define.sliders.3d: Choose points to "slide" along three-dimensional curves.

Description

An interactive function to define which digitized landmarks of an '*.nts' file will "slide" along three-dimensional (3D) curves.

Usage

define.sliders.3d(spec, nsliders, surfsliders = FALSE)

Arguments

spec

Name of specimen, as an object matrix containing 3D landmark coordinates

nsliders

Number of landmarks to be semilandmarks that slide along curves

surfsliders

Logical If spec contains landmarks that are "surface sliders", made by buildtemplate, "surfslide.csv" should be in working directory

Value

Function returns a 'curves x 3' matrix containing the landmark address of the curve sliders, indicating the points between which the selected point will "slide". Written to the working directory is this matrix as "curveslide.csv". Matrix (or "curveslide.csv") is designed for use by gpagen during GPA.

Details

Function takes a matrix of digitized landmark coordinates, such as made by digit.fixed, or buildtemplate and helps user choose which landmarks will be treated as "curve sliders" in Generalized Procrustes analysis gpagen. This type of semilandmark "slides" along curves lacking known landmarks (see Bookstein 1997 for algorithm details). Each sliding semilandmark ("sliders") will slide between two designated points, along a line tangent to the specified curvature. Selection{ Choosing which landmarks will be sliders involves landmark selection using a mouse in the rgl plot window. With a standard 3-button (PC) buildtemplate uses:

the RIGHT mouse button (primary) to choose points to be defined as sliders (click-drag a box around a vertex to select),
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 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.
the mouse SCROLLER or trackpad two finger scroll is used to zoom in an out.

To define the sliders, for each sliding landmark along the curve in the format 'before-slider-after':

Click-drag to choose the first landmark between which semi-landmark will "slide",
Click-drag to choose sliding landmark,
Click-drag to choose the last landmark between which semi-landmark will "slide", Screen will show lines connecting the three landmarks, and will highlight the sliding semilandmark in red.

This procedure is overlapping, so for example a curve defined by a sequence of semilandmarks, the user must select the 2nd point of the first three to be the 1st for the next e.g. 1 2 3 then 2 3 4, etc. }

References

Bookstein, F. J. 1997 Landmark Methods for Forms without Landmarks: Morphometrics of Group Differences in Outline Shape. Medical Image Analysis 1(3):225-243.