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.