Question on 3D coordinates derived from AMIRA and error in reading .ply files

[Pablo Fisichella]

Dear all

I have a couple of questions. First, I used AMIRA to digitize 3D landmarks/semilandmarks from human teeth. I used a script from another R package to read landmarks from AMIRA in R. Once the 3D coordinates appeared in the R console I copied such data in a format accepted in Geomorph. I loaded my data  sucessfully, but when I plotted the specimens using the function plotAllSpecimens() the five especimens were in quite different positions (see attached plot).  For me this kind of distribution of my specimens is so strange because in the past when I performed the same analysis using both 2D and 3D data all specimens were relatively aligned. Obviously, when I run a procrustes analysis the 5 specimens were aligned. My question is if is relatively normal that the 3D coordinates derived from 3D meshes present this distribution? o there exists some erros.

 Second, As I understand Geomorph only accept .ply ascii files. So I transformed in Meshlab my binary .ply into .ply ascii files. However, when I tried to read my ply file using  the function play <-read.ply I get this error Error in if (sum(normals[1:3, it[j, i]] * normal) < 0) normals[, it[j,  : 

  missing value where TRUE/FALSE needed

 How I can solve this error and read my ply files in Geomorph?

Thanks in advance for any suggestion

Best,

Pablo

[Emma Sherratt]

Dear Pablo,

I see no issue here. Answering "My question is if is relatively normal that the 3D coordinates derived from 3D meshes present this distribution?" - Yes. Every 3D scan of an object, whether it be using micro-CT or laser technology, will have the specimen scanned in it's own coordindate system. Therefore this is normal. However, if you have seen them more aligned in other software, that is likely then that those programs are centering the objects.

If you get an error message using read.ply about normals, just do addNormals = FALSE and it should work fine. Alternatively read in the ply file using morpho's functions (e.g. morpho::file2mesh) and use them the same way, since they are all mesh3d objects once imported.

Emma

[Pablo Fisichella]

Dear Emma

 Thank you very much for your answers and clarifications. Ok, I understand well the issue on the reference system of 3D meshes and when I added addNormals = FALSE, I can read my mesh in Geomorph. I also have used Morpho and Rvcg to read different kinds of files including ply both ascii and binary files.

Thanks for your time and kindness

Best regards,

Pablo