replaceEmptyImageDimensions-methods: Replace Subsetting from Empty Image Dimensions

In neuroconductor-devel-releases/neurobase: 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects

Description

Simple wrapper for subsetting an image with indices, dropping empty dimensions.

Usage

replaceEmptyImageDimensions(
  img,
  inds,
  target_dim,
  value = 0,
  reorient = FALSE,
  ...
)

## S4 method for signature 'nifti'
replaceEmptyImageDimensions(
  img,
  inds,
  target_dim,
  value = 0,
  reorient = FALSE,
  ...
)

## S4 method for signature 'character'
replaceEmptyImageDimensions(
  img,
  inds,
  target_dim,
  value = 0,
  reorient = FALSE,
  ...
)

## S4 method for signature 'factor'
replaceEmptyImageDimensions(
  img,
  inds,
  target_dim,
  value = 0,
  reorient = FALSE,
  ...
)

## S4 method for signature 'list'
replaceEmptyImageDimensions(
  img,
  inds,
  target_dim,
  value = 0,
  reorient = FALSE,
  ...
)

## S4 method for signature 'array'
replaceEmptyImageDimensions(
  img,
  inds,
  target_dim,
  value = 0,
  reorient = FALSE,
  ...
)

## S4 method for signature 'anlz'
replaceEmptyImageDimensions(
  img,
  inds,
  target_dim,
  value = 0,
  reorient = FALSE,
  ...
)

## S4 method for signature 'ANY'
replaceEmptyImageDimensions(
  img,
  inds,
  target_dim,
  value = 0,
  reorient = FALSE,
  ...
)

replace_empty_dim(img, ...)

Arguments

img	image, nifti object, or array
inds	indices of subset from getEmptyImageDimensions or dropEmptyImageDimensions.
target_dim	Original dimension from which the data was subset, the final dimension of the output
value	value to replace in the image where outside the indices
reorient	Should image be reoriented if a filename?
...	not used

Value

Object of class nifti or array if nifti is not supplied

Note

replace_empty_dim is a shorthand for replaceEmptyImageDimensions with all the same arguments.

See Also

getEmptyImageDimensions, dropEmptyImageDimensions

Examples

dims = rep(10, 3)
arr = array(rnorm(prod(dims)), dim = dims)
arr[,,10] = 0
nim = oro.nifti::nifti(arr)
rnifti = RNifti::asNifti(nim)
timg = tempimg(nim)
limg = list(factor(timg, timg))
inds = getEmptyImageDimensions(nim)
inds_arr = getEmptyImageDimensions(arr)
testthat::expect_equal(inds, inds_arr)

out = applyEmptyImageDimensions(nim, inds = inds)
result = replaceEmptyImageDimensions(out, inds = inds,
target_dim = dim(nim))
testthat::expect_equal(array(result, dim = dim(result)), 
array(nim, dim = dim(nim)))
replace_empty_dim(out, inds = inds,
target_dim = dim(nim))

target_dim = dim(nim)

arr = array(out, dim = dim(out))
nim = oro.nifti::nifti(arr)
rnifti = RNifti::asNifti(nim)
timg = tempimg(nim)
limg = list(factor(timg), factor(timg))
func = function(...) replaceEmptyImageDimensions(..., 
target_dim = target_dim, inds = inds)
func(arr)
func(nim)
func(rnifti)
func(timg)
func(limg)

neuroconductor-devel-releases/neurobase documentation built on May 6, 2020, 4:25 p.m.