161 lines
7.5 KiB
Python
Executable File
161 lines
7.5 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,itertools,math
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import numpy as np
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from optparse import OptionParser
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import damask
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scriptID = string.replace('$Id$','\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 quaternion and/or Bunge Euler angle representation of crystal lattice orientation.
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Orientation is given by quaternion, Euler angles, rotation matrix, or crystal frame coordinates (i.e. component vectors of rotation matrix).
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""", version = scriptID)
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outputChoices = ['quaternion','eulers']
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parser.add_option('-o', '--output',
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dest = 'output',
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action = 'extend', metavar = '<string LIST>',
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help = 'output orientation formats {%s}'%(','.join(outputChoices)))
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parser.add_option('-r', '--rotation',
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dest='rotation',
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type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
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help = 'angle and axis to (pre)rotate orientation')
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parser.add_option('-s', '--symmetry',
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dest = 'symmetry',
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type = 'choice', choices = damask.Symmetry.lattices[1:], metavar='string',
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help = 'crystal symmetry [%default] {{{}}} '.format(', '.join(damask.Symmetry.lattices[1:])))
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parser.add_option('-e', '--eulers',
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dest = 'eulers',
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type = 'string', metavar = 'string',
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help = 'Euler angles label')
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parser.add_option('-d', '--degrees',
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dest = 'degrees',
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action = 'store_true',
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help = 'Euler angles are given in degrees [%default]')
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parser.add_option('-m', '--matrix',
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dest = 'matrix',
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type = 'string', metavar = 'string',
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help = 'orientation matrix label')
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parser.add_option('-a',
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dest = 'a',
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type = 'string', metavar = 'string',
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help = 'crystal frame a vector label')
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parser.add_option('-b',
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dest = 'b',
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type = 'string', metavar = 'string',
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help = 'crystal frame b vector label')
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parser.add_option('-c',
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dest = 'c',
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type = 'string', metavar = 'string',
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help = 'crystal frame c vector label')
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parser.add_option('-q', '--quaternion',
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dest = 'quaternion',
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type = 'string', metavar = 'string',
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help = 'quaternion label')
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parser.set_defaults(output = [],
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symmetry = damask.Symmetry.lattices[-1],
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rotation = (0.,1.,1.,1.), # no rotation about 1,1,1
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degrees = False,
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)
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(options, filenames) = parser.parse_args()
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options.output = map(lambda x: x.lower(), options.output)
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if options.output == [] or (not set(options.output).issubset(set(outputChoices))):
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parser.error('output must be chosen from {}.'.format(', '.join(outputChoices)))
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input = [options.eulers != None,
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options.a != None and \
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options.b != None and \
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options.c != None,
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options.matrix != None,
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options.quaternion != None,
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]
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if np.sum(input) != 1: parser.error('needs exactly one input format.')
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(label,dim,inputtype) = [(options.eulers,3,'eulers'),
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([options.a,options.b,options.c],[3,3,3],'frame'),
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(options.matrix,9,'matrix'),
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(options.quaternion,4,'quaternion'),
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][np.where(input)[0][0]] # select input label that was requested
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toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
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r = damask.Quaternion().fromAngleAxis(toRadians*options.rotation[0],options.rotation[1:]) # pre-rotation
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# --- loop over input files ------------------------------------------------------------------------
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if filenames == []: filenames = ['STDIN']
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for name in filenames:
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if not (name == 'STDIN' or os.path.exists(name)): continue
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table = damask.ASCIItable(name = name, outname = name+'_tmp',
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buffered = False)
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table.croak('\033[1m'+scriptName+'\033[0m'+(': '+name if name != 'STDIN' else ''))
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# ------------------------------------------ read header ------------------------------------------
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table.head_read()
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# ------------------------------------------ sanity checks -----------------------------------------
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errors = []
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remarks = []
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if not np.all(table.label_dimension(label) == dim): errors.append('input {} has wrong dimension {}.'.format(label,dim))
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else: column = table.label_index(label)
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if remarks != []: table.croak(remarks)
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if errors != []:
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table.croak(errors)
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table.close(dismiss = True)
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continue
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# ------------------------------------------ assemble header ---------------------------------------
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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for output in options.output:
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if output == 'quaternion': table.labels_append(['{}_quat({})'.format( i+1,options.symmetry) for i in xrange(4)])
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if output == 'eulers': table.labels_append(['{}_eulers({})'.format(i+1,options.symmetry) for i in xrange(3)])
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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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if inputtype == 'eulers':
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o = damask.Orientation(Eulers = np.array(map(float,table.data[column:column+3]))*toRadians,
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symmetry = options.symmetry).reduced()
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elif inputtype == 'matrix':
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o = damask.Orientation(matrix = np.array(map(float,table.data[column:column+9])).reshape(3,3).transpose(),
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symmetry = options.symmetry).reduced()
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elif inputtype == 'frame':
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o = damask.Orientation(matrix = np.array(map(float,table.data[column[0]:column[0]+3] + \
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table.data[column[1]:column[1]+3] + \
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table.data[column[2]:column[2]+3])).reshape(3,3),
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symmetry = options.symmetry).reduced()
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elif inputtype == 'quaternion':
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o = damask.Orientation(quaternion = np.array(map(float,table.data[column:column+4])),
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symmetry = options.symmetry).reduced()
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o.quaternion = r*o.quaternion
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for output in options.output:
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if output == 'quaternion': table.data_append(o.asQuaternion())
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if output == 'eulers': table.data_append(o.asEulers('Bunge'))
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output finalization -----------------------------------
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table.close() # close ASCII tables
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if name != 'STDIN': os.rename(name+'_tmp',name) # overwrite old one with tmp new
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