Merge pull request #107 from VasLem/master

Added ability to prematurely terminate search

editdistance/__init__.pxd

@@ -1,2 +1,2 @@
 # cython: language_level=3
-from editdistance.bycython cimport eval
+from editdistance.bycython cimport eval, eval_criterion

editdistance/__init__.py

@@ -1,9 +1,12 @@
-from .bycython import eval
+from .bycython import eval, eval_criterion
 
 
 def distance(*args, **kwargs):
     """"An alias to eval"""
     return eval(*args, **kwargs)
 
+def distance_le_than(*args, **kwargs):
+    """"An alias to eval"""
+    return eval_criterion(*args, **kwargs)
 
-__all__ = ('eval', 'distance')
+__all__ = ('eval', 'distance', "eval_criterion", "distance_le_than")

editdistance/_editdistance.cpp

@@ -41,7 +41,7 @@ unsigned int edit_distance_bpv(T &cmap, int64_t const *vec, size_t const &vecsiz
     for(size_t i = 0; i < tlen; ++i) VP[tmax] |= (1LL << i);
     for(size_t i = 0; i < vecsize; ++i) {
         TVALUE &PM = cmap[vec[i]];
-        for(int r = 0; r <= tmax; ++r) {
+        for(unsigned int r = 0; r <= tmax; ++r) {
             uint64_t X = PM[r];
             if(r > 0 && (HN[r - 1] & lmb)) X |= 1LL;
             D0[r] = (((X & VP[r]) + VP[r]) ^ VP[r]) | X | VN[r];
@@ -76,6 +76,28 @@ unsigned int edit_distance_dp(int64_t const *str1, size_t const size1, int64_t c
     return d[size1&1][size2];
 }
 
+template<typename T>
+bool edit_distancec_dp(T const *str1, size_t const size1, T const *str2, size_t const size2, unsigned int const thr) {
+    vector< vector<uint32_t> > d(2, vector<uint32_t>(size2 + 1));
+    d[0][0] = 0;
+    d[1][0] = 1;
+    for (size_t i = 0; i < size2 + 1; i++) d[0][i] = i;
+    for (size_t i = 1; i < size1 + 1; i++) {
+        d[i&1][0] = d[(i-1)&1][0] + 1;
+        bool below_thr = false;
+        for (size_t j = 1; j < size2 + 1; j++) {
+            d[i&1][j] = min(min(d[(i-1)&1][j], d[i&1][j-1]) + 1, d[(i-1)&1][j-1] + (str1[i-1] == str2[j-1] ? 0 : 1));
+            if (d[i%1][j] <= thr) {
+                below_thr = true;
+            }
+        }
+        if (!below_thr) {
+            return false;
+        }
+    }
+    return d[size1&1][size2] <= thr;
+}
+
 template <size_t N>
 struct varr {
     uint64_t arr_[N];
@@ -129,3 +151,28 @@ unsigned int edit_distance(const int64_t *a, const unsigned int asize, const int
     else if(vsize == 10) return edit_distance_map_<10>(ap, *asizep, bp, *bsizep);
     return edit_distance_dp(ap, *asizep, bp, *bsizep);  // dynamic programmingに任せる
 }
+
+bool edit_distance_criterion(const int64_t *a, const unsigned int asize, const int64_t *b, const unsigned int bsize, const unsigned int thr) {
+    if(asize == 0) return bsize <= thr;
+    if(bsize == 0) return asize <= thr;
+    // 要素数の大きいほうがa
+    int64_t const *ap, *bp;
+    unsigned int const *asizep, *bsizep;
+    if(asize < bsize) ap = b, bp = a, asizep = &bsize, bsizep = &asize;
+    else ap = a, bp = b, asizep = &asize, bsizep = &bsize;
+    // 必要な配列サイズを調べる
+    size_t vsize = ((*asizep - 1) >> 6) + 1;  // 64までは1, 128までは2, ...
+    // bit-parallelでできそうな限界を超えたら要素数の小さい方をaとする。
+    if(vsize > 10) {
+        int64_t const *_ = ap;
+        unsigned int const *__ = asizep;
+        ap = bp, bp = _, asizep = bsizep, bsizep = __;
+        vsize = ((*asizep - 1) >> 6) + 1;
+    }
+
+    return edit_distancec_dp<int64_t>(ap, *asizep, bp, *bsizep, thr);  // dynamic programmingに任せる
+}
+
+
+
+

editdistance/_editdistance.h

@@ -8,6 +8,7 @@ extern "C" {
 #endif
 
 unsigned int edit_distance(const int64_t *a, const unsigned int asize, const int64_t *b, const unsigned int bsize);
+bool edit_distance_criterion(const int64_t *a, const unsigned int asize, const int64_t *b, const unsigned int bsize, const unsigned int thr);
 unsigned int edit_distance_dp(int64_t const *str1, size_t const size1, int64_t const *str2, size_t const size2);
 
 #ifdef __cplusplus

editdistance/bycython.pxd

@@ -1,2 +1,3 @@
 # cython: language_level=3
 cpdef unsigned int eval(object a, object b) except 0xffffffffffffffff
+cpdef bint eval_criterion(object a, object b, const unsigned int thr) except 0xffffffffffffffff

editdistance/bycython.pyx

@@ -2,11 +2,13 @@
 # distutils: sources = editdistance/_editdistance.cpp
 
 from libc.stdlib cimport malloc, free
+from libcpp cimport bool
 # from libc.stdint cimport int64_t
 
 cdef extern from "./_editdistance.h":
     ctypedef int int64_t
     unsigned int edit_distance(const int64_t *a, const unsigned int asize, const int64_t *b, const unsigned int bsize)
+    bool edit_distance_criterion(const int64_t *a, const unsigned int asize, const int64_t *b, const unsigned int bsize, const unsigned int thr)
     unsigned int edit_distance_dp(const int64_t *str1, const size_t size1, const int64_t *str2, const size_t size2)
 
 
@@ -22,9 +24,22 @@ cpdef unsigned int eval(object a, object b) except 0xffffffffffffffff:
     free(al)
     free(bl)
     return dist
+
+cpdef bint eval_criterion(object a, object b, const unsigned int thr) except 0xffffffffffffffff:
+    cdef unsigned int i
+    cdef bint ret
+    cdef int64_t *al = <int64_t *>malloc(len(a) * sizeof(int64_t))
+    for i in range(len(a)):
+        al[i] = hash(a[i])
+    cdef int64_t *bl = <int64_t *>malloc(len(b) * sizeof(int64_t))
+    for i in range(len(b)):
+        bl[i] = hash(b[i])
+    ret = edit_distance_criterion(al, len(a), bl, len(b), thr)
+    free(al)
+    free(bl)
+    return ret
 
-
-cpdef unsigned int eval_dp(object a, object b) except 0xffffffffffffffff:
+  cpdef unsigned int eval_dp(object a, object b) except 0xffffffffffffffff:
     cdef unsigned int i, dist
     cdef int64_t *al = <int64_t *>malloc(len(a) * sizeof(int64_t))
     for i in range(len(a)):
@@ -35,4 +50,4 @@ cpdef unsigned int eval_dp(object a, object b) except 0xffffffffffffffff:
     dist = edit_distance_dp(al, len(a), bl, len(b))
     free(al)
     free(bl)
-    return dist
+    return dist

setup.py

@@ -29,7 +29,7 @@
 
 setup(
     name="editdistance",
-    version="0.6.2",
+    version="0.7.0",
     python_requires=">=3.6",
     description="Fast implementation of the edit distance(Levenshtein distance)",
     long_description=readme,

test/test_editdistance.py

@@ -7,6 +7,11 @@ def test_editdistance(self):
         import editdistance
         self.assertEqual(1, editdistance.eval('abc', 'aec'))
 
+    def test_editdistance_criterion(self):
+        import editdistance
+        self.assertEqual(False, editdistance.eval_criterion('abcb', 'aeca', 1))
+        self.assertEqual(True, editdistance.eval_criterion('abc', 'aec', 1))
+
     def test_dp_editdistance(self):
         from editdistance.bycython import eval_dp
         self.assertEqual(3, eval_dp('bbb', 'a'))
@@ -20,7 +25,7 @@ def test_dp_vs_default(self):
             seq2 = random.choices([0, 1, 2], k=random.randint(10, 50))
 
             self.assertEqual(editdistance.eval(seq1, seq2), eval_dp(seq1, seq2))
-    
+
 
 if __name__ == '__main__':
     unittest.main()