R/splitNDImageToList.R

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

#' splitNDImageToList
#'
#' This function splits the dimensionality d input image into a list of images
#' with dimensonality d-1 by slicing the input image along its last dimension.
#'
#' @param img input image of class antsImage, last dimension will be split
#' @return output list filled with d-1 volumes of class antsImage
#' @author Pustina D, Avants B
#' @examples
#'
#' my4Dimage <- makeImage(c(5, 5, 5, 4))
#' my3Dlist <- splitNDImageToList(my4Dimage)
#'
#' @export splitNDImageToList
#'
splitNDImageToList <- function(img) {
  # check input is good
  if (!inherits(img, "antsImage")) stop("Input is not antsImage.")
  mydimv <- dim(img)
  mydim <- img@dimension
  if (img@dimension < 3) {
    stop("Input image dimensionality needs to be 3 or greater")
  }

  # put matrix to a list
  newimgs <- list()
  for (z in 1:mydimv[mydim]) {
    newimgs[[z]] <- extractSlice(img, z, mydim)
  }

  # copy headers to new images
  direction <- antsGetDirection(img)[-mydim, -mydim]
  spacing <- antsGetSpacing(img)[-mydim]
  origin <- antsGetOrigin(img)[-mydim]
  for (im in newimgs) {
    antsSetDirection(im, direction)
    antsSetSpacing(im, spacing)
    antsSetOrigin(im, origin)
  }
  return(newimgs)
}


#' mergeListToNDImage
#'
#' This function will copy a list of d-1 images into a d-dimension target image.
#' This function reverses the operation performed by \code{splitNDImageToList}.
#'
#' @param img input image of class antsImage, last dimension will be split
#' @param imgList input list to be merged back into dimension d space
#' @return output list filled with d-1 volumes of class antsImage
#' @author Pustina D, Avants B
#' @examples
#'
#' my4Dimage <- makeImage(c(5, 5, 5, 4), rnorm(5 * 5 * 5 * 4))
#' my3Dlist <- splitNDImageToList(my4Dimage)
#' my4DimageR <- mergeListToNDImage(my4Dimage, my3Dlist)
#'
#' @export mergeListToNDImage
#'
mergeListToNDImage <- function(img, imgList) {
  # check input is good
  if (!inherits(img, "antsImage")) stop("Input is not antsImage.")
  mydimv <- c(dim(imgList[[1]]), length(imgList))
  mydim <- img@dimension
  if (img@dimension < 3) {
    stop("Input image dimensionality needs to be 3 or greater")
  }

  iarr <- array(data = NA, dim = mydimv)
  for (i in 1:length(imgList))
  {
    temp <- as.array(imgList[[i]])
    if (mydim == 3) {
      iarr[, , i] <- temp
    }
    if (mydim == 4) {
      iarr[, , , i] <- temp
    }
  }
  iarr <- as.antsImage(iarr)
  antsCopyImageInfo(img, iarr)
  antsSetSpacing(
    iarr,
    c(antsGetSpacing(imgList[[1]]), tail(antsGetSpacing(img), 1))
  )
  antsSetOrigin(
    iarr,
    c(antsGetOrigin(imgList[[1]]), tail(antsGetOrigin(img), 1))
  )
  return(iarr)
}