Browsing by Author "Irwin M"

Now showing 1 - 12 of 12
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    Assessing the Leaf Blade Nutrient Status of Pinot Noir Using Hyperspectral Reflectance and Machine Learning Models
    (MDPI AG, 8/03/2023) Lyu H; Grafton MC; Ramilan T; Irwin M; Sandoval - Cruz E; Díaz-Varela, RA
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    Assessing the Leaf Blade Nutrient Status of Pinot Noir Using Hyperspectral Reflectance and Machine Learning Models
    (MDPI (Basel, Switzerland), 2023-03-08) Lyu H; Grafton M; Ramilan T; Irwin M; Sandoval E; Díaz-Varela RA
    Monitoring grape nutrient status, from flowering to veraison, is important for viticulturists when implementing vineyard management strategies, in order to produce quality wines. However, traditional methods for measuring nutrient elements incur high labour costs. The aim of this study is to explore the potential of predicting grapevine leaf blade nutrient concentration based on hyperspectral data. Leaf blades were collected at two Pinot Noir commercial vineyards at Martinborough, New Zealand. The leaf blade spectral data were obtained with a handheld spectroradiometer, to evaluate surface reflectance and derivative spectra in the spectrum range between 400 and 2400 nm. Afterwards, leaf blades nutrient concentrations (N, P, K, Ca, and Mg) were measured, and their relationships with the hyperspectral data were modelled by machine learning models; partial least squares regression (PLSR), random forest regression (RFR), and support vector regression (SVR) were used. Pearson correlation and recursive feature elimination, based on cross-validation, were used as feature selection methods for RFR and SVR, to improve the model’s performance. The variable importance score of PLSR, and permutation variable importance of RFR and SVR, were used to determine the most sensitive wavelengths, or spectral regions related to each biochemical variable. The results showed that the best predictive performance for leaf blade N concentration was based on PLSR to raw reflectance data (R2 = 0.66; RMSE = 0.15%). The combination of support vector regression with the Pearson correlation selected method and second derivative reflectance provided a high accuracy for K and Ca modelling (R2 = 0.7; RMSE = 0.06%; R2 = 0.62; RMSE = 0.11%, respectively). However, the modelling performance for P and Mg, by different feature groups and variable selection methods, was poor (R2 = 0.15; RMSE = 0.02%; R2 = 0.43; RMSE = 0.43%, respectively). Thus, a larger dataset is needed for improving the prediction of P and Mg. The results indicated that for Pinot Noir leaf blades, raw reflectance data had potential for the prediction of N concentration, while the second-derivative spectra were more suitable to predict K and Ca. This study led to the provision of rapid and non-destructive measurements of grapevine leaf nutrient status.
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    Comparing the Carbon Storage Potential of Naturally Regenerated Tea Trees with Default New Zealand Carbon Look-Up Tables: A Case Study
    (MDPI, 12/04/2023) Wilson T; Grafton M; Irwin M; Hatano, R
    The New Zealand Emissions Trading Scheme allows landowners to be remunerated for the carbon sequestration capabilities of eligible forests established post 1990. For afforested areas of 100 hectares or fewer, carbon sequestration is estimated with the use of default carbon look-up tables administered by the Ministry for Primary Industries. However, a disparity exists between exotic pines (Pinus radiata), where carbon sequestration predictions are regionally differentiated, and native species, where carbon sequestration estimations are neither distinguished by species or locality. This paper aims to highlight this inequality by comparing the calculated carbon storage of endemic tree species with the ‘Indigenous Forest’ category in the carbon look-up tables. The carbon storage of 12-year-old naturally regenerated tea trees (Leptospermum scoparium and Kunzea ericoides) was calculated using allometric measurements and compared to the look-up tables. The results suggest that carbon look-up tables underestimate the carbon sequestration of native tea trees by 81.8%. A bimodal data distribution suggests that carbon sequestration is heavily dependent on light interception levels. It is recommended that carbon sequestration data for specific native species in different environments are collected and integrated into such tables.
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    Evaluation of Point Hyperspectral Reflectance and Multivariate Regression Models for Grapevine Water Status Estimation
    (MDPI AG, 12/08/2021) Wei H-E; Grafton M; Bretherton M; Irwin M; Sandoval E
    Monitoring and management of plant water status over the critical period between flower-ing and veraison, plays a significant role in producing grapes of premium quality. Hyperspectral spectroscopy has been widely studied in precision farming, including for the prediction of grapevine water status. However, these studies were presented based on various combinations of transformed spectral data, feature selection methods, and regression models. To evaluate the performance of different modeling pipelines for estimating grapevine water status, a study spanning the critical period was carried out in two commercial vineyards at Martinborough, New Zealand. The modeling used six hyperspectral data groups (raw reflectance, first derivative reflectance, second derivative reflectance, continuum removal variables, simple ratio indices, and vegetation indices), two variable selection methods (Spearman correlation and recursive feature elimination based on cross-validation), an ensemble of selected variables, and three regression models (partial least squares regression, random forest regression, and support vector regression). Stem water potential (used as a proxy for vine water status) was measured by a pressure bomb. Hyperspectral reflectance was undertaken by a handheld spectroradiometer. The results show that the best predictive performance was achieved by applying partial least squares regression to simple ratio indices (R2 = 0.85; RMSE = 110 kPa). Models trained with an ensemble of selected variables comprising multicombination of transformed data and variable selection approaches outperformed those fitted using single combinations. Although larger data sizes are needed for further testing, this study compares 38 modeling pipelines and presents the best combination of procedures for estimating vine water status. This may lead to the provision of rapid estimation of vine water status in a nondestructive manner and highlights the possibility of applying hyperspectral data to precision irrigation in vineyards.
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    Evaluation of the use of two-stage calibrated PlanetScope images and environmental variables for the development of the grapevine water status prediction model
    (24/05/2023) Wei H-E; Grafton M; Bretherton M; Irwin M; Sandoval E
    Abstract Grapevine water status (GWS) assessment between flowering and veraison plays an important role in viticulture management in terms of producing high-quality grapes. Although satellites and uncrewed aerial vehicles (UAV) have successfully monitored GWS, these platforms are practically limited because data transfer is delayed due to post processing and UAV operation is weather dependent. This study focuses on addressing two issues: the unreliability of GWS estimation using satellite images with low-moderate spatial resolution and the inaccessibility of real-time satellite data. It aims to predict the temporal variation of GWS based on a prediction model using spectral information (calibrated PlanetScope (PS) images), soil/topography data (apparent electrical conductivity, elevation, slope), weather parameters (rainfall and potential evapotranspiration), cultivation practices (irrigation, fertigation, plucking, and trimming), and seasonality (day of the year) as predictors. Stem water potential (Ψstem) was used as a proxy for GWS. Two-stage calibration, including an initial calibration of UAV images with measured Ψstem and a subsequent calibration of satellite images with calibrated UAV data, was applied to calibrate the PS images. Three machine learning models (random forest regression, support vector regression, and multilayer perceptron) were used in the calibration and modeling process. The results showed that a two-stage calibration can generate reliable reference data, with a root mean square error of 113 kPa and 59 kPa on the test sets during the first and second calibration stage, respectively. The prediction model described the temporal variation of block Ψstem when compared with the measured Ψstem. In the similarity analysis, the Pearson correlation coefficient was 0.89 and 0.87 between predicted and reference Ψstem maps across four dates for the two study vineyards. This study supports the concept of developing an approach to predict grapevine Ψstem, which would enable growers to acquire Ψstem variation in advance during the growing season, leading to improved irrigation scheduling and optimal grape quality.
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    Evaluation of the use of UAV-derived Vegetation Indices and Environmental Variables for Grapevine Water Status Monitoring based on Machine Learning Algorithms and SHAP Analysis
    (1/06/2022) Wei H-E; Grafton MC; Bretherton M; Irwin M; Sandoval E; Horne, D; Singh, R
    Monitoring and management of grapevine water status (GWS) over the critical period between flowering and veraison plays a significant role in producing grapes of premium quality. The spatial and temporal variation of GWS, is conventionally characterized by using a pressure bomb. This is laborious and time-consuming, which limits the number of samples. Although unmanned aerial vehicles (UAVs) can provide mapping across the entire vineyards efficiently, most commercial UAV-based multispectral sensors do not contain a shortwave infrared band which makes the monitoring of GWS problematic. As GWS is an integrated response to vegetation characteristics, temporal trends, weather conditions, and soil/terrain data, it is assumed that these ancillary variables have the potential to enhance the capability of UAVs for GWS monitoring. The goal of this study is to explore whether and which of these ancillary variables may improve the accuracy of GWS estimation using UAV, and provide insights into the contribution that each selected variable contributes to the variation in GWS. A UAV was flown over two Pinot Noir vineyards in New Zealand to generate aerial images with 4.3 cm resolution, and 18 vegetation indices (VIs) were computed for every sampled grapevine. The strongly correlated VIs were used as the core input for later GWS modeling. Ancillary data included soil/terrain, weather, and temporal variables. Slope and elevation were extracted from a digital elevation model, and apparent electrical conductivity (ECa) was obtained from an EM38 survey. A local weather station provided continuous air temperature, humidity, rainfall, wind speed, and irradiance data, which were computed as variables at weekly and daily intervals. Day of the year (DOY) was used to represent the temporal trend along the growing season. Three machine learning algorithms (elastic net, random forest regression, and support vector regression) were used to regress the predictors against stem water potential (Ψstem), measured by a pressure bomb and used as a proxy for GWS. Shapley Additive exPlanations (SHAP) analysis (a statistical tool that weighs the importance of each variable in a model) was used to assess the relationship between selected variables and Ψstem. The results show that Transformed Chlorophyll Absorption Reflectance Index (TCARI) and Excess Green Index (ExG) are the best correlated VIs, but their correlation with Ψstem is poor (rTCARI = 0.6; rExG = 0.58). The coefficient of determination (R2) of the TCARI-based model increased from 0.35 to 0.7 when DOY and elevation were included as ancillary inputs. R2 of the ExG-based model increased from 0.3 to 0.74 when DOY, elevation, slope, ECa, and daily average windspeed, were included as ancillary inputs. Support vector regression was the best model to describe the relationship between Ψstem and selected predictors. This study has provided proof of the concept of developing GWS estimation models that potentially enhance the monitoring capacities of UAVs for GWS, as well as provide individual GWS mapping at the vineyard scale. This may enable growers to improve irrigation management, leading to controlled vegetative growth and optimized berry quality.
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    Hyperspectral Imaging Spectroscopy for Non-Destructive Determination of Grape Berry Total Soluble Solids and Titratable Acidity
    (MDPI AG, 2024-05-07) Lyu H; Grafton M; Ramilan T; Irwin M; Sandoval E; Krasuki K; Weirzbicki D
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    Mapping nutrient concentration in pasture using hyperspectral imaging
    (2015) Yule IJ; Pullanagari RR; Irwin M; McVeagh P; Kereszturi G; White M; Manning M
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    Towards better irrigation management for vineyards based on machine learning algorithms and SHAP analysis: a case study in New Zealand
    (19/09/2022) Wei H-E; Grafton MC; Bretherton M; Irwin M; Sandoval E
    Monitoring and management of grapevine water status (GWS) over the critical period between flowering and veraison plays a significant role in producing grapes of premium quality. GWS monitoring is critical to vineyard management, and so determines which variables are the main drivers of GWS variation. The goal of this study is to provide viticulturists with an approach to simulate the complex relationship between canopy GWS with vegetation, weather, day of the year (DOY), and soil/terrain variables, along with the interpretation of these relationships. A case study done in Martinborough, New Zealand is used for illustration. A UAV was flown over two Pinot Noir vineyards to generate aerial images with 4.3 cm resolution, and the vegetation index, Transformed Chlorophyll Absorption Reflectance Index (TCARI), was computed for every sampled grapevine. Slope and elevation were extracted from a digital elevation model, and apparent electrical conductivity (ECa) was obtained from an EM38 survey. A local weather station provided continuous air temperature, humidity, rainfall, wind speed, and irradiance data, which were computed as variables at weekly and daily intervals. DOY was used to represent temporal trends along the growing season. Hierarchical clustering and three machine learning algorithms (elastic net, random forest regression, support vector regression) were used to regress predictors against stem water potential (Ψstem), measured by a pressure bomb and used as a proxy for GWS. Shapley Additive exPlanations (SHAP) analysis (a statistical tool that weighs the importance of each variable in a model) was used to interpret the relationship between selected predictors and Ψstem. Our results showed that the coefficient of determination (R2) of the best-performed model reached 0.7 when simulated by support vector regression using TCARI, DOY, and elevation as inputs. This study has provided proof of concept of developing regression models that would be beneficial for grapevine irrigation systems via continuous GWS monitoring, while the identification and clarification of the relationship between statistically dominant variables would assist in decision-making to attain optimal grape quality.
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    Using Remote and Proximal Sensing Data and Vine Vigor Parameters for Non-Destructive and Rapid Prediction of Grape Quality
    (MDPI AG, 2023-11-19) Lyu H; Grafton M; Ramilan T; Irwin M; Wei H-E; Sandoval E; Zhang C; Liu D
    The traditional method for determining wine grape total soluble solid (TSS) is destructive laboratory analysis, which is time consuming and expensive. In this study, we explore the potential of using different predictor variables from various advanced techniques to predict the grape TSS in a non-destructive and rapid way. Calculating Pearson’s correlation coefficient between the vegetation indices (VIs) obtained from UAV multispectral imagery and grape TSS resulted in a strong correlation between OSAVI and grape TSS with a coefficient of 0.64. Additionally, seven machine learning models including ridge regression and lasso regression, k-Nearest neighbor (KNN), support vector regression (SVR), random forest regression (RFR), extreme gradient boosting (XGBoost), and artificial neural network (ANN) are used to build the prediction models. The predictor variables include the unmanned aerial vehicles (UAV) derived VIs, and other ancillary variables including normalized difference vegetation index (NDVI_proximal) and soil electrical conductivity (ECa) measured by proximal sensors, elevation, slope, trunk circumference, and day of the year for each sampling date. When using 23 VIs and other ancillary variables as input variables, the results show that ensemble learning models (RFR, and XGBoost) outperform other regression models when predicting grape TSS, with the average of root mean square error (RMSE) of 1.19 and 1.2 ◦Brix, and coefficient of determination (R2 ) of 0.52 and 0.52, respectively, during the 20 times testing process. In addition, this study examines the prediction performance of using optimized soil adjusted vegetation index (OSAVI) or normalized green-blue difference index (NGBDI) as the main input for different machine learning models with other ancillary variables. When using OSAVI-based models, the best prediction model is RFR with an average R2 of 0.51 and RMSE of 1.19 ◦Brix, respectively. For NGBDI-based model, the RFR model showed the best average result of predicting TSS were a R2 of 0.54 and a RMSE of 1.16 ◦Brix, respectively. The approach proposed in this study provides an opportunity to grape growers to estimate the whole vineyard grape TSS in a non-destructive way.
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    Using Remote and Proximal Sensing Data and Vine Vigor Parameters for Non-Destructive and Rapid Prediction of Grape Quality
    (MDPI (Basel, Switzerland), 2023-11-19) Lyu H; Grafton M; Ramilan T; Irwin M; Wei H-E; Sandoval E; Zhang C; Liu D
    The traditional method for determining wine grape total soluble solid (TSS) is destructive laboratory analysis, which is time consuming and expensive. In this study, we explore the potential of using different predictor variables from various advanced techniques to predict the grape TSS in a non-destructive and rapid way. Calculating Pearson’s correlation coefficient between the vegetation indices (VIs) obtained from UAV multispectral imagery and grape TSS resulted in a strong correlation between OSAVI and grape TSS with a coefficient of 0.64. Additionally, seven machine learning models including ridge regression and lasso regression, k-Nearest neighbor (KNN), support vector regression (SVR), random forest regression (RFR), extreme gradient boosting (XGBoost), and artificial neural network (ANN) are used to build the prediction models. The predictor variables include the unmanned aerial vehicles (UAV) derived VIs, and other ancillary variables including normalized difference vegetation index (NDVI_proximal) and soil electrical conductivity (ECa) measured by proximal sensors, elevation, slope, trunk circumference, and day of the year for each sampling date. When using 23 VIs and other ancillary variables as input variables, the results show that ensemble learning models (RFR, and XGBoost) outperform other regression models when predicting grape TSS, with the average of root mean square error (RMSE) of 1.19 and 1.2 °Brix, and coefficient of determination (R2) of 0.52 and 0.52, respectively, during the 20 times testing process. In addition, this study examines the prediction performance of using optimized soil adjusted vegetation index (OSAVI) or normalized green-blue difference index (NGBDI) as the main input for different machine learning models with other ancillary variables. When using OSAVI-based models, the best prediction model is RFR with an average R2 of 0.51 and RMSE of 1.19 °Brix, respectively. For NGBDI-based model, the RFR model showed the best average result of predicting TSS were a R2 of 0.54 and a RMSE of 1.16 °Brix, respectively. The approach proposed in this study provides an opportunity to grape growers to estimate the whole vineyard grape TSS in a non-destructive way.