SFMResults: SFMResults

In tommasojulitta/FieldSpectroscopyDP: R package for processing fieldspectroscopy data

Description

Calculate the optimized fluorescence and true reflectance

Usage

SFMResults(res, wl, output, fm, O2band)

Arguments

res	list object: as output from optim.
wl	numeric vector: wavelength vector
output	character value: FULL or VALUE referring to output expected. If FULL a data.fame of the spectrum in the considered range of fluorescence and true reflectance is returned. If VALUE the fluorescence and the true reflectance at the selected oxygen band is returned.
fm	object of class "lm", deriving from first guess functoin
O2band	character value: A or B referring to the oxygen absorption band where to compute the fluorescence estimation

Value

numeric vector or data.frame. If output = "FULL" a data.frame containing the spectra of the estimated true reflectance and fluorescence is returned. If output = "VALUE" a vector containing the fluorescence and the reflectance is returned.

Author(s)

Tommaso Julitta, Mirco Migliavacca, Thomas Wutzler

Examples

  





data("FloX_data")


data("up_coeff")


data("dw_coeff")


data("wl_FloX")





L<-GetRadiance(DNSignal=FloX_data$L-FloX_data$dcL,IntegrationTime=FloX_data$IT_L/1000,RadCalCoeff=dw_coeff);L<-L[,1]


#Get Solar Radiance 


E<-GetRadiance(DNSignal=FloX_data$E-FloX_data$dcE,IntegrationTime=FloX_data$IT_E/1000,RadCalCoeff=up_coeff);E<-E[,1]


#Estimate fluorescence using iFLD method, used as first guess for Spectral Fitting Methods


iFLD_O2B<-iFLD(wl=wl_FloX,E,L,fwhm =0.4,O2band="B")


#Define range used for =2B band


range<-which(wl_FloX>684& wl_FloX<700)


#Subset the wavelength vector


WL<-wl_FloX[range]


E_sfm<-as.numeric(E[range])


L_sfm<-as.numeric(L[range])


fluoFG<-iFLD_O2B$Fluo


#Compute the first guess parameter both for reflectance and fluorescence


fg<-FirstGuess(wl = WL,L = L_sfm,E = E_sfm, fluo = iFLD_O2B$Fluo,O2band= "B")


#Rescale parameters


pascales<-log10_ceiling(abs(fg$first_guess$FG)/10);  pascales[which(pascales==0)]<-1


#Optimise the modeled reflected radiance


res<-optim(fg$first_guess$FG,fn=SpecFit,wl=WL,E=E_sfm,L=L_sfm,fm=fg$fm,run="inverse", method="L-BFGS-B",lower=fg$first_guess$lb, 


           upper = fg$first_guess$ub,O2band ="B",control = list(parscale=pascales,fnscale=1e-14,factr=1e-1))


### Extract results


Results<-SFMResults(res = res,wl = WL,output = "VALUE",fm=fg$fm,O2band = "B") 

tommasojulitta/FieldSpectroscopyDP documentation built on March 12, 2020, 1:42 p.m.