def get_data_lazy(image: ImageWrapper, c_index: int = 0) -> da.Array:
"""Get n-dimensional dask array, with delayed reading from OMERO image."""
size_z = image.getSizeZ()
size_t = image.getSizeT()
size_x = image.getSizeX()
size_y = image.getSizeY()
pixels = image.getPrimaryPixels()
@delayed
@timer
def get_plane(plane_name):
z, c, t = [int(n) for n in plane_name.split(",")]
p = pixels.getPlane(z, c, t)
return p
dtype = PIXEL_TYPES.get(pixels.getPixelsType().value, None)
plane_names = [
f"{z},{c_index},{t}" for t in range(size_t) for z in range(size_z)
]
lazy_arrays = [get_plane(pn) for pn in plane_names]
dask_arrays = [
da.from_delayed(delayed_reader, shape=(size_y, size_x), dtype=dtype)
for delayed_reader in lazy_arrays
]
# Stack into one large dask.array
if size_z == 1 or size_t == 1:
return da.stack(dask_arrays, axis=0)
z_stacks = []
for t in range(size_t):
z_stacks.append(
da.stack(dask_arrays[t * size_z:(t + 1) * size_z], axis=0))
stack = da.stack(z_stacks, axis=0)
return stack
def get_data_lazy(image: ImageWrapper) -> da.Array:
"""Get 5D dask array, with delayed reading from OMERO image."""
nt, nc, nz, ny, nx = [getattr(image, f'getSize{x}')() for x in 'TCZYX']
pixels = image.getPrimaryPixels()
dtype = PIXEL_TYPES.get(pixels.getPixelsType().value, None)
get_plane = delayed(timer(lambda idx: pixels.getPlane(*idx)))
def get_lazy_plane(zct):
return da.from_delayed(get_plane(zct), shape=(ny, nx), dtype=dtype)
# 5D stack: TCZXY
t_stacks = []
for t in range(nt):
c_stacks = []
for c in range(nc):
z_stack = []
for z in range(nz):
z_stack.append(get_lazy_plane((z, c, t)))
c_stacks.append(da.stack(z_stack))
t_stacks.append(da.stack(c_stacks))
return da.stack(t_stacks)