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/ io / stata.py
"""
Module contains tools for processing Stata files into DataFrames
The StataReader below was originally written by Joe Presbrey as part of PyDTA.
It has been extended and improved by Skipper Seabold from the Statsmodels
project who also developed the StataWriter and was finally added to pandas in
a once again improved version.
You can find more information on http://presbrey.mit.edu/PyDTA and
http://www.statsmodels.org/devel/
"""
from collections import OrderedDict
import datetime
from io import BytesIO
import os
import struct
import sys
import warnings
from dateutil.relativedelta import relativedelta
import numpy as np
from pandas._libs.lib import infer_dtype
from pandas._libs.writers import max_len_string_array
from pandas.util._decorators import Appender, deprecate_kwarg
from pandas.core.dtypes.common import (
ensure_object,
is_categorical_dtype,
is_datetime64_dtype,
)
from pandas import (
Categorical,
DatetimeIndex,
NaT,
Timestamp,
concat,
isna,
to_datetime,
to_timedelta,
)
from pandas.core.frame import DataFrame
from pandas.core.series import Series
from pandas.io.common import BaseIterator, _stringify_path, get_filepath_or_buffer
_version_error = (
"Version of given Stata file is not 104, 105, 108, "
"111 (Stata 7SE), 113 (Stata 8/9), 114 (Stata 10/11), "
"115 (Stata 12), 117 (Stata 13), or 118 (Stata 14)"
)
_statafile_processing_params1 = """\
convert_dates : boolean, defaults to True
Convert date variables to DataFrame time values.
convert_categoricals : boolean, defaults to True
Read value labels and convert columns to Categorical/Factor variables."""
_encoding_params = """\
encoding : string, None or encoding
Encoding used to parse the files. None defaults to latin-1."""
_statafile_processing_params2 = """\
index_col : string, optional, default: None
Column to set as index.
convert_missing : boolean, defaults to False
Flag indicating whether to convert missing values to their Stata
representations. If False, missing values are replaced with nan.
If True, columns containing missing values are returned with
object data types and missing values are represented by
StataMissingValue objects.
preserve_dtypes : boolean, defaults to True
Preserve Stata datatypes. If False, numeric data are upcast to pandas
default types for foreign data (float64 or int64).
columns : list or None
Columns to retain. Columns will be returned in the given order. None
returns all columns.
order_categoricals : boolean, defaults to True
Flag indicating whether converted categorical data are ordered."""
_chunksize_params = """\
chunksize : int, default None
Return StataReader object for iterations, returns chunks with
given number of lines."""
_iterator_params = """\
iterator : boolean, default False
Return StataReader object."""
_read_stata_doc = """
Read Stata file into DataFrame.
Parameters
----------
filepath_or_buffer : str, path object or file-like object
Any valid string path is acceptable. The string could be a URL. Valid
URL schemes include http, ftp, s3, and file. For file URLs, a host is
expected. A local file could be: ``file://localhost/path/to/table.dta``.
If you want to pass in a path object, pandas accepts any ``os.PathLike``.
By file-like object, we refer to objects with a ``read()`` method,
such as a file handler (e.g. via builtin ``open`` function)
or ``StringIO``.
%s
%s
%s
%s
%s
Returns
-------
DataFrame or StataReader
See Also
--------
io.stata.StataReader : Low-level reader for Stata data files.
DataFrame.to_stata: Export Stata data files.
Examples
--------
Read a Stata dta file:
>>> df = pd.read_stata('filename.dta')
Read a Stata dta file in 10,000 line chunks:
>>> itr = pd.read_stata('filename.dta', chunksize=10000)
>>> for chunk in itr:
... do_something(chunk)
""" % (
_statafile_processing_params1,
_encoding_params,
_statafile_processing_params2,
_chunksize_params,
_iterator_params,
)
_data_method_doc = """\
Read observations from Stata file, converting them into a dataframe
.. deprecated::
This is a legacy method. Use `read` in new code.
Parameters
----------
%s
%s
Returns
-------
DataFrame
""" % (
_statafile_processing_params1,
_statafile_processing_params2,
)
_read_method_doc = """\
Reads observations from Stata file, converting them into a dataframe
Parameters
----------
nrows : int
Number of lines to read from data file, if None read whole file.
%s
%s
Returns
-------
DataFrame
""" % (
_statafile_processing_params1,
_statafile_processing_params2,
)
_stata_reader_doc = """\
Class for reading Stata dta files.
Parameters
----------
path_or_buf : path (string), buffer or path object
string, path object (pathlib.Path or py._path.local.LocalPath) or object
implementing a binary read() functions.
.. versionadded:: 0.23.0 support for pathlib, py.path.
%s
%s
%s
%s
""" % (
_statafile_processing_params1,
_statafile_processing_params2,
_encoding_params,
_chunksize_params,
)
@Appender(_read_stata_doc)
@deprecate_kwarg(old_arg_name="encoding", new_arg_name=None)
@deprecate_kwarg(old_arg_name="index", new_arg_name="index_col")
def read_stata(
filepath_or_buffer,
convert_dates=True,
convert_categoricals=True,
encoding=None,
index_col=None,
convert_missing=False,
preserve_dtypes=True,
columns=None,
order_categoricals=True,
chunksize=None,
iterator=False,
):
reader = StataReader(
filepath_or_buffer,
convert_dates=convert_dates,
convert_categoricals=convert_categoricals,
index_col=index_col,
convert_missing=convert_missing,
preserve_dtypes=preserve_dtypes,
columns=columns,
order_categoricals=order_categoricals,
chunksize=chunksize,
)
if iterator or chunksize:
data = reader
else:
try:
data = reader.read()
finally:
reader.close()
return data
_date_formats = ["%tc", "%tC", "%td", "%d", "%tw", "%tm", "%tq", "%th", "%ty"]
stata_epoch = datetime.datetime(1960, 1, 1)
def _stata_elapsed_date_to_datetime_vec(dates, fmt):
"""
Convert from SIF to datetime. http://www.stata.com/help.cgi?datetime
Parameters
----------
dates : Series
The Stata Internal Format date to convert to datetime according to fmt
fmt : str
The format to convert to. Can be, tc, td, tw, tm, tq, th, ty
Returns
Returns
-------
converted : Series
The converted dates
Examples
--------
>>> dates = pd.Series([52])
>>> _stata_elapsed_date_to_datetime_vec(dates , "%tw")
0 1961-01-01
dtype: datetime64[ns]
Notes
-----
datetime/c - tc
milliseconds since 01jan1960 00:00:00.000, assuming 86,400 s/day
datetime/C - tC - NOT IMPLEMENTED
milliseconds since 01jan1960 00:00:00.000, adjusted for leap seconds
date - td
days since 01jan1960 (01jan1960 = 0)
weekly date - tw
weeks since 1960w1
This assumes 52 weeks in a year, then adds 7 * remainder of the weeks.
The datetime value is the start of the week in terms of days in the
year, not ISO calendar weeks.
monthly date - tm
months since 1960m1
quarterly date - tq
quarters since 1960q1
half-yearly date - th
half-years since 1960h1 yearly
date - ty
years since 0000
If you don't have pandas with datetime support, then you can't do
milliseconds accurately.
"""
MIN_YEAR, MAX_YEAR = Timestamp.min.year, Timestamp.max.year
MAX_DAY_DELTA = (Timestamp.max - datetime.datetime(1960, 1, 1)).days
MIN_DAY_DELTA = (Timestamp.min - datetime.datetime(1960, 1, 1)).days
MIN_MS_DELTA = MIN_DAY_DELTA * 24 * 3600 * 1000
MAX_MS_DELTA = MAX_DAY_DELTA * 24 * 3600 * 1000
def convert_year_month_safe(year, month):
"""
Convert year and month to datetimes, using pandas vectorized versions
when the date range falls within the range supported by pandas.
Otherwise it falls back to a slower but more robust method
using datetime.
"""
if year.max() < MAX_YEAR and year.min() > MIN_YEAR:
return to_datetime(100 * year + month, format="%Y%m")
else:
index = getattr(year, "index", None)
return Series(
[datetime.datetime(y, m, 1) for y, m in zip(year, month)], index=index
)
def convert_year_days_safe(year, days):
"""
Converts year (e.g. 1999) and days since the start of the year to a
datetime or datetime64 Series
"""
if year.max() < (MAX_YEAR - 1) and year.min() > MIN_YEAR:
return to_datetime(year, format="%Y") + to_timedelta(days, unit="d")
else:
index = getattr(year, "index", None)
value = [
datetime.datetime(y, 1, 1) + relativedelta(days=int(d))
for y, d in zip(year, days)
]
return Series(value, index=index)
def convert_delta_safe(base, deltas, unit):
"""
Convert base dates and deltas to datetimes, using pandas vectorized
versions if the deltas satisfy restrictions required to be expressed
as dates in pandas.
"""
index = getattr(deltas, "index", None)
if unit == "d":
if deltas.max() > MAX_DAY_DELTA or deltas.min() < MIN_DAY_DELTA:
values = [base + relativedelta(days=int(d)) for d in deltas]
return Series(values, index=index)
elif unit == "ms":
if deltas.max() > MAX_MS_DELTA or deltas.min() < MIN_MS_DELTA:
values = [
base + relativedelta(microseconds=(int(d) * 1000)) for d in deltas
]
return Series(values, index=index)
else:
raise ValueError("format not understood")
base = to_datetime(base)
deltas = to_timedelta(deltas, unit=unit)
return base + deltas
# TODO: If/when pandas supports more than datetime64[ns], this should be
# improved to use correct range, e.g. datetime[Y] for yearly
bad_locs = np.isnan(dates)
has_bad_values = False
if bad_locs.any():
has_bad_values = True
data_col = Series(dates)
data_col[bad_locs] = 1.0 # Replace with NaT
dates = dates.astype(np.int64)
if fmt.startswith(("%tc", "tc")): # Delta ms relative to base
base = stata_epoch
ms = dates
conv_dates = convert_delta_safe(base, ms, "ms")
elif fmt.startswith(("%tC", "tC")):
warnings.warn("Encountered %tC format. Leaving in Stata " "Internal Format.")
conv_dates = Series(dates, dtype=np.object)
if has_bad_values:
conv_dates[bad_locs] = NaT
return conv_dates
# Delta days relative to base
elif fmt.startswith(("%td", "td", "%d", "d")):
base = stata_epoch
days = dates
conv_dates = convert_delta_safe(base, days, "d")
# does not count leap days - 7 days is a week.
# 52nd week may have more than 7 days
elif fmt.startswith(("%tw", "tw")):
year = stata_epoch.year + dates // 52
days = (dates % 52) * 7
conv_dates = convert_year_days_safe(year, days)
elif fmt.startswith(("%tm", "tm")): # Delta months relative to base
year = stata_epoch.year + dates // 12
month = (dates % 12) + 1
conv_dates = convert_year_month_safe(year, month)
elif fmt.startswith(("%tq", "tq")): # Delta quarters relative to base
year = stata_epoch.year + dates // 4
month = (dates % 4) * 3 + 1
conv_dates = convert_year_month_safe(year, month)
elif fmt.startswith(("%th", "th")): # Delta half-years relative to base
year = stata_epoch.year + dates // 2
month = (dates % 2) * 6 + 1
conv_dates = convert_year_month_safe(year, month)
elif fmt.startswith(("%ty", "ty")): # Years -- not delta
year = dates
month = np.ones_like(dates)
conv_dates = convert_year_month_safe(year, month)
else:
raise ValueError("Date fmt {fmt} not understood".format(fmt=fmt))
if has_bad_values: # Restore NaT for bad values
conv_dates[bad_locs] = NaT
return conv_dates
def _datetime_to_stata_elapsed_vec(dates, fmt):
"""
Convert from datetime to SIF. http://www.stata.com/help.cgi?datetime
Parameters
----------
dates : Series
Series or array containing datetime.datetime or datetime64[ns] to
convert to the Stata Internal Format given by fmt
fmt : str
The format to convert to. Can be, tc, td, tw, tm, tq, th, ty
"""
index = dates.index
NS_PER_DAY = 24 * 3600 * 1000 * 1000 * 1000
US_PER_DAY = NS_PER_DAY / 1000
def parse_dates_safe(dates, delta=False, year=False, days=False):
d = {}
if is_datetime64_dtype(dates.values):
if delta:
delta = dates - stata_epoch
d["delta"] = delta.values.astype(np.int64) // 1000 # microseconds
if days or year:
dates = DatetimeIndex(dates)
d["year"], d["month"] = dates.year, dates.month
if days:
days = dates.astype(np.int64) - to_datetime(
d["year"], format="%Y"
).astype(np.int64)
d["days"] = days // NS_PER_DAY
elif infer_dtype(dates, skipna=False) == "datetime":
if delta:
delta = dates.values - stata_epoch
f = lambda x: US_PER_DAY * x.days + 1000000 * x.seconds + x.microseconds
v = np.vectorize(f)
d["delta"] = v(delta)
if year:
year_month = dates.apply(lambda x: 100 * x.year + x.month)
d["year"] = year_month.values // 100
d["month"] = year_month.values - d["year"] * 100
if days:
f = lambda x: (x - datetime.datetime(x.year, 1, 1)).days
v = np.vectorize(f)
d["days"] = v(dates)
else:
raise ValueError(
"Columns containing dates must contain either "
"datetime64, datetime.datetime or null values."
)
return DataFrame(d, index=index)
bad_loc = isna(dates)
index = dates.index
if bad_loc.any():
dates = Series(dates)
if is_datetime64_dtype(dates):
dates[bad_loc] = to_datetime(stata_epoch)
else:
dates[bad_loc] = stata_epoch
if fmt in ["%tc", "tc"]:
d = parse_dates_safe(dates, delta=True)
conv_dates = d.delta / 1000
elif fmt in ["%tC", "tC"]:
warnings.warn("Stata Internal Format tC not supported.")
conv_dates = dates
elif fmt in ["%td", "td"]:
d = parse_dates_safe(dates, delta=True)
conv_dates = d.delta // US_PER_DAY
elif fmt in ["%tw", "tw"]:
d = parse_dates_safe(dates, year=True, days=True)
conv_dates = 52 * (d.year - stata_epoch.year) + d.days // 7
elif fmt in ["%tm", "tm"]:
d = parse_dates_safe(dates, year=True)
conv_dates = 12 * (d.year - stata_epoch.year) + d.month - 1
elif fmt in ["%tq", "tq"]:
d = parse_dates_safe(dates, year=True)
conv_dates = 4 * (d.year - stata_epoch.year) + (d.month - 1) // 3
elif fmt in ["%th", "th"]:
d = parse_dates_safe(dates, year=True)
conv_dates = 2 * (d.year - stata_epoch.year) + (d.month > 6).astype(np.int)
elif fmt in ["%ty", "ty"]:
d = parse_dates_safe(dates, year=True)
conv_dates = d.year
else:
raise ValueError(
"Format {fmt} is not a known Stata date format".format(fmt=fmt)
)
conv_dates = Series(conv_dates, dtype=np.float64)
missing_value = struct.unpack("<d", b"\x00\x00\x00\x00\x00\x00\xe0\x7f")[0]
conv_dates[bad_loc] = missing_value
return Series(conv_dates, index=index)
excessive_string_length_error = """
Fixed width strings in Stata .dta files are limited to 244 (or fewer)
characters. Column '%s' does not satisfy this restriction. Use the
'version=117' parameter to write the newer (Stata 13 and later) format.
"""
class PossiblePrecisionLoss(Warning):
pass
precision_loss_doc = """
Column converted from %s to %s, and some data are outside of the lossless
conversion range. This may result in a loss of precision in the saved data.
"""
class ValueLabelTypeMismatch(Warning):
pass
value_label_mismatch_doc = """
Stata value labels (pandas categories) must be strings. Column {0} contains
non-string labels which will be converted to strings. Please check that the
Stata data file created has not lost information due to duplicate labels.
"""
class InvalidColumnName(Warning):
pass
invalid_name_doc = """
Not all pandas column names were valid Stata variable names.
The following replacements have been made:
{0}
If this is not what you expect, please make sure you have Stata-compliant
column names in your DataFrame (strings only, max 32 characters, only
alphanumerics and underscores, no Stata reserved words)
"""
def _cast_to_stata_types(data):
"""Checks the dtypes of the columns of a pandas DataFrame for
compatibility with the data types and ranges supported by Stata, and
converts if necessary.
Parameters
----------
data : DataFrame
The DataFrame to check and convert
Notes
-----
Numeric columns in Stata must be one of int8, int16, int32, float32 or
float64, with some additional value restrictions. int8 and int16 columns
are checked for violations of the value restrictions and upcast if needed.
int64 data is not usable in Stata, and so it is downcast to int32 whenever
the value are in the int32 range, and sidecast to float64 when larger than
this range. If the int64 values are outside of the range of those
perfectly representable as float64 values, a warning is raised.
bool columns are cast to int8. uint columns are converted to int of the
same size if there is no loss in precision, otherwise are upcast to a
larger type. uint64 is currently not supported since it is concerted to
object in a DataFrame.
"""
ws = ""
# original, if small, if large
conversion_data = (
(np.bool, np.int8, np.int8),
(np.uint8, np.int8, np.int16),
(np.uint16, np.int16, np.int32),
(np.uint32, np.int32, np.int64),
)
float32_max = struct.unpack("<f", b"\xff\xff\xff\x7e")[0]
float64_max = struct.unpack("<d", b"\xff\xff\xff\xff\xff\xff\xdf\x7f")[0]
for col in data:
dtype = data[col].dtype
# Cast from unsupported types to supported types
for c_data in conversion_data:
if dtype == c_data[0]:
if data[col].max() <= np.iinfo(c_data[1]).max:
dtype = c_data[1]
else:
dtype = c_data[2]
if c_data[2] == np.float64: # Warn if necessary
if data[col].max() >= 2 ** 53:
ws = precision_loss_doc % ("uint64", "float64")
data[col] = data[col].astype(dtype)
# Check values and upcast if necessary
if dtype == np.int8:
if data[col].max() > 100 or data[col].min() < -127:
data[col] = data[col].astype(np.int16)
elif dtype == np.int16:
if data[col].max() > 32740 or data[col].min() < -32767:
data[col] = data[col].astype(np.int32)
elif dtype == np.int64:
if data[col].max() <= 2147483620 and data[col].min() >= -2147483647:
data[col] = data[col].astype(np.int32)
else:
data[col] = data[col].astype(np.float64)
if data[col].max() >= 2 ** 53 or data[col].min() <= -2 ** 53:
ws = precision_loss_doc % ("int64", "float64")
elif dtype in (np.float32, np.float64):
value = data[col].max()
if np.isinf(value):
raise ValueError(
"Column {col} has a maximum value of "
"infinity which is outside the range "
"supported by Stata.".format(col=col)
)
if dtype == np.float32 and value > float32_max:
data[col] = data[col].astype(np.float64)
elif dtype == np.float64:
if value > float64_max:
raise ValueError(
"Column {col} has a maximum value "
"({val}) outside the range supported by "
"Stata ({float64_max})".format(
col=col, val=value, float64_max=float64_max
)
)
if ws:
warnings.warn(ws, PossiblePrecisionLoss)
return data
class StataValueLabel:
"""
Parse a categorical column and prepare formatted output
Parameters
----------
value : int8, int16, int32, float32 or float64
The Stata missing value code
Attributes
----------
string : string
String representation of the Stata missing value
value : int8, int16, int32, float32 or float64
The original encoded missing value
Methods
-------
generate_value_label
"""
def __init__(self, catarray):
self.labname = catarray.name
categories = catarray.cat.categories
self.value_labels = list(zip(np.arange(len(categories)), categories))
self.value_labels.sort(key=lambda x: x[0])
self.text_len = np.int32(0)
self.off = []
self.val = []
self.txt = []
self.n = 0
# Compute lengths and setup lists of offsets and labels
for vl in self.value_labels:
category = vl[1]
if not isinstance(category, str):
category = str(category)
warnings.warn(
value_label_mismatch_doc.format(catarray.name),
ValueLabelTypeMismatch,
)
self.off.append(self.text_len)
self.text_len += len(category) + 1 # +1 for the padding
self.val.append(vl[0])
self.txt.append(category)
self.n += 1
if self.text_len > 32000:
raise ValueError(
"Stata value labels for a single variable must "
"have a combined length less than 32,000 "
"characters."
)
# Ensure int32
self.off = np.array(self.off, dtype=np.int32)
self.val = np.array(self.val, dtype=np.int32)
# Total length
self.len = 4 + 4 + 4 * self.n + 4 * self.n + self.text_len
def _encode(self, s):
"""
Python 3 compatibility shim
"""
return s.encode(self._encoding)
def generate_value_label(self, byteorder, encoding):
"""
Parameters
----------
byteorder : str
Byte order of the output
encoding : str
File encoding
Returns
-------
value_label : bytes
Bytes containing the formatted value label
"""
self._encoding = encoding
bio = BytesIO()
null_string = "\x00"
null_byte = b"\x00"
# len
bio.write(struct.pack(byteorder + "i", self.len))
# labname
labname = self._encode(_pad_bytes(self.labname[:32], 33))
bio.write(labname)
# padding - 3 bytes
for i in range(3):
bio.write(struct.pack("c", null_byte))
# value_label_table
# n - int32
bio.write(struct.pack(byteorder + "i", self.n))
# textlen - int32
bio.write(struct.pack(byteorder + "i", self.text_len))
# off - int32 array (n elements)
for offset in self.off:
bio.write(struct.pack(byteorder + "i", offset))
# val - int32 array (n elements)
for value in self.val:
bio.write(struct.pack(byteorder + "i", value))
# txt - Text labels, null terminated
for text in self.txt:
bio.write(self._encode(text + null_string))
bio.seek(0)
return bio.read()
class StataMissingValue:
"""
An observation's missing value.
Parameters
----------
value : int8, int16, int32, float32 or float64
The Stata missing value code
Attributes
----------
string : string
String representation of the Stata missing value
value : int8, int16, int32, float32 or float64
The original encoded missing value
Notes
-----
More information: <http://www.stata.com/help.cgi?missing>
Integer missing values make the code '.', '.a', ..., '.z' to the ranges
101 ... 127 (for int8), 32741 ... 32767 (for int16) and 2147483621 ...
2147483647 (for int32). Missing values for floating point data types are
more complex but the pattern is simple to discern from the following table.
np.float32 missing values (float in Stata)
0000007f .
0008007f .a
0010007f .b
...
00c0007f .x
00c8007f .y
00d0007f .z
np.float64 missing values (double in Stata)
000000000000e07f .
000000000001e07f .a
000000000002e07f .b
...
000000000018e07f .x
000000000019e07f .y
00000000001ae07f .z
"""
# Construct a dictionary of missing values
MISSING_VALUES = {}
bases = (101, 32741, 2147483621)
for b in bases:
# Conversion to long to avoid hash issues on 32 bit platforms #8968
MISSING_VALUES[b] = "."
for i in range(1, 27):
MISSING_VALUES[i + b] = "." + chr(96 + i)
float32_base = b"\x00\x00\x00\x7f"
increment = struct.unpack("<i", b"\x00\x08\x00\x00")[0]
for i in range(27):
value = struct.unpack("<f", float32_base)[0]
MISSING_VALUES[value] = "."
if i > 0:
MISSING_VALUES[value] += chr(96 + i)
int_value = struct.unpack("<i", struct.pack("<f", value))[0] + increment
float32_base = struct.pack("<i", int_value)
float64_base = b"\x00\x00\x00\x00\x00\x00\xe0\x7f"
increment = struct.unpack("q", b"\x00\x00\x00\x00\x00\x01\x00\x00")[0]
for i in range(27):
value = struct.unpack("<d", float64_base)[0]
MISSING_VALUES[value] = "."
if i > 0:
MISSING_VALUES[value] += chr(96 + i)
int_value = struct.unpack("q", struct.pack("<d", value))[0] + increment
float64_base = struct.pack("q", int_value)
BASE_MISSING_VALUES = {
"int8": 101,
"int16": 32741,
"int32": 2147483621,
"float32": struct.unpack("<f", float32_base)[0],
"float64": struct.unpack("<d", float64_base)[0],
}
def __init__(self, value):
self._value = value
# Conversion to int to avoid hash issues on 32 bit platforms #8968
value = int(value) if value < 2147483648 else float(value)
self._str = self.MISSING_VALUES[value]
string = property(
lambda self: self._str,
doc="The Stata representation of the missing value: " "'.', '.a'..'.z'",
)
value = property(
lambda self: self._value, doc="The binary representation of the missing value."
)
def __str__(self):
return self.string
def __repr__(self):
# not perfect :-/
return "{cls}({obj})".format(cls=self.__class__, obj=self)
def __eq__(self, other):
return (
isinstance(other, self.__class__)
and self.string == other.string
and self.value == other.value
)
@classmethod
def get_base_missing_value(cls, dtype):
if dtype == np.int8:
value = cls.BASE_MISSING_VALUES["int8"]
elif dtype == np.int16:
value = cls.BASE_MISSING_VALUES["int16"]
elif dtype == np.int32:
value = cls.BASE_MISSING_VALUES["int32"]
elif dtype == np.float32:
value = cls.BASE_MISSING_VALUES["float32"]
elif dtype == np.float64:
value = cls.BASE_MISSING_VALUES["float64"]
else:
raise ValueError("Unsupported dtype")
return value
class StataParser:
def __init__(self):
# type code.
# --------------------
# str1 1 = 0x01
# str2 2 = 0x02
# ...
# str244 244 = 0xf4
# byte 251 = 0xfb (sic)
# int 252 = 0xfc
# long 253 = 0xfd
# float 254 = 0xfe
# double 255 = 0xff
# --------------------
# NOTE: the byte type seems to be reserved for categorical variables
# with a label, but the underlying variable is -127 to 100
# we're going to drop the label and cast to int
self.DTYPE_MAP = dict(
list(zip(range(1, 245), ["a" + str(i) for i in range(1, 245)]))
+ [
(251, np.int8),
(252, np.int16),
(253, np.int32),
(254, np.float32),
(255, np.float64),
]
)
self.DTYPE_MAP_XML = dict(
[
(32768, np.uint8), # Keys to GSO
(65526, np.float64),
(65527, np.float32),
(65528, np.int32),
(65529, np.int16),
(65530, np.int8),
]
)
self.TYPE_MAP = list(range(251)) + list("bhlfd")
self.TYPE_MAP_XML = dict(
[
# Not really a Q, unclear how to handle byteswap
(32768, "Q"),
(65526, "d"),
(65527, "f"),
(65528, "l"),
(65529, "h"),
(65530, "b"),
]
)
# NOTE: technically, some of these are wrong. there are more numbers
# that can be represented. it's the 27 ABOVE and BELOW the max listed
# numeric data type in [U] 12.2.2 of the 11.2 manual
float32_min = b"\xff\xff\xff\xfe"
float32_max = b"\xff\xff\xff\x7e"
float64_min = b"\xff\xff\xff\xff\xff\xff\xef\xff"
float64_max = b"\xff\xff\xff\xff\xff\xff\xdf\x7f"
self.VALID_RANGE = {
"b": (-127, 100),
"h": (-32767, 32740),
"l": (-2147483647, 2147483620),
"f": (
np.float32(struct.unpack("<f", float32_min)[0]),
np.float32(struct.unpack("<f", float32_max)[0]),
),
"d": (
np.float64(struct.unpack("<d", float64_min)[0]),
np.float64(struct.unpack("<d", float64_max)[0]),
),
}
self.OLD_TYPE_MAPPING = {
98: 251, # byte
105: 252, # int
108: 253, # long
102: 254 # float
# don't know old code for double
}
# These missing values are the generic '.' in Stata, and are used
# to replace nans
self.MISSING_VALUES = {
"b": 101,
"h": 32741,
"l": 2147483621,
"f": np.float32(struct.unpack("<f", b"\x00\x00\x00\x7f")[0]),
"d": np.float64(
struct.unpack("<d", b"\x00\x00\x00\x00\x00\x00\xe0\x7f")[0]
),
}
self.NUMPY_TYPE_MAP = {
"b": "i1",
"h": "i2",
"l": "i4",
"f": "f4",
"d": "f8",
"Q": "u8",
}
# Reserved words cannot be used as variable names
self.RESERVED_WORDS = (
"aggregate",
"array",
"boolean",
"break",
"byte",
"case",
"catch",
"class",
"colvector",
"complex",
"const",
"continue",
"default",
"delegate",
"delete",
"do",
"double",
"else",
"eltypedef",
"end",
"enum",
"explicit",
"export",
"external",
"float",
"for",
"friend",
"function",
"global",
"goto",
"if",
"inline",
"int",
"local",
"long",
"NULL",
"pragma",
"protected",
"quad",
"rowvector",
"short",
"typedef",
"typename",
"virtual",
)
class StataReader(StataParser, BaseIterator):
__doc__ = _stata_reader_doc
@deprecate_kwarg(old_arg_name="encoding", new_arg_name=None)
@deprecate_kwarg(old_arg_name="index", new_arg_name="index_col")
def __init__(
self,
path_or_buf,
convert_dates=True,
convert_categoricals=True,
index_col=None,
convert_missing=False,
preserve_dtypes=True,
columns=None,
order_categoricals=True,
encoding=None,
chunksize=None,
):
super().__init__()
self.col_sizes = ()
# Arguments to the reader (can be temporarily overridden in
# calls to read).
self._convert_dates = convert_dates
self._convert_categoricals = convert_categoricals
self._index_col = index_col
self._convert_missing = convert_missing
self._preserve_dtypes = preserve_dtypes
self._columns = columns
self._order_categoricals = order_categoricals
self._encoding = None
self._chunksize = chunksize
# State variables for the file
self._has_string_data = False
self._missing_values = False
self._can_read_value_labels = False
self._column_selector_set = False
self._value_labels_read = False
self._data_read = False
self._dtype = None
self._lines_read = 0
self._native_byteorder = _set_endianness(sys.byteorder)
path_or_buf = _stringify_path(path_or_buf)
if isinstance(path_or_buf, str):
path_or_buf, encoding, _, should_close = get_filepath_or_buffer(path_or_buf)
if isinstance(path_or_buf, (str, bytes)):
self.path_or_buf = open(path_or_buf, "rb")
else:
# Copy to BytesIO, and ensure no encoding
contents = path_or_buf.read()
self.path_or_buf = BytesIO(contents)
self._read_header()
self._setup_dtype()
def __enter__(self):
""" enter context manager """
return self
def __exit__(self, exc_type, exc_value, traceback):
""" exit context manager """
self.close()
def close(self):
""" close the handle if its open """
try:
self.path_or_buf.close()
except IOError:
pass
def _set_encoding(self):
"""
Set string encoding which depends on file version
"""
if self.format_version < 118:
self._encoding = "latin-1"
else:
self._encoding = "utf-8"
def _read_header(self):
first_char = self.path_or_buf.read(1)
if struct.unpack("c", first_char)[0] == b"<":
self._read_new_header(first_char)
else:
self._read_old_header(first_char)
self.has_string_data = len([x for x in self.typlist if type(x) is int]) > 0
# calculate size of a data record
self.col_sizes = [self._calcsize(typ) for typ in self.typlist]
def _read_new_header(self, first_char):
# The first part of the header is common to 117 and 118.
self.path_or_buf.read(27) # stata_dta><header><release>
self.format_version = int(self.path_or_buf.read(3))
if self.format_version not in [117, 118]:
raise ValueError(_version_error)
self._set_encoding()
self.path_or_buf.read(21) # </release><byteorder>
self.byteorder = self.path_or_buf.read(3) == b"MSF" and ">" or "<"
self.path_or_buf.read(15) # </byteorder><K>
self.nvar = struct.unpack(self.byteorder + "H", self.path_or_buf.read(2))[0]
self.path_or_buf.read(7) # </K><N>
self.nobs = self._get_nobs()
self.path_or_buf.read(11) # </N><label>
self._data_label = self._get_data_label()
self.path_or_buf.read(19) # </label><timestamp>
self.time_stamp = self._get_time_stamp()
self.path_or_buf.read(26) # </timestamp></header><map>
self.path_or_buf.read(8) # 0x0000000000000000
self.path_or_buf.read(8) # position of <map>
self._seek_vartypes = (
struct.unpack(self.byteorder + "q", self.path_or_buf.read(8))[0] + 16
)
self._seek_varnames = (
struct.unpack(self.byteorder + "q", self.path_or_buf.read(8))[0] + 10
)
self._seek_sortlist = (
struct.unpack(self.byteorder + "q", self.path_or_buf.read(8))[0] + 10
)
self._seek_formats = (
struct.unpack(self.byteorder + "q", self.path_or_buf.read(8))[0] + 9
)
self._seek_value_label_names = (
struct.unpack(self.byteorder + "q", self.path_or_buf.read(8))[0] + 19
)
# Requires version-specific treatment
self._seek_variable_labels = self._get_seek_variable_labels()
self.path_or_buf.read(8) # <characteristics>
self.data_location = (
struct.unpack(self.byteorder + "q", self.path_or_buf.read(8))[0] + 6
)
self.seek_strls = (
struct.unpack(self.byteorder + "q", self.path_or_buf.read(8))[0] + 7
)
self.seek_value_labels = (
struct.unpack(self.byteorder + "q", self.path_or_buf.read(8))[0] + 14
)
self.typlist, self.dtyplist = self._get_dtypes(self._seek_vartypes)
self.path_or_buf.seek(self._seek_varnames)
self.varlist = self._get_varlist()
self.path_or_buf.seek(self._seek_sortlist)
self.srtlist = struct.unpack(
self.byteorder + ("h" * (self.nvar + 1)),
self.path_or_buf.read(2 * (self.nvar + 1)),
)[:-1]
self.path_or_buf.seek(self._seek_formats)
self.fmtlist = self._get_fmtlist()
self.path_or_buf.seek(self._seek_value_label_names)
self.lbllist = self._get_lbllist()
self.path_or_buf.seek(self._seek_variable_labels)
self._variable_labels = self._get_variable_labels()
# Get data type information, works for versions 117-118.
def _get_dtypes(self, seek_vartypes):
self.path_or_buf.seek(seek_vartypes)
raw_typlist = [
struct.unpack(self.byteorder + "H", self.path_or_buf.read(2))[0]
for i in range(self.nvar)
]
def f(typ):
if typ <= 2045:
return typ
try:
return self.TYPE_MAP_XML[typ]
except KeyError:
raise ValueError("cannot convert stata types [{0}]".format(typ))
typlist = [f(x) for x in raw_typlist]
def f(typ):
if typ <= 2045:
return str(typ)
try:
return self.DTYPE_MAP_XML[typ]
except KeyError:
raise ValueError("cannot convert stata dtype [{0}]".format(typ))
dtyplist = [f(x) for x in raw_typlist]
return typlist, dtyplist
def _get_varlist(self):
if self.format_version == 117:
b = 33
elif self.format_version == 118:
b = 129
return [self._decode(self.path_or_buf.read(b)) for i in range(self.nvar)]
# Returns the format list
def _get_fmtlist(self):
if self.format_version == 118:
b = 57
elif self.format_version > 113:
b = 49
elif self.format_version > 104:
b = 12
else:
b = 7
return [self._decode(self.path_or_buf.read(b)) for i in range(self.nvar)]
# Returns the label list
def _get_lbllist(self):
if self.format_version >= 118:
b = 129
elif self.format_version > 108:
b = 33
else:
b = 9
return [self._decode(self.path_or_buf.read(b)) for i in range(self.nvar)]
def _get_variable_labels(self):
if self.format_version == 118:
vlblist = [
self._decode(self.path_or_buf.read(321)) for i in range(self.nvar)
]
elif self.format_version > 105:
vlblist = [
self._decode(self.path_or_buf.read(81)) for i in range(self.nvar)
]
else:
vlblist = [
self._decode(self.path_or_buf.read(32)) for i in range(self.nvar)
]
return vlblist
def _get_nobs(self):
if self.format_version == 118:
return struct.unpack(self.byteorder + "Q", self.path_or_buf.read(8))[0]
else:
return struct.unpack(self.byteorder + "I", self.path_or_buf.read(4))[0]
def _get_data_label(self):
if self.format_version == 118:
strlen = struct.unpack(self.byteorder + "H", self.path_or_buf.read(2))[0]
return self._decode(self.path_or_buf.read(strlen))
elif self.format_version == 117:
strlen = struct.unpack("b", self.path_or_buf.read(1))[0]
return self._decode(self.path_or_buf.read(strlen))
elif self.format_version > 105:
return self._decode(self.path_or_buf.read(81))
else:
return self._decode(self.path_or_buf.read(32))
def _get_time_stamp(self):
if self.format_version == 118:
strlen = struct.unpack("b", self.path_or_buf.read(1))[0]
return self.path_or_buf.read(strlen).decode("utf-8")
elif self.format_version == 117:
strlen = struct.unpack("b", self.path_or_buf.read(1))[0]
return self._decode(self.path_or_buf.read(strlen))
elif self.format_version > 104:
return self._decode(self.path_or_buf.read(18))
else:
raise ValueError()
def _get_seek_variable_labels(self):
if self.format_version == 117:
self.path_or_buf.read(8) # <variable_lables>, throw away
# Stata 117 data files do not follow the described format. This is
# a work around that uses the previous label, 33 bytes for each
# variable, 20 for the closing tag and 17 for the opening tag
return self._seek_value_label_names + (33 * self.nvar) + 20 + 17
elif self.format_version == 118:
return struct.unpack(self.byteorder + "q", self.path_or_buf.read(8))[0] + 17
else:
raise ValueError()
def _read_old_header(self, first_char):
self.format_version = struct.unpack("b", first_char)[0]
if self.format_version not in [104, 105, 108, 111, 113, 114, 115]:
raise ValueError(_version_error)
self._set_encoding()
self.byteorder = (
struct.unpack("b", self.path_or_buf.read(1))[0] == 0x1 and ">" or "<"
)
self.filetype = struct.unpack("b", self.path_or_buf.read(1))[0]
self.path_or_buf.read(1) # unused
self.nvar = struct.unpack(self.byteorder + "H", self.path_or_buf.read(2))[0]
self.nobs = self._get_nobs()
self._data_label = self._get_data_label()
self.time_stamp = self._get_time_stamp()
# descriptors
if self.format_version > 108:
typlist = [ord(self.path_or_buf.read(1)) for i in range(self.nvar)]
else:
buf = self.path_or_buf.read(self.nvar)
typlistb = np.frombuffer(buf, dtype=np.uint8)
typlist = []
for tp in typlistb:
if tp in self.OLD_TYPE_MAPPING:
typlist.append(self.OLD_TYPE_MAPPING[tp])
else:
typlist.append(tp - 127) # bytes
try:
self.typlist = [self.TYPE_MAP[typ] for typ in typlist]
except ValueError:
raise ValueError(
"cannot convert stata types [{0}]".format(
",".join(str(x) for x in typlist)
)
)
try:
self.dtyplist = [self.DTYPE_MAP[typ] for typ in typlist]
except ValueError:
raise ValueError(
"cannot convert stata dtypes [{0}]".format(
",".join(str(x) for x in typlist)
)
)
if self.format_version > 108:
self.varlist = [
self._decode(self.path_or_buf.read(33)) for i in range(self.nvar)
]
else:
self.varlist = [
self._decode(self.path_or_buf.read(9)) for i in range(self.nvar)
]
self.srtlist = struct.unpack(
self.byteorder + ("h" * (self.nvar + 1)),
self.path_or_buf.read(2 * (self.nvar + 1)),
)[:-1]
self.fmtlist = self._get_fmtlist()
self.lbllist = self._get_lbllist()
self._variable_labels = self._get_variable_labels()
# ignore expansion fields (Format 105 and later)
# When reading, read five bytes; the last four bytes now tell you
# the size of the next read, which you discard. You then continue
# like this until you read 5 bytes of zeros.
if self.format_version > 104:
while True:
data_type = struct.unpack(
self.byteorder + "b", self.path_or_buf.read(1)
)[0]
if self.format_version > 108:
data_len = struct.unpack(
self.byteorder + "i", self.path_or_buf.read(4)
)[0]
else:
data_len = struct.unpack(
self.byteorder + "h", self.path_or_buf.read(2)
)[0]
if data_type == 0:
break
self.path_or_buf.read(data_len)
# necessary data to continue parsing
self.data_location = self.path_or_buf.tell()
def _setup_dtype(self):
"""Map between numpy and state dtypes"""
if self._dtype is not None:
return self._dtype
dtype = [] # Convert struct data types to numpy data type
for i, typ in enumerate(self.typlist):
if typ in self.NUMPY_TYPE_MAP:
dtype.append(("s" + str(i), self.byteorder + self.NUMPY_TYPE_MAP[typ]))
else:
dtype.append(("s" + str(i), "S" + str(typ)))
dtype = np.dtype(dtype)
self._dtype = dtype
return self._dtype
def _calcsize(self, fmt):
return type(fmt) is int and fmt or struct.calcsize(self.byteorder + fmt)
def _decode(self, s):
# have bytes not strings, so must decode
s = s.partition(b"\0")[0]
try:
return s.decode(self._encoding)
except UnicodeDecodeError:
# GH 25960, fallback to handle incorrect format produced when 117
# files are converted to 118 files in Stata
msg = """
One or more strings in the dta file could not be decoded using {encoding}, and
so the fallback encoding of latin-1 is being used. This can happen when a file
has been incorrectly encoded by Stata or some other software. You should verify
the string values returned are correct."""
warnings.warn(msg.format(encoding=self._encoding), UnicodeWarning)
return s.decode("latin-1")
def _read_value_labels(self):
if self._value_labels_read:
# Don't read twice
return
if self.format_version <= 108:
# Value labels are not supported in version 108 and earlier.
self._value_labels_read = True
self.value_label_dict = dict()
return
if self.format_version >= 117:
self.path_or_buf.seek(self.seek_value_labels)
else:
offset = self.nobs * self._dtype.itemsize
self.path_or_buf.seek(self.data_location + offset)
self._value_labels_read = True
self.value_label_dict = dict()
while True:
if self.format_version >= 117:
if self.path_or_buf.read(5) == b"</val": # <lbl>
break # end of value label table
slength = self.path_or_buf.read(4)
if not slength:
break # end of value label table (format < 117)
if self.format_version <= 117:
labname = self._decode(self.path_or_buf.read(33))
else:
labname = self._decode(self.path_or_buf.read(129))
self.path_or_buf.read(3) # padding
n = struct.unpack(self.byteorder + "I", self.path_or_buf.read(4))[0]
txtlen = struct.unpack(self.byteorder + "I", self.path_or_buf.read(4))[0]
off = np.frombuffer(
self.path_or_buf.read(4 * n), dtype=self.byteorder + "i4", count=n
)
val = np.frombuffer(
self.path_or_buf.read(4 * n), dtype=self.byteorder + "i4", count=n
)
ii = np.argsort(off)
off = off[ii]
val = val[ii]
txt = self.path_or_buf.read(txtlen)
self.value_label_dict[labname] = dict()
for i in range(n):
end = off[i + 1] if i < n - 1 else txtlen
self.value_label_dict[labname][val[i]] = self._decode(txt[off[i] : end])
if self.format_version >= 117:
self.path_or_buf.read(6) # </lbl>
self._value_labels_read = True
def _read_strls(self):
self.path_or_buf.seek(self.seek_strls)
# Wrap v_o in a string to allow uint64 values as keys on 32bit OS
self.GSO = {"0": ""}
while True:
if self.path_or_buf.read(3) != b"GSO":
break
if self.format_version == 117:
v_o = struct.unpack(self.byteorder + "Q", self.path_or_buf.read(8))[0]
else:
buf = self.path_or_buf.read(12)
# Only tested on little endian file on little endian machine.
if self.byteorder == "<":
buf = buf[0:2] + buf[4:10]
else:
buf = buf[0:2] + buf[6:]
v_o = struct.unpack("Q", buf)[0]
typ = struct.unpack("B", self.path_or_buf.read(1))[0]
length = struct.unpack(self.byteorder + "I", self.path_or_buf.read(4))[0]
va = self.path_or_buf.read(length)
if typ == 130:
va = va[0:-1].decode(self._encoding)
# Wrap v_o in a string to allow uint64 values as keys on 32bit OS
self.GSO[str(v_o)] = va
# legacy
@Appender(_data_method_doc)
def data(self, **kwargs):
warnings.warn("'data' is deprecated, use 'read' instead")
if self._data_read:
raise Exception("Data has already been read.")
self._data_read = True
return self.read(None, **kwargs)
def __next__(self):
return self.read(nrows=self._chunksize or 1)
def get_chunk(self, size=None):
"""
Reads lines from Stata file and returns as dataframe
Parameters
----------
size : int, defaults to None
Number of lines to read. If None, reads whole file.
Returns
-------
DataFrame
"""
if size is None:
size = self._chunksize
return self.read(nrows=size)
@Appender(_read_method_doc)
@deprecate_kwarg(old_arg_name="index", new_arg_name="index_col")
def read(
self,
nrows=None,
convert_dates=None,
convert_categoricals=None,
index_col=None,
convert_missing=None,
preserve_dtypes=None,
columns=None,
order_categoricals=None,
):
# Handle empty file or chunk. If reading incrementally raise
# StopIteration. If reading the whole thing return an empty
# data frame.
if (self.nobs == 0) and (nrows is None):
self._can_read_value_labels = True
self._data_read = True
self.close()
return DataFrame(columns=self.varlist)
# Handle options
if convert_dates is None:
convert_dates = self._convert_dates
if convert_categoricals is None:
convert_categoricals = self._convert_categoricals
if convert_missing is None:
convert_missing = self._convert_missing
if preserve_dtypes is None:
preserve_dtypes = self._preserve_dtypes
if columns is None:
columns = self._columns
if order_categoricals is None:
order_categoricals = self._order_categoricals
if index_col is None:
index_col = self._index_col
if nrows is None:
nrows = self.nobs
if (self.format_version >= 117) and (not self._value_labels_read):
self._can_read_value_labels = True
self._read_strls()
# Read data
dtype = self._dtype
max_read_len = (self.nobs - self._lines_read) * dtype.itemsize
read_len = nrows * dtype.itemsize
read_len = min(read_len, max_read_len)
if read_len <= 0:
# Iterator has finished, should never be here unless
# we are reading the file incrementally
if convert_categoricals:
self._read_value_labels()
self.close()
raise StopIteration
offset = self._lines_read * dtype.itemsize
self.path_or_buf.seek(self.data_location + offset)
read_lines = min(nrows, self.nobs - self._lines_read)
data = np.frombuffer(
self.path_or_buf.read(read_len), dtype=dtype, count=read_lines
)
self._lines_read += read_lines
if self._lines_read == self.nobs:
self._can_read_value_labels = True
self._data_read = True
# if necessary, swap the byte order to native here
if self.byteorder != self._native_byteorder:
data = data.byteswap().newbyteorder()
if convert_categoricals:
self._read_value_labels()
if len(data) == 0:
data = DataFrame(columns=self.varlist)
else:
data = DataFrame.from_records(data)
data.columns = self.varlist
# If index is not specified, use actual row number rather than
# restarting at 0 for each chunk.
if index_col is None:
ix = np.arange(self._lines_read - read_lines, self._lines_read)
data = data.set_index(ix)
if columns is not None:
try:
data = self._do_select_columns(data, columns)
except ValueError:
self.close()
raise
# Decode strings
for col, typ in zip(data, self.typlist):
if type(typ) is int:
data[col] = data[col].apply(self._decode, convert_dtype=True)
data = self._insert_strls(data)
cols_ = np.where(self.dtyplist)[0]
# Convert columns (if needed) to match input type
ix = data.index
requires_type_conversion = False
data_formatted = []
for i in cols_:
if self.dtyplist[i] is not None:
col = data.columns[i]
dtype = data[col].dtype
if dtype != np.dtype(object) and dtype != self.dtyplist[i]:
requires_type_conversion = True
data_formatted.append(
(col, Series(data[col], ix, self.dtyplist[i]))
)
else:
data_formatted.append((col, data[col]))
if requires_type_conversion:
data = DataFrame.from_dict(OrderedDict(data_formatted))
del data_formatted
data = self._do_convert_missing(data, convert_missing)
if convert_dates:
def any_startswith(x: str) -> bool:
return any(x.startswith(fmt) for fmt in _date_formats)
cols = np.where([any_startswith(x) for x in self.fmtlist])[0]
for i in cols:
col = data.columns[i]
try:
data[col] = _stata_elapsed_date_to_datetime_vec(
data[col], self.fmtlist[i]
)
except ValueError:
self.close()
raise
if convert_categoricals and self.format_version > 108:
data = self._do_convert_categoricals(
data, self.value_label_dict, self.lbllist, order_categoricals
)
if not preserve_dtypes:
retyped_data = []
convert = False
for col in data:
dtype = data[col].dtype
if dtype in (np.float16, np.float32):
dtype = np.float64
convert = True
elif dtype in (np.int8, np.int16, np.int32):
dtype = np.int64
convert = True
retyped_data.append((col, data[col].astype(dtype)))
if convert:
data = DataFrame.from_dict(OrderedDict(retyped_data))
if index_col is not None:
data = data.set_index(data.pop(index_col))
return data
def _do_convert_missing(self, data, convert_missing):
# Check for missing values, and replace if found
replacements = {}
for i, colname in enumerate(data):
fmt = self.typlist[i]
if fmt not in self.VALID_RANGE:
continue
nmin, nmax = self.VALID_RANGE[fmt]
series = data[colname]
missing = np.logical_or(series < nmin, series > nmax)
if not missing.any():
continue
if convert_missing: # Replacement follows Stata notation
missing_loc = np.argwhere(missing._ndarray_values)
umissing, umissing_loc = np.unique(series[missing], return_inverse=True)
replacement = Series(series, dtype=np.object)
for j, um in enumerate(umissing):
missing_value = StataMissingValue(um)
loc = missing_loc[umissing_loc == j]
replacement.iloc[loc] = missing_value
else: # All replacements are identical
dtype = series.dtype
if dtype not in (np.float32, np.float64):
dtype = np.float64
replacement = Series(series, dtype=dtype)
replacement[missing] = np.nan
replacements[colname] = replacement
if replacements:
columns = data.columns
replacements = DataFrame(replacements)
data = concat([data.drop(replacements.columns, 1), replacements], 1)
data = data[columns]
return data
def _insert_strls(self, data):
if not hasattr(self, "GSO") or len(self.GSO) == 0:
return data
for i, typ in enumerate(self.typlist):
if typ != "Q":
continue
# Wrap v_o in a string to allow uint64 values as keys on 32bit OS
data.iloc[:, i] = [self.GSO[str(k)] for k in data.iloc[:, i]]
return data
def _do_select_columns(self, data, columns):
if not self._column_selector_set:
column_set = set(columns)
if len(column_set) != len(columns):
raise ValueError("columns contains duplicate entries")
unmatched = column_set.difference(data.columns)
if unmatched:
raise ValueError(
"The following columns were not found in the "
"Stata data set: " + ", ".join(list(unmatched))
)
# Copy information for retained columns for later processing
dtyplist = []
typlist = []
fmtlist = []
lbllist = []
for col in columns:
i = data.columns.get_loc(col)
dtyplist.append(self.dtyplist[i])
typlist.append(self.typlist[i])
fmtlist.append(self.fmtlist[i])
lbllist.append(self.lbllist[i])
self.dtyplist = dtyplist
self.typlist = typlist
self.fmtlist = fmtlist
self.lbllist = lbllist
self._column_selector_set = True
return data[columns]
def _do_convert_categoricals(
self, data, value_label_dict, lbllist, order_categoricals
):
"""
Converts categorical columns to Categorical type.
"""
value_labels = list(value_label_dict.keys())
cat_converted_data = []
for col, label in zip(data, lbllist):
if label in value_labels:
# Explicit call with ordered=True
cat_data = Categorical(data[col], ordered=order_categoricals)
categories = []
for category in cat_data.categories:
if category in value_label_dict[label]:
categories.append(value_label_dict[label][category])
else:
categories.append(category) # Partially labeled
try:
cat_data.categories = categories
except ValueError:
vc = Series(categories).value_counts()
repeats = list(vc.index[vc > 1])
repeats = "-" * 80 + "\n" + "\n".join(repeats)
# GH 25772
msg = """
Value labels for column {col} are not unique. These cannot be converted to
pandas categoricals.
Either read the file with `convert_categoricals` set to False or use the
low level interface in `StataReader` to separately read the values and the
value_labels.
The repeated labels are:
{repeats}
"""
raise ValueError(msg.format(col=col, repeats=repeats))
# TODO: is the next line needed above in the data(...) method?
cat_data = Series(cat_data, index=data.index)
cat_converted_data.append((col, cat_data))
else:
cat_converted_data.append((col, data[col]))
data = DataFrame.from_dict(OrderedDict(cat_converted_data))
return data
@property
def data_label(self):
"""
Return data label of Stata file.
"""
return self._data_label
def variable_labels(self):
"""
Return variable labels as a dict, associating each variable name
with corresponding label.
Returns
-------
dict
"""
return dict(zip(self.varlist, self._variable_labels))
def value_labels(self):
"""
Return a dict, associating each variable name a dict, associating
each value its corresponding label.
Returns
-------
dict
"""
if not self._value_labels_read:
self._read_value_labels()
return self.value_label_dict
def _open_file_binary_write(fname):
"""
Open a binary file or no-op if file-like.
Parameters
----------
fname : string path, path object or buffer
Returns
-------
file : file-like object
File object supporting write
own : bool
True if the file was created, otherwise False
"""
if hasattr(fname, "write"):
# if 'b' not in fname.mode:
return fname, False
return open(fname, "wb"), True
def _set_endianness(endianness):
if endianness.lower() in ["<", "little"]:
return "<"
elif endianness.lower() in [">", "big"]:
return ">"
else: # pragma : no cover
raise ValueError("Endianness {endian} not understood".format(endian=endianness))
def _pad_bytes(name, length):
"""
Take a char string and pads it with null bytes until it's length chars.
"""
return name + "\x00" * (length - len(name))
def _convert_datetime_to_stata_type(fmt):
"""
Convert from one of the stata date formats to a type in TYPE_MAP.
"""
if fmt in [
"tc",
"%tc",
"td",
"%td",
"tw",
"%tw",
"tm",
"%tm",
"tq",
"%tq",
"th",
"%th",
"ty",
"%ty",
]:
return np.float64 # Stata expects doubles for SIFs
else:
raise NotImplementedError("Format {fmt} not implemented".format(fmt=fmt))
def _maybe_convert_to_int_keys(convert_dates, varlist):
new_dict = {}
for key in convert_dates:
if not convert_dates[key].startswith("%"): # make sure proper fmts
convert_dates[key] = "%" + convert_dates[key]
if key in varlist:
new_dict.update({varlist.index(key): convert_dates[key]})
else:
if not isinstance(key, int):
raise ValueError("convert_dates key must be a " "column or an integer")
new_dict.update({key: convert_dates[key]})
return new_dict
def _dtype_to_stata_type(dtype, column):
"""
Convert dtype types to stata types. Returns the byte of the given ordinal.
See TYPE_MAP and comments for an explanation. This is also explained in
the dta spec.
1 - 244 are strings of this length
Pandas Stata
251 - for int8 byte
252 - for int16 int
253 - for int32 long
254 - for float32 float
255 - for double double
If there are dates to convert, then dtype will already have the correct
type inserted.
"""
# TODO: expand to handle datetime to integer conversion
if dtype.type == np.object_: # try to coerce it to the biggest string
# not memory efficient, what else could we
# do?
itemsize = max_len_string_array(ensure_object(column.values))
return max(itemsize, 1)
elif dtype == np.float64:
return 255
elif dtype == np.float32:
return 254
elif dtype == np.int32:
return 253
elif dtype == np.int16:
return 252
elif dtype == np.int8:
return 251
else: # pragma : no cover
raise NotImplementedError(
"Data type {dtype} not supported.".format(dtype=dtype)
)
def _dtype_to_default_stata_fmt(dtype, column, dta_version=114, force_strl=False):
"""
Map numpy dtype to stata's default format for this type. Not terribly
important since users can change this in Stata. Semantics are
object -> "%DDs" where DD is the length of the string. If not a string,
raise ValueError
float64 -> "%10.0g"
float32 -> "%9.0g"
int64 -> "%9.0g"
int32 -> "%12.0g"
int16 -> "%8.0g"
int8 -> "%8.0g"
strl -> "%9s"
"""
# TODO: Refactor to combine type with format
# TODO: expand this to handle a default datetime format?
if dta_version < 117:
max_str_len = 244
else:
max_str_len = 2045
if force_strl:
return "%9s"
if dtype.type == np.object_:
inferred_dtype = infer_dtype(column, skipna=True)
if not (inferred_dtype in ("string", "unicode") or len(column) == 0):
raise ValueError(
"Column `{col}` cannot be exported.\n\nOnly "
"string-like object arrays containing all "
"strings or a mix of strings and None can be "
"exported. Object arrays containing only null "
"values are prohibited. Other object types"
"cannot be exported and must first be converted "
"to one of the supported "
"types.".format(col=column.name)
)
itemsize = max_len_string_array(ensure_object(column.values))
if itemsize > max_str_len:
if dta_version >= 117:
return "%9s"
else:
raise ValueError(excessive_string_length_error % column.name)
return "%" + str(max(itemsize, 1)) + "s"
elif dtype == np.float64:
return "%10.0g"
elif dtype == np.float32:
return "%9.0g"
elif dtype == np.int32:
return "%12.0g"
elif dtype == np.int8 or dtype == np.int16:
return "%8.0g"
else: # pragma : no cover
raise NotImplementedError(
"Data type {dtype} not supported.".format(dtype=dtype)
)
class StataWriter(StataParser):
"""
A class for writing Stata binary dta files
Parameters
----------
fname : path (string), buffer or path object
string, path object (pathlib.Path or py._path.local.LocalPath) or
object implementing a binary write() functions. If using a buffer
then the buffer will not be automatically closed after the file
is written.
.. versionadded:: 0.23.0 support for pathlib, py.path.
data : DataFrame
Input to save
convert_dates : dict
Dictionary mapping columns containing datetime types to stata internal
format to use when writing the dates. Options are 'tc', 'td', 'tm',
'tw', 'th', 'tq', 'ty'. Column can be either an integer or a name.
Datetime columns that do not have a conversion type specified will be
converted to 'tc'. Raises NotImplementedError if a datetime column has
timezone information
write_index : bool
Write the index to Stata dataset.
encoding : str
Default is latin-1. Only latin-1 and ascii are supported.
byteorder : str
Can be ">", "<", "little", or "big". default is `sys.byteorder`
time_stamp : datetime
A datetime to use as file creation date. Default is the current time
data_label : str
A label for the data set. Must be 80 characters or smaller.
variable_labels : dict
Dictionary containing columns as keys and variable labels as values.
Each label must be 80 characters or smaller.
.. versionadded:: 0.19.0
Returns
-------
writer : StataWriter instance
The StataWriter instance has a write_file method, which will
write the file to the given `fname`.
Raises
------
NotImplementedError
* If datetimes contain timezone information
ValueError
* Columns listed in convert_dates are neither datetime64[ns]
or datetime.datetime
* Column dtype is not representable in Stata
* Column listed in convert_dates is not in DataFrame
* Categorical label contains more than 32,000 characters
Examples
--------
>>> data = pd.DataFrame([[1.0, 1]], columns=['a', 'b'])
>>> writer = StataWriter('./data_file.dta', data)
>>> writer.write_file()
Or with dates
>>> from datetime import datetime
>>> data = pd.DataFrame([[datetime(2000,1,1)]], columns=['date'])
>>> writer = StataWriter('./date_data_file.dta', data, {'date' : 'tw'})
>>> writer.write_file()
"""
_max_string_length = 244
@deprecate_kwarg(old_arg_name="encoding", new_arg_name=None)
def __init__(
self,
fname,
data,
convert_dates=None,
write_index=True,
encoding="latin-1",
byteorder=None,
time_stamp=None,
data_label=None,
variable_labels=None,
):
super().__init__()
self._convert_dates = {} if convert_dates is None else convert_dates
self._write_index = write_index
self._encoding = "latin-1"
self._time_stamp = time_stamp
self._data_label = data_label
self._variable_labels = variable_labels
self._own_file = True
# attach nobs, nvars, data, varlist, typlist
self._prepare_pandas(data)
if byteorder is None:
byteorder = sys.byteorder
self._byteorder = _set_endianness(byteorder)
self._fname = _stringify_path(fname)
self.type_converters = {253: np.int32, 252: np.int16, 251: np.int8}
self._converted_names = {}
def _write(self, to_write):
"""
Helper to call encode before writing to file for Python 3 compat.
"""
self._file.write(to_write.encode(self._encoding or self._default_encoding))
def _prepare_categoricals(self, data):
"""Check for categorical columns, retain categorical information for
Stata file and convert categorical data to int"""
is_cat = [is_categorical_dtype(data[col]) for col in data]
self._is_col_cat = is_cat
self._value_labels = []
if not any(is_cat):
return data
get_base_missing_value = StataMissingValue.get_base_missing_value
data_formatted = []
for col, col_is_cat in zip(data, is_cat):
if col_is_cat:
self._value_labels.append(StataValueLabel(data[col]))
dtype = data[col].cat.codes.dtype
if dtype == np.int64:
raise ValueError(
"It is not possible to export "
"int64-based categorical data to Stata."
)
values = data[col].cat.codes.values.copy()
# Upcast if needed so that correct missing values can be set
if values.max() >= get_base_missing_value(dtype):
if dtype == np.int8:
dtype = np.int16
elif dtype == np.int16:
dtype = np.int32
else:
dtype = np.float64
values = np.array(values, dtype=dtype)
# Replace missing values with Stata missing value for type
values[values == -1] = get_base_missing_value(dtype)
data_formatted.append((col, values))
else:
data_formatted.append((col, data[col]))
return DataFrame.from_dict(OrderedDict(data_formatted))
def _replace_nans(self, data):
# return data
"""Checks floating point data columns for nans, and replaces these with
the generic Stata for missing value (.)"""
for c in data:
dtype = data[c].dtype
if dtype in (np.float32, np.float64):
if dtype == np.float32:
replacement = self.MISSING_VALUES["f"]
else:
replacement = self.MISSING_VALUES["d"]
data[c] = data[c].fillna(replacement)
return data
def _update_strl_names(self):
"""No-op, forward compatibility"""
pass
def _check_column_names(self, data):
"""
Checks column names to ensure that they are valid Stata column names.
This includes checks for:
* Non-string names
* Stata keywords
* Variables that start with numbers
* Variables with names that are too long
When an illegal variable name is detected, it is converted, and if
dates are exported, the variable name is propagated to the date
conversion dictionary
"""
converted_names = {}
columns = list(data.columns)
original_columns = columns[:]
duplicate_var_id = 0
for j, name in enumerate(columns):
orig_name = name
if not isinstance(name, str):
name = str(name)
for c in name:
if (
(c < "A" or c > "Z")
and (c < "a" or c > "z")
and (c < "0" or c > "9")
and c != "_"
):
name = name.replace(c, "_")
# Variable name must not be a reserved word
if name in self.RESERVED_WORDS:
name = "_" + name
# Variable name may not start with a number
if name[0] >= "0" and name[0] <= "9":
name = "_" + name
name = name[: min(len(name), 32)]
if not name == orig_name:
# check for duplicates
while columns.count(name) > 0:
# prepend ascending number to avoid duplicates
name = "_" + str(duplicate_var_id) + name
name = name[: min(len(name), 32)]
duplicate_var_id += 1
converted_names[orig_name] = name
columns[j] = name
data.columns = columns
# Check date conversion, and fix key if needed
if self._convert_dates:
for c, o in zip(columns, original_columns):
if c != o:
self._convert_dates[c] = self._convert_dates[o]
del self._convert_dates[o]
if converted_names:
conversion_warning = []
for orig_name, name in converted_names.items():
# need to possibly encode the orig name if its unicode
try:
orig_name = orig_name.encode("utf-8")
except (UnicodeDecodeError, AttributeError):
pass
msg = "{0} -> {1}".format(orig_name, name)
conversion_warning.append(msg)
ws = invalid_name_doc.format("\n ".join(conversion_warning))
warnings.warn(ws, InvalidColumnName)
self._converted_names = converted_names
self._update_strl_names()
return data
def _set_formats_and_types(self, data, dtypes):
self.typlist = []
self.fmtlist = []
for col, dtype in dtypes.items():
self.fmtlist.append(_dtype_to_default_stata_fmt(dtype, data[col]))
self.typlist.append(_dtype_to_stata_type(dtype, data[col]))
def _prepare_pandas(self, data):
# NOTE: we might need a different API / class for pandas objects so
# we can set different semantics - handle this with a PR to pandas.io
data = data.copy()
if self._write_index:
data = data.reset_index()
# Ensure column names are strings
data = self._check_column_names(data)
# Check columns for compatibility with stata, upcast if necessary
# Raise if outside the supported range
data = _cast_to_stata_types(data)
# Replace NaNs with Stata missing values
data = self._replace_nans(data)
# Convert categoricals to int data, and strip labels
data = self._prepare_categoricals(data)
self.nobs, self.nvar = data.shape
self.data = data
self.varlist = data.columns.tolist()
dtypes = data.dtypes
# Ensure all date columns are converted
for col in data:
if col in self._convert_dates:
continue
if is_datetime64_dtype(data[col]):
self._convert_dates[col] = "tc"
self._convert_dates = _maybe_convert_to_int_keys(
self._convert_dates, self.varlist
)
for key in self._convert_dates:
new_type = _convert_datetime_to_stata_type(self._convert_dates[key])
dtypes[key] = np.dtype(new_type)
self._set_formats_and_types(data, dtypes)
# set the given format for the datetime cols
if self._convert_dates is not None:
for key in self._convert_dates:
self.fmtlist[key] = self._convert_dates[key]
def write_file(self):
self._file, self._own_file = _open_file_binary_write(self._fname)
try:
self._write_header(time_stamp=self._time_stamp, data_label=self._data_label)
self._write_map()
self._write_variable_types()
self._write_varnames()
self._write_sortlist()
self._write_formats()
self._write_value_label_names()
self._write_variable_labels()
self._write_expansion_fields()
self._write_characteristics()
self._prepare_data()
self._write_data()
self._write_strls()
self._write_value_labels()
self._write_file_close_tag()
self._write_map()
except Exception as exc:
self._close()
try:
if self._own_file:
os.unlink(self._fname)
except Exception:
warnings.warn(
"This save was not successful but {0} could not "
"be deleted. This file is not "
"valid.".format(self._fname),
ResourceWarning,
)
raise exc
else:
self._close()
def _close(self):
"""
Close the file if it was created by the writer.
If a buffer or file-like object was passed in, for example a GzipFile,
then leave this file open for the caller to close. In either case,
attempt to flush the file contents to ensure they are written to disk
(if supported)
"""
# Some file-like objects might not support flush
try:
self._file.flush()
except AttributeError:
pass
if self._own_file:
self._file.close()
def _write_map(self):
"""No-op, future compatibility"""
pass
def _write_file_close_tag(self):
"""No-op, future compatibility"""
pass
def _write_characteristics(self):
"""No-op, future compatibility"""
pass
def _write_strls(self):
"""No-op, future compatibility"""
pass
def _write_expansion_fields(self):
"""Write 5 zeros for expansion fields"""
self._write(_pad_bytes("", 5))
def _write_value_labels(self):
for vl in self._value_labels:
self._file.write(vl.generate_value_label(self._byteorder, self._encoding))
def _write_header(self, data_label=None, time_stamp=None):
byteorder = self._byteorder
# ds_format - just use 114
self._file.write(struct.pack("b", 114))
# byteorder
self._write(byteorder == ">" and "\x01" or "\x02")
# filetype
self._write("\x01")
# unused
self._write("\x00")
# number of vars, 2 bytes
self._file.write(struct.pack(byteorder + "h", self.nvar)[:2])
# number of obs, 4 bytes
self._file.write(struct.pack(byteorder + "i", self.nobs)[:4])
# data label 81 bytes, char, null terminated
if data_label is None:
self._file.write(self._null_terminate(_pad_bytes("", 80)))
else:
self._file.write(self._null_terminate(_pad_bytes(data_label[:80], 80)))
# time stamp, 18 bytes, char, null terminated
# format dd Mon yyyy hh:mm
if time_stamp is None:
time_stamp = datetime.datetime.now()
elif not isinstance(time_stamp, datetime.datetime):
raise ValueError("time_stamp should be datetime type")
# GH #13856
# Avoid locale-specific month conversion
months = [
"Jan",
"Feb",
"Mar",
"Apr",
"May",
"Jun",
"Jul",
"Aug",
"Sep",
"Oct",
"Nov",
"Dec",
]
month_lookup = {i + 1: month for i, month in enumerate(months)}
ts = (
time_stamp.strftime("%d ")
+ month_lookup[time_stamp.month]
+ time_stamp.strftime(" %Y %H:%M")
)
self._file.write(self._null_terminate(ts))
def _write_variable_types(self):
for typ in self.typlist:
self._file.write(struct.pack("B", typ))
def _write_varnames(self):
# varlist names are checked by _check_column_names
# varlist, requires null terminated
for name in self.varlist:
name = self._null_terminate(name, True)
name = _pad_bytes(name[:32], 33)
self._write(name)
def _write_sortlist(self):
# srtlist, 2*(nvar+1), int array, encoded by byteorder
srtlist = _pad_bytes("", 2 * (self.nvar + 1))
self._write(srtlist)
def _write_formats(self):
# fmtlist, 49*nvar, char array
for fmt in self.fmtlist:
self._write(_pad_bytes(fmt, 49))
def _write_value_label_names(self):
# lbllist, 33*nvar, char array
for i in range(self.nvar):
# Use variable name when categorical
if self._is_col_cat[i]:
name = self.varlist[i]
name = self._null_terminate(name, True)
name = _pad_bytes(name[:32], 33)
self._write(name)
else: # Default is empty label
self._write(_pad_bytes("", 33))
def _write_variable_labels(self):
# Missing labels are 80 blank characters plus null termination
blank = _pad_bytes("", 81)
if self._variable_labels is None:
for i in range(self.nvar):
self._write(blank)
return
for col in self.data:
if col in self._variable_labels:
label = self._variable_labels[col]
if len(label) > 80:
raise ValueError(
"Variable labels must be 80 characters " "or fewer"
)
is_latin1 = all(ord(c) < 256 for c in label)
if not is_latin1:
raise ValueError(
"Variable labels must contain only "
"characters that can be encoded in "
"Latin-1"
)
self._write(_pad_bytes(label, 81))
else:
self._write(blank)
def _convert_strls(self, data):
"""No-op, future compatibility"""
return data
def _prepare_data(self):
data = self.data
typlist = self.typlist
convert_dates = self._convert_dates
# 1. Convert dates
if self._convert_dates is not None:
for i, col in enumerate(data):
if i in convert_dates:
data[col] = _datetime_to_stata_elapsed_vec(
data[col], self.fmtlist[i]
)
# 2. Convert strls
data = self._convert_strls(data)
# 3. Convert bad string data to '' and pad to correct length
dtypes = {}
native_byteorder = self._byteorder == _set_endianness(sys.byteorder)
for i, col in enumerate(data):
typ = typlist[i]
if typ <= self._max_string_length:
data[col] = data[col].fillna("").apply(_pad_bytes, args=(typ,))
stype = "S{type}".format(type=typ)
dtypes[col] = stype
data[col] = data[col].str.encode(self._encoding).astype(stype)
else:
dtype = data[col].dtype
if not native_byteorder:
dtype = dtype.newbyteorder(self._byteorder)
dtypes[col] = dtype
self.data = data.to_records(index=False, column_dtypes=dtypes)
def _write_data(self):
data = self.data
self._file.write(data.tobytes())
def _null_terminate(self, s, as_string=False):
null_byte = "\x00"
s += null_byte
if not as_string:
s = s.encode(self._encoding)
return s
def _dtype_to_stata_type_117(dtype, column, force_strl):
"""
Converts dtype types to stata types. Returns the byte of the given ordinal.
See TYPE_MAP and comments for an explanation. This is also explained in
the dta spec.
1 - 2045 are strings of this length
Pandas Stata
32768 - for object strL
65526 - for int8 byte
65527 - for int16 int
65528 - for int32 long
65529 - for float32 float
65530 - for double double
If there are dates to convert, then dtype will already have the correct
type inserted.
"""
# TODO: expand to handle datetime to integer conversion
if force_strl:
return 32768
if dtype.type == np.object_: # try to coerce it to the biggest string
# not memory efficient, what else could we
# do?
itemsize = max_len_string_array(ensure_object(column.values))
itemsize = max(itemsize, 1)
if itemsize <= 2045:
return itemsize
return 32768
elif dtype == np.float64:
return 65526
elif dtype == np.float32:
return 65527
elif dtype == np.int32:
return 65528
elif dtype == np.int16:
return 65529
elif dtype == np.int8:
return 65530
else: # pragma : no cover
raise NotImplementedError("Data type %s not supported." % dtype)
def _pad_bytes_new(name, length):
"""
Takes a bytes instance and pads it with null bytes until it's length chars.
"""
if isinstance(name, str):
name = bytes(name, "utf-8")
return name + b"\x00" * (length - len(name))
class StataStrLWriter:
"""
Converter for Stata StrLs
Stata StrLs map 8 byte values to strings which are stored using a
dictionary-like format where strings are keyed to two values.
Parameters
----------
df : DataFrame
DataFrame to convert
columns : list
List of columns names to convert to StrL
version : int, optional
dta version. Currently supports 117, 118 and 119
byteorder : str, optional
Can be ">", "<", "little", or "big". default is `sys.byteorder`
Notes
-----
Supports creation of the StrL block of a dta file for dta versions
117, 118 and 119. These differ in how the GSO is stored. 118 and
119 store the GSO lookup value as a uint32 and a uint64, while 117
uses two uint32s. 118 and 119 also encode all strings as unicode
which is required by the format. 117 uses 'latin-1' a fixed width
encoding that extends the 7-bit ascii table with an additional 128
characters.
"""
def __init__(self, df, columns, version=117, byteorder=None):
if version not in (117, 118, 119):
raise ValueError("Only dta versions 117, 118 and 119 supported")
self._dta_ver = version
self.df = df
self.columns = columns
self._gso_table = OrderedDict((("", (0, 0)),))
if byteorder is None:
byteorder = sys.byteorder
self._byteorder = _set_endianness(byteorder)
gso_v_type = "I" # uint32
gso_o_type = "Q" # uint64
self._encoding = "utf-8"
if version == 117:
o_size = 4
gso_o_type = "I" # 117 used uint32
self._encoding = "latin-1"
elif version == 118:
o_size = 6
else: # version == 119
o_size = 5
self._o_offet = 2 ** (8 * (8 - o_size))
self._gso_o_type = gso_o_type
self._gso_v_type = gso_v_type
def _convert_key(self, key):
v, o = key
return v + self._o_offet * o
def generate_table(self):
"""
Generates the GSO lookup table for the DataFRame
Returns
-------
gso_table : OrderedDict
Ordered dictionary using the string found as keys
and their lookup position (v,o) as values
gso_df : DataFrame
DataFrame where strl columns have been converted to
(v,o) values
Notes
-----
Modifies the DataFrame in-place.
The DataFrame returned encodes the (v,o) values as uint64s. The
encoding depends on teh dta version, and can be expressed as
enc = v + o * 2 ** (o_size * 8)
so that v is stored in the lower bits and o is in the upper
bits. o_size is
* 117: 4
* 118: 6
* 119: 5
"""
gso_table = self._gso_table
gso_df = self.df
columns = list(gso_df.columns)
selected = gso_df[self.columns]
col_index = [(col, columns.index(col)) for col in self.columns]
keys = np.empty(selected.shape, dtype=np.uint64)
for o, (idx, row) in enumerate(selected.iterrows()):
for j, (col, v) in enumerate(col_index):
val = row[col]
# Allow columns with mixed str and None (GH 23633)
val = "" if val is None else val
key = gso_table.get(val, None)
if key is None:
# Stata prefers human numbers
key = (v + 1, o + 1)
gso_table[val] = key
keys[o, j] = self._convert_key(key)
for i, col in enumerate(self.columns):
gso_df[col] = keys[:, i]
return gso_table, gso_df
def _encode(self, s):
"""
Python 3 compatibility shim
"""
return s.encode(self._encoding)
def generate_blob(self, gso_table):
"""
Generates the binary blob of GSOs that is written to the dta file.
Parameters
----------
gso_table : OrderedDict
Ordered dictionary (str, vo)
Returns
-------
gso : bytes
Binary content of dta file to be placed between strl tags
Notes
-----
Output format depends on dta version. 117 uses two uint32s to
express v and o while 118+ uses a uint32 for v and a uint64 for o.
"""
# Format information
# Length includes null term
# 117
# GSOvvvvooootllllxxxxxxxxxxxxxxx...x
# 3 u4 u4 u1 u4 string + null term
#
# 118, 119
# GSOvvvvooooooootllllxxxxxxxxxxxxxxx...x
# 3 u4 u8 u1 u4 string + null term
bio = BytesIO()
gso = bytes("GSO", "ascii")
gso_type = struct.pack(self._byteorder + "B", 130)
null = struct.pack(self._byteorder + "B", 0)
v_type = self._byteorder + self._gso_v_type
o_type = self._byteorder + self._gso_o_type
len_type = self._byteorder + "I"
for strl, vo in gso_table.items():
if vo == (0, 0):
continue
v, o = vo
# GSO
bio.write(gso)
# vvvv
bio.write(struct.pack(v_type, v))
# oooo / oooooooo
bio.write(struct.pack(o_type, o))
# t
bio.write(gso_type)
# llll
utf8_string = bytes(strl, "utf-8")
bio.write(struct.pack(len_type, len(utf8_string) + 1))
# xxx...xxx
bio.write(utf8_string)
bio.write(null)
bio.seek(0)
return bio.read()
class StataWriter117(StataWriter):
"""
A class for writing Stata binary dta files in Stata 13 format (117)
.. versionadded:: 0.23.0
Parameters
----------
fname : path (string), buffer or path object
string, path object (pathlib.Path or py._path.local.LocalPath) or
object implementing a binary write() functions. If using a buffer
then the buffer will not be automatically closed after the file
is written.
data : DataFrame
Input to save
convert_dates : dict
Dictionary mapping columns containing datetime types to stata internal
format to use when writing the dates. Options are 'tc', 'td', 'tm',
'tw', 'th', 'tq', 'ty'. Column can be either an integer or a name.
Datetime columns that do not have a conversion type specified will be
converted to 'tc'. Raises NotImplementedError if a datetime column has
timezone information
write_index : bool
Write the index to Stata dataset.
encoding : str
Default is latin-1. Only latin-1 and ascii are supported.
byteorder : str
Can be ">", "<", "little", or "big". default is `sys.byteorder`
time_stamp : datetime
A datetime to use as file creation date. Default is the current time
data_label : str
A label for the data set. Must be 80 characters or smaller.
variable_labels : dict
Dictionary containing columns as keys and variable labels as values.
Each label must be 80 characters or smaller.
convert_strl : list
List of columns names to convert to Stata StrL format. Columns with
more than 2045 characters are automatically written as StrL.
Smaller columns can be converted by including the column name. Using
StrLs can reduce output file size when strings are longer than 8
characters, and either frequently repeated or sparse.
Returns
-------
writer : StataWriter117 instance
The StataWriter117 instance has a write_file method, which will
write the file to the given `fname`.
Raises
------
NotImplementedError
* If datetimes contain timezone information
ValueError
* Columns listed in convert_dates are neither datetime64[ns]
or datetime.datetime
* Column dtype is not representable in Stata
* Column listed in convert_dates is not in DataFrame
* Categorical label contains more than 32,000 characters
Examples
--------
>>> from pandas.io.stata import StataWriter117
>>> data = pd.DataFrame([[1.0, 1, 'a']], columns=['a', 'b', 'c'])
>>> writer = StataWriter117('./data_file.dta', data)
>>> writer.write_file()
Or with long strings stored in strl format
>>> data = pd.DataFrame([['A relatively long string'], [''], ['']],
... columns=['strls'])
>>> writer = StataWriter117('./data_file_with_long_strings.dta', data,
... convert_strl=['strls'])
>>> writer.write_file()
"""
_max_string_length = 2045
@deprecate_kwarg(old_arg_name="encoding", new_arg_name=None)
def __init__(
self,
fname,
data,
convert_dates=None,
write_index=True,
encoding="latin-1",
byteorder=None,
time_stamp=None,
data_label=None,
variable_labels=None,
convert_strl=None,
):
# Shallow copy since convert_strl might be modified later
self._convert_strl = [] if convert_strl is None else convert_strl[:]
super().__init__(
fname,
data,
convert_dates,
write_index,
byteorder=byteorder,
time_stamp=time_stamp,
data_label=data_label,
variable_labels=variable_labels,
)
self._map = None
self._strl_blob = None
@staticmethod
def _tag(val, tag):
"""Surround val with <tag></tag>"""
if isinstance(val, str):
val = bytes(val, "utf-8")
return bytes("<" + tag + ">", "utf-8") + val + bytes("</" + tag + ">", "utf-8")
def _update_map(self, tag):
"""Update map location for tag with file position"""
self._map[tag] = self._file.tell()
def _write_header(self, data_label=None, time_stamp=None):
"""Write the file header"""
byteorder = self._byteorder
self._file.write(bytes("<stata_dta>", "utf-8"))
bio = BytesIO()
# ds_format - 117
bio.write(self._tag(bytes("117", "utf-8"), "release"))
# byteorder
bio.write(self._tag(byteorder == ">" and "MSF" or "LSF", "byteorder"))
# number of vars, 2 bytes
assert self.nvar < 2 ** 16
bio.write(self._tag(struct.pack(byteorder + "H", self.nvar), "K"))
# number of obs, 4 bytes
bio.write(self._tag(struct.pack(byteorder + "I", self.nobs), "N"))
# data label 81 bytes, char, null terminated
label = data_label[:80] if data_label is not None else ""
label_len = struct.pack(byteorder + "B", len(label))
label = label_len + bytes(label, "utf-8")
bio.write(self._tag(label, "label"))
# time stamp, 18 bytes, char, null terminated
# format dd Mon yyyy hh:mm
if time_stamp is None:
time_stamp = datetime.datetime.now()
elif not isinstance(time_stamp, datetime.datetime):
raise ValueError("time_stamp should be datetime type")
# Avoid locale-specific month conversion
months = [
"Jan",
"Feb",
"Mar",
"Apr",
"May",
"Jun",
"Jul",
"Aug",
"Sep",
"Oct",
"Nov",
"Dec",
]
month_lookup = {i + 1: month for i, month in enumerate(months)}
ts = (
time_stamp.strftime("%d ")
+ month_lookup[time_stamp.month]
+ time_stamp.strftime(" %Y %H:%M")
)
# '\x11' added due to inspection of Stata file
ts = b"\x11" + bytes(ts, "utf8")
bio.write(self._tag(ts, "timestamp"))
bio.seek(0)
self._file.write(self._tag(bio.read(), "header"))
def _write_map(self):
"""Called twice during file write. The first populates the values in
the map with 0s. The second call writes the final map locations when
all blocks have been written."""
if self._map is None:
self._map = OrderedDict(
(
("stata_data", 0),
("map", self._file.tell()),
("variable_types", 0),
("varnames", 0),
("sortlist", 0),
("formats", 0),
("value_label_names", 0),
("variable_labels", 0),
("characteristics", 0),
("data", 0),
("strls", 0),
("value_labels", 0),
("stata_data_close", 0),
("end-of-file", 0),
)
)
# Move to start of map
self._file.seek(self._map["map"])
bio = BytesIO()
for val in self._map.values():
bio.write(struct.pack(self._byteorder + "Q", val))
bio.seek(0)
self._file.write(self._tag(bio.read(), "map"))
def _write_variable_types(self):
self._update_map("variable_types")
bio = BytesIO()
for typ in self.typlist:
bio.write(struct.pack(self._byteorder + "H", typ))
bio.seek(0)
self._file.write(self._tag(bio.read(), "variable_types"))
def _write_varnames(self):
self._update_map("varnames")
bio = BytesIO()
for name in self.varlist:
name = self._null_terminate(name, True)
name = _pad_bytes_new(name[:32], 33)
bio.write(name)
bio.seek(0)
self._file.write(self._tag(bio.read(), "varnames"))
def _write_sortlist(self):
self._update_map("sortlist")
self._file.write(self._tag(b"\x00\00" * (self.nvar + 1), "sortlist"))
def _write_formats(self):
self._update_map("formats")
bio = BytesIO()
for fmt in self.fmtlist:
bio.write(_pad_bytes_new(fmt, 49))
bio.seek(0)
self._file.write(self._tag(bio.read(), "formats"))
def _write_value_label_names(self):
self._update_map("value_label_names")
bio = BytesIO()
for i in range(self.nvar):
# Use variable name when categorical
name = "" # default name
if self._is_col_cat[i]:
name = self.varlist[i]
name = self._null_terminate(name, True)
name = _pad_bytes_new(name[:32], 33)
bio.write(name)
bio.seek(0)
self._file.write(self._tag(bio.read(), "value_label_names"))
def _write_variable_labels(self):
# Missing labels are 80 blank characters plus null termination
self._update_map("variable_labels")
bio = BytesIO()
blank = _pad_bytes_new("", 81)
if self._variable_labels is None:
for _ in range(self.nvar):
bio.write(blank)
bio.seek(0)
self._file.write(self._tag(bio.read(), "variable_labels"))
return
for col in self.data:
if col in self._variable_labels:
label = self._variable_labels[col]
if len(label) > 80:
raise ValueError(
"Variable labels must be 80 characters " "or fewer"
)
is_latin1 = all(ord(c) < 256 for c in label)
if not is_latin1:
raise ValueError(
"Variable labels must contain only "
"characters that can be encoded in "
"Latin-1"
)
bio.write(_pad_bytes_new(label, 81))
else:
bio.write(blank)
bio.seek(0)
self._file.write(self._tag(bio.read(), "variable_labels"))
def _write_characteristics(self):
self._update_map("characteristics")
self._file.write(self._tag(b"", "characteristics"))
def _write_data(self):
self._update_map("data")
data = self.data
self._file.write(b"<data>")
self._file.write(data.tobytes())
self._file.write(b"</data>")
def _write_strls(self):
self._update_map("strls")
strls = b""
if self._strl_blob is not None:
strls = self._strl_blob
self._file.write(self._tag(strls, "strls"))
def _write_expansion_fields(self):
"""No-op in dta 117+"""
pass
def _write_value_labels(self):
self._update_map("value_labels")
bio = BytesIO()
for vl in self._value_labels:
lab = vl.generate_value_label(self._byteorder, self._encoding)
lab = self._tag(lab, "lbl")
bio.write(lab)
bio.seek(0)
self._file.write(self._tag(bio.read(), "value_labels"))
def _write_file_close_tag(self):
self._update_map("stata_data_close")
self._file.write(bytes("</stata_dta>", "utf-8"))
self._update_map("end-of-file")
def _update_strl_names(self):
"""Update column names for conversion to strl if they might have been
changed to comply with Stata naming rules"""
# Update convert_strl if names changed
for orig, new in self._converted_names.items():
if orig in self._convert_strl:
idx = self._convert_strl.index(orig)
self._convert_strl[idx] = new
def _convert_strls(self, data):
"""Convert columns to StrLs if either very large or in the
convert_strl variable"""
convert_cols = [
col
for i, col in enumerate(data)
if self.typlist[i] == 32768 or col in self._convert_strl
]
if convert_cols:
ssw = StataStrLWriter(data, convert_cols)
tab, new_data = ssw.generate_table()
data = new_data
self._strl_blob = ssw.generate_blob(tab)
return data
def _set_formats_and_types(self, data, dtypes):
self.typlist = []
self.fmtlist = []
for col, dtype in dtypes.items():
force_strl = col in self._convert_strl
fmt = _dtype_to_default_stata_fmt(
dtype, data[col], dta_version=117, force_strl=force_strl
)
self.fmtlist.append(fmt)
self.typlist.append(_dtype_to_stata_type_117(dtype, data[col], force_strl))