buildtemplate: Build 3D surface template

Description

A function to build 3D template to extract 3D surface sliding semilandmarks from all specimens

Usage

buildtemplate(specimen, fixed, surface.sliders)

Arguments

specimen

Name of matrix containing three-dimensional coordinates of a surface scan

fixed

numeric: the number of fixed template landmarks

surface.sliders

numeric: the number of template surface sliders desired

Value

Function returns a matrix containing the x,y,z coordinates of the down sampled points, which can be used as a template for digitizing other surface scans using the function digitsurface. Additionally, the file 'template.txt' is generated, and an NTS file with the name of the specimen containing the digitized points for the template specimen (for use in subsequent morphometric analsyes).

Details

Function buildtemplate constructs a template surface with which to down sample point clouds of specimens to be used in 3d shape analysis. builddtemplate allows users to choose a predetermined number of points with which to represent the structure of interest as sliding surface semilandmarks. Template surface is used in analyses of surface semi-landmarks outline in Gunz et al. (2005:90-92) and Mitteroecker and Gunz (2009:242). Landmark points are first digitized by the user (see Digitizing subsection), then a roughly equidistant set of predetermined number of points are automatically chosen. The now down-sampled mesh is used as a "template" to extract a mesh of similarly numbered points for analysis. Digitizing{Digitizing using buildtemplate 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 askesd to select it again. This can be repeated until the user is comfortable with the landmark chosen. NOTE: To ensure a strong match between the scan and the template, it is recommended that a reasonable number of fixed points be used. To digitize with a standard 3-button (PC) buildtemplate uses:

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

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.