12562.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug where :func:`mne.decoding.get_coef` did not work properly with :class:`mne.decoding.CSP`, by `Eric Larson`_. diff --git a/doc/changes/devel/12569.other.rst b/doc/changes/devel/12569.other.rst deleted file mode 100644 index acbd7d79663..00000000000 --- a/doc/changes/devel/12569.other.rst +++ /dev/null @@ -1 +0,0 @@ -Added `vulture `__ as a pre-commit hook and removed related dead code, by `Eric Larson`_. diff --git a/doc/changes/devel/12573.newfeature.rst b/doc/changes/devel/12573.newfeature.rst deleted file mode 100644 index 147db983edc..00000000000 --- a/doc/changes/devel/12573.newfeature.rst +++ /dev/null @@ -1,3 +0,0 @@ -When plotting EOG and ECG artifact scores for ICA in :meth:`mne.Report.add_ica`, -the channel names used for artifact detection are now displayed in the titles of -each respective subplot, by `Richard Höchenberger`_. \ No newline at end of file diff --git a/doc/changes/devel/12576.newfeature.rst b/doc/changes/devel/12576.newfeature.rst deleted file mode 100644 index 06ea4bb85b0..00000000000 --- a/doc/changes/devel/12576.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Use ``aseg='auto'`` for :meth:`mne.viz.Brain.add_volume_labels` and :func:`mne.get_montage_volume_labels` to use ``aparc+aseg`` by default or if not present use ``wmparc`` because freesurfer uses ``wmparc`` in the latest version, by `Alex Rockhill`_. diff --git a/doc/changes/devel/12578.bugfix.rst b/doc/changes/devel/12578.bugfix.rst deleted file mode 100644 index e22dffdd020..00000000000 --- a/doc/changes/devel/12578.bugfix.rst +++ /dev/null @@ -1,3 +0,0 @@ -The color scaling of Evoked topomaps added to reports via :meth:`mne.Report.add_evokeds` -was sometimes sub-optimal if bad channels were present in the data. This has now been fixed -and should be more consistent with the topomaps shown in the joint plots, by `Richard Höchenberger`_. diff --git a/doc/changes/devel/12583.apichange.rst b/doc/changes/devel/12583.apichange.rst deleted file mode 100644 index 92d64f5caf3..00000000000 --- a/doc/changes/devel/12583.apichange.rst +++ /dev/null @@ -1,2 +0,0 @@ -``mne.Info.ch_names`` will now return an empty list instead of raising a ``KeyError`` if no channels -are present, by `Richard Höchenberger`_. \ No newline at end of file diff --git a/doc/changes/devel/12583.newfeature.rst b/doc/changes/devel/12583.newfeature.rst deleted file mode 100644 index 27a0258f8ab..00000000000 --- a/doc/changes/devel/12583.newfeature.rst +++ /dev/null @@ -1,4 +0,0 @@ -The HTML representations of :class:`~mne.io.Raw`, :class:`~mne.Epochs`, -and :class:`~mne.Evoked` (which you will see e.g. when working with Jupyter Notebooks or -:class:`~mne.Report`) have been updated to be more consistent and contain -slightly more information, by `Richard Höchenberger`_. (:gh:`12624`) diff --git a/doc/changes/devel/12584.newfeature.rst b/doc/changes/devel/12584.newfeature.rst deleted file mode 100644 index 88f286afbbe..00000000000 --- a/doc/changes/devel/12584.newfeature.rst +++ /dev/null @@ -1,4 +0,0 @@ -When adding :class:`~mne.Evoked` data to a :class:`~mne.Report` via -:meth:`~mne.Report.add_evokeds`, we now also include an "Info" section -with some basic summary info, as has already been the case for raw and -epochs data, by `Richard Höchenberger`_. \ No newline at end of file diff --git a/doc/changes/devel/12593.bugfix.rst b/doc/changes/devel/12593.bugfix.rst deleted file mode 100644 index e43d6110716..00000000000 --- a/doc/changes/devel/12593.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix error causing :meth:`mne.Epochs.interpolate_bads` not to work for ``seeg`` channels and fix a single contact on neighboring shafts sometimes being included in interpolation, by `Alex Rockhill`_ \ No newline at end of file diff --git a/doc/changes/devel/12597.bugfix.rst b/doc/changes/devel/12597.bugfix.rst deleted file mode 100644 index 77997893f0f..00000000000 --- a/doc/changes/devel/12597.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug where :func:`mne.io.read_raw_fil` could not assign bad channels on import, by `George O'Neill`_. \ No newline at end of file diff --git a/doc/changes/devel/12600.other.rst b/doc/changes/devel/12600.other.rst deleted file mode 100644 index e31e0fa7030..00000000000 --- a/doc/changes/devel/12600.other.rst +++ /dev/null @@ -1 +0,0 @@ -Fixed issue template links by :newcontrib:`Michal Žák` diff --git a/doc/changes/devel/12605.bugfix.rst b/doc/changes/devel/12605.bugfix.rst deleted file mode 100644 index 0251eed410e..00000000000 --- a/doc/changes/devel/12605.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fixed a bug where :meth:`mne.Evoked.animate_topomap` did not work with :func:`mne.preprocessing.compute_current_source_density` - modified data, by `Michal Žák`_. diff --git a/doc/changes/devel/12609.bugfix.rst b/doc/changes/devel/12609.bugfix.rst deleted file mode 100644 index 1cd7e50d664..00000000000 --- a/doc/changes/devel/12609.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug where :func:`mne.stats.permutation_cluster_test` (and related functions) uses excessive amount of memory for large 2D data when TFCE method is selected, by :newcontrib:`Nicolas Fourcaud-Trocmé`. \ No newline at end of file diff --git a/doc/changes/devel/12612.bugfix.rst b/doc/changes/devel/12612.bugfix.rst deleted file mode 100644 index 5868fb93a2a..00000000000 --- a/doc/changes/devel/12612.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix overflow when plotting source estimates where data is all zero (or close to zero), and fix the range of allowed values for the colorbar sliders, by `Marijn van Vliet`_. diff --git a/doc/changes/devel/12616.bugfix.rst b/doc/changes/devel/12616.bugfix.rst deleted file mode 100644 index b7c5fc7fced..00000000000 --- a/doc/changes/devel/12616.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix adding channels to :class:`~mne.time_frequency.EpochsTFR` objects, by `Clemens Brunner`_. \ No newline at end of file diff --git a/doc/changes/devel/12620.bugfix.rst b/doc/changes/devel/12620.bugfix.rst deleted file mode 100644 index 0e8d53f02b1..00000000000 --- a/doc/changes/devel/12620.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix for new sklearn metadata routing protocol in decoding search_light, by `Alex Gramfort`_ diff --git a/doc/changes/devel/12628.newfeature.rst b/doc/changes/devel/12628.newfeature.rst deleted file mode 100644 index 82bab838318..00000000000 --- a/doc/changes/devel/12628.newfeature.rst +++ /dev/null @@ -1,4 +0,0 @@ -We added new installation variants for a full installation with the PySide6 Qt binding -(``"mne[full-pyside6]"``), with the PyQt6 binding (``"mne[full-pyqt6]"``, equivalent to -``"mne[full]"``), and without any Qt binding (``"mne[full-no-qt]"``), which may be useful -in certain situations by `Richard Höchenberger`_. diff --git a/doc/changes/devel/12633.bugfix.rst b/doc/changes/devel/12633.bugfix.rst deleted file mode 100644 index dfc69bc2fe7..00000000000 --- a/doc/changes/devel/12633.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix bug where :func:`mne.time_frequency.csd_multitaper`, :func:`mne.time_frequency.csd_fourier`, :func:`mne.time_frequency.csd_array_multitaper`, and :func:`mne.time_frequency.csd_array_fourier` would return cross-spectral densities with the ``fmin`` and ``fmax`` frequencies missing, by `Thomas Binns`_ \ No newline at end of file diff --git a/doc/changes/devel/12646.bugfix.rst b/doc/changes/devel/12646.bugfix.rst deleted file mode 100644 index a02ec58f77c..00000000000 --- a/doc/changes/devel/12646.bugfix.rst +++ /dev/null @@ -1,10 +0,0 @@ -Output types of sparse arrays were changed from ``matrix`` to ``array`` in -:func:`~mne.channels.read_ch_adjacency`, :func:`~mne.channels.find_ch_adjacency`, -:func:`~mne.stats.combine_adjacency`, :func:`~mne.spatio_temporal_src_adjacency`, -and related functions to comply with the pending deprecation of ``np.matrix``. -The returned objects now behave like standard :class:`~numpy.ndarray` objects, and -in particular ``*`` now operates element-wise instead of performing matrix -multiplication. You can use ``@`` as a backward compatible matrix multiplication -for both ``np.matrix`` and ``np.ndarray`` objects, and if a matrix is desired -the outputs can be cast directly, for example as ``scipy.sparse.csr_matrix(out)``. -Changed by `Eric Larson`_. diff --git a/doc/changes/devel/12649.newfeature.rst b/doc/changes/devel/12649.newfeature.rst deleted file mode 100644 index 33908f8dc89..00000000000 --- a/doc/changes/devel/12649.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Adding argument ``'random'`` to :func:`~mne.epochs.equalize_epoch_counts` and to :meth:`~mne.Epochs.equalize_event_counts` to randomly select epochs or events. By `Mathieu Scheltienne`_. diff --git a/doc/changes/devel/12650.other.rst b/doc/changes/devel/12650.other.rst deleted file mode 100644 index b97a204dff4..00000000000 --- a/doc/changes/devel/12650.other.rst +++ /dev/null @@ -1 +0,0 @@ -Enhance documentation on decimation filtering to prevent aliasing, by :newcontrib:`Xabier de Zuazo`. diff --git a/doc/changes/devel/12652.newfeature.rst b/doc/changes/devel/12652.newfeature.rst deleted file mode 100644 index 6273aa7b87f..00000000000 --- a/doc/changes/devel/12652.newfeature.rst +++ /dev/null @@ -1 +0,0 @@ -Add new parameter ``ignore_marker_types`` to :func:`~mne.io.read_raw_brainvision` to ignore marker types (and only use marker descriptions) when reading BrainVision files, by `Clemens Brunner`_. \ No newline at end of file diff --git a/doc/changes/devel/12655.newfeature.rst b/doc/changes/devel/12655.newfeature.rst deleted file mode 100644 index b2711d2f2ed..00000000000 --- a/doc/changes/devel/12655.newfeature.rst +++ /dev/null @@ -1,2 +0,0 @@ -Added support for passing ``axes`` to :func:`mne.viz.plot_head_positions` when -``mode='field'``, by `Eric Larson`_. diff --git a/doc/changes/devel/12659.other.rst b/doc/changes/devel/12659.other.rst deleted file mode 100644 index f538d3adc1e..00000000000 --- a/doc/changes/devel/12659.other.rst +++ /dev/null @@ -1 +0,0 @@ -Add link to BEst-Python in the list of related software. by `Ilian Azz`_. \ No newline at end of file diff --git a/doc/changes/devel/12661.bugfix.rst b/doc/changes/devel/12661.bugfix.rst deleted file mode 100644 index 5dae12d05ec..00000000000 --- a/doc/changes/devel/12661.bugfix.rst +++ /dev/null @@ -1 +0,0 @@ -Fix incorrect RuntimeWarning (different channel filter settings) in EDF/BDF import, by `Clemens Brunner`_. \ No newline at end of file diff --git a/doc/changes/devel/12664.other.rst b/doc/changes/devel/12664.other.rst deleted file mode 100644 index 1647e12cda0..00000000000 --- a/doc/changes/devel/12664.other.rst +++ /dev/null @@ -1 +0,0 @@ -Improved clarity of parameter documentation for `mne.decoding.SSD.fit`, by `Thomas Binns`_. \ No newline at end of file diff --git a/doc/changes/v0.10.rst b/doc/changes/v0.10.rst deleted file mode 100644 index ac4f2e42857..00000000000 --- a/doc/changes/v0.10.rst +++ /dev/null @@ -1,148 +0,0 @@ -.. _changes_0_10: - -Version 0.10 (2015-10-26) -------------------------- - -Changelog -~~~~~~~~~ - -- Add support for generalized M-way repeated measures ANOVA for fully balanced designs with :func:`mne.stats.f_mway_rm` by `Denis Engemann`_ - -- Add epochs browser to interactively view and manipulate epochs with :func:`mne.viz.plot_epochs` by `Jaakko Leppakangas`_ - -- Speed up TF-MxNE inverse solver with block coordinate descent by `Daniel Strohmeier`_ and `Yousra Bekhti`_ - -- Speed up zero-phase overlap-add (default) filtering by a factor of up to 2 using linearity by `Ross Maddox`_ and `Eric Larson`_ - -- Add support for scaling and adjusting the number of channels/time per view by `Jaakko Leppakangas`_ - -- Add support to toggle the show/hide state of all sections with a single keypress ('t') in :class:`mne.Report` by `Mainak Jas`_ - -- Add support for BEM model creation :func:`mne.make_bem_model` by `Eric Larson`_ - -- Add support for BEM solution computation :func:`mne.make_bem_solution` by `Eric Larson`_ - -- Add ICA plotters for raw and epoch components by `Jaakko Leppakangas`_ - -- Add new object ``mne.decoding.TimeDecoding`` for decoding sensors' evoked response across time by `Jean-Remi King`_ - -- Add command ``mne freeview_bem_surfaces`` to quickly check BEM surfaces with Freeview by `Alex Gramfort`_. - -- Add support for splitting epochs into multiple files in :func:`mne.Epochs.save` by `Mainak Jas`_ and `Alex Gramfort`_ - -- Add support for jointly resampling a raw object and event matrix to avoid issues with resampling status channels by `Marijn van Vliet`_ - -- Add new method :class:`mne.preprocessing.Xdawn` for denoising and decoding of ERP/ERF by `Alexandre Barachant`_ - -- Add support for plotting patterns/filters in :class:`mne.decoding.CSP` and :class:`mne.decoding.LinearModel` by `Romain Trachel`_ - -- Add new object :class:`mne.decoding.LinearModel` for decoding M/EEG data and interpreting coefficients of linear models with patterns attribute by `Romain Trachel`_ and `Alex Gramfort`_ - -- Add support to append new channels to an object from a list of other objects by `Chris Holdgraf`_ - -- Add interactive plotting of topomap from time-frequency representation by `Jaakko Leppakangas`_ - -- Add ``plot_topo`` method to ``Evoked`` object by `Jaakko Leppakangas`_ - -- Add fetcher :mod:`mne.datasets.brainstorm ` for datasets used by Brainstorm in their tutorials by `Mainak Jas`_ - -- Add interactive plotting of single trials by right clicking on channel name in epochs browser by `Jaakko Leppakangas`_ - -- New logos and logo generation script by `Daniel McCloy`_ - -- Add ability to plot topomap with a "skirt" (channels outside of the head circle) by `Marijn van Vliet`_ - -- Add multiple options to ICA infomax and extended infomax algorithms (number of subgaussian components, computation of bias, iteration status printing), enabling equivalent computations to those performed by EEGLAB by `Jair Montoya Martinez`_ - -- Add :func:`mne.Epochs.apply_baseline` method to ``Epochs`` objects by `Teon Brooks`_ - -- Add ``preload`` argument to :func:`mne.read_epochs` to enable on-demand reads from disk by `Eric Larson`_ - -- Big rewrite of simulation module by `Yousra Bekhti`_, `Mark Wronkiewicz`_, `Eric Larson`_ and `Alex Gramfort`_. Allows to simulate raw with artifacts (ECG, EOG) and evoked data, exploiting the forward solution. See :func:`mne.simulation.simulate_raw`, :func:`mne.simulation.simulate_evoked` and :func:`mne.simulation.simulate_sparse_stc` - -- Add :func:`mne.Epochs.load_data` method to :class:`mne.Epochs` by `Teon Brooks`_ - -- Add support for drawing topomaps by selecting an area in :func:`mne.Evoked.plot` by `Jaakko Leppakangas`_ - -- Add support for finding peaks in evoked data in :func:`mne.Evoked.plot_topomap` by `Jona Sassenhagen`_ and `Jaakko Leppakangas`_ - -- Add source space morphing in :func:`morph_source_spaces` and :func:`SourceEstimate.to_original_src` by `Eric Larson`_ and `Denis Engemann`_ - -- Adapt ``corrmap`` function (Viola et al. 2009) to semi-automatically detect similar ICs across data sets by `Jona Sassenhagen`_ and `Denis Engemann`_ and `Eric Larson`_ - -- Clarify docstring for :class:`mne.preprocessing.ICA` by `jeythekey`_ - -- New ``mne flash_bem`` command to compute BEM surfaces from Flash MRI images by `Lorenzo Desantis`_, `Alex Gramfort`_ and `Eric Larson`_. See :func:`mne.bem.make_flash_bem`. - -- New gfp parameter in :func:`mne.Evoked.plot` method to display Global Field Power (GFP) by `Eric Larson`_. - -- Add ``mne.Report.add_slider_to_section`` methods to :class:`mne.Report` by `Teon Brooks`_ - -BUG -~~~ - -- Fix ``mne.io.add_reference_channels`` not setting ``info[nchan]`` correctly by `Federico Raimondo`_ - -- Fix ``mne.stats.bonferroni_correction`` reject mask output to use corrected p-values by `Denis Engemann`_ - -- Fix FFT filter artifacts when using short windows in overlap-add by `Eric Larson`_ - -- Fix picking channels from forward operator could return a channel ordering different from ``info['chs']`` by `Chris Bailey`_ - -- Fix dropping of events after downsampling stim channels by `Marijn van Vliet`_ - -- 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`_ - -API -~~~ - -- Rename and deprecate ``mne.viz.plot_topo`` for ``mne.viz.plot_evoked_topo`` by `Jaakko Leppakangas`_ - -- Deprecated ``mne.decoding.transformer.ConcatenateChannels`` and replaced by ``mne.decoding.EpochsVectorizer`` by `Romain Trachel`_ - -- Deprecated ``lws`` and renamed ``ledoit_wolf`` for the ``reg`` argument in :class:`mne.decoding.CSP` by `Romain Trachel`_ - -- Redesigned and rewrote :meth:`mne.Epochs.plot` (no backwards compatibility) during the GSOC 2015 by `Jaakko Leppakangas`_, `Mainak Jas`_, `Federico Raimondo`_ and `Denis Engemann`_ - -- Deprecated and renamed ``mne.viz.plot_image_epochs`` for ``mne.plot.plot_epochs_image`` by `Teon Brooks`_ - -- ``picks`` argument has been added to :func:`mne.time_frequency.tfr_morlet`, :func:`mne.time_frequency.tfr_multitaper` by `Teon Brooks`_ - -- ``mne.io.Raw.preload_data`` has been deprecated for :func:`mne.io.Raw.load_data` by `Teon Brooks`_ - -- ``RawBrainVision`` objects now always have event channel ``'STI 014'``, and recordings with no events will have this channel set to zero by `Eric Larson`_ - -Authors -~~~~~~~ - -The committer list for this release is the following (preceded by number of commits): - -* 273 Eric Larson -* 270 Jaakko Leppakangas -* 194 Alexandre Gramfort -* 128 Denis A. Engemann -* 114 Jona Sassenhagen -* 107 Mark Wronkiewicz -* 97 Teon Brooks -* 81 Lorenzo De Santis -* 55 Yousra Bekhti -* 54 Jean-Remi King -* 48 Romain Trachel -* 45 Mainak Jas -* 40 Alexandre Barachant -* 32 Marijn van Vliet -* 26 Jair Montoya -* 22 Chris Holdgraf -* 16 Christopher J. Bailey -* 7 Christian Brodbeck -* 5 Natalie Klein -* 5 Fede Raimondo -* 5 Alan Leggitt -* 5 Roan LaPlante -* 5 Ross Maddox -* 4 Dan G. Wakeman -* 3 Daniel McCloy -* 3 Daniel Strohmeier -* 1 Jussi Nurminen diff --git a/doc/changes/v0.11.rst b/doc/changes/v0.11.rst deleted file mode 100644 index e3f9a67e3c4..00000000000 --- a/doc/changes/v0.11.rst +++ /dev/null @@ -1,92 +0,0 @@ -.. _changes_0_11: - -Version 0.11 (2015-12-24) -------------------------- - -Changelog -~~~~~~~~~ - -- Maxwell filtering (SSS) implemented in :func:`mne.preprocessing.maxwell_filter` by `Mark Wronkiewicz`_ as part of Google Summer of Code, with help from `Samu Taulu`_, `Jukka Nenonen`_, and `Jussi Nurminen`_. Our implementation includes support for: - - - Fine calibration - - - Cross-talk correction - - - Temporal SSS (tSSS) - - - Head position translation - - - Internal component regularization - -- Compensation for movements using Maxwell filtering on epoched data in :func:`mne.epochs.average_movements` by `Eric Larson`_ and `Samu Taulu`_ - -- Add reader for Nicolet files in :func:`mne.io.read_raw_nicolet` by `Jaakko Leppakangas`_ - -- Add FIFF persistence for ICA labels by `Denis Engemann`_ - -- Display ICA labels in :func:`mne.viz.plot_ica_scores` and :func:`mne.viz.plot_ica_sources` (for evoked objects) by `Denis Engemann`_ - -- Plot spatially color coded lines in :func:`mne.Evoked.plot` by `Jona Sassenhagen`_ and `Jaakko Leppakangas`_ - -- Add reader for CTF data in :func:`mne.io.read_raw_ctf` by `Eric Larson`_ - -- Add support for Brainvision v2 in :func:`mne.io.read_raw_brainvision` by `Teon Brooks`_ - -- Improve speed of generalization across time ``mne.decoding.GeneralizationAcrossTime`` decoding up to a factor of seven by `Jean-Remi King`_ and `Federico Raimondo`_ and `Denis Engemann`_. - -- Add the explained variance for each principal component, ``explained_var``, key to the :class:`mne.Projection` by `Teon Brooks`_ - -- Added methods ``mne.Epochs.add_eeg_average_proj``, ``mne.io.Raw.add_eeg_average_proj``, and ``mne.Evoked.add_eeg_average_proj`` to add an average EEG reference. - -- Add reader for EEGLAB data in :func:`mne.io.read_raw_eeglab` and :func:`mne.read_epochs_eeglab` by `Mainak Jas`_ - -BUG -~~~ - -- Fix bug that prevented homogeneous bem surfaces to be displayed in HTML reports by `Denis Engemann`_ - -- Added safeguards against ``None`` and negative values in reject and flat parameters in :class:`mne.Epochs` by `Eric Larson`_ - -- Fix train and test time window-length in ``mne.decoding.GeneralizationAcrossTime`` by `Jean-Remi King`_ - -- Added lower bound in :func:`mne.stats.linear_regression` on p-values ``p_val`` (and resulting ``mlog10_p_val``) using double floating point arithmetic limits by `Eric Larson`_ - -- Fix channel name pick in :func:`mne.Evoked.get_peak` method by `Alex Gramfort`_ - -- Fix drop percentages to take into account ``ignore`` option in :func:`mne.viz.plot_drop_log` and :func:`mne.Epochs.plot_drop_log` by `Eric Larson`_. - -- :class:`mne.EpochsArray` no longer has an average EEG reference silently added (but not applied to the data) by default. Use ``mne.EpochsArray.add_eeg_ref`` to properly add one. - -- Fix :func:`mne.io.read_raw_ctf` to read ``n_samp_tot`` instead of ``n_samp`` by `Jaakko Leppakangas`_ - -API -~~~ - -- :func:`mne.io.read_raw_brainvision` now has ``event_id`` argument to assign non-standard trigger events to a trigger value by `Teon Brooks`_ - -- :func:`mne.read_epochs` now has ``add_eeg_ref=False`` by default, since average EEG reference can be added before writing or after reading using the method ``mne.Epochs.add_eeg_ref``. - -- :class:`mne.EpochsArray` no longer has an average EEG reference silently added (but not applied to the data) by default. Use ``mne.EpochsArray.add_eeg_average_proj`` to properly add one. - -Authors -~~~~~~~ - -The committer list for this release is the following (preceded by number of commits): - -* 171 Eric Larson -* 117 Jaakko Leppakangas -* 58 Jona Sassenhagen -* 52 Mainak Jas -* 46 Alexandre Gramfort -* 33 Denis A. Engemann -* 28 Teon Brooks -* 24 Clemens Brunner -* 23 Christian Brodbeck -* 15 Mark Wronkiewicz -* 10 Jean-Remi King -* 5 Marijn van Vliet -* 3 Fede Raimondo -* 2 Alexander Rudiuk -* 2 emilyps14 -* 2 lennyvarghese -* 1 Marian Dovgialo diff --git a/doc/changes/v0.12.rst b/doc/changes/v0.12.rst deleted file mode 100644 index b3b7aba1a39..00000000000 --- a/doc/changes/v0.12.rst +++ /dev/null @@ -1,211 +0,0 @@ -.. _changes_0_12: - -Version 0.12 (2016-05-10) -------------------------- - -Changelog -~~~~~~~~~ - -- Add ``overlay_times`` parameter to :func:`mne.viz.plot_epochs_image` to be able to display for example reaction times on top of the images, by `Alex Gramfort`_ - -- Animation for evoked topomap in :func:`mne.Evoked.animate_topomap` by `Jaakko Leppakangas`_ - -- Make :func:`mne.channels.find_layout` more robust for KIT systems in the presence of bad or missing channels by `Jaakko Leppakangas`_ - -- Add raw movement compensation to :func:`mne.preprocessing.maxwell_filter` by `Eric Larson`_ - -- Add :class:`mne.Annotations` for for annotating segments of raw data by `Jaakko Leppakangas`_ - -- Add reading of .fif file montages by `Eric Larson`_ - -- Add system config utility :func:`mne.sys_info` by `Eric Larson`_ - -- Automatic cross-validation and scoring metrics in ``mne.decoding.GeneralizationAcrossTime``, by `Jean-Remi King`_ - -- ``mne.decoding.GeneralizationAcrossTime`` accepts non-deterministic cross-validations, by `Jean-Remi King`_ - -- Add plotting RMS of gradiometer pairs in :func:`mne.viz.plot_evoked_topo` by `Jaakko Leppakangas`_ - -- Add regularization methods to :func:`mne.compute_raw_covariance` by `Eric Larson`_. - -- Add command ``mne show_info`` to quickly show the measurement info from a .fif file from the terminal by `Alex Gramfort`_. - -- Add creating forward operator for dipole object :func:`mne.make_forward_dipole` by `Chris Bailey`_ - -- Add reading and estimation of fixed-position dipole time courses (similar to Elekta ``xfit``) using :func:`mne.read_dipole` and :func:`mne.fit_dipole` by `Eric Larson`_. - -- Accept ``mne.decoding.GeneralizationAcrossTime``'s ``scorer`` parameter to be a string that refers to a scikit-learn_ metric scorer by `Asish Panda`_. - -- Add method :func:`mne.Epochs.plot_image` calling :func:`mne.viz.plot_epochs_image` for better usability by `Asish Panda`_. - -- Add :func:`mne.io.read_raw_cnt` for reading Neuroscan CNT files by `Jaakko Leppakangas`_ - -- Add ``decim`` parameter to ``mne.time_frequency.cwt_morlet``, by `Jean-Remi King`_ - -- Add method :func:`mne.Epochs.plot_topo_image` by `Jaakko Leppakangas`_ - -- Add the ability to read events when importing raw EEGLAB files, by `Jona Sassenhagen`_. - -- Add function :func:`mne.viz.plot_sensors` and methods :func:`mne.Epochs.plot_sensors`, :func:`mne.io.Raw.plot_sensors` and :func:`mne.Evoked.plot_sensors` for plotting sensor positions and :func:`mne.viz.plot_layout` and :func:`mne.channels.Layout.plot` for plotting layouts by `Jaakko Leppakangas`_ - -- Add epoch rejection based on annotated segments by `Jaakko Leppakangas`_ - -- Add option to use new-style MEG channel names in ``mne.read_selection`` by `Eric Larson`_ - -- Add option for ``proj`` in :class:`mne.EpochsArray` by `Eric Larson`_ - -- Enable the usage of :func:`mne.viz.plot_topomap` with an :class:`mne.Info` instance for location information, by `Jona Sassenhagen`_. - -- Add support for electrocorticography (ECoG) channel type by `Eric Larson`_ - -- Add option for ``first_samp`` in :func:`mne.make_fixed_length_events` by `Jon Houck`_ - -- Add ability to auto-scale channel types for :func:`mne.viz.plot_raw` and :func:`mne.viz.plot_epochs` and corresponding object plotting methods by `Chris Holdgraf`_ - -BUG -~~~ - -- ``mne.time_frequency.compute_raw_psd``, ``mne.time_frequency.compute_epochs_psd``, ``mne.time_frequency.psd_multitaper``, and ``mne.time_frequency.psd_welch`` no longer remove rows/columns of the SSP matrix before applying SSP projectors when picks are provided by `Chris Holdgraf`_. - -- :func:`mne.Epochs.plot_psd` no longer calls a Welch PSD, and instead uses a Multitaper method which is more appropriate for epochs. Flags for this function are passed to ``mne.time_frequency.psd_multitaper`` by `Chris Holdgraf`_ - -- Time-cropping functions (e.g., :func:`mne.Epochs.crop`, :func:`mne.Evoked.crop`, :func:`mne.io.Raw.crop`, :func:`mne.SourceEstimate.crop`) made consistent with behavior of ``tmin`` and ``tmax`` of :class:`mne.Epochs`, where nearest sample is kept. For example, for MGH data acquired with ``sfreq=600.614990234``, constructing ``Epochs(..., tmin=-1, tmax=1)`` has bounds ``+/-1.00064103``, and now ``epochs.crop(-1, 1)`` will also have these bounds (previously they would have been ``+/-0.99897607``). Time cropping functions also no longer use relative tolerances when determining the boundaries. These changes have minor effects on functions that use cropping under the hood, such as :func:`mne.compute_covariance` and ``mne.connectivity.spectral_connectivity``. Changes by `Jaakko Leppakangas`_ and `Eric Larson`_ - -- Fix EEG spherical spline interpolation code to account for average reference by `Mainak Jas`_ - -- MEG projectors are removed after Maxwell filtering by `Eric Larson`_ - -- Fix ``mne.decoding.TimeDecoding`` to allow specifying ``clf`` by `Jean-Remi King`_ - -- Fix bug with units (uV) in 'Brain Vision Data Exchange Header File Version 1.0' by `Federico Raimondo`_ - -- Fix bug where :func:`mne.preprocessing.maxwell_filter` ``destination`` parameter did not properly set device-to-head transform by `Eric Larson`_ - -- Fix bug in rank calculation of ``mne.utils.estimate_rank``, ``mne.io.Raw.estimate_rank``, and covariance functions where the tolerance was set to slightly too small a value, new 'auto' mode uses values from ``scipy.linalg.orth`` by `Eric Larson`_. - -- Fix bug when specifying irregular ``train_times['slices']`` in ``mne.decoding.GeneralizationAcrossTime``, by `Jean-Remi King`_ - -- Fix colorbar range on norm data by `Jaakko Leppakangas`_ - -- Fix bug in ``mne.preprocessing.run_ica``, which used the ``ecg_criterion`` parameter for the EOG criterion instead of ``eog_criterion`` by `Christian Brodbeck`_ - -- Fix normals in CTF data reader by `Eric Larson`_ - -- Fix bug in :func:`mne.io.read_raw_ctf`, when omitting samples at the end by `Jaakko Leppakangas`_ - -- Fix ``info['lowpass']`` value for downsampled raw data by `Eric Larson`_ - -- Remove measurement date from :class:`mne.Info` in :func:`mne.io.Raw.anonymize` by `Eric Larson`_ - -- Fix bug that caused synthetic ecg channel creation even if channel was specified for ECG peak detection in :func:`mne.preprocessing.create_ecg_epochs` by `Jaakko Leppakangas`_ - -- Fix bug with vmin and vmax when None is passed in :func:`mne.viz.plot_topo_image_epochs` by `Jaakko Leppakangas`_ - -- Fix bug with :func:`mne.label_sign_flip` (and :func:`mne.extract_label_time_course`) by `Natalie Klein`_ and `Eric Larson`_ - -- Add copy parameter in :func:`mne.Epochs.apply_baseline` and :func:`mne.io.Raw.filter` methods by `Jona Sassenhagen`_ and `Alex Gramfort`_ - -- Fix bug in :func:`mne.merge_events` when using ``replace_events=False`` by `Alex Gramfort`_ - -- Fix bug in :class:`mne.Evoked` type setting in :func:`mne.stats.linear_regression_raw` by `Eric Larson`_ - -- Fix bug in ``mne.io.edf.RawEDF`` highpass filter setting to take max highpass to match warning message by `Teon Brooks`_ - -- Fix bugs with coordinane frame adjustments in ``mne.viz.plot_trans`` by `Eric Larson`_ - -- Fix bug in colormap selection in :func:`mne.Evoked.plot_projs_topomap` by `Jaakko Leppakangas`_ - -- Fix bug in source normal adjustment that occurred when 1) patch information is available (e.g., when distances have been calculated) and 2) points are excluded from the source space (by inner skull distance) by `Eric Larson`_ - -- Fix bug when merging info that has a field with list of dicts by `Jaakko Leppakangas`_ - -- The BTi/4D reader now considers user defined channel labels instead of the hard-ware names, however only for channels other than MEG. By `Denis Engemann`_ and `Alex Gramfort`_. - -- The BTi reader :func:`mne.io.read_raw_bti` can now read 2500 system data, by `Eric Larson`_ - -- Fix bug in :func:`mne.compute_raw_covariance` where rejection by non-data channels (e.g. EOG) was not done properly by `Eric Larson`_. - -- Change default scoring method of ``mne.decoding.GeneralizationAcrossTime`` and ``mne.decoding.TimeDecoding`` to estimate the scores within the cross-validation as in scikit-learn_ as opposed to across all cross-validated ``y_pred``. The method can be changed with the ``score_mode`` parameter by `Jean-Remi King`_ - -- 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 ``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`_ - -API -~~~ - -- The default ``picks=None`` in :func:`mne.viz.plot_epochs_image` now only plots the first 5 channels, not all channels, by `Jona Sassenhagen`_ - -- The ``mesh_color`` parameter in :func:`mne.viz.plot_dipole_locations` has been removed (use ``brain_color`` instead), by `Marijn van Vliet`_ - -- Deprecated functions ``mne.time_frequency.compute_raw_psd`` and ``mne.time_frequency.compute_epochs_psd``, replaced by ``mne.time_frequency.psd_welch`` by `Chris Holdgraf`_ - -- Deprecated function ``mne.time_frequency.multitaper_psd`` and replaced by ``mne.time_frequency.psd_multitaper`` by `Chris Holdgraf`_ - -- The ``y_pred`` attribute in ``mne.decoding.GeneralizationAcrossTime`` and ``mne.decoding.TimeDecoding`` is now a numpy array, by `Jean-Remi King`_ - -- The :func:`mne.bem.fit_sphere_to_headshape` function now default to ``dig_kinds='auto'`` which will use extra digitization points, falling back to extra plus eeg digitization points if there not enough extra points are available. - -- The :func:`mne.bem.fit_sphere_to_headshape` now has a ``units`` argument that should be set explicitly. This will default to ``units='mm'`` in 0.12 for backward compatibility but change to ``units='m'`` in 0.13. - -- Added default parameters in Epochs class namely ``event_id=None``, ``tmin=-0.2`` and ``tmax=0.5``. - -- To unify and extend the behavior of :func:`mne.compute_raw_covariance` relative to :func:`mne.compute_covariance`, the default parameter ``tstep=0.2`` now discards any epochs at the end of the :class:`mne.io.Raw` instance that are not the full ``tstep`` duration. This will slightly change the computation of :func:`mne.compute_raw_covariance`, but should only potentially have a big impact if the :class:`mne.io.Raw` instance is short relative to ``tstep`` and the last, too short (now discarded) epoch contained data inconsistent with the epochs that preceded it. - -- The default ``picks=None`` in :func:`mne.io.Raw.filter` now picks eeg, meg, seeg, and ecog channels, by `Jean-Remi King`_ and `Eric Larson`_ - -- EOG, ECG and EMG channels are now plotted by default (if present in data) when using :func:`mne.viz.plot_evoked` by `Marijn van Vliet`_ - -- Replace pseudoinverse-based solver with much faster Cholesky solver in :func:`mne.stats.linear_regression_raw`, by `Jona Sassenhagen`_. - -- CTF data reader now reads EEG locations from .pos file as HPI points by `Jaakko Leppakangas`_ - -- Subselecting channels can now emit a warning if many channels have been subselected from projection vectors. We recommend only computing projection vertors for and applying projectors to channels that will be used in the final analysis. However, after picking a subset of channels, projection vectors can be renormalized with :func:`mne.Info.normalize_proj` if necessary to avoid warnings about subselection. Changes by `Eric Larson`_ and `Alex Gramfort`_. - -- Rename and deprecate ``mne.Epochs.drop_bad_epochs`` to :func:`mne.Epochs.drop_bad`, and ``mne.Epochs.drop_epochs`` to :func:`mne.Epochs.drop` by `Alex Gramfort`_. - -- The C wrapper ``mne.do_forward_solution`` has been deprecated in favor of the native Python version :func:`mne.make_forward_solution` by `Eric Larson`_ - -- The ``events`` parameter of :func:`mne.EpochsArray` is set by default to chronological time-samples and event values to 1, by `Jean-Remi King`_ - -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 diff --git a/doc/changes/v0.13.rst b/doc/changes/v0.13.rst deleted file mode 100644 index aee297d9d2d..00000000000 --- a/doc/changes/v0.13.rst +++ /dev/null @@ -1,248 +0,0 @@ -.. _changes_0_13: - -Version 0.13 (2016-09-27) -------------------------- - -Changelog -~~~~~~~~~ - -- Add new class :class:`AcqParserFIF` to parse Elekta/Neuromag MEG acquisition info, allowing e.g. collecting epochs according to acquisition-defined averaging categories by `Jussi Nurminen`_ - -- Adds automatic determination of FIR filter parameters ``filter_length``, ``l_trans_bandwidth``, and ``h_trans_bandwidth`` and adds ``phase`` argument in e.g. in :meth:`mne.io.Raw.filter` by `Eric Larson`_ - -- Adds faster ``n_fft='auto'`` option to :meth:`mne.io.Raw.apply_hilbert` by `Eric Larson`_ - -- Adds new function ``mne.time_frequency.csd_array`` to compute the cross-spectral density of multivariate signals stored in an array, by `Nick Foti`_ - -- Add order params 'selection' and 'position' for :func:`mne.viz.plot_raw` to allow plotting of specific brain regions by `Jaakko Leppakangas`_ - -- Added the ability to decimate :class:`mne.Evoked` objects with :func:`mne.Evoked.decimate` by `Eric Larson`_ - -- Add generic array-filtering function :func:`mne.filter.filter_data` by `Eric Larson`_ - -- ``mne.viz.plot_trans`` now also shows head position indicators by `Christian Brodbeck`_ - -- Add label center of mass function :func:`mne.Label.center_of_mass` by `Eric Larson`_ - -- Added :func:`mne.viz.plot_ica_properties` that allows plotting of independent component properties similar to ``pop_prop`` in EEGLAB. Also :class:`mne.preprocessing.ICA` has :func:`mne.preprocessing.ICA.plot_properties` method now. Added by `Mikołaj Magnuski`_ - -- Add second-order sections (instead of ``(b, a)`` form) IIR filtering for reduced numerical error by `Eric Larson`_ - -- Add interactive colormap option to image plotting functions by `Jaakko Leppakangas`_ - -- Add support for the University of Maryland KIT system by `Christian Brodbeck`_ - -- Add support for \*.elp and \*.hsp files to the KIT2FIFF converter and ``mne.channels.read_dig_montage`` by `Teon Brooks`_ and `Christian Brodbeck`_ - -- Add option to preview events in the KIT2FIFF GUI by `Christian Brodbeck`_ - -- Add approximation of size of :class:`io.Raw`, :class:`Epochs`, and :class:`Evoked` in :func:`repr` by `Eric Larson`_ - -- Add possibility to select a subset of sensors by lasso selector to :func:`mne.viz.plot_sensors` and :func:`mne.viz.plot_raw` when using order='selection' or order='position' by `Jaakko Leppakangas`_ - -- Add the option to plot brain surfaces and source spaces to :func:`viz.plot_bem` by `Christian Brodbeck`_ - -- Add the ``--filterchpi`` option to :ref:`mne browse_raw`, by `Felix Raimundo`_ - -- Add the ``--no-decimate`` option to :ref:`mne make_scalp_surfaces` to skip the high-resolution surface decimation step, by `Eric Larson`_ - -- Add new class :class:`mne.decoding.EMS` to transform epochs with the event-matched spatial filters and add 'cv' parameter to :func:`mne.decoding.compute_ems`, by `Jean-Remi King`_ - -- Added :class:`mne.time_frequency.EpochsTFR` and average parameter in :func:`mne.time_frequency.tfr_morlet` and :func:`mne.time_frequency.tfr_multitaper` to compute time-frequency transforms on single trial epochs without averaging, by `Jean-Remi King`_ and `Alex Gramfort`_ - -- Added :class:`mne.decoding.TimeFrequency` to transform signals in scikit-learn pipelines, by `Jean-Remi King`_ - -- Added :class:`mne.decoding.UnsupervisedSpatialFilter` providing interface for scikit-learn decomposition algorithms to be used with MNE data, by `Jean-Remi King`_ and `Asish Panda`_ - -- Added support for multiclass decoding in :class:`mne.decoding.CSP`, by `Jean-Remi King`_ and `Alexandre Barachant`_ - -- Components obtained from :class:`mne.preprocessing.ICA` are now sorted by explained variance, by `Mikołaj Magnuski`_ - -- Adding an EEG reference channel using :func:`mne.add_reference_channels` will now use its digitized location from the FIFF file, if present, by `Chris Bailey`_ - -- Added interactivity to :func:`mne.preprocessing.ICA.plot_components` - passing an instance of :class:`io.Raw` or :class:`Epochs` in ``inst`` argument allows to open component properties by clicking on component topomaps, by `Mikołaj Magnuski`_ - -- Adds new function :func:`mne.viz.plot_compare_evokeds` to show multiple evoked time courses at a single location, or the mean over a ROI, or the GFP, automatically averaging and calculating a CI if multiple subjects are given, by `Jona Sassenhagen`_ - -- Added ``transform_into`` parameter into :class:`mne.decoding.CSP` to retrieve the average power of each source or the time course of each source, by `Jean-Remi King`_ - -- Added support for reading MaxShield (IAS) evoked data (e.g., from the acquisition machine) in :func:`mne.read_evokeds` by `Eric Larson`_ - -- Added support for functional near-infrared spectroscopy (fNIRS) channels by `Jaakko Leppakangas`_ - -- Added :attr:`mne.io.Raw.acqparser` convenience attribute for :class:`mne.AcqParserFIF` by `Eric Larson`_ - -- Added example of Representational Similarity Analysis, by `Jean-Remi King`_ - -BUG -~~~ - -- Fixed a bug where selecting epochs using hierarchical event IDs (HIDs) was *and*-like instead of *or*-like. When doing e.g. ``epochs[('Auditory', 'Left')]``, previously all trials that contain ``'Auditory'`` *and* ``'Left'`` (like ``'Auditory/Left'``) would be selected, but now any conditions matching ``'Auditory'`` *or* ``'Left'`` will be selected (like ``'Auditory/Left'``, ``'Auditory/Right'``, and ``'Visual/Left'``). This is now consistent with how epoch selection was done without HID tags, e.g. ``epochs[['a', 'b']]`` would select all epochs of type ``'a'`` and type ``'b'``. By `Eric Larson`_ - -- Fixed Infomax/Extended Infomax when the user provides an initial weights matrix by `Jair Montoya Martinez`_ - -- Fixed the default raw FIF writing buffer size to be 1 second instead of 10 seconds by `Eric Larson`_ - -- Fixed channel selection order when MEG channels do not come first in :func:`mne.preprocessing.maxwell_filter` by `Eric Larson`_ - -- Fixed color ranges to correspond to the colorbar when plotting several time instances with :func:`mne.viz.plot_evoked_topomap` by `Jaakko Leppakangas`_ - -- Added units to :func:`mne.io.read_raw_brainvision` for reading non-data channels and enable default behavior of inferring channel type by unit by `Jaakko Leppakangas`_ and `Pablo-Arias`_ - -- Fixed minor bugs with :func:`mne.Epochs.resample` and :func:`mne.Epochs.decimate` by `Eric Larson`_ - -- Fixed a bug where duplicate vertices were not strictly checked by :func:`mne.simulation.simulate_stc` by `Eric Larson`_ - -- Fixed a bug where some FIF files could not be read with :func:`mne.io.show_fiff` by `Christian Brodbeck`_ and `Eric Larson`_ - -- Fixed a bug where ``merge_grads=True`` causes :func:`mne.viz.plot_evoked_topo` to fail when plotting a list of evokeds by `Jaakko Leppakangas`_ - -- Fixed a bug when setting multiple bipolar references with :func:`set_bipolar_reference` by `Marijn van Vliet`_. - -- Fixed image scaling in :func:`mne.viz.plot_epochs_image` when plotting more than one channel by `Jaakko Leppakangas`_ - -- Fixed :class:`mne.preprocessing.Xdawn` to fit shuffled epochs by `Jean-Remi King`_ - -- Fixed a bug with channel order determination that could lead to an ``AssertionError`` when using :class:`mne.Covariance` matrices by `Eric Larson`_ - -- Fixed the check for CTF gradient compensation in :func:`mne.preprocessing.maxwell_filter` by `Eric Larson`_ - -- Fixed the import of EDF files with encoding characters in :func:`mne.io.read_raw_edf` by `Guillaume Dumas`_ - -- Fixed :class:`mne.Epochs` to ensure that detrend parameter is not a boolean by `Jean-Remi King`_ - -- Fixed bug with ``mne.realtime.FieldTripClient.get_data_as_epoch`` when ``picks=None`` which crashed the function by `Mainak Jas`_ - -- Fixed reading of units in ``.elc`` montage files (from ``UnitsPosition`` field) so that ``mne.channels.Montage`` objects are now returned with the ``pos`` attribute correctly in meters, by `Chris Mullins`_ - -- Fixed reading of BrainVision files by `Phillip Alday`_: - -- Greater support for BVA files, especially older ones: alternate text coding schemes with fallback to Latin-1 as well as units in column headers - -- Use online software filter information when present - -- Fix comparisons of filter settings for determining "strictest"/"weakest" filter - -- Weakest filter is now used for heterogeneous channel filter settings, leading to more consistent behavior with filtering methods applied to a subset of channels (e.g. ``Raw.filter`` with ``picks != None``). - -- Fixed plotting and timing of :class:`Annotations` and restricted addition of annotations outside data range to prevent problems with cropping and concatenating data by `Jaakko Leppakangas`_ - -- Fixed ICA plotting functions to refer to IC index instead of component number by `Andreas Hojlund`_ and `Jaakko Leppakangas`_ - -- Fixed bug with ``picks`` when interpolating MEG channels by `Mainak Jas`_. - -- Fixed bug in padding of Stockwell transform for signal of length a power of 2 by `Johannes Niediek`_ - -API -~~~ - -- The ``add_eeg_ref`` argument in core functions like :func:`mne.io.read_raw_fif` and :class:`mne.Epochs` has been deprecated in favor of using :func:`mne.set_eeg_reference` and equivalent instance methods like :meth:`raw.set_eeg_reference() `. In functions like :func:`mne.io.read_raw_fif` where the default in 0.13 and older versions is ``add_eeg_ref=True``, the default will change to ``add_eeg_ref=False`` in 0.14, and the argument will be removed in 0.15. - -- Multiple aspects of FIR filtering in MNE-Python has been refactored: - - 1. New recommended defaults for ``l_trans_bandwidth='auto'``, ``h_trans_bandwidth='auto'``, and ``filter_length='auto'``. This should generally reduce filter artifacts at the expense of slight decrease in effective filter stop-band attenuation. For details see :ref:`tut-filtering-in-python`. The default values of ``l_trans_bandwidth=h_trans_bandwidth=0.5`` and ``filter_length='10s'`` will change to ``'auto'`` in 0.14. - - 2. The ``filter_length=None`` option (i.e. use ``len(x)``) has been deprecated. - - 3. An improved ``phase='zero'`` zero-phase FIR filtering has been added. Instead of running the designed filter forward and backward, the filter is applied once and we compensate for the linear phase of the filter. The previous ``phase='zero-double'`` default will change to ``phase='zero'`` in 0.14. - - 4. A warning is provided when the filter is longer than the signal of interest, as this is unlikely to produce desired results. - - 5. Previously, if the filter was as long or longer than the signal of interest, direct FFT-based computations were used. Now a single code path (overlap-add filtering) is used for all FIR filters. This could cause minor changes in how short signals are filtered. - -- Support for Python 2.6 has been dropped, and the minimum supported dependencies are NumPy_ 1.8, SciPy_ 0.12, and Matplotlib_ 1.3 by `Eric Larson`_ - -- When CTF gradient compensation is applied to raw data, it is no longer reverted on save of :meth:`mne.io.Raw.save` by `Eric Larson`_ - -- Adds ``mne.time_frequency.csd_epochs`` to replace ``mne.time_frequency.csd_compute_epochs`` for naming consistency. ``mne.time_frequency.csd_compute_epochs`` is now deprecated and will be removed in mne 0.14, by `Nick Foti`_ - -- Weighted addition and subtraction of :class:`Evoked` as ``ev1 + ev2`` and ``ev1 - ev2`` have been deprecated, use explicit :func:`mne.combine_evoked(..., weights='nave') ` instead by `Eric Larson`_ - -- Deprecated support for passing a list of filenames to :class:`mne.io.Raw` constructor, use :func:`mne.io.read_raw_fif` and :func:`mne.concatenate_raws` instead by `Eric Larson`_ - -- Added options for setting data and date formats manually in :func:`mne.io.read_raw_cnt` by `Jaakko Leppakangas`_ - -- Now channels with units of 'C', 'µS', 'uS', 'ARU' and 'S' will be turned to misc by default in :func:`mne.io.read_raw_brainvision` by `Jaakko Leppakangas`_ - -- Add :func:`mne.io.anonymize_info` function to anonymize measurements and add methods to :class:`mne.io.Raw`, :class:`mne.Epochs` and :class:`mne.Evoked`, by `Jean-Remi King`_ - -- Now it is possible to plot only a subselection of channels in :func:`mne.viz.plot_raw` by using an array for order parameter by `Jaakko Leppakangas`_ - -- EOG channels can now be included when calling :func:`mne.preprocessing.ICA.fit` and a proper error is raised when trying to include unsupported channels by `Alexander Rudiuk`_ - -- :func:`mne.concatenate_epochs` and :func:`mne.compute_covariance` now check to see if all :class:`Epochs` instances have the same MEG-to-Head transformation, and errors by default if they do not by `Eric Larson`_ - -- Added option to pass a list of axes to :func:`mne.viz.plot_epochs_image` by `Mikołaj Magnuski`_ - -- Constructing IIR filters in :func:`mne.filter.construct_iir_filter` defaults to ``output='ba'`` in 0.13 but this will be changed to ``output='sos'`` by `Eric Larson`_ - -- Add ``zorder`` parameter to :func:`mne.Evoked.plot` and derived functions to sort allow sorting channels by e.g. standard deviation, by `Jona Sassenhagen`_ - -- The ``baseline`` parameter of :func:`mne.Epochs.apply_baseline` is set by default (None, 0), by `Felix Raimundo`_ - -- Adds :func:`mne.Evoked.apply_baseline` to be consistent with :func:`mne.Epochs.apply_baseline`, by `Felix Raimundo`_ - -- Deprecated the ``baseline`` parameter in :class:`mne.Evoked`, by `Felix Raimundo`_ - -- The API of :meth:`mne.SourceEstimate.plot` and :func:`mne.viz.plot_source_estimates` has been updated to reflect current PySurfer 0.6 API. The ``config_opts`` parameter is now deprecated and will be removed in mne 0.14, and the default representation for time will change from ``ms`` to ``s`` in mne 0.14. By `Christian Brodbeck`_ - -- The default dataset location has been changed from ``examples/`` in the MNE-Python root directory to ``~/mne_data`` in the user's home directory, by `Eric Larson`_ - -- A new option ``set_env`` has been added to :func:`mne.set_config` that defaults to ``False`` in 0.13 but will change to ``True`` in 0.14, by `Eric Larson`_ - -- The ``compensation`` parameter in :func:`mne.io.read_raw_fif` has been deprecated in favor of the method :meth:`mne.io.Raw.apply_gradient_compensation` by `Eric Larson`_ - -- ``mne.decoding.EpochsVectorizer`` has been deprecated in favor of :class:`mne.decoding.Vectorizer` by `Asish Panda`_ - -- The ``epochs_data`` parameter has been deprecated in :class:`mne.decoding.CSP`, in favour of the ``X`` parameter to comply to scikit-learn API, by `Jean-Remi King`_ - -- 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`_ - -- Extended Infomax is now the new default in :func:`mne.preprocessing.infomax` (``extended=True``), by `Clemens Brunner`_ - -- :func:`mne.io.read_raw_eeglab` and :func:`mne.read_epochs_eeglab` now take additional argument ``uint16_codec`` that allows to define the encoding of character arrays in set file. This helps in rare cases when reading a set file fails with ``TypeError: buffer is too small for requested array``. By `Mikołaj Magnuski`_ - -- Added :class:`mne.decoding.TemporalFilter` to filter data in scikit-learn pipelines, by `Asish Panda`_ - -- :func:`mne.preprocessing.create_ecg_epochs` now includes all the channels when ``picks=None`` by `Jaakko Leppakangas`_ - -- :func:`mne.set_eeg_reference` now allows moving from a custom to an average EEG reference by `Marijn van Vliet`_ - -Authors -~~~~~~~ - -The committer list for this release is the following (sorted by alphabetical order): - -* Alexander Rudiuk -* Alexandre Barachant -* Alexandre Gramfort -* Asish Panda -* Camilo Lamus -* Chris Holdgraf -* Christian Brodbeck -* Christopher J. Bailey -* Christopher Mullins -* Clemens Brunner -* Denis A. Engemann -* Eric Larson -* Federico Raimondo -* Félix Raimundo -* Guillaume Dumas -* Jaakko Leppakangas -* Jair Montoya -* Jean-Remi King -* Johannes Niediek -* Jona Sassenhagen -* Jussi Nurminen -* Keith Doelling -* Mainak Jas -* Marijn van Vliet -* Michael Krause -* Mikolaj Magnuski -* Nick Foti -* Phillip Alday -* Simon-Shlomo Poil -* Teon Brooks -* Yaroslav Halchenko diff --git a/doc/changes/v0.14.rst b/doc/changes/v0.14.rst deleted file mode 100644 index 7db46d27617..00000000000 --- a/doc/changes/v0.14.rst +++ /dev/null @@ -1,250 +0,0 @@ -.. _changes_0_14: - -Version 0.14 (2017-03-24) -------------------------- - -Changelog -~~~~~~~~~ - -- Add example of time-frequency decoding with CSP by `Laura Gwilliams`_ - -- Automatically create a legend in :func:`mne.viz.plot_evoked_topo` by `Jussi Nurminen`_ - -- Add I/O support for Artemis123 infant/toddler MEG data by `Luke Bloy`_ - -- Add filter plotting functions :func:`mne.viz.plot_filter` and :func:`mne.viz.plot_ideal_filter` as well as filter creation function :func:`mne.filter.create_filter` by `Eric Larson`_ - -- Add HCP-MMP1.0 parcellation dataset downloader by `Eric Larson`_ - -- Add option to project EEG electrodes onto the scalp in ``mne.viz.plot_trans`` by `Eric Larson`_ - -- Add option to plot individual sensors in :meth:`mne.io.Raw.plot_psd` by `Alex Gramfort`_ and `Eric Larson`_ - -- Add option to plot ECoG electrodes in ``mne.viz.plot_trans`` by `Eric Larson`_ - -- Add convenient default values to :meth:`mne.io.Raw.apply_hilbert` and :meth:`mne.io.Raw.apply_function` by `Denis Engemann`_ - -- Remove MNE-C requirement for :ref:`mne make_scalp_surfaces` by `Eric Larson`_ - -- Add support for FastTrack Polhemus ``.mat`` file outputs in ``hsp`` argument of ``mne.channels.read_dig_montage`` by `Eric Larson`_ - -- Add option to convert 3d electrode plots to a snapshot with 2d electrode positions with :func:`mne.viz.snapshot_brain_montage` by `Chris Holdgraf`_ - -- Add skull surface plotting option to ``mne.viz.plot_trans`` by `Jaakko Leppakangas`_ - -- Add minimum-phase filtering option in :meth:`mne.io.Raw.filter` by `Eric Larson`_ - -- Add support for reading ASCII BrainVision files in :func:`mne.io.read_raw_brainvision` by `Eric Larson`_ - -- Add method of ICA objects for retrieving the component maps :meth:`mne.preprocessing.ICA.get_components` by `Jona Sassenhagen`_ - -- Add option to plot events in :func:`mne.viz.plot_epochs` by `Jaakko Leppakangas`_ - -- Add dipole definitions for older phantom at Otaniemi in :func:`mne.dipole.get_phantom_dipoles` by `Eric Larson`_ - -- Add spatial colors option for :func:`mne.viz.plot_raw_psd` by `Jaakko Leppakangas`_ - -- Add functions like :func:`get_volume_labels_from_src` to handle mixed source spaces by `Annalisa Pascarella`_ - -- Add convenience function for opening MNE documentation :func:`open_docs` by `Eric Larson`_ - -- Add option in :meth:`mne.io.Raw.plot` to display the time axis relative to ``raw.first_samp`` by `Mainak Jas`_ - -- Add new :mod:`mne.datasets.visual_92_categories ` dataset by `Jaakko Leppakangas`_ - -- Add option in :func:`mne.io.read_raw_edf` to allow channel exclusion by `Jaakko Leppakangas`_ - -- Allow integer event codes in :func:`mne.read_epochs_eeglab` by `Jaakko Leppakangas`_ - -- Add ability to match channel names in a case insensitive manner when applying a ``mne.channels.Montage`` by `Marijn van Vliet`_ - -- Add ``yscale`` keyword argument to :meth:`mne.time_frequency.AverageTFR.plot` that allows specifying whether to present the frequency axis in linear (``'linear'``) or log (``'log'``) scale. The default value is ``'auto'`` which detects whether frequencies are log-spaced and sets yscale to log. Added by `Mikołaj Magnuski`_ - -- Add :ref:`Representational Similarity Analysis (RSA) ` example on :mod:`mne.datasets.visual_92_categories.data_path` dataset by `Jaakko Leppakangas`_, `Jean-Remi King`_ and `Alex Gramfort`_ - -- Add support for NeuroScan files with event type 3 in :func:`mne.io.read_raw_cnt` by `Marijn van Vliet`_ - -- Add interactive annotation mode to :meth:`mne.io.Raw.plot` (accessed by pressing 'a') by `Jaakko Leppakangas`_ - -- Add support for deleting all projectors or a list of indices in :meth:`mne.io.Raw.del_proj` by `Eric Larson`_ - -- Add source space plotting with :meth:`mne.SourceSpaces.plot` using ``mne.viz.plot_trans`` by `Eric Larson`_ - -- Add :func:`mne.decoding.get_coef` to retrieve and inverse the coefficients of a linear model - typically a spatial filter or pattern, by `Jean-Remi King`_ - -- Add support for reading in EGI MFF digitization coordinate files in ``mne.channels.read_dig_montage`` by `Matt Boggess`_ - -- Add ``n_per_seg`` keyword argument to ``mne.time_frequency.psd_welch`` and :func:`mne.time_frequency.psd_array_welch` that allows to control segment length independently of ``n_fft`` and use zero-padding when ``n_fft > n_per_seg`` by `Mikołaj Magnuski`_ - -- Add annotation aware data getter :meth:`mne.io.Raw.get_data` by `Jaakko Leppakangas`_ - -- Add support of dipole location visualization with MRI slice overlay with matplotlib to :func:`mne.viz.plot_dipole_locations` via mode='orthoview' parameter by `Jaakko Leppakangas`_ and `Alex Gramfort`_ - -- Add plotting of head positions as a function of time in :func:`mne.viz.plot_head_positions` by `Eric Larson`_ - -- Add ``real_filter`` option to ``mne.beamformer.dics``, ``mne.beamformer.dics_source_power``, ``mne.beamformer.tf_dics`` and ``mne.beamformer.dics_epochs`` by `Eric Larson`_, `Alex Gramfort`_ and `Andrea Brovelli`_. - -- Add a demo script showing how to use a custom inverse solver with MNE by `Alex Gramfort`_ - -- Functions :func:`mne.preprocessing.create_ecg_epochs`, :func:`mne.preprocessing.create_eog_epochs`, :func:`mne.compute_raw_covariance` and ICA methods :meth:`mne.preprocessing.ICA.score_sources`, :meth:`mne.preprocessing.ICA.find_bads_ecg`, :meth:`mne.preprocessing.ICA.find_bads_eog` are now annotation aware by `Jaakko Leppakangas`_ - -- Allow using ``spatial_colors`` for non-standard layouts by creating custom layouts from channel locations and add ``to_sphere`` keyword to :func:`mne.viz.plot_sensors` to allow plotting sensors that are not on the head surface by `Jaakko Leppakangas`_ - -- Concatenating raws with :func:`mne.concatenate_raws` now creates boundary annotations automatically by `Jaakko Leppakangas`_ - -- :func:`mne.viz.plot_projs_topomap` now supports plotting EEG topomaps by passing in :class:`mne.Info` by `Eric Larson`_ - -BUG -~~~ - -- Fix bug with DICS and LCMV (e.g., ``mne.beamformer.lcmv``, ``mne.beamformer.dics``) where regularization was done improperly. The default ``reg=0.01`` has been changed to ``reg=0.05``, by `Andrea Brovelli`_, `Alex Gramfort`_, and `Eric Larson`_ - -- Fix callback function call in ``mne.viz.topo._plot_topo_onpick`` by `Erkka Heinila`_ - -- Fix reading multi-file CTF recordings in :func:`mne.io.read_raw_ctf` by `Niklas Wilming`_ - -- Fix computation of AR coefficients across channels in :func:`mne.time_frequency.fit_iir_model_raw` by `Eric Larson`_ - -- Fix maxfilter channel names extra space bug in :func:`mne.preprocessing.maxwell_filter` by `Sheraz Khan`_ - -- :func:`mne.channels.find_layout` now leaves out the excluded channels by `Jaakko Leppakangas`_ - -- Array data constructors :class:`mne.io.RawArray` and :class:`EvokedArray` now make a copy of the info structure by `Jaakko Leppakangas`_ - -- Fix bug with finding layouts in :func:`mne.viz.plot_projs_topomap` by `Eric Larson`_ - -- Fix bug :func:`mne.io.anonymize_info` when Info does not contain 'file_id' or 'meas_id' fields by `Jean-Remi King`_ - -- Fix colormap selection in :func:`mne.viz.plot_evoked_topomap` when using positive vmin with negative data by `Jaakko Leppakangas`_ - -- Fix channel name comparison in ``mne.channels.read_montage`` so that if ``ch_names`` is provided, the returned montage will have channel names in the same letter case by `Jaakko Leppakangas`_ - -- Fix :meth:`inst.set_montage(montage) ` to only set ``inst.info['dev_head_t']`` if ``dev_head_t=True`` in ``mne.channels.read_dig_montage`` by `Eric Larson`_ - -- Fix handling of events in ``mne.realtime.RtEpochs`` when the triggers were split between two buffers resulting in missing and/or duplicate epochs by `Mainak Jas`_ and `Antti Rantala`_ - -- Fix bug with automatic decimation in :func:`mne.io.read_raw_kit` by `Keith Doelling`_ - -- Fix bug with :func:`setup_volume_source_space` where arguments ``subject`` and ``subjects_dir`` were ignored by `Jaakko Leppakangas`_ - -- Fix sanity check for incompatible ``threshold`` and ``tail`` values in clustering functions like :func:`mne.stats.spatio_temporal_cluster_1samp_test` by `Eric Larson`_ - -- Fix ``_bad_dropped`` not being set when loading eeglab epoched files via :func:`mne.read_epochs_eeglab` which resulted in :func:`len` not working by `Mikołaj Magnuski`_ - -- Fix a bug in :meth:`mne.time_frequency.AverageTFR.plot` when plotting without a colorbar by `Jaakko Leppakangas`_ - -- Fix ``_filenames`` attribute in creation of :class:`mne.io.RawArray` with :meth:`mne.preprocessing.ICA.get_sources` by `Paul Pasler`_ - -- Fix contour levels in :func:`mne.viz.plot_evoked_topomap` to be uniform across topomaps by `Jaakko Leppakangas`_ - -- Fix bug in :func:`mne.preprocessing.maxwell_filter` where fine calibration indices were mismatched leading to an ``AssertionError`` by `Eric Larson`_ - -- Fix bug in :func:`mne.preprocessing.fix_stim_artifact` where non-data channels were interpolated by `Eric Larson`_ - -- :class:`mne.decoding.Scaler` now scales each channel independently using data from all time points (epochs and times) instead of scaling all channels for each time point. It also now accepts parameter ``scalings`` to determine the data scaling method (default is ``None`` to use static channel-type-based scaling), by `Asish Panda`_, `Jean-Remi King`_, and `Eric Larson`_ - -- Raise error if the cv parameter of ``mne.decoding.GeneralizationAcrossTime`` and ``mne.decoding.TimeDecoding`` is not a partition and the predict_mode is "cross-validation" by `Jean-Remi King`_ - -- Fix bug in :func:`mne.io.read_raw_edf` when ``preload=False`` and channels have different sampling rates by `Jaakko Leppakangas`_ - -- Fix :func:`mne.read_labels_from_annot` to set ``label.values[:]=1`` rather than 0 for consistency with the :class:`Label` class by `Jon Houck`_ - -- Fix plotting non-uniform freqs (for example log-spaced) in :meth:`mne.time_frequency.AverageTFR.plot` by `Mikołaj Magnuski`_ - -- Fix :func:`mne.minimum_norm.compute_source_psd` when used with ``pick_ori=None`` by `Annalisa Pascarella`_ and `Alex Gramfort`_ - -- Fix bug in :class:`mne.Annotations` where concatenating two raws where ``orig_time`` of the second run is ``None`` by `Jaakko Leppakangas`_ - -- Fix reading channel location from eeglab ``.set`` files when some of the channels do not provide this information. Previously all channel locations were ignored in such case, now they are read - unless a montage is provided by the user in which case only channel names are read from set file. By `Mikołaj Magnuski`_ - -- Fix reading eeglab ``.set`` files when ``.chanlocs`` structure does not contain ``X``, ``Y`` or ``Z`` fields by `Mikołaj Magnuski`_ - -- Fix bug with :func:`mne.simulation.simulate_raw` when ``interp != 'zero'`` by `Eric Larson`_ - -- Fix :func:`mne.fit_dipole` to handle sphere model rank deficiency properly by `Alex Gramfort`_ - -- Raise error in :func:`mne.concatenate_epochs` when concatenated epochs have conflicting event_id by `Mikołaj Magnuski`_ - -- Fix handling of ``n_components=None`` in :class:`mne.preprocessing.ICA` by `Richard Höchenberger`_ - -- Fix reading of fiducials correctly from CTF data in :func:`mne.io.read_raw_ctf` by `Jaakko Leppakangas`_ - -- Fix :func:`mne.beamformer.rap_music` to return dipoles with amplitudes in Am instead of nAm by `Jaakko Leppakangas`_ - -- Fix computation of duality gap in ``mne.inverse_sparse.mxne_optim.dgap_l21`` by `Mathurin Massias`_ - -API -~~~ - -- The filtering functions ``band_pass_filter``, ``band_stop_filter``, ``low_pass_filter``, and ``high_pass_filter`` have been deprecated in favor of :func:`mne.filter.filter_data` by `Eric Larson`_ - -- :class:`EvokedArray` now has default value ``tmin=0.`` by `Jaakko Leppakangas`_ - -- The ``ch_type`` argument for ``mne.viz.plot_trans`` has been deprecated, use ``eeg_sensors`` and ``meg_sensors`` instead, by `Eric Larson`_ - -- The default ``tmax=60.`` in :meth:`mne.io.Raw.plot_psd` will change to ``tmax=np.inf`` in 0.15, by `Eric Larson`_ - -- Base classes :class:`mne.io.BaseRaw` and :class:`mne.BaseEpochs` are now public to allow easier typechecking, by `Daniel McCloy`_ - -- :func:`mne.io.read_raw_edf` now combines triggers from multiple tal channels to 'STI 014' by `Jaakko Leppakangas`_ - -- The measurement info :class:`Info` no longer contains a potentially misleading ``info['filename']`` entry. Use class properties like :attr:`mne.io.Raw.filenames` or :attr:`mne.Epochs.filename` instead by `Eric Larson`_ - -- Default fiducial name change from 'nz' to 'nasion' in ``mne.channels.read_montage``, so that it is the same for both ``mne.channels.Montage`` and :class: `mne.channels.DigMontage` by `Leonardo Barbosa`_ - -- MNE's additional files for the ``fsaverage`` head/brain model are now included in MNE-Python, and the now superfluous ``mne_root`` parameter to :func:`create_default_subject` has been deprecated by `Christian Brodbeck`_ - -- An ``overwrite=False`` default parameter has been added to :func:`write_source_spaces` to protect against accidental overwrites, by `Eric Larson`_ - -- The :class:`mne.decoding.LinearModel` class will no longer support ``plot_filters`` and ``plot_patterns``, use :class:`mne.EvokedArray` with :func:`mne.decoding.get_coef` instead, by `Jean-Remi King`_ - -- Made functions :func:`mne.time_frequency.tfr_array_multitaper`, :func:`mne.time_frequency.tfr_array_morlet`, :func:`mne.time_frequency.tfr_array_stockwell`, :func:`mne.time_frequency.psd_array_multitaper` and :func:`mne.time_frequency.psd_array_welch` public to allow computing TFRs and PSDs on numpy arrays by `Jaakko Leppakangas`_ - -- :meth:`mne.preprocessing.ICA.fit` now rejects data annotated bad by default. Turn off with ``reject_by_annotation=False``, by `Jaakko Leppakangas`_ - -- :func:`mne.io.read_raw_egi` now names channels with pattern 'E'. This behavior can be changed with parameter ``channel_naming`` by `Jaakko Leppakangas`_ - -- the ``name`` parameter in :class:`mne.Epochs` is deprecated, by `Jaakko Leppakangas`_ - -Authors -~~~~~~~ - -People who contributed to this release (in alphabetical order): - -* Alexander Rudiuk -* Alexandre Gramfort -* Annalisa Pascarella -* Antti Rantala -* Asish Panda -* Burkhard Maess -* Chris Holdgraf -* Christian Brodbeck -* Cristóbal Moënne-Loccoz -* Daniel McCloy -* Denis A. Engemann -* Eric Larson -* Erkka Heinila -* Hermann Sonntag -* Jaakko Leppakangas -* Jakub Kaczmarzyk -* Jean-Remi King -* Jon Houck -* Jona Sassenhagen -* Jussi Nurminen -* Keith Doelling -* Leonardo S. Barbosa -* Lorenz Esch -* Lorenzo Alfine -* Luke Bloy -* Mainak Jas -* Marijn van Vliet -* Matt Boggess -* Matteo Visconti -* Mikolaj Magnuski -* Niklas Wilming -* Paul Pasler -* Richard Höchenberger -* Sheraz Khan -* Stefan Repplinger -* Teon Brooks -* Yaroslav Halchenko diff --git a/doc/changes/v0.15.rst b/doc/changes/v0.15.rst deleted file mode 100644 index e2de7301973..00000000000 --- a/doc/changes/v0.15.rst +++ /dev/null @@ -1,329 +0,0 @@ -.. _changes_0_15: - -Version 0.15 (2017-10-20) -------------------------- - -Changelog -~~~~~~~~~ - -- :meth:`mne.channels.Layout.plot` and :func:`mne.viz.plot_layout` now allows plotting a subset of channels with ``picks`` argument by `Jaakko Leppakangas`_ - -- Add .bvef extension (BrainVision Electrodes File) to ``mne.channels.read_montage`` by `Jean-Baptiste Schiratti`_ - -- Add :func:`mne.decoding.cross_val_multiscore` to allow scoring of multiple tasks, typically used with :class:`mne.decoding.SlidingEstimator`, by `Jean-Remi King`_ - -- Add :class:`mne.decoding.ReceptiveField` module for modeling electrode response to input features by `Chris Holdgraf`_ - -- Add :class:`mne.decoding.TimeDelayingRidge` class, used by default by :class:`mne.decoding.ReceptiveField`, to speed up auto- and cross-correlation computations and enable Laplacian regularization by `Ross Maddox`_ and `Eric Larson`_ - -- Add new :mod:`mne.datasets.mtrf ` dataset by `Chris Holdgraf`_ - -- Add example of time-frequency decoding with CSP by `Laura Gwilliams`_ - -- Add :class:`mne.decoding.SPoC` to fit and apply spatial filters based on continuous target variables, by `Jean-Remi King`_ and `Alexandre Barachant`_ - -- Add Fieldtrip's electromyogram dataset, by `Alexandre Barachant`_ - -- Add ``reject_by_annotation`` option to :func:`mne.preprocessing.find_eog_events` (which is also utilised by :func:`mne.preprocessing.create_eog_epochs`) to omit data that is annotated as bad by `Jaakko Leppakangas`_ - -- Add example for fast screening of event-related dynamics in frequency bands by `Denis Engemann`_ - -- Add :meth:`mne.time_frequency.EpochsTFR.save` by `Jaakko Leppakangas`_ - -- Add butterfly mode (toggled with 'b' key) to :meth:`mne.io.Raw.plot` by `Jaakko Leppakangas`_ - -- Add ``axes`` parameter to plot_topo functions by `Jaakko Leppakangas`_ - -- Add options to change time windowing in :func:`mne.chpi.filter_chpi` by `Eric Larson`_ - -- ``mne.channels.Montage.plot``, :meth:`mne.channels.DigMontage.plot`, and :func:`mne.viz.plot_montage` now allow plotting channel locations as a topomap by `Clemens Brunner`_ - -- Add ``background_color`` parameter to :meth:`mne.Evoked.plot_topo` and :func:`mne.viz.plot_evoked_topo` and improve axes rendering as done in :func:`mne.viz.plot_compare_evokeds` by `Alex Gramfort`_ - -- Add support for GDF files in :func:`mne.io.read_raw_edf` by `Nicolas Barascud`_ - -- Add ``mne.io.find_edf_events`` for getting the events as they are in the EDF/GDF header by `Jaakko Leppakangas`_ - -- Speed up :meth:`mne.io.Raw.plot` and :meth:`mne.Epochs.plot` using (automatic) decimation based on low-passing with ``decim='auto'`` parameter by `Eric Larson`_ and `Jaakko Leppakangas`_ - -- Add ``mne.inverse_sparse.mxne_optim.dgap_l21l1`` for computing the duality gap for TF-MxNE as the new stopping criterion by `Daniel Strohmeier`_ - -- Add option to return a list of :class:`Dipole` objects in sparse source imaging methods by `Daniel Strohmeier`_ - -- Add :func:`mne.inverse_sparse.make_stc_from_dipoles` to generate stc objects from lists of dipoles by `Daniel Strohmeier`_ - -- Add ``mne.channels.find_ch_connectivity`` that tries to infer the correct connectivity template using channel info. If no template is found, it computes the connectivity matrix using :class:`Delaunay ` triangulation of the 2d projected channel positions by `Jaakko Leppakangas`_ - -- Add IO support for EGI MFF format by `Jaakko Leppakangas`_ and `ramonapariciog`_ - -- Add option to use matplotlib backend when plotting with :func:`mne.viz.plot_source_estimates` by `Jaakko Leppakangas`_ - -- Add ``mne.channels.Montage.get_pos2d`` to get the 2D positions of channels in a montage by `Clemens Brunner`_ - -- Add MGH 60- and 70-channel standard montages to ``mne.channels.read_montage`` by `Eric Larson`_ - -- Add option for embedding SVG instead of PNG in HTML for :class:`mne.Report` by `Eric Larson`_ - -- Add confidence intervals, number of free parameters, and χ² to :func:`mne.fit_dipole` and :func:`mne.read_dipole` by `Eric Larson`_ - -- :attr:`mne.SourceEstimate.data` is now writable, writing to it will also update :attr:`mne.SourceEstimate.times` by `Marijn van Vliet`_ - -- :meth:`mne.io.Raw.plot` and :meth:`mne.Epochs.plot` now use anti-aliasing to draw signals by `Clemens Brunner`_ - -- Allow using saved ``DigMontage`` to import digitization to :func:`mne.gui.coregistration` by `Jaakko Leppakangas`_ - -- Add function :func:`mne.channels.get_builtin_montages` to list all built-in montages by `Clemens Brunner`_ - -- :class:`mne.decoding.SlidingEstimator` and :class:`mne.decoding.GeneralizingEstimator` now accept ``**fit_params`` at fitting by `Jean-Remi King`_ - -- Add :class:`mne.VectorSourceEstimate` class which enables working with both source power and dipole orientations by `Marijn van Vliet`_ - -- Add option ``pick_ori='vector'`` to :func:`mne.minimum_norm.apply_inverse` to produce :class:`mne.VectorSourceEstimate` by `Marijn van Vliet`_ - -- Add support for :class:`numpy.random.RandomState` argument to ``seed`` in :mod:`statistical clustering functions ` and better documentation of exact 1-sample tests by `Eric Larson`_ - -- Extend :func:`mne.viz.plot_epochs_image`/:meth:`mne.Epochs.plot_image` with regards to grouping by or aggregating over channels. See the new example at ``examples/visualization/plot_roi_erpimage_by_rt.py`` by `Jona Sassenhagen`_ - -- Add bootstrapped confidence intervals to :func:`mne.viz.plot_compare_evokeds` by `Jona Sassenhagen`_ and `Denis Engemann`_ - -- Add example on how to plot ERDS maps (also known as ERSP) by `Clemens Brunner`_ - -- Add support for volume source spaces to ``spatial_src_connectivity`` and ``spatio_temporal_src_connectivity`` by `Alex Gramfort`_ - -- Plotting raw data (:func:`mne.viz.plot_raw` or :meth:`mne.io.Raw.plot`) with events now includes event numbers (if there are not more than 50 events on a page) by `Clemens Brunner`_ - -- Add filtering functions :meth:`mne.Epochs.filter` and :meth:`mne.Evoked.filter`, as well as ``pad`` argument to :meth:`mne.io.Raw.filter` by `Eric Larson`_ - -- Add high frequency somatosensory MEG dataset by `Jussi Nurminen`_ - -- Add reduced set of labels for HCPMMP-1.0 parcellation in :func:`mne.datasets.fetch_hcp_mmp_parcellation` by `Eric Larson`_ - -- Enable morphing between hemispheres with ``mne.compute_morph_matrix`` by `Christian Brodbeck`_ - -- Add ``return_residual`` to :func:`mne.minimum_norm.apply_inverse` by `Eric Larson`_ - -- Add ``return_drop_log`` to :func:`mne.preprocessing.compute_proj_eog` and :func:`mne.preprocessing.compute_proj_ecg` by `Eric Larson`_ - -- Add time cursor and category/amplitude status message into the single-channel evoked plot by `Jussi Nurminen`_ - -BUG -~~~ -- Fixed a bug when creating spherical volumetric grid source spaces in :func:`setup_volume_source_space` by improving the minimum-distance computations, which in general will decrease the number of used source space points by `Eric Larson`_ - -- Fix bug in :meth:`mne.io.read_raw_brainvision` read .vhdr files with ANSI codepage by `Okba Bekhelifi`_ and `Alex Gramfort`_ - -- Fix unit scaling when reading in EGI digitization files using ``mne.channels.read_dig_montage`` by `Matt Boggess`_ - -- Fix ``picks`` default in :meth:`mne.io.Raw.filter` to include ``ref_meg`` channels by default by `Eric Larson`_ - -- Fix :class:`mne.decoding.CSP` order of spatial filter in ``patterns_`` by `Alexandre Barachant`_ - -- :meth:`mne.concatenate_epochs` now maintains the relative position of events during concatenation by `Alexandre Barachant`_ - -- Fix bug in script ``mne make_scalp_surfaces`` by `Denis Engemann`_ (this bug prevented creation of high-resolution meshes when they were absent in the first place.) - -- Fix writing of raw files with empty set of annotations by `Jaakko Leppakangas`_ - -- Fix bug in :meth:`mne.preprocessing.ICA.plot_properties` where merging gradiometers would fail by `Jaakko Leppakangas`_ - -- Fix :func:`mne.viz.plot_sensors` to maintain proper aspect ratio by `Eric Larson`_ - -- Fix :func:`mne.viz.plot_topomap` to allow 0 contours by `Jaakko Leppakangas`_ - -- Fix :class:`mne.preprocessing.ICA` source-picking to increase threshold for rank estimation to 1e-14 by `Jesper Duemose Nielsen`_ - -- Fix :func:`mne.set_bipolar_reference` to support duplicates in anodes by `Jean-Baptiste Schiratti`_ and `Alex Gramfort`_ - -- Fix visuals of :func:`mne.viz.plot_evoked` and a bug where ylim changes when using interactive topomap plotting by `Jaakko Leppakangas`_ - -- Fix :meth:`mne.Evoked.plot_topomap` when using the ``mask`` argument with paired gradiometers by `Eric Larson`_ - -- Fix bug in :meth:`mne.Label.fill` where an empty label raised an error, by `Eric Larson`_ - -- Fix :func:`mne.io.read_raw_ctf` to also include the samples in the last block by `Jaakko Leppakangas`_ - -- Fix :meth:`mne.preprocessing.ICA.save` to close file before attempting to delete it when write fails by `Jesper Duemose Nielsen`_ - -- Fix :func:`mne.simulation.simulate_evoked` to use nave parameter instead of snr, by `Yousra Bekhti`_ - -- Fix :func:`mne.read_bem_surfaces` for BEM files missing normals by `Christian Brodbeck`_ - -- Fix :func:`mne.transform_surface_to` to actually copy when ``copy=True`` by `Eric Larson`_ - -- Fix :func:`mne.io.read_raw_brainvision` to read vectorized data correctly by `Jaakko Leppakangas`_ and `Phillip Alday`_ - -- Fix ``mne.connectivity.spectral_connectivity`` so that if ``n_jobs > 1`` it does not ignore last ``n_epochs % n_jobs`` epochs by `Mikołaj Magnuski`_ - -- Fix :func:`mne.io.read_raw_edf` to infer sampling rate correctly when reading EDF+ files where tal-channel has a higher sampling frequency by `Jaakko Leppakangas`_ - -- Fix default value of ``kind='topomap'`` in ``mne.channels.Montage.plot`` to be consistent with :func:`mne.viz.plot_montage` by `Clemens Brunner`_ - -- Fix bug in :meth:`to_data_frame ` where non-consecutive picks would make the function crash by `Jaakko Leppakangas`_ - -- Fix channel picking and drop in :class:`mne.time_frequency.EpochsTFR` by `Lukáš Hejtmánek`_ - -- Fix :func:`mne.SourceEstimate.transform` to properly update :attr:`mne.SourceEstimate.times` by `Marijn van Vliet`_ - -- Fix :func:`mne.viz.plot_evoked_joint` to allow custom titles without appending information about the channels by `Jaakko Leppakangas`_ - -- Fix writing a forward solution after being processed by :func:`mne.forward.restrict_forward_to_label` or :func:`mne.forward.restrict_forward_to_stc` by `Marijn van Vliet`_ - -- Fix bug in :func:`mne.viz.plot_compare_evokeds` where ``truncate_yaxis`` was ignored (default is now ``False``), by `Jona Sassenhagen`_ - -- Fix bug in :func:`mne.viz.plot_evoked` where all xlabels were removed when using ``spatial_colors=True``, by `Jesper Duemose Nielsen`_ - -- Fix field mapping :func:`mne.make_field_map` and MEG bad channel interpolation functions (e.g., :meth:`mne.Evoked.interpolate_bads`) to choose a better number of components during pseudoinversion when few channels are available, by `Eric Larson`_ - -- Fix bug in :func:`mne.io.read_raw_brainvision`, changed default to read coordinate information if available and added test, by `Jesper Duemose Nielsen`_ - -- Fix bug in :meth:`mne.SourceEstimate.to_original_src` where morphing failed if two vertices map to the same target vertex, by `Marijn van Vliet`_ - -- Fix :class:`mne.preprocessing.Xdawn` to give verbose error messages about rank deficiency and handle transforming :class:`mne.Evoked`, by `Eric Larson`_ - -- Fix bug in DC and Nyquist frequency multitaper PSD computations, e.g. in ``mne.time_frequency.psd_multitaper``, by `Eric Larson`_ - -- Fix default padding type for :meth:`mne.Epochs.resample` and :meth:`mne.Evoked.resample` to be ``'edge'`` by default, by `Eric Larson`_ - -- Fix :func:`mne.inverse_sparse.mixed_norm`, :func:`mne.inverse_sparse.tf_mixed_norm` and :func:`mne.inverse_sparse.gamma_map` to work with volume source space and sphere head models in MEG by `Alex Gramfort`_ and `Yousra Bekhti`_ - -- Fix :meth:`mne.Evoked.as_type` channel renaming to append ``'_v'`` instead of ``'_virtual'`` to channel names to comply with shorter naming (15 char) requirements, by `Eric Larson`_ - -- Fix treatment of CTF HPI coils as fiducial points in :func:`mne.gui.coregistration` by `Eric Larson`_ - -- Fix resampling of events along with raw in :func:`mne.io.Raw` to now take into consideration the value of ``first_samp`` by `Chris Bailey`_ - -- Fix labels of PSD plots in :func:`mne.viz.plot_raw_psd` by `Alejandro Weinstein`_ - -- Fix depth weighting of sparse solvers (:func:`mne.inverse_sparse.mixed_norm`, :func:`mne.inverse_sparse.tf_mixed_norm` and :func:`mne.inverse_sparse.gamma_map`) with free orientation source spaces to improve orientation estimation by `Alex Gramfort`_ and `Yousra Bekhti`_ - -- Fix the threshold in :func:`mne.beamformer.rap_music` to properly estimate the rank by `Yousra Bekhti`_ - -- Fix treatment of vector inverse in :func:`mne.minimum_norm.apply_inverse_epochs` by `Emily Stephen`_ - -- Fix :func:`mne.find_events` when passing a list as stim_channel parameter by `Alex Gramfort`_ - -- Fix parallel processing when computing covariance with shrinkage estimators by `Denis Engemann`_ - -API -~~~ -- Removed the ``mne.datasets.megsim`` dataset because it was taken down by its host (MRN). Use the :mod:`mne.simulation` functions instead, by `Eric Larson`_ - -- Add ``skip_by_annotation`` to :meth:`mne.io.Raw.filter` to process data concatenated with e.g. :func:`mne.concatenate_raws` separately. This parameter will default to the old behavior (treating all data as a single block) in 0.15 but will change to ``skip_by_annotation='edge'``, which will separately filter the concatenated chunks separately, in 0.16. This should help prevent potential problems with filter-induced ringing in concatenated files, by `Eric Larson`_ - -- ICA channel names have now been reformatted to start from zero, e.g. ``"ICA000"``, to match indexing schemes in :class:`mne.preprocessing.ICA` and related functions, by `Stefan Repplinger`_ and `Eric Larson`_ - -- Add :func:`mne.beamformer.make_lcmv` and :func:`mne.beamformer.apply_lcmv`, :func:`mne.beamformer.apply_lcmv_epochs`, and :func:`mne.beamformer.apply_lcmv_raw` to enable the separate computation and application of LCMV beamformer weights by `Britta Westner`_, `Alex Gramfort`_, and `Denis Engemann`_. - -- Add ``weight_norm`` parameter to enable both unit-noise-gain beamformer and neural activity index (weight normalization) and make whitening optional by allowing ``noise_cov=None`` in ``mne.beamformer.lcmv``, ``mne.beamformer.lcmv_epochs``, and ``mne.beamformer.lcmv_raw``, by `Britta Westner`_, `Alex Gramfort`_, and `Denis Engemann`_. - -- Add new filtering mode ``fir_design='firwin'`` (default in the next 0.16 release) that gets improved attenuation using fewer samples compared to ``fir_design='firwin2'`` (default in the current 0.15 release) by `Eric Larson`_ - -- Make the goodness of fit (GOF) of the dipoles returned by :func:`mne.beamformer.rap_music` consistent with the GOF of dipoles returned by :func:`mne.fit_dipole` by `Alex Gramfort`_. - -- :class:`mne.decoding.SlidingEstimator` will now replace ``mne.decoding.TimeDecoding`` to make it generic and fully compatible with scikit-learn, by `Jean-Remi King`_ and `Alex Gramfort`_ - -- :class:`mne.decoding.GeneralizingEstimator` will now replace ``mne.decoding.GeneralizationAcrossTime`` to make it generic and fully compatible with scikit-learn, by `Jean-Remi King`_ and `Alex Gramfort`_ - -- ``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`_ - -- 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`_ - -- Make function ``mne.io.eeglab.read_events_eeglab`` public to allow loading overlapping events from EEGLAB files, by `Jona Sassenhagen`_. - -- :func:`mne.find_events` ``mask_type`` parameter will change from ``'not_and'`` to ``'and'`` in 0.16. - -- Instead of raising an error, duplicate channel names in the data file are now appended with a running number by `Jaakko Leppakangas`_ - -- :func:`mne.io.read_raw_edf` has now ``'auto'`` option for ``stim_channel`` (default in version 0.16) that automatically detects if EDF annotations or GDF events exist in the header and constructs the stim channel based on these events by `Jaakko Leppakangas`_ - -- :meth:`mne.io.Raw.plot_psd` now rejects data annotated bad by default. Turn off with ``reject_by_annotation=False``, by `Eric Larson`_ - -- :func:`mne.set_eeg_reference` and the related methods (e.g., :meth:`mne.io.Raw.set_eeg_reference`) have a new argument ``projection``, which if set to False directly applies an average reference instead of adding an SSP projector, by `Clemens Brunner`_ - -- Deprecate ``plot_trans`` in favor of :func:`mne.viz.plot_alignment` and add ``bem`` parameter for plotting conductor model by `Jaakko Leppakangas`_ - -- ``mne.beamformer.tf_lcmv`` now has a ``raw`` parameter to accommodate epochs objects that already have data loaded with ``preload=True``, with :meth:`mne.Epochs.load_data`, or that are read from disk, by `Eric Larson`_ - -- ``mne.time_frequency.psd_welch`` and :func:`mne.time_frequency.psd_array_welch` now use a Hamming window (instead of a Hann window) by `Clemens Brunner`_ - -- ``picks`` parameter in ``mne.beamformer.lcmv``, ``mne.beamformer.lcmv_epochs``, ``mne.beamformer.lcmv_raw``, ``mne.beamformer.tf_lcmv`` and :func:`mne.beamformer.rap_music` is now deprecated and will be removed in 0.16, by `Britta Westner`_, `Alex Gramfort`_, and `Denis Engemann`_. - -- The keyword argument ``frequencies`` has been deprecated in favor of ``freqs`` in various time-frequency functions, e.g. :func:`mne.time_frequency.tfr_array_morlet`, by `Eric Larson`_ - -- Add ``patterns=False`` parameter in :class:`mne.decoding.ReceptiveField`. Turn on to compute inverse model coefficients, by `Nicolas Barascud`_ - -- The ``scale``, ``scale_time``, and ``unit`` parameters have been deprecated in favor of ``scalings``, ``scalings_time``, and ``units`` in :func:`mne.viz.plot_evoked_topomap` and related functions, by `Eric Larson`_ - -- ``loose`` parameter in inverse solvers has now a default value ``'auto'`` depending if the source space is a surface, volume, or discrete type by `Alex Gramfort`_ and `Yousra Bekhti`_ - -- The behavior of ``'mean_flip'`` label-flipping in :meth:`mne.extract_label_time_course` and related functions has been changed such that the flip, instead of having arbitrary sign, maximally aligns in the positive direction of the normals of the label, by `Eric Larson`_ - -- Deprecate force_fixed and surf_ori in :func:`mne.read_forward_solution` by `Daniel Strohmeier`_ - -- :func:`mne.convert_forward_solution` has a new argument ``use_cps``, which controls whether information on cortical patch statistics is applied while generating surface-oriented forward solutions with free and fixed orientation by `Daniel Strohmeier`_ - -- :func:`mne.write_forward_solution` writes a forward solution as a forward solution with free orientation in X/Y/Z RAS coordinates if it is derived from a forward solution with free orientation and as a forward solution with fixed orientation in surface-based local coordinates otherwise by `Daniel Strohmeier`_ - -- ``loose=None`` in inverse solvers is deprecated, use explicitly ``loose=0`` for fixed constraint and ``loose=1.0`` for free orientations by `Eric Larson`_ - -- Zero-channel-value in PSD calculation in :func:`mne.viz.plot_raw_psd` has been relaxed from error to warning by `Alejandro Weinstein`_ - -- Expose "rank" parameter in :func:`mne.viz.plot_evoked_white` to correct rank estimates on the spot during visualization by `Denis Engemann`_, `Eric Larson`_, `Alex Gramfort`_. - -- Show channel name under mouse cursor on topography plots by `Jussi Nurminen`_ - -- Return maximum response amplitude from :meth:`mne.Evoked.get_peak` - -Authors -~~~~~~~ - -People who contributed to this release (in alphabetical order): - -* akshay0724 -* Alejandro Weinstein -* Alexander Rudiuk -* Alexandre Barachant -* Alexandre Gramfort -* Andrew Dykstra -* Britta Westner -* Chris Bailey -* Chris Holdgraf -* Christian Brodbeck -* Christopher Holdgraf -* Clemens Brunner -* Cristóbal Moënne-Loccoz -* Daniel McCloy -* Daniel Strohmeier -* Denis A. Engemann -* Emily P. Stephen -* Eric Larson -* Fede Raimondo -* Jaakko Leppakangas -* Jean-Baptiste Schiratti -* Jean-Remi King -* Jesper Duemose Nielsen -* Joan Massich -* Jon Houck -* Jona Sassenhagen -* Jussi Nurminen -* Laetitia Grabot -* Laura Gwilliams -* Luke Bloy -* Lukáš Hejtmánek -* Mainak Jas -* Marijn van Vliet -* Mathurin Massias -* Matt Boggess -* Mikolaj Magnuski -* Nicolas Barascud -* Nicole Proulx -* Phillip Alday -* Ramonapariciog Apariciogarcia -* Robin Tibor Schirrmeister -* Rodrigo Hübner -* S. M. Gutstein -* Simon Kern -* Teon Brooks -* Yousra Bekhti diff --git a/doc/changes/v0.16.rst b/doc/changes/v0.16.rst deleted file mode 100644 index 4726b6d3efc..00000000000 --- a/doc/changes/v0.16.rst +++ /dev/null @@ -1,258 +0,0 @@ -.. _changes_0_16: - -Version 0.16 (2018-05-01) -------------------------- - -Changelog -~~~~~~~~~ - -- Add possibility to pass dict of floats as argument to :func:`mne.make_ad_hoc_cov` by `Nathalie Gayraud`_ - -- Add support for metadata in :class:`mne.Epochs` by `Chris Holdgraf`_, `Alex Gramfort`_, `Jona Sassenhagen`_, and `Eric Larson`_ - -- Add support for plotting a dense head in :func:`mne.viz.plot_alignment` by `Eric Larson`_ - -- Allow plotting in user-created mayavi Scene in :func:`mne.viz.plot_alignment` by `Daniel McCloy`_ - -- Reduce memory consumption and do not require data to be loaded in :meth:`mne.Epochs.apply_baseline` by `Eric Larson`_ - -- Add option ``render_bem`` to :meth:`mne.Report.parse_folder` by `Eric Larson`_ - -- Add to :func:`mne.viz.plot_alignment` plotting of coordinate frame axes via ``show_axes`` and terrain-style interaction via ``interaction``, by `Eric Larson`_ - -- Add option ``initial_event`` to :func:`mne.find_events` by `Clemens Brunner`_ - -- Left and right arrow keys now scroll by 25% of the visible data, whereas Shift+left/right scroll by a whole page in :meth:`mne.io.Raw.plot` by `Clemens Brunner`_ - -- Add support for gantry tilt angle determination from Elekta FIF file header by `Chris Bailey`_ - -- Add possibility to concatenate :class:`mne.Annotations` objects with ``+`` or ``+=`` operators by `Clemens Brunner`_ - -- Add support for MaxShield raw files in :class:`mne.Report` by `Eric Larson`_ - -- Add ability to plot whitened data in :meth:`mne.io.Raw.plot`, :meth:`mne.Epochs.plot`, :meth:`mne.Evoked.plot`, and :meth:`mne.Evoked.plot_topo` by `Eric Larson`_ - -- Workaround for reading EGI MFF files with physiological signals that also present a bug from the EGI system in :func:`mne.io.read_raw_egi` by `Federico Raimondo`_ - -- Add support for reading subject height and weight in ``info['subject_info']`` by `Eric Larson`_ - -- Improve online filtering of raw data when plotting with :meth:`mne.io.Raw.plot` to filter in segments in accordance with the default ``skip_by_annotation=('edge', 'bad_acq_skip')`` of :meth:`mne.io.Raw.filter` to avoid edge ringing by `Eric Larson`_ - -- Add support for multiple head position files, plotting of sensors, and control of plotting color and axes in :func:`mne.viz.plot_head_positions` by `Eric Larson`_ - -- Add ability to read and write :class:`Annotations` separate from :class:`mne.io.Raw` instances via :meth:`Annotations.save` and :func:`read_annotations` by `Eric Larson`_ - -- Add option to unset a montage by passing `None` to :meth:`mne.io.Raw.set_montage` by `Clemens Brunner`_ - -- Add sensor denoising via :func:`mne.preprocessing.oversampled_temporal_projection` by `Eric Larson`_ - -- Add ``mne.io.pick.get_channel_types`` which returns all available channel types in MNE by `Clemens Brunner`_ - -- Use standard PCA instead of randomized PCA whitening prior to ICA to increase reproducibility by `Clemens Brunner`_ - -- Plot sEEG electrodes in :func:`mne.viz.plot_alignment` by `Alex Gramfort`_ - -- Add support for any data type like sEEG or ECoG in covariance related functions (estimation, whitening and plotting) by `Alex Gramfort`_ and `Eric Larson`_ - -- Add function ``mne.io.read_annotations_eeglab`` to allow loading annotations from EEGLAB files, by `Alex Gramfort`_ - -- :meth:`mne.io.Raw.set_montage` now accepts a string as its ``montage`` argument; this will set a builtin montage, by `Clemens Brunner`_ - -- Add 4D BTi phantom dataset :func:`mne.datasets.phantom_4dbti.data_path`, by `Alex Gramfort`_ - -- Changed the background color to grey in :func:`mne.viz.plot_alignment` to make helmet more visible, by `Alex Gramfort`_ - -- Add :meth:`mne.io.Raw.reorder_channels`, :meth:`mne.Evoked.reorder_channels`, etc. to reorder channels, by `Eric Larson`_ - -- Add to ``mne coreg`` and :func:`mne.gui.coregistration` by `Eric Larson`_: - - - Improved visibility of points inside the head - - Projection of EEG electrodes - - Orientation of extra points toward the surface - - Scaling points by distance to the head surface - - Display of HPI points - - ICP fitting with convergence criteria - - Faster display updates - - Scaling of ``mri/*.mgz`` files - - Scaling of ``mri/trainsforms/talairach.xfm`` files for conversion to MNI space - -- Add ability to exclude components interactively by clicking on their labels in :meth:`mne.preprocessing.ICA.plot_components` by `Mikołaj Magnuski`_ - -- Add reader for manual annotations of raw data produced by Brainstorm by `Anne-Sophie Dubarry`_ - -- Add eLORETA noise normalization for minimum-norm solvers by `Eric Larson`_ - -- Tighter duality gap computation in ``mne.inverse_sparse.tf_mxne_optim`` and new parametrization with ``alpha`` and ``l1_ratio`` instead of ``alpha_space`` and ``alpha_time`` by `Mathurin Massias`_ and `Daniel Strohmeier`_ - -- Add ``dgap_freq`` parameter in ``mne.inverse_sparse.mxne_optim`` solvers to control the frequency of duality gap computation by `Mathurin Massias`_ and `Daniel Strohmeier`_ - -- Add support for reading Eximia files by `Eric Larson`_ and `Federico Raimondo`_ - -- Add the Picard algorithm to perform ICA for :class:`mne.preprocessing.ICA`, by `Pierre Ablin`_ and `Alex Gramfort`_ - -- Add ability to supply a mask to the plot in :func:`mne.viz.plot_evoked_image` by `Jona Sassenhagen`_ - -- Add ``connectivity=False`` to cluster-based statistical functions to perform non-clustering stats by `Eric Larson`_ - -- Add :func:`mne.time_frequency.csd_morlet` and :func:`mne.time_frequency.csd_array_morlet` to estimate cross-spectral density using Morlet wavelets, by `Marijn van Vliet`_ - -- Add multidictionary time-frequency support to :func:`mne.inverse_sparse.tf_mixed_norm` by `Mathurin Massias`_ and `Daniel Strohmeier`_ - -- Add new DICS implementation as :func:`mne.beamformer.make_dics`, :func:`mne.beamformer.apply_dics`, :func:`mne.beamformer.apply_dics_csd` and :func:`mne.beamformer.apply_dics_epochs`, by `Marijn van Vliet`_ and `Susanna Aro`_ - -Bug -~~~ - -- Fix bug in EEG interpolation code to do nothing if there is no channel to interpolate by `Mainak Jas`_ - -- Fix bug in ``mne.preprocessing.peak_finder`` to output datatype consistently and added input check for empty vectors by `Tommy Clausner`_ - -- Fix bug in :func:`mne.io.read_raw_brainvision` to use the correct conversion for filters from time constant to frequency by `Stefan Appelhoff`_ - -- Fix bug with events when saving split files using :meth:`mne.Epochs.save` by `Eric Larson`_ - -- Fix bug in :class:`mne.decoding.SlidingEstimator` and :class:`mne.decoding.GeneralizingEstimator` to allow :func:`mne.decoding.cross_val_multiscore` to automatically detect whether the ``base_estimator`` is a classifier and use a ``StratifiedKFold`` instead of a ``KFold`` when ``cv`` is not specified, by `Jean-Remi King`_ - -- Fix bug in :func:`mne.set_eeg_reference` to remove an average reference projector when setting the reference to ``[]`` (i.e. do not change the existing reference) by `Clemens Brunner`_ - -- Fix bug in threshold-free cluster enhancement parameter validation (:func:`mne.stats.permutation_cluster_1samp_test` and :func:`mne.stats.permutation_cluster_test`) by `Clemens Brunner`_ - -- Fix bug in :meth:`mne.io.Raw.plot` to correctly display event types when annotations are present by `Clemens Brunner`_ - -- Fix bug in :func:`mne.stats.spatio_temporal_cluster_test` default value for ``threshold`` is now calculated based on the array sizes in ``X``, by `Eric Larson`_ - -- Fix bug in :func:`mne.simulation.simulate_raw` with ``use_cps=True`` where CPS was not actually used by `Eric Larson`_ - -- Fix bug in :func:`mne.simulation.simulate_raw` where 1- and 3-layer BEMs were not properly transformed using ``trans`` by `Eric Larson`_ - -- Fix bug in :func:`mne.viz.plot_alignment` where the head surface file ``-head.fif`` was not used even though present by `Chris Bailey`_ - -- Fix bug when writing compressed sparse column matrices (e.g., Maxwell filtering cross-talk matrices) by `Marijn van Vliet`_ and `Eric Larson`_ - -- Fix bug in :meth:`mne.io.Raw.plot_psd` to correctly deal with ``reject_by_annotation=False`` by `Clemens Brunner`_ - -- Fix bug in :func:`mne.make_fixed_length_events` when hitting corner case problems rounding to sample numbers by `Eric Larson`_ - -- Fix bug in :class:`mne.Epochs` when passing events as list with ``event_id=None`` by `Alex Gramfort`_ - -- Fix bug in ``mne.Report.add_figs_to_section`` when passing :class:`numpy.ndarray` by `Eric Larson`_ - -- Fix bug in CSS class setting in `mne.Report` BEM section by `Eric Larson`_ - -- Fix bug in :class:`Annotations` where annotations that extend to the end of a recording were not extended properly by `Eric Larson`_ - -- Fix bug in :meth:`mne.io.Raw.filter` to properly raw data with acquisition skips in separate segments by `Eric Larson`_ - -- Fix bug in :func:`mne.preprocessing.maxwell_filter` where homogeneous fields were not removed for CTF systems by `Eric Larson`_ - -- Fix computation of average quaternions in :func:`mne.preprocessing.maxwell_filter` by `Eric Larson`_ - -- Fix bug in writing ``raw.annotations`` where empty annotations could not be written to disk, by `Eric Larson`_ - -- Fix support for writing FIF files with acquisition skips by using empty buffers rather than writing zeros by `Eric Larson`_ - -- Fix bug in the ``mne make_scalp_surfaces`` command where ``--force`` (to bypass topology check failures) was ignored by `Eric Larson`_ - -- Fix bug in :func:`mne.preprocessing.maxwell_filter` when providing ``origin`` in ``'meg'`` coordinate frame for recordings with a MEG to head transform (i.e., non empty-room recordings) by `Eric Larson`_ - -- Fix bug in :func:`mne.viz.plot_cov` that ignored ``colorbar`` argument by `Nathalie Gayraud`_ - -- Fix bug when picking CTF channels that could cause data saved to disk to be unreadable by `Eric Larson`_ - -- Fix bug when reading event latencies (in samples) from eeglab files didn't translate indices to 0-based python indexing by `Mikołaj Magnuski`_ - -- Fix consistency between :class:`mne.Epochs` and :func:`mne.stats.linear_regression_raw` in converting between samples and times (:func:`mne.stats.linear_regression_raw` now rounds, instead of truncating) by `Phillip Alday`_ - -- Fix bug in ``mne coreg`` where sphere surfaces were scaled by `Eric Larson`_ - -- Fix bug in :meth:`mne.Evoked.plot_topomap` when using ``proj='interactive'`` mode by `Eric Larson`_ - -- Fix bug when passing ``show_sensors=1`` to :func:`mne.viz.plot_compare_evokeds` resulted in sensors legend placed in lower right of the figure (position 4 in matplotlib), not upper right by `Mikołaj Magnuski`_ - -- Fix handling of annotations when cropping and concatenating raw data by `Alex Gramfort`_ and `Eric Larson`_ - -- Fix bug in :func:`mne.preprocessing.create_ecg_epochs` where ``keep_ecg=False`` was ignored by `Eric Larson`_ - -- Fix bug in :meth:`mne.io.Raw.plot_psd` when ``picks is not None`` and ``picks`` spans more than one channel type by `Eric Larson`_ - -- Fix bug in :class:`mne.make_forward_solution` when passing data with compensation channels (e.g. CTF) that contain bad channels by `Alex Gramfort`_ - -- Fix bug in :meth:`mne.SourceEstimate.get_peak` and :meth:`mne.VolSourceEstimate.get_peak` when there is only a single time point by `Marijn van Vliet`_ - -- Fix bug in :func:`mne.io.read_raw_edf` when reading BDF files stimulus channels are now not scaled anymore by `Clemens Brunner`_ - -API -~~~ - -- Channels with unknown locations are now assigned position ``[np.nan, np.nan, np.nan]`` instead of ``[0., 0., 0.]``, by `Eric Larson`_ - -- Removed unused ``image_mask`` argument from :func:`mne.viz.plot_topomap` by `Eric Larson`_ - -- Unknown measurement dates are now stored as ``info['meas_date'] = None`` rather than using the current date. ``None`` is also now used when anonymizing data and when determining the machine ID for writing files, by `Mainak Jas`_ and `Eric Larson`_ - -- :meth:`mne.Evoked.plot` will now append the number of epochs averaged for the evoked data in the first plot title, by `Eric Larson`_ - -- Changed the line width in :func:`mne.viz.plot_bem` from 2.0 to 1.0 for better visibility of underlying structures, by `Eric Larson`_ - -- Changed the behavior of :meth:`mne.io.Raw.pick_channels` and similar methods to be consistent with :func:`mne.pick_channels` to treat channel list as a set (ignoring order) -- if reordering is necessary use ``inst.reorder_channels``, by `Eric Larson`_ - -- Changed the labeling of some plotting functions to use more standard capitalization and units, e.g. "Time (s)" instead of "time [sec]" by `Eric Larson`_ - -- ``mne.time_frequency.csd_epochs`` has been refactored into :func:`mne.time_frequency.csd_fourier` and :func:`mne.time_frequency.csd_multitaper`, by `Marijn van Vliet`_ - -- ``mne.time_frequency.csd_array`` has been refactored into :func:`mne.time_frequency.csd_array_fourier` and :func:`mne.time_frequency.csd_array_multitaper`, by `Marijn van Vliet`_ - -- Added ``clean_names=False`` parameter to :func:`mne.io.read_raw_ctf` for control over cleaning of main channel names and compensation channel names from CTF suffixes by `Oleh Kozynets`_ - -- The functions ``lcmv``, ``lcmv_epochs``, and ``lcmv_raw`` are now deprecated in favor of :func:`mne.beamformer.make_lcmv` and :func:`mne.beamformer.apply_lcmv`, :func:`mne.beamformer.apply_lcmv_epochs`, and :func:`mne.beamformer.apply_lcmv_raw`, by `Britta Westner`_ - -- The functions ``mne.beamformer.dics``, ``mne.beamformer.dics_epochs`` and ``mne.beamformer.dics_source_power`` are now deprecated in favor of :func:`mne.beamformer.make_dics`, :func:`mne.beamformer.apply_dics`, and :func:`mne.beamformer.apply_dics_csd`, by `Marijn van Vliet`_ - - -Authors -~~~~~~~ - -People who contributed to this release (in alphabetical order): - -* Alejandro Weinstein -* Alexandre Gramfort -* Annalisa Pascarella -* Anne-Sophie Dubarry -* Britta Westner -* Chris Bailey -* Chris Holdgraf -* Christian Brodbeck -* Claire Braboszcz -* Clemens Brunner -* Daniel McCloy -* Denis A. Engemann -* Desislava Petkova -* Dominik Krzemiński -* Eric Larson -* Erik Hornberger -* Fede Raimondo -* Henrich Kolkhorst -* Jean-Remi King -* Jen Evans -* Joan Massich -* Jon Houck -* Jona Sassenhagen -* Juergen Dammers -* Jussi Nurminen -* Kambiz Tavabi -* Katrin Leinweber -* Kostiantyn Maksymenko -* Larry Eisenman -* Luke Bloy -* Mainak Jas -* Marijn van Vliet -* Mathurin Massias -* Mikolaj Magnuski -* Nathalie Gayraud -* Oleh Kozynets -* Phillip Alday -* Pierre Ablin -* Stefan Appelhoff -* Stefan Repplinger -* Tommy Clausner -* Yaroslav Halchenko diff --git a/doc/changes/v0.17.rst b/doc/changes/v0.17.rst deleted file mode 100644 index 49e722c584d..00000000000 --- a/doc/changes/v0.17.rst +++ /dev/null @@ -1,317 +0,0 @@ -.. _changes_0_17: - -Version 0.17 (2018-11-19) -------------------------- - -Changelog -~~~~~~~~~ - -- Add new tutorial for :class:`mne.Annotations` and ``events`` by `Joan Massich`_ and `Alex Gramfort`_ - -- Add support for saving :class:`mne.Annotations` as CSV and TXT files by `Joan Massich`_ and `Alex Gramfort`_ - -- Add :meth:`mne.Epochs.shift_time` that shifts the time axis of :class:`mne.Epochs` by `Thomas Hartmann`_ - -- Add :func:`mne.viz.plot_arrowmap` computes arrowmaps using Hosaka-Cohen transformation from magnetometer or gradiometer data, these arrows represents an estimation of the current flow underneath the MEG sensors by `Sheraz Khan`_ - -- Add :func:`mne.io.read_raw_fieldtrip`, :func:`mne.read_epochs_fieldtrip` and :func:`mne.read_evoked_fieldtrip` to import FieldTrip data. By `Thomas Hartmann`_ and `Dirk Gütlin`_. - -- Add ``rank`` parameter to :func:`mne.compute_covariance`, :func:`mne.cov.regularize` and related functions to preserve data rank and speed up computation using low-rank computations during regularization by `Eric Larson`_ and `Denis Engemann`_ - -- Add new function :func:`mne.read_annotations` that can read annotations in EEGLAB, BrainVision, EDF and Brainstorm formats by `Joan Massich`_ and `Alex Gramfort`_. - -- Add capability to read and save Epochs containing complex data (e.g. after Hilbert-transform) using :meth:`mne.Epochs.save` and :func:`mne.read_epochs`, by `Stefan Repplinger`_, `Eric Larson`_ and `Alex Gramfort`_ - -- Add optically pumped magnetometer dataset and example by `Rasmus Zetter`_ and `Eric Larson`_ - -- Add ``origin`` parameter to :meth:`mne.io.Raw.time_as_index` to allow ``times`` to be relative to this ``origin`` by `Joan Massich`_ - -- Add ``title`` argument to :meth:`mne.SourceEstimate.plot` by `Eric Larson`_ - -- :func:`mne.io.Raw.set_annotations` now changes ``orig_time`` to match ``meas_date`` and shift ``self.annotations.onset`` accordingly. Previous behavior is deprecated and would be removed in 0.18. Work by `Joan Massich`_ - -- Add :func:`mne.compute_source_morph` which creates a :class:`mne.SourceMorph` object to unify morphing any type of source estimates (surface or volume) from one subject to another for group studies. It is now possible to do group studies when working on the volume with MNE. Work by `Tommy Clausner`_ during GSOC 2018 with the help of `Alex Gramfort`_ and `Eric Larson`_. - -- Add ability to pass threshold for EOG to :func:`mne.preprocessing.find_eog_events` and :func:`mne.preprocessing.create_eog_epochs` by `Peter Molfese`_ - -- Add possibility to save :class:`mne.VolSourceEstimate` and :class:`mne.MixedSourceEstimate` to HDF5 format (file extension .h5) with :meth:`mne.VolSourceEstimate.save` and :meth:`mne.MixedSourceEstimate.save` by `Alex Gramfort`_ - -- Add ``replace`` parameter to :meth:`mne.io.Raw.add_events` to allow adding events while removing the old ones on the stim channel by `Alex Gramfort`_ - -- Add ability to pass ``axes`` to ``ts_args`` and ``topomap_args`` of :meth:`mne.viz.plot_evoked_joint` by `Jona Sassenhagen`_ - -- Add ability to pass a precomputed forward solution to :func:`mne.simulation.simulate_raw` by `Eric Larson`_ - -- Add ability to read and write beamformers with :func:`mne.beamformer.read_beamformer` and :class:`mne.beamformer.Beamformer.save` by `Eric Larson`_ - -- Add resting-state source power spectral estimation example ``sphx_glr_auto_examples_datasets_plot_opm_rest_data.py`` by `Eric Larson`_, `Denis Engemann`_, and `Luke Bloy`_ - -- Add :func:`mne.channels.make_1020_channel_selections` to group 10/20-named EEG channels by location, by `Jona Sassenhagen`_ - -- Add helmet for Artemis123 for :func:`mne.viz.plot_alignment` by `Eric Larson`_ - -- Add support for reading MATLAB ``v7.3+`` files in :func:`mne.io.read_raw_eeglab` and :func:`mne.read_epochs_eeglab` via `pymatreader`_ by `Steven Gutstein`_, `Eric Larson`_, and `Thomas Hartmann`_ - -- Add support for raw PSD plots in :meth:`mne.Report.parse_folder` via ``raw_psd`` argument of :class:`mne.Report` by `Eric Larson`_ - -- Add ``trig_shift_by_type`` parameter in :func:`mne.io.read_raw_brainvision` to allow to specify offsets for arbitrary marker types by `Henrich Kolkhorst`_ - -- Add progress bar support to :class:`mne.decoding.SlidingEstimator` and :class:`mne.decoding.GeneralizingEstimator` by `Eric Larson`_ - -- Add interactive visualization of volume source estimates using :func:`mne.viz.plot_volume_source_estimates` by `Mainak Jas`_ - -- Add :func:`mne.head_to_mri` to convert positions from head coordinates to MRI RAS coordinates, by `Joan Massich`_ and `Alex Gramfort`_ - -- Add improved CTF helmet for :func:`mne.viz.plot_alignment` by `Eric Larson`_ - -- Add handling in :func:`mne.combine_evoked` and :func:`mne.grand_average` for input with the same channels in different orders, if required, by `Jona Sassenhagen`_ - -- Add ``split_naming`` parameter to the `mne.io.Raw.save` method to allow for BIDS-compatible raw file name construction by `Teon Brooks`_ - -- Add ``origin`` parameter to :meth:`mne.Evoked.interpolate_bads` and related methods by `Eric Larson`_ - -- Add automated MEG helmet shape approximation to :func:`mne.viz.plot_alignment` by `Eric Larson`_ - -- Add capability to save a :class:`mne.Report` to an HDF5 file to :meth:`mne.Report.save` by `Marijn van Vliet`_ - -- Add :func:`mne.open_report` to read back a :class:`mne.Report` object that was saved to an HDF5 file by `Marijn van Vliet`_ - -- Add multi-taper estimation to :func:`mne.minimum_norm.compute_source_psd` by `Eric Larson`_ - -- Add support for custom, e.g. robust, averaging methods in :meth:`mne.Epochs.average` by `Jona Sassenhagen`_ - -- Add support for Neuromag 122 system by `Alex Gramfort`_ - -- Add function ``mne.io.read_annotations_brainvision`` for reading directly Brainvision marker files by `Alex Gramfort`_ - -- Add :meth:`mne.Report.remove` method to remove existing figures from a report, by `Marijn van Vliet`_ - -- Add sign to output of max-power orientation for :func:`mne.beamformer.make_dics` by `Eric Larson`_ - -- Add support for ``pick_ori='max-power'`` when ``weight_norm=None`` in :func:`mne.beamformer.make_lcmv` by `Marijn van Vliet`_ - -- Add support for ``weight_norm='nai'`` for all ``pick_ori`` options in :func:`mne.beamformer.make_lcmv` by `Marijn van Vliet`_ - -- Add support for ``weight_norm='nai'`` to :func:`mne.beamformer.make_dics` by `Marijn van Vliet`_ - -- Add parameter ``rank=None`` to :func:`mne.beamformer.make_dics` by `Marijn van Vliet`_ - -- Add parameter ``rank='full'`` to :func:`mne.beamformer.make_lcmv`, which can be set to ``None`` to auto-compute the rank of the covariance matrix before regularization by `Marijn van Vliet`_ - -- Handle different time vectors in topography plots using :func:`mne.viz.plot_evoked_topo` by `Jussi Nurminen`_ - -- Speed up :func:`mne.inverse_sparse.mixed_norm` if the ``solver`` parameter is set to ``bcd`` using :func:`scipy.linalg.get_blas_funcs` by `Quentin Bertrand`_ - -Bug -~~~ - -- Fix bug with scaling of data in ``mne.cov._compute_covariance_auto`` that was affecting the :class:`mne.decoding.SPoC` estimator by `David Sabbagh`_ - -- Fix :func:`mne.io.Raw.plot_projs_topomap` by `Joan Massich`_ - -- Fix bug in :func:`mne.minimum_norm.compute_source_psd` where the ``stc.times`` output was scaled by 1000, by `Eric Larson`_ - -- Fix default values for ``'diagonal_fixed'`` estimation method of :func:`mne.compute_covariance` to be ``0.1`` for all channel types, as in :func:`mne.cov.regularize` by `Eric Larson`_ - -- Fix reading edf file annotations by `Joan Massich`_ - -- Fix bug with reading events from BrainVision files by `Stefan Appelhoff`_ - -- Fix bug where :func:`mne.io.read_raw_eeglab` would warn when the stim channel is populated with an array of zeros by `Joan Massich`_ - -- Fix 2nd column of events in BrainVision to no longer store duration but rather be contained by ``raw.annotations`` by `Alex Gramfort`_ - -- Fix checking of the correctness of the ``prepared=True`` argument in :func:`mne.minimum_norm.apply_inverse` and related functions by `Eric Larson`_ - -- Fix bug of not showing ERD's in baseline rescaled tfr topomaps if grads are combined by `Erkka Heinila`_ - -- Fix bug with FIF I/O where strings were written in UTF-8 format instead of Latin-1 by `Eric Larson`_ - -- Fix bug with reading measurement dates from BrainVision files by `Stefan Appelhoff`_ - -- Fix bug with `mne.fit_dipole` where the residual was returned as ``ndarray`` instead of :class:`mne.Evoked` instance, by `Eric Larson`_ - -- Fix bug with ``mne flash_bem`` when ``flash30`` is not used by `Eric Larson`_ - -- Fix bug with :func:`mne.stats.permutation_cluster_test` and :func:`mne.stats.spatio_temporal_cluster_test` where ``threshold=None`` was not calculated properly for a f-oneway test by `Daniel McCloy`_ and `Eric Larson`_ - -- Fix bug with channel names in ``mgh70`` montage in ``mne.channels.read_montage`` by `Eric Larson`_ - -- Fix duplication of ``info['hpi_meas']`` and ``info['hpi_results']`` by `Sara Sommariva`_ - -- Fix bug in :func:`mne.io.read_raw_edf` when reading large files on Windows by `Marcin Koculak`_ - -- Fix check in :func:`mne.viz.plot_sensors` for invalid channel locations by `Eric Larson`_ - -- Fix bug in :func:`mne.io.read_raw_edf` where GDF files had ``info['highpass']`` and ``info['lowpass']`` set to NaN and ``info['meas_date']`` set incorrectly, by `Eric Larson`_ - -- Fix bug in :func:`mne.preprocessing.ICA.apply` to handle arrays as ``exclude`` property by `Joan Massich`_ - -- Fix bug in ``method='eLORETA'`` for :func:`mne.minimum_norm.apply_inverse` when using a sphere model and saved ``inv`` by `Eric Larson`_ - -- Fix bug in :class:`mne.io.Raw` where warnings were emitted when objects were deleted by `Eric Larson`_ - -- Fix vector data support for :class:`mne.VolSourceEstimate` by `Christian Brodbeck`_ - -- Fix bug with IIR filtering axis in :func:`mne.filter.filter_data` by `Eric Larson`_ - -- Fix bug with non-boxcar windows in :meth:`mne.io.Raw.resample` and :func:`mne.filter.resample` by `Eric Larson`_ - -- Fix bug in :func:`mne.minimum_norm.apply_inverse` where applying an MEG-only inverse would raise an error about needing an average EEG reference by `Eric Larson`_ - -- Fix bug in ``inst.apply_proj()`` where an average EEG reference was always added by `Eric Larson`_ - -- Fix bug in :func:`mne.time_frequency.tfr_morlet`, :func:`mne.time_frequency.tfr_multitaper`, and :func:`mne.time_frequency.tfr_stockwell` where not all data channels were picked by `Eric Larson`_ - -- Fix bug in :meth:`mne.preprocessing.ICA.plot_overlay` and :func:`mne.make_field_map` for CTF data with compensation by `Eric Larson`_ - -- Fix bug in :func:`mne.create_info` passing ``int`` as ``ch_names`` on Windows by `Eric Larson`_ - -- Fix bug in ``mne.realtime.RtEpochs`` where events during the buildup of the buffer were not correctly processed when incoming data buffers are smaller than the epochs by `Henrich Kolkhorst`_ - -- Fix bug in :func:`mne.io.read_raw_brainvision` where 1-indexed BrainVision events were not being converted into 0-indexed mne events by `Steven Bethard`_ - -- Fix bug in :func:`mne.viz.plot_snr_estimate` and :func:`mne.minimum_norm.estimate_snr` where the inverse rank was not properly utilized (especially affecting SSS'ed MEG data) by `Eric Larson`_ - -- Fix error when saving stc as nifti image when using volume source space formed by more than one label by `Alex Gramfort`_ - -- Fix error when interpolating MEG channels with compensation using reference channels (like for CTF data) by `Alex Gramfort`_ - -- Fix bug in :func:`mne.make_sphere_model` where EEG sphere model coefficients were not optimized properly by `Eric Larson`_ - -- Fix bug in :func:`mne.io.read_raw_ctf` to read bad channels and segments from CTF ds files by `Luke Bloy`_ - -- Fix problem with :meth:`mne.io.Raw.add_channels` where ``raw.info['bads']`` was replicated by `Eric Larson`_ - -- Fix bug with :class:`mne.Epochs` where an error was thrown when resizing data (e.g., during :meth:`mne.Epochs.drop_bad`) by `Eric Larson`_ - -- Fix naming of ``raw.info['buffer_size_sec']`` to be ``raw.buffer_size_sec`` as it is a writing parameter rather than a measurement parameter by `Eric Larson`_ - -- Fix EGI-MFF parser not to require ``dateutil`` package by `Eric Larson`_ - -- Fix error when running LCMV on MEG channels with compensation using reference channels (like for CTF data) by `Alex Gramfort`_ - -- Fix the use of :func:`sklearn.model_selection.cross_val_predict` with :class:`mne.decoding.SlidingEstimator` by `Alex Gramfort`_ - -- Fix event sample number increase when combining many Epochs objects with :func:`mne.concatenate_epochs` with by `Jasper van den Bosch`_ - -- Fix title of custom slider images to :class:`mne.Report` by `Marijn van Vliet`_ - -- Fix missing initialization of ``self._current`` in :class:`mne.Epochs` by `Henrich Kolkhorst`_ - -- Fix processing of data with bad segments and acquisition skips with new ``skip_by_annotation`` parameter in :func:`mne.preprocessing.maxwell_filter` by `Eric Larson`_ - -- Fix symlinking to use relative paths in ``mne flash_bem`` and ``mne watershed_bem`` by `Eric Larson`_ - -- Fix error in mne coreg when saving with scaled MRI if fiducials haven't been saved by `Ezequiel Mikulan`_ - -- Fix normalization error in :func:`mne.beamformer.make_lcmv` when ``pick_ori='normal', weight_norm='unit_noise_gain'`` by `Marijn van Vliet`_ - -- Fix MNE-C installation instructions by `buildqa`_ - -- Fix computation of max-power orientation in :func:`mne.beamformer.make_dics` when ``pick_ori='max-power', weight_norm='unit_noise_gain'`` by `Marijn van Vliet`_ - -API -~~~ - -- Deprecated separate reading of annotations and synthesis of STI014 channels in readers by `Joan Massich`_: - - - Deprecated ``mne.io.read_annotations_eeglab`` - - Deprecated ``annot`` and ``annotmap`` parameters in :meth:`~mne.io.read_raw_edf` - - Deprecated ``stim_channel`` parameters in :func:`~mne.io.read_raw_edf`, :func:`~mne.io.read_raw_brainvision`, and :func:`~mne.io.read_raw_eeglab` - - Annotations are now added to ``raw`` instances directly upon reading as :attr:`raw.annotations `. - They can also be read separately with :func:`mne.read_annotations` for EEGLAB, BrainVision, EDF, and Brainstorm formats. - Use :func:`mne.events_from_annotations(raw.annotations) ` - to convert these to events instead of the old way (using STI014 channel synthesis followed by :func:`mne.find_events(raw) `). - - In 0.17 (this release) - Use ``read_raw_...(stim_channel=False)`` to disable warnings (and stim channel synthesis), but other arguments for ``stim_channel`` will still be supported. - - In 0.18 - The only supported option will be ``read_raw_...(stim_channel=False)``, and all stim-channel-synthesis arguments will be removed. At this point, ``stim_channel`` should be removed from scripts for future compatibility, but ``stim_channel=False`` will still be acceptable for backward compatibility. - - In 0.19 - The ``stim_channel`` keyword arguments will be removed from ``read_raw_...`` functions. - -- 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`_ - -- Deprecated ``mne.SourceEstimate.morph_precomputed``, ``mne.SourceEstimate.morph``, ``mne.compute_morph_matrix``, ``mne.morph_data_precomputed`` and ``mne.morph_data`` in favor of :func:`mne.compute_source_morph`, by `Tommy Clausner`_ - -- Prepare transition to Python 3. This release will be the last release compatible with Python 2. The next version will be Python 3 only. - -- CUDA support now relies on CuPy_ instead of ``PyCUDA`` and ``scikits-cuda``. It can be installed using ``conda install cupy``. By `Eric Larson`_ - -- Functions requiring a color cycle will now default to Matplotlib rcParams colors, by `Stefan Appelhoff`_ - -- :meth:`mne.Evoked.plot_image` has gained the ability to ``show_names``, and if a selection is provided to ``group_by``, ``axes`` can now receive a `dict`, by `Jona Sassenhagen`_ - -- Calling :meth:`mne.Epochs.decimate` with ``decim=1`` no longer copies the data by `Henrich Kolkhorst`_ - -- Removed blocking (waiting for new epochs) in ``mne.realtime.RtEpochs.get_data()`` by `Henrich Kolkhorst`_ - -- Warning messages are now only emitted as :func:`warnings.warn_explicit` rather than also being emitted as ``logging`` messages (unless a logging file is being used) to avoid duplicate warning messages, by `Eric Larson`_ - -- Deprecated save_stc_as_volume function in favor of :meth:`mne.VolSourceEstimate.as_volume` and :meth:`mne.VolSourceEstimate.save_as_volume` by `Alex Gramfort`_ - -- ``src.kind`` now equals to ``'mixed'`` (and not ``'combined'``) for a mixed source space (made of surfaces and volume grids) by `Alex Gramfort`_ - -- Deprecation of :attr:`mne.io.Raw.annotations` property in favor of :meth:`mne.io.Raw.set_annotations` by `Joan Massich`_ - -- The default value of ``stop_receive_thread`` in ``mne.realtime.RtEpochs.stop`` has been changed to ``True`` by `Henrich Kolkhorst`_ - -- Using the :meth:`mne.io.Raw.add_channels` on an instance with memmapped data will now resize the memmap file to append the new channels on Windows and Linux, by `Eric Larson`_ - -- :attr:`mne.io.Raw.annotations` when missing is set to an empty :class:`mne.Annotations` rather than ``None`` by `Joan Massich`_ and `Alex Gramfort`_ - -- Mismatches in CTF compensation grade are now checked in inverse computation by `Eric Larson`_ - - -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 diff --git a/doc/changes/v0.18.rst b/doc/changes/v0.18.rst deleted file mode 100644 index 4e73e42239b..00000000000 --- a/doc/changes/v0.18.rst +++ /dev/null @@ -1,268 +0,0 @@ -.. _changes_0_18: - -Version 0.18 (2019-05-19) -------------------------- - -Changelog -~~~~~~~~~ - -- Add ``event_id='auto'`` in :func:`mne.events_from_annotations` to accommodate Brainvision markers by `Jona Sassenhagen`_, `Joan Massich`_ and `Eric Larson`_ - -- Add example on how to simulate raw data using subject anatomy, by `Ivana Kojcic`_, `Eric Larson`_, `Samuel Deslauriers-Gauthier`_ and `Kostiantyn Maksymenko`_ - -- :func:`mne.beamformer.apply_lcmv_cov` returns static source power after supplying a data covariance matrix to the beamformer filter by `Britta Westner`_ and `Marijn van Vliet`_ - -- Add ``butterfly`` and ``order`` arguments to :func:`mne.viz.plot_epochs` and offer separated traces for non-meg data (seeg, eeg, ecog) in butterfly view by `Stefan Repplinger`_ and `Eric Larson`_ - -- :meth:`mne.Epochs.get_data` now takes a ``picks`` parameter by `Jona Sassenhagen`_ - -- :func:`~mne.viz.plot_compare_evokeds` will generate topo plots if ``axes='topo'`` by `Jona Sassenhagen`_ - -- ``mne.viz.iter_topography`` can yield an additional axis, e.g., for plotting legends by `Jona Sassenhagen`_ and `Daniel McCloy`_ - -- Default plot title reflects channel type when ``picks`` is a channel type in :func:`~mne.viz.plot_compare_evokeds` by `Daniel McCloy`_ - -- Color scale limits in :func:`~mne.viz.plot_topo_image_epochs` are now computed separately per channel type in combined mag/grad plots, by `Daniel McCloy`_ - -- :func:`mne.simulation.simulate_stc` now allows for label overlaps by `Nathalie Gayraud`_, and `Ivana Kojcic`_ - -- Add ``long_format`` option to the pandas dataframe exporters, e.g :meth:`mne.Epochs.to_data_frame` by `Denis Engemann`_ - -- Add example on how to load standard montage :ref:`plot_montage` by `Joan Massich`_ - -- Add new tutorial on :ref:`tut-eeg-fsaverage-source-modeling` by `Alex Gramfort`_, and `Joan Massich`_ - -- Add :meth:`mne.Epochs.apply_hilbert` and :meth:`mne.Evoked.apply_hilbert` by `Eric Larson`_ - -- Add convenience ``fsaverage`` subject dataset fetcher / updater :func:`mne.datasets.fetch_fsaverage` by `Eric Larson`_ - -- Add ``fmin`` and ``fmax`` argument to :meth:`mne.time_frequency.AverageTFR.crop` and to :meth:`mne.time_frequency.EpochsTFR.crop` to crop TFR objects along frequency axis by `Dirk Gütlin`_ - -- Add support to :func:`mne.read_annotations` to read CNT formats by `Joan Massich`_ - -- Add ``reject`` parameter to :meth:`mne.preprocessing.ICA.plot_properties` to visualize rejected epochs by `Antoine Gauthier`_ - -- Add support for picking channels using channel name and type strings to functions with ``picks`` arguments, along with a convenience :meth:`mne.io.Raw.pick`, :meth:`mne.Epochs.pick`, and :meth:`mne.Evoked.pick` method, by `Eric Larson`_ - -- Add new tutorial on :ref:`tut-sleep-stage-classif` by `Alex Gramfort`_, `Stanislas Chambon`_ and `Joan Massich`_ - -- Add data fetchers for polysomnography (PSG) recordings from Physionet (:func:`mne.datasets.sleep_physionet.age.fetch_data` and :func:`mne.datasets.sleep_physionet.temazepam.fetch_data`) by `Alex Gramfort`_ and `Joan Massich`_ - -- Add envelope correlation code in ``mne.connectivity.envelope_correlation`` by `Denis Engemann`_, `Sheraz Khan`_, and `Eric Larson`_ - -- Add option to toggle all projectors in :meth:`mne.io.Raw.plot` and related functions by `Eric Larson`_ - -- Add support for indexing, slicing, and iterating :class:`mne.Annotations` by `Joan Massich`_ - -- :meth:`mne.io.Raw.plot` now uses the lesser of ``n_channels`` and ``raw.ch_names``, by `Joan Massich`_ - -- Add support for FIR filtering in :meth:`mne.io.Raw.plot` and :ref:`mne browse_raw` by passing ``filtorder=0`` or ``--filtorder 0``, respectively, by `Eric Larson`_ - -- Add ``chunk_duration`` parameter to :func:`mne.events_from_annotations` to allow multiple events from a single annotation by `Joan Massich`_ - -- Add :class:`mne.simulation.SourceSimulator` class to simplify simulating SourceEstimates, by `Samuel Deslauriers-Gauthier`_, `Kostiantyn Maksymenko`_, `Nathalie Gayraud`_, `Ivana Kojcic`_, `Alex Gramfort`_, and `Eric Larson`_ - -- :func:`mne.io.read_raw_edf` now detects analog stim channels labeled ``'STATUS'`` and sets them as stim channel. :func:`mne.io.read_raw_edf` no longer synthesize TAL annotations into stim channel but stores them in ``raw.annotations`` when reading by `Joan Massich`_ - -- Add `mne.simulation.add_noise` for ad-hoc noise addition to `io.Raw`, `Epochs`, and `Evoked` instances, by `Eric Larson`_ - -- Add ``drop_refs=True`` parameter to :func:`set_bipolar_reference` to drop/keep anode and cathode channels after applying the reference by `Cristóbal Moënne-Loccoz`_. - -- Add processing of reference MEG channels to :class:`mne.preprocessing.ICA` by `Jevri Hanna`_ - -- Add use of :func:`scipy.signal.windows.dpss` for faster multitaper window computations in PSD functions by `Eric Larson`_ - -- Add :func:`mne.morph_labels` to facilitate morphing label sets obtained from parcellations, by `Eric Larson`_ - -- Add :func:`mne.labels_to_stc` to facilitate working with label data, by `Eric Larson`_ - -- Add :func:`mne.label.select_sources` to simplify the selection of sources within a label, by `Samuel Deslauriers-Gauthier`_ - -- Add support for using :class:`mne.Info` in :func:`mne.simulation.simulate_raw` instead of :class:`mne.io.Raw` by `Eric Larson`_ - -- Add support for passing an iterable and stim channel values using ``stc`` parameter of :func:`mne.simulation.simulate_raw` by `Eric Larson`_ - -- Add ``overlap`` argument to :func:`mne.make_fixed_length_events` by `Eric Larson`_ - -- Add approximate distance-based ``spacing`` source space decimation algorithm to :func:`mne.setup_source_space` by `Eric Larson`_ - -- Add 448-labels subdivided aparc cortical parcellation by `Denis Engemann`_ and `Sheraz Khan`_ - -- Add option to improve rendering in :ref:`mne coreg` for modern graphics cards by `Eric Larson`_ - -- Add ``mne.preprocessing.mark_flat`` to automate marking of flat channels and segments of raw data by `Eric Larson`_ - -- Add support for CUDA-based correlation computations and progress bars in :class:`mne.decoding.ReceptiveField` by `Eric Larson`_ - -- Add support for file-like objects in :func:`mne.io.read_raw_fif` as long as preloading is used by `Eric Larson`_ - -- Add keyboard shortcuts to nativate volume source estimates in time using (shift+)left/right arrow keys by `Mainak Jas`_ - -- Add option to SSP preprocessing functions (e.g., :func:`mne.preprocessing.compute_proj_eog` and :func:`mne.compute_proj_epochs`) to process MEG channels jointly with ``meg='combined'`` by `Eric Larson`_ - -- Add Epoch selection and metadata functionality to :class:`mne.time_frequency.EpochsTFR` using new mixin class by `Keith Doelling`_ - -- Add ``reject_by_annotation`` argument to :func:`mne.preprocessing.find_ecg_events` by `Eric Larson`_ - -- Add ``pca`` argument to return the rank-reduced whitener in :func:`mne.cov.compute_whitener` by `Eric Larson`_ - -- Add ``extrapolate`` argument to :func:`mne.viz.plot_topomap` for better control of extrapolation points placement by `Mikołaj Magnuski`_ - -- Add ``channel_wise`` argument to :func:`mne.io.Raw.apply_function` to allow applying a function on multiple channels at once by `Hubert Banville`_ - -- Add option ``copy='auto'`` to control data copying in :class:`mne.io.RawArray` by `Eric Larson`_ - -- The ``mri`` parameter in :func:`mne.setup_volume_source_space` is now automatically set to ``T1.mgz`` if ``subject`` is provided. This allows to get a :class:`mne.SourceSpaces` of kind ``volume`` more automatically. By `Alex Gramfort`_ - -- Add better ``__repr__`` for constants, and :class:`info['dig'] ` entries via ``DigPoint`` by `Eric Larson`_ - -- Allow string argument in :meth:`mne.io.Raw.drop_channels` to remove a single channel by `Clemens Brunner`_ - -- Add additional depth weighting options for inverse solvers (e.g., :func:`mne.inverse_sparse.gamma_map` and :func:`mne.inverse_sparse.mixed_norm`) by `Eric Larson`_ - -- Add depth weighting to LCMV beamformers via ``depth`` argument in :func:`mne.beamformer.make_lcmv` by `Eric Larson`_ - -- Allow toggling of DC removal in :meth:`mne.io.Raw.plot` by pressing the 'd' key by `Clemens Brunner`_ - -- Improved clicking in :meth:`mne.io.Raw.plot` (left click on trace toggles bad, left click on background sets green line, right click anywhere removes green line) by `Clemens Brunner`_ - -- Add ``mne.realtime.LSLClient`` for realtime data acquisition with LSL streams of data by `Teon Brooks`_ and `Mainak Jas`_ - -- Add partial support for PyVista as a 3D backend using :func:`mne.viz.use_3d_backend` by `Guillaume Favelier`_ - -- Add option ``ids = None`` in :func:`mne.event.shift_time_events` for considering all events by `Nikolas Chalas`_ and `Joan Massich`_ - -- Add ``mne.realtime.MockLSLStream`` to simulate an LSL stream for testing and examples by `Teon Brooks`_ - -- Add support for file-like objects in :func:`mne.read_epochs` as long as preloading is used by `Paul Roujansky`_ - -Bug -~~~ - -- Fix annotations in split fif files :func:`mne.io.read_raw_fif` by `Joan Massich`_ - -- Fix :meth:`mne.Epochs.plot` with ``scalings='auto'`` to properly compute channel-wise scalings by `Stefan Repplinger`_ - -- Fix :func:`mne.gui.coregistration` and :ref:`mne coreg` crashing with segmentation fault when switching subjects by `Eric Larson`_ - -- Fix :func:`mne.io.read_raw_brainvision` to accommodate vmrk files which do not have any annotations by Alexander Kovrig - -- Fix :meth:`mne.io.Raw.plot` and :meth:`mne.Epochs.plot` to auto-scale ``misc`` channel types by default by `Eric Larson`_ - -- Fix filtering functions (e.g., :meth:`mne.io.Raw.filter`) to properly take into account the two elements in ``n_pad`` parameter by `Bruno Nicenboim`_ - -- Fix ``feature_names`` parameter change after fitting in :class:`mne.decoding.ReceptiveField` by `Jean-Remi King`_ - -- Fix index error in :func:`mne.io.read_raw_cnt` when creating stim_channel manually by `Joan Massich`_ - -- Fix bug with ``weight_norm='unit-gain'`` in :func:`mne.beamformer.make_lcmv` and :func:`mne.beamformer.make_dics` by `Britta Westner`_ - -- Fix 32bits annotations in :func:`mne.io.read_raw_cnt` by `Joan Massich`_ - -- Fix :func:`mne.events_from_annotations` to ignore ``'BAD_'`` and ``'EDGE_'`` annotations by default using a new default ``regexp`` by `Eric Larson`_ - -- Fix bug in ``mne.preprocessing.mark_flat`` where ``raw.first_samp`` was not taken into account by `kalenkovich`_ - -- Fix date parsing in :func:`mne.io.read_raw_cnt` by `Joan Massich`_ - -- Fix topological checks and error messages for BEM surfaces in :func:`mne.make_bem_model` by `Eric Larson`_ - -- Fix default HTML language of :class:`mne.Report` to be ``"en-us"`` instead of ``"fr"`` and allow setting via ``report.lang`` property by `Eric Larson`_ - -- Fix bug where loading epochs with ``preload=True`` and subsequently using :meth:`mne.Epochs.drop_bad` with new ``reject`` or ``flat`` entries leads to improper data (and ``epochs.selection``) since v0.16.0 by `Eric Larson`_. - If your code uses ``Epochs(..., preload=True).drop_bad(reject=..., flat=...)``, we recommend regenerating these data. - -- Fix :ref:`mne flash_bem` to properly utilize ``flash30`` images when conversion from DICOM images is used, and to properly deal with non-standard acquisition affines by `Eric Larson`_ - -- Fix :meth:`mne.io.Raw.set_annotations` with ``annotations=None`` to create an empty annotations object with ``orig_time`` that matches the :class:`mne.io.Raw` instance by `Eric Larson`_ - -- Fix :func:`mne.io.read_raw_edf` returning all the annotations with the same name in GDF files by `Joan Massich`_ - -- Fix boundaries during plotting of raw data with :func:`mne.io.Raw.plot` and :ref:`mne browse_raw` on scaled displays (e.g., macOS with HiDPI/Retina screens) by `Clemens Brunner`_ - -- Fix bug where filtering was not performed with ``lowpass`` or ``highpass`` in :meth:`mne.io.Raw.plot` and :ref:`mne browse_raw` by `Eric Larson`_ - -- Fix :func:`mne.simulation.simulate_evoked` that was failing to simulate the noise with heterogeneous sensor types due to poor conditioning of the noise covariance and make sure the projections from the noise covariance are taken into account `Alex Gramfort`_ - -- Fix checking of ``data`` dimensionality in :class:`mne.SourceEstimate` and related constructors by `Eric Larson`_ - -- Fix :meth:`mne.io.Raw.append` annotations miss-alignment by `Joan Massich`_ - -- Fix hash bug in the ``mne.io.edf`` module when installing on Windows by `Eric Larson`_ - -- Fix :func:`mne.io.read_raw_edf` reading duplicate channel names by `Larry Eisenman`_ - -- Fix :func:`set_bipolar_reference` in the case of generating all bipolar combinations and also in the case of repeated channels in both lists (anode and cathode) by `Cristóbal Moënne-Loccoz`_ - -- Fix missing code for computing the median when ``method='median'`` in :meth:`mne.Epochs.average` by `Cristóbal Moënne-Loccoz`_ - -- Fix CTF helmet plotting in :func:`mne.viz.plot_evoked_field` by `Eric Larson`_ - -- Fix saving of rejection parameters in :meth:`mne.Epochs.save` by `Eric Larson`_ - -- Fix orientations returned by :func:`mne.dipole.get_phantom_dipoles` (half were flipped 180 degrees) by `Eric Larson`_ - -- Fix bug in :func:`mne.viz.plot_compare_evokeds` when ``evoked.times[0] >= 0`` would cause a problem with ``vlines='auto'`` mode by `Eric Larson`_ - -- Fix path bugs in :func:`mne.bem.make_flash_bem` and :ref:`mne flash_bem` by `Eric Larson`_ - -- Fix :meth:`mne.time_frequency.AverageTFR.plot_joint` mishandling bad channels, by `David Haslacher`_ and `Jona Sassenhagen`_ - -- Fix :func:`mne.beamformer.make_lcmv` failing when full rank data is used (i.e., when no projection is done) with ``reg=0.``, by `Eric Larson`_ - -- Fix issue with bad channels ignored in :func:`mne.beamformer.make_lcmv` and :func:`mne.beamformer.make_dics` by `Alex Gramfort`_ - -- Fix :func:`mne.compute_proj_raw` when ``duration != None`` not to apply existing proj and to avoid using duplicate raw data samples by `Eric Larson`_ - -- Fix ``reject_by_annotation`` not being passed internally by :func:`mne.preprocessing.create_ecg_epochs` and :ref:`mne clean_eog_ecg` to :func:`mne.preprocessing.find_ecg_events` by `Eric Larson`_ - -- Fix :func:`mne.io.read_raw_edf` failing when EDF header fields (such as patient name) contained special characters, by `Clemens Brunner`_ - -- Fix :func:`mne.io.read_raw_eeglab` incorrectly parsing event durations by `Clemens Brunner`_ - -- Fix :func:`mne.io.read_raw_egi` when cropping non-preloaded EGI MFF data by `Alex Gramfort`_ - -- Fix :meth:`mne.io.Raw.interpolate_bads` for interpolating CTF MEG channels when reference sensors are present by `jeythekey`_ - -- Fix a bug in :meth:`mne.io.Raw.resample`, where resampling events could result in indices > n_times-1, by `jeythekey`_ - -- Fix :meth:`mne.preprocessing.ICA.score_sources` to use the ``sfreq`` of the raw data to filter rather than the ``sfreq`` when the ICA was fit, by `jeythekey`_ - -- Fix a bug in :class:`mne.preprocessing.ICA`, where manually setting the attribute ``ICA.exclude`` to an np.array resulted in the removal of random components when later also providing the ``exclude`` argument to any ``apply...``-method, by `jeythekey`_ - -- Ascending changed to descending sorting of scores for integer ``..._criterion`` arguments in ``mne.preprocessing.ICA.detect_artifacts`` and ``mne.preprocessing.run_ica``, as it used to be documented; the docstring in these functions was corrected for float ``..._criterion`` arguments, by `jeythekey`_ - -API -~~~ - -- Deprecate ``cov, iir_params, blink, ecg, chpi, random_state`` and support for :class:`mne.io.Raw` instance inputs in :func:`mne.simulation.simulate_raw`; use :func:`mne.simulation.add_noise`, :func:`mne.simulation.add_ecg`, :func:`mne.simulation.add_eog`, and :func:`mne.simulation.add_chpi` by `Eric Larson`_ - -- Add ``overwrite`` parameter in :func:`mne.Epochs.save` by `Katarina Slama`_ - -- Add ``stim_channel`` parameter in :func:`mne.io.read_raw_cnt` to toggle stim channel synthesis by `Joan Massich`_ - -- Python 2 is no longer supported; MNE-Python now requires Python 3.5+, by `Eric Larson`_ - -- A new class :class:`mne.VolVectorSourceEstimate` is returned by :func:`mne.minimum_norm.apply_inverse` (and related functions) when a volume source space and ``pick_ori='vector'`` is used, by `Eric Larson`_ - -- Converting a forward solution with a volume source space to fixed orientation using :func:`mne.convert_forward_solution` now raises an error, by `Eric Larson`_ - -- ``raw.estimate_rank`` has been deprecated and will be removed in 0.19 in favor of :func:`mne.compute_rank` by `Eric Larson`_ - -- :class:`Annotations` are now kept sorted (by onset time) during instantiation and :meth:`~Annotations.append` operations, by `Eric Larson`_ - -- Deprecate ``mne.io.find_edf_events`` by `Joan Massich`_ - -- Deprecate ``limit_depth_chs`` in :func:`mne.minimum_norm.make_inverse_operator` in favor of ``depth=dict(limit_depth_chs=...)`` by `Eric Larson`_ - -- Reading BDF and GDF files with :func:`mne.io.read_raw_edf` is deprecated and replaced by :func:`mne.io.read_raw_bdf` and :func:`mne.io.read_raw_gdf`, by `Clemens Brunner`_ - -- :func:`mne.forward.compute_depth_prior` has been reworked to operate directly on :class:`Forward` instance as ``forward`` rather than a representation scattered across the parameters ``G, is_fixed_ori, patch_info``, by `Eric Larson`_ - -- Deprecate ``method='extended-infomax'`` in :class:`mne.preprocessing.ICA`; Extended Infomax can now be computed with ``method='infomax'`` and ``fit_params=dict(extended=True)`` by `Clemens Brunner`_ - -- Fix support for supplying ``extrapolate`` via :meth:`ica.plot_properties(..., topomap_args=dict(extrapolate=...)) ` by `Sebastian Castano`_ - -- The peak finder that was formerly accessible via ``from mne.preprocessing.peak_finder import peak_finder`` should now be imported directly from the enclosing namespace as ``from mne.preprocessing import peak_finder`` by `Eric Larson`_ - -- Deprecate ``mne.realtime`` module to make a standalone module ``mne-realtime`` that will live outside of this package by `Teon Brooks`_ diff --git a/doc/changes/v0.19.rst b/doc/changes/v0.19.rst deleted file mode 100644 index 5e34210868a..00000000000 --- a/doc/changes/v0.19.rst +++ /dev/null @@ -1,232 +0,0 @@ -.. _changes_0_19: - -Version 0.19 (2019-09-24) -------------------------- - -Changelog -~~~~~~~~~ - -- Add :func:`mne.cuda.set_cuda_device` and config variable ``MNE_CUDA_DEVICE`` to select among multiple GPUs (by numeric device ID) by `Daniel McCloy`_. - -- Add :func:`mne.channels.make_standard_montage` to create :class:`mne.channels.DigMontage` from templates by `Joan Massich`_ and `Alex Gramfort`_. - -- Add :func:`mne.channels.compute_dev_head_t` to compute Device-to-Head transformation from a montage by `Joan Massich`_ and `Alex Gramfort`_. - -- Add :func:`mne.channels.read_dig_fif` to read digitization coordinates from ``.fif`` files by `Joan Massich`_ and `Alex Gramfort`_. - -- Add :func:`mne.channels.read_dig_egi` to read digitization coordinates from EGI ``.xml`` files by `Joan Massich`_ and `Alex Gramfort`_. - -- Add :func:`mne.channels.read_dig_polhemus_isotrak` and :func:`mne.channels.read_polhemus_fastscan` to read Polhemus data by `Joan Massich`_ - -- Add ``mne.channels.read_dig_captrack`` to read BrainVision CapTrak (BVCT) digitization coordinate files by `Stefan Appelhoff`_ and `Joan Massich`_ - -- Add :func:`mne.channels.make_dig_montage` to create :class:`mne.channels.DigMontage` objects out of np.arrays by `Joan Massich`_ - -- Add :func:`mne.channels.read_custom_montage` to read various EEG electrode locations files by `Joan Massich`_ and `Alex Gramfort`_. - -- Add support for making epochs with duplicated events, by allowing three policies: "error" (default), "drop", or "merge" in :class:`mne.Epochs` by `Stefan Appelhoff`_ - -- Allow :meth:`mne.Annotations.crop` to support negative ``tmin`` and ``tmax`` by `Joan Massich`_ - -- Unknown events code in GDF are now visible in the ``event_id`` by `Théodore Papadopoulo`_ - -- Now :func:`mne.io.read_raw_ctf` populates ``raw.annotations`` with the markers in ``MarkerFile.mrk`` if any by `Joan Massich`_ - -- Add options for controlling the use of the ``-T1`` flag and the location of the brainmask output in :ref:`mne watershed_bem` by `Eric Larson`_ - -- Add support to :func:`mne.read_annotations` to read CTF marker files by `Joan Massich`_ - -- Do not convert effective number of averages (``nave`` attribute of :class:`mne.Evoked`) to integer except when saving to FIFF file by `Daniel McCloy`_. - -- Add automatic fiducial position estimation in :ref:`mne coreg` using MNI Talairach fiducial locations in :func:`mne.coreg.get_mni_fiducials` by `Jon Houck`_ and `Eric Larson`_ - -- Add support for :ref:`mne coreg` scaling surrogate subjects without surface reconstructions, such as those created for volumetric analyses only (e.g., with ``recon-all -autorecon1``) by `Eric Larson`_ - -- Add reader for Curry data in :func:`mne.io.read_raw_curry` by `Dirk Gütlin`_ - -- Butterfly channel plots now possible for :meth:`mne.Epochs.plot_psd` with ``average=False``. Infrastructure for this function now shared with analogous Raw function, found in ``mne.viz.utils`` by `Jevri Hanna`_ - -- Add option not to orthogonalize power envelopes with ``orthogonalize=False`` in ``mne.connectivity.envelope_correlation`` by `Denis Engemann`_ - -- Accept filenames of raw .fif files that end in ``_meg.fif`` to enable complicance with the Brain Imaging Data Structure by `Stefan Appelhoff`_ - -- Add function to check the type of a FIF file using :func:`mne.what` and :ref:`mne what` by `Eric Larson`_ - -- Add support for specifying the initial time and/or position and providing a :class:`mne.SourceMorph` instead of :class:`mne.SourceSpaces` in :func:`mne.viz.plot_volume_source_estimates` by `Eric Larson`_ - -- Speed up morph map generation in :func:`mne.read_morph_map` by ~5-10x by using :func:`numba.jit` by `Eric Larson`_ - -- Speed up :func:`mne.setup_volume_source_space`, especially when ``volume_label is not None`` by `Eric Larson`_ - -- Speed up :ref:`mne coreg` interactive and automated (ICP) alignment by using nearest-neighbor calculations in the MRI coordinate frame, by `Eric Larson`_ - -- Add :func:`mne.dig_mri_distances` to compute the distances between digitized head points and the MRI head surface by `Alex Gramfort`_ and `Eric Larson`_ - -- Add scale bars for data channels in :func:`mne.io.Raw.plot` by `Eric Larson`_ - -- Add :func:`mne.viz.plot_brain_colorbar` to plot a colorbar appropriately matched to a :func:`mne.viz.plot_source_estimates` plot by `Eric Larson`_ - -- Add support for showing head surface (to visualize digitization fit) while showing a single-layer BEM to :func:`mne.viz.plot_alignment` by `Eric Larson`_ - -- Add option ``include_tmax=True`` to cropping methods :meth:`mne.io.Raw.crop`, :meth:`mne.Epochs.crop`, :meth:`mne.Evoked.crop`, :meth:`mne.SourceEstimate.crop`, :meth:`mne.Dipole.crop`, and :meth:`mne.time_frequency.AverageTFR.crop` by `Eric Larson`_ - -- Change the behavior of :meth:`mne.io.Raw.plot` for ``scalings='auto'`` and ``remove_dc=True`` to compute the scalings on the data with DC removed by `Clemens Brunner`_ - -- Allow creating annotations within existing annotations in :func:`mne.io.Raw.plot` by default (the old snapping behavior can be toggled by pressing 'p') by `Clemens Brunner`_ - -- Add plotting of rank estimates in :func:`mne.viz.plot_cov` by `Eric Larson`_ - -- Add a new ``mne.viz.plot_sensors_connectivity`` function to visualize the sensor connectivity in 3D by `Guillaume Favelier`_ and `Alex Gramfort`_ - -- Add support for ``info['utc_offset']``, ``info['device_info']``, and ``info['helium_info']`` components of :class:`mne.Info` by `Eric Larson`_ - -- Add control over dipole colors in :func:`mne.viz.plot_dipole_locations` when using orthoview mode by `Eric Larson`_ - -- Use second-order-sections filtering in :meth:`mne.io.Raw.plot` and :ref:`mne browse_raw` by `Eric Larson`_ - -- Add re-referencing functionality for ecog and seeg channel types in :func:`mne.set_eeg_reference` by `Keith Doelling`_ - -- Add support for median averaging and for returning unaggregated segments in ``mne.time_frequency.psd_welch`` by `Richard Höchenberger`_ - -- :func:`io.read_raw_kit`: add support for NYU New York 2019 system update, by `Christian Brodbeck`_ - - -Bug -~~~ - -- Fix setting montage eeg ref position for captrak by `Joan Massich`_ - -- Fix saving raw read from BDF file using ``tmin`` and ``tmax`` using ``preload=False`` by `Alex Gramfort`_ - -- Fix :func:`mne.grand_average` to use equal sum-to-one weights (like it used to, before changes to underlying :func:`mne.combine_evoked`) by `Daniel McCloy`_ - -- Fix :meth:`mne.io.Raw.filter` to deal with instances with no data channels properly by `Eric Larson`_ - -- Fix one-sample baseline issue in :class:`mne.BaseEpochs` when using ``tmin=0`` by `Milan Rybář`_ - -- Fix bug in :func:`mne.viz.plot_volume_source_estimates` where ``'glass_brain'`` MRIs were not transformed to MNI space, by `Eric Larson`_ - -- Fix bug in :func:`mne.viz.plot_volume_source_estimates` where MRIs with voxels not in RAS orientation could not be browsed properly, by `Eric Larson`_ - -- Fix bug in :meth:`mne.SourceMorph.apply` where output STCs had ``stc.vertices`` defined improperly, by `Eric Larson`_ - -- Fix bug in :meth:`mne.SourceMorph.apply` where the default was errantly ``mri_space=False`` instead of ``mri_space=None`` (as documented), by `Eric Larson`_ - -- Fix ``mne.VolVectorSourceEstimate.normal`` and :func:`mne.minimum_norm.apply_inverse` to only allow normal extraction/orientation for surface and discrete source spaces by `Eric Larson`_ - -- Fix :meth:`mne.io.Raw.set_annotations` for ``meas_date`` previous to 1970 by `Joan Massich`_ - -- Fix horizontal spacing issues in :meth:`mne.io.Raw.plot_psd` by `Jevri Hanna`_ - -- Fix reading of dates in BrainVision files if no "New Segment" marker is specified, no date is given, or data is missing, by `Stefan Appelhoff`_ - -- Fix bug with reading one-channel GDF files by `Abram Hindle`_ - -- Fix bug with y-axis labeling in :meth:`mne.io.Raw.plot_psd` by `Eric Larson`_ - -- Fix side-effect where :func:`mne.viz.plot_ica_sources` and :meth:`mne.preprocessing.ICA.plot_sources` changed the ``ICA.exclude`` attribute even when users didn't interact with the plot by `Daniel McCloy`_. - -- Fix scaling of sources in :meth:`ica.plot_sources(epochs) ` by `Eric Larson`_ - -- Fix wrong assumptions about units in BrainVision montages and add test asserting units in "mm" or "auto", by `Stefan Appelhoff`_ - -- Fix scaling issue with signals in mV in EDF files read with :func:`mne.io.read_raw_edf` by `Alex Gramfort`_ - -- Fix :func:`mne.extract_label_time_course` behavior when using STCs generated with ``apply_inverse(..., label=label)`` or ``stc.in_label`` by `Eric Larson`_ - -- Fix bug in :func:`mne.io.read_raw_brainvision` so that recording date timestamps are also recognized if channel reference data is negative, by `Stefan Appelhoff`_ - -- Fix order of ``info['dig']`` that was alphabetical based on channel names and not following the channel order when using :meth:`mne.io.Raw.set_montage` and a ``mne.channels.Montage`` object by `Joan Massich`_ and `Alex Gramfort`_. - -- Fix reading CNT files larger than 2Gb by `Joan Massich`_ - -- Fix reading of 4D/BTi data with different channel names and onsets in :func:`mne.io.read_raw_bti` by `Joshua Bear`_ and `Eberhard Eich`_ - -- Fix formula for effective number of averages in :func:`mne.combine_evoked` when ``weights='equal'`` by `Daniel McCloy`_. - -- Fix bug in :func:`mne.simulation.simulate_stc` to avoid empty stc if label vertices and source space do not intersect, by `Kostiantyn Maksymenko`_ - -- Fix ``event_id='auto'`` in :func:`mne.events_from_annotations` to recover Brainvision markers after saving it in ``.fif`` by `Joan Massich`_ - -- Fix :func:`mne.read_epochs_eeglab` when epochs are stored as float. By `Thomas Radman`_ - -- Fix :func:`mne.Evoked.resample` and :func:`mne.Epochs.resample` not setting ``inst.info['lowpass']`` properly by `Eric Larson`_ - -- Fix checks when constructing volumetric and surface source spaces with :func:`mne.setup_volume_source_space` and :func:`mne.setup_source_space`, respectively, by `Eric Larson`_ - -- Fix bug in handling of :class:`mne.Evoked` types that were not produced by MNE-Python (e.g., alternating average) by `Eric Larson`_ - -- Fix bug in :func:`mne.read_source_estimate` where vector volumetric source estimates could not be read by `Eric Larson`_ - -- Fix bug in :func:`mne.inverse_sparse.mixed_norm` and :func:`mne.inverse_sparse.tf_mixed_norm` where ``weights`` was supplied but ``weights_min`` was not, by `Eric Larson`_ - -- Fix bug in :func:`mne.set_eeg_reference` where non-EEG channels could be re-referenced by default if there were no EEG channels present, by `Eric Larson`_ - -- Fix bug in :func:`mne.io.Raw.plot` when using HiDPI displays and the MacOSX backend of matplotlib by `Eric Larson`_ - -- Fix bug in :func:`mne.viz.plot_compare_evokeds` when using Neuromag 122 system by `Eric Larson`_ - -- Fix bug in :func:`mne.Epochs.plot_psd` when some channels had zero/infinite ``psd`` values causing erroneous error messages by `Luke Bloy`_ - -- Fix :func:`mne.Evoked.decimate` not setting ``inst.first`` and ``inst.last`` properly by `Marijn van Vliet`_ - -- Fix :func:`mne.io.read_raw_brainvision` not handling ``Event`` markers created by PyCorder correctly by `Richard Höchenberger`_ - -- Fix support for string-like objects (such as :class:`python:pathlib.Path`) by `Eric Larson`_ - -- Fix :class:`mne.Report` silently suppressing exceptions when used as a context manager by `Marijn van Vliet`_ - -API -~~~ - -- Deprecate ``mne.channels.Montage`` class, ``mne.channels.read_montage`` and ``mne.channels.read_dig_montage`` function by `Joan Massich`_. - -- Deprecate passing ``Montage``, ``str`` as montage parameter in :meth:`mne.io.Raw.set_montage` by `Joan Massich`_. - -- Deprecate ``set_dig`` parameter in :meth:`mne.io.Raw.set_montage` and ``update_ch_names`` in ``mne.io.RawEEGLAB.set_montage`` when using :class:`mne.channels.DigMontage` as by `Joan Massich`_. - -- Now :meth:`mne.io.Raw.set_montage` raises an error when :class:`mne.channels.DigMontage` contains only a subset of the channels in ``raw.info``. It also adds ``raise_if_subset`` parameter to ensure backward compatibility (defaults to False in 0.19, to True in 0.20, and will be removed in 0.21) by `Joan Massich`_. - -- Minimum dependency versions for the following libraries have been bumped up (by `Eric Larson`_): - - - NumPy: 1.12.1 - - SciPy: 0.18.1 - - matplotlib: 2.0.2 - - scikit-learn: 0.18.2 - - pandas 0.19.2 - -- New boolean parameter ``show_scrollbars`` for :meth:`mne.io.Raw.plot`, :meth:`mne.Epochs.plot`, and :meth:`mne.preprocessing.ICA.plot_sources` (and associated functions) that allows hiding the scrollbars and buttons for a "zen mode" data browsing experience. When the plot window has focus, zen mode can be toggled by pressing :kbd:`z`, by `Daniel McCloy`_. - -- Deprecate ``mne.evoked.grand_average`` in favor of :func:`mne.grand_average` (which works on both :class:`~mne.Evoked` and :class:`~mne.time_frequency.AverageTFR`) by `Daniel McCloy`_ - -- Deprecate ``exclude`` parameter in :func:`mne.viz.plot_ica_sources` and :meth:`mne.preprocessing.ICA.plot_sources`, instead always use the ``exclude`` attribute of the ICA object by `Daniel McCloy`_. - -- Deprecate ``montage`` parameter in favor of the ``set_montage`` method in all EEG data readers :func:`mne.io.read_raw_cnt`, :func:`mne.io.read_raw_egi`, :func:`mne.io.read_raw_edf`, :func:`mne.io.read_raw_gdf`, :func:`mne.io.read_raw_nicolet`, :func:`mne.io.read_raw_eeglab` and :func:`mne.read_epochs_eeglab` by `Alex Gramfort`_ - -- New parameter ``clear`` in :func:`mne.viz.plot_epochs_image` for clearing pre-existing axes before plotting into them by `Daniel McCloy`_ - -- :func:`mne.viz.plot_epochs_image` no longer supports ``group_by='type'`` — combining by channel type is now the default when ``picks`` is a channel type string; to get individual plots for each channel, pass ``picks`` as a list of channel names or indices by `Daniel McCloy`_ - -- New parameter ``combine`` in :func:`mne.viz.plot_compare_evokeds` for specifying method to combine information across channels by `Daniel McCloy`_ - -- FIFF constants related to SmartShield (``*_SMSH_*`` and ``*_SMARTSHIELD``) have been renamed to ``IAS`` for consistency with MEGIN, by `Eric Larson`_ - -- The ``gfp`` parameter of :func:`mne.viz.plot_compare_evokeds` is deprecated; use ``combine='gfp'`` instead by `Daniel McCloy`_ - -- The ``truncate_yaxis='max_ticks'`` parameter of :func:`mne.viz.plot_compare_evokeds` is deprecated; use ``truncate_yaxis='auto'`` instead by `Daniel McCloy`_ - -- The ``truncate_xaxis`` and ``truncate_yaxis`` parameters of :func:`mne.viz.plot_compare_evokeds` now perform one-sided truncation unless both are ``True`` by `Daniel McCloy`_ - -- The ``show_legend`` parameter of :func:`mne.viz.plot_compare_evokeds` is renamed to ``legend`` by `Daniel McCloy`_ - -- :func:`mne.viz.plot_compare_evokeds` always returns a list of figures even when a single figure is generated by `Daniel McCloy`_ - -- Deprecate ``average=True`` and ``spatial_colors=False`` for :func:`mne.Epochs.plot_psd` by `Jevri Hanna`_ - -- :func:`mne.io.read_raw_brainvision` no longer raises an error when there are inconsistencies between ``info['chs']`` and ``montage`` but warns instead by `Joan Massich`_ - -- Add ``update_ch_names`` parameter to ``mne.io.RawEEGLAB.set_montage`` to allow updating the channel names based on the montage by `Joan Massich`_ - -- Reading annotations contained in GDF files with :func:`mne.io.read_raw_gdf` now returns numeric event codes as descriptions (instead of textual descriptions) due to restrictive licensing of the GDF event code table from BioSig by `Clemens Brunner`_ - -- ``channels.find_ch_connectivity`` now returns pre-built neighbor maps for KIT systems when available, by `Christian Brodbeck`_ diff --git a/doc/changes/v0.20.rst b/doc/changes/v0.20.rst deleted file mode 100644 index 7e6fa7d63c9..00000000000 --- a/doc/changes/v0.20.rst +++ /dev/null @@ -1,407 +0,0 @@ -.. _changes_0_20: - -Version 0.20 (2020-03-27) -------------------------- - -Changelog -~~~~~~~~~ - -- Improved :func:`mne.viz.plot_epochs` to label epoch counts starting from 0, by `Sophie Herbst`_ - -- Add :func:`minimum_norm.apply_inverse_cov` to compute static power by applying inverse solutions to a data covariance matrix by `Denis Engemann`_, `Luke Bloy`_, and `Eric Larson`_ - -- Add :func:`mne.minimum_norm.resolution_metrics` to compute various resolution metrics for inverse solutions, by `Olaf Hauk`_ - -- Add current source density :func:`mne.preprocessing.compute_current_source_density` to compute the surface Laplacian in order to reduce volume conduction in data by `Alex Rockhill`_ - -- Add :func:`mne.chpi.extract_chpi_locs_ctf` to extract cHPI coil locations from CTF data by `Luke Bloy`_ - -- Add :func:`mne.chpi.compute_chpi_amplitudes`, :func:`mne.chpi.compute_chpi_locs`, and :func:`mne.chpi.compute_head_pos` to compute head positions from cHPI coil locations by `Eric Larson`_ and `Luke Bloy`_ - -- Add ``allow_line_only`` option to :func:`mne.chpi.filter_chpi` to allow filtering line frequencies only in files that do not have cHPI information by `Eric Larson`_ - -- Add :func:`mne.io.Raw.set_meas_date` by `Eric Larson`_ - -- Add :meth:`mne.Epochs.as_type` to allow remapping data in MEG channels to virtual magnetometer or gradiometer channels by `Sophie Herbst`_ and `Alex Gramfort`_ - -- Add ``copy`` parameter to :meth:`mne.Epochs.iter_evoked` by `Alex Gramfort`_ - -- Add command :ref:`mne setup_source_space` to quickly set up bilateral hemisphere surface-based source space with subsampling by `Victor Ferat`_. - -- Add command :ref:`mne sys_info` to print system information by `Eric Larson`_ - -- Add function :func:`mne.make_fixed_length_epochs` to segment raw into fixed length epochs by `Mohammad Daneshzand`_ - -- Add support for computing patch information only in surface source space creation with ``add_dist='patch'`` in :func:`mne.setup_source_space` and ``dist_limit=0`` in :func:`mne.add_source_space_distances` by `Eric Larson`_ - -- Add :class:`mne.Label.restrict` to restrict a label to vertices within a source space by `Eric Larson`_ - -- Add support for passing a destination source space ``src_to`` in :func:`mne.compute_source_morph` to ensure morphing for multiple subjects results in consistent STCs, by `Eric Larson`_ - -- Add support for ``smooth='nearest'`` for surfaces in :func:`mne.compute_source_morph` by `Eric Larson`_ - -- Add support for plotting fNIRS channels in :func:`mne.viz.plot_alignment`, :func:`mne.viz.plot_evoked_topo` and :func:`mne.Evoked.animate_topomap` by `Eric Larson`_ and `Robert Luke`_ - -- Add command line tool :ref:`mne anonymize` for anonymizing raw fiff files by `Luke Bloy`_ - -- Add :func:`mne.preprocessing.find_bad_channels_maxwell` for automatic bad channel detection via Maxwell filtering by `Eric Larson`_ - -- Add support to :func:`mne.io.anonymize_info` to allow time offset to be applied to dates by `Luke Bloy`_ - -- Add support for computing resolution matrix to get point spread functions (PSF) and cross-talk functions (CTF) in :func:`mne.minimum_norm.make_inverse_resolution_matrix`, :func:`mne.beamformer.make_lcmv_resolution_matrix`, :func:`mne.minimum_norm.get_cross_talk`, :func:`mne.minimum_norm.get_point_spread` by `Olaf Hauk`_ - -- Add :func:`mne.preprocessing.read_ica_eeglab` to read EEGLAB ICA decompositions by `Christian O'Reilly`_ - -- Add keyboard functionality to interactive colorbar plotting TFRs by `Stefan Repplinger`_ - -- Add the ability to ``return_event_id`` in :func:`mne.read_events` for use with MNE-C produced ``-annot.fif`` files, by `Eric Larson`_ - -- Add option to ``mne.connectivity.spectral_connectivity`` to compute corrected imaginary PLV by `Adonay Nunes`_ - -- Add :func:`mne.SourceEstimate.estimate_snr` to estimate source-space SNR, by `Kaisu Lankinen`_ and `Padma Sundaram`_ - -- Add option to specify the coordinate frame in :func:`mne.channels.read_custom_montage` by `Eric Larson`_ - -- Add option to use ``match_case=False`` to :meth:`mne.io.Raw.set_montage` and related functions by `Eric Larson`_ - -- Add reader for NIRx data in :func:`mne.io.read_raw_nirx` by `Robert Luke`_ - -- Add function to convert NIRS data to optical density :func:`mne.preprocessing.nirs.optical_density` by `Robert Luke`_ - -- Add function to convert NIRS data to haemoglobin concentration :func:`mne.preprocessing.nirs.beer_lambert_law` by `Robert Luke`_ - -- Add ``fig`` argument to :func:`mne.viz.plot_evoked_field` by `Eric Larson`_ - -- Add functions to calculate spatial information of NIRS channels :func:`mne.preprocessing.nirs.source_detector_distances` and :func:`mne.preprocessing.nirs.short_channels` by `Robert Luke`_ - -- Add reader for ``*.dat`` electrode position files :func:`mne.channels.read_dig_dat` by `Christian Brodbeck`_ - -- Improved :func:`mne.viz.plot_events` to always show event counts by `Eric Larson`_ - -- Improved :ref:`limo-dataset` usage and :ref:`example ` for usage of :func:`mne.stats.linear_regression` by `Jose Alanis`_ - -- Add support for ``reduce_rank=True`` for vector beamformers by `Eric Larson`_ - -- Add ``method='sphere'`` support for using Freesurfer spherical inflation in :func:`mne.decimate_surface` to facilitate mesh downsampling for use with :func:`mne.make_bem_model` by `Eric Larson`_ - -- Speed up :func:`mne.beamformer.make_lcmv` and :func:`mne.beamformer.make_dics` calculations by vectorizing linear algebra calls by `Dmitrii Altukhov`_ and `Eric Larson`_ - -- Speed up :func:`mne.make_forward_solution` using Numba, by `Eric Larson`_ - -- Speed up :func:`mne.io.read_raw_fif` data reading when the recording is long and there are many data tags repeatedly accessed, by `Eric Larson`_ - -- For KIT systems without built-in layout, :func:`mne.channels.find_layout` now falls back on an automatically generated layout, by `Christian Brodbeck`_ - -- :meth:`mne.Epochs.plot` now takes a ``epochs_colors`` parameter to color specific epoch segments by `Mainak Jas`_ - -- Add command :ref:`mne setup_forward_model` to quickly create a BEM model for a subject by `Victor Ferat`_. - -- Add command :ref:`mne prepare_bem_model` to quickly create a BEM solution using the linear collocation approach by `Victor Ferat`_. - -- Add support for reading ``.bdip`` Xfit binary dipole fit files in :func:`mne.read_dipole` by `Eric Larson`_ - -- Allow returning vector source estimates from sparse inverse solvers through ``pick_ori='vector'`` by `Christian Brodbeck`_ - -- Add NIRS support to :func:`mne.viz.plot_topomap` and :func:`mne.viz.plot_ica_components` by `Robert Luke`_ - -- Add the ability to :func:`mne.channels.equalize_channels` to also re-order the channels and also operate on instances of :class:`mne.Info`, :class:`mne.Forward`, :class:`mne.Covariance` and :class:`mne.time_frequency.CrossSpectralDensity` by `Marijn van Vliet`_ - -- Allow `mne.channels.read_custom_montage` to handle fiducial points for BESA spherical (``.elp``) files by `Richard Höchenberger`_ - -- Add ``rank`` argument to :func:`mne.fit_dipole` by `Eric Larson`_ - -- Add function to convert events to annotations :func:`mne.annotations_from_events` by `Nicolas Barascud`_ - -- Add function to calculate scalp coupling index for fNIRS data :func:`mne.preprocessing.nirs.scalp_coupling_index` by `Robert Luke`_ - -- Add ``item`` argument to :meth:`mne.Epochs.get_data` for faster access to NumPy data arrays compared to :meth:`mne.Epochs.__getitem__` for frequent access on large :class:`mne.Epochs` objects, by `Eric Larson`_ - -- More accurate coordinate system for Easycap montages in :func:`mne.channels.make_standard_montage` by `Christian Brodbeck`_ - -- Add ``border`` argument to :func:`mne.viz.plot_topomap`. ``border`` controls the value of the edge points to which topomap values are extrapolated. ``border='mean'`` sets these points value to the average of their neighbours. By `Mikołaj Magnuski`_ - -- Add function :func:`mne.viz.link_brains` to link time properties of multiple brain objects interactively by `Guillaume Favelier`_ - -- Add function :func:`mne.preprocessing.annotate_movement` to annotate periods with head motion and :func:`mne.preprocessing.compute_average_dev_head_t` to re-estimate the device to head transform with average head position during segments with acceptable head movement. by `Adonay Nunes`_ - -- Make selected channels more distinguishable in :meth:`mne.Epochs.plot_sensors` when using ``kind='select'`` by `Mikołaj Magnuski`_ - -- Allow retrieval of the number of Infomax ICA iterations via the new ``return_n_iter`` keyword argument of :func:`mne.preprocessing.infomax` by `Richard Höchenberger`_ - -- Expose the number of ICA iterations during the fitting procedure via the ``n_iter_`` attribute of :class:`mne.preprocessing.ICA` by `Richard Höchenberger`_ - -- :func:`mne.grand_average` now produces a warning when only a single dataset was passed, instead of raising an error by `Richard Höchenberger`_ - -- Add ``nrows`` and ``ncols`` parameters to :func:`mne.viz.plot_evoked_topomap`, which allows to create multiline topomap plots for Evoked. By `Federico Raimondo`_ - -- Improve repr of :class:`mne.Info` (empty items are not shown anymore) by `Clemens Brunner`_ - -Bug -~~~ - -- Fix the ``reduce_rank`` parameter in :func:`mne.beamformer.make_lcmv` and :func:`mne.beamformer.make_dics` to reduce the rank of the leadfield first before then reducing the rank of the denominator of the beamformer formula for the inversion by `Britta Westner`_ and `Eric Larson`_. - -- Fix bug with :func:`mne.beamformer.make_lcmv` with data where rank was incorrectly checked by `Eric Larson`_. - -- Allow :func:`mne.channels.read_dig_hpts` to accept point categories (eg. EEG) to be specified in upper case by `Alex Gramfort`_. - -- Fix a bug in ``mne.MixedSourceEstimate.plot_surface`` that prevented plotting in latest PySurfer by `Christian O'Reilly`_. - -- Fix ``method='eLORETA'`` in :func:`mne.minimum_norm.apply_inverse`, by `Eric Larson`_: - - 1. regularization, which was off by roughly a factor of a square root - 2. units, which are now nAm instead of being arbitrary - 3. explained variance and residuals, which were previously unavailable - 4. ``force_equal`` in the case of loose orientations, which previously - defaulted to ``True`` now defaults to ``False``. - Reapplying orientation priors at each iteration of the algorithm - sufficiently preserves a smooth transition between loose=0. to loose=1. - without compromising localization accuracy in testing. - -- Fix bug in ``method='eLORETA'`` for :func:`mne.minimum_norm.apply_inverse` (and variants) to allow restricting source estimation to a label by `Luke Bloy`_ - -- Fix bug in :func:`mne.compute_covariance` and :func:`mne.compute_raw_covariance` where biased normalization (based on degrees of freedom) was used and ``cov.nfree`` was not set properly by `Eric Larson`_ - -- Fix ``mne.VectorSourceEstimate.normal`` to account for cortical patch statistics using ``use_cps=True`` by `Eric Larson`_ - -- Fix ``pick_ori='normal'`` for :func:`mne.minimum_norm.apply_inverse` when the inverse was computed with ``loose=1.`` and the forward solution was not in surface orientation, by `Eric Larson`_ - -- Fix missing xlabel for :func:`mne.io.Raw.plot_psd` and similar functions when passing a subset of axes from a figure by `Alex Gramfort`_ - -- Fix wrong DataFrame index when ``index=None`` in methods :meth:`mne.io.Raw.to_data_frame`, :meth:`mne.Epochs.to_data_frame`, :meth:`mne.Evoked.to_data_frame`, and :meth:`mne.SourceEstimate.to_data_frame`, by `Daniel McCloy`_. - -- Fix incorrect scaling of cluster temporal extent in :func:`mne.stats.summarize_clusters_stc` by `Daniel McCloy`_. - -- Fix :func:`mne.time_frequency.read_tfrs` to properly read :class:`~mne.Info` transforms by `Eric Larson`_ - -- Fix :func:`mne.viz.plot_sensors` to always plot in head coordinate frame by `Daniel McCloy`_. - -- Fix :func:`mne.io.read_raw_cnt` for version 1 of format in the presence of annotations by `Alex Gramfort`_. - -- Fix :class:`mne.decoding.GeneralizingEstimator` and related classes to support multi-class sklearn scorers such as ``'roc_auc_ovo'`` and ``'roc_auc_ovo_weighted'`` by `Eric Larson`_ - -- Fix :meth:`mne.io.read_raw_ctf` to set measurement date from CTF ds files by `Luke Bloy`_. - -- Fix :meth:`mne.read_epochs_eeglab` that ignored channel locations by `Alex Gramfort`_. - -- Fix :func:`mne.io.read_raw_brainvision` when channel names have spaces by `Sebastian Major`_. - -- Fix :func:`mne.io.read_raw_brainvision` when ``"Core"`` is in the data header by `Eric Larson`_ - -- Fix :meth:`mne.io.Raw.anonymize` to correctly reset ``raw.annotations.orig_time`` by `Luke Bloy`_. - -- Fix :meth:`mne.io.Raw.anonymize` to correctly avoid shifting ``raw.annotations.onset`` relative to ``raw.first_samp`` by `Eric Larson`_ - -- Fix :meth:`mne.io.Raw.set_channel_types` and :meth:`mne.io.Raw.rename_channels` and related methods to return the instance instead of ``None`` by `Eric Larson`_ - -- :meth:`mne.Epochs.iter_evoked` now does not return a copy of info when ``copy=False`` (default parameter) by `Alex Gramfort`_ - -- The attribute :class:`mne.Annotations.orig_time ` is now read-only, and is a :class:`~python:datetime.datetime` object (or None) rather than float, by `Eric Larson`_ - -- Fix bug where MRI distances were not properly initialized in :ref:`mne coreg` by `Eric Larson`_ - -- Fix ``xscale='log'`` in :meth:`mne.io.Raw.plot_psd` and related functions by `Alex Gramfort`_ - -- Unify behavior of ``raw.annotations.append(...)`` when ``raw.info['meas_date']`` is None to make onsets absolute relative to ``first_samp`` as they are when ``raw.info['meas_date']`` is not None; i.e., you might need to do ``raw.annotations.append(old_time + raw.first_time)``, by `Eric Larson`_ - -- The :class:`info['meas_date'] ` entry is now a :class:`~python:datetime.datetime` object (or None) rather than float, by `Eric Larson`_ - -- Fix :meth:`mne.time_frequency.AverageTFR.save` and related functions to deal with :class:`~python:datetime.datetime` objects properly by `Eric Larson`_ - -- Fix date reading before Unix time zero (1970 Jan 1) on Windows by `Alex Rockhill`_. - -- Fix bug running subprocesses (e.g., in :func:`mne.bem.make_watershed_bem`) in Jupyter notebooks, by `Eric Larson`_ - -- Fix :meth:`mne.io.read_raw_artemis123` to add HPI locations to digitization points, by `Luke Bloy`_ - -- Fix :meth:`mne.Epochs.shift_time` and :meth:`mne.Evoked.shift_time` to return the modified :class:`~mne.Epochs` or :class:`~mne.Evoked` instance (instead of ``None``) by `Daniel McCloy`_. - -- Fix :func:`mne.read_annotations` for text files with zero or one annotations, by `Adonay Nunes`_ - -- Fix bug in :class:`~mne.preprocessing.ICA` where requesting extended infomax via ``fit_params={'extended': True}`` was overridden, by `Daniel McCloy`_. - -- Fix bug in :meth:`mne.Epochs.interpolate_bads` where the ``origin`` was not used during MEG or EEG data interpolation by `Eric Larson`_. Old behavior can be achieved using ``origin=(0., 0., 0.)`` for EEG and ``origin=(0., 0., 0.04)`` for MEG, and the new default is ``origin='auto'``, which uses a head-digitization-based fit. - -- Fix bug in :func:`mne.write_evokeds` where ``evoked.nave`` was not saved properly when multiple :class:`~mne.Evoked` instances were written to a single file, by `Eric Larson`_ - -- Fix bug in ``mne.preprocessing.mark_flat`` where acquisition skips were not handled properly, by `Eric Larson`_ - -- Fix bug in :func:`mne.viz.plot_bem` where some sources were not plotted by `Jean-Remi King`_ and `Eric Larson`_ - -- Fix TAL channel parsing (annotations) for EDF-D files by `Clemens Brunner`_ - -- Fix bug with :func:`mne.viz.plot_dipole_locations` when plotting in head coordinates by `Eric Larson`_ - -- Fix handling in cases where no components are found in :func:`mne.preprocessing.corrmap` by `Eric Larson`_ - -- Fix handling of repeated events in :class:`mne.Epochs` by `Fahimeh Mamashli`_ and `Alex Gramfort`_ - -- Fix many bugs with plotting sensors overlaid on a head outline. All plotting is now done in head coordinates and scaled by ``head_radius``, which defaults to 0.095, by `Eric Larson`_ - -- Fix :func:`mne.io.anonymize_info` to allow shifting dates of service and to match anticipated changes in mne-cpp by `Luke Bloy`_ - -- Fix reading of cardinals in .htps files (identifier are int not strings) by `Alex Gramfort`_ - -- Fix IO of TFRs when event_id contain a / in one of the keys by `Alex Gramfort`_ - -- Fix plotting of TFRs with linear y-scale (misaligned frequency bins), by `Stefan Repplinger`_ and `Eric Larson`_ - -- Fix ``info['sfreq']`` when decimating in :func:`mne.time_frequency.tfr_multitaper` and :func:`mne.time_frequency.tfr_morlet` and make sure an error is raised when exceed Nyquist frequency by `Adonay Nunes`_ - -- Fix bug in EDF(+) loading, filter values ignored by insufficient regex, by `Demetres Kostas`_ - -- Fix missing scaling of tolerance parameter in :func:`mne.inverse_sparse.tf_mixed_norm` and :func:`mne.inverse_sparse.mixed_norm`, by `Mathurin Massias`_ - -- Fix the automatic scaling of the glyphs in :func:`mne.viz.plot_vector_source_estimates` by using 10% of the brain width, by `Guillaume Favelier`_ - -- Fix handling of missing values (NaNs) in ``mne.time_frequency.psd_welch`` by `Clemens Brunner`_ - -- Fix :class:`mne.decoding.LinearModel` to support the refitted estimator of ``GridSearchCV`` in ``sklearn`` by `Chun-Hui Li`_ - -- Fix :func:`mne.viz.plot_topomap` when there are bad channels in the provided :class:`mne.Info` instance by `Eric Larson`_ - -- Fix check for subject definition existing in source space in :func:`mne.compute_source_morph` and related functions by `Eric Larson`_ - -- Fix creation of new figures in :meth:`mne.Epochs.plot_image` and :func:`mne.viz.plot_epochs_image` by `Eric Larson`_ - -- Fix bug in :class:`~mne.preprocessing.Xdawn` where filters where selected along the incorrect axis, by `Henrich Kolkhorst`_ - -- Fix bug in :func:`mne.bem.make_watershed_bem` where some surfaces were saved incorrectly in the working directory by `Yu-Han Luo`_ - -- Fix support for multiple TAL (annotations) channels in BDF reader by `Clemens Brunner`_ - -- Fix missing ``brainmask`` file type in :func:`mne.bem.make_watershed_bem` by changing its default value to ``ws.mgz`` by `Fu-Te Wong`_ - -- Fix bug in :func:`mne.channels.make_standard_montage` which would return ``easycap-M1`` even when requesting ``easycap-M10`` by `Christian Brodbeck`_ - -- Fix the way planar gradiometers are combined in :func:`mne.viz.plot_tfr_topomap` and :meth:`mne.Epochs.plot_psd_topomap` by `Geoff Brookshire`_ - -- Improve error message when trying to load FieldTrip data from a cell array by `Thomas Hartmann`_ - -- Fix bug in :func:`mne.read_evoked_fieldtrip` causing it to crash when channels were present in the provided Info object but were not present in the data by `Thomas Hartmann`_ - -- Fix placement of extrapolation points in :meth:`mne.Evoked.plot_topomap` and related functions when exactly three channels were used by `Mikołaj Magnuski`_. - -- Fix bug in reading annotations in :func:`read_annotations`, which would not accept ";" character by `Adam Li`_ - -- Fix bug in :func:`mne.Report.parse_folder`, which would not recognize ``*meg.fif`` files by `Dmitrii Altukhov`_. - -- Include ``fit_params`` when saving an :class:`~mne.preprocessing.ICA` instance to disk by `Richard Höchenberger`_ - -- Update old url link in :func:`mne.datasets.eegbci.load_data` to ``EEGMI_URL = 'https://physionet.org/files/eegmmidb/1.0.0/'`` by `Ramiro Gatti`_ - -- Ensure corrected p-values calculated by :func:`mne.stats.bonferroni_correction` never exceed the value of 1.0 by `Richard Höchenberger`_ - -API -~~~ - -- ``mne.io.pick.get_channel_types`` is now called ``mne.io.pick.get_channel_type_constants`` to better reflect its return values, by `Daniel McCloy`_. - -- :meth:`mne.Evoked.as_type` now returns an instance of :class:`mne.EvokedArray` by `Sophie Herbst`_ and `Alex Gramfort`_ - -- Bumped minimum requirements to fall 2017 versions by `Eric Larson`_: - - - NumPy 1.13.3 - - SciPy 1.0.0 - - matplotlib 2.1 - - scikit-learn 0.19.1 (optional requirement) - - pandas 0.21 (optional requirement) - -- :meth:`mne.Epochs.plot` now accepts an ``event_id`` parameter (useful in tandem with ``event_colors`` for specifying event colors by name) by `Daniel McCloy`_. - -- Passing ``ch_types=None`` has been deprecated in favor of explicitly passing ``ch_types='misc'`` in :func:`mne.create_info` by `Eric Larson`_ - -- New time conversion options for methods :meth:`mne.io.Raw.to_data_frame`, :meth:`mne.Epochs.to_data_frame`, :meth:`mne.Evoked.to_data_frame`, and :meth:`mne.SourceEstimate.to_data_frame`, by `Daniel McCloy`_. - -- :meth:`mne.Epochs.shift_time` and :meth:`mne.Evoked.shift_time` now allow shifting times by arbitrary amounts (previously only by integer multiples of the sampling period), by `Daniel McCloy`_ and `Eric Larson`_. - -- The ``head_pos`` argument of :func:`mne.Evoked.plot_topomap` and related functions has been deprecated in favor of ``head_radius``, by `Eric Larson`_. - -- The ``layout`` argument to topomap-related functions such as :meth:`mne.Evoked.plot_topomap` and :func:`mne.viz.plot_tfr_topomap` has been deprecated in favor of channel-position based flattening based on the ``info`` and ``sphere`` argument, by `Eric Larson`_. - -- The APIs of :meth:`mne.io.Raw.plot_projs_topomap`, :meth:`mne.Epochs.plot_projs_topomap` and :meth:`mne.Evoked.plot_projs_topomap` are now more similar to :func:`mne.viz.plot_projs_topomap` by `Daniel McCloy`_. - -- The function :func:`mne.setup_volume_source_space` has a ``sphere_units`` argument that defaults to ``'mm'`` in 0.20 but will change to ``'m'`` in 0.21, set it to avoid a warning by `Eric Larson`_. - -- :func:`mne.viz.plot_projs_topomap` and the related methods :meth:`mne.io.Raw.plot_projs_topomap`, :meth:`mne.Epochs.plot_projs_topomap` and :meth:`mne.Evoked.plot_projs_topomap` now accept parameter ``vlim`` to control the colormap, with keyword ``'joint'`` computing the colormap jointly across all projectors of a given channel type, by `Daniel McCloy`_. - -- New methods :meth:`mne.io.Raw.get_channel_types`, :meth:`mne.Epochs.get_channel_types`, :meth:`mne.Evoked.get_channel_types` by `Daniel McCloy`_. - -- Deprecate ``mne.minimum_norm.point_spread_function`` and ``mne.minimum_norm.cross_talk_function`` by `Alex Gramfort`_ - -- Deprecate ``montage`` parameter of :func:`mne.create_info` in favor of :meth:`mne.io.Raw.set_montage`, :meth:`mne.Info.set_montage`, and related functions by `Eric Larson`_ - -- :func:`mne.channels.equalize_channels` no longer operates in-place by default, but instead makes copies of the objects when necessary (see ``copy`` parameter) by `Marijn van Vliet`_ - -- :func:`mne.channels.equalize_channels` now uses the first object in the list as a template for channel ordering by `Marijn van Vliet`_ - -- :func:`mne.channels.equalize_channels` now also re-orders the channels to match, in addition to dropping channels that are not shared by all objects by `Marijn van Vliet`_ - -- :meth:`mne.io.Raw.pick_channels`, :meth:`mne.Epochs.pick_channels` and :meth:`mne.Evoked.pick_channels` now have an ``ordered`` parameter to enforce the ordering of the picked channels by `Marijn van Vliet`_ - -- New methods :meth:`mne.Forward.pick_channels`, :meth:`mne.Covariance.pick_channels`, ``mne.Info.pick_channels``, :meth:`mne.time_frequency.CrossSpectralDensity.pick_channels` by `Marijn van Vliet`_ - -- New attributes ``mne.Forward.ch_names`` and ``mne.Info.ch_names`` by `Marijn van Vliet`_ - -- In :class:`~mne.preprocessing.Xdawn`, the components are stored in the rows of attributes ``filters_`` and ``patterns_`` to be consistent with :class:`~mne.decoding.CSP` and :class:`~mne.preprocessing.ICA` by `Henrich Kolkhorst`_ - -- Drop ``unit`` keyword argument from :func:`mne.channels.read_custom_montage`, as it was unused by `Richard Höchenberger`_ - -- Deprecate ``mne.preprocessing.run_ica``, use ``mne.preprocessing.ICA.detect_artifacts`` instead by `Richard Höchenberger`_ - -Authors -~~~~~~~ - -People who contributed to this release (in alphabetical order): - -* Adam Li -* Adonay Nunes -* Alex Rockhill -* Alexandre Gramfort -* Ariel Rokem -* Britta Westner -* Carlos de la Torre -* Christian Brodbeck -* Christian O'Reilly -* Chun-Hui Li -* Clemens Brunner -* Daniel McCloy -* Demetres Kostas -* Denis A. Engemann -* Dmitrii Altukhov -* Dominik Welke -* Eric Larson -* Ezequiel Mikulan -* Fahimeh Mamashli -* Fede Raimondo -* Fu-Te Wong -* Geoff Brookshire -* Guillaume Favelier -* Henrich Kolkhorst -* Joan Massich -* José C. García Alanis -* Jussi Nurminen -* Kaisu Lankinen -* Luke Bloy -* Mainak Jas -* Marijn van Vliet -* Mathurin Massias -* Mikolaj Magnuski -* Mohamed Sherif -* Mohammad Daneshzand -* Nataliia Kozhemiako -* Nicolas Barascud -* Nicolas Legrand -* Olaf Hauk -* Padma Sundaram -* Ramiro Gatti -* Richard Höchenberger -* Robert Luke -* Robert Oostenveld -* Sebastian Major -* Sophie Herbst -* Stefan Appelhoff -* Stefan Repplinger -* Thomas Hartmann -* Victor Férat -* Yu-Han Luo diff --git a/doc/changes/v0.21.rst b/doc/changes/v0.21.rst deleted file mode 100644 index 1d55c714f96..00000000000 --- a/doc/changes/v0.21.rst +++ /dev/null @@ -1,486 +0,0 @@ -.. _changes_0_21: - -Version 0.21 (2020-09-21) -------------------------- - -.. |Rahul Nadkarni| replace:: **Rahul Nadkarni** -.. |Lau Møller Andersen| replace:: **Lau Møller Andersen** -.. |Kyle Mathewson| replace:: **Kyle Mathewson** -.. |Jan Sedivy| replace:: **Jan Sedivy** -.. |Johann Benerradi| replace:: **Johann Benerradi** -.. |Martin Schulz| replace:: **Martin Schulz** -.. |Jeroen Van Der Donckt| replace:: **Jeroen Van Der Donckt** -.. |Simeon Wong| replace:: **Simeon Wong** -.. |Svea Marie Meyer| replace:: **Svea Marie Meyer** -.. |Lx37| replace:: **Lx37** -.. |Liberty Hamilton| replace:: **Liberty Hamilton** -.. |Steven Bierer| replace:: **Steven Bierer** - -Enhancements -~~~~~~~~~~~~ - -- Modified :meth:`mne.Epochs.pick_types` to remove dropped channel types from ``reject`` and ``flat`` dictionaries **by new contributor** |Rahul Nadkarni|_ - -- Add function :func:`mne.preprocessing.regress_artifact` to remove artifacts using linear regression **by new contributor** |Kyle Mathewson|_ and `Eric Larson`_ - -- Add ``sources`` and ``detectors`` options for fNIRS use of :meth:`mne.viz.plot_alignment` allowing plotting of optode locations in addition to channel midpoint ``channels`` and ``path`` between fNIRS optodes **by new contributor** |Kyle Mathewson|_ - -- BrainVision data format files are now parsed for EEG impedance values in :func:`mne.io.read_raw_brainvision` and provided as a ``.impedances`` attribute of ``raw`` **by new contributor** |Jan Sedivy|_ and `Stefan Appelhoff`_ - -- 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 new contributor** |Johann Benerradi|_ - -- Improved documentation building instructions and execution on Windows **by new contributor** |Martin Schulz|_, `kalenkovich`_, and `Eric Larson`_ - -- Speed up reading of annotations in EDF+ files **by new contributor** |Jeroen Van Der Donckt|_ - -- Add head to mri and mri to voxel space transform details to :ref:`tut-source-alignment` tutorial, by `Alex Rockhill`_ - -- Improve memory efficiency of :func:`mne.concatenate_epochs` by `Eric Larson`_ - -- Allow picking channels in raw instances (e.g., :meth:`mne.io.Raw.pick_types`) without preloading data, by `Eric Larson`_ - -- :meth:`mne.preprocessing.ICA.plot_sources` now plots annotation markers similar to :meth:`mne.io.Raw.plot` by `Luke Bloy`_ - -- Add support for scalar multiplication and division of :class:`mne.time_frequency.AverageTFR` instances by `Luke Bloy`_ - -- Add support for signals in mV for :func:`mne.io.read_raw_brainvision` by `Clemens Brunner`_ - -- :meth:`mne.Epochs.plot_psd_topomap` and :func:`mne.viz.plot_epochs_psd_topomap` now allow joint colorbar limits across subplots, by `Daniel McCloy`_. - -- Add support for using loose-orientation surface priors with free-orientation volume priors in mixed source space inverses by `Eric Larson`_ - -- Add :class:`mne.MixedVectorSourceEstimate` for vector source estimates for mixed source spaces, by `Eric Larson`_ - -- Add mixed and volumetric source estimate plotting using volumetric ray-casting to :meth:`mne.MixedSourceEstimate.plot` and :meth:`mne.VolSourceEstimate.plot_3d` by `Eric Larson`_ - -- Add :meth:`mne.MixedSourceEstimate.surface` and :meth:`mne.MixedSourceEstimate.volume` methods to allow surface and volume extraction by `Eric Larson`_ - -- Add :meth:`mne.VectorSourceEstimate.project` to project vector source estimates onto the direction of maximum source power by `Eric Larson`_ - -- Add support to :func:`mne.extract_label_time_course` for vector-valued and volumetric source estimates by `Eric Larson`_ - -- Add method :meth:`mne.VolSourceEstimate.in_label` by `Eric Larson`_ - -- Add support for mixed source spaces to :func:`mne.compute_source_morph` by `Eric Larson`_ - -- Add support for volume and mixed source spaces to :func:`mne.stats.summarize_clusters_stc` by `Eric Larson`_ - -- Add support for omitting the SDR step in volumetric morphing by passing ``n_iter_sdr=()`` to `mne.compute_source_morph` by `Eric Larson`_ - -- Add ``single_volume`` argument to :func:`mne.setup_volume_source_space` to facilitate creating source spaces with many volumes (e.g., all subvolumes of ``aseg.mgz``) by `Eric Larson`_ - -- Add support for passing a string argument to ``bg_img`` in `mne.viz.plot_volume_source_estimates` by `Eric Larson`_ - -- Add support for providing the destination surface source space in the ``src_to`` argument of :func:`mne.compute_source_morph` by `Eric Larson`_ - -- Add explained variance logging to :func:`mne.inverse_sparse.mixed_norm`, :func:`mne.inverse_sparse.gamma_map`, and :func:`mne.beamformer.rap_music` by `Eric Larson`_ - -- Add ``tol_kind`` option to :func:`mne.compute_rank` by `Eric Larson`_ - -- Allow resampling raw data with :func:`mne.io.Raw.resample` without preloading data, by `Eric Larson`_ - -- Allow using ``pick_ori='vector'`` with a fixed-orientation inverse to facilitate visualization with :func:`mne.viz.plot_vector_source_estimates` by `Eric Larson`_ - -- :func:`mne.viz.plot_dipole_locations` and :meth:`mne.Dipole.plot_locations` gained a ``title`` argument to specify a custom figure title in ``orthoview`` mode by `Richard Höchenberger`_ - -- Add orientations projected onto the MRI slices in :func:`mne.viz.plot_dipole_locations` in ``'orthoview'`` mode by `Eric Larson`_ - -- Add temporal derivative distribution repair (TDDR) :func:`mne.preprocessing.nirs.temporal_derivative_distribution_repair` with shortened alias ``mne.preprocessing.nirs.tddr`` by `Robert Luke`_ - -- Add :func:`mne.read_freesurfer_lut` to make it easier to work with volume atlases by `Eric Larson`_ - -- Add support for overlap-add processing when ``method='spectrum_fit'`` in :func:`mne.io.Raw.notch_filter` by `Eric Larson`_ - -- Add functionality to interpolate bad NIRS channels by `Robert Luke`_ - -- Add ability to interpolate EEG channels using minimum-norm projection in :meth:`mne.io.Raw.interpolate_bads` and related functions with ``method=dict(eeg='MNE')`` by `Eric Larson`_ - -- Added ability of :func:`mne.io.read_raw_nirx` to open data by passing path to header file `Robert Luke`_ - -- Add :meth:`mne.channels.DigMontage.rename_channels` to allow renaming montage channels by `Eric Larson`_ - -- Document :meth:`mne.channels.compute_native_head_t` to allow computing the native-to-head transformation that will be applied when doing :meth:`raw.set_montage ` and related functions by `Eric Larson`_ - -- Add support to in :meth:`mne.io.Raw.plot` for passing ``clipping`` as a float to clip to a proportion of the dedicated channel range by `Eric Larson`_ - -- Add function :func:`mne.preprocessing.annotate_muscle_zscore` to annotate periods with muscle artifacts. by `Adonay Nunes`_ - -- Add :func:`mne.stats.ttest_ind_no_p` to mirror :func:`mne.stats.ttest_1samp_no_p` with hat correction by `Eric Larson`_ - -- Add `mne.stats.combine_adjacency` to combine adjacency matrices for independent data dimensions to enable things like spatio-temporal-time-frequency clustering in `mne.stats.permutation_cluster_test` by `Eric Larson`_ - -- Speed up raw data reading without preload in :func:`mne.io.read_raw_nirx` by `Eric Larson`_ - -- Speed up :meth:`mne.Epochs.copy` and :meth:`mne.Epochs.__getitem__` by avoiding copying immutable attributes by `Eric Larson`_ - -- Speed up and reduce memory usage of :meth:`mne.SourceEstimate.plot` and related functions/methods when ``show_traces=True`` by `Eric Larson`_ - -- Reduce memory usage of `~mne.io.Raw.plot_psd`, ``mne.time_frequency.psd_welch``, and `~mne.time_frequency.psd_array_welch` for long segments of data by `Eric Larson`_ - -- Support for saving movies of source time courses (STCs) with ``brain.save_movie`` method and from graphical user interface by `Guillaume Favelier`_ - -- Add ``mri`` and ``show_orientation`` arguments to :func:`mne.viz.plot_bem` by `Eric Larson`_ - -- Add :func:`mne.viz.centers_to_edges` to help when using :meth:`matplotlib.axes.Axes.pcolormesh` with flat shading by `Eric Larson`_ - -- Add ``on_missing='raise'`` to :meth:`mne.io.Raw.set_montage` and related functions to allow ignoring of missing electrode coordinates by `Adam Li`_ - -- Add ``on_missing='raise'`` to :func:`mne.viz.plot_events` to allow ignoring missing events when passing ``event_id`` by `Eric Larson`_ - -- Add REST EEG infinity reference scheme to :meth:`mne.io.Raw.set_eeg_reference` and related functions by `Eric Larson`_ - -- Add better sanity checking of ``max_pca_components`` and ``n_components`` to provide more informative error messages for :class:`mne.preprocessing.ICA` by `Eric Larson`_ - -- Add ``plot`` option to :meth:`mne.viz.plot_filter` allowing selection of which filter properties are plotted and added option for user to supply ``axes`` by `Robert Luke`_ - -- Add estimation method legend to :func:`mne.viz.plot_snr_estimate` by `Eric Larson`_ - -- Add support to `mne.SourceSpaces.export_volume` for ``mri_resolution='sparse'`` to color only the nearest-neighbor voxels instead of entire regions by `Eric Larson`_ - -- Add ``axes`` argument to :func:`mne.viz.plot_evoked_white`, :meth:`mne.Evoked.plot_white`, and :func:`mne.viz.plot_snr_estimate` by `Eric Larson`_ - -- Change default to ``surfaces='auto'`` from ``surfaces='head'`` to allow :func:`mne.viz.plot_alignment` to work when just passing a :class:`mne.Info` as ``plot_alignment(info)`` by `Eric Larson`_ - -- Add ECoG misc EDF dataset to the :ref:`tut-working-with-ecog` tutorial to show snapshots of time-frequency activity by `Adam Li`_ - -- Add :func:`mne.viz.set_3d_options` and ``MNE_3D_OPTION_ANTIALIAS`` environment variable to control full-scene antialiasing (FXAA) in 3D functions like :ref:`mne coreg`, :func:`mne.viz.plot_alignment`, and :func:`mne.viz.plot_source_estimates`; this can be useful on systems where FXAA does not work well, such as some with MESA software rendering, by `Eric Larson`_ - -- Add config variable ``MNE_TQDM`` to support explicitly setting the TQDM backend to use, for example ``tqdm`` or ``tqdm.auto`` (default) by `Eric Larson`_ - -- Add better support for reading corrupted FIF files in :func:`mne.io.read_raw_fif` by `Eric Larson`_ - -- BIDS conformity: When saving FIF files to disk and the files are split into parts, the ``split_naming='bids'`` parameter now uses a "_split-%d" naming instead of the previous "_part-%d", by `Stefan Appelhoff`_ - -- Add support for whitening and multiple channel types in :func:`mne.beamformer.make_dics` by `Marijn van Vliet`_ - -- Add better error message when trying to save incompatible `~mne.Evoked` objects to the same file by `Eric Larson`_ - -- Add support for loading complex numbers from mat files by `Thomas Hartmann`_ - -- Add generic reader function :func:`mne.io.read_raw` that loads files based on their extensions (it wraps the underlying specific ``read_raw_xxx`` functions) by `Clemens Brunner`_ - -- Add automatic T3 magnetometer detection and application of :meth:`mne.io.Raw.fix_mag_coil_types` to :func:`mne.preprocessing.maxwell_filter` by `Eric Larson`_ - -- Add extended SSS (eSSS) support to :func:`mne.preprocessing.maxwell_filter` by `Eric Larson`_ - -- Add ``'auto'`` option to :meth:`mne.preprocessing.ICA.find_bads_ecg` to automatically determine the threshold for CTPS method by `Yu-Han Luo`_ - -- Add a ``notebook`` 3d backend for visualization in jupyter notebook with :func:`mne.viz.set_3d_backend` by `Guillaume Favelier`_ - -- Add support for reading and writing surfaces in Wavefront .obj format to the :func:`mne.read_surface` and :func:`mne.write_surface` by `Marijn van Vliet`_ - -- Add tutorial on how to manually fix BEM meshes in Blender by `Marijn van Vliet`_ and `Ezequiel Mikulan`_ - -- :func:`mne.write_evokeds` will now accept :class:`mne.Evoked` objects with differing channel orders in ``info['bads']``, which would previously raise an exception by `Richard Höchenberger`_ - -- Add support for reading channel names (e.g., for Ricoh data) to :func:`mne.io.read_raw_kit` by `Alex Gramfort`_ and `Eric Larson`_ - -- The ``reject_tmin`` and ``reject_tmax`` parameters of :class:`mne.Epochs` are now taken into account when using the ``reject_by_annotation`` parameter by `Stefan Appelhoff`_ - -- :func:`mne.preprocessing.find_bad_channels_maxwell` now automatically applies a low-pass filter before running bad channel detection. This can be disabled, restoring previous behavior by `Richard Höchenberger`_ - -- 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`_ - -- Add writing BEM surfaces and solutions in H5 format in :func:`mne.write_bem_surfaces` and :func:`mne.write_bem_solution` 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`_ - -- 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`_ - -- `~mne.Report.parse_folder` now accepts a path-like folder name (it used to work with strings only) by `Alex Gramfort`_ - -- Add ``component_order`` parameter to :class:`mne.decoding.CSP` which allows switching between ``mutual_info`` (default) and ``alternate`` (a simpler and frequently used option) by `Martin Billinger`_ and `Clemens Brunner`_ - -- Add memory size information to the ``repr`` of :class:`mne.SourceSpaces` and :class:`mne.SourceEstimate` and related classes by `Eric Larson`_ - -- Add reader for Persyst (.lay + .dat format) data in :func:`mne.io.read_raw_persyst` by `Adam Li`_ - -- Use PyVista as the default backend for 3D visualization instead of Mayavi by `Guillaume Favelier`_ - -- Add reader for SNIRF NIRS data in :func:`mne.io.read_raw_snirf` by `Robert Luke`_ - -- `~mne.Evoked` has gained ``tmin`` and ``tmax`` attributes for more consistency with `~mne.Epochs` by `Richard Höchenberger`_ - -Bugs -~~~~ - -- Fix bug for writing and reading complex evoked data modifying :func:`mne.write_evokeds` and :func:`mne.read_evokeds` **by new contributor** |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 new contributor** |Lau Møller Andersen|_ - -- Fix bug with logging in :meth:`mne.io.Raw.set_eeg_reference` and related functions **by new contributor** |Simeon Wong|_ - -- Fix bug with :func:`mne.io.read_raw_gdf` where birthdays were not parsed properly, leading to an error **by new contributor** |Svea Marie Meyer|_ - -- Fix bug with :func:`mne.io.read_raw_edf` where recording ID was not read properly for non-ASCII characters **by new contributor** |Lx37|_ - -- Fix bug in :func:`mne.set_eeg_reference` and related functions to set ``info['custom_ref_applied']`` to ``True`` for 'ecog' and 'seeg' channels in addition to 'eeg' **by new contributor** |Liberty Hamilton|_ - -- Fix bug with :func:`mne.chpi.compute_chpi_amplitudes` and :func:`mne.chpi.filter_chpi` to optimize time window length **by new contributor** |Steven Bierer|_ - -- Fix bug with :func:`mne.preprocessing.ICA.find_bads_eog` when more than one EOG components are present by `Christian O'Reilly`_ - -- Fix bug with non-preloaded data when using ``raw.apply_proj().load_data().get_data()`` where projectors were not applied by `Eric Larson`_ - -- Fix bug to permit :meth:`stc.project('nn', src) ` 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 :ref:`mne coreg` where reverse scalings were applied to ``src[0]['src_mri_t']`` for volume source spaces, so morphing and plotting did not work correctly 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 :meth:`mne.channels.DigMontage.plot` when reference channels with no defined position are present, by `Eric Larson`_ - -- Fix bug with :func:`mne.channels.read_custom_montage` where ``"headshape"`` points in SFP format were not read properly, by `Eric Larson`_ - -- Fix bug with setting HTML classes when using ``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 bug with :func:`mne.inverse_sparse.mixed_norm` and :func:`mne.inverse_sparse.gamma_map` with ``return_as_dipoles=True`` and :func:`mne.beamformer.rap_music` where ``dip.gof`` was the same for all dipoles. GOF values / explained variance across all dipoles now gets split among the dipoles using SVD of the lead fields. To get the total GOF, ``sum(dip.gof for dip in dipoles)`` can be used, by `Eric Larson`_ - -- Fix bug with :func:`mne.inverse_sparse.gamma_map` where output data was not assigned properly when using a free-orientation forward and ``xyz_same_gamma=False`` 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`_ - -- Fix bug with :func:`mne.viz.plot_vector_source_estimates` where ``clim='auto'`` and ``clim=dict(..., kind='percent')`` did not take into account the magnitude of the activation, 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 ` 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 topomap outlines in :meth:`mne.time_frequency.AverageTFR.plot_joint` and :meth:`mne.time_frequency.AverageTFR.plot_topo` 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.write_proj` where the number of columns was incorrectly written 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.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 with :func:`mne.viz.plot_sparse_source_estimates` when using ``'sphere'`` mode by `Eric Larson`_ and `Guillaume Favelier`_ - -- 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`_ - -- Fix bug with :func:`mne.events_from_annotations(raw.annotations) ` when ``orig_time`` of annotations is None and ``raw.first_time > 0``, by `Alex Gramfort`_ - -API changes -~~~~~~~~~~~ - -- 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``. - - The complete list of changed function names is: - - - ``mne.channels.find_ch_connectivity`` → `~mne.channels.find_ch_adjacency` - - ``mne.channels.read_ch_connectivity`` → `~mne.channels.read_ch_adjacency` - - ``mne.spatial_dist_connectivity`` → `~mne.spatial_dist_adjacency` - - ``mne.spatial_inter_hemi_connectivity`` → `~mne.spatial_inter_hemi_adjacency` - - ``mne.spatial_src_connectivity`` → `~mne.spatial_src_adjacency` - - ``mne.spatial_tris_connectivity`` → `~mne.spatial_tris_adjacency` - - ``mne.spatio_temporal_dist_connectivity`` → `~mne.spatio_temporal_dist_adjacency` - - ``mne.spatio_temporal_src_connectivity`` → `~mne.spatio_temporal_src_adjacency` - - ``mne.spatio_temporal_tris_connectivity`` → `~mne.spatio_temporal_tris_adjacency` - - "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`_ - -- The ``overwrite`` parameter of :func:`mne.write_bem_surfaces` and :func:`mne.write_bem_solution` defaults to ``True`` in 0.21 but will change to ``False`` in 0.22, 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(...) ` by `Eric Larson`_ - -- The method ``stc.normal`` for :class:`mne.VectorSourceEstimate` has been deprecated in favor of :meth:`stc.project('nn', src) ` 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 function ``mne.preprocessing.mark_flat`` has been deprecated in favor of ``mne.preprocessing.annotate_flat`` by `Eric Larson`_ - -- The default argument ``meg=True`` in :func:`mne.pick_types` will change to ``meg=False`` in version 0.22 by `Clemens Brunner`_ - -- Added :meth:`mne.io.Raw.get_montage`, which obtains the montage that an instance has, by `Adam Li`_ - - -Authors -~~~~~~~ - -People who contributed to this release in alphabetical order -(people with a + are first time contributors): - -* Adam Li -* Adonay Nunes -* Alejandro Weinstein -* Alex Rockhill -* Alexandre Gramfort -* Anton Nikolas Waniek -* Britta Westner -* Christian O'Reilly -* Clemens Brunner -* Daniel McCloy -* Eric Larson -* Evgenii Kalenkovich -* Fede Raimondo -* Guillaume Favelier -* Hubert Banville -* Jeroen Van Der Donckt + -* Johann Benerradi + -* Kyle Mathewson + -* Lau Møller Andersen + -* Liberty Hamilton + -* Luke Bloy -* Lx37 + -* Mainak Jas -* Marijn van Vliet -* Martin Billinger -* Martin Schulz + -* Martin van Harmelen -* Mikolaj Magnuski -* Olaf Hauk -* Rahul Nadkarni + -* Richard Höchenberger -* Robert Luke -* Sara Sommariva -* Simeon Wong + -* Stefan Appelhoff -* Steven Bierer + -* Svea Marie Meyer + -* Teon Brooks -* Thomas Hartmann -* Yu-Han Luo -* chapochn -* mshader diff --git a/doc/changes/v0.22.rst b/doc/changes/v0.22.rst deleted file mode 100644 index 1f4045ed780..00000000000 --- a/doc/changes/v0.22.rst +++ /dev/null @@ -1,263 +0,0 @@ -.. _changes_0_22: - -Version 0.22.0 (2020-12-17) ---------------------------- - -.. |Austin Hurst| replace:: **Austin Hurst** - -.. |Aniket Pradhan| replace:: **Aniket Pradhan** - -.. |Eduard Ort| replace:: **Eduard Ort** - -.. |Evan Hathaway| replace:: **Evan Hathaway** - -.. |Hongjiang Ye| replace:: **Hongjiang Ye** - -.. |Jeff Stout| replace:: **Jeff Stout** - -.. |Jonathan Kuziek| replace:: **Jonathan Kuziek** - -.. |Qianliang Li| replace:: **Qianliang Li** - -.. |Tod Flak| replace:: **Tod Flak** - -.. |Victoria Peterson| replace:: **Victoria Peterson** - - -Enhancements -~~~~~~~~~~~~ -- Add :func:`mne.read_evokeds_mff` to read averaged MFFs (requires mffpy >= 0.5.7) **by new contributor** |Evan Hathaway|_ (:gh:`8354`) - -- 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`_) - -- Add support for ``mri_fiducials='estimated'`` in :func:`mne.viz.plot_alignment` to allow estimating MRI fiducial locations using :func:`mne.coreg.get_mni_fiducials` (:gh:`8553` by `Eric Larson`_) - -- Update default values in :ref:`mne coreg` and :func:`mne.viz.plot_alignment` for clearer representation of MRI and digitized fiducial points (:gh:`8553` by `Alex Gramfort`_ and `Eric Larson`_) - -- Add ``n_pca_components`` argument to :func:`mne.viz.plot_ica_overlay` (:gh:`8351` by `Eric Larson`_) - -- Add :func:`mne.stc_near_sensors` to facilitate plotting ECoG data (:gh:`8190` by `Eric Larson`_) - -- Add ``proj`` argument to :func:`mne.make_fixed_length_epochs` (:gh:`8351` by `Eric Larson`_) - -- Add :func:`mne.preprocessing.realign_raw` to realign simultaneous raw recordings in the presence of clock drift (:gh:`8539` by `Eric Larson`_) - -- Reduce memory usage of volume source spaces (:gh:`8379` by `Eric Larson`_) - -- Speed up heavy use of :meth:`mne.SourceMorph.apply` for volumetric source spaces by use of the method :meth:`mne.SourceMorph.compute_vol_morph_mat` (:gh:`8366` by `Eric Larson`_) - -- Add support for non-uniform ``zooms`` (e.g., when using a surrogate MRI via :func:`mne.scale_mri`) in volumetric morphing (:gh:`8642` by `Eric Larson`_) - -- In :func:`mne.compute_source_morph` ``zooms`` are no longer required to match the spacing of ``src_to``, which is useful to ensure the morphing is accurate when the ``src_to`` spacing is large (e.g., 1 cm) (:gh:`8642` by `Eric Larson`_) - -- Add volumetric source space support to :func:`mne.labels_to_stc` (:gh:`8447` by `Eric Larson`_) - -- Speed up :class:`mne.decoding.TimeDelayingRidge` with edge correction using Numba (:gh:`8323` by `Eric Larson`_) - -- Add :meth:`mne.Epochs.reset_drop_log_selection` to facilitate writing epochs with many ignored entries in their drop log (:gh:`8449` by `Eric Larson`_) - -- Add sEEG source visualization using :func:`mne.stc_near_sensors` and sEEG working tutorial (:gh:`8402` by `Eric Larson`_ and `Adam Li`_) - -- Add :meth:`mne.channels.DigMontage.get_positions`, which will return a dictionary of channel positions, coordinate frame and fiducial locations (:gh:`8460` by `Adam Li`_) - -- Add support for writing digitization points in a coordinate frame other than head in :meth:`mne.channels.DigMontage.save` (:gh:`8532` by `Eric Larson`_) - -- Add ``picks`` parameter to :func:`mne.preprocessing.fix_stim_artifact` to specify which channel needs to be fixed (:gh:`8482` by `Alex Gramfort`_) - -- Add progress bar support to :func:`mne.time_frequency.csd_morlet` (:gh:`8608` by `Eric Larson`_) - -- Further improved documentation building instructions and execution on Windows (:gh:`8502` by `kalenkovich`_ and `Eric Larson`_) - -- Add option to disable TQDM entirely with ``MNE_TQDM='off'`` (:gh:`8515` by `Eric Larson`_) - -- Add option ``on_header_missing`` to :func:`mne.channels.read_polhemus_fastscan` (:gh:`8622` by `Eric Larson`_) - -- Add option ``window`` to ``mne.time_frequency.psd_welch`` and related functions (:gh:`8862` by `Eric Larson`_) - -- `mne.preprocessing.ICA.plot_sources` now displays an `mne.preprocessing.ICA.plot_properties` window when right-clicking on component names on the y-axis (:gh:`8381` by `Daniel McCloy`_) - -- :func:`mne.io.read_raw_edf`, :func:`mne.io.read_raw_bdf`, and :func:`mne.io.read_raw_gdf` now detect and handle invalid highpass/lowpass filter settings (:gh:`8584` by `Clemens Brunner`_) - -- If a ``baseline`` tuple containing one or two ``None`` values – e.g. ``(None, 0)``, ``(0, None)``, or ``(None, None)`` – is passed to `~mne.Epochs` or `~mne.Epochs.apply_baseline`, the ``None`` value(s) will be replaced with the actual time (i.e., :attr:`~mne.Epochs.tmin` and :attr:`~mne.Epochs.tmax`, respectively) when populating ``Epochs.baseline`` (:gh:`8442` by `Richard Höchenberger`_) - -- `~mne.Epochs` will now retain the information about an applied baseline correction, even if the baseline period is partially or completely removed through cropping later on (:gh:`8442` by `Richard Höchenberger`_) - -- Add :func:`mne.source_space.compute_distance_to_sensors` to compute distances between vertices and sensors (:gh:`8534` by `Olaf Hauk`_ and `Marijn van Vliet`_) - -- Annotations can now be shown/hidden interactively in raw plots (:gh:`8624` by `Daniel McCloy`_) - -- Added argument ``colors`` to `mne.grow_labels` (:gh:`8519` by `Olaf Hauk`_) - -- Added `mne.SourceEstimate.apply_baseline` method for baseline-correction of source estimates (:gh:`8452` by `Olaf Hauk`_) - -- New `mne.viz.Brain.set_time` method to set the displayed time in seconds (:gh:`8415` by `Daniel McCloy`_) - -- Update the ``backend`` parameter of :func:`mne.viz.plot_source_estimates` to integrate ``pyvista`` (:gh:`8395` by `Guillaume Favelier`_) - -- 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`_) - -Bugs -~~~~ -- Fix orthogonalization of power envelopes in ``mne.connectivity.envelope_correlation`` (:gh:`8658` **by new contributor** |Qianliang Li|_ and `Eric Larson`_) - -- Fix data overwrite of cascading simulation operations :`mne.simulation.simulate_raw` (:gh:`8633` **by new contributor** |Jeff Stout|_) - -- Fix a transpose issue of :func:`mne.decoding.CSP.plot_filters` (:gh:`8580` **by new contributor** |Hongjiang Ye|_) - -- Fix :func:`mne.io.read_raw_curry` to deal with Curry datasets that have channels that are listed in the labels file, but which are absent from the saved data file (e.g. 'Ref' channel). Also now populates info['meas_date'] if possible (:gh:`8400` **by new contributor** |Tod Flak|_) - -- Fix bug with mne.io.egi.tests/test_egi.py where it mandatorily downloaded testing data when it was not necessary (:gh:`8474` **by new contributor** |Aniket Pradhan|_) - -- Fix bug with reading split files that have dashes in the filename (:gh:`8339` **by new contributor** |Eduard Ort|_) - -- Fix bug with parsing EDF dates and date integers (:gh:`8558` **by new contributor** |Austin Hurst|_ and `Eric Larson`_) - -- Fix bug with reading EDF and KIT files on big endian architectures such as s390x (:gh:`8618` by `Eric Larson`_) - -- Fix bug with :func:`mne.beamformer.make_dics` where the ``rank`` parameter was not properly handled (:gh:`8594` by `Marijn van Vliet`_ and `Eric Larson`_) - -- Fix bug with :func:`mne.beamformer.apply_dics` where the whitener was not properly applied (:gh:`8610` by `Eric Larson`_) - -- Fix bug with `~mne.viz.plot_epochs_image` when ``order`` is supplied and multiple conditions are plotted (:gh:`8377` by `Daniel McCloy`_ ) - -- Fix bug with :func:`mne.viz.plot_source_estimates` when using the PyVista backend where singleton time points were not handled properly (:gh:`8285` by `Eric Larson`_) - -- Fix bug when passing ``axes`` to plotting functions, :func:`matplotlib.pyplot.tight_layout` will not be called when the figure was created using a constrained layout (:gh:`8344` by `Eric Larson`_) - -- Fix bug with compensated CTF data when picking channels without preload (:gh:`8318` by `Eric Larson`_) - -- Fix bug with plotting MEG topographies where the wrong extrapolation made was used in ICA (:gh:`8637` by `Eric Larson`_) - -- Fix bug when merging fNIRS channels in :func:`mne.viz.plot_evoked_topomap` and related functions (:gh:`8306` by `Robert Luke`_) - -- Fix bug where events could overflow when writing to FIF (:gh:`8448` by `Eric Larson`_) - -- :func:`mne.io.read_raw_edf` now supports EDF files with invalid recording dates (:gh:`8283` by `Clemens Brunner`_) - -- Fix bug with :func:`mne.io.Raw.save` when using ``split_naming='bids'`` where non-split files would still be named ``name_split-01_meg.fif`` instead of the requested ``name_meg.fif`` (:gh:`8464` by `Alex Gramfort`_ and `Eric Larson`_) - -- Fix bug with :class:`mne.preprocessing.ICA` where ``n_pca_components`` as a :class:`python:float` would give the number of components that explained less than or equal to the given variance. It now gives greater than the given number for better usability and consistency with :class:`sklearn.decomposition.PCA`. Generally this will mean that one more component will be included (:gh:`8326` by `Eric Larson`_) - -- Fix bug with :class:`mne.preprocessing.ICA` where projections were not tracked properly (:gh:`8343` by `Eric Larson`_) - -- Fix bug where extrapolation points created artifacts in :func:`mne.viz.plot_evoked_topomap` and related functions (:gh:`8425` by `Mikołaj Magnuski`_) - -- Fix bug with :func:`mne.preprocessing.read_ica_eeglab` where full-rank data were not handled properly (:gh:`8326` by `Eric Larson`_) - -- Fix bug with :ref:`somato-dataset` where the BEM was not included (:gh:`8317` by `Eric Larson`_) - -- Fix bug with coordinate frames when performing volumetric morphs via :func:`mne.compute_source_morph` and :meth:`mne.SourceMorph.apply` that could lead to ~5 mm bias (:gh:`8642` by `Eric Larson`_) - -- Fix bug with volumetric rendering alpha in :meth:`mne.VolSourceEstimate.plot_3d` and related functions (:gh:`8663` by `Eric Larson`_) - -- Fix missing documentation of :func:`mne.io.read_raw_nihon` in :ref:`tut-imorting-eeg-data` (:gh:`8320` by `Adam Li`_) - -- Fix bug with :func:`mne.add_reference_channels` when :func:`mne.io.Raw.reorder_channels` or related methods are used afterward (:gh:`8303`, :gh:`#8484` by `Eric Larson`_) - -- Fix bug where the ``verbose`` arguments to :meth:`mne.Evoked.apply_baseline` and :meth:`mne.Epochs.apply_baseline` were not keyword-only (:gh:`8349` by `Eric Larson`_) - -- ``ICA.max_pca_components`` will not be altered by calling `~mne.preprocessing.ICA.fit` anymore. Instead, the new attribute ``ICA.max_pca_components_`` will be set (:gh:`8321` by `Richard Höchenberger`_) - -- Fix bug that `~mne.viz.plot_ica_overlay` would sometimes not create red traces (:gh:`8341` by `Richard Höchenberger`_) - -- Fix bug with :class:`~mne.preprocessing.ICA` where ``n_components=None, n_pca_components=None`` could lead to unstable unmixing matrix inversion by making ``n_components=None`` also use the lesser of ``n_components=0.999999`` and ``n_components=n_pca_components`` (:gh:`8351` by `Eric Larson`_) - -- The ``ica.n_pca_components`` property is no longer be updated during :meth:`mne.preprocessing.ICA.fit`, instead ``ica.n_components_`` will be added to the instance (:gh:`8351` by `Eric Larson`_) - -- Pass ``rank`` everyhwere in forward preparation for source imaging. This bug affected sparse solvers when using maxfilter data (:gh:`8368` by `Alex Gramfort`_) - -- Fix bug in :func:`mne.viz.plot_alignment` where ECoG and sEEG channels were not plotted and fNIRS channels were always plotted in the head coordinate frame (:gh:`8393` by `Eric Larson`_) - -- Fix bug in :func:`mne.set_bipolar_reference` where ``ch_info`` could contain invalid channel information keys (:gh:`8416` by `Eric Larson`_) - -- When reading BrainVision raw data, the channel units and types were sometimes not inferred correctly (:gh:`8434` by `Richard Höchenberger`_) - -- Attempting to remove baseline correction from preloaded `~mne.Epochs` will now raise an exception (:gh:`8435` by `Richard Höchenberger`_) - -- :meth:`mne.Report.parse_folder` will now correctly handle split FIFF files (:gh:`8486`, :gh:`8491` by `Richard Höchenberger`_) - -- Fix bug where BrainVision channel names, event types, and event descriptions containing commas were incorrectly parsed (:gh:`8492` by `Stefan Appelhoff`_) - -- Fix bug in :func:`mne.preprocessing.compute_fine_calibration` where the magnetometer calibration coefficients were computed incorrectly (:gh:`8522` by `Eric Larson`_) - -- Fix bug in :func:`mne.io.read_raw_eeglab` where empty event durations led to an error (:gh:`8384` by `Mikołaj Magnuski`_) - -- Fix inset sensor plots to always use equal aspect (:gh:`8545` by `Daniel McCloy`_) - -- Fix bug in `mne.viz.plot_compare_evokeds` where evokeds with identical ``comment`` attributes would not plot properly if passed as a list (:gh:`8590` by `Daniel McCloy`_) - -- Fix bug in ``mne.time_frequency.psd_welch`` and related functions where the window default errantly changed from ``'hamming'`` to ``('tukey', 0.25)`` (:gh:`8862` by `Eric Larson`_) - -- Fix bug in :func:`mne.io.read_raw_kit` where scale factors for EEG channels could be set to zero (:gh:`8542` by `Eric Larson`_) - -- Fix reading GDF files with excluded channels in :func:`mne.io.read_raw_gdf` (:gh:`8520` by `Clemens Brunner`_) - -- Fix automatic selection of extrapolation mask type from channel type when plotting field maps (:gh:`8589` by `Daniel McCloy`_) - -- Fix bug in :func:`mne.viz.set_3d_title` where 3D plot could have multiple titles that overlap (:gh:`8564` by `Guillaume Favelier`_) - -- Fix bug in :func:`mne.viz.set_3d_view` where plotter is not updated properly causing camera issues in the doc (:gh:`8564` by `Guillaume Favelier`_) - -- :func:`mne.preprocessing.find_ecg_events` didn't take the ``tstart`` parameter value into account when calculating the average heart rate (:gh:`8605` by `Richard Höchenberger`_) - -API changes -~~~~~~~~~~~ - -- Minimum required versions were increased for core dependencies NumPy (1.15.4), SciPy (1.1.0), and Matplotlib (3.0) and for the optional dependencies scikit-learn (0.20.2) and pandas (0.23.4) (:gh:`8374` by `Eric Larson`_) - -- The parameter ``on_split_missing`` has been added to :func:`mne.io.read_raw_fif` and its default will change from ``'warn'`` to ``'raise'`` in 0.23, by (:gh:`8357` `Eric Larson`_) - -- The ``max_pca_components`` argument of :class:`~mne.preprocessing.ICA` has been deprecated, use ``n_components`` during initialization and ``n_pca_components`` in :meth:`~mne.preprocessing.ICA.apply` instead (:gh:`8351` by `Eric Larson`_) - -- The ``n_pca_components`` argument of :class:`~mne.preprocessing.ICA` has been deprecated, use ``n_pca_components`` in :meth:`~mne.preprocessing.ICA.apply` (:gh:`8356` by `Eric Larson`_) - -- The ``trans`` argument of :func:`mne.extract_label_time_course` is deprecated and will be removed in 0.23 as it is no longer necessary (:gh:`8389` by `Eric Larson`_) - -- 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`_) - -Authors -~~~~~~~ - -People who contributed to this release in alphabetical order -(people with a + are first time contributors): - -* Adam Li -* Alexandre Gramfort -* Aniket Pradhan + -* Austin Hurst + -* Christian Brodbeck -* Clemens Brunner -* Daniel McCloy -* Denis A. Engemann -* Eduard Ort + -* Eric Larson -* Evan Hathaway + -* Evgenii Kalenkovich -* Fede Raimondo -* Guillaume Favelier -* Hongjiang Ye + -* Jean-Remi King -* Jeff Stout + -* Jonathan Kuziek + -* Jussi Nurminen -* Justus Schwabedal -* Keith Doelling -* Kyle Mathewson -* Mads Jensen -* Mainak Jas -* Marijn van Vliet -* Mikolaj Magnuski -* Olaf Hauk -* Qianliang Li + -* Richard Höchenberger -* Robert Luke -* Stefan Appelhoff -* Thomas Hartmann -* Tod Flak + -* Victoria Peterson + diff --git a/doc/changes/v0.23.rst b/doc/changes/v0.23.rst deleted file mode 100644 index 0fa34b0dc2d..00000000000 --- a/doc/changes/v0.23.rst +++ /dev/null @@ -1,388 +0,0 @@ -.. _changes_0_23_0: - -Version 0.23.0 (2021-04-27) ---------------------------- - -.. |Jack Zhang| replace:: **Jack Zhang** - -.. |Sumalyo Datta| replace:: **Sumalyo Datta** - -.. |Anna Padee| replace:: **Anna Padee** - -.. |Richard Koehler| replace:: **Richard Koehler** - -.. |Zhi Zhang| replace:: **Zhi Zhang** - -.. |Rotem Falach| replace:: **Rotem Falach** - -.. |Andres Rodriguez| replace:: **Andres Rodriguez** - -.. |Matt Sanderson| replace:: **Matt Sanderson** - -.. |Enrico Varano| replace:: **Enrico Varano** - -.. |Dominik Welke| replace:: **Dominik Welke** - -.. |Judy D Zhu| replace:: **Judy D Zhu** - -.. |Valerii Chirkov| replace:: **Valerii Chirkov** - -.. |Matteo Anelli| replace:: **Matteo Anelli** - -.. |Apoorva Karekal| replace:: **Apoorva Karekal** - -.. |Cora Kim| replace:: **Cora Kim** - -.. |Silvia Cotroneo| replace:: **Silvia Cotroneo** - -.. |Ram Pari| replace:: **Ram Pari** - -.. |Erica Peterson| replace:: **Erica Peterson** - -.. |Maggie Clarke| replace:: **Maggie Clarke** - -.. |Felix Klotzsche| replace:: **Felix Klotzsche** - -Enhancements -~~~~~~~~~~~~ -- Add support for exporting to EEGLAB's set format with :mod:`eeglabio` with new methods :meth:`mne.io.Raw.export` and :meth:`mne.Epochs.export`. (:gh:`9192` **by new contributor** |Jack Zhang|_) - -- :func:`mne.viz.plot_evoked_topo` now uses a Minimum/Maximum of peaks for each channel type to calculate ylim when input param is None (:gh:`9285` **by new contributor** |Ram Pari|_) - -- Add exclude parameter to :func:`mne.viz.plot_evoked_topo` (:gh:`9278` **by new contributor** |Ram Pari|_) - -- Add :meth:`mne.time_frequency.EpochsTFR.to_data_frame` and :meth:`mne.time_frequency.AverageTFR.to_data_frame` methods (:gh:`9124` **by new contributor** |Felix Klotzsche|_) - -- Add ``selection`` and ``drop_log`` to :class:`mne.time_frequency.EpochsTFR` (:gh:`9124` **by new contributor** |Felix Klotzsche|_) - -- Add CSV, TSV, and XYZ support to :func:`mne.channels.read_custom_montage` (:gh:`9203` **by new contributor** |Jack Zhang|_) - -- Add HTML representation for `~mne.Epochs` in Jupyter Notebooks (:gh:`9174` **by new contributor** |Valerii Chirkov|_) - -- Speed up :func:`mne.viz.plot_ica_properties` by refactoring (:gh:`9174` **by new contributor** |Valerii Chirkov|_) - -- Add ``apply_function`` method to epochs and evoked objects (:gh:`9088` **by new contributor** |Erica Peterson|_ and `Victoria Peterson`_) - -- New tutorial for function :func:`mne.make_fixed_length_epochs` (:gh:`9156` **by new contributor** |Erica Peterson|_) - -- Add different colors for each volume source space in :func:`mne.viz.plot_alignment` (:gh:`9043` **by new contributor** |Valerii Chirkov|_) - -- Add ``overlap`` parameter to :func:`mne.make_fixed_length_epochs` to allow creating overlapping fixed length epochs (:gh:`9096` **by new contributor** |Silvia Cotroneo|_) - -- Add :meth:`mne.Dipole.to_mni` for more convenient dipole.pos to MNI conversion (:gh:`9043` **by new contributor** |Valerii Chirkov|_) - -- Update citations in maxwell.py (:gh:`9043` **by new contributor** |Valerii Chirkov|_) - -- New Tutorial for analyzing frequency-tagging data (:gh:`8867` **by new contributor** |Dominik Welke|_ and `kalenkovich`_) - -- Add dbs as new channel type for deep brain stimulation (DBS) recordings (:gh:`8739` **by new contributor** |Richard Koehler|_) - -- Add some preprocessing functions to the EEGLAB migration guide (:gh:`9169` **by new contributor** |Apoorva Karekal|_) - -- Add :func:`mne.chpi.extract_chpi_locs_kit` to read cHPI coil locations from KIT/Yokogawa data (:gh:`8813` **by new contributor** |Matt Sanderson|_, `Robert Seymour`_, and `Eric Larson`_) - -- Add ``match_alias`` parameter to :meth:`mne.io.Raw.set_montage` and related functions to match unrecognized channel location names to known aliases (:gh:`8799` **by new contributor** |Zhi Zhang|_) - -- Update the ``notebook`` 3d backend to use ``ipyvtk_simple`` for a better integration within ``Jupyter`` (:gh:`8503` by `Guillaume Favelier`_) - -- Remove the 15-character limitation for channel names when writing to FIF format. If you need the old 15-character names, you can use something like ``raw.rename_channels({n: n[:13] for n in raw.ch_names}, allow_duplicates=True)``, by `Eric Larson`_ (:gh:`8346`) - -- Add channel-specific annotation support to :class:`mne.Annotations` via ``ch_names`` parameter (:gh:`8896` by `Eric Larson`_) - -- Add toggle-all button to :class:`mne.Report` HTML and ``width`` argument to ``mne.Report.add_bem_to_section`` (:gh:`8723` by `Eric Larson`_) - -- Add infant template MRI dataset downloader :func:`mne.datasets.fetch_infant_template` (:gh:`8738` by `Eric Larson`_ and `Christian O'Reilly`_) - -- Add digitizer information to :func:`mne.io.read_raw_egi` (:gh:`8789` by `Christian Brodbeck`_) - -- Add support for reading some incomplete raw FIF files in :func:`mne.io.read_raw_fif` (:gh:`9268` by `Eric Larson`_) - -- Allow reading digitization from files other than ``*.fif`` in the coregistration GUI (:gh:`8790` by `Christian Brodbeck`_) - -- Speed up :func:`mne.inverse_sparse.tf_mixed_norm` using STFT/ISTFT linearity (:gh:`8697` by `Eric Larson`_) - -- Reduce memory consumption of `mne.io.Raw` and speed up epoching when thousands of events are present for `mne.Epochs` (:gh:`8801` by `Eric Larson`_) - -- Speed up ``import mne`` by reducing function creation overhead (:gh:`8829` by `Eric Larson`_) - -- `mne.Report.parse_folder` now processes supported non-FIFF files by default, too (:gh:`8744` by `Richard Höchenberger`_) - -- `mne.Report` has gained the new methods `~mne.Report.add_custom_js` and `~mne.Report.add_custom_css` for adding user-defined JavaScript and styles (:gh:`8762`, :gh:`9037` by `Richard Höchenberger`_) - -- Add option to control appearance of opaque inside surface of the head to :ref:`mne coreg` (:gh:`8793` by `Eric Larson`_) - -- Add option to disable projection using ``--projoff`` in :ref:`mne browse_raw` (:gh:`9262` by `Eric Larson`_) - -- Add keypress to toggle projection using ``shift+j`` in :meth:`mne.io.Raw.plot` and :ref:`mne browse_raw` (:gh:`9262` by `Eric Larson`_) - -- Add support for non-FIF files in :ref:`mne browse_raw` using :func:`mne.io.read_raw` (:gh:`8806` by `Eric Larson`_) - -- Add :func:`mne.io.read_raw_nedf` for reading StarStim / enobio NEDF files (:gh:`8734` by `Tristan Stenner`_) - -- Add :meth:`raw.describe() ` to display (or return) descriptive statistics for each channel (:gh:`8760` by `Clemens Brunner`_) - -- Add :meth:`annotations.to_data_frame() ` to return annotations as a pandas dataframe (:gh:`8783` by `Robert Luke`_) - -- Add :func:`mne.preprocessing.compute_maxwell_basis` to compute the SSS basis function (:gh:`8822` by `Eric Larson`_) - -- Add the ``silhouette`` parameter to :class:`mne.viz.Brain` to display sharp edges and improve perception (:gh:`8771` by `Guillaume Favelier`_) - -- Add warning to :func:`mne.cov.compute_whitener` when an explicit ``rank`` parameter leads to a large increase in condition number (:gh:`8805` by `Eric Larson`_) - -- Add parameter ``align=True`` to `mne.viz.Brain.show_view` to make views relative to the closest canonical (MNI) axes rather than the native MRI surface RAS coordinates (:gh:`8794` by `Eric Larson`_) - -- Add ``auto_close`` to ``mne.Report.add_figs_to_section`` and ``mne.Report.add_slider_to_section`` to manage closing figures (:gh:`8730` by `Guillaume Favelier`_) - -- Add :func:`mne.write_head_bem` to support writing head surface files (:gh:`8841` by `Yu-Han Luo`_) - -- The signal of ``resp`` (respiratory) channels is now assumed to be in the unit Volt (:gh:`8858` by `Richard Höchenberger`_) - -- Static type checkers like Pylance (comes with VS Code) now display the parameters of many more functions correctly, largely improving overall usability for VS Code users (:gh:`8862` by `Richard Höchenberger`_) - -- Support new EEGLAB file format (:gh:`8874` by `Clemens Brunner`_) - -- Reading and writing FIFF files whose filenames end with ``_meg.fif.gz``, ``_eeg.fif(.gz)``, and ``_ieeg.fif(.gz)`` doesn't emit a warning anymore; this improves interobaility with BIDS-formatted datasets (:gh:`8868` by `Richard Höchenberger`_) - -- On macOS, we now set the environment variable ``QT_MAC_WANTS_LAYER`` to ``"1"`` if it hasn't been set explicitly by the user, in order to ensure that `~mne.SourceEstimate` plots work on macOS 11 with older versions of Qt and PyQt (:gh:`8959` by `Richard Höchenberger`_) - -- :func:`mne.time_frequency.EpochsTFR.average` now allows different ways of averaging, such as "median", or callable functions (:gh:`8879` by `Adam Li`_) - -- `~mne.Epochs` metadata can now be generated automatically from events using `mne.epochs.make_metadata` (:gh:`8834` by `Richard Höchenberger`_) - -- Interactions with sliders in `mne.Report` will now continuously update the linked content (it was updated only on mouse button release before) (:gh:`9023` by `Richard Höchenberger`_) - -- `mne.viz.plot_drop_log` and :meth:`mne.Epochs.plot_drop_log` now omit displaying the subject name in the title if ``subject=None`` is passed (:gh:`9015` by `Richard Höchenberger`_) - -- Plot ECoG tutorial now uses a real epilepsy seizure dataset and visualizes the seizure onset (:gh:`9087` by `Eric Larson`_, `Adam Li`_, `Alex Rockhill`_ and `Liberty Hamilton`_) - -- Improve documentation of Report-Class (:gh:`9113` by `Martin Schulz`_) - -- Add :func:`mne.channels.DigMontage.add_estimated_fiducials` which will add LPA, RPA and Nasion fiducial points to the ``DigMontage`` object in ``mri`` coordinate frame (:gh:`9118` by `Adam Li`_) - -- :func:`mne.io.anonymize_info` now anonymizes also sex and hand fields when ``keep_his`` is ``False`` (:gh:`9103`, :gh:`9175` **by new contributor** |Rotem Falach|_ and `Richard Höchenberger`_) - -- Add parameter ``theme`` to :class:`mne.viz.Brain` for optional Dark-Mode (:gh:`9149` by `Martin Schulz`_, `Guillaume Favelier`_) - -- Add first_samp support for raw simulations with `mne.simulation.simulate_raw` and `mne.simulation.SourceSimulator` (:gh:`9166` by `Steven Bierer`_) - -- `~mne.Evoked` gained a ``baseline`` attribute that is automatically assembled based on the baseline of the averaged `~mne.Epochs` (:gh:`9210` by `Richard Höchenberger`_) - -- Add ``units`` parameter to :meth:`mne.io.Raw.get_data` to return data in the desired unit (:gh:`9136` by `Johann Benerradi`_ and `Stefan Appelhoff`_) - -- Add :func:`mne.preprocessing.equalize_bads` to interpolate bad channels in a list of `~mne.Evoked`, `~mne.Epochs` or `~mne.io.Raw` having different sets of bad channels (:gh:`9241` by `Alex Gramfort`_) - -- :meth:`mne.Epochs.equalize_event_counts` can now be called without providing a list of event names, and will equalize the counts of **all** event types present in the `~mne.Epochs` (:gh:`9261` by `Richard Höchenberger`_) - -- :func:`mne.preprocessing.find_eog_events` and :func:`mne.preprocessing.create_eog_epochs` now accept a list of channel names, allowing you to specify multiple EOG channels at once (:gh:`9269` by `Richard Höchenberger`_) - -- Improve performance of :func:`mne.set_bipolar_reference` (:gh:`9270` by `Martin Schulz`_) - -- Add support for setting montages on fNIRS data, with built in standard montages for Artinis OctaMon and Artinis Brite23 devices (:gh:`9141` by `Johann Benerradi`_, `Robert Luke`_ and `Eric Larson`_) - -- Enable support for reading SNIRF files with 2D optode positions (:gh:`9347` `Robert Luke`_) - - -Bugs -~~~~ -- Fix bug with :func:`mne.time_frequency.tfr` where plot misbehaved. Plot now always returns a list of figures instead of a single figure handle (:gh:`8013` **by new contributor** `Eduard Ort`_) - -- Fix bug with :func:`mne.viz.plot_evoked_topo` where set ylim parameters gets swapped across channel types. (:gh:`9207` **by new contributor** |Ram Pari|_) - -- Fix bug with :func:`mne.io.read_raw_edf` where µV was not correctly recognized (:gh:`9187` **by new contributor** |Sumalyo Datta|_) - -- Fix bug with :func:`mne.viz.plot_compare_evokeds` did not check type of combine. (:gh:`9151` **by new contributor** |Matteo Anelli|_) - -- Fix bug with :func:`mne.viz.plot_evoked_topo` where ``ylim`` was only being applied to the first channel in the dataset (:gh:`9162` **by new contributor** |Ram Pari|_ ) - -- Fix bug with :func:`mne.Epochs.plot_image` allowing interactive zoom to work properly (:gh:`9152` by **by new contributor** |Maggie Clarke|_ and `Daniel McCloy`_) - -- Fix bug with :func:`mne.Epochs.plot_image` where the ``x_label`` was different depending on the evoked parameter (:gh:`9115` **by new contributor** |Matteo Anelli|_) - -- Fix bug with restricting :func:`mne.io.Raw.save` saving options to .fif and .fif.gz extensions (:gh:`9062` **by new contributor** |Valerii Chirkov|_) - -- Fix bug with :func:`mne.io.read_raw_kit` where missing marker coils were not handled (:gh:`8989` **by new contributor** |Judy D Zhu|_) - -- Fix bug with ``mne.connectivity.spectral_connectivity`` where time axis in Epochs data object was dropped. (:gh:`8839` **by new contributor** |Anna Padee|_) - -- Fix bug with `mne.io.Raw.resample` to allow passing ``stim_picks='misc'`` (:gh:`8844` **by new contributor** |Enrico Varano|_ and `Eric Larson`_) - -- Fix bugs with `mne.io.read_raw_persyst` where multiple ``Comments`` with the same name are allowed, and ``Comments`` with a "," character are now allowed (:gh:`8311` and :gh:`8806` **by new contributor** |Andres Rodriguez|_ and `Adam Li`_) - -- Fix zen mode and scalebar toggling for :meth:`raw.plot() ` when using the ``macosx`` matplotlib backend (:gh:`8688` by `Daniel McCloy`_) - -- Fix bug with :func:`mne.viz.snapshot_brain_montage` where the positions were incorrect (:gh:`8983` by `Eric Larson`_) - -- Fix bug with :func:`mne.preprocessing.maxwell_filter` where the eSSS basis had to exactly match the good channels instead of being a superset (:gh:`8675` by `Eric Larson`_) - -- Fix bug with ``mne.Report.add_bem_to_section`` where ``n_jobs != 1`` would cause ``n_jobs`` subsets of MRI images in some orientations to be flipped (:gh:`8713` by `Eric Larson`_) - -- Fix bug with :meth:`raw.plot() ` where annotations didn't immediately appear when changing window duration (:gh:`8689` by `Daniel McCloy`_) - -- Fix bug with :meth:`raw.plot() ` where ``scalings='auto'`` did not compute scalings using the full range of data (:gh:`8806` by `Eric Larson`_) - -- Fix bug with :meth:`raw.plot() ` where setting a ``lowpass`` could lead to non-data-channels not plotting (:gh:`8954` by `Eric Larson`_) - -- Fix bug with :meth:`mne.io.Raw.load_data` and :meth:`mne.Epochs.drop_bad` where ``verbose`` logging was not handled properly (:gh:`8884` by `Eric Larson`_) - -- Fix bug with :func:`mne.io.read_raw_nicolet` where header type values such as num_sample and duration_in_sec where not parsed properly (:gh:`8712` by `Alex Gramfort`_) - -- Fix bug with :func:`mne.preprocessing.read_ica_eeglab` when reading decompositions using PCA dimensionality reduction (:gh:`8780` by `Alex Gramfort`_ and `Eric Larson`_) - -- Fix bug with :func:`mne.minimum_norm.make_inverse_operator` where ``depth`` was errantly restricted to be less than or equal to 1. (:gh:`8804` by `Eric Larson`_) - -- Fix bug with :func:`mne.stats.permutation_cluster_1samp_test` and related clustering functions when ``adjacency=None`` and ``out_type='indices'`` (:gh:`#8842` by `Eric Larson`_) - -- Fix bug with :func:`mne.viz.plot_alignment` where plotting a sphere model could ignore the ``brain`` argument (:gh:`8857` by `Eric Larson`_) - -- Fix bug with :func:`mne.SourceEstimate.plot` where flatmaps were not positioned properly when using ``hemi='both'`` (:gh:`9315` by `Eric Larson`_) - -- Fix bug with :meth:`mne.Annotations.save` where files could be overwritten accidentally, it can now be controlled via the ``overwrite`` argument (:gh:`8896` by `Eric Larson`_) - -- Fix bug with ``replace`` argument of ``mne.Report.add_bem_to_section`` and ``mne.Report.add_slider_to_section`` (:gh:`8723` by `Eric Larson`_) - -- Fix bug with :func:`mne.chpi.compute_chpi_locs` where all cHPI coils being off would lead to an empty array of the wrong dimensionality (:gh:`8956` by `Eric Larson`_) - -- Fix bug with :func:`mne.extract_label_time_course` where labels, STCs, and the source space were not checked for compatible ``subject`` attributes (:gh:`9284` by `Eric Larson`_) - -- Fix bug with :func:`mne.grow_labels` where ``overlap=False`` could run forever or raise an error (:gh:`9317` by `Eric Larson`_) - -- Fix compatibility bugs with ``mne_realtime`` (:gh:`8845` by `Eric Larson`_) - -- Fix bug with `mne.viz.Brain` where non-inflated surfaces had an X-offset imposed by default (:gh:`8794` by `Eric Larson`_) - -- Fix bug with :ref:`mne coreg` where nasion values were not updated when clicking (:gh:`8793` by `Eric Larson`_) - -- Fix bug with matplotlib-based 3D plotting where ``Axes3D`` were not properly initialized in :func:`mne.viz.plot_source_estimates` (:gh:`8811` by `Chris Bailey`_) - -- Allow sEEG channel types in :meth:`mne.Evoked.plot_joint` (:gh:`8736` by `Daniel McCloy`_) - -- Fix bug where hidden annotations could be deleted interactively in :meth:`mne.io.Raw.plot` windows (:gh:`8831` by `Daniel McCloy`_) - -- Function :func:`mne.set_bipolar_reference` was not working when passing ``Epochs`` constructed with some ``picks`` (:gh:`8728` by `Alex Gramfort`_) - -- Fix anonymization issue of FIF files after IO round trip (:gh:`8731` by `Alex Gramfort`_) - -- Fix bug in `mne.preprocessing.ICA.plot_sources` where right-clicking component names could yield `~mne.preprocessing.ICA.plot_properties` windows for the wrong component if ``picks`` had been specified (:gh:`8996` by `Daniel McCloy`_) - -- Fix title not shown in :func:`mne.viz.plot_montage` (:gh:`8752` by `Clemens Brunner`_) - -- `mne.io.read_raw_egi` now correctly handles `pathlib.Path` filenames (:gh:`8759` by `Richard Höchenberger`_) - -- `mne.viz.plot_evoked` and `mne.Evoked.plot` now correctly plot global field power (GFP) for EEG data when ``gfp=True`` or ``gfp='only'`` is passed (used to plot RMS). For MEG data, we continue to plot the RMS, but now label it correctly as such (:gh:`8775` by `Richard Höchenberger`_) - -- Fix bug with :ref:`mne make_scalp_surfaces` where ``--overwrite`` was not functional (:gh:`8800` by `Yu-Han Luo`_) - -- Fix bug with :func:`mne.viz.plot_topomap` when plotting gradiometers with a missing channel in a pair (:gh:`8817` by `Alex Gramfort`_) - -- :meth:`epochs.crop() ` now also adjusts the ``reject_tmin`` and ``reject_tmax`` attributes if necessary (:gh:`8821` by `Richard Höchenberger`_) - -- When creating `~mne.Epochs`, we now ensure that ``reject_tmin`` and ``reject_tmax`` cannot fall outside of the epochs' time interval anymore (:gh:`8821` by `Richard Höchenberger`_) - -- `~mne.io.read_raw_bti` erroneously treated response channels as respiratory channels (:gh:`8856` by `Richard Höchenberger`_) - -- The RMS trace shown in the time viewer of `~mne.SourceEstimate` plots is now correctly labeled as ``RMS`` (was ``GFP`` before) (:gh:`8965` by `Richard Höchenberger`_) - -- Fix bug with :meth:`mne.SourceEstimate.plot` and related functions where the scalars were not interactively updated properly (:gh:`8985` by `Eric Larson`_) - -- Fix bug with mne.channels.find_ch_adjacency() returning wrong adjacency for Neuromag122-Data (:gh:`8891` by `Martin Schulz`_) - -- Fix :func:`mne.read_dipole` yielding :class:`mne.Dipole` objects that could not be indexed (:gh:`8963` by `Marijn van Vliet`_) - -- Fix bug when setting n_jobs > 1 in :meth:`mne.Report.parse_folder` (:gh:`9109` by `Martin Schulz`_) - -- Fix bug with :meth:`mne.Evoked.plot_image` where an incorrect clim parameter did not raise any error (:gh:`9115` **by new contributor** |Matteo Anelli|_) - -- Fix bug with ``mne.io.Raw.pick`` where incorrect fnirs types were returned (:gh:`9178` by `Robert Luke`_) - -- Fix bug when passing both axes and picks to `mne.viz.plot_compare_evokeds` (:gh:`9252` by `Daniel McCloy`_) - -- Improved string representation of `~mne.Epochs` containing multiple event types; improved (and more mathematically correct) ``evoked.comment`` in the `mne.combine_evoked` output; and better (and often more concise) legend labels in the figures created via `~mne.viz.plot_compare_evokeds` (:gh:`9027` by `Richard Höchenberger`_) - -- :func:`mne.preprocessing.find_ecg_events` now correctly handles situation where no ECG activity could be detected, and correctly returns an empty array of ECG events (:gh:`9236` by `Richard Höchenberger`_) - -- Fix bug with ``picks`` attribute for `~mne.Epochs` after calling :meth:`mne.Epochs.add_channels` (:gh:`9246` by `Alex Gramfort`_) - -- Fix bug where ``backend='notebook'`` could not be used in :meth:`mne.SourceEstimate.plot` (:gh:`9305` by `Jean-Remi King`_) - -- `mne.preprocessing.compute_proj_eog` and `mne.preprocessing.compute_proj_ecg` now return empty lists if no EOG or ECG events, respectively, could be found. Previously, we'd return ``None`` in these situations, which does not match the documented behavior of returning a list of projectors (:gh:`9277` by `Richard Höchenberger`_) - -API changes -~~~~~~~~~~~ -- Introduced new ``'auto'`` settings for ``ICA.max_iter``. The old default ``max_iter=200`` will be removed in MNE-Python 0.24 (:gh:`9099` **by new contributor** |Cora Kim|_) - -- ``mne.viz.plot_sensors_connectivity`` now allows setting the colorbar label via the ``cbar_label`` parameter (:gh:`9248` by `Daniel McCloy`_) - -- ``mne.read_selection`` has been deprecated in favor of `mne.read_vectorview_selection`. ``mne.read_selection`` will be removed in MNE-Python 0.24 (:gh:`8870` by `Richard Höchenberger`_) - -- ``mne.beamformer.tf_dics`` has been deprecated and will be removed in MNE-Python 0.24 (:gh:`9122` by `Britta Westner`_) - -- Fitting `~mne.preprocessing.ICA` on baseline-corrected `~mne.Epochs`, and / or applying it on baseline-corrected `~mne.Epochs` or `~mne.Evoked` data will now display a warning. Users are advised to only baseline correct their data after cleaning is completed (:gh:`9033` by `Richard Höchenberger`_) - -- Supplying multiple channel names to `mne.preprocessing.find_eog_events` or `mne.preprocessing.compute_proj_eog` as a string of comma-separated channel names has been deprecated; please pass a list of channel names instead. Support for comma-separated strings will be removed in MNE-Python 0.24 (:gh:`9269` by `Richard Höchenberger`_) - -- The default in :func:`mne.beamformer.make_dics` of ``real_filter=False`` will change to ``real_filter=True`` in 0.24 (:gh:`9340` by `Britta Westner`_) - -Authors -~~~~~~~ - -People who contributed to this release in alphabetical order -(people with a + are first time contributors): - -* Adam Li -* Alex Rockhill -* Alexandre Gramfort -* Ana Radanovic -* Andres Rodriguez+ -* Anna Padee+ -* Apoorva Karekal+ -* Britta Westner -* Catalina Magalvan -* Christian Brodbeck -* Christian Mista -* Christian O'Reilly -* Christina Zhao -* Christopher J. Bailey -* Clemens Brunner -* Cora Kim+ -* Daniel McCloy -* Denis A. Engemann -* Dominik Welke+ -* Eduard Ort -* Enrico Varano+ -* Eric Larson -* Erica Peterson+ -* Evgenii Kalenkovich -* Felix Klotzsche+ -* Giorgio Marinato -* Guillaume Favelier -* Jack Zhang+ -* Jean-Remi King -* Johann Benerradi -* Joris Van den Bossche -* Judy D Zhu+ -* Liberty Hamilton -* Luke Bloy -* Maggie Clarke+ -* Mainak Jas -* Manorama Kadwani -* Marijn van Vliet -* Martin Schulz -* Matt Sanderson+ -* Matteo Anelli+ -* Nicolas Gensollen -* Ram Pari+ -* Richard Höchenberger -* Richard Koehler+ -* Robert Luke -* Rotem Falach+ -* Sebastien Treguer -* Silvia Cotroneo+ -* Stefan Appelhoff -* Steven Bierer -* Sumalyo Datta+ -* Timon Merk -* Tristan Stenner -* Valerii Chirkov+ -* Victoria Peterson -* Yu-Han Luo -* Zhi Zhang+ diff --git a/doc/changes/v0.24.rst b/doc/changes/v0.24.rst deleted file mode 100644 index 5f92e3dbdf6..00000000000 --- a/doc/changes/v0.24.rst +++ /dev/null @@ -1,411 +0,0 @@ -.. _changes_0_24_0: - -Version 0.24.0 (2021-11-03) ---------------------------- - -.. |David Julien| replace:: **David Julien** - -.. |Dominique Makowski| replace:: **Dominique Makowski** - -.. |Romain Derollepot| replace:: **Romain Derollepot** - -.. |Jan Sosulski| replace:: **Jan Sosulski** - -.. |Xiaokai Xia| replace:: **Xiaokai Xia** - -.. |Marian Dovgialo| replace:: **Marian Dovgialo** - -.. |Pierre-Antoine Bannier| replace:: **Pierre-Antoine Bannier** - -.. |Darin Erat Sleiter| replace:: **Darin Erat Sleiter** - -.. |Mathieu Scheltienne| replace:: **Mathieu Scheltienne** - -.. |Timothy Gates| replace:: **Timothy Gates** - -.. |Reza Shoorangiz| replace:: **Reza Shoorangiz** - -.. |Evgeny Goldstein| replace:: **Evgeny Goldstein** - -.. |Joshua Teves| replace:: **Joshua Teves** - -.. |Riessarius Stargardsky| replace:: **Riessarius Stargardsky** - -.. |John Samuelsson| replace:: **John Samuelsson** - -Enhancements -~~~~~~~~~~~~ -.. - Add something cool (:gh:`9192` **by new contributor** |New Contributor|_) - -- Add ``pooch`` to system information reports (:gh:`9801` **by new contributor** |Joshua Teves|_) - -- Get annotation descriptions from the name field of SNIRF stimulus groups when reading SNIRF files via `mne.io.read_raw_snirf` (:gh:`9575` **by new contributor** |Darin Erat Sleiter|_) - -- Add support for NIRSport and NIRSport2 devices to `mne.io.read_raw_nirx` (:gh:`9348` and :gh:`9401` **by new contributor** |David Julien|_, **new contributor** |Romain Derollepot|_, `Robert Luke`_, and `Eric Larson`_) - -- New function :func:`mne.Dipole.to_volume_labels` to get atlas label for MRI coordinates. (:gh:`9376` by **new contributor** |Marian Dovgialo|_) - -- Add support for SURE parameter selection in :func:`mne.inverse_sparse.mixed_norm` and make ``alpha`` parameter now default to ``'sure'`` (:gh:`9430` by **new contributor** |Pierre-Antoine Bannier|_ and `Alex Gramfort`_) - -- Speed up BCD solver in :func:`mne.inverse_sparse.mixed_norm` by adding Anderson acceleration (:gh:`9481` by **new contributor** |Pierre-Antoine Bannier|_ and `Alex Gramfort`_) - -- Add support for list of channel types for EEG/sEEG/ECoG/DBS referencing (:gh:`9637` **by new contributor** |Mathieu Scheltienne|_) - -- Add the ability to set point size and line width in :func:`mne.viz.plot_sensors` and related functions (:gH:`9872` **by new contributor** |Dominique Makowski|_) - -- Add support for changing the default event id used by :func:`mne.make_fixed_length_epochs` (:gh:`9782` **by new contributor** |Mathieu Scheltienne|_) - -- Improve documentation for arguments ``threshold``, ``method`` and ``measure`` of ICA methods `~mne.preprocessing.ICA.find_bads_ecg`, `~mne.preprocessing.ICA.find_bads_ref` and `~mne.preprocessing.ICA.find_bads_eog` (:gh:`9858` **by new contributor** |Mathieu Scheltienne|_) - -- Add support for more than 3 source estimates in :func:`mne.viz.plot_sparse_source_estimates` (:gh:`9640` **by new contributor** |Pierre-Antoine Bannier|_ and `Alex Gramfort`_) - -- Add cortical signal suppression (CSS) :func:`mne.preprocessing.cortical_signal_suppression` (:gh:`6888`, :gh:`9892` **by new contributor** |John Samuelsson|_ and `Eric Larson`_) - -- Show all good channel types and counts when printing a :class:`mne.Info` in the notebook (:gh:`9725` by `Valerii Chirkov`_ and `Eric Larson`_) - -- Speed up point decimation in :func:`mne.io.read_raw_kit` by vectorization and use of :class:`scipy.spatial.cKDTree` (:gh:`9568` by `Jean-Remi King`_ and `Eric Larson`_) - -- Add ability to export EDF+ files using :func:`mne.export.export_raw` (:gh:`9643` by `Adam Li`_) - -- New function :func:`mne.chpi.get_chpi_info` to retrieve basic information about the cHPI system used when recording MEG data (:gh:`9369` by `Richard Höchenberger`_) - -- New namespace `mne.export` created to contain functions (such as `mne.export.export_raw` and `mne.export.export_epochs`) for exporting data to non-FIF formats (:gh:`9427` by `Eric Larson`_) - -- Add support for Hitachi fNIRS devices in `mne.io.read_raw_hitachi` (:gh:`9391` by `Eric Larson`_) - -- Add support for ``picks`` in :func:`mne.stc_near_sensors` (:gh:`9396` by `Eric Larson`_) - -- Add label methods `mne.Label.compute_area` and `mne.Label.distances_to_outside` (:gh:`9424` by `Eric Larson`_) - -- Add projections when printing a :class:`mne.Info` in the notebook (:gh:`9403` by `Alex Gramfort`_) - -- Add new function :func:`mne.bem.make_scalp_surfaces` to compute scalp surfaces for coregistration (:gh:`9463` by `Alex Gramfort`_) - -- Add support for interpolating oxy and deoxyhaemoglobin data types (:gh:`9431` by `Robert Luke`_) - -- Add support for SNIRF files in :class:`mne.Report` (:gh:`9443` by `Robert Luke`_) - -- Add support for exporting MFF evoked files using `mne.export.export_evokeds` and `mne.export.export_evokeds_mff` (:gh:`9406` by `Evan Hathaway`_) - -- :func:`mne.concatenate_raws`, :func:`mne.concatenate_epochs`, and :func:`mne.write_evokeds` gained a new parameter ``on_mismatch``, which controls behavior in case not all of the supplied instances share the same device-to-head transformation (:gh:`9438` by `Richard Höchenberger`_) - -- Add support for multiple datablocks (acquisitions with pauses) in :func:`mne.io.read_raw_nihon` (:gh:`9437` by `Federico Raimondo`_) - -- Add new function :func:`mne.preprocessing.annotate_break` to automatically detect and mark "break" periods without any marked experimental events in the continuous data (:gh:`9445` by `Richard Höchenberger`_) - -- Add "time_format" to :meth:`mne.io.Raw.plot` and :meth:`mne.preprocessing.ICA.plot_sources` to display acquisition time on x-axis (:gh:`9419` by `Martin Schulz`_) - -- Speed up :meth:`mne.decoding.TimeDelayingRidge.predict` by switching to FFT-based convolution (:gh:`9458` by `Ross Maddox`_) - -- Show multiple colors and linestyles for excluded components with :class:`mne.Evoked` in :meth:`mne.preprocessing.ICA.plot_sources` (:gh:`9444` by `Martin Schulz`_) - -- Add functions for aligning MRI and CT data `mne.transforms.compute_volume_registration` and `mne.transforms.apply_volume_registration` (:gh:`9503` by `Alex Rockhill`_ and `Eric Larson`_) - -- Add tutorial for how to processes image (CT and MR) files in order to localize electrode contacts for intracranial recordings :ref:`tut-ieeg-localize` (:gh:`9484` by `Alex Rockhill`_) - -- Add vertex number in source space for :meth:`mne.VolSourceEstimate.plot` and :func:`mne.viz.plot_volume_source_estimates` (:gh:`9697` by `Eric Larson`_) - -- Add support for colormap normalization in :func:`mne.viz.plot_topomap` (:gh:`9468` by `Clemens Brunner`_) - -- Update :func:`mne.preprocessing.realign_raw` with Numpy-recommended polynomial fitting method (:gh:`9514` by `Erica Peterson`_) - -- Add a warning to `mne.preprocessing.nirs.beer_lambert_law` when source-detector distances are zero (:gh:`9541` by `Eric Larson`_) - -- Add ``exclude`` parameter to :meth:`mne.io.Raw.plot_psd` and :meth:`mne.Epochs.plot_psd` (:gh:`9519` by `Clemens Brunner`_) - -- Add `mne.Annotations.rename` to rename annotation descriptions (:gh:`9525` by `Robert Luke`_) - -- Add `mne.Annotations.set_durations` to set annotation durations (:gh:`9529` by `Robert Luke`_) - -- The ``exclude`` parameter in `mne.io.read_raw_edf`, `mne.io.read_raw_bdf`, and `mne.io.read_raw_gdf` now also accepts a regular expression (:gh:`9558` by `Clemens Brunner`_) - -- Add :meth:`mne.Evoked.get_data` method to :class:`mne.Evoked` (:gh:`9555` by `Stefan Appelhoff`_) - -- The :meth:`mne.Epochs.get_data` method now has a ``units`` parameter (:gh:`9553` by `Stefan Appelhoff`_) - -- Add ``mne.warp_montage_volume`` to use an anatomical volume with channel locations at high or low insensities to apply a symmetric diffeomorphic registration to a template (e.g. fsaverage) space (:gh:`9544` by `Alex Rockhill`_) - -- :meth:`mne.io.Raw.get_data`, :meth:`mne.Epochs.get_data`, and :meth:`mne.Evoked.get_data` methods now have ``tmin`` and ``tmax`` parameters to specify data window in seconds to get (:gh:`9556` by `Stefan Appelhoff`_) - -- The :meth:`mne.Evoked.get_data` method now has a ``units`` parameter (:gh:`9578` by `Stefan Appelhoff`_) - -- Add `mne.chpi.compute_chpi_snr` and `mne.viz.plot_chpi_snr` for computing and plotting the time-varying SNR of continuously-active HPI coils (:gh:`9570` by `Daniel McCloy`_ and `Jussi Nurminen`_) - -- Add :func:`mne.get_montage_volume_labels` to find the regions of interest in a Freesurfer atlas anatomical segmentation for an intracranial electrode montage and :func:`mne.viz.plot_channel_labels_circle` to plot them (:gh:`9545` by `Alex Rockhill`_) - -- Add :func:`mne.viz.Brain.add_volume_labels` to plot subcortical surfaces and other regions of interest (:gh:`9540` by `Alex Rockhill`_ and `Eric Larson`_) - -- Add custom cortex curvature colors in :class:`mne.viz.Brain` via the ``cortex`` argument (:gh:`9750` by `Eric Larson`_) - -- Add :meth:`mne.channels.DigMontage.apply_trans` to apply a transform directly to a montage (:gh:`9601` by `Alex Rockhill`_) - -- :meth:`mne.preprocessing.ICA.fit` now emits a warning if any of the ``start``, ``stop``, ``reject``, and ``flat`` parameters are passed when performing ICA on `~mne.Epochs`. These parameters only have an effect on `~mne.io.Raw` data and were previously silently ignored in the case of `~mne.Epochs` (:gh:`9605` by `Richard Höchenberger`_) - -- :func:`mne.viz.plot_alignment` now emits a warning (instead of aborting with an exception) if the surfaces contain topological defects (:gh:`9614` by `Richard Höchenberger`_) - -- The coregistration GUI can now display the head surface even if there are topological defects. Previously, a low-resolution standard head unsuitable for individualized coregistration was displayed (:gh:`9614` by `Richard Höchenberger`_) - -- New :class:`mne.coreg.Coregistration` object to allow coregistration scripting without a dependency on mayavi (:gh:`9516` by `Guillaume Favelier`_). - -- Add :meth:`mne.viz.Brain.add_head` to plot the head surface (:gh:`9618` by `Alex Rockhill`_) - -- Add :func:`mne.channels.read_dig_localite` to read Localite electrode location files (:gh:`9658` by `Clemens Brunner`_) - -- Add :meth:`mne.viz.Brain.add_sensors` to plot sensor locations (:gh:`9585` by `Alex Rockhill`_) - -- Add :func:`mne.coreg.estimate_head_mri_t` to estimate the head->mri transform from fsaverage fiducials (:gh:`9585` by `Alex Rockhill`_) - -- Add :meth:`mne.channels.DigMontage.add_mni_fiducials` to add fiducials to a montage in MNI coordinates (:gh:`9682` by `Alex Rockhill`_) - -- Add :meth:`mne.channels.DigMontage.remove_fiducials` to remove fiducials under rare circumstances when the coordinate frame should not be set to "head" (:gh:`9684` by `Alex Rockhill`_) - -- Add remove methods for mesh objects in :class:`mne.viz.Brain` (:gh:`9688` by `Alex Rockhill`_) - -- Add ``--show-paths`` and ``--developer`` options to :ref:`mne sys_info` (:gh:`9789` by `Eric Larson`_) - -- Add ability to export EDF+ files using :func:`mne.export.export_raw` (:gh:`9643` by `Adam Li`_) - -- Reading EDF files via :func:`mne.io.read_raw_edf` now can infer channel type from the signal label in the EDF header (:gh:`9694` by `Adam Li`_) - -- Add ``mne.gui.locate_ieeg`` to locate intracranial electrode contacts from a CT, an MRI (with Freesurfer ``recon-all``) and the channel names from an :class:`mne.Info` object (:gh:`9586` by `Alex Rockhill`_) - -- All data fetching code now relies on ``pooch``, which is an added optional requirement for dataset fetchers (:gh:`9742` by `Adam Li`_ and `Daniel McCloy`_) - -- Add phantom FreeSurfer subject fetcher :func:`mne.datasets.fetch_phantom` to allow fetching the Otaniemi phantom (:gh:`9796` by `Eric Larson`_) - -- Add :func:`mne.datasets.fetch_dataset` to allow packages to fetch datasets in a similar fashion to MNE (:gh:`9763` by `Adam Li`_) - -- Add full ECoG dataset to MNE-misc-data and demonstrate its use in :ref:`ex-electrode-pos-2d` and :ref:`tut-ieeg-localize` (:gh:`9784` by `Alex Rockhill`_) - -- Add options ``tol`` and ``accuracy`` to :func:`mne.fit_dipole` to control optimization (:gh:`9810` by `Eric Larson`_) - -- Completely revamp the `~mne.Report` experience: new HTML layout, many new methods, more flexibility; the functionality is demonstrated in :ref:`tut-report` (:gh:`9754`, :gh:`9828`, :gh:`9847`, :gh:`9860`, :gh:`9861`, :gh:`9862`, :gh:`9863`, :gh:`9871`, :gh:`9881`, :gh:`9891`, :gh:`9901` by `Richard Höchenberger`_, `Eric Larson`_, and `Alex Gramfort`_) - -- Add basic HTML representations of `~mne.Forward` and `~mne.minimum_norm.InverseOperator` instances for a nicer Jupyter experience (:gh:`9754` by `Richard Höchenberger`_) - -- `mne.io.read_raw_brainvision` now handles ASCII data with comma-separated values, as may be exported from BrainVision Analyzer (:gh:`9795` by `Richard Höchenberger`_) - -- Add :func:`mne.preprocessing.ieeg.project_sensors_onto_brain` to project ECoG sensors onto the pial surface to compensate for brain shift (:gh:`9800` by `Alex Rockhill`_) - -- Add support for data acquired with NIRx devices using Aurora software version 2021.9 (:gh:`9800` by `Robert Luke`_, and `Eric Larson`_) - -- All functions for reading and writing files should now automatically handle ``~`` (the tilde character) and expand it to the user's home directory. Should you come across any function that doesn't do it, please do let us know! (:gh:`9613`, :gh:`9845` by `Richard Höchenberger`_) - -- All functions accepting a FreeSurfer subjects directory via a ``subjects_dir`` parameter can now consume :class:`pathlib.Path` objects too (used to be only strings) (:gh:`9613` by `Richard Höchenberger`_) - -- Add support for colormap normalization in :meth:`mne.time_frequency.AverageTFR.plot` (:gh:`9851` by `Clemens Brunner`_) - -- Add support for BIDS-compatible filenames when splitting big epochs files via the new ``split_naming`` parameter in :meth:`mne.Epochs.save` (:gh:`9869` by `Denis Engemann`_) - -- Add ``by_event_type`` parameter to :meth:`mne.Epochs.average` to create a list containing an :class:`mne.Evoked` object for each event type (:gh:`9859` by `Marijn van Vliet`_) - -- Add pyqtgraph as a new backend for :meth:`mne.io.Raw.plot` (:gh:`9687` by `Martin Schulz`_) - -- Add :func:`mne.viz.set_browser_backend`, :func:`mne.viz.use_browser_backend` and :func:`mne.viz.get_browser_backend` to set matplotlib or pyqtgraph as backend for :meth:`mne.io.Raw.plot` (:gh:`9687` by `Martin Schulz`_) - -Bugs -~~~~ -- Fix bug in :meth:`mne.io.Raw.pick` and related functions when parameter list contains channels which are not in info instance (:gh:`9708` **by new contributor** |Evgeny Goldstein|_) - -- Fix a few typos (:gh:`9706` **by new contributor** |Timothy Gates|_) - -- Fix bug with :meth:`mne.Epochs.crop` and :meth:`mne.Evoked.crop` when ``include_tmax=False``, where the last sample was always cut off, even when ``tmax > epo.times[-1]`` (:gh:`9378` **by new contributor** |Jan Sosulski|_) - -- Fix bug with `mne.io.read_raw_curry` to allow reading Curry 7 and 8 event files with '.ceo' and '.cdt.ceo' extensions (:gh:`9381`, :gh:`9712` by **new contributor** |Xiaokai Xia|_, `Daniel McCloy`_, and **by new contributor** |Reza Shoorangiz|_) - -- Fix bug with `mne.compute_rank`, `mne.cov.compute_whitener` and `mne.preprocessing.ICA.fit` when explicit picks including bad channels are provided (:gh:`9719` **by new contributor** |Mathieu Scheltienne|_) - -- Fix bug with :func:`mne.concatenate_epochs` where the concatenated events could end up in non-chronological order. (:gh:`9765` **by new contributor** |Jan Sosulski|_) - -- Fix bug where :func:`mne.time_frequency.psd_array_welch` and :func:`mne.time_frequency.psd_array_multitaper` failed to handle negative integer for ``n_jobs`` argument (:gh:`9849` **by new contributor** |Riessarius Stargardsky|_) - -- Fix bug where resampling returns empty instances (:gh:`9897` **by new contributor** |Mathieu Scheltienne|_ and `Eric Larson`_) - -- Fix bug with `mne.io.Raw.get_montage` now returning both good and bad channels in the montage. (:gh:`9920` **by new contributor** |Mathieu Scheltienne|_) - -- Fix bug with :func:`mne.io.read_raw_nihon` where latin-1 annotations could not be read (:gh:`9384` by `Alex Gramfort`_) - -- Fix bug when printing a :class:`mne.io.RawArray` in the notebook (:gh:`9404` by `Alex Gramfort`_) - -- Fix bug when computing rank from info for SSS data with only gradiometers or magnetometers (:gh:`9435` by `Alex Gramfort`_) - -- Fix bug with `mne.preprocessing.find_bad_channels_maxwell` where all-flat segments could lead to an error (:gh:`9531` by `Eric Larson`_) - -- Fix bug with `mne.io.Raw.set_montage` and related functions where the channel coordinate frame was not properly set to head (:gh:`9447` by `Eric Larson`_) - -- Fix bug with `mne.io.read_raw_fieldtrip` and `mne.read_epochs_fieldtrip` where channel positions were not set properly (:gh:`9447` by `Eric Larson`_) - -- Fix bug with :func:`mne.io.read_raw_kit` where omitting HPI coils could lead to an :exc:`python:AssertionError` on reading (:gh:`9612` by `Eric Larson`_) - -- Fix bug with :func:`mne.io.read_raw_edf` where reading only stimulus channels would lead to an error (:gh:`9831` by `Eric Larson`_) - -- Fix bug with `mne.preprocessing.nirs.optical_density` where protection against zero values was not guaranteed (:gh:`9522` by `Eric Larson`_) - -- :func:`mne.concatenate_raws` now raises an exception if ``raw.info['dev_head_t']`` differs between files. This behavior can be controlled using the new ``on_mismatch`` parameter (:gh:`9438` by `Richard Höchenberger`_) - -- Fixed bug in :meth:`mne.Epochs.drop_bad` where subsequent rejections failed if they only specified thresholds for a subset of the channel types used in a previous rejection (:gh:`9485` by `Richard Höchenberger`_). - -- Fix bug with `mne.simulation.simulate_evoked`, `mne.apply_forward`, and `mne.apply_forward_raw` where systems with EEG channels that come before MEG channels would have them mixed up in the output evoked or raw object (:gh:`#9513` by `Eric Larson`_) - -- In :func:`mne.viz.plot_ica_scores` and :meth:`mne.preprocessing.ICA.plot_scores`, the figure and axis titles no longer overlap when plotting only a single EOG or ECG channel (:gh:`9489` by `Richard Höchenberger`_). - -- Ensure `mne.io.Raw.get_montage` works with SNIRF data (:gh:`9524` by `Robert Luke`_) - -- Fix bug in :func:`mne.setup_volume_source_space` where non-finite positions could be used in a discrete source space (:gh:`9603` by `Eric Larson`_) - -- Fix bug in :func:`mne.viz.plot_topomap` (and related methods like :meth:`mne.Evoked.plot_topomap`) where large distances between electrodes (higher than head radius) would lead to an error (:gh:`9528` by `Mikołaj Magnuski`_). - -- Fix bug in `mne.viz.plot_topomap` (and related methods) where passing ``axes`` that are part of a matplotlib figure that uses a constrained layout would emit warnings (:gh:`9558` by `Eric Larson`_) - -- Fix bug in :func:`mne.make_forward_solution` where impossible sensor-BEM geometries were not checked (:gh:`9893` by `Eric Larson`_) - -- Fix bug in :func:`mne.concatenate_epochs` when concatenating :class:`mne.Epochs` objects with 0 events (:gh:`9535` by `Marijn van Vliet`_) - -- Fix bug in :func:`mne.viz.Brain.screenshot` where the RGBA mode was not supported (:gh:`9564` by `Guillaume Favelier`_). - -- Fix bug in :func:`mne.io.read_raw_egi` where reading data from a data segment that is part of an acquisition skip would lead to an error (:gh:`9565` by `Eric Larson`_) - -- Prevent :meth:`mne.io.Raw.plot` windows from spawning at sizes too small to properly render (:gh:`9629` by `Daniel McCloy`_) - -- Fix bug where :meth:`mne.io.Raw.plot` raised an error when plotting raw dipole data (:gh:`9771` by `Eric Larson`_) - -- Fix bug in ::meth:`mne.preprocessing.ICA.find_bads_ecg` where passing ``start`` and ``stop`` lead to erroneous data windows depending on the combination of Raw, Epochs, Evoked, and the type (int, float, None) of ``start`` and ``stop`` (:gh:`9556` by `Stefan Appelhoff`_) - -- Fix bug in :func:`mne.viz.set_3d_backend` and :func:`mne.viz.get_3d_backend` where the PyVistaQt-based backend was ambiguously named ``'pyvista'`` instead of ``'pyvistaqt'``; use ``set_3d_backend('pyvistaqt')`` and expect ``'pyvistaqt'`` as the output of :func:`mne.viz.get_3d_backend` instead of ``'pyvista'``, and consider using ``get_3d_backend().startswith('pyvista')`` for example for backward-compatible conditionals (:gh:`9607` by `Guillaume Favelier`_) - -- Fix bug in :func:`mne.viz.plot_compare_evokeds` where confidence bands were not drawn if only one condition was plotted (:gh:`9663` by `Daniel McCloy`_) - -- Fix bug where setting of a montage with fNIRS data got set to "unknown" coordinate frame when it should have been in "head" (:gh:`9630` by `Alex Rockhill`_) - -- Fix bug where "seeg", "ecog", "dbs" and "fnirs" data had coordinate frame unknown upon loading from a file when it should have been in "head" (:gh:`9580` by `Alex Rockhill`_) - -- Raise error when no ``trans`` is provided to :func:`mne.viz.plot_alignment` when required instead of assuming identity head->mri transform (:gh:`9585` by `Alex Rockhill`_) - -- Fix bug where :meth:`mne.Epochs.equalize_event_counts` failed when only one good epoch existed for one of the event types (:gh:`9758` by `Daniel McCloy`_) - -- Fix bug where channels with a dollar sign ($) were not being labeled "misc" in :func:`mne.io.read_raw_nihon` (:gh:`9695` by `Adam Li`_) - -- Fix bug where :func:`mne.io.read_raw_persyst` was lower-casing events it found in the ``.lay`` file (:gh:`9746` by `Adam Li`_) - -- Fix bug with Qhull when plotting OPM sensors in :func:`mne.viz.plot_alignment` (:gh:`9799` and :gh:`9804` by `Eric Larson`_) - -- Fix bug where :func:`mne.io.read_raw_snirf` was including the landmark index as a spatial coordinate (:gh:`9777` by `Robert luke`_) - -- Fix bug where `mne.Annotations` were not appending channel names when being added together (:gh:`9780` by `Adam Li`_) - -- `mne.viz.plot_evoked_joint` now correctly handles a ``times='peaks'`` parameter value (:gh:`9754` by `Richard Höchenberger`_) - -- In `mne.viz.plot_compare_evokeds`, slightly adjust the x-axis limit calculation to avoid drawing an axis that is too short (:gh:`9754` by `Richard Höchenberger`_) - -- Fix a bug with :func:`mne.viz.snapshot_brain_montage` with the Mayavi backend where electrodes were shown in the wrong positions, and with the PyVista backend where the snapshot always contained the electrodes but could be missing a hemisphere (:gh:`9933` by `Eric Larson`_) - -- In :meth:`mne.io.Raw.plot_psd` and :meth:`mne.Epochs.plot_psd`, avoid overlap between subplot titles and x-axis tick labels (:gh:`9864` by `Richard Höchenberger`_) - -- In :meth:`mne.Epochs.plot_psd_topomap`, the data is now scaled to match the output of :meth:`mne.Epochs.plot_psd` (:gh:`9873` by `Richard Höchenberger`_) - -- Fix channel locations with ``NaN`` values causing all channel locations not to be plotted in :func:`mne.viz.Brain.add_sensors` (:gh:`9911` by `Alex Rockhill`_) - -- Fix infinite loop bug in :func:`mne.get_montage_volume_labels` (:gh:`9940` by `Alex Rockhill`_) - -API changes -~~~~~~~~~~~ -- The :class:`mne.Info` class is now more strictly checked when attributes are set. Setting most attributes directly will lead to an error in the next release. See the docstring of :class:`mne.Info` for more information (:gh:`9867` **by new contributor** |Mathieu Scheltienne|_) - -- The Mayavi 3D backend has been deprecated (:gh:`9904` by `Eric Larson`_): - - - In 3D plotting functions, use PyVista-based backends (``'pyvistaqt'`` and ``'notebook'``) as PySurfer/Mayavi will be removed in the next version - - - To use the :ref:`mne kit2fiff` command-line GUI for fiducial markers, install the separate ``mne-kit-gui`` module, which can still be launched via ``$ mne kit2fiff`` - - - The ``mne.gui.fiducials`` GUI has been deprecated, use :ref:`mne coreg` or ``mne_kit_gui.fiducials()`` to set MRI fiducials instead - -- In `mne.compute_source_morph`, the ``niter_affine`` and ``niter_sdr`` parameters have been replaced by ``niter`` and ``pipeline`` parameters for more consistent and finer-grained control of registration/warping steps and iteration (:gh:`9505` by `Alex Rockhill`_ and `Eric Larson`_) - -- Split :func:`mne.viz.Brain.show_view` argument ``view`` into ``azimuth``, ``elevation`` and ``focalpoint`` for clearer view setting and make the default for ``row`` and ``col`` apply to all rows and columns (:gh:`9596` by `Alex Rockhill`_) - -- Deprecate ``solver='prox'`` in :func:`mne.inverse_sparse.mixed_norm` in favor of ``solver='cd'`` and ``solver='bcd'`` as coordinate descent solvers consistently outperform proximal gradient descent (:gh:`9608` by `Pierre-Antoine Bannier`_) - -- All ``mne.connectivity`` functions have moved to the ``mne-connectivity`` package; they are deprecated in MNE-Python and will be removed in version 0.25 (:gh:`9493` by `Adam Li`_). - -- :func:`mne.inverse_sparse.mixed_norm` now simply warns when source estimates contain no dipole, e.g. if data are too noisy and alpha is based on SURE (:gh:`9685` by `Alex Gramfort`_) - -- Deprecate functions :samp:`mne.datasets.{DATASET_NAME}.has_{DATASET_NAME}_data()` for these datasets: ``epilepsy_ecog``, ``fnirs_motor``, ``multimodal``, ``opm``, ``phantom_4dbti``, ``refmeg_noise``, ``sample``, ``somato``, and ``ssvep``. Use the generic :func:`mne.datasets.has_dataset` instead (:gh:`9781` by `Daniel McCloy`_ and `Adam Li`_) - -- :class:`mne.Report` modernization has led to multiple deprecations (:gh:`9754` by `Richard Höchenberger`_): - - - ``mne.Report.add_figs_to_section`` and ``mne.Report.add_slider_to_section`` have been deprecated in favor of :meth:`mne.Report.add_figure` - - - ``mne.Report.add_images_to_section`` has been deprecated in favor of :meth:`mne.Report.add_image` - - - ``mne.Report.add_bem_to_section`` has been deprecated in favor of :meth:`mne.Report.add_bem` - - - ``mne.Report.add_htmls_to_section`` has been deprecated in favor of :meth:`mne.Report.add_html` - - - In :meth:`mne.Report.parse_folder`, the ``sort_sections`` parameter has been deprecated in favor of ``sort_content`` - - - In :meth:`mne.Report.remove`, the ``caption`` and ``section`` parameters have been deprecated in favor of ``title`` and ``tags``, respectively - - - The ``mne.Report.sections`` attribute has been deprecated in favor of ``mne.Report.tags`` - - - The ``mne.Report.fnames`` attribute has been deprecated without replacement - -- :meth:`mne.Epochs.plot` and :func:`mne.viz.plot_epochs` gained parameter ``show_scalebars`` analogous to :meth:`mne.viz.plot_raw` (:gh:`9815` by `Daniel McCloy`_) - -- The output folder name for HF_SEF datasets is now ``hf_sef`` instead of ``HF_SEF`` (:gh:`9763` by `Adam Li`_) - -- Deprecate ``mne.viz.utils.center_cmap`` (:gh:`9851` by `Clemens Brunner`_) - -- The default partial pathlength factor of :func:`mne.preprocessing.nirs.beer_lambert_law` will change from 0.1 in 0.24 to 6.0 in the next release (:gh:`9843` by `Robert Luke`_) - -- ``mne.preprocessing.ICA.detect_artifacts`` has been deprecated. Please use `~mne.preprocessing.ICA.find_bads_eog` and `~mne.preprocessing.ICA.find_bads_ecg` instead (:gh:`9909` by `Richard Höchenberger`_) - -Authors -~~~~~~~ -People who contributed to this release in alphabetical order -(people with a + are first time contributors): - -* Adam Li -* Alex Rockhill -* Alexandre Gramfort -* Britta Westner -* Clemens Brunner -* Daniel McCloy -* Darin Erat Sleiter+ -* David Julien+ -* Denis A. Engemann -* Dominique Makowski+ -* Eric Larson -* Erica Peterson -* Evan Hathaway -* Evgeny Goldstein+ -* Fede Raimondo -* Gansheng Tan+ -* Guillaume Favelier -* Hubert Banville -* Jan Sosulski+ -* Jean-Remi King -* Jeff Stout -* Johann Benerradi -* John Samuelsson+ -* Josh Koen+ -* Joshua Teves+ -* Lukas Hecker+ -* Luke Bloy -* Marian Dovgialo+ -* Marijn van Vliet -* Martin Schulz -* Mathieu Scheltienne+ -* Mikołaj Magnuski -* Pierre-Antoine Bannier+ -* Reza Shoorangiz+ -* Richard Höchenberger -* Riessarius Stargardsky+ -* Robert Luke -* Romain Derollepot+ -* Ross Maddox -* Ryan Law+ -* Stefan Appelhoff -* Steve Matindi+ -* Timothy Gates+ -* Valerii Chirkov -* Xiaokai Xia+ diff --git a/doc/changes/v0.3.rst b/doc/changes/v0.3.rst deleted file mode 100644 index 9c61d8c482b..00000000000 --- a/doc/changes/v0.3.rst +++ /dev/null @@ -1,40 +0,0 @@ -.. _changes_0_3: - -Version 0.3 (2012-03-23) ------------------------- - -Changelog -~~~~~~~~~ - -- Sign flip computation for robust label average of signed values by `Alex Gramfort`_. - -- Reading and writing of .w files by `Martin Luessi`_. - -- Support for modifying Raw object and allow raw data preloading with memory mapping by `Martin Luessi`_ and `Alex Gramfort`_. - -- Support of arithmetic of Evoked data (useful to concatenate between runs and compute contrasts) by `Alex Gramfort`_. - -- Support for computing sensor space data from a source estimate using an MNE forward solution by `Martin Luessi`_. - -- Support of arithmetic of Covariance by `Alex Gramfort`_. - -- Write BEM surfaces in Python by `Alex Gramfort`_. - -- Filtering operations and apply_function interface for Raw object by `Martin Luessi`_. - -- Support for complex valued raw fiff files and computation of analytic signal for Raw object by `Martin Luessi`_. - -- Write inverse operators (surface and volume) by `Alex Gramfort`_. - -- Covariance matrix computation with multiple event types by `Martin Luessi`_. - -- New tutorial in the documentation and new classes and functions reference page by `Alex Gramfort`_. - -Authors -~~~~~~~ - -The committer list for this release is the following (preceded by number -of commits): - -* 80 Alexandre Gramfort -* 51 Martin Luessi diff --git a/doc/changes/v0.4.rst b/doc/changes/v0.4.rst deleted file mode 100644 index 680e5fe8123..00000000000 --- a/doc/changes/v0.4.rst +++ /dev/null @@ -1,52 +0,0 @@ -.. _changes_0_4: - -Version 0.4 (2012-08-24) ------------------------- - -Changelog -~~~~~~~~~ - -- Add function to compute source PSD using minimum norm by `Alex Gramfort`_ - -- L21 Mixed Norm Estimates (MxNE) by `Alex Gramfort`_ and `Daniel Strohmeier`_ - -- Generation of simulated evoked responses by `Alex Gramfort`_, `Daniel Strohmeier`_, and `Martin Luessi`_ - -- Fit AR models to raw data for temporal whitening by `Alex Gramfort`_. - -- speedup + reduce memory of mne.morph_data by `Alex Gramfort`_. - -- Backporting scipy.signal.firwin2 so filtering works with old scipy by `Alex Gramfort`_. - -- LCMV Beamformer for evoked data, single trials, and raw data by `Alex Gramfort`_ and `Martin Luessi`_. - -- Add support for reading named channel selections by `Martin Luessi`_. - -- Add Raw.filter method to more easily band pass data by `Alex Gramfort`_. - -- Add tmin + tmax parameters in mne.compute_covariance to estimate noise covariance in epochs baseline without creating new epochs by `Alex Gramfort`_. - -- Add support for sLORETA in apply_inverse, apply_inverse_raw, apply_inverse_epochs (API Change) by `Alex Gramfort`_. - -- Add method to regularize a noise covariance by `Alex Gramfort`_. - -- Read and write measurement info in forward and inverse operators for interactive visualization in mne_analyze by `Alex Gramfort`_. - -- New mne_compute_proj_ecg.py and mne_compute_proj_eog.py scripts to estimate ECG/EOG PCA/SSP vectors by `Alex Gramfort`_ and `Martin Luessi`_. - -- Wrapper function and script (mne_maxfilter.py) for Elekta Neuromag MaxFilter(TM) by `Martin Luessi`_ - -- Add method to eliminate stimulation artifacts from raw data by linear interpolation or windowing by `Daniel Strohmeier`_. - -Authors -~~~~~~~ - -The committer list for this release is the following (preceded by number -of commits): - -* 118 Alexandre Gramfort -* 81 Martin Luessi -* 15 Daniel Strohmeier -* 4 Christian Brodbeck -* 4 Louis Thibault -* 2 Brad Buran diff --git a/doc/changes/v0.5.rst b/doc/changes/v0.5.rst deleted file mode 100644 index 9d6a8b3b856..00000000000 --- a/doc/changes/v0.5.rst +++ /dev/null @@ -1,125 +0,0 @@ -.. _changes_0_5: - -Version 0.5 (2012-12-27) ------------------------- - -Changelog -~~~~~~~~~ - -- Multi-taper PSD estimation for single epochs in source space using minimum norm by `Martin Luessi`_ - -- Read and visualize .dip files obtained with xfit or mne_dipole_fit by `Alex Gramfort`_ - -- Make EEG layout by `Eric Larson`_ - -- Ability to specify SSP projectors when computing covariance from raw by `Eric Larson`_ - -- Read and write txt based event files (.eve or .txt) by `Eric Larson`_ - -- Pass qrs threshold to preprocessing functions by `Eric Larson`_ - -- Compute SSP projections from continuous raw data by `Eric Larson`_ - -- Support for applied SSP projections when loading Raw by `Eric Larson`_ and `Alex Gramfort`_ - -- Support for loading Raw stored in different fif files by `Eric Larson`_ - -- IO of many Evoked in a single fif file + compute Epochs.standard_error by `Eric Larson`_ and `Alex Gramfort`_ - -- ICA computation on Raw and Epochs with automatic component selection by `Denis Engemann`_ and `Alex Gramfort`_ - -- Saving ICA sources to fif files and creating ICA topography layouts by `Denis Engemann`_ - -- Save and restore ICA session to and from fif by `Denis Engemann`_ - -- Export raw, epochs and evoked data as data frame to the pandas library by `Denis Engemann`_ - -- Export raw, epochs and evoked data to the nitime library by `Denis Engemann`_ - -- Copy methods for raw and epochs objects by `Denis Engemann`_, `Martin Luessi`_ and `Alex Gramfort`_ - -- New raw objects method to get the time at certain indices by `Denis Engemann`_ and `Alex Gramfort`_ - -- Plot method for evoked objects by `Denis Engemann`_ - -- Enhancement of cluster-level stats (speed and memory efficiency) by `Eric Larson`_ and `Martin Luessi`_ - -- Reading of source space distances by `Eric Larson`_ - -- Support for filling / smoothing labels and speedup of morphing by `Eric Larson`_ - -- Adding options for morphing by `Eric Larson`_ - -- Plotting functions for time frequency and epochs image topographies by `Denis Engemann`_ and `Alex Gramfort`_ - -- Plotting ERP/ERF images by `Alex Gramfort`_ - -- See detailed subplot when cliking on a channel inside a topography plot by `Martin Luessi`_, `Eric Larson`_ and `Denis Engemann`_ - -- Misc channel type support plotting functions by `Denis Engemann`_ - -- Improved logging support by `Eric Larson`_ - -- Whitening of evoked data for plotting and quality checking by `Alex Gramfort`_ - -- Transparent I/O of gzipped fif files (as .fif.gz) by `Eric Larson`_ - -- Spectral connectivity estimation in sensor and source space by `Martin Luessi`_ - -- Read and write Epochs in FIF files by `Alex Gramfort`_ - -- Resampling of Raw, Epochs, and Evoked by `Eric Larson`_ - -- Creating epochs objects for different conditions and accessing conditions via user-defined name by `Denis Engemann`_ , `Eric Larson`_, `Alex Gramfort`_ and `Christian Brodbeck`_ - -- Visualizing evoked responses from different conditions in one topography plot by `Denis Engemann`_ and `Alex Gramfort`_ - -- Support for L21 MxNE solver using coordinate descent using scikit-learn by `Alex Gramfort`_ and `Daniel Strohmeier`_ - -- Support IIR filters (butterworth, chebyshev, bessel, etc.) by `Eric Larson`_ - -- Read labels from FreeSurfer parcellation by `Martin Luessi`_ - -- Combining labels in source space by `Christian Brodbeck`_ - -- Read and write source spaces, surfaces and coordinate transforms to and from files by `Christian Brodbeck`_ - -- Downsample epochs by `Christian Brodbeck`_ and `Eric Larson`_ - -- New labels class for handling source estimates by `Christian Brodbeck`_, `Martin Luessi`_ and `Alex Gramfort`_ - -- New plotting routines to easily display SourceEstimates using PySurfer by `Alex Gramfort`_ - -- Function to extract label time courses from SourceEstimate(s) by `Martin Luessi`_ - -- Function to visualize connectivity as circular graph by `Martin Luessi`_ and `Alex Gramfort`_ - -- Time-frequency Mixed Norm Estimates (TF-MxNE) by `Alex Gramfort`_ and `Daniel Strohmeier`_ - - -API -~~~ -- Added nave parameter to source_induced_power() and source_band_induced_power(), use nave=1 by default (wrong nave was used before). - -- Use mne.layout.read_layout instead of mne.layout.Layout to read a layout file (.lout) - -- Use raw.time_as_index instead of time_to_index (still works but is deprecated). - -- The artifacts module (mne.artifacts) is now merged into mne.preprocessing - -- Epochs objects now also take dicts as values for the event_id argument. They now can represent multiple conditions. - -Authors -~~~~~~~ - -The committer list for this release is the following (preceded by number -of commits): - -* 313 Eric Larson -* 226 Alexandre Gramfort -* 219 Denis A. Engemann -* 104 Christian Brodbeck -* 85 Martin Luessi -* 6 Daniel Strohmeier -* 4 Teon Brooks -* 1 Dan G. Wakeman diff --git a/doc/changes/v0.6.rst b/doc/changes/v0.6.rst deleted file mode 100644 index eeb2ef87c8b..00000000000 --- a/doc/changes/v0.6.rst +++ /dev/null @@ -1,156 +0,0 @@ -.. _changes_0_6: - -Version 0.6 (2013-06-15) ------------------------- - -Changelog -~~~~~~~~~ - -- Linear (and zeroth-order) detrending for Epochs and Evoked by `Eric Larson`_ - -- Label morphing between subjects by `Eric Larson`_ - -- Define events based on time lag between reference and target event by `Denis Engemann`_ - -- ICA convenience function implementing an automated artifact removal workflow by `Denis Engemann`_ - -- Bad channels no longer included in epochs by default by `Eric Larson`_ - -- Support for diagonal noise covariances in inverse methods and rank computation by `Eric Larson`_ - -- Support for using CUDA in FFT-based FIR filtering (method='fft') and resampling by `Eric Larson`_ - -- Optimized FFT length selection for faster overlap-add filtering by `Martin Luessi`_ - -- Ability to exclude bad channels from evoked plots or shown them in red by `Martin Luessi`_ - -- Option to show both hemispheres when plotting SourceEstimate with PySurfer by `Martin Luessi`_ - -- Optimized Raw reading and epoching routines to limit memory copies by `Eric Larson`_ - -- Advanced options to save raw files in short or double precision by `Eric Larson`_ - -- Option to detect decreasing events using find_events by `Simon Kornblith`_ - -- Option to change default stim_channel used for finding events by `Eric Larson`_ - -- Use average patch normal from surface-oriented forward solution in inverse calculation when possible by `Eric Larson`_ - -- Function to plot drop_log from Epochs instance by `Eric Larson`_ - -- Estimate rank of Raw data by `Eric Larson`_ - -- Support reading of BTi/4D data by `Denis Engemann`_ - -- Wrapper for generating forward solutions by `Eric Larson`_ - -- Averaging forward solutions by `Eric Larson`_ - -- Events now contain the pre-event stim channel value in the middle column, by `Christian Brodbeck`_ - -- New function ``mne.find_stim_steps`` for finding all steps in a stim channel by `Christian Brodbeck`_ - -- Get information about FIFF files using mne.fiff.show_fiff() by `Eric Larson`_ - -- Compute forward fields sensitivity maps by `Alex Gramfort`_ and `Eric Larson`_ - -- Support reading of KIT data by `Teon Brooks`_ and `Christian Brodbeck`_ - -- Raw data visualization by `Eric Larson`_ - -- Smarter SourceEstimate object that contains linear inverse kernel and sensor space data for fast time-frequency transforms in source space by `Martin Luessi`_ - -- Add example of decoding/MVPA on MEG sensor data by `Alex Gramfort`_ - -- Add support for non-paired tests in spatiotemporal cluster stats by `Alex Gramfort`_ - -- Add unified SSP-projector API for Raw, Epochs and Evoked objects by `Denis Engemann`_, `Alex Gramfort`_ `Eric Larson`_ and `Martin Luessi`_ - -- Add support for delayed SSP application at evoked stage `Denis Engemann`_, `Alex Gramfort`_, `Eric Larson`_ and `Martin Luessi`_ - -- Support selective parameter updating in functions taking dicts as arguments by `Denis Engemann`_ - -- New ICA method ``sources_as_epochs`` to create Epochs in ICA space by `Denis Engemann`_ - -- New method in Evoked and Epoch classes to shift time scale by `Mainak Jas`_ - -- Added option to specify EOG channel(s) when computing PCA/SSP projections for EOG artifacts by `Mainak Jas`_ - -- Improved connectivity interface to allow combinations of signals, e.g., seed time series and source estimates, by `Martin Luessi`_ - -- Effective connectivity estimation using Phase Slope Index (PSI) by `Martin Luessi`_ - -- Support for threshold-free cluster enhancement (TFCE) by `Eric Larson`_ - -- Support for "hat" variance regularization by `Eric Larson`_ - -- Access source estimates as Pandas DataFrame by `Denis Engemann`_. - -- Add example of decoding/MVPA on MEG source space data by `Denis Engemann`_ - -- Add support for --tstart option in mne_compute_proj_eog.py by `Alex Gramfort`_ - -- Add two-way repeated measures ANOVA for mass-univariate statistics by `Denis Engemann`_, `Eric Larson`_ and `Alex Gramfort`_ - -- Add function for summarizing clusters from spatio-temporal-cluster permutation tests by `Denis Engemann`_ and `Eric Larson`_ - -- Add generator support for ``lcmv_epochs`` by `Denis Engemann`_ - -- Gamma-MAP sparse source localization method by `Martin Luessi`_ and `Alex Gramfort`_ - -- Add regular expression and substring support for selecting parcellation labels by `Denis Engemann`_ - -- New plot_evoked option for interactive and reversible selection of SSP projection vectors by `Denis Engemann`_ - -- Plot 2D flat topographies with interpolation for evoked and SSPs by `Christian Brodbeck`_ and `Alex Gramfort`_ - -- Support delayed SSP applicationon for 2D flat topographies by `Denis Engemann`_ and `Christian Brodbeck`_ and `Alex Gramfort`_ - -- Allow picking maximum power source, a.k.a. "optimal", orientation in LCMV beamformers by `Roman Goj`_, `Alex Gramfort`_, `Denis Engemann`_ and `Martin Luessi`_ - -- Add sensor type scaling parameter to plot_topo by `Andrew Dykstra`_, `Denis Engemann`_ and `Eric Larson`_ - -- Support delayed SSP application in plot_topo by `Denis Engemann`_ - -API -~~~ - -- Deprecated use of fiff.pick_types without specifying exclude -- use either [] (none), ``bads`` (bad channels), or a list of string (channel names). - -- Depth bias correction in dSPM/MNE/sLORETA make_inverse_operator is now done like in the C code using only gradiometers if present, else magnetometers, and EEG if no MEG channels are present. - -- Fixed-orientation inverse solutions need to be made using ``fixed=True`` option (using non-surface-oriented forward solutions if no depth weighting is used) to maintain compatibility with MNE C code. - -- Raw.save() will only overwrite the destination file, if it exists, if option overwrite=True is set. - -- mne.utils.set_config(), get_config(), get_config_path() moved to mne namespace. - -- Raw constructor argument proj_active deprecated -- use proj argument instead. - -- Functions from the mne.mixed_norm module have been moved to the mne.inverse_sparse module. - -- Deprecate CTF compensation (keep_comp and dest_comp) in Epochs and move it to Raw with a single compensation parameter. - -- Remove artifacts module. Artifacts- and preprocessing related functions can now be found in mne.preprocessing. - -Authors -~~~~~~~ - -The committer list for this release is the following (preceded by number -of commits): - -* 340 Eric Larson -* 330 Denis A. Engemann -* 204 Alexandre Gramfort -* 72 Christian Brodbeck -* 66 Roman Goj -* 65 Martin Luessi -* 37 Teon Brooks -* 18 Mainak Jas -* 9 Simon Kornblith -* 7 Daniel Strohmeier -* 6 Romain Trachel -* 5 Yousra BEKHTI -* 5 Brad Buran -* 1 Andrew Dykstra -* 1 Christoph Dinh diff --git a/doc/changes/v0.7.rst b/doc/changes/v0.7.rst deleted file mode 100644 index 7fde706f2cd..00000000000 --- a/doc/changes/v0.7.rst +++ /dev/null @@ -1,136 +0,0 @@ -.. _changes_0_7: - -Version 0.7 (2013-11-26) ------------------------- - -Changelog -~~~~~~~~~ - -- Add capability for real-time feedback via trigger codes using StimServer and StimClient classes by `Mainak Jas`_ - -- New decoding module for MEG analysis containing sklearn compatible transformers by `Mainak Jas`_ and `Alex Gramfort`_ - -- New realtime module containing RtEpochs, RtClient and MockRtClient class by `Martin Luessi`_, `Christopher Dinh`_, `Alex Gramfort`_, `Denis Engemann`_ and `Mainak Jas`_ - -- Allow picking normal orientation in LCMV beamformers by `Roman Goj`_, `Alex Gramfort`_, `Denis Engemann`_ and `Martin Luessi`_ - -- Add printing summary to terminal for measurement info by `Denis Engemann`_ - -- Add read and write info attribute ICA objects by `Denis Engemann`_ - -- Decoding with Common Spatial Patterns (CSP) by `Romain Trachel`_ and `Alex Gramfort`_ - -- Add ICA ``plot_topomap`` function and method for displaying the spatial sensitivity of ICA sources by `Denis Engemann`_ - -- Plotting multiple brain views at once by `Eric Larson`_ - -- Reading head positions from raw FIFF files by `Eric Larson`_ - -- Add decimation parameter to ICA.decompose* methods by `Denis Engemann`_ and `Alex Gramfort`_ - -- Add rejection buffer to ICA.decompose* methods by `Denis Engemann`_ and `Alex Gramfort`_ - -- Improve ICA computation speed and memory usage by `Denis Engemann`_ and `Alex Gramfort`_ - -- Add polygonal surface decimation function to preprocess head surfaces for coregistration by `Denis Engemann`_ and `Alex Gramfort`_ - -- DICS time-frequency beamforming for epochs, evoked and for estimating source power by `Roman Goj`_, `Alex Gramfort`_ and `Denis Engemann`_ - -- Add method for computing cross-spectral density (CSD) from epochs and class for storing CSD data by `Roman Goj`_, `Alex Gramfort`_ and `Denis Engemann`_ - -- Add trellis plot function and method for visualizing single epochs by `Denis Engemann`_ - -- Add fiducials read/write support by `Christian Brodbeck`_ and `Alex Gramfort`_ - -- Add select / drop bad channels in ``plot_raw`` on click by `Denis Engemann`_ - -- Add ``ico`` and ``oct`` source space creation in native Python by `Eric Larson`_ - -- Add interactive rejection of bad trials in ``plot_epochs`` by `Denis Engemann`_ - -- Add morph map calculation by `Eric Larson`_ and `Martin Luessi`_ - -- Add volume and discrete source space creation and I/O support by `Eric Larson`_ - -- Time-frequency beamforming to obtain spectrograms in source space using LCMV and DICS by `Roman Goj`_, `Alex Gramfort`_ and `Denis Engemann`_ - -- Compute epochs power spectral density function by `Denis Engemann`_ - -- Plot raw power spectral density by `Eric Larson`_ - -- Computing of distances along the cortical surface by `Eric Larson`_ - -- Add reading BEM solutions by `Eric Larson`_ - -- Add forward solution calculation in native Python by `Eric Larson`_ - -- Add (Neuro)debian license compatibility by `Eric Larson`_ - -- Automatic QRS threshold selection for ECG events by `Eric Larson`_ - -- Add Travis continuous integration service by `Denis Engemann`_ - -- Add SPM face data set by `Denis Engemann`_ `Martin Luessi`_ and `Alex Gramfort`_ - -- Support reading of EDF+,BDF data by `Teon Brooks`_ - -- Tools for scaling MRIs (mne.scale_mri) by `Christian Brodbeck`_ - -- GUI for head-MRI coregistration (mne.gui.coregistration) by `Christian Brodbeck`_ - -- GUI for ki2fiff conversion (mne.gui.kit2fiff) by `Christian Brodbeck`_ - -- Support reading of EEG BrainVision data by `Teon Brooks`_ - -- Improve CTF compensation handling by `Martin Luessi`_ and `Eric Larson`_ - -- Improve and extend automated layout guessing by `Denis Engemann`_ - -- Add Continuum Analytics Anaconda support by `Denis Engemann`_ - -- Add ``subtract evoked`` option to beamformers by `Andrew Dykstra`_ - -- Add new ``transform`` method to SourceEstimate(s) by `Andrew Dykstra`_ - -API -~~~ - -- The pick_normal parameter for minimum norm solvers has been renamed as ``pick_ori`` and normal orientation picking is now achieved by passing the value "normal" for the ``pick_ori`` parameter. - -- ICA objects now expose the measurement info of the object fitted. - -- Average EEG reference is now added by default to Raw instances. - -- Removed deprecated read/write_stc/w, use SourceEstimate methods instead - -- The ``chs`` argument in ``mne.layouts.find_layout`` is deprecated and will be removed in MNE-Python 0.9. Use ``info`` instead. - -- ``plot_evoked`` and ``Epochs.plot`` now open a new figure by default. To plot on an existing figure please specify the ``axes`` parameter. - - -Authors -~~~~~~~ - -The committer list for this release is the following (preceded by number -of commits): - -* 336 Denis A. Engemann -* 202 Eric Larson -* 193 Roman Goj -* 138 Alexandre Gramfort -* 99 Mainak Jas -* 75 Christian Brodbeck -* 60 Martin Luessi -* 40 Teon Brooks -* 29 Romain Trachel -* 28 Andrew Dykstra -* 12 Mark Wronkiewicz -* 10 Christoph Dinh -* 8 Alan Leggitt -* 3 Yaroslav Halchenko -* 3 Daniel Strohmeier -* 2 Mads Jensen -* 2 Praveen Sripad -* 1 Luke Bloy -* 1 Emanuele Olivetti -* 1 Yousra BEKHTI diff --git a/doc/changes/v0.8.rst b/doc/changes/v0.8.rst deleted file mode 100644 index c1de1638fdf..00000000000 --- a/doc/changes/v0.8.rst +++ /dev/null @@ -1,194 +0,0 @@ -.. _changes_0_8: - -Version 0.8 (2014-06-25) ------------------------- - -Changelog -~~~~~~~~~ - -- Add Python3 support by `Nick Ward`_, `Alex Gramfort`_, `Denis Engemann`_, and `Eric Larson`_ - -- 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 `Tal Linzen`_, `Alex Gramfort`_ 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 `Alex Gramfort`_ - -- 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`_ - -- Add ``plot_events`` function to visually display paradigm by `Alex Gramfort`_ - -- Improved connectivity circle plot by `Martin Luessi`_ - -- Add ability to anonymize measurement info by `Eric Larson`_ - -- Add callback to connectivity circle plot to isolate connections to clicked nodes `Roan LaPlante`_ - -- Add ability to add patch information to source spaces by `Eric Larson`_ - -- Add ``split_label`` function to divide labels into multiple parts by `Christian Brodbeck`_ - -- Add ``color`` attribute to ``Label`` objects by `Christian Brodbeck`_ - -- Add ``max`` mode for ``extract_label_time_course`` by `Mads Jensen`_ - -- Add ``rename_channels`` function to change channel names and types in info object by `Dan Wakeman`_ and `Denis Engemann`_ - -- Add ``compute_ems`` function to extract the time course of experimental effects by `Denis Engemann`_, `Sébastien Marti`_ and `Alex Gramfort`_ - -- Add option to expand Labels defined in a source space to the original surface (``Label.fill()``) by `Christian Brodbeck`_ - -- GUIs can be invoked form the command line using ``$ mne coreg`` and ``$ mne kit2fiff`` by `Christian Brodbeck`_ - -- Add ``add_channels_epochs`` function to combine different recordings at the Epochs level by `Christian Brodbeck`_ and `Denis Engemann`_ - -- Add support for EGI Netstation simple binary files by `Denis Engemann`_ - -- Add support for treating arbitrary data (numpy ndarray) as a Raw instance by `Eric Larson`_ - -- Support for parsing the EDF+ annotation channel by `Martin Billinger`_ - -- Add EpochsArray constructor for creating epochs from numpy arrays by `Denis Engemann`_ and `Federico Raimondo`_ - -- Add connector to FieldTrip realtime client by `Mainak Jas`_ - -- Add color and event_id with legend options in plot_events in viz.py by `Cathy Nangini`_ - -- Add ``events_list`` parameter to ``mne.concatenate_raws`` to concatenate events corresponding to runs by `Denis Engemann`_ - -- Add ``read_ch_connectivity`` function to read FieldTrip neighbor template .mat files and obtain sensor adjacency matrices by `Denis Engemann`_ - -- Add display of head in helmet from -trans.fif file to check coregistration quality by `Mainak Jas`_ - -- Add ``raw.add_events`` to allow adding events to a raw file by `Eric Larson`_ - -- Add ``plot_image`` method to Evoked object to display data as images by `Jean-Remi King`_ and `Alex Gramfort`_ and `Denis Engemann`_ - -- Add BCI demo with CSP on motor imagery by `Martin Billinger`_ - -- New ICA API with unified methods for processing ``Raw``, ``Epochs`` and ``Evoked`` objects by `Denis Engemann`_ - -- Apply ICA at the evoked stage by `Denis Engemann`_ - -- New ICA methods for visualizing unmixing quality, artifact detection and rejection by `Denis Engemann`_ - -- Add ``pick_channels`` and ``drop_channels`` mixin class to pick and drop channels from ``Raw``, ``Epochs``, and ``Evoked`` objects by `Andrew Dykstra`_ and `Denis Engemann`_ - -- Add ``EvokedArray`` class to create an Evoked object from an array by `Andrew Dykstra`_ - -- Add ``plot_bem`` method to visualize BEM contours on MRI anatomical images by `Mainak Jas`_ and `Alex Gramfort`_ - -- Add automated ECG detection using cross-trial phase statistics by `Denis Engemann`_ and `Juergen Dammers`_ - -- Add Forward class to succinctly display gain matrix info by `Andrew Dykstra`_ - -- Add reading and writing of split raw files by `Martin Luessi`_ - -- Add OLS regression function by `Tal Linzen`_, `Teon Brooks`_ and `Denis Engemann`_ - -- Add computation of point spread and cross-talk functions for MNE type solutions by `Alex Gramfort`_ and `Olaf Hauk`_ - -- Add mask parameter to ``plot_evoked_topomap`` and ``evoked.plot_topomap`` by `Denis Engemann`_ and `Alex Gramfort`_ - -- Add infomax and extended infomax ICA by `Denis Engemann`_, `Juergen Dammers`_ and `Lukas Breuer`_ and `Federico Raimondo`_ - -- Aesthetically redesign interpolated topography plots by `Denis Engemann`_ and `Alex Gramfort`_ - -- Simplify sensor space time-frequency analysis API with ``tfr_morlet`` function by `Alex Gramfort`_ and `Denis Engemann`_ - -- Add new somatosensory MEG dataset with nice time-frequency content by `Alex Gramfort`_ - -- Add HDF5 write/read support for SourceEstimates by `Eric Larson`_ - -- Add InverseOperator class to display inverse operator info by `Mainak Jas`_ - -- Add ``$ mne report`` command to generate html reports of MEG/EEG data analysis pipelines by `Mainak Jas`_, `Alex Gramfort`_ and `Denis Engemann`_ - -- Improve ICA verbosity with regard to rank reduction by `Denis Engemann`_ - -BUG -~~~ - -- Fix incorrect ``times`` attribute when stc was computed using ``apply_inverse`` after decimation at epochs stage for certain, arbitrary sample frequencies by `Denis Engemann`_ - -- Fix corner case error for step-down-in-jumps permutation test (when step-down threshold was high enough to include all clusters) by `Eric Larson`_ - -- Fix selection of total number of components via float when picking ICA sources by `Denis Engemann`_ and `Qunxi Dong`_ - -- Fix writing and reading transforms after modification in measurement info by `Denis Engemann`_ and `Martin Luessi`_ and `Eric Larson`_ - -- Fix pre-whitening / rescaling when estimating ICA on multiple channels without covariance by `Denis Engemann`_ - -- Fix ICA pre-whitening, avoid recomputation when applying ICA to new data by `Denis Engemann`_ - -API -~~~ - -- The minimum numpy version has been increased to 1.6 from 1.4. - -- Epochs object now has a selection attribute to track provenance of selected Epochs. The length of the drop_log attribute is now the same as the length of the original events passed to Epochs. In earlier versions it had the length of the events filtered by event_id. Epochs has also now a plot_drop_log method. - -- Deprecate Epochs.drop_picks in favor of a new method called drop_channels - -- Deprecate ``labels_from_parc`` and ``parc_from_labels`` in favor of ``read_labels_from_annot`` and ``write_labels_to_annot`` - -- The default of the new add_dist option of ``setup_source_space`` to add patch information will change from False to True in MNE-Python 0.9 - -- Deprecate ``read_evoked`` and ``write_evoked`` in favor of ``read_evokeds`` and ``write_evokeds``. read_evokeds will return all `Evoked` instances in a file by default. - -- Deprecate ``setno`` in favor of ``condition`` in the initialization of an Evoked instance. This affects ``mne.fiff.Evoked`` and ``read_evokeds``, but not ``read_evoked``. - -- Deprecate ``mne.fiff`` module, use ``mne.io`` instead e.g. ``mne.io.Raw`` instead of ``mne.fiff.Raw``. - -- Pick functions (e.g., ``pick_types``) are now in the mne namespace (e.g. use ``mne.pick_types``). - -- Deprecated ICA methods specific to one container type. Use ICA.fit, ICA.get_sources ICA.apply and ``ICA.plot_*`` for processing Raw, Epochs and Evoked objects. - -- The default smoothing method for ``mne.stc_to_label`` will change in v0.9, and the old method is deprecated. - -- As default, for ICA the maximum number of PCA components equals the number of channels passed. The number of PCA components used to reconstruct the sensor space signals now defaults to the maximum number of PCA components estimated. - -Authors -~~~~~~~ - -The committer list for this release is the following (preceded by number of commits): - -* 418 Denis A. Engemann -* 284 Alexandre Gramfort -* 242 Eric Larson -* 155 Christian Brodbeck -* 144 Mainak Jas -* 49 Martin Billinger -* 49 Andrew Dykstra -* 44 Tal Linzen -* 37 Dan G. Wakeman -* 36 Martin Luessi -* 26 Teon Brooks -* 20 Cathy Nangini -* 15 Hari Bharadwaj -* 15 Roman Goj -* 10 Ross Maddox -* 9 Marmaduke Woodman -* 8 Praveen Sripad -* 8 Tanay -* 8 Roan LaPlante -* 5 Saket Choudhary -* 4 Nick Ward -* 4 Mads Jensen -* 3 Olaf Hauk -* 3 Brad Buran -* 2 Daniel Strohmeier -* 2 Federico Raimondo -* 2 Alan Leggitt -* 1 Jean-Remi King -* 1 Matti Hämäläinen diff --git a/doc/changes/v0.9.rst b/doc/changes/v0.9.rst deleted file mode 100644 index 0d8cc565472..00000000000 --- a/doc/changes/v0.9.rst +++ /dev/null @@ -1,239 +0,0 @@ -.. _changes_0_9: - -Version 0.9 (2015-05-22) ------------------------- - -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 ``mne.Report.add_bem_to_section``, ``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 consequence, ``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 diff --git a/doc/changes/v1.1.rst b/doc/changes/v1.1.rst deleted file mode 100644 index de0f597c0ee..00000000000 --- a/doc/changes/v1.1.rst +++ /dev/null @@ -1,271 +0,0 @@ -.. _changes_1_1_0: - -Version 1.1.0 (2022-08-03) --------------------------- - -Enhancements -~~~~~~~~~~~~ -- Added new built-in montage R-Net 128 Ch (Brain Products) (:gh:`10974` by :newcontrib:`Ilias Machairas`) - -- :class:`~mne.channels.DigMontage` objects can now be checked for equality via ``==`` (:gh:`10942` by :newcontrib:`Tziona NessAiver`) - -- Add a note to clarify the inclusion of average referencing gain matrix during whitening (:gh:`10922` by :newcontrib:`Mingjian He`) - -- Add time axis scale bar for :meth:`mne.Epochs.plot` using matplotlib backend (:gh:`10736` by :newcontrib:`Jordan Drew`) - -- Add :func:`mne.bem.distance_to_bem` to find depth of source positions (:gh:`10632` by :newcontrib:`Matt Courtemanche`) - -- Add support for ahdr files in :func:`mne.io.read_raw_brainvision` (:gh:`10515` by :newcontrib:`Alessandro Tonin`) - -- Add support for reading data from Gowerlabs devices to :func:`mne.io.read_raw_snirf` (:gh:`10555` by :newcontrib:`Samuel Powell` and `Robert Luke`_) - -- Add built-in sensor layout files for Geodesic Head Web 130 and 280 devices (:gh:`10627` by `Evan Hathaway`_) - -- Add ``mne-icalabel`` to :func:`mne.sys_info` (:gh:`10615` by `Adam Li`_) - -- Add support for ``overview_mode`` in :meth:`raw.plot() ` and related functions/methods (:gh:`10501` by `Eric Larson`_) - -- Add :meth:`mne.io.Raw.crop_by_annotations` method to get chunks of Raw data based on :class:`mne.Annotations`. (:gh:`10460` by `Alex Gramfort`_) - -- The ``pick_channels`` method gained a ``verbose`` parameter, allowing e.g. to suppress messages about removed projectors (:gh:`10544` by `Richard Höchenberger`_) - -- Add :func:`mne.viz.plot_projs_joint` for joint plotting of projectors and Evoked (:gh:`10720` by `Eric Larson`_) - -- The :func:`mne.make_forward_dipole` function can now take a list of dipoles to make a multi-dipole forward models (:gh:`10464` by `Marijn van Vliet`_) - -- Add ``mode='outlines'`` support to :meth:`mne.Dipole.plot_locations` and :func:`mne.viz.plot_dipole_locations` (:gh:`10699` by `Eric Larson`_) - -- Add :meth:`mne.preprocessing.ICA.find_bads_muscle` to find muscle-related ICA components with an example, :ref:`ex-muscle-ica` (:gh:`10534` by `Alex Rockhill`_) - -- Add example of Xfit-style ECD modeling using multiple dipoles (:gh:`10464` by `Marijn van Vliet`_) - -- Add ``head_source`` argument to :func:`mne.make_field_map` to allow selecting which head source to use (:gh:`10568` by `Eric Larson`_) - -- Add support for ``n_jobs=None`` to support ``joblib:joblib.parallel_backend`` for more precise control over parallelization (:gh:`10567` by `Eric Larson`_) - -- It is now possible to compute inverse solutions with restricted source orientations using discrete forward models (:gh:`10464` by `Marijn van Vliet`_) - -- The new function :func:`mne.preprocessing.maxwell_filter_prepare_emptyroom` simplifies the preconditioning of an empty-room recording for our Maxwell filtering operations (:gh:`10533` by `Richard Höchenberger`_ and `Eric Larson`_) - -- Add keyboard shortcuts to toggle :meth:`mne.preprocessing.ICA.plot_properties` topomap channel types ('t') and power spectral density log-scale ('l') (:gh:`10557` by `Alex Rockhill`_) - -- Add ``--mri``, and ``--threshold`` options to :ref:`mne make_scalp_surfaces` to improve head surface mesh extraction (:gh:`10591` by `Eric Larson`_) - -- Add :func:`mne.preprocessing.compute_bridged_electrodes` to detect EEG electrodes with shared spatial sources due to a conductive medium connecting two or more electrodes, add :ref:`ex-eeg-bridging` for an example and :func:`mne.viz.plot_bridged_electrodes` to help visualize (:gh:`10571` by `Alex Rockhill`_) - -- Add ``'nearest'`` as an option for the ``image_interp`` argument in :func:`mne.viz.plot_topomap` to plot a topomap without interpolation using a Voronoi parcelation (:gh:`10571` by `Alex Rockhill`_) - -- Add :func:`mne.preprocessing.interpolate_bridged_electrodes` to use the spatially smeared signal to get a better interpolation rather than dropping those channels (:gh:`10587` by `Alex Rockhill`_) - -- Add support for hemoglobin type fNIRS data to temporal derivative distribution repair (TDDR) :func:`mne.preprocessing.nirs.temporal_derivative_distribution_repair` (:gh:`10125` by `Johann Benerradi`_) - -- :func:`mne.viz.plot_evoked_topomap` and :meth:`mne.Evoked.plot_topomap` now display the time range the map was averaged over if ``average`` was passed (:gh:`10606` by `Richard Höchenberger`_) - -- :func:`mne.viz.plot_evoked_topomap` and :meth:`mne.Evoked.plot_topomap` can now average the topographic maps across different time periods for each time point. To do this, pass a list of periods via the ``average`` parameter (:gh:`10610` by `Richard Höchenberger`_) - -- :func:`mne.viz.plot_evoked` and :meth:`mne.Evoked.plot` gained a new parameter, ``highlight``, to visually highlight time periods of interest (:gh:`10614` by `Richard Höchenberger`_) - -- Added fNIRS support to :func:`mne.Info.get_montage` (:gh:`10611` by `Robert Luke`_) - -- Add :func:`mne.viz.plot_ch_adjacency` to visualize and manually edit the channel adjacency matrix (:gh:`10633` by `Mikołaj Magnuski`_) - -- Add :meth:`mne.viz.Brain.get_view` to get the current camera parameters such that they can be passed to :meth:`mne.viz.Brain.show_view` (:gh:`10661` by `Alex Rockhill`_) - -- Added support for Aurora version 2021.9.0.6 to :func:`mne.io.read_raw_nirx` (:gh:`10668` by `Robert Luke`_) - -- Added BrainVision format (``.vhdr``, ``.vmrk``, ``.eeg``) to :func:`mne.export.export_raw` (:gh:`10681` by `Stefan Appelhoff`_) - -- Added ``export`` method to :class:`mne.Evoked` (:gh:`10681` by `Stefan Appelhoff`_) - -- Add timeformat ``YYYY/MM/DD`` to ``mne.io.ctf.info._convert_time`` (:gh:`10674` by `Simon Kern`_) - -- :meth:`mne.Report.add_figure` and :meth:`mne.Report.add_image` gained a new parameter, ``section``, allowing to put multiple figures or images into the same "content block". Previously, the only way to group figures and images was by means of a slider, which sometimes made content hard to discover. The slider remains available as an alternative (:gh:`10694` by `Richard Höchenberger`_) - -- All functions and methods that plot topographic maps for EEG (2D projections of the EEG sensor locations) now accept the parameter value ``sphere='eeglab'`` to lay out the sensors with respect to the head circle in a similar way to how EEGLAB does, i.e., T7/T8 and Fpz/Oz are placed directly on the circle for template montages (:gh:`10572` by `Richard Höchenberger`_) - -- :func:`mne.channels.get_builtin_montages` gained a new parameter, ``descriptions``, which allows to retrieve the descriptions of the montages in addition to their names (:gh:`10373` by `Richard Höchenberger`_) - -- Add ``include`` option to :meth:`mne.io.read_raw_edf`, :meth:`mne.io.read_raw_bdf` and :meth:`mne.io.read_raw_gdf`. (:gh:`10734` by `Michiru Kaneda`_) - -- :func:`mne.gui.coregistration` gained a new parameter, ``fullscreen``, to start the GUI in fullscreen mode (:gh:`10284` by `Richard Höchenberger`_) - -- The built-in FieldTrip channel adjacency matrices, which can be read via :func:`~mne.channels.read_ch_adjacency`, have been synchronized with FieldTrip again. This means that numerous new adjacencies have been added, most notably those for standard 10-05 and 10-20 montages (:gh:`10749` by `Richard Höchenberger`_) - -- :meth:`mne.Evoked.plot_field` gained a new parameter, ``interaction``, to control the rotation axes when interacting with the head (:gh:`10788` by `Richard Höchenberger`_) - -- Add :func:`mne.read_evoked_besa` for reading evokeds from BESA ``.avr`` and ``.mul`` files. (:gh:`10892` by `Marijn van Vliet`_) - -- Add :meth:`mne.time_frequency.EpochsTFR.decimate` to reduce size of time-frequency epochs objects (:gh:`10940` by `Alex Rockhill`_) - -- Add an alias that maps EGI reference channel names (``VREF`` or ``Vertex Reference``) to the electrode name in the standard EGI montages (``Cz``). Now setting standard EGI montages with :meth:`~mne.io.Raw.set_montage` with ``match_alias=True`` will avoid raising an error (:gh:`10823` by `Scott Huberty`_) - -- Add provenance in :func:`mne.time_frequency.EpochsTFR.apply_baseline` (:gh:`10979` by `Alex Rockhill`_) - -Bugs -~~~~ -- Fix bug in ``mne.surface._project_onto_surface`` for the condition ``method != 'accurate' and return_nn`` (:gh:`10930` by `Christian O'Reilly`_) - -- Fix bug in :func:`mne.export.export_raw` to ignore None value in filenames attribute of :class:`mne.io.RawArray` (:gh:`10927` by :newcontrib:`Reza Nasri`) - -- Fix bug in :func:`mne.io.read_raw_edf` to allow reading in all Hypnodyne ZMax EDFs to be read in without issues (:gh:`10754` by :newcontrib:`Frederik Weber`) - -- Fix bug in :func:`mne.Epochs.drop_bad` where data was loaded although no rejection had to be performed (:gh:`10718` by :newcontrib:`Lukas Gemein`) - -- Pick also bad channels when selecting T1T2 magnetometers in :func:`mne.preprocessing.maxwell_filter` (:gh:`10639` by :newcontrib:`Matti Toivonen`) - -- Make ``color`` parameter check in in :func:`mne.viz.plot_evoked_topo` consistent (:gh:`10217` by :newcontrib:`T. Wang` and `Stefan Appelhoff`_) - -- Fix bug in :func:`mne.io.read_raw_brainvision` when BrainVision data are acquired with the Brain Products "V-Amp" amplifier and disabled lowpass filter is marked with value ``0`` (:gh:`10517` by :newcontrib:`Alessandro Tonin`) - -- Fix bug in :func:`mne.pick_types` and related methods where ``csd=True`` was not passed handled properly (:gh:`10470` by :newcontrib:`Matthias Dold`) - -- Fix bug where plots produced using the ``'qt'`` / ``mne_qt_browser`` backend could not be added using :meth:`mne.Report.add_figure` (:gh:`10485` by `Eric Larson`_) - -- Fix bug where ``theme`` was not handled properly in :meth:`mne.io.Raw.plot` (:gh:`10487`, :gh:`10500` by `Mathieu Scheltienne`_ and `Eric Larson`_) - -- Fix bug in :meth:`raw.crop(start, stop) ` that would cause annotations to be erroneously shifted when ``start != 0`` and no measurement date was set. (:gh:`10491` by `Eric Larson`_) - -- Fix bug in :func:`mne.io.read_raw_bti` where unknown electrode locations were not handled properly (:gh:`10662` by `Eric Larson`_) - -- Fix bug in :func:`mne.io.read_raw_ctf` on Windows where large files could not be read (:gh:`10866` by `Eric Larson`_) - -- Fix bug in :func:`mne.io.read_raw_ctf` where invalid measurement dates were not handled properly (:gh:`10957` by `Jean-Remi King`_ and `Eric Larson`_) - -- Rendering issues with recent MESA releases can be avoided by setting the new environment variable ``MNE_3D_OPTION_MULTI_SAMPLES=1`` or using :func:`mne.viz.set_3d_options` (:gh:`10513` by `Eric Larson`_) - -- Fix behavior for the ``pyvista`` 3D renderer's ``quiver3D`` function so that default arguments plot a glyph in ``arrow`` mode (:gh:`10493` by `Alex Rockhill`_) - -- Retain epochs metadata when using :func:`mne.channels.combine_channels` (:gh:`10504` by `Clemens Brunner`_) - -- Fix epochs indexing with metadata containing boolean type and missing values (:gh:`10705` by `Clemens Brunner`_ and `Alex Gramfort`_) - -- Fix reading of fiducial locations in :func:`mne.io.read_raw_eeglab` (:gh:`10521` by `Alex Gramfort`_) - -- Prevent creation of montage with invalid ``[x, y, z]`` coordinates with :func:`mne.channels.make_dig_montage` (:gh:`10547` by `Mathieu Scheltienne`_) - -- Fix bug in coregistration GUI that prevented it from starting up if only a high-resolution head model was available (:gh:`10543` by `Richard Höchenberger`_) - -- Fix bug with :class:`mne.Epochs.add_reference_channels` where attributes were not updated properly so subsequent `~mne.Epochs.pick_types` calls were broken (:gh:`10912` by `Eric Larson`_) -- -- Fix bug in the :class:`mne.viz.Brain` tool bar that prevented the buttons to call the corresponding feature (:gh:`10560` by `Guillaume Favelier`_) - -- Fix issue with saving epochs once :func:`~mne.preprocessing.compute_current_source_density` has been used if a rejection threshold was used first (:gh:`10619` by `Alex Rockhill`_ and `Richard Höchenberger`_) - -- Fix bug in :func:`mne.viz.plot_evoked_image` that would cause incorrect sub-titles when using ``group_by`` (:gh:`10618` by `Reza Shoorangiz`_) - -- Reduce memory usage when loading an EDF file with ``preload=False`` (:gh:`10638` by `Clemens Brunner`_) - -- Fix bug in :meth:`mne.io.Raw.get_channel_types` and related methods where ``unique=True`` would return a :class:`python:set` with arbitrary order rather than a :class:`python:list` that preserves the same order as ``inst.ch_names`` (:gh:`10720` by `Eric Larson`_) - -- In :func:`mne.preprocessing.find_bad_channels_maxwell`, do not re-filter the data if a low-pass filter with the requested frequency has already been applied (:gh:`10664` by `Richard Höchenberger`_) - -- Fix a problem in :meth:`mne.Evoked.get_peak`, where under certain circumstances the ``mode`` parameters ``'pos'`` and ``'neg'`` were not honored when ``tmin`` and/or ``tmax`` were passed as well (:gh:`10686` by `Richard Höchenberger`_) - -- :func:`mne.read_evokeds`, :func:`mne.channels.read_custom_montage`, :func:`mne.channels.read_dig_hpts`, :func:`mne.channels.read_dig_polhemus_isotrak`, and :func:`mne.channels.read_polhemus_fastscan` now correctly expand ``~`` in the provided path to the user's home directory (:gh:`10685`, :gh:`10688` by `Richard Höchenberger`_) - -- Fix bug in :func:`mne.io.read_raw_eeglab` and :func:`mne.read_epochs_eeglab`, where the presence of channels without position in the ``.set`` file caused positions incorrectly assigned to all further channels (:gh:`8754` by `Mikołaj Magnuski`_) - -- Combining channels of :class:`mne.Epochs` or :class:`mne.Evoked` objects now properly retains baseline information (:gh:`10703` by `Clemens Brunner`_) - -- In :class:`mne.Report`, some figures would have an undesired border added to the edges; this has now been resolved (:gh:`10730` by `Richard Höchenberger`_) - -- Fix selection of EEG channels and selected sphere when plotting bridged electrodes with :func:`mne.viz.plot_bridged_electrodes` (:gh:`10753` by `Mathieu Scheltienne`_) - -- Fix broken links in :ref:`tut-fix-meshes` (:gh:`10765` by `Alex Rockhill`_) - -- The built-in FieldTrip channel adjacency matrix for ``easycapM1`` had a bug, where the channel ``PO8`` was incorrectly labeled as ``PO6`` This has been resolved by updating the adjacency matrix to the latest version provided by FieldTrip (:gh:`10749` by `Richard Höchenberger`_) - -- Add a YouTube video tutorial for editing Freesurfer surfaces in Blender to :ref:`tut-fix-meshes` (:gh:`10778` by `Alex Rockhill`_) - -- The default interaction style of :meth:`mne.Evoked.plot_field` has been changed such that if behaves like :func:`~mne.viz.plot_alignment` when trying to rotate the head (:gh:`10788` by `Richard Höchenberger`_) - -- Add a video on how to operate the intracranial electrode contact location GUI in :ref:`tut-ieeg-localize` (:gh:`10800` by `Alex Rockhill`_) - -- Add a video on how to operate the coregistration GUI in :ref:`tut-source-alignment` (:gh:`10802` by `Alex Rockhill`_) - -- Add ``show`` and ``block`` arguments to :func:`mne.gui.coregistration` and ``mne.gui.locate_ieeg`` to pop up the GUIs and halt execution of subsequent code respectively (:gh:`10802` by `Alex Rockhill`_) - -- Correctly report the number of available projections when printing measurement info in a Jupyter notebook (:gh:`10471` by `Clemens Brunner`_) - -- Fix value set in ``raw.orig_format`` for readers of BrainVision (ASCII format), EGI and Artemis123 files (:gh:`10851` by `Mathieu Scheltienne`_) - -- When reading EGI MFF files, channel names are no longer ignored and reference channel information is properly incorporated (:gh:`10898` by `Scott Huberty`_ and `Daniel McCloy`_) - -- Fix bug in :func:`mne.time_frequency.psd_array_welch` and related functions/methods where the bias was not accounted for when ``average='median'`` (:gh:`10990` by `Eric Larson`_) - -- Fix bug in :class:`mne.decoding.TemporalFilter` where filter parameters were not handled properly (:gh:`10968` by `Eric Larson`_) - -- Fix documentation bug in ``ica.plot_sources`` to specify that ``picks`` keyword argument is for picking ICA components to plot (:gh:`10936` by `Adam Li`_) - -- Annotations contained in EDF files are correctly read as UTF-8 according to the EDF specification (:gh:`10963` by `Clemens Brunner`_) - -- Fix bug where complex-valued topoplots caused an error, convert to amplitude instead (:gh:`10978` by `Alex Rockhill`_) - -API and behavior changes -~~~~~~~~~~~~~~~~~~~~~~~~ -- When creating BEM surfaces via :func:`mne.bem.make_watershed_bem` and :func:`mne.bem.make_flash_bem`, the ``copy`` parameter now defaults to ``True``. This means that instead of creating symbolic links inside the FreeSurfer subject's ``bem`` folder, we now create "actual" files. This should avoid troubles when sharing files across different operating systems and file systems (:gh:`10531` by `Richard Höchenberger`_) - -- The ordering of channels returned by :func:`mne.io.read_raw_nirx` is now ordered by channel name, rather than the order provided by the manufacturer. This enables consistent ordering of channels across different file types (:gh:`10555` by `Robert Luke`_) - -- For :func:`mne.viz.plot_topomap`, :func:`mne.viz.plot_evoked_topomap`, :func:`mne.viz.plot_arrowmap`, :func:`mne.viz.plot_ica_components`, :meth:`mne.Covariance.plot_topomap`, :meth:`mne.Evoked.plot_topomap`, :meth:`mne.Evoked.animate_topomap`, :meth:`mne.decoding.CSP.plot_patterns`, :meth:`mne.Projection.plot_topomap` and :meth:`mne.preprocessing.ICA.plot_components` the topomap image interpolation was previously a cubic interpolation but now can be ``'linear'`` and ``'nearest'`` as well. Unless ``image_interp='nearest'`` is passed mne uses a subsequent matplotlib bilinear interpolation to make the interpolated image smoother. Previously, ``'image_interp'`` controlled this second interpolation step and, for the first interpolation, the only option was cubic. To simplify, ``image_interp`` is now responsible for the main interpolation and the subsequent matplotlib image interpolation is bilinear but can be changed afterward using ``im.set_interpolation`` (:gh:`10617` by `Alex Rockhill`_) - -- The FLASH BEM surface generation via :func:`mne.bem.make_flash_bem` or the :ref:`mne flash_bem` command has now been clarified in terms of expected inputs. In :func:`mne.bem.convert_flash_mris` the ``convert`` parameter is now deprecated and the ``flash5`` and ``flash30`` now accept list of file names or nibabel images. One breaking change is that now the flash files are looked for as mef05_*.mgz and mef30_*.mgz in mri/flash folder (:gh:`10715` by `Alex Gramfort`_) - -- :func:`~mne.viz.plot_compare_evokeds` gets a new parameter ``time_unit`` which can be ``"s"`` or ``"ms"`` (:gh:`10950` by `Daniel McCloy`_) - -- The ``to_data_frame`` methods for :meth:`Raw `, :meth:`Epochs `, :meth:`Evoked `, :meth:`SourceEstimate `, :meth:`EpochsTFR `, and :meth:`AverageTFR ` all now have default ``time_format=None`` (keep time in seconds) instead of ``time_format='ms'`` (convert time to milliseconds) (:gh:`10925` by `Daniel McCloy`_) - -- :func:`mne.Evoked.decimate` now aligns to the sample at time=0 (so that the exact sample when the event occurred is preserved) to be consistent with :func:`mne.Epochs.decimate` (:gh:`10945` by `Alex Rockhill`_) - -Authors -~~~~~~~ - -* Adam Li -* Adeline Fecker+ -* Alessandro Tonin+ -* Alex Ciok+ -* Alex Rockhill -* Alexandre Gramfort -* Archit Singhal+ -* Ashley Drew+ -* Ben Beasley+ -* Carina Forster+ -* Christian O'Reilly -* Clemens Brunner -* Cora Kim -* Daniel McCloy -* Dominik Welke -* Dominique Makowski -* Eric Larson -* Evan Hathaway -* Frederik D. Weber+ -* Guillaume Favelier -* Hamid Maymandi+ -* Ilias Machairas+ -* Jean-Remi King -* Johann Benerradi -* Jon Houck -* Jona Sassenhagen -* Jordan Drew+ -* Lukas Gemein+ -* Marijn van Vliet -* Martin Schulz -* Mathieu Scheltienne -* Matt Courtemanche+ -* Matthias Dold+ -* Matti Toivonen+ -* Michiru Kaneda+ -* Mikołaj Magnuski -* Mingjian He+ -* Naveen Srinivasan+ -* Phillip Alday -* Reza Nasri+ -* Reza Shoorangiz -* Richard Höchenberger -* Rob Luke -* Scott Huberty+ -* Simon Kern -* Sondre Foslien+ -* Stefan Appelhoff -* T. Wang+ -* Tziona NessAiver+ diff --git a/doc/changes/v1.2.rst b/doc/changes/v1.2.rst deleted file mode 100644 index e292b472b03..00000000000 --- a/doc/changes/v1.2.rst +++ /dev/null @@ -1,116 +0,0 @@ -.. _changes_1_2_0: - -Version 1.2.0 (2022-10-11) --------------------------- - -Enhancements -~~~~~~~~~~~~ -- Add ``vmin`` and ``vmax`` parameters to :meth:`mne.Evoked.animate_topomap` (:gh:`11073` by :newcontrib:`Mats van Es`) -- Enable common average reference projection for ECoG, sEEG, and DBS data (optionally jointly with ``joint=True``) in :meth:`~mne.io.Raw.set_eeg_reference` and related functions/methods (:gh:`10656` by :newcontrib:`Moritz Gerster` and `Eric Larson`_) -- The ``trans`` parameter in :func:`mne.make_field_map` now accepts a :class:`~pathlib.Path` object, and uses standardised loading logic (:gh:`10784` by :newcontrib:`Andrew Quinn`) -- Add support for computing forward solutions using OpenMEEG_ (:gh:`11011` by `Alex Gramfort`_ and `Eric Larson`_) -- EEGLAB files (saved as MAT versions less than v7.3) can now be imported with :func:`mne.io.read_raw_eeglab` without the optional dependency ``pymatreader`` (:gh:`11006` by `Clemens Brunner`_) -- Add eight source estimate comparison metrics to new submodule :mod:`mne.simulation.metrics` (:gh:`6233` by `Kostiantyn Maksymenko`_ and `Alex Gramfort`_) -- Add :func:`mne.time_frequency.csd_tfr` to compute cross-spectral density from :class:`mne.time_frequency.EpochsTFR` (:gh:`10986` by `Alex Rockhill`_) -- Improve ``repr()`` for :class:`mne.minimum_norm.InverseOperator` when loose orientation is used (:gh:`11048` by `Eric Larson`_) -- Add support for vector and volume source estimates in :func:`mne.minimum_norm.get_point_spread` and :func:`mne.minimum_norm.get_cross_talk` (:gh:`8639`, :gh:`11083` by `Olaf Hauk`_, `Marijn van Vliet`_, `Alex Gramfort`_, and `Eric Larson`_) -- :meth:`mne.Epochs.plot_psd_topomap` now suppresses redundant colorbars when ``vlim='joint'`` (:gh:`11051` by `Daniel McCloy`_) -- Add ``starting_affine`` keyword argument to :func:`mne.transforms.compute_volume_registration` to initialize an alignment with an affine (:gh:`11020` by `Alex Rockhill`_) -- Add HTML representation for `~mne.Evoked` in Jupyter Notebooks (:gh:`11075` by `Valerii Chirkov`_ and `Andrew Quinn`_) -- Add support for ``temperature`` and ``gsr`` (galvanic skin response, i.e., electrodermal activity) channel types (:gh:`11090`, :gh:`11108` by `Eric Larson`_ and `Richard Höchenberger`_) -- Allow :func:`mne.beamformer.make_dics` to take ``pick_ori='vector'`` to compute vector source estimates (:gh:`10980` by `Alex Rockhill`_) -- Add ``units`` parameter to :func:`mne.io.read_raw_edf` in case units are missing from the file (:gh:`11099` by `Alex Gramfort`_) -- Add ``on_missing`` functionality to all of our classes that have a ``drop_channels`` method, to control what happens when channel names are not in the object (:gh:`11077` by `Andrew Quinn`_) -- Improve interpolation of bridged electrodes with `~mne.preprocessing.interpolate_bridged_electrodes` (:gh:`11094` by `Mathieu Scheltienne`_) -- Add :func:`mne.minimum_norm.apply_inverse_tfr_epochs` to apply inverse methods to time-frequency resolved epochs (:gh:`11095` by `Alex Rockhill`_) -- Add support for multiple probes via multiple CSV files passed to :func:`mne.io.read_raw_hitachi` (:gh:`11186` by `Eric Larson`_) -- Add :func:`mne.chpi.get_active_chpi` to retrieve the number of active hpi coils for each time point (:gh:`11122` by `Eduard Ort`_) -- Add example of how to obtain time-frequency decomposition using narrow bandpass Hilbert transforms to :ref:`ex-tfr-comparison` (:gh:`11116` by `Alex Rockhill`_) -- Add ``==`` and ``!=`` comparison between `mne.Projection` objects (:gh:`11147` by `Mathieu Scheltienne`_) -- Parse automatically temperature channel with :func:`mne.io.read_raw_edf` (:gh:`11150` by `Eric Larson`_ and `Alex Gramfort`_) -- Add ``unscale`` option to :func:`mne.head_to_mri` to facilitate working with surrogate MRI data (:gh:`11185` by `Eric Larson`_) -- Add ``encoding`` parameter to :func:`mne.io.read_raw_edf` and :func:`mne.io.read_raw_bdf` to support custom (non-UTF8) annotation channel encodings (:gh:`11154` by `Clemens Brunner`_) -- :class:`mne.preprocessing.ICA` gained a new method, :meth:`~mne.preprocessing.ICA.get_explained_variance_ratio`, that allows the retrieval of the proportion of variance explained by ICA components (:gh:`11141` by `Richard Höchenberger`_) -- Add ``on_baseline`` to :meth:`mne.preprocessing.ICA.apply`, :meth:`mne.preprocessing.ICA.plot_overlay`, and :func:`mne.viz.plot_ica_overlay` to allow reapplying baseline correction after applying ICA (:gh:`11232` by `Eric Larson`_) -- Add config option ``MNE_REPR_HTML`` to disable HTML repr in notebook environments (:gh:`11159` by `Clemens Brunner`_) - -Bugs -~~~~ -- Fix bug in :meth:`mne.io.Raw.crop` where argument ``include_tmax`` was not considered in checking ``tmax`` in bounds (:gh:`11196` by `Lukas Gemein`_) -- Fix bug in :func:`mne.io.read_raw_eeglab` where unlabeled fiducials caused reading errors (:gh:`11074` by :newcontrib:`Sebastiaan Mathot`) -- Fix bug in :func:`mne.time_frequency.read_csd` that returned ``projs`` as a list of dict instead of :class:`mne.Projection` (:gh:`11072` by :newcontrib:`Chetan Gohil`) -- Fix bug in :func:`mne.decoding.TimeFrequency` that prevented cloning if constructor arguments were modified (:gh:`11004` by :newcontrib:`Daniel Carlström Schad`) -- Fix bug in ``repr`` of decoding estimator classes (e.g., :class:`mne.decoding.SlidingEstimator`) where the parameters where not stored in the result string but instead just printed to ``sys.stdout`` (:gh:`11190` by :newcontrib:`Dominik Wetzel`) -- Document ``height`` and ``weight`` keys of ``subject_info`` entry in :class:`mne.Info` (:gh:`11019` by :newcontrib:`Sena Er`) -- Fix bug in :class:`mne.viz.Brain` constructor where the first argument was named ``subject_id`` instead of ``subject`` (:gh:`11049` by `Eric Larson`_) -- Fix bug in :ref:`mne coreg` where the MEG helmet position was not updated during ICP fitting (:gh:`11084` by `Eric Larson`_) -- Fix bug in :func:`~mne.io.read_raw_curry`, and :func:`~mne.io.read_raw_cnt` where digitization points were not read properly (:gh:`11145` by `Eric Larson`_) -- Fix bug in :func:`mne.minimum_norm.apply_inverse_epochs` where the average EEG projector was not checked properly (:gh:`11182` by `Eric Larson`_) -- Fix bug in :func:`mne.viz.plot_filter` when plotting filters created using ``output='ba'`` mode with ``compensation`` turned on. (:gh:`11040` by `Marian Dovgialo`_) -- Fix bugs in documentation of surface :class:`~mne.SourceSpaces` (:gh:`11171` by `Eric Larson`_) -- Fix bug in :func:`mne.viz.plot_compare_evokeds` where automatic legend labels could be excessively long; they are now abbreviated with ``...`` when necessary (:gh:`11181` by `Eric Larson`_) -- Fix bugs with ``verbose='error'`` not being used properly and allowing warnings through (:gh:`11193` by `Eric Larson`_) -- Fix bug in :func:`mne.io.read_raw_bti` where EEG, EMG, and H/VEOG channels were not detected properly, and many non-ECG channels were called ECG. The logic has been improved, and any channels of unknown type are now labeled as ``misc`` (:gh:`11102` by `Eric Larson`_) -- Fix bug in :func:`mne.viz.plot_topomap` when providing ``sphere="eeglab"`` (:gh:`11081` by `Mathieu Scheltienne`_) -- Fix bug in :meth:`mne.Dipole.to_mri` where MRI RAS rather than MRI surface RAS was returned (:gh:`11185` by `Eric Larson`_) -- Fix bug in :meth:`epochs.save ` where the ``verbose`` parameter defaulted to ``True`` instead of ``None`` (:gh:`11191` by `Eric Larson`_) -- The string and HTML representation of :class:`mne.preprocessing.ICA` reported incorrect values for the explained variance. This information has been removed from the representations, and should instead be retrieved via the new :meth:`~mne.preprocessing.ICA.get_explained_variance_ratio` method (:gh:`11141` by `Richard Höchenberger`_) -- Fix bug in :meth:`mne.Evoked.plot` and related methods where a ``np.nan`` location value in any channel causes spatial colours to fail (:gh:`6870` by `Simeon Wong`_) -- Fix bug in :meth:`mne.preprocessing.ICA.find_bads_muscle` where epochs caused an error when passed as the ``inst`` (:gh:`11197` by `Alex Rockhill`_) -- Fix bug in readers where EEG coordinates were assumed to be in head coordinates but no fiducial points were present. Estimated fiducial locations will now be added automatically to reflect the assumption of locations being in the head coordinate frame (:gh:`11212` by `Stefan Appelhoff`_ and `Eric Larson`_) -- The duration of raw data sometimes wasn't displayed correctly in Jupyter notebooks by omitting fractions of a second. We now always round up to the next full second so a duration of less than 1 second will not be displayed as a duration of zero anymore (:gh:`11203` by `Richard Höchenberger`_) -- Fix bug in :meth:`mne.Report.add_ica` and where baselines were not reapplied to the data when ``inst`` is Epochs or Evoked (:gh:`11232` by `Eric Larson`_) - -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`_) -- 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`_) -- The :func:`mne.head_to_mri` new function parameter ``kind`` default will change from ``'ras'`` to ``'mri'`` (:gh:`11185` by `Eric Larson`_) -- The ``show_toolbar`` argument to :class:`mne.viz.Brain` is being removed by deprecation (:gh:`11049` by `Eric Larson`_) -- New classes :class:`~mne.time_frequency.Spectrum` and :class:`~mne.time_frequency.EpochsSpectrum`, created via new methods :meth:`Raw.compute_psd()`, :meth:`Epochs.compute_psd()`, and :meth:`Evoked.compute_psd()` (:gh:`10184` by `Daniel McCloy`_) -- Functions/methods for plotting topomaps now have more consistent signatures; most have gained parameters for finer control of the topomap image and/or colorbar. See docstrings for details (:gh:`11123` by `Daniel McCloy`_) -- In :func:`mne.viz.plot_topomap`, passing ``axes=None`` will now create a new :class:`~matplotlib.figure.Figure` instead of plotting into the current axes (:gh:`11123` by `Daniel McCloy`_) -- In :func:`mne.viz.plot_topomap`, the parameter ``show_names`` has been deprecated, use the ``names`` parameter instead (:gh:`11123` by `Daniel McCloy`_) -- In :func:`mne.viz.plot_topomap`, :func:`~mne.viz.plot_tfr_topomap`, :func:`~mne.viz.plot_evoked_topomap`, and related class methods :meth:`mne.Covariance.plot_topomap`, :meth:`mne.Evoked.plot_topomap`, and :meth:`mne.time_frequency.AverageTFR.plot_topomap`: the parameters ``vmin`` and ``vmax`` are deprecated in favor of ``vlim``, for consistency with other ``plot_topomap`` functions and methods (:gh:`11123` by `Daniel McCloy`_) -- In :func:`mne.viz.plot_tfr_topomap`, :func:`~mne.viz.plot_evoked_topomap`, and related class methods :meth:`mne.Covariance.plot_topomap`, :meth:`mne.Evoked.plot_topomap`, and :meth:`mne.time_frequency.AverageTFR.plot_topomap`: the ``title`` parameter has been deprecated; use matplotlib's :meth:`fig.suptitle()` instead (:gh:`11123` by `Daniel McCloy`_) -- In functions/methods for plotting topomaps, the ``outlines='skirt'`` option is deprecated; use ``sphere='eeglab'`` for similar functionality (:gh:`11123` by `Daniel McCloy`_) -- The ``mne.epochs.add_channels_epochs`` function has been deprecated in favor of :meth:`epochs.add_channels ` (:gh:`11180` by `Eric Larson`_) -- The PSD functions that operate on Raw/Epochs/Evoked instances (``mne.time_frequency.psd_welch`` and ``mne.time_frequency.psd_multitaper``) are deprecated; for equivalent functionality create :class:`~mne.time_frequency.Spectrum` or :class:`~mne.time_frequency.EpochsSpectrum` objects instead and then run ``spectrum.get_data(return_freqs=True)`` (:gh:`10184` by `Daniel McCloy`_) -- Added new class :class:`mne.preprocessing.EOGRegression` to allow more flexibility when using regression to reduce EOG artifacts (:gh:`11046` by `Marijn van Vliet`_) -- New parameter ``exclude`` added to :func:`mne.preprocessing.regress_artifact` to prevent regression from being applied to certain channels (:gh:`11046` by `Marijn van Vliet`_) - -Authors -~~~~~~~ - -* Alex Rockhill -* Alexandre Gramfort -* Andrew Quinn+ -* Chetan Gohil+ -* Christian Brodbeck -* Clemens Brunner -* Daniel Carlström Schad+ -* Daniel McCloy -* Dominik Wetzel+ -* Eduard Ort -* Eric Larson -* Hüseyin Orkun Elmas+ -* Jack Zhang -* Joan Massich -* Julius Welzel+ -* Kostiantyn Maksymenko -* Lukas Gemein -* Marian Dovgialo -* Marijn van Vliet -* Mathieu Scheltienne -* Mats van Es+ -* Moritz Gerster+ -* Olaf Hauk -* Richard Höchenberger -* Sebastiaan Mathot+ -* Sena Er+ -* Simeon Wong -* Stefan Appelhoff -* Valerii Chirkov -* luzpaz+ diff --git a/doc/changes/v1.3.rst b/doc/changes/v1.3.rst deleted file mode 100644 index d5923e12aa9..00000000000 --- a/doc/changes/v1.3.rst +++ /dev/null @@ -1,89 +0,0 @@ -.. _changes_1_3_0: - -Version 1.3.0 (2022-12-21) --------------------------- - -Enhancements -~~~~~~~~~~~~ -- Improve default line width used in :func:`mne.viz.plot_filter` (:gh:`11333` by :newcontrib:`Toomas Erik Anijärv`) -- Add the argument ``max_iter`` to :func:`~mne.time_frequency.psd_array_multitaper` and to :func:`~mne.time_frequency.csd_array_multitaper` to increase the maximum number of iterations to reach convergence when using ``adaptive=True`` (:gh:`11237` by `Mathieu Scheltienne`_) -- Add a warning to the docstring of :func:`mne.channels.find_ch_adjacency` to encourage users to validate their outputs (:gh:`11236` by `Felix Klotzsche`_ and `Eric Larson`_) -- Mixed, cortical + discrete source spaces with fixed orientations are now allowed. (:gh:`11241` by `Jevri Hanna`_) -- Add size information to the ``repr`` of :class:`mne.Report` (:gh:`11357` by `Eric Larson`_) -- Add support for ``image_format='webp'`` to :class:`mne.Report` when using Matplotlib 3.6+, which can reduce file sizes by up to 50% compared to ``'png'``. The new default ``image_format='auto'`` will automatically use this format if it's available on the system (:gh:`11359` by `Eric Larson`_) -- Add :func:`mne.beamformer.apply_dics_tfr_epochs` to apply a DICS beamformer to time-frequency resolved epochs (:gh:`11096` by `Alex Rockhill`_) -- Add :func:`mne.time_frequency.fwhm` to determine the full-width half maximum for :func:`mne.time_frequency.morlet` (:gh:`11353` by `Britta Westner`_, `Daniel McCloy`_, and `Eric Larson`_) -- Check whether head radius (estimated from channel positions) is correct when reading EEGLAB data with :func:`~mne.io.read_raw_eeglab` and :func:`~mne.read_epochs_eeglab`. If head radius is not within likely values, warn informing about possible units mismatch and the new ``montage_units`` argument (:gh:`11283` by `Mikołaj Magnuski`_). -- Add support for a callable passed in ``combine`` for `mne.time_frequency.AverageTFR.plot` and `mne.time_frequency.AverageTFR.plot_joint` (:gh:`11329` by `Mathieu Scheltienne`_) - -Bugs -~~~~ -- Fix bug in :func:`mne.export.export_raw` when exporting raw to EDF with EDFLib when subject ``sex`` is missing (:gh:`11375` by :newcontrib:`Mark Alexander Henney`) -- Fix bugs in documentation of :func:`mne.time_frequency.tfr_array_multitaper` and related functions/methods (:gh:`11310` by :newcontrib:`Santeri Ruuskanen`) -- Fix bug to be able to customize legends when using :meth:`mne.viz.Brain.add_volume_labels` (:gh:`11289` by :newcontrib:`Mauricio Cespedes Tenorio`) -- Fix bug in documentation of :func:`mne.channels.make_dig_montage` (:gh:`11235` by :newcontrib:`Daniel Hasegan`) -- Add support for bad channel handling in :func:`mne.set_bipolar_reference` (:gh:`11245` by `Moritz Gerster`_, :newcontrib:`Dinara Issagaliyeva`, :newcontrib:`Jennifer Behnke`, :newcontrib:`Hakimeh Aslsardroud`, and :newcontrib:`Pavel Navratil`) -- Fix X coordinates of ear_left and ear_right in head outlines dict (:gh:`11255` by :newcontrib:`Tom Ma`) -- Add type checking for ``tmin`` and ``tmax`` arguments for ``crop`` (:gh:`11263` by :newcontrib:`Carlos de la Torre-Ortiz`). -- Fix bug where trying to setup projection without an EEG average reference projector would fail (:gh:`11351` by :newcontrib:`Enzo Altamiranda`) -- Fix bug where ``ica.reject_`` was not saved to disk, and the ``ica.reject_`` property was not inherited from ``Epochs`` when doing ``ICA.fit(epochs)`` (:gh:`11244` by `Eric Larson`_) -- Fix bug in automatic MESA detection for disabling advanced 3D options (:gh:`11271` by `Eric Larson`_) -- Fix bug in :func:`mne.head_to_mri` when ``unscale=True`` (:gh:`11303` by `Eric Larson`_) -- Fix bug in :meth:`set_montage('mgh60') ` and related functions where the ``'mgh60'`` sensor positions were incorrectly ordered (:gh:`11290` by `Eric Larson`_) -- Fix bug in the ``.compute_psd()`` methods where the number of unaggregated Welch segments was wrongly computed for some inputs, leading to an assertion error when computing the PSD (:gh:`11248` by `Daniel McCloy`_) -- Fix bug in the :func:`~mne.viz.plot_evoked_topo` and :meth:`~mne.Evoked.plot_topo`, where legend colors where shown incorrectly on newer matplotlib versions (:gh:`11258` by `Erkka Heinila`_) -- Fix bug where EEGLAB channel positions were read as meters, while they are commonly in millimeters, leading to head outlies of the size of one channel when plotting topomaps. Now ``montage_units`` argument has been added to :func:`~mne.io.read_raw_eeglab` and :func:`~mne.read_epochs_eeglab` to control in what units EEGLAB channel positions are read. The default is millimeters, ``'mm'`` (:gh:`11283` by `Mikołaj Magnuski`_) -- Fix bug where computing PSD with welch's method with more jobs than channels would fail (:gh:`11298` by `Mathieu Scheltienne`_) -- Fix bug where the default FFT length changed for spectrum plots (:gh:`11345` by `Daniel McCloy`_) -- Fix bug with :func:`mne.decoding.cross_val_multiscore` where progress bars were not displayed correctly (:gh:`11311` by `Eric Larson`_) -- Fix channel selection edge-cases in `~mne.preprocessing.ICA.find_bads_muscle` (:gh:`11300` by `Mathieu Scheltienne`_) -- Fix bug with :func:`mne.io.read_raw_curry` where a dot in the parent folders prevented files from being read (:gh:`11340` by `Eric Larson`_) -- Fix bug with :class:`mne.Report` with ``replace=True`` where the wrong content was replaced and ``section`` was not respected (:gh:`11318`, :gh:`11346` by `Eric Larson`_) -- Fix bug with unit conversion when setting reference MEG as the channel type in :meth:`mne.io.Raw.set_channel_types` and related methods (:gh:`11344` by `Eric Larson`_) -- Fix bug where reference MEG channels could not be plotted using :func:`mne.viz.plot_epochs_image` (:gh:`11344` by `Eric Larson`_) -- Fix bug where ``image_format='gif'`` was errantly documented as being supported by :class:`mne.Report`, it is now only supported in :meth:`mne.Report.add_image` (:gh:`11347` by `Eric Larson`_) -- Multitaper spectral estimation now uses periodic (rather than symmetric) taper windows. This also necessitated changing the default ``max_iter`` of our cross-spectral density functions from 150 to 250. (:gh:`11293` by `Daniel McCloy`_) -- Fix :meth:`mne.Epochs.plot_image` and :func:`mne.viz.plot_epochs_image` when using EMG signals (:gh:`11322` by `Alex Gramfort`_) -- Fix selection of ICA components in :func:`mne.viz.plot_ica_components` and :meth:`mne.preprocessing.ICA.plot_components` (:gh:`11369` by `Mathieu Scheltienne`_) -- Fix bug where a Freesurfer reconstruction run with both a T1 and a T2 caused :class:`mne.viz.Brain` not to initialize pial surfaces properly (:gh:`11361` by `Alex Rockhill`_) - -API changes -~~~~~~~~~~~ -- In :func:`mne.time_frequency.dpss_windows`, interpolating is deprecated (nowadays SciPy's computations are fast enough for large ``N`` without interpolation). This affects parameters ``interp_from`` and ``interp_kind``. Two new parameters of the underlying SciPy :func:`~scipy.signal.windows.dpss` function are also exposed: ``sym`` (for choosing symmetric vs. periodic windows) and ``norm`` (window normalization method). (:gh:`11293` by `Daniel McCloy`_) -- In :meth:`mne.decoding.CSP.plot_patterns`, :meth:`mne.decoding.CSP.plot_filters`, :meth:`mne.preprocessing.ICA.plot_components`, and :func:`mne.viz.plot_ica_components`, the parameters ``vmin`` and ``vmax`` are deprecated in favor of ``vlim``, for consistency with other topomap-plotting functions and methods (:gh:`11371` by `Daniel McCloy`_) -- In :meth:`mne.decoding.CSP.plot_patterns` and :meth:`mne.decoding.CSP.plot_filters` the ``title`` parameter is deprecated and will be removed in version 1.4 (:gh:`11371` by `Daniel McCloy`_) -- The APIs of :meth:`mne.preprocessing.ICA.plot_components` and :func:`mne.viz.plot_ica_components` gained new parameters ``show_names``, ``extrapolate``, ``border``, ``size``, ``cnorm``, ``cbar_fmt``, ``axes``, ``nrows``, ``ncols``, for consistency with other topomap-plotting functions and methods (:gh:`11371` by `Daniel McCloy`_) -- The APIs of :meth:`mne.decoding.CSP.plot_patterns` and :meth:`mne.decoding.CSP.plot_filters` gained new parameters ``extrapolate``, ``border``, ``cnorm``, ``axes``, ``nrows``, ``ncols``, for consistency with other topomap-plotting functions and methods (:gh:`11371` by `Daniel McCloy`_) - -Authors -~~~~~~~ - -* Alex Rockhill -* Alexandre Gramfort -* Britta Westner -* Carlos de la Torre+ -* Daniel Hasegan+ -* Daniel McCloy -* Dinara Issagaliyeva+ -* Enzo Altamiranda+ -* Eric Brayet+ -* Eric Larson -* Erkka Heinila -* Felix Klotzsche -* Hakimeh Aslsardroud+ -* Jennifer Behnke+ -* Jevri Hanna -* Lukas Hecker -* Mark Alexander Henney+ -* Mathieu Scheltienne -* Mauricio Cespedes+ -* Mikołaj Magnuski -* Moritz Gerster -* Omer Shubi+ -* Pavel Navratil+ -* Richard Höchenberger -* Santeri Ruuskanen+ -* Stefan Appelhoff -* Timon Merk -* Tom Ma+ -* Toomas Erik Anijärv+ diff --git a/doc/changes/v1.4.rst b/doc/changes/v1.4.rst deleted file mode 100644 index 2fa9ec2a0d1..00000000000 --- a/doc/changes/v1.4.rst +++ /dev/null @@ -1,133 +0,0 @@ -.. _changes_1_4_0: - -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("") ` 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+ diff --git a/doc/changes/v1.5.rst b/doc/changes/v1.5.rst deleted file mode 100644 index c607aefe26d..00000000000 --- a/doc/changes/v1.5.rst +++ /dev/null @@ -1,107 +0,0 @@ -.. NOTE: we use cross-references to highlight new functions and classes. - Please follow the examples below like :func:`mne.stats.f_mway_rm`, so the - whats_new page will have a link to the function/class documentation. - -.. NOTE: there are 3 separate sections for changes, based on type: - - "Enhancements" for new features - - "Bugs" for bug fixes - - "API changes" for backward-incompatible changes - -.. NOTE: changes from first-time contributors should be added to the TOP of - the relevant section (Enhancements / Bugs / API changes), and should look - like this (where xxxx is the pull request number): - - - description of enhancement/bugfix/API change (:gh:`xxxx` by - :newcontrib:`Firstname Lastname`) - - Also add a corresponding entry for yourself in doc/changes/names.inc - -.. _changes_1_5_0: - -Version 1.5.0 (2023-08-14) --------------------------- - -Enhancements -~~~~~~~~~~~~ -- Add reader for NSx files (Blackrock Microsystems Data Acquisition Systems) (:gh:`11432` by :newcontrib:`Proloy Das`) -- Add ``cmap`` argument for the :func:`mne.viz.plot_sensors` (:gh:`11720` by :newcontrib:`Gennadiy Belonosov`) -- Return unmodified instance if new sampling frequency is identical to the original in :meth:`mne.io.Raw.resample`, :meth:`mne.Epochs.resample`, :meth:`mne.Evoked.resample` and :meth:`mne.SourceEstimate.resample` (:gh:`11736` by :newcontrib:`Gennadiy Belonosov`) -- When failing to locate a file, we now print the full path in quotation marks to help spot accidentally added trailing spaces (:gh:`11718` by `Richard Höchenberger`_) -- Add standard montage lookup table for ``easycap-M43`` (:gh:`11744` by :newcontrib:`Diptyajit Das`) -- Added :class:`mne.preprocessing.eyetracking.Calibration` to store eye-tracking calibration info, and :func:`mne.preprocessing.eyetracking.read_eyelink_calibration` to read calibration data from EyeLink systems (:gh:`11719` by `Scott Huberty`_) -- Ocular :class:`mne.Annotations` read in by :func:`mne.io.read_raw_eyelink` are now channel aware. This means if the left eye blinked, the associated annotation will store this in the ``'ch_names'`` key. (:gh:`11746` by `Scott Huberty`_) -- Added :func:`mne.preprocessing.eyetracking.interpolate_blinks` to linear interpolate eyetrack signals during blink periods. (:gh:`11740` by `Scott Huberty`_) -- Added a section for combining eye-tracking and EEG data to the preprocessing tutorial "working with eye tracker data in MNE-Python" (:gh:`11770` by `Scott Huberty`_) -- Added a ``show_bytes`` option to :ref:`mne show_fiff` to show byte offsets (:gh:`11800` by `Eric Larson`_) -- Add :meth:`mne.Annotations.count` and :func:`mne.count_annotations` to count unique annotations (:gh:`11796` by `Clemens Brunner`_) -- Split the display of :meth:`mne.preprocessing.ICA.plot_overlay` between sensor types and display the RMS for MEG sensors and the :term:`GFP` for EEG sensors in the second panel instead of the channel average (:gh:`11830` by `Mathieu Scheltienne`_) -- Add :meth:`mne.Info.set_channel_types`, :meth:`mne.Info.rename_channels`, :meth:`mne.Info.plot_sensors`, :meth:`mne.Info.anonymize`, :meth:`mne.Info.set_meas_date` (:gh:`11839` by `Alex Rockhill`_) -- Curry and NEDF raw files can now also be read with the generic :func:`mne.io.read_raw` function (:gh:`11841` by `Richard Höchenberger`_) - -Bugs -~~~~ -- Fix bug in :func:`mne.bem.convert_flash_mris` to handle missing "flash5_reg.mgz" when processing "flash30" data. (:gh:`11842` by :newcontrib:`Hamza Abdelhedi`) -- Fix bug where epochs ``event_id`` was not kept by :func:`mne.channels.combine_channels` (:gh:`11786` by :newcontrib:`Samuel Louviot`) -- Fix bug where user-provided codec was not used to read annotations when loading EEGLAB ``.set`` files (:gh:`11773` by :newcontrib:`Yiping Zuo`) -- Fix bug that required curv.*h files to create Brain object (:gh:`11704` by :newcontrib:`Aaron Earle-Richardson`) -- Extended test to highlight bug in :func:`mne.stats.permutation_t_test` (:gh:`11575` by :newcontrib:`Joshua Calder-Travis`) -- Fix bug that used wrong indices for line/label styles (sometimes causing an ``IndexError``) in :meth:`mne.preprocessing.ICA.plot_sources` under certain conditions (:gh:`11808` by :newcontrib:`Joshua Calder-Travis`) -- Fix bug with :func:`~mne.io.read_raw_snirf` to handle files with measurement time containing milliseconds (:gh:`11804` by :newcontrib:`Daniel Tse`) -- Fix loading of EDF with mixed sampling frequencies with :func:`mne.io.read_raw_edf`: Upsampling is now applied to the entire signal and no longer block based, significantly reducing edge artifacts (:gh:`11549` by `Simon Kern`_) -- Fix bug where :func:`mne.io.read_raw_cnt` imports unnecessary durations (:gh:`11828` by `Jacob Woessner`_) -- Fix bug where :meth:`mne.viz.Brain.add_volume_labels` used an incorrect orientation (:gh:`11730` by `Alex Rockhill`_) -- Fix bug with :func:`mne.forward.restrict_forward_to_label` where cortical patch information was not adjusted (:gh:`11694` by `Eric Larson`_) -- Fix bug with PySide6 compatibility (:gh:`11721` by `Eric Larson`_) -- Fix bug with :class:`mne.io.Raw`, :class:`mne.SourceEstimate`, and related classes where the ``decimate`` and ``shift_time`` methods were errantly added (:gh:`11853` by `Eric Larson`_) -- Fix hanging interpreter with matplotlib figures using ``mne/viz/_mpl_figure.py`` in spyder console and jupyter notebooks (:gh:`11696` by `Mathieu Scheltienne`_) -- Fix bug with overlapping text for :meth:`mne.Evoked.plot` (:gh:`11698` by `Alex Rockhill`_) -- Fix bug with :func:`mne.preprocessing.corrmap` where the template iteration had non-standard map averaging (:gh:`11857` by `Eric Larson`_) -- For :func:`mne.io.read_raw_eyelink`, the default value of the ``gap_description`` parameter is now ``'BAD_ACQ_SKIP'``, following MNE convention (:gh:`11719` by `Scott Huberty`_) -- Fix bug with :func:`mne.io.read_raw_fil` where datasets without sensor positions would not import (:gh:`11733` by `George O'Neill`_) -- Fix bug with :func:`mne.chpi.compute_chpi_snr` where cHPI being off for part of the recording or bad channels being defined led to an error or incorrect behavior (:gh:`11754`, :gh:`11755` by `Eric Larson`_) -- Allow int-like for the argument ``id`` of `~mne.make_fixed_length_events` (:gh:`11748` by `Mathieu Scheltienne`_) -- Fix bugs with :mod:`mne.decoding` classes (:gh:`11846` by `Eric Larson`_): - - :class:`mne.decoding.ReceptiveField` now sets ``rf.fit_intercept_`` during ``fit()`` rather than overwriting ``rf.fit_intercept`` - - :class:`mne.decoding.SlidingEstimator` now returns the same ``dtype`` as ``X`` (usually ``float64``) in ``sl.transform(X)`` rather than always returning ``int`` -- Fix bug with :func:`mne.beamformer.make_lcmv` where the source space was not checked properly when the ``label`` argument was provided (:gh:`11852` by `Eric Larson`_) -- Fix bug where :func:`mne.io.read_raw_egi` did not properly set the EEG reference location for the reference channel itself (:gh:`11822` by `Eric Larson`_) -- Fix bug with legacy :meth:`~mne.io.Raw.plot_psd` method where passed axes were not used (:gh:`11778` by `Daniel McCloy`_) -- blink :class:`mne.Annotations` read in by :func:`mne.io.read_raw_eyelink` now begin with ``'BAD_'``, i.e. ``'BAD_blink'``, because ocular data are missing during blinks. (:gh:`11746` by `Scott Huberty`_) -- Fix bug where :ref:`mne show_fiff` could fail with an ambiguous error if the file is corrupt (:gh:`11800` by `Eric Larson`_) -- Fix bug where annotation FIF files lacked an end block tag (:gh:`11800` by `Eric Larson`_) -- Fix display of :class:`~mne.Annotations` in `mne.preprocessing.ICA.plot_sources` when the ``raw`` has ``raw.first_samp != 0`` and doesn't have a measurement date (:gh:`11766` by `Mathieu Scheltienne`_) -- Fix bug in read_raw_eyelink, where STATUS information of samples was always assumed to be in the file. Performance and memory improvements were also made. (:gh:`11823` by `Scott Huberty`_) -- Fix closing of a topographic map created from an interactive drag on an Evoked or PSD plot (:gh:`11862` by `Mathieu Scheltienne`_) - -API changes -~~~~~~~~~~~ -- The ``baseline`` argument can now be array-like (e.g. ``list``, ``tuple``, ``np.ndarray``, ...) instead of only a ``tuple`` (:gh:`11713` by `Clemens Brunner`_) -- The ``events`` and ``event_id`` parameters of :meth:`Epochs.plot() ` now accept boolean values; see docstring for details (:gh:`11445` by `Daniel McCloy`_ and `Clemens Brunner`_) -- Deprecated ``gap_description`` keyword argument of :func:`mne.io.read_raw_eyelink`, which will be removed in mne version 1.6, in favor of using :meth:`mne.Annotations.rename` (:gh:`11719` by `Scott Huberty`_) - -Authors -~~~~~~~ -* Aaron Earle-Richardson+ -* Alex Rockhill -* Alexandre Gramfort -* Britta Westner -* Clemens Brunner -* Daniel McCloy -* Daniel Tse+ -* Diptyajit Das+ -* Eric Larson -* Gennadiy Belonosov+ -* George O'Neill -* Hamza Abdelhedi+ -* Jacob Woessner -* Joshua Calder-Travis+ -* Mathieu Scheltienne -* Proloy Das -* Richard Höchenberger -* Rob Luke -* Samuel Louviot+ -* Scott Huberty -* Simon Kern -* Stefan Appelhoff -* Thomas Moreau -* Yiping Zuo+ diff --git a/doc/changes/v1.6.rst b/doc/changes/v1.6.rst deleted file mode 100644 index f770b5046d2..00000000000 --- a/doc/changes/v1.6.rst +++ /dev/null @@ -1,132 +0,0 @@ -.. _changes_1_6_0: - -Version 1.6.0 (2023-11-20) --------------------------- - -Enhancements -~~~~~~~~~~~~ -- Add support for Neuralynx data files with :func:`mne.io.read_raw_neuralynx` (:gh:`11969` by :newcontrib:`Kristijan Armeni` and :newcontrib:`Ivan Skelin`) -- Improve tests for saving splits with :class:`mne.Epochs` (:gh:`11884` by `Dmitrii Altukhov`_) -- Added functionality for linking interactive figures together, such that changing one figure will affect another, see :ref:`tut-ui-events` and :mod:`mne.viz.ui_events`. Current figures implementing UI events are :func:`mne.viz.plot_topomap` and :func:`mne.viz.plot_source_estimates` (:gh:`11685` :gh:`11891` by `Marijn van Vliet`_) -- HTML anchors for :class:`mne.Report` now reflect the ``section-title`` of the report items rather than using a global incrementor ``global-N`` (:gh:`11890` by `Eric Larson`_) -- Added public :func:`mne.io.write_info` to complement :func:`mne.io.read_info` (:gh:`11918` by `Eric Larson`_) -- Added option ``remove_dc`` to to :meth:`Raw.compute_psd() `, :meth:`Epochs.compute_psd() `, and :meth:`Evoked.compute_psd() `, to allow skipping DC removal when computing Welch or multitaper spectra (:gh:`11769` by `Nikolai Chapochnikov`_) -- Add the possibility to provide a float between 0 and 1 as ``n_grad``, ``n_mag`` and ``n_eeg`` in `~mne.compute_proj_raw`, `~mne.compute_proj_epochs` and `~mne.compute_proj_evoked` to select the number of vectors based on the cumulative explained variance (:gh:`11919` by `Mathieu Scheltienne`_) -- Add extracting all time courses in a label using :func:`mne.extract_label_time_course` without applying an aggregation function (like ``mean``) (:gh:`12001` by `Hamza Abdelhedi`_) -- Added support for Artinis fNIRS data files to :func:`mne.io.read_raw_snirf` (:gh:`11926` by `Robert Luke`_) -- Add helpful error messages when using methods on empty :class:`mne.Epochs`-objects (:gh:`11306` by `Martin Schulz`_) -- Add support for passing a :class:`python:dict` as ``sensor_color`` to specify per-channel-type colors in :func:`mne.viz.plot_alignment` (:gh:`12067` by `Eric Larson`_) -- Add inferring EEGLAB files' montage unit automatically based on estimated head radius using :func:`read_raw_eeglab(..., montage_units="auto") ` (:gh:`11925` by `Jack Zhang`_, :gh:`11951` by `Eric Larson`_) -- Add :class:`~mne.time_frequency.EpochsSpectrumArray` and :class:`~mne.time_frequency.SpectrumArray` to support creating power spectra from :class:`NumPy array ` data (:gh:`11803` by `Alex Rockhill`_) -- Add support for writing forward solutions to HDF5 and convenience function :meth:`mne.Forward.save` (:gh:`12036` by `Eric Larson`_) -- Refactored internals of :func:`mne.read_annotations` (:gh:`11964` by `Paul Roujansky`_) -- Add support for drawing MEG sensors in :ref:`mne coreg` (:gh:`12098` by `Eric Larson`_) -- Improve string representation of :class:`mne.Covariance` (:gh:`12181` by `Eric Larson`_) -- Add ``check_version=True`` to :ref:`mne sys_info` to check for a new release on GitHub (:gh:`12146` by `Eric Larson`_) -- Bad channels are now colored gray in addition to being dashed when spatial colors are used in :func:`mne.viz.plot_evoked` and related functions (:gh:`12142` by `Eric Larson`_) -- By default MNE-Python creates matplotlib figures with ``layout='constrained'`` rather than the default ``layout='tight'`` (:gh:`12050`, :gh:`12103` by `Mathieu Scheltienne`_ and `Eric Larson`_) -- Enhance :func:`~mne.viz.plot_evoked_field` with a GUI that has controls for time, colormap, and contour lines (:gh:`11942` by `Marijn van Vliet`_) -- Add :class:`mne.viz.ui_events.UIEvent` linking for interactive colorbars, allowing users to link figures and change the colormap and limits interactively. This supports :func:`~mne.viz.plot_evoked_topomap`, :func:`~mne.viz.plot_ica_components`, :func:`~mne.viz.plot_tfr_topomap`, :func:`~mne.viz.plot_projs_topomap`, :meth:`~mne.Evoked.plot_image`, and :meth:`~mne.Epochs.plot_image` (:gh:`12057` by `Santeri Ruuskanen`_) -- Add example KIT phantom dataset in :func:`mne.datasets.phantom_kit.data_path` and :ref:`tut-phantom-kit` (:gh:`12105` by `Judy D Zhu`_ and `Eric Larson`_) -- :func:`~mne.epochs.make_metadata` now accepts ``tmin=None`` and ``tmax=None``, which will bound the time window used for metadata generation by event names (instead of a fixed time). That way, you can now for example generate metadata spanning from one cue or fixation cross to the next, even if trial durations vary throughout the recording (:gh:`12118` by `Richard Höchenberger`_) -- Add support for passing multiple labels to :func:`mne.minimum_norm.source_induced_power` (:gh:`12026` by `Erica Peterson`_, `Eric Larson`_, and `Daniel McCloy`_ ) -- Added documentation to :meth:`mne.io.Raw.set_montage` and :func:`mne.add_reference_channels` to specify that montages should be set after adding reference channels (:gh:`12160` by `Jacob Woessner`_) -- Add argument ``splash`` to the function using the ``qt`` browser backend to allow enabling/disabling the splash screen (:gh:`12185` by `Mathieu Scheltienne`_) -- :class:`~mne.preprocessing.ICA`'s HTML representation (displayed in Jupyter notebooks and :class:`mne.Report`) now includes all optional fit parameters (e.g., max. number of iterations) (:gh:`12194`, by `Richard Höchenberger`_) - -Bugs -~~~~ -- Fix bug where :func:`mne.io.read_raw_gdf` would fail due to improper usage of ``np.clip`` (:gh:`12168` by :newcontrib:`Rasmus Aagaard`) -- Fix bugs with :func:`mne.preprocessing.realign_raw` where the start of ``other`` was incorrectly cropped; and onsets and durations in ``other.annotations`` were left unsynced with the resampled data (:gh:`11950` by :newcontrib:`Qian Chu`) -- Fix bug where ``encoding`` argument was ignored when reading annotations from an EDF file (:gh:`11958` by :newcontrib:`Andrew Gilbert`) -- Mark tests ``test_adjacency_matches_ft`` and ``test_fetch_uncompressed_file`` as network tests (:gh:`12041` by :newcontrib:`Maksym Balatsko`) -- Fix bug with :func:`mne.channels.read_ch_adjacency` (:gh:`11608` by :newcontrib:`Ivan Zubarev`) -- Fix bug where ``epochs.get_data(..., scalings=...)`` would errantly modify the preloaded data (:gh:`12121` by :newcontrib:`Pablo Mainar` and `Eric Larson`_) -- Fix bugs with saving splits for :class:`~mne.Epochs` (:gh:`11876` by `Dmitrii Altukhov`_) -- Fix bug with multi-plot 3D rendering where only one plot was updated (:gh:`11896` by `Eric Larson`_) -- Fix bug where ``verbose`` level was not respected inside parallel jobs (:gh:`12154` by `Eric Larson`_) -- Fix bug where subject birthdays were not correctly read by :func:`mne.io.read_raw_snirf` (:gh:`11912` by `Eric Larson`_) -- Fix bug where warnings were emitted when computing spectra for channels marked as bad (:gh:`12186` by `Eric Larson`_) -- Fix bug with :func:`mne.chpi.compute_head_pos` for CTF data where digitization points were modified in-place, producing an incorrect result during a save-load round-trip (:gh:`11934` by `Eric Larson`_) -- Fix bug where non-compliant stimulus data streams were not ignored by :func:`mne.io.read_raw_snirf` (:gh:`11915` by `Johann Benerradi`_) -- Fix bug with ``pca=False`` in :func:`mne.minimum_norm.compute_source_psd` (:gh:`11927` by `Alex Gramfort`_) -- Fix bug with notebooks when using PyVista 0.42 by implementing ``trame`` backend support (:gh:`11956` by `Eric Larson`_) -- Removed preload parameter from :func:`mne.io.read_raw_eyelink`, because data are always preloaded no matter what preload is set to (:gh:`11910` by `Scott Huberty`_) -- Fix bug with :meth:`mne.viz.Brain.get_view` where calling :meth:`~mne.viz.Brain.show_view` with returned parameters would change the view (:gh:`12000` by `Eric Larson`_) -- Fix bug with :meth:`mne.viz.Brain.show_view` where ``distance=None`` would change the view distance (:gh:`12000` by `Eric Larson`_) -- Fix bug with :meth:`~mne.viz.Brain.add_annotation` when reading an annotation from a file with both hemispheres shown (:gh:`11946` by `Marijn van Vliet`_) -- Fix bug with reported component number and errant reporting of PCA explained variance as ICA explained variance in :meth:`mne.Report.add_ica` (:gh:`12155`, :gh:`12167` by `Eric Larson`_ and `Richard Höchenberger`_) -- Fix bug with axis clip box boundaries in :func:`mne.viz.plot_evoked_topo` and related functions (:gh:`11999` by `Eric Larson`_) -- Fix bug with ``subject_info`` when loading data from and exporting to EDF file (:gh:`11952` by `Paul Roujansky`_) -- Fix bug where :class:`mne.Info` HTML representations listed all channel counts instead of good channel counts under the heading "Good channels" (:gh:`12145` by `Eric Larson`_) -- Fix rendering glitches when plotting Neuromag/TRIUX sensors in :func:`mne.viz.plot_alignment` and related functions (:gh:`12098` by `Eric Larson`_) -- Fix bug with delayed checking of :class:`info["bads"] ` (:gh:`12038` by `Eric Larson`_) -- Fix bug with :ref:`mne coreg` where points inside the head surface were not shown (:gh:`12147`, :gh:`12164` by `Eric Larson`_) -- Fix bug with :func:`mne.viz.plot_alignment` where ``sensor_colors`` were not handled properly on a per-channel-type basis (:gh:`12067` by `Eric Larson`_) -- Fix handling of channel information in annotations when loading data from and exporting to EDF file (:gh:`11960` :gh:`12017` :gh:`12044` by `Paul Roujansky`_) -- Add missing ``overwrite`` and ``verbose`` parameters to :meth:`Transform.save() ` (:gh:`12004` by `Marijn van Vliet`_) -- Fix parsing of eye-link :class:`~mne.Annotations` when ``apply_offsets=False`` is provided to :func:`~mne.io.read_raw_eyelink` (:gh:`12003` by `Mathieu Scheltienne`_) -- Correctly prune channel-specific :class:`~mne.Annotations` when creating :class:`~mne.Epochs` without the channel(s) included in the channel specific annotations (:gh:`12010` by `Mathieu Scheltienne`_) -- Fix :func:`~mne.viz.plot_volume_source_estimates` with :class:`~mne.VolSourceEstimate` which include a list of vertices (:gh:`12025` by `Mathieu Scheltienne`_) -- Add support for non-ASCII characters in Annotations, Evoked comments, etc when saving to FIFF format (:gh:`12080` by `Daniel McCloy`_) -- Correctly handle passing ``"eyegaze"`` or ``"pupil"`` to :meth:`mne.io.Raw.pick` (:gh:`12019` by `Scott Huberty`_) -- Fix bug with :func:`mne.time_frequency.Spectrum.plot` and related functions where bad channels were not marked (:gh:`12142` by `Eric Larson`_) -- Fix bug with :func:`~mne.viz.plot_raw` where changing ``MNE_BROWSER_BACKEND`` via :func:`~mne.set_config` would have no effect within a Python session (:gh:`12078` by `Santeri Ruuskanen`_) -- Improve handling of ``method`` argument in the channel interpolation function to support :class:`str` and raise helpful error messages (:gh:`12113` by `Mathieu Scheltienne`_) -- Fix combination of ``DIN`` event channels into a single synthetic trigger channel ``STI 014`` by the MFF reader of :func:`mne.io.read_raw_egi` (:gh:`12122` by `Mathieu Scheltienne`_) -- Fix bug with :func:`mne.io.read_raw_eeglab` and :func:`mne.read_epochs_eeglab` where automatic fiducial detection would fail for certain files (:gh:`12165` by `Clemens Brunner`_) -- Fix concatenation of ``raws`` with ``np.nan`` in the device to head transformation (:gh:`12198` by `Mathieu Scheltienne`_) -- Fix bug with :func:`mne.viz.plot_compare_evokeds` where the title was not displayed when ``axes='topo'`` (:gh:`12192` by `Jacob Woessner`_) -- Fix bug with :func:`mne.io.read_raw_cnt` where the bad channels were not properly read (:gh:`12189` by `Jacob Woessner`_) -- Fix bug where iterating over :class:`~mne.io.Raw` would result in an error (:gh:`12205` by `Clemens Brunner`_) - - -API changes -~~~~~~~~~~~ -- The default for :meth:`mne.Epochs.get_data` of ``copy=False`` will change to ``copy=True`` in 1.7. Set it explicitly to avoid a warning (:gh:`12121` by :newcontrib:`Pablo Mainar` and `Eric Larson`_) -- ``mne.preprocessing.apply_maxfilter`` and ``mne maxfilter`` have been deprecated and will be removed in 1.7. Use :func:`mne.preprocessing.maxwell_filter` (see :ref:`this tutorial `) in Python or the command-line utility from MEGIN ``maxfilter`` and :func:`mne.bem.fit_sphere_to_headshape` instead (:gh:`11938` by `Eric Larson`_) -- :func:`mne.io.kit.read_mrk` reading pickled files is deprecated using something like ``np.savetxt(fid, pts, delimiter="\t", newline="\n")`` to save your points instead (:gh:`11937` by `Eric Larson`_) -- Replace legacy ``inst.pick_channels`` and ``inst.pick_types`` with ``inst.pick`` (where ``inst`` is an instance of :class:`~mne.io.Raw`, :class:`~mne.Epochs`, or :class:`~mne.Evoked`) wherever possible (:gh:`11907` by `Clemens Brunner`_) -- The ``reset_camera`` parameter has been removed in favor of ``distance="auto"`` in :func:`mne.viz.set_3d_view`, :meth:`mne.viz.Brain.show_view`, and related functions (:gh:`12000` by `Eric Larson`_) -- Several unused parameters from :func:`mne.gui.coregistration` are now deprecated: tabbed, split, scrollable, head_inside, guess_mri_subject, scale, and ``advanced_rendering``. All arguments are also now keyword-only. (:gh:`12147` by `Eric Larson`_) - -Authors -~~~~~~~ -* Adam Li -* Alex Rockhill -* Alexandre Gramfort -* Ana Radanovic -* Andy Gilbert+ -* Clemens Brunner -* Daniel McCloy -* Denis A. Engemann -* Dimitri Papadopoulos Orfanos -* Dmitrii Altukhov -* Dominik Welke -* Eric Larson -* Erica Peterson -* Gonzalo Reina -* Hamza Abdelhedi -* Ivan Skelin+ -* Ivan Zubarev+ -* Jack Zhang -* Jacob Woessner -* Johann Benerradi -* John Veillette -* Judy D Zhu -* Kristijan Armeni+ -* Mainak Jas -* Maksym Balatsko+ -* Marijn van Vliet -* Martin Schulz -* Mathieu Scheltienne -* Nikolai Chapochnikov -* Pablo Mainar+ -* Paul Roujansky -* Qian Chu+ -* Rasmus Aagaard+ -* Richard Höchenberger -* Rob Luke -* Santeri Ruuskanen -* Scott Huberty -* Stefan Appelhoff