Script to calculate Quaternion from input orientation matrix
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Harsha Phukan
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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# Copyright 2011-14 Max-Planck-Institut für Eisenforschung GmbH
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#
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# This file is part of DAMASK,
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# the Düsseldorf Advanced Material Simulation Kit.
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#
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# DAMASK is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# DAMASK is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with DAMASK. If not, see <http://www.gnu.org/licenses/>.
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#
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import os,sys,math,string,numpy as np
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from collections import defaultdict
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from optparse import OptionParser
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import damask
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scriptID = string.replace('$Id: addQuaternions.py 3828M 2015-05-15 07:28:21Z (local) $','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Add Quaternions based on Crystal Frame Coordinates.
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""", version = scriptID)
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parser.add_option('-f','--frame', dest='frame', nargs=4, type='string', metavar='<string string string string>',
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help='heading of columns containing b* vector components and three frame vectors in that order')
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parser.add_option('-s','--symmetry', dest='crysym', nargs=1,type='string',metavar='<string>',
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help='crystal symmetry definition')
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parser.set_defaults(frame = None)
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(options,filenames) = parser.parse_args()
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if options.frame == None:
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parser.error('no data column specified...')
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datainfo = {'len':4,
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'label':[]
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}
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if options.frame != None: datainfo['label'] += options.frame
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []:
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filenames = ['STDIN']
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for name in filenames:
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if name == 'STDIN':
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file = {'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}
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file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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else:
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if not os.path.exists(name): continue
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file = {'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr}
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file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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table = damask.ASCIItable(file['input'],file['output'],buffered=False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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# --------------- figure out columns to process ---------------------------------------------------
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active = []
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column = {}
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for label in datainfo['label']:
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key = '1_'+label if datainfo['len'] > 1 else label # non-special labels have to start with '1_'
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if key in table.labels:
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active.append(label)
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column[label] = table.labels.index(key) # remember columns of requested data
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else:
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file['croak'].write('column %s not found...\n'%label)
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# ------------------------------------------ assemble header ---------------------------------------
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table.labels_append(['Q_%i'%(i+1) for i in xrange(4)]) # extend ASCII header with new labels [1 real, 3 imaginary components]
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table.head_write()
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# ------------------------------------------ process data ------------------------------------------
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outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
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vec = np.zeros([4,3])
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for i,label in enumerate(active):
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vec[i,:] = np.array(table.data[column[label]:
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column[label]+3])
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if sys.argv[1:][6]=='hexagonal': # Ensure Input matrix is orthogonal
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M=np.dot(vec[0,:],vec[2,:])
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vec[1,:]=vec[1,:]/np.linalg.norm(vec[1,:])
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vec[2,:]=M*(vec[0,:]/np.linalg.norm(vec[0,:]))
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vec[3,:]=vec[3,:]/np.linalg.norm(vec[3,:])
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else:
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vec[1,:]=vec[1,:]/np.linalg.norm(vec[1,:])
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vec[2,:]=vec[2,:]/np.linalg.norm(vec[2,:])
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vec[3,:]=vec[3,:]/np.linalg.norm(vec[3,:])
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Ori=damask.Orientation(matrix=vec[1:,:],symmetry=sys.argv[1:][6])
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table.data_append(np.asarray(Ori.asQuaternion()))
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output result -----------------------------------------
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outputAlive and table.output_flush() # just in case of buffered ASCII table
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table.input_close() # close input ASCII table (works for stdin)
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table.output_close() # close output ASCII table (works for stdout)
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if file['name'] != 'STDIN':
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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