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
#--------------------------------------------------------------------------------------------------
identifiers = {
'grid': ['a','b','c'],
'size': ['x','y','z'],
'origin': ['x','y','z'],
}
mappings = {
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'grid': lambda x: int(x),
'size': lambda x: float(x),
'origin': lambda x: float(x),
'homogenization': lambda x: int(x),
'microstructures': lambda x: int(x),
}
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,
help='offset from old to new origin of grid', metavar=' '.join(['float']*3))
parser.add_option('-m', '--microstructure', dest='microstructure', type='int',
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help='offset from old to new microstructure indices', metavar='int')
parser.add_option('-s', '--substitute', action='extend', dest='substitute',
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help='substitutions of microstructure indices from,to,from,to,...', metavar='<string LIST>')
parser.set_defaults(origin = (0.0,0.0,0.0))
parser.set_defaults(microstructure = 0)
parser.set_defaults(substitute = [])
parser.set_defaults(twoD = False)
(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])
#--- setup file handles ---------------------------------------------------------------------------
files = []
if filenames == []:
files.append({'name':'STDIN',
'input':sys.stdin,
'output':sys.stdout,
'croak':sys.stderr,
})
else:
for name in filenames:
if os.path.exists(name):
files.append({'name':name,
'input':open(name),
'output':open(name+'_tmp','w'),
'croak':sys.stdout,
})
#--- loop over input files ------------------------------------------------------------------------
for file in files:
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file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
theTable = damask.ASCIItable(file['input'],file['output'],labels=False)
theTable.head_read()
#--- interpret header ----------------------------------------------------------------------------
info = {
'grid': np.zeros(3,'i'),
'size': np.zeros(3,'d'),
'origin': np.zeros(3,'d'),
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'homogenization': 0,
'microstructures': 0,
}
newInfo = {
'origin': np.zeros(3,'d'),
'microstructures': 0,
}
extra_header = []
for header in theTable.info:
headitems = map(str.lower,header.split())
if len(headitems) == 0: continue
if headitems[0] in mappings.keys():
if headitems[0] in identifiers.keys():
for i in xrange(len(identifiers[headitems[0]])):
info[headitems[0]][i] = \
mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
else:
info[headitems[0]] = mappings[headitems[0]](headitems[1])
else:
extra_header.append(header)
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
'homogenization: %i\n'%info['homogenization'] + \
'microstructures: %i\n'%info['microstructures'])
if np.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
continue
if np.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
continue
#--- read data ------------------------------------------------------------------------------------
microstructure = np.zeros(info['grid'].prod(),'i')
i = 0
theTable.data_rewind()
while theTable.data_read():
items = theTable.data
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if len(items) > 2:
if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
else: items = map(int,items)
else: items = map(int,items)
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s = len(items)
microstructure[i:i+s] = items
i += s
#--- do work ------------------------------------------------------------------------------------
substituted = np.copy(microstructure)
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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 ---------------------------------------------------------------------------------------
if (any(newInfo['origin'] != info['origin'])):
file['croak'].write('--> origin x y z: %s\n'%(' : '.join(map(str,newInfo['origin']))))
if (newInfo['microstructures'] != info['microstructures']):
file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
#--- write header ---------------------------------------------------------------------------------
theTable.labels_clear()
theTable.info_clear()
theTable.info_append(extra_header+[
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scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
"origin\tx %f\ty %f\tz %f"%(newInfo['origin'][0],newInfo['origin'][1],newInfo['origin'][2],),
"homogenization\t%i"%info['homogenization'],
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"microstructures\t%i"%(newInfo['microstructures']),
])
theTable.head_write()
theTable.output_flush()
# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(substituted.max())+1))
theTable.data = substituted.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
theTable.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
theTable.input_close()
theTable.output_close()
os.rename(file['name']+'_tmp',file['name'])