fixLMmirror: estimate missing landmarks from their bilateral counterparts

In zarquon42b/Morpho: Calculations and Visualisations Related to Geometric Morphometrics

estimate missing landmarks from their bilateral counterparts

Description

estimate missing landmarks from their bilateral counterparts

Usage

fixLMmirror(x, pairedLM, ...)

## S3 method for class 'array'
fixLMmirror(x, pairedLM, ...)

## S3 method for class 'matrix'
fixLMmirror(x, pairedLM, ...)

Arguments

x	a matrix or an array containing landmarks (3D or 2D)
pairedLM	a k x 2 matrix containing the indices (rownumbers) of the paired LM. E.g. the left column contains the lefthand landmarks, while the right side contains the corresponding right hand landmarks.
...	additional arguments

Details

the configurations are mirrored and the relabled version is matched onto the original using a thin-plate spline deformation. The missing landmark is now estimated using its bilateral counterpart. If one side is completely missing, the landmarks will be mirrored and aligned by the unilateral landmarks.

Value

a matrix or array with fixed missing bilateral landmarks.

Note

in case both landmarks of a bilateral pair are missing a message will be issued. As well if there are missing landmarks on the midsaggital plane are detected.

Examples

data(boneData)
left <- c(4,6,8)
## determine corresponding Landmarks on the right side:
# important: keep same order
right <- c(3,5,7)
pairedLM <- cbind(left, right)
exampmat <- boneLM[,,1]
exampmat[4,] <- NA #set 4th landmark to be NA
fixed <- fixLMmirror(exampmat, pairedLM=pairedLM)
## Not run: 
deformGrid3d(fixed, boneLM[,,1],ngrid=0)
## result is a bit off due to actual asymmetry

## End(Not run)
## example with one side completely missing
oneside <- boneLM[,,1]
oneside[pairedLM[,1],] <- NA
onesidefixed <- fixLMmirror(oneside,pairedLM)
## Not run: 
deformGrid3d(onesidefixed, boneLM[,,1],ngrid=0)
## result is a bit off due to actual asymmetry

## End(Not run)

zarquon42b/Morpho documentation built on Jan. 28, 2024, 2:11 p.m.