SplineSmoothGapfilling: SplineSmoothGapfilling

In tommasojulitta/FieldSpectroscopyCC: R package for Characterization and Calibration of spectrometers

Description

Apply a spline smoothing and gap filling in the region where NA are found

Usage

SplineSmoothGapfilling(wl, spectrum, df = length(wl)/50)

Arguments

wl	numeric vector: wavelength vector
spectrum	numeric data.frame: First column wavelength vector, second column spectrum vector
df	numeric value: the desired equivalent number of degrees of freedom (trace of the smoother matrix)

Value

numeric vector containing the smoothed spectrum.

Author(s)

Tommaso Julitta, Mirco Migliavacca, Thomas Wutzler

Examples

  





data("outdoor_rad_cal_data")


data("atmospheric_absorption_regions")


integration_time<-450


#Create matrix for radiometric calibration


DN_mat<-DNSpectralMatrixRadCal(spectra = outdoor_rad_cal_data$DN_matrix,IntegrationTime = integration_time)


#calculate mean of several spectra


radiance_mean<-StatsOnSpectra(wl=outdoor_rad_cal_data$radiance_wl,spectra=outdoor_rad_cal_data$radiance_matrix,fun='mean')


#linear resample at refrence radiance wavelength 


radiance_mean_res<-LinearResample(wl = outdoor_rad_cal_data$radiance_wl,spectrum = radiance_mean,wlRef = outdoor_rad_cal_data$DN_wl)


wp_coeff_res<-LinearResample(outdoor_rad_cal_data$wp_coef$V1,outdoor_rad_cal_data$wp_coef$V2,outdoor_rad_cal_data$DN_wl)


#calculate mean of several spectra


DN_mean<-StatsOnSpectra(wl=outdoor_rad_cal_data$DN_wl,spectra=outdoor_rad_cal_data$DN_matrix,fun='mean')


#calculate calibration coefficients


rad_cal<-RadiometricCalibration(type=1,wl=outdoor_rad_cal_data$DN_wl,radiance = radiance_mean_res,DN = DN_mean)


#exclude regions of the spectrum affected by atmospheric absorptions and noisy pixels


range_to_exclude<-data.frame(wl_start=c(outdoor_rad_cal_data$DN_wl[1],outdoor_rad_cal_data$DN_wl[length(outdoor_rad_cal_data$DN_wl)-35]),wl_end=c(outdoor_rad_cal_data$DN_wl[30],outdoor_rad_cal_data$DN_wl[length(outdoor_rad_cal_data$DN_wl)]))


atmospheric_absorption_regions<-rbind(atmospheric_absorption_regions,c(range_to_exclude))


exclude_atmospheric_absorption_features<-ExcludeSpectralRegions(wl=outdoor_rad_cal_data$DN_wl, spectrum = rad_cal,SpectralRegion = atmospheric_absorption_regions)


#smooth results


rad_cal_coeff<-SplineSmoothGapfilling(wl=outdoor_rad_cal_data$DN_wl,spectrum = exclude_atmospheric_absorption_features) 


x11()


plot(outdoor_rad_cal_data$DN_wl,rad_cal,ylim=c(0,0.000025),xlab="WL [nm]",ylab="Conversion coefficients")


points(outdoor_rad_cal_data$DN_wl,exclude_atmospheric_absorption_features,pch=20,col="red")


lines(outdoor_rad_cal_data$DN_wl,rad_cal_coeff,col="green",lwd=2)

tommasojulitta/FieldSpectroscopyCC documentation built on May 31, 2019, 6:19 p.m.