Merge branch 'vectorize_rotation' into 'development'
Vectorize rotation See merge request damask/DAMASK!171
This commit is contained in:
Karo
commit
f63e412bcf
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@ -2,6 +2,7 @@
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import os
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import sys
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from io import StringIO
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from optparse import OptionParser
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import numpy as np
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@ -24,14 +25,8 @@ Additional (globally fixed) rotations of the lab frame and/or crystal frame can
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""", version = scriptID)
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representations = {
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'quaternion': ['qu',4],
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'rodrigues': ['ro',4],
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'Rodrigues': ['Ro',3],
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'eulers': ['eu',3],
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'matrix': ['om',9],
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'angleaxis': ['ax',4],
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}
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representations = ['quaternion', 'rodrigues', 'eulers', 'matrix', 'axisangle']
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parser.add_option('-o',
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'--output',
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@ -93,10 +88,10 @@ parser.set_defaults(output = [],
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)
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(options, filenames) = parser.parse_args()
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if filenames == []: filenames = [None]
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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(representations))):
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parser.error('output must be chosen from {}.'.format(', '.join(representations)))
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parser.error('output must be chosen from {}.'.format(', '.join(representations)))
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input = [options.eulers is not None,
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options.rodrigues is not None,
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@ -109,95 +104,47 @@ input = [options.eulers is not None,
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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,representations['eulers'][1],'eulers'),
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(options.rodrigues,representations['rodrigues'][1],'rodrigues'),
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([options.x,options.y,options.z],[3,3,3],'frame'),
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(options.matrix,representations['matrix'][1],'matrix'),
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(options.quaternion,representations['quaternion'][1],'quaternion'),
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][np.where(input)[0][0]] # select input label that was requested
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r = damask.Rotation.fromAxisAngle(np.array(options.crystalrotation),options.degrees,normalise=True)
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R = damask.Rotation.fromAxisAngle(np.array(options.labrotation),options.degrees,normalise=True)
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# --- loop over input files ------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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r = damask.Rotation.from_axis_angle(np.array(options.crystalrotation),options.degrees,normalise=True)
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R = damask.Rotation.from_axis_angle(np.array(options.labrotation),options.degrees,normalise=True)
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name)
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except IOError:
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continue
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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# ------------------------------------------ read header ------------------------------------------
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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table.head_read()
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if options.eulers is not None:
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label = options.eulers
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print(np.max(table.get(options.eulers),axis=0))
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o = damask.Rotation.from_Eulers(table.get(options.eulers), options.degrees)
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elif options.rodrigues is not None:
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label = options.rodrigues
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o = damask.Rotation.from_Rodrigues(table.get(options.rodrigues))
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elif options.matrix is not None:
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label = options.matrix
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o = damask.Rotation.from_matrix(table.get(options.matrix).reshape(-1,3,3))
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elif options.x is not None:
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label = '<{},{},{}>'.format(options.x,options.y,options.z)
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M = np.block([table.get(options.x),table.get(options.y),table.get(options.z)]).reshape(-1,3,3)
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o = damask.Rotation.from_matrix(M/np.linalg.norm(M,axis=0))
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elif options.quaternion is not None:
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label = options.quaternion
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o = damask.Rotation.from_quaternion(table.get(options.quaternion))
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# ------------------------------------------ sanity checks -----------------------------------------
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o = r.broadcast_to(o.shape) @ o @ R.broadcast_to(o.shape)
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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 options.lattice is not None:
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# o = damask.Orientation(rotation = o,lattice = options.lattice).reduced().rotation
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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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if 'rodrigues' in options.output:
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table.add('ro({})'.format(label),o.as_Rodrigues(), scriptID+' '+' '.join(sys.argv[1:]))
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if 'eulers' in options.output:
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table.add('eu({})'.format(label),o.as_Eulers(options.degrees), scriptID+' '+' '.join(sys.argv[1:]))
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if 'quaternion' in options.output:
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table.add('qu({})'.format(label),o.as_quaternion(), scriptID+' '+' '.join(sys.argv[1:]))
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if 'matrix' in options.output:
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table.add('om({})'.format(label),o.as_matrix(), scriptID+' '+' '.join(sys.argv[1:]))
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if 'axisangle' in options.output:
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table.add('om({})'.format(label),o.as_axisangle(options.degrees), scriptID+' '+' '.join(sys.argv[1:]))
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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 representations:
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table.labels_append(['{}_{}({})'.format(i+1,representations[output][0],label) \
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for i in range(representations[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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d = representations['eulers'][1]
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o = damask.Rotation.fromEulers(list(map(float,table.data[column:column+d])),options.degrees)
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elif inputtype == 'rodrigues':
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d = representations['rodrigues'][1]
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o = damask.Rotation.fromRodrigues(list(map(float,table.data[column:column+d])))
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elif inputtype == 'matrix':
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d = representations['matrix'][1]
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o = damask.Rotation.fromMatrix(np.array(list(map(float,table.data[column:column+d]))).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.Rotation.fromMatrix(M/np.linalg.norm(M,axis=0))
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elif inputtype == 'quaternion':
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d = representations['quaternion'][1]
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o = damask.Rotation.fromQuaternion(list(map(float,table.data[column:column+d])))
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o = r*o*R # apply additional lab and crystal frame rotations
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if options.lattice is not None:
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o = damask.Orientation(rotation = o,lattice = options.lattice).reduced().rotation
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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 == 'Rodrigues': table.data_append(o.asRodrigues(vector=True))
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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.asAxisAngle(degrees=options.degrees))
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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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table.to_ASCII(sys.stdout if name is None else name)
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@ -37,27 +37,26 @@ parser.add_option('--degrees',
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parser.set_defaults(rotation = (1.,1.,1.,0), # 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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if filenames == []: filenames = [None]
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if options.data is None:
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parser.error('no data column specified.')
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parser.error('no data column specified.')
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r = damask.Rotation.fromAxisAngle(options.rotation,options.degrees,normalise=True)
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r = damask.Rotation.from_axis_angle(options.rotation,options.degrees,normalise=True)
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for name in filenames:
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damask.util.report(scriptName,name)
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table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
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for data in options.data:
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d = table.get(data)
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if table.shapes[data] == (9,): d=d.reshape(-1,3,3)
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for i,l in enumerate(d):
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d[i] = r*l
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d = r.broadcast_to(d.shape[0:1]) @ d
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if table.shapes[data] == (9,): d=d.reshape(-1,9)
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table.set(data,d,scriptID+' '+' '.join(sys.argv[1:]))
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table.to_ASCII(sys.stdout if name is None else name)
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@ -84,9 +84,9 @@ if [options.angleaxis,options.quaternion].count(None) == 0:
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parser.error('more than one rotation specified.')
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if options.angleaxis is not None:
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rotation = damask.Rotation.fromAxisAngle(np.array(options.angleaxis),options.degrees,normalise=True)
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rotation = damask.Rotation.from_axis_angle(np.array(options.angleaxis),options.degrees,normalise=True)
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elif options.quaternion is not None:
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rotation = damask.Rotation.fromQuaternion(options.quaternion)
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rotation = damask.Rotation.from_quaternion(options.quaternion)
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else:
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rotation = damask.Rotation()
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@ -97,7 +97,7 @@ for name in filenames:
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dataset = os.path.join(group_pointwise,options.quaternion)
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try:
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quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
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rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
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rot = [damask.Rotation.from_quaternion(q,True,P=+1) for q in quats]
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except KeyError:
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errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
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@ -123,7 +123,7 @@ for name in filenames:
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dataset = os.path.join(group_average,options.quaternion)
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try:
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rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]] # skip first entry (unindexed)
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rot = [damask.Rotation.from_quaternion(q,True,P=+1) for q in inFile[dataset][...][1:]] # skip first entry (unindexed)
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except KeyError:
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errors.append('Average orientation data ({}) not readable'.format(dataset))
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@ -140,7 +140,7 @@ for name in filenames:
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config_header = ['<texture>']
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for i in range(np.nanmax(microstructure)):
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config_header += ['[{}{}]'.format(label,i+1),
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'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*rot[i].asEulers(degrees = True)),
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'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*rot[i].as_Eulers(degrees = True)),
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]
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config_header += ['<microstructure>']
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for i in range(np.nanmax(microstructure)):
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@ -89,7 +89,7 @@ for name in filenames:
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for i,data in enumerate(unique):
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ori = damask.Rotation(data[0:4])
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config_header += ['[Grain{}]'.format(i+1),
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'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*ori.asEulers(degrees = True)),
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'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*ori.as_Eulers(degrees = True)),
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]
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if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)]
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@ -59,15 +59,15 @@ if [options.rotation,options.eulers,options.matrix,options.quaternion].count(Non
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parser.error('no rotation specified.')
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if options.quaternion is not None:
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rot = damask.Rotation.fromQuaternion(np.array(options.quaternion)) # we might need P=+1 here, too...
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rot = damask.Rotation.from_quaternion(np.array(options.quaternion)) # we might need P=+1 here, too...
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if options.rotation is not None:
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rot = damask.Rotation.fromAxisAngle(np.array(options.rotation),degrees=options.degrees,normalise=True,P=+1)
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rot = damask.Rotation.from_axis_angle(np.array(options.rotation),degrees=options.degrees,normalise=True,P=+1)
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if options.matrix is not None:
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rot = damask.Rotation.fromMatrix(np.array(options.Matrix))
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rot = damask.Rotation.from_matrix(np.array(options.Matrix))
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if options.eulers is not None:
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rot = damask.Rotation.fromEulers(np.array(options.eulers),degrees=options.degrees)
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rot = damask.Rotation.from_Eulers(np.array(options.eulers),degrees=options.degrees)
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eulers = rot.asEulers(degrees=True)
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eulers = rot.as_Eulers(degrees=True)
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if filenames == []: filenames = [None]
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@ -635,6 +635,6 @@ class Lattice:
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otherDir = miller[otherDir_id]/ np.linalg.norm(miller[otherDir_id])
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otherMatrix = np.array([otherDir,np.cross(otherPlane,otherDir),otherPlane])
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r['rotations'].append(Rotation.fromMatrix(np.dot(otherMatrix.T,myMatrix)))
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r['rotations'].append(Rotation.from_matrix(np.dot(otherMatrix.T,myMatrix)))
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return r
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@ -37,7 +37,7 @@ class Orientation:
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if isinstance(rotation, Rotation):
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self.rotation = rotation
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else:
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self.rotation = Rotation.fromQuaternion(rotation) # assume quaternion
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self.rotation = Rotation.from_quaternion(rotation) # assume quaternion
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if self.rotation.quaternion.shape != (4,):
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raise NotImplementedError('Support for multiple rotations missing')
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@ -68,8 +68,8 @@ class Orientation:
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r = b*aInv
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for k in range(2):
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r.inverse()
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breaker = self.lattice.symmetry.inFZ(r.asRodrigues(vector=True)) \
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and (not SST or other.lattice.symmetry.inDisorientationSST(r.asRodrigues(vector=True)))
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breaker = self.lattice.symmetry.inFZ(r.as_Rodrigues(vector=True)) \
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and (not SST or other.lattice.symmetry.inDisorientationSST(r.as_Rodrigues(vector=True)))
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if breaker: break
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if breaker: break
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if breaker: break
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@ -78,7 +78,7 @@ class Orientation:
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# ... own sym, other sym,
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# self-->other: True, self<--other: False
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def inFZ(self):
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return self.lattice.symmetry.inFZ(self.rotation.asRodrigues(vector=True))
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return self.lattice.symmetry.inFZ(self.rotation.as_Rodrigues(vector=True))
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def equivalentOrientations(self,members=[]):
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@ -100,7 +100,7 @@ class Orientation:
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def reduced(self):
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"""Transform orientation to fall into fundamental zone according to symmetry."""
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for me in self.equivalentOrientations():
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if self.lattice.symmetry.inFZ(me.rotation.asRodrigues(vector=True)): break
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if self.lattice.symmetry.inFZ(me.rotation.as_Rodrigues(vector=True)): break
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return self.__class__(me.rotation,self.lattice)
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File diff suppressed because it is too large
Load Diff
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@ -8,13 +8,8 @@ import damask
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from damask import Rotation
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from damask import Orientation
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from damask import Lattice
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n = 1000
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@pytest.fixture
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def default():
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"""A set of n random rotations."""
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return [Rotation.fromRandom() for r in range(n)]
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n = 1000
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@pytest.fixture
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def reference_dir(reference_dir_base):
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@ -28,15 +23,15 @@ class TestOrientation:
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{'label':'green','RGB':[0,1,0],'direction':[0,1,1]},
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{'label':'blue', 'RGB':[0,0,1],'direction':[1,1,1]}])
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@pytest.mark.parametrize('lattice',['fcc','bcc'])
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def test_IPF_cubic(self,default,color,lattice):
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def test_IPF_cubic(self,color,lattice):
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cube = damask.Orientation(damask.Rotation(),lattice)
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for direction in set(permutations(np.array(color['direction']))):
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assert np.allclose(cube.IPFcolor(direction),np.array(color['RGB']))
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assert np.allclose(cube.IPFcolor(np.array(direction)),np.array(color['RGB']))
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@pytest.mark.parametrize('lattice',Lattice.lattices)
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def test_IPF(self,lattice):
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direction = np.random.random(3)*2.0-1
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for rot in [Rotation.fromRandom() for r in range(n//100)]:
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for rot in [Rotation.from_random() for r in range(n//100)]:
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R = damask.Orientation(rot,lattice)
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color = R.IPFcolor(direction)
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for equivalent in R.equivalentOrientations():
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@ -45,7 +40,7 @@ class TestOrientation:
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@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
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@pytest.mark.parametrize('lattice',['fcc','bcc'])
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def test_relationship_forward_backward(self,model,lattice):
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ori = Orientation(Rotation.fromRandom(),lattice)
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ori = Orientation(Rotation.from_random(),lattice)
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for i,r in enumerate(ori.relatedOrientations(model)):
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||||
ori2 = r.relatedOrientations(model)[i]
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misorientation = ori.rotation.misorientation(ori2.rotation)
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@ -56,8 +51,8 @@ class TestOrientation:
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|||
def test_relationship_reference(self,update,reference_dir,model,lattice):
|
||||
reference = os.path.join(reference_dir,'{}_{}.txt'.format(lattice,model))
|
||||
ori = Orientation(Rotation(),lattice)
|
||||
eu = np.array([o.rotation.asEulers(degrees=True) for o in ori.relatedOrientations(model)])
|
||||
if update:
|
||||
eu = np.array([o.rotation.as_Eulers(degrees=True) for o in ori.relatedOrientations(model)])
|
||||
if update:
|
||||
coords = np.array([(1,i+1) for i,x in enumerate(eu)])
|
||||
table = damask.Table(eu,{'Eulers':(3,)})
|
||||
table.add('pos',coords)
|
||||
|
|
|
|||
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Reference in New Issue