Sky-glint Removal (SR) for WISPstation reflectance data

This function implements a sky-glint Removal algorithm based on the methodology proposed by Jiang et al. (2020). The function operates on spectra that have already been filtered through the Quality Control process and applies a correction to obtain glint-corrected remote sensing reflectance. Following this correction, all algorithms are re-applied using the corrected reflectance, ensuring more accurate and physically consistent estimates of water constituents.

Usage

wisp_sr_reflectance_data(
  qc_data,
  calc_scatt = TRUE,
  calc_SPM = TRUE,
  calc_TUR = TRUE,
  calc_TSS = TRUE,
  calc_gons = TRUE,
  calc_gons740 = TRUE,
  calc_NDCI = TRUE,
  calc_mishra = TRUE,
  calc_dom_wave = TRUE,
  calc_OWT = TRUE,
  save_csv = FALSE,
  out_dir = "outputs"
)

Arguments

qc_data

A tibble from wisp_qc_reflectance_data() function.

calc_scatt

A logical. If TRUE, the function calculates the peak due to phytoplankton scattering (690-710 nm) and the ratio of the latter to the second chlorophyll absorption peak (670-680 nm). Default is TRUE.

calc_SPM

A logical. If TRUE, the function calculates the SPM concentrations in according to Novoa et al., (2017). Default is TRUE.

calc_TUR

A logical. If TRUE, the function calculates the turbidity (FNU) in according to Novoa et al., (2017). Default is TRUE.

calc_TSS

A logical. If TRUE, the function calculates the TSS concentrations in according to Jiang et al., (2021). Default is TRUE.

calc_gons

A logical. If TRUE, the function calculates chlorophyll using Gons et al. (2002) algorithm (NIR ~782 nm). Default is TRUE.

calc_gons740

A logical. If TRUE, the function calculates chlorophyll using Gons et al. (2002) algorithm (NIR ~740 nm). Default is TRUE.

calc_NDCI

A logical. If TRUE, the function calculates The Normalised Difference Chlorophyll Index algorithm by Mishra and Mishra (2012). Default is TRUE.

calc_mishra

A logical. If TRUE, the function calculates chlorophyll using Mishra and Mishra (2012) algorithm. Default is TRUE.

calc_dom_wave

A logical. If TRUE, the function calculates the hue angle and the dominant wavelength. Default is TRUE.

calc_OWT

A logical. If TRUE, the function calculates the Optical Water Type classification in according to Bi and Hieronymi (2024) (OWT_class), the membership probability (OWT_score), and the average Z-score (OWT_z_dist). In addition, it adds a column with the description of the corresponding OWT class. "OWT_class" represents the optical category to which the analyzed spectral signature belongs based on Gaussian Likelihood. "OWT_score" is a value between 0 and 1 representing the fuzzy membership grade; it indicates the probability of belonging to the selected class relative to the other available classes. "OWT_z_dist" indicates the statistical distance between the observed spectrum and the class mean, weighted by its standard deviation. 0-1.5 indicate an excellent fit with the OWT reference. Values above 3 suggest that the spectral signature is an outlier or deviates significantly from the typical range of that class. Default is TRUE.

save_csv

A logical. If TRUE, the function saves the reflectance data.

out_dir

A character. The directory where the CSV file will be saved. Default is "outputs" within the working directory.

Value

A tibble with the spectral signatures after the SR operation and all the extra parameters that were requested. If parameter save_csv is TRUE, the function saves the reflectance data in a CSV file.

Author

Alessandro Oggioni, phD alessandro.oggioni@cnr.it

Nicola Ghirardi, phD nicola.ghirardi@cnr.it

Examples

# example code
if (FALSE) { # \dontrun{
## Not run:
reflect_data_sr <- wisp_sr_reflectance_data(
  qc_data = reflect_data_qc,
  calc_scatt = TRUE,
  calc_SPM = TRUE,
  calc_TUR = TRUE,
  calc_TSS = TRUE,
  calc_gons  = TRUE,
  calc_gons740 = TRUE,
  calc_NDCI = TRUE,
  calc_mishra = FALSE,
  calc_dom_wave = TRUE,
  calc_OWT = TRUE,
  save_csv = FALSE,
  out_dir = "outputs"
)
} # }
## End (Not run)