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.


[Package AIUQ version 0.5.1 Index]