pandas df.loc [z，x] = y如何提高速度? [英] pandas df.loc[z,x]=y how to improve speed?

问题描述

我确定了一个熊猫命令

timeseries.loc[z, x] = y

负责迭代中花费的大部分时间.现在，我正在寻找更好的方法来加速它.该循环甚至无法覆盖5万个元素(并且生产目标约为25万个或更多)，但已经需要20秒钟.

to be responsible for most of the time spent in an iteration. And now I am looking for better approaches to accelerate it. The loop covers not even 50k elements (and production goal is ~250k or more), but already needs a sad 20 seconds.

这是我的代码(忽略上半部分，它只是计时助手)

Here is my code (ignore the top half, it is just the timing helper)

def populateTimeseriesTable(df, observable, timeseries):
    """
    Go through all rows of df and 
    put the observable into the timeseries 
    at correct row (symbol), column (tsMean).
    """

    print "len(df.index)=", len(df.index)  # show number of rows

    global bf, t
    bf = time.time()                       # set 'before' to now
    t = dict([(i,0) for i in range(5)])    # fill category timing with zeros

    def T(i):
        """
        timing helper: Add passed time to category 'i'. Then set 'before' to now.
        """
        global bf, t 
        t[i] = t[i] + (time.time()-bf)
        bf = time.time()        

    for i in df.index:             # this is the slow loop
        bf = time.time()

        sym = df["symbol"][i]
        T(0)

        tsMean = df["tsMean"][i]
        T(1)

        tsMean = tsFormatter(tsMean)
        T(2)

        o = df[observable][i]
        T(3)

        timeseries.loc[sym, tsMean] = o
        T(4)

    from pprint import pprint
    print "times needed (total = %.1f seconds) for each command:" % sum(t.values())
    pprint (t)

    return timeseries

具有(不重要，不慢)

def tsFormatter(ts):
    "as human readable string, only up to whole seconds"
    return time.strftime("%Y-%m-%d %H:%M:%S", time.gmtime(ts))

.

-> 待优化的代码位于for循环中.

(T和t只是计时的辅助函数&dict.)

(T, and t are just helper function & dict, for the timing.)

我已经为每一步计时了.绝大多数时间:

I have timed every step. The vast majority of time:

len(df.index)= 47160
times needed (total = 20.2 seconds) for each command:
{0: 1.102,
 1: 0.741,
 2: 0.243,
 3: 0.792,
 4: 17.371}

在最后一步中花费了

timeseries.loc[sym, tsMean] = o

我已经下载并安装了 pypy -但是可惜的是，它还不支持熊猫.

I have already downloaded and install pypy - but sadly, that doesn't support pandas yet.

有什么想法可以加快填充2D数组的速度吗?

Any ideas how to speed up populating a 2D array?

谢谢！

对不起，没有提到-时间序列"也是一个数据框:

Sorry, hadn't mentioned - 'timeseries' is a dataframe too:

timeseries = pd.DataFrame({"name": titles}, index=index)

推荐答案

更新:从Pandas 0.20.1开始

UPDATE: starting from Pandas 0.20.1 the .ix indexer is deprecated, in favor of the more strict .iloc and .loc indexers.

================================================ =====================

=====================================================================

@jezrael提供了一个有趣的比较，我决定使用更多的索引方法并针对10M行DF(实际上大小在这种情况下无关紧要)重复进行此操作:

@jezrael has provided an interesting comparison and i decided to repeat it using more indexing methods and against 10M rows DF (actually the size doesn't matter in this particular case):

设置:

In [15]: df = pd.DataFrame(np.random.rand(10**7, 5), columns=list('abcde'))

In [16]: df.info()
<class 'pandas.core.frame.DataFrame'>
RangeIndex: 10000000 entries, 0 to 9999999
Data columns (total 5 columns):
a    float64
b    float64
c    float64
d    float64
e    float64
dtypes: float64(5)
memory usage: 381.5 MB

In [17]: df.shape
Out[17]: (10000000, 5)

时间:

In [37]: %timeit df.loc[random.randint(0, 10**7), 'b']
1000 loops, best of 3: 502 µs per loop

In [38]: %timeit df.iloc[random.randint(0, 10**7), 1]
1000 loops, best of 3: 394 µs per loop

In [39]: %timeit df.at[random.randint(0, 10**7), 'b']
10000 loops, best of 3: 66.8 µs per loop

In [41]: %timeit df.iat[random.randint(0, 10**7), 1]
10000 loops, best of 3: 32.9 µs per loop

In [42]: %timeit df.ix[random.randint(0, 10**7), 'b']
10000 loops, best of 3: 64.8 µs per loop

In [43]: %timeit df.ix[random.randint(0, 10**7), 1]
1000 loops, best of 3: 503 µs per loop

结果显示为条形图:

将数据命名为DF:

In [88]: r
Out[88]:
       method  timing
0         loc   502.0
1        iloc   394.0
2          at    66.8
3         iat    32.9
4    ix_label    64.8
5  ix_integer   503.0

In [89]: r.to_dict()
Out[89]:
{'method': {0: 'loc',
  1: 'iloc',
  2: 'at',
  3: 'iat',
  4: 'ix_label',
  5: 'ix_integer'},
 'timing': {0: 502.0,
  1: 394.0,
  2: 66.799999999999997,
  3: 32.899999999999999,
  4: 64.799999999999997,
  5: 503.0}}

绘图

ax = sns.barplot(data=r, x='method', y='timing')
ax.tick_params(labelsize=16)
[ax.annotate(str(round(p.get_height(),2)), (p.get_x() + 0.2, p.get_height() + 5)) for p in ax.patches]
ax.set_xlabel('indexing method', size=20)
ax.set_ylabel('timing (microseconds)', size=20)

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