diff --git a/.setup b/.setup index 4a26132..bcbe9aa 100644 --- a/.setup +++ b/.setup @@ -1,2 +1 @@ export PATH=$PWD/bin:$PWD/test:$PATH -export PYTHONPATH=$PWD/lib diff --git a/bin/driver.py b/bin/driver.py index 764c388..b5c12eb 100755 --- a/bin/driver.py +++ b/bin/driver.py @@ -6,18 +6,18 @@ from optparse import OptionParser import numpy as np from baker.tools import rms, exact_func -import grid +from grid.DD import simple_random_grid, simple_rect_grid def get_mesh(source, destination, use_structured_grid = False): mesh_source = None mesh_dest = None if use_structured_grid: - mesh_source = grid.simple_rect_grid(source, source) - mesh_dest = grid.simple_rect_grid(destination, destination) + mesh_source = simple_rect_grid(source, source) + mesh_dest = simple_rect_grid(destination, destination) else: - mesh_source = grid.simple_random_grid(source) - mesh_dest = grid.simple_random_grid(destination) + mesh_source = simple_random_grid(source) + mesh_dest = simple_random_grid(destination) if not (mesh_dest and mesh_source): raise smberror('problem creating mesh objects') @@ -39,35 +39,33 @@ if __name__ == '__main__': dest="extra", type='int', default = 3, - help = "how many extra points") + help = "how many extra points (%default)") parser.add_option("-s", "--source-total", dest="source_total", type='int', default = 100, - help = "total number of source points for random,\ - resolution for structured") + help = "total number of source points for random, resolution for structured (%default)") parser.add_option("-d", "--destination-total", dest="destination_total", type='int', default = 100, - help = "total number of destination points,\ - resolution for structured") + help = "total number of destination points, resolution for structured (%default)") parser.add_option("-r", "--structured", action = 'store_true', default = False, - help = "use a structured grid instead of random point cloud") + help = "use a structured grid instead of random point cloud (%default)") parser.add_option("-v", "--verbose", action = 'store_true', default = False, - help = "verbosity") + help = "verbosity (%default)") (options, args) = parser.parse_args() diff --git a/bin/grid_regular.py b/bin/grid_regular.py index 515fc68..f25087d 100755 --- a/bin/grid_regular.py +++ b/bin/grid_regular.py @@ -1,9 +1,9 @@ -#!/usr/bin/python +#!/usr/bin/python2.6 import sys import pickle -from grid import simple_rect_grid, simple_random_grid +from grid.DD import simple_rect_grid, simple_random_grid from baker import run_baker from baker.tools import smberror diff --git a/lib/baker/baker.py b/lib/baker/baker.py index d2289fb..023e757 100644 --- a/lib/baker/baker.py +++ b/lib/baker/baker.py @@ -41,9 +41,14 @@ def get_phis_3D(X, r): X -- the destination point (3D) X = [0,0,0] r -- the four points that make up the tetrahedron (3D) - r = [[-1, -1], [0, 2], [1, -1]] + r = [ + [0.0, 0.0, 1.0], + [0.94280904333606508, 0.0, -0.3333333283722672], + [-0.47140452166803232, 0.81649658244673617, -0.3333333283722672], + [-0.47140452166803298, -0.81649658244673584, -0.3333333283722672], + ] - this will return [0.333, 0.333, 0.333] + this will return [0.25, 0.25, 0.25, 0.25] """ # baker: eq 7 @@ -82,7 +87,7 @@ def qlinear(X, R): qlin = sum([q_i * phi_i for q_i, phi_i in zip(R.q, phis)]) return phis, qlin -def qlinear_3D(X, R, q): +def qlinear_3D(X, R): """ this calculates the linear portion of q from X to r @@ -91,8 +96,8 @@ def qlinear_3D(X, R, q): q = CFD quantities of interest at the simplex points(R) """ - phis = get_phis_3D(X, R) - qlin = sum([q_i * phi_i for q_i, phi_i in zip(q, phis)]) + phis = get_phis_3D(X, R.points) + qlin = sum([q_i * phi_i for q_i, phi_i in zip(R.q, phis)]) return phis, qlin def run_baker(X, R, S): @@ -103,13 +108,11 @@ def run_baker(X, R, S): X = [0,0] R = Simplex - S = extra points - """ # calculate values only for the triangle - phi, qlin = qlinear (X, R) + phi, qlin = qlinear(X, R) if len(S.points) == 0: answer = { @@ -129,7 +132,13 @@ def run_baker(X, R, S): cur_phi, cur_qlin = qlinear(s, R) (phi1, phi2, phi3) = cur_phi - B.append([phi1 * phi2, phi2 * phi3, phi3 * phi1]) + B.append( + [ + phi1 * phi2, + phi2 * phi3, + phi3 * phi1, + ] + ) w.append(q - cur_qlin) B = np.array(B) @@ -161,3 +170,87 @@ def run_baker(X, R, S): } return answer + +def run_baker_3D(X, R, S): + """ + This is the main function to call to get an interpolation to X from the input meshes + + X -- the destination point (3D) + X = [0,0,0] + + R = Simplex (4 points, contains X) + S = extra points (surrounding, in some manner, R and X, but not in R) + """ + + # calculate values only for the triangle + phi, qlin = qlinear_3D(X, R) + + if len(S.points) == 0: + answer = { + 'a': None, + 'b': None, + 'c': None, + 'd': None, + 'e': None, + 'f': None, + 'qlin': qlin, + 'error': None, + 'final': None, + } + return answer + + B = [] # baker eq 9 + w = [] # baker eq 11 + + for (s, q) in zip(S.points, S.q): + cur_phi, cur_qlin = qlinear_3D(s, R) + (phi1, phi2, phi3, phi4) = cur_phi + + B.append( + [ + phi1 * phi2, + phi1 * phi3, + phi1 * phi4, + phi2 * phi3, + phi2 * phi4, + phi3 * phi4, + ] + ) + + w.append(q - cur_qlin) + + B = np.array(B) + w = np.array(w) + + A = np.dot(B.T, B) + b = np.dot(B.T, w) + + # baker solve eq 10 + try: + (a, b, c, d, e, f) = np.linalg.solve(A,b) + except: + print >> sys.stderr, "warning: run_baker: linear calculation went bad, resorting to np.linalg.pinv" + (a, b, c, d, e, f) = np.dot(np.linalg.pinv(A), b) + + error_term = a * phi[0] * phi[1]\ + + b * phi[0] * phi[2]\ + + c * phi[0] * phi[3]\ + + d * phi[1] * phi[2]\ + + e * phi[1] * phi[3]\ + + f * phi[2] * phi[3] + + q_final = qlin + error_term + + answer = { + 'a': a, + 'b': b, + 'c': c, + 'd': d, + 'e': e, + 'f': f, + 'qlin': qlin, + 'error': error_term, + 'final': q_final, + } + + return answer diff --git a/lib/baker/tools.py b/lib/baker/tools.py index 3ad8a4c..b7f2e34 100644 --- a/lib/baker/tools.py +++ b/lib/baker/tools.py @@ -24,3 +24,12 @@ def exact_func(x, y): the exact function used from baker's article (for testing) """ return np.power((np.sin(x * np.pi) * np.cos(y * np.pi)), 2) + +def exact_func_3D(X): + """ + the exact function (3D) used from baker's article (for testing) + """ + x = X[0] + y = X[1] + z = X[2] + return np.power((np.sin(x * np.pi / 2.0) * np.sin(y * np.pi / 2.0) * np.sin(z * np.pi / 2.0)), 2) diff --git a/lib/grid/grid.py b/lib/grid/grid.py index 6cbd413..58a39be 100755 --- a/lib/grid/grid.py +++ b/lib/grid/grid.py @@ -7,49 +7,11 @@ from collections import defaultdict import numpy as np import scipy.spatial -from baker import run_baker, get_phis +from baker import run_baker from baker.tools import exact_func, smberror +from simplex import face from smcqdelaunay import * -class face(object): - def __init__(self, name): - self.name = name - self.verts = [] - self.neighbors = [] - - def add_vert(self, v): - """ - v should be an index into grid.points - """ - self.verts.append(v) - - def add_neighbor(self, n): - """ - reference to another face object - """ - self.neighbors.append(n) - - def contains(self, X, grid): - R = [grid.points[i] for i in self.verts] - - phis = get_phis(X, R) - - r = True - if [i for i in phis if i < 0.0]: - r = False - return r - - def __str__(self): - neighbors = [i.name for i in self.neighbors] - return '%s: verts: %s neighbors: [%s]' %\ - ( - self.name, - self.verts, - ", ".join(neighbors) - ) - - - class grid(object): @@ -97,7 +59,7 @@ class grid(object): R is a grid object that is the (a) containing simplex around point X S is S_j from baker's paper : some points from all point that are not the simplex """ - (dist, indicies) = self.tree.query(X, 3 + extra_points) + (dist, indicies) = self.tree.query(X, simplex_size + extra_points) # get the containing simplex @@ -152,7 +114,7 @@ class grid(object): try: (R, S) = self.get_simplex_and_nearest_points(X) answer = run_baker(X, R, S) - except smberror as e: + except smberror, e: print "caught error: %s, trying with connectivity-based mesh" % e (R, S) = self.get_points_conn(X) answer = run_baker(X, R, S) @@ -199,27 +161,6 @@ class grid(object): # self.facets_for_point[int(point[1:])] = [i for i in neighboring_facets.split() if i in self.faces] - def for_qhull_generator(self): - """ - this returns a generator that should be fed into qdelaunay - """ - - yield '2'; - yield '%d' % len(self.points) - - for p in self.points: - yield "%f %f" % (p[0], p[1]) - - def for_qhull(self): - """ - this returns a single string that should be fed into qdelaunay - """ - r = '2\n' - r += '%d\n' % len(self.points) - for p in self.points: - r += "%f %f\n" % (p[0], p[1]) - return r - def __str__(self): r = '' assert( len(self.points) == len(self.q) ) @@ -233,49 +174,7 @@ class grid(object): r += "%s\n" % v return r -class simple_rect_grid(grid): - def __init__(self, xres = 5, yres = 5): - xmin = -1.0 - xmax = 1.0 - xspan = xmax - xmin - xdel = xspan / float(xres - 1) - ymin = -1.0 - ymay = 1.0 - yspan = ymay - ymin - ydel = yspan / float(yres - 1) - - - points = [] - q = [] - for x in xrange(xres): - cur_x = xmin + (x * xdel) - for y in xrange(yres): - cur_y = ymin + (y * ydel) - points.append([cur_x, cur_y]) - q.append(exact_func(cur_x, cur_y)) - grid.__init__(self, points, q) - self.construct_connectivity() - - - -class simple_random_grid(simple_rect_grid): - def __init__(self, num_points = 10): - points = [] - q = [] - - r = np.random - - for i in xrange(num_points): - cur_x = r.rand() - cur_y = r.rand() - - points.append([cur_x, cur_y]) - q.append(exact_func(cur_x, cur_y)) - grid.__init__(self, points, q) - - self.points = np.array(self.points) - self.q = np.array(self.q) if __name__ == '__main__': diff --git a/setup.py b/setup.py index d305283..e815ff2 100644 --- a/setup.py +++ b/setup.py @@ -4,7 +4,7 @@ use_setuptools() from setuptools import setup, find_packages setup( - name = 'bakinterp', + name = 'interpolosion', version = '0.01', package_dir = {'':'lib'}, packages = find_packages('lib'), diff --git a/test/baker.test.py b/test/baker.test.py index 95cff5b..addfcaf 100755 --- a/test/baker.test.py +++ b/test/baker.test.py @@ -10,7 +10,6 @@ import scipy.spatial class TestSequenceFunctions(unittest.TestCase): def setUp(self): self.l = [[-1, 1], [-1, 0], [-1, 1], [0, -1], [0, 0], [0, 1], [1, -1], [1, 0], [1, 1]] - self.approx_fmt = "%0.6f" self.all_points = [ [ 0, 0], # 0 [ 1, 0], # 1 @@ -37,9 +36,9 @@ class TestSequenceFunctions(unittest.TestCase): r = [[-1, -1], [0, 2], [1, -1]] result = baker.get_phis(X, r) - result = [self.approx_fmt % i for i in result] + result = [round(i, 5) for i in result] - right_answer = [self.approx_fmt % i for i in [1/3.0, 1/3.0, 1/3.0]] + right_answer = [round(i, 5) for i in [1/3.0, 1/3.0, 1/3.0]] for a,b in zip(result, right_answer): self.assertEqual(a,b) @@ -78,13 +77,13 @@ class TestSequenceFunctions(unittest.TestCase): self.q[size_of_simplex:size_of_simplex + extra_points]) answer = baker.run_baker(self.X, R, S) - a = self.approx_fmt % answer['a'] - b = self.approx_fmt % answer['b'] - c = self.approx_fmt % answer['c'] + a = round(answer['a'], 5) + b = round(answer['b'], 5) + c = round(answer['c'], 5) self.assertEqual(a, c) - self.assertEqual(c, self.approx_fmt % 0.00) - self.assertEqual(b, self.approx_fmt % (1/3.0)) + self.assertEqual(c, round(0.00 , 5)) + self.assertEqual(b, round(1/3.0, 5)) def testRunBaker_2(self): size_of_simplex = 3 @@ -98,12 +97,12 @@ class TestSequenceFunctions(unittest.TestCase): answer = baker.run_baker(self.X, R, S) - a = self.approx_fmt % answer['a'] - b = self.approx_fmt % answer['b'] - c = self.approx_fmt % answer['c'] + a = round(answer['a'], 5) + b = round(answer['b'], 5) + c = round(answer['c'], 5) self.assertEqual(a, c) - self.assertEqual(c, self.approx_fmt % float(2/3.0)) + self.assertEqual(c, round(float(2/3.0), 5)) def testRunBaker_3(self): size_of_simplex = 3 @@ -116,13 +115,13 @@ class TestSequenceFunctions(unittest.TestCase): self.q[size_of_simplex:size_of_simplex + extra_points]) answer = baker.run_baker(self.X, R, S) - a = self.approx_fmt % answer['a'] - b = self.approx_fmt % answer['b'] - c = self.approx_fmt % answer['c'] + a = round(answer['a'], 5) + b = round(answer['b'], 5) + c = round(answer['c'], 5) - self.assertEqual(a, self.approx_fmt % float(13/14.0)) - self.assertEqual(b, self.approx_fmt % float(2 / 7.0)) - self.assertEqual(c, self.approx_fmt % float(15/14.0)) + self.assertEqual(a, round(float(13/14.0), 5)) + self.assertEqual(b, round(float(2 / 7.0), 5)) + self.assertEqual(c, round(float(15/14.0), 5)) def testRunBaker_4(self): size_of_simplex = 3 @@ -135,13 +134,13 @@ class TestSequenceFunctions(unittest.TestCase): self.q[size_of_simplex:size_of_simplex + extra_points]) answer = baker.run_baker(self.X, R, S) - a = self.approx_fmt % answer['a'] - b = self.approx_fmt % answer['b'] - c = self.approx_fmt % answer['c'] + a = round(answer['a'], 5) + b = round(answer['b'], 5) + c = round(answer['c'], 5) - self.assertEqual(a, self.approx_fmt % float(48/53.0)) - self.assertEqual(b, self.approx_fmt % float(15/53.0)) - self.assertEqual(c, self.approx_fmt % float(54/53.0)) + self.assertEqual(a, round(float(48/53.0), 5)) + self.assertEqual(b, round(float(15/53.0), 5)) + self.assertEqual(c, round(float(54/53.0), 5)) if __name__ == '__main__': suite = unittest.TestLoader().loadTestsFromTestCase(TestSequenceFunctions)