def _fitRotation_lsq(Rparams, gI_spots, U,wavelength):
out = []
Rmat = Rotations.rotMatOfExpMap(Rparams)
Fmat = dot(Rmat,U)
for gI,spot in gI_spots:
try:
angCOM, angCOM_unc = spot.angCOM(useFit=True, getUncertainties=True)
except RuntimeError:
continue
r_i = _fitR_residual(angCOM.flatten(),gI, Fmat, wavelength)
if weighting:
weight = uncertainty_analysis.propagateUncertainty(_fitR_residual, angCOM_unc, 1e-8,angCOM.flatten(),gI,Fmat,wavelength)
#print 'Rotation using weight', weight, r_i, r_i/weight, angCOM_unc
else:
weight = 1.
out.append(r_i/weight)
return num.array(out)
def _fitC(Cparams,gI_spots,wavelength):
Cmat = vec_to_sym(Cparams)
invCmat = inv(Cmat)
out = []
for gI, spot in gI_spots:
try:
angCOM, angCOM_unc = spot.angCOM(useFit=True, getUncertainties=True)
except RuntimeError:
continue
r_i = _fitC_residual(angCOM.flatten(),gI, invCmat, wavelength)
if weighting:
weight = uncertainty_analysis.propagateUncertainty(_fitC_residual, angCOM_unc, 1e-8,angCOM.flatten(),gI,invCmat,wavelength)
#print 'using weight', weight, r_i, r_i/weight, angCOM_unc
else:
weight = 1
out.append(r_i/weight)
return num.array(out)
def associateRecipVectors_w_Uncertainty(self, forceReRead = False):
"""
pairs up gI from B.[h,k,l] to the measured rI for that [h,k,l].
For use with rotation/strain refinement functions.
stores results in self.gI_rIs
"""
if self.vecs_associated_w_uncertainty == True and forceReRead == False:
return self.gI_rIs_u_rIs
'else do the association'
self.fitGrainSpotUncertainties()
wavelength = self.planeData.wavelength
masterReflInfo = self.grainSpots
hitRelfId = num.where(masterReflInfo['iRefl'] >= 0)[0]
measHKLs = masterReflInfo['hkl'][hitRelfId, :]
gIs = num.dot(self.bMat, measHKLs.T)
gI_rIs_u_rIs=[]
for i in range(len(hitRelfId)):
Id = hitRelfId[i]
spotId = masterReflInfo['iRefl'][Id]
spot = self.spots._Spots__spots[spotId]
try:
angCOM, angCOM_unc = spot.angCOM(useFit=True, getUncertainties=True)
except RuntimeError:
continue
mus = num.hstack(angCOM).flatten()
mu_uncs = num.hstack(angCOM_unc).flatten()
meas_tth, meas_eta, meas_ome = mus
rI = makeARecipVector([meas_tth,meas_eta,meas_ome], wavelength)
u_rI = uncertainty_analysis.propagateUncertainty(makeARecipVector, mu_uncs, 1e-8, mus,wavelength )
gI = gIs[:,i]
gI_rIs_u_rIs.append([gI, rI, u_rI])
self.vecs_associated_w_uncertainty = True
self.gI_rIs_u_rIs = gI_rIs_u_rIs
return gI_rIs_u_rIs
