VTK/Titan may have most of the components that you need, but they are not currently available in ParaView. Titan (<a href="http://titan.sandia.gov">titan.sandia.gov</a>) has a generic hdf5 reader that loads data into a vtkTable that may suit your needs. There are also utilities for converting a vtkTable into a vtkGraph which can then be visualized in vtkGraphLayoutView, which can do 2D or 3D layout. As far as animation goes, graph layout on time-changing graphs is a tricky problem since it's easy to lose your frame-of-reference if you redo layout each time. But if you want to do the layout once, fix the node positions, then just animate properties like colors, that is more doable.<div>
<br></div><div>The other option is to manually get the data into one of the several geometry formats ParaView supports, then you could use ParaView directly. For example, you could produce a legacy vtkPolyData format where you define neurons as points and connections as lines, then you load it in ParaView and do things like glyph the points with spheres, color lines by attributes, etc.<br>
<div><br></div><div>Jeff<br><br><div class="gmail_quote">On Tue, Nov 16, 2010 at 4:54 AM, Benjamin Auffarth <span dir="ltr"><<a href="mailto:auffarth@csc.kth.se">auffarth@csc.kth.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi all, <br> my question is
about suitability of <span>ParaView</span> for visualization of neural network
models. I saw the gallery, looked at the supported file formats,
available tools and filters, and looked over the user guide (1.7). My
impression is that <span>ParaView</span> is typically used for visualization of
data that is layed out in a grid, say 3D matrices, especially particles,
however I noticed there is the possibility to interactively create 3D
objects and output them to povray and I I saw that ITK R4 at one point
had support for neural network visualization (<a href="http://www.paraview.org/Wiki/ITK_Release_4/Discussion_Points#Neural_Networks" target="_blank">http://www.<span>paraview</span>.org/Wiki/ITK_Release_4/Discussion_Points#Neural_Networks</a>). <br>
Our aim is to visualize a network model consisting of neurons and
connections between neurons and show time dynamics of evolving
attractors, etc. The visualization should basically colorcode neurons
and synapses, possibly in 3D and possibly raytraced. We run our
simulations in parallel and would like to use a binary format like hdf5
or netcdf to store data of neural activations and connection strengths.
These should then be used to create a 3D representations (images and
videos). I think Povray (+ pevious binary2text conversion) could be simply setup
to do network visualization for our purpose. Can this visualization be done in
<span>ParaView</span>? (If yes, how?) <br>
thanks, <br>Benjamin.<br><br><br clear="all">----<br><font color="#888888">Benjamin Auffarth<br>KTH, Computational Biology and Neurocomputing (CBN), <br>Albanova Universitetscentrum, Roslagstullsbacken 35, <br>S-100 44 Stockholm, Sweden<br>
room 162:021B, tel. +46 8 790 8699<br>
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