def GetPeelActor(self, p):
lut = vtk.vtkWindowLevelLookupTable()
lut.SetWindow(self.window_width)
lut.SetLevel(self.window_level)
lut.Build()
init = self.window_level - self.window_width / 2
end = self.window_level + self.window_width / 2
# Set mapper auto
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(self.peel[p])
mapper.SetScalarRange(init, end)
mapper.SetLookupTable(lut)
mapper.InterpolateScalarsBeforeMappingOn()
# Set actor
self.currentPeelActor.SetMapper(mapper)
currentPeel = self.TransformPeelPosition(p)
self.locator.SetDataSet(currentPeel)
self.locator.BuildLocator()
self.GetCenters(currentPeel)
self.GetNormals(currentPeel)
return self.currentPeelActor
def polyShowScalars(ren,obj):
#@c Show scalar values on poly in renderer in grayscale
#@a ren: renderer
#@a obj: object name
if isinstance(obj,list):
tag = "%s_%s" % (ren[0],obj[0])
elif isinstance(obj,str):
tag = "%s_%s" % (ren[0],obj)
else:
raise ValueError("Argument type unsupported.")
lookupGrayscale = [None]*2
lookupGrayscale[0] = "p_grayscaleLUT_"+tag
lookupGrayscale[1] = vtk.vtkWindowLevelLookupTable()
lookupGrayscale[1].SetWindow(1023)
lookupGrayscale[1].SetLevel(512)
lookupGrayscale[1].SetWindow(0.5)
lookupGrayscale[1].SetLevel(0.5)
lookupGrayscale[1].SetHueRange(0.,0.)
lookupGrayscale[1].SetSaturationRange(0.,0.)
lookupGrayscale[1].SetValueRange(0.,1.)
lookupGrayscale[1].SetNumberOfColors(16384)
lookupGrayscale[1].Build()
act = polyGetActor(ren,obj)
act[1].GetMapper().SetLookupTable(lookupGrayscale[1])
act[1].GetMapper().ScalarVisibilityOn()
Range = act[1].GetMapper().GetInput().GetPointData().GetScalars().GetRange()
act[1].GetMapper().SetScalarRange(Range[0],Range[1])
vis.render(ren)
setattr(vis,act[0],act)
setattr(vis,lookupGrayscale[0],lookupGrayscale)
return
def createGridActor(grid, showScalar=False, range=None, showEdges=False, colorMap='colors'):
mapper = vtk.vtkDataSetMapper()
mapper.SetInput(grid)
actor = vtk.vtkActor()
if showScalar:
scalars = grid.GetPointData().GetScalars()
if scalars==None:
scalars = grid.GetCellData().GetScalars()
if scalars==None:
scalars = grid.GetPointData().GetArray(0)
grid.GetPointData().SetScalars(scalars)
if scalars==None:
scalars = grid.GetCellData().GetArray(0)
grid.GetCellData().SetScalars(scalars)
if range==None: range = [scalars.GetRange()[0],.8*scalars.GetRange()[1]]
mapper.SetScalarRange(*range)
if colorMap=='GrayScale':wl = vtk.vtkWindowLevelLookupTable()
else:
wl = vtk.vtkLookupTable()
wl.SetScaleToLinear()
wl.SetRange(*range)
wl.SetHueRange(0.6667,0.0)#blue to red
wl.Build()
mapper.SetLookupTable(wl)
else:
mapper.ScalarVisibilityOff()
actor.GetProperty().SetColor(.6, .6, .6)
actor.SetMapper(mapper)
if showEdges: actor.GetProperty().EdgeVisibilityOn()
return actor
def CreateImageActor(actor, colorWindow, colorLevel):
wlut = vtk.vtkWindowLevelLookupTable()
wlut.SetWindow(colorWindow)
wlut.SetLevel(colorLevel)
wlut.Build()
# Map the image through the lookup table.
color = vtk.vtkImageMapToColors()
color.SetLookupTable(wlut)
color.SetInputData(actor.GetMapper().GetInput())
actor.GetMapper().SetInputConnection(color.GetOutputPort())
return
def CreateHighlightLookupTable(self):
# Create colour table for histogram overlay
table = vtk.vtkWindowLevelLookupTable()
table.SetSaturationRange(0, 0)
table.SetHueRange(0, 0)
table.SetValueRange(0, 1)
table.SetLevel(0.5)
table.SetWindow(1.0)
table.SetNumberOfColors(2)
table.SetTableValue(0, 0.0, 0.0, 0.0, 0.0)
table.SetTableValue(1, 1.0, 0.0, 0.0, 1.0)
table.Build()
return table
def createPolyDataActor(polydata, showScalar=False, range=None):
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(polydata)
if showScalar:
wl = vtk.vtkWindowLevelLookupTable()
if range == None:
range = polydata.GetPointData().GetScalars().GetRange()
mapper.SetScalarRange(*range)
mapper.SetLookupTable(wl)
else:
mapper.ScalarVisibilityOff()
actor = vtk.vtkActor()
actor.SetMapper(mapper)
return actor
def createClipActor(grid, plane, showScalar=False, range=None, showEdges=False, colorMap='GrayScale'):
clipMapper = vtk.vtkDataSetMapper()
clipMapper.SetInput(grid)
cutMapper = vtk.vtkDataSetMapper()
clipActor = vtk.vtkActor()
cutActor = vtk.vtkActor()
if showScalar:
scalars = grid.GetPointData().GetScalars()
if scalars==None:
scalars = grid.GetCellData().GetScalars()
if scalars==None:
scalars = grid.GetPointData().GetArray(0)
grid.GetPointData().SetScalars(scalars)
if scalars==None:
scalars = grid.GetCellData().GetArray(0)
grid.GetCellData().SetScalars(scalars)
if range==None: range = [scalars.GetRange()[0],.8*scalars.GetRange()[1]]
cutMapper.SetScalarRange(*range)
clipMapper.SetScalarRange(*range)
if colorMap=='GrayScale':wl = vtk.vtkWindowLevelLookupTable()
else:
wl = vtk.vtkLookupTable()
wl.SetScaleToLinear()
wl.SetRange(*range)
wl.SetHueRange(0.6667,0.0)#blue to red
wl.Build()
clipMapper.SetLookupTable(wl)
cutMapper.SetLookupTable(wl)
else:
clipMapper.ScalarVisibilityOff()
cutMapper.ScalarVisibilityOff()
clipActor.GetProperty().SetColor(.6, .6, .6)
cutActor.GetProperty().SetColor(.6, .6, .6)
clipMapper.AddClippingPlane(plane)
clipActor.SetMapper(clipMapper)
cutter = vtk.vtkCutter()
cutter.SetCutFunction(plane)
cutter.SetInput(grid)
cutter.Update()
cutMapper.SetInputConnection(cutter.GetOutputPort())
cutActor.SetMapper(cutMapper)
if showEdges:
cutActor.GetProperty().EdgeVisibilityOn()
clipActor.GetProperty().EdgeVisibilityOn()
return [cutActor,clipActor]
def __init__( self, color, plane, reslice, range ):
self._color = color
self._source = plane
self._mapper = vtk.vtkPolyDataMapper()
self._mapper.SetInput( self._source.GetOutput() )
self.SetMapper( self._mapper )
self._lut = vtk.vtkWindowLevelLookupTable()
self._lut.SetNumberOfColors( 256 )
self._lut.SetTableRange( range[0], range[1] )
self._lut.SetHueRange( 0.0, 0.0 )
self._lut.SetSaturationRange( 0.0, 0.0 )
self._lut.SetValueRange( 0.0, 1.0 )
self._lut.SetAlphaRange( 0.0, 1.0 )
self._lut.Build()
self._colormap = vtk.vtkImageMapToColors()
self._colormap.SetInputConnection( reslice.GetOutputPort() )
self._colormap.SetLookupTable( self._lut )
self._colormap.SetOutputFormatToRGBA()
self._colormap.PassAlphaToOutputOn()
self._texture = vtk.vtkTexture()
self._texture.SetInterpolate( True )
self._texture.SetQualityTo32Bit()
self._texture.MapColorScalarsThroughLookupTableOff()
self._texture.RepeatOff()
self._texture.SetInput( self._colormap.GetOutput() )
self._texture.SetLookupTable( self._lut )
self.SetTexture( self._texture )
self._property = vtk.vtkProperty()
self._property.SetOpacity( 0.9 )
self._property.EdgeVisibilityOn()
self._property.SetEdgeColor( self._color[0], self._color[1], self._color[2] )
self.SetProperty( self._property )
def GetCurrentPeelActor(self, currentPeel):
lut = vtk.vtkWindowLevelLookupTable()
lut.SetWindow(self.window_width)
lut.SetLevel(self.window_level)
lut.Build()
init = self.window_level - self.window_width / 2
end = self.window_level + self.window_width / 2
# Set mapper auto
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(currentPeel)
mapper.SetScalarRange(init, end)
mapper.SetLookupTable(lut)
mapper.InterpolateScalarsBeforeMappingOn()
# Set actor
self.currentPeelActor.SetMapper(mapper)
self.currentPeelActor.GetProperty().SetBackfaceCulling(1)
self.currentPeelActor.GetProperty().SetOpacity(0.5)
self.currentPeelActor.GetProperty().SetSpecular(0.25)
return self.currentPeelActor
def main(data_folder, slice_number):
colors = vtk.vtkNamedColors()
path = Path(data_folder)
if path.is_dir():
s = ''
fn_1 = path.joinpath('frog').with_suffix('.mhd')
if not fn_1.is_file():
s += 'The file: {:s} does not exist.\n'.format(str(fn_1))
print(s)
fn_2 = path.joinpath('frogtissue').with_suffix('.mhd')
if not fn_2.is_file():
s += 'The file: {:s} does not exist.'.format(str(fn_2))
if s:
print(s)
return
else:
print('Expected a path to frog.mhs and frogtissue.mhd')
return
so = SliceOrder()
# Now create the RenderWindow, Renderer and Interactor
#
ren1 = vtk.vtkRenderer()
ren2 = vtk.vtkRenderer()
ren3 = vtk.vtkRenderer()
ren_win = vtk.vtkRenderWindow()
ren_win.AddRenderer(ren1)
ren_win.AddRenderer(ren2)
ren_win.AddRenderer(ren3)
ren_win.SetWindowName('FrogSlice')
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(ren_win)
grey_reader = vtk.vtkMetaImageReader()
grey_reader.SetFileName(str(fn_1))
grey_reader.Update()
grey_padder = vtk.vtkImageConstantPad()
grey_padder.SetInputConnection(grey_reader.GetOutputPort())
grey_padder.SetOutputWholeExtent(0, 511, 0, 511, slice_number,
slice_number)
grey_padder.SetConstant(0)
grey_plane = vtk.vtkPlaneSource()
grey_transform = vtk.vtkTransformPolyDataFilter()
grey_transform.SetTransform(so.get('hfsi'))
grey_transform.SetInputConnection(grey_plane.GetOutputPort())
grey_normals = vtk.vtkPolyDataNormals()
grey_normals.SetInputConnection(grey_transform.GetOutputPort())
grey_normals.FlipNormalsOff()
wllut = vtk.vtkWindowLevelLookupTable()
wllut.SetWindow(255)
wllut.SetLevel(128)
wllut.SetTableRange(0, 255)
wllut.Build()
grey_mapper = vtk.vtkPolyDataMapper()
grey_mapper.SetInputConnection(grey_plane.GetOutputPort())
grey_texture = vtk.vtkTexture()
grey_texture.SetInputConnection(grey_padder.GetOutputPort())
grey_texture.SetLookupTable(wllut)
grey_texture.SetColorModeToMapScalars()
grey_texture.InterpolateOn()
grey_actor = vtk.vtkActor()
grey_actor.SetMapper(grey_mapper)
grey_actor.SetTexture(grey_texture)
segment_reader = vtk.vtkMetaImageReader()
segment_reader.SetFileName(str(fn_2))
segment_reader.Update()
segment_padder = vtk.vtkImageConstantPad()
segment_padder.SetInputConnection(segment_reader.GetOutputPort())
segment_padder.SetOutputWholeExtent(0, 511, 0, 511, slice_number,
slice_number)
segment_padder.SetConstant(0)
segment_plane = vtk.vtkPlaneSource()
segment_transform = vtk.vtkTransformPolyDataFilter()
segment_transform.SetTransform(so.get('hfsi'))
segment_transform.SetInputConnection(segment_plane.GetOutputPort())
segment_normals = vtk.vtkPolyDataNormals()
segment_normals.SetInputConnection(segment_transform.GetOutputPort())
segment_normals.FlipNormalsOn()
lut = create_frog_lut(colors)
segment_mapper = vtk.vtkPolyDataMapper()
segment_mapper.SetInputConnection(segment_plane.GetOutputPort())
segment_texture = vtk.vtkTexture()
segment_texture.SetInputConnection(segment_padder.GetOutputPort())
segment_texture.SetLookupTable(lut)
segment_texture.SetColorModeToMapScalars()
segment_texture.InterpolateOff()
segment_actor = vtk.vtkActor()
segment_actor.SetMapper(segment_mapper)
segment_actor.SetTexture(segment_texture)
segment_overlay_actor = vtk.vtkActor()
segment_overlay_actor.SetMapper(segment_mapper)
segment_overlay_actor.SetTexture(segment_texture)
segment_overlay_actor.GetProperty().SetOpacity(.5)
ren1.SetBackground(0, 0, 0)
ren1.SetViewport(0, 0.5, 0.5, 1)
ren_win.SetSize(640, 480)
ren1.AddActor(grey_actor)
ren2.SetBackground(0, 0, 0)
ren2.SetViewport(0.5, 0.5, 1, 1)
ren2.AddActor(segment_actor)
cam1 = vtk.vtkCamera()
cam1.SetViewUp(0, -1, 0)
cam1.SetPosition(0, 0, -1)
ren1.SetActiveCamera(cam1)
ren1.ResetCamera()
cam1.SetViewUp(0, -1, 0)
cam1.SetPosition(0.0554068, -0.0596001, -0.491383)
cam1.SetFocalPoint(0.0554068, -0.0596001, 0)
ren1.ResetCameraClippingRange()
ren3.AddActor(grey_actor)
ren3.AddActor(segment_overlay_actor)
segment_overlay_actor.SetPosition(0, 0, -0.01)
ren1.SetBackground(colors.GetColor3d('SlateGray'))
ren2.SetBackground(colors.GetColor3d('SlateGray'))
ren3.SetBackground(colors.GetColor3d('SlateGray'))
ren3.SetViewport(0, 0, 1, 0.5)
ren2.SetActiveCamera(ren1.GetActiveCamera())
ren3.SetActiveCamera(ren1.GetActiveCamera())
ren_win.Render()
iren.Start()
def main():
# colors = vtk.vtkNamedColors()
filename1 = "C:\\Users\\chenjiaxing\\Desktop\\Python\\Edge220\\"
filename2 = "C:\\Users\\chenjiaxing\\Desktop\\Python\\JPEG220\\6\\"
rows = 128
columns = 128
slicenumber = 19
start_slice = 1
end_slice = 51
pixel_size = 1
spacing = 1
endx = rows - 1
endy = columns - 1
endz = end_slice - 1
sliceOrder = SliceOrder()
# Now create the RenderWindow, Renderer and Interactor
#
ren1 = vtk.vtkRenderer()
ren2 = vtk.vtkRenderer()
ren3 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.AddRenderer(ren2)
renWin.AddRenderer(ren3)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
greyReader = vtk.vtkJPEGReader()
greyReader.SetFilePrefix(filename1)
greyReader.SetFilePattern("%s%d.jpg")
greyReader.SetDataSpacing(pixel_size, pixel_size, spacing)
greyReader.SetDataExtent(0, endx, 0, endy, slicenumber, slicenumber)
greyReader.DebugOn()
greyPadder = vtk.vtkImageConstantPad()
greyPadder.SetInputConnection(greyReader.GetOutputPort())
greyPadder.SetOutputWholeExtent(0, 127, 0, 127, slicenumber, slicenumber)
greyPadder.SetConstant(0)
greyPlane = vtk.vtkPlaneSource()
greyTransform = vtk.vtkTransformPolyDataFilter()
greyTransform.SetTransform(sliceOrder["hfsi"])
greyTransform.SetInputConnection(greyPlane.GetOutputPort())
greyNormals = vtk.vtkPolyDataNormals()
greyNormals.SetInputConnection(greyTransform.GetOutputPort())
greyNormals.FlipNormalsOff()
wllut = vtk.vtkWindowLevelLookupTable()
wllut.SetWindow(255)
wllut.SetLevel(128)
wllut.SetTableRange(0, 255)
wllut.Build()
greyMapper = vtk.vtkPolyDataMapper()
greyMapper.SetInputConnection(greyPlane.GetOutputPort())
greyTexture = vtk.vtkTexture()
greyTexture.SetInputConnection(greyPadder.GetOutputPort())
greyTexture.SetLookupTable(wllut)
greyTexture.SetColorModeToMapScalars()
greyTexture.InterpolateOn()
greyActor = vtk.vtkActor()
greyActor.SetMapper(greyMapper)
greyActor.SetTexture(greyTexture)
segmentReader = vtk.vtkJPEGReader()
segmentReader.SetFilePrefix(filename2)
segmentReader.SetFilePattern("%s%d.jpg")
segmentReader.SetDataSpacing(pixel_size, pixel_size, spacing)
#segmentReader.SetDataVOI(0, endx, 0, endy, slicenumber, slicenumber)
segmentReader.SetDataExtent(0, endx, 0, endy, slicenumber, slicenumber)
segmentReader.Update()
#imageThreshold filter
LowThreshold = 1
UpperThreshold = 16
selectTissue = vtk.vtkImageThreshold()
selectTissue.ThresholdBetween(LowThreshold, UpperThreshold)
selectTissue.SetInValue(UpperThreshold)
selectTissue.SetOutValue(0)
selectTissue.SetInputConnection(segmentReader.GetOutputPort())
segmentPadder = vtk.vtkImageConstantPad()
#segmentPadder.SetInputConnection(segmentReader.GetOutputPort())
segmentPadder.SetInputConnection(selectTissue.GetOutputPort())
segmentPadder.SetOutputWholeExtent(0, 127, 0, 127, slicenumber,
slicenumber)
segmentPadder.SetConstant(0)
segmentPlane = vtk.vtkPlaneSource()
segmentTransform = vtk.vtkTransformPolyDataFilter()
segmentTransform.SetTransform(sliceOrder["hfsi"])
segmentTransform.SetInputConnection(segmentPlane.GetOutputPort())
segmentNormals = vtk.vtkPolyDataNormals()
segmentNormals.SetInputConnection(segmentTransform.GetOutputPort())
segmentNormals.FlipNormalsOn()
colorLut = CreateFrogLut()
segmentMapper = vtk.vtkPolyDataMapper()
segmentMapper.SetInputConnection(segmentPlane.GetOutputPort())
segmentTexture = vtk.vtkTexture()
segmentTexture.SetInputConnection(segmentPadder.GetOutputPort())
segmentTexture.SetLookupTable(colorLut)
segmentTexture.SetColorModeToMapScalars()
segmentTexture.InterpolateOff()
segmentActor = vtk.vtkActor()
segmentActor.SetMapper(segmentMapper)
segmentActor.SetTexture(segmentTexture)
segmentOverlayActor = vtk.vtkActor()
segmentOverlayActor.SetMapper(segmentMapper)
segmentOverlayActor.SetTexture(segmentTexture)
segmentOverlayActor.GetProperty().SetOpacity(.5)
ren1.SetBackground(0, 0, 0)
ren1.SetViewport(0, .5, .5, 1)
renWin.SetSize(640, 480)
ren1.AddActor(greyActor)
ren2.SetBackground(0, 0, 0)
ren2.SetViewport(.5, .5, 1, 1)
ren2.AddActor(segmentActor)
cam1 = vtk.vtkCamera()
cam1.SetViewUp(0, -1, 0)
cam1.SetPosition(0, 0, -1)
ren1.SetActiveCamera(cam1)
ren1.ResetCamera()
cam1.SetViewUp(0, -1, 0)
cam1.SetPosition(0.0554068, -0.0596001, -0.491383)
cam1.SetFocalPoint(0.0554068, -0.0596001, 0)
ren1.ResetCameraClippingRange()
ren3.AddActor(greyActor)
ren3.AddActor(segmentOverlayActor)
segmentOverlayActor.SetPosition(0, 0, -.01)
ren3.SetBackground(0, 0, 0)
ren3.SetViewport(0, 0, 1, .5)
ren2.SetActiveCamera(ren1.GetActiveCamera())
ren3.SetActiveCamera(ren1.GetActiveCamera())
renWin.Render()
iren.Start()
# lookup table ''' table = vtk.vtkWindowLevelLookupTable() range_l = img1.GetOutput().GetScalarRange[0] range_h = img1.GetOutput().GetScalarRange[1] print range_h print range_l ''' colorSeries = vtk.vtkColorSeries() colorSeriesEnum = colorSeries.BREWER_QUALITATIVE_SET3 colorSeries.SetColorScheme(colorSeriesEnum) lut = vtk.vtkLookupTable() colorSeries.BuildLookupTable(lut) lut.SetNanColor(1,0,0,1) # lut = vtk.vtkWindowLevelLookupTable() lut.SetWindow(1000) lut.SetLevel(500) mapper1 = vtk.vtkDataSetMapper() mapper1.SetInputData(slicer1.GetOutput()) mapper1.SetLookupTable(lut) mapper2 = vtk.vtkDataSetMapper() mapper2.SetInputData(slicer2.GetOutput()) mapper2.SetLookupTable(lut) actor1 = vtk.vtkActor() actor1.SetMapper(mapper1)
def main():
# colors = vtk.vtkNamedColors()
fileName1, fileName2, sliceNumber = get_program_parameters()
sliceOrder = SliceOrder()
# Now create the RenderWindow, Renderer and Interactor
#
ren1 = vtk.vtkRenderer()
ren2 = vtk.vtkRenderer()
ren3 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.AddRenderer(ren2)
renWin.AddRenderer(ren3)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
greyReader = vtk.vtkMetaImageReader()
greyReader.SetFileName(fileName1)
greyReader.Update()
greyPadder = vtk.vtkImageConstantPad()
greyPadder.SetInputConnection(greyReader.GetOutputPort())
greyPadder.SetOutputWholeExtent(0, 511, 0, 511, sliceNumber, sliceNumber)
greyPadder.SetConstant(0)
greyPlane = vtk.vtkPlaneSource()
greyTransform = vtk.vtkTransformPolyDataFilter()
greyTransform.SetTransform(sliceOrder["hfsi"])
greyTransform.SetInputConnection(greyPlane.GetOutputPort())
greyNormals = vtk.vtkPolyDataNormals()
greyNormals.SetInputConnection(greyTransform.GetOutputPort())
greyNormals.FlipNormalsOff()
wllut = vtk.vtkWindowLevelLookupTable()
wllut.SetWindow(255)
wllut.SetLevel(128)
wllut.SetTableRange(0, 255)
wllut.Build()
greyMapper = vtk.vtkPolyDataMapper()
greyMapper.SetInputConnection(greyPlane.GetOutputPort())
greyTexture = vtk.vtkTexture()
greyTexture.SetInputConnection(greyPadder.GetOutputPort())
greyTexture.SetLookupTable(wllut)
greyTexture.SetColorModeToMapScalars()
greyTexture.InterpolateOn()
greyActor = vtk.vtkActor()
greyActor.SetMapper(greyMapper)
greyActor.SetTexture(greyTexture)
segmentReader = vtk.vtkMetaImageReader()
segmentReader.SetFileName(fileName2)
segmentReader.Update()
segmentPadder = vtk.vtkImageConstantPad()
segmentPadder.SetInputConnection(segmentReader.GetOutputPort())
segmentPadder.SetOutputWholeExtent(0, 511, 0, 511, sliceNumber,
sliceNumber)
segmentPadder.SetConstant(0)
segmentPlane = vtk.vtkPlaneSource()
segmentTransform = vtk.vtkTransformPolyDataFilter()
segmentTransform.SetTransform(sliceOrder["hfsi"])
segmentTransform.SetInputConnection(segmentPlane.GetOutputPort())
segmentNormals = vtk.vtkPolyDataNormals()
segmentNormals.SetInputConnection(segmentTransform.GetOutputPort())
segmentNormals.FlipNormalsOn()
colorLut = CreateFrogLut()
segmentMapper = vtk.vtkPolyDataMapper()
segmentMapper.SetInputConnection(segmentPlane.GetOutputPort())
segmentTexture = vtk.vtkTexture()
segmentTexture.SetInputConnection(segmentPadder.GetOutputPort())
segmentTexture.SetLookupTable(colorLut)
segmentTexture.SetColorModeToMapScalars()
segmentTexture.InterpolateOff()
segmentActor = vtk.vtkActor()
segmentActor.SetMapper(segmentMapper)
segmentActor.SetTexture(segmentTexture)
segmentOverlayActor = vtk.vtkActor()
segmentOverlayActor.SetMapper(segmentMapper)
segmentOverlayActor.SetTexture(segmentTexture)
segmentOverlayActor.GetProperty().SetOpacity(.5)
ren1.SetBackground(0, 0, 0)
ren1.SetViewport(0, .5, .5, 1)
renWin.SetSize(640, 480)
ren1.AddActor(greyActor)
ren2.SetBackground(0, 0, 0)
ren2.SetViewport(.5, .5, 1, 1)
ren2.AddActor(segmentActor)
cam1 = vtk.vtkCamera()
cam1.SetViewUp(0, -1, 0)
cam1.SetPosition(0, 0, -1)
ren1.SetActiveCamera(cam1)
ren1.ResetCamera()
cam1.SetViewUp(0, -1, 0)
cam1.SetPosition(0.0554068, -0.0596001, -0.491383)
cam1.SetFocalPoint(0.0554068, -0.0596001, 0)
ren1.ResetCameraClippingRange()
ren3.AddActor(greyActor)
ren3.AddActor(segmentOverlayActor)
segmentOverlayActor.SetPosition(0, 0, -.01)
ren3.SetBackground(0, 0, 0)
ren3.SetViewport(0, 0, 1, .5)
ren2.SetActiveCamera(ren1.GetActiveCamera())
ren3.SetActiveCamera(ren1.GetActiveCamera())
renWin.Render()
iren.Start()
def main():
# colors = vtk.vtkNamedColors()
fileName1 = "C:\\Users\\chenjiaxing\\Desktop\\VTKTextBook\\Data\\Frog\\frog"
fileName2 = "C:\\Users\\chenjiaxing\\Desktop\\VTKTextBook\\Data\\Frog\\frogTissue"
rows = 500
columns = 470
sliceNumber = 33
start_slice = 1
end_slice = 138
pixel_size = 1
spacing = 1.5
endX = rows - 1
endY = columns - 1
endZ = end_slice - 1
sliceOrder = SliceOrder()
# Now create the RenderWindow, Renderer and Interactor
#
ren1 = vtk.vtkRenderer()
ren2 = vtk.vtkRenderer()
ren3 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.AddRenderer(ren2)
renWin.AddRenderer(ren3)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
#greyReader = vtk.vtkMetaImageReader()
#greyReader.SetFileName(fileName1)
#greyReader.Update()
greyReader = vtk.vtkPNMReader()
greyReader.SetFilePrefix(fileName1)
greyReader.SetDataSpacing(pixel_size, pixel_size, spacing)
greyReader.SetDataVOI(0, endX, 0, endY, sliceNumber, sliceNumber)
greyReader.SetDataExtent(0, endX, 0, endY, sliceNumber, sliceNumber)
greyReader.DebugOn()
greyPadder = vtk.vtkImageConstantPad()
greyPadder.SetInputConnection(greyReader.GetOutputPort())
greyPadder.SetOutputWholeExtent(0, 511, 0, 511, 0, 0)
greyPadder.SetConstant(0)
greyPlane = vtk.vtkPlaneSource()
greyTransform = vtk.vtkTransformPolyDataFilter()
greyTransform.SetTransform(sliceOrder["hfsi"])
greyTransform.SetInputConnection(greyPlane.GetOutputPort())
greyNormals = vtk.vtkPolyDataNormals()
greyNormals.SetInputConnection(greyTransform.GetOutputPort())
greyNormals.FlipNormalsOff()
wllut = vtk.vtkWindowLevelLookupTable()
wllut.SetWindow(255)
wllut.SetLevel(128)
wllut.SetTableRange(0, 255)
wllut.Build()
greyMapper = vtk.vtkPolyDataMapper()
greyMapper.SetInputConnection(greyPlane.GetOutputPort())
greyTexture = vtk.vtkTexture()
greyTexture.SetInputConnection(greyPadder.GetOutputPort())
greyTexture.SetLookupTable(wllut)
greyTexture.SetColorModeToMapScalars()
greyTexture.InterpolateOn()
greyActor = vtk.vtkActor()
greyActor.SetMapper(greyMapper)
greyActor.SetTexture(greyTexture)
segmentReader = vtk.vtkPNMReader()
segmentReader.SetFilePrefix(fileName2)
segmentReader.SetDataSpacing(pixel_size, pixel_size, spacing)
segmentReader.SetDataVOI(0, endX, 0, endY, sliceNumber, sliceNumber)
segmentReader.SetDataExtent(0, endX, 0, endY, sliceNumber, sliceNumber)
segmentReader.Update()
segmentPadder = vtk.vtkImageConstantPad()
segmentPadder.SetInputConnection(segmentReader.GetOutputPort())
segmentPadder.SetOutputWholeExtent(0, 511, 0, 511, 0, 0)
segmentPadder.SetConstant(0)
segmentPlane = vtk.vtkPlaneSource()
segmentTransform = vtk.vtkTransformPolyDataFilter()
segmentTransform.SetTransform(sliceOrder["hfsi"])
segmentTransform.SetInputConnection(segmentPlane.GetOutputPort())
segmentNormals = vtk.vtkPolyDataNormals()
segmentNormals.SetInputConnection(segmentTransform.GetOutputPort())
segmentNormals.FlipNormalsOn()
colorLut = CreateFrogLut()
segmentMapper = vtk.vtkPolyDataMapper()
segmentMapper.SetInputConnection(segmentPlane.GetOutputPort())
segmentTexture = vtk.vtkTexture()
segmentTexture.SetInputConnection(segmentPadder.GetOutputPort())
segmentTexture.SetLookupTable(colorLut)
segmentTexture.SetColorModeToMapScalars()
segmentTexture.InterpolateOff()
segmentActor = vtk.vtkActor()
segmentActor.SetMapper(segmentMapper)
segmentActor.SetTexture(segmentTexture)
segmentOverlayActor = vtk.vtkActor()
segmentOverlayActor.SetMapper(segmentMapper)
segmentOverlayActor.SetTexture(segmentTexture)
segmentOverlayActor.GetProperty().SetOpacity(.5)
ren1.SetBackground(0, 0, 0)
ren1.SetViewport(0, .5, .5, 1)
renWin.SetSize(640, 480)
ren1.AddActor(greyActor)
ren2.SetBackground(0, 0, 0)
ren2.SetViewport(.5, .5, 1, 1)
ren2.AddActor(segmentActor)
cam1 = vtk.vtkCamera()
cam1.SetViewUp(0, -1, 0)
cam1.SetPosition(0, 0, -1)
ren1.SetActiveCamera(cam1)
ren1.ResetCamera()
cam1.SetViewUp(0, -1, 0)
cam1.SetPosition(0.0554068, -0.0596001, -0.491383)
cam1.SetFocalPoint(0.0554068, -0.0596001, 0)
ren1.ResetCameraClippingRange()
ren3.AddActor(greyActor)
ren3.AddActor(segmentOverlayActor)
segmentOverlayActor.SetPosition(0, 0, -.01)
ren3.SetBackground(0, 0, 0)
ren3.SetViewport(0, 0, 1, .5)
ren2.SetActiveCamera(ren1.GetActiveCamera())
ren3.SetActiveCamera(ren1.GetActiveCamera())
renWin.Render()
iren.Start()
def __init__(self, parent, *args, **kw):
VTKPlotWindowGUI.VTKPlotWindowGUI.__init__(self, parent)
# ------------------------------------------------------------------------------------
# Set up some zope event handlers
# ------------------------------------------------------------------------------------
component.provideHandler(self.OnImageChangeEvent)
self._voxel_volume_set = False
self._voxel_volume = 1.0
if ('bar' in kw):
self._usebar = True
else:
self._usebar = False
self._scale = 1.0
self._unit = kw.get('units', 'pixels')
self._dragging = 0 # is this needed?
self._x0 = None
self._y0 = None
self._x1 = None
self._y1 = None
self._select_x0 = None
self._select_x1 = None
self._select_i0 = None
self._select_i1 = None
self.xdata = []
self.ydata = []
self._line = [None, None]
self._liney = None
self._title = "This is the title"
self.filename = ''
self._xlabel = ""
self._ylabel = ""
self._usesymbols = False
# indicates whether nearest data point should be highlighted or not
self._use_highlight_data = True
self._isROI = False
self._linelength = None
self._inputname = ""
self._highlight_visible = False
self.__shortname__ = 'VTKPlot'
self._otsu_threshold = None
self._otsu_marker = None
self._unit_scalings = {'pixels': 1.0, 'mm': 1.0, 'wavelength': 1.0}
self.plot_data = None
self.legend = None
if ('scale' in kw):
self._scale = float(kw['scale'])
if ('title' in kw):
self._title = kw['title']
if ('xlabel' in kw):
self._xlabel = kw['xlabel']
if ('ylabel' in kw):
self._ylabel = kw['ylabel']
# get icon factory
self._stockicons = StockItems.StockIconFactory()
# create info panel - it'll depend on whether this is a line plot or
# histogram window
self.lower_panel = self.CreateLowerPanel()
self.GetSizer().Add(self.lower_panel, 0, wx.EXPAND, 5)
# create a matplotlib panel
self.dpi = 100
self.fig = Figure((3.0, 3.0), dpi=self.dpi)
# self.fig.subplots_adjust(left=0.07, right=0.97, bottom=0.08, top=0.95)
self.fig.subplots_adjust(left=0.0, right=1, bottom=0.0, top=1)
self.axes = self.fig.add_subplot(111)
# default labels
self.axes.set_title(self._title, size=10)
self.axes.set_ylabel(self._ylabel, size=8)
self.line_tool = None # A red, horizontal line tool
self.end_markers = None # Markers that go at the end of each line
self.data_markers = None # Marks that indicate nearest data point
pylab.setp(self.axes.get_xticklabels(), fontsize=8)
pylab.setp(self.axes.get_yticklabels(), fontsize=8)
sizer = wx.BoxSizer(wx.VERTICAL)
# create canvas for plot widget
self.canvas = FigCanvas(self.m_panelMatplotPanel, -1, self.fig)
self.m_panelMatplotPanel.SetSizer(sizer)
self.m_panelMatplotPanel.Fit()
# activate interactive navigation
self.toolbar = MicroViewNavigationToolbar(self.canvas)
self.toolbar.Realize()
tw, th = self.toolbar.GetSizeTuple()
fw, fh = self.canvas.GetSizeTuple()
self.toolbar.SetSize(wx.Size(fw, th))
sizer.Add(self.toolbar, 0, wx.LEFT | wx.EXPAND)
sizer.Add(self.canvas, 1, wx.EXPAND)
self.toolbar.update()
# adjust toolbar
self.EnableToolbar()
# wire up events
self.canvas.mpl_connect('motion_notify_event', self.MouseMoveEvent)
self.canvas.mpl_connect('key_press_event', self.KeyPressEvent)
self.canvas.mpl_connect('figure_leave_event', self.LeaveCanvasEvent)
# wire up events here
self.toolbar.Bind(
wx.EVT_TOOL, self.SaveData, id=self.toolbar.SAVE_DATA)
self.toolbar.Bind(
wx.EVT_TOOL, self.SaveSnapShot, id=self.toolbar.SAVE_SNAPSHOT)
self.toolbar.Bind(
wx.EVT_TOOL, self.symbolsOnOff, id=self.toolbar.VIEW_SYMBOLS)
# self.toolbar.Bind(wx.EVT_TOOL, self.Reset, id=self.toolbar.RESET_VIEW)
self.toolbar.Bind(
wx.EVT_TOOL, self.AutoThreshold, id=self.toolbar.AUTO_THRESHOLD)
self.toolbar.Bind(
wx.EVT_TOOL, self.onCopyHighlightToolbarButton, id=self.toolbar.COPY_HIGHLIGHT)
self.toolbar.Bind(
wx.EVT_TOOL, self.onShowHighlightToolbarToogle, id=self.toolbar.SHOW_HIGHLIGHT)
self.toolbar.Bind(
wx.EVT_TOOL, self.NearestDataSymbolsOnOff, id=self.toolbar.VIEW_NEARESTDATA)
self.toolbar.Bind(
wx.EVT_TOOL, self.select_roi, id=self.toolbar.SELECT_ROI)
# listen to size events
self.Bind(wx.EVT_PAINT, self.OnPaint)
self._plotData = None
# This table is used to make the input invisible
self._wlTableInvisible = vtk.vtkWindowLevelLookupTable()
self._wlTableInvisible.SetSaturationRange(0, 0)
self._wlTableInvisible.SetHueRange(0, 0)
self._wlTableInvisible.SetValueRange(0, 1)
self._wlTableInvisible.SetNumberOfColors(2)
self._wlTableInvisible.SetTableValue(0, 0.0, 0.0, 0.0, 0.0)
self._wlTableInvisible.SetTableValue(1, 0.0, 0.0, 0.0, 0.0)
self._wlTableInvisible.Build()
# Invoke an event to react to currently loaded image
mv = component.getUtility(IMicroViewMainFrame)
current_image = mv.GetCurrentImageIndex()
number_images_displayed = mv.GetNumberOfImagesCurrentlyLoaded()
title = mv.GetCurrentImageTitle()
self.OnImageChangeEvent(CurrentImageChangeEvent(
current_image, number_images_displayed, title))