## 4 Materials and Methods
### Correction for the PSI Fluorescence  
The rMLR model is only valid for fluorescence emissions from PSII [31]; the contribution of the PSI fluorescence should be excluded from all actively and passively induced ChlF related to Equation (3). Using the far-red method, [PERSON] et al. [67] showed that the PSI fluorescence yield (F\({}_{1}\)) detected by the PAM fluorometer for C\({}_{3}\) species can be estimated as:  
\[\mathrm{F}_{{}_{1}}=0.24\times\mathrm{F}_{{}_{0}}, \tag{4}\]  
By subtracting F\({}_{1}\) from the fluorescence yields (F\({}_{0}\), F\({}_{\mathrm{m}}\), F\({}_{\mathrm{m}}\)\({}^{\prime}\), F\({}_{\mathrm{I}}\)) directly measured by the PAM fluorometer, we were able to correct them for PSI fluorescence. Accordingly, all other yields/parameters derived from these four yields, \(\phi_{\mathrm{P}}\), \(\phi_{\mathrm{F}}\), \(\phi_{\mathrm{N}}\), \(\phi_{\mathrm{D}}\), and NPQ, were also corrected for PSI fluorescence. See the details in Note S1. Hereafter, all of the active fluorescence parameters in this study only contain the PSII contribution unless otherwise specified. The leaf-scale concurrent measurement system (Figure 11) provides the passive ChlF spectrum in the range 640 to 850 nm at the leaf scale (Chlf\({}_{\mathrm{L}}\)(\(\lambda\)), mW m\({}^{-2}\) nm\({}^{-1}\) sr\({}^{-1}\)):  
\[\mathrm{Chlf}\mathrm{F}_{{}_{\mathrm{L}}}(\lambda)\mathrm{=Chlf}\mathrm{F}_{{}_ {\mathrm{L}}\mathrm{U}}(\lambda)+\mathrm{Chlf}\mathrm{F}_{{}_{\mathrm{L}} \mathrm{D}}(\lambda), \tag{5}\]  
where Chlf\({}_{\mathrm{L}}\)(\(\lambda\)) and Chlf\({}_{\mathrm{L}}\),D(\(\lambda\)) represent the fluorescence radiance emitted fromaxial and abaxial leaf surfaces (\(\mu\)W cm\({}^{-2}\) nm\({}^{-1}\) sr\({}^{-1}\)), respectively, and \(\lambda\) is the wavelength (nm). Figure 12: Flowchart for quantifying the net CO\({}_{2}\) assimilation rate \(A_{\mathrm{net}}\) (umol m\({}^{-2}\) s\({}^{-1}\)) from the passive ChlF spectrum. The definitions of the variables are listed in Appendix A. Due to the strong linear relationships between spectral fluorescence yields and the original PAM F\({}_{\rm t}\) yields [68; 69], deriving the ratio of F\({}_{\rm t}\) yields before and after correction for PSI fluorescence can also allow for an approximate separation of the PSI and PSII spectral fluorescence yields. Further, [PERSON] [70] showed that the ratio of F\({}_{\rm t}\) to F\({}_{\rm 0}\) was 14% and 45% in the spectral ranges below 700 nm (SW) and above 700 nm (LW), respectively. Considering the wavelength-dependent relationships among spectral and PAM fluorescence yields [69], the contribution of PSII (ChIF\({}_{\rm L\_PSII}(\lambda)\)) to measurements of ChIF\({}_{\rm L}\)(\(\lambda\)) can be estimated as:  
\[{\rm ChIF}_{{}_{\rm L\_PSII}}(\lambda)=\left\{ \begin{array}{ll}{\rm ChIF}_{{}_{ \rm L}}(\lambda)\times\frac{{\rm F}_{{}_{\rm t}}-{\rm F}_{{}_{\rm 1},{}_{\rm SW}}}{{\rm F}_{\rm t}}& \lambda\leq 700\,{\rm nm}\\ {\rm ChIF}_{{}_{\rm L}}(\lambda)\times\frac{{\rm F}_{{}_{\rm t}}-{\rm F}_{{}_{ \rm 1},{}_{\rm LW}}}{{\rm F}_{\rm t}}&\lambda>700\,{\rm nm}\end{array} \right., \tag{6}\]  
where F\({}_{\rm t}\) is the steady-state fluorescence yield, and F\({}_{\rm 1\_SW}\) (F\({}_{\rm 1\_SW}\) = 0.14 \(\times\) F\({}_{\rm 0}\)) and F\({}_{\rm 1\_LW}\) (F\({}_{\rm 1\_LW}\) = 0.45 \(\times\) F\({}_{\rm 0}\)) represent the PSI contribution at SW wavelengths and LW wavelengths, respectively. Note that F\({}_{\rm t}\) and F\({}_{\rm 0}\) used in Equation (6) were directly measured by the PAM fluorometer and thus contain contributions from both PSI and PSII.