Handle raw and nm calibrated banc coordinates

banc_voxdims returns the image voxel dimensions which are normally used to scale between raw and nm coordinates.

Usage

banc_voxdims(url = choose_banc(set = FALSE)[["fafbseg.sampleurl"]])

banc_nm2raw(x, vd = banc_voxdims())

banc_raw2nm(x, vd = banc_voxdims())

Arguments

url

Optional neuroglancer URL containing voxel size. Defaults to getOption("fafbseg.sampleurl") as set by choose_banc.

x

3D coordinates in any form compatible with xyzmatrix

vd

The voxel dimensions in nm. Expert use only. Normally found automatically.

Value

For banc_voxdims A 3-vector

for banc_raw2nm and banc_nm2raw an Nx3 matrix of coordinates

Details

relies on nat >= 1.10.4

Examples

banc_voxdims()
#> Warning: running command ''/home/runner/.cache/R/reticulate/uv/cache/archive-v0/JkX5z3gbyfY8htJhnhin1/bin/python' -m pip freeze' had status 1
#> Warning: using default setting
#> Warning: Multiple segmentation layers. Choosing first!
#>  x  y  z 
#>  4  4 45 
#> attr(,"units")
#> [1] "nm"
banc_raw2nm(c(159144, 22192, 3560))
#> Warning: running command ''/home/runner/.cache/R/reticulate/uv/cache/archive-v0/JkX5z3gbyfY8htJhnhin1/bin/python' -m pip freeze' had status 1
#> Warning: using default setting
#>           X     Y      Z
#> [1,] 636576 88768 160200
banc_raw2nm('159144 22192 3560')
#> Warning: running command ''/home/runner/.cache/R/reticulate/uv/cache/archive-v0/JkX5z3gbyfY8htJhnhin1/bin/python' -m pip freeze' had status 1
#> Warning: using default setting
#>           X     Y      Z
#> [1,] 636576 88768 160200
if (FALSE) { # \dontrun{
banc_nm2raw(clipr::read_clip())
} # }