def test_anonymize(self):
header = highlevel.make_header(technician='tech',
recording_additional='radd',
patientname='name',
patient_additional='padd',
patientcode='42',
equipment='eeg',
admincode='420',
gender='Male',
birthdate='05.09.1980')
annotations = [[0.01, -1, 'begin'], [0.5, -1, 'middle'],
[10, -1, 'end']]
header['annotations'] = annotations
signal_headers = highlevel.make_signal_headers(
['ch' + str(i) for i in range(3)])
signals = np.random.rand(3, 256 * 300) * 200 #5 minutes of eeg
highlevel.write_edf(self.personalized, signals, signal_headers, header)
highlevel.anonymize_edf(self.personalized,
new_file=self.anonymized,
to_remove=[
'patientname', 'birthdate', 'admincode',
'patientcode', 'technician'
],
new_values=['x', '', 'xx', 'xxx', 'xxxx'],
verify=True,
verbose=True)
new_header = highlevel.read_edf_header(self.anonymized)
self.assertEqual(new_header['birthdate'], '')
self.assertEqual(new_header['patientname'], 'x')
self.assertEqual(new_header['admincode'], 'xx')
self.assertEqual(new_header['patientcode'], 'xxx')
self.assertEqual(new_header['technician'], 'xxxx')
highlevel.anonymize_edf(self.personalized,
to_remove=[
'patientname', 'birthdate', 'admincode',
'patientcode', 'technician'
],
new_values=['x', '', 'xx', 'xxx', 'xxxx'],
verify=True)
new_header = highlevel.read_edf_header(self.personalized[:-4] +
'_anonymized.edf')
self.assertEqual(new_header['birthdate'], '')
self.assertEqual(new_header['patientname'], 'x')
self.assertEqual(new_header['admincode'], 'xx')
self.assertEqual(new_header['patientcode'], 'xxx')
self.assertEqual(new_header['technician'], 'xxxx')
with self.assertRaises(AssertionError):
highlevel.anonymize_edf(self.personalized,
new_file=self.anonymized,
to_remove=[
'patientname', 'birthdate',
'admincode', 'patientcode',
'technician'
],
new_values=['x', '', 'xx', 'xxx'],
verify=True)
"""
Created on Thu Feb 27 14:40:36 2020
add
@author: skjerns
"""
import config
import os
from tqdm import tqdm
import ospath
from pyedflib import highlevel
folder = "Z:/NT1-HRV-data"
new_folder = ospath.join(folder, "new")
os.makedirs(new_folder, exist_ok=True)
mapping = config.mapping_channels
files = ospath.list_files(folder, exts='edf')
for file in tqdm(files):
name = ospath.basename(file)[:-4]
new_file = ospath.join(new_folder, name + ".edf")
if os.path.exists(new_file):
print(f"{new_file} exists, skipping")
continue
highlevel.anonymize_edf(file, new_file, to_remove = ['patientcode', 'patientname'],
new_values = [name, name], verify=False)
highlevel.rename_channels(new_file, mapping=mapping, new_file=new_file)