DAMASK_EICMD/processing/pre/seeds_fromGeom.py

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#!/usr/bin/env python3
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import os
import sys
from io import StringIO
from optparse import OptionParser
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import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Create seed file taking microstructure indices from given geom file.
Indices can be black-listed or white-listed.
""", version = scriptID)
parser.add_option('-w',
'--white',
action = 'extend', metavar = '<int LIST>',
dest = 'whitelist',
help = 'whitelist of grain IDs')
parser.add_option('-b',
'--black',
action = 'extend', metavar = '<int LIST>',
dest = 'blacklist',
help = 'blacklist of grain IDs')
parser.set_defaults(whitelist = [],
blacklist = [],
)
(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]
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options.whitelist = [int(i) for i in options.whitelist]
options.blacklist = [int(i) for i in options.blacklist]
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for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
microstructure = geom.get_microstructure().reshape((-1,1),order='F')
mask = np.logical_and(np.in1d(microstructure,options.whitelist,invert=False) if options.whitelist else \
np.full(geom.grid.prod(),True,dtype=bool),
np.in1d(microstructure,options.blacklist,invert=True) if options.blacklist else \
np.full(geom.grid.prod(),True,dtype=bool))
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seeds = np.concatenate((damask.grid_filters.cell_coord0(geom.grid,geom.size).reshape(-1,3),
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microstructure),
axis=1)[mask]
comments = geom.comments \
+ [scriptID + ' ' + ' '.join(sys.argv[1:]),
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"grid\ta {}\tb {}\tc {}".format(*geom.grid),
"size\tx {}\ty {}\tz {}".format(*geom.size),
"origin\tx {}\ty {}\tz {}".format(*geom.origin),
"homogenization\t{}".format(geom.homogenization)]
table = damask.Table(seeds,{'pos':(3,),'microstructure':(1,)},comments)
table.to_ASCII(sys.stdout if name is None else \
os.path.splitext(name)[0]+'.seeds')