use existing geom file and produce seed points from each voxel (filtering possible)
This commit is contained in:
Philip Eisenlohr
parent
c99ca8b0ee
commit
eda9076157
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#!/usr/bin/env python
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import os,sys,string,numpy,damask
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from optparse import OptionParser, Option
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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# -----------------------------
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class extendableOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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synonyms = {
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'grid': ['resolution'],
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'size': ['dimension'],
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}
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'grid': lambda x: int(x),
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'size': lambda x: float(x),
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'origin': lambda x: float(x),
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'homogenization': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
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Create seed file taking microstructure indices from given geom file but excluding black-listed grains.
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Examples:
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-w','--white', dest='whitelist', action='extend', type='string', \
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help='white list of column labels (a,b,c,...)', metavar='<LIST>')
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parser.add_option('-b','--black', dest='blacklist', action='extend', type='string', \
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help='black list of column labels (a,b,c,...)', metavar='<LIST>')
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parser.set_defaults(whitelist = [])
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parser.set_defaults(blacklist = [])
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(options,filenames) = parser.parse_args()
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options.whitelist = map(int,options.whitelist)
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options.blacklist = map(int,options.blacklist)
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#--- setup file handles --------------------------------------------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN',
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'input':sys.stdin,
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'output':sys.stdout,
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'croak':sys.stderr,
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})
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else:
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name,
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'input':open(name),
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'output':open(os.path.splitext(name)[0]+'.seeds','w'),
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'croak':sys.stdout,
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})
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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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theTable = damask.ASCIItable(file['input'],file['output'],labels=False,buffered=False)
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theTable.head_read()
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#--- interpret header ----------------------------------------------------------------------------
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info = {
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'grid': numpy.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'homogenization': 0,
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'microstructures': 0,
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}
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newInfo = {
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'grid': numpy.zeros(3,'i'),
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'origin': numpy.zeros(3,'d'),
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'microstructures': 0,
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}
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extra_header = []
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for header in theTable.info:
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headitems = map(str.lower,header.split())
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if len(headitems) == 0: continue # skip blank lines
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for synonym,alternatives in synonyms.iteritems():
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if headitems[0] in alternatives: headitems[0] = synonym
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if headitems[0] in mappings.keys():
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if headitems[0] in identifiers.keys():
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for i in xrange(len(identifiers[headitems[0]])):
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info[headitems[0]][i] = \
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mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
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else:
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info[headitems[0]] = mappings[headitems[0]](headitems[1])
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else:
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extra_header.append(header)
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file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n'%info['microstructures'])
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if numpy.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
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continue
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
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continue
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(info['grid'].prod(),'i') # initialize as flat array
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i = 0
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theTable.data_rewind()
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while theTable.data_read():
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items = theTable.data
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if len(items) > 2:
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if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
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elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
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else: items = map(int,items)
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else: items = map(int,items)
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s = len(items)
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microstructure[i:i+s] = items
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i += s
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# ------------------------------------------ assemble header ---------------------------------------
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theTable.info = [
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scriptID,
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"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
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]
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theTable.labels_clear()
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theTable.labels_append(['x','y','z','microstructure']) # implicitly switching label processing/writing on
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theTable.head_write()
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#--- filtering of grain voxels ------------------------------------------------------------------------------------
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theTable.data_clear()
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i = 0
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coord = numpy.zeros(3,'d')
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for coord[2] in xrange(info['grid'][2]):
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for coord[1] in xrange(info['grid'][1]):
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for coord[0] in xrange(info['grid'][0]):
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if (options.whitelist == [] and options.blacklist == []) or \
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(options.whitelist != [] and microstructure[i] in options.whitelist) or \
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(options.blacklist != [] and microstructure[i] not in options.blacklist):
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theTable.data = list((coord+0.5)/info['grid']*info['size'])+[microstructure[i]]
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theTable.data_write()
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i += 1
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# ------------------------------------------ output result ---------------------------------------
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file['input'].close() # close input ASCII table
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if file['name'] != 'STDIN':
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file['output'].close() # close output ASCII table
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