def test_nwb_file_builder_failed_due_to_None_parameter(self):
NWBFileBuilder(data_path=str(path) + '/test_data/',
animal_name='beans',
date=None,
nwb_metadata=self.metadata,
process_dio=True,
process_mda=True,
process_analog=True)
def build_nwb(self,
process_mda_valid_time=True,
process_mda_invalid_time=True,
process_pos_valid_time=True,
process_pos_invalid_time=True):
"""Builds nwb file for experiments from given dates.
Args:
process_mda_valid_time (boolean): True if the mda valid times should be build and append to nwb.
Need the mda data inside the nwb. (default True)
process_mda_invalid_time (boolean): True if the mda invalid times should be build and append to nwb.
Need the mda data inside the nwb. (default True)
process_pos_valid_time (boolean): True if the pos valid times should be build and append to nwb.
Need the pos data inside the nwb. (default True)
process_pos_invalid_time (boolean): True if the pos invalid times should be build and append to nwb.
Need the pos data inside the nwb. (default True)
"""
self.__preprocess_data()
os.makedirs(self.output_path, exist_ok=True)
os.makedirs(self.video_path, exist_ok=True)
for date in self.dates:
nwb_builder = NWBFileBuilder(
data_path=self.data_path,
animal_name=self.animal_name,
date=date,
nwb_metadata=self.nwb_metadata,
output_file=self.output_path + self.animal_name + date +
".nwb",
process_mda=self.extract_mda,
process_dio=self.extract_dio,
process_analog=self.extract_analog,
video_path=self.video_path,
reconfig_header=self.__get_header_path()
#reconfig_header=self.__is_rec_config_valid()
)
content = nwb_builder.build()
nwb_builder.write(content)
self.append_to_nwb(
nwb_builder=nwb_builder,
process_mda_valid_time=process_mda_valid_time,
process_mda_invalid_time=process_mda_invalid_time,
process_pos_valid_time=process_pos_valid_time,
process_pos_invalid_time=process_pos_invalid_time)
def test_old_nwb_file_builder_failed_due_to_incorrect_type_of_parameters(
self):
NWBFileBuilder(data_path=str(path) + '/test_data/',
animal_name='beans',
date=123,
nwb_metadata=self.metadata,
process_dio=True,
process_mda=True,
process_analog=True)
def setUpClass(cls):
cls.metadata = MetadataManager(
'C:/Users/wmery/PycharmProjects/rec_to_nwb/rec_to_nwb/test/test_data/KF2/raw/20170120/kibbles20170216_metadata.yml',
[
'C:/Users/wmery/PycharmProjects/rec_to_nwb/rec_to_nwb/test/test_data/KF2/raw/20170120/64c-3s6mm6cm-20um-40um-sl.yml',
'C:/Users/wmery/PycharmProjects/rec_to_nwb/rec_to_nwb/test/test_data/KF2/raw/20170120/64c-4s6mm6cm-20um-40um-dl.yml'
])
cls.nwb_builder = NWBFileBuilder(data_path=str(path) + '/test_data/',
animal_name='KF2',
date='20170120',
nwb_metadata=cls.metadata,
process_dio=True,
process_mda=True,
process_analog=True,
process_pos_timestamps=True,
video_path=str(path) + '/test_data')
def setUpClass(cls):
cls.metadata = MetadataManager(
str(path) + '/processing/res/metadata.yml', [
str(path) + '/processing/res/probe1.yml',
str(path) + '/processing/res/probe2.yml',
str(path) + '/processing/res/probe3.yml'
])
cls.nwb_builder = NWBFileBuilder(data_path=str(path) + '/test_data/',
animal_name='beans',
date='20190718',
nwb_metadata=cls.metadata,
process_dio=True,
process_mda=True,
process_analog=True,
process_pos_timestamps=True,
video_path=str(path) + '/test_data')
def get_nwb_builder(self, date):
if self.is_old_dataset:
old_dataset_kwargs = dict(
is_old_dataset=True,
session_start_time=_DEFAULT_SESSION_START_TIME)
else:
old_dataset_kwargs = dict()
return NWBFileBuilder(
data_path=self.data_path,
animal_name=self.animal_name,
date=date,
nwb_metadata=self.nwb_metadata,
output_file=os.path.join(self.output_path,
self.animal_name + date + ".nwb"),
process_mda=self.extract_mda,
process_dio=self.extract_dio,
process_analog=self.extract_analog,
preprocessing_path=self.preprocessing_path,
video_path=self.video_path,
reconfig_header=self.__get_header_path(),
# reconfig_header=self.__is_rec_config_valid()
**old_dataset_kwargs)