def fill_holes(self, hole_size=10.0):
print('filling holes')
filling_filter = vtk.vtkFillHolesFilter()
filling_filter.SetInputConnection(self.mesh.GetOutputPort())
filling_filter.SetHoleSize(hole_size)
filling_filter.Update()
self.mesh = filling_filter
def FillHoles(self, hole_size, inplace=True):
"""
Fill holes in a vtkInterface.PolyData or vtk.vtkPolyData object.
Holes are identified by locating boundary edges, linking them together
into loops, and then triangulating the resulting loops. Note that you
can specify an approximate limit to the size of the hole that can be
filled.
Parameters
----------
hole_size : float
Specifies the maximum hole size to fill. This is represented as a
radius to the bounding circumsphere containing the hole. Note that
this is an approximate area; the actual area cannot be computed
without first triangulating the hole.
inplace : bool, optional
Updates mesh in-place while returning nothing.
Returns
-------
mesh : vtkInterface.PolyData
Mesh with holes filled. None when inplace=True
"""
fill = vtk.vtkFillHolesFilter()
fill.SetHoleSize(hole_size)
fill.SetInputData(self)
fill.Update()
if inplace:
self.OverwriteMesh(fill.GetOutput())
else:
return PolyData(fill.GetOutput())
def make_mesh_watertight(self, hole_size=None, filename=None, write=True):
"""This method reads a ply mesh from an external file and converts it into a watertight mesh
"""
self.to_ply(filename="temp.ply")
logger.info(f"Making the mesh read from {filename} watertight")
reader = vtk.vtkPLYReader()
if filename is None:
filename = Path.cwd() / "output/temp.ply"
reader.SetFileName(str(filename))
reader.Update()
polydata = reader.GetOutput()
fill = vtk.vtkFillHolesFilter()
fill.SetInputData(polydata)
hole_size = hole_size if hole_size else config.stl_from_point_cloud.watertight_mesh.hole_size if config.stl_from_point_cloud.watertight_mesh.hole_size else 1.0
fill.SetHoleSize(hole_size)
fill.Update()
self.vtk_filled = fill.GetOutput()
if write:
writer = vtk.vtkPLYWriter()
writer.SetInputData(self.vtk_filled)
writer.SetFileName(f"temp-watertight.ply")
writer.Write()
self.stl_mesh = o3d.io.read_triangle_mesh("temp-watertight.ply")
print(self.stl_mesh)
# Path.unlink(Path("temp-watertight.ply"))
# Path.unlink(filename)
return fill.GetOutput()
def fillholes(polydata,size):
filler = vtk.vtkFillHolesFilter()
filler.SetInputData(polydata)
filler.SetHoleSize(size)
filler.Update()
return filler.GetOutput()
def fillholes(surface, holesize=1000):
"""Fill holes in surface. Use holesize to specify the max 'radius' of the
holes to be filled."""
filler = vtk.vtkFillHolesFilter()
filler.SetInput(surface)
filler.SetHoleSize(holesize)
filler.Update()
return filler.GetOutput()
def fillholes(surface, holesize=1000):
"""Fill holes in surface. Use holesize to specify the max 'radius' of the
holes to be filled."""
filler = vtk.vtkFillHolesFilter()
filler.SetInput(surface)
filler.SetHoleSize(holesize)
filler.Update()
return filler.GetOutput()
def FillSurfaceHole(polydata):
"""
Fill holes in the given polydata.
"""
# Filter used to detect and fill holes. Only fill
print "Filling polydata"
filled_polydata = vtk.vtkFillHolesFilter()
filled_polydata.SetInputData(polydata)
filled_polydata.SetHoleSize(500)
return filled_polydata.GetOutput()
def refineBreastPolyData(self, polyData, holeSize):
holeFiller = vtk.vtkFillHolesFilter()
holeFiller.SetInputData(polyData)
holeFiller.SetHoleSize(holeSize)
holeFiller.Update()
normalFilter = vtk.vtkPolyDataNormals()
normalFilter.SetInputConnection(holeFiller.GetOutputPort())
normalFilter.ComputePointNormalsOn()
normalFilter.SplittingOff()
normalFilter.Update()
return normalFilter.GetOutput()
def fillHoles(actor, size=None, legend=None): # not tested properly
fh = vtk.vtkFillHolesFilter()
if not size:
mb = maxBoundSize(actor)
size = mb / 20
fh.SetHoleSize(size)
poly = polydata(actor)
setInput(fh, poly)
fh.Update()
fpoly = fh.GetOutput()
factor = makeActor(fpoly, legend=legend)
factor.SetProperty(actor.GetProperty())
return factor
def fillHoles(inputModel, outputModel, maximumHoleSize=1000.0):
"""Fills up a hole in a open mesh.
"""
fill = vtk.vtkFillHolesFilter()
fill.SetInputData(inputModel.GetPolyData())
fill.SetHoleSize(maximumHoleSize)
# Need to auto-orient normals, otherwise holes could appear to be unfilled when
# only front-facing elements are chosen to be visible.
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(fill.GetOutputPort())
normals.SetAutoOrientNormals(True)
normals.Update()
outputModel.SetAndObservePolyData(normals.GetOutput())
def wrapOpImp(self):
fill = vtk.vtkFillHolesFilter();
fill.SetInputData(self.data);
fill.Update()
"""
consistenNormal = vtk.vtkPolyDataNormals();
consistenNormal.ConsistencyOn();
consistenNormal.SplittingOff();
consistenNormal.SetInputConnection(fill.GetOutputPort());
consistenNormal.Update();
output = consistenNormal.GetOutput();
output.GetPointData().SetNormals(self.data.GetPointData().GetNormals());
"""
output = fill.GetOutput();
return output;
def fill_hole(poly, size=10000000.):
"""
Fill holes in VTK PolyData
Args:
poly: VTK PolyData to fill
size: max size of the hole to fill
Returns:
poly: filled VTK PolyData
"""
filler = vtk.vtkFillHolesFilter()
filler.SetInputData(poly)
filler.SetHoleSize(size)
filler.Update()
return filler.GetOutput()
def _build_vtkcontours(self):
# fill holes
filledHoles = vtk.vtkFillHolesFilter()
filledHoles.SetInputData(self._mesh.vtk_obj)
filledHoles.SetHoleSize(1000)
filledHoles.Update()
filledHolesOutput = filledHoles.GetOutput()
# first generate normals
self._normals = vtk.vtkPolyDataNormals()
self._normals.SetInputData(filledHolesOutput)
self._normals.Update()
cut_meshes = dict()
for d in self._axes:
"""
:TODO: parallelise
"""
# the configure the cutter
self._cutter = vtk.vtkCutter()
self._cutter.SetInputConnection(self._normals.GetOutputPort())
self._cutter.SetCutFunction(self.__getattribute__('%s_plane' % d))
# determine the number of z-contours to generate from the bounds
d_max = math.floor(self.__getattribute__('%smax' % d.upper()))
d_count = int(2 * d_max + 1)
# generate the cuts on the mesh
self._cutter.GenerateValues(d_count, -d_max, d_max)
# pass through vtk.vtkStripper to ensure we have triangel strips
self._stripper = vtk.vtkStripper()
self._stripper.SetInputConnection(self._cutter.GetOutputPort())
self._stripper.Update()
# the actual cuts
colour = self._mesh.colour
args = self._mesh.vtk_args
cut_meshes[d] = VTKMesh(colour, args)
stripper_output = self._stripper.GetOutput()
cut_meshes[d].vtk_obj.SetPoints(stripper_output.GetPoints())
cut_meshes[d].vtk_obj.SetPolys(stripper_output.GetLines())
return cut_meshes
#fill_holes.SetInputConnection(subdivide.GetOutputPort())
#fill_holes.SetHoleSize(1000.0);
#fill_holes.Update()
triangle = vtk.vtkTriangleFilter()
triangle.SetInputConnection(subdivide.GetOutputPort())
triangle.PassLinesOff()
triangle.PassVertsOff()
triangle.Update()
if (vmtk_avail):
#creates round outlet region caps
capper = vtkvmtk.vtkvmtkSmoothCapPolyData()
capper.SetInputConnection(triangle.GetOutputPort())
capper.SetConstraintFactor(1.0)
capper.SetNumberOfRings(8)
else:
capper = vtk.vtkFillHolesFilter()
capper.SetInputConnection(triangle.GetOutputPort())
capper.SetHoleSize(1000.0)
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputConnection(capper.GetOutputPort())
cleaner.Update()
n_cells = cleaner.GetOutput().GetNumberOfCells()
print("surface cells", n_cells)
# Setup the colors array
colors = vtk.vtkIntArray()
colors.SetNumberOfComponents(1)
colors.SetNumberOfValues(n_cells)
colors.SetName("RegionId")
cellId = i - 1 + yRes * (j - 1)
if (cellId != 48 and cellId != 12 and cellId != 13 and cellId != 23
and cellId != 60 and cellId != 83 and cellId != 72
and cellId != 76 and cellId != 77 and cellId != 78
and cellId != 87):
polys.InsertNextCell(4)
polys.InsertCellPoint(i - 1 + ((j - 1) * yPtsRes))
polys.InsertCellPoint(i + ((j - 1) * yPtsRes))
polys.InsertCellPoint(i + (j * yPtsRes))
polys.InsertCellPoint(i - 1 + (j * yPtsRes))
pass
i += 1
j += 1
# Fill the holes
fill = vtk.vtkFillHolesFilter()
fill.SetInputData(pd)
fill.SetHoleSize(20.0)
# Mapping and actor
map = vtk.vtkPolyDataMapper()
# map SetInput pd
map.SetInputConnection(fill.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(map)
actor.GetProperty().SetColor(1, 0, 0)
# Add the actors to the renderer, set the background and size
#
ren1.AddActor(actor)
def join_process_surface(filenames, algorithm, smooth_iterations,
smooth_relaxation_factor, decimate_reduction,
keep_largest, fill_holes, options, msg_queue):
def send_message(msg):
try:
msg_queue.put_nowait(msg)
except queue.Full as e:
print(e)
send_message('Joining surfaces ...')
polydata_append = vtk.vtkAppendPolyData()
for f in filenames:
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(f)
reader.Update()
polydata = reader.GetOutput()
polydata_append.AddInputData(polydata)
del reader
del polydata
polydata_append.Update()
# polydata_append.GetOutput().ReleaseDataFlagOn()
polydata = polydata_append.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del polydata_append
send_message('Cleaning surface ...')
clean = vtk.vtkCleanPolyData()
# clean.ReleaseDataFlagOn()
# clean.GetOutput().ReleaseDataFlagOn()
clean_ref = weakref.ref(clean)
# clean_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(clean_ref(), _("Creating 3D surface...")))
clean.SetInputData(polydata)
clean.PointMergingOn()
clean.Update()
del polydata
polydata = clean.GetOutput()
# polydata.SetSource(None)
del clean
if algorithm == 'ca_smoothing':
send_message('Calculating normals ...')
normals = vtk.vtkPolyDataNormals()
normals_ref = weakref.ref(normals)
# normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(normals_ref(), _("Creating 3D surface...")))
normals.SetInputData(polydata)
# normals.ReleaseDataFlagOn()
#normals.SetFeatureAngle(80)
#normals.AutoOrientNormalsOn()
normals.ComputeCellNormalsOn()
# normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
del polydata
polydata = normals.GetOutput()
# polydata.SetSource(None)
del normals
clean = vtk.vtkCleanPolyData()
# clean.ReleaseDataFlagOn()
# clean.GetOutput().ReleaseDataFlagOn()
clean_ref = weakref.ref(clean)
# clean_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(clean_ref(), _("Creating 3D surface...")))
clean.SetInputData(polydata)
clean.PointMergingOn()
clean.Update()
del polydata
polydata = clean.GetOutput()
# polydata.SetSource(None)
del clean
# try:
# polydata.BuildLinks()
# except TypeError:
# polydata.BuildLinks(0)
# polydata = ca_smoothing.ca_smoothing(polydata, options['angle'],
# options['max distance'],
# options['min weight'],
# options['steps'])
send_message('Context Aware smoothing ...')
mesh = cy_mesh.Mesh(polydata)
cy_mesh.ca_smoothing(mesh, options['angle'], options['max distance'],
options['min weight'], options['steps'])
# polydata = mesh.to_vtk()
# polydata.SetSource(None)
# polydata.DebugOn()
else:
#smoother = vtk.vtkWindowedSincPolyDataFilter()
send_message('Smoothing ...')
smoother = vtk.vtkSmoothPolyDataFilter()
smoother_ref = weakref.ref(smoother)
# smoother_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(smoother_ref(), _("Creating 3D surface...")))
smoother.SetInputData(polydata)
smoother.SetNumberOfIterations(smooth_iterations)
smoother.SetRelaxationFactor(smooth_relaxation_factor)
smoother.SetFeatureAngle(80)
#smoother.SetEdgeAngle(90.0)
#smoother.SetPassBand(0.1)
smoother.BoundarySmoothingOn()
smoother.FeatureEdgeSmoothingOn()
#smoother.NormalizeCoordinatesOn()
#smoother.NonManifoldSmoothingOn()
# smoother.ReleaseDataFlagOn()
# smoother.GetOutput().ReleaseDataFlagOn()
smoother.Update()
del polydata
polydata = smoother.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del smoother
if decimate_reduction:
print("Decimating", decimate_reduction)
send_message('Decimating ...')
decimation = vtk.vtkQuadricDecimation()
# decimation.ReleaseDataFlagOn()
decimation.SetInputData(polydata)
decimation.SetTargetReduction(decimate_reduction)
decimation_ref = weakref.ref(decimation)
# decimation_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(decimation_ref(), _("Creating 3D surface...")))
#decimation.PreserveTopologyOn()
#decimation.SplittingOff()
#decimation.BoundaryVertexDeletionOff()
# decimation.GetOutput().ReleaseDataFlagOn()
decimation.Update()
del polydata
polydata = decimation.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del decimation
#to_measure.Register(None)
# to_measure.SetSource(None)
if keep_largest:
send_message('Finding the largest ...')
conn = vtk.vtkPolyDataConnectivityFilter()
conn.SetInputData(polydata)
conn.SetExtractionModeToLargestRegion()
conn_ref = weakref.ref(conn)
# conn_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(conn_ref(), _("Creating 3D surface...")))
conn.Update()
# conn.GetOutput().ReleaseDataFlagOn()
del polydata
polydata = conn.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del conn
#Filter used to detect and fill holes. Only fill boundary edges holes.
#TODO: Hey! This piece of code is the same from
#polydata_utils.FillSurfaceHole, we need to review this.
if fill_holes:
send_message('Filling holes ...')
filled_polydata = vtk.vtkFillHolesFilter()
# filled_polydata.ReleaseDataFlagOn()
filled_polydata.SetInputData(polydata)
filled_polydata.SetHoleSize(300)
filled_polydata_ref = weakref.ref(filled_polydata)
# filled_polydata_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(filled_polydata_ref(), _("Creating 3D surface...")))
filled_polydata.Update()
# filled_polydata.GetOutput().ReleaseDataFlagOn()
del polydata
polydata = filled_polydata.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
# polydata.DebugOn()
del filled_polydata
to_measure = polydata
normals = vtk.vtkPolyDataNormals()
# normals.ReleaseDataFlagOn()
# normals_ref = weakref.ref(normals)
# normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(normals_ref(), _("Creating 3D surface...")))
normals.SetInputData(polydata)
# normals.SetFeatureAngle(80)
# normals.SplittingOff()
# normals.AutoOrientNormalsOn()
# normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
del polydata
polydata = normals.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del normals
# Improve performance
stripper = vtk.vtkStripper()
# stripper.ReleaseDataFlagOn()
# stripper_ref = weakref.ref(stripper)
# stripper_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(stripper_ref(), _("Creating 3D surface...")))
stripper.SetInputData(polydata)
stripper.PassThroughCellIdsOn()
stripper.PassThroughPointIdsOn()
# stripper.GetOutput().ReleaseDataFlagOn()
stripper.Update()
del polydata
polydata = stripper.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del stripper
send_message('Calculating area and volume ...')
measured_polydata = vtk.vtkMassProperties()
measured_polydata.SetInputData(to_measure)
measured_polydata.Update()
volume = float(measured_polydata.GetVolume())
area = float(measured_polydata.GetSurfaceArea())
del measured_polydata
filename = tempfile.mktemp(suffix='_full.vtp')
writer = vtk.vtkXMLPolyDataWriter()
writer.SetInputData(polydata)
writer.SetFileName(filename)
writer.Write()
del writer
print("MY PID", os.getpid())
return filename, {'volume': volume, 'area': area}
def AddNewActor(self, slice_, mask, surface_parameters):
"""
Create surface actor, save into project and send it to viewer.
"""
matrix = slice_.matrix
filename_img = slice_.matrix_filename
spacing = slice_.spacing
algorithm = surface_parameters['method']['algorithm']
options = surface_parameters['method']['options']
surface_name = surface_parameters['options']['name']
quality = surface_parameters['options']['quality']
fill_holes = surface_parameters['options']['fill']
keep_largest = surface_parameters['options']['keep_largest']
mode = 'CONTOUR' # 'GRAYSCALE'
min_value, max_value = mask.threshold_range
colour = mask.colour[:3]
try:
overwrite = surface_parameters['options']['overwrite']
except KeyError:
overwrite = False
mask.matrix.flush()
if quality in const.SURFACE_QUALITY.keys():
imagedata_resolution = const.SURFACE_QUALITY[quality][0]
smooth_iterations = const.SURFACE_QUALITY[quality][1]
smooth_relaxation_factor = const.SURFACE_QUALITY[quality][2]
decimate_reduction = const.SURFACE_QUALITY[quality][3]
#if imagedata_resolution:
#imagedata = iu.ResampleImage3D(imagedata, imagedata_resolution)
pipeline_size = 4
if decimate_reduction:
pipeline_size += 1
if (smooth_iterations and smooth_relaxation_factor):
pipeline_size += 1
if fill_holes:
pipeline_size += 1
if keep_largest:
pipeline_size += 1
## Update progress value in GUI
UpdateProgress = vu.ShowProgress(pipeline_size)
UpdateProgress(0, _("Creating 3D surface..."))
language = ses.Session().language
if (prj.Project().original_orientation == const.CORONAL):
flip_image = False
else:
flip_image = True
n_processors = multiprocessing.cpu_count()
pipe_in, pipe_out = multiprocessing.Pipe()
o_piece = 1
piece_size = 2000
n_pieces = int(round(matrix.shape[0] / piece_size + 0.5, 0))
q_in = multiprocessing.Queue()
q_out = multiprocessing.Queue()
p = []
for i in range(n_processors):
sp = surface_process.SurfaceProcess(
pipe_in, filename_img, matrix.shape, matrix.dtype,
mask.temp_file, mask.matrix.shape, mask.matrix.dtype, spacing,
mode, min_value, max_value, decimate_reduction,
smooth_relaxation_factor, smooth_iterations, language,
flip_image, q_in, q_out, algorithm != 'Default', algorithm,
imagedata_resolution)
p.append(sp)
sp.start()
for i in range(n_pieces):
init = i * piece_size
end = init + piece_size + o_piece
roi = slice(init, end)
q_in.put(roi)
print("new_piece", roi)
for i in p:
q_in.put(None)
none_count = 1
while 1:
msg = pipe_out.recv()
if (msg is None):
none_count += 1
else:
UpdateProgress(msg[0] / (n_pieces * pipeline_size), msg[1])
if none_count > n_pieces:
break
polydata_append = vtk.vtkAppendPolyData()
# polydata_append.ReleaseDataFlagOn()
t = n_pieces
while t:
filename_polydata = q_out.get()
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(filename_polydata)
# reader.ReleaseDataFlagOn()
reader.Update()
# reader.GetOutput().ReleaseDataFlagOn()
polydata = reader.GetOutput()
# polydata.SetSource(None)
polydata_append.AddInputData(polydata)
del reader
del polydata
t -= 1
polydata_append.Update()
# polydata_append.GetOutput().ReleaseDataFlagOn()
polydata = polydata_append.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del polydata_append
if algorithm == 'ca_smoothing':
normals = vtk.vtkPolyDataNormals()
normals_ref = weakref.ref(normals)
normals_ref().AddObserver(
"ProgressEvent", lambda obj, evt: UpdateProgress(
normals_ref(), _("Creating 3D surface...")))
normals.SetInputData(polydata)
# normals.ReleaseDataFlagOn()
#normals.SetFeatureAngle(80)
#normals.AutoOrientNormalsOn()
normals.ComputeCellNormalsOn()
# normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
del polydata
polydata = normals.GetOutput()
# polydata.SetSource(None)
del normals
clean = vtk.vtkCleanPolyData()
# clean.ReleaseDataFlagOn()
# clean.GetOutput().ReleaseDataFlagOn()
clean_ref = weakref.ref(clean)
clean_ref().AddObserver(
"ProgressEvent", lambda obj, evt: UpdateProgress(
clean_ref(), _("Creating 3D surface...")))
clean.SetInputData(polydata)
clean.PointMergingOn()
clean.Update()
del polydata
polydata = clean.GetOutput()
# polydata.SetSource(None)
del clean
# try:
# polydata.BuildLinks()
# except TypeError:
# polydata.BuildLinks(0)
# polydata = ca_smoothing.ca_smoothing(polydata, options['angle'],
# options['max distance'],
# options['min weight'],
# options['steps'])
mesh = cy_mesh.Mesh(polydata)
cy_mesh.ca_smoothing(mesh, options['angle'],
options['max distance'],
options['min weight'], options['steps'])
# polydata = mesh.to_vtk()
# polydata.SetSource(None)
# polydata.DebugOn()
else:
#smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother = vtk.vtkSmoothPolyDataFilter()
smoother_ref = weakref.ref(smoother)
smoother_ref().AddObserver(
"ProgressEvent", lambda obj, evt: UpdateProgress(
smoother_ref(), _("Creating 3D surface...")))
smoother.SetInputData(polydata)
smoother.SetNumberOfIterations(smooth_iterations)
smoother.SetRelaxationFactor(smooth_relaxation_factor)
smoother.SetFeatureAngle(80)
#smoother.SetEdgeAngle(90.0)
#smoother.SetPassBand(0.1)
smoother.BoundarySmoothingOn()
smoother.FeatureEdgeSmoothingOn()
#smoother.NormalizeCoordinatesOn()
#smoother.NonManifoldSmoothingOn()
# smoother.ReleaseDataFlagOn()
# smoother.GetOutput().ReleaseDataFlagOn()
smoother.Update()
del polydata
polydata = smoother.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del smoother
if decimate_reduction:
print("Decimating", decimate_reduction)
decimation = vtk.vtkQuadricDecimation()
# decimation.ReleaseDataFlagOn()
decimation.SetInputData(polydata)
decimation.SetTargetReduction(decimate_reduction)
decimation_ref = weakref.ref(decimation)
decimation_ref().AddObserver(
"ProgressEvent", lambda obj, evt: UpdateProgress(
decimation_ref(), _("Creating 3D surface...")))
#decimation.PreserveTopologyOn()
#decimation.SplittingOff()
#decimation.BoundaryVertexDeletionOff()
# decimation.GetOutput().ReleaseDataFlagOn()
decimation.Update()
del polydata
polydata = decimation.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del decimation
#to_measure.Register(None)
# to_measure.SetSource(None)
if keep_largest:
conn = vtk.vtkPolyDataConnectivityFilter()
conn.SetInputData(polydata)
conn.SetExtractionModeToLargestRegion()
conn_ref = weakref.ref(conn)
conn_ref().AddObserver(
"ProgressEvent", lambda obj, evt: UpdateProgress(
conn_ref(), _("Creating 3D surface...")))
conn.Update()
# conn.GetOutput().ReleaseDataFlagOn()
del polydata
polydata = conn.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del conn
#Filter used to detect and fill holes. Only fill boundary edges holes.
#TODO: Hey! This piece of code is the same from
#polydata_utils.FillSurfaceHole, we need to review this.
if fill_holes:
filled_polydata = vtk.vtkFillHolesFilter()
# filled_polydata.ReleaseDataFlagOn()
filled_polydata.SetInputData(polydata)
filled_polydata.SetHoleSize(300)
filled_polydata_ref = weakref.ref(filled_polydata)
filled_polydata_ref().AddObserver(
"ProgressEvent", lambda obj, evt: UpdateProgress(
filled_polydata_ref(), _("Creating 3D surface...")))
filled_polydata.Update()
# filled_polydata.GetOutput().ReleaseDataFlagOn()
del polydata
polydata = filled_polydata.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
# polydata.DebugOn()
del filled_polydata
to_measure = polydata
# If InVesalius is running without GUI
if wx.GetApp() is None:
proj = prj.Project()
#Create Surface instance
if overwrite:
surface = Surface(index=self.last_surface_index)
proj.ChangeSurface(surface)
else:
surface = Surface(name=surface_name)
index = proj.AddSurface(surface)
surface.index = index
self.last_surface_index = index
surface.colour = colour
surface.polydata = polydata
# With GUI
else:
normals = vtk.vtkPolyDataNormals()
# normals.ReleaseDataFlagOn()
normals_ref = weakref.ref(normals)
normals_ref().AddObserver(
"ProgressEvent", lambda obj, evt: UpdateProgress(
normals_ref(), _("Creating 3D surface...")))
normals.SetInputData(polydata)
normals.SetFeatureAngle(80)
normals.AutoOrientNormalsOn()
# normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
del polydata
polydata = normals.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del normals
# Improve performance
stripper = vtk.vtkStripper()
# stripper.ReleaseDataFlagOn()
stripper_ref = weakref.ref(stripper)
stripper_ref().AddObserver(
"ProgressEvent", lambda obj, evt: UpdateProgress(
stripper_ref(), _("Creating 3D surface...")))
stripper.SetInputData(polydata)
stripper.PassThroughCellIdsOn()
stripper.PassThroughPointIdsOn()
# stripper.GetOutput().ReleaseDataFlagOn()
stripper.Update()
del polydata
polydata = stripper.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del stripper
# Map polygonal data (vtkPolyData) to graphics primitives.
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(polydata)
mapper.ScalarVisibilityOff()
# mapper.ReleaseDataFlagOn()
mapper.ImmediateModeRenderingOn() # improve performance
# Represent an object (geometry & properties) in the rendered scene
actor = vtk.vtkActor()
actor.SetMapper(mapper)
del mapper
#Create Surface instance
if overwrite:
surface = Surface(index=self.last_surface_index)
else:
surface = Surface(name=surface_name)
surface.colour = colour
surface.polydata = polydata
del polydata
# Set actor colour and transparency
actor.GetProperty().SetColor(colour)
actor.GetProperty().SetOpacity(1 - surface.transparency)
prop = actor.GetProperty()
interpolation = int(ses.Session().surface_interpolation)
prop.SetInterpolation(interpolation)
proj = prj.Project()
if overwrite:
proj.ChangeSurface(surface)
else:
index = proj.AddSurface(surface)
surface.index = index
self.last_surface_index = index
session = ses.Session()
session.ChangeProject()
measured_polydata = vtk.vtkMassProperties()
# measured_polydata.ReleaseDataFlagOn()
measured_polydata.SetInputData(to_measure)
volume = float(measured_polydata.GetVolume())
area = float(measured_polydata.GetSurfaceArea())
surface.volume = volume
surface.area = area
self.last_surface_index = surface.index
del measured_polydata
del to_measure
Publisher.sendMessage('Load surface actor into viewer',
actor=actor)
# Send actor by pubsub to viewer's render
if overwrite and self.actors_dict.keys():
old_actor = self.actors_dict[self.last_surface_index]
Publisher.sendMessage('Remove surface actor from viewer',
actor=old_actor)
# Save actor for future management tasks
self.actors_dict[surface.index] = actor
Publisher.sendMessage('Update surface info in GUI',
surface=surface)
#When you finalize the progress. The bar is cleaned.
UpdateProgress = vu.ShowProgress(1)
UpdateProgress(0, _("Ready"))
Publisher.sendMessage('Update status text in GUI',
label=_("Ready"))
Publisher.sendMessage('End busy cursor')
del actor
def AddNewActor(self, pubsub_evt):
"""
Create surface actor, save into project and send it to viewer.
"""
slice_, mask, surface_parameters = pubsub_evt.data
matrix = slice_.matrix
filename_img = slice_.matrix_filename
spacing = slice_.spacing
algorithm = surface_parameters['method']['algorithm']
options = surface_parameters['method']['options']
surface_name = surface_parameters['options']['name']
quality = surface_parameters['options']['quality']
fill_holes = surface_parameters['options']['fill']
keep_largest = surface_parameters['options']['keep_largest']
mode = 'CONTOUR' # 'GRAYSCALE'
min_value, max_value = mask.threshold_range
colour = mask.colour
try:
overwrite = surface_parameters['options']['overwrite']
except KeyError:
overwrite = False
mask.matrix.flush()
if quality in const.SURFACE_QUALITY.keys():
imagedata_resolution = const.SURFACE_QUALITY[quality][0]
smooth_iterations = const.SURFACE_QUALITY[quality][1]
smooth_relaxation_factor = const.SURFACE_QUALITY[quality][2]
decimate_reduction = const.SURFACE_QUALITY[quality][3]
#if imagedata_resolution:
#imagedata = iu.ResampleImage3D(imagedata, imagedata_resolution)
pipeline_size = 4
if decimate_reduction:
pipeline_size += 1
if (smooth_iterations and smooth_relaxation_factor):
pipeline_size += 1
if fill_holes:
pipeline_size += 1
if keep_largest:
pipeline_size += 1
## Update progress value in GUI
UpdateProgress = vu.ShowProgress(pipeline_size)
UpdateProgress(0, _("Creating 3D surface..."))
language = ses.Session().language
if (prj.Project().original_orientation == const.CORONAL):
flip_image = False
else:
flip_image = True
n_processors = multiprocessing.cpu_count()
pipe_in, pipe_out = multiprocessing.Pipe()
o_piece = 1
piece_size = 2000
n_pieces = int(round(matrix.shape[0] / piece_size + 0.5, 0))
q_in = multiprocessing.Queue()
q_out = multiprocessing.Queue()
p = []
for i in xrange(n_processors):
sp = surface_process.SurfaceProcess(pipe_in, filename_img,
matrix.shape, matrix.dtype,
mask.temp_file,
mask.matrix.shape,
mask.matrix.dtype,
spacing,
mode, min_value, max_value,
decimate_reduction,
smooth_relaxation_factor,
smooth_iterations, language,
flip_image, q_in, q_out,
algorithm != 'Default',
algorithm,
imagedata_resolution)
p.append(sp)
sp.start()
for i in xrange(n_pieces):
init = i * piece_size
end = init + piece_size + o_piece
roi = slice(init, end)
q_in.put(roi)
print "new_piece", roi
for i in p:
q_in.put(None)
none_count = 1
while 1:
msg = pipe_out.recv()
if(msg is None):
none_count += 1
else:
UpdateProgress(msg[0]/(n_pieces * pipeline_size), msg[1])
if none_count > n_pieces:
break
polydata_append = vtk.vtkAppendPolyData()
polydata_append.ReleaseDataFlagOn()
t = n_pieces
while t:
filename_polydata = q_out.get()
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(filename_polydata)
reader.ReleaseDataFlagOn()
reader.Update()
reader.GetOutput().ReleaseDataFlagOn()
polydata = reader.GetOutput()
polydata.SetSource(None)
polydata_append.AddInput(polydata)
del reader
del polydata
t -= 1
polydata_append.Update()
polydata_append.GetOutput().ReleaseDataFlagOn()
polydata = polydata_append.GetOutput()
#polydata.Register(None)
polydata.SetSource(None)
del polydata_append
if algorithm == 'ca_smoothing':
normals = vtk.vtkPolyDataNormals()
normals_ref = weakref.ref(normals)
normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
UpdateProgress(normals_ref(), _("Creating 3D surface...")))
normals.SetInput(polydata)
normals.ReleaseDataFlagOn()
#normals.SetFeatureAngle(80)
#normals.AutoOrientNormalsOn()
normals.ComputeCellNormalsOn()
normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
del polydata
polydata = normals.GetOutput()
polydata.SetSource(None)
del normals
clean = vtk.vtkCleanPolyData()
clean.ReleaseDataFlagOn()
clean.GetOutput().ReleaseDataFlagOn()
clean_ref = weakref.ref(clean)
clean_ref().AddObserver("ProgressEvent", lambda obj,evt:
UpdateProgress(clean_ref(), _("Creating 3D surface...")))
clean.SetInput(polydata)
clean.PointMergingOn()
clean.Update()
del polydata
polydata = clean.GetOutput()
polydata.SetSource(None)
del clean
try:
polydata.BuildLinks()
except TypeError:
polydata.BuildLinks(0)
polydata = ca_smoothing.ca_smoothing(polydata, options['angle'],
options['max distance'],
options['min weight'],
options['steps'])
polydata.SetSource(None)
polydata.DebugOn()
else:
#smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother = vtk.vtkSmoothPolyDataFilter()
smoother_ref = weakref.ref(smoother)
smoother_ref().AddObserver("ProgressEvent", lambda obj,evt:
UpdateProgress(smoother_ref(), _("Creating 3D surface...")))
smoother.SetInput(polydata)
smoother.SetNumberOfIterations(smooth_iterations)
smoother.SetRelaxationFactor(smooth_relaxation_factor)
smoother.SetFeatureAngle(80)
#smoother.SetEdgeAngle(90.0)
#smoother.SetPassBand(0.1)
smoother.BoundarySmoothingOn()
smoother.FeatureEdgeSmoothingOn()
#smoother.NormalizeCoordinatesOn()
#smoother.NonManifoldSmoothingOn()
smoother.ReleaseDataFlagOn()
smoother.GetOutput().ReleaseDataFlagOn()
smoother.Update()
del polydata
polydata = smoother.GetOutput()
#polydata.Register(None)
polydata.SetSource(None)
del smoother
if decimate_reduction:
print "Decimating", decimate_reduction
decimation = vtk.vtkQuadricDecimation()
decimation.ReleaseDataFlagOn()
decimation.SetInput(polydata)
decimation.SetTargetReduction(decimate_reduction)
decimation_ref = weakref.ref(decimation)
decimation_ref().AddObserver("ProgressEvent", lambda obj,evt:
UpdateProgress(decimation_ref(), _("Creating 3D surface...")))
#decimation.PreserveTopologyOn()
#decimation.SplittingOff()
#decimation.BoundaryVertexDeletionOff()
decimation.GetOutput().ReleaseDataFlagOn()
decimation.Update()
del polydata
polydata = decimation.GetOutput()
#polydata.Register(None)
polydata.SetSource(None)
del decimation
to_measure = polydata
#to_measure.Register(None)
to_measure.SetSource(None)
if keep_largest:
conn = vtk.vtkPolyDataConnectivityFilter()
conn.SetInput(polydata)
conn.SetExtractionModeToLargestRegion()
conn_ref = weakref.ref(conn)
conn_ref().AddObserver("ProgressEvent", lambda obj,evt:
UpdateProgress(conn_ref(), _("Creating 3D surface...")))
conn.Update()
conn.GetOutput().ReleaseDataFlagOn()
del polydata
polydata = conn.GetOutput()
#polydata.Register(None)
polydata.SetSource(None)
del conn
#Filter used to detect and fill holes. Only fill boundary edges holes.
#TODO: Hey! This piece of code is the same from
#polydata_utils.FillSurfaceHole, we need to review this.
if fill_holes:
filled_polydata = vtk.vtkFillHolesFilter()
filled_polydata.ReleaseDataFlagOn()
filled_polydata.SetInput(polydata)
filled_polydata.SetHoleSize(300)
filled_polydata_ref = weakref.ref(filled_polydata)
filled_polydata_ref().AddObserver("ProgressEvent", lambda obj,evt:
UpdateProgress(filled_polydata_ref(), _("Creating 3D surface...")))
filled_polydata.Update()
filled_polydata.GetOutput().ReleaseDataFlagOn()
del polydata
polydata = filled_polydata.GetOutput()
#polydata.Register(None)
polydata.SetSource(None)
polydata.DebugOn()
del filled_polydata
normals = vtk.vtkPolyDataNormals()
normals.ReleaseDataFlagOn()
normals_ref = weakref.ref(normals)
normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
UpdateProgress(normals_ref(), _("Creating 3D surface...")))
normals.SetInput(polydata)
normals.SetFeatureAngle(80)
normals.AutoOrientNormalsOn()
normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
del polydata
polydata = normals.GetOutput()
#polydata.Register(None)
polydata.SetSource(None)
del normals
# Improve performance
stripper = vtk.vtkStripper()
stripper.ReleaseDataFlagOn()
stripper_ref = weakref.ref(stripper)
stripper_ref().AddObserver("ProgressEvent", lambda obj,evt:
UpdateProgress(stripper_ref(), _("Creating 3D surface...")))
stripper.SetInput(polydata)
stripper.PassThroughCellIdsOn()
stripper.PassThroughPointIdsOn()
stripper.GetOutput().ReleaseDataFlagOn()
stripper.Update()
del polydata
polydata = stripper.GetOutput()
#polydata.Register(None)
polydata.SetSource(None)
del stripper
# Map polygonal data (vtkPolyData) to graphics primitives.
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(polydata)
mapper.ScalarVisibilityOff()
mapper.ReleaseDataFlagOn()
mapper.ImmediateModeRenderingOn() # improve performance
# Represent an object (geometry & properties) in the rendered scene
actor = vtk.vtkActor()
actor.SetMapper(mapper)
del mapper
#Create Surface instance
if overwrite:
surface = Surface(index = self.last_surface_index)
else:
surface = Surface(name=surface_name)
surface.colour = colour
surface.polydata = polydata
del polydata
# Set actor colour and transparency
actor.GetProperty().SetColor(colour)
actor.GetProperty().SetOpacity(1-surface.transparency)
prop = actor.GetProperty()
interpolation = int(ses.Session().surface_interpolation)
prop.SetInterpolation(interpolation)
proj = prj.Project()
if overwrite:
proj.ChangeSurface(surface)
else:
index = proj.AddSurface(surface)
surface.index = index
self.last_surface_index = index
session = ses.Session()
session.ChangeProject()
# The following lines have to be here, otherwise all volumes disappear
measured_polydata = vtk.vtkMassProperties()
measured_polydata.ReleaseDataFlagOn()
measured_polydata.SetInput(to_measure)
volume = float(measured_polydata.GetVolume())
surface.volume = volume
self.last_surface_index = surface.index
del measured_polydata
del to_measure
Publisher.sendMessage('Load surface actor into viewer', actor)
# Send actor by pubsub to viewer's render
if overwrite and self.actors_dict.keys():
old_actor = self.actors_dict[self.last_surface_index]
Publisher.sendMessage('Remove surface actor from viewer', old_actor)
# Save actor for future management tasks
self.actors_dict[surface.index] = actor
Publisher.sendMessage('Update surface info in GUI',
(surface.index, surface.name,
surface.colour, surface.volume,
surface.transparency))
#When you finalize the progress. The bar is cleaned.
UpdateProgress = vu.ShowProgress(1)
UpdateProgress(0, _("Ready"))
Publisher.sendMessage('Update status text in GUI', _("Ready"))
Publisher.sendMessage('End busy cursor')
del actor
def fillCaps(self):
# read the .obj and center it
# polydata = Helpers.centerPolyData(Helpers.getObjData(modelFn))
# TODO: centering seems to glitch the tetgen somewhy
polydata = Helpers.getObjData(modelFn)
size = Helpers.getBounds(polydata)
print "Model sizes:" + str(size)
fillHolesFilter = vtk.vtkFillHolesFilter()
fillHolesFilter.SetInputData(polydata)
fillHolesFilter.SetHoleSize(
1000.0
) # TODO: hole size: compute using model size (some factor of it)
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(fillHolesFilter.GetOutputPort())
normals.ConsistencyOn()
normals.SplittingOff()
normals.Update()
normals.GetOutput().GetPointData().SetNormals(
polydata.GetPointData().GetNormals())
numOriginalCells = polydata.GetNumberOfCells()
numNewCells = normals.GetOutput().GetNumberOfCells()
it = normals.GetOutput().NewCellIterator()
numCells = 0
it.InitTraversal()
# Iterate over the original cells
while (not it.IsDoneWithTraversal()) and numCells < numOriginalCells:
it.GoToNextCell()
numCells += 1
holePolyData = vtk.vtkPolyData()
holePolyData.Allocate(normals.GetOutput(),
numNewCells - numOriginalCells)
holePolyData.SetPoints(normals.GetOutput().GetPoints())
cell = vtk.vtkGenericCell()
# The remaining cells are the new ones from the hole filler
while not it.IsDoneWithTraversal():
it.GetCell(cell)
holePolyData.InsertNextCell(it.GetCellType(), cell.GetPointIds())
it.GoToNextCell()
connectivity = vtk.vtkConnectivityFilter()
connectivity.SetInputData(holePolyData)
connectivity.SetExtractionModeToAllRegions()
connectivity.ColorRegionsOn()
connectivity.Update()
capRegions = connectivity.GetOutput()
outPD = vtk.vtkPolyData()
outPD.Allocate(normals.GetOutput(), numNewCells)
outPD.SetPoints(capRegions.GetPoints())
numOfCaps = connectivity.GetNumberOfExtractedRegions()
print "Found " + str(numOfCaps) + " holes."
# create the cap polydatas
capPDs = []
for i in range(0, numOfCaps):
capPD = vtk.vtkPolyData()
capPD.Allocate(normals.GetOutput(), numNewCells)
capPD.SetPoints(capRegions.GetPoints())
capPDs.append(capPD)
capScalars = capRegions.GetCellData().GetScalars()
cell = vtk.vtkGenericCell()
it = capRegions.NewCellIterator()
i = 0
while not it.IsDoneWithTraversal():
it.GetCell(cell)
# outPD.InsertNextCell(it.GetCellType(), cell.GetPointIds())
capIdx = capScalars.GetValue(i)
capPDs[capIdx].InsertNextCell(it.GetCellType(), cell.GetPointIds())
it.GoToNextCell()
i = i + 1
sortedCaps = []
for i in range(0, len(capPDs)):
capPD = capPDs[i]
cleanFilter = vtk.vtkCleanPolyData()
cleanFilter.SetInputData(capPD)
cleanFilter.Update()
cleanedPD = cleanFilter.GetOutput()
area = Helpers.getArea(cleanedPD)
radius = math.sqrt(area / math.pi)
sortedCaps.append([cleanedPD, area, radius])
capPDs[i] = cleanedPD
sortedCaps = sorted(sortedCaps, key=lambda x: x[1], reverse=True)
[lastPd, area, radius] = sortedCaps[len(capPDs) - 1]
print "Recommended edge size: " + str(radius / 2)
scalarsName = "ModelFaceID"
Helpers.appendScalars(polydata, 1, scalarsName) # 1 for the walls
appendFilter = vtk.vtkAppendPolyData()
appendFilter.AddInputData(outPD)
appendFilter.AddInputData(polydata)
scalarIdx = 2
for [capPD, area, radius] in sortedCaps:
# if radius < 0.1:
# Helpers.appendScalars(capPD, 1, scalarsName) # append the face ID idx
# else:
# Helpers.appendScalars(capPD, scalarIdx, scalarsName) # append the face ID idx
Helpers.appendScalars(capPD, scalarIdx,
scalarsName) # append the face ID idx
appendFilter.AddInputData(capPD)
print "Cap radius: " + str(radius)
scalarIdx += 1
appendFilter.Update()
cleanFilter = vtk.vtkCleanPolyData()
cleanFilter.SetInputConnection(appendFilter.GetOutputPort())
cleanFilter.Update()
joinedPD = cleanFilter.GetOutput()
# joinedPD.GetCellData().SetScalars(scalars)
# Write as VTP
Helpers.writeVTP(meshFn, joinedPD)
return [
polydata, [[capPD, radius] for [capPD, area, radius] in sortedCaps]
]
def applyFilters(self, state):
surface = None
surface = state.inputModelNode.GetPolyDataConnection()
if state.decimation:
triangle = vtk.vtkTriangleFilter()
triangle.SetInputConnection(surface)
decimation = vtk.vtkDecimatePro()
decimation.SetTargetReduction(state.reduction)
decimation.SetBoundaryVertexDeletion(state.boundaryDeletion)
decimation.PreserveTopologyOn()
decimation.SetInputConnection(triangle.GetOutputPort())
surface = decimation.GetOutputPort()
if state.smoothing:
if state.smoothingMethod == "Laplace":
smoothing = vtk.vtkSmoothPolyDataFilter()
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.laplaceIterations)
smoothing.SetRelaxationFactor(state.laplaceRelaxation)
smoothing.SetInputConnection(surface)
surface = smoothing.GetOutputPort()
elif state.smoothingMethod == "Taubin":
smoothing = vtk.vtkWindowedSincPolyDataFilter()
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.taubinIterations)
smoothing.SetPassBand(state.taubinPassBand)
smoothing.SetInputConnection(surface)
surface = smoothing.GetOutputPort()
if state.normals:
normals = vtk.vtkPolyDataNormals()
normals.SetAutoOrientNormals(state.autoOrientNormals)
normals.SetFlipNormals(state.flipNormals)
normals.SetSplitting(state.splitting)
normals.SetFeatureAngle(state.featureAngle)
normals.ConsistencyOn()
normals.SetInputConnection(surface)
surface = normals.GetOutputPort()
if state.mirror:
mirrorTransformMatrix = vtk.vtkMatrix4x4()
mirrorTransformMatrix.SetElement(0, 0, -1 if state.mirrorX else 1)
mirrorTransformMatrix.SetElement(1, 1, -1 if state.mirrorY else 1)
mirrorTransformMatrix.SetElement(2, 2, -1 if state.mirrorZ else 1)
mirrorTransform = vtk.vtkTransform()
mirrorTransform.SetMatrix(mirrorTransformMatrix)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputConnection(surface)
transformFilter.SetTransform(mirrorTransform)
surface = transformFilter.GetOutputPort()
if mirrorTransformMatrix.Determinant() < 0:
reverse = vtk.vtkReverseSense()
reverse.SetInputConnection(surface)
surface = reverse.GetOutputPort()
if state.cleaner:
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputConnection(surface)
surface = cleaner.GetOutputPort()
if state.fillHoles:
fillHoles = vtk.vtkFillHolesFilter()
fillHoles.SetHoleSize(state.fillHolesSize)
fillHoles.SetInputConnection(surface)
# Need to auto-orient normals, otherwise holes
# could appear to be unfilled when only front-facing elements
# are chosen to be visible.
normals = vtk.vtkPolyDataNormals()
normals.AutoOrientNormalsOn()
normals.ConsistencyOn()
normals.SetInputConnection(fillHoles.GetOutputPort())
surface = normals.GetOutputPort()
if state.connectivity:
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetExtractionModeToLargestRegion()
connectivity.SetInputConnection(surface)
surface = connectivity.GetOutputPort()
state.outputModelNode.SetPolyDataConnection(surface)
return True
def mergeBreastAndBoundary(self, breastPolyData, wallPolyData):
# 先移除最外圍的點 避免與胸部data重疊
_, edgeIds = self.extractBoundaryPoints(wallPolyData)
rippedWallPolyData = self.deletePoint(wallPolyData, edgeIds)
rippedWallEdge, _ = self.extractBoundaryPoints(rippedWallPolyData)
wallStrips = vtk.vtkStripper()
wallStrips.SetInputData(rippedWallEdge)
wallStrips.Update()
edge1 = wallStrips.GetOutput()
breastEdge, _ = self.extractBoundaryPoints(breastPolyData)
boundaryStrips = vtk.vtkStripper()
boundaryStrips.SetInputData(breastEdge)
boundaryStrips.Update()
edge2 = boundaryStrips.GetOutput()
stitcer = PolyDataStitcher()
stitchPolyData = stitcer.stitch(edge1, edge2)
#self.createNewModelNode(stitchPolyData, "Stitch")
#先將胸壁與縫合面合併
appendFilter = vtk.vtkAppendPolyData()
appendFilter.AddInputData(rippedWallPolyData)
appendFilter.AddInputData(stitchPolyData)
appendFilter.Update()
normalFilter = vtk.vtkPolyDataNormals()
normalFilter.SetInputConnection(appendFilter.GetOutputPort())
normalFilter.Update()
cleanFilter = vtk.vtkCleanPolyData()
cleanFilter.SetInputConnection(normalFilter.GetOutputPort())
cleanFilter.ConvertLinesToPointsOn()
cleanFilter.ConvertPolysToLinesOn()
cleanFilter.ConvertStripsToPolysOn()
cleanFilter.Update()
holeFilter = vtk.vtkFillHolesFilter()
holeFilter.SetInputConnection(cleanFilter.GetOutputPort())
holeFilter.Update()
#self.createNewModelNode(holeFilter.GetOutput(), "Stitch_Combine")
#再次合併胸壁和胸部
appendFilter = vtk.vtkAppendPolyData()
appendFilter.AddInputData(breastPolyData)
appendFilter.AddInputData(holeFilter.GetOutput())
appendFilter.Update()
cleanFilter = vtk.vtkCleanPolyData()
cleanFilter.SetInputConnection(appendFilter.GetOutputPort())
cleanFilter.ConvertLinesToPointsOn()
cleanFilter.ConvertPolysToLinesOn()
cleanFilter.ConvertStripsToPolysOn()
cleanFilter.Update()
connectFilter = vtk.vtkPolyDataConnectivityFilter()
connectFilter.SetInputConnection(cleanFilter.GetOutputPort())
connectFilter.SetExtractionModeToLargestRegion()
connectFilter.Update()
holeFilter = vtk.vtkFillHolesFilter()
holeFilter.SetInputConnection(connectFilter.GetOutputPort())
holeFilter.Update()
cleanFilter = vtk.vtkCleanPolyData()
cleanFilter.SetInputConnection(holeFilter.GetOutputPort())
cleanFilter.ConvertLinesToPointsOn()
cleanFilter.ConvertPolysToLinesOn()
cleanFilter.ConvertStripsToPolysOn()
cleanFilter.Update()
normalFilter = vtk.vtkPolyDataNormals()
normalFilter.SetInputConnection(cleanFilter.GetOutputPort())
normalFilter.Update()
return normalFilter.GetOutput()
folder = os.path.basename(os.path.dirname(file))
if folder == "train":
out_folder = os.path.join(out_path, sub_folders[0])
elif folder == "val":
out_folder = os.path.join(out_path, sub_folders[1])
elif folder == "test":
out_folder = os.path.join(out_path, sub_folders[2])
new_name = '_'.join(os.path.basename(file).split('_')[0:2]) + '.vtk'
reader = vtk.vtkPolyDataReader()
reader.SetFileName(file)
reader.ReadAllScalarsOn()
reader.Update()
filler = vtk.vtkFillHolesFilter()
filler.SetInputData(reader.GetOutput())
filler.SetHoleSize(1000)
filler.Update()
filt = vtk.vtkConnectivityFilter()
filt.SetInputData(filler.GetOutput())
filt.SetExtractionModeToLargestRegion()
filt.Update()
TriangleFilter = vtk.vtkTriangleFilter()
TriangleFilter.SetInputData(filt.GetOutput())
TriangleFilter.Update()
cleanPolyData = vtk.vtkCleanPolyData()
cleanPolyData.ToleranceIsAbsoluteOn()
def CreateSurface(self):
_ = i18n.InstallLanguage(self.language)
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName(self.filename)
reader.Update()
image = reader.GetOutput()
if (self.flip_image):
# Flip original vtkImageData
flip = vtk.vtkImageFlip()
flip.SetInput(reader.GetOutput())
flip.SetFilteredAxis(1)
flip.FlipAboutOriginOn()
image = flip.GetOutput()
# Create vtkPolyData from vtkImageData
if self.mode == "CONTOUR":
contour = vtk.vtkContourFilter()
contour.SetInput(image)
contour.SetValue(0, self.min_value) # initial threshold
contour.SetValue(1, self.max_value) # final threshold
contour.GetOutput().ReleaseDataFlagOn()
contour.AddObserver("ProgressEvent", lambda obj,evt:
self.SendProgress(obj, _("Generating 3D surface...")))
polydata = contour.GetOutput()
else: #mode == "GRAYSCALE":
mcubes = vtk.vtkMarchingCubes()
mcubes.SetInput(image)
mcubes.SetValue(0, 255)
mcubes.ComputeScalarsOn()
mcubes.ComputeGradientsOn()
mcubes.ComputeNormalsOn()
mcubes.ThresholdBetween(self.min_value, self.max_value)
mcubes.GetOutput().ReleaseDataFlagOn()
mcubes.AddObserver("ProgressEvent", lambda obj,evt:
self.SendProgress(obj, _("Generating 3D surface...")))
polydata = mcubes.GetOutput()
if self.decimate_reduction:
decimation = vtk.vtkQuadricDecimation()
decimation.SetInput(polydata)
decimation.SetTargetReduction(self.decimate_reduction)
decimation.GetOutput().ReleaseDataFlagOn()
decimation.AddObserver("ProgressEvent", lambda obj,evt:
self.SendProgress(obj, _("Generating 3D surface...")))
polydata = decimation.GetOutput()
if self.smooth_iterations and self.smooth_relaxation_factor:
smoother = vtk.vtkSmoothPolyDataFilter()
smoother.SetInput(polydata)
smoother.SetNumberOfIterations(self.smooth_iterations)
smoother.SetFeatureAngle(80)
smoother.SetRelaxationFactor(self.smooth_relaxation_factor)
smoother.FeatureEdgeSmoothingOn()
smoother.BoundarySmoothingOn()
smoother.GetOutput().ReleaseDataFlagOn()
smoother.AddObserver("ProgressEvent", lambda obj,evt:
self.SendProgress(obj, _("Generating 3D surface...")))
polydata = smoother.GetOutput()
if self.keep_largest:
conn = vtk.vtkPolyDataConnectivityFilter()
conn.SetInput(polydata)
conn.SetExtractionModeToLargestRegion()
conn.AddObserver("ProgressEvent", lambda obj,evt:
self.SendProgress(obj, _("Generating 3D surface...")))
polydata = conn.GetOutput()
# Filter used to detect and fill holes. Only fill boundary edges holes.
#TODO: Hey! This piece of code is the same from
# polydata_utils.FillSurfaceHole, we need to review this.
if self.fill_holes:
filled_polydata = vtk.vtkFillHolesFilter()
filled_polydata.SetInput(polydata)
filled_polydata.SetHoleSize(300)
filled_polydata.AddObserver("ProgressEvent", lambda obj,evt:
self.SendProgress(obj, _("Generating 3D surface...")))
polydata = filled_polydata.GetOutput()
filename = tempfile.mktemp()
writer = vtk.vtkXMLPolyDataWriter()
writer.SetInput(polydata)
writer.SetFileName(filename)
writer.Write()
self.pipe.send(None)
self.pipe.send(filename)
def join_process_surface(filenames, algorithm, smooth_iterations, smooth_relaxation_factor, decimate_reduction, keep_largest, fill_holes, options, msg_queue):
def send_message(msg):
try:
msg_queue.put_nowait(msg)
except queue.Full as e:
print(e)
log_path = tempfile.mktemp('vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
send_message('Joining surfaces ...')
polydata_append = vtk.vtkAppendPolyData()
for f in filenames:
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(f)
reader.Update()
polydata = reader.GetOutput()
polydata_append.AddInputData(polydata)
del reader
del polydata
polydata_append.Update()
# polydata_append.GetOutput().ReleaseDataFlagOn()
polydata = polydata_append.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del polydata_append
send_message('Cleaning surface ...')
clean = vtk.vtkCleanPolyData()
# clean.ReleaseDataFlagOn()
# clean.GetOutput().ReleaseDataFlagOn()
clean_ref = weakref.ref(clean)
# clean_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(clean_ref(), _("Creating 3D surface...")))
clean.SetInputData(polydata)
clean.PointMergingOn()
clean.Update()
del polydata
polydata = clean.GetOutput()
# polydata.SetSource(None)
del clean
if algorithm == 'ca_smoothing':
send_message('Calculating normals ...')
normals = vtk.vtkPolyDataNormals()
normals_ref = weakref.ref(normals)
# normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(normals_ref(), _("Creating 3D surface...")))
normals.SetInputData(polydata)
# normals.ReleaseDataFlagOn()
#normals.SetFeatureAngle(80)
#normals.AutoOrientNormalsOn()
normals.ComputeCellNormalsOn()
# normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
del polydata
polydata = normals.GetOutput()
# polydata.SetSource(None)
del normals
clean = vtk.vtkCleanPolyData()
# clean.ReleaseDataFlagOn()
# clean.GetOutput().ReleaseDataFlagOn()
clean_ref = weakref.ref(clean)
# clean_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(clean_ref(), _("Creating 3D surface...")))
clean.SetInputData(polydata)
clean.PointMergingOn()
clean.Update()
del polydata
polydata = clean.GetOutput()
# polydata.SetSource(None)
del clean
# try:
# polydata.BuildLinks()
# except TypeError:
# polydata.BuildLinks(0)
# polydata = ca_smoothing.ca_smoothing(polydata, options['angle'],
# options['max distance'],
# options['min weight'],
# options['steps'])
send_message('Context Aware smoothing ...')
mesh = cy_mesh.Mesh(polydata)
cy_mesh.ca_smoothing(mesh, options['angle'],
options['max distance'],
options['min weight'],
options['steps'])
# polydata = mesh.to_vtk()
# polydata.SetSource(None)
# polydata.DebugOn()
# else:
# #smoother = vtk.vtkWindowedSincPolyDataFilter()
# send_message('Smoothing ...')
# smoother = vtk.vtkSmoothPolyDataFilter()
# smoother_ref = weakref.ref(smoother)
# # smoother_ref().AddObserver("ProgressEvent", lambda obj,evt:
# # UpdateProgress(smoother_ref(), _("Creating 3D surface...")))
# smoother.SetInputData(polydata)
# smoother.SetNumberOfIterations(smooth_iterations)
# smoother.SetRelaxationFactor(smooth_relaxation_factor)
# smoother.SetFeatureAngle(80)
# #smoother.SetEdgeAngle(90.0)
# #smoother.SetPassBand(0.1)
# smoother.BoundarySmoothingOn()
# smoother.FeatureEdgeSmoothingOn()
# #smoother.NormalizeCoordinatesOn()
# #smoother.NonManifoldSmoothingOn()
# # smoother.ReleaseDataFlagOn()
# # smoother.GetOutput().ReleaseDataFlagOn()
# smoother.Update()
# del polydata
# polydata = smoother.GetOutput()
# #polydata.Register(None)
# # polydata.SetSource(None)
# del smoother
if not decimate_reduction:
print("Decimating", decimate_reduction)
send_message('Decimating ...')
decimation = vtk.vtkQuadricDecimation()
# decimation.ReleaseDataFlagOn()
decimation.SetInputData(polydata)
decimation.SetTargetReduction(decimate_reduction)
decimation_ref = weakref.ref(decimation)
# decimation_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(decimation_ref(), _("Creating 3D surface...")))
#decimation.PreserveTopologyOn()
#decimation.SplittingOff()
#decimation.BoundaryVertexDeletionOff()
# decimation.GetOutput().ReleaseDataFlagOn()
decimation.Update()
del polydata
polydata = decimation.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del decimation
#to_measure.Register(None)
# to_measure.SetSource(None)
if keep_largest:
send_message('Finding the largest ...')
conn = vtk.vtkPolyDataConnectivityFilter()
conn.SetInputData(polydata)
conn.SetExtractionModeToLargestRegion()
conn_ref = weakref.ref(conn)
# conn_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(conn_ref(), _("Creating 3D surface...")))
conn.Update()
# conn.GetOutput().ReleaseDataFlagOn()
del polydata
polydata = conn.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del conn
#Filter used to detect and fill holes. Only fill boundary edges holes.
#TODO: Hey! This piece of code is the same from
#polydata_utils.FillSurfaceHole, we need to review this.
if fill_holes:
send_message('Filling holes ...')
filled_polydata = vtk.vtkFillHolesFilter()
# filled_polydata.ReleaseDataFlagOn()
filled_polydata.SetInputData(polydata)
filled_polydata.SetHoleSize(300)
filled_polydata_ref = weakref.ref(filled_polydata)
# filled_polydata_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(filled_polydata_ref(), _("Creating 3D surface...")))
filled_polydata.Update()
# filled_polydata.GetOutput().ReleaseDataFlagOn()
del polydata
polydata = filled_polydata.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
# polydata.DebugOn()
del filled_polydata
to_measure = polydata
normals = vtk.vtkPolyDataNormals()
# normals.ReleaseDataFlagOn()
# normals_ref = weakref.ref(normals)
# normals_ref().AddObserver("ProgressEvent", lambda obj,evt:
# UpdateProgress(normals_ref(), _("Creating 3D surface...")))
normals.SetInputData(polydata)
normals.SetFeatureAngle(80)
normals.SplittingOn()
normals.AutoOrientNormalsOn()
normals.NonManifoldTraversalOn()
normals.ComputeCellNormalsOn()
# normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
del polydata
polydata = normals.GetOutput()
#polydata.Register(None)
# polydata.SetSource(None)
del normals
# # Improve performance
# stripper = vtk.vtkStripper()
# # stripper.ReleaseDataFlagOn()
# # stripper_ref = weakref.ref(stripper)
# # stripper_ref().AddObserver("ProgressEvent", lambda obj,evt:
# # UpdateProgress(stripper_ref(), _("Creating 3D surface...")))
# stripper.SetInputData(polydata)
# stripper.PassThroughCellIdsOn()
# stripper.PassThroughPointIdsOn()
# # stripper.GetOutput().ReleaseDataFlagOn()
# stripper.Update()
# del polydata
# polydata = stripper.GetOutput()
# #polydata.Register(None)
# # polydata.SetSource(None)
# del stripper
send_message('Calculating area and volume ...')
measured_polydata = vtk.vtkMassProperties()
measured_polydata.SetInputData(to_measure)
measured_polydata.Update()
volume = float(measured_polydata.GetVolume())
area = float(measured_polydata.GetSurfaceArea())
del measured_polydata
filename = tempfile.mktemp(suffix='_full.vtp')
writer = vtk.vtkXMLPolyDataWriter()
writer.SetInputData(polydata)
writer.SetFileName(filename)
writer.Write()
del writer
print("MY PID", os.getpid())
return filename, {'volume': volume, 'area': area}
def applyFilters(self, state):
surface = None
surface = state.inputModelNode.GetPolyDataConnection()
if state.decimation:
triangle = vtk.vtkTriangleFilter()
triangle.SetInputConnection(surface)
decimation = vtk.vtkDecimatePro()
decimation.SetTargetReduction(state.reduction)
decimation.SetBoundaryVertexDeletion(state.boundaryDeletion)
decimation.PreserveTopologyOn()
decimation.SetInputConnection(triangle.GetOutputPort())
surface = decimation.GetOutputPort()
if state.smoothing:
if state.smoothingMethod == "Laplace":
smoothing = vtk.vtkSmoothPolyDataFilter()
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.laplaceIterations)
smoothing.SetRelaxationFactor(state.laplaceRelaxation)
smoothing.SetInputConnection(surface)
surface = smoothing.GetOutputPort()
elif state.smoothingMethod == "Taubin":
smoothing = vtk.vtkWindowedSincPolyDataFilter()
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.taubinIterations)
smoothing.SetPassBand(state.taubinPassBand)
smoothing.SetInputConnection(surface)
surface = smoothing.GetOutputPort()
if state.normals:
normals = vtk.vtkPolyDataNormals()
normals.SetAutoOrientNormals(state.autoOrientNormals)
normals.SetFlipNormals(state.flipNormals)
normals.SetSplitting(state.splitting)
normals.SetFeatureAngle(state.featureAngle)
normals.ConsistencyOn()
normals.SetInputConnection(surface)
surface = normals.GetOutputPort()
if state.mirror:
mirrorTransformMatrix = vtk.vtkMatrix4x4()
mirrorTransformMatrix.SetElement(0, 0, -1 if state.mirrorX else 1)
mirrorTransformMatrix.SetElement(1, 1, -1 if state.mirrorY else 1)
mirrorTransformMatrix.SetElement(2, 2, -1 if state.mirrorZ else 1)
mirrorTransform = vtk.vtkTransform()
mirrorTransform.SetMatrix(mirrorTransformMatrix)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputConnection(surface)
transformFilter.SetTransform(mirrorTransform)
surface = transformFilter.GetOutputPort()
if mirrorTransformMatrix.Determinant()<0:
reverse = vtk.vtkReverseSense()
reverse.SetInputConnection(surface)
surface = reverse.GetOutputPort()
if state.cleaner:
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputConnection(surface)
surface = cleaner.GetOutputPort()
if state.fillHoles:
fillHoles = vtk.vtkFillHolesFilter()
fillHoles.SetHoleSize(state.fillHolesSize)
fillHoles.SetInputConnection(surface)
# Need to auto-orient normals, otherwise holes
# could appear to be unfilled when only front-facing elements
# are chosen to be visible.
normals = vtk.vtkPolyDataNormals()
normals.AutoOrientNormalsOn()
normals.ConsistencyOn()
normals.SetInputConnection(fillHoles.GetOutputPort())
surface = normals.GetOutputPort()
if state.connectivity:
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetExtractionModeToLargestRegion()
connectivity.SetInputConnection(surface)
surface = connectivity.GetOutputPort()
state.outputModelNode.SetPolyDataConnection(surface)
return True
cellId = i - 1 + yRes * (j - 1)
if (cellId != 48 and cellId != 12 and cellId != 13
and cellId != 23 and cellId != 60 and cellId != 83
and cellId != 72 and cellId != 76 and cellId != 77
and cellId != 78 and cellId != 87):
polys.InsertNextCell(4)
polys.InsertCellPoint(i - 1 + ((j - 1) * yPtsRes))
polys.InsertCellPoint(i + ((j - 1) * yPtsRes))
polys.InsertCellPoint(i + (j * yPtsRes))
polys.InsertCellPoint(i - 1 + (j * yPtsRes))
pass
i += 1
j += 1
# Fill the holes
fill = vtk.vtkFillHolesFilter()
fill.SetInputData(pd)
fill.SetHoleSize(20.0)
# Mapping and actor
map = vtk.vtkPolyDataMapper()
# map SetInput pd
map.SetInputConnection(fill.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(map)
actor.GetProperty().SetColor(1, 0, 0)
# Add the actors to the renderer, set the background and size
#
ren1.AddActor(actor)
reader.SetFileName(file_name)
reader.Update()
model = reader.GetOutput()
clean_filter = vtk.vtkCleanPolyData()
clean_filter.SetPointMerging(True)
clean_filter.SetInputData(model)
clean_filter.Update()
model = clean_filter.GetOutput()
model.BuildLinks()
create_node_coord_hash(model)
#find_holes(model)
fill_hole_filter = vtk.vtkFillHolesFilter()
fill_hole_filter.SetInputData(model)
fill_hole_filter.SetHoleSize(float(1e10))
fill_hole_filter.Update()
model = fill_hole_filter.GetOutput()
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(model)
normals.ConsistencyOn()
normals.SplittingOn()
normals.Update()
model = normals.GetOutput()
clean_filter = vtk.vtkCleanPolyData()
clean_filter.SetPointMerging(True)
clean_filter.SetInputData(model)
