Phase unwrapping with a rapid opensource minimum spanning tree algorithm (ROMEO)

PURPOSE: To develop a rapid and accurate MRI phase-unwrapping technique for challenging phase topographies encountered at high magnetic fields, around metal implants, or postoperative cavities, which is sufficiently fast to be applied to large-group studies including Quantitative Susceptibility Mapping and functional MRI (with phase-based distortion correction). METHODS: The proposed path-following phase-unwrapping algorithm, ROMEO, estimates the coherence of the signal both in space-using MRI magnitude and phase information-and over time, assuming approximately linear temporal phase evolution. This information is combined to form a quality map that guides the unwrapping along a 3D path through the object using a computationally efficient minimum spanning tree algorithm. ROMEO was tested against the two most commonly used exact phase-unwrapping methods, PRELUDE and BEST PATH, in simulated topographies and at several field strengths: in 3T and 7T in vivo human head images and 9.4T ex vivo rat head images. RESULTS: ROMEO was more reliable than PRELUDE and BEST PATH, yielding unwrapping results with excellent temporal stability for multi-echo or multi-time-point data. It does not require image masking and delivers results within seconds, even in large, highly wrapped multi-echo data sets (eg, 9 seconds for a 7T head data set with 31 echoes and a 208 × 208 × 96 matrix size). CONCLUSION: Overall, ROMEO was both faster and more accurate than PRELUDE and BEST PATH, delivering exact results within seconds, which is well below typical image acquisition times, enabling potential on-console application

Three-Dimensional Nepal Earthquake Displacement Using Hybrid Genetic Algorithm Phase Unwrapping from Sentinel-1A Satellite

Introduction: Geophysicists had forewarned for decades that Nepal was exposed to a deadly earthquake, exceptionally despite its geology, urbanization and architecture. Gorkha earthquake is the most horrible natural disaster to crash into Nepal since the 1934 Nepal-Bihar earthquake. Gorkha earthquake occurred on April 25, 2015, at 11:56 NST and killed more than 10,000 people and injured more than 23,000 population. Objective: The main objective of this work is to utilize hybrid genetic algorithm for three-dimensional phase unwrapping of Nepal earthquake displacement using Sentinel-1A satellite. The three-dimensional best-path avoiding singularity loops (3DBPASL) algorithm was implemented to perform 3D Sentinel-1A satellite phase unwrapping. The hybrid genetic algorithm (HGA) was used to achieve 3DBPASL phase matching. Advancely, the errors in phase decorrelation were reduced by optimization of 3DBPASL using HGA. Results: The findings indicate a few cm of ground deformation and vertical northern of Kathmandu. Approximately, an area of 12,000 km2 has been drifted also the northern of Kathmandu. Further, each fringe of colour represents about 2.5 cm of deformation. The large amount of fringes indicates a large deformation pattern with ground motions of 3 m. Conclusion: In conclusion, HGA can be used to produce accurate 3D quake deformation using Sentinel-1A satellite

High-Fidelity and Perfect Reconstruction Techniques for Synthesizing Modulation Domain Filtered Images

Biomimetic processing inspired by biological vision systems has long been a goal of the image processing research community, both to further understanding of what it means to perceive and interpret image content and to facilitate advancements in applications ranging from processing large volumes of image data to engineering artificial intelligence systems. In recent years, the AM-FM transform has emerged as a useful tool that enables processing that is intuitive to human observers but would be difficult or impossible to achieve using traditional linear processing methods. The transform makes use of the multicomponent AM-FM image model, which represents imagery in terms of amplitude modulations, representative of local image contrast, and frequency modulations, representative of local spacing and orientation of lines and patterns. The model defines image components using an array of narrowband filterbank channels that is designed to be similar to the spatial frequency channel decomposition that occurs in the human visual system. The AM-FM transform entails the computation of modulation functions for all components of an image and the subsequent exact recovery of the image from those modulation functions. The process of modifying the modulation functions to alter visual information in a predictable way and then recovering the modified image through the AM-FM transform is known as modulation domain filtering. Past work in modulation domain filtering has produced dramatic results, but has faced challenges due to phase wrapping inherent in the transform computations and due to unknown integration constants associated with modified frequency content. The approaches developed to overcome these challenges have led to a loss of both stability and intuitive simplicity within the AM-FM model. In this dissertation, I have made significant advancements in the underlying processes that comprise the AM-FM transform. I have developed a new phase unwrapping method that increases the stability of the AM-FM transform, allowing higher quality modulation domain filtering results. I have designed new reconstruction techniques that allow for successful recovery from modified frequency modulations. These developments have allowed the design of modulation domain filters that, for the first time, do not require any departure from the simple and intuitive nature of the basic AM-FM model. Using the new modulation domain filters, I have produced new and striking results that achieve a variety of image processing tasks which are motivated by biological visual perception. These results represent a significant advancement relative to the state of the art and are a foundation from which future advancements in the field may be attained

Visualization and Localization of Interventional Devices with MRI by Susceptibility Mapping

Recently, interventional procedures can be performed with the visual assistance of MRI. However, the devices used in these procedures, such as brachytherapy seeds, biopsy needles, markers, and stents, have a large magnetic susceptibility that leads to severe signal loss and distortion in the MRI images and degrades the accuracy of the localization. Right now, there is no effective way to correctly identify, localize and visualize these interventional devices in MRI images. In this dissertation, we proposed a method to improve the accuracy of localization and visualization by generating positive contrast of the interventional devices using a regularized L1 minimization algorithm. Specifically, the spin-echo sequence with a shifted 180-degree pulse is used to acquire high SNR data. A short shift time is used to avoid severe phase wrap. A phase unwrapping method based on Markov Random Field using Highest-Confidence-First algorithm is proposed to unwrap the phase image. Then the phase images with different shifted time are used to calculate the field map. Next, L1 regularized deconvolution is performed to calculate the susceptibility map. With much higher susceptibility of the interventional devices than the background tissue, the interventional devices show positive-contrast in the susceptibility image. Computer simulations were performed to study the effect of the signal-to-noise ratio, resolution, orientation and size of the interventional devices on the accuracy of the results. Experiments were performed using gelatin and tissue phantom with brachytherapy seeds, gelatin phantoms with platinum wires, and water phantom with titanium needles. The results show that the proposed method provide positive contrast images of these interventional devices, differentiate them from other structures in the MRI images, and improves the visualization and localization of the devices

Efficient phase unwrapping

In the field of optical interferometry, two-dimensional projections of light interference patterns are often analysed in order to obtain measurements of interest. Such interference patterns, or interferograms, contain phase information which is inherently wrapped onto the range -t to it. Phase unwrapping is the processes of the restoration of the unknown multiple of 2ir, and therefore plays a major role in the overall process of interferogram analysis. Unwrapping phase information correctly becomes a challenging process in the presence of noise. This is particularly the case for speckle interferograms, which are noisy by nature. Many phase unwrapping algorithms have been devised by workers in the field, in order to achieve better noise rejection and improve the computational performance. This thesis focuses on the computational efficiency aspect, and picks as a starting point an existing phase unwrapping algorithm which has been shown to have inherent noise immunity. This is, namely, the tile-based phase unwrapping method, which attains its enhanced noise immunity through the application of the minimum spanning tree concept from graph theory. The thesis examines the problem of finding a minimum spanning tree, for this particular application, from a graph theory perspective, and shows that a more efficient class of minimum spanning tree algorithms can be applied to the problem. The thesis then goes on to show how a novel algorithm can be used to significantly reduce the size of the minimum spanning tree problem in an efficient manner.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

2D Phase Unwrapping via Graph Cuts

Phase imaging technologies such as interferometric synthetic aperture radar (InSAR), magnetic resonance imaging (MRI), or optical interferometry, are nowadays widespread and with an increasing usage. The so-called phase unwrapping, which consists in the in- ference of the absolute phase from the modulo-2π phase, is a critical step in many of their processing chains, yet still one of its most challenging problems. We introduce an en- ergy minimization based approach to 2D phase unwrapping. In this approach we address the problem by adopting a Bayesian point of view and a Markov random field (MRF) to model the phase. The maximum a posteriori estimation of the absolute phase gives rise to an integer optimization problem, for which we introduce a family of efficient algo- rithms based on existing graph cuts techniques. We term our approach and algorithms PUMA, for Phase Unwrapping MAx flow. As long as the prior potential of the MRF is convex, PUMA guarantees an exact global solution. In particular it solves exactly all the minimum L p norm (p ≥ 1) phase unwrapping problems, unifying in that sense, a set of existing independent algorithms. For non convex potentials we introduce a version of PUMA that, while yielding only approximate solutions, gives very useful phase unwrap- ping results. The main characteristic of the introduced solutions is the ability to blindly preserve discontinuities. Extending the previous versions of PUMA, we tackle denoising by exploiting a multi-precision idea, which allows us to use the same rationale both for phase unwrapping and denoising. Finally, the last presented version of PUMA uses a frequency diversity concept to unwrap phase images having large phase rates. A representative set of experiences illustrates the performance of PUMA

Numerical and Geometric Optimizations for Surface and Tolerance Modeling

Optimization techniques are widely used in many research and engineering areas. This dissertation presents numerical and geometric optimization methods for solving geometric and solid modeling problems. Geometric optimization methods are designed for manufacturing process planning, which optimizes the process by changing dependency relationships among geometric primitives from the original design diagram. Geometric primitives are used to represent part features, and dependencies in the dimensions between parts are represented by a topological graph. The ordering of these dependencies can have a significant effect on the tolerance zones in the part. To obtain tolerance zones from the dependencies, the conventional parametric method of tolerance analysis is de-composed into a set of geometric computations, which are combined and cascaded to obtain the tolerance zones in the geometric representations. Geometric optimization is applied to the topological graph in order to find a solution that provides not only an optimal dimensioning scheme but also an optimal plan for manufacturing the physical part. The applications of our method include tolerance analysis, dimension scheme optimization, and process planning. Two numerical optimization methods are proposed for local and global surface parameterizations. One is the nonlinear optimization, which is used for building the local field-aware parameterization. Given a local chart of the surface, a two-phase method is proposed, which generates a folding-free parameterization while still being aware of the geodesic metric. The parameterization method is applied in a view-dependent 3D painting system, which constitutes a local, adaptive and interactive painting environment. The other is the mixed-integer quadratic optimization, which is used for generating a quad mesh from a given triangular mesh. With a given cross field, the computation of parametric coordinates is formulated to be a mixed-integer optimization problem, which parameterizes the surface with good quality by adding redundant integer variables. The mixed integer system is solved more efficiently by an improved adaptive rounding solver. To obtain the final quadrangular mesh, an isoline tracing method and a breadth-first traversal mesh generation method are proposed so that the final mesh result has face information, which is useful for further model processing

A real-time multi-sensor 3D surface shape measurement system using fringe analysis

This thesis presents a state-of-the-art multi-sensor, 3D surface shape measurement system that is based upon fringe projection/analysis and which operates at speeds approaching real-time. The research programme was carried out as part of MEGURATH (www.megurath.org), a collaborative research project with the aim of improving the treatment of cancer by radiotherapy. The aim of this research programme was to develop a real-time, multi-sensor 3D surface shape measurement system that is based on fringe analysis, which provides the flexibility to choose from amongst several different fringe profilometry methods and to manipulate their settings interactively. The system has been designed specifically to measure dynamic 3D human body surface shape and to act as an enabling technology for the purpose of performing Metrology Guided Radiotherapy (MGRT). However, the system has a wide variety of other potential applications, including 3D modelling and visualisation, verbatim replication, reverse engineering and industrial inspection. It can also be used as a rapid prototyping tool for algorithm development and testing, within the field of fringe pattern profilometry. The system that has been developed provides single, or multi-sensor, measurement modes that are adaptable to the specific requirements of a desired application. The multi-sensor mode can be useful for covering a larger measurement area, by providing a multi-viewpoint measurement. The overall measurement accuracy of the system is better than O.5mm, with measurement speeds of up to 3 million XYZ points/second using the single-sensor mode and rising to up to 4.6 million XYZ points/second when measuring in parallel using the three sensor multi-sensor mode. In addition the system provides a wide-ranging catalogue of fringe profilometry methods and techniques, that enables the reconstruction of 3D information through an interactive user selection of 183 possible different paths of main combinations. The research aspects behind the development of the system are presented in this thesis, along with the author's contribution to this field of research, which has included the provision of a comprehensive framework for producing such a novel optical profilometry system, and the specific techniques that were developed to fulfil the aims of this research programme. This mainly included the following advanced methods: a transversal calibration method for the optical system, an adaptive filtering technique for the Fourier Transform Profilometry (FTP) method, and a method to synthetically restore the locations of the triangulation spots. Similarly, potential applications for the system have been presented and feasibility and accuracy analyses have been conducted, presenting both qualitative and quantitative measurement results. To this end, the high robustness levels exhibited by the system have been demonstrated (in terms of adaptability, accuracy and measurement capability) by performing extensive real experiments and laboratory testing. Finally, a number of potential future system developments are described, with the intention of further extending the system capabilities

An insight in cloud computing solutions for intensive processing of remote sensing data

The investigation of Earth's surface deformation phenomena provides critical insights into several processes of great interest for science and society, especially from the perspective of further understanding the Earth System and the impact of the human activities. Indeed, the study of ground deformation phenomena can be helpful for the comprehension of the geophysical dynamics dominating natural hazards such as earthquakes, volcanoes and landslide. In this context, the microwave space-borne Earth Observation (EO) techniques represent very powerful instruments for the ground deformation estimation. In particular, Small BAseline Subset (SBAS) is regarded as one of the key techniques, for its ability to investigate surface deformation affecting large areas of the Earth with a centimeter to millimeter accuracy in different scenarios (volcanoes, tectonics, landslides, anthropogenic induced land motions). The current Remote Sensing scenario is characterized by the availability of huge archives of radar data that are going to increase with the advent of Sentinel-1 satellites. The effective exploitation of this large amount of data requires both adequate computing resources as well as advanced algorithms able to properly exploit such facilities. In this work we concentrated on the use of the P-SBAS algorithm (a parallel version of SBAS) within HPC infrastructure, to finally investigate the effectiveness of such technologies for EO applications. In particular we demonstrated that the cloud computing solutions represent a valid alternative for scientific application and a promising research scenario, indeed, from all the experiments that we have conducted and from the results obtained performing Parallel Small Baseline Subset (P-SBAS) processing, the cloud technologies and features result to be absolutely competitive in terms of performance with in-house HPC cluster solution

Design of decorative 3D models: from geodesic ornaments to tangible assemblies

L'obiettivo di questa tesi è sviluppare strumenti utili per creare opere d'arte decorative digitali in 3D. Uno dei processi decorativi più comunemente usati prevede la creazione di pattern decorativi, al fine di abbellire gli oggetti. Questi pattern possono essere dipinti sull'oggetto di base o realizzati con l'applicazione di piccoli elementi decorativi. Tuttavia, la loro realizzazione nei media digitali non è banale. Da un lato, gli utenti esperti possono eseguire manualmente la pittura delle texture o scolpire ogni decorazione, ma questo processo può richiedere ore per produrre un singolo pezzo e deve essere ripetuto da zero per ogni modello da decorare. D'altra parte, gli approcci automatici allo stato dell'arte si basano sull'approssimazione di questi processi con texturing basato su esempi o texturing procedurale, o con sistemi di riproiezione 3D. Tuttavia, questi approcci possono introdurre importanti limiti nei modelli utilizzabili e nella qualità dei risultati. Il nostro lavoro sfrutta invece i recenti progressi e miglioramenti delle prestazioni nel campo dell'elaborazione geometrica per creare modelli decorativi direttamente sulle superfici. Presentiamo una pipeline per i pattern 2D e una per quelli 3D, e dimostriamo come ognuna di esse possa ricreare una vasta gamma di risultati con minime modifiche dei parametri. Inoltre, studiamo la possibilità di creare modelli decorativi tangibili. I pattern 3D generati possono essere stampati in 3D e applicati a oggetti realmente esistenti precedentemente scansionati. Discutiamo anche la creazione di modelli con mattoncini da costruzione, e la possibilità di mescolare mattoncini standard e mattoncini custom stampati in 3D. Ciò consente una rappresentazione precisa indipendentemente da quanto la voxelizzazione sia approssimativa. I principali contributi di questa tesi sono l'implementazione di due diverse pipeline decorative, un approccio euristico alla costruzione con mattoncini e un dataset per testare quest'ultimo.The aim of this thesis is to develop effective tools to create digital decorative 3D artworks. Real-world art often involves the use of decorative patterns to enrich objects. These patterns can be painted on the base or might be realized with the application of small decorative elements. However, their creation in digital media is not trivial. On the one hand, users can manually perform texture paint or sculpt each decoration, in a process that can take hours to produce a single piece and needs to be repeated from the ground up for every model that needs to be decorated. On the other hand, automatic approaches in state of the art rely on approximating these processes with procedural or by-example texturing or with 3D reprojection. However, these approaches can introduce significant limitations in the models that can be used and in the quality of the results. Instead, our work exploits the recent advances and performance improvements in the geometry processing field to create decorative patterns directly on surfaces. We present a pipeline for 2D and one for 3D patterns and demonstrate how each of them can recreate a variety of results with minimal tweaking of the parameters. Furthermore, we investigate the possibility of creating decorative tangible models. The 3D patterns we generate can be 3D printed and applied to previously scanned real-world objects. We also discuss the creation of models with standard building bricks and the possibility of mixing standard and custom 3D-printed bricks. This allows for a precise representation regardless of the coarseness of the voxelization. The main contributions of this thesis are the implementation of two different decorative pipelines, a heuristic approach to brick construction, and a dataset to test the latter