simulation-class {AIUQ}R Documentation

Simulation class

Description

S4 class for 2D particle movement simulation.

Details

intensity should has structure 'T_SS_mat', matrix with dimension len_t by sz\timessz.

pos should be the position matrix with dimension M\timeslen_t. See bm_particle_intensity, ou_particle_intensity, fbm_particle_intensity, fbm_ou_particle_intensity.

Slots

sz

vector. Frame size of the intensity profile, number of pixels contained in each frame equals sz[1] by sz[2].

len_t

integer. Number of time steps.

noise

character. Background noise, options from ('uniform','gaussian').

model_name

character. Simulated stochastic process, options from ('BM','OU','FBM','OU+FBM').

M

integer. Number of particles.

pxsz

numeric. Size of one pixel in unit of micron, 1 for simulated data.

mindt

numeric. Minimum lag time, 1 for simulated data.

pos

matrix. Position matrix for particle trajectory, see 'Details'.

intensity

matrix. Filled intensity profile, see 'Details'.

num_msd

vector. Numerical mean squared displacement (MSD).

param

vector. Parameters for simulated stochastic process.

theor_msd

vector. Theoretical MSD.

sigma_2_0

vector. Variance of background noise.

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]