Compute voxel colors based on colortable.

Use the intensity values of the voxels in volume and lookup the respective colors in a colortable.

Usage

vol.overlay.colors.from.colortable(
  volume,
  colortable,
  ignored_struct_indices = c(),
  ignored_struct_names = c("unknown", "Unknown")
)

Arguments

volume

numeric 3D array, the values should be integers present in the struct_index column of the colortable. All other values will be assigned NA as a color.

colortable

a colortable, as returned by read.fs.colortable, or a character string representing a path to a colortable file.

ignored_struct_indices

integer vector, struct_index entries in the colortable that should be ignored

ignored_struct_names

vector of character strings, struct_name entries in the colortable that should be ignored. Can be combined with ignored_struct_indices.

Value

character string 3D array, the colors. Voxels in the volume which were not matched by the colortable are set to NA in it.