Trying to read and process eye-tracking data currently stored in the HDF5 format. Pandas supports HDFStore, see also here.

The problem is that somehow the python/anaconda installation on my mac is out of date or out of sync. It won’t read the .hdf5 file, complaining the following:

>>> import pandas as pd
p>>> pd.HDFStore("test.hdf5")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/garyfeng/anaconda/lib/python2.7/site-packages/pandas/io/pytables.py", line 389, in __init__
    'importing'.format(ex=str(ex)))
ImportError: HDFStore requires PyTables, "dlopen(/Users/garyfeng/anaconda/lib/python2.7/site-packages/tables/utilsextension.so, 2): Library not loaded: @rpath/./libhdf5.10.dylib
  Referenced from: /Users/garyfeng/anaconda/lib/python2.7/site-packages/tables/utilsextension.so
  Reason: image not found" problem importing
>>>

So I thought I’d reinstall PyTabls, using:

brew tap homebrew/science
brew install hdf5

This installed hdf5 version 1.8.16, after which python complains that hdf5 version conflicts – between 1.8.15_patch1 and the newly installed 1.8.16. So I had to downgrade.

Found the hdf5.rb old version at https://raw.githubusercontent.com/Homebrew/homebrew-science/80f77e2ab89da3351c91af93fcf1f8c40b858628/hdf5.rb. Copy the content.

Edit /usr/local/Library/Taps/homebrew/homebrew-science/hdf5.rb, which after brew tap is of version 1.8.16. Paste in the above older version, and make the following changes at the very top:

class Hdf5 < Formula
  desc "File format designed to store large amounts of data"
  homepage "http://www.hdfgroup.org/HDF5"
  url "https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.5-patch1/src/hdf5-1.8.15-patch1.tar.bz2"
  version "1.8.15"

Save. Then back in terminal, do:

brew unlink hdf5
brew install hdf5

This now installs the older version 1.8.15. It also warns that we don’t have sha256. It reminds us the SHA256:

class Hdf5 < Formula
  desc "File format designed to store large amounts of data"
  homepage "http://www.hdfgroup.org/HDF5"
  url "https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.5-patch1/src/hdf5-1.8.15-patch1.tar.bz2"
  version "1.8.15"
  sha256 "1028be671e24dcd9826d3eabe6c0ebe674282368689dcf0f6bb5926bc8d3be25"

Done. However, PyTables still doesn’t run. At least we have got HDF5 running.

After this, I renamed the hdf5.rb to hdf5.1.8.15.rb, and restored the v1.8.16 to hdf5.rb.