.. _begin-badges:
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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 Standard. More
information on the ASDF Standard itself can be found
here <https://asdf-standard.readthedocs.io>__.
The ASDF format has the following features:
YAML <http://yaml.org>__)JSON Schema <http://json-schema.org>__).. _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>.
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=int64The 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()
TrueBy default, uncompressed data blocks are memory mapped for efficient
access. Memory mapping can be disabled by using the memmap
option of open when reading:
.. code:: python
af = asdf.open("example.asdf", memmap=False).. _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 Standard 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-developers>`_
If you are looking for the **A**\ daptable **S**\ eismic **D**\ ata
**F**\ ormat, information can be found
`here <https://seismic-data.org/>`__.
License
-------
ASDF is licensed under a BSD 3-clause style license. See `LICENSE.rst <LICENSE.rst>`_
for the `licenses folder <licenses>`_ 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 <CONTRIBUTING.rst>`__ 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 <CODE_OF_CONDUCT.md>`__.