Concatenate Voxel Time Series Across Runs (Generic)

Concatenate Voxel Time Series Across Runs (Generic)

Usage

series_concat(experiment, mask_idx, run_indices = NULL, ...)

# S4 method for class 'H5ClusterExperiment,numeric'
series_concat(experiment, mask_idx, run_indices = NULL)

Arguments

experiment

The experiment object (typically H5ClusterExperiment-class).

mask_idx

Indices of voxels within the mask of the experiment.

run_indices

Optional: A numeric or character vector specifying which runs to include.

...

Additional arguments for methods.

Value

A concatenated matrix (typically time x voxels).

Methods (by class)

• series_concat(experiment = H5ClusterExperiment, mask_idx = numeric): Concatenate voxel time series for H5ClusterExperiment

See also

Other H5Cluster: $,H5ClusterExperiment-method, H5ClusterExperiment, H5ClusterExperiment-class, H5ClusterRun-class, H5ClusterRunSummary-class, H5ClusteredArray-class, [,H5ClusterRun,ANY,ANY,ANY-method, [,H5ClusterRun,ANY,missing,ANY-method, as.data.frame(), as.matrix(), close(), cluster_metadata,H5ClusterExperiment-method, clusters(), dim(), h5file,H5ClusteredArray-method, linear_access-methods, make_run_full(), make_run_summary(), mask(), matrix_concat(), n_scans,H5ClusterExperiment-method, scan_metadata,H5ClusterExperiment-method, scan_names,H5ClusterExperiment-method, series(), show,H5ClusterRun-method

Examples

if (FALSE) { # \dontrun{
if (!is.null(fmristore:::create_minimal_h5_for_H5ClusterExperiment)) {
  temp_exp_file <- NULL
  exp_obj <- NULL
  tryCatch({
    temp_exp_file <- fmristore:::create_minimal_h5_for_H5ClusterExperiment(
      master_mask_dims = c(4L,4L,2L), # Smaller mask for example
      n_time_run1 = 5L # Shorter time series for Run1_Full
    )
    exp_obj <- fmristore::H5ClusterExperiment(file_path = temp_exp_file)

    # Get some valid voxel indices from the mask
    # The master mask is created by the helper.
    # exp_mask <- mask(exp_obj)
    # valid_mask_indices <- which(exp_mask@.Data)
    # For simplicity, let's assume first few indices if mask is not empty.
    # If mask has at least 2 voxels:
    # selected_vox_indices <- valid_mask_indices[1:min(2, length(valid_mask_indices))]
    # A more robust way for an example without directly loading mask here:
    # The H5ClusterExperiment has a mask, and its linear indices are 1:sum(mask_data)
    # For a 4x4x2 mask, if 50% are true, there are 16 true voxels. Indices are 1 to 16.
    # Let's pick first 2 voxels in the mask's internal indexing (1-based).

    # Note: series_concat typically works on runs with full data (H5ClusterRun)
    # The helper creates "Run1_Full".
    # concatenated_series <- series_concat(exp_obj, mask_idx = c(1, 2), 
    #                                       run_indices = "Run1_Full")
    # print(dim(concatenated_series)) # Should be n_time_run1 x 2
    # print(head(concatenated_series))

    # For a fully runnable example, need to ensure mask_idx is valid for the created object.
    # Since the helper creates a mask, we can try to use mask_idx = 1 (first voxel in mask).
    # The `series_concat` method for H5ClusterExperiment handles this.
    if (n_voxels(exp_obj) > 0) { # n_voxels from H5ClusteredArray slot
       conc_series <- series_concat(exp_obj, mask_idx = 1, run_indices = "Run1_Full")
       print(paste("Dimensions of concatenated series for voxel 1 from Run1_Full:",
                   paste(dim(conc_series), collapse="x")))
    } else {
       message("Skipping series_concat demonstration as experiment mask is empty.")
    }

  }, error = function(e) {
    message("series_concat example failed: ", e$message)
  }, finally = {
    if (!is.null(exp_obj)) try(close(exp_obj), silent = TRUE)
    if (!is.null(temp_exp_file) && file.exists(temp_exp_file)) {
      unlink(temp_exp_file)
    }
  })
} else {
  message("Skipping series_concat example: helper not available.")
}
} # }