otherside: Apply a list of mirroring, affine and warping registrations...

In alexanderbates/deformetricar: R wrapper for elements of the Deformetrica registration tool

Description

Apply a list of mirroring, affine and warping registrations to an object in 3D space

Usage

otherside(x, method = c("saved", "tps3d", "deformetrica"), ...)

## Default S3 method:
otherside(x, method = c("saved", "tps3d", "deformetrica"),
  regdir = system.file("extdata/reg_output/", package = "deformetricar"),
  object.type = "NonOrientedPolyLine", ...)

## S3 method for class 'neuron'
otherside(x, method = c("saved", "tps3d", "deformetrica"),
  object.type = "NonOrientedPolyLine", ...)

## S3 method for class 'neuronlist'
otherside(x, method = c("saved", "tps3d",
  "deformetrica"), object.type = "NonOrientedPolyLine", ...)

Arguments

x	a set of 3D coordinates (Nx3 matrix), a neuron, neuronlist, dotprops, hxsurf, igraph or mesh3d object. currently point replacement is only supported for neuron and neuronlist objects.
method	Whether to use the 3D thin plate spline mapping function from package Morpho, or, more accurately but much more slowly, Deformetrica (must be installed separately) in order to recapitulate a Deformetricar deformation.
...	additional arguments passed to: shootflow apply.mirror.affine
regdir	Path to directory containing deformetrica registration.
object.type	Type of object for Deformetrica deformation. See Deformetrica's documentation. Default is appropriate for neuron skeletons.

Value

a set of 3D cordinates (or a neuron/neuronlist object if that was given as input), that has undergone sequential mirroring affine and warping (via Deformetrica, see http://www.deformetrica.org/?page_id=232) transformations. The default is to flip points in the l1 larval central nervous system from one side to the other, and apply a previousy generated Deformetrica deformation based on the registering of a set of flipped, large neuroanatomical regions unto their un-flipped counterparts.

See Also

shootflow apply.mirror.affine

alexanderbates/deformetricar documentation built on May 11, 2019, 11:26 p.m.