def __get_mda_timestamps(nwb_content):
try:
timestamps = np.array(
nwb_content.acquisition['e-series'].timestamps)
except KeyError:
raise MissingDataException('MDA timestamps are not found')
if timestamps.any():
return timestamps
raise MissingDataException('MDA timestamps are not found')
def __extract_data_for_single_dataset(self, dataset):
data_from_current_dataset = self.__get_data_from_current_dataset(dataset)
if not self.__data_exist(data_from_current_dataset, dataset):
raise MissingDataException("Incomplete data in dataset " + str(dataset.name) + ", missing mda files")
return data_from_current_dataset, [dataset.get_mda_timestamps()], dataset.get_continuous_time()
def create_summary(self):
missing_metadata = self.__get_missing_metadata()
if missing_metadata:
message = ''
for missing_metadata_file in missing_metadata:
message += missing_metadata_file + '\n'
raise (MissingDataException(message))
return MetadataValidationSummary(missing_metadata)
def __build_fl_shanks(self, probe_metadata, shanks_electrodes):
for shank in probe_metadata['shanks']:
shanks_electrodes_in_shank = []
for _ in shank['electrodes']:
if shanks_electrodes:
shanks_electrodes_in_shank.append(shanks_electrodes.pop(0))
else:
raise MissingDataException('Not enough shanks_electrodes')
yield self.__build_single_fl_shank(shank['shank_id'],
shanks_electrodes_in_shank)
def __get_pos_timestamps(nwb_content):
timestamps = [
np.array(spatial_series.timestamps)
for spatial_series in nwb_content.processing['behavior'].
data_interfaces['position'].spatial_series.values()
]
timestamp = np.hstack(timestamps)
if timestamp.any():
return timestamp
raise MissingDataException('POS timestamps are not found!')
def create_summary(self):
"""Creates ValidationSummary object with the results of validation
Returns:
PreprocessingValidationSummary: missing preprocessing files
"""
missing_preprocessing_data = self.__get_missing_preprocessing_data()
message = ''
if missing_preprocessing_data:
for missing_preprocessing_file in missing_preprocessing_data:
message += missing_preprocessing_file[
0] + ' from epoch ' + missing_preprocessing_file[1] + '\n'
raise MissingDataException(message + "are missing")
return PreprocessingValidationSummary(missing_preprocessing_data)
def __extract_data(self):
all_pos = []
continuous_time = []
for dataset in self.datasets:
data_from_current_dataset = [
dataset.get_data_path_from_dataset('pos') + pos_file for pos_file in
dataset.get_all_data_from_dataset('pos') if
(pos_file.endswith('.pos_online.dat'))]
if dataset.get_continuous_time() is None:
raise MissingDataException(
'Incomplete data in dataset '
+ str(dataset.name)
+ 'missing continuous time file')
all_pos.append(data_from_current_dataset)
continuous_time.append(dataset.get_continuous_time())
return all_pos, continuous_time
def __extract_data(self):
"""Gets online position tracking file and corresponding continuous
time file"""
all_position_directories = []
continuous_time_directories = []
for dataset in self.datasets:
pos_online_paths = [
os.path.join(dataset.get_data_path_from_dataset('pos'),
pos_file)
for pos_file in dataset.get_all_data_from_dataset('pos')
if pos_file.endswith('.pos_online.dat')
]
if dataset.get_continuous_time() is None:
raise MissingDataException('Incomplete data in dataset ' +
str(dataset.name) +
'missing continuous time file')
all_position_directories.append(pos_online_paths)
continuous_time_directories.append(dataset.get_continuous_time())
return all_position_directories, continuous_time_directories
def validate_sections(self):
if 'experimenter_name' not in self.metadata:
raise MissingDataException('metadata is missing experimenter_name')
if 'lab' not in self.metadata:
raise MissingDataException('metadata is missing lab')
if 'institution' not in self.metadata:
raise MissingDataException('metadata is missing institution')
if 'experiment_description' not in self.metadata:
raise MissingDataException(
'metadata is missing experiment_description')
if 'session_description' not in self.metadata:
raise MissingDataException(
'metadata is missing session_description')
if 'session_id' not in self.metadata:
raise MissingDataException('metadata is missing session_id')
if 'subject' not in self.metadata:
raise MissingDataException('metadata is missing subject')
if 'units' not in self.metadata:
raise MissingDataException('metadata is missing units')
if 'data_acq_device' not in self.metadata:
raise MissingDataException('metadata is missing data_acq_device')
if 'cameras' not in self.metadata:
raise MissingDataException('metadata is missing cameras')
if 'tasks' not in self.metadata:
raise MissingDataException('metadata is missing tasks')
if 'associated_files' not in self.metadata:
raise MissingDataException('metadata is missing associated_files')
if 'associated_video_files' not in self.metadata:
raise MissingDataException(
'metadata is missing associated_video_files')
if 'times_period_multiplier' not in self.metadata:
raise MissingDataException(
'metadata is missing times_period_multiplier')
if 'behavioral_events' not in self.metadata:
raise MissingDataException('metadata is missing behavioral_events')
if 'electrode_groups' not in self.metadata:
raise MissingDataException('metadata is missing electrode_groups')
if 'ntrode_electrode_group_channel_map' not in self.metadata:
raise MissingDataException(
'metadata is missing ntrode_electrode_group_channel_map')
def __check_if_path_exists(self, path):
if not (os.path.exists(path)):
raise MissingDataException('missing ' + self.data_path +
' directory')
def create_summary(self):
if not os.path.exists(self.path):
raise MissingDataException('xml file ' + self.path + ' does not exist!')
return XmlFilesValidationSummary()