R/bin_subtraction.R

In espadon: Easy Study of Patient DICOM Data in Oncology

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#' Subtraction of two binaries
#' @description The \code{bin.subtraction} function creates a "volume" class 
#' object of "binary" modality, representing the subtraction of two binary objects.
#' @param vol1,vol2 "volume" class objects of "binary" modality.
#' @param alias Character string, \code{$alias} of the created object.
#' @param description Character string, describing the created object. If 
#' \code{description = NULL} (default value), it will be set to 
#' \code{paste (vol1$object.alias, "-", vol2$object.alias)}.

#' @return Returns a "volume" class object of "binary" modality (see 
#' \link[espadon]{espadon.class} for class definitions), with the same grid as 
#' \code{vol1} and \code{vol2}, in which \code{vol2} is subtracted from \code{vol1}.
#'
#' @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))
#' MR <- patient$mr[[1]]
#' S <- patient$rtstruct[[1]]
#'
#' z.ptv <- S$roi.info$Gz[S$roi.info$roi.pseudo == "ptv"]
#'
#' # binaries
#' bin.patient <- bin.from.roi (MR, struct = S, roi.name = "patient",
#'                            alias = "patient", T.MAT = patient$T.MAT,
#'                            verbose = FALSE)
#' bin.ptv <- bin.from.roi (MR, struct = S, roi.name = "ptv",
#'                            alias = "ptv", T.MAT = patient$T.MAT,
#'                            verbose = FALSE)
#'
#' #' calculation of the 'patient - ptv' binary
#' bin <- bin.subtraction (bin.patient, bin.ptv, alias = "patient - ptv")
#' display.plane (MR, top = bin, view.coord = z.ptv, 
#'                display.ref = S$ref.pseudo, T.MAT = patient$T.MAT,
#'                interpolate = FALSE)

#' @export
#' @importFrom methods is
bin.subtraction <- function (vol1, vol2 , alias = "", description = NULL) {
  
  if ((!is (vol1, "volume") & !is.null(vol1)) | (!is (vol2, "volume") & !is.null(vol1))) 
    stop ("vol1 or vol2 should be volume class objects.")
  if (!is.null(vol1)){
    if (vol1$modality!="binary") stop ("vol1 must be of binary modality.")
    if (is.null(vol1$vol3D.data)) stop ("empty vol1$vol3D.data.")
  }
  if (!is.null(vol2)){
    if (vol2$modality!="binary") stop ("vol2 must be of binary modality.")
    if (is.null(vol2$vol3D.data)) stop ("empty vol2$vol3D.data.")
  }
  
  if (is.null(vol1)) return (NULL)
  if (is.null(vol2)) return (vol1)
  
  #verifier que les volumes ont le même support
  if (!grid.equal (vol1, vol2)) stop ("both volumes must share the same grid.")
 
  if (is.null(description))  description <-  paste (vol1$object.alias, "-", vol2$object.alias)
  Vb <- vol.copy (vol1, alias = alias, modality = "binary", description = description)
  
  Vb$vol3D.data <- vol1$vol3D.data & (!vol2$vol3D.data)
  # Vb$vol3D.data[is.na(Vb$vol3D.data)] <- FALSE
  Vb$min.pixel <- all(Vb$vol3D.data)
  Vb$max.pixel <- any(Vb$vol3D.data)
  
  if (alias=="") return(Vb)
  return(.set.ref.obj(Vb,list(vol2)))
}