Unwind: Interactive Fish Straightening

The ScanAllFish project is a large-scale effort to scan all the world's 33,100 known species of fishes. It has already generated thousands of volumetric CT scans of fish species which are available on open access platforms such as the Open Science Framework. To achieve a scanning rate required for a project of this magnitude, many specimens are grouped together into a single tube and scanned all at once. The resulting data contain many fish which are often bent and twisted to fit into the scanner. Our system, Unwind, is a novel interactive visualization and processing tool which extracts, unbends, and untwists volumetric images of fish with minimal user interaction. Our approach enables scientists to interactively unwarp these volumes to remove the undesired torque and bending using a piecewise-linear skeleton extracted by averaging isosurfaces of a harmonic function connecting the head and tail of each fish. The result is a volumetric dataset of a individual, straight fish in a canonical pose defined by the marine biologist expert user. We have developed Unwind in collaboration with a team of marine biologists: Our system has been deployed in their labs, and is presently being used for dataset construction, biomechanical analysis, and the generation of figures for scientific publication

Three-dimensional structure of a low-Reynolds-number turbulent boundary layer

A low-Reynolds-number zero-pressure-gradient incompressible turbulent boundary layer was investigated using a volumetric imaging technique. The Reynolds number based on momentum thickness was 700. The flow was tagged with a passive scalar from two spanwise dye slots to distinguish between fluid motions originating in the inner and outer portions of the boundary layer. The resulting volumetric scalar field was interrogated using a laser sheet scanner developed for this study. Two- and three-dimensional time-dependent visualizations of a 50 volume time series are presented (equivalent to 17δ in length). In the outer portion of the boundary layer, scalar structures were observed to lie along lines in the (x, z)-plane, inclined to the streamwise (x-)direction in the range ±50°. The ejection of brightly dyed fluid packets from the near-wall region was observed to be spatially organized, and related to the passage of the large-scale scalar structures.Carl J Delo, Richard M Kelson and Alexander J Smit

Interaction of weak shock waves with cylindrical and spherical gas inhomogeneities

The interaction of a plane weak shock wave with a single discrete gaseous inhomogeneity is studied as a model of the mechanisms by which finite-amplitude waves in random media generate turbulence and intensify mixing. The experiments are treated as an example of the shock-induced Rayleigh-Taylor instability. or Richtmyer-Meshkov instability, with large initial distortions of the gas interfaces. The inhomogeneities are made by filling large soap bubbles and cylindrical refraction cells (5 cm diameter) whose walls are thin plastic membranes with gases both lighter and heavier than the ambient air in a square (8.9 cm side shock-tube text section. The wavefront geometry and the deformation of the gas volume are visualized by shadowgraph photography. Wave configurations predicted by geometrical acoustics, including the effects of refraction, reflection and diffraction, are compared to the observations. Departures from the predictions of acoustic theory are discussed in terms of gasdynamic nonlinearity. The pressure field on the axis of symmetry downstream of the inhomogeneity is measured by piezoelectric pressure transducers. In the case of a cylindrical or spherical volume filled with heavy low-sound-speed gas the wave which passes through the interior focuses just behind the cylinder. On the other hand, the wave which passes through the light high-sound-speed volume strongly diverges. Visualization of the wavefronts reflected from and diffracted around the inhomogeneities exhibit many features known in optical and acoustic scattering. Rayleigh-Taylor instability induced by shock acceleration deforms the initially circular cross-section of the volume. In the case of the high-sound-speed sphere, a strong vortex ring forms and separates from the main volume of gas. Measurements of the wave and gas-interface velocities are compared to values calculated for one-dimensional interactions and for a simple model of shock-induced Rayleigh-Taylor instability. The circulation and Reynolds number of the vortical structures are calculated from the measured velocities by modeling a piston vortex generator. The results of the flow visualization are also compared with contemporary numerical simulations

An exact general remeshing scheme applied to physically conservative voxelization

We present an exact general remeshing scheme to compute analytic integrals of polynomial functions over the intersections between convex polyhedral cells of old and new meshes. In physics applications this allows one to ensure global mass, momentum, and energy conservation while applying higher-order polynomial interpolation. We elaborate on applications of our algorithm arising in the analysis of cosmological N-body data, computer graphics, and continuum mechanics problems. We focus on the particular case of remeshing tetrahedral cells onto a Cartesian grid such that the volume integral of the polynomial density function given on the input mesh is guaranteed to equal the corresponding integral over the output mesh. We refer to this as "physically conservative voxelization". At the core of our method is an algorithm for intersecting two convex polyhedra by successively clipping one against the faces of the other. This algorithm is an implementation of the ideas presented abstractly by Sugihara (1994), who suggests using the planar graph representations of convex polyhedra to ensure topological consistency of the output. This makes our implementation robust to geometric degeneracy in the input. We employ a simplicial decomposition to calculate moment integrals up to quadratic order over the resulting intersection domain. We also address practical issues arising in a software implementation, including numerical stability in geometric calculations, management of cancellation errors, and extension to two dimensions. In a comparison to recent work, we show substantial performance gains. We provide a C implementation intended to be a fast, accurate, and robust tool for geometric calculations on polyhedral mesh elements.Comment: Code implementation available at https://github.com/devonmpowell/r3