NiftiArray: Realize NIfTI images as DelayedArray objects, using HDF5Array

In neuroconductor/NiftiArray: HDF5 Delayed Array for Nifti Objects

Description

NiftiArray, a HDF5Array::HDF5Array with a header.

Usage

NiftiArray(
  filepath,
  name = "image",
  header_name = "hdr",
  type = NA,
  header = NULL,
  extendible = FALSE
)

Arguments

filepath	The path (as a single character string) to the NIfTI or HDF5 file where the dataset is located. If a path to the NIfTI is provided we call RNifti::readNifti() and NiftiArray::writeNiftiArray() to convert to the HDF5 and more memory and time are used. If a path to a HDF5 file the data is simply loaded into R as an object of class NiftiArray. A path to the HDF5 file is more memory and time efficient.
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.
type	NA or the R atomic type, passed to HDF5Array::HDF5Array() corresponding to the type of the HDF5 dataset. Default is set to NA. Unless you want different types of HDF5 storage files there is no need to change default settings.
header	List of NIfTI header information to override call of nifti_header.
extendible	Should a single empty dimension be added to the array? Currently necessary for easy reshaping.

Value

A NiftiArray object

Note

All the operations available for HDF5Array::HDF5Array objects work on NiftiArray objects.

Examples

nii_fname = system.file("extdata",
"example.nii.gz", package = "RNifti")
res = NiftiArray(nii_fname)
res2 = NiftiArray(slot(slot(res, "seed"), "filepath"))
res2 = NiftiArray(slot(res, "seed"))

neuroconductor/NiftiArray documentation built on May 23, 2021, 8:40 a.m.