From 565c5325463a31b2020e7c98736665f72383caf3 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Wed, 27 Feb 2013 10:56:30 +0000 Subject: [PATCH] fixed bugs (grain index start, alpha orientation for elliptic osteons). added option to rotate osteon relative to periodic box. --- processing/pre/geom_Osteon.py | 65 +++++++++++++++----------- processing/setup/symLink_Processing.py | 1 + 2 files changed, 39 insertions(+), 27 deletions(-) diff --git a/processing/pre/geom_Osteon.py b/processing/pre/geom_Osteon.py index 243c18918..990a639c4 100755 --- a/processing/pre/geom_Osteon.py +++ b/processing/pre/geom_Osteon.py @@ -31,38 +31,41 @@ class extendedOption(Option): 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 orientation is oscillating by +/- amplitude within one period. -""" + string.replace('$Id: geom_fromMinimalSurface.py 2078 2013-01-18 12:59:26Z MPIE\p.eisenlohr $','\n','\\n') +Its fiber orientation is oscillating by +/- amplitude within one period. +""" + string.replace('$Id$','\n','\\n') ) parser.add_option('-c', '--canal', dest='canal', type='float', \ - help='Haversian canal radius') + help='Haversian canal radius') parser.add_option('-o', '--osteon', dest='osteon', type='float', \ - help='Osteon radius (horizontal)') + help='Osteon radius (horizontal)') parser.add_option('-r', '--aspect', dest='aspect', type='float', \ - help='Osteon aspect ratio (vert/horiz)') -parser.add_option('-s', '--size', dest='size', type='float', \ - help='box size (horizontal)') + 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') + help='margin width') parser.add_option('-N', '--resolution', dest='resolution', type='int', \ - help='box size in pixels (horizontal)') + help='box size in pixels (horizontal)') parser.add_option('-a', '--amplitude', dest='amplitude', type='float', \ - help='Amplitude of twisted plywood wiggle in deg') + help='Amplitude of twisted plywood wiggle in deg') parser.add_option('-p', '--period', dest='period', type='float', \ - help='lamella width') + 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') + 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') + help='output material configuration') parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \ - help='output geom file with two-dimensional data arrangement') + 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) @@ -117,27 +120,35 @@ else: 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 -X = numpy.tile(range(info['resolution'][0]),(info['resolution'][0],1)) - info['resolution'][0]/2 + 0.5 -Y = numpy.tile(range(info['resolution'][1]),(info['resolution'][1],1)).transpose() - info['resolution'][1]/2 + 0.5 radius = numpy.sqrt(X*X/options.aspect/options.aspect + Y*Y) -alpha = numpy.degrees(numpy.arctan2(Y,X)) +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'] = 2 +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: - info['grains'] += 1 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())) @@ -145,7 +156,7 @@ sys.stderr.write('micro assemble %f\n'%(time.clock())) # -------------------------------------- switch according to task ---------------------------------- -formatwidth = 1+int(math.floor(math.log10(info['grains']))) +formatwidth = 1+int(math.floor(math.log10(info['grains']-1))) if options.config: file['output'].write('\n') @@ -155,16 +166,16 @@ if options.config: file['output'].write('\n[interstitial]\n' + \ 'crystallite %i\n'%options.crystallite + \ '(constituent)\tphase 2\ttexture 2\tfraction 1.0\n') - for i in xrange(2,info['grains']): - file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \ + 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+1).rjust(formatwidth))) + '(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(2,info['grains']): - file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \ + 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])) diff --git a/processing/setup/symLink_Processing.py b/processing/setup/symLink_Processing.py index 02cf757eb..938c7b69b 100755 --- a/processing/setup/symLink_Processing.py +++ b/processing/setup/symLink_Processing.py @@ -20,6 +20,7 @@ bin_link = { \ 'geom_fromAng.py', 'geom_fromMinimalSurface.py', 'geom_fromVoronoiTessellation.py', + 'geom_Osteon.py', 'geom_canvas.py', 'geom_check.py', 'geom_rescale.py',