Taking an Object-Centric View on Dynamic Information with Object Flow Analysis

A large body of research analyzes the runtime execution of a system to extract abstract behavioral views. Those approaches primarily analyze control flow by tracing method execution events or they analyze object graphs of heap snapshots. However, they do not capture how objects are passed through the system at runtime. We refer to the exchange of objects as the object flow, and we claim that object flow is necessary to analyze if we are to understand the runtime of an object-oriented application. We propose and detail Object Flow Analysis, a novel dynamic analysis technique that takes this new information into account. To evaluate its usefulness, we present a visual approach that allows a developer to study classes and components in terms of how they exchange objects at runtime. We illustrate our approach on three case studies.

Composing New Abstractions From Object Fragments

As object-oriented languages are extended with novel modularization mechanisms, better underlying models are required to implement these high-level features. This paper describes CELL, a language model that builds on delegation-based chains of object fragments. Composition of groups of cells is used: 1) to represent objects, 2) to realize various forms of method lookup, and 3) to keep track of method references. A running prototype of CELL is provided and used to realize the basic kernel of a Smalltalk system. The paper shows, using several examples, how higher-level features such as traits can be supported by the lower-level model.

Senseo: Enriching Eclipse's Static Source Views with Dynamic Metrics

Maintaining object-oriented systems that use inheritance and polymorphism is difficult, since runtime information, such as which methods are actually invoked at a call site, is not visible in the static source code. We have implemented Senseo, an Eclipse plugin enhancing Eclipse's static source views with various dynamic metrics, such as runtime types, the number of objects created, or the amount of memory allocated in particular methods.

The Moldable Inspector: a framework for domain-specific object inspection

Answering run-time questions in object-oriented systems involves reasoning about and exploring connections between multiple objects. Developer questions exercise various aspects of an object and require multiple kinds of interactions depending on the relationships between objects, the application domain and the differing developer needs. Nevertheless, traditional object inspectors, the essential tools often used to reason about objects, favor a generic view that focuses on the low-level details of the state of individual objects. This leads to an inefficient effort, increasing the time spent in the inspector. To improve the inspection process, we propose the Moldable Inspector, a novel approach for an extensible object inspector. The Moldable Inspector allows developers to look at objects using multiple interchangeable presentations and supports a workflow in which multiple levels of connecting objects can be seen together. Both these aspects can be tailored to the domain of the objects and the question at hand. We further exemplify how the proposed solution improves the inspection process, introduce a prototype implementation and discuss new directions for extending the Moldable Inspector.

Towards cheap, accurate polymorphism detection

Polymorphism, along with inheritance, is one of the most important features in object-oriented languages, but it is also one of the biggest obstacles to source code comprehension. Depending on the run-time type of the receiver of a message, any one of a number of possible methods may be invoked. Several algorithms for creating accurate call-graphs using static analysis already exist, however, they consume significant time and memory resources. We propose an approach that will combine static and dynamic analysis and yield the best possible precision with a minimal trade-off between used resources and accuracy.

Computer Assisted Diagnosis and Treatment Planning of Femoroacetabular Impingement (FAI)

Femoroacetabular impingement (FAI) is a dynamic conflict of the hip defined by a pathological, early abutment of the proximal femur onto the acetabulum or pelvis. In the past two decades, FAI has received increasing focus in both research and clinical practice as a cause of hip pain and prearthrotic deformity. Anatomical abnormalities such as an aspherical femoral head (cam-type FAI), a focal or general overgrowth of the acetabulum (pincer-type FAI), a high riding greater or lesser trochanter (extra-articular FAI), or abnormal torsion of the femur have been identified as underlying pathomorphologies. Open and arthroscopic treatment options are available to correct the deformity and to allow impingement-free range of motion. In routine practice, diagnosis and treatment planning of FAI is based on clinical examination and conventional imaging modalities such as standard radiography, magnetic resonance arthrography (MRA), and computed tomography (CT). Modern software tools allow three-dimensional analysis of the hip joint by extracting pelvic landmarks from two-dimensional antero-posterior pelvic radiographs. An object-oriented cross-platform program (Hip2Norm) has been developed and validated to standardize pelvic rotation and tilt on conventional AP pelvis radiographs. It has been shown that Hip2Norm is an accurate, consistent, reliable and reproducible tool for the correction of selected hip parameters on conventional radiographs. In contrast to conventional imaging modalities, which provide only static visualization, novel computer assisted tools have been developed to allow the dynamic analysis of FAI pathomechanics. In this context, a validated, CT-based software package (HipMotion) has been introduced. HipMotion is based on polygonal three-dimensional models of the patient’s pelvis and femur. The software includes simulation methods for range of motion, collision detection and accurate mapping of impingement areas. A preoperative treatment plan can be created by performing a virtual resection of any mapped impingement zones both on the femoral head-neck junction, as well as the acetabular rim using the same three-dimensional models. The following book chapter provides a summarized description of current computer-assisted tools for the diagnosis and treatment planning of FAI highlighting the possibility for both static and dynamic evaluation, reliability and reproducibility, and its applicability to routine clinical use.

Identification of logically related heap regions

This paper introduces a novel technique for identifying logically related sections of the heap such as recursive data structures, objects that are part of the same multi-component structure, and related groups of objects stored in the same collection/array. When combined withthe lifetime properties of these structures, this information can be used to drive a range of program optimizations including pool allocation, object co-location, static deallocation, and region-based garbage collection. The technique outlined in this paper also improves the efficiency of the static analysis by providing a normal form for the abstract models (speeding the convergence of the static analysis). We focus on two techniques for grouping parts of the heap. The first is a technique for precisely identifying recursive data structures in object-oriented programs based on the types declared in the program. The second technique is a novel method for grouping objects that make up the same composite structure and that allows us to partition the objects stored in a collection/array into groups based on a similarity relation. We provide a parametric component in the similarity relation in order to support specific analysis applications (such as a numeric analysis which would need to partition the objects based on numeric properties of the fields). Using the Barnes-Hut benchmark from the JOlden suite we show how these grouping methods can be used to identify various types of logical structures allowing the application of many region-based program optimizations.

Advanced Topics in Resource Analysis: Certification, Incrementality, Concurrency and Array-Sensitivity

El Análisis de Consumo de Recursos o Análisis de Coste trata de aproximar el coste de ejecutar un programa como una función dependiente de sus datos de entrada. A pesar de que existen trabajos previos a esta tesis doctoral que desarrollan potentes marcos para el análisis de coste de programas orientados a objetos, algunos aspectos avanzados, como la eficiencia, la precisión y la fiabilidad de los resultados, todavía deben ser estudiados en profundidad. Esta tesis aborda estos aspectos desde cuatro perspectivas diferentes: (1) Las estructuras de datos compartidas en la memoria del programa son una pesadilla para el análisis estático de programas. Trabajos recientes proponen una serie de condiciones de localidad para poder mantener de forma consistente información sobre los atributos de los objetos almacenados en memoria compartida, reemplazando éstos por variables locales no almacenadas en la memoria compartida. En esta tesis presentamos dos extensiones a estos trabajos: la primera es considerar, no sólo los accesos a los atributos, sino también los accesos a los elementos almacenados en arrays; la segunda se centra en los casos en los que las condiciones de localidad no se cumplen de forma incondicional, para lo cual, proponemos una técnica para encontrar las precondiciones necesarias para garantizar la consistencia de la información acerca de los datos almacenados en memoria. (2) El objetivo del análisis incremental es, dado un programa, los resultados de su análisis y una serie de cambios sobre el programa, obtener los nuevos resultados del análisis de la forma más eficiente posible, evitando reanalizar aquellos fragmentos de código que no se hayan visto afectados por los cambios. Los analizadores actuales todavía leen y analizan el programa completo de forma no incremental. Esta tesis presenta un análisis de coste incremental, que, dado un cambio en el programa, reconstruye la información sobre el coste del programa de todos los métodos afectados por el cambio de forma incremental. Para esto, proponemos (i) un algoritmo multi-dominio y de punto fijo que puede ser utilizado en todos los análisis globales necesarios para inferir el coste, y (ii) una novedosa forma de almacenar las expresiones de coste que nos permite reconstruir de forma incremental únicamente las funciones de coste de aquellos componentes afectados por el cambio. (3) Las garantías de coste obtenidas de forma automática por herramientas de análisis estático no son consideradas totalmente fiables salvo que la implementación de la herramienta o los resultados obtenidos sean verificados formalmente. Llevar a cabo el análisis de estas herramientas es una tarea titánica, ya que se trata de herramientas de gran tamaño y complejidad. En esta tesis nos centramos en el desarrollo de un marco formal para la verificación de las garantías de coste obtenidas por los analizadores en lugar de analizar las herramientas. Hemos implementado esta idea mediante la herramienta COSTA, un analizador de coste para programas Java y KeY, una herramienta de verificación de programas Java. De esta forma, COSTA genera las garantías de coste, mientras que KeY prueba la validez formal de los resultados obtenidos, generando de esta forma garantías de coste verificadas. (4) Hoy en día la concurrencia y los programas distribuidos son clave en el desarrollo de software. Los objetos concurrentes son un modelo de concurrencia asentado para el desarrollo de sistemas concurrentes. En este modelo, los objetos son las unidades de concurrencia y se comunican entre ellos mediante llamadas asíncronas a sus métodos. La distribución de las tareas sugiere que el análisis de coste debe inferir el coste de los diferentes componentes distribuidos por separado. En esta tesis proponemos un análisis de coste sensible a objetos que, utilizando los resultados obtenidos mediante un análisis de apunta-a, mantiene el coste de los diferentes componentes de forma independiente. Abstract Resource Analysis (a.k.a. Cost Analysis) tries to approximate the cost of executing programs as functions on their input data sizes and without actually having to execute the programs. While a powerful resource analysis framework on object-oriented programs existed before this thesis, advanced aspects to improve the efficiency, the accuracy and the reliability of the results of the analysis still need to be further investigated. This thesis tackles this need from the following four different perspectives. (1) Shared mutable data structures are the bane of formal reasoning and static analysis. Analyses which keep track of heap-allocated data are referred to as heap-sensitive. Recent work proposes locality conditions for soundly tracking field accesses by means of ghost non-heap allocated variables. In this thesis we present two extensions to this approach: the first extension is to consider arrays accesses (in addition to object fields), while the second extension focuses on handling cases for which the locality conditions cannot be proven unconditionally by finding aliasing preconditions under which tracking such heap locations is feasible. (2) The aim of incremental analysis is, given a program, its analysis results and a series of changes to the program, to obtain the new analysis results as efficiently as possible and, ideally, without having to (re-)analyze fragments of code that are not affected by the changes. During software development, programs are permanently modified but most analyzers still read and analyze the entire program at once in a non-incremental way. This thesis presents an incremental resource usage analysis which, after a change in the program is made, is able to reconstruct the upper-bounds of all affected methods in an incremental way. To this purpose, we propose (i) a multi-domain incremental fixed-point algorithm which can be used by all global analyses required to infer the cost, and (ii) a novel form of cost summaries that allows us to incrementally reconstruct only those components of cost functions affected by the change. (3) Resource guarantees that are automatically inferred by static analysis tools are generally not considered completely trustworthy, unless the tool implementation or the results are formally verified. Performing full-blown verification of such tools is a daunting task, since they are large and complex. In this thesis we focus on the development of a formal framework for the verification of the resource guarantees obtained by the analyzers, instead of verifying the tools. We have implemented this idea using COSTA, a state-of-the-art cost analyzer for Java programs and KeY, a state-of-the-art verification tool for Java source code. COSTA is able to derive upper-bounds of Java programs while KeY proves the validity of these bounds and provides a certificate. The main contribution of our work is to show that the proposed tools cooperation can be used for automatically producing verified resource guarantees. (4) Distribution and concurrency are today mainstream. Concurrent objects form a well established model for distributed concurrent systems. In this model, objects are the concurrency units that communicate via asynchronous method calls. Distribution suggests that analysis must infer the cost of the diverse distributed components separately. In this thesis we propose a novel object-sensitive cost analysis which, by using the results gathered by a points-to analysis, can keep the cost of the diverse distributed components separate.

A survey of agent-oriented methodologies

This article introduces the current agent-oriented methodologies. It discusses what approaches have been followed (mainly extending existing object oriented and knowledge engineering methodologies), the suitability of these approaches for agent modelling, and some conclusions drawn from the survey.

UER technique: conceptualisation for agent oriented development

The problem of conceptualisation is the first step towards the identication of the functional requirements of a system. This article proposes two extensions of well-known object oriented techniques: UER (User-Environment-Responsibility) technique and enhanced CRC (Class-ResponsibilityCollaboration) cards. UER technique consists of (a) looking for the users of systems and describing the ways the system is used; (b) looking for the objects of the environment and describing the possible interactions; and (c) looking for the general requirements or goals of the system, the actions that it should carry out without explicit interaction. The enhanced CRC cards together with the internal use cases technique is used for dening collaborations between agents. These techniques can be easily integrated in UML (Unied Modelling Language) [2], dening the new notation symbols as stereotypes.

Estudio cinemático del cuerpo humano mediante Kinect

La cámara Kinect está desarrollada por Prime Sense en colaboración con Microsoft para la consola XBox, ofrece imágenes de profundidad gracias a un sensor infrarrojo. Este dispositivo también incluye una cámara RGB que ofrece imágenes a color además de una serie de micrófonos colocados de tal manera que son capaces de saber de qué ángulo proviene el sonido. En un principio Kinect se creó para el ocio doméstico pero su bajo precio (en comparación con otras cámaras de iguales características) y la aceptación por parte de desarrolladores han explotado sus posibilidades. El objetivo de este proyecto es, partiendo de estos datos, la obtención de variables cinemáticas tales como posición, velocidad y aceleración de determinados puntos de control del cuerpo de un individuo como pueden ser el cabeza, cuello, hombros, codos, muñecas, caderas, rodillas y tobillos a partir de los cuales poder extraer patrones de movimiento. Para ello se necesita un middleware mediante el entorno de libre distribución (GNU) multiplataforma. Como IDE se ha utilizado Processing, un entorno open source creado para proyectos de diseño. Además se ha utilizado el contenedor SimpleOpenNI, desarrollado por estudiantes e investigadores que trabajan con Kinect. Esto ofrece la posibilidad de prescindir del SDK de Microsoft, el cual es propietario y obliga a utilizar su sistema operativo, Windows. Usando estas herramientas se consigue una solución viable para varios sistemas operativos. Se han utilizado métodos y facilidades que ofrece el lenguaje orientado a objetos Java (Proccesing hereda de este), y se ha planteado una solución basada en un modelo cliente servidor que dota de escalabilidad al proyecto. El resultado del proyecto es útil en aplicaciones para poblaciones con riesgo de exclusión (como es el espectro autista), en telediagnóstico, y en general entornos donde se necesite estudiar hábitos y comportamientos a partir del movimiento humano. Con este proyecto se busca tener una continuidad mediante otras aplicaciones que analicen los datos ofrecidos. ABSTRACT. The Kinect camera is developed by PrimeSense in collaboration with Microsoft for the xBox console provides depth images thanks to an infrared sensor. This device also includes an RGB camera that provides color images in addition to a number of microphones placed such that they are able to know what angle the sound comes. Kinect initially created for domestic leisure but its low prices (compared to other cameras with the same characteristics) and acceptance by developers have exploited its possibilities. The objective of this project is based on this data to obtain kinematic variables such as position, velocity and acceleration of certain control points of the body of an individual from which to extract movement patterns. These points can be the head, neck, shoulders, elbows, wrists, hips, knees and ankles. This requires a middleware using freely distributed environment (GNU) platform. Processing has been used as a development environment, and open source environment created for design projects. Besides the container SimpleOpenNi has been used, it developed by students and researchers working with Kinect. This offers the possibility to dispense with the Microsoft SDK which owns and agrees to use its operating system, Windows. Using these tools will get a viable solution for multiple operating systems. We used methods and facilities of the Java object-oriented language (Processing inherits from this) and has proposed a solution based on a client-server model which provides scalability to the project. The result of the project is useful in applications to populations at risk of exclusion (such as autistic spectrum), in remote diagnostic, and in general environments that need study habits and behaviors from human motion. This project aims to have continuity using other applications to analyze the data provided.

The Role of Knowledge Modeling Techniques in Software Development: A General Approach Based on a Knowledge Management Tool

The aim of the paper is to discuss the use of knowledge models to formulate general applications. First, the paper presents the recent evolution of the software field where increasing attention is paid to conceptual modeling. Then, the current state of knowledge modeling techniques is described where increased reliability is available through the modern knowledge acquisition techniques and supporting tools. The KSM (Knowledge Structure Manager) tool is described next. First, the concept of knowledge area is introduced as a building block where methods to perform a collection of tasks are included together with the bodies of knowledge providing the basic methods to perform the basic tasks. Then, the CONCEL language to define vocabularies of domains and the LINK language for methods formulation are introduced. Finally, the object oriented implementation of a knowledge area is described and a general methodology for application design and maintenance supported by KSM is proposed. To illustrate the concepts and methods, an example of system for intelligent traffic management in a road network is described. This example is followed by a proposal of generalization for reuse of the resulting architecture. Finally, some concluding comments are proposed about the feasibility of using the knowledge modeling tools and methods for general application design.

The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research

The Zebrafish Information Network, ZFIN, is a WWW community resource of zebrafish genetic, genomic and developmental research information (http://zfin.org). ZFIN provides an anatomical atlas and dictionary, developmental staging criteria, research methods, pathology information and a link to the ZFIN relational database (http://zfin.org/ZFIN/). The database, built on a relational, object-oriented model, provides integrated information about mutants, genes, genetic markers, mapping panels, publications and contact information for the zebrafish research community. The database is populated with curated published data, user submitted data and large dataset uploads. A broad range of data types including text, images, graphical representations and genetic maps supports the data. ZFIN incorporates links to other genomic resources that provide sequence and ortholog data. Zebrafish nomenclature guidelines and an automated registration mechanism for new names are provided. Extensive usability testing has resulted in an easy to learn and use forms interface with complex searching capabilities.

Modelado de estrategias de personalización en OO-H

The consideration of personalization politics in the context of any web application modelling method obliges to the revision of its different modelling activities, which must be adapted to take into account the information regarding the user (usually gathered in a user model) to define aspects such as navigation or presentation. Additionally, they must provide a set of techniques to populate such user model. Finally, and because of the rapid pace at which personalization politics usually change, the modelling process should provide support not only for static personalization rules (known at design time) but also for the definition or change of these rules once the application has been deployed. This article presents, in the context of the Object Oriented Hypermedia Method (OO-H), a personalization framework that fulfils these requirements, and is organized around four main concepts: (1) a set of design activities that capture the personalization requirements known at design time, (2) a mechanism for the specification of personalization rules, defined by means of an XML template, that decouples the definition of the personalization model from the remaining models, (3) an execution architecture that supports the change at execution time of these rules and (4) an extensible repository that includes a set of register mechanisms for the user activity in the system. The possibility of extension of this repository facilitates its adaptation to the particular characteristics of any particular application.