R/load_obj_data.R

In espadon: Easy Study of Patient DICOM Data in Oncology

#' Load data of an \pkg{espadon} class object
#' @description The \code{load.obj.data} function loads all the data of an \pkg{espadon} 
#' object of class '\code{struct}' or '\code{volume}'.
#' @param obj  \code{struct} or "volume" class object
#' @param tag.dictionary Dataframe, by default equal to 
#' \link[espadon]{dicom.tag.dictionary}, whose structure it must keep. 
#' This dataframe is used to parse DICOM files in case obj was extracted from DICOM files.

#' @return Returns the \pkg{espadon} object with data \code{$vol3D.data} or \code{$roi.data}
#' @seealso \link[espadon]{load.obj.from.dicom} and \link[espadon]{load.obj.from.Rdcm}

#' @examples
#' # First, save toy patient objects to a temporary file pat.dir for testing.
#' pat.dir <- file.path(tempdir(), "PM_Rdcm") 
#' dir.create(pat.dir, recursive = TRUE) 
#' patient <- toy.load.patient(modality = c("ct", "mr"), roi.name = "", 
#'                             dxyz = c (4, 4, 4))
#' save.to.Rdcm(patient$ct[[1]], dirname = pat.dir)
#' rm( patient)
#' 
#' 
#' patient <- load.patient.from.Rdcm (pat.dir, data = FALSE)
#' CT <- load.obj.data(patient$ct[[1]])
#' str(CT, max.level = 2)
#' # Cleaning  temporary directory
#' unlink(pat.dir, recursive = TRUE)

#' @export
#' @importFrom methods is
load.obj.data <- function(obj, tag.dictionary = dicom.tag.dictionary()) {

  if (!(is(obj, "volume") | is(obj, "struct"))) return(obj)
    #stop ("obj must be of class 'struct' or 'volume'")
  fp <- file.path(obj$file.dirname, obj$file.basename)
  ref.pseudo <- obj$ref.pseudo
  if (grepl("[.]Rdcm$",fp[1])) return(load.obj.from.Rdcm(fp[1]))
  obj <- load.obj.from.dicom(fp,ref.pseudo = ref.pseudo, 
                             tag.dictionary = tag.dictionary,
                             verbose = FALSE)
  return(obj)  
}