PyNX: high performance computing toolkit for coherent X-ray imaging based on operators

Abstract

The open-source PyNX toolkit [Favre-Nicolin et al (2011) arXiv:1010.2641, Mandula et al (2016)] has been extended to provide tools for coherent X-ray imaging data analysis and simulation. All calculations can be executed on graphical processing units (GPU) to achieve high performance computing speeds. This can be used for Coherent Diffraction Imaging (CDI), Ptychography and wavefront propagation, in the far or near field regime. Moreover, all imaging operations (propagation, projections, algorithm cycles..) can be used in Python as simple mathematical operators, an approach which can be used to easily combine basic algorithms in a tailored chain. Calculations can also be distributed to multiple GPUs, e.g. for large Ptychography datasets. Command-line scripts are also available for on-line CDI and Ptychography analysis, either from raw beamline datasets or using the Coherent X-ray Imaging data format [Maia (2012)].

23 pages, 11 figures. To be published in Journal of Applied Crystallography

References in corpus (12)

• X-ray image reconstruction from a diffraction pattern alone
• High-resolution ab initio three-dimensional X-ray diffraction microscopy
• A unified evaluation of iterative projection algorithms for phase retrieval
• Relaxed Averaged Alternating Reflections for Diffraction Imaging
• SHARP: a distributed, GPU-based ptychographic solver
• High resolution three dimensional structural microscopy by single angle Bragg ptychography
• Alternating Projection, Ptychographic Imaging and Phase Synchronization
• Analysis of strain and stacking faults in single nanowires using Bragg coherent diffraction imaging
• Augmented projections for ptychographic imaging
• Fast computing of scattering maps of nanostructures using graphical processing units
• Free log-likelihood as an unbiased metric for coherent diffraction imaging
• Generalized Proximal Smoothing for Phase Retrieval

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• Soft X-ray phase nano-microscopy of micrometre-thick magnets
• Lattice deformation at the sub-micron scale: X-ray nanobeam measurements of elastic strain in electron shuttling devices
• Micromagnetics of magnetic chemical modulations in soft-magnetic cylindrical nanowires
• Fractional Skyrmion Tubes in Chiral-Interfaced Three-Dimensional Magnetic Nanowires
• A modular software framework for the design and implementation of ptychography algorithms
• Magnetic X-ray imaging using a single polarization and multimodal-ptychography
• Self-probed ptychography from semiconductor high-harmonic generation
• 3D tomographic imaging of skyrmionic cocoons using HERALDO