R/placeDowels.r

In zarquon42b/mesheR: Meshing Operations on Triangular Meshes

#' Place Dowels representing tissue depth on a skull
#'
#' Place Dowels representing tissue depth on a skull by using predefined tissue-values
#'
#' @param lm k x 3landmarks representing dowel locations
#' @param mesh triangular mesh (object of class 'mesh3d')
#' @param ldowel vector of length k giving a length for each dowel
#' @param render logical: if TRUE, the result will be rendered in an rgl window
#' @param col color of the dowels
#' @param radius numeric: diameter of dowels
#' @param meshcol mesh color
#' @param fine integer: amount of vertices to generate the cylinders representing tissue thickness.
#' @param smooth logical: use smoothed normals for dowel orientation
#' 
#' @details For orientation of the dowels, the (angle weighted) normal vectors of the surface is used. 
#' @return an invisible list with
#' \item{dowels }{a list containing the meshes for all dowels}
#' \item{endpoints }{a matrix containing the coordinates of the dowels endpoints}
#' 
#' @examples
#' require(Rvcg)
#' data(humface)
#' lms <- matrix(c(17.6061 , 9.2072 , -6.9917 , 44.7959 , 37.1135 ,
#'                 76.0469 , 3.7734 , 12.8234 , 81.3138 , 63.4207 ,
#'                 47.5009 , 44.6468), 4, 3)
#' #place markers of 5mm length
#' \dontrun{
#' placeDowels(lms, humface, rep(5, 4))
#' }
#' @seealso \code{\link{cylinder}}
#' @importFrom rgl shade3d
#' @export placeDowels
placeDowels <- function(lm, mesh, ldowel, render=TRUE,col=1,radius=1,meshcol=3, fine=50, smooth=TRUE, dowelcol=NULL)
{

    ldo <- FALSE
    colvec <- FALSE
    projLM <- vcgClost(lm,mesh,smoothNormals=smooth)
    ##projLM <- closemeshKD(lm,mesh)
                                        #projLM <- projRead(lm,mesh,smooth=TRUE)
    if (length(ldowel) > 1)
        ldo <- TRUE
    
    if (length(col) == nrow(lm))
        colvec <- TRUE
    else
        col <- rep(col[1],nrow(lm))

    dowels <- list()
    endpoints <- matrix(NA, dim(lm)[1] ,3)
    endpoints <- vert2points(projLM)+t(projLM$normals[1:3,])*ldowel
### create dowels and render them if required
    for (i in 1:dim(lm)[1])
    {
        if (ldo)
            ltmp <-ldowel[i]
        else
            ltmp=ldowel

        dowels[[i]] <- cylinder(projLM$vb[1:3,i],projLM$normals[1:3,i],length=ltmp,radius=radius,fine=fine,addNormals=FALSE)
        
        
        dowels[[i]]$material$color <- rep(rgb(t(col2rgb(col[i])),maxColorValue=255),ncol(dowels[[i]]$vb))
        
        if (render) {
            shade3d(dowels[[i]])
        }
    }
    if (render) ## render mesh ##
        shade3d(mesh,col=meshcol)

    invisible(list(dowels=dowels, endpoints=endpoints))
}