def sparse_block_mask_for_labels(self, labels, clip=True):
"""
Determine which bricks (each with our ``preferred_message_shape``)
would need to be accessed download all data for the given labels,
and return the result as a ``SparseBlockMask`` object.
This function uses a dask to fetch the coarse sparsevols in parallel.
The sparsevols are extracted directly from the labelindex.
If the ``self.supervoxels`` is True, the labels are grouped
by body before fetching the labelindexes,
to avoid fetching the same labelindexes more than once.
Args:
labels:
A list of body IDs (if ``self.supervoxels`` is False),
or supervoxel IDs (if ``self.supervoxels`` is True).
clip:
If True, filter the results to exclude any coordinates
that fall outside this service's bounding-box.
Otherwise, all brick coordinates that encompass the given label groups
will be returned, whether or not they fall within the bounding box.
Returns:
``SparseBlockMask``
"""
from neuclease.util import SparseBlockMask
coords_df = self.sparse_brick_coords_for_labels(labels, clip)
coords_df.drop_duplicates(['z', 'y', 'x'], inplace=True)
brick_shape = self.preferred_message_shape
coords_df[['z', 'y', 'x']] //= brick_shape
coords = coords_df[['z', 'y', 'x']].values
return SparseBlockMask.create_from_lowres_coords(coords, brick_shape)
def init_brickwall(self, volume_service, subset_groups):
try:
brick_coords_df = volume_service.sparse_brick_coords_for_label_groups(
subset_groups)
np.save('brick-coords.npy',
brick_coords_df.to_records(index=False))
brick_shape = volume_service.preferred_message_shape
brick_indexes = brick_coords_df[['z', 'y', 'x'
]].values // brick_shape
sbm = SparseBlockMask.create_from_lowres_coords(
brick_indexes, brick_shape)
except NotImplementedError:
logger.warning(
"The volume service does not support sparse fetching. All bricks will be analyzed."
)
sbm = None
with Timer("Initializing BrickWall", logger):
# Aim for 2 GB RDD partitions when loading segmentation
GB = 2**30
target_partition_size_voxels = 2 * GB // np.uint64().nbytes
# Apply halo WHILE downloading the data.
# TODO: Allow the user to configure whether or not the halo should
# be fetched from the outset, or added after the blocks are loaded.
halo = self.config["findadjacencies"]["halo"]
brickwall = BrickWall.from_volume_service(
volume_service,
0,
None,
self.client,
target_partition_size_voxels,
halo,
sbm,
compression='lz4_2x')
return brickwall