using new table class + vectorized rotation

This commit is contained in:
Martin Diehl 2020-05-16 09:40:44 +02:00
parent e2ba294b75
commit 347e3b8c60
2 changed files with 46 additions and 100 deletions

View File

@ -2,6 +2,7 @@
import os import os
import sys import sys
from io import StringIO
from optparse import OptionParser from optparse import OptionParser
import numpy as np import numpy as np
@ -24,14 +25,8 @@ Additional (globally fixed) rotations of the lab frame and/or crystal frame can
""", version = scriptID) """, version = scriptID)
representations = { representations = ['quaternion', 'rodrigues', 'eulers', 'matrix', 'axisangle']
'quaternion': ['qu',4],
'rodrigues': ['ro',4],
'Rodrigues': ['Ro',3],
'eulers': ['eu',3],
'matrix': ['om',9],
'angleaxis': ['ax',4],
}
parser.add_option('-o', parser.add_option('-o',
'--output', '--output',
@ -93,8 +88,8 @@ parser.set_defaults(output = [],
) )
(options, filenames) = parser.parse_args() (options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
#options.output = list(map(lambda x: x.lower(), options.output))
if options.output == [] or (not set(options.output).issubset(set(representations))): if options.output == [] or (not set(options.output).issubset(set(representations))):
parser.error('output must be chosen from {}.'.format(', '.join(representations))) parser.error('output must be chosen from {}.'.format(', '.join(representations)))
@ -109,95 +104,47 @@ input = [options.eulers is not None,
if np.sum(input) != 1: parser.error('needs exactly one input format.') if np.sum(input) != 1: parser.error('needs exactly one input format.')
(label,dim,inputtype) = [(options.eulers,representations['eulers'][1],'eulers'), r = damask.Rotation.from_axis_angle(np.array(options.crystalrotation),options.degrees,normalise=True)
(options.rodrigues,representations['rodrigues'][1],'rodrigues'), R = damask.Rotation.from_axis_angle(np.array(options.labrotation),options.degrees,normalise=True)
([options.x,options.y,options.z],[3,3,3],'frame'),
(options.matrix,representations['matrix'][1],'matrix'),
(options.quaternion,representations['quaternion'][1],'quaternion'),
][np.where(input)[0][0]] # select input label that was requested
r = damask.Rotation.fromAxisAngle(np.array(options.crystalrotation),options.degrees,normalise=True)
R = damask.Rotation.fromAxisAngle(np.array(options.labrotation),options.degrees,normalise=True)
# --- loop over input files ------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
try:
table = damask.ASCIItable(name = name)
except IOError:
continue
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------ table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.head_read() if options.eulers is not None:
label = options.eulers
print(np.max(table.get(options.eulers),axis=0))
o = damask.Rotation.from_Eulers(table.get(options.eulers), options.degrees)
elif options.rodrigues is not None:
label = options.rodrigues
o = damask.Rotation.from_Rodrigues(table.get(options.rodrigues))
elif options.matrix is not None:
label = options.matrix
o = damask.Rotation.from_matrix(table.get(options.matrix).reshape(-1,3,3))
elif options.x is not None:
label = '<{},{},{}>'.format(options.x,options.y,options.z)
M = np.block([table.get(options.x),table.get(options.y),table.get(options.z)]).reshape(-1,3,3)
o = damask.Rotation.from_matrix(M/np.linalg.norm(M,axis=0))
elif options.quaternion is not None:
label = options.quaternion
o = damask.Rotation.from_quaternion(table.get(options.quaternion))
# ------------------------------------------ sanity checks ----------------------------------------- o = r.broadcast_to(o.shape) @ o @ R.broadcast_to(o.shape)
errors = [] #if options.lattice is not None:
remarks = [] # o = damask.Orientation(rotation = o,lattice = options.lattice).reduced().rotation
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 'rodrigues' in options.output:
if errors != []: table.add('ro({})'.format(label),o.as_rodrigues(), scriptID+' '+' '.join(sys.argv[1:]))
damask.util.croak(errors) if 'eulers' in options.output:
table.close(dismiss = True) table.add('eu({})'.format(label),o.as_Eulers(options.degrees), scriptID+' '+' '.join(sys.argv[1:]))
continue if 'quaternion' in options.output:
table.add('qu({})'.format(label),o.as_quaternion(), scriptID+' '+' '.join(sys.argv[1:]))
if 'matrix' in options.output:
table.add('om({})'.format(label),o.as_matrix(), scriptID+' '+' '.join(sys.argv[1:]))
if 'axisangle' in options.output:
table.add('om({})'.format(label),o.as_axisangle(options.degrees), scriptID+' '+' '.join(sys.argv[1:]))
# ------------------------------------------ assemble header --------------------------------------- table.to_ASCII(sys.stdout if name is None else name)
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
for output in options.output:
if output in representations:
table.labels_append(['{}_{}({})'.format(i+1,representations[output][0],label) \
for i in range(representations[output][1])])
table.head_write()
# ------------------------------------------ process data ------------------------------------------
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
if inputtype == 'eulers':
d = representations['eulers'][1]
o = damask.Rotation.fromEulers(list(map(float,table.data[column:column+d])),options.degrees)
elif inputtype == 'rodrigues':
d = representations['rodrigues'][1]
o = damask.Rotation.fromRodrigues(list(map(float,table.data[column:column+d])))
elif inputtype == 'matrix':
d = representations['matrix'][1]
o = damask.Rotation.fromMatrix(np.array(list(map(float,table.data[column:column+d]))).reshape(3,3))
elif inputtype == 'frame':
M = np.array(list(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).T
o = damask.Rotation.fromMatrix(M/np.linalg.norm(M,axis=0))
elif inputtype == 'quaternion':
d = representations['quaternion'][1]
o = damask.Rotation.fromQuaternion(list(map(float,table.data[column:column+d])))
o = r*o*R # apply additional lab and crystal frame rotations
if options.lattice is not None:
o = damask.Orientation(rotation = o,lattice = options.lattice).reduced().rotation
for output in options.output:
if output == 'quaternion': table.data_append(o.asQuaternion())
elif output == 'rodrigues': table.data_append(o.asRodrigues())
elif output == 'Rodrigues': table.data_append(o.asRodrigues(vector=True))
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.asAxisAngle(degrees=options.degrees))
outputAlive = table.data_write() # output processed line
# ------------------------------------------ output finalization -----------------------------------
table.close() # close ASCII tables

View File

@ -44,7 +44,7 @@ if filenames == []: filenames = [None]
if options.data is None: if options.data is None:
parser.error('no data column specified.') parser.error('no data column specified.')
r = damask.Rotation.fromAxisAngle(options.rotation,options.degrees,normalise=True) r = damask.Rotation.from_axis_angle(options.rotation,options.degrees,normalise=True)
for name in filenames: for name in filenames:
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
@ -54,8 +54,7 @@ for name in filenames:
for data in options.data: for data in options.data:
d = table.get(data) d = table.get(data)
if table.shapes[data] == (9,): d=d.reshape(-1,3,3) if table.shapes[data] == (9,): d=d.reshape(-1,3,3)
for i,l in enumerate(d): d = r.broadcast_to(d.shape[0:1]) @ d
d[i] = r*l
if table.shapes[data] == (9,): d=d.reshape(-1,9) if table.shapes[data] == (9,): d=d.reshape(-1,9)
table.set(data,d,scriptID+' '+' '.join(sys.argv[1:])) table.set(data,d,scriptID+' '+' '.join(sys.argv[1:]))