Interpolating a 3d array in Python. How to avoid for loops?

问题

I have an array which I want to interpolate over the 1st axes. At the moment I am doing it like this example:

import numpy as np
from scipy.interpolate import interp1d

array = np.random.randint(0, 9, size=(100, 100, 100))
new_array = np.zeros((1000, 100, 100))
x = np.arange(0, 100, 1)
x_new = np.arange(0, 100, 0.1)

for i in x:
    for j in x:
        f = interp1d(x, array[:, i, j])
        new_array[:, i, j] = f(xnew)

The data I use represents 10 years of 5-day averaged values for each latitude and longitude in a domain. I want to create an array of daily values.

I have also tried using splines. I don't really know how they work but it was not much faster.

Is there a way to do this without using for loops? If for loops must be used, are there other ways to speed this up?

Thank you in advance for any suggestions.

回答1:

You can specify an axis argument to interp1d:

import numpy as np
from scipy.interpolate import interp1d
array = np.random.randint(0, 9, size=(100, 100, 100))
x = np.linspace(0, 100, 100)
x_new = np.linspace(0, 100, 1000)
new_array = interp1d(x, array, axis=0)(x_new)
new_array.shape # -> (1000, 100, 100)

回答2:

Because you're interpolating regularly-gridded data, have a look at using scipy.ndimage.map_coordinates.

As a quick example:

import numpy as np
import scipy.ndimage as ndimage

interp_factor = 10
nx, ny, nz = 100, 100, 100
array = np.random.randint(0, 9, size=(nx, ny, nz))

# If you're not familiar with mgrid: 
# http://docs.scipy.org/doc/numpy/reference/generated/numpy.mgrid.html
new_indicies = np.mgrid[0:nx:interp_factor*nx*1j, 0:ny, 0:nz]

# order=1 indicates bilinear interpolation. Default is 3 (cubic interpolation)
# We're also indicating the output array's dtype should be the same as the 
# original array's. Otherwise, a new float array would be created.
interp_array = ndimage.map_coordinates(array, new_indicies, 
                                       order=1, output=array.dtype)
interp_array = interp_array.reshape((interp_factor * nx, ny, nz))

来源：https://stackoverflow.com/questions/7755871/interpolating-a-3d-array-in-python-how-to-avoid-for-loops

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python

arrays

numpy

scipy

interpolation