Map xyz points to fish2 body ids via DVID

Look up the segmentation body id at each 3D point. Thin wrapper around malevnc::manc_xyz2bodyid that targets the active fish2 DVID node. Input may be in emraw (default), raw, nm or microns; see fish_coords for what each means.

Usage

fish_xyz2bodyid(
  xyz,
  units = c("emraw", "raw", "nm", "microns"),
  node = "neutu",
  cache = FALSE
)

Arguments

xyz

Point coordinates: a length-3 numeric vector for a single point, an Nx3 numeric matrix / data.frame, or anything else accepted by xyzmatrix (including "x,y,z" strings).

units

Units of the input coordinates. "emraw" (the default) matches coordinates copied from neuroglancer URLs against the fish2 EM imagery; "raw" matches the neuprint segmentation grid; "nm" and "microns" are self-explanatory. See fish_coords for the underlying voxel sizes.

node

The DVID node (UUID) to query. The default "neutu" uses the active neutu node, normally the most up-to-date.

cache

Whether to cache the result of this call for 5 minutes (default FALSE).

Value

A character vector of body ids, one per input point. NA_character_ where the input row had any NA.

Details

The DVID segmentation/labels endpoint accepts coordinates on the neuprint (16, 16, 15) "raw" grid, so input coordinates are first converted to raw via fish_coords and then rounded to integer voxel positions before the call (as in manc_xyz2bodyid). Points with NA coordinates yield NA_character_ in the output.

See also

fish_neuprint_meta, fish_coords, malevnc::manc_xyz2bodyid

Other coords: fish_coords()

Examples

if (FALSE) { # \dontrun{
# default emraw matches a point copied from a fish2 EM neuroglancer URL
fish_xyz2bodyid(c(115560, 56056, 5492))                # -> 100001043

# same body looked up via neuprint-raw coordinates
fish_xyz2bodyid(c(57780, 28028, 10984), units = "raw") # -> 100001043
} # }