Hello,
you can try the code below, it works fine with my data.
Ondrej
# functions
mat2arr <- function(mat) aperm(array(t(mat), c(3, ncol(mat) / 3,
nrow(mat))), c(2,1,3))
supplylm <- function(X, midplane, rightside, leftside) {
p <- nrow(X)
shift <- colMeans(X[midplane,])
rrot <- eigen(var(X[midplane,]))$vectors
rrot[,3] <- sign(det(rrot)) * rrot[,3]
CX <- X - rep(1, p) %*% t(shift)
RX <- CX %*% rrot
rna <- which(is.na(RX[rightside,1]))
lna <- which(is.na(RX[leftside,1]))
if (length(rna) > 0) {
RX[rightside[rna],] <- RX[leftside[rna],] %*% diag(c(1,1,-1))
}
if (length(lna) > 0) {
RX[leftside[lna],] <- RX[rightside[lna],] %*% diag(c(1,1,-1))
}
CX <- RX %*% solve(rrot)
X <- CX + rep(1, p) %*% t(shift)
return(X)
}
# create M, R, L = vectors with numbers of midplane, right side and left
side landmarks, respectively; corresponding right side and left side
landmarks have to be given in the same order
# read in your data
A <- mat2arr(read.csv("fossilseeds.csv", row.names=1))
# supply missing landmarks
for (i in 1:dim(A)[3]) {
A[,,i] <- supplylm(A[,,i], midplane=M, rightside=R, leftside=L)
}
On Monday, September 21, 2020 at 2:11:37 AM UTC+2 [email protected]
wrote:
> Hi everyone, I'm new here!
>
> I have a landmark dataset created in Amira for seeds with bilateral
> symmetry. Some specimens are fossils with missing landmarks. I converted
> the Amira datasets to text files formatted like TPS 3D landmarks and as a
> csv file (see screenshots below).
> ->sample TPS formatted 3D landmark file (1 specimen)
>
> [image: sample_landmark.jpg]
> -> sample landmark csv file (4 specimens, landmarks 1-2)
> [image: sample_landmarkcsv.jpg]
>
> I successfully imported them into R geomorph, used estimate.missing with
> TPS, gpagen for Procrustes fit, and bilat.symmetry to look at the effects
> of size. However, I'm not happy with the precision of the landmark
> estimation (see screenshots of estimated landmarks-above and without
> estimated landmarks-below).
>
> [image: landmarks_procrustes_Page_2.jpg]
> [image: landmarks_procrustes_Page_3.jpg]
> I'd like to try Morpho for estimating landmarks considering bilaterial
> symmetry with fixLMmirror, but I'm not able to load my data into Morpho.
> ->When loading my TPS-formatted landmark file using readallTPS, I get the
> error: Error in if (nLM[i] > 0) { : missing value where TRUE/FALSE needed.
> ->When loading landmark csv file using readLandmarks.csv, I get the error:
> Error in dimnames(arr) <- list(rown, c("X", "Y", "Z")) : length of
> 'dimnames' [2] not equal to array extent.
> -->I assumed the 2nd error means that XYZ coordinates for each landmark
> should be combined in the csv file, so I reformatted the data (screenshot
> below) and tried again.
> [image: sample_landmarkcsv2.jpg]
> -->New error: Error in h(simpleError(msg, call)) : error in evaluating the
> argument 'x' in selecting a method for function 'as.matrix': undefined
> columns selected
>
> *Summary*
> I am not sure why my TPS-formatted landmark file isn't working with
> Morpho, because it looks like all examples I've seen and works in geomorph.
> I also haven't been able to find a sample landmark csv dataset to compare
> with.
> *->Does anyone have small sample datasets of either they could share with
> me or show me screenshots of?*
>
> PS I also tried LOST, but am having some problems with dependencies and my
> R version so I'd prefer to use Morpho.
>
> Thanks in advance,
>
> Katie
>
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