def compose(self, t):
"""calculate state and derivatives for model at image number t"""
# Extract orientation from the initial state
U0 = self._initial_state
# extract parameter sets from the internal list
phi1_set, phi2_set, phi3_set = self._param
# extract angles and other data at time t using the smoother
phi1, phi1_weights, phi1_sumweights = self._smoother.value_weight(t, phi1_set)
phi2, phi2_weights, phi2_sumweights = self._smoother.value_weight(t, phi2_set)
phi3, phi3_weights, phi3_sumweights = self._smoother.value_weight(t, phi3_set)
# calculate derivatives of angles wrt underlying parameters.
# FIXME write up notes in orange notebook
dphi1_dp = phi1_weights * (1.0 / phi1_sumweights)
dphi2_dp = phi2_weights * (1.0 / phi2_sumweights)
dphi3_dp = phi3_weights * (1.0 / phi3_sumweights)
# calculate state and derivatives using the helper class
coc = CrystalOrientationCompose(U0, phi1, phi1_set.axis, phi2, phi2_set.axis, phi3, phi3_set.axis)
self._U_at_t = coc.U()
dU_dphi1 = coc.dU_dphi1()
dU_dphi2 = coc.dU_dphi2()
dU_dphi3 = coc.dU_dphi3()
# calculate derivatives of state wrt underlying parameters
dU_dp1 = [None] * dphi1_dp.size
for (i, v) in dphi1_dp:
dU_dp1[i] = dU_dphi1 * v
dU_dp2 = [None] * dphi2_dp.size
for (i, v) in dphi2_dp:
dU_dp2[i] = dU_dphi2 * v
dU_dp3 = [None] * dphi3_dp.size
for (i, v) in dphi3_dp:
dU_dp3[i] = dU_dphi3 * v
# store derivatives as list-of-lists
self._dstate_dp = [dU_dp1, dU_dp2, dU_dp3]
return
def compose(self):
"""calculate state and derivatives"""
# Extract orientation from the initial state
U0 = self._initial_state
# extract parameters from the internal list
phi1, phi2, phi3 = self._param
# calculate using the helper class
coc = CrystalOrientationCompose(U0, phi1.value, phi1.axis,
phi2.value, phi2.axis,
phi3.value, phi3.axis)
# compose new state
self._model.set_U(coc.U())
# store derivatives
self._dstate_dp = [coc.dU_dphi1(), coc.dU_dphi2(), coc.dU_dphi3()]
return
def compose(self, t):
"""calculate state and derivatives for model at image number t"""
# Extract orientation from the initial state
U0 = self._initial_state
# extract parameter sets from the internal list
phi1_set, phi2_set, phi3_set = self._param
# extract angles and other data at time t using the smoother
phi1, phi1_weights, phi1_sumweights = self._smoother.value_weight(
t, phi1_set)
phi2, phi2_weights, phi2_sumweights = self._smoother.value_weight(
t, phi2_set)
phi3, phi3_weights, phi3_sumweights = self._smoother.value_weight(
t, phi3_set)
# calculate derivatives of angles wrt underlying parameters.
# FIXME write up notes in orange notebook
dphi1_dp = phi1_weights * (1. / phi1_sumweights)
dphi2_dp = phi2_weights * (1. / phi2_sumweights)
dphi3_dp = phi3_weights * (1. / phi3_sumweights)
# calculate state and derivatives using the helper class
coc = CrystalOrientationCompose(U0, phi1, phi1_set.axis, phi2,
phi2_set.axis, phi3, phi3_set.axis)
self._U_at_t = coc.U()
dU_dphi1 = coc.dU_dphi1()
dU_dphi2 = coc.dU_dphi2()
dU_dphi3 = coc.dU_dphi3()
# calculate derivatives of state wrt underlying parameters
dU_dp1 = [None] * dphi1_dp.size
for (i, v) in dphi1_dp:
dU_dp1[i] = dU_dphi1 * v
dU_dp2 = [None] * dphi2_dp.size
for (i, v) in dphi2_dp:
dU_dp2[i] = dU_dphi2 * v
dU_dp3 = [None] * dphi3_dp.size
for (i, v) in dphi3_dp:
dU_dp3[i] = dU_dphi3 * v
# store derivatives as list-of-lists
self._dstate_dp = [dU_dp1, dU_dp2, dU_dp3]
return
def compose(self):
# Extract orientation from the initial state
U0 = self._initial_state
# extract parameters from the internal list
phi1, phi2, phi3 = self._param
# calculate using the helper class
coc = CrystalOrientationCompose(U0, phi1.value, phi1.axis, phi2.value,
phi2.axis, phi3.value, phi3.axis)
# compose new state
self._model.set_U(coc.U())
# store derivatives
self._dstate_dp = [coc.dU_dphi1(), coc.dU_dphi2(), coc.dU_dphi3()]
return
