Apply Subsetting from Empty Image Dimensions

Description

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

Usage

applyEmptyImageDimensions(img, inds, reorient = FALSE, ...)

## S4 method for signature 'nifti'
applyEmptyImageDimensions(img, inds, reorient = FALSE, ...)

## S4 method for signature 'character'
applyEmptyImageDimensions(img, inds, reorient = FALSE, ...)

## S4 method for signature 'factor'
applyEmptyImageDimensions(img, inds, reorient = FALSE, ...)

## S4 method for signature 'list'
applyEmptyImageDimensions(img, inds, reorient = FALSE, ...)

## S4 method for signature 'array'
applyEmptyImageDimensions(img, inds, reorient = FALSE, ...)

## S4 method for signature 'anlz'
applyEmptyImageDimensions(img, inds, reorient = FALSE, ...)

## S4 method for signature 'ANY'
applyEmptyImageDimensions(img, inds, reorient = FALSE, ...)

apply_empty_dim(img, ...)

Arguments

Value

Object of class nifti or array if nifti is not supplied

Note

apply_empty_dim is a shorthand for applyEmptyImageDimensions with all the same arguments.

See Also

getEmptyImageDimensions, dropEmptyImageDimensions

Examples

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

out = applyEmptyImageDimensions(nim, inds = inds)
out_arr = applyEmptyImageDimensions(arr, inds = inds)
testthat::expect_equal(out_arr, array(out, dim = dim(out)))
out = apply_empty_dim(nim, inds = inds)

set.seed(5)
dims = rep(10, 3)
arr = array(rnorm(prod(dims)), dim = dims)
arr[,,10] = 0
nim = oro.nifti::nifti(arr)
inds = getEmptyImageDimensions(nim)
rnifti = RNifti::asNifti(nim)
timg = tempimg(nim)
limg = list(factor(timg), factor(timg))
apply_empty_dim(nim, inds = inds)
func = function(...) applyEmptyImageDimensions(..., inds = inds)
func(arr)
func(nim)
func(rnifti)
func(timg)
func(limg)

Boxplot of Values in an Image

Description

Computes the boxplot of values of an image with the option for a mask.

Usage

## S3 method for class 'nifti'
boxplot(x, ..., mask)

## S3 method for class 'anlz'
boxplot(x, ..., mask)

Arguments

Value

Output of boxplot

Examples

img = nifti(array(rnorm(10^3), dim = rep(10, 3)))
mask = img > 0
boxplot(img)
boxplot(img, mask = mask)
boxplot(as.anlz(img))

Find Breaks for nifti Image Plotting

Description

Helper function for plotting - returns breaks for image plot function for object of class nifti

Usage

breaker(x, zlim, col, breaks = NULL)

Arguments

Value

Vector of length 2

If breaks = NULL, then vector of length(col) + 1, otherwise returns breaks

Check Mask is Binary

Description

Determine if only values in a mask are 0/1

Usage

check_mask(mask, allow.NA = FALSE, allow.array = TRUE)

Arguments

Value

Logical indicating if object is binary mask with only 0, 1, and NA if applicable

Examples

arr = array(rbinom(1000, size = 1, prob = 0.2), dim = c(10,10,10))
nim = oro.nifti::nifti(arr)
check_mask(nim)

Check Mask is Binary, Fail otherwise

Description

Determine if only values in a mask are 0/1. Will error otherwise.

Usage

check_mask_fail(...)

Arguments

Value

Either will error if conditions not met or an invisible NULL

Examples

arr = array(rbinom(1000, size = 1, prob = 0.2), dim = c(10,10,10))
nim = oro.nifti::nifti(arr)
check_mask_fail(nim)

Check if nifti image or read in a nifti image

Description

Simple check to see if input is character or of class nifti

Usage

check_nifti(
  x,
  reorient = FALSE,
  allow.array = FALSE,
  fast = FALSE,
  need_header = TRUE,
  ...
)

## S4 method for signature 'nifti'
check_nifti(
  x,
  reorient = FALSE,
  allow.array = FALSE,
  fast = FALSE,
  need_header = TRUE,
  ...
)

## S4 method for signature 'character'
check_nifti(
  x,
  reorient = FALSE,
  allow.array = FALSE,
  fast = FALSE,
  need_header = TRUE,
  ...
)

## S4 method for signature 'factor'
check_nifti(
  x,
  reorient = FALSE,
  allow.array = FALSE,
  fast = FALSE,
  need_header = TRUE,
  ...
)

## S4 method for signature 'list'
check_nifti(
  x,
  reorient = FALSE,
  allow.array = FALSE,
  fast = FALSE,
  need_header = TRUE,
  ...
)

## S4 method for signature 'array'
check_nifti(
  x,
  reorient = FALSE,
  allow.array = FALSE,
  fast = FALSE,
  need_header = FALSE,
  ...
)

## S4 method for signature 'anlz'
check_nifti(
  x,
  reorient = FALSE,
  allow.array = FALSE,
  fast = FALSE,
  need_header = TRUE,
  ...
)

## S4 method for signature 'ANY'
check_nifti(
  x,
  reorient = FALSE,
  allow.array = FALSE,
  fast = FALSE,
  need_header = TRUE,
  ...
)

Arguments

Value

nifti object or array if allow.array=TRUE and x is an array

Author(s)

John Muschelli muschellij2@gmail.com

See Also

readnii

Examples

x = nifti()
check_nifti(x)
set.seed(5)
dims = rep(10, 4)
arr = array(rpois(prod(dims), lambda = 2), dim = dims)
nim = oro.nifti::nifti(arr)
check_nifti(nim)
check_nifti(as.anlz(nim))
testthat::expect_error(check_nifti(arr, allow.array = FALSE))
tfile = tempimg(nim)
check_nifti(c(tfile, tfile))
check_nifti(list(tfile, tfile))
check_nifti(factor(c(tfile, tfile)))
check_nifti(RNifti::readNifti(tfile))

Check if nifti image or read in a nifti header

Description

Simple check to see if input is character or of class nifti and read in the header

Usage

check_nifti_header(x)

## S4 method for signature 'nifti'
check_nifti_header(x)

## S4 method for signature 'character'
check_nifti_header(x)

## S4 method for signature 'factor'
check_nifti_header(x)

## S4 method for signature 'list'
check_nifti_header(x)

## S4 method for signature 'array'
check_nifti_header(x)

## S4 method for signature 'anlz'
check_nifti_header(x)

## S4 method for signature 'ANY'
check_nifti_header(x)

Arguments

Value

nifti object or character

Author(s)

John Muschelli muschellij2@gmail.com

Examples

set.seed(5)
dims = rep(10, 4)
arr = array(rpois(prod(dims), lambda = 2), dim = dims)
nim = oro.nifti::nifti(arr)
check_nifti_header(nim)
check_nifti_header(as.anlz(nim))
testthat::expect_error(check_nifti_header(arr))
tfile = tempimg(nim)
check_nifti_header(tfile)
check_nifti_header(RNifti::readNifti(tfile))
check_nifti_header(c(tfile, tfile))
check_nifti_header(list(tfile, tfile))
check_nifti_header(factor(tfile))

Check output filename

Description

This function checks if an output filename is not NULL in conjunction whether the user would like to return an image

Usage

check_outfile(outfile, retimg, fileext = ".nii.gz")

Arguments

Value

Filename of output file or a temporary filename

Force object to filename

Description

Ensures the output to be a character filename (or vector) from an input image or nifti.

Usage

checkimg(file, allow_array = FALSE, ...)

## S4 method for signature 'nifti'
checkimg(file, allow_array = FALSE, ...)

## S4 method for signature 'ANY'
checkimg(file, allow_array = FALSE, ...)

## S4 method for signature 'character'
checkimg(file, allow_array = FALSE, ...)

## S4 method for signature 'list'
checkimg(file, allow_array = FALSE, ...)

Arguments

Value

character filename of image or temporary nii, with .nii extension

Author(s)

John Muschelli muschellij2@gmail.com

Force object to filename with .nii extension

Description

Ensures the output to be a character filename (or vector) from an input image or nifti, but not gzipped and has .nii extension

Usage

checknii(file, ...)

## S4 method for signature 'nifti'
checknii(file, ...)

## S4 method for signature 'factor'
checknii(file, ...)

## S4 method for signature 'character'
checknii(file, ...)

## S4 method for signature 'list'
checknii(file, ...)

## S4 method for signature 'ANY'
checknii(file, ...)

ensure_nii(file, ...)

Arguments

Value

character filename of image or temporary nii, with .nii extension

Author(s)

John Muschelli muschellij2@gmail.com

Examples

set.seed(5)
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), factor(timg))
func = checknii
func(nim)
func(rnifti)
func(timg)
func(limg)

Force object to filename with .nii.gz extension

Description

Ensures the output to be a character filename (or vector) from an input image or nifti, to be gzipped and has .nii.gz extension

Usage

checkniigz(file, ...)

## S4 method for signature 'nifti'
checkniigz(file, ...)

## S4 method for signature 'ANY'
checkniigz(file, ...)

## S4 method for signature 'factor'
checkniigz(file, ...)

## S4 method for signature 'character'
checkniigz(file, ...)

## S4 method for signature 'list'
checkniigz(file, ...)

ensure_nii_gz(file, ...)

Arguments

Value

Character filename of image or temporary nii, with .nii.gz extension

Author(s)

John Muschelli muschellij2@gmail.com

Examples

set.seed(5)
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), factor(timg))
func = checkniigz
func(nim)
func(rnifti)
func(timg)
func(limg)

Image Center of Gravity

Description

Find Center of Gravity of Image, after thresholding

Usage

cog(img, thresh = 0, ceil = FALSE, warn = TRUE)

Arguments

Value

Vector of length 3

Examples

dims = rep(20, 3)
x = array(rnorm(prod(dims)), dim = dims)
img = nifti(x, dim= dims, 
datatype = convert.datatype()$FLOAT32, cal.min = min(x), 
cal.max = max(x), pixdim = rep(1, 4))
cog(img)

Add a colorbar to an ortho2 object

Description

Adds a series of colors mapped to a value

Usage

colorbar(breaks, col, text.col = "white", labels = TRUE, maxleft = 0.95)

Arguments

Value

A plot

Note

Much of this was taken from vertical.image.legend from the aqfig package

Copy NIfTI Header to an array

Description

Copies slots of a nifti object to an array. This is useful if you're subsetting 4D data and getting an array out

Usage

copyNIfTIHeader(
  img,
  arr,
  drop_slots = c(".Data", "dim_"),
  drop = TRUE,
  onlylast = TRUE,
  warn = TRUE,
  ...
)

Arguments

Value

Object of class nifti the size of arr

Examples

img = nifti(img = array(rnorm(10^4), dim=rep(10, 4)), dim=rep(10, 4), datatype = 16)
sub = img[,,,1:3]
copyNIfTIHeader(img, sub)
sub = img[,,,1, drop=FALSE]
copyNIfTIHeader(img, sub) 
copyNIfTIHeader(img, sub, drop = FALSE) 

Perform Cut on an image

Description

Cuts a numeric image into an integer factor, with the option of a mask.

Usage

## S3 method for class 'nifti'
cut(x, breaks, ..., mask)

## S3 method for class 'anlz'
cut(x, ..., mask)

Arguments

Value

Object of class nifti with an attribute of levels

Examples

img = nifti(array(rnorm(10^3), dim = rep(10, 3)))
mask = img > 0
cut(img, mask = mask, breaks = 4)

Change Data type for img

Description

Tries to figure out the correct datatype for image. Useful for image masks - makes them binary if

Usage

datatyper(
  img,
  type_string = NULL,
  datatype = NULL,
  bitpix = NULL,
  trybyte = TRUE,
  warn = TRUE
)

Arguments

Value

object of type nifti

Examples

img = nifti(array(rnorm(10^3, sd = 1000), dim = rep(10, 3)))
rimg = round(img)
newnii(datatyper(rimg))
rimg = datatyper(rimg, type_string= "FLOAT32")

Density of Values in an Image

Description

Computes the density of values of an image with the option for a mask.

Usage

## S3 method for class 'nifti'
density(x, ..., mask)

## S3 method for class 'anlz'
density(x, ..., mask)

Arguments

Value

Output of density

Examples

img = nifti(array(rnorm(10^3), dim = rep(10, 3)))
mask = img > 0
density(img, mask = mask)
density(img)

density(as.anlz(img), mask = mask)
density(as.anlz(img))

Calculate Dice from a Table

Description

Simple wrapper to calculate the Dice Coefficient/Similarity Index from a table

Usage

dicer(tab, verbose = TRUE)

Arguments

Value

Numeric scalar (one number)

Examples

tab = matrix(c(1000, 20, 20, 400), ncol = 2)
dicer(tab)

Double Orthographic Display

Description

Copy of oro.nifti's orthographic function with some tweaks such as adding L/R designations for left and right

Usage

double_ortho(
  x,
  y = NULL,
  col.y = gray(0:64/64),
  NA.x = TRUE,
  mfrow = c(2, 4),
  add = FALSE,
  ...
)

Arguments

See Also

orthographic

Drop Empty Image Dimensions

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

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)}
)

Make Mask from Empty Image Dimensions

Description

Make a mask of an image that has all irrelevant values

Usage

emptyImageDimensionsMask(img, ..., reorient = FALSE)

empty_dim_mask(img, ..., reorient = FALSE)

Arguments

Value

Object of class nifti, with binary values

Note

empty_dim_mask is a shorthand for emptyImageDimensionsMask with all the same arguments.

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)
out = emptyImageDimensionsMask(nim)
out_arr = emptyImageDimensionsMask(arr)
testthat::expect_equal(out_arr, array(out, dim = dim(out)))
out_arr = empty_dim_mask(arr)

Ensure an array output

Description

Forces an array output for manipulation and overall conversion

Usage

ensure_array(img)

Arguments

Value

Array of same dimensions as image object

Examples

set.seed(5)
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), factor(timg))
func = ensure_array
func(arr)
func(nim)
func(rnifti)
func(timg)
func(limg[[1]])

Fast Dice Tabulation

Description

Fast Dice Tabulation

Usage

fast_dice_tab(x, y)

fast_dice(x, y, verbose = FALSE)

Arguments

Value

A table object

Examples

library(oro.nifti)
set.seed(20161007)
dims = rep(10, 3)
arr = array(rnorm(10*10*10), dim = dims)
nim = oro.nifti::nifti(arr) > -1
fast_dice_tab(nim, nim)
fast_dice(nim, nim) == 1

Reading NIfTI images through RNifti

Description

This function calls the readNifti function from the RNifti package, and then converts the image to a nifti object

Usage

fast_readnii(fname, dtype = TRUE, drop_dim = TRUE)

Arguments

Value

A nifti object

Examples

set.seed(5)
dims = rep(10, 4)
arr = array(rpois(prod(dims), lambda = 2), dim = dims)
nim = oro.nifti::nifti(arr)
tfile = tempfile(fileext = ".nii.gz")
write_nifti(nim, tfile)
rimg = fast_readnii(tfile)

Get Image file extension

Description

Get the image file extension, either .nii, .hdr, .nii.gz, or .hdr.gz

Usage

file_imgext(file, withdot = TRUE)

Arguments

Value

Vector of extensions. If withdot = FALSE, then will return nii instead of .nii

Finite Image

Description

Simple wrapper for setting non-finite values to zero

Usage

finite_img(img, replace = 0)

## S4 method for signature 'nifti'
finite_img(img, replace = 0)

## S4 method for signature 'array'
finite_img(img, replace = 0)

## S4 method for signature 'ANY'
finite_img(img, replace = 0)

## S4 method for signature 'character'
finite_img(img, replace = 0)

## S4 method for signature 'list'
finite_img(img, replace = 0)

Arguments

Value

nifti object

Author(s)

John Muschelli muschellij2@gmail.com

Examples

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)
finite_img(arr)
tfile = tempimg(nim)
checkimg(c(tfile, tfile))
checkimg(list(tfile, tfile))
finite_img(list(tfile, tfile))
finite_img(c(tfile, tfile))
img = RNifti::readNifti(tfile)
checkimg(img)
img[c(5, 6, 7, 8)] = c(NA, NaN, Inf, -Inf)
stopifnot(!any(c(is.na(c(finite_img(img))))))

Flip NifTI Image

Description

This image will flip x, y, or z direction

Usage

flip_img(img, x = FALSE, y = FALSE, z = FALSE, ...)

Arguments

Value

Object of class nifti

Examples

img = random_nifti(rep(15, 3))
flipped = flip_img(img, x = TRUE, y = TRUE, z = TRUE)
img = random_nifti(rep(15, 2))
flipped = flip_img(img, x = TRUE)
testthat::expect_error(flip_img(img, z= TRUE))

Get Empty Image Dimensions

Description

Creates a list of indices of an image that has all irrelevant values

Usage

getEmptyImageDimensions(img, value = 0, threshold = 0, reorient = FALSE, ...)

get_empty_dim(img, value = 0, threshold = 0, reorient = FALSE, ...)

Arguments

Value

List of length 3 of indices.

Note

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

Examples

arr = array(rbinom(1000, size = 1, prob = 0.2), dim = c(10,10,10))
arr[,,1] = 0
arr[2:3,,] = 0
getEmptyImageDimensions(arr)

Histogram of Values in an Image

Description

Computes and displays a histogram of the values of an image with the option for a mask.

Usage

## S3 method for class 'nifti'
hist(x, ..., mask)

## S3 method for class 'anlz'
hist(x, ..., mask)

Arguments

Value

Output of hist

Examples

img = nifti(array(rnorm(10^3), dim = rep(10, 3)))
mask = img > 0
hist(img, mask = mask)

Transform set of images to matrix

Description

Creates a matrix, where the voxels are on the rows and images are on the columns

Usage

images2matrix(imgs, mask = NULL)

Arguments

Value

Matrix of V by p, where V is the product of the dimensions of one image or the number of voxels in the mask, and p is the number of images

Examples

set.seed(5)
dims = rep(10, 3)
arr = array(rpois(prod(dims), lambda = 2), dim = dims)
nim = oro.nifti::nifti(arr)
imgs = list(nim, arr)
mask = nim > 2
mat1 = images2matrix(imgs)
mat2 = images2matrix(list(nim, nim))
if (packageVersion("oro.nifti") >= package_version("0.10.2")) {
testthat::expect_equal(mat1, mat2)
} else {
testthat::expect_error(testthat::expect_equal(mat1, mat2))
}
mat1 = images2matrix(imgs, mask = mask)
mat2 = images2matrix(list(nim, nim), mask)

Convert Image to Data.frame with Colors

Description

Takes in an image and a color scheme, converts that image into a data.frame with the data and a color mapping.

Usage

img_colour_df(img, zlim = NULL, breaks = NULL, col = gray(0:64/64))

img_color_df(...)

Arguments

Value

A data.frame with the first columns being the x,y,z (maybe t) coordinates (named dim and the dimension number), a value column that contains the intensity information, and a colour column representing the color that voxel maps to

Note

img_color_df is a duplicate of img_colour_df

Examples

img = nifti(array(rnorm(10^3), dim = rep(10, 3)))
df = img_colour_df(img)
df = img_color_df(img)

Retrieve Image Indices

Description

Extract image xyz indices (in voxels or millimeters), with the option to append the values

Usage

img_indices(img, mask = NULL, add_values = FALSE, units = c("index", "mm"))

Arguments

Value

Matrix of 3 columns if add_values = FALSE or 4 columns, otherwise.

Examples

set.seed(5)
dims = rep(10, 4)
arr = array(rpois(prod(dims), lambda = 2), dim = dims)
nim = oro.nifti::nifti(arr)
ind = img_indices(nim)
ind2 = img_indices(nim, mask = nim > 2)
# 3d example
set.seed(5)
dims = rep(10, 3)
arr = array(rpois(prod(dims), lambda = 2), dim = dims)
nim = oro.nifti::nifti(arr)
ind = img_indices(nim)
ind2 = img_indices(nim, mask = nim > 2)
testthat::expect_equal(colnames(ind2), c("x", "y", "z"))
ind2 = img_indices(nim, mask = nim > 2, add_values = TRUE)
testthat::expect_equal(colnames(ind2), c("x", "y", "z", "value"))

Image List to Time Series

Description

Turns a a list of 3D images into a 4D time series image

Usage

img_list_to_ts(imgs, copy_nifti = TRUE, warn = TRUE)

Arguments

Value

Object of class nifti

Note

If the object is not of class list, then the object is returned

Image Time Series to Data.frame

Description

Turns a 4D time series image to a Data.frame

Usage

img_ts_to_df(imgs, warn = FALSE)

Arguments

Value

Matrix of values

Image Time Series to list

Description

Turns a 4D time series image to a list of 3D images

Usage

img_ts_to_list(imgs, copy_nifti = TRUE, warn = TRUE)

Arguments

Value

List of images

Note

If the object is not of class nifti or have 4 dimensions, then the object is returned

Examples

set.seed(5)
dims = rep(10, 4)
arr = array(rpois(prod(dims), lambda = 2), dim = dims)
nim = oro.nifti::nifti(arr)
simg = img_ts_to_list(nim)
simg_arr = img_ts_to_list(arr)
back = img_list_to_ts(simg_arr)
slist = lapply(simg, function(x) array(x, dim(x)))
testthat::expect_equal(slist, simg_arr)
simg_arr = img_ts_to_matrix(arr)
simg_arr = img_ts_to_df(arr)

Image Time Series to Matrix

Description

Turns a 4D time series image to a Matrix

Usage

img_ts_to_matrix(imgs, warn = FALSE)

Arguments

Value

Matrix of values

Apply Masking from Empty Image Dimensions

Description

Simple wrapper for replacing indices with a value

Usage

maskEmptyImageDimensions(img, inds, reorient = FALSE, mask.value = 0, ...)

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

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

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

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

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

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

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

mask_empty_dim(img, ...)

Arguments

Value

Object of class nifti or array if nifti is not supplied

Note

mask_empty_dim is a shorthand for maskEmptyImageDimensions with all the same arguments.

See Also

getEmptyImageDimensions, dropEmptyImageDimensions

Examples

set.seed(5)
dims = rep(10, 3)
arr = array(rnorm(prod(dims)), dim = dims)
arr[,,10] = 0
nim = oro.nifti::nifti(arr)
inds = getEmptyImageDimensions(nim)
inds_arr = getEmptyImageDimensions(arr)
res = maskEmptyImageDimensions(nim, inds = inds, mask.value = NA)
res2 = maskEmptyImageDimensions(arr, inds = inds_arr, mask.value = NA)
testthat::expect_equal(array(res, dim = dim(res)), 
array(res2, dim = dim(res2)))

set.seed(5)
dims = rep(10, 3)
arr = array(rnorm(prod(dims)), dim = dims)
arr[,,10] = 0
nim = oro.nifti::nifti(arr)
inds = getEmptyImageDimensions(nim)
rnifti = RNifti::asNifti(nim)
timg = tempimg(nim)
limg = list(factor(timg), factor(timg))
mask_empty_dim(nim, inds = inds)
func = function(...) maskEmptyImageDimensions(..., inds = inds)
func(arr)
func(nim)
func(rnifti)
func(timg)
func(limg)

Mask Image

Description

Takes an image, masks it by mask, and returns an object of class nifti

Usage

mask_img(img, mask, allow.NA = TRUE)

Arguments

Value

Object of class nifti with values outside mask set to 0 if mask is 0 and NA if mask is NA and img if mask == 1

Examples

  set.seed(5)
  dims = rep(10, 3)
  arr = array(rnorm(prod(dims)), dim = dims)
  nim = oro.nifti::nifti(arr)
  mask = abs(nim) > 1
  masked = mask_img(nim, mask)
  mask[mask == 0] = NA
  na_masked = mask_img(nim, mask, allow.NA = TRUE)
  
set.seed(5)
dims = rep(10, 3)
arr = array(rnorm(prod(dims)), dim = dims)
arr[,,10] = 0
nim = oro.nifti::nifti(arr)
rnifti = RNifti::asNifti(nim)
mask = nim > 0
timg = tempimg(nim)
limg = list(factor(timg), factor(timg))
func = function(...) mask_img(..., mask = mask)
func(arr)
func(nim)
func(rnifti)
func(timg)
lapply(limg, func)

Extract or Replace Values Inside a Mask

Description

Methods that act on the .Data field in a NIfTI/ANALYZE image but only on values inside a mask.

Usage

mask_vals(object, mask)

mask_vals(object, mask) <- value

## S4 replacement method for signature 'nifti'
mask_vals(object, mask) <- value

## S4 replacement method for signature 'anlz'
mask_vals(object, mask) <- value

## S4 replacement method for signature 'array'
mask_vals(object, mask) <- value

Arguments

Examples

set.seed(2022)
img = nifti(array(rnorm(10^3), dim = rep(10, 3)))
mask = img > 1.5
mask_vals(img, mask)
testthat::expect_equal(sum(mask_vals(img, mask)), 117.628200302518)
mask_vals(img, mask) = rep(4, sum(mask))
mask_vals(img, as(mask, "array")) = rep(4, sum(mask))
mask_vals(as(img, "array"), 
    as(mask, "array")) = rep(4, sum(mask))

Mean of Values in an Image

Description

Computes the mean of values of an image with the option for a mask.

Usage

## S3 method for class 'nifti'
mean(x, ..., mask)

## S3 method for class 'anlz'
mean(x, ..., mask)

Arguments

Value

Output of mean

Examples

img = nifti(array(rnorm(10^3), dim = rep(10, 3)))
mask = img > 0
mean(img, mask = mask)

Normalize Image using Range

Description

Calculates the range of values in an image, then scales the image minimum to 0 and maximum to 1

Usage

minmax_img(img)

## S4 method for signature 'nifti'
minmax_img(img)

## S4 method for signature 'array'
minmax_img(img)

## S4 method for signature 'ANY'
minmax_img(img)

## S4 method for signature 'character'
minmax_img(img)

## S4 method for signature 'factor'
minmax_img(img)

## S4 method for signature 'list'
minmax_img(img)

Arguments

Value

A nifti object (or list of them) or class of object passed in if not specified

Examples

set.seed(5)
dims = rep(10, 4)
arr = array(rpois(prod(dims), lambda = 2), dim = dims)
nim = oro.nifti::nifti(arr)
mimg = minmax_img(nim)
marr = minmax_img(arr)
testthat::expect_equal(array(mimg, dim = dim(mimg)), marr)

set.seed(5)
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), factor(timg))
func = minmax_img
func(arr)
func(nim)
func(rnifti)
func(timg)
func(limg)

Create Multi-Image Plot with Overlays

Description

Creates a multi-row or multi-column plot with image slices and the potential for overlays as well.

Usage

multi_overlay(
  x,
  y = NULL,
  z = NULL,
  w = 1,
  mask = NULL,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  ybreaks = NULL,
  plane = c("axial", "coronal", "sagittal"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  direction = c("horizontal", "vertical"),
  par.opts = list(oma = c(0, 0, 0, 0), mar = rep(0, 4), bg = "black"),
  text = NULL,
  text.x = 0.5,
  text.y = 1.4,
  text.cex = 2.5,
  text.col = "white",
  main = NULL,
  main.col = text.col,
  main.cex = text.cex,
  NA.x = TRUE,
  NA.y = TRUE,
  pdim = NULL,
  useRaster = TRUE,
  ...
)

multi_overlay_center(x, y = NULL, ...)

Arguments

Examples

set.seed(5)
dims = rep(10, 4)
arr = array(rnorm(prod(dims)), dim = dims)
arr[,,,c(3, 5)] = rpois(1000*2, lambda = 2)
nim = oro.nifti::nifti(arr)
mask = nim > 2
add_mask = nim[,,,1] > 0
imgs = img_ts_to_list(nim) 
masks = img_ts_to_list(mask) 
multi_overlay(imgs, masks)
multi_overlay(imgs, masks, 
main = "hey", direction = "vertical", plane = "coronal")
multi_overlay(imgs, masks, mask = add_mask, 
main = "hey")



## Not run: 

 if (requireNamespace("brainR", quietly = TRUE)) {
   visits = 1:3
   y = paste0("Visit_", visits, ".nii.gz")
   y = system.file(y, package = "brainR")
   y = lapply(y, readnii)

   y = lapply(y, function(r){
     pixdim(r) = c(0, rep(1, 3), rep(0, 4))
     dropImageDimension(r)
   })

   x = system.file("MNI152_T1_1mm_brain.nii.gz", 
                 package = "brainR")
   x = readnii(x)
   mask = x >0
   x = lapply(visits, function(tmp){
       x
   })
   alpha = function(col, alpha = 1) {
       cols = t(col2rgb(col, alpha = FALSE)/255)
       rgb(cols, alpha = alpha)
   }
   multi_overlay(x, y, 
         col.y = alpha(hotmetal(), 0.5),
         mask = mask, 
         main = paste0("\n", "Visit ", visits),
         text = LETTERS[visits],
         text.x = 0.9,
         text.y = 0.1,
         text.cex = 3)
 }

## End(Not run)

Resets image parameters for a copied nifti object

Description

Resets the slots of a nifti object, usually because an image was loaded, then copied and filled in with new data instead of making a nifti object from scratch. Just a wrapper for smaller functions

Usage

newnii(img, ...)

Arguments

Value

object of type nifti

Make new nifti from array

Description

Make new nifti object by passing in old nifti and array

Usage

niftiarr(img, arr)

Arguments

Value

object of class nifti

Grab nii file stubname

Description

Quick helper function to strip off .nii or .nii.gz from filename

Usage

nii.stub(x, bn = FALSE)

Arguments

Value

A character vector with the same length as x

Reorient an Image to RPI orientation

Description

Reorient an Image to RPI orientation

Usage

orient_rpi(file, verbose = TRUE)

orient_rpi_file(file, verbose = TRUE)

is_rpi_oriented(file, verbose = FALSE)

Arguments

Value

List of 3 elements

• img: Reoriented image of class nifti

• convention: Convention (Neurological/Radiological) of original image

• orientation: Original image orientations

Note

'orient_rpi' and 'orient_rpi_file' uses 'RNifti' to ensure the reading orientation

Examples

lr_fname = system.file( "nifti", "mniLR.nii.gz", package = "oro.nifti")
img = readnii(lr_fname)

rl_fname = system.file( "nifti", "mniRL.nii.gz", package = "oro.nifti")
rl_img = readnii(rl_fname)
stopifnot(all(rl_img[nrow(rl_img):1,,] == img))

reor = orient_rpi(rl_fname)
stopifnot(all(img == reor$img))

rev = reverse_orient_rpi(reor$img, convention = reor$convention,
orientation = reor$orientation)
stopifnot(all(rev == rl_img))

Orthographic Display, added options

Description

Copy of oro.nifti's orthographic function with some tweaks such as adding L/R designations for left and right

Usage

ortho2(
  x,
  y = NULL,
  xyz = NULL,
  w = 1,
  col = gray(0:64/64),
  col.y = oro.nifti::hotmetal(),
  zlim = NULL,
  zlim.y = NULL,
  NA.x = FALSE,
  NA.y = TRUE,
  crosshairs = TRUE,
  col.crosshairs = "red",
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = c(0, 0, 0, ifelse(ycolorbar, 5, 0)),
  mar = rep(0, 4),
  bg = "black",
  text = NULL,
  text.color = "white",
  text.cex = 2,
  text.x = 32,
  text.y = 32,
  add.orient = FALSE,
  mfrow = c(2, 2),
  ybreaks = NULL,
  breaks = NULL,
  addlegend = FALSE,
  leg.x = 32,
  leg.y = 32,
  legend,
  leg.col,
  leg.title = NULL,
  leg.cex,
  window = NULL,
  ycolorbar = FALSE,
  clabels = TRUE,
  add = TRUE,
  pdim = NULL,
  useRaster = is.null(y),
  mask = NULL,
  ...
)

Arguments

See Also

orthographic

Examples

set.seed(10)
x = oro.nifti::nifti(array(rnorm(1000), dim = rep(10, 3)))
ortho2(x)
y = x > 2
mask = x > 2.5
ortho2(x, y)
ortho2(x, y, mask = mask, add.orient = TRUE)
ortho2(x, y, mask = mask, add.orient = TRUE, add = FALSE)
nim = RNifti::asNifti(x, internal = FALSE)
ortho2(nim, y, mask = mask)
neurobase::ortho2(nim, x, mask = mask, 
ybreaks = seq(min(x), max(x), length.out = 65), ycolorbar = TRUE)

ortho2(nim, y, mask = mask, add = FALSE)
arr_x = as.array(x)
arr_y = as.array(y)
ortho2( arr_x)
ortho2( arr_x, arr_y, useRaster = FALSE)

set.seed(10)
x = oro.nifti::nifti(array(rnorm(10000), dim = rep(10, 4)))
y = x > 2
mask = x > 2.5
ortho2(x, y)

set.seed(10)
x = oro.nifti::nifti(array(rnorm(100), dim = rep(10, 2)))
y = x > 2
mask = x > 2.5
ortho2(x, y)

Plot differences for Prediction and Gold Standard

Description

Uses ortho2 to plot differences between a predicted binary image and the assumed ground truth (roi).

Usage

ortho_diff(
  img,
  pred,
  roi,
  xyz = NULL,
  cols = c("#56B4E9", "#D55E00", "#009E73"),
  levels = c("False Negative", "False Positive", "True Positive"),
  addlegend = TRUE,
  center = TRUE,
  leg.cex = 1.5,
  ...
)

multi_overlay_diff(
  x,
  pred,
  roi,
  z = NULL,
  cols = c("#56B4E9", "#D55E00", "#009E73"),
  ...
)

Arguments

See Also

ortho2

Examples

set.seed(5)
dims = rep(10, 3)
arr = array(rpois(prod(dims), lambda = 2), dim = dims)
nim = oro.nifti::nifti(arr)
roi = nim > 2
pred = nim > 1.5
ortho_diff(nim, pred, roi)
set.seed(5)
dims = rep(10, 3)
arr = array(rnorm(prod(dims)), dim = dims)
nim = oro.nifti::nifti(arr)
mask = nim > 2
pred = nim > 1.5
multi_overlay_diff(nim, roi = mask, pred = pred)



 if (requireNamespace("brainR", quietly = TRUE)) {
   visits = 1:3
   y = paste0("Visit_", visits, ".nii.gz")
   y = system.file(y, package = "brainR")
   y = lapply(y, readnii)

   y = lapply(y, function(r){
     pixdim(r) = c(0, rep(1, 3), rep(0, 4))
     dropImageDimension(r)
   })

   x = system.file("MNI152_T1_1mm_brain.nii.gz", 
                 package = "brainR")
   x = readnii(x)
   mask = x > 0
   alpha = function(col, alpha = 1) {
       cols = t(col2rgb(col, alpha = FALSE)/255)
       rgb(cols, alpha = alpha)
   }
   roi = y[[2]]
   pred = y
   multi_overlay_diff(x, roi = roi, pred = pred)
   multi_overlay_diff(x, roi = roi, pred = pred, 
         mask = mask, 
         main = paste0("\n", "Visit ", visits),
         text = LETTERS[visits],
         text.x = 0.9,
         text.y = 0.1,
         text.cex = 3)
 }

Parse Image Extensions

Description

Get image extensions from a filename

Usage

parse_img_ext(file)

Arguments

Value

Extension of file

Examples

parse_img_ext("blah.nii.gz")
parse_img_ext("blah.mnc")
parse_img_ext("blah.nii")
parse_img_ext("blah")
parse_img_ext("blah.img")
parse_img_ext("blah.hdr")
parse_img_ext("blah.hdr.gz")

Sample Quantiles

Description

Computes sample quantiles for an image, with the option of a mask.

Usage

## S3 method for class 'nifti'
quantile(x, ..., mask)

## S3 method for class 'anlz'
quantile(x, ..., mask)

Arguments

Value

Output of quantile

Examples

img = nifti(array(rnorm(10^3), dim = rep(10, 3)))
mask = img > 0
quantile(img, mask = mask)

Create Quantile Image

Description

Creates output image of the quantiles that each voxel is in, after applying the mask

Usage

quantile_img(img, mask = NULL, ...)

Arguments

Value

Object of class nifti

Examples

set.seed(5)
dims = rep(10, 3)
arr = array(rnorm(prod(dims)), dim = dims)
nim = oro.nifti::nifti(arr)
qimg = quantile_img(nim)
qarr = quantile_img(arr)
testthat::expect_equal(qarr, array(qimg, dim = dim(qarr)))
qimg = quantile_img(nim, mask = nim > 0)

Create Random 'nifti' object

Description

Create Random 'nifti' object

Usage

random_nifti(dim, ...)

Arguments

Value

A 'nifti' object

Examples

random_nifti(c(10, 10, 2))
random_nifti(c(10, 10))

Randomize Image based on Mask

Description

Randomize the values within a mask

Usage

randomize_mask(img, mask)

Arguments

Value

Object of class nifti

Examples

  set.seed(5)
  dims = rep(10, 3)
  arr = array(rnorm(prod(dims)), dim = dims)
  nim = oro.nifti::nifti(arr)
  mask = abs(nim) > 1
  randomize_mask(nim, mask)

readNIfTI with default non-reorientation

Description

This function calls the readNIfTI function from the oro.nifti package, but sets the reorientation to FALSE by default

Usage

readNIfTI2(..., reorient = FALSE)

readnii(
  ...,
  reorient = FALSE,
  dtype = TRUE,
  drop_dim = TRUE,
  reset_slope = FALSE,
  warn = FALSE,
  rm_extensions = TRUE
)

Arguments

Value

nifti object

Read NIfTI file reoriented to RPI

Description

This function calls the readnii function after calling orient_rpi_file to force RPI orientation.

Usage

read_rpi(file, ..., verbose = TRUE)

Arguments

Note

'read_rpi' uses 'RNifti' to ensure the reading orientation

Remake Image from Vector

Description

Wrapper function to take a vector of values and result in a nifti object

Usage

remake_img(vec, img, mask = NULL, warn = FALSE, ...)

Arguments

Value

Object of class nifti

See Also

niftiarr

Examples

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

Build Filename (usually for images)

Description

This is a simple function that helps with the case where you want to construct a filename (usually for an image) with the same base of the filename, the same directory (default), but things added to the front or end of that base filename, with the same extension.

Usage

remap_filename(x, sub_dir = NULL, prefix = "", suffix = "")

Arguments

Value

Character vector

Examples

fname = file.path("/path/to/file", "original.nii.gz")
remap_filename(fname, prefix = "preproc_", "_with_gz")
fname = "original.nii"
remap_filename(fname, prefix = "note_", "_has_directory")
remap_filename(c(fname, "other.nii.gz"), prefix = "note_", "_has_directory")

Replace Subsetting from Empty Image Dimensions

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

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)

Remake Dropped Dimensions

Description

This function is the reverse of dropEmptyImageDimensions. If dropEmptyImageDimensions was run, and the output is a list, usually if keep_ind = TRUE, this function reverses that.

Usage

replace_dropped_dimensions(img, inds, orig.dim)

Arguments

Value

Object of class nifti

Examples

## Not run: 
# nim is an object of class nifti
dd = dropEmptyImageDimensions(nim, keep_ind = TRUE)
remake = replace_dropped_dimensions(img = dd$outimg, 
inds = dd$inds,
orig.dim = dd$orig.dim)
all.equal(nim, remake)

## End(Not run)

Replace Values Outside Surface of image

Description

Determines values outside the surface of an image and gives a mask back with those values set to a replacement.

Usage

replace_outside_surface(
  img,
  value = 0,
  threshold = 0,
  replace_value = NA,
  reorient = FALSE
)

Arguments

Value

Creates an array of binary values. If img is a nifti object, then a nifti is returned

Examples

set.seed(5)
dims = rep(10, 3)
arr = array(0, dim = dims)

arr[ 3:5, 4:6, c(2, 6:8, 5)] = 1
nim = oro.nifti::nifti(arr)
out = replace_outside_surface(nim, replace_value = 0)
out_arr = replace_outside_surface(arr, replace_value = 0)
testthat::expect_equal(out_arr, array(out, dim = dim(out)))

Image Rescaler

Description

Rescales an image to be in certain value range. This was created as sometimes DICOM scale and slope parameters may be inconsistent across sites and the data need to be value restricted

Usage

rescale_img(
  filename,
  pngname = NULL,
  write.nii = FALSE,
  outfile = NULL,
  min.val = -1024,
  max.val = 3071,
  ROIformat = FALSE,
  drop_dim = TRUE,
  writer = "dcm2nii",
  ...
)

Arguments

Value

Object of class nifti

Examples

img = nifti(array(rnorm(10^3, sd = 1000), dim = rep(10, 3)))
outfile = tempfile(fileext = ".nii.gz")
pngname = tempfile(fileext = ".png")
rescale_img(img, write.nii = TRUE, outfile = outfile,
pngname = pngname)

Reverse Reorientation an Image to RPI orientation

Description

Reverse Reorientation an Image to RPI orientation

Usage

reverse_orient_rpi(
  file,
  convention = c("NEUROLOGICAL", "RADIOLOGICAL"),
  orientation,
  verbose = TRUE
)

reverse_orient_rpi_file(
  file,
  convention = c("NEUROLOGICAL", "RADIOLOGICAL"),
  orientation,
  verbose = TRUE
)

Arguments

Value

Object of class nifti

Note

'reverse_orient_rpi' and 'reverse_orient_rpi_file' uses 'RNifti' to ensure the reading orientation

Window image based on quantiles of Image

Description

Takes an image, finds the quantiles given by probs, then sets values outside these values to other values, as determined by replace argument passed to to window_img

Usage

robust_window(img, non_zero = FALSE, probs = c(0, 0.999), ..., mask = NULL)

Arguments

Value

Object of class nifti with values outside quantiles replaced by values depending on replace argument passed to window_img

Check if Objects have Same Dimensions

Description

Wrapper to check if multiple objects all have the same dimensions

Usage

same_dims(...)

Arguments

Value

Logical indicating if all have the same dimensions or not

Examples

mat1 = matrix(1:9, ncol = 3)
mat2 = matrix(rnorm(9), ncol = 3)
mat3 = matrix(rnorm(16), ncol = 4)
mat4 = matrix(rnorm(9), ncol = 3)
same_dims(mat1, mat2)
same_dims(mat1, mat3)
same_dims(mat1, mat2, mat4)

Separate Labeled Image into Multiple Binary Images

Description

Takes in an image, gets the unique values, then creates a list of binary images for each one of those values.

Usage

separate_img(img, levels = NULL, drop_zero = TRUE)

## S4 method for signature 'nifti'
separate_img(img, levels = NULL, drop_zero = TRUE)

## S4 method for signature 'array'
separate_img(img, levels = NULL, drop_zero = TRUE)

## S4 method for signature 'ANY'
separate_img(img, levels = NULL, drop_zero = TRUE)

## S4 method for signature 'factor'
separate_img(img, levels = NULL, drop_zero = TRUE)

## S4 method for signature 'character'
separate_img(img, levels = NULL, drop_zero = TRUE)

## S4 method for signature 'list'
separate_img(img, levels = NULL, drop_zero = TRUE)

Arguments

Value

A nifti object (or list of them) or class of object passed in if not specified

Note

Exact equalling is using ==

Examples

set.seed(5)
dims = rep(10, 3)
arr = array(rpois(prod(dims), lambda = 2), dim = dims)
nim = oro.nifti::nifti(arr)
simg = separate_img(nim)
simg_arr = separate_img(arr)
slist = lapply(simg, function(x) array(x, dim(x)))
testthat::expect_equal(slist, simg_arr)

rnifti = RNifti::asNifti(nim)
timg = tempimg(nim)
limg = list(factor(timg), factor(timg))
func = separate_img
func(arr)
func(nim)
func(rnifti)
func(timg)
func(limg)

Slice a Image Color Data.frame

Description

Slices a image color data.frame along the 3 planes (axial, coronal, sagittal) and returns it in a ggplot-ready format for faceting.

Usage

slice_colour_df(img_df, xyz = NULL)

Arguments

Value

A data.frame with x and y coordinates, colour, and intensity values, along with the associated planes that were sliced.

Examples

img = nifti(array(rnorm(10^3), dim = rep(10, 3)))
df = img_colour_df(img)
sliced = slice_colour_df(df, c(5, 5, 4))

Subset DTI data based on b-values #'

Description

Subset DTI data based on b-values #'

Usage

subset_dti(
  img,
  bvals,
  bvecs,
  b_step = 1,
  maximum = Inf,
  shells = NULL,
  verbose = TRUE,
  ...
)

## S4 method for signature 'nifti'
subset_dti(
  img,
  bvals,
  bvecs,
  b_step = 1,
  maximum = Inf,
  shells = NULL,
  verbose = TRUE,
  ...
)

## S4 method for signature 'ANY'
subset_dti(
  img,
  bvals,
  bvecs,
  b_step = 1,
  maximum = Inf,
  shells = NULL,
  verbose = TRUE,
  ...
)

## S4 method for signature 'character'
subset_dti(
  img,
  bvals,
  bvecs,
  b_step = 1,
  maximum = Inf,
  shells = NULL,
  verbose = TRUE,
  ...
)

## S4 method for signature 'list'
subset_dti(
  img,
  bvals,
  bvecs,
  b_step = 1,
  maximum = Inf,
  shells = NULL,
  verbose = TRUE,
  ...
)

Arguments

Value

List of filenames of image, b-values, and b-vectors that were subsetted.

Author(s)

John Muschelli muschellij2@gmail.com

Examples

## Not run: 
img = "~/Downloads/data.nii.gz"
bvals = "~/Downloads/bvals"
bvecs = "~/Downloads/bvals"
verbose = TRUE
b_step = 50
maximum = 1500
shells = NULL
sub = subset_dti(img = img, bvals = bvals, bvecs = bvecs, 
maximum = 1500,
b_step = 50)


## End(Not run)

Create temporary nii.gz file

Description

Takes in a object of class nifti, writes it to a temp file, appends .nii.gz as writenii adds it.

Usage

tempimg(
  nim,
  gzipped = TRUE,
  checknan = TRUE,
  check_type = FALSE,
  warn = FALSE,
  drop_dim = TRUE,
  dtype = TRUE,
  ...
)

Arguments

Value

filename of output nii.gz

nifti image windower

Description

Windows an image to min and max values and also changes cal_max and cal_min parameters

Usage

window_img(
  x,
  window = c(0, 100),
  replace = c("window", "missing", "zero"),
  ...
)

Arguments

Value

Object of class nifti

See Also

readnii

Examples

  set.seed(5)
  dims = rep(10, 3)
  arr = array(rnorm(prod(dims)), dim = dims)
  nim = oro.nifti::nifti(arr)
  window_img(nim, window = c(1, 5))
  window_img(nim, window = c(1, 5), replace = "missing")
  tfile = tempimg(nim)
  window_img(tfile)
  window_img(as.factor(tfile))
  arr = window_img(img_data(nim))
  rnim = RNifti::readNifti(tfile)
  window_img(rnim, window = c(1, 5))
  range(window_img(rnim, window = c(1, 5)))
  window_img(rnim, window = c(1, 5), replace = "missing")
  range(window_img(rnim, window = c(1, 5), replace = "missing"))
   

writeNIfTI with default non-reorientation

Description

This function calls the writeNIfTI function from the oro.nifti package, but makes sure to remove .nii extension and warnings can be suppressed.

Usage

writeNIfTI2(nim, filename, dtype = FALSE, compression = 9, ...)

writenii(
  nim,
  filename,
  dtype = TRUE,
  drop_dim = TRUE,
  warn = FALSE,
  compression = 9,
  rm_extensions = TRUE,
  ...
)

Arguments

Value

Nothing

Note

While writeNIfTI2 does not run datatyper as default, writenii does. Additional functionality will be added to writenii likely but will not to writeNIfTI2

Examples

set.seed(5)
dims = rep(10, 3)
arr = array(rnorm(prod(dims)), dim = dims)
nim = oro.nifti::nifti(arr)
rnifti = RNifti::asNifti(nim)
tfile = tempfile(fileext = ".nii.gz")
timg = writenii(nim, tfile, rm_extensions = TRUE, warn = TRUE)
timg = writeNIfTI2(nim, tfile, dtype = TRUE)

General NIfTI Writer

Description

Writes out NIfTI files for multiple formats. Currently, for nifti objects and niftiImage objects from RNifti

Usage

write_nifti(nim, filename, ...)

Arguments

Value

Output from NIfTI writer

Examples

set.seed(5)
dims = rep(10, 4)
arr = array(rpois(prod(dims), lambda = 2), dim = dims)
nim = oro.nifti::nifti(arr)
tfile = tempfile(fileext = ".nii.gz")
write_nifti(nim, tfile)
rimg = RNifti::readNifti(tfile)
write_nifti(rimg, tfile)

Image Center of Gravity Wrapper

Description

Find Center of Gravity of Image, after thresholding and take ceiling (wrapper for cog)

Usage

xyz(...)

Arguments

Value

Vector of length 3

Note

Just a convenience wrapper for cog(ceil=TRUE)

Zero pads an image

Description

This function zero pads an image by a certain number of dimensions, usually for convolution

Usage

zero_pad(img, kdim, invert = FALSE, pad_value = 0L, ...)

Arguments

Value

Object of class nifti

Examples

kdim = c(3,3,5)
img = array(rnorm(30*30*36), dim = c(30, 30, 36))
pad = zero_pad(img, kdim)
back = zero_pad(pad, kdim, invert=TRUE)
all.equal(back, img)

Find Image z-limits

Description

Helper function for plotting - returns zlim for image plot function

Usage

zlimmer(x, zlim = NULL, computed_range = NULL)

Arguments

Value

If zlim = NULL, then vector of length 2, otherwise returns zlim

Get Z-score over a margin of an img

Description

Standardizes an image either by the axial, sagittal, or coronal slice or whole image

Usage

zscore_img(
  img,
  mask = NULL,
  margin = NULL,
  centrality = c("mean", "median", "trimmed_mean"),
  variability = c("sd", "iqrdiff", "mad", "maddiff", "iqr", "trimmed_sd"),
  trim = 0.2,
  remove.na = TRUE,
  remove.nan = TRUE,
  remove.inf = TRUE,
  remove.val = 0,
  remask = TRUE
)

Arguments

Value

Array of object of class nifti

See Also

aperm

Examples

dim = c(100, 30, 5)
img = array(rnorm(prod(dim), mean=4, sd=4), 
dim=dim)

truth2 = img
for (i in 1:dim(img)[2]) {
truth2[,i,] = (truth2[,i,]- mean(truth2[,i,]))/sd(truth2[,i,])
}

truth1 = img
for (i in 1:dim(img)[1]) {
truth1[i,,] = (truth1[i,,]- mean(truth1[i,,]))/sd(truth1[i,,])
}

truth3 = img
for (i in 1:dim(img)[3]) {
truth3[,,i] = (truth3[,,i]- mean(truth3[,,i]))/sd(truth3[,,i])
}
try3 = zscore_img(img, margin=3)
stopifnot(all.equal(try3, truth3))
try2 = zscore_img(img, margin=2)
stopifnot(all.equal(try2, truth2))
try1 = zscore_img(img, margin=1)
stopifnot(all.equal(try1, truth1))
  
z = zscore_img(img, margin=NULL)
ztrim = zscore_img(img, margin=NULL, 
centrality = "trimmed_mean", variability = "trimmed_sd")

z = zscore_img(img, centrality = "median", variability = "iqr")
z = zscore_img(img, centrality = "median", variability = "iqrdiff")
z = zscore_img(img, centrality = "median", variability = "maddiff")