mirror: Mirror 3D object about a given axis, optionally using a...

In natverse/nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

Mirror 3D object about a given axis, optionally using a warping registration

Description

mirroring with a warping registration can be used to account e.g. for the asymmetry between brain hemispheres.

mirror.character handles images on disk

Usage

mirror(x, ...)

## S3 method for class 'character'
mirror(x, output, mirrorAxisSize = NULL, target = x, ...)

## Default S3 method:
mirror(
  x,
  mirrorAxisSize,
  mirrorAxis = c("X", "Y", "Z"),
  warpfile = NULL,
  transform = c("warp", "affine", "flip"),
  ...
)

## S3 method for class 'neuronlist'
mirror(x, subset = NULL, OmitFailures = NA, ...)

Arguments

x	Object with 3D points (with named cols X,Y,Z) or path to image on disk.
...	additional arguments passed to methods or eventually to xform
output	Path to the output image
mirrorAxisSize	A single number specifying the size of the axis to mirror or a 2 vector (recommended) or 2x3 matrix specifying the boundingbox (see details).
target	Path to the image defining the target grid (defaults to the input image - hard to see when this would not be wanted).
mirrorAxis	Axis to mirror (default "X"). Can also be an integer in range 1:3.
warpfile	Optional registration or reglist to be applied after the simple mirroring.. It is called warpfile for historical reasons, since it is normally the path to a CMTK registration that specifies a non-rigid transformation to correct asymmetries in an image.
transform	whether to use warp (default) or affine component of registration, or simply flip about midplane of axis.
subset	For mirror.neuronlist indices (character/logical/integer) that specify a subset of the members of x to be transformed.
OmitFailures	Whether to omit neurons for which FUN gives an error. The default value (NA) will result in nlapply stopping with an error message the moment there is an error. For other values, see details.

Details

The mirrorAxisSize argument can be specified in 3 ways for the x axis with extreme values, x0+x1:

• a single number equal to x0+x1

• a 2-vector c(x0, x1) (recommended)

• the boundingbox for the 3D data to be mirrored: the relevant axis specified by mirrorAxis will be extracted.

This function is agnostic re node vs cell data, but for node data BoundingBox should be supplied while for cell, it should be bounds. See boundingbox for details of BoundingBox vs bounds.

See nlapply for details of the subset and OmitFailures arguments.

Value

Object with transformed points

See Also

xform, boundingbox

nlapply

Examples

nopen3d()
x=Cell07PNs[[1]]
mx=mirror(x,168)

plot3d(x,col='red')
plot3d(mx,col='green')


# also works with dotprops objects
nclear3d()
y=kcs20[[1]]
my=mirror(y,mirrorAxisSize=564.2532,transform='flip')

plot3d(y, col='red')
plot3d(my, col='green')


## Not run: 
## Example with an image
# note that we must specify an output image (obviously) but that as a
# convenience mirror calculates the mirrorAxisSize for us
mirror('myimage.nrrd', output='myimage-mirrored.nrrd', 
  warpfile='myimage_mirror.list')

# Simple flip along a different axis
mirror('myimage.nrrd', output='myimage-flipped.nrrd', mirrorAxis="Y", 
  transform='flip')

## End(Not run)

natverse/nat documentation built on Feb. 19, 2024, 7:19 a.m.