This file was created from the following Jupyter-notebook: importdata_edf.ipynb
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Importing Data from Eyelink EDF files Example¶
[1]:
import sys, os
sys.path.insert(0,"..") # this is not needed if you have installed pypillometry
import pypillometry as pp
import pandas as pd
import numpy as np
import pylab as plt
The easiest way is to use a local filename or a URL where the EDF file is stored:
[6]:
url='https://osf.io/trsuq/download' # will download the file from OSF
d = pp.EyeData.from_eyelink(url)
d
tmpfxwzpzg0: 100%|██████████| 14.2M/14.2M [00:01<00:00, 11.6MiB/s]
pp: 10:45:45 | INFO | read_eyelink:582 | Loading EDF file: /tmp/tmpfxwzpzg0 (current log level: INFO, set to DEBUG to see eyelinkio output)
[6]:
EyeData(tmpfxwzpzg0, 61.1MiB):
n : 598885
sampling_rate : 500.0
data : ['left_x', 'left_y', 'left_pupil', 'right_x', 'right_y', 'right_pupil']
nevents : 1685
screen_limits : ((0, 1280), (0, 1024))
physical_screen_size: not set
screen_eye_distance : not set
duration_minutes : 19.962833333333336
start_min : 0.0
end_min : 19.9628
parameters : {}
glimpse : EyeDataDict(vars=6,n=598885,shape=(598885,)):
left_x (float64): 668.2000122070312, 660.5999755859375, 650.0, 639.0999755859375, 628.4000244140625...
left_y (float64): 491.1000061035156, 490.1000061035156, 489.3999938964844, 488.5, 488.0...
left_pupil (float64): 724.0, 724.0, 725.0, 727.0, 727.0...
right_x (float64): 682.7999877929688, 679.5, 674.5, 662.7000122070312, 644.2999877929688...
right_y (float64): 505.20001220703125, 502.8999938964844, 501.29998779296875, 499.0, 496.3999938964844...
right_pupil (float64): 637.0, 642.0, 644.0, 639.0, 636.0...
eyes : ['right', 'left']
nblinks : {}
blinks : {'right': None, 'left': None}
params : {}
Info: 1 keys: eyelink_info
History:
*
└ fill_time_discontinuities()
You can also cache a local copy of the file to avoid further downloads. The following command will download the file only the first time and read it from the local file the second time it is run:
[4]:
d=pp.EyeData.from_eyelink(url, cache_file="example_data/test.edf")
pp: 10:43:39 | INFO | read_eyelink:582 | Loading EDF file: example_data/test.edf (current log level: INFO, set to DEBUG to see eyelinkio output)
This works for publicly shared EDF files such as the one under the link https://osf.io/trsuq/download. If you want to load data from a private OSF repository, you will need to authenticate first. To do that, create a “Personal access token” on your OSF page under https://osf.io/settings/tokens.
Copy that token and store it in a variable or a protected file (CAUTION: if you share that token, they will be able to access your private OSF data). Here, I stored my token in a file “my_osf_token.secret” so that the token is not revealed in the documentation:
[2]:
private_url = "https://osf.io/5vkj3/download"
# read the token from the file
with open("my_osf_token.secret") as f:
token = f.read().strip()
# use the token to authenticate to OSF
session = pp.osf_authenticate(token, validate=True)
d = pp.EyeData.from_eyelink(private_url, session=session)
pp: 10:47:38 | INFO | osf_authenticate:81 | OSF token validation succeeded.
tmpml4svjq1: 100%|██████████| 43.9M/43.9M [00:05<00:00, 8.24MiB/s]
pp: 10:47:46 | INFO | read_eyelink:582 | Loading EDF file: /tmp/tmpml4svjq1 (current log level: INFO, set to DEBUG to see eyelinkio output)
pp: 10:48:20 | INFO | from_eyelink:682 | Filtering out Eyelink triggers
The result is an EyeData object containing all the data and samples.
[ ]:
# plot the timeseries for a minute of data (min 10-11)
d.plot_timeseries( (10, 11), units="min")
Note: The EyeData.from_eyelink() function removes Eyelink’s triggers related to calibration and validation. If you want those, you can use keyword arguments
remove_eyelink_triggers=Falseto keep thosereturn_edf_obj=Trueto return the originaleyelinkioobject that contains all information (including saccade detection etc)
[8]:
d,edfobj = pp.EyeData.from_eyelink(private_url, session=session, return_edf_obj=True)
edfobj
tmpr8bngegk: 100%|██████████| 43.9M/43.9M [00:03<00:00, 14.0MiB/s]
pp: 10:53:42 | INFO | read_eyelink:582 | Loading EDF file: /tmp/tmpr8bngegk (current log level: INFO, set to DEBUG to see eyelinkio output)
pp: 10:54:17 | INFO | from_eyelink:682 | Filtering out Eyelink triggers
[8]:
<EDF | tmpr8bngegk>
Version: EYELINK II 1
Eye: BINOCULAR
Pupil unit: PUPIL_AREA
Sampling frequency: 1000.0 Hz
Calibrations: 4
Length: 1905.643 seconds
[10]:
edfobj["discrete"]
[10]:
{'messages': array([( 0. , b'!CAL \n>>>>>>> CALIBRATION (HV9,P-CR) FOR LEFT: <<<<<<<<<'),
( 0. , b'!CAL Calibration points: '),
( 0. , b'!CAL -15.8, -58.2 0, 264 '), ...,
(1875.54 , b'TRIG_TASK_END_253'),
(1905.633, b'TRIG_SESSION_END_249'), (1905.642, b'RECORDING_STOP')],
dtype=[('stime', '<f8'), ('msg', 'S260')]),
'buttons': array([(0., 0.), (0., 0.), (0., 0.), (0., 0.)],
dtype=[('stime', '<f8'), ('buttons', '<f8')]),
'inputs': array([(0., 0.), (0., 0.), (0., 0.), (0., 0.)],
dtype=[('stime', '<f8'), ('input', '<f8')]),
'fixations': array([(0., 7.000000e-03, 2.590000e-01, 971.09997559, 628.5 ),
(1., 1.000000e-02, 2.590000e-01, 986.29998779, 627.59997559),
(1., 3.190000e-01, 4.480000e-01, 644.40002441, 532.20001221), ...,
(1., 1.905359e+03, 1.905453e+03, 1068.19995117, 514.79998779),
(0., 1.905515e+03, 1.905641e+03, 853.5 , 488.5 ),
(1., 1.905506e+03, 1.905641e+03, 858.70001221, 567.40002441)],
dtype=[('eye', '<f8'), ('stime', '<f8'), ('etime', '<f8'), ('axp', '<f8'), ('ayp', '<f8')]),
'saccades': array([(1., 2.600000e-01, 3.180000e-01, 978.70001221, 627.09997559, 655.09997559, 535.70001221, 349.5 ),
(0., 2.600000e-01, 3.490000e-01, 974. , 628.29998779, 651.90002441, 494.1000061 , 265.3999939 ),
(1., 4.490000e-01, 5.050000e-01, 649.70001221, 530.20001221, 405.79998779, 517.59997559, 295.70001221),
...,
(1., 1.905350e+03, 1.905358e+03, 1027.19995117, 563.5 , 1043.90002441, 545.40002441, 76.90000153),
(1., 1.905454e+03, 1.905505e+03, 1074.80004883, 502.70001221, 873.90002441, 562.79998779, 474.3999939 ),
(0., 1.905452e+03, 1.905514e+03, 1045.90002441, 441.20001221, 852.40002441, 488.70001221, 352. )],
dtype=[('eye', '<f8'), ('stime', '<f8'), ('etime', '<f8'), ('sxp', '<f8'), ('syp', '<f8'), ('exp', '<f8'), ('eyp', '<f8'), ('pv', '<f8')]),
'blinks': array([(1., 7.771, 7.866), (0., 7.769, 7.867),
(1., 12.847, 12.948), ..., (1., 1904.197, 1904.301),
(0., 1905.097, 1905.194), (1., 1904.869, 1905.205)],
dtype=[('eye', '<f8'), ('stime', '<f8'), ('etime', '<f8')])}
This file was created from the following Jupyter-notebook: importdata_edf.ipynb
Interactive version:
Interactive version:
