DAMASK_EICMD/processing/pre/seeds_fromGeom.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string
import numpy as np
from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
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 = """
Create seed file taking microstructure indices from given geom file but excluding black-listed grains.
""", version = scriptID)
parser.add_option('-w','--white', dest='whitelist', action='extend', \
help='white list of grain IDs', metavar='<LIST>')
parser.add_option('-b','--black', dest='blacklist', action='extend', \
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:
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file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
table = damask.ASCIItable(file['input'],file['output'],labels = False,buffered = False)
table.head_read()
#--- interpret header ----------------------------------------------------------------------------
info = {
'grid': np.zeros(3,'i'),
'size': np.zeros(3,'d'),
'origin': np.zeros(3,'d'),
'homogenization': 0,
'microstructures': 0,
}
newInfo = {
'grid': np.zeros(3,'i'),
'origin': np.zeros(3,'d'),
'microstructures': 0,
}
extra_header = []
for header in table.info:
headitems = map(str.lower,header.split())
if len(headitems) == 0: continue # skip blank lines
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 np.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n')
continue
if np.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
continue
if 'origin' not in info:
info['origin'] = np.zeros(3)
#--- read data ------------------------------------------------------------------------------------
microstructure = np.zeros(info['grid'].prod(),'i') # initialize as flat array
i = 0
while table.data_read():
items = table.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 ---------------------------------------
table.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],),
]
table.labels_clear()
table.labels_append(['1_coords','2_coords','3_coords','microstructure']) # implicitly switching label processing/writing on
table.head_write()
#--- filtering of grain voxels ------------------------------------------------------------------------------------
table.data_clear()
i = 0
outputDead = False
coord = np.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):
table.data = list((coord+0.5)/info['grid'])+[microstructure[i]]
outputDead = not table.data_write()
i += 1
if outputDead: break
if outputDead: break
if outputDead: break
# ------------------------------------------ output result ---------------------------------------
outputDead or table.output_flush() # just in case of buffered ASCII table
table.input_close() # close input ASCII table
if file['name'] != 'STDIN':
table.output_close() # close output ASCII table