#' @title Parse BrainModel from CIFTI
#' @description Extracts information about BrainModels from CIFTI file
#' @param nodeset Set of XML nodes corresponding to \code{BrainModel}
#' @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, "./BrainModel")
#' }
#' @importFrom xml2 xml_attrs xml_find_all xml_text
parse_brain_model = function(nodeset) {
if (is.list(nodeset) &&
!inherits(nodeset, "xml_nodes") &&
!inherits(nodeset, "xml_nodeset")) {
return(lapply(nodeset, parse_brain_model))
}
n_nodes = length(nodeset)
all_attrs = xml_attrs(nodeset)
all_attrs = lapply(all_attrs, as.list)
all_attrs = lapply(all_attrs, function(x) {
nums = is_cifti_numeric(names(x))
if (any(nums)) {
x[nums] = lapply(x[nums], as.numeric)
}
return(x)
})
vert_nodes = lapply(nodeset,
xml_find_all,
xpath = "./VertexIndices")
get_verts = function(node) {
verts = xml_text(node)
if (length(verts) > 0) {
verts = lapply(verts, strsplit,
split = " ")
verts = lapply(verts, `[[`, 1)
verts = lapply(verts, as.numeric)
if (length(verts) > 1){
stop(paste0(
"Multiple vertice indices ",
"in BrainModel"))
}
verts = verts[[1]]
}
return(verts)
}
verts = lapply(vert_nodes, get_verts)
vox_nodes = lapply(nodeset,
xml_find_all,
xpath = "./VoxelIndicesIJK")
get_vox_ijks = function(node) {
verts = xml_text(node)
if (length(verts) > 0) {
verts = strsplit(verts,
split = "\n")[[1]]
verts = lapply(verts, function(x){
x = strsplit(x, " ")[[1]]
x = as.numeric(x)
})
## === mjm 20200717
# Originally, the code expected newlines in the XML separating
# triples of voxel ijk indices, but many CIFTI files I've encountered
# (ones produced by the FieldTrip MATLAB functions) don't have these
# newlines but rather a long string of space-delimited values of length
# 3 x n_vertices. Adding the below condition to accommodate this possibility.
element_lengths = sapply(verts, length)
if (all(element_lengths == 3))
verts = do.call("rbind", verts)
else if (all(element_lengths == 1))
verts = data.frame(
matrix(unlist(verts), ncol = 3, byrow = TRUE)
)
else
stop("Unrecognized or inconsistent voxel IJK sequence")
colnames(verts) = c("i", "j", "k")
}
return(verts)
}
vox = lapply(vox_nodes, get_vox_ijks)
### double_check
n_vert = sapply(verts, length) > 0
n_vox = lapply(vox, length) > 0
if (!all(!(n_vox & n_vert)) ) {
stop(paste0("Bad specification for ",
"Vox IJK or Vertices"))
}
verts = mapply(function(i, l){
attributes(i) = l
return(i)
}, verts, all_attrs, SIMPLIFY = FALSE)
vox[n_vox] <- mapply(FUN = function(i,j) {
attributes(i)$VoxelIndicesIJK <- j
return(i)
}, verts[n_vox], vox[n_vox])
verts[n_vox] = vox[n_vox]
# =====
return(verts)
}
#' @rdname parse_brain_model
#' @param fname filename of CIFTI file
#' @export
get_brain_model = function(fname, verbose = TRUE) {
nodes = matrix_ind_map_nodes(fname)
nodeset = lapply(nodes, xml_find_all, xpath = "./BrainModel")
nodeset = keep_sub_nodeset(nodeset)
if (verbose) {
message("Parsing Brain Model Data")
}
parse_brain_model(nodeset)
}
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