LabeledVolumeSet Class

A class representing a multi-volume dataset stored in HDF5, where each volume is labeled (similar to a named 4th dimension). We store:

a 3D mask
a set of label strings
for each label, data only at the mask's nonzero entries

This extends NeuroVec, so it is logically a 4D object with dimension [X, Y, Z, #labels].

Slots

obj: An H5File reference (the file handle).
mask: A LogicalNeuroVol of shape [X, Y, Z].
labels: A character vector for the volume labels.
load_env: An environment storing references for lazy loading.

Examples

if (FALSE) { # \dontrun{
if (requireNamespace("neuroim2", quietly = TRUE) &&
    requireNamespace("hdf5r", quietly = TRUE) &&
    exists("read_labeled_vec", where = "package:fmristore") &&
    !is.null(fmristore:::create_minimal_h5_for_LabeledVolumeSet)) {

  # Setup: Create a temporary HDF5 file suitable for read_labeled_vec
  temp_h5_path <- NULL
  lvs <- NULL
  tryCatch({
    temp_h5_path <- fmristore:::create_minimal_h5_for_LabeledVolumeSet(
      vol_dims = c(5L, 4L, 3L),
      labels = c("CondA", "CondB"),
      num_vols_per_label = 2L
    )

    # Create a LabeledVolumeSet object using the constructor
    lvs <- fmristore::read_labeled_vec(file_name = temp_h5_path)

    print(lvs)
    print(labels(lvs)) # Access labels

    # Access data for a specific label (returns a NeuroVol or similar)
    # data_cond_a <- lvs[["CondA"]]
    # print(dim(data_cond_a)) # Should be 3D x num_vols_per_label

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

Slots

See also

Examples