#!/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('-r', '--resolution', dest='resolution', type='int', nargs=2, \ help='resolution (a,b) of grid') parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs=2, \ help='physical dimension (x,y) of periodic patch') 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('-l', '--lamella', dest='period', type='float', \ help='lamella width') parser.add_option('-a', '--amplitude', dest='amplitude', type='float', \ help='amplitude of twisted plywood wiggle in deg') parser.add_option( '--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('--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='use two-dimensional geom data arrangement') 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(dimension = numpy.array([300e-6,300e-6],'d')) parser.set_defaults(resolution = 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.resolution < 2): file['croak'].write('resolution 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) sys.stderr.write("bounding box: %s\n"%(numpy.sqrt(numpy.sum(box*box,0)))) info = {'grains': 0, 'resolution': numpy.ones(3,'i'), 'dimension': numpy.ones(3,'d'), 'origin': numpy.zeros(3,'d'), 'homogenization': options.homogenization, } info['resolution'][:2] = options.resolution info['dimension'][:2] = options.dimension info['dimension'][2] = min(info['dimension'][0]/info['resolution'][0],info['dimension'][1]/info['resolution'][1]) info['origin'] = -info['dimension']/2.0 X0 = info['dimension'][0]/info['resolution'][0]*\ (numpy.tile(numpy.arange(info['resolution'][0]),(info['resolution'][1],1)) - info['resolution'][0]/2 + 0.5) Y0 = info['dimension'][1]/info['resolution'][1]*\ (numpy.tile(numpy.arange(info['resolution'][1]),(info['resolution'][0],1)).transpose() - info['resolution'][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['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[y,x] == 0: microstructure[y,x] = info['grains'] alphaOfGrain[info['grains']] = alpha[y,x] betaOfGrain[ info['grains']] = beta[y,x] info['grains'] += 1 # -------------------------------------- switch according to task ---------------------------------- formatwidth = 1+int(math.floor(math.log10(info['grains']-1))) if options.config: file['output'].write('\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\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],info['resolution'][2]) + \ "dimension\tx %g\ty %g\tz %g\n"%(info['dimension'][0],info['dimension'][1],info['dimension'][2]) + \ "origin\tx %g\ty %g\tz %g\n"%(info['origin'][0],info['origin'][1],info['origin'][2]) + \ "homogenization 1\n" ) for y in xrange(info['resolution'][1]): for x in xrange(info['resolution'][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()