Changelogs » Eelbrain

Eelbrain

0.31

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* :mod:`testnd` API:  For permutation tests, the ``samples`` parameter now defaults to 10,000 (previously 0)
* :mod:`plot` API:  Additional arguments for :class:`plot.Boxplot` to control plotting of outliers (``whis`` and ``label_fliers``).
* Horizontal bar-plot: :class:`plot.BarplotHorizontal`

0.30

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* Support for vector data (with many contributions from `Proloy Das`_):

- :class:`Space` dimension to represent physical space
- :class:`VolumeSourceSpace` to represent volume source spaces
- Statistical tests: :class:`testnd.Vector`, :class:`testnd.VectorDifferenceRelated`
- Plotting with :class:`plot.GlassBrain`

* ICA-GUI: tool to find high amplitude signals
* Documentation: New :ref:`examples` section
* :meth:`Dataset.summary` method
* .. currentmodule:: eelbrain.pipeline
:class:`MneExperiment` pipeline:

- :class:`RawApplyICA` preprocessing pipe to apply ICA estimated in a different branch of the pipeline.
- :meth:`MneExperiment.load_evoked_stc` API more closely matches :meth:`MneExperiment.load_epochs_stc`
- :meth:`MneExperiment.load_neighbor_correlation`

0.29

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.. currentmodule:: eelbrain

* API: Better default parameters for :func:`resample`
* Predictor-specific stopping for :func:`boosting`
* New :class:`NDVar` function :func:`correlation_coefficient`
* Plotting:

- :ref:`general-layout-parameters` for plot size relative to screen size
- Better plots for masked statistic maps

* .. currentmodule:: eelbrain.pipeline
:class:`MneExperiment` pipeline:

- API: :meth:`MneExperiment.make_rej` renamed to :meth:`MneExperiment.make_epoch_selection`
- Object-based definitions (see :ref:`experiment-class-guide`)
- New method :meth:`MneExperiment.plot_raw`

0.28

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.. currentmodule:: eelbrain

* Transition to `Python 3.6 <https://docs.python.org/3.6/>`_
* API changes:

- :class:`testnd.anova`: The ``match`` parameter is now determined
automatically and does not need to be specified anymore in most cases.
- :attr:`testnd.ttest_1samp.diff` renamed to
:attr:`testnd.ttest_1samp.difference`.
- :class:`plot.Histogram`: following :mod:`matplotlib`, the ``normed``
parameter was renamed to ``density``.
- Previously capitalized argument and attribute names ``Y``, ``X`` and ``Xax``
are now lowercase.
- Topomap-plot argument order changed to provide consistency between different
plots.

* :class:`NDVar` and :class:`Var` support for ``round(x)``
* .. currentmodule:: eelbrain.pipeline
:class:`MneExperiment` pipeline:

- Independent measures t-test

0.27

-----------

.. currentmodule:: eelbrain

* API changes:

- To change the parcellation of an :class:`NDVar` with source-space data,
use the new function :func:`set_parc`. The :meth:`SourceSpace.set_parc`
method has been removed because dimension objects should be treated
as immutable, as they can be shared between different :class:`NDVar`
instances. Analogously, :meth:`UTS.set_tmin` is now :func:`set_tmin`.
- :func:`table.frequencies`: If the input ``y`` is a :class:`Var` object, the
output will also be a :class:`Var` (was :class:`Factor`).
- :meth:`NDVar.smooth`: window-based smoothing now uses a symmetric window,
which can lead to slightly different results.

* :func:`concatenate`: concatenate multiple :class:`NDVar` objects to form a
new dimension.
* :meth:`NDVar.ols`: regress on a dimension.
* :class:`plot.brain.SequencePlotter` to plot multiple anatomical images on one
figure.
* New functions and objects:

- :func:`complete_source_space`
- :func:`psd_welch`
- :func:`frequency_response`
- :class:`test.Correlation`, :func:`test.pairwise_correlations`
- :func:`xhemi`

* New methods:

- :meth:`Dataset.zip`, :meth:`Dataset.tile`
- :meth:`Factor.sort_cells`

0.26

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* API changes:

- A new global :func:`configure` function replaces module-level configuration
functions.
- :class:`Dataset`: when a one-dimensional array is assigned to an unused
key, the array is now automatically converted to a :class:`Var` object.
- :attr:`SourceSpace.vertno` has been renamed to
:attr:`SourceSpace.vertices`.

* Plotting:

- The new ``name`` argument allows setting the window title without adding a
title to the figure.
- Plots that reresent time have a new method to synchronize the time axis on
multiple plots: :meth:`~plot.Butterfly.link_time_axis`.
- Plot source space time series: :func:`plot.brain.butterfly`

* ANOVAs now support mixed models with between- and within-subjects factors
(see examples at :func:`test.anova`).
* :mod:`load.fiff`: when generating epochs from raw data, a new ``tstop``
argument allows specifying the time interval exclusive of the last sample.
* New functions:

- :func:`table.cast_to_ndvar`
- :func:`test.TTestInd`

* New methods:

- :meth:`NDVar.log`
- :meth:`NDVar.smooth`

* .. currentmodule:: eelbrain.pipeline
:class:`MneExperiment` pipeline:

- :meth:`MneExperiment.reset` (replacing :meth:`MneExperiment.store_state`
and :meth:`MneExperiment.restore_state`)
- New :attr:`MneExperiment.auto_delete_results` attribute to control whether
invalidated results are automatically deleted.
- :attr:`MneExperiment.screen_log_level`

0.25

-----------

.. currentmodule:: eelbrain

* Installation with ``conda`` (see :doc:`installing`) and ``$ eelbrain`` launch
script (see :doc:`getting_started`).
* API:

- :class:`NDVar` objects now inherit names through operations.
- Assignment to a :class:`Dataset` overwrites variable ``.name`` attributes,
unless the :class:`Dataset` key is a pythonified version of ``.name``.

* GUI/plotting:

- When using iPython 5 or later, GUI start and stop is now automatic. It is
possible to revert to the old behavior with :func:`plot.configure`.
- There are new hotkeys for most plots (see the individual plots' help for
details).
- Plots automatically rescale when the window is resized.

* :class:`MneExperiment`:

- A new :attr:`MneExperiment.sessions` attribute replaces
``defaults['experiment']``, with support for multiple sessions in one
experiment (see :ref:`MneExperiment-filestructure`).
- The :attr:`MneExperiment.epochs` parameter ``sel_epoch`` has been removed,
use ``base`` instead.
- The setting ``raw='clm'`` has been renamed to ``raw='raw'``.
- Custom preprocessing pipelines (see :attr:`MneExperiment.raw`).
- The ``model`` parameter for ANOVA tests is now optional (see
:attr:`MneExperiment.tests`).

* Reverse correlation using :func:`boosting`.
* Loading and saving ``*.wav`` files (:func:`load.wav` and :func:`save.wav`).

0.24

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* API:

- :class:`MneExperiment`: For data from the NYU New York system converted
with :mod:`mne` < 0.13, the :attr:`MneExperiment.meg_system` attribute needs
to be set to ``"KIT-157"`` to distinguish it from data collected with the
KIT UMD system.
- :meth:`~testnd.ttest_rel.masked_parameter_map` method of cluster-based test
results: use of ``pmin=None`` is deprecated, use ``pmin=1`` instead.

* New test: :class:`test.TTestRel`.
* :meth:`MneExperiment.make_report_rois` includes corrected p-values in reports
for tests in more than one ROI
* :meth:`MneExperiment.make_rej` now has a ``decim`` parameter to improve
display performance.
* :class:`MneExperiment`: BEM-solution files are now created dynamically with
:mod:`mne` and are not cached any more. This can lead to small changes
in results due to improved numerical precision. Delete old files to free up
space with ``mne_experiment.rm('bem-sol-file', subject='*')``.
* New :meth:`MneExperiment.make_report_coreg` method.
* New :class:`MneExperiment`: analysis parameter
:ref:`state-connectivity`
* :class:`plot.TopoButterfly`: press ``Shift-T`` for a large topo-map with
sensor names.

0.23

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* API :func:`plot.colors_for_twoway` and :func:`plot.colors_for_categorial`:
new color model, different options.
* :class:`testnd.t_contrast_rel` contrasts can contain ``*`` to include the
average of multiple cells.
* New :class:`NDVar` methods:  :meth:`NDVar.envelope`, :meth:`NDVar.fft`.

0.22

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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:`MneExperiment`: new method :meth:`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`.

0.21

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* :class:`MneExperiment`:

- New epoch parameters: ``trigger_shift`` and ``vars`` (see
:attr:`MneExperiment.epochs`).
- :meth:`~MneExperiment.load_selected_events`: new ``vardef`` parameter to
load variables from a test definition.
- Log files stored in the root directory.
- Parcellations (:attr:`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``.

0.20

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* :class:`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.

0.19

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* Two-stage tests (see :attr:`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.

0.18

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* API: The first argument for :meth:`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:`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.

0.17

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* :attr:`MneExperiment.brain_plot_defaults` can be used to customize PySurfer
plots in movies and reports.
* :attr:`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:`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:`MneExperiment.variables` entries with unspecified values.

0.16

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* New function for plotting a legend for annot-files:
:func:`plot.brain.annot_legend` (automatically used in reports).
* Epoch definitions in :attr:`MneExperiment.epochs` can now include a ``'base'``
parameter, which will copy the given "base" epoch and modify it with the
current definition.
* :meth:`MneExperiment.make_mov_ttest` and
:meth:`MneExperiment.make_mov_ga_dspm` are fixed but require PySurfer 0.6.
* New function: :func:`table.melt_ndvar`.
* API: :mod:`plot.brain` function signatures changed slightly to accommodate
more layout-related arguments.
* API: use :meth:`Brain.image` instead of :func:`plot.brain.image`.

0.15

-----------

* The Eelbrain package on the PYPI is now compiled with Anaconda. This means
that the package can now be installed into an Anaconda distribution with
``pip``, whereas ``easy_install`` has to be used for the Canopy distribution.
* GUI :func:`gui.select_epochs`: Set marked channels through menu (View > Mark
Channels)
* Datasets can be saved as tables in RTF format (:meth:`Dataset.save_rtf`).
* API :class:`plot.Timeplot`: the default spread indicator changed to SEM, and
there is a new argument for `timelabels`.
* API: :func:`test.anova` is now a function with a slightly changed signature.
The old class has been renamed to :class:`test.ANOVA`.
* API: :func:`test.oneway` was removed. Use :func:`test.anova`.
* API: the default value of the :class:`plot.Timeplot` parameter `bottom`
changed from `0` to `None` (determined by the data).
* API: :meth:`Factor.relabel` renamed to :meth:`Factor.update_labels`.
* Plotting: New option for the figure legend ``'draggable'`` (drag the legend
with the mouse pointer).

0.14

-----------

* API: the :class:`plot.Topomap` argument `sensors` changed to `sensorlabels`.
* GUI: The *python/Quit Eelbrain* menu command now closes all windows to ensure
that unsaved documents are handled properly. In order to yield to the terminal
without closing windows, use the *Go/Yield to Terminal* command
(Command-Alt-Q).
* :class:`testnd.t_contrast_rel`:  support for unary operation `abs`.

0.13

-----------

* The :func:`gui.select_epochs` GUI can now also be used to set bad channels.
:class:`MneExperiment` subclasses will combine bad channel information from
rejection files with bad channel information from bad channel files. Note
that while bad channel files set bad channels for a given raw file
globally, rejection files set bad channels only for the given epoch.
* :class:`Factor` objects can now remember a custom cell order which determines
the order in tables and plots.
* The :meth:`Var.as_factor` method can now assign all unmentioned codes to a
default value.
* :class:`MneExperiment`:

- API: Subclasses should remove the ``subject`` and ``experiment`` parameters
from :meth:`MneExperiment.label_events`.
- API: :class:`MneExperiment` can now be imported directly from
:mod:`eelbrain`.
- API: The :attr:`MneExperiment._defaults` attribute should be renamed to
:attr:`MneExperiment.defaults`.
- A draft for a guide at :ref:`experiment-class-guide`.
- Cached files are now saved in a separate folder at ``root/eelbrain-cache``.
The cache can be cleared using :meth:`MneExperiment.clear_cache`. To
preserve cached test results, move the ``root/test`` folder into the
``root/eelbrain-cache`` folder.

0.12

-----------

* API: :class:`Dataset` construction changed, allows setting the number of
cases in the Dataset.
* API:  :class:`plot.SensorMap2d` was renamed to :class:`plot.SensorMap`.
* :class:`~experiment.MneExperiment`:

- API: The default number of samples for reports is now 10'000.
- New epoch parameter ``'n_cases'``:  raise an error if an epoch definition
does not yield expected number of trials.
- A custom baseline period for epochs can now be specified as a parameter in
the epoch definition (e.g., ``'baseline': (-0.2, -0.1)``). When loading
data, specifying ``baseline=True`` uses the epoch's custom baseline.

0.11

-----------

* :class:`~experiment.MneExperiment`:

- Change in the way the covariance matrix
is defined:  The epoch for the covariance matrix should be specified in
``MneExperiment.epochs['cov']``. The regularization is no longer part of
:meth:`~experiment.MneExperiment.set_inv`, but is instead set with
``MneExperiment.set(cov='reg')`` or ``MneExperiment.set(cov='noreg')``.
- New option ``cov='bestreg'`` automatically selects the regularization
parameter for each subejct.

* :meth:`Var.as_factor` allows more efficient labeling when multiple values
share the same label.
* API: Previously :func:`plot.configure_backend` is now :func:`plot.configure`

0.10

-----------

* Tools for generating colors for categories (see :ref:`ref-plotting`).
* Plots now all largely respect matplotlib rc-parameters (see
`Customizing Matplotlib <http://matplotlib.org/users/customizing.html>`_).
* Fixed an issue in the :mod:`testnd` module that could affect permutation based
p-values when multiprocessing was used.

0.9

----------

* :class:`Factor` API change:  The ``rep`` argument was renamed to ``repeat``.
* T-values for regression coefficients through :meth:`NDVar.ols_t`.
* :class:`~experiment.MneExperiment`: subject name patterns and eog_sns are
now handled automatically.
* :class:`~plot.uts.UTSStat` and :class:`~plot.uv.Barplot` plots can use pooled
error for variability estimates (on by default for related measures designs,
can be turned off using the ``pool_error`` argument).

- API: for consistency, the argument to specify the kind of error to plot
changed to ``error`` in both plots.

0.8

----------

* A new GUI application controls plots as well as the epoch selection GUI (see
notes in the reference sections on :ref:`ref-plotting` and :ref:`ref-guis`).
* Randomization/Monte Carlo tests now seed the random state to make results replicable.

0.6

----------

* New recipes for :ref:`recipe-regression`.

0.5

----------

* The :mod:`eelbrain.lab` and :mod:`eelbrain.eellab` modules are deprecated.
Everything can now me imported from :mod:`eelbrain` directly.

0.4

----------

* Optimized ANOVA evaluation, support for unbalanced fixed effects models.
* `rpy2 <http://rpy.sourceforge.net>`_ interaction: :meth:`Dataset.from_r` to
create a :class:`Dataset` from an R Data Frame, and :meth:`Dataset.to_r` to
cerate an R Data Frame from a :class:`Dataset`.

0.3

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* Optimized clustering for cluster permutation tests.

0.2

----------

* :class:`gui.SelectEpochs` Epoch rejection GIU has a new "GA" button to plot
the grand average of all accepted trials
* Cluster permutation tests in :mod:`testnd` use multiple cores; To disable
multiprocessing set ``eelbrain._stats.testnd.multiprocessing = False``.

0.1.7

------------

* :class:`gui.SelectEpochs` can now be initialized with a single
:class:`mne.Epochs` instance (data needs to be preloaded).
* Parameters that take :class:`NDVar` objects now also accept
:class:`mne.Epochs` and :class:`mne.fiff.Evoked` objects.

0.1.5

------------

* :py:class:`plot.topo.TopoButterfly` plot: new keyboard commands (``t``,
``left arrow``, ``right arrow``).


.. _Proloy Das: https://ece.umd.edu/~proloy/