Resampling data¶

When performing experiments where timing is critical, a signal with a high sampling rate is desired. However, having a signal with a much higher sampling rate than is necessary needlessly consumes memory and slows down computations operating on the data.

This example downsamples from 600 Hz to 100 Hz. This achieves a 6-fold reduction in data size, at the cost of an equal loss of temporal resolution.

# Authors: Marijn van Vliet <w.m.vanvliet@gmail.com>
#
#
from __future__ import print_function

from matplotlib import pyplot as plt

import mne
from mne.io import Raw
from mne.datasets import sample


data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif'


Since downsampling reduces the timing precision of events, we recommend first extracting epochs and downsampling the Epochs object:

events = mne.find_events(raw)
epochs = mne.Epochs(raw, events, event_id=2, tmin=-0.1, tmax=0.8, preload=True)

# Downsample to 100 Hz
print('Original sampling rate:', epochs.info['sfreq'], 'Hz')
epochs_resampled = epochs.resample(100, copy=True)
print('New sampling rate:', epochs_resampled.info['sfreq'], 'Hz')

# Plot a piece of data to see the effects of downsampling
plt.figure(figsize=(7, 3))

n_samples_to_plot = int(0.5 * epochs.info['sfreq'])  # plot 0.5 seconds of data
plt.plot(epochs.times[:n_samples_to_plot],
epochs.get_data()[0, 0, :n_samples_to_plot], color='black')

n_samples_to_plot = int(0.5 * epochs_resampled.info['sfreq'])
plt.plot(epochs_resampled.times[:n_samples_to_plot],
epochs_resampled.get_data()[0, 0, :n_samples_to_plot],
'-o', color='red')

plt.xlabel('time (s)')
plt.legend(['original', 'downsampled'], loc='best')
plt.title('Effect of downsampling')
mne.viz.tight_layout()


Script output:

Original sampling rate: 600.614990234 Hz
New sampling rate: 100 Hz


When resampling epochs is unwanted or impossible, for example when the data doesn’t fit into memory or your analysis pipeline doesn’t involve epochs at all, the alternative approach is to resample the continous data. This can also be done on non-preloaded data.

# Resample to 300 Hz
raw_resampled = raw.resample(300, copy=True)


Because resampling also affects the stim channels, some trigger onsets might be lost in this case. While MNE attempts to downsample the stim channels in an intelligent manner to avoid this, the recommended approach is to find events on the original data before downsampling.

print('Number of events before resampling:', len(mne.find_events(raw)))

# Resample to 100 Hz (generates warning)
raw_resampled = raw.resample(100, copy=True)
print('Number of events after resampling:',
len(mne.find_events(raw_resampled)))

# To avoid losing events, jointly resample the data and event matrix
events = mne.find_events(raw)
raw_resampled, events_resampled = raw.resample(100, events=events, copy=True)
print('Number of events after resampling:', len(events_resampled))


Script output:

Number of events before resampling: 320
Number of events after resampling: 319
Number of events after resampling: 320


Total running time of the script: (0 minutes 30.897 seconds)

Download Python source code: plot_resample.py