有eucl_dist软件包(免责声明:我是它的作者),它基本上包含两种方法来解决计算平方欧几里德距离的问题,该方法比SciPy的cdist更有效,尤其是对于大型数组(具有适当的列数).
我们将使用其source code中的一些代码来适应此处的问题,从而为我们提供两种方法.
方法1
def pdist_squareformed_numpy(a):
a_sumrows = np.einsum('ij,ij->i',a,a)
dist = a_sumrows[:,None] + a_sumrows -2*np.dot(a,a.T)
np.fill_diagonal(dist,0)
return dist
方法#2
另一种方法是创建输入数组的“扩展”版本,在github源代码链接中再次进行了详细讨论,以获取第二种方法,这种方法适用于较少的列,例如此处所示-
def ext_arrs(A,B, precision="float64"):
nA,dim = A.shape
A_ext = np.ones((nA,dim*3),dtype=precision)
A_ext[:,dim:2*dim] = A
A_ext[:,2*dim:] = A**2
nB = B.shape[0]
B_ext = np.ones((dim*3,nB),dtype=precision)
B_ext[:dim] = (B**2).T
B_ext[dim:2*dim] = -2.0*B.T
return A_ext, B_ext
def pdist_squareformed_numpy_v2(a):
A_ext, B_ext = ext_arrs(a,a)
dist = A_ext.dot(B_ext)
np.fill_diagonal(dist,0)
return dist
请注意,这些给出了平方欧几里德距离.因此,对于实际距离,如果需要最终输出,我们想使用np.sqrt().
样品运行-
In [380]: np.random.seed(0)
...: a = np.random.rand(5,3)
In [381]: from scipy.spatial.distance import cdist
In [382]: cdist(a,a)
Out[382]:
array([[0. , 0.29, 0.42, 0.2 , 0.57],
[0.29, 0. , 0.58, 0.42, 0.76],
[0.42, 0.58, 0. , 0.45, 0.9 ],
[0.2 , 0.42, 0.45, 0. , 0.51],
[0.57, 0.76, 0.9 , 0.51, 0. ]])
In [383]: np.sqrt(pdist_squareformed_numpy(a))
Out[383]:
array([[0. , 0.29, 0.42, 0.2 , 0.57],
[0.29, 0. , 0.58, 0.42, 0.76],
[0.42, 0.58, 0. , 0.45, 0.9 ],
[0.2 , 0.42, 0.45, 0. , 0.51],
[0.57, 0.76, 0.9 , 0.51, 0. ]])
In [384]: np.sqrt(pdist_squareformed_numpy_v2(a))
Out[384]:
array([[0. , 0.29, 0.42, 0.2 , 0.57],
[0.29, 0. , 0.58, 0.42, 0.76],
[0.42, 0.58, 0. , 0.45, 0.9 ],
[0.2 , 0.42, 0.45, 0. , 0.51],
[0.57, 0.76, 0.9 , 0.51, 0. ]])
1万点的计时-
In [385]: a = np.random.rand(10000,3)
In [386]: %timeit cdist(a,a)
1 loop, best of 3: 309 ms per loop
# Approach #1
In [388]: %timeit pdist_squareformed_numpy(a) # squared eucl distances
1 loop, best of 3: 668 ms per loop
In [389]: %timeit np.sqrt(pdist_squareformed_numpy(a)) # actual eucl distances
1 loop, best of 3: 812 ms per loop
# Approach #2
In [390]: %timeit pdist_squareformed_numpy_v2(a) # squared eucl distances
1 loop, best of 3: 237 ms per loop
In [391]: %timeit np.sqrt(pdist_squareformed_numpy_v2(a)) # actual eucl distances
1 loop, best of 3: 395 ms per loop
第二种方法似乎在性能上接近cdist!