R/neuron-mesh.R

In jefferis/nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

# internal function
# read a mesh representing a neuron and return a mesh3d object
read.neuron.mesh <- function(x, updateNormals=FALSE, clean=FALSE, ...) {
  ext=tools::file_ext(x)
  
  if(ext=="ply") {
    if(!requireNamespace('Rvcg', quietly = TRUE))
      stop("Please install suggested library Rvcg to read .ply files!")
    m=Rvcg::vcgPlyRead(x, updateNormals=updateNormals, clean=clean, ...)
    if(!inherits(m, 'shape3d'))
      class(m)=union(class(m), 'shape3d')
    m
  } else if(ext=="obj") {
    if(!requireNamespace('readobj', quietly = TRUE))
      stop("Please install suggested library readobj to read .obj files!")
    res=readobj::read.obj(x, convert.rgl = TRUE)
    if(length(res)>1)
      warning("Only reading 1/",length(res)," objects in: ",x)
    res[[1]]
  } else {
    stop("Unrecognised mesh file format!")
  }
}

is.ply<-function(f=NULL, bytes=NULL) {
  if(!is.null(bytes) && is.character(f) && length(f)>1)
    stop("Can only check bytes for a single file")
  tocheck=if(is.null(bytes)) f else bytes
  generic_magic_check(tocheck, "ply")
}

write.neuron.ply <- function(x, file, binary=TRUE, ...) {
  write.neuron.mesh(x, file=file, format="ply", binary=binary, ...)
}

write.neuron.obj <- function(x, file, ... ) {
  write.neuron.mesh(x, file=file, format="obj", ...)
}

write.neuron.mesh <- function(x, file, format=c("ply", "obj"), ...) {
  if(!requireNamespace('Rvcg', quietly = TRUE))
    stop("Please install suggested library Rvcg to write .",format," files!")
  if(!inherits(x, 'mesh3d')) {
    x=tryCatch(as.mesh3d(x), error=function(e) stop("Unable to convert x to mesh3d object! Only neuron meshes can be written in ",format," format!"))
  }
  if(format=="ply") {
    if(!isTRUE(tools::file_ext(file)=="ply")) {
      # ply format must end in .ply 
      origfile=file
      file=tempfile(fileext = '.ply')
      on.exit(file.copy(file, origfile, overwrite = T), add = T)
      on.exit(unlink(file), add = T)
    }
    Rvcg::vcgPlyWrite(x, filename=file, writeCol = F, writeNormals = F, ...)
  }
  else if(format=="obj")
    Rvcg::vcgObjWrite(x, filename=file, writeNormals=F, ...)
  else stop("Unknown format")
  
}