DAMASK_EICMD/processing/pre/geom_fromMinimalSurface.py

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

import os,sys,string,math,numpy
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP

#--------------------------------------------------------------------------------------------------
class extendedOption(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
#--------------------------------------------------------------------------------------------------
minimal_surfaces = ['primitive','gyroid','diamond',]

surface = {
            'primitive': lambda x,y,z: math.cos(x)+math.cos(y)+math.cos(z),
            'gyroid':    lambda x,y,z: math.sin(x)*math.cos(y)+math.sin(y)*math.cos(z)+math.cos(x)*math.sin(z),
            'diamond':   lambda x,y,z: math.cos(x-y)*math.cos(z)+math.sin(x+y)*math.sin(z),
          }
  

parser = OptionParser(option_class=extendedOption, usage='%prog', description = """
Generate a geometry file of a bicontinuous structure of given type.
""" + string.replace('$Id$','\n','\\n')
)

parser.add_option('-t','--type', dest='type', choices=minimal_surfaces, \
                  help='type of minimal surface (%s) [primitive]' %(','.join(minimal_surfaces)))
parser.add_option('-f','--threshold', dest='threshold', type='float', \
                  help='threshold value defining minimal surface [%default]')
parser.add_option('-g', '--grid', dest='grid', type='int', nargs=3, \
                  help='a,b,c grid of hexahedral box %default')
parser.add_option('-s', '--size', dest='size', type='float', nargs=3, \
                  help='x,y,z size of hexahedral box %default')
parser.add_option('-p', '--periods', dest='periods', type='int', \
                  help='number of repetitions of unit cell [%default]')
parser.add_option('--homogenization', dest='homogenization', type='int', \
                  help='homogenization index to be used [%default]')
parser.add_option('--m', dest='microstructure', type='int', nargs = 2, \
                  help='two microstructure indices to be used %default')
parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
                  help='output geom file with two-dimensional data arrangement [%default]')

parser.set_defaults(type = minimal_surfaces[0])
parser.set_defaults(threshold = 0.0)
parser.set_defaults(periods = 1)
parser.set_defaults(grid = numpy.array([16,16,16]))
parser.set_defaults(size = numpy.array([1.0,1.0,1.0]))
parser.set_defaults(homogenization = 1)
parser.set_defaults(microstructure = [1,2])
parser.set_defaults(twoD  = False)

(options, args) = parser.parse_args()

#--- setup file handles ---------------------------------------------------------------------------
file = {'name':'STDIN',
        'input':sys.stdin,
        'output':sys.stdout,
        'croak':sys.stderr,
       }
info = {
        'grid':   numpy.array(options.grid),
        'size':   numpy.array(options.size),
        'origin': numpy.zeros(3,'d'),
        'microstructures': max(options.microstructure),
        'homogenization':  options.homogenization
       }

#--- 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()

#--- write header ---------------------------------------------------------------------------------
header = ['$Id$\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))

#--- write data -----------------------------------------------------------------------------------
for z in xrange(options.grid[2]):
  Z = options.periods*2.0*math.pi*(z+0.5)/options.grid[2]
  for y in xrange(options.grid[1]):
    Y = options.periods*2.0*math.pi*(y+0.5)/options.grid[1]
    for x in xrange(options.grid[0]):
      X = options.periods*2.0*math.pi*(x+0.5)/options.grid[0]
      file['output'].write(\
        str({True:options.microstructure[0],False:options.microstructure[1]}[options.threshold > \
            surface[options.type](X,Y,Z)]) + {True:' ',False:'\n'}[options.twoD] )
    file['output'].write({True:'\n',False:''}[options.twoD])