Code forked from Julia Winchester (https://github.com/JuliaWinchester/auto3dgm-fork).

Code has been changed to:

Write out the transormation matrix and origin into the './Results/Aligned_Shapes' folder. 

Code has been used in the following scientific publications:

Exploring age-related variations during talar growth (2019) https://meeting.physanth.org/program/2019/session51/gabanini-2019-exploring-age-related-variations-during-calcaneal-growth.html

Trabecular bone patterning across the human hand (2018) JHE, 123 1-23 https://doi.org/10.1016/j.jhevol.2018.05.004

Signals of loading and function in the human hand: a multi-method analysis of the external cortical and internal trabecular bone of the metacarpals.


################################################################################
#
# auto3dgm-fork
#
# Original auto3dgm package authors: Chris Glynn, Jesus Puente, Doug Boyer,
# Sayan Mukherjee, Ingrid Daubechies, and Justin Gladman
# Departments of Statistical Science, Mathematics, and Evolutionary Anthropology
# Duke University
#
# Fork author: Julia Winchester
# Department of Evolutionary Anthropology
# Duke University
################################################################################ 

auto3dgm-fork is a branch of the R version of auto3dgm that implements a number 
of "quality of life" improvements while maintaining the full capability of the
original auto3dgm R package. These improvements include:

	- Optional disabling of specimen mirroring/reflection during alignment
	- Reading specimens as PLY files in addition to OFF files
	- Lists of file names and IDs are not required for align_shapes() function

#######################
# Loading auto3dgm-fork
#######################

auto3dgm-fork has not been uploaded to CRAN. This means it can't be installed 
using R's install.packages() function, or loaded using R's library() or 
require() functions. Instead, auto3dgm-fork files must be loaded as needed into 
an active R session to be used. The easiest way to do this is to load the 
included file 'source_auto3dgm-fork.R' using R's source() function, like so:

	source("/Users/Julie/Code/auto3dgm-fork/source_auto3dgm-fork.R")

On sourcing, this file should load all auto3dgm-fork files into the active R 
workspace.

########################################
# Using auto3dgm-fork and align_shapes()
########################################

Like standard auto3dgm, auto3dgm-fork is used by calling the align_shapes() 
function (see http://www2.stat.duke.edu/~sayan/auto3dgm/Instructions/index.html 
for more information, this document assumes some familiarity with the standard 
package), as so:

	result = align_shapes(Data_dir, Output_dir, Levels, Ids, Names, Mirror)

The function arguments (Data_dir, Output_dir, Levels, *Ids*, *Names*, *Mirror*) 
are similar to standard auto3dgm with some changes. Arguments enclosed with 
asterisks are optional, and may be excluded in some cases. Each argument will be
described and differences noted.

	Data_dir ("http://stat.duke.edu/~sayan/auto3dgm/data/meshes/teeth_dataset"): 
	A string path to a directory (local or web) of surface mesh files. These 
	files can be in OFF or PLY format.

	Output_dir ("/Users/sayanm/Desktop/Bones"): A directory to which files are 
	exported. 

	Levels (64, 128): Numbers of points for subsampled data.

	Ids ('001','002','003','004','005'):  A list of data file names, excluding 
	file type. If loading files from a local directory, this argument is 
	optional and may be excluded.

	Names ('a01','a02','a03','a04','a05'): A list of names for surfaces 
	corresponding to data files. This argument is optional, and if excluded 
	file names will be used as surface names. 

	Mirror: This argument is boolean (0 or 1) and specifies whether specimen 
	mirroring/reflection should be used when attempting to align surfaces. It is
	optional and by default mirroring is enabled. To disable mirroring, Mirror
	should be 0. Please note that if mirroring is disabled, then only 4 initial
	alignment "guesses" will be used instead of 8. It is possible that this may
	decrease alignment accuracy.

Because the new Mirror argument is optional and reflection is enabled by 
default, any use of the align_shapes() function that conforms to previous 
examples given for using auto3dgm will produce identical results in 
auto3dgm-fork compared with the standard package. As an example, the 
Web_Example.R file provided in the instructions for the standard package 
produces the same results for both the standard and fork packages. The 
advantages of this package are in control over specimen reflection, ability to 
use PLY files as well as OFF files, and being able to exclude long lists of file
names and Ids when calling align_shapes(). Several examples are given below for 
different possible ways of calling align_shapes() as necessary:

Standard auto3dgm behavior, mirroring enabled by default:
	result = align_shapes(Data_dir, Output_dir, Levels, Ids, Names)

Loading local or web files specifying Ids and Names, mirroring enabled, produces
the same results as previous example:
	result = align_shapes(Data_dir, Output_dir, Levels, Ids, Names, Mirror=1)

Loading local files not specifying Ids and Names, mirroring disabled:
	result = align_shapes(Data_dir, Output_dir, Levels, Mirror=0)

Loading web files not specifying Names, mirroring disabled:
	result = align_shapes(Data_dir, Output_dir, Levels, Ids, Mirror=0)