R/ifcb_download_test_data.R

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

#' Download Test IFCB Data
#'
#' This function downloads a zip archive containing MATLAB files from the `iRfcb`
#' dataset available in the SMHI IFCB Plankton Image Reference Library (Torstensson et al. 2024),
#' unzips them into the specified folder and extracts png images. These data can be used, for instance,
#' for testing iRfcb and for creating the tutorial vignette
#' using \code{vignette("a-general-tutorial", package = "iRfcb")}
#'
#' @param dest_dir The destination directory where the files will be unzipped.
#' @param figshare_article The file article number at the SciLifeLab Figshare data repository.
#' By default, the iRfcb test dataset (48158716) from Torstensson et al. (2024) is used.
#' @param max_retries The maximum number of retry attempts in case of download failure. Default is 5.
#' @param sleep_time The sleep time between download attempts, in seconds. Default is 10.
#' @param verbose A logical indicating whether to print progress messages. Default is TRUE.
#'
#' @return No return value. This function is called for its side effect of downloading, extracting, and organizing IFCB test data.
#'
#' @references Torstensson, Anders; Skjevik, Ann-Turi; Mohlin, Malin; Karlberg, Maria; Karlson, Bengt (2024). SMHI IFCB Plankton Image Reference Library. Version 3. SciLifeLab. Dataset.
#' \doi{10.17044/scilifelab.25883455.v3}
#'
#' @examples
#' \dontrun{
#' # Download and unzip IFCB test data into the "data" directory
#' ifcb_download_test_data("data")
#' }
#'
#' @export
ifcb_download_test_data <- function(dest_dir, figshare_article = "48158716", max_retries = 5, sleep_time = 10, verbose = TRUE) {
  # URL of the zip file
  url <- paste0("https://figshare.scilifelab.se/ndownloader/files/", figshare_article)

  # Create destination directories if they do not exist
  if (!dir.exists(dest_dir)) {
    dir.create(dest_dir, recursive = TRUE)
  }

  # Determine the local destination file path
  dest_file <- file.path(dest_dir, paste0(basename(url), ".zip"))

  # Initialize retry counter
  attempts <- 0
  success <- FALSE

  # Implement retry logic
  while (attempts < max_retries && !success) {
    try({
      # Attempt the download using curl with resume capability
      handle <- new_handle(resume_from = if (file.exists(dest_file)) file.info(dest_file)$size else 0)
      curl_download(url, dest_file, handle = handle, quiet = TRUE)

      # Check if the download was successful
      if (file.exists(dest_file)) {
        success <- TRUE
      }
    }, silent = TRUE)

    # Increment the attempt counter
    attempts <- attempts + 1

    if (!success) {
      if (verbose) {
        message("Attempt ", attempts, " failed. Retrying in ", sleep_time, " seconds...")
      }

      Sys.sleep(sleep_time)
    }
  }

  # If download failed after max_retries, stop the function
  if (!success) {
    stop("Download failed after ", max_retries, " attempts.")
  }


  # Unzip the file into the appropriate subdirectory
  unzip(dest_file, exdir = dest_dir)

  # Remove the downloaded zip file
  file.remove(dest_file)

  # Extract png images
  ifcb_extract_annotated_images(file.path(dest_dir, "manual"),
                                file.path(dest_dir, "config", "class2use.mat"),
                                file.path(dest_dir, "data"),
                                file.path(dest_dir, "png"),
                                skip_class = "unclassified",
                                verbose = FALSE)

  # Define source files
  class_file <- system.file("exdata/example.mat", package = "iRfcb")
  summary_file <- system.file("exdata/example_summary.mat", package = "iRfcb")
  correction_file <- system.file("exdata/example.txt", package = "iRfcb")
  ferrybox_file <- system.file("exdata/example_ferrybox.txt", package = "iRfcb")

  # Define destination directories
  classified_dir <- file.path(dest_dir, "classified", "2023")
  summary_dir <- file.path(classified_dir, "summary")
  manual_dir <- file.path(dest_dir, "manual", "correction")
  ferrybox_dir <- file.path(dest_dir, "ferrybox_data")

  # Create necessary directories
  dir.create(summary_dir, recursive = TRUE, showWarnings = FALSE)
  dir.create(manual_dir, recursive = TRUE, showWarnings = FALSE)
  dir.create(ferrybox_dir, recursive = TRUE, showWarnings = FALSE)

  # Define destination files
  dest_class_file <- file.path(classified_dir, "D20230314T001205_IFCB134_class_v1.mat")
  dest_summary_file <- file.path(summary_dir, "summary_allTB_2023.mat")
  dest_correction_file <- file.path(manual_dir, "Alexandrium_pseudogonyaulax_selected_images.txt")
  dest_ferrybox_file <- file.path(ferrybox_dir, "SveaFB_38059_20220501000100_20220531235800_OK.txt")

  # Copy files to their respective destinations
  file.copy(class_file, dest_class_file)
  file.copy(summary_file, dest_summary_file)
  file.copy(correction_file, dest_correction_file)
  file.copy(ferrybox_file, dest_ferrybox_file)

  if (verbose) {
    cat("Download and extraction complete.\n")
  }
}