DAMASK_EICMD/processing/pre/geom_fromAng.py

#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-

import os,sys,math,string,numpy
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')
)


parser.add_option('--column',              dest='column', type='int', \
                  help='data column to discriminate phase 1 from 2 [%default]')
parser.add_option('-t','--threshold',      dest='threshold', type='float', \
                  help='threshold value to discriminate phase 1 from 2 [%default]')
parser.add_option('--homogenization',      dest='homogenization', type='int', \
                  help='homogenization index to be used [%default]')
parser.add_option('--phase',               dest='phase', type='int', nargs = 2, \
                  help='two phase indices to be used %default')
parser.add_option('--crystallite',         dest='crystallite', type='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('-a', '--axes',         dest='axes', type='string', nargs = 3, \
                  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(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':   numpy.ones (3,'i'),
          'size':   numpy.zeros(3,'d'),
          'origin': numpy.zeros(3,'d'),
          'microstructures': 0,
          'homogenization':  options.homogenization
         }

  microstructure = ['<microstructure>']
  texture        = ['<texture>']
  step           = [0,0]

  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]); formatwidth = 1+int(math.log10(info['grid'][0]*info['grid'][1]))
        if words[1] == 'NROWS:':         
          info['grid'][1] = int(words[2]); formatwidth = 1+int(math.log10(info['grid'][0]*info['grid'][1]))
    else:                                                                                           # finished with comments block
      point += 1
      me = str(point).zfill(formatwidth)
      microstructure += ['[Grain%s]\n'%me + \
                         'crystallite\t%i\n'%options.crystallite + \
                         '(constituent)\tphase %i\ttexture %s\tfraction 1.0\n'%(options.phase[{True:0,False:1}[float(words[options.column-1])<options.threshold]],me)
                        ]
      texture +=        ['[Grain%s]\n'%me + \
                         '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(map(lambda x: float(x)*180.0/math.pi, words[:3]))
                        ]

  info['microstructures'] = info['grid'][0]*info['grid'][1]
  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 numpy.any(info['grid'] < 1):
    file['croak'].write('invalid grid a b c.\n')
    sys.exit()
  if numpy.any(info['size'] <= 0.0):
    file['croak'].write('invalid size x y z.\n')
    sys.exit()
  if info['grid'].prod() != len(microstructure) -1:
    file['croak'].write('found %s microstructures. Header info in ang file might be wrong.\n'%point)
    sys.exit()

#--- write data -----------------------------------------------------------------------------------
  if options.config:
    file['output'].write('\n'.join(microstructure) + \
                         '\n'.join(texture))
  else:
    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'])
    file['output'].write('%i\theader\n'%(len(header))+''.join(header))
    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] + \
                                  {True: '_material.config',
                                   False:'.geom'}[options.config])