Eelbrain

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* Epoch Rejection GUI:

- New "Tools" menu.
- New "Info" tool to show summary info on the rejection.
- New "Find Bad Channels" tool to automatically find bad channels.
- Set marked channels by clicking on topo-map.
- Faster page redraw.

* :class:`plot.Barplot` and :class:`plot.Boxplot`: new ``cells`` argument to
customize the order of bars/boxes.
* :class:`pipeline.MneExperiment`: new method :meth:`pipeline.MneExperiment.show_rej_info`.
* :class:`NDVar`: new method :meth:`NDVar.label_clusters`.
* :func:`plot.configure`: option to revert to wxPython backend for
:mod:`plot.brain`.

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* :class:`MneExperiment`:

- New epoch parameters: ``trigger_shift`` and ``vars`` (see
:attr:`pipeline.MneExperiment.epochs`).
- :meth:`~pipeline.MneExperiment.load_selected_events`: new ``vardef`` parameter to
load variables from a test definition.
- Log files stored in the root directory.
- Parcellations (:attr:`pipeline.MneExperiment.parcs`) based on combinations can also
include split commands.

* New :class:`Factor` method: :meth:`Factor.floodfill`.
* :class:`Model` methods: :meth:`~Model.get_table` replaced with
:meth:`~Model.as_table`, new :meth:`~Model.head` and :meth:`~Model.tail`.
* API: ``.sort_idx`` methods renamed to ``.sort_index``.

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* :class:`pipeline.MneExperiment`: new analysis parameter ``select_clusters='all'`` to
keep all clusters in cluster tests (see
:ref:`state-select_clusters`).
* Use :func:`testnd.configure` to limit the number of CPUs that are used in
permutation cluster tests.

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* Two-stage tests (see :attr:`pipeline.MneExperiment.tests`).
* Safer cache-handling. See note at :ref:`MneExperiment-intro-analysis`.
* :meth:`Dataset.head` and :meth:`Dataset.tail` methods for more efficiently
inspecting partial Datasets.
* The default format for plots in reports is now SVG since they are displayed
correctly in Safari 9.0. Use :func:`plot.configure` to change the default
format.
* API: Improvements in :class:`plot.Topomap` with concomitant changes in the
constructor signature. For examples see the `meg/topographic plotting
<https://github.com/christianbrodbeck/Eelbrain/blob/r/0.19/examples/meg/topographic%20plotting.py>`_
example.
* API: :class:`plot.ColorList` has a new argument called `labels`.
* API: :class:`testnd.ANOVA` attribute :attr:`~testnd.ANOVA.probability_maps`
renamed to :attr:`~testnd.ANOVA.p` analogous to other :mod:`testnd` results.
* Rejection-GUI: The option to plot the data range only has been removed.

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* API: The first argument for :meth:`pipeline.MneExperiment.plot_annot` is now `parc`.
* API: the ``fill_in_missing`` parameter to :func:`combine` has been deprecated
and replaced with a new parameter called ``incomplete``.
* API: Several plotting functions have a new ``xticklabels`` parameter to
suppress x-axis tick labels (e.g. :class:`plot.UTSStat`).
* The objects returned by :mod:`plot.brain` plotting functions now contain
a :meth:`~plot._brain_object.Brain.plot_colorbar` method to create a
corresponding :class:`plot.ColorBar` plot.
* New function :func:`choose` to combine data in different :class:`NDVars`
on a case by case basis.
* Rejection-GUI (:func:`gui.select_epochs`): Press Shift-i when hovering over
an epoch to enter channels for interpolation manually.
* :meth:`pipeline.MneExperiment.show_file_status` now shows the last modification date
of each file.
* Under OS X 10.8 and newer running code under a notifier statement now
automatically prevents the computer from going to sleep.

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* :attr:`pipeline.MneExperiment.brain_plot_defaults` can be used to customize PySurfer
plots in movies and reports.
* :attr:`pipeline.MneExperiment.trigger_shift` can now also be a dictionary mapping
subject name to shift value.
* The rejection GUI now allows selecting individual channels for interpolation
using the 'i' key.
* Parcellations based on combinations of existing labels, as well as
parcellations based on regions around points specified in MNI coordinates can
now be defined in :attr:`pipeline.MneExperiment.parcs`.
* Source space :class:`NDVar` can be indexed with lists of region names, e.g.,
``ndvar.sub(source=['cuneus-lh', 'lingual-lh'])``.
* API: :func:`plot.brain.bin_table` function signature changed slightly (more
parameters, new ``hemi`` parameter inserted to match other functions' argument
order).
* API: :func:`combine` now raises ``KeyError`` when trying to combine
:class:`Dataset` objects with unequal keys; set ``fill_in_missing=True`` to
reproduce previous behavior.
* API: Previously, :meth:`Var.as_factor` mapped unspecified values to
``str(value)``. Now they are mapped to ``''``. This also applies to
:attr:`pipeline.MneExperiment.variables` entries with unspecified values.