smbinterp/interp/grid/delaunay.py

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import re
import logging
from interp.grid import grid as basegrid, cell
from subprocess import Popen, PIPE
def get_qdelaunay_dump(g):
"""
pass in interp.grid g, and get back lines from a qhull triangulation:
qdelaunay Qt f
"""
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))
class grid(basegrid):
cell_re = re.compile(r'''
-\s+(?P<cell>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, verts, q = None):
basegrid.__init__(self, verts,q)
def get_containing_simplex(self, X):
if not self.cells:
self.construct_connectivity()
# get closest point
(dist, indicies) = self.tree.query(X, 2)
closest_point = indicies[0]
logging.debug('X: %s' % X)
logging.debug('point index: %d' % closest_point)
logging.debug('actual point %s' % self.verts[closest_point])
logging.debug('distance = %0.4f' % dist[0])
simplex = None
checked_cells = []
cells_to_check = self.cells_for_vert[closest_point]
attempts = 0
while not simplex and cells_to_check:
attempts += 1
# if attempts > 20:
# raise Exception("probably recursing to many times")
cur_cell = cells_to_check.pop(0)
checked_cells.append(cur_cell)
if cur_cell.contains(X, self):
simplex = cur_cell
continue
for neighbor in cur_cell.neighbors:
if (neighbor not in checked_cells) and (neighbor not in cells_to_check):
cells_to_check.append(neighbor)
if not simplex:
raise Exception('no containing simplex found')
R = self.create_mesh(simplex.verts)
logging.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 verts from all point that are not the simplex
"""
logging.debug("extra verts: %d" % extra_points)
logging.debug("simplex size: %d" % simplex_size)
r_mesh = self.get_containing_simplex(X)
# logging.debug("R:\n%s" % r_mesh)
# and some UNIQUE extra verts
(dist, indicies) = self.tree.query(X, simplex_size + extra_points)
unique_indicies = []
for index in indicies:
if self.verts[index] not in r_mesh.verts:
unique_indicies.append(index)
logging.debug("indicies: %s" % ",".join([str(i) for i in indicies]))
logging.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.verts:
if point in r_mesh.verts:
logging.error("ERROR")
logging.error("\n%s\nin\n%s" % (point, r_mesh))
raise Exception("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 verts based on
connectivity information, not just nearest-neighbor.
in theory, this will work much better for situations like
verts near a short edge in a boundary layer cell where the
nearest verts 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 verts
"""
if not self.cells:
self.construct_connectivity()
# get closest point
(dist, indicies) = self.tree.query(X, 2)
simplex = None
for cell in self.cells_for_vert[indicies[0]]:
if cell.contains(X, self):
simplex = cell
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.verts):
raise Exception("run_baker with get_simplex_and_nearest_points returned non-containing simplex")
answer = run_baker(X, R, S, order)
except Exception, e:
logging.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
"""
logging.debug('start')
qdelaunay_string = get_qdelaunay_dump_str(self)
with open('/tmp/qdel.out', 'w') as of:
of.write(qdelaunay_string)
cell_to_cells = []
for matcher in grid.cell_re.finditer(qdelaunay_string):
d = matcher.groupdict()
cell_name = d['cell']
verticies = d['verts']
neighboring_cells = d['neigh']
cur_cell = cell(cell_name)
self.cells[cell_name] = cur_cell
for v in grid.vert_re.findall(verticies):
vertex_index = int(v[1:])
cur_cell.add_vert(vertex_index)
self.cells_for_vert[vertex_index].append(cur_cell)
nghbrs = [(cell_name, i) for i in neighboring_cells.split()]
cell_to_cells.extend(nghbrs)
logging.debug(cell_to_cells)
for rel in cell_to_cells:
if rel[1] in self.cells:
self.cells[rel[0]].add_neighbor(self.cells[rel[1]])
logging.debug(self.cells)
logging.debug('end')