Integrated Software Framework Research Articles

New digital low-level RF controls based on the Red Pitaya STEMlab for the TLS Linac system

The Linac system at Taiwan Light Source (TLS) has been in operation for almost a quarter of a century and requires upgrades to improve its reliability. To achieve this, some components of the control system have been replaced with new digital low-level RF control units that use emerging technologies. A new unit is based on the open-source hardware platform which is named “Red Pitaya STEMlab” and offers a compact size and low power consumption. The unit features DAC (Digital-to-Analog Converter) blocks for downloading arbitrary waveforms with external trigger play and ADC (Analog-to-Digital Converter) blocks for waveform acquisition, enabling the development of real-time diagnostic toolkits. The new low-level RF control interface has been fully integrated into the existing EPICS software framework for system integration. The new digital low-level RF control system supports I/Q (in-phase/quadra-ture-phase) data with online amplitude and phase set-tings, and a waveform digitizer for inspecting low-level RF signals from the klystron modulator. Specific graphical applications have been designed and integrated into the existing operation interfaces. The system has been successfully achieved during routine operations. This paper describes the details of these efforts.

HIPPYlib-MUQ: A Bayesian Inference Software Framework for Integration of Data with Complex Predictive Models under Uncertainty

Bayesian inference provides a systematic framework for integration of data with mathematical models to quantify the uncertainty in the solution of the inverse problem. However, the solution of Bayesian inverse problems governed by complex forward models described bypartial differential equations (PDEs)remains prohibitive with black-boxMarkov chain Monte Carlo (MCMC)methods. We present hIPPYlib-MUQ, an extensible and scalable software framework that contains implementations of state-of-the art algorithms aimed to overcome the challenges of high-dimensional, PDE-constrained Bayesian inverse problems. These algorithms accelerate MCMC sampling by exploiting the geometry and intrinsic low-dimensionality of parameter space via derivative information and low rank approximation. The software integrates two complementary open-source software packages, hIPPYlib and MUQ. hIPPYlib solves PDE-constrained inverse problems using automatically-generated adjoint-based derivatives, but it lacks full Bayesian capabilities. MUQ provides a spectrum of powerful Bayesian inversion models and algorithms, but expects forward models to come equipped with gradients and Hessians to permit large-scale solution. By combining these two complementary libraries, we created a robust, scalable, and efficient software framework that realizes the benefits of each and allows us to tackle complex large-scale Bayesian inverse problems across a broad spectrum of scientific and engineering disciplines. To illustrate the capabilities of hIPPYlib-MUQ, we present a comparison of a number of MCMC methods available in the integrated software on several high-dimensional Bayesian inverse problems. These include problems characterized by both linear and nonlinear PDEs, various noise models, and different parameter dimensions. The results demonstrate that large (∼ 50×) speedups over conventional black box and gradient-based MCMC algorithms can be obtained by exploiting Hessian information (from the log-posterior), underscoring the power of the integrated hIPPYlib-MUQ framework.

Lorenzetti Showers - A general-purpose framework for supporting signal reconstruction and triggering with calorimeters

Calorimeters play an important role in high-energy physics experiments. Their design includes electronic instrumentation, signal processing chain, computing infrastructure, and also a good understanding of their response to particle showers produced by the interaction of incoming particles. This is usually supported by full simulation frameworks developed for specific experiments so that their access is restricted to the collaboration members only. Such restrictions limit the general-purpose developments that aim to propose innovative approaches to signal processing, which may include machine learning and advanced stochastic signal processing models. This work presents the Lorenzetti Showers, a general-purpose framework that mainly targets supporting novel signal reconstruction and triggering strategies using segmented calorimeter information. This framework fully incorporates developments down to the signal processing chain level (signal shaping, energy estimation, and noise mitigation techniques) to allow advanced signal processing approaches in modern calorimetry and triggering systems. The developed framework is flexible enough to be extended in different directions. For instance, it can become a tool for the phenomenology community to go beyond the usual detector design and physics process generation approaches. Program summaryProgram Title: Lorenzetti ShowersCPC Library link to program files:https://doi.org/10.17632/sy64367452.1Developer's repository link:https://github.com/lorenzetti-hep/lorenzettiLicensing provisions: GPLv3Programming language: Python, C++.Nature of problem: In experimental high-energy physics, simulation is essential for experiment preparation, design and interpretations of ongoing acquisitions. Especially for calorimeters, an accurate simulation that can describe detector geometry, behavior to different physics processes and signal generation close to the readout electronics and data acquisition levels is required to properly develop signal processing and computational methods. Such detectors may face very challenging demands arising from the new designs, such as pileup mitigation and noise reduction tasks under unprecedented levels. In this sense, simulation requirements continuously increase in complexity and performance, because new physics searches require large datasets and accurate modeling to experimental effects.Solution method: The Lorenzetti Showers is an integrated software framework that provides complete calorimeter information close enough to the electronic readout chain. Thus, the proposed framework allows users to access cell readout values, configurable sensor pulse-shapes, crosstalk modeling, and different energy estimation methods. It aims at supporting designs that target low or high pileup operation conditions in an easy-to-use modular structure. The developed framework is based on Pythia 8 (particle generation) and Geant4 (interactions with the calorimeter technique under analysis). An efficient data recording structure was used to allow full access to the Lorenzetti Showers outputs. In summary, the Lorenzetti Showers tool provides to the scientific community a user-friendly, flexible, user-oriented, and low-level calorimeter simulation framework.Additional comments including restrictions and unusual features: The framework current version provides the implementation of a generic segmented calorimeter (electromagnetic and hadronic sections), which may be modified by the user, if desired. It allows the generation of particles interactions using Pythia 8 (native) or any generator compatible with the HepMC format (which may be integrated using an external input file) and propagation through a user-configurable calorimeter using Geant4.

3D ion gyro-orbit heat load predictions for NSTX-U

High power tokamaks operate with divertor heat loads capable of destroying the plasma facing components (PFCs). High fidelity heat load predictions are necessary to ascertain the PFC state for design and during operation. Typical heat flux calculations are 2D, time invariant, and assume that power flows directly along the magnetic field lines (the optical approximation). These assumptions neglect the complex 3D geometries employed to protect the PFCs, the time varying nature of the plasma and PFC thermal state, and the helical trajectories of ions with finite Larmor radii (the gyro-orbit approximation). An integrated software framework, the heat flux engineering analysis toolkit (HEAT), was developed to generate time varying optical heat loads applied to real engineering computer aided design (CAD) (Looby et al 2022 Fusion Sci. Technol. 78 10–27). Recently, an ion-gyro orbit module has been added to HEAT. This module calculates the helical trajectories of ions as they gyrate about the magnetic field lines using kinetic theory macro-particles to accelerate the calculation. First, the new gyro-orbit module will be presented. Next, a comparison to existing research is performed. Finally, an analysis of the gyro-orbit heat loads for NSTX-U is presented for diverted discharges using the engineering CAD models utilized for PFC fabrication. Including these gyro-orbit effects can enhance the PFC performance by ‘smearing’ out the magnetic shadows associated with the castellated fish-scaled geometry. Simultaneously, the helical trajectories can degrade performance when they load narrow regions on edges and corners with high heat fluxes. Analysis of the trade-offs between these competing effects is included, and regions for further investigation are identified.

Design and Implementation of a SoC Embedded Waveform Acquisition System for Surveillance and Diagnostics of Pulsed Magnet Power Supplies

Pulsed magnet power supply systems used for electron beam injection and extraction have been developed for the Taiwan Photon Source (TPS) and the Taiwan Light Source (TLS). Control systems for these supplies have been implemented with well-functioning operations interfaces. To accomplish higher reliable operation, advanced real-time diagnostic toolkits for pulsed magnet power supplies had to be developed. A SoC (System-on-Chip) embedded waveform acquisition system has been designed, implemented and applied to inspect pulsed magnet power supplies during routine operation. This waveform acquisition system not only operates at the 125 MS/s sample rate, 50 MHz bandwidth and 14 bits resolution, but supports also the EPICS software framework for complete system integration. The acquired current waveforms can be immediately extracted specific characteristics to examine the status of pulsed magnet power supplies. In this paper, we summarize the design, implementation and real-time data analysis of the SoC embedded waveform acquisition system for the pulsed magnet power supplies.

Design and testing of a monolithic compliant constant force mechanism

This paper reports the design of a monolithic long-stroke constant force compliant mechanism (CM). The device is suitable for applications requiring a predefined force magnitude at the contact interface, such as manipulation systems. Starting from a compliant slider-crank mechanism providing a constant force within a rather limited deflection range, the paper describes the shape optimization carried out with the aim of extending the CM available stroke. In the first design step, the pseudo-rigid body (PRB) method is used to synthesize a sub-optimal lumped compliance solution. Secondly, two improved beam-based alternatives are evaluated by means of an integrated software framework, comprising Matlab and ANSYS. These new embodiments make use of a variable thickness beam, whose shape and dimensions have been optimized so as to provide a constant reaction force in an extended range. In particular, straight and spline segments are respectively used for the first and second prototype. With reference to the lumped compliance configuration, the available stroke has been increased of amounts equalling to 467% in the straight segments version (namely, from 3 mm to 14 mm) and to 833% in the spline segments version (namely, from 3 mm to 25 mm). All the predicted behaviors have been validated via physical experiments on 3D printed specimens. The proposed multi-step design flow may also be applied to a large variety of CMs, starting from their PRB model.

A Unified Pipeline for ECG Imaging Testing.

The Consortium for ECG Imaging (CEI) has formed several collaborative projects to evaluate and improve technical aspects of Electrocardiographic Imaging (ECGI), but these efforts are not yet implemented into an integrated software framework. We developed a framework to unify the multiple techniques and stages of ECGI into one pipeline. This framework merges existing open source packages: SCIRun, a problem solving environment; the Forward/Inverse toolkit, a series of SCIRun modules for ECGI; and PFEIFER, a cardiac signal pre-processing tool. The Unified ECGI Toolkit (UETK), combined with the EDGAR dataset, allows users to test and validate a vast array of parameters within each stage of the ECGI pipeline. We expect that this unified tool will help introduce new researchers to ECGI, facilitate interaction between the various groups working on ECGI, and establish a common approach for researchers to test and validate their ECGI techniques.

Complete coverage path planning for aerial vehicle flocks deployed in outdoor environments

This paper presents a system for Complete Coverage Path Planning to survey an outdoor area with a flock of Unmanned Aerial Vehicles (UAVs). The proposed system is able to manage the presence of no-fly zones, by decomposing the area into smaller subregions via a Morse-based decomposition approach. Furthermore, negotiation for UAV-subregion assignment is managed, taking into account environment geometry and both starting and desired final positions for the UAVs, once the coverage mission is completed. The back-and-forth motion is chosen as coverage pattern inside each subregion. All these features have been implemented with an integrated software framework, capable of working with georeferenced maps and data structures, thus obtaining a software tool compatible with commonly used geographic information systems.

Software Framework for the Creation and Application of Personalized Bone and Plate Implant Geometrical Models.

Computer-Assisted Orthopaedic Surgery (CAOS) defines a set of techniques that use computers and other devices for planning, guiding, and performing surgical interventions. The important components of CAOS are accurate geometrical models of human bones and plate implants, which can be used in preoperational planning or for surgical guiding during an intervention. Software framework which is introduced in this study is based on the Model-View-Controller (MVC) architectural pattern, and it uses 3D models of bones and plate implants developed by the application of the Method of Anatomical Features (MAF). The presented framework may be used for preoperative planning processes and for the production of personalized plate implants. The main idea of the research was to develop a novel integrated software framework which will provide improved personalized healthcare to the patient, and at the same time, provide the surgeon with more control over the patient's treatment and recovery.

Precise photorealistic visualization for restoration of historic buildings based on tacheometry data

This paper puts forward a 3D reconstruction methodology applied to the restoration of historic buildings taking advantage of the speed, range and accuracy of a total geodetic station. The measurements representing geo-referenced points produced an interactive and photorealistic geometric mesh of a monument named ‘Neoria.’ ‘Neoria’ is a Venetian building located by the old harbor at Chania, Crete, Greece. The integration of tacheometry acquisition and computer graphics puts forward a novel integrated software framework for the accurate 3D reconstruction of a historical building. The main technical challenge of this work was the production of a precise 3D mesh based on a sufficient number of tacheometry measurements acquired fast and at low cost, employing a combination of surface reconstruction and processing methods. A fully interactive application based on game engine technologies was developed. The user can visualize and walk through the monument and the area around it as well as photorealistically view it at different times of day and night. Advanced interactive functionalities are offered to the user in relation to identifying restoration areas and visualizing the outcome of such works. The user could visualize the coordinates of the points measured, calculate distances and navigate through the complete 3D mesh of the monument. The geographical data are stored in a database connected with the application. Features referencing and associating the database with the monument are developed. The goal was to utilize a small number of acquired data points and present a fully interactive visualization of a geo-referenced 3D model.

Intelligent Autonomous Vehicles in digital supply chains: A framework for integrating innovations towards sustainable value networks

Abstract The principal objective of this research is to provide a framework that captures the main software architecture elements for developing highly customised simulation tools that support the effective integration of Intelligent Autonomous Vehicles (IAVs) in sustainable supply networks, as an emerging field in the operations management agenda. To that end, the study's contribution is fourfold including: (i) a review of software simulation tools and platforms used in assessing the performance of IAVs interlinked with sustainability ramifications in supply chain (SC) ecosystems, (ii) an integrated software framework for monitoring and assessing the sustainability performance of SCs defined by the utilisation of innovative IAVs in operations, (iii) a translation of the proposed SC framework into a corresponding software application through a robust five-stage stepwise process, and (iv) a demonstration of the developed software tool through its application on the case of an IAV system operating in a customisable warehouse model. Our analysis highlights the flexibility resulting from a decentralised software management architecture, thus enabling the dynamic reconfiguration of a SC network. In addition, the developed pilot simulation tool can assist operations managers in capturing the operational needs of facilities and assessing the performance of IAV systems while considering sustainability parameters.

"Wink to grasp" - comparing eye, voice & EMG gesture control of grasp with soft-robotic gloves.

The ability of robotic rehabilitation devices to support paralysed end-users is ultimately limited by the degree to which human-machine-interaction is designed to be effective and efficient in translating user intention into robotic action. Specifically, we evaluate the novel possibility of binocular eye-tracking technology to detect voluntary winks from involuntary blink commands, to establish winks as a novel low-latency control signal to trigger robotic action. By wearing binocular eye-tracking glasses we enable users to directly observe their environment or the actuator and trigger movement actions, without having to interact with a visual display unit or user interface. We compare our novel approach to two conventional approaches for controlling robotic devices based on electromyo-graphy (EMG) and speech-based human-computer interaction technology. We present an integrated software framework based on ROS that allows transparent integration of these multiple modalities with a robotic system. We use a soft-robotic SEM glove (Bioservo Technologies AB, Sweden) to evaluate how the 3 modalities support the performance and subjective experience of the end-user when movement assisted. All 3 modalities are evaluated in streaming, closed-loop control operation for grasping physical objects. We find that wink control shows the lowest error rate mean with lowest standard deviation of (0.23 ± 0.07, mean ± SEM) followed by speech control (0.35 ± 0. 13) and EMG gesture control (using the Myo armband by Thalamic Labs), with the highest mean and standard deviation (0.46 ± 0.16). We conclude that with our novel own developed eye-tracking based approach to control assistive technologies is a well suited alternative to conventional approaches, especially when combined with 3D eye-tracking based robotic end-point control.

An Integrated Software Framework to Support Semantic Modeling and Reasoning of Spatiotemporal Change of Geographical Objects: A Use Case of Land Use and Land Cover Change Study

Evolving Earth observation and change detection techniques enable the automatic identification of Land Use and Land Cover Change (LULCC) over a large extent from massive amounts of remote sensing data. It at the same time poses a major challenge in effective organization, representation and modeling of such information. This study proposes and implements an integrated computational framework to support the modeling, semantic and spatial reasoning of change information with regard to space, time and topology. We first proposed a conceptual model to formally represent the spatiotemporal variation of change data, which is essential knowledge to support various environmental and social studies, such as deforestation and urbanization studies. Then, a spatial ontology was created to encode these semantic spatiotemporal data in a machine-understandable format. Based on the knowledge defined in the ontology and related reasoning rules, a semantic platform was developed to support the semantic query and change trajectory reasoning of areas with LULCC. This semantic platform is innovative, as it integrates semantic and spatial reasoning into a coherent computational and operational software framework to support automated semantic analysis of time series data that can go beyond LULC datasets. In addition, this system scales well as the amount of data increases, validated by a number of experimental results. This work contributes significantly to both the geospatial Semantic Web and GIScience communities in terms of the establishment of the (web-based) semantic platform for collaborative question answering and decision-making.

A scalable software framework for data integration in bioprocess development.

Effectiveness in lab workflows-despite progresses made in automation and lab informatics-is often hindered by insufficient integration of devices and data. The iLAB software framework, a middleware connecting and integrating devices and data, provides a plugin architecture that can be adapted to individual lab environments. Integration of devices is preferably based on standardized data and communication protocols. In addition to device integration, process data and result data from different sources (e.g. readers) are converted to a standard format and administered by a powerful database for further processing. In this paper, the use of iLAB in a bioprocess development application is described. Process parameters and measured values of two high-throughput bioreactor systems (96-well plates and 10 mL reactor vessels) are collected in the iLAB database. Data from screening experiments and offline data are visualized, analyzed, and compared. A filter algorithm allows searching for matching parameters in experiments as well as the comparison of correlated datasets, independently from the used bioreactor system. The database model enables the consolidation of data, the transition from data to information, and a solid base for management decisions on enterprise level.

Deploying Islandora as a Digital Repository Platform: a Multifaceted Experience at the University of Denver Libraries

The purpose of a highly integrated software framework such as Islandora is to satisfy as many workflows as possible in a single ecosystem for a digital repository. The Library Technology Department at the University of Denver was tasked with implementing an Islandora open-source framework for its Special Collections Department because the current host was being retired. Although Islandora's front-end is tailored for librarians, its back-end is complex, and built upon many subsystems. A failure in any of the subsystems guarantees a domino effect and a chain reaction which can obfuscate the root cause of the issue. Though product documentation and support communication channels exist, many of the problems we faced were unique to our specific hardware and software configuration. The development team had to learn fast, and be innovative, agile, and systematic in order to work with such a complicated system. This article describes the tactics used in this repository development effort, as well as the library's stakeholder relationship management. We believe our experience will be illustrative for administrators, librarians and developers, and help them better understand the many facets of an in-house, open-source digital repository development project.

An autonomous observation and control system based on EPICS and RTS2 for Antarctic telescopes

For an unattended telescopes in Antarctic, the remote operation, autonomous observation and control are essential. An EPICS (Experimental Physics and Industrial Control System) and RTS2(Remote Telescope System, 2nd Version) based autonomous observation and control system with remoted operation is introduced in this paper. EPICS is a set of Open Source software tools, libraries and applications developed collaboratively and used worldwide to create distributed soft real-time control systems for scientific instruments while RTS2 is an open source environment for control of a fully autonomous observatory. Using the advantage of EPICS and RTS2 respectively, a combined integrated software framework for autonomous observation and control is established that use RTS2 to fulfill the function of astronomical observation and use EPICS to fulfill the device control of telescope. A command and status interface for EPICS and RTS2 is designed to make the EPICS IOC (Input/Output Controller) components integrate to RTS2 directly. For the specification and requirement of control system of telescope in Antarctic, core components named Executor and Auto-focus for autonomous observation is designed and implemented with remote operation user interface based on Browser-Server mode. The whole system including the telescope is tested in Lijiang Observatory in Yunnan Province for practical observation to complete the autonomous observation and control, including telescope control, camera control, dome control, weather information acquisition with the local and remote operation.

Visual workflows for 13 C-metabolic flux analysis

The precise quantification of intracellular metabolic flow rates is of fundamental importance in bio(techno)logy and medical research. The gold standard in the field is metabolic flux analysis (MFA) with 13C-labeling experiments. 13C-MFA workflows orchestrate several, mainly human-in-the-loop, software applications, integrating them with plenty of heterogeneous information. In practice, this had posed a major practical barrier for evaluating, interpreting and understanding isotopic data from carbon labeling experiments. Graphical modeling, interactive model exploration and visual data analysis are the key to overcome this limitation. We have developed a first-of-its-kind graphical tool suite providing scientists with an integrated software framework for all aspects of 13C-MFA. Almost 30 modules (plug-ins) have been implemented for the Omix visualization software. Several advanced graphical workflows and ergonomic user interfaces support major domain-specific modeling and proofreading tasks. With that, the graphical suite is a productivity enhancing tool and an original educational training instrument supporting the adoption of 13C-MFA applications in all life science fields. The Omix Light Edition is freely available at http://www.omix-visualization.com k.noeh@fz-juelich.de, p.droste@omix-visualization.com Supplementary data are available at Bioinformatics online.

OpenStructure: an integrated software framework for computational structural biology.

Research projects in structural biology increasingly rely on combinations of heterogeneous sources of information, e.g. evolutionary information from multiple sequence alignments, experimental evidence in the form of density maps and proximity constraints from proteomics experiments. The OpenStructure software framework, which allows the seamless integration of information of different origin, has previously been introduced. The software consists of C++ libraries which are fully accessible from the Python programming language. Additionally, the framework provides a sophisticated graphics module that interactively displays molecular structures and density maps in three dimensions. In this work, the latest developments in the OpenStructure framework are outlined. The extensive capabilities of the framework will be illustrated using short code examples that show how information from molecular-structure coordinates can be combined with sequence data and/or density maps. The framework has been released under the LGPL version 3 license and is available for download from http://www.openstructure.org.

SU-FF-T-504: An Integrated Software Framework for Radiotherapy Research and Outcome Analysis for Stereotactic Body Radiotherapy

Purpose: To develop a software framework which allows analysis and evaluation of outcomes for patients treated with hypo‐fractionated stereotactic body radiotherapy(SBRT)Method and Materials: An outcomes‐study database was designed, under IRB‐approval, to collect and analyze medical information for lungcancer patients undergoing SBRT. The outcomes‐study database incorporates a variety of patient information, including demographic, social, diagnostic, treatment and follow‐up data. A software tool with a graphical user interface was developed to calculate biological dose indices, including TCP, EUD (Niemierko) and NTCP (Lyman‐Kutcher‐Burman and relative seriality models). Biologically effective doses are determined from dose distributions and DVHs, automatically imported from the treatment planning systems. Results: Approximately 200 SBRT patients' medical records have been populated into the outcomes database. To demonstrate the functionality of the software framework, 11 lungcancer patients treated with SBRT (12 Gy/fraction × 4 fractions) for central lesions (tumors within a 2 cm zone of the proximal bronchial tree) were reviewed. The linear‐quadratic (LQ) adjusted mean lungdose was 13.38 Gy (range: 9.24 Gy to 16.50 Gy) with an α/β ratio of 3.0 Gy. Observed lung toxicities were reviewed using the database and showed the regimen to be well tolerated: none of the patients developed grades 3–5 toxicities and only 2 lower‐grade toxicities were noted. The calculated NTCP ranged from 1.73% to 8.22% using the LKB model, with parameters n=1, m=0.33, TD50 =30.5 Gy. Conclusions: One of the goals of the outcomes database is to enable the investigation of correlation between dose, volume and effect for patients treated with SBRT, using non‐standard, hypo‐fractionated RT doses. Parameters specific to biological dose models are being updated using maximum likelihood analysis of calculated probabilities vs. observed outcomes for this large cohort of patients. Such outcomes studies are important in understanding the efficacy of new treatment paradigms.

Horses for courses [industrial bus

This paper examines the question of whether there is an ideal bus technology that can be applied to all test systems. While some companies may claim that a single technology is the ideal bus for all application needs, each bus has its strengths and is suited for different applications. With the variety of bus technologies available, engineers should consider key bus attributes such as latency, bandwidth, software support, distance support and availability when determining the appropriate bus for an application. Using a layered test architecture, with an integrated software framework, engineers can meet varying system needs by integrating buses to create a hybrid multiplatform system.