X-ray crystallography is a technique for determining the structure (positions of atoms in space) of molecules. It is a well developed technique, and is applied routinely to both small inorganic and large organic molecules. However, the determination of the structures of large biological molecules by x-ray crystallography can still be an experimentally and computationally expensive task. The data in an x-ray experiment are the amplitudes of the Fourier transform of the electron density in the crystalline specimen. The structure determination problem in x-ray crystallography is therefore identical to a phase retrieval problem in image reconstruction, for which iterative transform algorithms are a common solution method. This thesis is concerned with iterative projection algorithms, a generalized and more powerful version of iterative transform algorithms, and their application to macromolecular x-ray crystallography. A detailed study is made of iterative projection algorithms, including their properties, convergence, and implementations. Two applications to macromolecular crystallography are then investigated. The first concerns reconstruction of binary image and the application of iterative projection algorithms to determining molecular envelopes from x-ray solvent contrast variation data. An effective method for determining molecular envelopes is developed. The second concerns the use of symmetry constraints and the application of iterative projection algorithms to ab initio determination of macromolecular structures from crystal diffraction data. The algorithm is tested on an icosahedral virus and a protein tetramer. The results indicate that ab initio phasing is feasible for structures containing 4-fold or 5-fold non-crystallographic symmetry using these algorithms if an estimate of the molecular envelope is available.

New quantitative methods are developed for analyser-based phase contrast imaging (ABI) with hard X-rays. In the first instance we show that quantitative ABI may be implemented using an extended incoherent source. Next, we outline how complex Green’s functions may be reconstructed from phase contrast images and we apply this method to reconstruct the thick perfect crystal Green’s function associated with an ABI imaging system. The use of quantitative ABI with incoherent X-ray sources is not widespread and the first set of results pertains to the feasibility of quantitative ABI imaging and phase retrieval using a rotating anode X-ray source. The necessary conditions for observation of ABI phase contrast are deduced from elementary coherence considerations and numerical simulations. We then focus on the problem of extracting quantitative information from ABI images recorded using an extended incoherent X-ray source. The results of an experiment performed at Friedrich-Schiller University, Germany using a rotating anode X-ray source demonstrate the validity of our approach. It is shown that quantitative information may be extracted from such images under quite general and practicable conditions. We then develop a new use for phase contrast imaging systems that allows the Green’s function associated with a linear shift-invariant imaging system to be deduced from two phase contrast images of a known weak object. This new approach is applied to X-ray crystallography where the development of efficient methods of inferring the phase of rocking curves is an important open problem. We show how the complex Green’s function describing Bragg reflection of a coherent scalar X-ray wavefield from a crystal may be recovered from a single image over a wide range of reciprocal space simultaneously. The solution we derive is fast, non-iterative and deterministic. When applied to crystalline structures for which the kinematic scattering approximation is valid, such as thin crystalline films, our technique is shown to solve the famous one-dimensional phase retrieval problem which allows us to directly invert the Green’s function to retrieve the depth-dependent interplanar spacing. Finally we implement our Green’s function retrieval method on experimental data collected at the SPring-8 synchrotron in Hyogo, Japan. In the experiment we recorded analyser-based phase contrast images of a known weak object using a thick perfect silicon analyser crystal. It is then demonstrated that these measurements can be inverted to recover the complex Green’s function associated with the analyser crystal Bragg peak. The reconstructed Green’s function is found to be in good agreement with the prediction of dynamical diffraction theory.

X-ray crystallography is a form of microscopy that allows the three-dimensional arrangement of atoms belonging to molecules within crystals to be determined. In this method, a crystal is illuminated with a beam of X-rays and the diffracted amplitudes resulting from the illumination are measured and computationally processed to enable the electron density of the unit molecule, or the unit cell, constituting the crystal to be calculated. The recent development of the X-ray free-electron laser (XFEL) provides new routes for determining molecular structures via its ability to generate intense but brief X-ray pulses. These new instruments enable diffraction measurements to be obtained from crystals that have a small number of unit cells, referred to as nanocrystals, and molecular structure determination via this technique is known as serial femtosecond nanocrystallography (SFX). This thesis is concerned with the characterisation of diffraction data obtained from SFX experiments and the techniques for reconstructing the electron density of the molecule from such data. The noise characteristics of diffraction measurements from nanocrystals is developed. Methods for directly inverting nanocrystal diffraction to obtain the electron density of the molecule are analysed and an approach to ameliorate the effect of noise is proposed and evaluated by simulation. A model for diffraction by nanocrystals that include the effects of different unit cell arrangements and incomplete unit cells on the crystal surface is also developed and explored by simulation. The diffraction by finite crystals is shown to be equal to the incoherent average over a set of unit cells that contain different molecular arrangements related to the symmetry of the crystal at hand. The problem of image reconstruction under this circumstance is investigated. The more general problem of reconstructing multiple, unrelated, objects from their averaged diffraction is also explored and uniqueness properties along with reconstruction algorithms developed. The problem of reconstructing multiple, related, unit cells is studied and preliminary results are obtained. These results show that iterative phase retrieval algorithms can in principle be adapted to reconstruct the electron density of a crystalline specimen from the data obtained in SFX and the retrieval of phases from the diffracted intensity averaged over multiple objects is feasible.

This thesis focuses on the use of phaseless (magnitude-only) planar near-field antenna measurements for the far-field characterization of an antenna under test (AUT). This is important since the use of phaseless data only requires power measurements, thus, removing the need of using expensive instruments, such as vector network analyzers which can measure both magnitude and phase. In addition, as opposed to far-field measurement techniques, performing measurements in the near-field zone of an AUT makes the measurement system more compact. / February 2016

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Les tâches qui consistent à comprendre automatiquement le contenu d’un signal naturel, comme une image ou un son, sont en général difficiles. En effet, dans leur représentation naïve, les signaux sont des objets compliqués, appartenant à des espaces de grande dimension. Représentés différemment, ils peuvent en revanche être plus faciles à interpréter. Cette thèse s’intéresse à une représentation fréquemment utilisée dans ce genre de situations, notamment pour analyser des signaux audio : le module de la transformée en ondelettes. Pour mieux comprendre son comportement, nous considérons, d’un point de vue théorique et algorithmique, le problème inverse correspondant : la reconstruction d’un signal à partir du module de sa transformée en ondelettes. Ce problème appartient à une classe plus générale de problèmes inverses : les problèmes de reconstruction de phase. Dans un premier chapitre, nous décrivons un nouvel algorithme, PhaseCut, qui résout numériquement un problème de reconstruction de phase générique. Comme l’algorithme similaire PhaseLift, PhaseCut utilise une relaxation convexe, qui se trouve en l’occurence être de la même forme que les relaxations du problème abondamment étudié MaxCut. Nous comparons les performances de PhaseCut et PhaseLift, en termes de précision et de rapidité. Dans les deux chapitres suivants, nous étudions le cas particulier de la reconstruction de phase pour la transformée en ondelettes. Nous montrons que toute fonction sans fréquence négative est uniquement déterminée (à une phase globale près) par le module de sa transformée en ondelettes, mais que la reconstruction à partir du module n’est pas stable au bruit, pour une définition forte de la stabilité. On démontre en revanche une propriété de stabilité locale. Nous présentons également un nouvel algorithme de reconstruction de phase, non-convexe, qui est spécifique à la transformée en ondelettes, et étudions numériquement ses performances. Enfin, dans les deux derniers chapitres, nous étudions une représentation plus sophistiquée, construite à partir du module de transformée en ondelettes : la transformée de scattering. Notre but est de comprendre quelles propriétés d’un signal sont caractérisées par sa transformée de scattering. On commence par démontrer un théorème majorant l’énergie des coefficients de scattering d’un signal, à un ordre donné, en fonction de l’énergie du signal initial, convolé par un filtre passe-haut qui dépend de l’ordre. On étudie ensuite une généralisation de la transformée de scattering, qui s’applique à des processus stationnaires. On montre qu’en dimension finie, cette transformée généralisée préserve la norme. En dimension un, on montre également que les coefficients de scattering généralisés d’un processus caractérisent la queue de distribution du processus. / Automatically understanding the content of a natural signal, like a sound or an image, is in general a difficult task. In their naive representation, signals are indeed complicated objects, belonging to high-dimensional spaces. With a different representation, they can however be easier to interpret. This thesis considers a representation commonly used in these cases, in particular for theanalysis of audio signals: the modulus of the wavelet transform. To better understand the behaviour of this operator, we study, from a theoretical as well as algorithmic point of view, the corresponding inverse problem: the reconstruction of a signal from the modulus of its wavelet transform. This problem belongs to a wider class of inverse problems: phase retrieval problems. In a first chapter, we describe a new algorithm, PhaseCut, which numerically solves a generic phase retrieval problem. Like the similar algorithm PhaseLift, PhaseCut relies on a convex relaxation of the phase retrieval problem, which happens to be of the same form as relaxations of the widely studied problem MaxCut. We compare the performances of PhaseCut and PhaseLift, in terms of precision and complexity. In the next two chapters, we study the specific case of phase retrieval for the wavelet transform. We show that any function with no negative frequencies is uniquely determined (up to a global phase) by the modulus of its wavelet transform, but that the reconstruction from the modulus is not stable to noise, for a strong notion of stability. However, we prove a local stability property. We also present a new non-convex phase retrieval algorithm, which is specific to the case of the wavelet transform, and we numerically study its performances. Finally, in the last two chapters, we study a more sophisticated representation, built from the modulus of the wavelet transform: the scattering transform. Our goal is to understand which properties of a signal are characterized by its scattering transform. We first prove that the energy of scattering coefficients of a signal, at a given order, is upper bounded by the energy of the signal itself, convolved with a high-pass filter that depends on the order. We then study a generalization of the scattering transform, for stationary processes. We show that, in finite dimension, this generalized transform preserves the norm. In dimension one, we also show that the generalized scattering coefficients of a process characterize the tail of its distribution.

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Research has shown that a frame for an n-dimensional real Hilbert space offers phase retrieval if and only if it has the complement property. There is a geometric characterization of general frames, the Han-Larson-Naimark Dilation Theorem, which gives us the necessary and sufficient conditions required to dilate a frame for an n-dimensional Hilbert space to a frame for a Hilbert space of higher dimension k. However, a frame having the complement property in an n-dimensional real Hilbert space does not ensure that its dilation will offer phase retrieval. In this thesis, we will explore and provide what necessary and sufficient conditions must be satisfied to dilate a phase retrieval frame for an n-dimensional real Hilbert space to a phase retrieval frame for a k-dimensional real Hilbert.

Electron Ptychography is a technique to retrieve the phase information of the medium through which the electron wave travels in a Transmission Electron Microscope (TEM). Phase calculation is carried out by acquiring an oversampled dataset of diffraction patterns from the sample and execution of a Fourier-based mathematical solution or algorithm using the collected dataset of intensity patterns. The phase of the electron wave contains valuable information about the structure of the material under study. In this contribution, we provide a scientific background necessary for understanding the phase calculation method, examine the capabilities and limitations of the Electron Ptychography in experimental setup and introduce two novel methods to increase the signal to noise ratio by using the same dose budget used in a classic Ptychography experiment. / Thesis / Master of Applied Science (MASc)