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99 lines
4.1 KiB
Python
99 lines
4.1 KiB
Python
6 years ago
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"""This module contains all the functions needed for variogram analysis """
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import sklearn.metrics.pairwise as pairwise
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import numpy as np
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def lagindices(pwdist, lag, tol):
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'''
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Input: (pwdist) square NumPy array of pairwise distances
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(lag) the distance, h, between points
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(tol) the tolerance we are comfortable with around (lag)
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Output: (ind) list of tuples; the first element is the row of
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(data) for one point, the second element is the row
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of a point (lag)+/-(tol) away from the first point,
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e.g., (3,5) corresponds fo data[3,:], and data[5,:]
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'''
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# grab the coordinates in a given range: lag +/- tolerance
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i, j = np.where((pwdist >= lag - tol) & (pwdist < lag + tol))
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# zip the coordinates into a list
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indices = list(zip(i, j))
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# take out the repeated elements,
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# since p is a *symmetric* distance matrix
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indices = np.array([i for i in indices if i[1] > i[0]])
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return indices
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def semivariance(data, indices):
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'''
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Input: (data) NumPy array where the fris t two columns
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are the spatial coordinates, x and y, and
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the third column is the variable of interest
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(indices) indices of paired data points in (data)
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Output: (z) semivariance value at lag (h) +/- (tol)
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'''
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# take the squared difference between
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# the values of the variable of interest
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z = [(data[i] - data[j])**2.0 for i, j in indices]
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# the semivariance is half the mean squared difference
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return np.mean(z) / 2.0
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def semivariogram(t, data, lags, tol):
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'''
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Input: (data) NumPy array where the fris t two columns
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are the spatial coordinates, x and y
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(lag) the distance, h, between points
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(tol) the tolerance we are comfortable with around (lag)
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Output: (sv) <2xN> NumPy array of lags and semivariogram values
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'''
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return variogram(t, data, lags, tol, 'semivariogram')
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def covariance(data, indices):
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'''
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Input: (data) NumPy array where the fris t two columns
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are the spatial coordinates, x and y
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(lag) the distance, h, between points
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(tol) the tolerance we are comfortable with around (lag)
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Output: (z) covariance value at lag (h) +/- (tol)
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'''
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# grab the indices of the points
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# that are lag +/- tolerance apart
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m_tail = np.mean([data[i] for i, j in indices])
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m_head = np.mean([data[j] for i, j in indices])
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m = m_tail * m_head
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z = [data[i] * data[j] - m for i, j in indices]
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return np.mean(z)
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def covariogram(t, data, lags, tol):
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'''
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Input: (data) NumPy array where the fris t two columns
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are the spatial coordinates, x and y
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(lag) the distance, h, between points
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(tol) the tolerance we are comfortable with around (lag)
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Output: (cv) <2xN> NumPy array of lags and covariogram values
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'''
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return variogram(t, data, lags, tol, 'covariogram')
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def variogram(t, data, lags, tol, method):
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'''
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Input: (data) NumPy array where the fris t two columns
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are the spatial coordinates, x and y
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(lag) the distance, h, between points
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(tol) the tolerance we are comfortable with around (lag)
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(method) either 'semivariogram', or 'covariogram'
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Output: (cv) <2xN> NumPy array of lags and variogram values
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'''
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# calculate the pairwise distances
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pwdist = pairwise.pairwise_distances(np.reshape(np.array(t), (-1,1)))
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# create a list of lists of indices of points having the ~same lag
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index = [lagindices(pwdist, lag, tol) for lag in lags]
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# calculate the variogram at different lags given some tolerance
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if method in ['semivariogram', 'semi', 'sv', 's']:
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v = [semivariance(data, indices) for indices in index]
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elif method in ['covariogram', 'cov', 'co', 'cv', 'c']:
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v = [covariance(data, indices) for indices in index]
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# bundle the semivariogram values with their lags
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return np.array(list(zip(lags, v))).T
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