def _read_raw(path_: Path, volume_: Volume):
# from pymicro
return file_utils.HST_read(
str(path_), # it doesn't accept paths...
# pre-loaded kwargs
autoparse_filename=False, # the file names are not properly formatted
data_type=volume.metadata.dtype,
dims=volume.metadata.dimensions,
verbose=True,
)
volume = Volume.with_check(
name=args.volume_name, version=args.volume_version
)
logger.info(f"volume\n{dict2str(asdict(volume))}")
assert volume.nclasses == model_nclasses, f"{model_nclasses=} {volume.nclasses=}"
logger.info("Loading data from disk.")
# Data
voldata = file_utils.HST_read(
str(volume.data_path), # it doesn't accept paths...
autoparse_filename=False, # the file names are not properly formatted
data_type=volume.metadata.dtype,
dims=volume.metadata.dimensions,
verbose=False,
) / volume.normalization_factor
logger.debug(f"{voldata.shape=}")
voldata_train = volume[args.partition_train].get_volume_partition(voldata)
voldata_val = volume[args.partition_val].get_volume_partition(voldata)
logger.debug(f"{voldata_train.shape=}")
logger.debug(f"{voldata_val.shape=}")
del voldata
logger.info("done")
# ##### data
logger.info(f"Loading data from disk at file: {volume.data_path.name}")
logger.debug(f"{volume.data_path=}")
normalization_factor = volume_sequence.NORMALIZE_FACTORS[
volume.metadata.dtype]
logger.debug(f"{normalization_factor=}")
data_volume = file_utils.HST_read(
str(volume.data_path), # it doesn't accept paths...
autoparse_filename=False, # the file names are not properly formatted
data_type=volume.metadata.dtype,
dims=volume.metadata.dimensions,
verbose=True,
) / normalization_factor # normalize
logger.debug(f"{data_volume.shape=}")
if partition is not None:
logger.info(f"Cutting data with {partition.alias=}")
logger.debug(f"{partition=}")
data_volume = partition.get_volume_partition(data_volume)
else:
logger.debug(f"No partition. The whole volume will be processed.")
