def imagefeature():
'''
图像的水平集分割，生成等值面
'''
input_datadir = 'C:/Users/chenjiaxing/Desktop/CT-Data/png/WU_Lung_Vessel_Ext/'
reader = imagereader.vmtkImageReader()
# 图像序
filelist = os.listdir(input_datadir)
reader.InputFilePrefix = input_datadir
reader.InputFilePattern = "%s%d.png"
reader.DataExtent = [0, 512, 0, 512, 1, len(filelist)]
reader.Format = "png"
reader.UseITKIO = 0
reader.Execute()
feature = imageFeatures.vmtkImageFeatures()
feature.Image = reader.Image
feature.FWHMRadius = [0.5, 0.5, 0.5]
feature.FeatureImageType = "gradient" # '["vtkgradient","gradient","upwind","fwhm"]'
feature.Execute()
viewer = imageviewer.vmtkImageViewer()
viewer.Image = reader.Image
viewer.Execute()
def test_features_types(aorta_image, compare_images, featureType, paramid, write_image):
name = __name__ + '_test_features_types_' + paramid + '.mha'
featurer = imagefeatures.vmtkImageFeatures()
featurer.Image = aorta_image
featurer.FeatureImageType = featureType
featurer.Execute()
assert compare_images(featurer.Image, name) == True
def test_features_types_upwind(aorta_image, compare_images, featureType, paramid, write_image):
name = __name__ + '_test_features_types_' + paramid + '.mha'
featurer = imagefeatures.vmtkImageFeatures()
featurer.Image = aorta_image
featurer.FeatureImageType = featureType
featurer.Execute()
assert compare_images(featurer.Image, name) == True
def test_upwind_factor_values_for_upwind(aorta_image, compare_images, upwindValue, paramid, write_image):
name = __name__ + '_test_upwind_factor_values_for_upwind_' + paramid + '.mha'
featurer = imagefeatures.vmtkImageFeatures()
featurer.Image = aorta_image
featurer.FeatureImageType = 'upwind'
featurer.UpwindFactor = upwindValue
featurer.Execute()
assert compare_images(featurer.Image, name) == True
def test_derivative_sigma_values_for_gradient(aorta_image, compare_images, derivativeValue, paramid, write_image):
name = __name__ + '_test_derivative_sigma_values_for_gradient_' + paramid + '.mha'
featurer = imagefeatures.vmtkImageFeatures()
featurer.Image = aorta_image
featurer.FeatureImageType = 'gradient'
featurer.DerivativeSigma = derivativeValue
featurer.Execute()
assert compare_images(featurer.Image, name) == True
def test_sigmoid_on_for_gradient_and_upwind(aorta_image, compare_images, featureType, paramid, write_image):
name = __name__ + '_test_sigmoid_on_for_gradient_and_upwind_' + paramid + '.mha'
featurer = imagefeatures.vmtkImageFeatures()
featurer.Image = aorta_image
featurer.FeatureImageType = featureType
featurer.SigmoidRemapping = 1
featurer.Execute()
assert compare_images(featurer.Image, name) == True
def test_upwind_factor_values_for_upwind(aorta_image, compare_images, upwindValue, paramid, write_image):
name = __name__ + '_test_upwind_factor_values_for_upwind_' + paramid + '.mha'
featurer = imagefeatures.vmtkImageFeatures()
featurer.Image = aorta_image
featurer.FeatureImageType = 'upwind'
featurer.UpwindFactor = upwindValue
featurer.Execute()
assert compare_images(featurer.Image, name) == True
def test_derivative_sigma_values_for_gradient(aorta_image, compare_images, derivativeValue, paramid, write_image):
name = __name__ + '_test_derivative_sigma_values_for_gradient_' + paramid + '.mha'
featurer = imagefeatures.vmtkImageFeatures()
featurer.Image = aorta_image
featurer.FeatureImageType = 'gradient'
featurer.DerivativeSigma = derivativeValue
featurer.Execute()
assert compare_images(featurer.Image, name) == True
def test_sigmoid_on_for_upwind(aorta_image, compare_images, featureType, paramid, write_image):
name = __name__ + '_test_sigmoid_on_for_gradient_and_upwind_' + paramid + '.mha'
featurer = imagefeatures.vmtkImageFeatures()
featurer.Image = aorta_image
featurer.FeatureImageType = featureType
featurer.SigmoidRemapping = 1
featurer.Execute()
assert compare_images(featurer.Image, name) == True
def Execute(self):
if not self.Network:
self.Network = vtk.vtkPolyData()
networkPoints = vtk.vtkPoints()
networkLines = vtk.vtkCellArray()
radiusArray = vtk.vtkDoubleArray()
radiusArray.SetName(self.RadiusArrayName)
self.Network.SetPoints(networkPoints)
self.Network.SetLines(networkLines)
self.Network.GetPointData().AddArray(radiusArray)
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.ExitAfterTextInputMode = False
self.vmtkRenderer.RegisterScript(self)
if self.Image and (not self.PlaneWidgetX or not self.PlaneWidgetY or not self.PlaneWidgetZ):
imageViewer = vmtkimageviewer.vmtkImageViewer()
imageViewer.Image = self.Image
imageViewer.vmtkRenderer = self.vmtkRenderer
imageViewer.Display = 0
imageViewer.Execute()
self.PlaneWidgetX = imageViewer.PlaneWidgetX
self.PlaneWidgetY = imageViewer.PlaneWidgetY
self.PlaneWidgetZ = imageViewer.PlaneWidgetZ
if self.Image:
spacing = self.Image.GetSpacing()
self.CurrentRadius = min(spacing)
if self.UseActiveTubes and not self.FeatureImage:
imageFeatures = vmtkimagefeatures.vmtkImageFeatures()
imageFeatures.Image = self.Image
imageFeatures.FeatureImageType = 'vtkgradient'
imageFeatures.Execute()
self.FeatureImage = imageFeatures.FeatureImage
self.NetworkRadiusArray = self.Network.GetPointData().GetArray(self.RadiusArrayName)
self.Network.GetPointData().SetActiveScalars(self.RadiusArrayName)
networkMapper = vtk.vtkPolyDataMapper()
networkMapper.SetInputData(self.Network)
networkMapper.SetScalarModeToUseCellData()
self.NetworkActor = vtk.vtkActor()
self.NetworkActor.SetMapper(networkMapper)
self.vmtkRenderer.Renderer.AddActor(self.NetworkActor)
self.NetworkTube = vtk.vtkTubeFilter()
self.NetworkTube.SetInputData(self.Network)
self.NetworkTube.SetVaryRadiusToVaryRadiusByAbsoluteScalar()
self.NetworkTube.SetNumberOfSides(20)
networkTubeMapper = vtk.vtkPolyDataMapper()
networkTubeMapper.SetInputConnection(self.NetworkTube.GetOutputPort())
networkTubeMapper.ScalarVisibilityOff()
networkTubeActor = vtk.vtkActor()
networkTubeActor.SetMapper(networkTubeMapper)
networkTubeActor.PickableOff()
networkTubeActor.GetProperty().SetOpacity(0.2)
self.vmtkRenderer.Renderer.AddActor(networkTubeActor)
self.Selection = vtk.vtkPolyData()
self.SelectionPoints = vtk.vtkPoints()
self.SelectionRadiusArray = vtk.vtkDoubleArray()
self.SelectionRadiusArray.SetName(self.RadiusArrayName)
self.Selection.SetPoints(self.SelectionPoints)
self.Selection.GetPointData().AddArray(self.SelectionRadiusArray)
self.Selection.GetPointData().SetActiveScalars(self.RadiusArrayName)
glyphs = vtk.vtkGlyph3D()
glyphSource = vtk.vtkSphereSource()
glyphSource.SetRadius(1.0)
glyphSource.SetThetaResolution(20)
glyphSource.SetPhiResolution(20)
glyphs.SetInputData(self.Selection)
glyphs.SetSourceConnection(glyphSource.GetOutputPort())
glyphs.SetScaleModeToScaleByScalar()
glyphs.SetScaleFactor(1.0)
selectionMapper = vtk.vtkPolyDataMapper()
selectionMapper.SetInputConnection(glyphs.GetOutputPort())
self.SelectionActor = vtk.vtkActor()
self.SelectionActor.SetMapper(selectionMapper)
self.SelectionActor.GetProperty().SetColor(1.0,0.0,0.0)
self.SelectionActor.GetProperty().SetOpacity(0.5)
self.SelectionActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.SelectionActor)
self.ActiveSegmentSeeds = vtk.vtkPolyData()
self.ActiveSegmentSeedsPoints = vtk.vtkPoints()
self.ActiveSegmentSeedsRadiusArray = vtk.vtkDoubleArray()
self.ActiveSegmentSeedsRadiusArray.SetName(self.RadiusArrayName)
self.ActiveSegmentSeeds.SetPoints(self.ActiveSegmentSeedsPoints)
self.ActiveSegmentSeeds.GetPointData().AddArray(self.ActiveSegmentSeedsRadiusArray)
self.ActiveSegmentSeeds.GetPointData().SetActiveScalars(self.RadiusArrayName)
activeSegmentSeedsGlyphs = vtk.vtkGlyph3D()
activeSegmentSeedsGlyphSource = vtk.vtkSphereSource()
activeSegmentSeedsGlyphSource.SetRadius(1.0)
activeSegmentSeedsGlyphSource.SetThetaResolution(20)
activeSegmentSeedsGlyphSource.SetPhiResolution(20)
activeSegmentSeedsGlyphs.SetInputData(self.ActiveSegmentSeeds)
activeSegmentSeedsGlyphs.SetSourceConnection(activeSegmentSeedsGlyphSource.GetOutputPort())
activeSegmentSeedsGlyphs.SetScaleModeToScaleByScalar()
activeSegmentSeedsGlyphs.SetScaleFactor(1.0)
activeSegmentSeedsMapper = vtk.vtkPolyDataMapper()
activeSegmentSeedsMapper.SetInputConnection(activeSegmentSeedsGlyphs.GetOutputPort())
activeSegmentSeedsMapper.ScalarVisibilityOff()
self.ActiveSegmentSeedsActor = vtk.vtkActor()
self.ActiveSegmentSeedsActor.SetMapper(activeSegmentSeedsMapper)
self.ActiveSegmentSeedsActor.GetProperty().SetColor(1.0,0.0,0.0)
self.ActiveSegmentSeedsActor.GetProperty().SetOpacity(0.5)
self.ActiveSegmentSeedsActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.ActiveSegmentSeedsActor)
self.ActiveSegment = vtk.vtkPolyData()
self.ActiveSegmentPoints = vtk.vtkPoints()
self.ActiveSegmentCellArray = vtk.vtkCellArray()
self.ActiveSegmentRadiusArray = vtk.vtkDoubleArray()
self.ActiveSegmentRadiusArray.SetName(self.RadiusArrayName)
self.ActiveSegment.SetPoints(self.ActiveSegmentPoints)
self.ActiveSegment.SetLines(self.ActiveSegmentCellArray)
self.ActiveSegment.GetPointData().AddArray(self.ActiveSegmentRadiusArray)
self.ActiveSegment.GetPointData().SetActiveScalars(self.RadiusArrayName)
activeSegmentMapper = vtk.vtkPolyDataMapper()
activeSegmentMapper.ScalarVisibilityOff()
if self.SplineInterpolation and self.Image != None:
splineFilter = vtk.vtkSplineFilter()
splineFilter.SetInputData(self.ActiveSegment)
splineFilter.SetSubdivideToLength()
splineFilter.SetLength(2.0*min(self.Image.GetSpacing()))
activeSegmentMapper.SetInputConnection(splineFilter.GetOutputPort())
else:
activeSegmentMapper.SetInputData(self.ActiveSegment)
self.ActiveSegmentActor = vtk.vtkActor()
self.ActiveSegmentActor.SetMapper(activeSegmentMapper)
self.ActiveSegmentActor.GetProperty().SetColor(1.0,1.0,1.0)
self.ActiveSegmentActor.GetProperty().SetLineWidth(3.0)
self.ActiveSegmentActor.PickableOff()
self.vmtkRenderer.Renderer.AddActor(self.ActiveSegmentActor)
activeTube = vtk.vtkTubeFilter()
activeTube.SetInputConnection(activeSegmentMapper.GetInputPort())
activeTube.SetVaryRadiusToVaryRadiusByAbsoluteScalar()
activeTube.SetNumberOfSides(20)
activeTubeMapper = vtk.vtkPolyDataMapper()
activeTubeMapper.SetInputConnection(activeTube.GetOutputPort())
activeTubeMapper.ScalarVisibilityOff()
activeTubeActor = vtk.vtkActor()
activeTubeActor.SetMapper(activeTubeMapper)
activeTubeActor.PickableOff()
activeTubeActor.GetProperty().SetOpacity(0.6)
self.vmtkRenderer.Renderer.AddActor(activeTubeActor)
self.NetworkLabelsArray = vtk.vtkStringArray.SafeDownCast(self.Network.GetCellData().GetAbstractArray(self.LabelsArrayName))
if not self.NetworkLabelsArray:
self.NetworkLabelsArray = vtk.vtkStringArray()
self.NetworkLabelsArray.SetName(self.LabelsArrayName)
self.NetworkLabelsArray.SetNumberOfValues(self.Network.GetNumberOfCells())
for i in range(self.Network.GetNumberOfCells()):
self.NetworkLabelsArray.SetValue(i,'')
self.Network.GetCellData().AddArray(self.NetworkLabelsArray)
self.CellCenters = vtk.vtkCellCenters()
self.CellCenters.SetInputData(self.Network)
self.CellCenters.VertexCellsOff()
self.CellCenters.Update()
labeledMapper = vtk.vtkLabeledDataMapper()
labeledMapper.SetInputConnection(self.CellCenters.GetOutputPort())
labeledMapper.SetLabelModeToLabelFieldData()
labeledMapper.SetFieldDataName(self.LabelsArrayName)
labeledMapper.GetLabelTextProperty().SetFontFamilyToArial()
labeledMapper.GetLabelTextProperty().BoldOff()
labeledMapper.GetLabelTextProperty().ItalicOff()
labeledMapper.GetLabelTextProperty().ShadowOff()
self.LabelsActor = vtk.vtkActor2D()
self.LabelsActor.SetMapper(labeledMapper)
self.LabelsActor.VisibilityOff()
self.vmtkRenderer.Renderer.AddActor(self.LabelsActor)
self.CellPicker = vtk.vtkCellPicker()
self.CellPicker.SetTolerance(1E-2)
self.CellPicker.InitializePickList()
self.CellPicker.AddPickList(self.NetworkActor)
self.CellPicker.PickFromListOn()
self.vmtkRenderer.AddKeyBinding('a','Add mode.',self.AddCallback)
self.vmtkRenderer.AddKeyBinding('d','Delete mode.',self.DeleteCallback)
self.vmtkRenderer.AddKeyBinding('m','Merge mode.',self.MergeCallback)
self.vmtkRenderer.AddKeyBinding('s','Split mode.',self.SplitCallback)
self.vmtkRenderer.AddKeyBinding('l','Label mode.',self.LabelCallback)
self.vmtkRenderer.AddKeyBinding('Tab','Show labels.',self.ShowLabelCallback)
self.vmtkRenderer.RenderWindowInteractor.AddObserver("KeyReleaseEvent", self.KeyReleaseCallback)
self.vmtkRenderer.RenderWindowInteractor.AddObserver("LeftButtonPressEvent", self.LeftButtonPressCallback)
self.vmtkRenderer.RenderWindowInteractor.AddObserver("MouseMoveEvent", self.MouseMoveCallback)
if self.PlaneWidgetX:
self.PlaneWidgetX.UseContinuousCursorOn()
self.PlaneWidgetX.AddObserver("StartInteractionEvent", self.PlaneStartInteractionCallback)
if self.PlaneWidgetY:
self.PlaneWidgetY.UseContinuousCursorOn()
self.PlaneWidgetY.AddObserver("StartInteractionEvent", self.PlaneStartInteractionCallback)
if self.PlaneWidgetZ:
self.PlaneWidgetZ.UseContinuousCursorOn()
self.PlaneWidgetZ.AddObserver("StartInteractionEvent", self.PlaneStartInteractionCallback)
self.FirstRender()
self.Surface = self.NetworkTube.GetOutput()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
