DAMASK_EICMD/processing/pre/seeds_check.py

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

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

scriptID   = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
     
#--------------------------------------------------------------------------------------------------
#                                MAIN
#--------------------------------------------------------------------------------------------------
identifiers = {
        'grid':   ['a','b','c'],
        'size':   ['x','y','z'],
        'origin': ['x','y','z'],
          }
mappings = {
        'grid':            lambda x: int(x),
        'size':            lambda x: float(x),
        'origin':          lambda x: float(x),
        'microstructures': lambda x: int(x),
          }


parser = OptionParser(option_class=damask.extendableOption, usage='%prog [seedsfile[s]]', description = """
Produce VTK point mesh from seeds file

""", version = scriptID)

parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, metavar='float float float',\
                  help='x,y,z size of hexahedral box [1.0 along largest grid point number]')

parser.set_defaults(size = [0.0,0.0,0.0])

(options, filenames) = parser.parse_args()

# --- loop over input files -------------------------------------------------------------------------
if filenames == []:
  filenames = ['STDIN']

for name in filenames:
  if name == 'STDIN':
    file = {'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}
    file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
  else:
    if not os.path.exists(name): continue
    file = {'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr}
    file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')

  table = damask.ASCIItable(file['input'],file['output'],buffered = False)
  table.head_read()


  if np.all(table.label_index(['1_coords','2_coords','3_coords']) != -1):
    labels = ['1_coords','2_coords','3_coords']
  elif np.all(table.label_index(['x','y','z']) != -1):
    labels = ['x','y','z']
  else:
    file['croak'].write('no coordinate data (1/2/3_coords | x/y/z) found ...')
    continue

  hasGrains = table.label_index('microstructure') != -1
  labels += ['microstructure'] if hasGrains else []

  table.data_readArray(labels)                                                                      # read ASCIItable columns
  coords = table.data[:,:3]                                                                         # assign coordinates
  grain = table.data[:,3].astype('i') if hasGrains else 1+np.arange(len(coords),dtype='i')          # assign grains
  grainIDs = np.unique(grain).astype('i')                                                           # find all grainIDs present
  
#--- interpret header ----------------------------------------------------------------------------
  info = {
          'grid':    np.zeros(3,'i'),
          'size':    np.array(options.size),
          'origin':  np.zeros(3,'d'),
          'microstructures':  0,
         }

  for header in table.info:
    headitems = map(str.lower,header.split())
    if len(headitems) == 0: continue
    if headitems[0] in mappings.keys():
      if headitems[0] in identifiers.keys():
        for i in xrange(len(identifiers[headitems[0]])):
          info[headitems[0]][i] = \
            mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
      else:
        info[headitems[0]] = mappings[headitems[0]](headitems[1])

  if info['microstructures'] != len(grainIDs):
    file['croak'].write('grain data not matching grain count (%i)...\n'%(len(grainIDs)))
    info['microstructures'] = len(grainIDs)
  if np.any(info['grid'] < 1):
    file['croak'].write('invalid grid a b c.\n')
    continue

  for i in xrange(3):
    if info['size'][i] <= 0.0:                                                                      # any invalid size?
      info['size'][i] = float(info['grid'][i])/max(info['grid'])
      file['croak'].write('rescaling size %s...\n'%{0:'x',1:'y',2:'z'}[i])

#--- generate grid --------------------------------------------------------------------------------
  grid = vtk.vtkUnstructuredGrid()
  pts = vtk.vtkPoints()

#--- process microstructure information --------------------------------------------------------------
  IDs = vtk.vtkIntArray()
  IDs.SetNumberOfComponents(1)
  IDs.SetName("GrainID")

  for i,item in enumerate(coords):
    pid = pts.InsertNextPoint(item[0:3])
    pointIds = vtk.vtkIdList()
    pointIds.InsertId(0, pid)
    grid.InsertNextCell(1, pointIds)
    IDs.InsertNextValue(grain[i])

  grid.SetPoints(pts)
  grid.GetCellData().AddArray(IDs)

#--- write data -----------------------------------------------------------------------------------
  if file['name'] == 'STDIN':
    writer = vtk.vtkUnstructuredGridWriter()
    writer.WriteToOutputStringOn()
    writer.SetFileTypeToASCII()
    writer.SetHeader('# powered by '+scriptID)
    if vtk.VTK_MAJOR_VERSION <= 5:
      writer.SetInput(grid)
    else:
      writer.SetInputData(grid)
    writer.Write()
    sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
  else:
    table.close(dismiss=True)
    (head,tail) = os.path.split(file['name'])
    writer = vtk.vtkXMLUnstructuredGridWriter()
    writer.SetDataModeToBinary()
    writer.SetCompressorTypeToZLib()
    writer.SetFileName(os.path.join(head,'seeds_'+os.path.splitext(tail)[0]
                                                   +'.'+writer.GetDefaultFileExtension()))
    if vtk.VTK_MAJOR_VERSION <= 5:
      writer.SetInput(grid)
    else:
      writer.SetInputData(grid)
    writer.Write()