class R2(FreeParameterTemplate): """R2 = 1/T2, for linear T2Dec or other models.""" init_value = 5 lower_bound = 0.5 upper_bound = 500.0 parameter_transform = ScaleTransform(1e2)
class D_12(FreeParameterTemplate): init_value = 0.1e-9 lower_bound = 0 upper_bound = 5e-9 parameter_transform = ScaleTransform(1e10) sampling_proposal_std = 1e-10 numdiff_info = {'scale_factor': 1e10, 'use_upper_bound': False}
class R2s(FreeParameterTemplate): """R2s = 1/T2s, for lineaR T2sDec or other models.""" init_value = 10 lower_bound = 1 upper_bound = 50.0 parameter_transform = ScaleTransform(1e2)
class time_dependent_characteristic_coefficient(FreeParameterTemplate): """The time dependent characteristic as used in the TimeDependentZeppelin model. Values are in m^2.""" init_value = 1e-6 lower_bound = 1e-7 upper_bound = 1e-5 parameter_transform = ScaleTransform(1e7) sampling_proposal_std = 1e-7
class R1(FreeParameterTemplate): """R1 = 1/T1, for linear T1Dec or other models. """ init_value = 2 lower_bound = 0.25 upper_bound = 100.0 parameter_transform = ScaleTransform(1e2)
class matrix_element_param(FreeParameterTemplate): name = 'W_{}{}{}{}'.format(*index) init_value = _init_value lower_bound = _lower_bound upper_bound = 1e20 parameter_transform = ScaleTransform(100) sampling_prior = _sampling_prior sampling_proposal_std = 0.01
class d_exvivo(FreeParameterTemplate): """For use in ExpT1DecSTEAM model. It assumes ex-vivo values. For in-vivo use ``d`` instead.""" init_value = 5.0e-10 lower_bound = 0.0 upper_bound = 1.0e-8 parameter_transform = ScaleTransform(1e10) sampling_proposal_std = 1e-11 numdiff_info = {'scale_factor': 1e10, 'use_upper_bound': False}
class dperp1(FreeParameterTemplate): init_value = 1.7e-11 lower_bound = 0 upper_bound = 1.0e-8 parameter_transform = ScaleTransform(1e10) sampling_proposal_std = 1e-10 numdiff_info = {'scale_factor': 1e10, 'use_upper_bound': False}
class kw(FreeParameterTemplate): """We optimize the ratio w = k1/k2 in the Ball&Racket and NODDI Bingham model""" init_value = 2 lower_bound = 1 upper_bound = 64 sampling_proposal_std = 0.01 numdiff_info = {'use_upper_bound': False} parameter_transform = ScaleTransform(1 / 64.)
class k1(FreeParameterTemplate): """The kappa parameter for the Ball&Racket and NODDI Bingham model""" init_value = 1 lower_bound = 0 upper_bound = 64 sampling_proposal_std = 0.01 numdiff_info = {'use_upper_bound': False} parameter_transform = ScaleTransform(1 / 64.)
class T2_b(FreeParameterTemplate): """T2_b""" init_value = 10e-6 lower_bound = 1e-7 upper_bound = 100e-6 parameter_transform = ScaleTransform(1e6) numdiff_info = { 'scale_factor': 1e5, 'use_upper_bound': False, 'use_lower_bound': False }
class kappa(FreeParameterTemplate): """The kappa parameter used in the NODDI Watson model. The NODDI-Watson model computes the spherical harmonic (SH) coefficients of the Watson distribution with the concentration parameter k (kappa) up to the 12th order. Truncating at the 12th order gives good approximation for kappa up to 64, as such we define kappa to be between zero and 64. """ init_value = 1 lower_bound = 0 upper_bound = 64 sampling_proposal_std = 0.01 numdiff_info = {'use_upper_bound': False} parameter_transform = ScaleTransform(1 / 64.)
class scale(FreeParameterTemplate): init_value = 1e-6 lower_bound = 0.01e-6 upper_bound = 20e-6 parameter_transform = ScaleTransform(1e6) sampling_proposal_std = 0.01e-6
class T2(FreeParameterTemplate): init_value = 0.05 lower_bound = 1e-5 upper_bound = 2.0 parameter_transform = ScaleTransform(1e4)
class R(FreeParameterTemplate): init_value = 1.0e-6 lower_bound = 1e-7 upper_bound = 20e-6 parameter_transform = ScaleTransform(1e7) sampling_proposal_std = 1e-7