refactored the term 'face' to 'cell' to match what I've found in literature
This commit is contained in:
Stephen Mardson McQuay
parent
075dd586a3
commit
93fec67cc7
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@ -8,7 +8,7 @@ import scipy.spatial
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from interp.baker import run_baker
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from interp.tools import log
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from simplex import face, contains
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from simplex import cell, contains
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from smcqdelaunay import *
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@ -32,12 +32,12 @@ class grid(object):
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if q:
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self.q = np.array(q)
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self.faces = {}
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self.faces_for_vert = defaultdict(list)
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self.cells = {}
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self.cells_for_vert = defaultdict(list)
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def get_containing_simplex(self, X):
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if not self.faces:
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raise Exception("face connectivity is not set up")
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if not self.cells:
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raise Exception("cell connectivity is not set up")
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# get closest point
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(dist, indicies) = self.tree.query(X, 2)
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@ -49,26 +49,26 @@ class grid(object):
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log.debug('distance = %0.4f' % dist[0])
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simplex = None
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checked_faces = []
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faces_to_check = list(self.faces_for_vert[closest_point])
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checked_cells = []
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cells_to_check = list(self.cells_for_vert[closest_point])
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attempts = 0
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while not simplex and faces_to_check:
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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_face = faces_to_check.pop(0)
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checked_faces.append(cur_face)
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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_face.contains(X, self):
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simplex = cur_face
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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_face.neighbors:
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if (neighbor not in checked_faces) and (neighbor not in faces_to_check):
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faces_to_check.append(neighbor)
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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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@ -137,21 +137,21 @@ class grid(object):
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assert( len(self.verts) == len(self.q) )
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for c, i in enumerate(zip(self.verts, self.q)):
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r += "%d vert(%s): q(%0.4f)" % (c,i[0], i[1])
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face_str = ", ".join([str(f.name) for f in self.faces_for_vert[c]])
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r += " faces: [%s]" % face_str
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cell_str = ", ".join([str(f.name) for f in self.cells_for_vert[c]])
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r += " cells: [%s]" % cell_str
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r += "\n"
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if self.faces:
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for v in self.faces.itervalues():
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if self.cells:
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for v in self.cells.itervalues():
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r += "%s\n" % v
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return r
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class delaunay_grid(grid):
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face_re = re.compile(r'''
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-\s+(?P<face>f\d+).*?
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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 faces:\s+(?P<neigh>[\sf\d]*)
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neighboring\s cells:\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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@ -168,7 +168,7 @@ class delaunay_grid(grid):
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def get_containing_simplex(self, X):
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if not self.faces:
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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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@ -181,24 +181,24 @@ class delaunay_grid(grid):
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log.debug('distance = %0.4f' % dist[0])
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simplex = None
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checked_faces = []
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faces_to_check = self.faces_for_vert[closest_point]
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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 faces_to_check:
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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_face = faces_to_check.pop(0)
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checked_faces.append(cur_face)
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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_face.contains(X, self):
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simplex = cur_face
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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_face.neighbors:
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if (neighbor not in checked_faces) and (neighbor not in faces_to_check):
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faces_to_check.append(neighbor)
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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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@ -262,16 +262,16 @@ class delaunay_grid(grid):
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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.faces:
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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 face in self.faces_for_vert[indicies[0]]:
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if face.contains(X, self):
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simplex = face
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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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@ -312,27 +312,27 @@ class delaunay_grid(grid):
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"""
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log.debug('start')
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qdelaunay_string = get_qdelaunay_dump_str(self)
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face_to_faces = []
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for matcher in grid.face_re.finditer(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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face_name = d['face']
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cell_name = d['cell']
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verticies = d['verts']
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neighboring_faces = d['neigh']
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neighboring_cells = d['neigh']
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cur_face = face(face_name)
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self.faces[face_name] = cur_face
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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_face.add_vert(vertex_index)
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self.faces_for_vert[vertex_index].append(cur_face)
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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 = [(face_name, i) for i in neighboring_faces.split()]
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face_to_faces.extend(nghbrs)
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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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for rel in face_to_faces:
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if rel[1] in self.faces:
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self.faces[rel[0]].add_neighbor(self.faces[rel[1]])
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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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log.debug('end')
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@ -7,7 +7,7 @@ import numpy as np
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from scipy.spatial import KDTree
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from interp.grid import grid
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from interp.grid.simplex import face
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from interp.grid.simplex import cell
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from interp.tools import exact_func, exact_func_3D
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@ -58,45 +58,45 @@ class gmsh_grid(grid):
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gmsh_file.readline() # $EndNodes
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gmsh_file.readline() # $Elements
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# temporary dict used to compute face connectivity
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# temporary dict used to compute cell connectivity
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neighbors = {}
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element_count = int(gmsh_file.readline())
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for i in xrange(element_count):
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cur_line = gmsh_file.readline()
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cur_line = cur_line.split()
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cur_face_index, node_type, rest = (int(cur_line[0]),
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cur_cell_index, node_type, rest = (int(cur_line[0]),
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int(cur_line[1]),
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[int(j) for j in cur_line[2:]])
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if(node_type == THREE_NODE_TRIANGLE):
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points_for_cur_face = [i-1 for i in rest[rest[0]+1:]]
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points_for_cur_cell = [i-1 for i in rest[rest[0]+1:]]
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cur_face = face(cur_face_index)
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cur_cell = cell(cur_cell_index)
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for cur_point in points_for_cur_face:
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self.faces_for_vert[cur_point].append(cur_face)
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for cur_point in points_for_cur_cell:
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self.cells_for_vert[cur_point].append(cur_cell)
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cur_face.verts = points_for_cur_face
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cur_cell.verts = points_for_cur_cell
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self.faces[cur_face_index] = cur_face
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edges = [tuple(sorted(i)) for i in combinations(points_for_cur_face, EDGES_FOR_FACE_CONNECTIVITY)]
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self.cells[cur_cell_index] = cur_cell
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edges = [tuple(sorted(i)) for i in combinations(points_for_cur_cell, EDGES_FOR_FACE_CONNECTIVITY)]
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# edge is two verts
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for edge in edges:
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if edge in neighbors:
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neighbors[edge].append(cur_face_index)
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neighbors[edge].append(cur_cell_index)
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else:
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neighbors[edge] = [cur_face_index]
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neighbors[edge] = [cur_cell_index]
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for k,v in neighbors.iteritems():
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if len(v) > 1:
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self.faces[v[0]].add_neighbor(self.faces[v[1]])
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self.faces[v[1]].add_neighbor(self.faces[v[0]])
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self.cells[v[0]].add_neighbor(self.cells[v[1]])
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self.cells[v[1]].add_neighbor(self.cells[v[0]])
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def dump_to_blender_files(self, pfile = '/tmp/points.p', ffile = '/tmp/faces.p'):
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def dump_to_blender_files(self, pfile = '/tmp/points.p', ffile = '/tmp/cells.p'):
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pickle.dump([(p[0], p[1], p[2]) for p in self.verts], open(pfile, 'w'))
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pickle.dump([f.verts for f in self.faces.itervalues()], open(ffile, 'w'))
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pickle.dump([f.verts for f in self.cells.itervalues()], open(ffile, 'w'))
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class gmsh_grid3D(grid):
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@ -136,41 +136,41 @@ class gmsh_grid3D(grid):
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gmsh_file.readline() # $EndNodes
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gmsh_file.readline() # $Elements
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# temporary dict used to compute face connectivity
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# temporary dict used to compute cell connectivity
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neighbors = {}
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element_count = int(gmsh_file.readline())
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for i in xrange(element_count):
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cur_line = gmsh_file.readline()
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cur_line = cur_line.split()
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cur_face_index, node_type, rest = (int(cur_line[0]),
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cur_cell_index, node_type, rest = (int(cur_line[0]),
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int(cur_line[1]),
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[int(j) for j in cur_line[2:]])
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if(node_type == FOUR_NODE_TET):
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points_for_cur_face = [i-1 for i in rest[rest[0]+1:]]
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points_for_cur_cell = [i-1 for i in rest[rest[0]+1:]]
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cur_face = face(cur_face_index)
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cur_cell = cell(cur_cell_index)
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for cur_point in points_for_cur_face:
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self.faces_for_vert[cur_point].append(cur_face)
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for cur_point in points_for_cur_cell:
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self.cells_for_vert[cur_point].append(cur_cell)
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cur_face.verts = points_for_cur_face
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cur_cell.verts = points_for_cur_cell
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self.faces[cur_face_index] = cur_face
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edges = [tuple(sorted(i)) for i in combinations(points_for_cur_face, EDGES_FOR_VOLUME_CONNECTIVITY)]
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self.cells[cur_cell_index] = cur_cell
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edges = [tuple(sorted(i)) for i in combinations(points_for_cur_cell, EDGES_FOR_VOLUME_CONNECTIVITY)]
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for edge in edges:
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if edge in neighbors:
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neighbors[edge].append(cur_face_index)
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neighbors[edge].append(cur_cell_index)
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else:
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neighbors[edge] = [cur_face_index]
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neighbors[edge] = [cur_cell_index]
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for k,v in neighbors.iteritems():
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if len(v) > 1:
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self.faces[v[0]].add_neighbor(self.faces[v[1]])
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self.faces[v[1]].add_neighbor(self.faces[v[0]])
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self.cells[v[0]].add_neighbor(self.cells[v[1]])
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self.cells[v[1]].add_neighbor(self.cells[v[0]])
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def dump_to_blender_files(self, pfile = '/tmp/points.p', ffile = '/tmp/faces.p'):
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def dump_to_blender_files(self, pfile = '/tmp/points.p', ffile = '/tmp/cells.p'):
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pickle.dump([(p[0], p[1], p[2]) for p in self.verts], open(pfile, 'w'))
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pickle.dump([f.verts for f in self.faces.itervalues()], open(ffile, 'w'))
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pickle.dump([f.verts for f in self.cells.itervalues()], open(ffile, 'w'))
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@ -21,7 +21,7 @@ def contains(X, R):
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return r
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class face(object):
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class cell(object):
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def __init__(self, name):
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self.name = name
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self.verts = []
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@ -35,7 +35,7 @@ class face(object):
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def add_neighbor(self, n):
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"""
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reference to another face object
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reference to another cell object
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"""
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self.neighbors.append(n)
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@ -44,7 +44,7 @@ class face(object):
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X = point of interest
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G = corrensponding grid object (G.verts)
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because of the way i'm storing things,
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a face simply stores indicies, and so one
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a cell simply stores indicies, and so one
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must pass in a reference to the grid object
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containing real verts.
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@ -54,7 +54,7 @@ class face(object):
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def __str__(self):
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neighbors = [str(i.name) for i in self.neighbors]
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return '<face %s: verts: %s neighbors: [%s]>' %\
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return '<cell %s: verts: %s neighbors: [%s]>' %\
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(
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self.name,
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self.verts,
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