1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245
|
import os
import pickle
import unittest
import numpy as np
import hnswlib
class RandomSelfTestCase(unittest.TestCase):
def testRandomSelf(self):
"""
Tests if replace of deleted elements works correctly
Tests serialization of the index with replaced elements
"""
dim = 16
num_elements = 5000
max_num_elements = 2 * num_elements
recall_threshold = 0.98
# Generating sample data
print("Generating data")
# batch 1
first_id = 0
last_id = num_elements
labels1 = np.arange(first_id, last_id)
data1 = np.float32(np.random.random((num_elements, dim)))
# batch 2
first_id += num_elements
last_id += num_elements
labels2 = np.arange(first_id, last_id)
data2 = np.float32(np.random.random((num_elements, dim)))
# batch 3
first_id += num_elements
last_id += num_elements
labels3 = np.arange(first_id, last_id)
data3 = np.float32(np.random.random((num_elements, dim)))
# batch 4
first_id += num_elements
last_id += num_elements
labels4 = np.arange(first_id, last_id)
data4 = np.float32(np.random.random((num_elements, dim)))
# Declaring index
hnsw_index = hnswlib.Index(space='l2', dim=dim)
hnsw_index.init_index(max_elements=max_num_elements, ef_construction=200, M=16, allow_replace_deleted=True)
hnsw_index.set_ef(100)
hnsw_index.set_num_threads(4)
# Add batch 1 and 2
print("Adding batch 1")
hnsw_index.add_items(data1, labels1)
print("Adding batch 2")
hnsw_index.add_items(data2, labels2) # maximum number of elements is reached
# Delete nearest neighbors of batch 2
print("Deleting neighbors of batch 2")
labels2_deleted, _ = hnsw_index.knn_query(data2, k=1)
# delete probable duplicates from nearest neighbors
labels2_deleted_no_dup = set(labels2_deleted.flatten())
num_duplicates = len(labels2_deleted) - len(labels2_deleted_no_dup)
for l in labels2_deleted_no_dup:
hnsw_index.mark_deleted(l)
labels1_found, _ = hnsw_index.knn_query(data1, k=1)
items = hnsw_index.get_items(labels1_found)
diff_with_gt_labels = np.mean(np.abs(data1 - items))
self.assertAlmostEqual(diff_with_gt_labels, 0, delta=1e-3)
labels2_after, _ = hnsw_index.knn_query(data2, k=1)
for la in labels2_after:
if la[0] in labels2_deleted_no_dup:
print(f"Found deleted label {la[0]} during knn search")
self.assertTrue(False)
print("All the neighbors of data2 are removed")
# Replace deleted elements
print("Inserting batch 3 by replacing deleted elements")
# Maximum number of elements is reached therefore we cannot add new items
# but we can replace the deleted ones
# Note: there may be less than num_elements elements.
# As we could delete less than num_elements because of duplicates
labels3_tr = labels3[0:labels3.shape[0] - num_duplicates]
data3_tr = data3[0:data3.shape[0] - num_duplicates]
hnsw_index.add_items(data3_tr, labels3_tr, replace_deleted=True)
# After replacing, all labels should be retrievable
print("Checking that remaining labels are in index")
# Get remaining data from batch 1 and batch 2 after deletion of elements
remaining_labels = (set(labels1) | set(labels2)) - labels2_deleted_no_dup
remaining_labels_list = list(remaining_labels)
comb_data = np.concatenate((data1, data2), axis=0)
remaining_data = comb_data[remaining_labels_list]
returned_items = hnsw_index.get_items(remaining_labels_list)
self.assertTrue((remaining_data == returned_items).all())
returned_items = hnsw_index.get_items(labels3_tr)
self.assertTrue((data3_tr == returned_items).all())
# Check index serialization
# Delete batch 3
print("Deleting batch 3")
for l in labels3_tr:
hnsw_index.mark_deleted(l)
# Save index
index_path = "index.bin"
print(f"Saving index to {index_path}")
hnsw_index.save_index(index_path)
del hnsw_index
# Reinit and load the index
hnsw_index = hnswlib.Index(space='l2', dim=dim) # the space can be changed - keeps the data, alters the distance function.
hnsw_index.set_num_threads(4)
print(f"Loading index from {index_path}")
hnsw_index.load_index(index_path, max_elements=max_num_elements, allow_replace_deleted=True)
# Insert batch 4
print("Inserting batch 4 by replacing deleted elements")
labels4_tr = labels4[0:labels4.shape[0] - num_duplicates]
data4_tr = data4[0:data4.shape[0] - num_duplicates]
hnsw_index.add_items(data4_tr, labels4_tr, replace_deleted=True)
# Check recall
print("Checking recall")
labels_found, _ = hnsw_index.knn_query(data4_tr, k=1)
recall = np.mean(labels_found.reshape(-1) == labels4_tr)
print(f"Recall for the 4 batch: {recall}")
self.assertGreater(recall, recall_threshold)
# Delete batch 4
print("Deleting batch 4")
for l in labels4_tr:
hnsw_index.mark_deleted(l)
print("Testing pickle serialization")
hnsw_index_pckl = pickle.loads(pickle.dumps(hnsw_index))
del hnsw_index
# Insert batch 3
print("Inserting batch 3 by replacing deleted elements")
hnsw_index_pckl.add_items(data3_tr, labels3_tr, replace_deleted=True)
# Check recall
print("Checking recall")
labels_found, _ = hnsw_index_pckl.knn_query(data3_tr, k=1)
recall = np.mean(labels_found.reshape(-1) == labels3_tr)
print(f"Recall for the 3 batch: {recall}")
self.assertGreater(recall, recall_threshold)
os.remove(index_path)
def test_recall_degradation(self):
"""
Compares recall of the index with replaced elements and without
Measures recall degradation
"""
dim = 16
num_elements = 10_000
max_num_elements = 2 * num_elements
query_size = 1_000
k = 100
recall_threshold = 0.98
max_recall_diff = 0.02
# Generating sample data
print("Generating data")
# batch 1
first_id = 0
last_id = num_elements
labels1 = np.arange(first_id, last_id)
data1 = np.float32(np.random.random((num_elements, dim)))
# batch 2
first_id += num_elements
last_id += num_elements
labels2 = np.arange(first_id, last_id)
data2 = np.float32(np.random.random((num_elements, dim)))
# batch 3
first_id += num_elements
last_id += num_elements
labels3 = np.arange(first_id, last_id)
data3 = np.float32(np.random.random((num_elements, dim)))
# query to test recall
query_data = np.float32(np.random.random((query_size, dim)))
# Declaring index
hnsw_index_no_replace = hnswlib.Index(space='l2', dim=dim)
hnsw_index_no_replace.init_index(max_elements=max_num_elements, ef_construction=200, M=16, allow_replace_deleted=False)
hnsw_index_with_replace = hnswlib.Index(space='l2', dim=dim)
hnsw_index_with_replace.init_index(max_elements=max_num_elements, ef_construction=200, M=16, allow_replace_deleted=True)
bf_index = hnswlib.BFIndex(space='l2', dim=dim)
bf_index.init_index(max_elements=max_num_elements)
hnsw_index_no_replace.set_ef(100)
hnsw_index_no_replace.set_num_threads(50)
hnsw_index_with_replace.set_ef(100)
hnsw_index_with_replace.set_num_threads(50)
# Add data
print("Adding data")
hnsw_index_with_replace.add_items(data1, labels1)
hnsw_index_with_replace.add_items(data2, labels2) # maximum number of elements is reached
bf_index.add_items(data1, labels1)
bf_index.add_items(data3, labels3) # maximum number of elements is reached
for l in labels2:
hnsw_index_with_replace.mark_deleted(l)
hnsw_index_with_replace.add_items(data3, labels3, replace_deleted=True)
hnsw_index_no_replace.add_items(data1, labels1)
hnsw_index_no_replace.add_items(data3, labels3) # maximum number of elements is reached
# Query the elements and measure recall:
labels_hnsw_with_replace, _ = hnsw_index_with_replace.knn_query(query_data, k)
labels_hnsw_no_replace, _ = hnsw_index_no_replace.knn_query(query_data, k)
labels_bf, distances_bf = bf_index.knn_query(query_data, k)
# Measure recall
correct_with_replace = 0
correct_no_replace = 0
for i in range(query_size):
for label in labels_hnsw_with_replace[i]:
for correct_label in labels_bf[i]:
if label == correct_label:
correct_with_replace += 1
break
for label in labels_hnsw_no_replace[i]:
for correct_label in labels_bf[i]:
if label == correct_label:
correct_no_replace += 1
break
recall_with_replace = float(correct_with_replace) / (k*query_size)
recall_no_replace = float(correct_no_replace) / (k*query_size)
print("recall with replace:", recall_with_replace)
print("recall without replace:", recall_no_replace)
recall_diff = abs(recall_with_replace - recall_with_replace)
self.assertGreater(recall_no_replace, recall_threshold)
self.assertLess(recall_diff, max_recall_diff)
|