Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Automatic Data Processing”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 757 records · Page 42

SU-F-T-139: Meeting the Challenges of Quality Control in the TOPAS Monte Carlo Simulation Toolkit for Proton Therapy

Purpose: Monte Carlo particle transport simulation (MC) codes have become important tools in proton therapy and biology, both for research and practice. TOPAS is an MC toolkit serving users worldwide (213 licensed users at 95 institutions in 21 countries). It provides unprecedented ease in 4D placement of geometry components, beam sources and scoring through its user-friendly and reproducible parameter file interface. Quality control (QC) of stochastic simulation software is inherently difficult, and the versatility of TOPAS introduces additional challenges. But QC is vital as the TOPAS development team implements new features, addresses user feedback and reacts to upgrades of underlying software (i.e. Geant4). Methods: Whenever code is committed to our repository, over 50 separate module tests are automatically triggered via a continuous integration service. They check that the various module options execute successfully and that their results are statistically consistent with previous reference values. Prior to each software release, longer end-to-end tests automatically validate TOPAS against experimental data and a TOPAS benchmark. These include simulating multiple properties of spread-out Bragg peaks, validating nuclear models, and searching for differences in patient simulations. Results: Continuous integration has proven effective in catching regressions at the time they are introduced, particularly when implementing new features that involve refactoring code (e.g. multithreading and ntuple output). Code coverage statistics highlight untested portions of code and guide development of new tests. The various end-to-end tests demonstrate that TOPAS accurately describes the physics of proton therapy within clinical tolerances. Conclusion: The TOPAS QC strategy of frequent short tests and pre-release long tests has led to a more reliable tool. However, the versatility of TOPAS makes it difficult to predict how users might combine different modules, and so QC ultimately remains a partnership between the developer and the user. This work was funded by National Cancer Institute grant R01 CA 140735.

60 APPLIED LIFE SCIENCES↗

Deep learning-driven super-resolution in Raman hyperspectral imaging: Efficient high-resolution reconstruction from low-resolution data

Deep learning (DL) has become an indispensable tool in hyperspectral data analysis, automatically extracting valuable features from complex, high-dimensional datasets. Super-resolution reconstruction, an essential aspect of hyperspectral data, involves enhancing spatial resolution, particularly relevant to low-resolution hyperspectral data. Yet, the pursuit of super-resolution in hyperspectral analysis is fraught with challenges, including acquiring ground truth high-resolution data for training, generalization, and scalability. The pressing issue of extended spectral acquisition times, notably for high-resolution scans, is a significant roadblock in hyperspectral imaging. Super-resolution methods offer a promising solution by providing higher spatial resolution data to expedite data collection and yield more efficient outcomes. This paper delves into a practical application of these concepts using Raman imaging, where spectral acquisition times can be prohibitively long. In this context, DL-based super-resolution models demonstrate their efficacy by predicting and reconstructing high-resolution Raman data from low-resolution input, eliminating the need for resource-intensive high-resolution scans. While previous work often relied on substantial high-resolution datasets, this study showcases the ability to achieve similar outcomes even with limited data, presenting a more practical and cost-effective approach. In conclusion, the results offer a glimpse into the transformative potential of this technology to streamline hyperspectral imaging applications by saving valuable time and resources through the successful generation of high-resolution data from low-resolution inputs.

42 ENGINEERING↗

An adaptive regularization parameter choice strategy for multispectral bioluminescence tomography

Purpose: Bioluminescence tomography (BLT) provides an effective tool for monitoring physiological and pathological activities in vivo. However, the measured data in bioluminescence imaging are corrupted by noise. Therefore, regularization methods are commonly used to find a regularized solution. Nevertheless, for the quality of the reconstructed bioluminescent source obtained by regularization methods, the choice of the regularization parameters is crucial. To date, the selection of regularization parameters remains challenging. With regards to the above problems, the authors proposed a BLT reconstruction algorithm with an adaptive parameter choice rule. Methods: The proposed reconstruction algorithm uses a diffusion equation for modeling the bioluminescent photon transport. The diffusion equation is solved with a finite element method. Computed tomography (CT) images provide anatomical information regarding the geometry of the small animal and its internal organs. To reduce the ill-posedness of BLT, spectral information and the optimal permissible source region are employed. Then, the relationship between the unknown source distribution and multiview and multispectral boundary measurements is established based on the finite element method and the optimal permissible source region. Since the measured data are noisy, the BLT reconstruction is formulated as l{sub 2} data fidelity and a general regularization term. When choosing the regularization parameters for BLT, an efficient model function approach is proposed, which does not require knowledge of the noise level. This approach only requests the computation of the residual and regularized solution norm. With this knowledge, we construct the model function to approximate the objective function, and the regularization parameter is updated iteratively. Results: First, the micro-CT based mouse phantom was used for simulation verification. Simulation experiments were used to illustrate why multispectral data were used rather than monochromatic data. Furthermore, the study conducted using an adaptive regularization parameter demonstrated our ability to accurately localize the bioluminescent source. With the adaptively estimated regularization parameter, the reconstructed center position of the source was (20.37, 31.05, 12.95) mm, and the distance to the real source was 0.63 mm. The results of the dual-source experiments further showed that our algorithm could localize the bioluminescent sources accurately. The authors then presented experimental evidence that the proposed algorithm exhibited its calculated efficiency over the heuristic method. The effectiveness of the new algorithm was also confirmed by comparing it with the L-curve method. Furthermore, various initial speculations regarding the regularization parameter were used to illustrate the convergence of our algorithm. Finally, in vivo mouse experiment further illustrates the effectiveness of the proposed algorithm. Conclusions: Utilizing numerical, physical phantom and in vivo examples, we demonstrated that the bioluminescent sources could be reconstructed accurately with automatic regularization parameters. The proposed algorithm exhibited superior performance than both the heuristic regularization parameter choice method and L-curve method based on the computational speed and localization error.

61 RADIATION PROTECTION AND DOSIMETRY↗

Toward tsunami early warning system in Indonesia by using rapid rupture durations estimation

Indonesia has Indonesian Tsunami Early Warning System (Ina-TEWS) since 2008. The Ina-TEWS has used automatic processing on hypocenter; Mwp, Mw (mB) and Mj. If earthquake occurred in Ocean, depth < 70 km and magnitude > 7, then Ina-TEWS announce early warning that the earthquake can generate tsunami. However, the announcement of the Ina-TEWS is still not accuracy. Purposes of this research are to estimate earthquake rupture duration of large Indonesia earthquakes that occurred in Indian Ocean, Java, Timor sea, Banda sea, Arafura sea and Pasific ocean. We analyzed at least 330 vertical seismogram recorded by IRIS-DMC network using a direct procedure for rapid assessment of earthquake tsunami potential using simple measures on P-wave vertical seismograms on the velocity records, and the likelihood that the high-frequency, apparent rupture duration, T{sub dur}. T{sub dur} can be related to the critical parameters rupture length (L), depth (z), and shear modulus ({mu}) while T{sub dur} may be related to wide (W), slip (D), z or {mu}. Our analysis shows that the rupture duration has a stronger influence to generate tsunami than Mw and depth. The rupture duration gives more information on tsunami impact, Mo/{mu}, depth and size than Mw and other currently used discriminants. We show more information which known from the rupture durations. The longer rupture duration, the shallower source of the earthquake. For rupture duration greater than 50 s, the depth less than 50 km, Mw greater than 7, the longer rupture length, because T{sub dur} is proportional L and greater Mo/{mu}. Because Mo/{mu} is proportional L. So, with rupture duration information can be known information of the four parameters. We also suggest that tsunami potential is not directly related to the faulting type of source and for events that have rupture duration greater than 50 s, the earthquakes generated tsunami. With available real-time seismogram data, rapid calculation, rupture duration discriminant can be completed within 4-5 min after an earthquake occurs and thus can aid in effective, accuracy and reliable tsunami early warning for Indonesia region.

58 GEOSCIENCES↗

Autonomous Radiological Survey Systems for Locating Fired Depleted Uranium Munitions - 19212

An ensemble of autonomous radiological survey platforms that utilize a suite of scintillation detectors that can be used to conduct radiological site characterization, assist with remediation efforts, or conduct site clearance in accordance with the Multi-Agency Radiologic Survey and Site Investigation Manual are described. The overall systems are composed of inorganic scintillators, light detection and ranging, global positioning, inertial guidance, wireless telemetry, and signal processing systems. Two primary designs are discussed: a three-meter wide platform and multiple half-meter-wide systems. The survey systems are used to conduct radiological surveys over large areas autonomously, without human involvement. The three-meter system has been designed to cover large, open areas free of obstacles. Smaller robotic platforms are designed to handle a large range of terrain types and to conduct surveys in areas that are plagued with obstacles, such as bushes and trees. The primary design criteria for these systems were accurate locating of fired depleted uranium (DU) munitions. Several U.S. Army facilities have remnant DU material on active firing ranges where DU rounds have been used in performance evaluations. Many ranges also have unexploded ordinance (UXO) challenges which are problematic for conducting walkover surveys. The combination of having active DU impacted firing ranges with UXO make conducting site characterization surveys very difficult and hazardous. The autonomous surveying systems allow radiological scanning data collection to be scheduled around range activities and reduces human exposure to ionizing radiation and UXO. All of the robotic platforms act independently, and are controlled by a centralized computer system via a wireless telemetry system. The central computer system is responsible for setting up survey units, survey paths, and scheduling which platform is to complete the scheduled survey. Unit selection and scheduling are completed by technicians, and the work is conducted autonomously by these survey platforms. The survey areas and survey paths are transmitted to each platform through the telemetry system. Radiological and positional data are collected by the systems and transmitted back to the central computer system in real-time. Collected data is saved to a database for post-survey analysis or can be analyzed in real-time. Analysis of the radiological data is used to construct radiation intensity and estimated DU concentration maps. Automatically generated reports for each survey unit will provide range managers with: survey coverage data maps, estimated uranium concentration maps, and a detailed list of areas that are above a user defined concentration. This paper describes the components of each of the surveying systems, their capabilities, and limitations. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

TU-AB-BRA-11: Evaluation of Fully Automatic Volumetric GBM Segmentation in the TCGA-GBM Dataset: Prognosis and Correlation with VASARI Features

Purpose: Reproducible definition and quantification of imaging biomarkers is essential. We evaluated a fully automatic MR-based segmentation method by comparing it to manually defined sub-volumes by experienced radiologists in the TCGA-GBM dataset, in terms of sub-volume prognosis and association with VASARI features. Methods: MRI sets of 67 GBM patients were downloaded from the Cancer Imaging archive. GBM sub-compartments were defined manually and automatically using the Brain Tumor Image Analysis (BraTumIA), including necrosis, edema, contrast enhancing and non-enhancing tumor. Spearman’s correlation was used to evaluate the agreement with VASARI features. Prognostic significance was assessed using the C-index. Results: Auto-segmented sub-volumes showed high agreement with manually delineated volumes (range (r): 0.65 – 0.91). Also showed higher correlation with VASARI features (auto r = 0.35, 0.60 and 0.59; manual r = 0.29, 0.50, 0.43, for contrast-enhancing, necrosis and edema, respectively). The contrast-enhancing volume and post-contrast abnormal volume showed the highest C-index (0.73 and 0.72), comparable to manually defined volumes (p = 0.22 and p = 0.07, respectively). The non-enhancing region defined by BraTumIA showed a significantly higher prognostic value (CI = 0.71) than the edema (CI = 0.60), both of which could not be distinguished by manual delineation. Conclusion: BraTumIA tumor sub-compartments showed higher correlation with VASARI data, and equivalent performance in terms of prognosis compared to manual sub-volumes. This method can enable more reproducible definition and quantification of imaging based biomarkers and has a large potential in high-throughput medical imaging research.

60 APPLIED LIFE SCIENCES↗

Fishing for Clickbaits in Social Images and Texts with Linguistically-Infused Neural Network Models

This paper presents the results and conclusions of our participation in the Clickbait Challenge 2017 on automatic clickbait detection in social media. We first describe linguistically-infused neural network models and identify informative representations to predict the level of clickbaiting present in Twitter posts. Our models allow to answer the question not only whether a post is a clickbait or not, but to what extent it is a clickbait post e.g., not at all, slightly, considerably, or heavily clickbaity using a score ranging from 0 to 1. We evaluate the predictive power of models trained on varied text and image representations extracted from tweets. Our best performing model that relies on the tweet text and linguistic markers of biased language extracted from the tweet and the corresponding page yields mean squared error (MSE) of 0.04, mean absolute error (MAE) of 0.16 and R2 of 0.43 on the held-out test data. For the binary classification setup (clickbait vs. non-clickbait), our model achieved F1 score of 0.69. We have not found that image representations combined with text yield significant performance improvement yet. Nevertheless, this work is the first to present preliminary analysis of objects extracted using Google Tensorflow object detection API from images in clickbait vs. non-clickbait Twitter posts. Finally, we outline several steps to improve model performance as a part of the future work.

dlickbait challenge, Twitter, neural networks, mac↗

Theoretical Plasma Physics

Lattice Boltzmann algorithms are a mesoscopic method to solve problems in nonlinear physics which are highly parallelized – unlike the direction solution of the original problem. These methods are applied to both fluid and magnetohydrodynamic turbulence. By introducing entropic constraints one can enforce the positive definiteness of the distribution functions and so be able to simulate fluids at high Reynolds numbers without numerical instabilities. By introducing a vector distribution function for the magnetic field one can enforce the divergence free condition on the magnetic field automatically, without the need of divergence cleaning as needed in most direct numerical solutions of the resistive magnetohydrodynamic equations. The principal reason for the high parallelization of lattice Boltzmann codes is that they consist of a kinetic collisional relaxation step (which is purely local) followed by a simple shift of the relaxed data to neighboring lattice sites. In large eddy simulations, the closure schemes are highly nonlocal – the most famous of these schemes is that due to Smagorinsky. Under a lattice Boltzmann representation the Smagorinsky closure is purely local – being simply a particular moment on the perturbed distribution fucntions. After nonlocal fluid moment models were discovered to represent Landau damping, it was found possible to model these fluid models using an appropriate lattice Boltzmann algorithm. The close to ideal parallelization of the lattice Boltzmann codes permitted us to be Gordon Bell finalists on using the Earth Simulation in Japan. We have also been involved in the radio frequency propagation of waves into a tokamak and into a spherical overdense tokamak plasma. Initially we investigated the use of a quasi-optical grill for the launching of lower hybrid waves into a tokamak. It was found that the conducting walls do not prevent the rods from being properly irradiated, the overloading of the quasi-optical grill is not severe with the electric field only being about three times higher than in the ideal case. Moreover, the quasi-optical grill was significantly fewer structural elements that the multijunction grill. Nevertheless there has not been much interest from experimental fusion groups to implementing these structures. Hence we have returned to optimizing the multijunction grill so that the large number of coupling matrix elements can be efficiently evaluated using symmetry arguments. In overdense plasmas, the standard electromagnetic waves cannot propagate into the plasma center, but are reflected at the plasma edge. By optimizing mode conversion processes (in particular, the O-X-B wave propagation of Ordinary Mode converting to an Extraordinary mode which then converts into an electrostatic Bernstein wave) one can excite within the plasma an electrostatic Bernstein wave that does not suffer density cutoffs and is absorbed on the electron cyclotron harmonics. Finally we have started looking at other mesoscopic lattice algorithms that involve unitary collision and streaming steps. Because these algorithms are unitary they can be run on quantum computers when they become available – unlike their computational cousin of lattice Boltzmann which is a purely classical code. These quantum lattice gas algorithms have been tested successfully on exact analytic soliton collision solution. These calculations are hoped to be able to study Bose Einstein condensed atomic gases and their ground states in an optical lattice.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Data Locality Enhancement of Dynamic Simulations for Exascale Computing (Final Report)

The development of modern processors exhibits two trends that complicate the optimizations of modern software. The first is the increasing sensitivity of processors' throughput to irregularities in computation. With more processors produced through a massive integration of simple cores, future systems will increasingly favor regular data-level parallel computations, but deviate from the needs of applications with complex patterns. Some evidences are already shown on Graphic Processing Units (GPU): Irregular data accesses (e.g., indirect references A[D[i]]) and conditional branches are limiting many GPU applications' performance at a level an order of magnitude lower than the peak of GPU. The second hardware trend is the growing gap between memory bandwidth and the aggregate speed—that is, the sum of all cores' computing power—of a Chip Multiprocessor (CMP). Despite the capped growth of the peak CPU speed, the aggregate speed of a CMP keeps increasing as more cores get into a single chip. It is expected that by 2018, node concurrency in an exascale system will increase by hundreds of times, whereas, memory bandwidth will expand by only 10 to 20 times. Consequently, data movement and storage is expected to consume more than 70% of the total system power. Bridging this gap is difficult; the complexities of modern CMP memory hierarchy make it even harder: Data cache becomes shared among computing units, and the sharing is often non-uniform—whether two computing units share a cache depends on their proximity and the level of the cache. On the recent IBM Power7 architecture, for instance, four hardware contexts (or SMT threads) in a core share the entire memory hierarchy, all cores in one chip share an on-chip L3 cache, and cores across chips share L3 and main memory through off-chip connections. These two trends complicate the translation of computing power into performance, especially for a program with either intensive data accesses or complex patterns in data accesses or control flow paths. Unfortunately, both attributes present and will persist in a class of important applications. For instance, many scientific simulations deal with a large volume of data. And meanwhile, as most real-world processes are non-uniform and evolving (e.g., the evolution of a galaxy or the process of a drug injection), both the computations and data accesses of these programs tend to be irregular and dynamically changing. Currently, the lack of support to these applications on modern CMP severely limits their performance. On GPU, as our recent study shows and other studies echo, performance enhancement of a factor of integers is possible when memory accesses or control flows are streamlined for a set of GPU applications. On multicore CPU, our studies show that traditional locality enhancement, for being oblivious to the new features of multicore memory hierarchy, may even cause large slowdown to data-intensive dynamic applications. The severity of the issues is expected to worsen as the two hardware trends continue. Some recent studies try to match software with the trends, but in a limited scope or manner. For irregularities on GPU, most studies focus on irregularities analyzable through static analysis (e.g., data accesses in regular loops). Dynamic irregularities are harder to address because the needed analysis and transformations typically have to happen at run time. Some other research resorts to hardware extensions, an actual adoption of which is unclear for the entailed space cost and complexity. For data locality, recent years have seen some exploitations of the new memory hierarchy on multicore for performance, but most of them are on process or thread scheduling, rather than program transformations. Our recent study reveals that program-level transformations may magnify the scheduling benefits by a factor of seven, concluding that program-level transformation should play a central role for data locality enhancement on modern CMP. But research in this direction has been sparse, and most have focused on data layout or cache performance modeling, rather than program transformations to match with the new memory hierarchy features. Overall, it is still an open question how to bridge the gap between dynamic computations and the two prominent properties of modern processors. The goal of this project is to develop a set of techniques and software tools to enhance the matching between memory accesses in dynamic simulations and the prominent features of modern and future CMP, alleviating the memory performance issues for petascale and exascale computing. This report summarizes the discoveries and products produced throughout this project. It includes free launch, a new software approach to overcoming the shortcomings of both methods; coherence-free multiview, an approach that allows multiple views of a single data object to co-exist on GPU memory during a GPU kernel execution; algorithmic optimizations to data analytics problems, especially those that involve lots of distance calculations. Supporting dynamic parallelism is important for GPU to benefit a broad range of applications. There are currently two fundamental ways for programs to exploit dynamic parallelism on GPU: a software-based approach with software-managed worklists, and a hardware-based approach through dynamic subkernel launches. Neither is satisfactory. The former is complicated to program and is often subject to some load imbalance; the latter suffers large runtime overhead. In this work, we propose free launch, a new software approach to overcoming the shortcomings of both methods. It allows programmers to use subkernel launches to express dynamic parallelism. It employs a novel compiler-based code transformation named subkernel launch removal to replace the subkernel launches with the reuse of parent threads. Coupled with an adaptive task assignment mechanism, the transformation reassigns the tasks in the subkernels to the parent threads with a good load balance. The technique requires no hardware extensions, immediately deployable on existing GPUs. It keeps the programming convenience of the subkernel launch-based approach while avoiding its large runtime overhead. Meanwhile, its superior load balancing makes it outperform manual worklist-based techniques by 3X on average. The work was published at the 48th Annual IEEE/ACM International Symposium on Microarchitecture (Micro'2015). A Graphic Processing Unit (GPU) system is typically equipped with many types of memory (e.g., global, constant, texture, shared, cache). Data placement determines what data are placed on which type of memory, essential for GPU memory performance. Prior optimizations of data placement always require a single view of a data object on memory, which limits the optimization effectiveness. In this work, we propose coherence-free multiview, an approach that allows multiple views of a single data object to co-exist on GPU memory during a GPU kernel execution. We demonstrate that under certain conditions, the multiple views can remain incoherent while facilitating enhanced data placement. We present a theorem and some compiler support to ensure the soundness of the usage of coherence-free multiview. We further develop reference-discerning data placement, a new way to enhance data placements on GPU. It enables more flexible data placements by using coherence-free multiview to leverage the slack in coherence requirement of some GPU programs. Experiments on three types of GPU systems show that, with less than 200KB space cost, the new data placement technique can provide a 1.6X average (up to 4.27X) speedup. In addition, we have examined algorithmic optimizations to data analytics problems, especially those that involve lots of distance calculations. Computing distances among data points is an essential part of many important algorithms in data analytics, graph analysis, and other domains. In each of these domains, developers have spent significant manual effort optimizing algorithms, often through novel applications of the triangle equality, in order to minimize the number of distance computations in the algorithms. In this work, we observe that many algorithms across these domains can be generalized as an instance of a generic distance-related abstraction. Based on this abstraction, we derive seven principles for correctly applying the triangular inequality to optimize distance-related algorithms. Guided by the findings, we develop Triangular OPtimizer (TOP), the first software framework that is able to automatically produce optimized algorithms that either matches or outperforms manually designed algorithms for solving distance-related problems. TOP achieves up to 237x speedups and 2.5X on average. The work has been published at the 32nd International Conference on Machine Learning (ICML'15) and the 41st International Conference on Very Large Data Bases (VLDB'15).

42 ENGINEERING↗

Rapid Identification of X-ray Diffraction Patterns Based on Very Limited Data by Interpretable Convolutional Neural Networks

Large volumes of data from material characterizations call for rapid and automatic data analysis to accelerate materials discovery. Herein, we report a convolutional neural network (CNN) that was trained based on theoretical data and very limited experimental data for fast identification of experimental X-ray diffraction (XRD) patterns of metal–organic frameworks (MOFs). To augment the data for training the model, noise was extracted from experimental data and shuffled; then it was merged with the main peaks that were extracted from theoretical spectra to synthesize new spectra. For the first time, one-to-one material identification was achieved. Theoretical MOFs patterns (1012) were augmented to a whole data set of 72 864 samples. It was then randomly shuffled and split into training (58 292 samples) and validation (14 572 samples) data sets at a ratio of 4:1. For the task of discriminating, the optimized model showed the highest identification accuracy of 96.7% for the top 5 ranking on a test data set of 30 hold-out samples. Neighborhood component analysis (NCA) on the experimental XRD samples shows that the samples from the same material are clustered in groups in the NCA map. Analysis on the class activation maps of the last CNN layer further discloses the mechanism by which the CNN model successfully identifies individual MOFs from the XRD patterns. Furthermore, this CNN model trained by the data augmentation technique would not only open numerous potential applications for identifying XRD patterns for different materials, but also pave avenues to autonomously analyze data by other characterization tools such as FTIR, Raman, and NMR spectroscopies.

36 MATERIALS SCIENCE↗

Build and Execute Environment

At exascale, the challenge becomes to develop applications that run at scale and use exascale platforms reliably, efficiently, and flexibly. Workflows become much more complex because they must seamlessly integrate simulation and data analytics. They must include down-sampling, post-processing, feature extraction, and visualization. Power and data transfer limitations require these analysis tasks to be run in-situ or in-transit. We expect successful workflows will comprise multiple linked simulations along with tens of analysis routines. Users will have limited development time at scale and, therefore, must have rich tools to develop, debug, test, and deploy applications. At this scale, successful workflows will compose linked computations from an assortment of reliable, well-defined computation elements, ones that can come and go as required, based on the needs of the workflow over time. We propose a novel framework that utilizes both virtual machines (VMs) and software containers to create a workflow system that establishes a uniform build and execution environment (BEE) beyond the capabilities of current systems. In this environment, applications will run reliably and repeatably across heterogeneous hardware and software. Containers, both commercial (Docker and Rocket) and open-source (LXC and LXD), define a runtime that isolates all software dependencies from the machine operating system. Workflows may contain multiple containers that run different operating systems, different software, and even different versions of the same software. We will run containers in open-source virtual machines (KVM) and emulators (QEMU) so that workflows run on any machine entirely in user-space. On this platform of containers and virtual machines, we will deliver workflow software that provides services, including repeatable execution, provenance, checkpointing, and future proofing. We will capture provenance about how containers were launched and how they interact to annotate workflows for repeatable and partial re-execution. We will coordinate the physical snapshots of virtual machines with parallel programming constructs, such as barriers, to automate checkpoint and restart. We will also integrate with HPC-specific container runtimes to gain access to accelerators and other specialized hardware to preserve native performance. Containers will link development to continuous integration. When application developers check code in, it will automatically be tested on a suite of different software and hardware architectures.

Guan, Qiang↗

Build and Execute Environment

At exascale, the challenge becomes to develop applications that run at scale and use exascale platforms reliably, efficiently, and flexibly. Workflows become much more complex because they must seamlessly integrate simulation and data analytics. They must include down-sampling, post-processing, feature extraction, and visualization. Power and data transfer limitations require these analysis tasks to be run in-situ or in-transit. We expect successful workflows will comprise multiple linked simulations along with tens of analysis routines. Users will have limited development time at scale and, therefore, must have rich tools to develop, debug, test, and deploy applications. At this scale, successful workflows will compose linked computations from an assortment of reliable, well-defined computation elements, ones that can come and go as required, based on the needs of the workflow over time. We propose a novel framework that utilizes both virtual machines (VMs) and software containers to create a workflow system that establishes a uniform build and execution environment (BEE) beyond the capabilities of current systems. In this environment, applications will run reliably and repeatably across heterogeneous hardware and software. Containers, both commercial (Docker and Rocket) and open-source (LXC and LXD), define a runtime that isolates all software dependencies from the machine operating system. Workflows may contain multiple containers that run different operating systems, different software, and even different versions of the same software. We will run containers in open-source virtual machines (KVM) and emulators (QEMU) so that workflows run on any machine entirely in user-space. On this platform of containers and virtual machines, we will deliver workflow software that provides services, including repeatable execution, provenance, checkpointing, and future proofing. We will capture provenance about how containers were launched and how they interact to annotate workflows for repeatable and partial re-execution. We will coordinate the physical snapshots of virtual machines with parallel programming constructs, such as barriers, to automate checkpoint and restart. We will also integrate with HPC-specific container runtimes to gain access to accelerators and other specialized hardware to preserve native performance. Containers will link development to continuous integration. When application developers check code in, it will automatically be tested on a suite of different software and hardware architectures.

Guan, Qiang↗

WE-D-9A-01: A Novel Mesh-Based Deformable Surface-Contour Registration

Purpose: Initial guess is vital for 3D-2D deformable image registration (DIR) while dealing with large deformations for adaptive radiation therapy. A fast procedure has been developed to deform body surface to match 2D body contour on projections. This surface-contour DIR will provide an initial deformation for further complete 3D DIR or image reconstruction. Methods: Both planning CT images and come-beam CT (CBCT) projections are preprocessed to create 0–1 binary mask. Then the body surface and CBCT projection body contours are extracted by Canny edge detector. A finite element modeling system was developed to automatically generate adaptive meshes based on the image surface. After that, the projections of the CT surface voxels are computed and compared with corresponding 2D projection contours from CBCT scans. As a result, the displacement vector field (DVF) on mesh vertices around the surface was optimized iteratively until the shortest Euclidean distance between the pixels on the projections of the deformed CT surface and the corresponding CBCT projection contour is minimized. With the help of the tetrahedral meshes, we can smoothly diffuse the deformation from the surface into the interior of the volume. Finally, the deformed CT images are obtained by the optimal DVF applied on the original planning CT images. Results: The accuracy of the surface-contour registration is evaluated by 3D normalized cross correlation increased from 0.9176 to 0.9957 (sphere-ellipsoid phantom) and from 0.7627 to 0.7919 (H and N cancer patient data). Under the GPU-based implementation, our surface-contour-guided method on H and N cancer patient data takes 8 seconds/iteration, about 7.5 times faster than direct 3D method (60 seconds/iteration), and it needs fewer optimization iterations (30 iterations vs 50 iterations). Conclusion: The proposed surface-contour DIR method can substantially improve both the accuracy and the speed of reconstructing volumetric images, which is helpful for applying in adaptive radiotherapy. This research is supported by CPRIT individual investigator award RP110329.

60 APPLIED LIFE SCIENCES↗

Automatic tracking of implanted fiducial markers in cone beam CT projection images

Purpose: This paper describes a novel method for simultaneous intrafraction tracking of multiple fiducial markers. Although the proposed method is generic and can be adopted for a number of applications including fluoroscopy based patient position monitoring and gated radiotherapy, the tracking results presented in this paper are specific to tracking fiducial markers in a sequence of cone beam CT projection images. Methods: The proposed method is accurate and robust thanks to utilizing the mean shift and random sampling principles, respectively. The performance of the proposed method was evaluated with qualitative and quantitative methods, using data from two pancreatic and one prostate cancer patients and a moving phantom. The ground truth, for quantitative evaluation, was calculated based on manual tracking preformed by three observers. Results: The average dispersion of marker position error calculated from the tracking results for pancreas data (six markers tracked over 640 frames, 3840 marker identifications) was 0.25 mm (at iscoenter), compared with an average dispersion for the manual ground truth estimated at 0.22 mm. For prostate data (three markers tracked over 366 frames, 1098 marker identifications), the average error was 0.34 mm. The estimated tracking error in the pancreas data was < 1 mm (2 pixels) in 97.6% of cases where nearby image clutter was detected and in 100.0% of cases with no nearby image clutter. Conclusions: The proposed method has accuracy comparable to that of manual tracking and, in combination with the proposed batch postprocessing, superior robustness. Marker tracking in cone beam CT (CBCT) projections is useful for a variety of purposes, such as providing data for assessment of intrafraction motion, target tracking during rotational treatment delivery, motion correction of CBCT, and phase sorting for 4D CBCT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Automatic detection of low surface brightness galaxies from Sloan Digital Sky Survey images

ABSTRACT Low surface brightness (LSB) galaxies are galaxies with central surface brightness fainter than the night sky. Due to the faint nature of LSB galaxies and the comparable sky background, it is difficult to search LSB galaxies automatically and efficiently from large sky survey. In this study, we established the low surface brightness galaxies autodetect (LSBG-AD) model, which is a data-driven model for end-to-end detection of LSB galaxies from Sloan Digital Sky Survey (SDSS) images. Object-detection techniques based on deep learning are applied to the SDSS field images to identify LSB galaxies and estimate their coordinates at the same time. Applying LSBG-AD to 1120 SDSS images, we detected 1197 LSB galaxy candidates, of which 1081 samples are already known and 116 samples are newly found candidates. The B-band central surface brightness of the candidates searched by the model ranges from 22 to 24 mag arcsec−2, quite consistent with the surface brightness distribution of the standard sample. A total of 96.46 per cent of LSB galaxy candidates have an axial ratio (b/a) greater than 0.3, and 92.04 per cent of them have $fracDev\_r$ < 0.4, which is also consistent with the standard sample. The results show that the LSBG-AD model learns the features of LSB galaxies of the training samples well, and can be used to search LSB galaxies without using photometric parameters. Next, this method will be used to develop efficient algorithms to detect LSB galaxies from massive images of the next-generation observatories.

79 ASTRONOMY AND ASTROPHYSICS↗

Innovative Patient Room Lighting System with Integrated Spectrally Adaptive Control

In December of 2013, the U.S. Department of Energy’s SSL R&D Program released a Funding Opportunity Announcement (FOA), that for the first time, contained opportunities for comprehensive application-specific system development. The FOA included opportunities for two applications, one of which was a Patient Room. Philips Lighting Research North America, submitted a proposal for the Patient Room application, and was selected for the complete project award. The award amount was for $497,127, with a Philips Research co-funding commitment 165,709 dollars. The total project value was 662,836 dollars. This project sought to redefine lighting for the patient room application. The goal was to deliver an innovative LED patient suite (patient room and bathroom) lighting system solution that was 40% more energy-efficient than traditional fluorescent incumbent technologies, and would meet all the visual and non-visual needs of patients, caregivers and visitors, and improve the patient experience. State-of-the-art multichannel LED platforms and control technologies that would provide spectral tuning and become part of an intelligent, connected lighting system drove the solution. The project was scoped into four main task areas that included a) System Concept Creation, b) Identification of the Luminaire Portfolio, c) Development of the Connected Lighting Infrastructure, and d) System Performance Validation. Each of the four main tasks were completed and validated extensively over the course the 2 ½ year project. The system concept was created by first developing a lighting design that demonstrated best practices for patient room lighting – illuminance and uniformity for task performance, reduced glare, and convenient controls, in addition to giving patients control over the lighting in their environment. A framework was defined to deliver circadian support via software behaviors. Through that process luminaires were identified from the Philips portfolio that were adaptable – by their form, dimensions, and optical materials – to mix multicolor LED platforms uniformly and deliver target design lumen levels. The Blue Sky luminaire was selected for the patient bed area to give the illusion of skylight while providing white light on the patient bed. Luminaires used existing 2-channel tunable white LED boards, and newly developed 4-channel LED boards. Red-Orange, Blue, Green, and Blue-shifted Yellow LED chips were selected based on spectral characteristics and their ability to produce high quality white light. 4-channel Power over Ethernet (PoE) drivers were developed and firmware written so they would communicate with both 2- and 4-channel boards. These components formed the backbone of the connected lighting infrastructure. Software, flexible and nuanced in its complexity, was written to set behaviors for myriad lighting scenes in the room throughout the 24 hour day – and all could be overridden by manual controls. This included a dynamic tunable white program, three color changing automatic programs that simulated degrees of sunrise to sunset palettes, and an amber night lighting system that offered visual cues for postural stability to minimize the risk of falls. All programs were carefully designed to provide visual comfort for all occupants, support critical task performance for staff, and to support the patient’s 24hr rhythms. A full scale mockup room was constructed in the Philips Cambridge Lab. The lighting system was installed, tested and functionality demonstrated to ensure smooth operation of system components – luminaires, drivers, PoE switches, wall controls, patient remote, and daylight and occupancy sensors. How did the system perform? It met visual criteria, confirmed by calculations, simulations and measurements in the field. It met non-visual criteria, confirmed by setting circadian stimulus (CS) targets and performing calculations using the calculator developed by the Lighting Research Center. Finally, human factors validation studies were conducted to gain insight from real end users in the healthcare profession; surveys were administered, data analyzed, and audio comments captured. The general consensus was positive, with requests to pilot the system in their hospitals. The importance of the research completed under this grant is that it allowed the exploration and development of a unique lighting system, one that would deliver a blend of visual and non-visual criteria in patient room design for today’s healthcare environment. The research investigated the area of multichannel LED technology, multichannel Power over Ethernet (PoE) drivers and their integration with automatic and manual controls as a system – uncovering and meeting challenges along the way. It married visual needs of patients and staff with support for 24 hour rhythms, placing value on the wellbeing of the patient – while successfully saving energy over incumbent technologies. Indications are that the market is ready and willing to invest – multiple healthcare facilities are in line to pilot this system, recognizing its value beyond energy to patient and staff well-being. Its value to the public can best be expressed by a patient support coordinator who, after spending several hours in the room being immersed in the lighting, analyzing all its features, commented: “This re-writes lighting for healthcare”.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Efficient ptychographic phase retrieval via a matrix-free Levenberg-Marquardt algorithm

The phase retrieval problem, where one aims to recover a complex-valued image from far-field intensity measurements, is a classic problem encountered in a range of imaging applications. Modern phase retrieval approaches usually rely on gradient descent methods in a nonlinear minimization framework. Calculating closed-form gradients for use in these methods is tedious work, and formulating second order derivatives is even more laborious. Additionally, second order techniques often require the storage and inversion of large matrices of partial derivatives, with memory requirements that can be prohibitive for data-rich imaging modalities. We use a reverse-mode automatic differentiation (AD) framework to implement an efficient matrix-free version of the Levenberg-Marquardt (LM) algorithm, a longstanding method that finds popular use in nonlinear least-square minimization problems but which has seen little use in phase retrieval. Furthermore, we extend the basic LM algorithm so that it can be applied for more general constrained optimization problems (including phase retrieval problems) beyond just the least-square applications. Since we use AD, we only need to specify the physics-based forward model for a specific imaging application; the first and second-order derivative terms are calculated automatically through matrix-vector products, without explicitly forming the large Jacobian or Gauss-Newton matrices typically required for the LM method. We demonstrate that this algorithm can be used to solve both the unconstrained ptychographic object retrieval problem and the constrained “blind” ptychographic object and probe retrieval problems, under the popular Gaussian noise model as well as the Poisson noise model. We compare this algorithm to state-of-the-art first order ptychographic reconstruction methods to demonstrate empirically that this method outperforms best-in-class first-order methods: it provides excellent convergence guarantees with (in many cases) a superlinear rate of convergence, all with a computational cost comparable to, or lower than, the tested first-order algorithms.

36 MATERIALS SCIENCE↗

The influence of respiratory motion on CT image volume definition

Purpose: Radiotherapy treatments are based on geometric and density information acquired from patient CT scans. It is well established that breathing motion during scan acquisition induces motion artifacts in CT images, which can alter the size, shape, and density of a patient's anatomy. The aim of this work is to examine and evaluate the impact of breathing motion on multislice CT imaging with respiratory synchronization (4DCT) and without it (3DCT). Methods: A specific phantom with a movable insert was used. Static and dynamic phantom acquisitions were obtained with a multislice CT. Four sinusoidal breath patterns were simulated to move known geometric structures longitudinally. Respiratory synchronized acquisitions (4DCT) were performed to generate images during inhale, intermediate, and exhale phases using prospective and retrospective techniques. Static phantom data were acquired in helical and sequential mode to define a baseline for each type of respiratory 4DCT technique. Taking into account the fact that respiratory 4DCT is not always available, 3DCT helical image studies were also acquired for several CT rotation periods. To study breath and acquisition coupling when respiratory 4DCT was not performed, the beginning of the CT image acquisition was matched with inhale, intermediate, or exhale respiratory phases, for each breath pattern. Other coupling scenarios were evaluated by simulating different phantom and CT acquisition parameters. Motion induced variations in shape and density were quantified by automatic threshold volume generation and Dice similarity coefficient calculation. The structure mass center positions were also determined to make a comparison with their theoretical expected position. Results: 4DCT acquisitions provided volume and position accuracies within ±3% and ±2 mm for structure dimensions >2 cm, breath amplitude ≤15 mm, and breath period ≥3 s. The smallest object (1 cm diameter) exceeded 5% volume variation for the breath patterns of higher frequency and amplitude motion. Larger volume differences (>10%) and inconsistencies between the relative positions of objects were detected in image studies acquired without respiratory control. Increasing the 3DCT rotation period caused a higher distortion in structures without obtaining their envelope. Simulated data showed that the slice acquisition time should be at least twice the breath period to average object movement. Conclusions: Respiratory 4DCT images provide accurate volume and position of organs affected by breath motion detecting higher volume discrepancies as amplitude length or breath frequency are increased. For 3DCT acquisitions, a CT should be considered slow enough to include lesion envelope as long as the slice acquisition time exceeds twice the breathing period. If this requirement cannot be satisfied, a fast CT (along with breath-hold inhale and exhale CTs to estimate roughly the ITV) is recommended in order to minimize structure distortion. Even with an awareness of a patient's respiratory cycle, its coupling with 3DCT acquisition cannot be predicted since patient anatomy is not accurately known.

62 RADIOLOGY AND NUCLEAR MEDICINE↗