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

  • Copyright (C) 2019,2022 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: 0.9 (code name: Daseot - Korean 5)
  • URL: http://github.com/NeuroJSON/easyh5
  • Compatibility: MATLAB R2010b or newer
  • Acknowledgement: This project is supported by US National Institute of Health (NIH) grant U24-NS124027 (NeuroJSON)

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-valued 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

    ['/hdf5/path/.../varname',num2str(idx1d)]

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 below.

Installation

The EasyH5 toolbox can be installed using a single command

    addpath('/path/to/easyh5');

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.

Example:

  a=struct('a',rand(5),'c','string','b',true,'d',2+3i,'e',{'test',[],1:5});
  saveh5(a,'test.h5');
  saveh5(a(1),'test2.h5','rootname','');
  saveh5(a(1),'test2.h5','compression','deflate','compressarraysize',1);
  saveh5('appending data to existing file','test.h5','rootname','/name','append',1);
  saveh5(a,'test.h5j','jdata',1);

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

Load data in an HDF5 file to a MATLAB structure.

Example:

  a={rand(2), struct('va',1,'vb','string'), 1+2i};
  saveh5(a,'test.h5');
  a2=loadh5('test.h5')
  a3=loadh5('test.h5','regroup',1)
  isequaln(a,a3.a)
  a4=loadh5('test.h5','/a1')

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.

Example:

  a=struct('a1',rand(5),'a2','string','a3',true,'d',2+3i,'e',{'test',[],1:5});
  a(1).a1=0; a(2).a2='test';
  data=regrouph5(a)
  saveh5(a,'test.h5');
  rawdata=loadh5('test.h5')
  data=regrouph5(rawdata)

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
  • When saving a dynamic expression instead of a named variable, the data are stored under path /data

Contribute to EasyH5

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

https://github.com/NeuroJSON/easyh5/issues

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