Write mesh data (cell data) with python - it is not working?

Algorithms
1

Hi guys,
I’m trying to write the mesh data with point and cell data using python (based on C++).
This is my Python codes:

from itk import BinaryMask3DMeshSource

MeshType = itk.Mesh[itk.F, 3]
ImageType = itk.Image[itk.UC, 3]

MeshSourceType = itk.BinaryMask3DMeshSource[ImageType, MeshType]
meshSource = MeshSourceType.New()
meshSource.SetObjectValue(objectValue)
meshSource.SetInput(inputImage)

NodeNum = meshSource.GetNumberOfNodes()
CellNum = meshSource.GetNumberOfCells()
print("\tNodes =", NodeNum)
print("\tCells =", CellNum)

mesh = meshSource.GetOutput()

outputMeshFile = 'a.dat'
OutMesh = open(outputMeshFile, 'w')

points = mesh.GetPoints()
cells = mesh.GetCells()
numCells = mesh.GetNumberOfCells()

#it works for points
for i in range(points.Size()):
    p = points.ElementAt(i)
    OutMesh.write(str(p[0]) + " " + str(p[1]) + " " + str(p[2]) + "\n")
    points.SetElement(i, p)
    
    
for i in range(numCells):
    cell = cells.GetElement(i)
    numPts = cell.GetNumberOfPoints()
    point_ids = cell.GetPointIds()

    line = ""
    for j in range(numPts):
        line += str(point_ids.GetId(j) + 1) + " "
    OutMesh.write(line + "\n")

OutMesh.close()

I got the error like this:

---> 21         line += str(point_ids.GetId(j) + 1) + " "
     22     OutMesh.write(line + "\n")
     25 OutMesh.close()

AttributeError: 'SwigPyObject' object has no attribute 'GetId'

I follow CellIterator from this examplehttps://itk.org/Doxygen/html/Examples_2DataRepresentation_2Mesh_2MeshCellsIteration_8cxx-example.html.
In C++, it is like this:

    while(PointIterator != points->End() )
    {
       PointType p=(PointIterator++).Value();
       OutMesh<<p[0]<<" "<<p[1]<<" "<<p[2]<<std::endl;
    }

    while(cellIterator != end)  
    {
       CellType *cell=cellIterator.Value();

       TriangleType *triangle= dynamic_cast<TriangleType *>(cell);
       TriangleType::PointIdIterator pit=triangle->PointIdsBegin();

       while(pit !=triangle->PointIdsEnd())
	  OutMesh<<(*pit++)+1<<" ";
	  OutMesh<<std::endl;
      ++cellIterator;
    }
    OutMesh.close();

Do you have any idea?

Thank you,

2

@Pranjal_Sahu is there some example or unit test in Python which does this, or something similar?

3

Hi there,

All you need is:

output_mesh = itk.binary_mask3_d_mesh_source(input_image)
itk.meshwrite(output_mesh, args.output_mesh)

Here is a full example:

4

Thanks @matt.mccormick ,
I did the same as you mentioned,

output_mesh = itk.binary_mask3_d_mesh_source(inputImage)
itk.meshwrite(output_mesh,'a.vtk') #cannot write .dat file

It wrote the “a.vtk” mesh file with the information:

# vtk DataFile Version 2.0
File written by itkPolyDataMeshIO
ASCII
DATASET POLYDATA

And it does not include any points and cells.
Could you guide me more?

5

It may be helpful to verify that there is content in the mesh before writing, e.g.:

print(output_mesh.GetNumberOfCells())
print(output_mesh.GetNumberOfPoints())
6

hi @matt.mccormick ,
As you can see from my first post:

MeshSourceType = itk.BinaryMask3DMeshSource[ImageType, MeshType]
meshSource = MeshSourceType.New()
meshSource.SetObjectValue(objectValue)
meshSource.SetInput(inputImage)

NodeNum = meshSource.GetNumberOfNodes()
CellNum = meshSource.GetNumberOfCells()
print("\tNodes =", NodeNum)
print("\tCells =", CellNum)

The output is:

	Nodes = 119740
	Cells = 239488

Thanks,

7

Hi,
I fixed it by following this example:https://github.com/InsightSoftwareConsortium/ITKSphinxExamples/blob/master/src/Core/Mesh/AddPointsAndEdges/Code.py

for i in range(numCells):
    cell = cells.GetElement(i)
    numPts = cell.GetNumberOfPoints()
    point_ids = cell.GetPointIdsContainer()
    for j in range(num_pts):
        line += str(point_ids[j] + 1) + " "
    OutMesh.write(line + "\n")

Thank you =))

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