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 2011-10-11 17:35:53 +00:00
parent 98c9bf9c15
commit ba0488638b
1 changed files with 154 additions and 0 deletions

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,math,numpy
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
# -----------------------------
class extendedOption(Option):
# -----------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
# ----------------------- MAIN -------------------------------
identifiers = {
'resolution': ['a','b','c'],
'dimension': ['x','y','z'],
}
mappings = {
'resolution': lambda x: int(x),
'dimension': lambda x: float(x),
}
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
Offset microstructure index for points which see a microstructure different from themselves within a given (cubic) vicinity,
i.e. within the region close to a grain/phase boundary.
""" + string.replace('$Id: spectral_geomCheck 994 2011-09-05 13:38:10Z MPIE\p.eisenlohr $','\n','\\n')
)
parser.add_option('-v', '--vicinity', dest='vicinity', type='int', \
help='voxel distance checked for presence of other microstructure')
parser.add_option('-o', '--offset', dest='offset', type='int', \
help='integer offset for tagged microstructure')
parser.set_defaults(vicinity = 1)
(options, filenames) = parser.parse_args()
# ------------------------------------------ setup file handles ---------------------------------------
files = []
if filenames == []:
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
else:
for name in filenames:
if os.path.exists(name):
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w')})
# ------------------------------------------ loop over input files ---------------------------------------
for file in files:
if file['name'] != 'STDIN': print file['name']
# get labels by either read the first row, or - if keyword header is present - the last line of the header
firstline = file['input'].readline()
m = re.search('(\d+)\s*head', firstline.lower())
if m:
headerlines = int(m.group(1))
headers = [firstline]+[file['input'].readline() for i in range(headerlines)]
else:
headerlines = 1
headers = firstline
content = file['input'].readlines()
file['input'].close()
resolution = [0,0,0]
dimension = [0.0,0.0,0.0]
for header in headers:
headitems = header.split()
if headitems[0] == 'resolution': # located resolution entry
for i in xrange(3):
resolution[i] = mappings['resolution'](headitems[headitems.index(identifiers['resolution'][i])+1])
if headitems[0] == 'dimension': # located dimension entry
for i in xrange(3):
dimension[i] = mappings['dimension'](headitems[headitems.index(identifiers['dimension'][i])+1])
if resolution == [0,0,0]:
print 'no resolution info found.'
sys.exit(1)
if dimension == [0.0,0.0,0.0]:
print 'no dimension info found.'
sys.exit(1)
if file['name'] != 'STDIN':
print 'resolution: %s'%(' x '.join(map(str,resolution)))
print 'dimension: %s'%(' x '.join(map(str,dimension)))
microstructure = numpy.zeros(resolution,'i')
i = 0
for line in content:
for item in map(int,line.split()):
microstructure[i%resolution[0],(i/resolution[0])%resolution[1],i/resolution[0]/resolution[1]] = item
i += 1
formatwidth = int(math.floor(math.log10(microstructure.max())))
for x in xrange(resolution[0]):
for y in xrange(resolution[1]):
for z in xrange(resolution[2]):
me = microstructure[x,y,z]
breaker = False
for dx in xrange(-options.vicinity,options.vicinity+1):
for dy in xrange(-options.vicinity,options.vicinity+1):
for dz in xrange(-options.vicinity,options.vicinity+1):
they = microstructure[(x+dx)%resolution[0],(y+dy)%resolution[1],(z+dz)%resolution[2]]
if they != me and they != me+options.offset: # located alien microstructure in vicinity
microstructure[x,y,z] += options.offset # tag myself as close to aliens!
breaker = True
break
if breaker: break
if breaker: break
# ------------------------------------------ assemble header ---------------------------------------
output = ''.join(headers)
# ------------------------------------- regenerate texture information ----------------------------------
for z in xrange(resolution[2]):
for y in xrange(resolution[2]):
output += ' '.join(map(lambda x: ('%%%ii'%formatwidth)%x, microstructure[:,y,z])) + '\n'
output += '\n'
# ------------------------------------------ output result ---------------------------------------
file['output'].write(output)
if file['name'] != 'STDIN':
file['output'].close
os.rename(file['name']+'_tmp',file['name'])