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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('-g', '--grid', dest='grid', type='int', nargs=2, \
help='a,b grid of hexahedral box %default')
parser.add_option('-s', '--size', dest='size', type='float', nargs=2, \
help='x,y size of hexahedral box %default')
parser.add_option('-c', '--canal', dest='canal', type='float', \
help='Haversian canal radius [%default]')
parser.add_option('-o', '--osteon', dest='osteon', type='float', \
help='osteon radius (horizontal) [%default]')
parser.add_option('-l', '--lamella', dest='period', type='float', \
help='lamella width [%default]')
parser.add_option('-a', '--amplitude', dest='amplitude', type='float', \
help='amplitude of twisted plywood wiggle in deg [%default]')
parser.add_option( '--aspect', dest='aspect', type='float', \
help='osteon aspect ratio (vert/horiz) [%default]')
parser.add_option('-w', '--omega', dest='omega', type='float', \
help='rotation angle (around normal) of osteon [%default]')
parser.add_option('--homogenization', dest='homogenization', type='int', \
help='homogenization index to be used [%default]')
parser.add_option('--crystallite', dest='crystallite', type='int', \
help='crystallite index to be used [%default]')
parser.add_option('--configuration', dest='config', action='store_true', \
help='output material configuration [%default]')
parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
help='use two-dimensional geom data arrangement [%default]')
parser.set_defaults(canal = 25e-6)
parser.set_defaults(osteon = 100e-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 = numpy.array([300e-6,300e-6],'d'))
parser.set_defaults(grid = numpy.array([512,512],'i'))
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 numpy.any(options.grid < 2):
file['croak'].write('grid too low...\n')
sys.exit()
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')
box = numpy.dot(numpy.array([[options.canal,0.],[0.,options.aspect*options.canal]]).transpose(),rotation)
info = {
'grid': numpy.ones(3,'i'),
'size': numpy.ones(3,'d'),
'origin': numpy.zeros(3,'d'),
'microstructures': 0,
'homogenization': options.homogenization,
}
info['grid'][:2] = options.grid
info['size'][:2] = options.size
info['size'][2] = min(info['size'][0]/info['grid'][0],info['size'][1]/info['grid'][1])
info['origin'] = -info['size']/2.0
X0 = info['size'][0]/info['grid'][0]*\
(numpy.tile(numpy.arange(info['grid'][0]),(info['grid'][1],1)) - info['grid'][0]/2 + 0.5)
Y0 = info['size'][1]/info['grid'][1]*\
(numpy.tile(numpy.arange(info['grid'][1]),(info['grid'][0],1)).transpose() - info['grid'][1]/2 + 0.5)
X = X0*rotation[0,0] + Y0*rotation[0,1] # rotate by omega
Y = X0*rotation[1,0] + Y0*rotation[1,1] # rotate by omega
radius = numpy.sqrt(X*X + Y*Y/options.aspect/options.aspect)
alpha = numpy.degrees(numpy.arctan2(Y/options.aspect,X))
beta = options.amplitude*numpy.sin(2.0*math.pi*(radius-options.canal)/options.period)
microstructure = numpy.where(radius < float(options.canal),1,0) + numpy.where(radius > float(options.osteon),2,0)
info['microstructures'] = 3
alphaOfGrain = numpy.zeros(info['grid'][0]*info['grid'][1],'d')
betaOfGrain = numpy.zeros(info['grid'][0]*info['grid'][1],'d')
for y in xrange(info['grid'][1]):
for x in xrange(info['grid'][0]):
if microstructure[y,x] == 0:
microstructure[y,x] = info['microstructures']
alphaOfGrain[info['microstructures']] = alpha[y,x]
betaOfGrain[ info['microstructures']] = beta[y,x]
info['microstructures'] += 1
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']))) + \
'microstructures: %i\n'%info['microstructures'] + \
'homogenization: %i\n'%info['homogenization'])
file['croak'].write("bounding box: %s\n"%(numpy.sqrt(numpy.sum(box*box,0))))
# -------------------------------------- switch according to task ----------------------------------
formatwidth = 1+int(math.floor(math.log10(info['microstructures']-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['microstructures']):
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['microstructures']):
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("6 header\n" + \
"$Id$\n" + \
"grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2]) + \
"size\tx %g\ty %g\tz %g\n"%(info['size'][0],info['size'][1],info['size'][2]) + \
"origin\tx %g\ty %g\tz %g\n"%(info['origin'][0],info['origin'][1],info['origin'][2]) + \
"microstructures\t%i\n"%(info['microstructures']) + \
"homogenization\t%i\n"%(info['homogenization'])
)
for y in xrange(info['grid'][1]):
for x in xrange(info['grid'][0]):
file['output'].write(\
str(microstructure[y,x]).rjust(formatwidth) + \
{True:' ',False:'\n'}[options.twoD] )
file['output'].write({True:'\n',False:''}[options.twoD])
# ------------------------------------------ output finalization ---------------------------------------
file['output'].close()
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