## 2 System Description and Data Collection
### Data Collection  
The central controlling software includes several modules that implement different functions. An open\(-\)close module is required to manage the computer and the measurement process. The solar zenith angle (SZA) is calculated based on the latitude, longitude, and the local time so that the time when the measurements should start and stop can be determined. Once the SZA is larger than 85\({}^{\circ}\), the spectra acquisition process will stop. Two alternative observation modes, manual and automatic, are provided. The automatic mode is used mainly during the making of continuous, long-term field measurements. The manual mode is more suitable for use during the calibration process or when making a single measurement for a specific purpose. In the automatic observation mode, the single beam sandwiched method is employed to collect the down-welling and up-welling spectra following the method proposed by the previous works [25; 32]. The schematic observation sequence is displayed in Figure 2. The first down-welling solar irradiance, the up-welling radiance, and the second down-welling irradiance are sequentially collected by controlling the shutters. The effect of the variation in the solar irradiance resulting from the time delay can be reduced by averaging the two down-welling irradiance measurements. Typically, an entire measurement can be accomplished within 15 s at noon and within 2 min at sunrise and sunset. The integration time is a key parameter for determining the amount of light entering the spectrometer via the optical fibers and has to be set corresponding to the incident irradiance. In order to maximize the SNR, the incoming energy has to make full use of the dynamic range of the spectrometer. A range for the ratio of the measured intensity to the saturation value of the spectrometer is set to automatically determine the integration time. A simple integration time optimization method ([33]) is used in this system. Iterations are not required for this algorithm and this helps to reduce the time delay to as little as possible. \[\Pi_{opt}=\frac{DN_{opt}}{DN_{default}}\Pi_{default}, \tag{1}\]  
where IT\({}_{opt}\) is the optimized integration time and \(\Pi_{default}\) is the default integration time measured previously. \(DN_{default}\) is the maximum value of the spectral range at the default integration time. \(DN_{opt}\) is the optimized count value with a variable range from 80% to 90% of the spectrometer saturation  
Figure 2: Flow diagram showing the data collection sequence used in the automated observation mode of the SIFSpec system. The circles and squares represent the downward and upward channels, respectively. The \(\surd\) and \(\times\) symbols indicate that the light channel is open and closed, respectively. ORT and DN indicate the optimization process of the integration time and the digital number measured by the spectrometer, respectively. value (~65,000). In general, the integration times are around 600 ms and 500 ms at noon under clear-sky conditions for the downward and upward channels, respectively. However, the integration time will significantly increase under low light conditions, especially in the early morning and late afternoon or if it is cloudy, which will increase the risk of a time mismatch between the downward irradiance and upward radiance measurements. The solar irradiance, in particular, fluctuates rapidly as a result of moving clouds, as well as in the early morning and late afternoon. This can cause a large bias in the retrieved spectral reflectance and, as a result, there is the potential for making inaccurate SIF retrievals. Thus, a maximum integration time (IT) of 8 s is set for any illumination conditions. By default, the IT is about 0.6 s at noon and 3 s in the morning and afternoon for the down-welling channel on a cloud-free day. For the up-welling channel, the IT is around 0.4 s and 1.8 s at these times. The dark currents (DCs) resulting from the thermal noises and readout noises continuously vary with the integration time and the temperature.