Engineering topics

Li, Shuang

Publications and source records attributed to Li, Shuang.

16 records

DOE OSTI2024

RNA-Puzzles Round V: blind predictions of 23 RNA structures

RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between prediction and experiment. Our analyses reveal some critical steps to be overcome to achieve good accuracy in modeling RNA structures: identification of helix-forming pairs and of non-Watson–Crick modules, correct coaxial stacking between helices and avoidance of entanglements. Three of the top four modeling groups in this round also ranked among the top four in the CASP15 contest.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2019

Transfer Learning to Generate True Color Images from GOES-16

Along with scientific applications, Geostationary imagery is often used to learn about weather patterns through true color visualizations. NOAA/NASA's GOES-R series of satellites uses the advanced baseline imager with 16-bands which, unlike previous generations, does not include the green wavelength (500-565 nm) and hence cannot directly generate true color images. However, Himawari, Japan's geostationary satellite, uses a similar 16-band advanced Himawari imager that does include a green band (but missing cirrus). In this work, we show how transfer learning with convolutional neural networks can be applied across satellites to generate "virtual sensors". We apply this approach to generate a green band for GOES-16 and present near true color images.

transfer learning↗

NASA NTRS2019

Surface Reflectance Product from Geostationary Satellite

We have generated provisional Himawari-8 AHI surface reflectance (SR) product for land and vegetation monitoring. The Himawari-8 AHI surface reflectance product is part of our GeoNEX land products, which integrate level 2 and higher remote sensing data from a set of geostationary satellite sensors (i.e. GOES-16, -17 ABI, Himawari-8 AHI, FY4-A AGRI, and MTG-I). Adapted Multiangle Implementation of Atmospheric Correction (MAIAC) algorithm is used to process time series Himawari-8 AHI observations. Himawari-8 AHI SR provides gridded and tiled land SR in 1-km resolution with high frequency (every 10 minutes during daylight time). There are three subdatasets: 1) retrieved atmospheric properties (e.g. column water vapor at 0.86 m, aerosol optical depth at 0.47m and 0.51m); 2) spectral (AHI bands 1-6) surface reflectance, kernels of RTLS BRDF model; 3)spectral BRDF kernel weights, and extensive quality assurance flags. The evaluation results show that Himawari-8 AHI data yield much more valid pixels in a single day in the characterization of land surface, when compare to NASA flagship satellite MODIS Terra/Aqua. This observation frequency and resolution of geostationary data should allow for using continuous ecosystem monitoring in diurnal studies at continental scale. Initial evaluations indicate a stable Himawari-8 AHI land SR product.

Li, Shuang↗

NASA NTRS2019

Generating Accurate and Consistent Top-Of-Atmosphere Reflectance Products from the New Generation Geostationary Satellite Sensors

GeoNEX is a collaborative project by scientists from NASA, NOAA, JAXA, and other organizations around the world with the purpose of generating a suite of Earth-monitoring products using data streams from the latest geostationary (GEO) sensors including the GOES-16/17 ABI and the Himawari-8/9 AHI. An accurate and consistent top-of-atmosphere (TOA) reflectance product, in particular the bidirectional reflectance factor (BRF), is the starting point in the scientific processing chain. We describe the main considerations and corresponding algorithms in generating the GeoNEX TOA BRF product. First, a special advantage of geostationary data streams is their high temporal resolution (~10 minutes per full-disk scan), providing a key source of information for many downstream products. To fully utilize this high temporal frequency demands a high georegistration accuracy for every acquired image. Our analysis shows that there can be substantial georegistration uncertainties in both GOES and Himawari L1b data which we addressed by implementing a phase-based correction algorithm to remove residual errors. Second, geostationary sensors have distinct illumination-view geometry features in that the solar angle changes for every pixel. Therefore, to accurately derive a BRF requires a solar position algorithm and the estimation of the pixel-wise acquisition time within an uncertainty of 10 seconds. Third, we discuss the measures we adopted to check and correct residual radiometric calibration issues of individual sensors to enable time-series analysis as well as the cross calibration between different satellite sensors (including those from low-Earth orbit). Finally, we also explain the rationale for the choice of the global grid/tile system of the GeoNEX TOA BRF product.

Wang, Weile↗

NASA NTRS2019

Deep Learning Emulation of Atmospheric Correction for Geostationary Sensors

New generation geostationary satellites make reflectance observations available at a continental scale with unprecedented spatiotemporal resolution and spectral range. Generating Earth monitoring products from these observations requires retrieval of the basic parameter, surface reflectance (SR), by atmospheric correction (AC). Algorithms for atmospheric correction, including Multi-Angle Implementation of Atmospheric Correction (MAIAC), are adapted for each sensor and are too computationally complex to be run in real time, relying instead on look-up tables with precomputed values. Machine learning methods, including convolutional neural networks, have demonstrated performance in learning complex, nonlinear mappings and extracting insight from high-dimensional remote sensing data. In this work, we present a deep learning emulator of MAIAC to retrieve both SR and cloud products. Using this adaptation of deep learning-based emulation to remote sensing, we demonstrate stable SR retrieval over a variety of land covers and viewing conditions and accurate cloud detection. Further, a comparison of computation time suggests emulation as a compelling alternative for expensive physical simulation, especially for applications benefited by near-real time data, such as agricultural management and disaster response.

Duffy, Kate↗

NASA NTRS2018

GEONEX: Challenges in Producing MODIS-Like Land Products from a New Generation of Geostationary Sensors

The new generation geostationary (GEO) remote sensors (GOES-R ABI, Himawari AHI, and FY4 AGRI) provide high frequency (5-15 minute) observations spatially/spectrally similar to MODIS/VIIRS for land monitoring. These new features of GEO satellite sensors make producing MODIS like land products for terrestrial monitoring possible. The NASA Earth Exchange (NEX) team developed the GEONEX pipeline that is containerized, deployable on NASA Pleiades supercomputer as well as public cloud platforms (e.g. AWS). The processing pipeline is designed to take Himawari Standard Data (HSD) and GOES-16 L1b to generate surface reflectance (SR) and other high-level land remote sensing products. In order to produce low-Earth-orbiting (LEO) remote sensing compatible land products, inter-comparison between Himawari AHI and MODIS Terra/Aqua has been conducted in this research work. Comparisons of TOA reflectance and surface reflectance between AHI and Terra/Aqua are presented. Ray-Matching method was used to locate the co-located pixels, where GEO and LEO sensors look at the land target with similar Viewing Zenith Angle (VZA) and Viewing Azimuth Angle (VAA) simultaneously. Here, we address challenges associated with the selection of qualified pixels of similar solar illumination condition and atmosphere path. We used strict criterion to constrain the pixel selection: the time difference between GEO and LEO observations is less than +-2.5 mins, the cosine of VZA difference is less than 1%, and the VAA difference is less than 10 deg. We also discuss the strong radiometric consistency that the new generation GEO sensors along with the popular LEO sensors would benefit the environmental remote sensing community.

Li, Shuang↗

NASA NTRS2018

Land Surface Reflectances from Geostationary Sensors

GEONEX is a processing pipeline that produces a suite of satellite land surface products using data streams from the latest geostationary (GEO) sensors including the GOES016/ABI and the Himawari-8/AHI. The suite, created collaboratively by scientists from NASA and NOAA, includes top-of-atmosphere (TOA) reflectances, land surface reflectances (LSRs), vegetation indices, LAI/fPAR, and other downstream products. As a key component of the GEONEX product processing, we have adapted the Multi-Angle Implementation of Atmospheric Correction (MAIAC) algorithm to produce LSRs from the TOA data. Because the algorithm depends on building "stacks" of images, we first run internal geo-registration checks to ensure geo-spatial accuracy and consistency of the input (L1B) data before transferring them from the geostationary projection into a tile system in geographic grids. Scan-time is inferred from metadata and applied to calculate the sun-sensor angles for each grid cell. The MAIAC algorithm is run to detect clouds/shadows, estimate aerosol optical thickness (AOT), perform atmospheric corrections, and generate LSRs. We have processed 18-months (from 2016/04 onward) of AHI data over East Asia and Oceania at a 10-minute time step and 10-months (from 2018/01 onward) of ABI data over North and South Americas at a 15-minute time step. As a verification measure, we compare the GEONEX (AHI/ABI) surface reflectances with the standard MODIS products (MOD09GA) and the MODIS MAIAC products over pixels that have similar sun-view geometries. The results indicate general linear relationships between GEONEX and corresponding MODIS LSRs. In particular, the RMSEs between GEONEX and MOD09 data are comparable to those between MOD09 and MODIS MAIAC products, suggesting that the uncertainties of GEONEX LSRs fall into an acceptable range. However, direct comparisons of LSRs over pixels with different sun-view angles are not as straightforward and require more modeling efforts to correct the directional effects. Evaluation of such angular influences on the downstream products (e.g., vegetation indices) is also under investigation.

Geostationary satellite; Remote Sensing; Atmospher↗

NASA NTRS2018

GEONEX: Progressive Conditional Generative Adversarial Training Using Transfer learning

Obtaining accurate segmentation on large scale images is an open problem in deep learning. The main problem is the amount of labeled data that exists for large scale images. Traditionally, the common solution to this problem is to crop the large images into smaller images to increase the amount of available data and train a Conditional Generative Adversarial Network (CGAN). CGANs are currently the state of the art in image to image translation and provide better accuracy than the traditional method of training a encoder based conv-net architecture to minimize the loss at each pixel. This method can produce noisy and discontinuous images with inaccurate results. We seek to solve this problem by utilizing the concepts of transfer learning and progressive training to create a CGAN that can segment large scale images with a limited amount of labeled data. In transfer learning we recognize that many learned features are applicable to many classes from multiple domains. This introduces the concept of feature reusability, which is the basis for finetuning. Progressive training got its start in training models on the same images at different resolutions. In this work we instead train a GAN on increasing image scales by transferring the weights from the smaller scales to the larger scales. The learned features at the smaller scales are continually reused and applied to larger scales to create a CGAN that can perform accurate segmentation on large scale images. We apply this method to detect building footprints on very high-resolution overhead imagery (e.g Digital Globe and high resolution airborne platforms).

GEONEX↗

NASA NTRS2018

GEONEX: Webpage to Display NASA-NOAA Collaboration of Producing Land Surface Products from Geostationary Sensors

The latest generation of geostationary satellites carry sensors such as the Advanced Baseline Imager (GOES-16/17) and the Advanced Himawari Imager (Himawari-8/9) that closely mimic the spatial and spectral characteristics of MODIS and VIIRS, useful for monitoring land surface conditions. The NASA Earth Exchange (NEX) team at Ames Research Center has embarked on a collaborative effort among scientists from NASA and NOAA exploring the feasibility of producing operational land surface products similar to those from MODIS/VIIRS. The team built a processing pipeline called GEONEX that is capable of converting raw geostationary data into routine products of Fires, surface reflectances, vegetation indices, LAI/FPAR, ET and GPP/NPP using algorithms adapted from both NASA/EOS and NOAA/GOES-R programs. The GEONEX pipeline has been deployed on Amazon Web Services cloud platform and it currently leverages near-realtime geostationary data hosted in AWS public datasets under a NOAA-AWS agreement.In order to better introduce the GEONEX products to the science community, we set up a simple webpage (www.geonex.org) to describe the background and the motivation of the project, the algorithms used in deriving the products, and user manuals to the data files. We will also update the status of the data processing, in particular the near-real-time products, on the website and provide links (in text or json files) to the latest datasets.

geostationary↗

NASA NTRS2017

H31G-1596: DeepSAT's CloudCNN: A Deep Neural Network for Rapid Cloud Detection from Geostationary Satellites

Cloud and cloud shadow detection has important applications in weather and climate studies. It is even more crucial when we introduce geostationary satellites into the field of terrestrial remote sensing. With the challenges associated with data acquired in very high frequency (10-15 mins per scan), the ability to derive an accurate cloud shadow mask from geostationary satellite data is critical. The key to the success for most of the existing algorithms depends on spatially and temporally varying thresholds,which better capture local atmospheric and surface effects.However, the selection of proper threshold is difficult and may lead to erroneous results. In this work, we propose a deep neural network based approach called CloudCNN to classify cloudshadow from Himawari-8 AHI and GOES-16 ABI multispectral data. DeepSAT's CloudCNN consists of an encoderdecoder based architecture for binary-class pixel wise segmentation. We train CloudCNN on multi-GPU Nvidia Devbox cluster, and deploy the prediction pipeline on NASA Earth Exchange (NEX) Pleiades supercomputer. We achieved an overall accuracy of 93.29% on test samples. Since, the predictions take only a few seconds to segment a full multispectral GOES-16 or Himawari-8 Full Disk image, the developed framework can be used for real-time cloud detection, cyclone detection, or extreme weather event predictions.

GOES-1↗

NASA NTRS2017

GEONEX: Land Monitoring From a New Generation of Geostationary Satellite Sensors

The latest generation of geostationary satellites carry sensors such as ABI (Advanced Baseline Imager on GOES-16) and the AHI (Advanced Himawari Imager on Himawari) that closely mimic the spatial and spectral characteristics of Earth Observing System flagship MODIS for monitoring land surface conditions. More importantly they provide observations at 5-15 minute intervals. Such high frequency data offer exciting possibilities for producing robust estimates of land surface conditions by overcoming cloud cover, enabling studies of diurnally varying local-to-regional biosphere-atmosphere interactions, and operational decision-making in agriculture, forestry and disaster management. But the data come with challenges that need special attention. For instance, geostationary data feature changing sun angle at constant view for each pixel, which is reciprocal to sun-synchronous observations, and thus require careful adaptation of EOS algorithms. Our goal is to produce a set of land surface products from geostationary sensors by leveraging NASA's investments in EOS algorithms and in the data/compute facility NEX. The land surface variables of interest include atmospherically corrected surface reflectances, snow cover, vegetation indices and leaf area index (LAI)/fraction of photosynthetically absorbed radiation (FPAR), as well as land surface temperature and fires. In order to get ready to produce operational products over the US from GOES-16 starting 2018, we have utilized 18 months of data from Himawari AHI over Australia to test the production pipeline and the performance of various algorithms for our initial tests. The end-to-end processing pipeline consists of a suite of modules to (a) perform calibration and automatic georeference correction of the AHI L1b data, (b) adopt the Multi-Angle Implementation of Atmospheric Correction (MAIAC) algorithm to produce surface spectral reflectances along with compositing schemes and QA, and (c) modify relevant EOS retrieval algorithms (e.g., LAI and FPAR, GPP, etc.) for subsequent science product generation. Initial evaluation of Himawari AHI products against standard MODIS products indicate general agreement, suggesting that data from geostationary sensors can augment low earth orbit (LEO) satellite observations.

geostationary↗

NASA NTRS2017

Very High Resolution Tree Cover Mapping for Continental United States using Deep Convolutional Neural Networks

Uncertainties in input land cover estimates contribute to a significant bias in modeled above ground biomass (AGB) and carbon estimates from satellite-derived data. The resolution of most currently used passive remote sensing products is not sufficient to capture tree canopy cover of less than ca. 10-20 percent, limiting their utility to estimate canopy cover and AGB for trees outside of forest land. In our study, we created a first of its kind Continental United States (CONUS) tree cover map at a spatial resolution of 1-m for the 2010-2012 epoch using the USDA NAIP imagery to address the present uncertainties in AGB estimates. The process involves different tasks including data acquisition ingestion to pre-processing and running a state-of-art encoder-decoder based deep convolutional neural network (CNN) algorithm for automatically generating a tree non-tree map for almost a quarter million scenes. The entire processing chain including generation of the largest open source existing aerial satellite image training database was performed at the NEX supercomputing and storage facility. We believe the resulting forest cover product will substantially contribute to filling the gaps in ongoing carbon and ecological monitoring research and help quantifying the errors and uncertainties in derived products.

High Resolution↗

NASA NTRS2017

Generating Land Surface Reflectance for the New Generation of Geostationary Satellite Sensors with the MAIAC Algorithm

The latest generation of geostationary satellite sensors, including the GOES-16/ABI and the Himawari 8/AHI, provide exciting capability to monitor land surface at very high temporal resolutions (5-15 minute intervals) and with spatial and spectral characteristics that mimic the Earth Observing System flagship MODIS. However, geostationary data feature changing sun angles at constant view geometry, which is almost reciprocal to sun-synchronous observations. Such a challenge needs to be carefully addressed before one can exploit the full potential of the new sources of data. Here we take on this challenge with Multi-Angle Implementation of Atmospheric Correction (MAIAC) algorithm, recently developed for accurate and globally robust applications like the MODIS Collection 6 re-processing. MAIAC first grids the top-of- atmosphere measurements to a fixed grid so that the spectral and physical signatures of each grid cell are stacked (“remembered”) over time and used to dramatically improve cloud/shadow/snow detection, which is by far the dominant error source in the remote sensing. It also exploits the changing sun-view geometry of the geostationary sensor to characterize surface BRDF with augmented angular resolution for accurate aerosol retrievals and atmospheric correction. The high temporal resolutions of the geostationary data indeed make the BRDF retrieval much simpler and more robust as compared with sun-synchronous sensors such as MODIS. As a prototype test for the geostationary-data processing pipeline on NASA Earth Exchange (GEONEX), we apply MAIAC to process 18 months of data from Himawari 8/AHI over Australia. We generate a suite of test results, including the input TOA reflectance and the output cloud mask, aerosol optical depth (AOD), and the atmospherically-corrected surface reflectance for a variety of geographic locations, terrain, and land cover types. Comparison with MODIS data indicates a general agreement between the retrieved surface reflectance products. Furthermore, the geostationary results satisfactorily capture the movement of clouds and variations in atmospheric dust/aerosol concentrations, suggesting that high quality land surface and vegetation datasets from the advanced geostationary sensors can help complement and improve the corresponding EOS products.

geostationary satellite sensors↗

NASA NTRS2016

The Sentinel-2 MSI Can Increase the Temporal Resolution of 30m Satellite-Derived LAI Estimates

The successful launch of the European Space Agency (ESA) Sentinel-2A (S2-A) on 23 June 2015 with its MultiSpectral Instrument (MSI) provides an important means to augment Earth-observation capabilities following the legacy of Landsat. After the three-month satellite commissioning campaign, the MSI onboard S-2A is performing very well (ESA, 2015). By 3 December 2015, the sensor data records have achieved provisional maturity status and have been accessed in level-1C Top-Of-Atmosphere (TOA) reflectance by the remote sensing community worldwide. Near-nadir observations by the MSI onboard S-2A and the Operational Land Imager (OLI) onboard Landsat 8 were collected during Simultaneous Nadir Overpasses as well as nearly coincident overpasses. This paper presents a processing chain using harmonized S-2A MSI and Landsat 8 OLI sensors to obtain increased temporal resolution in Leaf Area Index (LAI) estimates using the red-edge band B8A of MSI to replace the NIR band B08. Results demonstrate that LAI estimates from the MSI and OLI are comparable, and, given sufficient preprocessing for atmospheric correction and geometric rectification, can be used interchangeably to improve the frequency with which low LAI canopies can be monitored.

Dungan, Jennifer L.↗

NASA NTRS2014

High Resolution Mapping of Soils and Landforms for the Desert Renewable Energy Conservation Plan (DRECP)

The Desert Renewable Energy Conservation Plan (DRECP), a major component of California's renewable energy planning efforts, is intended to provide effective protection and conservation of desert ecosystems, while allowing for the sensible development of renewable energy projects. This NASA mapping report was developed to support the DRECP and the Bureau of Land Management (BLM). We outline in this document remote sensing image processing methods to deliver new maps of biological soils crusts, sand dune movements, desert pavements, and sub-surface water sources across the DRECP area. We focused data processing first on the largely unmapped areas most likely to be used for energy developments, such as those within Renewable Energy Study Areas (RESA) and Solar Energy Zones (SEZs). We used imagery (multispectral and radar) mainly from the years 2009-2011.

Mapping↗

NASA NTRSDate not supplied

GeoNEX: A geostationary earth observatory at NASA Earth eXchange: Earth monitoring from operational geostationary satellite systems

The latest generation of geostationary satellites (Himawari 8/9, GOES-16/17, FY-4, GK-2A) carries sensors that closely mimic the spatial and spectral characteristics of widely used polar-orbiting, global monitoring sensors such as MODIS and VIIRS. When combined, data from various currently operating/planned geostationary platforms provide a geo-ring of hyper-temporal (5-10 minutes), multispectral observations at spatial resolutions as high as 500 m. These high frequency observations offer exciting new possibilities for monitoring our planet, including better retrievals of geophysical variables by overcoming cloud cover, enabling studies of diurnally varying phenomena in the atmosphere, land, and the oceans, and support operational decision-making in agriculture, hydrology and disaster management. The NASA Earth Exchange (NEX) team, in collaboration with scientists from JAXA, KARI, NOAA and other international institutions, created the GeoNEX (www.nasa.gov/geonex) pipeline to integrate data from all available geostationary platforms and produce and distribute spatially, temporally, and radiometrically consistent data for the earth science community. We envision various institutions adapting the Geo component (e.g., GeoNOAA, GeoKARI, GeoChiba, GeoJAXA, GeoCMA) and customizing the pipeline and downstream products to serve the local/regional research and applied science communities.

Ramakrishna R Nemani↗