astropy:docs

ASCII Tables (astropy.io.ascii)

Introduction

astropy.io.ascii provides methods for reading and writing a wide range of ASCII data table formats via built-in Extension Reader classes. The emphasis is on flexibility and ease of use.

The following shows a few of the ASCII formats that are available, while the section on Supported formats contains the full list.

The astropy.io.ascii package is built on a modular and extensible class structure with independent Base class elements so that new formats can be easily accommodated.

Note

It is also possible to use the functionality from astropy.io.ascii through a higher-level interface in the astropy.table package. See Unified file read/write interface for more details.

Getting Started

Reading Tables

The majority of commonly encountered ASCII tables can be easily read with the read() function. Assume you have a file named sources.dat with the following contents:

obsid redshift  X      Y     object
3102  0.32      4167  4085   Q1250+568-A
877   0.22      4378  3892   "Source 82"

This table can be read with the following:

>>> from astropy.io import ascii
>>> data = ascii.read("sources.dat")  
>>> print data  
obsid redshift  X    Y      object
----- -------- ---- ---- -----------
 3102     0.32 4167 4085 Q1250+568-A
  877     0.22 4378 3892   Source 82

The first argument to the read() function can be the name of a file, a string representation of a table, or a list of table lines. By default read() will try to guess the table format by trying all the supported formats. If this does not work (for unusually formatted tables) then one needs give astropy.io.ascii additional hints about the format, for example:

>>> lines = ['objID                   & osrcid            & xsrcid       ',
...          '----------------------- & ----------------- & -------------',
...          '              277955213 & S000.7044P00.7513 & XS04861B6_005',
...          '              889974380 & S002.9051P14.7003 & XS03957B7_004']
>>> data = ascii.read(lines, data_start=2, delimiter='&')
>>> print(data)
  objID         osrcid          xsrcid
--------- ----------------- -------------
277955213 S000.7044P00.7513 XS04861B6_005
889974380 S002.9051P14.7003 XS03957B7_004

If the format of a file is known (e.g. it is a fixed width table or an IPAC table), then it is more efficient and reliable to provide a value for the format argument from one of the values in the supported formats. For example:

>>> data = ascii.read(lines, format='fixed_width_two_line', delimiter='&')

Writing Tables

The write() function provides a way to write a data table as a formatted ASCII table. For example the following writes a table as a simple space-delimited file:

>>> import numpy as np
>>> from astropy.table import Table
>>> x = np.array([1, 2, 3])
>>> y = x ** 2
>>> data = Table([x, y], names=['x', 'y'])
>>> ascii.write(data, 'values.dat')

The values.dat file will then contain:

x y
1 1
2 4
3 9

All of the input Reader formats supported by astropy.io.ascii for reading are also supported for writing. This provides a great deal of flexibility in the format for writing. The example below writes the data as a LaTeX table, using the option to send the output to sys.stdout instead of a file:

>>> import sys
>>> ascii.write(data, sys.stdout, format='latex')
\begin{table}
\begin{tabular}{cc}
x & y \\
1 & 1 \\
2 & 4 \\
3 & 9 \\
\end{tabular}
\end{table}

Supported formats

A full list of the supported format values and corresponding format types for ASCII tables is given below. The Write column indicates which formats support write functionality.

Format Write Description
aastex Yes AASTex: AASTeX deluxetable used for AAS journals
basic Yes Basic: Basic table with custom delimiters
cds   Cds: CDS format table
commented_header Yes CommentedHeader: Column names in a commented line
csv Yes Csv: Basic table with comma-separated values
daophot   Daophot: IRAF DAOphot format table
fixed_width Yes FixedWidth: Fixed width
fixed_width_no_header Yes FixedWidthNoHeader: Fixed width with no header
fixed_width_two_line Yes FixedWidthTwoLine: Fixed width with second header line
html Yes HTML: HTML format table
ipac Yes Ipac: IPAC format table
latex Yes Latex: LaTeX table
no_header Yes NoHeader: Basic table with no headers
rdb Yes Rdb: Tab-separated with a type definition header line
sextractor   SExtractor: SExtractor format table
tab Yes Tab: Basic table with tab-separated values

Reference/API

astropy.io.ascii Module

An extensible ASCII table reader and writer.

Functions

convert_numpy(numpy_type) Return a tuple (converter_func, converter_type).
get_reader([Reader, Inputter, Outputter]) Initialize a table reader allowing for common customizations.
get_writer([Writer]) Initialize a table writer allowing for common customizations.
read(table[, guess]) Read the input table and return the table.
set_guess(guess) Set the default value of the guess parameter for read()
write(table[, output, format, Writer]) Write the input table to filename.

Classes

AASTex(**kwargs) Write and read AASTeX tables.
AllType Subclass of all other data types.
BaseData() Base table data reader.
BaseHeader() Base table header reader
BaseInputter Get the lines from the table input and return a list of lines.
BaseOutputter Output table as a dict of column objects keyed on column name.
BaseReader() Class providing methods to read and write an ASCII table using the specified header, data, inputter, and outputter instances.
BaseSplitter Base splitter that uses python’s split method to do the work.
Basic() Read a character-delimited table with a single header line at the top followed by data lines to the end of the table.
BasicData() Basic table Data Reader
BasicHeader() Basic table Header Reader
Cds([readme]) Read a CDS format table.
Column(name) Table column.
CommentedHeader() Read a file where the column names are given in a line that begins with the header comment character.
ContinuationLinesInputter Inputter where lines ending in continuation_char are joined with the subsequent line.
Csv() Read a CSV (comma-separated-values) file.
Daophot() Read a DAOphot file.
DefaultSplitter Default class to split strings into columns using python csv.
FixedWidth([col_starts, col_ends, ...]) Read or write a fixed width table with a single header line that defines column names and positions.
FixedWidthData() Base table data reader.
FixedWidthHeader() Fixed width table header reader.
FixedWidthNoHeader([col_starts, col_ends, ...]) Read or write a fixed width table which has no header line.
FixedWidthSplitter Split line based on fixed start and end positions for each col in self.cols.
FixedWidthTwoLine([position_line, ...]) Read or write a fixed width table which has two header lines.
FloatType Describes floating-point data.
HTML([htmldict]) Read and write HTML tables.
InconsistentTableError Indicates that an input table is inconsistent in some way.
IntType Describes integer data.
Ipac([definition, DBMS]) Read or write an IPAC format table.
Latex([ignore_latex_commands, latexdict, ...]) Write and read LaTeX tables.
NoHeader() Read a table with no header line.
NoType Superclass for StrType and NumType classes.
NumType Indicates that a column consists of numerical data.
Rdb() Read a tab-separated file with an extra line after the column definition line.
SExtractor() Read a SExtractor file.
StrType Indicates that a column consists of text data.
Tab() Read a tab-separated file.
TableOutputter Output the table as an astropy.table.Table object.
WhitespaceSplitter

Class Inheritance Diagram

Inheritance diagram of astropy.io.ascii.latex.AASTex, astropy.io.ascii.core.AllType, astropy.io.ascii.core.BaseData, astropy.io.ascii.core.BaseHeader, astropy.io.ascii.core.BaseInputter, astropy.io.ascii.core.BaseOutputter, astropy.io.ascii.core.BaseReader, astropy.io.ascii.core.BaseSplitter, astropy.io.ascii.basic.Basic, astropy.io.ascii.basic.BasicData, astropy.io.ascii.basic.BasicHeader, astropy.io.ascii.cds.Cds, astropy.io.ascii.core.Column, astropy.io.ascii.basic.CommentedHeader, astropy.io.ascii.core.ContinuationLinesInputter, astropy.io.ascii.basic.Csv, astropy.io.ascii.daophot.Daophot, astropy.io.ascii.core.DefaultSplitter, astropy.io.ascii.fixedwidth.FixedWidth, astropy.io.ascii.fixedwidth.FixedWidthData, astropy.io.ascii.fixedwidth.FixedWidthHeader, astropy.io.ascii.fixedwidth.FixedWidthNoHeader, astropy.io.ascii.fixedwidth.FixedWidthSplitter, astropy.io.ascii.fixedwidth.FixedWidthTwoLine, astropy.io.ascii.core.FloatType, astropy.io.ascii.html.HTML, astropy.io.ascii.core.InconsistentTableError, astropy.io.ascii.core.IntType, astropy.io.ascii.ipac.Ipac, astropy.io.ascii.latex.Latex, astropy.io.ascii.basic.NoHeader, astropy.io.ascii.core.NoType, astropy.io.ascii.core.NumType, astropy.io.ascii.basic.Rdb, astropy.io.ascii.sextractor.SExtractor, astropy.io.ascii.core.StrType, astropy.io.ascii.basic.Tab, astropy.io.ascii.core.TableOutputter, astropy.io.ascii.core.WhitespaceSplitter