Roberto Cavicchioli

Efficient deconvolution methods for astronomical imaging: algorithms and IDL-GPU codes

Context. The Richardson-Lucy method is the most popular deconvolution method in astronomy because it preserves the number of counts and the non-negativity of the original object. Regularization is, in general, obtained by an early stopping of Richardson-Lucy iterations. In the case of point-wise objects such as binaries or open star clusters, iterations can be pushed to convergence. However, it is well-known that Richardson-Lucy is an inefficient method. In most cases and, in particular, for low noise levels, acceptable solutions are obtained at the cost of hundreds or thousands of iterations, thus several approaches to accelerating Richardson-Lucy have been proposed. They are mainly based on Richardson-Lucy being a scaled gradient method for the minimization of the Kullback-Leibler divergence, or Csiszar I-divergence, which represents the data-fidelity function in the case of Poisson noise. In this framework, a line search along the descent direction is considered for reducing the number of iterations. Aims. A general optimization method, referred to as the scaled gradient projection method, has been proposed for the constrained minimization of continuously differentiable convex functions. It is applicable to the non-negative minimization of the Kullback-Leibler divergence. If the scaling suggested by Richardson-Lucy is used in this method, then it provides a considerable increase in the efficiency of Richardson-Lucy. Therefore the aim of this paper is to apply the scaled gradient projection method to a number of imaging problems in astronomy such as single image deconvolution, multiple image deconvolution, and boundary effect correction. Methods. Deconvolution methods are proposed by applying the scaled gradient projection method to the minimization of the Kullback-Leibler divergence for the imaging problems mentioned above and the corresponding algorithms are derived and implemented in interactive data language. For all the algorithms, several stopping rules are introduced, including one based on a recently proposed discrepancy principle for Poisson data. To attempt to achieve a further increase in efficiency, we also consider an implementation on graphic processing units. Results. The proposed algorithms are tested on simulated images. The acceleration of scaled gradient projection methods achieved with respect to the corresponding Richardson-Lucy methods strongly depends on both the problem and the specific object to be reconstructed, and in our simulations the improvement achieved ranges from about a factor of 4 to more than 30. Moreover, significant accelerations of up to two orders of magnitude have been observed between the serial and parallel implementations of the algorithms. The codes are available upon request.

Towards real-time image deconvolution: application to confocal and STED microscopy

Although deconvolution can improve the quality of any type of microscope, the high computational time required has so far limited its massive spreading. Here we demonstrate the ability of the scaled-gradient-projection (SGP) method to provide accelerated versions of the most used algorithms in microscopy. To achieve further increases in efficiency, we also consider implementations on graphic processing units (GPUs). We test the proposed algorithms both on synthetic and real data of confocal and STED microscopy. Combining the SGP method with the GPU implementation we achieve a speed-up factor from about a factor 25 to 690 (with respect the conventional algorithm). The excellent results obtained on STED microscopy images demonstrate the synergy between super-resolution techniques and image-deconvolution. Further, the real-time processing allows conserving one of the most important property of STED microscopy, i.e the ability to provide fast sub-diffraction resolution recordings.

ML estimation of wavelet regularization hyperparameters in inverse problems

In this paper we are interested in regularizing hyperparameter estimation by maximum likelihood in inverse problems with wavelet regularization. One parameter per subband will be estimated by gradient ascent algorithm. We have to face with two main difficulties: i) sampling the a posteriori image distribution to compute the gradient; ii) choosing a suited step-size to ensure good convergence properties. We first show that introducing an auxiliary variable makes the sampling feasible using classical Metropolis-Hastings algorithm and Gibbs sampler. Secondly, we propose an adaptive step-size selection and a line-search strategy to improve the gradient-based method. Good performances of the proposed approach are demonstrated on both synthetic and real data.

An efficient algorithm for planted structured motif extraction

In this paper we present an algorithm for the problem of planted structured motif extraction from a set of sequences. This problem is strictly related to the structured motif extraction problem, which has many important applications in molecular biology. We propose an algorithm that uses a simple two-stage approach: first it extracts simple motifs, then the simple motifs are combined in order to extract structured motifs. We compare our algorithm with existing algorithms whose code is available, and which are based on more complex approaches. Our experiments show that, even if in general the problem is NP-hard, our algorithm is able to handle complex instances of the problem in a reasonable amount of time.

A Survey on Shared I/O Management in Virtualized Environments under Real Time Constraints

In the embedded systems domain, hypervisors are increasingly being adopted to guarantee timing isolation and appropriate hardware resource sharing among different software components. However, managing concurrent and parallel requests to shared hardware resources in a predictable way still represents an open issue. We argue that hypervisors can be an effective means to achieve an efficient and predictable arbitration of competing requests to shared devices in order to satisfy real-time requirements. As a representative example, we consider the case for mass storage (I/O) devices like Hard Disk Drives (HDD) and Solid State Disks (SSD), whose access times are orders of magnitude higher than those of central memory and CPU caches, therefore having a greater impact on overall task delays. We provide a comprehensive and up-to-date survey of the literature on I/O management within virtualized environments, focusing on software solutions proposed in the open source community, and discussing their main limitations in terms of realtime performance. Then, we discuss how the research in this subject may evolve in the future, highlighting the importance of techniques that are focused on scheduling not uniquely the processing bandwidth, but also the access to other important shared resources, like I/O devices.

SiGAMMA: server based integrated GPU arbitration mechanism for memory accesses

In embedded systems, CPUs and GPUs typically share main memory. The resulting memory contention may significantly inflate the duration of CPU tasks in a hard-to-predict way. Despite initial solutions have been devised to control this undesired inflation, these approaches do not consider the interference due to memory-intensive components in COTS embedded systems like integrated Graphical Processing Units. Dealing with this kind of interference might require custom-made hardware components that are not integrated in off-the-shelf platforms. We address these important issues by proposing a memory-arbitration mechanism, SiGAMMA (SiΓ), for eliminating the interference on CPU tasks caused by conflicting memory requests from the GPU. Tasks on the CPU are assumed to comply with a prefetch-based execution model (PREM) proposed in the real-time literature, while memory accesses from the GPU are arbitrated through a predictable mechanism that avoids contention. Our experiments show that SiΓ proves to be very effective in guaranteeing almost null inflation to memory phases of CPU tasks, while at the same time avoiding excessive starvation of GPU tasks.

A software stack for next-generation automotive systems on many-core heterogeneous platforms☆

The advent of commercial-of-the-shelf (COTS) heterogeneous many-core platforms is opening up a series of opportunities in the embedded computing market. Integrating multiple computing elements running at lower frequencies allows obtaining impressive performance capabilities at a reduced power consumption. These platforms can be successfully adopted to build the next-generation of self-driving vehicles, where Advanced Driver Assistance Systems (ADAS) need to process unprecedently higher computing workloads at low power budgets. Unfortunately, the current methodologies for providing real-time guarantees are uneffective when applied to the complex architectures of modern many-cores. Having impressive average performances with no guaranteed bounds on the response times of the critical computing activities is of little if no use to these applications. Project HERCULES will provide the required technological infrastructure to obtain an order-of-magnitude improvement in the cost and power consumption of next generation automotive systems. This paper presents the integrated software framework of the project, which allows achieving predictable performance on top of cutting-edge heterogeneous COTS platforms. The proposed software stack will let both real-time and non real-time application coexist on next-generation, power-efficient embedded platform, with preserved timing guarantees.