relaxLM: relax one specific landmark configuration against a reference

Description

relax one specific landmark configuration against a reference (e.g. a sample mean)

Usage

relaxLM(lm, reference, SMvector, outlines = NULL, surp = NULL,
  sur.name = NULL, mesh = NULL, tol = 1e-05, deselect = FALSE,
  inc.check = TRUE, iterations = 0, fixRepro = TRUE)

Arguments

k x 3 or k x 2 matrix containing landmark data to be slidden.

reference

k x 3 or k x 2 matrix containing landmark of the reference

SMvector

A vector containing the landmarks on the curve(s) that are allowed to slide

outlines

A vector (or if threre are several curves) a list of vectors (containing the rowindices) of the (Semi-)landmarks forming the curve(s) in the successive position on the curve - including the beginning and end points, that are not allowed to slide.

surp

A vector containing Semilandmarks positioned on surfaces.

sur.name

character: containing the filename of the corresponding surface.When specified, mesh has to be NULL.

mesh

triangular mesh of class "mesh3d" loaded into the R workspace, when specified, "sur.name" has to be NULL. The function closemeshKD will be used for reprojection onto the surface.

tol

numeric: Threshold for convergence in the sliding proces. Full Procrustes distance between actual result and previous iteration.

deselect

Logical: if TRUE, the SMvector is interpreted as those landmarks, that are not allowed to slide.

inc.check

Logical: if TRUE, the program stops when convergence criterion starts increasing and reports result from last iteration.

iterations

integer: maximum amounts the algorithm runs - even when 'tol' is not reached. When iterations=0, the algorithm runs until convergence.

fixRepro

logical: if TRUE, fix landmarks will also be projected onto the surface. If you have landmarks not on the surface, select fixRepro=FALSE

Value

returns kx3 matrix of slidden landmarks

References

Gunz, P., P. Mitteroecker, and F. L. Bookstein. 2005. Semilandmarks in Three Dimensions, in Modern Morphometrics in Physical Anthropology. Edited by D. E. Slice, pp. 73-98. New York: Kluwer Academic/Plenum Publishers.

Examples

Run this code

require(rgl)
data(nose)
### relax shornose against longnose

# define fix landmarks
fix <- c(1:5,20:21)
# define surface patch by specifying row indices of matrices
# all except those defined as fix
surp <- c(1:dim(shortnose.lm)[1])[-fix]
## to reduce this example's computation time,
# we only use the right hand semi-landmarks
# (which keeps the left hand ones fix)
surp <- surp[1:316]

relax <- relaxLM(shortnose.lm[1:323, ],
         longnose.lm[1:323, ], mesh=shortnose.mesh, iterations=1,
         SMvector=fix, deselect=TRUE, surp=surp)

# visualize differences red=before and green=after sliding
deformGrid3d(shortnose.lm[1:323, ], relax, ngrid=0)
# add surface
wire3d(shortnose.mesh, col="white")