Simple wrapper for setting non-finite values to zero
finite_img(img, replace = 0)
# S4 method for nifti
finite_img(img, replace = 0)
# S4 method for array
finite_img(img, replace = 0)
# S4 method for ANY
finite_img(img, replace = 0)
# S4 method for character
finite_img(img, replace = 0)
# S4 method for list
finite_img(img, replace = 0)| img | character path of image or
an object of class |
|---|---|
| replace | Value to replace non-finite values to |
nifti object
John Muschelli muschellij2@gmail.com
set.seed(5)
dims = rep(10, 3)
arr = array(rpois(prod(dims), lambda = 2), dim = dims)
arr[c(5, 6, 7, 8)] = c(NA, NaN, Inf, -Inf)
nim = nifti(arr)
finite_img(nim)
#> NIfTI-1 format
#> Type : nifti
#> Data Type : 2 (UINT8)
#> Bits per Pixel : 8
#> Slice Code : 0 (Unknown)
#> Intent Code : 0 (None)
#> Qform Code : 0 (Unknown)
#> Sform Code : 0 (Unknown)
#> Dimension : 10 x 10 x 10
#> Pixel Dimension : 1 x 1 x 1
#> Voxel Units : Unknown
#> Time Units : Unknown
finite_img(arr)
#> , , 1
#>
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 4 2 3 1 2 3 4 3
#> [2,] 3 2 3 0 1 2 1 3 3 1
#> [3,] 4 1 1 1 3 4 4 1 1 1
#> [4,] 1 2 1 0 2 5 6 3 0 1
#> [5,] 0 1 1 0 4 4 6 0 2 1
#> [6,] 0 1 2 2 2 1 4 4 0 3
#> [7,] 0 1 2 2 3 1 4 0 5 1
#> [8,] 0 4 5 2 0 1 1 3 3 2
#> [9,] 5 2 1 1 3 1 4 2 1 2
#> [10,] 0 3 5 1 2 1 3 1 2 2
#>
#> , , 2
#>
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 4 1 0 1 2 2 3 1 3 2
#> [2,] 3 2 5 1 1 2 1 4 3 3
#> [3,] 2 3 3 0 2 3 0 6 1 1
#> [4,] 4 1 4 3 4 0 4 0 2 4
#> [5,] 3 2 1 1 2 2 3 1 3 1
#> [6,] 1 1 0 0 3 3 2 4 0 1
#> [7,] 1 2 3 0 2 2 2 2 3 2
#> [8,] 2 0 3 2 2 1 1 5 1 2
#> [9,] 2 2 1 1 2 1 3 1 3 2
#> [10,] 1 1 1 2 3 3 5 0 1 2
#>
#> , , 3
#>
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 0 3 1 3 4 2 4 2 1 1
#> [2,] 0 3 2 0 1 0 2 1 1 2
#> [3,] 4 2 5 0 3 1 0 2 2 2
#> [4,] 3 2 1 4 6 1 1 1 1 2
#> [5,] 3 0 6 3 0 4 0 1 6 2
#> [6,] 2 1 3 1 2 0 0 1 1 2
#> [7,] 2 1 2 2 0 0 2 3 3 0
#> [8,] 1 0 3 0 0 4 1 1 3 0
#> [9,] 2 4 0 2 3 0 3 2 1 1
#> [10,] 1 0 1 3 1 2 2 3 4 4
#>
#> , , 4
#>
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 3 4 0 1 0 2 6 1 3 4
#> [2,] 1 1 3 0 1 1 3 1 1 3
#> [3,] 3 1 6 2 2 4 1 2 2 3
#> [4,] 1 2 1 5 1 2 1 3 1 3
#> [5,] 1 4 2 2 0 1 3 1 1 2
#> [6,] 5 2 0 1 1 2 4 2 2 5
#> [7,] 3 1 5 2 0 3 3 3 2 1
#> [8,] 0 0 2 2 2 0 5 1 4 4
#> [9,] 1 2 1 1 2 1 0 0 2 3
#> [10,] 3 0 3 1 4 0 2 3 4 1
#>
#> , , 5
#>
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 2 2 4 1 2 2 1 5 2 1
#> [2,] 1 2 2 2 3 4 0 6 0 2
#> [3,] 1 3 3 2 2 0 3 4 2 3
#> [4,] 0 0 1 3 1 2 3 3 4 4
#> [5,] 3 3 3 4 5 1 1 1 2 2
#> [6,] 1 2 1 3 0 2 5 3 2 1
#> [7,] 1 1 1 3 1 1 1 1 4 0
#> [8,] 0 3 2 2 0 1 2 2 2 5
#> [9,] 2 3 3 3 0 0 1 4 0 2
#> [10,] 2 3 1 1 0 0 5 3 2 1
#>
#> , , 6
#>
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 0 0 6 1 2 2 1 2 1
#> [2,] 1 0 2 4 0 1 3 3 2 2
#> [3,] 1 1 2 3 1 0 1 4 3 3
#> [4,] 2 1 3 2 4 0 2 4 1 3
#> [5,] 2 1 3 1 1 2 1 2 3 3
#> [6,] 0 1 1 2 2 2 5 2 5 3
#> [7,] 1 3 1 0 4 2 3 5 2 2
#> [8,] 2 0 1 2 4 2 2 1 1 2
#> [9,] 0 2 2 1 5 2 1 1 2 2
#> [10,] 4 0 3 1 3 5 3 1 3 1
#>
#> , , 7
#>
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 4 1 1 4 1 0 0 1 0 1
#> [2,] 1 1 0 3 3 2 2 1 2 0
#> [3,] 2 4 4 4 4 3 2 0 0 1
#> [4,] 4 5 1 1 2 5 1 1 3 1
#> [5,] 5 1 3 1 2 2 2 2 0 0
#> [6,] 2 2 1 1 4 0 1 3 1 2
#> [7,] 2 2 1 0 3 0 1 3 3 2
#> [8,] 2 4 4 3 1 4 2 1 3 2
#> [9,] 0 3 2 2 1 1 3 2 1 4
#> [10,] 2 4 3 0 0 2 4 5 2 3
#>
#> , , 8
#>
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 0 3 1 4 2 4 5 4 1 0
#> [2,] 6 3 3 1 2 2 2 4 1 1
#> [3,] 2 5 5 1 3 1 4 3 2 1
#> [4,] 1 0 2 5 2 2 0 1 2 2
#> [5,] 3 0 2 2 0 4 3 1 1 3
#> [6,] 1 0 1 3 2 0 2 4 2 1
#> [7,] 1 2 3 3 3 3 3 1 3 0
#> [8,] 5 1 2 4 3 2 2 2 3 2
#> [9,] 2 2 1 2 1 1 5 1 2 1
#> [10,] 2 0 1 2 3 5 7 0 0 2
#>
#> , , 9
#>
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 1 1 3 6 2 2 1 3 1 2
#> [2,] 2 0 2 2 2 4 2 2 2 2
#> [3,] 3 1 1 1 5 3 0 4 0 4
#> [4,] 0 2 1 0 0 0 2 1 2 2
#> [5,] 0 5 1 2 2 0 2 5 2 1
#> [6,] 1 0 4 2 4 2 0 3 2 3
#> [7,] 1 1 3 2 0 3 2 3 3 5
#> [8,] 3 3 2 2 3 1 1 2 1 3
#> [9,] 2 0 2 0 2 3 5 3 3 2
#> [10,] 0 4 1 2 5 0 4 2 2 0
#>
#> , , 10
#>
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 3 2 1 3 4 4 2 1 1 2
#> [2,] 3 1 3 3 2 1 1 1 2 4
#> [3,] 1 0 0 3 1 2 1 1 1 1
#> [4,] 3 2 3 1 1 1 4 2 1 3
#> [5,] 2 3 2 0 0 2 1 1 1 4
#> [6,] 2 2 4 0 3 3 1 4 2 3
#> [7,] 2 0 0 3 1 3 2 3 1 2
#> [8,] 1 0 5 1 2 0 1 4 2 0
#> [9,] 2 2 5 1 1 3 0 2 4 0
#> [10,] 4 2 1 3 3 2 1 1 4 1
#>
tfile = tempimg(nim)
#> Warning: NAs and NaNs in image file, replacing with zeros
#> Warning: NAs introduced by coercion to integer range
checkimg(c(tfile, tfile))
#> /tmp/RtmpBb1B9G/file16b731fb2bee4.nii.gz
#> "/tmp/RtmpBb1B9G/file16b731fb2bee4.nii.gz"
#> /tmp/RtmpBb1B9G/file16b731fb2bee4.nii.gz
#> "/tmp/RtmpBb1B9G/file16b731fb2bee4.nii.gz"
checkimg(list(tfile, tfile))
#> [1] "/tmp/RtmpBb1B9G/file16b731fb2bee4.nii.gz"
#> [2] "/tmp/RtmpBb1B9G/file16b731fb2bee4.nii.gz"
finite_img(list(tfile, tfile))
#> Warning: NAs introduced by coercion to integer range
#> Warning: NAs introduced by coercion to integer range
#> [[1]]
#> NIfTI-1 format
#> Type : nifti
#> Data Type : 16 (FLOAT32)
#> Bits per Pixel : 32
#> Slice Code : 0 (Unknown)
#> Intent Code : 0 (None)
#> Qform Code : 0 (Unknown)
#> Sform Code : 0 (Unknown)
#> Dimension : 10 x 10 x 10
#> Pixel Dimension : 1 x 1 x 1
#> Voxel Units : Unknown
#> Time Units : Unknown
#>
#> [[2]]
#> NIfTI-1 format
#> Type : nifti
#> Data Type : 16 (FLOAT32)
#> Bits per Pixel : 32
#> Slice Code : 0 (Unknown)
#> Intent Code : 0 (None)
#> Qform Code : 0 (Unknown)
#> Sform Code : 0 (Unknown)
#> Dimension : 10 x 10 x 10
#> Pixel Dimension : 1 x 1 x 1
#> Voxel Units : Unknown
#> Time Units : Unknown
#>
finite_img(c(tfile, tfile))
#> Warning: NAs introduced by coercion to integer range
#> Warning: NAs introduced by coercion to integer range
#> [[1]]
#> NIfTI-1 format
#> Type : nifti
#> Data Type : 16 (FLOAT32)
#> Bits per Pixel : 32
#> Slice Code : 0 (Unknown)
#> Intent Code : 0 (None)
#> Qform Code : 0 (Unknown)
#> Sform Code : 0 (Unknown)
#> Dimension : 10 x 10 x 10
#> Pixel Dimension : 1 x 1 x 1
#> Voxel Units : Unknown
#> Time Units : Unknown
#>
#> [[2]]
#> NIfTI-1 format
#> Type : nifti
#> Data Type : 16 (FLOAT32)
#> Bits per Pixel : 32
#> Slice Code : 0 (Unknown)
#> Intent Code : 0 (None)
#> Qform Code : 0 (Unknown)
#> Sform Code : 0 (Unknown)
#> Dimension : 10 x 10 x 10
#> Pixel Dimension : 1 x 1 x 1
#> Voxel Units : Unknown
#> Time Units : Unknown
#>
img = RNifti::readNifti(tfile)
checkimg(img)
#> [1] "/tmp/RtmpBb1B9G/file16b7357445518.nii.gz"
img[c(5, 6, 7, 8)] = c(NA, NaN, Inf, -Inf)
stopifnot(!any(c(is.na(c(finite_img(img))))))