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- VOTable XML handling (`astropy.io.votable`)

# 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 `parse`:

    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 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 `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 `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 `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:

    <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>

Note

The mapping from VOTable `name` and `ID` attributes to Numpy dtype `names` and `titles` is highly confusing.

In VOTable, `ID` is guaranteed to be unique, but is not required. `name` is not guaranteed to be unique, but is required.

In Numpy record dtypes, `names` are required to be unique and are required. `titles` are not required, and are not required to be unique.

Therefore, VOTable’s `ID` most closely maps to Numpy’s `names`, and VOTable’s `name` most closely maps to Numpy’s `titles`. However, in some cases where a VOTable `ID` is not provided, a Numpy `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 a `astropy.io.votable.tree.Table` object to an `astropy.table.Table` object, one can specify whether to give preference to `name` or `ID` attributes when naming the columns. By default, `ID` is given preference. To give `name` preference, pass the keyword argument `use_names_over_ids=True`:

    >>> votable.get_first_table().to_table(use_names_over_ids=True)

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 `to_xml` method. It accepts either a string or Unicode path, or a Python file-like object:

    votable.to_xml('output.xml')

There are a number of 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. VOTable version 1.3 adds the `BINARY2` format, which allows for masking of any data type, including integers and bit fields which can not be masked in the older `BINARY` format. The storage format can be set on a per-table basis using the `format` attribute, or globally using the `set_all_tables_format` method:

    votable.get_first_table().format = 'binary'
    votable.set_all_tables_format('binary')
    votable.to_xml('binary.xml')

## Using `astropy.io.votable`

### Standard compliance

`astropy.io.votable.tree.Table` supports the VOTable Format Definition Version 1.1, Version 1.2, and the Version 1.3 proposed recommendation. 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 Warnings and Exceptions.

Output always conforms to the 1.1, 1.2 or 1.3 spec, depending on the input.

#### 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 `parse` or `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 `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 `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 `get_field_by_id` method, which returns the `Field` object with the given ID. For example:

    >>> field = table.get_field_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.

### 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 `base64`-encoded blob.
- 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.
- FITS stores the data in an external FITS file. This serialization is not supported by the `astropy.io.votable` writer, since it requires writing multiple files.

The serialization format can be selected in two ways:

> 1) By setting the `format` attribute of a `astropy.io.votable.tree.Table` object:

>     votable.get_first_table().format = "binary"
>     votable.to_xml("new_votable.xml")

> 2) By overriding the format of all tables using the `tabledata_format` keyword argument when writing out a VOTable file:

>     votable.to_xml("new_votable.xml", tabledata_format="binary")

### 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")

Note

By default, `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, set the `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 thus `astropy.table.Table` objects), the names may be renamed by appending numbers to the end in some cases.

### 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.

## See Also

- VOTable Format Definition Version 1.1
- VOTable Format Definition Version 1.2
- VOTable Format Definition Version 1.3, Proposed Recommendatation

## Reference/API

### astropy.io.votable Package

This package reads and writes data formats used by the Virtual Observatory (VO) initiative, particularly the VOTable XML format.

#### Functions

`parse`(source[, columns, invalid, pedantic, ...]) | Parses a VOTABLE xml file (or file-like object), and returns a `VOTableFile` object.
`parse_single_table`(source, **kwargs) | Parses a VOTABLE xml file (or file-like object), reading and returning only the first `Table` instance.
`validate`(source[, output, xmllint, filename]) | Prints a validation report for the given file.
`from_table`(table[, table_id]) | Given an `Table` object, return a `VOTableFile` file structure containing just that single table.
`is_votable`(source) | Reads the header of a file to determine if it is a VOTable file.
`writeto`(table, file[, tabledata_format]) | Writes a `VOTableFile` to a VOTABLE xml file.

#### Classes

`Conf` | Configuration parameters for `astropy.io.votable`.

### astropy.io.votable.tree Module

#### Classes

`Link` | LINK elements: used to reference external documents and servers through a URI.
`Info` | INFO elements: arbitrary key-value pairs for extensions to the standard.
`Values` | VALUES element: used within FIELD and PARAM elements to define the domain of values.
`Field` | FIELD element: describes the datatype of a particular column of data.
`Param` | PARAM element: constant-valued columns in the data.
`CooSys` | COOSYS element: defines a coordinate system.
`FieldRef`(table, ref[, ucd, utype, config, pos]) | FIELDref element: used inside of GROUP elements to refer to remote FIELD elements.
`ParamRef` | PARAMref element: used inside of GROUP elements to refer to remote PARAM elements.
`Group` | GROUP element: groups FIELD and PARAM elements.
`Table` | TABLE element: optionally contains data.
`Resource` | RESOURCE element: Groups TABLE and RESOURCE elements.
`VOTableFile` | VOTABLE element: represents an entire file.

### astropy.io.votable.converters Module

This module handles the conversion of various VOTABLE datatypes to/from TABLEDATA and BINARY formats.

#### Functions

`get_converter`(field[, config, pos]) | Get an appropriate converter instance for a given field.
`table_column_to_votable_datatype`(column) | Given a `astropy.table.Column` instance, returns the attributes necessary to create a VOTable FIELD element that corresponds to the type of the column.

#### Classes

`Converter`(field[, config, pos]) | The base class for all converters.

### astropy.io.votable.ucd Module

This file contains routines to verify the correctness of UCD strings.

#### Functions

`parse_ucd`(ucd[, ...]) | Parse the UCD into its component parts.
`check_ucd`(ucd[, ...]) | Returns False if ucd is not a valid unified content descriptor.

### astropy.io.votable.util Module

Various utilities and cookbook-like things.

#### Functions

`convert_to_writable_filelike`(*args, **kwds) | Returns a writable file-like object suitable for streaming output.
`coerce_range_list_param`(p[, frames, numeric]) | Coerces and/or verifies the object p into a valid range-list-format parameter.

### astropy.io.votable.validator Package

Validates a large collection of web-accessible VOTable files, and generates a report as a directory tree of HTML files.

#### Functions

`make_validation_report`([urls, destdir, ...]) | Validates a large collection of web-accessible VOTable files.

### astropy.io.votable.xmlutil Module

Various XML-related utilities

#### Functions

`check_id`(ID[, name, config, pos]) | Raises a `VOTableSpecError` if ID is not a valid XML ID.
`fix_id`(ID[, config, pos]) | Given an arbitrary string, create one that can be used as an xml id.
`check_token`(token, attr_name[, config, pos]) | Raises a `ValueError` if token is not a valid XML token.
`check_mime_content_type`(content_type[, ...]) | Raises a `VOTableSpecError` if content_type is not a valid MIME content type.
`check_anyuri`(uri[, config, pos]) | Raises a `VOTableSpecError` if uri is not a valid URI.
`validate_schema`(filename[, version]) | Validates the given file against the appropriate VOTable schema.

### astropy.io.votable.exceptions Module

- `astropy.io.votable.exceptions`