Convert xyz locations to CRANT root or supervoxel ids

Usage

crant_xyz2id(
  xyz,
  rawcoords = FALSE,
  root = TRUE,
  integer64 = FALSE,
  fast_root = TRUE,
  method = c("cloudvolume", "spine"),
  ...
)

Arguments

xyz: One or more xyz locations as an Nx3 matrix or in any form compatible with xyzmatrix including neuron or mesh3d surface objects.
rawcoords: whether the input values are raw voxel indices or in nm
root: Whether to return the root id of the whole segment rather than the supervoxel id.
integer64: Whether to return ids as integer64 type (more compact but a little fragile) rather than character (default FALSE).
fast_root: Whether to use a fast but two-step look-up procedure when finding roots. This is strongly recommended and the alternative approach has only been retained for validation purposes.
method: Whether to use the spine transform-service API or cloudvolume for lookup. "auto" is presently a synonym for "spine".
...: additional arguments passed to pbapply when looking up multiple positions.

Value

A character vector of segment ids, NA when lookup fails.

Details

This used to be very slow because we do not have a supervoxel field on spine.

I am somewhat puzzled by the voxel dimensions for crant. Neuroglancer clearly shows voxel coordinates of 4.3x4.3x45. But in this function, the voxel coordinates must be set to 4.25 in x-y to give the correct answers.

Examples

if (FALSE) { # \dontrun{
# a point from neuroglancer, should map to 576460752684030043
crant_xyz2id(cbind(37306, 31317, 1405), rawcoords=TRUE)
} # }