def test_neighboring_tiles():
# fmt: off
arr = Array5D(np.asarray(
[[10, 11, 12, 20, 21, 22, 30], [13, 14, 15, 23, 24, 25, 33],
[16, 17, 18, 26, 27, 28, 36], [40, 41, 42, 50, 51, 52, 60],
[43, 44, 45, 53, 54, 55, 63], [46, 47, 48, 56, 57, 58, 66],
[70, 71, 72, 80, 81, 82, 90], [73, 74, 75, 83, 84, 85, 93],
[76, 77, 78, 86, 87, 88, 96], [0, 1, 2, 3, 4, 5, 6]],
dtype=np.uint8),
axiskeys="yx")
ds = DataSource.create(create_png(arr))
fifties_slice = DataSourceSlice(ds).clamped(
Slice5D(x=slice(3, 6), y=slice(3, 6)))
expected_fifties_slice = Array5D(np.asarray([[50, 51, 52], [53, 54, 55],
[56, 57, 58]]),
axiskeys="yx")
# fmt: on
top_slice = DataSourceSlice(ds, x=slice(3, 6), y=slice(0, 3))
bottom_slice = DataSourceSlice(ds, x=slice(3, 6), y=slice(6, 9))
right_slice = DataSourceSlice(ds, x=slice(6, 7), y=slice(3, 6))
left_slice = DataSourceSlice(ds, x=slice(0, 3), y=slice(3, 6))
# fmt: off
fifties_neighbor_data = {
top_slice:
Array5D(np.asarray([[20, 21, 22], [23, 24, 25], [26, 27, 28]]),
axiskeys="yx"),
right_slice:
Array5D(np.asarray([[60], [63], [66]]), axiskeys="yx"),
bottom_slice:
Array5D(np.asarray([[80, 81, 82], [83, 84, 85], [86, 87, 88]]),
axiskeys="yx"),
left_slice:
Array5D(np.asarray([[40, 41, 42], [43, 44, 45], [46, 47, 48]]),
axiskeys="yx"),
}
expected_fifties_neighbors = {}
# fmt: on
assert (fifties_slice.retrieve().raw("yx") == expected_fifties_slice.raw(
"yx")).all()
for neighbor in fifties_slice.get_neighboring_tiles(
tile_shape=Shape5D(x=3, y=3)):
try:
expected_slice = fifties_neighbor_data.pop(neighbor)
assert (expected_slice.raw("yx") == neighbor.retrieve().raw("yx")
).all()
except KeyError:
print(f"\nWas searching for ", neighbor, "\n")
for k in fifties_neighbor_data.keys():
print("--->>> ", k)
assert len(fifties_neighbor_data) == 0
def test_h5_datasource():
data_2d = Array5D(np.arange(100).reshape(10, 10), axiskeys="yx")
h5_path = create_h5(data_2d, axiskeys_style="vigra", chunk_shape=Shape5D(x=3, y=3))
ds = DataSource.create(h5_path)
assert ds.shape == data_2d.shape
assert ds.tile_shape == Shape5D(x=3, y=3)
slc = Slice5D(x=slice(0, 3), y=slice(0, 2))
assert (ds.retrieve(slc).raw("yx") == data_2d.cut(slc).raw("yx")).all()
data_3d = Array5D(np.arange(10 * 10 * 10).reshape(10, 10, 10), axiskeys="zyx")
h5_path = create_h5(data_3d, axiskeys_style="vigra", chunk_shape=Shape5D(x=3, y=3))
ds = DataSource.create(h5_path)
assert ds.shape == data_3d.shape
assert ds.tile_shape == Shape5D(x=3, y=3)
slc = Slice5D(x=slice(0, 3), y=slice(0, 2), z=3)
assert (ds.retrieve(slc).raw("yxz") == data_3d.cut(slc).raw("yxz")).all()
def test_retrieve_roi_smaller_than_tile():
# fmt: off
data = Array5D(np.asarray([
[[1, 2, 3, 4, 5], [6, 7, 8, 9, 10], [11, 12, 13, 14, 15],
[16, 17, 18, 19, 20]],
[[100, 200, 300, 400, 500], [600, 700, 800, 900, 1000],
[1100, 1200, 1300, 1400, 1500], [1600, 1700, 1800, 1900, 2000]],
]).astype(np.uint32),
axiskeys="cyx")
# fmt: on
path = Path(create_n5(data, chunk_size=Shape5D(c=2, y=4, x=4)))
ds = DataSource.create(path)
print(f"\n\n====>> tile shape: {ds.roi}")
smaller_than_tile = ds.retrieve(
Slice5D.all(c=1, y=slice(0, 4), x=slice(0, 4)))
print(smaller_than_tile.raw("cyx"))
def test_n5_datasource():
# fmt: off
data = Array5D(np.asarray([[1, 2, 3, 4, 5], [6, 7, 8, 9, 10],
[11, 12, 13, 14, 15], [16, 17, 18, 19,
20]]).astype(np.uint8),
axiskeys="yx")
# fmt: on
path = Path(create_n5(data))
ds = DataSource.create(path)
assert ds.shape == data.shape
# fmt: off
expected_raw_piece = Array5D(np.asarray([[1, 2, 3], [6, 7,
8]]).astype(np.uint8),
axiskeys="yx")
# fmt: on
assert ds.retrieve(Slice5D(x=slice(0, 3),
y=slice(0, 2))) == expected_raw_piece
ds2 = pickle.loads(pickle.dumps(ds))
assert ds2.retrieve(Slice5D(x=slice(0, 3),
y=slice(0, 2))) == expected_raw_piece
def tile_equals(tile: DataSource, axiskeys: str, raw: np.ndarray):
return (tile.retrieve().raw(axiskeys) == raw).all()