def test_custom_initialization() -> None:
assert Vec3Int.zeros() == Vec3Int(0, 0, 0)
assert Vec3Int.ones() == Vec3Int(1, 1, 1)
assert Vec3Int.full(4) == Vec3Int(4, 4, 4)
assert Vec3Int.ones() - Vec3Int.ones() == Vec3Int.zeros()
assert Vec3Int.full(4) == Vec3Int.ones() * 4
def test_buffered_slice_writer() -> None:
test_img = np.arange(24 * 24).reshape(24, 24).astype(np.uint16) + 1
dtype = test_img.dtype
origin = Vec3Int.zeros()
layer_name = "color"
mag = Mag(1)
dataset_dir = TESTOUTPUT_DIR / "buffered_slice_writer"
dataset_path = str(dataset_dir / layer_name / mag.to_layer_name())
rmtree(dataset_dir)
ds = Dataset(dataset_dir, voxel_size=(1, 1, 1))
mag_view = ds.add_layer("color", COLOR_CATEGORY,
dtype_per_channel=dtype).add_mag(mag)
with mag_view.get_buffered_slice_writer(absolute_offset=origin) as writer:
for i in range(13):
writer.send(test_img)
with wkw.Dataset.open(dataset_path, wkw.Header(dtype)) as data:
try:
read_data = data.read(origin, (24, 24, 13))
if read_data[read_data.nonzero()].size != 0:
raise AssertionError(
"Nothing should be written on the disk. But found data with shape: {}"
.format(read_data.shape))
except wkw.wkw.WKWException:
pass
for i in range(13, 32):
writer.send(test_img)
with wkw.Dataset.open(dataset_path, wkw.Header(dtype)) as data:
read_data = data.read(origin, (24, 24, 32))
assert np.squeeze(read_data).shape == (24, 24, 32), (
"The read data should have the shape: (24, 24, 32) "
"but has a shape of: {}".format(np.squeeze(read_data).shape))
assert read_data.size == read_data[read_data.nonzero()].size, (
"The read data contains zeros while the "
"written image has no zeros")
for i in range(32, 35):
writer.send(test_img)
with wkw.Dataset.open(dataset_path, wkw.Header(dtype)) as data:
read_data = data.read(origin, (24, 24, 35))
read_data = np.squeeze(read_data)
assert read_data.shape == (24, 24, 35), (
"The read data should have the shape: (24, 24, 35) "
"but has a shape of: {}".format(np.squeeze(read_data).shape))
assert read_data.size == read_data[read_data.nonzero()].size, (
"The read data contains zeros while the "
"written image has no zeros")
test_img_3d = np.zeros((test_img.shape[0], test_img.shape[1], 35))
for i in np.arange(35):
test_img_3d[:, :, i] = test_img
# check if the data are correct
assert np.array_equal(
test_img_3d, read_data), ("The data from the disk is not the same "
"as the data that should be written.")
def __init__(
self,
view: "View",
offset: Optional[Vec3IntLike] = None,
# buffer_size specifies, how many slices should be aggregated until they are flushed.
buffer_size: int = 32,
dimension: int = 2, # z
*,
relative_offset: Optional[Vec3IntLike] = None, # in mag1
absolute_offset: Optional[Vec3IntLike] = None, # in mag1
use_logging: bool = False,
) -> None:
"""see `View.get_buffered_slice_writer()`"""
self.view = view
self.buffer_size = buffer_size
self.dtype = self.view.get_dtype()
self.use_logging = use_logging
if offset is None and relative_offset is None and absolute_offset is None:
relative_offset = Vec3Int.zeros()
if offset is not None:
warnings.warn(
"[DEPRECATION] Using offset for a buffered slice writer is deprecated. "
+ "Please use the parameter relative_offset or absolute_offset in Mag(1) instead.",
DeprecationWarning,
)
self.offset = None if offset is None else Vec3Int(offset)
self.relative_offset = (
None if relative_offset is None else Vec3Int(relative_offset)
)
self.absolute_offset = (
None if absolute_offset is None else Vec3Int(absolute_offset)
)
self.dimension = dimension
assert 0 <= dimension <= 2
self.buffer: List[np.ndarray] = []
self.current_slice: Optional[int] = None
self.buffer_start_slice: Optional[int] = None
