asdf

ASDF (Advanced Scientific Data Format) is a next generation interchange format for scientific data

https://github.com/asdf-format/asdf

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ASDF (Advanced Scientific Data Format) is a next generation interchange format for scientific data

README.rst

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 `__.

The ASDF format has the following features:

* Hierarchical and human-readable metadata in `YAML `__ format
* Efficient binary array storage with support for memory mapping
  and flexible compression.
* Content validation using schemas (using `JSON Schema `__)
* 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
`__. 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 `__ 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 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 `__.

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

.. _begin-pip-install-text:

Stable releases of the ASDF Python package are registered `at
PyPi `__. 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 `__. To clone the project:

::

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

To install:

::

    $ cd asdf
    $ pip install .

To install 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
`__.

::

   $ pip install tox

To list all available environments:

::

   $ tox -va

To run a specific environment:

::

   $ tox -e 


.. _end-testing-text:

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

More detailed documentation on this software package can be found
`here `__.

More information on the ASDF file format itself can be found
`here `__.

There are two mailing lists for ASDF:

* `asdf-users `_
* `asdf-developers `_

    If you are looking for the **A**\ daptable **S**\ eismic **D**\ ata
    **F**\ ormat, information can be found
    `here `__.

License
-------

ASDF is licensed under a BSD 3-clause style license. See `LICENSE.rst `_
for the `licenses folder `_ for
licenses for any included software.

Contributing
------------

We welcome feedback and contributions to the project. Contributions of
code, documentation, or general feedback are all appreciated. Please
follow the `contributing guidelines `__ to submit an
issue or a pull request.

We strive to provide a welcoming community to all of our users by
abiding to the `Code of Conduct `__.

Owner

Citation (CITATION.rst)

If you use ASDF for work/research presented in a publication (whether directly,
as a dependency to another package), please cite the Zenodo DOI for the appropriate
version of ASDF.  The versions (and their BibTeX entries) can be found at:

.. only:: html

    .. include:: ../../README.rst
        :start-after: begin-zenodo:
        :end-before: end-zenodo:

.. only:: latex

    .. admonition:: Zenodo DOI

        https://zenodo.org/badge/latestdoi/18112754

We also recommend and encourage you to cite the general ASDF paper and/or its update:

.. code:: bibtex

    @article{GREENFIELD2015240,
    title = {ASDF: A new data format for astronomy},
    journal = {Astronomy and Computing},
    volume = {12},
    pages = {240-251},
    year = {2015},
    issn = {2213-1337},
    doi = {https://doi.org/10.1016/j.ascom.2015.06.004},
    url = {https://www.sciencedirect.com/science/article/pii/S2213133715000645},
    author = {P. Greenfield and M. Droettboom and E. Bray},
    keywords = {FITS, File formats, Standards, World coordinate system},
    abstract = {We present the case for developing a successor format for the immensely successful FITS format. We first review existing alternative formats and discuss why we do not believe they provide an adequate solution. The proposed format is called the Advanced Scientific Data Format (ASDF) and is based on an existing text format, YAML, that we believe removes most of the current problems with the FITS format. An overview of the capabilities of the new format is given along with specific examples. This format has the advantage that it does not limit the size of attribute names (akin to FITS keyword names) nor place restrictions on the size or type of values attributes have. Hierarchical relationships are explicit in the syntax and require no special conventions. Finally, it is capable of storing binary data within the file in its binary form. At its basic level, the format proposed has much greater applicability than for just astronomical data.}
    }

    @InProceedings{ 00_greenfield-proc-scipy-2022,
    author    = { {P}erry {G}reenfield and {E}dward {S}lavich and {W}illiam {J}amieson and {N}adia {D}encheva },
    title     = { {T}he {A}dvanced {S}cientific {D}ata {F}ormat ({A}{S}{D}{F}): {A}n {U}pdate },
    booktitle = { {P}roceedings of the 21st {P}ython in {S}cience {C}onference },
    pages     = { 1 - 6 },
    year      = { 2022 },
    editor    = { {M}eghann {A}garwal and {C}hris {C}alloway and {D}illon {N}iederhut and {D}avid {S}hupe },
    doi       = { 10.25080/majora-212e5952-000 }
    }

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