coord2ind: Find 1D indices into a 3D image given spatial coordinates

Description Usage Arguments Details See Also Examples

View source: R/coordinates.R

Description

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

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
coord2ind(coords, ...)

## Default S3 method:
coord2ind(
  coords,
  imdims,
  voxdims = NULL,
  origin = NULL,
  aperm,
  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.

aperm

permutation order for axes.

Clamp

???

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

1
2
3
4
5
6
7
8
coord2ind(cbind(1,2,3), imdims = c(1024,512,218), 
  voxdims = c(0.622088, 0.622088, 0.622088), origin = c(0,0,0))
## Not run: 
## repeat but using a templatebrain object to specify the coordinate system
library(nat.flybrains)
coord2ind(cbind(1,2,3), JFRC2)

## End(Not run)

nat documentation built on Sept. 6, 2021, 5:09 p.m.