def _do_surface_creation(self, mask, mask_sFormMatrix=None):
if mask_sFormMatrix is None:
mask_sFormMatrix = vtkMatrix4x4()
value = np.mean(mask.GetScalarRange())
# Use the mask to create isosurface
mc = vtkContourFilter()
mc.SetInputData(mask)
mc.SetValue(0, value)
mc.ComputeNormalsOn()
mc.Update()
# Mask isosurface
refSurface = mc.GetOutput()
# Create a uniformly meshed surface
tmpPeel = downsample(refSurface)
# Standard space coordinates
# Apply coordinate transform to the meshed mask
mask_ijk2xyz = vtkTransform()
mask_ijk2xyz.SetMatrix(mask_sFormMatrix)
mask_ijk2xyz_filter = vtkTransformPolyDataFilter()
mask_ijk2xyz_filter.SetInputData(tmpPeel)
mask_ijk2xyz_filter.SetTransform(mask_ijk2xyz)
mask_ijk2xyz_filter.Update()
# Smooth the mesh
tmpPeel = smooth(mask_ijk2xyz_filter.GetOutput())
# Configure calculation of normals
tmpPeel = fixMesh(tmpPeel)
# Remove duplicate points etc
# tmpPeel = cleanMesh(tmpPeel)
# Generate triangles
tmpPeel = upsample(tmpPeel)
tmpPeel = smooth(tmpPeel)
tmpPeel = fixMesh(tmpPeel)
tmpPeel = cleanMesh(tmpPeel)
refImageSpace2_xyz_transform = vtkTransform()
refImageSpace2_xyz_transform.SetMatrix(vtk_utils.numpy_to_vtkMatrix4x4(np.linalg.inv(self.affine)))
self.refImageSpace2_xyz = vtkTransformPolyDataFilter()
self.refImageSpace2_xyz.SetTransform(refImageSpace2_xyz_transform)
xyz2_refImageSpace_transform = vtkTransform()
xyz2_refImageSpace_transform.SetMatrix(vtk_utils.numpy_to_vtkMatrix4x4(self.affine))
self.xyz2_refImageSpace = vtkTransformPolyDataFilter()
self.xyz2_refImageSpace.SetTransform(xyz2_refImageSpace_transform)
currentPeel = tmpPeel
self.currentPeelNo = 0
currentPeel= self.MapImageOnCurrentPeel(currentPeel)
newPeel = vtkPolyData()
newPeel.DeepCopy(currentPeel)
newPeel.DeepCopy(currentPeel)
self.peel_normals = vtkFloatArray()
self.peel_centers = vtkFloatArray()
self.peel.append(newPeel)
self.currentPeelActor = vtkActor()
if not np.all(np.equal(self.affine, np.eye(4))):
affine_vtk = self.CreateTransformedVTKAffine()
self.currentPeelActor.SetUserMatrix(affine_vtk)
self.GetCurrentPeelActor(currentPeel)
self.peelActors.append(self.currentPeelActor)
# locator will later find the triangle on the peel surface where the coil's normal intersect
self.locator = vtkCellLocator()
self.PeelDown(currentPeel)
def CreateSurfaceFromPolydata(self, polydata, overwrite=False, index=None,
name=None, colour=None, transparency=None,
volume=None, area=None, scalar=False):
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(polydata)
normals.SetFeatureAngle(80)
normals.AutoOrientNormalsOn()
normals.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(normals.GetOutput())
if scalar:
mapper.ScalarVisibilityOn()
else:
mapper.ScalarVisibilityOff()
# mapper.ImmediateModeRenderingOn() # improve performance
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetBackfaceCulling(1)
if self.convert2inv:
# convert between invesalius and world space with shift in the Y coordinate
affine = sl.Slice().affine
# TODO: Check that this is needed with the new way of using affine
# now the affine should be at least the identity(4) and never None
if affine is not None:
matrix_shape = sl.Slice().matrix.shape
spacing = sl.Slice().spacing
img_shift = spacing[1] * (matrix_shape[1] - 1)
affine = sl.Slice().affine.copy()
affine[1, -1] -= img_shift
affine_vtk = vtk_utils.numpy_to_vtkMatrix4x4(affine)
actor.SetUserMatrix(affine_vtk)
if overwrite:
if index is None:
index = self.last_surface_index
surface = Surface(index=index)
else:
surface = Surface()
if not colour:
surface.colour = random.choice(const.SURFACE_COLOUR)
else:
surface.colour = colour
surface.polydata = polydata
if transparency:
surface.transparency = transparency
if name:
surface.name = name
# Append surface into Project.surface_dict
proj = prj.Project()
if overwrite:
proj.ChangeSurface(surface)
else:
index = proj.AddSurface(surface)
surface.index = index
self.last_surface_index = index
# Set actor colour and transparency
actor.GetProperty().SetColor(surface.colour)
actor.GetProperty().SetOpacity(1-surface.transparency)
if overwrite and self.actors_dict.keys():
try:
old_actor = self.actors_dict[index]
Publisher.sendMessage('Remove surface actor from viewer', actor=old_actor)
except KeyError:
pass
self.actors_dict[surface.index] = actor
session = ses.Session()
session.ChangeProject()
# The following lines have to be here, otherwise all volumes disappear
if not volume or not area:
triangle_filter = vtk.vtkTriangleFilter()
triangle_filter.SetInputData(polydata)
triangle_filter.Update()
measured_polydata = vtk.vtkMassProperties()
measured_polydata.SetInputConnection(triangle_filter.GetOutputPort())
measured_polydata.Update()
volume = measured_polydata.GetVolume()
area = measured_polydata.GetSurfaceArea()
surface.volume = volume
surface.area = area
print(">>>>", surface.volume)
else:
surface.volume = volume
surface.area = area
self.last_surface_index = surface.index
Publisher.sendMessage('Load surface actor into viewer', actor=actor)
Publisher.sendMessage('Update surface info in GUI', surface=surface)
return surface.index