DAMASK_EICMD/processing/pre/geom_fromVoronoiTessellatio...

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#!/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('<microstructure>\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<texture>\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))
#--- 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])