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 (aldcroft@head.cfa.harvard.edu)
"""
import re
from . import core
[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
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))
class TabHeaderSplitter(core.DefaultSplitter):
"""Split lines on tab and do not remove whitespace"""
delimiter = "\t"
def process_line(self, line):
return line + "\n"
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 ``--``.
Since the `CSV format <https://tools.ietf.org/html/rfc4180>`_ does not
formally support comments, any comments defined for the table via
``tbl.meta['comments']`` are ignored by default. If you would still like to
write those comments then include a keyword ``comment='#'`` to the
``write()`` call.
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://www.drdobbs.com/rdb-a-unix-command-line-database/199101326
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