DAMASK_EICMD/processing/pre/geom_vicinityOffset.py

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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'],
'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])
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if numpy.all(info['resolution'] == 0):
file['croak'].write('no resolution info found.\n')
continue
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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'])