R/struct_in_new_ref.R

In espadon: Easy Study of Patient DICOM Data in Oncology

#' Change of frame of reference of a "struct" class object.
#' @description The \code{struct.in.new.ref} function allows you to change the 
#' frame of reference of a struct.
#' @param struct "struct" class object.
#' @param new.ref.pseudo pseudonym of the frame of reference in which the struct 
#' should be located. This \code{new.ref.pseudo} must exist in the \code{T.MAT} list.
#' @param T.MAT "t.mat" class object, created by 
#' \link[espadon]{load.patient.from.dicom}, \link[espadon]{load.patient.from.Rdcm},
#' \link[espadon]{load.T.MAT} or \link[espadon]{ref.add}.
#' @param alias Character string, \code{$alias} of the created object.
#' @return Returns "struct" class object in the new frame of reference 
#' \code{new.ref.pseudo}.
#' @seealso \link[espadon]{vol.in.new.ref}
#' @examples
#' # loading of toy-patient objects (decrease dxyz for better result)
#' step <- 4
#' patient <- toy.load.patient (modality = c("mr", "rtstruct"), roi.name = "", 
#'                              dxyz = rep (step, 3))
#' S <- patient$rtstruct[[1]]
#' S.in.new.ref <- struct.in.new.ref (S, patient$mr[[1]]$ref.pseudo, patient$T.MAT)

#' @export
#' @importFrom methods is

struct.in.new.ref <- function (struct, new.ref.pseudo, T.MAT, alias="") {
  if (is.null (struct)) return (NULL)
  if (!is (struct, "struct")) stop ("struct should be a struct class object.")
  
  if (new.ref.pseudo!=struct$ref.pseudo){
    if (!is (T.MAT, "t.mat")) stop ("T.MAT should be a t.mat class object.")
    }
  
  if (is.null(struct$roi.data))  {
    warning ("struct$roi.data is NULL.")
  }
  
  
  if (new.ref.pseudo==struct$ref.pseudo){
    struct$object.alias <- alias
    return (struct)
  }
  M <- get.rigid.M (T.MAT, struct$ref.pseudo, new.ref.pseudo)

  if (is.null (M)) stop("no transfer matrix between struct$ref.pseudo and new.ref.pseudo")

  struct_ <- list(object.alias=struct$object.alias,object.info=struct$object.info)
  class(struct_) <- "struct"
  struct$file.basename <- ""
  struct$file.dirname <- ""
  struct$object.name <- alias
  struct$object.alias <- alias
  struct$object.info <- NULL
  struct$ref.object.alias <- NULL
  struct$ref.object.info <- NULL
  struct$ref.pseudo <- new.ref.pseudo
  struct$frame.of.reference <- T.MAT$ref.info[T.MAT$ref.info$ref.pseudo==new.ref.pseudo, ]$ref
  
  struct$ref.from.contour <- M %*% struct$ref.from.contour
  struct$ref.from.contour [abs (struct$ref.from.contour) < 1.0e-6] <- 0
  if (!is.null(struct$roi.data))
    struct$roi.info[ , 7:17] <- .struct.moreinfo(struct$roi.data,
                                                 struct$ref.from.contour,
                                                 struct$thickness)
  
  if (alias=="") return(struct)
  return(.set.ref.obj(struct,list(struct_)))
  
}