#!/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.set_defaults(d = 1)
parser.set_defaults(N = 1)
(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)
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
theTable.data_rewind()
while theTable.data_read():
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 ---------------------------------------------------------------------
nMicrostuctures = numpy.prod([2 if i == 1 else i for i in info['grid']])
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')
#--- domain decomposition -------------------------------------------------------------------------
stride = numpy.array([2 if i == 1 else i for i in info['grid']],'i')
if numpy.any(numpy.floor(stride) != stride):
file['croak'].write('invalid domain decomposition.\n')
continue
#--- initialize helper data -----------------------------------------------------------------------
window = 0
X,Y,Z = numpy.mgrid[0:stride[0]+2*window,0:stride[1]+2*window,0:stride[2]+2*window]
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[:,:,(stride[2]+2*window)/2::] = gauss[:,:,(stride[2]+2*window)/2-1::-1]
gauss[:,(stride[1]+2*window)/2::,:] = gauss[:,(stride[1]+2*window)/2-1::-1,:]
gauss[(stride[0]+2*window)/2::,:,:] = gauss[(stride[0]+2*window)/2-1::-1,:,:]
gauss = numpy.fft.rfftn(gauss)
for smoothIter in xrange(options.N):
interfacialEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0
struc = ndimage.generate_binary_structure(3,1)
microExt = numpy.zeros([microstructure.shape[0]+2,microstructure.shape[1]+2,microstructure.shape[2]+2])
microExt[1:-1,1:-1,1:-1] = microstructure
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,microExt[i:microstructure.shape[0]+i,\
j:microstructure.shape[1]+j,\
k:microstructure.shape[2]+k]))
index = ndimage.morphology.distance_transform_edt(boundary == 0.,return_distances=False,return_indices=True)
boundary = numpy.fft.irfftn(numpy.fft.rfftn(numpy.where(ndimage.morphology.binary_dilation(boundary!=0.,\
structure=struc,\
iterations=2*options.d-1),\
boundary[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructure.shape),\
0.))*gauss)
index = ndimage.morphology.distance_transform_edt(boundary >= 0.5,return_distances=False,return_indices=True)
microstructure = microstructure[index[0].flatten(),index[1].flatten(),index[2].flatten()].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()
theTable.output_flush()
# --- 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'])