smbinterp/lib/grid/__init__.py

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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):
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):
"""
this thing eats two pre-constructed arrays of stuff:
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.facets_for_point = defaultdict(list)
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.facets_for_point[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.facets_for_point[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.facets_for_point[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.facets_for_point[c]])
r += " faces: [%s]" % facet_str
r += "\n"
if self.faces:
for v in self.faces.itervalues():
r += "%s\n" % v
return r