## 4 The Data-Collection, Processing, and Display Software
### Operating--Data Acquisition  
Upon completion of system configuration, CDAP begins collecting GPS and data logger data streams, and saving them to files. Whether in calibration or observation mode, CDAP configures the radiometers and takes an initial spectral scan to determine incoming downwelling irradiance and to appropriately set instrument integration times. Once set, CDAP performs a spectral scan and writes the data obtained to a file. At the same time, if so selected, CDAP executes a shutter trigger command to the digital camera in order to capture the scene in the radiometer field of view. The program is equipped to automatically download data from the camera or to retrieve the picture file from a directory if camera software controls the download. In the calibrating and observing modes, CDAP provides to the operator both real-time quick-look reflectance and (quasi) absorption spectra (Figure 6), as well as camera images. The operator can use this information to ascertain correct operation and equipment configuration. Figure 6: This screen capture shows CALMIT Data Acquisition Program (CDAPTM) during field observation. The graphs at the top show, left to right, the upwelling radiance and downwelling irradiance; calculated reflectance and reciprocal reflectance (a proxy of absorbance). The last 25 observations are plotted on the right two screens. The plots are colorcoded with the latest being bright white to distinguish them. Operating parameters and activating buttons are shown in the control screen. The panel at the right center can contain a camera image preview. The lower part of the screen shows raw data and the status of data collection. Prior to actual data collection, a Spectralon (North Sutton, NH, USA) 99% reflective reference panel is positioned beneath the sensor and scanned in order not only to assure that both Ocean Optics radiometers are spectrally coincident (levels of sensitivity as well as band centers) but also to link all subsequent measurements of downwelling irradiance to national standards (via the documented characteristics of the reference surface). The median reflectance spectrum from the Spectralon panel is adjusted as required based on the manufacturer's coefficients that describe the spectral reflectivity of the panel at a given wavelength. All other calibration is based upon the simultaneous measurement of upwelling radiance and downwelling irradiance. The procedure, as described in [PERSON] [8] (and in preceding text), involves Radiometer \(\#1\), equipped with a 25\({}^{\circ}\) field-of-view optical fiber being pointed downward to measure the radiance upwelling from the crop canopy (\(L_{\lambda}\)_maie_). Radiometer \(\#2\), equipped with an optical fiber and cosine diffuser (yielding a hemispherical field of view), is pointed upward to simultaneously measure incident irradiance (\(E_{\lambda}^{\textit{inc}}\)). To match their transfer functions, the inter-calibration of the radiometers is accomplished by measuring the upwelling radiance (\(L_{\lambda}^{\textit{cal}}\)) of the white Spectralon reflectance standard, simultaneously with incident irradiance (\(E_{\lambda}^{\textit{cal}}\)). Percent reflectance, \(\rho_{\lambda}\), is computed as:  
\[\rho_{\lambda}=\left(\frac{L_{\lambda}^{\textit{maieze}}}{E_{\lambda}^{\textit{ inc}}}\right)\times\left(\frac{E_{\lambda}^{\textit{cal}}}{L_{\lambda}^{\textit{cal}}} \right)\times 100\times\rho_{\lambda}^{\textit{cal}} \tag{1}\]  
One critical issue with regard to the dual-fiber approach is that the transfer functions of both radiometers must be identical. We tested our Ocean Optics instruments under laboratory and field conditions and found that over a four-hour period the coefficient of variation of the ratio of the two transfer functions did not exceed 0.4%. During operation, CDAP may be configured to operate in a manual mode or an automatic mode where measurements are taken repeatedly at a specified rate. CDAP has been successfully used in diverse field venues for several years.