.. _io:
.. currentmodule:: pandas
.. ipython:: python
:suppress:
import os
import csv
from StringIO import StringIO
import numpy as np
np.random.seed(123456)
randn = np.random.randn
np.set_printoptions(precision=4, suppress=True)
import matplotlib.pyplot as plt
plt.close('all')
from pandas import *
import pandas.util.testing as tm
clipdf = DataFrame({'A':[1,2,3],'B':[4,5,6],'C':['p','q','r']},
index=['x','y','z'])
*******************************
IO Tools (Text, CSV, HDF5, ...)
*******************************
Clipboard
---------
.. _io.clipboard:
A handy way to grab data is to use the ``read_clipboard`` method, which takes
the contents of the clipboard buffer and passes them to the ``read_table``
method described in the next section. For instance, you can copy the following
text to the clipboard (CTRL-C on many operating systems):
.. code-block:: python
A B C
x 1 4 p
y 2 5 q
z 3 6 r
And then import the data directly to a DataFrame by calling:
.. code-block:: python
clipdf = read_clipboard(sep='\s*')
.. ipython:: python
clipdf
.. _io.read_csv_table:
CSV & Text files
----------------
The two workhorse functions for reading text files (a.k.a. flat files) are
:func:`~pandas.io.parsers.read_csv` and :func:`~pandas.io.parsers.read_table`.
They both use the same parsing code to intelligently convert tabular
data into a DataFrame object. They can take a number of arguments:
- ``filepath_or_buffer``: Either a string path to a file, or any object with a
``read`` method (such as an open file or ``StringIO``).
- ``sep`` or ``delimiter``: A delimiter / separator to split fields
on. `read_csv` is capable of inferring the delimiter automatically in some
cases by "sniffing." The separator may be specified as a regular
expression; for instance you may use '\s*' to indicate arbitrary
whitespace.
- ``dialect``: string or :class:`python:csv.Dialect` instance to expose more ways to specify
the file format
- ``header``: row number to use as the column names, and the start of the data.
Defaults to 0 (first row); specify None if there is no header row.
- ``skiprows``: A collection of numbers for rows in the file to skip. Can
also be an integer to skip the first ``n`` rows
- ``index_col``: column number, column name, or list of column numbers/names,
to use as the ``index`` (row labels) of the resulting DataFrame. By default,
it will number the rows without using any column, unless there is one more
data column than there are headers, in which case the first column is taken
as the index.
- ``names``: List of column names to use. If passed, header will be
implicitly set to None.
- ``na_values``: optional list of strings to recognize as NaN (missing
values), either in addition to or in lieu of the default set.
- ``keep_default_na``: whether to include the default set of missing values
in addition to the ones specified in ``na_values``
- ``parse_dates``: if True then index will be parsed as dates
(False by default). You can specify more complicated options to parse
a subset of columns or a combination of columns into a single date column
(list of ints or names, list of lists, or dict)
[1, 2, 3] -> try parsing columns 1, 2, 3 each as a separate date column
[[1, 3]] -> combine columns 1 and 3 and parse as a single date column
{'foo' : [1, 3]} -> parse columns 1, 3 as date and call result 'foo'
- ``keep_date_col``: if True, then date component columns passed into
``parse_dates`` will be retained in the output (False by default).
- ``date_parser``: function to use to parse strings into datetime
objects. If ``parse_dates`` is True, it defaults to the very robust
``dateutil.parser``. Specifying this implicitly sets ``parse_dates`` as True.
You can also use functions from community supported date converters from
date_converters.py
- ``dayfirst``: if True then uses the DD/MM international/European date format
(This is False by default)
- ``thousands``: sepcifies the thousands separator. If not None, then parser
will try to look for it in the output and parse relevant data to integers.
Because it has to essentially scan through the data again, this causes a
significant performance hit so only use if necessary.
- ``comment``: denotes the start of a comment and ignores the rest of the line.
Currently line commenting is not supported.
- ``nrows``: Number of rows to read out of the file. Useful to only read a
small portion of a large file
- ``iterator``: If True, return a ``TextParser`` to enable reading a file
into memory piece by piece
- ``chunksize``: An number of rows to be used to "chunk" a file into
pieces. Will cause an ``TextParser`` object to be returned. More on this
below in the section on :ref:`iterating and chunking <io.chunking>`
- ``skip_footer``: number of lines to skip at bottom of file (default 0)
- ``converters``: a dictionary of functions for converting values in certain
columns, where keys are either integers or column labels
- ``encoding``: a string representing the encoding to use if the contents are
non-ascii
- ``verbose``: show number of NA values inserted in non-numeric columns
- ``squeeze``: if True then output with only one column is turned into Series
.. ipython:: python
:suppress:
f = open('foo.csv','w')
f.write('date,A,B,C\n20090101,a,1,2\n20090102,b,3,4\n20090103,c,4,5')
f.close()
Consider a typical CSV file containing, in this case, some time series data:
.. ipython:: python
print open('foo.csv').read()
The default for `read_csv` is to create a DataFrame with simple numbered rows:
.. ipython:: python
read_csv('foo.csv')
In the case of indexed data, you can pass the column number or column name you
wish to use as the index:
.. ipython:: python
read_csv('foo.csv', index_col=0)
.. ipython:: python
read_csv('foo.csv', index_col='date')
You can also use a list of columns to create a hierarchical index:
.. ipython:: python
read_csv('foo.csv', index_col=[0, 'A'])
.. _io.dialect:
The ``dialect`` keyword gives greater flexibility in specifying the file format.
By default it uses the Excel dialect but you can specify either the dialect name
or a :class:`python:csv.Dialect` instance.
.. ipython:: python
:suppress:
data = ('label1,label2,label3\n'
'index1,"a,c,e\n'
'index2,b,d,f')
Suppose you had data with unenclosed quotes:
.. ipython:: python
print data
By default, ``read_csv`` uses the Excel dialect and treats the double quote as
the quote character, which causes it to fail when it finds a newline before it
finds the closing double quote.
We can get around this using ``dialect``
.. ipython:: python
dia = csv.excel()
dia.quoting = csv.QUOTE_NONE
read_csv(StringIO(data), dialect=dia)
The parsers make every attempt to "do the right thing" and not be very
fragile. Type inference is a pretty big deal. So if a column can be coerced to
integer dtype without altering the contents, it will do so. Any non-numeric
columns will come through as object dtype as with the rest of pandas objects.
.. _io.parse_dates:
Specifying Date Columns
~~~~~~~~~~~~~~~~~~~~~~~
To better facilitate working with datetime data, :func:`~pandas.io.parsers.read_csv` and :func:`~pandas.io.parsers.read_table`
uses the keyword arguments ``parse_dates`` and ``date_parser`` to allow users
to specify a variety of columns and date/time formats to turn the input text
data into ``datetime`` objects.
The simplest case is to just pass in ``parse_dates=True``:
.. ipython:: python
# Use a column as an index, and parse it as dates.
df = read_csv('foo.csv', index_col=0, parse_dates=True)
df
# These are python datetime objects
df.index
.. ipython:: python
:suppress:
os.remove('foo.csv')
It is often the case that we may want to store date and time data separately,
or store various date fields separately. the ``parse_dates`` keyword can be
used to specify a combination of columns to parse the dates and/or times from.
You can specify a list of column lists to ``parse_dates``, the resulting date
columns will be prepended to the output (so as to not affect the existing column
order) and the new column names will be the concatenation of the component
column names:
.. ipython:: python
:suppress:
data = ("KORD,19990127, 19:00:00, 18:56:00, 0.8100\n"
"KORD,19990127, 20:00:00, 19:56:00, 0.0100\n"
"KORD,19990127, 21:00:00, 20:56:00, -0.5900\n"
"KORD,19990127, 21:00:00, 21:18:00, -0.9900\n"
"KORD,19990127, 22:00:00, 21:56:00, -0.5900\n"
"KORD,19990127, 23:00:00, 22:56:00, -0.5900")
with open('tmp.csv', 'w') as fh:
fh.write(data)
.. ipython:: python
print open('tmp.csv').read()
df = read_csv('tmp.csv', header=None, parse_dates=[[1, 2], [1, 3]])
df
By default the parser removes the component date columns, but you can choose
to retain them via the ``keep_date_col`` keyword:
.. ipython:: python
df = read_csv('tmp.csv', header=None, parse_dates=[[1, 2], [1, 3]],
keep_date_col=True)
df
Note that if you wish to combine multiple columns into a single date column, a
nested list must be used. In other words, ``parse_dates=[1, 2]`` indicates that
the second and third columns should each be parsed as separate date columns
while ``parse_dates=[[1, 2]]`` means the two columns should be parsed into a
single column.
You can also use a dict to specify custom name columns:
.. ipython:: python
date_spec = {'nominal': [1, 2], 'actual': [1, 3]}
df = read_csv('tmp.csv', header=None, parse_dates=date_spec)
df
It is important to remember that if multiple text columns are to be parsed into
a single date column, then a new column is prepended to the data. The `index_col`
specification is based off of this new set of columns rather than the original
data columns:
.. ipython:: python
date_spec = {'nominal': [1, 2], 'actual': [1, 3]}
df = read_csv('tmp.csv', header=None, parse_dates=date_spec,
index_col=0) #index is the nominal column
df
**Note**: When passing a dict as the `parse_dates` argument, the order of
the columns prepended is not guaranteed, because `dict` objects do not impose
an ordering on their keys. On Python 2.7+ you may use `collections.OrderedDict`
instead of a regular `dict` if this matters to you. Because of this, when using a
dict for 'parse_dates' in conjunction with the `index_col` argument, it's best to
specify `index_col` as a column label rather then as an index on the resulting frame.
Date Parsing Functions
~~~~~~~~~~~~~~~~~~~~~~
Finally, the parser allows you can specify a custom ``date_parser`` function to
take full advantage of the flexiblity of the date parsing API:
.. ipython:: python
import pandas.io.date_converters as conv
df = read_csv('tmp.csv', header=None, parse_dates=date_spec,
date_parser=conv.parse_date_time)
df
You can explore the date parsing functionality in ``date_converters.py`` and
add your own. We would love to turn this module into a community supported set
of date/time parsers. To get you started, ``date_converters.py`` contains
functions to parse dual date and time columns, year/month/day columns,
and year/month/day/hour/minute/second columns. It also contains a
``generic_parser`` function so you can curry it with a function that deals with
a single date rather than the entire array.
.. ipython:: python
:suppress:
os.remove('tmp.csv')
.. _io.dayfirst:
International Date Formats
~~~~~~~~~~~~~~~~~~~~~~~~~~
While US date formats tend to be MM/DD/YYYY, many international formats use
DD/MM/YYYY instead. For convenience, a ``dayfirst`` keyword is provided:
.. ipython:: python
:suppress:
data = "date,value,cat\n1/6/2000,5,a\n2/6/2000,10,b\n3/6/2000,15,c"
with open('tmp.csv', 'w') as fh:
fh.write(data)
.. ipython:: python
print open('tmp.csv').read()
read_csv('tmp.csv', parse_dates=[0])
read_csv('tmp.csv', dayfirst=True, parse_dates=[0])
.. _io.thousands:
Thousand Separators
~~~~~~~~~~~~~~~~~~~
For large integers that have been written with a thousands separator, you can
set the ``thousands`` keyword to ``True`` so that integers will be parsed
correctly:
.. ipython:: python
:suppress:
data = ("ID|level|category\n"
"Patient1|123,000|x\n"
"Patient2|23,000|y\n"
"Patient3|1,234,018|z")
with open('tmp.csv', 'w') as fh:
fh.write(data)
By default, integers with a thousands separator will be parsed as strings
.. ipython:: python
print open('tmp.csv').read()
df = read_csv('tmp.csv', sep='|')
df
df.level.dtype
The ``thousands`` keyword allows integers to be parsed correctly
.. ipython:: python
print open('tmp.csv').read()
df = read_csv('tmp.csv', sep='|', thousands=',')
df
df.level.dtype
.. ipython:: python
:suppress:
os.remove('tmp.csv')
.. _io.comments:
Comments
~~~~~~~~
Sometimes comments or meta data may be included in a file:
.. ipython:: python
:suppress:
data = ("ID,level,category\n"
"Patient1,123000,x # really unpleasant\n"
"Patient2,23000,y # wouldn't take his medicine\n"
"Patient3,1234018,z # awesome")
with open('tmp.csv', 'w') as fh:
fh.write(data)
.. ipython:: python
print open('tmp.csv').read()
By default, the parse includes the comments in the output:
.. ipython:: python
df = read_csv('tmp.csv')
df
We can suppress the comments using the ``comment`` keyword:
.. ipython:: python
df = read_csv('tmp.csv', comment='#')
df
.. ipython:: python
:suppress:
os.remove('tmp.csv')
Returning Series
~~~~~~~~~~~~~~~~
Using the ``squeeze`` keyword, the parser will return output with a single column
as a ``Series``:
.. ipython:: python
:suppress:
data = ("level\n"
"Patient1,123000\n"
"Patient2,23000\n"
"Patient3,1234018")
with open('tmp.csv', 'w') as fh:
fh.write(data)
.. ipython:: python
print open('tmp.csv').read()
output = read_csv('tmp.csv', squeeze=True)
output
type(output)
.. ipython:: python
:suppress:
os.remove('tmp.csv')
.. _io.fwf:
Files with Fixed Width Columns
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
While `read_csv` reads delimited data, the :func:`~pandas.io.parsers.read_fwf`
function works with data files that have known and fixed column widths.
The function parameters to `read_fwf` are largely the same as `read_csv` with
two extra parameters:
- ``colspecs``: a list of pairs (tuples), giving the extents of the
fixed-width fields of each line as half-open intervals [from, to[
- ``widths``: a list of field widths, which can be used instead of
``colspecs`` if the intervals are contiguous
.. ipython:: python
:suppress:
f = open('bar.csv', 'w')
data1 = ("id8141 360.242940 149.910199 11950.7\n"
"id1594 444.953632 166.985655 11788.4\n"
"id1849 364.136849 183.628767 11806.2\n"
"id1230 413.836124 184.375703 11916.8\n"
"id1948 502.953953 173.237159 12468.3")
f.write(data1)
f.close()
Consider a typical fixed-width data file:
.. ipython:: python
print open('bar.csv').read()
In order to parse this file into a DataFrame, we simply need to supply the
column specifications to the `read_fwf` function along with the file name:
.. ipython:: python
#Column specifications are a list of half-intervals
colspecs = [(0, 6), (8, 20), (21, 33), (34, 43)]
df = read_fwf('bar.csv', colspecs=colspecs, header=None, index_col=0)
df
Note how the parser automatically picks column names X.<column number> when
``header=None`` argument is specified. Alternatively, you can supply just the
column widths for contiguous columns:
.. ipython:: python
#Widths are a list of integers
widths = [6, 14, 13, 10]
df = read_fwf('bar.csv', widths=widths, header=None)
df
The parser will take care of extra white spaces around the columns
so it's ok to have extra separation between the columns in the file.
.. ipython:: python
:suppress:
os.remove('bar.csv')
Files with an "implicit" index column
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. ipython:: python
:suppress:
f = open('foo.csv', 'w')
f.write('A,B,C\n20090101,a,1,2\n20090102,b,3,4\n20090103,c,4,5')
f.close()
Consider a file with one less entry in the header than the number of data
column:
.. ipython:: python
print open('foo.csv').read()
In this special case, ``read_csv`` assumes that the first column is to be used
as the index of the DataFrame:
.. ipython:: python
read_csv('foo.csv')
Note that the dates weren't automatically parsed. In that case you would need
to do as before:
.. ipython:: python
df = read_csv('foo.csv', parse_dates=True)
df.index
.. ipython:: python
:suppress:
os.remove('foo.csv')
Reading DataFrame objects with ``MultiIndex``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. _io.csv_multiindex:
Suppose you have data indexed by two columns:
.. ipython:: python
print open('data/mindex_ex.csv').read()
The ``index_col`` argument to ``read_csv`` and ``read_table`` can take a list of
column numbers to turn multiple columns into a ``MultiIndex``:
.. ipython:: python
df = read_csv("data/mindex_ex.csv", index_col=[0,1])
df
df.ix[1978]
.. _io.sniff:
Automatically "sniffing" the delimiter
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``read_csv`` is capable of inferring delimited (not necessarily
comma-separated) files. YMMV, as pandas uses the :class:`python:csv.Sniffer`
class of the csv module.
.. ipython:: python
:suppress:
df = DataFrame(np.random.randn(10, 4))
df.to_csv('tmp.sv', sep='|')
df.to_csv('tmp2.sv', sep=':')
.. ipython:: python
print open('tmp2.sv').read()
read_csv('tmp2.sv')
.. _io.chunking:
Iterating through files chunk by chunk
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Suppose you wish to iterate through a (potentially very large) file lazily
rather than reading the entire file into memory, such as the following:
.. ipython:: python
print open('tmp.sv').read()
table = read_table('tmp.sv', sep='|')
table
By specifiying a ``chunksize`` to ``read_csv`` or ``read_table``, the return
value will be an iterable object of type ``TextParser``:
.. ipython:: python
reader = read_table('tmp.sv', sep='|', chunksize=4)
reader
for chunk in reader:
print chunk
Specifying ``iterator=True`` will also return the ``TextParser`` object:
.. ipython:: python
reader = read_table('tmp.sv', sep='|', iterator=True)
reader.get_chunk(5)
.. ipython:: python
:suppress:
os.remove('tmp.sv')
os.remove('tmp2.sv')
Writing to CSV format
~~~~~~~~~~~~~~~~~~~~~
.. _io.store_in_csv:
The Series and DataFrame objects have an instance method ``to_csv`` which
allows storing the contents of the object as a comma-separated-values file. The
function takes a number of arguments. Only the first is required.
- ``path``: A string path to the file to write
``nanRep``: A string representation of a missing value (default '')
- ``cols``: Columns to write (default None)
- ``header``: Whether to write out the column names (default True)
- ``index``: whether to write row (index) names (default True)
- ``index_label``: Column label(s) for index column(s) if desired. If None
(default), and `header` and `index` are True, then the index names are
used. (A sequence should be given if the DataFrame uses MultiIndex).
- ``mode`` : Python write mode, default 'w'
- ``sep`` : Field delimiter for the output file (default ",")
- ``encoding``: a string representing the encoding to use if the contents are
non-ascii, for python versions prior to 3
Writing a formatted string
~~~~~~~~~~~~~~~~~~~~~~~~~~
.. _io.formatting:
The DataFrame object has an instance method ``to_string`` which allows control
over the string representation of the object. All arguments are optional:
- ``buf`` default None, for example a StringIO object
- ``columns`` default None, which columns to write
- ``col_space`` default None, number of spaces to write between columns
- ``na_rep`` default ``NaN``, representation of NA value
- ``formatters`` default None, a dictionary (by column) of functions each of
which takes a single argument and returns a formatted string
- ``float_format`` default None, a function which takes a single (float)
argument and returns a formatted string; to be applied to floats in the
DataFrame.
- ``sparsify`` default True, set to False for a DataFrame with a hierarchical
index to print every multiindex key at each row.
- ``index_names`` default True, will print the names of the indices
- ``index`` default True, will print the index (ie, row labels)
- ``header`` default True, will print the column labels
- ``justify`` default ``left``, will print column headers left- or
right-justified
The Series object also has a ``to_string`` method, but with only the ``buf``,
``na_rep``, ``float_format`` arguments. There is also a ``length`` argument
which, if set to ``True``, will additionally output the length of the Series.
Writing to HTML format
~~~~~~~~~~~~~~~~~~~~~~
.. _io.html:
DataFrame object has an instance method ``to_html`` which renders the contents
of the DataFrame as an html table. The function arguments are as in the method
``to_string`` described above.
Excel files
----------------
The ``ExcelFile`` class can read an Excel 2003 file using the ``xlrd`` Python
module and use the same parsing code as the above to convert tabular data into
a DataFrame. To use it, create the ``ExcelFile`` object:
.. code-block:: python
xls = ExcelFile('path_to_file.xls')
Then use the ``parse`` instance method with a sheetname, then use the same
additional arguments as the parsers above:
.. code-block:: python
xls.parse('Sheet1', index_col=None, na_values=['NA'])
To read sheets from an Excel 2007 file, you can pass a filename with a ``.xlsx``
extension, in which case the ``openpyxl`` module will be used to read the file.
It is often the case that users will insert columns to do temporary computations
in Excel and you may not want to read in those columns. `ExcelFile.parse` takes
a `parse_cols` keyword to allow you to specify a subset of columns to parse.
If `parse_cols` is an integer, then it is assumed to indicate the last column
to be parsed.
.. code-block:: python
xls.parse('Sheet1', parse_cols=2, index_col=None, na_values=['NA'])
If `parse_cols` is a list of integers, then it is assumed to be the file column
indices to be parsed.
.. code-block:: python
xls.parse('Sheet1', parse_cols=[0, 2, 3], index_col=None, na_values=['NA'])
To write a DataFrame object to a sheet of an Excel file, you can use the
``to_excel`` instance method. The arguments are largely the same as ``to_csv``
described above, the first argument being the name of the excel file, and the
optional second argument the name of the sheet to which the DataFrame should be
written. For example:
.. code-block:: python
df.to_excel('path_to_file.xlsx', sheet_name='sheet1')
Files with a ``.xls`` extension will be written using ``xlwt`` and those with
a ``.xlsx`` extension will be written using ``openpyxl``.
The Panel class also has a ``to_excel`` instance method,
which writes each DataFrame in the Panel to a separate sheet.
In order to write separate DataFrames to separate sheets in a single Excel file,
one can use the ExcelWriter class, as in the following example:
.. code-block:: python
writer = ExcelWriter('path_to_file.xlsx')
df1.to_excel(writer, sheet_name='sheet1')
df2.to_excel(writer, sheet_name='sheet2')
writer.save()
HDF5 (PyTables)
---------------
``HDFStore`` is a dict-like object which reads and writes pandas to the high
performance HDF5 format using the excellent `PyTables
<http://www.pytables.org/>`__ library.
.. ipython:: python
:suppress:
:okexcept:
os.remove('store.h5')
.. ipython:: python
store = HDFStore('store.h5')
print store
Objects can be written to the file just like adding key-value pairs to a dict:
.. ipython:: python
index = date_range('1/1/2000', periods=8)
s = Series(randn(5), index=['a', 'b', 'c', 'd', 'e'])
df = DataFrame(randn(8, 3), index=index,
columns=['A', 'B', 'C'])
wp = Panel(randn(2, 5, 4), items=['Item1', 'Item2'],
major_axis=date_range('1/1/2000', periods=5),
minor_axis=['A', 'B', 'C', 'D'])
store['s'] = s
store['df'] = df
store['wp'] = wp
store
In a current or later Python session, you can retrieve stored objects:
.. ipython:: python
store['df']
.. ipython:: python
:suppress:
store.close()
import os
os.remove('store.h5')
.. Storing in Table format
.. ~~~~~~~~~~~~~~~~~~~~~~~
.. Querying objects stored in Table format
.. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~