Writing tables

astropy.io.ascii is able to write ASCII tables out to a file or file-like object using the same class structure and basic user interface as for reading tables.

The write() function provides a way to write a data table as a formatted ASCII table. For example:

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

The values.dat file will then contain:

x y
1 1
2 4
3 9

Most of the input table Supported formats for reading are also available 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:

>>> ascii.write(data, 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)

Input data format

The input table argument to write() can be any value that is supported for initializing a Table object. This is documented in detail in the Constructing a table section and includes creating a table with a list of columns, a dictionary of columns, or from numpy arrays (either structured or homogeneous). The sections below show a few examples.

Table or NumPy structured array

An Astropy Table object or a NumPy structured array (or record array) can serve as input to the write() function.

>>> from astropy.io import ascii
>>> from astropy.table import Table

>>> data = Table({'a': [1, 2, 3],
...               'b': [4.0, 5.0, 6.0]},
...              names=['a', 'b'])
>>> ascii.write(data)
a b
1 4.0
2 5.0
3 6.0

>>> data = np.array([(1, 2., 'Hello'), (2, 3., "World")],
...                 dtype=('i4,f4,a10'))
>>> ascii.write(data)
f0 f1 f2
1 2.0 Hello
2 3.0 World

The output of astropy.io.ascii.read is a Table or NumPy array data object that can be an input to the write() function.

>>> data = ascii.read('data/daophot.dat', format='daophot')  
>>> ascii.write(data, 'space_delimited_table.dat')

List of lists

A list of Python lists (or any iterable object) can be used as input:

>>> x = [1, 2, 3]
>>> y = [4, 5.2, 6.1]
>>> z = ['hello', 'world', '!!!']
>>> data = [x, y, z]

>>> ascii.write(data)
col0 col1 col2
1 4.0 hello
2 5.2 world
3 6.1 !!!

The data object does not contain information about the column names so Table has chosen them automatically. To specify the names, provide the names keyword argument. This example also shows excluding one of the columns from the output:

>>> ascii.write(data, names=['x', 'y', 'z'], exclude_names=['y'])
x z
1 hello
2 world
3 !!!

Dict of lists

A dictionary containing iterable objects can serve as input to write(). Each dict key is taken as the column name while the value must be an iterable object containing the corresponding column values.

Since a Python dictionary is not ordered the output column order will be unpredictable unless the names argument is provided.

>>> data = {'x': [1, 2, 3],
...         'y': [4, 5.2, 6.1],
...         'z': ['hello', 'world', '!!!']}
>>> ascii.write(data, names=['x', 'y', 'z'])
x y z
1 4.0 hello
2 5.2 world
3 6.1 !!!

Parameters for write()

The write() function accepts a number of parameters that specify the detailed output table format. Each of the Supported formats is handled by a corresponding Writer class that can define different defaults, so the descriptions below sometimes mention “typical” default values. This refers to the Basic writer and other similar Writer classes.

Some output format Writer classes, e.g. Latex or AASTex accept additional keywords, that can customize the output further. See the documentation of these classes for details.

outputoutput specifier

There are two ways to specify the output for the write operation:

  • Name of a file (string)

  • File-like object (from open(), StringIO, etc)

tableinput table

Any value that is supported for initializing a Table object (see Constructing a table).

formatoutput format (default=’basic’)

This specifies the format of the ASCII table to be written, for example if it is a basic character delimited table, fixed format table, or a CDS-compatible table, etc. The value of this parameter must be one of the Supported formats.

delimitercolumn delimiter string

A one-character string used to separate fields which typically defaults to the space character. Other common values might be “,” or “|” or “\t”.

commentstring defining start of a comment line in output table

For the Basic Writer this defaults to “# “. Which and how comments are written depends on the format chosen. The comments are defined as a list of strings in the input table meta['comments'] element. Comments in the metadata of the given Table will normally be written before the header, although CommentedHeader writes table comments after the commented header. To disable writing comments, set comment=False.

formats: dict of data type converters

For each key (column name) use the given value to convert the column data to a string. If the format value is string-like then it is used as a Python format statement, e.g. ‘%0.2f’ % value. If it is a callable function then that function is called with a single argument containing the column value to be converted. Example:

astropy.io.ascii.write(table, sys.stdout, formats={'XCENTER': '%12.1f',
                                             'YCENTER': lambda x: round(x, 1)},
names: list of names corresponding to each data column

Define the complete list of names for each data column. This will override names determined from the data table (if available). If not supplied then use names from the data table or auto-generated names.

include_names: list of names to include in output

From the list of column names found from the data table or the names parameter, select for output only columns within this list. If not supplied then include all names.

exclude_names: list of names to exclude from output

Exclude these names from the list of output columns. This is applied after the include_names filtering. If not specified then no columns are excluded.

fill_values: list of fill value specifiers

This can be used to fill missing values in the table or replace values with special meaning.

See the Bad or missing values section for more information on the syntax. The syntax is almost the same as when reading a table. There is a special value astropy.io.ascii.masked that is used a say “output this string for all masked values in a masked table (the default is to use an empty string ""):

>>> import sys
>>> from astropy.table import Table, Column, MaskedColumn
>>> from astropy.io import ascii
>>> t = Table([(1, 2), (3, 4)], names=('a', 'b'), masked=True)
>>> t['a'].mask = [True, False]
>>> ascii.write(t, sys.stdout)
a b
"" 3
2 4
>>> ascii.write(t, sys.stdout, fill_values=[(ascii.masked, 'N/A')])
a b
N/A 3
2 4

Note that when writing a table all values are converted to strings, before any value is replaced. Because fill_values only replaces cells that are an exact match to the specification, you need to provide the string representation (stripped of whitespace) for each value. For example, in the following commands -99 is formatted with two digits after the comma, so we need to replace -99.00 and not -99:

>>> t = Table([(-99, 2), (3, 4)], names=('a', 'b'))
>>> ascii.write(t, sys.stdout, fill_values = [('-99.00', 'no data')],
...             formats={'a': '%4.2f'})
a b
"no data" 3
2.00 4

Similarly, if you replace a value in a column that has a fixed length format, e.g. 'f4.2', then the string you want to replace must have the same number of characters, in the example above fill_values=[(' nan',' N/A')] would work.

fill_include_names: list of column names, which are affected by fill_values.

If not supplied, then fill_values can affect all columns.

fill_exclude_names: list of column names, which are not affected by fill_values.

If not supplied, then fill_values can affect all columns.

fast_writer: whether to use the fast Cython writer

If this parameter is None (which it is by default), write() will attempt to use the faster writer (described in Fast ASCII I/O) if possible. Specifying fast_writer=False disables this behavior.

WriterWriter class (deprecated in favor of format)

This specifies the top-level format of the ASCII table to be written, for example if it is a basic character delimited table, fixed format table, or a CDS-compatible table, etc. The value of this parameter must be a Writer class. For basic usage this means one of the built-in Extension Reader classes. Note: Reader classes and Writer classes are synonymous, in other words Reader classes can also write, but for historical reasons they are often called Reader classes.

ECSV format

The Enhanced Character-Separated Values (ECSV) format can be used to write astropy Table or QTable datasets to a text-only data file and then read the table back without loss of information. The format handles the key issue of serializing column specifications and table metadata by using a YAML-encoded data structure. The actual tabular data are stored in a standard character separated values (CSV) format, giving compatibility with a wide variety of non-specialized CSV table readers.

Mixin columns

Starting with astropy 2.0 it is possible to store not only standard Column objects to ECSV but also the following Mixin columns:

In general a mixin column may contain multiple data components as well as object attributes beyond the standard Column attributes like format or description. Storing such mixin columns is done by replacing the mixin column with column(s) representing the underlying data component(s) and then inserting meta data which informs the reader how to reconstruct the original column. For example a SkyCoord mixin column in 'spherical' representation would have data attributes ra, dec, distance, along with object attributes like representation_type or frame. For example:

>>> from astropy.io import ascii
>>> from astropy.coordinates import SkyCoord
>>> import astropy.units as u
>>> from astropy.time import Time
>>> from astropy.table import QTable, Column

>>> sc = SkyCoord(ra=[1,2]*u.deg, dec=[3,4]*u.deg, distance=[5,6]*u.m,
...               frame='fk4', obstime=Time('2000:001'))
>>> sc.info.description = 'flying circus'
>>> c = Column([1,2])
>>> q = [1,2]*u.m
>>> q.info.format = '.2f'
>>> t = QTable([c, q, sc], names=['c', 'q', 'sc'])

>>> ascii.write(t, format='ecsv')   
# %ECSV 0.9
# ---
# datatype:
# - {name: c, datatype: int64}
# - {name: q, unit: m, datatype: float64}
# - {name: sc.ra, unit: deg, datatype: float64}
# - {name: sc.dec, unit: deg, datatype: float64}
# - {name: sc.distance, unit: m, datatype: float64}
# meta: !!omap
# - __serialized_columns__:
#     q:
#       __class__: astropy.units.quantity.Quantity
#       value: !astropy.table.SerializedColumn {name: q}
#     sc:
#       __class__: astropy.coordinates.sky_coordinate.SkyCoord
#       __info__: {description: flying circus}
#       dec: !astropy.table.SerializedColumn
#         __class__: astropy.coordinates.angles.Latitude
#         value: !astropy.table.SerializedColumn {name: sc.dec}
#       distance: !astropy.table.SerializedColumn
#         __class__: astropy.coordinates.distances.Distance
#         value: !astropy.table.SerializedColumn {name: sc.distance}
#       equinox: !astropy.time.Time {format: byear_str, in_subfmt: '*', jd1: 2400000.5,
#         jd2: 33281.92345905, out_subfmt: '*', precision: 3, scale: tai}
#       frame: fk4
#       obstime: !astropy.time.Time {format: yday, in_subfmt: '*', jd1: 2451544.5, jd2: 0.0,
#         out_subfmt: '*', precision: 3, scale: utc}
#       ra: !astropy.table.SerializedColumn
#         __class__: astropy.coordinates.angles.Longitude
#         value: !astropy.table.SerializedColumn {name: sc.ra}
#         wrap_angle: !astropy.coordinates.Angle
#           unit: !astropy.units.Unit {unit: deg}
#           value: 360.0
#       representation: spherical
# schema: astropy-2.0
c q sc.ra sc.dec sc.distance
1 1.0 1.0 3.0 5.0
2 2.0 2.0 4.0 6.0

The '__class__' keyword gives the fully-qualified class name, and must be one of the specifically-allowed astropy classes. There is no option to add user-specified allowed classes. The '__info__' keyword contains values for standard Column attributes like description or format, for any mixin columns that are represented by more than one serialized column.

Masked columns

By default, the ECSV format uses an empty (zero-length) string in the output table to represent masked or missing data in MaskedColumn columns. In certain cases this may not be sufficient:

  • String column that contains empty (zero-length) string(s) as valid data.

  • Masked data values must be stored so those values can later be unmasked.

In this case there is an available mechanism to specify that the full data and the mask itself should be written as columns in the output table as shown in the example below. For further context see the section on Table serialization methods.

>>> from astropy.table.table_helpers import simple_table
>>> t = simple_table(masked=True)
>>> t['c'][0] = ""  # Valid empty string in data
>>> t
<Table masked=True length=3>
  a      b     c
int64 float64 str1
----- ------- ----
   --     1.0
    2     2.0   --
    3      --    e

Now we tell ECSV writer to output separate data and mask columns for the string column 'c':

>>> t['c'].info.serialize_method['ecsv'] = 'data_mask'

When this is written out notice that the output shows all the data values for the 'c' column (include the masked 'd' value) and a new column 'c.masked'. It also stores metadata that tells the ECSV reader to interpret the 'c' and 'c.masked' columns as components of one MaskedColumn object:

>>> ascii.write(t, format='ecsv')
# %ECSV 0.9
# ---
# datatype:
# - {name: a, datatype: int64}
# - {name: b, datatype: float64}
# - {name: c, datatype: string}
# - {name: c.mask, datatype: bool}
# meta: !!omap
# - __serialized_columns__:
#     c:
#       __class__: astropy.table.column.MaskedColumn
#       data: !astropy.table.SerializedColumn {name: c}
#       mask: !astropy.table.SerializedColumn {name: c.mask}
# schema: astropy-2.0
a b c c.mask
"" 1.0 "" False
2 2.0 d True
3 "" e False

When you read this back in, the empty (zero-length) string in the first row of column 'c' will be preserved. One can easily write all the columns out as data and mask pairs using the Unified I/O interface for tables with the serialize_method keyword argument:

>>> t.write('out.ecsv', format='ascii.ecsv', serialize_method='data_mask')

In this case all data values, including those “under the mask” in the original table, will be restored exactly when you read the file back.