From 1af176a6e08cedc900c9f9b18a967f92b8850d15 Mon Sep 17 00:00:00 2001 From: "Stephen M. McQuay" Date: Tue, 27 Sep 2011 15:23:42 -0600 Subject: [PATCH] Primarily: fixed the gmsh module to use integer indices also did some pep8/pyflakes cleanup --- interp/baker/__init__.py | 11 +- interp/bootstrap.py | 4 +- interp/grid/__init__.py | 34 +- interp/grid/delaunay.py | 9 +- interp/grid/gmsh.py | 160 +-- interp/tools.py | 9 +- test/baker2d.py | 1 - test/delaunay.py | 2012 +++++++++++++++++++------------------- test/quadratic2d.py | 1 - 9 files changed, 1131 insertions(+), 1110 deletions(-) diff --git a/interp/baker/__init__.py b/interp/baker/__init__.py index 3e4d8d7..7bc3b7d 100644 --- a/interp/baker/__init__.py +++ b/interp/baker/__init__.py @@ -142,10 +142,10 @@ def interpolate(X, R, R_q, S=None, S_q=None, order=2): order - order of interpolation - 1 """ - qlin=None - error_term=None - final=None - abc={} + qlin = None + error_term = None + final = None + abc = {} # calculate values only for the simplex triangle phi, qlin = qlinear(X, R, R_q) @@ -161,10 +161,9 @@ def interpolate(X, R, R_q, S=None, S_q=None, order=2): raise np.linalg.LinAlgError("Pathological Vertex Config") else: final = qlin + error_term - elif order not in xrange(2,11): + elif order not in xrange(2, 11): raise Exception('unsupported order "%d" for baker method' % order) - return Answer(qlin=qlin, error=error_term, final=final, abc=abc) diff --git a/interp/bootstrap.py b/interp/bootstrap.py index a9868e6..78f9d22 100644 --- a/interp/bootstrap.py +++ b/interp/bootstrap.py @@ -13,5 +13,7 @@ def save_history(historyPath=historyPath): if os.path.exists(historyPath): readline.read_history_file(historyPath) +rl = rlcompleter + atexit.register(save_history) -del os, atexit, readline, rlcompleter, save_history, historyPath +del os, atexit, readline, rl, save_history, historyPath diff --git a/interp/grid/__init__.py b/interp/grid/__init__.py index 8110024..3b23934 100644 --- a/interp/grid/__init__.py +++ b/interp/grid/__init__.py @@ -16,7 +16,18 @@ class grid(object): pass def get_simplex_extra_points(self, X, extra_points=8): - pass + # I need two things: find_simplex, and self.simplices + simplex_id = self.find_simplex(X) + simplex_verts_ids = set(self.simplices[simplex_id]) + + distances, kdt_ids \ + = self.tree.query(X, extra_points + len(simplex_verts_ids)) + kdt_ids = set(kdt_ids) + + simplex_ids = list(simplex_verts_ids) + extra_points_ids = list(kdt_ids - simplex_verts_ids) + + return simplex_ids, extra_points_ids def interpolate(self, X, order=2, extra_points=3): r, s = self.get_simplex_extra_points(X, extra_points=extra_points) @@ -25,27 +36,16 @@ class grid(object): def dump_to_blender_files(self, pfile='/tmp/points.p', cfile='/tmp/cells.p'): - if len(self.verts[0]) == 2: - pickle.dump([(p[0], p[1], 0.0) for p in self.verts], + if len(self.points[0]) == 2: + pickle.dump([(p[0], p[1], 0.0) for p in self.points.tolist()], open(pfile, 'w')) else: - pickle.dump([(p[0], p[1], p[2]) for p in self.verts], + pickle.dump([(p[0], p[1], p[2]) for p in self.points.tolist()], open(pfile, 'w')) - pickle.dump([f.verts for f in self.cells.itervalues()], - open(cfile, 'w')) + pickle.dump([face for face in self.simplices.tolist()], + open(cfile, 'w')) -def get_simplex_extra_points(X, points, triangulation, kdtree, extra_points=8): - simplex_id = triangulation.find_simplex(X) - simplex_verts_ids = set(triangulation.vertices[simplex_id]) - - distances, kdt_ids = kdtree.query(X, extra_points + len(simplex_verts_ids)) - kdt_ids = set(kdt_ids) - - simplex_ids = list(simplex_verts_ids) - extra_points_ids = list(kdt_ids - simplex_verts_ids) - - return simplex_ids, extra_points_ids def contains(X, R): """ diff --git a/interp/grid/delaunay.py b/interp/grid/delaunay.py index f3f9078..8e36ba8 100644 --- a/interp/grid/delaunay.py +++ b/interp/grid/delaunay.py @@ -1,7 +1,6 @@ import scipy.spatial from interp.grid import grid as basegrid -from interp.grid import get_simplex_extra_points class dgrid(basegrid): @@ -9,8 +8,8 @@ class dgrid(basegrid): self.points = points self.values = values self.triangulation = scipy.spatial.Delaunay(points) - self.kdtree = scipy.spatial.KDTree(points) + self.simplices = self.triangulation.vertices + self.tree = scipy.spatial.KDTree(points) - def get_simplex_extra_points(self, X, extra_points=8): - return get_simplex_extra_points(X, self.points, self.triangulation, - self.kdtree, extra_points=extra_points) + def find_simplex(self, X): + return self.triangulation.find_simplex(X) diff --git a/interp/grid/gmsh.py b/interp/grid/gmsh.py index 6b8e818..9842c8b 100644 --- a/interp/grid/gmsh.py +++ b/interp/grid/gmsh.py @@ -1,101 +1,121 @@ -from itertools import combinations +from itertools import combinations import numpy as np -from scipy.spatial import KDTree - -from interp.grid import grid -from interp.grid import cell - -import logging -log = logging.getLogger('interp') - +from scipy.spatial import KDTree +from interp.grid import grid, contains THREE_NODE_TRIANGLE = 2 -FOUR_NODE_TET = 4 - -EDGES_FOR_FACE_CONNECTIVITY = 2 -EDGES_FOR_VOLUME_CONNECTIVITY = 3 - +FOUR_NODE_TET = 4 +MAX_SEARCH_COUNT = 256 class ggrid(grid): + def __init__(self, filename, values=None, dimension=3): + """ + construct an interp.grid.grid-compliant grid + object out of a {2,3}D gmsh file + """ + self.dim = dimension + self.values = None - def __init__(self, filename, dimension = 3): - """ - construct an interp.grid.grid-compliant grid - object out of a {2,3}D gmsh file - """ - self.dim = dimension - log.debug("dimension: %d", self.dim) + gmsh_file = open(filename, 'r') - gmsh_file = open(filename, 'r') + gmsh_file.readline() # $MeshFormat + fmt = gmsh_file.readline() + self.version, self.file_type, self.data_size = fmt.split() + gmsh_file.readline() # $EndMeshFormat + gmsh_file.readline() # $Nodes - gmsh_file.readline() # $MeshFormat - gmsh_file.readline() - gmsh_file.readline() # $EndMeshFormat + node_count = int(gmsh_file.readline()) - gmsh_file.readline() # $Nodes + self.points = np.empty((node_count, dimension), dtype=np.float64) + self.q = np.empty(node_count) - node_count = int(gmsh_file.readline()) + for i in xrange(node_count): + cur_line = gmsh_file.readline() + (index, x, y, z) = cur_line.split() + index = int(index) - 1 - self.verts = np.empty((node_count, dimension)) - self.q = np.empty(node_count) + self.points[i][0] = float(x) + self.points[i][1] = float(y) + if self.dim == 3: + self.points[i][2] = float(z) - for i in xrange(node_count): - cur_line = gmsh_file.readline() - (index, x,y,z) = cur_line.split() - index = int(index) - 1 + self.tree = KDTree(self.points) - self.verts[i][0] = float(x) - self.verts[i][1] = float(y) + gmsh_file.readline() # $EndNodes + gmsh_file.readline() # $Elements - if self.dim == 3: - self.verts[i][2] = float(z) + neighbors = {} + simplices = [] + self.point_to_simplex = [[] for i in xrange(len(self.points))] + simplex_counter = 0 + element_count = int(gmsh_file.readline()) + for simplex_id in xrange(element_count): + cur_line = gmsh_file.readline() + cur_line = cur_line.split() + simplex_index, node_type, rest = (int(cur_line[0]), + int(cur_line[1]), + [int(j) for j in cur_line[2:]]) + if (node_type == THREE_NODE_TRIANGLE and self.dim == 2) \ + or (node_type == FOUR_NODE_TET and self.dim == 3): + points_for_simplex = [i - 1 for i in rest[rest[0] + 1:]] + for point in points_for_simplex: + self.point_to_simplex[point].append(simplex_counter) + simplices.append(points_for_simplex) + simplex_counter += 1 - self.tree = KDTree(self.verts) + self.simplex_to_simplex = [[] for i in xrange(len(simplices))] - # initialize rest of structures about to be populated (cells, - # cells_for_vert) - grid.__init__(self) + for simplex in xrange(len(simplices)): + edges = [tuple(sorted(i)) for i in \ + combinations(simplices[simplex], self.dim)] + for edge in edges: + if edge in neighbors: + neighbors[edge].append(simplex) + else: + neighbors[edge] = [simplex] - gmsh_file.readline() # $EndNodes - gmsh_file.readline() # $Elements + for k, v in neighbors.iteritems(): + if len(v) > 1: + self.simplex_to_simplex[v[0]].append(v[1]) + self.simplex_to_simplex[v[1]].append(v[0]) - # temporary dict used to compute cell connectivity - neighbors = {} + self.simplices = np.array(simplices, dtype=np.int32) - element_count = int(gmsh_file.readline()) - for i in xrange(element_count): - cur_line = gmsh_file.readline() - cur_line = cur_line.split() - cur_cell_index, node_type, rest = (int(cur_line[0]), - int(cur_line[1]), - [int(j) for j in cur_line[2:]]) + def find_simplex(self, X, max_search_count=MAX_SEARCH_COUNT): + # get closest point + (dist, indicies) = self.tree.query(X, 2) + closest_point = indicies[0] - if (node_type == THREE_NODE_TRIANGLE and self.dim == 2) \ - or (node_type == FOUR_NODE_TET and self.dim == 3): - points_for_cur_cell = [i-1 for i in rest[rest[0]+1:]] + simplex = None + checked_cells = [] + cells_to_check = list(self.point_to_simplex[closest_point]) - cur_cell = cell(cur_cell_index) + attempts = 0 + while not simplex and cells_to_check: + cur_cell = cells_to_check.pop(0) + checked_cells.append(cur_cell) - for cur_point in points_for_cur_cell: - self.cells_for_vert[cur_point].append(cur_cell) + R = self.points[self.simplices[cur_cell]] + if contains(X, R): + simplex = cur_cell + continue - cur_cell.verts = points_for_cur_cell + attempts += 1 + if attempts >= max_search_count: + raise Exception("Is the search becoming exhaustive?" + " (%dth attempt)" % attempts) - self.cells[cur_cell_index] = cur_cell - edges = [tuple(sorted(i)) for i in combinations(points_for_cur_cell, self.dim)] + for neighbor in self.simplex_to_simplex[cur_cell]: + if (neighbor not in checked_cells) \ + and (neighbor not in cells_to_check): + cells_to_check.append(neighbor) - for edge in edges: - if edge in neighbors: - neighbors[edge].append(cur_cell_index) - else: - neighbors[edge] = [cur_cell_index] + if not simplex: + raise Exception('no containing simplex found') - for k,v in neighbors.iteritems(): - if len(v) > 1: - self.cells[v[0]].add_neighbor(self.cells[v[1]]) - self.cells[v[1]].add_neighbor(self.cells[v[0]]) + return simplex diff --git a/interp/tools.py b/interp/tools.py index 647499e..5130b08 100644 --- a/interp/tools.py +++ b/interp/tools.py @@ -45,8 +45,9 @@ def baker_exact_3D(X): np.sin(z * np.pi / 2.0)), 2) return answer -def exact_me(X, f): - a = np.array([f(i) for i in X]) + +def exact_me(points, f): + a = np.array([f(i) for i in points]) return a @@ -71,10 +72,12 @@ def improved_answer(answer, exact): else: return False -def identical_points(a,b): + +def identical_points(a, b): return all(set(j[i] for j in a) \ == set(j[i] for j in b) for i in xrange(len(a[0]))) + def improved(qlin, err, final, exact): if np.abs(final - exact) <= np.abs(qlin - exact): return True diff --git a/test/baker2d.py b/test/baker2d.py index 40ba2b5..13aaeac 100644 --- a/test/baker2d.py +++ b/test/baker2d.py @@ -75,7 +75,6 @@ class Test(unittest.TestCase): R, R_q = (self.all_points[:size_of_simplex], self.q[:size_of_simplex]) - answer = baker.interpolate(self.X, R, R_q) good_answer = Answer(qlin=0.5, final=None, error=None, abc={}) self.assertEqual(answer, good_answer) diff --git a/test/delaunay.py b/test/delaunay.py index d220609..63c1cf3 100644 --- a/test/delaunay.py +++ b/test/delaunay.py @@ -5,1006 +5,1006 @@ import numpy as np from interp.grid.delaunay import dgrid from interp.tools import baker_exact_3D, exact_me, improved_answer -points = np.array([[ 0.11428445, 0.28754022, 0.21450866], - [ 0.70777361, 0.97113801, 0.70142999], - [ 0.9678696 , 0.8752588 , 0.61011066], - [ 0.28114508, 0.56494346, 0.10472855], - [ 0.87320653, 0.60442285, 0.77830118], - [ 0.54868101, 0.06763191, 0.36992336], - [ 0.74785868, 0.01445301, 0.36157087], - [ 0.37893801, 0.2798186 , 0.66882913], - [ 0.40288033, 0.43632989, 0.68307495], - [ 0.05443145, 0.69825395, 0.75788844], - [ 0.72652183, 0.46143234, 0.92496808], - [ 0.98215309, 0.74919871, 0.26359922], - [ 0.64446603, 0.03215349, 0.71585739], - [ 0.74583664, 0.17934764, 0.48514102], - [ 0.02953106, 0.26222083, 0.84447849], - [ 0.92558287, 0.86491041, 0.00388493], - [ 0.48458751, 0.18263645, 0.10020616], - [ 0.50691704, 0.29474261, 0.05317139], - [ 0.13503481, 0.45742548, 0.89879376], - [ 0.42092092, 0.50429495, 0.93224069], - [ 0.38495379, 0.6395474 , 0.67431922], - [ 0.10397544, 0.05895451, 0.9875192 ], - [ 0.06942965, 0.86935731, 0.29390551], - [ 0.08325816, 0.37391508, 0.94985739], - [ 0.70791782, 0.62839051, 0.80202258], - [ 0.49957473, 0.84219751, 0.88040138], - [ 0.91766782, 0.48387821, 0.08503156], - [ 0.36803798, 0.3877998 , 0.24104388], - [ 0.1526318 , 0.01782609, 0.04233187], - [ 0.24389489, 0.35547378, 0.86487884], - [ 0.79969989, 0.86603222, 0.12417413], - [ 0.07748739, 0.40214123, 0.26731593], - [ 0.22738297, 0.71726456, 0.26570381], - [ 0.05918811, 0.07212692, 0.55623921], - [ 0.36451404, 0.58232176, 0.71326058], - [ 0.1194748 , 0.30536944, 0.06718068], - [ 0.15832267, 0.8887553 , 0.72702744], - [ 0.64205779, 0.63270873, 0.84104407], - [ 0.6598406 , 0.64223508, 0.4446435 ], - [ 0.27005486, 0.92531167, 0.41231729], - [ 0.32309501, 0.36187601, 0.29635482], - [ 0.82053702, 0.18239855, 0.31045463], - [ 0.89756268, 0.40578409, 0.24500909], - [ 0.91924702, 0.84409983, 0.52950817], - [ 0.45169706, 0.8790168 , 0.65692569], - [ 0.96988179, 0.45284828, 0.98161877], - [ 0.67214891, 0.43246417, 0.36161494], - [ 0.91771824, 0.13570763, 0.30358442], - [ 0.00856081, 0.46164223, 0.89603726], - [ 0.95545709, 0.17282928, 0.83199973], - [ 0.56650153, 0.89603536, 0.45668853], - [ 0.9542778 , 0.12299014, 0.41592707], - [ 0.06352572, 0.94850064, 0.33634642], - [ 0.93951017, 0.43484399, 0.37270086], - [ 0.67236423, 0.16673231, 0.82524789], - [ 0.84371993, 0.41819289, 0.28587838], - [ 0.61771884, 0.84808589, 0.22994513], - [ 0.17655356, 0.76040647, 0.66896936], - [ 0.39594309, 0.30225809, 0.56655642], - [ 0.26509525, 0.48602892, 0.4414201 ], - [ 0.01230335, 0.47860405, 0.43923575], - [ 0.92014909, 0.99002187, 0.3740484 ], - [ 0.88845505, 0.68630333, 0.37397556], - [ 0.11044038, 0.28907405, 0.51466146], - [ 0.11092469, 0.20020453, 0.75125346], - [ 0.27536249, 0.60320668, 0.6360586 ], - [ 0.94241002, 0.00823361, 0.05984616], - [ 0.24263625, 0.93050725, 0.54862345], - [ 0.12049839, 0.16584759, 0.94799531], - [ 0.43141746, 0.77530968, 0.89400203], - [ 0.43453017, 0.72250458, 0.30855848], - [ 0.58327876, 0.30410605, 0.21529569], - [ 0.6906952 , 0.88501704, 0.33122977], - [ 0.59582838, 0.23855177, 0.25562364], - [ 0.84408793, 0.7565708 , 0.18566003], - [ 0.71847225, 0.78348879, 0.01394492], - [ 0.2157923 , 0.0878241 , 0.53304275], - [ 0.65077817, 0.73134788, 0.47375731], - [ 0.15480248, 0.04877231, 0.84551572], - [ 0.18828918, 0.34674004, 0.11989061], - [ 0.78564365, 0.30275406, 0.09642356], - [ 0.82960515, 0.73738278, 0.24500901], - [ 0.63381853, 0.78702512, 0.44869516], - [ 0.60875909, 0.38448521, 0.11101309], - [ 0.25896923, 0.86776042, 0.99926272], - [ 0.44865064, 0.47424466, 0.51402304], - [ 0.44738627, 0.413574 , 0.58787803], - [ 0.42558597, 0.18098633, 0.44647855], - [ 0.6197636 , 0.40172899, 0.82633434], - [ 0.19667605, 0.9592378 , 0.31371263], - [ 0.44543992, 0.36630682, 0.96721493], - [ 0.00113251, 0.74157699, 0.83322406], - [ 0.02975107, 0.82937627, 0.80524179], - [ 0.39907603, 0.53267979, 0.53531684], - [ 0.8342222 , 0.9169928 , 0.81969662], - [ 0.13888135, 0.67287953, 0.45754592], - [ 0.4873301 , 0.02399868, 0.79007014], - [ 0.48908379, 0.01660648, 0.88531733], - [ 0.06064489, 0.15676077, 0.57462736], - [ 0.46347854, 0.50204698, 0.92260013], - [ 0.30769454, 0.91413535, 0.71872948], - [ 0.54766355, 0.99080514, 0.23629655], - [ 0.29504561, 0.69239956, 0.11541326], - [ 0.06638065, 0.44583771, 0.40993712], - [ 0.78546547, 0.39669903, 0.70850067], - [ 0.57490847, 0.01931911, 0.95229857], - [ 0.36478595, 0.51095616, 0.4450777 ], - [ 0.27962055, 0.5670248 , 0.73430206], - [ 0.08512962, 0.92858697, 0.16280465], - [ 0.35404686, 0.26061171, 0.90922437], - [ 0.36088532, 0.67658412, 0.3225552 ], - [ 0.21179329, 0.78877855, 0.52533685], - [ 0.72919654, 0.30032783, 0.35231397], - [ 0.98164664, 0.14363536, 0.70022392], - [ 0.52173619, 0.80860274, 0.50831038], - [ 0.38294836, 0.0077242 , 0.73545865], - [ 0.88265733, 0.43355191, 0.20679372], - [ 0.90846836, 0.51886944, 0.38919361], - [ 0.92039147, 0.66254952, 0.65083492], - [ 0.70248187, 0.10121166, 0.89420336], - [ 0.89448921, 0.88377854, 0.46296508], - [ 0.35057331, 0.12859417, 0.02405395], - [ 0.99091684, 0.54648747, 0.03855661], - [ 0.26477678, 0.84030298, 0.5826511 ], - [ 0.14283269, 0.30983103, 0.76758542], - [ 0.95578979, 0.17808405, 0.33390006], - [ 0.09878404, 0.22161407, 0.65968794], - [ 0.04496103, 0.66141433, 0.16798657], - [ 0.15300491, 0.48347774, 0.6682864 ], - [ 0.55398838, 0.2255844 , 0.93903814], - [ 0.93418825, 0.5798594 , 0.34924861], - [ 0.01206828, 0.44051883, 0.63147375], - [ 0.08048752, 0.70924834, 0.36574764], - [ 0.03811209, 0.44101423, 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0.73187941, 0.99794175], + [0.84381799, 0.50563945, 0.2338819], + [0.64879475, 0.11428564, 0.65671366], + [0.23384312, 0.66965284, 0.19456637], + [0.53093166, 0.95852386, 0.98772503], + [0.98463144, 0.03103187, 0.86130255], + [0.06819395, 0.49299943, 0.06459917], + [0.91893265, 0.49085647, 0.52698672], + [0.98981069, 0.90960177, 0.54153429], + [0.28101046, 0.06888627, 0.84965766], + [0.62303017, 0.21383628, 0.98395503], + [0.51816527, 0.10226694, 0.2760039], + [0.27242839, 0.98456279, 0.43348216], + [0.8505522, 0.06138676, 0.92275804], + [0.2688598, 0.68773136, 0.63179621]]) class Test(unittest.TestCase): @@ -1015,37 +1015,37 @@ class Test(unittest.TestCase): def run_point(self, X, extra_points=32): exact = baker_exact_3D(X) answers = [] - for o in (2,3,4,5): + for o in (2, 3, 4, 5): r = self.g.interpolate(X, order=o, extra_points=extra_points) answers.append(improved_answer(r, exact)) return answers def test_point_1(self): - X = [0.2,0.2,0.2] + X = [0.2, 0.2, 0.2] answers = self.run_point(X) expected_answers = [True, True, True, False] self.assertEqual(answers, expected_answers) def test_point_2(self): - X = [0.1,0.8,0.9] + X = [0.1, 0.8, 0.9] answers = self.run_point(X) expected_answers = [True, True, True, False] self.assertEqual(answers, expected_answers) def test_point_3(self): - X = [0.5,0.5,0.99999] + X = [0.5, 0.5, 0.99999] answers = self.run_point(X) expected_answers = [True, True, True, True] self.assertEqual(answers, expected_answers) def test_point_4(self): - X = [0.5,0.5,0.99999] + X = [0.5, 0.5, 0.99999] answers = self.run_point(X, extra_points=64) expected_answers = [True, True, True, True] self.assertEqual(answers, expected_answers) def test_point_5(self): - X = [0.5,0.5,0.5] + X = [0.5, 0.5, 0.5] answers = self.run_point(X, extra_points=128) expected_answers = [True, True, True, True] self.assertEqual(answers, expected_answers) diff --git a/test/quadratic2d.py b/test/quadratic2d.py index eafc5f1..533f81d 100644 --- a/test/quadratic2d.py +++ b/test/quadratic2d.py @@ -3,7 +3,6 @@ import unittest from interp.baker import interpolate -from interp.grid import grid from interp.grid import contains