Related: Check HDF5 files for corruption
The options for graphically browsing and editing HDF5 data files from Linux, Mac and Windows include:
HDFview is maintained by the curators of the HDF5 format, the HDF Group. HDFView enables editing (writing) as well as reading HDF5.
apt install hdfview
- Mac, Windows download
HDFview needs compiling if running from source, unlike ImageJ, which is a pure platform-independent Java program.
Ubuntu 18.04 (still!) has a broken
hdfview such that the program opens, but silently fails to read any HDF5/NetCDF4 files.
the CentOS HDFView binary–it will work on Ubuntu / Debian as well.
HDF Compass is also by the HDF Group. Unlike HDFView, HDF Compass is read-only.
apt install hdf-compass
Instead of using the menus, I typically open one or more HDF5/NetCDF4 files from Terminal like:
HDFCompass f1.h5 f2.nc
ViTables is a Python-based HDF5 viewing program.
apt install libhdf5-dev python -m pip install pyqt5 python -m pip install vitables
Unfortunately at this time PyQT5 doesn’t have a
armhf, so that means ViTables only works on non-ARM systems (laptops, desktops, NOT Raspberry Pi).
PanoplyJ is downloaded for Mac, Linux or Windows. PanoplyJ does not require compiling, just run it using Java. Linux PanoplyJ requires Java 8 or newer, and can also work with Java 9.
apt install openjdk-8-jre
Extract PanoplyJ and make executable:
unzip PanoplyJ-4*.zip -d ~ chmod +x ~/PanoplyJ/panoply.sh
Run PanoplyJ by:
Make a command-line shortcut by adding to
If you get PanoplyJ error
Unknown superblock version=3
You may have an older version of PanoplyJ whose NetCDF-Java library isn’t ready for HDF5 1.10.
If you’re writing the HDF5 files from
h5py, you can use in your Python program writing the data:
with h5py.File('myfile.h5', libver='earliest') as f: ....
which should write in an HDF5 1.8-compatible way.