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PointerTree, FaceDiv, Visualization
This commit is contained in:
Rowan Cockett
@@ -0,0 +1,415 @@
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import scurve
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from SimPEG import np, sp, Utils, Solver
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import matplotlib.pyplot as plt
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import matplotlib
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class Tree(object):
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def __init__(self, h_in, levels=3):
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assert type(h_in) is list, 'h_in must be a list'
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assert len(h_in) > 1, "len(h_in) must be greater than 1"
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h = range(len(h_in))
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for i, h_i in enumerate(h_in):
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if type(h_i) in [int, long, float]:
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# This gives you something over the unit cube.
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h_i = np.ones(int(h_i))/int(h_i)
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assert isinstance(h_i, np.ndarray), ("h[%i] is not a numpy array." % i)
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assert len(h_i.shape) == 1, ("h[%i] must be a 1D numpy array." % i)
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assert len(h_i) == 2**levels, "must make h and levels match"
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h[i] = h_i[:] # make a copy.
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self.h = h
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self._levels = levels
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self._levelBits = int(np.ceil(np.sqrt(levels)))+1
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self._z = scurve.zorder.ZOrder(self.dim,20)
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self._treeInds = set()
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self._treeInds.add(0)
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@property
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def dim(self): return len(self.h)
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@property
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def levels(self): return self._levels
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@property
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def _sortedInds(self):
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if getattr(self, '__sortedInds', None) is None:
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self.__sortedInds = sorted(self._treeInds)
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return self.__sortedInds
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def _structureChange(self):
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deleteThese = ['__sortedInds', '_gridCC', '_gridFx']
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for p in deleteThese:
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if hasattr(self, p): delattr(self, p)
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def _index(self, pointer):
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assert len(pointer) is self.dim+1
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assert pointer[-1] <= self.levels
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x = self._z.index([p for p in pointer[:-1]]) # copy
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return (x << self._levelBits) + pointer[-1]
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def _pointer(self, index):
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assert type(index) in [int, long]
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n = index & (2**self._levelBits-1)
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p = self._z.point(index >> self._levelBits)
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return p + [n] #[p[1],p[0],p[2]]
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def refine(self, function=None, recursive=True, cells=None):
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cells = cells if cells is not None else sorted(self._treeInds)
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recurse = []
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for cell in cells:
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p = self._pointer(cell)
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do = function(self._cellC(cell)) > p[-1]
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if do:
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recurse += self._refineCell(cell)
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if recursive and len(recurse) > 0:
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self.refine(function=function, recursive=True, cells=recurse)
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return recurse
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def _refineCell(self, pointer):
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self._structureChange()
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pointer = self._asPointer(pointer)
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ind = self._asIndex(pointer)
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assert ind in self
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h = self._levelWidth(pointer[-1])/2 # halfWidth
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nL = pointer[-1] + 1 # new level
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add = lambda p:p[0]+p[1]
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added = []
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def addCell(p):
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i = self._index(p+[nL])
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self._treeInds.add(i)
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added.append(i)
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addCell(map(add, zip(pointer[:-1], [0,0,0][:self.dim])))
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addCell(map(add, zip(pointer[:-1], [h,0,0][:self.dim])))
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addCell(map(add, zip(pointer[:-1], [0,h,0][:self.dim])))
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addCell(map(add, zip(pointer[:-1], [h,h,0][:self.dim])))
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if self.dim == 3:
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addCell(map(add, zip(pointer[:-1], [0,0,h])))
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addCell(map(add, zip(pointer[:-1], [h,0,h])))
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addCell(map(add, zip(pointer[:-1], [0,h,h])))
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addCell(map(add, zip(pointer[:-1], [h,h,h])))
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self._treeInds.remove(ind)
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return added
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def _corsenCell(self, pointer):
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self._structureChange()
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raise Exception('Not yet implemented')
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def _asPointer(self, ind):
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if type(ind) in [int, long]:
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return self._pointer(ind)
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if type(ind) is list:
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return ind
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if isinstance(ind, np.ndarray):
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return ind.tolist()
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raise Exception
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def _asIndex(self, pointer):
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if type(pointer) in [int, long]:
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return pointer
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if type(pointer) is list:
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return self._index(pointer)
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raise Exception
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def _parentPointer(self, pointer):
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mod = self._levelWidth(pointer[-1]-1)
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return [p - (p % mod) for p in pointer[:-1]] + [pointer[-1]-1]
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def _levelWidth(self, level):
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return 2**(self.levels - level)
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def _isInsideMesh(self, pointer):
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inside = True
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for p in pointer[:-1]:
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inside = inside and p >= 0 and p < 2**self.levels
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return inside
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def _getNextCell(self, ind, direction=0, positive=True):
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"""
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Returns a None, int, list, or nested list
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The int is the cell number.
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"""
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pointer = self._asPointer(ind)
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step = (1 if positive else -1) * self._levelWidth(pointer[-1])
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nextCell = [p if ii is not direction else p + step for ii, p in enumerate(pointer)]
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if not self._isInsideMesh(nextCell): return None
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# it might be the same size as me?
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if nextCell in self: return self._index(nextCell)
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# it might be smaller than me?
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if nextCell[-1] + 1 <= self.levels: # if I am not the smallest.
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nextCell[-1] += 1
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if not positive:
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nextCell[direction] -= step/2 # Get the closer one
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if nextCell in self: # there is at least one
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hw = self._levelWidth(pointer[-1]) / 2
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nextCell = np.array([p if ii is not direction else p + (step/2 if positive else 0) for ii, p in enumerate(pointer)])
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if self.dim == 3: raise Exception
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if direction == 0: children = [0,0,1], [0,hw,1]
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if direction == 1: children = [0,0,1], [hw,0,1]
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nextCells = []
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for child in children:
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nextCells.append(self._getNextCell(nextCell + child, direction=direction,positive=positive))
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return nextCells
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# it might be bigger than me?
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return self._getNextCell(self._parentPointer(pointer),
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direction=direction, positive=positive)
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def __contains__(self, v):
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if type(v) in [int, long]:
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return v in self._treeInds
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return self._index(v) in self._treeInds
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def plotGrid(self, ax=None, showIt=False):
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if ax is None:
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fig = plt.figure()
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ax = plt.subplot(111)
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else:
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assert isinstance(ax,matplotlib.axes.Axes), "ax must be an Axes!"
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fig = ax.figure
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for ind in self._sortedInds:
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p = self._asPointer(ind)
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n = self._cellN(p)
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h = self._cellH(p)
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x = [n[0] , n[0] + h[0], n[0] + h[0], n[0] , n[0]]
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y = [n[1] , n[1] , n[1] + h[1], n[1] + h[1], n[1]]
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ax.plot(x,y, 'b-')
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ax.plot(self.gridCC[[0,-1],0], self.gridCC[[0,-1],1], 'ro')
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ax.plot(self.gridCC[:,0], self.gridCC[:,1], 'r.')
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ax.plot(self.gridCC[:,0], self.gridCC[:,1], 'r:')
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ax.plot(self.gridFx[self._hangingFacesX,0], self.gridFx[self._hangingFacesX,1], 'gs', ms=10, mfc='none', mec='green')
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ax.plot(self.gridFx[:,0], self.gridFx[:,1], 'g>')
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ax.plot(self.gridFy[self._hangingFacesY,0], self.gridFy[self._hangingFacesY,1], 'gs', ms=10, mfc='none', mec='green')
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ax.plot(self.gridFy[:,0], self.gridFy[:,1], 'g^')
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if showIt:plt.show()
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def _cellN(self, p):
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p = self._asPointer(p)
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return [hi[:p[ii]].sum() for ii, hi in enumerate(self.h)]
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def _cellH(self, p):
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p = self._asPointer(p)
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w = self._levelWidth(p[-1])
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return [hi[p[ii]:p[ii]+w].sum() for ii, hi in enumerate(self.h)]
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def _cellC(self, p):
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return (np.array(self._cellH(p))/2.0 + self._cellN(p)).tolist()
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@property
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def gridCC(self):
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if getattr(self, '_gridCC', None) is None:
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self._gridCC = np.zeros((len(self._treeInds),self.dim))
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for ii, ind in enumerate(self._sortedInds):
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p = self._asPointer(ind)
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self._gridCC[ii, :] = self._cellC(p)
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return self._gridCC
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@property
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def gridFx(self):
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if getattr(self, '_gridFx', None) is None:
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self.number()
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return self._gridFx
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@property
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def gridFy(self):
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if getattr(self, '_gridFy', None) is None:
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self.number()
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return self._gridFy
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def _onSameLevel(self, i0, i1):
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p0 = self._asPointer(i0)
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p1 = self._asPointer(i1)
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return p0[-1] == p1[-1]
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def number(self):
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facesX, facesY = [], []
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hangingFacesX, hangingFacesY = [], []
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faceXCount, faceYCount = -1, -1
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fXm,fXp,fYm,fYp,fZm,fZp = range(6)
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area, vol = [], []
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def addXFace(count, p, positive=True):
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n = self._cellN(p)
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w = self._cellH(p)
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area.append(w[1] if self.dim == 2 else w[1]*w[2])
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facesX.append([n[0] + (w[0] if positive else 0), n[1] + w[1]/2.0])
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return count + 1
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def addYFace(count, p, positive=True):
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n = self._cellN(p)
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w = self._cellH(p)
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area.append(w[0] if self.dim == 2 else w[0]*w[2])
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facesY.append([n[0] + w[0]/2.0, n[1] + (w[1] if positive else 0)])
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return count + 1
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# c2cn = dict()
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c2f = dict()
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def gc2f(ind):
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if ind in c2f: return c2f[ind]
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c2f_ind = [list() for _ in xrange(2*self.dim)]
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c2f[ind] = c2f_ind
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return c2f_ind
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def processCell(ind, faceCount, addFace, hangingFaces, DIR=0):
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fM,fP=(0,1) if DIR == 0 else (2,3) if DIR == 1 else (4,5)
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p = self._asPointer(ind)
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if self._getNextCell(p, direction=DIR, positive=False) is None:
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faceCount = addFace(faceCount, p, positive=False)
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gc2f(ind)[fM] += [faceCount]
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nextCell = self._getNextCell(p, direction=DIR)
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# Add the next Xface
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if nextCell is None:
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# on the boundary
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faceCount = addFace(faceCount, p)
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gc2f(ind)[fP] += [faceCount]
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elif type(nextCell) in [int, long] and self._onSameLevel(p,nextCell):
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# same sized cell
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faceCount = addFace(faceCount, p)
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gc2f(ind)[fP] += [faceCount]
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gc2f(nextCell)[fM] += [faceCount]
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elif type(nextCell) in [int, long] and not self._onSameLevel(p,nextCell):
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# the cell is bigger than me
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faceCount = addFace(faceCount, p)
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gc2f(ind)[fP] += [faceCount]
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gc2f(nextCell)[fM] += [faceCount]
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hangingFaces.append(faceCount)
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elif type(nextCell) is list:
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# the cell is smaller than me
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# TODO: ensure that things are balanced.
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p0 = self._pointer(nextCell[0])
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p1 = self._pointer(nextCell[1])
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faceCount = addFace(faceCount, p0, positive=False)
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gc2f(nextCell[0])[fM] += [faceCount]
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faceCount = addFace(faceCount, p1, positive=False)
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gc2f(nextCell[1])[fM] += [faceCount]
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gc2f(ind)[fP] += [faceCount-1,faceCount]
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hangingFaces += [faceCount-1, faceCount]
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return faceCount
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for ii, ind in enumerate(self._sortedInds):
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# c2cn[ind] = ii
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vol.append(np.prod(self._cellH(ind)))
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faceXCount = processCell(ind, faceXCount, addXFace, hangingFacesX, DIR=0)
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faceYCount = processCell(ind, faceYCount, addYFace, hangingFacesY, DIR=1)
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self._c2f = c2f
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self.area = np.array(area)
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self.vol = np.array(vol)
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self._gridFx = np.array(facesX)
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self._gridFy = np.array(facesY)
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self.nC = len(self._sortedInds)
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self.nFx = self._gridFx.shape[0]
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self.nFy = self._gridFy.shape[0]
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self.nF = self.nFx + self.nFy
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self._hangingFacesX = hangingFacesX
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self._hangingFacesY = hangingFacesY
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@property
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def faceDiv(self):
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print self._c2f
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if getattr(self, '_faceDiv', None) is None:
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self.number()
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# TODO: Preallocate!
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I, J, V = [], [], []
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PM = [-1,1]*self.dim # plus / minus
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offset = [0,0,self.nFx,self.nFx]
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for ii, ind in enumerate(self._sortedInds):
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faces = self._c2f[ind]
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for off, pm, face in zip(offset,PM,faces):
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j = [_ + off for _ in face]
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I += [ii]*len(j)
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J += j
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V += [pm]*len(j)
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VOL = self.vol
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D = sp.csr_matrix((V,(I,J)), shape=(self.nC, self.nF))
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S = self.area
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self._faceDiv = Utils.sdiag(1.0/VOL)*D*Utils.sdiag(S)
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return self._faceDiv
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if __name__ == '__main__':
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def function(xc):
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r = xc - np.r_[0.5,0.5]
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dist = np.sqrt(r.dot(r))
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# if dist < 0.05:
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# return 5
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if dist < 0.1:
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return 4
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if dist < 0.3:
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return 3
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if dist < 1.0:
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return 2
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else:
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return 0
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# T = Tree([16,16],levels=4)
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# T.refine(function,recursive=True)
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# T.plotGrid(showIt=True)
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# BREAK
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T = Tree([np.r_[1,2,1,5,2,3,1,1],8])
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T._refineCell([0,0,0])
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T._refineCell([4,4,1])
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T._refineCell([0,0,1])
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T._refineCell([2,2,2])
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T.plotGrid(showIt=True)
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T.number()
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print sorted(T._treeInds) == [32, 40, 48, 60, 61, 62, 63, 68, 132, 224, 232, 240, 248]
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print len(T._hangingFacesX) == 7
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print T.nFx == 18
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print T.vol == 1.0
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print T.area
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T.faceDiv
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plt.subplot(211)
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plt.spy(T.faceDiv)
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T.plotGrid(ax=plt.subplot(212), showIt=True)
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print T._getNextCell([4,0,1]) is None
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print T._getNextCell([0,4,1]) == [T._index([4,4,2]), T._index([4,6,2])]
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print T._getNextCell([0,2,2]) == [T._index([2,2,3]), T._index([2,3,3])]
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print T._getNextCell([4,4,2]) == T._index([6,4,2])
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print T._getNextCell([6,4,2]) is None
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print T._getNextCell([2,0,2]) == T._index([4,0,1])
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print T._getNextCell([4,0,1], positive=False) == [T._index([2,0,2]), [T._index([3,2,3]), T._index([3,3,3])]]
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print T._getNextCell([3,3,3]) == T._index([4,0,1])
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print T._getNextCell([3,2,3]) == T._index([4,0,1])
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print T._getNextCell([2,2,3]) == T._index([3,2,3])
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print T._getNextCell([3,2,3], positive=False) == T._index([2,2,3])
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print T._getNextCell([0,0,2], direction=1) == T._index([0,2,2])
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print T._getNextCell([0,2,2], direction=1, positive=False) == T._index([0,0,2])
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print T._getNextCell([0,2,2], direction=1) == T._index([0,4,1])
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print T._getNextCell([0,4,1], direction=1, positive=False) == [T._index([0,2,2]), [T._index([2,3,3]), T._index([3,3,3])]]
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