DAMASK_EICMD/processing/pre/geom_clean.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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from scipy import ndimage
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
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def mostFrequent(arr):
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unique, inverse = np.unique(arr, return_inverse=True)
return unique[np.argmax(np.bincount(inverse))]
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
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Smooth microstructure by selecting most frequent index within given stencil at each location.
""", version=scriptID)
parser.add_option('-s','--stencil',
dest = 'stencil',
type = 'int', metavar = 'int',
help = 'size of smoothing stencil [%default]')
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parser.set_defaults(stencil = 3)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
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geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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damask.util.croak(geom.update(ndimage.filters.generic_filter(
geom.microstructure,mostFrequent,
size=(options.stencil,)*3).astype(geom.microstructure.dtype)))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)