DAMASK_EICMD/processing/post/addCauchy

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#!/usr/bin/python
import os,re,sys,math,numpy,string
from optparse import OptionParser, Option
# -----------------------------
class extendableOption(Option):
# -----------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
def prefixMultiply(what,len):
return {True: ['%i_%s'%(i+1,what) for i in range(len)],
False:[what]}[len>1]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
Add column(s) containing Cauchy stress based on given column(s) of
deformation gradient and first Piola--Kirchhoff stress.
$Id: addCauchy 263 2011-05-25 17:42:50Z MPIE\p.eisenlohr $
""")
parser.add_option('-m','--memory', dest='memory', action='store_true', \
help='load complete file into memory [%default]')
parser.add_option('-f','--defgrad', dest='defgrad', type='string', \
help='heading of columns containing deformation gradient [%default]')
parser.add_option('-p','--stress', dest='stress', type='string', \
help='heading of columns containing first Piola--Kirchhoff stress [%default]')
parser.set_defaults(memory = False)
parser.set_defaults(defgrad = 'f')
parser.set_defaults(stress = 'p')
(options,filenames) = parser.parse_args()
if options.defgrad == None or options.stress == None:
parser.error('missing data column...')
datainfo = { # list of requested labels per datatype
'defgrad': {'len':9,
'label':[]},
'stress': {'len':9,
'label':[]},
}
datainfo['defgrad']['label'].append(options.defgrad)
datainfo['stress']['label'].append(options.stress)
# ------------------------------------------ setup file handles ---------------------------------------
files = []
if filenames == []:
files.append({'name':'STDIN', 'handle':sys.stdin})
else:
for name in filenames:
if os.path.exists(name):
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w')})
# ------------------------------------------ loop over input files ---------------------------------------
for file in files:
print file['name']
# get labels by either read the first row, or - if keyword header is present - the last line of the header
firstline = file['input'].readline()
m = re.search('(\d+)\s*head', firstline.lower())
if m:
headerlines = int(m.group(1))
passOn = [file['input'].readline() for i in range(1,headerlines)]
headers = file['input'].readline().split()
else:
headerlines = 1
passOn = []
headers = firstline.split()
if options.memory:
data = file['input'].readlines()
else:
data = []
for i,l in enumerate(headers):
if l.startswith('1_'):
if re.match('\d+_',l[2:]) or i == len(headers)-1 or not headers[i+1].endswith(l[2:]):
headers[i] = l[2:]
active = {}
column = {}
head = []
for datatype,info in datainfo.items():
for label in info['label']:
key = {True :'1_%s',
False:'%s' }[info['len']>1]%label
if key not in headers:
sys.stderr.write('column %s not found...\n'%key)
else:
if datatype not in active: active[datatype] = []
if datatype not in column: column[datatype] = {}
active[datatype].append(label)
column[datatype][label] = headers.index(key)
head += prefixMultiply('Cauchy',datainfo[datatype]['len'])
# ------------------------------------------ assemble header ---------------------------------------
output = '%i\theader'%(headerlines+1) + '\n' + \
''.join(passOn) + \
string.replace('$Id: addCauchy 263 2011-05-25 17:42:50Z MPIE\p.eisenlohr $','\n','\\n')+ '\t' + \
' '.join(sys.argv[1:]) + '\n' + \
'\t'.join(headers + head) + '\n' # build extended header
if not options.memory:
file['output'].write(output)
output = ''
# ------------------------------------------ read file ---------------------------------------
for line in {True : data,
False : file['input']}[options.memory]:
items = line.split()[:len(headers)]
if len(items) < len(headers):
continue
output += '\t'.join(items)
F = numpy.array(map(float,items[column['defgrad'][active['defgrad'][0]]:
column['defgrad'][active['defgrad'][0]]+datainfo['defgrad']['len']]),'d').reshape(3,3)
P = numpy.array(map(float,items[column['stress'][active['stress'][0]]:
column['stress'][active['stress'][0]]+datainfo['stress']['len']]),'d').reshape(3,3)
output += '\t'+'\t'.join(map(str,1.0/numpy.linalg.det(F)*numpy.dot(P,F.T).reshape(9))) # [Cauchy] = (1/det(F)) * [P].[F_transpose]
output += '\n'
if not options.memory:
file['output'].write(output)
output = ''
file['input'].close()
# ------------------------------------------ output result ---------------------------------------
if options.memory:
file['output'].write(output)
if file['name'] != 'STDIN':
file['output'].close
os.rename(file['name']+'_tmp',file['name'])