757 lines
27 KiB
Python
757 lines
27 KiB
Python
"""
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Read SAS7BDAT files
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Based on code written by Jared Hobbs:
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https://bitbucket.org/jaredhobbs/sas7bdat
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See also:
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https://github.com/BioStatMatt/sas7bdat
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Partial documentation of the file format:
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https://cran.r-project.org/package=sas7bdat/vignettes/sas7bdat.pdf
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Reference for binary data compression:
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http://collaboration.cmc.ec.gc.ca/science/rpn/biblio/ddj/Website/articles/CUJ/1992/9210/ross/ross.htm
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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 (
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datetime,
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timedelta,
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)
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import sys
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from typing import TYPE_CHECKING
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import numpy as np
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from pandas._libs.byteswap import (
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read_double_with_byteswap,
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read_float_with_byteswap,
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read_uint16_with_byteswap,
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read_uint32_with_byteswap,
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read_uint64_with_byteswap,
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)
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from pandas._libs.sas import (
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Parser,
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get_subheader_index,
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)
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from pandas._libs.tslibs.conversion import cast_from_unit_vectorized
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from pandas.errors import EmptyDataError
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import pandas as pd
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from pandas import (
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DataFrame,
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Timestamp,
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isna,
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)
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from pandas.io.common import get_handle
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import pandas.io.sas.sas_constants as const
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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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FilePath,
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ReadBuffer,
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)
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_unix_origin = Timestamp("1970-01-01")
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_sas_origin = Timestamp("1960-01-01")
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def _parse_datetime(sas_datetime: float, unit: str):
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if isna(sas_datetime):
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return pd.NaT
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if unit == "s":
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return datetime(1960, 1, 1) + timedelta(seconds=sas_datetime)
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elif unit == "d":
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return datetime(1960, 1, 1) + timedelta(days=sas_datetime)
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else:
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raise ValueError("unit must be 'd' or 's'")
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def _convert_datetimes(sas_datetimes: pd.Series, unit: str) -> pd.Series:
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"""
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Convert to Timestamp if possible, otherwise to datetime.datetime.
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SAS float64 lacks precision for more than ms resolution so the fit
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to datetime.datetime is ok.
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Parameters
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----------
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sas_datetimes : {Series, Sequence[float]}
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Dates or datetimes in SAS
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unit : {'d', 's'}
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"d" if the floats represent dates, "s" for datetimes
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Returns
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-------
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Series
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Series of datetime64 dtype or datetime.datetime.
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"""
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td = (_sas_origin - _unix_origin).as_unit("s")
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if unit == "s":
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millis = cast_from_unit_vectorized(
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sas_datetimes._values, unit="s", out_unit="ms"
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)
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dt64ms = millis.view("M8[ms]") + td
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return pd.Series(dt64ms, index=sas_datetimes.index, copy=False)
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else:
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vals = np.array(sas_datetimes, dtype="M8[D]") + td
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return pd.Series(vals, dtype="M8[s]", index=sas_datetimes.index, copy=False)
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class _Column:
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col_id: int
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name: str | bytes
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label: str | bytes
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format: str | bytes
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ctype: bytes
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length: int
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def __init__(
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self,
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col_id: int,
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# These can be bytes when convert_header_text is False
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name: str | bytes,
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label: str | bytes,
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format: str | bytes,
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ctype: bytes,
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length: int,
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) -> None:
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self.col_id = col_id
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self.name = name
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self.label = label
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self.format = format
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self.ctype = ctype
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self.length = length
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# SAS7BDAT represents a SAS data file in SAS7BDAT format.
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class SAS7BDATReader(ReaderBase, abc.Iterator):
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"""
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Read SAS files in SAS7BDAT format.
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Parameters
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----------
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path_or_buf : path name or buffer
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Name of SAS file or file-like object pointing to SAS file
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contents.
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index : column identifier, defaults to None
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Column to use as index.
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convert_dates : bool, defaults to True
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Attempt to convert dates to Pandas datetime values. Note that
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some rarely used SAS date formats may be unsupported.
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blank_missing : bool, defaults to True
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Convert empty strings to missing values (SAS uses blanks to
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indicate missing character variables).
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chunksize : int, defaults to None
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Return SAS7BDATReader object for iterations, returns chunks
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with given number of lines.
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encoding : str, 'infer', defaults to None
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String encoding acc. to Python standard encodings,
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encoding='infer' tries to detect the encoding from the file header,
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encoding=None will leave the data in binary format.
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convert_text : bool, defaults to True
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If False, text variables are left as raw bytes.
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convert_header_text : bool, defaults to True
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If False, header text, including column names, are left as raw
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bytes.
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"""
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_int_length: int
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_cached_page: bytes | None
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def __init__(
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self,
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path_or_buf: FilePath | ReadBuffer[bytes],
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index=None,
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convert_dates: bool = True,
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blank_missing: bool = True,
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chunksize: int | None = None,
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encoding: str | None = None,
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convert_text: bool = True,
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convert_header_text: bool = True,
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compression: CompressionOptions = "infer",
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) -> None:
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self.index = index
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self.convert_dates = convert_dates
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self.blank_missing = blank_missing
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self.chunksize = chunksize
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self.encoding = encoding
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self.convert_text = convert_text
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self.convert_header_text = convert_header_text
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self.default_encoding = "latin-1"
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self.compression = b""
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self.column_names_raw: list[bytes] = []
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self.column_names: list[str | bytes] = []
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self.column_formats: list[str | bytes] = []
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self.columns: list[_Column] = []
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self._current_page_data_subheader_pointers: list[tuple[int, int]] = []
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self._cached_page = None
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self._column_data_lengths: list[int] = []
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self._column_data_offsets: list[int] = []
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self._column_types: list[bytes] = []
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self._current_row_in_file_index = 0
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self._current_row_on_page_index = 0
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self._current_row_in_file_index = 0
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self.handles = get_handle(
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path_or_buf, "rb", is_text=False, compression=compression
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)
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self._path_or_buf = self.handles.handle
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# Same order as const.SASIndex
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self._subheader_processors = [
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self._process_rowsize_subheader,
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self._process_columnsize_subheader,
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self._process_subheader_counts,
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self._process_columntext_subheader,
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self._process_columnname_subheader,
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self._process_columnattributes_subheader,
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self._process_format_subheader,
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self._process_columnlist_subheader,
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None, # Data
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]
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try:
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self._get_properties()
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self._parse_metadata()
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except Exception:
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self.close()
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raise
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def column_data_lengths(self) -> np.ndarray:
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"""Return a numpy int64 array of the column data lengths"""
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return np.asarray(self._column_data_lengths, dtype=np.int64)
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def column_data_offsets(self) -> np.ndarray:
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"""Return a numpy int64 array of the column offsets"""
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return np.asarray(self._column_data_offsets, dtype=np.int64)
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def column_types(self) -> np.ndarray:
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"""
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Returns a numpy character array of the column types:
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s (string) or d (double)
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"""
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return np.asarray(self._column_types, dtype=np.dtype("S1"))
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def close(self) -> None:
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self.handles.close()
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def _get_properties(self) -> None:
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# Check magic number
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self._path_or_buf.seek(0)
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self._cached_page = self._path_or_buf.read(288)
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if self._cached_page[0 : len(const.magic)] != const.magic:
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raise ValueError("magic number mismatch (not a SAS file?)")
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# Get alignment information
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buf = self._read_bytes(const.align_1_offset, const.align_1_length)
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if buf == const.u64_byte_checker_value:
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self.U64 = True
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self._int_length = 8
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self._page_bit_offset = const.page_bit_offset_x64
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self._subheader_pointer_length = const.subheader_pointer_length_x64
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else:
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self.U64 = False
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self._page_bit_offset = const.page_bit_offset_x86
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self._subheader_pointer_length = const.subheader_pointer_length_x86
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self._int_length = 4
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buf = self._read_bytes(const.align_2_offset, const.align_2_length)
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if buf == const.align_1_checker_value:
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align1 = const.align_2_value
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else:
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align1 = 0
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# Get endianness information
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buf = self._read_bytes(const.endianness_offset, const.endianness_length)
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if buf == b"\x01":
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self.byte_order = "<"
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self.need_byteswap = sys.byteorder == "big"
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else:
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self.byte_order = ">"
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self.need_byteswap = sys.byteorder == "little"
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# Get encoding information
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buf = self._read_bytes(const.encoding_offset, const.encoding_length)[0]
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if buf in const.encoding_names:
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self.inferred_encoding = const.encoding_names[buf]
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if self.encoding == "infer":
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self.encoding = self.inferred_encoding
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else:
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self.inferred_encoding = f"unknown (code={buf})"
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# Timestamp is epoch 01/01/1960
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epoch = datetime(1960, 1, 1)
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x = self._read_float(
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const.date_created_offset + align1, const.date_created_length
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)
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self.date_created = epoch + pd.to_timedelta(x, unit="s")
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x = self._read_float(
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const.date_modified_offset + align1, const.date_modified_length
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)
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self.date_modified = epoch + pd.to_timedelta(x, unit="s")
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self.header_length = self._read_uint(
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const.header_size_offset + align1, const.header_size_length
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)
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# Read the rest of the header into cached_page.
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buf = self._path_or_buf.read(self.header_length - 288)
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self._cached_page += buf
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# error: Argument 1 to "len" has incompatible type "Optional[bytes]";
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# expected "Sized"
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if len(self._cached_page) != self.header_length: # type: ignore[arg-type]
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raise ValueError("The SAS7BDAT file appears to be truncated.")
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self._page_length = self._read_uint(
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const.page_size_offset + align1, const.page_size_length
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)
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def __next__(self) -> DataFrame:
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da = self.read(nrows=self.chunksize or 1)
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if da.empty:
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self.close()
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raise StopIteration
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return da
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# Read a single float of the given width (4 or 8).
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def _read_float(self, offset: int, width: int):
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assert self._cached_page is not None
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if width == 4:
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return read_float_with_byteswap(
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self._cached_page, offset, self.need_byteswap
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)
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elif width == 8:
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return read_double_with_byteswap(
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self._cached_page, offset, self.need_byteswap
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)
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else:
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self.close()
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raise ValueError("invalid float width")
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# Read a single unsigned integer of the given width (1, 2, 4 or 8).
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def _read_uint(self, offset: int, width: int) -> int:
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assert self._cached_page is not None
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if width == 1:
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return self._read_bytes(offset, 1)[0]
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elif width == 2:
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return read_uint16_with_byteswap(
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self._cached_page, offset, self.need_byteswap
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)
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elif width == 4:
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return read_uint32_with_byteswap(
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self._cached_page, offset, self.need_byteswap
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)
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elif width == 8:
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return read_uint64_with_byteswap(
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self._cached_page, offset, self.need_byteswap
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)
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else:
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self.close()
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raise ValueError("invalid int width")
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def _read_bytes(self, offset: int, length: int):
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assert self._cached_page is not None
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if offset + length > len(self._cached_page):
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self.close()
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raise ValueError("The cached page is too small.")
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return self._cached_page[offset : offset + length]
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def _read_and_convert_header_text(self, offset: int, length: int) -> str | bytes:
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return self._convert_header_text(
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self._read_bytes(offset, length).rstrip(b"\x00 ")
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)
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def _parse_metadata(self) -> None:
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done = False
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while not done:
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self._cached_page = self._path_or_buf.read(self._page_length)
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if len(self._cached_page) <= 0:
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break
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if len(self._cached_page) != self._page_length:
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raise ValueError("Failed to read a meta data page from the SAS file.")
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done = self._process_page_meta()
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def _process_page_meta(self) -> bool:
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self._read_page_header()
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pt = const.page_meta_types + [const.page_amd_type, const.page_mix_type]
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if self._current_page_type in pt:
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self._process_page_metadata()
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is_data_page = self._current_page_type == const.page_data_type
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is_mix_page = self._current_page_type == const.page_mix_type
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return bool(
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is_data_page
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or is_mix_page
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or self._current_page_data_subheader_pointers != []
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)
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def _read_page_header(self) -> None:
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bit_offset = self._page_bit_offset
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tx = const.page_type_offset + bit_offset
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self._current_page_type = (
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self._read_uint(tx, const.page_type_length) & const.page_type_mask2
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)
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tx = const.block_count_offset + bit_offset
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self._current_page_block_count = self._read_uint(tx, const.block_count_length)
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tx = const.subheader_count_offset + bit_offset
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self._current_page_subheaders_count = self._read_uint(
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tx, const.subheader_count_length
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)
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def _process_page_metadata(self) -> None:
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bit_offset = self._page_bit_offset
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for i in range(self._current_page_subheaders_count):
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offset = const.subheader_pointers_offset + bit_offset
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total_offset = offset + self._subheader_pointer_length * i
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subheader_offset = self._read_uint(total_offset, self._int_length)
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total_offset += self._int_length
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subheader_length = self._read_uint(total_offset, self._int_length)
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total_offset += self._int_length
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subheader_compression = self._read_uint(total_offset, 1)
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total_offset += 1
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subheader_type = self._read_uint(total_offset, 1)
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if (
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subheader_length == 0
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or subheader_compression == const.truncated_subheader_id
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):
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continue
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subheader_signature = self._read_bytes(subheader_offset, self._int_length)
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subheader_index = get_subheader_index(subheader_signature)
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subheader_processor = self._subheader_processors[subheader_index]
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if subheader_processor is None:
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f1 = subheader_compression in (const.compressed_subheader_id, 0)
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f2 = subheader_type == const.compressed_subheader_type
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if self.compression and f1 and f2:
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self._current_page_data_subheader_pointers.append(
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(subheader_offset, subheader_length)
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)
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else:
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self.close()
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raise ValueError(
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f"Unknown subheader signature {subheader_signature}"
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)
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else:
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subheader_processor(subheader_offset, subheader_length)
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def _process_rowsize_subheader(self, offset: int, length: int) -> None:
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int_len = self._int_length
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lcs_offset = offset
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lcp_offset = offset
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if self.U64:
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lcs_offset += 682
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lcp_offset += 706
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else:
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lcs_offset += 354
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lcp_offset += 378
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self.row_length = self._read_uint(
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offset + const.row_length_offset_multiplier * int_len,
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int_len,
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)
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self.row_count = self._read_uint(
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offset + const.row_count_offset_multiplier * int_len,
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int_len,
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)
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self.col_count_p1 = self._read_uint(
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offset + const.col_count_p1_multiplier * int_len, int_len
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)
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self.col_count_p2 = self._read_uint(
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offset + const.col_count_p2_multiplier * int_len, int_len
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)
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mx = const.row_count_on_mix_page_offset_multiplier * int_len
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self._mix_page_row_count = self._read_uint(offset + mx, int_len)
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self._lcs = self._read_uint(lcs_offset, 2)
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self._lcp = self._read_uint(lcp_offset, 2)
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def _process_columnsize_subheader(self, offset: int, length: int) -> None:
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int_len = self._int_length
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offset += int_len
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self.column_count = self._read_uint(offset, int_len)
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if self.col_count_p1 + self.col_count_p2 != self.column_count:
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print(
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f"Warning: column count mismatch ({self.col_count_p1} + "
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f"{self.col_count_p2} != {self.column_count})\n"
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)
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# Unknown purpose
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def _process_subheader_counts(self, offset: int, length: int) -> None:
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pass
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|
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def _process_columntext_subheader(self, offset: int, length: int) -> None:
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offset += self._int_length
|
|
text_block_size = self._read_uint(offset, const.text_block_size_length)
|
|
|
|
buf = self._read_bytes(offset, text_block_size)
|
|
cname_raw = buf[0:text_block_size].rstrip(b"\x00 ")
|
|
self.column_names_raw.append(cname_raw)
|
|
|
|
if len(self.column_names_raw) == 1:
|
|
compression_literal = b""
|
|
for cl in const.compression_literals:
|
|
if cl in cname_raw:
|
|
compression_literal = cl
|
|
self.compression = compression_literal
|
|
offset -= self._int_length
|
|
|
|
offset1 = offset + 16
|
|
if self.U64:
|
|
offset1 += 4
|
|
|
|
buf = self._read_bytes(offset1, self._lcp)
|
|
compression_literal = buf.rstrip(b"\x00")
|
|
if compression_literal == b"":
|
|
self._lcs = 0
|
|
offset1 = offset + 32
|
|
if self.U64:
|
|
offset1 += 4
|
|
buf = self._read_bytes(offset1, self._lcp)
|
|
self.creator_proc = buf[0 : self._lcp]
|
|
elif compression_literal == const.rle_compression:
|
|
offset1 = offset + 40
|
|
if self.U64:
|
|
offset1 += 4
|
|
buf = self._read_bytes(offset1, self._lcp)
|
|
self.creator_proc = buf[0 : self._lcp]
|
|
elif self._lcs > 0:
|
|
self._lcp = 0
|
|
offset1 = offset + 16
|
|
if self.U64:
|
|
offset1 += 4
|
|
buf = self._read_bytes(offset1, self._lcs)
|
|
self.creator_proc = buf[0 : self._lcp]
|
|
if hasattr(self, "creator_proc"):
|
|
self.creator_proc = self._convert_header_text(self.creator_proc)
|
|
|
|
def _process_columnname_subheader(self, offset: int, length: int) -> None:
|
|
int_len = self._int_length
|
|
offset += int_len
|
|
column_name_pointers_count = (length - 2 * int_len - 12) // 8
|
|
for i in range(column_name_pointers_count):
|
|
text_subheader = (
|
|
offset
|
|
+ const.column_name_pointer_length * (i + 1)
|
|
+ const.column_name_text_subheader_offset
|
|
)
|
|
col_name_offset = (
|
|
offset
|
|
+ const.column_name_pointer_length * (i + 1)
|
|
+ const.column_name_offset_offset
|
|
)
|
|
col_name_length = (
|
|
offset
|
|
+ const.column_name_pointer_length * (i + 1)
|
|
+ const.column_name_length_offset
|
|
)
|
|
|
|
idx = self._read_uint(
|
|
text_subheader, const.column_name_text_subheader_length
|
|
)
|
|
col_offset = self._read_uint(
|
|
col_name_offset, const.column_name_offset_length
|
|
)
|
|
col_len = self._read_uint(col_name_length, const.column_name_length_length)
|
|
|
|
name_raw = self.column_names_raw[idx]
|
|
cname = name_raw[col_offset : col_offset + col_len]
|
|
self.column_names.append(self._convert_header_text(cname))
|
|
|
|
def _process_columnattributes_subheader(self, offset: int, length: int) -> None:
|
|
int_len = self._int_length
|
|
column_attributes_vectors_count = (length - 2 * int_len - 12) // (int_len + 8)
|
|
for i in range(column_attributes_vectors_count):
|
|
col_data_offset = (
|
|
offset + int_len + const.column_data_offset_offset + i * (int_len + 8)
|
|
)
|
|
col_data_len = (
|
|
offset
|
|
+ 2 * int_len
|
|
+ const.column_data_length_offset
|
|
+ i * (int_len + 8)
|
|
)
|
|
col_types = (
|
|
offset + 2 * int_len + const.column_type_offset + i * (int_len + 8)
|
|
)
|
|
|
|
x = self._read_uint(col_data_offset, int_len)
|
|
self._column_data_offsets.append(x)
|
|
|
|
x = self._read_uint(col_data_len, const.column_data_length_length)
|
|
self._column_data_lengths.append(x)
|
|
|
|
x = self._read_uint(col_types, const.column_type_length)
|
|
self._column_types.append(b"d" if x == 1 else b"s")
|
|
|
|
def _process_columnlist_subheader(self, offset: int, length: int) -> None:
|
|
# unknown purpose
|
|
pass
|
|
|
|
def _process_format_subheader(self, offset: int, length: int) -> None:
|
|
int_len = self._int_length
|
|
text_subheader_format = (
|
|
offset + const.column_format_text_subheader_index_offset + 3 * int_len
|
|
)
|
|
col_format_offset = offset + const.column_format_offset_offset + 3 * int_len
|
|
col_format_len = offset + const.column_format_length_offset + 3 * int_len
|
|
text_subheader_label = (
|
|
offset + const.column_label_text_subheader_index_offset + 3 * int_len
|
|
)
|
|
col_label_offset = offset + const.column_label_offset_offset + 3 * int_len
|
|
col_label_len = offset + const.column_label_length_offset + 3 * int_len
|
|
|
|
x = self._read_uint(
|
|
text_subheader_format, const.column_format_text_subheader_index_length
|
|
)
|
|
format_idx = min(x, len(self.column_names_raw) - 1)
|
|
|
|
format_start = self._read_uint(
|
|
col_format_offset, const.column_format_offset_length
|
|
)
|
|
format_len = self._read_uint(col_format_len, const.column_format_length_length)
|
|
|
|
label_idx = self._read_uint(
|
|
text_subheader_label, const.column_label_text_subheader_index_length
|
|
)
|
|
label_idx = min(label_idx, len(self.column_names_raw) - 1)
|
|
|
|
label_start = self._read_uint(
|
|
col_label_offset, const.column_label_offset_length
|
|
)
|
|
label_len = self._read_uint(col_label_len, const.column_label_length_length)
|
|
|
|
label_names = self.column_names_raw[label_idx]
|
|
column_label = self._convert_header_text(
|
|
label_names[label_start : label_start + label_len]
|
|
)
|
|
format_names = self.column_names_raw[format_idx]
|
|
column_format = self._convert_header_text(
|
|
format_names[format_start : format_start + format_len]
|
|
)
|
|
current_column_number = len(self.columns)
|
|
|
|
col = _Column(
|
|
current_column_number,
|
|
self.column_names[current_column_number],
|
|
column_label,
|
|
column_format,
|
|
self._column_types[current_column_number],
|
|
self._column_data_lengths[current_column_number],
|
|
)
|
|
|
|
self.column_formats.append(column_format)
|
|
self.columns.append(col)
|
|
|
|
def read(self, nrows: int | None = None) -> DataFrame:
|
|
if (nrows is None) and (self.chunksize is not None):
|
|
nrows = self.chunksize
|
|
elif nrows is None:
|
|
nrows = self.row_count
|
|
|
|
if len(self._column_types) == 0:
|
|
self.close()
|
|
raise EmptyDataError("No columns to parse from file")
|
|
|
|
if nrows > 0 and self._current_row_in_file_index >= self.row_count:
|
|
return DataFrame()
|
|
|
|
nrows = min(nrows, self.row_count - self._current_row_in_file_index)
|
|
|
|
nd = self._column_types.count(b"d")
|
|
ns = self._column_types.count(b"s")
|
|
|
|
self._string_chunk = np.empty((ns, nrows), dtype=object)
|
|
self._byte_chunk = np.zeros((nd, 8 * nrows), dtype=np.uint8)
|
|
|
|
self._current_row_in_chunk_index = 0
|
|
p = Parser(self)
|
|
p.read(nrows)
|
|
|
|
rslt = self._chunk_to_dataframe()
|
|
if self.index is not None:
|
|
rslt = rslt.set_index(self.index)
|
|
|
|
return rslt
|
|
|
|
def _read_next_page(self):
|
|
self._current_page_data_subheader_pointers = []
|
|
self._cached_page = self._path_or_buf.read(self._page_length)
|
|
if len(self._cached_page) <= 0:
|
|
return True
|
|
elif len(self._cached_page) != self._page_length:
|
|
self.close()
|
|
msg = (
|
|
"failed to read complete page from file (read "
|
|
f"{len(self._cached_page):d} of {self._page_length:d} bytes)"
|
|
)
|
|
raise ValueError(msg)
|
|
|
|
self._read_page_header()
|
|
if self._current_page_type in const.page_meta_types:
|
|
self._process_page_metadata()
|
|
|
|
if self._current_page_type not in const.page_meta_types + [
|
|
const.page_data_type,
|
|
const.page_mix_type,
|
|
]:
|
|
return self._read_next_page()
|
|
|
|
return False
|
|
|
|
def _chunk_to_dataframe(self) -> DataFrame:
|
|
n = self._current_row_in_chunk_index
|
|
m = self._current_row_in_file_index
|
|
ix = range(m - n, m)
|
|
rslt = {}
|
|
|
|
js, jb = 0, 0
|
|
for j in range(self.column_count):
|
|
name = self.column_names[j]
|
|
|
|
if self._column_types[j] == b"d":
|
|
col_arr = self._byte_chunk[jb, :].view(dtype=self.byte_order + "d")
|
|
rslt[name] = pd.Series(col_arr, dtype=np.float64, index=ix, copy=False)
|
|
if self.convert_dates:
|
|
if self.column_formats[j] in const.sas_date_formats:
|
|
rslt[name] = _convert_datetimes(rslt[name], "d")
|
|
elif self.column_formats[j] in const.sas_datetime_formats:
|
|
rslt[name] = _convert_datetimes(rslt[name], "s")
|
|
jb += 1
|
|
elif self._column_types[j] == b"s":
|
|
rslt[name] = pd.Series(self._string_chunk[js, :], index=ix, copy=False)
|
|
if self.convert_text and (self.encoding is not None):
|
|
rslt[name] = self._decode_string(rslt[name].str)
|
|
js += 1
|
|
else:
|
|
self.close()
|
|
raise ValueError(f"unknown column type {repr(self._column_types[j])}")
|
|
|
|
df = DataFrame(rslt, columns=self.column_names, index=ix, copy=False)
|
|
return df
|
|
|
|
def _decode_string(self, b):
|
|
return b.decode(self.encoding or self.default_encoding)
|
|
|
|
def _convert_header_text(self, b: bytes) -> str | bytes:
|
|
if self.convert_header_text:
|
|
return self._decode_string(b)
|
|
else:
|
|
return b
|