Thanks a lot, Jeff. I will think over, which option to use. Using titan I could even do visualization at runtime (for analysis of the network) and for bigger networks I could just store the network state and visualize offline. Now I have somewhere to start. That helped a lot.
---- Benjamin Auffarth KTH, Computational Biology and Neurocomputing (CBN), Albanova Universitetscentrum, Roslagstullsbacken 35, S-100 44 Stockholm, Sweden room 162:021B, tel. +46 8 790 8699 On Tue, Nov 16, 2010 at 4:56 PM, Jeff Baumes <[email protected]>wrote: > VTK/Titan may have most of the components that you need, but they are not > currently available in ParaView. Titan (titan.sandia.gov) 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. > > 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. > > Jeff > > On Tue, Nov 16, 2010 at 4:54 AM, Benjamin Auffarth <[email protected]>wrote: > >> Hi all, >> my question is about suitability of ParaView 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 ParaView 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 (http://www.paraview >> .org/Wiki/ITK_Release_4/Discussion_Points#Neural_Networks). >> 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 ParaView? (If yes, >> how?) >> thanks, >> Benjamin. >> >> >> ---- >> Benjamin Auffarth >> KTH, Computational Biology and Neurocomputing (CBN), >> Albanova Universitetscentrum, Roslagstullsbacken 35, >> S-100 44 Stockholm, Sweden >> room 162:021B, tel. +46 8 790 8699 >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Please keep messages on-topic and check the ParaView Wiki at: >> http://paraview.org/Wiki/ParaView >> >> Follow this link to subscribe/unsubscribe: >> http://www.paraview.org/mailman/listinfo/paraview >> >> > > > -- > Jeff Baumes, Ph.D. > Technical Lead, Kitware Inc. > (518) 881-4932 > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Please keep messages on-topic and check the ParaView Wiki at: > http://paraview.org/Wiki/ParaView > > Follow this link to subscribe/unsubscribe: > http://www.paraview.org/mailman/listinfo/paraview > >
_______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
