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, although readers can optionally use a less flexible C/Cython engine for reading and writing for improved performance.

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

• Basic: basic table with customizable delimiters and header configurations
• Cds: CDS format table (also Vizier and ApJ machine readable tables)
• Daophot: table from the IRAF DAOphot package
• Ecsv: ECSV format for lossless round-trip of data tables
• FixedWidth: table with fixed-width columns (see also Fixed-width Gallery)
• Ipac: IPAC format table
• HTML: HTML format table contained in a <table> tag
• Latex: LaTeX table with datavalue in the tabular environment
• Rdb: tab-separated values with an extra line after the column definition line
• SExtractor: SExtractor format table

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 (and encouraged) to use the functionality from astropy.io.ascii through a higher-level interface in the Data Tables 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. The return value (data in this case) is a Table object.

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='&')

For simpler formats such as CSV, read() will automatically try reading with the Cython/C parsing engine, which is significantly faster than the ordinary Python implementation (described in Fast ASCII I/O). If the fast engine fails, read() will fall back on the Python reader by default. The argument fast_reader can be specified to control this behavior. For example, to disable the fast engine:

>>> data = ascii.read(lines, format='csv', fast_reader=False)

For reading very large tables see the section on Reading large tables in chunks.

Note

Reading a table which contains unicode characters is supported; if you need a different encoding, you can specify the encoding parameter in the pure-Python readers.

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, Column, MaskedColumn
>>> 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

Most 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}

There is also a faster Cython engine for writing simple formats, which is enabled by default for these formats (see Fast ASCII I/O). To disable this engine, use the parameter fast_writer:

>>> ascii.write(data, 'values.csv', format='csv', fast_writer=False)  

Finally, one can write data in the ECSV format which allows preserving table meta-data such as column data types and units. In this way a data table (including one with masked entries) can be stored and read back as ASCII with no loss of information.

>>> t = Table(masked=True)
>>> t['x'] = MaskedColumn([1.0, 2.0], unit='m', dtype='float32')
>>> t['x'][1] = np.ma.masked
>>> t['y'] = MaskedColumn([False, True], dtype='bool')

>>> import io
>>> fh = io.StringIO()
>>> t.write(fh, format='ascii.ecsv')  # doctest: +SKIP
>>> table_string = fh.getvalue()      # doctest: +SKIP
>>> print(table_string)               # doctest: +SKIP
# %ECSV 0.9
# ---
# datatype:
# - {name: x, unit: m, datatype: float32}
# - {name: y, datatype: bool}
x y
1.0 False
"" True

>>> Table.read(table_string, format='ascii')  # doctest: +SKIP
<Table masked=True length=2>
   x      y
   m
float32  bool
------- -----
    1.0 False
     --  True

Note

For most supported formats one can write a masked table and then read it back without losing information about the masked table entries. This is accomplished by using a blank string entry to indicate a masked (missing) value. See the Bad or missing values section for more information.

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, and the Fast column indicates which formats are compatible with the fast Cython/C engine for reading and writing.

Format	Write	Fast	Description
aastex	Yes		AASTex: AASTeX deluxetable used for AAS journals
basic	Yes	Yes	Basic: Basic table with custom delimiters
cds			Cds: CDS format table
commented_header	Yes	Yes	CommentedHeader: Column names in a commented line
csv	Yes	Yes	Csv: Basic table with comma-separated values
daophot			Daophot: IRAF DAOphot format table
ecsv	Yes		Ecsv: Enhanced CSV format
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	Yes	NoHeader: Basic table with no headers
rdb	Yes	Yes	Rdb: Tab-separated with a type definition header line
rst	Yes		RST: reStructuredText simple format table
sextractor			SExtractor: SExtractor format table
tab	Yes	Yes	Tab: Basic table with tab-separated values

Attention

ECSV is recommended

For writing and reading tables to ASCII in a way that fully reproduces the table data, types and metadata (i.e. the table will “round-trip”), we highly recommend using the ECSV format. This writes the actual data in a simple space-delimited format (the basic format) that any ASCII table reader can parse, but also includes metadata encoded in a comment block that allows full reconstruction of the original columns. This includes support for Mixin columns (such as SkyCoord or Time) and Masked columns.

Using astropy.io.ascii

The details of using astropy.io.ascii are provided in the following sections:

Reading tables

• Reading tables
  • Parameters for read()
  • Specifying header and data location
  • Bad or missing values
  • Guess table format
  • Comments and metadata
  • Converters
  • Fortran-style exponents
  • Advanced customization
  • Reading large tables in chunks

Writing tables

• Writing tables
  • Input data format
  • Parameters for write()
  • ECSV format

Fixed-width Gallery

• Fixed-width Gallery
  • Reading
  • Writing

Fast ASCII Engine

• Fast ASCII I/O
  • Reading
  • Writing
  • Speed gains

Base class elements

• Base class elements

Extension Reader classes

• Extension Reader classes

Performance Tips

By default, when trying to read a file, the reader will guess the format, which involves trying to read it with many different readers. Especially when dealing with large tables, it is much better performance-wise if you can specify the format and any options explicitly, and also turn off guessing. For example, if you are reading a simple CSV file with a one-line header with column names, the following:

read('example.csv', format='basic', delimiter=',', guess=False)  # doctest: +SKIP

can be at least an order of magnitude faster than:

read('example.csv')  # doctest: +SKIP

Reference/API

astropy.io.ascii Package

An extensible ASCII table reader and writer.

Functions

convert_numpy(numpy_type)	Return a tuple containing a function which converts a list into a numpy array and the type produced by the converter function.
get_read_trace()	Return a traceback of the attempted read formats for the last call to read where guessing was enabled.
get_reader([Reader, Inputter, Outputter])	Initialize a table reader allowing for common customizations.
get_writer([Writer, fast_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.
Ecsv()	Read a file which conforms to the ECSV (Enhanced Character Separated Values) format.
FastBasic([default_kwargs])	This class is intended to handle the same format addressed by the ordinary Basic writer, but it acts as a wrapper for underlying C code and is therefore much faster.
FastCommentedHeader(**kwargs)	A faster version of the CommentedHeader reader, which looks for column names in a commented line.
FastCsv(**kwargs)	A faster version of the ordinary Csv writer that uses the optimized C parsing engine.
FastNoHeader(**kwargs)	This class uses the fast C engine to read tables with no header line.
FastRdb(**kwargs)	A faster version of the Rdb reader.
FastTab(**kwargs)	A faster version of the ordinary Tab reader that uses the optimized C parsing engine.
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.
ParameterError	Indicates that a reader cannot handle a passed parameter.
RST()	Read or write a reStructuredText simple format table.
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