def load_rg_chunk_affinities(regiongraph_storage: Storage,
chunk_path: str) -> np.ndarray:
"""
Extract weighted supervoxel edges from zstd compressed Region Graph
file `chunk_path`.
The unversioned, custom binary file format shall be called RanStruct,
which, as of 2018-08-03, looks like this:
struct RanStruct # Little Endian, not aligned -> 56 Byte
segA1::UInt64
segB1::UInt64
sum_aff1::Float32
sum_area1::UInt64
segA2::UInt64 # same as segA1
segB2::UInt64 # same as segB1
sum_aff2::Float32 # same as sum_aff1
sum_area2::UInt64 # same as sum_area1
end
The big top level Region Graph chunks get requested almost every time,
thus the memoization.
"""
f = regiongraph_storage.get_file(chunk_path)
if not f:
Warning("%s doesn't exist" % chunk_path)
return np.array([], dtype='uint64, uint64, float32, uint64')
dctx = zstd.ZstdDecompressor()
decompressed = dctx.decompress(f)
buf = np.frombuffer(decompressed, dtype='uint64, uint64, float32, uint64')
return np.lib.stride_tricks.as_strided(buf,
shape=tuple(x // 2
for x in buf.shape),
strides=tuple(x * 2
for x in buf.strides),
writeable=False)
def _download_input_chunk(self, bounds):
storage = Storage(self.layer_path, n_threads=0)
relpath = 'build/{}'.format(bounds.to_filename())
return storage.get_file(relpath)