Convert xyz points between fish2 coordinate systems

fish2 uses three distinct voxel scales that all turn up in day-to-day work: nm (the canonical unit for spatial transforms like mirror_fish), raw (the (16, 16, 15) nm voxel grid stored in neuprint's somaLocation and friends, and accepted by the DVID segmentation/labels endpoint), and emraw (the (8, 8, 30) nm voxel grid of the EM imagery and the Clio / Neuroglancer URL conventions). fish_coords converts between any of these, plus microns.

Usage

fish_coords(xyz, from = "nm", to = "nm", as_character = FALSE)

Arguments

xyz: Point coordinates. Anything accepted by xyzmatrix (vector, matrix, data.frame, "x,y,z" strings).
from, to: Source and target units. One of "nm" (default), "raw" (16, 16, 15 nm voxels, the neuprint grid), "emraw" (8, 8, 30 nm voxels, the EM acquisition grid), "microns".
as_character: If TRUE, return a character vector of "x,y,z" strings via xyzmatrix2str.

Value

An Nx3 numeric matrix in the requested units, or a character vector when as_character = TRUE.

Details

fish2 has two "raw" voxel grids. raw is the (16, 16, 15) nm grid used by neuprint (it stores somaLocation and friends in raw, and the DVID segmentation/labels endpoint accepts raw coordinates). emraw is the (8, 8, 30) nm acquisition grid of the EM imagery and the convention used in Clio / Neuroglancer URLs. The two grids differ per axis (emraw is twice the XY resolution of raw and half the Z resolution): emraw = raw * c(2, 2, 0.5).

Examples

# neuprint "raw" -> EM "emraw"
fish_coords(c(57780, 28028, 10984), from = "raw", to = "emraw")
#>           X     Y    Z
#> [1,] 115560 56056 5492

# emraw -> nm
fish_coords(c(115560, 56056, 5492), from = "emraw", to = "nm")
#>           X      Y      Z
#> [1,] 924480 448448 164760

# batch + character output
fish_coords(rbind(c(115560, 56056, 5492), c(0, 0, 0)),
            from = "emraw", to = "raw", as_character = TRUE)
#> [1] "57780,28028,10984" "0,0,0"