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#' extract information about fixed landmarks, curves and patches from and atlas
#' generated by "landmark"
#'
#' After exporting the pts file of the atlas from "landmark" and importing it
#' into R via "read.pts" cExtract gets information which rows of the landmark
#' datasets belong to curves or patches.
#'
#'
#' @param pts.file either a character naming the path to a pts.file or the name
#' of an object imported via read.pts.
#' @return returns a list containing the vectors with the indices of matrix
#' rows belonging to the in "landmark" defined curves, patches and fix
#' landmarks and a matrix containing landmark coordinates.
#' @author Stefan Schlager
#' @seealso \code{\link{read.lmdta}} ,\code{\link{read.pts}}
#' @export
cExtract <- function(pts.file)
{
if (is.character(pts.file))
x <- read.pts(pts.file)
else
x <- pts.file
allnames <- row.names(x)
cs <- grep("C",allnames)
ps <- grep("P",allnames)
S <- grep("S",allnames)
if (length(ps))
cs <- c(cs,ps)
if (length(cs)) {
cnames <- row.names(x)[cs]
olevels <- levels(as.factor(substr(cnames,1,4)))
} else {
warning("no curves or patches found")
olevels <- NULL
}
S <- grep("S",allnames)
if (!length(S)) {
S <- NULL
} else {
S <- "S"
}
olevels <- c(S, olevels)
tl <- length(olevels)
out <- list()
for (i in 1:tl)
out[[olevels[i]]] <- grep(olevels[i],allnames)
out$coords <- x
return(out)
}
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