DAMASK_EICMD/processing/pre/geom_fromAng.py

215 lines
11 KiB
Python
Raw Normal View History

#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,math,string,numpy as np
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
scriptID = '$Id$'
scriptName = scriptID.split()[1]
#--------------------------------------------------------------------------------------------------
class extendableOption(Option):
#--------------------------------------------------------------------------------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
Generate geometry description and material configuration from EBSD data in given square-gridded 'ang' file.
Two phases can be discriminated based on threshold value in a given data column.
""" + string.replace(scriptID,'\n','\\n')
)
2014-01-20 20:11:56 +05:30
parser.add_option('--column', dest='column', type='int', metavar = 'int', \
help='data column to discriminate phase 1 from 2 [%default]')
2014-01-20 20:11:56 +05:30
parser.add_option('-t','--threshold', dest='threshold', type='float', metavar = 'float', \
help='threshold value to discriminate phase 1 from 2 [%default]')
2014-01-20 20:11:56 +05:30
parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', \
help='homogenization index to be used [%default]')
2014-01-20 20:11:56 +05:30
parser.add_option('--phase', dest='phase', type='int', nargs = 2, metavar = 'int int', \
help='two phase indices to be used %default')
2014-01-20 20:11:56 +05:30
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('--compress', dest='compress', action='store_true', \
help='search for matching mircrostructure and texture and lump them [%default]')
2014-01-20 20:11:56 +05:30
parser.add_option('-a', '--axes', dest='axes', type='string', nargs = 3, metavar = 'string string string', \
help='axes assignement of eulerangles x,y,z = %default')
parser.set_defaults(column = 11)
parser.set_defaults(threshold = 0.5)
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(axes = ['y','x','-z'])
(options,filenames) = parser.parse_args()
for i in options.axes:
if i.lower() not in ['x','+x','-x','y','+y','-y','z','+z','-z']:
file['croak'].write('invalid axes %s %s %s' %(options.axes[0],options.axes[1],options.axes[2]))
sys.exit()
#--- 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:
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')
info = {
'grid': np.ones (3,'i'),
'size': np.zeros(3,'d'),
'origin': np.zeros(3,'d'),
'microstructures': 0,
'homogenization': options.homogenization
}
step = [0,0]
2013-05-14 23:21:53 +05:30
point = 0
for line in file['input']:
words = line.split()
if words[0] == '#': # process initial comments block
if len(words) > 2:
if words[2].lower() == 'hexgrid':
file['croak'].write('The file has HexGrid format. Please first convert to SquareGrid...\n')
sys.exit()
if words[1] == 'XSTEP:': step[0] = float(words[2])
if words[1] == 'YSTEP:': step[1] = float(words[2])
if words[1] == 'NCOLS_ODD:':
info['grid'][0] = int(words[2])
eulerangles = np.zeros((info['grid'][0]*info['grid'][1],3),dtype='f')
phase = np.zeros(info['grid'][0]*info['grid'][1],dtype='i')
if words[1] == 'NROWS:':
info['grid'][1] = int(words[2])
eulerangles = np.zeros((info['grid'][0]*info['grid'][1],3),dtype='f')
phase = np.zeros(info['grid'][0]*info['grid'][1],dtype='i')
else: # finished with comments block
phase[point] = options.phase[{True:0,False:1}[float(words[options.column-1])<options.threshold]]
eulerangles[point,...] = map(lambda x: float(x)*180.0/math.pi, words[:3])
point += 1
if info['grid'].prod() != point:
file['croak'].write('Error: found %s microstructures. Header info in ang file might be wrong.\n'%point)
sys.exit()
if options.compress:
texture = []
microstructure = []
otherPoint=-1 # ensure to create first microstructure
matPoints = np.zeros(info['grid'][0]*info['grid'][1],dtype='i')
for myPoint in xrange(info['grid'][0]*info['grid'][1]):
myTexture=-1
for otherPoint in xrange(len(microstructure)):
otherEulers = eulerangles[texture[microstructure[otherPoint][0]]]
otherPhase = phase[[microstructure[otherPoint][1]]]
if all(eulerangles[myPoint]==otherEulers) and phase[myPoint] == otherPhase: # common microstructure
matPoints[myPoint] = otherPoint+1 # use other points microstructure
otherPoint =-4 # in no case, create new microstructure
break
elif all(eulerangles[myPoint]==otherEulers): # found common texture and store it
myTexture = microstructure[otherPoint][0]
if otherPoint == len(microstructure)-1 or otherPoint == -2: #
if myTexture == -1:
texture.append(myPoint)
myTexture = len(texture)-1
microstructure.append([myTexture,myPoint])
matPoints[myPoint] = len(microstructure) # use the new microstructure
else:
texture = [i for i in xrange(info['grid'][0]*info['grid'][1])]
microstructure = [[i+1,phase[i]] for i in xrange(info['grid'][0]*info['grid'][1])]
matPoints = np.arange(info['grid'][0]*info['grid'][1],dtype='i')
formatOut = 1+int(math.log10(len(texture)))
textureOut =['\n\n<texture>']
for i in xrange(len(texture)):
textureOut += ['[Texture%s]\n'%str(i+1).zfill(formatOut) + \
'axes %s %s %s\n'%(options.axes[0],options.axes[1],options.axes[2]) +\
'(gauss)\tphi1 %4.2f\tPhi %4.2f\tphi2 %4.2f\tscatter 0.0\tfraction 1.0\n'%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 %s\tfraction 1.0\n'%(phase[microstructure[i][1]],microstructure[i][0]+1)
]
info['microstructures'] = len(microstructure)
info['size'] = step[0]*info['grid'][0],step[1]*info['grid'][1],min(step)
#--- 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')
sys.exit()
if np.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
sys.exit()
#--- write data -----------------------------------------------------------------------------------
if options.config:
file['output'].write('\n'.join(microstructureOut) + \
'\n'.join(textureOut))
else:
2014-01-15 20:40:13 +05:30
header = [scriptID + ' ' + ' '.join(sys.argv[1:]) + '\n']
header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))
header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],))
header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],))
header.append("microstructures\t%i\n"%info['microstructures'])
header.append("homogenization\t%i\n"%info['homogenization'])
2013-05-14 23:21:53 +05:30
file['output'].write('%i\theader\n'%(len(header))+''.join(header))
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':
table.output_close()
os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] + \
{True: '_material.config',
False:'.geom'}[options.config])