SAM-class {AIUQ} | R Documentation |
SAM class
Description
S4 class for fast parameter estimation in scattering analysis of microscopy,
using either AIUQ
or DDM
method.
Slots
pxsz
numeric. Size of one pixel in unit of micron with default value 1.
mindt
numeric. Minimum lag time with default value 1.
sz
vector. Frame size of the intensity profile in x and y directions, number of pixels contained in each frame equals sz_x by sz_y.
len_t
integer. Number of time steps.
len_q
integer. Number of wave vector.
q
vector. Wave vector in unit of um^-1.
d_input
vector. Sequence of lag times.
B_est_ini
numeric. Estimation of B. This parameter is determined by the noise in the system. See 'References'.
A_est_ini
vector. Estimation of A(q). Note this parameter is determined by the properties of the imaged material and imaging optics. See 'References'.
I_o_q_2_ori
vector. Absolute square of Fourier transformed intensity profile, ensemble over time.
q_ori_ring_loc_unique_index
list. List of location index of non-duplicate values for each q ring.
model_name
character. Fitted model, options from ('BM','OU','FBM','OU+FBM', 'user_defined').
param_est
vector. Estimated parameters contained in MSD.
sigma_2_0_est
numeric. Estimated variance of background noise.
msd_est
vector. Estimated MSD.
uncertainty
logical. A logical evaluating to TRUE or FALSE indicating whether parameter uncertainty should be computed.
msd_lower
vector. Lower bound of 95% confidence interval of MSD.
msd_upper
vector. Upper bound of 95% confidence interval of MSD.
msd_truth
vector. True MSD or reference MSD value.
sigma_2_0_truth
vector. True variance of background noise, non NA for simulated data using
simulation
.param_truth
vector. True parameters used to construct MSD, non NA for simulated data using
simulation
.index_q
vector. Selected index of wave vector.
Dqt
matrix. Dynamic image structure function D(q,delta t).
ISF
matrix. Empirical intermediate scattering function f(q,delta t).
I_q
matrix. Fourier transformed intensity profile with structure 'SS_T_mat'.
AIC
numeric. Akaike information criterion score.
mle
numeric. Maximum log likelihood value.
param_uq_range
matrix. 95% confidence interval for estimated parameters.
modeled_Dqt
matrix. Modeled dynamic image structure function D(q,delta t).
modeled_ISF
matrix. Modeled intermediate scattering function f(q,delta t).
Author(s)
Yue He [aut], Xubo Liu [aut], Mengyang Gu [aut, cre]
References
Gu, M., He, Y., Liu, X., & Luo, Y. (2023). Ab initio uncertainty quantification in scattering analysis of microscopy. arXiv preprint arXiv:2309.02468.
Gu, M., Luo, Y., He, Y., Helgeson, M. E., & Valentine, M. T. (2021). Uncertainty quantification and estimation in differential dynamic microscopy. Physical Review E, 104(3), 034610.
Cerbino, R., & Trappe, V. (2008). Differential dynamic microscopy: probing wave vector dependent dynamics with a microscope. Physical review letters, 100(18), 188102.