H5NeuroVec Class

A class representing a four-dimensional brain image backed by an HDF5 file. H5NeuroVec objects provide efficient storage and access for large-scale 4D neuroimaging data using the HDF5 file format.

Details

H5NeuroVec inherits a space slot from NeuroVec-class, defining the 4D dimensions (e.g., x, y, z, time). Data are stored in an HDF5 dataset and accessed on demand.

Slots

obj

An instance of class H5File from the hdf5r package, representing the underlying HDF5 file containing the 4D brain image data.

Inheritance

H5NeuroVec inherits from:

• NeuroVec-class: Base class for 4D brain images

• ArrayLike4D-class: Interface for 4D array-like operations

See also

NeuroVec-class for the base 4D brain image class. H5NeuroVol-class for the 3D counterpart. H5File for details on HDF5 file objects.

Examples

if (FALSE) { # \dontrun{
if (requireNamespace("neuroim2", quietly = TRUE) &&
  requireNamespace("hdf5r", quietly = TRUE) &&
  exists("H5NeuroVec", where = "package:fmristore") &&
  !is.null(fmristore:::create_minimal_h5_for_H5NeuroVec)) {
  # Setup: Create a temporary HDF5 file using a helper
  temp_h5_path <- NULL
  h5_vec <- NULL
  tryCatch({
    temp_h5_path <- fmristore:::create_minimal_h5_for_H5NeuroVec(dims = c(5L, 5L, 3L, 4L))

    # Create an H5NeuroVec object using the constructor
    # Constructor defaults: dataset_name = "data/elements", space from HDF5 /space group
    h5_vec <- fmristore::H5NeuroVec(file_name = temp_h5_path)

    print(h5_vec)

    # Access a subset of the data
    subset_data <- h5_vec[1:2, 1:2, 1, 1:2]
    print(subset_data)

  }, error = function(e) {
    message("H5NeuroVec example failed: ", e$message)
  }, finally = {
    # Close HDF5 handle owned by H5NeuroVec object
    if (!is.null(h5_vec) && inherits(h5_vec, "H5NeuroVec")) {
      try(close(h5_vec), silent = TRUE)
    }
    # Cleanup temporary file
    if (!is.null(temp_h5_path) && file.exists(temp_h5_path)) {
      unlink(temp_h5_path)
    }
  })
} else {
  message("Skipping H5NeuroVec example: fmristore, neuroim2, hdf5r, or helper not available.")
}
} # }