CODEWITHSUNDEEP
pythonpython-3.xpandas
tinproject
tinproject

Reputation: 1014

Create a pandas DataFrame from generator?

I've create a tuple generator that extract information from a file filtering only the records of interest and converting it to a tuple that generator returns. Using python 3.3/ pandas 0.12

I've try to create a DataFrame from:

import pandas as pd
df = pd.DataFrame.from_records(tuple_generator, columns = tuple_fields_name_list)

but throws an error:

... 
C:\Anaconda\envs\py33\lib\site-packages\pandas\core\frame.py in from_records(cls, data, index, exclude, columns, coerce_float, nrows)
   1046                 values.append(row)
   1047                 i += 1
-> 1048                 if i >= nrows:
   1049                     break
   1050 

TypeError: unorderable types: int() >= NoneType()

I managed it to work consuming the generator in a list, but uses twice memory:

df = pd.DataFrame.from_records(list(tuple_generator), columns = tuple_fields_name_list)

The files I want to load are big, and memory consumption matters. The last try my computer spends two hours trying to increment virtual memory :(

The question: Anyone knows a method to create a DataFrame from a record generator directly, without previously convert it to a list?

Note: I'm using python 3.3 and pandas 0.12 with Anaconda on Windows.

Update:

It's not problem of reading the file, my tuple generator do it well, it scan a text compressed file of intermixed records line by line and convert only the wanted data to the correct types, then it yields fields in a generator of tuples form. Some numbers, it scans 2111412 records on a 130MB gzip file, about 6.5GB uncompressed, in about a minute and with little memory used.

Pandas 0.12 does not allow generators, dev version allows it but put all the generator in a list and then convert to a frame. It's not efficient but it's something that have to deal internally pandas. Meanwhile I've must think about buy some more memory.

Upvotes: 46

Views: 75439

Answers (5)

C8H10N4O2
C8H10N4O2

Reputation: 19005

You certainly can construct a pandas.DataFrame() from a generator of tuples, as of version 0.19 (and probably earlier). Don't use .from_records(); just use the constructor, for example:

import pandas as pd
someGenerator = ( (x, chr(x)) for x in range(48,127) )
someDf = pd.DataFrame(someGenerator)

Produces:

type(someDf) #pandas.core.frame.DataFrame

someDf.dtypes
#0     int64
#1    object
#dtype: object

someDf.tail(10)
#      0  1
#69  117  u
#70  118  v
#71  119  w
#72  120  x
#73  121  y
#74  122  z
#75  123  {
#76  124  |
#77  125  }
#78  126  ~

Upvotes: 32

Natalia Sashnikova
Natalia Sashnikova

Reputation: 31

If generator is just like a list of DataFrames, you need just to create a new DataFrame concatenating elements of the list:

result = pd.concat(list)

Recently I've faced the same problem.

Upvotes: 3

Guilherme Freitas
Guilherme Freitas

Reputation: 361

You can also use something like (Python tested in 2.7.5)

from itertools import izip

def dataframe_from_row_iterator(row_iterator, colnames):
    col_iterator = izip(*row_iterator)
    return pd.DataFrame({cn: cv for (cn, cv) in izip(colnames, col_iterator)})

You can also adapt this to append rows to a DataFrame.

-- Edit, Dec 4th: s/row/rows in last line

Upvotes: 2

Jeff
Jeff

Reputation: 129018

To get it to be memory efficient, read in chunks. Something like this, using Viktor's Reader class from above.

df = pd.concat(list(pd.read_csv(Reader(gen()),chunksize=10000)),axis=1)

Upvotes: 7

Viktor Kerkez
Viktor Kerkez

Reputation: 46616

You cannot create a DataFrame from a generator with the 0.12 version of pandas. You can either update yourself to the development version (get it from the github and compile it - which is a little bit painful on windows but I would prefer this option).

Or you can, since you said you are filtering the lines, first filter them, write them to a file and then load them using read_csv or something else...

If you want to get super complicated you can create a file like object that will return the lines:

def gen():
    lines = [
        'col1,col2\n',
        'foo,bar\n',
        'foo,baz\n',
        'bar,baz\n'
    ]
    for line in lines:
        yield line

class Reader(object):
    def __init__(self, g):
        self.g = g
    def read(self, n=0):
        try:
            return next(self.g)
        except StopIteration:
            return ''

And then use the read_csv:

>>> pd.read_csv(Reader(gen()))
  col1 col2
0  foo  bar
1  foo  baz
2  bar  baz

Upvotes: 20

Related Questions