fixed bugs (grain index start, alpha orientation for elliptic osteons).
added option to rotate osteon relative to periodic box.
This commit is contained in:
Philip Eisenlohr
parent
62e55483f7
commit
565c532546
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@ -31,38 +31,41 @@ class extendedOption(Option):
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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 $','\n','\\n')
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Its fiber orientation is oscillating by +/- amplitude within one period.
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""" + string.replace('$Id$','\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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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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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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help='Osteon aspect ratio (vert/horiz)')
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parser.add_option('-w', '--omega', dest='omega', type='float', \
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help='rotation angle (around normal) of osteon')
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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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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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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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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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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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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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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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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(omega = 0.0)
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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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@ -117,27 +120,35 @@ else:
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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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options.omega *= math.pi/180.0 # rescale ro radians
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rotation = numpy.array([[ math.cos(options.omega),math.sin(options.omega),],
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[-math.sin(options.omega),math.cos(options.omega),]],'d')
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X0 = numpy.tile(range(info['resolution'][0]),(info['resolution'][0],1)) - info['resolution'][0]/2 + 0.5
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Y0 = numpy.tile(range(info['resolution'][1]),(info['resolution'][1],1)).transpose() - info['resolution'][1]/2 + 0.5
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X = X0*rotation[0,0] + Y0*rotation[1,0] # rotate by omega
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Y = X0*rotation[0,1] + Y0*rotation[1,1] # rotate by omega
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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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alpha = numpy.degrees(numpy.arctan2(X/options.aspect,Y))
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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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info['grains'] = 3
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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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info['grains'] += 1
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sys.stderr.write('micro assemble %f\n'%(time.clock()))
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@ -145,7 +156,7 @@ 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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formatwidth = 1+int(math.floor(math.log10(info['grains']-1)))
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if options.config:
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file['output'].write('<microstructure>\n')
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@ -155,16 +166,16 @@ if options.config:
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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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for i in xrange(3,info['grains']):
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file['output'].write('\n[Grain%s]\n'%(str(i).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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'(constituent)\tphase 3\ttexture %s\tfraction 1.0\n'%(str(i).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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for i in xrange(3,info['grains']):
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file['output'].write('\n[Grain%s]\n'%(str(i).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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@ -20,6 +20,7 @@ bin_link = { \
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'geom_fromAng.py',
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'geom_fromMinimalSurface.py',
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'geom_fromVoronoiTessellation.py',
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'geom_Osteon.py',
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'geom_canvas.py',
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'geom_check.py',
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'geom_rescale.py',
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