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geomorph (version 1.1-1)

digitsurface: Digitize 3D fixed landmarks and surface semilandmarks.

Description

A function to digitize three dimensional fixed landmarks and surface semilandmarks.

Usage

digitsurface(specimen, fixed)

Arguments

specimen
Name of data matrix in working directory containing three-dimensional landmark coordinates.
fixed
numeric: the number of fixed template landmarks

Details

Function to digitize landmarks on 3D pointclouds. "n" Landmark points are selected by user akin to landmarks selected to construct template using function buildtemplate. Following selection of points, function digitsurface 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 semi-landmarks 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. 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. To digitize with a standard 3-button (PC) buildtemplate uses:
  1. the RIGHT mouse button (primary) to select points to be digitized First,
  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:
  1. press button to rotate 3D mesh,
  2. press button while pressing CONTROL key to select points to be digitized,
  3. 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. } When completed, an ".nts" file is created in working directory using the specimen name, adding "coords.nts" as a suffix. This file contains the specimen coordinates to be used by GPA.

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