def TransferTask(
src_path,
dest_path,
mip,
shape,
offset,
translate=(0, 0, 0), # change of origin
fill_missing=False,
skip_first=False,
skip_downsamples=False,
delete_black_uploads=False,
background_color=0,
sparse=False,
axis='z',
agglomerate=False,
timestamp=None,
compress='gzip',
factor=None):
shape = Vec(*shape)
offset = Vec(*offset)
fill_missing = bool(fill_missing)
translate = Vec(*translate)
delete_black_uploads = bool(delete_black_uploads)
sparse = bool(sparse)
skip_first = bool(skip_first)
skip_downsamples = bool(skip_downsamples)
srccv = CloudVolume(src_path,
fill_missing=fill_missing,
mip=mip,
bounded=False)
destcv = CloudVolume(dest_path,
fill_missing=fill_missing,
mip=mip,
delete_black_uploads=delete_black_uploads,
background_color=background_color,
compress=compress)
dst_bounds = Bbox(offset, shape + offset)
dst_bounds = Bbox.clamp(dst_bounds, destcv.bounds)
src_bounds = dst_bounds - translate
image = srccv.download(src_bounds,
agglomerate=agglomerate,
timestamp=timestamp)
if skip_downsamples:
destcv[dst_bounds] = image
else:
downsample_and_upload(image,
dst_bounds,
destcv,
shape,
mip=mip,
skip_first=skip_first,
sparse=sparse,
axis=axis,
factor=factor)
def execute(self):
self._volume = CloudVolume(
self.layer_path, self.options['mip'], bounded=False,
parallel=self.options['parallel_download'],
fill_missing=self.options['fill_missing']
)
self._bounds = Bbox(self.offset, self.shape + self.offset)
self._bounds = Bbox.clamp(self._bounds, self._volume.bounds)
self.progress = bool(self.options['progress'])
self._mesher = zmesh.Mesher(self._volume.resolution)
# Marching cubes loves its 1vx overlaps.
# This avoids lines appearing between
# adjacent chunks.
data_bounds = self._bounds.clone()
data_bounds.minpt -= self.options['low_padding']
data_bounds.maxpt += self.options['high_padding']
self._mesh_dir = self.get_mesh_dir()
if self.options['encoding'] == 'draco':
self.draco_encoding_settings = draco_encoding_settings(
shape=(self.shape + self.options['low_padding'] + self.options['high_padding']),
offset=self.offset,
resolution=self._volume.resolution,
compression_level=self.options["draco_compression_level"],
create_metadata=self.options['draco_create_metadata'],
uses_new_draco_bin_size=False,
)
# chunk_position includes the overlap specified by low_padding/high_padding
# agglomerate, timestamp, stop_layer only applies to graphene volumes,
# no-op for precomputed
data = self._volume.download(
data_bounds,
agglomerate=self.options['agglomerate'],
timestamp=self.options['timestamp'],
stop_layer=self.options['stop_layer']
)
if not np.any(data):
if self.options['spatial_index']:
self._upload_spatial_index(self._bounds, {})
return
data = self._remove_dust(data, self.options['dust_threshold'])
data = self._remap(data)
if self.options['object_ids']:
data = fastremap.mask_except(data, self.options['object_ids'], in_place=True)
data, renumbermap = fastremap.renumber(data, in_place=True)
renumbermap = { v:k for k,v in renumbermap.items() }
self.compute_meshes(data, renumbermap)
def execute(self):
srccv = CloudVolume(self.src_path, fill_missing=self.fill_missing, mip=self.mip)
destcv = CloudVolume(self.dest_path, fill_missing=self.fill_missing, mip=self.mip)
bounds = Bbox(self.offset, self.shape + self.offset)
bounds = Bbox.clamp(bounds, srccv.bounds)
image = srccv[bounds.to_slices()]
bounds += self.translate
bounds = Bbox.clamp(bounds, destcv.bounds)
downsample_and_upload(image, bounds, destcv, self.shape, mip=self.mip)
def test_slices_from_global_coords():
delete_layer()
cv, data = create_layer(size=(1024, 1024, 5, 1), offset=(7,0,0))
bbox = Bbox( (10, 10, 1), (100, 100, 2) )
scale = cv.info['scales'][0]
scale = copy.deepcopy(scale)
scale['voxel_offset'] = [ 3, 0, 0 ]
scale['volume_size'] = [ 512, 512, 5 ]
scale['resolution'] = [ 2, 2, 1 ]
scale['key'] = '2_2_1'
cv.info['scales'].append(scale)
cv.commit_info()
assert len(cv.available_mips) == 2
cv.mip = 1
slices = cv.slices_from_global_coords( Bbox( (100, 100, 1), (500, 512, 2) ) )
result = Bbox.from_slices(slices)
assert result == Bbox( (50, 50, 1), (250, 256, 2) )
cv.mip = 0
slices = cv.slices_from_global_coords( Bbox( (100, 100, 1), (500, 512, 2) ) )
result = Bbox.from_slices(slices)
assert result == Bbox( (100, 100, 1), (500, 512, 2) )
slices = cv.slices_from_global_coords( np.s_[:,:,:] )
result = Bbox.from_slices(slices)
assert result == Bbox( (7, 0, 0), ( 1031, 1024, 5) )
def execute(self):
srcvol = CloudVolume(self.source_layer_path, mip=0, fill_missing=self.fill_missing)
bounds = Bbox( self.offset, self.shape + self.offset )
bounds = Bbox.clamp(bounds, srcvol.bounds)
image = srcvol[ bounds.to_slices() ][ :, :, :, :1 ] # only use x affinity
image = (image * 255.0).astype(np.uint8)
destvol = CloudVolume(self.dest_layer_path, mip=0)
downsample_and_upload(image, bounds, destvol, self.shape, mip=0, axis='z')
def execute(self):
vol = CloudVolume(self.layer_path, self.mip,
fill_missing=self.fill_missing)
bounds = Bbox(self.offset, self.shape + self.offset)
bounds = Bbox.clamp(bounds, vol.bounds)
image = vol[ bounds.to_slices() ]
downsample_and_upload(
image, bounds, vol,
self.shape, self.mip, self.axis,
skip_first=True, sparse=self.sparse
)
def BlackoutTask( cloudpath, mip, shape, offset, value=0, non_aligned_writes=False ): shape = Vec(*shape) offset = Vec(*offset) vol = CloudVolume(cloudpath, mip, non_aligned_writes=non_aligned_writes) bounds = Bbox(offset, shape + offset) bounds = Bbox.clamp(bounds, vol.bounds) img = np.zeros(bounds.size3(), dtype=vol.dtype) + value vol[bounds] = img
def execute(self):
vol = CloudVolume(self.layer_path)
highres_bbox = Bbox(self.offset, self.offset + self.shape)
for mip in vol.available_mips:
vol.mip = mip
slices = vol.slices_from_global_coords(highres_bbox.to_slices())
bbox = Bbox.from_slices(slices).round_to_chunk_size(
vol.underlying, offset=vol.bounds.minpt)
vol.delete(bbox)
def compute_build_bounding_box(storage, prefix='build/'):
bboxes = []
for filename in tqdm(storage.list_files(prefix=prefix), desc='Computing Bounds'):
bbox = Bbox.from_filename(filename)
bboxes.append(bbox)
bounds = Bbox.expand(*bboxes)
chunk_size = reduce(max2, map(lambda bbox: bbox.size3(), bboxes))
print('bounds={} (size: {}); chunk_size={}'.format(bounds, bounds.size3(), chunk_size))
return bounds, chunk_size
def execute(self):
self.cv = CloudVolume(
self.cloudpath,
mip=self.mip,
bounded=False,
fill_missing=self.options['fill_missing'],
mesh_dir=self.options['mesh_dir'],
)
if self.cv.mesh.meta.is_sharded() == False:
raise ValueError("The mesh sharding parameter must be defined.")
self.bounds = Bbox(self.offset, self.shape + self.offset)
self.bounds = Bbox.clamp(self.bounds, self.cv.bounds)
self.progress = bool(self.options['progress'])
self.mesher = zmesh.Mesher(self.cv.resolution)
# Marching cubes needs 1 voxel overlap to properly
# stitch adjacent meshes.
# data_bounds = self.bounds.clone()
# data_bounds.maxpt += self.overlap_vx
self.mesh_dir = self.get_mesh_dir()
self.draco_encoding_settings = draco_encoding_settings(
shape=(self.shape + self.overlap_vx),
offset=self.offset,
resolution=self.cv.resolution,
compression_level=1,
create_metadata=True,
uses_new_draco_bin_size=self.cv.meta.uses_new_draco_bin_size,
)
chunk_pos = self.cv.meta.point_to_chunk_position(self.bounds.center(),
mip=self.mip)
img = mesh_graphene_remap.remap_segmentation(
self.cv,
chunk_pos.x,
chunk_pos.y,
chunk_pos.z,
mip=self.mip,
overlap_vx=self.overlap_vx,
time_stamp=self.timestamp,
progress=self.progress,
)
if not np.any(img):
return
self.upload_meshes(self.compute_meshes(img))
def create_blackout_tasks(cloudpath: str,
bounds: Bbox,
mip: int = 0,
shape: ShapeType = (2048, 2048, 64),
value: int = 0,
non_aligned_writes: bool = False):
vol = CloudVolume(cloudpath, mip=mip)
shape = Vec(*shape)
bounds = Bbox.create(bounds)
bounds = vol.bbox_to_mip(bounds, mip=0, to_mip=mip)
if not non_aligned_writes:
bounds = bounds.expand_to_chunk_size(vol.chunk_size, vol.voxel_offset)
bounds = Bbox.clamp(bounds, vol.mip_bounds(mip))
class BlackoutTaskIterator(FinelyDividedTaskIterator):
def task(self, shape, offset):
bounded_shape = min2(shape, vol.bounds.maxpt - offset)
return partial(
igneous.tasks.BlackoutTask,
cloudpath=cloudpath,
mip=mip,
shape=shape.clone(),
offset=offset.clone(),
value=value,
non_aligned_writes=non_aligned_writes,
)
def on_finish(self):
vol.provenance.processing.append({
'method': {
'task': 'BlackoutTask',
'cloudpath': cloudpath,
'mip': mip,
'non_aligned_writes': non_aligned_writes,
'value': value,
'shape': shape.tolist(),
'bounds': [
bounds.minpt.tolist(),
bounds.maxpt.tolist(),
],
},
'by':
operator_contact(),
'date':
strftime('%Y-%m-%d %H:%M %Z'),
})
return BlackoutTaskIterator(bounds, shape)
def child_upload_process(
meta,
cache,
img_shape,
offset,
mip,
compress,
cdn_cache,
progress,
location,
location_bbox,
location_order,
delete_black_uploads,
background_color,
green,
chunk_ranges,
compress_level=None,
):
global fs_lock
reset_connection_pools()
shared_shape = img_shape
if location_bbox:
shared_shape = list(location_bbox.size3()) + [meta.num_channels]
array_like, renderbuffer = shm.ndarray(shape=shared_shape,
dtype=meta.dtype,
location=location,
order=location_order,
lock=fs_lock,
readonly=True)
if location_bbox:
cutout_bbox = Bbox(offset, offset + img_shape[:3])
delta_box = cutout_bbox.clone() - location_bbox.minpt
renderbuffer = renderbuffer[delta_box.to_slices()]
threaded_upload_chunks(
meta,
cache,
renderbuffer,
mip,
chunk_ranges,
compress=compress,
cdn_cache=cdn_cache,
progress=progress,
delete_black_uploads=delete_black_uploads,
background_color=background_color,
green=green,
compress_level=compress_level,
)
array_like.close()
def upload_build_chunks(storage, volume, offset=[0, 0, 0], build_chunk_size=[1024,1024,128]):
offset = Vec(*offset)
shape = Vec(*volume.shape[:3])
build_chunk_size = Vec(*build_chunk_size)
for spt in xyzrange( (0,0,0), shape, build_chunk_size):
ept = min2(spt + build_chunk_size, shape)
bbox = Bbox(spt, ept)
chunk = volume[ bbox.to_slices() ]
bbox += offset
filename = 'build/{}'.format(bbox.to_filename())
storage.put_file(filename, chunks.encode_npz(chunk))
storage.wait()
def select_bounding_boxes(self, dataset_bounds):
# Sample 1024x1024x1 patches until coverage factor is
# satisfied. Ensure the patches are non-overlapping and
# random.
sample_shape = Bbox( (0,0,0), (2048, 2048, 1) )
area = self.shape.rectVolume()
total_patches = int(math.ceil(area / sample_shape.volume()))
N = int(math.ceil(float(total_patches) * self.coverage_factor))
# Simplification: We are making patch selection against a discrete
# grid instead of a continuous space. This removes the influence of
# overlap in a less complex fashion.
patch_indicies = set()
while len(patch_indicies) < N:
ith_patch = random.randint(0, (total_patches - 1))
patch_indicies.add(ith_patch)
gridx = int(math.ceil(self.shape.x / sample_shape.size3().x))
bboxes = []
for i in patch_indicies:
patch_start = Vec( i % gridx, i // gridx, 0 )
patch_start *= sample_shape.size3()
patch_start += self.offset
bbox = Bbox( patch_start, patch_start + sample_shape.size3() )
bbox = Bbox.clamp(bbox, dataset_bounds)
bboxes.append(bbox)
return bboxes
def create_blackout_tasks(cloudpath,
bounds,
mip=0,
shape=(2048, 2048, 64),
value=0,
non_aligned_writes=False):
vol = CloudVolume(cloudpath, mip=mip)
shape = Vec(*shape)
bounds = Bbox.create(bounds)
bounds = vol.bbox_to_mip(bounds, mip=0, to_mip=mip)
bounds = Bbox.clamp(bounds, vol.mip_bounds(mip))
class BlackoutTaskIterator():
def __len__(self):
return num_tasks(bounds, shape)
def __iter__(self):
for startpt in xyzrange(bounds.minpt, bounds.maxpt, shape):
bounded_shape = min2(shape, vol.bounds.maxpt - startpt)
yield igneous.tasks.BlackoutTask(
cloudpath=cloudpath,
mip=mip,
shape=shape.clone(),
offset=startpt.clone(),
value=value,
non_aligned_writes=non_aligned_writes,
)
vol.provenance.processing.append({
'method': {
'task': 'BlackoutTask',
'cloudpath': cloudpath,
'mip': mip,
'non_aligned_writes': non_aligned_writes,
'value': value,
'shape': shape.tolist(),
'bounds': [
bounds.minpt.tolist(),
bounds.maxpt.tolist(),
],
},
'by':
OPERATOR_CONTACT,
'date':
strftime('%Y-%m-%d %H:%M %Z'),
})
return BlackoutTaskIterator()
def create_touch_tasks(self,
cloudpath,
mip=0,
shape=(2048, 2048, 64),
bounds=None):
vol = CloudVolume(cloudpath, mip=mip)
shape = Vec(*shape)
if bounds is None:
bounds = vol.bounds.clone()
bounds = Bbox.create(bounds)
bounds = vol.bbox_to_mip(bounds, mip=0, to_mip=mip)
bounds = Bbox.clamp(bounds, vol.mip_bounds(mip))
class TouchTaskIterator():
def __len__(self):
return num_tasks(bounds, shape)
def __iter__(self):
for startpt in xyzrange(bounds.minpt, bounds.maxpt, shape):
bounded_shape = min2(shape, vol.bounds.maxpt - startpt)
yield igneous.tasks.TouchTask(
cloudpath=cloudpath,
shape=bounded_shape.clone(),
offset=startpt.clone(),
mip=mip,
)
vol.provenance.processing.append({
'method': {
'task': 'TouchTask',
'mip': mip,
'shape': shape.tolist(),
'bounds': [
bounds.minpt.tolist(),
bounds.maxpt.tolist(),
],
},
'by':
OPERATOR_CONTACT,
'date':
strftime('%Y-%m-%d %H:%M %Z'),
})
vol.commit_provenance()
return TouchTaskIterator()
def get_bounds(vol, bounds, shape, mip, chunk_size=None):
if bounds is None:
bounds = vol.bounds.clone()
else:
bounds = Bbox.create(bounds)
bounds = vol.bbox_to_mip(bounds, mip=0, to_mip=mip)
if chunk_size is not None:
bounds = bounds.expand_to_chunk_size(chunk_size,
vol.mip_voxel_offset(mip))
bounds = Bbox.clamp(bounds, vol.mip_bounds(mip))
print("Volume Bounds: ", vol.mip_bounds(mip))
print("Selected ROI: ", bounds)
return bounds
def test_compute_build_bounding_box():
delete_layer()
storage = create_storage()
random_data = np.random.randint(255, size=(256, 256, 128), dtype=np.uint8)
# Easy, power of two, 0 offsets
task_creation.upload_build_chunks(storage,
random_data,
offset=(0, 0, 0),
build_chunk_size=(128, 128, 32))
bounds, chunk_size = task_creation.compute_build_bounding_box(storage)
assert np.all(chunk_size == (128, 128, 32))
assert bounds == Bbox((0, 0, 0), (256, 256, 128))
# Prime offsets
delete_layer()
task_creation.upload_build_chunks(storage,
random_data,
offset=(3, 23, 5),
build_chunk_size=(128, 128, 32))
bounds, chunk_size = task_creation.compute_build_bounding_box(storage)
assert np.all(chunk_size == (128, 128, 32))
assert bounds == Bbox((3, 23, 5), (256 + 3, 256 + 23, 128 + 5))
# Non-power of two edges, 0 offsets
random_data2 = random_data[:100, :100, :106]
delete_layer()
task_creation.upload_build_chunks(storage,
random_data2,
offset=(0, 0, 0),
build_chunk_size=(32, 32, 32))
bounds, chunk_size = task_creation.compute_build_bounding_box(storage)
assert np.all(chunk_size == (32, 32, 32))
assert bounds == Bbox((0, 0, 0), (100, 100, 106))
# Non-power of two edges, offsets
delete_layer()
task_creation.upload_build_chunks(storage,
random_data2,
offset=(3, 23, 5),
build_chunk_size=(64, 64, 32))
bounds, chunk_size = task_creation.compute_build_bounding_box(storage)
assert np.all(chunk_size == (64, 64, 32))
assert bounds == Bbox((3, 23, 5), (100 + 3, 100 + 23, 106 + 5))
def fetch_z_levels(self):
bounds = Bbox(self.offset, self.shape[:3] + self.offset)
levelfilenames = [
'levels/{}/{}'.format(self.mip, z) \
for z in range(bounds.minpt.z, bounds.maxpt.z)
]
with Storage(self.levels_path) as stor:
levels = stor.get_files(levelfilenames)
errors = [
level['filename'] \
for level in levels if level['content'] == None
]
if len(errors):
raise Exception(", ".join(
errors) + " were not defined. Did you run a LuminanceLevelsTask for these slices?")
levels = [(
int(os.path.basename(item['filename'])),
json.loads(item['content'].decode('utf-8'))
) for item in levels ]
levels.sort(key=lambda x: x[0])
levels = [x[1] for x in levels]
return [ np.array(x['levels'], dtype=np.uint64) for x in levels ]
def _create_thumbnail(self, chunk):
logging.info('creating thumbnail...')
thumbnail_layer_path = os.path.join(self.volume_path, 'thumbnail')
thumbnail_volume = CloudVolume(thumbnail_layer_path,
compress='gzip',
fill_missing=True,
bounded=False,
autocrop=True,
mip=self.mip,
cache=False,
green_threads=True,
progress=False)
# only use the last channel, it is the Z affinity
# if this is affinitymap
image = chunk[-1, :, :, :]
if np.issubdtype(image.dtype, np.floating):
image = (image * 255).astype(np.uint8)
#self.thumbnail_operator(image)
# transpose to xyzc
image = np.transpose(image)
image_bbox = Bbox.from_slices(chunk.slices[::-1][:3])
downsample_and_upload(image,
image_bbox,
thumbnail_volume,
Vec(*(image.shape)),
mip=self.mip,
max_mip=6,
axis='z',
skip_first=True,
only_last_mip=True)
def agglomerate_group(seg_map, merge_output, gid=None, relabel=True):
if seg_map == {}:
return {}
G = nx.Graph()
G.add_nodes_from(seg_map.keys())
# find neighbors
for k1, k2 in itertools.product(seg_map.keys(), seg_map.keys()):
bb1, p1 = seg_map[k1]['bbox'], seg_map[k1]['output']
bb2, p2 = seg_map[k2]['bbox'], seg_map[k2]['output']
int_bb = Bbox.intersection(bb1, bb2)
if not int_bb.empty() and k1 != k2:
G.add_edge(k1, k2)
# agglomerate each pair and rewrite cloud volume
for k1, k2 in G.edges():
p1 = seg_map[k1]['output']
p2 = seg_map[k2]['output']
if relabel:
remap_label = agglomerate(p1,
p2,
contiguous=False,
inplace=True,
no_zero=True)
return merge(seg_map, merge_output, gid)
def __iter__(self):
for x, y, z in xyzrange(grid_size):
output_bounds = Bbox.from_slices(
tuple(
slice(s + x * b, s + x * b + b)
for (s, x, b) in zip(output_block_start, (
z, y, x), output_block_size)))
yield MaskAffinitymapTask(
aff_input_layer_path=aff_input_layer_path,
aff_output_layer_path=aff_output_layer_path,
aff_mip=aff_mip,
mask_layer_path=mask_layer_path,
mask_mip=mask_mip,
output_bounds=output_bounds,
)
vol = CloudVolume(output_layer_path, mip=aff_mip)
vol.provenance.processing.append({
'method': {
'task': 'InferenceTask',
'aff_input_layer_path': aff_input_layer_path,
'aff_output_layer_path': aff_output_layer_path,
'aff_mip': aff_mip,
'mask_layer_path': mask_layer_path,
'mask_mip': mask_mip,
'output_block_start': output_block_start,
'output_block_size': output_block_size,
'grid_size': grid_size,
},
'by':
OPERATOR_CONTACT,
'date':
strftime('%Y-%m-%d %H:%M %Z'),
})
vol.commit_provenance()
def execute(self):
vol = CloudVolume(self.cloudpath,
mip=self.mip,
info=self.info,
cdn_cache=False)
bbox = Bbox.clamp(self.bounds, vol.bounds)
path = skeldir(self.cloudpath)
path = os.path.join(self.cloudpath, path)
all_labels = vol[bbox.to_slices()]
all_labels = all_labels[:, :, :, 0]
skeletons = kimimaro.skeletonize(all_labels,
self.teasar_params,
object_ids=self.object_ids,
anisotropy=vol.resolution,
dust_threshold=1000,
cc_safety_factor=0.25,
progress=False,
fix_branching=self.fix_branching)
for segid, skel in six.iteritems(skeletons):
skel.vertices[:, 0] += bbox.minpt.x * vol.resolution.x
skel.vertices[:, 1] += bbox.minpt.y * vol.resolution.y
skel.vertices[:, 2] += bbox.minpt.z * vol.resolution.z
self.upload(vol, path, bbox, skeletons.values())
def from_array(cls, arr: np.ndarray):
bboxes = []
for idx in range(arr.shape(0)):
bbox = Bbox.from_vec(arr[idx, :])
bboxes.append(bbox)
return cls(bboxes)
def _create_mesh(self, obj_id, left_bound_offset):
mesh = self._mesher.get_mesh(
obj_id,
simplification_factor=self.options['simplification_factor'],
max_simplification_error=self.options['max_simplification_error'],
voxel_centered=True,
)
self._mesher.erase(obj_id)
resolution = self._volume.resolution
offset = (self._bounds.minpt - self.options['low_padding']).astype(
np.float32)
mesh.vertices[:] += (offset - left_bound_offset) * resolution
mesh_bounds = Bbox(np.amin(mesh.vertices, axis=0),
np.amax(mesh.vertices, axis=0))
if self.options['encoding'] == 'draco':
mesh_binary = DracoPy.encode(mesh.vertices, mesh.faces,
**self.draco_encoding_settings)
elif self.options['encoding'] == 'precomputed':
mesh_binary = mesh.to_precomputed()
return mesh_binary, mesh_bounds
def crop(self, bbox):
"""
Crop away all vertices and edges that lie outside of the given bbox.
The edge counts as inside.
Returns: new PrecomputedSkeleton
"""
skeleton = self.clone()
bbox = Bbox.create(bbox)
if skeleton.empty():
return skeleton
nodes_valid_mask = np.array(
[bbox.contains(vtx) for vtx in skeleton.vertices], dtype=np.bool)
nodes_valid_idx = np.where(nodes_valid_mask)[0]
# Set invalid vertices to be duplicates
# so they'll be removed during consolidation
if nodes_valid_idx.shape[0] == 0:
return PrecomputedSkeleton()
first_node = nodes_valid_idx[0]
skeleton.vertices[~nodes_valid_mask] = skeleton.vertices[first_node]
edges_valid_mask = np.isin(skeleton.edges, nodes_valid_idx)
edges_valid_idx = edges_valid_mask[:, 0] * edges_valid_mask[:, 1]
skeleton.edges = skeleton.edges[edges_valid_idx, :]
return skeleton.consolidate()
def execute(self):
vol = CloudVolume(
self.cloudpath, mip=self.mip,
info=self.info, cdn_cache=False,
parallel=self.parallel
)
bbox = Bbox.clamp(self.bounds, vol.bounds)
path = skeldir(self.cloudpath)
path = os.path.join(self.cloudpath, path)
all_labels = vol[ bbox.to_slices() ]
all_labels = all_labels[:,:,:,0]
if self.mask_ids:
all_labels = fastremap.mask(all_labels, self.mask_ids)
skeletons = kimimaro.skeletonize(
all_labels, self.teasar_params,
object_ids=self.object_ids, anisotropy=vol.resolution,
dust_threshold=self.dust_threshold, cc_safety_factor=0.25,
progress=self.progress,
fix_branching=self.fix_branching,
fix_borders=self.fix_borders,
parallel=self.parallel,
)
for segid, skel in six.iteritems(skeletons):
skel.vertices[:] += bbox.minpt * vol.resolution
self.upload(vol, path, bbox, skeletons.values())
def __call__(self, chunk):
assert 3 == chunk.ndim
voxel_offset = chunk.voxel_offset
num_mips = self.stop_mip - self.chunk_mip
# tinybrain use F order and require 4D array!
chunk2 = np.transpose(chunk)
# chunk2 = np.reshape(chunk2, (*chunk2.shape, 1))
chunk2 = np.expand_dims(chunk2, 3)
if np.issubdtype(chunk.dtype, np.floating) or chunk.dtype == np.uint8:
pyramid = tinybrain.downsample_with_averaging(
chunk2, factor=self.factor[::-1], num_mips=num_mips)
else:
pyramid = tinybrain.downsample_segmentation(
chunk2, factor=self.factor[::-1], num_mips=num_mips)
for mip in range(self.start_mip, self.stop_mip):
# the first chunk in pyramid is already downsampled!
downsampled_chunk = pyramid[mip - self.chunk_mip - 1]
# compute new offset, only downsample the y,x dimensions
offset = np.divide(
voxel_offset,
np.asarray([
self.factor[0]**(mip - self.chunk_mip),
self.factor[1]**(mip - self.chunk_mip),
self.factor[2]**(mip - self.chunk_mip)
]))
bbox = Bbox.from_delta(offset, downsampled_chunk.shape[0:3][::-1])
# upload downsampled chunk, note that we should use F order in the indexing
self.vols[mip][bbox.to_slices()[::-1]] = downsampled_chunk
def test_bbox_hashing():
bbx = Bbox.from_list([1, 2, 3, 4, 5, 6])
d = {}
d[bbx] = 1
assert len(d) == 1
for k, v in d.items():
assert v == 1
bbx = Bbox((1., 1.3, 2.), (3., 4., 4.))
d = {}
d[bbx] = 1
assert len(d) == 1
for k, v in d.items():
assert v == 1
def to_volumecutout(img,
image_type,
resolution=None,
offset=None,
hostname='localhost'):
from cloudvolume.volumecutout import VolumeCutout
if type(img) == VolumeCutout:
try:
img.dataset_name # check if it's an intact VolumeCutout
return img
except AttributeError:
pass
resolution = getresolution(img, resolution)
offset = getoffset(img, offset)
return VolumeCutout(
buf=img,
path=ExtractedPath('mem', hostname, '/', '', '', '', ''),
cloudpath='IN MEMORY',
resolution=resolution,
mip=-1,
layer_type=image_type,
bounds=Bbox(offset, offset + Vec(*(img.shape[:3]))),
handle=None,
)
