Merge pull request #103 from boeddeker/master

Fix bug for long sequences (> 640)

editdistance/_editdistance.cpp

@@ -61,15 +61,15 @@ unsigned int edit_distance_bpv(T &cmap, int64_t const *vec, size_t const &vecsiz
 
 
 /// c.f. http://handasse.blogspot.com/2009/04/c_29.html
-template<typename T>
-unsigned int edit_distance_dp(T const *str1, size_t const size1, T const *str2, size_t const size2) {
+unsigned int edit_distance_dp(int64_t const *str1, size_t const size1, int64_t const *str2, size_t const size2) {
     // vectorより固定長配列の方が速いが、文字列が長い時の保険でのみ呼ばれるのでサイズを決め打ちできない
     vector< vector<uint32_t> > d(2, vector<uint32_t>(size2 + 1));
     d[0][0] = 0;
     d[1][0] = 1;
-    for (int i = 0; i < size2 + 1; i++) d[0][i] = i;
-    for (int i = 1; i < size1 + 1; i++) {
-        for (int j = 1; j < size2 + 1; j++) {
+    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;
+        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));
         }
     }
@@ -127,5 +127,5 @@ unsigned int edit_distance(const int64_t *a, const unsigned int asize, const int
     else if(vsize == 8) return edit_distance_map_<8>(ap, *asizep, bp, *bsizep);
     else if(vsize == 9) return edit_distance_map_<9>(ap, *asizep, bp, *bsizep);
     else if(vsize == 10) return edit_distance_map_<10>(ap, *asizep, bp, *bsizep);
-    return edit_distance_dp<int64_t>(ap, *asizep, bp, *bsizep);  // dynamic programmingに任せる
+    return edit_distance_dp(ap, *asizep, bp, *bsizep);  // 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);
+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.pyx

@@ -7,6 +7,8 @@ from libc.stdlib cimport malloc, free
 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)
+    unsigned int edit_distance_dp(const int64_t *str1, const size_t size1, const int64_t *str2, const size_t size2)
+
 
 cpdef unsigned int eval(object a, object b) except 0xffffffffffffffff:
     cdef unsigned int i, dist
@@ -20,3 +22,17 @@ cpdef unsigned int eval(object a, object b) except 0xffffffffffffffff:
     free(al)
     free(bl)
     return dist
+
+
+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)):
+        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])
+    dist = edit_distance_dp(al, len(a), bl, len(b))
+    free(al)
+    free(bl)
+    return dist

test/test_editdistance.py

@@ -1,9 +1,25 @@
 import unittest
+import random
+
 
 class TestEditDistance(unittest.TestCase):
     def test_editdistance(self):
         import editdistance
         self.assertEqual(1, editdistance.eval('abc', 'aec'))
+
+    def test_dp_editdistance(self):
+        from editdistance.bycython import eval_dp
+        self.assertEqual(3, eval_dp('bbb', 'a'))
+        self.assertEqual(3, eval_dp('a', 'bbb'))
+
+    def test_dp_vs_default(self):
+        for _ in range(10):
+            import editdistance
+            from editdistance.bycython import eval_dp
+            seq1 = random.choices([0, 1, 2], k=random.randint(10, 50))
+            seq2 = random.choices([0, 1, 2], k=random.randint(10, 50))
+
+            self.assertEqual(editdistance.eval(seq1, seq2), eval_dp(seq1, seq2))
 
 
 if __name__ == '__main__':