def test_list_folders(self):
path = ospath.abspath('.')
folder1 = ospath.join(path, 'folder1') + '/'
sub1 = ospath.join(path, 'folder1', 'subfolder') + '/'
folders = ospath.list_folders(path, subfolders=False, add_parent=False)
self.assertEqual(folders, [folder1])
folders = ospath.list_folders(path, subfolders=False, add_parent=True)
self.assertEqual(folders, [path, folder1])
folders = ospath.list_folders(path, subfolders=True, add_parent=False)
self.assertEqual(folders, [folder1, sub1])
folders = ospath.list_folders(path, subfolders=True, add_parent=True)
self.assertEqual(folders, [path, folder1, sub1])
def __init__(self, patient_list: list = None, readonly=False):
"""
Load a list of Patients (edf format). Resample if necessary.
:param patient_list: A list of strings pointing to Patients
"""
if isinstance(patient_list, str):
patient_list = ospath.list_folders(patient_list)
assert isinstance(patient_list, list), 'patient_list must be type list'
self.patients = []
# return if list is empty
if len(patient_list) == 0: return None
# must be either Patients or strings to make patients from.
all_patients = all(['Patient' in str(type(x)) for x in patient_list])
all_strings = all([isinstance(x, str) for x in patient_list])
assert all_patients or all_strings, \
"patient_list must be either strings or Patients"
if all_strings: # natural sorting of file list
patient_list = sorted(patient_list, key=natsort_key)
tqdm_loop = tqdm if all_strings else lambda x, *args, **kwargs: x
for patient in tqdm_loop(patient_list, desc='Loading Patients'):
try:
patient = Patient(patient, readonly=readonly)
self.add(patient)
except Exception as e:
print('Error in', patient)
raise e
return None
def index(folder):
folders = ospath.list_folders(folder)
folders = [f for f in folders if not any([x in f for x in EXCLUDED])]
files = folders + ospath.list_files(folder, relative=True)
fnames = [fname for fname in sorted(files) if fname not in EXCLUDED]
header = os.path.basename(folder)
html = Template(INDEX_TEMPLATE).render(names=fnames, header=header)
return html
def main(root):
folders = ospath.list_folders(root, subfolders=True, add_parent=True)
folders = [f for f in folders if not any([exc in f for exc in EXCLUDED])]
for folder in folders:
print(f'index for {folder}')
if '.git' in folder: continue
if 'joblib' in folder: continue
html = index(folder)
with open(folder + '/index.html', 'w') as f:
f.write(html)
import numpy as np
import config as cfg
import scipy
import scipy.signal as signal
from sleep import SleepSet
import seaborn as sns
import matplotlib.pyplot as plt
from tqdm import tqdm
import plotting
import ospath
from itertools import permutations
plt.close('all')
stimer.start('All calculations')
files = ospath.list_folders(cfg.folder_unisens)
stimer.start()
ss = SleepSet(files, readonly=True)
stimer.stop()
# ss = ss.filter(lambda x: 'body' in x) # only take patients with body position sensors
# ss = ss.filter(lambda x: x.drug_hrv==0 and x.drug_sleep==0)
ss = ss.stratify() # only use matched participants
p = ss[2]
# apply this type of pvalue correction per table,
# see from statsmodels.stats.multitest.multipletests
correction = 'holm'
# only analyse the first 3 REM cycles
max_epochs = int(2 * 60 * 4.5)