voxel_colormap: Color maps for volume or surface data

In threeBrain: 3D Brain Visualization

Color maps for volume or surface data

Description

Color maps for volume or surface data

Usage

create_colormap(
  gtype = c("surface", "volume"),
  dtype = c("continuous", "discrete"),
  key,
  color,
  value,
  alpha = FALSE,
  con = NULL,
  auto_rescale = FALSE,
  ...
)

save_colormap(cmap, con)

freeserfer_colormap(con)

load_colormap(con)

Arguments

gtype	geometry type, choices are "surface", "volume"
dtype	data type, "continuous" or "discrete"
key	non-negative integer vector corresponding to color values; its length must exceed 1; see 'Details'
color	characters, corresponding to color strings for each key
value	actual value for each key
alpha	whether to respect transparency
con	a file path to write results to or to read from. The file path can be passed as voxel_colormap into threejs_brain.
auto_rescale	automatically scale the color according to image values; only valid for continuous color maps
...	used by continuous color maps, passed to colorRampPalette
cmap	color map object

Details

Internal 'JavaScript' shader implementation uses integer color keys to connect color palettes and corresponding values. The keys must be non-negative.

Zero key is a special color key reserved by system. Please avoid using it for valid values.

Value

A list of color map information

Examples

# Creates a symmetric continuous colormap with 3 keys
# The color range is -10 to 10
# The colors are 'blue','white','red' for these keys

pal <- create_colormap(
  gtype = "volume", dtype = "continuous",
  key = c(1,2,3), value = c(-10,0,10),
  color = c('blue','white','red'))

print( pal )

# ---------------- Get colormap key from a value ------------

# returns key index starting from
pal$get_key( -10 )

# nearest value
pal$get_key( 2 )

# set threshold, key is now 0 (no color)
pal$get_key( 2, max_delta = 1 )


# ---------------- Save and load ----------------
f <- tempfile( fileext = '.json' )
save_colormap( pal, f )
cat(readLines(f), sep = '\n')

load_colormap(f)

threeBrain documentation built on July 9, 2023, 6:32 p.m.