def __init__(self,
path: Path,
*,
location: Point5D = Point5D.zero(),
filesystem: FS):
url = filesystem.geturl(path.as_posix())
match = re.search(r"[^/]+\.n5/.*$", url, re.IGNORECASE)
if not match:
raise UnsupportedUrlException(url)
name = match.group(0)
self.filesystem = filesystem.opendir(path.as_posix())
with self.filesystem.openbin("attributes.json", "r") as f:
attributes_json_bytes = f.read()
attributes = json.loads(attributes_json_bytes.decode("utf8"))
dimensions = attributes["dimensions"][::-1]
blockSize = attributes["blockSize"][::-1]
axiskeys = "".join(attributes["axes"]).lower(
)[::-1] if "axes" in attributes else guess_axiskeys(dimensions)
super().__init__(
url=url,
name=name,
tile_shape=Shape5D.create(raw_shape=blockSize, axiskeys=axiskeys),
shape=Shape5D.create(raw_shape=dimensions, axiskeys=axiskeys),
dtype=np.dtype(attributes["dataType"]).newbyteorder(">"),
location=location,
axiskeys=axiskeys,
)
self.compression_type = attributes["compression"]["type"]
if self.compression_type not in N5Block.DECOMPRESSORS.keys():
raise NotImplementedError(
f"Don't know how to decompress from {self.compression_type}")
def from_filesystem(cls, filesystem: FileSystem) -> "Protocol":
if isinstance(filesystem, OSFS):
return Protocol.FILE
return Url.parse(filesystem.geturl("")).protocol #FIXME: is this reliable ?
