def MC_fitAll_Angles_wrap(allparams,agrain,wmin,wmax,angles, weighting = True):
pVec = allparams[0:3]
Rparams = allparams[3:6]
Uparams = allparams[6:12]
U = gw.vec_to_sym(Uparams)
R = Rotations.rotMatOfExpMap(Rparams)
#angles = MC_make_angles_from_spots_grain(R,U,agrain,pVec,wmin,wmax,tweak = False)
return MC_Angle_Fit(R,U,agrain,pVec,wmin,wmax,angles,weighting)
def _fitC(Cparams,gIs,angles,wavelength):
Cmat = gw.vec_to_sym(Cparams)
invCmat = inv(Cmat)
out = []
for i in range(len(gIs)):
gI = gIs[i]
angCOM = angles[i] #, spot in gI_spots:
r_i = _fitC_residual(angCOM,gI, invCmat, wavelength)
if weighting:
weight = uncertainty_analysis.propagateUncertainty(_fitC_residual, weighting[i], 1e-8,angCOM,gI,invCmat,wavelength)
else:
weight = 1
out.append(r_i/weight)
return num.array(out)
def MC_fitC_angle_weights(Rparams, Uparams, gIs,angles0, wavelength, weighting = False, report = True, evaluate = False):
"""
alternate fitting approach for U, uses no Rotation information.
Cparams: [C11,C22,C33,C12,C23,C13]
"""
from Vector_funcs import Mag
from numpy import dot,sqrt
import uncertainty_analysis
'internal objective function'
def _fitC_residual(angles, r0, invCmat, wavelength):
rI = gw.makeARecipVector(angles, wavelength)
#print rI
df = 1./Mag(rI)
d0 = 1./Mag(r0)
gii_0 = dot(r0,r0)
gii = dot(dot(invCmat,r0),r0)
r_i = df/d0 - sqrt(gii_0)/(sqrt(gii))
return r_i
def _fitC(Cparams,gIs,angles,wavelength):
Cmat = gw.vec_to_sym(Cparams)
invCmat = inv(Cmat)
out = []
for i in range(len(gIs)):
gI = gIs[i]
angCOM = angles[i] #, spot in gI_spots:
r_i = _fitC_residual(angCOM,gI, invCmat, wavelength)
if weighting:
weight = uncertainty_analysis.propagateUncertainty(_fitC_residual, weighting[i], 1e-8,angCOM,gI,invCmat,wavelength)
else:
weight = 1
out.append(r_i/weight)
return num.array(out)
if Rparams == 'default':
angl,axxx = Rotations.angleAxisOfRotMat(num.eye(3))
Rparams = (angl*axxx).flatten()
else:
Rparams = Rparams
if Uparams=='default':
Uparams = sym_to_vec(num.eye(3))
else:
Uparams = Uparams
U = gw.vec_to_sym(Uparams)
R = Rotations.rotMatOfExpMap(Rparams)
F = num.dot(R,U)
C_ = num.dot(F.T,F)
Cparams = gw.sym_to_vec(C_)
if evaluate:
return _fitC(Cparams,gIs,angles0,wavelength)
optResults = optimize.leastsq(_fitC, x0 = Cparams, args = (gIs,angles0,wavelength), full_output = 1)
Cparams = optResults[0]
C = gw.vec_to_sym(Cparams)
from scipy.linalg import eig
'spectral decomposition to get U'
eval,evec = eig(C)
l1_sqr,l2_sqr,l3_sqr = num.asarray(eval,dtype = 'float')
u1,u2,u3 = evec[:,0],evec[:,1],evec[:,2]
U = sqrt(l1_sqr)*num.outer(u1,u1) + sqrt(l2_sqr)*num.outer(u2,u2) + sqrt(l3_sqr)*num.outer(u3,u3)
if report:
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], )
return optResults
def MC_fitU_Angle_wrap(Uparams,R,agrain,pVec,wmin,wmax,angles,weighting = True):
uMat = gw.vec_to_sym(Uparams)
#angles = MC_make_angles_from_spots_grain(R,U,agrain,pVec,wmin,wmax,tweak = False)
return MC_Angle_Fit(R,uMat,agrain,pVec,wmin,wmax,angles, weighting)
def MC_fitRotation_angles(Rparams, Uparams, gIs,angles0, wavelength, weighting = False, report = True,evaluate = False):
assert len(gIs)==len(angles0), 'different lengths'
def _fitR_residual(angles, r0, Fmat, wavelength):
Cmat = dot(Fmat.T,Fmat)
rI = gw.makeARecipVector(angles,wavelength)
n = Unit(rI)
N = Unit(r0)
#print Fmat,Cmat
alpha_ = sqrt(Inner_Prod(Star(Cmat),N,N))
#print alpha_
r_i = Inner_Prod(Star(Fmat),n,N) - alpha_
#print 'r_i'
return r_i
def _fitRotation_lsq(Rparams, gIs,angles0, U,wavelength):
out = []
Rmat = Rotations.rotMatOfExpMap(Rparams)
Fmat = dot(Rmat,U)
for i in range(len(gIs)):
gI,angles = gIs[i], angles0[i]
r_i = _fitR_residual(angles,gI, Fmat, wavelength)
if weighting:
weight = uncertainty_analysis.propagateUncertainty(_fitR_residual, weighting[i], 1e-8,angles,gI,Fmat,wavelength)
maxiter = 100
ct = 0
while weight==0:
weight = uncertainty_analysis.propagateUncertainty(_fitR_residual, weighting[i], 1e-8,angles,gI,Fmat,wavelength)
ct+=1
if ct>=maxiter:
print 'zero weight error, i = ',i
weight = 1
break
else:
weight = 1.
out.append(r_i/weight)
if weight == 0:
print 'wefiht0',i,weighting[i],Fmat
out = num.array(out)
# print out
return out
if Rparams == 'default':
angl,axxx = Rotations.angleAxisOfRotMat(num.eye(3))
Rparams = (angl*axxx).flatten()
else:
Rparams = Rparams
if Uparams=='default':
Uparams = sym_to_vec(num.eye(3))
else:
Uparams = Uparams
U = gw.vec_to_sym(Uparams)
if evaluate:
return _fitRotation_lsq(Rparams,gIs,angles0,U,wavelength)
optResults = optimize.leastsq(_fitRotation_lsq, x0 = Rparams, args = (gIs,angles0, 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], )
return optResults
