auto3dgmBLE

#auto3dgm for Perdiz points from Toyah sites
library(Matrix)
library(clue)
library(linprog)
library(igraph)
library(MASS)

rm(list=ls())
library(auto3dgm)
setwd(getwd())
Data_dir = "data"
Output_dir = "3dgm"

Levels=c(75,150)
Ids = c('EF01', 'EF02', 'EFO3', 'EF05', 'EF06', 'EF08', 'EF09', 'EF10', 'EF11', 
        'EF12', 'FT01', 'FT02', 'FT03', 'FT04', 'FT05', 'FT06', 'FT07', 'FT08', 'FT10',
        'FT11', 'FT12')  
Names = c('EF01', 'EF02', 'EFO3', 'EF05', 'EF06', 'EF08', 'EF09', 'EF10', 'EF11', 
          'EF12', 'FT01', 'FT02', 'FT03', 'FT04', 'FT05', 'FT06', 'FT07', 'FT08', 'FT10',
          'FT11', 'FT12')


#FULL is a list of 3 returned elements.  User gets to specify what is returned.
FULL = align_shapes(Data_dir, Output_dir, Levels, Ids, Names)


ds = FULL[[1]]  #the whole shape dataset.
ga_full=FULL[[2]]  #the global alignment 
pa=FULL[[3]] #the pairwise alignments.  

#Each of these three returned items is useful in identifying and fixing 
#misaligned shapes. 

#vcgPlyRead to import ascii PLY Files
vcgPlyRead(file, updateNormals = TRUE, clean = TRUE)

#vcguniformremesh to resample a mesh uniformly
data(dataname)
resample <- vcgUniformRemesh(x, voxelSize = NULL, offset = 0, discretize = FALSE, multiSample = FALSE, mergeClost = False, silent = False)
require(rgl)
shade3d(humresample, col=#)

#create a loop
x <- c(#,#,#)

#vcgOFFWrite to Export meshes to OFF-files
data(dataname)
vcgOffWrite(mesh,filename = dataname)