digitsurface: Digitize 3D fixed landmarks and surface semilandmarks

In geomorph: Geometric Morphometric Analyses of 2D and 3D Landmark Data

Digitize 3D fixed landmarks and surface semilandmarks

Description

An interactive function to digitize three-dimensional (3D) landmarks on a surface lacking known landmarks. Input for the function is either a matrix of vertex coordinates defining a 3D surface object or a mesh3d object as obtained from read.ply.

Usage

digitsurface(spec, fixed, ptsize = 1, center = TRUE)

Arguments

spec	An object of class shape3d/mesh3d, or matrix of 3D vertex coordinates
fixed	Either a numeric value designating the number of fixed landmarks to be selected by digit.fixed, or a matrix of 3D coordinates collected previously
ptsize	Size of mesh points (vertices), e.g. 0.1 for dense meshes, 3 for sparse meshes
center	Should the object 'spec' be centered prior to digitizing?

Details

Function for digitizing fixed 3D landmarks and placing surface sliding semilandmarks using a previously created template. Following the selection of fixed points (see digitizing below), the function finds surface semilandmarks following the algorithm outlined in Gunz et al. (2005) and Mitteroecker and Gunz (2009). digitsurface finds the same number of surface semilandmarks as the template (created by buildtemplate) by downsampling the scanned mesh, after registering the template with the current specimen via GPA. A nearest neighbor algorithm is used to match template surface semilandmarks to mesh points of the current specimen. To use function digitsurface, the template must be constructed first, and 'template.txt' be in the working directory. Because template matching is based on the correspondence of fixed landmark points in the template and the specimen, a minimum of four fixed landmarks must be used.

For details on the full procedure for digitizing fixed 3D landmarks and surface sliding semilandmarks, see the relevant vignette by running vignette("geomorph.digitize3D").

NOTE: Function centers the mesh before digitizing by default (center=TRUE). If one chooses not to center, specimen may be difficult to manipulate in rgl window.

Digitizing

Digitizing of fixed landmarks is interactive. Once a point is selected, the user is asked if the system should keep or discard the selection (y/n). If "y", the user is asked to continue to select the next landmark. If "n" the removes the last chosen landmark, and the user is asked to select it again. This can be repeated until the user is comfortable with the landmark chosen.

To digitize with a standard 3-button (PC):

1. the RIGHT mouse button (primary) to select points to be digitized,

2. the LEFT mouse button (secondary) is used to rotate mesh,

3. the mouse SCROLLER (third/middle) is used to zoom in and out.

NOTE: Digitizing functions on MACINTOSH computers using a standard 3-button mice works as specified. Macs using platform specific single button mice, XQuartz must be configured: go to Preferences > Input > tick "Emulate three button mouse":

1. press button to rotate 3D mesh,

2. press button while pressing COMMAND key to select vertex to be used as a landmark,

3. press button while pressing OPTION key to adjust mesh perspective.

4. the mouse SCROLLER or trackpad two finger scroll is used to zoom in an out.

NOTE: there is no pan (translate) functionality in rgl library for all platforms at this time.

AUTO mode

The function as described above (for interactive mode) calls digit.fixed, prompting the user to select fixed landmarks in the rgl window. However if the user has digitized these fixed landmark elsewhere (e.g., in other software), then the input for parameter 'fixed' can be a p-x-k matrix of 3D coordinates. In this case, the function the function will automatically use these landmarks and fit the template of sliding semilandmarks.

Value

Function returns (if assigned to an object) and writes to the working directory an NTS file, containing the landmark coordinates. The file name corresponds to the name of the specimen.

Author(s)

Erik Otarola-Castillo & Emma Sherratt

References

Gunz P, Mitteroecker P, & Bookstein FJ (2005) Semilandmarks in Three Dimensions. Modern Morphometrics in Physical Anthropology, ed Slice DE (Springer-Verlag, New York), pp 73-98.

Mitteroecker P & Gunz P (2009) Advances in Geometric Morphometrics. Evolutionary Biology 36(2):235-247.

See Also

buildtemplate

read.ply

digit.fixed

rgl-package (used in 3D plotting)

geomorph documentation built on Sept. 1, 2023, 1:07 a.m.