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.
digitsurface(spec, fixed, ptsize = 1, center = TRUE)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.
An object of class shape3d/mesh3d, or matrix of 3D vertex coordinates
Either a numeric value designating the number of fixed landmarks to be selected by digit.fixed, or a matrix of 3D coordinates collected previously
Size of mesh points (vertices), e.g. 0.1 for dense meshes, 3 for sparse meshes
Should the object 'spec' be centered prior to digitizing?
Erik Otarola-Castillo & Emma Sherratt
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 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):
the RIGHT mouse button (primary) to select points to be digitized,
the LEFT mouse button (secondary) is used to rotate mesh,
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":
press button to rotate 3D mesh,
press button while pressing COMMAND key to select vertex to be used as a landmark,
press button while pressing OPTION key to adjust mesh perspective.
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.
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.
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.
buildtemplate
read.ply
digit.fixed
rgl-package (used in 3D plotting)