How to export vtk file in biodynamo

Hello. I am working with biodynamo, and I would like to use some other tool instead of ParaView for visualization. I there any way I can get a .vtk file and not .pvsm file?

Hi,

BioDynaMo outputs agent attributes in (p)vtu and diffusion data in (p)vti format. These are XML-based formats. The pdf at [1] provides more information. The file is a bit dated, but maybe helpful for you.

The pvsm file is optional and contains the information about the rendering pipeline for ParaView.

If you require another file format you can add your own implementation of VisualizationAdaptor [2].
Currently, BioDynaMo provides the ParaView visualization adapter and a ROOT one which we use for web-based notebooks.

Lukas

[1] https://vtk.org/wp-content/uploads/2015/04/file-formats.pdf
[2] biodynamo/src/core/visualization at master · BioDynaMo/biodynamo · GitHub

Sorry for the late answer.
Thank you for clarification. It still leaves a problem because, as I understand, biodynamo produces (p)vtu and (p)vti files for each separate time step. If I want to make an animation from them, I can use paraview, provided that files are in the format as here:Animating legacy VTK file series - KitwarePublic. But what if I want to use some other tool. Is there a way of creating some generic vtk-file which represents an animation, and so I can run in any app supporting vtk??

You can create ParaView animations directly with the files that BioDynaMo produces. [1]
There is no need to use the legacy vtk format.

What are you trying to achieve with the other tool?
You can try the following to convert the files to vtk format:

  1. Open paraview and load the pvsm file
  2. Select the data object in the pipeline browser (e.g. Cells-data)
  3. Click on FileSave Data
  4. Select Legacy Vtk Files
  5. Follow the instructions of the dialog

[1] 7. Animation — ParaView Documentation 5.8.1 documentation