https://fisica.cab.cnea.gov.ar/gpgpu/images/charlas/medical_image_processing_on_the_gpu.pdf

Medical Image Processing on the GPU : Past, Present and Future

Micro Aerial Vehicles (MAVs) that operate in unstructured, unexplored environments require fast and flexible local planning, which can replan when new parts of the map are explored. Trajectory optimization methods fulfill these needs, but require obstacle distance information, which can be given by Euclidean Signed Distance Fields (ESDFs). We propose a method to incrementally build ESDFs from Truncated Signed Distance Fields (TSDFs), a common implicit surface representation used in computer graphics and vision. TSDFs are fast to build and smooth out sensor noise over many observations, and are designed to produce surface meshes. We show that we can build TSDFs faster than Octomaps, and that it is more accurate to build ESDFs out of TSDFs than occupancy maps. Our complete system, called voxblox, is available as open source and runs in real-time on a single CPU core. We validate our approach on-board an MAV, by using our system with a trajectory optimization local planner, entirely on-board and in real-time.

Voxblox: Incremental 3D Euclidean Signed Distance Fields for on-board MAV planning

Micro Aerial Vehicles (MAVs) that operate in unstructured, unexplored environments require fast and flexible local planning, which can replan when new parts of the map are explored. Trajectory optimization methods fulfill these needs, but require obstacle distance information, which can be given by Euclidean Signed Distance Fields (ESDFs). 
We propose a method to incrementally build ESDFs from Truncated Signed Distance Fields (TSDFs), a common implicit surface representation used in computer graphics and vision. TSDFs are fast to build and smooth out sensor noise over many observations, and are designed to produce surface meshes. Meshes allow human operators to get a better assessment of the robot's environment, and set high-level mission goals. 
We show that we can build TSDFs faster than Octomaps, and that it is more accurate to build ESDFs out of TSDFs than occupancy maps. Our complete system, called voxblox, will be available as open source and runs in real-time on a single CPU core. We validate our approach on-board an MAV, by using our system with a trajectory optimization local planner, entirely on-board and in real-time.

Voxblox: Incremental 3D Euclidean Signed Distance Fields for On-Board MAV Planning

Given a shape, a skeleton is a thin centered structure which jointly describes the topology and the geometry of the shape. Skeletons provide an alternative to classical boundary or volumetric representations, which is especially effective for applications where one needs to reason about, and manipulate, the structure of a shape. These skeleton properties make them powerful tools for many types of shape analysis and processing tasks. For a given shape, several skeleton types can be defined, each having its own properties, advantages, and drawbacks. Similarly, a large number of methods exist to compute a given skeleton type, each having its own requirements, advantages, and limitations. While using skeletons for two-dimensional (2D) shapes is a relatively well covered area, developments in the skeletonization of three-dimensional (3D) shapes make these tasks challenging for both researchers and practitioners. This survey presents an overview of 3D shape skeletonization. We start by presenting the definition and properties of various types of 3D skeletons. We propose a taxonomy of 3D skeletons which allows us to further analyze and compare them with respect to their properties. We next overview methods and techniques used to compute all described 3D skeleton types, and discuss their assumptions, advantages, and limitations. Finally, we describe several applications of 3D skeletons, which illustrate their added value for different shape analysis and processing tasks.

/pdf/3d-skeletons-a-state-of-the-art-report-23xi7o6x4j.pdf

3D skeletons: a state-of-the-art report

In this paper, we present a novel approach for constructing bundled layouts of general graphs. As layout cues for bundles, we use medial axes, or skeletons, of edges which are similar in terms of position information. We combine edge clustering, distance fields, and 2D skeletonization to construct progressively bundled layouts for general graphs by iteratively attracting edges towards the centerlines of level sets of their distance fields. Apart from clustering, our entire pipeline is image-based with an efficient implementation in graphics hardware. Besides speed and implementation simplicity, our method allows explicit control of the emphasis on structure of the bundled layout, i.e. the creation of strongly branching (organic-like) or smooth bundles. We demonstrate our method on several large real-world graphs.

/pdf/skeleton-based-edge-bundling-for-graph-visualization-kx9v9iqoc9.pdf

Skeleton-Based Edge Bundling for Graph Visualization

We propose a Parallel Banding Algorithm (PBA) on the GPU to compute the exact Euclidean Distance Transform (EDT) for a binary image in 2D and higher dimensions. Partitioning the image into small bands to process and then merging them concurrently, PBA computes the exact EDT with optimal linear total work, high level of parallelism and a good memory access pattern. This work is the first attempt to exploit the enormous power of the GPU in computing the exact EDT, while prior works are only on approximation. Compared to these other algorithms in our experiments, our exact algorithm is still a few times faster in 2D and 3D for most input sizes. We illustrate the use of our algorithm in applications such as computing the Euclidean skeleton using the integer medial axis transform, performing morphological operations of 3D volumetric data, and constructing 2D weighted centroidal Voronoi diagrams.

/pdf/parallel-banding-algorithm-to-compute-exact-distance-dgajwxpz3x.pdf

Parallel Banding Algorithm to compute exact distance transform with the GPU

The proliferation of data in graph form calls for the development of scalable graph algorithms that exploit parallel processing environments. One such problem is the computation of a graph's minimum spanning forest (MSF). Past research has proposed several parallel algorithms for this problem, yet none of them scales to large, high-density graphs. In this paper we propose a novel, scalable, parallel MSF algorithm for undirected weighted graphs. Our algorithm leverages Prim's algorithm in a parallel fashion, concurrently expanding several subsets of the computed MSF. Our effort focuses on minimizing the communication among different processors without constraining the local growth of a processor's computed subtree. In effect, we achieve a scalability that previous approaches lacked. We implement our algorithm in CUDA, running on a GPU and study its performance using real and synthetic, sparse as well as dense, structured and unstructured graph data. Our experimental study demonstrates that our algorithm outperforms the previous state-of-the-art GPU-based MSF algorithm, while being several orders of magnitude faster than sequential CPU-based algorithms.

http://karras.rutgers.edu/ppo143-nobari.pdf

Scalable parallel minimum spanning forest computation

This paper presents a novel approach to compute, for a given point set S in R2, its Delaunay triangulation T (S). Though prior work mentions the possibility of using the graphics processing unit (GPU) to compute Delaunay triangulations, no known implementation and performance have been reported. Our work uncovers various challenges in the use of GPU for such a purpose. In practice, our approach exploits the GPU to assist in the computation of a triangulation T of S that is a good approximation to T (S). From that, the approach employs the CPU to transform T ' to T (S). As a major part of the total work is done by the GPU with parallel computing capability, it is a fast and practical approach, particularly for a large number of points (millions with the current state-of-the-art GPU). For such cases, our current implementation can run up to 53% faster on a Core2 Duo machine when compared to Triangle, the well-known fastest Delaunay triangulation implementation.

/pdf/computing-two-dimensional-delaunay-triangulation-using-4xqpjlthdz.pdf

Computing two-dimensional Delaunay triangulation using graphics hardware

We propose the first graphics processing unit (GPU) solution to compute the 2D constrained Delaunay triangulation (CDT) of a planar straight line graph (PSLG) consisting of points and edges. There are many existing CPU algorithms to solve the CDT problem in computational geometry, yet there has been no prior approach to solve this problem efficiently using the parallel computing power of the GPU. For the special case of the CDT problem where the PSLG consists of just points, which is simply the normal Delaunay triangulation (DT) problem, a hybrid approach using the GPU together with the CPU to partially speed up the computation has already been presented in the literature. Our work, on the other hand, accelerates the entire computation on the GPU. Our implementation using the CUDA programming model on NVIDIA GPUs is numerically robust, and runs up to an order of magnitude faster than the best sequential implementations on the CPU. This result is reflected in our experiment with both randomly generated PSLGs and real-world GIS data having millions of points and edges.

/pdf/computing-2d-constrained-delaunay-triangulation-using-the-3uuvngn9cs.pdf

Computing 2D Constrained Delaunay Triangulation Using the GPU

We propose the first algorithm to compute the 3D Delaunay triangulation (DT) on the GPU. Our algorithm uses massively parallel point insertion followed by bilateral flipping, a powerful local operation in computational geometry. Although a flipping algorithm is very amenable to parallel processing and has been employed to construct the 2D DT and the 3D convex hull on the GPU, to our knowledge there is no such successful attempt for constructing the 3D DT. This is because in 3D when many points are inserted in parallel, flipping gets stuck long before reaching the DT, and thus any further correction to obtain the DT is costly. In contrast, we show that by alternating between parallel point insertion and flipping, together with picking an appropriate point insertion order, one can still obtain a triangulation very close to Delaunay. We further propose an adaptive star splaying approach to subsequently transform this result into the 3D DT efficiently. In addition, we introduce several GPU speedup techniques for our implementation, which are also useful for general computational geometry algorithms. On the whole, our hybrid approach, with the GPU accelerating the main work of constructing a near-Delaunay structure and the CPU transforming that into the 3D DT, outperforms all existing sequential CPU algorithms by up to an order of magnitude, in both synthetic and real-world inputs. We also adapt our approach to the 2D DT problem and obtain similar speedup over the best sequential CPU algorithms, and up to 2 times over previous GPU algorithms.

/pdf/a-gpu-accelerated-algorithm-for-3d-delaunay-triangulation-4x6ndgeq3d.pdf

Thanh-Tung Cao

Papers

Parallel Banding Algorithm to compute exact distance transform with the GPU

Scalable parallel minimum spanning forest computation

Computing two-dimensional Delaunay triangulation using graphics hardware

Computing 2D Constrained Delaunay Triangulation Using the GPU

A GPU accelerated algorithm for 3D Delaunay triangulation