#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,itertools,re,math,numpy
import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
scriptID = '$Id$'
scriptName = scriptID.split()[1]
#--------------------------------------------------------------------------------------------------
class extendedOption(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)
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """\
Add quaternion and/or Bunge Euler angle representation of crystal lattice orientation.
Orientation is given by quaternion, Euler angles,
rotation matrix, or crystal frame coordinates (i.e. component vectors of rotation matrix).
""" + string.replace(scriptID,'\n','\\n')
)
parser.add_option('-o', '--orientations', dest='output', action='append', metavar='<LIST>',
help = 'output orientation formats')
parser.add_option('-s', '--symmetry', dest='symmetry', type='string',
help = 'crystal symmetry [%default]')
parser.add_option('-e', '--eulers', dest='eulers', type='string', metavar='LABEL',
help = 'Euler angles')
parser.add_option('-d', '--degrees', dest='degrees', action='store_true',
help = 'Euler angles are given in degrees [%default]')
parser.add_option('-m', '--matrix', dest='matrix', type='string', metavar='LABEL',
help = 'orientation matrix')
parser.add_option('-a', dest='a', type='string', metavar='LABEL',
help = 'crystal frame a vector')
parser.add_option('-b', dest='b', type='string', metavar='LABEL',
help = 'crystal frame b vector')
parser.add_option('-c', dest='c', type='string', metavar='LABEL',
help = 'crystal frame c vector')
parser.add_option('-q', '--quaternion', dest='quaternion', type='string', metavar='LABEL',
help = 'quaternion')
parser.set_defaults(output = [])
parser.set_defaults(symmetry = 'cubic')
parser.set_defaults(degrees = False)
(options, filenames) = parser.parse_args()
datainfo = { # list of requested labels per datatype
'tensor': {'len':9,
'label':[]},
'vector': {'len':3,
'label':[]},
'quaternion': {'len':4,
'label':[]},
}
if options.eulers != None: datainfo['vector']['label'] += [options.eulers]; input = 'eulers'
if options.a != None and \
options.b != None and \
options.c != None: datainfo['vector']['label'] += [options.a,options.b,options.c]; input = 'frame'
if options.matrix != None: datainfo['tensor']['label'] += [options.matrix]; input = 'matrix'
if options.quaternion != None: datainfo['quaternion']['label'] += [options.quaternion]; input = 'quaternion'
toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
options.output = map(lambda x: x.lower(), options.output)
# ------------------------------------------ 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'],buffered = False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info
table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
# --------------- figure out columns to process
active = {}
column = {}
head = []
for datatype,info in datainfo.items():
for label in info['label']:
foundIt = False
for key in ['1_'+label,label]:
if key in table.labels:
foundIt = True
if datatype not in active: active[datatype] = []
if datatype not in column: column[datatype] = {}
active[datatype].append(label)
column[datatype][label] = table.labels.index(key) # remember columns of requested data
if not foundIt:
file['croak'].write('column %s not found...\n'%label)
break
for output in options.output:
if output == 'quaternion':
table.labels_append(['%i_quaternion_%s'%(i+1,options.symmetry) for i in xrange(4)])
if output == 'eulers':
table.labels_append(['%i_eulers_%s'%(i+1,options.symmetry) for i in xrange(3)])
# ------------------------------------------ assemble header ---------------------------------------
table.head_write()
# ------------------------------------------ process data ---------------------------------------
while table.data_read(): # read next data line of ASCII table
if input == 'eulers':
o = damask.Orientation(Eulers=toRadians*numpy.array(map(float,table.data[column['vector'][options.eulers]:\
column['vector'][options.eulers]+datainfo['vector']['len']])),
symmetry=options.symmetry).reduced()
elif input == 'matrix':
o = damask.Orientation(matrix=numpy.array([map(float,table.data[column['tensor'][options.matrix]:\
column['tensor'][options.matrix]+datainfo['tensor']['len']])]),
symmetry=options.symmetry).reduced()
elif input == 'frame':
o = damask.Orientation(matrix=numpy.array([map(float,table.data[column['vector'][options.a]:\
column['vector'][options.a]+datainfo['vector']['len']] + \
table.data[column['vector'][options.b]:\
column['vector'][options.b]+datainfo['vector']['len']] + \
table.data[column['vector'][options.c]:\
column['vector'][options.c]+datainfo['vector']['len']]
)]).reshape(3,3),
symmetry=options.symmetry).reduced()
elif input == 'quaternion':
o = damask.Orientation(quaternion=numpy.array(map(float,table.data[column['quaternion'][options.quaternion]:\
column['quaternion'][options.quaternion]+datainfo['quaternion']['len']])),
symmetry=options.symmetry).reduced()
for output in options.output:
if output == 'quaternion':
table.data_append(o.asQuaternion())
if output == 'eulers':
table.data_append(o.asEulers('Bunge'))
table.data_write() # output processed line
# ------------------------------------------ output result ---------------------------------------
table.output_flush() # just in case of buffered ASCII table
if file['name'] != 'STDIN':
file['input'].close() # close input ASCII table
file['output'].close() # close output ASCII table
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new