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h5pack virtual documentation

Note

If you're new to h5pack, please consult our Quickstart guide. Please note that this page is just a quick reference to explain different tool options.

This tool takes two or more .h5 partition files created with h5pack and creates a Virtual Dataset (VDS), allowing you to access all the data through a single logical file.

Basic usage

h5pack virtual <input-file-0> <input-file-1> ... --output <output-h5-file>

or using aliases:

h5pack virtual <input-file-0> <input-file-1> ... -o <output-h5-file>

This will result in a single .h5 file that acts as a link to all the data from each input file.

Warning

When using relative paths in Virtual Dataset (VDS), they are typically resolved relative to the location of the VDS file itself. If you run a script from a different location and attempt to load the data, the relative paths are still anchored to the VDS file's location, not the location from which the script is executed.

If for your specific use case using absolute paths is more convenient, you can use the --force-abspath flag. Additionally, you can use h5pack info to check the validity of your file paths.

Advanced settings

Adding additional attributes

You can add additional attributes to the VDS by using the -a/--attrs option. The arguments to this option should be key/value pairs. All values will be parsed as a string. 

h5pack virtual <input-file-0> <input-file-1> --attrs key0 value0 key1 value1 ... --output <output-h5-file>

or using aliases: 

h5pack virtual <input-file-0> <input-file-1> -a key0 value0 key1 value1 ... -o <output-h5-file>

Oftentimes you may have folders or nested folders containing multiple .h5 files that you want to use to create a VDS. In such cases, you can provide the parent folder as input and use the -r/--recursive option to make the search recursive.

h5pack virtual <input-folder> --output <output-h5-file> --recursive

or sing aliases: 

h5pack virtual <input-folder> -o <output-h5-file> -r

Selecting or filtering multiple files from a folder

You may also want to easily select or filter a subset of all files. In these cases you can use the -s/--select or -f/--filter option.

For selecting a subset of files you can run: 

h5pack virtual <input-folder> --output <output-h5-file> --select <select-expression> --recursive

or using aliases: 

h5pack virtual <input-folder> -o <output-h5-file> -s <select-expression> -r

For filtering out a subset of files you can run: 

h5pack virtual <input-folder> --output <output-h5-file> --filter <filter-expression> --recursive

or using aliases: 

h5pack virtual <input-folder> -o <output-h5-file> -f <filter-expression> -r

Forcing absolute paths

If you want to force all the paths included in the VDS to be absolute paths regardless of how they are provided, you can use the --force-absppath flag as follows:

h5pack virtual <input-folder> --output <output-h5-file> --force-abspath

Help

To see all available options, run: 

h5pack virtual --help

or using aliases: 

h5pack virtual -h