[VincentG]

Hi, apologies for the late response, I did not try 64-bit again as 32-bit works fine. Also, all the system search pathes are now set to 32-bit and our project must go on of course, so I’d rather leave it this way. I however found an old CMakeCache.txt file. The only lines involving Qt5Xml are as follows:

//The directory containing a CMake configuration file for Qt5Xml.
Qt5Xml_DIR:PATH=D:/Programs/Qt_5_9_1/5.9.9/msvc2017_64/lib/cmake/Qt5Xml

The path actually exists and I do not see specific error messages in CMakeCache.txt. If you are still interested in the contents of this file then you can download it at https://www.dropbox.com/s/e0h3vv7ld60yrca/CMakeCache.txt

[VincentG]

Switching target to 32-bit seems to workaround the issue. Still I’d like to know why 64-bit target gives these errors. After all, your Windows instructions page uses 64-bit.

[VincentG]

Already solved. By luck, I figured out I could right-click on a node and choose ‘Save Node’, the resulting .scn also contains the vonMisesStress. Happy now 🙂

[VincentG]

Is it possible to export vonMises stress data to a file, or to visualize the vonMises stress in a section view of the model? I am able to rainbow-colorize the tetrahedra, but only see those on the outside of the model (and a bit of the inside through the gaps) which hides the important information. I can view the vonMisesPerNode data, but there is no way to export it to a file as the Export Graph feature is broken, everythime when I click ‘Export’ (also with other models) the console says “[ERROR] [GNodeVisitor] Node is not a GNode.”. And I can use a monitor only for exporting position, velocity and/or force data, not for vonMises stress.

[VincentG]

Thanks, yes I am understanding things better now! It just takes time to climb the steep learning curve. The many hundreds of examples are really helpful, these more than makes up for the missing pieces in the main documentation! Keep up the good work 🙂

[VincentG]

Importing meshes now works. I wrote my own Matlat scripts to export in VTK format with correct field names. Because there were still some errors, I also wrote a script for gmesh export, but this didn’t matter because it turned out that some tetras were too small. Now I can focus on making good quality meshes from DICOM data.

In case anyone else is interested in Matlab to VTK/gmesh export, here is the code:

function saveTetraVtk(filename,nodes,elements)
fileID = fopen(filename,'w');
fprintf(fileID,'# vtk DataFile Version 3.0\n');
fprintf(fileID,'VTK by Vincent\n');
fprintf(fileID,'ASCII\n');
fprintf(fileID,'DATASET UNSTRUCTURED_GRID\n');
fprintf(fileID,'POINTS %d float\n',size(nodes,1));
fprintf(fileID,'%3.3f %3.3f %3.3f\n',nodes');
fprintf(fileID,'\n');
fprintf(fileID,'CELLS %d %d\n',size(elements,1),5*size(elements,1));
fprintf(fileID,'4 %d %d %d %d\n',elements(:,1:4)'-1);
fprintf(fileID,'\n');
fprintf(fileID,'CELL_TYPES %d\n',size(elements,1));
fprintf(fileID,'%d\n',10*ones(size(elements,1),1));
fclose(fileID);
end

function saveTetraMesh(filename,nodes,elements)
% first column is 1..#nodes
nodes(:,2:4)=nodes(:,1:3);
nodes(:,1)=1:size(nodes,1);
elements(:,2:5)=elements(:,1:4);
elements(:,1)=1:size(elements,1);
fileID = fopen(filename,'w');
fprintf(fileID,'$NOD\n');
fprintf(fileID,'%d\n',size(nodes,1));
fprintf(fileID,'%d %3.3f %3.3f %3.3f\n',nodes');
fprintf(fileID,'$ENDNOD\n');
fprintf(fileID,'$ELM\n');
fprintf(fileID,'%d\n',size(elements,1));
fprintf(fileID,'%d 4 1 1 4 %d %d %d %d\n',elements(:,1:5)');
fprintf(fileID,'$ENDELM\n');
fclose(fileID);
end

[VincentG]

I see that the word “POLYGONS” in phantom_volume.vtk makes the file reader think that it is a surface mesh, but the data itself is actually a volumetric mesh. Now I understand why Paraview consistently shows only two faces of each tetrahedra! I’m now trying to get the field names right to get it work…

[VincentG]

Looks like I was a bit too quick. While I can produce VTK output files, I consistently get the error:
[WARNING] [TetrahedralCorotationalFEMForceField] ERROR(TetrahedralCorotationalFEMForceField): object must have a Tetrahedral Set Topology.

Comparing my phantom_volume.vkt file contents with the provided HeartTetra_200k.vtk (which works), I see a lot of differences. Apparently, more information is needed in the output. Any specific documentation on this point? I hope there is still a way to import Matlab-meshed data into SOFA.

######### phantom_volume.vtk #########

# vtk DataFile Version 2.0
VTK from Matlab
ASCII
DATASET POLYDATA
POINTS 591 float
-81.13 92.76 -32.01 -92.76 85.00 -20.98 -81.17 92.33 -32.19
…

POLYGONS 2282 11410
4 422 544 528 79
…

######### HeartTetra_200k.vtk #########

# vtk DataFile Version 3.0
vtk output
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 37923 float
71.0287 51.4427 26.4789 31.9127 65.3531 31.8623 72.5554 39.0259 56.9355
…

CELLS 204841 1024205
4 8170 8171 8172 8173
…

CELL_TYPES 204841
10
…

CELL_DATA 204841
FIELD FieldData 1
Zones 1 204841 int
6 6 6 21 6 21 21 25 7
…

POINT_DATA 37923
FIELD FieldData 1
DTI_Fibres 3 37923 double
0.204005 -0.779598 0.592123
…

[VincentG]

Thanks for the quick reply! I found a VTK export module (vtkwrite) for Matlab, which can write the iso2mesh data arrays to a VTK file. This seems to work fine.

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