CodeSet for deduping large datasets (facebookresearch#2949)

Summary:
Pull Request resolved: facebookresearch#2949

A more scalable alternative to `np.unique` for deduping large datasets with a quantized code.

Reviewed By: mlomeli1

Differential Revision: D47443953

fbshipit-source-id: 4a1554d4d4200b5fa657e9d8b7395bba9856a8e3

faiss/python/__init__.py

@@ -41,6 +41,7 @@
 class_wrappers.handle_IDSelectorSubset(IDSelectorBatch, class_owns=True)
 class_wrappers.handle_IDSelectorSubset(IDSelectorArray, class_owns=False)
 class_wrappers.handle_IDSelectorSubset(IDSelectorBitmap, class_owns=False, force_int64=False)
+class_wrappers.handle_CodeSet(CodeSet)
 
 this_module = sys.modules[__name__]
 

faiss/python/class_wrappers.py

@@ -1102,3 +1102,21 @@ def replacement_init(self, *args):
         self.original_init(*args)
 
     the_class.__init__ = replacement_init
+
+
+def handle_CodeSet(the_class):
+
+    def replacement_insert(self, codes, inserted=None):
+        n, d = codes.shape
+        assert d == self.d
+        codes = np.ascontiguousarray(codes, dtype=np.uint8)
+
+        if inserted is None:
+            inserted = np.empty(n, dtype=bool)
+        else:
+            assert inserted.shape == (n, )
+
+        self.insert_c(n, swig_ptr(codes), swig_ptr(inserted))
+        return inserted
+
+    replace_method(the_class, 'insert', replacement_insert)

faiss/utils/utils.cpp

@@ -28,6 +28,7 @@
 #include <omp.h>
 
 #include <algorithm>
+#include <set>
 #include <type_traits>
 #include <vector>
 
@@ -623,4 +624,12 @@ void CombinerRangeKNN<T>::write_result(T* D_res, int64_t* I_res) {
 template struct CombinerRangeKNN<float>;
 template struct CombinerRangeKNN<int16_t>;
 
+void CodeSet::insert(size_t n, const uint8_t* codes, bool* inserted) {
+    for (size_t i = 0; i < n; i++) {
+        auto res = s.insert(
+                std::vector<uint8_t>(codes + i * d, codes + i * d + d));
+        inserted[i] = res.second;
+    }
+}
+
 } // namespace faiss

faiss/utils/utils.h

@@ -17,7 +17,9 @@
 #define FAISS_utils_h
 
 #include <stdint.h>
+#include <set>
 #include <string>
+#include <vector>
 
 #include <faiss/impl/platform_macros.h>
 #include <faiss/utils/Heap.h>
@@ -209,6 +211,14 @@ struct CombinerRangeKNN {
     void write_result(T* D_res, int64_t* I_res);
 };
 
+struct CodeSet {
+    size_t d;
+    std::set<std::vector<uint8_t>> s;
+
+    explicit CodeSet(size_t d) : d(d) {}
+    void insert(size_t n, const uint8_t* codes, bool* inserted);
+};
+
 } // namespace faiss
 
 #endif /* FAISS_utils_h */

tests/test_contrib.py

@@ -630,3 +630,17 @@ def test_hnsw_permute(self):
         np.testing.assert_equal(Dnew, Dref)
         Inew_remap = perm[Inew]
         np.testing.assert_equal(Inew_remap, Iref)
+
+
+class TestCodeSet(unittest.TestCase):
+
+    def test_code_set(self):
+        """ CodeSet and np.unique should produce the same output """
+        d = 8
+        n = 1000  # > 256 and using only 0 or 1 so there must be duplicates
+        codes = np.random.randint(0, 2, (n, d), dtype=np.uint8)
+        s = faiss.CodeSet(d)
+        inserted = s.insert(codes)
+        np.testing.assert_equal(
+            np.sort(np.unique(codes, axis=0), axis=None),
+            np.sort(codes[inserted], axis=None))