192 lines
8.4 KiB
Python
192 lines
8.4 KiB
Python
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,math,numpy,time
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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# -----------------------------
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class extendedOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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# ----------------------- MAIN -------------------------------
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parser = OptionParser(option_class=extendedOption, usage='%prog', description = """
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Generate a geometry file of an osteon enclosing the Harvesian canal and separated by interstitial tissue.
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The osteon phase is lamellar with a twisted plywood structure.
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Its orientation is oscillating by +/- amplitude within one period.
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""" + string.replace('$Id: geom_fromMinimalSurface.py 2078 2013-01-18 12:59:26Z MPIE\p.eisenlohr $','\n','\\n')
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)
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parser.add_option('-c', '--canal', dest='canal', type='float', \
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help='Haversian canal radius')
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parser.add_option('-o', '--osteon', dest='osteon', type='float', \
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help='Osteon radius (horizontal)')
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parser.add_option('-r', '--aspect', dest='aspect', type='float', \
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help='Osteon aspect ratio (vert/horiz)')
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parser.add_option('-s', '--size', dest='size', type='float', \
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help='box size (horizontal)')
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parser.add_option('-m', '--margin', dest='margin', type='float', \
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help='margin width')
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parser.add_option('-N', '--resolution', dest='resolution', type='int', \
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help='box size in pixels (horizontal)')
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parser.add_option('-a', '--amplitude', dest='amplitude', type='float', \
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help='Amplitude of twisted plywood wiggle in deg')
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parser.add_option('-p', '--period', dest='period', type='float', \
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help='lamella width')
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parser.add_option('--homogenization', dest='homogenization', type='int', \
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help='homogenization index to be used')
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parser.add_option('--crystallite', dest='crystallite', type='int', \
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help='crystallite index to be used')
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parser.add_option('--configuration', dest='config', action='store_true', \
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help='output material configuration')
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parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
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help='output geom file with two-dimensional data arrangement')
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parser.set_defaults(canal = 25e-6)
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parser.set_defaults(osteon = 75e-6)
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parser.set_defaults(aspect = 1.0)
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parser.set_defaults(period = 5e-6)
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parser.set_defaults(amplitude = 60)
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parser.set_defaults(size = 300e-6)
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parser.set_defaults(margin = 0.0)
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parser.set_defaults(resolution = 256)
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parser.set_defaults(homogenization = 1)
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parser.set_defaults(crystallite = 1)
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parser.set_defaults(config = False)
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parser.set_defaults(twoD = False)
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(options, args) = parser.parse_args()
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# ------------------------------------------ setup file handles ---------------------------------------
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file = {'name':'STDIN',
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'input':sys.stdin,
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'output':sys.stdout,
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'croak':sys.stderr,
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}
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if (options.resolution < 2):
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file['croak'].write('resolution too low...\n')
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sys.exit()
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if (options.size < options.canal):
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file['croak'].write('canal larger than box...\n')
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sys.exit()
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if (options.osteon < options.canal):
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file['croak'].write('canal larger than osteon...\n')
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sys.exit()
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info = {'grains': 0,
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'resolution': numpy.zeros(3,'i'),
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'dimension': numpy.ones(3,'d'),
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'origin': numpy.ones(3,'d'),
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'homogenization': options.homogenization,
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}
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if options.margin > 0.0:
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info['resolution'][0] = options.resolution
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info['resolution'][1] = round(options.resolution*(options.aspect * options.osteon + options.margin) / \
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(options.osteon + options.margin) )
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info['dimension'][0] = options.osteon + options.margin
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info['dimension'][1] = options.aspect * options.osteon + options.margin
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else:
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info['resolution'][0] = options.resolution
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info['resolution'][1] = options.resolution
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info['dimension'][0] = options.size
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info['dimension'][1] = options.size
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options.canal *= info['resolution'][0]/info['dimension'][0] # rescale to pixel dimension
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options.osteon *= info['resolution'][0]/info['dimension'][0] # rescale to pixel dimension
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options.period *= info['resolution'][0]/info['dimension'][0] # rescale to pixel dimension
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X = numpy.tile(range(info['resolution'][0]),(info['resolution'][0],1)) - info['resolution'][0]/2 + 0.5
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Y = numpy.tile(range(info['resolution'][1]),(info['resolution'][1],1)).transpose() - info['resolution'][1]/2 + 0.5
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radius = numpy.sqrt(X*X/options.aspect/options.aspect + Y*Y)
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alpha = numpy.degrees(numpy.arctan2(Y,X))
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beta = options.amplitude*numpy.sin(math.pi*(radius-options.canal)/options.period)
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microstructure = numpy.where(radius < float(options.canal),1,0) + numpy.where(radius > float(options.osteon),2,0)
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sys.stderr.write('micro %f\n'%(time.clock()))
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info['grains'] = 2
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alphaOfGrain = numpy.zeros(info['resolution'][0]*info['resolution'][1],'d')
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betaOfGrain = numpy.zeros(info['resolution'][0]*info['resolution'][1],'d')
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for y in xrange(info['resolution'][1]):
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for x in xrange(info['resolution'][0]):
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if microstructure[x,y] == 0:
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info['grains'] += 1
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microstructure[x,y] = info['grains']
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alphaOfGrain[info['grains']] = alpha[x,y]
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betaOfGrain[ info['grains']] = beta[x,y]
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sys.stderr.write('micro assemble %f\n'%(time.clock()))
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# -------------------------------------- switch according to task ----------------------------------
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formatwidth = 1+int(math.floor(math.log10(info['grains'])))
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if options.config:
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file['output'].write('<microstructure>\n')
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file['output'].write('\n[canal]\n' + \
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'crystallite %i\n'%options.crystallite + \
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'(constituent)\tphase 1\ttexture 1\tfraction 1.0\n')
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file['output'].write('\n[interstitial]\n' + \
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'crystallite %i\n'%options.crystallite + \
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'(constituent)\tphase 2\ttexture 2\tfraction 1.0\n')
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for i in xrange(2,info['grains']):
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file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \
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'crystallite %i\n'%options.crystallite + \
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'(constituent)\tphase 3\ttexture %s\tfraction 1.0\n'%(str(i+1).rjust(formatwidth)))
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file['output'].write('\n<texture>\n')
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file['output'].write('\n[canal]\n')
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file['output'].write('\n[interstitial]\n')
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for i in xrange(2,info['grains']):
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file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \
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'(gauss)\tphi1 %g\tPhi %g\tphi2 0\tscatter 0.0\tfraction 1.0\n'%(\
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alphaOfGrain[i],\
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betaOfGrain[i]))
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else:
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file['output'].write("4 header\n" + \
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"resolution\ta %i\tb %i\tc %i\n"%(info['resolution'][0],info['resolution'][1],1,) + \
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"dimension\tx %g\ty %g\tz %g\n"%(info['dimension'][0],info['dimension'][1],info['dimension'][0]/info['resolution'][0],) + \
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"origin\tx 0\ty 0\tz 0\n" + \
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"homogenization 1\n"
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)
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for y in xrange(info['resolution'][1]):
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for x in xrange(info['resolution'][0]):
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file['output'].write(\
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str(microstructure[x,y]).rjust(formatwidth) + \
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{True:' ',False:'\n'}[options.twoD] )
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file['output'].write({True:'\n',False:''}[options.twoD])
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# ------------------------------------------ output finalization ---------------------------------------
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file['output'].close()
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