I won't get back to my office, and the hard drive where the files are
stored, for about a week. I'll send something along then.
Thanks, Emma.
David
On Wed, Jan 20, 2016 at 12:08 AM, Emma Sherratt <emma.sherr...@gmail.com>
wrote:
> Hi David,
>
> Not sure what the file actually looks like since you’ve not included a
> sample here. However I suggest taking a look at the readland functions in
> geomorph R package to see how we tackle the different types. If you want,
> send it through to us and we can take a look. If there’s a lot of people
> using AVIZO for digitising, we can include a function in geomorph.
>
> Regarding a read function writing? Nope, never heard of that.
>
> Em
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Emma Sherratt, PhD.
>
> Lecturer in Zoology,
> Zoology Division, School of Environmental and Rural Science,
> Room L112 Bldg C02,
> University of New England,
> Armidale, NSW, Australia, 2351
> Tel: +61 2 6773 5041
> email: emma.sherr...@une.edu.au
> Twitter: @DrEmSherratt
>
> Caecilians are legless amphibians...
>
> * __
> (\ .-. .-. /_")
> \\_//^\\_//^\\_//
> `"` `"` `"`*
>
> learn more about them here: www.emmasherratt.com/caecilians
>
>
> On 20 January 2016 at 14:50:38, David Katz (dck...@ucdavis.edu) wrote:
>
> 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
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--
David Katz
Doctoral Candidate
Evolutionary Anthropology
University of California, Davis
Young Hall 204
ResearchGate profile <https://www.researchgate.net/profile/David_Katz29>
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