im3d {nat}

Construct an im3d object representing 3D image data, densities etc

Description

im3d objects consist of a data array with attributes defining the spatial positions at which the voxels are located. There should always be a BoundingBox attribute which defines the physical extent of the volume in the same manner as the Amira 3D visualisation and analysis software. This corresponds to the node centers option in the NRRD format.

Usage

im3d(
  x = numeric(0),
  dims = NULL,
  voxdims = NULL,
  origin = NULL,
  BoundingBox = NULL,
  bounds = NULL,
  ...
)

Arguments

x

The object to turn into an im3d

dims

The dimensions of the image array either as an integer vector or as an im3d object, whose attributes will provide defaults for dims, origin, BoundingBox, bounds arguments. The default (dims=NULL) will result in dims being set to x if x is an im3d object or dim(x) otherwise.

voxdims

The voxel dimensions

origin

the location (or centre) of the first voxel

BoundingBox

Physical extent of the image. See the details section of boundingbox's help for the distinction between BoundingBox and bounds.

bounds

Physical extent of image

...

Additional attributes such as units or materials

Details

We follow Amira's convention of setting the bounding box equal to voxel dimension (rather than 0) for any dimension with only 1 voxel.

Value

An array with additional class im3d

See Also

Other im3d: as.im3d(), boundingbox(), im3d-coords, im3d-io, imexpand.grid(), imslice(), is.im3d(), mask(), origin(), projection(), threshold(), unmask(), voxdims()