R/cropImage.R

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

#' crop a sub-image via a mask
#'
#' uses a label image to crop a smaller image from within a larger image
#'
#' @param image antsImage to crop
#' @param labelImage antsImage with label values.
#'  If not supplied, estimated from data.
#' @param label the label value to use
#' @return subimage
#' @author Brian B. Avants, Nicholas J. Tustison
#' @keywords crop, extract sub-image
#' @examples
#'
#' fi <- antsImageRead(getANTsRData("r16"))
#' cropped <- cropImage(fi)
#' cropped <- cropImage(fi, fi, 100)
#'
#' @export cropImage
cropImage <- function(image, labelImage, label = 1) {
  image <- check_ants(image)

  if (missing(labelImage)) {
    labelImage <- getMask(image)
  }
  labelImage <- check_ants(labelImage)
  if (image@pixeltype != "float" | labelImage@pixeltype != "float") {
    stop("input images must have float pixeltype")
  }
  ANTsRCore::cropImage(image, labelImage, label, 0, NULL, NULL)
}


#' crop a sub-image by image indices
#'
#' create a proper antsImage sub-image by indexing the image with indices.
#' this is similar to but different from array sub-setting in that the resulting
#' sub-image can be decropped back into its place without having to store its
#' original index locations explicitly.
#'
#' @param image antsImage to crop
#' @param lowerind vector of lower index, should be length image dimensionality
#' @param upperind vector of upper index, should be length image dimensionality
#' @return subimage
#' @author Brian B. Avants, Nicholas J. Tustison
#' @keywords crop, extract sub-image
#' @examples
#'
#' fi <- antsImageRead(getANTsRData("r16"))
#' cropped <- cropIndices(fi, c(10, 10), c(100, 100))
#' cropped <- smoothImage(cropped, 5)
#' decropped <- decropImage(cropped, fi)
#'
#' @export cropIndices
cropIndices <- function(image, lowerind, upperind) {
  image <- check_ants(image)
  if (image@pixeltype != "float") {
    stop("input images must have float pixeltype")
  }
  if (image@dimension != length(lowerind) |
    image@dimension != length(upperind)) {
    stop("dimensionality and index length dont match")
  }
  if (any(lowerind < 1) |
    any(upperind > dim(image))) {
    stop("lowerind is < 1 or upperind is > dim(image)")
  }
  if (image@components == 1) {
    return(ANTsRCore::cropImage(
      image, image, 1, 2, lowerind, upperind
    ))
  }
  ilist <- splitChannels(image)
  for (k in 1:image@components) {
    ilist[[k]] <- ANTsRCore::cropImage(
      ilist[[k]], ilist[[k]], 1, 2,
      lowerind, upperind
    )
  }
  return(mergeChannels(ilist))
}


#' decrop a sub-image back into the full image
#'
#' the inverse function for \code{cropImage}
#'
#' @param croppedImage cropped antsImage
#' @param fullImage antsImage to put back into
#' @return decroppedImage
#' @author Brian B. Avants, Nicholas J. Tustison
#' @keywords decrop, extract sub-image
#' @examples
#'
#' fi <- antsImageRead(getANTsRData("r16"))
#' mask <- getMask(fi)
#' cropped <- cropImage(fi, mask, 1)
#' cropped <- smoothImage(cropped, 1)
#' decropped <- decropImage(cropped, fi)
#'
#' @export decropImage
decropImage <- function(croppedImage, fullImage) {
  croppedImage <- check_ants(croppedImage)
  fullImage <- check_ants(fullImage)
  if (croppedImage@pixeltype != "float" | fullImage@pixeltype != "float") {
    stop("input images must have float pixeltype")
  }
  ANTsRCore::cropImage(
    croppedImage, fullImage, 1, 1, NULL, NULL
  )
}




#' extract a slice from an image
#'
#' extract a slice from an image and return an image of dimensionality, d-1
#'
#' @param image antsImage to crop
#' @param slice which slice, integer
#' @param direction which axis, integer
#' @param collapseStrategy collapse sub-matrix.
#' 0: Collapse sub-matrix if positive definite.  Otherwise, thrown exception. Default.
#' 1: Set sub-matrix to identity.  2: Collapse if positive definite.  Otherwise,
#' set to identity.
#' @return antsImage of dimension - 1
#' @author Brian B. Avants, Nicholas J. Tustison
#' @keywords extract
#' @examples
#'
#' fi <- makeImage(c(10, 10, 10), rnorm(1000))
#' slice <- extractSlice(fi, 1, 1)
#'
#' @export extractSlice
extractSlice <- function(image, slice, direction, collapseStrategy = 0) {
  image <- check_ants(image)
  if (image@pixeltype != "float") {
    stop("input images must have float pixeltype")
  }
  if (image@dimension < 3) stop("can't extract 1-d image")
  if (direction > image@dimension) {
    stop("dimensionality and index length dont match")
  }
  if (collapseStrategy != 0 && collapseStrategy != 1 && collapseStrategy != 2) {
    stop("collapseStrategy must be 0, 1, or 2.")
  }
  ANTsRCore::extractSlice(image, slice - 1, direction - 1, collapseStrategy)
}