R/tempimg.R

In neuroconductor/neurobase: 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects

#' @title Create temporary nii.gz file 
#' @description Takes in a object of class nifti, writes it 
#' to a temp file, appends
#' .nii.gz as \code{\link{writenii}} adds it.
#' @param nim object of class nifti
#' @param gzipped Should file be gzipped? Passed to 
#' \code{\link{writenii}}
#' @param checknan Check for NAs or NaNs
#' @param check_type Check the datatype for an image.  Will run \code{\link{datatyper}}.
#' @param warn Should warnings be displayed if \code{\link{writenii}} has
#' any?  Passed to \code{\link{writenii}}.
#' @param drop_dim Should \code{\link{drop_img_dim}} be applied?
#' @param ... Passed to \code{\link{writenii}}.
#' @return filename of output nii.gz
#' @export
tempimg = function(nim, gzipped = TRUE, checknan = TRUE, 
                   check_type = FALSE, warn = FALSE, 
                   drop_dim = TRUE,
                   ...){
  f = tempfile()
  nim = cal_img(nim)
  nim = zero_trans(nim)
  if (checknan) {
    cnim = c(nim)
    if (any(is.na(cnim) | is.nan(cnim))) {
      warning("NAs and NaNs in image file, replacing with zeros")
      nim[is.na(nim) | is.nan(cnim)] = 0
    }
  }
  if (check_type) {
    nim = datatyper(nim, warn = warn)
  }
  ########### added for weird stuff of NIfTI
  if (drop_dim) {
    nim = drop_img_dim(nim)
  }
  writenii(nim, filename = f, 
           onefile = TRUE, gzipped = gzipped,
           warn = warn,
           drop_dim = drop_dim,
           ...)
  ext = ".nii"
  if (gzipped) ext = paste0(ext, '.gz')
  f = paste0(f, ext)
  f = normalizePath(f)
  return(f)
}