Two methods for optical flow estimation

summary:In this paper we describe two methods for optical flow estimation between two images. Both methods are based on the backward tracking of characteristics for advection equation and the difference is on the choice of advection vector field. We present numerical experiments on 2D data of cell nucleus

High resolution compact implicit numerical scheme for conservation laws

We present a novel implicit scheme for the numerical solution of time-dependent conservation laws. The core idea of the presented method is to exploit and approximate the mixed spatial-temporal derivative of the solution that occurs naturally when deriving some second order accurate schemes in time. Such an approach is introduced in the context of the Lax-Wendroff (or Cauchy-Kowalevski) procedure when the second time derivative is not completely replaced by space derivatives using the PDE, but the mixed derivative is kept. If approximated in a suitable way, the resulting compact implicit scheme produces algebraic systems that have a more convenient structure than the systems derived by fully implicit schemes. We derive a high resolution TVD form of the implicit scheme for some representative hyperbolic equations in the one-dimensional case, including illustrative numerical experiments.Comment: Significantly revised version that is accepted to AMC journa

Unconditionally stable higher order semi-implicit level set method for advection equations

We present compact semi-implicit finite difference schemes on structured grids for numerical solutions of the advection by an external velocity and by a speed in normal direction that are applicable in level set methods. The most involved numerical scheme is third order accurate for the linear advection with a space dependent velocity and unconditionally stable in the sense of von Neumann stability analysis. We also present a simple high-resolution scheme that gives a TVD (Total Variation Diminishing) approximation of the spatial derivative for the advected level set function. In the case of nonlinear advection, the semi-implicit discretization is proposed to linearize the problem. The compact form of implicit stencil in numerical schemes containing unknowns only in the upwind direction allows applications of efficient algebraic solvers like fast sweeping methods. Numerical tests to evolve a smooth and non-smooth interface and an example with a large variation of velocity confirm the good accuracy of the methods and fast convergence of the algebraic solver even in the case of very large Courant numbers

Laplacian regularized eikonal equation with Soner boundary condition on polyhedral meshes

In this paper, we propose a numerical algorithm based on a cell-centered finite volume method to compute a distance from given objects on a three-dimensional computational domain discretized by polyhedral cells. Inspired by the vanishing viscosity method, a Laplacian regularized eikonal equation is solved and the Soner boundary condition is applied to the boundary of the domain to avoid a non-viscosity solution. As the regularization parameter depending on a characteristic length of the discretized domain is reduced, a corresponding numerical solution is calculated. A convergence to the viscosity solution is verified numerically as the characteristic length becomes smaller and the regularization parameter accordingly becomes smaller. From the numerical experiments, the second experimental order of convergence in the $L^1$ norm error is confirmed for smooth solutions. Compared to solve a time-dependent form of eikonal equation, the Laplacian regularized eikonal equation has the advantage of reducing computational cost dramatically when a more significant number of cells is used or a region of interest is far away from the given objects. Moreover, the implementation of parallel computing using domain decomposition with $1$-ring face neighborhood structure can be done straightforwardly by a standard cell-centered finite volume code

Counting number of cells and cell segmentation using advection-diffusion equations

summary:We develop a method for counting number of cells and extraction of approximate cell centers in 2D and 3D images of early stages of the zebra-fish embryogenesis. The approximate cell centers give us the starting points for the subjective surface based cell segmentation. We move in the inner normal direction all level sets of nuclei and membranes images by a constant speed with slight regularization of this flow by the (mean) curvature. Such multi- scale evolutionary process is represented by a geometrical advection-diffusion equation which gives us at a certain scale the desired information on the number of cells. For solving the problems computationally we use flux-based finite volume level set method developed by Frolkovič and Mikula in [FM1] and semi-implicit co-volume subjective surface method given in [CMSSg, MSSgCVS, MSSgchapter]. Computational experiments on testing and real 2D and 3D embryogenesis images are presented and the results are discussed

Semi-implicit methods for advection equations with explicit forms of numerical solution

We present a parametric family of semi-implicit second order accurate numerical methods for non-conservative and conservative advection equation for which the numerical solutions can be obtained in a fixed number of forward and backward alternating substitutions. The methods use a novel combination of implicit and explicit time discretizations for one-dimensional case and the Strang splitting method in several dimensional case. The methods are described for advection equations with a continuous variable velocity that can change its sign inside of computational domain. The methods are unconditionally stable in the non-conservative case for variable velocity and for variable numerical parameter. Several numerical experiments confirm the advantages of presented methods including an involvement of differential programming to find optimized values of the variable numerical parameter

A global method for coupling transport with chemistry in heterogeneous porous media

Modeling reactive transport in porous media, using a local chemical equilibrium assumption, leads to a system of advection-diffusion PDE's coupled with algebraic equations. When solving this coupled system, the algebraic equations have to be solved at each grid point for each chemical species and at each time step. This leads to a coupled non-linear system. In this paper a global solution approach that enables to keep the software codes for transport and chemistry distinct is proposed. The method applies the Newton-Krylov framework to the formulation for reactive transport used in operator splitting. The method is formulated in terms of total mobile and total fixed concentrations and uses the chemical solver as a black box, as it only requires that on be able to solve chemical equilibrium problems (and compute derivatives), without having to know the solution method. An additional advantage of the Newton-Krylov method is that the Jacobian is only needed as an operator in a Jacobian matrix times vector product. The proposed method is tested on the MoMaS reactive transport benchmark.Comment: Computational Geosciences (2009) http://www.springerlink.com/content/933p55085742m203/?p=db14bb8c399b49979ba8389a3cae1b0f&pi=1

Numerical error in groundwater flow and solute transport simulation

Models of groundwater flow and solute transport may be affected by numerical error, leading to quantitative and qualitative changes in behavior. In this paper we compare and combine three methods of assessing the extent of numerical error: grid refinement, mathematical analysis, and benchmark test problems. In particular, we assess the popular solute transport code SUTRA [ Voss, 1984 ] as being a typical finite element code. Our numerical analysis suggests that SUTRA incorporates a numerical dispersion error and that its mass-lumped numerical scheme increases the numerical error. This is confirmed using a Gaussian test problem. A modified SUTRA code, in which the numerical dispersion is calculated and subtracted, produces better results. The much more challenging Elder problem [ Elder, 1967 ; Voss and Souza, 1987 ] is then considered. Calculation of its numerical dispersion coefficients and numerical stability show that the Elder problem is prone to error. We confirm that Elder problem results are extremely sensitive to the simulation method used.Juliette A. Woods, Michael D. Teubner, Craig T. Simmons and Kumar A. Naraya