R/spectralCalculations.R

In nickmckay/specimR: R tools for working with specim sediment core hyperspectral data

# ##Script for taking normalized data output from normalize.R function and calculating indices
#
# #choose desired outputs
#
#
# #transpose normalized dataset and get normalized values
# getNormValues <- function(normalized){
#   norm <- t(normalized$normalized)
#   data <- raster::getValues(norm,row = 1)
#   colnames(data) <- names(normalized$spectra)
# return(data)
# }
#
# #and subsetted bands
# subsetBands <- function(data){
# bands <- gsub("X","",colnames(data))%>%as.numeric()
# bands <- data.table::data.table(Value=bands)
# bands[,merge:=Value]
# data.table::setkeyv(bands,c('merge'))
# return(bands)
# }
#
# #RABD660
# getRABD660 <- function(data,bands, normalized,indices){
#   if (indices[grepl("RABD660",indices)]!="RABD660"){ print("next")
# } else{
# vals_660 <- data.table::data.table(Value = c(590,660,730))
# vals_660[,merge:=Value]
# data.table::setkeyv(vals_660,c('merge'))
# r660 <-bands[vals_660,roll='nearest']
# r660n <- as.character(paste0("X",r660$Value))
# r660v <- data[,r660n]
#
# dBtwnLo <- sum(normalized$allbands < r660$Value[2] & normalized$allbands > r660$Value[1])
# dBtwnHi <- sum(normalized$allbands < r660$Value[3] & normalized$allbands > r660$Value[2])
# dBtwnTot <- sum(normalized$allbands < r660$Value[3] & normalized$allbands > r660$Value[1])
# RABD_660 <- as.data.frame((((dBtwnLo*r660v[,3])+(dBtwnHi*r660v[,1]))/dBtwnTot)/r660v[,2])
# colnames(RABD_660) <- "RABD660"
# return(RABD_660)
# }
# }
# #RABD 845
# getRABD845 <- function(data,bands, normalized,indices){
#   if (indices[grepl("RABD845",indices)]!="RABD845"){ print("next")
#   } else{
# vals_845 <- data.table::data.table(Value = c(790,845,900))
# vals_845[,merge:=Value]
# data.table::setkeyv(vals_845,c('merge'))
# r845 <-bands[vals_845,roll='nearest']
# r845n <- as.character(paste0("X",r845$Value))
# r845v <- data[,r845n]
#
# dBtwnLo <- sum(normalized$allbands < r845$Value[2] & normalized$allbands > r845$Value[1])
# dBtwnHi <- sum(normalized$allbands < r845$Value[3] & normalized$allbands > r845$Value[2])
# dBtwnTot <- sum(normalized$allbands < r845$Value[3] & normalized$allbands > r845$Value[1])
# RABD_845 <- as.data.frame((((dBtwnLo*r845v[,3])+(dBtwnHi*r845v[,1]))/dBtwnTot)/r845v[,2])
# colnames(RABD_845) <- "RABD845"
# return(RABD_845)
# }
# }
#
# getR570R630 <-function(data,bands,indices){
#   if (indices[grepl("R570R630",indices)]!="R570R630"){ print("next")
#   } else{
#   vals_r570r630 <- data.table::data.table(Value = c(570,630))
#   vals_r570r630[,merge:=Value]
#   data.table::setkeyv(vals_r570r630,c('merge'))
#   r570r630 <-bands[vals_r570r630,roll='nearest']
#   r570r630n <- as.character(paste0("X",r570r630$Value))
#   r570r630v <- data[,r570r630n]
#   R570_R630 <-as.data.frame(r570r630v[,1]/r570r630v[,2])
#   colnames(R570_R630) <- "R570_R630"
# return(R570_R630)
# }
# }
#
# getR590R690 <-function(data,bands, indices){
#   if (indices[grepl("R590R690",indices)]!="R590R690"){ print("next")
#   } else{
#   vals_r590r690 <- data.table::data.table(Value = c(590,690))
#   vals_r590r690[,merge:=Value]
#   data.table::setkeyv(vals_r590r690,c('merge'))
#   r590r690 <-bands[vals_r590r690,roll='nearest']
#   r590r690n <- as.character(paste0("X",r590r690$Value))
#   r590r690v <- data[,r590r690n]
#   R590_R690 <-as.data.frame(r590r690v[,1]/r590r690v[,2])
#   colnames(R590_R690) <- "R590_R690"
#   return(R590_R690)
# }
# }
# GetIndices <- function(normalized,indices){
#   data <- getNormValues(normalized = normalized)
#   bands <- subsetBands(data = data)
#   RABD_660 <-getRABD660(data=data,bands = bands,normalized = normalized,indices=indices)
#   RABD_845 <-getRABD845(data=data,bands = bands,normalized = normalized,indices=indices)
#   R570_R630 <- getR570R630(data=data,bands=bands,indices=indices)
#   R590_R690 <- getR590R690(data=data,bands=bands,indices = indices)
#   scaleY <- normalized$scaleY
#   ext <- extent(normalized$normalized)
#   yseq <- seq(ext@ymin,ext@ymax, by= 1)
#   yseq <- yseq[-1]
#   indicesVals <- cbind(yseq, scaleY,RABD_660,RABD_845,R570_R630,R590_R690)
#  # write.csv(indicesVals, paste0(id,"_Spectral_Calculations",format(Sys.time(),"%d-%b-%Y %H.%M"),".csv"))
#   return(list(indicesVals=indicesVals,bands=bands))
# }
#