#' @title Parse Volume from CIFTI
#' @description Extracts information about Volumes from CIFTI file
#' @param nodeset Set of XML nodes corresponding to \code{Volume}
#' @param verbose print diagnostic messages
#'
#' @return List of values
#' @export
#'
#' @examples \dontrun{
#' doc = cifti_xml(fname)
#' nodes = xml_find_all(doc, "/CIFTI/Matrix/MatrixIndicesMap")
#' nodeset = xml_find_all(nodes, "./Volume")
#' parse_volume(nodeset)
#' }
parse_volume = function(nodeset) {
if (is.list(nodeset) &&
!inherits(nodeset, "xml_nodes") &&
!inherits(nodeset, "xml_nodeset")) {
return(lapply(nodeset, parse_volume))
}
n_nodes = length(nodeset)
all_names = xml_attrs(nodeset,
"VolumeDimensions")
all_names = unlist(all_names)
vert_nodes = lapply(nodeset,
xml_find_all,
xpath = "./TransformationMatrixVoxelIndicesIJKtoXYZ")
get_mat = function(node) {
vert_attr = xml_attrs(node)
if (length(vert_attr) > 1){
vert_attr = lapply(vert_attr,
as.list)
} else {
if (length(vert_attr) == 0) {
vert_attr = NULL
}
vert_attr = as.list(vert_attr[[1]])
}
verts = xml_text(node)
if (length(verts) > 0) {
verts = strsplit(verts, split = "\n")[[1]]
verts = verts[ !(verts %in% "")]
verts = strsplit(verts, " ")
verts = lapply(verts, as.numeric)
verts = do.call("rbind", verts)
# attributes(vert) = vert_attr
}
return(verts)
}
verts = lapply(vert_nodes, get_mat)
verts = mapply(function(x, a) {
list(mat = x, VolumeDimensions = a)
}, verts, all_names, SIMPLIFY = FALSE)
if (length(verts) == 1) {
verts = verts[[1]]
}
return(verts)
}
#' @rdname parse_volume
#' @param fname filename of CIFTI file
#' @export
get_volume = function(fname, verbose = TRUE) {
nodes = matrix_ind_map_nodes(fname)
nodeset = lapply(nodes, xml_find_all, xpath = "./Volume")
nodeset = keep_sub_nodeset(nodeset)
if (verbose) {
message("Parsing Volume Data")
}
parse_volume(nodeset)
}
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