add IPF color tuple for HDF5 file
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#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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import os
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import sys
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import math
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import damask
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import numpy as np
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from optparse import OptionParser
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName, damask.version])
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# TODO
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# This implementation will have to iterate through the array one
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# element at a time, maybe there are some other ways to make this
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# faster.
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# ----- Helper functions ----- #
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# ref: http://stackoverflow.com/questions/16801322/how-can-i-check-that-a-list-
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# has-one-and-only-one-truthy-value
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# NOTE:
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# These functions might be useful in the future
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def n_trues(iterable, n=1):
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"""N(trues) = n"""
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i = iter(iterable)
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return all(any(i) for j in range(n)) and not any(i)
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def up_to_n_trues(iterable, n=1):
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i = iter(iterable)
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all(any(i) for j in range(n))
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return not any(i)
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def at_least_n_trues(iterable, n=1):
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i = iter(iterable)
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return all(any(i) for j in range(n))
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def m_to_n_trues(iterable, m=1, n=1):
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i = iter(iterable)
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assert m <= n
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return at_least_n_trues(i, m) and up_to_n_trues(i, n - m)
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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desp = "Add RGB color value corresponding to TSL-OIM scheme for IPF."
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parser = OptionParser(option_class=damask.extendableOption,
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usage='%prog options [file[s]]',
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description=desp,
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version=scriptID)
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parser.add_option('-p', '--pole',
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dest='pole',
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type='float', nargs=3, metavar='float float float',
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help='lab frame direction for IPF [%default]')
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msg = ', '.join(damask.Symmetry.lattices[1:])
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parser.add_option('-s', '--symmetry',
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dest='symmetry',
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type='choice', choices=damask.Symmetry.lattices[1:],
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metavar='string',
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help='crystal symmetry [%default] {{{}}} '.format(msg))
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parser.add_option('-e', '--eulers',
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dest='eulers',
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type='string', metavar='string',
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help='Euler angles label')
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parser.add_option('-d', '--degrees',
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dest='degrees',
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action='store_true',
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help='Euler angles are given in degrees [%default]')
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parser.add_option('-m', '--matrix',
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dest='matrix',
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type='string', metavar='string',
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help='orientation matrix label')
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parser.add_option('-a',
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dest='a',
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type='string', metavar='string',
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help='crystal frame a vector label')
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parser.add_option('-b',
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dest='b',
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type='string', metavar='string',
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help='crystal frame b vector label')
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parser.add_option('-c',
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dest='c',
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type='string', metavar='string',
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help='crystal frame c vector label')
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parser.add_option('-q', '--quaternion',
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dest='quaternion',
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type='string', metavar='string',
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help='quaternion label')
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parser.set_defaults(pole=(0.0, 0.0, 1.0),
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symmetry=damask.Symmetry.lattices[-1],
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degrees=False)
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(options, filenames) = parser.parse_args()
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# safe guarding to have only one orientation representation
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# use dynamic typing to group a,b,c into frame
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options.frame = [options.a, options.b, options.c]
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input = [options.eulers is not None,
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all(options.frame),
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options.matrix is not None,
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options.quaternion is not None]
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if np.sum(input) != 1:
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parser.error('needs exactly one input format.')
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# select input label that was requested (active)
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label_active = np.where(input)[0][0]
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(label, dim, inputtype) = [(options.eulers, 3, 'eulers'),
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(options.frame, [3, 3, 3], 'frame'),
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(options.matrix, 9, 'matrix'),
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(options.quaternion, 4, 'quaternion')][label_active]
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# rescale degrees to radians
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toRadians = math.pi/180.0 if options.degrees else 1.0
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# only use normalized pole
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pole = np.array(options.pole)
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pole /= np.linalg.norm(pole)
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# ----- Loop over input files ----- #
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for name in filenames:
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try:
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h5f = damask.H5Table(name, new_file=False)
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except:
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continue
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damask.util.report(scriptName, name)
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# extract data from HDF5 file
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if inputtype == 'eulers':
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orieData = h5f.get_data(label)
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elif inputtype == 'matrix':
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orieData = h5f.get_data(label)
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orieData = orieData.reshape(orieData.shape[0], 3, 3)
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elif inputtype == 'frame':
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vctr_a = h5f.get_data(label[0])
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vctr_b = h5f.get_data(label[1])
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vctr_c = h5f.get_data(label[2])
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frame = np.column_stack((vctr_a, vctr_b, vctr_c))
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orieData = frame.reshape(frame.shape[0], 3, 3)
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elif inputtype == 'quaternion':
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orieData = h5f.get_data(label)
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# calculate the IPF color
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rgbArrays = np.zeros((orieData.shape[0], 3))
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for ci in xrange(rgbArrays.shape[0]):
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if inputtype == 'eulers':
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o = damask.Orientation(Eulers=np.array(orieData[ci, :])*toRadians,
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symmetry=options.symmetry).reduced()
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elif inputtype == 'matrix':
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o = damask.Orientation(matrix=orieData[ci, :, :].transpose(),
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symmetry=options.symmetry).reduced()
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elif inputtype == 'frame':
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o = damask.Orientation(matrix=orieData[ci, :, :],
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symmetry=options.symmetry).reduced()
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elif inputtype == 'quaternion':
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o = damask.Orientation(quaternion=orieData[ci, :],
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symmetry=options.symmetry).reduced()
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rgbArrays[ci, :] = o.IPFcolor(pole)
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# compose labels/headers for IPF color (RGB)
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labelIPF = 'IPF_{:g}{:g}{:g}_{sym}'.format(*options.pole,
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sym=options.symmetry.lower())
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# compose cmd history (go with dataset)
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cmd_log = scriptID + '\t' + ' '.join(sys.argv[1:])
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# write data to HDF5 file
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h5f.add_data(labelIPF, rgbArrays, cmd_log=cmd_log)
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