DAMASK_EICMD/processing/pre/geom_fromVPSC.py

177 lines
9.2 KiB
Python
Raw Normal View History

#!/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')
2014-11-18 21:01:39 +05:30
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 <microstructure> configuration [%default]')
parser.add_option('--phase', dest='phase', type='int', nargs = 2, metavar = 'int int',
help='phase indices for <microstructure> configuration %default')
parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int',
help='crystallite index for <microstructure> 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()
2013-05-14 23:21:53 +05:30
#--- 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:
2014-11-18 21:01:39 +05:30
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
}
phase = []
eulerangles = []
point = 0
for line in file['input']:
if line.strip():
words = line.split()
currPos = map(float,words[3:6])
for i in xrange(3):
if currPos[i] > info['grid'][i]:
info['size'][i] = currPos[i]
info['grid'][i]+=1
eulerangles.append(map(float,words[:3]))
phase.append(options.phase[int(float(words[options.column-1]) > options.threshold)])
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<texture>']
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 =['<microstructure>']
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'][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'))