DAMASK_EICMD/processing/post/addCompatibilityMismatch.py

175 lines
7.7 KiB
Python
Executable File

#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,re,sys,math,string,numpy,damask
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 location(idx,res):
return ( idx % res[0], \
(idx // res[0]) % res[1], \
(idx // res[0] // res[1]) % res[2] )
def index(location,res):
return ( location[0] % res[0] + \
(location[1] % res[1]) * res[0] + \
(location[2] % res[2]) * res[0] * res[1] )
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options file[s]', description = """
Add column containing debug information
Operates on periodic ordered three-dimensional data sets.
""" + string.replace('$Id$','\n','\\n')
)
parser.add_option('--no-shape','-s', dest='noShape', action='store_false', \
help='do not calcuate shape mismatch [%default]')
parser.add_option('--no-volume','-v', dest='noVolume', action='store_false', \
help='do not calculate volume mismatch [%default]')
parser.add_option('-c','--coordinates', dest='coords', type='string',\
help='column heading for coordinates [%default]')
parser.add_option('-f','--deformation', dest='F', action='extend', type='string', \
help='heading(s) of columns containing deformation tensor values %default')
parser.set_defaults(noVolume = False)
parser.set_defaults(noShape = False)
parser.set_defaults(coords = 'ip')
parser.set_defaults(F = 'f')
(options,filenames) = parser.parse_args()
datainfo = { # list of requested labels per datatype
'F': {'len':9,
'label':[]},
}
if options.F != None: datainfo['F']['label'] += options.F
# ------------------------------------------ setup file handles ---------------------------------------
files = []
if filenames == []:
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout})
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:
if file['name'] != 'STDIN': print file['name'],
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info
table.info_append(string.replace('$Id$','\n','\\n') + \
'\t' + ' '.join(sys.argv[1:]))
# --------------- figure out dimension and resolution
try:
locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data
except ValueError:
print 'no coordinate data found...'
continue
grid = [{},{},{}]
while table.data_read(): # read next data line of ASCII table
for j in xrange(3):
grid[j][str(table.data[locationCol+j])] = True # remember coordinate along x,y,z
res = numpy.array([len(grid[0]),\
len(grid[1]),\
len(grid[2]),],'i') # resolution is number of distinct coordinates found
geomdim = res/numpy.maximum(numpy.ones(3,'d'),res-1.0)* \
numpy.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),\
],'d') # dimension from bounding box, corrected for cell-centeredness
if res[2] == 1:
geomdim[2] = min(geomdim[:2]/res[:2])
N = res.prod()
print '\t%s @ %s'%(geomdim,res)
# --------------- figure out columns to process
key = '1_%s' %options.F
if key not in table.labels:
sys.stderr.write('column %s not found...\n'%key)
else:
F = numpy.array([0.0 for i in xrange(N*9)]).reshape([3,3]+list(res))
if not options.noShape: table.labels_append(['shapeMismatch(%s)' %options.F])
if not options.noVolume: table.labels_append(['volMismatch(%s)'%options.F])
column = table.labels.index(key)
# ------------------------------------------ assemble header ---------------------------------------
table.head_write()
# ------------------------------------------ read deformation gradient field -----------------------
table.data_rewind()
idx = 0
while table.data_read(): # read next data line of ASCII table
(x,y,z) = location(idx,res) # figure out (x,y,z) position from line count
idx += 1
F[0:3,0:3,x,y,z] = numpy.array(map(float,table.data[column:column+9]),'d').reshape(3,3)
Favg = damask.core.math.tensorAvg(F)
if (res[0]%2 != 0 or res[1]%2 != 0 or (res[2] != 1 and res[2]%2 !=0)):
print 'using linear reconstruction for uneven resolution'
centres = damask.core.mesh.deformedCoordsLin(geomdim,F,Favg)
else:
centres = damask.core.mesh.deformedCoordsFFT(geomdim,F,1.0,Favg)
nodes = damask.core.mesh.nodesAroundCentres(geomdim,Favg,centres)
if not options.noShape: shapeMismatch = damask.core.mesh.shapeMismatch( geomdim,F,nodes,centres)
if not options.noVolume: volumeMismatch = damask.core.mesh.volumeMismatch(geomdim,F,nodes)
# ------------------------------------------ process data ---------------------------------------
table.data_rewind()
idx = 0
while table.data_read(): # read next data line of ASCII table
(x,y,z) = location(idx,res) # figure out (x,y,z) position from line count
idx += 1
if not options.noShape: table.data_append( shapeMismatch[x,y,z])
if not options.noVolume: table.data_append(volumeMismatch[x,y,z])
table.data_write() # output processed line
# ------------------------------------------ output result ---------------------------------------
table.output_flush() # just in case of buffered ASCII table
file['input'].close() # close input ASCII table
if file['name'] != 'STDIN':
file['output'].close # close output ASCII table
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new