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2018 | OriginalPaper | Chapter

GPU-Based Implementation of Ptycho-ADMM for High Performance X-Ray Imaging

Authors : Pablo Enfedaque, Huibin Chang, Hari Krishnan, Stefano Marchesini

Published in: Computational Science – ICCS 2018

Publisher: Springer International Publishing

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Abstract

X-ray imaging allows biologists to retrieve the atomic arrangement of proteins and doctors the capability to view broken bones in full detail. In this context, ptychography has risen as a reference imaging technique. It provides resolutions of one billionth of a meter, macroscopic field of view, or the capability to retrieve chemical or magnetic contrast, among other features. The goal is to reconstruct a 2D visualization of a sample from a collection of diffraction patterns generated from the interaction of a light source with the sample. The data collected is typically two orders of magnitude bigger than the final image reconstructed, so high performance solutions are normally desired. One of the latest advances in ptychography imaging is the development of Ptycho-ADMM, a new ptychography reconstruction algorithm based on the Alternating Direction Method of Multipliers (ADMM). Ptycho-ADMM provides faster convergence speed and better quality reconstructions, all while being more resilient to noise in comparison with state-of-the-art methods. The downside of Ptycho-ADMM is that it requires additional computation and a larger memory footprint compared to simpler solutions. In this paper we tackle the computational requirements of Ptycho-ADMM, and design the first high performance multi-GPU solution of the method. We analyze and exploit the parallelism of Ptycho-ADMM to make use of multiple GPU devices. The proposed implementation achieves reconstruction times comparable to other GPU-accelerated high performance solutions, while providing the enhanced reconstruction quality of the Ptycho-ADMM method.

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Footnotes
1
Ratio of number of arithmetic operations computed per memory access.
 
2
The experiment with a single GPU and more than 200 million input samples is not reported because it does not fit into the device main memory.
 
Literature
1.
go back to reference Shi, X., Fischer, P., Neu, V., Elefant, D., Lee, J., Shapiro, D., Farmand, M., Tyliszczak, T., Shiu, H.-W., Marchesini, S., et al.: Soft x-ray ptychography studies of nanoscale magnetic and structural correlations in thin \(\rm {SmCo}_{5}\) films. Appl. Phys. Lett. 108(9), 094103 (2016)CrossRef Shi, X., Fischer, P., Neu, V., Elefant, D., Lee, J., Shapiro, D., Farmand, M., Tyliszczak, T., Shiu, H.-W., Marchesini, S., et al.: Soft x-ray ptychography studies of nanoscale magnetic and structural correlations in thin \(\rm {SmCo}_{5}\) films. Appl. Phys. Lett. 108(9), 094103 (2016)CrossRef
2.
go back to reference Giewekemeyer, K., Thibault, P., Kalbfleisch, S., Beerlink, A., Kewish, C.M., Dierolf, M., Pfeiffer, F., Salditt, T.: Quantitative biological imaging by ptychographic x-ray diffraction microscopy. Proc. Natl. Acad. Sci. 107(2), 529–534 (2010)CrossRef Giewekemeyer, K., Thibault, P., Kalbfleisch, S., Beerlink, A., Kewish, C.M., Dierolf, M., Pfeiffer, F., Salditt, T.: Quantitative biological imaging by ptychographic x-ray diffraction microscopy. Proc. Natl. Acad. Sci. 107(2), 529–534 (2010)CrossRef
3.
go back to reference Shapiro, D.A., Yu, Y.-S., Tyliszczak, T., Cabana, J., Celestre, R., Chao, W., Kaznatcheev, K., Kilcoyne, A.D., Maia, F., Marchesini, S., et al.: Chemical composition mapping with nanometre resolution by soft x-ray microscopy. Nat. Photonics 8(10), 765–769 (2014)CrossRef Shapiro, D.A., Yu, Y.-S., Tyliszczak, T., Cabana, J., Celestre, R., Chao, W., Kaznatcheev, K., Kilcoyne, A.D., Maia, F., Marchesini, S., et al.: Chemical composition mapping with nanometre resolution by soft x-ray microscopy. Nat. Photonics 8(10), 765–769 (2014)CrossRef
4.
go back to reference Holler, M., Guizar-Sicairos, M., Tsai, E.H., Dinapoli, R., Müller, E., Bunk, O., Raabe, J., Aeppli, G.: High-resolution non-destructive three-dimensional imaging of integrated circuits. Nature 543(7645), 402–406 (2017)CrossRef Holler, M., Guizar-Sicairos, M., Tsai, E.H., Dinapoli, R., Müller, E., Bunk, O., Raabe, J., Aeppli, G.: High-resolution non-destructive three-dimensional imaging of integrated circuits. Nature 543(7645), 402–406 (2017)CrossRef
5.
go back to reference Marchesini, S.: Invited article: a unified evaluation of iterative projection algorithms for phase retrieval. Rev. Sci. Instr. 78(1), 011301 (2007)CrossRef Marchesini, S.: Invited article: a unified evaluation of iterative projection algorithms for phase retrieval. Rev. Sci. Instr. 78(1), 011301 (2007)CrossRef
6.
go back to reference Marchesini, S., Krishnan, H., Daurer, B.J., Shapiro, D.A., Perciano, T., Sethian, J.A., Maia, F.R.: Sharp: a distributed GPU-based ptychographic solver. J. Appl. Crystallogr. 49(4), 1245–1252 (2016)CrossRef Marchesini, S., Krishnan, H., Daurer, B.J., Shapiro, D.A., Perciano, T., Sethian, J.A., Maia, F.R.: Sharp: a distributed GPU-based ptychographic solver. J. Appl. Crystallogr. 49(4), 1245–1252 (2016)CrossRef
7.
go back to reference Glowinski, R., Tallec, P.L.: Augmented Lagrangian and Operator-Splitting Methods in Nonlinear Mechanics. SIAM Studies in Applied Mathematics, Society for Industrial and Applied Mathematics, Philadelphia (1989)CrossRef Glowinski, R., Tallec, P.L.: Augmented Lagrangian and Operator-Splitting Methods in Nonlinear Mechanics. SIAM Studies in Applied Mathematics, Society for Industrial and Applied Mathematics, Philadelphia (1989)CrossRef
8.
go back to reference Chang, H., Enfedaque, P., Marchesini, S.: Blind Ptychographic Phase Retrieval via Convergent Alternating Direction Method of Multipliers (2018, submitted) Chang, H., Enfedaque, P., Marchesini, S.: Blind Ptychographic Phase Retrieval via Convergent Alternating Direction Method of Multipliers (2018, submitted)
10.
go back to reference Thibault, P., Dierolf, M., Bunk, O., Menzel, A., Pfeiffer, F.: Probe retrieval in ptychographic coherent diffractive imaging. Ultramicroscopy 109(4), 338–343 (2009)CrossRef Thibault, P., Dierolf, M., Bunk, O., Menzel, A., Pfeiffer, F.: Probe retrieval in ptychographic coherent diffractive imaging. Ultramicroscopy 109(4), 338–343 (2009)CrossRef
11.
go back to reference Hesse, R., Luke, D.R., Sabach, S., Tam, M.K.: Proximal heterogeneous block implicit-explicit method and application to blind ptychographic diffraction imaging. SIAM J. Imaging Sci. 8(1), 426–457 (2015)MathSciNetCrossRef Hesse, R., Luke, D.R., Sabach, S., Tam, M.K.: Proximal heterogeneous block implicit-explicit method and application to blind ptychographic diffraction imaging. SIAM J. Imaging Sci. 8(1), 426–457 (2015)MathSciNetCrossRef
12.
go back to reference Enfedaque, P., Auli-Llinas, F., Moure, J.C.: Implementation of the DWT in a GPU through a register-based strategy. IEEE Trans. Parallel Distrib. Syst. 26(12), 3394–3406 (2015)CrossRef Enfedaque, P., Auli-Llinas, F., Moure, J.C.: Implementation of the DWT in a GPU through a register-based strategy. IEEE Trans. Parallel Distrib. Syst. 26(12), 3394–3406 (2015)CrossRef
13.
Metadata
Title
GPU-Based Implementation of Ptycho-ADMM for High Performance X-Ray Imaging
Authors
Pablo Enfedaque
Huibin Chang
Hari Krishnan
Stefano Marchesini
Copyright Year
2018
DOI
https://doi.org/10.1007/978-3-319-93698-7_41

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