def parse_ieeg(data, i):
#parsing data DataFrame to get iEEG information
sub_ID = data.iloc[i].RID
iEEG_filename = data.iloc[i].file
ignore_electrodes = data.iloc[i].ignore_electrodes.split(",")
start_time_usec = int(data.iloc[i].connectivity_start_time_seconds * 1e6)
stop_time_usec = int(data.iloc[i].connectivity_end_time_seconds * 1e6)
descriptor = data.iloc[i].descriptor
#Output filename EEG
ofpath_EEG_sub_ID = ospj(ofpath_EEG, f"sub-{sub_ID}")
if not (os.path.isdir(ofpath_EEG_sub_ID)):
os.mkdir(ofpath_EEG_sub_ID
) #if the path doesn't exists, then make the directory
outputfile_EEG = ospj(
f"{ofpath_EEG_sub_ID}",
f"sub-{sub_ID}_{iEEG_filename}_{start_time_usec}_{stop_time_usec}_EEG.csv"
)
print(f"\n\n\nID: {sub_ID}\nDescriptor: {descriptor}")
if (os.path.exists(outputfile_EEG)):
print(f"File already exists: {outputfile_EEG}")
else: #if file already exists, don't run below
get_iEEG_data(username, password, iEEG_filename, start_time_usec,
stop_time_usec, ignore_electrodes, outputfile_EEG)
password = sys.argv[2]
#%% Load Study Meta Data
data = pd.read_excel(ifname_EEG_times)
#%% Get iEEG data
for i in range(len(data)):
#parsing data DataFrame to get iEEG information
sub_ID = data.iloc[i].RID
iEEG_filename = data.iloc[i].file
ignore_electrodes = data.iloc[i].ignore_electrodes.split(",")
start_time_usec = int(data.iloc[i].connectivity_start_time_seconds * 1e6)
stop_time_usec = int(data.iloc[i].connectivity_end_time_seconds * 1e6)
descriptor = data.iloc[i].descriptor
#Output filename EEG
ofpath_EEG_sub_ID = ospj(ofpath_EEG, "sub-{0}".format(sub_ID))
if not (os.path.isdir(ofpath_EEG_sub_ID)):
os.mkdir(ofpath_EEG_sub_ID
) #if the path doesn't exists, then make the directory
outputfile_EEG = "{0}/sub-{1}_{2}_{3}_{4}_EEG.pickle".format(
ofpath_EEG_sub_ID, sub_ID, iEEG_filename, start_time_usec,
stop_time_usec)
print("\n\n\nID: {0}\nDescriptor: {1}".format(sub_ID, descriptor))
if (os.path.exists(outputfile_EEG)):
print("File already exists: {0}".format(outputfile_EEG))
else: #if file already exists, don't run below
get_iEEG_data(username, password, iEEG_filename, start_time_usec,
stop_time_usec, ignore_electrodes, outputfile_EEG)
#%%
if not os.path.exists(patient_directory):
os.makedirs(eeg_directory)
outputfile = os.path.join(
eeg_directory,
"sub-{}_{}_{}_{}_EEG.pickle".format(rid, iEEG_filename,
start_time_usec,
stop_time_usec))
# download data if the file does not already exist
if not os.path.isfile(outputfile):
# start timer
start = time.time()
get_iEEG_data(username, password, iEEG_filename,
start_time_usec, stop_time_usec,
removed_channels, outputfile)
# stop timer
end = time.time()
# report time elapsed
print("Time elapsed = {}".format(
convertSeconds(int(end - start))))
process_count = process_count + 1
else:
print("{} exists, skipping...".format(outputfile))
total_end = time.time()
outputfile = os.path.join(eeg_directory,"sub-{}_{}_{}_{}_EEG.pickle".format(rid,iEEG_filename,start_time_usec,stop_time_usec))
bids_root = os.path.join(parent_directory,'bids_output')
edf_filename = os.path.join(bids_root,"sub-{}".format(rid),"ses-presurgery","ieeg","sub-{}.edf".format(interval_name))
if overwrite_files or not os.path.isfile(edf_filename):
# download data if the file does not already exist
#if not os.path.isfile(outputfile):
# start timer
start = time.time()
try:
true_ignore_electrodes = get_iEEG_data(username, password, iEEG_filename, start_time_usec, stop_time_usec, removed_channels, outputfile, get_all_channels = True, redownload = redownload)
except KeyError:
print("Encountered KeyError: ignore_electrodes are probably named differently on ieeg.org. Skipping...")
continue
except KeyboardInterrupt:
print('Interrupted')
try:
sys.exit()
except SystemExit:
os._exit()
# stop timer
end = time.time()
# report time elapsed
print("Time elapsed = {}".format(convertSeconds(int(end - start))))