DAMASK_EICMD/processing/pre/geom_unpack.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,math
import numpy as np
from optparse import OptionParser
import damask
scriptID = '$Id$'
scriptName = scriptID.split()[1]
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
synonyms = {
'grid': ['resolution'],
'size': ['dimension'],
}
identifiers = {
'grid': ['a','b','c'],
'size': ['x','y','z'],
'origin': ['x','y','z'],
}
mappings = {
'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 = """
Unpack geometry files containing ranges "a to b" and/or "n of x" multiples (exclusively in one line).
""", version = scriptID)
parser.add_option('-1', '--onedimensional', dest='oneD', action='store_true', \
help='output geom file with one-dimensional data arrangement [%default]')
parser.set_defaults(oneD = False)
(options, filenames) = parser.parse_args()
# ------------------------------------------ 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.stderr})
# ------------------------------------------ loop over input files ---------------------------------
for file in files:
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
table = damask.ASCIItable(file['input'],file['output'],labels = False,buffered = False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info
#--- interpret header ----------------------------------------------------------------------------
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info = {
'grid': np.zeros(3,'i'),
'size': np.zeros(3,'d'),
'origin': np.zeros(3,'d'),
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'homogenization': 0,
'microstructures': 0,
}
extra_header = []
for header in table.info:
headitems = map(str.lower,header.split())
if len(headitems) == 0: continue
for synonym,alternatives in synonyms.iteritems():
if headitems[0] in alternatives: headitems[0] = synonym
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):
file['croak'].write('invalid grid a b c.\n')
continue
if np.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
continue
#--- read data ------------------------------------------------------------------------------------
microstructure = np.zeros(info['grid'].prod(),'i')
i = 0
while table.data_read(): # read next data line of ASCII table
items = table.data
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)
s = len(items)
microstructure[i:i+s] = items
i += s
#--- write header ---------------------------------------------------------------------------------
table.labels_clear()
table.info_clear()
table.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 %e\ty %e\tz %e"%(info['size'][0],info['size'][1],info['size'][2],),
"origin\tx %e\ty %e\tz %e"%(info['origin'][0],info['origin'][1],info['origin'][2],),
"homogenization\t%i"%info['homogenization'],
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"microstructures\t%i"%(info['microstructures']),
])
table.head_write()
# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
if options.oneD:
table.data = microstructure
else:
table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
table.input_close() # close input ASCII table
table.output_close() # close input ASCII table
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new