R/clean_mesh.R

In lcrawlab/SINATRA: Sub Image Analysis using Topological Summary Statistics (SINATRA)

#### Aligning and Scaling the meshes ####
#' Scale & Translate Meshes
#'
#' @export
#'
#' @import Rvcg
#' @import Morpho
#' @import rgl
#'
#' @description Scales the meshes to have unit surface area and translates the meshes to the origin.
#'
#' @param input_dir The input directory of the files to scale & translate.
#' @param output_dir The output directory to put the files post scaling and translating.
#' @return None; files written in output path.
clean_files=function(input_dir,output_dir){
  files=list.files(path = dir,full.names = TRUE)
  filenames=list.files(path=dir,full.names = FALSE)
  num_files=length(files)
  for (i in seq_len(num_files)){
    print(files[i])
    file=Rvcg::vcgImport(files[i])
    filename=paste(output_dir,filenames[i],sep='')
    area=Rvcg::vcgArea(file)
    file2=Morpho::scalemesh(file,1/sqrt(area),center='mean')
    centroid <- colMeans(Morpho::vert2points(file2))
    file3=rgl::translate3d(file2,-centroid[1],-centroid[2],-centroid[3])
    print(filename)
    Rvcg::vcgOffWrite(file3,filename = filename)
  }
}