def test_index_to_slices(self):
bounds = (slice(0, 70), slice(0, 70))
chunk_shape = (30, 30)
overlap = (10, 10)
block = Block(bounds=bounds, chunk_shape=chunk_shape, overlap=overlap)
assert block.unit_index_to_slices((0, 0)) == (slice(0,
30), slice(0, 30))
assert block.unit_index_to_slices((0, 1)) == (slice(0,
30), slice(20, 50))
assert block.unit_index_to_slices((1, 0)) == (slice(20,
50), slice(0, 30))
def test_iterator(self):
bounds = (slice(0, 70), slice(0, 70))
chunk_shape = (30, 30)
overlap = (10, 10)
start = (0, 0)
block = Block(bounds=bounds,
chunk_shape=chunk_shape,
overlap=overlap,
base_iterator=IdentityIterator())
chunks = list(block.chunk_iterator(start))
assert len(chunks) == 1
assert chunks[0].unit_index == start
def test_overlap_slices_3d(self):
bounds = (slice(0, 7), slice(0, 7), slice(0, 7))
chunk_shape = (3, 3, 3)
overlap = (1, 1, 1)
block = Block(bounds=bounds, chunk_shape=chunk_shape, overlap=overlap)
assert block.num_chunks == (3, 3, 3)
fake_data = GlobalOffsetArray(np.zeros(block.shape),
global_offset=(0, 0, 0))
for chunk in block.chunk_iterator((1, 0, 1)):
for edge_slice in block.overlap_slices(chunk):
fake_data[edge_slice] += 1
fake_data[block.core_slices(chunk)] += 1
assert fake_data.sum() == np.product(fake_data.shape)
def test_get_border_slices_3d(self):
bounds = (slice(0, 70), slice(0, 70), slice(0, 70))
chunk_shape = (30, 30, 30)
overlap = (10, 10, 10)
block = Block(bounds=bounds, chunk_shape=chunk_shape, overlap=overlap)
chunk = Chunk(block, (0, 0, 0))
borders = list(itertools.product(range(0, len(bounds)), [-1, 1]))
fake_data = np.zeros(chunk.shape)
for slices in chunk.border_slices(borders):
fake_data[slices] += 1
fake_data[chunk.core_slices(borders)] += 1
assert fake_data.sum() == np.product(fake_data.shape)
def test_get_border_slices_3d_overlapping(self):
bounds = (slice(0, 7), slice(0, 7), slice(0, 7))
chunk_shape = (3, 3, 3)
overlap = (1, 1, 1)
block = Block(bounds=bounds, chunk_shape=chunk_shape, overlap=overlap)
chunk = Chunk(block, (0, 0, 0))
borders = list(itertools.product(range(0, len(bounds)), [-1, 1]))
fake_data = np.zeros(chunk.shape)
for slices in chunk.border_slices(borders, nonintersecting=False):
fake_data[slices] += 1
fake_data[chunk.core_slices(borders)] += 1
assert np.array_equal(fake_data, [[[3, 2, 3], [2, 1, 2], [3, 2, 3]],
[[2, 1, 2], [1, 1, 1], [2, 1, 2]],
[[3, 2, 3], [2, 1, 2], [3, 2, 3]]])
def test_init(self):
bounds = (slice(0, 70), slice(0, 70))
offset = (0, 0)
num_chunks = (3, 3)
overlap = (10, 10)
chunk_shape = (30, 30)
# test with bounds
Block(bounds=bounds, chunk_shape=chunk_shape, overlap=overlap)
# test with offset/num_chunks
Block(offset=offset,
num_chunks=num_chunks,
chunk_shape=chunk_shape,
overlap=overlap)
# test with both offset/num_chunks
Block(bounds=bounds,
offset=offset,
num_chunks=num_chunks,
chunk_shape=chunk_shape,
overlap=overlap)
# test fail with neither block and offset offset/num_chunks
with pytest.raises(ValueError):
Block(chunk_shape=chunk_shape, overlap=overlap)
# test fail with only offset no num_chunks
with pytest.raises(ValueError):
Block(offset=offset, chunk_shape=chunk_shape, overlap=overlap)
# test fail with only num_chuks no offset
with pytest.raises(ValueError):
Block(num_chunks=num_chunks,
chunk_shape=chunk_shape,
overlap=overlap)
# test incorrect matching bounds with offset/num_chunks
with pytest.raises(Exception):
Block(bounds=(slice(b.start, b.stop + 1) for b in bounds),
offset=offset,
num_chunks=num_chunks,
chunk_shape=chunk_shape,
overlap=overlap)
def test_checkpoints(self):
bounds = (slice(0, 7), slice(0, 7), slice(0, 7))
chunk_shape = (3, 3, 3)
overlap = (1, 1, 1)
block = Block(bounds=bounds, chunk_shape=chunk_shape, overlap=overlap)
for chunk in block.chunk_iterator((1, 0, 1)):
block.checkpoint(chunk)
assert block.is_checkpointed(chunk)
assert block.is_checkpointed(chunk, stage=0)
for chunk in block.chunk_iterator((1, 0, 1)):
assert not block.is_checkpointed(chunk, stage=1)
assert not block.checkpoint(chunk, stage=1)
assert block.all_neighbors_checkpointed(chunk, stage=0)
block.checkpoint(chunk, stage=1)
stage = 0
for chunk in block.chunk_iterator((1, 0, 1)):
print(block.checkpoints[stage][chunk.unit_index])
for c in block.get_all_neighbors(chunk):
print(c.unit_index, block.checkpoints[stage][c.unit_index])
assert block.all_neighbors_checkpointed(chunk, stage=0)
def test_init_wrong_size_no_overlap(self):
bounds = (slice(0, 70), slice(0, 70))
chunk_shape = (30, 30)
with pytest.raises(ValueError):
Block(bounds=bounds, chunk_shape=chunk_shape)
def test_slices_to_indices(self):
bounds_1 = (slice(0, 16), slice(0, 16), slice(0, 16))
chunk_shape_1 = (4, 4, 4)
overlap_1 = (1, 1, 1)
block_1 = Block(bounds=bounds_1,
chunk_shape=chunk_shape_1,
overlap=overlap_1)
bounds_2 = (slice(-1, 25), slice(-1, 25), slice(-1, 25))
chunk_shape_2 = (6, 6, 6)
overlap_2 = (1, 1, 1)
block_2 = Block(bounds=bounds_2,
chunk_shape=chunk_shape_2,
overlap=overlap_2)
index = 1
for unit_index in range(0, block_2.num_chunks[index]):
chunk_2 = Chunk(block_2, (0, unit_index))
chunk_2_coords = set(
filter(
lambda x: x >= block_1.bounds[index].start and x < block_1.
bounds[index].stop,
range(chunk_2.slices[index].start,
chunk_2.slices[index].stop)))
print('expect:', chunk_2.slices, chunk_2_coords)
for unit_index in block_1.slices_to_unit_indices(chunk_2.slices):
chunk_1 = Chunk(block_1, unit_index)
chunk_1_coords = set(
filter(
lambda x: x >= block_1.bounds[index].start and x <
block_1.bounds[index].stop,
range(chunk_1.slices[index].start,
chunk_1.slices[index].stop)))
print(chunk_1.slices, chunk_1_coords)
chunk_2_coords.difference_update(chunk_1_coords)
assert all(
tuple(u >= 0 and u <= n
for u, n in zip(unit_index, block_1.num_chunks)))
print('left', chunk_2_coords)
assert len(chunk_2_coords) == 0
# Test reverse direction
block_2_temp = block_2
block_2 = block_1
block_1 = block_2_temp
index = 1
for unit_index in range(0, block_2.num_chunks[index]):
chunk_2 = Chunk(block_2, (0, unit_index))
chunk_2_coords = set(
filter(
lambda x: x >= block_1.bounds[index].start and x < block_1.
bounds[index].stop,
range(chunk_2.slices[index].start,
chunk_2.slices[index].stop)))
print('expect:', chunk_2.slices, chunk_2_coords)
for unit_index in block_1.slices_to_unit_indices(chunk_2.slices):
chunk_1 = Chunk(block_1, unit_index)
chunk_1_coords = set(
filter(
lambda x: x >= block_1.bounds[index].start and x <
block_1.bounds[index].stop,
range(chunk_1.slices[index].start,
chunk_1.slices[index].stop)))
print(chunk_1.slices, chunk_1_coords)
chunk_2_coords.difference_update(chunk_1_coords)
assert all(
tuple(u >= 0 and u <= n
for u, n in zip(unit_index, block_1.num_chunks)))
print('left', chunk_2_coords)
assert len(chunk_2_coords) == 0
# Test None
index = 1
for unit_index in range(0, block_2.num_chunks[index]):
chunk_2 = Chunk(block_2, (0, unit_index))
# use fake slices with None here!
chunk_2_slices = (slice(None, None), ) + chunk_2.slices[1:]
chunk_2_coords = set(
filter(
lambda x: x >= block_1.bounds[index].start and x < block_1.
bounds[index].stop,
range(chunk_2_slices[index].start,
chunk_2_slices[index].stop)))
print('expect:', chunk_2_slices, chunk_2_coords)
for unit_index in block_1.slices_to_unit_indices(chunk_2_slices):
chunk_1 = Chunk(block_1, unit_index)
chunk_1_coords = set(
filter(
lambda x: x >= block_1.bounds[index].start and x <
block_1.bounds[index].stop,
range(chunk_1.slices[index].start,
chunk_1.slices[index].stop)))
print(chunk_1.slices, chunk_1_coords)
chunk_2_coords.difference_update(chunk_1_coords)
assert all(
tuple(u >= 0 and u <= n
for u, n in zip(unit_index, block_1.num_chunks)))
print('left', chunk_2_coords)
assert len(chunk_2_coords) == 0