hdfuse 1.0.1

hdfuse5

What is hdfuse5?

hdfuse5 is a filesystem in userspace (FUSE https://github.com/libfuse/libfuse or MacFUSE https://osxfuse.github.io/) to explore data stored in hierarchical hdf5 files (see https://www.hdfgroup.org/solutions/hdf5/).

All files in the directory given as the hdfuse5 root are mirrored into the mountpoint with all hdf5 files being presented as a directories. HDF5 Groups within the files are mapped into further directories, data arrays are files, and attributes are shown as extended filesystem attributes. Non-hdf5 files and directories are just mirrored unchanged.

The main purpose is to enable a quick access to the contents of hdf5 files with normal system tools (grep, find, cat, file browser, etc.).

What do I need to run hdfuse5?

• python (https://www.python.org/)
• h5py (https://www.h5py.org/)
• fusepy (see below)
• FUSE or MacFUSE support in you operating system and the required permissions to use it. That rules out any Windows variants.

This software uses fusepy available from https://github.com/fusepy/fusepy It provides a simple python interface to FUSE and MacFUSE in a single file. fusepy is under the ISC License so it could be included here for convenience. There have been a few updates to it since, that are not incorporated.

Most distributions have a 'fuse' user group you need to be a member of in order to be allowed to use fuse (and therefore hdfuse5).

What do I need to do?

Provided the above requirements are met you can do this from within the source directory:

    $ ls
    exampleroot  fuse.py  fuse.pyc  hdfuse5.py  LICENSE  README
    $ ls -l exampleroot # contains an hdf5 file
    total 16
    -rw-r--r-- 1 user user 14704 2011-06-17 16:55 NXtest.h5
    $ mkdir mnt # create mountpoint
    $ python hdfuse5.py exampleroot mnt # mount
    $ # what's in the mountpoint now? a directory for the file!
    $ ls -l mnt
    total 0
    drwxr-xr-x 1 user user 14704 2011-06-17 16:55 NXtest.h5
    $ # explore the structure
    $ find mnt -ls
         1    0 drwxr-xr-x   2 user user     4096 Jun 17 16:55 mnt
         2    0 drwxr-xr-x   1 user user    14704 Jun 17 16:55 mnt/NXtest.h5
         3    0 drwxr-xr-x   1 user user        0 Jun 17 16:55 mnt/NXtest.h5/entry
         4    0 -rw-r--r--   1 user user       10 Jun 17 16:55 mnt/NXtest.h5/entry/ch_data
         5    0 drwxr-xr-x   1 user user        0 Jun 17 16:55 mnt/NXtest.h5/entry/data
         6    0 -rw-r--r--   1 user user     8000 Jun 17 16:55 mnt/NXtest.h5/entry/data/comp_data
         7    0 -rw-r--r--   1 user user       28 Jun 17 16:55 mnt/NXtest.h5/entry/data/flush_data
         8    0 -rw-r--r--   1 user user      160 Jun 17 16:55 mnt/NXtest.h5/entry/data/r8_data
         9    0 -rw-r--r--   1 user user        4 Jun 17 16:55 mnt/NXtest.h5/entry/i1_data
        10    0 -rw-r--r--   1 user user        8 Jun 17 16:55 mnt/NXtest.h5/entry/i2_data
        11    0 -rw-r--r--   1 user user       16 Jun 17 16:55 mnt/NXtest.h5/entry/i4_data
        12    0 -rw-r--r--   1 user user       32 Jun 17 16:55 mnt/NXtest.h5/entry/i8_data
        13    0 -rw-r--r--   1 user user       80 Jun 17 16:55 mnt/NXtest.h5/entry/r4_data
        14    0 -rw-r--r--   1 user user      160 Jun 17 16:55 mnt/NXtest.h5/entry/r8_data
        15    0 drwxr-xr-x   1 user user        0 Jun 17 16:55 mnt/NXtest.h5/entry/sample
        16    0 -rw-r--r--   1 user user       20 Jun 17 16:55 mnt/NXtest.h5/entry/sample/ch_data
        17    0 drwxr-xr-x   1 user user        0 Jun 17 16:55 mnt/NXtest.h5/link
        18    0 -rw-r--r--   1 user user      160 Jun 17 16:55 mnt/NXtest.h5/link/renLinkData
        19    0 drwxr-xr-x   1 user user        0 Jun 17 16:55 mnt/NXtest.h5/link/renLinkGroup
        20    0 -rw-r--r--   1 user user       20 Jun 17 16:55 mnt/NXtest.h5/link/renLinkGroup/ch_data
        21    0 drwxr-xr-x   1 user user        0 Jun 17 16:55 mnt/NXtest.h5/link/sample
        22    0 -rw-r--r--   1 user user       20 Jun 17 16:55 mnt/NXtest.h5/link/sample/ch_data
    $ # find out the attributes of a dataset
    $ getfattr -d mnt/NXtest.h5/entry/data/comp_data
    # file: mnt/NXtest.h5/entry/data/comp_data
    user.dtype="int32"
    user.dtype.itemsize="4"
    user.itemsize="4"
    user.ndim="2"
    user.shape="(100, 20)"
    user.size="2000"
    $ # explore the data (see "man od")
    $ od -t dI -w4 -v mnt/NXtest.h5/entry/data/comp_data | head -30
    0000000           0
    0000004           0
    0000010           0
    0000014           0
    0000020           0
    0000024           0
    0000030           0
    0000034           0
    0000040           0
    0000044           0
    0000050           0
    0000054           0
    0000060           0
    0000064           0
    0000070           0
    0000074           0
    0000100           0
    0000104           0
    0000110           0
    0000114           0
    0000120           1
    0000124           1
    0000130           1
    0000134           1
    0000140           1
    0000144           1
    0000150           1
    0000154           1
    0000160           1
    0000164           1
    $ grep -ar sample mnt # find some sample information
    mnt/NXtest.h5/entry/sample/ch_data:NeXus sample
    mnt/NXtest.h5/link/renLinkGroup/ch_data:NeXus sample
    mnt/NXtest.h5/link/sample/ch_data:NeXus sample
    $ fusermount -u mnt  # get rid of the mount after you are done
    $

Random other questions

What kind of performance can I expect?

None. hdfuse5 was coded as a proof of principle. It holds no state, there is no caching, no optimisations whatsoever. This left the code quite simple and concise but still proved to be good enough for the main application: quick inspection of the file structure of a limited number of files.

Why do I have to mount a directory? Why can't I mount a single file?

This would be simple to support. The motivation at the time was to be able explore to multiple files easily with "grep" or similar tools.

Can I have write support?

Setting up the data storage in hdf5 properly requires some knowledge or at least good assumptions about your data. As a generic tool hdfuse5 make any good guesses. Using h5py is not that hard.

Any drawbacks?

hdf5 files cannot be opened "normally" by HDF5 aware tools in the tree mounted via hdfuse5, because to the operating system they look like directories.

Any future plans?

Links in hdf5 could be presented as symbolic link in the mounted directory. Pull requests welcome.

Another idea would get to present data that could be interpreted as image data in the hdf5 in a format that could be read by standard image file readers, e.g. as tiff.