.. doctest-skip-all
.. _table_io:
Unified file read/write interface
===================================
Astropy provides a unified interface for reading and writing data in different formats.
For many common cases this will simplify the process of file I/O and reduce the need to
master the separate details of all the I/O packages within Astropy. This functionality is
still in active development and the number of supported formats will be increasing. For
details on the implementation see :ref:`io_registry`.
Getting started with Table I/O
------------------------------
The :class:`~astropy.table.Table` class includes two methods,
:meth:`~astropy.table.Table.read` and
:meth:`~astropy.table.Table.write`, that make it possible to read from
and write to files. A number of formats are automatically supported (see
`Built-in table readers/writers`_) and new file formats and extensions can be
registered with the :class:`~astropy.table.Table` class (see
:ref:`io_registry`).
To use this interface, first import the :class:`~astropy.table.Table` class, then
simply call the :class:`~astropy.table.Table`
:meth:`~astropy.table.Table.read` method with the name of the file and
the file format, for instance ``'ascii.daophot'``::
>>> from astropy.table import Table
>>> t = Table.read('photometry.dat', format='ascii.daophot')
It is possible to load tables directly from the Internet using URLs. For example,
download tables from Vizier catalogues in CDS format (``'ascii.cds'``)::
>>> t = Table.read("ftp://cdsarc.u-strasbg.fr/pub/cats/VII/253/snrs.dat",
... readme="ftp://cdsarc.u-strasbg.fr/pub/cats/VII/253/ReadMe",
... format="ascii.cds")
For certain file formats, the format can be automatically detected, for
example from the filename extension::
>>> t = Table.read('table.tex')
Similarly, for writing, the format can be explicitly specified::
>>> t.write(filename, format='latex')
As for the :meth:`~astropy.table.Table.read` method, the format may
be automatically identified in some cases.
The underlying file handler will also automatically detect various
compressed data formats and transparently uncompress them as far as
supported by the Python installation (see
:meth:`~astropy.utils.data.get_readable_fileobj`).
Any additional arguments specified will depend on the format. For examples of this see the
section `Built-in table readers/writers`_. This section also provides the full list of
choices for the ``format`` argument.
.. _built_in_readers_writers:
Built-in table readers/writers
------------------------------
The full list of built-in readers and writers is shown in the table below:
=========================== ==== ===== ============= ==========
Format Read Write Auto-identify Deprecated
=========================== ==== ===== ============= ==========
aastex Yes Yes No Yes
ascii Yes Yes No
ascii.aastex Yes Yes No
ascii.basic Yes Yes No
ascii.cds Yes No No
ascii.commented_header Yes Yes No
ascii.daophot Yes No No
ascii.ecsv Yes Yes No
ascii.fixed_width Yes Yes No
ascii.fixed_width_no_header Yes Yes No
ascii.fixed_width_two_line Yes Yes No
ascii.html Yes Yes Yes
ascii.ipac Yes Yes No
ascii.latex Yes Yes Yes
ascii.no_header Yes Yes No
ascii.rdb Yes Yes Yes
ascii.sextractor Yes No No
ascii.tab Yes Yes No
ascii.csv Yes Yes Yes
cds Yes No No Yes
daophot Yes No No Yes
fits Yes Yes Yes
hdf5 Yes Yes Yes
html Yes Yes No Yes
ipac Yes Yes No Yes
latex Yes Yes No Yes
rdb Yes Yes No Yes
votable Yes Yes Yes
=========================== ==== ===== ============= ==========
Deprecated format names like ``aastex`` will be removed in a future version.
Use the full name (e.g. ``ascii.aastex``) instead.
.. _table_io_ascii:
ASCII formats
^^^^^^^^^^^^^^
The :meth:`~astropy.table.Table.read` and
:meth:`~astropy.table.Table.write` methods can be used to read and write formats
supported by `astropy.io.ascii`.
Use ``format='ascii'`` in order to interface to the generic
:func:`~astropy.io.ascii.read` and :func:`~astropy.io.ascii.write`
functions from `astropy.io.ascii`. When reading a table this means
that all supported ASCII table formats will be tried in order to successfully
parse the input. For example::
>>> t = Table.read('astropy/io/ascii/tests/t/latex1.tex', format='ascii')
>>> print(t)
cola colb colc
---- ---- ----
a 1 2
b 3 4
When writing a table with ``format='ascii'`` the output is a basic
character-delimited file with a single header line containing the
column names.
All additional arguments are passed to the `astropy.io.ascii`
:func:`~astropy.io.ascii.read` and :func:`~astropy.io.ascii.write`
functions. Further details are available in the sections on
:ref:`io_ascii_read_parameters` and :ref:`io_ascii_write_parameters`. For example, to change
column delimiter and the output format for the ``colc`` column use::
>>> t.write(sys.stdout, format='ascii', delimiter='|', formats={'colc': '%0.2f'})
cola|colb|colc
a|1|2.00
b|3|4.00
A full list of the supported ``format`` values and corresponding format types
for ASCII tables is given below. The ``Suffix`` column indicates the filename
suffix where the format will be auto-detected, while the ``Write`` column
indicates which support write functionality.
=============================== ====== ===== ============================================================================================
Format Suffix Write Description
=============================== ====== ===== ============================================================================================
``ascii`` Yes ASCII table in any supported format (uses guessing)
``ascii.aastex`` Yes :class:`~astropy.io.ascii.AASTex`: AASTeX deluxetable used for AAS journals
``ascii.basic`` Yes :class:`~astropy.io.ascii.Basic`: Basic table with custom delimiters
``ascii.cds`` :class:`~astropy.io.ascii.Cds`: CDS format table
``ascii.commented_header`` Yes :class:`~astropy.io.ascii.CommentedHeader`: Column names in a commented line
``ascii.daophot`` :class:`~astropy.io.ascii.Daophot`: IRAF DAOphot format table
``ascii.fixed_width`` Yes :class:`~astropy.io.ascii.FixedWidth`: Fixed width
``ascii.fixed_width_no_header`` Yes :class:`~astropy.io.ascii.FixedWidthNoHeader`: Fixed width with no header
``ascii.fixed_width_two_line`` Yes :class:`~astropy.io.ascii.FixedWidthTwoLine`: Fixed width with second header line
``ascii.ipac`` Yes :class:`~astropy.io.ascii.Ipac`: IPAC format table
``ascii.html`` .html Yes :class:`~astropy.io.ascii.HTML`: HTML table
``ascii.latex`` .tex Yes :class:`~astropy.io.ascii.Latex`: LaTeX table
``ascii.no_header`` Yes :class:`~astropy.io.ascii.NoHeader`: Basic table with no headers
``ascii.rdb`` .rdb Yes :class:`~astropy.io.ascii.Rdb`: Tab-separated with a type definition header line
``ascii.sextractor`` :class:`~astropy.io.ascii.SExtractor`: SExtractor format table
``ascii.tab`` Yes :class:`~astropy.io.ascii.Tab`: Basic table with tab-separated values
``ascii.csv`` .csv Yes :class:`~astropy.io.ascii.Csv`: Basic table with comma-separated values
``ascii.ecsv`` .ecsv Yes :class:`~astropy.io.ascii.Ecsv`: Basic table with Enhanced CSV (supporting metadata)
=============================== ====== ===== ============================================================================================
.. note::
When specifying a specific ASCII table format using the unified interface, the format name is
prefixed with ``ascii.`` in order to identify the format as ASCII-based. Compare the
table above to the `astropy.io.ascii` list of :ref:`supported_formats`. Therefore the following
are equivalent::
>>> dat = ascii.read('file.dat', format='daophot')
>>> dat = Table.read('file.dat', format='ascii.daophot')
For compatibility with astropy version 0.2 and earlier, the following format
values are also allowed in ``Table.read()``: ``daophot``, ``ipac``, ``html``, ``latex``, and ``rdb``.
.. _table_io_fits:
FITS
^^^^
Reading and writing tables in `FITS `_ format is
supported with ``format='fits'``. In most cases, existing FITS files should be
automatically identified as such based on the header of the file, but if not,
or if writing to disk, then the format should be explicitly specified.
Reading
""""""""
If a FITS table file contains only a single table, then it can be read in
with::
>>> from astropy.table import Table
>>> t = Table.read('data.fits')
If more than one table is present in the file, you can select the HDU
as follows::
>>> t = Table.read('data.fits', hdu=3)
In this case if the ``hdu`` argument is omitted then the first table found will be
read in and a warning will be emitted::
>>> t = Table.read('data.fits')
WARNING: hdu= was not specified but multiple tables are present, reading in first available table (hdu=1) [astropy.io.fits.connect]
Writing
""""""""
To write a table ``t`` to a new file::
>>> t.write('new_table.fits')
If the file already exists and you want to overwrite it, then set the
``overwrite`` keyword::
>>> t.write('existing_table.fits', overwrite=True)
At this time there is no support for appending an HDU to an existing file or
writing multi-HDU files using the Table interface. Instead one can use the
lower-level :ref:`astropy.io.fits ` interface.
Keywords
"""""""""
The FITS keywords associated with an HDU table are represented in the ``meta``
ordered dictionary attribute of a :ref:`Table `. After reading
a table one can view the available keywords in a readable format using::
>>> for key, value in t.meta.items():
... print('{0} = {1}'.format(key, value))
This does not include the "internal" FITS keywords that are required to specify
the FITS table properties (e.g. ``NAXIS``, ``TTYPE1``). ``HISTORY`` and
``COMMENT`` keywords are treated specially and are returned as a list of
values.
Conversely, the following shows examples of setting user keyword values for a
table ``t``::
>>> t.meta['MY_KEYWD'] = 'my value'
>>> t.meta['COMMENT'] = ['First comment', 'Second comment', 'etc']
>>> t.write('my_table.fits', overwrite=True)
The keyword names (e.g. ``MY_KEYWD``) will be automatically capitalized prior
to writing.
At this time, the ``meta`` attribute of the :class:`~astropy.table.Table` class
is simply an ordered dictionary and does not fully represent the structure of a
FITS header (for example, keyword comments are dropped).
.. _table_io_hdf5:
HDF5
^^^^^^^^
Reading/writing from/to `HDF5 `_ files is
supported with ``format='hdf5'`` (this requires `h5py
`_ to be installed). However, the ``.hdf5``
file extension is automatically recognized when writing files, and HDF5 files
are automatically identified (even with a different extension) when reading
in (using the first few bytes of the file to identify the format), so in most
cases you will not need to explicitly specify ``format='hdf5'``.
Since HDF5 files can contain multiple tables, the full path to the table
should be specified via the ``path=`` argument when reading and writing.
For example, to read a table called ``data`` from an HDF5 file named
``observations.hdf5``, you can do::
>>> t = Table.read('observations.hdf5', path='data')
To read a table nested in a group in the HDF5 file, you can do::
>>> t = Table.read('observations.hdf5', path='group/data')
To write a table to a new file, the path should also be specified::
>>> t.write('new_file.hdf5', path='updated_data')
It is also possible to write a table to an existing file using ``append=True``::
>>> t.write('observations.hdf5', path='updated_data', append=True)
As with other formats, the ``overwrite=True`` argument is supported for
overwriting existing files. To overwrite only a single table within an HDF5
file that has multiple datasets, use *both* the ``overwrite=True`` and
``append=True`` arguments.
If the metadata of the table cannot be written directly to the HDF5 file
(e.g. dictionaries), or if you want to preserve the units and description
of tables and columns, use using ``serialize_meta=True``::
>>> t.write('observations.hdf5', path='updated_data', serialize_meta=True)
Finally, when writing to HDF5 files, the ``compression=`` argument can be
used to ensure that the data is compressed on disk::
>>> t.write('new_file.hdf5', path='updated_data', compression=True)
.. _table_io_votable:
VO Tables
^^^^^^^^^^^
Reading/writing from/to `VO table `_
files is supported with ``format='votable'``. In most cases, existing VO
tables should be automatically identified as such based on the header of the
file, but if not, or if writing to disk, then the format should be explicitly
specified.
If a VO table file contains only a single table, then it can be read in with::
>>> t = Table.read('aj285677t3_votable.xml')
If more than one table is present in the file, an error will be raised,
unless the table ID is specified via the ``table_id=`` argument::
>>> t = Table.read('catalog.xml')
Traceback (most recent call last):
...
ValueError: Multiple tables found: table id should be set via the table_id= argument. The available tables are twomass, spitzer
>>> t = Table.read('catalog.xml', table_id='twomass')
To write to a new file, the ID of the table should also be specified (unless
``t.meta['ID']`` is defined)::
>>> t.write('new_catalog.xml', table_id='updated_table', format='votable')
When writing, the ``compression=True`` argument can be used to force
compression of the data on disk, and the ``overwrite=True`` argument can be
used to overwrite an existing file.