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DAMASK_EICMD
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more output options, frame input changed to "lab expressed in crystal"

This commit is contained in:
Philip Eisenlohr 2018-12-07 22:03:14 -05:00
parent 3d7a73a0de
commit ac45a9e2d3
1 changed files with 38 additions and 38 deletions
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76
processing/post/addOrientations.py
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@ -21,19 +21,22 @@ Additional (globally fixed) rotations of the lab frame and/or crystal frame can
""", version = scriptID) """, version = scriptID)
outputChoices = ['quaternion','rodrigues','eulers'] outputChoices = {
'quaternion': ['quat',4],
'rodrigues': ['rodr',3],
'eulers': ['eulr',3],
'matrix': ['mtrx',9],
'angleaxis': ['aaxs',4],
}
parser.add_option('-o', '--output', parser.add_option('-o', '--output',
dest = 'output', dest = 'output',
action = 'extend', metavar = '<string LIST>', action = 'extend', metavar = '<string LIST>',
help = 'output orientation formats {{{}}}'.format(', '.join(outputChoices))) 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', parser.add_option('-d', '--degrees',
dest = 'degrees', dest = 'degrees',
action = 'store_true', action = 'store_true',
help = 'angles are given in degrees [%default]') help = 'all angles in degrees')
parser.add_option('-R', '--labrotation', parser.add_option('-R', '--labrotation',
dest='labrotation', dest='labrotation',
type = 'float', nargs = 4, metavar = ' '.join(['float']*4), type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
@ -58,21 +61,20 @@ parser.add_option( '--quaternion',
dest = 'quaternion', dest = 'quaternion',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
help = 'quaternion label') help = 'quaternion label')
parser.add_option('-a', parser.add_option('-x',
dest = 'a', dest = 'x',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
help = 'crystal frame a vector label') help = 'label of lab x vector (expressed in crystal coords)')
parser.add_option('-b', parser.add_option('-y',
dest = 'b', dest = 'y',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
help = 'crystal frame b vector label') help = 'label of lab y vector (expressed in crystal coords)')
parser.add_option('-c', parser.add_option('-z',
dest = 'c', dest = 'z',
type = 'string', metavar = 'string', type = 'string', metavar = 'string',
help = 'crystal frame c vector label') help = 'label of lab z vector (expressed in crystal coords)')
parser.set_defaults(output = [], parser.set_defaults(output = [],
symmetry = damask.Symmetry.lattices[-1],
labrotation = (0.,1.,1.,1.), # no rotation about 1,1,1 labrotation = (0.,1.,1.,1.), # no rotation about 1,1,1
crystalrotation = (0.,1.,1.,1.), # no rotation about 1,1,1 crystalrotation = (0.,1.,1.,1.), # no rotation about 1,1,1
degrees = False, degrees = False,
@ -86,9 +88,9 @@ if options.output == [] or (not set(options.output).issubset(set(outputChoices))
input = [options.eulers is not None, input = [options.eulers is not None,
options.rodrigues is not None, options.rodrigues is not None,
options.a is not None and \ options.x is not None and \
options.b is not None and \ options.y is not None and \
options.c is not None, options.z is not None,
options.matrix is not None, options.matrix is not None,
options.quaternion is not None, options.quaternion is not None,
] ]
@ -97,13 +99,13 @@ if np.sum(input) != 1: parser.error('needs exactly one input format.')
(label,dim,inputtype) = [(options.eulers,3,'eulers'), (label,dim,inputtype) = [(options.eulers,3,'eulers'),
(options.rodrigues,3,'rodrigues'), (options.rodrigues,3,'rodrigues'),
([options.a,options.b,options.c],[3,3,3],'frame'), ([options.x,options.y,options.z],[3,3,3],'frame'),
(options.matrix,9,'matrix'), (options.matrix,9,'matrix'),
(options.quaternion,4,'quaternion'), (options.quaternion,4,'quaternion'),
][np.where(input)[0][0]] # select input label that was requested ][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 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.crystalrotation[0],options.crystalrotation[1:]) # crystal frame rotation
R = damask.Quaternion().fromAngleAxis(toRadians*options. labrotation[0],options. labrotation[1:]) # lab frame rotation R = damask.Quaternion.fromAngleAxis(toRadians*options. labrotation[0],options. labrotation[1:]) # lab frame rotation
# --- loop over input files ------------------------------------------------------------------------ # --- loop over input files ------------------------------------------------------------------------
@ -137,32 +139,28 @@ for name in filenames:
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:])) table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
for output in options.output: for output in options.output:
if output == 'quaternion': table.labels_append(['{}_{}_{}({})'.format(i+1,'quat',options.symmetry,label) for i in range(4)]) if output in outputChoices:
elif output == 'rodrigues': table.labels_append(['{}_{}_{}({})'.format(i+1,'rodr',options.symmetry,label) for i in range(3)]) table.labels_append(['{}_{}({})'.format(i+1,outputChoices[output][0],label) \
elif output == 'eulers': table.labels_append(['{}_{}_{}({})'.format(i+1,'eulr',options.symmetry,label) for i in range(3)]) for i in range(outputChoices[output][1])])
table.head_write() table.head_write()
# ------------------------------------------ process data ------------------------------------------ # ------------------------------------------ process data ------------------------------------------
outputAlive = True outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table while outputAlive and table.data_read(): # read next data line of ASCII table
if inputtype == 'eulers': if inputtype == 'eulers':
o = damask.Orientation(Eulers = np.array(list(map(float,table.data[column:column+3])))*toRadians, o = damask.Orientation(Eulers = np.array(list(map(float,table.data[column:column+3])))*toRadians)
symmetry = options.symmetry).reduced()
elif inputtype == 'rodrigues': elif inputtype == 'rodrigues':
o = damask.Orientation(Rodrigues= np.array(list(map(float,table.data[column:column+3]))), o = damask.Orientation(Rodrigues= np.array(list(map(float,table.data[column:column+3]))))
symmetry = options.symmetry).reduced()
elif inputtype == 'matrix': elif inputtype == 'matrix':
o = damask.Orientation(matrix = np.array(list(map(float,table.data[column:column+9]))).reshape(3,3).transpose(), o = damask.Orientation(matrix = np.array(list(map(float,table.data[column:column+9]))).reshape(3,3))
symmetry = options.symmetry).reduced()
elif inputtype == 'frame': elif inputtype == 'frame':
o = damask.Orientation(matrix = np.array(list(map(float,table.data[column[0]:column[0]+3] + \ M = np.array(list(map(float,table.data[column[0]:column[0]+3] + \
table.data[column[1]:column[1]+3] + \ table.data[column[1]:column[1]+3] + \
table.data[column[2]:column[2]+3]))).reshape(3,3), table.data[column[2]:column[2]+3]))).reshape(3,3).T
symmetry = options.symmetry).reduced() o = damask.Orientation(matrix = M/np.linalg.norm(M,axis=0))
elif inputtype == 'quaternion': elif inputtype == 'quaternion':
o = damask.Orientation(quaternion = np.array(list(map(float,table.data[column:column+4]))), o = damask.Orientation(quaternion = np.array(list(map(float,table.data[column:column+4]))))
symmetry = options.symmetry).reduced()
o.quaternion = r*o.quaternion*R # apply additional lab and crystal frame rotations o.quaternion = r*o.quaternion*R # apply additional lab and crystal frame rotations
@ -170,6 +168,8 @@ for name in filenames:
if output == 'quaternion': table.data_append(o.asQuaternion()) if output == 'quaternion': table.data_append(o.asQuaternion())
elif output == 'rodrigues': table.data_append(o.asRodrigues()) elif output == 'rodrigues': table.data_append(o.asRodrigues())
elif output == 'eulers': table.data_append(o.asEulers(degrees=options.degrees)) elif output == 'eulers': table.data_append(o.asEulers(degrees=options.degrees))
elif output == 'matrix': table.data_append(o.asMatrix())
elif output == 'angleaxis': table.data_append(o.asAngleAxis(degrees=options.degrees,flat=True))
outputAlive = table.data_write() # output processed line outputAlive = table.data_write() # output processed line
# ------------------------------------------ output finalization ----------------------------------- # ------------------------------------------ output finalization -----------------------------------