#!/usr/bin/env python2.7 # -*- coding: UTF-8 no BOM -*- import os,sys,math import numpy as np from optparse import OptionParser import damask scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptID = ' '.join([scriptName,damask.version]) # -------------------------------------------------------------------- # 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). Additional (globally fixed) rotations of the lab frame and/or crystal frame can be applied. """, version = scriptID) outputChoices = ['quaternion','rodrigues','eulers'] parser.add_option('-o', '--output', dest = 'output', action = 'extend', metavar = '', help = 'output orientation formats {{{}}}'.format(', '.join(outputChoices))) parser.add_option('-s', '--symmetry', dest = 'symmetry', type = 'choice', choices = damask.Symmetry.lattices[1:], metavar='string', help = 'crystal symmetry [%default] {{{}}} '.format(', '.join(damask.Symmetry.lattices[1:]))) parser.add_option('-d', '--degrees', dest = 'degrees', action = 'store_true', help = 'angles are given in degrees [%default]') parser.add_option('-R', '--labrotation', dest='labrotation', type = 'float', nargs = 4, metavar = ' '.join(['float']*4), help = 'angle and axis of additional lab frame rotation') parser.add_option('-r', '--crystalrotation', dest='crystalrotation', type = 'float', nargs = 4, metavar = ' '.join(['float']*4), help = 'angle and axis of additional crystal frame rotation') parser.add_option( '--eulers', dest = 'eulers', type = 'string', metavar = 'string', help = 'Euler angles label') parser.add_option( '--rodrigues', dest = 'rodrigues', type = 'string', metavar = 'string', help = 'Rodrigues vector label') parser.add_option( '--matrix', dest = 'matrix', type = 'string', metavar = 'string', help = 'orientation matrix label') parser.add_option( '--quaternion', dest = 'quaternion', type = 'string', metavar = 'string', help = 'quaternion label') parser.add_option('-a', dest = 'a', type = 'string', metavar = 'string', help = 'crystal frame a vector label') parser.add_option('-b', dest = 'b', type = 'string', metavar = 'string', help = 'crystal frame b vector label') parser.add_option('-c', dest = 'c', type = 'string', metavar = 'string', help = 'crystal frame c vector label') parser.set_defaults(output = [], symmetry = damask.Symmetry.lattices[-1], labrotation = (0.,1.,1.,1.), # no rotation about 1,1,1 crystalrotation = (0.,1.,1.,1.), # no rotation about 1,1,1 degrees = False, ) (options, filenames) = parser.parse_args() options.output = map(lambda x: x.lower(), options.output) if options.output == [] or (not set(options.output).issubset(set(outputChoices))): parser.error('output must be chosen from {}.'.format(', '.join(outputChoices))) input = [options.eulers is not None, options.rodrigues is not None, options.a is not None and \ options.b is not None and \ options.c is not None, options.matrix is not None, options.quaternion is not None, ] if np.sum(input) != 1: parser.error('needs exactly one input format.') (label,dim,inputtype) = [(options.eulers,3,'eulers'), (options.rodrigues,3,'rodrigues'), ([options.a,options.b,options.c],[3,3,3],'frame'), (options.matrix,9,'matrix'), (options.quaternion,4,'quaternion'), ][np.where(input)[0][0]] # select input label that was requested toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians r = damask.Quaternion().fromAngleAxis(toRadians*options.crystalrotation[0],options.crystalrotation[1:]) # crystal frame rotation R = damask.Quaternion().fromAngleAxis(toRadians*options. labrotation[0],options. labrotation[1:]) # lab frame rotation # --- loop over input files ------------------------------------------------------------------------ if filenames == []: filenames = [None] for name in filenames: try: table = damask.ASCIItable(name = name, buffered = False) except: continue damask.util.report(scriptName,name) # ------------------------------------------ read header ------------------------------------------ table.head_read() # ------------------------------------------ sanity checks ----------------------------------------- errors = [] remarks = [] if not np.all(table.label_dimension(label) == dim): errors.append('input {} does not have dimension {}.'.format(label,dim)) else: column = table.label_index(label) if remarks != []: damask.util.croak(remarks) if errors != []: damask.util.croak(errors) table.close(dismiss = True) continue # ------------------------------------------ assemble header --------------------------------------- table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:])) for output in options.output: if output == 'quaternion': table.labels_append(['{}_{}_{}({})'.format(i+1,'quat',options.symmetry,label) for i in range(4)]) elif output == 'rodrigues': table.labels_append(['{}_{}_{}({})'.format(i+1,'rodr',options.symmetry,label) for i in range(3)]) elif output == 'eulers': table.labels_append(['{}_{}_{}({})'.format(i+1,'eulr',options.symmetry,label) for i in range(3)]) table.head_write() # ------------------------------------------ process data ------------------------------------------ outputAlive = True while outputAlive and table.data_read(): # read next data line of ASCII table if inputtype == 'eulers': o = damask.Orientation(Eulers = np.array(map(float,table.data[column:column+3]))*toRadians, symmetry = options.symmetry).reduced() elif inputtype == 'rodrigues': o = damask.Orientation(Rodrigues= np.array(map(float,table.data[column:column+3])), symmetry = options.symmetry).reduced() elif inputtype == 'matrix': o = damask.Orientation(matrix = np.array(map(float,table.data[column:column+9])).reshape(3,3).transpose(), symmetry = options.symmetry).reduced() elif inputtype == 'frame': o = damask.Orientation(matrix = np.array(map(float,table.data[column[0]:column[0]+3] + \ table.data[column[1]:column[1]+3] + \ table.data[column[2]:column[2]+3])).reshape(3,3), symmetry = options.symmetry).reduced() elif inputtype == 'quaternion': o = damask.Orientation(quaternion = np.array(map(float,table.data[column:column+4])), symmetry = options.symmetry).reduced() o.quaternion = r*o.quaternion*R # apply additional lab and crystal frame rotations for output in options.output: if output == 'quaternion': table.data_append(o.asQuaternion()) elif output == 'rodrigues': table.data_append(o.asRodrigues()) elif output == 'eulers': table.data_append(o.asEulers('Bunge', degrees=options.degrees)) outputAlive = table.data_write() # output processed line # ------------------------------------------ output finalization ----------------------------------- table.close() # close ASCII tables