Merge pull request #90 from williamsyy/localmap

fix: Fixing the Issue #89

source/pacmap/pacmap.py

@@ -1115,6 +1115,7 @@ def sample_FP_nearby(n_samples, maximum, reject_ind, self_ind, Y, low_dist_thres
     result = np.empty(n_samples, dtype=np.int32)
     for i in range(n_samples):
         reject_sample = True
+        count = 0
         while reject_sample:
             j = np.random.randint(maximum)
             if j == self_ind:
@@ -1126,15 +1127,20 @@ def sample_FP_nearby(n_samples, maximum, reject_ind, self_ind, Y, low_dist_thres
                 for k in range(reject_ind.shape[0]):
                     if j == reject_ind[k]:
                         break
-                if euclid_dist(Y[self_ind], Y[j]) > low_dist_thres:
-                    continue
                 else:
-                    reject_sample = False
+                    if euclid_dist(Y[self_ind], Y[j]) > low_dist_thres:
+                        continue
+                    else:
+                        reject_sample = False
+            count += 1
+            if count > 100:
+                j = -1
+                reject_sample = False
         result[i] = j
     return result
 
-@numba.njit("i4[:,:](f4[:,:],i4[:,:],i4,i4, f4[:,:], f4)", parallel=True, nogil=True, cache=True)
-def sample_FP_pair_nearby(X, pair_neighbors, n_neighbors, n_FP, Y, low_dist_thres):
+@numba.njit("i4[:,:](f4[:,:],i4[:,:],i4[:,:],i4,i4, f4[:,:], f4)", parallel=True, nogil=True, cache=True)
+def sample_FP_pair_nearby(X, pair_neighbors, old_pair_FP, n_neighbors, n_FP, Y, low_dist_thres):
     '''Resample Further pairs for local graph adjustment'''
     n = X.shape[0]
     pair_FP = np.empty((n * n_FP, 2), dtype=np.int32)
@@ -1149,7 +1155,10 @@ def sample_FP_pair_nearby(X, pair_neighbors, n_neighbors, n_FP, Y, low_dist_thre
         )
         for k in numba.prange(n_FP):
             pair_FP[i*n_FP + k][0] = i
-            pair_FP[i*n_FP + k][1] = FP_index[k]
+            if FP_index[k] == -1:
+                pair_FP[i*n_FP + k][1] = old_pair_FP[i*n_FP + k][1]
+            else:
+                pair_FP[i*n_FP + k][1] = FP_index[k]
     return pair_FP
 
 @numba.njit("f4[:,:](f4[:,:],i4[:,:],i4[:,:],i4[:,:],f4,f4,f4,f4)", parallel=True, nogil=True, cache=True)
@@ -1281,7 +1290,7 @@ def localmap(
         update_embedding_adam(Y, grad, m, v, beta1, beta2, lr, itr)
 
         if (itr > num_iters[0] + num_iters[1]) and (itr % 10 == 0):
-            pair_FP = sample_FP_pair_nearby(X, pair_neighbors, n_neighbors, n_FP, Y, low_dist_thres)
+            pair_FP = sample_FP_pair_nearby(X, pair_neighbors, pair_FP, n_neighbors, n_FP, Y, low_dist_thres)
 
         if intermediate:
             if (itr + 1) == inter_snapshots[itr_ind]:
@@ -1462,7 +1471,4 @@ def fit(self, X, init=None, save_pairs=True):
         )
         if not save_pairs:
             self.del_pairs()
-        return self
-
-
-
+        return self