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 test_mag_constructor() -> None:
mag = Mag(16)
assert mag.to_list() == [16, 16, 16]
mag = Mag("256")
assert mag.to_list() == [256, 256, 256]
mag = Mag("16-2-4")
assert mag.to_list() == [16, 2, 4]
mag1 = Mag("16-2-4")
mag2 = Mag("8-2-4")
assert mag1 > mag2
assert mag1.to_layer_name() == "16-2-4"
assert np.all(mag1.to_np() == np.array([16, 2, 4]))
assert mag1 == Mag(mag1)
assert mag1 == Mag(mag1.to_np())
def _setup_mag(self, mag: Mag) -> None:
# This method is used to initialize the mag when opening the Dataset. This does not create e.g. the wk_header.
mag_name = mag.to_layer_name()
self._assert_mag_does_not_exist_yet(mag)
try:
cls_array = BaseArray.get_class(self._properties.data_format)
info = cls_array.open(
_find_mag_path_on_disk(self.dataset.path, self.name,
mag_name)).info
self._mags[mag] = MagView(
self,
mag,
info.chunk_size,
info.chunks_per_shard,
info.compression_mode,
)
self._mags[mag]._read_only = self._dataset.read_only
except ArrayException as e:
logging.error(
f"Failed to setup magnification {mag_name}, which is specified in the datasource-properties.json. See {e}"
)