DAMASK_EICMD/processing/post/addIPFcolor.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string
import numpy as np
from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Add RGB color value corresponding to TSL-OIM scheme for inverse pole figures.
""", version = scriptID)
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parser.add_option('-p', '--pole', dest='pole', action='store', type='float', nargs=3, metavar='float float float',
help = 'lab frame direction for inverse pole figure %default')
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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('-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]')
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parser.add_option('-m', '--matrix', dest='matrix', action='store', type='string', metavar='string',
help = 'orientation matrix label')
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parser.add_option('-a', dest='a', action='store', type='string', metavar='string',
help = 'crystal frame a vector label')
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parser.add_option('-b', dest='b', action='store', type='string', metavar='string',
help = 'crystal frame b vector label')
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parser.add_option('-c', dest='c', action='store', type='string', metavar='string',
help = 'crystal frame c vector label')
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parser.add_option('-q', '--quaternion', dest='quaternion', action='store', type='string', metavar='string',
help = 'quaternion label')
parser.set_defaults(pole = [0.0,0.0,1.0])
parser.set_defaults(symmetry = 'cubic')
parser.set_defaults(degrees = False)
(options, filenames) = parser.parse_args()
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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'
inputGiven = 0
for datatype,info in datainfo.items():
inputGiven += len(info['label'])
if inputGiven != 1: parser.error('select exactly one input format...')
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toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
pole = np.array(options.pole)
pole /= np.linalg.norm(pole)
# ------------------------------------------ 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})
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# ------------------------------------------ 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 ---------------------------------------
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table.labels_append(['%i_IPF_%g%g%g'%(i+1,options.pole[0],options.pole[1],options.pole[2]) 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()
table.data_append(o.IPFcolor(pole))
outputAlive = table.data_write() # output processed line
# ------------------------------------------ output result -----------------------------------------
outputAlive and 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)
if file['name'] != 'STDIN':
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new