def fitU(self, Rparams = 'default', Uparams = 'default'):
if Uparams=='default':
Uparams = sym_to_vec(self.uMat)
else:
Uparams = Uparams
if Rparams == 'default':
angl, axxx = Rotations.angleAxisOfRotMat(self.rMat)
Rparams = (angl*axxx).flatten()
else:
Rparams = Rparams
optResults = optimize.leastsq(self._fitU_objFunc_lsq, x0 = Uparams, args = (Rparams, self.planeData.wavelength), xtol=1e-5, ftol=1e-5, full_output = 1)
Uparams = optResults[0]
U = vec_to_sym(Uparams)
print "refined stretch matrix: \n%g, %g, %g\n%g, %g, %g\n%g, %g, %g\n" \
% (U[0, 0], U[0, 1], U[0, 2], \
U[1, 0], U[1, 1], U[1, 2], \
U[2, 0], U[2, 1], U[2, 2], )
self.uMat = U
def fitRotationStar_angle_weights(self, Rparams = 'default', Uparams = 'default', report = True, weighting = True, evaluate = False):
"""
uses F*N = \alpha n to refine rotation
"""
def _fitR_residual(angles, r0, Fmat, wavelength):
Cmat = dot(Fmat.T,Fmat)
rI = makeARecipVector(angles,wavelength)
n = Unit(rI)
N = Unit(r0)
alpha_ = sqrt(Inner_Prod(Star(Cmat),N,N))
r_i = Inner_Prod(Star(Fmat),n,N) - alpha_
return r_i
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)
if Rparams == 'default':
angl,axxx = Rotations.angleAxisOfRotMat(self.rMat)
Rparams = (angl*axxx).flatten()
else:
Rparams = Rparams
if Uparams=='default':
Uparams = sym_to_vec(self.uMat)
else:
Uparams = Uparams
self.fitGrainSpotUncertainties()
gI_spots = self.associateRecipVector_Spots()
U = vec_to_sym(Uparams)
wavelength = self.planeData.wavelength
if evaluate:
return _fitRotation_lsq(Rparams,gI_spots,U,wavelength)
optResults = optimize.leastsq(_fitRotation_lsq, x0 = Rparams, args = (gI_spots, U, wavelength), full_output = 1)
r1 = optResults[0]
U1 = Rotations.rotMatOfExpMap(r1)
if report:
print "refined orientation matrix: \n%g, %g, %g\n%g, %g, %g\n%g, %g, %g\n" \
% (U1[0, 0], U1[0, 1], U1[0, 2], \
U1[1, 0], U1[1, 1], U1[1, 2], \
U1[2, 0], U1[2, 1], U1[2, 2], )
self.rMat = U1
return optResults
def fitRotation_Angles_(self, Rparams = 'default', Uparams = 'default', report = True, weighting = True, evaluate = False):
"""
"""
if Rparams == 'default':
angl,axxx = Rotations.angleAxisOfRotMat(self.rMat)
Rparams = (angl*axxx).flatten()
else:
Rparams = Rparams
if Uparams=='default':
Uparams = sym_to_vec(self.uMat)
else:
Uparams = Uparams
U = vec_to_sym(Uparams)
def _lsq_Rotation(Rparams, U, weighting = True):
return self.fitAngles_lsq(Rparams, U, weighting)
if evaluate:
return _lsq_Rotation(Rparams,U,weighting)
optResults = optimize.leastsq(_lsq_Rotation, x0 = Rparams, args = (U,weighting), full_output = 1)
r1 = optResults[0]
U1 = Rotations.rotMatOfExpMap(r1)
if report:
print "refined orientation matrix: \n%g, %g, %g\n%g, %g, %g\n%g, %g, %g\n" \
% (U1[0, 0], U1[0, 1], U1[0, 2], \
U1[1, 0], U1[1, 1], U1[1, 2], \
U1[2, 0], U1[2, 1], U1[2, 2], )
# reset pVec in self
self.rMat = U1
return optResults
def fitU_Angles_(self, Rparams = 'default', Uparams = 'default', weighting = True, report = True,evaluate = False):
if Uparams=='default':
Uparams = sym_to_vec(self.uMat)
else:
Uparams = Uparams
if Rparams == 'default':
angl, axxx = Rotations.angleAxisOfRotMat(self.rMat)
Rparams = (angl*axxx).flatten()
else:
Rparams = Rparams
def _lsq_U(Uparams, Rparams):
U = vec_to_sym(Uparams)
return self.fitAngles_lsq(Rparams, U, weighting)
if evaluate:
return _lsq_U(Uparams, Rparams, weighting)
optResults = optimize.leastsq(_lsq_U, x0 = Uparams, args = Rparams, full_output = 1)
r1 = optResults[0]
U1 = vec_to_sym(r1)
if report:
print "refined U matrix: \n%g, %g, %g\n%g, %g, %g\n%g, %g, %g\n" \
% (U1[0, 0], U1[0, 1], U1[0, 2], \
U1[1, 0], U1[1, 1], U1[1, 2], \
U1[2, 0], U1[2, 1], U1[2, 2], )
self.uMat = U1
return optResults
def fitRotation(self, Rparams = 'default', Uparams = 'default', report = True,evaluate = False):
"""
uses F*N = \alpha n to refine rotation
"""
if Rparams == 'default':
angl,axxx = Rotations.angleAxisOfRotMat(self.rMat)
Rparams = (angl*axxx).flatten()
else:
Rparams = Rparams
if Uparams=='default':
Uparams = sym_to_vec(self.uMat)
else:
Uparams = Uparams
def _fitRotation_lsq(Rparams, vecs, U):
out = []
Rmat = Rotations.rotMatOfExpMap(Rparams)
Fmat = dot(Rmat,U)
Cmat = dot(Fmat.T,Fmat)
for r0,rd in vecs:
N = Unit(r0)
n = Unit(rd)
alpha_ = sqrt(Inner_Prod(Star(Cmat),N,N))
r_i = Inner_Prod(Star(Fmat),n,N) - alpha_
out.append(r_i)
return num.array(out)
gI_rIs = self.associateRecipVectors()
U = vec_to_sym(Uparams)
if evaluate:
return _fitRotation_lsq(Rparams,gI_rIs,U)
optResults = optimize.leastsq(_fitRotation_lsq, x0 = Rparams, args = (gI_rIs, U), full_output = 1)
r1 = optResults[0]
U1 = Rotations.rotMatOfExpMap(r1)
if report:
print "refined orientation matrix: \n%g, %g, %g\n%g, %g, %g\n%g, %g, %g\n" \
% (U1[0, 0], U1[0, 1], U1[0, 2], \
U1[1, 0], U1[1, 1], U1[1, 2], \
U1[2, 0], U1[2, 1], U1[2, 2], )
# reset pVec in self
self.rMat = U1
return optResults
def fitF(self):
def _fitF(FParams, vecs):
Rparams = FParams[0:3]
Uparams = FParams[3:9]
rMat = Rotations.rotMatOfExpMap(Rparams)
uMat = vec_to_sym(Uparams)
F = dot(rMat,uMat)
FinvT = inv(F).T
out = []
for r0,rd in vecs:
diff = dot(FinvT,r0) - rd
out.append(diff[0])
out.append(diff[1])
out.append(diff[2])
return num.array(out)
gI_rIs = self.associateRecipVectors()
angle,axxx = Rotations.angleAxisOfRotMat(self.rMat)
Rparams = (angle*axxx).flatten()
Uparams = sym_to_vec(self.uMat)
Fparams = []
Fparams.extend(list(Rparams))
Fparams.extend(list(Uparams))
optResults = optimize.leastsq(_fitF, x0 = Fparams, args = gI_rIs, full_output = 1)
Rparams = optResults[0][0:3]
Uparams = optResults[0][3:9]
rMat = Rotations.rotMatOfExpMap(Rparams)
uMat = vec_to_sym(Uparams)
F = dot(rMat,uMat)
print 'finalF'
print F
R_,U = polarDecomposition(F)
print R_,'\n',U
return optResults