DAMASK_EICMD/processing/post/addOrientations.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,itertools
import numpy as np
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from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
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# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, 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).
""", version = scriptID)
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outputChoices = ['quaternion','eulers']
parser.add_option('-o', '--output', dest='output', action='extend', type='string', metavar='<string LIST>',
help = 'output orientation formats (%s)'%(','.join(outputChoices)))
parser.add_option('-s', '--symmetry', dest='symmetry', action='store', type='choice',
choices=damask.Symmetry.lattices[1:], metavar='string',
help = 'crystal symmetry (%s) [cubic]'%(', '.join(damask.Symmetry.lattices[1:])))
parser.add_option('-r', '--rotation', dest='rotation', action='store', type='float', nargs=4, metavar='float float float float',
help = 'angle and axis to (pre)rotate orientation')
parser.add_option('-e', '--eulers', dest='eulers', action='store', type='string', metavar='string',
help = 'Euler angles label')
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', action='store', type='string', metavar='string',
help = 'orientation matrix label')
parser.add_option('-a', dest='a', action='store', type='string', metavar='string',
help = 'crystal frame a vector label')
parser.add_option('-b', dest='b', action='store', type='string', metavar='string',
help = 'crystal frame b vector label')
parser.add_option('-c', dest='c', action='store', type='string', metavar='string',
help = 'crystal frame c vector label')
parser.add_option('-q', '--quaternion', dest='quaternion', action='store', type='string', metavar='string',
help = 'quaternion label')
parser.set_defaults(output = [])
parser.set_defaults(symmetry = 'cubic')
parser.set_defaults(rotation = [0.,1.,1.,1.]) # no rotation about 1,1,1
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':[]},
}
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if not set(options.output).issubset(set(outputChoices)):
parser.error('output must be chosen from %s...'%(', '.join(outputChoices)))
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'
inputGiven = 0
for datatype,info in datainfo.items():
inputGiven += len(info['label'])
if inputGiven != 1: parser.error('select exactly one input format...')
toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
options.output = map(lambda x: x.lower(), options.output)
r = damask.Quaternion().fromAngleAxis(toRadians*options.rotation[0],options.rotation[1:])
# ------------------------------------------ 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')
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
column = {}
missingColumns = False
for datatype,info in datainfo.items():
for label in info['label']:
key = '1_%s'%label
if key not in table.labels:
file['croak'].write('column %s not found...\n'%key)
missingColumns = True # break if label not found
else:
column[label] = table.labels.index(key) # remember columns of requested data
if missingColumns:
continue
# ------------------------------------------ assemble header ---------------------------------------
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)])
table.head_write()
# ------------------------------------------ process data ------------------------------------------
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outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
if input == 'eulers':
o = damask.Orientation(Eulers=toRadians*\
np.array(map(float,table.data[column[options.eulers]:\
column[options.eulers]+datainfo['vector']['len']])),
symmetry=options.symmetry).reduced()
elif input == 'matrix':
o = damask.Orientation(matrix=\
np.array([map(float,table.data[column[options.matrix]:\
column[options.matrix]+datainfo['tensor']['len']])]),
symmetry=options.symmetry).reduced()
elif input == 'frame':
o = damask.Orientation(matrix=\
np.array([map(float,table.data[column[options.a]:\
column[options.a]+datainfo['vector']['len']] + \
table.data[column[options.b]:\
column[options.b]+datainfo['vector']['len']] + \
table.data[column[options.c]:\
column[options.c]+datainfo['vector']['len']]
)]).reshape(3,3),
symmetry=options.symmetry).reduced()
elif input == 'quaternion':
o = damask.Orientation(quaternion=\
np.array(map(float,table.data[column[options.quaternion]:\
column[options.quaternion]+datainfo['quaternion']['len']])),
symmetry=options.symmetry).reduced()
o.quaternion = r*o.quaternion
for output in options.output:
if output == 'quaternion':
table.data_append(o.asQuaternion())
if output == 'eulers':
table.data_append(o.asEulers('Bunge'))
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outputAlive = table.data_write() # output processed line
# ------------------------------------------ output result -----------------------------------------
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outputAlive and table.output_flush() # just in case of buffered ASCII table
table.input_close() # close input ASCII table (works for stdin)
table.output_close() # close output ASCII table (works for stdout)
if file['name'] != 'STDIN':
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new