VOTable XML Handling (
astropy.io.votable sub-package converts VOTable XML files to and
numpy record arrays. This subpackage was originally developed
This section provides a quick introduction of using
goal is to demonstrate the package’s basic features without getting into too
Reading a VOTable File#
To read in a VOTable file, pass a file path to
from astropy.io.votable import parse votable = parse("votable.xml")
votable is a
VOTableFile object, which
can be used to retrieve and manipulate the data and save it back out
VOTable files are made up of nested
RESOURCE elements, each of
which may contain one or more
TABLE elements. The
elements contain the arrays of data.
To get at the
TABLE elements, you can write a loop over the
resources in the
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,
you can use
return a flat list of all tables:
for table in votable.iter_tables(): # ... do something with the table ... pass
Finally, if you expect only one table in the file, it might be most convenient
table = votable.get_first_table()
Alternatively, 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")
TableElement object, you can get the data itself
array member variable:
data = table.array
This data is a
numpy record array.
The columns get their names from both the
attributes of the
FIELD elements in the
Suppose we had a
FIELD specified as follows:
<FIELD ID="Dec" name="dec_targ" datatype="char" ucd="POS_EQ_DEC_MAIN" unit="deg"> <DESCRIPTION> representing the ICRS declination of the center of the image. </DESCRIPTION> </FIELD>
The mapping from VOTable
ID attributes to
titles is highly confusing.
ID is guaranteed to be unique, but is not
name is not guaranteed to be unique, but is
numpy record dtypes,
names are required to be unique and
titles are not required, and are not required
to be unique.
ID most closely maps to
names, and VOTable’s
name most closely maps to
titles. However, in some cases where a VOTable
ID is not
name will be generated based on the VOTable
name. Unfortunately, VOTable fields do not have an attribute
that is both unique and required, which would be the most
convenient mechanism to uniquely identify a column.
When converting from an
astropy.io.votable.tree.TableElement object to
astropy.table.Table object, you can specify whether to give
ID attributes when naming the
columns. By default,
ID is given preference. To give
name preference, pass the keyword argument
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)
>>> 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.
To build a new table from a VOTable file:
from astropy.io.votable.tree import VOTableFile, Resource, TableElement, Field # Create a new VOTable file... votable = VOTableFile() # ...with one resource... resource = Resource() votable.resources.append(resource) # ... with one table table = TableElement(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 = ('test1.xml', [[1, 0], [0, 1]]) table.array = ('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#
This section describes writing table data in the VOTable format using the
votable package directly. For some cases, however, the high-level
Unified File Read/Write Interface will often suffice and is somewhat more convenient to use. See
the Unified I/O VOTable section for details.
To save a VOTable file, call the
to_xml method. It accepts
either a string or Unicode path, or a Python file-like object:
There are a number of data storage formats supported by
TABLEDATA format is XML-based and
stores values as strings representing numbers. The
is more compact, and stores numbers in base64-encoded binary. VOTable
version 1.3 adds the
BINARY2 format, which allows for masking of
any data type, including integers and bit fields which cannot be
masked in the older
BINARY format. The storage format can be set
on a per-table basis using the
attribute, or globally using the
votable.get_first_table().format = 'binary' votable.set_all_tables_format('binary') votable.to_xml('binary.xml')
astropy.io.votable.tree.TableElement supports the VOTable Format Definition
and Version 1.4.
Some flexibility is provided to support the 1.0 draft version and
other nonstandard usage in the wild, see Verifying VOTables for more
Output always conforms to the 1.1, 1.2, 1.3, or 1.4 spec, depending on the input.
Many VOTable files in the wild do not conform to the VOTable specification. You
can set what should happen when a violation is encountered with the
keyword, which can take three values:
'ignore'- Attempt to parse the VOTable silently. This is the default setting.
'warn'- Attempt to parse the VOTable, but raise appropriate Warnings. It is possible to limit the number of warnings of the same type to a maximum value using the
astropy.io.votable.exceptions.conf.max_warningsitem in the Configuration System (astropy.config).
'exception'- Do not parse the VOTable and raise an exception.
from astropy.io.votable import parse votable = parse("votable.xml", verify='warn')
'warn' mean that
astropy will attempt to
parse the VOTable, but if the specification has been violated then success
cannot be guaranteed.
It is good practice to report any errors to the author of the application that generated the VOTable file to bring the file into compliance with the specification.
Any value in the table may be “missing”.
numpy masked array in each
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 because variable-length columns are not directly supported
numpy masked arrays.
The datatype specified by a
FIELD element is mapped to a
type according to the following table:
char (variable length)
O - A
char (fixed length)
unicodeChar (variable length)
O - A
unicodeChar (fixed length)
If the field is a fixed-size array, the data is stored as a
If the field is a variable-size array (that is,
a ‘*’), the cell will contain a Python list of
numpy values. Each
value may be either an array or scalar depending on the
Examining Field Types#
To look up more information about a field:
>>> field = table.get_field_by_id('Dec') >>> field.datatype 'char' >>> field.unit 'deg'
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.
Data Serialization Formats#
VOTable supports a number of different serialization formats.
TABLEDATA stores the data in pure XML, where the numerical values are written as human-readable strings.
BINARY is a binary representation of the data, stored in the XML as an opaque
BINARY2 was added in VOTable 1.3, and is identical to “BINARY”, except that it explicitly records the position of missing values rather than identifying them by a special value.
PARQUETstores the data in an external PARQUET file, similar to FITS serialization. Reading and writing is fully supported by the
astropy.io.votablewriter and the
astropy.io.votable.parsereader. The parquet file can be referenced with either absolute and relative paths. The parquet serialization can be used as part of the unified Table I/O (see next section), by setting the
The serialization format can be selected in two ways:
1) By setting the
formatattribute of a
astropy.io.votable.tree.TableElementobject:votable.get_first_table().format = "binary" votable.to_xml("new_votable.xml")
2) By overriding the format of all tables using the
tabledata_formatkeyword argument when writing out a VOTable file:votable.to_xml("new_votable.xml", tabledata_format="binary")
Converting to/from an
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")
to_table will use the
ID attribute from the files to
create the column names for the
Table object. However,
it may be that you want to use the
name attributes instead. For this,
use_names_over_ids keyword to
True. Note that since field
names are not guaranteed to be unique in the VOTable specification,
but column names are required to be unique in
numpy structured arrays (and
astropy.table.Table objects), the names may be renamed by appending
numbers to the end in some cases.
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.
Reading and writing VO model annotations#
Model Instances in VOTables (MIVOT) defines a syntax to map VOTable data to any model serialised in VO-DML (Virtual Observatory Data Modeling Language). This annotation schema operates as a bridge between data and the models. It associates both column/param metadata and data from the VOTable to the data model elements (class, attributes, types, etc.). It also brings up VOTable data or metadata that were possibly missing in the table, e.g., coordinate system description, or curation tracing. The data model elements are grouped in an independent annotation block complying with the MIVOT XML schema which is added as an extra resource above the table element. The MIVOT syntax allows to describe a data structure as a hierarchy of classes. It is also able to represent relations and compositions between them. It can moreover build up data model objects by aggregating instances from different tables of the VOTable.
The purpose of Astropy is not to process VO annotations. It is just to allow related packages to get and set MIVOT blocks from/into VOTables. For this reason, in this implementation MIVOT annotations are both imported and exported as strings. The current implementation prevents client code from injecting into VOTables strings that are not MIVOT serializations.
MIVOT blocks are handled by the
A MivotBlock instance can only be carried by a resource with “type=meta”.
This instance holds the XML mapping block as a string.
MivotBlock objects are instanced by the Resource parser.
The MivotBlock class has its own logic that operates both parsing and IO functionalities.
<VOTABLE xmlns="http://www.ivoa.net/xml/VOTable/v1.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="1.3"> <RESOURCE> <RESOURCE type="meta"> <VODML xmlns="http://www.ivoa.net/xml/mivot"> ... </VODML> </RESOURCE> <TABLE name="myDataTable"> .... </TABLE> </RESOURCE> </VOTABLE>
Reading a VOTable containing a MIVOT block#
To read in a VOTable file containing or not a MIVOT Resource, pass a file path to`~astropy.io.votable.parse`:
>>> from astropy.io.votable import parse >>> from astropy.utils.data import get_pkg_data_filename >>> votable = parse(get_pkg_data_filename("data/test.order.xml", package="astropy.io.votable.tests")) <VODML xmlns="http://www.ivoa.net/xml/mivot"> </VODML> <VODML xmlns="http://www.ivoa.net/xml/mivot"> </VODML>
The parse function will call the MIVOT parser if it detects a MIVOT block.
Building a Resource containing a MIVOT block#
Construct the MIVOT block by passing the XML block as a parameter:
>>> from astropy.io.votable import tree >>> from astropy.io.votable.tree import MivotBlock, Resource, VOTableFile >>> mivot_block = MivotBlock(""" <VODML xmlns="http://www.ivoa.net/xml/mivot" > <REPORT status="OK">Unit test mapping block</REPORT> <GLOBALS> </GLOBALS> </VODML> """)
Build a new resource:
>>> mivot_resource = Resource()
Give it the type meta:
>>> mivot_resource.type = "meta"
Then add it the MIVOT block:
>>> mivot_resource.mivot_block = mivot_block
Now you have a MIVOT resource that you can add to an object Resource creating a new Resource:
>>> votable = VOTableFile() >>> r1 = Resource() >>> r1.type = "results" >>> r1.resources.append(mivot_resource)
You can add an
astropy.io.votable.tree.TableElement to the resource:
>>> table = tree.TableElement(votable) >>> r1.tables.append(t1) >>> votable.resources.append(r1) >>> for resource in votable.resources: ... print(resource.mivot_block.content) <VODML xmlns="http://www.ivoa.net/xml/mivot" > <REPORT status="OK">Unit test mapping block</REPORT> <GLOBALS> </GLOBALS> </VODML>