minc.ray.trace: Call ray_trace to get an image of a rendered slice

In Mouse-Imaging-Centre/RMINC: Statistical Tools for Medical Imaging NetCDF (MINC) Files

Call ray_trace to get an image of a rendered slice

Description

This function provides an interface to the ray_trace command written by David MacDonald. As such it needs both ray_trace and make_slice to be on the path upon startup of R, and the bicpl library has to be compiled with image output enabled.

Usage

minc.ray.trace(
  volume,
  output = "slice.rgb",
  size = c(400, 400),
  slice = list(pos = 0, wv = "w", axis = "z"),
  threshold = NULL,
  colourmap = "-spectral",
  background = NULL,
  background.threshold = NULL,
  background.colourmap = "-gray",
  display = TRUE
)

Arguments

volume	The filename of a volume to render.
output	The output filename.
size	A vector of two elements specifying the output size
slice	A list of three elements, pos being the slice number, wv whether the specification is in voxel or world space, and the axis.
threshold	A vector of two elements containing the threshold. If NULL, the full range of the volume will be used.
colourmap	The colourmap to be used by ray_trace.
background	An optional filename of a background volume. Used, for example, to render statistical results on top of background anatomy.
background.threshold	Threshold to use for the background volume. If NULL the whole range will be used.
background.colourmap	The colourmap argument to be passed to ray_trace for the background image.
display	Boolean argument which determines whether display (from ImageMagick) will be called on the output.

Details

Behaviour of minc.ray.trace varies depending on whether a background image is specified. If background=NULL, then the specified slice is rendered using the supplied (or automatically determined) threshold argument. If there is a background image, then the slice from the input volume is rendered semi-transparently on top of the background.

Note that cropping in ray_trace is on by default, so the output image size will not necessarily be the same as the size argument to minc.ray.trace.

Value

output

The filename of the output image is returned.

Mouse-Imaging-Centre/RMINC documentation built on Feb. 24, 2025, 1:22 a.m.