major refactoring

--HG--
rename : lib/baker/__init__.py => interp/baker/__init__.py
rename : lib/grid/DD.py => interp/grid/DD.py
rename : lib/grid/DDD.py => interp/grid/DDD.py
rename : lib/grid/__init__.py => interp/grid/__init__.py
rename : lib/grid/qhull.py => interp/grid/qhull.py
rename : lib/grid/simplex.py => interp/grid/simplex.py
rename : lib/grid/smcqdelaunay.py => interp/grid/smcqdelaunay.py
rename : lib/baker/tools.py => interp/tools.py

bin/parse_gmsh.py

@@ -21,50 +21,15 @@ del os, atexit, readline, rlcompleter, save_history, historyPath
 import sys
 import pickle
 from itertools import combinations
+from collections import defaultdict
+from scipy.spatial import KDTree
+
+from grid.simplex import face
 
 import numpy as np
 
 THREE_NODE_TRIANGLE = 2
 
-class point(object):
-  def __init__(self, xyz):
-    self.index = index
-
-    self.xyz    = xyz
-    self.faces  = []
-
-  def __getitem__(self, i):
-    if isinstance(i, int):
-      if   i == 0:
-        return self.xyz[0]
-      elif i == 1:
-        return self.xyz[1]
-      elif i == 2:
-        return self.xyz[2]
-      else:
-        raise IndexError("there are only (x,y,z)")
-    else:
-      raise TypeError("only point.x and point[0] access allowed")
-
-  def _getx(self):
-    return self.xyz[0]
-  x = property(_getx)
-  def _gety(self):
-    return self.xyz[1]
-  y = property(_gety)
-  def _getz(self):
-    return self.xyz[2]
-  z = property(_getz)
-
-  def __str__(self):
-    return '%s' % self.xyz
-  __repr__ = __str__
-
-class face(object):
-  def __init__(self):
-    self.neighbors = []
-    self.points = []
-
 if __name__ == '__main__':
   if len(sys.argv) != 2:
     print >> sys.stderr, "usage: %s <gmsh file>" % sys.argv[0]
@@ -81,8 +46,7 @@ if __name__ == '__main__':
 
   node_count = int(gmsh_file.readline())
 
-  points = []
-  nppoints = np.zeros((node_count, 3))
+  verts = np.zeros((node_count, 3))
   for i in xrange(node_count):
     cur_line = gmsh_file.readline()
     (index, x,y,z) = cur_line.split()
@@ -91,19 +55,20 @@ if __name__ == '__main__':
     y     = float(y)
     z     = float(z)
 
-    nppoints[i][0] = x
-    nppoints[i][1] = y
-    nppoints[i][2] = z
-    points.append(point(nppoints[i]))
+    verts[i][0] = x
+    verts[i][1] = y
+    verts[i][2] = z
 
+  tree = KDTree(verts)
 
-  gmsh_file.readline() # $EndNodes
-  gmsh_file.readline() # $Elements
+  gmsh_file.readline() # $E   ndNodes
+  gmsh_file.readline() # $E   lements
 
   element_count = int(gmsh_file.readline())
 
-  faceobjs        = {}
-  neighbors       = {}
+  faces     = {}
+  neighbors = {}
+  faces_for_vert = defaultdict(list)
 
   for i in xrange(element_count):
     cur_line = gmsh_file.readline()
@@ -115,17 +80,17 @@ if __name__ == '__main__':
     if(node_type == THREE_NODE_TRIANGLE):
       points_for_cur_face = [i-1 for i in rest[rest[0]+1:]]
 
-      cur_face = face()
+      cur_face = face(cur_face_index)
 
       for cur_point in points_for_cur_face:
-        points[cur_point].faces.append(cur_face_index)
+        faces_for_vert[cur_point].append(cur_face_index)
 
-      cur_face.points       = points_for_cur_face
+      cur_face.verts       = points_for_cur_face
 
-      faceobjs[cur_face_index] = cur_face
+      faces[cur_face_index] = cur_face
       edges = [tuple(sorted(i)) for i in combinations(points_for_cur_face, 2)]
 
-      # edge is two points
+      # edge is two verts 
       for edge in edges:
         if edge in neighbors:
           neighbors[edge].append(cur_face_index)
@@ -134,8 +99,8 @@ if __name__ == '__main__':
 
   for k,v in neighbors.iteritems():
     if len(v) > 1:
-      faceobjs[v[0]].neighbors.append(v[1])
-      faceobjs[v[1]].neighbors.append(v[0])
+      faces[v[0]].add_neighbor(faces[v[1]])
+      faces[v[1]].add_neighbor(faces[v[0]])
 
-  pickle.dump([(p[0], p[1], p[2]) for p in points], open('/tmp/points.p', 'w'))
-  pickle.dump([f.points for f in faceobjs.itervalues()], open('/tmp/faces.p',  'w'))
+  pickle.dump([(p[0], p[1], p[2]) for p in verts], open('/tmp/points.p', 'w'))
+  pickle.dump([f.verts for f in faces.itervalues()], open('/tmp/faces.p',  'w'))

bin/test2d-connectivity.py

@@ -67,4 +67,3 @@ if __name__ == '__main__':
     good.append(d[True])
 
   draw_gb(bad = bad, good = good)
-

bin/test2d-qhull-specific.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python2.6
+#!/usr/bin/env python
 
 import sys
 from grid.DD import grid
@@ -24,6 +24,8 @@ g = grid(verts,q)
 
 exact = exact_func(X)
 
+d = {True:0, False:0}
+
 try:
   answer =  g.run_baker(X)
   d[improved_answer(answer, exact)] += 1