Roel Wuyts

Bio: Roel Wuyts is an academic researcher from Katholieke Universiteit Leuven. The author has contributed to research in topics: Software development & Smalltalk. The author has an hindex of 26, co-authored 119 publications receiving 2390 citations. Previous affiliations of Roel Wuyts include Vrije Universiteit Brussel & Université libre de Bruxelles.

Traits: A mechanism for fine-grained reuse

Abstract: Inheritance is well-known and accepted as a mechanism for reuse in object-oriented languages. Unfortunately, due to the coarse granularity of inheritance, it may be difficult to decompose an application into an optimal class hierarchy that maximizes software reuse. Existing schemes based on single inheritance, multiple inheritance, or mixins, all pose numerous problems for reuse. To overcome these problems we propose traits, pure units of reuse consisting only of methods. We develop a formal model of traits that establishes how traits can be composed, either to form other traits, or to form classes. We also outline an experimental validation in which we apply traits to refactor a nontrivial application into composable units.

Declarative reasoning about the structure of object-oriented systems

Abstract: The structure of object-oriented systems typically forms a complicated tangled web of interdependent classes. Understanding this implicit and hidden structure poses severe problems to developers and maintainers who want to use, extend or adapt those systems. This paper advocates the use of a logic meta-language to express and extract structural relationships in class-based object-oriented systems. As validation the logic meta-language SOUL was implemented and used to construct a declarative framework that allows reasoning about the structure of Smalltalk programs. The declarative framework's usefulness is illustrated by expressing different high-level structural relationships such as those described by design patterns.

Components for embedded software: the PECOS approach

Abstract: Software is more and more becoming the major cost factor for embedded devices. Already today, software accounts for more than 50 percent of the development costs of such a device. However, software development practices in this area lag far behind those in the traditional software industry. Reuse is hardly ever heard of in some areas, development from scratch is common practice and component-based software is usually a foreign word. PECOS is a collaborative project between industrial and research partners that seeks to enable component-based technology for a certain class of embedded systems known as "field devices" by taking into account the specific properties of this application area. In this paper we introduce a component model for field device software. Furthermore we report on the PECOS component composition language CoCo and the mapping from CoCo to Java and C++.

A Component Model for Field Devices

Abstract: Component-based software development is becoming mainstream for conventional applications However, components can be difficult to deploy in embedded systems because of non-functional requirements Pecos is a collaborative project between industrial and research partners that seeks to enable component-based technology for a class of embedded systems known as "field devices" In this paper we introduce a component model for field devices that captures a range of non-functional properties and constraints

Phd by thesis

Abstract: Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

An overview of AspectJ

Abstract: Aspect] is a simple and practical aspect-oriented extension to Java With just a few new constructs, AspectJ provides support for modular implementation of a range of crosscutting concerns. In AspectJ's dynamic join point model, join points are well-defined points in the execution of the program; pointcuts are collections of join points; advice are special method-like constructs that can be attached to pointcuts; and aspects are modular units of crosscutting implementation, comprising pointcuts, advice, and ordinary Java member declarations. AspectJ code is compiled into standard Java bytecode. Simple extensions to existing Java development environments make it possible to browse the crosscutting structure of aspects in the same kind of way as one browses the inheritance structure of classes. Several examples show that AspectJ is powerful, and that programs written using it are easy to understand.

Test Driven Development: By Example

Abstract: From the Book: “Clean code that works” is Ron Jeffries’ pithy phrase. The goal is clean code that works, and for a whole bunch of reasons: Clean code that works is a predictable way to develop. You know when you are finished, without having to worry about a long bug trail.Clean code that works gives you a chance to learn all the lessons that the code has to teach you. If you only ever slap together the first thing you think of, you never have time to think of a second, better, thing. Clean code that works improves the lives of users of our software.Clean code that works lets your teammates count on you, and you on them.Writing clean code that works feels good.But how do you get to clean code that works? Many forces drive you away from clean code, and even code that works. Without taking too much counsel of our fears, here’s what we do—drive development with automated tests, a style of development called “Test-Driven Development” (TDD for short). In Test-Driven Development, you: Write new code only if you first have a failing automated test.Eliminate duplication. Two simple rules, but they generate complex individual and group behavior. Some of the technical implications are:You must design organically, with running code providing feedback between decisionsYou must write your own tests, since you can’t wait twenty times a day for someone else to write a testYour development environment must provide rapid response to small changesYour designs must consist of many highly cohesive, loosely coupled components, just to make testing easy The two rules imply an order to the tasks ofprogramming: 1. Red—write a little test that doesn’t work, perhaps doesn’t even compile at first 2. Green—make the test work quickly, committing whatever sins necessary in the process 3. Refactor—eliminate all the duplication created in just getting the test to work Red/green/refactor. The TDD’s mantra. Assuming for the moment that such a style is possible, it might be possible to dramatically reduce the defect density of code and make the subject of work crystal clear to all involved. If so, writing only code demanded by failing tests also has social implications: If the defect density can be reduced enough, QA can shift from reactive to pro-active workIf the number of nasty surprises can be reduced enough, project managers can estimate accurately enough to involve real customers in daily developmentIf the topics of technical conversations can be made clear enough, programmers can work in minute-by-minute collaboration instead of daily or weekly collaborationAgain, if the defect density can be reduced enough, we can have shippable software with new functionality every day, leading to new business relationships with customers So, the concept is simple, but what’s my motivation? Why would a programmer take on the additional work of writing automated tests? Why would a programmer work in tiny little steps when their mind is capable of great soaring swoops of design? Courage. Courage Test-driven development is a way of managing fear during programming. I don’t mean fear in a bad way, pow widdle prwogwammew needs a pacifiew, but fear in the legitimate, this-is-a-hard-problem-and-I-can’t-see-the-end-from-the-beginning sense. If pain is nature’s way of saying “Stop!”, fear is nature’s way of saying “Be careful.” Being careful is good, but fear has a host of other effects: Makes you tentativeMakes you want to communicate lessMakes you shy from feedbackMakes you grumpy None of these effects are helpful when programming, especially when programming something hard. So, how can you face a difficult situation and: Instead of being tentative, begin learning concretely as quickly as possible.Instead of clamming up, communicate more clearly.Instead of avoiding feedback, search out helpful, concrete feedback.(You’ll have to work on grumpiness on your own.) Imagine programming as turning a crank to pull a bucket of water from a well. When the bucket is small, a free-spinning crank is fine. When the bucket is big and full of water, you’re going to get tired before the bucket is all the way up. You need a ratchet mechanism to enable you to rest between bouts of cranking. The heavier the bucket, the closer the teeth need to be on the ratchet. The tests in test-driven development are the teeth of the ratchet. Once you get one test working, you know it is working, now and forever. You are one step closer to having everything working than you were when the test was broken. Now get the next one working, and the next, and the next. By analogy, the tougher the programming problem, the less ground should be covered by each test. Readers of Extreme Programming Explained will notice a difference in tone between XP and TDD. TDD isn’t an absolute like Extreme Programming. XP says, “Here are things you must be able to do to be prepared to evolve further.” TDD is a little fuzzier. TDD is an awareness of the gap between decision and feedback during programming, and techniques to control that gap. “What if I do a paper design for a week, then test-drive the code? Is that TDD?” Sure, it’s TDD. You were aware of the gap between decision and feedback and you controlled the gap deliberately. That said, most people who learn TDD find their programming practice changed for good. “Test Infected” is the phrase Erich Gamma coined to describe this shift. You might find yourself writing more tests earlier, and working in smaller steps than you ever dreamed would be sensible. On the other hand, some programmers learn TDD and go back to their earlier practices, reserving TDD for special occasions when ordinary programming isn’t making progress. There are certainly programming tasks that can’t be driven solely by tests (or at least, not yet). Security software and concurrency, for example, are two topics where TDD is not sufficient to mechanically demonstrate that the goals of the software have been met. Security relies on essentially defect-free code, true, but also on human judgement about the methods used to secure the software. Subtle concurrency problems can’t be reliably duplicated by running the code. Once you are finished reading this book, you should be ready to: Start simplyWrite automated testsRefactor to add design decisions one at a time This book is organized into three sections. An example of writing typical model code using TDD. The example is one I got from Ward Cunningham years ago, and have used many times since, multi-currency arithmetic. In it you will learn to write tests before code and grow a design organically.An example of testing more complicated logic, including reflection and exceptions, by developing a framework for automated testing. This example also serves to introduce you to the xUnit architecture that is at the heart of many programmer-oriented testing tools. In the second example you will learn to work in even smaller steps than in the first example, including the kind of self-referential hooha beloved of computer scientists.Patterns for TDD. Included are patterns for the deciding what tests to write, how to write tests using xUnit, and a greatest hits selection of the design patterns and refactorings used in the examples. I wrote the examples imagining a pair programming session. If you like looking at the map before wandering around, you may want to go straight to the patterns in Section 3 and use the examples as illustrations. If you prefer just wandering around and then looking at the map to see where you’ve been, try reading the examples through and refering to the patterns when you want more detail about a technique, then using the patterns as a reference. Several reviewers have commented they got the most out of the examples when they started up a programming environment and entered the code and ran the tests as they read. A note about the examples. Both examples, multi-currency calculation and a testing framework, appear simple. There are (and I have seen) complicated, ugly, messy ways of solving the same problems. I could have chosen one of those complicated, ugly, messy solutions to give the book an air of “reality.” However, my goal, and I hope your goal, is to write clean code that works. Before teeing off on the examples as being too simple, spend 15 seconds imagining a programming world in which all code was this clear and direct, where there were no complicated solutions, only apparently complicated problems begging for careful thought. TDD is a practice that can help you lead yourself to exactly that careful thought.

Deep learning for cellular image analysis

Abstract: Recent advances in computer vision and machine learning underpin a collection of algorithms with an impressive ability to decipher the content of images. These deep learning algorithms are being applied to biological images and are transforming the analysis and interpretation of imaging data. These advances are positioned to render difficult analyses routine and to enable researchers to carry out new, previously impossible experiments. Here we review the intersection between deep learning and cellular image analysis and provide an overview of both the mathematical mechanics and the programming frameworks of deep learning that are pertinent to life scientists. We survey the field's progress in four key applications: image classification, image segmentation, object tracking, and augmented microscopy. Last, we relay our labs' experience with three key aspects of implementing deep learning in the laboratory: annotating training data, selecting and training a range of neural network architectures, and deploying solutions. We also highlight existing datasets and implementations for each surveyed application.