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DAMASK_EICMD
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DAMASK_EICMD/processing/pre/geom_Osteon.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,math,numpy,time
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 -------------------------------
parser = OptionParser(option_class=extendedOption, usage='%prog', description = """
Generate a geometry file of an osteon enclosing the Harvesian canal and separated by interstitial tissue.
The osteon phase is lamellar with a twisted plywood structure.
Its fiber orientation is oscillating by +/- amplitude within one period.
""" + string.replace('$Id$','\n','\\n')
)
parser.add_option('-c', '--canal', dest='canal', type='float', \
help='Haversian canal radius')
parser.add_option('-o', '--osteon', dest='osteon', type='float', \
help='Osteon radius (horizontal)')
parser.add_option('-r', '--aspect', dest='aspect', type='float', \
help='Osteon aspect ratio (vert/horiz)')
parser.add_option('-w', '--omega', dest='omega', type='float', \
help='rotation angle (around normal) of osteon')
parser.add_option('-s', '--size', dest='size', type='float', \
help='box size (horizontal)')
parser.add_option('-m', '--margin', dest='margin', type='float', \
help='margin width')
parser.add_option('-N', '--resolution', dest='resolution', type='int', \
help='box size in pixels (horizontal)')
parser.add_option('-a', '--amplitude', dest='amplitude', type='float', \
help='Amplitude of twisted plywood wiggle in deg')
parser.add_option('-p', '--period', dest='period', type='float', \
help='lamella width')
parser.add_option('--homogenization', dest='homogenization', type='int', \
help='homogenization index to be used')
parser.add_option('--crystallite', dest='crystallite', type='int', \
help='crystallite index to be used')
parser.add_option('--configuration', dest='config', action='store_true', \
help='output material configuration')
parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
help='output geom file with two-dimensional data arrangement')
parser.set_defaults(canal = 25e-6)
parser.set_defaults(osteon = 75e-6)
parser.set_defaults(aspect = 1.0)
parser.set_defaults(omega = 0.0)
parser.set_defaults(period = 5e-6)
parser.set_defaults(amplitude = 60)
parser.set_defaults(size = 300e-6)
parser.set_defaults(margin = 0.0)
parser.set_defaults(resolution = 256)
parser.set_defaults(homogenization = 1)
parser.set_defaults(crystallite = 1)
parser.set_defaults(config = False)
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,
}
if (options.resolution < 2):
file['croak'].write('resolution too low...\n')
sys.exit()
if (options.size < options.canal):
file['croak'].write('canal larger than box...\n')
sys.exit()
if (options.osteon < options.canal):
file['croak'].write('canal larger than osteon...\n')
sys.exit()
info = {'grains': 0,
'resolution': numpy.zeros(3,'i'),
'dimension': numpy.ones(3,'d'),
'origin': numpy.ones(3,'d'),
'homogenization': options.homogenization,
}
if options.margin > 0.0:
info['resolution'][0] = options.resolution
info['resolution'][1] = round(options.resolution*(options.aspect * options.osteon + options.margin) / \
(options.osteon + options.margin) )
info['dimension'][0] = options.osteon + options.margin
info['dimension'][1] = options.aspect * options.osteon + options.margin
else:
info['resolution'][0] = options.resolution
info['resolution'][1] = options.resolution
info['dimension'][0] = options.size
info['dimension'][1] = options.size
options.canal *= info['resolution'][0]/info['dimension'][0] # rescale to pixel dimension
options.osteon *= info['resolution'][0]/info['dimension'][0] # rescale to pixel dimension
options.period *= info['resolution'][0]/info['dimension'][0] # rescale to pixel dimension
options.omega *= math.pi/180.0 # rescale ro radians
rotation = numpy.array([[ math.cos(options.omega),math.sin(options.omega),],
[-math.sin(options.omega),math.cos(options.omega),]],'d')
X0 = numpy.tile(range(info['resolution'][0]),(info['resolution'][0],1)) - info['resolution'][0]/2 + 0.5
Y0 = numpy.tile(range(info['resolution'][1]),(info['resolution'][1],1)).transpose() - info['resolution'][1]/2 + 0.5
X = X0*rotation[0,0] + Y0*rotation[1,0] # rotate by omega
Y = X0*rotation[0,1] + Y0*rotation[1,1] # rotate by omega
radius = numpy.sqrt(X*X/options.aspect/options.aspect + Y*Y)
alpha = numpy.degrees(numpy.arctan2(X/options.aspect,Y))
beta = options.amplitude*numpy.sin(math.pi*(radius-options.canal)/options.period)
microstructure = numpy.where(radius < float(options.canal),1,0) + numpy.where(radius > float(options.osteon),2,0)
sys.stderr.write('micro %f\n'%(time.clock()))
info['grains'] = 3
alphaOfGrain = numpy.zeros(info['resolution'][0]*info['resolution'][1],'d')
betaOfGrain = numpy.zeros(info['resolution'][0]*info['resolution'][1],'d')
for y in xrange(info['resolution'][1]):
for x in xrange(info['resolution'][0]):
if microstructure[x,y] == 0:
microstructure[x,y] = info['grains']
alphaOfGrain[info['grains']] = alpha[x,y]
betaOfGrain[ info['grains']] = beta[x,y]
info['grains'] += 1
sys.stderr.write('micro assemble %f\n'%(time.clock()))
# -------------------------------------- switch according to task ----------------------------------
formatwidth = 1+int(math.floor(math.log10(info['grains']-1)))
if options.config:
file['output'].write('<microstructure>\n')
file['output'].write('\n[canal]\n' + \
'crystallite %i\n'%options.crystallite + \
'(constituent)\tphase 1\ttexture 1\tfraction 1.0\n')
file['output'].write('\n[interstitial]\n' + \
'crystallite %i\n'%options.crystallite + \
'(constituent)\tphase 2\ttexture 2\tfraction 1.0\n')
for i in xrange(3,info['grains']):
file['output'].write('\n[Grain%s]\n'%(str(i).zfill(formatwidth)) + \
'crystallite %i\n'%options.crystallite + \
'(constituent)\tphase 3\ttexture %s\tfraction 1.0\n'%(str(i).rjust(formatwidth)))
file['output'].write('\n<texture>\n')
file['output'].write('\n[canal]\n')
file['output'].write('\n[interstitial]\n')
for i in xrange(3,info['grains']):
file['output'].write('\n[Grain%s]\n'%(str(i).zfill(formatwidth)) + \
'(gauss)\tphi1 %g\tPhi %g\tphi2 0\tscatter 0.0\tfraction 1.0\n'%(\
alphaOfGrain[i],\
betaOfGrain[i]))
else:
file['output'].write("4 header\n" + \
"resolution\ta %i\tb %i\tc %i\n"%(info['resolution'][0],info['resolution'][1],1,) + \
"dimension\tx %g\ty %g\tz %g\n"%(info['dimension'][0],info['dimension'][1],info['dimension'][0]/info['resolution'][0],) + \
"origin\tx 0\ty 0\tz 0\n" + \
"homogenization 1\n"
)
for y in xrange(info['resolution'][1]):
for x in xrange(info['resolution'][0]):
file['output'].write(\
str(microstructure[x,y]).rjust(formatwidth) + \
{True:' ',False:'\n'}[options.twoD] )
file['output'].write({True:'\n',False:''}[options.twoD])
# ------------------------------------------ output finalization ---------------------------------------
file['output'].close()
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