1_preppingScanData.Rmd

---
title: "Supplemental script: preparing face data for analyses in main script"
output: html_notebook
---

```{r message=FALSE}
library(tidyverse)
library(geomorph)
library(Morpho)
library(rgl)
```

# Full Face
## Load surface scans
Face scans were converted from OBJ to PLY format in a prior step so they can be read into R.

```{r}
# Create list of ids/files
ids<-substr(list.files("./", pattern="*.ply"),1,8)

ids.table<-data.frame(id=ids)
#write_csv(ids.table,"ids.csv")

files <- list.files("./", pattern="*.ply")

# Define dimensions of data
k<-60541 # number of vertices
d<-3 # number of dimensions
n<-length(files) # number of specimen

# Create empty array of the right dimensions
data.array<-array(0,c(k,d,n))

# Populate array by importing ply files as mesh3d objects
for(i in 1:length(files)){
  temp.mesh <- file2mesh(files[i])
  temp.vert <- t(temp.mesh$vb[1:3,]) # last row seems to be a 1 for every point...?
  data.array[,,i]<-temp.vert
}

# Save array, so next time it can be loaded right away
saveRDS(data.array, "fullFace_scans.rds")
dimnames(data.array)[[3]]<-ids
```

## GPA
Morpho::ProcGPA with default settings is used for GPA
```{r eval=FALSE}
data.gpa<-ProcGPA(data.array)
#plot3d(data.gpa$mshape, box=FALSE, axes=FALSE)
#rm(data.array) # to make some space
saveRDS(data.gpa, "fullFace_gpa.rds")
```

# Facial regions
```{r}
regions<-c("eyes","nose","mouth")

for (j in 1:length(regions)){
  
  files <- list.files(path=paste0("./_regions/",regions[j]), pattern="*.ply",full.names = TRUE)
  
  mesh <- file2mesh(files[1])
  vert <- t(mesh$vb[1:3,])
  k<-dim(vert)[1]
  
  data.array<-array(0,c(k,d,n))
  
  for(i in 1:length(files)){
    temp.mesh <- file2mesh(files[i])
    temp.vert <- t(temp.mesh$vb[1:3,])
    
    k<-dim(temp.vert)[1]
    
    data.array[,,i]<-temp.vert
  }
  dimnames(data.array)[[3]]<-ids
  saveRDS(data.array, paste0("./",regions[j],"_scans.rds"))
  
  data.gpa<-ProcGPA(data.array)
  
  saveRDS(data.gpa, paste0("./",regions[j],"_gpa.rds"))
  
}
```