PyKrige 1.4.0

Installation

PyKrige requires Python 2.7 or 3.5+ as well as numpy, scipy and matplotlib. It can be installed from PyPi with,

pip install pykrige

scikit-learn is an optional dependency needed for parameter tuning and regression kriging.

If you use conda, PyKrige can be installed from the conda-forge channel with,

conda install -c conda-forge pykrige

Ordinary Kriging Example

First we will create a 2D dataset together with the associated x, y grids,

import numpy as np
import pykrige.kriging_tools as kt

data = np.array([[0.3, 1.2, 0.47],
                 [1.9, 0.6, 0.56],
                 [1.1, 3.2, 0.74],
                 [3.3, 4.4, 1.47],
                 [4.7, 3.8, 1.74]])

gridx = np.arange(0.0, 5.5, 0.5)
gridy = np.arange(0.0, 5.5, 0.5)

# Create the ordinary kriging object. Required inputs are the X-coordinates of
# the data points, the Y-coordinates of the data points, and the Z-values of the
# data points. If no variogram model is specified, defaults to a linear variogram
# model. If no variogram model parameters are specified, then the code automatically
# calculates the parameters by fitting the variogram model to the binned
# experimental semivariogram. The verbose kwarg controls code talk-back, and
# the enable_plotting kwarg controls the display of the semivariogram.
OK = OrdinaryKriging(data[:, 0], data[:, 1], data[:, 2], variogram_model='linear',
                     verbose=False, enable_plotting=False)

# Creates the kriged grid and the variance grid. Allows for kriging on a rectangular
# grid of points, on a masked rectangular grid of points, or with arbitrary points.
# (See OrdinaryKriging.__doc__ for more information.)
z, ss = OK.execute('grid', gridx, gridy)

# Writes the kriged grid to an ASCII grid file.
kt.write_asc_grid(gridx, gridy, z, filename="output.asc")

Universal Kriging Example

from pykrige.uk import UniversalKriging
import numpy as np

data = np.array([[0.3, 1.2, 0.47],
                 [1.9, 0.6, 0.56],
                 [1.1, 3.2, 0.74],
                 [3.3, 4.4, 1.47],
                 [4.7, 3.8, 1.74]])

gridx = np.arange(0.0, 5.5, 0.5)
gridy = np.arange(0.0, 5.5, 0.5)

# Create the ordinary kriging object. Required inputs are the X-coordinates of
# the data points, the Y-coordinates of the data points, and the Z-values of the
# data points. Variogram is handled as in the ordinary kriging case.
# drift_terms is a list of the drift terms to include; currently supported terms
# are 'regional_linear', 'point_log', and 'external_Z'. Refer to
# UniversalKriging.__doc__ for more information.
UK = UniversalKriging(data[:, 0], data[:, 1], data[:, 2], variogram_model='linear',
                      drift_terms=['regional_linear'])

# Creates the kriged grid and the variance grid. Allows for kriging on a rectangular
# grid of points, on a masked rectangular grid of points, or with arbitrary points.
# (See UniversalKriging.__doc__ for more information.)
z, ss = UK.execute('grid', gridx, gridy)

Three-Dimensional Kriging Example

from pykrige.ok3d import OrdinaryKriging3D
from pykrige.uk3d import UniversalKriging3D
import numpy as np

data = np.array([[0.1, 0.1, 0.3, 0.9],
                                 [0.2, 0.1, 0.4, 0.8],
                                 [0.1, 0.3, 0.1, 0.9],
                                 [0.5, 0.4, 0.4, 0.5],
                                 [0.3, 0.3, 0.2, 0.7]])

gridx = np.arange(0.0, 0.6, 0.05)
gridy = np.arange(0.0, 0.6, 0.01)
gridz = np.arange(0.0, 0.6, 0.1)

# Create the 3D ordinary kriging object and solves for the three-dimension kriged
# volume and variance. Refer to OrdinaryKriging3D.__doc__ for more information.
ok3d = OrdinaryKriging3D(data[:, 0], data[:, 1], data[:, 2], data[:, 3],
                                                 variogram_model='linear')
k3d, ss3d = ok3d.execute('grid', gridx, gridy, gridz)

# Create the 3D universal kriging object and solves for the three-dimension kriged
# volume and variance. Refer to UniversalKriging3D.__doc__ for more information.
uk3d = UniversalKriging3D(data[:, 0], data[:, 1], data[:, 2], data[:, 3],
                                                  variogram_model='linear', drift_terms=['regional_linear'])
k3d, ss3d = uk3d.execute('grid', gridx, gridy, gridz)

# To use the generic 'specified' drift term, the user must provide the drift values
# at each data point and at every grid point. The following example is equivalent to
# using a linear drift in all three spatial dimensions. Refer to
# UniversalKriging3D.__doc__ for more information.
zg, yg, xg = np.meshgrid(gridz, gridy, gridx, indexing='ij')
uk3d = UniversalKriging3D(data[:, 0], data[:, 1], data[:, 2], data[:, 3],
                                                  variogram_model='linear', drift_terms=['specified'],
                                                  specified_drift=[data[:, 0], data[:, 1]])
k3d, ss3d = uk3d.execute('grid', gridx, gridy, gridz, specified_drift_arrays=[xg, yg, zg])

# To use the generic 'functional' drift term, the user must provide a callable
# function that takes only the spatial dimensions as arguments. The following example
# is equivalent to using a linear drift only in the x-direction. Refer to
# UniversalKriging3D.__doc__ for more information.
func = lambda x, y, z: x
uk3d = UniversalKriging3D(data[:, 0], data[:, 1], data[:, 2], data[:, 3],
                                                  variogram_model='linear', drift_terms=['functional'],
                                                  functional_drift=[func])
k3d, ss3d = uk3d.execute('grid', gridx, gridy, gridz)

# Note that the use of the 'specified' and 'functional' generic drift capabilities is
# essentially identical in the two-dimensional universal kriging class (except for a
# difference in the number of spatial coordinates for the passed drift functions).
# See UniversalKriging.__doc__ for more information.

Kriging Parameters Tuning

A scikit-learn compatible API for parameter tuning by cross-validation is exposed in sklearn.model_selection.GridSearchCV. See the Krige CV example for a more practical illustration.

Regression Kriging

Regression kriging can be performed with pykrige.rk.RegressionKriging. This class takes as parameters a scikit-learn regression model, and details of either either the OrdinaryKriging or the UniversalKriging class, and performs a correction steps on the ML regression prediction.

A demonstration of the regression kriging is provided in the corresponding example.

License

PyKrige uses the BSD 3-Clause License.