Running a loop for landmarking with Geomorph

[Helen Ryan]

Hi! 

I have a heap (~600) specimens to landmark so have created a loop to streamline the landmarking process. 

for(i in 1:length(ply_files)) {
  spec3D <- vcgPlyRead(ply_files[i], updateNormals = TRUE)
  surf.pts <- digitsurface(spec = spec3D, fixed = 12)
}

I am having two issues. 1) once I have placed the 12th fixed landmark, it opens the next specimen in the RGL window, without showing me how the sliding landmarks placed on the specimen so I can't check for errors, and 2) the landmark file saves as spec3D.nts instead of the original file number (eg HS051.nts) which would mean all subsequent files will overwrite the previous one.

I would love some advice on how to correct the code to fix these two issues.

Cheers,

Helen

[Adams, Dean [EEOB]]

Helen,

The first issue is unavoidable when putting this into a loop. However, you can call the specimens up post-digitizing using the 'plotspec' function to visualize.

To the second issue, your loop hasn't specified things in a specimen-specific manner, so it has no way of knowing which specimen is which.  Please have a look at the 3D digitizing vignette which comes with geomorph. In that example we add a line or two of code that specifies 2 specimens. Then, when digitsurface is called, the output *.nts have different names.  You should be able to follow this logic and add a line or two of code in your loop to allow for this.

The alternative is to add a line of code after 'digitsurface' where you brute-force change the name to what you want. 

Dean

-- 
Dr. Dean C. Adams
Distinguished Professor
Director, Ecology and Evolutionary Biology Graduate Program
Department of Ecology, Evolution, and Organismal Biology
Iowa State University
www.public.iastate.edu/~dcadams/
phone: 515-294-3834

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From: geomorph-...@googlegroups.com <geomorph-...@googlegroups.com> on behalf of Helen Ryan <mrsry...@gmail.com>
Sent: Thursday, December 11, 2025 2:29 AM
To: geomorph R package <geomorph-...@googlegroups.com>
Subject: [geomorph-r-package] Running a loop for landmarking with Geomorph

 

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