title: Repair corrupted hdf5 file
body: <p>We are saving time of flight mass spectra in hdf5 files. For more than 99% of the cases this works without any errors. But sometimes measurements crashes.</p>
  <p>We save different (meta-) data but my question is about one incrementing table:</p>
  <ul>
  <li>Storage Layout: CHUNKED: 1x1x10x248584</li>
  <li>Compression: 8,312:1GZIP: level=5</li>
  </ul>
  <p>Values are inserted each time step (usually 10 seconds). After 1min the layout is 6x1x10x248584.</p>
  <p>But the corrupted table has size: 0x1x10x248584 (Tried with h5py 2.10.0 and HDFView 3.1.0).</p>
  <p>My question: Is there any low-level library (python preferred) where I can try to access the lost data? The file size (measuring several hours --&gt; several GB) promises the data is there, but cannot be read with those two programs I tried.
  Thank you.</p>
  <p>[Update]:
  In HDFView it looks like this for the corrupted File. From file size I expect the first dimension to be &gt;1000.
  <a href="https://i.stack.imgur.com/rw3gQ.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/rw3gQ.png" alt="enter image description here" /></a></p>