diff --git a/interp/grid/__init__.py b/interp/grid/__init__.py index 4491cb5..692f9ed 100644 --- a/interp/grid/__init__.py +++ b/interp/grid/__init__.py @@ -7,31 +7,123 @@ import numpy as np import scipy.spatial from interp.baker import run_baker -from interp.tools import exact_func, smberror, log +from interp.tools import exact_func, log from simplex import face, contains from smcqdelaunay import * class grid(object): - def __init__(self, points, q): + def __init__(self, verts = None, q = None): """ this thing eats two pre-constructed arrays of floats: - points = array of arrays (i will convert to numpy.array) - [[x0,y0], [x1,y1], ...] - q = array (1D) of important values + + verts = array of arrays (if passed in, will convert to numpy.array) + [ + [x0,y0], + [x1,y1], ... + ] + + q = array (1D) of physical values """ - self.points = np.array(points) - self.q = np.array(q) - self.tree = scipy.spatial.KDTree(self.points) - self.faces = {} + if verts: + self.verts = np.array(verts) + if q: + self.q = np.array(q) + + self.tree = scipy.spatial.KDTree(self.verts) + self.faces = {} self.faces_for_vert = defaultdict(list) + def get_containing_simplex(self, X): + if not self.faces: + self.construct_connectivity() + + # get closest point + (dist, indicies) = self.tree.query(X, 2) + closest_point = indicies[0] + + log.debug('X: %s' % X) + log.debug('point index: %d' % closest_point) + log.debug('actual point %s' % self.verts[closest_point]) + log.debug('distance = %0.4f' % dist[0]) + + simplex = None + checked_faces = [] + faces_to_check = self.faces_for_vert[closest_point] + + attempts = 0 + while not simplex and faces_to_check: + attempts += 1 + + # if attempts > 20: + # raise Exception("probably recursing to many times") + + cur_face = faces_to_check.pop(0) + checked_faces.append(cur_face) + + if cur_face.contains(X, self): + simplex = cur_face + continue + + new_facest = [] + for neighbor in cur_face.neighbors: + if (neighbor not in checked_faces) and (neighbor not in faces_to_check): + faces_to_check.append(neighbor) + + if not simplex: + raise AssertionError('no containing simplex found') + + R = self.create_mesh(simplex.verts) + + log.debug('total attempts before finding simplex: %d' % attempts) + return R + + def create_mesh(self, indicies): + """ + this function takes a list of indicies, and then creates + and returns a grid object (collection of verts and q). + + note: the input is indicies, the grid contains verts + """ + p = [self.verts[i] for i in indicies] + q = [self.q[i] for i in indicies] + return grid(p, q) + + 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 + """ + raise Exception("abstract base class: override this method") + + def run_baker(self, X, extra_points = 3, order = 2): + raise Exception("abstract base class: override this method") + + def __str__(self): + r = '' + assert( len(self.verts) == len(self.q) ) + for c, i in enumerate(zip(self.verts, self.q)): + r += "%d %r: %0.4f" % (c,i[0], i[1]) + face_str = ", ".join([str(f.name) for f in self.faces_for_vert[c]]) + r += " faces: [%s]" % face_str + r += "\n" + if self.faces: + for v in self.faces.itervalues(): + r += "%s\n" % v + return r + + + class delaunay_grid(grid): - facet_re = re.compile(r''' - -\s+(?Pf\d+).*? + face_re = re.compile(r''' + -\s+(?Pf\d+).*? vertices:\s(?P.*?)\n.*? - neighboring\s facets:\s+(?P[\sf\d]*) + neighboring\s faces:\s+(?P[\sf\d]*) ''', re.S|re.X) point_re = re.compile(r''' @@ -43,21 +135,10 @@ class delaunay_grid(grid): (p\d+) ''', re.S|re.X) - def __init__(self, points, q): - grid.__init__(self, points,q) + def __init__(self, verts, q): + grid.__init__(self, verts,q) - def create_mesh(self, indicies): - """ - this function takes a list of indicies, and then creates - and returns a grid object (collection of points and q). - - note: the input is indicies, the grid contains points - """ - p = [self.points[i] for i in indicies] - q = [self.q[i] for i in indicies] - return grid(p, q) - def get_containing_simplex(self, X): if not self.faces: self.construct_connectivity() @@ -66,38 +147,38 @@ class delaunay_grid(grid): (dist, indicies) = self.tree.query(X, 2) closest_point = indicies[0] - smblog.debug('X: %s' % X) - smblog.debug('point index: %d' % closest_point) - smblog.debug('actual point %s' % self.points[closest_point]) - smblog.debug('distance = %0.4f' % dist[0]) + log.debug('X: %s' % X) + log.debug('point index: %d' % closest_point) + log.debug('actual point %s' % self.verts[closest_point]) + log.debug('distance = %0.4f' % dist[0]) simplex = None - checked_facets = [] - facets_to_check = self.faces_for_vert[closest_point] + checked_faces = [] + faces_to_check = self.faces_for_vert[closest_point] attempts = 0 - while not simplex and facets_to_check: + while not simplex and faces_to_check: attempts += 1 # if attempts > 20: - # raise smberror("probably recursing to many times") - cur_facet = facets_to_check.pop(0) - checked_facets.append(cur_facet) + # raise Exception("probably recursing to many times") + cur_face = faces_to_check.pop(0) + checked_faces.append(cur_face) - if cur_facet.contains(X, self): - simplex = cur_facet + if cur_face.contains(X, self): + simplex = cur_face continue new_facest = [] - for neighbor in cur_facet.neighbors: - if (neighbor not in checked_facets) and (neighbor not in facets_to_check): - facets_to_check.append(neighbor) + for neighbor in cur_face.neighbors: + if (neighbor not in checked_faces) and (neighbor not in faces_to_check): + faces_to_check.append(neighbor) if not simplex: raise AssertionError('no containing simplex found') R = self.create_mesh(simplex.verts) - smblog.debug('total attempts before finding simplex: %d' % attempts) + log.debug('total attempts before finding simplex: %d' % attempts) return R @@ -108,33 +189,33 @@ class delaunay_grid(grid): 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 points from all point that are not the simplex + S is S_j from baker's paper : some verts from all point that are not the simplex """ - smblog.debug(inspect.stack()[1][3]) - smblog.debug("extra points: %d" % extra_points) - smblog.debug("simplex size: %d" % simplex_size) + log.debug(inspect.stack()[1][3]) + log.debug("extra verts: %d" % extra_points) + log.debug("simplex size: %d" % simplex_size) r_mesh = self.get_containing_simplex(X) - # smblog.debug("R:\n%s" % r_mesh) + # log.debug("R:\n%s" % r_mesh) - # and some UNIQUE extra points + # and some UNIQUE extra verts (dist, indicies) = self.tree.query(X, simplex_size + extra_points) unique_indicies = [] for index in indicies: - if self.points[index] not in r_mesh.points: + if self.verts[index] not in r_mesh.verts: unique_indicies.append(index) - smblog.debug("indicies: %s" % ",".join([str(i) for i in indicies])) - smblog.debug("indicies: %s" % ",".join([str(i) for i in unique_indicies])) + log.debug("indicies: %s" % ",".join([str(i) for i in indicies])) + log.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.points: - if point in r_mesh.points: - smblog.error("ERROR") - smblog.error("\n%s\nin\n%s" % (point, r_mesh)) - raise smberror("repeating point S and R") + for point in s_mesh.verts: + if point in r_mesh.verts: + log.error("ERROR") + log.error("\n%s\nin\n%s" % (point, r_mesh)) + raise Exception("repeating point S and R") return (r_mesh, s_mesh) @@ -143,16 +224,16 @@ class delaunay_grid(grid): 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 points based on + 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 - points near a short edge in a boundary layer cell where the - nearest points would all be colinear + 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 points + S is a connectivity-based nearest-neighbor lookup, limited to 3 extra verts """ if not self.faces: self.construct_connectivity() @@ -161,9 +242,9 @@ class delaunay_grid(grid): (dist, indicies) = self.tree.query(X, 2) simplex = None - for facet in self.faces_for_vert[indicies[0]]: - if facet.contains(X, self): - simplex = facet + for face in self.faces_for_vert[indicies[0]]: + if face.contains(X, self): + simplex = face break if not simplex: @@ -184,11 +265,11 @@ class delaunay_grid(grid): try: (R, S) = self.get_simplex_and_nearest_points(X) - if not contains(X, R.points): - raise smberror("run_baker with get_simplex_and_nearest_points returned non-containing simplex") + 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 smberror, e: - smblog.error("caught error: %s, trying with connectivity-based mesh" % e) + except Exception, e: + log.error("caught error: %s, trying with connectivity-based mesh" % e) (R, S) = self.get_points_conn(X) answer = run_baker(X, R, S, order) @@ -202,43 +283,29 @@ class delaunay_grid(grid): this is part of the __init__ for a rect_grid, but can be called from any grid object """ - smblog.debug('start') + log.debug('start') qdelaunay_string = get_qdelaunay_dump_str(self) - facet_to_facets = [] - for matcher in grid.facet_re.finditer(qdelaunay_string): + face_to_faces = [] + for matcher in grid.face_re.finditer(qdelaunay_string): d = matcher.groupdict() - facet_name = d['facet'] + face_name = d['face'] verticies = d['verts'] - neighboring_facets = d['neigh'] + neighboring_faces = d['neigh'] - cur_face = face(facet_name) - self.faces[facet_name] = cur_face + cur_face = face(face_name) + self.faces[face_name] = cur_face for v in grid.vert_re.findall(verticies): vertex_index = int(v[1:]) cur_face.add_vert(vertex_index) self.faces_for_vert[vertex_index].append(cur_face) - nghbrs = [(facet_name, i) for i in neighboring_facets.split()] - facet_to_facets.extend(nghbrs) + nghbrs = [(face_name, i) for i in neighboring_faces.split()] + face_to_faces.extend(nghbrs) - for rel in facet_to_facets: + for rel in face_to_faces: if rel[1] in self.faces: self.faces[rel[0]].add_neighbor(self.faces[rel[1]]) - smblog.debug('end') - - - def __str__(self): - r = '' - assert( len(self.points) == len(self.q) ) - for c, i in enumerate(zip(self.points, self.q)): - r += "%d %r: %0.4f" % (c,i[0], i[1]) - facet_str = ", ".join([f.name for f in self.faces_for_vert[c]]) - r += " faces: [%s]" % facet_str - r += "\n" - if self.faces: - for v in self.faces.itervalues(): - r += "%s\n" % v - return r + log.debug('end')