def write_recording(recording: RecordingExtractor,
save_path: PathType,
dtype: DtypeType = None,
**write_binary_kwargs):
"""
Convert and save the recording extractor to Neuroscope format.
Parameters
----------
recording: RecordingExtractor
The recording extractor to be converted and saved.
save_path: str
Path to desired target folder. The name of the files will be the same as the final directory.
dtype: dtype
Optional. Data type to be used in writing; must be int16 or int32 (default).
Will throw a warning if stored recording type from get_traces() does not match.
**write_binary_kwargs: keyword arguments for write_to_binary_dat_format function
- chunk_size
- chunk_mb
"""
save_path = Path(save_path)
save_path.mkdir(parents=True, exist_ok=True)
if save_path.suffix == "":
recording_name = save_path.name
else:
recording_name = save_path.stem
xml_name = recording_name
save_xml_filepath = save_path / f"{xml_name}.xml"
recording_filepath = save_path / recording_name
# create parameters file if none exists
if save_xml_filepath.is_file():
raise FileExistsError(f"{save_xml_filepath} already exists!")
xml_root = et.Element('xml')
et.SubElement(xml_root, 'acquisitionSystem')
et.SubElement(xml_root.find('acquisitionSystem'), 'nBits')
et.SubElement(xml_root.find('acquisitionSystem'), 'nChannels')
et.SubElement(xml_root.find('acquisitionSystem'), 'samplingRate')
recording_dtype = str(recording.get_dtype())
int_loc = recording_dtype.find('int')
recording_n_bits = recording_dtype[(int_loc + 3):(int_loc + 5)]
valid_dtype = ["16", "32"]
if dtype is None:
if int_loc != -1 and recording_n_bits in valid_dtype:
n_bits = recording_n_bits
else:
print(
"Warning: Recording data type must be int16 or int32! Defaulting to int32."
)
n_bits = "32"
dtype = f"int{n_bits}" # update dtype in pass to BinDatRecordingExtractor.write_recording
else:
dtype = str(dtype) # if user passed numpy data type
int_loc = dtype.find('int')
assert int_loc != -1, "Data type must be int16 or int32! Non-integer received."
n_bits = dtype[(int_loc + 3):(int_loc + 5)]
assert n_bits in valid_dtype, "Data type must be int16 or int32!"
xml_root.find('acquisitionSystem').find('nBits').text = n_bits
xml_root.find('acquisitionSystem').find('nChannels').text = str(
recording.get_num_channels())
xml_root.find('acquisitionSystem').find('samplingRate').text = str(
recording.get_sampling_frequency())
et.ElementTree(xml_root).write(str(save_xml_filepath),
pretty_print=True)
recording.write_to_binary_dat_format(recording_filepath,
dtype=dtype,
**write_binary_kwargs)
def write_recording(recording: RecordingExtractor, save_path: PathType, dtype: DtypeType = None,
**write_binary_kwargs):
"""
Convert and save the recording extractor to Neuroscope format.
Parameters
----------
recording: RecordingExtractor
The recording extractor to be converted and saved.
save_path: str
Path to desired target folder. The name of the files will be the same as the final directory.
dtype: dtype
Optional. Data type to be used in writing; must be int16 or int32 (default).
Will throw a warning if stored recording type from get_traces() does not match.
**write_binary_kwargs: keyword arguments for write_to_binary_dat_format function
- chunk_size
- chunk_mb
"""
save_path = Path(save_path)
if not save_path.is_dir():
os.makedirs(save_path)
if save_path.suffix == '':
recording_name = save_path.name
else:
recording_name = save_path.stem
xml_name = recording_name
save_xml_filepath = save_path / (str(xml_name) + '.xml')
recording_filepath = save_path / recording_name
# create parameters file if none exists
if save_xml_filepath.is_file():
raise FileExistsError(f'{save_xml_filepath} already exists!')
soup = BeautifulSoup("", 'xml')
new_tag = soup.new_tag('nbits')
recording_dtype = str(recording.get_dtype())
int_loc = recording_dtype.find('int')
recording_n_bits = recording_dtype[(int_loc + 3):(int_loc + 5)]
if dtype is None: # user did not specify data type
if int_loc != -1 and recording_n_bits in ['16', '32']:
n_bits = recording_n_bits
else:
print('Warning: Recording data type must be int16 or int32! Defaulting to int32.')
n_bits = '32'
dtype = 'int' + n_bits # update dtype in pass to BinDatRecordingExtractor.write_recording
else:
dtype = str(dtype) # if user passed numpy data type
int_loc = dtype.find('int')
assert int_loc != -1, 'Data type must be int16 or int32! Non-integer received.'
n_bits = dtype[(int_loc + 3):(int_loc + 5)]
assert n_bits in ['16', '32'], 'Data type must be int16 or int32!'
new_tag.string = n_bits
soup.append(new_tag)
new_tag = soup.new_tag('nchannels')
new_tag.string = str(recording.get_num_channels())
soup.append(new_tag)
new_tag = soup.new_tag('samplingrate')
new_tag.string = str(recording.get_sampling_frequency())
soup.append(new_tag)
# write parameters file
# create parameters file if none exists
with save_xml_filepath.open("w") as f:
f.write(str(soup))
recording.write_to_binary_dat_format(recording_filepath, dtype=dtype, **write_binary_kwargs)
