Version: 0.1.1
Date: 2022-11-04
Title: A Pipe-Friendly Image Calculator
Maintainer: Jon Clayden <code@clayden.org>
Imports: Rcpp, RNifti, magrittr
LinkingTo: Rcpp, RNifti
Suggests: mmand, tinytest, covr
Description: Provides a set of fast, chainable image-processing operations which are applicable to images of two, three or four dimensions, particularly medical images.
License: BSD_3_clause + file LICENCE
URL: https://github.com/jonclayden/imbibe
BugReports: https://github.com/jonclayden/imbibe/issues
Encoding: UTF-8
RoxygenNote: 7.2.1
NeedsCompilation: yes
Packaged: 2022-11-06 12:26:15 UTC; jon
Author: Jon Clayden ORCID iD [aut, cre], Chris Rorden ORCID iD [aut], John Muschelli ORCID iD [ctb], Exstrom Laboratories LLC [cph]
Repository: CRAN
Date/Publication: 2022-11-09 21:50:16 UTC

Basic binary operations

Description

Basic binary operations

Usage

add(image, arg)

subtract(image, arg)

multiply(image, arg)

divide(image, arg)

remainder(image, arg)

mask(image, arg)

maximum(image, arg)

minimum(image, arg)

Arguments

image

An image object or pipeline.

arg

Numeric or image argument.

Value

An updated pipeline.

Mathematical morphology and filtering operations

Description

Mathematical morphology and filtering operations

Usage

dilate(image, kernel = NULL, ..., max = FALSE, nonzero = TRUE)

dilateall(image, kernel = NULL, ...)

erode(image, kernel = NULL, ..., min = FALSE)

filter_median(image, kernel = NULL, ...)

filter_mean(image, kernel = NULL, ..., norm = TRUE)

smooth_gauss(image, sigma)

subsample(image, offset = FALSE)

Arguments

image

An image object or pipeline.

kernel

A suitable kernel function (see kernels). If NULL, the most recently set kernel in the pipeline is used, if any, otherwise the default kernel (kernel_3d).

...

Additional arguments to the kernel function, if any.

max

Logical value: if TRUE, maximum filtering is used for dilation; otherwise mean filtering is used. Mean filtering is always used by dilateall.

nonzero

Logical value: if TRUE, the default, dilation is only applied to nonzero pixels/voxels. Otherwise it is applied everywhere (and maximum filtering is always used).

min

Logical value: if TRUE, minimum filtering is used for erosion; otherwise nonzero voxels overlapping with the kernel are simply zeroed.

norm

Logical value indicating whether the mean filter will be normalised or not.

sigma

Numeric value giving the standard deviation of the Gaussian smoothing kernel.

offset

Logical value indicating whether subsampled pixels should be offset from the original locations or not.

Value

An updated pipeline.

Dimensionality reduction operations

Description

Dimensionality reduction operations

Usage

dim_mean(image, dim = 4L)

dim_sd(image, dim = 4L)

dim_max(image, dim = 4L)

dim_whichmax(image, dim = 4L)

dim_min(image, dim = 4L)

dim_median(image, dim = 4L)

dim_quantile(image, dim = 4L, prob)

dim_AR1(image, dim = 4L)

Arguments

image

An image object or pipeline.

dim

Integer value between 1 and 4, giving the dimension to apply the reduction along.

prob

For drt_quantile, the quantile probability to extract (analogously to quantile).

Value

An updated pipeline.

Expectation for testing pipeline output

Description

This function provides an expectation for use with the "tinytest" package, which runs the pipeline specified in its first argument and compares the result to its second.

Usage

expect_pipeline_result(current, target, precision = "double", ...)

Arguments

current

The pipeline to run, which should have class "imbibe".

target

The target value to compare against, a numeric array of some kind, which will be converted to a "niftiImage" object.

precision

A string specifying the working precision. Passed to run.

...

Further arguments to expect_equal.

Value

A "tinytest" object.

Basic unary operations

Description

Basic unary operations

Usage

exponent(image)

logarithm(image)

sine(image)

cosine(image)

tangent(image)

arcsine(image)

arccosine(image)

arctangent(image)

square(image)

squareroot(image)

reciprocal(image)

absolute(image)

binarise(image, invert = FALSE)

binarize(image, invert = FALSE)

Arguments

image

An image object or pipeline.

invert

Logical value: if TRUE, binarising will also perform logical inversion so that only zeroes in the original image will be nonzero; if FALSE, the default, the usual sense is used, in which zeroes remain as they are, and everything else is converted to 1.

Value

An updated pipeline.

Create an operation pipeline

Description

Create an operation pipeline

Usage

imbibe(image)

## S3 method for class 'imbibe'
asNifti(x, ...)

## S3 method for class 'imbibe'
as.array(x, ...)

## S3 method for class 'imbibe'
print(x, ...)

Arguments

image

An image object or existing pipeline.

x

An "imbibe" object.

...

Additional arguments to methods.

Mathematical morphology kernels

Description

Mathematical morphology kernels

Usage

kernel_3d(image)

kernel_2d(image)

kernel_box(image, width, voxels = FALSE)

kernel_gauss(image, sigma)

kernel_sphere(image, radius)

kernel_file(image, file)

Arguments

image

An image object or pipeline.

width

The width of the kernel in appropriate units. If voxels is FALSE a value can be specified for each of the three dimensions; otherwise only a single value should be given and the kernel will be isotropic.

voxels

Logical value: if TRUE, the width is given in pixels/voxels and must be an odd integer; otherwise, the units are millimetres and can take any value.

sigma

Numeric value giving the standard deviation of a Gaussian kernel, in millimetres.

radius

Numeric value giving the radius of a sphere kernel, in millimetres.

file

Name of a NIfTI file containing the kernel.

Value

An updated pipeline.

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

magrittr

%>%

Run a pipeline and return an image result

Description

Run a pipeline and return an image result

Usage

run(pipe, precision = getOption("imbibe.precision", "double"))

Arguments

pipe

An operation pipeline.

precision

The internal precision used for calculations. May be "double", "float" or "single"; the latter two are equivalent.

Value

An image

Examples

im <- RNifti::readNifti(system.file("extdata", "example.nii.gz", package="RNifti"))
pipe <- im %>% threshold_below(500) %>% binarise()
run(pipe)

Image thresholding

Description

Image thresholding

Usage

threshold(
  image,
  value,
  reference = c("none", "image", "nonzero"),
  above = FALSE
)

threshold_below(image, value, reference = c("none", "image", "nonzero"))

threshold_above(image, value, reference = c("none", "image", "nonzero"))

Arguments

image

An image object or pipeline.

value

Numeric threshold value.

reference

String indicating what the value should be referenced against, if anything. If "none", the default, the value is taken literally. If "image", it is interpreted as a proportion of the "robust range" of the current image's intensities. If "nonzero" it is interpreted as a proportion of the "robust range" of the nonzero pixel intensities.

above

Logical value: if TRUE the operation zeroes values above the threshold; otherwise it zeroes values below it. The threshold_below and threshold_above function variants set argument implicitly.

Value

An updated pipeline.