def initialize(self):
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Create default pipeline (Only once for all the session)
if not _WebCone.view:
# VTK specific code
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderWindowInteractor.GetInteractorStyle().SetCurrentStyleToTrackballCamera()
cone = vtk.vtkConeSource()
mapper = vtk.vtkPolyDataMapper()
actor = vtk.vtkActor()
mapper.SetInputConnection(cone.GetOutputPort())
actor.SetMapper(mapper)
renderer.AddActor(actor)
renderer.ResetCamera()
renderWindow.Render()
# VTK Web application specific
_WebCone.view = renderWindow
self.Application.GetObjectIdMap().SetActiveObject("VIEW", renderWindow)
def initialize(self):
print "initialize"
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
self.registerVtkWebProtocol(protocols.vtkWebFileBrowser('.', '.'))
# Create default pipeline (Only once for all the session)
# Update authentication key to use
self.updateSecret(_WebCone.authKey)
if not _WebCone.view:
# # VTK specific code
# renderer = vtk.vtkRenderer()
# renderWindow = vtk.vtkRenderWindow()
# renderWindow.AddRenderer(renderer)
# renderWindowInteractor = vtk.vtkRenderWindowInteractor()
# renderWindowInteractor.SetRenderWindow(renderWindow)
# renderWindowInteractor.GetInteractorStyle().SetCurrentStyleToTrackballCamera()
# cone = vtk.vtkConeSource()
# mapper = vtk.vtkPolyDataMapper()
# actor = vtk.vtkActor()
# mapper.SetInputConnection(cone.GetOutputPort())
# actor.SetMapper(mapper)
# renderer.AddActor(actor)
# renderer.ResetCamera()
# renderWindow.Render()
# VCS specific code
import vcs, cdms2, sys
x = vcs.init(bg=1)
f = cdms2.open(vcs.sample_data + "/geos5-sample.nc")
v = f["uwnd"]
dv3d = vcs.get3d_scalar()
dv3d.ToggleClipping = (40, 360, -28, 90)
dv3d.YSlider = (0.0, vcs.off)
dv3d.XSlider = (180.0, vcs.on)
dv3d.ZSlider = (0.0, vcs.on)
dv3d.ToggleVolumePlot = vcs.on
dv3d.ToggleSurfacePlot = vcs.on
dv3d.IsosurfaceValue = 31.0
dv3d.ScaleOpacity = [0.0, 1.0]
dv3d.BasemapOpacity = 0.5
dv3d.Camera = {
'Position': (-161, -171, 279),
'ViewUp': (.29, 0.67, 0.68),
'FocalPoint': (146.7, 8.5, -28.6)
}
dv3d.VerticalScaling = 5.0
dv3d.ScaleColormap = [-46.0, 48.0]
dv3d.ScaleTransferFunction = [12.0, 77.0]
x.plot(v, dv3d)
renderWindow = x.backend.renWin
# VTK Web application specific
_WebCone.view = renderWindow
self.getApplication().GetObjectIdMap().SetActiveObject(
"VIEW", renderWindow)
def initialize(self):
print "initialize"
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
self.registerVtkWebProtocol(protocols.vtkWebFileBrowser('.', '.'))
# Create default pipeline (Only once for all the session)
# Update authentication key to use
self.updateSecret(_WebCone.authKey)
if not _WebCone.view:
# # VTK specific code
# renderer = vtk.vtkRenderer()
# renderWindow = vtk.vtkRenderWindow()
# renderWindow.AddRenderer(renderer)
# renderWindowInteractor = vtk.vtkRenderWindowInteractor()
# renderWindowInteractor.SetRenderWindow(renderWindow)
# renderWindowInteractor.GetInteractorStyle().SetCurrentStyleToTrackballCamera()
# cone = vtk.vtkConeSource()
# mapper = vtk.vtkPolyDataMapper()
# actor = vtk.vtkActor()
# mapper.SetInputConnection(cone.GetOutputPort())
# actor.SetMapper(mapper)
# renderer.AddActor(actor)
# renderer.ResetCamera()
# renderWindow.Render()
# VCS specific code
import vcs, cdms2, sys
x = vcs.init(bg=1)
f = cdms2.open( vcs.sample_data+"/geos5-sample.nc" )
v = f["uwnd"]
dv3d = vcs.get3d_scalar()
dv3d.ToggleClipping = ( 40, 360, -28, 90 )
dv3d.YSlider = ( 0.0, vcs.off)
dv3d.XSlider = ( 180.0, vcs.on )
dv3d.ZSlider = ( 0.0, vcs.on )
dv3d.ToggleVolumePlot = vcs.on
dv3d.ToggleSurfacePlot = vcs.on
dv3d.IsosurfaceValue = 31.0
dv3d.ScaleOpacity = [0.0, 1.0]
dv3d.BasemapOpacity = 0.5
dv3d.Camera={ 'Position': (-161, -171, 279),
'ViewUp': (.29, 0.67, 0.68),
'FocalPoint': (146.7, 8.5, -28.6) }
dv3d.VerticalScaling = 5.0
dv3d.ScaleColormap = [ -46.0, 48.0 ]
dv3d.ScaleTransferFunction = [ 12.0, 77.0 ]
x.plot( v, dv3d )
renderWindow = x.backend.renWin
# VTK Web application specific
_WebCone.view = renderWindow
self.getApplication().GetObjectIdMap().SetActiveObject("VIEW", renderWindow)
def initialize(self):
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(_PhylogeneticTree.authKey)
# Create default pipeline (Only once for all the session)
if not _PhylogeneticTree.view:
# read in a tree
treeReader = vtk.vtkNewickTreeReader()
treeReader.SetFileName(_PhylogeneticTree.treeFilePath)
treeReader.Update()
reader = treeReader.GetOutput()
# read in a table
tableReader = vtk.vtkDelimitedTextReader()
tableReader.SetFileName(_PhylogeneticTree.csvFilePath)
tableReader.SetHaveHeaders(True)
tableReader.DetectNumericColumnsOn()
tableReader.Update()
table = tableReader.GetOutput()
# play with the heatmap vis
treeHeatmapItem = vtk.vtkTreeHeatmapItem()
treeHeatmapItem.SetTree(reader)
treeHeatmapItem.SetTable(table)
# setup the window
view = vtk.vtkContextView()
view.GetRenderer().SetBackground(1, 1, 1)
view.GetRenderWindow().SetSize(800, 600)
iren = view.GetInteractor()
iren.SetRenderWindow(view.GetRenderWindow())
transformItem = vtk.vtkContextTransform()
transformItem.AddItem(treeHeatmapItem)
transformItem.SetInteractive(1)
view.GetScene().AddItem(transformItem)
view.GetRenderWindow().SetMultiSamples(0)
iren.Initialize()
view.GetRenderWindow().Render()
# VTK Web application specific
_PhylogeneticTree.view = view.GetRenderWindow()
self.Application.GetObjectIdMap().SetActiveObject(
"VIEW", view.GetRenderWindow())
def initialize(self):
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(_PhylogeneticTree.authKey)
# Create default pipeline (Only once for all the session)
if not _PhylogeneticTree.view:
# read in a tree
treeReader = vtk.vtkNewickTreeReader()
treeReader.SetFileName(_PhylogeneticTree.treeFilePath)
treeReader.Update()
reader = treeReader.GetOutput()
# read in a table
tableReader = vtk.vtkDelimitedTextReader()
tableReader.SetFileName(_PhylogeneticTree.csvFilePath)
tableReader.SetHaveHeaders(True)
tableReader.DetectNumericColumnsOn()
tableReader.Update()
table = tableReader.GetOutput()
# play with the heatmap vis
treeHeatmapItem = vtk.vtkTreeHeatmapItem()
treeHeatmapItem.SetTree(reader);
treeHeatmapItem.SetTable(table);
# setup the window
view = vtk.vtkContextView()
view.GetRenderer().SetBackground(1,1,1)
view.GetRenderWindow().SetSize(800,600)
iren = view.GetInteractor()
iren.SetRenderWindow(view.GetRenderWindow())
transformItem = vtk.vtkContextTransform()
transformItem.AddItem(treeHeatmapItem)
transformItem.SetInteractive(1)
view.GetScene().AddItem(transformItem)
view.GetRenderWindow().SetMultiSamples(0)
iren.Initialize()
view.GetRenderWindow().Render()
# VTK Web application specific
_PhylogeneticTree.view = view.GetRenderWindow()
self.Application.GetObjectIdMap().SetActiveObject("VIEW", view.GetRenderWindow())
def initialize(self):
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(
protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(
protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(VTKWebApp.authKey)
if "initialize" in self.app.__dict__:
self.app.initialize(self, VTKWebApp, self.args)
def initialize(self):
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(
protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(
protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(VTKWebApp.authKey)
if "initialize" in self.app.__dict__:
self.app.initialize(self, VTKWebApp, self.args)
def initialize(self):
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(
protocols.vtkWebPublishImageDelivery(decode=False))
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(_WebCone.authKey)
# tell the C++ web app to use no encoding.
# ParaViewWebPublishImageDelivery must be set to decode=False to match.
self.getApplication().SetImageEncoding(0)
# Create default pipeline (Only once for all the session)
if not _WebCone.view:
# VTK specific code
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
# renderWindow.SetOffScreenRendering(1)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderWindowInteractor.GetInteractorStyle(
).SetCurrentStyleToTrackballCamera()
cone = vtk.vtkConeSource()
mapper = vtk.vtkPolyDataMapper()
actor = vtk.vtkActor()
mapper.SetInputConnection(cone.GetOutputPort())
actor.SetMapper(mapper)
renderer.AddActor(actor)
renderer.ResetCamera()
renderWindow.Render()
# VTK Web application specific
_WebCone.view = renderWindow
self.getApplication().GetObjectIdMap().SetActiveObject(
"VIEW", renderWindow)
def initialize(self):
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Create default pipeline (Only once for all the session)
if not _WebCone.view:
# VTK specific code
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderWindowInteractor.GetInteractorStyle(
).SetCurrentStyleToTrackballCamera()
cone = vtk.vtkConeSource()
mapper = vtk.vtkPolyDataMapper()
actor = vtk.vtkActor()
mapper.SetInputConnection(cone.GetOutputPort())
actor.SetMapper(mapper)
renderer.AddActor(actor)
renderer.ResetCamera()
renderWindow.Render()
# VTK Web application specific
_WebCone.view = renderWindow
self.Application.GetObjectIdMap().SetActiveObject(
"VIEW", renderWindow)
def initialize(self):
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(
protocols.vtkWebPublishImageDelivery(decode=False))
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(_WebCone.authKey)
# tell the C++ web app to use no encoding.
# ParaViewWebPublishImageDelivery must be set to decode=False to match.
self.getApplication().SetImageEncoding(0)
# Create default pipeline (Only once for all the session)
if not _WebCone.view:
# VTK specific code
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderWindowInteractor.GetInteractorStyle(
).SetCurrentStyleToTrackballCamera()
# cone = vtk.vtkConeSource()
# mapper = vtk.vtkPolyDataMapper()
# actor = vtk.vtkActor()
# mapper.SetInputConnection(cone.GetOutputPort())
# actor.SetMapper(mapper)
# renderer.AddActor(actor)
# load nrrd
reader = vtk.vtkNrrdReader()
reader.SetFileName('C:\\Users\\Mat\\Desktop\\tardiva3.0.nrrd')
reader.Update()
# The volume will be displayed by ray-cast alpha compositing.
# A ray-cast mapper is needed to do the ray-casting.
# volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
volume_mapper = vtk.vtkSmartVolumeMapper()
volume_mapper.SetInputConnection(reader.GetOutputPort())
volume_mapper.SetSampleDistance(0.5)
# The color transfer function maps voxel intensities to colors.
# It is modality-specific, and often anatomy-specific as well.
# The goal is to one color for flesh (between 500 and 1000)
# and another color for bone (1150 and over).
volume_color = vtk.vtkColorTransferFunction()
volume_color.AddRGBPoint(0, 0.2, 0.2, 0.7)
volume_color.AddRGBPoint(500, 240.0 / 255.0, 184.0 / 255.0,
160.0 / 255.0)
volume_color.AddRGBPoint(1000, 240.0 / 255.0, 184.0 / 255.0,
160.0 / 255.0)
volume_color.AddRGBPoint(1150, 1.0, 1.0, 240.0 / 255.0) # Ivory
# The opacity transfer function is used to control the opacity
# of different tissue types.
volume_scalar_opacity = vtk.vtkPiecewiseFunction()
volume_scalar_opacity.AddPoint(0, 0.00)
volume_scalar_opacity.AddPoint(500, 0.15)
volume_scalar_opacity.AddPoint(1000, 0.15)
volume_scalar_opacity.AddPoint(1150, 0.85)
# The gradient opacity function is used to decrease the opacity
# in the 'flat' regions of the volume while maintaining the opacity
# at the boundaries between tissue types. The gradient is measured
# as the amount by which the intensity changes over unit distance.
# For most medical data, the unit distance is 1mm.
volume_gradient_opacity = vtk.vtkPiecewiseFunction()
volume_gradient_opacity.AddPoint(0, 0.0)
volume_gradient_opacity.AddPoint(90, 0.5)
volume_gradient_opacity.AddPoint(100, 1.0)
# The VolumeProperty attaches the color and opacity functions to the
# volume, and sets other volume properties. The interpolation should
# be set to linear to do a high-quality rendering. The ShadeOn option
# turns on directional lighting, which will usually enhance the
# appearance of the volume and make it look more '3D'. However,
# the quality of the shading depends on how accurately the gradient
# of the volume can be calculated, and for noisy data the gradient
# estimation will be very poor. The impact of the shading can be
# decreased by increasing the Ambient coefficient while decreasing
# the Diffuse and Specular coefficient. To increase the impact
# of shading, decrease the Ambient and increase the Diffuse and Specular.
volume_property = vtk.vtkVolumeProperty()
volume_property.SetColor(volume_color)
volume_property.SetScalarOpacity(volume_scalar_opacity)
volume_property.SetGradientOpacity(volume_gradient_opacity)
volume_property.SetInterpolationTypeToLinear()
volume_property.ShadeOn()
volume_property.SetAmbient(0.4)
volume_property.SetDiffuse(0.6)
volume_property.SetSpecular(0.2)
# The vtkVolume is a vtkProp3D (like a vtkActor) and controls the position
# and orientation of the volume in world coordinates.
volumeActor = vtk.vtkVolume()
volumeActor.SetMapper(volume_mapper)
volumeActor.SetProperty(volume_property)
# Finally, add the volume to the renderer
renderer.AddActor(volumeActor)
##########################
# renderer.AddActor(actor)
# render
renderer.ResetCamera()
renderWindow.Render()
# VTK Web application specific
_WebCone.view = renderWindow
self.getApplication().GetObjectIdMap().SetActiveObject(
"VIEW", renderWindow)
def initialize(self):
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(_WebCone.authKey)
# Create default pipeline (Only once for all the session)
if not _WebCone.view:
try:
# Create the renderer, the render window, and the interactor. The renderer
# draws into the render window, the interactor enables mouse- and
# keyboard-based interaction with the scene.
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
iren.GetInteractorStyle().SetCurrentStyleToTrackballCamera()
cred = credentials()
mydb = mysql.connector.connect(host="localhost",
user=cred[0],
password=cred[1],
database="iqweb")
mycursor = mydb.cursor()
sql = "SELECT path FROM image WHERE seriesuid = %s"
params = (self.uid, )
mycursor.execute(sql, params)
files = mycursor.fetchall()
fileset = vtk.vtkStringArray()
for file in files:
fileset.InsertNextValue(file[0])
sorter = vtk.vtkDICOMFileSorter()
sorter.SetInputFileNames(fileset)
sorter.Update()
sortedFiles = vtk.vtkStringArray()
sortedFiles = sorter.GetFileNamesForSeries(0)
reader = vtk.vtkDICOMReader()
reader.AutoRescaleOff() #only because our preset is shifted
reader.SetFileNames(sortedFiles)
reader.Update()
# The volume will be displayed by ray-cast alpha compositing.
# A ray-cast mapper is needed to do the ray-casting, and a
# compositing function is needed to do the compositing along the ray.
volumeMapper = vtk.vtkGPUVolumeRayCastMapper()
volumeMapper.SetInputConnection(reader.GetOutputPort())
volumeMapper.SetBlendModeToComposite()
volumeMapper.AutoAdjustSampleDistancesOff()
volumeMapper.UseJitteringOn()
# The color transfer function maps voxel intensities to colors.
# It is modality-specific, and often anatomy-specific as well.
# The goal is to one color for flesh (between 500 and 1000)
# and another color for bone (1150 and over).
volumeColor = vtk.vtkColorTransferFunction()
volumeColor.AddRGBPoint(1024, 0.53125, 0.171875, 0.0507813)
volumeColor.AddRGBPoint(1031, 0.488281, 0.148438, 0.0351563)
volumeColor.AddRGBPoint(1000, 0.589844, 0.0257813, 0.0148438)
volumeColor.AddRGBPoint(1170, 0.589844, 0.0257813, 0.0148438)
volumeColor.AddRGBPoint(1181, 0.957031, 0.996094, 0.878906)
volumeColor.AddRGBPoint(2024, 0.976563, 0.996094, 0.929688)
volumeColor.AddRGBPoint(3014, 0.488281, 0.488281, 0.488281)
# The opacity transfer function is used to control the opacity
# of different tissue types.
volumeScalarOpacity = vtk.vtkPiecewiseFunction()
#volumeScalarOpacity.AddPoint(0, 0.00)
#volumeScalarOpacity.AddPoint(500, 0.15)
#volumeScalarOpacity.AddPoint(1000, 0.15)
#volumeScalarOpacity.AddPoint(1150, 0.85)
volumeScalarOpacity.AddPoint(1131, 0)
volumeScalarOpacity.AddPoint(1463, 1)
volumeScalarOpacity.AddPoint(3135, 1)
# The gradient opacity function is used to decrease the opacity
# in the "flat" regions of the volume while maintaining the opacity
# at the boundaries between tissue types. The gradient is measured
# as the amount by which the intensity changes over unit distance.
# For most medical data, the unit distance is 1mm.
volumeGradientOpacity = vtk.vtkPiecewiseFunction()
volumeGradientOpacity.AddPoint(0, 0.0)
volumeGradientOpacity.AddPoint(90, 0.9)
volumeGradientOpacity.AddPoint(100, 1.0)
# The VolumeProperty attaches the color and opacity functions to the
# volume, and sets other volume properties. The interpolation should
# be set to linear to do a high-quality rendering. The ShadeOn option
# turns on directional lighting, which will usually enhance the
# appearance of the volume and make it look more "3D". However,
# the quality of the shading depends on how accurately the gradient
# of the volume can be calculated, and for noisy data the gradient
# estimation will be very poor. The impact of the shading can be
# decreased by increasing the Ambient coefficient while decreasing
# the Diffuse and Specular coefficient. To increase the impact
# of shading, decrease the Ambient and increase the Diffuse and Specular.
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(volumeColor)
volumeProperty.SetScalarOpacity(volumeScalarOpacity)
volumeProperty.SetGradientOpacity(volumeGradientOpacity)
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.ShadeOn()
volumeProperty.SetAmbient(0.4) # 0.1
volumeProperty.SetDiffuse(0.5) # 0.9
volumeProperty.SetSpecular(0.2) # 0.2
volumeProperty.SetSpecularPower(10)
# The vtkVolume is a vtkProp3D (like a vtkActor) and controls the position
# and orientation of the volume in world coordinates.
volume = vtk.vtkVolume()
volume.SetMapper(volumeMapper)
volume.SetProperty(volumeProperty)
# Finally, add the volume to the renderer
ren.AddViewProp(volume)
# Set up an initial view of the volume. The focal point will be the
# center of the volume, and the camera position will be 400mm to the
# patient's left (which is our right).
camera = ren.GetActiveCamera()
c = volume.GetCenter()
camera.SetFocalPoint(c[0], c[1], c[2])
camera.SetPosition(c[0] + 400, c[1], c[2])
camera.SetViewUp(0, 0, -1)
# Increase the size of the render window
#renWin.SetSize(640, 480)
#renWin.SetSize(432, 336)
renWin.SetSize(320, 240)
# Interact with the data.
#iren.Initialize()
renWin.Render()
# vtkweb
self.getApplication().GetObjectIdMap().SetActiveObject(
"VIEW", renWin)
except:
print("Unexpected error:", sys.exc_info()[0])
def initialize(self):
print(sys.version)
global renderer, renderWindow, renderWindowInteractor #, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
# self.registerVtkWebProtocol(protocols.vtkWebPublishImageDelivery(decode=False))
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(_WebCone.authKey)
# tell the C++ web app to use no encoding. vtkWebPublishImageDelivery must be set to decode=False to match.
# self.getApplication().SetImageEncoding(0)
# Create default pipeline (Only once for all the session)
if not _WebCone.view:
TEST_HORIZON = False
if not TEST_HORIZON:
showm = window.ShowManager()
showm.initialize()
slider_demo = self.build_slider_demo()
brain_demo = self.build_brain_demo(showm)
bundle_demo = self.build_bundle_demo()
surface_demo = self.build_surface_demo(showm)
examples = [slider_demo, brain_demo]
examples_names = [name for name, act in examples]
listbox = ui.ListBox2D(values=examples_names,
position=(10, 300),
size=(300, 80),
multiselection=False)
def hide_all_examples():
for _, l_act in examples:
for element in l_act:
if hasattr(element, 'add_to_scene'):
element.set_visibility(False)
else:
element.SetVisibility(False)
def display_element():
hide_all_examples()
example = examples[examples_names.index(
listbox.selected[0])]
for element in example[1]:
if hasattr(element, 'add_to_scene'):
element.set_visibility(True)
else:
element.SetVisibility(True)
listbox.on_change = display_element
listbox.panel.color = (1.0, 1.0, 1.0)
listbox.panel.opacity = 0.3
hide_all_examples()
showm.scene.add(listbox)
for _, l_act in examples:
for element in l_act:
showm.scene.add(element)
# VTK specific code
renderer = showm.scene
renderWindow = showm.window
renderWindowInteractor = showm.iren
else:
affine = np.diag([2., 1, 1, 1]).astype('f8')
data = 255 * np.random.rand(150, 150, 150)
images = [(data, affine)]
from dipy.segment.tests.test_bundles import f1
streamlines = f1.copy()
tractograms = [streamlines]
Horizon(tractograms,
images=images,
cluster=True,
cluster_thr=5,
random_colors=False,
length_lt=np.inf,
length_gt=0,
clusters_lt=np.inf,
clusters_gt=0,
world_coords=True)
def calc_suare(numbers, showm):
print("Calculate square numbers")
for n in numbers:
time.sleep(1)
print("square:", n * n)
showm.scene.GetActiveCamera().Azimuth(10)
# showm.render()
# view = self.getApplication().GetObjectIdMap().GetActiveObject("VIEW")
# arr = np.random.rand(100)
# t1 = threading.Thread(target=calc_suare, args=(arr, showm))
# t1.start()
print("Auth-key {}".format(_WebCone.authKey))
print('Initialization --- OK')
print('Starting FURY SERVER')
# VTK Web application specific
_WebCone.view = renderWindow
self.getApplication().GetObjectIdMap().SetActiveObject(
"VIEW", renderWindow)
def initialize(self):
global renderer, renderWindow, renderWindowInteractor, cone, mapper, actor
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(_WebCone.authKey)
# Create default pipeline (Only once for all the session)
if not _WebCone.view:
def GetDiagonalFromBounds(bounds):
box = vtk.vtkBoundingBox(bounds)
box.SetBounds(bounds)
distance = box.GetDiagonalLength()
return distance
def setupCamera( renWin, ren, width, height ):
print("setting up camera")
renWin.SetSize( width, height )
camera = ren.GetActiveCamera()
cameraDistance = 10
sliceHalfThickness = 1
xFocal = ( width - 1 ) / 2.0
yFocal = ( height - 1 ) / 2.0
#camera.SetFocalPoint( xFocal, yFocal, 0.0 )
camera.SetPosition( xFocal, yFocal, cameraDistance )
camera.SetViewUp( 0, 1, 0 )
camera.SetClippingRange( cameraDistance - sliceHalfThickness, cameraDistance + sliceHalfThickness )
#camera.SetParallelScale( ( height - 1 ) / 2.0 )
camera.ParallelProjectionOn()
try:
# Create the renderer, the render window, and the interactor. The renderer
# draws into the render window, the interactor enables mouse- and
# keyboard-based interaction with the scene.
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
interactorStyle = vtk.vtkInteractorStyleImage()
iren.SetInteractorStyle(interactorStyle)
cred = credentials()
mydb = mysql.connector.connect(
host="localhost",
user=cred[0],
password=cred[1],
database="iqweb"
)
mycursor = mydb.cursor()
sql = "SELECT path FROM image WHERE seriesuid = %s"
params = (self.uid,)
mycursor.execute(sql, params)
files = mycursor.fetchall()
fileset = vtk.vtkStringArray()
for file in files:
fileset.InsertNextValue(file[0])
sorter = vtk.vtkDICOMFileSorter()
sorter.SetInputFileNames(fileset)
sorter.Update()
sortedFiles = vtk.vtkStringArray()
sortedFiles = sorter.GetFileNamesForSeries(0)
reader = vtk.vtkDICOMReader()
reader.SetFileNames(sortedFiles);
reader.Update()
# Calculate the center of the volume
reader.Update()
(xMin, xMax, yMin, yMax, zMin, zMax) = reader.GetExecutive().GetWholeExtent(reader.GetOutputInformation(0))
(xSpacing, ySpacing, zSpacing) = reader.GetOutput().GetSpacing()
(x0, y0, z0) = reader.GetOutput().GetOrigin()
origin = [x0, y0, z0]
spacing = [xSpacing, ySpacing, zSpacing]
extent = [xMin, xMax, yMin, yMax, zMin, zMax]
bounds = [ extent[0]/spacing[0], extent[1]/spacing[0], extent[2]/spacing[1], extent[3]/spacing[1], extent[4]/spacing[2], extent[5]/spacing[2] ]
diagonal = GetDiagonalFromBounds(bounds)
originOut = [diagonal * spacing[0]/2, -diagonal * spacing[1]/2]
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))
# Extract a slice in the desired orientation
reslice = vtk.vtkImageReslice()
reslice.SetInputConnection(reader.GetOutputPort())
reslice.SetOutputDimensionality(2)
#reslice.SetOutputOrigin(origin)
reslice.SetResliceAxes(axial)
if self.orientation == "coronal":
reslice.SetResliceAxes(coronal)
if self.orientation == "sagittal":
reslice.SetResliceAxes(sagittal)
reslice.SetInterpolationModeToLinear()
meta = reader.GetMetaData();
level = meta.Get(vtk.vtkDICOMTag(0x0028,0x1050)).AsUTF8String().split("\\")[0]
window = meta.Get(vtk.vtkDICOMTag(0x0028,0x1051)).AsUTF8String().split("\\")[0]
range1 = int(level) - int(window)/2
range2 = int(level) + int(window)/2
# Create a greyscale lookup table
table = vtk.vtkLookupTable()
table.SetRange(range1, range2) # 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())
ren.AddActor(actor)
# Create callbacks for slicing the image
actions = {}
actions["Slicing"] = 0
def ButtonCallback(obj, event):
if event == "LeftButtonPressEvent":
actions["Slicing"] = 1
else:
actions["Slicing"] = 0
def MouseMoveCallback(obj, event):
(lastX, lastY) = iren.GetLastEventPosition()
(mouseX, mouseY) = iren.GetEventPosition()
if actions["Slicing"] == 1:
deltaY = mouseY - lastY
reslice.Update()
sliceSpacing = reslice.GetOutput().GetSpacing()[2]
matrix = reslice.GetResliceAxes()
# move the center point that we are slicing through
center = matrix.MultiplyPoint((0, 0, sliceSpacing*deltaY, 1))
matrix.SetElement(0, 3, center[0])
matrix.SetElement(1, 3, center[1])
matrix.SetElement(2, 3, center[2])
window.Render()
else:
interactorStyle.OnMouseMove()
interactorStyle.AddObserver("MouseMoveEvent", MouseMoveCallback)
interactorStyle.AddObserver("LeftButtonPressEvent", ButtonCallback)
interactorStyle.AddObserver("LeftButtonReleaseEvent", ButtonCallback)
xc = origin[0] + 0.5*(extent[0] + extent[1])*spacing[0]
yc = origin[1] + 0.5*(extent[2] + extent[3])*spacing[1]
xd = (extent[1] - extent[0] + 1)*spacing[0]
yd = (extent[3] - extent[2] + 1)*spacing[1]
ren.ResetCamera()
camera = ren.GetActiveCamera()
camera.Zoom(1.4)
#d = camera.GetDistance()
#camera.SetParallelScale(0.5 * yd)
#camera.SetFocalPoint(xc, yc, 0.0)
#camera.SetPosition(xc, yc, d)
#setupCamera(renWin, ren, 320, 240)
renWin.Render()
# vtkweb
self.getApplication().GetObjectIdMap().SetActiveObject("VIEW", renWin)
except:
print("Unexpected error:", sys.exc_info()[0])
exit()
def initialize(self):
# Bring used components
self.registerVtkWebProtocol(protocols.vtkWebMouseHandler())
self.registerVtkWebProtocol(protocols.vtkWebViewPort())
self.registerVtkWebProtocol(protocols.vtkWebViewPortImageDelivery())
self.registerVtkWebProtocol(protocols.vtkWebViewPortGeometryDelivery())
# Update authentication key to use
self.updateSecret(_WebSpheres.authKey)
# Create default pipeline (Only once for all the session)
if not _WebSpheres.view:
# FURY specific code
scene = window.Scene()
scene.background((1, 1, 1))
n_points = 1000000
translate = 100
colors = 255 * np.random.rand(n_points, 3)
centers = translate * np.random.rand(n_points, 3) - translate / 2
radius = np.random.rand(n_points) / 10
polydata = vtk.vtkPolyData()
verts = np.array([[0.0, 0.0, 0.0], [0.0, 1.0, 0.0],
[1.0, 1.0, 0.0], [1.0, 0.0, 0.0]])
verts -= np.array([0.5, 0.5, 0])
big_verts = np.tile(verts, (centers.shape[0], 1))
big_cents = np.repeat(centers, verts.shape[0], axis=0)
big_verts += big_cents
# print(big_verts)
big_scales = np.repeat(radius, verts.shape[0], axis=0)
# print(big_scales)
big_verts *= big_scales[:, np.newaxis]
# print(big_verts)
tris = np.array([[0, 1, 2], [2, 3, 0]], dtype='i8')
big_tris = np.tile(tris, (centers.shape[0], 1))
shifts = np.repeat(
np.arange(0, centers.shape[0] * verts.shape[0],
verts.shape[0]), tris.shape[0])
big_tris += shifts[:, np.newaxis]
# print(big_tris)
big_cols = np.repeat(colors, verts.shape[0], axis=0)
# print(big_cols)
big_centers = np.repeat(centers, verts.shape[0], axis=0)
# print(big_centers)
big_centers *= big_scales[:, np.newaxis]
# print(big_centers)
set_polydata_vertices(polydata, big_verts)
set_polydata_triangles(polydata, big_tris)
set_polydata_colors(polydata, big_cols)
vtk_centers = numpy_to_vtk(big_centers, deep=True)
vtk_centers.SetNumberOfComponents(3)
vtk_centers.SetName("center")
polydata.GetPointData().AddArray(vtk_centers)
canvas_actor = get_actor_from_polydata(polydata)
canvas_actor.GetProperty().BackfaceCullingOff()
mapper = canvas_actor.GetMapper()
mapper.MapDataArrayToVertexAttribute(
"center", "center", vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,
-1)
vtk_major_version = vtk.vtkVersion.GetVTKMajorVersion()
vtk_minor_version = vtk.vtkVersion.GetVTKMinorVersion()
if vtk_major_version > 8 or (vtk_major_version == 8
and vtk_minor_version >= 90):
mapper = canvas_actor.GetShaderProperty()
mapper.AddShaderReplacement(
vtk.vtkShader.Vertex, "//VTK::ValuePass::Dec", True, """
//VTK::ValuePass::Dec
in vec3 center;
out vec3 centeredVertexMC;
""", False)
mapper.AddShaderReplacement(
vtk.vtkShader.Vertex, "//VTK::ValuePass::Impl", True, """
//VTK::ValuePass::Impl
centeredVertexMC = vertexMC.xyz - center;
float scalingFactor = 1. / abs(centeredVertexMC.x);
centeredVertexMC *= scalingFactor;
vec3 cameraRight = vec3(MCVCMatrix[0][0], MCVCMatrix[1][0],
MCVCMatrix[2][0]);
vec3 cameraUp = vec3(MCVCMatrix[0][1], MCVCMatrix[1][1],
MCVCMatrix[2][1]);
vec2 squareVertices = vec2(.5, -.5);
vec3 vertexPosition = center + cameraRight * squareVertices.x *
vertexMC.x + cameraUp * squareVertices.y *
vertexMC.y;
gl_Position = MCDCMatrix * vec4(vertexPosition, 1.);
gl_Position /= gl_Position.w;
""", False)
mapper.AddShaderReplacement(
vtk.vtkShader.Fragment, "//VTK::ValuePass::Dec", True, """
//VTK::ValuePass::Dec
in vec3 centeredVertexMC;
""", False)
mapper.AddShaderReplacement(
vtk.vtkShader.Fragment, "//VTK::Light::Impl", True, """
// Renaming variables passed from the Vertex Shader
vec3 color = vertexColorVSOutput.rgb;
vec3 point = centeredVertexMC;
float len = length(point);
// VTK Fake Spheres
float radius = 1.;
if(len > radius)
discard;
vec3 normalizedPoint = normalize(vec3(point.xy, sqrt(1. - len)));
vec3 direction = normalize(vec3(1., -1., 1.));
float df = max(0, dot(direction, normalizedPoint));
float sf = pow(df, 24);
fragOutput0 = vec4(max(df * color, sf * vec3(1)), 1);
""", False)
scene.add(canvas_actor)
#scene.add(actor.axes())
showm = window.ShowManager(scene)
renderWindow = showm.window
# VTK Web application specific
_WebSpheres.view = renderWindow
self.getApplication().GetObjectIdMap().\
SetActiveObject('VIEW', renderWindow)
