GUI programs to view HDF5 data

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

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

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 .whl for armhf, so that means ViTables only works on non-ARM systems (laptops, desktops, NOT Raspberry Pi).

PanoplyJ

PanoplyJ is downloaded for Mac, Linux or Windows. PanoplyJ does not require compiling, just run it using Java.

  1. Linux PanoplyJ requires Java 8 or newer.
    apt install openjdk-8-jre
    
  2. extract PanoplyJ and make executable
    unzip PanoplyJ-4*.zip -d ~
    
    chmod +x ~/PanoplyJ/panoply.sh
    
  3. run PanoplyJ
    ~/PanoplyJ/panoply.sh
    
  4. Make a command-line shortcut by adding to ~/.bash_aliases
    alias panoply='$HOME/PanoplyJ/panoply.sh'
    

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.

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