finally added proper (in my opinon) exception handling to the grid's run_baker method. it should properly autocorrect, and switch the extra point lookup scheme to connectivity-based if solving the system of equations yields a singular solution

bin/grid_regular.py

@@ -6,30 +6,38 @@ import pickle
 from grid import simple_rect_grid, simple_random_grid
 from baker import run_baker
 
+from tools import smberror
+
 qfile = '/tmp/grid_regular.txt'
 
 if __name__ == '__main__':
   try:
     rx = int(sys.argv[1])
     ry = int(sys.argv[2])
-  except ValueError as e:
+  except (IndexError, ValueError) as e:
-    print e
+    print "problem with argv: %s" % e
     rx = 4
     ry = 4 * rx
 
   source_mesh = simple_rect_grid(rx, ry)
-  print source_mesh
+
+  # print source_mesh
 
   X = [0.1, 0.1]
 
-  (R, S) = source_mesh.get_simplex_and_nearest_points(X, extra_points=4)
+  try:
-  print "R for nearest-neighbor:\n", R
+    (R, S) = source_mesh.get_simplex_and_nearest_points(X, extra_points=4)
-  print "S for nearest-neighbor:\n", S
+    print "R for nearest-neighbor:\n", R
-  print run_baker(X, R, S)
+    print "S for nearest-neighbor:\n", S
+    print run_baker(X, R, S)
+  except smberror as e:
+    print "caught error: %s" % e
+    (R, S) =  source_mesh.get_points_conn(X)
+    print "R for connectivity:\n", R
+    print "S for connectivity:\n", S
+    print run_baker(X, R, S)
 
-  (R, S) =  source_mesh.get_points_conn(X)
-  print "R for connectivity:\n", R
-  print "S for connectivity:\n", S
-  print run_baker(X, R, S)
 
+  print "repeating the above just using the grid object:"
+  print source_mesh.run_baker(X)
   open(qfile, 'w').write(source_mesh.for_qhull())

lib/baker.py

@@ -1,6 +1,8 @@
 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.
@@ -26,7 +28,8 @@ def get_phis(X, R):
   try:
     phi = np.linalg.solve(A,b)
   except:
-    print >> sys.stderr, "warning: calculation of phis yielded a linearly dependant system"
+    print >> sys.stderr, "warning: get_phis: calculation of phis yielded a linearly dependant system"
+    raise smberror('get_phis')
     phi = np.dot(np.linalg.pinv(A), b)
 
   return phi
@@ -58,13 +61,13 @@ def get_phis_3D(X, r):
   try:
     phi = np.linalg.solve(A,b)
   except:
-    print >> sys.stderr, "warning: calculation of phis yielded a linearly dependant system"
+    print >> sys.stderr, "warning: get_phis_3D: calculation of phis yielded a linearly dependant system"
     phi = np.dot(np.linalg.pinv(A), b)
 
   return phi
 
 
-def qlinear(X, R, q):
+def qlinear(X, R):
   """
     this calculates the linear portion of q from X to r
 
@@ -75,9 +78,9 @@ def qlinear(X, R, q):
     q = CFD quantities of interest at the simplex points
   """
 
-  phis = get_phis(X, R)
+  phis = get_phis(X, R.points)
-  qlin = sum([q_i * phi_i for q_i, phi_i in zip(q, phis)])
+  qlin = sum([q_i * phi_i for q_i, phi_i in zip(R.q, phis)])
-  return qlin
+  return phis, qlin
 
 def qlinear_3D(X, R, q):
   """
@@ -90,7 +93,7 @@ def qlinear_3D(X, R, q):
 
   phis = get_phis_3D(X, R)
   qlin = sum([q_i * phi_i for q_i, phi_i in zip(q, phis)])
-  return qlin
+  return phis, qlin
 
 def run_baker(X, R, S):
   """
@@ -106,8 +109,7 @@ def run_baker(X, R, S):
   """
 
   # calculate values only for the triangle
-  phi  = get_phis(X, R.points)
+  phi, qlin = qlinear (X, R)
-  qlin = qlinear (X, R.points, R.q)
 
   if len(S.points) == 0:
     answer = {
@@ -124,10 +126,11 @@ def run_baker(X, R, S):
   w = [] # baker eq 11
 
   for (s, q) in zip(S.points, S.q):
-    (phi1, phi2, phi3) = get_phis(s, R.points)
+    cur_phi, cur_qlin = qlinear(s, R)
-    B.append([phi1 * phi2, phi2*phi3, phi3*phi1])
+    (phi1, phi2, phi3) = cur_phi
 
-    w.append(q - qlinear(s, R.points, R.q))
+    B.append([phi1 * phi2, phi2 * phi3, phi3 * phi1])
+    w.append(q - cur_qlin)
 
   B = np.array(B)
   w = np.array(w)
@@ -139,7 +142,7 @@ def run_baker(X, R, S):
   try:
     (a, b, c) = np.linalg.solve(A,b)
   except:
-    print >> sys.stderr, "warning: linear calculation went bad, resorting to np.linalg.pinv"
+    print >> sys.stderr, "warning: run_baker: linear calculation went bad, resorting to np.linalg.pinv"
     (a, b, c) = np.dot(np.linalg.pinv(A), b)
 
   error_term =  a * phi[0] * phi[1]\

lib/grid.py

@@ -8,7 +8,7 @@ import numpy as np
 import scipy.spatial
 
 from baker import run_baker, get_phis
-from tools import exact_func
+from tools import exact_func, smberror
 from smcqdelaunay import *
 
 class face(object):
@@ -146,13 +146,20 @@ class grid(object):
 
     return R, S
 
-  def run_baker(self, X, connectivity_based = False):
+  def run_baker(self, X):
-    print >>sys.stderr, "suxor"
+    answer = None
-    if connectivity_based:
+
-      (R, S) = self.get_points_conn(X)
+    try:
-    else:
       (R, S) = self.get_simplex_and_nearest_points(X)
-    return run_baker(X, R, S)
+      answer = run_baker(X, R, S)
+    except smberror as 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):
     """

test/baker.test.py

@@ -30,7 +30,6 @@ class TestSequenceFunctions(unittest.TestCase):
     import scipy
     import grid
     import baker
-    import delaunay
 
   def testGetPhis(self):
 
@@ -62,7 +61,7 @@ class TestSequenceFunctions(unittest.TestCase):
     r = [[0, 0], [1, 0], [1, 1]]
     q = [1, 0, 0]
 
-    result = baker.qlinear(X, r, q)
+    phi, result = baker.qlinear(X, grid.grid(r,q))
 
     right_answer = 0.5