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#' Combine \code{"xifti"}s with non-overlapping brain structures
#'
#' Combine two to three \code{"xifti"}s with non-overlapping brain structures into
#' a single \code{"xifti"}. The names, intent, and surfaces of the first will be used,
#' if present. To add more surfaces to the result, use \code{\link{add_surf}}.
#'
#' @param ... The \code{"xifti"} objects
#' @param xii_list Alternatively, a list of \code{"xifti"} objects. If specified,
#' will ignore \code{...}
#' @param meta \code{"first"} (default) to just use the metadata from the first
#' argument, or \code{"all"} to include the other metadata in a list.
#' @return A \code{"xifti"} with data from the inputs
#'
#' @family manipulating xifti
#' @export
#'
combine_xifti <- function(..., xii_list=NULL, meta=c("first", "all")) {
meta <- match.arg(meta, c("first", "all"))
if (!is.null(xii_list)) { xiis <- xii_list } else { xiis <- list(...) }
# Check validity of inputs. --------------------------------------------------
if (length(xiis) > 3) {
stop(
"Inputs must be `xifti` objects with non-overlapping brain structures.",
"So, there should be 3 or less inputs."
)
}
# Each input must be a \code{"xifti"}.
bad_xiis <- !vapply(xiis, is.xifti, FALSE, messages=FALSE)
if (any(bad_xiis)) {
is.xifti(xiis[[which(bad_xiis)[1]]])
stop_msg <- paste0(
"Arguments at these indices were not `xifti` objects: ",
paste(which(bad_xiis), collapse=", "), "."
)
if (sum(bad_xiis) >= 1) {
stop_msg <- paste(
stop_msg,
"The error message for the first invalid xifti is printed above."
)
}
stop(stop_msg)
}
# Combine. -------------------------------------------------------------------
out <- xiis[[1]]
# Handle `dlabel`.
dlabel_out <- (!is.null(out$meta$cifti$intent)) && (out$meta$cifti$intent == 3007)
if (dlabel_out) {
dlabel_vals <- unique(do.call(c, lapply(out$meta$cifti$labels, function(x){x$Key})))
}
T_ <- ncol_xifti(out)
for (ii in seq(2, length(xiis))) {
# More validity checks.
if (ncol_xifti(xiis[[ii]]) != T_) {
stop(
"The input at index ", ii, " had ", ncol_xifti(xiis[[ii]]),
" columns, whereas the first input had ", T_, " columns."
)
}
bsidx_out <- !vapply(out$data, is.null, FALSE)
bsidx_ii <- !vapply(xiis[[ii]]$data, is.null, FALSE)
if (any(bsidx_out & bsidx_ii)) {
bs_both <- c("left cortex", "right cortex", "subcortex")[bsidx_out & bsidx_ii]
stop("These brain structures were present in more than one argument: ", paste(bs_both, collapse=", "), ".")
}
# Intent.
dlabel_ii <- (!is.null(xiis[[ii]]$meta$cifti$intent)) && (xiis[[ii]]$meta$cifti$intent == 3007)
if (dlabel_out && (!dlabel_ii)) {
xiis[[ii]] <- convert_to_dlabel(xiis[[ii]], levels=dlabel_vals)
}
# Combine data.
if (!is.null(xiis[[ii]]$data$cortex_left)) {
out$data$cortex_left <- xiis[[ii]]$data$cortex_left
if (!is.null(xiis[[ii]]$meta$cortex$medial_wall_mask$left)) {
out$meta$cortex$medial_wall_mask$left <- xiis[[ii]]$meta$cortex$medial_wall_mask$left
}
}
if (!is.null(xiis[[ii]]$data$cortex_right)) {
out$data$cortex_right <- xiis[[ii]]$data$cortex_right
if (!is.null(xiis[[ii]]$meta$cortex$medial_wall_mask$right)) {
out$meta$cortex$medial_wall_mask$right <- xiis[[ii]]$meta$cortex$medial_wall_mask$right
}
}
if (!is.null(xiis[[ii]]$data$subcort)) {
out$data$subcort <- xiis[[ii]]$data$subcort
out$meta$subcort <- xiis[[ii]]$meta$subcort
}
}
# Combine metadata.
if (meta == "all") {
if (!is.null(out$meta$cifti$misc$combined)) {
warning("`$meta$cifti$misc$combined` will be overwritten.")
}
out$meta$cifti$misc$combined <- lapply(xiis, function(x){ x$meta$cifti })
}
stopifnot(is.xifti(out))
out
}
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