Rice crop phenology mapping at high spatial and temporal resolution using downscaled MODIS time-series

Satellite data holds considerable potential as a source of information on rice crop growth which can be used to inform agronomy. However, given the typical field sizes in many rice-growing countries such as China, data from coarse spatial resolution satellite systems such as the Moderate Resolution Imaging Spectroradiometer (MODIS) are inadequate for resolving crop growth variability at the field scale. Nevertheless, systems such as MODIS do provide images with sufficient frequency to be able to capture the detail of rice crop growth trajectories throughout a growing season. In order to generate high spatial and temporal resolution data suitable for mapping rice crop phenology, this study fused MODIS data with lower frequency, higher spatial resolution Landsat data. An overall workflow was developed which began with image preprocessing, calculation of multi-temporal normalized difference vegetation index (NDVI) images, and spatiotemporal fusion of data from the two sensors. The Spatial and Temporal Adaptive Reflectance Fusion Model was used to effectively downscale the MODIS data to deliver a time-series of 30 m spatial resolution NDVI data at 8-day intervals throughout the rice-growing season. Zonal statistical analysis was used to extract NDVI time-series for individual fields and signal filtering was applied to the time-series to generate rice phenology curves. The downscaled MODIS NDVI products were able to characterize the development of paddy rice at fine spatial and temporal resolutions, across wide spatial extents over multiple growing seasons. These data permitted the extraction of key crop seasonality parameters that quantified inter-annual growth variability for a whole agricultural region and enabled mapping of the variability in crop performance between and within fields. Hence, this approach can provide rice crop growth data that is suitable for informing agronomic policy and practice across a wide range of scales

Mapping of multitemporal rice (Oryza sativa L.) growth stages using remote sensing with multi-sensor and machine learning : a thesis dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Earth Science at Massey University, Manawatū, New Zealand

Figure 2.1 is adapted and re-used under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.Rice (Oryza Sativa) plays a pivotal role in food security for Asian countries, especially in Indonesia. Due to the increasing pressure of environmental changes, such as land use and climate, rice cultivation areas need to be monitored regularly and spatially to ensure sustainable rice production. Moreover, timely information of rice growth stages (RGS) can lead to more efficient of inputs distribution from water, seed, fertilizer, and pesticide. One of the efficient solutions for regularly mapping the rice crop is using Earth observation satellites. Moreover, the increasing availability of open access satellite images such as Landsat-8, Sentinel-1, and Sentinel-2 provides ample opportunities to map continuous and high-resolution rice growth stages with greater accuracy. The majority of the literature has focused on mapping rice area, cropping patterns and relied mainly on the phenology of vegetation. However, the mapping process of RGS was difficult to assess the accuracy, time-consuming, and depended on only one sensor. In this work, we discuss the use of machine learning algorithms (MLA) for mapping paddy RGS with multiple remote sensing data in near-real-time. The study area was Java Island, which is the primary rice producer in Indonesia. This study has investigated: (1) the mapping of RGS using Landsat-8 imagery and different MLAs, and their rigorous performance was evaluated by conducting a multitemporal analysis; (2) the temporal consistency of predicting RGS using Sentinel-2, MOD13Q1, and Sentinel-1 data; (3) evaluating the correlation of local statistics data and paddy RGS using Sentinel-2, PROBA-V, and Sentinel-1 with MLAs. The ground truth datasets were collected from multi-year web camera data (2014-2016) and three months of the field campaign in different regions of Java (2018). The study considered the RGS in the analysis to be vegetative, reproductive, ripening, bare land, and flooding, and MLAs such as support vector machines (SVMs), random forest (RF), and artificial neural network (ANN) were used. The temporal consistency matrix was used to compare the classification maps within three sensor datasets (Landsat-8 OLI, Sentinel-2, and Sentinel-2, MOD13Q1, Sentinel-1) and in four periods (5, 10, 15, 16 days). Moreover, the result of the RGS map was also compared with monthly data from local statistics within each sub-district using cross-correlation analysis. The result from the analysis shows that SVM with a radial base function outperformed the RF and ANN and proved to be a robust method for small-size datasets (< 1,000 points). Compared to Sentinel-2, Landsat-8 OLI gives less accuracy due to the lack of a red-edge band and larger pixel size (30 x 30 m). Integration of Sentinel-2, MOD13Q1, and Sentinel-1 improved the classification performance and increased the temporal availability of cloud-free maps. The integration of PROBA-V and Sentinel-1 improved the classification accuracy from the Landsat-8 result, consistent with the monthly rice planting area statistics at the sub-district level. The western area of Java has the highest accuracy and consistency since the cropping pattern only relied on rice cultivation. In contrast, less accuracy was noticed in the eastern area because of upland rice cultivation due to limited irrigation facilities and mixed cropping. In addition, the cultivation of shallots to the north of Nganjuk Regency interferes with the model predictions because the cultivation of shallots resembles the vegetative phase due to the water banks. One future research idea is the auto-detection of the cropping index in the complex landscape to be able to use it for mapping RGS on a global scale. Detection of the rice area and RGS using Google Earth Engine (GEE) can be an action plan to disseminate the information quickly on a planetary scale. Our results show that the multitemporal Sentinel-1 combined with RF can detect rice areas with high accuracy (>91%). Similarly, accurate RGS maps can be detected by integrating multiple remote sensing (Sentinel-2, Landsat-8 OLI, and MOD13Q1) data with acceptable accuracy (76.4%), with high temporal frequency and lower cloud interference (every 16 days). Overall, this study shows that remote sensing combined with the machine learning methodology can deliver information on RGS in a timely fashion, which is easy to scale up and consistent both in time and space and matches the local statistics. This thesis is also in line with the existing rice monitoring projects such as Crop Monitor, Crop Watch, AMIS, and Sen4Agri to support disseminating information over a large area. To sum up, the proposed workflow and detailed map provide a more accurate method and information in near real-time for stakeholders, such as governmental agencies against the existing mapping method. This method can be introduced to provide accurate information to rice farmers promptly with sufficient inputs such as irrigation, seeds, and fertilisers for ensuring national food security from the shifting planting time due to climate change

Characterising maize and intercropped maize spectral signatures for cropping pattern classification

Intercropping – the planting of more than one crop in the same plot of land – is a prevalent agricultural management practice which can be used for risk reduction. Despite its widespread use, intercropping is not commonly reported in agricultural statistics, resulting to very limited spatially disaggregated information about its prevalence. Remote sensing-based approaches to detect and estimate the area of cropping patterns like intercropping require good understanding of the spectral response of (intercropped) crops at different crop growth phases. This study integrates field surveys, farmer interviews and temporal Sentinel-2 data from four crop growth phases and the post-harvest period of maize and intercropped maize (imaize). The goal is to identify the optimal crop growth phases, spectral regions and vegetation indices (VIs) that can accurately discriminate the two cropping patterns. We computed p-values for the spectral bands using Mann-Whitney U test and identified critical crop growth phases. Classification of maize and imaize cropping patterns was performed using random forest classifier. Our spectral analysis revealed effective discrimination between maize and imaize cropping patterns during the vegetative (in all spectral bands) and flowering-yield phases (in Blue, Green, Red, RE704, RE783, NIR833, NIR865). The most suitable VIs contained red-edge and near-infrared spectal bands. Utilizing spectral data and VIs from vegetative and flowering-yield phases, we achieved optimal discrimination during the vegetative phase (user’s accuracy of 100 % and producer’s accuracy of 100 %). However, accuracy decreased during the flowering yield phase (overall accuracy of 87 % for all spectral bands). The highest classification results using all spectral bands at the flowering yield phase resulted in 80 % producer’s accuracy for maize and 100 % for imaize. This study illustrates the utility of temporal Sentinel-2 spectral data for identifying the critical crop growth phase, spectral regions and VIs for cropping patterns classification, particularly for intercropping

National wetland mapping in China: a new product resulting from object-based and hierarchical classification of Landsat 8 OLI images

Spatially and thematically explicit information of wetlands is important to understanding ecosystem functions and services, as well as for establishment of management policy and implementation. However, accurate wetland mapping is limited due to lacking an operational classification system and an effective classification approach at a large scale. This study was aimed to map wetlands in China by developing a hybrid object-based and hierarchical classification approach (HOHC) and a new wetland classification system for remote sensing. Application of the hybrid approach and the wetland classification system to Landsat 8 Operational Land Imager data resulted in a wetland map of China with an overall classification accuracy of 95.1%. This national scale wetland map, so named CAS_Wetlands, reveals that China’s wetland area is estimated to be 451,084 ± 2014 km2, of which 70.5% is accounted by inland wetlands. Of the 14 sub-categories, inland marsh has the largest area (152,429 ± 373 km2), while coastal swamp has the smallest coverage (259 ± 15 km2). Geospatial variations in wetland areas at multiple scales indicate that China’s wetlands mostly present in Tibet, Qinghai, Inner Mongolia, Heilongjiang, and Xinjiang Provinces. This new map provides a new baseline data to establish multi-temporal and continuous datasets for China’s wetlands and biodiversity conservation

Crop growth and yield monitoring in smallholder agricultural systems:a multi-sensor data fusion approach

Smallholder agricultural systems are highly vulnerable to production risks posed by the intensification of extreme weather events such as drought and flooding, soil degradation, pests, lack of access to agricultural inputs, and political instability. Monitoring the spatial and temporal variability of crop growth and yield is crucial for farm management, national-level food security assessments, and famine early warning. However, agricultural monitoring is difficult in fragmented agricultural landscapes because of scarcity and uncertainty of data to capture small crop fields. Traditional pre- and post-harvest crop monitoring and yield estimation based on fieldwork is costly, slow, and can be unrepresentative of heterogeneous agricultural landscapes as found in smallholder systems in sub-Saharan Africa. Devising accurate and timely crop phenology detection and yield estimation methods can improve our understanding of the status of crop production and food security in these regions.Satellite-based Earth observation (EO) data plays a key role in monitoring the spatial and temporal variability of crop growth and yield over large areas. The small field sizes and variability in management practices in fragmented landscapes requires high spatial and high temporal resolution EO data. This thesis develops and demonstrates methods to investigate the spatiotemporal variability of crop phenology detection and yield estimation using Landsat and MODIS data fusion in smallholder agricultural systems in the Lake Tana sub-basin of Ethiopia. The overall aim is to further broaden the application of multi-sensor EO data for crop growth monitoring in smallholder agricultural systems.The thesis addressed two important aspects of crop monitoring applications of EO data: phenology detection and yield estimation. First, the ESTARFM data fusion workflow was modified based on local knowledge of crop calendars and land cover to improve crop phenology monitoring in fragmented agricultural landscapes. The approach minimized data fusion uncertainties in predicting temporal reflectance change of crops during the growing season and the reflectance value of fused data was comparable to the original Landsat image reserved for validation. The main sources of uncertainty in data fusion are the small field size and abrupt crop growth changes between the base andviiprediction dates due to flooding, weeding, fertiliser application, and harvesting. The improved data fusion approach allowed us to determine crop phenology and estimate LAI more accurately than both the standard ESTARFM data fusion method and when using MODIS data without fusion. We also calibrated and validated a dynamic threshold phenology detection method using maize and rice crop sowing and harvest date information. Crop-specific phenology determined from data fusion minimized the mismatch between EO-derived phenometrics and the actual crop calendar. The study concluded that accurate phenology detection and LAI estimation from Landsat–MODIS data fusion demonstrates the feasibility of crop growth monitoring using multi-sensor data fusion in fragmented and persistently cloudy agricultural landscapes.Subsequently, the validated data fusion and phenology detection methods were implemented to understand crop phenology trends from 2000 to 2020. These trends are often less understood in smallholder agricultural systems due to the lack of high spatial resolution data to distinguish crops from the surrounding natural vegetation. Trends based on Landsat–MODIS fusion were compared with those detected using MODIS alone to assess the contribution of data fusion to discern crop phenometric change. Landsat and MODIS fusion discerned crop and environment-specific trends in the magnitude and direction of crop phenology change. The results underlined the importance of high spatial and temporal resolution EO data to capture environment-specific crop phenology change, which has implications in designing adaptation and crop management practices in these regions.The second important aspect of the crop monitoring problem addressed in this thesis is improving crop yield estimation in smallholder agricultural systems. The large input requirements of crop models and lack of spatial information about the heterogeneous crop-growing environment and agronomic management practices are major challenges to the accurate estimation of crop yield. We assimilated leaf area index (LAI) and phenology information from Landsat–MODIS fusion in a crop model (simple algorithm for yield estimation: SAFY) to obtain reasonably reliable crop yield estimates. The SAFY model is sensitive to the spatial and temporal resolution of the calibration input LAI, phenology information, and the effective light use efficiency (ELUE) parameter, which needs accurate field level inputs during modelviiioptimization. Assimilating fused EO-based phenology information minimized model uncertainty and captured the large management and environmental variation in smallholder agricultural systems.In the final research chapter of the thesis, we analysed the contribution of assimilating LAI at different phenological stages. The frequency and timing of LAI observations influences the retrieval accuracy of the assimilating LAI in crop growth simulation models. The use of (optical) EO data to estimate LAI is constrained by limited repeat frequency and cloud cover, which can reduce yield estimation accuracy. We evaluated the relative contribution of EO observations at different crop growth stages for accurate calibration of crop model parameters. We found that LAI between jointing and grain filling has the highest contribution to SAFY yield estimation and that the distribution of LAI during the key development stages was more useful than the frequency of LAI to improve yield estimation. This information on the optimal timing of EO data assimilation is important to develop better in-season crop yield forecasting in smallholder systems

Rice crop classification and yield estimation using multi-temporal sentinel-2 data: a case study of Terai districts of Nepal

Dissertation submitted in partial fulfilment of the requirements for the degree of Master of Science in Geospatial TechnologiesCrop monitoring, especially in developing countries, can improve food production, address food security issues, and support sustainable development goals. Crop type mapping and yield estimation are the two major aspects of crop monitoring that remain challenging due to the problem of timely and adequate data availability. Existing approaches rely on ground-surveys and traditional means which are time-consuming and costly. In this context, we introduce the use of freely available Sentinel-2 (S2) imagery with high spatial, spectral and temporal resolution to classify crop and estimate its yield through a deep learning approach. In particular, this study uses patch-based 2D and 3D Convolutional Neural Network (CNN) algorithms to map rice crop and predict its yield in the Terai districts of Nepal. Firstly, the study reviews the existing state-of-art technologies in this field and selects suitable CNN architectures. Secondly, the selected architectures are implemented and trained using S2 imagery, groundtruth and auxiliary data in addition for yield estimation.We also introduce a variation in the chosen 3D CNN architecture to enhance its performance in estimating rice yield. The performance of the models is validated and then evaluated using performance metrics namely overall accuracy and F1-score for classification and Root Mean Squared Error (RMSE) for yield estimation. In consistency with the existing works, the results demonstrate recommendable performance of the models with remarkable accuracy, indicating the suitability of S2 data for crop mapping and yield estimation in developing countries. Reproducibility self-assessment (https://osf.io/j97zp/): 2, 2, 2, 1, 2 (input data, preprocessing, methods, computational environment, results)

Big Earth Data and Machine Learning for Sustainable and Resilient Agriculture

Big streams of Earth images from satellites or other platforms (e.g., drones and mobile phones) are becoming increasingly available at low or no cost and with enhanced spatial and temporal resolution. This thesis recognizes the unprecedented opportunities offered by the high quality and open access Earth observation data of our times and introduces novel machine learning and big data methods to properly exploit them towards developing applications for sustainable and resilient agriculture. The thesis addresses three distinct thematic areas, i.e., the monitoring of the Common Agricultural Policy (CAP), the monitoring of food security and applications for smart and resilient agriculture. The methodological innovations of the developments related to the three thematic areas address the following issues: i) the processing of big Earth Observation (EO) data, ii) the scarcity of annotated data for machine learning model training and iii) the gap between machine learning outputs and actionable advice. This thesis demonstrated how big data technologies such as data cubes, distributed learning, linked open data and semantic enrichment can be used to exploit the data deluge and extract knowledge to address real user needs. Furthermore, this thesis argues for the importance of semi-supervised and unsupervised machine learning models that circumvent the ever-present challenge of scarce annotations and thus allow for model generalization in space and time. Specifically, it is shown how merely few ground truth data are needed to generate high quality crop type maps and crop phenology estimations. Finally, this thesis argues there is considerable distance in value between model inferences and decision making in real-world scenarios and thereby showcases the power of causal and interpretable machine learning in bridging this gap.Comment: Phd thesi

Remote Sensing of Surface Water Dynamics in the Context of Global Change - A Review

Inland surface water is often the most accessible freshwater source. As opposed to groundwater, surface water is replenished in a comparatively quick cycle, which makes this vital resource—if not overexploited—sustainable. From a global perspective, freshwater is plentiful. Still, depending on the region, surface water availability is severely limited. Additionally, climate change and human interventions act as large-scale drivers and cause dramatic changes in established surface water dynamics. Actions have to be taken to secure sustainable water availability and usage. This requires informed decision making based on reliable environmental data. Monitoring inland surface water dynamics is therefore more important than ever. Remote sensing is able to delineate surface water in a number of ways by using optical as well as active and passive microwave sensors. In this review, we look at the proceedings within this discipline by reviewing 233 scientific works. We provide an extensive overview of used sensors, the spatial and temporal resolution of studies, their thematic foci, and their spatial distribution. We observe that a wide array of available sensors and datasets, along with increasing computing capacities, have shaped the field over the last years. Multiple global analysis-ready products are available for investigating surface water area dynamics, but so far none offer high spatial and temporal resolution

Climate Change and Environmental Sustainability-Volume 4

Anthropogenic activities are significant drivers of climate change and environmental degradation. Such activities are particularly influential in the context of the land system that is an important medium connecting earth surface, atmospheric dynamics, ecological systems, and human activities. Assessment of land use land cover changes and associated environmental, economic, and social consequences is essential to provide references for enhancing climate resilience and improving environmental sustainability. On the one hand, this book touches on various environmental topics, including soil erosion, crop yield, bioclimatic variation, carbon emission, natural vegetation dynamics, ecosystem and biodiversity degradation, and habitat quality caused by both climate change and earth surface modifications. On the other hand, it explores a series of socioeconomic facts, such as education equity, population migration, economic growth, sustainable development, and urban structure transformation, along with urbanization. The results of this book are of significance in terms of revealing the impact of land use land cover changes and generating policy recommendations for land management. More broadly, this book is important for understanding the interrelationships among life on land, good health and wellbeing, quality education, climate actions, economic growth, sustainable cities and communities, and responsible consumption and production according to the United Nations Sustainable Development Goals. We expect the book to benefit decision makers, practitioners, and researchers in different fields, such as climate governance, crop science and agricultural engineering, forest ecosystem, land management, urban planning and design, urban governance, and institutional operation.Prof. Bao-Jie He acknowledges the Project NO. 2021CDJQY-004 supported by the Fundamental Research Funds for the Central Universities and the Project NO. 2022ZA01 supported by the State Key Laboratory of Subtropical Building Science, South China University of Technology, China. We appreciate the assistance of Mr. Lifeng Xiong, Mr. Wei Wang, Ms. Xueke Chen, and Ms. Anxian Chen at School of Architecture and Urban Planning, Chongqing University, China

Monitoring wetlands and water bodies in semi-arid Sub-Saharan regions

Surface water in wetlands is a critical resource in semi-arid West-African regions that are frequently exposed to droughts. Wetlands are of utmost importance for the population as well as the environment, and are subject to rapidly changing seasonal fluctuations. Dynamics of wetlands in the study area are still poorly understood, and the potential of remote sensing-derived information as a large-scale, multi-temporal, comparable and independent measurement source is not exploited. This work shows successful wetland monitoring with remote sensing in savannah and Sahel regions in Burkina Faso, focusing on the main study site Lac Bam (Lake Bam). Long-term optical time series from MODIS with medium spatial resolution (MR), and short-term synthetic aperture radar (SAR) time series from TerraSAR-X and RADARSAT-2 with high spatial resolution (HR) successfully demonstrate the classification and dynamic monitoring of relevant wetland features, e.g. open water, flooded vegetation and irrigated cultivation. Methodological highlights are time series analysis, e.g. spatio-temporal dynamics or multitemporal-classification, as well as polarimetric SAR (polSAR) processing, i.e. the Kennaugh elements, enabling physical interpretation of SAR scattering mechanisms for dual-polarized data. A multi-sensor and multi-frequency SAR data combination provides added value, and reveals that dual-co-pol SAR data is most recommended for monitoring wetlands of this type. The interpretation of environmental or man-made processes such as water areas spreading out further but retreating or evaporating faster, co-occurrence of droughts with surface water and vegetation anomalies, expansion of irrigated agriculture or new dam building, can be detected with MR optical and HR SAR time series. To capture long-term impacts of water extraction, sedimentation and climate change on wetlands, remote sensing solutions are available, and would have great potential to contribute to water management in Africa