R/vol_in_new_ref.R

In espadon: Easy Study of Patient DICOM Data in Oncology

#' Change of frame of reference of a volume
#' @description The \code{vol.in.new.ref} function allows you to change the 
#' frame of reference of a volume.
#' @param vol "volume" class object.
#' @param new.ref.pseudo pseudonym of the frame of reference in which the volume 
#' 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{$alias} of the created object.
#' @param description Character string, describing the created object. If 
#' \code{description = NULL} (default value), it will be that of the \code{vol} volume.
#' @return Returns "volume" class object in the new frame of reference 
#' \code{new.ref.pseudo}.
#' @seealso \link[espadon]{struct.in.new.ref}
#' @examples
#' # loading of toy-patient objects (decrease dxyz for  better result)
#' patient <- toy.load.patient(modality = c("ct", "mr"), roi.name = "", 
#'                             dxyz = c(4, 4, 4))
#' CT <- patient$ct[[1]]
#' CT.in.new.ref <- vol.in.new.ref(CT, patient$mr[[1]]$ref.pseudo, patient$T.MAT)

#' @export
#' @importFrom methods is

vol.in.new.ref <- function(vol, new.ref.pseudo, T.MAT, alias="", description = NULL) {
  
  if (is.null(vol)) return(NULL)
  if (!is(vol, "volume")) stop("vol should be a volume class object.")
  
  if (new.ref.pseudo != vol$ref.pseudo) {
    if (!is(T.MAT, "t.mat")) stop("T.MAT should be a t.mat class object.")
  }
  
  if (is.null(vol$vol3D.data)) message("vol$vol3D.data is NULL.")

  
  M <- get.rigid.M(T.MAT, vol$ref.pseudo, new.ref.pseudo)
  if (is.null(M)) stop("no transfer matrix between vol$ref.pseudo and new.ref.pseudo")
  
  V <- vol.copy(vol, alias = alias, description = description)
  V$ref.pseudo <- new.ref.pseudo
  V$frame.of.reference <- T.MAT$ref.info[T.MAT$ref.info$ref.pseudo == new.ref.pseudo, ]$ref
  V$xyz.from.ijk <- M %*% vol$xyz.from.ijk
  V$xyz.from.ijk[abs(V$xyz.from.ijk) < 1.0e-6] <- 0
  V$xyz0 <- matrix((as.matrix(expand.grid(0, 0, vol$k.idx, 1)) %*% t(V$xyz.from.ijk))[ ,1:3],ncol = 3)
  V$orientation <- c(V$xyz.from.ijk[1:3, 1]/vol$dxyz[1], V$xyz.from.ijk[1:3, 2] / vol$dxyz[2])

  if (!is.null(V$beam.source)) {
    V$beam.source <- round(matrix((as.matrix(cbind(V$beam.source,1)) %*% t(M))[,1:3], 
                                  byrow = TRUE, ncol = 3), 6)
    V$beam.orientation <- as.numeric((M %*% cbind(c(V$beam.orientation[1:3],0),
                                                  c(V$beam.orientation[4:6],0)))[1:3,])
  }
  return(V)
}