def test_copysegmentation_from_hdf5_to_dvid_input_mask(
setup_hdf5_segmentation_input, disable_auto_retry):
template_dir, config, volume, dvid_address, repo_uuid, _output_segmentation_name = setup_hdf5_segmentation_input
# make sure we get a fresh output
output_segmentation_name = 'copyseg-with-input-mask'
config["output"]["dvid"]["segmentation-name"] = output_segmentation_name
# Select only even IDs
all_labels = pd.unique(volume.reshape(-1))
even_labels = all_labels[all_labels % 2 == 0]
config["copysegmentation"]["input-mask-labels"] = even_labels.tolist()
# Add an offset, which is added to both the input volume AND the mask labels
offset = 2000
config["copysegmentation"]["add-offset-to-ids"] = offset
input_box = np.array(config["input"]["geometry"]["bounding-box"])[:, ::-1]
volume = np.where((volume % 2) == 0, volume + offset, 0)
expected_vol = np.zeros_like(volume)
overwrite_subvol(expected_vol, input_box,
extract_subvol(volume, input_box))
setup = template_dir, config, expected_vol, dvid_address, repo_uuid, output_segmentation_name
_box_zyx, _expected_vol, _output_vol = _run_to_dvid(setup)
def test_copysegmentation_from_dvid_to_dvid_input_mask(
setup_dvid_segmentation_input, disable_auto_retry):
template_dir, config, volume, dvid_address, repo_uuid, _output_segmentation_name = setup_dvid_segmentation_input
# make sure we get a fresh output
output_segmentation_name = 'copyseg-with-input-mask-from-dvid'
config["output"]["dvid"]["segmentation-name"] = output_segmentation_name
# Add an offset, which is added to both the input volume AND the mask labels
offset = 2000
config["copysegmentation"]["add-offset-to-ids"] = offset
# Select some labels that don't extend throughout the whole volume
selected_labels = pd.unique(volume[150, 64:128, 64:128].reshape(-1))
assert 0 not in selected_labels
selected_coords = np.array(
mask_for_labels(volume, selected_labels).nonzero()).transpose()
selected_box = np.array(
[selected_coords.min(axis=0), 1 + selected_coords.max(axis=0)])
input_box = np.array(config["input"]["geometry"]["bounding-box"])[:, ::-1]
subvol_box = box_intersection(input_box, selected_box)
selected_subvol = extract_subvol(volume, subvol_box).copy()
selected_subvol = apply_mask_for_labels(selected_subvol, selected_labels)
config["copysegmentation"]["input-mask-labels"] = selected_labels.tolist()
selected_subvol = np.where(selected_subvol, selected_subvol + offset, 0)
expected_vol = np.zeros(volume.shape, np.uint64)
overwrite_subvol(expected_vol, subvol_box, selected_subvol)
setup = template_dir, config, expected_vol, dvid_address, repo_uuid, output_segmentation_name
_box_zyx, _expected_vol, _output_vol = _run_to_dvid(setup)
def test_dvid_volume_service_grayscale(setup_dvid_repo, disable_auto_retry):
server, uuid = setup_dvid_repo
instance_name = 'test-dvs-grayscale'
volume = np.random.randint(100, size=(256, 192, 128), dtype=np.uint8)
max_scale = 2
voxel_dimensions = [4.0, 4.0, 32.0]
config_text = textwrap.dedent(f"""\
dvid:
server: {server}
uuid: {uuid}
grayscale-name: {instance_name}
create-if-necessary: true
creation-settings:
max-scale: {max_scale}
voxel-size: {voxel_dimensions}
geometry:
bounding-box: [[0,0,0], {list(volume.shape[::-1])}]
""")
yaml = YAML()
with StringIO(config_text) as f:
volume_config = yaml.load(f)
assert instance_name not in fetch_repo_instances(server, uuid)
service = VolumeService.create_from_config(volume_config)
repo_instances = fetch_repo_instances(server, uuid)
info = fetch_instance_info(server, uuid, instance_name)
assert info["Extended"]["VoxelSize"] == voxel_dimensions
scaled_volumes = {}
for scale in range(max_scale + 1):
if scale == 0:
assert instance_name in repo_instances
assert repo_instances[instance_name] == 'uint8blk'
else:
assert f"{instance_name}_{scale}" in repo_instances
assert repo_instances[f"{instance_name}_{scale}"] == 'uint8blk'
vol = downsample(volume, 2**scale,
'label') # label downsampling is easier to test with
aligned_shape = (np.ceil(np.array(vol.shape) / 64) * 64).astype(int)
aligned_vol = np.zeros(aligned_shape, np.uint8)
overwrite_subvol(aligned_vol, [(0, 0, 0), aligned_shape], aligned_vol)
service.write_subvolume(aligned_vol, (0, 0, 0), scale)
scaled_volumes[scale] = aligned_vol
box = np.array([[40, 80, 40], [240, 160, 100]])
for scale in range(max_scale + 1):
scaled_box = box // 2**scale
vol = service.get_subvolume(scaled_box, scale)
assert (vol == extract_subvol(scaled_volumes[scale], scaled_box)).all()
def assemble_brick_fragments( fragments ):
"""
Given a list of Bricks with identical logical_boxes, splice their volumes
together into a final Brick that contains a full volume containing all of
the fragments.
Note: Brick 'fragments' are also just Bricks, whose physical_box does
not cover the entire logical_box for the brick.
Each fragment's physical_box indicates where that fragment's data
should be located within the final returned Brick.
Returns: A Brick containing the data from all fragments,
UNLESS the fully assembled fragments would not intersect
with the Brick's own logical_box (i.e. all fragments fall
within the halo), in which case None is returned.
Note: If the fragment physical_boxes are not disjoint, the results
are undefined.
"""
fragments = list(fragments)
# All logical boxes must be the same
logical_boxes = np.asarray([frag.logical_box for frag in fragments])
assert (logical_boxes == logical_boxes[0]).all(), \
"Cannot assemble brick fragments from different logical boxes. "\
"They belong to different bricks!"
final_logical_box = logical_boxes[0]
# The final physical box is the min/max of all fragment physical extents.
physical_boxes = np.array([frag.physical_box for frag in fragments])
assert physical_boxes.ndim == 3 # (N, 2, Dim)
assert physical_boxes.shape == ( len(fragments), 2, final_logical_box.shape[1] )
final_physical_box = np.asarray( ( np.min( physical_boxes[:,0,:], axis=0 ),
np.max( physical_boxes[:,1,:], axis=0 ) ) )
interior_box = box_intersection(final_physical_box, final_logical_box)
if (interior_box[1] - interior_box[0] < 1).any():
# All fragments lie completely within the halo
return None
final_volume_shape = final_physical_box[1] - final_physical_box[0]
dtype = fragments[0].volume.dtype
final_volume = np.zeros(final_volume_shape, dtype)
for frag in fragments:
internal_box = frag.physical_box - final_physical_box[0]
overwrite_subvol(final_volume, internal_box, frag.volume)
# Destroy original to save RAM
frag.destroy()
brick = Brick( final_logical_box, final_physical_box, final_volume )
brick.compress()
return brick
def zero_fill(vol, box, full_box):
"""
Given a volume, it's corresponding box, and a 'full box' that encompasses it,
Return a volume that fills the full box, padding with zeros if necessary.
"""
if (box == full_box).all():
return vol
else:
full_vol = np.zeros(full_box[1] - full_box[0], vol.dtype)
overwrite_subvol(full_vol, box - full_box[0], vol)
return full_vol
def download(bounding_box_zyx, output_path):
shape = bounding_box_zyx[1] - bounding_box_zyx[0]
with h5py.File(output_path, 'w') as f:
gray_dset = f.create_dataset('grayscale',
shape=shape,
dtype=np.uint8,
chunks=True)
seg_dset = f.create_dataset('segmentation',
shape=shape,
dtype=np.uint64,
chunks=True,
compression='gzip')
print("Downloading grayscale...")
block_shape = (256, 256, 256)
block_boxes = boxes_from_grid(bounding_box_zyx,
block_shape,
clipped=True)
for block_box in tqdm(block_boxes):
relative_box = block_box - bounding_box_zyx[0]
block_gray = fetch_raw(*GRAYSCALE, block_box)
overwrite_subvol(gray_dset, relative_box, block_gray)
print("")
print("Downloading segmentation...")
block_boxes = boxes_from_grid(bounding_box_zyx,
block_shape,
clipped=True)
for block_box in tqdm(block_boxes):
relative_box = block_box - bounding_box_zyx[0]
block_seg = fetch_labelmap_voxels(*SEGMENTATION, block_box)
overwrite_subvol(seg_dset, relative_box, block_seg)
print("")
print("DONE")
def setup_dvid_segmentation_input(setup_dvid_repo, random_segmentation):
dvid_address, repo_uuid = setup_dvid_repo
input_segmentation_name = 'labelmapcopy-segmentation-input'
output_segmentation_name = 'labelmapcopy-segmentation-output'
partial_output_segmentation_name = 'labelmapcopy-segmentation-partial-output'
max_scale = 3
already_exists = False
try:
create_labelmap_instance(dvid_address,
repo_uuid,
input_segmentation_name,
max_scale=max_scale)
create_labelmap_instance(dvid_address,
repo_uuid,
partial_output_segmentation_name,
max_scale=max_scale)
except HTTPError as ex:
if ex.response is not None and 'already exists' in ex.response.content.decode(
'utf-8'):
already_exists = True
expected_vols = {}
for scale in range(1 + max_scale):
if scale == 0:
scaled_vol = random_segmentation
else:
scaled_vol = downsample(scaled_vol, 2, 'labels-numba')
expected_vols[scale] = scaled_vol
if not already_exists:
scaled_box = round_box([(0, 0, 0), scaled_vol.shape], 64, 'out')
aligned_vol = np.zeros(scaled_box[1], np.uint64)
overwrite_subvol(aligned_vol, [(0, 0, 0), scaled_vol.shape],
scaled_vol)
post_labelmap_voxels(dvid_address,
repo_uuid,
input_segmentation_name, (0, 0, 0),
aligned_vol,
scale=scale)
if not already_exists:
# Create a 'partial' output volume that is the same (bitwise) as the input except for some blocks.
scaled_box = np.array([(0, 0, 0), random_segmentation.shape])
scaled_box[1, -1] = 192
for scale in range(1 + max_scale):
scaled_box = round_box(scaled_box // (2**scale), 64, 'out')
raw_blocks = fetch_labelmap_voxels(dvid_address,
repo_uuid,
input_segmentation_name,
scaled_box,
scale,
supervoxels=True,
format='raw-response')
post_labelmap_blocks(dvid_address,
repo_uuid,
partial_output_segmentation_name, [(0, 0, 0)],
raw_blocks,
scale,
is_raw=True)
block = np.random.randint(1_000_000,
1_000_010,
size=(64, 64, 64),
dtype=np.uint64)
post_labelmap_voxels(dvid_address,
repo_uuid,
partial_output_segmentation_name, (0, 128, 64),
block,
0,
downres=True)
partial_vol = fetch_labelmap_voxels(dvid_address,
repo_uuid,
partial_output_segmentation_name,
[(0, 0, 0), random_segmentation.shape],
supervoxels=True)
template_dir = tempfile.mkdtemp(suffix="labelmapcopy-template")
config_text = textwrap.dedent(f"""\
workflow-name: labelmapcopy
cluster-type: {CLUSTER_TYPE}
input:
dvid:
server: {dvid_address}
uuid: {repo_uuid}
segmentation-name: {input_segmentation_name}
supervoxels: true
geometry:
message-block-shape: [512,64,64]
available-scales: [0,1,2,3]
output:
dvid:
server: {dvid_address}
uuid: {repo_uuid}
segmentation-name: {output_segmentation_name}
supervoxels: true
disable-indexing: true
create-if-necessary: true
labelmapcopy:
slab-shape: [512,128,64]
dont-overwrite-identical-blocks: true
""")
with open(f"{template_dir}/workflow.yaml", 'w') as f:
f.write(config_text)
yaml = YAML()
with StringIO(config_text) as f:
config = yaml.load(f)
return template_dir, config, expected_vols, partial_vol, dvid_address, repo_uuid, output_segmentation_name, partial_output_segmentation_name
def pad_brick_data_from_volume_source( padding_grid, volume_accessor_func, brick ):
"""
Expand the given Brick's data until its physical_box is aligned with the given padding_grid.
The data in the expanded region will be sourced from the given volume_accessor_func.
Note: padding_grid need not be identical to the grid the Brick was created with,
but it must divide evenly into that grid.
For instance, if padding_grid happens to be the same as the brick's own native grid,
then the phyiscal_box is expanded to align perfectly with the logical_box on all sides:
+-------------+ +-------------+
| physical | | | same |
|__________| | | physical |
| | --> | and |
| logical | | logical |
|_____________| |_____________|
Args:
brick: Brick
padding_grid: Grid
volume_accessor_func: Callable with signature: f(box) -> ndarray
Returns: Brick
Note: It is not legal to call this function unless the Brick's physical_box
lies completely within the logical_box (i.e. no halos allowed).
Furthremore, the padding_grid is not permitted to use a halo, either.
(These restrictions could be fixed, but the current version of this
function has these requirements.)
Note: If no padding is necessary, then the original Brick is returned (no copy is made).
"""
assert isinstance(padding_grid, Grid)
assert not padding_grid.halo_shape.any()
block_shape = padding_grid.block_shape
assert ((brick.logical_box - padding_grid.offset) % block_shape == 0).all(), \
f"Padding grid {padding_grid.offset} must be aligned with brick logical_box: {brick.logical_box}"
# Subtract offset to calculate the needed padding
offset_physical_box = brick.physical_box - padding_grid.offset
if (offset_physical_box % block_shape == 0).all():
# Internal data is already aligned to the padding_grid.
return brick
offset_padded_box = np.array([offset_physical_box[0] // block_shape * block_shape,
(offset_physical_box[1] + block_shape - 1) // block_shape * block_shape])
# Re-add offset
padded_box = offset_padded_box + padding_grid.offset
assert (padded_box[0] >= brick.logical_box[0]).all()
assert (padded_box[1] <= brick.logical_box[1]).all()
# Initialize a new volume of the fully-padded shape
padded_volume_shape = padded_box[1] - padded_box[0]
padded_volume = np.zeros(padded_volume_shape, dtype=brick.volume.dtype)
# Overwrite the previously existing data in the new padded volume
orig_box = brick.physical_box
orig_box_within_padded = orig_box - padded_box[0]
overwrite_subvol(padded_volume, orig_box_within_padded, brick.volume)
# Check for a non-zero-volume halo on all six sides.
halo_boxes = []
for axis in range(padded_volume.ndim):
if orig_box[0,axis] != padded_box[0,axis]:
leading_halo_box = padded_box.copy()
leading_halo_box[1, axis] = orig_box[0,axis]
halo_boxes.append(leading_halo_box)
if orig_box[1,axis] != padded_box[1,axis]:
trailing_halo_box = padded_box.copy()
trailing_halo_box[0, axis] = orig_box[1,axis]
halo_boxes.append(trailing_halo_box)
assert halo_boxes, \
"How could halo_boxes be empty if there was padding needed?"
for halo_box in halo_boxes:
# Retrieve padding data for one halo side
halo_volume = volume_accessor_func(halo_box)
# Overwrite in the final padded volume
halo_box_within_padded = halo_box - padded_box[0]
overwrite_subvol(padded_volume, halo_box_within_padded, halo_volume)
return Brick( brick.logical_box, padded_box, padded_volume )
def _init_mask(self):
"""
- read the mask ROI as a volume
- dilate/erode it if necessary
- invert it if necessary
- save to .h5 (just for offline debug)
- return the scale-5 mask and its scale-5 bounding-box
"""
options = self.config["masksegmentation"]
roi = options["mask-roi"]
invert_mask = options["invert-mask"]
max_scale = options["max-pyramid-scale"]
roi_dilation = options["dilate-roi"]
roi_erosion = options["erode-roi"]
seg_dilation = options["dilate-segmentation"]
block_width = self.output_service.block_width
# Select a mask_box that's large enough to divide evenly into the
# block width even when reduced to the highest scale we'll be processing.
seg_box = round_box(self.input_service.bounding_box_zyx,
block_width * 2**max_scale)
seg_box_s5 = round_box(seg_box, 2**5) // (2**5)
with Timer(f"Loading ROI '{roi}'", logger):
roi_mask, _ = fetch_roi(self.input_service.server,
self.input_service.uuid,
roi,
format='mask',
mask_box=seg_box_s5)
with h5py.File('roi-mask.h5', 'w') as f:
f.create_dataset('mask',
data=roi_mask.view(np.uint8),
chunks=(128, 128, 128))
assert not (roi_dilation and roi_erosion)
if roi_dilation > 0:
with Timer(f"Dilating ROI by {roi_dilation}", logger):
roi_mask = vigra.filters.multiBinaryDilation(
roi_mask, roi_dilation)
with h5py.File('dilated-roi-mask.h5', 'w') as f:
f.create_dataset('mask',
data=roi_mask.view(np.uint8),
chunks=(128, 128, 128))
if roi_erosion > 0:
with Timer(f"Eroding ROI by {roi_erosion}", logger):
roi_mask = vigra.filters.multiBinaryErosion(
roi_mask, roi_erosion)
with h5py.File('eroded-roi-mask.h5', 'w') as f:
f.create_dataset('mask',
data=roi_mask.view(np.uint8),
chunks=(128, 128, 128))
assert not seg_dilation or invert_mask, \
"Can't use 'dilate-segmentation'. The segmentation isn't downloaded unless 'invert-mask' is used."
if invert_mask:
with Timer("Inverting mask", logger):
# Initialize the mask with entire segmentation at scale 5,
# then subtract the roi from it.
boxes = [
*boxes_from_grid(seg_box_s5, (64, 64, 2048), clipped=True)
]
input_service = self.input_service
def fetch_seg_mask_s5(box_s5):
seg_s5 = input_service.get_subvolume(box_s5, scale=5)
return box_s5, (seg_s5 != 0)
boxes_and_mask = dask.bag.from_sequence(
boxes, 1).map(fetch_seg_mask_s5).compute()
seg_mask = np.zeros(box_shape(seg_box_s5), bool)
for box_s5, box_mask in boxes_and_mask:
overwrite_subvol(seg_mask, box_s5, box_mask)
if seg_dilation == 0:
with h5py.File('segmentation-mask.h5', 'w') as f:
f.create_dataset('mask',
data=seg_mask.view(np.uint8),
chunks=(128, 128, 128))
else:
with Timer(f"Dilating segmentation by {seg_dilation}",
logger):
seg_mask = vigra.filters.multiBinaryDilation(
seg_mask, seg_dilation)
with h5py.File('dilated-segmentation-mask.h5', 'w') as f:
f.create_dataset('mask',
data=seg_mask.view(np.uint8),
chunks=(128, 128, 128))
seg_mask[roi_mask] = False
roi_mask = seg_mask
with h5py.File('final-mask.h5', 'w') as f:
f.create_dataset('mask',
data=roi_mask.view(np.uint8),
chunks=(128, 128, 128))
# Downsample the roi_mask to dvid-block resolution, just to see how many blocks it touches.
block_mask = view_as_blocks(roi_mask, (2, 2, 2)).any(axis=(3, 4, 5))
blocks_touched = block_mask.sum()
voxel_total = blocks_touched * (block_width**3)
logger.info(
f"Mask touches {blocks_touched} blocks ({voxel_total / 1e9:.1f} Gigavoxels)"
)
return roi_mask, seg_box_s5
def assemble_brick_fragments(fragments, output_accessor_fn=None):
"""
Given a list of Bricks with identical logical_boxes, splice their volumes
together into a final Brick that contains a full volume containing all of
the fragments.
Note:
Brick 'fragments' are also just Bricks, whose physical_box does
not cover the entire logical_box for the brick.
Each fragment's physical_box indicates where that fragment's data
should be located within the final returned Brick.
Args:
fragments:
TODO: docs.
output_accessor_fn:
Callable with signature: f(box) -> ndarray
TODO: docs.
Returns:
A Brick containing the data from all fragments,
UNLESS the fully assembled fragments would not intersect
with the Brick's own logical_box (i.e. all fragments fall
within the halo), in which case None is returned.
Note:
If the fragment physical_boxes are not disjoint, the results
are undefined. That is, if two fragments overlap, there's
no guarantee about which one "wins" for the overlapping region.
"""
fragments = list(fragments)
# All logical boxes must be the same
logical_boxes = np.asarray([frag.logical_box for frag in fragments])
assert (logical_boxes == logical_boxes[0]).all(), \
"Cannot assemble brick fragments from different logical boxes. "\
"They belong to different bricks!"
final_logical_box = fragments[0].logical_box
final_location_id = fragments[0].location_id
# The final physical box is the min/max of all fragment physical extents.
physical_boxes = np.array([frag.physical_box for frag in fragments])
assert physical_boxes.ndim == 3 # (N, 2, Dim)
assert physical_boxes.shape == (len(fragments), 2,
final_logical_box.shape[1])
final_physical_box = np.asarray(
(np.min(physical_boxes[:, 0, :],
axis=0), np.max(physical_boxes[:, 1, :], axis=0)))
intersects_interior = False
for frag_pbox in physical_boxes:
interior_box = box_intersection(frag_pbox, final_logical_box)
if (interior_box[1] - interior_box[0] > 0).all():
intersects_interior = True
if not intersects_interior:
# All fragments lie completely within the halo;
# none intersect with the interior logical_box,
# so we don't bother keeping this brick.
return None
final_volume_shape = final_physical_box[1] - final_physical_box[0]
dtype = fragments[0].volume.dtype
# If the physical boxes don't completely fill the final_box,
# then we will need to use the output_accessor_fn (if given).
if output_accessor_fn is None or is_box_coverage_complete(
physical_boxes, final_physical_box):
final_volume = np.zeros(final_volume_shape, dtype)
else:
final_volume = output_accessor_fn(final_physical_box)
for frag in fragments:
internal_box = frag.physical_box - final_physical_box[0]
overwrite_subvol(final_volume, internal_box, frag.volume)
# Recompress fragment now that we're done with it.
frag.compress()
## It's tempting to destroy the fragment to save RAM,
## but the fragment might be needed by more than one final brick.
## (Also, it might be needed twice if a Worker gets restarted.)
# frag.destroy()
compression = fragments[0].compression
brick = Brick(final_logical_box,
final_physical_box,
final_volume,
location_id=final_location_id,
compression=compression)
brick.compress()
return brick
def pad_brick_data_from_volume_source(padding_grid, volume_accessor_func,
brick):
"""
Expand the given Brick's data until its physical_box is aligned with the given padding_grid.
The data in the expanded region will be sourced from the given volume_accessor_func.
Note: padding_grid need not be identical to the grid the Brick was created with,
but it must divide evenly into that grid.
For instance, if padding_grid happens to be the same as the brick's own native grid,
then the phyiscal_box is expanded to align perfectly with the logical_box on all sides:
+-------------+ +-------------+
| physical | | | same |
|__________| | | physical |
| | --> | and |
| logical | | logical |
|_____________| |_____________|
Args:
brick: Brick
padding_grid: Grid
volume_accessor_func: Callable with signature: f(box) -> ndarray
Returns: Brick
Note: It is not legal to call this function unless the Brick's physical_box
lies completely within the logical_box (i.e. no halos allowed).
Furthremore, the padding_grid is not permitted to use a halo, either.
(These restrictions could be fixed, but the current version of this
function has these requirements.)
Note: If no padding is necessary, then the original Brick is returned (no copy is made).
"""
assert isinstance(padding_grid, Grid)
assert not padding_grid.halo_shape.any()
block_shape = padding_grid.block_shape
assert ((brick.logical_box - padding_grid.offset) % block_shape == 0).all(), \
f"Padding grid {padding_grid.offset} must be aligned with brick logical_box: {brick.logical_box}"
# Subtract offset to calculate the needed padding
offset_physical_box = brick.physical_box - padding_grid.offset
if (offset_physical_box % block_shape == 0).all():
# Internal data is already aligned to the padding_grid.
return brick
offset_padded_box = np.array([
offset_physical_box[0] // block_shape * block_shape,
(offset_physical_box[1] + block_shape - 1) // block_shape * block_shape
])
# Re-add offset
padded_box = offset_padded_box + padding_grid.offset
assert (padded_box[0] >= brick.logical_box[0]).all()
assert (padded_box[1] <= brick.logical_box[1]).all()
# Initialize a new volume of the fully-padded shape
padded_volume_shape = padded_box[1] - padded_box[0]
padded_volume = np.zeros(padded_volume_shape, dtype=brick.volume.dtype)
# Overwrite the previously existing data in the new padded volume
orig_box = brick.physical_box
orig_box_within_padded = orig_box - padded_box[0]
overwrite_subvol(padded_volume, orig_box_within_padded, brick.volume)
# Check for a non-zero-volume halo on all six sides.
halo_boxes = []
for axis in range(padded_volume.ndim):
if orig_box[0, axis] != padded_box[0, axis]:
leading_halo_box = padded_box.copy()
leading_halo_box[1, axis] = orig_box[0, axis]
halo_boxes.append(leading_halo_box)
if orig_box[1, axis] != padded_box[1, axis]:
trailing_halo_box = padded_box.copy()
trailing_halo_box[0, axis] = orig_box[1, axis]
halo_boxes.append(trailing_halo_box)
assert halo_boxes, \
"How could halo_boxes be empty if there was padding needed?"
for halo_box in halo_boxes:
# Retrieve padding data for one halo side
halo_volume = volume_accessor_func(halo_box)
# Overwrite in the final padded volume
halo_box_within_padded = halo_box - padded_box[0]
overwrite_subvol(padded_volume, halo_box_within_padded, halo_volume)
new_brick = Brick(brick.logical_box,
padded_box,
padded_volume,
location_id=brick.location_id,
compression=brick.compression)
brick.compress()
return new_brick
def test_dvid_volume_service_labelmap(setup_dvid_repo, random_segmentation,
disable_auto_retry):
server, uuid = setup_dvid_repo
instance_name = 'test-dvs-labelmap'
volume = random_segmentation[:256, :192, :128]
max_scale = 2
voxel_dimensions = [4.0, 4.0, 32.0]
config_text = textwrap.dedent(f"""\
dvid:
server: {server}
uuid: {uuid}
segmentation-name: {instance_name}
supervoxels: true
create-if-necessary: true
creation-settings:
max-scale: {max_scale}
voxel-size: {voxel_dimensions}
geometry:
bounding-box: [[0,0,0], {list(volume.shape[::-1])}]
message-block-shape: [64,64,64]
""")
yaml = YAML()
with StringIO(config_text) as f:
volume_config = yaml.load(f)
assert instance_name not in fetch_repo_instances(server, uuid)
service = VolumeService.create_from_config(volume_config)
repo_instances = fetch_repo_instances(server, uuid)
assert instance_name in repo_instances
assert repo_instances[instance_name] == 'labelmap'
info = fetch_instance_info(server, uuid, instance_name)
assert info["Extended"]["VoxelSize"] == voxel_dimensions
scaled_volumes = {}
for scale in range(max_scale + 1):
vol = downsample(volume, 2**scale, 'label')
aligned_shape = (np.ceil(np.array(vol.shape) / 64) * 64).astype(int)
aligned_vol = np.zeros(aligned_shape, np.uint64)
overwrite_subvol(aligned_vol, [(0, 0, 0), vol.shape], vol)
service.write_subvolume(aligned_vol, (0, 0, 0), scale)
scaled_volumes[scale] = aligned_vol
box = np.array([[40, 80, 40], [240, 160, 100]])
for scale in range(max_scale + 1):
scaled_box = box // 2**scale
vol = service.get_subvolume(scaled_box, scale)
assert (vol == extract_subvol(scaled_volumes[scale], scaled_box)).all()
#
# Check sparse coords function
#
labels = list({*pd.unique(volume.reshape(-1))} - {0})
brick_coords_df = service.sparse_brick_coords_for_labels(labels)
assert brick_coords_df.columns.tolist() == ['z', 'y', 'x', 'label']
assert set(brick_coords_df['label'].values) == set(labels), \
"Some labels were missing from the sparse brick coords!"
def ndi(shape):
return np.indices(shape).reshape(len(shape), -1).transpose()
expected_df = pd.DataFrame(ndi(volume.shape), columns=[*'zyx'])
expected_df['label'] = volume.reshape(-1)
expected_df['z'] //= 64
expected_df['y'] //= 64
expected_df['x'] //= 64
expected_df = expected_df.drop_duplicates()
expected_df['z'] *= 64
expected_df['y'] *= 64
expected_df['x'] *= 64
expected_df = expected_df.query('label != 0')
expected_df.sort_values(['z', 'y', 'x', 'label'], inplace=True)
brick_coords_df.sort_values(['z', 'y', 'x', 'label'], inplace=True)
expected_df.reset_index(drop=True, inplace=True)
brick_coords_df.reset_index(drop=True, inplace=True)
assert expected_df.shape == brick_coords_df.shape
assert (brick_coords_df == expected_df).all().all()
#
# Check sample_labels()
#
points = [np.random.randint(d, size=(10, )) for d in vol.shape]
points = np.transpose(points)
labels = service.sample_labels(points)
assert (labels == volume[(*points.transpose(), )]).all()
