Wrapper object for one or more HDF5 encoded transforms

Wrapping paths to one or more h5 registration files on disk in an antsreg object means that they can be used by nat::xform and inside nat::reglist objects.

Usage

h5reg(..., swap = NULL)

Arguments

...: Path to one or more HDF5 encoded registrations.
swap: When TRUE implies that the registration specifies the direction required for transforming points. When FALSE implies the inverse. The default implied by swap=NULL is swap=TRUE for all registrations.

Value

A character vector with additional class h5reg.

Details

h5 registrations contains both forward and inverse deformation fields along with the corresponding affine transforms wrapped in a single HDF5 file. They are therefore naively invertible just by picking out the correct registration field.

For historical reasons (based on the convention of CMTK), when swap=FALSE, we assume we are trying to specify a registration in the direction required for image transformation. This is the opposite of the direction required for point transformation, which is the convention for h5 registration files. We therefore set swap=TRUE when it is not specified.

If multiple registrations are specified, they are given in order from floating to template brain, reading from left to right. See nat::xform and nat::reglist for further details.

Examples

if (FALSE) {
# We will use sample Kenyon Cells in FCWB (FlyCircuit) space
library(nat)
head(kcs20)

# swap=FALSE, so this will map points onto JRC2018F
kcs20.jrc2018 = xform(kcs20,
                      reg = h5reg('JRC2018F_FCWB_transform_quant16.h5', swap=FALSE)
)

# map back again (round trip test)
kcs20.rt = xform(
  kcs20.jrc2018,
  reg = h5reg('JRC2018F_FCWB_transform_quant16.h5')
)

plot3d(kcs20.jrc2018, col='green')

clear3d()
plot3d(kcs20, col='red')
plot3d(kcs20.rt, col='blue')

diffs=xyzmatrix(kcs20)-xyzmatrix(kcs20.rt)
str(diffs)
plot(as.data.frame(diffs))
}