We present the PyHST2 code which is in service at ESRF for phase-contrast and absorption tomography. This code has been engineered to sustain the high data flow typical of the third generation synchrotron facilities (10 terabytes per experiment) by a
dopting a distributed and pipelined architecture. The code implements, beside a default filtered backprojection reconstruction, iterative reconstruction techniques with a-priori knowledge. These latter are used to improve the reconstruction quality or in order to reduce the required data volume and reach a given quality goal. The implemented a-priori knowledge techniques are based on the total variation penalisation and a new recently found convex functional which is based on overlapping patches. We give details of the different methods and their implementations while the code is distributed under free license. We provide methods for estimating, in the absence of ground-truth data, the optimal parameters values for a-priori techniques.
We investigate experimentally the mixing dynamics in a channel flow with a finite stirring region undergoing chaotic advection. We study the homogenization of dye in two variants of an eggbeater stirring protocol that differ in the extent of their mi
xing region. In the first case, the mixing region is separated from the side walls of the channel, while in the second it extends to the walls. For the first case, we observe the onset of a permanent concentration pattern that repeats over time with decaying intensity. A quantitative analysis of the concentration field of dye confirms the convergence to a self-similar pattern, akin to the strange eigenmodes previously observed in closed flows. We model this phenomenon using an idealized map, where an analysis of the mixing dynamics explains the convergence to an eigenmode. In contrast, for the second case the presence of no-slip walls and separation points on the frontier of the mixing region leads to non-self-similar mixing dynamics.
A stirring device consisting of a periodic motion of rods induces a mapping of the fluid domain to itself, which can be regarded as a homeomorphism of a punctured surface. Having the rods undergo a topologically-complex motion guarantees at least a m
inimum amount of stretching of material lines, which is important for chaotic mixing. We use topological considerations to describe the nature of the injection of unmixed material into a central mixing region, which takes place at injection cusps. A topological index formula allow us to predict the possible types of unstable foliations that can arise for a fixed number of rods.
Chaotic mixing in a closed vessel is studied experimentally and numerically in different 2-D flow configurations. For a purely hyperbolic phase space, it is well-known that concentration fluctuations converge to an eigenmode of the advection-diffusio
n operator and decay exponentially with time. We illustrate how the unstable manifold of hyperbolic periodic points dominates the resulting persistent pattern. We show for different physical viscous flows that, in the case of a fully chaotic Poincare section, parabolic periodic points at the walls lead to slower (algebraic) decay. A persistent pattern, the backbone of which is the unstable manifold of parabolic points, can be observed. However, slow stretching at the wall forbids the rapid propagation of stretched filaments throughout the whole domain, and hence delays the formation of an eigenmode until it is no longer experimentally observable. Inspired by the bakers map, we introduce a 1-D model with a parabolic point that gives a good account of the slow decay observed in experiments. We derive a universal decay law for such systems parametrized by the rate at which a particle approaches the no-slip wall.
