def fit(self, X):
if X.dtype != numpy.float32:
X = X.astype(numpy.float32)
if self._metric == 'angular':
X = sklearn.preprocessing.normalize(X, axis=1, norm='l2')
self._index_autotuned = mrpt.MRPTIndex(X)
self._index_autotuned.build_autotune_sample(target_recall = None, k = self._k, n_test = 1000)
def fit(self, X):
if self._metric == 'angular':
X = sklearn.preprocessing.normalize(X, axis=1, norm='l2')
self._index = mrpt.MRPTIndex(X,
depth=self._depth,
n_trees=self._n_trees)
self._index.build()
def RunAnnMrpt():
totalTimer = Timer()
# Load input dataset.
Log.Info("Loading dataset", self.verbose)
referenceData = np.genfromtxt(self.dataset[0], delimiter=',')
queryData = np.genfromtxt(self.dataset[1], delimiter=',')
train, label = SplitTrainData(self.dataset)
# Get all the parameters.
if "k" in options:
k = int(options.pop("k"))
if (k < 1 or k > referenceData.shape[0]):
Log.Fatal("Invalid k: " + k.group(1) +
"; must be greater than 0" +
" and less or equal than " +
str(referenceData.shape[0]))
return -1
else:
Log.Fatal(
"Required option: Number of furthest neighbors to find.")
return -1
build_dict = {}
run_dict = {}
if "num_trees" in options:
build_dict["n_trees"] = int(options.pop("num_trees"))
else:
Log.Fatal("Required option: Number of trees to build")
return -1
if "depth" in options:
build_dict["depth"] = int(options.pop("depth"))
else:
build_dict["depth"] = 2 # Not sure... just a default...
if "votes_required" in options:
run_dict["votes_required"] = int(options.pop("votes_required"))
if len(options) > 0:
Log.Fatal("Unknown parameters: " + str(options))
raise Exception("unknown parameters")
with totalTimer:
try:
# Perform Approximate Nearest-Neighbors.
acc = 0
index = mrpt.MRPTIndex(np.float32(train), **build_dict)
index.build()
approximate_neighbors = np.zeros((len(queryData), k))
for i in range(len(queryData)):
approximate_neighbors[i] = index.ann(
np.float32(queryData[i]), k, **run_dict)
except Exception as e:
return -1
return totalTimer.ElapsedTime()
def metric(self):
totalTimer = Timer()
with totalTimer:
index = mrpt.MRPTIndex(np.float32(self.data[0]))
index.build(**self.build_dict)
neighbors = np.zeros((len(self.data[1]), self.k))
for i in range(len(self.data[1])):
neighbors[i] = index.ann(np.float32(self.data[1][i]), self.k,
**self.run_dict)
metric = {}
metric["runtime"] = totalTimer.ElapsedTime()
return metric
def RunAnnMrpt(q):
totalTimer = Timer()
# Load input dataset.
Log.Info("Loading dataset", self.verbose)
referenceData = np.genfromtxt(self.dataset[0], delimiter=',')
queryData = np.genfromtxt(self.dataset[1], delimiter=',')
train, label = SplitTrainData(self.dataset)
# Get all the parameters.
k = re.search("-k (\d+)", options)
n = re.search("-n (\d+)", options) # Number of trees.
d = re.search("-d (\d+)", options) # The tree depth.
v = re.search("-v (\d+)", options) # Number of votes_required.
if not k:
Log.Fatal(
"Required option: Number of furthest neighbors to find.")
q.put(-1)
return -1
else:
k = int(k.group(1))
if (k < 1 or k > referenceData.shape[0]):
Log.Fatal("Invalid k: " + k.group(1) +
"; must be greater than 0" +
" and less or equal than " +
str(referenceData.shape[0]))
q.put(-1)
return -1
if not n:
Log.Fatal("Required option: Number of trees to build")
q.put(-1)
return -1
else:
n = int(n.group(1))
d = 5 if not d else int(d.group(1))
v = 4 if not v else int(v.group(1))
with totalTimer:
try:
# Perform Approximate Nearest-Neighbors.
acc = 0
index = mrpt.MRPTIndex(np.float32(train),
depth=d,
n_trees=n)
index.build()
approximate_neighbors = np.zeros((len(queryData), k))
for i in range(len(queryData)):
approximate_neighbors[i] = index.ann(np.float32(
queryData[i]),
k,
votes_required=v)
except Exception as e:
Log.Info(e)
q.put(-1)
return -1
time = totalTimer.ElapsedTime()
q.put(time)
return time
reacll.append(annoyRecall)
algorithm.append('Annoy-trees-' + str(numTrees))
construciotnTimes.append(constructionTime)
searchTimes.append(searchTime)
avgdistances.append(avgDist)
#mrpt multi RP-tree
import mrpt
for a in [(0.5, 5), (0.6, 6), (0.8, 8), (0.9, 10)]:
m = a[1]
target_recall = a[0]
startTime = time.perf_counter()
index = mrpt.MRPTIndex(train.astype(np.float32))
index.build_autotune_sample(0.65, k, trees_max=10)
end_time = time.perf_counter()
constructionTime = end_time - startTime
mrtpquery = query.astype(np.float32)
rez = []
dist = []
startTime = time.perf_counter()
for q in mrtpquery:
res, d = index.ann(q, return_distances=True)
rez.append(res)
dist.append(d)
end_time = time.perf_counter()
# Generate synthetic test data
k = 10; n_queries = 100
data = np.dot(np.random.rand(1e5,5), np.random.rand(5,100)).astype('float32')
queries = np.dot(np.random.rand(n_queries,5), np.random.rand(5,100)).astype('float32')
# Solve exact nearest neighbors with standard methods from scipy and numpy for reference
exact_search_time = time()
exact_neighbors = np.zeros((n_queries, k))
for i in range(n_queries):
exact_neighbors[i] = np.argsort(cdist([queries[i]], data))[0,:k]
exact_search_time = time() - exact_search_time
# Offline phase: Indexing the data. This might take some time.
indexing_time = time()
index = mrpt.MRPTIndex(data, depth=5, n_trees=100)
index.build()
indexing_time = time() - indexing_time
# Online phase: Finding nearest neighbors stupendously fast.
approximate_search_time = time()
approximate_neighbors = np.zeros((n_queries, k))
for i in range(n_queries):
approximate_neighbors[i] = index.ann(queries[i], k, votes_required=4)
approximate_search_time = time() - approximate_search_time
# Print some stats
print ('Indexing time: %1.3f seconds' %indexing_time)
print ('%d approximate queries time: %1.3f seconds' %(n_queries, approximate_search_time))
print ('%d exact queries time: %1.3f seconds' %(n_queries, exact_search_time))
def fit(self, X):
self._index = mrpt.MRPTIndex(X,
depth=self._depth,
n_trees=self._n_trees)
self._index.build()