#' @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)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.