def buildMisOriList(self, calcAxis=False):
quatCompsSym = Quat.calcSymEqvs(self.quatList, self.crystalSym)
if self.refOri is None:
self.refOri = Quat.calcAverageOri(quatCompsSym)
misOriArray, minQuatComps = Quat.calcMisOri(quatCompsSym, self.refOri)
self.averageMisOri = misOriArray.mean()
self.misOriList = list(misOriArray)
if calcAxis:
# Now for axis calulation
refOriInv = self.refOri.conjugate
misOriAxis = np.empty((3, minQuatComps.shape[1]))
Dq = np.empty((4, minQuatComps.shape[1]))
# refOriInv * minQuat for all points (* is quaternion product)
# change to minQuat * refOriInv
Dq[0, :] = (refOriInv[0] * minQuatComps[0, :] - refOriInv[1] * minQuatComps[1, :] -
refOriInv[2] * minQuatComps[2, :] - refOriInv[3] * minQuatComps[3, :])
Dq[1, :] = (refOriInv[1] * minQuatComps[0, :] + refOriInv[0] * minQuatComps[1, :] +
refOriInv[3] * minQuatComps[2, :] - refOriInv[2] * minQuatComps[3, :])
Dq[2, :] = (refOriInv[2] * minQuatComps[0, :] + refOriInv[0] * minQuatComps[2, :] +
refOriInv[1] * minQuatComps[3, :] - refOriInv[3] * minQuatComps[1, :])
Dq[3, :] = (refOriInv[3] * minQuatComps[0, :] + refOriInv[0] * minQuatComps[3, :] +
refOriInv[2] * minQuatComps[1, :] - refOriInv[1] * minQuatComps[2, :])
Dq[:, Dq[0] < 0] = -Dq[:, Dq[0] < 0]
# numpy broadcasting taking care of different array sizes
misOriAxis[:, :] = (2 * Dq[1:4, :] * np.arccos(Dq[0, :])) / np.sqrt(1 - np.power(Dq[0, :], 2))
# hack it back into a list. Need to change self.*List to be arrays, it was a bad decision to
# make them lists in the beginning
self.misOriAxisList = []
for row in misOriAxis.transpose():
self.misOriAxisList.append(row)
def calcAverageOri(self):
quatCompsSym = Quat.calcSymEqvs(self.quatList, self.crystalSym)
self.refOri = Quat.calcAverageOri(quatCompsSym)
