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[英]Speed up operations on a for loop with `coo` matrix and a numpy array in python
[英]Speed up getting edge matrix by index with numpy array
我想在原始矩陣中剪裁邊緣,不知道有沒有更快的方法。 由於我需要在相同的positions和positions_u中多次運行selectEdge函數,這意味着對於很多圖形來說索引不會改變嗎? 是否有可能生成一個可以解決所有問題的映射矩陣?
非常感謝你
def selectEdge(positions, positions_u, originalMat, selectedMat):
""" select Edge by neighbors of all points
many to many
m positions
n positions
would have m*n edges
update selectedMat
"""
for ele in positions:
for ele_u in positions_u:
selectedMat[ele][ele_u] += originalMat[ele][ele_u]
selectedMat[ele_u][ele] += originalMat[ele_u][ele]
return selectedMat
我只需要上三角矩陣,因為它是對稱的
def test_selectEdge(self):
positions, positions_u = np.array([0,1,5,7]), np.array([2,3,4,6])
originalMat, selectedMat = np.array([[1.0]*8]*8), np.array([[0.0]*8]*8)
selectedMat = selectEdge(positions, positions_u, originalMat, selectedMat)
print 'position, positions_u'
print positions, positions_u
print 'originalMat', originalMat
print 'selectedMat', selectedMat
這是我的測試結果
position, positions_u
[0 1 5 7] [2 3 4 6]
originalMat
[[ 1. 1. 1. 1. 1. 1. 1. 1.]
[ 1. 1. 1. 1. 1. 1. 1. 1.]
[ 1. 1. 1. 1. 1. 1. 1. 1.]
[ 1. 1. 1. 1. 1. 1. 1. 1.]
[ 1. 1. 1. 1. 1. 1. 1. 1.]
[ 1. 1. 1. 1. 1. 1. 1. 1.]
[ 1. 1. 1. 1. 1. 1. 1. 1.]
[ 1. 1. 1. 1. 1. 1. 1. 1.]]
selectedMat
[[ 0. 0. 1. 1. 1. 0. 1. 0.]
[ 0. 0. 1. 1. 1. 0. 1. 0.]
[ 1. 1. 0. 0. 0. 1. 0. 1.]
[ 1. 1. 0. 0. 0. 1. 0. 1.]
[ 1. 1. 0. 0. 0. 1. 0. 1.]
[ 0. 0. 1. 1. 1. 0. 1. 0.]
[ 1. 1. 0. 0. 0. 1. 0. 1.]
[ 0. 0. 1. 1. 1. 0. 1. 0.]]
對於后面的選擇相鄰邊的實現,它甚至會更慢
def selectNeighborEdges(originalMat, selectedMat, relation):
""" select Edge by neighbors of all points
one to many
Args:
relation: dict, {node1:[node i, node j,...], node2:[node i, node j, ...]}
update selectedMat
"""
for key in relation:
selectedMat = selectEdge([key], relation[key], originalMat, selectedMat)
return selectedMat
您可以使用“高級整數索引”消除double for-loop
:
X, Y = positions[:,None], positions_u[None,:]
selectedMat[X, Y] += originalMat[X, Y]
selectedMat[Y, X] += originalMat[Y, X]
例如,
import numpy as np
def selectEdge(positions, positions_u, originalMat, selectedMat):
for ele in positions:
for ele_u in positions_u:
selectedMat[ele][ele_u] += originalMat[ele][ele_u]
selectedMat[ele_u][ele] += originalMat[ele_u][ele]
return selectedMat
def alt_selectEdge(positions, positions_u, originalMat, selectedMat):
X, Y = positions[:,None], positions_u[None,:]
selectedMat[X, Y] += originalMat[X, Y]
selectedMat[Y, X] += originalMat[Y, X]
return selectedMat
N, M = 100, 50
positions = np.random.choice(np.arange(N), M, replace=False)
positions_u = np.random.choice(np.arange(N), M, replace=False)
originalMat = np.random.random((N, N))
selectedMat = np.zeros_like(originalMat)
首先檢查selectEdge
和alt_selectEdge
返回相同的結果:
expected = selectEdge(positions, positions_u, originalMat, selectedMat)
result = alt_selectEdge(positions, positions_u, originalMat, selectedMat)
assert np.allclose(expected, result)
這是一個timeit基准測試(使用IPython):
In [89]: %timeit selectEdge(positions, positions_u, originalMat, selectedMat)
100 loops, best of 3: 4.44 ms per loop
In [90]: %timeit alt_selectEdge(positions, positions_u, originalMat, selectedMat)
10000 loops, best of 3: 104 µs per loop
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