ASDF - Advanced Scientific Data Format

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.. _begin-summary-text:

The A\ dvanced S\ cientific D\ ata F\ ormat (ASDF) is a next-generation interchange format for scientific data. This package contains the Python implementation of the ASDF specification. More information on the ASDF file format including the specification can be found here <https://asdf-standard.readthedocs.io>__.

The ASDF format has the following features:

• Hierarchical and human-readable metadata in YAML <http://yaml.org>__ format
• Efficient binary array storage with support for memory mapping and flexible compression.
• Content validation using schemas (using JSON Schema <http://json-schema.org>__)
• Native and transparent support for most basic Python data types, with an extension API to add support for any custom Python object.

.. _end-summary-text:

ASDF is under active development on github <https://github.com/asdf-format/asdf>. More information on contributing can be found below <#contributing>.

Overview

This section outlines basic use cases of the ASDF package for creating and reading ASDF files.

Creating a file

.. _begin-create-file-text:

We're going to store several `numpy` arrays and other data to an ASDF file. We
do this by creating a "tree", which is simply a `dict`, and we provide it as
input to the constructor of `AsdfFile`:

.. code:: python

    import asdf
    import numpy as np

    # Create some data
    sequence = np.arange(100)
    squares = sequence**2
    random = np.random.random(100)

    # Store the data in an arbitrarily nested dictionary
    tree = {
        "foo": 42,
        "name": "Monty",
        "sequence": sequence,
        "powers": {"squares": squares},
        "random": random,
    }

    # Create the ASDF file object from our data tree
    af = asdf.AsdfFile(tree)

    # Write the data to a new file
    af.write_to("example.asdf")

If we open the newly created file's metadata section, we can see some of the key features
of ASDF on display:

.. _begin-example-asdf-metadata:

.. code:: yaml

    #ASDF 1.0.0
    #ASDF_STANDARD 1.2.0
    %YAML 1.1
    %TAG ! tag:stsci.edu:asdf/
    --- !core/asdf-1.1.0
    asdf_library: !core/software-1.0.0 {author: The ASDF Developers, homepage: 'http://github.com/asdf-format/asdf',
      name: asdf, version: 2.0.0}
    history:
      extensions:
      - !core/extension_metadata-1.0.0
        extension_class: asdf.extension.BuiltinExtension
        software: {name: asdf, version: 2.0.0}
    foo: 42
    name: Monty
    powers:
      squares: !core/ndarray-1.0.0
        source: 1
        datatype: int64
        byteorder: little
        shape: [100]
    random: !core/ndarray-1.0.0
      source: 2
      datatype: float64
      byteorder: little
      shape: [100]
    sequence: !core/ndarray-1.0.0
      source: 0
      datatype: int64
      byteorder: little
      shape: [100]
    ...

.. _end-example-asdf-metadata:

The metadata in the file mirrors the structure of the tree that was stored. It
is hierarchical and human-readable. Notice that metadata has been added to the
tree that was not explicitly given by the user. Notice also that the numerical
array data is not stored in the metadata tree itself. Instead, it is stored as
binary data blocks below the metadata section (not shown above).

.. _end-create-file-text:
.. _begin-compress-file:

It is possible to compress the array data when writing the file:

.. code:: python

    af.write_to("compressed.asdf", all_array_compression="zlib")

The built-in compression algorithms are ``'zlib'``, and ``'bzp2'``.  The
``'lz4'`` algorithm becomes available when the `lz4 <https://python-lz4.readthedocs.io/>`__ package
is installed.  Other compression algorithms may be available via extensions.

.. _end-compress-file:

Reading a file
~~~~~~~~~~~~~~

.. _begin-read-file-text:

To read an existing ASDF file, we simply use the top-level `open` function of
the `asdf` package:

.. code:: python

    import asdf

    af = asdf.open("example.asdf")

The `open` function also works as a context handler:

.. code:: python

    with asdf.open("example.asdf") as af:
        ...

.. warning::
    The ``memmap`` argument replaces ``copy_arrays`` as of ASDF 4.0
    (``memmap == not copy_arrays``).

To get a quick overview of the data stored in the file, use the top-level
`AsdfFile.info()` method:

.. code:: pycon

    >>> import asdf
    >>> af = asdf.open("example.asdf")
    >>> af.info()
    root (AsdfObject)
    ├─asdf_library (Software)
    │ ├─author (str): The ASDF Developers
    │ ├─homepage (str): http://github.com/asdf-format/asdf
    │ ├─name (str): asdf
    │ └─version (str): 2.8.0
    ├─history (dict)
    │ └─extensions (list)
    │   └─[0] (ExtensionMetadata)
    │     ├─extension_class (str): asdf.extension.BuiltinExtension
    │     └─software (Software)
    │       ├─name (str): asdf
    │       └─version (str): 2.8.0
    ├─foo (int): 42
    ├─name (str): Monty
    ├─powers (dict)
    │ └─squares (NDArrayType): shape=(100,), dtype=int64
    ├─random (NDArrayType): shape=(100,), dtype=float64
    └─sequence (NDArrayType): shape=(100,), dtype=int64

The `AsdfFile` behaves like a Python `dict`, and nodes are accessed like
any other dictionary entry:

.. code:: pycon

    >>> af["name"]
    'Monty'
    >>> af["powers"]
    {'squares': <array (unloaded) shape: [100] dtype: int64>}

Array data remains unloaded until it is explicitly accessed:

.. code:: pycon

    >>> af["powers"]["squares"]
    array([   0,    1,    4,    9,   16,   25,   36,   49,   64,   81,  100,
            121,  144,  169,  196,  225,  256,  289,  324,  361,  400,  441,
            484,  529,  576,  625,  676,  729,  784,  841,  900,  961, 1024,
           1089, 1156, 1225, 1296, 1369, 1444, 1521, 1600, 1681, 1764, 1849,
           1936, 2025, 2116, 2209, 2304, 2401, 2500, 2601, 2704, 2809, 2916,
           3025, 3136, 3249, 3364, 3481, 3600, 3721, 3844, 3969, 4096, 4225,
           4356, 4489, 4624, 4761, 4900, 5041, 5184, 5329, 5476, 5625, 5776,
           5929, 6084, 6241, 6400, 6561, 6724, 6889, 7056, 7225, 7396, 7569,
           7744, 7921, 8100, 8281, 8464, 8649, 8836, 9025, 9216, 9409, 9604,
           9801])

    >>> import numpy as np
    >>> expected = [x**2 for x in range(100)]
    >>> np.equal(af["powers"]["squares"], expected).all()
    True

Memory mapping can be enabled by providing ``memmap=True``
to `open`:

.. code:: python

    af = asdf.open("example.asdf", memmap=True)

.. _end-read-file-text:

For more information and for advanced usage examples, see the
`documentation <#documentation>`__.

Extending ASDF
~~~~~~~~~~~~~~

Out of the box, the ``asdf`` package automatically serializes and
deserializes native Python types. It is possible to extend ``asdf`` by
implementing custom tags that correspond to custom user types. More
information on extending ASDF can be found in the `official
documentation <http://asdf.readthedocs.io/en/latest/#extending-asdf>`__.

Installation
------------

.. _begin-pip-install-text:

Stable releases of the ASDF Python package are registered `at
PyPi <https://pypi.python.org/pypi/asdf>`__. The latest stable version
can be installed using ``pip``:

::

    $ pip install asdf

.. _begin-source-install-text:

The latest development version of ASDF is available from the ``main`` branch
`on github <https://github.com/asdf-format/asdf>`__. To clone the project:

::

    $ git clone https://github.com/asdf-format/asdf

To install:

::

    $ cd asdf
    $ pip install .

To install in `development
mode <https://packaging.python.org/tutorials/distributing-packages/#working-in-development-mode>`__::

    $ pip install -e .

.. _end-source-install-text:

Testing
-------

.. _begin-testing-text:

To install the test dependencies from a source checkout of the repository:

::

    $ pip install -e ".[tests]"

To run the unit tests from a source checkout of the repository:

::

    $ pytest

It is also possible to run the test suite from an installed version of
the package.

::

    $ pip install "asdf[tests]"
    $ pytest --pyargs asdf

It is also possible to run the tests using `tox
<https://tox.readthedocs.io/en/latest/>`__.

::

   $ pip install tox

To list all available environments:

::

   $ tox -va

To run a specific environment:

::

   $ tox -e <envname>


.. _end-testing-text:

Documentation
-------------

More detailed documentation on this software package can be found
`here <https://asdf.readthedocs.io>`__.

More information on the ASDF file format itself can be found
`here <https://asdf-standard.readthedocs.io>`__.

There are two mailing lists for ASDF:

* `asdf-users <https://groups.google.com/forum/#!forum/asdf-users>`_
* `asdf-developers <https://groups.google.com/forum/#!forum/asdf-developer