minc.ray.trace {RMINC}R Documentation

Call ray_trace to get a bitmap of a slice

Description

Call ray_trace to get an image of a rendered slice

Usage

minc.ray.trace("filename.mnc")
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

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.

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.

See Also

minc.apply, minc.write.volume, minc.model

Examples

## Not run: 
# get a file that could be used by glim_image
gf <- as.data.frame(read.table("filename.glim"))

# get a t-test at every voxel
t.stats <- minc.model(gf$V1, gf$V2, "t-test")

# and write to file
minc.write.volume("t-test.mnc", gf$V1[1], t.stats)

# create a pretty picture to include in the next Nature or Science
# article
minc.ray.trace("t-test.mnc", output="pretty.rgb", threshold=c(2.5,6),
               background="anatomy_image.mnc")

## End(Not run)

[Package RMINC version 0.5.1 Index]