Extract and display file hierarchy from HDF5

[pdurbin]

For now I left a note with some screenshots here: IQSS/dataverse-sample-data#35 (comment)

[JR-1991]

I found an example that uses JHDF to extract a file tree structure from an HDF5 file. The library does not rely on the HDF-Group C-Libs and is pure Java. Might be interesting to use for displaying contents of an HDF5 file.

[JR-1991]

I came across a very nice HDF5 viewer H5Web that displays the tree and its contents as graph/heatmap. It is a React component library and could be interesting for the upcoming SPA as a plugin.

[pdurbin]

@JR-1991 yes! @atrisovic and I talked about that silx-kit/h5web one a while back. Looks fancy! 🧐

[pdurbin]

I had a quick play with the EDcheck_CIRO-2022-12-08-Thu-20-03-14.hdf5 file I mentioned at IQSS/dataverse-sample-data#35 (comment)

Here's how the file hierarchy looks in HDFView

I wrote a little recursive function (uncommitted) to print the directories (groups) using the Java library we added to the codebase:

printGroups(netcdfFile.getRootGroup().getGroups());
...
public static void printGroups (ImmutableList<Group> groups) {
    if (groups.isEmpty()) {
        return;
    }
    for (Group group : groups) {
        System.out.println("group: " + group.getFullName());
        printGroups(group.getGroups());
    }
}

It seems to work well enough:

group: \.axes
group: \.config
group: \.environment
group: \.quantities
group: \.quantities/accept-flavourchange
group: \.quantities/accept-glob
group: \.quantities/accept-ins
group: \.quantities/accept-ins4
group: \.quantities/accept-pair-tau
group: \.quantities/accept-rem
group: \.quantities/accept-rem4
group: \.quantities/accept-shift
group: \.quantities/contrib-sst
group: \.quantities/contrib-state
group: \.quantities/energies-eigenstates
group: \.quantities/fiw
group: \.quantities/ftau
group: \.quantities/ftau-full
group: \.quantities/g0iw
group: \.quantities/g0iw-full
group: \.quantities/giw
group: \.quantities/giw-full
group: \.quantities/gleg
group: \.quantities/gleg-full
group: \.quantities/gtau
group: \.quantities/gtau-full
group: \.quantities/hist
group: \.quantities/hist-seg
group: \.quantities/hist-sst
group: \.quantities/hist-state
group: \.quantities/lhist
group: \.quantities/muimp
group: \.quantities/ntau-n0
group: \.quantities/occ
group: \.quantities/occbasis-mapping
group: \.quantities/rhist
group: \.quantities/sign
group: \.quantities/sign-sst
group: \.quantities/sign-state
group: \.quantities/siw
group: \.quantities/siw-full
group: \.quantities/smom
group: \.quantities/smom-full
group: \.quantities/ssts-states
group: \.quantities/time-qmc
group: \.quantities/time-sampling
group: \.quantities/time-simulation
group: \.quantities/time-warmup
group: start
group: stat-001
group: stat-001/ineq-001
group: stat-001/ineq-001/accept-flavourchange
group: stat-001/ineq-001/accept-glob
group: stat-001/ineq-001/accept-ins
group: stat-001/ineq-001/accept-ins4
group: stat-001/ineq-001/accept-pair-tau
group: stat-001/ineq-001/accept-rem
group: stat-001/ineq-001/accept-rem4
group: stat-001/ineq-001/accept-shift
group: stat-001/ineq-001/contrib-sst
group: stat-001/ineq-001/contrib-state
group: stat-001/ineq-001/energies-eigenstates
group: stat-001/ineq-001/fiw
group: stat-001/ineq-001/ftau
group: stat-001/ineq-001/ftau-full
group: stat-001/ineq-001/g0iw
group: stat-001/ineq-001/g0iw-full
group: stat-001/ineq-001/giw
group: stat-001/ineq-001/giw-full
group: stat-001/ineq-001/gleg
group: stat-001/ineq-001/gleg-full
group: stat-001/ineq-001/gtau
group: stat-001/ineq-001/gtau-full
group: stat-001/ineq-001/hist
group: stat-001/ineq-001/hist-seg
group: stat-001/ineq-001/hist-sst
group: stat-001/ineq-001/hist-state
group: stat-001/ineq-001/lhist
group: stat-001/ineq-001/muimp
group: stat-001/ineq-001/ntau-n0
group: stat-001/ineq-001/occ
group: stat-001/ineq-001/occbasis-mapping
group: stat-001/ineq-001/rhist
group: stat-001/ineq-001/sign
group: stat-001/ineq-001/sign-sst
group: stat-001/ineq-001/sign-state
group: stat-001/ineq-001/siw
group: stat-001/ineq-001/siw-full
group: stat-001/ineq-001/smom
group: stat-001/ineq-001/smom-full
group: stat-001/ineq-001/ssts-states
group: stat-001/ineq-001/time-qmc
group: stat-001/ineq-001/time-sampling
group: stat-001/ineq-001/time-simulation
group: stat-001/ineq-001/time-warmup

[pdurbin]

@atrisovic and I are at least soft closing this in favor of this one:

• Addition of H5Web viewer to preview HDF5 files gdcc/dataverse-previewers#30