multispline 0.8.0

Cubic splines in multiple dimensions

multispline

A Python package for generating cubic splines in one, two, or three (hence, multiple) dimensions. The package supports a number of boundary conditions, but is restricted to interpolating data that is spaced on a uniform grid. Documentation and useful examples are provided in the Jupyter notebook tutorial.ipynb. Minimal working examples are also provided below.

Installation

We recommend installing multispline through the package installer pip, but we also provide instructions for installing from source.

Using pip

The easiest way to install multispline is through pip

python3 -m pip install multispline

From source

multispline relies on a few dependencies to install and run, namely a C/C++ compiler (e.g., g++), Cython, numpy, and python >= 3.7, though we recommend using at least Python 3.9. To reduce package conflicts and ensure that the proper dependencies are installed, we recommend using conda and its virtual environments, which can be obtained through the Miniforge distribution.

Create a conda environment spline-env (or whatever name you would like) with the necessary dependencies to install multispline. For MACOSX Intel run:

conda create -n spline-env -c conda-forge Cython numpy clang_osx-64 clangxx_osx-64 python=3.9
conda activate spline-env

This may also work for MACOSX silicon, though alternatively one should use:

conda create -n spline-env -c conda-forge Cython numpy clang_osx-arm64 clangxx_osx-arm64 python=3.9
conda activate spline-env

See Troubleshooting. To instead include the necessary compiler on linux run:

conda create -n spline-env -c conda-forge Cython numpy gcc_linux-64 gxx_linux-64 python=3.9
conda activate spline-env

Next clone the :code:multispline repository from GitHub:

git clone https://github.com/znasipak/multspline.git
cd multispline

Finally, we recommend installing the package via pip:

pip install .

Conda Environments with Jupyter

To run the code in a jupyter notebook, we recommend installing the following dependencies through your preferred package manager, such as conda:

conda install ipykernel matplotlib

One can then make the environment accessible within Jupyter by running

python -m ipykernel install --user --name=multispline-env

Tutorial

Import basic packages

import numpy as np
import matplotlib.pyplot as plt

Cubic Spline (1D)

The class CubicSpline provides a method for interpolating data sampled on a uniform one-dimensional grid.

from multispline.spline import CubicSpline

As a first example we interpolate an oscillatory function, sampled at 100 equidistant points, using CubicSpline

def test_function(x):
    return np.sin(x) + 0.1 * np.cos(10*x)

sample_points = np.linspace(0, 5, 100)
sample_values = test_function(sample_points)

Constructing an interpolating cubic spline is then as simple as initializing the CubicSpline class

cspl = CubicSpline(sample_points, sample_values)

We can evaluate the spline to visually check how well the spline approximates our test function

plt.plot(sample_points, sample_values, '.', label='original')
plt.plot(sample_points, cspl(sample_points), label='spline')
plt.legend()
plt.xlabel('x')
plt.ylabel('f(x)')
plt.show()

To test the accuracy of the spline, we can also evaluate it at values that differ from the sample values

test_points = np.linspace(0, 5, 66)
test_values = test_function(test_points)

plt.plot(test_points, np.abs(test_values - cspl(test_points)), '.')
# plt.legend()
plt.xlabel('x')
plt.yscale('log')
plt.ylabel('Absolute error')
plt.show()

Cubic splines are not fully constrained by the sample data, but require a choice of boundary conditions. We can check the different types of boundary conditions offered by multispline by calling available_boundary_conditions()

from multispline.spline import available_boundary_conditions
available_boundary_conditions()

['natural', 'not-a-knot', 'clamped', 'E(3)']

The default choice is known as the "E(3)" boundary condition. Other boundary conditions may be specified using the optional bc argument when instantiating CubicSpline

cspl_natural = CubicSpline(sample_points, sample_values, bc='natural')

Notice that this new spline will not exactly agree with the original spline

print(cspl_natural(0.001) - cspl(0.001))

-0.00014990567110854947

Different boundary conditions may be better at approximating the behavior of the test function near the boundary. However, which boundary condition works best depends on the problem and the number of sample points. Below, we demonstrate how the "E(3)" boundary condition most accurately approximates the test function near the boundary, though the "not-a-knot" algorithm provides similarly well and more accurately approximates the test function at some points near the boundary.

cspl_bcs = {}
for bc in available_boundary_conditions():
    cspl_bcs[bc] = CubicSpline(sample_points, sample_values, bc=bc)

for bc in available_boundary_conditions():
    plt.plot(test_points[1:-1], np.abs(cspl_bcs[bc](test_points[1:-1]) - test_function(test_points[1:-1])), label=bc)
plt.legend()
plt.yscale('log')
plt.xlabel('x')
plt.ylabel('Absolute error')
plt.show()

We can also evaluate the first and second derivatives of the spline through the methods deriv and deriv2

print(cspl.deriv(0.4325))
print(cspl.deriv2(0.4325))

1.8338073517167228
3.3129057480026125

And we can directly access the spline coefficients through the class property coefficients---which returns a full array of coefficients---or the method coeff which returns a single coefficient for a given interval and polynomial power. (See documentation for more information.)

print(cspl.coefficients[:10, :10])
print(cspl.coefficients[43, 3])
print(cspl.coeff(43, 3))

[[ 1.00000000e-01  5.08213538e-02 -1.35749987e-02  7.52230981e-04]
 [ 1.37998586e-01  2.59280493e-02 -1.13183057e-02  1.40760863e-03]
 [ 1.54015938e-01  7.51426371e-03 -7.09547987e-03  2.06298627e-03]
 [ 1.56497708e-01 -4.87737213e-04 -9.06521058e-04  2.10237484e-03]
 [ 1.57205825e-01  4.00634520e-03  5.40060347e-03  1.63719121e-03]
 [ 1.68249965e-01  1.97191258e-02  1.03121771e-02  7.51166869e-04]
 [ 1.99032435e-01  4.25969806e-02  1.25656777e-02 -3.25688390e-04]
 [ 2.53869404e-01  6.67512708e-02  1.15886125e-02 -1.32673577e-03]
 [ 3.30882552e-01  8.59482885e-02  7.60840521e-03 -2.00129622e-03]
 [ 4.22437949e-01  9.51612103e-02  1.60451654e-03 -2.18099410e-03]]
5.912839775437061e-05
5.912839775437061e-05

More information can be found in the code documentation, which can be accessed, for example, via

?CubicSpline

?CubicSpline.coeff

Bicubic Spline (2D)

The class BicubicSpline provides a method for interpolating data sampled on a uniform two-dimensional grid.

from multispline.spline import BicubicSpline
import numpy as np
import matplotlib.pyplot as plt

As an example, we demonstrate how we can use this class to interpolate a two-dimensional test function

def test_function_2d(x, y):
    return np.sin(x) * np.cos(4*y)

NX = 100
NY = 101
sample_points_x = np.linspace(0, 5, NX)
sample_points_y = np.linspace(0, 5, NY)
sample_grid_xy = np.meshgrid(sample_points_x, sample_points_y, indexing='ij')
sample_values_z = test_function_2d(*sample_grid_xy)

Once again, interpolating the data is as simple as instantiating BicubicSpline. Note that the grid points are passed in as 1D-arrays, while the sample values must be passed on a 2D grid with dimensions (NX, NY)

bspl = BicubicSpline(sample_points_x, sample_points_y, sample_values_z)

We can visually inspect the performance of our interpolating function in one dimension by fixing the value of $x$ or $y$

plt.plot(sample_points_y, sample_values_z[10], '.', label='original')
plt.plot(sample_points_y, bspl(sample_points_x[10], sample_points_y), label='spline')
plt.legend()
plt.xlabel('y')
plt.ylabel(f'f({str(sample_points_x[10])[:7]}, y)')
plt.show()

Alternatively, we can compare the spline against the test function on a grid that differs from the sample grid

test_points_x = np.linspace(0, 5, 66)
test_points_y = np.linspace(0, 5, 66)
test_grid_xy = np.meshgrid(test_points_x, test_points_y, indexing='ij')
test_values_z = test_function_2d(*test_grid_xy)
bspl_values_z = bspl(*test_grid_xy)

Plotting the absolute error in two-dimensions, we see good agreement between the spline and the exact solution

from matplotlib.colors import LogNorm
plt.pcolormesh(*test_grid_xy, np.abs(bspl_values_z - test_values_z), shading='gouraud', norm=LogNorm())
cbar = plt.colorbar()
cbar.set_label('Absolute error', rotation=270, labelpad=15)
plt.xlabel('x')
plt.ylabel('y')
plt.show()

Like CubicSpline, a BicubicSpline can be created using different boundary conditions. At the moment, the code requires that the same boundary condition is used for all dimensions.

One can also evaluate up to two partial derivatives of the spline via the class methods deriv_x, deriv_y, deriv_xx, deriv_yy, and deriv_xy.

Lastly, one can access spline coefficients through the class property coefficients or method coeff

Tricubic Spline (3D)

The class TricubicSpline provides a method for interpolating data sampled on a uniform three-dimensional grid.

from multispline.spline import TricubicSpline

As before, we demonstrate its use by interpolating a three-dimensional test function

def test_function_3d(x, y, z):
    return np.sin(x) * np.cos(4*y) + np.i0(3.2*z)

NX = 65
NY = 100
NZ = 85
sample_points_x = np.linspace(0, 5, NX)
sample_points_y = np.linspace(0, 5, NY)
sample_points_z = np.linspace(-2, 2, NZ)
sample_points_grid = np.meshgrid(sample_points_x, sample_points_y, sample_points_z, indexing='ij')
sample_values_f = test_function_3d(*sample_points_grid)

Like the other spline classes, the spline is created by instantiating TricubicSpline. The grid points are passed in as 1D-arrays, while the sample values must be passed on a 3D grid with dimensions (NX, NY, NZ)

tspl = TricubicSpline(sample_points_x, sample_points_y, sample_points_z, sample_values_f)

We can compare the spline against the test function on a grid that differs from the sample grid

test_points_x = np.linspace(0, 5, 77)
test_points_y = np.linspace(0, 5, 81)
test_points_z = np.linspace(-2, 2, 59)
test_points_grid = np.meshgrid(test_points_x, test_points_y, test_points_z, indexing='ij')
test_values_f = test_function_3d(*test_points_grid)
tspl_values_f = tspl(*test_points_grid)

To make it easier to visualize the comparison, we take the maximum error along the x-axis to reduce the data down to two dimensions.

average_error = np.max(np.abs(tspl_values_f - test_values_f), axis=0)
plot_grid = np.meshgrid(test_points_y, test_points_z, indexing='ij')

Making it easy to plot the results

from matplotlib.colors import LogNorm
plt.pcolormesh(*plot_grid, average_error, shading='gouraud', norm=LogNorm())
cbar = plt.colorbar()
cbar.set_label('Max absolute error in x', rotation=270, labelpad=15)
plt.xlabel('y')
plt.ylabel('z')
plt.show()

Like the other classes, a TricubicSpline can be created using different boundary conditions. At the moment, the code requires that the same boundary condition is used for all dimensions.

One can also evaluate up to two partial derivatives of the spline via the class methods deriv_x, deriv_y , deriv_z, deriv_xx, deriv_yy, deriv_zz, deriv_xy, deriv_yz, and deriv_xz.

Lastly, one can access spline coefficients through the class property coefficients or method coeff

Contributing

Zachary Nasipak

Christian Chapman-Bird