def LoadVolumeData(self, data_set):
if data_set.endswith('nii') or data_set.endswith('nii.gz'):
try:
from nifti import NiftiImage
except ImportError:
print "Apparently you don't have PyNIfTI installed, see http://www.siafoo.net/snippet/310 for instructions"
exit(1)
nim = NiftiImage(data_set)
img_data = nim.data
elif data_set.endswith('hdr'):
# Use the header to figure out the shape of the data
# then load the raw data and reshape the array
shape = [int(x) for x in open(data_set).readline().split()]
img_data = numpy.frombuffer(open(data_set.replace('.hdr', '.dat'), 'rb').read(),
numpy.uint8)\
.reshape((shape[2], shape[1], shape[0]))
img = vtkImageImportFromArray()
img.SetArray(img_data)
return img
def LoadVolumeData(self, data_set):
if data_set.endswith('nii') or data_set.endswith('nii.gz'):
try:
from nifti import NiftiImage
except ImportError:
print "Apparently you don't have PyNIfTI installed, see http://www.siafoo.net/snippet/310 for instructions"
exit(1)
nim = NiftiImage(data_set)
img_data = nim.data
elif data_set.endswith('hdr'):
# Use the header to figure out the shape of the data
# then load the raw data and reshape the array
shape = [int(x) for x in open(data_set).readline().split()]
img_data = numpy.frombuffer(open(data_set.replace('.hdr', '.dat'), 'rb').read(),
numpy.uint8)\
.reshape((shape[2], shape[1], shape[0]))
img = vtkImageImportFromArray()
img.SetArray(img_data)
return img
def __init__(self, parent, data_set):
wxVTKRenderWindowInteractor.__init__(self,
parent,
-1,
size=parent.GetSize())
ren = vtk.vtkRenderer()
self.GetRenderWindow().AddRenderer(ren)
# prob should allow a string as data_set also, but for now assume it's a python or numpy array
#img = self.LoadVolumeData(data_set) # load from filename
img = vtkImageImportFromArray()
img.SetArray(data_set)
pix_diag = 5.0
# volMapper = vtk.vtkVolumeTextureMapper3D()
volMapper = vtk.vtkVolumeRayCastMapper()
compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
compositeFunction.SetCompositeMethodToInterpolateFirst()
volMapper.SetVolumeRayCastFunction(compositeFunction)
volMapper.SetSampleDistance(pix_diag / 5.0)
volMapper.SetInputConnection(img.GetOutputPort())
# Transfer Functions
self.opacity_tf = vtk.vtkPiecewiseFunction()
self.color_tf = vtk.vtkColorTransferFunction()
# The property describes how the data will look
self.volProperty = volProperty = vtk.vtkVolumeProperty()
volProperty.SetColor(self.color_tf)
volProperty.SetScalarOpacity(self.opacity_tf)
volProperty.ShadeOn()
volProperty.SetInterpolationTypeToLinear()
volProperty.SetScalarOpacityUnitDistance(pix_diag)
vol = vtk.vtkVolume()
vol.SetMapper(volMapper)
vol.SetProperty(volProperty)
ren.AddVolume(vol)
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(self)
boxWidget.SetPlaceFactor(1.0)
# The implicit function vtkPlanes is used in conjunction with the
# volume ray cast mapper to limit which portion of the volume is
# volume rendered.
planes = vtk.vtkPlanes()
def ClipVolumeRender(obj, event):
obj.GetPlanes(planes)
volMapper.SetClippingPlanes(planes)
# Place the interactor initially. The output of the reader is used to
# place the box widget.
boxWidget.SetInput(img.GetOutput())
boxWidget.PlaceWidget()
boxWidget.InsideOutOn()
boxWidget.AddObserver("InteractionEvent", ClipVolumeRender)
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(img.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineProperty = boxWidget.GetOutlineProperty()
outlineProperty.SetRepresentationToWireframe()
outlineProperty.SetAmbient(1.0)
outlineProperty.SetAmbientColor(1, 1, 1)
outlineProperty.SetLineWidth(3)
selectedOutlineProperty = boxWidget.GetSelectedOutlineProperty()
selectedOutlineProperty.SetRepresentationToWireframe()
selectedOutlineProperty.SetAmbient(1.0)
selectedOutlineProperty.SetAmbientColor(1, 0, 0)
selectedOutlineProperty.SetLineWidth(3)
ren.AddActor(outlineActor)
style = vtk.vtkInteractorStyleTrackballCamera()
self.SetInteractorStyle(style)
self.t_graph = TransferGraph(self)
self.SetFocus()
# So we know when new values are added / changed on the tgraph
self.t_graph.Connect(-1, -1, wx.wxEVT_COMMAND_SLIDER_UPDATED,
self.OnTGraphUpdate)
self.OnTGraphUpdate(None)
self.lighting = True
# This is the transfer graph
self.t_graph.Show()
def __init__(self, parent, data_set):
wxVTKRenderWindowInteractor.__init__(self, parent, -1, size=parent.GetSize())
ren = vtk.vtkRenderer()
self.GetRenderWindow().AddRenderer(ren)
# prob should allow a string as data_set also, but for now assume it's a python or numpy array
#img = self.LoadVolumeData(data_set) # load from filename
img = vtkImageImportFromArray()
img.SetArray(data_set)
pix_diag = 5.0
# volMapper = vtk.vtkVolumeTextureMapper3D()
volMapper = vtk.vtkVolumeRayCastMapper()
compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
compositeFunction.SetCompositeMethodToInterpolateFirst()
volMapper.SetVolumeRayCastFunction(compositeFunction)
volMapper.SetSampleDistance(pix_diag / 5.0)
volMapper.SetInputConnection(img.GetOutputPort())
# Transfer Functions
self.opacity_tf = vtk.vtkPiecewiseFunction()
self.color_tf = vtk.vtkColorTransferFunction()
# The property describes how the data will look
self.volProperty = volProperty = vtk.vtkVolumeProperty()
volProperty.SetColor(self.color_tf)
volProperty.SetScalarOpacity(self.opacity_tf)
volProperty.ShadeOn()
volProperty.SetInterpolationTypeToLinear()
volProperty.SetScalarOpacityUnitDistance(pix_diag)
vol = vtk.vtkVolume()
vol.SetMapper(volMapper)
vol.SetProperty(volProperty)
ren.AddVolume(vol)
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(self)
boxWidget.SetPlaceFactor(1.0)
# The implicit function vtkPlanes is used in conjunction with the
# volume ray cast mapper to limit which portion of the volume is
# volume rendered.
planes = vtk.vtkPlanes()
def ClipVolumeRender(obj, event):
obj.GetPlanes(planes)
volMapper.SetClippingPlanes(planes)
# Place the interactor initially. The output of the reader is used to
# place the box widget.
boxWidget.SetInput(img.GetOutput())
boxWidget.PlaceWidget()
boxWidget.InsideOutOn()
boxWidget.AddObserver("InteractionEvent", ClipVolumeRender)
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(img.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineProperty = boxWidget.GetOutlineProperty()
outlineProperty.SetRepresentationToWireframe()
outlineProperty.SetAmbient(1.0)
outlineProperty.SetAmbientColor(1, 1, 1)
outlineProperty.SetLineWidth(3)
selectedOutlineProperty = boxWidget.GetSelectedOutlineProperty()
selectedOutlineProperty.SetRepresentationToWireframe()
selectedOutlineProperty.SetAmbient(1.0)
selectedOutlineProperty.SetAmbientColor(1, 0, 0)
selectedOutlineProperty.SetLineWidth(3)
ren.AddActor(outlineActor)
style = vtk.vtkInteractorStyleTrackballCamera()
self.SetInteractorStyle(style)
self.t_graph = TransferGraph(self)
self.SetFocus()
# So we know when new values are added / changed on the tgraph
self.t_graph.Connect(-1, -1, wx.wxEVT_COMMAND_SLIDER_UPDATED,
self.OnTGraphUpdate)
self.OnTGraphUpdate(None)
self.lighting = True
# This is the transfer graph
self.t_graph.Show()
