def __init__(self, path: Path, *, location: Point5D = Point5D.zero(), filesystem: FS):
try:
raw_data = skimage.io.imread(filesystem.openbin(path.as_posix()))
except ValueError:
raise UnsupportedUrlException(path)
axiskeys = "yxc"[: len(raw_data.shape)]
super().__init__(url=filesystem.desc(path.as_posix()), data=raw_data, axiskeys=axiskeys, location=location)
def openDataset(cls, path: Path, filesystem: FS) -> Tuple[h5py.Dataset, Path, Path]:
outer_path = path
dataset_path_components: List[str] = []
while True:
try:
info = filesystem.getinfo(outer_path.as_posix())
if not info.is_file:
raise UnsupportedUrlException(path.as_posix())
break
except ResourceNotFound as e:
dataset_path_components.insert(0, outer_path.name)
parent = outer_path.parent
if parent == outer_path:
raise UnsupportedUrlException(path.as_posix())
outer_path = parent
try:
binfile = filesystem.openbin(outer_path.as_posix())
f = h5py.File(binfile, "r")
except OSError as e:
raise UnsupportedUrlException(path) from e
try:
inner_path = "/".join(dataset_path_components)
dataset = f[inner_path]
if not isinstance(dataset, h5py.Dataset):
raise ValueError(f"{inner_path} is not a h5py.Dataset")
except Exception as e:
f.close()
raise e
return dataset, outer_path, Path(inner_path)
def load(cls, path: Path, filesystem: FileSystem) -> "N5DatasetAttributes":
with filesystem.openbin(
path.joinpath("attributes.json").as_posix(), "r") as f:
attributes_json = f.read().decode("utf8")
raw_attributes = json.loads(attributes_json)
return cls.from_json_data(raw_attributes)
