How is HDF5 different from a folder with files?

Question

I\'m working on an open source project dealing with adding metadata to folders. The provided (Python) API lets you browse and access metadata like it was just another folder. Be

Answer 1

Thanks for asking this interesting question. Is a folder with files portable because I can copy a directory onto a stick on a Mac and then see the same directory and files on a PC? I agree that the file directory structure is portable, thanks to the people that write operating systems, but this is unrelated to the data in the files being portable. Now, if the files in this directory are pdf's, they are portable because there are tools that read and make sense of pdfs in multiple operating systems (thanks to Adobe). But, if those files are raw scientific data (in ASCII or binary doesn't matter) they are not at all portable. The ASCII file would look like a bunch of characters and the binary file would look like gibberish. If the were XML or json files, they would be readable, because json is ASCII, but the information they contain would likely not be portable because the meaning of the XML/json tags may not be clear to someone that did not write the file. This is an important point, the characters in an ASCII file are portable, but the information they represent is not.

HDF5 data are portable, just like the pdf, because there are tools in many operating systems that can read the data in HDF5 files (just like pdf readers, see http://www.hdfgroup.org/products/hdf5_tools/index.html). There are also libraries in many languages that can be used to read the data and present it in a way that makes sense to users – which is what Adobe reader does. There are hundreds of groups in the HDF5 community that do the same thing for their users (see http://www.hdfgroup.org/HDF5/users5.html).

There has been some discussion here of compression as well. The important thing about compressing in HDF5 files is that objects are compressed independently and only the objects that you need get decompressed on output. This is clearly more efficient than compressing the entire file and having to decompress the entire file to read it.

The other critical piece is that HDF5 files are self-describing – so, people that write the files can add information that helps users and tools know what is in the file. What are the variables, what are their types, what software wrote them, what instruments collected them, etc. It sounds like the tool you are working on can read metadata for files. Attributes in an HDF5 file can be attached to any object in the file – they are not just file level information. This is huge. And, of course, those, attributes can be read using tools written in many languages and many operating systems.