R/database_operations.R

In tjconstant/rindex: Refractive Index Database

install_database <- function(){

  install_path <- system.file("extdata",package = "rindex")
  install_file <- paste0(install_path, "/", "master.tar.gz")

  database_url <- "https://github.com/tjconstant/refractiveindex.info-database/archive/master.tar.gz"

  download.file(url = database_url, destfile = install_file)

  suppressWarnings(untar(tarfile = install_file, exdir = install_path, verbose = TRUE))

  unlink(install_file)

  message("Database Installed Sucessfully.")

}

load_database <- function(){

  database_index <- system.file("extdata/refractiveindex.info-database-master/database/library.yml",package = "rindex")
  con <- file(database_index, open = "rb", encoding = "UTF-8")
  db <- yaml::yaml.load(readLines(con))
  close(con)

  db_tree <- data.tree::as.Node(db)

  # Coinvert & Tidy Up the db index dataframe
  db_df <- data.tree::ToDataFrameTable(db_tree, "SHELF", "DIVIDER","BOOK", "name", "PAGE", "data")
  db_df <- db_df[!grepl(pattern = "Experimental",x = db_df$DIVIDER),]
  db_df <- db_df[!grepl(pattern = "Models and",x = db_df$DIVIDER),]
  db_df <- tidyr::fill(db_df,DIVIDER)
  db_df <- db_df[!is.na(db_df$data),]
  db_df <- data.frame(pageid = 1:length(db_df$SHELF), db_df)

  return(db_df)

}

read.index_file <- function(pageid){
  lookup <- db_df$data[db_df$pageid == pageid]

  x <- system.file(paste0("extdata/refractiveindex.info-database-master/database/data/",lookup),package = "rindex")
  x.raw <- yaml::read_yaml(x)

  data <- read.table(textConnection(x.raw$DATA[[1]]$data))
  names(data) <- c("wavelength (m)", "n", "k")
  data$`wavelength (m)` <- data$`wavelength (m)` * 1e-6

  list(material = db_df$BOOK[db_df$pageid == pageid],
       data = data,
       `minimum wavelength (m)`= min(data$`wavelength (m)`),
       `maximum wavelength (m)`= max(data$`wavelength (m)`),
       reference = x.raw$REFERENCES,
       comments = x.raw$COMMENTS,
       source = db_df$PAGE[db_df$pageid == pageid])
}