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Register a new userAb initio compressive phase retrieval
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S. Marchesini
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Any object on earth has two fundamental properties: it is finite, and it is made of atoms. Structural information about an object can be obtained from diffraction amplitude measurements that account for either one of these traits. Nyquist-sampling of the Fourier amplitudes is sufficient to image single particles of finite size at any resolution. Atomic resolution data is routinely used to image molecules replicated in a crystal structure. Here we report an algorithm that requires neither information, but uses the fact that an image of a natural object is compressible. Intended applications include tomographic diffractive imaging, crystallography, powder diffraction, small angle x-ray scattering and random Fourier amplitude measurements.
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When x-rays penetrate soft matter, their phase changes more rapidly than their amplitude. In- terference effects visible with high brightness sources creates higher contrast, edge enhanced images. When the object is piecewise smooth (made of big blocks of a few components), such higher con- trast datasets have a sparse solution. We apply basis pursuit solvers to improve SNR, remove ring artifacts, reduce the number of views and radiation dose from phase contrast datasets collected at the Hard X-Ray Micro Tomography Beamline at the Advanced Light Source. We report a GPU code for the most computationally intensive task, the gridding and inverse gridding algorithm (non uniform sampled Fourier transform).
In the compressive phase retrieval problem, or phaseless compressed sensing, or compressed sensing from intensity only measurements, the goal is to reconstruct a sparse or approximately $k$-sparse vector $x in mathbb{R}^n$ given access to $y= |Phi x|$, where $|v|$ denotes the vector obtained from taking the absolute value of $vinmathbb{R}^n$ coordinate-wise. In this paper we present sublinear-time algorithms for different variants of the compressive phase retrieval problem which are akin to the variants considered for the classical compressive sensing problem in theoretical computer science. Our algorithms use pure combinatorial techniques and near-optimal number of measurements.
Ultrafast nanocrystallography has the potential to revolutionize biology by enabling structural elucidation of proteins for which it is possible to grow crystals with 10 or fewer unit cells on the side. The success of nanocrystallography depends on robust orientation-determination procedures that allow us to average diffraction data from multiple nanocrystals to produce a three dimensional (3D) diffraction data volume with a high signal-to-noise ratio. Such a 3D diffraction volume can then be phased using standard crystallographic techniques. Indexing algorithms used in crystallography enable orientation determination of diffraction data from a single crystal when a relatively large number of reflections are recorded. Here we show that it is possible to obtain the exact lattice geometry from a smaller number of measurements than standard approaches using a basis pursuit solver.
Available simulation methods, suitable to describe solid-solid phase transitions occurring upon increasing of presssure and/or temperature, are based on empirical interatomic potentials: this restriction reduces the predictive power, and thus the general usefulness of numeric simulations in this very relevant field. We present a new simulation scheme which allows, for the first time, the simulation of these phenomena with the correct quantum-mechanical description of interatomic forces and internal stress, along with the correct statistical mechanics of ionic degrees of freedom. The method is obtained by efficiently combining the Car-Parrinello method for ab- initio molecular dynamics with the Parrinello Rahman method to account for a variable cell shape. Within this scheme phase trasformations may spontaneously take place during the simulation with variation of external pressure and/or temperature. The validity of the method is demonstrated by simulating the metal-insulator transition in Silicon (from diamond structure to simple hexagonal structure) under high pressure.
In this work we consider the problem of reconstruction of a signal from the magnitude of its Fourier transform, also known as phase retrieval. The problem arises in many areas of astronomy, crystallography, optics, and coherent diffraction imaging (CDI). Our main goal is to develop an efficient reconstruction method based on continuous optimization techniques. Unlike current reconstruction methods, which are based on alternating projections, our approach leads to a much faster and more robust method. However, all previous attempts to employ continuous optimization methods, such as Newton-type algorithms, to the phase retrieval problem failed. In this work we provide an explanation for this failure, and based on this explanation we devise a sufficient condition that allows development of new reconstruction methods---approximately known Fourier phase. We demonstrate that a rough (up to $pi/2$ radians) Fourier phase estimate practically guarantees successful reconstruction by any reasonable method. We also present a new reconstruction method whose reconstruction time is orders of magnitude faster than that of the current method-of-choice in phase retrieval---Hybrid Input-Output (HIO). Moreover, our method is capable of successful reconstruction even in the situations where HIO is known to fail. We also extended our method to other applications: Fourier domain holography, and interferometry. Additionally we developed a new sparsity-based method for sub-wavelength CDI. Using this method we demonstrated experimental resolution exceeding several times the physical limit imposed by the diffraction light properties (so called diffraction limit).
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