def write_sopath2skeleton(so_path, dest_path, scaling=None, comment=None):
"""
Writes very simple skeleton, each node represents the center of mass of a
SV, and edges are created in list order.
Parameters
----------
so_path : list of SegmentationObject
dest_path : str
scaling : np.ndarray or tuple
comment : str
"""
if scaling is None:
scaling = np.array(global_params.config["Dataset"]["scaling"])
skel = Skeleton()
anno = SkeletonAnnotation()
anno.scaling = scaling
rep_nodes = []
for so in so_path:
vert = so.mesh[1].reshape((-1, 3))
com = np.mean(vert, axis=0)
kd_tree = spatial.cKDTree(vert)
dist, nn_ix = kd_tree.query([com])
nn = vert[nn_ix[0]] / scaling
n = SkeletonNode().from_scratch(anno, nn[0], nn[1], nn[2])
anno.addNode(n)
rep_nodes.append(n)
for i in range(1, len(rep_nodes)):
anno.addEdge(rep_nodes[i - 1], rep_nodes[i])
if comment is not None:
anno.setComment(comment)
skel.add_annotation(anno)
skel.to_kzip(dest_path)
def coordpath2anno(coords, scaling=None, add_edges=True):
"""
Creates skeleton from scaled coordinates, assume coords are in order for
edge creation.
Parameters
----------
coords : np.array
scaled cooridnates
scaling : tuple
add_edges : bool
Returns
-------
SkeletonAnnotation
"""
if scaling is None:
scaling = global_params.config['scaling']
anno = SkeletonAnnotation()
anno.scaling = scaling
scaling = np.array(scaling, dtype=np.int)
rep_nodes = []
coords = np.array(coords, dtype=np.int)
for c in coords:
unscaled_c = c / scaling
n = SkeletonNode().from_scratch(anno, unscaled_c[0], unscaled_c[1],
unscaled_c[2])
anno.addNode(n)
rep_nodes.append(n)
if add_edges:
for i in range(1, len(rep_nodes)):
anno.addEdge(rep_nodes[i - 1], rep_nodes[i])
return anno
def coordpath2anno(coords, scaling=None):
"""
Creates skeleton from scaled coordinates, assume coords are in order for
edge creation.
Parameters
----------
coords : np.array
scaling : np.ndarray
Returns
-------
SkeletonAnnotation
"""
if scaling is None:
scaling = global_params.config["Dataset"]["scaling"]
anno = SkeletonAnnotation()
anno.scaling = scaling
rep_nodes = []
for c in coords:
n = SkeletonNode().from_scratch(anno, c[0] / scaling[0],
c[1] / scaling[1], c[2] / scaling[2])
anno.addNode(n)
rep_nodes.append(n)
for i in range(1, len(rep_nodes)):
anno.addEdge(rep_nodes[i - 1], rep_nodes[i])
return anno
def nxGraph2kzip(g, coords, kzip_path):
import tqdm
scaling = global_params.config.entries['Dataset']['scaling']()
coords = coords / scaling
skel = Skeleton()
anno = SkeletonAnnotation()
anno.scaling = scaling
node_mapping = {}
pbar = tqdm.tqdm(total=len(coords) + len(g.edges()))
for v in g.nodes():
c = coords[v]
n = SkeletonNode().from_scratch(anno, c[0], c[1], c[2])
node_mapping[v] = n
anno.addNode(n)
pbar.update(1)
for e in g.edges():
anno.addEdge(node_mapping[e[0]], node_mapping[e[1]])
pbar.update(1)
skel.add_annotation(anno)
skel.to_kzip(kzip_path)
pbar.close()