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

下面是一个例子:

chunkTemp = []
queryTemp = []
query = pd.DataFrame()

for chunk in pd.read_csv(file, header=0, chunksize=<your_chunksize>, iterator=True, low_memory=False):

    #REPLACING BLANK SPACES AT COLUMNS' NAMES FOR SQL OPTIMIZATION
    chunk = chunk.rename(columns = {c: c.replace(' ', '') for c in chunk.columns})

    #YOU CAN EITHER: 
    #1)BUFFER THE CHUNKS IN ORDER TO LOAD YOUR WHOLE DATASET 
    chunkTemp.append(chunk)

    #2)DO YOUR PROCESSING OVER A CHUNK AND STORE THE RESULT OF IT
    query = chunk[chunk[<column_name>].str.startswith(<some_pattern>)]   
    #BUFFERING PROCESSED DATA
    queryTemp.append(query)

#!  NEVER DO pd.concat OR pd.DataFrame() INSIDE A LOOP
print("Database: CONCATENATING CHUNKS INTO A SINGLE DATAFRAME")
chunk = pd.concat(chunkTemp)
print("Database: LOADED")

#CONCATENATING PROCESSED DATA
query = pd.concat(queryTemp)
print(query)

其他回答

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.

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

函数read_csv和read_table几乎是一样的。但在程序中使用read_table函数时,必须分配分隔符“,”。

def get_from_action_data(fname, chunk_size=100000):
    reader = pd.read_csv(fname, header=0, iterator=True)
    chunks = []
    loop = True
    while loop:
        try:
            chunk = reader.get_chunk(chunk_size)[["user_id", "type"]]
            chunks.append(chunk)
        except StopIteration:
            loop = False
            print("Iteration is stopped")

    df_ac = pd.concat(chunks, ignore_index=True)

您可以将数据读入为块,并将每个块保存为pickle。

import pandas as pd 
import pickle

in_path = "" #Path where the large file is
out_path = "" #Path to save the pickle files to
chunk_size = 400000 #size of chunks relies on your available memory
separator = "~"

reader = pd.read_csv(in_path,sep=separator,chunksize=chunk_size, 
                    low_memory=False)    


for i, chunk in enumerate(reader):
    out_file = out_path + "/data_{}.pkl".format(i+1)
    with open(out_file, "wb") as f:
        pickle.dump(chunk,f,pickle.HIGHEST_PROTOCOL)

在下一步中,读入pickle并将每个pickle附加到所需的数据框架中。

import glob
pickle_path = "" #Same Path as out_path i.e. where the pickle files are

data_p_files=[]
for name in glob.glob(pickle_path + "/data_*.pkl"):
   data_p_files.append(name)


df = pd.DataFrame([])
for i in range(len(data_p_files)):
    df = df.append(pd.read_pickle(data_p_files[i]),ignore_index=True)

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))