tps3d: thin plate spline mapping (2D and 3D) for coordinates and...

In Morpho: Calculations and Visualisations Related to Geometric Morphometrics

thin plate spline mapping (2D and 3D) for coordinates and triangular meshes

Description

maps landmarks or a triangular mesh via thin plate spline based on a reference and a target configuration in 2D and 3D

Usage

tps3d(x, refmat, tarmat, lambda = 1e-08, threads = 0, ...)

tps2d(x, refmat, tarmat, lambda = 1e-08, threads = 0, ...)

Arguments

x	matrix - e.g. the matrix information of vertices of a given surface or a triangular mesh of class "mesh3d"
refmat	reference matrix - e.g. landmark configuration on a surface
tarmat	target matrix - e.g. landmark configuration on a target surface
lambda	numeric: regularisation parameter of the TPS.
threads	threads to be used for parallel execution in tps deformation.
...	additional arguments, currently not used.

Value

returns the deformed input

Note

tps2d is simply an alias for tps3d that can handle both cases.

Author(s)

Stefan Schlager

References

Bookstein FL. 1989. Principal Warps: Thin-plate splines and the decomposition of deformations. IEEE Transactions on pattern analysis and machine intelligence 11(6).

See Also

computeTransform, applyTransform

Examples

data(nose)
## define some landmarks
refind <- c(1:3,4,19:20)
## use a subset of shortnose.lm as anchor points for a TPS-deformation
reflm <- shortnose.lm[refind,]
tarlm <- reflm
##replace the landmark at the tip of the nose with that of longnose.lm
tarlm[4,] <- longnose.lm[4,]
##  deform a set of semilandmarks by applying a TPS-deformation
##  based on 5 reference points
deformed <- tps3d(shortnose.lm, reflm, tarlm,threads=1)
## Not run: 
##visualize results by applying a deformation grid
deformGrid3d(shortnose.lm,deformed,ngrid = 5)


data(nose)##load data
##warp a mesh onto another landmark configuration:
longnose.mesh <- tps3d(shortnose.mesh,shortnose.lm,longnose.lm,threads=1)


require(rgl)
shade3d(longnose.mesh,col=skin1)

## End(Not run)

data(boneData)
## deform mesh belonging to the first specimen
## onto the landmark configuration of the 10th specimen

## Not run: 
warpskull <- tps3d(skull_0144_ch_fe.mesh,boneLM[,,1],
                     boneLM[,,10], threads=1)
## render deformed mesh and landmarks
shade3d(warpskull, col=2, specular=1)
spheres3d(boneLM[,,1])
## render original mesh
shade3d(skull_0144_ch_fe.mesh, col=3, specular=1)
spheres3d(boneLM[,,10])


## End(Not run)

Morpho documentation built on Feb. 16, 2023, 10:51 p.m.