Convert XYZ locations between FANC4 (autoseg) and FANC3 (CATMAID)

Usage

fanc4to3(
  xyz,
  rawcoords = FALSE,
  swap = FALSE,
  chunksize = 40000,
  method = c("mapmany", "map1"),
  ...
)

Arguments

xyz: An Nx3 matrix of coordinates
rawcoords: whether the input values are raw voxel indices or in nm
swap: When TRUE applies the deformation field in the opposite direction e.g. to give a coarse mapping of points FAFB->FlyWire. This is wrong but may be useful.
chunksize: The number of points to send to the server when mapping many points at once.
method: Whether to map many points at once (default) or just one
...: additional arguments for pbapply::pblapply (used to chunk requests for many points) and eventually the POST command against the transform services server.

Value

a Nx3 matrix of coordinates.

Examples

fanc3=xyzmatrix(cbind(194569.2, 470101.3, 117630))
fanc4=cbind(45224, 109317, 2614)*c(4.3,4.3,45)
fanc4to3(fanc4)-fanc3
#>          X    Y Z
#> [1,] 2.575 2.65 0
# can also pass in raw coordinates e.g. from neuroglancer
fanc4to3(c(45224, 109317, 2614), rawcoords = TRUE)
#>             X      Y      Z
#> [1,] 194571.8 470104 117630

# rather small error for the approx inverse in this case
fanc4to3(fanc3, swap=TRUE)-fanc4
#> Warning: Please note the FANC3->FANC4 transform is wrong but useful!
#>         X      Y Z
#> [1,] -5.8 -1.575 0
# \donttest{
# ... so reverse mapping works in this case, but not always
fanc_xyz2id(fanc4to3(fanc3, swap = TRUE))
#> [1] "648518346486614449"
# }