fanc4to3: Convert XYZ locations between FANC4 (autoseg) and FANC3...

In flyconnectome/fanc: Support Access to the Female Adult Nerve Cord (FANC) Dataset

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

Description

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
# can also pass in raw coordinates e.g. from neuroglancer
fanc4to3(c(45224, 109317, 2614), rawcoords = TRUE)

# rather small error for the approx inverse in this case
fanc4to3(fanc3, swap=TRUE)-fanc4

# ... so reverse mapping works in this case, but not always
fanc_xyz2id(fanc4to3(fanc3, swap = TRUE))

flyconnectome/fanc documentation built on Sept. 6, 2024, 9:56 a.m.