antsApplyTransformsToPoints: Apply transforms to points.

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

Apply transforms to points.

Description

Apply a transform list to map a pointset from one domain to another. In registration, one computes mappings between pairs of domains. These transforms are often a sequence of increasingly complex maps, e.g. from translation, to rigid, to affine to deformation. The list of such transforms is passed to this function to interpolate one image domain into the next image domain, as below. The order matters strongly and the user is advised to familiarize with the standards established in examples. Importantly, point mapping goes the opposite direction of image mapping, for both reasons of convention and engineering.

Usage

antsApplyTransformsToPoints(
  dim,
  points,
  transformlist = "",
  whichtoinvert = NA
)

Arguments

dim	dimensionality of the transformation.
points	moving point set with n-points in rows of at least dim columns - we maintain extra information in additional columns. this may be either a dataframe or a 2D antsImage - the latter may be better for large pointsets.
transformlist	character vector of transforms generated by antsRegistration where each transform is a filename.
whichtoinvert	vector of booleans, same length as transforms

Value

same type as input. 1 – Failure

Author(s)

Avants BB

See Also

antsRegistration

Examples

fixed <- antsImageRead(getANTsRData("r16"), 2)
moving <- antsImageRead(getANTsRData("r64"), 2)
fixed <- resampleImage(fixed, c(64, 64), 1, 0)
moving <- resampleImage(moving, c(64, 64), 1, 0)
mytx <- antsRegistration(
  fixed = fixed, moving = moving,
  typeofTransform = c("SyN"), verbose = FALSE
)
pts <- data.frame(
  x = c(110.5, 120, 130), y = c(108.1, 121.0, 130),
  label = c(1, 2, 3)
)
wpts <- antsApplyTransformsToPoints(
  dim = 2, points = pts,
  transformlist = mytx$fwdtransforms
)
wptsi <- antsApplyTransformsToPoints(
  dim = 2, points = wpts,
  transformlist = mytx$invtransforms
) # close to pts

## Not run: 
fixed <- antsImageRead(getANTsRData("r16"), 2)
moving <- antsImageRead(getANTsRData("r64"), 2)
fpts <- kmeansSegmentation(fixed, 3)$segmentation %>%
  thresholdImage(1, 1) %>%
  labelClusters(5) %>%
  getCentroids(5)
wpts <- antsApplyTransformsToPoints(
  dim = 2, points = fpts,
  transformlist = mytx$fwdtransforms
)
labimgf <- fixed * 0
labimgm <- moving * 0
for (p in 1:nrow(wpts))
{
  pt <- as.numeric(wpts[p, 1:2])
  idx <- round(antsTransformPhysicalPointToIndex(moving, pt))
  labimgm[idx[1], idx[2]] <- p
  pt <- as.numeric(fpts[p, 1:2])
  idx <- round(antsTransformPhysicalPointToIndex(fixed, pt))
  labimgf[idx[1], idx[2]] <- p
}
plot(fixed, labimgf %>% iMath("GD", 2))
plot(moving, labimgm %>% iMath("GD", 2))

## End(Not run)

stnava/ANTsR documentation built on April 16, 2024, 12:17 a.m.