175 lines
7.7 KiB
Python
Executable File
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
|