.. include:: references.txt
.. |join| replace:: :func:`~astropy.table.join`
.. |Quantity| replace:: :class:`~astropy.units.Quantity`
.. |Time| replace:: :class:`~astropy.time.Time`
.. |SkyCoord| replace:: :class:`~astropy.coordinates.SkyCoord`

.. _mixin_columns:

Mixin columns
***************

Version 1.0 of astropy introduces a new concept of the "Mixin
Column" in tables which allows integration of appropriate non-|Column| based
class objects within a |Table| object.  These mixin column objects are not
converted in any way but are used natively.

The available built-in mixin column classes are:

- |Quantity| and subclasses
- |SkyCoord| and coordinate frame classes
- |Time| and :class:`~astropy.time.TimeDelta`
- :class:`~astropy.coordinates.EarthLocation`
- `~astropy.table.NdarrayMixin`

As a first example we can create a table and add a time column::

  >>> from astropy.table import Table
  >>> from astropy.time import Time
  >>> t = Table()
  >>> t['index'] = [1, 2]
  >>> t['time'] = Time(['2001-01-02T12:34:56', '2001-02-03T00:01:02'])
  >>> print(t)
  index           time
  ----- -----------------------
      1 2001-01-02T12:34:56.000
      2 2001-02-03T00:01:02.000

The important point here is that the ``time`` column is a bona fide |Time| object::

  >>> t['time']
  <Time object: scale='utc' format='isot' value=['2001-01-02T12:34:56.000' '2001-02-03T00:01:02.000']>
  >>> t['time'].mjd  # doctest: +FLOAT_CMP
  array([51911.52425926, 51943.00071759])

.. _quantity_and_qtable:

Quantity and QTable
===================

The ability to natively handle |Quantity| objects within a table makes it
easier to manipulate tabular data with units in a natural and robust way.
However, this feature introduces an ambiguity because data with a unit
(e.g. from a FITS binary table) can be represented as either a |Column| with a
``unit`` attribute or as a |Quantity| object. In order to retain complete
backward compatibility with astropy versions prior to 1.0, a minor variant of
the |Table| class called |QTable| is available.  |QTable| is exactly the same
as |Table| except that |Quantity| is the default for any data column with a
defined unit.

If you take advantage of the |Quantity| infrastructure in your analysis then
|QTable| is the preferred way to create tables with units.  If instead you use
table column units more as a descriptive label then the plain |Table| class is
probably the best class to use.

To illustrate these concepts we first create a standard |Table| where we supply as input a
|Time| object and a |Quantity| object with units of ``m / s``.  In this case
the quantity is converted to a |Column| (which has a ``unit`` attribute but
does not have all the features of a |Quantity|)::

  >>> import astropy.units as u
  >>> t = Table()
  >>> t['index'] = [1, 2]
  >>> t['time'] = Time(['2001-01-02T12:34:56', '2001-02-03T00:01:02'])
  >>> t['velocity'] = [3, 4] * u.m / u.s

  >>> print(t)
  index           time          velocity
                                 m / s
  ----- ----------------------- --------
      1 2001-01-02T12:34:56.000      3.0
      2 2001-02-03T00:01:02.000      4.0

  >>> type(t['velocity'])
  <class 'astropy.table.column.Column'>

  >>> t['velocity'].unit
  Unit("m / s")

  >>> (t['velocity'] ** 2).unit  # WRONG because Column is not smart about unit
  Unit("m / s")

So instead let's do the same thing using a quantity table |QTable|::

  >>> from astropy.table import QTable

  >>> qt = QTable()
  >>> qt['index'] = [1, 2]
  >>> qt['time'] = Time(['2001-01-02T12:34:56', '2001-02-03T00:01:02'])
  >>> qt['velocity'] = [3, 4] * u.m / u.s

The ``velocity`` column is now a |Quantity| and behaves accordingly::

  >>> type(qt['velocity'])
  <class 'astropy.units.quantity.Quantity'>

  >>> qt['velocity'].unit
  Unit("m / s")

  >>> (qt['velocity'] ** 2).unit  # GOOD!
  Unit("m2 / s2")

You can easily convert |Table| to |QTable| and vice-versa::

  >>> qt2 = QTable(t)
  >>> type(qt2['velocity'])
  <class 'astropy.units.quantity.Quantity'>

  >>> t2 = Table(qt2)
  >>> type(t2['velocity'])
  <class 'astropy.table.column.Column'>

.. Note::

   To summarize: the **only** difference between `~astropy.table.QTable` and
   `~astropy.table.Table` is the behavior when adding a column that has a
   specified unit.  With `~astropy.table.QTable` such a column is always
   converted to a `~astropy.units.Quantity` object before being added to the
   table.  Likewise if a unit is specified for an existing unit-less
   `~astropy.table.Column` in a `~astropy.table.QTable`, then the column is
   converted to `~astropy.units.Quantity`.

   The converse is that if one adds a `~astropy.units.Quantity` column to an
   ordinary `~astropy.table.Table` then it gets converted to an ordinary
   `~astropy.table.Column` with the corresponding ``unit`` attribute.

.. _mixin_attributes:

Mixin Attributes
================

The usual column attributes ``name``, ``dtype``, ``unit``, ``format``, and
``description`` are available in any mixin column via the ``info`` property::

  >>> qt['velocity'].info.name
  'velocity'

This ``info`` property is a key bit of glue that allows for a
non-Column object to behave much like a column.

The same ``info`` property is also available in standard
`~astropy.table.Column` objects.  These ``info`` attributes like
``t['a'].info.name`` simply refer to the direct `~astropy.table.Column`
attribute (e.g. ``t['a'].name``) and can be used interchangeably.
Likewise in a `~astropy.units.Quantity` object, ``info.dtype``
attribute refers to the native ``dtype`` attribute of the object.

.. Note::

   When writing generalized code that handles column objects which
   might be mixin columns, one must *always* use the ``info``
   property to access column attributes.


.. _details_and_caveats:

Details and caveats
===================

Most common table operations behave as expected when mixin columns are part of
the table.  However, there are limitations in the current implementation.

**Adding or inserting a row**

Adding or inserting a row works as expected only for mixin classes that are
mutable (data can changed internally) and that have an ``insert()`` method.
|Quantity| and |Time| support ``insert()`` but for example |SkyCoord| does not.
If one tried to insert a row into a table with a |SkyCoord| column then
an exception like the following would occur::

  ValueError: Unable to insert row because of exception in column 'skycoord':
  'SkyCoord' object has no attribute 'insert'

**Initializing from a list of rows or a list of dicts**

This mode of initializing a table does not work with mixin columns, so both of
the following will fail::

   >>> qt = QTable([{'a': 1 * u.m, 'b': 2},
   ...              {'a': 2 * u.m, 'b': 3}])  # doctest: +SKIP
   Traceback (most recent call last):
    ...
   TypeError: only dimensionless scalar quantities can be converted to Python scalars

   >>> qt = QTable(rows=[[1 * u.m, 2],
   ...                   [2 * u.m, 3]])  # doctest: +SKIP
   Traceback (most recent call last):
    ...
   TypeError: only dimensionless scalar quantities can be converted to Python scalars

The problem lies in knowing if and how to assemble the individual elements
for each column into an appropriate mixin column.  The current code uses
numpy to perform this function on numerical or string types, but it
does not handle mixin column types like |Quantity| or |SkyCoord|.

**Masking**

Mixin columns do not generally support masking (with the exception of |Time|),
but there is limited support for use of
mixins within a masked table.  In this case a ``mask`` attribute is assigned to
the mixin column object.  This ``mask`` is a special object that is a boolean
array of ``False`` corresponding to the mixin data shape.  The ``mask`` looks
like a normal numpy array but an exception will be raised if ``True`` is assigned
to any element.  The consequences of the limitation are most apparent in the
high-level table operations.

**High-level table operations**

The table below gives a summary of support for high-level operations on tables
that contain mixin columns:

.. list-table::
   :header-rows: 1
   :widths: 28 72

   * - Operation
     - Support
   * - :ref:`grouped-operations`
     - Not implemented yet, but no fundamental limitation
   * - :ref:`stack-vertically`
     - Available for `~astropy.units.Quantity` subclasses, |Time|
       and any other mixin classes that provide a
       `new_like() method`_ in the ``info`` descriptor.
   * - :ref:`stack-horizontally`
     - Works if output mixin column supports masking or if no masking is required
   * - :ref:`table-join`
     - Works if output mixin column supports masking or if no masking is required; key
       columns must be subclasses of `numpy.ndarray`.
   * - :ref:`unique-rows`
     - Not implemented yet, uses grouped operations

**ASCII table writing**

Tables with mixin columns can be written out to file using the `astropy.io.ascii` module,
but the fast C-based writers are not available.  Instead the pure-Python
writers will be used.  For writing tables with mixin columns it is recommended
to use the ``'ecsv'`` ASCII format.  This will fully serialize the table data and
metadata, allowing full "round-trip" of the table when it is read back.  See
:ref:`ecsv_format` for details.

**Binary table writing**

Starting with astropy 3.0, tables with mixin columns can be written in binary
format to file using both FITS and HDF5 formats.  These can be read back to
recover exactly the original Table including mixin columns and metadata. See
:ref:`table_io` for details.

.. _mixin_protocol:

Mixin protocol
==============

A key idea behind mixin columns is that any class which satisfies a specified
protocol can be used.  That means many user-defined class objects which handle
array-like data can be used natively within a |Table|.  The protocol is
relatively simple and requires that a class behave like a minimal numpy array
with the following properties:

- Contains array-like data
- Implements ``__getitem__`` to support getting data as a
  single item, slicing, or index array access
- Has a ``shape`` attribute
- Has a ``__len__`` method for length
- Has an ``info`` class descriptor which is a subclass of the
  ``astropy.utils.data_info.MixinInfo`` class.

The `Example: ArrayWrapper`_ section shows a working minimal example of a class
which can be used as a mixin column.  A `pandas.Series
<http://pandas.pydata.org/pandas-docs/stable/generated/pandas.Series.html>`_
object can function as a mixin column as well.

Other interesting possibilities for mixin columns include:

- Columns which are dynamically computed as a function of other columns (AKA
  spreadsheet)
- Columns which are themselves a |Table|, i.e. nested tables.  A `proof of
  concept <https://github.com/astropy/astropy/pull/3963>`_ is available.

new_like() method
~~~~~~~~~~~~~~~~~

In order to support high-level operations like `~astropy.table.join` and
`~astropy.table.vstack`, a mixin class must provide a ``new_like()`` method
in the ``info`` class descriptor.  A key part of the functionality is to ensure
that the input column metadata are merged appropriately and that the columns
have consistent properties such as the shape.

A mixin class that provides ``new_like()`` must also implement ``__setitem__``
to support setting via a single item, slicing, or index array.

The ``new_like`` method has the following signature::

    def new_like(self, cols, length, metadata_conflicts='warn', name=None):
        """
        Return a new instance of this class which is consistent with the
        input ``cols`` and has ``length`` rows.

        This is intended for creating an empty column object whose elements can
        be set in-place for table operations like join or vstack.

        Parameters
        ----------
        cols : list
            List of input columns
        length : int
            Length of the output column object
        metadata_conflicts : str ('warn'|'error'|'silent')
            How to handle metadata conflicts
        name : str
            Output column name

        Returns
        -------
        col : object
            New instance of this class consistent with ``cols``
        """

Examples of this are found in the `~astropy.table.column.ColumnInfo` and
`~astropy.units.quantity.QuantityInfo` classes.


.. _arraywrapper_example:

Example: ArrayWrapper
=====================

The code listing below shows a example of a data container class which acts as
a mixin column class.  This class is a simple wrapper around a numpy array.  It
is used in the astropy mixin test suite and is fully compliant as a mixin
column.

::

  from astropy.utils.data_info import ParentDtypeInfo

  class ArrayWrapper(object):
      """
      Minimal mixin using a simple wrapper around a numpy array
      """
      info = ParentDtypeInfo()

      def __init__(self, data):
          self.data = np.array(data)
          if 'info' in getattr(data, '__dict__', ()):
              self.info = data.info

      def __getitem__(self, item):
          if isinstance(item, (int, np.integer)):
              out = self.data[item]
          else:
              out = self.__class__(self.data[item])
              if 'info' in self.__dict__:
                  out.info = self.info
          return out

      def __setitem__(self, item, value):
          self.data[item] = value

      def __len__(self):
          return len(self.data)

      @property
      def dtype(self):
          return self.data.dtype

      @property
      def shape(self):
          return self.data.shape

      def __repr__(self):
          return ("<{0} name='{1}' data={2}>"
                  .format(self.__class__.__name__, self.info.name, self.data))