def setup_root_new(mesh, is_soma_pt=None, soma_d=None, is_valid=None):
if is_valid is not None:
valid = np.copy(is_valid)
else:
valid = np.ones(len(mesh.vertices), np.bool)
root = None
# soma mode
if is_soma_pt is not None:
# pick the first soma as root
is_valid_root = is_soma_pt & valid
valid_root_inds = np.where(is_valid_root)[0]
if len(valid_root_inds) > 0:
min_valid_root = np.nanargmin(soma_d[valid_root_inds])
root = valid_root_inds[min_valid_root]
root_ds, pred = sparse.csgraph.dijkstra(mesh.csgraph,
False,
root,
return_predecessors=True)
else:
start_ind = np.where(valid)[0][0]
root, target, pred, dm, root_ds = utils.find_far_points(
mesh, start_ind=start_ind)
valid[is_soma_pt] = False
if root is None:
# there is no soma close, so use far point heuristic
start_ind = np.where(valid)[0][0]
root, target, pred, dm, root_ds = utils.find_far_points(
mesh, start_ind=start_ind)
valid[root] = False
assert (np.all(~np.isinf(root_ds[valid])))
return root, root_ds, pred, valid
def setup_root(mesh, soma_pt=None, soma_thresh=7500, valid_inds=None):
if valid_inds is not None:
valid = np.zeros(len(mesh.vertices), np.bool)
valid[valid_inds] = True
else:
valid = np.ones(len(mesh.vertices), np.bool)
root = None
# soma mode
if soma_pt is not None:
# pick the first soma as root
soma_d, soma_i = mesh.kdtree.query(soma_pt,
k=len(mesh.vertices),
distance_upper_bound=soma_thresh)
if valid_inds is not None:
soma_i, valid_soma_ind, soma_valid_ind = np.intersect1d(
soma_i, valid_inds, return_indices=True)
soma_d = soma_d[valid_soma_ind]
if (len(soma_d) > 0):
min_d = np.min(soma_d)
else:
min_d = np.inf
if (min_d < soma_thresh):
root = soma_i[np.argmin(soma_d)]
root_ds, pred = sparse.csgraph.dijkstra(mesh.csgraph,
False,
root,
return_predecessors=True)
else:
if valid_inds is not None:
root, target, pred, dm, root_ds = utils.find_far_points(
mesh, start_ind=valid_inds[0])
else:
root, target, pred, dm, root_ds = utils.find_far_points(mesh)
if root is None:
# there is no soma close, so use far point heuristic
root, target, pred, dm, root_ds = find_far_points(mesh)
valid[root] = False
return root, root_ds, pred, valid