R/file_catalogue.R

In Nature40/tRackIT: Process data recorded with automatic radio-tracking stations

#' create file and parameter catalogue from raw logger data
#'
#' @description Creates a catalogue of all raw logger files in folder
#'
#'
#' @author Jannis Gottwald
#'
#' @param station string, station of hich the files should be catagolized
#' @param projList list, generatet by initProject function
#' @param collection string, path to data collection in station folder from which the files should be catagolized
#'
#' @export
#'
#'



file.catalogue <- function(projList, station = ".", collection = ".") {
  root <- paste0(projList$path$raw, station, "/", collection, "/")

  tmp_files <- list.files(root, full.names = T)

  all_files <- unlist(strsplit(tmp_files, split = "/"))

  all_csv <- all_files[grepl("*\\.csv", all_files)]
  all_sig <- as.data.frame(stringr::str_split_fixed(all_csv, "_", 2))
  all_sig$file <- all_csv
  all_time <- as.data.frame(stringr::str_split_fixed(all_sig$V1, "T", 2))
  all_time$time <- NA

  for (j in seq_len(all_time))
  {
    x <- as.character(all_time$V2[j])
    x2 <- substring(as.character(all_time$V2[j]), seq(1, nchar(x) - 1, 2), seq(2, nchar(x), 2))
    all_time$time[j] <- paste0(x2[1], ":", x2[2], ":", x2[3])
  }

  all_sig$time <- paste(all_time$V1, all_time$time)

  colnames(all_sig) <- c("conf_match", "receiver", "signals", "time")

  all_sig$receiver <- stringr::str_replace(all_sig$receiver, ".csv", "")

  all_conf <- all_files[grepl("*\\.conf", all_files)]

  conf_df <- data.frame(config = all_conf, conf_match = stringr::str_replace(all_conf, ".conf", ""))

  catalogue <- merge(all_sig, conf_df, by = "conf_match")

  catalogue$GAIN <- NA

  catalogue$THRESHOLD <- NA

  catalogue$FREQUENCY <- NA

  for (m in unique(catalogue$conf_match))
  {
    if (file.exists(paste0(root, "/", catalogue$config[catalogue$conf_match == m][1]))) {
      conf <- read.csv(paste0(root, "/", catalogue$config[catalogue$conf_match == m][1]), header = F, sep = "=")
      catalogue$GAIN[catalogue$conf_match == m] <- conf$V2[conf$V1 == "GAIN"]
      catalogue$THRESHOLD[catalogue$conf_match == m] <- conf$V2[conf$V1 == "THRESHOLD"]
      catalogue$FREQUENCY[catalogue$conf_match == m] <- conf$V2[conf$V1 == "FREQUENCY"]
    } else {
      next
    }
  }

  catalogue$station <- station
  catalogue$time <- as.POSIXct(catalogue$time)
  write.csv(catalogue, paste0(paste0(projList$path$catalogues, station, "_collection_", collection, "_FROM_", as.Date(min(catalogue$time)), "_TO_", as.Date(max(catalogue$time)), "_file_catalogue.csv")))
}