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Arbitrarily large tomography with iterative algorithms on multiple GPUs using the TIGRE toolbox

Journal of Parallel and Distributed Computing 2020年 146卷 52-63页

作者： Biguri, Ander Lindroos, Reuben Bryll, Robert Towsyfyan, Hossein Deyhle, Hans Harrane, Ibrahim El khalil Boardman, Richard Mavrogordato, Mark Dosanjh, Manjit Hancock, Steven Blumensath, Thomas Institute of Sound and Vibration Research University of Southampton Southampton United Kingdom Micro Encoder Inc United States mu-Vis X-ray Imaging Laboratory University of Southampton Southampton United Kingdom CERN Switzerland

3D tomographic imaging requires the computation of solutions to very large inverse problems. In many applications, iterative algorithms provide superior results, however, memory limits in available computing hardware restrict the size of problems that can be solved. For this reason, iterative methods are not normally used to reconstruct typical data sets acquired with lab based CT systems. We thus use state of the art techniques such as dual buffering to develop an efficient strategy to compute the required operations for iterative reconstruction. This allows the iterative reconstruction of volumetric images of arbitrary size using any number of GPUs, each with arbitrarily small memory. Strategies for both the forward and backprojection operators are presented, along with two regularization approaches that are easily generalized to other projection types or regularizers. The proposed improvement also accelerates reconstruction of smaller images on single or multiple GPU systems, providing faster code for time-critical applications. The resulting algorithm has been added to the TIGRE toolbox, a repository for iterative reconstruction algorithms for general CT, but this memory-saving and problem-splitting strategy can be easily adapted for use with other GPU-based tomographic reconstruction code. © 2020 Elsevier inc.

关键词： Graphics processing unit

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High-speed 3d inspection with liquid lenses

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Photonics Spectra 2019年第11期53卷 35-38页

作者： Senekerimyan, Vahan Gladnick, Paul Nuara, Paul MITUTOYO AMERICA CORP Micro Encoder Inc

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Comparison of the generalized centroid with Gaussian and quadratic peak localization methods

arXiv

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arXiv 2018年

作者： Campbell, Shannon Micro Encoder Inc

We examine a new method for peak localization, the centroid of the data raised to some power, which we call the generalized centroid. We derive the peak localization uncertainty for the generalized centroid and compare it with the Cramer-Rao lower bound for both Gaussian and quadratic fits (with Gaussian signal and noise). We find that the centroid of squares and the Gaussian fit yield the best results in both one and two dimensions. We perform similar analysis with a Lorentz-like signal and find that the centroid of cubes and the nonlinear least squares fit provide the best results. We support our derivations with simulations, and also show simulation results when the maximum function is used to initially estimate the peak location. Copyright © 2018, The Authors. All rights reserved.

关键词： Gaussian distribution

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Arbitrarily large iterative tomographic reconstruction on multiple GPUS using the TIGRE toolbox

arXiv

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arXiv 2019年

作者： Biguri, Ander Lindroos, Reuben Bryll, Robert Towsyfyan, Hossein Deyhle, Hans Boardman, Richard Mavrogordato, Mark Dosanjh, Manjit Hancock, Steven Blumensath, Thomas University of Southampton SouthamptonSO17 1BJ United Kingdom Micro Encoder Inc United States CERN Meyrin1211 Switzerland µ-VIS X-ray Imaging Centre University of Southampton SouthamptonSO17 1BJ United Kingdom

Tomographic image sizes keep increasing over time and while the GPUs that compute the tomographic reconstruction are also increasing in memory size, they are not doing so fast enough to reconstruct the largest datasets. This problem is often solved by reconstructing data in large clusters of GPUs with enough devices to fit the measured X-ray projections and reconstructed volume. Often this requires tens of GPUs, which is a very economically expensive solution. Access to single-node machines designed to reconstruct using just one or a few GPUs is more common in the field, but current software does not allow iterative reconstruction of volumes that do not fit in those GPUs. In this work, we propose a strategy to execute efficiently the required operations for iterative reconstruction for arbitrarily large images with any number of GPUs with arbitrarily small memories in a single node. Strategies for both the forward and backprojection operators are presented, along with two regularization approaches that are easily generalized to other projection types or regularizers. The proposed improvement also accelerates reconstruction of smaller images on single or multiple GPUs, providing faster code for time-critical medical applications. The resulting algorithm has been added to the TIGRE toolbox, a repository for iterative reconstruction algorithms for general CT, but this memory-saving and problem-splitting strategy can be easily adapted for any other GPU-based CT code. Copyright © 2019, The Authors. All rights reserved.

关键词： Program processors

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Introduction to the JSTQE Issue on Indium Phosphide Integrated Photonics

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IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS 2018年第1期24卷

作者： Williams, K. Grote, N. Mashanovitch, M. Matsuo, S. Nakano, Y. Summers, J. Eindhoven Univ Technol Univ Inst Photon Integrat NL-5612 AZ Eindhoven Netherlands Fraunhofer Heinrich Hertz Inst Dept Photon Components D-10587 Berlin Germany Freedom Photon Goleta CA 93117 USA Nippon Telegraph & Telecom Device Technol Labs Atsugi Kanagawa Japan Univ Tokyo Grad Sch Engn Dept Elect Engn & Informat Syst Tokyo 1138654 Japan Micro Encoder Inc Kirkland WA 98034 USA

This special issue includes 19 papers on InP integrated photonics capturing some of the most important recent advances, and providing a reference point for current state of the art.

关键词： Special issues and sections Photonics Indium phosphide Integrated optics

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The geometry of Niggli reduction: BGAOL - embedding Niggli reduction and analysis of boundaries. (vol 47, pg 346, 2014)

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JOURNAL OF APPLIED CRYSTALLOGRAPHY 2014年第1期47卷 1477-1477页

作者： Andrews, Lawrence C. Bernstein, Herbert J. Micro Encoder Inc Kirkland WA 98034 USA Dowling Coll Shirley NY 11967 USA

Niggli reduction can be viewed as a series of operations in a six-dimensional space derived from the metric tensor. An implicit embedding of the space of Niggli-reduced cells in a higher-dimensional space to facilitate calculation of distances between cells is described. This distance metric is used to create a program, BGAOL, for Bravais lattice determination. Results from BGAOL are compared with results from other metric based Bravais lattice determination algorithms. This embedding depends on understanding the boundary polytopes of the Niggli-reduced cone N in the six-dimensional space G6. This article describes an investigation of the boundary polytopes of the Niggli-reduced cone N in the six-dimensional space G6 by algebraic analysis and organized random probing of regions near one-, two-, three-, four-, five-, six-, seven- and eightfold boundary polytope intersections. The discussion of valid boundary polytopes is limited to those avoiding the mathematically interesting but crystallographically impossible cases of zero-length cell edges. Combinations of boundary polytopes without a valid intersection in the closure of the Niggli cone or with an intersection that would force a cell edge to zero or without neighboring probe points are eliminated. In all, 216 boundary polytopes are found. There are 15 five-dimensional boundary polytopes of the full G6 Niggli cone N.

关键词： Niggli reduction Bravais lattice determination computer programs

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The geometry of Niggli reduction: SAUC - search of alternative unit cells

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JOURNAL OF APPLIED CRYSTALLOGRAPHY 2014年第1期47卷 360-364页

作者： McGill, Keith J. Asadi, Mojgan Karakasheva, Maria T. Andrews, Lawrence C. Bernstein, Herbert J. Dowling Coll Shirley NY 11967 USA Micro Encoder Inc Kirkland WA 98034 USA

A database of lattices using the G(6) representation of the Niggli-reduced cell as the search key provides a more robust and complete search than older techniques. Searching is implemented by finding the distance from the probe cell to other cells using a topological embedding of the Niggli reduction in G(6), so that all cells representing similar lattices will be found. The embedding provides the first fully linear measure of distances between unit cells. Comparison of results with those from older cell-based search algorithms suggests significant value in the new approach.

关键词： Niggli reduction Bravais lattice determination computer programs

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The geometry of Niggli reduction: SAUC - search of alternative unit cells

The geometry of Niggli reduction: SAUC - search of alternati...

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作者： McGill, Keith J. Asadi, Mojgan Karakasheva, Maria T. Andrews, Lawrence C. Bernstein, Herbert J. Dowling College 1300 William Floyd Parkway Shirley NY 11967 United States Micro Encoder Inc. 11533 NE 118th Street Kirkland WA 98034 United States

A database of lattices using the G 6 representation of the Niggli-reduced cell as the search key provides a more robust and complete search than older techniques. Searching is implemented by finding the distance from the probe cell to other cells using a topological embedding of the Niggli reduction in G 6, so that all cells representing similar lattices will be found. The embedding provides the first fully linear measure of distances between unit cells. Comparison of results with those from older cell-based search algorithms suggests significant value in the new approach. © 2014 International Union of Crystallography.

关键词： Cells

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The geometry of Niggli reduction: BGAOL -embedding Niggli reduction and analysis of boundaries

The geometry of Niggli reduction: BGAOL -embedding Niggli re...

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作者： Andrews, Lawrence C. Bernstein, Herbert J. Micro Encoder Inc. 11533 NE 118th Street Kirkland WA 98034 United States Dowling College 1300 William Floyd Parkway Shirley NY 11967 United States

Niggli reduction can be viewed as a series of operations in a six-dimensional space derived from the metric tensor. An implicit embedding of the space of Niggli-reduced cells in a higher-dimensional space to facilitate calculation of distances between cells is described. This distance metric is used to create a program, BGAOL, for Bravais lattice determination. Results from BGAOL are compared with results from other metric based Bravais lattice determination algorithms. This embedding depends on understanding the boundary polytopes of the Niggli-reduced cone N in the six-dimensional space G 6. This article describes an investigation of the boundary polytopes of the Niggli-reduced cone N in the six-dimensional space G 6 by algebraic analysis and organized random probing of regions near one-, two-, three-, four-, five-, six-, seven- and eightfold boundary polytope intersections. The discussion of valid boundary polytopes is limited to those avoiding the mathematically interesting but crystallographically impossible cases of zero-length cell edges. Combinations of boundary polytopes without a valid intersection in the closure of the Niggli cone or with an intersection that would force a cell edge to zero or without neighboring probe points are eliminated. In all, 216 boundary polytopes are found. There are 15 five-dimensional boundary polytopes of the full G 6 Niggli cone N. © 2014 International Union of Crystallography.

关键词： Cytology

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Measurement comparisons between optical and mechanical edges for a silicon micromachined dimensional calibration standard

Measurement comparisons between optical and mechanical edges...

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26th Annual Meeting of the American Society for Precision Engineering, ASPE 2011

作者： Tran, Hy D. Emtman, Casey Salsbury, James G. Wright, William Zwilling, Avron Primary Physical Standards Sandia National Laboratories Albuquerque NM United States Micro Encoder Inc. Kirkland WA United States Mitutoyo America Corporation Aurora IL United States

ISBN: (纸本)9781887706582

A mesoscale dimensional artifact based on silicon bulk micromachining fabrication has been developed and manufactured with the intention of evaluating the artifact both on a high precision coordinate measuring machine (CMM) and video-probe based measuring systems. This hybrid artifact has features that can be located by both a touch probe and a video probe system. A key feature is that the physical edge can be located using a touch probe CMM, and this same physical edge can also be located using a video probe. While video-probe based systems are commonly used to inspect mesoscale mechanical components, a video-probe system's certified accuracy is generally much worse than its repeatability. To solve this problem, an artifact has been developed which can be calibrated using a commercially available high-accuracy tactile system and then be used to calibrate typical production vision-based measurement systems. This allows for error mapping to a higher degree of accuracy than is possible with a typical chrome-on-glass reference artifact. Details of the designed features and manufacturing process of the hybrid dimensional artifact are given, and a comparison of the designed features to the measured features of the manufactured artifact is presented and discussed. Measurement results are presented using a meter-scale CMM with submicron measurement uncertainty;an optical CMM with submicron measurement uncertainty;a micro-CMM with submicron measurement uncertainty using three different probes;and a form contour instrument.

关键词： Probes

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