Potential Fields as an External Force and Algorithmic Improvements in Deformable Models

Deformable Models are extensively used as a Pattern Recognition technique. They are curves defined within an image domain that can be moved under the influence of internal and external forces. Some trade-offs of standard deformable models algorithms are the selection of image energy function (external force), the location of initial snake and the attraction of contour points to local energy minima when the snake is being deformed. This paper proposes a new procedure using potential fields as external forces. In addition, standard Deformable Models algorithm has been enhanced with both this new external force and algorithmic improvements. The performance of the presented approach has been successfully proved to extract muscles from Magnetic Resonance Imaging (MRI) sequences of Iberian ham at different maturation stages in order to calculate their volume change. The main conclusions of this paper are the practical viability of potential fields used as external forces, as well as the validation of the algorithmic improvements developed. The feasibility of applying Computer Vision techniques, in conjunction with MRI, for determining automatically the optimal ripening time of the Iberian ham is a practical conclusion reached with the proposed approach

A parallel interaction potential approach coupled with the immersed boundary method for fully resolved simulations of deformable interfaces and membranes

In this paper we show and discuss the use of a versatile interaction potential approach coupled with an immersed boundary method to simulate a variety of flows involving deformable bodies. In particular, we focus on two kinds of problems, namely (i) deformation of liquid-liquid interfaces and (ii) flow in the left ventricle of the heart with either a mechanical or a natural valve. Both examples have in common the two-way interaction of the flow with a deformable interface or a membrane. The interaction potential approach (de Tullio & Pascazio, Jou. Comp. Phys., 2016; Tanaka, Wada and Nakamura, Computational Biomechanics, 2016) with minor modifications can be used to capture the deformation dynamics in both classes of problems. We show that the approach can be used to replicate the deformation dynamics of liquid-liquid interfaces through the use of ad-hoc elastic constants. The results from our simulations agree very well with previous studies on the deformation of drops in standard flow configurations such as deforming drop in a shear flow or a cross flow. We show that the same potential approach can also be used to study the flow in the left ventricle of the heart. The flow imposed into the ventricle interacts dynamically with the mitral valve (mechanical or natural) and the ventricle which are simulated using the same model. Results from these simulations are compared with ad- hoc in-house experimental measurements. Finally, a parallelisation scheme is presented, as parallelisation is unavoidable when studying large scale problems involving several thousands of simultaneously deforming bodies on hundreds of distributed memory computing processors

Evaluation of a mesh-based contact model for optimal control problems using automatic differentiation

In recent years, there has been a growing research interest in the field of musculoskeletal gait, with a focus on enhancing the walking ability of older adults and individuals with disabilities due to accidents or illnesses. This research endeavours to comprehend the physical behaviour of muscles, ligaments, and joints that contribute to this movement. The objective of this thesis is to examine and compare the various contact model approaches used to analyse and simulate the contact forces and moments arising on the contact of human joints, particularly in the knee and knee prosthesis. Additionally, the study aims to integrate tangential forces into the original model which only considers normal forces in pressure contact models, and to evaluate and analyse the resulting differences in a tracking problem. To accomplish the objectives of this study, an automatic differentiation tools were employed calculate derivatives to solve an optimal control problem (OCP) using the CasADi library in a Matlab program. Therefore, the model needed to be continuously differentiable. The contact models developed within the group were tested, the results show that the original model had moderate accuracy in predicting lateral knee contact force (��� 2 value of 0.46 and an RMSE of 259.7 N) and better accuracy in predicting medial knee contact force (��� 2 value of 0.62 and an RMSE of 132.6 N). The inclusion of tangential forces in the pressure contact model led to mixed results, such as improved performance in hip flexion, but a decrease in accuracy for predicting both lateral and medial knee contact forces. The study indicates the need for further improvement in mesh-based contact models for knee joint simulation, especially in the inclusion of tangential forces.En els darrers anys, hi ha hagut un interès creixent en la recerca en el camp de la marxa humana i l’estudi de la biomecànica musculoesquelètica, centrada en millorar la capacitat de caminar de les persones grans i les persones amb discapacitats a causa d'accidents o malalties. Aquesta recerca s’esforça per comprendre el comportament físic dels músculs, lligaments i articulacions que contribueixen a aquest moviment. L'objectiu d'aquesta tesi és examinar i comparar les diferents aproximacions del model de contacte utilitzades per analitzar i simular les forces i moments que es produeixen a les superfícies de contacte de les articulacions humanes, especialment al genoll i a una pròtesi de genoll. A més, l'estudi té com a objectiu integrar les forces tangencials al model original, que només considera les forces normals en els models de contacte, i avaluar i analitzar les diferències obtingudes en un problema de seguiment de dades experimentals. Per aconseguir els objectius d'aquest estudi s'ha emprat un mètode de diferenciació automàtica per calcular les derivades de les expressions matemàtiques i resoldre un problema de control òptim (OCP) utilitzant la llibreria CasADi en Matlab. Es van analitzar els models de contacte desenvolupats al grup SIMMA Lab. Els resultats mostren que el model original va tenir una precisió moderada en la predicció de la força de contacte lateral del genoll (valor �� 2 de 0.46 i un RMSE de 259.7 N) i una millor precisió en la predicció de la força de contacte medial del genoll (valor �� 2 de 0.62 i un RMSE de 132.6 N). La inclusió de les forces tangencials en el model de pressió de contacte va donar resultats regulars. Per una banda es va obtenir una millora en la flexió del maluc, però una disminució en la precisió per predir les forces de contacte lateral i medial del genoll. L'estudi indica la necessitat de millores addicionals en els models de contacte basats en malles per a la simulació de l'articulació del genoll, especialment en la integració de les forces tangencials.En los últimos años, ha habido un creciente número de investigaciones en el campo de investigación de la marcha humana y la biomecánica musculoesquelética, con el objetivo de mejorar la capacidad de caminar de personas mayores y personas con discapacidades debido a accidentes o enfermedades. Esta investigación se esfuerza en comprender el comportamiento físico de los músculos, ligamentos y articulaciones que contribuyen a este movimiento. El objetivo de esta tesis es examinar y comparar las diferentes metodologías de modelos de contacto utilizadas para analizar y simular las fuerzas y momentos de contacto en las articulaciones humanas, especialmente en la rodilla y en la prótesis de rodilla. Además, el estudio busca integrar las fuerzas tangenciales en el modelo original, que solo considera las fuerzas normales en los modelos de contacto de presión, y evaluar y analizar las diferencias resultantes en un problema de seguimiento. Para lograr los objetivos de esta investigación, se utilizó un método de diferenciación automática para calcular las derivadas de expresiones matemáticas y resolver un problema de control óptimo (OCP) utilizando la librería CasADi en Matlab. Se analizaron los modelos de contacto desarrollados dentro del grupo SIMMA Lab. Los resultados muestran que el modelo original tuvo una precisión moderada en la predicción de la fuerza de contacto lateral de la rodilla (valor � 2 de 0.46 y un RMSE de 259.7 N) y una mejor precisión en la predicción de la fuerza de contacto medial de la rodilla (valor � 2 de 0.62 y un RMSE de 132.6 N). La inclusión de fuerzas tangenciales en el modelo de contacto dio resultados regulares. Por un lado, se obtuvo un mejor seguimiento de la flexión de cadera, pero por otro lado se obtuvo una disminución en la precisión para predecir tanto la fuerza de contacto lateral como medial de la rodilla. El estudio indica la necesidad de mejorar los modelos de contacto basados en malla para la simulación de la articulación de la rodilla, especialmente en la incorporación de fuerzas tangenciales

SOFA: A Multi-Model Framework for Interactive Physical Simulation

International audienceSOFA (Simulation Open Framework Architecture) is an open-source C++ library primarily targeted at interactive computational medical simulation. SOFA facilitates collaborations between specialists from various domains, by decomposing complex simulators into components designed independently and organized in a scenegraph data structure. Each component encapsulates one of the aspects of a simulation, such as the degrees of freedom, the forces and constraints, the differential equations, the main loop algorithms, the linear solvers, the collision detection algorithms or the interaction devices. The simulated objects can be represented using several models, each of them optimized for a different task such as the computation of internal forces, collision detection, haptics or visual display. These models are synchronized during the simulation using a mapping mechanism. CPU and GPU implementations can be transparently combined to exploit the computational power of modern hardware architectures. Thanks to this flexible yet efficient architecture, \sofa{} can be used as a test-bed to compare models and algorithms, or as a basis for the development of complex, high-performance simulators

Doctor of Philosophy

dissertationStochastic methods, dense free-form mapping, atlas construction, and total variation are examples of advanced image processing techniques which are robust but computationally demanding. These algorithms often require a large amount of computational power as well as massive memory bandwidth. These requirements used to be ful lled only by supercomputers. The development of heterogeneous parallel subsystems and computation-specialized devices such as Graphic Processing Units (GPUs) has brought the requisite power to commodity hardware, opening up opportunities for scientists to experiment and evaluate the in uence of these techniques on their research and practical applications. However, harnessing the processing power from modern hardware is challenging. The di fferences between multicore parallel processing systems and conventional models are signi ficant, often requiring algorithms and data structures to be redesigned signi ficantly for efficiency. It also demands in-depth knowledge about modern hardware architectures to optimize these implementations, sometimes on a per-architecture basis. The goal of this dissertation is to introduce a solution for this problem based on a 3D image processing framework, using high performance APIs at the core level to utilize parallel processing power of the GPUs. The design of the framework facilitates an efficient application development process, which does not require scientists to have extensive knowledge about GPU systems, and encourages them to harness this power to solve their computationally challenging problems. To present the development of this framework, four main problems are described, and the solutions are discussed and evaluated: (1) essential components of a general 3D image processing library: data structures and algorithms, as well as how to implement these building blocks on the GPU architecture for optimal performance; (2) an implementation of unbiased atlas construction algorithms|an illustration of how to solve a highly complex and computationally expensive algorithm using this framework; (3) an extension of the framework to account for geometry descriptors to solve registration challenges with large scale shape changes and high intensity-contrast di fferences; and (4) an out-of-core streaming model, which enables developers to implement multi-image processing techniques on commodity hardware

A Framework for Dynamic Terrain with Application in Off-road Ground Vehicle Simulations

The dissertation develops a framework for the visualization of dynamic terrains for use in interactive real-time 3D systems. Terrain visualization techniques may be classified as either static or dynamic. Static terrain solutions simulate rigid surface types exclusively; whereas dynamic solutions can also represent non-rigid surfaces. Systems that employ a static terrain approach lack realism due to their rigid nature. Disregarding the accurate representation of terrain surface interaction is rationalized because of the inherent difficulties associated with providing runtime dynamism. Nonetheless, dynamic terrain systems are a more correct solution because they allow the terrain database to be modified at run-time for the purpose of deforming the surface. Many established techniques in terrain visualization rely on invalid assumptions and weak computational models that hinder the use of dynamic terrain. Moreover, many existing techniques do not exploit the capabilities offered by current computer hardware. In this research, we present a component framework for terrain visualization that is useful in research, entertainment, and simulation systems. In addition, we present a novel method for deforming the terrain that can be used in real-time, interactive systems. The development of a component framework unifies disparate works under a single architecture. The high-level nature of the framework makes it flexible and adaptable for developing a variety of systems, independent of the static or dynamic nature of the solution. Currently, there are only a handful of documented deformation techniques and, in particular, none make explicit use of graphics hardware. The approach developed by this research offloads extra work to the graphics processing unit; in an effort to alleviate the overhead associated with deforming the terrain. Off-road ground vehicle simulation is used as an application domain to demonstrate the practical nature of the framework and the deformation technique. In order to realistically simulate terrain surface interactivity with the vehicle, the solution balances visual fidelity and speed. Accurately depicting terrain surface interactivity in off-road ground vehicle simulations improves visual realism; thereby, increasing the significance and worth of the application. Systems in academia, government, and commercial institutes can make use of the research findings to achieve the real-time display of interactive terrain surfaces

High performance computing for 3D image segmentation

Digital image processing is a very popular and still very promising eld of science, which has been successfully applied to numerous areas and problems, reaching elds like forensic analysis, security systems, multimedia processing, aerospace, automotive, and many more. A very important part of the image processing area is image segmentation. This refers to the task of partitioning a given image into multiple regions and is typically used to locate and mark objects and boundaries in input scenes. After segmentation the image represents a set of data far more suitable for further algorithmic processing and decision making. Image segmentation algorithms are a very broad eld and they have received signi cant amount of research interest A good example of an area, in which image processing plays a constantly growing role, is the eld of medical solutions. The expectations and demands that are presented in this branch of science are very high and dif cult to meet for the applied technology. The problems are challenging and the potential bene ts are signi cant and clearly visible. For over thirty years image processing has been applied to different problems and questions in medicine and the practitioners have exploited the rich possibilities that it offered. As a result, the eld of medicine has seen signi cant improvements in the interpretation of examined medical data. Clearly, the medical knowledge has also evolved signi cantly over these years, as well as the medical equipment that serves doctors and researchers. Also the common computer hardware, which is present at homes, of ces and laboratories, is constantly evolving and changing. All of these factors have sculptured the shape of modern image processing techniques and established in which ways it is currently used and developed. Modern medical image processing is centered around 3D images with high spatial and temporal resolution, which can bring a tremendous amount of data for medical practitioners. Processing of such large sets of data is not an easy task, requiring high computational power. Furthermore, in present times the computational power is not as easily available as in recent years, as the growth of possibilities of a single processing unit is very limited - a trend towards multi-unit processing and parallelization of the workload is clearly visible. Therefore, in order to continue the development of more complex and more advanced image processing techniques, a new direction is necessary. A very interesting family of image segmentation algorithms, which has been gaining a lot of focus in the last three decades, is called Deformable Models. They are based on the concept of placing a geometrical object in the scene of interest and deforming it until it assumes the shape of objects of interest. This process is usually guided by several forces, which originate in mathematical functions, features of the input images and other constraints of the deformation process, like object curvature or continuity. A range of very desired features of Deformable Models include their high capability for customization and specialization for different tasks and also extensibility with various approaches for prior knowledge incorporation. This set of characteristics makes Deformable Models a very ef cient approach, which is capable of delivering results in competitive times and with very good quality of segmentation, robust to noisy and incomplete data. However, despite the large amount of work carried out in this area, Deformable Models still suffer from a number of drawbacks. Those that have been gaining the most focus are e.g. sensitivity to the initial position and shape of the model, sensitivity to noise in the input images and to awed input data, or the need for user supervision over the process. The work described in this thesis aims at addressing the problems of modern image segmentation, which has raised from the combination of above-mentioned factors: the signi cant growth of image volumes sizes, the growth of complexity of image processing algorithms, coupled with the change in processor development and turn towards multi-processing units instead of growing bus speeds and the number of operations per second of a single processing unit. We present our innovative model for 3D image segmentation, called the The Whole Mesh Deformation model, which holds a set of very desired features that successfully address the above-mentioned requirements. Our model has been designed speci cally for execution on parallel architectures and with the purpose of working well with very large 3D images that are created by modern medical acquisition devices. Our solution is based on Deformable Models and is characterized by a very effective and precise segmentation capability. The proposed Whole Mesh Deformation (WMD) model uses a 3D mesh instead of a contour or a surface to represent the segmented shapes of interest, which allows exploiting more information in the image and obtaining results in shorter times. The model offers a very good ability for topology changes and allows effective parallelization of work ow, which makes it a very good choice for large data-sets. In this thesis we present a precise model description, followed by experiments on arti cial images and real medical data

Robot Learning for Manipulation of Deformable Linear Objects

Deformable Object Manipulation (DOM) is a challenging problem in robotics. Until recently there has been limited research on the subject, with most robotic manipulation methods being developed for rigid objects. Part of the challenge in DOM is that non-rigid objects require solutions capable of generalizing to changes in shape and mechanical properties. Recently, Machine Learning (ML) has been proven successful in other fields where generalization is important such as computer vision, thus encouraging the application of ML to robotics as well. Notably, Reinforcement Learning (RL) has shown promise in finding control policies for manipulation of rigid objects. However, RL requires large amounts of data that are better satisfied in simulation while deformable objects are inherently more difficult to model and simulate. This thesis presents ReForm, a simulation sandbox for robotic manipulation of Deformable Linear Objects (DLOs) such as cables, ropes, and wires. DLO manipulation is an interesting problem for a variety of applications throughout manufacturing, agriculture, and medicine. Currently, this sandbox includes six shape control tasks, which are classified as explicit when a precise shape is to be achieved, or implicit when the deformation is just a consequence of a more abstract goal, e.g. wrapping a DLO around another object. The proposed simulation environments aim to facilitate comparison and reproducibility of robot learning research. To that end, an RL algorithm is tested on each simulated task providing initial benchmarking results. ReForm is one of three concurrent frameworks to first support DOM problems. This thesis also addresses the problem of DLO state representation for an explicit shape control problem. Moreover, the effects of elastoplastic properties on the RL reward definition are investigated. From a control perspective, DLOs with these properties are particularly challenging to manipulate due to their nonlinear behavior, acting elastic up to a yield point after which they become permanently deformed. A low-dimensional representation from discrete differential geometry is proposed, offering more descriptive shape information than a simple point-cloud while avoiding the need for curve fitting. Empirical results show that this representation leads to a better goal description in the presence of elastoplasticity, preventing the RL algorithm from converging to local minima which correspond to incorrect shapes of the DLO

Robuste Berechnungsverfahren zur nichtlinearen dynamischen Analyse von Balken- und Schalenstrukturen

Gegenwärtige und zukünftige dynamisch beanspruchte, schlanke Strukturen aus mehrschichtig verbundenen, hyperelastischen Werkstoffen, z. B. Windenergieanlagen und Hubschrauber usw., sind sehr komplex. Eine genaue Untersuchung im Zeitbereich erfordert den Einsatz von Methoden, die kinematische, geometrische sowie, bis zu einem gewissen Grad, materielle Nichtlinearitäten berücksichtigen sollten. Daher könnten Simulationen mit Beachtung von großen Verschiebungen, Drehungen und Verzerrungen nötig sein, um das mechanische Verhalten akkurat zu vorhersagen zu vermögen. Zunächst werden die Bewegungsgleichungen räumlich diskretisiert. Dann werden die zum Teil diskretisierten Gleichungen mittels eines Integrationsverfahrens zeitlich diskretisiert. Solche diskreten Gleichungen sind sehr steif, sodass sich die Berechnung der langzeitigen Lösung erschwert. Darüber hinaus ist die Einführung von Nebenbedingungen oft nötig, um komplexere Strukturen aufstellen zu können, wodurch sich die Komplexität erhöht wird und unerwünschte Eigenschaften noch verschärft werden. Um Robustheit zu gewinnen, sollen Berechnungsverfahren hergeleitet werden, die die zugrunde legende Physik in gewissem Maße erhalten können und gleichzeitig den hochfrequenten Anteil der Lösung unterdrücken können. Die Erfüllung dieser Anforderungen stellt sich als sehr herausfordernd dar. Das Hauptziel dieser Arbeit liegt an der Entwicklung von Berechnungsverfahren zur Vertiefung des Verständnises des dynamischen Verhaltens von Balken- und Schalenstrukturen. Um dieses Ziel zu erreichen, wird ein umfassender Ansatz vorgeschlagen. Dieser besteht aus: i) Einer auf Direktoren basierenden, Finite-Elemente-Formulierung für den geometrisch exakten Balken mit allgemeinen Querschnittseigenschaften; ii) einer auf Direktoren basierenden, Finite-Elemente-Formulierung für die Kontinuumsmechanik-basierte Schale aus mehrschichtig verbundenen, hyperelastischen Werkstoffen; iii) einer vereinheitlichten Beschreibung von Starrkörpern, Balken und Schalen und deren Kopplung mittels kinematischer Nebenbedingungen; und, iv) einem robusten Integrationsverfahren basierend auf dem gemittelten Vektorfeld. Des Weiteren wird Folgendes ebenfalls vorgeschlagen: v) Die Partikularisierung der Hauptgeodätenanalyse zur nichtlinearen Identifikation von Bewegungsmoden an Balkenstrukturen; und, vi) ein neues konservatives/dissipatives Integrationsverfahren für allgemeine nichtlineare mechanische Systeme basierend auf optimierten Modifizierungen höherer Ordnung, die die Defizite der Mittelpunktsregel beheben. Die sehr gute Leistung des vorgeschlagenen Ansatzes wird durch mehrere Beispiele unterschiedlicher Komplexität nachgewiesen.Existing and new slender structures made of hyperelastic multilayer composite materials subject to highly dynamic loads, e.g., wind turbines, helicopters, cars, speedboats or submarines inter alia, are very complex. Their dynamic analysis requires fully nonlinear formulations, at least from the kinematic and geometric point of view, and also to some extent from the material point of view. Thus, simulations in time-domain involving large displacements, rotations and strains could be necessary to predict their mechanical behavior accurately. Numerical procedures to carry out such simulations rely firstly on the partial discretization in space of the governing equations, for instance with finite elements. These semi discrete equations are further discretized in time with an integration scheme. The resulting discrete equations are in fact very stiff and therefore, the computation of the long-term behavior could be problematic. In many applications, the introduction of constraints is also necessary for rendering more complex structures. Besides introducing a new level of complexity, this can sharpen conditioning problems already present in the fully discrete problem. Additionally, we also require procedures able to annihilate the unwanted unresolved high-frequency content without upsetting of the underlying physics. However, the simultaneous satisfaction of all these requirements is a very challenging task. The main objective of this work is to provide means intended for helping to understand further the nonlinear dynamics of beam and shell structures made of hyperelastic multilayer composite materials subject to highly dynamic loads. To accomplish this main goal, we propose a unifying computational approach that relies on: i) a director-based finite-element formulation for geometrically exact beams with general cross-section properties; ii) a director-based finite-element formulation for solid-degenerate shells made of hyperelastic multilayer composite materials; iii) a unifying description of rigid bodies, geometrically exact beams and solid-degenerate shells and their combination with kinematic pairs, which avoids inherently the necessity of rotational degrees of freedom; and, iv) a robust integration scheme based on the average vector field. Additionally, we propose: v) the particularization of the principal geodesic analysis to identify motion patters exhibited by beam structures in a purely nonlinear setting; and, vi) a new conservative/dissipative integration method for general nonlinear mechanical systems, which relies on high-order correction terms that optimally modify the midpoint rule. Moreover, the excellent numerical performance of the proposed unifying framework and procedures is illustrated by means of a good number of examples with different difficulty levels