major refactoring
--HG-- rename : lib/baker/__init__.py => interp/baker/__init__.py rename : lib/grid/DD.py => interp/grid/DD.py rename : lib/grid/DDD.py => interp/grid/DDD.py rename : lib/grid/__init__.py => interp/grid/__init__.py rename : lib/grid/qhull.py => interp/grid/qhull.py rename : lib/grid/simplex.py => interp/grid/simplex.py rename : lib/grid/smcqdelaunay.py => interp/grid/smcqdelaunay.py rename : lib/baker/tools.py => interp/tools.py
This commit is contained in:
@@ -0,0 +1,382 @@
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from baker import *
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from baker.tools import smblog
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import numpy as np
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import sys
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import itertools
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from tools import smberror
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def get_phis(X, R):
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"""
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The get_phis function is used to get barycentric coordonites for a point on a triangle.
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X -- the destination point (2D)
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X = [0,0]
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r -- the three points that make up the containing triangular simplex (2D)
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r = [[-1, -1], [0, 2], [1, -1]]
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this will return [0.333, 0.333, 0.333]
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"""
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# baker: eq 7
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A = np.array([
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[ 1, 1, 1],
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[R[0][0], R[1][0], R[2][0]],
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[R[0][1], R[1][1], R[2][1]],
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])
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b = np.array([ 1,
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X[0],
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X[1]
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])
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try:
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phi = np.linalg.solve(A,b)
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except np.linalg.LinAlgError as e:
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msg = "calculation of phis yielded a linearly dependant system (%s)" % e
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smblog.error(msg)
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raise smberror(msg)
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phi = np.dot(np.linalg.pinv(A), b)
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return phi
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def get_phis_3D(X, R):
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"""
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The get_phis function is used to get barycentric coordonites for a point on a tetrahedron.
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X -- the destination point (3D)
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X = [0,0,0]
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R -- the four points that make up the containing simplex, tetrahedron (3D)
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R = [
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[0.0, 0.0, 1.0],
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[0.94280904333606508, 0.0, -0.3333333283722672],
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[-0.47140452166803232, 0.81649658244673617, -0.3333333283722672],
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[-0.47140452166803298, -0.81649658244673584, -0.3333333283722672],
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]
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this (should) will return [0.25, 0.25, 0.25, 0.25]
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"""
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# baker: eq 7
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A = np.array([
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[ 1, 1, 1, 1 ],
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[R[0][0], R[1][0], R[2][0], R[3][0]],
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[R[0][1], R[1][1], R[2][1], R[3][1]],
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[R[0][2], R[1][2], R[2][2], R[3][2]],
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])
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b = np.array([ 1,
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X[0],
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X[1],
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X[2]
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])
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try:
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phi = np.linalg.solve(A,b)
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except np.linalg.LinAlgError as e:
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smblog.error("calculation of phis yielded a linearly dependant system: %s" % e)
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phi = np.dot(np.linalg.pinv(A), b)
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return phi
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def qlinear(X, R):
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"""
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this calculates the linear portion of q from X to R
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also, this is baker eq 3
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X = destination point
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R = simplex points
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q = CFD quantities of interest at the simplex points
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"""
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phis = get_phis(X, R.points)
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qlin = np.sum([q_i * phi_i for q_i, phi_i in zip(R.q, phis)])
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return phis, qlin
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def qlinear_3D(X, R):
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"""
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this calculates the linear portion of q from X to R
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X = destination point
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R = simplex points
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q = CFD quantities of interest at the simplex points(R)
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"""
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phis = get_phis_3D(X, R.points)
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qlin = sum([q_i * phi_i for q_i, phi_i in zip(R.q, phis)])
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return phis, qlin
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def get_error_quadratic(phi, R, S):
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B = [] # baker eq 9
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w = [] # baker eq 11
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for (s, q) in zip(S.points, S.q):
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cur_phi, cur_qlin = qlinear(s, R)
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(phi1, phi2, phi3) = cur_phi
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B.append(
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[
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phi1 * phi2,
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phi2 * phi3,
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phi3 * phi1,
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]
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)
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w.append(q - cur_qlin)
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B = np.array(B)
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w = np.array(w)
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A = np.dot(B.T, B)
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b = np.dot(B.T, w)
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# baker solve eq 10
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try:
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(a, b, c) = np.linalg.solve(A,b)
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except np.linalg.LinAlgError as e:
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smblog.error("linear calculation went bad, resorting to np.linalg.pinv: %s" % e)
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(a, b, c) = np.dot(np.linalg.pinv(A), b)
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error_term = a * phi[0] * phi[1]\
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+ b * phi[1] * phi[2]\
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+ c * phi[2] * phi[0]
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return error_term
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def get_error_cubic(phi, R, S):
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B = [] # baker eq 9
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w = [] # baker eq 11
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for (s, q) in zip(S.points, S.q):
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cur_phi, cur_qlin = qlinear(s, R)
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(phi1, phi2, phi3) = cur_phi
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# basing this on eq 17
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B.append(
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[
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phi1 * phi2 * phi2, # a
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phi1 * phi3 * phi3, # b
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phi2 * phi1 * phi1, # c
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phi2 * phi3 * phi3, # d
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phi3 * phi1 * phi1, # e
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phi3 * phi2 * phi2, # f
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phi1 * phi2 * phi3, # g
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]
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)
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w.append(q - cur_qlin)
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B = np.array(B)
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w = np.array(w)
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A = np.dot(B.T, B)
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b = np.dot(B.T, w)
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# baker solve eq 10
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try:
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(a, b, c, d, e, f, g) = np.linalg.solve(A,b)
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except np.linalg.LinAlgError as e:
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smblog.error("linear calculation went bad, resorting to np.linalg.pinv: %s" % e)
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(a, b, c, d, e, f, g) = np.dot(np.linalg.pinv(A), b)
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error_term = a * phi[0] * phi[1] * phi[1]\
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+ b * phi[0] * phi[2] * phi[2]\
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+ c * phi[1] * phi[0] * phi[0]\
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+ d * phi[1] * phi[2] * phi[2]\
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+ e * phi[2] * phi[0] * phi[0]\
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+ f * phi[2] * phi[1] * phi[1]\
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+ g * phi[0] * phi[1] * phi[2]\
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return error_term
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def get_error_sauron(phi, R, S, order = 2):
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smblog.debug("len(phi): %d"% len(phi))
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B = [] # baker eq 9
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w = [] # baker eq 11
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p = pattern(order, len(phi), offset = -1)
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smblog.debug("pattern: %s" % p)
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for (s,q) in zip(S.points, S.q):
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cur_phi, cur_qlin = qlinear(s, R)
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l = []
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for i in p:
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cur_sum = cur_phi[i[0]]
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for j in i[1:]:
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cur_sum *= cur_phi[j]
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l.append(cur_sum)
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B.append(l)
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w.append(q - cur_qlin)
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smblog.debug("B: %s" % B)
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smblog.debug("w: %s" % w)
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B = np.array(B)
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w = np.array(w)
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A = np.dot(B.T, B)
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b = np.dot(B.T, w)
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# baker solve eq 10
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try:
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abc = np.linalg.solve(A,b)
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except np.linalg.LinAlgError as e:
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smblog.error("linear calculation went bad, resorting to np.linalg.pinv: %s" % e)
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abc = np.dot(np.linalg.pinv(A), b)
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smblog.debug(len(abc) == len(p))
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error_term = 0.0
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for (a, i) in zip(abc, p):
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cur_sum = a
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for j in i:
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cur_sum *= phi[j]
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error_term += cur_sum
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smblog.debug("error_term smb: %s" % error_term)
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return error_term, abc
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def run_baker(X, R, S, order=2):
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"""
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This is the main function to call to get an interpolation to X from the input meshes
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X -- the destination point (2D)
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X = [0,0]
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R = Simplex
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S = extra points
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"""
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smblog.debug("order = %d" % order)
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answer = {
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'qlin': None,
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'error': None,
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'final': None,
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}
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# calculate values only for the simplex triangle
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phi, qlin = qlinear(X, R)
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if order == 1:
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answer['qlin'] = qlin
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return answer
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elif order in (2,3):
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error_term, abc = get_error_sauron(phi, R, S, order)
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else:
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raise smberror('unsupported order for baker method')
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q_final = qlin + error_term
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answer['qlin' ] = qlin
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answer['error'] = error_term
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answer['final'] = q_final
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return answer
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def run_baker_3D(X, R, S):
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"""
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This is the main function to call to get an interpolation to X from the input meshes
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X -- the destination point (3D)
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X = [0,0,0]
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R = Simplex (4 points, contains X)
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S = extra points (surrounding, in some manner, R and X, but not in R)
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"""
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# calculate values only for the triangle
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phi, qlin = qlinear_3D(X, R)
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if len(S.points) == 0:
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answer = {
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'a': None,
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'b': None,
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'c': None,
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'd': None,
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'e': None,
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'f': None,
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'qlin': qlin,
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'error': None,
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'final': None,
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}
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return answer
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B = [] # baker eq 9
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w = [] # baker eq 11
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for (s, q) in zip(S.points, S.q):
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cur_phi, cur_qlin = qlinear_3D(s, R)
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(phi1, phi2, phi3, phi4) = cur_phi
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B.append(
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[
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phi1 * phi2,
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phi1 * phi3,
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phi1 * phi4,
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phi2 * phi3,
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phi2 * phi4,
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phi3 * phi4,
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]
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)
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w.append(q - cur_qlin)
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B = np.array(B)
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w = np.array(w)
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A = np.dot(B.T, B)
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b = np.dot(B.T, w)
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# baker solve eq 10
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try:
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(a, b, c, d, e, f) = np.linalg.solve(A,b)
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except np.linalg.LinAlgError as e:
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smblog.error("linear calculation went bad, resorting to np.linalg.pinv: %s", e)
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(a, b, c, d, e, f) = np.dot(np.linalg.pinv(A), b)
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error_term = a * phi[0] * phi[1]\
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+ b * phi[0] * phi[2]\
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+ c * phi[0] * phi[3]\
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+ d * phi[1] * phi[2]\
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+ e * phi[1] * phi[3]\
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+ f * phi[2] * phi[3]
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q_final = qlin + error_term
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answer = {
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'a': a,
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'b': b,
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'c': c,
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'd': d,
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'e': e,
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'f': f,
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'qlin': qlin,
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'error': error_term,
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'final': q_final,
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}
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return answer
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def _boxings(n, k):
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"""\
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source for this function:
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http://old.nabble.com/Simple-combinatorics-with-Numpy-td20086915.html
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http://old.nabble.com/Re:-Simple-combinatorics-with-Numpy-p20099736.html
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"""
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seq, i = [n] * k + [0], k
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while i:
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yield tuple(seq[i] - seq[i+1] for i in xrange(k))
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i = seq.index(0) - 1
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seq[i:k] = [seq[i] - 1] * (k-i)
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def _samples_ur(items, k, offset = 0):
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"""Returns k unordered samples (with replacement) from items."""
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n = len(items)
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for sample in _boxings(k, n):
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selections = [[items[i]]*count for i,count in enumerate(sample)]
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yield tuple([x + offset for sel in selections for x in sel])
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def pattern(power, phicount, offset = 0):
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smblog.debug("(power = %s, phicount = %s)" % (power, phicount))
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r = []
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for i in _samples_ur(range(1, phicount + 1), power, offset):
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if not len(set(i)) == 1:
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r.append(i)
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return r
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@@ -0,0 +1,92 @@
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from grid import grid as basegrid
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from baker.tools import exact_func, smblog
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import numpy as np
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class grid(basegrid):
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def __init__(self, points, q):
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basegrid.__init__(self, points, q)
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def for_qhull_generator(self):
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"""
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this returns a generator that should be fed into qdelaunay
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"""
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yield '2';
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yield '%d' % len(self.points)
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for p in self.points:
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yield "%f %f" % (p[0], p[1])
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def for_qhull(self):
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"""
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this returns a single string that should be fed into qdelaunay
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"""
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r = '2\n'
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r += '%d\n' % len(self.points)
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for p in self.points:
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r += "%f %f\n" % (p[0], p[1])
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return r
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class rect_grid(grid):
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def __init__(self, xres = 5, yres = 5):
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xmin = -1.0
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xmax = 1.0
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xspan = xmax - xmin
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xdel = xspan / float(xres - 1)
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ymin = -1.0
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ymay = 1.0
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yspan = ymay - ymin
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ydel = yspan / float(yres - 1)
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points = []
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q = []
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for x in xrange(xres):
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cur_x = xmin + (x * xdel)
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for y in xrange(yres):
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cur_y = ymin + (y * ydel)
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points.append([cur_x, cur_y])
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q.append(exact_func((cur_x, cur_y)))
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grid.__init__(self, points, q)
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self.construct_connectivity()
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class random_grid(rect_grid):
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def __init__(self, num_points = 10):
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smblog.debug("number of points: %d" % num_points)
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points = []
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q = []
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r = np.random
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appx_side_res = int(np.sqrt(num_points))
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smblog.debug("appx_side_res: %d" % appx_side_res)
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delta = 1.0 / float(appx_side_res)
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for x in xrange(appx_side_res + 1):
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cur_x = x * delta
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for cur_y in (0, 1):
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new_point = [cur_x, cur_y]
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points.append(new_point)
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q.append(exact_func(new_point))
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for y in xrange(appx_side_res + 1):
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cur_y = y * delta
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for cur_x in (0, 1):
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new_point = [cur_x, cur_y]
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points.append(new_point)
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q.append(exact_func(new_point))
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for i in xrange(num_points):
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cur_x = r.rand()
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cur_y = r.rand()
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points.append([cur_x, cur_y])
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q.append( exact_func( (cur_x, cur_y) ) )
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grid.__init__(self, points, q)
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|
||||
self.points = np.array(self.points)
|
||||
self.q = np.array(self.q)
|
||||
@@ -0,0 +1,108 @@
|
||||
from grid import grid as basegrid
|
||||
from baker.tools import exact_func_3D, smblog
|
||||
|
||||
import numpy as np
|
||||
|
||||
|
||||
class grid(basegrid):
|
||||
def __init__(self, points, q):
|
||||
basegrid.__init__(self, points, q)
|
||||
|
||||
def for_qhull_generator(self):
|
||||
"""
|
||||
this returns a generator that should be fed into qdelaunay
|
||||
"""
|
||||
|
||||
yield '3';
|
||||
yield '%d' % len(self.points)
|
||||
|
||||
for p in self.points:
|
||||
yield "%f %f %f" % tuple(p)
|
||||
|
||||
def for_qhull(self):
|
||||
"""
|
||||
this returns a single string that should be fed into qdelaunay
|
||||
"""
|
||||
r = '3\n'
|
||||
r += '%d\n' % len(self.points)
|
||||
for p in self.points:
|
||||
r += "%f %f %f\n" % tuple(p)
|
||||
return r
|
||||
|
||||
class rect_grid(grid):
|
||||
def __init__(self, xres = 5, yres = 5, zres = 5):
|
||||
xmin = -1.0
|
||||
xmax = 1.0
|
||||
xspan = xmax - xmin
|
||||
xdel = xspan / float(xres - 1)
|
||||
|
||||
ymin = -1.0
|
||||
ymay = 1.0
|
||||
yspan = ymay - ymin
|
||||
ydel = yspan / float(yres - 1)
|
||||
|
||||
zmin = -1.0
|
||||
zmaz = 1.0
|
||||
zspan = zmaz - zmin
|
||||
zdel = zspan / float(zres - 1)
|
||||
|
||||
|
||||
points = []
|
||||
q = []
|
||||
for x in xrange(xres):
|
||||
cur_x = xmin + (x * xdel)
|
||||
for y in xrange(yres):
|
||||
cur_y = ymin + (y * ydel)
|
||||
for z in xrange(zres):
|
||||
cur_z = zmin + (z * zdel)
|
||||
points.append([cur_x, cur_y, cur_z])
|
||||
q.append(exact_func_3D((cur_x, cur_y, cur_z)))
|
||||
grid.__init__(self, points, q)
|
||||
# self.construct_connectivity()
|
||||
|
||||
def for_qhull_generator(self):
|
||||
"""
|
||||
this returns a generator that should be fed into qdelaunay
|
||||
"""
|
||||
|
||||
yield '3';
|
||||
yield '%d' % len(self.points)
|
||||
|
||||
for p in self.points:
|
||||
yield "%f %f %f" % tuple(p)
|
||||
|
||||
def for_qhull(self):
|
||||
"""
|
||||
this returns a single string that should be fed into qdelaunay
|
||||
"""
|
||||
r = '3\n'
|
||||
r += '%d\n' % len(self.points)
|
||||
for p in self.points:
|
||||
r += "%f %f %f\n" % tuple(p)
|
||||
return r
|
||||
|
||||
class random_grid(rect_grid):
|
||||
def __init__(self, num_points = 10):
|
||||
points = []
|
||||
q = []
|
||||
|
||||
r = np.random
|
||||
|
||||
appx_side_res = int(np.power(num_points, 1/3.0))
|
||||
smblog.debug("appx_side_res: %d" % appx_side_res)
|
||||
delta = 1.0 / float(appx_side_res)
|
||||
|
||||
for x in xrange(appx_side_res + 1):
|
||||
pass
|
||||
|
||||
for i in xrange(num_points):
|
||||
cur_x = r.rand()
|
||||
cur_y = r.rand()
|
||||
cur_z = r.rand()
|
||||
|
||||
points.append([cur_x, cur_y, cur_z])
|
||||
q.append(exact_func_3D((cur_x, cur_y, cur_z)))
|
||||
grid.__init__(self, points, q)
|
||||
|
||||
self.points = np.array(self.points)
|
||||
self.q = np.array(self.q)
|
||||
@@ -0,0 +1,244 @@
|
||||
import sys
|
||||
import re
|
||||
from collections import defaultdict
|
||||
import inspect
|
||||
|
||||
import numpy as np
|
||||
import scipy.spatial
|
||||
|
||||
from baker import run_baker
|
||||
from baker.tools import exact_func, smberror, smblog
|
||||
from simplex import face, contains
|
||||
from smcqdelaunay import *
|
||||
|
||||
|
||||
class grid(object):
|
||||
def __init__(self, points, q):
|
||||
"""
|
||||
this thing eats two pre-constructed arrays of floats:
|
||||
points = array of arrays (i will convert to numpy.array)
|
||||
[[x0,y0], [x1,y1], ...]
|
||||
q = array (1D) of important values
|
||||
"""
|
||||
|
||||
self.points = np.array(points)
|
||||
self.q = np.array(q)
|
||||
self.tree = scipy.spatial.KDTree(self.points)
|
||||
self.faces = {}
|
||||
self.faces_for_vert = defaultdict(list)
|
||||
|
||||
class delaunay_grid(grid):
|
||||
facet_re = re.compile(r'''
|
||||
-\s+(?P<facet>f\d+).*?
|
||||
vertices:\s(?P<verts>.*?)\n.*?
|
||||
neighboring\s facets:\s+(?P<neigh>[\sf\d]*)
|
||||
''', re.S|re.X)
|
||||
|
||||
point_re = re.compile(r'''
|
||||
-\s+(?P<point>p\d+).*?
|
||||
neighbors:\s+(?P<neigh>[\sf\d]*)
|
||||
''', re.S|re.X)
|
||||
|
||||
vert_re = re.compile(r'''
|
||||
(p\d+)
|
||||
''', re.S|re.X)
|
||||
|
||||
def __init__(self, points, q):
|
||||
grid.__init__(self, points,q)
|
||||
|
||||
|
||||
def create_mesh(self, indicies):
|
||||
"""
|
||||
this function takes a list of indicies, and then creates
|
||||
and returns a grid object (collection of points and q).
|
||||
|
||||
note: the input is indicies, the grid contains points
|
||||
"""
|
||||
p = [self.points[i] for i in indicies]
|
||||
q = [self.q[i] for i in indicies]
|
||||
return grid(p, q)
|
||||
|
||||
def get_containing_simplex(self, X):
|
||||
if not self.faces:
|
||||
self.construct_connectivity()
|
||||
|
||||
# get closest point
|
||||
(dist, indicies) = self.tree.query(X, 2)
|
||||
closest_point = indicies[0]
|
||||
|
||||
smblog.debug('X: %s' % X)
|
||||
smblog.debug('point index: %d' % closest_point)
|
||||
smblog.debug('actual point %s' % self.points[closest_point])
|
||||
smblog.debug('distance = %0.4f' % dist[0])
|
||||
|
||||
simplex = None
|
||||
checked_facets = []
|
||||
facets_to_check = self.faces_for_vert[closest_point]
|
||||
|
||||
attempts = 0
|
||||
while not simplex and facets_to_check:
|
||||
attempts += 1
|
||||
# if attempts > 20:
|
||||
# raise smberror("probably recursing to many times")
|
||||
cur_facet = facets_to_check.pop(0)
|
||||
checked_facets.append(cur_facet)
|
||||
|
||||
if cur_facet.contains(X, self):
|
||||
simplex = cur_facet
|
||||
continue
|
||||
|
||||
new_facest = []
|
||||
for neighbor in cur_facet.neighbors:
|
||||
if (neighbor not in checked_facets) and (neighbor not in facets_to_check):
|
||||
facets_to_check.append(neighbor)
|
||||
|
||||
if not simplex:
|
||||
raise AssertionError('no containing simplex found')
|
||||
|
||||
R = self.create_mesh(simplex.verts)
|
||||
|
||||
smblog.debug('total attempts before finding simplex: %d' % attempts)
|
||||
return R
|
||||
|
||||
|
||||
def get_simplex_and_nearest_points(self, X, extra_points = 3, simplex_size = 3):
|
||||
"""
|
||||
this returns two grid objects: R and S.
|
||||
|
||||
R is a grid object that is supposedly a containing simplex
|
||||
around point X (it tends not to be)
|
||||
|
||||
S is S_j from baker's paper : some points from all point that are not the simplex
|
||||
"""
|
||||
smblog.debug(inspect.stack()[1][3])
|
||||
smblog.debug("extra points: %d" % extra_points)
|
||||
smblog.debug("simplex size: %d" % simplex_size)
|
||||
|
||||
r_mesh = self.get_containing_simplex(X)
|
||||
# smblog.debug("R:\n%s" % r_mesh)
|
||||
|
||||
# and some UNIQUE extra points
|
||||
(dist, indicies) = self.tree.query(X, simplex_size + extra_points)
|
||||
|
||||
unique_indicies = []
|
||||
for index in indicies:
|
||||
if self.points[index] not in r_mesh.points:
|
||||
unique_indicies.append(index)
|
||||
|
||||
smblog.debug("indicies: %s" % ",".join([str(i) for i in indicies]))
|
||||
smblog.debug("indicies: %s" % ",".join([str(i) for i in unique_indicies]))
|
||||
s_mesh = self.create_mesh(unique_indicies)# indicies[simplex_size:])
|
||||
|
||||
# TODO: eventually remove this test:
|
||||
for point in s_mesh.points:
|
||||
if point in r_mesh.points:
|
||||
smblog.error("ERROR")
|
||||
smblog.error("\n%s\nin\n%s" % (point, r_mesh))
|
||||
raise smberror("repeating point S and R")
|
||||
|
||||
return (r_mesh, s_mesh)
|
||||
|
||||
def get_points_conn(self, X):
|
||||
"""
|
||||
this returns two grid objects: R and S.
|
||||
|
||||
this function differes from the get_simplex_and_nearest_points
|
||||
function in that it builds up the extra points based on
|
||||
connectivity information, not just nearest-neighbor.
|
||||
in theory, this will work much better for situations like
|
||||
points near a short edge in a boundary layer cell where the
|
||||
nearest points would all be colinear
|
||||
|
||||
also, it guarantees that we find a containing simplex
|
||||
|
||||
R is a grid object that is the (a) containing simplex around point X
|
||||
S is a connectivity-based nearest-neighbor lookup, limited to 3 extra points
|
||||
"""
|
||||
if not self.faces:
|
||||
self.construct_connectivity()
|
||||
|
||||
# get closest point
|
||||
(dist, indicies) = self.tree.query(X, 2)
|
||||
|
||||
simplex = None
|
||||
for facet in self.faces_for_vert[indicies[0]]:
|
||||
if facet.contains(X, self):
|
||||
simplex = facet
|
||||
break
|
||||
|
||||
if not simplex:
|
||||
raise AssertionError('no containing simplex found')
|
||||
|
||||
# self.create_mesh(simplex.verts)
|
||||
R = self.get_containing_simplex(X)
|
||||
|
||||
s = []
|
||||
for c,i in enumerate(simplex.neighbors):
|
||||
s.extend([guy for guy in i.verts if not guy in simplex.verts])
|
||||
S = self.create_mesh(s)
|
||||
|
||||
return R, S
|
||||
|
||||
def run_baker(self, X, extra_points = 3, order = 2):
|
||||
answer = None
|
||||
|
||||
try:
|
||||
(R, S) = self.get_simplex_and_nearest_points(X)
|
||||
if not contains(X, R.points):
|
||||
raise smberror("run_baker with get_simplex_and_nearest_points returned non-containing simplex")
|
||||
answer = run_baker(X, R, S, order)
|
||||
except smberror, e:
|
||||
smblog.error("caught error: %s, trying with connectivity-based mesh" % e)
|
||||
(R, S) = self.get_points_conn(X)
|
||||
answer = run_baker(X, R, S, order)
|
||||
|
||||
return answer
|
||||
|
||||
|
||||
|
||||
def construct_connectivity(self):
|
||||
"""
|
||||
a call to this method prepares the internal connectivity structure.
|
||||
|
||||
this is part of the __init__ for a rect_grid, but can be called from any grid object
|
||||
"""
|
||||
smblog.debug('start')
|
||||
qdelaunay_string = get_qdelaunay_dump_str(self)
|
||||
facet_to_facets = []
|
||||
for matcher in grid.facet_re.finditer(qdelaunay_string):
|
||||
d = matcher.groupdict()
|
||||
|
||||
facet_name = d['facet']
|
||||
verticies = d['verts']
|
||||
neighboring_facets = d['neigh']
|
||||
|
||||
cur_face = face(facet_name)
|
||||
self.faces[facet_name] = cur_face
|
||||
|
||||
for v in grid.vert_re.findall(verticies):
|
||||
vertex_index = int(v[1:])
|
||||
cur_face.add_vert(vertex_index)
|
||||
self.faces_for_vert[vertex_index].append(cur_face)
|
||||
|
||||
nghbrs = [(facet_name, i) for i in neighboring_facets.split()]
|
||||
facet_to_facets.extend(nghbrs)
|
||||
|
||||
for rel in facet_to_facets:
|
||||
if rel[1] in self.faces:
|
||||
self.faces[rel[0]].add_neighbor(self.faces[rel[1]])
|
||||
|
||||
smblog.debug('end')
|
||||
|
||||
|
||||
def __str__(self):
|
||||
r = ''
|
||||
assert( len(self.points) == len(self.q) )
|
||||
for c, i in enumerate(zip(self.points, self.q)):
|
||||
r += "%d %r: %0.4f" % (c,i[0], i[1])
|
||||
facet_str = ", ".join([f.name for f in self.faces_for_vert[c]])
|
||||
r += " faces: [%s]" % facet_str
|
||||
r += "\n"
|
||||
if self.faces:
|
||||
for v in self.faces.itervalues():
|
||||
r += "%s\n" % v
|
||||
return r
|
||||
@@ -0,0 +1,15 @@
|
||||
|
||||
def parse_qhull_file(filename, verbose=False):
|
||||
f = open(filename, 'r')
|
||||
|
||||
if verbose:
|
||||
print 'filename: ', filename
|
||||
degree = int(f.readline().strip())
|
||||
print "degree:", degree
|
||||
print "number of points", f.readline().strip()
|
||||
|
||||
verts = []
|
||||
for p in f:
|
||||
v = [float(i) for i in p.strip().split()]
|
||||
verts.append(v)
|
||||
return verts
|
||||
@@ -0,0 +1,64 @@
|
||||
from baker import get_phis, get_phis_3D
|
||||
from baker.tools import smblog
|
||||
|
||||
TOL = 1e-8
|
||||
|
||||
def contains(X, R):
|
||||
"""
|
||||
tests if X (point) is in R (a simplex,
|
||||
represented by a list of n-degree coordinates)
|
||||
|
||||
it now correctly checks for 2/3-D points
|
||||
"""
|
||||
if len(X) == 2:
|
||||
phis = get_phis(X, R)
|
||||
elif len(X) == 3:
|
||||
phis = get_phis_3D(X, R)
|
||||
|
||||
r = True
|
||||
if [i for i in phis if i < 0.0 - TOL]:
|
||||
r = False
|
||||
return r
|
||||
|
||||
|
||||
class face(object):
|
||||
def __init__(self, name):
|
||||
self.name = name
|
||||
self.verts = []
|
||||
self.neighbors = []
|
||||
|
||||
def add_vert(self, v):
|
||||
"""
|
||||
v should be an index into grid.points
|
||||
"""
|
||||
self.verts.append(v)
|
||||
|
||||
def add_neighbor(self, n):
|
||||
"""
|
||||
reference to another face object
|
||||
"""
|
||||
self.neighbors.append(n)
|
||||
|
||||
def contains(self, X, G):
|
||||
"""
|
||||
X = point of interest
|
||||
G = corrensponding grid object (G.points)
|
||||
because of the way i'm storing things,
|
||||
a face simply stores indicies, and so one
|
||||
must pass in a reference to the grid object
|
||||
containing real points.
|
||||
|
||||
this simply calls grid.simplex.contains
|
||||
"""
|
||||
return contains(X, [G.points[i] for i in self.verts])
|
||||
|
||||
def __str__(self):
|
||||
neighbors = [str(i.name) for i in self.neighbors]
|
||||
return '<face %s: verts: %s neighbors: [%s]>' %\
|
||||
(
|
||||
self.name,
|
||||
self.verts,
|
||||
", ".join(neighbors)
|
||||
)
|
||||
|
||||
__repr__ = __str__
|
||||
@@ -0,0 +1,23 @@
|
||||
#!/usr/bin/python
|
||||
|
||||
from subprocess import Popen, PIPE
|
||||
|
||||
def get_qdelaunay_dump(g):
|
||||
cmd = 'qdelaunay Qt f'
|
||||
p = Popen(cmd.split(), bufsize=1, stdin=PIPE, stdout=PIPE)
|
||||
so, se = p.communicate(g.for_qhull())
|
||||
for i in so.splitlines():
|
||||
yield i
|
||||
|
||||
def get_qdelaunay_dump_str(g):
|
||||
return "\n".join(get_qdelaunay_dump(g))
|
||||
|
||||
def get_index_only(g):
|
||||
cmd = 'qdelaunay Qt i'
|
||||
p = Popen(cmd.split(), bufsize=1, stdin=PIPE, stdout=PIPE)
|
||||
so, se = p.communicate(g.for_qhull())
|
||||
for i in so.splitlines():
|
||||
yield i
|
||||
|
||||
def get_index_only_str(g):
|
||||
return "\n".join(get_index_only(g))
|
||||
@@ -0,0 +1,84 @@
|
||||
import os
|
||||
import logging
|
||||
import inspect
|
||||
import numpy as np
|
||||
|
||||
|
||||
class smbLog(object):
|
||||
interpolator = "%s ==> %s"
|
||||
def __init__(self, level = logging.DEBUG):
|
||||
logging.basicConfig(
|
||||
level = level,
|
||||
format = '%(asctime)s %(levelname)s %(message)s',
|
||||
filename = os.path.join(os.sep, 'tmp', 'baker.lol'),
|
||||
)
|
||||
self.log = logging.getLogger()
|
||||
def debug(self, message = None):
|
||||
msg = smbLog.interpolator % (inspect.stack()[1][3], message)
|
||||
self.log.debug(msg)
|
||||
|
||||
def info(self, message = None):
|
||||
msg = smbLog.interpolator % (inspect.stack()[1][3], message)
|
||||
self.log.info(msg)
|
||||
|
||||
def warn(self, message = None):
|
||||
msg = smbLog.interpolator % (inspect.stack()[1][3], message)
|
||||
self.log.warn(msg)
|
||||
|
||||
def error(self, message = None):
|
||||
msg = smbLog.interpolator % (inspect.stack()[1][3], message)
|
||||
self.log.error(msg)
|
||||
|
||||
|
||||
smblog = smbLog(logging.DEBUG)
|
||||
|
||||
class smberror(Exception):
|
||||
"""
|
||||
this is a silly little exception subclass
|
||||
"""
|
||||
def __init__(self, val):
|
||||
self.value = val
|
||||
def __str__(self):
|
||||
return repr(self.value)
|
||||
|
||||
def rms(errors):
|
||||
"""
|
||||
root mean square calculation
|
||||
"""
|
||||
r = 0.0
|
||||
for i in errors:
|
||||
r += np.power(i, 2)
|
||||
r = np.sqrt(r / len(errors))
|
||||
return r
|
||||
|
||||
def exact_func(X):
|
||||
"""
|
||||
the exact function used from baker's article (for testing)
|
||||
"""
|
||||
x = X[0]
|
||||
y = X[0]
|
||||
return np.power((np.sin(x * np.pi) * np.cos(y * np.pi)), 2)
|
||||
|
||||
def exact_func_3D(X):
|
||||
"""
|
||||
the exact function (3D) used from baker's article (for testing)
|
||||
"""
|
||||
x = X[0]
|
||||
y = X[1]
|
||||
z = X[2]
|
||||
return np.power((np.sin(x * np.pi / 2.0) * np.sin(y * np.pi / 2.0) * np.sin(z * np.pi / 2.0)), 2)
|
||||
|
||||
def improved_answer(answer, exact, verbose=False):
|
||||
if not answer['error']:
|
||||
return True
|
||||
smblog.debug('error: %s' % answer['error'])
|
||||
smblog.debug('qlin: %s' % answer['qlin'])
|
||||
smblog.debug('final: %s' % answer['final'])
|
||||
smblog.debug('exact: %s' % exact)
|
||||
|
||||
if np.abs(answer['final'] - exact) <= np.abs(answer['qlin'] - exact):
|
||||
smblog.debug(":) improved result")
|
||||
return True
|
||||
else:
|
||||
smblog.debug(":( damaged result")
|
||||
return False
|
||||
Reference in New Issue
Block a user