ieegio (version 0.0.9)

as_ieegio_volume: Convert objects to 'ieegio' image volumes

Description

Convert array, path, or 'NIfTI' images in other formats to 'ieegio' image volume instance

Usage

as_ieegio_volume(x, ...)
# S3 method for character
as_ieegio_volume(x, ...)
# S3 method for ieegio_volume
as_ieegio_volume(x, ...)
# S3 method for array
as_ieegio_volume(x, vox2ras = NULL, as_color = is.character(x), ...)
# S3 method for niftiImage
as_ieegio_volume(x, ...)
# S3 method for nifti
as_ieegio_volume(x, ...)
# S3 method for ants.core.ants_image.ANTsImage
as_ieegio_volume(x, ...)

Value

An ieegio volume object; see imaging-volume

Arguments

x

R object such as array, image path, or objects such as 'RNifti' or 'oro.nifti' image instances

...

passed to other methods

vox2ras

a 4x4 'affine' matrix representing the transform from 'voxel' index (column-row-slice) to 'RAS' (right-anterior-superior) coordinate. This transform is often called 'xform', 'sform', 'qform' in 'NIfTI' terms, or 'Norig' in 'FreeSurfer'

as_color

for converting arrays to volume, whether to treat x as array of colors; default is true when x is a raster matrix ( matrix of color strings) and false when x is not a character array.

Examples

shape <- c(50, 50, 50)
vox2ras <- matrix(
  c(-1, 0, 0, 25,
    0, 0, 1, -25,
    0, -1, 0, 25,
    0, 0, 0, 1),
  nrow = 4, byrow = TRUE
)

# continuous
x <- array(rnorm(125000), shape)

volume <- as_ieegio_volume(x, vox2ras = vox2ras)
plot(volume, zoom = 3, pixel_width = 0.5)

# color rgb(a)
x <- array(
  sample(c("red","blue", "green", "cyan", "yellow"),
         12500, replace = TRUE),
  shape
)
rgb <- as_ieegio_volume(x, vox2ras = vox2ras)
plot(rgb, zoom = 3, pixel_width = 0.5)



# ---- When RNifti package is not available ---------------------------

# Emulate WebAssemply when RNifti is unavailable, using oro.nifti instead
old_opt <- options("ieegio.debug.emscripten" = TRUE)
on.exit({ options(old_opt) }, add = TRUE)

shape <- c(50, 50, 50)
vox2ras <- matrix(
  c(-1, 0, 0, 25,
    0, 0, 1, -25,
    0, -1, 0, 25,
    0, 0, 0, 1),
  nrow = 4, byrow = TRUE
)

# continuous
x <- array(rnorm(125000), shape)

# In WebAssemply, RNifti is not available, using oro.nifti instead
volume <- as_ieegio_volume(x, vox2ras = vox2ras)

stopifnot(volume$type[[1]] == "oro")

plot(volume, zoom = 3, pixel_width = 0.5)

# Cleanup: make sure the options are reset
options(old_opt)