Structural and photosynthetic dynamics mediate the response of SIF to water stress in a potato crop

Publication is now online and open access at: https://www.sciencedirect.com/science/article/pii/S0034425721002753 <strong>1. Introduction</strong> We provide data and processing code associated with Xu et al. (2021) study investigating the structural and photosynthetic response of SIF to water stress in a potato crop. Two platforms were used to measure VNIR spectra using a Piccolo Doppio system, one is a hydraulic lift for diurnal analysis, and another is an Unmanned Aerial Vehicle (UAV) for spatial analysis. Physiological measurements were obtained from a host of instruments (including PAM fluorometers) on the ground. Structural measurements were obtained from point clouds. Due to the large file size (10s GB), please contact the authors if interested in the raw point cloud data. <strong>2. Description of files</strong> Datasets includes raw and processed canopy scale spectra for SIF, in addition to scripts and analysis results. Code was run on MATLAB R2019a. Spectral data is saved in folder ‘Spectrum process’, which contains Piccolo Doppio canopy spectra and the scripts for processing. These data were used to derive SIF from UAV and hydraulic lift platforms. The folder also contains leaf spectra used for model inversions (described below). The canopy spectra are saved in folder ‘Canopy spectrum’. In this folder, we provide calibration data, raw data, scripts and products. Then calibration data are saved in folder ‘CalibrationData’, which are used to conduct wavelength and radiometric correction from digital numbers of raw data to calibrated radiometric values. Raw data are saved in folder ‘RawDATA’, which contains two UAV flights and lift raw spectrums. The UAV data were conducted in 10 plots (W1-W10), and the batch number corresponding plots are: W1-batch 6, W2-batch 7, W3-batch 8, W4-batch 9, W5-batch 10, W6-batch 11, W7-batch 17, W8-batch 18, W9-batch 13, W10-batch 12, Soil-batch 14. The lift data were conducted in plots W7 and W8 in diurnal scales. We generate two level products: Level1_Product1 contains the calibrated radiance and irradiance, and Level1_Product1 contains reflectance, SIF, NDVI, fPAR, NIRv and FCVI. Leaf reflectance, transmittance and absorption data are also saved in folder ‘Leaf absorption’, which are used to invert leaf biochemical properties through model ‘fluspect_B_CX_PSI_PSII_combined’. In this folder, folder ‘RawDATA’ contains 3 replicates of leaf reflectance and transmittance of 10 plots (W1-W10). Folder ‘Fluspect_inversion’ contains the inversion code in MATLAB scripts, and the main function is ‘myinversion.m’. Analysis results data are saved in folder ‘Results’ in the ‘.xlsx’ format. The file ‘Canopy diurnal temperature.xlsx’ contains diurnal canopy temperature data of plots W7 and W8. The file ‘Diurnal key parameters.xlsx’ contains diurnal physiological and structural parameters, which is used to make figure 5 in linked paper. The file ‘Spatial key parameters.xlsx’ contains saptial physiological and structural parameters, which is used to make figure 4 in linked paper. The file ‘LAD_estiamtion.xlsx’ contains leaf angle distribution (LAD) of 10 plots estimated using point cloud. The file ‘Leaf_inversion.xlsx’ contains leaf biochemical parameters inverted from leaf reflectance and transmittance. The file ‘Observed diurnal SIF_fPAR_NIRv_FCVI.xlsx’ contains estimated diurnal fPAR, NIRv, FCVI and F760 and F687 of plots W7 and W8 from lift diurnal spectrums. The file ‘Observed spatial SIF_fPAR_NIRv_FCVI.xlsx’ contains estimated saptial fPAR, NIRv, FCVI and F760 and F687 of 10 plots (W1-W10) from lift diurnal spectrums. Three files ‘Q1_relative_influence’, Q2_stress_driver.xlsx, and ‘’Q3_SIF_GPP_relationships.xlsx are used to make figure 7, figure 8, figure 9 and figure 10 in linked paper. ‘Simulated diurnal SIF.xlsx’ and ‘Simulated spatial SIF.xlsx’ are simulated SIF under different scenarios using SCOPE model.本研究成果现已在线开放获取，发表链接：https://www.sciencedirect.com/science/article/pii/S0034425721002753 <strong>1. 引言</strong> 本数据集配套于Xu等人（2021）的研究，该研究旨在探究日光诱导叶绿素荧光（Solar-Induced Chlorophyll Fluorescence, SIF）对马铃薯作物水分胁迫的结构与光合响应。本研究采用两套平台结合Piccolo Doppio系统开展可见光-近红外光谱（Visible and Near-Infrared, VNIR）测量：一套为用于日变化分析的液压升降台，另一套为用于空间分析的无人机（Unmanned Aerial Vehicle, UAV）。地面生理参数测量借助多款仪器完成（包括脉冲振幅调制荧光仪（Pulse Amplitude Modulation fluorometer, PAM)），结构参数则通过点云数据获取。由于原始点云数据文件体量较大（达数十GB），若需获取此类数据，请联系论文作者。 <strong>2. 数据集文件说明</strong> 本数据集包含日光诱导叶绿素荧光（SIF）的原始与预处理冠层尺度光谱数据，同时配套相关脚本与分析结果。代码基于MATLAB R2019a运行。 光谱数据存储于"Spectrum process"文件夹，内含Piccolo Doppio冠层光谱数据与预处理脚本，用于从无人机与液压升降台平台获取SIF数据；该文件夹同时包含用于模型反演的叶片光谱数据（详见下文）。 冠层光谱数据存储于"Canopy spectrum"文件夹，内含校正数据、原始数据、脚本与产品文件。其中校正数据存储于"CalibrationData"文件夹，用于将原始数据的数字量化值校正为辐射亮度值，完成波长与辐射定标。原始数据存储于"RawDATA"文件夹，包含两次无人机飞行与液压升降台的原始光谱数据。 无人机数据采集于10个样地（W1-W10），各批次对应样地如下：W1-批次6，W2-批次7，W3-批次8，W4-批次9，W5-批次10，W6-批次11，W7-批次17，W8-批次18，W9-批次13，W10-批次12，土壤样地-批次14。液压升降台数据采集于W7与W8样地的日变化尺度。 本数据集生成两级产品：Level1_Product1包含校正后的辐射亮度与辐照度数据，另一级产品（原文笔误仍标注为Level1_Product1）包含反射率、SIF、归一化差异植被指数（Normalized Difference Vegetation Index, NDVI）、光合有效辐射吸收比率（Fraction of Absorbed Photosynthetically Active Radiation, fPAR）、近红外植被指数（Near-Infrared Vegetation Index, NIRv）与植被覆盖度植被指数（Fractional Cover Vegetation Index, FCVI）。 叶片反射率、透射率与吸收系数数据存储于"Leaf absorption"文件夹，用于通过"fluspect_B_CX_PSI_PSII_combined"模型反演叶片生化参数。该文件夹内的"RawDATA"子文件夹包含10个样地（W1-W10）的叶片反射率与透射率的3次重复测量数据；"Fluspect_inversion"子文件夹包含MATLAB格式的反演脚本，主函数为"myinversion.m"。 分析结果数据存储于"Results"文件夹，格式为Excel表格（.xlsx）： - "Canopy diurnal temperature.xlsx"：包含W7与W8样地的冠层日变化温度数据； - "Diurnal key parameters.xlsx"：包含日变化生理与结构参数，用于绘制关联论文中的图5； - "Spatial key parameters.xlsx"（原文笔误：saptial应为spatial）：包含空间尺度生理与结构参数，用于绘制关联论文中的图4； - "LAD_estimation.xlsx"（原文笔误：estiamtion应为estimation）：包含通过点云数据估算的10个样地的叶角分布（Leaf Angle Distribution, LAD）； - "Leaf_inversion.xlsx"：包含通过叶片反射率与透射率反演得到的叶片生化参数； - "Observed diurnal SIF_fPAR_NIRv_FCVI.xlsx"：包含基于液压升降台日变化光谱数据估算的W7与W8样地的日变化fPAR、NIRv、FCVI、F760与F687数据； - "Observed spatial SIF_fPAR_NIRv_FCVI.xlsx"（原文笔误：saptial应为spatial）：包含基于液压升降台日变化光谱数据估算的10个样地（W1-W10）的空间尺度fPAR、NIRv、FCVI、F760与F687数据； - "Q1_relative_influence.xlsx"、"Q2_stress_driver.xlsx"与"Q3_SIF_GPP_relationships.xlsx"：用于绘制关联论文中的图7、图8、图9与图10； - "Simulated diurnal SIF.xlsx"与"Simulated spatial SIF.xlsx"：为基于SCOPE模型模拟的不同情境下的SIF数据。