Note
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Define an electrophysiological dataset using MNE-Python structures#
This example illustrates how to define a dataset using MNE-Python Epochs.
import numpy as np
from mne import EpochsArray, create_info
from frites.dataset import DatasetEphy
from frites import set_mpl_style
import matplotlib.pyplot as plt
set_mpl_style()
Create artificial data#
We start by creating some random data for several subjects. To do that, each subject is going have a 3 dimensional array of shape (n_epochs, n_channels, n_times). Then, all of the arrays are grouped together in a list of length (n_subjects,)
n_subjects = 5
n_epochs = 10
n_channels = 5
n_times = 100
sf = 512
x, ch = [], []
for k in range(n_subjects):
# generate single subject data
x_suj = np.random.rand(n_epochs, n_channels, n_times)
# generate some random channel names
ch_suj = np.array([f"ch_{r}" for r in range(n_channels)])
# concatenate in a list
x.append(x_suj)
ch.append(ch_suj)
# finally lets create a time vector
times = np.arange(n_times) / sf
MNE conversion to Epoch#
Here, we convert our illustrative data into EpochsArray. With real data, you are probbaly going to have mne.Epochs objects which also going to work just the same
x_mne = []
for k in range(n_subjects):
# create some informations
info = create_info(ch[k].tolist(), sf)
# create the Epoch of this subject
epoch = EpochsArray(x[k], info, tmin=times[0], verbose=False)
# finally, replace it in the original list
x_mne.append(epoch)
print(x_mne[0])
<EpochsArray | 10 events (all good), 0 – 0.193359 s, baseline off, ~49 kB, data loaded,
'1': 10>
Build the dataset#
Finally, we pass the data to the frites.dataset.DatasetEphy class
in order to create the dataset
dt = DatasetEphy(x_mne)
print(dt)
print('Time vector : ', dt.times)
print('ROI DataFrame\n: ', dt.df_rs)
<xarray.DataArray 'subject_0' (trials: 10, roi: 5, times: 100)>
array([[[0.24392333, 0.65495435, 0.35150695, ..., 0.75384745,
0.93627024, 0.3299055 ],
[0.3110566 , 0.87868043, 0.06982022, ..., 0.90765657,
0.67911187, 0.19209818],
[0.36660264, 0.02974329, 0.95329504, ..., 0.48321024,
0.60814371, 0.93922705],
[0.79902297, 0.37618136, 0.58825882, ..., 0.43421206,
0.33749481, 0.94168455],
[0.76155977, 0.80324398, 0.25562594, ..., 0.24869778,
0.9335653 , 0.22747919]],
[[0.71605324, 0.92937511, 0.91069937, ..., 0.99355173,
0.22700501, 0.49485814],
[0.12091355, 0.10959777, 0.00516555, ..., 0.47622637,
0.17127595, 0.68506362],
[0.70785012, 0.38955529, 0.76906054, ..., 0.16161444,
0.06978964, 0.23431213],
[0.72875621, 0.87612937, 0.03940922, ..., 0.19273235,
0.76165237, 0.43280645],
[0.59328406, 0.80146893, 0.63416803, ..., 0.89278915,
...
0.31650509, 0.03652929],
[0.41709039, 0.90968837, 0.35487336, ..., 0.83509349,
0.74766765, 0.17380476],
[0.97159376, 0.7545753 , 0.10104604, ..., 0.93820243,
0.62185655, 0.19636822],
[0.21483059, 0.74461171, 0.2580803 , ..., 0.45927542,
0.30866759, 0.39530782],
[0.1791466 , 0.32694537, 0.15613618, ..., 0.89519947,
0.07556917, 0.47114553]],
[[0.1810615 , 0.54071795, 0.63001438, ..., 0.24662136,
0.45418379, 0.80146086],
[0.28820267, 0.12738988, 0.41164697, ..., 0.51239921,
0.49802141, 0.18298122],
[0.61265254, 0.27139124, 0.70616473, ..., 0.36432601,
0.43102553, 0.70709125],
[0.22926219, 0.66829409, 0.26836332, ..., 0.55201116,
0.59011918, 0.46382726],
[0.01851871, 0.38966844, 0.11513355, ..., 0.78412312,
0.61925482, 0.15752893]]])
Coordinates:
* trials (trials) int64 0 1 2 3 4 5 6 7 8 9
* roi (roi) <U4 'ch_0' 'ch_1' 'ch_2' 'ch_3' 'ch_4'
agg_ch (roi) int64 0 0 0 0 0
* times (times) float64 0.0 0.001953 0.003906 ... 0.1895 0.1914 0.1934
subject (trials) int64 0 0 0 0 0 0 0 0 0 0
Attributes:
__version__: 0.4.5
modality: electrophysiology
dtype: SubjectEphy
y_dtype: none
z_dtype: none
mi_type: none
mi_repr: none
sfreq: 512.0
agg_ch: 1
multivariate: 0
<xarray.DataArray 'subject_1' (trials: 10, roi: 5, times: 100)>
array([[[0.01109675, 0.00176979, 0.15505512, ..., 0.45284762,
0.59954199, 0.2719661 ],
[0.96102724, 0.04345081, 0.72659793, ..., 0.52574985,
0.00683546, 0.86238922],
[0.12650748, 0.74559266, 0.72083238, ..., 0.0294278 ,
0.53947405, 0.21383679],
[0.61218365, 0.45715353, 0.35434214, ..., 0.16090124,
0.87208857, 0.01881678],
[0.97678488, 0.12174478, 0.16746949, ..., 0.29672356,
0.04980363, 0.62885735]],
[[0.53937919, 0.06376116, 0.03691362, ..., 0.94779467,
0.85471542, 0.41874634],
[0.55564718, 0.83965301, 0.23306488, ..., 0.4001393 ,
0.7145485 , 0.29302891],
[0.60144183, 0.29616752, 0.1655798 , ..., 0.62902752,
0.93831673, 0.26722398],
[0.94567553, 0.15444464, 0.78849142, ..., 0.42681579,
0.37615727, 0.57259254],
[0.10025302, 0.99448565, 0.87103453, ..., 0.72900585,
...
0.5213406 , 0.43386368],
[0.91233447, 0.88570529, 0.86468671, ..., 0.84050424,
0.66784162, 0.17469976],
[0.50634435, 0.12160911, 0.52991834, ..., 0.69923107,
0.85486006, 0.98326732],
[0.24818939, 0.3976172 , 0.06209891, ..., 0.88555227,
0.33731101, 0.47106099],
[0.5582356 , 0.57802422, 0.68296597, ..., 0.08616856,
0.38576078, 0.75506298]],
[[0.24089265, 0.76595472, 0.00714221, ..., 0.14817551,
0.36155844, 0.40182818],
[0.94620349, 0.07018871, 0.80118731, ..., 0.13793289,
0.89391399, 0.67439013],
[0.40669996, 0.68865767, 0.4992233 , ..., 0.13865445,
0.73507301, 0.18129449],
[0.18627529, 0.45228337, 0.42723941, ..., 0.4991425 ,
0.60134917, 0.77386409],
[0.26973761, 0.14448086, 0.78933364, ..., 0.59208601,
0.45728648, 0.55747382]]])
Coordinates:
* trials (trials) int64 0 1 2 3 4 5 6 7 8 9
* roi (roi) <U4 'ch_0' 'ch_1' 'ch_2' 'ch_3' 'ch_4'
agg_ch (roi) int64 0 0 0 0 0
* times (times) float64 0.0 0.001953 0.003906 ... 0.1895 0.1914 0.1934
subject (trials) int64 1 1 1 1 1 1 1 1 1 1
Attributes:
__version__: 0.4.5
modality: electrophysiology
dtype: SubjectEphy
y_dtype: none
z_dtype: none
mi_type: none
mi_repr: none
sfreq: 512.0
agg_ch: 1
multivariate: 0
<xarray.DataArray 'subject_2' (trials: 10, roi: 5, times: 100)>
array([[[0.51581483, 0.95028891, 0.3888361 , ..., 0.10959219,
0.47453192, 0.44606687],
[0.65847037, 0.47130979, 0.67203554, ..., 0.62118374,
0.46666992, 0.26672759],
[0.64807381, 0.24777647, 0.11131784, ..., 0.93289054,
0.46018623, 0.40699517],
[0.90758875, 0.30291291, 0.24209164, ..., 0.03279871,
0.75713367, 0.37236105],
[0.02202746, 0.00932916, 0.01339035, ..., 0.46286979,
0.85665419, 0.4872235 ]],
[[0.7777711 , 0.55748914, 0.98574848, ..., 0.91798246,
0.25489224, 0.50705835],
[0.36248442, 0.50160319, 0.99962982, ..., 0.92314743,
0.81968621, 0.46867419],
[0.48178369, 0.18603546, 0.26248367, ..., 0.90772469,
0.84959545, 0.48859922],
[0.46675039, 0.58862497, 0.97976884, ..., 0.18438617,
0.14433657, 0.98559311],
[0.06389391, 0.42291312, 0.90768166, ..., 0.4520585 ,
...
0.23274637, 0.85764766],
[0.86262341, 0.36115707, 0.31575497, ..., 0.55765498,
0.07969845, 0.24284618],
[0.40113791, 0.36688194, 0.20798164, ..., 0.15687717,
0.33361071, 0.73073486],
[0.34390796, 0.08748721, 0.49332186, ..., 0.15175538,
0.43770247, 0.88636801],
[0.08106464, 0.25920657, 0.43460526, ..., 0.37084312,
0.98002021, 0.38036088]],
[[0.31787268, 0.33901538, 0.16138566, ..., 0.63222269,
0.8402969 , 0.44492924],
[0.59753713, 0.52374904, 0.00125058, ..., 0.38727654,
0.9537937 , 0.83938407],
[0.39440674, 0.48919191, 0.005361 , ..., 0.88669946,
0.75097974, 0.40812447],
[0.2985188 , 0.45829102, 0.12191161, ..., 0.46862567,
0.51352981, 0.79236877],
[0.43251311, 0.00900492, 0.18810681, ..., 0.56425734,
0.60526059, 0.93545513]]])
Coordinates:
* trials (trials) int64 0 1 2 3 4 5 6 7 8 9
* roi (roi) <U4 'ch_0' 'ch_1' 'ch_2' 'ch_3' 'ch_4'
agg_ch (roi) int64 0 0 0 0 0
* times (times) float64 0.0 0.001953 0.003906 ... 0.1895 0.1914 0.1934
subject (trials) int64 2 2 2 2 2 2 2 2 2 2
Attributes:
__version__: 0.4.5
modality: electrophysiology
dtype: SubjectEphy
y_dtype: none
z_dtype: none
mi_type: none
mi_repr: none
sfreq: 512.0
agg_ch: 1
multivariate: 0
<xarray.DataArray 'subject_3' (trials: 10, roi: 5, times: 100)>
array([[[0.19112391, 0.05854766, 0.43681052, ..., 0.98285116,
0.75960944, 0.56082868],
[0.68743319, 0.95944606, 0.54110355, ..., 0.85549807,
0.63384251, 0.12465387],
[0.07699636, 0.52816128, 0.58944985, ..., 0.21595938,
0.04935497, 0.848193 ],
[0.85337132, 0.23613114, 0.85887024, ..., 0.63804154,
0.57225554, 0.05314667],
[0.86561985, 0.80783732, 0.73797733, ..., 0.72411739,
0.96091459, 0.1326284 ]],
[[0.42140534, 0.37790698, 0.00808216, ..., 0.13832723,
0.52820552, 0.01815526],
[0.83772931, 0.89204519, 0.85892773, ..., 0.27244483,
0.64041396, 0.62111615],
[0.39675014, 0.55016239, 0.03579929, ..., 0.21352248,
0.16069066, 0.56689289],
[0.92848866, 0.72602818, 0.57983457, ..., 0.79242554,
0.34400905, 0.35637945],
[0.26435496, 0.09152404, 0.41832919, ..., 0.30127874,
...
0.47819327, 0.62576883],
[0.27082248, 0.5636694 , 0.4572046 , ..., 0.21566352,
0.20891019, 0.84209603],
[0.80166917, 0.3996219 , 0.85685233, ..., 0.09643161,
0.20417991, 0.11488457],
[0.52324762, 0.63761337, 0.42255344, ..., 0.42335149,
0.14261326, 0.44492949],
[0.17777531, 0.20606367, 0.05732538, ..., 0.61222859,
0.2601258 , 0.02038846]],
[[0.95433104, 0.07217132, 0.09010197, ..., 0.40614839,
0.2623648 , 0.8129389 ],
[0.14624277, 0.16398797, 0.83541745, ..., 0.48746753,
0.90240508, 0.92632065],
[0.84035788, 0.9764717 , 0.85184826, ..., 0.34881195,
0.32055504, 0.59203046],
[0.5991912 , 0.96951956, 0.39432461, ..., 0.91030387,
0.42970534, 0.73500405],
[0.38844779, 0.0480029 , 0.15251854, ..., 0.49011981,
0.0430546 , 0.64650278]]])
Coordinates:
* trials (trials) int64 0 1 2 3 4 5 6 7 8 9
* roi (roi) <U4 'ch_0' 'ch_1' 'ch_2' 'ch_3' 'ch_4'
agg_ch (roi) int64 0 0 0 0 0
* times (times) float64 0.0 0.001953 0.003906 ... 0.1895 0.1914 0.1934
subject (trials) int64 3 3 3 3 3 3 3 3 3 3
Attributes:
__version__: 0.4.5
modality: electrophysiology
dtype: SubjectEphy
y_dtype: none
z_dtype: none
mi_type: none
mi_repr: none
sfreq: 512.0
agg_ch: 1
multivariate: 0
<xarray.DataArray 'subject_4' (trials: 10, roi: 5, times: 100)>
array([[[0.96313608, 0.61881857, 0.11579477, ..., 0.10670696,
0.37226264, 0.66481021],
[0.71629345, 0.30617858, 0.84802591, ..., 0.02707331,
0.32840594, 0.01588814],
[0.88415412, 0.5712669 , 0.28411945, ..., 0.55713675,
0.67094586, 0.86149949],
[0.59120621, 0.56605371, 0.51685115, ..., 0.76287029,
0.59916864, 0.51235271],
[0.95963307, 0.3884158 , 0.15728345, ..., 0.75118109,
0.55464832, 0.26593243]],
[[0.02760775, 0.08173029, 0.293669 , ..., 0.9336578 ,
0.45489323, 0.16932518],
[0.04195368, 0.16490623, 0.25099848, ..., 0.29583988,
0.49688914, 0.54716939],
[0.52323549, 0.28077145, 0.20884221, ..., 0.92226945,
0.58961377, 0.32022785],
[0.85765427, 0.61893106, 0.43780174, ..., 0.58446624,
0.18915154, 0.84550671],
[0.54754623, 0.25526766, 0.64168355, ..., 0.12260603,
...
0.13758326, 0.41077202],
[0.84638027, 0.98380405, 0.74107143, ..., 0.81495978,
0.78667031, 0.0113469 ],
[0.15206914, 0.14219443, 0.60842978, ..., 0.18452566,
0.67846034, 0.97917668],
[0.53046042, 0.90742149, 0.57439819, ..., 0.69266066,
0.09664642, 0.66421804],
[0.61849359, 0.27357108, 0.41722557, ..., 0.35432996,
0.48737692, 0.75225962]],
[[0.52289232, 0.48686443, 0.24256897, ..., 0.39883038,
0.8833534 , 0.7931012 ],
[0.16060307, 0.7799293 , 0.1054113 , ..., 0.64910971,
0.52654156, 0.02859812],
[0.1755579 , 0.07195134, 0.6645303 , ..., 0.00219381,
0.79661686, 0.15715099],
[0.16175203, 0.20587649, 0.93604932, ..., 0.44172662,
0.85701721, 0.17779312],
[0.07849112, 0.27611425, 0.0851793 , ..., 0.81013284,
0.55103228, 0.22575586]]])
Coordinates:
* trials (trials) int64 0 1 2 3 4 5 6 7 8 9
* roi (roi) <U4 'ch_0' 'ch_1' 'ch_2' 'ch_3' 'ch_4'
agg_ch (roi) int64 0 0 0 0 0
* times (times) float64 0.0 0.001953 0.003906 ... 0.1895 0.1914 0.1934
subject (trials) int64 4 4 4 4 4 4 4 4 4 4
Attributes:
__version__: 0.4.5
modality: electrophysiology
dtype: SubjectEphy
y_dtype: none
z_dtype: none
mi_type: none
mi_repr: none
sfreq: 512.0
agg_ch: 1
multivariate: 0
Time vector : [0. 0.00195312 0.00390625 0.00585938 0.0078125 0.00976562
0.01171875 0.01367188 0.015625 0.01757812 0.01953125 0.02148438
0.0234375 0.02539062 0.02734375 0.02929688 0.03125 0.03320312
0.03515625 0.03710938 0.0390625 0.04101562 0.04296875 0.04492188
0.046875 0.04882812 0.05078125 0.05273438 0.0546875 0.05664062
0.05859375 0.06054688 0.0625 0.06445312 0.06640625 0.06835938
0.0703125 0.07226562 0.07421875 0.07617188 0.078125 0.08007812
0.08203125 0.08398438 0.0859375 0.08789062 0.08984375 0.09179688
0.09375 0.09570312 0.09765625 0.09960938 0.1015625 0.10351562
0.10546875 0.10742188 0.109375 0.11132812 0.11328125 0.11523438
0.1171875 0.11914062 0.12109375 0.12304688 0.125 0.12695312
0.12890625 0.13085938 0.1328125 0.13476562 0.13671875 0.13867188
0.140625 0.14257812 0.14453125 0.14648438 0.1484375 0.15039062
0.15234375 0.15429688 0.15625 0.15820312 0.16015625 0.16210938
0.1640625 0.16601562 0.16796875 0.16992188 0.171875 0.17382812
0.17578125 0.17773438 0.1796875 0.18164062 0.18359375 0.18554688
0.1875 0.18945312 0.19140625 0.19335938]
ROI DataFrame
: #subjects subjects keep
roi
ch_0 5 [0, 1, 2, 3, 4] True
ch_1 5 [0, 1, 2, 3, 4] True
ch_2 5 [0, 1, 2, 3, 4] True
ch_3 5 [0, 1, 2, 3, 4] True
ch_4 5 [0, 1, 2, 3, 4] True
Total running time of the script: (0 minutes 0.593 seconds)
Estimated memory usage: 9 MB