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Speed improvements, cython, balancing.

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This commit is contained in:
Rowan Cockett
2015-11-07 16:47:19 -08:00
parent 109a5f0f86
commit e8ae516030
2 changed files with 160 additions and 83 deletions
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SimPEG/Mesh/PointerTree.py
+75 -83
View File
@@ -1,51 +1,10 @@
from SimPEG import np, sp, Utils, Solver
import matplotlib.pyplot as plt
import matplotlib
import TreeUtils
import time
class ZCurve(object):
"""
The Z-order curve is generated by interleaving the bits of an offset.
See:
https://github.com/cortesi/scurve
Aldo Cortesi <aldo@corte.si>
"""
def __init__(self, dimension, bits):
"""
dimension: Number of dimensions
bits: The number of bits per co-ordinate. Total number of points is
2**(bits*dimension).
"""
self.dimension, self.bits = dimension, bits
def bitrange(self, x, width, start, end):
"""
Extract a bit range as an integer.
(start, end) is inclusive lower bound, exclusive upper bound.
"""
return x >> (width-end) & ((2**(end-start))-1)
def index(self, p):
p.reverse()
idx = 0
iwidth = self.bits * self.dimension
for i in range(iwidth):
bitoff = self.bits-(i/self.dimension)-1
poff = self.dimension-(i%self.dimension)-1
b = self.bitrange(p[poff], self.bits, bitoff, bitoff+1) << i
idx |= b
return idx
def point(self, idx):
p = [0]*self.dimension
iwidth = self.bits * self.dimension
for i in range(iwidth):
b = self.bitrange(idx, iwidth, i, i+1) << (iwidth-i-1)/self.dimension
p[i%self.dimension] |= b
p.reverse()
return p
MAX_BITS = 20
def SortGrid(grid, offset=0):
"""
@@ -112,7 +71,6 @@ class Tree(object):
self.__dirty__ = True #: The numbering is dirty!
self._z = ZCurve(self.dim, 20)
self._treeInds = set()
self._treeInds.add(0)
@@ -216,8 +174,6 @@ class Tree(object):
raise Exception()
def _structureChange(self):
if self.__dirty__: return
deleteThese = ['__sortedInds', '_gridCC', '_gridN', '_gridFx', '_gridFy', '_gridFz', '_gridEx', '_gridEy', '_gridEz', '_area', '_edge', '_vol']
for p in deleteThese:
if hasattr(self, p): delattr(self, p)
@@ -226,39 +182,42 @@ class Tree(object):
def _index(self, pointer):
assert len(pointer) is self.dim+1
assert pointer[-1] <= self.levels
x = self._z.index([p for p in pointer[:-1]]) # copy
return (x << self._levelBits) + pointer[-1]
return TreeUtils.index(self.dim, MAX_BITS, self._levelBits, pointer[:-1], pointer[-1])
def _pointer(self, index):
assert type(index) in [int, long]
n = index & (2**self._levelBits-1)
p = self._z.point(index >> self._levelBits)
return p + [n]
return TreeUtils.point(self.dim, MAX_BITS, self._levelBits, index)
def __contains__(self, v):
if type(v) in [int, long]:
return v in self._treeInds
return self._index(v) in self._treeInds
def refine(self, function=None, recursive=True, cells=None, balance=True):
def refine(self, function=None, recursive=True, cells=None, balance=True, _inRecursion=False):
if not _inRecursion:
self._structureChange()
print 'Refining Mesh'
cells = cells if cells is not None else sorted(self._treeInds)
recurse = []
tic = time.time()
for cell in cells:
p = self._pointer(cell)
do = function(self._cellC(cell)) > p[-1]
if do:
recurse += self._refineCell(cell)
if recursive and len(recurse) > 0:
recurse += self.refine(function=function, recursive=True, cells=recurse, balance=balance)
print ' ', time.time() - tic
if balance:
recurse += self.balance(recursive=True)
if recursive and len(recurse) > 0:
recurse += self.refine(function=function, recursive=True, cells=recurse, balance=balance, _inRecursion=True)
if balance and not _inRecursion:
self.balance()
return recurse
def _refineCell(self, pointer):
self._structureChange()
pointer = self._asPointer(pointer)
ind = self._asIndex(pointer)
assert ind in self
@@ -283,10 +242,13 @@ class Tree(object):
self._treeInds.remove(ind)
return added
def _corsenCell(self, pointer):
def corsen(self, function=None):
self._structureChange()
raise Exception('Not yet implemented')
def _corsenCell(self, pointer):
raise Exception('Not yet implemented')
def _asPointer(self, ind):
if type(ind) in [int, long]:
return self._pointer(ind)
@@ -393,10 +355,24 @@ class Tree(object):
return self._getNextCell(self._parentPointer(pointer),
direction=direction, positive=positive)
def balance(self, recursive=True):
def balance(self, recursive=True, cells=None, _inRecursion=False):
tic = time.time()
if not _inRecursion:
self._structureChange()
print 'Balancing Mesh:'
cells = cells if cells is not None else sorted(self._treeInds)
# calcDepth = lambda i: lambda A: i if type(A) is not list else max(map(calcDepth(i+1), A))
# flatten = lambda A: A if calcDepth(0)(A) == 1 else flatten([_ for __ in A for _ in (__ if type(__) is list else [__])])
recurse = set()
for cell in cells:
p = self._asPointer(cell)
if p[-1] == self.levels: continue
recurse = []
for cell in sorted(self._treeInds):
cs = range(6)
cs[0] = self._getNextCell(cell, direction=0, positive=False)
cs[1] = self._getNextCell(cell, direction=0, positive=True)
@@ -410,14 +386,20 @@ class Tree(object):
for c in cs
if c is not None
])
# print cs, do
if do:
recurse += self._refineCell(cell)
# depth = calcDepth(0)(cs)
# print depth, depth > 2, do, [jj for jj in flatten(cs) if jj is not None]
# recurse += [jj for jj in flatten(cs) if jj is not None]
if do and cell in self:
newCells = self._refineCell(cell)
recurse.update([_ for _ in cs if type(_) in [int, long]]) # only add the bigger ones!
recurse.update(newCells)
print ' ', len(cells), time.time() - tic
if recursive and len(recurse) > 0:
# print 'here'
recurse += self.balance()
return recurse
self.balance(cells=sorted(recurse), _inRecursion=True)
@property
def gridCC(self):
@@ -961,7 +943,7 @@ class Tree(object):
facesX=False, facesY=False, facesZ=False,
edgesX=False, edgesY=False, edgesZ=False):
self.number()
# self.number()
axOpts = {'projection':'3d'} if self.dim == 3 else {}
if ax is None:
@@ -1070,7 +1052,7 @@ class Tree(object):
ax.plot(self.gridEz[ind,0], self.gridEz[ind,1], 'k:', zs=self.gridEz[ind,2])
ax.axis('equal')
# ax.axis('equal')
if showIt:plt.show()
@@ -1079,36 +1061,47 @@ if __name__ == '__main__':
def function(xc):
r = xc - np.r_[0.5*128,0.5*128]
r = xc - np.array([0.5*128]*len(xc))
dist = np.sqrt(r.dot(r))
# if dist < 0.05:
# return 5
if dist < 0.1*128:
return 5
return 7
if dist < 0.3*128:
return 3
# if dist < 1.0*128:
# return 2
return 5
if dist < 1.0*128:
return 2
else:
return 0
# T = Tree([[(1,8)],[(1,8)],[(1,8)]],levels=3)
T = Tree([[(1,128)],[(1,128)],[(1,128)]],levels=7)
# T = Tree([[(1,16)],[(1,16)]],levels=4)
T = Tree([[(1,128)],[(1,128)]],levels=7)
T.refine(lambda xc:2, balance=False)
T.refine(function)
# T = Tree([[(1,128)],[(1,128)]],levels=7)
# T.refine(lambda xc:6, balance=False)
# T._index([0,0,0])
# T._pointer(0)
tic = time.time()
T.refine(function)#, balance=False)
print time.time() - tic
print T.nC
asdf
# T._refineCell([8,0,1])
# T._refineCell([8,0,2])
# T._refineCell([12,0,2])
# T._refineCell([8,4,2])
# T._refineCell([6,0,3])
# T._refineCell([8,8,1])
# T._refineCell([4,4,4,1])
# T._refineCell([0,0,0,1])
ax = plt.subplot(211)
ax.spy(T.faceDiv)
# ax.spy(T.faceDiv)
T.plotGrid(ax=ax)
# R = deflationMatrix(T._facesX, T._hangingFx, T._fx2i)
# print R
@@ -1120,7 +1113,7 @@ if __name__ == '__main__':
# ax.spy(T.faceDiv[:,:T.nFx] * R)
T.balance()
T.plotGrid(ax=ax)
# cx = T._getNextCell([0,0,1],direction=0,positive=True)
@@ -1145,7 +1138,6 @@ if __name__ == '__main__':
# print T.nN
plt.show()
SimPEG/Mesh/TreeUtils.pyx
+85
View File
@@ -0,0 +1,85 @@
# from __future__ import division
# import numpy as np
# cimport numpy as np
# from libcpp.vector cimport vector
"""
The Z-order curve is generated by interleaving the bits of an offset.
See also:
https://github.com/cortesi/scurve
Aldo Cortesi <aldo@corte.si>
"""
def bitrange(long x, int width, int start, int end):
"""
Extract a bit range as an integer.
(start, end) is inclusive lower bound, exclusive upper bound.
"""
return x >> (width-end) & ((2**(end-start))-1)
def index(int dimension, int bits, int levelBits, list p, int level):
cdef long idx = 0
cdef int iwidth
cdef int i
cdef long b
cdef int bitoff
p = [_ for _ in p]
p.reverse()
iwidth = bits * dimension
for i in range(iwidth):
bitoff = bits-(i/dimension)-1
poff = dimension-(i%dimension)-1
b = bitrange(p[poff], bits, bitoff, bitoff+1) << i
idx |= b
return (idx << levelBits) + level
def point(int dimension, int bits, int levelBits, long idx):
cdef list p
cdef int iwidth
cdef int i, n
cdef long b
n = idx & (2**levelBits-1)
idx = idx >> levelBits
p = [0]*dimension
iwidth = bits * dimension
for i in range(iwidth):
b = bitrange(idx, iwidth, i, i+1) << (iwidth-i-1)/dimension
p[i%dimension] |= b
p.reverse()
return p + [n]
# def _refineCell(int dimension, int bits, self, pointer):
# self._structureChange()
# pointer = self._asPointer(pointer)
# ind = self._asIndex(pointer)
# assert ind in self
# h = self._levelWidth(pointer[-1])/2 # halfWidth
# nL = pointer[-1] + 1 # new level
# add = lambda p:p[0]+p[1]
# added = []
# def addCell(p):
# i = self._index(p+[nL])
# self._treeInds.add(i)
# added.append(i)
# addCell(map(add, zip(pointer[:-1], [0,0,0])))
# addCell(map(add, zip(pointer[:-1], [h,0,0])))
# addCell(map(add, zip(pointer[:-1], [0,h,0])))
# addCell(map(add, zip(pointer[:-1], [h,h,0])))
# if self.dim == 3:
# addCell(map(add, zip(pointer[:-1], [0,0,h])))
# addCell(map(add, zip(pointer[:-1], [h,0,h])))
# addCell(map(add, zip(pointer[:-1], [0,h,h])))
# addCell(map(add, zip(pointer[:-1], [h,h,h])))
# self._treeInds.remove(ind)
# return added