HDF5 I/O & Management

1 Overview

Creation, import, layout and management of HDF5 datasets and groups (I/O, metadata, subsetting, binding, moving, reducing).

2 Functions

2.1 bdImportData_hdf5

bdImportData_hdf5

2.2 bdBind_hdf5_datasets

bdBind_hdf5_datasets

2.3 bdCreate_hdf5_emptyDataset

Creates an HDF5 dataset of size inside with name , without writing data (allocation only). Honors file/dataset overwrite flags and supports unlimited datasets.

2.4 bdCreate_hdf5_group

Create a (nested) group inside an HDF5 file. The operation is idempotent: if the group already exists, no error is raised.

2.5 bdCreate_hdf5_matrix

bdCreate_hdf5_matrix

2.6 bdIsLocked_hdf5

Uses HDF5 file locking to check if can be opened in read/write mode. If opening fails under locking, the file is treated as “in use” and is returned. Non-existent files return .

2.7 bdgetDim_hdf5

Retrieves the dimensions (number of rows and columns) of a dataset stored in an HDF5 file.

2.8 bdgetDatasetsList_hdf5

Retrieves a list of all datasets within a specified HDF5 group, with optional filtering by prefix or suffix.

2.9 bdCheckMatrix_hdf5

Checks whether a matrix stored in HDF5 format is suitable for eigenvalue decomposition using Spectra. The function verifies that the matrix is square and optionally checks for symmetry to recommend the best solver type.

2.10 bdImportTextFile_hdf5

Converts a text file (e.g., CSV, TSV) to HDF5 format, providing efficient storage and access capabilities.

2.11 bdmove_hdf5_dataset

Moves an HDF5 dataset from one location to another within the same HDF5 file. This function automatically handles moving associated rownames and colnames datasets, creates parent groups if needed, and updates all internal references.

2.12 bdReduce_hdf5_dataset

Reduces multiple datasets within an HDF5 group using arithmetic operations (addition or subtraction).

2.13 bdRemove_hdf5_element

Removes specified groups or datasets from an HDF5 file.

2.14 bdSort_hdf5_dataset

Sorts a dataset in an HDF5 file based on a predefined ordering specified through a list of sorting blocks.

2.15 bdSplit_matrix_hdf5

Splits a large dataset in an HDF5 file into smaller submatrices, with support for both row-wise and column-wise splitting.

2.16 bdsubset_hdf5_dataset

Creates a new HDF5 dataset containing only the specified rows or columns from an existing dataset. This operation is memory efficient as it uses HDF5’s hyperslab selection for direct disk-to-disk copying without loading the entire dataset into memory.

2.17 bdWrite_hdf5_dimnames

Write row and/or column names metadata for an existing dataset in an HDF5 file. Empty vectors skip the corresponding dimnames.