183 lines
6.7 KiB
Python
Executable File
183 lines
6.7 KiB
Python
Executable File
#!/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'],
|
|
'origin': ['x','y','z'],
|
|
}
|
|
mappings = {
|
|
'resolution': lambda x: int(x),
|
|
'dimension': lambda x: float(x),
|
|
'origin': lambda x: float(x),
|
|
'homogenization': lambda x: int(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 [%default]')
|
|
parser.add_option('-o', '--offset', dest='offset', type='int', \
|
|
help='integer offset for tagged microstructure [%default]')
|
|
parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
|
|
help='output geom file with two-dimensional data arrangement')
|
|
|
|
parser.set_defaults(vicinity = 1)
|
|
parser.set_defaults(offset = 0)
|
|
parser.set_defaults(twoD = False)
|
|
|
|
(options, filenames) = parser.parse_args()
|
|
|
|
# ------------------------------------------ setup file handles ---------------------------------------
|
|
|
|
files = []
|
|
if filenames == []:
|
|
files.append({'name':'STDIN',
|
|
'input':sys.stdin,
|
|
'output':sys.stdout,
|
|
'croak':sys.stderr,
|
|
})
|
|
else:
|
|
for name in filenames:
|
|
if os.path.exists(name):
|
|
files.append({'name':name,
|
|
'input':open(name),
|
|
'output':open(name+'_tmp','w'),
|
|
'croak':sys.stdout,
|
|
})
|
|
|
|
|
|
# ------------------------------------------ loop over input files ---------------------------------------
|
|
|
|
for file in files:
|
|
if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
|
|
|
|
# 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()
|
|
|
|
info = {'resolution': numpy.array([0,0,0]),
|
|
'dimension': numpy.array([0.0,0.0,0.0]),
|
|
'origin': numpy.array([0.0,0.0,0.0]),
|
|
'homogenization': 1,
|
|
}
|
|
|
|
new_header = []
|
|
for header in headers:
|
|
headitems = map(str.lower,header.split())
|
|
if headitems[0] in mappings.keys():
|
|
if headitems[0] in identifiers.keys():
|
|
for i in xrange(len(identifiers[headitems[0]])):
|
|
info[headitems[0]][i] = \
|
|
mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
|
|
else:
|
|
info[headitems[0]] = mappings[headitems[0]](headitems[1])
|
|
|
|
if numpy.all(info['resolution'] == 0):
|
|
file['croak'].write('no resolution info found.\n')
|
|
continue
|
|
if numpy.all(info['dimension'] == 0.0):
|
|
file['croak'].write('no dimension info found.\n')
|
|
continue
|
|
|
|
file['croak'].write('resolution: %s\n'%(' x '.join(map(str,info['resolution']))) + \
|
|
'dimension: %s\n'%(' x '.join(map(str,info['dimension']))) + \
|
|
'origin: %s\n'%(' : '.join(map(str,info['origin']))) + \
|
|
'homogenization: %i\n'%info['homogenization'])
|
|
|
|
microstructure = numpy.zeros(info['resolution'],'i')
|
|
i = 0
|
|
for line in content:
|
|
for item in map(int,line.split()):
|
|
microstructure[i%info['resolution'][0],
|
|
(i/info['resolution'][0])%info['resolution'][1],
|
|
i/info['resolution'][0] /info['resolution'][1]] = item
|
|
i += 1
|
|
|
|
formatwidth = 1+int(math.floor(math.log10(abs(microstructure.max()+options.offset))))
|
|
if options.offset == 0:
|
|
options.offset = microstructure.max()
|
|
file['croak'].write('offset: %i\n'%options.offset)
|
|
|
|
for x in xrange(info['resolution'][0]):
|
|
for y in xrange(info['resolution'][1]):
|
|
for z in xrange(info['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)%info['resolution'][0],(y+dy)%info['resolution'][1],(z+dz)%info['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(info['resolution'][2]):
|
|
for y in xrange(info['resolution'][1]):
|
|
output += {True:' ',False:'\n'}[options.twoD].join(map(lambda x: str(x).rjust(formatwidth), 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'])
|