#!/usr/bin/env python # -*- coding: UTF-8 no BOM -*- import os,sys,string,re,math,numpy,itertools import damask from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP from scipy import ndimage from multiprocessing import Pool scriptID = '$Id$' scriptName = scriptID.split()[1] #-------------------------------------------------------------------------------------------------- class extendedOption(Option): #-------------------------------------------------------------------------------------------------- # used for definition of new option parser action 'extend', which enables to take multiple option arguments # taken from online tutorial http://docs.python.org/library/optparse.html ACTIONS = Option.ACTIONS + ("extend",) STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",) TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",) ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",) def take_action(self, action, dest, opt, value, values, parser): if action == "extend": lvalue = value.split(",") values.ensure_value(dest, []).extend(lvalue) else: Option.take_action(self, action, dest, opt, value, values, parser) #-------------------------------------------------------------------------------------------------- # MAIN #-------------------------------------------------------------------------------------------------- synonyms = { 'grid': ['resolution'], 'size': ['dimension'], } identifiers = { 'grid': ['a','b','c'], 'size': ['x','y','z'], 'origin': ['x','y','z'], } mappings = { 'grid': lambda x: int(x), 'size': lambda x: float(x), 'origin': lambda x: float(x), 'homogenization': lambda x: int(x), 'microstructures': lambda x: int(x), } parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """ Smoothens out interface roughness by simulated curvature flow. This is achieved by the diffusion of each initially sharply bounded grain volume within the periodic domain up to a given distance 'd' voxels. The final geometry is assembled by selecting at each voxel that grain index for which the concentration remains largest. """ + string.replace(scriptID,'\n','\\n') ) parser.add_option('-d', '--distance', dest='d', type='int', metavar='int', \ help='diffusion distance in voxels [%default]') parser.add_option('-N', '--smooth', dest='N', type='int', metavar='int', \ help='N for curvature flow [%default]') parser.add_option('-r', '--renumber', dest='renumber', action='store_true', \ help='renumber microstructure indices from 1...N [%default]') parser.add_option('-i', '--immutable', action='extend', dest='immutable', type='string', \ help='immutable microstructures') parser.set_defaults(d = 1) parser.set_defaults(N = 1) parser.set_defaults(renumber = False) parser.set_defaults(immutable = [0]) (options, filenames) = parser.parse_args() #--- setup file handles -------------------------------------------------------------------------- files = [] if filenames == []: files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr, }) else: for name in filenames: if os.path.exists(name): files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stdout, }) #--- loop over input files ------------------------------------------------------------------------ for file in files: if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n') else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n') theTable = damask.ASCIItable(file['input'],file['output'],labels = False,buffered = False) theTable.head_read() #--- interpret header ---------------------------------------------------------------------------- info = { 'grid': numpy.zeros(3,'i'), 'size': numpy.zeros(3,'d'), 'origin': numpy.zeros(3,'d'), 'homogenization': 0, 'microstructures': 0, } newInfo = { 'microstructures': 0, } extra_header = [] for header in theTable.info: headitems = map(str.lower,header.split()) if len(headitems) == 0: continue for synonym,alternatives in synonyms.iteritems(): if headitems[0] in alternatives: headitems[0] = synonym if headitems[0] in mappings.keys(): if headitems[0] in identifiers.keys(): for i in xrange(len(identifiers[headitems[0]])): info[headitems[0]][i] = \ mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1]) else: info[headitems[0]] = mappings[headitems[0]](headitems[1]) else: extra_header.append(header) file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \ 'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \ 'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \ 'homogenization: %i\n'%info['homogenization'] + \ 'microstructures: %i\n'%info['microstructures']) if numpy.any(info['grid'] < 1): file['croak'].write('invalid grid a b c.\n') continue if numpy.any(info['size'] <= 0.0): file['croak'].write('invalid size x y z.\n') continue #--- read data ------------------------------------------------------------------------------------ microstructure = numpy.zeros(numpy.prod([2 if i == 1 else i for i in info['grid']]),'i') # 2D structures do not work i = 0 while theTable.data_read(): # read next data line of ASCII table items = theTable.data if len(items) > 2: if items[1].lower() == 'of': items = [int(items[2])]*int(items[0]) elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2])) else: items = map(int,items) else: items = map(int,items) s = len(items) microstructure[i:i+s] = items i += s #--- reshape, if 2D make copy --------------------------------------------------------------------- expandedGrid = numpy.array([2 if i == 1 else i for i in info['grid']],'i') nMicrostuctures = numpy.prod(expandedGrid) if nMicrostuctures > info['grid'].prod(): microstructure[info['grid'].prod():nMicrostuctures] = microstructure[0:info['grid'].prod()] microstructure = microstructure.reshape([2 if i == 1 else i for i in info['grid']],order='F') grid = numpy.array([2 if i == 1 else i for i in info['grid']],'i') #--- initialize helper data ----------------------------------------------------------------------- X,Y,Z = numpy.mgrid[0:expandedGrid[0],0:expandedGrid[1],0:expandedGrid[2]] 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) gauss[:,:,(expandedGrid[2])/2::] = gauss[:,:,(expandedGrid[2])/2-1::-1] gauss[:,(expandedGrid[1])/2::,:] = gauss[:,(expandedGrid[1])/2-1::-1,:] gauss[(expandedGrid[0])/2::,:,:] = gauss[(expandedGrid[0])/2-1::-1,:,:] gauss = numpy.fft.rfftn(gauss) interfacialEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0 struc = ndimage.generate_binary_structure(3,1) microstructure_original = numpy.copy(microstructure) for smoothIter in xrange(options.N): boundary = numpy.zeros(microstructure.shape) for i in range(3): for j in range(3): for k in range(3): boundary = numpy.maximum(boundary, interfacialEnergy(microstructure,numpy.roll(numpy.roll(numpy.roll( microstructure,i-1,axis=0),j-1,axis=1),k-1,axis=2))) boundaryExt = numpy.tile(boundary,(3,3,3)) boundaryExt = boundaryExt[(expandedGrid[0])/2:-(expandedGrid[0])/2, (expandedGrid[1])/2:-(expandedGrid[1])/2, (expandedGrid[2])/2:-(expandedGrid[2])/2] index = ndimage.morphology.distance_transform_edt(boundaryExt == 0.,return_distances = False,return_indices = True) # array index of nearest voxel on periodically extended boundary boundaryExt = boundaryExt[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(boundaryExt.shape) # fill bulk with energy of nearest interface boundary = numpy.fft.irfftn(numpy.fft.rfftn(numpy.where(ndimage.morphology.binary_dilation(boundary > 0., structure = struc, iterations = 2*options.d-1), # fat boundary boundaryExt[(expandedGrid[0])/2:-(expandedGrid[0])/2, # retain filled energy on fat boundary (expandedGrid[1])/2:-(expandedGrid[1])/2, (expandedGrid[2])/2:-(expandedGrid[2])/2], 0.))*gauss) # zero everywhere else boundaryExt = numpy.tile(boundary,(3,3,3)) boundaryExt = boundaryExt[(expandedGrid[0])/2:-(expandedGrid[0])/2, (expandedGrid[1])/2:-(expandedGrid[1])/2, (expandedGrid[2])/2:-(expandedGrid[2])/2] microstructureExt = numpy.tile(microstructure,(3,3,3)) microstructureExt = microstructureExt[(expandedGrid[0])/2:-(expandedGrid[0])/2, (expandedGrid[1])/2:-(expandedGrid[1])/2, (expandedGrid[2])/2:-(expandedGrid[2])/2] index = ndimage.morphology.distance_transform_edt(boundaryExt >= 0.5,return_distances=False,return_indices=True) microstructureExt = microstructureExt[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructureExt.shape) microstructure = microstructureExt[(expandedGrid[0])/2:-(expandedGrid[0])/2, (expandedGrid[1])/2:-(expandedGrid[1])/2, (expandedGrid[2])/2:-(expandedGrid[2])/2] immutable = numpy.zeros(microstructure.shape, dtype=bool) for micro in options.immutable: immutable = numpy.logical_or(immutable, numpy.logical_or(microstructure == int(micro), microstructure_original == int(micro))) microstructure = numpy.where(immutable, microstructure_original,microstructure) # --- renumber to sequence 1...Ngrains if requested ------------------------------------------------ # http://stackoverflow.com/questions/10741346/numpy-frequency-counts-for-unique-values-in-an-array if options.renumber: newID=0 for microstructureID,count in enumerate(numpy.bincount(microstructure.reshape(info['grid'].prod()))): if count != 0: newID+=1 microstructure=numpy.where(microstructure==microstructureID,newID,microstructure).reshape(microstructure.shape) # --- assemble header ----------------------------------------------------------------------------- newInfo['microstructures'] = microstructure[0:info['grid'][0],0:info['grid'][1],0:info['grid'][2]].max() #--- report --------------------------------------------------------------------------------------- if (newInfo['microstructures'] != info['microstructures']): file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures']) #--- write header --------------------------------------------------------------------------------- theTable.labels_clear() theTable.info_clear() theTable.info_append(extra_header+[ scriptID+ ' ' + ' '.join(sys.argv[1:]), "grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],), "size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],), "origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],), "homogenization\t%i"%info['homogenization'], "microstructures\t%i"%(newInfo['microstructures']), ]) theTable.head_write() # --- write microstructure information ------------------------------------------------------------ formatwidth = int(math.floor(math.log10(microstructure.max())+1)) theTable.data = microstructure[0:info['grid'][0],0:info['grid'][1],0:info['grid'][2]].reshape(numpy.prod(info['grid']),order='F').transpose() theTable.data_writeArray('%%%ii'%(formatwidth),delimiter=' ') #--- output finalization -------------------------------------------------------------------------- if file['name'] != 'STDIN': file['input'].close() file['output'].close() os.rename(file['name']+'_tmp',file['name'])