179 lines
7.4 KiB
Python
Executable File
179 lines
7.4 KiB
Python
Executable File
#!/usr/bin/env python
|
|
# -*- coding: UTF-8 no BOM -*-
|
|
|
|
import os,sys,string,itertools,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 by taking microstructure indices from given ASCIItable column.
|
|
White and black-listing of microstructure indices is possible.
|
|
|
|
Examples:
|
|
--white 1,2,5 --index grainID isolates grainID entries of value 1, 2, and 5;
|
|
--black 1 --index grainID takes all grainID entries except for value 1.
|
|
""" + string.replace(scriptID,'\n','\\n')
|
|
)
|
|
|
|
|
|
parser.add_option('-p', '--positions', dest='pos', type='string',
|
|
help = 'coordinate label')
|
|
parser.add_option('-i', '--index', dest='index', type='string',
|
|
help = 'microstructure index label')
|
|
parser.add_option('-w','--white', dest='whitelist', action='extend', type='string', \
|
|
help='white list of microstructure indices', metavar='<LIST>')
|
|
parser.add_option('-b','--black', dest='blacklist', action='extend', type='string', \
|
|
help='black list of microstructure indices', metavar='<LIST>')
|
|
|
|
parser.set_defaults(pos = 'pos')
|
|
parser.set_defaults(index = 'microstructure')
|
|
parser.set_defaults(whitelist = [])
|
|
parser.set_defaults(blacklist = [])
|
|
|
|
(options,filenames) = parser.parse_args()
|
|
|
|
datainfo = { # list of requested labels per datatype
|
|
'scalar': {'len':1,
|
|
'label':[]},
|
|
'vector': {'len':3,
|
|
'label':[]},
|
|
}
|
|
|
|
if options.pos != None: datainfo['vector']['label'] += [options.pos]
|
|
if options.index != None: datainfo['scalar']['label'] += [options.index]
|
|
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'],buffered = False)
|
|
theTable.head_read()
|
|
|
|
# --------------- figure out columns to process
|
|
active = {}
|
|
column = {}
|
|
head = []
|
|
|
|
for datatype,info in datainfo.items():
|
|
for label in info['label']:
|
|
foundIt = False
|
|
for key in ['1_'+label,label]:
|
|
if key in theTable.labels:
|
|
foundIt = True
|
|
if datatype not in active: active[datatype] = []
|
|
if datatype not in column: column[datatype] = {}
|
|
active[datatype].append(label)
|
|
column[datatype][label] = theTable.labels.index(key) # remember columns of requested data
|
|
if not foundIt:
|
|
file['croak'].write('column %s not found...\n'%label)
|
|
break
|
|
|
|
|
|
# ------------------------------------------ process data ---------------------------------------
|
|
|
|
theTable.data_readArray(list(itertools.chain.from_iterable(map(lambda x:[x+i for i in range(datainfo['vector']['len'])],
|
|
[column['vector'][label] for label in active['vector']]))) +
|
|
[column['scalar'][label] for label in active['scalar']])
|
|
|
|
#--- finding bounding box ------------------------------------------------------------------------------------
|
|
boundingBox = numpy.array((numpy.amin(theTable.data[:,0:3],axis=0),numpy.amax(theTable.data[:,0:3],axis=0)))
|
|
|
|
#--- rescaling coordinates ------------------------------------------------------------------------------------
|
|
theTable.data[:,0:3] -= boundingBox[0,:]
|
|
theTable.data[:,0:3] /= boundingBox[1,:]-boundingBox[0,:]
|
|
|
|
|
|
#--- filtering of grain voxels ------------------------------------------------------------------------------------
|
|
mask = numpy.logical_and(\
|
|
numpy.ones_like(theTable.data[:,3],bool) \
|
|
if options.whitelist == [] \
|
|
else numpy.in1d(theTable.data[:,3].ravel(), options.whitelist).reshape(theTable.data[:,3].shape),
|
|
numpy.ones_like(theTable.data[:,3],bool) \
|
|
if options.blacklist == [] \
|
|
else numpy.invert(numpy.in1d(theTable.data[:,3].ravel(), options.blacklist).reshape(theTable.data[:,3].shape))
|
|
)
|
|
theTable.data = theTable.data[mask]
|
|
|
|
# ------------------------------------------ output result ---------------------------------------
|
|
|
|
# ------------------------------------------ assemble header ---------------------------------------
|
|
|
|
theTable.info = [
|
|
scriptID,
|
|
'size %s'%(' '.join(list(itertools.chain.from_iterable(zip(['x','y','z'],
|
|
map(str,boundingBox[1,:]-boundingBox[0,:])))))),
|
|
]
|
|
theTable.labels_clear()
|
|
theTable.labels_append(['x','y','z','microstructure']) # implicitly switching label processing/writing on
|
|
theTable.head_write()
|
|
|
|
theTable.data_writeArray()
|
|
theTable.output_flush()
|
|
|
|
file['input'].close() # close input ASCII table
|
|
if file['name'] != 'STDIN':
|
|
file['output'].close() # close output ASCII table
|