ndsplines

ndsplines: A Python Library for Tensor-Product B-Splines of Arbitrary Dimension - Published in JOSS (2019)

https://github.com/kb-press/ndsplines

Keywords from Contributors

Scientific Fields

Repository

Multi-dimensional B-splines

readme.rst

=========
ndsplines
=========

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This is a Python package for multivariate B-splines with a performant Cython
implementation. For a mathematical overview of tensor product B-splines, see the
|Splines| page of the documentation.

The primary goal of this package is to provide a unified API for tensor product
splines of arbitrary input and output dimension. For a list of related packages
see the |Comparisons| page.

.. |Splines| replace:: `Splines`_
.. _Splines: https://ndsplines.readthedocs.io/en/latest/math.html

.. |Comparisons| replace:: `Comparisons`_
.. _Comparisons: https://ndsplines.readthedocs.io/en/latest/compare.html

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

``ndsplines`` is available on PyPI as well as conda-forge.

pip
^^^

Install ``ndsplines`` with pip::

    $ pip install ndsplines

Wheels are provided for a range of Python versions and platforms, so no
compilation is required to get the better-performing Cython-based implementation
in many cases.

If no matching wheel is found, pip will install build dependencies and attempt
to compile the Cython-based extension module.

conda
^^^^^

Install ``ndsplines`` with conda::

    $ conda install -c conda-forge ndsplines

Usage
-----

The easiest way to use ``ndsplines`` is to use one of the ``make_*``
functions: ``make_interp_spline``, ``make_interp_spline_from_tidy``, or
``make_lsq_spline``, which return an ``NDSpline`` object which can be used to
evaluate the spline. For example, suppose we have data over a two-dimensional
mesh.

.. code:: python

    import ndsplines
    import numpy as np

    # generate grid of independent variables
    x = np.array([-1, -7/8, -3/4, -1/2, -1/4, -1/8, 0, 1/8, 1/4, 1/2, 3/4, 7/8, 1])*np.pi
    y = np.array([-1, -1/2, 0, 1/2, 1])
    meshx, meshy = np.meshgrid(x, y, indexing='ij')
    gridxy = np.stack((meshx, meshy), axis=-1)

    # evaluate a function to interpolate over input grid
    meshf = np.sin(meshx) * (meshy-3/8)**2 + 2


We can then use ``make_interp_spline`` to create an interpolating spline and
evaluate it over a denser mesh.

.. code:: python

    # create the interpolating spline
    interp = ndsplines.make_interp_spline(gridxy, meshf)

    # generate denser grid of independent variables to interpolate
    sparse_dense = 2**7
    xx = np.concatenate([np.linspace(x[i], x[i+1], sparse_dense) for i in range(x.size-1)])
    yy = np.concatenate([np.linspace(y[i], y[i+1], sparse_dense) for i in range(y.size-1)])
    gridxxyy = np.stack(np.meshgrid(xx, yy, indexing='ij'), axis=-1)

    # evaluate spline over denser grid
    meshff = interp(gridxxyy)


Generally, we construct data so that the first ``ndim`` axes index the
independent variables and the remaining axes index output. This is
a generalization of using rows to index time and columns to index output
variables for time-series data.

We can also create an interpolating spline from a `tidy data`_ format:

.. code:: python

    tidy_data = np.dstack((gridxy, meshf)).reshape((-1,3))
    tidy_interp = ndsplines.make_interp_spline_from_tidy(
        tidy_data,
        [0,1], # columns to use as independent variable data
        [2]    # columns to use as dependent variable data
    )

    print("\nCoefficients all same?",
          np.all(tidy_interp.coefficients == interp.coefficients))
    print("Knots all same?",
          np.all([np.all(k0 == k1) for k0, k1 in zip(tidy_interp.knots, interp.knots)]))

Note however, that the tidy dataset must be over a structured rectangular grid
equivalent to the N-dimensional tensor product representation. Also note that
Pandas dataframes can be used, in which case lists of column names can be used
instead of lists of column indices.

To see examples for creating least-squares regression splines
with ``make_lsq_spline``, see the |1D example| and |2D example|.

Derivatives of constructed splines can be evaluated in two ways: (1) by using
the ``nus`` parameter while calling the interpolator or (2) by creating a new spline
with the ``derivative`` method. In this codeblock, we show both ways of
evaluating derivatives in each direction.

.. code:: python

    # two ways to evaluate derivatives x-direction: create a derivative spline or call with nus:
    deriv_interp = interp.derivative(0)
    deriv1 = deriv_interp(gridxxy)
    deriv2 = interp(gridxy, nus=np.array([1,0]))

    # two ways to evaluate derivative - y direction
    deriv_interp = interp.derivative(1)
    deriv1 = deriv_interp(gridxy)
    deriv2 = interp(gridxxyy, nus=np.array([0,1]))

The ``NDSpline`` class also has an ``antiderivative`` method for creating a
spline representative of the anti-derivative in the specified direction.

.. code:: python

    # Calculus demonstration
    interp1 = deriv_interp.antiderivative(0)
    coeff_diff = interp1.coefficients - interp.coefficients
    print("\nAntiderivative of derivative:\n","Coefficients differ by constant?",
          np.allclose(interp1.coefficients+2.0, interp.coefficients))
    print("Knots all same?",
          np.all([np.all(k0 == k1) for k0, k1 in zip(interp1.knots, interp.knots)]))

    antideriv_interp = interp.antiderivative(0)
    interp2 = antideriv_interp.derivative(0)
    print("\nDerivative of antiderivative:\n","Coefficients the same?",
          np.allclose(interp2.coefficients, interp.coefficients))
    print("Knots all same?",
          np.all([np.all(k0 == k1) for k0, k1 in zip(interp2.knots, interp.knots)]))

.. _tidy data: https://www.jstatsoft.org/article/view/v059i10

.. |1D example| replace:: `1D example`_
.. _1D example: https://ndsplines.readthedocs.io/en/latest/auto_examples/1d-lsq.html

.. |2D example| replace:: `2D example`_
.. _2D example: https://ndsplines.readthedocs.io/en/latest/auto_examples/2d-lsq.html

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

Please feel free to share any thoughts or opinions about the design and
implementation of this software by `opening an issue on GitHub
`_. Constructive feedback is
welcomed and appreciated.

Bug fix pull requests are always welcome. For feature additions, breaking
changes, etc. check if there is an open issue discussing the change and
reference it in the pull request. If there isn't one, it is recommended to open
one with your rationale for the change before spending significant time
preparing the pull request.

Ideally, new/changed functionality should come with tests and documentation. If
you are new to contributing, it is perfectly fine to open a work-in-progress
pull request and have it iteratively reviewed.

Testing
-------

To test, install the package with the ``test`` extras and use ``pytest``::

    $ pip install .[test]
    $ pytest

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

Documentation is based on Sphinx and built and served by Read the Docs. To
build locally, install the ``docs`` requirements::

    $ pip install .[docs]
    $ cd docs
    $ make html

Owner

JOSS Publication

ndsplines: A Python Library for Tensor-Product B-Splines of Arbitrary Dimension

Published

October 25, 2019

DOI

10.21105/joss.01745

Volume 4, Issue 42, Page 1745

Authors

Benjamin W. l. Margolis
University of California, Davis

Kenneth R. Lyons
University of California, Davis

Editor

Monica Bobra

Tags

interpolation spline

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