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# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
""" a few tests for graph-based indices (HNSW, nndescent and NSG)"""
import numpy as np
import unittest
import faiss
import tempfile
import os
from common_faiss_tests import get_dataset_2
class TestHNSW(unittest.TestCase):
def __init__(self, *args, **kwargs):
unittest.TestCase.__init__(self, *args, **kwargs)
d = 32
nt = 0
nb = 1500
nq = 500
(_, self.xb, self.xq) = get_dataset_2(d, nt, nb, nq)
index = faiss.IndexFlatL2(d)
index.add(self.xb)
Dref, Iref = index.search(self.xq, 1)
self.Iref = Iref
def test_hnsw(self):
d = self.xq.shape[1]
index = faiss.IndexHNSWFlat(d, 16)
index.add(self.xb)
Dhnsw, Ihnsw = index.search(self.xq, 1)
self.assertGreaterEqual((self.Iref == Ihnsw).sum(), 460)
self.io_and_retest(index, Dhnsw, Ihnsw)
def test_range_search(self):
index_flat = faiss.IndexFlat(self.xb.shape[1])
index_flat.add(self.xb)
D, _ = index_flat.search(self.xq, 10)
radius = np.median(D[:, -1])
lims_ref, Dref, Iref = index_flat.range_search(self.xq, radius)
index = faiss.IndexHNSWFlat(self.xb.shape[1], 16)
index.add(self.xb)
lims, D, I = index.range_search(self.xq, radius)
nmiss = 0
# check if returned resutls are a subset of the reference results
for i in range(len(self.xq)):
ref = Iref[lims_ref[i]: lims_ref[i + 1]]
new = I[lims[i]: lims[i + 1]]
self.assertLessEqual(set(new), set(ref))
nmiss += len(ref) - len(new)
# currenly we miss 405 / 6019 neighbors
self.assertLessEqual(nmiss, lims_ref[-1] * 0.1)
def test_hnsw_unbounded_queue(self):
d = self.xq.shape[1]
index = faiss.IndexHNSWFlat(d, 16)
index.add(self.xb)
index.search_bounded_queue = False
Dhnsw, Ihnsw = index.search(self.xq, 1)
self.assertGreaterEqual((self.Iref == Ihnsw).sum(), 460)
self.io_and_retest(index, Dhnsw, Ihnsw)
def test_hnsw_no_init_level0(self):
d = self.xq.shape[1]
index = faiss.IndexHNSWFlat(d, 16)
index.init_level0 = False
index.add(self.xb)
Dhnsw, Ihnsw = index.search(self.xq, 1)
# This is expected to be smaller because we are not initializing
# vectors into level 0.
self.assertGreaterEqual((self.Iref == Ihnsw).sum(), 25)
self.io_and_retest(index, Dhnsw, Ihnsw)
def io_and_retest(self, index, Dhnsw, Ihnsw):
index2 = faiss.deserialize_index(faiss.serialize_index(index))
Dhnsw2, Ihnsw2 = index2.search(self.xq, 1)
self.assertTrue(np.all(Dhnsw2 == Dhnsw))
self.assertTrue(np.all(Ihnsw2 == Ihnsw))
# also test clone
index3 = faiss.clone_index(index)
Dhnsw3, Ihnsw3 = index3.search(self.xq, 1)
self.assertTrue(np.all(Dhnsw3 == Dhnsw))
self.assertTrue(np.all(Ihnsw3 == Ihnsw))
def test_hnsw_2level(self):
d = self.xq.shape[1]
quant = faiss.IndexFlatL2(d)
index = faiss.IndexHNSW2Level(quant, 256, 8, 8)
index.train(self.xb)
index.add(self.xb)
Dhnsw, Ihnsw = index.search(self.xq, 1)
self.assertGreaterEqual((self.Iref == Ihnsw).sum(), 307)
self.io_and_retest(index, Dhnsw, Ihnsw)
def test_hnsw_2level_mixed_search(self):
d = self.xq.shape[1]
quant = faiss.IndexFlatL2(d)
storage = faiss.IndexIVFPQ(quant, d, 32, 8, 8)
storage.make_direct_map()
index = faiss.IndexHNSW2Level(quant, 32, 8, 8)
index.storage = storage
index.train(self.xb)
index.add(self.xb)
Dhnsw, Ihnsw = index.search(self.xq, 1)
# It is expected that the mixed search will perform worse.
self.assertGreaterEqual((self.Iref == Ihnsw).sum(), 200)
self.io_and_retest(index, Dhnsw, Ihnsw)
def test_add_0_vecs(self):
index = faiss.IndexHNSWFlat(10, 16)
zero_vecs = np.zeros((0, 10), dtype='float32')
# infinite loop
index.add(zero_vecs)
def test_hnsw_IP(self):
d = self.xq.shape[1]
index_IP = faiss.IndexFlatIP(d)
index_IP.add(self.xb)
Dref, Iref = index_IP.search(self.xq, 1)
index = faiss.IndexHNSWFlat(d, 16, faiss.METRIC_INNER_PRODUCT)
index.add(self.xb)
Dhnsw, Ihnsw = index.search(self.xq, 1)
self.assertGreaterEqual((Iref == Ihnsw).sum(), 470)
mask = Iref[:, 0] == Ihnsw[:, 0]
assert np.allclose(Dref[mask, 0], Dhnsw[mask, 0])
def test_ndis_stats(self):
d = self.xq.shape[1]
index = faiss.IndexHNSWFlat(d, 16)
index.add(self.xb)
stats = faiss.cvar.hnsw_stats
stats.reset()
Dhnsw, Ihnsw = index.search(self.xq, 1)
self.assertGreater(stats.ndis, len(self.xq) * index.hnsw.efSearch)
def test_io_no_storage(self):
d = self.xq.shape[1]
index = faiss.IndexHNSWFlat(d, 16)
index.add(self.xb)
Dref, Iref = index.search(self.xq, 5)
# test writing without storage
index2 = faiss.deserialize_index(
faiss.serialize_index(index, faiss.IO_FLAG_SKIP_STORAGE)
)
self.assertEqual(index2.storage, None)
self.assertRaises(
RuntimeError,
index2.search, self.xb, 1)
# make sure we can store an index with empty storage
index4 = faiss.deserialize_index(
faiss.serialize_index(index2))
# add storage afterwards
index.storage = faiss.clone_index(index.storage)
index.own_fields = True
Dnew, Inew = index.search(self.xq, 5)
np.testing.assert_array_equal(Dnew, Dref)
np.testing.assert_array_equal(Inew, Iref)
if False:
# test reading without storage
# not implemented because it is hard to skip over an index
index3 = faiss.deserialize_index(
faiss.serialize_index(index), faiss.IO_FLAG_SKIP_STORAGE
)
self.assertEqual(index3.storage, None)
def test_hnsw_reset(self):
d = self.xb.shape[1]
index_flat = faiss.IndexFlat(d)
index_flat.add(self.xb)
self.assertEqual(index_flat.ntotal, self.xb.shape[0])
index_hnsw = faiss.IndexHNSW(index_flat)
index_hnsw.add(self.xb)
# * 2 because we add to storage twice. This is just for testing
# that storage gets cleared correctly.
self.assertEqual(index_hnsw.ntotal, self.xb.shape[0] * 2)
index_hnsw.reset()
self.assertEqual(index_flat.ntotal, 0)
self.assertEqual(index_hnsw.ntotal, 0)
class Issue3684(unittest.TestCase):
def test_issue3684(self):
np.random.seed(1234) # For reproducibility
d = 256 # Example dimension
nb = 10 # Number of database vectors
nq = 2 # Number of query vectors
xb = np.random.random((nb, d)).astype('float32')
xq = np.random.random((nq, d)).astype('float32')
faiss.normalize_L2(xb) # Normalize both query and database vectors
faiss.normalize_L2(xq)
hnsw_index_ip = faiss.IndexHNSWFlat(256, 16, faiss.METRIC_INNER_PRODUCT)
hnsw_index_ip.hnsw.efConstruction = 512
hnsw_index_ip.hnsw.efSearch = 512
hnsw_index_ip.add(xb)
# test knn
D, I = hnsw_index_ip.search(xq, 10)
self.assertTrue(np.all(D[:, :-1] >= D[:, 1:]))
# test range search
radius = 0.74 # Cosine similarity threshold
lims, D, I = hnsw_index_ip.range_search(xq, radius)
self.assertTrue(np.all(D >= radius))
class TestNSG(unittest.TestCase):
def __init__(self, *args, **kwargs):
unittest.TestCase.__init__(self, *args, **kwargs)
d = 32
nt = 0
nb = 1500
nq = 500
self.GK = 32
_, self.xb, self.xq = get_dataset_2(d, nt, nb, nq)
def make_knn_graph(self, metric):
n = self.xb.shape[0]
d = self.xb.shape[1]
index = faiss.IndexFlat(d, metric)
index.add(self.xb)
_, I = index.search(self.xb, self.GK + 1)
knn_graph = np.zeros((n, self.GK), dtype=np.int64)
# For the inner product distance, the distance between a vector and
# itself may not be the smallest, so it is not guaranteed that I[:, 0]
# is the query itself.
for i in range(n):
cnt = 0
for j in range(self.GK + 1):
if I[i, j] != i:
knn_graph[i, cnt] = I[i, j]
cnt += 1
if cnt == self.GK:
break
return knn_graph
def subtest_io_and_clone(self, index, Dnsg, Insg):
fd, tmpfile = tempfile.mkstemp()
os.close(fd)
try:
faiss.write_index(index, tmpfile)
index2 = faiss.read_index(tmpfile)
finally:
if os.path.exists(tmpfile):
os.unlink(tmpfile)
Dnsg2, Insg2 = index2.search(self.xq, 1)
np.testing.assert_array_equal(Dnsg2, Dnsg)
np.testing.assert_array_equal(Insg2, Insg)
# also test clone
index3 = faiss.clone_index(index)
Dnsg3, Insg3 = index3.search(self.xq, 1)
np.testing.assert_array_equal(Dnsg3, Dnsg)
np.testing.assert_array_equal(Insg3, Insg)
def subtest_connectivity(self, index, nb):
vt = faiss.VisitedTable(nb)
count = index.nsg.dfs(vt, index.nsg.enterpoint, 0)
self.assertEqual(count, nb)
def subtest_add(self, build_type, thresh, metric=faiss.METRIC_L2):
d = self.xq.shape[1]
metrics = {faiss.METRIC_L2: 'L2',
faiss.METRIC_INNER_PRODUCT: 'IP'}
flat_index = faiss.IndexFlat(d, metric)
flat_index.add(self.xb)
Dref, Iref = flat_index.search(self.xq, 1)
index = faiss.IndexNSGFlat(d, 16, metric)
index.verbose = True
index.build_type = build_type
index.GK = self.GK
index.add(self.xb)
Dnsg, Insg = index.search(self.xq, 1)
recalls = (Iref == Insg).sum()
self.assertGreaterEqual(recalls, thresh)
self.subtest_connectivity(index, self.xb.shape[0])
self.subtest_io_and_clone(index, Dnsg, Insg)
def subtest_build(self, knn_graph, thresh, metric=faiss.METRIC_L2):
d = self.xq.shape[1]
metrics = {faiss.METRIC_L2: 'L2',
faiss.METRIC_INNER_PRODUCT: 'IP'}
flat_index = faiss.IndexFlat(d, metric)
flat_index.add(self.xb)
Dref, Iref = flat_index.search(self.xq, 1)
index = faiss.IndexNSGFlat(d, 16, metric)
index.verbose = True
index.build(self.xb, knn_graph)
Dnsg, Insg = index.search(self.xq, 1)
recalls = (Iref == Insg).sum()
self.assertGreaterEqual(recalls, thresh)
self.subtest_connectivity(index, self.xb.shape[0])
def test_add_bruteforce_L2(self):
self.subtest_add(0, 475, faiss.METRIC_L2)
def test_add_nndescent_L2(self):
self.subtest_add(1, 475, faiss.METRIC_L2)
def test_add_bruteforce_IP(self):
self.subtest_add(0, 480, faiss.METRIC_INNER_PRODUCT)
def test_add_nndescent_IP(self):
self.subtest_add(1, 480, faiss.METRIC_INNER_PRODUCT)
def test_build_L2(self):
knn_graph = self.make_knn_graph(faiss.METRIC_L2)
self.subtest_build(knn_graph, 475, faiss.METRIC_L2)
def test_build_IP(self):
knn_graph = self.make_knn_graph(faiss.METRIC_INNER_PRODUCT)
self.subtest_build(knn_graph, 480, faiss.METRIC_INNER_PRODUCT)
def test_build_invalid_knng(self):
"""Make some invalid entries in the input knn graph.
It would cause a warning but IndexNSG should be able
to handle this.
"""
knn_graph = self.make_knn_graph(faiss.METRIC_L2)
knn_graph[:100, 5] = -111
self.subtest_build(knn_graph, 475, faiss.METRIC_L2)
knn_graph = self.make_knn_graph(faiss.METRIC_INNER_PRODUCT)
knn_graph[:100, 5] = -111
self.subtest_build(knn_graph, 480, faiss.METRIC_INNER_PRODUCT)
def test_reset(self):
"""test IndexNSG.reset()"""
d = self.xq.shape[1]
metrics = {faiss.METRIC_L2: 'L2',
faiss.METRIC_INNER_PRODUCT: 'IP'}
metric = faiss.METRIC_L2
flat_index = faiss.IndexFlat(d, metric)
flat_index.add(self.xb)
Dref, Iref = flat_index.search(self.xq, 1)
index = faiss.IndexNSGFlat(d, 16)
index.verbose = True
index.GK = 32
index.add(self.xb)
Dnsg, Insg = index.search(self.xq, 1)
recalls = (Iref == Insg).sum()
self.assertGreaterEqual(recalls, 475)
self.subtest_connectivity(index, self.xb.shape[0])
index.reset()
index.add(self.xb)
Dnsg, Insg = index.search(self.xq, 1)
recalls = (Iref == Insg).sum()
self.assertGreaterEqual(recalls, 475)
self.subtest_connectivity(index, self.xb.shape[0])
def test_order(self):
"""make sure that output results are sorted"""
d = self.xq.shape[1]
index = faiss.IndexNSGFlat(d, 32)
index.train(self.xb)
index.add(self.xb)
k = 10
nq = self.xq.shape[0]
D, _ = index.search(self.xq, k)
indices = np.argsort(D, axis=1)
gt = np.arange(0, k)[np.newaxis, :] # [1, k]
gt = np.repeat(gt, nq, axis=0) # [nq, k]
np.testing.assert_array_equal(indices, gt)
def test_nsg_supports_pre_built_knn_graph(self):
"""Test IndexNSGBuild"""
knn_graph = self.make_knn_graph(faiss.METRIC_L2)
d = self.xq.shape[1]
index = faiss.IndexNSGFlat(d, 16)
index.build(self.xb, knn_graph)
index.search(self.xq, k=1)
self.assertTrue(index.is_built)
def test_nsg_with_pre_built_knn_graph_throws_when_rebuilding_via_add(self):
"""Test IndexNSGBuild"""
knn_graph = self.make_knn_graph(faiss.METRIC_L2)
d = self.xq.shape[1]
index = faiss.IndexNSGFlat(d, 16)
index.build(self.xb, knn_graph)
index.search(self.xq, k=1)
self.assertTrue(index.is_built)
index.GK = 32
index.train(self.xb)
with self.assertRaises(RuntimeError) as context:
index.add(self.xb)
self.assertIn(
"NSG does not support incremental addition",
str(context.exception)
)
def test_nsg_rebuild_throws_with_pre_built_knn_graph(self):
"""Test IndexNSGBuild"""
knn_graph = self.make_knn_graph(faiss.METRIC_L2)
d = self.xq.shape[1]
index = faiss.IndexNSGFlat(d, 16)
index.build(self.xb, knn_graph)
index.search(self.xq, k=1)
with self.assertRaises(RuntimeError) as context:
index.build(self.xb, knn_graph)
self.assertIn("The IndexNSG is already built", str(context.exception))
def test_nsg_pq(self):
"""Test IndexNSGPQ"""
d = self.xq.shape[1]
R, pq_M = 32, 4
index = faiss.index_factory(d, f"NSG{R}_PQ{pq_M}np")
assert isinstance(index, faiss.IndexNSGPQ)
idxpq = faiss.downcast_index(index.storage)
assert index.nsg.R == R and idxpq.pq.M == pq_M
flat_index = faiss.IndexFlat(d)
flat_index.add(self.xb)
Dref, Iref = flat_index.search(self.xq, k=1)
index.GK = 32
index.train(self.xb)
index.add(self.xb)
D, I = index.search(self.xq, k=1)
# test accuracy
recalls = (Iref == I).sum()
self.assertGreaterEqual(recalls, 190) # 193
# test I/O
self.subtest_io_and_clone(index, D, I)
def test_nsg_sq(self):
"""Test IndexNSGSQ"""
d = self.xq.shape[1]
R = 32
index = faiss.index_factory(d, f"NSG{R}_SQ8")
assert isinstance(index, faiss.IndexNSGSQ)
idxsq = faiss.downcast_index(index.storage)
assert index.nsg.R == R
assert idxsq.sq.qtype == faiss.ScalarQuantizer.QT_8bit
flat_index = faiss.IndexFlat(d)
flat_index.add(self.xb)
Dref, Iref = flat_index.search(self.xq, k=1)
index.train(self.xb)
index.add(self.xb)
D, I = index.search(self.xq, k=1)
# test accuracy
recalls = (Iref == I).sum()
self.assertGreaterEqual(recalls, 405) # 411
# test I/O
self.subtest_io_and_clone(index, D, I)
class TestNNDescent(unittest.TestCase):
def __init__(self, *args, **kwargs):
unittest.TestCase.__init__(self, *args, **kwargs)
d = 32
nt = 0
nb = 1500
nq = 500
self.GK = 32
_, self.xb, self.xq = get_dataset_2(d, nt, nb, nq)
def test_nndescentflat(self):
d = self.xq.shape[1]
index = faiss.IndexNNDescentFlat(d, 32)
index.nndescent.search_L = 8
flat_index = faiss.IndexFlat(d)
flat_index.add(self.xb)
Dref, Iref = flat_index.search(self.xq, k=1)
index.train(self.xb)
index.add(self.xb)
D, I = index.search(self.xq, k=1)
# test accuracy
recalls = (Iref == I).sum()
self.assertGreaterEqual(recalls, 450) # 462
# do some IO tests
fd, tmpfile = tempfile.mkstemp()
os.close(fd)
try:
faiss.write_index(index, tmpfile)
index2 = faiss.read_index(tmpfile)
finally:
if os.path.exists(tmpfile):
os.unlink(tmpfile)
D2, I2 = index2.search(self.xq, 1)
np.testing.assert_array_equal(D2, D)
np.testing.assert_array_equal(I2, I)
# also test clone
index3 = faiss.clone_index(index)
D3, I3 = index3.search(self.xq, 1)
np.testing.assert_array_equal(D3, D)
np.testing.assert_array_equal(I3, I)
def test_order(self):
"""make sure that output results are sorted"""
d = self.xq.shape[1]
index = faiss.IndexNNDescentFlat(d, 32)
index.train(self.xb)
index.add(self.xb)
k = 10
nq = self.xq.shape[0]
D, _ = index.search(self.xq, k)
indices = np.argsort(D, axis=1)
gt = np.arange(0, k)[np.newaxis, :] # [1, k]
gt = np.repeat(gt, nq, axis=0) # [nq, k]
np.testing.assert_array_equal(indices, gt)
class TestNNDescentKNNG(unittest.TestCase):
def test_knng_L2(self):
self.subtest(32, 10, faiss.METRIC_L2)
def test_knng_IP(self):
self.subtest(32, 10, faiss.METRIC_INNER_PRODUCT)
def subtest(self, d, K, metric):
metric_names = {faiss.METRIC_L1: 'L1',
faiss.METRIC_L2: 'L2',
faiss.METRIC_INNER_PRODUCT: 'IP'}
nb = 1000
_, xb, _ = get_dataset_2(d, 0, nb, 0)
_, knn = faiss.knn(xb, xb, K + 1, metric)
knn = knn[:, 1:]
index = faiss.IndexNNDescentFlat(d, K, metric)
index.nndescent.S = 10
index.nndescent.R = 32
index.nndescent.L = K + 20
index.nndescent.iter = 5
index.verbose = True
index.add(xb)
graph = index.nndescent.final_graph
graph = faiss.vector_to_array(graph)
graph = graph.reshape(nb, K)
recalls = 0
for i in range(nb):
for j in range(K):
for k in range(K):
if graph[i, j] == knn[i, k]:
recalls += 1
break
recall = 1.0 * recalls / (nb * K)
assert recall > 0.99
def test_small_nndescent(self):
""" building a too small graph used to crash, make sure it raises
an exception instead.
TODO: build the exact knn graph for small cases
"""
d = 32
K = 10
index = faiss.IndexNNDescentFlat(d, K, faiss.METRIC_L2)
index.nndescent.S = 10
index.nndescent.R = 32
index.nndescent.L = K + 20
index.nndescent.iter = 5
index.verbose = True
xb = np.zeros((78, d), dtype='float32')
self.assertRaises(RuntimeError, index.add, xb)
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