Open VTK files for visualization in other software


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1
20 days ago by
JJ Yeo  
Dear CC3D users,

Are there any other visualization software that can be used to visualize the trajectory output from CC3D and make fancy movies? I've tried VMD to open the .vtk files and it seems to be work but probably some tweaks need to be done to get the correct visuals. Anyone has experience with that?
Community: CompuCell3D

2 Answers


3
19 days ago by
VTK is kind of a difficult format. Besides VMD there are also (at least);
In my experience these all work but they have a pretty steep learning curves.

I find it easier to have CC3D export screen shots of any displays that I want to make a movie out of. You can open multiple windows in CC3D for things like the cell types, fields, ... and then click the little camera icon to have CC3D save the screenshots at the frequency defined in Player's [Tools] [Configuration] menu. Every window in the simulation will get its own folder for screen shots. I then animate the images with, MovieMaker, Gimp, VLC Media Player, ImageMagick ...
Thank you very much for the advice! I'm testing out Paraview together with output from the cellsort_3D demo. I immediately ran into a problem when I tried to visualize by celltype, I get the error of

ERROR: In /Users/kitware/dashboards/buildbot-slave/8275bd07/build/superbuild/paraview/src/VTK/Rendering/Volume/vtkGPUVolumeRayCastMapper.cxx, line 353
vtkOpenGLGPUVolumeRayCastMapper (0x7ff64c9b5480): scalar of type VTK_CHAR is not supported because this type is platform dependent. Use VTK_SIGNED_CHAR or VTK_UNSIGNED_CHAR instead.​

CellId and ClusterID visualizes just fine. May I know how I can somehow convert the celltypes to VTK_SIGNED_CHAR or VTK_UNSIGNED_CHAR or is there a trick to getting Paraview to visualize by celltype?

EDIT:
I realised a simple solution was to change celltypes in each file to unsigned_char
find . -type f -name 'cellsort_3D_cc3d_*' -exec sed -i 's/char/unsigned_char/g' {} \;​
written 19 days ago by JJ Yeo  
0
19 days ago by
Yes, manually changing the celltype data type in the VTK file(s) appears to work, for example;
CellType 1 10000 char
to
CellType 1 10000 UNSIGNED_CHAR

What version of ParaView are you using (and what platform)? I tried version 3.98.0 and 5.4.1 on a 64-bit windows 7 computer and didn't get the "char" data type error.

I'm not sure why CC3D would be using that data type anyway, it really is just unsigned integer data and not character data. Perhaps we should change this in the next CC3D release?
I'm using the latest version of Paraview 5.4.1 on MacOSX Sierra.
written 19 days ago by JJ Yeo  
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