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OpenChemistry / tomviz

Cross platform, open source application for the processing, visualization, and analysis of 3D tomography data
https://tomviz.org/
BSD 3-Clause "New" or "Revised" License
325 stars 86 forks source link

HDF5/DXFile support? #1355

Open ghost opened 6 years ago

ghost commented 6 years ago

Hi, I've just been poking around at Tomviz and I like it very much! The best parts of Paraview, but made easier to use... nice!!

I was wondering though if you are planning to incorporate HDF5 support, particularly of the Data Exchange type in use at many synchrotron beamlines? I see that there was a thread on this a couple of years ago, but that was in reference to v0.6 and right now I am using v1.2. Probably many things change in a factor of 2. :-)

mathturtle commented 6 years ago

Hi,

There is some support in recent versions, EMD files are HDF5-based and they are supported now. If this is a commonly used format we probably should add support for it. @cryos?

cryos commented 6 years ago

Hi @jdgelb we will be working on adding some of the synchrotron data exchange formats, I have been talking with people about NeXuS, are there other formats you are thinking of, and do you have any links to the specification. Perhaps you are referring to this? https://github.com/data-exchange/dxfile

ghost commented 6 years ago

Hi all, thanks for considering this request! @cryos yes, that's the one. Here is a full description of the format: http://dxfile.readthedocs.io. The image data lives in /exchange/data, though there is a substantial amount of additional information that can be / is stored within the rest of the file structure. Let me know if you'd like an example file to tinker with and I will be happy to email something over... (jgelb at sigray dot com)

cryos commented 6 years ago

This looks like another great candidate for a Python reader/writer that could reuse the Python API mentioned. It would be great to get some sample files, especially ones that are CC0/CC-BY so that we could share them more readily/use them in testing.