190 lines
8.0 KiB
Python
Executable File
190 lines
8.0 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,re,math,numpy
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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from scipy import ndimage
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#--------------------------------------------------------------------------------------------------
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class extendedOption(Option):
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#--------------------------------------------------------------------------------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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identifiers = {
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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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'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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}
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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Smoothens out interface roughness by simulated curvature flow.
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This is achieved by the diffusion of each initially sharply bounded grain volume within the periodic domain for a given time,
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i.e. up to a diffusion distance of sqrt(t) voxels.
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The final geometry is assembled by selecting at each voxel that grain index for which the concentration is largest.
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('-t', '--time', dest='t', type='int', \
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help='time for curvature flow [%default]')
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parser.add_option('-b', '--black', dest='black', action='extend', type='string', \
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help='indices of stationary microstructures', metavar='<LIST>')
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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 [%default]')
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parser.set_defaults(t = 1)
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parser.set_defaults(black = [])
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parser.set_defaults(twoD = False)
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(options, filenames) = parser.parse_args()
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options.black = map(int,options.black)
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#--- setup file handles --------------------------------------------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN',
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'input':sys.stdin,
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'output':sys.stdout,
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'croak':sys.stderr,
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})
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else:
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name,
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'input':open(name),
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'output':open(name+'_tmp','w'),
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'croak':sys.stdout,
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})
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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
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firstline = file['input'].readline()
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m = re.search('(\d+)\s*head', firstline.lower())
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if m:
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headerlines = int(m.group(1))
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headers = [file['input'].readline() for i in range(headerlines)]
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else:
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headerlines = 1
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headers = firstline
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content = file['input'].readlines()
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file['input'].close()
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#--- interprete header ----------------------------------------------------------------------------
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info = {
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'grid': numpy.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'microstructures': 0,
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'homogenization': 0,
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}
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new_header = []
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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] = \
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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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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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if numpy.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
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sys.exit()
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
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sys.exit()
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(info['grid'],'i')
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i = 0
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for line in content:
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items = line.split()
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if len(items) > 2:
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if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
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elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
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else: items = map(int,items)
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else: items = map(int,items)
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for item in items:
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microstructure[i%info['grid'][0],
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(i/info['grid'][0])%info['grid'][1],
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i/info['grid'][0] /info['grid'][1]] = item
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i += 1
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#--- initialize helper data -----------------------------------------------------------------------
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winner = numpy.zeros(info['grid'],'i')
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diffusedMax = numpy.zeros(info['grid'])
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#--- diffuse each grain separately ----------------------------------------------------------------
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for theGrain in xrange(1,1+numpy.amax(microstructure)):
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diffused = ndimage.filters.gaussian_filter((microstructure == theGrain).astype(float),\
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{True:0.0,False:numpy.sqrt(options.t)}[theGrain in options.black],\
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mode='wrap')
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winner = numpy.where(diffused > diffusedMax, theGrain, winner)
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diffusedMax = numpy.where(diffused > diffusedMax, diffused, diffusedMax)
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microstructure = winner
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# --- assemble header -----------------------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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new_header.append('$Id$\n')
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new_header.append("grid\ta %i\tb %i\tc %i\n"%(
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info['grid'][0],info['grid'][1],info['grid'][2]))
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new_header.append("size\tx %f\ty %f\tz %f\n"%(
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info['size'][0],info['size'][1],info['size'][2]))
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new_header.append("origin\tx %f\ty %f\tz %f\n"%(
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info['origin'][0],info['origin'][1],info['origin'][2]))
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new_header.append("homogenization\t%i\n"%info['homogenization'])
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new_header.append("microstructures\t%i\n"%info['microstructures'])
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file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
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# --- write microstructure information ------------------------------------------------------------
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for z in xrange(info['grid'][2]):
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for y in xrange(info['grid'][1]):
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file['output'].write({True:' ',False:'\n'}[options.twoD].join(map(lambda x: \
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('%%%ii'%formatwidth)%x, microstructure[:,y,z])) + '\n')
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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file['output'].close()
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os.rename(file['name']+'_tmp',file['name'])
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