Call ray_trace to get an image of a rendered slice

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.

Value

output: The filename of the output image is returned.

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.