def test_multiple_tiles_of_different_kind():
with pytest.raises(TypeError):
ImageStack.synthetic_stack(
NUM_HYB,
NUM_CH,
NUM_Z,
HEIGHT,
WIDTH,
tile_data_provider=create_tile_data_provider(
np.uint32, np.float32),
)
def labeled_synthetic_dataset():
stp = synthesize.SyntheticSpotTileProvider()
image = ImageStack.synthetic_stack(tile_data_provider=stp.tile)
max_proj = image.max_proj(Indices.HYB, Indices.CH, Indices.Z)
view = max_proj.reshape((1, 1, 1) + max_proj.shape)
dots = ImageStack.from_numpy_array(view)
def labeled_synthetic_dataset_factory():
return deepcopy(image), deepcopy(dots), deepcopy(stp.codebook)
return labeled_synthetic_dataset_factory
def test_multiple_tiles_of_same_dtype():
stack = ImageStack.synthetic_stack(
NUM_HYB,
NUM_CH,
NUM_Z,
HEIGHT,
WIDTH,
tile_data_provider=create_tile_data_provider(np.uint32, np.uint32),
)
expected = np.ones((NUM_HYB, NUM_CH, NUM_Z, HEIGHT, WIDTH),
dtype=np.uint32)
assert np.array_equal(stack.numpy_array, expected)
def test_set_slice_range():
"""
Sets a slice across a range of one of the dimensions.
"""
stack = ImageStack.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 = ImageStack.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 = ImageStack.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_float_type_promotion():
with warnings.catch_warnings(record=True) as w:
stack = ImageStack.synthetic_stack(
NUM_HYB,
NUM_CH,
NUM_Z,
HEIGHT,
WIDTH,
tile_data_provider=create_tile_data_provider(
np.float64, np.float32),
)
assert len(w) == 1
assert issubclass(w[0].category, DataFormatWarning)
expected = np.ones((NUM_HYB, NUM_CH, NUM_Z, HEIGHT, WIDTH),
dtype=np.float64)
assert np.array_equal(stack.numpy_array, 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 = ImageStack.synthetic_stack(
num_hyb=NUM_HYB, num_ch=NUM_CH, num_z=NUM_Z, tile_extras_provider=tile_extras_provider,
)
with pytest.raises(ValueError):
stack.tile_metadata
def test_int_type_promotion():
with warnings.catch_warnings(record=True) as w:
stack = ImageStack.synthetic_stack(
NUM_HYB,
NUM_CH,
NUM_Z,
HEIGHT,
WIDTH,
tile_data_provider=create_tile_data_provider(np.int32, np.int8),
)
assert len(w) == 1
assert issubclass(w[0].category, DataFormatWarning)
expected = np.ones((NUM_HYB, NUM_CH, NUM_Z, HEIGHT, WIDTH), dtype=np.int32)
corner = np.empty((HEIGHT, WIDTH), dtype=np.int32)
corner.fill(16777216)
expected[0, 0, 0] = corner
assert np.array_equal(stack.numpy_array, expected)
def test_get_slice_range():
"""
Retrieve a slice across a range of one of the dimensions.
"""
stack = ImageStack.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 = ImageStack.synthetic_stack(
num_hyb=NUM_HYB, num_ch=NUM_CH, num_z=NUM_Z, tile_extras_provider=tile_extras_provider,
)
table = stack.tile_metadata
assert len(table) == NUM_HYB * NUM_CH * NUM_Z
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 = ImageStack.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_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 = ImageStack.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_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 = ImageStack.synthetic_stack(
num_hyb=NUM_HYB, num_ch=NUM_CH, num_z=NUM_Z, tile_extras_provider=tile_extras_provider,
)
table = stack.tile_metadata
assert len(table) == NUM_HYB * NUM_CH * NUM_Z
def test_apply_3d():
"""test that apply correctly applies a simple function across 3d volumes of a Stack"""
stack = ImageStack.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 = ImageStack.synthetic_stack()
assert (stack.numpy_array == 1).all()
stack.apply(multiply, value=2)
assert (stack.numpy_array == 2).all()