The Topology ToolKit

This system paper presents the Topology ToolKit (TTK), a software platform designed for topological data analysis in scientific visualization. TTK provides a unified, generic, efficient, and robust implementation of key algorithms for the topological analysis of scalar data, including: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces, and more. TTK is easily accessible to end users due to a tight integration with ParaView. It is also easily accessible to developers through a variety of bindings (Python, VTK/C++) for fast prototyping or through direct, dependence-free, C++, to ease integration into pre-existing complex systems. While developing TTK, we faced several algorithmic and software engineering challenges, which we document in this paper. In particular, we present an algorithm for the construction of a discrete gradient that complies to the critical points extracted in the piecewise-linear setting. This algorithm guarantees a combinatorial consistency across the topological abstractions supported by TTK, and importantly, a unified implementation of topological data simplification for multi-scale exploration and analysis. We also present a cached triangulation data structure, that supports time efficient and generic traversals, which self-adjusts its memory usage on demand for input simplicial meshes and which implicitly emulates a triangulation for regular grids with no memory overhead. Finally, we describe an original software architecture, which guarantees memory efficient and direct accesses to TTK features, while still allowing for researchers powerful and easy bindings and extensions. TTK is open source (BSD license) and its code, online documentation and video tutorials are available on TTK's website

Analysis of the contour structural irregularity of skin lesions using wavelet decomposition

The boundary irregularity of skin lesions is of clinical significance for the early detection of malignant melanomas and to distinguish them from other lesions such as benign moles. The structural components of the contour are of particular importance. To extract the structure from the contour, wavelet decomposition was used as these components tend to locate in the lower frequency sub-bands. Lesion contours were modeled as signatures with scale normalization to give position and frequency resolution invariance. Energy distributions among different wavelet sub-bands were then analyzed to extract those with significant levels and differences to enable maximum discrimination. Based on the coefficients in the significant sub-bands, structural components from the original contours were modeled, and a set of statistical and geometric irregularity descriptors researched that were applied at each of the significant sub-bands. The effectiveness of the descriptors was measured using the Hausdorff distance between sets of data from melanoma and mole contours. The best descriptor outputs were input to a back projection neural network to construct a combined classifier system. Experimental results showed that thirteen features from four sub-bands produced the best discrimination between sets of melanomas and moles, and that a small training set of nine melanomas and nine moles was optimum

Task-based Augmented Contour Trees with Fibonacci Heaps

This paper presents a new algorithm for the fast, shared memory, multi-core computation of augmented contour trees on triangulations. In contrast to most existing parallel algorithms our technique computes augmented trees, enabling the full extent of contour tree based applications including data segmentation. Our approach completely revisits the traditional, sequential contour tree algorithm to re-formulate all the steps of the computation as a set of independent local tasks. This includes a new computation procedure based on Fibonacci heaps for the join and split trees, two intermediate data structures used to compute the contour tree, whose constructions are efficiently carried out concurrently thanks to the dynamic scheduling of task parallelism. We also introduce a new parallel algorithm for the combination of these two trees into the output global contour tree. Overall, this results in superior time performance in practice, both in sequential and in parallel thanks to the OpenMP task runtime. We report performance numbers that compare our approach to reference sequential and multi-threaded implementations for the computation of augmented merge and contour trees. These experiments demonstrate the run-time efficiency of our approach and its scalability on common workstations. We demonstrate the utility of our approach in data segmentation applications

Director Field Model of the Primary Visual Cortex for Contour Detection

We aim to build the simplest possible model capable of detecting long, noisy contours in a cluttered visual scene. For this, we model the neural dynamics in the primate primary visual cortex in terms of a continuous director field that describes the average rate and the average orientational preference of active neurons at a particular point in the cortex. We then use a linear-nonlinear dynamical model with long range connectivity patterns to enforce long-range statistical context present in the analyzed images. The resulting model has substantially fewer degrees of freedom than traditional models, and yet it can distinguish large contiguous objects from the background clutter by suppressing the clutter and by filling-in occluded elements of object contours. This results in high-precision, high-recall detection of large objects in cluttered scenes. Parenthetically, our model has a direct correspondence with the Landau - de Gennes theory of nematic liquid crystal in two dimensions.Comment: 9 pages, 7 figure

NonAbelian Vortices, Large Winding Limits and Aharonov-Bohm Effects

Remarkable simplification arises from considering vortex equations in the large winding limit. This was recently used in [1] to display all sorts of vortex zeromodes, the orientational, translational, fermionic as well as semi-local, and to relate them to the apparently distinct phenomena of the Nielsen-Olesen-Ambjorn magnetic instabilities. Here we extend these analyses to more general types of BPS nonAbelian vortices, taking as a prototype a system with gauged U(1) x SU(N) x SU(N) symmetry where the VEV of charged scalar fields in the bifundamental representation breaks the symmetry to SU(N)_{l+r} . The presence of the massless SU(N)_{l+r} gauge fields in 4D bulk introduces all sorts of non-local, topological phenomena such as the nonAbelian Aharonov-Bohm effects, which in the theory with global SU(N)_r group (g_r=0) are washed away by the strongly fluctuating orientational zeromodes in the worldsheet. Physics changes qualitatively at the moment the right gauge coupling constant g_r is turned on.Comment: 31 pages, 4 figure