509 lines
15 KiB
Python
509 lines
15 KiB
Python
"""
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Read a SAS XPort format file into a Pandas DataFrame.
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Based on code from Jack Cushman (github.com/jcushman/xport).
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The file format is defined here:
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https://support.sas.com/content/dam/SAS/support/en/technical-papers/record-layout-of-a-sas-version-5-or-6-data-set-in-sas-transport-xport-format.pdf
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"""
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from __future__ import annotations
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from collections import abc
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from datetime import datetime
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import struct
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from typing import TYPE_CHECKING
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import warnings
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import numpy as np
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from pandas.util._decorators import Appender
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from pandas.util._exceptions import find_stack_level
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import pandas as pd
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from pandas.io.common import get_handle
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from pandas.io.sas.sasreader import ReaderBase
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if TYPE_CHECKING:
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from pandas._typing import (
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CompressionOptions,
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DatetimeNaTType,
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FilePath,
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ReadBuffer,
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)
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_correct_line1 = (
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"HEADER RECORD*******LIBRARY HEADER RECORD!!!!!!!"
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"000000000000000000000000000000 "
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)
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_correct_header1 = (
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"HEADER RECORD*******MEMBER HEADER RECORD!!!!!!!000000000000000001600000000"
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)
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_correct_header2 = (
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"HEADER RECORD*******DSCRPTR HEADER RECORD!!!!!!!"
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"000000000000000000000000000000 "
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)
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_correct_obs_header = (
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"HEADER RECORD*******OBS HEADER RECORD!!!!!!!"
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"000000000000000000000000000000 "
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)
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_fieldkeys = [
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"ntype",
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"nhfun",
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"field_length",
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"nvar0",
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"name",
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"label",
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"nform",
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"nfl",
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"num_decimals",
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"nfj",
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"nfill",
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"niform",
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"nifl",
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"nifd",
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"npos",
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"_",
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]
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_base_params_doc = """\
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Parameters
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----------
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filepath_or_buffer : str or file-like object
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Path to SAS file or object implementing binary read method."""
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_params2_doc = """\
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index : identifier of index column
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Identifier of column that should be used as index of the DataFrame.
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encoding : str
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Encoding for text data.
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chunksize : int
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Read file `chunksize` lines at a time, returns iterator."""
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_format_params_doc = """\
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format : str
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File format, only `xport` is currently supported."""
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_iterator_doc = """\
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iterator : bool, default False
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Return XportReader object for reading file incrementally."""
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_read_sas_doc = f"""Read a SAS file into a DataFrame.
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{_base_params_doc}
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{_format_params_doc}
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{_params2_doc}
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{_iterator_doc}
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Returns
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-------
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DataFrame or XportReader
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Examples
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--------
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Read a SAS Xport file:
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>>> df = pd.read_sas('filename.XPT')
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Read a Xport file in 10,000 line chunks:
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>>> itr = pd.read_sas('filename.XPT', chunksize=10000)
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>>> for chunk in itr:
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>>> do_something(chunk)
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"""
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_xport_reader_doc = f"""\
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Class for reading SAS Xport files.
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{_base_params_doc}
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{_params2_doc}
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Attributes
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----------
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member_info : list
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Contains information about the file
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fields : list
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Contains information about the variables in the file
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"""
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_read_method_doc = """\
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Read observations from SAS Xport file, returning as data frame.
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Parameters
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----------
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nrows : int
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Number of rows to read from data file; if None, read whole
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file.
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Returns
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-------
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A DataFrame.
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"""
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def _parse_date(datestr: str) -> DatetimeNaTType:
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"""Given a date in xport format, return Python date."""
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try:
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# e.g. "16FEB11:10:07:55"
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return datetime.strptime(datestr, "%d%b%y:%H:%M:%S")
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except ValueError:
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return pd.NaT
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def _split_line(s: str, parts):
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"""
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Parameters
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----------
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s: str
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Fixed-length string to split
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parts: list of (name, length) pairs
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Used to break up string, name '_' will be filtered from output.
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Returns
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-------
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Dict of name:contents of string at given location.
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"""
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out = {}
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start = 0
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for name, length in parts:
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out[name] = s[start : start + length].strip()
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start += length
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del out["_"]
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return out
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def _handle_truncated_float_vec(vec, nbytes):
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# This feature is not well documented, but some SAS XPORT files
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# have 2-7 byte "truncated" floats. To read these truncated
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# floats, pad them with zeros on the right to make 8 byte floats.
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#
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# References:
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# https://github.com/jcushman/xport/pull/3
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# The R "foreign" library
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if nbytes != 8:
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vec1 = np.zeros(len(vec), np.dtype("S8"))
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dtype = np.dtype(f"S{nbytes},S{8 - nbytes}")
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vec2 = vec1.view(dtype=dtype)
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vec2["f0"] = vec
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return vec2
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return vec
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def _parse_float_vec(vec):
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"""
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Parse a vector of float values representing IBM 8 byte floats into
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native 8 byte floats.
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"""
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dtype = np.dtype(">u4,>u4")
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vec1 = vec.view(dtype=dtype)
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xport1 = vec1["f0"]
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xport2 = vec1["f1"]
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# Start by setting first half of ieee number to first half of IBM
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# number sans exponent
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ieee1 = xport1 & 0x00FFFFFF
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# The fraction bit to the left of the binary point in the ieee
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# format was set and the number was shifted 0, 1, 2, or 3
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# places. This will tell us how to adjust the ibm exponent to be a
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# power of 2 ieee exponent and how to shift the fraction bits to
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# restore the correct magnitude.
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shift = np.zeros(len(vec), dtype=np.uint8)
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shift[np.where(xport1 & 0x00200000)] = 1
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shift[np.where(xport1 & 0x00400000)] = 2
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shift[np.where(xport1 & 0x00800000)] = 3
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# shift the ieee number down the correct number of places then
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# set the second half of the ieee number to be the second half
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# of the ibm number shifted appropriately, ored with the bits
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# from the first half that would have been shifted in if we
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# could shift a double. All we are worried about are the low
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# order 3 bits of the first half since we're only shifting by
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# 1, 2, or 3.
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ieee1 >>= shift
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ieee2 = (xport2 >> shift) | ((xport1 & 0x00000007) << (29 + (3 - shift)))
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# clear the 1 bit to the left of the binary point
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ieee1 &= 0xFFEFFFFF
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# set the exponent of the ieee number to be the actual exponent
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# plus the shift count + 1023. Or this into the first half of the
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# ieee number. The ibm exponent is excess 64 but is adjusted by 65
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# since during conversion to ibm format the exponent is
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# incremented by 1 and the fraction bits left 4 positions to the
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# right of the radix point. (had to add >> 24 because C treats &
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# 0x7f as 0x7f000000 and Python doesn't)
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ieee1 |= ((((((xport1 >> 24) & 0x7F) - 65) << 2) + shift + 1023) << 20) | (
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xport1 & 0x80000000
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)
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ieee = np.empty((len(ieee1),), dtype=">u4,>u4")
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ieee["f0"] = ieee1
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ieee["f1"] = ieee2
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ieee = ieee.view(dtype=">f8")
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ieee = ieee.astype("f8")
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return ieee
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class XportReader(ReaderBase, abc.Iterator):
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__doc__ = _xport_reader_doc
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def __init__(
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self,
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filepath_or_buffer: FilePath | ReadBuffer[bytes],
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index=None,
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encoding: str | None = "ISO-8859-1",
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chunksize: int | None = None,
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compression: CompressionOptions = "infer",
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) -> None:
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self._encoding = encoding
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self._lines_read = 0
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self._index = index
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self._chunksize = chunksize
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self.handles = get_handle(
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filepath_or_buffer,
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"rb",
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encoding=encoding,
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is_text=False,
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compression=compression,
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)
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self.filepath_or_buffer = self.handles.handle
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try:
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self._read_header()
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except Exception:
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self.close()
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raise
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def close(self) -> None:
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self.handles.close()
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def _get_row(self):
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return self.filepath_or_buffer.read(80).decode()
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def _read_header(self) -> None:
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self.filepath_or_buffer.seek(0)
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# read file header
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line1 = self._get_row()
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if line1 != _correct_line1:
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if "**COMPRESSED**" in line1:
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# this was created with the PROC CPORT method and can't be read
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# https://documentation.sas.com/doc/en/pgmsascdc/9.4_3.5/movefile/p1bm6aqp3fw4uin1hucwh718f6kp.htm
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raise ValueError(
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"Header record indicates a CPORT file, which is not readable."
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)
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raise ValueError("Header record is not an XPORT file.")
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line2 = self._get_row()
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fif = [["prefix", 24], ["version", 8], ["OS", 8], ["_", 24], ["created", 16]]
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file_info = _split_line(line2, fif)
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if file_info["prefix"] != "SAS SAS SASLIB":
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raise ValueError("Header record has invalid prefix.")
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file_info["created"] = _parse_date(file_info["created"])
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self.file_info = file_info
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line3 = self._get_row()
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file_info["modified"] = _parse_date(line3[:16])
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# read member header
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header1 = self._get_row()
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header2 = self._get_row()
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headflag1 = header1.startswith(_correct_header1)
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headflag2 = header2 == _correct_header2
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if not (headflag1 and headflag2):
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raise ValueError("Member header not found")
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# usually 140, could be 135
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fieldnamelength = int(header1[-5:-2])
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# member info
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mem = [
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["prefix", 8],
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["set_name", 8],
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["sasdata", 8],
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["version", 8],
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["OS", 8],
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["_", 24],
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["created", 16],
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]
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member_info = _split_line(self._get_row(), mem)
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mem = [["modified", 16], ["_", 16], ["label", 40], ["type", 8]]
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member_info.update(_split_line(self._get_row(), mem))
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member_info["modified"] = _parse_date(member_info["modified"])
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member_info["created"] = _parse_date(member_info["created"])
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self.member_info = member_info
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# read field names
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types = {1: "numeric", 2: "char"}
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fieldcount = int(self._get_row()[54:58])
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datalength = fieldnamelength * fieldcount
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# round up to nearest 80
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if datalength % 80:
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datalength += 80 - datalength % 80
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fielddata = self.filepath_or_buffer.read(datalength)
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fields = []
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obs_length = 0
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while len(fielddata) >= fieldnamelength:
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# pull data for one field
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fieldbytes, fielddata = (
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fielddata[:fieldnamelength],
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fielddata[fieldnamelength:],
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)
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# rest at end gets ignored, so if field is short, pad out
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# to match struct pattern below
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fieldbytes = fieldbytes.ljust(140)
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fieldstruct = struct.unpack(">hhhh8s40s8shhh2s8shhl52s", fieldbytes)
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field = dict(zip(_fieldkeys, fieldstruct))
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del field["_"]
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field["ntype"] = types[field["ntype"]]
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fl = field["field_length"]
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if field["ntype"] == "numeric" and ((fl < 2) or (fl > 8)):
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msg = f"Floating field width {fl} is not between 2 and 8."
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raise TypeError(msg)
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for k, v in field.items():
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try:
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field[k] = v.strip()
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except AttributeError:
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pass
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obs_length += field["field_length"]
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fields += [field]
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header = self._get_row()
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if not header == _correct_obs_header:
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raise ValueError("Observation header not found.")
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self.fields = fields
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self.record_length = obs_length
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self.record_start = self.filepath_or_buffer.tell()
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self.nobs = self._record_count()
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self.columns = [x["name"].decode() for x in self.fields]
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# Setup the dtype.
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dtypel = [
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("s" + str(i), "S" + str(field["field_length"]))
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for i, field in enumerate(self.fields)
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]
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dtype = np.dtype(dtypel)
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self._dtype = dtype
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def __next__(self) -> pd.DataFrame:
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return self.read(nrows=self._chunksize or 1)
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def _record_count(self) -> int:
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"""
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Get number of records in file.
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This is maybe suboptimal because we have to seek to the end of
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the file.
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Side effect: returns file position to record_start.
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"""
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self.filepath_or_buffer.seek(0, 2)
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total_records_length = self.filepath_or_buffer.tell() - self.record_start
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if total_records_length % 80 != 0:
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warnings.warn(
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"xport file may be corrupted.",
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stacklevel=find_stack_level(),
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)
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if self.record_length > 80:
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self.filepath_or_buffer.seek(self.record_start)
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return total_records_length // self.record_length
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self.filepath_or_buffer.seek(-80, 2)
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last_card_bytes = self.filepath_or_buffer.read(80)
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last_card = np.frombuffer(last_card_bytes, dtype=np.uint64)
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# 8 byte blank
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ix = np.flatnonzero(last_card == 2314885530818453536)
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if len(ix) == 0:
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tail_pad = 0
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else:
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tail_pad = 8 * len(ix)
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self.filepath_or_buffer.seek(self.record_start)
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return (total_records_length - tail_pad) // self.record_length
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def get_chunk(self, size: int | None = None) -> pd.DataFrame:
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"""
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Reads lines from Xport file and returns as dataframe
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Parameters
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----------
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size : int, defaults to None
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Number of lines to read. If None, reads whole file.
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Returns
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-------
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DataFrame
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"""
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if size is None:
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size = self._chunksize
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return self.read(nrows=size)
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def _missing_double(self, vec):
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v = vec.view(dtype="u1,u1,u2,u4")
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miss = (v["f1"] == 0) & (v["f2"] == 0) & (v["f3"] == 0)
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miss1 = (
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((v["f0"] >= 0x41) & (v["f0"] <= 0x5A))
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| (v["f0"] == 0x5F)
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| (v["f0"] == 0x2E)
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)
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miss &= miss1
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return miss
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@Appender(_read_method_doc)
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def read(self, nrows: int | None = None) -> pd.DataFrame:
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if nrows is None:
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nrows = self.nobs
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read_lines = min(nrows, self.nobs - self._lines_read)
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read_len = read_lines * self.record_length
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if read_len <= 0:
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self.close()
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raise StopIteration
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raw = self.filepath_or_buffer.read(read_len)
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data = np.frombuffer(raw, dtype=self._dtype, count=read_lines)
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df_data = {}
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for j, x in enumerate(self.columns):
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vec = data["s" + str(j)]
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ntype = self.fields[j]["ntype"]
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if ntype == "numeric":
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vec = _handle_truncated_float_vec(vec, self.fields[j]["field_length"])
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miss = self._missing_double(vec)
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v = _parse_float_vec(vec)
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v[miss] = np.nan
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elif self.fields[j]["ntype"] == "char":
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v = [y.rstrip() for y in vec]
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if self._encoding is not None:
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v = [y.decode(self._encoding) for y in v]
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df_data.update({x: v})
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df = pd.DataFrame(df_data)
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if self._index is None:
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df.index = pd.Index(range(self._lines_read, self._lines_read + read_lines))
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else:
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df = df.set_index(self._index)
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self._lines_read += read_lines
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return df
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