210 lines
9.7 KiB
Python
Executable File
210 lines
9.7 KiB
Python
Executable File
#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os,sys
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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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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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# --------------------------------------------------------------------
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# convention conformity checks
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# --------------------------------------------------------------------
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def check_Eulers(eulers):
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if np.any(eulers < 0.0) or np.any(eulers > 2.0*np.pi) or eulers[1] > np.pi: # Euler angles within valid range?
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raise ValueError('Euler angles outside of [0..2π],[0..π],[0..2π].\n{} {} {}.'.format(*eulers))
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return eulers
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def check_quaternion(q):
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if q[0] < 0.0: # positive first quaternion component?
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raise ValueError('quaternion has negative first component.\n{}'.format(q[0]))
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if not np.isclose(np.linalg.norm(q), 1.0): # unit quaternion?
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raise ValueError('quaternion is not of unit length.\n{} {} {} {}'.format(*q))
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return q
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def check_matrix(M):
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if not np.isclose(np.linalg.det(M),1.0): # proper rotation?
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raise ValueError('matrix is not a proper rotation.\n{}'.format(M))
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if not np.isclose(np.dot(M[0],M[1]), 0.0) \
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or not np.isclose(np.dot(M[1],M[2]), 0.0) \
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or not np.isclose(np.dot(M[2],M[0]), 0.0): # all orthogonal?
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raise ValueError('matrix is not orthogonal.\n{}'.format(M))
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return M
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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
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(i.e. component vectors of rotation matrix).
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Additional (globally fixed) rotations of the lab frame and/or crystal frame can be applied.
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""", version = scriptID)
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outputChoices = {
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'quaternion': ['quat',4],
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'rodrigues': ['rodr',3],
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'eulers': ['eulr',3],
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'matrix': ['mtrx',9],
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'angleaxis': ['aaxs',4],
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}
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parser.add_option('-o',
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'--output',
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dest = 'output',
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action = 'extend', metavar = '<string LIST>',
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help = 'output orientation formats {{{}}}'.format(', '.join(outputChoices)))
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parser.add_option('-d',
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'--degrees',
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dest = 'degrees',
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action = 'store_true',
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help = 'all angles in degrees')
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parser.add_option('-R',
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'--labrotation',
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dest='labrotation',
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type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
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help = 'angle and axis of additional lab frame rotation [%default]')
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parser.add_option('-r',
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'--crystalrotation',
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dest='crystalrotation',
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type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
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help = 'angle and axis of additional crystal frame rotation [%default]')
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parser.add_option('--eulers',
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dest = 'eulers',
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metavar = 'string',
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help = 'Euler angles label')
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parser.add_option('--rodrigues',
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dest = 'rodrigues',
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metavar = 'string',
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help = 'Rodrigues vector label')
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parser.add_option('--matrix',
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dest = 'matrix',
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metavar = 'string',
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help = 'orientation matrix label')
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parser.add_option('--quaternion',
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dest = 'quaternion',
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metavar = 'string',
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help = 'quaternion label')
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parser.add_option('-x',
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dest = 'x',
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metavar = 'string',
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help = 'label of lab x vector (expressed in crystal coords)')
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parser.add_option('-y',
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dest = 'y',
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metavar = 'string',
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help = 'label of lab y vector (expressed in crystal coords)')
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parser.add_option('-z',
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dest = 'z',
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metavar = 'string',
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help = 'label of lab z vector (expressed in crystal coords)')
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parser.set_defaults(output = [],
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labrotation = (0.,1.,1.,1.), # no rotation about 1,1,1
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crystalrotation = (0.,1.,1.,1.), # no rotation about 1,1,1
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)
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(options, filenames) = parser.parse_args()
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options.output = list(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 is not None,
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options.rodrigues is not None,
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options.x is not None and \
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options.y is not None and \
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options.z is not None,
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options.matrix is not None,
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options.quaternion is not 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.rodrigues,3,'rodrigues'),
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([options.x,options.y,options.z],[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 = np.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
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r = damask.Quaternion.fromAngleAxis(toRadians*options.crystalrotation[0],options.crystalrotation[1:]) # crystal frame rotation
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R = damask.Quaternion.fromAngleAxis(toRadians*options. labrotation[0],options. labrotation[1:]) # lab frame rotation
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# --- loop over input files ------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try: table = damask.ASCIItable(name = name,
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buffered = False)
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except: continue
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damask.util.report(scriptName,name)
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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 {} does not have dimension {}.'.format(label,dim))
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else: column = table.label_index(label)
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.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 in outputChoices:
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table.labels_append(['{}_{}({})'.format(i+1,outputChoices[output][0],label) \
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for i in range(outputChoices[output][1])])
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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 = check_Eulers(np.array(list(map(float,table.data[column:column+3])))*toRadians))
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elif inputtype == 'rodrigues':
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o = damask.Orientation(Rodrigues = np.array(list(map(float,table.data[column:column+3]))))
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elif inputtype == 'matrix':
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o = damask.Orientation(matrix = check_matrix(np.array(list(map(float,table.data[column:column+9]))).reshape(3,3)))
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elif inputtype == 'frame':
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M = np.array(list(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).T
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o = damask.Orientation(matrix = check_matrix(M/np.linalg.norm(M,axis=0)))
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elif inputtype == 'quaternion':
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o = damask.Orientation(quaternion = check_quaternion(np.array(list(map(float,table.data[column:column+4])))))
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o.quaternion = r*o.quaternion*R # apply additional lab and crystal frame rotations
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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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elif output == 'rodrigues': table.data_append(o.asRodrigues())
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elif output == 'eulers': table.data_append(o.asEulers(degrees=options.degrees))
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elif output == 'matrix': table.data_append(o.asMatrix())
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elif output == 'angleaxis': table.data_append(o.asAngleAxis(degrees=options.degrees,flat=True))
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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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