183 lines
6.7 KiB
Python
Executable File
183 lines
6.7 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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# -----------------------------
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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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# ----------------------- 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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'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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'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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Offset microstructure index for points which see a microstructure different from themselves within a given (cubic) vicinity,
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i.e. within the region close to a grain/phase boundary.
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('-v', '--vicinity', dest='vicinity', type='int', \
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help='voxel distance checked for presence of other microstructure [%default]')
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parser.add_option('-o', '--offset', dest='offset', type='int', \
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help='integer offset for tagged microstructure [%default]')
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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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parser.set_defaults(vicinity = 1)
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parser.set_defaults(offset = 0)
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parser.set_defaults(twoD = False)
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(options, filenames) = parser.parse_args()
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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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# get labels by either read the first row, or - if keyword header is present - the last line of the header
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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 = [firstline]+[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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info = {'resolution': numpy.array([0,0,0]),
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'dimension': numpy.array([0.0,0.0,0.0]),
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'origin': numpy.array([0.0,0.0,0.0]),
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'homogenization': 1,
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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] 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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if numpy.all(info['resolution'] == 0):
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file['croak'].write('no resolution 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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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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'homogenization: %i\n'%info['homogenization'])
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microstructure = numpy.zeros(info['resolution'],'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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microstructure[i%info['resolution'][0],
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(i/info['resolution'][0])%info['resolution'][1],
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i/info['resolution'][0] /info['resolution'][1]] = item
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i += 1
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formatwidth = 1+int(math.floor(math.log10(abs(microstructure.max()+options.offset))))
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if options.offset == 0:
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options.offset = microstructure.max()
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file['croak'].write('offset: %i\n'%options.offset)
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for x in xrange(info['resolution'][0]):
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for y in xrange(info['resolution'][1]):
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for z in xrange(info['resolution'][2]):
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me = microstructure[x,y,z]
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breaker = False
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for dx in xrange(-options.vicinity,options.vicinity+1):
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for dy in xrange(-options.vicinity,options.vicinity+1):
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for dz in xrange(-options.vicinity,options.vicinity+1):
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they = microstructure[(x+dx)%info['resolution'][0],(y+dy)%info['resolution'][1],(z+dz)%info['resolution'][2]]
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if they != me and they != me+options.offset: # located alien microstructure in vicinity
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microstructure[x,y,z] += options.offset # tag myself as close to aliens!
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breaker = True
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break
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if breaker: break
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if breaker: break
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# ------------------------------------------ assemble header ---------------------------------------
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output = ''.join(headers)
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# ------------------------------------- regenerate texture information ----------------------------------
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for z in xrange(info['resolution'][2]):
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for y in xrange(info['resolution'][1]):
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output += {True:' ',False:'\n'}[options.twoD].join(map(lambda x: str(x).rjust(formatwidth), microstructure[:,y,z])) + '\n'
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output += '\n'
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# ------------------------------------------ output result ---------------------------------------
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file['output'].write(output)
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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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