Source code for astropy.io.ascii.basic

# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""An extensible ASCII table reader and writer.

basic.py:
  Basic table read / write functionality for simple character
  delimited files with various options for column header definition.

:Copyright: Smithsonian Astrophysical Observatory (2011)
:Author: Tom Aldcroft ([email protected])
"""


import re

from . import core


[docs]class BasicHeader(core.BaseHeader): """ Basic table Header Reader Set a few defaults for common ascii table formats (start at line 0, comments begin with ``#`` and possibly white space) """ start_line = 0 comment = r'\s*#' write_comment = '# '
[docs]class BasicData(core.BaseData): """ Basic table Data Reader Set a few defaults for common ascii table formats (start at line 1, comments begin with ``#`` and possibly white space) """ start_line = 1 comment = r'\s*#' write_comment = '# '
[docs]class Basic(core.BaseReader): r"""Character-delimited table with a single header line at the top. Lines beginning with a comment character (default='#') as the first non-whitespace character are comments. Example table:: # Column definition is the first uncommented line # Default delimiter is the space character. apples oranges pears # Data starts after the header column definition, blank lines ignored 1 2 3 4 5 6 """ _format_name = 'basic' _description = 'Basic table with custom delimiters' _io_registry_format_aliases = ['ascii'] header_class = BasicHeader data_class = BasicData
class NoHeaderHeader(BasicHeader): """ Reader for table header without a header Set the start of header line number to `None`, which tells the basic reader there is no header line. """ start_line = None class NoHeaderData(BasicData): """ Reader for table data without a header Data starts at first uncommented line since there is no header line. """ start_line = 0
[docs]class NoHeader(Basic): """Character-delimited table with no header line. When reading, columns are autonamed using header.auto_format which defaults to "col%d". Otherwise this reader the same as the :class:`Basic` class from which it is derived. Example:: # Table data 1 2 "hello there" 3 4 world """ _format_name = 'no_header' _description = 'Basic table with no headers' header_class = NoHeaderHeader data_class = NoHeaderData
class CommentedHeaderHeader(BasicHeader): """ Header class for which the column definition line starts with the comment character. See the :class:`CommentedHeader` class for an example. """ def process_lines(self, lines): """ Return only lines that start with the comment regexp. For these lines strip out the matching characters. """ re_comment = re.compile(self.comment) for line in lines: match = re_comment.match(line) if match: yield line[match.end():] def write(self, lines): lines.append(self.write_comment + self.splitter.join(self.colnames))
[docs]class CommentedHeader(Basic): """Character-delimited table with column names in a comment line. When reading, ``header_start`` can be used to specify the line index of column names, and it can be a negative index (for example -1 for the last commented line). The default delimiter is the <space> character. This matches the format produced by ``np.savetxt()``, with ``delimiter=','``, and ``header='<comma-delimited-column-names-list>'``. Example:: # col1 col2 col3 # Comment line 1 2 3 4 5 6 """ _format_name = 'commented_header' _description = 'Column names in a commented line' header_class = CommentedHeaderHeader data_class = NoHeaderData
[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. """ out = super().read(table) # Strip off the comment line set as the header line for # commented_header format (first by default). if 'comments' in out.meta: idx = self.header.start_line if idx < 0: idx = len(out.meta['comments']) + idx out.meta['comments'] = out.meta['comments'][:idx] + out.meta['comments'][idx+1:] if not out.meta['comments']: del out.meta['comments'] return out
[docs] def write_header(self, lines, meta): """ Write comment lines after, rather than before, the header. """ self.header.write(lines) self.header.write_comments(lines, meta)
class TabHeaderSplitter(core.DefaultSplitter): """Split lines on tab and do not remove whitespace""" delimiter = '\t' process_line = None class TabDataSplitter(TabHeaderSplitter): """ Don't strip data value whitespace since that is significant in TSV tables """ process_val = None skipinitialspace = False class TabHeader(BasicHeader): """ Reader for header of tables with tab separated header """ splitter_class = TabHeaderSplitter class TabData(BasicData): """ Reader for data of tables with tab separated data """ splitter_class = TabDataSplitter
[docs]class Tab(Basic): """Tab-separated table. Unlike the :class:`Basic` reader, whitespace is not stripped from the beginning and end of either lines or individual column values. Example:: col1 <tab> col2 <tab> col3 # Comment line 1 <tab> 2 <tab> 5 """ _format_name = 'tab' _description = 'Basic table with tab-separated values' header_class = TabHeader data_class = TabData
class CsvSplitter(core.DefaultSplitter): """ Split on comma for CSV (comma-separated-value) tables """ delimiter = ',' class CsvHeader(BasicHeader): """ Header that uses the :class:`astropy.io.ascii.basic.CsvSplitter` """ splitter_class = CsvSplitter comment = None write_comment = None class CsvData(BasicData): """ Data that uses the :class:`astropy.io.ascii.basic.CsvSplitter` """ splitter_class = CsvSplitter fill_values = [(core.masked, '')] comment = None write_comment = None
[docs]class Csv(Basic): """CSV (comma-separated-values) table. This file format may contain rows with fewer entries than the number of columns, a situation that occurs in output from some spreadsheet editors. The missing entries are marked as masked in the output table. Masked values (indicated by an empty '' field value when reading) are written out in the same way with an empty ('') field. This is different from the typical default for `astropy.io.ascii` in which missing values are indicated by ``--``. Example:: num,ra,dec,radius,mag 1,32.23222,10.1211 2,38.12321,-88.1321,2.2,17.0 """ _format_name = 'csv' _io_registry_format_aliases = ['csv'] _io_registry_can_write = True _io_registry_suffix = '.csv' _description = 'Comma-separated-values' header_class = CsvHeader data_class = CsvData
[docs] def inconsistent_handler(self, str_vals, ncols): """ Adjust row if it is too short. If a data row is shorter than the header, add empty values to make it the right length. Note that this will *not* be called if the row already matches the header. Parameters ---------- str_vals : list A list of value strings from the current row of the table. ncols : int The expected number of entries from the table header. Returns ------- str_vals : list List of strings to be parsed into data entries in the output table. """ if len(str_vals) < ncols: str_vals.extend((ncols - len(str_vals)) * ['']) return str_vals
class RdbHeader(TabHeader): """ Header for RDB tables """ col_type_map = {'n': core.NumType, 's': core.StrType} def get_type_map_key(self, col): return col.raw_type[-1] def get_cols(self, lines): """ Initialize the header Column objects from the table ``lines``. This is a specialized get_cols for the RDB type: Line 0: RDB col names Line 1: RDB col definitions Line 2+: RDB data rows Parameters ---------- lines : list List of table lines Returns ------- None """ header_lines = self.process_lines(lines) # this is a generator header_vals_list = [hl for _, hl in zip(range(2), self.splitter(header_lines))] if len(header_vals_list) != 2: raise ValueError('RDB header requires 2 lines') self.names, raw_types = header_vals_list if len(self.names) != len(raw_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 raw_types): raise core.InconsistentTableError(f'RDB types definitions do not all match [num](N|S): {raw_types}') self._set_cols_from_names() for col, raw_type in zip(self.cols, raw_types): col.raw_type = raw_type col.type = self.get_col_type(col) def write(self, lines): lines.append(self.splitter.join(self.colnames)) rdb_types = [] for col in self.cols: # Check if dtype.kind is string or unicode. See help(np.core.numerictypes) rdb_type = 'S' if col.info.dtype.kind in ('S', 'U') else 'N' rdb_types.append(rdb_type) lines.append(self.splitter.join(rdb_types)) class RdbData(TabData): """ Data reader for RDB data. Starts reading at line 2. """ start_line = 2
[docs]class Rdb(Tab): """Tab-separated file with an extra line after the column definition line that specifies either numeric (N) or string (S) data. See: https://compbio.soe.ucsc.edu/rdb/ Example:: col1 <tab> col2 <tab> col3 N <tab> S <tab> N 1 <tab> 2 <tab> 5 """ _format_name = 'rdb' _io_registry_format_aliases = ['rdb'] _io_registry_suffix = '.rdb' _description = 'Tab-separated with a type definition header line' header_class = RdbHeader data_class = RdbData