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MathGroup Archive 2011

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HDF5

  • To: mathgroup at smc.vnet.net
  • Subject: [mg119840] HDF5
  • From: "Scot T. Martin" <smartin at seas.harvard.edu>
  • Date: Sat, 25 Jun 2011 05:27:27 -0400 (EDT)

I intend to make a small Mathematica package to do better with use of HDF5 data files in Mathematica.

Would anyone like to work on this with me in a partnership?

I have the broad scope sorted out (i.e., HDF5 Java library from www.hdfgroup.org, J/LINK in Mathematica). 

Partners who know Java as well as HDF5 would be most welcome.

My personal goals are to improve on Import[..., "HDF5"] in two ways:

- move past the limitation described in the Mathematica documentation for "compound data structures"

- get random access to large HDF5 files (i.e., MaxMemoryUsed[...] at present goes through the roof in the Import[..., "HDF5"] implementation even if you extract only a small part of the file).

Write back to me if you're interested to partner with me on this and include your areas of expertise relevant to this project.


________________________________________
From: Scot T. Martin [smartin at seas.harvard.edu]
Sent: Friday, June 10, 2011 06:38
To: mathgroup at smc.vnet.net
Subject: [mg119840] Import HDF5 file with "Compound Data Structures"

The documentation states that Import[...] for HDF5 does not accept "compound data structures".

Is there a workaround or alternative for this?

The file in question has the following format:

In[2]:= Import[filename, {"HDF5", "DataFormat"}]

Out[2]= {{"UnsignedInteger128", "String", "String"}, "Real32", "Real64", "Real64", "Real32", "Real32", {"String", "Real32", "Real32", "Real32"}, "Real64"}

In[3]:= Import[filename, {"HDF5", "Datasets", 1}]

>>During evaluation of In[3]:= Import::h5type: The datatype of the dataset "/AcquisitionLog/Log" is not currently supported.

Out[3]= $Failed



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