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#' Flatten a \code{"xifti"}
#'
#' Concatenates the data in a \code{"xifti"} object row-wise to form a single matrix.
#'
#' If all brain structures are present, and if
#' \code{is.null(medial_wall)} and \code{subcort_order=="alphabetical"}
#' (the default arguments), then the result will be identical to the matrix
#' obtained with the Connectome Workbench command
#' \code{-cifti-export-dense-mapping}.
#'
#' @inheritParams xifti_Param
#' @param medial_wall Should vertices for the medial wall be included with the
#' cortical data? If \code{NULL} (default), do not include them. If any other
#' value, use that value to fill rows corresponding to the medial wall mask.
#' @param subcort_order "alphabetical" (default) to match the Connectome
#' Workbench command \code{-cifti-export-dense-mapping}, or "spatial" which is
#' already the ordering used in the \code{"xifti"}.
#'
#' @return The flattened \code{"xifti"}, a data matrix
#'
#' @keywords internal
#'
flatten_xifti <- function(xifti, medial_wall=NULL, subcort_order="alphabetical") {
if (!is.xifti(xifti)) { stop("The input \"xifti\" object is invalid.") }
if (!is.null(medial_wall)) {
stopifnot(length(medial_wall) == 1)
if (!is.null(xifti$data$cortex_left)) {
cortex_dat <- matrix(medial_wall,
nrow=length(xifti$meta$cortex$medial_wall_mask$left),
ncol=ncol(xifti$data$cortex_left)
)
cortex_dat[xifti$meta$cortex$medial_wall_mask$left,] <- xifti$data$cortex_left
xifti$data$cortex_left <- cortex_dat
}
if (!is.null(xifti$data$cortex_right)) {
cortex_dat <- matrix(medial_wall,
nrow=length(xifti$meta$cortex$medial_wall_mask$right),
ncol=ncol(xifti$data$cortex_right)
)
cortex_dat[xifti$meta$cortex$medial_wall_mask$right,] <- xifti$data$cortex_right
xifti$data$cortex_right <- cortex_dat
}
}
if (subcort_order=="alphabetical" && !is.null(xifti$data$subcort)) {
alpha_order <- order(xifti$meta$subcort$labels)
xifti$data$subcort <- xifti$data$subcort[alpha_order,, drop=FALSE]
}
do.call(rbind, xifti$data)
}
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