using new table class + vectorized rotation
This commit is contained in:
Martin Diehl
parent
e2ba294b75
commit
347e3b8c60
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@ -2,6 +2,7 @@
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import os
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import os
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import sys
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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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from optparse import OptionParser
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import numpy as np
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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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""", version = scriptID)
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representations = {
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representations = ['quaternion', 'rodrigues', 'eulers', 'matrix', 'axisangle']
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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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parser.add_option('-o',
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parser.add_option('-o',
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'--output',
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'--output',
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@ -93,8 +88,8 @@ parser.set_defaults(output = [],
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)
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)
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(options, filenames) = parser.parse_args()
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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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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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@ -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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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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r = damask.Rotation.from_axis_angle(np.array(options.crystalrotation),options.degrees,normalise=True)
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(options.rodrigues,representations['rodrigues'][1],'rodrigues'),
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R = damask.Rotation.from_axis_angle(np.array(options.labrotation),options.degrees,normalise=True)
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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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for name in filenames:
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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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#if options.lattice is not None:
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remarks = []
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# o = damask.Orientation(rotation = o,lattice = options.lattice).reduced().rotation
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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 'rodrigues' in options.output:
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if errors != []:
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table.add('ro({})'.format(label),o.as_rodrigues(), scriptID+' '+' '.join(sys.argv[1:]))
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damask.util.croak(errors)
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if 'eulers' in options.output:
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table.close(dismiss = True)
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table.add('eu({})'.format(label),o.as_Eulers(options.degrees), scriptID+' '+' '.join(sys.argv[1:]))
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continue
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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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# ------------------------------------------ assemble header ---------------------------------------
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table.to_ASCII(sys.stdout if name is None else name)
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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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@ -44,7 +44,7 @@ if filenames == []: filenames = [None]
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if options.data is 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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for name in filenames:
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damask.util.report(scriptName,name)
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damask.util.report(scriptName,name)
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@ -54,8 +54,7 @@ for name in filenames:
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for data in options.data:
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for data in options.data:
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d = table.get(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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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 = r.broadcast_to(d.shape[0:1]) @ d
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d[i] = r*l
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if table.shapes[data] == (9,): d=d.reshape(-1,9)
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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.set(data,d,scriptID+' '+' '.join(sys.argv[1:]))
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