writeNiftiArray: Write NiftiArray Object

In muschellij2/niftiArray: HDF5 Delayed Array for Nifti Objects

Description

A function for writing NIfTI objects on disk to a specifically formatted HDF5 file. The HDF5 file will include a group for the NIfTI image or array and the NIfTI header.

Usage

writeNiftiArray(
  x,
  filepath = tempfile(fileext = ".h5"),
  name = "image",
  header_name = "hdr",
  chunkdim = NULL,
  level = NULL,
  verbose = FALSE,
  header = NULL,
  overwrite = FALSE,
  extendible = FALSE
)

Arguments

x	A niftiImage object loaded into R or a file path to a NIfTI file.
filepath	The file path (single character string) of where to save the HDF5 file converted from the NIfTI input as x. By default creates a temporary file on disk.
name	The name of the group for the NIfTI image in the HDF5 file. Default is set to "image". Unless you have to other "image" groups in the HDF5 file there is no need to change default settings.
header_name	The name of the group for the NIfTI header in the HDF5 file. Default is set to "header". Unless you have to other "header" groups in the HDF5 file there is no need to change default settings.
chunkdim	The dimensions of the chunks to use for writing the data to disk. Passed to HDF5Array::writeHDF5Array.
level	The compression level, passed to HDF5Array::writeHDF5Array.
verbose	Display progress, passed to HDF5Array::writeHDF5Array.
header	List of header information; overrides call of nifti_header.
overwrite	FALSE by default. In the event that an HDF5 file already exists for filepath input then do not overwrite it. If set to TRUE then the name and header_name group objects in the HDF5 file location will overwrite.
extendible	Should a single empty dimension be added to the array? Currently necessary for easy reshaping.

Value

A NiftiArray object.

Examples

nii_fname = system.file("extdata", "example.nii.gz", package = "RNifti")
res = writeNiftiArray(nii_fname)
filepath = tempfile(fileext = ".h5")
res = writeNiftiArray(nii_fname, filepath = filepath)
testthat::expect_error(
   writeNiftiArray(nii_fname, filepath = filepath),
   regexp = "already exist",
)
res = writeNiftiArray(nii_fname, filepath = filepath, overwrite = TRUE)
img = RNifti::readNifti(nii_fname)
writeNiftiArray(c(img), header = nifti_header(img))

muschellij2/niftiArray documentation built on June 12, 2020, 3:06 a.m.