如何以最有效的内存和时间方式获取大文件的行数?

def file_len(filename):
    with open(filename) as f:
        for i, _ in enumerate(f):
            pass
    return i + 1

当前回答

这是对其他一些答案的元评论。

The line-reading and buffered \n-counting techniques won't return the same answer for every file, because some text files have no newline at the end of the last line. You can work around this by checking the last byte of the last nonempty buffer and adding 1 if it's not b'\n'. In Python 3, opening the file in text mode and in binary mode can yield different results, because text mode by default recognizes CR, LF, and CRLF as line endings (converting them all to '\n'), while in binary mode only LF and CRLF will be counted if you count b'\n'. This applies whether you read by lines or into a fixed-size buffer. The classic Mac OS used CR as a line ending; I don't know how common those files are these days. The buffer-reading approach uses a bounded amount of RAM independent of file size, while the line-reading approach could read the entire file into RAM at once in the worst case (especially if the file uses CR line endings). In the worst case it may use substantially more RAM than the file size, because of overhead from dynamic resizing of the line buffer and (if you opened in text mode) Unicode decoding and storage. You can improve the memory usage, and probably the speed, of the buffered approach by pre-allocating a bytearray and using readinto instead of read. One of the existing answers (with few votes) does this, but it's buggy (it double-counts some bytes). The top buffer-reading answer uses a large buffer (1 MiB). Using a smaller buffer can actually be faster because of OS readahead. If you read 32K or 64K at a time, the OS will probably start reading the next 32K/64K into the cache before you ask for it, and each trip to the kernel will return almost immediately. If you read 1 MiB at a time, the OS is unlikely to speculatively read a whole megabyte. It may preread a smaller amount but you will still spend a significant amount of time sitting in the kernel waiting for the disk to return the rest of the data.

其他回答

这是我用的,看起来很干净:

import subprocess

def count_file_lines(file_path):
    """
    Counts the number of lines in a file using wc utility.
    :param file_path: path to file
    :return: int, no of lines
    """
    num = subprocess.check_output(['wc', '-l', file_path])
    num = num.split(' ')
    return int(num[0])

更新:这比使用纯python略快,但以内存使用为代价。子进程在执行您的命令时将派生一个与父进程具有相同内存占用的新进程。

为了完成上述方法,我尝试了fileinput模块的一个变体:

import fileinput as fi   
def filecount(fname):
        for line in fi.input(fname):
            pass
        return fi.lineno()

并将一个60mil行文件传递给上述所有方法:

mapcount : 6.1331050396
simplecount : 4.588793993
opcount : 4.42918205261
filecount : 43.2780818939
bufcount : 0.170812129974

这让我有点惊讶,fileinput是如此糟糕,比所有其他方法都要糟糕得多…

在perfplot分析之后,必须推荐缓冲读取解决方案

def buf_count_newlines_gen(fname):
    def _make_gen(reader):
        while True:
            b = reader(2 ** 16)
            if not b: break
            yield b

    with open(fname, "rb") as f:
        count = sum(buf.count(b"\n") for buf in _make_gen(f.raw.read))
    return count

它速度快,内存效率高。大多数其他解决方案大约要慢20倍。


代码重现情节:

import mmap
import subprocess
from functools import partial

import perfplot


def setup(n):
    fname = "t.txt"
    with open(fname, "w") as f:
        for i in range(n):
            f.write(str(i) + "\n")
    return fname


def for_enumerate(fname):
    i = 0
    with open(fname) as f:
        for i, _ in enumerate(f):
            pass
    return i + 1


def sum1(fname):
    return sum(1 for _ in open(fname))


def mmap_count(fname):
    with open(fname, "r+") as f:
        buf = mmap.mmap(f.fileno(), 0)

    lines = 0
    while buf.readline():
        lines += 1
    return lines


def for_open(fname):
    lines = 0
    for _ in open(fname):
        lines += 1
    return lines


def buf_count_newlines(fname):
    lines = 0
    buf_size = 2 ** 16
    with open(fname) as f:
        buf = f.read(buf_size)
        while buf:
            lines += buf.count("\n")
            buf = f.read(buf_size)
    return lines


def buf_count_newlines_gen(fname):
    def _make_gen(reader):
        b = reader(2 ** 16)
        while b:
            yield b
            b = reader(2 ** 16)

    with open(fname, "rb") as f:
        count = sum(buf.count(b"\n") for buf in _make_gen(f.raw.read))
    return count


def wc_l(fname):
    return int(subprocess.check_output(["wc", "-l", fname]).split()[0])


def sum_partial(fname):
    with open(fname) as f:
        count = sum(x.count("\n") for x in iter(partial(f.read, 2 ** 16), ""))
    return count


def read_count(fname):
    return open(fname).read().count("\n")


b = perfplot.bench(
    setup=setup,
    kernels=[
        for_enumerate,
        sum1,
        mmap_count,
        for_open,
        wc_l,
        buf_count_newlines,
        buf_count_newlines_gen,
        sum_partial,
        read_count,
    ],
    n_range=[2 ** k for k in range(27)],
    xlabel="num lines",
)
b.save("out.png")
b.show()

使用Numba

我们可以使用Numba来JIT(及时)编译我们的函数到机器代码。Def numbacountparallel(fname)运行速度快2.8倍 然后从问题中定义file_len(fname)。

注:

在运行基准测试之前,操作系统已经将文件缓存到内存中,因为我在我的PC上没有看到太多的磁盘活动。 第一次读取文件时,时间会慢得多,因此使用Numba的时间优势并不显著。

第一次调用函数时,JIT编译需要额外的时间。

如果我们不只是计算行数,这个就很有用了。

Cython是另一个选择。

http://numba.pydata.org/

结论

因为计算行数是IO绑定的,所以使用问题中的def file_len(fname),除非你想做的不仅仅是计算行数。

import timeit

from numba import jit, prange
import numpy as np

from itertools import (takewhile,repeat)

FILE = '../data/us_confirmed.csv' # 40.6MB, 371755 line file
CR = ord('\n')


# Copied from the question above. Used as a benchmark
def file_len(fname):
    with open(fname) as f:
        for i, l in enumerate(f):
            pass
    return i + 1


# Copied from another answer. Used as a benchmark
def rawincount(filename):
    f = open(filename, 'rb')
    bufgen = takewhile(lambda x: x, (f.read(1024*1024*10) for _ in repeat(None)))
    return sum( buf.count(b'\n') for buf in bufgen )


# Single thread
@jit(nopython=True)
def numbacountsingle_chunk(bs):

    c = 0
    for i in range(len(bs)):
        if bs[i] == CR:
            c += 1

    return c


def numbacountsingle(filename):
    f = open(filename, "rb")
    total = 0
    while True:
        chunk = f.read(1024*1024*10)
        lines = numbacountsingle_chunk(chunk)
        total += lines
        if not chunk:
            break

    return total


# Multi thread
@jit(nopython=True, parallel=True)
def numbacountparallel_chunk(bs):

    c = 0
    for i in prange(len(bs)):
        if bs[i] == CR:
            c += 1

    return c


def numbacountparallel(filename):
    f = open(filename, "rb")
    total = 0
    while True:
        chunk = f.read(1024*1024*10)
        lines = numbacountparallel_chunk(np.frombuffer(chunk, dtype=np.uint8))
        total += lines
        if not chunk:
            break

    return total

print('numbacountparallel')
print(numbacountparallel(FILE)) # This allows Numba to compile and cache the function without adding to the time.
print(timeit.Timer(lambda: numbacountparallel(FILE)).timeit(number=100))

print('\nnumbacountsingle')
print(numbacountsingle(FILE))
print(timeit.Timer(lambda: numbacountsingle(FILE)).timeit(number=100))

print('\nfile_len')
print(file_len(FILE))
print(timeit.Timer(lambda: rawincount(FILE)).timeit(number=100))

print('\nrawincount')
print(rawincount(FILE))
print(timeit.Timer(lambda: rawincount(FILE)).timeit(number=100))

每个函数调用100次的时间(以秒为单位)

numbacountparallel
371755
2.8007332000000003

numbacountsingle
371755
3.1508585999999994

file_len
371755
6.7945494

rawincount
371755
6.815438

与此答案类似的一行bash解决方案,使用了现代子进程。check_output功能:

def line_count(filename):
    return int(subprocess.check_output(['wc', '-l', filename]).split()[0])