From fafa69b846c097e0fc7930b6c898ada8b6532103 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Wed, 10 Jul 2013 09:12:00 +0000 Subject: [PATCH] added possibility to have microstructure indices for seed points. Hence, multiple seed points can belong to the same final grain. --- .../pre/geom_fromVoronoiTessellation.py | 98 +++++++++++++------ 1 file changed, 68 insertions(+), 30 deletions(-) diff --git a/processing/pre/geom_fromVoronoiTessellation.py b/processing/pre/geom_fromVoronoiTessellation.py index 8e503c77b..27ec065af 100755 --- a/processing/pre/geom_fromVoronoiTessellation.py +++ b/processing/pre/geom_fromVoronoiTessellation.py @@ -5,6 +5,9 @@ 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): #-------------------------------------------------------------------------------------------------- @@ -48,17 +51,26 @@ def meshgrid2(*arrs): #-------------------------------------------------------------------------------------------------- # MAIN #-------------------------------------------------------------------------------------------------- +synonyms = { + 'grid': ['resolution'], + 'size': ['dimension'], + } identifiers = { - 'grid': ['a','b','c'], + 'grid': ['a','b','c'], + 'size': ['x','y','z'], + 'origin': ['x','y','z'], } mappings = { - 'grid': lambda x: int(x), - 'grains': lambda x: int(x), + '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('$Id$','\n','\\n') +""" + string.replace(scriptID,'\n','\\n') ) parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \ @@ -103,25 +115,40 @@ else: #--- loop over input 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.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 ---------------------------------------------------------------------------- info = { 'grid': numpy.zeros(3,'i'), 'size': numpy.array(options.size), 'origin': numpy.zeros(3,'d'), - 'grains': 0, + '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 # skip blank lines - if headitems[0] == 'resolution': headitems[0] = 'grid' + 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]])): @@ -129,10 +156,12 @@ for file in files: 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['grains'] != len(theData): + if info['microstructures'] != len(grainIDs): 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 info['grid'] = numpy.array(options.grid) @@ -142,7 +171,7 @@ for file in files: 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['grains'] + \ + 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']))) + \ @@ -154,26 +183,30 @@ for file in files: if numpy.any(info['size'] <= 0.0): file['croak'].write('invalid size x y z.\n') continue - if info['grains'] == 0: + if info['microstructures'] == 0: file['croak'].write('no grain info found.\n') continue #--- prepare data --------------------------------------------------------------------------------- - coords = (theData[:,:3]*info['size']).transpose() - eulers = (theData[:,3:6]).transpose() + 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('\n') - for i in xrange(info['grains']): - file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \ + 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+1).rjust(formatwidth))) + '(constituent)\tphase %i\ttexture %s\tfraction 1.0\n'%(options.phase,str(i).rjust(formatwidth))) file['output'].write('\n\n') - for i in xrange(info['grains']): - file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \ - '(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0\n'%(eulers[0,i],eulers[1,i],eulers[2,i])) + 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] @@ -181,32 +214,37 @@ for file in files: 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('tesselating...\n') + 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 - missing = 0 - for i in xrange(info['grains']): - if i+1 not in indices: missing += 1 - file['croak'].write({True:'all',False:'only'}[missing == 0] + ' %i grains mapped.\n'%(info['grains']-missing)) + 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([ - "$Id$", + 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"%(info['grains']-missing), + "microstructures\t%i"%(newInfo['microstructures']), ]) theTable.head_write() theTable.output_flush() # --- 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_writeArray('%%%ii'%(formatwidth))