An easy-to-use HDF5 data interface (loadh5 and saveh5) for MATLAB


Updated 21 May 2023

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= EasyH5 Toolbox - An easy-to-use HDF5 data interface (loadh5 and saveh5) =

* Copyright (C) 2019 Qianqian Fang <q.fang at neu.edu>
* License: GNU General Public License version 3 (GPL v3) or 3-clause BSD license, see LICENSE*.txt
* Version: 0.8 (code name: Go - Japanese 5)
* URL: http://github.com/fangq/easyh5

== Overview ==

EasyH5 is a fully automated, fast, compact and portable MATLAB object to HDF5
exporter/importer. It contains two easy-to-use functions - `loadh5.m` and
`saveh5.m`. The `saveh5.m` can handle almost all MATLAB data types, including
structs, struct arrays, cells, cell arrays, real and complex arrays, strings,
and `containers.Map` objects. All other data classes (such as a table, digraph,
etc) can also be stored/loaded seemlessly using an undocumented data serialization
interface (MATLAB only).

EasyH5 stores complex numerical arrays using a special compound data type in an
HDF5 dataset. The real-part of the data are stored as `Real` and the imaginary
part is stored as the `Imag` component. The `loadh5.m` automatically converts
such data structure to a complex array. Starting from v0.8, EasyH5 also supports
saving and loading sparse arrays using a compound dataset with 2 or 3
specialized subfields: `SparseArray`, `Real`, and, in the case of a sparse
complex array, `Imag`. The sparse array dimension is stored as an attribute
named `SparseArraySize`, attached with the dataset. Using the `deflate` filter
to save compressed arrays is supported in v0.8 and later.

Because HDF5 does not directly support 1-D/N-D cell arrays or struct arrays,
EasyH5 converts these data structures into data groups with names in the
following format
where `varname` is the variable/field name to the cell/struct array object,
and `idx1d` is the 1-D integer index of the cell/struct array. We also provide
a function, `regrouph5.m` to automatically collapse these group/dataset names
into 1-D cell/struct arrays after loading the data using `loadh5.m`. See examples

== Installation ==

The EasyH5 toolbox can be installed using a single command
where the `/path/to/easyh5` should be replaced by the unzipped folder
of the toolbox (i.e. the folder containing `loadh5.m/saveh5.m`).

== Usage ==

=== `saveh5` - Save a MATLAB struct (array) or cell (array) into an HDF5 file
Save a MATLAB struct (array) or cell (array) into an HDF5 file.

=== `loadh5` - Load data in an HDF5 file to a MATLAB structure.
Load data in an HDF5 file to a MATLAB structure.

a={rand(2), struct('va',1,'vb','string'), 1+2i};
=== `regrouph5` - Processing an HDF5 based data and group indexed datasets into a cell array
Processing a loadh5 restored data and merge "indexed datasets", whose
names start with an ASCII string followed by a contiguous integer
sequence number starting from 1, into a cell array. For example,
datasets {data.a1, data.a2, data.a3} will be merged into a cell/struct
array data.a with 3 elements.

a(1).a1=0; a(2).a2='test';

== Known problems

- EasyH5 currently does not support 2D cell and struct arrays
- If a cell name ends with a number, such as `a10={...}`; `regrouph5` can not group the cell correctly
- If a database/group name is longer than 63 characters, it may have the risk of being truncated

== Contribute to EasyH5 ==

Please submit your bug reports, feature requests and questions to the Github Issues page at


Please feel free to fork our software, making changes, and submit your revision back
to us via "Pull Requests". EasyH5 is open-source and we welcome your contributions!

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Cite As

Qianqian Fang (2023). EasyH5 (https://github.com/fangq/easyh5), GitHub. Retrieved .

MATLAB Release Compatibility
Created with R2010a
Compatible with any release
Platform Compatibility
Windows macOS Linux

Inspired by: HDF5 data to struct reader

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Version Published Release Notes

- Link page to Github repository

To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.