dropEmptyImageDimensions: Drop Empty Image Dimensions

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

Description

Drops dimensions of an image that has all irrelevant values

Usage

dropEmptyImageDimensions(
  img,
  value = 0,
  threshold = 0,
  other.imgs = NULL,
  keep_ind = FALSE,
  reorient = FALSE
)

drop_empty_dim(
  img,
  value = 0,
  threshold = 0,
  other.imgs = NULL,
  keep_ind = FALSE,
  reorient = FALSE
)

Arguments

img	nifti object
value	Value to check against. If zero, then dropEmptyImageDimensions will drop any dimension that has fewer than threshold zeroes. May be a vector of values, matched with match
threshold	Drop dimension if fewer than threshold voxels are in the slice
other.imgs	List of other nifti objects or filenames to apply the same dropping as img.
keep_ind	keep indices in output. Will return list, even if other.imgs not specified
reorient	Should image be reoriented if a filename?

Value

List of output image indices, and other images if other.imgs not specified or keep_ind = TRUE. Otherwise object of class nifti

Note

drop_empty_dim is a shorthand for dropEmptyImageDimensions with all the same arguments. Also, NA are set to zero.

See Also

getEmptyImageDimensions

Examples

set.seed(5)
dims = rep(10, 3)
arr = array(rnorm(prod(dims)), dim = dims)
arr[,,10] = 0
nim = oro.nifti::nifti(arr)

dnim = dropEmptyImageDimensions(nim, keep_ind = TRUE)
new_nim = dnim$outimg
names(dnim)
dnim = dropEmptyImageDimensions(nim, keep_ind = TRUE, other.imgs = nim)
dims = rep(10, 4)
arr = array(rnorm(prod(dims)), dim = dims)
nim = oro.nifti::nifti(arr)

testthat::expect_error(
{dnim = dropEmptyImageDimensions(nim, keep_ind = TRUE)}
)

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