From 0d7f1e86236eb101d211a919d6f673cab29bf888 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Wed, 27 Feb 2013 18:43:53 +0000 Subject: [PATCH] killed "margin" option, now same as all others: resolution and dimension in x and y. can be non-square grid. --- processing/pre/geom_Osteon.py | 117 ++++++++++++++-------------------- 1 file changed, 48 insertions(+), 69 deletions(-) diff --git a/processing/pre/geom_Osteon.py b/processing/pre/geom_Osteon.py index 990a639c4..a18cd32df 100755 --- a/processing/pre/geom_Osteon.py +++ b/processing/pre/geom_Osteon.py @@ -35,24 +35,22 @@ 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('-r', '--aspect', dest='aspect', type='float', \ - help='Osteon aspect ratio (vert/horiz)') + 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('-s', '--size', dest='size', type='float', \ - help='box size (horizontal)') -parser.add_option('-m', '--margin', dest='margin', type='float', \ - help='margin width') -parser.add_option('-N', '--resolution', dest='resolution', type='int', \ - help='box size in pixels (horizontal)') -parser.add_option('-a', '--amplitude', dest='amplitude', type='float', \ - help='Amplitude of twisted plywood wiggle in deg') -parser.add_option('-p', '--period', dest='period', type='float', \ - 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', \ @@ -60,17 +58,16 @@ parser.add_option('--crystallite', dest='crystallite', type='int', \ parser.add_option('--configuration', dest='config', action='store_true', \ help='output material configuration') parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \ - help='output geom file with two-dimensional data arrangement') + help='use two-dimensional geom data arrangement') parser.set_defaults(canal = 25e-6) -parser.set_defaults(osteon = 75e-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 = 300e-6) -parser.set_defaults(margin = 0.0) -parser.set_defaults(resolution = 256) +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) @@ -86,74 +83,56 @@ file = {'name':'STDIN', 'croak':sys.stderr, } -if (options.resolution < 2): +if numpy.any(options.resolution < 2): file['croak'].write('resolution too low...\n') sys.exit() -if (options.size < options.canal): - file['croak'].write('canal larger than box...\n') - sys.exit() - -if (options.osteon < options.canal): - file['croak'].write('canal larger than osteon...\n') - sys.exit() - -info = {'grains': 0, - 'resolution': numpy.zeros(3,'i'), - 'dimension': numpy.ones(3,'d'), - 'origin': numpy.ones(3,'d'), - 'homogenization': options.homogenization, - } - -if options.margin > 0.0: - info['resolution'][0] = options.resolution - info['resolution'][1] = round(options.resolution*(options.aspect * options.osteon + options.margin) / \ - (options.osteon + options.margin) ) - info['dimension'][0] = options.osteon + options.margin - info['dimension'][1] = options.aspect * options.osteon + options.margin -else: - info['resolution'][0] = options.resolution - info['resolution'][1] = options.resolution - info['dimension'][0] = options.size - info['dimension'][1] = options.size - -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 +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)))) -X = X0*rotation[0,0] + Y0*rotation[1,0] # rotate by omega -Y = X0*rotation[0,1] + Y0*rotation[1,1] # rotate by omega +info = {'grains': 0, + 'resolution': numpy.ones(3,'i'), + 'dimension': numpy.ones(3,'d'), + 'origin': numpy.zeros(3,'d'), + 'homogenization': options.homogenization, + } -radius = numpy.sqrt(X*X/options.aspect/options.aspect + Y*Y) -alpha = numpy.degrees(numpy.arctan2(X/options.aspect,Y)) -beta = options.amplitude*numpy.sin(math.pi*(radius-options.canal)/options.period) +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) -sys.stderr.write('micro %f\n'%(time.clock())) 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: - microstructure[x,y] = info['grains'] - alphaOfGrain[info['grains']] = alpha[x,y] - betaOfGrain[ info['grains']] = beta[x,y] + 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 -sys.stderr.write('micro assemble %f\n'%(time.clock())) - - # -------------------------------------- switch according to task ---------------------------------- formatwidth = 1+int(math.floor(math.log10(info['grains']-1))) @@ -183,16 +162,16 @@ if options.config: else: file['output'].write("4 header\n" + \ - "resolution\ta %i\tb %i\tc %i\n"%(info['resolution'][0],info['resolution'][1],1,) + \ - "dimension\tx %g\ty %g\tz %g\n"%(info['dimension'][0],info['dimension'][1],info['dimension'][0]/info['resolution'][0],) + \ - "origin\tx 0\ty 0\tz 0\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[x,y]).rjust(formatwidth) + \ + str(microstructure[y,x]).rjust(formatwidth) + \ {True:' ',False:'\n'}[options.twoD] ) file['output'].write({True:'\n',False:''}[options.twoD])