Making a 3D model in VTK solid instead of hollow inside

Question

I'm trying to create 3D model of the skull using VTK [example]:(https://kitware.github.io/vtk-examples/site/Python/VisualizationAlgorithms/HeadBone/)

#!/usr/bin/env python

# noinspection PyUnresolvedReferences
import vtkmodules.vtkInteractionStyle
# noinspection PyUnresolvedReferences
import vtkmodules.vtkRenderingOpenGL2
from vtkmodules.vtkCommonColor import vtkNamedColors
from vtkmodules.vtkCommonCore import (
    VTK_VERSION_NUMBER,
    vtkVersion
)
from vtkmodules.vtkCommonDataModel import vtkMergePoints
from vtkmodules.vtkFiltersCore import (
    vtkFlyingEdges3D,
    vtkMarchingCubes
)
from vtkmodules.vtkFiltersModeling import vtkOutlineFilter
from vtkmodules.vtkIOImage import vtkMetaImageReader
from vtkmodules.vtkRenderingCore import (
    vtkActor,
    vtkPolyDataMapper,
    vtkRenderWindow,
    vtkRenderWindowInteractor,
    vtkRenderer
)


def main():
    # vtkFlyingEdges3D was introduced in VTK >= 8.2
    use_flying_edges = vtk_version_ok(8, 2, 0)

    file_name = get_program_parameters()

    colors = vtkNamedColors()

    # Create the RenderWindow, Renderer and Interactor.
    ren = vtkRenderer()
    ren_win = vtkRenderWindow()
    ren_win.AddRenderer(ren)
    iren = vtkRenderWindowInteractor()
    iren.SetRenderWindow(ren_win)

    # Create the pipeline.
    reader = vtkMetaImageReader()
    reader.SetFileName(file_name)
    reader.Update()

    locator = vtkMergePoints()
    locator.SetDivisions(64, 64, 92)
    locator.SetNumberOfPointsPerBucket(2)
    locator.AutomaticOff()

    if use_flying_edges:
        try:
            using_marching_cubes = False
            iso = vtkFlyingEdges3D()
        except AttributeError:
            using_marching_cubes = True
            iso = vtkMarchingCubes()
    else:
        using_marching_cubes = True
        iso = vtkMarchingCubes()
    iso.SetInputConnection(reader.GetOutputPort())
    iso.ComputeGradientsOn()
    iso.ComputeScalarsOff()
    iso.SetValue(0, 1150)
    if using_marching_cubes:
        iso.SetLocator(locator)

    iso_mapper = vtkPolyDataMapper()
    iso_mapper.SetInputConnection(iso.GetOutputPort())
    iso_mapper.ScalarVisibilityOff()

    iso_actor = vtkActor()
    iso_actor.SetMapper(iso_mapper)
    iso_actor.GetProperty().SetColor(colors.GetColor3d('Ivory'))

    outline = vtkOutlineFilter()
    outline.SetInputConnection(reader.GetOutputPort())

    outline_mapper = vtkPolyDataMapper()
    outline_mapper.SetInputConnection(outline.GetOutputPort())

    outline_actor = vtkActor()
    outline_actor.SetMapper(outline_mapper)

    # Add the actors to the renderer, set the background and size.
    #
    ren.AddActor(outline_actor)
    ren.AddActor(iso_actor)
    ren.SetBackground(colors.GetColor3d('SlateGray'))
    ren.GetActiveCamera().SetFocalPoint(0, 0, 0)
    ren.GetActiveCamera().SetPosition(0, -1, 0)
    ren.GetActiveCamera().SetViewUp(0, 0, -1)
    ren.ResetCamera()
    ren.GetActiveCamera().Dolly(1.5)
    ren.ResetCameraClippingRange()

    ren_win.SetSize(640, 480)
    ren_win.SetWindowName('HeadBone')

    ren_win.Render()
    iren.Start()


def get_program_parameters():
    import argparse
    description = 'Marching cubes surface of human bone.'
    epilogue = '''
    '''
    parser = argparse.ArgumentParser(description=description, epilog=epilogue,
                                     formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('filename', help='FullHead.mhd.')
    args = parser.parse_args()
    return args.filename


def vtk_version_ok(major, minor, build):
    """
    Check the VTK version.

    :param major: Major version.
    :param minor: Minor version.
    :param build: Build version.
    :return: True if the requested VTK version is greater or equal to the actual VTK version.
    """
    needed_version = 10000000000 * int(major) + 100000000 * int(minor) + int(build)
    try:
        vtk_version_number = VTK_VERSION_NUMBER
    except AttributeError:  # as error:
        ver = vtkVersion()
        vtk_version_number = 10000000000 * ver.GetVTKMajorVersion() + 100000000 * ver.GetVTKMinorVersion() \
                             + ver.GetVTKBuildVersion()
    if vtk_version_number >= needed_version:
        return True
    else:
        return False


if __name__ == '__main__':
    main()

It appears that model works just fine, but there is something that I want to know. The model of the skull works perfectly fine, but the model density is not solid (it hollow inside). It generates only the surface of the model.

I want to know how I can fill the gap in the surface to get the full solid model.

Answer 1

In this example, you are trying to extract the isosurface (hollow) from the data. vtkFlyingEdges3D() and vtkMarchingCubes() algorithms will create contours based on the iso.SetValue(0, 1150) and extract the surface for you. If you want to keep it filled, remove the contouring functions, i'e, vtkFlyingEdges3D() and vtkMarchingCubes() from your script and use some image data mapper instead of vtkPolydataMapper, it will show the entire object.