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

Multitemporal monitoring of plant area index in the Valencia Rice District with PocketLAI

Leaf area index (LAI) is a key biophysical parameter used to determine foliage cover and crop growth in environmental studies in order to assess crop yield. Frequently, plant canopy analyzers (LAI-2000) and digital cameras for hemispherical photography (DHP) are used for indirect effective plant area index (PAIeff ) estimates. Nevertheless, these instruments are expensive and have the disadvantages of low portability and maintenance. Recently, a smartphone app called PocketLAI was presented and tested for acquiring PAIeff measurements. It was used during an entire rice season for indirect PAIeff estimations and for deriving reference high-resolution PAIeff maps. Ground PAIeff values acquired with PocketLAI, LAI-2000, and DHP were well correlated (R2 = 0.95, RMSE = 0.21 m2/m2 for Licor-2000, and R2 = 0.94, RMSE = 0.6 m2/m2 for DHP). Complementary data such as phenology and leaf chlorophyll content were acquired to complement seasonal rice plant information provided by PAIeff. High-resolution PAIeff maps, which can be used for the validation of remote sensing products, have been derived using a global transfer function (TF) made of several measuring dates and their associated satellite radiances

Combining Multitemporal Microwave and Optical Remote Sensing Data. Mapping of Land Use / Land Cover, Crop Type, and Crop Traits

Humanity has changed the earth’s surface to a dramatic extent. This is especially true for the area used for agricultural production. Against the background of a growing world population and the associated increased demand for food, it is precisely this area that will become even more important in the future. In order not to have to allocate even more land to agricultural use, optimization and intensification is the only way out of the dilemma. In this context, precise Geoinformation of the agriculturally used area is of central importance. It is utilized for improving land use, producing yield forecasts for more stable food security, and optimizing agricultural management. Rapid developments in the field of satellite-based remote sensing sensors make it possible to monitor agricultural areas with increased spatial, spectral and temporal resolution. However, to retrieve the needed information from this data, new methods are needed. Furthermore, the quality of the data has to be verified. Only then can the presented geodata help to grow crops more sustainably and more efficiently. This thesis develops new approaches for monitoring agricultural areas using the technology of microwave remote sensing in combination with optical remote sensing and existing geodata. It is framed by the overall objective to obtain knowledge on how this combination of data can provide the necessary geoinformation for land use studies, precision farming, and agricultural monitoring systems. Hundreds of remote sensing images from more than eight different satellites were analyzed in six research studies from two different Areas of Interest (AOIs). The studies guide through various spatial scales. First, the general Land Use / Land Cover (LULC) on a regional level in a multi-sensor scenario is derived, evaluating different sensor combinations of varying resolutions. Next, an innovative method is proposed, through which the high geometric accuracy of radar-imaging satellite sensors is exploited to update the spatial accuracy of any external geodata of lower spatial accuracy. Such external data is then used in the next two studies, which focus on cost-effective crop type mapping using Synthetic Aperture Radar (SAR) images. The resulting enhanced LULC maps present the annually changing crop types of the region alongside external, official geoinformation that is not retrievable from remote sensing sensors. The last two research studies deal with a single maize field, on which high resolution optical WorldView-2 images and experimental bistatic SAR observations from TanDEM-X are assessed and combined with ground measurements. As a result, this thesis shows that, depending on the AOI and the application, different resolution demands need to be fulfilled before LULC, crop type, and crop traits mapping can be performed with adequate accuracy. The spatial resolution needs to be adapted to the particularities of the AOI. Evaluation of the sensors showed that SAR sensors proved beneficial for the study objective. Processing the SAR images is complicated, and the images are unintuitive at first sight. However, the advantage of SAR sensors is that they work even in cloudy conditions. This results in an increased temporal resolution, which is particularly important for monitoring the highly dynamic agricultural area. Furthermore, the high geometric accuracy of the SAR images proved ideal for implementing the Multi-Data Approach (MDA). Thus information-rich external geodata could be used to lower the remote sensing resolution needs, improve the accuracy of the LULC-maps, and to provide enhanced LULC-maps. The first study of the maize field demonstrates the potential of the WorldView-2 data in predicting in-field biomass variations, and its increased accuracy when fused with plant height measurements. The second study shows the potential of the TanDEM-X Constellation (TDM) to retrieve plant height from space. LULC, crop type and information on the spatial distribution of biomass can thus be derived efficiently and with high accuracy from the combination of SAR, optical satellites and external geodata. The shown analyses for acquiring such geoinformation represent a high potential for helping to solve the future challenges of agricultural production

Sustainable Agriculture and Advances of Remote Sensing (Volume 1)

Agriculture, as the main source of alimentation and the most important economic activity globally, is being affected by the impacts of climate change. To maintain and increase our global food system production, to reduce biodiversity loss and preserve our natural ecosystem, new practices and technologies are required. This book focuses on the latest advances in remote sensing technology and agricultural engineering leading to the sustainable agriculture practices. Earth observation data, in situ and proxy-remote sensing data are the main source of information for monitoring and analyzing agriculture activities. Particular attention is given to earth observation satellites and the Internet of Things for data collection, to multispectral and hyperspectral data analysis using machine learning and deep learning, to WebGIS and the Internet of Things for sharing and publishing the results, among others

High-throughput estimation of crop traits: A review of ground and aerial phenotyping platforms

Crop yields need to be improved in a sustainable manner to meet the expected worldwide increase in population over the coming decades as well as the effects of anticipated climate change. Recently, genomics-assisted breeding has become a popular approach to food security; in this regard, the crop breeding community must better link the relationships between the phenotype and the genotype. While high-throughput genotyping is feasible at a low cost, highthroughput crop phenotyping methods and data analytical capacities need to be improved. High-throughput phenotyping offers a powerful way to assess particular phenotypes in large-scale experiments, using high-tech sensors, advanced robotics, and imageprocessing systems to monitor and quantify plants in breeding nurseries and field experiments at multiple scales. In addition, new bioinformatics platforms are able to embrace large-scale, multidimensional phenotypic datasets. Through the combined analysis of phenotyping and genotyping data, environmental responses and gene functions can now be dissected at unprecedented resolution. This will aid in finding solutions to currently limited and incremental improvements in crop yields

Télédétection radar appliquée au suivi des rizières. Méthodes utilisant le rapport des intensités de rétrodiffusion.

Because of the importance of rice in global food security and of the role of rice paddies in methane emissions, a large-scale near-real-time monitoring system of rice fields appears to be particularly useful. The objective of this work is to develop methods aiming at an effective use of remote sensing data from past and future satellites for rice fields monitoring. Radar imagery is preferred to optical imagery, due to its all-weather ability. Two methods are considered, both involving a C-band SAR intensity ratio as a classification feature: the HH/VV polarization ratio and the co-polarized temporal change HHdate2/HHdate1. First, a statistical study of intensity ratios is done, leading to the development of an error model that estimates the performance of the classification methods. The error model is also used to assess the impact of SAR system parameters (calibration, ambiguity ratio, revisit frequency) on the classification accuracy. Then, these classification methods are applied to two datasets acquired by the ASAR instrument onboard ENVISAT over the Mekong Delta, Vietnam, in order to map rice fields at two scales. The first approach relies on the use of the HH/VV polarization ratio calculated from the Alternating Polarization mode of ASAR, and is applied to produce a rice map covering one province in the delta. The second approach uses the HH temporal change of Wide-Swath mode images from ASAR, and allows mapping rice fields over the whole delta. Both methods are validated with success through the use of the cultivated areas reported in national statistics.En raison de l'importance du riz dans l'alimentation mondiale et du rôle des rizières dans les émissions de méthane, un suivi à grande échelle et en temps quasi-réel des surfaces cultivées en riz semble particulièrement utile. L'objectif de cette thèse est de développer des méthodes permettant une utilisation effective des données de télédétection des satellites présents et futurs pour le suivi des rizières. L'imagerie radar est privilégiée car elle permet des acquisitions sous toutes les conditions météorologiques, contrairement à l'imagerie optique. Deux méthodes sont retenues qui font intervenir un rapport d'intensité de deux images SAR en bande C : le rapport de polarisation HH/VV ou le changement temporel en co-polarisation HHdate2/HHdate1. Dans un premier temps, une étude statistique des rapports d'intensité de rétrodiffusion est effectuée, qui conduit au développement d'un modèle d'erreur permettant d'estimer la performance des méthodes de classification. Ce modèle d'erreur est également utilisé pour évaluer l'impact des paramètres des systèmes SAR (Synthetic Aperture Radar) sur la performance de la classification. Il s'agit des paramètres concernant l'étalonnage, l'ambiguïté, la fréquence de revisite. Dans un second temps, les méthodes de classification ainsi développées sont appliquées à deux jeux de données de l'instrument ASAR du satellite ENVISAT sur le delta du Mékong au Vietnam, pour faire la cartographie des rizières à deux échelles différentes. La première méthode repose sur l'utilisation du rapport HH/VV à partir de données du mode Alternating Polarization d'ASAR, qui permet de produire une carte de rizières couvrant une province du delta. La seconde méthode tire parti du changement temporel de HH sur des images du mode Wide-Swath d'ASAR, et est utilisée pour cartographier les rizières de l'ensemble du delta. Les deux méthodes sont validées avec succès en utilisant les surfaces cultivées données par les statistiques nationales

Polarimetric Synthetic Aperture Radar

This open access book focuses on the practical application of electromagnetic polarimetry principles in Earth remote sensing with an educational purpose. In the last decade, the operations from fully polarimetric synthetic aperture radar such as the Japanese ALOS/PalSAR, the Canadian Radarsat-2 and the German TerraSAR-X and their easy data access for scientific use have developed further the research and data applications at L,C and X band. As a consequence, the wider distribution of polarimetric data sets across the remote sensing community boosted activity and development in polarimetric SAR applications, also in view of future missions. Numerous experiments with real data from spaceborne platforms are shown, with the aim of giving an up-to-date and complete treatment of the unique benefits of fully polarimetric synthetic aperture radar data in five different domains: forest, agriculture, cryosphere, urban and oceans