R/tension.R

In benharden27/sea: Process and plot data from the Sea Education Association's archive

#' Find maximum tension for wire files in a folder
#'
#' @param data_folder the folder where the tension files are kept
#'
#' @return
#' @export
#'
#' @examples
max_tension <- function(data_folder, cruiseID = NULL,
                        width = 8, thresh = 100,
                        plotFL = TRUE, check = TRUE) {

  # Create list of files to cycle through
  files <- list.files(data_folder,"^[CS]{1}[0-9]{3}")
  if(length(files)==0)
    stop("no files that meet criteria in folder")

  if(is.null(cruiseID))
    cruiseID <- stringr::str_extract(files[1],"^[CS][0-9]{3}")

  # create output data folder
  process_out <- file.path(data_folder,"processed")
  if (!file.exists(process_out))
    dir.create(process_out)

  # create output plotting folder
  if(plotFL) {
    plot_out <- file.path(process_out,"plots")
    if (!file.exists(plot_out))
      dir.create(plot_out)
  }

  # name output file
  file_out <- paste0(cruiseID, "_maxtension.csv")

  # check if file has already been processed
  if (check == TRUE & file.exists(file.path(process_out,file_out))) {
    max_tension <- readr::read_csv(file.path(process_out,file_out),
                                   col_types = "cd")
    files <- setdiff(files,max_tension$cast)
  }

  if(length(files)>0) {
    # cycle through data files, find max tension and plot
    max_tension2 <- tibble::tibble(cast = files, max_tension = NA)
    for (i in 1:length(files)) {

      # read and process data
      file <- file.path(data_folder,files[i])
      data <- readr::read_csv(file, col_names = F, col_types = readr::cols(.default = readr::col_double()), skip = 10)
      data$X3 <- oce::despike(data$X3)
      datasm <- runmed(data$X3, 121, endrule = "constant")
      tr <- range(which(datasm > thresh), na.rm = T)
      tr <- round(tr + c(1,-1)*diff(tr)/width)
      max_tension2$max_tension[i] = max(data$X3[tr[1]:tr[2]],na.rm = T)
      max_t_i <- tr[1] - 1 + which.max(data$X3[tr[1]:tr[2]])

      # plot data if required
      if(plotFL) {
        ggplot2::qplot(1:nrow(data),data$X3) +
        ggplot2::geom_point(ggplot2::aes(max_t_i, max_tension2$max_tension[i]),
                            color = "red", size = 5) +
        ggplot2::ylab("Wire Tension") +
        ggplot2::xlab("Index")
        ggplot2::ggsave(file.path(plot_out, paste0(files[i], ".png")))
      }
    }

    if(check == TRUE & file.exists(file.path(process_out,file_out))) {
      max_tension <- rbind(max_tension,max_tension2)
    } else {
      max_tension <- max_tension2
    }

    readr::write_csv(max_tension, file.path(process_out,file_out))
  }

}