putting together a simple test case so that I can test my quad/cubic interpolator

bin/driver.py

@@ -6,18 +6,18 @@ from optparse import OptionParser
 import numpy as np
 
 from baker.tools import rms, exact_func
-from grid.DD import simple_random_grid, simple_rect_grid
+from grid.DD import random_grid, rect_grid
 
 
 def get_mesh(source, destination, use_structured_grid = False):
   mesh_source = None
   mesh_dest   = None
   if use_structured_grid:
-    mesh_source = simple_rect_grid(source, source)
+    mesh_source = rect_grid(source, source)
-    mesh_dest   = simple_rect_grid(destination, destination)
+    mesh_dest   = rect_grid(destination, destination)
   else:
-    mesh_source = simple_random_grid(source)
+    mesh_source = random_grid(source)
-    mesh_dest   = simple_random_grid(destination)
+    mesh_dest   = random_grid(destination)
 
   if not (mesh_dest and mesh_source):
     raise smberror('problem creating mesh objects')
@@ -88,7 +88,7 @@ if __name__ == '__main__':
       errors.append(0)
       continue
 
-    exact = exact_func(X[0], X[1])
+    exact = exact_func(X)
     if np.abs(exact - answer['final']) <= np.abs(exact - answer['qlin']):
       success += 1
 

bin/generate_qhull.pl

@@ -1,16 +0,0 @@
-#!/usr/bin/perl
-
-use strict;
-use warnings;
-
-my $output_filename = $ARGV[0] or die "no args";
-my $tmp_grid_file   = "$output_filename.grid.txt";
-
-system("grid.py > $tmp_grid_file");
-
-
-system("cat $tmp_grid_file | qdelaunay  GD2 s > $output_filename.txt\n"       );
-system("cat $tmp_grid_file | qdelaunay GD2 s Qt > ${output_filename}_qt.txt\n");
-system("cat $tmp_grid_file | qdelaunay GD2 s QJ > ${output_filename}_qj.txt\n");
-
-unlink($tmp_grid_file);

bin/grid_regular.py

@@ -3,9 +3,9 @@
 import sys
 import pickle
 
-from grid.DD     import simple_rect_grid, simple_random_grid
+from grid.DD     import rect_grid, random_grid
 from baker       import run_baker
-from baker.tools import smberror
+from baker.tools import exact_func, smberror
 
 qfile = '/tmp/grid_regular.txt'
 
@@ -18,19 +18,23 @@ if __name__ == '__main__':
     rx = 4
     ry = 4 * rx
 
-  source_mesh = simple_rect_grid(rx, ry)
+  source_mesh = rect_grid(rx, ry)
 
   # print source_mesh
 
-  X = [0.1, 0.1]
+  X = [0.1, 0.01]
 
   try:
+    print "trying to get simplex and nearest points using nearest points (kdtree)"
     (R, S) = source_mesh.get_simplex_and_nearest_points(X, extra_points=4)
     print "R for nearest-neighbor:\n", R
     print "S for nearest-neighbor:\n", S
+    print "trying to run baker"
     print run_baker(X, R, S)
   except smberror as e:
     print "caught error: %s" % e
+
+    print "trying to get simplex and nearest points using connectivity scheme"
     (R, S) =  source_mesh.get_points_conn(X)
     print "R for connectivity:\n", R
     print "S for connectivity:\n", S
@@ -38,5 +42,16 @@ if __name__ == '__main__':
 
 
   print "repeating the above just using the grid object:"
-  print source_mesh.run_baker(X)
+  r = source_mesh.run_baker(X)
+  exact = exact_func(X)
+  print r
+  print 'exact', exact
+  print 'qlin' , r['qlin']
+  print 'error', r['error']
+  print 'final', r['final']
+
+  if abs(r['final'] - exact) <= abs(r['qlin'] - exact):
+    print "win"
+  else:
+    print "failure"
   open(qfile, 'w').write(source_mesh.for_qhull())

bin/test.py

@@ -1,9 +1,9 @@
 #!/usr/bin/python2.6
 
 import sys
-from grid.DDD import simple_random_grid
+from grid.DDD import random_grid
 from baker import get_phis_3D, run_baker_3D
-from baker.tools import exact_func_3D
+from baker.tools import exact_func_3D, smberror
 
 try:
   total_points = int(sys.argv[1])
@@ -12,7 +12,7 @@ except:
 
 
 print total_points
-g = simple_random_grid(total_points)
+g = random_grid(total_points)
 
 open('/tmp/for_qhull.txt', 'w').write(g.for_qhull())
 
@@ -31,13 +31,16 @@ print "phi values (should all be positive): ", phis, sum(phis)
 if [i for i in phis if i < 0.0]:
   print "problems"
 
-r = run_baker_3D(X, R, S)
+try:
+  r = run_baker_3D(X, R, S)
+  print 'qlin' , r['qlin']
+  print 'error', r['error']
+  print 'final', r['final']
 
-print 'qlin' , r['qlin']
+  if abs(r['final'] - exact) <= abs(r['qlin'] - exact):
-print 'error', r['error']
+    print "win"
-print 'final', r['final']
+  else:
-
+    print "failure"
-if abs(r['final'] - exact) <= abs(r['qlin'] - exact):
+except smberror as e:
-  print "win"
+  print e
-else:
+  print 'TAINT'
-  print "failure"

lib/baker/__init__.py

@@ -1 +1,274 @@
 from baker import *
+import numpy as np
+import sys
+
+from tools import smberror
+
+def get_phis(X, R):
+  """
+    The get_phis function is used to get barycentric coordonites for a point on a triangle.
+
+    X -- the destination point (2D)
+         X = [0,0]
+    r -- the three points that make up the containing triangular simplex (2D)
+         r = [[-1, -1], [0, 2], [1, -1]]
+
+    this will return [0.333, 0.333, 0.333]
+  """
+
+  # baker: eq 7
+  A = np.array([
+                [      1,       1,       1],
+                [R[0][0], R[1][0], R[2][0]],
+                [R[0][1], R[1][1], R[2][1]],
+                ])
+  b = np.array([    1,
+                  X[0],
+                  X[1]
+              ])
+  try:
+    phi = np.linalg.solve(A,b)
+  except np.linalg.LinAlgError as e:
+    msg = "warning: get_phis: calculation of phis yielded a linearly dependant system (%s)" % e
+    # TODO: log this -- > print >> sys.stderr, msg
+    raise smberror(msg)
+    phi = np.dot(np.linalg.pinv(A), b)
+
+  return phi
+
+def get_phis_3D(X, R):
+  """
+    The get_phis function is used to get barycentric coordonites for a point on a tetrahedron.
+
+    X -- the destination point (3D)
+         X = [0,0,0]
+    R -- the four points that make up the containing simplex, tetrahedron (3D)
+         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 (should) will return [0.25, 0.25, 0.25, 0.25]
+  """
+
+  # baker: eq 7
+  A = np.array([
+                [      1,       1,       1,       1 ],
+                [R[0][0], R[1][0], R[2][0], R[3][0]],
+                [R[0][1], R[1][1], R[2][1], R[3][1]],
+                [R[0][2], R[1][2], R[2][2], R[3][2]],
+                ])
+  b = np.array([    1,
+                  X[0],
+                  X[1],
+                  X[2]
+              ])
+  try:
+    phi = np.linalg.solve(A,b)
+  except np.linalg.LinAlgError as e:
+    print >> sys.stderr, "warning: get_phis_3D: calculation of phis yielded a linearly dependant system", e
+    phi = np.dot(np.linalg.pinv(A), b)
+
+  return phi
+
+
+def qlinear(X, R):
+  """
+    this calculates the linear portion of q from X to R
+
+    also, this is baker eq 3
+
+    X = destination point
+    R = simplex points
+    q = CFD quantities of interest at the simplex points
+  """
+
+  phis = get_phis(X, R.points)
+  qlin = sum([q_i * phi_i for q_i, phi_i in zip(R.q, phis)])
+  return phis, qlin
+
+def qlinear_3D(X, R):
+  """
+    this calculates the linear portion of q from X to R
+
+    X = destination point
+    R = simplex points
+    q = CFD quantities of interest at the simplex points(R)
+  """
+
+  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):
+  """
+    This is the main function to call to get an interpolation to X from the input meshes
+
+    X -- the destination point (2D)
+         X = [0,0]
+
+    R = Simplex
+    S = extra points
+  """
+
+  # calculate values only for the simplex triangle
+  phi, qlin = qlinear(X, R)
+
+  if [i for i in phi if i <= 0.0]:
+    s = "this is not a containing simplex:\n"
+    s += "  X: %s\n" % X
+    s += "  R: %s\n" % R
+    s += "  phi: %s, sum(%0.4e)\n" % (phi, sum(phi))
+    print >> sys.stderr, s
+    raise smberror("simplex does not contain point")
+
+  if len(S.points) == 0:
+    answer = {
+               'a': None,
+               'b': None,
+               'c': 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(s, R)
+    (phi1, phi2, phi3) = cur_phi
+
+    B.append(
+              [
+                phi1 * phi2,
+                phi2 * phi3,
+                phi3 * phi1,
+              ]
+            )
+    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) = np.linalg.solve(A,b)
+  except np.linalg.LinAlgError as e:
+    print >> sys.stderr, "warning: run_baker: linear calculation went bad, resorting to np.linalg.pinv", e
+    (a, b, c) = np.dot(np.linalg.pinv(A), b)
+
+  error_term =  a * phi[0] * phi[1]\
+              + b * phi[1] * phi[2]\
+              + c * phi[2] * phi[0]
+
+  q_final = qlin + error_term
+
+  answer = {
+             'a': a,
+             'b': b,
+             'c': c,
+             'qlin': qlin,
+             'error': error_term,
+             'final': q_final,
+            }
+
+  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 [i for i in phi if i <= 0.0]:
+    s = "this is not a containing simplex:\n"
+    s += "  X: %s\n" % X
+    s += "  R: %s\n" % R
+    s += "  phi: %s, sum(%0.4e)\n" % (phi, sum(phi))
+    print >> sys.stderr, s
+    raise smberror("not containing simplex")
+
+  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 np.linalg.LinAlgError as e:
+    print >> sys.stderr, "warning: run_baker: linear calculation went bad, resorting to np.linalg.pinv", e
+    (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

lib/baker/baker.py

@@ -1,272 +0,0 @@
-import numpy as np
-import sys
-
-from tools import smberror
-
-def get_phis(X, R):
-  """
-    The get_phis function is used to get barycentric coordonites for a point on a triangle.
-
-    X -- the destination point (2D)
-         X = [0,0]
-    r -- the three points that make up the triangular simplex (2D)
-         r = [[-1, -1], [0, 2], [1, -1]]
-
-    this will return [0.333, 0.333, 0.333]
-  """
-
-  # baker: eq 7
-  A = np.array([
-                [      1,       1,       1],
-                [R[0][0], R[1][0], R[2][0]],
-                [R[0][1], R[1][1], R[2][1]],
-                ])
-  b = np.array([    1,
-                  X[0],
-                  X[1]
-              ])
-  try:
-    phi = np.linalg.solve(A,b)
-  except np.linalg.LinAlgError as e:
-    print >> sys.stderr, "warning: get_phis: calculation of phis yielded a linearly dependant system", e
-    raise smberror('get_phis')
-    phi = np.dot(np.linalg.pinv(A), b)
-
-  return phi
-
-def get_phis_3D(X, r):
-  """
-    The get_phis function is used to get barycentric coordonites for a point on a triangle.
-
-    X -- the destination point (3D)
-         X = [0,0,0]
-    r -- the four points that make up the tetrahedron (3D)
-         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 [0.25, 0.25, 0.25, 0.25]
-  """
-
-  # baker: eq 7
-  A = np.array([
-                [      1,       1,       1,       1 ],
-                [r[0][0], r[1][0], r[2][0], r[3][0]],
-                [r[0][1], r[1][1], r[2][1], r[3][1]],
-                [r[0][2], r[1][2], r[2][2], r[3][2]],
-                ])
-  b = np.array([    1,
-                  X[0],
-                  X[1],
-                  X[2]
-              ])
-  try:
-    phi = np.linalg.solve(A,b)
-  except np.linalg.LinAlgError as e:
-    print >> sys.stderr, "warning: get_phis_3D: calculation of phis yielded a linearly dependant system", e
-    phi = np.dot(np.linalg.pinv(A), b)
-
-  return phi
-
-
-def qlinear(X, R):
-  """
-    this calculates the linear portion of q from X to r
-
-    also, this is baker eq 3
-
-    X = destination point
-    R = simplex points
-    q = CFD quantities of interest at the simplex points
-  """
-
-  phis = get_phis(X, R.points)
-  qlin = sum([q_i * phi_i for q_i, phi_i in zip(R.q, phis)])
-  return phis, qlin
-
-def qlinear_3D(X, R):
-  """
-    this calculates the linear portion of q from X to r
-
-    X = destination point
-    R = simplex points
-    q = CFD quantities of interest at the simplex points(R)
-  """
-
-  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):
-  """
-    This is the main function to call to get an interpolation to X from the input meshes
-
-    X -- the destination point (2D)
-         X = [0,0]
-
-    R = Simplex
-    S = extra points
-  """
-
-  # calculate values only for the simplex triangle
-  phi, qlin = qlinear(X, R)
-
-  if [i for i in phi if i <= 0.0]:
-    s = "this is not a containing simplex:\n"
-    s += "  X: %s\n" % X
-    s += "  R: %s\n" % R
-    s += "  phi: %s, sum(%0.4e)\n" % (phi, sum(phi))
-    print >> sys.stderr, s
-    raise smberror("not containing simplex")
-
-  if len(S.points) == 0:
-    answer = {
-               'a': None,
-               'b': None,
-               'c': 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(s, R)
-    (phi1, phi2, phi3) = cur_phi
-
-    B.append(
-              [
-                phi1 * phi2,
-                phi2 * phi3,
-                phi3 * phi1,
-              ]
-            )
-    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) = np.linalg.solve(A,b)
-  except np.linalg.LinAlgError as e:
-    print >> sys.stderr, "warning: run_baker: linear calculation went bad, resorting to np.linalg.pinv", e
-    (a, b, c) = np.dot(np.linalg.pinv(A), b)
-
-  error_term =  a * phi[0] * phi[1]\
-              + b * phi[1] * phi[2]\
-              + c * phi[2] * phi[0]
-
-  q_final = qlin + error_term
-
-  answer = {
-             'a': a,
-             'b': b,
-             'c': c,
-             'qlin': qlin,
-             'error': error_term,
-             'final': q_final,
-            }
-
-  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 [i for i in phi if i <= 0.0]:
-    s = "this is not a containing simplex:\n"
-    s += "  X: %s\n" % X
-    s += "  R: %s\n" % R
-    s += "  phi: %s, sum(%0.4e)\n" % (phi, sum(phi))
-    print >> sys.stderr, s
-    raise smberror("not containing simplex")
-
-  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 np.linalg.LinAlgError as e:
-    print >> sys.stderr, "warning: run_baker: linear calculation went bad, resorting to np.linalg.pinv", e
-    (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

lib/baker/tools.py

@@ -19,10 +19,12 @@ def rms(errors):
   r = np.sqrt(r / len(errors))
   return r
 
-def exact_func(x, y):
+def exact_func(X):
   """
     the exact function used from baker's article (for testing)
   """
+  x = X[0]
+  y = X[0]
   return np.power((np.sin(x * np.pi) * np.cos(y * np.pi)), 2)
 
 def exact_func_3D(X):

lib/grid/DD.py

@@ -1,32 +1,13 @@
-from grid import grid
+from grid import grid as basegrid
+
 from baker.tools import exact_func
 
 import numpy as np
 
 
-class simple_rect_grid(grid):
+class grid(basegrid):
-  def __init__(self, xres = 5, yres = 5):
+  def __init__(self, points, q):
-    xmin = -1.0
+    basegrid.__init__(self, points, q)
-    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()
 
   def for_qhull_generator(self):
     """
@@ -49,8 +30,32 @@ class simple_rect_grid(grid):
       r += "%f %f\n" % (p[0], p[1])
     return r
 
+class rect_grid(grid):
+  def __init__(self, xres = 5, yres = 5):
+    xmin = -1.0
+    xmax =  1.0
+    xspan = xmax - xmin
+    xdel = xspan / float(xres - 1)
 
-class simple_random_grid(simple_rect_grid):
+    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 random_grid(rect_grid):
   def __init__(self, num_points = 10):
     points = []
     q = []
@@ -62,7 +67,7 @@ class simple_random_grid(simple_rect_grid):
       cur_y = r.rand()
 
       points.append([cur_x, cur_y])
-      q.append(exact_func(cur_x, cur_y))
+      q.append( exact_func( (cur_x, cur_y) ) )
     grid.__init__(self, points, q)
 
     self.points = np.array(self.points)

lib/grid/DDD.py

@@ -1,10 +1,35 @@
-from grid import grid
+from grid import grid as basegrid
 from baker.tools import exact_func_3D
 
 import numpy as np
 
 
-class simple_rect_grid(grid):
+class grid(basegrid):
+  def __init__(self, points, q):
+    basegrid.__init__(self, points, q)
+
+  def for_qhull_generator(self):
+    """
+      this returns a generator that should be fed into qdelaunay
+    """
+
+    yield '3';
+    yield '%d' % len(self.points)
+
+    for p in self.points:
+      yield "%f %f %f" % tuple(p)
+
+  def for_qhull(self):
+    """
+      this returns a single string that should be fed into qdelaunay
+    """
+    r  = '3\n'
+    r += '%d\n' % len(self.points)
+    for p in self.points:
+      r += "%f %f %f\n" % tuple(p)
+    return r
+
+class rect_grid(grid):
   def __init__(self, xres = 5, yres = 5, zres = 5):
     xmin = -1.0
     xmax =  1.0
@@ -56,7 +81,7 @@ class simple_rect_grid(grid):
       r += "%f %f %f\n" % tuple(p)
     return r
 
-class simple_random_grid(simple_rect_grid):
+class random_grid(rect_grid):
   def __init__(self, num_points = 10):
     points = []
     q = []

lib/grid/__init__.py

@@ -1 +1,173 @@
-from grid import *
+import sys
+import re
+from   collections import defaultdict
+
+import numpy as np
+import scipy.spatial
+
+from baker        import run_baker
+from baker.tools  import exact_func, smberror
+from simplex      import face
+from smcqdelaunay import *
+
+
+
+class grid(object):
+  facet_re = re.compile(r'''
+                            -\s+(?P<facet>f\d+).*?
+                            vertices:\s(?P<verts>.*?)\n.*?
+                            neighboring\s facets:\s+(?P<neigh>[\sf\d]*)
+                         ''', re.S|re.X)
+
+  point_re = re.compile(r'''
+                            -\s+(?P<point>p\d+).*?
+                            neighbors:\s+(?P<neigh>[\sf\d]*)
+                         ''', re.S|re.X)
+
+  vert_re  = re.compile(r'''
+                            (p\d+)
+                         ''', re.S|re.X)
+
+
+  def __init__(self, points, q):
+    """
+      this thing eats two pre-constructed arrays of stuff:
+      points = array of arrays (i will convert to numpy.array)
+               [[x0,y0], [x1,y1], ...]
+      q      = array (1D) of important values
+    """
+
+    self.points           = np.array(points)
+    self.q                = np.array(q)
+    self.tree             = scipy.spatial.KDTree(self.points)
+    self.faces            = {}
+    self.facets_for_point = defaultdict(list)
+
+
+  def create_mesh(self, indicies):
+    p = [self.points[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 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, simplex_size + extra_points)
+
+
+    # get the containing simplex
+    r_mesh = self.create_mesh(indicies[:simplex_size])
+    # and some extra points
+    s_mesh = self.create_mesh(indicies[simplex_size:])
+
+    return (r_mesh, s_mesh)
+
+  def get_points_conn(self, X):
+    """
+      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
+      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
+
+      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
+    """
+    if not self.faces:
+      self.construct_connectivity()
+
+    # get closest point
+    (dist, indicies) = self.tree.query(X, 2)
+
+    simplex = None
+    for i in self.facets_for_point[indicies[0]]:
+      if i.contains(X, self):
+        simplex = i
+        break
+
+    if not simplex:
+      raise AssertionError('no containing simplex found')
+
+    R = self.create_mesh(simplex.verts)
+
+
+    s = []
+    for c,i in enumerate(simplex.neighbors):
+      s.extend([guy for guy in i.verts if not guy in simplex.verts])
+    S = self.create_mesh(s)
+
+    return R, S
+
+  def run_baker(self, X):
+    answer = None
+
+    try:
+      (R, S) = self.get_simplex_and_nearest_points(X)
+      answer = run_baker(X, R, S)
+    except smberror, e:
+      print >> sys.stderr, "caught error: %s, trying with connectivity-based mesh" % e
+      (R, S) = self.get_points_conn(X)
+      answer = run_baker(X, R, S)
+
+    return answer
+
+
+
+  def construct_connectivity(self):
+    """
+      a call to this method prepares the internal connectivity structure.
+
+      this is part of the __init__ for a rect_grid, but can be called from any grid object
+    """
+    qdelaunay_string = get_qdelaunay_dump_str(self)
+    facet_to_facets = []
+    for matcher in grid.facet_re.finditer(qdelaunay_string):
+      d = matcher.groupdict()
+
+      facet_name          = d['facet']
+      verticies           = d['verts']
+      neighboring_facets  = d['neigh']
+
+      cur_face = face(facet_name)
+      self.faces[facet_name] = cur_face
+
+      for v in grid.vert_re.findall(verticies):
+        vertex_index = int(v[1:])
+        cur_face.add_vert(vertex_index)
+        self.facets_for_point[vertex_index].append(cur_face)
+
+      nghbrs = [(facet_name, i) for i in  neighboring_facets.split()]
+      facet_to_facets.extend(nghbrs)
+
+    for rel in facet_to_facets:
+      if rel[1] in self.faces:
+        self.faces[rel[0]].add_neighbor(self.faces[rel[1]])
+
+    # for matcher in grid.point_re.finditer(qdelaunay_string):
+    #   d = matcher.groupdict()
+
+    #   point               = d['point']
+    #   neighboring_facets  = d['neigh']
+
+    #   self.facets_for_point[int(point[1:])] = [i for i in neighboring_facets.split() if i in self.faces]
+
+  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.facets_for_point[c]])
+      r += "  faces: [%s]" % facet_str
+      r += "\n"
+    if self.faces:
+      for v in self.faces.itervalues():
+        r += "%s\n" % v
+    return r

lib/grid/grid.py

@@ -1,186 +0,0 @@
-#!/usr/bin/python
-
-import sys
-import re
-from   collections import defaultdict
-
-import numpy as np
-import scipy.spatial
-
-from baker        import run_baker
-from baker.tools  import exact_func, smberror
-from simplex      import face
-from smcqdelaunay import *
-
-
-
-class grid(object):
-  facet_re = re.compile(r'''
-                            -\s+(?P<facet>f\d+).*?
-                            vertices:\s(?P<verts>.*?)\n.*?
-                            neighboring\s facets:\s+(?P<neigh>[\sf\d]*)
-                         ''', re.S|re.X)
-
-  point_re = re.compile(r'''
-                            -\s+(?P<point>p\d+).*?
-                            neighbors:\s+(?P<neigh>[\sf\d]*)
-                         ''', re.S|re.X)
-
-  vert_re  = re.compile(r'''
-                            (p\d+)
-                         ''', re.S|re.X)
-
-
-  def __init__(self, points, q):
-    """
-      this thing eats two pre-constructed arrays of stuff:
-      points = array of arrays (i will convert to numpy.array)
-               [[x0,y0], [x1,y1], ...]
-      q      = array (1D) of important values
-    """
-
-    self.points           = np.array(points)
-    self.q                = np.array(q)
-    self.tree             = scipy.spatial.KDTree(self.points)
-    self.faces            = {}
-    self.facets_for_point = defaultdict(list)
-
-
-  def create_mesh(self, indicies):
-    p = [self.points[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 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, simplex_size + extra_points)
-
-
-    # get the containing simplex
-    r_mesh = self.create_mesh(indicies[:simplex_size])
-    # and some extra points
-    s_mesh = self.create_mesh(indicies[simplex_size:])
-
-    return (r_mesh, s_mesh)
-
-  def get_points_conn(self, X):
-    """
-      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
-      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
-
-      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
-    """
-    if not self.faces:
-      self.construct_connectivity()
-
-    # get closest point
-    (dist, indicies) = self.tree.query(X, 2)
-
-    simplex = None
-    for i in self.facets_for_point[indicies[0]]:
-      if i.contains(X, self):
-        simplex = i
-        break
-
-    if not simplex:
-      raise AssertionError('no containing simplex found')
-
-    R = self.create_mesh(simplex.verts)
-
-
-    s = []
-    for c,i in enumerate(simplex.neighbors):
-      s.extend([guy for guy in i.verts if not guy in simplex.verts])
-    S = self.create_mesh(s)
-
-    return R, S
-
-  def run_baker(self, X):
-    answer = None
-
-    try:
-      (R, S) = self.get_simplex_and_nearest_points(X)
-      answer = run_baker(X, R, S)
-    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)
-
-    return answer
-
-
-
-  def construct_connectivity(self):
-    """
-      a call to this method prepares the internal connectivity structure.
-
-      this is part of the __init__ for a simple_rect_grid, but can be called from any grid object
-    """
-    qdelaunay_string = get_qdelaunay_dump_str(self)
-    facet_to_facets = []
-    for matcher in grid.facet_re.finditer(qdelaunay_string):
-      d = matcher.groupdict()
-
-      facet_name          = d['facet']
-      verticies           = d['verts']
-      neighboring_facets  = d['neigh']
-
-      cur_face = face(facet_name)
-      self.faces[facet_name] = cur_face
-
-      for v in grid.vert_re.findall(verticies):
-        vertex_index = int(v[1:])
-        cur_face.add_vert(vertex_index)
-        self.facets_for_point[vertex_index].append(cur_face)
-
-      nghbrs = [(facet_name, i) for i in  neighboring_facets.split()]
-      facet_to_facets.extend(nghbrs)
-
-    for rel in facet_to_facets:
-      if rel[1] in self.faces:
-        self.faces[rel[0]].add_neighbor(self.faces[rel[1]])
-
-    # for matcher in grid.point_re.finditer(qdelaunay_string):
-    #   d = matcher.groupdict()
-
-    #   point               = d['point']
-    #   neighboring_facets  = d['neigh']
-
-    #   self.facets_for_point[int(point[1:])] = [i for i in neighboring_facets.split() if i in self.faces]
-
-  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.facets_for_point[c]])
-      r += "  faces: [%s]" % facet_str
-      r += "\n"
-    if self.faces:
-      for v in self.faces.itervalues():
-        r += "%s\n" % v
-    return r
-
-
-
-
-if __name__ == '__main__':
-  try:
-    resolution = int(sys.argv[1])
-  except:
-    resolution = 10
-  g = simple_rect_grid(resolution, resolution)
-  print g.for_qhull()

lib/grid/simplex.py

@@ -1,5 +1,15 @@
 from baker import get_phis
 
+TOL = 1e-3
+
+def contains(X, R):
+    phis = get_phis(X, R)
+    r = True
+    if [i for i in phis if i < 0.0 - TOL]:
+      r = False
+    return r
+
+
 class face(object):
   def __init__(self, name):
     self.name      = name
@@ -19,14 +29,7 @@ class face(object):
     self.neighbors.append(n)
 
   def contains(self, X, grid):
-    R    = [grid.points[i] for i in self.verts]
+    return contains(X, grid.points)
-
-    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]

test/quad.test.py

@@ -0,0 +1,54 @@
+#!/usr/bin/python
+
+import unittest
+
+from baker        import run_baker
+from baker.tools  import exact_func
+
+from grid.DD      import grid
+from grid.simplex import contains
+
+
+class TestSequenceFunctions(unittest.TestCase):
+  def setUp(self):
+    self.points = [
+                        [ 0.25, 0.40], # 0
+                        [ 0.60, 0.80], # 1
+                        [ 0.65, 0.28], # 2
+                        [ 0.28, 0.65], # 3
+                        [ 1.00, 0.75], # 4
+                        [ 0.30, 0.95], # 5
+                        [ 0.80, 0.50], # 6
+                        [ 0.35, 0.15], # 7
+                      ]
+    self.q = [exact_func(p) for p in self.points]
+
+    self.X = [0.55, 0.45]
+    self.X = [0.25, 0.4001]
+
+    self.g = grid(self.points, self.q)
+    self.g.construct_connectivity()
+    self.R = self.g.create_mesh(range(3))
+    self.S = self.g.create_mesh(range(3,len(self.points)))
+
+    self.exact = exact_func(self.X)
+
+    self.answer = run_baker(self.X, self.R, self.S)
+
+    self.accuracy = 8
+
+  def test_R_contains_X(self):
+    self.assertTrue(contains(self.X, self.R.points))
+
+  def test_RunBaker(self):
+    print  
+    print "X\n", self.X
+    print "R\n", self.R
+    print "S\n", self.S
+    print "exact\n",self.exact
+    print "qlin\n",self.answer['qlin']
+    self.assertTrue(self.answer)
+
+if __name__ == '__main__':
+  suite = unittest.TestLoader().loadTestsFromTestCase(TestSequenceFunctions)
+  unittest.TextTestRunner(verbosity=3).run(suite)

tools/blender/plot_cloud.py

@@ -1,9 +1,9 @@
 from Blender import *
 import bpy
 
-from grid.test3d import simple_rect_grid
+from grid.test3d import rect_grid
 
-g = simple_rect_grid(10, 10, 20)
+g = rect_grid(10, 10, 20)
 
 me = bpy.data.meshes.new('points')
 me.verts.extend(g.points)