def _parse_vec3_int(value: str) -> Vec3Int:
parts = [int(part.strip()) for part in value.split(",")]
if len(parts) == 1:
return Vec3Int.full(parts[0])
elif len(parts) == 3:
return Vec3Int(*parts)
else:
raise TypeError(f"Cannot convert `{value}` to Vec3Int.")
def downsample_test_helper(WT1_path: Path, tmp_path: Path, use_compress: bool,
chunk_size: Vec3Int) -> None:
source_path = WT1_path
target_path = tmp_path / "WT1_wkw"
source_ds = Dataset.open(source_path)
target_ds = source_ds.copy_dataset(target_path,
chunk_size=chunk_size,
chunks_per_shard=16)
target_layer = target_ds.get_layer("color")
mag1 = target_layer.get_mag("1")
target_layer.delete_mag("2-2-1") # This is not needed for this test
# The bounding box has to be set here explicitly because the downsampled data is written to a different dataset.
target_layer.bounding_box = source_ds.get_layer("color").bounding_box
mag2 = target_layer._initialize_mag_from_other_mag("2", mag1, use_compress)
# The actual size of mag1 is (4600, 4600, 512).
# To keep this test case fast, we are only downsampling a small part
offset = (4096, 4096, 0)
size = (504, 504, 512)
source_buffer = mag1.read(
absolute_offset=offset,
size=size,
)[0]
assert np.any(source_buffer != 0)
downsample_cube_job(
(
mag1.get_view(absolute_offset=offset, size=size),
mag2.get_view(
absolute_offset=offset,
size=size,
),
0,
),
Vec3Int(2, 2, 2),
InterpolationModes.MAX,
Vec3Int.full(128),
)
assert np.any(source_buffer != 0)
target_buffer = mag2.read(absolute_offset=offset, size=size)[0]
assert np.any(target_buffer != 0)
assert np.all(target_buffer == downsample_cube(source_buffer, [2, 2, 2],
InterpolationModes.MAX))
def test_compressed_downsample_cube_job(WT1_path: Path,
tmp_path: Path) -> None:
with warnings.catch_warnings():
warnings.filterwarnings(
"error") # This escalates the warning to an error
downsample_test_helper(WT1_path, tmp_path, True, Vec3Int.full(32))
def test_downsample_cube_job(WT1_path: Path, tmp_path: Path) -> None:
downsample_test_helper(WT1_path, tmp_path, False, Vec3Int.full(16))
import pytest
from webknossos import COLOR_CATEGORY, Dataset, Mag, Vec3Int
from webknossos.dataset._downsampling_utils import (
InterpolationModes,
_mode,
calculate_default_coarsest_mag,
calculate_mags_to_downsample,
calculate_mags_to_upsample,
downsample_cube,
downsample_cube_job,
non_linear_filter_3d,
)
from webknossos.dataset.sampling_modes import SamplingModes
BUFFER_SHAPE = Vec3Int.full(256)
def test_downsample_cube() -> None:
buffer = np.zeros(BUFFER_SHAPE, dtype=np.uint8)
buffer[:, :, :] = np.arange(0, BUFFER_SHAPE.x)
output = downsample_cube(buffer, [2, 2, 2], InterpolationModes.MODE)
assert np.all(output.shape == (BUFFER_SHAPE.to_np() // 2))
assert buffer[0, 0, 0] == 0
assert buffer[0, 0, 1] == 1
assert np.all(output[:, :, :] == np.arange(0, BUFFER_SHAPE.x, 2))
def test_downsample_mode() -> None:
setup_logging(args)
if args.isotropic is not None:
raise DeprecationWarning(
"The flag 'isotropic' is deprecated. Consider using '--sampling_mode isotropic' instead."
)
if args.anisotropic_target_mag is not None:
raise DeprecationWarning(
"The 'anisotropic_target_mag' flag is deprecated. Use '--max' instead (and consider changing the 'sampling_mode')"
)
from_mag = Mag(args.from_mag)
target_mag = Mag(args.target_mag)
buffer_shape = (
Vec3Int.full(args.buffer_cube_size)
if args.buffer_cube_size is not None
else None
)
upsample_mags(
args.path,
args.layer_name,
from_mag,
target_mag,
buffer_shape=buffer_shape,
compress=not args.no_compress,
sampling_mode=args.sampling_mode,
args=args,
)
args = create_parser().parse_args()
setup_logging(args)
if args.isotropic is not None:
raise DeprecationWarning(
"The flag 'isotropic' is deprecated. Consider using '--sampling_mode isotropic' instead."
)
if args.anisotropic_target_mag is not None:
raise DeprecationWarning(
"The 'anisotropic_target_mag' flag is deprecated. Use '--max' instead (and consider changing the 'sampling_mode')"
)
from_mag = Mag(args.from_mag)
max_mag = None if args.max is None else Mag(args.max)
buffer_shape = (Vec3Int.full(args.buffer_cube_size)
if args.buffer_cube_size is not None else None)
downsample_mags(
path=args.path,
layer_name=args.layer_name,
from_mag=from_mag,
max_mag=max_mag,
interpolation_mode=args.interpolation_mode,
compress=not args.no_compress,
sampling_mode=args.sampling_mode,
buffer_shape=buffer_shape,
force_sampling_scheme=args.force_sampling_scheme,
args=get_executor_args(args),
)