def test_set_slice_range():
"""
Sets a slice across a range of one of the dimensions.
"""
stack = synthetic_stack()
zrange = slice(1, 3)
Y, X = stack.tile_shape
expected = np.ones((stack.shape[Indices.HYB], stack.shape[Indices.CH],
zrange.stop - zrange.start, Y, X)) * 10
index = {Indices.Z: zrange}
stack.set_slice(index, expected)
assert np.array_equal(stack.get_slice(index)[0], expected)
def test_set_slice_middle_index():
"""
Sets a slice across one of the indices in the middle. For instance, if the dimensions are
(P, Q0,..., Qn-1, R), slice across one of the Q axes.
"""
stack = synthetic_stack()
ch = 1
Y, X = stack.tile_shape
expected = np.ones(
(stack.shape[Indices.HYB], stack.shape[Indices.Z], Y, X)) * 2
index = {Indices.CH: ch}
stack.set_slice(index, expected)
assert np.array_equal(stack.get_slice(index)[0], expected)
def test_set_slice_simple_index():
"""
Sets a slice across one of the indices at the end. For instance, if the dimensions are
(P, Q0,..., Qn-1, R), sets a slice across either P or R.
"""
stack = synthetic_stack()
hyb = 1
Y, X = stack.tile_shape
expected = np.ones(
(stack.shape[Indices.CH], stack.shape[Indices.Z], Y, X)) * 2
index = {Indices.HYB: hyb}
stack.set_slice(index, expected)
assert np.array_equal(stack.get_slice(index)[0], expected)
def test_conflict():
"""
Tiles that have extras that conflict with indices should produce an error.
"""
def tile_extras_provider(hyb: int, ch: int, z: int) -> Any:
return {
Indices.HYB: hyb,
Indices.CH: ch,
Indices.Z: z,
}
stack = synthetic_stack(
tile_extras_provider=tile_extras_provider,
)
with pytest.raises(ValueError):
stack.tile_metadata
def test_get_slice_range():
"""
Retrieve a slice across a range of one of the dimensions.
"""
stack = synthetic_stack()
zrange = slice(1, 3)
imageslice, axes = stack.get_slice({Indices.Z: zrange})
Y, X = stack.tile_shape
assert axes == [Indices.HYB, Indices.CH, Indices.Z]
for hyb in range(stack.shape[Indices.HYB]):
for ch in range(stack.shape[Indices.CH]):
for z in range(zrange.stop - zrange.start):
data = np.empty((Y, X))
data.fill((hyb * stack.shape[Indices.CH] + ch) *
stack.shape[Indices.Z] + (z + zrange.start))
assert data.all() == imageslice[hyb, ch, z].all()
def test_metadata():
"""
Normal situation where all the tiles have uniform keys for both indices and extras.
"""
def tile_extras_provider(hyb: int, ch: int, z: int) -> Any:
return {
'random_key': {
Indices.HYB: hyb,
Indices.CH: ch,
Indices.Z: z,
}
}
stack = synthetic_stack(
tile_extras_provider=tile_extras_provider,
)
table = stack.tile_metadata
assert len(table) == DEFAULT_NUM_HYB * DEFAULT_NUM_CH * DEFAULT_NUM_Z
def test_get_slice_simple_index():
"""
Retrieve a slice across one of the indices at the end. For instance, if the dimensions are
(P, Q0,..., Qn-1, R), slice across either P or R.
"""
stack = synthetic_stack()
hyb = 1
imageslice, axes = stack.get_slice({Indices.HYB: hyb})
assert axes == [Indices.CH, Indices.Z]
Y, X = stack.tile_shape
for ch in range(stack.shape[Indices.CH]):
for z in range(stack.shape[Indices.Z]):
data = np.empty((Y, X))
data.fill((hyb * stack.shape[Indices.CH] + ch) *
stack.shape[Indices.Z] + z)
assert data.all() == imageslice[ch, z].all()
def test_get_slice_middle_index():
"""
Retrieve a slice across one of the indices in the middle. For instance, if the dimensions are
(P, Q0,..., Qn-1, R), slice across one of the Q axes.
"""
stack = synthetic_stack()
ch = 1
imageslice, axes = stack.get_slice({Indices.CH: ch})
assert axes == [Indices.HYB, Indices.Z]
Y, X = stack.tile_shape
for hyb in range(stack.shape[Indices.HYB]):
for z in range(stack.shape[Indices.Z]):
data = np.empty((Y, X))
data.fill((hyb * stack.shape[Indices.CH] + ch) *
stack.shape[Indices.Z] + z)
assert data.all() == imageslice[hyb, z].all()
def test_missing_extras():
"""
If the extras are not present on some of the tiles, it should still work.
"""
def tile_extras_provider(hyb: int, ch: int, z: int) -> Any:
if hyb == 0:
return {
'random_key': {
Indices.HYB: hyb,
Indices.CH: ch,
Indices.Z: z,
}
}
else:
return None
stack = synthetic_stack(
tile_extras_provider=tile_extras_provider,
)
table = stack.tile_metadata
assert len(table) == DEFAULT_NUM_HYB * DEFAULT_NUM_CH * DEFAULT_NUM_Z
def test_apply_3d():
"""test that apply correctly applies a simple function across 3d volumes of a Stack"""
stack = synthetic_stack()
assert np.all(stack.numpy_array == 1)
stack.apply(multiply, value=4, is_volume=True)
assert (stack.numpy_array == 4).all()
def test_apply():
"""test that apply correctly applies a simple function across 2d tiles of a Stack"""
stack = synthetic_stack()
assert (stack.numpy_array == 1).all()
stack.apply(multiply, value=2)
assert (stack.numpy_array == 2).all()