alter a spectral geom file such that any voxel that sees within a given vicinity a different microstructure than itself gets offset by a given value. this allows to identify/isolate grain boundary regions...
This commit is contained in:
Philip Eisenlohr
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98c9bf9c15
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ba0488638b
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#!/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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}
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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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}
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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: spectral_geomCheck 994 2011-09-05 13:38:10Z MPIE\p.eisenlohr $','\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')
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parser.add_option('-o', '--offset', dest='offset', type='int', \
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help='integer offset for tagged microstructure')
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parser.set_defaults(vicinity = 1)
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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', 'input':sys.stdin, 'output':sys.stdout})
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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, 'input':open(name), 'output':open(name+'_tmp','w')})
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# ------------------------------------------ loop over input files ---------------------------------------
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for file in files:
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if file['name'] != 'STDIN': print file['name']
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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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resolution = [0,0,0]
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dimension = [0.0,0.0,0.0]
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for header in headers:
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headitems = header.split()
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if headitems[0] == 'resolution': # located resolution entry
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for i in xrange(3):
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resolution[i] = mappings['resolution'](headitems[headitems.index(identifiers['resolution'][i])+1])
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if headitems[0] == 'dimension': # located dimension entry
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for i in xrange(3):
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dimension[i] = mappings['dimension'](headitems[headitems.index(identifiers['dimension'][i])+1])
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if resolution == [0,0,0]:
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print 'no resolution info found.'
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sys.exit(1)
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if dimension == [0.0,0.0,0.0]:
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print 'no dimension info found.'
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sys.exit(1)
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if file['name'] != 'STDIN':
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print 'resolution: %s'%(' x '.join(map(str,resolution)))
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print 'dimension: %s'%(' x '.join(map(str,dimension)))
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microstructure = numpy.zeros(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%resolution[0],(i/resolution[0])%resolution[1],i/resolution[0]/resolution[1]] = item
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i += 1
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formatwidth = int(math.floor(math.log10(microstructure.max())))
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for x in xrange(resolution[0]):
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for y in xrange(resolution[1]):
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for z in xrange(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)%resolution[0],(y+dy)%resolution[1],(z+dz)%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(resolution[2]):
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for y in xrange(resolution[2]):
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output += ' '.join(map(lambda x: ('%%%ii'%formatwidth)%x, 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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