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.
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)
| 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. |
The filename of the output image is returned.
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.