Morpho (version 1.0-1)

relaxLM: relax one specific 3D landmark configuration against a reference

Description

relax one specific 3D 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

lm

k x 3 matrix containing landmark data to be slidden.

reference

k x 3 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

Details

needs trimesh_project to be installed (http://sourceforge.net/projects/morpho-rpackage/files/Auxiliaries/)

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.

See Also

slider3d

Examples

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")