DAMASK_EICMD/processing/pre/geom_translate.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,math
import numpy as np
import damask
from optparse import OptionParser
scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
translate microstructure indices (shift or substitute) and/or geometry origin.
""", version=scriptID)
parser.add_option('-o', '--origin',
dest = 'origin',
type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
help = 'offset from old to new origin of grid')
parser.add_option('-m', '--microstructure',
dest = 'microstructure',
type = 'int', metavar = 'int',
help = 'offset from old to new microstructure indices')
parser.add_option('-s', '--substitute',
dest = 'substitute',
action = 'extend', metavar = '<string LIST>',
help = 'substitutions of microstructure indices from,to,from,to,...')
parser.set_defaults(origin = (0.0,0.0,0.0),
microstructure = 0,
substitute = [],
)
(options, filenames) = parser.parse_args()
sub = {}
for i in xrange(len(options.substitute)/2): # split substitution list into "from" -> "to"
sub[int(options.substitute[i*2])] = int(options.substitute[i*2+1])
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = ['STDIN']
for name in filenames:
if not (name == 'STDIN' or os.path.exists(name)): continue
table = damask.ASCIItable(name = name, outname = name+'_tmp',
buffered = False, labeled = False)
table.croak('\033[1m'+scriptName+'\033[0m'+(': '+name if name != 'STDIN' else ''))
# --- interpret header ----------------------------------------------------------------------------
table.head_read()
info,extra_header = table.head_getGeom()
table.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 != []:
table.croak(errors)
table.close(dismiss = True)
continue
# --- read data ------------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']) # read microstructure
# --- do work ------------------------------------------------------------------------------------
newInfo = {
'origin': np.zeros(3,'d'),
'microstructures': 0,
}
substituted = np.copy(microstructure)
for k, v in sub.iteritems(): substituted[microstructure==k] = v # substitute microstructure indices
substituted += options.microstructure # shift microstructure indices
newInfo['origin'] = info['origin'] + options.origin
newInfo['microstructures'] = substituted.max()
# --- report ---------------------------------------------------------------------------------------
remarks = []
if (any(newInfo['origin'] != info['origin'])): remarks.append('--> origin x y z: %s'%(' : '.join(map(str,newInfo['origin']))))
if ( newInfo['microstructures'] != info['microstructures']): remarks.append('--> microstructures: %i'%newInfo['microstructures'])
if remarks != []: file['croak'](remarks)
# --- 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=newInfo['origin']),
"homogenization\t{homog}".format(homog=info['homogenization']),
"microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']),
])
table.head_write()
table.output_flush()
# --- 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
if name != 'STDIN': os.rename(name+'_tmp',name) # overwrite old one with tmp new