def test_remove_from_index(self) -> None:
# Test that actual removal occurs.
i = LinearHashIndex()
i.index = {0, 1, 2}
# noinspection PyTypeChecker
i.remove_from_index([[0, 0], [1, 0]])
self.assertSetEqual(i.index, {1})
def test_from_config_with_cache(self) -> None:
c = LinearHashIndex.get_default_config()
c['cache_element'][
'type'] = 'smqtk_dataprovider.impls.data_element.memory.DataMemoryElement'
i = LinearHashIndex.from_config(c)
self.assertIsInstance(i.cache_element, DataMemoryElement)
self.assertEqual(i.index, set())
def test_build_index_with_cache(self) -> None:
cache_element = DataMemoryElement()
i = LinearHashIndex(cache_element)
# noinspection PyTypeChecker
i.build_index([[0, 1, 0], [1, 0, 0], [0, 1, 1], [0, 0, 1]])
self.assertEqual(i.index, {1, 2, 3, 4})
self.assertFalse(cache_element.is_empty())
def test_update_index_no_index(self) -> None:
# Test calling update index with no existing index. Should result the
# same as calling build_index with no index.
i = LinearHashIndex()
# noinspection PyTypeChecker
i.update_index([[0, 1, 0], [1, 0, 0], [0, 1, 1], [0, 0, 1]])
self.assertEqual(i.index, {1, 2, 3, 4})
self.assertIsNone(i.cache_element)
def test_remove_from_index_single_not_in_index(self) -> None:
# Test attempting to remove single hash not in the index.
i = LinearHashIndex()
i.index = {0, 1, 2}
self.assertRaises(
KeyError,
i.remove_from_index,
[[1, 0, 0]] # 4
)
self.assertSetEqual(i.index, {0, 1, 2})
def test_load_cache(self) -> None:
cache_element = DataMemoryElement()
i1 = LinearHashIndex(cache_element)
# noinspection PyTypeChecker
i1.build_index([[0, 1, 0], [1, 0, 0], [0, 1, 1], [0, 0, 1]])
# load called on initialization.
i2 = LinearHashIndex(cache_element)
self.assertEqual(i1.cache_element, i2.cache_element)
self.assertEqual(i1.index, i2.index)
def test_save_cache_build_index(self) -> None:
cache_element = DataMemoryElement()
self.assertTrue(cache_element.is_empty())
i = LinearHashIndex(cache_element)
# noinspection PyTypeChecker
i.build_index([[0, 1, 0], [1, 0, 0], [0, 1, 1], [0, 0, 1]])
self.assertFalse(cache_element.is_empty())
# Check byte content
expected_cache = {1, 2, 3, 4}
actual_cache = set(numpy.load(BytesIO(cache_element.get_bytes())))
self.assertSetEqual(expected_cache, actual_cache)
def test_nn(self) -> None:
i = LinearHashIndex()
# noinspection PyTypeChecker
i.build_index([[0, 1, 0], [1, 1, 0], [0, 1, 1], [0, 0, 1]])
# noinspection PyTypeChecker
near_codes, near_dists = i.nn([0, 0, 0], 4)
self.assertEqual(set(map(tuple, near_codes[:2])), {(0, 1, 0),
(0, 0, 1)})
self.assertEqual(set(map(tuple, near_codes[2:])), {(1, 1, 0),
(0, 1, 1)})
numpy.testing.assert_array_almost_equal(
near_dists, (1 / 3., 1 / 3., 2 / 3., 2 / 3.))
def test_remove_from_index_one_of_many_not_in_index(self) -> None:
# Test attempting to remove hashes where one of them is not in the
# index.
i = LinearHashIndex()
i.index = {0, 1, 2}
self.assertRaises(
KeyError,
i.remove_from_index,
[
[0, 0], # 0
[0, 1], # 1
[1, 1]
] # 3
)
# Check that the index has not been modified.
self.assertSetEqual(i.index, {0, 1, 2})
def test_update_index_with_hash_index(self) -> None:
# Similar test to `test_update_index_add_new_descriptors` but with a
# linear hash index.
descr_set = MemoryDescriptorSet()
hash_kvs = MemoryKeyValueStore()
linear_hi = LinearHashIndex() # simplest hash index, heap-sorts.
index = LSHNearestNeighborIndex(DummyHashFunctor(), descr_set,
hash_kvs, linear_hi)
descriptors1 = [
DescriptorMemoryElement('t', 0),
DescriptorMemoryElement('t', 1),
DescriptorMemoryElement('t', 2),
DescriptorMemoryElement('t', 3),
DescriptorMemoryElement('t', 4),
]
descriptors2 = [
DescriptorMemoryElement('t', 5),
DescriptorMemoryElement('t', 6),
]
# Vectors of length 1 for easy dummy hashing prediction.
for d in descriptors1 + descriptors2:
d.set_vector(np.ones(1, float) * d.uuid())
# Build initial index.
index.build_index(descriptors1)
# Initial hash index should only encode hashes for first batch of
# descriptors.
self.assertSetEqual(linear_hi.index, {0, 1, 2, 3, 4})
# Update index and check that components have new data.
index.update_index(descriptors2)
# Now the hash index should include all descriptor hashes.
self.assertSetEqual(linear_hi.index, {0, 1, 2, 3, 4, 5, 6})
def test_save_cache_remove_from_index(self) -> None:
# Test that the cache is updated appropriately on a removal.
cache_element = DataMemoryElement()
self.assertTrue(cache_element.is_empty())
i = LinearHashIndex(cache_element)
# noinspection PyTypeChecker
i.build_index([
[0, 1, 0], # 2
[0, 1, 1], # 3
[1, 0, 0], # 4
[1, 1, 0]
]) # 6
self.assertFalse(cache_element.is_empty())
self.assertSetEqual(
set(numpy.load(BytesIO(cache_element.get_bytes()))), {2, 3, 4, 6})
# noinspection PyTypeChecker
i.remove_from_index([
[0, 1, 1], # 3
[1, 0, 0]
]) # 4
self.assertFalse(cache_element.is_empty())
self.assertSetEqual(
set(numpy.load(BytesIO(cache_element.get_bytes()))), {2, 6})
def test_configuration(self) -> None:
i = LSHNearestNeighborIndex(
lsh_functor=ItqFunctor(), descriptor_set=MemoryDescriptorSet(),
hash2uuids_kvstore=MemoryKeyValueStore(),
hash_index=LinearHashIndex(), distance_method='euclidean',
read_only=True
)
for inst in configuration_test_helper(i): # type: LSHNearestNeighborIndex
assert isinstance(inst.lsh_functor, LshFunctor)
assert isinstance(inst.descriptor_set, MemoryDescriptorSet)
assert isinstance(inst.hash_index, LinearHashIndex)
assert isinstance(inst.hash2uuids_kvstore, MemoryKeyValueStore)
assert inst.distance_method == 'euclidean'
assert inst.read_only is True
def test_update_index_add_hashes(self) -> None:
i = LinearHashIndex()
# Build index with some initial hashes
# noinspection PyTypeChecker
i.build_index([[0, 0], [0, 1]])
self.assertSetEqual(i.index, {0, 1})
# Update index with new stuff
# noinspection PyTypeChecker
i.update_index([[1, 0], [1, 1]])
self.assertSetEqual(i.index, {0, 1, 2, 3})
def test_get_config(self) -> None:
i = LinearHashIndex()
# Without cache element
expected_c = LinearHashIndex.get_default_config()
self.assertEqual(i.get_config(), expected_c)
# With cache element
i.cache_element = DataMemoryElement()
expected_c['cache_element'][
'type'] = 'smqtk_dataprovider.impls.data_element.memory.DataMemoryElement'
self.assertEqual(i.get_config(), expected_c)
def test_build_index_fresh_build_with_hash_index(self) -> None:
descr_set = MemoryDescriptorSet()
hash_kvs = MemoryKeyValueStore()
linear_hi = LinearHashIndex() # simplest hash index, heap-sorts.
index = LSHNearestNeighborIndex(DummyHashFunctor(), descr_set,
hash_kvs, linear_hi)
descriptors = [
DescriptorMemoryElement('t', 0),
DescriptorMemoryElement('t', 1),
DescriptorMemoryElement('t', 2),
DescriptorMemoryElement('t', 3),
DescriptorMemoryElement('t', 4),
]
# Vectors of length 1 for easy dummy hashing prediction.
for i, d in enumerate(descriptors):
d.set_vector(np.ones(1, float) * i)
index.build_index(descriptors)
# Hash index should have been built with hash vectors, and linearHI
# converts those to integers for storage.
self.assertEqual(linear_hi.index, {0, 1, 2, 3, 4})
def _nn(
self,
d: DescriptorElement,
n: int = 1
) -> Tuple[Tuple[DescriptorElement, ...], Tuple[float, ...]]:
"""
Internal method to be implemented by sub-classes to return the nearest
`N` neighbors to the given descriptor element.
When this internal method is called, we have already checked that there
is a vector in ``d`` and our index is not empty.
:param d: Descriptor element to compute the neighbors of.
:param n: Number of nearest neighbors to find.
:return: Tuple of nearest N DescriptorElement instances, and a tuple of
the distance values to those neighbors.
"""
LOG.debug("generating hash for descriptor")
d_v = d.vector()
d_h = self.lsh_functor.get_hash(d_v)
def comp_descr_dist(d2_v: numpy.ndarray) -> float:
return self._distance_function(d_v, d2_v)
with self._model_lock:
LOG.debug("getting near hashes")
hi = self.hash_index
if hi is None:
# Make on-the-fly linear index
hi = LinearHashIndex()
# not calling ``build_index`` because we already have the int
# hashes.
hi.index = set(cast(Iterator[int], self.hash2uuids_kvstore.keys()))
near_hashes, _ = hi.nn(d_h, n)
LOG.debug("getting UUIDs of descriptors for nearby hashes")
neighbor_uuids: List[Hashable] = []
for h_int in map(bit_vector_to_int_large, near_hashes):
# If descriptor hash not in our map, we effectively skip it.
# Get set of descriptor UUIDs for a hash code.
near_uuids: Set[Hashable] = self.hash2uuids_kvstore.get(h_int, set())
# Accumulate matching descriptor UUIDs to a list.
neighbor_uuids.extend(near_uuids)
LOG.debug("-- matched %d UUIDs", len(neighbor_uuids))
LOG.debug("getting descriptors for neighbor_uuids")
neighbors = \
list(self.descriptor_set.get_many_descriptors(neighbor_uuids))
# Done with model parts at this point, so releasing lock.
LOG.debug(f"ordering descriptors via distance method {self.distance_method}")
LOG.debug('-- getting element vectors')
neighbor_vectors = numpy.asarray(list(
parallel_map(lambda d_: d_.vector(), neighbors)
))
LOG.debug('-- calculating distances')
distances = list(map(comp_descr_dist, neighbor_vectors))
LOG.debug('-- ordering')
ordered = sorted(zip(neighbors, distances),
key=lambda p: p[1])
LOG.debug(f'-- slicing top n={n}')
r_descrs: Tuple[DescriptorElement, ...]
r_dists: Tuple[float, ...]
r_descrs, r_dists = zip(*(ordered[:n]))
return r_descrs, r_dists
def test_update_index_no_input(self) -> None:
i = LinearHashIndex()
self.assertRaises(ValueError, i.update_index, [])
def _make_hi_linear(self) -> LinearHashIndex:
return LinearHashIndex()
def test_build_index_no_cache(self) -> None:
i = LinearHashIndex()
# noinspection PyTypeChecker
i.build_index([[0, 1, 0], [1, 0, 0], [0, 1, 1], [0, 0, 1]])
self.assertEqual(i.index, {1, 2, 3, 4})
self.assertIsNone(i.cache_element)
def test_is_usable(self) -> None:
# Should always be true since this impl does no have special deps.
self.assertTrue(LinearHashIndex.is_usable())
def test_default_config(self) -> None:
c = LinearHashIndex.get_default_config()
self.assertEqual(len(c), 1)
self.assertIsNone(c['cache_element']['type'])
def test_save_cache_readonly_update_index(self) -> None:
ro_cache = DataMemoryElement(readonly=True)
i = LinearHashIndex(ro_cache)
self.assertRaisesRegex(ValueError, "is read-only", i.update_index,
[[0, 1, 0], [1, 0, 0], [0, 1, 1], [0, 0, 1]])
def test_from_config_no_cache(self) -> None:
# Default config is valid and specifies no cache.
c = LinearHashIndex.get_default_config()
i = LinearHashIndex.from_config(c)
self.assertIsNone(i.cache_element)
self.assertEqual(i.index, set())