241 lines
12 KiB
Python
Executable File
241 lines
12 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,re,math,numpy,itertools
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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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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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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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#--------------------------------------------------------------------------------------------------
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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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}
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'grid': lambda x: int(x),
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'size': lambda x: float(x),
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'origin': lambda x: float(x),
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'homogenization': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Smoothens out interface roughness by simulated curvature flow.
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This is achieved by the diffusion of each initially sharply bounded grain volume within the periodic domain
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up to a given distance 'd' voxels.
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The final geometry is assembled by selecting at each voxel that grain index for which the concentration remains largest.
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-d', '--distance', dest='d', type='int', metavar='int', \
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help='diffusion distance in voxels [%default]')
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parser.add_option('-N', '--smooth', dest='N', type='int', metavar='int', \
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help='N for curvature flow [%default]')
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parser.add_option('-r', '--renumber', dest='renumber', action='store_true', \
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help='renumber microstructure indices from 1...N [%default]')
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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(renumber = False)
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(options, filenames) = parser.parse_args()
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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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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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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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theTable = damask.ASCIItable(file['input'],file['output'],labels = False,buffered = False)
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theTable.head_read()
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#--- interpret header ----------------------------------------------------------------------------
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info = {
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'grid': numpy.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'homogenization': 0,
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'microstructures': 0,
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}
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newInfo = {
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'microstructures': 0,
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}
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extra_header = []
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for header in theTable.info:
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headitems = map(str.lower,header.split())
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if len(headitems) == 0: continue
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for synonym,alternatives in synonyms.iteritems():
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if headitems[0] in alternatives: headitems[0] = synonym
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if headitems[0] in mappings.keys():
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if headitems[0] in identifiers.keys():
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for i in xrange(len(identifiers[headitems[0]])):
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info[headitems[0]][i] = \
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mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
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else:
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info[headitems[0]] = mappings[headitems[0]](headitems[1])
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else:
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extra_header.append(header)
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file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n'%info['microstructures'])
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if numpy.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
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continue
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
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continue
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(numpy.prod([2 if i == 1 else i for i in info['grid']]),'i') # 2D structures do not work
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i = 0
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while theTable.data_read(): # read next data line of ASCII table
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items = theTable.data
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if len(items) > 2:
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if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
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elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
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else: items = map(int,items)
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else: items = map(int,items)
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s = len(items)
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microstructure[i:i+s] = items
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i += s
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#--- reshape, if 2D make copy ---------------------------------------------------------------------
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expandedGrid = numpy.array([2 if i == 1 else i for i in info['grid']],'i')
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nMicrostuctures = numpy.prod(expandedGrid)
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if nMicrostuctures > info['grid'].prod():
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microstructure[info['grid'].prod():nMicrostuctures] = microstructure[0:info['grid'].prod()]
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microstructure = microstructure.reshape([2 if i == 1 else i for i in info['grid']],order='F')
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grid = numpy.array([2 if i == 1 else i for i in info['grid']],'i')
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#--- initialize helper data -----------------------------------------------------------------------
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X,Y,Z = numpy.mgrid[0:expandedGrid[0],0:expandedGrid[1],0:expandedGrid[2]]
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gauss = numpy.exp(-(X*X+Y*Y+Z*Z)/(2.0*options.d*options.d))/math.pow(2.0*numpy.pi*options.d*options.d,1.5)
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gauss[:,:,(expandedGrid[2])/2::] = gauss[:,:,(expandedGrid[2])/2-1::-1]
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gauss[:,(expandedGrid[1])/2::,:] = gauss[:,(expandedGrid[1])/2-1::-1,:]
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gauss[(expandedGrid[0])/2::,:,:] = gauss[(expandedGrid[0])/2-1::-1,:,:]
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gauss = numpy.fft.rfftn(gauss)
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interfacialEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0
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struc = ndimage.generate_binary_structure(3,1)
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for smoothIter in xrange(options.N):
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boundary = numpy.zeros(microstructure.shape)
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for i in range(3):
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for j in range(3):
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for k in range(3):
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boundary = numpy.maximum(boundary,
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interfacialEnergy(microstructure,numpy.roll(numpy.roll(numpy.roll(
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microstructure,i-1,axis=0),j-1,axis=1),k-1,axis=2)))
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index = ndimage.morphology.distance_transform_edt(boundary == 0.,return_distances = False,return_indices = True)
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boundary = numpy.fft.irfftn(numpy.fft.rfftn(numpy.where(ndimage.morphology.binary_dilation(boundary != 0.,
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structure = struc,
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iterations = 2*options.d-1),
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boundary[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructure.shape),
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0.))*gauss)
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boundaryExt = numpy.tile(boundary,(3,3,3))
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boundaryExt = boundaryExt[(expandedGrid[0])/2:-(expandedGrid[0])/2,
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(expandedGrid[1])/2:-(expandedGrid[1])/2,
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(expandedGrid[2])/2:-(expandedGrid[2])/2]
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microstructureExt = numpy.tile(microstructure,(3,3,3))
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microstructureExt = microstructureExt[(expandedGrid[0])/2:-(expandedGrid[0])/2,
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(expandedGrid[1])/2:-(expandedGrid[1])/2,
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(expandedGrid[2])/2:-(expandedGrid[2])/2]
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index = ndimage.morphology.distance_transform_edt(boundaryExt >= 0.5,return_distances=False,return_indices=True)
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microstructureExt = microstructureExt[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructureExt.shape)
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microstructure = microstructureExt[(expandedGrid[0])/2:-(expandedGrid[0])/2,
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(expandedGrid[1])/2:-(expandedGrid[1])/2,
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(expandedGrid[2])/2:-(expandedGrid[2])/2]
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# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
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# http://stackoverflow.com/questions/10741346/numpy-frequency-counts-for-unique-values-in-an-array
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if options.renumber:
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newID=0
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for microstructureID,count in enumerate(numpy.bincount(microstructure.reshape(info['grid'].prod()))):
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if count != 0:
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newID+=1
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microstructure=numpy.where(microstructure==microstructureID,newID,microstructure).reshape(microstructure.shape)
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# --- assemble header -----------------------------------------------------------------------------
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newInfo['microstructures'] = microstructure[0:info['grid'][0],0:info['grid'][1],0:info['grid'][2]].max()
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#--- report ---------------------------------------------------------------------------------------
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if (newInfo['microstructures'] != info['microstructures']):
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file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
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#--- write header ---------------------------------------------------------------------------------
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theTable.labels_clear()
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theTable.info_clear()
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theTable.info_append(extra_header+[
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scriptID+ ' ' + ' '.join(sys.argv[1:]),
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"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
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"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
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"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
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"homogenization\t%i"%info['homogenization'],
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"microstructures\t%i"%(newInfo['microstructures']),
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])
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theTable.head_write()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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theTable.data = microstructure[0:info['grid'][0],0:info['grid'][1],0:info['grid'][2]].reshape(numpy.prod(info['grid']),order='F').transpose()
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theTable.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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file['input'].close()
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file['output'].close()
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os.rename(file['name']+'_tmp',file['name'])
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