R/ifcb_replace_mat_values.R

In iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

utils::globalVariables("replace_value_in_classlist")
#' Replace Values in MATLAB Classlist
#'
#' This function replaces a target class ID with a new ID in MATLAB classlist files,
#' generated by the code in the `ifcb-analysis` repository (Sosik and Olson 2007).
#'
#' @details
#' Python must be installed to use this function. The required python packages can be installed in a virtual environment using `ifcb_py_install()`.
#'
#' @param manual_folder A character string specifying the path to the folder containing MAT classlist files to be updated.
#' @param out_folder A character string specifying the path to the folder where updated MAT classlist files will be saved.
#' @param target_id The target class ID to be replaced.
#' @param new_id The new class ID to replace the target ID.
#' @param column_index An integer value specifying which classlist column to edit. Default is 1 (manual).
#' @param do_compression A logical value indicating whether to compress the .mat file. Default is TRUE.
#'
#' @return This function does not return any value; it updates the classlist files in the specified directory.
#' @seealso \code{\link{ifcb_py_install}} \url{https://github.com/hsosik/ifcb-analysis}
#' @references Sosik, H. M. and Olson, R. J. (2007), Automated taxonomic classification of phytoplankton sampled with imaging-in-flow cytometry. Limnol. Oceanogr: Methods 5, 204–216.
#' @examples
#' \dontrun{
#' # Initialize a python session if not already set up
#' ifcb_py_install()
#'
#' # Replace class ID 99 with 1 in .mat classlist files
#' ifcb_replace_mat_values("output/manual", "output/manual", 99, 1, column_index = 1)
#' }
#' @export
ifcb_replace_mat_values <- function(manual_folder, out_folder, target_id, new_id, column_index = 1, do_compression = TRUE) {

  # Initialize python check
  check_python_and_module()

  # Import the Python function
  source_python(system.file("python", "replace_value_in_classlist.py", package = "iRfcb"))

  # Check if the manual_folder exists
  if (!dir.exists(manual_folder)) {
    stop(paste("The manual folder does not exist:", manual_folder))
  }

  # Create the output folder if it does not exist
  if (!dir.exists(out_folder)) {
    dir.create(out_folder, recursive = TRUE)
  }

  # List files to be updated
  files <- list.files(manual_folder, pattern = "\\.mat$", full.names = TRUE)

  if (length(files) == 0) {
    stop(paste("No files found in the manual folder:", manual_folder))
  }

  for (i in seq_along(files)) {
    file_path_in <- files[i]

    # Skip empty/corrupt files
    if (file.size(file_path_in) == 0) {
      warning(paste("Empty .mat file:", file_path_in, "Skipping."))
      next
    }

    file_path_out <- file.path(out_folder, basename(files[i]))

    replace_value_in_classlist(
      file_path_in,  # Ensure correct file path
      file_path_out,  # Ensure correct output file path
      as.integer(target_id),
      as.integer(new_id),
      as.integer(column_index),
      do_compression
    )
  }
}