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WIP first version of tps speedup #515

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WIP first version of tps speedup #515

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8aade1d
WIP first version of tps speedup
jefferis Oct 9, 2023
da771b0
switch to precomputing tps registration
jefferis Jan 16, 2024
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27 changes: 20 additions & 7 deletions R/xform.R
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Original file line number Diff line number Diff line change
Expand Up @@ -423,8 +423,12 @@ mirror.neuronlist<-function(x, subset=NULL, OmitFailures=NA, ...){
#' plot(da2pns.R.L, col='blue', add=TRUE)
#' }
tpsreg<-function(sample, reference, ...){
structure(list(refmat=data.matrix(sample), tarmat=data.matrix(reference), ...),
reg=structure(list(refmat=data.matrix(sample), tarmat=data.matrix(reference), ...),
class='tpsreg')
# precompute forward and reverse
attr(reg,'fwd')=Morpho::computeTransform(x=reg$tarmat, y=reg$refmat, type = "tps", ...)
attr(reg,'rev')=Morpho::computeTransform(x=reg$refmat, y=reg$tarmat, type = "tps", ...)
reg
}

#' @description \code{xformpoints.tpsreg} enables \code{\link[nat]{xform}} and
Expand All @@ -436,12 +440,21 @@ tpsreg<-function(sample, reference, ...){
#' @param points The 3D points to transform
#' @param swap Whether to change the direction of registration (default of
#' \code{NULL} checks if reg has a \code{attr('swap'=TRUE)}) otherwise
#' @param FallBackToAffine,na.action Not applicable to this function
#' @export
xformpoints.tpsreg <- function(reg, points, swap=NULL, ...){
if(isTRUE(swap) || isTRUE(attr(reg, 'swap'))) {
tmp=reg$refmat
reg$refmat=reg$tarmat
reg$tarmat=tmp
xformpoints.tpsreg <- function(reg, points, swap=NULL, FallBackToAffine = NULL, na.action = NULL, ...){

dir <- ifelse(isTRUE(swap) || isTRUE(attr(reg, 'swap')), 'rev', 'fwd')
trafo <- attr(reg, dir)
if(is.null(trafo)) {
warning("Incomplete thin plate splines registration!\n",
"I am recomputing, but please use `tpsreg()` to make a new registration")
trafo <- if(dir=='fwd') Morpho::computeTransform(x=reg$tarmat, y=reg$refmat, type = "tps", ...)
else
Morpho::computeTransform(x=reg$refmat, y=reg$tarmat, type = "tps", ...)
}
do.call(Morpho::tps3d, c(list(x=points), reg, list(...)))

Morpho::applyTransform(points, trafo, ...)
}


11 changes: 10 additions & 1 deletion man/tpsreg.Rd
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2 changes: 1 addition & 1 deletion tests/testthat/test-xformpoints.R
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Expand Up @@ -92,7 +92,7 @@ test_that("Thin plate spine registration", {
landmarks=xyz[sids,] #take some points as landmarks
landmarkst=scale(xyz[sids,], center = T, scale = rep(1.5, 3)) #now scale the landmarks..

#compute a transformation with sameple as scaled landmarks and reference as the original landmarks
#compute a transformation with sample as scaled landmarks and reference as the original landmarks
mytps=tpsreg(sample=landmarkst, reference = landmarks)

kcs20.t=xform(kcs20, mytps)
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