def SplitDisconectedParts(polydata): """ """ conn = vtk.vtkPolyDataConnectivityFilter() conn.SetInputData(polydata) conn.SetExtractionModeToAllRegions() conn.Update() nregions = conn.GetNumberOfExtractedRegions() conn.SetExtractionModeToSpecifiedRegions() conn.Update() polydata_collection = [] # Update progress value in GUI progress = nregions -1 if progress: UpdateProgress = vu.ShowProgress(progress) for region in xrange(nregions): conn.InitializeSpecifiedRegionList() conn.AddSpecifiedRegion(region) conn.Update() p = vtk.vtkPolyData() p.DeepCopy(conn.GetOutput()) polydata_collection.append(p) if progress: UpdateProgress(region, _("Splitting disconnected regions...")) return polydata_collection
def SelectLargestPart(polydata): """ """ UpdateProgress = vu.ShowProgress(1) conn = vtk.vtkPolyDataConnectivityFilter() conn.SetInputData(polydata) conn.SetExtractionModeToLargestRegion() conn.AddObserver("ProgressEvent", lambda obj, evt: UpdateProgress(conn, "Getting largest part...")) conn.Update() result = vtk.vtkPolyData() result.DeepCopy(conn.GetOutput()) return result
def JoinSeedsParts(polydata, point_id_list): """ The function require vtkPolyData and point id from vtkPolyData. """ conn = vtk.vtkPolyDataConnectivityFilter() conn.SetInputData(polydata) conn.SetExtractionModeToPointSeededRegions() UpdateProgress = vu.ShowProgress(1 + len(point_id_list)) pos = 1 for seed in point_id_list: conn.AddSeed(seed) UpdateProgress(pos, _("Analysing selected regions...")) pos += 1 conn.AddObserver("ProgressEvent", lambda obj, evt: UpdateProgress(conn, "Getting selected parts")) conn.Update() result = vtk.vtkPolyData() result.DeepCopy(conn.GetOutput()) return result
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.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']) # 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 = polydata #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 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() # The following lines have to be here, otherwise all volumes disappear 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) # 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.area, 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
# QUALQUER GARANTIA; sem mesmo a garantia implicita de # COMERCIALIZACAO ou de ADEQUACAO A QUALQUER PROPOSITO EM # PARTICULAR. Consulte a Licenca Publica Geral GNU para obter mais # detalhes. #-------------------------------------------------------------------------- import sys import vtk import wx from wx.lib.pubsub import pub as Publisher import vtk_utils as vu # Update progress value in GUI UpdateProgress = vu.ShowProgress() def ApplyDecimationFilter(polydata, reduction_factor): """ Reduce number of triangles of the given vtkPolyData, based on reduction_factor. """ # Important: vtkQuadricDecimation presented better results than # vtkDecimatePro decimation = vtk.vtkQuadricDecimation() decimation.SetInputData(polydata) decimation.SetTargetReduction(reduction_factor) decimation.GetOutput().ReleaseDataFlagOn() decimation.AddObserver("ProgressEvent", lambda obj, evt: UpdateProgress(decimation, "Reducing number of triangles...")) return decimation.GetOutput()