def kdconnect(root_nodes, trees=None, tol=0.75):
from networkx.algorithms.components import connected_components
import networkx as nx
cnt1, cnt2 = 0, 0
# make trees if they were not added before
if trees is None:
trees = []
for node in root_nodes:
tr = gp.KDTreeIndex(fwd=True, bkwd=True)(node)
trees.append(tr)
# get a node count for validation
for node in root_nodes:
cnt1 += len(list(node.__iter__(fwd=True, bkwd=True)))
gg = nx.Graph()
for i in range(len(trees)):
ti = trees[i]
for j in range(i+1, len(trees)):
tj = trees[j]
res_ij = ti.query_ball_tree(tj, tol)
adj = [(di, x) for di, x in enumerate(res_ij) if len(x) > 0]
if any(adj):
# unique indicies from tree_i and tree_j
un_tix = np.unique([i for i, j in adj])
un_tjx = np.unique([j for i, j in adj])
# closest points between unique positions
dists = distance.cdist(ti.data[un_tix], tj.data[un_tjx])
armi = np.unravel_index(np.argmin(dists, axis=None), dists.shape)
# retrieve node ids from respective trees, and connect
node_id1 = ti[un_tix[armi[0]]]
node_id2 = tj[un_tjx[armi[1]]]
ndi = gutil.node_with_id(root_nodes[i], node_id1)
ndj = gutil.node_with_id(root_nodes[j], node_id2)
ndi.connect_to(ndj, is_pipe=True)
# add root indexes to component graph
gg.add_edge(i, j)
final_roots = []
# gather new root nodes using connected_component algorithm
for component in connected_components(gg):
# pick a random index from the set ...
ix = list(component)[0]
a_root = root_nodes[ix]
cnt2 += len(list(a_root.__iter__(fwd=True, bkwd=True)))
final_roots.append(a_root)
# sanity check - number of nodes should not have changed
assert cnt1 == cnt2, 'unequal number of nodes before and after merge'
return final_roots
def test_elbow_1(self):
node_id = 9674342137
node = gutils.node_with_id(self.s.root, node_id)
print(node.get('$create'))
assert node is not None
mgr = rvt.make_actions_for(node)
print(mgr._state)
a = mgr.next_action()
print(a[0:3], '\n', mgr._state)
assert isinstance(a, list), msg('list', a)
assert a[0] == _Cmd_pipe, msg(_Cmd_pipe, a[0])
mgr.on_success(a)
a = mgr.next_action()
print(a[0:3], '\n', mgr._state)
assert a[0] == _Cmd_elb, msg(_Cmd_elb, a[0])
mgr.on_success(a)
print(mgr._state)
a = mgr.next_action()
print(a, '\n', mgr._state)
assert a is None, msg(None, a)
e = node.successors(edges=True, ix=0)
self._edge_stat(e, True, True, not True)
def resolve_heads(root_node, spr_points, tol=1.):
kdprop = gp.KDTreeIndex()(root_node)
data = np.array(kdprop.data)
for six, spr in enumerate(spr_points):
cdist = distance.cdist([spr], data)[0]
if np.min(cdist) < tol:
best_ix = np.argmin(cdist)
node = gutil.node_with_id(root_node, kdprop[best_ix])
connect_heads2(node)
return kdprop
def test_elbow_fail(self):
node_id = 9674342137
node = gutils.node_with_id(self.s.root, node_id)
# print(node.get('$create'))
assert node is not None
mgr = rvt.make_actions_for(node)
a = mgr.next_action()
# print(a)
assert a[0] == _Cmd_pipe, msg(_Cmd_pipe, a[0])
mgr.on_success(a)
a = mgr.next_action()
# print(a)
assert a[0] == _Cmd_elb, msg(_Cmd_elb, a[0])
mgr.on_fail(a)
a = mgr.next_action()
self._edge_stat(node.successors(edges=True, ix=0), True, True,
not True)
def test_elbow_f(self):
node_id = 9674342137
node = gutils.node_with_id(self.s.root, node_id)
res = [1, 0, 1, 1, 1]
self._test_scenario(node, res)
def test_tee2(self):
node_id = 5566475637
node = gutils.node_with_id(self.s.root, node_id)
self._single_node_success(node)
def test_tee1(self):
node_id = 390499279
node = gutils.node_with_id(self.s.root, node_id)
assert node is not None
self._test_node_success(node, _Cmd_tee)