#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,math,numpy
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
scriptID = '$Id$'
scriptName = scriptID.split()[1]
#--------------------------------------------------------------------------------------------------
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 = {
'grid': ['a','b','c'],
'size': ['x','y','z'],
'origin': ['x','y','z'],
}
mappings = {
'grid': lambda x: int(x),
'size': lambda x: float(x),
'origin': lambda x: float(x),
'homogenization': lambda x: int(x),
'microstructures': 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(scriptID,'\n','\\n')
)
parser.add_option('-v', '--vicinity', dest='vicinity', type='int', \
help='voxel distance checked for presence of other microstructure [%default]')
parser.add_option('-m', '--microstructureoffset', dest='offset', type='int', \
help='offset (positive or negative) for tagged microstructure. '+
'"0" selects maximum microstructure index [%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('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
firstline = file['input'].readline()
m = re.search('(\d+)\s*head', firstline.lower())
if m:
headerlines = int(m.group(1))
headers = [file['input'].readline() for i in range(headerlines)]
else:
headerlines = 1
headers = firstline
content = file['input'].readlines()
file['input'].close()
#--- interprete header ----------------------------------------------------------------------------
info = {
'grid': numpy.zeros(3,'i'),
'size': numpy.zeros(3,'d'),
'origin': numpy.zeros(3,'d'),
'microstructures': 0,
'homogenization': 0
}
newInfo = {
'microstructures': 0,
}
new_header = []
new_header.append(scriptID+'\n')
for header in headers:
headitems = map(str.lower,header.split())
if headitems[0] == 'resolution': headitems[0] = 'grid'
if headitems[0] == 'dimension': headitems[0] = 'size'
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])
else:
new_header.append(header)
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
'homogenization: %i\n'%info['homogenization'] + \
'microstructures: %i\n'%info['microstructures'])
if numpy.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n')
sys.exit()
if numpy.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
sys.exit()
#--- read data ------------------------------------------------------------------------------------
microstructure = numpy.zeros(info['grid'],'i')
i = 0
for line in content:
for item in map(int,line.split()):
microstructure[i%info['grid'][0],
(i/info['grid'][0])%info['grid'][1],
i/info['grid'][0] /info['grid'][1]] = item
i += 1
if options.offset == 0:
options.offset = microstructure.max()
formatwidth = 1+int(math.floor(math.log10(abs(microstructure.max()+options.offset))))
#--- search ---------------------------------------------------------------------------------------
for x in xrange(info['grid'][0]):
for y in xrange(info['grid'][1]):
for z in xrange(info['grid'][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['grid'][0],(y+dy)%info['grid'][1],(z+dz)%info['grid'][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
newInfo['microstructures'] = microstructure.max()
if (newInfo['microstructures'] != info['microstructures']):
file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
# --- assemble header -----------------------------------------------------------------------------
new_header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2]))
new_header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][0]))
new_header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2]))
new_header.append("microstructures\t%i\n"%newInfo['microstructures'])
new_header.append("homogenization\t%i\n"%info['homogenization'])
file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
# --- write microstructure information ------------------------------------------------------------
for z in xrange(info['grid'][2]):
for y in xrange(info['grid'][1]):
file['output'].write({True:' ',False:'\n'}[options.twoD].
join(map(lambda x: str(x).rjust(formatwidth), microstructure[:,y,z])) + '\n')
file['output'].write('\n')
#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
file['output'].close()
os.rename(file['name']+'_tmp',file['name'])