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NASA NTRS2005

Rover Sequencing and Visualization Program

The Rover Sequencing and Visualization Program (RSVP) is the software tool for use in the Mars Exploration Rover (MER) mission for planning rover operations and generating command sequences for accomplishing those operations. RSVP combines three-dimensional (3D) visualization for immersive exploration of the operations area, stereoscopic image display for high-resolution examination of the downlinked imagery, and a sophisticated command-sequence editing tool for analysis and completion of the sequences. RSVP is linked with actual flight-code modules for operations rehearsal to provide feedback on the expected behavior of the rover prior to committing to a particular sequence. Playback tools allow for review of both rehearsed rover behavior and downlinked results of actual rover operations. These can be displayed simultaneously for comparison of rehearsed and actual activities for verification. The primary inputs to RSVP are downlink data products from the Operations Storage Server (OSS) and activity plans generated by the science team. The activity plans are high-level goals for the next day s activities. The downlink data products include imagery, terrain models, and telemetered engineering data on rover activities and state. The Rover Sequence Editor (RoSE) component of RSVP performs activity expansion to command sequences, command creation and editing with setting of command parameters, and viewing and management of rover resources. The HyperDrive component of RSVP performs 2D and 3D visualization of the rover s environment, graphical and animated review of rover-predicted and telemetered state, and creation and editing of command sequences related to mobility and Instrument Deployment Device (IDD) operations. Additionally, RoSE and HyperDrive together evaluate command sequences for potential violations of flight and safety rules. The products of RSVP include command sequences for uplink that are stored in the Distributed Object Manager (DOM) and predicted rover state histories stored in the OSS for comparison and validation of downlinked telemetry. The majority of components comprising RSVP utilize the MER command and activity dictionaries to automatically customize the system for MER activities. Thus, RSVP, being highly data driven, may be tailored to other missions with minimal effort. In addition, RSVP uses a distributed, message-passing architecture to allow multitasking, and collaborative visualization and sequence development by scattered team members.

Cooper, Brian↗

NASA NTRS2005

Update on Rover Sequencing and Visualization Program

The Rover Sequencing and Visualization Program (RSVP) has been updated. RSVP was reported in Rover Sequencing and Visualization Program (NPO-30845), NASA Tech Briefs, Vol. 29, No. 4 (April 2005), page 38. To recapitulate: The Rover Sequencing and Visualization Program (RSVP) is the software tool to be used in the Mars Exploration Rover (MER) mission for planning rover operations and generating command sequences for accomplishing those operations. RSVP combines three-dimensional (3D) visualization for immersive exploration of the operations area, stereoscopic image display for high-resolution examination of the downlinked imagery, and a sophisticated command-sequence editing tool for analysis and completion of the sequences. RSVP is linked with actual flight code modules for operations rehearsal to provide feedback on the expected behavior of the rover prior to committing to a particular sequence. Playback tools allow for review of both rehearsed rover behavior and downlinked results of actual rover operations. These can be displayed simultaneously for comparison of rehearsed and actual activities for verification. The primary inputs to RSVP are downlink data products from the Operations Storage Server (OSS) and activity plans generated by the science team. The activity plans are high-level goals for the next day s activities. The downlink data products include imagery, terrain models, and telemetered engineering data on rover activities and state. The Rover Sequence Editor (RoSE) component of RSVP performs activity expansion to command sequences, command creation and editing with setting of command parameters, and viewing and management of rover resources. The HyperDrive component of RSVP performs 2D and 3D visualization of the rover s environment, graphical and animated review of rover predicted and telemetered state, and creation and editing of command sequences related to mobility and Instrument Deployment Device (robotic arm) operations. Additionally, RoSE and HyperDrive together evaluate command sequences for potential violations of flight and safety rules. The products of RSVP include command sequences for uplink that are stored in the Distributed Object Manager (DOM) and predicted rover state histories stored in the OSS for comparison and validation of downlinked telemetry. The majority of components comprising RSVP utilize the MER command and activity dictionaries to automatically customize the system for MER activities.

Cooper, Brian↗

DOE OSTI2017

User-Centered Evaluation of Visual Analytics

Visual analytics systems are becoming very popular. More domains now use interactive visualizations to analyze the ever-increasing amount and heterogeneity of data. More novel visualizations are being developed for more tasks and users. We need to ensure that these systems can be evaluated to determine that they are both useful and usable. A user-centered evaluation for visual analytics needs to be developed for these systems. While many of the typical human-computer interaction (HCI) evaluation methodologies can be applied as is, others will need modification. Additionally, new functionality in visual analytics systems needs new evaluation methodologies. There is a difference between usability evaluations and user-centered evaluations. Usability looks at the efficiency, effectiveness, and user satisfaction of users carrying out tasks with software applications. User-centered evaluation looks more specifically at the utility provided to the users by the software. This is reflected in the evaluations done and in the metrics used. In the visual analytics domain this is very challenging as users are most likely experts in a particular domain, the tasks they do are often not well defined, the software they use needs to support large amounts of different kinds of data, and often the tasks last for months. These difficulties are discussed more in the section on User-centered Evaluation. Our goal is to provide a discussion of user-centered evaluation practices for visual analytics, including existing practices that can be carried out and new methodologies and metrics that need to be developed and agreed upon by the visual analytics community. The material provided here should be of use for both researchers and practitioners in the field of visual analytics. Researchers and practitioners in HCI and interested in visual analytics will find this information useful as well as a discussion on changes that need to be made to current HCI practices to make them more suitable to visual analytics. A history of analysis and analysis techniques and problems is provided as well as an introduction to user-centered evaluation and various evaluation techniques for readers from different disciplines. The understanding of these techniques is imperative if we wish to support analysis in the visual analytics software we develop. Currently the evaluations that are conducted and published for visual analytics software are very informal and consist mainly of comments from users or potential users. Our goal is to help researchers in visual analytics to conduct more formal user-centered evaluations. While these are time-consuming and expensive to carryout, the outcomes of these studies will have a defining impact on the field of visual analytics and help point the direction for future features and visualizations to incorporate. While many researchers view work in user-centered evaluation as a less-than-exciting area to work, the opposite is true. First of all, the goal is user-centered evaluation is to help visual analytics software developers, researchers, and designers improve their solutions and discover creative ways to better accommodate their users. Working with the users is extremely rewarding as well. While we use the term “users” in almost all situations there are a wide variety of users that all need to be accommodated. Moreover, the domains that use visual analytics are varied and expanding. Just understanding the complexities of a number of these domains is exciting. Researchers are trying out different visualizations and interactions as well. And of course, the size and variety of data are expanding rapidly. User-centered evaluation in this context is rapidly changing. There are no standard processes and metrics and thus those of us working on user-centered evaluation must be creative in our work with both the users and with the researchers and developers.

intelligence analysis↗

NASA NTRS2018

Overview of the Digitization Workflow Post Image Acquisition of Apollo Lunar and Antarctic Meteorite Samples Using Agisoft Photoscan for the NASA 3D Astromaterials Virtual Samples Collection

The 3D Virtual Astromaterials Samples (3DVAS) collection is a multi-year funded project to create a digital database of sixty Apollo Lunar and Antarctic Meteorite samples following non-destructive documentation conservation protocols. After initial image processing, the photos are evaluated and processed using unique structure-from-motion photogrammetric techniques in a high performance modelling software designed to create a 3D model from 2D images: Agisoft Photoscan Pro. Agisoft Photoscan Pro uses image processing algorithms and techniques originating in computer vision to resolve 3D models for accurate and detailed visualization of a subject. The software provides a stepwise process that is tailored per model based on spatial and specular reflectance properties, for example. The process includes: photo alignment, creation of a dense point cloud, mesh, and finally texture. Photo alignment is dependent on model properties. The 3DVAS process requires a special rotation platform with calibrated photogrammetric targets, specific distance rotation protocols, and a contrasting background for alignment and scale accuracy. As a result of the photographic process, alignment will complete with two mirrored hemispheres that, in a sense, represent the 2D images overlapping to create a 3D model. Each dense point cloud is analyzed with provided statistical measures in a gradual selection process to eliminate outliers. The point cloud is reduced to include only data valuable to the final model. When a precise dense point cloud is achieved, a mesh and texture are applied. Each model is scaled with scale bar accuracies within 100 microns. Each sample has its own intimate process for modelling; there is no standard for the parameters required in the final creation of a high resolution model. By processing multiple samples, a skill is gained in practice to allow a close definition of the original sample and will result in the most detailed version of the sample shell. This process completes one-fifth of the 3DVAS protocol for providing accurate digital documentation. Each model shell is merged with X-ray Computed Tomography data to create a full volumetric sample. All 3DVAS data will be served on NASA's Astromaterials Acquisition and Curation website with an early subset of data available in 2019 and the 3D Virtual Astromaterials Samples Collection launch in 2020.

Thomas, Andi B.↗

NASA NTRS1986

Finite element solver for 3-D compressible viscous flows

The space shuttle main engine (SSME) has extremely complex internal flow structure. The geometry of the flow domain is three-dimensional with complicated topology. The flow is compressible, viscous, and turbulent with large gradients in flow quantities and regions of recirculations. The analysis of the flow field in SSME involves several tedious steps. One is the geometrical modeling of the particular zone of the SSME being studied. Accessing the geometry definition, digitalizing it, and developing surface interpolations suitable for an interior grid generator require considerable amount of manual labor. There are several types of grid generators available with some general-purpose finite element programs. An efficient and robust computational scheme for solving 3D Navier-Stokes equations has to be implemented. Post processing software has to be adapted to visualize and analyze the computed 3D flow field. The progress made in a project to develop software for the analysis of the flow is discussed. The technical approach to the development of the finite element scheme and the relaxation procedure are discussed. The three dimensional finite element code for the compressible Navier-Stokes equations is listed.

Reddy, K. C.↗

DOE OSTI2019

Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases

Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1989

Visualizing large data sets in the earth sciences

The authors describe the capabilities of McIDAS, an interactive visualization system that is vastly increasing the ability of earth scientists to manage and analyze data from remote sensing instruments and numerical simulation models. McIDAS provides animated three-dimensionsal images and highly interactive displays. The software can manage, analyze, and visualize large data sets that span many physical variables (such as temperature, pressure, humidity, and wind speed), as well as time and three spatial dimensions. The McIDAS system manages data from at least 100 different sources. The data management tools consist of data structures for storing different data types in files, libraries of routines for accessing these data structures, system commands for performing housekeeping functions on the data files, and reformatting programs for converting external data to the system's data structures. The McIDAS tools for three-dimensional visualization of meteorological data run on an IBM mainframe and can load up to 128-frame animation sequences into the workstations. A highly interactive version of the system can provide an interactive window into data sets containing tens of millions of points produced by numerical models and remote sensing instruments. The visualizations are being used for teaching as well as by scientists.

Hibbard, William↗

NASA NTRS2004

Overview of Transonic to Hypersonic Stage Separation Tool Development for Multi-Stage-to-Orbit Concepts

An overview of research efforts at NASA in support of the stage separation and ascent aerothermodynamics research program is presented. The objective of this work is to develop a synergistic suite of experimental, computational, and engineering tools and methods to apply to vehicle separation across the transonic to hypersonic speed regimes. Proximity testing of a generic bimese wing-body configuration is on-going in the transonic (Mach numbers 0.6, 1.05, and 1.1), supersonic (Mach numbers 2.3, 3.0, and 4.5) and hypersonic (Mach numbers 6 and 10) speed regimes in four wind tunnel facilities at the NASA Langley Research Center. An overset grid, Navier-Stokes flow solver has been enhanced and demonstrated on a matrix of proximity cases and on a dynamic separation simulation of the bimese configuration. Steady-state predictions with this solver were in excellent agreement with wind tunnel data at Mach 3 as were predictions via a Cartesian-grid Euler solver. Experimental and computational data have been used to evaluate multi-body enhancements to the widely-used Aerodynamic Preliminary Analysis System, an engineering methodology, and to develop a new software package, SepSim, for the simulation and visualization of vehicle motions in a stage separation scenario. Web-based software will be used for archiving information generated from this research program into a database accessible to the user community. Thus, a framework has been established to study stage separation problems using coordinated experimental, computational, and engineering tools.

Murphy, Kelly J.↗

DOE OSTI2019

GRACC: GRid ACcounting Collector

The OSG has long maintained a central accounting system called Gratia. It uses small probes on each computing and storage resource in order to collect resource usage. The probes report to a central collector which stores the usage in a database. The database is then queried to generate reports. As the OSG aged, the size of the database grew very large. It became too large for the database technology to efficiently query to generate detailed reports. The design of a replacement requires data storage that could be queried efficiently to generate multi-year reports. Additionally, it requires flexibilityto add new attributes to the collected data.In this paper we will describe updates to the GRACC architecture in the last 18 months. GRACC uses modern web technologies that were designed for large data storage, query, and visualization. That includes the open source database Elasticsearch, message broker software RabbitMQ, and Grafana and Kibana as data visualization platforms. It uses multiple agents that perform operations on the data to transform it for easier querying and summarization.

Weitzel, Derek↗

NASA NTRS2002

A Unified Overset Grid Generation Graphical Interface and New Concepts on Automatic Gridding Around Surface Discontinuities

For many years, generation of overset grids for complex configurations has required the use of a number of different independently developed software utilities. Results created by each step were then visualized using a separate visualization tool before moving on to the next. A new software tool called OVERGRID was developed which allows the user to perform all the grid generation steps and visualization under one environment. OVERGRID provides grid diagnostic functions such as surface tangent and normal checks as well as grid manipulation functions such as extraction, extrapolation, concatenation, redistribution, smoothing, and projection. Moreover, it also contains hyperbolic surface and volume grid generation modules that are specifically suited for overset grid generation. It is the first time that such a unified interface existed for the creation of overset grids for complex geometries. New concepts on automatic overset surface grid generation around surface discontinuities will also be briefly presented. Special control curves on the surface such as intersection curves, sharp edges, open boundaries, are called seam curves. The seam curves are first automatically extracted from a multiple panel network description of the surface. Points where three or more seam curves meet are automatically identified and are called seam corners. Seam corner surface grids are automatically generated using a singular axis topology. Hyperbolic surface grids are then grown from the seam curves that are automatically trimmed away from the seam corners.

Chan, William M.↗

NASA NTRS2011

A Hyperbolic Ontology Visualization Tool for Model Application Programming Interface Documentation

Spacecraft modeling, a critically important portion in validating planned spacecraft activities, is currently carried out using a time consuming method of mission to mission model implementations and integration. A current project in early development, Integrated Spacecraft Analysis (ISCA), aims to remedy this hindrance by providing reusable architectures and reducing time spent integrating models with planning and sequencing tools. The principle objective of this internship was to develop a user interface for an experimental ontology-based structure visualization of navigation and attitude control system modeling software. To satisfy this, a number of tree and graph visualization tools were researched and a Java based hyperbolic graph viewer was selected for experimental adaptation. Early results show promise in the ability to organize and display large amounts of spacecraft model documentation efficiently and effectively through a web browser. This viewer serves as a conceptual implementation for future development but trials with both ISCA developers and end users should be performed to truly evaluate the effectiveness of continued development of such visualizations.

mission operations system (MOS)↗

NASA NTRS1995

Development of a Prototype Simulation Executive with Zooming in the Numerical Propulsion System Simulation

A major difficulty in designing aeropropulsion systems is that of identifying and understanding the interactions between the separate engine components and disciplines (e.g., fluid mechanics, structural mechanics, heat transfer, material properties, etc.). The traditional analysis approach is to decompose the system into separate components with the interaction between components being evaluated by the application of each of the single disciplines in a sequential manner. Here, one discipline uses information from the calculation of another discipline to determine the effects of component coupling. This approach, however, may not properly identify the consequences of these effects during the design phase, leaving the interactions to be discovered and evaluated during engine testing. This contributes to the time and cost of developing new propulsion systems as, typically, several design-build-test cycles are needed to fully identify multidisciplinary effects and reach the desired system performance. The alternative to sequential isolated component analysis is to use multidisciplinary coupling at a more fundamental level. This approach has been made more plausible due to recent advancements in computation simulation along with application of concurrent engineering concepts. Computer simulation systems designed to provide an environment which is capable of integrating the various disciplines into a single simulation system have been proposed and are currently being developed. One such system is being developed by the Numerical Propulsion System Simulation (NPSS) project. The NPSS project, being developed at the Interdisciplinary Technology Office at the NASA Lewis Research Center is a 'numerical test cell' designed to provide for comprehensive computational design and analysis of aerospace propulsion systems. It will provide multi-disciplinary analyses on a variety of computational platforms, and a user-interface consisting of expert systems, data base management and visualization tools, to allow the designer to investigate the complex interactions inherent in these systems. An interactive programming software system, known as the Application Visualization System (AVS), was utilized for the development of the propulsion system simulation. The modularity of this system provides the ability to couple propulsion system components, as well as disciplines, and provides for the ability to integrate existing, well established analysis codes into the overall system simulation. This feature allows the user to customize the simulation model by inserting desired analysis codes. The prototypical simulation environment for multidisciplinary analysis, called Turbofan Engine System Simulation (TESS), which incorporates many of the characteristics of the simulation environment proposed herein, is detailed.

Reed, John A.↗

NASA NTRS2011

Core Recursive Hierarchical Image Segmentation

The Recursive Hierarchical Image Segmentation (RHSEG) software has been repackaged to provide a version of the RHSEG software that is not subject to patent restrictions and that can be released to the general public through NASA GSFC's Open Source release process. Like the Core HSEG Software Package, this Core RHSEG Software Package also includes a visualization program called HSEGViewer along with a utility program HSEGReader. It also includes an additional utility program called HSEGExtract. The unique feature of the Core RHSEG package is that it is a repackaging of the RHSEG technology designed to specifically avoid the inclusion of the certain software technology. Unlike the Core HSEG package, it includes the recursive portions of the technology, but does not include processing window artifact elimination technology.

Tilton, James↗

DOE OSTI2015

openPMD-viewer

Many simulation software produce data in the form of a set of field values or of a set of particle positions. (one such example is that of particle-in-cell codes, which produce data on the electromagnetic fields that they simulate.) However, each particular software uses its own particular format and layout, for the output data. This makes it difficult to compare the results of different simulation software, or to have a common visualization tool for these results. However, a standardized layout for fields and particles has recently been developed: the openPMD format ( HYPERLINK "http://www.openpmd.org/"www.openpmd.org) This format is open- source, and specifies a standard way in which field data and particle data should be written. The openPMD format is already implemented in the particle-in-cell code Warp (developed at LBL) and in PIConGPU (developed at HZDR, Germany). In this context, the proposed software (openPMD-viewer) is a Python package, which allows to access and visualize any data which has been formatted according to the openPMD standard. This package contains two main components: - a Python API, which allows to read and extract the data from a openPMD file, so as to be able to work with it within the Python environment. (e.g. plot the data and reprocess it with particular Python functions) - a graphical interface, which works with the ipython notebook, and allows to quickly visualize the data and browse through a set of openPMD files. The proposed software will be typically used when analyzing the results of numerical simulations. It will be useful to quickly extract scientific meaning from a set of numerical data.

Lehe, Remi↗

DOE OSTI2015

openPMD-viewer

Lehe, Remi↗

DOE OSTI2020

GNET2: an R package for constructing gene regulatory networks from transcriptomic data

Abstract Motivation The Gene Network Estimation Tool (GNET) is designed to build gene regulatory networks (GRNs) from transcriptomic gene expression data with a probabilistic graphical model. The data preprocessing, model construction and visualization modules of the original GNET software were developed on different programming platforms, which were inconvenient for users to deploy and use. Results Here, we present GNET2, an improved implementation of GNET as an integrated R package. GNET2 provides more flexibility for parameter initialization and regulatory module construction based on the core iterative modeling process of the original algorithm. The data exchange interface of GNET2 is handled within an R session automatically. Given the growing demand for regulatory network reconstruction from transcriptomic data, GNET2 offers a convenient option for GRN inference on large datasets. Availability and implementation The source code of GNET2 is available at https://github.com/jianlin-cheng/GNET2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

ML for microbiomes

The software provides machine learning analysis and visualization to detect patterns in microbiome data, including topic modeling, probabilistic graphical modeling, conventional machine learning methods, and deep learning. The software is written in python and R, it uses some python and R libraries as well as big open-source libraries like sklearn, networkX, pytorch (python), pgmpy (python), and bnlearn (R). It also has a script to use for MALLET and DTM (open-source packages for topic modeling, written in Java).

Kim, Anastasiia↗

NASA NTRS1995

Gravity Sensors and the Role of 3-D Visualization and Simulation in Biomedical Research

Ross 3.0 software was developed in the Biocomputation Center for semi-automated reconstruction of objects from serial thin sections. Data are captured directly from a transmission electron microscope via a video camera to a graphics workstation where the sections are mosaicked and contours are traced, registered and displayed by semi-automated methods. For the first time, macular type II cells are described completely for their innervation patterns. The purposes are to learn more about the fundamental circuitry of the macula and to demonstrate whether the terminals are altered morphologically by space flight. Current examples, from the medial part of the macula, are from maculas collected in-flight on the Space Life Sciences-2 mission, 4.5 hrs post-flight, and from a ground control. Results show that the typical type 11 cell receives processes from up to six nearby calyces or afferents. Nearly all the processes are elongated; some have bouton-like swellings and numerous vesicles. Multiple (2 to 4) processes from a single calyx to a type II cell are common, and approx. 1/3 of the processes innervate 2 type II cells of a neighboring cluster of 3 cells. About 2% of type II cells resemble type I cells morphologically and are surrounded by demicalyces. Differences in size or shape of the terminals under flight conditions could not be determined because the sample size is still too small; but it is clear that reconstruction methods provide insights into macular circuitry not obtainable by other techniques. The results demonstrate a morphological basis for interactions between adjacent receptive fields, through feedback-feedforward connections, during preprocessing of linear acceleratory information by the maculas. While the methods are currently being tested using vestibular maculas as the model system, it is clear that the technology is applicable to any tissue that can be physically or optically sectioned. ROSS software has already been implemented for reconstructing objects from tissues studied by confocal and by transmitted light microscopy, and research into magnetic resonance imaging-computational tomography combined visualization are underway.

Ross, Muriel D.↗