def vtk_marching_cube_multi(vtkLabel, bg_id, smooth=None, band=None):
"""
Use the VTK marching cube to create isosrufaces for all classes excluding the background
Args:
labels: vtk image contraining the label map
bg_id: id number of background class
smooth: smoothing iteration
Returns:
mesh: vtk PolyData of the surface mesh
"""
from vtk.util.numpy_support import vtk_to_numpy
ids = np.unique(vtk_to_numpy(vtkLabel.GetPointData().GetScalars()))
ids = np.delete(ids, np.where(ids==bg_id))
#smooth the label map
#vtkLabel = utils.gaussianSmoothImage(vtkLabel, 2.)
contour = vtk.vtkDiscreteMarchingCubes()
contour.SetInputData(vtkLabel)
for index, i in enumerate(ids):
print("Setting iso-contour value: ", i)
contour.SetValue(index, i)
contour.Update()
mesh = contour.GetOutput()
if smooth is not None:
if band is not None:
mesh = utils.windowed_sinc_smooth_vtk_polydata(mesh, smooth, band)
else:
mesh = utils.smooth_vtk_polydata(mesh, smooth)
return mesh
def vtk_marching_cube_union(vtkLabel, bg_id, smooth=True):
"""
Use the VTK marching cube to create isosrufaces for all classes excluding the background
Args:
labels: vtk image contraining the label map
bg_id: id number of background class
smooth: whether to smooth
Returns:
model: vtk PolyData of the surface mesh
"""
from vtk.util.numpy_support import vtk_to_numpy
ids = np.unique(vtk_to_numpy(vtkLabel.GetPointData().GetScalars()))
ids = np.delete(ids, np.where(ids==bg_id))
model = vtk.vtkPolyData()
from utils import boolean_vtk_polydata
for index, i in enumerate(ids):
mesh = vtk_marching_cube(vtkLabel, i, False)
if model.GetNumberOfCells()==0:
model.ShallowCopy(mesh)
print("Processing iso-contour value: ", i)
model = boolean_vtk_polydata(model, mesh, 'union')
if smooth:
model = utils.smooth_vtk_polydata(model)
return model
def process_wall(self, la_cutter, la_plane, aa_cutter, aa_plane):
if self.wall_processed:
print("Left ventricle wall has been processed!")
return
# cut with la and aorta cutter:
self.poly = utils.cut_polydata_with_another(self.poly, la_cutter,
la_plane)
self.poly = utils.cut_polydata_with_another(self.poly, aa_cutter,
aa_plane)
#fill small cutting artifacts:
self.poly = utils.fill_hole(self.poly, size=15.)
#improve valve opening geometry
id_lists, boundaries = utils.get_point_ids_on_boundaries(self.poly)
for idx, (ids, boundary) in enumerate(zip(id_lists, boundaries)):
boundary = utils.smooth_vtk_polyline(boundary, 5)
self.poly = utils.project_opening_to_fit_plane(
self.poly, ids, boundary.GetPoints(), self.edge_size)
# Remove the free cells and update the point lists
self.poly, id_lists[idx] = utils.remove_free_cells(
self.poly, [idx for sub_l in id_lists for idx in sub_l])
self.poly = utils.smooth_vtk_polydata(utils.clean_polydata(
self.poly, 0.),
iteration=50)
self.wall_processed = True
return
def vtk_continuous_marching_cube(vtkLabel, tol, smooth=None, band=None):
"""
Use the VTK marching cube implementation to create the surface mesh
Args:
vtkLabel: vtk structured array containing the label map
tol: threshold value for iso-surface
smooth: smoothing iterations
Returns:
mesh: vtk PolyData of the surface mesh
"""
contour = vtk.vtkMarchingCubes()
contour.SetInputData(vtkLabel)
contour.SetValue(0, tol)
contour.Update()
mesh = contour.GetOutput()
if smooth is not None:
if band is not None:
mesh = utils.windowed_sinc_smooth_vtk_polydata(mesh, smooth, band)
else:
mesh = utils.smooth_vtk_polydata(mesh, smooth)
return mesh