"""
.. _tut-epochs-dataframe:

Exporting Epochs to Pandas DataFrames
=====================================

This tutorial shows how to export the data in :class:`~mne.Epochs` objects to a
:class:`Pandas DataFrame <pandas.DataFrame>`, and applies a typical Pandas
:doc:`split-apply-combine <pandas:user_guide/groupby>` workflow to examine the
latencies of the response maxima across epochs and conditions.

We'll use the :ref:`sample-dataset` dataset, but load a version of the raw file
that has already been filtered and downsampled, and has an average reference
applied to its EEG channels. As usual we'll start by importing the modules we
need and loading the data:
"""
import os
import seaborn as sns
import mne

sample_data_folder = mne.datasets.sample.data_path()
sample_data_raw_file = os.path.join(sample_data_folder, 'MEG', 'sample',
                                    'sample_audvis_filt-0-40_raw.fif')
raw = mne.io.read_raw_fif(sample_data_raw_file, verbose=False)

###############################################################################
# Next we'll load a list of events from file, map them to condition names with
# an event dictionary, set some signal rejection thresholds (cf.
# :ref:`tut-reject-epochs-section`), and segment the continuous data into
# epochs:

sample_data_events_file = os.path.join(sample_data_folder, 'MEG', 'sample',
                                       'sample_audvis_filt-0-40_raw-eve.fif')
events = mne.read_events(sample_data_events_file)

event_dict = {'auditory/left': 1, 'auditory/right': 2, 'visual/left': 3,
              'visual/right': 4}

reject_criteria = dict(mag=3000e-15,     # 3000 fT
                       grad=3000e-13,    # 3000 fT/cm
                       eeg=100e-6,       # 100 µV
                       eog=200e-6)       # 200 µV

tmin, tmax = (-0.2, 0.5)  # epoch from 200 ms before event to 500 ms after it
baseline = (None, 0)      # baseline period from start of epoch to time=0

epochs = mne.Epochs(raw, events, event_dict, tmin, tmax, proj=True,
                    baseline=baseline, reject=reject_criteria, preload=True)
del raw

###############################################################################
# Converting an ``Epochs`` object to a ``DataFrame``
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
#
# Once we have our :class:`~mne.Epochs` object, converting it to a
# :class:`~pandas.DataFrame` is simple: just call :meth:`epochs.to_data_frame()
# <mne.Epochs.to_data_frame>`. Each channel's data will be a column of the new
# :class:`~pandas.DataFrame`, alongside three additional columns of event name,
# epoch number, and sample time. Here we'll just show the first few rows and
# columns:

df = epochs.to_data_frame()
df.iloc[:5, :10]

###############################################################################
# Scaling time and channel values
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# By default, time values are converted from seconds to milliseconds and
# then rounded to the nearest integer; if you don't want this, you can pass
# ``time_format=None`` to keep time as a :class:`float` value in seconds, or
# convert it to a :class:`~pandas.Timedelta` value via
# ``time_format='timedelta'``.
#
# Note also that, by default, channel measurement values are scaled so that EEG
# data are converted to µV, magnetometer data are converted to fT, and
# gradiometer data are converted to fT/cm. These scalings can be customized
# through the ``scalings`` parameter, or suppressed by passing
# ``scalings=dict(eeg=1, mag=1, grad=1)``.

df = epochs.to_data_frame(time_format=None,
                          scalings=dict(eeg=1, mag=1, grad=1))
df.iloc[:5, :10]

###############################################################################
# Notice that the time values are no longer integers, and the channel values
# have changed by several orders of magnitude compared to the earlier
# DataFrame.
#
#
# Setting the ``index``
# ~~~~~~~~~~~~~~~~~~~~~
#
# It is also possible to move one or more of the indicator columns (event name,
# epoch number, and sample time) into the :ref:`index <pandas:indexing>`, by
# passing a string or list of strings as the ``index`` parameter. We'll also
# demonstrate here the effect of ``time_format='timedelta'``, yielding
# :class:`~pandas.Timedelta` values in the "time" column.

df = epochs.to_data_frame(index=['condition', 'epoch'],
                          time_format='timedelta')
df.iloc[:5, :10]

###############################################################################
# Wide- versus long-format DataFrames
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
# Another parameter, ``long_format``, determines whether each channel's data is
# in a separate column of the :class:`~pandas.DataFrame`
# (``long_format=False``), or whether the measured values are pivoted into a
# single ``'value'`` column with an extra indicator column for the channel name
# (``long_format=True``). Passing ``long_format=True`` will also create an
# extra column ``ch_type`` indicating the channel type.

long_df = epochs.to_data_frame(time_format=None, index='condition',
                               long_format=True)
long_df.head()

###############################################################################
# Generating the :class:`~pandas.DataFrame` in long format can be helpful when
# using other Python modules for subsequent analysis or plotting. For example,
# here we'll take data from the "auditory/left" condition, pick a couple MEG
# channels, and use :func:`seaborn.lineplot` to automatically plot the mean and
# confidence band for each channel, with confidence computed across the epochs
# in the chosen condition:

channels = ['MEG 1332', 'MEG 1342']
data = long_df.loc['auditory/left'].query('channel in @channels')
# convert channel column (CategoryDtype → string; for a nicer-looking legend)
data['channel'] = data['channel'].astype(str)
sns.lineplot(x='time', y='value', hue='channel', data=data)

###############################################################################
# We can also now use all the power of Pandas for grouping and transforming our
# data. Here, we find the latency of peak activation of 2 gradiometers (one
# near auditory cortex and one near visual cortex), and plot the distribution
# of the timing of the peak in each channel as a :func:`~seaborn.violinplot`:

# sphinx_gallery_thumbnail_number = 2
df = epochs.to_data_frame(time_format=None)
peak_latency = (df.filter(regex=r'condition|epoch|MEG 1332|MEG 2123')
                .groupby(['condition', 'epoch'])
                .aggregate(lambda x: df['time'].iloc[x.idxmax()])
                .reset_index()
                .melt(id_vars=['condition', 'epoch'],
                      var_name='channel',
                      value_name='latency of peak')
                )

ax = sns.violinplot(x='channel', y='latency of peak', hue='condition',
                    data=peak_latency, palette='deep', saturation=1)
