DAMASK_EICMD/processing/pre/geom_vicinityOffset.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,math
import numpy as np
from scipy import ndimage
from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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#--------------------------------------------------------------------------------------------------
class extendedOption(Option):
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#--------------------------------------------------------------------------------------------------
# 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)
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#--------------------------------------------------------------------------------------------------
# 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=damask.extendableOption, 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.
""", version = scriptID)
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parser.add_option('-v', '--vicinity', dest='vicinity', type='int', metavar='int', \
help='voxel distance checked for presence of other microstructure [%default]')
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parser.add_option('-m', '--microstructureoffset', dest='offset', type='int', metavar='int', \
help='offset (positive or negative) for tagged microstructure. '+
'"0" selects maximum microstructure index [%default]')
parser.set_defaults(vicinity = 1)
parser.set_defaults(offset = 0)
(options, filenames) = parser.parse_args()
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#--- 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,
})
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#--- loop over input files ------------------------------------------------------------------------
for file in files:
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file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\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,
}
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newInfo = {
'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)
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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'])
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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
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#--- 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 ------------------------------------------------------------------------------------
microstructure = microstructure.reshape(info['grid'],order='F')
if options.offset == 0:
options.offset = microstructure.max()
microstructure = numpy.where(ndimage.filters.maximum_filter(microstructure,size=1+2*options.vicinity,mode='wrap') ==
ndimage.filters.minimum_filter(microstructure,size=1+2*options.vicinity,mode='wrap'),
microstructure, microstructure + options.offset)
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newInfo['microstructures'] = microstructure.max()
if (newInfo['microstructures'] != info['microstructures']):
file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
#--- write header ---------------------------------------------------------------------------------
theTable.labels_clear()
theTable.info_clear()
theTable.info_append(extra_header+[
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scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['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()
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# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
theTable.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
theTable.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
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#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
table.input_close()
table.output_close()
os.rename(file['name']+'_tmp',file['name'])