normalizeR

#load libraries
library(raster)
library(tictoc)
#library(devtools)
#devtools::install_github("timelyportfolio/svgPanZoom")
#devtools::install_github("duncantl/SVGAnnotation")
library(svglite)
library(svgPanZoom)
library(SVGAnnotation)
library(tcltk)
library(progress)

#internal functions
source('~/Desktop/INF_550_Notes/standardize.R')

#go to directory where raw files are saved
setwd()

#choose band_names
names <- c("X569.71","X589.88","X615.22","X630.49","X659.89","X665.02","X689.43","X730.74","X790.43","X845.12","X899.86")

#function
normalizeR <- function(names){
  tic()
  Filters <- matrix(c("*",".raw"),1, 2, byrow = TRUE)

  data <- tk_choose.files(caption="choose Data File",filter = Filters)
  filen <- brick(data)

  white <- tk_choose.files(caption="choose 'WHITEREF' File",filter = Filters)
  dark <-tk_choose.files(caption="choose 'DARKREF' File",filter = Filters)

  raw <- raster::subset(filen,names)

  #is there an option to add extra zoom?
  plotRGB(raw,c(1,5,8), axes=TRUE, stretch="hist", main="Raw Image")
  cropC <- drawExtent()
  stripe <- crop(raw,cropC)
  names(stripe) <- names(raw)

  #header file has to exist in same file or this breaks!
  whiteRow <- createReferenceMeanRow(white,stripe,"WhiteRow.tif",names)
  names(whiteRow) <- names(stripe)
  darkRow <- createReferenceMeanRow(dark,stripe,"DarkRow.tif",names)
  names(darkRow) <- names(stripe)

  #find length of core stripe to break up white
  len <- stripe@nrows

  #disaggregate whiterow to length
  whiteRef <- disaggregate(whiteRow,fact = c(1,len))
  darkRef <- disaggregate(darkRow,fact = c(1,len))

  #set extents to be the same between stripe and reference files
  extent(whiteRef) <- extent(stripe)
  extent(darkRef) <- extent(stripe)

  #normalization is fast! 47 seconds for Tutae
  normalized <- overlay(stripe,whiteRef,darkRef,fun = normFun,filename = "normalized.tif",overwrite = TRUE)
  names(normalized) <- names(stripe)

  return(normalized)
}

core_name <- normalizeR()