DAMASK_EICMD/processing/pre/geom_vicinityOffset.py

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#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
import numpy as np
from scipy import ndimage
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def taintedNeighborhood(stencil,trigger=[],size=1):
me = stencil[stencil.shape[0]//2]
if len(trigger) == 0:
return np.any(stencil != me)
if me in trigger:
trigger = set(trigger)
trigger.remove(me)
trigger = list(trigger)
return np.any(np.in1d(stencil,np.array(trigger)))
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#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Offset microstructure index for points which see a microstructure different from themselves
(or listed as triggers) within a given (cubic) vicinity, i.e. within the region close to a grain/phase boundary.
""", version = scriptID)
parser.add_option('-v', '--vicinity',
dest = 'vicinity',
type = 'int', metavar = 'int',
help = 'voxel distance checked for presence of other microstructure [%default]')
parser.add_option('-m', '--microstructureoffset',
dest='offset',
type = 'int', metavar = 'int',
help = 'offset (positive or negative) for tagged microstructure indices. '+
'"0" selects maximum microstructure index [%default]')
parser.add_option('-t', '--trigger',
action = 'extend', dest = 'trigger', metavar = '<int LIST>',
help = 'list of microstructure indices triggering a change')
parser.add_option('-n', '--nonperiodic',
dest = 'mode',
action = 'store_const', const = 'nearest',
help = 'assume geometry to be non-periodic')
parser.set_defaults(vicinity = 1,
offset = 0,
trigger = [],
mode = 'wrap',
)
(options, filenames) = parser.parse_args()
options.trigger = np.array(options.trigger, dtype=int)
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False, labeled = False)
except: continue
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damask.util.report(scriptName,name)
# --- interpret header ----------------------------------------------------------------------------
table.head_read()
info,extra_header = table.head_getGeom()
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damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
])
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
if errors != []:
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damask.util.croak(errors)
table.close(dismiss = True)
continue
# --- read data ------------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F') # read microstructure
# --- do work ------------------------------------------------------------------------------------
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newInfo = {
'microstructures': 0,
}
if options.offset == 0: options.offset = microstructure.max()
microstructure = np.where(ndimage.filters.generic_filter(microstructure,
taintedNeighborhood,
size=1+2*options.vicinity,mode=options.mode,
extra_arguments=(),
extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}),
microstructure + options.offset,microstructure)
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newInfo['microstructures'] = microstructure.max()
# --- report ---------------------------------------------------------------------------------------
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if (newInfo['microstructures'] != info['microstructures']):
damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])
# --- write header ---------------------------------------------------------------------------------
table.labels_clear()
table.info_clear()
table.info_append(extra_header+[
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scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
"homogenization\t{homog}".format(homog=info['homogenization']),
"microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']),
])
table.head_write()
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# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table