#!/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): 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('--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) (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: 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(np.asarray(table.labels_index(['1_coords','2_coords','3_coords'])) != -1): labels += ['1_coords','2_coords','3_coords'] coords = ['1_coords','2_coords','3_coords'] elif np.all(np.asarray(table.labels_index(['x','y','z'])) != -1): labels += ['x','y','z'] coords = ['x','y','z'] else: file['croak'].write('no coordinate data (1_coords/x) found ...') continue hasEulers = np.all(np.asarray(table.labels_index(['phi1','Phi','phi2'])) != -1) if hasEulers: labels += ['phi1','Phi','phi2'] hasGrains = table.labels_index('microstructure') != -1 if hasGrains: labels += ['microstructure'] hasWeight = table.labels_index('weight') != -1 if hasWeight: labels += ['weight'] table.data_readArray(labels) coords = table.data[:,table.labels_index(coords)] eulers = table.data[:,table.labels_index(['phi1','Phi','phi2'])] if hasEulers else np.zeros(3*len(coords)) grain = table.data[:,table.labels.index('microstructure')] if hasGrains else 1+np.arange(len(coords)) weights = table.data[:,table.labels.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 np.random.shuffle(phase) formatwidth = 1+int(math.log10(info['microstructures'])) file['output'].write('#' + scriptID + ' ' + ' '.join(sys.argv[1:])) file['output'].write('\n\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\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) 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 --------------------------------------------------------------------------------- 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'))