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At least 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Leveraging the checkpoint-restart technique for optimizing CPU efficiency of ATLAS production applications on opportunistic platforms

Data processing applications of the ATLAS experiment, such as event simulation and reconstruction, spend considerable amount of time in the initialization phase. This phase includes loading a large number of shared libraries, reading detector geometry and condition data from external databases, building a transient representation of the detector geometry and initializing various algorithms and services. In some cases the initialization step can take as long as 10-15 minutes. Such slow initialization has a significant negative impact on overall CPU efficiency of the production job, especially when the job is executed on opportunistic, often short-lived, resources such as commercial clouds or volunteer computing. In order to improve this situation, we can take advantage of the fact that ATLAS runs large numbers of production jobs with similar configuration parameters (e.g. jobs within the same production task). This allows us to checkpoint one job at the end of its configuration step and then use the generated checkpoint image for rapid startup of thousands of production jobs. By applying this technique we can bring the initialization time of a job from tens of minutes down to just a few seconds. In addition to that we can leverage container technology for restarting checkpointed applications on the variety of computing platforms, in particular of platforms different from the one on which the checkpoint image was created. We will describe the mechanism of creating checkpoint images of Geant4 simulation jobs with AthenaMP (the multi-process version of the ATLAS data simulation, reconstruction and analysis framework Athena) and the usage of these images for running ATLAS Simulation production jobs on volunteer computing resources (ATLAS@Home) and on Supercomputers.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

THEORY AND SIMULATIONS OF REFRACTIVE SUBSTRUCTURE IN RESOLVED SCATTER-BROADENED IMAGES

At radio wavelengths, scattering in the interstellar medium distorts the appearance of astronomical sources. Averaged over a scattering ensemble, the result is a blurred image of the source. However, Narayan and Goodman and Goodman and Narayan showed that for an incomplete average, scattering introduces refractive substructure in the image of a point source that is both persistent and wideband. We show that this substructure is quenched but not smoothed by an extended source. As a result, when the scatter-broadening is comparable to or exceeds the unscattered source size, the scattering can introduce spurious compact features into images. In addition, we derive efficient strategies to numerically compute realistic scattered images, and we present characteristic examples from simulations. Our results show that refractive substructure is an important consideration for ongoing missions at the highest angular resolutions, and we discuss specific implications for RadioAstron and the Event Horizon Telescope.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

Quantifying the margin sharpness of lesions on radiological images for content-based image retrieval

Purpose: To develop a method to quantify the margin sharpness of lesions on CT and to evaluate it in simulations and CT scans of liver and lung lesions. Methods: The authors computed two attributes of margin sharpness: the intensity difference between a lesion and its surroundings, and the sharpness of the intensity transition across the lesion boundary. These two attributes were extracted from sigmoid curves fitted along lines automatically drawn orthogonal to the lesion margin. The authors then represented the margin characteristics for each lesion by a feature vector containing histograms of these parameters. The authors created 100 simulated CT scans of lesions over a range of intensity difference and margin sharpness, and used the concordance correlation between the known parameter and the corresponding computed feature as a measure of performance. The authors also evaluated their method in 79 liver lesions (44 patients: 23 M, 21 F, mean age 61) and 58 lung nodules (57 patients: 24 M, 33 F, mean age 66). The methodology presented takes into consideration the boundary of the liver and lung during feature extraction in clinical images to ensure that the margin feature do not get contaminated by anatomy other than the normal organ surrounding the lesions. For evaluation in these clinical images, the authors created subjective independent reference standards for pairwise margin sharpness similarity in the liver and lung cohorts, and compared rank orderings of similarity used using our sharpness feature to that expected from the reference standards using mean normalized discounted cumulative gain (NDCG) over all query images. In addition, the authors compared their proposed feature with two existing techniques for lesion margin characterization using the simulated and clinical datasets. The authors also evaluated the robustness of their features against variations in delineation of the lesion margin by simulating five types of deformations of the lesion margin. Equivalence across deformations was assessed using Schuirmann's paired two one-sided tests. Results: In simulated images, the concordance correlation between measured gradient and actual gradient was 0.994. The mean (s.d.) and standard deviation NDCG score for the retrieval of K images, K = 5, 10, and 15, were 84% (8%), 85% (7%), and 85% (7%) for CT images containing liver lesions, and 82% (7%), 84% (6%), and 85% (4%) for CT images containing lung nodules, respectively. The authors' proposed method outperformed the two existing margin characterization methods in average NDCG scores over all K, by 1.5% and 3% in datasets containing liver lesion, and 4.5% and 5% in datasets containing lung nodules. Equivalence testing showed that the authors' feature is more robust across all margin deformations (p < 0.05) than the two existing methods for margin sharpness characterization in both simulated and clinical datasets. Conclusions: The authors have described a new image feature to quantify the margin sharpness of lesions. It has strong correlation with known margin sharpness in simulated images and in clinical CT images containing liver lesions and lung nodules. This image feature has excellent performance for retrieving images with similar margin characteristics, suggesting potential utility, in conjunction with other lesion features, for content-based image retrieval applications.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Dot tracking methodology for background-oriented schlieren (BOS)

We propose here a dot tracking methodology for processing background-oriented schlieren (BOS) images. The technique improves the accuracy, precision and spatial resolution compared to conventional cross-correlation algorithms. Our methodology utilizes the prior information about the dot pattern such as the location, size and number of dots to provide near 100% yield even for high dot densities (20 dots/32 × 32 pixels) and is robust to image noise. Furthermore, we propose an improvement to the displacement estimation step in the tracking process, especially for noisy images, using a “correlation correction”, whereby we combine the spatial resolution benefit of the tracking method and the smoothing property of the correlation method to increase the dynamic range of the overall measurement process. We evaluate the performance of the method with synthetic BOS images of buoyancy-driven turbulence rendered using ray-tracing simulations, and experimental images of flow in the exit plane of a converging–diverging nozzle. The results show that the improved spatial resolution results in a better accuracy of the tracking method compared to correlation-based methods in regions with sharp displacement gradients, and the correlation correction step reduces the noise floor of the measurement, resulting in a fourfold improvement in the dynamic range.

42 ENGINEERING↗
DOE OSTI2014

Exchange bias magnetism in films of NiFe/(Ni,Fe)O nanocrystallite dispersions

Ni{sub 3}Fe/(Ni,Fe)O thin films having a nanocrystallite dispersion morphology were prepared by a reactive ion beam-assisted deposition technique. The crystallite sizes of these dispersion-based films were observed to decrease from 8.4 ± 0.3 nm to 3.4 ± 0.3 nm as the deposition flow-rate increased from 2.78% to 7.89% O{sub 2}/Ar. Thin film composition was determined using selective area electron diffraction images and Multislice simulations. Through a detailed analysis of high resolution transmission electron microscopy images, the nanocrystallites were determined to be Ni{sub 3}Fe (a ferromagnet), NiO, and FeO (both antiferromagnets). It was determined that the interfacial molar Ni{sub 3}Fe ratio in the nanocrystallite dispersions increased slightly at first, then decreased as the oxygen content was increased; at 7.89% O{sub 2}/Ar, the interfacial molar ratio was essentially zero (only NiO and FeO remained). For nanocrystallite dispersion films grown with O{sub 2}/Ar flow-rate greater than 7.89%, no interfacial (intermixed) Ni{sub 3}Fe phase was detected, which resulted in no measurable exchange bias. Comparing the exchange bias field between the nanocrystallite dispersion films at 5 K, we observed a decrease in the magnitude of the exchange bias field as the nanocrystallite size decreased. The exchange bias coupling for all samples measured set in at essentially the same temperature (i.e., the exchange bias blocking temperature). Since the ferromagnetic/anti-ferromagnetic (FM/AFM) contact area in the nanocrystallite dispersion films increased as the nanocrystallite size decreased, the increase in the magnitude of the exchange bias could be attributed to larger regions of defects (vacancies and bond distortions) which occupied a significant portion of the FM/AFM interfaces in the nanocrystallite dispersion films.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Improvement of the optical image reconstruction based on multiplexed quantum ghost images

Ghost imaging allows one to obtain information on an object from the spatial correlation function between photons propagating through or reflected from the object and photons of the reference arm. In this case, detection in the object arm is performed over the entire aperture of the beam and, therefore, it does not give information on the object. The reference beam does not interact with the object, but is recorded with a scanning point detector or a CCD array permitting the measurement of the spatial correlation function of photons in two arms. The use of multimode entangled quantum light beams by illuminating the object by one beam and orienting other beams to reference arms makes it possible to obtain simultaneously several ghost images (GIs). Cross correlations of multiplexed GIs (MGIs) are determined by eighth-order field correlation functions. A special algorithm is developed for calculating higher-order correlations of Bose operators. The presence of GI cross correlations is used for improving the quality of the reconstructed object’s image by their processing using the measurement reduction method. An example of the computer simulation of the image reconstruction by MGIs formed in the field of four-frequency entangled quantum states is considered. It is found that in this case the reduced GI has a signal-to-noise ratio several times higher than that of GIs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Correction of Fluorescent Images of Biological Tissues for the Effects of Light Absorption and Scattering

A method for correcting the influence of light attenuation processes in biological tissues on their fluorescent images is proposed. The transfer function that takes into account the radiation losses in the medium at the wavelengths of excitation and emission of fluorescence is calculated analytically, depending on the transport scattering index and the hemoglobin tissue index. The latter is determined on the basis of a color image of the tissue in reflected visible light. Verification of the developed method was carried out on the basis of computer simulation of fluorescent images of biological tissue by the Monte Carlo method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Simulated JWST Data Sets for Multispectral and Hyperspectral Image Fusion

The James Webb Space Telescope (JWST) will provide multispectral and hyperspectral infrared images of a large number of astrophysical scenes. Multispectral images will have the highest angular resolution, while hyperspectral images (e.g., with integral field unit spectrometers) will provide the best spectral resolution. This paper aims at providing a comprehensive framework to generate an astrophysical scene and to simulate realistic hyperspectral and multispectral data acquired by two JWST instruments, namely, NIRCam Imager and NIRSpec IFU. We want to show that this simulation framework can be resorted to assess the benefits of fusing these images to recover an image of high spatial and spectral resolutions. To do so, we make a synthetic scene associated with a canonical infrared source, the Orion Bar. We develop forward models including corresponding noises for the two JWST instruments based on their physical features. JWST observations are then simulated by applying the forward models to the aforementioned synthetic scene. We test a dedicated fusion algorithm we developed on these simulated observations. We show that the fusion process reconstructs the high spatio-spectral resolution scene with a good accuracy on most areas, and we identify some limitations of the method to be tackled in future works. The synthetic scene and observations presented in the paper can be used, for instance, to evaluate instrument models, pipelines, or more sophisticated algorithms dedicated to JWST data analysis. Besides, fusion methods such as the one presented in this paper are shown to be promising tools to fully exploit the unprecedented capabilities of the JWST.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

Adsorption and dissociation of oxygen molecules on Si(111)-(7×7) surface

The adsorption and dissociation of O{sub 2} molecules on Si(111)-(7×7) surface have been studied by first-principles calculations. Our results show that all the O{sub 2} molecular species adsorbed on Si(111)-(7×7) surface are unstable and dissociate into atomic species with a small energy barrier about 0.1 eV. The single O{sub 2} molecule adsorption tends to form an ins×2 or a new metastable ins×2* structure on the Si adatom sites and the further coming O{sub 2} molecules adsorb on those structures to produce an ad-ins×3 structure. The ad-ins×3 structure is indeed highly stable and kinetically limited for diving into the subsurface layer to form the ins×3-tri structure by a large barrier of 1.3 eV. Unlike the previous views, we find that all the ad-ins, ins×2, and ad-ins×3 structures show bright images, while the ins×2*, ins×3, and ins×3-tri structures show dark images. The proposed oxidation pathways and simulated scanning tunneling microscope images account well for the experimental results and resolve the long-standing confusion and issue about the adsorption and reaction of O{sub 2} molecules on Si(111) surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

TH-CD-209-11: Simulation Study of Real-Time-Image Gating On Spot Scanning Proton Therapy for Lung Tumors

Purpose: To study the impact of a real-time-image gating on spot scanning proton therapy for lung tumors and to examine the suitable size of the gating window (GW). Methods: We investigated a real-time-image gated proton therapy (RGPT), in which two fluoroscopic units monitor a gold sphere fiducial in real-time, and the proton beam is irradiated only when the marker enters within the pre-assigned GW. We designed 5 treatment plans for 7 lung cancer patients: RGPT with a GW of ±1, 2, 5, and 8 mm and free-breathing proton therapy (FBPT) using the end-exhale and average images of 4-dimensional (4D) CT, respectively. 70 Gy(RBE)/10fr was prescribed to 99% of the targets. The time-series data of the three-dimensional marker positions (RTRT data) were grouped into 10 phases to associate with the phases of 4DCT. The 4D dose distributions were calculated using the plan information, RTRT Data, 4DCT, and modeled accelerator pattern. The dose distribution in each respiratory phase was deformed into the end-exhale CT. The D99 and D5-95 of CTV (with a criteria of D99>95% and D5-95<5%), V20 of Lung-GTV, and treatment times were evaluated. Results: GWs ≤ ±2 mm satisfied the criteria of CTV in all cases, whereas GWs ≥ ±5 mm did not satisfy the criteria in some cases. The V20 was reduced by more than 18.9% (relative to FBPT) for GW ≤ ±2 mm, but equaled or even surpassed the FBPT for GWs ≥ ±5 mm. The irradiation times for the ±1, 2, 5, and 8 mm GWs and FBPT were 372.4±208.3, 215.2±51.5, 180.9±31.6, 178.4±21.2, and 140.1±15.2 s, respectively. The GW of ±1 mm caused large variation in irradiation time among the patients. Conclusion: In RGPT for lung cancer, the most suitable GW, in terms of good dose preservation without prolonging the therapeutic beam delivery, is ±2 mm.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1999

Electric organ discharges and electric images during electrolocation

Weakly electric fish use active electrolocation - the generation and detection of electric currents - to explore their surroundings. Although electrosensory systems include some of the most extensively understood circuits in the vertebrate central nervous system, relatively little is known quantitatively about how fish electrolocate objects. We believe a prerequisite to understanding electrolocation and its underlying neural substrates is to quantify and visualize the peripheral electrosensory information measured by the electroreceptors. We have therefore focused on reconstructing both the electric organ discharges (EODs) and the electric images resulting from nearby objects and the fish's exploratory behaviors. Here, we review results from a combination of techniques, including field measurements, numerical and semi-analytical simulations, and video imaging of behaviors. EOD maps are presented and interpreted for six gymnotiform species. They reveal diverse electric field patterns that have significant implications for both the electrosensory and electromotor systems. Our simulations generated predictions of the electric images from nearby objects as well as sequences of electric images during exploratory behaviors. These methods are leading to the identification of image features and computational algorithms that could reliably encode electrosensory information and may help guide electrophysiological experiments exploring the neural basis of electrolocation.

Review, Tutorial↗
NASA NTRS2016

The Characterization of a DIRSIG Simulation Environment to Support the Inter-Calibration of Spaceborne Sensors

Climate change studies require long-term, continuous records that extend beyond the lifetime, and the temporal resolution, of a single remote sensing satellite sensor. The inter-calibration of spaceborne sensors is therefore desired to provide spatially, spectrally, and temporally homogeneous datasets. The Digital Imaging and Remote Sensing Image Generation (DIRSIG) tool is a first principle-based synthetic image generation model that has the potential to characterize the parameters that impact the accuracy of the inter-calibration of spaceborne sensors. To demonstrate the potential utility of the model, we compare the radiance observed in real image data to the radiance observed in simulated image from DIRSIG. In the present work, a synthetic landscape of the Algodones Sand Dunes System is created. The terrain is facetized using a 2-meter digital elevation model generated from NASA Goddard's LiDAR, Hyperspectral, and Thermal (G-LiHT) imager. The material spectra are assigned using hyperspectral measurements of sand collected from the Algodones Sand Dunes System. Lastly, the bidirectional reflectance distribution function (BRDF) properties are assigned to the modeled terrain using the Moderate Resolution Imaging Spectroradiometer (MODIS) BRDF product in conjunction with DIRSIG's Ross-Li capability. The results of this work indicate that DIRSIG is in good agreement with real image data. The potential sources of residual error are identified and the possibilities for future work are discussed..

Ambeau, Brittany L.↗
DOE OSTI2015

Theoretical investigation of the design and performance of a dual energy (kV and MV) radiotherapy imager

Purpose: In modern radiotherapy treatment rooms, megavoltage (MV) portal imaging and kilovoltage (kV) cone-beam CT (CBCT) imaging are performed using various active matrix flat-panel imager (AMFPI) designs. To expand the clinical utility of MV and kV imaging, MV AMFPIs incorporating thick, segmented scintillators and, separately, kV imaging using a beam’s eye view geometry have been investigated by a number of groups. Motivated by these previous studies, it is of interest to explore to what extent it is possible to preserve the benefits of kV and MV imaging using a single AMFPI design, given the considerably different x ray energy spectra used for kV and MV imaging. In this paper, considerations for the design of such a dual energy imager are explored through examination of the performance of a variety of hypothetical AMFPIs based on x ray converters employing segmented scintillators. Methods: Contrast, noise, and contrast-to-noise ratio performances were characterized through simulation modeling of CBCT imaging, while modulation transfer function, Swank factor, and signal performance were characterized through simulation modeling of planar imaging. The simulations were based on a previously reported hybrid modeling technique (accounting for both radiation and optical effects), augmented through modeling of electronic additive noise. All designs employed BGO scintillator material with thicknesses ranging from 0.25 to 4 cm and element-to-element pitches ranging from 0.508 to 1.016 mm. A series of studies were performed under both kV and MV imaging conditions to determine the most advantageous imager configuration (involving front or rear x ray illumination and use of a mirror or black reflector), converter design (pitch and thickness), and operating mode (pitch-binning combination). Results: Under the assumptions of the present study, the most advantageous imager design was found to employ rear illumination of the converter in combination with a black reflector, incorporate a BGO converter with a 0.508 mm pitch and a 2 cm thickness, and operate at full resolution for kV imaging and 2 × 2 binning mode for MV imaging. Such a dual energy imager design should provide soft tissue visualization at low, clinically practical doses under MV conditions, while helping to preserve the high spatial resolution and high contrast offered by kV imaging. Conclusions: The authors’ theoretical investigation suggests that a dual energy imager capable of largely preserving the desirable characteristics of both kV and MV imaging is feasible. Such an imager, when coupled to a dual energy radiation source, could facilitate simplification of current treatment room imaging systems (as well as their associated quality assurance), and facilitate more precise integration of kV and MV imaging information by virtue of reduced geometric uncertainties.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2021

A Fast Algorithm for Scanning Transmission Electron Microscopy Imaging and 4D-STEM Diffraction Simulations

Scanning transmission electron microscopy (STEM) is an extremely versatile method for studying materials on the atomic scale. Many STEM experiments are supported or validated with electron scattering simulations. However, using the conventional multislice algorithm to perform these simulations can require extremely large calculation times, particularly for experiments with millions of probe positions as each probe position must be simulated independently. Recently, the plane-wave reciprocal-space interpolated scattering matrix (PRISM) algorithm was developed to reduce calculation times for large STEM simulations. Here, we introduce a new method for STEM simulation: partitioning of the STEM probe into “beamlets,” given by a natural neighbor interpolation of the parent beams. This idea is compatible with PRISM simulations and can lead to even larger improvements in simulation time, as well requiring significantly less computer random access memory (RAM). We have performed various simulations to demonstrate the advantages and disadvantages of partitioned PRISM STEM simulations. We find that this new algorithm is particularly useful for 4D-STEM simulations of large fields of view. We also provide a reference implementation of the multislice, PRISM, and partitioned PRISM algorithms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Adsorption of PTCDA on Si(001) − 2 × 1 surface

Adsorption structures of the 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) molecule on the clean Si(001) − 2 × 1 surface were investigated using scanning tunneling microscopy (STM) experiments in conjunction with first principles theoretical calculations. Four dominant adsorption structures were observed in the STM experiments and their atomic coordinates on the Si(001) surface were determined by comparison between the experimental STM images and the theoretical simulations. Maximizing the number of the Si—O bonds is more crucial than that of the Si—C bonds in the PTCDA adsorption.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

SU-E-I-43: Pediatric CT Dose and Image Quality Optimization

Purpose: To design an approach to optimize radiation dose and image quality for pediatric CT imaging, and to evaluate expected performance. Methods: A methodology was designed to quantify relative image quality as a function of CT image acquisition parameters. Image contrast and image noise were used to indicate expected conspicuity of objects, and a wide-cone system was used to minimize scan time for motion avoidance. A decision framework was designed to select acquisition parameters as a weighted combination of image quality and dose. Phantom tests were used to acquire images at multiple techniques to demonstrate expected contrast, noise and dose. Anthropomorphic phantoms with contrast inserts were imaged on a 160mm CT system with tube voltage capabilities as low as 70kVp. Previously acquired clinical images were used in conjunction with simulation tools to emulate images at different tube voltages and currents to assess human observer preferences. Results: Examination of image contrast, noise, dose and tube/generator capabilities indicates a clinical task and object-size dependent optimization. Phantom experiments confirm that system modeling can be used to achieve the desired image quality and noise performance. Observer studies indicate that clinical utilization of this optimization requires a modified approach to achieve the desired performance. Conclusion: This work indicates the potential to optimize radiation dose and image quality for pediatric CT imaging. In addition, the methodology can be used in an automated parameter selection feature that can suggest techniques given a limited number of user inputs. G Stevens and R Singh are employees of GE Healthcare.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Rapid simulations of hyperspectral near-field images of three-dimensional heterogeneous surfaces – part II

The modeling of the near-field interaction in the scattering-type scanning near-field optical microscope (s-SNOM) is rapidly advancing, although an accurate yet versatile modeling framework that can be easily adapted to various complex situations is still lacking. In this work, we propose a time-efficient numerical scheme in the quasi-electrostatic limit to capture the tip-sample interaction in the near field. This method considers an extended tip geometry, which is a significant advantage compared to the previously reported method based on the point-dipole approximation. Using this formalism, we investigate, among others, nontrivial questions such as uniaxial and biaxial anisotropy in the near-field interaction, the relationship between various experimental parameters (e.g. tip radius, tapping amplitude, etc.), and the tip-dependent spatial resolution. The demonstrated method further sheds light on the understanding of the contrast mechanism in s-SNOM imaging and spectroscopy, while also representing a valuable platform for future quantitative analysis of the experimental observations.

Chen, Xinzhong (ORCID:0000000261033848)↗