moved the delaunay grid into it's own module

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+(?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)
+    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')