.. include:: references.txt
*******************************************
VOTable XML handling (`astropy.io.votable`)
*******************************************
Introduction
============
The `astropy.io.votable` subpackage converts VOTable XML files to and
from Numpy record arrays.
Getting Started
===============
Reading a VOTable file
----------------------
To read in a VOTable file, pass a file path to
`~astropy.io.votable.parse`::
from astropy.io.votable import parse
votable = parse("votable.xml")
``votable`` is a `~astropy.io.votable.tree.VOTableFile` object, which
can be used to retrieve and manipulate the data and save it back out
to disk.
VOTable files are made up of nested ``RESOURCE`` elements, each of
which may contain one or more ``TABLE`` elements. The ``TABLE``
elements contain the arrays of data.
To get at the ``TABLE`` elements, one can write a loop over the
resources in the ``VOTABLE`` file::
for resource in votable.resources:
for table in resource.tables:
# ... do something with the table ...
pass
However, if the nested structure of the resources is not important,
one can use `~astropy.io.votable.tree.VOTableFile.iter_tables` to
return a flat list of all tables::
for table in votable.iter_tables():
# ... do something with the table ...
pass
Finally, if there is expected to be only one table in the file, it
might be simplest to just use
`~astropy.io.votable.tree.VOTableFile.get_first_table`::
table = votable.get_first_table()
Even easier, there is a convenience method to parse a VOTable file and
return the first table all in one step::
from astropy.io.votable import parse_single_table
table = parse_single_table("votable.xml")
From a `~astropy.io.votable.tree.Table` object, one can get the data itself
in the ``array`` member variable::
data = table.array
This data is a Numpy record array. The columns get their names from
both the ``ID`` and ``name`` attributes of the ``FIELD`` elements in
the ``VOTABLE`` file. For example, suppose we had a ``FIELD``
specified as follows:
.. code-block:: xml
representing the ICRS declination of the center of the image.
This column of data can be extracted from the record array using::
>>> table.array['dec_targ']
array([17.15153360566, 17.15153360566, 17.15153360566, 17.1516686826,
17.1516686826, 17.1516686826, 17.1536197136, 17.1536197136,
17.1536197136, 17.15375479055, 17.15375479055, 17.15375479055,
17.1553884541, 17.15539736932, 17.15539752176,
17.25736014763,
# ...
17.2765703], dtype=object)
or equivalently::
>>> table.array['Dec']
array([17.15153360566, 17.15153360566, 17.15153360566, 17.1516686826,
17.1516686826, 17.1516686826, 17.1536197136, 17.1536197136,
17.1536197136, 17.15375479055, 17.15375479055, 17.15375479055,
17.1553884541, 17.15539736932, 17.15539752176,
17.25736014763,
# ...
17.2765703], dtype=object)
Building a new table from scratch
---------------------------------
It is also possible to build a new table, define some field datatypes
and populate it with data::
from astropy.io.votable.tree import VOTableFile, Resource, Table, Field
# Create a new VOTable file...
votable = VOTableFile()
# ...with one resource...
resource = Resource()
votable.resources.append(resource)
# ... with one table
table = Table(votable)
resource.tables.append(table)
# Define some fields
table.fields.extend([
Field(votable, name="filename", datatype="char", arraysize="*"),
Field(votable, name="matrix", datatype="double", arraysize="2x2")])
# Now, use those field definitions to create the numpy record arrays, with
# the given number of rows
table.create_arrays(2)
# Now table.array can be filled with data
table.array[0] = ('test1.xml', [[1, 0], [0, 1]])
table.array[1] = ('test2.xml', [[0.5, 0.3], [0.2, 0.1]])
# Now write the whole thing to a file.
# Note, we have to use the top-level votable file object
votable.to_xml("new_votable.xml")
Outputting a VOTable file
-------------------------
To save a VOTable file, simply call the
`~astropy.io.votable.tree.VOTableFile.to_xml` method. It accepts
either a string or unicode path, or a Python file-like object::
votable.to_xml('output.xml')
There are currently two data storage formats supported by
`astropy.io.votable`. The ``TABLEDATA`` format is XML-based and
stores values as strings representing numbers. The ``BINARY`` format
is more compact, and stores numbers in base64-encoded binary. The
storage format can be set on a per-table basis using the
`~astropy.io.votable.tree.Table.format` attribute, or globally using
the `~astropy.io.votable.tree.VOTableFile.set_all_tables_format`
method::
votable.get_first_table().format = 'binary'
votable.set_all_tables_format('binary')
votable.to_xml('binary.xml')
Using `io.votable`
==================
Standard compliance
-------------------
`astropy.io.votable.table` supports the `VOTable Format Definition
Version 1.1
`_
and `Version 1.2
`_.
Some flexibility is provided to support the 1.0 draft version and
other non-standard usage in the wild. To support these cases, set the
keyword argument ``pedantic`` to ``False`` when parsing.
.. note::
Each warning and VOTABLE-specific exception emitted has a number and
is documented in more detail in :ref:`warnings` and
:ref:`exceptions`.
Output always conforms to the 1.1 or 1.2 spec, depending on the input.
.. _pedantic-mode:
Pedantic mode
^^^^^^^^^^^^^
Many VOTABLE files in the wild do not conform to the VOTABLE
specification. If reading one of these files causes exceptions, you
may turn off pedantic mode in `astropy.io.votable` by passing
``pedantic=False`` to the `~astropy.io.votable.parse` or
`~astropy.io.votable.parse_single_table` functions::
from astropy.io.votable import parse
votable = parse("votable.xml", pedantic=False)
Note, however, that it is good practice to report these errors to the
author of the application that generated the VOTABLE file to bring the
file into compliance with the specification.
Even with ``pedantic`` turned off, many warnings may still be omitted.
These warnings are all of the type
`~astropy.io.votable.exceptions.VOTableSpecWarning` and can be turned
off using the standard Python `warnings` module.
Missing values
--------------
Any value in the table may be "missing". `astropy.io.votable` stores
a Numpy masked array in each `~astropy.io.votable.tree.Table`
instance. This behaves like an ordinary Numpy masked array, except
for variable-length fields. For those fields, the datatype of the
column is "object" and another Numpy masked array is stored there.
Therefore, operations on variable length columns will not work -- this
is simply because variable length columns are not directly supported
by Numpy masked arrays.
Datatype mappings
-----------------
The datatype specified by a ``FIELD`` element is mapped to a Numpy
type according to the following table:
================================ ========================================================================
VOTABLE type Numpy type
================================ ========================================================================
boolean b1
-------------------------------- ------------------------------------------------------------------------
bit b1
-------------------------------- ------------------------------------------------------------------------
unsignedByte u1
-------------------------------- ------------------------------------------------------------------------
char (*variable length*) O - In Python 2.x, a `str` object; in 3.x, a `bytes` object.
-------------------------------- ------------------------------------------------------------------------
char (*fixed length*) S
-------------------------------- ------------------------------------------------------------------------
unicodeChar (*variable length*) O - In Python 2.x, a `unicode` object, in utf-16; in 3.x a `str` object
-------------------------------- ------------------------------------------------------------------------
unicodeChar (*fixed length*) U
-------------------------------- ------------------------------------------------------------------------
short i2
-------------------------------- ------------------------------------------------------------------------
int i4
-------------------------------- ------------------------------------------------------------------------
long i8
-------------------------------- ------------------------------------------------------------------------
float f4
-------------------------------- ------------------------------------------------------------------------
double f8
-------------------------------- ------------------------------------------------------------------------
floatComplex c8
-------------------------------- ------------------------------------------------------------------------
doubleComplex c16
================================ ========================================================================
If the field is a fixed size array, the data is stored as a Numpy
fixed-size array.
If the field is a variable size array (that is ``arraysize`` contains
a '*'), the cell will contain a Python list of Numpy values. Each
value may be either an array or scalar depending on the ``arraysize``
specifier.
Examining field types
---------------------
To look up more information about a field in a table, one can use the
`~astropy.io.votable.tree.Table.get_field_by_id` method, which returns
the `~astropy.io.votable.tree.Field` object with the given ID. For
example::
>>> field = table.get_field_or_param_by_id('Dec')
>>> field.datatype
'char'
>>> field.unit
'deg'
.. note::
Field descriptors should not be mutated. To change the set of
columns, convert the Table to an `astropy.table.Table`, make the
changes, and then convert it back.
Converting to/from an `astropy.table.Table`
-------------------------------------------
The VOTable standard does not map conceptually to an
`astropy.table.Table`. However, a single table within the `VOTable`
file may be converted to and from an `astropy.table.Table`::
from astropy.io.votable import parse_single_table
table = parse_single_table("votable.xml").to_table()
As a convenience, there is also a function to create an entire VOTable
file with just a single table::
from astropy.io.votable import from_table, writeto
votable = from_table(table)
writeto(votable, "output.xml")
Performance considerations
--------------------------
File reads will be moderately faster if the ``TABLE`` element includes
an nrows_ attribute. If the number of rows is not specified, the
record array must be resized repeatedly during load.
.. _nrows: http://www.ivoa.net/Documents/REC/VOTable/VOTable-20040811.html#ToC10
See Also
========
- `VOTable Format Definition Version 1.1
`_
- `VOTable Format Definition Version 1.2
`_
Reference/API
=============
.. automodapi:: astropy.io.votable
:no-inheritance-diagram:
:skip: VOWarning
:skip: VOTableChangeWarning
:skip: VOTableSpecWarning
:skip: UnimplementedWarning
:skip: IOWarning
:skip: VOTableSpecError
.. automodapi:: astropy.io.votable.tree
:no-inheritance-diagram:
.. automodapi:: astropy.io.votable.converters
:no-inheritance-diagram:
.. automodapi:: astropy.io.votable.ucd
:no-inheritance-diagram:
.. automodapi:: astropy.io.votable.util
:no-inheritance-diagram:
.. automodapi:: astropy.io.votable.validator
:no-inheritance-diagram:
.. automodapi:: astropy.io.votable.xmlutil
:no-inheritance-diagram:
astropy.io.votable.exceptions Module
------------------------------------
.. toctree::
:maxdepth: 1
api_exceptions.rst