polish for inclusion into thesis

bin/iqmgr.py

@@ -2,9 +2,9 @@
 
 import sys
 import time
-import interp.bootstrap
-from   interp.cluster import QueueManager, get_qs
-from   optparse       import OptionParser
+
+from   interp.cluster   import QueueManager, get_qs
+from   optparse         import OptionParser
 
 if __name__ == '__main__':
   parser = OptionParser(usage = "usage: %s [options] <status|watch|add|fresult #|slay|clear|clearall|clearresults>")

bin/master.py

@@ -4,20 +4,18 @@ import sys
 import os
 
 import time
-
 import shelve
-from   progressbar import *
 from   collections import defaultdict
 from   optparse    import OptionParser
 
-import numpy as np
-
-import interp.bootstrap
-
 import logging
 log = logging.getLogger("interp")
 
-from interp.cluster import QueueManager, get_qs
+import numpy as np
+
+from   interp.cluster import QueueManager, get_qs
+
+from   progressbar import *
 
 if __name__ == '__main__':
   parser = OptionParser(usage = "usage: %s [options] <server> <interp count>")

bin/minion.py

@@ -11,7 +11,6 @@ import datetime
 
 import numpy as np
 
-import interp.bootstrap
 from   interp.grid.gmsh import ggrid
 from   interp.tools import baker_exact_3D as exact
 

bin/resolution.2D.py

@@ -6,8 +6,8 @@ import time
 from   progressbar import *
 
 from interp.grid.DD import *
-from interp.tools import *
-from interp import bootstrap
+from interp.tools   import *
+from interp         import bootstrap
 
 EXTRA_POINTS = 64
 

bin/shepherd.py

@@ -10,8 +10,6 @@ import pickle
 
 import numpy as np
 
-import interp.bootstrap
-
 from interp.cluster import QueueManager, get_qs
 
 if __name__ == '__main__':

interp/baker/__init__.py

@@ -11,37 +11,35 @@ log = logging.getLogger('interp')
 
 def get_phis(X, R):
   """
-    The get_phis function is used to get barycentric coordonites for a point on
-    a triangle or tetrahedron:
-
+    The get_phis function is used to get barycentric coordonites for a
+    point on a triangle or tetrahedron. This is equation (*\ref{eq:qlinarea}*)
 
     in 2D:
 
-    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]]
+    X - the destination point (2D)
+        X = [0,0]
+    R - the three points that make up the 2-D triangular simplex
+        R = [[-1, -1], [0, 2], [1, -1]]
 
     this will return [0.333, 0.333, 0.333]
 
 
     in 3D:
 
-    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],
-             ]
+    X - the destination point (3D)
+        X = [0,0,0]
+    R - the four points that make up the 3-D simplex (tetrahedron)
+        R = [
+           [ 0.0000,  0.0000,  1.0000],
+           [ 0.9428,  0.0000, -0.3333],
+           [-0.4714,  0.8165, -0.3333],
+           [-0.4714, -0.8165, -0.3333],
+         ]
 
     this will return [0.25, 0.25, 0.25, 0.25]
   """
 
-  # baker: eq 7
-  # TODO: perhaps also test len(R[0])  .. ?
+  # equations (*\ref{eq:lin3d}*) and (*\ref{eq:lin2d}*)
   if len(X) == 2:
     log.debug("running 2D")
     A = np.array([
@@ -85,7 +83,7 @@ def qlinear(X, R):
   """
     this calculates the linear portion of q from R to X
 
-    also, this is baker eq 3
+    This is equation (*\ref{eq:qlinbasis}*)
 
     X = destination point
     R = a inter.grid object; must have R.points and R.q
@@ -100,9 +98,12 @@ def qlinear(X, R):
   return phis, qlin
 
 def get_error(phi, R, S, order = 2):
-  #TODO: change the equation names in the comments
-  B = [] # baker eq 9
-  w = [] # baker eq 11
+  """
+    Calculate the error approximation terms, returning the unknowns
+    a,b, and c in equation (*\ref{eq:quadratic2d}*).
+  """
+  B = [] # equation ((*\ref{eq:B2d}*)
+  w = [] # equation ((*\ref{eq:w}*)
 
   cur_pattern  = pattern(len(phi), order)
   log.info("pattern: %s" % cur_pattern)
@@ -150,8 +151,7 @@ def run_baker(X, R, S, order=2):
     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]
+    X -- the destination point
 
     R = Simplex
     S = extra points
@@ -190,9 +190,7 @@ def run_baker(X, R, S, order=2):
 
 def memoize(f):
   """
-    for more information on what I'm doing here,
-    please read:
-
+    for more information on what I'm doing here, please read:
     http://en.wikipedia.org/wiki/Memoize
   """
   cache = {}

interp/grid/__init__.py

@@ -20,8 +20,9 @@ class grid(object):
     """
       verts = array of arrays (if passed in, will convert to numpy.array)
               [
-                [x0,y0],
-                [x1,y1], ...
+                [x0,y0 <, z0>],
+                [x1,y1 <, z1>],
+                ...
               ]
 
       q     = array (1D) of physical values
@@ -97,10 +98,9 @@ class grid(object):
     """
       this returns two grid objects: R and S.
 
-      R is a grid object that is supposedly a containing simplex around point X
+      R is a grid object that is a containing simplex around point X
 
-      S is S_j from baker's paper : some verts from all point that are not the
-      simplex
+      S : some verts from all points that are not the simplex
     """
     simplex_size = self.dim + 1
     log.debug("extra verts: %d" % extra_points)
@@ -228,8 +228,9 @@ class cell(object):
       X = point of interest
       G = corrensponding grid object (G.verts)
 
-      because of the way i'm storing things, a cell simply stores indicies, and
-      so one must pass in a reference to the grid object containing real verts.
+      because of the way i'm storing things, a cell simply stores indicies,
+      and so one must pass in a reference to the grid object containing real
+      verts.
 
       this simply calls grid.simplex.contains
     """
@@ -255,10 +256,6 @@ def contains(X, R):
     tests if X (point) is in R
 
     R is a simplex, represented by a list of n-degree coordinates
-
-    it now correctly checks for 2/3-D verts
-
-    TODO: write unit test ...
   """
   phis = get_phis(X, R)
 

interp/grid/delaunay.py

@@ -51,9 +51,6 @@ class dgrid(basegrid):
   def construct_connectivity(self):
     """
       a call to this method prepares the internal connectivity structure.
-
-      this is part of the __init__ for a interp.grid.delaunay.grid, but can be
-      called from any grid object
     """
     log.info('start')
     qdelaunay_string = get_qdelaunay_dump_str(self)

interp/grid/qhull.py

@@ -1,14 +0,0 @@
-def parse_qhull_file(filename, verbose=False):
-  f = open(filename, 'r')
-
-  if verbose:
-    print 'filename: ', filename
-    degree = int(f.readline().strip())
-    print "degree:", degree
-    print "number of points", f.readline().strip()
-
-  verts = []
-  for p in f:
-    v = [float(i) for i in p.strip().split()]
-    verts.append(v)
-  return verts

interp/tools.py

@@ -1,6 +1,5 @@
 import os
 
-import inspect
 import numpy as np
 
 import logging
@@ -27,8 +26,6 @@ def baker_exact_2D(X):
   """
   x ,y = X
 
-  # TODO: this is not baker's function!! this is:
-  #        np.power(np.sin(x*np.pi/2.0) * np.sin(y*np.pi/2.0),2)
   answer = np.power((np.sin(x * np.pi) * np.cos(y * np.pi)), 2)
   log.debug(answer)
   return answer
@@ -83,6 +80,3 @@ def improved(qlin, err, final, exact):
     return True
   else:
     return False
-
-def percent_improvement(answer, exact):
-  return np.abs(answer['error']) / exact