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

## 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.

`ind2coord`, `sub2ind`, `ijkpos`
 ```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) ```