HDF5 & NetCDF Explorer (H5 Viewer)

For climate and lab scientists who keep data in .nc or .h5 files, this extension shows the variables, their CF metadata, the values and a plot inside VS Code, without a line of Python.

A real VS Code 1.142 window running this extension on samples/era5-t2m-sample.nc, a 1.3 MB NetCDF-4 file made by scripts/make-samples.py.

• Made for NetCDF and climate data. Dimension names, coordinates, scale_factor, add_offset, _FillValue and CF time units are applied for you, so you see 263.75 K on 2024-12-04 06:00, not 1500 at index 13. The noleap, 360_day and all_leap calendars work too.
• Big files stay fast. The file is read slice by slice in a background thread. In our test a 37 GB array opens, shows a page and draws a sampled heatmap in about one second, and a slow read is stopped after 20 s instead of freezing the editor.
• One viewer for HDF5, NetCDF-4 and NetCDF-3, including HDF5 files with other names such as Julia .jld2, MATLAB 7.3 .mat and .loom. Groups, attributes, compound tables, strings, chunking and compression filters are all shown. Nothing leaves your machine.

Quick start

1. Install the extension.
2. Click a .nc or .h5 file in the Explorer. Pick a variable on the left.

Recorded in the same window. The white arrow is drawn in to show where each click lands.

What you can do

• Browse the group tree with a filter box. Coordinates, plain datasets, external links and NetCDF dimensions have their own icons.
• Read the file overview (format, dimensions, global attributes and a table of all variables with units and long names), much like ncdump -h.
• See type, shape with dimension names, chunk shape, compression (shuffle, deflate level, LZF, szip and others by name), size in memory and the full attribute list. Internal HDF5 and NetCDF attributes are hidden behind a checkbox.
• Pick any two dimensions as rows and columns. Sliders fix the others and show the decoded coordinate value next to the index.
• Page through values 100 rows by 30 columns at a time, with coordinate values as row and column headers.
• Plot 1D data as a line and 2D slices as a heatmap with a colour bar and hover readout. Arrays larger than 512 x 512 are sampled with a stride.
• See min, max, mean, std and the number of fill, NaN and Inf values for the slice on screen.
• Copy the path, or copy xarray or h5py code that loads the same slice.
• Export the slice on screen to CSV or JSON with "Export slice…". You get every row and column of the two chosen dimensions, with the coordinate values as headers. The sliders fix the other dimensions, and the JSON file records which index and value each of them had. Text from the file that starts with =, +, - or @ gets a leading ' in the CSV, so a spreadsheet does not run it as a formula.
• Turn CF decoding off to see the raw stored numbers.
• The view reloads when the file changes on disk, which helps while a model run is writing output. A script that deletes the file and writes it again also triggers a reload.

Supported files

The format is detected from the first bytes of the file, not from the extension, so a 512-byte user block (JLD2 and MATLAB 7.3 files have one) is fine. HDF4, NASA CDF, NetCDF CDF-5 and older MATLAB v5 .mat files get a clear message instead of an error.

Settings

Privacy and safety

The extension makes no network calls and has no telemetry. It never runs code from a file. Values go to the view as plain JSON and are drawn as text or canvas pixels, under a strict Content Security Policy with no remote scripts.

Known limits

• Files must be on this computer. Remote and virtual file systems are not supported yet.
• HDF5 filters that are not built into h5wasm (Blosc, Zstd, bitshuffle and other plugins) show the filter name and a read error.
• Zarr is not supported yet.
• MATLAB .mat files saved in the v5 format are not HDF5. Save them again with save(filename, '-v7.3').
• Export writes at most hdf5NetcdfExplorer.maxReadValues values (1,000,000 by default) per file.
• The standard calendar uses the proleptic Gregorian calendar for dates before 1582.

Credits

HDF5 reading uses h5wasm by the National Institute of Standards and Technology, which bundles the HDF5 library by The HDF Group. NetCDF-3 headers are parsed with netcdfjs (MIT). See THIRD-PARTY-NOTICES.txt.

License

MIT

Support

Zovo extensions have no ads and no tracking, and sponsors pay for the time that goes into fixes and new viewers. You can sponsor the work on GitHub Sponsors.

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