DOI: 10.5281/zenodo.13651607
title: Simulated submerged aquatic vegetation spectral signatures under different water quality conditions using Hydrolight

description: Reflectance spectra were simulated using the Hydrolight radiative transfer model (Sequoia Scientific, Bellevue, WA) for four different submerged macrophyte species under a range of water quality conditions at two different depths. We used the four-component case-2 model with spectral reflectance of four submerged species, Egeria densa, Ceratophyllum demersum, Cabomba caroliniana, and Stukenia pectinata. These four reflectance spectra were calculated from the median of 10 measurements of the canopies of the representative species placed in clear tap-water made with a handheld ASD FieldSpec Pro spectrometer. Total suspended solids concentration was varied from 1 to 40 g·m−3, chlorophyll-a concentration was varied from 0.5 to 50 mg·m−3, and colored dissolved organic matter (CDOM) was varied from 0.25 to 3.5 m−1. A total of 4,742 spectra were simulated for all four species and a mud substrate at two different depths, 1 m and 5 m, and for optically deep water.
description: The code included in this publication takes as input all six input files compiled from the output of Hydrolight models as described above. Spectra for each of the six classes, Cabomba caroliniana, Ceratophyllum demersum, Egeria densa, Stukenia pectinata, water, and mud substrate, were simulated using the following values for water quality parameters:Depth in meters: 1 and 5Total Suspended Sediment in g·m−3: 1, 7.4, 13.7, 20.1, 26.4, 32.8, 39.1Colored Dissolved Organic Matter per meter: 0.3, 0.5, 0.7, 0.9, 1.2, 1.4, 1.6, 1.9, 2.1, 2.3, 2.6, 2.8, 3, 3, 3.5Chlorophyll-a in mg·m−3: 0.5, 4, 7.6, 11.1, 14.6, 18.2, 21.7, 25.3, 28.8, 32.3, 35.9, 39.4, 42.9, 46.5, 50

There are 12 output files generated by the script:

test_PSI_summary_1m_20231027.csv - This file contains the summary of every PSI formulation tested, the slope and intercept values needed to calculate the index, and the accuracy achieved for separating water from submerged vegetation using each formulation. The metadata for this file is included in the .xml file in this publication.

test_PSIW_rsquared_1m_20231027.csv, test_PSIS_rsquared_1m_20231027.csv – These two files report the R2 values for the water line or the SAP line for each band-pair tested. For more information, see related citation.

test_PSIW_calcindx_1m_20231027.csv, test_PSIS_calcindx_1m_20231027.csv, test_PSID_calcindx_1m_20231027.csv – These three files have columns for each PSI index calculated using different band pairs. The column header includes the wavelengths of the two bands that were used to calculate the index.

test_PSIW_accgrid_1m_20231027.csv, test_PSIS_accgrid_1m_20231027.csv, test_PSID_accgrid_1m_20231027.csv - These three files report the overall accuracy values using each PSI formulation for each band-pair tested. The maximum accuracy value in each file indicates which band-pair works best for calculating PSI for the set of input data that are being tested. For more information, see related citation.

test_PSIW_kapgrid_1m_20231027.csv, test_PSIS_kapgrid_1m_20231027.csv, test_PSID_kapgrid_1m_20231027.csv - These three files report the Kappa coefficients using each PSI formulation for each band-pair tested. The maximum Kappa value in each file indicates which band-pair works best for calculating PSI for the set of input data that are being tested. For more information, see related citation.