221 lines
9.6 KiB
Python
Executable File
221 lines
9.6 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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import os,sys,math,string,re,numpy
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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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 meshgrid2(*arrs):
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'''
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code inspired by http://stackoverflow.com/questions/1827489/numpy-meshgrid-in-3d
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'''
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arrs = tuple(reversed(arrs))
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arrs = tuple(arrs)
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lens = numpy.array(map(len, arrs))
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dim = len(arrs)
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ans = []
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for i, arr in enumerate(arrs):
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slc = numpy.ones(dim,'i')
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slc[i] = lens[i]
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arr2 = numpy.asarray(arr).reshape(slc)
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for j, sz in enumerate(lens):
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if j != i:
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arr2 = arr2.repeat(sz, axis=j)
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ans.insert(0,arr2)
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return tuple(ans)
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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identifiers = {
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'grid': ['a','b','c'],
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}
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mappings = {
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'grid': lambda x: int(x),
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'grains': 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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Generate geometry description and material configuration by standard Voronoi tessellation of given seeds file.
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \
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help='a,b,c grid of hexahedral box [from seeds file]')
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parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, \
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help='x,y,z size of hexahedral box [1.0 along largest grid point number]')
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parser.add_option('--homogenization', dest='homogenization', type='int', \
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help='homogenization index to be used [%default]')
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parser.add_option('--phase', dest='phase', type='int', \
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help='phase index to be used [%default]')
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parser.add_option('--crystallite', dest='crystallite', type='int', \
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help='crystallite index to be used [%default]')
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parser.add_option('-c', '--configuration', dest='config', action='store_true', \
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help='output material configuration [%default]')
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parser.set_defaults(grid = [0,0,0])
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parser.set_defaults(size = [0.0,0.0,0.0])
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parser.set_defaults(homogenization = 1)
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parser.set_defaults(phase = 1)
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parser.set_defaults(crystallite = 1)
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parser.set_defaults(config = 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(file['name']+'\n')
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theTable = damask.ASCIItable(file['input'],file['output'])
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theTable.head_read()
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theData = theTable.data_asArray(['x','y','z','phi1','Phi','phi2'])
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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.array(options.size),
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'origin': numpy.zeros(3,'d'),
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'grains': 0,
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'homogenization': options.homogenization,
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}
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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 # skip blank lines
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if headitems[0] == 'resolution': headitems[0] = 'grid'
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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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if info['grains'] != len(theData):
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file['croak'].write('grain data not matching grain count...\n')
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info['grains'] = min(info['grains'],len(theData))
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if 0 not in options.grid: # user-specified grid
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info['grid'] = numpy.array(options.grid)
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for i in xrange(3):
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if info['size'][i] <= 0.0: # any invalid size?
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info['size'][i] = float(info['grid'][i])/max(info['grid'])
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file['croak'].write('rescaling size %s...\n'%{0:'x',1:'y',2:'z'}[i])
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file['croak'].write('grains to map: %i\n'%info['grains'] + \
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'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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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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if info['grains'] == 0:
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file['croak'].write('no grain info found.\n')
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continue
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#--- prepare data ---------------------------------------------------------------------------------
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coords = (theData[:,:3]*info['size']).transpose()
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eulers = (theData[:,3:6]).transpose()
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#--- switch according to task ---------------------------------------------------------------------
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if options.config: # write config file
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file['output'].write('<microstructure>\n')
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for i in xrange(info['grains']):
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file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \
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'crystallite %i\n'%options.crystallite + \
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'(constituent)\tphase %i\ttexture %s\tfraction 1.0\n'%(options.phase,str(i+1).rjust(formatwidth)))
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file['output'].write('\n<texture>\n')
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for i in xrange(info['grains']):
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file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \
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'(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0\n'%(eulers[0,i],eulers[1,i],eulers[2,i]))
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else: # write geometry file
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x = (numpy.arange(info['grid'][0])+0.5)*info['size'][0]/info['grid'][0]
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y = (numpy.arange(info['grid'][1])+0.5)*info['size'][1]/info['grid'][1]
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z = (numpy.arange(info['grid'][2])+0.5)*info['size'][2]/info['grid'][2]
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undeformed = numpy.vstack(map(numpy.ravel, meshgrid2(x, y, z)))
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file['croak'].write('tesselating...\n')
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indices = damask.core.math.periodicNearestNeighbor(\
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info['size'],\
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numpy.eye(3),\
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undeformed,coords)//3**3 + 1 # floor division to kill periodic images
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missing = 0
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for i in xrange(info['grains']):
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if i+1 not in indices: missing += 1
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file['croak'].write({True:'all',False:'only'}[missing == 0] + ' %i grains mapped.\n'%(info['grains']-missing))
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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([
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"$Id$",
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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"%(info['grains']-missing),
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])
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theTable.head_write()
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theTable.output_flush()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = 1+int(math.log10(info['grains']))
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theTable.data = indices.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
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theTable.data_writeArray('%%%ii'%(formatwidth))
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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',os.path.splitext(file['name'])[0] + \
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{True: '_material.config',
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False:'.geom'}[options.config])
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