warpRefMesh: Creates a mesh3d object warped to the mean shape

In EmSherratt/geomorph: Geometric Morphometric Analyses of 2D/3D Landmark Data

Creates a mesh3d object warped to the mean shape

Description

A function that uses the thin-plate spline to warp a 3D mesh into a shape defined by a set of landmark coordinates.

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 gray.
centered	Logical If the data in mesh.coords were collected from a centered mesh (see 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:

1. Calculate the mean shape using mshape

2. 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

3. Warp this specimen into the mean shape using warpRefMesh

4. Use this average mesh where it asks for a mesh= in the analysis functions and visualization functions

Users should ensure that their mesh and mesh.coord matrix are in the same scale (a common issue is that the mesh is in micrometers and coordinates are in mm or cm). Use range(mesh$vb[1:3,]) and range(mesh.coord) to check and adjust mesh.coord as necessary.

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 (picknplot.shape, two.b.pls, bilat.symmetry, and plotRefToTarget).

Value

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

Author(s)

Emma Sherratt

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.

Rohlf, F. J. 1998. On Applications of Geometric Morphometrics to Studies of Ontogeny and Phylogeny. Systematic Biology. 47:147-158.

See Also

findMeanSpec

rgl-package (used in 3D plotting)

EmSherratt/geomorph documentation built on June 24, 2022, 11:05 p.m.