## 3 Results
### Simulation Results by the Fluspect Model with/without the FQE Inversion Code
\begin{table}
\begin{tabular}{c c c c c c c} \hline \hline
**Sample** & **RMSE** & \multirow{2}{*}{**Pearson**} & **RMSE** & **\(R^{2}\)** & **Pearson** \\
**Setup** & \(\times 10^{-4}\) & & & **Improved \(\times 10^{-1}\)** & **Improved & **Improved** \\ \hline HT Up-A & 1.73 & 0.774 & 0.881 & 0.73 & 0.949 & 0.974 \\ HT Up-B & 2.28 & 0.813 & 0.901 & 0.52 & 0.966 & 0.983 \\ HT Up-C & 1.63 & 0.821 & 0.906 & 0.86 & 0.969 & 0.985 \\ HT Up-D & 1.54 & 0.786 & 0.887 & 0.53 & 0.962 & 0.981 \\ HT Down-A & 0.99 & 0.870 & 0.933 & 0.65 & 0.962 & 0.981 \\ HT Down-B & 1.49 & 0.953 & 0.976 & 0.43 & 0.977 & 0.988 \\ HT Down-C & 0.85 & 0.975 & 0.987 & 0.85 & 0.982 & 0.991 \\ HT Down-D & 0.78 & 0.923 & 0.961 & 0.42 & 0.974 & 0.987 \\ \hline HM Up-A & 2.49 & 0.813 & 0.902 & 0.36 & 0.969 & 0.985 \\ HM Up-B & 1.53 & 0.846 & 0.920 & 0.60 & 0.964 & 0.982 \\ HM Up-C & 1.79 & 0.827 & 0.909 & 0.48 & 0.960 & 0.980 \\ HM Up-D & 1.76 & 0.724 & 0.851 & 0.72 & 0.957 & 0.978 \\ HM & 1.68 & 0.943 & 0.971 & 0.28 & 0.975 & 0.987 \\ HM Down-B & 0.98 & 0.930 & 0.964 & 0.51 & 0.971 & 0.986 \\ HM Down-C & 1.40 & 0.938 & 0.969 & 0.38 & 0.973 & 0.986 \\ HM & 0.55 & 0.943 & 0.971 & 0.50 & 0.970 & 0.985 \\ Down-D & & & & & & \\ \hline LT Up-A & 3.00 & 0.922 & 0.960 & 0.31 & 0.980 & 0.990 \\ LT Up-B & 2.19 & 0.918 & 0.958 & 0.41 & 0.980 & 0.990 \\ LT Up-C & 1.88 & 0.740 & 0.860 & 1.00 & 0.904 & 0.946 \\ LT Up-D & 2.22 & 0.966 & 0.983 & 0.23 & 0.974 & 0.987 \\ LT Down-A & 2.81 & 0.868 & 0.932 & 0.34 & 0.967 & 0.983 \\ LT Down-B & 2.34 & 0.871 & 0.933 & 0.43 & 0.970 & 0.985 \\ LT Down-C & 2.41 & 0.942 & 0.971 & 0.98 & 0.966 & 0.983 \\ LT Down-D & 2.03 & 0.943 & 0.971 & 0.24 & 0.966 & 0.983 \\ \hline LM Up-A & 1.56 & 0.934 & 0.966 & 0.47 & 0.979 & 0.990 \\ LM Up-B & 1.09 & 0.907 & 0.952 & 0.69 & 0.975 & 0.988 \\ LM Up-C & 1.23 & 0.872 & 0.934 & 0.85 & 0.971 & 0.986 \\ LM Up-D & 2.97 & 0.978 & 0.989 & 0.37 & 0.984 & 0.992 \\ LM Down-A & 1.79 & 0.893 & 0.945 & 0.49 & 0.971 & 0.985 \\ LM Down-B & 1.31 & 0.917 & 0.958 & 0.68 & 0.978 & 0.989 \\ LM Down-C & 1.78 & 0.855 & 0.925 & 0.82 & 0.973 & 0.987 \\ LM Down-D & 2.72 & 0.948 & 0.973 & 0.30 & 0.969 & 0.984 \\ \hline \hline \end{tabular} Note: HT is high (WT) top, HM is high (WT) middle, LT is low (MG) top, LM is low (MG) middle.  
\end{table} 
Table 2: The statistical relationship between the measured and modeled fluorescence for the representative leaf samples, before and after adding the FQE inversion code (root mean square error (RMSE) unit: Wm\({}^{-2}\)um\({}^{-1}\)sr\({}^{-1}\)). of the leaves for both the top and middle layers. For these leaves, the first and second peaks of fluorescence were also overestimated in the upward and downward directions. Only in the second peak of the upward fluorescence were the simulations for the two leaves underestimated (see Figure 4). In general, the simulated fluorescence for low-chlorophyll-content leaves was overestimated over the entire wavelength range. The simulation results without inversion code show that the model always overestimated the fluorescence, especially in the first and second peaks. PS II and PS I greatly influenced the emissions of these components. The photosystem plays an important role in fluorescence emissions. When plants photosynthesize, PS II is responsible for the emission of fluorescence at around 680 nm, while the fluorescence of PS I peaks at around 700 nm. The photosystems play a role in the occurrence of fluorescence peaks and influence the fluorescence over the entire wavelength range. Larger values of FQE II and I result in more fluorescence, especially in the first and second peaks of the fluorescence curve. It is necessary to adjust the default FQE values to obtain a better agreement between the simulated and measured fluorescence. Hence, to improve the model, the emission efficiencies of PS II and PS I were considered. The latest version of Fluspect uses a doubling algorithm that generates the fluorescence matrices of the leaf to simulate fluorescence.