Source code for astropy.io.ascii.fastbasic

# Licensed under a 3-clause BSD style license - see LICENSE.rst

import re
import copy
from collections import OrderedDict

from . import core
from astropy.table import Table
from . import cparser
from astropy.utils.misc import _set_locale


[docs]class FastBasic(metaclass=core.MetaBaseReader): """ This class is intended to handle the same format addressed by the ordinary :class:`Basic` writer, but it acts as a wrapper for underlying C code and is therefore much faster. Unlike the other ASCII readers and writers, this class is not very extensible and is restricted by optimization requirements. """ _format_name = 'fast_basic' _description = 'Basic table with custom delimiter using the fast C engine' _fast = True fill_extra_cols = False guessing = False strict_names = False def __init__(self, default_kwargs={}, **user_kwargs): # Make sure user does not set header_start to None for a reader # that expects a non-None value (i.e. a number >= 0). This mimics # what happens in the Basic reader. if (default_kwargs.get('header_start', 0) is not None and user_kwargs.get('header_start', 0) is None): raise ValueError('header_start cannot be set to None for this Reader') # Set up kwargs and copy any user kwargs. Use deepcopy user kwargs # since they may contain a dict item which would end up as a ref to the # original and get munged later (e.g. in cparser.pyx validation of # fast_reader dict). kwargs = copy.deepcopy(default_kwargs) kwargs.update(copy.deepcopy(user_kwargs)) delimiter = kwargs.pop('delimiter', ' ') self.delimiter = str(delimiter) if delimiter is not None else None self.write_comment = kwargs.get('comment', '# ') self.comment = kwargs.pop('comment', '#') if self.comment is not None: self.comment = str(self.comment) self.quotechar = str(kwargs.pop('quotechar', '"')) self.header_start = kwargs.pop('header_start', 0) # If data_start is not specified, start reading # data right after the header line data_start_default = user_kwargs.get('data_start', self.header_start + 1 if self.header_start is not None else 1) self.data_start = kwargs.pop('data_start', data_start_default) self.kwargs = kwargs self.strip_whitespace_lines = True self.strip_whitespace_fields = True def _read_header(self): # Use the tokenizer by default -- this method # can be overridden for specialized headers self.engine.read_header()
[docs] def read(self, table): """ Read input data (file-like object, filename, list of strings, or single string) into a Table and return the result. """ if self.comment is not None and len(self.comment) != 1: raise core.ParameterError("The C reader does not support a comment regex") elif self.data_start is None: raise core.ParameterError("The C reader does not allow data_start to be None") elif self.header_start is not None and self.header_start < 0 and \ not isinstance(self, FastCommentedHeader): raise core.ParameterError("The C reader does not allow header_start to be " "negative except for commented-header files") elif self.data_start < 0: raise core.ParameterError("The C reader does not allow data_start to be negative") elif len(self.delimiter) != 1: raise core.ParameterError("The C reader only supports 1-char delimiters") elif len(self.quotechar) != 1: raise core.ParameterError("The C reader only supports a length-1 quote character") elif 'converters' in self.kwargs: raise core.ParameterError("The C reader does not support passing " "specialized converters") elif 'encoding' in self.kwargs: raise core.ParameterError("The C reader does not use the encoding parameter") elif 'Outputter' in self.kwargs: raise core.ParameterError("The C reader does not use the Outputter parameter") elif 'Inputter' in self.kwargs: raise core.ParameterError("The C reader does not use the Inputter parameter") elif 'data_Splitter' in self.kwargs or 'header_Splitter' in self.kwargs: raise core.ParameterError("The C reader does not use a Splitter class") self.strict_names = self.kwargs.pop('strict_names', False) # Process fast_reader kwarg, which may or may not exist (though ui.py will always # pass this as a dict with at least 'enable' set). fast_reader = self.kwargs.get('fast_reader', True) if not isinstance(fast_reader, dict): fast_reader = {} fast_reader.pop('enable', None) self.return_header_chars = fast_reader.pop('return_header_chars', False) # Put fast_reader dict back into kwargs. self.kwargs['fast_reader'] = fast_reader self.engine = cparser.CParser(table, self.strip_whitespace_lines, self.strip_whitespace_fields, delimiter=self.delimiter, header_start=self.header_start, comment=self.comment, quotechar=self.quotechar, data_start=self.data_start, fill_extra_cols=self.fill_extra_cols, **self.kwargs) conversion_info = self._read_header() self.check_header() if conversion_info is not None: try_int, try_float, try_string = conversion_info else: try_int = {} try_float = {} try_string = {} with _set_locale('C'): data, comments = self.engine.read(try_int, try_float, try_string) out = self.make_table(data, comments) if self.return_header_chars: out.meta['__ascii_fast_reader_header_chars__'] = self.engine.header_chars return out
[docs] def make_table(self, data, comments): """Actually make the output table give the data and comments.""" meta = OrderedDict() if comments: meta['comments'] = comments return Table(data, names=list(self.engine.get_names()), meta=meta)
[docs] def check_header(self): names = self.engine.get_header_names() or self.engine.get_names() if self.strict_names: # Impose strict requirements on column names (normally used in guessing) bads = [" ", ",", "|", "\t", "'", '"'] for name in names: if (core._is_number(name) or len(name) == 0 or name[0] in bads or name[-1] in bads): raise ValueError('Column name {!r} does not meet strict name requirements' .format(name)) # When guessing require at least two columns if self.guessing and len(names) <= 1: raise ValueError('Table format guessing requires at least two columns, got {}' .format(names))
[docs] def write(self, table, output): """ Use a fast Cython method to write table data to output, where output is a filename or file-like object. """ self._write(table, output, {})
def _write(self, table, output, default_kwargs, header_output=True, output_types=False): write_kwargs = {'delimiter': self.delimiter, 'quotechar': self.quotechar, 'strip_whitespace': self.strip_whitespace_fields, 'comment': self.write_comment } write_kwargs.update(default_kwargs) # user kwargs take precedence over default kwargs write_kwargs.update(self.kwargs) writer = cparser.FastWriter(table, **write_kwargs) writer.write(output, header_output, output_types)
[docs]class FastCsv(FastBasic): """ A faster version of the ordinary :class:`Csv` writer that uses the optimized C parsing engine. Note that this reader will append empty field values to the end of any row with not enough columns, while :class:`FastBasic` simply raises an error. """ _format_name = 'fast_csv' _description = 'Comma-separated values table using the fast C engine' _fast = True fill_extra_cols = True def __init__(self, **kwargs): super().__init__({'delimiter': ',', 'comment': None}, **kwargs)
[docs] def write(self, table, output): """ Override the default write method of `FastBasic` to output masked values as empty fields. """ self._write(table, output, {'fill_values': [(core.masked, '')]})
[docs]class FastTab(FastBasic): """ A faster version of the ordinary :class:`Tab` reader that uses the optimized C parsing engine. """ _format_name = 'fast_tab' _description = 'Tab-separated values table using the fast C engine' _fast = True def __init__(self, **kwargs): super().__init__({'delimiter': '\t'}, **kwargs) self.strip_whitespace_lines = False self.strip_whitespace_fields = False
[docs]class FastNoHeader(FastBasic): """ This class uses the fast C engine to read tables with no header line. If the names parameter is unspecified, the columns will be autonamed with "col{}". """ _format_name = 'fast_no_header' _description = 'Basic table with no headers using the fast C engine' _fast = True def __init__(self, **kwargs): super().__init__({'header_start': None, 'data_start': 0}, **kwargs)
[docs] def write(self, table, output): """ Override the default writing behavior in `FastBasic` so that columns names are not included in output. """ self._write(table, output, {}, header_output=None)
[docs]class FastCommentedHeader(FastBasic): """ A faster version of the :class:`CommentedHeader` reader, which looks for column names in a commented line. ``header_start`` denotes the index of the header line among all commented lines and is 0 by default. """ _format_name = 'fast_commented_header' _description = 'Columns name in a commented line using the fast C engine' _fast = True def __init__(self, **kwargs): super().__init__({}, **kwargs) # Mimic CommentedHeader's behavior in which data_start # is relative to header_start if unspecified; see #2692 if 'data_start' not in kwargs: self.data_start = 0
[docs] def make_table(self, data, comments): """ Actually make the output table give the data and comments. This is slightly different from the base FastBasic method in the way comments are handled. """ meta = OrderedDict() if comments: idx = self.header_start if idx < 0: idx = len(comments) + idx meta['comments'] = comments[:idx] + comments[idx+1:] if not meta['comments']: del meta['comments'] return Table(data, names=list(self.engine.get_names()), meta=meta)
def _read_header(self): tmp = self.engine.source commented_lines = [] for line in tmp.splitlines(): line = line.lstrip() if line and line[0] == self.comment: # line begins with a comment commented_lines.append(line[1:]) if len(commented_lines) == self.header_start + 1: break if len(commented_lines) <= self.header_start: raise cparser.CParserError('not enough commented lines') self.engine.setup_tokenizer([commented_lines[self.header_start]]) self.engine.header_start = 0 self.engine.read_header() self.engine.setup_tokenizer(tmp)
[docs] def write(self, table, output): """ Override the default writing behavior in `FastBasic` so that column names are commented. """ self._write(table, output, {}, header_output='comment')
[docs]class FastRdb(FastBasic): """ A faster version of the :class:`Rdb` reader. This format is similar to tab-delimited, but it also contains a header line after the column name line denoting the type of each column (N for numeric, S for string). """ _format_name = 'fast_rdb' _description = 'Tab-separated with a type definition header line' _fast = True def __init__(self, **kwargs): super().__init__({'delimiter': '\t', 'data_start': 2}, **kwargs) self.strip_whitespace_lines = False self.strip_whitespace_fields = False def _read_header(self): tmp = self.engine.source line1 = '' line2 = '' for line in tmp.splitlines(): # valid non-comment line if not line1 and line.strip() and line.lstrip()[0] != self.comment: line1 = line elif not line2 and line.strip() and line.lstrip()[0] != self.comment: line2 = line break else: # less than 2 lines in table raise ValueError('RDB header requires 2 lines') # tokenize the two header lines separately self.engine.setup_tokenizer([line2]) self.engine.header_start = 0 self.engine.read_header() types = self.engine.get_names() self.engine.setup_tokenizer([line1]) self.engine.set_names([]) self.engine.read_header() if len(self.engine.get_names()) != len(types): raise core.InconsistentTableError('RDB header mismatch between number of ' 'column names and column types') if any(not re.match(r'\d*(N|S)$', x, re.IGNORECASE) for x in types): raise core.InconsistentTableError('RDB type definitions do not all match ' '[num](N|S): {}'.format(types)) try_int = {} try_float = {} try_string = {} for name, col_type in zip(self.engine.get_names(), types): if col_type[-1].lower() == 's': try_int[name] = 0 try_float[name] = 0 try_string[name] = 1 else: try_int[name] = 1 try_float[name] = 1 try_string[name] = 0 self.engine.setup_tokenizer(tmp) return (try_int, try_float, try_string)
[docs] def write(self, table, output): """ Override the default writing behavior in `FastBasic` to output a line with column types after the column name line. """ self._write(table, output, {}, output_types=True)