86 lines
3.2 KiB
Python
Executable File
86 lines
3.2 KiB
Python
Executable File
#!/usr/bin/env python3
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import os
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import sys
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from io import StringIO
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from optparse import OptionParser
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from scipy import ndimage
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import numpy as np
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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def taintedNeighborhood(stencil,trigger=[],size=1):
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me = stencil[stencil.shape[0]//2]
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if len(trigger) == 0:
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return np.any(stencil != me)
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if me in trigger:
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trigger = set(trigger)
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trigger.remove(me)
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trigger = list(trigger)
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return np.any(np.in1d(stencil,np.array(trigger)))
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
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Offset microstructure index for points which see a microstructure different from themselves
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(or listed as triggers) within a given (cubic) vicinity, i.e. within the region close to a grain/phase boundary.
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""", version = scriptID)
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parser.add_option('-v', '--vicinity',
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dest = 'vicinity',
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type = 'int', metavar = 'int',
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help = 'voxel distance checked for presence of other microstructure [%default]')
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parser.add_option('-o', '--offset',
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dest='offset',
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type = 'int', metavar = 'int',
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help='offset (positive or negative) to tag microstructure indices, defaults to max microstructure index')
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parser.add_option('-t', '--trigger',
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dest = 'trigger',
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action = 'extend', metavar = '<int LIST>',
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help = 'list of microstructure indices triggering a change')
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parser.add_option('-n', '--nonperiodic',
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dest = 'mode',
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action = 'store_const', const = 'nearest',
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help = 'assume geometry to be non-periodic')
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parser.set_defaults(vicinity = 1,
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trigger = [],
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mode = 'wrap',
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)
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(options, filenames) = parser.parse_args()
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options.trigger = np.array(options.trigger, dtype=int)
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if filenames == []: filenames = [None]
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for name in filenames:
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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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offset = np.nanmax(geom.microstructure) if options.offset is None else options.offset
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damask.util.croak(geom.update(np.where(ndimage.filters.generic_filter(
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geom.microstructure,
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taintedNeighborhood,
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size=1+2*options.vicinity,mode=options.mode,
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extra_arguments=(),
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extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}),
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geom.microstructure + offset,geom.microstructure)))
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geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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geom.to_file(sys.stdout if name is None else name,pack=False)
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