save_slices: Save the Same Slice Across Images

In avalcarcel9/aliviateR: A package to automate my R workflow

Description

Save the same slice across a set of images provided. Saves images in png or PDF formats. Others can be added upon request through a GitHub issue. Wraps [oro.nifti::image()].

Usage

save_slices(
  imgs,
  outfiles,
  format = c("png", "pdf"),
  width = NULL,
  height = NULL,
  units = NULL,
  ...
)

Arguments

imgs	A 'character' 'vector' of file paths to the image(s) or local 'list' of 'nifti' class objects.
outfiles	A 'character' 'vector' of file paths corresponding to the name of the output file(s).
format	The format in which to save the image slice. Only 'png' and 'pdf' are supported currently. Users can include the image format in the file path (i.e. test.png) or exclude. If excluded 'outfiles' pasted with the 'format' input.
width	The width of the device. The default is 480 px for 'format = 'png'‘ and 7 inches for 'format = ’pdf''.
height	The height of the device. The default is 480 px for 'format = 'png'‘ and 7 inches for 'format = ’pdf''.
units	The units in which height and width are given. Can be 'px' (pixels, the default), 'in' (inches), 'cm' or 'mm'. This is only allowed with ‘format = ’png''. Specifying a unit will be ignored with 'format = 'pdf'' will be ignored and instead inches are used. The default is set to 'px'.
...	Arguments passed to the [oro.nifti::image()] function may be provided here. Common useful arguments include 'z' is the slice to be displayed (ignored when plot.type = "multiple"), 'col' is grayscale (by default), 'plane' is the plane of acquisition to be displayed (choices are 'axial', 'coronal', 'sagittal').

Value

A list of simple output from [grDevices::png()] or [grDevices::pdf()]. Image slice(s) are saved to 'outfiles'.

Examples

## Not run: 
# `rtapas` has example probability map data available for use
# Load and create a list of 2 example NIFTI objects from `rtapas`
images = list(rtapas::pmap1, rtapas::pmap2)
save_slices(imgs = images,
            outfiles = c('/Users/alval/Desktop/test_pmap1',
            '/Users/alval/Desktop/test_pmap2.png'),
#  Change to a file path where you would like to save the example images.
# Note we can include or exclude the file extension.
            format = 'png',
            width = 480,
            height = 480,
            units = 'px',
            z = 2,
            col = oro.nifti::hotmetal(70),
            plane = 'axial',
            plot.type = 'single')

## End(Not run)

avalcarcel9/aliviateR documentation built on July 10, 2020, 12:32 p.m.