From 336a80091fc4fd6fc6fa5857541429a49a4aa79d Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 12 Feb 2019 08:58:23 +0100 Subject: [PATCH] rodrigues is 4-vector with rotation being the last component established a single source of truth for length --- processing/post/addOrientations.py | 42 ++++++++++++++++-------------- python/damask/orientation.py | 14 +++++----- 2 files changed, 30 insertions(+), 26 deletions(-) diff --git a/processing/post/addOrientations.py b/processing/post/addOrientations.py index 65444bcb9..8353e0403 100755 --- a/processing/post/addOrientations.py +++ b/processing/post/addOrientations.py @@ -21,19 +21,19 @@ Additional (globally fixed) rotations of the lab frame and/or crystal frame can """, version = scriptID) -outputChoices = { - 'quaternion': ['quat',4], - 'rodrigues': ['rodr',3], +representations = { + 'quaternion': ['quat',4], #ToDo: Use here Rowenhorst names (qu/ro/om/ax?) + 'rodrigues': ['rodr',4], 'eulers': ['eulr',3], 'matrix': ['mtrx',9], 'angleaxis': ['aaxs',4], - } + } parser.add_option('-o', '--output', dest = 'output', action = 'extend', metavar = '', - help = 'output orientation formats {{{}}}'.format(', '.join(outputChoices))) + help = 'output orientation formats {{{}}}'.format(', '.join(representations))) parser.add_option('-d', '--degrees', dest = 'degrees', @@ -87,8 +87,8 @@ parser.set_defaults(output = [], (options, filenames) = parser.parse_args() options.output = list(map(lambda x: x.lower(), options.output)) -if options.output == [] or (not set(options.output).issubset(set(outputChoices))): - parser.error('output must be chosen from {}.'.format(', '.join(outputChoices))) +if options.output == [] or (not set(options.output).issubset(set(representations))): + parser.error('output must be chosen from {}.'.format(', '.join(representations))) input = [options.eulers is not None, options.rodrigues is not None, @@ -101,11 +101,11 @@ input = [options.eulers is not None, if np.sum(input) != 1: parser.error('needs exactly one input format.') -(label,dim,inputtype) = [(options.eulers,3,'eulers'), - (options.rodrigues,3,'rodrigues'), +(label,dim,inputtype) = [(options.eulers,representations['eulers'][1],'eulers'), + (options.rodrigues,representations['rodrigues'][1],'rodrigues'), ([options.x,options.y,options.z],[3,3,3],'frame'), - (options.matrix,9,'matrix'), - (options.quaternion,4,'quaternion'), + (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.fromAngleAxis(options.crystalrotation,options.degrees) # crystal frame rotation @@ -143,9 +143,9 @@ for name in filenames: table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:])) for output in options.output: - if output in outputChoices: - table.labels_append(['{}_{}({})'.format(i+1,outputChoices[output][0],label) \ - for i in range(outputChoices[output][1])]) + 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 ------------------------------------------ @@ -153,13 +153,16 @@ for name in filenames: outputAlive = True while outputAlive and table.data_read(): # read next data line of ASCII table if inputtype == 'eulers': - o = damask.Rotation.fromEulers(list(map(float,table.data[column:column+3])),options.degrees) + l = representations['eulers'][1] + o = damask.Rotation.fromEulers(list(map(float,table.data[column:column+l])),options.degrees) elif inputtype == 'rodrigues': - o = damask.Rotation.fromRodrigues(list(map(float,table.data[column:column+3]))) + l = representations['rodrigues'][1] + o = damask.Rotation.fromRodrigues(list(map(float,table.data[column:column+l]))) elif inputtype == 'matrix': - o = damask.Rotation.fromMatrix(list(map(float,table.data[column:column+9])).reshape(3,3)) + l = representations['matrix'][1] + o = damask.Rotation.fromMatrix(list(map(float,table.data[column:column+l]))) elif inputtype == 'frame': M = np.array(list(map(float,table.data[column[0]:column[0]+3] + \ @@ -168,7 +171,8 @@ for name in filenames: o = damask.Rotation.fromMatrix(M/np.linalg.norm(M,axis=0)) elif inputtype == 'quaternion': - o = damask.Rotation.fromQuaternion(list(map(float,table.data[column:column+4]))) + l = representations['quaternion'][1] + o = damask.Rotation.fromQuaternion(list(map(float,table.data[column:column+l]))) o= r*o*R # apply additional lab and crystal frame rotations @@ -177,7 +181,7 @@ for name in filenames: elif output == 'rodrigues': table.data_append(o.asRodrigues()) 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)) + elif output == 'angleaxis': table.data_append(o.asAngleAxis(degrees=options.degrees)) outputAlive = table.data_write() # output processed line # ------------------------------------------ output finalization ----------------------------------- diff --git a/python/damask/orientation.py b/python/damask/orientation.py index e53915b13..6f1b12671 100644 --- a/python/damask/orientation.py +++ b/python/damask/orientation.py @@ -336,7 +336,7 @@ class Rotation: matrix, containsStretch = False): #ToDo: better name? - om = matrix if isinstance(matrix, np.ndarray) else np.array(matrix) + om = matrix if isinstance(matrix, np.ndarray) else np.array(matrix).reshape((3,3)) # ToDo: Reshape here or require explicit? if containsStretch: (U,S,Vh) = np.linalg.svd(om) # singular value decomposition om = np.dot(U,Vh) @@ -356,12 +356,12 @@ class Rotation: P = -1): ro = rodrigues if isinstance(rodrigues, np.ndarray) else np.array(rodrigues) - if P > 0: ro[1:4] *= -1 # convert from P=1 to P=-1 - if normalise: ro[1:4] /=np.linalg.norm(ro[1:4]) - if not np.isclose(np.linalg.norm(ro[1:4]), 1.0): - raise ValueError('Rodrigues rotation axis is not of unit length.\n{} {} {}'.format(*ro[1:4])) - if ro[0] < 0.0: - raise ValueError('Rodriques rotation angle not positive.\n'.format(ro[0])) + if P > 0: ro[0:3] *= -1 # convert from P=1 to P=-1 + if normalise: ro[0:3] /=np.linalg.norm(ro[0:3]) + if not np.isclose(np.linalg.norm(ro[0:3]), 1.0): + raise ValueError('Rodrigues rotation axis is not of unit length.\n{} {} {}'.format(*ro[0:3])) + if ro[3] < 0.0: + raise ValueError('Rodriques rotation angle not positive.\n'.format(ro[3])) return cls(ro2qu(ro))