Lab Reflectance spectra of hand samples (with probe) from Puig del Roser

• Agustin.Lobo@geo3bcn.csic.es
• 20230717

require(ggplot2)
require(plotly)
library(RColorBrewer)
require(prospectr)
library(soilspec)
#NOTE: there is also asdreader::get_spectra() (see EspCrater_FS3_nb.Rmd)

# > getwd()
# [1] "/media/alobo/DecepNTFS2/HSI_Lab/Testllum_20230717/Rtestllum_20230717"

dirRSpect <- "/home/alobo/owncloudRSpect/RSpect"
dirdat <- "../EspCrater_HandSamples/FS3"

1. Reading data

f <- read.csv(file.path(dirdat,"FS3spectra.csv"), stringsAsFactors = FALSE)
f$ID <- paste(f$smple,f$point,f$replicate, sep="_")
f$file <- paste0(f$file,".asd")

2. Build data frame (long format)

d.lf <-  NULL
for (i in 1:nrow(f)) {
  r <- readASD(file.path(dirdat,f$file[i]), out_format = 'list')[[1]]$radiance
  rf <- readASD(file.path(dirdat,f$file[i]), out_format = 'list')[[1]]$reference
  s <- readASD(file.path(dirdat,f$file[i]), out_format = 'list')[[1]]$reflectance
  w <- readASD(file.path(dirdat,f$file[i]), out_format = 'list')[[1]]$wavelength
  sc <- spliceCorrection(s,wav=w, splice = c(1000, 1800))
  d.lf <- rbind(d.lf,data.frame(f[i,],w,r,rf,s,sc))
  #d <- cbind(d,)
}
head(d.lf,3)

EspCratHandSamplesProbe.lf <- d.lf

3. Reflectance Spectra

glabprobe <- ggplot(data=d.lf[d.lf$sample!="w",]) +
  geom_line(aes(x=w, y=sc, color=sample, group=file), linewidth=0.3) +
  xlab("Wavelength") + ylab("Reflectance") + 
  ggtitle("Espai Crater: lab (probe) Reflectance spectra")
  #scale_color_brewer(palette = "Set1")
#ggplotly(g2)
ggplotly(glabprobe + facet_wrap(~sample))