R/save.ANTsR.R

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

#' @rdname save.ANTsR
#' @title Save R sessions including ANTsR objects
#' @description
#' Use this function to save an object or a full R session for
#' later use. Any object can be saved (list, antsImage, data frame,
#' etc.). The function will save all antsImage objects as nifti
#' files with random filenames (to avoid using (sub)variable names,
#' which can be identical). These files is what load.ANTsR uses
#' later to fill back the original antsImage variables. For variables
#' that contain filenames, you can choose to copy those files
#' in your saved folder so you can completely recreate the environment
#' even if you change computer or the temporary folder is deleted.
#'
#' @param filename Prefix for folder to store data.
#' @param objects Vector of character names of objects to store.  Can be antsImages.
#' @param env Environment to save from or load to.
#' @param overwrite logical to select whether overwriting existing data is allowed.
#' @param clonediskfiles logical enables the copying of disk files that are not loaded
#'      in workspace but where character variables point. Set to TRUE if moving sessions
#'      from one computer to another or if you save antsRegistration() outputs. Set to
#'      FALSE if you save temporary sessions to continue later on the same computer.
#' @param ... Additional arguments to pass to \code{save}.
#'
#' @author Dorian Pustina
#'
#' @examples
#' \dontrun{
#' # causes problems with devtools::run_examples()
#' # a <- 1
#' # b <- c( 2, 3, 4)
#' # save.ANTsR(objects=c('b', 'a'))
#' # load.ANTsR("./.ANTsRsession")
#' }
#'
#' @export
save.ANTsR <- function(filename = file.path(".", ".ANTsRsession"),
                       objects = NA,
                       env = as.environment(1),
                       overwrite = FALSE,
                       clonediskfiles = TRUE,
                       ...) {
  # convert to absolute path
  filename <- suppressWarnings(file.path(dirname(normalizePath(filename)), basename(filename)))
  fremove1234567890 <- NULL

  # create or empty the target folder
  if (file.exists(file.path(filename, "ANTSLOAD.Rdata")) & overwrite) {
    fnames <- list.files(filename)
    assign("fremove1234567890", file.path(filename, fnames), envir = env)
  } else {
    dir.create(filename, showWarnings = F)
    assign("fremove1234567890", "", envir = env)
  }
  if (file.exists(file.path(filename, "ANTSLOAD.Rdata")) & !overwrite) {
    stop(paste("Folder", filename, "not empty and overwrite is false."))
  }


  antslist <- as.list(env)
  if (all(!is.na(objects))) {
    index <- match(objects, names(antslist))
    antslist <- antslist[index]
  }


  funimgS <- function(x, fold = filename) {
    file <- paste0(paste(sample(c(0:9, letters, LETTERS), 20, replace = T), collapse = ""), ".nii.gz")
    fn <- file.path(fold, file)
    antsImageWrite(x, fn)
    return(paste0("ANTSload", file))
  }

  funimgSf <- function(x, fold = filename) {
    index <- which(file.exists(x))
    if (length(index) == 0) {
      return(x)
    }

    nocopy <- file.exists(file.path(fold, basename(x[index])))
    noremovef <- file.path(fold, basename(x[index[nocopy]]))
    noremoveindx <- match(noremovef, fremove1234567890)
    assign("fremove1234567890", fremove1234567890[-(noremoveindx)], envir = env)
    x[index[nocopy]] <- paste0("ANTSrepl", basename(x[index[nocopy]]))
    index <- index[!nocopy]
    if (length(index) == 0) {
      return(x)
    }

    for (indx in index) {
      file <- paste0(
        paste(sample(c(0:9, letters, LETTERS), 20, replace = T), collapse = ""),
        "_", basename(x[indx])
      )
      fn <- file.path(fold, file)
      file.copy(x[indx], fn)
      x[indx] <- paste0("ANTSrepl", file)
    }
    return(x)
  }

  if (clonediskfiles) antslist <- rapply(antslist, funimgSf, classes = "character", how = "replace")
  ANTSLOAD <- rapply(antslist, funimgS, classes = "antsImage", how = "replace")

  if (file.exists(file.path(filename, "ANTSLOAD.Rdata")) && overwrite && length(fremove1234567890) > 0) {
    drop <- file.remove(fremove1234567890) # cleanup remaining files in folder
    rm(fremove1234567890, envir = env)
  }

  save(ANTSLOAD, file = file.path(filename, "ANTSLOAD.Rdata"), ...)
}


#' @rdname load.ANTsR
#' @title Load R sessions with ANTsR objects
#' @description
#' Loads a previously saved ANTsR session or object. Simply
#' point the function to the folder where you previously
#' saved the data with save.ANTsR.
#'
#' @param filename path of the saved ANTsR session. If not
#' specified, the default behavior is to search for the
#' folder \".ANTsRsesssion\" in the current working directory.
#'
#' @param env the environment level. Don't change unless you know
#' what are you doing.
#'
#' @usage
#' load.ANTsR(filename=file.path('.','.ANTsRsession'), env=as.environment(1))
#'
#' @author Dorian Pustina
#'
#' @export
load.ANTsR <- function(filename = file.path(".", ".ANTsRsession"),
                       env = as.environment(1)) {
  # convert to absolute path
  filename <- file.path(dirname(normalizePath(filename)), basename(filename))
  ANTSLOAD <- NULL

  funimgL <- function(x, fold = filename) {
    if (length(x) == 1 && substr(x, 1, 8) == "ANTSload") {
      fn <- file.path(fold, substr(x, 9, nchar(x)))
      x <- antsImageRead(fn)
      return(x)
    }

    # here we replace file names in variables
    # starting with ANTSrepl, which were filename vectors
    # when the data were saved with save.ANTsR
    #
    if (any(grepl("^ANTSrepl", x))) x <- file.path(fold, gsub("^ANTSrepl", "", x))
    return(x)
  }

  load(file.path(filename, "ANTSLOAD.Rdata"))
  antslist <- rapply(ANTSLOAD, funimgL, classes = "character", how = "replace")
  envir <- list2env(antslist, envir = env)
}