Find 1D or 3D voxel indices into a 3D image given spatial coordinates

Source: R/coordinates.R

Find 1D or 3D voxel indices into a 3D image given spatial coordinates

coord2ind(coords, ...)

# S3 method for default
coord2ind(
  coords,
  imdims,
  voxdims = NULL,
  origin = NULL,
  linear.indices = TRUE,
  aperm = NULL,
  Clamp = FALSE,
  CheckRanges = !Clamp,
  ...
)

Arguments

coords

spatial coordinates of image voxels.

...

extra arguments passed to methods.

imdims

array dimensions of 3D image OR an object for which a as.im3d object has been defined (see Details).

voxdims

vector of 3 voxels dimensions (width, height, depth).

origin

the origin of the 3D image.

linear.indices

Whether or not to convert the voxel indices into a linear 1D form (the default) or to keep as 3D indices.

aperm

permutation order for axes.

Clamp

Whether or not to map out of range coordinates to the nearest in range index (default FALSE)

CheckRanges

whether to check if coordinates are out of range.

Details

coord2ind is designed to cope with any user-defined class for which an as.im3d method exists. Presently the only example in the nat.* ecosystem is nat.templatebrains::as.im3d.templatebrain. The existence of an as.im3d method implies that voxdims,origin, and dim functions can be called. This is the necessary information required to convert i,j,k logical indices into x,y,z spatial indices.

See also

ind2coord, sub2ind, ijkpos

Examples

coord2ind(cbind(1,2,3), imdims = c(1024,512,218), 
  voxdims = c(0.622088, 0.622088, 0.622088), origin = c(0,0,0))
#> [1] 2624515
if (FALSE) {
## repeat but using a templatebrain object to specify the coordinate system
library(nat.flybrains)
coord2ind(cbind(1,2,3), JFRC2)
}