#!/usr/bin/env python # -*- coding: utf-8 -*- import os,sys,math,string,re,numpy import damask from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP 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) def meshgrid2(*arrs): ''' code inspired by http://stackoverflow.com/questions/1827489/numpy-meshgrid-in-3d ''' arrs = tuple(reversed(arrs)) arrs = tuple(arrs) lens = numpy.array(map(len, arrs)) dim = len(arrs) ans = [] for i, arr in enumerate(arrs): slc = numpy.ones(dim,'i') slc[i] = lens[i] arr2 = numpy.asarray(arr).reshape(slc) for j, sz in enumerate(lens): if j != i: arr2 = arr2.repeat(sz, axis=j) ans.insert(0,arr2) return tuple(ans) #-------------------------------------------------------------------------------------------------- # MAIN #-------------------------------------------------------------------------------------------------- synonyms = { 'grid': ['resolution'], 'size': ['dimension'], 'microstructures': ['grains'], } 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 = """ Generate geometry description and material configuration by standard Voronoi tessellation of given seeds file. """ + string.replace(scriptID,'\n','\\n') ) parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \ help='a,b,c grid of hexahedral box [from seeds file]') parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, \ help='x,y,z size of hexahedral box [1.0 along largest grid point number]') parser.add_option('--homogenization', dest='homogenization', type='int', \ help='homogenization index to be used [%default]') parser.add_option('--phase', dest='phase', type='int', \ help='phase index to be used [%default]') parser.add_option('--crystallite', dest='crystallite', type='int', \ help='crystallite index to be used [%default]') parser.add_option('-c', '--configuration', dest='config', action='store_true', \ help='output material configuration [%default]') parser.set_defaults(grid = [0,0,0]) parser.set_defaults(size = [0.0,0.0,0.0]) parser.set_defaults(homogenization = 1) parser.set_defaults(phase = 1) parser.set_defaults(crystallite = 1) parser.set_defaults(config = False) (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']) theTable.head_read() coords = theTable.data_asArray(['x','y','z']) if numpy.all(theTable.labels_index(['phi1','Phi','phi2']) != -1): eulers = theTable.data_asArray(['phi1','Phi','phi2']) if theTable.labels_index('microstructure') != -1: grain = theTable.data_asArray(['microstructure']) grainIDs = numpy.unique(grain).astype('i') else: grain = 1+numpy.arange(len(eulers)) grainIDs = grain #--- interpret header ---------------------------------------------------------------------------- info = { 'grid': numpy.zeros(3,'i'), 'size': numpy.array(options.size), 'origin': numpy.zeros(3,'d'), 'microstructures': 0, 'homogenization': options.homogenization, } 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) if info['microstructures'] != len(grainIDs): file['croak'].write('grain data not matching grain count (%i)...\n'%(len(grainIDs))) info['microstructures'] = len(grainIDs) if 0 not in options.grid: # user-specified grid info['grid'] = numpy.array(options.grid) for i in xrange(3): if info['size'][i] <= 0.0: # any invalid size? info['size'][i] = float(info['grid'][i])/max(info['grid']) file['croak'].write('rescaling size %s...\n'%{0:'x',1:'y',2:'z'}[i]) file['croak'].write('grains to map: %i\n'%info['microstructures'] + \ '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']) 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 if info['microstructures'] == 0: file['croak'].write('no grain info found.\n') continue #--- prepare data --------------------------------------------------------------------------------- coords = (coords*info['size']).transpose() eulers = eulers.transpose() #--- switch according to task --------------------------------------------------------------------- if options.config: # write config file formatwidth = 1+int(math.log10(info['microstructures'])) file['output'].write('\n') for i in grainIDs: file['output'].write('\n[Grain%s]\n'%(str(i).zfill(formatwidth)) + \ 'crystallite %i\n'%options.crystallite + \ '(constituent)\tphase %i\ttexture %s\tfraction 1.0\n'%(options.phase,str(i).rjust(formatwidth))) file['output'].write('\n\n') for i in grainIDs: eulerID = numpy.nonzero(grain == i)[0][0] # find first occurrence of this grain id file['output'].write('\n[Grain%s]\n'%(str(i).zfill(formatwidth)) + \ '(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0\n'%(eulers[0,eulerID], eulers[1,eulerID], eulers[2,eulerID])) else: # write geometry file x = (numpy.arange(info['grid'][0])+0.5)*info['size'][0]/info['grid'][0] y = (numpy.arange(info['grid'][1])+0.5)*info['size'][1]/info['grid'][1] z = (numpy.arange(info['grid'][2])+0.5)*info['size'][2]/info['grid'][2] undeformed = numpy.vstack(map(numpy.ravel, meshgrid2(x, y, z))) file['croak'].write('tessellating...\n') indices = damask.core.math.periodicNearestNeighbor(\ info['size'],\ numpy.eye(3),\ undeformed,coords)//3**3 + 1 # floor division to kill periodic images indices = grain[indices-1] newInfo['microstructures'] = info['microstructures'] for i in grainIDs: if i not in indices: newInfo['microstructures'] -= 1 file['croak'].write({True:'all',False:'only'}[newInfo['microstructures'] == info['microstructures'] ] + ' %i'%newInfo['microstructures'] + {True:'',False:' out of %i'%info['microstructures']}[newInfo['microstructures'] == info['microstructures']] + ' grains mapped.\n') #--- write header --------------------------------------------------------------------------------- theTable.labels_clear() theTable.info_clear() theTable.info_append(extra_header+[ scriptID, "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() theTable.output_flush() # --- write microstructure information ------------------------------------------------------------ formatwidth = 1+int(math.log10(newInfo['microstructures'])) theTable.data = indices.reshape(info['grid'][1]*info['grid'][2],info['grid'][0]) theTable.data_writeArray('%%%ii'%(formatwidth),delimiter=' ') #--- output finalization -------------------------------------------------------------------------- if file['name'] != 'STDIN': file['input'].close() file['output'].close() os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] + \ {True: '_material.config', False:'.geom'}[options.config])