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daisea

A package for decomposing total non-water absorption spectra into CDM and phytoplankton absorption.

The daisea package utilizes derivative analysis, iterative spectral evaluation and Gaussian decomposition of total non-water absorption spectra to provide an estimate of colored detrital material (CDM) absorption and phytoplankton absorption.

The primary function is daisea (Derivative Analysis and Iterative Spectral Evaluation of Absorption) as described in the manuscript Deriving inherent optical properties from decomposition of hyperspectral non-water absorption (Grunert et al. 2019, https://doi.org/10.1016/j.rse.2019.03.004). We encourage users to refer to this document for a detailed description of steps along with a flow chart; additional information on function output can be found in this document as well. As the main executable function, daisea utilizes a variety of custom sub-functions as well as the following Matlab Toolboxes: Curve Fitting Toolbox and Signal Processing Toolbox. Input spectra should be hyperspectral, ideally at a wavelength range of ≤ 5 nm. Spectral range should extend to approximately 350 nm and up to 690 nm or greater. All function files include a detailed description of required input variables.

Primary function

daisea

Sub-functions

build_daisea_model

Function utilizes an estimated single exponential model and pre-defined number of estimated Gaussian curves to fit total non-water absorption using a least squares approach.

build_phy_model

Function optimizes a pre-defined number of estimated Gaussian curves for a given signal using a least squares approach.

cdom_model_lam0_noK

Function models a colored dissolved organic matter (CDOM), non-algal particulate (NAP), or CDM absorption spectra with a single exponential following a defined initial wavelength, absorption at that wavelength, and no offset value (K value).

spectral_slope_nogauss_noK

Function estimates spectral slope (S) for a CDOM, NAP or CDM absorption spectra assuming the spectra can be fit with a single exponential model, no Gaussian components and K value.

cdom_model_0gaussian_noK

Function models an absorption spectra best approximated with a single exponential and no Gaussian components with no K value.

cdom_model_1gaussian_noK

Function models an absorption spectra best approximated with a single exponential and one Gaussian component with no K value.

cdom_model_2gaussian_noK

Function models an absorption spectra best approximated with a single exponential and two Gaussian components with no K value.

cdom_model_3gaussian_noK

Function models an absorption spectra best approximated with a single exponential and three Gaussian components with no K value.

cdom_model_4gaussian_noK

Function models an absorption spectra best approximated with a single exponential and four Gaussian components with no K value.

cdom_model_5gaussian_noK

Function models an absorption spectra best approximated with a single exponential and five Gaussian components with no K value.

cdom_model_6gaussian_noK

Function models an absorption spectra best approximated with a single exponential and six Gaussian components with no K value.

cdom_model_7gaussian_noK

Function models an absorption spectra best approximated with a single exponential and seven Gaussian components with no K value.

cdom_model_8gaussian_noK

Function models an absorption spectra best approximated with a single exponential and eight Gaussian components with no K value.

cdom_model_9gaussian_noK

Function models an absorption spectra best approximated with a single exponential and nine Gaussian components with no K value.

cdom_model_10gaussian_noK

Function models an absorption spectra best approximated with a single exponential and ten Gaussian components with no K value.

cdom_model_11gaussian_noK

Function models an absorption spectra best approximated with a single exponential and eleven Gaussian components with no K value.

cdom_model_12gaussian_noK

Function models an absorption spectra best approximated with a single exponential and twelve Gaussian components with no K value.

cdom_model_13gaussian_noK

Function models an absorption spectra best approximated with a single exponential and thirteen Gaussian components with no K value.

cdom_model_14gaussian_noK

Function models an absorption spectra best approximated with a single exponential and fourteen Gaussian components with no K value.

cdom_model_15gaussian_noK

Function models an absorption spectra best approximated with a single exponential and fifteen Gaussian components with no K value.

cdom_model_16gaussian_noK

Function models an absorption spectra best approximated with a single exponential and sixteen Gaussian components with no K value.

gauss

Function models a single Gaussian curve.

gauss1

Function models a single Gaussian curve.

gauss2

Function models two Gaussian curves.

gauss3

Function models three Gaussian curves.

gauss4

Function models four Gaussian curves.

gauss5

Function models five Gaussian curves.

gauss6

Function models six Gaussian curves.

gauss7

Function models seven Gaussian curves.

gauss8

Function models eight Gaussian curves.

gauss9

Function models nine Gaussian curves.

gauss10

Function models ten Gaussian curves.

gauss11

Function models eleven Gaussian curves.

gauss12

Function models twelve Gaussian curves.

gauss13

Function models thirteen Gaussian curves.

gauss14

Function models fourteen Gaussian curves.

gauss15

Function models fifteen Gaussian curves.

gauss16

Function models sixteen Gaussian curves.

How to use example spectra

for ii=1:length(example_spectra)
	output(ii)=daisea(example_spectra(ii).at_nw,example_spectra(ii).wavelength,350,700);
end

How to plot results

for ii=1:length(output)
	figure;
	plot(output(ii).lam,output(ii).at_nw,’--k’)
	hold on;
	plot(output(ii).lam,output(ii).agd_final_estimate,’-‘,’color’,[140 81 10]/255)
	plot(output(ii).lam, output(ii).agd_final_estimate+output(ii).aphy_final_estimate,’-‘,’color’,[35 139 69]/255)
end

How to cite this package

This algorithm/package was released with an accompanying publication, Deriving inherent optical properties from decomposition of hyperspectral non-water absorption (Grunert et al. 2019, https://doi.org/10.1016/j.rse.2019.03.004). Please cite this paper when using this package for presentations, publications, etc.

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A package for decomposing total non-water absorption spectra into CDM and phytoplankton absorption.

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