def synthetic_stack(
cls,
num_round: int = 4,
num_ch: int = 4,
num_z: int = 12,
tile_height: int = 50,
tile_width: int = 40,
tile_fetcher: TileFetcher = None,
) -> "ImageStack":
"""generate a synthetic ImageStack
Returns
-------
ImageStack :
imagestack containing a tensor whose default shape is (2, 3, 4, 30, 20)
and whose default values are all 1.
"""
if tile_fetcher is None:
tile_fetcher = tile_fetcher_factory(
OnesTile,
False,
(tile_height, tile_width),
)
collection = build_image(
1,
num_round,
num_ch,
num_z,
tile_fetcher,
)
tileset = list(collection.all_tilesets())[0][1]
return ImageStack(tileset)
def test_missing_extras():
"""
If the extras are not present on some of the tiles, it should still work.
"""
class OnesTilesWithExtrasMostly(OnesTile):
def __init__(self, fov, r, ch, z, extras: dict) -> None:
super().__init__((10, 10))
self.fov = fov
self._extras = extras
@property
def extras(self):
if self.fov == 0:
return None
return self._extras
tile_fetcher = tile_fetcher_factory(OnesTilesWithExtrasMostly, True,
{'random_key': {
'hello': "world",
}})
stack = ImageStack.synthetic_stack(
num_round=NUM_ROUND,
num_ch=NUM_CH,
num_z=NUM_Z,
tile_fetcher=tile_fetcher,
)
table = stack.tile_metadata
assert len(table) == NUM_ROUND * NUM_CH * NUM_Z
def test_conflict():
"""
Tiles that have extras that conflict with indices should produce an error.
"""
tile_fetcher = tile_fetcher_factory(OnesTilesWithExtras, False,
{Indices.ROUND: {
'hello': "world",
}})
stack = ImageStack.synthetic_stack(
num_round=NUM_ROUND,
num_ch=NUM_CH,
num_z=NUM_Z,
tile_fetcher=tile_fetcher,
)
with pytest.raises(ValueError):
stack.tile_metadata
def test_metadata():
"""
Normal situation where all the tiles have uniform keys for both indices and extras.
"""
tile_fetcher = tile_fetcher_factory(OnesTilesWithExtras, False,
{'random_key': {
'hello': "world",
}})
stack = ImageStack.synthetic_stack(
num_round=NUM_ROUND,
num_ch=NUM_CH,
num_z=NUM_Z,
tile_fetcher=tile_fetcher,
)
table = stack.tile_metadata
assert len(table) == NUM_ROUND * NUM_CH * NUM_Z