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DAMASK_EICMD
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added possibility to have microstructure indices for seed points. Hence, multiple seed points can belong to the same final grain.

This commit is contained in:
Philip Eisenlohr 2013-07-10 09:12:00 +00:00
parent b7e86f5c23
commit fafa69b846
1 changed files with 68 additions and 30 deletions
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98
processing/pre/geom_fromVoronoiTessellation.py
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@ -5,6 +5,9 @@ import os,sys,math,string,re,numpy
import damask import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
scriptID = '$Id$'
scriptName = scriptID.split()[1]
#-------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------
class extendedOption(Option): class extendedOption(Option):
#-------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------
@ -48,17 +51,26 @@ def meshgrid2(*arrs):
#-------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------
# MAIN # MAIN
#-------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------
synonyms = {
'grid': ['resolution'],
'size': ['dimension'],
}
identifiers = { identifiers = {
'grid': ['a','b','c'], 'grid': ['a','b','c'],
'size': ['x','y','z'],
'origin': ['x','y','z'],
} }
mappings = { mappings = {
'grid': lambda x: int(x), 'grid': lambda x: int(x),
'grains': 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 = """ 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. Generate geometry description and material configuration by standard Voronoi tessellation of given seeds file.
""" + string.replace('$Id$','\n','\\n') """ + string.replace(scriptID,'\n','\\n')
) )
parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \ parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \
@ -103,25 +115,40 @@ else:
#--- loop over input files ------------------------------------------------------------------------ #--- loop over input files ------------------------------------------------------------------------
for file in files: for file in files:
if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n') 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 = damask.ASCIItable(file['input'],file['output'])
theTable.head_read() theTable.head_read()
theData = theTable.data_asArray(['x','y','z','phi1','Phi','phi2'])
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)
else:
grain = 1+numpy.arange(len(eulers))
grainIDs = grain
#--- interpret header ---------------------------------------------------------------------------- #--- interpret header ----------------------------------------------------------------------------
info = { info = {
'grid': numpy.zeros(3,'i'), 'grid': numpy.zeros(3,'i'),
'size': numpy.array(options.size), 'size': numpy.array(options.size),
'origin': numpy.zeros(3,'d'), 'origin': numpy.zeros(3,'d'),
'grains': 0, 'microstructures': 0,
'homogenization': options.homogenization, 'homogenization': options.homogenization,
} }
newInfo = {
'microstructures': 0,
}
extra_header = []
for header in theTable.info: for header in theTable.info:
headitems = map(str.lower,header.split()) headitems = map(str.lower,header.split())
if len(headitems) == 0: continue # skip blank lines if len(headitems) == 0: continue
if headitems[0] == 'resolution': headitems[0] = 'grid' for synonym,alternatives in synonyms.iteritems():
if headitems[0] in alternatives: headitems[0] = synonym
if headitems[0] in mappings.keys(): if headitems[0] in mappings.keys():
if headitems[0] in identifiers.keys(): if headitems[0] in identifiers.keys():
for i in xrange(len(identifiers[headitems[0]])): for i in xrange(len(identifiers[headitems[0]])):
@ -129,10 +156,12 @@ for file in files:
mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1]) mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
else: else:
info[headitems[0]] = mappings[headitems[0]](headitems[1]) info[headitems[0]] = mappings[headitems[0]](headitems[1])
else:
extra_header.append(header)
if info['grains'] != len(theData): if info['microstructures'] != len(grainIDs):
file['croak'].write('grain data not matching grain count...\n') file['croak'].write('grain data not matching grain count...\n')
info['grains'] = min(info['grains'],len(theData)) info['microstructures'] = min(info['microstructures'],len(grainIDs))
if 0 not in options.grid: # user-specified grid if 0 not in options.grid: # user-specified grid
info['grid'] = numpy.array(options.grid) info['grid'] = numpy.array(options.grid)
@ -142,7 +171,7 @@ for file in files:
info['size'][i] = float(info['grid'][i])/max(info['grid']) 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('rescaling size %s...\n'%{0:'x',1:'y',2:'z'}[i])
file['croak'].write('grains to map: %i\n'%info['grains'] + \ file['croak'].write('grains to map: %i\n'%info['microstructures'] + \
'grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \ 'grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \ 'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \ 'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
@ -154,26 +183,30 @@ for file in files:
if numpy.any(info['size'] <= 0.0): if numpy.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n') file['croak'].write('invalid size x y z.\n')
continue continue
if info['grains'] == 0: if info['microstructures'] == 0:
file['croak'].write('no grain info found.\n') file['croak'].write('no grain info found.\n')
continue continue
#--- prepare data --------------------------------------------------------------------------------- #--- prepare data ---------------------------------------------------------------------------------
coords = (theData[:,:3]*info['size']).transpose() coords = (coords*info['size']).transpose()
eulers = (theData[:,3:6]).transpose() eulers = eulers.transpose()
#--- switch according to task --------------------------------------------------------------------- #--- switch according to task ---------------------------------------------------------------------
if options.config: # write config file if options.config: # write config file
formatwidth = 1+int(math.log10(info['microstructures']))
file['output'].write('<microstructure>\n') file['output'].write('<microstructure>\n')
for i in xrange(info['grains']): for i in grainIDs:
file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \ file['output'].write('\n[Grain%s]\n'%(str(i).zfill(formatwidth)) + \
'crystallite %i\n'%options.crystallite + \ 'crystallite %i\n'%options.crystallite + \
'(constituent)\tphase %i\ttexture %s\tfraction 1.0\n'%(options.phase,str(i+1).rjust(formatwidth))) '(constituent)\tphase %i\ttexture %s\tfraction 1.0\n'%(options.phase,str(i).rjust(formatwidth)))
file['output'].write('\n<texture>\n') file['output'].write('\n<texture>\n')
for i in xrange(info['grains']): for i in grainIDs:
file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \ eulerID = numpy.nonzero(grain == i)[0][0] # find first occurrence of this grain id
'(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0\n'%(eulers[0,i],eulers[1,i],eulers[2,i])) 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 else: # write geometry file
x = (numpy.arange(info['grid'][0])+0.5)*info['size'][0]/info['grid'][0] x = (numpy.arange(info['grid'][0])+0.5)*info['size'][0]/info['grid'][0]
@ -181,32 +214,37 @@ for file in files:
z = (numpy.arange(info['grid'][2])+0.5)*info['size'][2]/info['grid'][2] z = (numpy.arange(info['grid'][2])+0.5)*info['size'][2]/info['grid'][2]
undeformed = numpy.vstack(map(numpy.ravel, meshgrid2(x, y, z))) undeformed = numpy.vstack(map(numpy.ravel, meshgrid2(x, y, z)))
file['croak'].write('tesselating...\n') file['croak'].write('tessellating...\n')
indices = damask.core.math.periodicNearestNeighbor(\ indices = damask.core.math.periodicNearestNeighbor(\
info['size'],\ info['size'],\
numpy.eye(3),\ numpy.eye(3),\
undeformed,coords)//3**3 + 1 # floor division to kill periodic images undeformed,coords)//3**3 + 1 # floor division to kill periodic images
missing = 0 indices = grain[indices-1]
for i in xrange(info['grains']):
if i+1 not in indices: missing += 1 newInfo['microstructures'] = info['microstructures']
file['croak'].write({True:'all',False:'only'}[missing == 0] + ' %i grains mapped.\n'%(info['grains']-missing)) 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 --------------------------------------------------------------------------------- #--- write header ---------------------------------------------------------------------------------
theTable.labels_clear() theTable.labels_clear()
theTable.info_clear() theTable.info_clear()
theTable.info_append([ theTable.info_append(extra_header+[
"$Id$", scriptID,
"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],), "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],), "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],), "origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
"homogenization\t%i"%info['homogenization'], "homogenization\t%i"%info['homogenization'],
"microstructures\t%i"%(info['grains']-missing), "microstructures\t%i"%(newInfo['microstructures']),
]) ])
theTable.head_write() theTable.head_write()
theTable.output_flush() theTable.output_flush()
# --- write microstructure information ------------------------------------------------------------ # --- write microstructure information ------------------------------------------------------------
formatwidth = 1+int(math.log10(info['grains'])) formatwidth = 1+int(math.log10(newInfo['microstructures']))
theTable.data = indices.reshape(info['grid'][1]*info['grid'][2],info['grid'][0]) theTable.data = indices.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
theTable.data_writeArray('%%%ii'%(formatwidth)) theTable.data_writeArray('%%%ii'%(formatwidth))