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 get_bounds(vol, bounds, mip, bounds_mip=0, chunk_size=None):
"""Return bounds of vol at mip, or snap bounds at src_mip to chunk_size
Args:
vol (CloudVolume)
bounds (Bbox-like object)
mip (int): mip level of returned bounds
bounds_mip (int): mip level of input bounds
chunk_size (Vec-like object): if bounds are set, can set chunk_size for snapping
Returns:
Bbox for bounds
"""
if bounds is None:
bounds = vol.meta.bounds(mip)
else:
bounds = Bbox.create(bounds)
bounds = vol.bbox_to_mip(bounds, mip=bounds_mip, to_mip=mip)
if chunk_size is not None:
bounds = bounds.expand_to_chunk_size(chunk_size,
vol.meta.voxel_offset(mip))
bounds = Bbox.clamp(bounds, vol.meta.bounds(mip))
print("Volume Bounds: ", vol.meta.bounds(mip))
print("Selected ROI: ", bounds)
return bounds
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 ImageShardTransferTask(
src_path: str,
dst_path: str,
shape: ShapeType,
offset: ShapeType,
mip: int = 0,
fill_missing: bool = False,
translate: ShapeType = (0, 0, 0),
agglomerate: bool = False,
timestamp: Optional[int] = None,
):
"""
Generates a sharded image volume from
a preexisting CloudVolume readable data
source. Downsamples are not generated.
The sharded specification can be read here:
Shard Container:
https://github.com/google/neuroglancer/blob/056a3548abffc3c76c93c7a906f1603ce02b5fa3/src/neuroglancer/datasource/precomputed/sharded.md
Sharded Images:
https://github.com/google/neuroglancer/blob/056a3548abffc3c76c93c7a906f1603ce02b5fa3/src/neuroglancer/datasource/precomputed/volume.md#unsharded-chunk-storage
"""
shape = Vec(*shape)
offset = Vec(*offset)
mip = int(mip)
fill_missing = bool(fill_missing)
translate = Vec(*translate)
src_vol = CloudVolume(
src_path, fill_missing=fill_missing,
mip=mip, bounded=False
)
dst_vol = CloudVolume(
dst_path,
fill_missing=fill_missing,
mip=mip,
compress=None
)
dst_bbox = Bbox(offset, offset + shape)
dst_bbox = Bbox.clamp(dst_bbox, dst_vol.meta.bounds(mip))
dst_bbox = dst_bbox.expand_to_chunk_size(
dst_vol.meta.chunk_size(mip),
offset=dst_vol.meta.voxel_offset(mip)
)
src_bbox = dst_bbox - translate
img = src_vol.download(
src_bbox, agglomerate=agglomerate, timestamp=timestamp
)
(filename, shard) = dst_vol.image.make_shard(
img, dst_bbox, mip, progress=False
)
del img
basepath = dst_vol.meta.join(
dst_vol.cloudpath, dst_vol.meta.key(mip)
)
CloudFiles(basepath).put(filename, shard)
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, zero_as_background=self.zero_as_background)
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[:3] + self.offset )
bounds = Bbox.clamp(bounds, srccv.bounds)
image = srccv[ bounds.to_slices() ].astype(np.float32)
zlevels = self.fetch_z_levels()
nbits = np.dtype(srccv.dtype).itemsize * 8
maxval = float(2 ** nbits - 1)
for z in range(bounds.minpt.z, bounds.maxpt.z):
imagez = z - bounds.minpt.z
zlevel = zlevels[ imagez ]
(lower, upper) = self.find_section_clamping_values(zlevel, self.clip_fraction, 1 - self.clip_fraction)
if lower == upper:
continue
img = image[:,:,imagez]
img = (img - float(lower)) * (maxval / (float(upper) - float(lower)))
image[:,:,imagez] = img
image = np.round(image)
image = np.clip(image, 0.0, maxval).astype(destcv.dtype)
bounds += self.translate
downsample_and_upload(image, bounds, destcv, self.shape)
def execute(self):
self._mesher = Mesher()
self._volume = CloudVolume(self.layer_path, self.mip, bounded=False)
self._bounds = Bbox( self.offset, self.shape + self.offset )
self._bounds = Bbox.clamp(self._bounds, self._volume.bounds)
# Marching cubes loves its 1vx overlaps.
# This avoids lines appearing between
# adjacent chunks.
data_bounds = self._bounds.clone()
data_bounds.minpt -= 1
data_bounds.maxpt += 1
self._mesh_dir = None
if 'meshing' in self._volume.info:
self._mesh_dir = self._volume.info['meshing']
elif 'mesh' in self._volume.info:
self._mesh_dir = self._volume.info['mesh']
if not self._mesh_dir:
raise ValueError("The mesh destination is not present in the info file.")
self._data = self._volume[data_bounds.to_slices()] # chunk_position includes a 1 pixel overlap
self._compute_meshes()
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 execute(self):
srccv = CloudVolume(self.src_path)
destcv = CloudVolume(self.dest_path)
bounds = Bbox( self.offset, self.shape + self.offset )
bounds = Bbox.clamp(bounds, srccv.bounds)
remap = self._get_map()
watershed_data = srccv[ bounds.to_slices() ]
# Here's how the remapping works. Numpy has a special
# indexing that can be used to perform the remap.
# The remap array is a key:value mapping where the
# array index is the key and the value is the contents.
# The watershed_data array contains only data values that
# are within the length of the remap array.
#
# e.g.
#
# remap = np.array([1,2,3]) # i.e. 0=>1, 1=>2, 1=>3
# vals = np.array([0,1,1,1,2,0,2,1,2])
#
# remap[vals] # array([1, 2, 2, 2, 3, 1, 3, 2, 3])
image = remap[watershed_data]
downsample_and_upload(image, bounds, destcv, self.shape)
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 execute(self):
self._volume = CloudVolume(
self.layer_path, self.options['mip'], bounded=False,
parallel=self.options['parallel_download'])
self._bounds = Bbox(self.offset, self.shape + self.offset)
self._bounds = Bbox.clamp(self._bounds, self._volume.bounds)
self._mesher = 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 = None
if self.options['mesh_dir'] is not None:
self._mesh_dir = self.options['mesh_dir']
elif 'mesh' in self._volume.info:
self._mesh_dir = self._volume.info['mesh']
if not self._mesh_dir:
raise ValueError("The mesh destination is not present in the info file.")
# chunk_position includes the overlap specified by low_padding/high_padding
self._data = self._volume[data_bounds.to_slices()]
self._remap()
self._compute_meshes()
def generate_chunks(meta, img, offset, mip):
shape = Vec(*img.shape)[:3]
offset = Vec(*offset)[:3]
bounds = Bbox(offset, shape + offset)
alignment_check = bounds.round_to_chunk_size(meta.chunk_size(mip),
meta.voxel_offset(mip))
if not np.all(alignment_check.minpt == bounds.minpt):
raise AlignmentError("""
Only chunk aligned writes are supported by this function.
Got: {}
Volume Offset: {}
Nearest Aligned: {}
""".format(bounds, meta.voxel_offset(mip), alignment_check))
bounds = Bbox.clamp(bounds, meta.bounds(mip))
img_offset = bounds.minpt - offset
img_end = Vec.clamp(bounds.size3() + img_offset, Vec(0, 0, 0), shape)
for startpt in xyzrange(img_offset, img_end, meta.chunk_size(mip)):
startpt = startpt.clone()
endpt = min2(startpt + meta.chunk_size(mip), shape)
spt = (startpt + bounds.minpt).astype(int)
ept = (endpt + bounds.minpt).astype(int)
yield (startpt, endpt, spt, ept)
def MeshSpatialIndex(
cloudpath:str,
shape:Tuple[int,int,int],
offset:Tuple[int,int,int],
mip:int = 0,
fill_missing:bool=False,
compress:Optional[Union[str,bool]] = 'gzip',
mesh_dir:Optional[str] = None
) -> None:
"""
The main way to add a spatial index is to use the MeshTask,
but old datasets or broken datasets may need it to be
reconstituted. An alternative use is create the spatial index
over a different area size than the mesh task.
"""
cv = CloudVolume(
cloudpath, mip=mip,
bounded=False, fill_missing=fill_missing
)
cf = CloudFiles(cloudpath)
bounds = Bbox(Vec(*offset), Vec(*shape) + Vec(*offset))
bounds = Bbox.clamp(bounds, cv.bounds)
data_bounds = bounds.clone()
data_bounds.maxpt += 1 # match typical Marching Cubes overlap
precision = cv.mesh.spatial_index.precision
resolution = cv.resolution
if not mesh_dir:
mesh_dir = cv.info["mesh"]
# remap: old img -> img
img, remap = cv.download(data_bounds, renumber=True)
img = img[...,0]
slcs = find_objects(img)
del img
reverse_map = { v:k for k,v in remap.items() } # img -> old img
bboxes = {}
for label, slc in enumerate(slcs):
if slc is None:
continue
mesh_bounds = Bbox.from_slices(slc)
mesh_bounds += Vec(*offset)
mesh_bounds *= Vec(*resolution, dtype=np.float32)
bboxes[str(reverse_map[label+1])] = \
mesh_bounds.astype(resolution.dtype).to_list()
bounds = bounds.astype(resolution.dtype) * resolution
cf.put_json(
f"{mesh_dir}/{bounds.to_filename(precision)}.spatial",
bboxes,
compress=compress,
cache_control=False,
)
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 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):
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):
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 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 create_connected_component_tasks(
descpath, segpath, storagestr, storagedir,
cc_thresh, sz_thresh, bounds, shape,
mip=(8, 8, 40), parallel=1, hashmax=1):
shape = Vec(*shape)
vol = CloudVolume(segpath, mip=mip)
# bounds = vol.bbox_to_mip(bounds, mip=0, to_mip=mip)
bounds = Bbox.clamp(bounds, vol.bounds)
class ConnectedComponentsTaskIterator(object):
def __init__(self, level_start, level_end):
self.level_start = level_start
self.level_end = level_end
def __len__(self):
return self.level_end - self.level_start
def __getitem__(self, slc):
itr = copy.deepcopy(self)
itr.level_start = self.level_start + slc.start
itr.level_end = self.level_start + slc.stop
return itr
def __iter__(self):
self.bounds = bounds.clone()
self.bounds.minpt.z = bounds.minpt.z + self.level_start * shape.z
self.bounds.maxpt.z = bounds.minpt.z + self.level_end * shape.z
for startpt in xyzrange( self.bounds.minpt, self.bounds.maxpt, shape ):
task_shape = min2(shape.clone(), self.bounds.maxpt - startpt)
task_bounds = Bbox( startpt, startpt + task_shape )
if task_bounds.volume() < 1:
continue
chunk_begin = tup2str(task_bounds.minpt)
chunk_end = tup2str(task_bounds.maxpt)
mip_str = tup2str(mip)
cmd = (f"chunk_ccs {descpath} {segpath} {storagestr}"
f" {cc_thresh} {sz_thresh} --chunk_begin {chunk_begin}"
f" --chunk_end {chunk_end} --hashmax {hashmax}"
f" --parallel {parallel} --mip {mip_str}"
f" --storagedir {storagedir}")
yield SynaptorTask(cmd)
level_end = int(math.ceil(bounds.size3().z / shape.z))
return ConnectedComponentsTaskIterator(0, level_end)
def QuantizeTask(
source_layer_path, dest_layer_path,
shape, offset, mip, fill_missing=False
):
shape = Vec(*shape)
offset = Vec(*offset)
srcvol = CloudVolume(source_layer_path, mip=mip,
fill_missing=fill_missing)
bounds = Bbox(offset, shape + 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(dest_layer_path, mip=mip)
downsample_and_upload(image, bounds, destvol, shape, mip=mip, axis='z')
def execute(self):
vol = CloudVolume(self.layer_path, mip=self.mip)
highres_bbox = Bbox( self.offset, self.offset + self.shape )
top_mip = min(vol.available_mips[-1], self.mip + self.num_mips)
for mip in range(self.mip, top_mip + 1):
vol.mip = mip
bbox = vol.bbox_to_mip(highres_bbox, self.mip, mip)
bbox = bbox.round_to_chunk_size(vol.underlying, offset=vol.bounds.minpt)
bbox = Bbox.clamp(bbox, vol.bounds)
if bbox.volume() == 0:
continue
vol.delete(bbox)
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(FinelyDividedTaskIterator):
def task(self, shape, offset):
bounded_shape = min2(shape, vol.bounds.maxpt - offset)
return igneous.tasks.TouchTask(
cloudpath=cloudpath,
shape=bounded_shape.clone(),
offset=offset.clone(),
mip=mip,
)
def on_finish(self):
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(bounds, shape)
def generate_chunks(meta, img, offset, mip):
shape = Vec(*img.shape)[:3]
offset = Vec(*offset)[:3]
bounds = Bbox(offset, shape + offset)
alignment_check = bounds.round_to_chunk_size(meta.chunk_size(mip),
meta.voxel_offset(mip))
if not np.all(alignment_check.minpt == bounds.minpt):
raise AlignmentError(f"""
Only chunk aligned writes are supported by this function.
Got: {bounds}
Volume Offset: {meta.voxel_offset(mip)}
Nearest Aligned: {alignment_check}
""")
bounds = Bbox.clamp(bounds, meta.bounds(mip))
img_offset = bounds.minpt - offset
img_end = Vec.clamp(bounds.size3() + img_offset, Vec(0, 0, 0), shape)
class ChunkIterator():
def __len__(self):
csize = meta.chunk_size(mip)
bbox = Bbox(img_offset, img_end)
# round up and avoid conversion to float
n_chunks = (bbox.dx + csize[0] - 1) // csize[0]
n_chunks *= (bbox.dy + csize[1] - 1) // csize[1]
n_chunks *= (bbox.dz + csize[2] - 1) // csize[2]
return n_chunks
def __iter__(self):
for startpt in xyzrange(img_offset, img_end, meta.chunk_size(mip)):
startpt = startpt.clone()
endpt = min2(startpt + meta.chunk_size(mip), shape)
spt = (startpt + bounds.minpt).astype(int)
ept = (endpt + bounds.minpt).astype(int)
yield (startpt, endpt, spt, ept)
return ChunkIterator()
def DeleteTask(layer_path:str, shape, offset, mip=0, num_mips=5):
"""Delete a block of images inside a layer on all mip levels."""
shape = Vec(*shape)
offset = Vec(*offset)
vol = CloudVolume(layer_path, mip=mip, max_redirects=0)
highres_bbox = Bbox( offset, offset + shape )
top_mip = min(vol.available_mips[-1], mip + num_mips)
for mip_i in range(mip, top_mip + 1):
vol.mip = mip_i
bbox = vol.bbox_to_mip(highres_bbox, mip, mip_i)
bbox = bbox.round_to_chunk_size(vol.chunk_size, offset=vol.bounds.minpt)
bbox = Bbox.clamp(bbox, vol.bounds)
if bbox.volume() == 0:
continue
vol.delete(bbox)
def execute(self):
srccv = CloudVolume(self.src_path, mip=self.mip, fill_missing=True)
# Accumulate a histogram of the luminance levels
nbits = np.dtype(srccv.dtype).itemsize * 8
levels = np.zeros(shape=(2 ** nbits,), dtype=np.uint64)
bounds = Bbox(self.offset, self.shape[:3] + self.offset)
bounds = Bbox.clamp(bounds, srccv.bounds)
bboxes = self.select_bounding_boxes(bounds)
for bbox in bboxes:
img2d = srccv[bbox.to_slices()].reshape((bbox.volume()))
cts = np.bincount(img2d)
levels[0:len(cts)] += cts.astype(np.uint64)
covered_area = sum([bbx.volume() for bbx in bboxes])
bboxes = [(bbox.volume(), bbox.size3()) for bbox in bboxes]
bboxes.sort(key=lambda x: x[0])
biggest = bboxes[-1][1]
output = {
"levels": levels.tolist(),
"patch_size": biggest.tolist(),
"num_patches": len(bboxes),
"coverage_ratio": covered_area / self.shape.rectVolume(),
}
path = self.levels_path if self.levels_path else self.src_path
path = os.path.join(path, 'levels')
cf = CloudFiles(path)
cf.put_json(
path="{}/{}".format(self.mip, self.offset.z),
content=output,
cache_control='no-cache'
)
def create_transfer_tasks(src_layer_path,
dest_layer_path,
chunk_size=None,
shape=Vec(2048, 2048, 64),
fill_missing=False,
translate=(0, 0, 0),
bounds=None,
mip=0,
preserve_chunk_size=True,
encoding=None):
"""
Transfer data from one data layer to another. It's possible
to transfer from a lower resolution mip level within a given
bounding box. The bounding box should be specified in terms of
the highest resolution.
"""
shape = Vec(*shape)
vol = CloudVolume(src_layer_path, mip=mip)
translate = Vec(*translate) // vol.downsample_ratio
if not chunk_size:
chunk_size = vol.info['scales'][mip]['chunk_sizes'][0]
chunk_size = Vec(*chunk_size)
try:
dvol = CloudVolume(dest_layer_path, mip=mip)
except Exception: # no info file
info = copy.deepcopy(vol.info)
dvol = CloudVolume(dest_layer_path, info=info)
dvol.commit_info()
if encoding is not None:
dvol.info['scales'][mip]['encoding'] = encoding
dvol.info['scales'] = dvol.info['scales'][:mip + 1]
dvol.info['scales'][mip]['chunk_sizes'] = [chunk_size.tolist()]
dvol.commit_info()
create_downsample_scales(dest_layer_path,
mip=mip,
ds_shape=shape,
preserve_chunk_size=preserve_chunk_size,
encoding=encoding)
if bounds is None:
bounds = vol.bounds.clone()
else:
bounds = vol.bbox_to_mip(bounds, mip=0, to_mip=mip)
bounds = Bbox.clamp(bounds, dvol.bounds)
dvol_bounds = dvol.mip_bounds(mip).clone()
class TransferTaskIterator(object):
def __len__(self):
return int(reduce(operator.mul, np.ceil(bounds.size3() / shape)))
def __iter__(self):
for startpt in xyzrange(bounds.minpt, bounds.maxpt, shape):
task_shape = min2(shape.clone(), dvol_bounds.maxpt - startpt)
yield TransferTask(
src_path=src_layer_path,
dest_path=dest_layer_path,
shape=task_shape,
offset=startpt.clone(),
fill_missing=fill_missing,
translate=translate,
mip=mip,
)
job_details = {
'method': {
'task': 'TransferTask',
'src': src_layer_path,
'dest': dest_layer_path,
'shape': list(map(int, shape)),
'fill_missing': fill_missing,
'translate': list(map(int, translate)),
'bounds': [bounds.minpt.tolist(),
bounds.maxpt.tolist()],
'mip': mip,
},
'by': OPERATOR_CONTACT,
'date': strftime('%Y-%m-%d %H:%M %Z'),
}
dvol = CloudVolume(dest_layer_path)
dvol.provenance.sources = [src_layer_path]
dvol.provenance.processing.append(job_details)
dvol.commit_provenance()
if vol.path.protocol != 'boss':
vol.provenance.processing.append(job_details)
vol.commit_provenance()
return TransferTaskIterator()