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duality-group / pandas python
Repository URL to install this package:
|
Version:
1.4.3 ▾
|
# Copyright (c) 2012, Lambda Foundry, Inc.
# See LICENSE for the license
from csv import (
QUOTE_MINIMAL,
QUOTE_NONE,
QUOTE_NONNUMERIC,
)
from errno import ENOENT
import sys
import time
import warnings
from libc.stdlib cimport free
from libc.string cimport (
strcasecmp,
strlen,
strncpy,
)
import cython
from cython import Py_ssize_t
from cpython.bytes cimport (
PyBytes_AsString,
PyBytes_FromString,
)
from cpython.exc cimport (
PyErr_Fetch,
PyErr_Occurred,
)
from cpython.object cimport PyObject
from cpython.ref cimport (
Py_INCREF,
Py_XDECREF,
)
from cpython.unicode cimport (
PyUnicode_AsUTF8String,
PyUnicode_Decode,
PyUnicode_DecodeUTF8,
)
cdef extern from "Python.h":
object PyUnicode_FromString(char *v)
import numpy as np
cimport numpy as cnp
from numpy cimport (
float64_t,
int64_t,
ndarray,
uint8_t,
uint64_t,
)
cnp.import_array()
from pandas._libs cimport util
from pandas._libs.util cimport (
INT64_MAX,
INT64_MIN,
UINT64_MAX,
)
import pandas._libs.lib as lib
from pandas._libs.khash cimport (
kh_destroy_float64,
kh_destroy_str,
kh_destroy_str_starts,
kh_destroy_strbox,
kh_exist_str,
kh_float64_t,
kh_get_float64,
kh_get_str,
kh_get_str_starts_item,
kh_get_strbox,
kh_init_float64,
kh_init_str,
kh_init_str_starts,
kh_init_strbox,
kh_put_float64,
kh_put_str,
kh_put_str_starts_item,
kh_put_strbox,
kh_resize_float64,
kh_resize_str_starts,
kh_str_starts_t,
kh_str_t,
kh_strbox_t,
khiter_t,
)
from pandas.errors import (
EmptyDataError,
ParserError,
ParserWarning,
)
from pandas.core.dtypes.common import (
is_bool_dtype,
is_datetime64_dtype,
is_extension_array_dtype,
is_float_dtype,
is_integer_dtype,
is_object_dtype,
)
from pandas.core.dtypes.dtypes import CategoricalDtype
from pandas.core.dtypes.inference import is_dict_like
cdef:
float64_t INF = <float64_t>np.inf
float64_t NEGINF = -INF
int64_t DEFAULT_CHUNKSIZE = 256 * 1024
cdef extern from "headers/portable.h":
# I *think* this is here so that strcasecmp is defined on Windows
# so we don't get
# `parsers.obj : error LNK2001: unresolved external symbol strcasecmp`
# in Appveyor.
# In a sane world, the `from libc.string cimport` above would fail
# loudly.
pass
cdef extern from "parser/tokenizer.h":
ctypedef enum ParserState:
START_RECORD
START_FIELD
ESCAPED_CHAR
IN_FIELD
IN_QUOTED_FIELD
ESCAPE_IN_QUOTED_FIELD
QUOTE_IN_QUOTED_FIELD
EAT_CRNL
EAT_CRNL_NOP
EAT_WHITESPACE
EAT_COMMENT
EAT_LINE_COMMENT
WHITESPACE_LINE
SKIP_LINE
FINISHED
enum: ERROR_OVERFLOW
ctypedef enum BadLineHandleMethod:
ERROR,
WARN,
SKIP
ctypedef void* (*io_callback)(void *src, size_t nbytes, size_t *bytes_read,
int *status, const char *encoding_errors)
ctypedef int (*io_cleanup)(void *src)
ctypedef struct parser_t:
void *source
io_callback cb_io
io_cleanup cb_cleanup
int64_t chunksize # Number of bytes to prepare for each chunk
char *data # pointer to data to be processed
int64_t datalen # amount of data available
int64_t datapos
# where to write out tokenized data
char *stream
uint64_t stream_len
uint64_t stream_cap
# Store words in (potentially ragged) matrix for now, hmm
char **words
int64_t *word_starts # where we are in the stream
uint64_t words_len
uint64_t words_cap
uint64_t max_words_cap # maximum word cap encountered
char *pword_start # pointer to stream start of current field
int64_t word_start # position start of current field
int64_t *line_start # position in words for start of line
int64_t *line_fields # Number of fields in each line
uint64_t lines # Number of lines observed
uint64_t file_lines # Number of lines observed (with bad/skipped)
uint64_t lines_cap # Vector capacity
# Tokenizing stuff
ParserState state
int doublequote # is " represented by ""? */
char delimiter # field separator */
int delim_whitespace # consume tabs / spaces instead
char quotechar # quote character */
char escapechar # escape character */
char lineterminator
int skipinitialspace # ignore spaces following delimiter? */
int quoting # style of quoting to write */
char commentchar
int allow_embedded_newline
int usecols
Py_ssize_t expected_fields
BadLineHandleMethod on_bad_lines
# floating point options
char decimal
char sci
# thousands separator (comma, period)
char thousands
int header # Boolean: 1: has header, 0: no header
int64_t header_start # header row start
uint64_t header_end # header row end
void *skipset
PyObject *skipfunc
int64_t skip_first_N_rows
int64_t skipfooter
# pick one, depending on whether the converter requires GIL
float64_t (*double_converter)(const char *, char **,
char, char, char,
int, int *, int *) nogil
# error handling
char *warn_msg
char *error_msg
int64_t skip_empty_lines
ctypedef struct coliter_t:
char **words
int64_t *line_start
int64_t col
ctypedef struct uint_state:
int seen_sint
int seen_uint
int seen_null
void uint_state_init(uint_state *self)
int uint64_conflict(uint_state *self)
void coliter_setup(coliter_t *it, parser_t *parser,
int64_t i, int64_t start) nogil
void COLITER_NEXT(coliter_t, const char *) nogil
parser_t* parser_new()
int parser_init(parser_t *self) nogil
void parser_free(parser_t *self) nogil
void parser_del(parser_t *self) nogil
int parser_add_skiprow(parser_t *self, int64_t row)
int parser_set_skipfirstnrows(parser_t *self, int64_t nrows)
void parser_set_default_options(parser_t *self)
int parser_consume_rows(parser_t *self, size_t nrows)
int parser_trim_buffers(parser_t *self)
int tokenize_all_rows(parser_t *self, const char *encoding_errors) nogil
int tokenize_nrows(parser_t *self, size_t nrows, const char *encoding_errors) nogil
int64_t str_to_int64(char *p_item, int64_t int_min,
int64_t int_max, int *error, char tsep) nogil
uint64_t str_to_uint64(uint_state *state, char *p_item, int64_t int_max,
uint64_t uint_max, int *error, char tsep) nogil
float64_t xstrtod(const char *p, char **q, char decimal,
char sci, char tsep, int skip_trailing,
int *error, int *maybe_int) nogil
float64_t precise_xstrtod(const char *p, char **q, char decimal,
char sci, char tsep, int skip_trailing,
int *error, int *maybe_int) nogil
float64_t round_trip(const char *p, char **q, char decimal,
char sci, char tsep, int skip_trailing,
int *error, int *maybe_int) nogil
int to_boolean(const char *item, uint8_t *val) nogil
cdef extern from "parser/io.h":
void *new_rd_source(object obj) except NULL
int del_rd_source(void *src)
void* buffer_rd_bytes(void *source, size_t nbytes,
size_t *bytes_read, int *status, const char *encoding_errors)
cdef class TextReader:
"""
# source: StringIO or file object
..versionchange:: 1.2.0
removed 'compression', 'memory_map', and 'encoding' argument.
These arguments are outsourced to CParserWrapper.
'source' has to be a file handle.
"""
cdef:
parser_t *parser
object na_fvalues
object true_values, false_values
object handle
object orig_header
bint na_filter, keep_default_na, verbose, has_usecols, has_mi_columns
bint mangle_dupe_cols, allow_leading_cols
uint64_t parser_start # this is modified after __init__
list clocks
const char *encoding_errors
kh_str_starts_t *false_set
kh_str_starts_t *true_set
int64_t buffer_lines, skipfooter
list dtype_cast_order # list[np.dtype]
list names # can be None
set noconvert # set[int]
cdef public:
int64_t leading_cols, table_width
object delimiter # bytes or str
object converters
object na_values
list header # list[list[non-negative integers]]
object index_col
object skiprows
object dtype
object usecols
set unnamed_cols # set[str]
def __cinit__(self, source,
delimiter=b',', # bytes | str
header=0,
int64_t header_start=0,
uint64_t header_end=0,
index_col=None,
names=None,
tokenize_chunksize=DEFAULT_CHUNKSIZE,
bint delim_whitespace=False,
converters=None,
bint skipinitialspace=False,
escapechar=None, # bytes | str
bint doublequote=True,
quotechar=b'"',
quoting=0, # int
lineterminator=None, # bytes | str
comment=None,
decimal=b'.', # bytes | str
thousands=None, # bytes | str
dtype=None,
usecols=None,
on_bad_lines=ERROR,
bint na_filter=True,
na_values=None,
na_fvalues=None,
bint keep_default_na=True,
true_values=None,
false_values=None,
bint allow_leading_cols=True,
skiprows=None,
skipfooter=0, # int64_t
bint verbose=False,
bint mangle_dupe_cols=True,
float_precision=None,
bint skip_blank_lines=True,
encoding_errors=b"strict"):
# set encoding for native Python and C library
if isinstance(encoding_errors, str):
encoding_errors = encoding_errors.encode("utf-8")
elif encoding_errors is None:
encoding_errors = b"strict"
Py_INCREF(encoding_errors)
self.encoding_errors = PyBytes_AsString(encoding_errors)
self.parser = parser_new()
self.parser.chunksize = tokenize_chunksize
self.mangle_dupe_cols = mangle_dupe_cols
# For timekeeping
self.clocks = []
self.parser.usecols = (usecols is not None)
self._setup_parser_source(source)
parser_set_default_options(self.parser)
parser_init(self.parser)
if delim_whitespace:
self.parser.delim_whitespace = delim_whitespace
else:
if len(delimiter) > 1:
raise ValueError('only length-1 separators excluded right now')
self.parser.delimiter = <char>ord(delimiter)
# ----------------------------------------
# parser options
self.parser.doublequote = doublequote
self.parser.skipinitialspace = skipinitialspace
self.parser.skip_empty_lines = skip_blank_lines
if lineterminator is not None:
if len(lineterminator) != 1:
raise ValueError('Only length-1 line terminators supported')
self.parser.lineterminator = <char>ord(lineterminator)
if len(decimal) != 1:
raise ValueError('Only length-1 decimal markers supported')
self.parser.decimal = <char>ord(decimal)
if thousands is not None:
if len(thousands) != 1:
raise ValueError('Only length-1 thousands markers supported')
self.parser.thousands = <char>ord(thousands)
if escapechar is not None:
if len(escapechar) != 1:
raise ValueError('Only length-1 escapes supported')
self.parser.escapechar = <char>ord(escapechar)
self._set_quoting(quotechar, quoting)
dtype_order = ['int64', 'float64', 'bool', 'object']
if quoting == QUOTE_NONNUMERIC:
# consistent with csv module semantics, cast all to float
dtype_order = dtype_order[1:]
self.dtype_cast_order = [np.dtype(x) for x in dtype_order]
if comment is not None:
if len(comment) > 1:
raise ValueError('Only length-1 comment characters supported')
self.parser.commentchar = <char>ord(comment)
self.parser.on_bad_lines = on_bad_lines
self.skiprows = skiprows
if skiprows is not None:
self._make_skiprow_set()
self.skipfooter = skipfooter
# suboptimal
if usecols is not None:
self.has_usecols = 1
# GH-20558, validate usecols at higher level and only pass clean
# usecols into TextReader.
self.usecols = usecols
# TODO: XXX?
if skipfooter > 0:
self.parser.on_bad_lines = SKIP
self.delimiter = delimiter
self.na_values = na_values
if na_fvalues is None:
na_fvalues = set()
self.na_fvalues = na_fvalues
self.true_values = _maybe_encode(true_values) + _true_values
self.false_values = _maybe_encode(false_values) + _false_values
self.true_set = kset_from_list(self.true_values)
self.false_set = kset_from_list(self.false_values)
self.keep_default_na = keep_default_na
self.converters = converters
self.na_filter = na_filter
self.verbose = verbose
if float_precision == "round_trip":
# see gh-15140
self.parser.double_converter = round_trip
elif float_precision == "legacy":
self.parser.double_converter = xstrtod
elif float_precision == "high" or float_precision is None:
self.parser.double_converter = precise_xstrtod
else:
raise ValueError(f'Unrecognized float_precision option: '
f'{float_precision}')
# Caller is responsible for ensuring we have one of
# - None
# - DtypeObj
# - dict[Any, DtypeObj]
self.dtype = dtype
# XXX
self.noconvert = set()
self.index_col = index_col
# ----------------------------------------
# header stuff
self.allow_leading_cols = allow_leading_cols
self.leading_cols = 0 # updated in _get_header
# TODO: no header vs. header is not the first row
self.has_mi_columns = 0
self.orig_header = header
if header is None:
# sentinel value
self.parser.header_start = -1
self.parser.header_end = -1
self.parser.header = -1
self.parser_start = 0
prelim_header = []
else:
if isinstance(header, list):
if len(header) > 1:
# need to artificially skip the final line
# which is still a header line
header = list(header)
header.append(header[-1] + 1)
self.parser.header_end = header[-1]
self.has_mi_columns = 1
else:
self.parser.header_end = header[0]
self.parser_start = header[-1] + 1
self.parser.header_start = header[0]
self.parser.header = header[0]
prelim_header = header
else:
self.parser.header_start = header
self.parser.header_end = header
self.parser_start = header + 1
self.parser.header = header
prelim_header = [header]
self.names = names
header, table_width, unnamed_cols = self._get_header(prelim_header)
# header, table_width, and unnamed_cols are set here, never changed
self.header = header
self.table_width = table_width
self.unnamed_cols = unnamed_cols
if not self.table_width:
raise EmptyDataError("No columns to parse from file")
# Compute buffer_lines as function of table width.
heuristic = 2**20 // self.table_width
self.buffer_lines = 1
while self.buffer_lines * 2 < heuristic:
self.buffer_lines *= 2
def __init__(self, *args, **kwargs):
pass
def __dealloc__(self):
_close(self)
parser_del(self.parser)
def close(self):
_close(self)
def _set_quoting(self, quote_char: str | bytes | None, quoting: int):
if not isinstance(quoting, int):
raise TypeError('"quoting" must be an integer')
if not QUOTE_MINIMAL <= quoting <= QUOTE_NONE:
raise TypeError('bad "quoting" value')
if not isinstance(quote_char, (str, bytes)) and quote_char is not None:
dtype = type(quote_char).__name__
raise TypeError(f'"quotechar" must be string, not {dtype}')
if quote_char is None or quote_char == '':
if quoting != QUOTE_NONE:
raise TypeError("quotechar must be set if quoting enabled")
self.parser.quoting = quoting
self.parser.quotechar = -1
elif len(quote_char) > 1: # 0-len case handled earlier
raise TypeError('"quotechar" must be a 1-character string')
else:
self.parser.quoting = quoting
self.parser.quotechar = <char>ord(quote_char)
cdef _make_skiprow_set(self):
if util.is_integer_object(self.skiprows):
parser_set_skipfirstnrows(self.parser, self.skiprows)
elif not callable(self.skiprows):
for i in self.skiprows:
parser_add_skiprow(self.parser, i)
else:
self.parser.skipfunc = <PyObject *>self.skiprows
cdef _setup_parser_source(self, source):
cdef:
void *ptr
ptr = new_rd_source(source)
self.parser.source = ptr
self.parser.cb_io = &buffer_rd_bytes
self.parser.cb_cleanup = &del_rd_source
cdef _get_header(self, list prelim_header):
# header is now a list of lists, so field_count should use header[0]
#
# modifies:
# self.parser attributes
# self.parser_start
# self.leading_cols
cdef:
Py_ssize_t i, start, field_count, passed_count, unnamed_count, level
char *word
str name, old_name
uint64_t hr, data_line = 0
list header = []
set unnamed_cols = set()
if self.parser.header_start >= 0:
# Header is in the file
for level, hr in enumerate(prelim_header):
this_header = []
if self.parser.lines < hr + 1:
self._tokenize_rows(hr + 2)
if self.parser.lines == 0:
field_count = 0
start = self.parser.line_start[0]
# e.g., if header=3 and file only has 2 lines
elif (self.parser.lines < hr + 1
and not isinstance(self.orig_header, list)) or (
self.parser.lines < hr):
msg = self.orig_header
if isinstance(msg, list):
joined = ','.join(str(m) for m in msg)
msg = f"[{joined}], len of {len(msg)},"
raise ParserError(
f'Passed header={msg} but only '
f'{self.parser.lines} lines in file')
else:
field_count = self.parser.line_fields[hr]
start = self.parser.line_start[hr]
unnamed_count = 0
unnamed_col_indices = []
for i in range(field_count):
word = self.parser.words[start + i]
name = PyUnicode_DecodeUTF8(word, strlen(word),
self.encoding_errors)
if name == '':
if self.has_mi_columns:
name = f'Unnamed: {i}_level_{level}'
else:
name = f'Unnamed: {i}'
unnamed_count += 1
unnamed_col_indices.append(i)
this_header.append(name)
if not self.has_mi_columns and self.mangle_dupe_cols:
# Ensure that regular columns are used before unnamed ones
# to keep given names and mangle unnamed columns
col_loop_order = [i for i in range(len(this_header))
if i not in unnamed_col_indices
] + unnamed_col_indices
counts = {}
for i in col_loop_order:
col = this_header[i]
old_col = col
cur_count = counts.get(col, 0)
if cur_count > 0:
while cur_count > 0:
counts[old_col] = cur_count + 1
col = f'{old_col}.{cur_count}'
if col in this_header:
cur_count += 1
else:
cur_count = counts.get(col, 0)
if (
self.dtype is not None
and is_dict_like(self.dtype)
and self.dtype.get(old_col) is not None
and self.dtype.get(col) is None
):
self.dtype.update({col: self.dtype.get(old_col)})
this_header[i] = col
counts[col] = cur_count + 1
if self.has_mi_columns:
# If we have grabbed an extra line, but it's not in our
# format, save in the buffer, and create an blank extra
# line for the rest of the parsing code.
if hr == prelim_header[-1]:
lc = len(this_header)
ic = (len(self.index_col) if self.index_col
is not None else 0)
# if wrong number of blanks or no index, not our format
if (lc != unnamed_count and lc - ic > unnamed_count) or ic == 0:
hr -= 1
self.parser_start -= 1
this_header = [None] * lc
data_line = hr + 1
header.append(this_header)
unnamed_cols.update({this_header[i] for i in unnamed_col_indices})
if self.names is not None:
header = [self.names]
elif self.names is not None:
# Names passed
if self.parser.lines < 1:
self._tokenize_rows(1)
header = [self.names]
if self.parser.lines < 1:
field_count = len(header[0])
else:
field_count = self.parser.line_fields[data_line]
# Enforce this unless usecols
if not self.has_usecols:
self.parser.expected_fields = max(field_count, len(self.names))
else:
# No header passed nor to be found in the file
if self.parser.lines < 1:
self._tokenize_rows(1)
return None, self.parser.line_fields[0], unnamed_cols
# Corner case, not enough lines in the file
if self.parser.lines < data_line + 1:
field_count = len(header[0])
else: # not self.has_usecols:
field_count = self.parser.line_fields[data_line]
# #2981
if self.names is not None:
field_count = max(field_count, len(self.names))
passed_count = len(header[0])
if (self.has_usecols and self.allow_leading_cols and
not callable(self.usecols)):
nuse = len(self.usecols)
if nuse == passed_count:
self.leading_cols = 0
elif self.names is None and nuse < passed_count:
self.leading_cols = field_count - passed_count
elif passed_count != field_count:
raise ValueError('Number of passed names did not match number of '
'header fields in the file')
# oh boy, #2442, #2981
elif self.allow_leading_cols and passed_count < field_count:
self.leading_cols = field_count - passed_count
return header, field_count, unnamed_cols
def read(self, rows: int | None = None) -> dict[int, "ArrayLike"]:
"""
rows=None --> read all rows
"""
# Don't care about memory usage
columns = self._read_rows(rows, 1)
return columns
def read_low_memory(self, rows: int | None)-> list[dict[int, "ArrayLike"]]:
"""
rows=None --> read all rows
"""
# Conserve intermediate space
# Caller is responsible for concatenating chunks,
# see c_parser_wrapper._concatenate_chunks
cdef:
size_t rows_read = 0
list chunks = []
if rows is None:
while True:
try:
chunk = self._read_rows(self.buffer_lines, 0)
if len(chunk) == 0:
break
except StopIteration:
break
else:
chunks.append(chunk)
else:
while rows_read < rows:
try:
crows = min(self.buffer_lines, rows - rows_read)
chunk = self._read_rows(crows, 0)
if len(chunk) == 0:
break
rows_read += len(list(chunk.values())[0])
except StopIteration:
break
else:
chunks.append(chunk)
parser_trim_buffers(self.parser)
if len(chunks) == 0:
raise StopIteration
return chunks
cdef _tokenize_rows(self, size_t nrows):
cdef:
int status
with nogil:
status = tokenize_nrows(self.parser, nrows, self.encoding_errors)
if self.parser.warn_msg != NULL:
print(self.parser.warn_msg, file=sys.stderr)
free(self.parser.warn_msg)
self.parser.warn_msg = NULL
if status < 0:
raise_parser_error('Error tokenizing data', self.parser)
# -> dict[int, "ArrayLike"]
cdef _read_rows(self, rows, bint trim):
cdef:
int64_t buffered_lines
int64_t irows
self._start_clock()
if rows is not None:
irows = rows
buffered_lines = self.parser.lines - self.parser_start
if buffered_lines < irows:
self._tokenize_rows(irows - buffered_lines)
if self.skipfooter > 0:
raise ValueError('skipfooter can only be used to read '
'the whole file')
else:
with nogil:
status = tokenize_all_rows(self.parser, self.encoding_errors)
if self.parser.warn_msg != NULL:
print(self.parser.warn_msg, file=sys.stderr)
free(self.parser.warn_msg)
self.parser.warn_msg = NULL
if status < 0:
raise_parser_error('Error tokenizing data', self.parser)
if self.parser_start >= self.parser.lines:
raise StopIteration
self._end_clock('Tokenization')
self._start_clock()
columns = self._convert_column_data(rows)
self._end_clock('Type conversion')
self._start_clock()
if len(columns) > 0:
rows_read = len(list(columns.values())[0])
# trim
parser_consume_rows(self.parser, rows_read)
if trim:
parser_trim_buffers(self.parser)
self.parser_start -= rows_read
self._end_clock('Parser memory cleanup')
return columns
cdef _start_clock(self):
self.clocks.append(time.time())
cdef _end_clock(self, str what):
if self.verbose:
elapsed = time.time() - self.clocks.pop(-1)
print(f'{what} took: {elapsed * 1000:.2f} ms')
def set_noconvert(self, i: int) -> None:
self.noconvert.add(i)
def remove_noconvert(self, i: int) -> None:
self.noconvert.remove(i)
def _convert_column_data(self, rows: int | None) -> dict[int, "ArrayLike"]:
cdef:
int64_t i
int nused
kh_str_starts_t *na_hashset = NULL
int64_t start, end
object name, na_flist, col_dtype = None
bint na_filter = 0
int64_t num_cols
dict result
start = self.parser_start
if rows is None:
end = self.parser.lines
else:
end = min(start + rows, self.parser.lines)
num_cols = -1
# Py_ssize_t cast prevents build warning
for i in range(<Py_ssize_t>self.parser.lines):
num_cols = (num_cols < self.parser.line_fields[i]) * \
self.parser.line_fields[i] + \
(num_cols >= self.parser.line_fields[i]) * num_cols
usecols_not_callable_and_exists = not callable(self.usecols) and self.usecols
names_larger_num_cols = (self.names and
len(self.names) - self.leading_cols > num_cols)
if self.table_width - self.leading_cols > num_cols:
if (usecols_not_callable_and_exists
and self.table_width - self.leading_cols < len(self.usecols)
or names_larger_num_cols):
raise ParserError(f"Too many columns specified: expected "
f"{self.table_width - self.leading_cols} "
f"and found {num_cols}")
if (usecols_not_callable_and_exists and
all(isinstance(u, int) for u in self.usecols)):
missing_usecols = [col for col in self.usecols if col >= num_cols]
if missing_usecols:
warnings.warn(
"Defining usecols with out of bounds indices is deprecated "
"and will raise a ParserError in a future version.",
FutureWarning,
stacklevel=6,
)
results = {}
nused = 0
for i in range(self.table_width):
if i < self.leading_cols:
# Pass through leading columns always
name = i
elif (self.usecols and not callable(self.usecols) and
nused == len(self.usecols)):
# Once we've gathered all requested columns, stop. GH5766
break
else:
name = self._get_column_name(i, nused)
usecols = set()
if callable(self.usecols):
if self.usecols(name):
usecols = {i}
else:
usecols = self.usecols
if self.has_usecols and not (i in usecols or
name in usecols):
continue
nused += 1
conv = self._get_converter(i, name)
col_dtype = None
if self.dtype is not None:
if isinstance(self.dtype, dict):
if name in self.dtype:
col_dtype = self.dtype[name]
elif i in self.dtype:
col_dtype = self.dtype[i]
else:
if self.dtype.names:
# structured array
col_dtype = np.dtype(self.dtype.descr[i][1])
else:
col_dtype = self.dtype
if conv:
if col_dtype is not None:
warnings.warn((f"Both a converter and dtype were specified "
f"for column {name} - only the converter will "
f"be used."), ParserWarning,
stacklevel=5)
results[i] = _apply_converter(conv, self.parser, i, start, end)
continue
# Collect the list of NaN values associated with the column.
# If we aren't supposed to do that, or none are collected,
# we set `na_filter` to `0` (`1` otherwise).
na_flist = set()
if self.na_filter:
na_list, na_flist = self._get_na_list(i, name)
if na_list is None:
na_filter = 0
else:
na_filter = 1
na_hashset = kset_from_list(na_list)
else:
na_filter = 0
# Attempt to parse tokens and infer dtype of the column.
# Should return as the desired dtype (inferred or specified).
try:
col_res, na_count = self._convert_tokens(
i, start, end, name, na_filter, na_hashset,
na_flist, col_dtype)
finally:
# gh-21353
#
# Cleanup the NaN hash that we generated
# to avoid memory leaks.
if na_filter:
self._free_na_set(na_hashset)
# don't try to upcast EAs
if na_count > 0 and not is_extension_array_dtype(col_dtype):
col_res = _maybe_upcast(col_res)
if col_res is None:
raise ParserError(f'Unable to parse column {i}')
results[i] = col_res
self.parser_start += end - start
return results
# -> tuple["ArrayLike", int]:
cdef inline _convert_tokens(self, Py_ssize_t i, int64_t start,
int64_t end, object name, bint na_filter,
kh_str_starts_t *na_hashset,
object na_flist, object col_dtype):
if col_dtype is not None:
col_res, na_count = self._convert_with_dtype(
col_dtype, i, start, end, na_filter,
1, na_hashset, na_flist)
# Fallback on the parse (e.g. we requested int dtype,
# but its actually a float).
if col_res is not None:
return col_res, na_count
if i in self.noconvert:
return self._string_convert(i, start, end, na_filter, na_hashset)
else:
col_res = None
for dt in self.dtype_cast_order:
try:
col_res, na_count = self._convert_with_dtype(
dt, i, start, end, na_filter, 0, na_hashset, na_flist)
except ValueError:
# This error is raised from trying to convert to uint64,
# and we discover that we cannot convert to any numerical
# dtype successfully. As a result, we leave the data
# column AS IS with object dtype.
col_res, na_count = self._convert_with_dtype(
np.dtype('object'), i, start, end, 0,
0, na_hashset, na_flist)
except OverflowError:
col_res, na_count = self._convert_with_dtype(
np.dtype('object'), i, start, end, na_filter,
0, na_hashset, na_flist)
if col_res is not None:
break
# we had a fallback parse on the dtype, so now try to cast
if col_res is not None and col_dtype is not None:
# If col_res is bool, it might actually be a bool array mixed with NaNs
# (see _try_bool_flex()). Usually this would be taken care of using
# _maybe_upcast(), but if col_dtype is a floating type we should just
# take care of that cast here.
if col_res.dtype == np.bool_ and is_float_dtype(col_dtype):
mask = col_res.view(np.uint8) == na_values[np.uint8]
col_res = col_res.astype(col_dtype)
np.putmask(col_res, mask, np.nan)
return col_res, na_count
# NaNs are already cast to True here, so can not use astype
if col_res.dtype == np.bool_ and is_integer_dtype(col_dtype):
if na_count > 0:
raise ValueError(
f"cannot safely convert passed user dtype of "
f"{col_dtype} for {np.bool_} dtyped data in "
f"column {i} due to NA values"
)
# only allow safe casts, eg. with a nan you cannot safely cast to int
try:
col_res = col_res.astype(col_dtype, casting='safe')
except TypeError:
# float -> int conversions can fail the above
# even with no nans
col_res_orig = col_res
col_res = col_res.astype(col_dtype)
if (col_res != col_res_orig).any():
raise ValueError(
f"cannot safely convert passed user dtype of "
f"{col_dtype} for {col_res_orig.dtype.name} dtyped data in "
f"column {i}")
return col_res, na_count
cdef _convert_with_dtype(self, object dtype, Py_ssize_t i,
int64_t start, int64_t end,
bint na_filter,
bint user_dtype,
kh_str_starts_t *na_hashset,
object na_flist):
if isinstance(dtype, CategoricalDtype):
# TODO: I suspect that _categorical_convert could be
# optimized when dtype is an instance of CategoricalDtype
codes, cats, na_count = _categorical_convert(
self.parser, i, start, end, na_filter, na_hashset)
# Method accepts list of strings, not encoded ones.
true_values = [x.decode() for x in self.true_values]
array_type = dtype.construct_array_type()
cat = array_type._from_inferred_categories(
cats, codes, dtype, true_values=true_values)
return cat, na_count
elif is_extension_array_dtype(dtype):
result, na_count = self._string_convert(i, start, end, na_filter,
na_hashset)
array_type = dtype.construct_array_type()
try:
# use _from_sequence_of_strings if the class defines it
if is_bool_dtype(dtype):
true_values = [x.decode() for x in self.true_values]
false_values = [x.decode() for x in self.false_values]
result = array_type._from_sequence_of_strings(
result, dtype=dtype, true_values=true_values,
false_values=false_values)
else:
result = array_type._from_sequence_of_strings(result, dtype=dtype)
except NotImplementedError:
raise NotImplementedError(
f"Extension Array: {array_type} must implement "
f"_from_sequence_of_strings in order "
f"to be used in parser methods")
return result, na_count
elif is_integer_dtype(dtype):
try:
result, na_count = _try_int64(self.parser, i, start,
end, na_filter, na_hashset)
if user_dtype and na_count is not None:
if na_count > 0:
raise ValueError(f"Integer column has NA values in column {i}")
except OverflowError:
result = _try_uint64(self.parser, i, start, end,
na_filter, na_hashset)
na_count = 0
if result is not None and dtype != 'int64':
result = result.astype(dtype)
return result, na_count
elif is_float_dtype(dtype):
result, na_count = _try_double(self.parser, i, start, end,
na_filter, na_hashset, na_flist)
if result is not None and dtype != 'float64':
result = result.astype(dtype)
return result, na_count
elif is_bool_dtype(dtype):
result, na_count = _try_bool_flex(self.parser, i, start, end,
na_filter, na_hashset,
self.true_set, self.false_set)
if user_dtype and na_count is not None:
if na_count > 0:
raise ValueError(f"Bool column has NA values in column {i}")
return result, na_count
elif dtype.kind == 'S':
# TODO: na handling
width = dtype.itemsize
if width > 0:
result = _to_fw_string(self.parser, i, start, end, width)
return result, 0
# treat as a regular string parsing
return self._string_convert(i, start, end, na_filter,
na_hashset)
elif dtype.kind == 'U':
width = dtype.itemsize
if width > 0:
raise TypeError(f"the dtype {dtype} is not supported for parsing")
# unicode variable width
return self._string_convert(i, start, end, na_filter,
na_hashset)
elif is_object_dtype(dtype):
return self._string_convert(i, start, end, na_filter,
na_hashset)
elif is_datetime64_dtype(dtype):
raise TypeError(f"the dtype {dtype} is not supported "
f"for parsing, pass this column "
f"using parse_dates instead")
else:
raise TypeError(f"the dtype {dtype} is not supported for parsing")
# -> tuple[ndarray[object], int]
cdef _string_convert(self, Py_ssize_t i, int64_t start, int64_t end,
bint na_filter, kh_str_starts_t *na_hashset):
return _string_box_utf8(self.parser, i, start, end, na_filter,
na_hashset, self.encoding_errors)
def _get_converter(self, i: int, name):
if self.converters is None:
return None
if name is not None and name in self.converters:
return self.converters[name]
# Converter for position, if any
return self.converters.get(i)
cdef _get_na_list(self, Py_ssize_t i, name):
# Note: updates self.na_values, self.na_fvalues
if self.na_values is None:
return None, set()
if isinstance(self.na_values, dict):
key = None
values = None
if name is not None and name in self.na_values:
key = name
elif i in self.na_values:
key = i
else: # No na_values provided for this column.
if self.keep_default_na:
return _NA_VALUES, set()
return list(), set()
values = self.na_values[key]
if values is not None and not isinstance(values, list):
values = list(values)
fvalues = self.na_fvalues[key]
if fvalues is not None and not isinstance(fvalues, set):
fvalues = set(fvalues)
return _ensure_encoded(values), fvalues
else:
if not isinstance(self.na_values, list):
self.na_values = list(self.na_values)
if not isinstance(self.na_fvalues, set):
self.na_fvalues = set(self.na_fvalues)
return _ensure_encoded(self.na_values), self.na_fvalues
cdef _free_na_set(self, kh_str_starts_t *table):
kh_destroy_str_starts(table)
cdef _get_column_name(self, Py_ssize_t i, Py_ssize_t nused):
cdef int64_t j
if self.has_usecols and self.names is not None:
if (not callable(self.usecols) and
len(self.names) == len(self.usecols)):
return self.names[nused]
else:
return self.names[i - self.leading_cols]
else:
if self.header is not None:
j = i - self.leading_cols
# generate extra (bogus) headers if there are more columns than headers
if j >= len(self.header[0]):
return j
elif self.has_mi_columns:
return tuple(header_row[j] for header_row in self.header)
else:
return self.header[0][j]
else:
return None
# Factor out code common to TextReader.__dealloc__ and TextReader.close
# It cannot be a class method, since calling self.close() in __dealloc__
# which causes a class attribute lookup and violates best parctices
# https://cython.readthedocs.io/en/latest/src/userguide/special_methods.html#finalization-method-dealloc
cdef _close(TextReader reader):
# also preemptively free all allocated memory
parser_free(reader.parser)
if reader.true_set:
kh_destroy_str_starts(reader.true_set)
reader.true_set = NULL
if reader.false_set:
kh_destroy_str_starts(reader.false_set)
reader.false_set = NULL
cdef:
object _true_values = [b'True', b'TRUE', b'true']
object _false_values = [b'False', b'FALSE', b'false']
def _ensure_encoded(list lst):
cdef:
list result = []
for x in lst:
if isinstance(x, str):
x = PyUnicode_AsUTF8String(x)
elif not isinstance(x, bytes):
x = str(x).encode('utf-8')
result.append(x)
return result
# common NA values
# no longer excluding inf representations
# '1.#INF','-1.#INF', '1.#INF000000',
STR_NA_VALUES = {
"-1.#IND",
"1.#QNAN",
"1.#IND",
"-1.#QNAN",
"#N/A N/A",
"#N/A",
"N/A",
"n/a",
"NA",
"<NA>",
"#NA",
"NULL",
"null",
"NaN",
"-NaN",
"nan",
"-nan",
"",
}
_NA_VALUES = _ensure_encoded(list(STR_NA_VALUES))
def _maybe_upcast(arr):
"""
"""
if issubclass(arr.dtype.type, np.integer):
na_value = na_values[arr.dtype]
arr = arr.astype(float)
np.putmask(arr, arr == na_value, np.nan)
elif arr.dtype == np.bool_:
mask = arr.view(np.uint8) == na_values[np.uint8]
arr = arr.astype(object)
np.putmask(arr, mask, np.nan)
return arr
# ----------------------------------------------------------------------
# Type conversions / inference support code
# -> tuple[ndarray[object], int]
cdef _string_box_utf8(parser_t *parser, int64_t col,
int64_t line_start, int64_t line_end,
bint na_filter, kh_str_starts_t *na_hashset,
const char *encoding_errors):
cdef:
int error, na_count = 0
Py_ssize_t i, lines
coliter_t it
const char *word = NULL
ndarray[object] result
int ret = 0
kh_strbox_t *table
object pyval
object NA = na_values[np.object_]
khiter_t k
table = kh_init_strbox()
lines = line_end - line_start
result = np.empty(lines, dtype=np.object_)
coliter_setup(&it, parser, col, line_start)
for i in range(lines):
COLITER_NEXT(it, word)
if na_filter:
if kh_get_str_starts_item(na_hashset, word):
# in the hash table
na_count += 1
result[i] = NA
continue
k = kh_get_strbox(table, word)
# in the hash table
if k != table.n_buckets:
# this increments the refcount, but need to test
pyval = <object>table.vals[k]
else:
# box it. new ref?
pyval = PyUnicode_Decode(word, strlen(word), "utf-8", encoding_errors)
k = kh_put_strbox(table, word, &ret)
table.vals[k] = <PyObject *>pyval
result[i] = pyval
kh_destroy_strbox(table)
return result, na_count
@cython.boundscheck(False)
cdef _categorical_convert(parser_t *parser, int64_t col,
int64_t line_start, int64_t line_end,
bint na_filter, kh_str_starts_t *na_hashset):
"Convert column data into codes, categories"
cdef:
int na_count = 0
Py_ssize_t i, size, lines
coliter_t it
const char *word = NULL
int64_t NA = -1
int64_t[:] codes
int64_t current_category = 0
char *errors = "strict"
int ret = 0
kh_str_t *table
khiter_t k
lines = line_end - line_start
codes = np.empty(lines, dtype=np.int64)
# factorize parsed values, creating a hash table
# bytes -> category code
with nogil:
table = kh_init_str()
coliter_setup(&it, parser, col, line_start)
for i in range(lines):
COLITER_NEXT(it, word)
if na_filter:
if kh_get_str_starts_item(na_hashset, word):
# is in NA values
na_count += 1
codes[i] = NA
continue
k = kh_get_str(table, word)
# not in the hash table
if k == table.n_buckets:
k = kh_put_str(table, word, &ret)
table.vals[k] = current_category
current_category += 1
codes[i] = table.vals[k]
# parse and box categories to python strings
result = np.empty(table.n_occupied, dtype=np.object_)
for k in range(table.n_buckets):
if kh_exist_str(table, k):
result[table.vals[k]] = PyUnicode_FromString(table.keys[k])
kh_destroy_str(table)
return np.asarray(codes), result, na_count
# -> ndarray[f'|S{width}']
cdef _to_fw_string(parser_t *parser, int64_t col, int64_t line_start,
int64_t line_end, int64_t width):
cdef:
char *data
ndarray result
result = np.empty(line_end - line_start, dtype=f'|S{width}')
data = <char*>result.data
with nogil:
_to_fw_string_nogil(parser, col, line_start, line_end, width, data)
return result
cdef inline void _to_fw_string_nogil(parser_t *parser, int64_t col,
int64_t line_start, int64_t line_end,
size_t width, char *data) nogil:
cdef:
int64_t i
coliter_t it
const char *word = NULL
coliter_setup(&it, parser, col, line_start)
for i in range(line_end - line_start):
COLITER_NEXT(it, word)
strncpy(data, word, width)
data += width
cdef:
char* cinf = b'inf'
char* cposinf = b'+inf'
char* cneginf = b'-inf'
char* cinfty = b'Infinity'
char* cposinfty = b'+Infinity'
char* cneginfty = b'-Infinity'
# -> tuple[ndarray[float64_t], int] | tuple[None, None]
cdef _try_double(parser_t *parser, int64_t col,
int64_t line_start, int64_t line_end,
bint na_filter, kh_str_starts_t *na_hashset, object na_flist):
cdef:
int error, na_count = 0
Py_ssize_t lines
float64_t *data
float64_t NA = na_values[np.float64]
kh_float64_t *na_fset
ndarray[float64_t] result
bint use_na_flist = len(na_flist) > 0
lines = line_end - line_start
result = np.empty(lines, dtype=np.float64)
data = <float64_t *>result.data
na_fset = kset_float64_from_list(na_flist)
with nogil:
error = _try_double_nogil(parser, parser.double_converter,
col, line_start, line_end,
na_filter, na_hashset, use_na_flist,
na_fset, NA, data, &na_count)
kh_destroy_float64(na_fset)
if error != 0:
return None, None
return result, na_count
cdef inline int _try_double_nogil(parser_t *parser,
float64_t (*double_converter)(
const char *, char **, char,
char, char, int, int *, int *) nogil,
int64_t col, int64_t line_start, int64_t line_end,
bint na_filter, kh_str_starts_t *na_hashset,
bint use_na_flist,
const kh_float64_t *na_flist,
float64_t NA, float64_t *data,
int *na_count) nogil:
cdef:
int error = 0,
Py_ssize_t i, lines = line_end - line_start
coliter_t it
const char *word = NULL
char *p_end
khiter_t k64
na_count[0] = 0
coliter_setup(&it, parser, col, line_start)
if na_filter:
for i in range(lines):
COLITER_NEXT(it, word)
if kh_get_str_starts_item(na_hashset, word):
# in the hash table
na_count[0] += 1
data[0] = NA
else:
data[0] = double_converter(word, &p_end, parser.decimal,
parser.sci, parser.thousands,
1, &error, NULL)
if error != 0 or p_end == word or p_end[0]:
error = 0
if (strcasecmp(word, cinf) == 0 or
strcasecmp(word, cposinf) == 0 or
strcasecmp(word, cinfty) == 0 or
strcasecmp(word, cposinfty) == 0):
data[0] = INF
elif (strcasecmp(word, cneginf) == 0 or
strcasecmp(word, cneginfty) == 0):
data[0] = NEGINF
else:
return 1
if use_na_flist:
k64 = kh_get_float64(na_flist, data[0])
if k64 != na_flist.n_buckets:
na_count[0] += 1
data[0] = NA
data += 1
else:
for i in range(lines):
COLITER_NEXT(it, word)
data[0] = double_converter(word, &p_end, parser.decimal,
parser.sci, parser.thousands,
1, &error, NULL)
if error != 0 or p_end == word or p_end[0]:
error = 0
if (strcasecmp(word, cinf) == 0 or
strcasecmp(word, cposinf) == 0 or
strcasecmp(word, cinfty) == 0 or
strcasecmp(word, cposinfty) == 0):
data[0] = INF
elif (strcasecmp(word, cneginf) == 0 or
strcasecmp(word, cneginfty) == 0):
data[0] = NEGINF
else:
return 1
data += 1
return 0
cdef _try_uint64(parser_t *parser, int64_t col,
int64_t line_start, int64_t line_end,
bint na_filter, kh_str_starts_t *na_hashset):
cdef:
int error
Py_ssize_t lines
coliter_t it
uint64_t *data
ndarray result
uint_state state
lines = line_end - line_start
result = np.empty(lines, dtype=np.uint64)
data = <uint64_t *>result.data
uint_state_init(&state)
coliter_setup(&it, parser, col, line_start)
with nogil:
error = _try_uint64_nogil(parser, col, line_start, line_end,
na_filter, na_hashset, data, &state)
if error != 0:
if error == ERROR_OVERFLOW:
# Can't get the word variable
raise OverflowError('Overflow')
return None
if uint64_conflict(&state):
raise ValueError('Cannot convert to numerical dtype')
if state.seen_sint:
raise OverflowError('Overflow')
return result
cdef inline int _try_uint64_nogil(parser_t *parser, int64_t col,
int64_t line_start,
int64_t line_end, bint na_filter,
const kh_str_starts_t *na_hashset,
uint64_t *data, uint_state *state) nogil:
cdef:
int error
Py_ssize_t i, lines = line_end - line_start
coliter_t it
const char *word = NULL
coliter_setup(&it, parser, col, line_start)
if na_filter:
for i in range(lines):
COLITER_NEXT(it, word)
if kh_get_str_starts_item(na_hashset, word):
# in the hash table
state.seen_null = 1
data[i] = 0
continue
data[i] = str_to_uint64(state, word, INT64_MAX, UINT64_MAX,
&error, parser.thousands)
if error != 0:
return error
else:
for i in range(lines):
COLITER_NEXT(it, word)
data[i] = str_to_uint64(state, word, INT64_MAX, UINT64_MAX,
&error, parser.thousands)
if error != 0:
return error
return 0
cdef _try_int64(parser_t *parser, int64_t col,
int64_t line_start, int64_t line_end,
bint na_filter, kh_str_starts_t *na_hashset):
cdef:
int error, na_count = 0
Py_ssize_t lines
coliter_t it
int64_t *data
ndarray result
int64_t NA = na_values[np.int64]
lines = line_end - line_start
result = np.empty(lines, dtype=np.int64)
data = <int64_t *>result.data
coliter_setup(&it, parser, col, line_start)
with nogil:
error = _try_int64_nogil(parser, col, line_start, line_end,
na_filter, na_hashset, NA, data, &na_count)
if error != 0:
if error == ERROR_OVERFLOW:
# Can't get the word variable
raise OverflowError('Overflow')
return None, None
return result, na_count
cdef inline int _try_int64_nogil(parser_t *parser, int64_t col,
int64_t line_start,
int64_t line_end, bint na_filter,
const kh_str_starts_t *na_hashset, int64_t NA,
int64_t *data, int *na_count) nogil:
cdef:
int error
Py_ssize_t i, lines = line_end - line_start
coliter_t it
const char *word = NULL
na_count[0] = 0
coliter_setup(&it, parser, col, line_start)
if na_filter:
for i in range(lines):
COLITER_NEXT(it, word)
if kh_get_str_starts_item(na_hashset, word):
# in the hash table
na_count[0] += 1
data[i] = NA
continue
data[i] = str_to_int64(word, INT64_MIN, INT64_MAX,
&error, parser.thousands)
if error != 0:
return error
else:
for i in range(lines):
COLITER_NEXT(it, word)
data[i] = str_to_int64(word, INT64_MIN, INT64_MAX,
&error, parser.thousands)
if error != 0:
return error
return 0
# -> tuple[ndarray[bool], int]
cdef _try_bool_flex(parser_t *parser, int64_t col,
int64_t line_start, int64_t line_end,
bint na_filter, const kh_str_starts_t *na_hashset,
const kh_str_starts_t *true_hashset,
const kh_str_starts_t *false_hashset):
cdef:
int error, na_count = 0
Py_ssize_t lines
uint8_t *data
ndarray result
uint8_t NA = na_values[np.bool_]
lines = line_end - line_start
result = np.empty(lines, dtype=np.uint8)
data = <uint8_t *>result.data
with nogil:
error = _try_bool_flex_nogil(parser, col, line_start, line_end,
na_filter, na_hashset, true_hashset,
false_hashset, NA, data, &na_count)
if error != 0:
return None, None
return result.view(np.bool_), na_count
cdef inline int _try_bool_flex_nogil(parser_t *parser, int64_t col,
int64_t line_start,
int64_t line_end, bint na_filter,
const kh_str_starts_t *na_hashset,
const kh_str_starts_t *true_hashset,
const kh_str_starts_t *false_hashset,
uint8_t NA, uint8_t *data,
int *na_count) nogil:
cdef:
int error = 0
Py_ssize_t i, lines = line_end - line_start
coliter_t it
const char *word = NULL
na_count[0] = 0
coliter_setup(&it, parser, col, line_start)
if na_filter:
for i in range(lines):
COLITER_NEXT(it, word)
if kh_get_str_starts_item(na_hashset, word):
# in the hash table
na_count[0] += 1
data[0] = NA
data += 1
continue
if kh_get_str_starts_item(true_hashset, word):
data[0] = 1
data += 1
continue
if kh_get_str_starts_item(false_hashset, word):
data[0] = 0
data += 1
continue
error = to_boolean(word, data)
if error != 0:
return error
data += 1
else:
for i in range(lines):
COLITER_NEXT(it, word)
if kh_get_str_starts_item(true_hashset, word):
data[0] = 1
data += 1
continue
if kh_get_str_starts_item(false_hashset, word):
data[0] = 0
data += 1
continue
error = to_boolean(word, data)
if error != 0:
return error
data += 1
return 0
cdef kh_str_starts_t* kset_from_list(list values) except NULL:
# caller takes responsibility for freeing the hash table
cdef:
Py_ssize_t i
kh_str_starts_t *table
int ret = 0
object val
table = kh_init_str_starts()
for i in range(len(values)):
val = values[i]
# None creeps in sometimes, which isn't possible here
if not isinstance(val, bytes):
kh_destroy_str_starts(table)
raise ValueError('Must be all encoded bytes')
kh_put_str_starts_item(table, PyBytes_AsString(val), &ret)
if table.table.n_buckets <= 128:
# Resize the hash table to make it almost empty, this
# reduces amount of hash collisions on lookup thus
# "key not in table" case is faster.
# Note that this trades table memory footprint for lookup speed.
kh_resize_str_starts(table, table.table.n_buckets * 8)
return table
cdef kh_float64_t* kset_float64_from_list(values) except NULL:
# caller takes responsibility for freeing the hash table
cdef:
khiter_t k
kh_float64_t *table
int ret = 0
float64_t val
object value
table = kh_init_float64()
for value in values:
val = float(value)
k = kh_put_float64(table, val, &ret)
if table.n_buckets <= 128:
# See reasoning in kset_from_list
kh_resize_float64(table, table.n_buckets * 8)
return table
cdef raise_parser_error(object base, parser_t *parser):
cdef:
object old_exc
object exc_type
PyObject *type
PyObject *value
PyObject *traceback
if PyErr_Occurred():
PyErr_Fetch(&type, &value, &traceback)
Py_XDECREF(traceback)
if value != NULL:
old_exc = <object>value
Py_XDECREF(value)
# PyErr_Fetch only returned the error message in *value,
# so the Exception class must be extracted from *type.
if isinstance(old_exc, str):
if type != NULL:
exc_type = <object>type
else:
exc_type = ParserError
Py_XDECREF(type)
raise exc_type(old_exc)
else:
Py_XDECREF(type)
raise old_exc
message = f'{base}. C error: '
if parser.error_msg != NULL:
message += parser.error_msg.decode('utf-8')
else:
message += 'no error message set'
raise ParserError(message)
# ----------------------------------------------------------------------
# NA values
def _compute_na_values():
int64info = np.iinfo(np.int64)
int32info = np.iinfo(np.int32)
int16info = np.iinfo(np.int16)
int8info = np.iinfo(np.int8)
uint64info = np.iinfo(np.uint64)
uint32info = np.iinfo(np.uint32)
uint16info = np.iinfo(np.uint16)
uint8info = np.iinfo(np.uint8)
na_values = {
np.float64: np.nan,
np.int64: int64info.min,
np.int32: int32info.min,
np.int16: int16info.min,
np.int8: int8info.min,
np.uint64: uint64info.max,
np.uint32: uint32info.max,
np.uint16: uint16info.max,
np.uint8: uint8info.max,
np.bool_: uint8info.max,
np.object_: np.nan # oof
}
return na_values
na_values = _compute_na_values()
for k in list(na_values):
na_values[np.dtype(k)] = na_values[k]
# -> ArrayLike
cdef _apply_converter(object f, parser_t *parser, int64_t col,
int64_t line_start, int64_t line_end):
cdef:
Py_ssize_t i, lines
coliter_t it
const char *word = NULL
ndarray[object] result
object val
lines = line_end - line_start
result = np.empty(lines, dtype=np.object_)
coliter_setup(&it, parser, col, line_start)
for i in range(lines):
COLITER_NEXT(it, word)
val = PyUnicode_FromString(word)
result[i] = f(val)
return lib.maybe_convert_objects(result)
cdef list _maybe_encode(list values):
if values is None:
return []
return [x.encode('utf-8') if isinstance(x, str) else x for x in values]
def sanitize_objects(ndarray[object] values, set na_values) -> int:
"""
Convert specified values, including the given set na_values to np.nan.
Parameters
----------
values : ndarray[object]
na_values : set
Returns
-------
na_count : int
"""
cdef:
Py_ssize_t i, n
object val, onan
Py_ssize_t na_count = 0
dict memo = {}
n = len(values)
onan = np.nan
for i in range(n):
val = values[i]
if val in na_values:
values[i] = onan
na_count += 1
elif val in memo:
values[i] = memo[val]
else:
memo[val] = val
return na_count