# coord2ind: Find 1D indices into a 3D image given spatial coordinates In nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

 coord2ind R Documentation

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

### Description

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

### Usage

``````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

``````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 May 29, 2024, 10:36 a.m.