def test_list_vs(bedmaster_reader: BedmasterReader, empty_matfile: h5py.File):
expected_vs = ["CO", "CUFF", "HR", "SPO2%", "SPO2R"]
assert bedmaster_reader.list_vs() == expected_vs
# No vs on file:
empty_reader = BedmasterReader(empty_matfile.name)
assert empty_reader.list_vs() == []
def test_list_wv(bedmaster_reader: BedmasterReader, empty_matfile: h5py.File):
expected_dict = {
"I": "ch7",
"II": "ch8",
"III": "ch9",
"V": "ch10",
"SPO2": "ch39",
"RESP": "ch40",
}
assert bedmaster_reader.list_wv() == expected_dict
# No wv on file:
empty_reader = BedmasterReader(empty_matfile.name)
assert empty_reader.list_vs() == []
def _write_bedmaster_data(
bedmaster_files: List[str],
writer: Writer,
scaling_and_units: Dict,
):
all_files = True
previous_max = None
untensorized_files: Dict[str, List[str]] = {"file": [], "error": []}
for bedmaster_file in bedmaster_files:
try:
with BedmasterReader(bedmaster_file, scaling_and_units) as reader:
if previous_max:
reader.get_interbundle_correction(previous_max)
# These blocks can be easily parallelized with MPI:
# >>> rank = MPI.COMM_WORLD.rank
# >>> if rank == 1:
vs_signals = reader.list_vs()
for vs_signal_name in vs_signals:
vs_signal = reader.get_vs(vs_signal_name)
if vs_signal:
writer.write_signal(vs_signal)
# >>> if rank == 2
wv_signals = reader.list_wv()
for wv_signal_name, channel in wv_signals.items():
wv_signal = reader.get_wv(channel, wv_signal_name)
if wv_signal:
writer.write_signal(wv_signal)
previous_max = reader.max_segment
except Exception as error:
untensorized_files["file"].append(bedmaster_file)
untensorized_files["error"].append(repr(error))
if len(untensorized_files["file"]) > 0:
all_files = False
return all_files, untensorized_files
def bedmaster_reader(
test_scale_units: Dict[str, Dict[str, Union[int, float, str]]],
) -> Iterator[BedmasterReader]:
with h5py.File(pytest.mat_file, "r") as mat_file:
reader = BedmasterReader(mat_file.filename, test_scale_units)
yield reader