moved the delaunay grid into it's own module
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305b1c82cf
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12e7b16102
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import re
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import logging
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from interp.grid import grid as basegrid, cell
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from subprocess import Popen, PIPE
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def get_qdelaunay_dump(g):
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"""
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pass in interp.grid g, and get back lines from a qhull triangulation:
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qdelaunay Qt f
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"""
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cmd = 'qdelaunay Qt f'
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p = Popen(cmd.split(), bufsize=1, stdin=PIPE, stdout=PIPE)
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so, se = p.communicate(g.for_qhull())
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for i in so.splitlines():
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yield i
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def get_qdelaunay_dump_str(g):
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return "\n".join(get_qdelaunay_dump(g))
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def get_index_only(g):
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cmd = 'qdelaunay Qt i'
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p = Popen(cmd.split(), bufsize=1, stdin=PIPE, stdout=PIPE)
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so, se = p.communicate(g.for_qhull())
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for i in so.splitlines():
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yield i
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def get_index_only_str(g):
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return "\n".join(get_index_only(g))
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class grid(basegrid):
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cell_re = re.compile(r'''
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-\s+(?P<cell>f\d+).*?
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vertices:\s(?P<verts>.*?)\n.*?
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neighboring\s facets:\s+(?P<neigh>[\sf\d]*)
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''', re.S|re.X)
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point_re = re.compile(r'''
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-\s+(?P<point>p\d+).*?
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neighbors:\s+(?P<neigh>[\sf\d]*)
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''', re.S|re.X)
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vert_re = re.compile(r'''
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(p\d+)
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''', re.S|re.X)
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def __init__(self, verts, q = None):
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basegrid.__init__(self, verts,q)
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def get_containing_simplex(self, X):
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if not self.cells:
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self.construct_connectivity()
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# get closest point
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(dist, indicies) = self.tree.query(X, 2)
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closest_point = indicies[0]
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logging.debug('X: %s' % X)
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logging.debug('point index: %d' % closest_point)
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logging.debug('actual point %s' % self.verts[closest_point])
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logging.debug('distance = %0.4f' % dist[0])
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simplex = None
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checked_cells = []
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cells_to_check = self.cells_for_vert[closest_point]
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attempts = 0
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while not simplex and cells_to_check:
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attempts += 1
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# if attempts > 20:
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# raise Exception("probably recursing to many times")
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cur_cell = cells_to_check.pop(0)
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checked_cells.append(cur_cell)
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if cur_cell.contains(X, self):
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simplex = cur_cell
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continue
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for neighbor in cur_cell.neighbors:
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if (neighbor not in checked_cells) and (neighbor not in cells_to_check):
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cells_to_check.append(neighbor)
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if not simplex:
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raise Exception('no containing simplex found')
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R = self.create_mesh(simplex.verts)
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logging.debug('total attempts before finding simplex: %d' % attempts)
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return R
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def get_simplex_and_nearest_points(self, X, extra_points = 3, simplex_size = 3):
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"""
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this returns two grid objects: R and S.
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R is a grid object that is supposedly a containing simplex
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around point X (it tends not to be)
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S is S_j from baker's paper : some verts from all point that are not the simplex
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"""
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logging.debug("extra verts: %d" % extra_points)
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logging.debug("simplex size: %d" % simplex_size)
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r_mesh = self.get_containing_simplex(X)
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# logging.debug("R:\n%s" % r_mesh)
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# and some UNIQUE extra verts
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(dist, indicies) = self.tree.query(X, simplex_size + extra_points)
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unique_indicies = []
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for index in indicies:
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if self.verts[index] not in r_mesh.verts:
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unique_indicies.append(index)
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logging.debug("indicies: %s" % ",".join([str(i) for i in indicies]))
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logging.debug("indicies: %s" % ",".join([str(i) for i in unique_indicies]))
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s_mesh = self.create_mesh(unique_indicies)# indicies[simplex_size:])
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# TODO: eventually remove this test:
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for point in s_mesh.verts:
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if point in r_mesh.verts:
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logging.error("ERROR")
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logging.error("\n%s\nin\n%s" % (point, r_mesh))
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raise Exception("repeating point S and R")
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return (r_mesh, s_mesh)
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def get_points_conn(self, X):
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"""
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this returns two grid objects: R and S.
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this function differes from the get_simplex_and_nearest_points
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function in that it builds up the extra verts based on
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connectivity information, not just nearest-neighbor.
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in theory, this will work much better for situations like
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verts near a short edge in a boundary layer cell where the
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nearest verts would all be colinear
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also, it guarantees that we find a containing simplex
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R is a grid object that is the (a) containing simplex around point X
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S is a connectivity-based nearest-neighbor lookup, limited to 3 extra verts
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"""
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if not self.cells:
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self.construct_connectivity()
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# get closest point
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(dist, indicies) = self.tree.query(X, 2)
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simplex = None
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for cell in self.cells_for_vert[indicies[0]]:
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if cell.contains(X, self):
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simplex = cell
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break
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if not simplex:
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raise AssertionError('no containing simplex found')
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# self.create_mesh(simplex.verts)
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R = self.get_containing_simplex(X)
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s = []
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for c,i in enumerate(simplex.neighbors):
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s.extend([guy for guy in i.verts if not guy in simplex.verts])
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S = self.create_mesh(s)
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return R, S
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def run_baker(self, X, extra_points = 3, order = 2):
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answer = None
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try:
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(R, S) = self.get_simplex_and_nearest_points(X)
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if not contains(X, R.verts):
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raise Exception("run_baker with get_simplex_and_nearest_points returned non-containing simplex")
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answer = run_baker(X, R, S, order)
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except Exception, e:
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logging.error("caught error: %s, trying with connectivity-based mesh" % e)
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(R, S) = self.get_points_conn(X)
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answer = run_baker(X, R, S, order)
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return answer
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def construct_connectivity(self):
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"""
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a call to this method prepares the internal connectivity structure.
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this is part of the __init__ for a rect_grid, but can be called from any grid object
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"""
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logging.debug('start')
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qdelaunay_string = get_qdelaunay_dump_str(self)
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logging.info(qdelaunay_string)
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with open('/tmp/qdel.out', 'w') as of:
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of.write(qdelaunay_string)
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cell_to_cells = []
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for matcher in grid.cell_re.finditer(qdelaunay_string):
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d = matcher.groupdict()
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cell_name = d['cell']
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verticies = d['verts']
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neighboring_cells = d['neigh']
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cur_cell = cell(cell_name)
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self.cells[cell_name] = cur_cell
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for v in grid.vert_re.findall(verticies):
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vertex_index = int(v[1:])
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cur_cell.add_vert(vertex_index)
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self.cells_for_vert[vertex_index].append(cur_cell)
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nghbrs = [(cell_name, i) for i in neighboring_cells.split()]
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cell_to_cells.extend(nghbrs)
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logging.debug(cell_to_cells)
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for rel in cell_to_cells:
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if rel[1] in self.cells:
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self.cells[rel[0]].add_neighbor(self.cells[rel[1]])
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logging.debug(self.cells)
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logging.debug('end')
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