R/construct_subj_dir.R

In freesurfer: Wrapper Functions for 'Freesurfer'

#' @title Construct Subject Directory
#' @description This function copies files specified by the types of data, 
#' determined by the folder Freesurfer put them in, into a temporary directory
#' for easier separation of data and different structuring of data.
#' @param label Files to copy to \code{subj_root_dir/subj/label} folder
#' @param mri Files to copy to \code{subj_root_dir/subj/mri} folder
#' @param stats Files to copy to \code{subj_root_dir/subj/stats} folder
#' @param surf Files to copy to \code{subj_root_dir/subj/surf} folder
#' @param touch Files to copy to \code{subj_root_dir/subj/touch} folder
#' @param subj Name of subject to make folder for to use for Freesurfer functions.
#' If \code{NULL}, a temporary id will be generated
#' @param subj_root_dir Directory to put folder with contents of \code{subj}
#'
#' @return List with the subject name, the SUBJECTS_DIR to use (the directory
#' that contains the subject name), and the types of objects copied
#' @export
#'
#' @examples \dontrun{
#' library(freesurfer)
#' label = "/Applications/freesurfer/subjects/bert/label/aparc.annot.a2009s.ctab"
#' mri = c(
#'   "/Applications/freesurfer/subjects/bert/mri/aparc.a2009s+aseg.mgz",
#'   "/Applications/freesurfer/subjects/bert/mri/aseg.auto.mgz")
#' stats = c("/Applications/freesurfer/subjects/bert/stats/lh.aparc.stats",
#'           "/Applications/freesurfer/subjects/bert/stats/aseg.stats")
#' surf = "/Applications/freesurfer/subjects/bert/surf/lh.thickness"
#' touch = NULL
#' }
construct_subj_dir = function(label = NULL,
                              mri = NULL,
                              stats = NULL,
                              surf = NULL,
                              touch = NULL,
                              subj = NULL,
                              subj_root_dir = tempdir()) {
  if (is.null(subj)) {
    subj = basename(tempfile())
  }
  base_dir = file.path(subj_root_dir, subj)
  dir.create(base_dir)
  
  L = list(label = label,
           mri = mri,
           stats = stats,
           surf = surf,
           touch = touch)
  # REMOVE NULL
  nulls = sapply(L, is.null)
  L = L[!nulls]
  type_names = fol_names = names(L)
  fol_names = file.path(base_dir, fol_names)
  
  sapply(fol_names, dir.create)
  
  res = mapply(function(y, fol){
    N = length(y)
    res = rep(TRUE, length = N)
    out_names = file.path(fol, basename(y))
    for (ix in seq(N)) {
      x = y[ix]
      if (!file.exists(x)) {
        stop(paste0(x)) 
      }
      out = out_names[ix]
      res[ix] = file.copy(from = x, to = out)
    }
    R = list(
      res = res,
      out_names = out_names
    )
    return(R)
  }, L, fol_names, SIMPLIFY = FALSE)
  out_names = lapply(res, `[[`, "out_names")
  res = lapply(res,  `[[`, "res")
  res = unlist(res )
  stopifnot(all(res))  
  
  R = list(subj = subj,
           subj_dir = subj_root_dir,
           types = type_names)
}
# 
# aparcstats2table(subjects = subj, subj_dir = subj_dir,
#                  measure = "thickness")
# asegstats2table(subjects = subj, subj_dir = subj_dir,
#                  measure = "mean")
# out =