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

Applications of satellite ‘hyper-sensing’ in Chinese agriculture:Challenges and opportunities

Ensuring adequate food supplies to a large and increasing population continues to be the key challenge for China. Given the increasing integration of China within global markets for agricultural products, this issue is of considerable significance for global food security. Over the last 50 years, China has increased the production of its staple crops mainly by increasing yield per unit land area. However, this has largely been achieved through inappropriate agricultural practices, which have caused environmental degradation, with deleterious consequences for future agricultural productivity. Hence, there is now a pressing need to intensify agriculture in China using practices that are environmentally and economically sustainable. Given the dynamic nature of crops over space and time, the use of remote sensing technology has proven to be a valuable asset providing end-users in many countries with information to guide sustainable agricultural practices. Recently, the field has experienced considerable technological advancements reflected in the availability of ‘hyper-sensing’ (high spectral, spatial and temporal) satellite imagery useful for monitoring, modelling and mapping of agricultural crops. However, there still remains a significant challenge in fully exploiting such technologies for addressing agricultural problems in China. This review paper evaluates the potential contributions of satellite ‘hyper-sensing’ to agriculture in China and identifies the opportunities and challenges for future work. We perform a critical evaluation of current capabilities in satellite ‘hyper-sensing’ in agriculture with an emphasis on Chinese sensors. Our analysis draws on a series of in-depth examples based on recent and on-going projects in China that are developing ‘hyper-sensing’ approaches for (i) measuring crop phenology parameters and predicting yields; (ii) specifying crop fertiliser requirements; (iii) optimising management responses to abiotic and biotic stress in crops; (iv) maximising yields while minimising water use in arid regions; (v) large-scale crop/cropland mapping; and (vi) management zone delineation. The paper concludes with a synthesis of these application areas in order to define the requirements for future research, technological innovation and knowledge exchange in order to deliver yield sustainability in China

Multi-Temporal Dual- and Quad-Polarimetric Synthetic Aperture Radar Data for Crop-Type Mapping

Land-cover monitoring is one of the core applications of remote sensing. Monitoring and mapping changes in the distribution of agricultural land covers provide a reliable source of information that helps environmental sustainability and supports agricultural policies. Synthetic Aperture Radar (SAR) can contribute considerably to this monitoring effort. The first objective of this research is to extend the use of time series of polarimetric data for land-cover classification using a decision tree classification algorithm. With this aim, RADARSAT-2 (quad-pol) and Sentinel-1 (dual-pol) data were acquired over an area of 600 km2 in central Spain. Ten polarimetric observables were derived from both datasets and seven scenarios were created with different sets of observables to evaluate a multitemporal parcel-based approach for classifying eleven land-cover types, most of which were agricultural crops. The study demonstrates that good overall accuracies, greater than 83%, were achieved for all of the different proposed scenarios and the scenario with all RADARSAT-2 polarimetric observables was the best option (89.1%). Very high accuracies were also obtained when dual-pol data from RADARSAT-2 or Sentinel-1 were used to classify the data, with overall accuracies of 87.1% and 86%, respectively. In terms of individual crop accuracy, rapeseed achieved at least 95% of a producer’s accuracy for all scenarios and that was followed by the spring cereals (wheat and barley), which achieved high producer’s accuracies (79.9%-95.3%) and user’s accuracies (85.5% and 93.7%).All RADARSAT-2 images have been provided by MDA and CSA in the framework of the SOAR-EU2 Project ref. 16375. This study was supported by the Spanish Ministry of Science, Innovation and Universities, State Research Agency (AEI) and the European Regional Development Fund under projects TEC2017-85244-C2-1-P, ESP2015-67549-C3-3 and ESP2017-89463-C3-3-R

Towards a set of agrosystem-specific cropland mapping methods to address the global cropland diversity

Accurate cropland information is of paramount importance for crop monitoring. This study compares five existing cropland mapping methodologies over five contrasting Joint Experiment for Crop Assessment and Monitoring (JECAM) sites of medium to large average field size using the time series of 7-day 250 m Moderate Resolution Imaging Spectroradiometer (MODIS) mean composites (red and near-infrared channels). Different strategies were devised to assess the accuracy of the classification methods: confusion matrices and derived accuracy indicators with and without equalizing class proportions, assessing the pairwise difference error rates and accounting for the spatial resolution bias. The robustness of the accuracy with respect to a reduction of the quantity of calibration data available was also assessed by a bootstrap approach in which the amount of training data was systematically reduced. Methods reached overall accuracies ranging from 85% to 95%, which demonstrates the ability of 250 m imagery to resolve fields down to 20 ha. Despite significantly different error rates, the site effect was found to persistently dominate the method effect. This was confirmed even after removing the share of the classification due to the spatial resolution of the satellite data (from 10% to 30%). This underlines the effect of other agrosystems characteristics such as cloudiness, crop diversity, and calendar on the ability to perform accurately. All methods have potential for large area cropland mapping as they provided accurate results with 20% of the calibration data, e.g. 2% of the study area in Ukraine. To better address the global cropland diversity, results advocate movement towards a set of cropland classification methods that could be applied regionally according to their respective performance in specific landscapes.Instituto de Clima y AguaFil: Waldner, François. Université catholique de Louvain. Earth and Life Institute - Environment, Croix du Sud; BelgicaFil: De Abelleyra, Diego. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Clima y Agua; ArgentinaFil: Veron, Santiago Ramón. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Clima y Agua; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Métodos Cuantitativos y Sistemas de Información; ArgentinaFil: Zhang, Miao. Chinese Academy of Science. Institute of Remote Sensing and Digital Earth; ChinaFil: Wu, Bingfang. Chinese Academy of Science. Institute of Remote Sensing and Digital Earth; ChinaFil: Plotnikov, Dmitry. Russian Academy of Sciences. Space Research Institute. Terrestrial Ecosystems Monitoring Laboratory; RusiaFil: Bartalev, Sergey. Russian Academy of Sciences. Space Research Institute. Terrestrial Ecosystems Monitoring Laboratory; RusiaFil: Lavreniuk, Mykola. Space Research Institute NAS and SSA. Department of Space Information Technologies; UcraniaFil: Skakun, Sergii. Space Research Institute NAS and SSA. Department of Space Information Technologies; Ucrania. University of Maryland. Department of Geographical Sciences; Estados UnidosFil: Kussul, Nataliia. Space Research Institute NAS and SSA. Department of Space Information Technologies; UcraniaFil: Le Maire, Guerric. UMR Eco&Sols, CIRAD; Francia. Empresa Brasileira de Pesquisa Agropecuária. Meio Ambiante; BrasilFil: Dupuy, Stéphane. Centre de Coopération Internationale en Recherche Agronomique pour le Développement. Territoires, Environnement, Télédétection et Information Spatiale; FranciaFil: Jarvis, Ian. Agriculture and Agri-Food Canada. Science and Technology Branch. Agri-Climate, Geomatics and Earth Observation; CanadáFil: Defourny, Pierre. Université Catholique de Louvain. Earth and Life Institute - Environment, Croix du Sud; Belgic

Improvement in Land Cover and Crop Classification based on Temporal Features Learning from Sentinel-2 Data Using Recurrent-Convolutional Neural Network (R-CNN)

Understanding the use of current land cover, along with monitoring change over time, is vital for agronomists and agricultural agencies responsible for land management. The increasing spatial and temporal resolution of globally available satellite images, such as provided by Sentinel-2, creates new possibilities for researchers to use freely available multi-spectral optical images, with decametric spatial resolution and more frequent revisits for remote sensing applications such as land cover and crop classification (LC&CC), agricultural monitoring and management, environment monitoring. Existing solutions dedicated to cropland mapping can be categorized based on per-pixel based and object-based. However, it is still challenging when more classes of agricultural crops are considered at a massive scale. In this paper, a novel and optimal deep learning model for pixel-based LC&CC is developed and implemented based on Recurrent Neural Networks (RNN) in combination with Convolutional Neural Networks (CNN) using multi-temporal sentinel-2 imagery of central north part of Italy, which has diverse agricultural system dominated by economic crop types. The proposed methodology is capable of automated feature extraction by learning time correlation of multiple images, which reduces manual feature engineering and modeling crop phenological stages. Fifteen classes, including major agricultural crops, were considered in this study. We also tested other widely used traditional machine learning algorithms for comparison such as support vector machine SVM, random forest (RF), Kernal SVM, and gradient boosting machine, also called XGBoost. The overall accuracy achieved by our proposed Pixel R-CNN was 96.5%, which showed considerable improvements in comparison with existing mainstream methods. This study showed that Pixel R-CNN based model offers a highly accurate way to assess and employ time-series data for multi-temporal classification tasks

Automatic Sub-Pixel Co-Registration of LandSat-8 OLI and Sentinel-2A MSI Images Using Phase Correlation and Machine Learning Based Mapping

This study investigates misregistration issues between Landsat-8/OLI and Sentinel-2A/MSI at 30 m resolution, and between multi-temporal Sentinel-2A images at 10 m resolution using a phase correlation approach and multiple transformation functions. Co-registration of 45 Landsat-8 to Sentinel-2A pairs and 37 Sentinel-2A to Sentinel-2A pairs were analyzed. Phase correlation proved to be a robust approach that allowed us to identify hundreds and thousands of control points on images acquired more than 100 days apart. Overall, misregistration of up to 1.6 pixels at 30 m resolution between Landsat-8 and Sentinel-2A images, and 1.2 pixels and 2.8 pixels at 10 m resolution between multi-temporal Sentinel-2A images from the same and different orbits, respectively, were observed. The non-linear Random Forest regression used for constructing the mapping function showed best results in terms of root mean square error (RMSE), yielding an average RMSE error of 0.07+/-0.02 pixels at 30 m resolution, and 0.09+/-0.05 and 0.15+/-0.06 pixels at 10 m resolution for the same and adjacent Sentinel-2A orbits, respectively, for multiple tiles and multiple conditions. A simpler 1st order polynomial function (affine transformation) yielded RMSE of 0.08+/-0.02 pixels at 30 m resolution and 0.12+/-0.06 (same Sentinel-2A orbits) and 0.20+/-0.09 (adjacent orbits) pixels at 10 m resolution

Despeckling of Multitemporal Sentinel SAR Images and Its Impact on Agricultural Area Classification

This chapter addresses an important practical task of classification of multichannel remote sensing data with application to multitemporal dual-polarization Sentinel radar images acquired for agricultural regions in Ukraine. We first consider characteristics of dual-polarization Sentinel radar images and discuss what kind of filters can be applied to such data. Several examples of denoising are presented with analysis of what properties of filters are desired and what can be provided in practice. It is also demonstrated that the use of preliminary denoising produces improvement of classification accuracy where despeckling that is more efficient in terms of standard filtering criteria results in better classification

A systematic review of the use of Deep Learning in Satellite Imagery for Agriculture

Agricultural research is essential for increasing food production to meet the requirements of an increasing population in the coming decades. Recently, satellite technology has been improving rapidly and deep learning has seen much success in generic computer vision tasks and many application areas which presents an important opportunity to improve analysis of agricultural land. Here we present a systematic review of 150 studies to find the current uses of deep learning on satellite imagery for agricultural research. Although we identify 5 categories of agricultural monitoring tasks, the majority of the research interest is in crop segmentation and yield prediction. We found that, when used, modern deep learning methods consistently outperformed traditional machine learning across most tasks; the only exception was that Long Short-Term Memory (LSTM) Recurrent Neural Networks did not consistently outperform Random Forests (RF) for yield prediction. The reviewed studies have largely adopted methodologies from generic computer vision, except for one major omission: benchmark datasets are not utilised to evaluate models across studies, making it difficult to compare results. Additionally, some studies have specifically utilised the extra spectral resolution available in satellite imagery, but other divergent properties of satellite images - such as the hugely different scales of spatial patterns - are not being taken advantage of in the reviewed studies.Comment: 25 pages, 2 figures and lots of large tables. Supplementary materials section included here in main pd