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#' Read a CIFTI file quickly
#'
#' Read a CIFTI file by exporting it as a single GIFTI
#' using \code{-cifti-convert -to-gifti-ext} (\code{\link{read_cifti_flat}}),
#' and obtaining the brainordinate mapping using
#' \code{-cifti-export-dense-mapping} (\code{\link{info_cifti}}).
#'
#' @inheritParams cifti_fname_Param
#' @inheritParams surfL_fname_Param
#' @inheritParams surfR_fname_Param
#' @inheritParams brainstructures_Param_all
#' @inheritParams idx_Param
#' @param mwall_values If the medial wall mask is not present in the CIFTI,
#' infer it from these data values. Default: \code{c(NA, NaN)}. If \code{NULL},
#' do not attempt to infer the medial wall mask from the data values.
#' @inheritParams verbose_Param_FALSE
#' @param ... Additional arguments to \code{read_cifti_flat}.
#'
#' @return A \code{"xifti"} object. See \code{\link{is.xifti}}.
#'
#' @keywords internal
#'
read_cifti_convert <- function(
cifti_fname,
surfL_fname=NULL, surfR_fname=NULL,
brainstructures="all", idx=NULL,
mwall_values=c(NA, NaN), verbose=FALSE, ...){
# Check arguments.
brainstructures <- match_input(
brainstructures, c("left","right","subcortical","all"),
user_value_label="brainstructures"
)
if ("all" %in% brainstructures) {
brainstructures <- c("left","right","subcortical")
}
# Create the template.
xifti <- template_xifti()
# ----------------------------------------------------------------------------
# Read files. ----------------------------------------------------------------
# ----------------------------------------------------------------------------
if (verbose) { exec_time <- Sys.time() }
if (verbose) { cat("Reading CIFTI file.\n") }
# Read the CIFTI info.
xifti$meta <- info_cifti(cifti_fname)
bs_present <- brainstructures %in% xifti$meta$cifti$brainstructures
if (!all(bs_present)) {
warning(paste0(
"Only the following brainstructures are present in the CIFTI file: ",
paste(xifti$meta$cifti$brainstructures, collapse=", "), "\n"
))
brainstructures <- brainstructures[bs_present]
}
# Select metadata columns if only some data columns will be read in.
if (!is.null(idx)) {
if (!is.null(xifti$meta$cifti$names)) {
if (!all(idx %in% seq(length(xifti$meta$cifti$names)))) {
stop(
"`idx` is invalid: must be positive integer(s) indicating column(s) of ",
"the `xifti`. There are ", length(xifti$meta$cifti$names), " columns."
)
}
xifti$meta$cifti$names <- xifti$meta$cifti$names[idx]
}
if (!is.null(xifti$meta$cifti$labels)) {
xifti$meta$cifti$labels <- xifti$meta$cifti$labels[idx]
}
xifti$meta$cifti$misc$idx <- idx
}
# Read the CIFTI data.
xifti_data <- read_cifti_flat(cifti_fname, idx=idx, ...)
if (get_cifti_extn(cifti_fname) == "dlabel.nii") {
if (!all(round(xifti_data) == xifti_data)) {
warning("The CIFTI file extension was \"dlabel.nii\" but the data values were not integers.")
} else {
mode(xifti_data) <- "integer"
}
}
# Place cortex data into the \code{"xifti"} object.
last_left <- sum(xifti$meta$cortex$medial_wall_mask$left)
last_right <- last_left + sum(xifti$meta$cortex$medial_wall_mask$right)
if ("left" %in% brainstructures) {
cortex <- make_cortex(
xifti_data[1:last_left,, drop=FALSE],
side = "left",
mwall = xifti$meta$cortex$medial_wall_mask$left,
mwall_values=mwall_values,
mwall_source="the CIFTI being read in",
)
xifti$data$cortex_left <- cortex$data
xifti$meta$cortex$medial_wall_mask["left"] <- list(cortex$mwall)
} else {
xifti$meta$cortex$medial_wall_mask["left"] <- list(template_xifti()$meta$cortex$medial_wall_mask$left)
}
if ("right" %in% brainstructures) {
cortex <- make_cortex(
xifti_data[(1+last_left):last_right,, drop=FALSE],
side = "right",
mwall = xifti$meta$cortex$medial_wall_mask$right,
mwall_values=mwall_values,
mwall_source="the CIFTI being read in",
)
xifti$data$cortex_right <- cortex$data
xifti$meta$cortex$medial_wall_mask["right"] <- list(cortex$mwall)
} else {
xifti$meta$cortex$medial_wall_mask["right"] <- list(template_xifti()$meta$cortex$medial_wall_mask$right)
}
# Place subcortical data into the \code{"xifti"} object.
if ("subcortical" %in% brainstructures) {
alpha_to_spatial <- order(order(xifti$meta$subcort$labels))
subcort_order <- c((1+last_right):nrow(xifti_data))[alpha_to_spatial]
xifti$data$subcort <- xifti_data[subcort_order,, drop=FALSE]
} else {
xifti$meta$subcort <- template_xifti()$meta$subcort
}
# Read surfaces.
if (!is.null(surfL_fname) | !is.null(surfR_fname)) {
if(verbose) { cat("...and surface(s).\n") }
}
if (!is.null(surfL_fname)) { xifti <- add_surf(xifti, surfL=surfL_fname) }
if (!is.null(surfR_fname)) { xifti <- add_surf(xifti, surfR=surfR_fname) }
# Finish.
if (!is.xifti(xifti)) { stop("The \"xifti\" object was invalid.") }
if (verbose) {
print(Sys.time() - exec_time)
exec_time <- Sys.time()
}
structure(xifti, class="xifti")
}
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