Note
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Apply bipolar montage to depth electrodesΒΆ
This scripts shows a very simple example on how to create an Interface wrapping a desired function of a Matlab toolbox (FieldTrip).
The input data should be a .mat file containing a FieldTrip data struct
# Authors: Annalisa Pascarella <a.pascarella@iac.cnr.it>
# License: BSD (3-clause)
import os.path as op
import ephypype
from ephypype.nodes.FT_tools import Reference
from ephypype.datasets import fetch_ieeg_dataset
Let us fetch the data first. It is around 675 MB download.
base_path = op.join(op.dirname(ephypype.__file__), '..', 'examples')
data_path = fetch_ieeg_dataset(base_path)
import json # noqa
import pprint # noqa
params = json.load(open("params.json"))
pprint.pprint({'time frequency parameters': params["tfr"]})
ft_path = params["tfr"]['fieldtrip_path']
refmethod = params["tfr"]['refmethod']
channels_name = params["tfr"]['channels_name']
# channels_name = '{\'RAM*\', \'RHH*\', \'RTH*\', \'ROC*\', \'LAM*\',\'LHH*\', \'LTH*\'}' # noqa
# Now we call the interface Reference to apply a bipolar montage to sEEG data
reference_if = Reference()
reference_if.inputs.data_file = op.join(data_path, 'SubjectUCI29_data.mat')
reference_if.inputs.channels = channels_name
reference_if.inputs.ft_path = ft_path
reference_if.inputs.refmethod = refmethod
reference_if.inputs.script = ''
out = reference_if.run()
print('Rereferenced data saved at {}'.format(out.outputs.data_output))
Total running time of the script: ( 0 minutes 0.000 seconds)