def __init__(self, module_manager):
"""Standard constructor. All DeVIDE modules have these, we do
the required setup actions.
"""
# we record the setting here, in case the user changes it
# during the lifetime of this model, leading to different
# states at init and shutdown.
self.IMAGE_VIEWER = IMAGE_VIEWER
# we need all this for our contours
self.mask_data = None
self.image_data = None
self.lungVolume = None
self.contour_severe_actor = vtk.vtkActor()
self.contour_moderate_actor = vtk.vtkActor()
self.contour_lungedge_actor = vtk.vtkActor()
self.severe_mapper = vtk.vtkPolyDataMapper()
self.severe_mapper.ScalarVisibilityOff()
self.moderate_mapper = vtk.vtkPolyDataMapper()
self.moderate_mapper.ScalarVisibilityOff()
self.lung_mapper = vtk.vtkPolyDataMapper()
self.lung_mapper.ScalarVisibilityOff()
self.contour_severe_actor.SetMapper(self.severe_mapper)
self.contour_severe_actor.GetProperty().SetColor(1, 0, 0)
self.contour_severe_actor.GetProperty().SetOpacity(0.5)
self.contour_moderate_actor.SetMapper(self.moderate_mapper)
self.contour_moderate_actor.GetProperty().SetColor(0.5, 0, 1)
self.contour_moderate_actor.GetProperty().SetOpacity(0.25)
self.contour_lungedge_actor.SetMapper(self.lung_mapper)
self.contour_lungedge_actor.GetProperty().SetColor(0.9, 0.9, 0.9)
self.contour_lungedge_actor.GetProperty().SetOpacity(0.1)
ModuleBase.__init__(self, module_manager)
# create the view frame
self._view_frame = module_utils.instantiate_module_view_frame(
self, self._module_manager,
EmphysemaViewerFrame.EmphysemaViewerFrame)
# change the title to something more spectacular (or at least something non-default)
self._view_frame.SetTitle('EmphysemaViewer')
# create the necessary VTK objects: we only need a renderer,
# the RenderWindowInteractor in the view_frame has the rest.
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(0.5, 0.5, 0.5)
self._view_frame.rwi.GetRenderWindow().AddRenderer(self.ren)
self.ren.AddActor(self.contour_severe_actor)
self.ren.AddActor(self.contour_moderate_actor)
self.ren.AddActor(self.contour_lungedge_actor)
self.ren2 = vtk.vtkRenderer()
self.ren2.SetBackground(0.5, 0.5, 0.5)
self._view_frame.overlay.GetRenderWindow().AddRenderer(self.ren2)
self.slice_viewer1 = CMSliceViewer(self._view_frame.overlay, self.ren2)
self.ren3 = vtk.vtkRenderer()
self.ren3.SetBackground(0.5, 0.5, 0.5)
self._view_frame.original.GetRenderWindow().AddRenderer(self.ren3)
self.slice_viewer2 = CMSliceViewer(self._view_frame.original,
self.ren3)
self.slice_viewer3 = CMSliceViewer(self._view_frame.rwi, self.ren)
self.sync = SyncSliceViewers()
self.sync.add_slice_viewer(self.slice_viewer1)
self.sync.add_slice_viewer(self.slice_viewer2)
self.sync.add_slice_viewer2(self.slice_viewer3)
# hook up all event handlers
self._bind_events()
# anything you stuff into self._config will be saved
self._config.last_used_dir = ''
# make our window appear (this is a viewer after all)
self.view()
# all modules should toggle this once they have shown their
# views.
self.view_initialised = True
# apply config information to underlying logic
self.sync_module_logic_with_config()
# then bring it all the way up again to the view
self.sync_module_view_with_logic()
class EmphysemaViewer(IntrospectModuleMixin, ModuleBase):
"""Module to visualize lungemphysema in a CT scan. A lung mask is also needed.
EmphysemaViewer consists of a volume rendering and two linked slice-based views; one with the original data and one with an emphysema overlay. The volume rendering shows 3
contours: the lungedges and 2 different contours of emphysema; a normal one and a severe one.
There are two ways of setting the emphysema values.
- The first way is choosing the 'default' values, which are literature-based. They are set on -950 HU (emphysema) and -970 HU (severe).
- The other way is a computational way: The lowest 11% values, that are present in the data are marked as emphysema, the lowest 8,5% values are marked as severe emphysema.
The theory behind this is the hypothesis that the histograms of emphysema patients differ from healthy people in a way that in emphysema patients there are relatively more
lower values present. In both ways you can finetune the values, or completely change them (if you want to).
After loading your image data and mask data, you can inspect the data and examine the severity of the emphysema of the patient.
Controls:
LMB: The left mouse button can be used to rotate objects in the 3D scene, or to poll Houndsfield Units in areas of interest (click and hold to see the values)\n
RMB: For the slice viewers, you can set the window and level values by clicking and holding the right mouse button in a slice and moving your mouse. You can see the current
window and level values in the bottom of the viewer. Outside of the slice, this zooms the camera in and out\n
MMB: The middle mouse button enables stepping through the slices if clicked and held in the center of the slice. When clicking on de edges of a slice, this re-orients the
entire slice. Outside of the slice, this pans the camera\n
Scrollwheel: The scrollwheel can be used for zooming in and out of a scene, but also for sliceviewing if used with the CTRL- or SHIFT-key\n
SHIFT: By holding the SHIFT-key, it is possible to use the mouse scrollwheel to scroll through the slices.\n
CTRL: Holding the CTRL-key does the same, but enables stepping through the data in steps of 10 slices.\n
"""
def __init__(self, module_manager):
"""Standard constructor. All DeVIDE modules have these, we do
the required setup actions.
"""
# we record the setting here, in case the user changes it
# during the lifetime of this model, leading to different
# states at init and shutdown.
self.IMAGE_VIEWER = IMAGE_VIEWER
# we need all this for our contours
self.mask_data = None
self.image_data = None
self.lungVolume = None
self.contour_severe_actor = vtk.vtkActor()
self.contour_moderate_actor = vtk.vtkActor()
self.contour_lungedge_actor = vtk.vtkActor()
self.severe_mapper = vtk.vtkPolyDataMapper()
self.severe_mapper.ScalarVisibilityOff()
self.moderate_mapper = vtk.vtkPolyDataMapper()
self.moderate_mapper.ScalarVisibilityOff()
self.lung_mapper = vtk.vtkPolyDataMapper()
self.lung_mapper.ScalarVisibilityOff()
self.contour_severe_actor.SetMapper(self.severe_mapper)
self.contour_severe_actor.GetProperty().SetColor(1, 0, 0)
self.contour_severe_actor.GetProperty().SetOpacity(0.5)
self.contour_moderate_actor.SetMapper(self.moderate_mapper)
self.contour_moderate_actor.GetProperty().SetColor(0.5, 0, 1)
self.contour_moderate_actor.GetProperty().SetOpacity(0.25)
self.contour_lungedge_actor.SetMapper(self.lung_mapper)
self.contour_lungedge_actor.GetProperty().SetColor(0.9, 0.9, 0.9)
self.contour_lungedge_actor.GetProperty().SetOpacity(0.1)
ModuleBase.__init__(self, module_manager)
# create the view frame
self._view_frame = module_utils.instantiate_module_view_frame(
self, self._module_manager,
EmphysemaViewerFrame.EmphysemaViewerFrame)
# change the title to something more spectacular (or at least something non-default)
self._view_frame.SetTitle('EmphysemaViewer')
# create the necessary VTK objects: we only need a renderer,
# the RenderWindowInteractor in the view_frame has the rest.
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(0.5, 0.5, 0.5)
self._view_frame.rwi.GetRenderWindow().AddRenderer(self.ren)
self.ren.AddActor(self.contour_severe_actor)
self.ren.AddActor(self.contour_moderate_actor)
self.ren.AddActor(self.contour_lungedge_actor)
self.ren2 = vtk.vtkRenderer()
self.ren2.SetBackground(0.5, 0.5, 0.5)
self._view_frame.overlay.GetRenderWindow().AddRenderer(self.ren2)
self.slice_viewer1 = CMSliceViewer(self._view_frame.overlay, self.ren2)
self.ren3 = vtk.vtkRenderer()
self.ren3.SetBackground(0.5, 0.5, 0.5)
self._view_frame.original.GetRenderWindow().AddRenderer(self.ren3)
self.slice_viewer2 = CMSliceViewer(self._view_frame.original,
self.ren3)
self.slice_viewer3 = CMSliceViewer(self._view_frame.rwi, self.ren)
self.sync = SyncSliceViewers()
self.sync.add_slice_viewer(self.slice_viewer1)
self.sync.add_slice_viewer(self.slice_viewer2)
self.sync.add_slice_viewer2(self.slice_viewer3)
# hook up all event handlers
self._bind_events()
# anything you stuff into self._config will be saved
self._config.last_used_dir = ''
# make our window appear (this is a viewer after all)
self.view()
# all modules should toggle this once they have shown their
# views.
self.view_initialised = True
# apply config information to underlying logic
self.sync_module_logic_with_config()
# then bring it all the way up again to the view
self.sync_module_view_with_logic()
def close(self):
"""Clean-up method called on all DeVIDE modules when they are
deleted.
FIXME: Still get a nasty X error :(
"""
# with this complicated de-init, we make sure that VTK is
# properly taken care of
self.ren.RemoveAllViewProps()
self.ren2.RemoveAllViewProps()
self.ren3.RemoveAllViewProps()
# this finalize makes sure we don't get any strange X
# errors when we kill the module.
self.slice_viewer1.close()
self.slice_viewer2.close()
self.slice_viewer3.close()
self._view_frame.rwi.GetRenderWindow().Finalize()
self._view_frame.rwi.SetRenderWindow(None)
self._view_frame.overlay.GetRenderWindow().Finalize()
self._view_frame.overlay.SetRenderWindow(None)
self._view_frame.original.GetRenderWindow().Finalize()
self._view_frame.original.SetRenderWindow(None)
del self._view_frame.rwi
del self._view_frame.overlay
del self._view_frame.original
del self.slice_viewer3
del self.slice_viewer2
del self.slice_viewer1
# done with VTK de-init
# now take care of the wx window
self._view_frame.close()
# then shutdown our introspection mixin
IntrospectModuleMixin.close(self)
def get_input_descriptions(self):
# define this as a tuple of input descriptions if you want to
# take input data e.g. return ('vtkPolyData', 'my kind of
# data')
return ()
def get_output_descriptions(self):
# define this as a tuple of output descriptions if you want to
# generate output data.
return ()
def set_input(self, idx, input_stream):
# this gets called right before you get executed. take the
# input_stream and store it so that it's available during
# execute_module()
pass
def get_output(self, idx):
# this can get called at any time when a consumer module wants
# you output data.
pass
def execute_module(self):
# when it's you turn to execute as part of a network
# execution, this gets called.
pass
def logic_to_config(self):
pass
def config_to_logic(self):
pass
def config_to_view(self):
pass
def view_to_config(self):
pass
def view(self):
self._view_frame.Show()
self._view_frame.Raise()
# because we have an RWI involved, we have to do this
# SafeYield, so that the window does actually appear before we
# call the render. If we don't do this, we get an initial
# empty renderwindow.
wx.SafeYield()
self.render()
def create_volumerender(self, contourValueModerate, contourValueSevere):
"""Creates a volumerender of the masked data using iso-contour surfaces
created by the Marching Cubes algorithm at the specified contourvalues.
"""
self._view_frame.SetStatusText("Creating Volumerender...")
self.image_data
mask = vtk.vtkImageMask()
severeFraction = 0.10
moderateFraction = 0.12
# We only want to contour the lungs, so mask it
mask.SetMaskInput(self.mask_data)
mask.SetInput(self.image_data)
mask.Update()
self.lungVolume = mask.GetOutput()
if contourValueModerate == 0 and contourValueSevere == 0: # This means we get to calculate the percentual values ourselves!
scalars = self.lungVolume.GetScalarRange()
range = scalars[1] - scalars[0]
contourValueSevere = scalars[0] + range * severeFraction
contourValueModerate = scalars[0] + range * moderateFraction
self._view_frame.upper_slider.SetValue(contourValueModerate)
self._view_frame.lower_slider.SetValue(contourValueSevere)
self.create_overlay(contourValueModerate, contourValueSevere)
# Create the contours
self.adjust_contour(self.lungVolume, contourValueSevere,
self.severe_mapper)
self.adjust_contour(self.lungVolume, contourValueModerate,
self.moderate_mapper)
#self.adjust_contour(self.mask_data, 0.5, self.lung_mapper)
self.create_lungcontour()
# Set the camera to a nice view
cam = self.ren.GetActiveCamera()
cam.SetPosition(0, -100, 0)
cam.SetFocalPoint(0, 0, 0)
cam.SetViewUp(0, 0, 1)
self.ren.ResetCamera()
self.render()
self._view_frame.SetStatusText("Created Volumerender")
def adjust_contour(self, volume, contourValue, mapper):
"""Adjust or create an isocontour using the Marching Cubes surface at the given
value using the given mapper
"""
self._view_frame.SetStatusText("Calculating new volumerender...")
contour = vtk.vtkMarchingCubes()
contour.SetValue(0, contourValue)
contour.SetInput(volume)
mapper.SetInput(contour.GetOutput())
mapper.Update()
self.render()
self._view_frame.SetStatusText("Calculated new volumerender")
def create_lungcontour(self):
"""Create a lungcontour using the Marching Cubes algorithm and smooth the surface
"""
self._view_frame.SetStatusText("Calculating lungcontour...")
contourLung = vtk.vtkMarchingCubes()
contourLung.SetValue(0, 1)
contourLung.SetInput(self.mask_data)
smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother.SetInput(contourLung.GetOutput())
smoother.BoundarySmoothingOn()
smoother.SetNumberOfIterations(40)
smoother.Update()
self.lung_mapper.SetInput(smoother.GetOutput())
self.lung_mapper.Update()
self._view_frame.SetStatusText("Calculated lungcontour")
def create_overlay(self, emphysemavalue, severeemphysemavalue):
"""Creates an overlay for the slice-based volume view
0: no emphysema
1: moderate emphysema
2: severe emphysema
"""
self._view_frame.SetStatusText("Creating Overlay...")
mask = vtk.vtkImageMask()
mask2 = vtk.vtkImageMask()
threshold = vtk.vtkImageThreshold()
threshold2 = vtk.vtkImageThreshold()
math = vtk.vtkImageMathematics()
mask.SetInput(self.image_data)
mask.SetMaskInput(self.mask_data)
threshold.SetInput(mask.GetOutput())
threshold.ThresholdByLower(emphysemavalue)
threshold.SetOutValue(0)
threshold.SetInValue(1)
threshold2.SetInput(mask.GetOutput())
threshold2.ThresholdByLower(severeemphysemavalue)
threshold2.SetOutValue(1)
threshold2.SetInValue(2)
math.SetOperationToMultiply()
math.SetInput1(threshold.GetOutput())
math.SetInput2(threshold2.GetOutput())
math.Update()
overlay = math.GetOutput()
self.slice_viewer1.set_overlay_input(None)
self.slice_viewer1.set_overlay_input(overlay)
self.render()
self._view_frame.SetStatusText("Created Overlay")
def load_data_from_file(self, file_path):
"""Loads scanvolume data from file. Also sets the volume as input for the sliceviewers
"""
self._view_frame.SetStatusText("Opening file: %s..." % (file_path))
filename = os.path.split(file_path)[1]
fileBaseName = os.path.splitext(filename)[0]
reader = vtk.vtkMetaImageReader()
reader.SetFileName(file_path)
reader.Update()
self.image_data = reader.GetOutput()
self.slice_viewer1.set_input(self.image_data)
self.slice_viewer1.reset_camera()
self.slice_viewer1.render()
self.slice_viewer2.set_input(self.image_data)
self.slice_viewer2.reset_camera()
self.slice_viewer2.render()
self.slice_viewer3.set_input(self.image_data)
self.slice_viewer3.render()
self.slice_viewer3.set_opacity(0.1)
cam = self.ren.GetActiveCamera()
cam.SetPosition(0, -100, 0)
cam.SetFocalPoint(0, 0, 0)
cam.SetViewUp(0, 0, 1)
self.ren.ResetCamera()
if (self.mask_data
) is not None: # We can start calculating the volumerender
self.create_volumerender(0, 0)
else:
self._view_frame.SetStatusText("Opened file")
def load_mask_from_file(self, file_path):
"""Loads mask file
"""
self._view_frame.SetStatusText("Opening mask: %s..." % (file_path))
filename = os.path.split(file_path)[1]
fileBaseName = os.path.splitext(filename)[0]
reader = vtk.vtkMetaImageReader()
reader.SetFileName(file_path)
reader.Update()
self.mask_data = reader.GetOutput()
if (self.image_data) is not None:
self.create_volumerender(0, 0)
else:
self._view_frame.SetStatusText("Opened mask file")
def save_to_file(self, file_path):
"""Save data from main renderwindow (the contour one) to a PNG-file
"""
w2i = vtk.vtkWindowToImageFilter()
w2i.SetInput(self._view_frame.rwi.GetRenderWindow())
w2i.Update()
writer = vtk.vtkPNGWriter()
writer.SetInput(w2i.GetOutput())
writer.SetFileName(file_path)
writer.Update()
result = writer.Write()
if result == 0:
self._view_frame.SetStatusText("Saved file")
else:
self._view_frame.SetStatusText("Saved file to: %s..." %
(file_path))
def _bind_events(self):
"""Bind wx events to Python callable object event handlers.
"""
vf = self._view_frame
vf.Bind(wx.EVT_MENU, self._handler_file_open, id=vf.id_file_open)
vf.Bind(wx.EVT_MENU, self._handler_mask_open, id=vf.id_mask_open)
vf.Bind(wx.EVT_MENU, self._handler_file_save, id=vf.id_mask_save)
self._view_frame.button1.Bind(wx.EVT_BUTTON, self._handler_button1)
self._view_frame.button2.Bind(wx.EVT_BUTTON, self._handler_button2)
self._view_frame.button3.Bind(wx.EVT_BUTTON, self._handler_button3)
self._view_frame.button4.Bind(wx.EVT_BUTTON, self._handler_button4)
self._view_frame.button5.Bind(wx.EVT_BUTTON, self._handler_button5)
self._view_frame.button6.Bind(wx.EVT_BUTTON, self._handler_button6)
self._view_frame.upper_slider.Bind(wx.EVT_SCROLL_CHANGED,
self._handler_slider1)
self._view_frame.lower_slider.Bind(wx.EVT_SCROLL_CHANGED,
self._handler_slider2)
def _handler_button1(self, event):
"""Reset the camera of the main render window
"""
self.ren.ResetCamera()
self.render()
def _handler_button2(self, event):
"""Reset all for the main render window
"""
cam = self.ren.GetActiveCamera()
cam.SetPosition(0, -100, 0)
cam.SetFocalPoint(0, 0, 0)
cam.SetViewUp(0, 0, 1)
self.ren.ResetCamera()
self.render()
def _handler_button3(self, event):
"""Reset the camera for the sliceviewers
"""
self.slice_viewer1.reset_camera()
self.slice_viewer2.reset_camera()
self.render()
def _handler_button4(self, event):
"""Reset all for the sliceviewers
"""
self.slice_viewer1.reset_to_default_view(2)
self.slice_viewer2.reset_to_default_view(2)
orientations = [2, 0, 1]
for i, ipw in enumerate(self.slice_viewer1.ipws):
ipw.SetPlaneOrientation(orientations[i]) # axial
ipw.SetSliceIndex(0)
self.render()
for i, ipw in enumerate(self.slice_viewer2.ipws):
ipw.SetPlaneOrientation(orientations[i]) # axial
ipw.SetSliceIndex(0)
self.render()
def _handler_button5(self, event):
"""Adjust the contourvalues to values recommended in literature
"""
if self.lungVolume == None:
return
else:
self._view_frame.upper_slider.SetValue(-950)
self._view_frame.lower_slider.SetValue(-970)
self.adjust_contour(self.lungVolume, -950, self.moderate_mapper)
self.adjust_contour(self.lungVolume, -970, self.severe_mapper)
self.create_overlay(-950, -970)
def _handler_button6(self, event):
"""Adjust the contourvalues to values calculated from data
"""
if self.lungVolume == None:
return
else:
self.create_volumerender(0, 0)
def _handler_file_open(self, event):
"""Handler for file opening
"""
filters = 'Volume files (*.mhd)|*.mhd;'
dlg = wx.FileDialog(self._view_frame, "Please choose a CT-thorax file",
self._config.last_used_dir, "", filters, wx.OPEN)
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetFilename()
self._config.last_used_dir = dlg.GetDirectory()
full_file_path = "%s/%s" % (self._config.last_used_dir, filename)
self.load_data_from_file(full_file_path)
dlg.Destroy()
def _handler_mask_open(self, event):
"""Handler for mask opening
"""
filters = 'Mask files (*.mhd;#.mha)|*.mhd;*mha;'
dlg = wx.FileDialog(self._view_frame,
"Please choose a CT-thorax mask file",
self._config.last_used_dir, "", filters, wx.OPEN)
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetFilename()
self._config.last_used_dir = dlg.GetDirectory()
full_file_path = "%s/%s" % (self._config.last_used_dir, filename)
self.load_mask_from_file(full_file_path)
dlg.Destroy()
def _handler_file_save(self, event):
"""Handler for filesaving
"""
self._view_frame.SetStatusText("Saving file...")
filters = 'png file (*.png)|*.png'
dlg = wx.FileDialog(self._view_frame, "Choose a destination",
self._config.last_used_dir, "", filters, wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetFilename()
self._config.last_used_dir = dlg.GetDirectory()
file_path = "%s/%s" % (self._config.last_used_dir, filename)
self.save_to_file(file_path)
dlg.Destroy()
self._view_frame.SetStatusText("Saved file")
def _handler_slider1(self, event):
"""Handler for slider adjustment (Severe emphysema)
"""
if self.lungVolume == None:
return
else:
contourValue = self._view_frame.upper_slider.GetValue()
self.adjust_contour(self.lungVolume, contourValue,
self.moderate_mapper)
self.create_overlay(contourValue,
self._view_frame.lower_slider.GetValue())
def _handler_slider2(self, event):
"""Handler for slider adjustment (Moderate emphysema)
"""
if self.lungVolume == None:
return
else:
contourValue = self._view_frame.lower_slider.GetValue()
self.adjust_contour(self.lungVolume, contourValue,
self.severe_mapper)
self.create_overlay(self._view_frame.upper_slider.GetValue(),
contourValue)
def render(self):
"""Method that calls Render() on the embedded RenderWindow.
Use this after having made changes to the scene.
"""
self._view_frame.render()
self.slice_viewer1.render()
def _init_frame():
# call base constructor
ModuleBase.__init__(self, module_manager)
self._numDataInputs = self.NUM_INPUTS
# use list comprehension to create list keeping track of inputs
self._inputs = [{'Connected' : None, 'inputData' : None,
'vtkActor' : None, 'ipw' : None}
for i in range(self._numDataInputs)]
# create the view frame
self.frame = module_utils.instantiate_module_view_frame(
self, self._module_manager,
multiDirectionalSlicedViewSegmentation3dVieWeRFrame.multiDirectionalSlicedViewSegmentation3dVieWeRFrame)
#THE FRAME (reference)
frame = self.frame
# change the title to something more spectacular (or at least something non-default)
frame.SetTitle('multiDirectionalSlicedViewSegmentation3dVieWeR')
# predefine this
self.selectedData = []
self.controlIsCurrentlyDown = 0
# list of objects that want to be contoured by this slice
self._contourObjectsDict1 = {}
self._contourObjectsDict2 = {}
self._contourObjectsDict3 = {}
# anything you stuff into self._config will be saved
self._config.last_used_dir = ''
#color definitions
twoD_bg_color = (0.19,0.19,0.19)
threeD_bg_color = (0.62,0.62,0.62)
contour_color = (0.6,0.6,0.6)
# create the necessary VTK objects
# setup the Top Renderer (id: 1)
self.renderer_top = vtk.vtkRenderer()
self.renderer_top.SetBackground(twoD_bg_color)
frame.top.GetRenderWindow().AddRenderer(self.renderer_top)
self.slice_viewer_top = CMSliceViewer(frame.top, self.renderer_top)
self.slice_viewer_top.set_parallel()
# setup the Side Renderer (id: 2)
self.renderer_side = vtk.vtkRenderer()
self.renderer_side.SetBackground(twoD_bg_color)
frame.side.GetRenderWindow().AddRenderer(self.renderer_side)
self.slice_viewer_side = CMSliceViewer(frame.side, self.renderer_side)
self.slice_viewer_side.set_parallel()
# setup the Front Renderer (id: 3)
self.renderer_front = vtk.vtkRenderer()
self.renderer_front.SetBackground(twoD_bg_color)
frame.front.GetRenderWindow().AddRenderer(self.renderer_front)
self.slice_viewer_front = CMSliceViewer(frame.front, self.renderer_front)
self.slice_viewer_front.set_parallel()
# setup the 3D Renderer (id: 4)
self.contour_actor = vtk.vtkActor()
self.contour_mapper = vtk.vtkPolyDataMapper()
self.contour_mapper.ScalarVisibilityOff()
self.contour_selected_actors = []
self.contour_actor.SetMapper(self.contour_mapper)
self.contour_actor.GetProperty().SetColor(contour_color)
self._on_slide_transparency()
self.renderer_3d = vtk.vtkRenderer()
self.renderer_3d.SetBackground(threeD_bg_color)
self.renderer_3d.AddActor(self.contour_actor)
frame.view3d.GetRenderWindow().AddRenderer(self.renderer_3d)
frame.view3d._outline_source = vtk.vtkOutlineSource()
om = vtk.vtkPolyDataMapper()
om.SetInput(frame.view3d._outline_source.GetOutput())
frame.view3d._outline_actor = vtk.vtkActor()
frame.view3d._outline_actor.SetMapper(om)
frame.view3d._cInteractorStyle = vtk.vtkInteractorStyleTrackballCamera()
frame.view3d.SetInteractorStyle(frame.view3d._cInteractorStyle)
frame.view3d._orientation_widget.On()
# make our window appear (this is a viewer after all)
self.view()
# all modules should toggle this once they have shown their views.
self.view_initialised = True
# apply config information to underlying logic
self.sync_module_logic_with_config()
# then bring it all the way up again to the view
self.sync_module_view_with_logic()
self.clearSeedPoints()
class multiDirectionalSlicedViewSegmentation3dVieWeR(IntrospectModuleMixin, ModuleBase):
"""Module to visualize VTI images, easily combining axial, coronal and sagittal data in one screen,
and giving the possibility to select seedpoints that will grow into contours on the 3D screen.
The multiDirectionalSlicedViewSegmentation3dVieWeR consists of three sliceviewers, and a 3D viewer.
There are two ways of setting the input.
- The first way is using a vtiRDR, to load the data via the network.
- The other way is just using the file browser to collect a VTI file from your file system.
After loading your image data , you can inspect the data and examine the patient, by highlighting one or multiple areas by your choice.
Controls:
LMB: The left mouse button can be used to select a seedpoint from the different 2D views\n
CTRL + LMB: Holding the CTRL-key does the same, but adds a seedpoint to your selection, LMB then returns your selection to a single point\n
RMB: For the slice viewers, you can set the window and level values by clicking and holding the right mouse button in a slice and moving your mouse. You can see the current
window and level values in the bottom of the viewer. Outside of the slice, this zooms the camera in and out\n
MMB: The middle mouse button enables stepping through the slices if clicked and held in the center of the slice. When clicking on de edges of a slice, this re-orients the
entire slice. Outside of the slice, this pans the camera\n
Scrollwheel: The scrollwheel can be used for zooming in and out of a scene\n
"""
NUM_INPUTS = 1
PARTS_TO_INPUTS = {0 : tuple(range(NUM_INPUTS))}
# PARTS_TO_OUTPUTS = {0 : (3,4), 1 : (0,4), 2 : (1,4), 3 : (2,4)}
def __init__(self, module_manager):
"""Standard constructor. All DeVIDE modules have these, we do
the required setup actions.
"""
def _init_frame():
# call base constructor
ModuleBase.__init__(self, module_manager)
self._numDataInputs = self.NUM_INPUTS
# use list comprehension to create list keeping track of inputs
self._inputs = [{'Connected' : None, 'inputData' : None,
'vtkActor' : None, 'ipw' : None}
for i in range(self._numDataInputs)]
# create the view frame
self.frame = module_utils.instantiate_module_view_frame(
self, self._module_manager,
multiDirectionalSlicedViewSegmentation3dVieWeRFrame.multiDirectionalSlicedViewSegmentation3dVieWeRFrame)
#THE FRAME (reference)
frame = self.frame
# change the title to something more spectacular (or at least something non-default)
frame.SetTitle('multiDirectionalSlicedViewSegmentation3dVieWeR')
# predefine this
self.selectedData = []
self.controlIsCurrentlyDown = 0
# list of objects that want to be contoured by this slice
self._contourObjectsDict1 = {}
self._contourObjectsDict2 = {}
self._contourObjectsDict3 = {}
# anything you stuff into self._config will be saved
self._config.last_used_dir = ''
#color definitions
twoD_bg_color = (0.19,0.19,0.19)
threeD_bg_color = (0.62,0.62,0.62)
contour_color = (0.6,0.6,0.6)
# create the necessary VTK objects
# setup the Top Renderer (id: 1)
self.renderer_top = vtk.vtkRenderer()
self.renderer_top.SetBackground(twoD_bg_color)
frame.top.GetRenderWindow().AddRenderer(self.renderer_top)
self.slice_viewer_top = CMSliceViewer(frame.top, self.renderer_top)
self.slice_viewer_top.set_parallel()
# setup the Side Renderer (id: 2)
self.renderer_side = vtk.vtkRenderer()
self.renderer_side.SetBackground(twoD_bg_color)
frame.side.GetRenderWindow().AddRenderer(self.renderer_side)
self.slice_viewer_side = CMSliceViewer(frame.side, self.renderer_side)
self.slice_viewer_side.set_parallel()
# setup the Front Renderer (id: 3)
self.renderer_front = vtk.vtkRenderer()
self.renderer_front.SetBackground(twoD_bg_color)
frame.front.GetRenderWindow().AddRenderer(self.renderer_front)
self.slice_viewer_front = CMSliceViewer(frame.front, self.renderer_front)
self.slice_viewer_front.set_parallel()
# setup the 3D Renderer (id: 4)
self.contour_actor = vtk.vtkActor()
self.contour_mapper = vtk.vtkPolyDataMapper()
self.contour_mapper.ScalarVisibilityOff()
self.contour_selected_actors = []
self.contour_actor.SetMapper(self.contour_mapper)
self.contour_actor.GetProperty().SetColor(contour_color)
self._on_slide_transparency()
self.renderer_3d = vtk.vtkRenderer()
self.renderer_3d.SetBackground(threeD_bg_color)
self.renderer_3d.AddActor(self.contour_actor)
frame.view3d.GetRenderWindow().AddRenderer(self.renderer_3d)
frame.view3d._outline_source = vtk.vtkOutlineSource()
om = vtk.vtkPolyDataMapper()
om.SetInput(frame.view3d._outline_source.GetOutput())
frame.view3d._outline_actor = vtk.vtkActor()
frame.view3d._outline_actor.SetMapper(om)
frame.view3d._cInteractorStyle = vtk.vtkInteractorStyleTrackballCamera()
frame.view3d.SetInteractorStyle(frame.view3d._cInteractorStyle)
frame.view3d._orientation_widget.On()
# make our window appear (this is a viewer after all)
self.view()
# all modules should toggle this once they have shown their views.
self.view_initialised = True
# apply config information to underlying logic
self.sync_module_logic_with_config()
# then bring it all the way up again to the view
self.sync_module_view_with_logic()
self.clearSeedPoints()
# END OF _INIT_FRAME
_init_frame()
self._reset_frame()
self._bind_events()
def _bind_events(self):
"""Bind wx events to Python callable object event handlers.
"""
frame = self.frame
#CONTROL check
frame.top.Bind(wx.EVT_LEFT_UP, self.onLeftUp)
frame.side.Bind(wx.EVT_LEFT_UP, self.onLeftUp)
frame.front.Bind(wx.EVT_LEFT_UP, self.onLeftUp)
# bind onClickedAViewer
self.slice_viewer_top.ipws[0].AddObserver('StartInteractionEvent', lambda e, o: self._ipwStartInteractionCallback(1))
self.slice_viewer_top.ipws[0].AddObserver('InteractionEvent', lambda e, o: self._ipwInteractionCallback(1))
self.slice_viewer_top.ipws[0].AddObserver('EndInteractionEvent', lambda e, o: self._ipwEndInteractionCallback(1, e))
self.slice_viewer_side.ipws[0].AddObserver('StartInteractionEvent', lambda e, o: self._ipwStartInteractionCallback(2))
self.slice_viewer_side.ipws[0].AddObserver('InteractionEvent', lambda e, o: self._ipwInteractionCallback(2))
self.slice_viewer_side.ipws[0].AddObserver('EndInteractionEvent', lambda e, o: self._ipwEndInteractionCallback(2, e))
self.slice_viewer_front.ipws[0].AddObserver('StartInteractionEvent', lambda e, o: self._ipwStartInteractionCallback(3))
self.slice_viewer_front.ipws[0].AddObserver('InteractionEvent', lambda e, o: self._ipwInteractionCallback(3))
self.slice_viewer_front.ipws[0].AddObserver('EndInteractionEvent', lambda e, o: self._ipwEndInteractionCallback(3, e))
# bind onScrollViewer
frame.view3d.Unbind(wx.EVT_MOUSEWHEEL)
frame.view3d.Bind(wx.EVT_MOUSEWHEEL, lambda evt: self._on_scroll_viewer(evt, 4))
# bind onChangeSliderSlice
frame.top_zoomer.Bind(wx.EVT_SLIDER, lambda evt: self._on_slide_slice(evt, 1))
frame.side_zoomer.Bind(wx.EVT_SLIDER, lambda evt: self._on_slide_slice(evt, 2))
frame.front_zoomer.Bind(wx.EVT_SLIDER, lambda evt: self._on_slide_slice(evt, 3))
frame.top_zoomer.Bind(wx.EVT_SCROLL_CHANGED, lambda evt: self._on_zoomer_released(evt, 1))
frame.side_zoomer.Bind(wx.EVT_SCROLL_CHANGED, lambda evt: self._on_zoomer_released(evt, 2))
frame.front_zoomer.Bind(wx.EVT_SCROLL_CHANGED, lambda evt: self._on_zoomer_released(evt, 3))
# bind onChangeSliderToleranceLow
frame.lower_slider.Bind(wx.EVT_SCROLL_CHANGED, self._on_slide_tolerance_low)
# bind onChangeSliderToleranceHigh
frame.upper_slider.Bind(wx.EVT_SCROLL_CHANGED, self._on_slide_tolerance_high)
# bind onChangeSliderTransparency
frame.transparency_slider.Bind(wx.EVT_SCROLL_CHANGED, self._on_slide_transparency)
# bind onChangeSelectionColor
frame.color_picker.Bind(wx.EVT_COLOURPICKER_CHANGED, self._on_select_new_color)
# bind onCheckContinuous
frame.continuous_check.Bind(wx.EVT_CHECKBOX, self._on_check_continuous)
# bind onClickresetViewer
frame.reset_top.Bind(wx.EVT_BUTTON, lambda x: self._reset_viewer(1, False))
frame.reset_side.Bind(wx.EVT_BUTTON, lambda x: self._reset_viewer(2, False))
frame.reset_front.Bind(wx.EVT_BUTTON, lambda x: self._reset_viewer(3, False))
frame.reset_view3d.Bind(wx.EVT_BUTTON, lambda x: self._reset_viewer(4, False))
# bind onClickFileButton
frame.file_button.Bind(wx.EVT_BUTTON, self._on_clicked_btn_new_file)
# bind onClickSaveSnapshotButton
frame.save_button.Bind(wx.EVT_BUTTON, self._save_snapshot)
# bind onClickRemoveSeedPointsButtom
frame.seedpoint_button.Bind(wx.EVT_BUTTON, self.removeSeedPoints)
def _ipwStartInteractionCallback(self, viewer_id):
"""Method for handling seedpoint selection in the ipw
"""
self.tempCursorData = None
self._ipwInteractionCallback(viewer_id)
def _ipwInteractionCallback(self, viewer_id):
"""Method for handling seedpoint selection in the ipw
"""
cd = 4 * [0.0]
if viewer_id == 1 and self.slice_viewer_top.ipws[0].GetCursorData(cd):
self.tempCursorData = cd
elif viewer_id == 2 and self.slice_viewer_side.ipws[0].GetCursorData(cd):
self.tempCursorData = cd
elif viewer_id == 3 and self.slice_viewer_front.ipws[0].GetCursorData(cd):
self.tempCursorData = cd
def onLeftUp(self, evt):
"""Method for handling seedpoint selection in the ipw
"""
self.controlIsCurrentlyDown = evt.ControlDown()
evt.Skip()
def _ipwEndInteractionCallback(self, viewer_id, event):
"""Method for handling seedpoint selection in the ipw
"""
if not (self.controlIsCurrentlyDown):
self.clearSeedPoints()
self.addSeedPoint(self.tempCursorData)
self._calculate_selection()
def clearSeedPoints(self):
"""Method for clearing the seedpoint list
"""
self.seedPoints = []
self.frame.seedpoint_list.DeleteAllItems()
def addSeedPoint(self, point):
"""Method for adding a point to the seedpoint list
"""
self.seedPoints.append(point)
index = len(self.seedPoints) - 1
self.frame.seedpoint_list.InsertStringItem(index, str(point[0]).rstrip('0').rstrip('.'))
self.frame.seedpoint_list.SetStringItem(index, 1, str(point[1]).rstrip('0').rstrip('.'))
self.frame.seedpoint_list.SetStringItem(index, 2, str(point[2]).rstrip('0').rstrip('.'))
self.frame.seedpoint_list.SetStringItem(index, 3, str(point[3]).rstrip('0').rstrip('.'))
def removeSeedPoints(self, event):
"""Event method call to remove selected seedpoints from list
"""
points = self.frame.seedpoint_list
count = points.GetSelectedItemCount()
if count <= 0:
return
while (count > 0) :
itemIndex = points.GetFirstSelected()
#recreate point to be able to remove from array
point = []
for i in range(0,points.GetColumnCount()):
point.append(float(points.GetItem(itemIndex, i).GetText()))
#delete item
self.seedPoints.remove(point)
points.DeleteItem(itemIndex)
count -= 1
self._reset_viewer(4, False)
def _on_scroll_viewer(self, event, viewer_id):
if viewer_id == 1: # Top Viewer
return
elif viewer_id == 2: # Side Viewer
return
elif viewer_id == 3: # Front Viewer
return
elif viewer_id == 4: # 3D Viewer
# event.GetWheelRotation() is + or - 120 depending on
# direction of turning.
if event.ControlDown():
delta = 10
elif event.ShiftDown():
delta = 1
else:
# if user is NOT doing shift / control, we pass on to the
# default handling which will give control to the VTK
# mousewheel handlers.
self.frame.view3d.OnMouseWheel(event)
return
selected_sds = self.sliceDirections.getSelectedSliceDirections()
if len(selected_sds) == 0:
if len(self.sliceDirections._sliceDirectionsDict) == 1:
# convenience: nothing selected, but there is only one SD, use that then!
sd = self.sliceDirections._sliceDirectionsDict.items()[0][1]
else:
return
else:
sd = selected_sds[0]
if event.GetWheelRotation() > 0:
sd.delta_slice(+delta)
else:
sd.delta_slice(-delta)
self.render()
def _on_slide_slice(self, event, viewer_id):
"""Handler for zoomer interaction (sliders on 2D views)
"""
if self._inputs[0]['inputData'] == None:
return
sv = None
slicer_max = 0
if viewer_id == 1: # Top Viewer
sv = self.slice_viewer_top
slicer_max = self.top_zoomer_max
elif viewer_id == 2: # Side Viewer
sv = self.slice_viewer_side
slicer_max = self.side_zoomer_max
elif viewer_id == 3: # Front Viewer
sv = self.slice_viewer_front
slicer_max = self.front_zoomer_max
if not(sv == None):
value = slicer_max - event.GetEventObject().GetValue()
sv.ipws[0].SetSliceIndex(value)
self.render()
def _on_zoomer_released(self, event, viewerIndex):
"""Handler for slider adjustment end (Zoomers)
"""
for data in self.selectedData:
self.syncContourToObject(viewerIndex, data)
def _on_slide_tolerance_low(self, event):
"""Handler for slider adjustment (Lower Threshold)
"""
if len(self.seedPoints) == 0:
return
else:
self._calculate_selection()
def _on_slide_tolerance_high(self, event):
"""Handler for slider adjustment (Upper Threshold)
"""
if len(self.seedPoints) == 0:
return
else:
self._calculate_selection()
def _on_select_new_color(self, event = None):
"""Handler for color adjustment (Color of selection)
"""
for actor in self.contour_selected_actors:
actor.GetProperty().SetColor(self.frame.color_picker.GetColour().Get())
def _on_slide_transparency(self, event = None):
"""Handler for slider adjustment (Transparency of unselected Actors)
"""
self.contour_actor.GetProperty().SetOpacity(float(self.frame.transparency_slider.GetValue()) / 100)
def _on_check_continuous(self, event):
"""Handler for checkbox adjustment (Continous selection)
"""
if len(self.seedPoints) == 0:
return
else:
self._calculate_selection()
def _on_clicked_btn_new_file(self, event):
"""Handler for file opening
"""
filters = 'Volume files (*.vti)|*.vti;'
dlg = wx.FileDialog(self.frame, "Please choose a VTI file", self._config.last_used_dir, "", filters, wx.OPEN)
if dlg.ShowModal() == wx.ID_OK:
filename=dlg.GetFilename()
self._config.last_used_dir=dlg.GetDirectory()
full_file_path = "%s/%s" % (self._config.last_used_dir, filename)
self._load_data_from_file(full_file_path)
dlg.Destroy()
def _load_data_from_file(self, file_path):
"""Loads scanvolume data from file. Also sets the volume as input for the sliceviewers
"""
#self.frame.SetStatusText("Opening file: %s..." % (file_path))
filename = os.path.split(file_path)[1]
fileBaseName = os.path.splitext(filename)[0]
self.frame._set_filename(filename)
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName(file_path)
reader.Update()
self.set_input(0, reader.GetOutput())
def _save_snapshot(self, event):
"""Handler for filesaving
"""
filters = 'png file (*.png)|*.png'
dlg = wx.FileDialog(self.frame, "Choose a destination", self._config.last_used_dir, "", filters, wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
filename=dlg.GetFilename()
self._config.last_used_dir=dlg.GetDirectory()
file_path = "%s/%s" % (self._config.last_used_dir, filename)
w2i = vtk.vtkWindowToImageFilter()
w2i.SetInput(self.frame.view3d.GetRenderWindow());
w2i.Update()
writer = vtk.vtkPNGWriter()
writer.SetInput(w2i.GetOutput())
writer.SetFileName(file_path)
writer.Update()
result = writer.Write()
dlg.Destroy()
def _reset_frame(self, event = None):
"""Handler for resetting the frame
"""
self._reset_controls()
self._reset_all_viewers()
def _reset_controls(self, event = None):
"""Handler for resetting the controls
"""
self.frame._reset_controls()
self._calculate_selection()
def _reset_all_viewers(self, event = None):
"""Handler for resetting all viewer
"""
self._reset_viewer(1, True)
self._reset_viewer(2, True)
self._reset_viewer(3, True)
self._reset_viewer(4, True)
def _reset_viewer(self, viewer_id, reset_zoom, event = None):
"""Handler for resetting a specific viewer
"""
def resetCamera(viewerIndex):
sliceViewer = None
renderer = None
if(viewerIndex == 1):
sliceViewer = self.slice_viewer_top
renderer = self.renderer_top
elif(viewerIndex == 2):
sliceViewer = self.slice_viewer_side
renderer = self.renderer_side
elif(viewerIndex ==3):
sliceViewer = self.slice_viewer_front
renderer = self.renderer_front
elif(viewerIndex ==4):
sliceViewer = self.frame.view3d;
renderer = self.renderer_3d
cam = renderer.GetActiveCamera()
# then make sure it's up is the right way
if(viewerIndex == 1):
cam.SetViewUp(0, 1 ,0)
posX = 0
posY = 0
posZ = 1
cam.SetPosition(posX, posY, posZ)
cam.SetFocalPoint(0, 0, 0)
elif(viewerIndex == 2):
cam.SetViewUp(0, 1 ,0)
posX = 1
posY = 0
posZ = 0
cam.SetPosition(posX, posY, posZ)
cam.SetFocalPoint(0, 0, 0)
elif(viewerIndex ==3):
cam.SetViewUp(0,1,0)
posX = 0
posY = -1
posZ = 0
cam.SetPosition(posX, posY, posZ)
cam.SetFocalPoint(0, 0, 0)
if(viewerIndex == 4):
cam.SetViewUp(0, 1, 0)
fp = cam.GetFocalPoint()
cp = cam.GetPosition()
if cp[2] < fp[2]:
z = fp[2] + (fp[2] - cp[2])
else:
z = cp[2]
posX = fp[0]
posY = fp[1]
posZ = z
cam.SetFocalPoint(0, 99999999, 0) #Look towards infinity
cam.SetPosition(posX, posY, posZ)
#print("Setting camera " + str(viewerIndex) + " to (" + str(posX) + ", " + str(posY) + ", " + str(posZ) + ")")
# first reset the camera
renderer.ResetCamera()
if(viewerIndex == 4):
sliceViewer.Render()
else:
sliceViewer.render()
if self._inputs[0]['inputData'] == None:
return
else:
size = self._inputs[0]['inputData'].GetDimensions()
colorRange = self._inputs[0]['inputData'].GetScalarRange()
if viewer_id == 1: # Top Viewer
if(reset_zoom):
self.top_zoomer_max = size[2]-1
self.frame.top_zoomer.SetMax(self.top_zoomer_max)
value = self.top_zoomer_max / 2
self.frame.top_zoomer.SetValue(value)
self.slice_viewer_top.ipws[0].SetPlaneOrientation(2)
for i, ipw in enumerate(self.slice_viewer_top.ipws):
ipw.SetSliceIndex(value)
ipw.GetColorMap().GetLookupTable().SetRange(colorRange[0], colorRange[1])
resetCamera(1)
elif viewer_id == 2: # Side Viewer
if(reset_zoom):
self.side_zoomer_max = size[0]-1
self.frame.side_zoomer.SetMax(self.side_zoomer_max)
value = self.side_zoomer_max / 2
self.frame.side_zoomer.SetValue(value)
self.slice_viewer_side.ipws[0].SetPlaneOrientation(0)
for i, ipw in enumerate(self.slice_viewer_side.ipws):
ipw.SetSliceIndex(value)
ipw.GetColorMap().GetLookupTable().SetRange(colorRange[0], colorRange[1])
resetCamera(2)
elif viewer_id == 3: # Front Viewer
if(reset_zoom):
self.front_zoomer_max = size[1]-1
self.frame.front_zoomer.SetMax(self.front_zoomer_max)
value = self.front_zoomer_max / 2
self.frame.front_zoomer.SetValue(value)
self.slice_viewer_front.ipws[0].SetPlaneOrientation(1)
for i, ipw in enumerate(self.slice_viewer_front.ipws):
ipw.SetSliceIndex(value)
ipw.GetColorMap().GetLookupTable().SetRange(colorRange[0], colorRange[1])
resetCamera(3)
elif viewer_id == 4: # 3D Viewer
self._update_3d_renderer(self._inputs[0]['inputData'])
resetCamera(4)
self.render()
return
def set_input(self, idx, input_stream):
# this gets called right before you get executed. take the
# input_stream and store it so that it's available during execute_module()
def add_primary_init(input_stream):
"""After a new primary has been added, a number of other
actions have to be performed.
"""
# add outline actor to renderer
self.renderer_3d.AddActor(self.frame.view3d._outline_actor)
self.frame.view3d._outline_actor.PickableOff()
# end of method add_primary_init()
def _handleNewImageDataInput():
connecteds = [i['Connected'] for i in self._inputs]
# if we already have a primary, make sure the new inputStream
# is added at a higher port number than all existing
# primaries and overlays
if 'vtkImageDataPrimary' in connecteds:
highestPortIndex = connecteds.index('vtkImageDataPrimary')
for i in range(highestPortIndex, len(connecteds)):
if connecteds[i] == 'vtkImageDataOverlay':
highestPortIndex = i
if idx <= highestPortIndex:
raise Exception, \
"Please add overlay data at higher input " \
"port numbers " \
"than existing primary data and overlays."
# find out whether this is primary or an overlay, record it
if 'vtkImageDataPrimary' in connecteds:
# there's no way there can be only overlays in the list,
# the check above makes sure of that
self._inputs[idx]['Connected'] = 'vtkImageDataOverlay'
else:
# there are no primaries or overlays, this must be
# a primary then
self._inputs[idx]['Connected'] = 'vtkImageDataPrimary'
# also store binding to the data itself
self._inputs[idx]['inputData'] = input_stream
if self._inputs[idx]['Connected'] == 'vtkImageDataPrimary':
# things to setup when primary data is added
add_primary_init(input_stream)
if self.frame._get_filename() == None:
self.frame._set_filename('FROM NETWORK')
self.selectedData = []
self.contour_selected_actors = []
self._contourObjectsDict1 = {}
self._contourObjectsDict2 = {}
self._contourObjectsDict3 = {}
self.clearSeedPoints()
#set the input on the 2d slice viewers
self._update_2d_renderers(input_stream)
#update our 3d renderer
self._update_3d_renderer(input_stream)
self._reset_all_viewers()
# end of function _handleImageDataInput()
if not(input_stream == None):
if input_stream.IsA('vtkImageData'):
if self._inputs[idx]['Connected'] is None:
_handleNewImageDataInput()
else:
# take necessary actions to refresh
prevData = self._inputs[idx]['inputData']
#set the input on the 2d slice viewers
self._update_2d_renderers(input_stream)
#update our 3d renderer
self._update_3d_renderer(input_stream)
# record it in our main structure
self._inputs[idx]['inputData'] = input_stream
if self.frame._get_filename() == None:
self.frame._set_filename('FROM NETWORK')
self._reset_all_viewers()
else:
print "ERROR: input_stream isn't vtkImageData!"
else:
self.frame._set_filename()
print "No input_stream"
# end of set_input
def _update_2d_renderers(self, input_stream):
"""Convenience method to pass the input stream to the 2d slice viewers
"""
try:
self.slice_viewer_top.set_input(input_stream)
self.slice_viewer_side.set_input(input_stream)
self.slice_viewer_front.set_input(input_stream)
except:
print "ISSUE: adding input_streams"
def _update_3d_renderer(self, input_stream):
"""Calculate the contour based on the input data
"""
self._config.iso_value = 128
contourFilter = vtk.vtkContourFilter()
contourFilter.SetInput(input_stream)
contourFilter.Update()
data = contourFilter.GetOutput()
self.contour_mapper.SetInput(data)
self.contour_mapper.Update()
self._calculate_selection()
self.renderer_3d.ResetCamera()
return data
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
def addSelectionTo2DViewers(self, data, actor):
self.addContourObject(1, data, actor)
self.addContourObject(2, data, actor)
self.addContourObject(3, data, actor)
def addContourObject(self, viewerIndex, contourObject, prop3D):
"""Activate contouring for the contourObject. The contourObject
is usually a tdObject and specifically a vtkPolyData. We also
need the prop3D that represents this polydata in the 3d scene.
"""
#TODO include this to show selection in 2d renders
#if self._contourObjectsDict.has_key(contourObject):
# # we already have this, thanks
# return
#prop3D = vtk.vtkActor()
renderer = None
if viewerIndex == 1:
renderer = self.renderer_top
elif viewerIndex == 2:
renderer = self.renderer_side
elif viewerIndex == 3:
renderer = self.renderer_front
try:
contourable = contourObject.IsA('vtkPolyData')
except:
contourable = False
if contourable:
# we need a cutter to calculate the contours and then a stripper
# to string them all together
cutter = vtk.vtkCutter()
plane = vtk.vtkPlane()
cutter.SetCutFunction(plane)
trfm = vtk.vtkTransform()
trfm.SetMatrix(prop3D.GetMatrix())
trfmFilter = vtk.vtkTransformPolyDataFilter()
trfmFilter.SetTransform(trfm)
trfmFilter.SetInput(contourObject)
cutter.SetInput(trfmFilter.GetOutput())
stripper = vtk.vtkStripper()
stripper.SetInput(cutter.GetOutput())
cutter.SetValue(0, 1)
#
#tubef = vtk.vtkTubeFilter()
#tubef.SetNumberOfSides(12)
#tubef.SetRadius(0.5)
#tubef.SetInput(stripper.GetOutput())
# and create the overlay at least for the 3d renderer
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(stripper.GetOutput())
mapper.ScalarVisibilityOff()
actor = vtk.vtkActor()
actor.SetMapper(mapper)
#color = self.sliceDirections.slice3dVWR._tdObjects.getObjectColour(
# contourObject)
actor.GetProperty().SetColor(self.frame.color_picker.GetColour().Get())
actor.GetProperty().SetInterpolationToFlat()
# add it to the renderer
self.contour_selected_actors.append(actor)
renderer.AddActor(actor)
# add all necessary metadata to our dict
contourDict = {'contourObject' : contourObject,
'contourObjectProp' : prop3D,
'trfmFilter' : trfmFilter,
'cutter' : cutter,
'tdActor' : actor}
if viewerIndex == 1:
self._contourObjectsDict1[contourObject] = contourDict
elif viewerIndex == 2:
self._contourObjectsDict2[contourObject] = contourDict
elif viewerIndex == 3:
self._contourObjectsDict3[contourObject] = contourDict
# now sync the bugger
self.syncContourToObject(viewerIndex, contourObject)
else:
print "Error: polyData is not Contourable!!!"
def syncContourToObject(self, viewerIndex, contourObject):
"""Update the contour for the given contourObject. contourObject
corresponds to a tdObject in tdObjects.py.
"""
# yes, in and not in work on dicts, doh
#if contourObject not in self._contourObjectsDict:
# print "Error!! contourObject not in _contourobjects!"
# return
#else:
# print "syncContourToObject!"
slicerPlane = None
contourDict = None
if viewerIndex == 1:
slicerPlane = self.slice_viewer_top.ipws[0]
contourDict = self._contourObjectsDict1[contourObject]
elif viewerIndex == 2:
slicerPlane = self.slice_viewer_side.ipws[0]
contourDict = self._contourObjectsDict2[contourObject]
elif viewerIndex == 3:
slicerPlane = self.slice_viewer_front.ipws[0]
contourDict = self._contourObjectsDict3[contourObject]
# get the contourObject metadata
cutter = contourDict['cutter']
plane = cutter.GetCutFunction()
# adjust the implicit plane (if we got this far (i.e.
plane.SetNormal(slicerPlane.GetNormal())
plane.SetOrigin(slicerPlane.GetOrigin())
# hack to turn around normal for front-view.
if viewerIndex == 3:
normal = slicerPlane.GetNormal()
plane.SetNormal((-normal[0], -normal[1], -normal[2]))
# also make sure the transform knows about the new object position
contourDict['trfmFilter'].GetTransform().SetMatrix(contourDict['contourObjectProp'].GetMatrix())
# calculate it
cutter.Update()
###################################################################################
# _____ _______ ____ _____ _____ ______ _____ _____ _ _ _____ #
# / ____|__ __/ __ \| __ \ | __ \| ____| /\ | __ \_ _| \ | |/ ____| #
# | (___ | | | | | | |__) | | |__) | |__ / \ | | | || | | \| | | __ #
# \___ \ | | | | | | ___/ | _ /| __| / /\ \ | | | || | | . ` | | |_ | #
# ____) | | | | |__| | | | | \ \| |____ / ____ \| |__| || |_| |\ | |__| | #
# |_____/ |_| \____/|_| |_| \_\______/_/ \_\_____/_____|_| \_|\_____| #
# #
###################################################################################
def view(self):
self.frame.Show()
self.frame.Raise()
# because we have an RWI involved, we have to do this
# SafeYield, so that the window does actually appear before we
# call the render. If we don't do this, we get an initial
# empty renderwindow.
wx.SafeYield()
self.render()
def render(self):
"""Method that calls Render() on the embedded RenderWindow.
Use this after having made changes to the scene.
"""
self.frame.render()
self.renderer_3d.Render()
self.slice_viewer_top.render()
self.slice_viewer_side.render()
self.slice_viewer_front.render()
def get_input_descriptions(self):
# define this as a tuple of input descriptions if you want to
# take input data e.g. return ('vtkPolyData', 'my kind of
# data')
# concatenate it num_inputs times (but these are shallow copies!)
return self._numDataInputs * ('vtkImageData',)
def get_output_descriptions(self):
# define this as a tuple of output descriptions if you want to
# generate output data.
return ()
def get_output(self, idx):
# this can get called at any time when a consumer module wants
# you output data.
pass
def execute_module(self):
# when it's you turn to execute as part of a network
# execution, this gets called.
pass
def logic_to_config(self):
pass
def config_to_logic(self):
pass
def config_to_view(self):
pass
def view_to_config(self):
pass
def close(self):
"""Clean-up method called on all DeVIDE modules when they are
deleted.
FIXME: Still get a nasty X error :(
"""
#THE FRAME (reference)
frame = self.frame
# with this complicated de-init, we make sure that VTK is
# properly taken care of
self.renderer_top.RemoveAllViewProps()
self.renderer_side.RemoveAllViewProps()
self.renderer_front.RemoveAllViewProps()
self.renderer_3d.RemoveAllViewProps()
# this finalize makes sure we don't get any strange X
# errors when we kill the module.
self.slice_viewer_top.close()
self.slice_viewer_side.close()
self.slice_viewer_front.close()
frame.top.GetRenderWindow().Finalize()
frame.top.SetRenderWindow(None)
frame.side.GetRenderWindow().Finalize()
frame.side.SetRenderWindow(None)
frame.front.GetRenderWindow().Finalize()
frame.front.SetRenderWindow(None)
frame.view3d.GetRenderWindow().Finalize()
frame.view3d.SetRenderWindow(None)
del frame.top
del frame.side
del frame.front
del frame.view3d
del self.slice_viewer_top
del self.slice_viewer_side
del self.slice_viewer_front
# done with VTK de-init
# now take care of the wx window
frame.close()
# then shutdown our introspection mixin
IntrospectModuleMixin.close(self)
def __init__(self, module_manager):
"""Standard constructor. All DeVIDE modules have these, we do
the required setup actions.
"""
# we record the setting here, in case the user changes it
# during the lifetime of this model, leading to different
# states at init and shutdown.
self.IMAGE_VIEWER = IMAGE_VIEWER
# we need all this for our contours
self.mask_data = None
self.image_data = None
self.lungVolume = None
self.contour_severe_actor = vtk.vtkActor()
self.contour_moderate_actor = vtk.vtkActor()
self.contour_lungedge_actor = vtk.vtkActor()
self.severe_mapper = vtk.vtkPolyDataMapper()
self.severe_mapper.ScalarVisibilityOff()
self.moderate_mapper = vtk.vtkPolyDataMapper()
self.moderate_mapper.ScalarVisibilityOff()
self.lung_mapper = vtk.vtkPolyDataMapper()
self.lung_mapper.ScalarVisibilityOff()
self.contour_severe_actor.SetMapper(self.severe_mapper)
self.contour_severe_actor.GetProperty().SetColor(1,0,0)
self.contour_severe_actor.GetProperty().SetOpacity(0.5)
self.contour_moderate_actor.SetMapper(self.moderate_mapper)
self.contour_moderate_actor.GetProperty().SetColor(0.5,0,1)
self.contour_moderate_actor.GetProperty().SetOpacity(0.25)
self.contour_lungedge_actor.SetMapper(self.lung_mapper)
self.contour_lungedge_actor.GetProperty().SetColor(0.9,0.9,0.9)
self.contour_lungedge_actor.GetProperty().SetOpacity(0.1)
ModuleBase.__init__(self, module_manager)
# create the view frame
self._view_frame = module_utils.instantiate_module_view_frame(
self, self._module_manager,
EmphysemaViewerFrame.EmphysemaViewerFrame)
# change the title to something more spectacular (or at least something non-default)
self._view_frame.SetTitle('EmphysemaViewer')
# create the necessary VTK objects: we only need a renderer,
# the RenderWindowInteractor in the view_frame has the rest.
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(0.5,0.5,0.5)
self._view_frame.rwi.GetRenderWindow().AddRenderer(self.ren)
self.ren.AddActor(self.contour_severe_actor)
self.ren.AddActor(self.contour_moderate_actor)
self.ren.AddActor(self.contour_lungedge_actor)
self.ren2 = vtk.vtkRenderer()
self.ren2.SetBackground(0.5,0.5,0.5)
self._view_frame.overlay.GetRenderWindow().AddRenderer(self.ren2)
self.slice_viewer1 = CMSliceViewer(self._view_frame.overlay, self.ren2)
self.ren3 = vtk.vtkRenderer()
self.ren3.SetBackground(0.5,0.5,0.5)
self._view_frame.original.GetRenderWindow().AddRenderer(self.ren3)
self.slice_viewer2 = CMSliceViewer(self._view_frame.original, self.ren3)
self.slice_viewer3 = CMSliceViewer(self._view_frame.rwi, self.ren)
self.sync = SyncSliceViewers()
self.sync.add_slice_viewer(self.slice_viewer1)
self.sync.add_slice_viewer(self.slice_viewer2)
self.sync.add_slice_viewer2(self.slice_viewer3)
# hook up all event handlers
self._bind_events()
# anything you stuff into self._config will be saved
self._config.last_used_dir = ''
# make our window appear (this is a viewer after all)
self.view()
# all modules should toggle this once they have shown their
# views.
self.view_initialised = True
# apply config information to underlying logic
self.sync_module_logic_with_config()
# then bring it all the way up again to the view
self.sync_module_view_with_logic()
class EmphysemaViewer(IntrospectModuleMixin, ModuleBase):
"""Module to visualize lungemphysema in a CT scan. A lung mask is also needed.
EmphysemaViewer consists of a volume rendering and two linked slice-based views; one with the original data and one with an emphysema overlay. The volume rendering shows 3
contours: the lungedges and 2 different contours of emphysema; a normal one and a severe one.
There are two ways of setting the emphysema values.
- The first way is choosing the 'default' values, which are literature-based. They are set on -950 HU (emphysema) and -970 HU (severe).
- The other way is a computational way: The lowest 11% values, that are present in the data are marked as emphysema, the lowest 8,5% values are marked as severe emphysema.
The theory behind this is the hypothesis that the histograms of emphysema patients differ from healthy people in a way that in emphysema patients there are relatively more
lower values present. In both ways you can finetune the values, or completely change them (if you want to).
After loading your image data and mask data, you can inspect the data and examine the severity of the emphysema of the patient.
Controls:
LMB: The left mouse button can be used to rotate objects in the 3D scene, or to poll Houndsfield Units in areas of interest (click and hold to see the values)\n
RMB: For the slice viewers, you can set the window and level values by clicking and holding the right mouse button in a slice and moving your mouse. You can see the current
window and level values in the bottom of the viewer. Outside of the slice, this zooms the camera in and out\n
MMB: The middle mouse button enables stepping through the slices if clicked and held in the center of the slice. When clicking on de edges of a slice, this re-orients the
entire slice. Outside of the slice, this pans the camera\n
Scrollwheel: The scrollwheel can be used for zooming in and out of a scene, but also for sliceviewing if used with the CTRL- or SHIFT-key\n
SHIFT: By holding the SHIFT-key, it is possible to use the mouse scrollwheel to scroll through the slices.\n
CTRL: Holding the CTRL-key does the same, but enables stepping through the data in steps of 10 slices.\n
"""
def __init__(self, module_manager):
"""Standard constructor. All DeVIDE modules have these, we do
the required setup actions.
"""
# we record the setting here, in case the user changes it
# during the lifetime of this model, leading to different
# states at init and shutdown.
self.IMAGE_VIEWER = IMAGE_VIEWER
# we need all this for our contours
self.mask_data = None
self.image_data = None
self.lungVolume = None
self.contour_severe_actor = vtk.vtkActor()
self.contour_moderate_actor = vtk.vtkActor()
self.contour_lungedge_actor = vtk.vtkActor()
self.severe_mapper = vtk.vtkPolyDataMapper()
self.severe_mapper.ScalarVisibilityOff()
self.moderate_mapper = vtk.vtkPolyDataMapper()
self.moderate_mapper.ScalarVisibilityOff()
self.lung_mapper = vtk.vtkPolyDataMapper()
self.lung_mapper.ScalarVisibilityOff()
self.contour_severe_actor.SetMapper(self.severe_mapper)
self.contour_severe_actor.GetProperty().SetColor(1,0,0)
self.contour_severe_actor.GetProperty().SetOpacity(0.5)
self.contour_moderate_actor.SetMapper(self.moderate_mapper)
self.contour_moderate_actor.GetProperty().SetColor(0.5,0,1)
self.contour_moderate_actor.GetProperty().SetOpacity(0.25)
self.contour_lungedge_actor.SetMapper(self.lung_mapper)
self.contour_lungedge_actor.GetProperty().SetColor(0.9,0.9,0.9)
self.contour_lungedge_actor.GetProperty().SetOpacity(0.1)
ModuleBase.__init__(self, module_manager)
# create the view frame
self._view_frame = module_utils.instantiate_module_view_frame(
self, self._module_manager,
EmphysemaViewerFrame.EmphysemaViewerFrame)
# change the title to something more spectacular (or at least something non-default)
self._view_frame.SetTitle('EmphysemaViewer')
# create the necessary VTK objects: we only need a renderer,
# the RenderWindowInteractor in the view_frame has the rest.
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(0.5,0.5,0.5)
self._view_frame.rwi.GetRenderWindow().AddRenderer(self.ren)
self.ren.AddActor(self.contour_severe_actor)
self.ren.AddActor(self.contour_moderate_actor)
self.ren.AddActor(self.contour_lungedge_actor)
self.ren2 = vtk.vtkRenderer()
self.ren2.SetBackground(0.5,0.5,0.5)
self._view_frame.overlay.GetRenderWindow().AddRenderer(self.ren2)
self.slice_viewer1 = CMSliceViewer(self._view_frame.overlay, self.ren2)
self.ren3 = vtk.vtkRenderer()
self.ren3.SetBackground(0.5,0.5,0.5)
self._view_frame.original.GetRenderWindow().AddRenderer(self.ren3)
self.slice_viewer2 = CMSliceViewer(self._view_frame.original, self.ren3)
self.slice_viewer3 = CMSliceViewer(self._view_frame.rwi, self.ren)
self.sync = SyncSliceViewers()
self.sync.add_slice_viewer(self.slice_viewer1)
self.sync.add_slice_viewer(self.slice_viewer2)
self.sync.add_slice_viewer2(self.slice_viewer3)
# hook up all event handlers
self._bind_events()
# anything you stuff into self._config will be saved
self._config.last_used_dir = ''
# make our window appear (this is a viewer after all)
self.view()
# all modules should toggle this once they have shown their
# views.
self.view_initialised = True
# apply config information to underlying logic
self.sync_module_logic_with_config()
# then bring it all the way up again to the view
self.sync_module_view_with_logic()
def close(self):
"""Clean-up method called on all DeVIDE modules when they are
deleted.
FIXME: Still get a nasty X error :(
"""
# with this complicated de-init, we make sure that VTK is
# properly taken care of
self.ren.RemoveAllViewProps()
self.ren2.RemoveAllViewProps()
self.ren3.RemoveAllViewProps()
# this finalize makes sure we don't get any strange X
# errors when we kill the module.
self.slice_viewer1.close()
self.slice_viewer2.close()
self.slice_viewer3.close()
self._view_frame.rwi.GetRenderWindow().Finalize()
self._view_frame.rwi.SetRenderWindow(None)
self._view_frame.overlay.GetRenderWindow().Finalize()
self._view_frame.overlay.SetRenderWindow(None)
self._view_frame.original.GetRenderWindow().Finalize()
self._view_frame.original.SetRenderWindow(None)
del self._view_frame.rwi
del self._view_frame.overlay
del self._view_frame.original
del self.slice_viewer3
del self.slice_viewer2
del self.slice_viewer1
# done with VTK de-init
# now take care of the wx window
self._view_frame.close()
# then shutdown our introspection mixin
IntrospectModuleMixin.close(self)
def get_input_descriptions(self):
# define this as a tuple of input descriptions if you want to
# take input data e.g. return ('vtkPolyData', 'my kind of
# data')
return ()
def get_output_descriptions(self):
# define this as a tuple of output descriptions if you want to
# generate output data.
return ()
def set_input(self, idx, input_stream):
# this gets called right before you get executed. take the
# input_stream and store it so that it's available during
# execute_module()
pass
def get_output(self, idx):
# this can get called at any time when a consumer module wants
# you output data.
pass
def execute_module(self):
# when it's you turn to execute as part of a network
# execution, this gets called.
pass
def logic_to_config(self):
pass
def config_to_logic(self):
pass
def config_to_view(self):
pass
def view_to_config(self):
pass
def view(self):
self._view_frame.Show()
self._view_frame.Raise()
# because we have an RWI involved, we have to do this
# SafeYield, so that the window does actually appear before we
# call the render. If we don't do this, we get an initial
# empty renderwindow.
wx.SafeYield()
self.render()
def create_volumerender(self, contourValueModerate, contourValueSevere):
"""Creates a volumerender of the masked data using iso-contour surfaces
created by the Marching Cubes algorithm at the specified contourvalues.
"""
self._view_frame.SetStatusText("Creating Volumerender...")
self.image_data
mask = vtk.vtkImageMask()
severeFraction = 0.10
moderateFraction = 0.12
# We only want to contour the lungs, so mask it
mask.SetMaskInput(self.mask_data)
mask.SetInput(self.image_data)
mask.Update()
self.lungVolume = mask.GetOutput()
if contourValueModerate == 0 and contourValueSevere == 0: # This means we get to calculate the percentual values ourselves!
scalars = self.lungVolume.GetScalarRange()
range = scalars[1]-scalars[0]
contourValueSevere = scalars[0]+range*severeFraction
contourValueModerate = scalars[0]+range*moderateFraction
self._view_frame.upper_slider.SetValue(contourValueModerate)
self._view_frame.lower_slider.SetValue(contourValueSevere)
self.create_overlay(contourValueModerate,contourValueSevere)
# Create the contours
self.adjust_contour(self.lungVolume, contourValueSevere, self.severe_mapper)
self.adjust_contour(self.lungVolume, contourValueModerate, self.moderate_mapper)
#self.adjust_contour(self.mask_data, 0.5, self.lung_mapper)
self.create_lungcontour()
# Set the camera to a nice view
cam = self.ren.GetActiveCamera()
cam.SetPosition(0,-100,0)
cam.SetFocalPoint(0,0,0)
cam.SetViewUp(0,0,1)
self.ren.ResetCamera()
self.render()
self._view_frame.SetStatusText("Created Volumerender")
def adjust_contour(self, volume, contourValue, mapper):
"""Adjust or create an isocontour using the Marching Cubes surface at the given
value using the given mapper
"""
self._view_frame.SetStatusText("Calculating new volumerender...")
contour = vtk.vtkMarchingCubes()
contour.SetValue(0,contourValue)
contour.SetInput(volume)
mapper.SetInput(contour.GetOutput())
mapper.Update()
self.render()
self._view_frame.SetStatusText("Calculated new volumerender")
def create_lungcontour(self):
"""Create a lungcontour using the Marching Cubes algorithm and smooth the surface
"""
self._view_frame.SetStatusText("Calculating lungcontour...")
contourLung = vtk.vtkMarchingCubes()
contourLung.SetValue(0,1)
contourLung.SetInput(self.mask_data)
smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother.SetInput(contourLung.GetOutput())
smoother.BoundarySmoothingOn()
smoother.SetNumberOfIterations(40)
smoother.Update()
self.lung_mapper.SetInput(smoother.GetOutput())
self.lung_mapper.Update()
self._view_frame.SetStatusText("Calculated lungcontour")
def create_overlay(self, emphysemavalue, severeemphysemavalue):
"""Creates an overlay for the slice-based volume view
0: no emphysema
1: moderate emphysema
2: severe emphysema
"""
self._view_frame.SetStatusText("Creating Overlay...")
mask = vtk.vtkImageMask()
mask2 = vtk.vtkImageMask()
threshold = vtk.vtkImageThreshold()
threshold2 = vtk.vtkImageThreshold()
math=vtk.vtkImageMathematics()
mask.SetInput(self.image_data)
mask.SetMaskInput(self.mask_data)
threshold.SetInput(mask.GetOutput())
threshold.ThresholdByLower(emphysemavalue)
threshold.SetOutValue(0)
threshold.SetInValue(1)
threshold2.SetInput(mask.GetOutput())
threshold2.ThresholdByLower(severeemphysemavalue)
threshold2.SetOutValue(1)
threshold2.SetInValue(2)
math.SetOperationToMultiply()
math.SetInput1(threshold.GetOutput())
math.SetInput2(threshold2.GetOutput())
math.Update()
overlay = math.GetOutput()
self.slice_viewer1.set_overlay_input(None)
self.slice_viewer1.set_overlay_input(overlay)
self.render()
self._view_frame.SetStatusText("Created Overlay")
def load_data_from_file(self, file_path):
"""Loads scanvolume data from file. Also sets the volume as input for the sliceviewers
"""
self._view_frame.SetStatusText("Opening file: %s..." % (file_path))
filename = os.path.split(file_path)[1]
fileBaseName =os.path.splitext(filename)[0]
reader = vtk.vtkMetaImageReader()
reader.SetFileName(file_path)
reader.Update()
self.image_data = reader.GetOutput()
self.slice_viewer1.set_input(self.image_data)
self.slice_viewer1.reset_camera()
self.slice_viewer1.render()
self.slice_viewer2.set_input(self.image_data)
self.slice_viewer2.reset_camera()
self.slice_viewer2.render()
self.slice_viewer3.set_input(self.image_data)
self.slice_viewer3.render()
self.slice_viewer3.set_opacity(0.1)
cam = self.ren.GetActiveCamera()
cam.SetPosition(0,-100,0)
cam.SetFocalPoint(0,0,0)
cam.SetViewUp(0,0,1)
self.ren.ResetCamera()
if (self.mask_data) is not None: # We can start calculating the volumerender
self.create_volumerender(0,0)
else:
self._view_frame.SetStatusText("Opened file")
def load_mask_from_file(self, file_path):
"""Loads mask file
"""
self._view_frame.SetStatusText( "Opening mask: %s..." % (file_path))
filename = os.path.split(file_path)[1]
fileBaseName =os.path.splitext(filename)[0]
reader = vtk.vtkMetaImageReader()
reader.SetFileName(file_path)
reader.Update()
self.mask_data = reader.GetOutput()
if (self.image_data) is not None:
self.create_volumerender(0,0)
else:
self._view_frame.SetStatusText("Opened mask file")
def save_to_file(self, file_path):
"""Save data from main renderwindow (the contour one) to a PNG-file
"""
w2i = vtk.vtkWindowToImageFilter()
w2i.SetInput(self._view_frame.rwi.GetRenderWindow());
w2i.Update()
writer = vtk.vtkPNGWriter()
writer.SetInput(w2i.GetOutput())
writer.SetFileName(file_path)
writer.Update()
result = writer.Write()
if result == 0:
self._view_frame.SetStatusText( "Saved file")
else:
self._view_frame.SetStatusText( "Saved file to: %s..." % (file_path))
def _bind_events(self):
"""Bind wx events to Python callable object event handlers.
"""
vf = self._view_frame
vf.Bind(wx.EVT_MENU, self._handler_file_open,
id = vf.id_file_open)
vf.Bind(wx.EVT_MENU, self._handler_mask_open,
id = vf.id_mask_open)
vf.Bind(wx.EVT_MENU, self._handler_file_save,
id = vf.id_mask_save)
self._view_frame.button1.Bind(wx.EVT_BUTTON,
self._handler_button1)
self._view_frame.button2.Bind(wx.EVT_BUTTON,
self._handler_button2)
self._view_frame.button3.Bind(wx.EVT_BUTTON,
self._handler_button3)
self._view_frame.button4.Bind(wx.EVT_BUTTON,
self._handler_button4)
self._view_frame.button5.Bind(wx.EVT_BUTTON,
self._handler_button5)
self._view_frame.button6.Bind(wx.EVT_BUTTON,
self._handler_button6)
self._view_frame.upper_slider.Bind(wx.EVT_SCROLL_CHANGED, self._handler_slider1)
self._view_frame.lower_slider.Bind(wx.EVT_SCROLL_CHANGED, self._handler_slider2)
def _handler_button1(self, event):
"""Reset the camera of the main render window
"""
self.ren.ResetCamera()
self.render()
def _handler_button2(self, event):
"""Reset all for the main render window
"""
cam = self.ren.GetActiveCamera()
cam.SetPosition(0,-100,0)
cam.SetFocalPoint(0,0,0)
cam.SetViewUp(0,0,1)
self.ren.ResetCamera()
self.render()
def _handler_button3(self, event):
"""Reset the camera for the sliceviewers
"""
self.slice_viewer1.reset_camera()
self.slice_viewer2.reset_camera()
self.render()
def _handler_button4(self, event):
"""Reset all for the sliceviewers
"""
self.slice_viewer1.reset_to_default_view(2)
self.slice_viewer2.reset_to_default_view(2)
orientations = [2, 0, 1]
for i, ipw in enumerate(self.slice_viewer1.ipws):
ipw.SetPlaneOrientation(orientations[i]) # axial
ipw.SetSliceIndex(0)
self.render()
for i, ipw in enumerate(self.slice_viewer2.ipws):
ipw.SetPlaneOrientation(orientations[i]) # axial
ipw.SetSliceIndex(0)
self.render()
def _handler_button5(self, event):
"""Adjust the contourvalues to values recommended in literature
"""
if self.lungVolume == None:
return
else:
self._view_frame.upper_slider.SetValue(-950)
self._view_frame.lower_slider.SetValue(-970)
self.adjust_contour(self.lungVolume, -950, self.moderate_mapper)
self.adjust_contour(self.lungVolume, -970, self.severe_mapper)
self.create_overlay(-950,-970)
def _handler_button6(self, event):
"""Adjust the contourvalues to values calculated from data
"""
if self.lungVolume == None:
return
else:
self.create_volumerender(0, 0)
def _handler_file_open(self, event):
"""Handler for file opening
"""
filters = 'Volume files (*.mhd)|*.mhd;'
dlg = wx.FileDialog(self._view_frame, "Please choose a CT-thorax file", self._config.last_used_dir, "", filters, wx.OPEN)
if dlg.ShowModal() == wx.ID_OK:
filename=dlg.GetFilename()
self._config.last_used_dir=dlg.GetDirectory()
full_file_path = "%s/%s" % (self._config.last_used_dir, filename)
self.load_data_from_file(full_file_path)
dlg.Destroy()
def _handler_mask_open(self, event):
"""Handler for mask opening
"""
filters = 'Mask files (*.mhd;#.mha)|*.mhd;*mha;'
dlg = wx.FileDialog(self._view_frame, "Please choose a CT-thorax mask file", self._config.last_used_dir, "", filters, wx.OPEN)
if dlg.ShowModal() == wx.ID_OK:
filename=dlg.GetFilename()
self._config.last_used_dir=dlg.GetDirectory()
full_file_path = "%s/%s" % (self._config.last_used_dir, filename)
self.load_mask_from_file(full_file_path)
dlg.Destroy()
def _handler_file_save(self, event):
"""Handler for filesaving
"""
self._view_frame.SetStatusText( "Saving file...")
filters = 'png file (*.png)|*.png'
dlg = wx.FileDialog(self._view_frame, "Choose a destination", self._config.last_used_dir, "", filters, wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
filename=dlg.GetFilename()
self._config.last_used_dir=dlg.GetDirectory()
file_path = "%s/%s" % (self._config.last_used_dir, filename)
self.save_to_file(file_path)
dlg.Destroy()
self._view_frame.SetStatusText( "Saved file")
def _handler_slider1(self, event):
"""Handler for slider adjustment (Severe emphysema)
"""
if self.lungVolume == None:
return
else:
contourValue = self._view_frame.upper_slider.GetValue()
self.adjust_contour(self.lungVolume, contourValue, self.moderate_mapper)
self.create_overlay(contourValue, self._view_frame.lower_slider.GetValue())
def _handler_slider2(self, event):
"""Handler for slider adjustment (Moderate emphysema)
"""
if self.lungVolume == None:
return
else:
contourValue = self._view_frame.lower_slider.GetValue()
self.adjust_contour(self.lungVolume, contourValue, self.severe_mapper)
self.create_overlay(self._view_frame.upper_slider.GetValue(),contourValue)
def render(self):
"""Method that calls Render() on the embedded RenderWindow.
Use this after having made changes to the scene.
"""
self._view_frame.render()
self.slice_viewer1.render()