h5web presentation

h5web: a web-based viewer of HDF5 files

Loïc Huder

European Synchrotron Radiation Facility, Grenoble, France

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 823852

International synchrotron (driven by 13 member states and 9 associate states)

Zdora M.-C. et al. (2020) highlighted in ESRF's Spotlight on Science 18/09/2020

Provides X-rays for many scientific applications

The HDF5 files follow NeXus specifications, a standard for HDF5 file structure at neutron/X-ray facilities.

Example of NeXus hierarchy

(while practical for many other reasons...)

It can be hard to retrieve/browse data as NeXus adds several levels of hierarchy.
Data analysis/acquisition tools need to be adapted to this new format.

→ Need for a software (GUI) to easily visualise and browse HDF5 file contents

A web application written in React, a component-based front-end framework

Development started in February 2020 in the PaNOSC project

Open-source: https://github.com/silx-kit/h5web

Requests HDF5 metadata/data to a server-side provider (such as HSDS)

This is mock data.
Show basic layout: display/inspect, the explorer tree, the inspect panel to look at HDF5 metadata.
Move in the explorer tree to show the exploration
Select a 1D dataset and show the display panel
The LineVis is based on WebGL (computation can be on GPU). Fully develop by us using R3F (React wrapper of WebGL).
Has all basic features: toolbar, zoom and pan
Move to a 2d dataset and show the Heatmap. 1 000 000 points computed in ~1s
Again, also fully developed by us with basic features: colormap, domain changes...
Show nD support with the LineVis for example of the same dataset for profiles

Browsing and inspecting
Displaying n-dimensional datasets with Lines and Heatmaps (WebGL-based visualisations with React-three-fiber and visx)
Basic tools for UI: pan/zoom, colormap changes, scale type selection...
Visualisation components available as npm packages

Using the WebGL-based visualisation components outside the app:

Other web apps at ESRF, in a JupyterLab extension

NeXus support: default plots, axis labels

Some links:

This project is funded by PaNOSC

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 823852