141 lines
5.9 KiB
Python
Executable File
141 lines
5.9 KiB
Python
Executable File
#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
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import numpy as np
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from scipy import ndimage
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from optparse import OptionParser
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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 [file[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('-m', '--microstructureoffset',
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dest='offset',
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type = 'int', metavar = 'int',
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help = 'offset (positive or negative) for tagged microstructure indices. '+
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'"0" selects maximum microstructure index [%default]')
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parser.add_option('-t', '--trigger',
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action = 'extend', dest = 'trigger', 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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offset = 0,
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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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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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buffered = False, labeled = False)
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except: continue
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damask.util.report(scriptName,name)
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# --- interpret header ----------------------------------------------------------------------------
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table.head_read()
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info,extra_header = table.head_getGeom()
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damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
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'size x y z: %s'%(' x '.join(map(str,info['size']))),
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'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
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'homogenization: %i'%info['homogenization'],
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'microstructures: %i'%info['microstructures'],
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])
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errors = []
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if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
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if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# --- read data ------------------------------------------------------------------------------------
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microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F') # read microstructure
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# --- do work ------------------------------------------------------------------------------------
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newInfo = {
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'microstructures': 0,
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}
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if options.offset == 0: options.offset = microstructure.max()
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microstructure = np.where(ndimage.filters.generic_filter(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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microstructure + options.offset,microstructure)
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newInfo['microstructures'] = microstructure.max()
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# --- report ---------------------------------------------------------------------------------------
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if (newInfo['microstructures'] != info['microstructures']):
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damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])
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# --- write header ---------------------------------------------------------------------------------
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table.labels_clear()
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table.info_clear()
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table.info_append(extra_header+[
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scriptID + ' ' + ' '.join(sys.argv[1:]),
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"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
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"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
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"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
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"homogenization\t{homog}".format(homog=info['homogenization']),
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"microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']),
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])
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table.head_write()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
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table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
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# --- output finalization --------------------------------------------------------------------------
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table.close() # close ASCII table
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