def sparse_init_from_random(
n_neighbors,
inds,
indptr,
data,
query_inds,
query_indptr,
query_data,
heap,
rng_state,
sparse_dist,
):
for i in range(query_indptr.shape[0] - 1):
indices = rejection_sample(n_neighbors, indptr.shape[0] - 1, rng_state)
to_inds = query_inds[query_indptr[i]:query_indptr[i + 1]]
to_data = query_data[query_indptr[i]:query_indptr[i + 1]]
for j in range(indices.shape[0]):
if indices[j] < 0:
continue
from_inds = inds[indptr[indices[j]]:indptr[indices[j] + 1]]
from_data = data[indptr[indices[j]]:indptr[indices[j] + 1]]
d = sparse_dist(from_inds, from_data, to_inds, to_data)
heap_push(heap, i, d, indices[j], 1)
return
def nn_descent(
data,
n_neighbors,
rng_state,
max_candidates=50,
dist=dist.euclidean,
n_iters=10,
delta=0.001,
rho=0.5,
rp_tree_init=True,
leaf_array=None,
low_memory=False,
verbose=False,
):
tried = set([(-1, -1)])
current_graph = make_heap(data.shape[0], n_neighbors)
for i in range(data.shape[0]):
indices = rejection_sample(n_neighbors, data.shape[0], rng_state)
for j in range(indices.shape[0]):
d = dist(data[i], data[indices[j]])
heap_push(current_graph, i, d, indices[j], 1)
heap_push(current_graph, indices[j], d, i, 1)
tried.add((i, indices[j]))
tried.add((indices[j], i))
if rp_tree_init:
init_rp_tree(data, dist, current_graph, leaf_array, tried=tried)
if low_memory:
nn_descent_internal_low_memory(
current_graph,
data,
n_neighbors,
rng_state,
max_candidates=max_candidates,
dist=dist,
n_iters=n_iters,
delta=delta,
rho=rho,
verbose=verbose,
)
else:
nn_descent_internal_high_memory(
current_graph,
data,
n_neighbors,
rng_state,
tried,
max_candidates=max_candidates,
dist=dist,
n_iters=n_iters,
delta=delta,
rho=rho,
verbose=verbose,
)
return deheap_sort(current_graph)
def init_current_graph(data, dist, n_neighbors, rng_state):
current_graph = make_heap(data.shape[0], n_neighbors)
for i in range(data.shape[0]):
indices = rejection_sample(n_neighbors, data.shape[0], rng_state)
for j in range(indices.shape[0]):
d = dist(data[i], data[indices[j]])
heap_push(current_graph, i, d, indices[j], 1)
heap_push(current_graph, indices[j], d, i, 1)
return current_graph
def init_from_random(n_neighbors, data, query_points, heap, rng_state, dist):
for i in range(query_points.shape[0]):
indices = rejection_sample(n_neighbors, data.shape[0], rng_state)
for j in range(indices.shape[0]):
if indices[j] < 0:
continue
d = dist(data[indices[j]], query_points[i])
heap_push(heap, i, d, indices[j], 1)
return
def sparse_nn_descent(
inds,
indptr,
data,
n_vertices,
n_neighbors,
rng_state,
max_candidates=50,
sparse_dist=Jvis.sparse.sparse_euclidean,
n_iters=10,
delta=0.001,
rho=0.5,
low_memory=False,
rp_tree_init=True,
leaf_array=None,
verbose=False,
):
tried = set([(-1, -1)])
current_graph = make_heap(n_vertices, n_neighbors)
for i in range(n_vertices):
indices = rejection_sample(n_neighbors, n_vertices, rng_state)
for j in range(indices.shape[0]):
from_inds = inds[indptr[i]:indptr[i + 1]]
from_data = data[indptr[i]:indptr[i + 1]]
to_inds = inds[indptr[indices[j]]:indptr[indices[j] + 1]]
to_data = data[indptr[indices[j]]:indptr[indices[j] + 1]]
d = sparse_dist(from_inds, from_data, to_inds, to_data)
heap_push(current_graph, i, d, indices[j], 1)
heap_push(current_graph, indices[j], d, i, 1)
tried.add((i, indices[j]))
tried.add((indices[j], i))
if rp_tree_init:
sparse_init_rp_tree(
inds,
indptr,
data,
sparse_dist,
current_graph,
leaf_array,
tried=tried,
)
if low_memory:
sparse_nn_descent_internal_low_memory(
current_graph,
inds,
indptr,
data,
n_vertices,
n_neighbors,
rng_state,
max_candidates=max_candidates,
sparse_dist=sparse_dist,
n_iters=n_iters,
delta=delta,
rho=rho,
verbose=verbose,
)
else:
sparse_nn_descent_internal_high_memory(
current_graph,
inds,
indptr,
data,
n_vertices,
n_neighbors,
rng_state,
tried,
max_candidates=max_candidates,
sparse_dist=sparse_dist,
n_iters=n_iters,
delta=delta,
rho=rho,
verbose=verbose,
)
return deheap_sort(current_graph)