def test_build_and_read_nwb(self):
metadata = MetadataManager(
str(path) +
'/rec_to_nwb/rec_to_nwb/test/processing/res/metadata.yml', [
str(path) +
'/rec_to_nwb/rec_to_nwb/test/processing/res/probe1.yml',
str(path) +
'/rec_to_nwb/rec_to_nwb/test/processing/res/probe2.yml',
str(path) +
'/rec_to_nwb/rec_to_nwb/test/processing/res/probe3.yml'
])
builder = RawToNWBBuilder(
animal_name='beans',
data_path=str(path) + '/rec_to_nwb/rec_to_nwb/test/test_data/',
dates=['20190718'],
nwb_metadata=metadata,
output_path='',
extract_spikes=False,
extract_mda=True,
extract_lfps=False,
extract_analog=True,
extract_dio=True,
overwrite=True,
trodes_rec_export_args=_DEFAULT_TRODES_REC_EXPORT_ARGS,
video_path=str(path) + '/rec_to_nwb/rec_to_nwb/test/test_data')
builder.build_nwb()
self.assertTrue(os.path.exists('beans20190718.nwb'))
with pynwb.NWBHDF5IO('beans20190718.nwb', 'r',
load_namespaces=True) as nwb_file_handler:
nwb_file = nwb_file_handler.read()
print(nwb_file)
if os.path.isfile('beans20190718.nwb'):
os.remove('beans20190718.nwb')
class TestRawToNWBGeneration(unittest.TestCase):
def setUp(self):
self.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'
])
self.builder = RawToNWBBuilder(
animal_name='KF2',
data_path=str(path) + '/../test_data/',
dates=['20170120'],
nwb_metadata=self.metadata,
output_path='',
video_path=str(path) + '/../test_data',
extract_spikes=False,
extract_mda=True,
extract_lfps=False,
extract_analog=True,
extract_dio=True,
overwrite=True,
trodes_rec_export_args=_DEFAULT_TRODES_REC_EXPORT_ARGS)
def test_from_raw_to_nwb_generation(self):
self.builder.build_nwb(process_mda_valid_time=False,
process_mda_invalid_time=False,
process_pos_valid_time=False,
process_pos_invalid_time=False)
self.assertTrue(os.path.exists('beans20190718.nwb'),
'NWBFile did not build')
@should_raise(TypeError)
def test_raw_to_nwb_builder_failed_due_to_none_parameters(self):
RawToNWBBuilder(
animal_name='beans',
data_path=str(path) + '/../test_data/',
dates=['20190718'],
nwb_metadata=None,
)
@should_raise(TypeError)
def test_raw_to_nwb_builder_failed_due_to_incorrect_type_parameters(self):
RawToNWBBuilder(animal_name=11111,
data_path=str(path) + '/../test_data/',
dates=['20190718'],
nwb_metadata=self.metadata,
output_path='',
extract_spikes=False,
extract_mda=True,
extract_lfps=False,
extract_analog=True,
extract_dio=True,
overwrite=True,
trodes_rec_export_args=_DEFAULT_TRODES_REC_EXPORT_ARGS)
def convert_kibbles_single_day(animal_name: str,
date: str,
yaml_path='../yaml',
reconfig_file=None):
dates = [date] # single date for now
# Specify the paths for the data, the output nwb file, and the video files
# data are saved in data_path/animal_name/raw/date/*.*
# data_path = '/data2/data1_backup/jason/'
data_path = '/stelmo/jhbak/Data/' # temporary copy with renamed files
out_path = '/stelmo/jhbak/nwb/conversion/' # both preprocessing and NWB
output_path = out_path + animal_name + '/out/'
video_path = out_path + animal_name + '/video/'
# Specify metadata files
animal_metadata_file = '{}_{}_metadata.yml'.format(animal_name, date)
probe_metadata_files = [
'tetrode_12.5.yml',
'32c-2s8mm6cm-20um-40um-dl.yml',
'64c-3s6mm6cm-20um-40um-sl.yml', # kibbles
'64c-4s6mm6cm-20um-40um-dl.yml', # kibbles
]
# specify the locations of the metadata files for the animal and the probe(s).
# Note that specifying all possible probes is fine
animal_metadata = os.path.join(yaml_path, animal_metadata_file)
probe_metadata = [
os.path.join(yaml_path, file) for file in probe_metadata_files
]
# Specify any optional trodes export flags
if reconfig_file is None:
trodes_rec_export_args = ()
else:
trodes_rec_export_args = ('-reconfig', reconfig_file)
metadata = MetadataManager(animal_metadata, probe_metadata)
builder = RawToNWBBuilder(
animal_name=animal_name,
data_path=data_path,
dates=dates,
nwb_metadata=metadata,
overwrite=OVERWRITE,
preprocessing_path=out_path, # new
output_path=output_path,
video_path=video_path,
trodes_rec_export_args=trodes_rec_export_args)
_ = builder.build_nwb(run_preprocessing=RUN_PREPROCESSING)
def test_raw_to_nwb_builder_failed_due_to_none_parameters(self):
RawToNWBBuilder(
animal_name='beans',
data_path=str(path) + '/../test_data/',
dates=['20190718'],
nwb_metadata=None,
)
def setUp(self):
self.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'
])
self.builder = RawToNWBBuilder(
animal_name='KF2',
data_path=str(path) + '/../test_data/',
dates=['20170120'],
nwb_metadata=self.metadata,
output_path='',
video_path=str(path) + '/../test_data',
extract_spikes=False,
extract_mda=True,
extract_lfps=False,
extract_analog=True,
extract_dio=True,
overwrite=True,
trodes_rec_export_args=_DEFAULT_TRODES_REC_EXPORT_ARGS)
def test_raw_to_nwb_builder_failed_due_to_incorrect_type_parameters(self):
RawToNWBBuilder(animal_name=11111,
data_path=str(path) + '/../test_data/',
dates=['20190718'],
nwb_metadata=self.metadata,
output_path='',
extract_spikes=False,
extract_mda=True,
extract_lfps=False,
extract_analog=True,
extract_dio=True,
overwrite=True,
trodes_rec_export_args=_DEFAULT_TRODES_REC_EXPORT_ARGS)
def setUp(self):
self.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'
]
)
self.builder = RawToNWBBuilder(
animal_name='beans',
data_path=str(path) + '/../test_data/',
dates=['20190718'],
nwb_metadata=self.metadata,
output_path='',
video_path=str(path) + '/../test_data',
extract_spikes=False,
extract_mda=True,
extract_lfps=False,
extract_analog=True,
extract_dio=True,
overwrite=True,
trodes_rec_export_args=_DEFAULT_TRODES_REC_EXPORT_ARGS
)
def main():
print('Setting variables', flush=True)
# set the animal name and the date or list of dates to process
# animal_name = 'beans'
# date = '20190718'
# animal_metadata_file = 'beans20190718_metadata.yml'
# reconfig_file = '/stelmo/loren/beans/Probe_128ch_allnT_DIOs_PTP_reconfig_export_shanks.xml'
animal_name = 'despereaux'
date = '20191125'
animal_metadata_file = 'despereaux20191125.yml'
reconfig_file = None
#reconfig_file = '/stelmo/loren/despereaux/raw/20191125/20191125_despereaux_01_s1.rec_header.xml'
# animal_name = 'Jaq'
# date = '20190826'
# animal_metadata_file = 'jaq20190826.yml'
# reconfig_file = None
yaml_path = '/home/loren/Src/NWB/franklabnwb/yaml'
probe1_metadata_file = '128c-4s8mm6cm-20um-40um-sl.yml'
probe2_metadata_file = 'tetrode_12.5.yml'
#Specify the paths for the data, the output nwb file, and the video files
data_path = '/stelmo/loren/'
output_path = '/stelmo/nwb/'
video_path = '/stelmo/nwb/video/'
# data_path = '/Users/loren/data/nwb_builder_test_data/'
# output_path='//Users/loren/data/nwb_builder_test_data/tmp'
# video_path='/Users/loren/data/nwb_builder_test_data/tmp'
# specify the locations of the metadata files for the animal and the probe(s).
# Note that specifying all possible probes is fine
animal_metadata = os.path.join(yaml_path, animal_metadata_file)
probe_metadata = [
os.path.join(yaml_path, probe1_metadata_file),
os.path.join(yaml_path, probe2_metadata_file)
]
print(probe_metadata)
# Specify whether data should be reextracted.
overwrite = False
# metadata parameters
metadata = MetadataManager(animal_metadata, probe_metadata)
print(metadata, flush=True)
print('Creating Builder', flush=True)
if reconfig_file is not None:
# Specify any optional trodes export flags
trodes_rec_export_args = ('-reconfig', reconfig_file)
builder = RawToNWBBuilder(
animal_name=animal_name,
data_path=data_path,
dates=[date],
nwb_metadata=metadata,
overwrite=overwrite,
output_path=output_path,
video_path=video_path,
extract_analog=True,
trodes_rec_export_args=trodes_rec_export_args)
else:
builder = RawToNWBBuilder(animal_name=animal_name,
data_path=data_path,
dates=[date],
nwb_metadata=metadata,
overwrite=overwrite,
output_path=output_path,
video_path=video_path,
extract_analog=True)
print('Building and Writing', flush=True)
builder.build_nwb(process_mda_valid_time='False',
process_mda_invalid_time='False',
process_pos_valid_time='False',
process_pos_invalid_time='False')
print('Done', flush=True)
class TestRawToNWBGeneration(unittest.TestCase):
def setUp(self):
self.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'
]
)
self.builder = RawToNWBBuilder(
animal_name='beans',
data_path=str(path) + '/../test_data/',
dates=['20190718'],
nwb_metadata=self.metadata,
output_path='',
video_path=str(path) + '/../test_data',
extract_spikes=False,
extract_mda=True,
extract_lfps=False,
extract_analog=True,
extract_dio=True,
overwrite=True,
trodes_rec_export_args=_DEFAULT_TRODES_REC_EXPORT_ARGS
)
def test_from_raw_to_nwb_generation(self):
self.builder.build_nwb(
process_mda_valid_time=True,
process_mda_invalid_time=True,
process_pos_valid_time=True,
process_pos_invalid_time=True
)
self.assertTrue(os.path.exists('beans20190718.nwb'), 'NWBFile did not build')
@should_raise(TypeError)
def test_raw_to_nwb_builder_failed_due_to_none_parameters(self):
RawToNWBBuilder(
animal_name='beans',
data_path=str(path) + '/../test_data/',
dates=['20190718'],
nwb_metadata=None,
)
@should_raise(TypeError)
def test_raw_to_nwb_builder_failed_due_to_incorrect_type_parameters(self):
RawToNWBBuilder(
animal_name=11111,
data_path=str(path) + '/../test_data/',
dates=['20190718'],
nwb_metadata=self.metadata,
output_path='',
extract_spikes=False,
extract_mda=True,
extract_lfps=False,
extract_analog=True,
extract_dio=True,
overwrite=True,
trodes_rec_export_args=_DEFAULT_TRODES_REC_EXPORT_ARGS
)
def tearDown(self):
self.builder.cleanup()