fixed bug and re-reverted to faster version. added python multiprocessing functionality. polishing and renaming
This commit is contained in:
Pratheek Shanthraj
parent
8ccdfb27f3
commit
5ff8a7067e
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@ -5,30 +5,63 @@ import os,sys,string,re,math,numpy
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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from scipy import ndimage
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from multiprocessing import Pool
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#--------------------------------------------------------------------------------------------------
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class extendedOption(Option):
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#--------------------------------------------------------------------------------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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def grainCoarsenLocal(microLocal,ix,iy,iz,window):
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winner = numpy.zeros(microLocal.shape).astype(int)
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winner = numpy.where(numpy.reshape(numpy.in1d(microLocal,options.black),microLocal.shape),
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microLocal,0) # zero out non-blacklisted microstructures
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diffusedMax = (winner > 0).astype(float) # concentration of immutable microstructures
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boundingSlice = ndimage.measurements.find_objects(microLocal) # bounding boxes of each distinct microstructure region
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for grain in set(numpy.unique(microLocal)).difference(set(options.black).union(set([0]))): # diffuse all microstructures except immutable ones
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mini = [max(0, boundingSlice[grain-1][i].start - window) for i in range(3)] # upper right of expanded bounding box
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maxi = [min(microLocal.shape[i], boundingSlice[grain-1][i].stop + window) for i in range(3)] # lower left of expanded bounding box
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diffused = ndimage.filters.gaussian_filter((microLocal[mini[0]:maxi[0],\
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mini[1]:maxi[1],\
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mini[2]:maxi[2]]==grain).astype(float),\
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options.d) # diffuse microstructure inside extended bounding box
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isMax = diffused > diffusedMax[mini[0]:maxi[0],\
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mini[1]:maxi[1],\
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mini[2]:maxi[2]] # me at highest concentration?
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winner[mini[0]:maxi[0],\
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mini[1]:maxi[1],\
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mini[2]:maxi[2]][isMax] = grain # remember me ...
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diffusedMax[mini[0]:maxi[0],\
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mini[1]:maxi[1],\
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mini[2]:maxi[2]] = numpy.where(isMax,\
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diffused,\
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diffusedMax[mini[0]:maxi[0],\
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mini[1]:maxi[1],\
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mini[2]:maxi[2]]) # ... and my concentration
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return [winner[window:-window,window:-window,window:-window],ix,iy,iz]
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def log_result(result):
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ix = result[1]; iy = result[2]; iz = result[3]
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microstructure[ix*stride[0]:(ix+1)*stride[0],iy*stride[1]:(iy+1)*stride[1],iz*stride[2]:(iz+1)*stride[2]] = \
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result[0]
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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synonyms = {
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'grid': ['resolution'],
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'size': ['dimension'],
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@ -54,12 +87,18 @@ The final geometry is assembled by selecting at each voxel that grain index for
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('-d', '--distance', dest='d', type='float', \
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parser.add_option('-d', '--distance', dest='d', type='int', \
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help='diffusion distance in voxels [%default]', metavar='float')
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parser.add_option('-N', '--smooth', dest='N', type='int', \
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help='N for curvature flow [%default]')
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parser.add_option('-p', '--processors', dest='p', type='int', nargs = 3, \
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help='number of threads in x,y,z direction')
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parser.add_option('-b', '--black', dest='black', action='extend', type='string', \
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help='indices of stationary microstructures', metavar='<LIST>')
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help='indices of stationary microstructures', metavar='<LIST>')
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parser.set_defaults(t = 1)
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parser.set_defaults(d = 1)
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parser.set_defaults(N = 1)
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parser.set_defaults(p = [1,1,1])
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parser.set_defaults(black = [])
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(options, filenames) = parser.parse_args()
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@ -69,19 +108,19 @@ options.black = map(int,options.black)
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#--- setup file handles --------------------------------------------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN',
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'input':sys.stdin,
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'output':sys.stdout,
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'croak':sys.stderr,
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})
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files.append({'name':'STDIN',
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'input':sys.stdin,
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'output':sys.stdout,
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'croak':sys.stderr,
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})
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else:
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name,
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'input':open(name),
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'output':open(name+'_tmp','w'),
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'croak':sys.stdout,
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})
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name,
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'input':open(name),
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'output':open(name+'_tmp','w'),
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'croak':sys.stdout,
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})
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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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@ -147,22 +186,37 @@ for file in files:
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microstructure[i:i+s] = items
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i += s
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#--- do work ------------------------------------------------------------------------------------
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#--- do work -------------------------------------------------------------------------------------
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microstructure = microstructure.reshape(info['grid'],order='F')
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#--- domain decomposition -------------------------------------------------------------------------
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numProc = int(options.p[0]*options.p[1]*options.p[2])
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stride = info['grid']/options.p
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if numpy.any(numpy.floor(stride) != stride):
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file['croak'].write('invalid domain decomposition.\n')
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continue
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#--- initialize helper data -----------------------------------------------------------------------
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winner = numpy.zeros(info['grid'],'i')
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diffusedMax = numpy.zeros(info['grid'])
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window = 4*options.d
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for smoothIter in xrange(options.N):
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extendedMicro = numpy.tile(microstructure,[3,3,3])
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extendedMicro = extendedMicro[(info['grid'][0]-window):-(info['grid'][0]-window),
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(info['grid'][1]-window):-(info['grid'][1]-window),
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(info['grid'][2]-window):-(info['grid'][2]-window)]
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pool = Pool(processes=numProc)
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for iz in xrange(options.p[2]):
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for iy in xrange(options.p[1]):
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for ix in xrange(options.p[0]):
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pool.apply_async(grainCoarsenLocal,(extendedMicro[ix*stride[0]:(ix+1)*stride[0]+2*window,\
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iy*stride[1]:(iy+1)*stride[1]+2*window,\
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iz*stride[2]:(iz+1)*stride[2]+2*window],\
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ix,iy,iz,window), callback=log_result)
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pool.close()
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pool.join()
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#--- diffuse each grain separately ----------------------------------------------------------------
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for theGrain in xrange(1,1+numpy.amax(microstructure)):
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diffused = ndimage.filters.gaussian_filter((microstructure == theGrain).astype(float),\
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{True:0.0,False:options.d}[theGrain in options.black],\
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mode='wrap')
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winner = numpy.where(diffused > diffusedMax, theGrain, winner)
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diffusedMax = numpy.where(diffused > diffusedMax, diffused, diffusedMax)
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newInfo['microstructures'] = winner.max()
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# --- assemble header -----------------------------------------------------------------------------
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newInfo['microstructures'] = microstructure.max()
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#--- report ---------------------------------------------------------------------------------------
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if (newInfo['microstructures'] != info['microstructures']):
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@ -183,8 +237,8 @@ for file in files:
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theTable.output_flush()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(winner.max())+1))
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theTable.data = winner.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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theTable.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
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theTable.data_writeArray('%%%ii'%(formatwidth))
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#--- output finalization --------------------------------------------------------------------------
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@ -30,7 +30,7 @@ bin_link = { \
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'geom_unpack.py',
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'geom_translate.py',
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'geom_vicinityOffset.py',
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'geom_stretchInterfaces.py',
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'geom_grainGrowth.py',
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],
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'post' : [
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'3Dvisualize.py',
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