def test_kdtree_k1():
kdtree = KDTree([X1, X2])
dists, inds = kdtree.query([
[0] * 10,
[10] * 10,
[0] * 10
])
assert len(inds) == 3
for subind in inds:
assert len(subind) == 2
# traj i
assert inds[0][0] == 0
assert inds[1][0] == 1
assert inds[2][0] == 0
# framei
assert 0 <= inds[0][1] < 500
assert 0 <= inds[1][1] < 1000
assert 0 <= inds[2][1] < 500
# distances
assert len(dists) == 3
for d in dists:
assert 0 <= d < 0.5
def test_kdtree_k2():
kdtree = KDTree([X1, X2])
dists, inds = kdtree.query([
[0] * 10,
[10] * 10,
[0] * 10
], k=2)
assert len(inds) == 3
# traj i
for qp in inds[0]: assert qp[0] == 0
for qp in inds[1]: assert qp[0] == 1
for qp in inds[2]: assert qp[0] == 0
# frame i
for qp in inds[0]: assert 0 <= qp[1] < 500
for qp in inds[1]: assert 0 <= qp[1] < 1000
for qp in inds[2]: assert 0 <= qp[1] < 500
# distances
assert len(dists) == 3
for d in dists:
assert 0 <= d[0] < 0.5
assert 0 <= d[1] < 0.5
def test_kdtree_k2():
kdtree = KDTree([X1, X2])
dists, inds = kdtree.query([[0] * 10, [10] * 10, [0] * 10], k=2)
assert len(inds) == 3
# traj i
for qp in inds[0]:
assert qp[0] == 0
for qp in inds[1]:
assert qp[0] == 1
for qp in inds[2]:
assert qp[0] == 0
# frame i
for qp in inds[0]:
assert 0 <= qp[1] < 500
for qp in inds[1]:
assert 0 <= qp[1] < 1000
for qp in inds[2]:
assert 0 <= qp[1] < 500
# distances
assert len(dists) == 3
for d in dists:
assert 0 <= d[0] < 0.5
assert 0 <= d[1] < 0.5
def test_kdtree_k1():
kdtree = KDTree([X1, X2])
dists, inds = kdtree.query([[0] * 10, [10] * 10, [0] * 10])
assert len(inds) == 3
for subind in inds:
assert len(subind) == 2
# traj i
assert inds[0][0] == 0
assert inds[1][0] == 1
assert inds[2][0] == 0
# framei
assert 0 <= inds[0][1] < 500
assert 0 <= inds[1][1] < 1000
assert 0 <= inds[2][1] < 500
# distances
assert len(dists) == 3
for d in dists:
assert 0 <= d < 0.5
def find_closest_indices_to_cluster_center(tica_coords, clusterer_file, k=1):
tica = compat_verboseload(tica_coords)
clusterer = compat_verboseload(clusterer_file)
kd = KDTree(tica)
dist, inds = kd.query(clusterer.cluster_centers_, k=k)
return inds