Function to read and write Meshlab picked points (*.pp) with R

07 May 2017

Recently, I’ve been using the ‘PickPoints’ feature of Meshlab to collect landmarks from 3D surface models of primate skulls. Meshlab exports landmark coordinates in uniquely formatted ‘PickedPoints’ files, which I want to read into R as 3D coordinate matrices. Here is an example of the files I am working with- this one decribes 3 points, or landmarks, named “p1”, “p2”, and “p3”:

<!DOCTYPE PickedPoints>
<PickedPoints>
  <DocumentData>
    <DataFileName name="surface.ply"/>
    <templateName name="template.pptpl"/>
  </DocumentData>
  <point x="0.58" y="187.8" z="46.3" name="p1" active="1"/>
  <point x="0.09" y="169.2" z="31.9" name="p2" active="1"/>
  <point x="0.96" y="161.2" z="34.8" name="p3" active="1"/>
</PickedPoints>

For some reason, the order of the <point/> parameters, x, y, z, name, and active, varies unpredictably in saved *.pp files. Failure to recognize this quirk doomed my first attempt at writing an import function. Below is the successful version of the function,read.pp, for reading *.pp files into R.

# function to read Meshlab *.pp files into R
read.pp <- function (file) {
	file <- readLines(file)
	lines <- file[grep("point", file)]
	x <- strsplit(lines, "x=\"")
	y <- strsplit(lines, "y=\"")
	z <- strsplit(lines, "z=\"")
	name <- strsplit(lines, "name=\"")
	mat <- matrix(0, length(x), 3)
	r <- c()
	for (i in 1:length(lines)) {
		mat[i,1] <- as.numeric(strsplit(x[[i]][2], "\"")[[1]][1])
		mat[i,2] <- as.numeric(strsplit(y[[i]][2], "\"")[[1]][1])
		mat[i,3] <- as.numeric(strsplit(z[[i]][2], "\"")[[1]][1])
		r <- c(r, strsplit(name[[i]][2], "\"")[[1]][1])
	}
	rownames(mat) <- r 
	colnames(mat) <- c("x","y","z")
	return(mat)
}

Amd here is a function to write Meshlab *.pp files from R. This function takes a matrix with 3 columns, and assumes the coordinates are in the order: x, y, z.

# function to write Meshlap *.pp files from R
write.pp <- function (mat, file) {
  # create text for each point
   pp <- c()
   for (i in 1:nrow(mat)) {
     point <- paste0("  <point x=\"", mat[i,1],
                     "\" y=\"", mat[i,2],
                     "\" z=\"", mat[i,3],
                     "\" name=\"p", i,
                     "\" active=\"1\"/>")
     pp <- append(pp, point)
   }
  # add supporting markup
   pp <- c("<!DOCTYPE PickedPoints>",
          "<PickedPoints>",
          "  <DocumentData>",
          paste0("    <DataFileName name=\"", tail(strsplit(file,"/")[[1]],1), "\"/>"),
          "    <templateName name=\"template.pptpl\"/>",
          "  </DocumentData>",
          pp,
          "</PickedPoints>")
  # write the file
  write(pp, file=file)
}

You can now import a single *.pp file like this:

# import a single file
coords <- read.pp("~/path/to/file.pp")

And export individual *.pp files like this:

# export a single file
write.pp(coords, "~/path/to/file.pp")

To import a set of *.pp files from a directory and format them as a 3D array, use read.pp and abind in a loop:

# load abind package
library(abind)

# list all the *.pp files in the specified directory
path = "~/path/to/directory/"
files <- paste(path, list.files(path, ".pp"), sep="")

# loop to import each *.pp file and bind it to an array
landmarks <- NULL
for (i in 1:length(files)) {
  landmarks <- abind(landmarks, read.pp(files[i]), along=3)
}

And that’s how you can import and export Meshlab landmark files with R!

Footnotes:

The Morpho package has the function read.mpp for reading Meshlab picked points files into R, but it didn’t work for me. Maybe the “picked points” output changed under more recent versions of Meshlab? I am currently using Meshlab 2016, which produces files with the extension \*.pp, not \*.mpp.

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Randi H Griffin, PhD

Function to read and write Meshlab picked points (*.pp) with R