Skip to contents

read_vec

Source: R/neurovec.R
read_vec.Rd

Loads a neuroimaging volume from one or more files, with support for various input formats and memory management strategies.

Usage

read_vec(
  file_name,
  indices = NULL,
  mask = NULL,
  mode = c("normal", "mmap", "bigvec", "filebacked")
)

Arguments

file_name

A character vector of one or more file paths to load. A 3D file is promoted to a 4D NeuroVec with a single time point (see Details). When multiple paths are supplied the result is always a NeuroVecSeq (which itself extends NeuroVec), regardless of whether the individual files are 3D, 4D, or a mix of both.

indices

The indices of the sub-volumes to load (e.g. if the file is 4-dimensional). Only supported in "normal" mode.

mask

A logical mask defining which spatial elements to load. Required for "bigvec" mode and optional for other modes.

mode

The IO mode which is one of: * "normal": Standard in-memory loading * "mmap": Memory-mapped access (more memory efficient) * "bigvec": Optimized for large datasets with masking * "filebacked": File-backed storage with on-demand loading

Value

The return type depends on how many files are supplied:

  • Single 3D file — a NeuroVec with dim(x)[4] == 1 (concrete class depends on mode: e.g. DenseNeuroVec for "normal", MappedNeuroVec for "mmap", BigNeuroVec for "bigvec", FileBackedNeuroVec for "filebacked").

  • Single 4D file — a NeuroVec of the same concrete class as above, with dim(x)[4] equal to the 4th dimension of the file (or length(indices) when indices is supplied).

  • Multiple files (any mix of 3D and 4D) — a NeuroVecSeq wrapping one NeuroVec per input file in the order given. Because NeuroVecSeq extends NeuroVec, it can be used wherever a NeuroVec is accepted, but its underlying storage is segmented rather than a single contiguous 4D array. For example, read_vec(c(vol, vec, vec, vol)) returns a 4-element NeuroVecSeq whose segments have time lengths c(1, T2, T3, 1).

Details

This function supports multiple file formats: * .nii: Standard NIfTI format * .nii.gz: Compressed NIfTI (not supported in mmap mode)

Memory management modes: * "normal": Loads entire dataset into memory. Best for smaller datasets or when memory is not a constraint. * "mmap": Memory-maps the file, providing efficient access for large files without loading entirely into memory. Not available for compressed files. * "bigvec": Optimized for large datasets where only a subset of voxels are of interest. Requires a mask to specify which voxels to load. * "filebacked": Similar to mmap but with more flexible caching strategies.

3D inputs: A path pointing at a 3D image is not rejected. It is promoted to a 4D NeuroVec whose fourth dimension has length 1, so the return type is always a NeuroVec, never a NeuroVol. If you want a true volume, use read_vol (or vec[[1]]).

Multiple files: When file_name has length > 1, each file is loaded independently and the results are wrapped with NeuroVecSeq. No data is copied or re-concatenated into a single dense 4D array; the returned NeuroVecSeq holds the constituent NeuroVecs in its @vecs slot and exposes them as a single logical time series. Time-point lookups (e.g. x[[i]], sub_vector(x, i), linear_access(x, i)) transparently walk across the segments. The per-file time lengths may differ (e.g. a 3D file contributes 1 time point, a 4D file contributes dim(file)[4]); all spatial dimensions must match.

Note

* Memory-mapping (.mmap mode) is not supported for gzipped files * The bigvec mode requires a mask to be specified * When loading multiple files, they must have compatible dimensions

Examples


# Load a single NIfTI file
img <- read_vec(system.file("extdata", "global_mask_v4.nii", package="neuroim2"))


# Memory-mapped loading for large files
big_img <- read_vec(system.file("extdata", "global_mask_v4.nii", package="neuroim2"), mode="mmap")
#> loading /home/runner/work/_temp/Library/neuroim2/extdata/global_mask_v4.nii as mmaped file 

# Load masked data for memory efficiency
mask <- as.logical(big_img[[1]])
masked_data <- read_vec(system.file("extdata", "global_mask_v4.nii", package="neuroim2"),
               mask=mask, mode="bigvec")
#> loading /home/runner/work/_temp/Library/neuroim2/extdata/global_mask_v4.nii as bigvec