From 12e7b1610272625ee0ccccff56d3682ef69eb39c Mon Sep 17 00:00:00 2001 From: Stephen Mardson McQuay Date: Mon, 21 Mar 2011 16:55:45 -0600 Subject: [PATCH] moved the delaunay grid into it's own module --- interp/grid/delaunay.py | 225 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 225 insertions(+) create mode 100644 interp/grid/delaunay.py diff --git a/interp/grid/delaunay.py b/interp/grid/delaunay.py new file mode 100644 index 0000000..ff2f77e --- /dev/null +++ b/interp/grid/delaunay.py @@ -0,0 +1,225 @@ +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+(?Pf\d+).*? + vertices:\s(?P.*?)\n.*? + neighboring\s facets:\s+(?P[\sf\d]*) + ''', re.S|re.X) + + point_re = re.compile(r''' + -\s+(?Pp\d+).*? + neighbors:\s+(?P[\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) + logging.info(qdelaunay_string) + 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')