def create_h5(array: Array5D, axiskeys_style: str, chunk_shape: Optional[Shape5D] = None, axiskeys: str = "xyztc"):
raw_chunk_shape = (chunk_shape or Shape5D() * 2).clamped(maximum=array.shape).to_tuple(axiskeys)
path = tempfile.mkstemp()[1] + ".h5"
f = h5py.File(path, "w")
ds = f.create_dataset("data", chunks=raw_chunk_shape, data=array.raw(axiskeys))
if axiskeys_style == "dims":
for key, dim in zip(axiskeys, ds.dims):
dim.label = key
elif axiskeys_style == "vigra":
type_flags = {"x": 2, "y": 2, "z": 2, "t": 2, "c": 1}
axistags = [{"key": key, "typeflags": type_flags[key], "resolution": 0, "description": ""} for key in axiskeys]
ds.attrs["axistags"] = json.dumps({"axes": axistags})
else:
raise Exception(f"Bad axiskeys_style: {axiskeys_style}")
return PurePosixPath(path)
def encode(self, data: Array5D) -> bytes:
return data.raw("xyzc").tobytes("F")
def create_png(array: Array5D) -> PurePosixPath:
png_path = tempfile.mkstemp()[1] + ".png"
skimage.io.imsave(png_path, array.raw("yxc"))
return PurePosixPath(png_path)
def from_array5d(data: Array5D, labels: Optional[Set[int]] = None) -> "ConnectedComponents":
return ConnectedComponents(
data.raw(Point5D.LABELS), axiskeys=Point5D.LABELS, location=data.location, labels=labels
)
