added ID information of creator script to header, changed keywords (resolution->grid, dimension->size)
This commit is contained in:
Martin Diehl
parent
4314ab236e
commit
7bcf1d6072
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@ -35,30 +35,30 @@ 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('-r', '--resolution', dest='resolution', type='int', nargs=2, \
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help='resolution (a,b) of grid')
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parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs=2, \
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help='physical dimension (x,y) of periodic patch')
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parser.add_option('-g', '--grid', dest='grid', type='int', nargs=2, \
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help='a,b grid of hexahedral box %default')
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parser.add_option('-s', '--size', dest='size', type='float', nargs=2, \
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help='x,y size of hexahedral box %default')
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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 [%default]')
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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) [%default]')
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parser.add_option('-l', '--lamella', dest='period', type='float', \
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help='lamella width')
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help='lamella width [%default]')
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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 [%default]')
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parser.add_option( '--aspect', dest='aspect', type='float', \
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help='osteon aspect ratio (vert/horiz)')
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help='osteon aspect ratio (vert/horiz) [%default]')
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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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help='rotation angle (around normal) of osteon [%default]')
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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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help='homogenization index to be used [%default]')
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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='crystallite index to be used [%default]')
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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 [%default]')
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parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
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help='use two-dimensional geom data arrangement')
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help='use two-dimensional geom data arrangement [%default]')
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parser.set_defaults(canal = 25e-6)
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parser.set_defaults(osteon = 100e-6)
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@ -66,8 +66,8 @@ 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(dimension = numpy.array([300e-6,300e-6],'d'))
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parser.set_defaults(resolution = numpy.array([512,512],'i'))
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parser.set_defaults(size = numpy.array([300e-6,300e-6],'d'))
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parser.set_defaults(grid = numpy.array([512,512],'i'))
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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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@ -83,8 +83,8 @@ file = {'name':'STDIN',
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'croak':sys.stderr,
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}
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if numpy.any(options.resolution < 2):
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file['croak'].write('resolution too low...\n')
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if numpy.any(options.grid < 2):
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file['croak'].write('grid too low...\n')
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sys.exit()
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options.omega *= math.pi/180.0 # rescale ro radians
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@ -92,25 +92,26 @@ 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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box = numpy.dot(numpy.array([[options.canal,0.],[0.,options.aspect*options.canal]]).transpose(),rotation)
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sys.stderr.write("bounding box: %s\n"%(numpy.sqrt(numpy.sum(box*box,0))))
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info = {'grains': 0,
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'resolution': numpy.ones(3,'i'),
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'dimension': numpy.ones(3,'d'),
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info = {
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'grid': numpy.ones(3,'i'),
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'size': numpy.ones(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'microstructures': 0,
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'homogenization': options.homogenization,
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}
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info['resolution'][:2] = options.resolution
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info['dimension'][:2] = options.dimension
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info['dimension'][2] = min(info['dimension'][0]/info['resolution'][0],info['dimension'][1]/info['resolution'][1])
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info['origin'] = -info['dimension']/2.0
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info['grid'][:2] = options.grid
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info['size'][:2] = options.size
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info['size'][2] = min(info['size'][0]/info['grid'][0],info['size'][1]/info['grid'][1])
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info['origin'] = -info['size']/2.0
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X0 = info['dimension'][0]/info['resolution'][0]*\
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(numpy.tile(numpy.arange(info['resolution'][0]),(info['resolution'][1],1)) - info['resolution'][0]/2 + 0.5)
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Y0 = info['dimension'][1]/info['resolution'][1]*\
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(numpy.tile(numpy.arange(info['resolution'][1]),(info['resolution'][0],1)).transpose() - info['resolution'][1]/2 + 0.5)
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X0 = info['size'][0]/info['grid'][0]*\
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(numpy.tile(numpy.arange(info['grid'][0]),(info['grid'][1],1)) - info['grid'][0]/2 + 0.5)
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Y0 = info['size'][1]/info['grid'][1]*\
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(numpy.tile(numpy.arange(info['grid'][1]),(info['grid'][0],1)).transpose() - info['grid'][1]/2 + 0.5)
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X = X0*rotation[0,0] + Y0*rotation[0,1] # rotate by omega
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Y = X0*rotation[1,0] + Y0*rotation[1,1] # rotate by omega
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@ -121,22 +122,26 @@ beta = options.amplitude*numpy.sin(2.0*math.pi*(radius-options.canal)/options.pe
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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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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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info['microstructures'] = 3
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alphaOfGrain = numpy.zeros(info['grid'][0]*info['grid'][1],'d')
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betaOfGrain = numpy.zeros(info['grid'][0]*info['grid'][1],'d')
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for y in xrange(info['grid'][1]):
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for x in xrange(info['grid'][0]):
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if microstructure[y,x] == 0:
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microstructure[y,x] = info['grains']
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alphaOfGrain[info['grains']] = alpha[y,x]
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betaOfGrain[ info['grains']] = beta[y,x]
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info['grains'] += 1
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microstructure[y,x] = info['microstructures']
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alphaOfGrain[info['microstructures']] = alpha[y,x]
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betaOfGrain[ info['microstructures']] = beta[y,x]
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info['microstructures'] += 1
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file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
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'microstructures: %i\n'%info['microstructures'] + \
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'homogenization: %i\n'%info['homogenization'])
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file['croak'].write("bounding box: %s\n"%(numpy.sqrt(numpy.sum(box*box,0))))
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# -------------------------------------- switch according to task ----------------------------------
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formatwidth = 1+int(math.floor(math.log10(info['grains']-1)))
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formatwidth = 1+int(math.floor(math.log10(info['microstructures']-1)))
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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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@ -161,15 +166,17 @@ if options.config:
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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],info['resolution'][2]) + \
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"dimension\tx %g\ty %g\tz %g\n"%(info['dimension'][0],info['dimension'][1],info['dimension'][2]) + \
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file['output'].write("6 header\n" + \
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"$Id$\n" + \
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"grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2]) + \
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"size\tx %g\ty %g\tz %g\n"%(info['size'][0],info['size'][1],info['size'][2]) + \
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"origin\tx %g\ty %g\tz %g\n"%(info['origin'][0],info['origin'][1],info['origin'][2]) + \
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"homogenization 1\n"
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"microstructures\t%i\n"%(info['microstructures']) + \
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"homogenization\t%i\n"%(info['homogenization'])
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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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for y in xrange(info['grid'][1]):
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for x in xrange(info['grid'][0]):
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file['output'].write(\
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str(microstructure[y,x]).rjust(formatwidth) + \
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{True:' ',False:'\n'}[options.twoD] )
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@ -92,14 +92,16 @@ def vtk_writeASCII_mesh(dim,res,origin,data):
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# ----------------------- MAIN -------------------------------
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identifiers = {
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'resolution': ['a','b','c'],
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'dimension': ['x','y','z'],
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'resolution': lambda x: int(x),
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'dimension': lambda x: float(x),
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'grid': lambda x: int(x),
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'size': lambda x: float(x),
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'origin': lambda x: float(x),
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'homogenization': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog [geomfile[s]]', description = """
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@ -145,39 +147,49 @@ for file in files:
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content = file['input'].readlines()
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file['input'].close()
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info = {'resolution': [0,0,0],
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'dimension': [0.0,0.0,0.0],
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info = {'grid': [0,0,0],
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'size': [0.0,0.0,0.0],
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'origin': [0.0,0.0,0.0],
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'homogenization': 1,
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'microstructures': 0,
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}
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for header in headers:
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headitems = map(str.lower,header.split())
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if headitems[0] == 'resolution': headitems[0] = 'grid'
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if headitems[0] == 'dimension': headitems[0] = 'size'
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if headitems[0] in mappings.keys():
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if headitems[0] in identifiers.keys():
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for i in xrange(len(identifiers[headitems[0]])):
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info[headitems[0]][i] = mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
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info[headitems[0]][i] = \
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mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
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else:
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info[headitems[0]] = mappings[headitems[0]](headitems[1])
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if numpy.all(info['resolution'] == 0):
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file['croak'].write('no resolution info found.\n')
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if numpy.all(info['grid'] == 0):
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file['croak'].write('no grid info found.\n')
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continue
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if numpy.all(info['dimension'] == 0.0):
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file['croak'].write('no dimension info found.\n')
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if numpy.all(info['size'] == 0.0):
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file['croak'].write('no size info found.\n')
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continue
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file['croak'].write('resolution: %s\n'%(' x '.join(map(str,info['resolution']))) + \
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'dimension: %s\n'%(' x '.join(map(str,info['dimension']))) + \
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'origin: %s\n'%(' : '.join(map(str,info['origin'])))
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)
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file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n'%info['microstructures'])
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data = {'scalar':{'structure':numpy.zeros(info['resolution'],'i')}}
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data = {'scalar':{'structure':numpy.zeros(info['grid'],'i')}}
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i = 0
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for line in content:
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for item in map(int,line.split()):
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data['scalar']['structure'][i%info['resolution'][0],(i/info['resolution'][0])%info['resolution'][1],i/info['resolution'][0]/info['resolution'][1]] = item
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data['scalar']['structure'][i%info['grid'][0],(i/info['grid'][0])%info['grid'][1],i/info['grid'][0]/info['grid'][1]] = item
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i += 1
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out = {}
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out['mesh'] = vtk_writeASCII_mesh(info['dimension'],info['resolution'],info['origin'],data)
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out['mesh'] = vtk_writeASCII_mesh(info['size'],info['grid'],info['origin'],data)
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for what in out.keys():
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if file['name'] == 'STDIN':
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