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added addPK2 script to test

This commit is contained in:
Martin Diehl 2014-07-24 21:42:13 +00:00
parent 7954c9a4a3
commit d0ecc0943c
1 changed files with 47 additions and 71 deletions
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102
processing/post/addPK2.py
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@ -1,54 +1,35 @@
#!/usr/bin/env python #!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*- # -*- coding: UTF-8 no BOM -*-
import os,re,sys,math,numpy,string,damask import os,re,sys,math,string
from optparse import OptionParser, Option import numpy as np
from collections import defaultdict
# ----------------------------- from optparse import OptionParser
class extendableOption(Option): import damask
# -----------------------------
# 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)
scriptID = '$Id$'
scriptName = scriptID.split()[1]
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# MAIN # MAIN
# -------------------------------------------------------------------- # --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """ parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Add column(s) containing Second Piola--Kirchhoff stress based on given column(s) of Add column(s) containing Second Piola--Kirchhoff stress based on given column(s) of
deformation gradient and first Piola--Kirchhoff stress. deformation gradient and first Piola--Kirchhoff stress.
""" + string.replace('$Id$','\n','\\n') """, version = string.replace(scriptID,'\n','\\n')
) )
parser.add_option('-f','--defgrad', dest='defgrad', action='store', type='string', metavar='string',
parser.add_option('-f','--defgrad', dest='defgrad', type='string', \
help='heading of columns containing deformation gradient [%default]') help='heading of columns containing deformation gradient [%default]')
parser.add_option('-p','--stress', dest='stress', type='string', \ parser.add_option('-p','--stress', dest='stress', action='store', type='string', metavar='string',
help='heading of columns containing first Piola--Kirchhoff stress [%default]') help='heading of columns containing first Piola--Kirchhoff stress [%default]')
parser.set_defaults(defgrad = 'f') parser.set_defaults(defgrad = 'f')
parser.set_defaults(stress = 'p') parser.set_defaults(stress = 'p')
(options,filenames) = parser.parse_args() (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 datainfo = { # list of requested labels per datatype
'defgrad': {'len':9, 'defgrad': {'len':9,
'label':[]}, 'label':[]},
@ -56,71 +37,66 @@ datainfo = { # lis
'label':[]}, 'label':[]},
} }
datainfo['defgrad']['label'].append(options.defgrad) datainfo['defgrad']['label'].append(options.defgrad)
datainfo['stress']['label'].append(options.stress) datainfo['stress']['label'].append(options.stress)
# ------------------------------------------ setup file handles --------------------------------------- # ------------------------------------------ setup file handles ---------------------------------------
files = [] files = []
if filenames == []: if filenames == []:
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout}) files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
else: else:
for name in filenames: for name in filenames:
if os.path.exists(name): if os.path.exists(name):
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w')}) files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
# ------------------------------------------ loop over input files --------------------------------------- # ------------------------------------------ loop over input files ---------------------------------------
for file in files: for file in files:
if file['name'] != 'STDIN': print file['name'] 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'],False) # make unbuffered ASCII_table table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info table.head_read() # read ASCII header info
table.info_append(string.replace('$Id$','\n','\\n') + \ table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
'\t' + ' '.join(sys.argv[1:]))
active = {} active = defaultdict(list)
column = {} column = defaultdict(dict)
head = [] missingColumns = False
for datatype,info in datainfo.items(): for datatype,info in datainfo.items():
for label in info['label']: for label in info['label']:
key = {True :'1_%s', key = {True :'1_%s',
False:'%s' }[info['len']>1]%label False:'%s' }[info['len']>1]%label
if key not in table.labels: if key not in table.labels:
sys.stderr.write('column %s not found...\n'%key) file['croak'].write('column %s not found...\n'%key)
missingColumns = True # break if label not found
else: else:
if datatype not in active: active[datatype] = []
if datatype not in column: column[datatype] = {}
active[datatype].append(label) active[datatype].append(label)
column[datatype][label] = table.labels.index(key) # remember columns of requested data column[datatype][label] = table.labels.index(key) # remember columns of requested data
table.labels_append(['%i_S'%(i+1) if missingColumns:
for i in xrange(datainfo['defgrad']['len'])]) # extend ASCII header with new labels continue
# ------------------------------------------ assemble header ---------------------------------------
# ------------------------------------------ assemble header ------------------------------------
table.labels_append(['%i_S'%(i+1) for i in xrange(datainfo['stress']['len'])]) # extend ASCII header with new labels
table.head_write() table.head_write()
# ------------------------------------------ process data --------------------------------------- # ------------------------------------------ process data ----------------------------------------
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
F = np.array(map(float,table.data[column['defgrad'][active['defgrad'][0]]:
column['defgrad'][active['defgrad'][0]]+
datainfo['defgrad']['len']]),'d').reshape(3,3)
P = np.array(map(float,table.data[column['stress'][active['stress'][0]]:
column['stress'][active['stress'][0]]+
datainfo['stress']['len']]),'d').reshape(3,3)
while table.data_read(): # read next data line of ASCII table table.data_append(list(np.dot(np.linalg.inv(F),P).reshape(9))) # [S] =[P].[F-1]
outputAlive = table.data_write() # output processed line
F = numpy.array(map(float,table.data[column['defgrad'][active['defgrad'][0]]:
column['defgrad'][active['defgrad'][0]]+datainfo['defgrad']['len']]),'d').reshape(3,3)
P = numpy.array(map(float,table.data[column['stress'][active['stress'][0]]:
column['stress'][active['stress'][0]]+datainfo['stress']['len']]),'d').reshape(3,3)
table.data_append(list(numpy.dot(numpy.linalg.inv(F),P).reshape(9))) # [S] =[P].[F-1]
table.data_write() # output processed line
# ------------------------------------------ output result --------------------------------------- # ------------------------------------------ output result ---------------------------------------
outputAlive and table.output_flush() # just in case of buffered ASCII table
table.output_flush() # just in case of buffered ASCII table file['input'].close() # close input ASCII table (works for stdin)
file['output'].close() # close output ASCII table (works for stdout)
file['input'].close() # close input ASCII table
if file['name'] != 'STDIN': if file['name'] != 'STDIN':
file['output'].close # close output ASCII table
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new