#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,re,sys,math,string
import numpy as np
from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
def meshgrid2(*arrs):
'''
code inspired by http://stackoverflow.com/questions/1827489/numpy-meshgrid-in-3d
'''
arrs = tuple(reversed(arrs))
arrs = tuple(arrs)
lens = np.array(map(len, arrs))
dim = len(arrs)
ans = []
for i, arr in enumerate(arrs):
slc = np.ones(dim,'i')
slc[i] = lens[i]
arr2 = np.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)
def laguerreTessellation(undeformed, coords, weights):
bestdist = np.ones(len(undeformed)) * np.finfo('d').max
bestseed = np.zeros(len(undeformed))
for i,seed in enumerate(coords):
for copy in np.array([[1, 0, 0, ],
[0, 1, 0, ],
[0, 0, 1, ],
[-1, 0, 0, ],
[0, -1, 0, ],
[0, 0, -1, ],
[1, 1, 0, ],
[1, 0, 1, ],
[0, 1, 1, ],
[-1, 1, 0, ],
[-1, 0, 1, ],
[0, -1, 1, ],
[-1, -1, 0, ],
[-1, 0, -1, ],
[0, -1, -1, ],
[1, -1, 0, ],
[1, 0, -1, ],
[0, 1, -1, ],
[1, 1, 1, ],
[-1, 1, 1, ],
[1, -1, 1, ],
[1, 1, -1, ],
[-1, -1, -1, ],
[1, -1, -1, ],
[-1, 1, -1, ],
[-1, -1, 1, ]]).astype(float):
diff = undeformed - np.repeat((seed+info['size']*copy).reshape(3,1),len(undeformed),axis=1).T
dist = np.sum(diff*diff,axis=1) - weights[i]
bestseed = np.where(dist < bestdist, np.ones(len(undeformed))*(i+1),bestseed)
bestdist = np.where(dist < bestdist, dist,bestdist)
return bestseed
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
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=damask.extendableOption, usage='%prog options [file[s]]', description = """
Generate geometry description and material configuration by standard Voronoi tessellation of given seeds file.
""", version = scriptID)
parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, metavar=' '.join(['int']*3),
help='a,b,c grid of hexahedral box [from seeds file]')
parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, metavar=' '.join(['float']*3),
help='x,y,z size of hexahedral box [1.0 along largest grid point number]')
parser.add_option('-o', '--origin', dest='origin', type='float', nargs = 3, metavar=' '.join(['float']*3),
help='offset from old to new origin of grid')
parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int',
help='homogenization index to be used [%default]')
parser.add_option('--phase', dest='phase', type='int', metavar = 'int',
help='phase index to be used [%default]')
parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int',
help='crystallite index to be used [%default]')
parser.add_option('-c', '--configuration', dest='config', action='store_true',
help='output material configuration [%default]')
parser.add_option('-r', '--rnd', dest='randomSeed', type='int', metavar='int',
help='seed of random number generator for second phase distribution [%default]')
parser.add_option('--secondphase', type='float', dest='secondphase', metavar= 'float',
help='volume fraction of randomly distribute second phase [%default]')
parser.add_option('--laguerre', dest='laguerre', action='store_true',
help='for weighted voronoi (Laguerre) tessellation [%default]')
parser.set_defaults(grid = (0,0,0))
parser.set_defaults(size = (0.0,0.0,0.0))
parser.set_defaults(origin = (0.0,0.0,0.0))
parser.set_defaults(homogenization = 1)
parser.set_defaults(phase = 1)
parser.set_defaults(crystallite = 1)
parser.set_defaults(secondphase = 0.0)
parser.set_defaults(config = False)
parser.set_defaults(laguerre = False)
parser.set_defaults(randomSeed = None)
(options,filenames) = parser.parse_args()
if options.secondphase > 1.0 or options.secondphase < 0.0:
parser.error('volume fraction of second phase (%f) out of bounds...'%options.secondphase)
#--- 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:
file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
table = damask.ASCIItable(file['input'],file['output'],buffered = False)
table.head_read()
labels = []
if np.all(table.label_index(['1_coords','2_coords','3_coords']) != -1):
coords = ['1_coords','2_coords','3_coords']
elif np.all(table.label_index(['x','y','z']) != -1):
coords = ['x','y','z']
else:
file['croak'].write('no coordinate data (1/2/3_coords | x/y/z) found ...')
continue
labels += coords
hasEulers = np.all(table.label_index(['phi1','Phi','phi2']) != -1)
if hasEulers:
labels += ['phi1','Phi','phi2']
hasGrains = table.label_index('microstructure') != -1
if hasGrains:
labels += ['microstructure']
hasWeight = table.label_index('weight') != -1
if hasWeight:
labels += ['weight']
table.data_readArray(labels)
coords = table.data[:,table.label_index(coords)]
eulers = table.data[:,table.label_index(['phi1','Phi','phi2'])] if hasEulers else np.zeros(3*len(coords))
grain = table.data[:,table.label_index('microstructure')] if hasGrains else 1+np.arange(len(coords))
weights = table.data[:,table.label_index('weight')] if hasWeight else np.zeros(len(coords))
grainIDs = np.unique(grain).astype('i')
#--- interpret header ----------------------------------------------------------------------------
info = {
'grid': np.zeros(3,'i'),
'size': np.array(options.size),
'origin': np.zeros(3,'d'),
'microstructures': 0,
'homogenization': options.homogenization,
}
newInfo = {
'microstructures': 0,
}
extra_header = []
for header in table.info:
headitems = map(str.lower,header.split())
if len(headitems) == 0: continue
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'] = np.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 np.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n')
continue
if np.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 ---------------------------------------------------------------------------------
eulers = eulers.T
#--- switch according to task ---------------------------------------------------------------------
if options.config: # write config file
phase=np.empty(info['microstructures'],'i')
phase.fill(options.phase)
phase[0:int(float(info['microstructures'])*options.secondphase)] = options.phase+1
randomSeed = int(os.urandom(4).encode('hex'), 16) if options.randomSeed == None else options.randomSeed # radom seed per file for second phase
np.random.seed(randomSeed)
np.random.shuffle(phase)
formatwidth = 1+int(math.log10(info['microstructures']))
file['output'].write('#' + scriptID + ' ' + ' '.join(sys.argv[1:])+'\n')
if options.secondphase > 0.0: file['output'].write('# random seed for second phase %i\n'%randomSeed)
file['output'].write('\n<microstructure>\n')
for i,ID in enumerate(grainIDs):
file['output'].write('\n[Grain%s]\n'%(str(ID).zfill(formatwidth)) + \
'crystallite %i\n'%options.crystallite + \
'(constituent)\tphase %i\ttexture %s\tfraction 1.0\n'%(phase[i],str(ID).rjust(formatwidth)))
file['output'].write('\n<texture>\n')
for ID in grainIDs:
eulerID = np.nonzero(grain == ID)[0][0] # find first occurrence of this grain id
file['output'].write('\n[Grain%s]\n'%(str(ID).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 = (np.arange(info['grid'][0])+0.5)*info['size'][0]/info['grid'][0]
y = (np.arange(info['grid'][1])+0.5)*info['size'][1]/info['grid'][1]
z = (np.arange(info['grid'][2])+0.5)*info['size'][2]/info['grid'][2]
if not options.laguerre:
coords = (coords*info['size']).T
undeformed = np.vstack(map(np.ravel, meshgrid2(x, y, z)))
file['croak'].write('tessellating...\n')
indices = damask.core.math.periodicNearestNeighbor(\
info['size'],\
np.eye(3),\
undeformed,coords)//3**3 + 1 # floor division to kill periodic images
indices = grain[indices-1]
else :
undeformed = np.vstack(np.meshgrid(x, y, z)).reshape(3,-1).T
indices = laguerreTessellation(undeformed, coords, weights)
newInfo['microstructures'] = info['microstructures']
for i in grainIDs:
if i not in indices: newInfo['microstructures'] -= 1
file['croak'].write('all' if [newInfo['microstructures'] == info['microstructures'] ] else 'only' +
' %i'%newInfo['microstructures'] +
'' if [newInfo['microstructures'] == info['microstructures']] else \
'out of %i'%info['microstructures'] +
' grains mapped.\n')
#--- write header ---------------------------------------------------------------------------------
table.labels_clear()
table.info_clear()
table.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']),
])
table.head_write()
# --- write microstructure information ------------------------------------------------------------
formatwidth = 1+int(math.log10(newInfo['microstructures']))
table.data = indices.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
table.input_close()
table.output_close()
os.rename(file['name']+'_tmp',
os.path.splitext(file['name'])[0] +'%s'%('_material.config' if options.config else '.geom'))