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