Related: Check HDF5 files for corruption
Here are a few options for graphically browsing and editing HDF5 data files from Linux, Mac and Windows.
HDFview normally works fine, and it’s maintained by the curators of the HDF5 format.
apt install hdfview
HDFview needs compiling if running from source, unlike ImageJ, which is a pure platform-independent Java program.
ViTables is a Python-based HDF5 viewing program.
apt install libhdf5-dev pip install pyqt5 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.
apt install openjdk-8-jre
- extract PanoplyJ and make executable
unzip PanoplyJ-4*.zip -d ~ chmod +x ~/PanoplyJ/panoply.sh
- run PanoplyJ
- Make a command-line shortcut by adding to
If you get PanoplyJ error
Unknown superblock version=3
This is because PanoplyJ ≤ 4.8.5:
- isn’t yet ready for the new HDF5 1.10 library.
- is compatible with legacy HDF5 1.8 library.
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 HDF5 1.8-compatible way.