Sparse Matrix-Based HPC Tomography

Marchesini, Stefano; Trivedi, Anuradha; Enfedaque, Pablo; Perciano, Talita; Parkinson, Dilworth

doi:10.1007/978-3-030-50371-0_18

Sparse Matrix-Based HPC Tomography

Journal Article · Mon Jun 15 00:00:00 EDT 2020 · Lecture Notes in Computer Science

DOI:https://doi.org/10.1007/978-3-030-50371-0_18· OSTI ID:1650080

Marchesini, Stefano ^[1]; Trivedi, Anuradha ^[2]; Enfedaque, Pablo ^[3]; Perciano, Talita ^[3]; Parkinson, Dilworth ^[4]

Sigray Inc., Concord, CA (United States)
Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)

Tomographic imaging has benefited from advances in X-ray sources, detectors and optics to enable novel observations in science, engineering and medicine. These advances have come with a dramatic increase of input data in the form of faster frame rates, larger fields of view or higher resolution, so high performance solutions are currently widely used for analysis. Tomographic instruments can vary significantly from one to another, including the hardware employed for reconstruction: from single CPU workstations to large scale hybrid CPU/GPU supercomputers. Furthermore, flexibility on the software interfaces and reconstruction engines are also highly valued to allow for easy development and prototyping. This paper presents a novel software framework for tomographic analysis that tackles all aforementioned requirements. The proposed solution capitalizes on the increased performance of sparse matrix-vector multiplication and exploits multi-CPU and GPU reconstruction over MPI. Furthermore, the solution is implemented in Python and relies on CuPy for fast GPU operators and CUDA kernel integration, and on SciPy for CPU sparse matrix computation. As opposed to previous tomography solutions that are tailor-made for specific use cases or hardware, the proposed software is designed to provide flexible, portable and high-performance operators that can be used for continuous integration at different production environments, but also for prototyping new experimental settings or for algorithmic development. The experimental results demonstrate how our implementation can even outperform state-of-the-art software packages used at advanced X-ray sources worldwide.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1650080

Journal Information:: Lecture Notes in Computer Science, Journal Name: Lecture Notes in Computer Science Vol. 12137; ISSN 0302-9743

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

References (20)

Tomographic reconstruction with arbitrary directions Davison, M. E.; Grunbaum, F. A. Communications on Pure and Applied Mathematics, Vol. 34, Issue 1 https://doi.org/10.1002/cpa.3160340105	journal	January 1981
Electron tomography at 2.4-ångström resolution Scott, M. C.; Chen, Chien-Chun; Mecklenburg, Matthew Nature, Vol. 483, Issue 7390 https://doi.org/10.1038/nature10934	journal	March 2012
Using X-ray tomoscopy to explore the dynamics of foaming metal García-Moreno, Francisco; Kamm, Paul Hans; Neu, Tillmann Robert Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11521-1	journal	August 2019
Two-Point Step Size Gradient Methods Barzilai, Jonathan; Borwein, Jonathan M. IMA Journal of Numerical Analysis, Vol. 8, Issue 1 https://doi.org/10.1093/imanum/8.1.141	journal	January 1988
TomoPy: a framework for the analysis of synchrotron tomographic data Gürsoy, Dogˇa; De Carlo, Francesco; Xiao, Xianghui Journal of Synchrotron Radiation, Vol. 21, Issue 5 https://doi.org/10.1107/S1600577514013939	journal	August 2014
Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data Pelt, Daniël M.; Gürsoy, Dogˇa; Palenstijn, Willem Jan Journal of Synchrotron Radiation, Vol. 23, Issue 3 https://doi.org/10.1107/S1600577516005658	journal	April 2016
Selection of a convolution function for Fourier inversion using gridding (computerised tomography application) Jackson, J. I.; Meyer, C. H.; Nishimura, D. G. IEEE Transactions on Medical Imaging, Vol. 10, Issue 3 https://doi.org/10.1109/42.97598	journal	January 1991
A generalized Gaussian image model for edge-preserving MAP estimation Bouman, C.; Sauer, K. IEEE Transactions on Image Processing, Vol. 2, Issue 3 https://doi.org/10.1109/83.236536	journal	July 1993
Plug-and-Play priors for model based reconstruction Venkatakrishnan, Singanallur V.; Bouman, Charles A.; Wohlberg, Brendt 2013 IEEE Global Conference on Signal and Information Processing (GlobalSIP) https://doi.org/10.1109/GlobalSIP.2013.6737048	conference	December 2013
Model-based iterative reconstruction for synchrotron X-ray tomography Mohan, K. Aditya; Venkatakrishnan, S. V.; Drummy, Lawrence F. ICASSP 2014 - 2014 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) https://doi.org/10.1109/ICASSP.2014.6854939	conference	May 2014
Image Denoising by Sparse 3-D Transform-Domain Collaborative Filtering Dabov, Kostadin; Foi, Alessandro; Katkovnik, Vladimir IEEE Transactions on Image Processing, Vol. 16, Issue 8 https://doi.org/10.1109/TIP.2007.901238	journal	August 2007
Improving Filtered Backprojection Reconstruction by Data-Dependent Filtering Pelt, Daniel M.; Batenburg, Kees Joost IEEE Transactions on Image Processing, Vol. 23, Issue 11 https://doi.org/10.1109/TIP.2014.2341971	journal	November 2014
Nonuniform fast fourier transforms using min-max interpolation Fessler, J. A.; Sutton, B. P. IEEE Transactions on Signal Processing, Vol. 51, Issue 2 https://doi.org/10.1109/TSP.2002.807005	journal	February 2003
Compressive phase contrast tomography Maia, F.; MacDowell, A.; Marchesini, S. SPIE Optical Engineering + Applications, SPIE Proceedings https://doi.org/10.1117/12.861946	conference	August 2010
The Split Bregman Method for L1-Regularized Problems Goldstein, Tom; Osher, Stanley SIAM Journal on Imaging Sciences, Vol. 2, Issue 2 https://doi.org/10.1137/080725891	journal	January 2009
CGS, A Fast Lanczos-Type Solver for Nonsymmetric Linear systems Sonneveld, Peter SIAM Journal on Scientific and Statistical Computing, Vol. 10, Issue 1 https://doi.org/10.1137/0910004	journal	January 1989
Optimization of sparse matrix-vector multiplication on emerging multicore platforms Williams, Samuel; Oliker, Leonid; Vuduc, Richard Proceedings of the 2007 ACM/IEEE conference on Supercomputing - SC '07 https://doi.org/10.1145/1362622.1362674	conference	January 2007
Fast and flexible X-ray tomography using the ASTRA toolbox van Aarle, Wim; Palenstijn, Willem Jan; Cant, Jeroen Optics Express, Vol. 24, Issue 22 https://doi.org/10.1364/OE.24.025129	journal	January 2016
Making Advanced Scientific Algorithms and Big Scientific Data Management More Accessible Venkatakrishnan, S. V.; Mohan, K. Aditya; Beattie, Keith Electronic Imaging, Vol. 2016, Issue 19 https://doi.org/10.2352/ISSN.2470-1173.2016.19.COIMG-155	journal	February 2016
Generalized fourier slice theorem for cone-beam image reconstruction Zhao, Shuang-Ren; Jiang, Dazong; Yang, Kevin Journal of X-Ray Science and Technology, Vol. 23, Issue 2 https://doi.org/10.3233/XST-150479	journal	January 2015

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