#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,numpy,damask
from optparse import OptionParser, Option
scriptID = '$Id$'
scriptName = scriptID.split()[1]
# -----------------------------
class extendableOption(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
#--------------------------------------------------------------------------------------------------
synonyms = {
'grid': ['resolution'],
'size': ['dimension'],
}
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=extendableOption, usage='%prog options [file[s]]', description = """
Create seed file taking microstructure indices from given geom file but excluding black-listed grains.
Examples:
""" + string.replace(scriptID,'\n','\\n')
)
parser.add_option('-w','--white', dest='whitelist', action='extend', type='string', \
help='white list of grain IDs', metavar='<LIST>')
parser.add_option('-b','--black', dest='blacklist', action='extend', type='string', \
help='black list of grain IDs', metavar='<LIST>')
parser.set_defaults(whitelist = [])
parser.set_defaults(blacklist = [])
(options,filenames) = parser.parse_args()
options.whitelist = map(int,options.whitelist)
options.blacklist = map(int,options.blacklist)
#--- 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(os.path.splitext(name)[0]+'.seeds','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')
theTable = damask.ASCIItable(file['input'],file['output'],labels = False,buffered = False)
theTable.head_read()
#--- interpret header ----------------------------------------------------------------------------
info = {
'grid': numpy.zeros(3,'i'),
'size': numpy.zeros(3,'d'),
'origin': numpy.zeros(3,'d'),
'homogenization': 0,
'microstructures': 0,
}
newInfo = {
'grid': numpy.zeros(3,'i'),
'origin': numpy.zeros(3,'d'),
'microstructures': 0,
}
extra_header = []
for header in theTable.info:
headitems = map(str.lower,header.split())
if len(headitems) == 0: continue # skip blank lines
for synonym,alternatives in synonyms.iteritems():
if headitems[0] in alternatives: headitems[0] = synonym
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:
extra_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')
continue
if numpy.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
continue
if 'origin' not in info:
info['origin'] = numpy.zeros(3)
#--- read data ------------------------------------------------------------------------------------
microstructure = numpy.zeros(info['grid'].prod(),'i') # initialize as flat array
i = 0
while theTable.data_read():
items = theTable.data
if len(items) > 2:
if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
else: items = map(int,items)
else: items = map(int,items)
s = len(items)
microstructure[i:i+s] = items
i += s
# ------------------------------------------ assemble header ---------------------------------------
theTable.info = [
scriptID,
"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
"size\tx %i\ty %i\tz %i"%(info['size'][0],info['size'][1],info['size'][2],),
"origin\tx %i\ty %i\tz %i"%(info['origin'][0],info['origin'][1],info['origin'][2],),
]
theTable.labels_clear()
theTable.labels_append(['x','y','z','microstructure']) # implicitly switching label processing/writing on
theTable.head_write()
#--- filtering of grain voxels ------------------------------------------------------------------------------------
theTable.data_clear()
i = 0
outputDead = False
coord = numpy.zeros(3,'d')
for coord[2] in xrange(info['grid'][2]):
for coord[1] in xrange(info['grid'][1]):
for coord[0] in xrange(info['grid'][0]):
if (options.whitelist == [] and options.blacklist == []) or \
(options.whitelist != [] and microstructure[i] in options.whitelist) or \
(options.blacklist != [] and microstructure[i] not in options.blacklist):
theTable.data = list((coord+0.5)/info['grid'])+[microstructure[i]]
outputDead = not theTable.data_write()
i += 1
if outputDead: break
if outputDead: break
if outputDead: break
# ------------------------------------------ output result ---------------------------------------
outputDead or theTable.output_flush() # just in case of buffered ASCII table
file['input'].close() # close input ASCII table
if file['name'] != 'STDIN':
file['output'].close() # close output ASCII table