Hi everyone,
I've collected 3D landmarks on a series of cranial surface models in Avizo.
Avizo's landmark editor outputs .landmarkAscii files, which I would like to
read into R. The way I've done the reading has the following very
unexpected effect: *sometimes, *it* writes *additional data to my
.landmarkAscii files. I'd like to understand why, but am mostly interested
in finding a solution.
To read in the landmark files for a specimen...
# Below, avz.file is the filepath for the .landmarkAscii
# file for a single specimen.
# The code reads the .landmarkAscii file with read.csv.
# This is useful because the object created lays out
# the informational data that precedes the coordinate data
# predictably. This makes it easy to lop off the
# informational data.
read.lms <- read.csv(avz.file, header=FALSE)[,1]
# The last row of informational data will contain the
# text "@1" and nothing else.
lm.start <- which(read.lms=="@1")+1
# Now it is possible to create an object with landmark
# data only. R interprets each landmark (all three
# coordinates together) as a factor. I convert the factor
# vector to a character vector.
lm.char <-
as.character(droplevels(
read.lms[(lm.start):length(read.lms)]))
# Then I create an empty matrix for the landmark data
lm.mat <- matrix(NA, nrow=length(lm.char), ncol=3)
# Then fill lm.mat with the landmark data. As mentioned,
# lm.char is a vector. Each element of that vector
# contains the X, Y, and Z coordinate for a landmark.
# The coordinates are separated by spaces
# (or maybe tabs)
for(i in 1:nrow(lm.mat))
{lm.mat[i,] <-
as.numeric(unlist(strsplit(ctlm.char[i], " ")))}
That's it. The code above will read in the data and make a landmark matrix.
Unfortunately, it sometimes also writes additional lines to the
.landmarkAscii file. The first added element is "@2." Thereafter, the
landmark file adds as many three-coordinate triplets as there are landmarks
in the original data file. The values of these triplets are 0,0,1 (or maybe
1,0,0).
This is really strange behavior. A read function shouldn't write.
My issue may be better suited to an R forum, but I am hoping someone here
has reliable code for reading Avizo landmarks into R.
Thanks in advance.
David
--
David Katz
University of California, Davis
--
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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