diff --git a/processing/pre/geom_fromAng.py b/processing/pre/geom_fromAng.py index e69de29bb..0261f94f1 100755 --- a/processing/pre/geom_fromAng.py +++ b/processing/pre/geom_fromAng.py @@ -0,0 +1,189 @@ +#!/usr/bin/env python +# -*- coding: UTF-8 no BOM -*- + +import os,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] + +#-------------------------------------------------------------------------------------------------- +# MAIN +#-------------------------------------------------------------------------------------------------- +parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """ +Generate geometry description and material configuration from input files used by R.A. Lebensohn. + +""", version = scriptID) + +parser.add_option('--column', dest='column', type='int', metavar = 'int', + help='data column to discriminate between both phases [%default]') +parser.add_option('-t','--threshold', dest='threshold', type='float', metavar = 'float', + help='threshold value for phase discrimination [%default]') +parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', + help='homogenization index for configuration [%default]') +parser.add_option('--phase', dest='phase', type='int', nargs = 2, metavar = 'int int', + help='phase indices for configuration %default') +parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int', + help='crystallite index for configuration [%default]') +parser.add_option('-c', '--configuration', dest='config', action='store_true', + help='output material configuration [%default]') +parser.add_option('--compress', dest='compress', action='store_true', + help='lump identical microstructure and texture information [%default]') +parser.add_option('-p', '--precision', dest='precision', choices=['0','1','2','3'], metavar = 'int', + help = 'euler angles decimal places for output format and compressing (0,1,2,3) [2]') + +parser.set_defaults(column = 7) +parser.set_defaults(threshold = 1.0) +parser.set_defaults(homogenization = 1) +parser.set_defaults(phase = [1,2]) +parser.set_defaults(crystallite = 1) +parser.set_defaults(config = False) +parser.set_defaults(compress = False) +parser.set_defaults(precision = '2') + +(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') + + info = { + 'grid': np.zeros(3,'i'), + 'size': np.zeros(3,'d'), + 'origin': np.zeros(3,'d'), + 'microstructures': 0, + 'homogenization': options.homogenization + } + + coords = [{},{},{}] + pos = {'min':[ float("inf"), float("inf"), float("inf")], + 'max':[-float("inf"),-float("inf"),-float("inf")]} + + phase = [] + eulerangles = [] +# --------------- read data ----------------------------------------------------------------------- + for line in file['input']: + if line.strip(): + words = line.split() + currPos = words[3:6] + for i in xrange(3): + coords[i][currPos[i]] = True + currPos = map(float,currPos) + for i in xrange(3): + pos['min'][i] = min(pos['min'][i],currPos[i]) + pos['max'][i] = max(pos['max'][i],currPos[i]) + eulerangles.append(map(math.degrees,map(float,words[:3]))) + phase.append(options.phase[int(float(words[options.column-1]) > options.threshold)]) + +# --------------- determine size and grid --------------------------------------------------------- + info['grid'] = np.array(map(len,coords),'i') + info['size'] = info['grid']/np.maximum(np.ones(3,'d'),info['grid']-1.0)* \ + np.array([pos['max'][0]-pos['min'][0], + pos['max'][1]-pos['min'][1], + pos['max'][2]-pos['min'][2]],'d') + eulerangles = np.array(eulerangles,dtype='f').reshape(info['grid'].prod(),3) + phase = np.array(phase,dtype='i').reshape(info['grid'].prod()) + + limits = [360,180,360] + if any([np.any(eulerangles[:,i]>=limits[i]) for i in [0,1,2]]): + file['croak'].write('Error: euler angles out of bound. Ang file might contain unidexed poins.\n') + for i,angle in enumerate(['phi1','PHI','phi2']): + for n in np.nditer(np.where(eulerangles[:,i]>=limits[i]),['zerosize_ok']): + file['croak'].write('%s in line %i (%4.2f %4.2f %4.2f)\n' + %(angle,n,eulerangles[n,0],eulerangles[n,1],eulerangles[n,2])) + continue + eulerangles=np.around(eulerangles,int(options.precision)) # round to desired precision + for i,angle in enumerate(['phi1','PHI','phi2']): + eulerangles[:,i]%=limits[i] # ensure, that rounded euler angles are not out of bounds (modulo by limits) + + if options.compress: + formatString='{0:0>'+str(int(options.precision)+3)+'}' + euleranglesRadInt = (eulerangles*10**int(options.precision)).astype('int') # scale by desired precision and convert to int + eulerKeys = np.array([int(''.join(map(formatString.format,euleranglesRadInt[i,:]))) \ + for i in xrange(info['grid'].prod())]) # create unique integer key from three euler angles by concatenating the string representation with leading zeros and store as integer + devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)# search unique euler angle keys. Texture IDs are the indices of the first occurence, the inverse is used to construct the microstructure + msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in xrange(info['grid'].prod())],'i8') # create a microstructure (texture/phase pair) for each point using unique texture IDs. Use longInt (64bit, i8) because the keys might be long + devNull,msUnique,matPoints = np.unique(msFull.view('c16'),True,True) + matPoints+=1 + microstructure = np.array([msFull[i] for i in msUnique]) # pick only unique microstructures + else: + texture = np.arange(info['grid'].prod()) + microstructure = np.hstack( zip(texture,phase) ).reshape(info['grid'].prod(),2) # create texture/phase pairs + formatOut = 1+int(math.log10(len(texture))) + textureOut =['\n\n'] + + eulerFormatOut='%%%i.%if'%(int(options.precision)+4,int(options.precision)) + outStringAngles='(gauss) phi1 '+eulerFormatOut+' Phi '+eulerFormatOut+' phi2 '+eulerFormatOut+' scatter 0.0 fraction 1.0\n' + for i in xrange(len(texture)): + textureOut += ['[Texture%s]\n'%str(i+1).zfill(formatOut) + + outStringAngles%tuple(eulerangles[texture[i],...]) + ] + formatOut = 1+int(math.log10(len(microstructure))) + microstructureOut =[''] + for i in xrange(len(microstructure)): + microstructureOut += ['[Grain%s]\n'%str(i+1).zfill(formatOut) + + 'crystallite\t%i\n'%options.crystallite + + '(constituent)\tphase %i\ttexture %i\tfraction 1.0\n'%(microstructure[i,1],microstructure[i,0]+1) + ] + + info['microstructures'] = len(microstructure) + +#--- report --------------------------------------------------------------------------------------- + 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\n'%info['microstructures']) + + 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 + + +#--- write data ----------------------------------------------------------------------------------- + if options.config: + file['output'].write('\n'.join(microstructureOut+ textureOut) + '\n') + else: + header = [' '.join([scriptID] + 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],), + "microstructures\t%i"%info['microstructures'], + "homogenization\t%i"%info['homogenization'], + ] + file['output'].write('\n'.join(['%i\theader'%(len(header))] + header) + '\n') + if options.compress: + matPoints = matPoints.reshape([info['grid'][1]*info['grid'][2],info['grid'][0]]) + np.savetxt(file['output'],matPoints,fmt='%0'+str(1+int(math.log10(np.amax(matPoints))))+'d') + else: + file['output'].write("1 to %i\n"%(info['microstructures'])) + +#--- output finalization -------------------------------------------------------------------------- + if file['name'] != 'STDIN': + file['output'].close() + os.rename(file['name']+'_tmp', + os.path.splitext(file['name'])[0] +'%s'%('_material.config' if options.config else '.geom')) + diff --git a/processing/pre/geom_fromVPSC.py b/processing/pre/geom_fromVPSC.py index e69de29bb..0261f94f1 100755 --- a/processing/pre/geom_fromVPSC.py +++ b/processing/pre/geom_fromVPSC.py @@ -0,0 +1,189 @@ +#!/usr/bin/env python +# -*- coding: UTF-8 no BOM -*- + +import os,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] + +#-------------------------------------------------------------------------------------------------- +# MAIN +#-------------------------------------------------------------------------------------------------- +parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """ +Generate geometry description and material configuration from input files used by R.A. Lebensohn. + +""", version = scriptID) + +parser.add_option('--column', dest='column', type='int', metavar = 'int', + help='data column to discriminate between both phases [%default]') +parser.add_option('-t','--threshold', dest='threshold', type='float', metavar = 'float', + help='threshold value for phase discrimination [%default]') +parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', + help='homogenization index for configuration [%default]') +parser.add_option('--phase', dest='phase', type='int', nargs = 2, metavar = 'int int', + help='phase indices for configuration %default') +parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int', + help='crystallite index for configuration [%default]') +parser.add_option('-c', '--configuration', dest='config', action='store_true', + help='output material configuration [%default]') +parser.add_option('--compress', dest='compress', action='store_true', + help='lump identical microstructure and texture information [%default]') +parser.add_option('-p', '--precision', dest='precision', choices=['0','1','2','3'], metavar = 'int', + help = 'euler angles decimal places for output format and compressing (0,1,2,3) [2]') + +parser.set_defaults(column = 7) +parser.set_defaults(threshold = 1.0) +parser.set_defaults(homogenization = 1) +parser.set_defaults(phase = [1,2]) +parser.set_defaults(crystallite = 1) +parser.set_defaults(config = False) +parser.set_defaults(compress = False) +parser.set_defaults(precision = '2') + +(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') + + info = { + 'grid': np.zeros(3,'i'), + 'size': np.zeros(3,'d'), + 'origin': np.zeros(3,'d'), + 'microstructures': 0, + 'homogenization': options.homogenization + } + + coords = [{},{},{}] + pos = {'min':[ float("inf"), float("inf"), float("inf")], + 'max':[-float("inf"),-float("inf"),-float("inf")]} + + phase = [] + eulerangles = [] +# --------------- read data ----------------------------------------------------------------------- + for line in file['input']: + if line.strip(): + words = line.split() + currPos = words[3:6] + for i in xrange(3): + coords[i][currPos[i]] = True + currPos = map(float,currPos) + for i in xrange(3): + pos['min'][i] = min(pos['min'][i],currPos[i]) + pos['max'][i] = max(pos['max'][i],currPos[i]) + eulerangles.append(map(math.degrees,map(float,words[:3]))) + phase.append(options.phase[int(float(words[options.column-1]) > options.threshold)]) + +# --------------- determine size and grid --------------------------------------------------------- + info['grid'] = np.array(map(len,coords),'i') + info['size'] = info['grid']/np.maximum(np.ones(3,'d'),info['grid']-1.0)* \ + np.array([pos['max'][0]-pos['min'][0], + pos['max'][1]-pos['min'][1], + pos['max'][2]-pos['min'][2]],'d') + eulerangles = np.array(eulerangles,dtype='f').reshape(info['grid'].prod(),3) + phase = np.array(phase,dtype='i').reshape(info['grid'].prod()) + + limits = [360,180,360] + if any([np.any(eulerangles[:,i]>=limits[i]) for i in [0,1,2]]): + file['croak'].write('Error: euler angles out of bound. Ang file might contain unidexed poins.\n') + for i,angle in enumerate(['phi1','PHI','phi2']): + for n in np.nditer(np.where(eulerangles[:,i]>=limits[i]),['zerosize_ok']): + file['croak'].write('%s in line %i (%4.2f %4.2f %4.2f)\n' + %(angle,n,eulerangles[n,0],eulerangles[n,1],eulerangles[n,2])) + continue + eulerangles=np.around(eulerangles,int(options.precision)) # round to desired precision + for i,angle in enumerate(['phi1','PHI','phi2']): + eulerangles[:,i]%=limits[i] # ensure, that rounded euler angles are not out of bounds (modulo by limits) + + if options.compress: + formatString='{0:0>'+str(int(options.precision)+3)+'}' + euleranglesRadInt = (eulerangles*10**int(options.precision)).astype('int') # scale by desired precision and convert to int + eulerKeys = np.array([int(''.join(map(formatString.format,euleranglesRadInt[i,:]))) \ + for i in xrange(info['grid'].prod())]) # create unique integer key from three euler angles by concatenating the string representation with leading zeros and store as integer + devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)# search unique euler angle keys. Texture IDs are the indices of the first occurence, the inverse is used to construct the microstructure + msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in xrange(info['grid'].prod())],'i8') # create a microstructure (texture/phase pair) for each point using unique texture IDs. Use longInt (64bit, i8) because the keys might be long + devNull,msUnique,matPoints = np.unique(msFull.view('c16'),True,True) + matPoints+=1 + microstructure = np.array([msFull[i] for i in msUnique]) # pick only unique microstructures + else: + texture = np.arange(info['grid'].prod()) + microstructure = np.hstack( zip(texture,phase) ).reshape(info['grid'].prod(),2) # create texture/phase pairs + formatOut = 1+int(math.log10(len(texture))) + textureOut =['\n\n'] + + eulerFormatOut='%%%i.%if'%(int(options.precision)+4,int(options.precision)) + outStringAngles='(gauss) phi1 '+eulerFormatOut+' Phi '+eulerFormatOut+' phi2 '+eulerFormatOut+' scatter 0.0 fraction 1.0\n' + for i in xrange(len(texture)): + textureOut += ['[Texture%s]\n'%str(i+1).zfill(formatOut) + + outStringAngles%tuple(eulerangles[texture[i],...]) + ] + formatOut = 1+int(math.log10(len(microstructure))) + microstructureOut =[''] + for i in xrange(len(microstructure)): + microstructureOut += ['[Grain%s]\n'%str(i+1).zfill(formatOut) + + 'crystallite\t%i\n'%options.crystallite + + '(constituent)\tphase %i\ttexture %i\tfraction 1.0\n'%(microstructure[i,1],microstructure[i,0]+1) + ] + + info['microstructures'] = len(microstructure) + +#--- report --------------------------------------------------------------------------------------- + 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\n'%info['microstructures']) + + 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 + + +#--- write data ----------------------------------------------------------------------------------- + if options.config: + file['output'].write('\n'.join(microstructureOut+ textureOut) + '\n') + else: + header = [' '.join([scriptID] + 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],), + "microstructures\t%i"%info['microstructures'], + "homogenization\t%i"%info['homogenization'], + ] + file['output'].write('\n'.join(['%i\theader'%(len(header))] + header) + '\n') + if options.compress: + matPoints = matPoints.reshape([info['grid'][1]*info['grid'][2],info['grid'][0]]) + np.savetxt(file['output'],matPoints,fmt='%0'+str(1+int(math.log10(np.amax(matPoints))))+'d') + else: + file['output'].write("1 to %i\n"%(info['microstructures'])) + +#--- output finalization -------------------------------------------------------------------------- + if file['name'] != 'STDIN': + file['output'].close() + os.rename(file['name']+'_tmp', + os.path.splitext(file['name'])[0] +'%s'%('_material.config' if options.config else '.geom')) + diff --git a/processing/pre/geom_fromVoronoiTessellation.py b/processing/pre/geom_fromVoronoiTessellation.py index a598e4e6d..5a02e4940 100755 --- a/processing/pre/geom_fromVoronoiTessellation.py +++ b/processing/pre/geom_fromVoronoiTessellation.py @@ -174,7 +174,7 @@ parser.set_defaults(grid = None, position = 'pos', weight = 'weight', microstructure = 'microstructure', - eulers = 'Euler', + eulers = 'eulerangles', homogenization = 1, crystallite = 1, phase = 1,