scene4d: Wrapper to write a 4D scene

In brainR: Helper Functions to 'misc3d' and 'rgl' Packages for Brain Imaging

Description

This function takes in filenames, levels, and creates an output html file, with 4D elements. The html is based on XTK (https://github.com/xtk/X#readme)

Usage

scene4d(
  files,
  fnames = NULL,
  outfile = "index_4D_stl.html",
  levels = NULL,
  alpha = NULL,
  color = "white",
  useTemp = FALSE,
  MNITemp = c("1mm", "2mm"),
  objtype = "stl",
  ...
)

Arguments

files	(character) vector of filenames (first being a brain file if useTemp=FALSE)
fnames	(character) filenames for the 3D surfaces in the scene - needs to be the same length as files
outfile	(character) html filename
levels	(numeric/list) levels to make contours/surfaces for each file. Either a numeric vector may be passed, one level for each file. Or a list of numeric vectors of multiple levels for each file. Will be coerced to a list.
alpha	(numeric/list) alpha opacities for each contours/surface for each file. Will be coerced to list similarly as levels
color	(character/list) colors for each contours/surface for each file. Will be coerced to list similarly as levels
useTemp	(logical) whether to use template from brainR as the brain figure
MNITemp	(character) if (useTemp = TRUE) either "1mm" or "2mm" denoting the resolution of the template used
objtype	(character) object type to write the files to. Either "stl", "obj", or "ply" to write.
...	other options to be passed to write4D

Examples

### Faster - 8mm resampled but very coarse
imgs <- paste("Visit_", 1:5, "_8mm.nii.gz", sep="") 
ifiles <- sapply(imgs, system.file, package='brainR')
files = file.path(tempdir(), basename(ifiles))
file.copy(ifiles, files)
outfile <-  file.path(tempdir(), "index_4D_stl.html")
scene4d(files, levels=rep(0.99, length(files)), 
outfile = outfile, color= rep("blue", length(files)), useTemp=TRUE, 
MNITemp = "8mm", alpha = rep(1, length(files)), rescale=TRUE  )
## Not run: 
imgs <- paste("Visit_", 1:5, ".nii.gz", sep="") 
ifiles <- sapply(imgs, system.file, package='brainR')
files = file.path(tempdir(), basename(ifiles))
file.copy(ifiles, files)
scene4d(files, levels=rep(0.99, length(files)), 
outfile = outfile,
color= rep("blue", length(files)), useTemp=TRUEge, 
MNITemp = "8mm", alpha = rep(1, length(files)), rescale=TRUE  )

## End(Not run)

brainR documentation built on Dec. 5, 2019, 9:07 a.m.