IO tools (text, CSV, HDF5, …)#
The pandas I/O API is a set of top level reader
functions accessed like
pandas.read_csv()
that generally return a pandas object. The corresponding
writer
functions are object methods that are accessed like
DataFrame.to_csv()
. Below is a table containing available readers
and
writers
.
Format Type |
Data Description |
Reader |
Writer |
---|---|---|---|
text |
|||
text |
Fixed-Width Text File |
NA |
|
text |
|||
text |
|||
text |
NA |
||
text |
|||
text |
Local clipboard |
||
binary |
|||
binary |
NA |
||
binary |
|||
binary |
|||
binary |
|||
binary |
|||
binary |
|||
binary |
NA |
||
binary |
NA |
||
binary |
|||
SQL |
Here is an informal performance comparison for some of these IO methods.
Note
For examples that use the StringIO
class, make sure you import it
with from io import StringIO
for Python 3.
CSV & text files#
The workhorse function for reading text files (a.k.a. flat files) is
read_csv()
. See the cookbook for some advanced strategies.
Parsing options#
read_csv()
accepts the following common arguments:
Basic#
- filepath_or_buffervarious
Either a path to a file (a
str
,pathlib.Path
) URL (including http, ftp, and S3 locations), or any object with aread()
method (such as an open file orStringIO
).- sepstr, defaults to
','
forread_csv()
,\t
forread_table()
Delimiter to use. If sep is
None
, the C engine cannot automatically detect the separator, but the Python parsing engine can, meaning the latter will be used and automatically detect the separator by Python’s builtin sniffer tool,csv.Sniffer
. In addition, separators longer than 1 character and different from'\s+'
will be interpreted as regular expressions and will also force the use of the Python parsing engine. Note that regex delimiters are prone to ignoring quoted data. Regex example:'\\r\\t'
.- delimiterstr, default
None
Alternative argument name for sep.
Column and index locations and names#
- headerint or list of ints, default
'infer'
Row number(s) to use as the column names, and the start of the data. Default behavior is to infer the column names: if no names are passed the behavior is identical to
header=0
and column names are inferred from the first line of the file, if column names are passed explicitly then the behavior is identical toheader=None
. Explicitly passheader=0
to be able to replace existing names.The header can be a list of ints that specify row locations for a MultiIndex on the columns e.g.
[0,1,3]
. Intervening rows that are not specified will be skipped (e.g. 2 in this example is skipped). Note that this parameter ignores commented lines and empty lines ifskip_blank_lines=True
, so header=0 denotes the first line of data rather than the first line of the file.- namesarray-like, default
None
List of column names to use. If file contains no header row, then you should explicitly pass
header=None
. Duplicates in this list are not allowed.- index_colint, str, sequence of int / str, or False, optional, default
None
Column(s) to use as the row labels of the
DataFrame
, either given as string name or column index. If a sequence of int / str is given, a MultiIndex is used.Note
index_col=False
can be used to force pandas to not use the first column as the index, e.g. when you have a malformed file with delimiters at the end of each line.The default value of
None
instructs pandas to guess. If the number of fields in the column header row is equal to the number of fields in the body of the data file, then a default index is used. If it is larger, then the first columns are used as index so that the remaining number of fields in the body are equal to the number of fields in the header.The first row after the header is used to determine the number of columns, which will go into the index. If the subsequent rows contain less columns than the first row, they are filled with
NaN
.This can be avoided through
usecols
. This ensures that the columns are taken as is and the trailing data are ignored.- usecolslist-like or callable, default
None
Return a subset of the columns. If list-like, all elements must either be positional (i.e. integer indices into the document columns) or strings that correspond to column names provided either by the user in
names
or inferred from the document header row(s). Ifnames
are given, the document header row(s) are not taken into account. For example, a valid list-likeusecols
parameter would be[0, 1, 2]
or['foo', 'bar', 'baz']
.Element order is ignored, so
usecols=[0, 1]
is the same as[1, 0]
. To instantiate a DataFrame fromdata
with element order preserved usepd.read_csv(data, usecols=['foo', 'bar'])[['foo', 'bar']]
for columns in['foo', 'bar']
order orpd.read_csv(data, usecols=['foo', 'bar'])[['bar', 'foo']]
for['bar', 'foo']
order.If callable, the callable function will be evaluated against the column names, returning names where the callable function evaluates to True:
In [1]: import pandas as pd In [2]: from io import StringIO In [3]: data = "col1,col2,col3\na,b,1\na,b,2\nc,d,3" In [4]: pd.read_csv(StringIO(data)) Out[4]: col1 col2 col3 0 a b 1 1 a b 2 2 c d 3 In [5]: pd.read_csv(StringIO(data), usecols=lambda x: x.upper() in ["COL1", "COL3"]) Out[5]: col1 col3 0 a 1 1 a 2 2 c 3
Using this parameter results in much faster parsing time and lower memory usage when using the c engine. The Python engine loads the data first before deciding which columns to drop.
General parsing configuration#
- dtypeType name or dict of column -> type, default
None
Data type for data or columns. E.g.
{'a': np.float64, 'b': np.int32, 'c': 'Int64'}
Usestr
orobject
together with suitablena_values
settings to preserve and not interpret dtype. If converters are specified, they will be applied INSTEAD of dtype conversion.Added in version 1.5.0: Support for defaultdict was added. Specify a defaultdict as input where the default determines the dtype of the columns which are not explicitly listed.
- dtype_backend{“numpy_nullable”, “pyarrow”}, defaults to NumPy backed DataFrames
Which dtype_backend to use, e.g. whether a DataFrame should have NumPy arrays, nullable dtypes are used for all dtypes that have a nullable implementation when “numpy_nullable” is set, pyarrow is used for all dtypes if “pyarrow” is set.
The dtype_backends are still experimental.
Added in version 2.0.
- engine{
'c'
,'python'
,'pyarrow'
} Parser engine to use. The C and pyarrow engines are faster, while the python engine is currently more feature-complete. Multithreading is currently only supported by the pyarrow engine.
Added in version 1.4.0: The “pyarrow” engine was added as an experimental engine, and some features are unsupported, or may not work correctly, with this engine.
- convertersdict, default
None
Dict of functions for converting values in certain columns. Keys can either be integers or column labels.
- true_valueslist, default
None
Values to consider as
True
.- false_valueslist, default
None
Values to consider as
False
.- skipinitialspaceboolean, default
False
Skip spaces after delimiter.
- skiprowslist-like or integer, default
None
Line numbers to skip (0-indexed) or number of lines to skip (int) at the start of the file.
If callable, the callable function will be evaluated against the row indices, returning True if the row should be skipped and False otherwise:
In [6]: data = "col1,col2,col3\na,b,1\na,b,2\nc,d,3" In [7]: pd.read_csv(StringIO(data)) Out[7]: col1 col2 col3 0 a b 1 1 a b 2 2 c d 3 In [8]: pd.read_csv(StringIO(data), skiprows=lambda x: x % 2 != 0) Out[8]: col1 col2 col3 0 a b 2
- skipfooterint, default
0
Number of lines at bottom of file to skip (unsupported with engine=’c’).
- nrowsint, default
None
Number of rows of file to read. Useful for reading pieces of large files.
- low_memoryboolean, default
True
Internally process the file in chunks, resulting in lower memory use while parsing, but possibly mixed type inference. To ensure no mixed types either set
False
, or specify the type with thedtype
parameter. Note that the entire file is read into a singleDataFrame
regardless, use thechunksize
oriterator
parameter to return the data in chunks. (Only valid with C parser)- memory_mapboolean, default False
If a filepath is provided for
filepath_or_buffer
, map the file object directly onto memory and access the data directly from there. Using this option can improve performance because there is no longer any I/O overhead.
NA and missing data handling#
- na_valuesscalar, str, list-like, or dict, default
None
Additional strings to recognize as NA/NaN. If dict passed, specific per-column NA values. See na values const below for a list of the values interpreted as NaN by default.
- keep_default_naboolean, default
True
Whether or not to include the default NaN values when parsing the data. Depending on whether
na_values
is passed in, the behavior is as follows:If
keep_default_na
isTrue
, andna_values
are specified,na_values
is appended to the default NaN values used for parsing.If
keep_default_na
isTrue
, andna_values
are not specified, only the default NaN values are used for parsing.If
keep_default_na
isFalse
, andna_values
are specified, only the NaN values specifiedna_values
are used for parsing.If
keep_default_na
isFalse
, andna_values
are not specified, no strings will be parsed as NaN.
Note that if
na_filter
is passed in asFalse
, thekeep_default_na
andna_values
parameters will be ignored.- na_filterboolean, default
True
Detect missing value markers (empty strings and the value of na_values). In data without any NAs, passing
na_filter=False
can improve the performance of reading a large file.- verboseboolean, default
False
Indicate number of NA values placed in non-numeric columns.
- skip_blank_linesboolean, default
True
If
True
, skip over blank lines rather than interpreting as NaN values.
Datetime handling#
- parse_datesboolean or list of ints or names or list of lists or dict, default
False
. If
True
-> try parsing the index.If
[1, 2, 3]
-> try parsing columns 1, 2, 3 each as a separate date column.
Note
A fast-path exists for iso8601-formatted dates.
- date_formatstr or dict of column -> format, default
None
If used in conjunction with
parse_dates
, will parse dates according to this format. For anything more complex, please read in asobject
and then applyto_datetime()
as-needed.Added in version 2.0.0.
- dayfirstboolean, default
False
DD/MM format dates, international and European format.
- cache_datesboolean, default True
If True, use a cache of unique, converted dates to apply the datetime conversion. May produce significant speed-up when parsing duplicate date strings, especially ones with timezone offsets.
Iteration#
- iteratorboolean, default
False
Return
TextFileReader
object for iteration or getting chunks withget_chunk()
.- chunksizeint, default
None
Return
TextFileReader
object for iteration. See iterating and chunking below.
Quoting, compression, and file format#
- compression{
'infer'
,'gzip'
,'bz2'
,'zip'
,'xz'
,'zstd'
,None
,dict
}, default'infer'
For on-the-fly decompression of on-disk data. If ‘infer’, then use gzip, bz2, zip, xz, or zstandard if
filepath_or_buffer
is path-like ending in ‘.gz’, ‘.bz2’, ‘.zip’, ‘.xz’, ‘.zst’, respectively, and no decompression otherwise. If using ‘zip’, the ZIP file must contain only one data file to be read in. Set toNone
for no decompression. Can also be a dict with key'method'
set to one of {'zip'
,'gzip'
,'bz2'
,'zstd'
} and other key-value pairs are forwarded tozipfile.ZipFile
,gzip.GzipFile
,bz2.BZ2File
, orzstandard.ZstdDecompressor
. As an example, the following could be passed for faster compression and to create a reproducible gzip archive:compression={'method': 'gzip', 'compresslevel': 1, 'mtime': 1}
.Changed in version 1.2.0: Previous versions forwarded dict entries for ‘gzip’ to
gzip.open
.- thousandsstr, default
None
Thousands separator.
- decimalstr, default
'.'
Character to recognize as decimal point. E.g. use
','
for European data.- float_precisionstring, default None
Specifies which converter the C engine should use for floating-point values. The options are
None
for the ordinary converter,high
for the high-precision converter, andround_trip
for the round-trip converter.- lineterminatorstr (length 1), default
None
Character to break file into lines. Only valid with C parser.
- quotecharstr (length 1)
The character used to denote the start and end of a quoted item. Quoted items can include the delimiter and it will be ignored.
- quotingint or
csv.QUOTE_*
instance, default0
Control field quoting behavior per
csv.QUOTE_*
constants. Use one ofQUOTE_MINIMAL
(0),QUOTE_ALL
(1),QUOTE_NONNUMERIC
(2) orQUOTE_NONE
(3).- doublequoteboolean, default
True
When
quotechar
is specified andquoting
is notQUOTE_NONE
, indicate whether or not to interpret two consecutivequotechar
elements inside a field as a singlequotechar
element.- escapecharstr (length 1), default
None
One-character string used to escape delimiter when quoting is
QUOTE_NONE
.- commentstr, default
None
Indicates remainder of line should not be parsed. If found at the beginning of a line, the line will be ignored altogether. This parameter must be a single character. Like empty lines (as long as
skip_blank_lines=True
), fully commented lines are ignored by the parameterheader
but not byskiprows
. For example, ifcomment='#'
, parsing ‘#empty\na,b,c\n1,2,3’ withheader=0
will result in ‘a,b,c’ being treated as the header.- encodingstr, default
None
Encoding to use for UTF when reading/writing (e.g.
'utf-8'
). List of Python standard encodings.- dialectstr or
csv.Dialect
instance, defaultNone
If provided, this parameter will override values (default or not) for the following parameters:
delimiter
,doublequote
,escapechar
,skipinitialspace
,quotechar
, andquoting
. If it is necessary to override values, a ParserWarning will be issued. Seecsv.Dialect
documentation for more details.
Error handling#
- on_bad_lines(‘error’, ‘warn’, ‘skip’), default ‘error’
Specifies what to do upon encountering a bad line (a line with too many fields). Allowed values are :
‘error’, raise an ParserError when a bad line is encountered.
‘warn’, print a warning when a bad line is encountered and skip that line.
‘skip’, skip bad lines without raising or warning when they are encountered.
Added in version 1.3.0.
Specifying column data types#
You can indicate the data type for the whole DataFrame
or individual
columns:
In [9]: import numpy as np
In [10]: data = "a,b,c,d\n1,2,3,4\n5,6,7,8\n9,10,11"
In [11]: print(data)
a,b,c,d
1,2,3,4
5,6,7,8
9,10,11
In [12]: df = pd.read_csv(StringIO(data), dtype=object)
In [13]: df
Out[13]:
a b c d
0 1 2 3 4
1 5 6 7 8
2 9 10 11 NaN
In [14]: df["a"][0]
Out[14]: '1'
In [15]: df = pd.read_csv(StringIO(data), dtype={"b": object, "c": np.float64, "d": "Int64"})
In [16]: df.dtypes
Out[16]:
a int64
b object
c float64
d Int64
dtype: object
Fortunately, pandas offers more than one way to ensure that your column(s)
contain only one dtype
. If you’re unfamiliar with these concepts, you can
see here to learn more about dtypes, and
here to learn more about object
conversion in
pandas.
For instance, you can use the converters
argument
of read_csv()
:
In [17]: data = "col_1\n1\n2\n'A'\n4.22"
In [18]: df = pd.read_csv(StringIO(data), converters={"col_1": str})
In [19]: df
Out[19]:
col_1
0 1
1 2
2 'A'
3 4.22
In [20]: df["col_1"].apply(type).value_counts()
Out[20]:
col_1
<class 'str'> 4
Name: count, dtype: int64
Or you can use the to_numeric()
function to coerce the
dtypes after reading in the data,
In [21]: df2 = pd.read_csv(StringIO(data))
In [22]: df2["col_1"] = pd.to_numeric(df2["col_1"], errors="coerce")
In [23]: df2
Out[23]:
col_1
0 1.00
1 2.00
2 NaN
3 4.22
In [24]: df2["col_1"].apply(type).value_counts()
Out[24]:
col_1
<class 'float'> 4
Name: count, dtype: int64
which will convert all valid parsing to floats, leaving the invalid parsing
as NaN
.
Ultimately, how you deal with reading in columns containing mixed dtypes
depends on your specific needs. In the case above, if you wanted to NaN
out
the data anomalies, then to_numeric()
is probably your best option.
However, if you wanted for all the data to be coerced, no matter the type, then
using the converters
argument of read_csv()
would certainly be
worth trying.
Note
In some cases, reading in abnormal data with columns containing mixed dtypes will result in an inconsistent dataset. If you rely on pandas to infer the dtypes of your columns, the parsing engine will go and infer the dtypes for different chunks of the data, rather than the whole dataset at once. Consequently, you can end up with column(s) with mixed dtypes. For example,
In [25]: col_1 = list(range(500000)) + ["a", "b"] + list(range(500000))
In [26]: df = pd.DataFrame({"col_1": col_1})
In [27]: df.to_csv("foo.csv")
In [28]: mixed_df = pd.read_csv("foo.csv")
In [29]: mixed_df["col_1"].apply(type).value_counts()
Out[29]:
col_1
<class 'int'> 737858
<class 'str'> 262144
Name: count, dtype: int64
In [30]: mixed_df["col_1"].dtype
Out[30]: dtype('O')
will result with mixed_df
containing an int
dtype for certain chunks
of the column, and str
for others due to the mixed dtypes from the
data that was read in. It is important to note that the overall column will be
marked with a dtype
of object
, which is used for columns with mixed dtypes.
Setting dtype_backend="numpy_nullable"
will result in nullable dtypes for every column.
In [31]: data = """a,b,c,d,e,f,g,h,i,j
....: 1,2.5,True,a,,,,,12-31-2019,
....: 3,4.5,False,b,6,7.5,True,a,12-31-2019,
....: """
....:
In [32]: df = pd.read_csv(StringIO(data), dtype_backend="numpy_nullable", parse_dates=["i"])
In [33]: df
Out[33]:
a b c d e f g h i j
0 1 2.5 True a <NA> <NA> <NA> <NA> 2019-12-31 <NA>
1 3 4.5 False b 6 7.5 True a 2019-12-31 <NA>
In [34]: df.dtypes
Out[34]:
a Int64
b Float64
c boolean
d string[python]
e Int64
f Float64
g boolean
h string[python]
i datetime64[s]
j Int64
dtype: object
Specifying categorical dtype#
Categorical
columns can be parsed directly by specifying dtype='category'
or
dtype=CategoricalDtype(categories, ordered)
.
In [35]: data = "col1,col2,col3\na,b,1\na,b,2\nc,d,3"
In [36]: pd.read_csv(StringIO(data))
Out[36]:
col1 col2 col3
0 a b 1
1 a b 2
2 c d 3
In [37]: pd.read_csv(StringIO(data)).dtypes
Out[37]:
col1 object
col2 object
col3 int64
dtype: object
In [38]: pd.read_csv(StringIO(data), dtype="category").dtypes
Out[38]:
col1 category
col2 category
col3 category
dtype: object
Individual columns can be parsed as a Categorical
using a dict
specification:
In [39]: pd.read_csv(StringIO(data), dtype={"col1": "category"}).dtypes
Out[39]:
col1 category
col2 object
col3 int64
dtype: object
Specifying dtype='category'
will result in an unordered Categorical
whose categories
are the unique values observed in the data. For more
control on the categories and order, create a
CategoricalDtype
ahead of time, and pass that for
that column’s dtype
.
In [40]: from pandas.api.types import CategoricalDtype
In [41]: dtype = CategoricalDtype(["d", "c", "b", "a"], ordered=True)
In [42]: pd.read_csv(StringIO(data), dtype={"col1": dtype}).dtypes
Out[42]:
col1 category
col2 object
col3 int64
dtype: object
When using dtype=CategoricalDtype
, “unexpected” values outside of
dtype.categories
are treated as missing values.
In [43]: dtype = CategoricalDtype(["a", "b", "d"]) # No 'c'
In [44]: pd.read_csv(StringIO(data), dtype={"col1": dtype}).col1
Out[44]:
0 a
1 a
2 NaN
Name: col1, dtype: category
Categories (3, object): ['a', 'b', 'd']
This matches the behavior of Categorical.set_categories()
.
Note
With dtype='category'
, the resulting categories will always be parsed
as strings (object dtype). If the categories are numeric they can be
converted using the to_numeric()
function, or as appropriate, another
converter such as to_datetime()
.
When dtype
is a CategoricalDtype
with homogeneous categories
(
all numeric, all datetimes, etc.), the conversion is done automatically.
In [45]: df = pd.read_csv(StringIO(data), dtype="category")
In [46]: df.dtypes
Out[46]:
col1 category
col2 category
col3 category
dtype: object
In [47]: df["col3"]
Out[47]:
0 1
1 2
2 3
Name: col3, dtype: category
Categories (3, object): ['1', '2', '3']
In [48]: new_categories = pd.to_numeric(df["col3"].cat.categories)
In [49]: df["col3"] = df["col3"].cat.rename_categories(new_categories)
In [50]: df["col3"]
Out[50]:
0 1
1 2
2 3
Name: col3, dtype: category
Categories (3, int64): [1, 2, 3]
Naming and using columns#
Handling column names#
A file may or may not have a header row. pandas assumes the first row should be used as the column names:
In [51]: data = "a,b,c\n1,2,3\n4,5,6\n7,8,9"
In [52]: print(data)
a,b,c
1,2,3
4,5,6
7,8,9
In [53]: pd.read_csv(StringIO(data))
Out[53]:
a b c
0 1 2 3
1 4 5 6
2 7 8 9
By specifying the names
argument in conjunction with header
you can
indicate other names to use and whether or not to throw away the header row (if
any):
In [54]: print(data)
a,b,c
1,2,3
4,5,6
7,8,9
In [55]: pd.read_csv(StringIO(data), names=["foo", "bar", "baz"], header=0)
Out[55]:
foo bar baz
0 1 2 3
1 4 5 6
2 7 8 9
In [56]: pd.read_csv(StringIO(data), names=["foo", "bar", "baz"], header=None)
Out[56]:
foo bar baz
0 a b c
1 1 2 3
2 4 5 6
3 7 8 9
If the header is in a row other than the first, pass the row number to
header
. This will skip the preceding rows:
In [57]: data = "skip this skip it\na,b,c\n1,2,3\n4,5,6\n7,8,9"
In [58]: pd.read_csv(StringIO(data), header=1)
Out[58]:
a b c
0 1 2 3
1 4 5 6
2 7 8 9
Note
Default behavior is to infer the column names: if no names are
passed the behavior is identical to header=0
and column names
are inferred from the first non-blank line of the file, if column
names are passed explicitly then the behavior is identical to
header=None
.
Duplicate names parsing#
If the file or header contains duplicate names, pandas will by default distinguish between them so as to prevent overwriting data:
In [59]: data = "a,b,a\n0,1,2\n3,4,5"
In [60]: pd.read_csv(StringIO(data))
Out[60]:
a b a.1
0 0 1 2
1 3 4 5
There is no more duplicate data because duplicate columns ‘X’, …, ‘X’ become ‘X’, ‘X.1’, …, ‘X.N’.
Filtering columns (usecols
)#
The usecols
argument allows you to select any subset of the columns in a
file, either using the column names, position numbers or a callable:
In [61]: data = "a,b,c,d\n1,2,3,foo\n4,5,6,bar\n7,8,9,baz"
In [62]: pd.read_csv(StringIO(data))
Out[62]:
a b c d
0 1 2 3 foo
1 4 5 6 bar
2 7 8 9 baz
In [63]: pd.read_csv(StringIO(data), usecols=["b", "d"])
Out[63]:
b d
0 2 foo
1 5 bar
2 8 baz
In [64]: pd.read_csv(StringIO(data), usecols=[0, 2, 3])
Out[64]:
a c d
0 1 3 foo
1 4 6 bar
2 7 9 baz
In [65]: pd.read_csv(StringIO(data), usecols=lambda x: x.upper() in ["A", "C"])
Out[65]:
a c
0 1 3
1 4 6
2 7 9
The usecols
argument can also be used to specify which columns not to
use in the final result:
In [66]: pd.read_csv(StringIO(data), usecols=lambda x: x not in ["a", "c"])
Out[66]:
b d
0 2 foo
1 5 bar
2 8 baz
In this case, the callable is specifying that we exclude the “a” and “c” columns from the output.
Dealing with Unicode data#
The encoding
argument should be used for encoded unicode data, which will
result in byte strings being decoded to unicode in the result:
In [86]: from io import BytesIO
In [87]: data = b"word,length\n" b"Tr\xc3\xa4umen,7\n" b"Gr\xc3\xbc\xc3\x9fe,5"
In [88]: data = data.decode("utf8").encode("latin-1")
In [89]: df = pd.read_csv(BytesIO(data), encoding="latin-1")
In [90]: df
Out[90]:
word length
0 Träumen 7
1 Grüße 5
In [91]: df["word"][1]
Out[91]: 'Grüße'
Some formats which encode all characters as multiple bytes, like UTF-16, won’t parse correctly at all without specifying the encoding. Full list of Python standard encodings.
Index columns and trailing delimiters#
If a file has one more column of data than the number of column names, the
first column will be used as the DataFrame
’s row names:
In [92]: data = "a,b,c\n4,apple,bat,5.7\n8,orange,cow,10"
In [93]: pd.read_csv(StringIO(data))
Out[93]:
a b c
4 apple bat 5.7
8 orange cow 10.0
In [94]: data = "index,a,b,c\n4,apple,bat,5.7\n8,orange,cow,10"
In [95]: pd.read_csv(StringIO(data), index_col=0)
Out[95]:
a b c
index
4 apple bat 5.7
8 orange cow 10.0
Ordinarily, you can achieve this behavior using the index_col
option.
There are some exception cases when a file has been prepared with delimiters at
the end of each data line, confusing the parser. To explicitly disable the
index column inference and discard the last column, pass index_col=False
:
In [96]: data = "a,b,c\n4,apple,bat,\n8,orange,cow,"
In [97]: print(data)
a,b,c
4,apple,bat,
8,orange,cow,
In [98]: pd.read_csv(StringIO(data))
Out[98]:
a b c
4 apple bat NaN
8 orange cow NaN
In [99]: pd.read_csv(StringIO(data), index_col=False)
Out[99]:
a b c
0 4 apple bat
1 8 orange cow
If a subset of data is being parsed using the usecols
option, the
index_col
specification is based on that subset, not the original data.
In [100]: data = "a,b,c\n4,apple,bat,\n8,orange,cow,"
In [101]: print(data)
a,b,c
4,apple,bat,
8,orange,cow,
In [102]: pd.read_csv(StringIO(data), usecols=["b", "c"])
Out[102]:
b c
4 bat NaN
8 cow NaN
In [103]: pd.read_csv(StringIO(data), usecols=["b", "c"], index_col=0)
Out[103]:
b c
4 bat NaN
8 cow NaN
Date Handling#
Specifying date columns#
To better facilitate working with datetime data, read_csv()
uses the keyword arguments parse_dates
and date_format
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
:
In [104]: with open("foo.csv", mode="w") as f:
.....: f.write("date,A,B,C\n20090101,a,1,2\n20090102,b,3,4\n20090103,c,4,5")
.....:
# Use a column as an index, and parse it as dates.
In [105]: df = pd.read_csv("foo.csv", index_col=0, parse_dates=True)
In [106]: df
Out[106]:
A B C
date
2009-01-01 a 1 2
2009-01-02 b 3 4
2009-01-03 c 4 5
# These are Python datetime objects
In [107]: df.index
Out[107]: DatetimeIndex(['2009-01-01', '2009-01-02', '2009-01-03'], dtype='datetime64[s]', name='date', freq=None)
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 columns to parse the dates and/or times.
Note
If a column or index contains an unparsable date, the entire column or
index will be returned unaltered as an object data type. For non-standard
datetime parsing, use to_datetime()
after pd.read_csv
.
Note
read_csv has a fast_path for parsing datetime strings in iso8601 format, e.g “2000-01-01T00:01:02+00:00” and similar variations. If you can arrange for your data to store datetimes in this format, load times will be significantly faster, ~20x has been observed.
Date parsing functions#
Finally, the parser allows you to specify a custom date_format
.
Performance-wise, you should try these methods of parsing dates in order:
If you know the format, use
date_format
, e.g.:date_format="%d/%m/%Y"
ordate_format={column_name: "%d/%m/%Y"}
.If you different formats for different columns, or want to pass any extra options (such as
utc
) toto_datetime
, then you should read in your data asobject
dtype, and then useto_datetime
.
Parsing a CSV with mixed timezones#
pandas cannot natively represent a column or index with mixed timezones. If your CSV
file contains columns with a mixture of timezones, the default result will be
an object-dtype column with strings, even with parse_dates
.
To parse the mixed-timezone values as a datetime column, read in as object
dtype and
then call to_datetime()
with utc=True
.
In [108]: content = """\
.....: a
.....: 2000-01-01T00:00:00+05:00
.....: 2000-01-01T00:00:00+06:00"""
.....:
In [109]: df = pd.read_csv(StringIO(content))
In [110]: df["a"] = pd.to_datetime(df["a"], utc=True)
In [111]: df["a"]
Out[111]:
0 1999-12-31 19:00:00+00:00
1 1999-12-31 18:00:00+00:00
Name: a, dtype: datetime64[s, UTC]
Inferring datetime format#
Here are some examples of datetime strings that can be guessed (all representing December 30th, 2011 at 00:00:00):
“20111230”
“2011/12/30”
“20111230 00:00:00”
“12/30/2011 00:00:00”
“30/Dec/2011 00:00:00”
“30/December/2011 00:00:00”
Note that format inference is sensitive to dayfirst
. With
dayfirst=True
, it will guess “01/12/2011” to be December 1st. With
dayfirst=False
(default) it will guess “01/12/2011” to be January 12th.
If you try to parse a column of date strings, pandas will attempt to guess the format
from the first non-NaN element, and will then parse the rest of the column with that
format. If pandas fails to guess the format (for example if your first string is
'01 December US/Pacific 2000'
), then a warning will be raised and each
row will be parsed individually by dateutil.parser.parse
. The safest
way to parse dates is to explicitly set format=
.
In [112]: df = pd.read_csv(
.....: "foo.csv",
.....: index_col=0,
.....: parse_dates=True,
.....: )
.....:
In [113]: df
Out[113]:
A B C
date
2009-01-01 a 1 2
2009-01-02 b 3 4
2009-01-03 c 4 5
In the case that you have mixed datetime formats within the same column, you can
pass format='mixed'
In [114]: data = StringIO("date\n12 Jan 2000\n2000-01-13\n")
In [115]: df = pd.read_csv(data)
In [116]: df['date'] = pd.to_datetime(df['date'], format='mixed')
In [117]: df
Out[117]:
date
0 2000-01-12
1 2000-01-13
or, if your datetime formats are all ISO8601 (possibly not identically-formatted):
In [118]: data = StringIO("date\n2020-01-01\n2020-01-01 03:00\n")
In [119]: df = pd.read_csv(data)
In [120]: df['date'] = pd.to_datetime(df['date'], format='ISO8601')
In [121]: df
Out[121]:
date
0 2020-01-01 00:00:00
1 2020-01-01 03:00:00
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:
In [122]: data = "date,value,cat\n1/6/2000,5,a\n2/6/2000,10,b\n3/6/2000,15,c"
In [123]: print(data)
date,value,cat
1/6/2000,5,a
2/6/2000,10,b
3/6/2000,15,c
In [124]: with open("tmp.csv", "w") as fh:
.....: fh.write(data)
.....:
In [125]: pd.read_csv("tmp.csv", parse_dates=[0])
Out[125]:
date value cat
0 2000-01-06 5 a
1 2000-02-06 10 b
2 2000-03-06 15 c
In [126]: pd.read_csv("tmp.csv", dayfirst=True, parse_dates=[0])
Out[126]:
date value cat
0 2000-06-01 5 a
1 2000-06-02 10 b
2 2000-06-03 15 c
Writing CSVs to binary file objects#
Added in version 1.2.0.
df.to_csv(..., mode="wb")
allows writing a CSV to a file object
opened binary mode. In most cases, it is not necessary to specify
mode
as pandas will auto-detect whether the file object is
opened in text or binary mode.
In [127]: import io
In [128]: data = pd.DataFrame([0, 1, 2])
In [129]: buffer = io.BytesIO()
In [130]: data.to_csv(buffer, encoding="utf-8", compression="gzip")
Specifying method for floating-point conversion#
The parameter float_precision
can be specified in order to use
a specific floating-point converter during parsing with the C engine.
The options are the ordinary converter, the high-precision converter, and
the round-trip converter (which is guaranteed to round-trip values after
writing to a file). For example:
In [131]: val = "0.3066101993807095471566981359501369297504425048828125"
In [132]: data = "a,b,c\n1,2,{0}".format(val)
In [133]: abs(
.....: pd.read_csv(
.....: StringIO(data),
.....: engine="c",
.....: float_precision=None,
.....: )["c"][0] - float(val)
.....: )
.....:
Out[133]: 5.551115123125783e-17
In [134]: abs(
.....: pd.read_csv(
.....: StringIO(data),
.....: engine="c",
.....: float_precision="high",
.....: )["c"][0] - float(val)
.....: )
.....:
Out[134]: 5.551115123125783e-17
In [135]: abs(
.....: pd.read_csv(StringIO(data), engine="c", float_precision="round_trip")["c"][0]
.....: - float(val)
.....: )
.....:
Out[135]: 0.0
Thousand separators#
For large numbers that have been written with a thousands separator, you can
set the thousands
keyword to a string of length 1 so that integers will be parsed
correctly:
By default, numbers with a thousands separator will be parsed as strings:
In [136]: data = (
.....: "ID|level|category\n"
.....: "Patient1|123,000|x\n"
.....: "Patient2|23,000|y\n"
.....: "Patient3|1,234,018|z"
.....: )
.....:
In [137]: with open("tmp.csv", "w") as fh:
.....: fh.write(data)
.....:
In [138]: df = pd.read_csv("tmp.csv", sep="|")
In [139]: df
Out[139]:
ID level category
0 Patient1 123,000 x
1 Patient2 23,000 y
2 Patient3 1,234,018 z
In [140]: df.level.dtype
Out[140]: dtype('O')
The thousands
keyword allows integers to be parsed correctly:
In [141]: df = pd.read_csv("tmp.csv", sep="|", thousands=",")
In [142]: df
Out[142]:
ID level category
0 Patient1 123000 x
1 Patient2 23000 y
2 Patient3 1234018 z
In [143]: df.level.dtype
Out[143]: dtype('int64')
NA values#
To control which values are parsed as missing values (which are signified by
NaN
), specify a string in na_values
. If you specify a list of strings,
then all values in it are considered to be missing values. If you specify a
number (a float
, like 5.0
or an integer
like 5
), the
corresponding equivalent values will also imply a missing value (in this case
effectively [5.0, 5]
are recognized as NaN
).
To completely override the default values that are recognized as missing, specify keep_default_na=False
.
Let us consider some examples:
pd.read_csv("path_to_file.csv", na_values=[5])
In the example above 5
and 5.0
will be recognized as NaN
, in
addition to the defaults. A string will first be interpreted as a numerical
5
, then as a NaN
.
pd.read_csv("path_to_file.csv", keep_default_na=False, na_values=[""])
Above, only an empty field will be recognized as NaN
.
pd.read_csv("path_to_file.csv", keep_default_na=False, na_values=["NA", "0"])
Above, both NA
and 0
as strings are NaN
.
pd.read_csv("path_to_file.csv", na_values=["Nope"])
The default values, in addition to the string "Nope"
are recognized as
NaN
.
Infinity#
inf
like values will be parsed as np.inf
(positive infinity), and -inf
as -np.inf
(negative infinity).
These will ignore the case of the value, meaning Inf
, will also be parsed as np.inf
.
Boolean values#
The common values True
, False
, TRUE
, and FALSE
are all
recognized as boolean. Occasionally you might want to recognize other values
as being boolean. To do this, use the true_values
and false_values
options as follows:
In [144]: data = "a,b,c\n1,Yes,2\n3,No,4"
In [145]: print(data)
a,b,c
1,Yes,2
3,No,4
In [146]: pd.read_csv(StringIO(data))
Out[146]:
a b c
0 1 Yes 2
1 3 No 4
In [147]: pd.read_csv(StringIO(data), true_values=["Yes"], false_values=["No"])
Out[147]:
a b c
0 1 True 2
1 3 False 4
Handling “bad” lines#
Some files may have malformed lines with too few fields or too many. Lines with too few fields will have NA values filled in the trailing fields. Lines with too many fields will raise an error by default:
In [148]: data = "a,b,c\n1,2,3\n4,5,6,7\n8,9,10"
In [149]: pd.read_csv(StringIO(data))
---------------------------------------------------------------------------
ParserError Traceback (most recent call last)
Cell In[149], line 1
----> 1 pd.read_csv(StringIO(data))
File ~/work/pandas/pandas/pandas/io/parsers/readers.py:849, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, skip_blank_lines, parse_dates, date_format, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, on_bad_lines, low_memory, memory_map, float_precision, storage_options, dtype_backend)
837 kwds_defaults = _refine_defaults_read(
838 dialect,
839 delimiter,
(...)
845 dtype_backend=dtype_backend,
846 )
847 kwds.update(kwds_defaults)
--> 849 return _read(filepath_or_buffer, kwds)
File ~/work/pandas/pandas/pandas/io/parsers/readers.py:716, in _read(filepath_or_buffer, kwds)
713 return parser
715 with parser:
--> 716 return parser.read(nrows)
File ~/work/pandas/pandas/pandas/io/parsers/readers.py:1496, in TextFileReader.read(self, nrows)
1489 nrows = validate_integer("nrows", nrows)
1490 try:
1491 # error: "ParserBase" has no attribute "read"
1492 (
1493 index,
1494 columns,
1495 col_dict,
-> 1496 ) = self._engine.read( # type: ignore[attr-defined]
1497 nrows
1498 )
1499 except Exception:
1500 self.close()
File ~/work/pandas/pandas/pandas/io/parsers/c_parser_wrapper.py:237, in CParserWrapper.read(self, nrows)
235 try:
236 if self.low_memory:
--> 237 chunks = self._reader.read_low_memory(nrows)
238 # destructive to chunks
239 data = _concatenate_chunks(chunks, self.names) # type: ignore[has-type]
File parsers.pyx:830, in pandas._libs.parsers.TextReader.read_low_memory()
File parsers.pyx:895, in pandas._libs.parsers.TextReader._read_rows()
File parsers.pyx:866, in pandas._libs.parsers.TextReader._tokenize_rows()
File parsers.pyx:883, in pandas._libs.parsers.TextReader._check_tokenize_status()
File parsers.pyx:2037, in pandas._libs.parsers.raise_parser_error()
ParserError: Error tokenizing data. C error: Expected 3 fields in line 3, saw 4
You can elect to skip bad lines:
In [150]: data = "a,b,c\n1,2,3\n4,5,6,7\n8,9,10"
In [151]: pd.read_csv(StringIO(data), on_bad_lines="skip")
Out[151]:
a b c
0 1 2 3
1 8 9 10
Added in version 1.4.0.
Or pass a callable function to handle the bad line if engine="python"
.
The bad line will be a list of strings that was split by the sep
:
In [152]: external_list = []
In [153]: def bad_lines_func(line):
.....: external_list.append(line)
.....: return line[-3:]
.....:
In [154]: external_list
Out[154]: []
Note
The callable function will handle only a line with too many fields. Bad lines caused by other errors will be silently skipped.
In [155]: bad_lines_func = lambda line: print(line)
In [156]: data = 'name,type\nname a,a is of type a\nname b,"b\" is of type b"'
In [157]: data
Out[157]: 'name,type\nname a,a is of type a\nname b,"b" is of type b"'
In [158]: pd.read_csv(StringIO(data), on_bad_lines=bad_lines_func, engine="python")
Out[158]:
name type
0 name a a is of type a
The line was not processed in this case, as a “bad line” here is caused by an escape character.
You can also use the usecols
parameter to eliminate extraneous column
data that appear in some lines but not others:
In [159]: pd.read_csv(StringIO(data), usecols=[0, 1, 2])
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[159], line 1
----> 1 pd.read_csv(StringIO(data), usecols=[0, 1, 2])
File ~/work/pandas/pandas/pandas/io/parsers/readers.py:849, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, skip_blank_lines, parse_dates, date_format, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, on_bad_lines, low_memory, memory_map, float_precision, storage_options, dtype_backend)
837 kwds_defaults = _refine_defaults_read(
838 dialect,
839 delimiter,
(...)
845 dtype_backend=dtype_backend,
846 )
847 kwds.update(kwds_defaults)
--> 849 return _read(filepath_or_buffer, kwds)
File ~/work/pandas/pandas/pandas/io/parsers/readers.py:710, in _read(filepath_or_buffer, kwds)
707 _validate_names(kwds.get("names", None))
709 # Create the parser.
--> 710 parser = TextFileReader(filepath_or_buffer, **kwds)
712 if chunksize or iterator:
713 return parser
File ~/work/pandas/pandas/pandas/io/parsers/readers.py:1192, in TextFileReader.__init__(self, f, engine, **kwds)
1189 self.options["has_index_names"] = kwds["has_index_names"]
1191 self.handles: IOHandles | None = None
-> 1192 self._engine = self._make_engine(f, self.engine)
File ~/work/pandas/pandas/pandas/io/parsers/readers.py:1471, in TextFileReader._make_engine(self, f, engine)
1468 raise ValueError(msg)
1470 try:
-> 1471 return mapping[engine](f, **self.options)
1472 except Exception:
1473 if self.handles is not None:
File ~/work/pandas/pandas/pandas/io/parsers/c_parser_wrapper.py:160, in CParserWrapper.__init__(self, src, **kwds)
157 # error: Cannot determine type of 'names'
158 if len(self.names) < len(usecols): # type: ignore[has-type]
159 # error: Cannot determine type of 'names'
--> 160 self._validate_usecols_names(
161 usecols,
162 self.names, # type: ignore[has-type]
163 )
165 # error: Cannot determine type of 'names'
166 validate_parse_dates_presence(self.parse_dates, self.names) # type: ignore[has-type]
File ~/work/pandas/pandas/pandas/io/parsers/base_parser.py:657, in ParserBase._validate_usecols_names(self, usecols, names)
655 missing = [c for c in usecols if c not in names]
656 if len(missing) > 0:
--> 657 raise ValueError(
658 f"Usecols do not match columns, columns expected but not found: "
659 f"{missing}"
660 )
662 return usecols
ValueError: Usecols do not match columns, columns expected but not found: [0, 1, 2]
In case you want to keep all data including the lines with too many fields, you can
specify a sufficient number of names
. This ensures that lines with not enough
fields are filled with NaN
.
In [160]: pd.read_csv(StringIO(data), names=['a', 'b', 'c', 'd'])
Out[160]:
a b c d
0 name type NaN NaN
1 name a a is of type a NaN NaN
2 name b b is of type b" NaN NaN
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 csv.Dialect
instance.
Suppose you had data with unenclosed quotes:
In [161]: data = "label1,label2,label3\n" 'index1,"a,c,e\n' "index2,b,d,f"
In [162]: print(data)
label1,label2,label3
index1,"a,c,e
index2,b,d,f
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
:
In [163]: import csv
In [164]: dia = csv.excel()
In [165]: dia.quoting = csv.QUOTE_NONE
In [166]: pd.read_csv(StringIO(data), dialect=dia)
Out[166]:
label1 label2 label3
index1 "a c e
index2 b d f
All of the dialect options can be specified separately by keyword arguments:
In [167]: data = "a,b,c~1,2,3~4,5,6"
In [168]: pd.read_csv(StringIO(data), lineterminator="~")
Out[168]:
a b c
0 1 2 3
1 4 5 6
Another common dialect option is skipinitialspace
, to skip any whitespace
after a delimiter:
In [169]: data = "a, b, c\n1, 2, 3\n4, 5, 6"
In [170]: print(data)
a, b, c
1, 2, 3
4, 5, 6
In [171]: pd.read_csv(StringIO(data), skipinitialspace=True)
Out[171]:
a b c
0 1 2 3
1 4 5 6
The parsers make every attempt to “do the right thing” and not be fragile. Type inference is a pretty big deal. If a column can be coerced to integer dtype without altering the contents, the parser will do so. Any non-numeric columns will come through as object dtype as with the rest of pandas objects.
Quoting and Escape Characters#
Quotes (and other escape characters) in embedded fields can be handled in any
number of ways. One way is to use backslashes; to properly parse this data, you
should pass the escapechar
option:
In [172]: data = 'a,b\n"hello, \\"Bob\\", nice to see you",5'
In [173]: print(data)
a,b
"hello, \"Bob\", nice to see you",5
In [174]: pd.read_csv(StringIO(data), escapechar="\\")
Out[174]:
a b
0 hello, "Bob", nice to see you 5
Files with fixed width columns#
While read_csv()
reads delimited data, the 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, and
a different usage of the delimiter
parameter:
colspecs
: A list of pairs (tuples) giving the extents of the fixed-width fields of each line as half-open intervals (i.e., [from, to[ ). String value ‘infer’ can be used to instruct the parser to try detecting the column specifications from the first 100 rows of the data. Default behavior, if not specified, is to infer.widths
: A list of field widths which can be used instead of ‘colspecs’ if the intervals are contiguous.delimiter
: Characters to consider as filler characters in the fixed-width file. Can be used to specify the filler character of the fields if it is not spaces (e.g., ‘~’).
Consider a typical fixed-width data file:
In [175]: 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"
.....: )
.....:
In [176]: with open("bar.csv", "w") as f:
.....: f.write(data1)
.....:
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:
# Column specifications are a list of half-intervals
In [177]: colspecs = [(0, 6), (8, 20), (21, 33), (34, 43)]
In [178]: df = pd.read_fwf("bar.csv", colspecs=colspecs, header=None, index_col=0)
In [179]: df
Out[179]:
1 2 3
0
id8141 360.242940 149.910199 11950.7
id1594 444.953632 166.985655 11788.4
id1849 364.136849 183.628767 11806.2
id1230 413.836124 184.375703 11916.8
id1948 502.953953 173.237159 12468.3
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:
# Widths are a list of integers
In [180]: widths = [6, 14, 13, 10]
In [181]: df = pd.read_fwf("bar.csv", widths=widths, header=None)
In [182]: df
Out[182]:
0 1 2 3
0 id8141 360.242940 149.910199 11950.7
1 id1594 444.953632 166.985655 11788.4
2 id1849 364.136849 183.628767 11806.2
3 id1230 413.836124 184.375703 11916.8
4 id1948 502.953953 173.237159 12468.3
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.
By default, read_fwf
will try to infer the file’s colspecs
by using the
first 100 rows of the file. It can do it only in cases when the columns are
aligned and correctly separated by the provided delimiter
(default delimiter
is whitespace).
In [183]: df = pd.read_fwf("bar.csv", header=None, index_col=0)
In [184]: df
Out[184]:
1 2 3
0
id8141 360.242940 149.910199 11950.7
id1594 444.953632 166.985655 11788.4
id1849 364.136849 183.628767 11806.2
id1230 413.836124 184.375703 11916.8
id1948 502.953953 173.237159 12468.3
read_fwf
supports the dtype
parameter for specifying the types of
parsed columns to be different from the inferred type.
In [185]: pd.read_fwf("bar.csv", header=None, index_col=0).dtypes
Out[185]:
1 float64
2 float64
3 float64
dtype: object
In [186]: pd.read_fwf("bar.csv", header=None, dtype={2: "object"}).dtypes
Out[186]:
0 object
1 float64
2 object
3 float64
dtype: object
Indexes#
Files with an “implicit” index column#
Consider a file with one less entry in the header than the number of data column:
In [187]: data = "A,B,C\n20090101,a,1,2\n20090102,b,3,4\n20090103,c,4,5"
In [188]: print(data)
A,B,C
20090101,a,1,2
20090102,b,3,4
20090103,c,4,5
In [189]: with open("foo.csv", "w") as f:
.....: f.write(data)
.....:
In this special case, read_csv
assumes that the first column is to be used
as the index of the DataFrame
:
In [190]: pd.read_csv("foo.csv")
Out[190]:
A B C
20090101 a 1 2
20090102 b 3 4
20090103 c 4 5
Note that the dates weren’t automatically parsed. In that case you would need to do as before:
In [191]: df = pd.read_csv("foo.csv", parse_dates=True)
In [192]: df.index
Out[192]: DatetimeIndex(['2009-01-01', '2009-01-02', '2009-01-03'], dtype='datetime64[s]', freq=None)
Reading an index with a MultiIndex
#
Suppose you have data indexed by two columns:
In [193]: data = 'year,indiv,zit,xit\n1977,"A",1.2,.6\n1977,"B",1.5,.5'
In [194]: print(data)
year,indiv,zit,xit
1977,"A",1.2,.6
1977,"B",1.5,.5
In [195]: with open("mindex_ex.csv", mode="w") as f:
.....: f.write(data)
.....:
The index_col
argument to read_csv
can take a list of
column numbers to turn multiple columns into a MultiIndex
for the index of the
returned object:
In [196]: df = pd.read_csv("mindex_ex.csv", index_col=[0, 1])
In [197]: df
Out[197]:
zit xit
year indiv
1977 A 1.2 0.6
B 1.5 0.5
In [198]: df.loc[1977]
Out[198]:
zit xit
indiv
A 1.2 0.6
B 1.5 0.5
Reading columns with a MultiIndex
#
By specifying list of row locations for the header
argument, you
can read in a MultiIndex
for the columns. Specifying non-consecutive
rows will skip the intervening rows.
In [199]: mi_idx = pd.MultiIndex.from_arrays([[1, 2, 3, 4], list("abcd")], names=list("ab"))
In [200]: mi_col = pd.MultiIndex.from_arrays([[1, 2], list("ab")], names=list("cd"))
In [201]: df = pd.DataFrame(np.ones((4, 2)), index=mi_idx, columns=mi_col)
In [202]: df.to_csv("mi.csv")
In [203]: print(open("mi.csv").read())
c,,1,2
d,,a,b
a,b,,
1,a,1.0,1.0
2,b,1.0,1.0
3,c,1.0,1.0
4,d,1.0,1.0
In [204]: pd.read_csv("mi.csv", header=[0, 1, 2, 3], index_col=[0, 1])
Out[204]:
c 1 2
d a b
a Unnamed: 2_level_2 Unnamed: 3_level_2
1 1.0 1.0
2 b 1.0 1.0
3 c 1.0 1.0
4 d 1.0 1.0
read_csv
is also able to interpret a more common format
of multi-columns indices.
In [205]: data = ",a,a,a,b,c,c\n,q,r,s,t,u,v\none,1,2,3,4,5,6\ntwo,7,8,9,10,11,12"
In [206]: print(data)
,a,a,a,b,c,c
,q,r,s,t,u,v
one,1,2,3,4,5,6
two,7,8,9,10,11,12
In [207]: with open("mi2.csv", "w") as fh:
.....: fh.write(data)
.....:
In [208]: pd.read_csv("mi2.csv", header=[0, 1], index_col=0)
Out[208]:
a b c
q r s t u v
one 1 2 3 4 5 6
two 7 8 9 10 11 12
Note
If an index_col
is not specified (e.g. you don’t have an index, or wrote it
with df.to_csv(..., index=False)
, then any names
on the columns index will
be lost.
Automatically “sniffing” the delimiter#
read_csv
is capable of inferring delimited (not necessarily
comma-separated) files, as pandas uses the csv.Sniffer
class of the csv module. For this, you have to specify sep=None
.
In [209]: df = pd.DataFrame(np.random.randn(10, 4))
In [210]: df.to_csv("tmp2.csv", sep=":", index=False)
In [211]: pd.read_csv("tmp2.csv", sep=None, engine="python")
Out[211]:
0 1 2 3
0 0.469112 -0.282863 -1.509059 -1.135632
1 1.212112 -0.173215 0.119209 -1.044236
2 -0.861849 -2.104569 -0.494929 1.071804
3 0.721555 -0.706771 -1.039575 0.271860
4 -0.424972 0.567020 0.276232 -1.087401
5 -0.673690 0.113648 -1.478427 0.524988
6 0.404705 0.577046 -1.715002 -1.039268
7 -0.370647 -1.157892 -1.344312 0.844885
8 1.075770 -0.109050 1.643563 -1.469388
9 0.357021 -0.674600 -1.776904 -0.968914
Reading multiple files to create a single DataFrame#
It’s best to use concat()
to combine multiple files.
See the cookbook for an example.
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:
In [212]: df = pd.DataFrame(np.random.randn(10, 4))
In [213]: df.to_csv("tmp.csv", index=False)
In [214]: table = pd.read_csv("tmp.csv")
In [215]: table
Out[215]:
0 1 2 3
0 -1.294524 0.413738 0.276662 -0.472035
1 -0.013960 -0.362543 -0.006154 -0.923061
2 0.895717 0.805244 -1.206412 2.565646
3 1.431256 1.340309 -1.170299 -0.226169
4 0.410835 0.813850 0.132003 -0.827317
5 -0.076467 -1.187678 1.130127 -1.436737
6 -1.413681 1.607920 1.024180 0.569605
7 0.875906 -2.211372 0.974466 -2.006747
8 -0.410001 -0.078638 0.545952 -1.219217
9 -1.226825 0.769804 -1.281247 -0.727707
By specifying a chunksize
to read_csv
, the return
value will be an iterable object of type TextFileReader
:
In [216]: with pd.read_csv("tmp.csv", chunksize=4) as reader:
.....: print(reader)
.....: for chunk in reader:
.....: print(chunk)
.....:
<pandas.io.parsers.readers.TextFileReader object at 0x7f65c888f5e0>
0 1 2 3
0 -1.294524 0.413738 0.276662 -0.472035
1 -0.013960 -0.362543 -0.006154 -0.923061
2 0.895717 0.805244 -1.206412 2.565646
3 1.431256 1.340309 -1.170299 -0.226169
0 1 2 3
4 0.410835 0.813850 0.132003 -0.827317
5 -0.076467 -1.187678 1.130127 -1.436737
6 -1.413681 1.607920 1.024180 0.569605
7 0.875906 -2.211372 0.974466 -2.006747
0 1 2 3
8 -0.410001 -0.078638 0.545952 -1.219217
9 -1.226825 0.769804 -1.281247 -0.727707
Changed in version 1.2: read_csv/json/sas
return a context-manager when iterating through a file.
Specifying iterator=True
will also return the TextFileReader
object:
In [217]: with pd.read_csv("tmp.csv", iterator=True) as reader:
.....: print(reader.get_chunk(5))
.....:
0 1 2 3
0 -1.294524 0.413738 0.276662 -0.472035
1 -0.013960 -0.362543 -0.006154 -0.923061
2 0.895717 0.805244 -1.206412 2.565646
3 1.431256 1.340309 -1.170299 -0.226169
4 0.410835 0.813850 0.132003 -0.827317
Specifying the parser engine#
pandas currently supports three engines, the C engine, the python engine, and an experimental
pyarrow engine (requires the pyarrow
package). In general, the pyarrow engine is fastest
on larger workloads and is equivalent in speed to the C engine on most other workloads.
The python engine tends to be slower than the pyarrow and C engines on most workloads. However,
the pyarrow engine is much less robust than the C engine, which lacks a few features compared to the
Python engine.
Where possible, pandas uses the C parser (specified as engine='c'
), but it may fall
back to Python if C-unsupported options are specified.
Currently, options unsupported by the C and pyarrow engines include:
sep
other than a single character (e.g. regex separators)skipfooter
Specifying any of the above options will produce a ParserWarning
unless the
python engine is selected explicitly using engine='python'
.
Options that are unsupported by the pyarrow engine which are not covered by the list above include:
float_precision
chunksize
comment
nrows
thousands
memory_map
dialect
on_bad_lines
quoting
lineterminator
converters
decimal
iterator
dayfirst
verbose
skipinitialspace
low_memory
Specifying these options with engine='pyarrow'
will raise a ValueError
.
Reading/writing remote files#
You can pass in a URL to read or write remote files to many of pandas’ IO functions - the following example shows reading a CSV file:
df = pd.read_csv("https://download.bls.gov/pub/time.series/cu/cu.item", sep="\t")
Added in version 1.3.0.
A custom header can be sent alongside HTTP(s) requests by passing a dictionary
of header key value mappings to the storage_options
keyword argument as shown below:
headers = {"User-Agent": "pandas"}
df = pd.read_csv(
"https://download.bls.gov/pub/time.series/cu/cu.item",
sep="\t",
storage_options=headers
)
All URLs which are not local files or HTTP(s) are handled by fsspec, if installed, and its various filesystem implementations (including Amazon S3, Google Cloud, SSH, FTP, webHDFS…). Some of these implementations will require additional packages to be installed, for example S3 URLs require the s3fs library:
df = pd.read_json("s3://pandas-test/adatafile.json")
When dealing with remote storage systems, you might need
extra configuration with environment variables or config files in
special locations. For example, to access data in your S3 bucket,
you will need to define credentials in one of the several ways listed in
the S3Fs documentation. The same is true
for several of the storage backends, and you should follow the links
at fsimpl1 for implementations built into fsspec
and fsimpl2
for those not included in the main fsspec
distribution.
You can also pass parameters directly to the backend driver. Since fsspec
does not
utilize the AWS_S3_HOST
environment variable, we can directly define a
dictionary containing the endpoint_url and pass the object into the storage
option parameter:
storage_options = {"client_kwargs": {"endpoint_url": "http://127.0.0.1:5555"}}
df = pd.read_json("s3://pandas-test/test-1", storage_options=storage_options)
More sample configurations and documentation can be found at S3Fs documentation.
If you do not have S3 credentials, you can still access public data by specifying an anonymous connection, such as
Added in version 1.2.0.
pd.read_csv(
"s3://ncei-wcsd-archive/data/processed/SH1305/18kHz/SaKe2013"
"-D20130523-T080854_to_SaKe2013-D20130523-T085643.csv",
storage_options={"anon": True},
)
fsspec
also allows complex URLs, for accessing data in compressed
archives, local caching of files, and more. To locally cache the above
example, you would modify the call to
pd.read_csv(
"simplecache::s3://ncei-wcsd-archive/data/processed/SH1305/18kHz/"
"SaKe2013-D20130523-T080854_to_SaKe2013-D20130523-T085643.csv",
storage_options={"s3": {"anon": True}},
)
where we specify that the “anon” parameter is meant for the “s3” part of the implementation, not to the caching implementation. Note that this caches to a temporary directory for the duration of the session only, but you can also specify a permanent store.
Writing out data#
Writing to CSV format#
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_or_buf
: A string path to the file to write or a file object. If a file object it must be opened withnewline=''
sep
: Field delimiter for the output file (default “,”)na_rep
: A string representation of a missing value (default ‘’)float_format
: Format string for floating point numberscolumns
: 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), andheader
andindex
are True, then the index names are used. (A sequence should be given if theDataFrame
uses MultiIndex).mode
: Python write mode, default ‘w’encoding
: a string representing the encoding to use if the contents are non-ASCII, for Python versions prior to 3lineterminator
: Character sequence denoting line end (defaultos.linesep
)quoting
: Set quoting rules as in csv module (default csv.QUOTE_MINIMAL). Note that if you have set afloat_format
then floats are converted to strings and csv.QUOTE_NONNUMERIC will treat them as non-numericquotechar
: Character used to quote fields (default ‘”’)doublequote
: Control quoting ofquotechar
in fields (default True)escapechar
: Character used to escapesep
andquotechar
when appropriate (default None)chunksize
: Number of rows to write at a timedate_format
: Format string for datetime objects
Writing a formatted string#
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 objectcolumns
default None, which columns to writecol_space
default None, minimum width of each column.na_rep
defaultNaN
, representation of NA valueformatters
default None, a dictionary (by column) of functions each of which takes a single argument and returns a formatted stringfloat_format
default None, a function which takes a single (float) argument and returns a formatted string; to be applied to floats in theDataFrame
.sparsify
default True, set to False for aDataFrame
with a hierarchical index to print every MultiIndex key at each row.index_names
default True, will print the names of the indicesindex
default True, will print the index (ie, row labels)header
default True, will print the column labelsjustify
defaultleft
, 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.
JSON#
Read and write JSON
format files and strings.
Writing JSON#
A Series
or DataFrame
can be converted to a valid JSON string. Use to_json
with optional parameters:
path_or_buf
: the pathname or buffer to write the output. This can beNone
in which case a JSON string is returned.orient
:Series
:default is
index
allowed values are {
split
,records
,index
}
DataFrame
:default is
columns
allowed values are {
split
,records
,index
,columns
,values
,table
}
The format of the JSON string
split
dict like {index -> [index]; columns -> [columns]; data -> [values]}
records
list like [{column -> value}; … ]
index
dict like {index -> {column -> value}}
columns
dict like {column -> {index -> value}}
values
just the values array
table
adhering to the JSON Table Schema
date_format
: string, type of date conversion, ‘epoch’ for timestamp, ‘iso’ for ISO8601.double_precision
: The number of decimal places to use when encoding floating point values, default 10.force_ascii
: force encoded string to be ASCII, default True.date_unit
: The time unit to encode to, governs timestamp and ISO8601 precision. One of ‘s’, ‘ms’, ‘us’ or ‘ns’ for seconds, milliseconds, microseconds and nanoseconds respectively. Default ‘ms’.default_handler
: The handler to call if an object cannot otherwise be converted to a suitable format for JSON. Takes a single argument, which is the object to convert, and returns a serializable object.lines
: Ifrecords
orient, then will write each record per line as json.mode
: string, writer mode when writing to path. ‘w’ for write, ‘a’ for append. Default ‘w’
Note NaN
’s, NaT
’s and None
will be converted to null
and datetime
objects will be converted based on the date_format
and date_unit
parameters.
In [218]: dfj = pd.DataFrame(np.random.randn(5, 2), columns=list("AB"))
In [219]: json = dfj.to_json()
In [220]: json
Out[220]: '{"A":{"0":-0.1213062281,"1":0.6957746499,"2":0.9597255933,"3":-0.6199759194,"4":-0.7323393705},"B":{"0":-0.0978826728,"1":0.3417343559,"2":-1.1103361029,"3":0.1497483186,"4":0.6877383895}}'
Orient options#
There are a number of different options for the format of the resulting JSON
file / string. Consider the following DataFrame
and Series
:
In [221]: dfjo = pd.DataFrame(
.....: dict(A=range(1, 4), B=range(4, 7), C=range(7, 10)),
.....: columns=list("ABC"),
.....: index=list("xyz"),
.....: )
.....:
In [222]: dfjo
Out[222]:
A B C
x 1 4 7
y 2 5 8
z 3 6 9
In [223]: sjo = pd.Series(dict(x=15, y=16, z=17), name="D")
In [224]: sjo
Out[224]:
x 15
y 16
z 17
Name: D, dtype: int64
Column oriented (the default for DataFrame
) serializes the data as
nested JSON objects with column labels acting as the primary index:
In [225]: dfjo.to_json(orient="columns")
Out[225]: '{"A":{"x":1,"y":2,"z":3},"B":{"x":4,"y":5,"z":6},"C":{"x":7,"y":8,"z":9}}'
# Not available for Series
Index oriented (the default for Series
) similar to column oriented
but the index labels are now primary:
In [226]: dfjo.to_json(orient="index")
Out[226]: '{"x":{"A":1,"B":4,"C":7},"y":{"A":2,"B":5,"C":8},"z":{"A":3,"B":6,"C":9}}'
In [227]: sjo.to_json(orient="index")
Out[227]: '{"x":15,"y":16,"z":17}'
Record oriented serializes the data to a JSON array of column -> value records,
index labels are not included. This is useful for passing DataFrame
data to plotting
libraries, for example the JavaScript library d3.js
:
In [228]: dfjo.to_json(orient="records")
Out[228]: '[{"A":1,"B":4,"C":7},{"A":2,"B":5,"C":8},{"A":3,"B":6,"C":9}]'
In [229]: sjo.to_json(orient="records")
Out[229]: '[15,16,17]'
Value oriented is a bare-bones option which serializes to nested JSON arrays of values only, column and index labels are not included:
In [230]: dfjo.to_json(orient="values")
Out[230]: '[[1,4,7],[2,5,8],[3,6,9]]'
# Not available for Series
Split oriented serializes to a JSON object containing separate entries for
values, index and columns. Name is also included for Series
:
In [231]: dfjo.to_json(orient="split")
Out[231]: '{"columns":["A","B","C"],"index":["x","y","z"],"data":[[1,4,7],[2,5,8],[3,6,9]]}'
In [232]: sjo.to_json(orient="split")
Out[232]: '{"name":"D","index":["x","y","z"],"data":[15,16,17]}'
Table oriented serializes to the JSON Table Schema, allowing for the preservation of metadata including but not limited to dtypes and index names.
Note
Any orient option that encodes to a JSON object will not preserve the ordering of
index and column labels during round-trip serialization. If you wish to preserve
label ordering use the split
option as it uses ordered containers.
Date handling#
Writing in ISO date format:
In [233]: dfd = pd.DataFrame(np.random.randn(5, 2), columns=list("AB"))
In [234]: dfd["date"] = pd.Timestamp("20130101")
In [235]: dfd = dfd.sort_index(axis=1, ascending=False)
In [236]: json = dfd.to_json(date_format="iso")
In [237]: json
Out[237]: '{"date":{"0":"2013-01-01T00:00:00.000","1":"2013-01-01T00:00:00.000","2":"2013-01-01T00:00:00.000","3":"2013-01-01T00:00:00.000","4":"2013-01-01T00:00:00.000"},"B":{"0":0.403309524,"1":0.3016244523,"2":-1.3698493577,"3":1.4626960492,"4":-0.8265909164},"A":{"0":0.1764443426,"1":-0.1549507744,"2":-2.1798606054,"3":-0.9542078401,"4":-1.7431609117}}'
Writing in ISO date format, with microseconds:
In [238]: json = dfd.to_json(date_format="iso", date_unit="us")
In [239]: json
Out[239]: '{"date":{"0":"2013-01-01T00:00:00.000000","1":"2013-01-01T00:00:00.000000","2":"2013-01-01T00:00:00.000000","3":"2013-01-01T00:00:00.000000","4":"2013-01-01T00:00:00.000000"},"B":{"0":0.403309524,"1":0.3016244523,"2":-1.3698493577,"3":1.4626960492,"4":-0.8265909164},"A":{"0":0.1764443426,"1":-0.1549507744,"2":-2.1798606054,"3":-0.9542078401,"4":-1.7431609117}}'
Writing to a file, with a date index and a date column:
In [240]: dfj2 = dfj.copy()
In [241]: dfj2["date"] = pd.Timestamp("20130101")
In [242]: dfj2["ints"] = list(range(5))
In [243]: dfj2["bools"] = True
In [244]: dfj2.index = pd.date_range("20130101", periods=5)
In [245]: dfj2.to_json("test.json", date_format="iso")
In [246]: with open("test.json") as fh:
.....: print(fh.read())
.....:
{"A":{"2013-01-01T00:00:00.000":-0.1213062281,"2013-01-02T00:00:00.000":0.6957746499,"2013-01-03T00:00:00.000":0.9597255933,"2013-01-04T00:00:00.000":-0.6199759194,"2013-01-05T00:00:00.000":-0.7323393705},"B":{"2013-01-01T00:00:00.000":-0.0978826728,"2013-01-02T00:00:00.000":0.3417343559,"2013-01-03T00:00:00.000":-1.1103361029,"2013-01-04T00:00:00.000":0.1497483186,"2013-01-05T00:00:00.000":0.6877383895},"date":{"2013-01-01T00:00:00.000":"2013-01-01T00:00:00.000","2013-01-02T00:00:00.000":"2013-01-01T00:00:00.000","2013-01-03T00:00:00.000":"2013-01-01T00:00:00.000","2013-01-04T00:00:00.000":"2013-01-01T00:00:00.000","2013-01-05T00:00:00.000":"2013-01-01T00:00:00.000"},"ints":{"2013-01-01T00:00:00.000":0,"2013-01-02T00:00:00.000":1,"2013-01-03T00:00:00.000":2,"2013-01-04T00:00:00.000":3,"2013-01-05T00:00:00.000":4},"bools":{"2013-01-01T00:00:00.000":true,"2013-01-02T00:00:00.000":true,"2013-01-03T00:00:00.000":true,"2013-01-04T00:00:00.000":true,"2013-01-05T00:00:00.000":true}}
Fallback behavior#
If the JSON serializer cannot handle the container contents directly it will fall back in the following manner:
if the dtype is unsupported (e.g.
np.complex_
) then thedefault_handler
, if provided, will be called for each value, otherwise an exception is raised.if an object is unsupported it will attempt the following:
check if the object has defined a
toDict
method and call it. AtoDict
method should return adict
which will then be JSON serialized.invoke the
default_handler
if one was provided.convert the object to a
dict
by traversing its contents. However this will often fail with anOverflowError
or give unexpected results.
In general the best approach for unsupported objects or dtypes is to provide a default_handler
.
For example:
>>> DataFrame([1.0, 2.0, complex(1.0, 2.0)]).to_json() # raises
RuntimeError: Unhandled numpy dtype 15
can be dealt with by specifying a simple default_handler
:
In [247]: pd.DataFrame([1.0, 2.0, complex(1.0, 2.0)]).to_json(default_handler=str)
Out[247]: '{"0":{"0":"(1+0j)","1":"(2+0j)","2":"(1+2j)"}}'
Reading JSON#
Reading a JSON string to pandas object can take a number of parameters.
The parser will try to parse a DataFrame
if typ
is not supplied or
is None
. To explicitly force Series
parsing, pass typ=series
filepath_or_buffer
: a VALID JSON string or file handle / StringIO. The string could be a URL. Valid URL schemes include http, ftp, S3, and file. For file URLs, a host is expected. For instance, a local file could be file ://localhost/path/to/table.jsontyp
: type of object to recover (series or frame), default ‘frame’orient
:- Series :
default is
index
allowed values are {
split
,records
,index
}
- DataFrame
default is
columns
allowed values are {
split
,records
,index
,columns
,values
,table
}
The format of the JSON string
split
dict like {index -> [index]; columns -> [columns]; data -> [values]}
records
list like [{column -> value} …]
index
dict like {index -> {column -> value}}
columns
dict like {column -> {index -> value}}
values
just the values array
table
adhering to the JSON Table Schema
dtype
: if True, infer dtypes, if a dict of column to dtype, then use those, ifFalse
, then don’t infer dtypes at all, default is True, apply only to the data.convert_axes
: boolean, try to convert the axes to the proper dtypes, default isTrue
convert_dates
: a list of columns to parse for dates; IfTrue
, then try to parse date-like columns, default isTrue
.keep_default_dates
: boolean, defaultTrue
. If parsing dates, then parse the default date-like columns.precise_float
: boolean, defaultFalse
. Set to enable usage of higher precision (strtod) function when decoding string to double values. Default (False
) is to use fast but less precise builtin functionality.date_unit
: string, the timestamp unit to detect if converting dates. Default None. By default the timestamp precision will be detected, if this is not desired then pass one of ‘s’, ‘ms’, ‘us’ or ‘ns’ to force timestamp precision to seconds, milliseconds, microseconds or nanoseconds respectively.lines
: reads file as one json object per line.encoding
: The encoding to use to decode py3 bytes.chunksize
: when used in combination withlines=True
, return apandas.api.typing.JsonReader
which reads inchunksize
lines per iteration.engine
: Either"ujson"
, the built-in JSON parser, or"pyarrow"
which dispatches to pyarrow’spyarrow.json.read_json
. The"pyarrow"
is only available whenlines=True
The parser will raise one of ValueError/TypeError/AssertionError
if the JSON is not parseable.
If a non-default orient
was used when encoding to JSON be sure to pass the same
option here so that decoding produces sensible results, see Orient Options for an
overview.
Data conversion#
The default of convert_axes=True
, dtype=True
, and convert_dates=True
will try to parse the axes, and all of the data into appropriate types,
including dates. If you need to override specific dtypes, pass a dict to
dtype
. convert_axes
should only be set to False
if you need to
preserve string-like numbers (e.g. ‘1’, ‘2’) in an axes.
Note
Large integer values may be converted to dates if convert_dates=True
and the data and / or column labels appear ‘date-like’. The exact threshold depends on the date_unit
specified. ‘date-like’ means that the column label meets one of the following criteria:
it ends with
'_at'
it ends with
'_time'
it begins with
'timestamp'
it is
'modified'
it is
'date'
Warning
When reading JSON data, automatic coercing into dtypes has some quirks:
an index can be reconstructed in a different order from serialization, that is, the returned order is not guaranteed to be the same as before serialization
a column that was
float
data will be converted tointeger
if it can be done safely, e.g. a column of1.
bool columns will be converted to
integer
on reconstruction
Thus there are times where you may want to specify specific dtypes via the dtype
keyword argument.
Reading from a JSON string:
In [248]: from io import StringIO
In [249]: pd.read_json(StringIO(json))
Out[249]:
date B A
0 2013-01-01 0.403310 0.176444
1 2013-01-01 0.301624 -0.154951
2 2013-01-01 -1.369849 -2.179861
3 2013-01-01 1.462696 -0.954208
4 2013-01-01 -0.826591 -1.743161
Reading from a file:
In [250]: pd.read_json("test.json")
Out[250]:
A B date ints bools
2013-01-01 -0.121306 -0.097883 2013-01-01 0 True
2013-01-02 0.695775 0.341734 2013-01-01 1 True
2013-01-03 0.959726 -1.110336 2013-01-01 2 True
2013-01-04 -0.619976 0.149748 2013-01-01 3 True
2013-01-05 -0.732339 0.687738 2013-01-01 4 True
Don’t convert any data (but still convert axes and dates):
In [251]: pd.read_json("test.json", dtype=object).dtypes
Out[251]:
A object
B object
date datetime64[ns]
ints object
bools object
dtype: object
Specify dtypes for conversion:
In [252]: pd.read_json("test.json", dtype={"A": "float32", "bools": "int8"}).dtypes
Out[252]:
A float32
B float64
date datetime64[ns]
ints int64
bools int8
dtype: object
Preserve string indices:
In [253]: from io import StringIO
In [254]: si = pd.DataFrame(
.....: np.zeros((4, 4)), columns=list(range(4)), index=[str(i) for i in range(4)]
.....: )
.....:
In [255]: si
Out[255]:
0 1 2 3
0 0.0 0.0 0.0 0.0
1 0.0 0.0 0.0 0.0
2 0.0 0.0 0.0 0.0
3 0.0 0.0 0.0 0.0
In [256]: si.index
Out[256]: Index(['0', '1', '2', '3'], dtype='object')
In [257]: si.columns
Out[257]: Index([0, 1, 2, 3], dtype='int64')
In [258]: json = si.to_json()
In [259]: sij = pd.read_json(StringIO(json), convert_axes=False)
In [260]: sij
Out[260]:
0 1 2 3
0 0 0 0 0
1 0 0 0 0
2 0 0 0 0
3 0 0 0 0
In [261]: sij.index
Out[261]: Index(['0', '1', '2', '3'], dtype='object')
In [262]: sij.columns
Out[262]: Index(['0', '1', '2', '3'], dtype='object')
Dates written in nanoseconds need to be read back in nanoseconds:
In [263]: from io import StringIO
In [264]: json = dfj2.to_json(date_format="iso", date_unit="ns")
# Try to parse timestamps as milliseconds -> Won't Work
In [265]: dfju = pd.read_json(StringIO(json), date_unit="ms")
In [266]: dfju
Out[266]:
A B date ints bools
2013-01-01 -0.121306 -0.097883 2013-01-01 0 True
2013-01-02 0.695775 0.341734 2013-01-01 1 True
2013-01-03 0.959726 -1.110336 2013-01-01 2 True
2013-01-04 -0.619976 0.149748 2013-01-01 3 True
2013-01-05 -0.732339 0.687738 2013-01-01 4 True
# Let pandas detect the correct precision
In [267]: dfju = pd.read_json(StringIO(json))
In [268]: dfju
Out[268]:
A B date ints bools
2013-01-01 -0.121306 -0.097883 2013-01-01 0 True
2013-01-02 0.695775 0.341734 2013-01-01 1 True
2013-01-03 0.959726 -1.110336 2013-01-01 2 True
2013-01-04 -0.619976 0.149748 2013-01-01 3 True
2013-01-05 -0.732339 0.687738 2013-01-01 4 True
# Or specify that all timestamps are in nanoseconds
In [269]: dfju = pd.read_json(StringIO(json), date_unit="ns")
In [270]: dfju
Out[270]:
A B date ints bools
2013-01-01 -0.121306 -0.097883 2013-01-01 0 True
2013-01-02 0.695775 0.341734 2013-01-01 1 True
2013-01-03 0.959726 -1.110336 2013-01-01 2 True
2013-01-04 -0.619976 0.149748 2013-01-01 3 True
2013-01-05 -0.732339 0.687738 2013-01-01 4 True
By setting the dtype_backend
argument you can control the default dtypes used for the resulting DataFrame.
In [271]: data = (
.....: '{"a":{"0":1,"1":3},"b":{"0":2.5,"1":4.5},"c":{"0":true,"1":false},"d":{"0":"a","1":"b"},'
.....: '"e":{"0":null,"1":6.0},"f":{"0":null,"1":7.5},"g":{"0":null,"1":true},"h":{"0":null,"1":"a"},'
.....: '"i":{"0":"12-31-2019","1":"12-31-2019"},"j":{"0":null,"1":null}}'
.....: )
.....:
In [272]: df = pd.read_json(StringIO(data), dtype_backend="pyarrow")
In [273]: df
Out[273]:
a b c d e f g h i j
0 1 2.5 True a <NA> <NA> <NA> <NA> 12-31-2019 None
1 3 4.5 False b 6 7.5 True a 12-31-2019 None
In [274]: df.dtypes
Out[274]:
a int64[pyarrow]
b double[pyarrow]
c bool[pyarrow]
d string[pyarrow]
e int64[pyarrow]
f double[pyarrow]
g bool[pyarrow]
h string[pyarrow]
i string[pyarrow]
j null[pyarrow]
dtype: object
Normalization#
pandas provides a utility function to take a dict or list of dicts and normalize this semi-structured data into a flat table.
In [275]: data = [
.....: {"id": 1, "name": {"first": "Coleen", "last": "Volk"}},
.....: {"name": {"given": "Mark", "family": "Regner"}},
.....: {"id": 2, "name": "Faye Raker"},
.....: ]
.....:
In [276]: pd.json_normalize(data)
Out[276]:
id name.first name.last name.given name.family name
0 1.0 Coleen Volk NaN NaN NaN
1 NaN NaN NaN Mark Regner NaN
2 2.0 NaN NaN NaN NaN Faye Raker
In [277]: data = [
.....: {
.....: "state": "Florida",
.....: "shortname": "FL",
.....: "info": {"governor": "Rick Scott"},
.....: "county": [
.....: {"name": "Dade", "population": 12345},
.....: {"name": "Broward", "population": 40000},
.....: {"name": "Palm Beach", "population": 60000},
.....: ],
.....: },
.....: {
.....: "state": "Ohio",
.....: "shortname": "OH",
.....: "info": {"governor": "John Kasich"},
.....: "county": [
.....: {"name": "Summit", "population": 1234},
.....: {"name": "Cuyahoga", "population": 1337},
.....: ],
.....: },
.....: ]
.....:
In [278]: pd.json_normalize(data, "county", ["state", "shortname", ["info", "governor"]])
Out[278]:
name population state shortname info.governor
0 Dade 12345 Florida FL Rick Scott
1 Broward 40000 Florida FL Rick Scott
2 Palm Beach 60000 Florida FL Rick Scott
3 Summit 1234 Ohio OH John Kasich
4 Cuyahoga 1337 Ohio OH John Kasich
The max_level parameter provides more control over which level to end normalization. With max_level=1 the following snippet normalizes until 1st nesting level of the provided dict.
In [279]: data = [
.....: {
.....: "CreatedBy": {"Name": "User001"},
.....: "Lookup": {
.....: "TextField": "Some text",
.....: "UserField": {"Id": "ID001", "Name": "Name001"},
.....: },
.....: "Image": {"a": "b"},
.....: }
.....: ]
.....:
In [280]: pd.json_normalize(data, max_level=1)
Out[280]:
CreatedBy.Name Lookup.TextField Lookup.UserField Image.a
0 User001 Some text {'Id': 'ID001', 'Name': 'Name001'} b
Line delimited json#
pandas is able to read and write line-delimited json files that are common in data processing pipelines using Hadoop or Spark.
For line-delimited json files, pandas can also return an iterator which reads in chunksize
lines at a time. This can be useful for large files or to read from a stream.
In [281]: from io import StringIO
In [282]: jsonl = """
.....: {"a": 1, "b": 2}
.....: {"a": 3, "b": 4}
.....: """
.....:
In [283]: df = pd.read_json(StringIO(jsonl), lines=True)
In [284]: df
Out[284]:
a b
0 1 2
1 3 4
In [285]: df.to_json(orient="records", lines=True)
Out[285]: '{"a":1,"b":2}\n{"a":3,"b":4}\n'
# reader is an iterator that returns ``chunksize`` lines each iteration
In [286]: with pd.read_json(StringIO(jsonl), lines=True, chunksize=1) as reader:
.....: reader
.....: for chunk in reader:
.....: print(chunk)
.....:
Empty DataFrame
Columns: []
Index: []
a b
0 1 2
a b
1 3 4
Line-limited json can also be read using the pyarrow reader by specifying engine="pyarrow"
.
In [287]: from io import BytesIO
In [288]: df = pd.read_json(BytesIO(jsonl.encode()), lines=True, engine="pyarrow")
In [289]: df
Out[289]:
a b
0 1 2
1 3 4
Added in version 2.0.0.
Table schema#
Table Schema is a spec for describing tabular datasets as a JSON
object. The JSON includes information on the field names, types, and
other attributes. You can use the orient table
to build
a JSON string with two fields, schema
and data
.
In [290]: df = pd.DataFrame(
.....: {
.....: "A": [1, 2, 3],
.....: "B": ["a", "b", "c"],
.....: "C": pd.date_range("2016-01-01", freq="D", periods=3),
.....: },
.....: index=pd.Index(range(3), name="idx"),
.....: )
.....:
In [291]: df
Out[291]:
A B C
idx
0 1 a 2016-01-01
1 2 b 2016-01-02
2 3 c 2016-01-03
In [292]: df.to_json(orient="table", date_format="iso")
Out[292]: '{"schema":{"fields":[{"name":"idx","type":"integer"},{"name":"A","type":"integer"},{"name":"B","type":"string"},{"name":"C","type":"datetime"}],"primaryKey":["idx"],"pandas_version":"1.4.0"},"data":[{"idx":0,"A":1,"B":"a","C":"2016-01-01T00:00:00.000"},{"idx":1,"A":2,"B":"b","C":"2016-01-02T00:00:00.000"},{"idx":2,"A":3,"B":"c","C":"2016-01-03T00:00:00.000"}]}'
The schema
field contains the fields
key, which itself contains
a list of column name to type pairs, including the Index
or MultiIndex
(see below for a list of types).
The schema
field also contains a primaryKey
field if the (Multi)index
is unique.
The second field, data
, contains the serialized data with the records
orient.
The index is included, and any datetimes are ISO 8601 formatted, as required
by the Table Schema spec.
The full list of types supported are described in the Table Schema spec. This table shows the mapping from pandas types:
pandas type |
Table Schema type |
---|---|
int64 |
integer |
float64 |
number |
bool |
boolean |
datetime64[ns] |
datetime |
timedelta64[ns] |
duration |
categorical |
any |
object |
str |
A few notes on the generated table schema:
The
schema
object contains apandas_version
field. This contains the version of pandas’ dialect of the schema, and will be incremented with each revision.All dates are converted to UTC when serializing. Even timezone naive values, which are treated as UTC with an offset of 0.
In [293]: from pandas.io.json import build_table_schema In [294]: s = pd.Series(pd.date_range("2016", periods=4)) In [295]: build_table_schema(s) Out[295]: {'fields': [{'name': 'index', 'type': 'integer'}, {'name': 'values', 'type': 'datetime'}], 'primaryKey': ['index'], 'pandas_version': '1.4.0'}
datetimes with a timezone (before serializing), include an additional field
tz
with the time zone name (e.g.'US/Central'
).In [296]: s_tz = pd.Series(pd.date_range("2016", periods=12, tz="US/Central")) In [297]: build_table_schema(s_tz) Out[297]: {'fields': [{'name': 'index', 'type': 'integer'}, {'name': 'values', 'type': 'datetime', 'tz': 'US/Central'}], 'primaryKey': ['index'], 'pandas_version': '1.4.0'}
Periods are converted to timestamps before serialization, and so have the same behavior of being converted to UTC. In addition, periods will contain and additional field
freq
with the period’s frequency, e.g.'A-DEC'
.In [298]: s_per = pd.Series(1, index=pd.period_range("2016", freq="Y-DEC", periods=4)) In [299]: build_table_schema(s_per) Out[299]: {'fields': [{'name': 'index', 'type': 'datetime', 'freq': 'YE-DEC'}, {'name': 'values', 'type': 'integer'}], 'primaryKey': ['index'], 'pandas_version': '1.4.0'}
Categoricals use the
any
type and anenum
constraint listing the set of possible values. Additionally, anordered
field is included:In [300]: s_cat = pd.Series(pd.Categorical(["a", "b", "a"])) In [301]: build_table_schema(s_cat) Out[301]: {'fields': [{'name': 'index', 'type': 'integer'}, {'name': 'values', 'type': 'any', 'constraints': {'enum': ['a', 'b']}, 'ordered': False}], 'primaryKey': ['index'], 'pandas_version': '1.4.0'}
A
primaryKey
field, containing an array of labels, is included if the index is unique:In [302]: s_dupe = pd.Series([1, 2], index=[1, 1]) In [303]: build_table_schema(s_dupe) Out[303]: {'fields': [{'name': 'index', 'type': 'integer'}, {'name': 'values', 'type': 'integer'}], 'pandas_version': '1.4.0'}
The
primaryKey
behavior is the same with MultiIndexes, but in this case theprimaryKey
is an array:In [304]: s_multi = pd.Series(1, index=pd.MultiIndex.from_product([("a", "b"), (0, 1)])) In [305]: build_table_schema(s_multi) Out[305]: {'fields': [{'name': 'level_0', 'type': 'string'}, {'name': 'level_1', 'type': 'integer'}, {'name': 'values', 'type': 'integer'}], 'primaryKey': FrozenList(['level_0', 'level_1']), 'pandas_version': '1.4.0'}
The default naming roughly follows these rules:
For series, the
object.name
is used. If that’s none, then the name isvalues
For
DataFrames
, the stringified version of the column name is usedFor
Index
(notMultiIndex
),index.name
is used, with a fallback toindex
if that is None.For
MultiIndex
,mi.names
is used. If any level has no name, thenlevel_<i>
is used.
read_json
also accepts orient='table'
as an argument. This allows for
the preservation of metadata such as dtypes and index names in a
round-trippable manner.
In [306]: df = pd.DataFrame(
.....: {
.....: "foo": [1, 2, 3, 4],
.....: "bar": ["a", "b", "c", "d"],
.....: "baz": pd.date_range("2018-01-01", freq="D", periods=4),
.....: "qux": pd.Categorical(["a", "b", "c", "c"]),
.....: },
.....: index=pd.Index(range(4), name="idx"),
.....: )
.....:
In [307]: df
Out[307]:
foo bar baz qux
idx
0 1 a 2018-01-01 a
1 2 b 2018-01-02 b
2 3 c 2018-01-03 c
3 4 d 2018-01-04 c
In [308]: df.dtypes
Out[308]:
foo int64
bar object
baz datetime64[ns]
qux category
dtype: object
In [309]: df.to_json("test.json", orient="table")
In [310]: new_df = pd.read_json("test.json", orient="table")
In [311]: new_df
Out[311]:
foo bar baz qux
idx
0 1 a 2018-01-01 a
1 2 b 2018-01-02 b
2 3 c 2018-01-03 c
3 4 d 2018-01-04 c
In [312]: new_df.dtypes
Out[312]:
foo int64
bar object
baz datetime64[ns]
qux category
dtype: object
Please note that the literal string ‘index’ as the name of an Index
is not round-trippable, nor are any names beginning with 'level_'
within a
MultiIndex
. These are used by default in DataFrame.to_json()
to
indicate missing values and the subsequent read cannot distinguish the intent.
In [313]: df.index.name = "index"
In [314]: df.to_json("test.json", orient="table")
In [315]: new_df = pd.read_json("test.json", orient="table")
In [316]: print(new_df.index.name)
None
When using orient='table'
along with user-defined ExtensionArray
,
the generated schema will contain an additional extDtype
key in the respective
fields
element. This extra key is not standard but does enable JSON roundtrips
for extension types (e.g. read_json(df.to_json(orient="table"), orient="table")
).
The extDtype
key carries the name of the extension, if you have properly registered
the ExtensionDtype
, pandas will use said name to perform a lookup into the registry
and re-convert the serialized data into your custom dtype.
HTML#
Reading HTML content#
Warning
We highly encourage you to read the HTML Table Parsing gotchas below regarding the issues surrounding the BeautifulSoup4/html5lib/lxml parsers.
The top-level read_html()
function can accept an HTML
string/file/URL and will parse HTML tables into list of pandas DataFrames
.
Let’s look at a few examples.
Note
read_html
returns a list
of DataFrame
objects, even if there is
only a single table contained in the HTML content.
Read a URL with no options:
In [320]: url = "https://www.fdic.gov/resources/resolutions/bank-failures/failed-bank-list"
In [321]: pd.read_html(url)
Out[321]:
[ Bank NameBank CityCity StateSt ... Acquiring InstitutionAI Closing DateClosing FundFund
0 Almena State Bank Almena KS ... Equity Bank October 23, 2020 10538
1 First City Bank of Florida Fort Walton Beach FL ... United Fidelity Bank, fsb October 16, 2020 10537
2 The First State Bank Barboursville WV ... MVB Bank, Inc. April 3, 2020 10536
3 Ericson State Bank Ericson NE ... Farmers and Merchants Bank February 14, 2020 10535
4 City National Bank of New Jersey Newark NJ ... Industrial Bank November 1, 2019 10534
.. ... ... ... ... ... ... ...
558 Superior Bank, FSB Hinsdale IL ... Superior Federal, FSB July 27, 2001 6004
559 Malta National Bank Malta OH ... North Valley Bank May 3, 2001 4648
560 First Alliance Bank & Trust Co. Manchester NH ... Southern New Hampshire Bank & Trust February 2, 2001 4647
561 National State Bank of Metropolis Metropolis IL ... Banterra Bank of Marion December 14, 2000 4646
562 Bank of Honolulu Honolulu HI ... Bank of the Orient October 13, 2000 4645
[563 rows x 7 columns]]
Note
The data from the above URL changes every Monday so the resulting data above may be slightly different.
Read a URL while passing headers alongside the HTTP request:
In [322]: url = 'https://www.sump.org/notes/request/' # HTTP request reflector
In [323]: pd.read_html(url)
Out[323]:
[ 0 1
0 Remote Socket: 51.15.105.256:51760
1 Protocol Version: HTTP/1.1
2 Request Method: GET
3 Request URI: /notes/request/
4 Request Query: NaN,
0 Accept-Encoding: identity
1 Host: www.sump.org
2 User-Agent: Python-urllib/3.8
3 Connection: close]
In [324]: headers = {
In [325]: 'User-Agent':'Mozilla Firefox v14.0',
In [326]: 'Accept':'application/json',
In [327]: 'Connection':'keep-alive',
In [328]: 'Auth':'Bearer 2*/f3+fe68df*4'
In [329]: }
In [340]: pd.read_html(url, storage_options=headers)
Out[340]:
[ 0 1
0 Remote Socket: 51.15.105.256:51760
1 Protocol Version: HTTP/1.1
2 Request Method: GET
3 Request URI: /notes/request/
4 Request Query: NaN,
0 User-Agent: Mozilla Firefox v14.0
1 AcceptEncoding: gzip, deflate, br
2 Accept: application/json
3 Connection: keep-alive
4 Auth: Bearer 2*/f3+fe68df*4]
Note
We see above that the headers we passed are reflected in the HTTP request.
Read in the content of the file from the above URL and pass it to read_html
as a string:
In [317]: html_str = """
.....: <table>
.....: <tr>
.....: <th>A</th>
.....: <th colspan="1">B</th>
.....: <th rowspan="1">C</th>
.....: </tr>
.....: <tr>
.....: <td>a</td>
.....: <td>b</td>
.....: <td>c</td>
.....: </tr>
.....: </table>
.....: """
.....:
In [318]: with open("tmp.html", "w") as f:
.....: f.write(html_str)
.....:
In [319]: df = pd.read_html("tmp.html")
In [320]: df[0]
Out[320]:
A B C
0 a b c
You can even pass in an instance of StringIO
if you so desire:
In [321]: dfs = pd.read_html(StringIO(html_str))
In [322]: dfs[0]
Out[322]:
A B C
0 a b c
Note
The following examples are not run by the IPython evaluator due to the fact that having so many network-accessing functions slows down the documentation build. If you spot an error or an example that doesn’t run, please do not hesitate to report it over on pandas GitHub issues page.
Read a URL and match a table that contains specific text:
match = "Metcalf Bank"
df_list = pd.read_html(url, match=match)
Specify a header row (by default <th>
or <td>
elements located within a
<thead>
are used to form the column index, if multiple rows are contained within
<thead>
then a MultiIndex is created); if specified, the header row is taken
from the data minus the parsed header elements (<th>
elements).
dfs = pd.read_html(url, header=0)
Specify an index column:
dfs = pd.read_html(url, index_col=0)
Specify a number of rows to skip:
dfs = pd.read_html(url, skiprows=0)
Specify a number of rows to skip using a list (range
works
as well):
dfs = pd.read_html(url, skiprows=range(2))
Specify an HTML attribute:
dfs1 = pd.read_html(url, attrs={"id": "table"})
dfs2 = pd.read_html(url, attrs={"class": "sortable"})
print(np.array_equal(dfs1[0], dfs2[0])) # Should be True
Specify values that should be converted to NaN:
dfs = pd.read_html(url, na_values=["No Acquirer"])
Specify whether to keep the default set of NaN values:
dfs = pd.read_html(url, keep_default_na=False)
Specify converters for columns. This is useful for numerical text data that has leading zeros. By default columns that are numerical are cast to numeric types and the leading zeros are lost. To avoid this, we can convert these columns to strings.
url_mcc = "https://en.wikipedia.org/wiki/Mobile_country_code?oldid=899173761"
dfs = pd.read_html(
url_mcc,
match="Telekom Albania",
header=0,
converters={"MNC": str},
)
Use some combination of the above:
dfs = pd.read_html(url, match="Metcalf Bank", index_col=0)
Read in pandas to_html
output (with some loss of floating point precision):
df = pd.DataFrame(np.random.randn(2, 2))
s = df.to_html(float_format="{0:.40g}".format)
dfin = pd.read_html(s, index_col=0)
The lxml
backend will raise an error on a failed parse if that is the only
parser you provide. If you only have a single parser you can provide just a
string, but it is considered good practice to pass a list with one string if,
for example, the function expects a sequence of strings. You may use:
dfs = pd.read_html(url, "Metcalf Bank", index_col=0, flavor=["lxml"])
Or you could pass flavor='lxml'
without a list:
dfs = pd.read_html(url, "Metcalf Bank", index_col=0, flavor="lxml")
However, if you have bs4 and html5lib installed and pass None
or ['lxml',
'bs4']
then the parse will most likely succeed. Note that as soon as a parse
succeeds, the function will return.
dfs = pd.read_html(url, "Metcalf Bank", index_col=0, flavor=["lxml", "bs4"])
Links can be extracted from cells along with the text using extract_links="all"
.
In [323]: html_table = """
.....: <table>
.....: <tr>
.....: <th>GitHub</th>
.....: </tr>
.....: <tr>
.....: <td><a href="https://github.com/pandas-dev/pandas">pandas</a></td>
.....: </tr>
.....: </table>
.....: """
.....:
In [324]: df = pd.read_html(
.....: StringIO(html_table),
.....: extract_links="all"
.....: )[0]
.....:
In [325]: df
Out[325]:
(GitHub, None)
0 (pandas, https://github.com/pandas-dev/pandas)
In [326]: df[("GitHub", None)]
Out[326]:
0 (pandas, https://github.com/pandas-dev/pandas)
Name: (GitHub, None), dtype: object
In [327]: df[("GitHub", None)].str[1]
Out[327]:
0 https://github.com/pandas-dev/pandas
Name: (GitHub, None), dtype: object
Added in version 1.5.0.
Writing to HTML files#
DataFrame
objects have 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.
Note
Not all of the possible options for DataFrame.to_html
are shown here for
brevity’s sake. See DataFrame.to_html()
for the
full set of options.
Note
In an HTML-rendering supported environment like a Jupyter Notebook, display(HTML(...))`
will render the raw HTML into the environment.
In [328]: from IPython.display import display, HTML
In [329]: df = pd.DataFrame(np.random.randn(2, 2))
In [330]: df
Out[330]:
0 1
0 -0.345352 1.314232
1 0.690579 0.995761
In [331]: html = df.to_html()
In [332]: print(html) # raw html
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>0</th>
<th>1</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>-0.345352</td>
<td>1.314232</td>
</tr>
<tr>
<th>1</th>
<td>0.690579</td>
<td>0.995761</td>
</tr>
</tbody>
</table>
In [333]: display(HTML(html))
<IPython.core.display.HTML object>
The columns
argument will limit the columns shown:
In [334]: html = df.to_html(columns=[0])
In [335]: print(html)
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>0</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>-0.345352</td>
</tr>
<tr>
<th>1</th>
<td>0.690579</td>
</tr>
</tbody>
</table>
In [336]: display(HTML(html))
<IPython.core.display.HTML object>
float_format
takes a Python callable to control the precision of floating
point values:
In [337]: html = df.to_html(float_format="{0:.10f}".format)
In [338]: print(html)
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>0</th>
<th>1</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>-0.3453521949</td>
<td>1.3142323796</td>
</tr>
<tr>
<th>1</th>
<td>0.6905793352</td>
<td>0.9957609037</td>
</tr>
</tbody>
</table>
In [339]: display(HTML(html))
<IPython.core.display.HTML object>
bold_rows
will make the row labels bold by default, but you can turn that
off:
In [340]: html = df.to_html(bold_rows=False)
In [341]: print(html)
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>0</th>
<th>1</th>
</tr>
</thead>
<tbody>
<tr>
<td>0</td>
<td>-0.345352</td>
<td>1.314232</td>
</tr>
<tr>
<td>1</td>
<td>0.690579</td>
<td>0.995761</td>
</tr>
</tbody>
</table>
In [342]: display(HTML(html))
<IPython.core.display.HTML object>
The classes
argument provides the ability to give the resulting HTML
table CSS classes. Note that these classes are appended to the existing
'dataframe'
class.
In [343]: print(df.to_html(classes=["awesome_table_class", "even_more_awesome_class"]))
<table border="1" class="dataframe awesome_table_class even_more_awesome_class">
<thead>
<tr style="text-align: right;">
<th></th>
<th>0</th>
<th>1</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>-0.345352</td>
<td>1.314232</td>
</tr>
<tr>
<th>1</th>
<td>0.690579</td>
<td>0.995761</td>
</tr>
</tbody>
</table>
The render_links
argument provides the ability to add hyperlinks to cells
that contain URLs.
In [344]: url_df = pd.DataFrame(
.....: {
.....: "name": ["Python", "pandas"],
.....: "url": ["https://www.python.org/", "https://pandas.pydata.org"],
.....: }
.....: )
.....:
In [345]: html = url_df.to_html(render_links=True)
In [346]: print(html)
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>name</th>
<th>url</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>Python</td>
<td><a href="https://www.python.org/" target="_blank">https://www.python.org/</a></td>
</tr>
<tr>
<th>1</th>
<td>pandas</td>
<td><a href="https://pandas.pydata.org" target="_blank">https://pandas.pydata.org</a></td>
</tr>
</tbody>
</table>
In [347]: display(HTML(html))
<IPython.core.display.HTML object>
Finally, the escape
argument allows you to control whether the
“<”, “>” and “&” characters escaped in the resulting HTML (by default it is
True
). So to get the HTML without escaped characters pass escape=False
In [348]: df = pd.DataFrame({"a": list("&<>"), "b": np.random.randn(3)})
Escaped:
In [349]: html = df.to_html()
In [350]: print(html)
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>a</th>
<th>b</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>&</td>
<td>2.396780</td>
</tr>
<tr>
<th>1</th>
<td><</td>
<td>0.014871</td>
</tr>
<tr>
<th>2</th>
<td>></td>
<td>3.357427</td>
</tr>
</tbody>
</table>
In [351]: display(HTML(html))
<IPython.core.display.HTML object>
Not escaped:
In [352]: html = df.to_html(escape=False)
In [353]: print(html)
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>a</th>
<th>b</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>&</td>
<td>2.396780</td>
</tr>
<tr>
<th>1</th>
<td><</td>
<td>0.014871</td>
</tr>
<tr>
<th>2</th>
<td>></td>
<td>3.357427</td>
</tr>
</tbody>
</table>
In [354]: display(HTML(html))
<IPython.core.display.HTML object>
Note
Some browsers may not show a difference in the rendering of the previous two HTML tables.
HTML Table Parsing Gotchas#
There are some versioning issues surrounding the libraries that are used to
parse HTML tables in the top-level pandas io function read_html
.
Issues with lxml
Benefits
Drawbacks
lxml does not make any guarantees about the results of its parse unless it is given strictly valid markup.
In light of the above, we have chosen to allow you, the user, to use the lxml backend, but this backend will use html5lib if lxml fails to parse
It is therefore highly recommended that you install both BeautifulSoup4 and html5lib, so that you will still get a valid result (provided everything else is valid) even if lxml fails.
Issues with BeautifulSoup4 using lxml as a backend
The above issues hold here as well since BeautifulSoup4 is essentially just a wrapper around a parser backend.
Issues with BeautifulSoup4 using html5lib as a backend
Benefits
html5lib is far more lenient than lxml and consequently deals with real-life markup in a much saner way rather than just, e.g., dropping an element without notifying you.
html5lib generates valid HTML5 markup from invalid markup automatically. This is extremely important for parsing HTML tables, since it guarantees a valid document. However, that does NOT mean that it is “correct”, since the process of fixing markup does not have a single definition.
html5lib is pure Python and requires no additional build steps beyond its own installation.
Drawbacks
The biggest drawback to using html5lib is that it is slow as molasses. However consider the fact that many tables on the web are not big enough for the parsing algorithm runtime to matter. It is more likely that the bottleneck will be in the process of reading the raw text from the URL over the web, i.e., IO (input-output). For very large tables, this might not be true.
LaTeX#
Added in version 1.3.0.
Currently there are no methods to read from LaTeX, only output methods.
Writing to LaTeX files#
Note
DataFrame and Styler objects currently have a to_latex
method. We recommend
using the Styler.to_latex() method
over DataFrame.to_latex() due to the former’s greater flexibility with
conditional styling, and the latter’s possible future deprecation.
Review the documentation for Styler.to_latex, which gives examples of conditional styling and explains the operation of its keyword arguments.
For simple application the following pattern is sufficient.
In [355]: df = pd.DataFrame([[1, 2], [3, 4]], index=["a", "b"], columns=["c", "d"])
In [356]: print(df.style.to_latex())
\begin{tabular}{lrr}
& c & d \\
a & 1 & 2 \\
b & 3 & 4 \\
\end{tabular}
To format values before output, chain the Styler.format method.
In [357]: print(df.style.format("€ {}").to_latex())
\begin{tabular}{lrr}
& c & d \\
a & € 1 & € 2 \\
b & € 3 & € 4 \\
\end{tabular}
XML#
Reading XML#
Added in version 1.3.0.
The top-level read_xml()
function can accept an XML
string/file/URL and will parse nodes and attributes into a pandas DataFrame
.
Note
Since there is no standard XML structure where design types can vary in
many ways, read_xml
works best with flatter, shallow versions. If
an XML document is deeply nested, use the stylesheet
feature to
transform XML into a flatter version.
Let’s look at a few examples.
Read an XML string:
In [358]: from io import StringIO
In [359]: xml = """<?xml version="1.0" encoding="UTF-8"?>
.....: <bookstore>
.....: <book category="cooking">
.....: <title lang="en">Everyday Italian</title>
.....: <author>Giada De Laurentiis</author>
.....: <year>2005</year>
.....: <price>30.00</price>
.....: </book>
.....: <book category="children">
.....: <title lang="en">Harry Potter</title>
.....: <author>J K. Rowling</author>
.....: <year>2005</year>
.....: <price>29.99</price>
.....: </book>
.....: <book category="web">
.....: <title lang="en">Learning XML</title>
.....: <author>Erik T. Ray</author>
.....: <year>2003</year>
.....: <price>39.95</price>
.....: </book>
.....: </bookstore>"""
.....:
In [360]: df = pd.read_xml(StringIO(xml))
In [361]: df
Out[361]:
category title author year price
0 cooking Everyday Italian Giada De Laurentiis 2005 30.00
1 children Harry Potter J K. Rowling 2005 29.99
2 web Learning XML Erik T. Ray 2003 39.95
Read a URL with no options:
In [362]: df = pd.read_xml("https://www.w3schools.com/xml/books.xml")
In [363]: df
Out[363]:
category title author year price cover
0 cooking Everyday Italian Giada De Laurentiis 2005 30.00 None
1 children Harry Potter J K. Rowling 2005 29.99 None
2 web XQuery Kick Start Vaidyanathan Nagarajan 2003 49.99 None
3 web Learning XML Erik T. Ray 2003 39.95 paperback
Read in the content of the “books.xml” file and pass it to read_xml
as a string:
In [364]: file_path = "books.xml"
In [365]: with open(file_path, "w") as f:
.....: f.write(xml)
.....:
In [366]: with open(file_path, "r") as f:
.....: df = pd.read_xml(StringIO(f.read()))
.....:
In [367]: df
Out[367]:
category title author year price
0 cooking Everyday Italian Giada De Laurentiis 2005 30.00
1 children Harry Potter J K. Rowling 2005 29.99
2 web Learning XML Erik T. Ray 2003 39.95
Read in the content of the “books.xml” as instance of StringIO
or
BytesIO
and pass it to read_xml
:
In [368]: with open(file_path, "r") as f:
.....: sio = StringIO(f.read())
.....:
In [369]: df = pd.read_xml(sio)
In [370]: df
Out[370]:
category title author year price
0 cooking Everyday Italian Giada De Laurentiis 2005 30.00
1 children Harry Potter J K. Rowling 2005 29.99
2 web Learning XML Erik T. Ray 2003 39.95
In [371]: with open(file_path, "rb") as f:
.....: bio = BytesIO(f.read())
.....:
In [372]: df = pd.read_xml(bio)
In [373]: df
Out[373]:
category title author year price
0 cooking Everyday Italian Giada De Laurentiis 2005 30.00
1 children Harry Potter J K. Rowling 2005 29.99
2 web Learning XML Erik T. Ray 2003 39.95
Even read XML from AWS S3 buckets such as NIH NCBI PMC Article Datasets providing Biomedical and Life Science Journals:
>>> df = pd.read_xml(
... "s3://pmc-oa-opendata/oa_comm/xml/all/PMC1236943.xml",
... xpath=".//journal-meta",
...)
>>> df
journal-id journal-title issn publisher
0 Cardiovasc Ultrasound Cardiovascular Ultrasound 1476-7120 NaN
With lxml as default parser
, you access the full-featured XML library
that extends Python’s ElementTree API. One powerful tool is ability to query
nodes selectively or conditionally with more expressive XPath:
In [374]: df = pd.read_xml(file_path, xpath="//book[year=2005]")
In [375]: df
Out[375]:
category title author year price
0 cooking Everyday Italian Giada De Laurentiis 2005 30.00
1 children Harry Potter J K. Rowling 2005 29.99
Specify only elements or only attributes to parse:
In [376]: df = pd.read_xml(file_path, elems_only=True)
In [377]: df
Out[377]:
title author year price
0 Everyday Italian Giada De Laurentiis 2005 30.00
1 Harry Potter J K. Rowling 2005 29.99
2 Learning XML Erik T. Ray 2003 39.95
In [378]: df = pd.read_xml(file_path, attrs_only=True)
In [379]: df
Out[379]:
category
0 cooking
1 children
2 web
XML documents can have namespaces with prefixes and default namespaces without
prefixes both of which are denoted with a special attribute xmlns
. In order
to parse by node under a namespace context, xpath
must reference a prefix.
For example, below XML contains a namespace with prefix, doc
, and URI at
https://example.com
. In order to parse doc:row
nodes,
namespaces
must be used.
In [380]: xml = """<?xml version='1.0' encoding='utf-8'?>
.....: <doc:data xmlns:doc="https://example.com">
.....: <doc:row>
.....: <doc:shape>square</doc:shape>
.....: <doc:degrees>360</doc:degrees>
.....: <doc:sides>4.0</doc:sides>
.....: </doc:row>
.....: <doc:row>
.....: <doc:shape>circle</doc:shape>
.....: <doc:degrees>360</doc:degrees>
.....: <doc:sides/>
.....: </doc:row>
.....: <doc:row>
.....: <doc:shape>triangle</doc:shape>
.....: <doc:degrees>180</doc:degrees>
.....: <doc:sides>3.0</doc:sides>
.....: </doc:row>
.....: </doc:data>"""
.....:
In [381]: df = pd.read_xml(StringIO(xml),
.....: xpath="//doc:row",
.....: namespaces={"doc": "https://example.com"})
.....:
In [382]: df
Out[382]:
shape degrees sides
0 square 360 4.0
1 circle 360 NaN
2 triangle 180 3.0
Similarly, an XML document can have a default namespace without prefix. Failing
to assign a temporary prefix will return no nodes and raise a ValueError
.
But assigning any temporary name to correct URI allows parsing by nodes.
In [383]: xml = """<?xml version='1.0' encoding='utf-8'?>
.....: <data xmlns="https://example.com">
.....: <row>
.....: <shape>square</shape>
.....: <degrees>360</degrees>
.....: <sides>4.0</sides>
.....: </row>
.....: <row>
.....: <shape>circle</shape>
.....: <degrees>360</degrees>
.....: <sides/>
.....: </row>
.....: <row>
.....: <shape>triangle</shape>
.....: <degrees>180</degrees>
.....: <sides>3.0</sides>
.....: </row>
.....: </data>"""
.....:
In [384]: df = pd.read_xml(StringIO(xml),
.....: xpath="//pandas:row",
.....: namespaces={"pandas": "https://example.com"})
.....:
In [385]: df
Out[385]:
shape degrees sides
0 square 360 4.0
1 circle 360 NaN
2 triangle 180 3.0
However, if XPath does not reference node names such as default, /*
, then
namespaces
is not required.
Note
Since xpath
identifies the parent of content to be parsed, only immediate
descendants which include child nodes or current attributes are parsed.
Therefore, read_xml
will not parse the text of grandchildren or other
descendants and will not parse attributes of any descendant. To retrieve
lower level content, adjust xpath to lower level. For example,
In [386]: xml = """
.....: <data>
.....: <row>
.....: <shape sides="4">square</shape>
.....: <degrees>360</degrees>
.....: </row>
.....: <row>
.....: <shape sides="0">circle</shape>
.....: <degrees>360</degrees>
.....: </row>
.....: <row>
.....: <shape sides="3">triangle</shape>
.....: <degrees>180</degrees>
.....: </row>
.....: </data>"""
.....:
In [387]: df = pd.read_xml(StringIO(xml), xpath="./row")
In [388]: df
Out[388]:
shape degrees
0 square 360
1 circle 360
2 triangle 180
shows the attribute sides
on shape
element was not parsed as
expected since this attribute resides on the child of row
element
and not row
element itself. In other words, sides
attribute is a
grandchild level descendant of row
element. However, the xpath
targets row
element which covers only its children and attributes.
With lxml as parser, you can flatten nested XML documents with an XSLT script which also can be string/file/URL types. As background, XSLT is a special-purpose language written in a special XML file that can transform original XML documents into other XML, HTML, even text (CSV, JSON, etc.) using an XSLT processor.
For example, consider this somewhat nested structure of Chicago “L” Rides
where station and rides elements encapsulate data in their own sections.
With below XSLT, lxml
can transform original nested document into a flatter
output (as shown below for demonstration) for easier parse into DataFrame
:
In [389]: xml = """<?xml version='1.0' encoding='utf-8'?>
.....: <response>
.....: <row>
.....: <station id="40850" name="Library"/>
.....: <month>2020-09-01T00:00:00</month>
.....: <rides>
.....: <avg_weekday_rides>864.2</avg_weekday_rides>
.....: <avg_saturday_rides>534</avg_saturday_rides>
.....: <avg_sunday_holiday_rides>417.2</avg_sunday_holiday_rides>
.....: </rides>
.....: </row>
.....: <row>
.....: <station id="41700" name="Washington/Wabash"/>
.....: <month>2020-09-01T00:00:00</month>
.....: <rides>
.....: <avg_weekday_rides>2707.4</avg_weekday_rides>
.....: <avg_saturday_rides>1909.8</avg_saturday_rides>
.....: <avg_sunday_holiday_rides>1438.6</avg_sunday_holiday_rides>
.....: </rides>
.....: </row>
.....: <row>
.....: <station id="40380" name="Clark/Lake"/>
.....: <month>2020-09-01T00:00:00</month>
.....: <rides>
.....: <avg_weekday_rides>2949.6</avg_weekday_rides>
.....: <avg_saturday_rides>1657</avg_saturday_rides>
.....: <avg_sunday_holiday_rides>1453.8</avg_sunday_holiday_rides>
.....: </rides>
.....: </row>
.....: </response>"""
.....:
In [390]: xsl = """<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
.....: <xsl:output method="xml" omit-xml-declaration="no" indent="yes"/>
.....: <xsl:strip-space elements="*"/>
.....: <xsl:template match="/response">
.....: <xsl:copy>
.....: <xsl:apply-templates select="row"/>
.....: </xsl:copy>
.....: </xsl:template>
.....: <xsl:template match="row">
.....: <xsl:copy>
.....: <station_id><xsl:value-of select="station/@id"/></station_id>
.....: <station_name><xsl:value-of select="station/@name"/></station_name>
.....: <xsl:copy-of select="month|rides/*"/>
.....: </xsl:copy>
.....: </xsl:template>
.....: </xsl:stylesheet>"""
.....:
In [391]: output = """<?xml version='1.0' encoding='utf-8'?>
.....: <response>
.....: <row>
.....: <station_id>40850</station_id>
.....: <station_name>Library</station_name>
.....: <month>2020-09-01T00:00:00</month>
.....: <avg_weekday_rides>864.2</avg_weekday_rides>
.....: <avg_saturday_rides>534</avg_saturday_rides>
.....: <avg_sunday_holiday_rides>417.2</avg_sunday_holiday_rides>
.....: </row>
.....: <row>
.....: <station_id>41700</station_id>
.....: <station_name>Washington/Wabash</station_name>
.....: <month>2020-09-01T00:00:00</month>
.....: <avg_weekday_rides>2707.4</avg_weekday_rides>
.....: <avg_saturday_rides>1909.8</avg_saturday_rides>
.....: <avg_sunday_holiday_rides>1438.6</avg_sunday_holiday_rides>
.....: </row>
.....: <row>
.....: <station_id>40380</station_id>
.....: <station_name>Clark/Lake</station_name>
.....: <month>2020-09-01T00:00:00</month>
.....: <avg_weekday_rides>2949.6</avg_weekday_rides>
.....: <avg_saturday_rides>1657</avg_saturday_rides>
.....: <avg_sunday_holiday_rides>1453.8</avg_sunday_holiday_rides>
.....: </row>
.....: </response>"""
.....:
In [392]: df = pd.read_xml(StringIO(xml), stylesheet=StringIO(xsl))
In [393]: df
Out[393]:
station_id station_name ... avg_saturday_rides avg_sunday_holiday_rides
0 40850 Library ... 534.0 417.2
1 41700 Washington/Wabash ... 1909.8 1438.6
2 40380 Clark/Lake ... 1657.0 1453.8
[3 rows x 6 columns]
For very large XML files that can range in hundreds of megabytes to gigabytes, pandas.read_xml()
supports parsing such sizeable files using lxml’s iterparse and etree’s iterparse
which are memory-efficient methods to iterate through an XML tree and extract specific elements and attributes.
without holding entire tree in memory.
Added in version 1.5.0.
To use this feature, you must pass a physical XML file path into read_xml
and use the iterparse
argument.
Files should not be compressed or point to online sources but stored on local disk. Also, iterparse
should be
a dictionary where the key is the repeating nodes in document (which become the rows) and the value is a list of
any element or attribute that is a descendant (i.e., child, grandchild) of repeating node. Since XPath is not
used in this method, descendants do not need to share same relationship with one another. Below shows example
of reading in Wikipedia’s very large (12 GB+) latest article data dump.
In [1]: df = pd.read_xml(
... "/path/to/downloaded/enwikisource-latest-pages-articles.xml",
... iterparse = {"page": ["title", "ns", "id"]}
... )
... df
Out[2]:
title ns id
0 Gettysburg Address 0 21450
1 Main Page 0 42950
2 Declaration by United Nations 0 8435
3 Constitution of the United States of America 0 8435
4 Declaration of Independence (Israel) 0 17858
... ... ... ...
3578760 Page:Black cat 1897 07 v2 n10.pdf/17 104 219649
3578761 Page:Black cat 1897 07 v2 n10.pdf/43 104 219649
3578762 Page:Black cat 1897 07 v2 n10.pdf/44 104 219649
3578763 The History of Tom Jones, a Foundling/Book IX 0 12084291
3578764 Page:Shakespeare of Stratford (1926) Yale.djvu/91 104 21450
[3578765 rows x 3 columns]
Writing XML#
Added in version 1.3.0.
DataFrame
objects have an instance method to_xml
which renders the
contents of the DataFrame
as an XML document.
Note
This method does not support special properties of XML including DTD,
CData, XSD schemas, processing instructions, comments, and others.
Only namespaces at the root level is supported. However, stylesheet
allows design changes after initial output.
Let’s look at a few examples.
Write an XML without options:
In [394]: geom_df = pd.DataFrame(
.....: {
.....: "shape": ["square", "circle", "triangle"],
.....: "degrees": [360, 360, 180],
.....: "sides": [4, np.nan, 3],
.....: }
.....: )
.....:
In [395]: print(geom_df.to_xml())
<?xml version='1.0' encoding='utf-8'?>
<data>
<row>
<index>0</index>
<shape>square</shape>
<degrees>360</degrees>
<sides>4.0</sides>
</row>
<row>
<index>1</index>
<shape>circle</shape>
<degrees>360</degrees>
<sides/>
</row>
<row>
<index>2</index>
<shape>triangle</shape>
<degrees>180</degrees>
<sides>3.0</sides>
</row>
</data>
Write an XML with new root and row name:
In [396]: print(geom_df.to_xml(root_name="geometry", row_name="objects"))
<?xml version='1.0' encoding='utf-8'?>
<geometry>
<objects>
<index>0</index>
<shape>square</shape>
<degrees>360</degrees>
<sides>4.0</sides>
</objects>
<objects>
<index>1</index>
<shape>circle</shape>
<degrees>360</degrees>
<sides/>
</objects>
<objects>
<index>2</index>
<shape>triangle</shape>
<degrees>180</degrees>
<sides>3.0</sides>
</objects>
</geometry>
Write an attribute-centric XML:
In [397]: print(geom_df.to_xml(attr_cols=geom_df.columns.tolist()))
<?xml version='1.0' encoding='utf-8'?>
<data>
<row index="0" shape="square" degrees="360" sides="4.0"/>
<row index="1" shape="circle" degrees="360"/>
<row index="2" shape="triangle" degrees="180" sides="3.0"/>
</data>
Write a mix of elements and attributes:
In [398]: print(
.....: geom_df.to_xml(
.....: index=False,
.....: attr_cols=['shape'],
.....: elem_cols=['degrees', 'sides'])
.....: )
.....:
<?xml version='1.0' encoding='utf-8'?>
<data>
<row shape="square">
<degrees>360</degrees>
<sides>4.0</sides>
</row>
<row shape="circle">
<degrees>360</degrees>
<sides/>
</row>
<row shape="triangle">
<degrees>180</degrees>
<sides>3.0</sides>
</row>
</data>
Any DataFrames
with hierarchical columns will be flattened for XML element names
with levels delimited by underscores:
In [399]: ext_geom_df = pd.DataFrame(
.....: {
.....: "type": ["polygon", "other", "polygon"],
.....: "shape": ["square", "circle", "triangle"],
.....: "degrees": [360, 360, 180],
.....: "sides": [4, np.nan, 3],
.....: }
.....: )
.....:
In [400]: pvt_df = ext_geom_df.pivot_table(index='shape',
.....: columns='type',
.....: values=['degrees', 'sides'],
.....: aggfunc='sum')
.....:
In [401]: pvt_df
Out[401]:
degrees sides
type other polygon other polygon
shape
circle 360.0 NaN 0.0 NaN
square NaN 360.0 NaN 4.0
triangle NaN 180.0 NaN 3.0
In [402]: print(pvt_df.to_xml())
<?xml version='1.0' encoding='utf-8'?>
<data>
<row>
<shape>circle</shape>
<degrees_other>360.0</degrees_other>
<degrees_polygon/>
<sides_other>0.0</sides_other>
<sides_polygon/>
</row>
<row>
<shape>square</shape>
<degrees_other/>
<degrees_polygon>360.0</degrees_polygon>
<sides_other/>
<sides_polygon>4.0</sides_polygon>
</row>
<row>
<shape>triangle</shape>
<degrees_other/>
<degrees_polygon>180.0</degrees_polygon>
<sides_other/>
<sides_polygon>3.0</sides_polygon>
</row>
</data>
Write an XML with default namespace:
In [403]: print(geom_df.to_xml(namespaces={"": "https://example.com"}))
<?xml version='1.0' encoding='utf-8'?>
<data xmlns="https://example.com">
<row>
<index>0</index>
<shape>square</shape>
<degrees>360</degrees>
<sides>4.0</sides>
</row>
<row>
<index>1</index>
<shape>circle</shape>
<degrees>360</degrees>
<sides/>
</row>
<row>
<index>2</index>
<shape>triangle</shape>
<degrees>180</degrees>
<sides>3.0</sides>
</row>
</data>
Write an XML with namespace prefix:
In [404]: print(
.....: geom_df.to_xml(namespaces={"doc": "https://example.com"},
.....: prefix="doc")
.....: )
.....:
<?xml version='1.0' encoding='utf-8'?>
<doc:data xmlns:doc="https://example.com">
<doc:row>
<doc:index>0</doc:index>
<doc:shape>square</doc:shape>
<doc:degrees>360</doc:degrees>
<doc:sides>4.0</doc:sides>
</doc:row>
<doc:row>
<doc:index>1</doc:index>
<doc:shape>circle</doc:shape>
<doc:degrees>360</doc:degrees>
<doc:sides/>
</doc:row>
<doc:row>
<doc:index>2</doc:index>
<doc:shape>triangle</doc:shape>
<doc:degrees>180</doc:degrees>
<doc:sides>3.0</doc:sides>
</doc:row>
</doc:data>
Write an XML without declaration or pretty print:
In [405]: print(
.....: geom_df.to_xml(xml_declaration=False,
.....: pretty_print=False)
.....: )
.....:
<data><row><index>0</index><shape>square</shape><degrees>360</degrees><sides>4.0</sides></row><row><index>1</index><shape>circle</shape><degrees>360</degrees><sides/></row><row><index>2</index><shape>triangle</shape><degrees>180</degrees><sides>3.0</sides></row></data>
Write an XML and transform with stylesheet:
In [406]: xsl = """<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
.....: <xsl:output method="xml" omit-xml-declaration="no" indent="yes"/>
.....: <xsl:strip-space elements="*"/>
.....: <xsl:template match="/data">
.....: <geometry>
.....: <xsl:apply-templates select="row"/>
.....: </geometry>
.....: </xsl:template>
.....: <xsl:template match="row">
.....: <object index="{index}">
.....: <xsl:if test="shape!='circle'">
.....: <xsl:attribute name="type">polygon</xsl:attribute>
.....: </xsl:if>
.....: <xsl:copy-of select="shape"/>
.....: <property>
.....: <xsl:copy-of select="degrees|sides"/>
.....: </property>
.....: </object>
.....: </xsl:template>
.....: </xsl:stylesheet>"""
.....:
In [407]: print(geom_df.to_xml(stylesheet=StringIO(xsl)))
<?xml version="1.0"?>
<geometry>
<object index="0" type="polygon">
<shape>square</shape>
<property>
<degrees>360</degrees>
<sides>4.0</sides>
</property>
</object>
<object index="1">
<shape>circle</shape>
<property>
<degrees>360</degrees>
<sides/>
</property>
</object>
<object index="2" type="polygon">
<shape>triangle</shape>
<property>
<degrees>180</degrees>
<sides>3.0</sides>
</property>
</object>
</geometry>
XML Final Notes#
All XML documents adhere to W3C specifications. Both
etree
andlxml
parsers will fail to parse any markup document that is not well-formed or follows XML syntax rules. Do be aware HTML is not an XML document unless it follows XHTML specs. However, other popular markup types including KML, XAML, RSS, MusicML, MathML are compliant XML schemas.For above reason, if your application builds XML prior to pandas operations, use appropriate DOM libraries like
etree
andlxml
to build the necessary document and not by string concatenation or regex adjustments. Always remember XML is a special text file with markup rules.With very large XML files (several hundred MBs to GBs), XPath and XSLT can become memory-intensive operations. Be sure to have enough available RAM for reading and writing to large XML files (roughly about 5 times the size of text).
Because XSLT is a programming language, use it with caution since such scripts can pose a security risk in your environment and can run large or infinite recursive operations. Always test scripts on small fragments before full run.
The etree parser supports all functionality of both
read_xml
andto_xml
except for complex XPath and any XSLT. Though limited in features,etree
is still a reliable and capable parser and tree builder. Its performance may traillxml
to a certain degree for larger files but relatively unnoticeable on small to medium size files.
Excel files#
The read_excel()
method can read Excel 2007+ (.xlsx
) files
using the openpyxl
Python module. Excel 2003 (.xls
) files
can be read using xlrd
. Binary Excel (.xlsb
)
files can be read using pyxlsb
. All formats can be read
using calamine engine.
The to_excel()
instance method is used for
saving a DataFrame
to Excel. Generally the semantics are
similar to working with csv data.
See the cookbook for some advanced strategies.
Note
When engine=None
, the following logic will be used to determine the engine:
If
path_or_buffer
is an OpenDocument format (.odf, .ods, .odt), then odf will be used.Otherwise if
path_or_buffer
is an xls format,xlrd
will be used.Otherwise if
path_or_buffer
is in xlsb format,pyxlsb
will be used.Otherwise
openpyxl
will be used.
Reading Excel files#
In the most basic use-case, read_excel
takes a path to an Excel
file, and the sheet_name
indicating which sheet to parse.
When using the engine_kwargs
parameter, pandas will pass these arguments to the
engine. For this, it is important to know which function pandas is
using internally.
For the engine openpyxl, pandas is using
openpyxl.load_workbook()
to read in (.xlsx
) and (.xlsm
) files.For the engine xlrd, pandas is using
xlrd.open_workbook()
to read in (.xls
) files.For the engine pyxlsb, pandas is using
pyxlsb.open_workbook()
to read in (.xlsb
) files.For the engine odf, pandas is using
odf.opendocument.load()
to read in (.ods
) files.For the engine calamine, pandas is using
python_calamine.load_workbook()
to read in (.xlsx
), (.xlsm
), (.xls
), (.xlsb
), (.ods
) files.
# Returns a DataFrame
pd.read_excel("path_to_file.xls", sheet_name="Sheet1")
ExcelFile
class#
To facilitate working with multiple sheets from the same file, the ExcelFile
class can be used to wrap the file and can be passed into read_excel
There will be a performance benefit for reading multiple sheets as the file is
read into memory only once.
xlsx = pd.ExcelFile("path_to_file.xls")
df = pd.read_excel(xlsx, "Sheet1")
The ExcelFile
class can also be used as a context manager.
with pd.ExcelFile("path_to_file.xls") as xls:
df1 = pd.read_excel(xls, "Sheet1")
df2 = pd.read_excel(xls, "Sheet2")
The sheet_names
property will generate
a list of the sheet names in the file.
The primary use-case for an ExcelFile
is parsing multiple sheets with
different parameters:
data = {}
# For when Sheet1's format differs from Sheet2
with pd.ExcelFile("path_to_file.xls") as xls:
data["Sheet1"] = pd.read_excel(xls, "Sheet1", index_col=None, na_values=["NA"])
data["Sheet2"] = pd.read_excel(xls, "Sheet2", index_col=1)
Note that if the same parsing parameters are used for all sheets, a list
of sheet names can simply be passed to read_excel
with no loss in performance.
# using the ExcelFile class
data = {}
with pd.ExcelFile("path_to_file.xls") as xls:
data["Sheet1"] = pd.read_excel(xls, "Sheet1", index_col=None, na_values=["NA"])
data["Sheet2"] = pd.read_excel(xls, "Sheet2", index_col=None, na_values=["NA"])
# equivalent using the read_excel function
data = pd.read_excel(
"path_to_file.xls", ["Sheet1", "Sheet2"], index_col=None, na_values=["NA"]
)
ExcelFile
can also be called with a xlrd.book.Book
object
as a parameter. This allows the user to control how the excel file is read.
For example, sheets can be loaded on demand by calling xlrd.open_workbook()
with on_demand=True
.
import xlrd
xlrd_book = xlrd.open_workbook("path_to_file.xls", on_demand=True)
with pd.ExcelFile(xlrd_book) as xls:
df1 = pd.read_excel(xls, "Sheet1")
df2 = pd.read_excel(xls, "Sheet2")
Specifying sheets#
Note
The second argument is sheet_name
, not to be confused with ExcelFile.sheet_names
.
Note
An ExcelFile’s attribute sheet_names
provides access to a list of sheets.
The arguments
sheet_name
allows specifying the sheet or sheets to read.The default value for
sheet_name
is 0, indicating to read the first sheetPass a string to refer to the name of a particular sheet in the workbook.
Pass an integer to refer to the index of a sheet. Indices follow Python convention, beginning at 0.
Pass a list of either strings or integers, to return a dictionary of specified sheets.
Pass a
None
to return a dictionary of all available sheets.
# Returns a DataFrame
pd.read_excel("path_to_file.xls", "Sheet1", index_col=None, na_values=["NA"])
Using the sheet index:
# Returns a DataFrame
pd.read_excel("path_to_file.xls", 0, index_col=None, na_values=["NA"])
Using all default values:
# Returns a DataFrame
pd.read_excel("path_to_file.xls")
Using None to get all sheets:
# Returns a dictionary of DataFrames
pd.read_excel("path_to_file.xls", sheet_name=None)
Using a list to get multiple sheets:
# Returns the 1st and 4th sheet, as a dictionary of DataFrames.
pd.read_excel("path_to_file.xls", sheet_name=["Sheet1", 3])
read_excel
can read more than one sheet, by setting sheet_name
to either
a list of sheet names, a list of sheet positions, or None
to read all sheets.
Sheets can be specified by sheet index or sheet name, using an integer or string,
respectively.
Reading a MultiIndex
#
read_excel
can read a MultiIndex
index, by passing a list of columns to index_col
and a MultiIndex
column by passing a list of rows to header
. If either the index
or columns
have serialized level names those will be read in as well by specifying
the rows/columns that make up the levels.
For example, to read in a MultiIndex
index without names:
In [408]: df = pd.DataFrame(
.....: {"a": [1, 2, 3, 4], "b": [5, 6, 7, 8]},
.....: index=pd.MultiIndex.from_product([["a", "b"], ["c", "d"]]),
.....: )
.....:
In [409]: df.to_excel("path_to_file.xlsx")
In [410]: df = pd.read_excel("path_to_file.xlsx", index_col=[0, 1])
In [411]: df
Out[411]:
a b
a c 1 5
d 2 6
b c 3 7
d 4 8
If the index has level names, they will be parsed as well, using the same parameters.
In [412]: df.index = df.index.set_names(["lvl1", "lvl2"])
In [413]: df.to_excel("path_to_file.xlsx")
In [414]: df = pd.read_excel("path_to_file.xlsx", index_col=[0, 1])
In [415]: df
Out[415]:
a b
lvl1 lvl2
a c 1 5
d 2 6
b c 3 7
d 4 8
If the source file has both MultiIndex
index and columns, lists specifying each
should be passed to index_col
and header
:
In [416]: df.columns = pd.MultiIndex.from_product([["a"], ["b", "d"]], names=["c1", "c2"])
In [417]: df.to_excel("path_to_file.xlsx")
In [418]: df = pd.read_excel("path_to_file.xlsx", index_col=[0, 1], header=[0, 1])
In [419]: df
Out[419]:
c1 a
c2 b d
lvl1 lvl2
a c 1 5
d 2 6
b c 3 7
d 4 8
Missing values in columns specified in index_col
will be forward filled to
allow roundtripping with to_excel
for merged_cells=True
. To avoid forward
filling the missing values use set_index
after reading the data instead of
index_col
.
Parsing specific columns#
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. read_excel
takes
a usecols
keyword to allow you to specify a subset of columns to parse.
You can specify a comma-delimited set of Excel columns and ranges as a string:
pd.read_excel("path_to_file.xls", "Sheet1", usecols="A,C:E")
If usecols
is a list of integers, then it is assumed to be the file column
indices to be parsed.
pd.read_excel("path_to_file.xls", "Sheet1", usecols=[0, 2, 3])
Element order is ignored, so usecols=[0, 1]
is the same as [1, 0]
.
If usecols
is a list of strings, it is assumed that each string corresponds
to a column name provided either by the user in names
or inferred from the
document header row(s). Those strings define which columns will be parsed:
pd.read_excel("path_to_file.xls", "Sheet1", usecols=["foo", "bar"])
Element order is ignored, so usecols=['baz', 'joe']
is the same as ['joe', 'baz']
.
If usecols
is callable, the callable function will be evaluated against
the column names, returning names where the callable function evaluates to True
.
pd.read_excel("path_to_file.xls", "Sheet1", usecols=lambda x: x.isalpha())
Parsing dates#
Datetime-like values are normally automatically converted to the appropriate
dtype when reading the excel file. But if you have a column of strings that
look like dates (but are not actually formatted as dates in excel), you can
use the parse_dates
keyword to parse those strings to datetimes:
pd.read_excel("path_to_file.xls", "Sheet1", parse_dates=["date_strings"])
Cell converters#
It is possible to transform the contents of Excel cells via the converters
option. For instance, to convert a column to boolean:
pd.read_excel("path_to_file.xls", "Sheet1", converters={"MyBools": bool})
This options handles missing values and treats exceptions in the converters as missing data. Transformations are applied cell by cell rather than to the column as a whole, so the array dtype is not guaranteed. For instance, a column of integers with missing values cannot be transformed to an array with integer dtype, because NaN is strictly a float. You can manually mask missing data to recover integer dtype:
def cfun(x):
return int(x) if x else -1
pd.read_excel("path_to_file.xls", "Sheet1", converters={"MyInts": cfun})
Dtype specifications#
As an alternative to converters, the type for an entire column can
be specified using the dtype
keyword, which takes a dictionary
mapping column names to types. To interpret data with
no type inference, use the type str
or object
.
pd.read_excel("path_to_file.xls", dtype={"MyInts": "int64", "MyText": str})
Writing Excel files#
Writing Excel files to disk#
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:
df.to_excel("path_to_file.xlsx", sheet_name="Sheet1")
Files with a
.xlsx
extension will be written using xlsxwriter
(if available) or
openpyxl
.
The DataFrame
will be written in a way that tries to mimic the REPL output.
The index_label
will be placed in the second
row instead of the first. You can place it in the first row by setting the
merge_cells
option in to_excel()
to False
:
df.to_excel("path_to_file.xlsx", index_label="label", merge_cells=False)
In order to write separate DataFrames
to separate sheets in a single Excel file,
one can pass an ExcelWriter
.
with pd.ExcelWriter("path_to_file.xlsx") as writer:
df1.to_excel(writer, sheet_name="Sheet1")
df2.to_excel(writer, sheet_name="Sheet2")
When using the engine_kwargs
parameter, pandas will pass these arguments to the
engine. For this, it is important to know which function pandas is using internally.
For the engine openpyxl, pandas is using
openpyxl.Workbook()
to create a new sheet andopenpyxl.load_workbook()
to append data to an existing sheet. The openpyxl engine writes to (.xlsx
) and (.xlsm
) files.For the engine xlsxwriter, pandas is using
xlsxwriter.Workbook()
to write to (.xlsx
) files.For the engine odf, pandas is using
odf.opendocument.OpenDocumentSpreadsheet()
to write to (.ods
) files.
Writing Excel files to memory#
pandas supports writing Excel files to buffer-like objects such as StringIO
or
BytesIO
using ExcelWriter
.
from io import BytesIO
bio = BytesIO()
# By setting the 'engine' in the ExcelWriter constructor.
writer = pd.ExcelWriter(bio, engine="xlsxwriter")
df.to_excel(writer, sheet_name="Sheet1")
# Save the workbook
writer.save()
# Seek to the beginning and read to copy the workbook to a variable in memory
bio.seek(0)
workbook = bio.read()
Note
engine
is optional but recommended. Setting the engine determines
the version of workbook produced. Setting engine='xlrd'
will produce an
Excel 2003-format workbook (xls). Using either 'openpyxl'
or
'xlsxwriter'
will produce an Excel 2007-format workbook (xlsx). If
omitted, an Excel 2007-formatted workbook is produced.
Excel writer engines#
pandas chooses an Excel writer via two methods:
the
engine
keyword argumentthe filename extension (via the default specified in config options)
By default, pandas uses the XlsxWriter for .xlsx
, openpyxl
for .xlsm
. If you have multiple
engines installed, you can set the default engine through setting the
config options io.excel.xlsx.writer
and
io.excel.xls.writer
. pandas will fall back on openpyxl for .xlsx
files if Xlsxwriter is not available.
To specify which writer you want to use, you can pass an engine keyword
argument to to_excel
and to ExcelWriter
. The built-in engines are:
openpyxl
: version 2.4 or higher is requiredxlsxwriter
# By setting the 'engine' in the DataFrame 'to_excel()' methods.
df.to_excel("path_to_file.xlsx", sheet_name="Sheet1", engine="xlsxwriter")
# By setting the 'engine' in the ExcelWriter constructor.
writer = pd.ExcelWriter("path_to_file.xlsx", engine="xlsxwriter")
# Or via pandas configuration.
from pandas import options # noqa: E402
options.io.excel.xlsx.writer = "xlsxwriter"
df.to_excel("path_to_file.xlsx", sheet_name="Sheet1")
Style and formatting#
The look and feel of Excel worksheets created from pandas can be modified using the following parameters on the DataFrame
’s to_excel
method.
float_format
: Format string for floating point numbers (defaultNone
).freeze_panes
: A tuple of two integers representing the bottommost row and rightmost column to freeze. Each of these parameters is one-based, so (1, 1) will freeze the first row and first column (defaultNone
).
Note
As of pandas 3.0, by default spreadsheets created with the to_excel
method
will not contain any styling. Users wishing to bold text, add bordered styles,
etc in a worksheet output by to_excel
can do so by using Styler.to_excel()
to create styled excel files. For documentation on styling spreadsheets, see
here.
css = "border: 1px solid black; font-weight: bold;"
df.style.map_index(lambda x: css).map_index(lambda x: css, axis=1).to_excel("myfile.xlsx")
Using the Xlsxwriter engine provides many options for controlling the
format of an Excel worksheet created with the to_excel
method. Excellent examples can be found in the
Xlsxwriter documentation here: https://xlsxwriter.readthedocs.io/working_with_pandas.html
OpenDocument Spreadsheets#
The io methods for Excel files also support reading and writing OpenDocument spreadsheets
using the odfpy module. The semantics and features for reading and writing
OpenDocument spreadsheets match what can be done for Excel files using
engine='odf'
. The optional dependency ‘odfpy’ needs to be installed.
The read_excel()
method can read OpenDocument spreadsheets
# Returns a DataFrame
pd.read_excel("path_to_file.ods", engine="odf")
Similarly, the to_excel()
method can write OpenDocument spreadsheets
# Writes DataFrame to a .ods file
df.to_excel("path_to_file.ods", engine="odf")
Binary Excel (.xlsb) files#
The read_excel()
method can also read binary Excel files
using the pyxlsb
module. The semantics and features for reading
binary Excel files mostly match what can be done for Excel files using
engine='pyxlsb'
. pyxlsb
does not recognize datetime types
in files and will return floats instead (you can use calamine
if you need recognize datetime types).
# Returns a DataFrame
pd.read_excel("path_to_file.xlsb", engine="pyxlsb")
Note
Currently pandas only supports reading binary Excel files. Writing is not implemented.
Calamine (Excel and ODS files)#
The read_excel()
method can read Excel file (.xlsx
, .xlsm
, .xls
, .xlsb
)
and OpenDocument spreadsheets (.ods
) using the python-calamine
module.
This module is a binding for Rust library calamine
and is faster than other engines in most cases. The optional dependency ‘python-calamine’ needs to be installed.
# Returns a DataFrame
pd.read_excel("path_to_file.xlsb", engine="calamine")
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_csv
method. For instance, you can copy the following text to the
clipboard (CTRL-C on many operating systems):
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:
>>> clipdf = pd.read_clipboard()
>>> clipdf
A B C
x 1 4 p
y 2 5 q
z 3 6 r
The to_clipboard
method can be used to write the contents of a DataFrame
to
the clipboard. Following which you can paste the clipboard contents into other
applications (CTRL-V on many operating systems). Here we illustrate writing a
DataFrame
into clipboard and reading it back.
>>> df = pd.DataFrame(
... {"A": [1, 2, 3], "B": [4, 5, 6], "C": ["p", "q", "r"]}, index=["x", "y", "z"]
... )
>>> df
A B C
x 1 4 p
y 2 5 q
z 3 6 r
>>> df.to_clipboard()
>>> pd.read_clipboard()
A B C
x 1 4 p
y 2 5 q
z 3 6 r
We can see that we got the same content back, which we had earlier written to the clipboard.
Note
You may need to install xclip or xsel (with PyQt5, PyQt4 or qtpy) on Linux to use these methods.
Pickling#
All pandas objects are equipped with to_pickle
methods which use Python’s
cPickle
module to save data structures to disk using the pickle format.
In [420]: df
Out[420]:
c1 a
c2 b d
lvl1 lvl2
a c 1 5
d 2 6
b c 3 7
d 4 8
In [421]: df.to_pickle("foo.pkl")
The read_pickle
function in the pandas
namespace can be used to load
any pickled pandas object (or any other pickled object) from file:
In [422]: pd.read_pickle("foo.pkl")
Out[422]:
c1 a
c2 b d
lvl1 lvl2
a c 1 5
d 2 6
b c 3 7
d 4 8
Warning
Loading pickled data received from untrusted sources can be unsafe.
Warning
read_pickle()
is only guaranteed backwards compatible back to a few minor release.
Compressed pickle files#
read_pickle()
, DataFrame.to_pickle()
and Series.to_pickle()
can read
and write compressed pickle files. The compression types of gzip
, bz2
, xz
, zstd
are supported for reading and writing.
The zip
file format only supports reading and must contain only one data file
to be read.
The compression type can be an explicit parameter or be inferred from the file extension.
If ‘infer’, then use gzip
, bz2
, zip
, xz
, zstd
if filename ends in '.gz'
, '.bz2'
, '.zip'
,
'.xz'
, or '.zst'
, respectively.
The compression parameter can also be a dict
in order to pass options to the
compression protocol. It must have a 'method'
key set to the name
of the compression protocol, which must be one of
{'zip'
, 'gzip'
, 'bz2'
, 'xz'
, 'zstd'
}. All other key-value pairs are passed to
the underlying compression library.
In [423]: df = pd.DataFrame(
.....: {
.....: "A": np.random.randn(1000),
.....: "B": "foo",
.....: "C": pd.date_range("20130101", periods=1000, freq="s"),
.....: }
.....: )
.....:
In [424]: df
Out[424]:
A B C
0 -0.317441 foo 2013-01-01 00:00:00
1 -1.236269 foo 2013-01-01 00:00:01
2 0.896171 foo 2013-01-01 00:00:02
3 -0.487602 foo 2013-01-01 00:00:03
4 -0.082240 foo 2013-01-01 00:00:04
.. ... ... ...
995 -0.171092 foo 2013-01-01 00:16:35
996 1.786173 foo 2013-01-01 00:16:36
997 -0.575189 foo 2013-01-01 00:16:37
998 0.820750 foo 2013-01-01 00:16:38
999 -1.256530 foo 2013-01-01 00:16:39
[1000 rows x 3 columns]
Using an explicit compression type:
In [425]: df.to_pickle("data.pkl.compress", compression="gzip")
In [426]: rt = pd.read_pickle("data.pkl.compress", compression="gzip")
In [427]: rt
Out[427]:
A B C
0 -0.317441 foo 2013-01-01 00:00:00
1 -1.236269 foo 2013-01-01 00:00:01
2 0.896171 foo 2013-01-01 00:00:02
3 -0.487602 foo 2013-01-01 00:00:03
4 -0.082240 foo 2013-01-01 00:00:04
.. ... ... ...
995 -0.171092 foo 2013-01-01 00:16:35
996 1.786173 foo 2013-01-01 00:16:36
997 -0.575189 foo 2013-01-01 00:16:37
998 0.820750 foo 2013-01-01 00:16:38
999 -1.256530 foo 2013-01-01 00:16:39
[1000 rows x 3 columns]
Inferring compression type from the extension:
In [428]: df.to_pickle("data.pkl.xz", compression="infer")
In [429]: rt = pd.read_pickle("data.pkl.xz", compression="infer")
In [430]: rt
Out[430]:
A B C
0 -0.317441 foo 2013-01-01 00:00:00
1 -1.236269 foo 2013-01-01 00:00:01
2 0.896171 foo 2013-01-01 00:00:02
3 -0.487602 foo 2013-01-01 00:00:03
4 -0.082240 foo 2013-01-01 00:00:04
.. ... ... ...
995 -0.171092 foo 2013-01-01 00:16:35
996 1.786173 foo 2013-01-01 00:16:36
997 -0.575189 foo 2013-01-01 00:16:37
998 0.820750 foo 2013-01-01 00:16:38
999 -1.256530 foo 2013-01-01 00:16:39
[1000 rows x 3 columns]
The default is to ‘infer’:
In [431]: df.to_pickle("data.pkl.gz")
In [432]: rt = pd.read_pickle("data.pkl.gz")
In [433]: rt
Out[433]:
A B C
0 -0.317441 foo 2013-01-01 00:00:00
1 -1.236269 foo 2013-01-01 00:00:01
2 0.896171 foo 2013-01-01 00:00:02
3 -0.487602 foo 2013-01-01 00:00:03
4 -0.082240 foo 2013-01-01 00:00:04
.. ... ... ...
995 -0.171092 foo 2013-01-01 00:16:35
996 1.786173 foo 2013-01-01 00:16:36
997 -0.575189 foo 2013-01-01 00:16:37
998 0.820750 foo 2013-01-01 00:16:38
999 -1.256530 foo 2013-01-01 00:16:39
[1000 rows x 3 columns]
In [434]: df["A"].to_pickle("s1.pkl.bz2")
In [435]: rt = pd.read_pickle("s1.pkl.bz2")
In [436]: rt
Out[436]:
0 -0.317441
1 -1.236269
2 0.896171
3 -0.487602
4 -0.082240
...
995 -0.171092
996 1.786173
997 -0.575189
998 0.820750
999 -1.256530
Name: A, Length: 1000, dtype: float64
Passing options to the compression protocol in order to speed up compression:
In [437]: df.to_pickle("data.pkl.gz", compression={"method": "gzip", "compresslevel": 1})
msgpack#
pandas support for msgpack
has been removed in version 1.0.0. It is
recommended to use pickle instead.
Alternatively, you can also the Arrow IPC serialization format for on-the-wire transmission of pandas objects. For documentation on pyarrow, see here.
HDF5 (PyTables)#
HDFStore
is a dict-like object which reads and writes pandas using
the high performance HDF5 format using the excellent PyTables library. See the cookbook
for some advanced strategies
Warning
pandas uses PyTables for reading and writing HDF5 files, which allows serializing object-dtype data with pickle. Loading pickled data received from untrusted sources can be unsafe.
See: https://docs.python.org/3/library/pickle.html for more.
In [438]: store = pd.HDFStore("store.h5")
In [439]: print(store)
<class 'pandas.io.pytables.HDFStore'>
File path: store.h5
Objects can be written to the file just like adding key-value pairs to a dict:
In [440]: index = pd.date_range("1/1/2000", periods=8)
In [441]: s = pd.Series(np.random.randn(5), index=["a", "b", "c", "d", "e"])
In [442]: df = pd.DataFrame(np.random.randn(8, 3), index=index, columns=["A", "B", "C"])
# store.put('s', s) is an equivalent method
In [443]: store["s"] = s
In [444]: store["df"] = df
In [445]: store
Out[445]:
<class 'pandas.io.pytables.HDFStore'>
File path: store.h5
In a current or later Python session, you can retrieve stored objects:
# store.get('df') is an equivalent method
In [446]: store["df"]
Out[446]:
A B C
2000-01-01 0.858644 -0.851236 1.058006
2000-01-02 -0.080372 -1.268121 1.561967
2000-01-03 0.816983 1.965656 -1.169408
2000-01-04 0.712795 -0.062433 0.736755
2000-01-05 -0.298721 -1.988045 1.475308
2000-01-06 1.103675 1.382242 -0.650762
2000-01-07 -0.729161 -0.142928 -1.063038
2000-01-08 -1.005977 0.465222 -0.094517
# dotted (attribute) access provides get as well
In [447]: store.df
Out[447]:
A B C
2000-01-01 0.858644 -0.851236 1.058006
2000-01-02 -0.080372 -1.268121 1.561967
2000-01-03 0.816983 1.965656 -1.169408
2000-01-04 0.712795 -0.062433 0.736755
2000-01-05 -0.298721 -1.988045 1.475308
2000-01-06 1.103675 1.382242 -0.650762
2000-01-07 -0.729161 -0.142928 -1.063038
2000-01-08 -1.005977 0.465222 -0.094517
Deletion of the object specified by the key:
# store.remove('df') is an equivalent method
In [448]: del store["df"]
In [449]: store
Out[449]:
<class 'pandas.io.pytables.HDFStore'>
File path: store.h5
Closing a Store and using a context manager:
In [450]: store.close()
In [451]: store
Out[451]:
<class 'pandas.io.pytables.HDFStore'>
File path: store.h5
In [452]: store.is_open
Out[452]: False
# Working with, and automatically closing the store using a context manager
In [453]: with pd.HDFStore("store.h5") as store:
.....: store.keys()
.....:
Read/write API#
HDFStore
supports a top-level API using read_hdf
for reading and to_hdf
for writing,
similar to how read_csv
and to_csv
work.
In [454]: df_tl = pd.DataFrame({"A": list(range(5)), "B": list(range(5))})
In [455]: df_tl.to_hdf("store_tl.h5", key="table", append=True)
In [456]: pd.read_hdf("store_tl.h5", "table", where=["index>2"])
Out[456]:
A B
3 3 3
4 4 4
HDFStore will by default not drop rows that are all missing. This behavior can be changed by setting dropna=True
.
In [457]: df_with_missing = pd.DataFrame(
.....: {
.....: "col1": [0, np.nan, 2],
.....: "col2": [1, np.nan, np.nan],
.....: }
.....: )
.....:
In [458]: df_with_missing
Out[458]:
col1 col2
0 0.0 1.0
1 NaN NaN
2 2.0 NaN
In [459]: df_with_missing.to_hdf("file.h5", key="df_with_missing", format="table", mode="w")
In [460]: pd.read_hdf("file.h5", "df_with_missing")
Out[460]:
col1 col2
0 0.0 1.0
1 NaN NaN
2 2.0 NaN
In [461]: df_with_missing.to_hdf(
.....: "file.h5", key="df_with_missing", format="table", mode="w", dropna=True
.....: )
.....:
In [462]: pd.read_hdf("file.h5", "df_with_missing")
Out[462]:
col1 col2
0 0.0 1.0
2 2.0 NaN
Fixed format#
The examples above show storing using put
, which write the HDF5 to PyTables
in a fixed array format, called
the fixed
format. These types of stores are not appendable once written (though you can simply
remove them and rewrite). Nor are they queryable; they must be
retrieved in their entirety. They also do not support dataframes with non-unique column names.
The fixed
format stores offer very fast writing and slightly faster reading than table
stores.
This format is specified by default when using put
or to_hdf
or by format='fixed'
or format='f'
.
Warning
A fixed
format will raise a TypeError
if you try to retrieve using a where
:
In [463]: pd.DataFrame(np.random.randn(10, 2)).to_hdf("test_fixed.h5", key="df")
In [464]: pd.read_hdf("test_fixed.h5", "df", where="index>5")
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[464], line 1
----> 1 pd.read_hdf("test_fixed.h5", "df", where="index>5")
File ~/work/pandas/pandas/pandas/io/pytables.py:444, in read_hdf(path_or_buf, key, mode, errors, where, start, stop, columns, iterator, chunksize, **kwargs)
439 raise ValueError(
440 "key must be provided when HDF5 "
441 "file contains multiple datasets."
442 )
443 key = candidate_only_group._v_pathname
--> 444 return store.select(
445 key,
446 where=where,
447 start=start,
448 stop=stop,
449 columns=columns,
450 iterator=iterator,
451 chunksize=chunksize,
452 auto_close=auto_close,
453 )
454 except (ValueError, TypeError, LookupError):
455 if not isinstance(path_or_buf, HDFStore):
456 # if there is an error, close the store if we opened it.
File ~/work/pandas/pandas/pandas/io/pytables.py:916, in HDFStore.select(self, key, where, start, stop, columns, iterator, chunksize, auto_close)
902 # create the iterator
903 it = TableIterator(
904 self,
905 s,
(...)
913 auto_close=auto_close,
914 )
--> 916 return it.get_result()
File ~/work/pandas/pandas/pandas/io/pytables.py:2102, in TableIterator.get_result(self, coordinates)
2099 where = self.where
2101 # directly return the result
-> 2102 results = self.func(self.start, self.stop, where)
2103 self.close()
2104 return results
File ~/work/pandas/pandas/pandas/io/pytables.py:900, in HDFStore.select.<locals>.func(_start, _stop, _where)
899 def func(_start, _stop, _where):
--> 900 return s.read(start=_start, stop=_stop, where=_where, columns=columns)
File ~/work/pandas/pandas/pandas/io/pytables.py:3349, in BlockManagerFixed.read(self, where, columns, start, stop)
3341 def read(
3342 self,
3343 where=None,
(...)
3347 ) -> DataFrame:
3348 # start, stop applied to rows, so 0th axis only
-> 3349 self.validate_read(columns, where)
3350 select_axis = self.obj_type()._get_block_manager_axis(0)
3352 axes = []
File ~/work/pandas/pandas/pandas/io/pytables.py:2992, in GenericFixed.validate_read(self, columns, where)
2987 raise TypeError(
2988 "cannot pass a column specification when reading "
2989 "a Fixed format store. this store must be selected in its entirety"
2990 )
2991 if where is not None:
-> 2992 raise TypeError(
2993 "cannot pass a where specification when reading "
2994 "from a Fixed format store. this store must be selected in its entirety"
2995 )
TypeError: cannot pass a where specification when reading from a Fixed format store. this store must be selected in its entirety
Table format#
HDFStore
supports another PyTables
format on disk, the table
format. Conceptually a table
is shaped very much like a DataFrame,
with rows and columns. A table
may be appended to in the same or
other sessions. In addition, delete and query type operations are
supported. This format is specified by format='table'
or format='t'
to append
or put
or to_hdf
.
This format can be set as an option as well pd.set_option('io.hdf.default_format','table')
to
enable put/append/to_hdf
to by default store in the table
format.
In [465]: store = pd.HDFStore("store.h5")
In [466]: df1 = df[0:4]
In [467]: df2 = df[4:]
# append data (creates a table automatically)
In [468]: store.append("df", df1)
In [469]: store.append("df", df2)
In [470]: store
Out[470]:
<class 'pandas.io.pytables.HDFStore'>
File path: store.h5
# select the entire object
In [471]: store.select("df")
Out[471]:
A B C
2000-01-01 0.858644 -0.851236 1.058006
2000-01-02 -0.080372 -1.268121 1.561967
2000-01-03 0.816983 1.965656 -1.169408
2000-01-04 0.712795 -0.062433 0.736755
2000-01-05 -0.298721 -1.988045 1.475308
2000-01-06 1.103675 1.382242 -0.650762
2000-01-07 -0.729161 -0.142928 -1.063038
2000-01-08 -1.005977 0.465222 -0.094517
# the type of stored data
In [472]: store.root.df._v_attrs.pandas_type
Out[472]: 'frame_table'
Note
You can also create a table
by passing format='table'
or format='t'
to a put
operation.
Hierarchical keys#
Keys to a store can be specified as a string. These can be in a
hierarchical path-name like format (e.g. foo/bar/bah
), which will
generate a hierarchy of sub-stores (or Groups
in PyTables
parlance). Keys can be specified without the leading ‘/’ and are always
absolute (e.g. ‘foo’ refers to ‘/foo’). Removal operations can remove
everything in the sub-store and below, so be careful.
In [473]: store.put("foo/bar/bah", df)
In [474]: store.append("food/orange", df)
In [475]: store.append("food/apple", df)
In [476]: store
Out[476]:
<class 'pandas.io.pytables.HDFStore'>
File path: store.h5
# a list of keys are returned
In [477]: store.keys()
Out[477]: ['/df', '/food/apple', '/food/orange', '/foo/bar/bah']
# remove all nodes under this level
In [478]: store.remove("food")
In [479]: store
Out[479]:
<class 'pandas.io.pytables.HDFStore'>
File path: store.h5
You can walk through the group hierarchy using the walk
method which
will yield a tuple for each group key along with the relative keys of its contents.
In [480]: for (path, subgroups, subkeys) in store.walk():
.....: for subgroup in subgroups:
.....: print("GROUP: {}/{}".format(path, subgroup))
.....: for subkey in subkeys:
.....: key = "/".join([path, subkey])
.....: print("KEY: {}".format(key))
.....: print(store.get(key))
.....:
GROUP: /foo
KEY: /df
A B C
2000-01-01 0.858644 -0.851236 1.058006
2000-01-02 -0.080372 -1.268121 1.561967
2000-01-03 0.816983 1.965656 -1.169408
2000-01-04 0.712795 -0.062433 0.736755
2000-01-05 -0.298721 -1.988045 1.475308
2000-01-06 1.103675 1.382242 -0.650762
2000-01-07 -0.729161 -0.142928 -1.063038
2000-01-08 -1.005977 0.465222 -0.094517
GROUP: /foo/bar
KEY: /foo/bar/bah
A B C
2000-01-01 0.858644 -0.851236 1.058006
2000-01-02 -0.080372 -1.268121 1.561967
2000-01-03 0.816983 1.965656 -1.169408
2000-01-04 0.712795 -0.062433 0.736755
2000-01-05 -0.298721 -1.988045 1.475308
2000-01-06 1.103675 1.382242 -0.650762
2000-01-07 -0.729161 -0.142928 -1.063038
2000-01-08 -1.005977 0.465222 -0.094517
Warning
Hierarchical keys cannot be retrieved as dotted (attribute) access as described above for items stored under the root node.
In [481]: store.foo.bar.bah
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[481], line 1
----> 1 store.foo.bar.bah
File ~/work/pandas/pandas/pandas/io/pytables.py:605, in HDFStore.__getattr__(self, name)
603 """allow attribute access to get stores"""
604 try:
--> 605 return self.get(name)
606 except (KeyError, ClosedFileError):
607 pass
File ~/work/pandas/pandas/pandas/io/pytables.py:817, in HDFStore.get(self, key)
815 if group is None:
816 raise KeyError(f"No object named {key} in the file")
--> 817 return self._read_group(group)
File ~/work/pandas/pandas/pandas/io/pytables.py:1951, in HDFStore._read_group(self, group)
1950 def _read_group(self, group: Node):
-> 1951 s = self._create_storer(group)
1952 s.infer_axes()
1953 return s.read()
File ~/work/pandas/pandas/pandas/io/pytables.py:1825, in HDFStore._create_storer(self, group, format, value, encoding, errors)
1823 tt = "generic_table"
1824 else:
-> 1825 raise TypeError(
1826 "cannot create a storer if the object is not existing "
1827 "nor a value are passed"
1828 )
1829 else:
1830 if isinstance(value, Series):
TypeError: cannot create a storer if the object is not existing nor a value are passed
# you can directly access the actual PyTables node but using the root node
In [482]: store.root.foo.bar.bah
Out[482]:
/foo/bar/bah (Group) ''
children := ['axis0' (Array), 'axis1' (Array), 'block0_items' (Array), 'block0_values' (Array)]
Instead, use explicit string based keys:
In [483]: store["foo/bar/bah"]
Out[483]:
A B C
2000-01-01 0.858644 -0.851236 1.058006
2000-01-02 -0.080372 -1.268121 1.561967
2000-01-03 0.816983 1.965656 -1.169408
2000-01-04 0.712795 -0.062433 0.736755
2000-01-05 -0.298721 -1.988045 1.475308
2000-01-06 1.103675 1.382242 -0.650762
2000-01-07 -0.729161 -0.142928 -1.063038
2000-01-08 -1.005977 0.465222 -0.094517
Storing types#
Storing mixed types in a table#
Storing mixed-dtype data is supported. Strings are stored as a
fixed-width using the maximum size of the appended column. Subsequent attempts
at appending longer strings will raise a ValueError
.
Passing min_itemsize={`values`: size}
as a parameter to append
will set a larger minimum for the string columns. Storing floats,
strings, ints, bools, datetime64
are currently supported. For string
columns, passing nan_rep = 'nan'
to append will change the default
nan representation on disk (which converts to/from np.nan
), this
defaults to nan
.
In [484]: df_mixed = pd.DataFrame(
.....: {
.....: "A": np.random.randn(8),
.....: "B": np.random.randn(8),
.....: "C": np.array(np.random.randn(8), dtype="float32"),
.....: "string": "string",
.....: "int": 1,
.....: "bool": True,
.....: "datetime64": pd.Timestamp("20010102"),
.....: },
.....: index=list(range(8)),
.....: )
.....:
In [485]: df_mixed.loc[df_mixed.index[3:5], ["A", "B", "string", "datetime64"]] = np.nan
In [486]: store.append("df_mixed", df_mixed, min_itemsize={"values": 50})
In [487]: df_mixed1 = store.select("df_mixed")
In [488]: df_mixed1
Out[488]:
A B C string int bool datetime64
0 0.013747 -1.166078 -1.292080 string 1 True 2001-01-02
1 -0.712009 0.247572 1.526911 string 1 True 2001-01-02
2 -0.645096 1.687406 0.288504 string 1 True 2001-01-02
3 NaN NaN 0.097771 NaN 1 True NaT
4 NaN NaN 1.536408 NaN 1 True NaT
5 -0.023202 0.043702 0.926790 string 1 True 2001-01-02
6 2.359782 0.088224 -0.676448 string 1 True 2001-01-02
7 -0.143428 -0.813360 -0.179724 string 1 True 2001-01-02
In [489]: df_mixed1.dtypes.value_counts()
Out[489]:
float64 2
float32 1
object 1
int64 1
bool 1
datetime64[s] 1
Name: count, dtype: int64
# we have provided a minimum string column size
In [490]: store.root.df_mixed.table
Out[490]:
/df_mixed/table (Table(8,)) ''
description := {
"index": Int64Col(shape=(), dflt=0, pos=0),
"values_block_0": Float64Col(shape=(2,), dflt=0.0, pos=1),
"values_block_1": Float32Col(shape=(1,), dflt=0.0, pos=2),
"values_block_2": StringCol(itemsize=50, shape=(1,), dflt=b'', pos=3),
"values_block_3": Int64Col(shape=(1,), dflt=0, pos=4),
"values_block_4": BoolCol(shape=(1,), dflt=False, pos=5),
"values_block_5": Int64Col(shape=(1,), dflt=0, pos=6)}
byteorder := 'little'
chunkshape := (689,)
autoindex := True
colindexes := {
"index": Index(6, mediumshuffle, zlib(1)).is_csi=False}
Storing MultiIndex DataFrames#
Storing MultiIndex DataFrames
as tables is very similar to
storing/selecting from homogeneous index DataFrames
.
In [491]: index = pd.MultiIndex(
.....: levels=[["foo", "bar", "baz", "qux"], ["one", "two", "three"]],
.....: codes=[[0, 0, 0, 1, 1, 2, 2, 3, 3, 3], [0, 1, 2, 0, 1, 1, 2, 0, 1, 2]],
.....: names=["foo", "bar"],
.....: )
.....:
In [492]: df_mi = pd.DataFrame(np.random.randn(10, 3), index=index, columns=["A", "B", "C"])
In [493]: df_mi
Out[493]:
A B C
foo bar
foo one -1.303456 -0.642994 -0.649456
two 1.012694 0.414147 1.950460
three 1.094544 -0.802899 -0.583343
bar one 0.410395 0.618321 0.560398
two 1.434027 -0.033270 0.343197
baz two -1.646063 -0.695847 -0.429156
three -0.244688 -1.428229 -0.138691
qux one 1.866184 -1.446617 0.036660
two -1.660522 0.929553 -1.298649
three 3.565769 0.682402 1.041927
In [494]: store.append("df_mi", df_mi)
In [495]: store.select("df_mi")
Out[495]:
A B C
foo bar
foo one -1.303456 -0.642994 -0.649456
two 1.012694 0.414147 1.950460
three 1.094544 -0.802899 -0.583343
bar one 0.410395 0.618321 0.560398
two 1.434027 -0.033270 0.343197
baz two -1.646063 -0.695847 -0.429156
three -0.244688 -1.428229 -0.138691
qux one 1.866184 -1.446617 0.036660
two -1.660522 0.929553 -1.298649
three 3.565769 0.682402 1.041927
# the levels are automatically included as data columns
In [496]: store.select("df_mi", "foo=bar")
Out[496]:
A B C
foo bar
bar one 0.410395 0.618321 0.560398
two 1.434027 -0.033270 0.343197
Note
The index
keyword is reserved and cannot be use as a level name.
Querying#
Querying a table#
select
and delete
operations have an optional criterion that can
be specified to select/delete only a subset of the data. This allows one
to have a very large on-disk table and retrieve only a portion of the
data.
A query is specified using the Term
class under the hood, as a boolean expression.
index
andcolumns
are supported indexers ofDataFrames
.if
data_columns
are specified, these can be used as additional indexers.level name in a MultiIndex, with default name
level_0
,level_1
, … if not provided.
Valid comparison operators are:
=, ==, !=, >, >=, <, <=
Valid boolean expressions are combined with:
|
: or&
: and(
and)
: for grouping
These rules are similar to how boolean expressions are used in pandas for indexing.
Note
=
will be automatically expanded to the comparison operator==
~
is the not operator, but can only be used in very limited circumstancesIf a list/tuple of expressions is passed they will be combined via
&
The following are valid expressions:
'index >= date'
"columns = ['A', 'D']"
"columns in ['A', 'D']"
'columns = A'
'columns == A'
"~(columns = ['A', 'B'])"
'index > df.index[3] & string = "bar"'
'(index > df.index[3] & index <= df.index[6]) | string = "bar"'
"ts >= Timestamp('2012-02-01')"
"major_axis>=20130101"
The indexers
are on the left-hand side of the sub-expression:
columns
, major_axis
, ts
The right-hand side of the sub-expression (after a comparison operator) can be:
functions that will be evaluated, e.g.
Timestamp('2012-02-01')
strings, e.g.
"bar"
date-like, e.g.
20130101
, or"20130101"
lists, e.g.
"['A', 'B']"
variables that are defined in the local names space, e.g.
date
Note
Passing a string to a query by interpolating it into the query expression is not recommended. Simply assign the string of interest to a variable and use that variable in an expression. For example, do this
string = "HolyMoly'"
store.select("df", "index == string")
instead of this
string = "HolyMoly'"
store.select('df', f'index == {string}')
The latter will not work and will raise a SyntaxError
.Note that
there’s a single quote followed by a double quote in the string
variable.
If you must interpolate, use the '%r'
format specifier
store.select("df", "index == %r" % string)
which will quote string
.
Here are some examples:
In [497]: dfq = pd.DataFrame(
.....: np.random.randn(10, 4),
.....: columns=list("ABCD"),
.....: index=pd.date_range("20130101", periods=10),
.....: )
.....:
In [498]: store.append("dfq", dfq, format="table", data_columns=True)
Use boolean expressions, with in-line function evaluation.
In [499]: store.select("dfq", "index>pd.Timestamp('20130104') & columns=['A', 'B']")
Out[499]:
A B
2013-01-05 -0.830545 -0.457071
2013-01-06 0.431186 1.049421
2013-01-07 0.617509 -0.811230
2013-01-08 0.947422 -0.671233
2013-01-09 -0.183798 -1.211230
2013-01-10 0.361428 0.887304
Use inline column reference.
In [500]: store.select("dfq", where="A>0 or C>0")
Out[500]:
A B C D
2013-01-02 0.658179 0.362814 -0.917897 0.010165
2013-01-03 0.905122 1.848731 -1.184241 0.932053
2013-01-05 -0.830545 -0.457071 1.565581 1.148032
2013-01-06 0.431186 1.049421 0.383309 0.595013
2013-01-07 0.617509 -0.811230 -2.088563 -1.393500
2013-01-08 0.947422 -0.671233 -0.847097 -1.187785
2013-01-10 0.361428 0.887304 0.266457 -0.399641
The columns
keyword can be supplied to select a list of columns to be
returned, this is equivalent to passing a
'columns=list_of_columns_to_filter'
:
In [501]: store.select("df", "columns=['A', 'B']")
Out[501]:
A B
2000-01-01 0.858644 -0.851236
2000-01-02 -0.080372 -1.268121
2000-01-03 0.816983 1.965656
2000-01-04 0.712795 -0.062433
2000-01-05 -0.298721 -1.988045
2000-01-06 1.103675 1.382242
2000-01-07 -0.729161 -0.142928
2000-01-08 -1.005977 0.465222
start
and stop
parameters can be specified to limit the total search
space. These are in terms of the total number of rows in a table.
Note
select
will raise a ValueError
if the query expression has an unknown
variable reference. Usually this means that you are trying to select on a column
that is not a data_column.
select
will raise a SyntaxError
if the query expression is not valid.
Query timedelta64[ns]#
You can store and query using the timedelta64[ns]
type. Terms can be
specified in the format: <float>(<unit>)
, where float may be signed (and fractional), and unit can be
D,s,ms,us,ns
for the timedelta. Here’s an example:
In [502]: from datetime import timedelta
In [503]: dftd = pd.DataFrame(
.....: {
.....: "A": pd.Timestamp("20130101"),
.....: "B": [
.....: pd.Timestamp("20130101") + timedelta(days=i, seconds=10)
.....: for i in range(10)
.....: ],
.....: }
.....: )
.....:
In [504]: dftd["C"] = dftd["A"] - dftd["B"]
In [505]: dftd
Out[505]:
A B C
0 2013-01-01 2013-01-01 00:00:10 -1 days +23:59:50
1 2013-01-01 2013-01-02 00:00:10 -2 days +23:59:50
2 2013-01-01 2013-01-03 00:00:10 -3 days +23:59:50
3 2013-01-01 2013-01-04 00:00:10 -4 days +23:59:50
4 2013-01-01 2013-01-05 00:00:10 -5 days +23:59:50
5 2013-01-01 2013-01-06 00:00:10 -6 days +23:59:50
6 2013-01-01 2013-01-07 00:00:10 -7 days +23:59:50
7 2013-01-01 2013-01-08 00:00:10 -8 days +23:59:50
8 2013-01-01 2013-01-09 00:00:10 -9 days +23:59:50
9 2013-01-01 2013-01-10 00:00:10 -10 days +23:59:50
In [506]: store.append("dftd", dftd, data_columns=True)
In [507]: store.select("dftd", "C<'-3.5D'")
Out[507]:
Empty DataFrame
Columns: [A, B, C]
Index: []
Query MultiIndex#
Selecting from a MultiIndex
can be achieved by using the name of the level.
In [508]: df_mi.index.names
Out[508]: FrozenList(['foo', 'bar'])
In [509]: store.select("df_mi", "foo=baz and bar=two")
Out[509]:
A B C
foo bar
baz two -1.646063 -0.695847 -0.429156
If the MultiIndex
levels names are None
, the levels are automatically made available via
the level_n
keyword with n
the level of the MultiIndex
you want to select from.
In [510]: index = pd.MultiIndex(
.....: levels=[["foo", "bar", "baz", "qux"], ["one", "two", "three"]],
.....: codes=[[0, 0, 0, 1, 1, 2, 2, 3, 3, 3], [0, 1, 2, 0, 1, 1, 2, 0, 1, 2]],
.....: )
.....:
In [511]: df_mi_2 = pd.DataFrame(np.random.randn(10, 3), index=index, columns=["A", "B", "C"])
In [512]: df_mi_2
Out[512]:
A B C
foo one -0.219582 1.186860 -1.437189
two 0.053768 1.872644 -1.469813
three -0.564201 0.876341 0.407749
bar one -0.232583 0.179812 0.922152
two -1.820952 -0.641360 2.133239
baz two -0.941248 -0.136307 -1.271305
three -0.099774 -0.061438 -0.845172
qux one 0.465793 0.756995 -0.541690
two -0.802241 0.877657 -2.553831
three 0.094899 -2.319519 0.293601
In [513]: store.append("df_mi_2", df_mi_2)
# the levels are automatically included as data columns with keyword level_n
In [514]: store.select("df_mi_2", "level_0=foo and level_1=two")
Out[514]:
A B C
foo two 0.053768 1.872644 -1.469813
Indexing#
You can create/modify an index for a table with create_table_index
after data is already in the table (after and append/put
operation). Creating a table index is highly encouraged. This will
speed your queries a great deal when you use a select
with the
indexed dimension as the where
.
Note
Indexes are automagically created on the indexables
and any data columns you specify. This behavior can be turned off by passing
index=False
to append
.
# we have automagically already created an index (in the first section)
In [515]: i = store.root.df.table.cols.index.index
In [516]: i.optlevel, i.kind
Out[516]: (6, 'medium')
# change an index by passing new parameters
In [517]: store.create_table_index("df", optlevel=9, kind="full")
In [518]: i = store.root.df.table.cols.index.index
In [519]: i.optlevel, i.kind
Out[519]: (9, 'full')
Oftentimes when appending large amounts of data to a store, it is useful to turn off index creation for each append, then recreate at the end.
In [520]: df_1 = pd.DataFrame(np.random.randn(10, 2), columns=list("AB"))
In [521]: df_2 = pd.DataFrame(np.random.randn(10, 2), columns=list("AB"))
In [522]: st = pd.HDFStore("appends.h5", mode="w")
In [523]: st.append("df", df_1, data_columns=["B"], index=False)
In [524]: st.append("df", df_2, data_columns=["B"], index=False)
In [525]: st.get_storer("df").table
Out[525]:
/df/table (Table(20,)) ''
description := {
"index": Int64Col(shape=(), dflt=0, pos=0),
"values_block_0": Float64Col(shape=(1,), dflt=0.0, pos=1),
"B": Float64Col(shape=(), dflt=0.0, pos=2)}
byteorder := 'little'
chunkshape := (2730,)
Then create the index when finished appending.
In [526]: st.create_table_index("df", columns=["B"], optlevel=9, kind="full")
In [527]: st.get_storer("df").table
Out[527]:
/df/table (Table(20,)) ''
description := {
"index": Int64Col(shape=(), dflt=0, pos=0),
"values_block_0": Float64Col(shape=(1,), dflt=0.0, pos=1),
"B": Float64Col(shape=(), dflt=0.0, pos=2)}
byteorder := 'little'
chunkshape := (2730,)
autoindex := True
colindexes := {
"B": Index(9, fullshuffle, zlib(1)).is_csi=True}
In [528]: st.close()
See here for how to create a completely-sorted-index (CSI) on an existing store.
Query via data columns#
You can designate (and index) certain columns that you want to be able
to perform queries (other than the indexable
columns, which you can
always query). For instance say you want to perform this common
operation, on-disk, and return just the frame that matches this
query. You can specify data_columns = True
to force all columns to
be data_columns
.
In [529]: df_dc = df.copy()
In [530]: df_dc["string"] = "foo"
In [531]: df_dc.loc[df_dc.index[4:6], "string"] = np.nan
In [532]: df_dc.loc[df_dc.index[7:9], "string"] = "bar"
In [533]: df_dc["string2"] = "cool"
In [534]: df_dc.loc[df_dc.index[1:3], ["B", "C"]] = 1.0
In [535]: df_dc
Out[535]:
A B C string string2
2000-01-01 0.858644 -0.851236 1.058006 foo cool
2000-01-02 -0.080372 1.000000 1.000000 foo cool
2000-01-03 0.816983 1.000000 1.000000 foo cool
2000-01-04 0.712795 -0.062433 0.736755 foo cool
2000-01-05 -0.298721 -1.988045 1.475308 NaN cool
2000-01-06 1.103675 1.382242 -0.650762 NaN cool
2000-01-07 -0.729161 -0.142928 -1.063038 foo cool
2000-01-08 -1.005977 0.465222 -0.094517 bar cool
# on-disk operations
In [536]: store.append("df_dc", df_dc, data_columns=["B", "C", "string", "string2"])
In [537]: store.select("df_dc", where="B > 0")
Out[537]:
A B C string string2
2000-01-02 -0.080372 1.000000 1.000000 foo cool
2000-01-03 0.816983 1.000000 1.000000 foo cool
2000-01-06 1.103675 1.382242 -0.650762 NaN cool
2000-01-08 -1.005977 0.465222 -0.094517 bar cool
# getting creative
In [538]: store.select("df_dc", "B > 0 & C > 0 & string == foo")
Out[538]:
A B C string string2
2000-01-02 -0.080372 1.0 1.0 foo cool
2000-01-03 0.816983 1.0 1.0 foo cool
# this is in-memory version of this type of selection
In [539]: df_dc[(df_dc.B > 0) & (df_dc.C > 0) & (df_dc.string == "foo")]
Out[539]:
A B C string string2
2000-01-02 -0.080372 1.0 1.0 foo cool
2000-01-03 0.816983 1.0 1.0 foo cool
# we have automagically created this index and the B/C/string/string2
# columns are stored separately as ``PyTables`` columns
In [540]: store.root.df_dc.table
Out[540]:
/df_dc/table (Table(8,)) ''
description := {
"index": Int64Col(shape=(), dflt=0, pos=0),
"values_block_0": Float64Col(shape=(1,), dflt=0.0, pos=1),
"B": Float64Col(shape=(), dflt=0.0, pos=2),
"C": Float64Col(shape=(), dflt=0.0, pos=3),
"string": StringCol(itemsize=3, shape=(), dflt=b'', pos=4),
"string2": StringCol(itemsize=4, shape=(), dflt=b'', pos=5)}
byteorder := 'little'
chunkshape := (1680,)
autoindex := True
colindexes := {
"index": Index(6, mediumshuffle, zlib(1)).is_csi=False,
"B": Index(6, mediumshuffle, zlib(1)).is_csi=False,
"C": Index(6, mediumshuffle, zlib(1)).is_csi=False,
"string": Index(6, mediumshuffle, zlib(1)).is_csi=False,
"string2": Index(6, mediumshuffle, zlib(1)).is_csi=False}
There is some performance degradation by making lots of columns into
data columns
, so it is up to the user to designate these. In addition,
you cannot change data columns (nor indexables) after the first
append/put operation (Of course you can simply read in the data and
create a new table!).
Iterator#
You can pass iterator=True
or chunksize=number_in_a_chunk
to select
and select_as_multiple
to return an iterator on the results.
The default is 50,000 rows returned in a chunk.
In [541]: for df in store.select("df", chunksize=3):
.....: print(df)
.....:
A B C
2000-01-01 0.858644 -0.851236 1.058006
2000-01-02 -0.080372 -1.268121 1.561967
2000-01-03 0.816983 1.965656 -1.169408
A B C
2000-01-04 0.712795 -0.062433 0.736755
2000-01-05 -0.298721 -1.988045 1.475308
2000-01-06 1.103675 1.382242 -0.650762
A B C
2000-01-07 -0.729161 -0.142928 -1.063038
2000-01-08 -1.005977 0.465222 -0.094517
Note
You can also use the iterator with read_hdf
which will open, then
automatically close the store when finished iterating.
for df in pd.read_hdf("store.h5", "df", chunksize=3):
print(df)
Note, that the chunksize keyword applies to the source rows. So if you are doing a query, then the chunksize will subdivide the total rows in the table and the query applied, returning an iterator on potentially unequal sized chunks.
Here is a recipe for generating a query and using it to create equal sized return chunks.
In [542]: dfeq = pd.DataFrame({"number": np.arange(1, 11)})
In [543]: dfeq
Out[543]:
number
0 1
1 2
2 3
3 4
4 5
5 6
6 7
7 8
8 9
9 10
In [544]: store.append("dfeq", dfeq, data_columns=["number"])
In [545]: def chunks(l, n):
.....: return [l[i: i + n] for i in range(0, len(l), n)]
.....:
In [546]: evens = [2, 4, 6, 8, 10]
In [547]: coordinates = store.select_as_coordinates("dfeq", "number=evens")
In [548]: for c in chunks(coordinates, 2):
.....: print(store.select("dfeq", where=c))
.....:
number
1 2
3 4
number
5 6
7 8
number
9 10
Advanced queries#
Select a single column#
To retrieve a single indexable or data column, use the
method select_column
. This will, for example, enable you to get the index
very quickly. These return a Series
of the result, indexed by the row number.
These do not currently accept the where
selector.
In [549]: store.select_column("df_dc", "index")
Out[549]:
0 2000-01-01
1 2000-01-02
2 2000-01-03
3 2000-01-04
4 2000-01-05
5 2000-01-06
6 2000-01-07
7 2000-01-08
Name: index, dtype: datetime64[ns]
In [550]: store.select_column("df_dc", "string")
Out[550]:
0 foo
1 foo
2 foo
3 foo
4 NaN
5 NaN
6 foo
7 bar
Name: string, dtype: object
Selecting coordinates#
Sometimes you want to get the coordinates (a.k.a the index locations) of your query. This returns an
Index
of the resulting locations. These coordinates can also be passed to subsequent
where
operations.
In [551]: df_coord = pd.DataFrame(
.....: np.random.randn(1000, 2), index=pd.date_range("20000101", periods=1000)
.....: )
.....:
In [552]: store.append("df_coord", df_coord)
In [553]: c = store.select_as_coordinates("df_coord", "index > 20020101")
In [554]: c
Out[554]:
Index([732, 733, 734, 735, 736, 737, 738, 739, 740, 741,
...
990, 991, 992, 993, 994, 995, 996, 997, 998, 999],
dtype='int64', length=268)
In [555]: store.select("df_coord", where=c)
Out[555]:
0 1
2002-01-02 0.007717 1.168386
2002-01-03 0.759328 -0.638934
2002-01-04 -1.154018 -0.324071
2002-01-05 -0.804551 -1.280593
2002-01-06 -0.047208 1.260503
... ... ...
2002-09-22 -1.139583 0.344316
2002-09-23 -0.760643 -1.306704
2002-09-24 0.059018 1.775482
2002-09-25 1.242255 -0.055457
2002-09-26 0.410317 2.194489
[268 rows x 2 columns]
Selecting using a where mask#
Sometime your query can involve creating a list of rows to select. Usually this mask
would
be a resulting index
from an indexing operation. This example selects the months of
a datetimeindex which are 5.
In [556]: df_mask = pd.DataFrame(
.....: np.random.randn(1000, 2), index=pd.date_range("20000101", periods=1000)
.....: )
.....:
In [557]: store.append("df_mask", df_mask)
In [558]: c = store.select_column("df_mask", "index")
In [559]: where = c[pd.DatetimeIndex(c).month == 5].index
In [560]: store.select("df_mask", where=where)
Out[560]:
0 1
2000-05-01 1.479511 0.516433
2000-05-02 -0.334984 -1.493537
2000-05-03 0.900321 0.049695
2000-05-04 0.614266 -1.077151
2000-05-05 0.233881 0.493246
... ... ...
2002-05-27 0.294122 0.457407
2002-05-28 -1.102535 1.215650
2002-05-29 -0.432911 0.753606
2002-05-30 -1.105212 2.311877
2002-05-31 2.567296 2.610691
[93 rows x 2 columns]
Storer object#
If you want to inspect the stored object, retrieve via
get_storer
. You could use this programmatically to say get the number
of rows in an object.
In [561]: store.get_storer("df_dc").nrows
Out[561]: 8
Multiple table queries#
The methods append_to_multiple
and
select_as_multiple
can perform appending/selecting from
multiple tables at once. The idea is to have one table (call it the
selector table) that you index most/all of the columns, and perform your
queries. The other table(s) are data tables with an index matching the
selector table’s index. You can then perform a very fast query
on the selector table, yet get lots of data back. This method is similar to
having a very wide table, but enables more efficient queries.
The append_to_multiple
method splits a given single DataFrame
into multiple tables according to d
, a dictionary that maps the
table names to a list of ‘columns’ you want in that table. If None
is used in place of a list, that table will have the remaining
unspecified columns of the given DataFrame. The argument selector
defines which table is the selector table (which you can make queries from).
The argument dropna
will drop rows from the input DataFrame
to ensure
tables are synchronized. This means that if a row for one of the tables
being written to is entirely np.nan
, that row will be dropped from all tables.
If dropna
is False, THE USER IS RESPONSIBLE FOR SYNCHRONIZING THE TABLES.
Remember that entirely np.Nan
rows are not written to the HDFStore, so if
you choose to call dropna=False
, some tables may have more rows than others,
and therefore select_as_multiple
may not work or it may return unexpected
results.
In [562]: df_mt = pd.DataFrame(
.....: np.random.randn(8, 6),
.....: index=pd.date_range("1/1/2000", periods=8),
.....: columns=["A", "B", "C", "D", "E", "F"],
.....: )
.....:
In [563]: df_mt["foo"] = "bar"
In [564]: df_mt.loc[df_mt.index[1], ("A", "B")] = np.nan
# you can also create the tables individually
In [565]: store.append_to_multiple(
.....: {"df1_mt": ["A", "B"], "df2_mt": None}, df_mt, selector="df1_mt"
.....: )
.....:
In [566]: store
Out[566]:
<class 'pandas.io.pytables.HDFStore'>
File path: store.h5
# individual tables were created
In [567]: store.select("df1_mt")
Out[567]:
A B
2000-01-01 0.162291 -0.430489
2000-01-02 NaN NaN
2000-01-03 0.429207 -1.099274
2000-01-04 1.869081 -1.466039
2000-01-05 0.092130 -1.726280
2000-01-06 0.266901 -0.036854
2000-01-07 -0.517871 -0.990317
2000-01-08 -0.231342 0.557402
In [568]: store.select("df2_mt")
Out[568]:
C D E F foo
2000-01-01 -2.502042 0.668149 0.460708 1.834518 bar
2000-01-02 0.130441 -0.608465 0.439872 0.506364 bar
2000-01-03 -1.069546 1.236277 0.116634 -1.772519 bar
2000-01-04 0.137462 0.313939 0.748471 -0.943009 bar
2000-01-05 0.836517 2.049798 0.562167 0.189952 bar
2000-01-06 1.112750 -0.151596 1.503311 0.939470 bar
2000-01-07 -0.294348 0.335844 -0.794159 1.495614 bar
2000-01-08 0.860312 -0.538674 -0.541986 -1.759606 bar
# as a multiple
In [569]: store.select_as_multiple(
.....: ["df1_mt", "df2_mt"],
.....: where=["A>0", "B>0"],
.....: selector="df1_mt",
.....: )
.....:
Out[569]:
Empty DataFrame
Columns: [A, B, C, D, E, F, foo]
Index: []
Delete from a table#
You can delete from a table selectively by specifying a where
. In
deleting rows, it is important to understand the PyTables
deletes
rows by erasing the rows, then moving the following data. Thus
deleting can potentially be a very expensive operation depending on the
orientation of your data. To get optimal performance, it’s
worthwhile to have the dimension you are deleting be the first of the
indexables
.
Data is ordered (on the disk) in terms of the indexables
. Here’s a
simple use case. You store panel-type data, with dates in the
major_axis
and ids in the minor_axis
. The data is then
interleaved like this:
- date_1
id_1
id_2
.
id_n
- date_2
id_1
.
id_n
It should be clear that a delete operation on the major_axis
will be
fairly quick, as one chunk is removed, then the following data moved. On
the other hand a delete operation on the minor_axis
will be very
expensive. In this case it would almost certainly be faster to rewrite
the table using a where
that selects all but the missing data.
Warning
Please note that HDF5 DOES NOT RECLAIM SPACE in the h5 files automatically. Thus, repeatedly deleting (or removing nodes) and adding again, WILL TEND TO INCREASE THE FILE SIZE.
To repack and clean the file, use ptrepack.
Notes & caveats#
Compression#
PyTables
allows the stored data to be compressed. This applies to
all kinds of stores, not just tables. Two parameters are used to
control compression: complevel
and complib
.
complevel
specifies if and how hard data is to be compressed.complevel=0
andcomplevel=None
disables compression and0<complevel<10
enables compression.complib
specifies which compression library to use. If nothing is specified the default libraryzlib
is used. A compression library usually optimizes for either good compression rates or speed and the results will depend on the type of data. Which type of compression to choose depends on your specific needs and data. The list of supported compression libraries:zlib: The default compression library. A classic in terms of compression, achieves good compression rates but is somewhat slow.
lzo: Fast compression and decompression.
bzip2: Good compression rates.
blosc: Fast compression and decompression.
Support for alternative blosc compressors:
blosc:blosclz This is the default compressor for
blosc
blosc:lz4: A compact, very popular and fast compressor.
blosc:lz4hc: A tweaked version of LZ4, produces better compression ratios at the expense of speed.
blosc:snappy: A popular compressor used in many places.
blosc:zlib: A classic; somewhat slower than the previous ones, but achieving better compression ratios.
blosc:zstd: An extremely well balanced codec; it provides the best compression ratios among the others above, and at reasonably fast speed.
If
complib
is defined as something other than the listed libraries aValueError
exception is issued.
Note
If the library specified with the complib
option is missing on your platform,
compression defaults to zlib
without further ado.
Enable compression for all objects within the file:
store_compressed = pd.HDFStore(
"store_compressed.h5", complevel=9, complib="blosc:blosclz"
)
Or on-the-fly compression (this only applies to tables) in stores where compression is not enabled:
store.append("df", df, complib="zlib", complevel=5)
ptrepack#
PyTables
offers better write performance when tables are compressed after
they are written, as opposed to turning on compression at the very
beginning. You can use the supplied PyTables
utility
ptrepack
. In addition, ptrepack
can change compression levels
after the fact.
ptrepack --chunkshape=auto --propindexes --complevel=9 --complib=blosc in.h5 out.h5
Furthermore ptrepack in.h5 out.h5
will repack the file to allow
you to reuse previously deleted space. Alternatively, one can simply
remove the file and write again, or use the copy
method.
Caveats#
Warning
HDFStore
is not-threadsafe for writing. The underlying
PyTables
only supports concurrent reads (via threading or
processes). If you need reading and writing at the same time, you
need to serialize these operations in a single thread in a single
process. You will corrupt your data otherwise. See the (GH 2397) for more information.
If you use locks to manage write access between multiple processes, you may want to use
fsync()
before releasing write locks. For convenience you can usestore.flush(fsync=True)
to do this for you.Once a
table
is created columns (DataFrame) are fixed; only exactly the same columns can be appendedBe aware that timezones (e.g.,
zoneinfo.ZoneInfo('US/Eastern')
) are not necessarily equal across timezone versions. So if data is localized to a specific timezone in the HDFStore using one version of a timezone library and that data is updated with another version, the data will be converted to UTC since these timezones are not considered equal. Either use the same version of timezone library or usetz_convert
with the updated timezone definition.
Warning
PyTables
will show a NaturalNameWarning
if a column name
cannot be used as an attribute selector.
Natural identifiers contain only letters, numbers, and underscores,
and may not begin with a number.
Other identifiers cannot be used in a where
clause
and are generally a bad idea.
DataTypes#
HDFStore
will map an object dtype to the PyTables
underlying
dtype. This means the following types are known to work:
Type |
Represents missing values |
---|---|
floating : |
|
integer : |
|
boolean |
|
|
|
|
|
categorical : see the section below |
|
object : |
|
unicode
columns are not supported, and WILL FAIL.
Categorical data#
You can write data that contains category
dtypes to a HDFStore
.
Queries work the same as if it was an object array. However, the category
dtyped data is
stored in a more efficient manner.
In [570]: dfcat = pd.DataFrame(
.....: {"A": pd.Series(list("aabbcdba")).astype("category"), "B": np.random.randn(8)}
.....: )
.....:
In [571]: dfcat
Out[571]:
A B
0 a -1.520478
1 a -1.069391
2 b -0.551981
3 b 0.452407
4 c 0.409257
5 d 0.301911
6 b -0.640843
7 a -2.253022
In [572]: dfcat.dtypes
Out[572]:
A category
B float64
dtype: object
In [573]: cstore = pd.HDFStore("cats.h5", mode="w")
In [574]: cstore.append("dfcat", dfcat, format="table", data_columns=["A"])
In [575]: result = cstore.select("dfcat", where="A in ['b', 'c']")
In [576]: result
Out[576]:
A B
2 b -0.551981
3 b 0.452407
4 c 0.409257
6 b -0.640843
In [577]: result.dtypes
Out[577]:
A category
B float64
dtype: object
String columns#
min_itemsize
The underlying implementation of HDFStore
uses a fixed column width (itemsize) for string columns.
A string column itemsize is calculated as the maximum of the
length of data (for that column) that is passed to the HDFStore
, in the first append. Subsequent appends,
may introduce a string for a column larger than the column can hold, an Exception will be raised (otherwise you
could have a silent truncation of these columns, leading to loss of information). In the future we may relax this and
allow a user-specified truncation to occur.
Pass min_itemsize
on the first table creation to a-priori specify the minimum length of a particular string column.
min_itemsize
can be an integer, or a dict mapping a column name to an integer. You can pass values
as a key to
allow all indexables or data_columns to have this min_itemsize.
Passing a min_itemsize
dict will cause all passed columns to be created as data_columns automatically.
Note
If you are not passing any data_columns
, then the min_itemsize
will be the maximum of the length of any string passed
In [578]: dfs = pd.DataFrame({"A": "foo", "B": "bar"}, index=list(range(5)))
In [579]: dfs
Out[579]:
A B
0 foo bar
1 foo bar
2 foo bar
3 foo bar
4 foo bar
# A and B have a size of 30
In [580]: store.append("dfs", dfs, min_itemsize=30)
In [581]: store.get_storer("dfs").table
Out[581]:
/dfs/table (Table(5,)) ''
description := {
"index": Int64Col(shape=(), dflt=0, pos=0),
"values_block_0": StringCol(itemsize=30, shape=(2,), dflt=b'', pos=1)}
byteorder := 'little'
chunkshape := (963,)
autoindex := True
colindexes := {
"index": Index(6, mediumshuffle, zlib(1)).is_csi=False}
# A is created as a data_column with a size of 30
# B is size is calculated
In [582]: store.append("dfs2", dfs, min_itemsize={"A": 30})
In [583]: store.get_storer("dfs2").table
Out[583]:
/dfs2/table (Table(5,)) ''
description := {
"index": Int64Col(shape=(), dflt=0, pos=0),
"values_block_0": StringCol(itemsize=3, shape=(1,), dflt=b'', pos=1),
"A": StringCol(itemsize=30, shape=(), dflt=b'', pos=2)}
byteorder := 'little'
chunkshape := (1598,)
autoindex := True
colindexes := {
"index": Index(6, mediumshuffle, zlib(1)).is_csi=False,
"A": Index(6, mediumshuffle, zlib(1)).is_csi=False}
nan_rep
String columns will serialize a np.nan
(a missing value) with the nan_rep
string representation. This defaults to the string value nan
.
You could inadvertently turn an actual nan
value into a missing value.
In [584]: dfss = pd.DataFrame({"A": ["foo", "bar", "nan"]})
In [585]: dfss
Out[585]:
A
0 foo
1 bar
2 nan
In [586]: store.append("dfss", dfss)
In [587]: store.select("dfss")
Out[587]:
A
0 foo
1 bar
2 NaN
# here you need to specify a different nan rep
In [588]: store.append("dfss2", dfss, nan_rep="_nan_")
In [589]: store.select("dfss2")
Out[589]:
A
0 foo
1 bar
2 nan
Performance#
tables
format come with a writing performance penalty as compared tofixed
stores. The benefit is the ability to append/delete and query (potentially very large amounts of data). Write times are generally longer as compared with regular stores. Query times can be quite fast, especially on an indexed axis.You can pass
chunksize=<int>
toappend
, specifying the write chunksize (default is 50000). This will significantly lower your memory usage on writing.You can pass
expectedrows=<int>
to the firstappend
, to set the TOTAL number of rows thatPyTables
will expect. This will optimize read/write performance.Duplicate rows can be written to tables, but are filtered out in selection (with the last items being selected; thus a table is unique on major, minor pairs)
A
PerformanceWarning
will be raised if you are attempting to store types that will be pickled by PyTables (rather than stored as endemic types). See Here for more information and some solutions.
Feather#
Feather provides binary columnar serialization for data frames. It is designed to make reading and writing data frames efficient, and to make sharing data across data analysis languages easy.
Feather is designed to faithfully serialize and de-serialize DataFrames, supporting all of the pandas dtypes, including extension dtypes such as categorical and datetime with tz.
Several caveats:
The format will NOT write an
Index
, orMultiIndex
for theDataFrame
and will raise an error if a non-default one is provided. You can.reset_index()
to store the index or.reset_index(drop=True)
to ignore it.Duplicate column names and non-string columns names are not supported
Actual Python objects in object dtype columns are not supported. These will raise a helpful error message on an attempt at serialization.
See the Full Documentation.
In [590]: import pytz
In [591]: df = pd.DataFrame(
.....: {
.....: "a": list("abc"),
.....: "b": list(range(1, 4)),
.....: "c": np.arange(3, 6).astype("u1"),
.....: "d": np.arange(4.0, 7.0, dtype="float64"),
.....: "e": [True, False, True],
.....: "f": pd.Categorical(list("abc")),
.....: "g": pd.date_range("20130101", periods=3),
.....: "h": pd.date_range("20130101", periods=3, tz=pytz.timezone("US/Eastern")),
.....: "i": pd.date_range("20130101", periods=3, freq="ns"),
.....: }
.....: )
.....:
In [592]: df
Out[592]:
a b c ... g h i
0 a 1 3 ... 2013-01-01 2013-01-01 00:00:00-05:00 2013-01-01 00:00:00.000000000
1 b 2 4 ... 2013-01-02 2013-01-02 00:00:00-05:00 2013-01-01 00:00:00.000000001
2 c 3 5 ... 2013-01-03 2013-01-03 00:00:00-05:00 2013-01-01 00:00:00.000000002
[3 rows x 9 columns]
In [593]: df.dtypes
Out[593]:
a object
b int64
c uint8
d float64
e bool
f category
g datetime64[ns]
h datetime64[ns, US/Eastern]
i datetime64[ns]
dtype: object
Write to a feather file.
In [594]: df.to_feather("example.feather")
Read from a feather file.
In [595]: result = pd.read_feather("example.feather")
In [596]: result
Out[596]:
a b c ... g h i
0 a 1 3 ... 2013-01-01 2013-01-01 00:00:00-05:00 2013-01-01 00:00:00.000000000
1 b 2 4 ... 2013-01-02 2013-01-02 00:00:00-05:00 2013-01-01 00:00:00.000000001
2 c 3 5 ... 2013-01-03 2013-01-03 00:00:00-05:00 2013-01-01 00:00:00.000000002
[3 rows x 9 columns]
# we preserve dtypes
In [597]: result.dtypes
Out[597]:
a object
b int64
c uint8
d float64
e bool
f category
g datetime64[ns]
h datetime64[ns, US/Eastern]
i datetime64[ns]
dtype: object
Parquet#
Apache Parquet provides a partitioned binary columnar serialization for data frames. It is designed to make reading and writing data frames efficient, and to make sharing data across data analysis languages easy. Parquet can use a variety of compression techniques to shrink the file size as much as possible while still maintaining good read performance.
Parquet is designed to faithfully serialize and de-serialize DataFrame
s, supporting all of the pandas
dtypes, including extension dtypes such as datetime with tz.
Several caveats.
Duplicate column names and non-string columns names are not supported.
The
pyarrow
engine always writes the index to the output, butfastparquet
only writes non-default indexes. This extra column can cause problems for non-pandas consumers that are not expecting it. You can force including or omitting indexes with theindex
argument, regardless of the underlying engine.Index level names, if specified, must be strings.
In the
pyarrow
engine, categorical dtypes for non-string types can be serialized to parquet, but will de-serialize as their primitive dtype.The
pyarrow
engine preserves theordered
flag of categorical dtypes with string types.fastparquet
does not preserve theordered
flag.Non supported types include
Interval
and actual Python object types. These will raise a helpful error message on an attempt at serialization.Period
type is supported with pyarrow >= 0.16.0.The
pyarrow
engine preserves extension data types such as the nullable integer and string data type (requiring pyarrow >= 0.16.0, and requiring the extension type to implement the needed protocols, see the extension types documentation).
You can specify an engine
to direct the serialization. This can be one of pyarrow
, or fastparquet
, or auto
.
If the engine is NOT specified, then the pd.options.io.parquet.engine
option is checked; if this is also auto
,
then pyarrow
is tried, and falling back to fastparquet
.
See the documentation for pyarrow and fastparquet.
Note
These engines are very similar and should read/write nearly identical parquet format files.
pyarrow>=8.0.0
supports timedelta data, fastparquet>=0.1.4
supports timezone aware datetimes.
These libraries differ by having different underlying dependencies (fastparquet
by using numba
, while pyarrow
uses a c-library).
In [598]: df = pd.DataFrame(
.....: {
.....: "a": list("abc"),
.....: "b": list(range(1, 4)),
.....: "c": np.arange(3, 6).astype("u1"),
.....: "d": np.arange(4.0, 7.0, dtype="float64"),
.....: "e": [True, False, True],
.....: "f": pd.date_range("20130101", periods=3),
.....: "g": pd.date_range("20130101", periods=3, tz="US/Eastern"),
.....: "h": pd.Categorical(list("abc")),
.....: "i": pd.Categorical(list("abc"), ordered=True),
.....: }
.....: )
.....:
In [599]: df
Out[599]:
a b c d e f g h i
0 a 1 3 4.0 True 2013-01-01 2013-01-01 00:00:00-05:00 a a
1 b 2 4 5.0 False 2013-01-02 2013-01-02 00:00:00-05:00 b b
2 c 3 5 6.0 True 2013-01-03 2013-01-03 00:00:00-05:00 c c
In [600]: df.dtypes
Out[600]:
a object
b int64
c uint8
d float64
e bool
f datetime64[ns]
g datetime64[ns, US/Eastern]
h category
i category
dtype: object
Write to a parquet file.
In [601]: df.to_parquet("example_pa.parquet", engine="pyarrow")
In [602]: df.to_parquet("example_fp.parquet", engine="fastparquet")
Read from a parquet file.
In [603]: result = pd.read_parquet("example_fp.parquet", engine="fastparquet")
In [604]: result = pd.read_parquet("example_pa.parquet", engine="pyarrow")
In [605]: result.dtypes
Out[605]:
a object
b int64
c uint8
d float64
e bool
f datetime64[ns]
g datetime64[ns, US/Eastern]
h category
i category
dtype: object
By setting the dtype_backend
argument you can control the default dtypes used for the resulting DataFrame.
In [606]: result = pd.read_parquet("example_pa.parquet", engine="pyarrow", dtype_backend="pyarrow")
In [607]: result.dtypes
Out[607]:
a string[pyarrow]
b int64[pyarrow]
c uint8[pyarrow]
d double[pyarrow]
e bool[pyarrow]
f timestamp[ns][pyarrow]
g timestamp[ns, tz=US/Eastern][pyarrow]
h dictionary<values=string, indices=int32, order...
i dictionary<values=string, indices=int32, order...
dtype: object
Note
Note that this is not supported for fastparquet
.
Read only certain columns of a parquet file.
In [608]: result = pd.read_parquet(
.....: "example_fp.parquet",
.....: engine="fastparquet",
.....: columns=["a", "b"],
.....: )
.....:
In [609]: result = pd.read_parquet(
.....: "example_pa.parquet",
.....: engine="pyarrow",
.....: columns=["a", "b"],
.....: )
.....:
In [610]: result.dtypes
Out[610]:
a object
b int64
dtype: object
Handling indexes#
Serializing a DataFrame
to parquet may include the implicit index as one or
more columns in the output file. Thus, this code:
In [611]: df = pd.DataFrame({"a": [1, 2], "b": [3, 4]})
In [612]: df.to_parquet("test.parquet", engine="pyarrow")
creates a parquet file with three columns if you use pyarrow
for serialization:
a
, b
, and __index_level_0__
. If you’re using fastparquet
, the
index may or may not
be written to the file.
This unexpected extra column causes some databases like Amazon Redshift to reject the file, because that column doesn’t exist in the target table.
If you want to omit a dataframe’s indexes when writing, pass index=False
to
to_parquet()
:
In [613]: df.to_parquet("test.parquet", index=False)
This creates a parquet file with just the two expected columns, a
and b
.
If your DataFrame
has a custom index, you won’t get it back when you load
this file into a DataFrame
.
Passing index=True
will always write the index, even if that’s not the
underlying engine’s default behavior.
Partitioning Parquet files#
Parquet supports partitioning of data based on the values of one or more columns.
In [614]: df = pd.DataFrame({"a": [0, 0, 1, 1], "b": [0, 1, 0, 1]})
In [615]: df.to_parquet(path="test", engine="pyarrow", partition_cols=["a"], compression=None)
The path
specifies the parent directory to which data will be saved.
The partition_cols
are the column names by which the dataset will be partitioned.
Columns are partitioned in the order they are given. The partition splits are
determined by the unique values in the partition columns.
The above example creates a partitioned dataset that may look like:
test
├── a=0
│ ├── 0bac803e32dc42ae83fddfd029cbdebc.parquet
│ └── ...
└── a=1
├── e6ab24a4f45147b49b54a662f0c412a3.parquet
└── ...
ORC#
Similar to the parquet format, the ORC Format is a binary columnar serialization
for data frames. It is designed to make reading data frames efficient. pandas provides both the reader and the writer for the
ORC format, read_orc()
and to_orc()
. This requires the pyarrow library.
Warning
It is highly recommended to install pyarrow using conda due to some issues occurred by pyarrow.
to_orc()
requires pyarrow>=7.0.0.read_orc()
andto_orc()
are not supported on Windows yet, you can find valid environments on install optional dependencies.For supported dtypes please refer to supported ORC features in Arrow.
Currently timezones in datetime columns are not preserved when a dataframe is converted into ORC files.
In [616]: df = pd.DataFrame(
.....: {
.....: "a": list("abc"),
.....: "b": list(range(1, 4)),
.....: "c": np.arange(4.0, 7.0, dtype="float64"),
.....: "d": [True, False, True],
.....: "e": pd.date_range("20130101", periods=3),
.....: }
.....: )
.....:
In [617]: df
Out[617]:
a b c d e
0 a 1 4.0 True 2013-01-01
1 b 2 5.0 False 2013-01-02
2 c 3 6.0 True 2013-01-03
In [618]: df.dtypes
Out[618]:
a object
b int64
c float64
d bool
e datetime64[ns]
dtype: object
Write to an orc file.
In [619]: df.to_orc("example_pa.orc", engine="pyarrow")
Read from an orc file.
In [620]: result = pd.read_orc("example_pa.orc")
In [621]: result.dtypes
Out[621]:
a object
b int64
c float64
d bool
e datetime64[ns]
dtype: object
Read only certain columns of an orc file.
In [622]: result = pd.read_orc(
.....: "example_pa.orc",
.....: columns=["a", "b"],
.....: )
.....:
In [623]: result.dtypes
Out[623]:
a object
b int64
dtype: object
SQL queries#
The pandas.io.sql
module provides a collection of query wrappers to both
facilitate data retrieval and to reduce dependency on DB-specific API.
Where available, users may first want to opt for Apache Arrow ADBC drivers. These drivers should provide the best performance, null handling, and type detection.
Added in version 2.2.0: Added native support for ADBC drivers
For a full list of ADBC drivers and their development status, see the ADBC Driver Implementation Status documentation.
Where an ADBC driver is not available or may be missing functionality, users should opt for installing SQLAlchemy alongside their database driver library. Examples of such drivers are psycopg2 for PostgreSQL or pymysql for MySQL. For SQLite this is included in Python’s standard library by default. You can find an overview of supported drivers for each SQL dialect in the SQLAlchemy docs.
If SQLAlchemy is not installed, you can use a sqlite3.Connection
in place of
a SQLAlchemy engine, connection, or URI string.
See also some cookbook examples for some advanced strategies.
The key functions are:
|
Read SQL database table into a DataFrame. |
|
Read SQL query into a DataFrame. |
|
Read SQL query or database table into a DataFrame. |
|
Write records stored in a DataFrame to a SQL database. |
Note
The function read_sql()
is a convenience wrapper around
read_sql_table()
and read_sql_query()
(and for
backward compatibility) and will delegate to specific function depending on
the provided input (database table name or sql query).
Table names do not need to be quoted if they have special characters.
In the following example, we use the SQlite SQL database engine. You can use a temporary SQLite database where data are stored in “memory”.
To connect using an ADBC driver you will want to install the adbc_driver_sqlite
using your
package manager. Once installed, you can use the DBAPI interface provided by the ADBC driver
to connect to your database.
import adbc_driver_sqlite.dbapi as sqlite_dbapi
# Create the connection
with sqlite_dbapi.connect("sqlite:///:memory:") as conn:
df = pd.read_sql_table("data", conn)
To connect with SQLAlchemy you use the create_engine()
function to create an engine
object from database URI. You only need to create the engine once per database you are
connecting to.
For more information on create_engine()
and the URI formatting, see the examples
below and the SQLAlchemy documentation
In [624]: from sqlalchemy import create_engine
# Create your engine.
In [625]: engine = create_engine("sqlite:///:memory:")
If you want to manage your own connections you can pass one of those instead. The example below opens a connection to the database using a Python context manager that automatically closes the connection after the block has completed. See the SQLAlchemy docs for an explanation of how the database connection is handled.
with engine.connect() as conn, conn.begin():
data = pd.read_sql_table("data", conn)
Warning
When you open a connection to a database you are also responsible for closing it. Side effects of leaving a connection open may include locking the database or other breaking behaviour.
Writing DataFrames#
Assuming the following data is in a DataFrame
data
, we can insert it into
the database using to_sql()
.
id |
Date |
Col_1 |
Col_2 |
Col_3 |
---|---|---|---|---|
26 |
2012-10-18 |
X |
25.7 |
True |
42 |
2012-10-19 |
Y |
-12.4 |
False |
63 |
2012-10-20 |
Z |
5.73 |
True |
In [626]: import datetime
In [627]: c = ["id", "Date", "Col_1", "Col_2", "Col_3"]
In [628]: d = [
.....: (26, datetime.datetime(2010, 10, 18), "X", 27.5, True),
.....: (42, datetime.datetime(2010, 10, 19), "Y", -12.5, False),
.....: (63, datetime.datetime(2010, 10, 20), "Z", 5.73, True),
.....: ]
.....:
In [629]: data = pd.DataFrame(d, columns=c)
In [630]: data
Out[630]:
id Date Col_1 Col_2 Col_3
0 26 2010-10-18 X 27.50 True
1 42 2010-10-19 Y -12.50 False
2 63 2010-10-20 Z 5.73 True
In [631]: data.to_sql("data", con=engine)
Out[631]: 3
With some databases, writing large DataFrames can result in errors due to
packet size limitations being exceeded. This can be avoided by setting the
chunksize
parameter when calling to_sql
. For example, the following
writes data
to the database in batches of 1000 rows at a time:
In [632]: data.to_sql("data_chunked", con=engine, chunksize=1000)
Out[632]: 3
SQL data types#
Ensuring consistent data type management across SQL databases is challenging. Not every SQL database offers the same types, and even when they do the implementation of a given type can vary in ways that have subtle effects on how types can be preserved.
For the best odds at preserving database types users are advised to use ADBC drivers when available. The Arrow type system offers a wider array of types that more closely match database types than the historical pandas/NumPy type system. To illustrate, note this (non-exhaustive) listing of types available in different databases and pandas backends:
numpy/pandas |
arrow |
postgres |
sqlite |
---|---|---|---|
int16/Int16 |
int16 |
SMALLINT |
INTEGER |
int32/Int32 |
int32 |
INTEGER |
INTEGER |
int64/Int64 |
int64 |
BIGINT |
INTEGER |
float32 |
float32 |
REAL |
REAL |
float64 |
float64 |
DOUBLE PRECISION |
REAL |
object |
string |
TEXT |
TEXT |
bool |
|
BOOLEAN |
|
datetime64[ns] |
timestamp(us) |
TIMESTAMP |
|
datetime64[ns,tz] |
timestamp(us,tz) |
TIMESTAMPTZ |
|
date32 |
DATE |
||
month_day_nano_interval |
INTERVAL |
||
binary |
BINARY |
BLOB |
|
decimal128 |
DECIMAL [1] |
||
list |
ARRAY [1] |
||
struct |
|
Footnotes
If you are interested in preserving database types as best as possible
throughout the lifecycle of your DataFrame, users are encouraged to
leverage the dtype_backend="pyarrow"
argument of read_sql()
# for roundtripping
with pg_dbapi.connect(uri) as conn:
df2 = pd.read_sql("pandas_table", conn, dtype_backend="pyarrow")
This will prevent your data from being converted to the traditional pandas/NumPy type system, which often converts SQL types in ways that make them impossible to round-trip.
In case an ADBC driver is not available, to_sql()
will try to map your data to an appropriate SQL data type based on the dtype of
the data. When you have columns of dtype object
, pandas will try to infer
the data type.
You can always override the default type by specifying the desired SQL type of
any of the columns by using the dtype
argument. This argument needs a
dictionary mapping column names to SQLAlchemy types (or strings for the sqlite3
fallback mode).
For example, specifying to use the sqlalchemy String
type instead of the
default Text
type for string columns:
In [633]: from sqlalchemy.types import String
In [634]: data.to_sql("data_dtype", con=engine, dtype={"Col_1": String})
Out[634]: 3
Note
Due to the limited support for timedelta’s in the different database
flavors, columns with type timedelta64
will be written as integer
values as nanoseconds to the database and a warning will be raised. The only
exception to this is when using the ADBC PostgreSQL driver in which case a
timedelta will be written to the database as an INTERVAL
Note
Columns of category
dtype will be converted to the dense representation
as you would get with np.asarray(categorical)
(e.g. for string categories
this gives an array of strings).
Because of this, reading the database table back in does not generate
a categorical.
Datetime data types#
Using ADBC or SQLAlchemy, to_sql()
is capable of writing
datetime data that is timezone naive or timezone aware. However, the resulting
data stored in the database ultimately depends on the supported data type
for datetime data of the database system being used.
The following table lists supported data types for datetime data for some common databases. Other database dialects may have different data types for datetime data.
Database |
SQL Datetime Types |
Timezone Support |
---|---|---|
SQLite |
|
No |
MySQL |
|
No |
PostgreSQL |
|
Yes |
When writing timezone aware data to databases that do not support timezones, the data will be written as timezone naive timestamps that are in local time with respect to the timezone.
read_sql_table()
is also capable of reading datetime data that is
timezone aware or naive. When reading TIMESTAMP WITH TIME ZONE
types, pandas
will convert the data to UTC.
Insertion method#
The parameter method
controls the SQL insertion clause used.
Possible values are:
None
: Uses standard SQLINSERT
clause (one per row).'multi'
: Pass multiple values in a singleINSERT
clause. It uses a special SQL syntax not supported by all backends. This usually provides better performance for analytic databases like Presto and Redshift, but has worse performance for traditional SQL backend if the table contains many columns. For more information check the SQLAlchemy documentation.callable with signature
(pd_table, conn, keys, data_iter)
: This can be used to implement a more performant insertion method based on specific backend dialect features.
Example of a callable using PostgreSQL COPY clause:
# Alternative to_sql() *method* for DBs that support COPY FROM
import csv
from io import StringIO
def psql_insert_copy(table, conn, keys, data_iter):
"""
Execute SQL statement inserting data
Parameters
----------
table : pandas.io.sql.SQLTable
conn : sqlalchemy.engine.Engine or sqlalchemy.engine.Connection
keys : list of str
Column names
data_iter : Iterable that iterates the values to be inserted
"""
# gets a DBAPI connection that can provide a cursor
dbapi_conn = conn.connection
with dbapi_conn.cursor() as cur:
s_buf = StringIO()
writer = csv.writer(s_buf)
writer.writerows(data_iter)
s_buf.seek(0)
columns = ', '.join(['"{}"'.format(k) for k in keys])
if table.schema:
table_name = '{}.{}'.format(table.schema, table.name)
else:
table_name = table.name
sql = 'COPY {} ({}) FROM STDIN WITH CSV'.format(
table_name, columns)
cur.copy_expert(sql=sql, file=s_buf)
Reading tables#
read_sql_table()
will read a database table given the
table name and optionally a subset of columns to read.
Note
In order to use read_sql_table()
, you must have the
ADBC driver or SQLAlchemy optional dependency installed.
In [635]: pd.read_sql_table("data", engine)
Out[635]:
index id Date Col_1 Col_2 Col_3
0 0 26 2010-10-18 X 27.50 True
1 1 42 2010-10-19 Y -12.50 False
2 2 63 2010-10-20 Z 5.73 True
Note
ADBC drivers will map database types directly back to arrow types. For other drivers
note that pandas infers column dtypes from query outputs, and not by looking
up data types in the physical database schema. For example, assume userid
is an integer column in a table. Then, intuitively, select userid ...
will
return integer-valued series, while select cast(userid as text) ...
will
return object-valued (str) series. Accordingly, if the query output is empty,
then all resulting columns will be returned as object-valued (since they are
most general). If you foresee that your query will sometimes generate an empty
result, you may want to explicitly typecast afterwards to ensure dtype
integrity.
You can also specify the name of the column as the DataFrame
index,
and specify a subset of columns to be read.
In [636]: pd.read_sql_table("data", engine, index_col="id")
Out[636]:
index Date Col_1 Col_2 Col_3
id
26 0 2010-10-18 X 27.50 True
42 1 2010-10-19 Y -12.50 False
63 2 2010-10-20 Z 5.73 True
In [637]: pd.read_sql_table("data", engine, columns=["Col_1", "Col_2"])
Out[637]:
Col_1 Col_2
0 X 27.50
1 Y -12.50
2 Z 5.73
And you can explicitly force columns to be parsed as dates:
In [638]: pd.read_sql_table("data", engine, parse_dates=["Date"])
Out[638]:
index id Date Col_1 Col_2 Col_3
0 0 26 2010-10-18 X 27.50 True
1 1 42 2010-10-19 Y -12.50 False
2 2 63 2010-10-20 Z 5.73 True
If needed you can explicitly specify a format string, or a dict of arguments
to pass to pandas.to_datetime()
:
pd.read_sql_table("data", engine, parse_dates={"Date": "%Y-%m-%d"})
pd.read_sql_table(
"data",
engine,
parse_dates={"Date": {"format": "%Y-%m-%d %H:%M:%S"}},
)
You can check if a table exists using has_table()
Schema support#
Reading from and writing to different schemas is supported through the schema
keyword in the read_sql_table()
and to_sql()
functions. Note however that this depends on the database flavor (sqlite does not
have schemas). For example:
df.to_sql(name="table", con=engine, schema="other_schema")
pd.read_sql_table("table", engine, schema="other_schema")
Querying#
You can query using raw SQL in the read_sql_query()
function.
In this case you must use the SQL variant appropriate for your database.
When using SQLAlchemy, you can also pass SQLAlchemy Expression language constructs,
which are database-agnostic.
In [639]: pd.read_sql_query("SELECT * FROM data", engine)
Out[639]:
index id Date Col_1 Col_2 Col_3
0 0 26 2010-10-18 00:00:00.000000 X 27.50 1
1 1 42 2010-10-19 00:00:00.000000 Y -12.50 0
2 2 63 2010-10-20 00:00:00.000000 Z 5.73 1
Of course, you can specify a more “complex” query.
In [640]: pd.read_sql_query("SELECT id, Col_1, Col_2 FROM data WHERE id = 42;", engine)
Out[640]:
id Col_1 Col_2
0 42 Y -12.5
The read_sql_query()
function supports a chunksize
argument.
Specifying this will return an iterator through chunks of the query result:
In [641]: df = pd.DataFrame(np.random.randn(20, 3), columns=list("abc"))
In [642]: df.to_sql(name="data_chunks", con=engine, index=False)
Out[642]: 20
In [643]: for chunk in pd.read_sql_query("SELECT * FROM data_chunks", engine, chunksize=5):
.....: print(chunk)
.....:
a b c
0 -0.395347 -0.822726 -0.363777
1 1.676124 -0.908102 -1.391346
2 -1.094269 0.278380 1.205899
3 1.503443 0.932171 -0.709459
4 -0.645944 -1.351389 0.132023
a b c
0 0.210427 0.192202 0.661949
1 1.690629 -1.046044 0.618697
2 -0.013863 1.314289 1.951611
3 -1.485026 0.304662 1.194757
4 -0.446717 0.528496 -0.657575
a b c
0 -0.876654 0.336252 0.172668
1 0.337684 -0.411202 -0.828394
2 -0.244413 1.094948 0.087183
3 1.125934 -1.480095 1.205944
4 -0.451849 0.452214 -2.208192
a b c
0 -2.061019 0.044184 -0.017118
1 1.248959 -0.675595 -1.908296
2 -0.125934 1.491974 0.648726
3 0.391214 0.438609 1.634248
4 1.208707 -1.535740 1.620399
Engine connection examples#
To connect with SQLAlchemy you use the create_engine()
function to create an engine
object from database URI. You only need to create the engine once per database you are
connecting to.
from sqlalchemy import create_engine
engine = create_engine("postgresql://scott:tiger@localhost:5432/mydatabase")
engine = create_engine("mysql+mysqldb://scott:tiger@localhost/foo")
engine = create_engine("oracle://scott:[email protected]:1521/sidname")
engine = create_engine("mssql+pyodbc://mydsn")
# sqlite://<nohostname>/<path>
# where <path> is relative:
engine = create_engine("sqlite:///foo.db")
# or absolute, starting with a slash:
engine = create_engine("sqlite:////absolute/path/to/foo.db")
For more information see the examples the SQLAlchemy documentation
Advanced SQLAlchemy queries#
You can use SQLAlchemy constructs to describe your query.
Use sqlalchemy.text()
to specify query parameters in a backend-neutral way
In [644]: import sqlalchemy as sa
In [645]: pd.read_sql(
.....: sa.text("SELECT * FROM data where Col_1=:col1"), engine, params={"col1": "X"}
.....: )
.....:
Out[645]:
index id Date Col_1 Col_2 Col_3
0 0 26 2010-10-18 00:00:00.000000 X 27.5 1
If you have an SQLAlchemy description of your database you can express where conditions using SQLAlchemy expressions
In [646]: metadata = sa.MetaData()
In [647]: data_table = sa.Table(
.....: "data",
.....: metadata,
.....: sa.Column("index", sa.Integer),
.....: sa.Column("Date", sa.DateTime),
.....: sa.Column("Col_1", sa.String),
.....: sa.Column("Col_2", sa.Float),
.....: sa.Column("Col_3", sa.Boolean),
.....: )
.....:
In [648]: pd.read_sql(sa.select(data_table).where(data_table.c.Col_3 is True), engine)
Out[648]:
Empty DataFrame
Columns: [index, Date, Col_1, Col_2, Col_3]
Index: []
You can combine SQLAlchemy expressions with parameters passed to read_sql()
using sqlalchemy.bindparam()
In [649]: import datetime as dt
In [650]: expr = sa.select(data_table).where(data_table.c.Date > sa.bindparam("date"))
In [651]: pd.read_sql(expr, engine, params={"date": dt.datetime(2010, 10, 18)})
Out[651]:
index Date Col_1 Col_2 Col_3
0 1 2010-10-19 Y -12.50 False
1 2 2010-10-20 Z 5.73 True
Sqlite fallback#
The use of sqlite is supported without using SQLAlchemy. This mode requires a Python database adapter which respect the Python DB-API.
You can create connections like so:
import sqlite3
con = sqlite3.connect(":memory:")
And then issue the following queries:
data.to_sql("data", con)
pd.read_sql_query("SELECT * FROM data", con)
Google BigQuery#
The pandas-gbq
package provides functionality to read/write from Google BigQuery.
Full documentation can be found here.
Stata format#
Writing to stata format#
The method DataFrame.to_stata()
will write a DataFrame
into a .dta file. The format version of this file is always 115 (Stata 12).
In [652]: df = pd.DataFrame(np.random.randn(10, 2), columns=list("AB"))
In [653]: df.to_stata("stata.dta")
Stata data files have limited data type support; only strings with
244 or fewer characters, int8
, int16
, int32
, float32
and float64
can be stored in .dta
files. Additionally,
Stata reserves certain values to represent missing data. Exporting a
non-missing value that is outside of the permitted range in Stata for
a particular data type will retype the variable to the next larger
size. For example, int8
values are restricted to lie between -127
and 100 in Stata, and so variables with values above 100 will trigger
a conversion to int16
. nan
values in floating points data
types are stored as the basic missing data type (.
in Stata).
Note
It is not possible to export missing data values for integer data types.
The Stata writer gracefully handles other data types including int64
,
bool
, uint8
, uint16
, uint32
by casting to
the smallest supported type that can represent the data. For example, data
with a type of uint8
will be cast to int8
if all values are less than
100 (the upper bound for non-missing int8
data in Stata), or, if values are
outside of this range, the variable is cast to int16
.
Warning
Conversion from int64
to float64
may result in a loss of precision
if int64
values are larger than 2**53.
Warning
StataWriter
and
DataFrame.to_stata()
only support fixed width
strings containing up to 244 characters, a limitation imposed by the version
115 dta file format. Attempting to write Stata dta files with strings
longer than 244 characters raises a ValueError
.
Reading from Stata format#
The top-level function read_stata
will read a dta file and return
either a DataFrame
or a pandas.api.typing.StataReader
that can
be used to read the file incrementally.
In [654]: pd.read_stata("stata.dta")
Out[654]:
index A B
0 0 -0.165614 0.490482
1 1 -0.637829 0.067091
2 2 -0.242577 1.348038
3 3 0.647699 -0.644937
4 4 0.625771 0.918376
5 5 0.401781 -1.488919
6 6 -0.981845 -0.046882
7 7 -0.306796 0.877025
8 8 -0.336606 0.624747
9 9 -1.582600 0.806340
Specifying a chunksize
yields a
pandas.api.typing.StataReader
instance that can be used to
read chunksize
lines from the file at a time. The StataReader
object can be used as an iterator.
In [655]: with pd.read_stata("stata.dta", chunksize=3) as reader:
.....: for df in reader:
.....: print(df.shape)
.....:
(3, 3)
(3, 3)
(3, 3)
(1, 3)
For more fine-grained control, use iterator=True
and specify
chunksize
with each call to
read()
.
In [656]: with pd.read_stata("stata.dta", iterator=True) as reader:
.....: chunk1 = reader.read(5)
.....: chunk2 = reader.read(5)
.....:
Currently the index
is retrieved as a column.
The parameter convert_categoricals
indicates whether value labels should be
read and used to create a Categorical
variable from them. Value labels can
also be retrieved by the function value_labels
, which requires read()
to be called before use.
The parameter convert_missing
indicates whether missing value
representations in Stata should be preserved. If False
(the default),
missing values are represented as np.nan
. If True
, missing values are
represented using StataMissingValue
objects, and columns containing missing
values will have object
data type.
Note
read_stata()
and
StataReader
support .dta formats 113-115
(Stata 10-12), 117 (Stata 13), and 118 (Stata 14).
Note
Setting preserve_dtypes=False
will upcast to the standard pandas data types:
int64
for all integer types and float64
for floating point data. By default,
the Stata data types are preserved when importing.
Note
All StataReader
objects, whether created by read_stata()
(when using iterator=True
or chunksize
) or instantiated by hand, must be used as context
managers (e.g. the with
statement).
While the close()
method is available, its use is unsupported.
It is not part of the public API and will be removed in with future without warning.
Categorical data#
Categorical
data can be exported to Stata data files as value labeled data.
The exported data consists of the underlying category codes as integer data values
and the categories as value labels. Stata does not have an explicit equivalent
to a Categorical
and information about whether the variable is ordered
is lost when exporting.
Warning
Stata only supports string value labels, and so str
is called on the
categories when exporting data. Exporting Categorical
variables with
non-string categories produces a warning, and can result a loss of
information if the str
representations of the categories are not unique.
Labeled data can similarly be imported from Stata data files as Categorical
variables using the keyword argument convert_categoricals
(True
by default).
The keyword argument order_categoricals
(True
by default) determines
whether imported Categorical
variables are ordered.
Note
When importing categorical data, the values of the variables in the Stata
data file are not preserved since Categorical
variables always
use integer data types between -1
and n-1
where n
is the number
of categories. If the original values in the Stata data file are required,
these can be imported by setting convert_categoricals=False
, which will
import original data (but not the variable labels). The original values can
be matched to the imported categorical data since there is a simple mapping
between the original Stata data values and the category codes of imported
Categorical variables: missing values are assigned code -1
, and the
smallest original value is assigned 0
, the second smallest is assigned
1
and so on until the largest original value is assigned the code n-1
.
Note
Stata supports partially labeled series. These series have value labels for
some but not all data values. Importing a partially labeled series will produce
a Categorical
with string categories for the values that are labeled and
numeric categories for values with no label.
SAS formats#
The top-level function read_sas()
can read (but not write) SAS
XPORT (.xpt) and SAS7BDAT (.sas7bdat) format files.
SAS files only contain two value types: ASCII text and floating point
values (usually 8 bytes but sometimes truncated). For xport files,
there is no automatic type conversion to integers, dates, or
categoricals. For SAS7BDAT files, the format codes may allow date
variables to be automatically converted to dates. By default the
whole file is read and returned as a DataFrame
.
Specify a chunksize
or use iterator=True
to obtain reader
objects (XportReader
or SAS7BDATReader
) for incrementally
reading the file. The reader objects also have attributes that
contain additional information about the file and its variables.
Read a SAS7BDAT file:
df = pd.read_sas("sas_data.sas7bdat")
Obtain an iterator and read an XPORT file 100,000 lines at a time:
def do_something(chunk):
pass
with pd.read_sas("sas_xport.xpt", chunk=100000) as rdr:
for chunk in rdr:
do_something(chunk)
The specification for the xport file format is available from the SAS web site.
No official documentation is available for the SAS7BDAT format.
SPSS formats#
The top-level function read_spss()
can read (but not write) SPSS
SAV (.sav) and ZSAV (.zsav) format files.
SPSS files contain column names. By default the
whole file is read, categorical columns are converted into pd.Categorical
,
and a DataFrame
with all columns is returned.
Specify the usecols
parameter to obtain a subset of columns. Specify convert_categoricals=False
to avoid converting categorical columns into pd.Categorical
.
Read an SPSS file:
df = pd.read_spss("spss_data.sav")
Extract a subset of columns contained in usecols
from an SPSS file and
avoid converting categorical columns into pd.Categorical
:
df = pd.read_spss(
"spss_data.sav",
usecols=["foo", "bar"],
convert_categoricals=False,
)
More information about the SAV and ZSAV file formats is available here.
Other file formats#
pandas itself only supports IO with a limited set of file formats that map cleanly to its tabular data model. For reading and writing other file formats into and from pandas, we recommend these packages from the broader community.
netCDF#
xarray provides data structures inspired by the pandas DataFrame
for working
with multi-dimensional datasets, with a focus on the netCDF file format and
easy conversion to and from pandas.
Performance considerations#
This is an informal comparison of various IO methods, using pandas 0.24.2. Timings are machine dependent and small differences should be ignored.
In [1]: sz = 1000000
In [2]: df = pd.DataFrame({'A': np.random.randn(sz), 'B': [1] * sz})
In [3]: df.info()
<class 'pandas.DataFrame'>
RangeIndex: 1000000 entries, 0 to 999999
Data columns (total 2 columns):
A 1000000 non-null float64
B 1000000 non-null int64
dtypes: float64(1), int64(1)
memory usage: 15.3 MB
The following test functions will be used below to compare the performance of several IO methods:
import numpy as np
import os
sz = 1000000
df = pd.DataFrame({"A": np.random.randn(sz), "B": [1] * sz})
sz = 1000000
np.random.seed(42)
df = pd.DataFrame({"A": np.random.randn(sz), "B": [1] * sz})
def test_sql_write(df):
if os.path.exists("test.sql"):
os.remove("test.sql")
sql_db = sqlite3.connect("test.sql")
df.to_sql(name="test_table", con=sql_db)
sql_db.close()
def test_sql_read():
sql_db = sqlite3.connect("test.sql")
pd.read_sql_query("select * from test_table", sql_db)
sql_db.close()
def test_hdf_fixed_write(df):
df.to_hdf("test_fixed.hdf", key="test", mode="w")
def test_hdf_fixed_read():
pd.read_hdf("test_fixed.hdf", "test")
def test_hdf_fixed_write_compress(df):
df.to_hdf("test_fixed_compress.hdf", key="test", mode="w", complib="blosc")
def test_hdf_fixed_read_compress():
pd.read_hdf("test_fixed_compress.hdf", "test")
def test_hdf_table_write(df):
df.to_hdf("test_table.hdf", key="test", mode="w", format="table")
def test_hdf_table_read():
pd.read_hdf("test_table.hdf", "test")
def test_hdf_table_write_compress(df):
df.to_hdf(
"test_table_compress.hdf", key="test", mode="w", complib="blosc", format="table"
)
def test_hdf_table_read_compress():
pd.read_hdf("test_table_compress.hdf", "test")
def test_csv_write(df):
df.to_csv("test.csv", mode="w")
def test_csv_read():
pd.read_csv("test.csv", index_col=0)
def test_feather_write(df):
df.to_feather("test.feather")
def test_feather_read():
pd.read_feather("test.feather")
def test_pickle_write(df):
df.to_pickle("test.pkl")
def test_pickle_read():
pd.read_pickle("test.pkl")
def test_pickle_write_compress(df):
df.to_pickle("test.pkl.compress", compression="xz")
def test_pickle_read_compress():
pd.read_pickle("test.pkl.compress", compression="xz")
def test_parquet_write(df):
df.to_parquet("test.parquet")
def test_parquet_read():
pd.read_parquet("test.parquet")
When writing, the top three functions in terms of speed are test_feather_write
, test_hdf_fixed_write
and test_hdf_fixed_write_compress
.
In [4]: %timeit test_sql_write(df)
3.29 s ± 43.2 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [5]: %timeit test_hdf_fixed_write(df)
19.4 ms ± 560 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [6]: %timeit test_hdf_fixed_write_compress(df)
19.6 ms ± 308 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [7]: %timeit test_hdf_table_write(df)
449 ms ± 5.61 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [8]: %timeit test_hdf_table_write_compress(df)
448 ms ± 11.9 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [9]: %timeit test_csv_write(df)
3.66 s ± 26.2 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [10]: %timeit test_feather_write(df)
9.75 ms ± 117 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
In [11]: %timeit test_pickle_write(df)
30.1 ms ± 229 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [12]: %timeit test_pickle_write_compress(df)
4.29 s ± 15.9 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [13]: %timeit test_parquet_write(df)
67.6 ms ± 706 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
When reading, the top three functions in terms of speed are test_feather_read
, test_pickle_read
and
test_hdf_fixed_read
.
In [14]: %timeit test_sql_read()
1.77 s ± 17.7 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [15]: %timeit test_hdf_fixed_read()
19.4 ms ± 436 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [16]: %timeit test_hdf_fixed_read_compress()
19.5 ms ± 222 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [17]: %timeit test_hdf_table_read()
38.6 ms ± 857 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [18]: %timeit test_hdf_table_read_compress()
38.8 ms ± 1.49 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)
In [19]: %timeit test_csv_read()
452 ms ± 9.04 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [20]: %timeit test_feather_read()
12.4 ms ± 99.7 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
In [21]: %timeit test_pickle_read()
18.4 ms ± 191 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
In [22]: %timeit test_pickle_read_compress()
915 ms ± 7.48 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
In [23]: %timeit test_parquet_read()
24.4 ms ± 146 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
The files test.pkl.compress
, test.parquet
and test.feather
took the least space on disk (in bytes).
29519500 Oct 10 06:45 test.csv
16000248 Oct 10 06:45 test.feather
8281983 Oct 10 06:49 test.parquet
16000857 Oct 10 06:47 test.pkl
7552144 Oct 10 06:48 test.pkl.compress
34816000 Oct 10 06:42 test.sql
24009288 Oct 10 06:43 test_fixed.hdf
24009288 Oct 10 06:43 test_fixed_compress.hdf
24458940 Oct 10 06:44 test_table.hdf
24458940 Oct 10 06:44 test_table_compress.hdf
Comments and empty lines#
Ignoring line comments and empty lines#
If the
comment
parameter is specified, then completely commented lines will be ignored. By default, completely blank lines will be ignored as well.If
skip_blank_lines=False
, thenread_csv
will not ignore blank lines:Warning
The presence of ignored lines might create ambiguities involving line numbers; the parameter
header
uses row numbers (ignoring commented/empty lines), whileskiprows
uses line numbers (including commented/empty lines):If both
header
andskiprows
are specified,header
will be relative to the end ofskiprows
. For example:Comments#
Sometimes comments or meta data may be included in a file:
By default, the parser includes the comments in the output:
We can suppress the comments using the
comment
keyword: