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Resolve #544 : refactor RawToNWBBuilder for easier workflow #545

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Resolve #544 : refactor RawToNWBBuilder for easier workflow #545

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88c1edc
separate a private method __build_nwb_files
jihyunbak Nov 7, 2020
ab5a682
add method get_nwb_builder to RawToNWBBuilder
jihyunbak Nov 12, 2020
ab5cd41
Merge branch 'master' into refactor-raw-to-nwb-builder
jihyunbak Nov 24, 2020
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40 changes: 27 additions & 13 deletions rec_to_nwb/processing/builder/raw_to_nwb_builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -147,19 +147,20 @@ def build_nwb(self, process_mda_valid_time=True, process_mda_invalid_time=True,
"""

self.__preprocess_data()

self.__build_nwb_file(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 __build_nwb_file(self, process_mda_valid_time=True, process_mda_invalid_time=True,
process_pos_valid_time=True, process_pos_invalid_time=True):
logger.info('Building NWB files')
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.__is_rec_config_valid()
)
logger.info('Date: {}'.format(date))
nwb_builder = self.get_nwb_builder(date)
content = nwb_builder.build()
nwb_builder.write(content)
self.append_to_nwb(
Expand All @@ -170,6 +171,20 @@ def build_nwb(self, process_mda_valid_time=True, process_mda_invalid_time=True,
process_pos_invalid_time=process_pos_invalid_time
)

def get_nwb_builder(self, date):
return 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.__is_rec_config_valid()
)

def __preprocess_data(self):
"""process data with rec_to_binaries library"""

Expand Down Expand Up @@ -241,4 +256,3 @@ def cleanup(self):
preprocessing = self.data_path + '/' + self.animal_name + '/preprocessing'
if os.path.exists(preprocessing):
shutil.rmtree(preprocessing)