digitsurface: 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)

Arguments

spec

Name of surface file, as either an object of class shape3d/mesh3d, or matrix of three-dimensional vertex coordinates.

fixed

numeric: The number of fixed template landmarks

ptsize

numeric: Size to plot the mesh points (vertices), e.g. 0.1 for dense meshes, 3 for sparse meshes

Value

Function writes to the working directory an NTS file with the name of the specimen and .nts suffix containing the landmark coordinates. Function also returns a list:
FIX.LANDMARKSan n x 3 matrix containing the x,y,z coordinates of the digitized landmarks
SURFSLIDERSxyza matrix of addresses for landmarks that are "surface sliders"

Details

Function for digitizing fixed 3D landmarks and placing "surface sliders", semilandmarks that slide over a surface. Following selection of fixed points (see digitizing below), function finds surface semilandmarks following algorithm outlined in Gunz et al. (2005:90-92) and Mitteroecker and Gunz (2009:242). digitsurface finds the same number of surface semilandmarks as the template (created by buildtemplate) by downsampling scanned mesh, registering template with current specimen via GPA. A nearest neighbor algorithm is used to match template surface landmarks to current specimen's. To use function digitsurface, the template must be constructed first, and 'template.txt' be in the working directory. Some of the "fixed" landmarks digitized with digitsurface can be later designated as "curve sliders" using function define.sliders.3d if required (see details in digit.fixed). NOTE: Function centers the mesh before digitizing (required for further operations). Digitizing{ Digitizing is interactive between landmark selection using a mouse (see below for instructions), and the R console. 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 (click-drag a box around a vertex to select as landmark),
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:

press button to rotate 3D mesh,
press button while pressing CONTROL key to select points to be digitized (click-drag a box around a vertex to select as landmark),
press button while pressing OPTION key to adjust mesh perspective.

Mac mouse settings need adjustment to acquire zooming functions of the "middle/third" mouse button/scroller. Some instructions can be found at http://blog.boastr.net/. In addition, freeware providing "Middle Click" functionality is available at http://magicprefs.com/ for "magicmice" now standard on many Macintosh machines. NOTE: there is no pan (translate) functionality in rgl library for all platforms at this time. }

References