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file_utility.py
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import glob
import os
def find_the_file(file_path, pattern, type):
name = None
file_found = True
file_name = None
file_counter = 0
for name in glob.glob(file_path + pattern):
file_counter += 1
pass
if file_counter > 1:
print('There are more than one ' + type + ' files in this folder. This may not be okay.')
if name is not None:
file_name = name.rsplit('\\', 1)[1]
else:
print('The '+ type + ' file(such as ' + pattern + ' )is not here, or it has an unusual name.')
file_found = False
return file_name, file_found
def init_data_file_names(prm, beginning, end):
prm.set_continuous_file_name(beginning)
prm.set_continuous_file_name_end(end)
def set_continuous_data_path(prm):
file_path = prm.get_filepath()
continuous_file_name_1 = '105_CH'
continuous_file_name_end_1 = '_0'
continuous_file_name_2 = '100_CH'
continuous_file_name_end_2 = ''
recording_path = file_path + continuous_file_name_1 + str(1) + continuous_file_name_end_1 + '.continuous'
if os.path.isfile(recording_path) is True:
init_data_file_names(prm, continuous_file_name_1, continuous_file_name_end_1)
recording_path = file_path + continuous_file_name_2 + str(1) + continuous_file_name_end_2 + '.continuous'
if os.path.isfile(recording_path) is True:
init_data_file_names(prm, continuous_file_name_2, continuous_file_name_end_2)
def set_dead_channel_path(prm):
file_path = prm.get_filepath()
dead_ch_path = file_path + "/dead_channels.txt"
prm.set_dead_channel_path(dead_ch_path)
def create_behaviour_folder_structure(prm):
movement_path = prm.get_filepath() + 'Behaviour'
prm.set_behaviour_path(movement_path)
data_path = movement_path + '/Data'
analysis_path = movement_path + '/Analysis'
prm.set_behaviour_data_path(data_path)
prm.set_behaviour_analysis_path(analysis_path)
if os.path.exists(movement_path) is False:
print('Behavioural data will be saved in {}.'.format(movement_path))
os.makedirs(movement_path)
os.makedirs(data_path)
os.makedirs(analysis_path)
# main path is the folder that contains 'recordings' and 'sorting_files'
def get_main_path(prm):
file_path = prm.get_filepath()
main_path = file_path.rsplit('/', 3)[-4]
return main_path
def get_raw_mda_path_all_channels(prm):
raw_mda_path = prm.get_filepath() + 'Electrophysiology/' + prm.get_spike_sorter() + '/raw.mda'
return raw_mda_path
def get_raw_mda_path_separate_tetrodes(prm):
raw_mda_path = '/data/raw.mda'
return raw_mda_path
def folders_for_separate_tetrodes(prm):
ephys_path = prm.get_filepath() + 'Electrophysiology'
spike_path = ephys_path + '/Spike_sorting'
data_path = ephys_path + '/Data'
sorting_t1_path_continuous = spike_path + '/t1'
sorting_t2_path_continuous = spike_path + '/t2'
sorting_t3_path_continuous = spike_path + '/t3'
sorting_t4_path_continuous = spike_path + '/t4'
mountain_data_folder_t1 = spike_path + '/t1/data'
mountain_data_folder_t2 = spike_path + '/t2/data'
mountain_data_folder_t3 = spike_path + '/t3/data'
mountain_data_folder_t4 = spike_path + '/t4/data'
if os.path.exists(ephys_path) is False:
os.makedirs(ephys_path)
os.makedirs(spike_path)
os.makedirs(data_path)
if os.path.exists(sorting_t1_path_continuous) is False:
os.makedirs(sorting_t1_path_continuous)
os.makedirs(sorting_t2_path_continuous)
os.makedirs(sorting_t3_path_continuous)
os.makedirs(sorting_t4_path_continuous)
os.makedirs(mountain_data_folder_t1)
os.makedirs(mountain_data_folder_t2)
os.makedirs(mountain_data_folder_t3)
os.makedirs(mountain_data_folder_t4)
def create_ephys_folder_structure(prm):
ephys_path = prm.get_filepath() + 'Electrophysiology'
prm.set_ephys_path(ephys_path)
data_path = ephys_path + '/' + prm.get_spike_sorter()
if os.path.exists(ephys_path) is False:
os.makedirs(ephys_path)
if os.path.exists(data_path) is False:
os.makedirs(data_path)
def create_folder_structure(prm):
create_behaviour_folder_structure(prm)
create_ephys_folder_structure(prm)
def dead_channels_from_txt_file(dead_channel_txt_file_path):
dead_channels=[]
if os.path.isfile(dead_channel_txt_file_path) is True:
if os.stat(dead_channel_txt_file_path).st_size == 0:
print("theres a dead channel file but no dead channel is given")
else:
dead_channel_reader = open(dead_channel_txt_file_path, 'r')
dead_channels = dead_channel_reader.readlines()
dead_channels = list([x.strip() for x in dead_channels])
return dead_channels