DAMASK_EICMD/processing/pre/geom_toTable.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
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import os,sys
import numpy as np
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile[s]]', description = """
Translate geom description into ASCIItable containing 1/2/3_pos and microstructure.
""", version = scriptID)
parser.add_option('-p','--position',
dest = 'position',
type = 'string', metavar = 'string',
help = 'column label for position [%default]')
parser.add_option('-m','--microstructure',
dest = 'microstructure',
type = 'string', metavar = 'string',
help = 'column label for microstructure index [%default]')
parser.set_defaults(position = 'pos',
microstructure = 'microstructure',
)
(options, filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
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try:
table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.txt' if name else 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: %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 != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# --- read data ------------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']) # read microstructure
# ------------------------------------------ assemble header ---------------------------------------
table.info_clear()
table.info_append(extra_header + [scriptID + '\t' + ' '.join(sys.argv[1:])])
table.labels_clear()
table.labels_append(['{}_{}'.format(1+i,options.position) for i in xrange(3)]+[options.microstructure])
table.head_write()
table.output_flush()
#--- generate grid --------------------------------------------------------------------------------
x = (0.5 + np.arange(info['grid'][0],dtype=float))/info['grid'][0]*info['size'][0]+info['origin'][0]
y = (0.5 + np.arange(info['grid'][1],dtype=float))/info['grid'][1]*info['size'][1]+info['origin'][1]
z = (0.5 + np.arange(info['grid'][2],dtype=float))/info['grid'][2]*info['size'][2]+info['origin'][2]
xx = np.tile( x, info['grid'][1]* info['grid'][2])
yy = np.tile(np.repeat(y,info['grid'][0] ),info['grid'][2])
zz = np.repeat(z,info['grid'][0]*info['grid'][1])
table.data = np.squeeze(np.dstack((xx,yy,zz,microstructure)))
table.data_writeArray()
# ------------------------------------------ finalize output ---------------------------------------
table.close()