def addT2transvisualize(self, T2images, image_pos_pat, image_ori_pat, T2dims, T2spacing, sideBreast, interact):
'''Added to build second reference frame and display T2 overlayed into T1 reference frame'''
# Proceed to build reference frame for display objects based on DICOM coords
[transformed_T2image, transform_cube] = self.dicomTransform(T2images, image_pos_pat, image_ori_pat)
#alignR = int(raw_input('\nAlign right? Yes:1 No:0 : '))
#if alignR:
if(sideBreast=="Right"):
zf1 = self.T1spacing[2]*self.T1extent[5] + self.T1origin[2]
self.T2origin[2] = zf1 - T2spacing[2]*self.T2extent[5] # this is z-span
else:
self.T2origin[2] = self.T1origin[2]
# Change info origin
translated_T2image = vtk.vtkImageChangeInformation()
translated_T2image.SetInput( transformed_T2image )
translated_T2image.SetOutputOrigin(self.T2origin)
translated_T2image.Update()
# Set up ortogonal planes
self.xImagePlaneWidget.SetInput( translated_T2image.GetOutput() )
self.xImagePlaneWidget.SetSliceIndex(0)
self.yImagePlaneWidget.SetInput( translated_T2image.GetOutput() )
self.yImagePlaneWidget.SetSliceIndex(0)
self.zImagePlaneWidget.SetInput( translated_T2image.GetOutput() )
self.zImagePlaneWidget.SetSliceIndex(0)
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(0.5, 0.5, 0)
tprop.ShadowOff()
# Update the reneder window to receive new image !Important*****
self.renderer1.Modified()
self.renWin1.Modified()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axesT2 = vtk.vtkCubeAxesActor2D()
axesT2.SetInput(translated_T2image.GetOutput())
axesT2.SetCamera(self.renderer1.GetActiveCamera())
axesT2.SetLabelFormat("%6.4g")
axesT2.SetFlyModeToOuterEdges()
axesT2.SetFontFactor(1.2)
axesT2.SetAxisTitleTextProperty(tprop)
axesT2.SetAxisLabelTextProperty(tprop)
self.renderer1.AddViewProp(axesT2)
### Update T2Images
t_T2images = vtk.vtkImageChangeInformation()
t_T2images.SetInput( T2images )
t_T2images.SetOutputOrigin(self.T2origin)
t_T2images.Update()
############
if(interact==True):
interactor = self.renWin1.GetInteractor()
interactor.Start()
return
def run(self):
self.vtk_renderer = vtkRenderer()
self.setup_gui()
self.setup_grid()
# Handle any deferred configuration
# Overlaid polygons
for args in self.conf_overlaidPolygons:
self.overlay_polygon_internal(*args)
# Draw (and maybe alter) the axes
if self.vtk_drawAxes:
self.vtk_axes = vtkCubeAxesActor2D()
# Perform all of the alterations required, by applying func to the vtk_axes instance (with the given args).
for func, args in self.conf_axesAlterations:
func(*((self.vtk_axes,) + args))
# Alter the Tk root as necessary.
for func, args in self.conf_tkAlterations:
func(*((self.tk_root,) + args))
# Finished with deferred configuration.
# Draw Height Quantities
for q in self.height_quantities:
self.update_height_quantity(q, self.height_dynamic[q])
self.draw_height_quantity(q)
self.tk_root.mainloop()
def addAxes(self, obj):
"""Add axes"""
tprop = self.textProperty(fontsize = self.opt.axes_fontsize)
axes = vtk.vtkCubeAxesActor2D()
axes.SetInput(obj.GetOutput())
axes.SetLabelFormat(self.opt.axes_format)
axes.SetFlyModeToOuterEdges()
axes.SetFontFactor(1.5)
axes.SetCornerOffset(0.0)
axes.GetProperty().SetColor(tprop.GetColor())
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
if self.opt.axes_levels:
axes.SetNumberOfLabels()
if self.opt.axes_xlabel:
axes.SetXLabel(self.opt.axes_xlabel)
if self.opt.axes_ylabel:
axes.SetYLabel(self.opt.axes_ylabel)
if self.opt.axes_zlabel:
axes.SetZLabel(self.opt.axes_zlabel)
return axes
def __init__ (self, mod_m):
debug ("In Axes::__init__ ()")
Common.state.busy ()
Base.Objects.Module.__init__ (self, mod_m)
self.axes = vtk.vtkCubeAxesActor2D ()
txt = ("X", "Y", "Z")
for i in range (0, 3):
eval ("self.axes.%sAxisVisibilityOn ()"%(txt[i]))
self.axes.SetNumberOfLabels (2)
self.axes.SetFontFactor (1.35)
self.axes.SetFlyModeToOuterEdges ()
self.axes.SetCornerOffset (0.0)
self.axes.ScalingOff ()
self.axes.GetProperty ().SetColor (*Common.config.fg_color)
self.axes.SetCamera (self.renwin.get_active_camera ())
if hasattr(self.axes, "GetAxisTitleTextProperty"):
ttp = self.axes.GetAxisTitleTextProperty()
ltp = self.axes.GetAxisLabelTextProperty()
ttp.ShadowOff()
fg_color = Common.config.fg_color
ttp.SetColor(fg_color)
ltp.SetColor(fg_color)
ltp.ShadowOff()
else:
self.axes.ShadowOff ()
self.renwin.add_actors (self.axes)
self.axes.SetInput (self.mod_m.GetOutput ())
self.actor = self.axes
# used for the pipeline browser
self.pipe_objs = self.axes
self._gui_init ()
Common.state.idle ()
def cube_axes(size):
render = vtk.vtkRenderer()
cube = vtk.vtkCubeSource()
cube.SetXLength(size)
cube.SetYLength(size)
cube.SetZLength(size)
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(layer_color, layer_color, layer_color)
tprop.ShadowOn()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axes = vtk.vtkCubeAxesActor2D()
axes.SetInputConnection(cube.GetOutputPort())
axes.SetCamera(render.GetActiveCamera())
axes.SetLabelFormat("%6.4g")
axes.SetFlyModeToOuterEdges()
axes.SetFontFactor(0.8)
axes.GetAxisLabelTextProperty().SetColor(cube_color, cube_color,
cube_color)
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
axes.GetProperty().SetColor(cube_color, cube_color, cube_color)
return axes
def run(self):
self.vtk_renderer = vtkRenderer()
self.setup_gui()
self.setup_grid()
# Handle any deferred configuration
# Overlaid polygons
for args in self.conf_overlaidPolygons:
self.overlay_polygon_internal(*args)
# Draw (and maybe alter) the axes
if self.vtk_drawAxes:
self.vtk_axes = vtkCubeAxesActor2D()
# Perform all of the alterations required, by applying func to the vtk_axes instance (with the given args).
for func, args in self.conf_axesAlterations:
func(*((self.vtk_axes, ) + args))
# Alter the Tk root as necessary.
for func, args in self.conf_tkAlterations:
func(*((self.tk_root, ) + args))
# Finished with deferred configuration.
# Draw Height Quantities
for q in self.height_quantities:
self.update_height_quantity(q, self.height_dynamic[q])
self.draw_height_quantity(q)
self.tk_root.mainloop()
def __init__(self, parent):
QVTKRenderWindowInteractor.__init__(self, parent)
self.renderer = vtk.vtkRenderer()
self.GetRenderWindow().AddRenderer(self.renderer)
interactor = vtk.vtkInteractorStyleSwitch()
self._Iren.SetInteractorStyle(interactor)
self.surface = None
# Remainng calls set up axes.
tprop = vtk.vtkTextProperty()
tprop.SetColor(1,1,1)
# Create a faint outline to go with the axes.
self.outline = vtk.vtkOutlineFilter()
# Initially set up with a box as input. This will be changed
# to a plot once the user clicks something.
self.box = vtk.vtkBox()
self.box.SetBounds(0,10,0,10,0,10)
sample = vtk.vtkSampleFunction()
sample.SetImplicitFunction(self.box)
sample.SetSampleDimensions(2,2,2)
sample.SetModelBounds(0,10,0,10,0,5)
sample.ComputeNormalsOff()
self.outline.SetInputConnection(sample.GetOutputPort())
mapOutline = vtk.vtkPolyDataMapper()
mapOutline.SetInputConnection(self.outline.GetOutputPort())
self.outlineActor = vtk.vtkActor()
self.outlineActor.SetMapper(mapOutline)
self.outlineActor.GetProperty().SetColor(1,1,1)
self.outlineActor.GetProperty().SetOpacity(.25)
self.renderer.AddActor(self.outlineActor)
self.axes = vtk.vtkCubeAxesActor2D()
self.axes.SetCamera(self.renderer.GetActiveCamera())
self.axes.SetFlyModeToOuterEdges()
self.axes.SetLabelFormat("%6.4g")
self.axes.SetFontFactor(0.8)
self.axes.SetAxisTitleTextProperty(tprop)
self.axes.SetAxisLabelTextProperty(tprop)
self.axes.SetXLabel("MPI Rank")
self.axes.SetYLabel("Progress")
self.axes.SetZLabel("Effort")
self.axes.SetInput(sample.GetOutput())
self.renderer.AddViewProp(self.axes)
# Keep original camera around in case it gets changed
self.originalCamera = self.renderer.GetActiveCamera()
self.renderer.GetActiveCamera().Pitch(90) # Want effort to be vertical
self.renderer.GetActiveCamera().OrthogonalizeViewUp()
self.renderer.ResetCamera()
self.renderer.GetActiveCamera().Elevation(15) # Be slightly above the data
def __init__(self,
plots=None,
las_header=None,
axes_on=False,
app=None,
background=(.2, .3, .4)):
"""
:param plots: list of VTKPointClouds to plot
:param las_header: a las_header that is optionally supplied if reading from a las file, helpful for saving
:param axes_on: flag for turning axes on/off
:param app: the main QApplication driving the GUI
:param background: tuple of 0-1's for background color
"""
super().__init__()
self.plots = plots
self.las_header = las_header
self.background = background
self.default_viewup = (0.0, 1.0, 0.0)
self.axes_on = axes_on
# self.app = Qt.QApplication(sys.argv)
self.app = app
self.main = Qt.QMainWindow()
self.main.__init__()
self.frame = Qt.QFrame()
self.hl = Qt.QHBoxLayout()
self.bl = Qt.QVBoxLayout()
self.widgets = []
self.widget_defaults = []
self.widget_point_actors = []
self.axes_actors = []
if self.plots is not None:
for i in range(len(plots)):
vtk_widget = QVTKRenderWindowInteractor(self.frame)
self.widgets.append(vtk_widget)
self.hl.addWidget(vtk_widget)
self.axes_actors.append(vtk.vtkCubeAxesActor2D())
self.plot_point_cloud_qt(plots[i], vtk_widget)
for w in self.widgets:
position = w.GetRenderWindow().GetInteractor(
).GetInteractorStyle().camera.GetPosition()
focus = w.GetRenderWindow().GetInteractor().GetInteractorStyle(
).camera.GetFocalPoint()
viewup = w.GetRenderWindow().GetInteractor(
).GetInteractorStyle().camera.GetViewUp()
self.widget_defaults.append((position, focus, viewup))
self.hl.addLayout(self.bl)
self.add_buttons()
self.frame.setLayout(self.hl)
self.main.setCentralWidget(self.frame)
self.main.show()
for w in self.widgets:
w.GetRenderWindow().GetInteractor().Initialize()
w.GetRenderWindow().GetInteractor().Start()
def scale_bar_actor(center,
camera,
length=10000,
color=(0, 0, 0),
linewidth=5,
font_size=20):
"""Creates a xyz 3d scale bar actor located at a specific location with a given size
Parameters
----------
center : iterable
a length 3 iterable of xyz position
camera : vtk.vtkCamera
the camera the scale bar should follow
length : int, optional
length of each of the xyz axis, by default 10000
color : tuple, optional
color of text and lines, by default (0,0,0)
linewidth : int, optional
width of line in pixels, by default 5
font_size : int, optional
font size of xyz labels, by default 20
Returns
-------
vtk.vktActor
scale bar actor to add to render_actors
"""
axes_actor = vtk.vtkCubeAxesActor2D()
axes_actor.SetBounds(center[0], center[0] + length, center[1],
center[1] + length, center[2], center[2] + length)
# this means no real labels
axes_actor.SetLabelFormat("")
axes_actor.SetCamera(camera)
# this turns off the tick marks and labelled numbers
axes_actor.SetNumberOfLabels(0)
# this affects whether the corner of the 3 axis
# changes as you rotate the view
# this option makes it stay constant
axes_actor.SetFlyModeToNone()
axes_actor.SetFontFactor(1.0)
axes_actor.GetProperty().SetColor(*color)
axes_actor.GetProperty().SetLineWidth(linewidth)
# this controls the color of text
tprop = vtk.vtkTextProperty()
tprop.SetColor(*color)
# no shadows on text
tprop.ShadowOff()
tprop.SetFontSize(font_size)
# makes the xyz and labels the same
axes_actor.SetAxisTitleTextProperty(tprop)
axes_actor.SetAxisLabelTextProperty(tprop)
return axes_actor
def visualize_map(self, VOIclip):
# get info from image before visualization
VOIclip.UpdateInformation()
self.dims = VOIclip.GetDimensions()
(xMin, xMax, yMin, yMax, zMin, zMax) = VOIclip.GetWholeExtent()
self.spacing = VOIclip.GetSpacing()
# Set up ortogonal planes
self.xImagePlaneWidget.SetInput( VOIclip )
self.xImagePlaneWidget.SetPlaneOrientationToXAxes()
self.xImagePlaneWidget.SetSliceIndex(0)
self.yImagePlaneWidget.SetInput( VOIclip )
self.yImagePlaneWidget.SetPlaneOrientationToYAxes()
self.yImagePlaneWidget.SetSliceIndex(0)
self.zImagePlaneWidget.SetInput( VOIclip )
self.zImagePlaneWidget.SetPlaneOrientationToZAxes()
self.zImagePlaneWidget.SetSliceIndex(0)
self.xImagePlaneWidget.On()
self.yImagePlaneWidget.On()
self.zImagePlaneWidget.On()
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(1, 1, 1)
tprop.ShadowOff()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axes = vtk.vtkCubeAxesActor2D()
axes.SetInput(VOIclip)
axes.SetCamera(self.renderer1.GetActiveCamera())
axes.SetLabelFormat("%6.4g")
axes.SetFlyModeToOuterEdges()
axes.SetFontFactor(1.2)
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
self.renderer1.AddViewProp(axes)
############
# bounds and initialize camera
bounds = VOIclip.GetBounds()
self.renderer1.ResetCamera(bounds)
self.renderer1.ResetCameraClippingRange()
self.camera.SetViewUp(0.0,-1.0,0.0)
self.camera.Azimuth(360)
# Initizalize
#self.renWin1.Render()
self.renderer1.Render()
self.iren1.Start()
return
def new_axes_actor(ren: vtk.vtkRenderer, data_source):
axes = vtk.vtkCubeAxesActor2D()
axes.SetInputConnection(data_source.GetOutputPort())
axes.SetCamera(ren.GetActiveCamera())
axes.SetLabelFormat("%6.4g")
axes.SetFlyModeToOuterEdges()
axes.SetFontFactor(0.8)
tprop = vtk.vtkTextProperty()
tprop.SetColor(1, 1, 1)
tprop.ShadowOn()
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
return axes
def displayPolyAnd3Planes(poly, image, title = 'Polydata and 3 Planes'):
"""
display a poly and 3 planes
"""
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(poly)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetRepresentationToWireframe()
actor.GetProperty().SetColor(0,0,0) #RED
ren= vtk.vtkRenderer()
ren.AddActor(actor)
ren.SetBackground(1,1,1)
renwin = vtk.vtkRenderWindow()
renwin.AddRenderer(ren)
renwin.SetSize( 700, 700 )
renwin.SetWindowName(title)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renwin)
style = vtk.vtkInteractorStyleTrackballCamera()
iren.SetInteractorStyle(style)
wX,wY,wZ = create3Planes(image)
wX.SetInteractor(iren); wX.On()
wY.SetInteractor(iren); wY.On()
wZ.SetInteractor(iren); wZ.On()
outline = createOutlineActor(image)
ren.AddActor(outline)
axes = vtk.vtkCubeAxesActor2D()
axes.SetCamera(ren.GetActiveCamera())
axes.SetViewProp(outline)
ren.AddActor(axes)
ren.ResetCamera()
cam1 = ren.GetActiveCamera()
cam1.Elevation(-90)
cam1.SetViewUp(0, 0, 1)
cam1.Azimuth(45)
ren.ResetCameraClippingRange()
iren.Initialize()
renwin.Render()
iren.Start()
def visualizemha(self, img_path, image_pos_pat, image_ori_pat, interact):
'''Display and render volumes, reference frames, actors and widgets'''
# Proceed to build reference frame for display objects based on DICOM coords
mhareader = vtk.vtkMetaImageReader()
mhareader.SetFileName(img_path)
mhareader.Update()
self.warpT2_mha = self.mhaTransform(mhareader.GetOutput(), image_pos_pat, image_ori_pat)
self.T2origin = list(self.warpT2_mha.GetOrigin())
print "T2 Extent"
self.T2extent = list(self.warpT2_mha.GetExtent())
print self.T2extent
# Initizalize
self.xImagePlaneWidget.Modified()
self.yImagePlaneWidget.Modified()
self.zImagePlaneWidget.Modified()
# Set up ortogonal planes
self.xImagePlaneWidget.SetInputData(self.warpT2_mha )
self.xImagePlaneWidget.SetSliceIndex(0)
self.yImagePlaneWidget.SetInputData(self.warpT2_mha )
self.yImagePlaneWidget.SetSliceIndex(0)
self.zImagePlaneWidget.SetInputData( self.warpT2_mha )
self.zImagePlaneWidget.SetSliceIndex(0)
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(0.5, 0.5, 0)
tprop.ShadowOff()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axesT2 = vtk.vtkCubeAxesActor2D()
axesT2.SetInputData(self.warpT2_mha)
axesT2.SetCamera(self.renderer1.GetActiveCamera())
axesT2.SetLabelFormat("%6.4g")
axesT2.SetFlyModeToOuterEdges()
axesT2.SetFontFactor(1.2)
axesT2.SetAxisTitleTextProperty(tprop)
axesT2.SetAxisLabelTextProperty(tprop)
self.renderer1.AddViewProp(axesT2)
if(interact==True):
interactor = self.renWin1.GetInteractor()
interactor.Start()
return
def __create_axes(self):
axes = vtk.vtkCubeAxesActor2D()
axes.SetBounds(numpy.array([0.0, 1.0, 0.0, 1.0, 0.0, 1.0]) * self.settings.scaling)
axes.SetRanges(0.0, self.__world_size, 0.0, self.__world_size, 0.0, self.__world_size)
axes.SetLabelFormat("%g")
axes.SetFontFactor(1.5)
tprop = vtk.vtkTextProperty()
tprop.SetColor(self.settings.axis_annotation_color)
tprop.ShadowOn()
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
axes.UseRangesOn()
axes.SetCornerOffset(0.0)
return axes
def makeAxes(self, outline, outlinefilter):
""" create axes """
tprop = vtk.vtkTextProperty()
tprop.SetColor(self.fgColor)
tprop.ShadowOff()
prop = vtk.vtkProperty2D()
prop.SetColor(self.fgColor)
zax = vtk.vtkCubeAxesActor()
zax.SetBounds(outline.GetBounds()[0], outline.GetBounds()[1], outline.GetBounds()[2], outline.GetBounds()[3],
outline.GetBounds()[4], outline.GetBounds()[4])
zax.SetDragable(False)
zax.SetCamera(self.renderer.GetActiveCamera())
zax.SetFlyModeToOuterEdges()
zax.DrawXGridlinesOn()
zax.DrawYGridlinesOn()
zax.DrawZGridlinesOn()
zax.SetXTitle('')
zax.SetYTitle('')
zax.SetZTitle('')
zax.SetXAxisMinorTickVisibility(0)
zax.SetYAxisMinorTickVisibility(0)
zax.SetZAxisMinorTickVisibility(0)
zax.SetXAxisLabelVisibility(0)
zax.SetYAxisLabelVisibility(0)
zax.SetZAxisLabelVisibility(0)
axes = vtk.vtkCubeAxesActor2D()
axes.SetDragable(False)
axes.SetInputConnection(outlinefilter.GetOutputPort())
axes.SetCamera(self.renderer.GetActiveCamera())
axes.SetLabelFormat(self.config.LabelFormat())
axes.SetFlyModeToOuterEdges()
axes.SetFontFactor(self.fontFactor)
axes.SetNumberOfLabels(self.config.NLabels())
axes.SetXLabel(self.config.XLabel())
axes.SetYLabel(self.config.YLabel())
axes.SetZLabel(self.config.ZLabel())
axes.SetRanges(self.out.GetBounds())
axes.SetUseRanges(True)
axes.SetProperty(prop)
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
return zax, axes
def initArea(self):
'''
Sets up the VTK simulation area
:return:None
'''
# Zoom items
self.zitems = []
self.actors_dict = {}
self.cellTypeActors={}
self.outlineActor = vtk.vtkActor()
self.outlineDim=[0,0,0]
self.invisibleCellTypes={}
self.typesInvisibleStr=""
self.set3DInvisibleTypes()
self.axesActor = vtk.vtkCubeAxesActor2D()
self.clut = vtk.vtkLookupTable()
self.clut.SetHueRange(0.67, 0.0)
self.clut.SetSaturationRange(1.0,1.0)
self.clut.SetValueRange(1.0,1.0)
self.clut.SetAlphaRange(1.0,1.0)
self.clut.SetNumberOfColors(1024)
self.clut.Build()
## Set up the mapper and actor (3D) for concentration field.
# self.conMapper = vtk.vtkPolyDataMapper()
self.conActor = vtk.vtkActor()
self.glyphsActor=vtk.vtkActor()
# self.glyphsMapper=vtk.vtkPolyDataMapper()
self.cellGlyphsActor = vtk.vtkActor()
self.FPPLinksActor = vtk.vtkActor()
# Weird attributes
self.typeActors = {} # vtkActor
# self.smootherFilters = {} # vtkSmoothPolyDataFilter
# self.polyDataNormals = {} # vtkPolyDataNormals
# self.typeExtractors = {} # vtkDiscreteMarchingCubes
# self.typeExtractorMappers = {} # vtkPolyDataMapper
self.actors_dict['cellsActor'] = {}
def initArea(self):
'''
Sets up the VTK simulation area
:return:None
'''
# Zoom items
self.zitems = []
self.actors_dict = {}
self.cellTypeActors = {}
self.outlineActor = vtk.vtkActor()
self.outlineDim = [0, 0, 0]
self.invisibleCellTypes = {}
self.typesInvisibleStr = ""
self.set3DInvisibleTypes()
self.axesActor = vtk.vtkCubeAxesActor2D()
self.clut = vtk.vtkLookupTable()
self.clut.SetHueRange(0.67, 0.0)
self.clut.SetSaturationRange(1.0, 1.0)
self.clut.SetValueRange(1.0, 1.0)
self.clut.SetAlphaRange(1.0, 1.0)
self.clut.SetNumberOfColors(1024)
self.clut.Build()
## Set up the mapper and actor (3D) for concentration field.
# self.conMapper = vtk.vtkPolyDataMapper()
self.conActor = vtk.vtkActor()
self.glyphsActor = vtk.vtkActor()
# self.glyphsMapper=vtk.vtkPolyDataMapper()
self.cellGlyphsActor = vtk.vtkActor()
self.FPPLinksActor = vtk.vtkActor()
# Weird attributes
self.typeActors = {} # vtkActor
# self.smootherFilters = {} # vtkSmoothPolyDataFilter
# self.polyDataNormals = {} # vtkPolyDataNormals
# self.typeExtractors = {} # vtkDiscreteMarchingCubes
# self.typeExtractorMappers = {} # vtkPolyDataMapper
self.actors_dict['cellsActor'] = {}
def addT2visualize(self, T2images, image_pos_pat, image_ori_pat, T2dims, T2spacing, interact):
'''Added to build second reference frame and display T2 overlayed into T1 reference frame'''
# Proceed to build reference frame for display objects based on DICOM coords
[self.transformed_T2image, transform_cube] = self.dicomTransform(T2images, image_pos_pat, image_ori_pat)
self.T2origin = list(self.transformed_T2image.GetOrigin())
print "T2 Extent"
self.T2extent = list(self.transformed_T2image.GetExtent())
print self.T2extent
# Set up ortogonal planes
self.xImagePlaneWidget.SetInputData( self.transformed_T2image )
self.xImagePlaneWidget.SetSliceIndex(0)
self.yImagePlaneWidget.SetInputData( self.transformed_T2image )
self.yImagePlaneWidget.SetSliceIndex(0)
self.zImagePlaneWidget.SetInputData( self.transformed_T2image )
self.zImagePlaneWidget.SetSliceIndex(0)
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(0, 1, 1)
tprop.ShadowOff()
# Update the reneder window to receive new image !Important*****
self.renderer1.Modified()
self.renWin1.Modified()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axesT2 = vtk.vtkCubeAxesActor2D()
axesT2.SetInputData(self.transformed_T2image)
axesT2.SetCamera(self.renderer1.GetActiveCamera())
axesT2.SetLabelFormat("%6.4g")
axesT2.SetFlyModeToOuterEdges()
axesT2.SetFontFactor(1.2)
axesT2.SetAxisTitleTextProperty(tprop)
axesT2.SetAxisLabelTextProperty(tprop)
self.renderer1.AddViewProp(axesT2)
############
if(interact==True):
interactor = self.renWin1.GetInteractor()
interactor.Start()
return
def addT2visualize(self, T2images, image_pos_pat, image_ori_pat, T2dims, T2spacing, interact):
'''Added to build second reference frame and display T2 overlayed into T1 reference frame'''
# Proceed to build reference frame for display objects based on DICOM coords
[transformed_T2image, transform_cube] = self.dicomTransform(T2images, image_pos_pat, image_ori_pat)
self.T2origin = list(transformed_T2image.GetOrigin())
print "T2 Extent"
self.T2extent = list(transformed_T2image.GetExtent())
print self.T2extent
# Set up ortogonal planes
self.xImagePlaneWidget.SetInput( transformed_T2image )
self.xImagePlaneWidget.SetSliceIndex(0)
self.yImagePlaneWidget.SetInput( transformed_T2image )
self.yImagePlaneWidget.SetSliceIndex(0)
self.zImagePlaneWidget.SetInput( transformed_T2image )
self.zImagePlaneWidget.SetSliceIndex(0)
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(0, 1, 1)
tprop.ShadowOff()
# Update the reneder window to receive new image !Important*****
self.renderer1.Modified()
self.renWin1.Modified()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axesT2 = vtk.vtkCubeAxesActor2D()
axesT2.SetInput(transformed_T2image)
axesT2.SetCamera(self.renderer1.GetActiveCamera())
axesT2.SetLabelFormat("%6.4g")
axesT2.SetFlyModeToOuterEdges()
axesT2.SetFontFactor(1.2)
axesT2.SetAxisTitleTextProperty(tprop)
axesT2.SetAxisLabelTextProperty(tprop)
self.renderer1.AddViewProp(axesT2)
############
if(interact==True):
interactor = self.renWin1.GetInteractor()
interactor.Start()
return
def __init__(self, data_reader, renderer):
# Create a text property for cube axes
self.tprop = vtk.vtkTextProperty()
self.tprop.SetColor(1, 1, 1)
self.tprop.ShadowOn()
# Create a vtkCubeAxesActor2D. Use the closest vertex to the camera to
# determine where to draw the axes. Add the actor to the renderer.
self.actor = vtk.vtkCubeAxesActor2D()
self.actor.SetInput(data_reader.get_data_set())
self.actor.SetCamera(renderer.GetActiveCamera())
self.actor.SetLabelFormat("%6.4g")
self.actor.SetFlyModeToClosestTriad()
self.actor.SetFontFactor(0.8)
self.actor.GetProperty().SetColor(0, 0, 0)
self.actor.ScalingOff()
self.actor.SetAxisTitleTextProperty(self.tprop)
self.actor.SetAxisLabelTextProperty(self.tprop)
def _create_axes(self):
axes = vtk.vtkCubeAxesActor2D()
axes.SetBounds(
numpy.array([0.0, 1.0, 0.0, 1.0, 0.0, 1.0]) *
self.settings.scaling)
axes.SetRanges(0.0, self._world_size, 0.0, self._world_size, 0.0,
self._world_size)
axes.SetLabelFormat('%g')
axes.SetFontFactor(1.5)
tprop = vtk.vtkTextProperty()
tprop.SetColor(self.settings.axis_annotation_color)
tprop.ShadowOn()
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
axes.UseRangesOn()
axes.SetCornerOffset(0.0)
return axes
def __init__(self,data_reader,renderer):
# Create a text property for cube axes
self.tprop=vtk.vtkTextProperty()
self.tprop.SetColor(1,1,1)
self.tprop.ShadowOn()
# Create a vtkCubeAxesActor2D. Use the closest vertex to the camera to
# determine where to draw the axes. Add the actor to the renderer.
self.actor=vtk.vtkCubeAxesActor2D()
self.actor.SetInput(data_reader.get_data_set())
self.actor.SetCamera(renderer.GetActiveCamera())
self.actor.SetLabelFormat("%6.4g")
self.actor.SetFlyModeToClosestTriad()
self.actor.SetFontFactor(0.8)
self.actor.GetProperty().SetColor(0,0,0)
self.actor.ScalingOff()
self.actor.SetAxisTitleTextProperty(self.tprop)
self.actor.SetAxisLabelTextProperty(self.tprop)
def view3Planes(image, title = 'Image and 3 Planes'):
"""
display and image and 3 planes
"""
xMin, xMax, yMin, yMax, zMin, zMax = image.GetWholeExtent()
ren= vtk.vtkRenderer()
ren.SetBackground(0.2,0.3,0.6)
renwin = vtk.vtkRenderWindow()
renwin.AddRenderer(ren)
renwin.SetSize( 700, 700 )
renwin.SetWindowName(title)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renwin)
style = vtk.vtkInteractorStyleTrackballCamera()
iren.SetInteractorStyle(style)
wX,wY,wZ = create3Planes(image)
wX.SetInteractor(iren); wX.On()
wY.SetInteractor(iren); wY.On()
wZ.SetInteractor(iren); wZ.On()
outline = createOutlineActor(image)
ren.AddActor(outline)
axes = vtk.vtkCubeAxesActor2D()
axes.SetCamera(ren.GetActiveCamera())
axes.SetViewProp(outline)
ren.AddActor(axes)
ren.ResetCamera()
cam1 = ren.GetActiveCamera()
cam1.Elevation(-70)
cam1.SetViewUp(0, 0, 1)
cam1.Azimuth(30)
ren.ResetCameraClippingRange()
iren.Initialize()
renwin.Render()
iren.Start()
def simple_axis(self, ren):
"""Show axes."""
if self.mesh is not None:
tprop = vtk.vtkTextProperty()
tprop.SetColor(0, 0, 0)
tprop.ShadowOff()
outline = vtk.vtkOutlineFilter()
outline.SetInput(self.vtkgrid[self.dim])
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(outline.GetOutputPort())
self.axes = vtk.vtkCubeAxesActor2D()
self.axes.SetInput(normals.GetOutput())
self.axes.SetCamera(ren.GetActiveCamera())
self.axes.GetProperty().SetColor(0, 0, 0)
self.axes.SetAxisTitleTextProperty(tprop)
self.axes.SetAxisLabelTextProperty(tprop)
self.axes.SetCornerOffset(0)
if self.dim == 2:
self.axes.ZAxisVisibilityOff()
ren.AddViewProp(self.axes)
def create_axes(bounds, **params):
# bounds = (minpos[0], maxpos[0], minpos[1],
# maxpos[1], minpos[2], maxpos[2])
ranges = bounds
axes = vtk.vtkCubeAxesActor2D()
axes.SetBounds(bounds)
axes.SetRanges(ranges)
axes.SetLabelFormat('%g')
# axes.SetFontFactor(1.5)
axes.UseRangesOn()
# axes.SetCornerOffset(0.0)
tprop = vtk.vtkTextProperty()
if 'color' in params.keys():
tprop.SetColor(params['color'])
# tprop.ShadowOn()
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
return axes
def _create_axes(self):
axes = vtk.vtkCubeAxesActor2D()
axes.SetBounds(
[0.0, self._scalings[0],
0.0, self._scalings[1],
0.0, self._scalings[2]])
axes.SetRanges(
0.0, self._world_sizes[0],
0.0, self._world_sizes[1],
0.0, self._world_sizes[2])
axes.SetLabelFormat('%g')
axes.SetFontFactor(1.5)
tprop = vtk.vtkTextProperty()
tprop.SetColor(self.settings.axis_annotation_color)
tprop.ShadowOn()
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
axes.UseRangesOn()
axes.SetCornerOffset(0.0)
return axes
def main ():
# example code...
import vtk
from vtk.wx.wxVTKRenderWindow import wxVTKRenderWindow
cone = vtk.vtkConeSource()
cone.SetResolution(8)
transform = vtk.vtkTransformFilter ()
transform.SetInput ( cone.GetOutput() )
transform.SetTransform ( vtk.vtkTransform() )
coneMapper = vtk.vtkPolyDataMapper()
coneMapper.SetInput(transform.GetOutput())
l = vtk.vtkLookupTable ()
coneMapper.SetLookupTable (l)
coneActor = vtk.vtkActor()
coneActor.SetMapper(coneMapper)
axes = vtk.vtkCubeAxesActor2D ()
app = wx.PySimpleApp()
frame = wx.Frame(None, -1, "wx.RenderWindow", size=wx.Size(400,400))
wid = wxVTKRenderWindow(frame, -1)
ren = vtk.vtkRenderer()
renWin = wid.GetRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(300,300)
ren.AddActor (coneActor)
ren.AddActor (axes)
axes.SetCamera (ren.GetActiveCamera ())
renWin.Render ()
debug ("Starting VTK Pipeline Browser...")
pipe = vtkPipelineBrowser (frame, renWin)
pipe.show()
pipe_segment = vtkPipelineBrowser(frame, renWin, (coneActor, axes))
pipe_segment.show()
app.MainLoop()
def main():
# example code...
import vtk
from vtk.wx.wxVTKRenderWindow import wxVTKRenderWindow
cone = vtk.vtkConeSource()
cone.SetResolution(8)
transform = vtk.vtkTransformFilter()
transform.SetInput(cone.GetOutput())
transform.SetTransform(vtk.vtkTransform())
coneMapper = vtk.vtkPolyDataMapper()
coneMapper.SetInput(transform.GetOutput())
l = vtk.vtkLookupTable()
coneMapper.SetLookupTable(l)
coneActor = vtk.vtkActor()
coneActor.SetMapper(coneMapper)
axes = vtk.vtkCubeAxesActor2D()
app = wx.PySimpleApp()
frame = wx.Frame(None, -1, "wx.RenderWindow", size=wx.Size(400, 400))
wid = wxVTKRenderWindow(frame, -1)
ren = vtk.vtkRenderer()
renWin = wid.GetRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(300, 300)
ren.AddActor(coneActor)
ren.AddActor(axes)
axes.SetCamera(ren.GetActiveCamera())
renWin.Render()
debug("Starting VTK Pipeline Browser...")
pipe = vtkPipelineBrowser(frame, renWin)
pipe.show()
pipe_segment = vtkPipelineBrowser(frame, renWin, (coneActor, axes))
pipe_segment.show()
app.MainLoop()
def show_axes(self):
"""Shows the axes around the main object"""
tprop = vtk.vtkTextProperty()
tprop.SetColor(0., 0., 0.)
tprop.ShadowOn()
axes = vtk.vtkCubeAxesActor2D()
if vtk.VTK_MAJOR_VERSION <= 5:
axes.SetInput(self.polydatas[0])
else:
axes.SetInputData(self.polydatas[0])
axes.SetCamera(self.renderer.GetActiveCamera())
axes.SetLabelFormat("%6.4g")
axes.SetFlyModeToOuterEdges()
axes.SetFontFactor(0.8)
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
# axes.DrawGridLinesOn()
self.renderer.AddViewProp(axes)
self.axes.append(axes)
def _createIPW(self):
# we have to do this to get the correct log range
self._histogram.GetOutput().Update()
# this means we have newly valid input and should setup an ipw
self._ipw = vtk.vtkImagePlaneWidget()
self._histogram.GetOutput().Update()
self._ipw.SetInput(self._histogram.GetOutput())
self._ipw.SetInteractor(self._viewFrame.rwi)
# normal to the Z-axis
self._ipw.SetPlaneOrientation(2)
self._ipw.SetSliceIndex(0)
# setup specific lut
srange = self._histogram.GetOutput().GetScalarRange()
lut = vtk.vtkLookupTable()
lut.SetScaleToLog10()
lut.SetTableRange(srange)
lut.SetSaturationRange(1.0, 1.0)
lut.SetValueRange(1.0, 1.0)
lut.SetHueRange(0.1, 1.0)
lut.Build()
self._ipw.SetUserControlledLookupTable(1)
self._ipw.SetLookupTable(lut)
self._ipw.SetDisplayText(1)
# if we use ContinousCursor, we get OffImage when zoomed
# on Linux (really irritating) but not on Windows. A VTK
# recompile might help, we'll see.
self._ipw.SetUseContinuousCursor(1)
# make sure the user can't twist the plane out of sight
self._ipw.SetMiddleButtonAction(0)
self._ipw.SetRightButtonAction(0)
# add an observer
self._ipw.AddObserver("StartInteractionEvent", self._observerIPWInteraction)
self._ipw.AddObserver("InteractionEvent", self._observerIPWInteraction)
self._ipw.AddObserver("EndInteractionEvent", self._observerIPWInteraction)
self._ipw.On()
self._axes = vtk.vtkCubeAxesActor2D()
self._axes.SetFlyModeToOuterEdges()
# NOBODY will ever know why we have to switch off the Y axis when
# we actually want the Z-axis to go away.
self._axes.YAxisVisibilityOff()
self._axes.SetBounds(self._ipw.GetResliceOutput().GetBounds())
self._renderer.AddActor(self._axes)
self._axes.SetCamera(self._renderer.GetActiveCamera())
self._axes.PickableOff()
if 0:
# now add a scalarbar
self._scalarBarWidget = vtk.vtkScalarBarWidget()
self._scalarBarWidget.SetInteractor(self._viewFrame.rwi)
self._scalarBarWidget.GetScalarBarActor().SetTitle("Frequency")
self._scalarBarWidget.GetScalarBarActor().SetLookupTable(lut)
# and activate
self._scalarBarWidget.On()
self._resetCamera()
self._render()
def simpleVisualize(self, volume, interact):
""" simpleVisualize will load a 3D ortoghonal planes visualization of a volume"""
# get info from image before visualization
volume.UpdateInformation()
self.dims = volume.GetDimensions()
print "Image Dimensions"
print self.dims
(xMin, xMax, yMin, yMax, zMin, zMax) = volume.GetWholeExtent()
print "Image Extension"
print xMin, xMax, yMin, yMax, zMin, zMax
self.spacing = volume.GetSpacing()
print "Image Spacing"
print self.spacing
self.origin = volume.GetOrigin()
print "Image Origin"
print self.origin
# Set up ortogonal planes
self.xImagePlaneWidget.SetInput(volume)
self.xImagePlaneWidget.SetPlaneOrientationToXAxes()
self.xImagePlaneWidget.SetSliceIndex(0)
self.yImagePlaneWidget.SetInput(volume)
self.yImagePlaneWidget.SetPlaneOrientationToYAxes()
self.yImagePlaneWidget.SetSliceIndex(0)
self.zImagePlaneWidget.SetInput(volume)
self.zImagePlaneWidget.SetPlaneOrientationToZAxes()
self.zImagePlaneWidget.SetSliceIndex(0)
self.xImagePlaneWidget.On()
self.yImagePlaneWidget.On()
self.zImagePlaneWidget.On()
# Set UP the axes
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(1, 1, 1)
tprop.ShadowOff()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axes = vtk.vtkCubeAxesActor2D()
axes.SetInput(volume)
axes.SetCamera(self.renderer1.GetActiveCamera())
axes.SetLabelFormat("%6.4g")
axes.SetFlyModeToOuterEdges()
axes.SetFontFactor(1.2)
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
self.renderer1.AddViewProp(axes)
############
# bounds and initialize camera
bounds = volume.GetBounds()
self.renderer1.ResetCamera(bounds)
self.renderer1.ResetCameraClippingRange()
self.camera.SetViewUp(0.0, -1.0, 0.0)
self.camera.Azimuth(315)
# Initizalize
self.renWin1.Render()
self.renderer1.Render()
if (interact == True):
self.iren1.Initialize()
self.iren1.Start()
return
def display(image, image_pos_pat, image_ori_pat):
global xMin, xMax, yMin, yMax, zMin, zMax, xSpacing, ySpacing, zSpacing, interactor, actions, reslice, interactorStyle
# The box widget observes the events invoked by the render window
# interactor. These events come from user interaction in the render
# window.
# boxWidget = vtk.vtkBoxWidget()
# boxWidget.SetInteractor(iren1)
# boxWidget.SetPlaceFactor(1)
# Initialize Image orienation
IO = matrix( [[0, 0,-1, 0],
[1, 0, 0, 0],
[0,-1, 0, 0],
[0, 0, 0, 1]])
# Assign the 6-Image orientation patient coordinates (from Dicomtags)
IO[0,0] = image_ori_pat[0]; IO[1,0] = image_ori_pat[1]; IO[2,0] = image_ori_pat[2];
IO[0,1] = image_ori_pat[3]; IO[1,1] = image_ori_pat[4]; IO[2,1] = image_ori_pat[5];
# obtain thrid column as the cross product of column 1 y 2
IO_col1 = [image_ori_pat[0], image_ori_pat[1], image_ori_pat[2]]
IO_col2 = [image_ori_pat[3], image_ori_pat[4], image_ori_pat[5]]
IO_col3 = cross(IO_col1, IO_col2)
# assign column 3
IO[0,2] = IO_col3[0]; IO[1,2] = IO_col3[1]; IO[2,2] = IO_col3[2];
IP = array([0, 0, 0, 1]) # Initialization Image Position
IP[0] = image_pos_pat[0]; IP[1] = image_pos_pat[1]; IP[2] = image_pos_pat[2];
IO[0,3] = image_pos_pat[0]; IO[1,3] = image_pos_pat[1]; IO[2,3] = image_pos_pat[2]
print "image_pos_pat :"
print image_pos_pat
print "image_ori_pat:"
print image_ori_pat
origin = IP*IO.I
print "Volume Origin:"
print origin[0,0], origin[0,1], origin[0,2]
# Create matrix 4x4
DICOM_mat = vtk.vtkMatrix4x4();
DICOM_mat.SetElement(0, 0, IO[0,0])
DICOM_mat.SetElement(0, 1, IO[0,1])
DICOM_mat.SetElement(0, 2, IO[0,2])
DICOM_mat.SetElement(0, 3, IO[0,3])
DICOM_mat.SetElement(1, 0, IO[1,0])
DICOM_mat.SetElement(1, 1, IO[1,1])
DICOM_mat.SetElement(1, 2, IO[1,2])
DICOM_mat.SetElement(1, 3, IO[1,3])
DICOM_mat.SetElement(2, 0, IO[2,0])
DICOM_mat.SetElement(2, 1, IO[2,1])
DICOM_mat.SetElement(2, 2, IO[2,2])
DICOM_mat.SetElement(2, 3, IO[2,3])
DICOM_mat.SetElement(3, 0, IO[3,0])
DICOM_mat.SetElement(3, 1, IO[3,1])
DICOM_mat.SetElement(3, 2, IO[3,2])
DICOM_mat.SetElement(3, 3, IO[3,3])
#DICOM_mat.Invert()
# Set up the axes
transform = vtk.vtkTransform()
transform.Concatenate(DICOM_mat)
transform.Update()
# Set up the cube (set up the translation back to zero
DICOM_mat_cube = vtk.vtkMatrix4x4();
DICOM_mat_cube.DeepCopy(DICOM_mat)
DICOM_mat_cube.SetElement(0, 3, 0)
DICOM_mat_cube.SetElement(1, 3, 0)
DICOM_mat_cube.SetElement(2, 3, 0)
transform_cube = vtk.vtkTransform()
transform_cube.Concatenate(DICOM_mat_cube)
transform_cube.Update()
##########################
# Calculate the center of the volume
(xMin, xMax, yMin, yMax, zMin, zMax) = image.GetWholeExtent()
(xSpacing, ySpacing, zSpacing) = image.GetSpacing()
(x0, y0, z0) = image.GetOrigin()
center = [x0 + xSpacing * 0.5 * (xMin + xMax),
y0 + ySpacing * 0.5 * (yMin + yMax),
z0 + zSpacing * 0.5 * (zMin + zMax)]
# Matrices for axial, coronal, sagittal, oblique view orientations
axial = vtk.vtkMatrix4x4()
axial.DeepCopy((1, 0, 0, center[0],
0, 1, 0, center[1],
0, 0, 1, center[2],
0, 0, 0, 1))
coronal = vtk.vtkMatrix4x4()
coronal.DeepCopy((1, 0, 0, center[0],
0, 0, 1, center[1],
0,-1, 0, center[2],
0, 0, 0, 1))
sagittal = vtk.vtkMatrix4x4()
sagittal.DeepCopy((0, 0,-1, center[0],
1, 0, 0, center[1],
0,-1, 0, center[2],
0, 0, 0, 1))
oblique = vtk.vtkMatrix4x4()
oblique.DeepCopy((1, 0, 0, center[0],
0, 0.866025, -0.5, center[1],
0, 0.5, 0.866025, center[2],
0, 0, 0, 1))
# Extract a slice in the desired orientation
reslice = vtk.vtkImageReslice()
reslice.SetInput(image)
reslice.SetOutputDimensionality(2)
reslice.SetResliceAxes(sagittal)
reslice.SetInterpolationModeToLinear()
# Create a greyscale lookup table
table = vtk.vtkLookupTable()
table.SetRange(0, 2000) # image intensity range
table.SetValueRange(0.0, 1.0) # from black to white
table.SetSaturationRange(0.0, 0.0) # no color saturation
table.SetRampToLinear()
table.Build()
# Map the image through the lookup table
color = vtk.vtkImageMapToColors()
color.SetLookupTable(table)
color.SetInputConnection(reslice.GetOutputPort())
# Display the image
actor = vtk.vtkImageActor()
actor.GetMapper().SetInputConnection(color.GetOutputPort())
renderer1 = vtk.vtkRenderer()
renderer1.AddActor(actor)
################
# set up cube actor with Orientation(R-L, A-P, S-O) using transform_cube
# Set up to ALS (+X=A, +Y=S, +Z=L) source:
cube = vtk.vtkAnnotatedCubeActor()
cube.SetXPlusFaceText( "S" );
cube.SetXMinusFaceText( "I" );
cube.SetYPlusFaceText( "L" );
cube.SetYMinusFaceText( "R" );
cube.SetZPlusFaceText( "A" );
cube.SetZMinusFaceText( "P" );
cube.SetFaceTextScale( 0.5 );
cube.GetAssembly().SetUserTransform( transform_cube );
# Set UP the axes
axes2 = vtk.vtkAxesActor()
axes2.SetShaftTypeToCylinder();
#axes2.SetUserTransform( transform_cube );
axes2.SetTotalLength( 1.5, 1.5, 1.5 );
axes2.SetCylinderRadius( 0.500 * axes2.GetCylinderRadius() );
axes2.SetConeRadius( 1.025 * axes2.GetConeRadius() );
axes2.SetSphereRadius( 1.500 * axes2.GetSphereRadius() );
tprop2 = axes2.GetXAxisCaptionActor2D()
tprop2.GetCaptionTextProperty();
assembly = vtk.vtkPropAssembly();
assembly.AddPart( axes2 );
assembly.AddPart( cube );
widget = vtk.vtkOrientationMarkerWidget();
widget.SetOutlineColor( 0.9300, 0.5700, 0.1300 );
widget.SetOrientationMarker( assembly );
widget.SetInteractor( iren1 );
widget.SetViewport( 0.0, 0.0, 0.4, 0.4 );
widget.SetEnabled( 1 );
widget.InteractiveOff();
# Set Up Camera view
renderer1.SetBackground(0.0, 0.0, 0.0)
camera = renderer1.GetActiveCamera()
# bounds and initialize camera
b = image.GetBounds()
renderer1.ResetCamera(b)
renderer1.ResetCameraClippingRange()
camera.SetViewUp(0.0,-1.0,0.0)
camera.Azimuth(315)
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(1, 1, 1)
tprop.ShadowOff()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axes = vtk.vtkCubeAxesActor2D()
axes.SetInput(image)
axes.SetCamera(renderer1.GetActiveCamera())
axes.SetLabelFormat("%6.4g")
axes.SetFlyModeToOuterEdges()
axes.SetFontFactor(1.2)
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
renderer1.AddViewProp(axes)
############
# Place the interactor initially. The input to a 3D widget is used to
# initially position and scale the widget. The "EndInteractionEvent" is
# observed which invokes the SelectPolygons callback.
# boxWidget.SetInput(image)
# boxWidget.PlaceWidget()
# boxWidget.AddObserver("InteractionEvent", SelectPolygons)
# boxWidget.On()
# Initizalize
# Set up the interaction
interactorStyle = vtk.vtkInteractorStyleImage()
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetInteractorStyle(interactorStyle)
renWin1.SetInteractor(interactor)
renWin1.Render()
renderer1.Render()
interactor.Start()
renderer1.RemoveViewProp(axes)
return transform_cube, zImagePlaneWidget.GetSliceIndex()
def visualize(self, images, image_pos_pat, image_ori_pat, sub, postS, interact):
'''Display and render volumes, reference frames, actors and widgets'''
if(sub):
#subtract volumes based on indicated postS
# define image based on subtraction of postS -preS
image = self.subImage(images, postS)
else:
image = images[postS]
# Proceed to build reference frame for display objects based on DICOM coords
[self.transformed_image, transform_cube] = self.dicomTransform(image, image_pos_pat, image_ori_pat)
# get info from image before visualization
self.transformed_image.UpdateInformation()
self.dims = self.transformed_image.GetDimensions()
print "Image Dimensions"
print self.dims
self.T1spacing = self.transformed_image.GetSpacing()
print "Image Spacing"
print self.T1spacing
self.T1origin = self.transformed_image.GetOrigin()
print "Image Origin"
print self.T1origin
self.T1extent = list(self.transformed_image.GetWholeExtent())
print "Image Extent"
print self.T1extent
# Set up ortogonal planes
self.xImagePlaneWidget.SetInput( self.transformed_image )
self.xImagePlaneWidget.SetPlaneOrientationToXAxes()
self.xImagePlaneWidget.SetSliceIndex(0)
self.yImagePlaneWidget.SetInput( self.transformed_image )
self.yImagePlaneWidget.SetPlaneOrientationToYAxes()
self.yImagePlaneWidget.SetSliceIndex(0)
self.zImagePlaneWidget.SetInput( self.transformed_image )
self.zImagePlaneWidget.SetPlaneOrientationToZAxes()
self.zImagePlaneWidget.SetSliceIndex(0)
self.xImagePlaneWidget.On()
self.yImagePlaneWidget.On()
self.zImagePlaneWidget.On()
# set up cube actor with Orientation(A-P, S-I, L-R) using transform_cube
# Set up to ALS (+X=A, +Y=S, +Z=L) source:
cube = vtk.vtkAnnotatedCubeActor()
cube.SetXPlusFaceText( "L" );
cube.SetXMinusFaceText( "R" );
cube.SetYPlusFaceText( "A" );
cube.SetYMinusFaceText( "P" );
cube.SetZPlusFaceText( "S" );
cube.SetZMinusFaceText( "I" );
cube.SetFaceTextScale( 0.5 );
cube.GetAssembly().SetUserTransform( transform_cube );
# Set UP the axes
axes2 = vtk.vtkAxesActor()
axes2.SetShaftTypeToCylinder();
#axes2.SetUserTransform( transform_cube );
axes2.SetTotalLength( 1.5, 1.5, 1.5 );
axes2.SetCylinderRadius( 0.500 * axes2.GetCylinderRadius() );
axes2.SetConeRadius( 1.025 * axes2.GetConeRadius() );
axes2.SetSphereRadius( 1.500 * axes2.GetSphereRadius() );
tprop2 = axes2.GetXAxisCaptionActor2D()
tprop2.GetCaptionTextProperty();
assembly = vtk.vtkPropAssembly();
assembly.AddPart( axes2 );
assembly.AddPart( cube );
widget = vtk.vtkOrientationMarkerWidget();
widget.SetOutlineColor( 0.9300, 0.5700, 0.1300 );
widget.SetOrientationMarker( assembly );
widget.SetInteractor( self.iren1 );
widget.SetViewport( 0.0, 0.0, 0.4, 0.4 );
widget.SetEnabled( 1 );
widget.InteractiveOff();
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(1, 1, 1)
tprop.ShadowOff()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axes = vtk.vtkCubeAxesActor2D()
axes.SetInput(self.transformed_image)
axes.SetCamera(self.renderer1.GetActiveCamera())
axes.SetLabelFormat("%6.4g")
axes.SetFlyModeToOuterEdges()
axes.SetFontFactor(1.2)
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
self.renderer1.AddViewProp(axes)
############
# bounds and initialize camera
bounds = self.transformed_image.GetBounds()
self.renderer1.ResetCamera(bounds)
self.renderer1.ResetCameraClippingRange()
self.camera.SetViewUp(0.0,-1.0,0.0)
self.camera.Azimuth(315)
# Initizalize
self.renWin1.Modified()
self.renWin1.Render()
self.renderer1.Render()
if(interact==True):
interactor = self.renWin1.GetInteractor()
interactor.Start()
return
def __init__(self, module_manager):
# call base constructor
ModuleBase.__init__(self, module_manager)
ColourDialogMixin.__init__(
self, module_manager.get_module_view_parent_window())
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)]
# then the window containing the renderwindows
self.threedFrame = None
# the renderers corresponding to the render windows
self._threedRenderer = None
self._outline_source = vtk.vtkOutlineSource()
om = vtk.vtkPolyDataMapper()
om.SetInputConnection(self._outline_source.GetOutputPort())
self._outline_actor = vtk.vtkActor()
self._outline_actor.SetMapper(om)
self._cube_axes_actor2d = vtk.vtkCubeAxesActor2D()
self._cube_axes_actor2d.SetFlyModeToOuterEdges()
#self._cube_axes_actor2d.SetFlyModeToClosestTriad()
# use box widget for VOI selection
self._voi_widget = vtk.vtkBoxWidget()
# we want to keep it aligned with the cubic volume, thanks
self._voi_widget.SetRotationEnabled(0)
self._voi_widget.AddObserver('InteractionEvent',
self.voiWidgetInteractionCallback)
self._voi_widget.AddObserver('EndInteractionEvent',
self.voiWidgetEndInteractionCallback)
self._voi_widget.NeedsPlacement = True
# also create the VTK construct for actually extracting VOI from data
#self._extractVOI = vtk.vtkExtractVOI()
self._currentVOI = 6 * [0]
# set the whole UI up!
self._create_window()
# our interactor styles (we could add joystick or something too)
self._cInteractorStyle = vtk.vtkInteractorStyleTrackballCamera()
# set the default
self.threedFrame.threedRWI.SetInteractorStyle(self._cInteractorStyle)
rwi = self.threedFrame.threedRWI
rwi.Unbind(wx.EVT_MOUSEWHEEL)
rwi.Bind(wx.EVT_MOUSEWHEEL, self._handler_mousewheel)
# initialise our sliceDirections, this will also setup the grid and
# bind all slice UI events
self.sliceDirections = sliceDirections(
self, self.controlFrame.sliceGrid)
self.selectedPoints = selectedPoints(
self, self.controlFrame.pointsGrid)
# we now have a wx.ListCtrl, let's abuse it
self._tdObjects = tdObjects(self,
self.controlFrame.objectsListGrid)
self._implicits = implicits(self,
self.controlFrame.implicitsGrid)
# setup orientation widget stuff
# NB NB NB: we switch interaction with this off later
# (InteractiveOff()), thus disabling direct translation and
# scaling. If we DON'T do this, interaction with software
# raycasters are greatly slowed down.
self._orientation_widget = vtk.vtkOrientationMarkerWidget()
self._annotated_cube_actor = aca = vtk.vtkAnnotatedCubeActor()
#aca.TextEdgesOff()
aca.GetXMinusFaceProperty().SetColor(1,0,0)
aca.GetXPlusFaceProperty().SetColor(1,0,0)
aca.GetYMinusFaceProperty().SetColor(0,1,0)
aca.GetYPlusFaceProperty().SetColor(0,1,0)
aca.GetZMinusFaceProperty().SetColor(0,0,1)
aca.GetZPlusFaceProperty().SetColor(0,0,1)
self._axes_actor = vtk.vtkAxesActor()
self._orientation_widget.SetInteractor(
self.threedFrame.threedRWI)
self._orientation_widget.SetOrientationMarker(
self._axes_actor)
self._orientation_widget.On()
# make sure interaction is off; when on, interaction with
# software raycasters is greatly slowed down!
self._orientation_widget.InteractiveOff()
def __init__(self, module_manager):
# call base constructor
ModuleBase.__init__(self, module_manager)
ColourDialogMixin.__init__(
self, module_manager.get_module_view_parent_window())
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)]
# then the window containing the renderwindows
self.threedFrame = None
# the renderers corresponding to the render windows
self._threedRenderer = None
self._outline_source = vtk.vtkOutlineSource()
om = vtk.vtkPolyDataMapper()
om.SetInputConnection(self._outline_source.GetOutputPort())
self._outline_actor = vtk.vtkActor()
self._outline_actor.SetMapper(om)
self._cube_axes_actor2d = vtk.vtkCubeAxesActor2D()
self._cube_axes_actor2d.SetFlyModeToOuterEdges()
#self._cube_axes_actor2d.SetFlyModeToClosestTriad()
# use box widget for VOI selection
self._voi_widget = vtk.vtkBoxWidget()
# we want to keep it aligned with the cubic volume, thanks
self._voi_widget.SetRotationEnabled(0)
self._voi_widget.AddObserver('InteractionEvent',
self.voiWidgetInteractionCallback)
self._voi_widget.AddObserver('EndInteractionEvent',
self.voiWidgetEndInteractionCallback)
self._voi_widget.NeedsPlacement = True
# also create the VTK construct for actually extracting VOI from data
#self._extractVOI = vtk.vtkExtractVOI()
self._currentVOI = 6 * [0]
# set the whole UI up!
self._create_window()
# our interactor styles (we could add joystick or something too)
self._cInteractorStyle = vtk.vtkInteractorStyleTrackballCamera()
# set the default
self.threedFrame.threedRWI.SetInteractorStyle(self._cInteractorStyle)
rwi = self.threedFrame.threedRWI
rwi.Unbind(wx.EVT_MOUSEWHEEL)
rwi.Bind(wx.EVT_MOUSEWHEEL, self._handler_mousewheel)
# initialise our sliceDirections, this will also setup the grid and
# bind all slice UI events
self.sliceDirections = sliceDirections(self,
self.controlFrame.sliceGrid)
self.selectedPoints = selectedPoints(self,
self.controlFrame.pointsGrid)
# we now have a wx.ListCtrl, let's abuse it
self._tdObjects = tdObjects(self, self.controlFrame.objectsListGrid)
self._implicits = implicits(self, self.controlFrame.implicitsGrid)
# setup orientation widget stuff
# NB NB NB: we switch interaction with this off later
# (InteractiveOff()), thus disabling direct translation and
# scaling. If we DON'T do this, interaction with software
# raycasters are greatly slowed down.
self._orientation_widget = vtk.vtkOrientationMarkerWidget()
self._annotated_cube_actor = aca = vtk.vtkAnnotatedCubeActor()
#aca.TextEdgesOff()
aca.GetXMinusFaceProperty().SetColor(1, 0, 0)
aca.GetXPlusFaceProperty().SetColor(1, 0, 0)
aca.GetYMinusFaceProperty().SetColor(0, 1, 0)
aca.GetYPlusFaceProperty().SetColor(0, 1, 0)
aca.GetZMinusFaceProperty().SetColor(0, 0, 1)
aca.GetZPlusFaceProperty().SetColor(0, 0, 1)
self._axes_actor = vtk.vtkAxesActor()
self._orientation_widget.SetInteractor(self.threedFrame.threedRWI)
self._orientation_widget.SetOrientationMarker(self._axes_actor)
self._orientation_widget.On()
# make sure interaction is off; when on, interaction with
# software raycasters is greatly slowed down!
self._orientation_widget.InteractiveOff()
def addT2transvisualize(self, T2images, image_pos_pat, image_ori_pat, T2dims, T2spacing, interact):
'''Added to build second reference frame and display T2 overlayed into T1 reference frame'''
# Proceed to build reference frame for display objects based on DICOM coords
[transformed_T2image, transform_cube] = self.dicomTransform(T2images, image_pos_pat, image_ori_pat)
self.T2origin = list(transformed_T2image.GetOrigin())
print "T2 Extent"
self.T2extent = list(transformed_T2image.GetExtent())
print self.T2extent
alignR = int(raw_input('\nAlign right? Yes:1 or align with T1w: !=1 : '))
if alignR:
zf1 = self.T1spacing[2]*self.T1extent[5] + self.T1origin[2]
self.T2origin[2] = zf1 - T2spacing[2]*self.T2extent[5] # this is z-span
else:
self.T2origin[2] = self.T1origin[2]
# Change info origin
transformedInfo_T2image = vtk.vtkImageChangeInformation()
transformedInfo_T2image.SetInputData( transformed_T2image )
transformedInfo_T2image.SetOutputOrigin(self.T2origin)
transformedInfo_T2image.Update()
self.transformed_T2image = transformedInfo_T2image.GetOutput()
# Set up ortogonal planes
self.xImagePlaneWidget.SetInputData( self.transformed_T2image )
self.xImagePlaneWidget.SetSliceIndex(0)
self.yImagePlaneWidget.SetInputData( self.transformed_T2image )
self.yImagePlaneWidget.SetSliceIndex(0)
self.zImagePlaneWidget.SetInputData( self.transformed_T2image )
self.zImagePlaneWidget.SetSliceIndex(0)
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(0.5, 0.5, 0)
tprop.ShadowOff()
# Update the reneder window to receive new image !Important*****
self.renderer1.Modified()
self.renWin1.Modified()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axesT2 = vtk.vtkCubeAxesActor2D()
axesT2.SetInputData(self.transformed_T2image)
axesT2.SetCamera(self.renderer1.GetActiveCamera())
axesT2.SetLabelFormat("%6.4g")
axesT2.SetFlyModeToOuterEdges()
axesT2.SetFontFactor(1.2)
axesT2.SetAxisTitleTextProperty(tprop)
axesT2.SetAxisLabelTextProperty(tprop)
self.renderer1.AddViewProp(axesT2)
### Update T2Images
t_T2images = vtk.vtkImageChangeInformation()
t_T2images.SetInputData( T2images )
t_T2images.SetOutputOrigin(self.T2origin)
t_T2images.Update()
############
if(interact==True):
interactor = self.renWin1.GetInteractor()
interactor.Start()
return
class TestGL2PSExporter(Testing.vtkTest):
# Create these as class attributes so that they are only created
# once and not for every test.
cs = vtk.vtkConeSource()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(cs.GetOutputPort())
act = vtk.vtkActor()
act.SetMapper(mapper)
act.GetProperty().SetColor(0.5, 0.5, 1.0)
axes = vtk.vtkCubeAxesActor2D()
axes.SetInput(cs.GetOutput())
axes.SetFontFactor(2.0)
axes.SetCornerOffset(0.0)
axes.GetProperty().SetColor(0,0,0)
txt = vtk.vtkTextActor()
txt.SetDisplayPosition(45, 150)
txt.SetInput("This is test\nmultiline\ninput\ndata.")
tprop = txt.GetTextProperty()
tprop.SetFontSize(18)
tprop.SetFontFamilyToArial()
tprop.SetJustificationToCentered()
tprop.BoldOn()
tprop.ItalicOn()
tprop.ShadowOn()
tprop.SetColor(0, 0, 1)
ren = vtk.vtkRenderer()
ren.AddActor(act)
ren.AddActor(txt)
axes.SetCamera(ren.GetActiveCamera())
ren.AddActor(axes)
ren.SetBackground(0.8, 0.8, 0.8)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
cam = ren.GetActiveCamera()
ren.ResetCamera()
cam.Azimuth(30)
iren.Initialize()
iren.Render()
def _cleanup(self, files):
"""Remove the list of given files."""
for f in files:
if os.path.isfile(f):
os.remove(f)
def testVectorEPS(self):
"""Test vector EPS output."""
# Get a temporary file name. Set the extension to empty since
# the exporter appends a suitable extension.
tmp_eps = tempfile.mktemp('')
# Write an EPS file.
exp = vtk.vtkGL2PSExporter()
exp.SetRenderWindow(self.renWin)
exp.SetFilePrefix(tmp_eps)
# Turn off compression so PIL can read file.
exp.CompressOff()
exp.SetSortToBSP()
exp.DrawBackgroundOn()
exp.Write()
# Now read the EPS file using PIL.
tmp_eps += '.eps'
im = Image.open(tmp_eps)
# Get a temporary name for the PNG file.
tmp_png = tempfile.mktemp('.png')
im.save(tmp_png)
# Now read the saved image and compare it for the test.
png_r = vtk.vtkPNGReader()
png_r.SetFileName(tmp_png)
png_r.Update()
img = png_r.GetOutput()
# Cleanup. Do this first because if the test fails, an
# exception is raised and the temporary files won't be
# removed.
self._cleanup([tmp_eps, tmp_png])
img_file = "TestGL2PSExporter.png"
Testing.compareImageWithSavedImage(img,
Testing.getAbsImagePath(img_file))
# Interact if necessary.
Testing.interact()
def testRasterEPS(self):
"""Test EPS output when Write3DPropsAsRasterImage is on."""
# Get a temporary file name. Set the extension to empty since
# the exporter appends a suitable extension.
tmp_eps = tempfile.mktemp('')
# Write an EPS file.
exp = vtk.vtkGL2PSExporter()
exp.SetRenderWindow(self.renWin)
exp.SetFilePrefix(tmp_eps)
# Turn off compression so PIL can read file.
exp.CompressOff()
exp.SetSortToOff()
exp.DrawBackgroundOn()
exp.Write3DPropsAsRasterImageOn()
exp.Write()
# Now read the EPS file using PIL.
tmp_eps += '.eps'
im = Image.open(tmp_eps)
# Get a temporary name for the PNG file.
tmp_png = tempfile.mktemp('.png')
im.save(tmp_png)
# Now read the saved image and compare it for the test.
png_r = vtk.vtkPNGReader()
png_r.SetFileName(tmp_png)
png_r.Update()
img = png_r.GetOutput()
# Cleanup. Do this first because if the test fails, an
# exception is raised and the temporary files won't be
# removed.
self._cleanup([tmp_eps, tmp_png])
img_file = "TestGL2PSExporter.png"
Testing.compareImageWithSavedImage(img,
Testing.getAbsImagePath(img_file))
# Interact if necessary.
Testing.interact()
def visualize(self, images, image_pos_pat, image_ori_pat, sub, postS, interact=True):
'''Display and render volumes, reference frames, actors and widgets'''
if(sub):
#subtract volumes based on indicated postS
# define image based on subtraction of postS -preS
image = self.subImage(images, postS)
else:
image = images[postS]
# Proceed to build reference frame for display objects based on DICOM coords
[self.transformed_image, transform_cube] = self.dicomTransform(image, image_pos_pat, image_ori_pat)
# get info from image before visualization
self.dims = self.transformed_image.GetDimensions()
print "Image Dimensions"
print self.dims
self.T1spacing = self.transformed_image.GetSpacing()
print "Image Spacing"
print self.T1spacing
self.T1origin = self.transformed_image.GetOrigin()
print "Image Origin"
print self.T1origin
self.T1extent = list(self.transformed_image.GetExtent())
print "Image Extent"
print self.T1extent
# Set up ortogonal planes
self.xImagePlaneWidget.SetInputData( self.transformed_image )
self.xImagePlaneWidget.SetPlaneOrientationToXAxes()
self.xImagePlaneWidget.SetSliceIndex(0)
self.yImagePlaneWidget.SetInputData( self.transformed_image )
self.yImagePlaneWidget.SetPlaneOrientationToYAxes()
self.yImagePlaneWidget.SetSliceIndex(0)
self.zImagePlaneWidget.SetInputData( self.transformed_image )
self.zImagePlaneWidget.SetPlaneOrientationToZAxes()
self.zImagePlaneWidget.SetSliceIndex(0)
self.xImagePlaneWidget.On()
self.yImagePlaneWidget.On()
self.zImagePlaneWidget.On()
# set up cube actor with Orientation(A-P, S-I, L-R) using transform_cube
# Set up to ALS (+X=A, +Y=S, +Z=L) source:
cube = vtk.vtkAnnotatedCubeActor()
cube.SetXPlusFaceText( "L" );
cube.SetXMinusFaceText( "R" );
cube.SetYPlusFaceText( "A" );
cube.SetYMinusFaceText( "P" );
cube.SetZPlusFaceText( "S" );
cube.SetZMinusFaceText( "I" );
cube.SetFaceTextScale( 0.5 );
cube.GetAssembly().SetUserTransform( transform_cube );
# Set UP the axes
axes2 = vtk.vtkAxesActor()
axes2.SetShaftTypeToCylinder();
#axes2.SetUserTransform( transform_cube );
axes2.SetTotalLength( 1.5, 1.5, 1.5 );
axes2.SetCylinderRadius( 0.500 * axes2.GetCylinderRadius() );
axes2.SetConeRadius( 1.025 * axes2.GetConeRadius() );
axes2.SetSphereRadius( 1.500 * axes2.GetSphereRadius() );
tprop2 = axes2.GetXAxisCaptionActor2D()
tprop2.GetCaptionTextProperty();
assembly = vtk.vtkPropAssembly();
assembly.AddPart( axes2 );
assembly.AddPart( cube );
widget = vtk.vtkOrientationMarkerWidget();
widget.SetOutlineColor( 0.9300, 0.5700, 0.1300 );
widget.SetOrientationMarker( assembly );
widget.SetInteractor( self.iren1 );
widget.SetViewport( 0.0, 0.0, 0.4, 0.4 );
widget.SetEnabled( 1 );
widget.InteractiveOff();
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(1, 1, 1)
tprop.ShadowOff()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axes = vtk.vtkCubeAxesActor2D()
axes.SetInputData(self.transformed_image)
axes.SetCamera(self.renderer1.GetActiveCamera())
axes.SetLabelFormat("%6.4g")
axes.SetFlyModeToOuterEdges()
axes.SetFontFactor(1.2)
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
self.renderer1.AddViewProp(axes)
############
# bounds and initialize camera
bounds = self.transformed_image.GetBounds()
self.renderer1.ResetCamera(bounds)
self.renderer1.ResetCameraClippingRange()
self.camera.SetViewUp(0.0,-1.0,0.0)
self.camera.Azimuth(315)
# Initizalize
self.renWin1.Modified()
self.renWin1.Render()
self.renderer1.Render()
if(interact==True):
interactor = self.renWin1.GetInteractor()
interactor.Start()
return
def run(self):
doImports()
self.renWin = vtk.vtkRenderWindow()
self.ren = vtk.vtkRenderer()
self.renWin.AddRenderer(self.ren)
self.renWin.SetSize(600, 600)
self.ren.SetBackground(0.7, 0.7, 0.7)
self.ren.ResetCamera()
self.cam = self.ren.GetActiveCamera()
self.axes = vtk.vtkCubeAxesActor2D()
self.axes.SetCamera(self.ren.GetActiveCamera())
self.undefinedActor=vtk.vtkTextActor()
self.undefinedActor.GetPositionCoordinate().SetCoordinateSystemToNormalizedDisplay()
self.undefinedActor.GetPositionCoordinate().SetValue(0.05,0.2)
self.undefinedActor.GetTextProperty().SetColor(1.,0.,0.)
self.undefinedActor.SetInput("")
try:
self.readFile()
except Exception:
e = sys.exc_info()[1] # Needed because python 2.5 does not support 'as e'
warning("While reading",self.parser.getArgs()[0],"this happened:",e)
raise e
self.ren.ResetCamera()
self.root = tkinter.Tk()
self.root.withdraw()
# Create the toplevel window
self.top = tkinter.Toplevel(self.root)
self.top.title("blockMesh-Viewer")
self.top.protocol("WM_DELETE_WINDOW", self.quit)
# Create some frames
self.f1 = tkinter.Frame(self.top)
self.f2 = tkinter.Frame(self.top)
self.f1.pack(side="top", anchor="n", expand=1, fill="both")
self.f2.pack(side="bottom", anchor="s", expand="f", fill="x")
# Create the Tk render widget, and bind the events
self.rw = vtkTkRenderWindowInteractor(self.f1, width=400, height=400, rw=self.renWin)
self.rw.pack(expand="t", fill="both")
self.blockHigh=tkinter.IntVar()
self.blockHigh.set(-1)
self.oldBlock=-1
self.blockActor=None
self.blockTextActor=None
self.patchHigh=tkinter.IntVar()
self.patchHigh.set(-1)
self.oldPatch=-1
self.patchActor=None
self.patchTextActor=vtk.vtkTextActor()
self.patchTextActor.GetPositionCoordinate().SetCoordinateSystemToNormalizedDisplay()
self.patchTextActor.GetPositionCoordinate().SetValue(0.05,0.1)
self.patchTextActor.GetTextProperty().SetColor(0.,0.,0.)
self.patchTextActor.SetInput("Patch: <none>")
self.scroll=tkinter.Scale(self.f2,orient='horizontal',
from_=-1,to=len(self.blocks)-1,resolution=1,tickinterval=1,
label="Block (-1 is none)",
variable=self.blockHigh,command=self.colorBlock)
self.scroll.pack(side="top", expand="t", fill="x")
self.scroll2=tkinter.Scale(self.f2,orient='horizontal',
from_=-1,to=len(list(self.patches.keys()))-1,resolution=1,tickinterval=1,
label="Patch (-1 is none)",
variable=self.patchHigh,command=self.colorPatch)
self.scroll2.pack(side="top", expand="t", fill="x")
self.f3 = tkinter.Frame(self.f2)
self.f3.pack(side="bottom", anchor="s", expand="f", fill="x")
self.b1 = tkinter.Button(self.f3, text="Quit", command=self.quit)
self.b1.pack(side="left", expand="t", fill="x")
self.b2 = tkinter.Button(self.f3, text="Reread blockMeshDict", command=self.reread)
self.b2.pack(side="left", expand="t", fill="x")
self.root.update()
self.iren = self.renWin.GetInteractor()
self.istyle = vtk.vtkInteractorStyleSwitch()
self.iren.SetInteractorStyle(self.istyle)
self.istyle.SetCurrentStyleToTrackballCamera()
self.addProps()
self.iren.Initialize()
self.renWin.Render()
self.iren.Start()
self.root.mainloop()
def set_initial_display(self):
if self.renwininter is None:
self.renwininter = MEQ_QVTKRenderWindowInteractor(self.winsplitter)
self.renwininter.setWhatsThis(rendering_control_instructions)
self.renwin = self.renwininter.GetRenderWindow()
self.inter = self.renwin.GetInteractor()
self.winsplitter.insertWidget(0,self.renwininter)
self.winsplitter.addWidget(self.v_box_controls)
self.winsplitter.setSizes([500,100])
self.renwininter.show()
# Paul Kemper suggested the following:
camstyle = vtk.vtkInteractorStyleTrackballCamera()
self.renwininter.SetInteractorStyle(camstyle)
self.extents = self.image_array.GetDataExtent()
self.spacing = self.image_array.GetDataSpacing()
self.origin = self.image_array.GetDataOrigin()
# An outline is shown for context.
if self.warped_surface:
self.index_selector.initWarpContextmenu()
sx, sy, sz = self.image_array.GetDataSpacing()
xMin, xMax, yMin, yMax, zMin, zMax = self.image_array.GetDataExtent()
xMin = sx * xMin
xMax = sx * xMax
yMin = sy * yMin
yMax = sy * yMax
self.scale_factor = 0.5 * ((xMax-xMin) + (yMax-yMin)) / (self.data_max - self.data_min)
zMin = self.data_min * self.scale_factor
zMax = self.data_max * self.scale_factor
self.outline = vtk.vtkOutlineSource();
self.outline.SetBounds(xMin, xMax, yMin, yMax, zMin, zMax)
else:
self.index_selector.init3DContextmenu()
self.outline = vtk.vtkOutlineFilter()
self.outline.SetInput(self.image_array.GetOutput())
outlineMapper = vtk.vtkPolyDataMapper();
outlineMapper.SetInput(self.outline.GetOutput() );
outlineActor = vtk.vtkActor();
outlineActor.SetMapper(outlineMapper);
# create blue to red color table
self.lut = vtk.vtkLookupTable()
self.lut.SetHueRange(0.6667, 0.0)
self.lut.SetNumberOfColors(256)
self.lut.Build()
# here is where the 2-D image gets warped
if self.warped_surface:
geometry = vtk.vtkImageDataGeometryFilter()
geometry.SetInput(self.image_array.GetOutput())
self.warp = vtk.vtkWarpScalar()
self.warp.SetInput(geometry.GetOutput())
self.warp.SetScaleFactor(self.scale_factor)
self.mapper = vtk.vtkPolyDataMapper();
self.mapper.SetInput(self.warp.GetPolyDataOutput())
self.mapper.SetScalarRange(self.data_min,self.data_max)
self.mapper.SetLookupTable(self.lut)
self.mapper.ImmediateModeRenderingOff()
warp_actor = vtk.vtkActor()
# warp_actor.SetScale(2,1,1)
warp_actor.SetMapper(self.mapper)
min_range = 0.5 * self.scale_factor
max_range = 2.0 * self.scale_factor
self.index_selector.set_emit(False)
self.index_selector.setMaxValue(max_range,False)
self.index_selector.setMinValue(min_range)
self.index_selector.setTickInterval( (max_range - min_range) / 10 )
self.index_selector.setRange(max_range, False)
self.index_selector.setValue(self.scale_factor)
self.index_selector.setLabel('display gain')
self.index_selector.hideNDControllerOption()
self.index_selector.reset_scale_toggle()
self.index_selector.set_emit(True)
else:
# set up ImagePlaneWidgets ...
# The shared picker enables us to use 3 planes at one time
# and gets the picking order right
picker = vtk.vtkCellPicker()
picker.SetTolerance(0.005)
# get locations for initial slices
xMin, xMax, yMin, yMax, zMin, zMax = self.extents
x_index = (xMax-xMin) / 2
y_index = (yMax-yMin) / 2
z_index = (zMax-zMin) / 2
# The 3 image plane widgets are used to probe the dataset.
self.planeWidgetX = vtk.vtkImagePlaneWidget()
self.planeWidgetX.DisplayTextOn()
self.planeWidgetX.SetInput(self.image_array.GetOutput())
self.planeWidgetX.SetPlaneOrientationToXAxes()
self.planeWidgetX.SetSliceIndex(x_index)
self.planeWidgetX.SetPicker(picker)
self.planeWidgetX.SetKeyPressActivationValue("x")
self.planeWidgetX.SetLookupTable(self.lut)
self.planeWidgetX.TextureInterpolateOff()
self.planeWidgetX.SetResliceInterpolate(0)
self.planeWidgetY = vtk.vtkImagePlaneWidget()
self.planeWidgetY.DisplayTextOn()
self.planeWidgetY.SetInput(self.image_array.GetOutput())
self.planeWidgetY.SetPlaneOrientationToYAxes()
self.planeWidgetY.SetSliceIndex(y_index)
self.planeWidgetY.SetPicker(picker)
self.planeWidgetY.SetKeyPressActivationValue("y")
self.planeWidgetY.SetLookupTable(self.planeWidgetX.GetLookupTable())
self.planeWidgetY.TextureInterpolateOff()
self.planeWidgetY.SetResliceInterpolate(0)
self.planeWidgetZ = vtk.vtkImagePlaneWidget()
self.planeWidgetZ.DisplayTextOn()
self.planeWidgetZ.SetInput(self.image_array.GetOutput())
self.planeWidgetZ.SetPlaneOrientationToZAxes()
self.planeWidgetZ.SetSliceIndex(z_index)
self.planeWidgetZ.SetPicker(picker)
self.planeWidgetZ.SetKeyPressActivationValue("z")
self.planeWidgetZ.SetLookupTable(self.planeWidgetX.GetLookupTable())
self.planeWidgetZ.TextureInterpolateOff()
self.planeWidgetZ.SetResliceInterpolate(0)
self.current_widget = self.planeWidgetZ
self.mode_widget = self.planeWidgetZ
self.index_selector.set_emit(False)
self.index_selector.setMinValue(zMin)
self.index_selector.setMaxValue(zMax,False)
self.index_selector.setTickInterval( (zMax-zMin) / 10 )
self.index_selector.setRange(zMax, False)
self.index_selector.setValue(z_index)
self.index_selector.setLabel('Z axis')
self.index_selector.reset_scale_toggle()
self.index_selector.set_emit(True)
# create scalar bar for display of intensity range
self.scalar_bar = vtk.vtkScalarBarActor()
self.scalar_bar.SetLookupTable(self.lut)
self.scalar_bar.SetOrientationToVertical()
self.scalar_bar.SetWidth(0.1)
self.scalar_bar.SetHeight(0.8)
self.scalar_bar.SetTitle("Intensity")
self.scalar_bar.GetPositionCoordinate().SetCoordinateSystemToNormalizedViewport()
self.scalar_bar.GetPositionCoordinate().SetValue(0.01, 0.1)
# Create the RenderWindow and Renderer
self.ren = vtk.vtkRenderer()
self.renwin.AddRenderer(self.ren)
# Add the outline actor to the renderer, set the background color and size
if self.warped_surface:
self.ren.AddActor(warp_actor)
self.ren.AddActor(outlineActor)
self.ren.SetBackground(0.1, 0.1, 0.2)
self.ren.AddActor2D(self.scalar_bar)
# Create a text property for cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(1, 1, 1)
tprop.ShadowOn()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
self.axes = vtk.vtkCubeAxesActor2D()
if self.warped_surface:
if zMin < 0.0 and zMax > 0.0:
zLoc = 0.0
else:
zLoc = zMin
self.axes.SetBounds(xMin, xMax, yMin, yMax, zLoc, zLoc)
self.axes.SetZLabel(" ")
else:
self.axes.SetInput(self.image_array.GetOutput())
self.axes.SetZLabel("Z")
self.axes.SetCamera(self.ren.GetActiveCamera())
self.axes.SetLabelFormat("%6.4g")
self.axes.SetFlyModeToOuterEdges()
self.axes.SetFontFactor(0.8)
self.axes.SetAxisTitleTextProperty(tprop)
self.axes.SetAxisLabelTextProperty(tprop)
self.axes.SetXLabel("X")
self.axes.SetYLabel("Y")
self.ren.AddProp(self.axes)
# Set the interactor for the widgets
if not self.warped_surface:
self.planeWidgetX.SetInteractor(self.inter)
self.planeWidgetX.On()
self.planeWidgetY.SetInteractor(self.inter)
self.planeWidgetY.On()
self.planeWidgetZ.SetInteractor(self.inter)
self.planeWidgetZ.On()
self.initialize_camera()
def show_neurons(tree_dict,
label_nodes_dict={},
labels_dict={},
priorities_dict={},
pos_dict={},
rot_dict={},
nodecolor=ng.nodecolor_4cp,
background=(0, 0, 0),
lines=False,
relative=True,
stereo=False,
axes=True,
fullscreen=True):
"""
tree_dict: dict containing {cell_name: morphology tree}
label_nodes_dict: {cell_name: list of label nodes}
labels_dict: {cell_name: list of labels corresponding to label nodes}
priorities_dict: {cell_name: list of priorities of the labels}
axes: If true, show axis with scale bar info
"""
label_actors = {}
neuron_actors = {}
renderer = vtk.vtkRenderer()
renderer.SetBackground(*background)
for cell, neurotree in tree_dict.items():
label_nodes = label_nodes_dict.get(cell, [])
labels = labels_dict.get(cell, [])
priorities = priorities_dict.get(cell, [])
pos = pos_dict.get(cell, [0, 0, 0])
rot = rot_dict.get(cell, [])
neuron_actor, label_actor = neuron3d(neurotree,
label_nodes=label_nodes,
labels=labels,
priorities=priorities,
pos=pos,
rot=rot,
nodecolor=nodecolor,
lines=lines,
relative=relative)
neuron_actors[cell] = neuron_actor
label_actors[cell] = label_actor
renderer.AddActor(neuron_actor)
if label_actor is not None:
renderer.AddActor2D(label_actor)
if axes: # show axis with scale bar info
_ax = vtk.vtkCubeAxesActor2D()
_ax.SetLabelFormat('%3.0f')
_ax.SetNumberOfLabels(0)
# _ax.SetYAxisVisibility(False)
# _ax.SetZAxisVisibility(False)
_ax.SetBounds(0, 200, 0, 200, 0, 200)
_ax.SetXLabel('X')
_ax.SetYLabel('Y')
_ax.SetZLabel('Z')
_ax.SetXOrigin(0)
_ax.SetYOrigin(0)
_ax.SetZOrigin(0)
color = (1.0 - background[0], 1.0 - background[1], 1.0 - background[2])
tprop = vtk.vtkTextProperty()
tprop.SetColor(color)
_ax.SetAxisLabelTextProperty(tprop)
_ax.GetProperty().SetColor(*color)
# _ax.SetFlyModeToClosestTriad()
_ax.SetCamera(renderer.GetActiveCamera())
renderer.AddActor(_ax)
renderer.ResetCamera()
win = vtk.vtkRenderWindow()
win.AddRenderer(renderer)
if fullscreen:
win.FullScreenOn()
if stereo:
win.GetStereoCapableWindow()
win.StereoCapableWindowOn()
win.SetStereoRender(1)
win.SetStereoTypeToCrystalEyes()
win.SetFullScreen(1)
#win.SetStereoTypeToRedBlue()
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(win)
win.Render()
interactor.Initialize()
interactor.Start()
def set_initial_display(self):
if self.renwininter is None:
self.renwininter = MEQ_QVTKRenderWindowInteractor(self.winsplitter)
self.renwininter.setWhatsThis(rendering_control_instructions)
self.renwin = self.renwininter.GetRenderWindow()
self.inter = self.renwin.GetInteractor()
self.winsplitter.insertWidget(0, self.renwininter)
self.winsplitter.addWidget(self.v_box_controls)
self.winsplitter.setSizes([500, 100])
self.renwininter.show()
# Paul Kemper suggested the following:
camstyle = vtk.vtkInteractorStyleTrackballCamera()
self.renwininter.SetInteractorStyle(camstyle)
self.extents = self.image_array.GetDataExtent()
self.spacing = self.image_array.GetDataSpacing()
self.origin = self.image_array.GetDataOrigin()
# An outline is shown for context.
if self.warped_surface:
self.index_selector.initWarpContextmenu()
sx, sy, sz = self.image_array.GetDataSpacing()
xMin, xMax, yMin, yMax, zMin, zMax = self.image_array.GetDataExtent(
)
xMin = sx * xMin
xMax = sx * xMax
yMin = sy * yMin
yMax = sy * yMax
self.scale_factor = 0.5 * (
(xMax - xMin) +
(yMax - yMin)) / (self.data_max - self.data_min)
zMin = self.data_min * self.scale_factor
zMax = self.data_max * self.scale_factor
self.outline = vtk.vtkOutlineSource()
self.outline.SetBounds(xMin, xMax, yMin, yMax, zMin, zMax)
else:
self.index_selector.init3DContextmenu()
self.outline = vtk.vtkOutlineFilter()
self.outline.SetInput(self.image_array.GetOutput())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInput(self.outline.GetOutput())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
# create blue to red color table
self.lut = vtk.vtkLookupTable()
self.lut.SetHueRange(0.6667, 0.0)
self.lut.SetNumberOfColors(256)
self.lut.Build()
# here is where the 2-D image gets warped
if self.warped_surface:
geometry = vtk.vtkImageDataGeometryFilter()
geometry.SetInput(self.image_array.GetOutput())
self.warp = vtk.vtkWarpScalar()
self.warp.SetInput(geometry.GetOutput())
self.warp.SetScaleFactor(self.scale_factor)
self.mapper = vtk.vtkPolyDataMapper()
self.mapper.SetInput(self.warp.GetPolyDataOutput())
self.mapper.SetScalarRange(self.data_min, self.data_max)
self.mapper.SetLookupTable(self.lut)
self.mapper.ImmediateModeRenderingOff()
warp_actor = vtk.vtkActor()
# warp_actor.SetScale(2,1,1)
warp_actor.SetMapper(self.mapper)
min_range = 0.5 * self.scale_factor
max_range = 2.0 * self.scale_factor
self.index_selector.set_emit(False)
self.index_selector.setMaxValue(max_range, False)
self.index_selector.setMinValue(min_range)
self.index_selector.setTickInterval((max_range - min_range) / 10)
self.index_selector.setRange(max_range, False)
self.index_selector.setValue(self.scale_factor)
self.index_selector.setLabel('display gain')
self.index_selector.hideNDControllerOption()
self.index_selector.reset_scale_toggle()
self.index_selector.set_emit(True)
else:
# set up ImagePlaneWidgets ...
# The shared picker enables us to use 3 planes at one time
# and gets the picking order right
picker = vtk.vtkCellPicker()
picker.SetTolerance(0.005)
# get locations for initial slices
xMin, xMax, yMin, yMax, zMin, zMax = self.extents
x_index = (xMax - xMin) / 2
y_index = (yMax - yMin) / 2
z_index = (zMax - zMin) / 2
# The 3 image plane widgets are used to probe the dataset.
self.planeWidgetX = vtk.vtkImagePlaneWidget()
self.planeWidgetX.DisplayTextOn()
self.planeWidgetX.SetInput(self.image_array.GetOutput())
self.planeWidgetX.SetPlaneOrientationToXAxes()
self.planeWidgetX.SetSliceIndex(x_index)
self.planeWidgetX.SetPicker(picker)
self.planeWidgetX.SetKeyPressActivationValue("x")
self.planeWidgetX.SetLookupTable(self.lut)
self.planeWidgetX.TextureInterpolateOff()
self.planeWidgetX.SetResliceInterpolate(0)
self.planeWidgetY = vtk.vtkImagePlaneWidget()
self.planeWidgetY.DisplayTextOn()
self.planeWidgetY.SetInput(self.image_array.GetOutput())
self.planeWidgetY.SetPlaneOrientationToYAxes()
self.planeWidgetY.SetSliceIndex(y_index)
self.planeWidgetY.SetPicker(picker)
self.planeWidgetY.SetKeyPressActivationValue("y")
self.planeWidgetY.SetLookupTable(
self.planeWidgetX.GetLookupTable())
self.planeWidgetY.TextureInterpolateOff()
self.planeWidgetY.SetResliceInterpolate(0)
self.planeWidgetZ = vtk.vtkImagePlaneWidget()
self.planeWidgetZ.DisplayTextOn()
self.planeWidgetZ.SetInput(self.image_array.GetOutput())
self.planeWidgetZ.SetPlaneOrientationToZAxes()
self.planeWidgetZ.SetSliceIndex(z_index)
self.planeWidgetZ.SetPicker(picker)
self.planeWidgetZ.SetKeyPressActivationValue("z")
self.planeWidgetZ.SetLookupTable(
self.planeWidgetX.GetLookupTable())
self.planeWidgetZ.TextureInterpolateOff()
self.planeWidgetZ.SetResliceInterpolate(0)
self.current_widget = self.planeWidgetZ
self.mode_widget = self.planeWidgetZ
self.index_selector.set_emit(False)
self.index_selector.setMinValue(zMin)
self.index_selector.setMaxValue(zMax, False)
self.index_selector.setTickInterval((zMax - zMin) / 10)
self.index_selector.setRange(zMax, False)
self.index_selector.setValue(z_index)
self.index_selector.setLabel('Z axis')
self.index_selector.reset_scale_toggle()
self.index_selector.set_emit(True)
# create scalar bar for display of intensity range
self.scalar_bar = vtk.vtkScalarBarActor()
self.scalar_bar.SetLookupTable(self.lut)
self.scalar_bar.SetOrientationToVertical()
self.scalar_bar.SetWidth(0.1)
self.scalar_bar.SetHeight(0.8)
self.scalar_bar.SetTitle("Intensity")
self.scalar_bar.GetPositionCoordinate(
).SetCoordinateSystemToNormalizedViewport()
self.scalar_bar.GetPositionCoordinate().SetValue(0.01, 0.1)
# Create the RenderWindow and Renderer
self.ren = vtk.vtkRenderer()
self.renwin.AddRenderer(self.ren)
# Add the outline actor to the renderer, set the background color and size
if self.warped_surface:
self.ren.AddActor(warp_actor)
self.ren.AddActor(outlineActor)
self.ren.SetBackground(0.1, 0.1, 0.2)
self.ren.AddActor2D(self.scalar_bar)
# Create a text property for cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(1, 1, 1)
tprop.ShadowOn()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
self.axes = vtk.vtkCubeAxesActor2D()
if self.warped_surface:
if zMin < 0.0 and zMax > 0.0:
zLoc = 0.0
else:
zLoc = zMin
self.axes.SetBounds(xMin, xMax, yMin, yMax, zLoc, zLoc)
self.axes.SetZLabel(" ")
else:
self.axes.SetInput(self.image_array.GetOutput())
self.axes.SetZLabel("Z")
self.axes.SetCamera(self.ren.GetActiveCamera())
self.axes.SetLabelFormat("%6.4g")
self.axes.SetFlyModeToOuterEdges()
self.axes.SetFontFactor(0.8)
self.axes.SetAxisTitleTextProperty(tprop)
self.axes.SetAxisLabelTextProperty(tprop)
self.axes.SetXLabel("X")
self.axes.SetYLabel("Y")
self.ren.AddProp(self.axes)
# Set the interactor for the widgets
if not self.warped_surface:
self.planeWidgetX.SetInteractor(self.inter)
self.planeWidgetX.On()
self.planeWidgetY.SetInteractor(self.inter)
self.planeWidgetY.On()
self.planeWidgetZ.SetInteractor(self.inter)
self.planeWidgetZ.On()
self.initialize_camera()
def initializeVTK(self):
"""
Code to initialize VTK portions of this widget
"""
self.renWin = self.wxrenwin.GetRenderWindow()
ren = self.renderer = self.wxrenwin.getRenderer()
ren.SetBackground(0, 0, 0)
self.wxrenwin.Render()
self.iren = iren = self.renWin.GetInteractor()
self.iren.SetSize(self.renWin.GetSize())
self.dataExtensionX = 50
self.dataExtensionY = 50
self.dataExtensionZ = 50
self.data = None
self.interactionCallback = None
self.spline = spline = vtk.vtkSplineWidget()
self.spline.GetLineProperty().SetColor(1, 0, 0)
self.spline.GetHandleProperty().SetColor(0, 1, 0)
self.spline.SetResolution(10000)
self.spline.SetInteractor(self.iren)
self.style = self.iren.GetInteractorStyle()
self.spline.AddObserver("EndInteractionEvent", self.endInteraction)
self.spline.AddObserver("InteractionEvent", self.endInteraction)
self.style.AddObserver("EndInteractionEvent", self.endInteraction)
self.style.AddObserver("InteractionEvent", self.endInteraction)
self.iren.AddObserver("EndInteractionEvent", self.endInteraction)
self.iren.AddObserver("InteractionEvent", self.endInteraction)
self.spline.On()
self.spline.SetEnabled(1)
self.style.SetEnabled(1)
self.outline = vtk.vtkOutlineFilter ()
self.outlinemapper = vtk.vtkPolyDataMapper ()
self.outlineactor = vtk.vtkActor ()
self.axes = vtk.vtkCubeAxesActor2D ()
self.initCamera()
self.arrow = vtk.vtkArrowSource()
self.arrowTransform = vtk.vtkTransform()
self.arrowTransform.RotateX(90.0)
self.arrowTransform.Scale(80.0, 200.0, 200.0)
self.transformFilter = vtk.vtkTransformFilter()
self.transformFilter.SetTransform(self.arrowTransform)
self.transformFilter.SetInput(self.arrow.GetOutput())
self.arrowMapper = vtk.vtkPolyDataMapper()
self.arrowMapper.SetInput(self.transformFilter.GetOutput())
self.arrowActor = vtk.vtkActor()
self.arrowActor.GetProperty().SetColor((0, 0, 1))
self.arrowActor.SetMapper(self.arrowMapper)
self.renderer.AddActor(self.arrowActor)
self.arrowActor.SetVisibility(0)
self.wxrenwin.Render()
vprop.ShadeOn()
vprop.SetAmbient(0.1)
vprop.SetDiffuse(0.7)
vprop.SetSpecular(0.4)
vprop.SetSpecularPower(60) # 10
volume = vtkVolume()
volume.SetProperty(vprop)
volume.SetMapper(splatmapper)
ren = vtkRenderer()
ren.SetBackground(0.5, 0.5, 0.5)
ren.AddVolume(volume)
#ren.GetActiveCamera().ParallelProjectionOn()
cubeAxesActor2d = vtk.vtkCubeAxesActor2D()
cubeAxesActor2d.SetFlyModeToOuterEdges()
ren.AddActor(cubeAxesActor2d)
cubeAxesActor2d.VisibilityOff() # turn on here!
v16.Update()
cubeAxesActor2d.SetBounds(v16.GetOutput().GetBounds())
cubeAxesActor2d.SetCamera(ren.GetActiveCamera())
renwin = vtkRenderWindow()
renwin.SetSize(512, 512)
renwin.AddRenderer(ren)
rwi = vtkRenderWindowInteractor()
rwi.SetRenderWindow(renwin)
rwi.AddObserver('CharEvent', ce_cb)
ren.AddViewProp(foheActor)
ren.AddViewProp(outlineActor)
ren2.AddViewProp(foheActor)
ren2.AddViewProp(outlineActor)
ren.SetBackground(0.1, 0.2, 0.4)
ren2.SetBackground(0.1, 0.2, 0.4)
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(1, 1, 1)
tprop.ShadowOn()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axes = vtk.vtkCubeAxesActor2D()
axes.SetInputConnection(normals.GetOutputPort())
axes.SetCamera(ren.GetActiveCamera())
axes.SetLabelFormat("%6.4g")
axes.SetFlyModeToOuterEdges()
axes.SetFontFactor(0.8)
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
ren.AddViewProp(axes)
# Create a vtkCubeAxesActor2D. Use the closest vertex to the camera to
# determine where to draw the axes. Add the actor to the renderer.
axes2 = vtk.vtkCubeAxesActor2D()
axes2.SetViewProp(foheActor)
axes2.SetCamera(ren2.GetActiveCamera())
axes2.SetLabelFormat("%6.4g")
def neuron3d(neuron_graph,
label_nodes=[],
labels=[],
priorities=[],
nodecolor=nodecolor_4cp,
background=(0, 0, 0),
lines=False,
stereo=False,
axes=True,
fullscreen=True):
"""axes: If true, show axis with scale bar info
"""
renderer, actor = nrngraph2vtk(neuron_graph,
label_nodes=label_nodes,
labels=labels,
priorities=priorities,
nodecolor=nodecolor,
background=background,
lines=lines)
if axes: # show axis with scale bar info
_ax = vtk.vtkCubeAxesActor2D()
_ax.SetLabelFormat('%3.0f')
_ax.SetNumberOfLabels(0)
_ax.SetYAxisVisibility(False)
_ax.SetZAxisVisibility(False)
_ax.SetBounds(0, 200, -600, -400, 0, 200)
_ax.SetXLabel('')
_ax.SetXOrigin(0)
_ax.SetYOrigin(-600)
_ax.SetZOrigin(0)
color = (1.0 - background[0], 1.0 - background[1], 1.0 - background[2])
tprop = vtk.vtkTextProperty()
tprop.SetColor(color)
_ax.SetAxisLabelTextProperty(tprop)
_ax.GetProperty().SetColor(*color)
_ax.SetFlyModeToClosestTriad()
_ax.SetCamera(renderer.GetActiveCamera())
renderer.AddActor(_ax)
renderer.ResetCamera()
win = vtk.vtkRenderWindow()
win.AddRenderer(renderer)
if fullscreen:
win.FullScreenOn()
if stereo:
win.GetStereoCapableWindow()
win.StereoCapableWindowOn()
win.SetStereoRender(1)
win.SetStereoTypeToCrystalEyes()
win.SetFullScreen(1)
#win.SetStereoTypeToRedBlue()
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(win)
win.Render()
# exporter = vtk.vtkX3DExporter()
# exporter.SetFileName('ggn.x3d')
# exporter.SetRenderWindow(win)
# exporter.Write()
interactor.Initialize()
interactor.Start()
ren.AddViewProp(foheActor)
ren.AddViewProp(outlineActor)
ren2.AddViewProp(foheActor)
ren2.AddViewProp(outlineActor)
ren.SetBackground(0.1, 0.2, 0.4)
ren2.SetBackground(0.1, 0.2, 0.4)
# Create a text property for both cube axes
tprop = vtk.vtkTextProperty()
tprop.SetColor(1, 1, 1)
tprop.ShadowOn()
# Create a vtkCubeAxesActor2D. Use the outer edges of the bounding box to
# draw the axes. Add the actor to the renderer.
axes = vtk.vtkCubeAxesActor2D()
axes.SetInputConnection(normals.GetOutputPort())
axes.SetCamera(ren.GetActiveCamera())
axes.SetLabelFormat("%6.4g")
axes.SetFlyModeToOuterEdges()
axes.SetFontFactor(0.8)
axes.SetAxisTitleTextProperty(tprop)
axes.SetAxisLabelTextProperty(tprop)
ren.AddViewProp(axes)
# Create a vtkCubeAxesActor2D. Use the closest vertex to the camera to
# determine where to draw the axes. Add the actor to the renderer.
axes2 = vtk.vtkCubeAxesActor2D()
axes2.SetViewProp(foheActor)
axes2.SetCamera(ren2.GetActiveCamera())
axes2.SetLabelFormat("%6.4g")
def initializeVTK(self):
"""
Code to initialize VTK portions of this widget
"""
self.renWin = self.wxrenwin.GetRenderWindow()
ren = self.renderer = self.wxrenwin.getRenderer()
ren.SetBackground(0, 0, 0)
self.wxrenwin.Render()
self.iren = iren = self.renWin.GetInteractor()
self.iren.SetSize(self.renWin.GetSize())
self.dataExtensionX = 50
self.dataExtensionY = 50
self.dataExtensionZ = 50
self.data = None
self.interactionCallback = None
self.spline = spline = vtk.vtkSplineWidget()
self.spline.GetLineProperty().SetColor(1, 0, 0)
self.spline.GetHandleProperty().SetColor(0, 1, 0)
self.spline.SetResolution(10000)
self.spline.SetInteractor(self.iren)
self.style = self.iren.GetInteractorStyle()
self.spline.AddObserver("EndInteractionEvent", self.endInteraction)
self.spline.AddObserver("InteractionEvent", self.endInteraction)
self.style.AddObserver("EndInteractionEvent", self.endInteraction)
self.style.AddObserver("InteractionEvent", self.endInteraction)
self.iren.AddObserver("EndInteractionEvent", self.endInteraction)
self.iren.AddObserver("InteractionEvent", self.endInteraction)
self.spline.On()
self.spline.SetEnabled(1)
self.style.SetEnabled(1)
self.outline = vtk.vtkOutlineFilter()
self.outlinemapper = vtk.vtkPolyDataMapper()
self.outlineactor = vtk.vtkActor()
self.axes = vtk.vtkCubeAxesActor2D()
self.initCamera()
self.arrow = vtk.vtkArrowSource()
self.arrowTransform = vtk.vtkTransform()
self.arrowTransform.RotateX(90.0)
self.arrowTransform.Scale(80.0, 200.0, 200.0)
self.transformFilter = vtk.vtkTransformFilter()
self.transformFilter.SetTransform(self.arrowTransform)
self.transformFilter.SetInput(self.arrow.GetOutput())
self.arrowMapper = vtk.vtkPolyDataMapper()
self.arrowMapper.SetInput(self.transformFilter.GetOutput())
self.arrowActor = vtk.vtkActor()
self.arrowActor.GetProperty().SetColor((0, 0, 1))
self.arrowActor.SetMapper(self.arrowMapper)
self.renderer.AddActor(self.arrowActor)
self.arrowActor.SetVisibility(0)
self.wxrenwin.Render()
vprop.ShadeOn()
vprop.SetAmbient(0.1)
vprop.SetDiffuse(0.7)
vprop.SetSpecular(0.4)
vprop.SetSpecularPower(60) # 10
volume = vtkVolume()
volume.SetProperty(vprop)
volume.SetMapper(splatmapper)
ren = vtkRenderer()
ren.SetBackground(0.5, 0.5, 0.5)
ren.AddVolume(volume)
#ren.GetActiveCamera().ParallelProjectionOn()
cubeAxesActor2d = vtk.vtkCubeAxesActor2D()
cubeAxesActor2d.SetFlyModeToOuterEdges()
ren.AddActor(cubeAxesActor2d)
cubeAxesActor2d.VisibilityOff() # turn on here!
v16.Update()
cubeAxesActor2d.SetBounds(v16.GetOutput().GetBounds())
cubeAxesActor2d.SetCamera(ren.GetActiveCamera())
renwin = vtkRenderWindow()
renwin.SetSize(512, 512)
renwin.AddRenderer(ren)
rwi = vtkRenderWindowInteractor()
rwi.SetRenderWindow(renwin)
rwi.AddObserver('CharEvent', ce_cb)
def _createIPW(self):
# we have to do this to get the correct log range
self._histogram.GetOutput().Update()
# this means we have newly valid input and should setup an ipw
self._ipw = vtk.vtkImagePlaneWidget()
self._histogram.GetOutput().Update()
self._ipw.SetInput(self._histogram.GetOutput())
self._ipw.SetInteractor(self._viewFrame.rwi)
# normal to the Z-axis
self._ipw.SetPlaneOrientation(2)
self._ipw.SetSliceIndex(0)
# setup specific lut
srange = self._histogram.GetOutput().GetScalarRange()
lut = vtk.vtkLookupTable()
lut.SetScaleToLog10()
lut.SetTableRange(srange)
lut.SetSaturationRange(1.0,1.0)
lut.SetValueRange(1.0, 1.0)
lut.SetHueRange(0.1, 1.0)
lut.Build()
self._ipw.SetUserControlledLookupTable(1)
self._ipw.SetLookupTable(lut)
self._ipw.SetDisplayText(1)
# if we use ContinousCursor, we get OffImage when zoomed
# on Linux (really irritating) but not on Windows. A VTK
# recompile might help, we'll see.
self._ipw.SetUseContinuousCursor(1)
# make sure the user can't twist the plane out of sight
self._ipw.SetMiddleButtonAction(0)
self._ipw.SetRightButtonAction(0)
# add an observer
self._ipw.AddObserver('StartInteractionEvent',
self._observerIPWInteraction)
self._ipw.AddObserver('InteractionEvent',
self._observerIPWInteraction)
self._ipw.AddObserver('EndInteractionEvent',
self._observerIPWInteraction)
self._ipw.On()
self._axes = vtk.vtkCubeAxesActor2D()
self._axes.SetFlyModeToOuterEdges()
# NOBODY will ever know why we have to switch off the Y axis when
# we actually want the Z-axis to go away.
self._axes.YAxisVisibilityOff()
self._axes.SetBounds(self._ipw.GetResliceOutput().GetBounds())
self._renderer.AddActor(self._axes)
self._axes.SetCamera(self._renderer.GetActiveCamera())
self._axes.PickableOff()
if 0:
# now add a scalarbar
self._scalarBarWidget = vtk.vtkScalarBarWidget()
self._scalarBarWidget.SetInteractor(self._viewFrame.rwi)
self._scalarBarWidget.GetScalarBarActor().SetTitle('Frequency')
self._scalarBarWidget.GetScalarBarActor().SetLookupTable(
lut)
# and activate
self._scalarBarWidget.On()
self._resetCamera()
self._render()