Create a Template for Surface Semi-landmarks

Creating a template in R using geomorph:

I am using morton1306 as my template

Make sure the landmark txt files is in .tps file format:

LM3: 109

x y z

x y z

x y z

Open up R:

-change the working directory to the folder with the landmark and surface files of the template

setwd("~/Documents/FinalEndocastAnalysis")
load("~/Documents/CompletedEndocastsFinal/FinalAnalysisRData")
library(geomorph)

-read in the specimen's landmarks and endocast files

morton1306_fixed_curve_landmarks <- readland.tps(file.choose())

morton1306ply <- read.ply(file.choose()) 

-Build the template using the buildtemplate() function.

buildtemplate(morton1306ply, morton1306_fixed_curve_landmarks, 900, ptsize=1, center=FALSE)

- This places 900 semilandmarks on the template surface and creates a template.txt file of the landmark points, an .nts file of the points and a surfslide.csv file that tells which ones slide

- read the template file into R

template <- as.matrix(read.table("template.txt", header=T, sep=" "))

To edit the template and remove landmarks you do not want:
- use the editTemplate() function in geomorph
     - it will allow you to choose a set number of landmarks to remove from the template and overwrite the template.txt file
     - it will not edit the surfslide.csv file, you will need to edit this by hand

To edit the surfslide.csv file:
- open in excel
- determine how many surface semilandmarks you now have
- edit the file so that it shows a continous column of numbers from the next number after your fixed and curve semilandmarks to the number of surface semilandmarks there are
(I have 109 fixed/curve landmarks so my surfslide file goes from 110 to 969)




To view the endocast surface with the semilandmarks and landmarks:

>morton1306alllandmarks<- readland.nts("morton1306ply.nts")

> morton1306alllandmarks2d <- two.d.array(morton1306alllandmarks)

>plotspec(spec=morton1306ply, digitspec=morton11306alllandmarks2d, fixed=109 centered=FALSE)

a window will pop up with the surface and landmarks