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