def from_json_data(cls,
data: JsonValue,
location_override: Optional[Point5D] = None
) -> "N5DatasetAttributes":
raw_attributes = ensureJsonObject(data)
dimensions = ensureJsonIntArray(raw_attributes.get("dimensions"))
blockSize = ensureJsonIntArray(raw_attributes.get("blockSize"))
axes = raw_attributes.get("axes")
if axes is None:
axiskeys = guess_axiskeys(dimensions)
else:
axiskeys = "".join(ensureJsonStringArray(axes)[::-1]).lower()
location = raw_attributes.get("location")
if location is None:
location_5d = Point5D.zero()
else:
location_5d = Point5D.zero(
**dict(zip(axiskeys,
ensureJsonIntArray(location)[::-1])))
return N5DatasetAttributes(
blockSize=Shape5D.create(raw_shape=blockSize[::-1],
axiskeys=axiskeys),
dimensions=Shape5D.create(raw_shape=dimensions[::-1],
axiskeys=axiskeys),
dataType=np.dtype(ensureJsonString(raw_attributes.get(
"dataType"))).newbyteorder(">"), # type: ignore
axiskeys=axiskeys,
compression=N5Compressor.from_json_data(
raw_attributes["compression"]),
location=location_override or location_5d,
)
def __init__(self,
*,
outer_path: PurePosixPath,
inner_path: PurePosixPath,
location: Point5D = Point5D.zero(),
filesystem: JsonableFilesystem,
spatial_resolution: Optional[Tuple[int, int, int]] = None):
self.outer_path = outer_path
self.inner_path = inner_path
self.filesystem = filesystem
binfile = filesystem.openbin(outer_path.as_posix())
# FIXME: h5py might not like this if the filesystem isn't OSFS
f = h5py.File(binfile, "r") #type: ignore
try:
dataset = f[inner_path.as_posix()]
if not isinstance(dataset, h5py.Dataset):
raise ValueError(f"{inner_path} is not a Dataset")
self.axiskeys = self.getAxisKeys(dataset)
self._dataset = dataset
tile_shape = Shape5D.create(raw_shape=self._dataset.chunks
or self._dataset.shape,
axiskeys=self.axiskeys)
base_url = Url.parse(filesystem.geturl(outer_path.as_posix()))
assert base_url is not None
super().__init__(
c_axiskeys_on_disk=self.axiskeys,
tile_shape=tile_shape,
interval=Shape5D.create(
raw_shape=self._dataset.shape,
axiskeys=self.axiskeys).to_interval5d(location),
dtype=self._dataset.dtype,
spatial_resolution=spatial_resolution or (1, 1, 1), # FIXME
filesystem=filesystem,
path=self.outer_path)
except Exception as e:
f.close()
raise e