#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,math,numpy
import damask
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
#--------------------------------------------------------------------------------------------------
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=extendedOption, usage='%prog options [file[s]]', description = """
Scales a geometry description independently in x, y, and z direction in terms of grid and/or size.
Either absolute values or relative factors (like "0.25x") can be used.
""" + string.replace(scriptID,'\n','\\n')
)
parser.add_option('-g', '--grid', dest='grid', type='string', nargs = 3, metavar = 'string string string', \
help='a,b,c grid of hexahedral box [unchanged]')
parser.add_option('-s', '--size', dest='size', type='string', nargs = 3, metavar = 'string string string', \
help='x,y,z size of hexahedral box [unchanged]')
parser.add_option('-r', '--renumber', dest='renumber', action='store_true', \
help='renumber microstructure indices from 1...N [%default]')
parser.set_defaults(renumber = False)
parser.set_defaults(grid = ['0','0','0'])
parser.set_defaults(size = ['0.0','0.0','0.0'])
(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')
theTable = damask.ASCIItable(file['input'],file['output'],labels=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'),
'size': numpy.zeros(3,'d'),
'microstructures': 0,
}
extra_header = []
for header in theTable.info:
headitems = map(str.lower,header.split())
if len(headitems) == 0: continue
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
#--- read data ------------------------------------------------------------------------------------
microstructure = numpy.zeros(info['grid'].prod(),'i')
i = 0
theTable.data_rewind()
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
#--- do work ------------------------------------------------------------------------------------
newInfo['grid'] = numpy.array([{True:round(o*float(n.translate(None,'xX'))), False: round(float(n.translate(None,'xX')))}[n[-1].lower() == 'x'] for o,n in zip(info['grid'],options.grid)],'i')
newInfo['size'] = numpy.array([{True: o*float(n.translate(None,'xX')) , False: float(n.translate(None,'xX')) }[n[-1].lower() == 'x'] for o,n in zip(info['size'],options.size)],'d')
newInfo['grid'] = numpy.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
newInfo['size'] = numpy.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
multiplicity = []
for j in xrange(3):
multiplicity.append([])
last = 0
for i in xrange(info['grid'][j]):
this = int((i+1)*float(newInfo['grid'][j])/info['grid'][j])
multiplicity[j].append(this-last)
last = this
microstructure = microstructure.reshape(info['grid'],order='F')
microstructure = numpy.repeat(
numpy.repeat(
numpy.repeat(microstructure,multiplicity[0], axis=0),
multiplicity[1], axis=1),
multiplicity[2], axis=2)
# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
# http://stackoverflow.com/questions/10741346/numpy-frequency-counts-for-unique-values-in-an-array
if options.renumber:
newID=0
for microstructureID,count in enumerate(numpy.bincount(microstructure.reshape(newInfo['grid'].prod()))):
if count != 0:
newID+=1
microstructure=numpy.where(microstructure==microstructureID,newID,microstructure).reshape(microstructure.shape)
newInfo['microstructures'] = microstructure.max()
#--- report ---------------------------------------------------------------------------------------
if (any(newInfo['grid'] != info['grid'])):
file['croak'].write('--> grid a b c: %s\n'%(' x '.join(map(str,newInfo['grid']))))
if (any(newInfo['size'] != info['size'])):
file['croak'].write('--> size x y z: %s\n'%(' x '.join(map(str,newInfo['size']))))
if (newInfo['microstructures'] != info['microstructures']):
file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
if numpy.any(newInfo['grid'] < 1):
file['croak'].write('invalid new grid a b c.\n')
continue
if numpy.any(newInfo['size'] <= 0.0):
file['croak'].write('invalid new size x y z.\n')
continue
#--- write header ---------------------------------------------------------------------------------
theTable.labels_clear()
theTable.info_clear()
theTable.info_append(extra_header+[
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta %i\tb %i\tc %i"%(newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2],),
"size\tx %f\ty %f\tz %f"%(newInfo['size'][0],newInfo['size'][1],newInfo['size'][2],),
"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
"homogenization\t%i"%info['homogenization'],
"microstructures\t%i"%(newInfo['microstructures']),
])
theTable.head_write()
theTable.output_flush()
# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
theTable.data = microstructure.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose()
theTable.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
file['input'].close()
file['output'].close()
os.rename(file['name']+'_tmp',file['name'])