warpRefMesh: Creates a mesh3d object warped to the mean shape

Description

A function to take a 3D mesh and use thin-plate spline method to warp the file into the estimated mean shape for a set of aligned specimens

Usage

warpRefMesh(mesh, mesh.coord, ref, color = NULL, centered = FALSE)

Arguments

mesh

A mesh3d object (e.g. made by read.ply)

mesh.coord

A p x k matrix of 3D coordinates digitized on the ply file.

ref

A p x k matrix of 3D coordinates made by mshape

color

Color to set the ply file $material. If the ply already has color, use NULL. For ply files without color, color=NULL will be plotted as grey.

centered

Logical If the data in mesh.coords were collected from a centered mesh (see details).

Value

Function returns a mesh3d object, which is a list of class mesh3d (see rgl for details)

Details

Function takes a 3D mesh (class mesh3d or shape3d, e.g. from read.ply) and its digitized landmark coordinates and uses the thin-plate spline method (Bookstein 1989) to warp the mesh into the shape defined by a second set of landmark coordinates, usually those of the mean shape for a set of aligned specimens. It is highly recommended that the mean shape is used as the reference for warping (see Rohlf 1998). The workflow is as follows:

Calculate the mean shape using mshape
Choose an actual specimen to use for the warping. The specimen used as the template for this warping is recommended as one most similar in shape to the average of the sample, but can be any reasonable specimen - do this by eye, or use findMeanSpec
Warp this specimen into the mean shape using warpRefMesh
Use this average mesh where it asks for a mesh= in the analysis functions and visualization functions

For landmark coordinates digitized with geomorph digitizing functions, centered = TRUE. This refers to the specimen being centered prior to landmark acquisition in the RGL window. For landmark data collected outside of geomorph, centered=FALSE will usually be the case. The returned mesh3d object is for use in geomorph functions where shape deformations are plotted (plotTangentSpace, two.b.pls, bilat.symmetry, and plotRefToTarget).

References

Bookstein, F. L. 1989 Principal Warps: Thin-Plate Splines and the Decomposition of Deformations. IEEE Transactions on Pattern Analysis and Machine Intelligence 11(6):567-585.