DAMASK_EICMD/processing/pre/geom_toTable.py

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

import os,sys
import numpy as np
from optparse import OptionParser
import damask

scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID   = ' '.join([scriptName,damask.version])


#--------------------------------------------------------------------------------------------------
#                                MAIN
#--------------------------------------------------------------------------------------------------

parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile[s]]', description = """
Translate geom description into ASCIItable containing 1/2/3_pos and microstructure.

""", version = scriptID)

parser.add_option('-p','--position',
                  dest = 'position',
                  type = 'string', metavar = 'string',
                  help = 'column label for position [%default]')
parser.add_option('-m','--microstructure',
                  dest = 'microstructure',
                  type = 'string', metavar = 'string',
                  help = 'column label for microstructure index [%default]')

parser.set_defaults(position = 'pos',
                    microstructure = 'microstructure',
                   )

(options, filenames) = parser.parse_args()

# --- loop over input files -------------------------------------------------------------------------

if filenames == []: filenames = [None]

for name in filenames:
  try:
    table = damask.ASCIItable(name = name,
                              outname = os.path.splitext(name)[0]+'.txt' if name else name,
                              buffered = False, labeled = False)
  except: continue
  damask.util.report(scriptName,name)

# --- interpret header ----------------------------------------------------------------------------

  table.head_read()
  info,extra_header = table.head_getGeom()
  
  damask.util.croak(['grid     a b c:  %s'%(' x '.join(map(str,info['grid']))),
                     'size     x y z:  %s'%(' x '.join(map(str,info['size']))),
                     'origin   x y z:  %s'%(' : '.join(map(str,info['origin']))),
                     'homogenization:  %i'%info['homogenization'],
                     'microstructures: %i'%info['microstructures'],
                    ])

  errors = []
  if np.any(info['grid'] < 1):    errors.append('invalid grid a b c.')
  if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
  if errors != []:
    damask.util.croak(errors)
    table.close(dismiss = True)
    continue

# --- read data ------------------------------------------------------------------------------------

  microstructure = table.microstructure_read(info['grid'])                                          # read microstructure

# ------------------------------------------ assemble header ---------------------------------------

  table.info_clear()
  table.info_append(extra_header + [scriptID + '\t' + ' '.join(sys.argv[1:])])
  table.labels_clear()
  table.labels_append(['{}_{}'.format(1+i,options.position) for i in xrange(3)]+[options.microstructure])
  table.head_write()
  table.output_flush()

#--- generate grid --------------------------------------------------------------------------------

  x = (0.5 + np.arange(info['grid'][0],dtype=float))/info['grid'][0]*info['size'][0]+info['origin'][0]
  y = (0.5 + np.arange(info['grid'][1],dtype=float))/info['grid'][1]*info['size'][1]+info['origin'][1]
  z = (0.5 + np.arange(info['grid'][2],dtype=float))/info['grid'][2]*info['size'][2]+info['origin'][2]

  xx = np.tile(          x,                info['grid'][1]* info['grid'][2])
  yy = np.tile(np.repeat(y,info['grid'][0]                ),info['grid'][2])
  zz =         np.repeat(z,info['grid'][0]*info['grid'][1])

  table.data = np.squeeze(np.dstack((xx,yy,zz,microstructure)))
  table.data_writeArray()

# ------------------------------------------ finalize output ---------------------------------------

  table.close()