The Raw data structure: continuous data

from __future__ import print_function

import mne
import os.path as op
from matplotlib import pyplot as plt

Continuous data is stored in objects of type Raw. The core data structure is simply a 2D numpy array (channels × samples, ._data) combined with an Info object (.info) (The Info data structure.

The most common way to load continuous data is from a .fif file. For more information on loading data from other formats, or creating it from scratch.

Loading continuous data

# Load an example dataset, the preload flag loads the data into memory now
data_path = op.join(mne.datasets.sample.data_path(), 'MEG',
                    'sample', 'sample_audvis_raw.fif')
raw = mne.io.RawFIF(data_path, preload=True, verbose=False)

# Give the sample rate
print('sample rate:', raw.info['sfreq'], 'Hz')
# Give the size of the data matrix
print('channels x samples:', raw._data.shape)

Out:

sample rate: 600.614990234 Hz
channels x samples: (376, 166800)

Information about the channels contained in the Raw object is contained in the Info attribute. This is essentially a dictionary with a number of relevant fields (see The Info data structure).

Indexing data

There are two ways to access the data stored within Raw objects. One is by accessing the underlying data array, and the other is to index the Raw object directly.

To access the data array of Raw objects, use the _data attribute. Note that this is only present if preload==True.

print('Shape of data array:', raw._data.shape)
array_data = raw._data[0, :1000]
_ = plt.plot(array_data)
../_images/sphx_glr_plot_raw_objects_001.png

Out:

Shape of data array: (376, 166800)

You can also pass an index directly to the Raw object. This will return an array of times, as well as the data representing those timepoints. This may be used even if the data is not preloaded:

# Extract data from the first 5 channels, from 1 s to 3 s.
sfreq = raw.info['sfreq']
data, times = raw[:5, int(sfreq * 1):int(sfreq * 3)]
_ = plt.plot(times, data.T)
_ = plt.title('Sample channels')
../_images/sphx_glr_plot_raw_objects_002.png

Selecting subsets of channels and samples

It is possible to use more intelligent indexing to extract data, using channel names, types or time ranges.

# Pull all MEG gradiometer channels:
# Make sure to use copy==True or it will overwrite the data
meg_only = raw.pick_types(meg=True, copy=True)
eeg_only = raw.pick_types(meg=False, eeg=True, copy=True)

# The MEG flag in particular lets you specify a string for more specificity
grad_only = raw.pick_types(meg='grad', copy=True)

# Or you can use custom channel names
pick_chans = ['MEG 0112', 'MEG 0111', 'MEG 0122', 'MEG 0123']
specific_chans = raw.pick_channels(pick_chans, copy=True)
print(meg_only, eeg_only, grad_only, specific_chans, sep='\n')

Out:

<RawFIF  |  n_channels x n_times : 305 x 166800>
<RawFIF  |  n_channels x n_times : 59 x 166800>
<RawFIF  |  n_channels x n_times : 203 x 166800>
<RawFIF  |  n_channels x n_times : 4 x 166800>

Notice the different scalings of these types

f, (a1, a2) = plt.subplots(2, 1)
eeg, times = eeg_only[0, :int(sfreq * 2)]
meg, times = meg_only[0, :int(sfreq * 2)]
a1.plot(times, meg[0])
a2.plot(times, eeg[0])
../_images/sphx_glr_plot_raw_objects_003.png

You can restrict the data to a specific time range

restricted = raw.crop(5, 7)  # in seconds
print('New time range from', restricted.times.min(), 's to',
      restricted.times.max(), 's')

Out:

New time range from 0.0 s to 1.99795213158 s

And drop channels by name

restricted = restricted.drop_channels(['MEG 0241', 'EEG 001'])
print('Number of channels reduced from', raw.info['nchan'], 'to',
      restricted.info['nchan'])

Out:

Number of channels reduced from 376 to 374

Concatenating Raw objects

Raw objects can be concatenated in time by using the append function. For this to work, they must have the same number of channels and their Info structures should be compatible.

# Create multiple :class:`Raw <mne.io.RawFIF>` objects
raw1 = raw.copy().crop(0, 10)
raw2 = raw.copy().crop(10, 20)
raw3 = raw.copy().crop(20, 100)

# Concatenate in time (also works without preloading)
raw1.append([raw2, raw3])
print('Time extends from', raw1.times.min(), 's to', raw1.times.max(), 's')

Out:

Time extends from 0.0 s to 100.000834106 s

Total running time of the script: (0 minutes 5.813 seconds)

Download Python source code: plot_raw_objects.py
Download IPython notebook: plot_raw_objects.ipynb