def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImageSeedConnectivity(), 'Processing.',
('vtkImageData',), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkImageSeedConnectivity(),
'Processing.', ('vtkImageData', ),
('vtkImageData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def __init__(self, module_manager):
# call parent constructor
ModuleBase.__init__(self, module_manager)
self._imageCast = vtk.vtkImageCast()
self._imageCast.SetOutputScalarTypeToUnsignedChar()
self._seedConnect = vtk.vtkImageSeedConnectivity()
self._seedConnect.SetInput(self._imageCast.GetOutput())
module_utils.setup_vtk_object_progress(self, self._seedConnect,
'Performing region growing')
module_utils.setup_vtk_object_progress(self, self._imageCast,
'Casting data to unsigned char')
# we'll use this to keep a binding (reference) to the passed object
self._inputPoints = None
# this will be our internal list of points
self._seedPoints = []
# now setup some defaults before our sync
self._config.inputConnectValue = 1
self._config.outputConnectedValue = 1
self._config.outputUnconnectedValue = 0
config_list = [
('Input connect value:', 'inputConnectValue', 'base:int', 'text',
'Points connected to seed points with this value will be '
'included.'),
('Output connected value:', 'outputConnectedValue', 'base:int',
'text', 'Included points will get this value.'),
('Output unconnected value:', 'outputUnconnectedValue',
'base:int', 'text', 'Non-included points will get this value.')]
ScriptedConfigModuleMixin.__init__(
self, config_list,
{'Module (self)' : self,
'vtkImageSeedConnectivity' : self._seedConnect,
'vtkImageCast' : self._imageCast})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._image_threshold = vtk.vtkImageThreshold()
# seedconnect wants unsigned char at input
self._image_threshold.SetOutputScalarTypeToUnsignedChar()
self._image_threshold.SetInValue(1)
self._image_threshold.SetOutValue(0)
self._seed_connect = vtk.vtkImageSeedConnectivity()
self._seed_connect.SetInputConnectValue(1)
self._seed_connect.SetOutputConnectedValue(1)
self._seed_connect.SetOutputUnconnectedValue(0)
self._seed_connect.SetInput(self._image_threshold.GetOutput())
module_utils.setup_vtk_object_progress(self, self._seed_connect,
'Performing region growing')
module_utils.setup_vtk_object_progress(self, self._image_threshold,
'Thresholding data')
# we'll use this to keep a binding (reference) to the passed object
self._input_points = None
# this will be our internal list of points
self._seed_points = []
self._config._thresh_interval = 5
config_list = [
('Auto threshold interval:', '_thresh_interval', 'base:float',
'text', 'Used to calculate automatic threshold (unit %).')
]
ScriptedConfigModuleMixin.__init__(
self, config_list, {
'Module (self)': self,
'vtkImageSeedConnectivity': self._seed_connect,
'vtkImageThreshold': self._image_threshold
})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._image_threshold = vtk.vtkImageThreshold()
# seedconnect wants unsigned char at input
self._image_threshold.SetOutputScalarTypeToUnsignedChar()
self._image_threshold.SetInValue(1)
self._image_threshold.SetOutValue(0)
self._seed_connect = vtk.vtkImageSeedConnectivity()
self._seed_connect.SetInputConnectValue(1)
self._seed_connect.SetOutputConnectedValue(1)
self._seed_connect.SetOutputUnconnectedValue(0)
self._seed_connect.SetInput(self._image_threshold.GetOutput())
module_utils.setup_vtk_object_progress(self, self._seed_connect,
'Performing region growing')
module_utils.setup_vtk_object_progress(self, self._image_threshold,
'Thresholding data')
# we'll use this to keep a binding (reference) to the passed object
self._input_points = None
# this will be our internal list of points
self._seed_points = []
self._config._thresh_interval = 5
config_list = [
('Auto threshold interval:', '_thresh_interval', 'base:float',
'text',
'Used to calculate automatic threshold (unit %).')]
ScriptedConfigModuleMixin.__init__(
self, config_list,
{'Module (self)' : self,
'vtkImageSeedConnectivity' : self._seed_connect,
'vtkImageThreshold' : self._image_threshold})
self.sync_module_logic_with_config()
def main():
# colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
# Read the image.
readerFactory = vtk.vtkImageReader2Factory()
reader = readerFactory.CreateImageReader2(fileName)
reader.SetFileName(fileName)
reader.Update()
# Dilate
dilate = vtk.vtkImageDilateErode3D()
dilate.SetInputConnection(reader.GetOutputPort())
dilate.SetDilateValue(0)
dilate.SetErodeValue(255)
dilate.SetKernelSize(31, 31, 1)
# Erode
erode = vtk.vtkImageDilateErode3D()
erode.SetInputConnection(reader.GetOutputPort())
erode.SetDilateValue(255)
erode.SetErodeValue(0)
erode.SetKernelSize(31, 31, 1)
# Opening - dilate then erode.
dilate1 = vtk.vtkImageDilateErode3D()
dilate1.SetInputConnection(reader.GetOutputPort())
dilate1.SetDilateValue(0)
dilate1.SetErodeValue(255)
dilate1.SetKernelSize(31, 31, 1)
erode1 = vtk.vtkImageDilateErode3D()
erode1.SetInputConnection(dilate1.GetOutputPort())
erode1.SetDilateValue(255)
erode1.SetErodeValue(0)
erode1.SetKernelSize(31, 31, 1)
# Closing - erode then dilate.
erode2 = vtk.vtkImageDilateErode3D()
erode2.SetInputConnection(reader.GetOutputPort())
erode2.SetDilateValue(255)
erode2.SetErodeValue(0)
erode2.SetKernelSize(31, 31, 1)
dilate2 = vtk.vtkImageDilateErode3D()
dilate2.SetInputConnection(erode2.GetOutputPort())
dilate2.SetDilateValue(0)
dilate2.SetErodeValue(255)
dilate2.SetKernelSize(31, 31, 1)
# Connectivity
con = vtk.vtkImageSeedConnectivity()
con.SetInputConnection(reader.GetOutputPort())
con.AddSeed(300, 200)
con.SetInputConnectValue(0)
con.SetOutputConnectedValue(0)
con.SetOutputUnconnectedValue(255)
# Actors
originalActor = vtk.vtkImageActor()
originalActor.GetMapper().SetInputConnection(reader.GetOutputPort())
originalActor.GetProperty().SetInterpolationTypeToNearest()
connectedActor = vtk.vtkImageActor()
connectedActor.GetMapper().SetInputConnection(con.GetOutputPort())
connectedActor.GetProperty().SetInterpolationTypeToNearest()
erodeActor = vtk.vtkImageActor()
erodeActor.GetMapper().SetInputConnection(erode.GetOutputPort())
erodeActor.GetProperty().SetInterpolationTypeToNearest()
dilateActor = vtk.vtkImageActor()
dilateActor.GetMapper().SetInputConnection(dilate.GetOutputPort())
dilateActor.GetProperty().SetInterpolationTypeToNearest()
openingActor = vtk.vtkImageActor()
openingActor.GetMapper().SetInputConnection(dilate2.GetOutputPort())
openingActor.GetProperty().SetInterpolationTypeToNearest()
closingActor = vtk.vtkImageActor()
closingActor.GetMapper().SetInputConnection(erode1.GetOutputPort())
closingActor.GetProperty().SetInterpolationTypeToNearest()
# Setup renderers
originalRenderer = vtk.vtkRenderer()
originalRenderer.AddActor(originalActor)
connectedRenderer = vtk.vtkRenderer()
connectedRenderer.AddActor(connectedActor)
dilateRenderer = vtk.vtkRenderer()
dilateRenderer.AddActor(dilateActor)
erodeRenderer = vtk.vtkRenderer()
erodeRenderer.AddActor(erodeActor)
closingRenderer = vtk.vtkRenderer()
closingRenderer.AddActor(closingActor)
openingRenderer = vtk.vtkRenderer()
openingRenderer.AddActor(openingActor)
renderers = list()
renderers.append(originalRenderer)
renderers.append(connectedRenderer)
renderers.append(erodeRenderer)
renderers.append(dilateRenderer)
renderers.append(openingRenderer)
renderers.append(closingRenderer)
# Setup viewports for the renderers
rendererSize = 300
xGridDimensions = 2
yGridDimensions = 3
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(rendererSize * xGridDimensions,
rendererSize * yGridDimensions)
for row in range(0, yGridDimensions):
for col in range(xGridDimensions):
index = row * xGridDimensions + col
# (xmin, ymin, xmax, ymax)
viewport = [
float(col) / xGridDimensions,
float(yGridDimensions - (row + 1)) / yGridDimensions,
float(col + 1) / xGridDimensions,
float(yGridDimensions - row) / yGridDimensions
]
renderers[index].SetViewport(viewport)
renderWindow.AddRenderer(renderers[index])
renderWindow.SetWindowName('MorphologyComparison')
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
style = vtk.vtkInteractorStyleImage()
renderWindowInteractor.SetInteractorStyle(style)
renderWindowInteractor.SetRenderWindow(renderWindow)
# The renderers share one camera.
renderWindow.Render()
renderers[0].GetActiveCamera().Dolly(1.5)
renderers[0].ResetCameraClippingRange()
for r in range(1, len(renderers)):
renderers[r].SetActiveCamera(renderers[0].GetActiveCamera())
renderWindowInteractor.Initialize()
renderWindowInteractor.Start()
def _calculate_selection(self):
"""Calculate the selection contour based on the input data and seedpoints
"""
for actor in self.contour_selected_actors:
self.renderer_top.RemoveActor(actor)
self.renderer_side.RemoveActor(actor)
self.renderer_front.RemoveActor(actor)
self.renderer_3d.RemoveActor(actor)
# initial cleanup
self.selectedData = []
self.contour_selected_actors = []
self._contourObjectsDict1 = {}
self._contourObjectsDict2 = {}
self._contourObjectsDict3 = {}
if self.frame.continuous_check.GetValue():
for seed_point in self.seedPoints:
#self._config._thresh_interval = 5
_image_threshold = vtk.vtkImageThreshold()
# seedconnect wants unsigned char at input
_image_threshold.SetOutputScalarTypeToUnsignedChar()
_image_threshold.SetInValue(1)
_image_threshold.SetOutValue(0)
_image_threshold.SetInput(self._inputs[0]['inputData'])
_seed_connect = vtk.vtkImageSeedConnectivity()
_seed_connect.SetInputConnectValue(1)
_seed_connect.SetOutputConnectedValue(1)
_seed_connect.SetOutputUnconnectedValue(0)
_seed_connect.SetInput(_image_threshold.GetOutput())
# extract a list from the input points
_seed_connect.RemoveAllSeeds()
# we need to call Modified() explicitly as RemoveAllSeeds()
# doesn't. AddSeed() does, but sometimes the list is empty at
# this stage and AddSeed() isn't called.
_seed_connect.Modified()
for seedPoint in self.seedPoints:
if not seedPoint == None:
_seed_connect.AddSeed(seedPoint[0], seedPoint[1], seedPoint[2])
#Determine threshold
iso_value = seed_point[3]
lower_thresh = iso_value + self.frame.lower_slider.GetValue()
upper_thresh = iso_value + self.frame.upper_slider.GetValue()
_image_threshold.ThresholdBetween(lower_thresh, upper_thresh)
#Update all stuff
_image_threshold.GetInput().Update()
_image_threshold.Update()
_seed_connect.Update()
#Create the contour
contourFilter = vtk.vtkContourFilter()
contourFilter.SetInput(_seed_connect.GetOutput())
contourFilter.GenerateValues(contourFilter.GetNumberOfContours(), 1, 1) #because 1 is output in-value
contourFilter.Update()
# Setup Actor and Mapper
actor = vtk.vtkActor()
mapper = vtk.vtkPolyDataMapper()
mapper.ScalarVisibilityOff()
actor.SetMapper(mapper)
self.renderer_3d.AddActor(actor)
# Set output to mapper
data = contourFilter.GetOutput()
mapper.SetInput(data)
mapper.Update()
self.addSelectionTo2DViewers(data, actor)
# Save result
self.selectedData.append(data)
self.contour_selected_actors.append(actor)
#End for-loop
else:
for seedPoint in self.seedPoints:
if not seedPoint == None:
iso_value = seedPoint[3]
#print "working on seedpoint with iso" + str(iso_value)
# Setup Actor and Mapper
actor = vtk.vtkActor()
mapper = vtk.vtkPolyDataMapper()
mapper.ScalarVisibilityOff()
actor.SetMapper(mapper)
self.renderer_3d.AddActor(actor)
# Calculate Polydata
contourFilter = vtk.vtkContourFilter()
contourFilter.SetInput(self._inputs[0]['inputData'])
contourFilter.GenerateValues(contourFilter.GetNumberOfContours(), iso_value + self.frame.lower_slider.GetValue(), iso_value + self.frame.upper_slider.GetValue())
contourFilter.Update()
# Set output to mapper
data = contourFilter.GetOutput()
mapper.SetInput(data)
mapper.Update()
self.addSelectionTo2DViewers(data, actor)
# Save result
self.selectedData.append(data)
self.contour_selected_actors.append(actor)
# Set colors
self._on_select_new_color()
self.render()
return self.selectedData
extractImage = vtk.vtkImageExtractComponents()
extractImage.SetInputConnection(toHSV.GetOutputPort())
extractImage.SetComponents(2)
extractImage.GetExecutive().SetReleaseDataFlag(0, 0)
threshold1 = vtk.vtkImageThreshold()
threshold1.SetInputConnection(extractImage.GetOutputPort())
threshold1.ThresholdByUpper(230)
threshold1.SetInValue(255)
threshold1.SetOutValue(0)
threshold1.Update()
extent = threshold1.GetExecutive().GetWholeExtent(
threshold1.GetOutputInformation(0))
connect = vtk.vtkImageSeedConnectivity()
connect.SetInputConnection(threshold1.GetOutputPort())
connect.SetInputConnectValue(255)
connect.SetOutputConnectedValue(255)
connect.SetOutputUnconnectedValue(0)
connect.AddSeed(extent[0], extent[2])
connect.AddSeed(extent[1], extent[2])
connect.AddSeed(extent[1], extent[3])
connect.AddSeed(extent[0], extent[3])
smooth = vtk.vtkImageGaussianSmooth()
smooth.SetDimensionality(2)
smooth.SetStandardDeviation(1, 1)
smooth.SetInputConnection(connect.GetOutputPort())
shrink = vtk.vtkImageShrink3D()
imagePowerOf2.SetOutputWholeExtent(0,expr.expr(globals(), locals(),["padX","-","1"]),0,expr.expr(globals(), locals(),["padY","-","1"]),0,0) toHSV = vtk.vtkImageRGBToHSV() toHSV.SetInputConnection(imageIn.GetOutputPort()) toHSV.GetExecutive().SetReleaseDataFlag(0,0) extractImage = vtk.vtkImageExtractComponents() extractImage.SetInputConnection(toHSV.GetOutputPort()) extractImage.SetComponents(2) extractImage.GetExecutive().SetReleaseDataFlag(0,0) threshold1 = vtk.vtkImageThreshold() threshold1.SetInputConnection(extractImage.GetOutputPort()) threshold1.ThresholdByUpper(230) threshold1.SetInValue(255) threshold1.SetOutValue(0) threshold1.Update() extent = threshold1.GetExecutive().GetWholeExtent(threshold1.GetOutputInformation(0)) connect = vtk.vtkImageSeedConnectivity() connect.SetInputConnection(threshold1.GetOutputPort()) connect.SetInputConnectValue(255) connect.SetOutputConnectedValue(255) connect.SetOutputUnconnectedValue(0) connect.AddSeed(lindex(extent,0),lindex(extent,2)) connect.AddSeed(lindex(extent,1),lindex(extent,2)) connect.AddSeed(lindex(extent,1),lindex(extent,3)) connect.AddSeed(lindex(extent,0),lindex(extent,3)) smooth = vtk.vtkImageGaussianSmooth() smooth.SetDimensionality(2) smooth.SetStandardDeviation(1,1) smooth.SetInputConnection(connect.GetOutputPort()) shrink = vtk.vtkImageShrink3D() shrink.SetInputConnection(smooth.GetOutputPort()) shrink.SetShrinkFactors(2,2,1)
