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