我试图读取一个大的csv文件(aprox。6 GB)在熊猫和我得到一个内存错误:

MemoryError                               Traceback (most recent call last)
<ipython-input-58-67a72687871b> in <module>()
----> 1 data=pd.read_csv('aphro.csv',sep=';')

...

MemoryError: 

有什么帮助吗?


当前回答

在使用chunksize选项之前,如果你想确定你想要在@unutbu提到的分块for循环中写入的进程函数,你可以简单地使用nrows选项。

small_df = pd.read_csv(filename, nrows=100)

一旦确定流程块准备好了,就可以将其放入整个数据帧的分块for循环中。

其他回答

除了上面的答案,对于那些想要处理CSV然后导出到CSV、parquet或SQL的人来说,d6tstack是另一个不错的选择。您可以加载多个文件,它处理数据模式更改(添加/删除列)。核心支持已经被剔除。

def apply(dfg):
    # do stuff
    return dfg

c = d6tstack.combine_csv.CombinerCSV([bigfile.csv], apply_after_read=apply, sep=',', chunksize=1e6)

# or
c = d6tstack.combine_csv.CombinerCSV(glob.glob('*.csv'), apply_after_read=apply, chunksize=1e6)

# output to various formats, automatically chunked to reduce memory consumption
c.to_csv_combine(filename='out.csv')
c.to_parquet_combine(filename='out.pq')
c.to_psql_combine('postgresql+psycopg2://usr:pwd@localhost/db', 'tablename') # fast for postgres
c.to_mysql_combine('mysql+mysqlconnector://usr:pwd@localhost/db', 'tablename') # fast for mysql
c.to_sql_combine('postgresql+psycopg2://usr:pwd@localhost/db', 'tablename') # slow but flexible

如果您使用pandas将大文件读入块,然后逐行yield,这是我所做的

import pandas as pd

def chunck_generator(filename, header=False,chunk_size = 10 ** 5):
   for chunk in pd.read_csv(filename,delimiter=',', iterator=True, chunksize=chunk_size, parse_dates=[1] ): 
        yield (chunk)

def _generator( filename, header=False,chunk_size = 10 ** 5):
    chunk = chunck_generator(filename, header=False,chunk_size = 10 ** 5)
    for row in chunk:
        yield row

if __name__ == "__main__":
filename = r'file.csv'
        generator = generator(filename=filename)
        while True:
           print(next(generator))

分块不应该总是解决这个问题的第一步。

Is the file large due to repeated non-numeric data or unwanted columns? If so, you can sometimes see massive memory savings by reading in columns as categories and selecting required columns via pd.read_csv usecols parameter. Does your workflow require slicing, manipulating, exporting? If so, you can use dask.dataframe to slice, perform your calculations and export iteratively. Chunking is performed silently by dask, which also supports a subset of pandas API. If all else fails, read line by line via chunks. Chunk via pandas or via csv library as a last resort.

解决方案1:

使用大数据的熊猫

解决方案2:

TextFileReader = pd.read_csv(path, chunksize=1000)  # the number of rows per chunk

dfList = []
for df in TextFileReader:
    dfList.append(df)

df = pd.concat(dfList,sort=False)

如果有人还在寻找这样的东西,我发现这个名为modin的新库可以提供帮助。它使用分布式计算来帮助读取。这里有一篇不错的文章将其功能与熊猫进行了比较。它本质上使用与熊猫相同的功能。

import modin.pandas as pd
pd.read_csv(CSV_FILE_NAME)