将 numpy 数组写入文本文件的速度

Question

我需要将一个非常“高”的两列数组写入文本文件，而且速度非常慢。我发现如果我将数组重塑为更宽的数组，写入速度会快得多。例如

import time
import numpy as np
dataMat1 = np.random.rand(1000,1000)
dataMat2 = np.random.rand(2,500000)
dataMat3 = np.random.rand(500000,2)
start = time.perf_counter()
with open('test1.txt','w') as f:
    np.savetxt(f,dataMat1,fmt='%g',delimiter=' ')
end = time.perf_counter()
print(end-start)

start = time.perf_counter()
with open('test2.txt','w') as f:
    np.savetxt(f,dataMat2,fmt='%g',delimiter=' ')
end = time.perf_counter()
print(end-start)

start = time.perf_counter()
with open('test3.txt','w') as f:
    np.savetxt(f,dataMat3,fmt='%g',delimiter=' ')
end = time.perf_counter()
print(end-start)

在三个数据矩阵中元素数量相同的情况下，为什么最后一个比其他两个更耗时？有没有办法加快写入“高”数据数组的速度？

Answer 1

正如hpaulj 指出的那样，savetxt正在循环遍历X每一行并单独格式化每一行：

for row in X:
    try:
        v = format % tuple(row) + newline
    except TypeError:
        raise TypeError("Mismatch between array dtype ('%s') and "
                        "format specifier ('%s')"
                        % (str(X.dtype), format))
    fh.write(v)

我认为这里的主要时间杀手是所有的字符串插值调用。如果我们将所有字符串插值打包到一个调用中，事情会变得更快：

with open('/tmp/test4.txt','w') as f:
    fmt = ' '.join(['%g']*dataMat3.shape[1])
    fmt = '\n'.join([fmt]*dataMat3.shape[0])
    data = fmt % tuple(dataMat3.ravel())
    f.write(data)

import io
import time
import numpy as np

dataMat1 = np.random.rand(1000,1000)
dataMat2 = np.random.rand(2,500000)
dataMat3 = np.random.rand(500000,2)
start = time.perf_counter()
with open('/tmp/test1.txt','w') as f:
    np.savetxt(f,dataMat1,fmt='%g',delimiter=' ')
end = time.perf_counter()
print(end-start)

start = time.perf_counter()
with open('/tmp/test2.txt','w') as f:
    np.savetxt(f,dataMat2,fmt='%g',delimiter=' ')
end = time.perf_counter()
print(end-start)

start = time.perf_counter()
with open('/tmp/test3.txt','w') as f:
    np.savetxt(f,dataMat3,fmt='%g',delimiter=' ')
end = time.perf_counter()
print(end-start)

start = time.perf_counter()
with open('/tmp/test4.txt','w') as f:
    fmt = ' '.join(['%g']*dataMat3.shape[1])
    fmt = '\n'.join([fmt]*dataMat3.shape[0])
    data = fmt % tuple(dataMat3.ravel())        
    f.write(data)
end = time.perf_counter()
print(end-start)

报告

0.1604848340011813
0.17416274400056864
0.6634929459996783
0.16207673999997496