DAMASK_EICMD/processing/pre/geom_clean.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
import numpy as np
import damask
from scipy import ndimage
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def mostFrequent(arr):
return np.argmax(np.bincount(arr))
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Smooth geometry by selecting most frequent microstructure 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]')
parser.set_defaults(stencil = 3,
)
(options, filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,
buffered = False,
labeled = False)
except: continue
damask.util.report(scriptName,name)
# --- interpret header ----------------------------------------------------------------------------
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.croak(['grid a b c: {}'.format(' x '.join(map(str,info['grid']))),
'size x y z: {}'.format(' x '.join(map(str,info['size']))),
'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
'homogenization: {}'.format(info['homogenization']),
'microstructures: {}'.format(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 != []:
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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microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,size=(options.stencil,)*3)
# --- write header ---------------------------------------------------------------------------------
table.info_clear()
table.info_append([scriptID + ' ' + ' '.join(sys.argv[1:]),])
table.head_putGeom(info)
table.info_append([extra_header])
table.labels_clear()
table.head_write()
# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
table.data = microstructure.reshape((info['grid'][0],np.prod(info['grid'][1:])),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table