Removing duplicate points from Purkinje mesh

[edorachlee]

Hi Lucas,

When encountering duplicate point errors, what is the best way to fix them?

Currently I am trying to manually edit the .VTK file, but I am having trouble identifying the duplicate points.

For example, if we have the following message,

[purkinje] Duplicates are indexes: 2446 and 2318 --> (60000,46500,81550) x (60000,46500,81550) || 2446 has 2 edges || 2318 has 2 edges ||

I am having trouble finding 60000,46500,81550 in the .VTK file. Are these are cell centers instead of vertices?

[bergolho]

Hi @edorachlee,

To identify the duplicate points that can appear in MonoAlg3D the procedure that I did was this one:

1. Inside the MonoAlg3D source file "src/purkinje_library/purkinje.c" just after line 46, I included a debug function that writes the discretized Purkinje network mesh into a VTK file. This function is called "write_purkinje_network_to_vtk()"

// Before returning test if there is an error in Purkinje mesh
int success = check_purkinje_mesh_for_errors(the_grid->purkinje->network);
write_purkinje_network_to_vtk(the_grid->purkinje->network);

2. Compile MonoAlg3D again with the code change. Execute your MonoAlg3D configuration file again.

3. It should appear a new file called "purkinje_mesh.vtk" on your "/outputs" folder. Therefore, you can use this new VTK file to identify the exact position where the duplicate point appears and compare with the network generate by Shocker.

4. Check the indexes that are involved in the collision and try to solve by renumbering manually the Shocker Purkinje network VTK.

Another detail that I noticed in your Purkinje networks in particular, is that if you increase the space discretization of the Purkinje mesh ('dx' parameter inside the [purkinje] section in the MonoAlg3D configuration file) you can reduce the number of duplicate points.

I will try to fix this duplicate points in Shocker when I am more free after 09/12/24. Sorry for any incovenience that this might have caused.

Best regards,
Lucas

[edorachlee]

Hi Lucas, thanks for your help.

When going through #3 and comparing the two meshes, I see that the number of points in the files are different. For example, purkinje_mesh.vtk will have 25097 points and my original purkinje will have 4153 points. In this case, how will we compare the indices?

In #4, when you are renumbering, are you required to delete the duplicate points? If so, how did you handle the Line elements connecting to the duplicate points?

[edorachlee]

Just figured it out. I needed to go into Paraview and check the indices visually with the two meshes. Now I know how to fix the mesh.

Was your workflow significantly different? Also, is there another visualizing program you like to use besides Paraview?

[bergolho]

Hi @edorachlee,

Sorry for the delay in answering you. My workflow was similar to yours, I had to use Paraview to visually inspect the duplicate points and make the necessary changes.

During the following weeks I will try to revise the Shocker code to solve the duplicate points problem and improve the program with more guides and tutorials.

Best regards,
Lucas