def read_slc_file(filename):
print("Reading SLC file")
reader = vtk.vtkSLCReader()
reader.SetFileName(filename)
reader.Update()
return reader
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkSLCReader(), 'Reading vtkSLC.',
(), ('vtkSLC',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def loadImageData(filename, spacing=()):
"""Read and return a ``vtkImageData`` object from file.
Use ``load`` instead.
E.g. `img = load('myfile.tif').imagedata()`
"""
if ".tif" in filename.lower():
reader = vtk.vtkTIFFReader()
elif ".slc" in filename.lower():
reader = vtk.vtkSLCReader()
if not reader.CanReadFile(filename):
colors.printc("~prohibited Sorry bad slc file " + filename, c=1)
return None
elif ".vti" in filename.lower():
reader = vtk.vtkXMLImageDataReader()
elif ".mhd" in filename.lower():
reader = vtk.vtkMetaImageReader()
elif ".dem" in filename.lower():
reader = vtk.vtkDEMReader()
elif ".nii" in filename.lower():
reader = vtk.vtkNIFTIImageReader()
elif ".nrrd" in filename.lower():
reader = vtk.vtkNrrdReader()
if not reader.CanReadFile(filename):
colors.printc("~prohibited Sorry bad nrrd file " + filename, c=1)
return None
reader.SetFileName(filename)
reader.Update()
image = reader.GetOutput()
if len(spacing) == 3:
image.SetSpacing(spacing[0], spacing[1], spacing[2])
return image
def read_SLC_file(filename):
# vtkSLCReader to read.
read = vtk.vtkSLCReader()
read.SetFileName(filename)
read.Update()
return read
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkSLCReader(),
'Reading vtkSLC.', (), ('vtkSLC', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def main():
InputFilename = get_program_parameters()
colors = vtk.vtkNamedColors()
# vtkSLCReader to read.
reader = vtk.vtkSLCReader()
reader.SetFileName(InputFilename)
reader.Update()
# Create a mapper.
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(reader.GetOutputPort())
# Implementing Marching Cubes Algorithm to create the surface using vtkContourFilter object.
contourFilter = vtk.vtkContourFilter()
contourFilter.SetInputConnection(reader.GetOutputPort())
contourFilter.SetValue(0, 72.0)
outliner = vtk.vtkOutlineFilter()
outliner.SetInputConnection(reader.GetOutputPort())
outliner.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(contourFilter.GetOutputPort())
mapper.SetScalarVisibility(0)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
# Create a rendering window and renderer.
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindow.SetSize(500, 500)
# Create a renderwindowinteractor.
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
# Assign actor to the renderer.
renderer.AddActor(actor)
renderer.SetBackground(colors.GetColor3d("lemon_chiffon"))
# Pick a good view
renderer.GetActiveCamera().SetPosition(-382.606608, -3.308563, 223.475751)
renderer.GetActiveCamera().SetFocalPoint(77.311562, 72.821162, 100.000000)
renderer.GetActiveCamera().SetViewUp(0.235483, 0.137775, 0.962063)
renderer.GetActiveCamera().SetDistance(482.25171)
renderer.GetActiveCamera().SetClippingRange(27.933848, 677.669341)
renderWindow.Render()
# Enable user interface interactor.
renderWindowInteractor.Initialize()
renderWindow.Render()
renderWindowInteractor.Start()
def load_slc(filename):
""" Load a slc file and return its content
Args:
source: Path and filename
Returns:
vtkSLCReader
"""
slc = vtk.vtkSLCReader()
slc.SetFileName(filename)
slc.Update()
return slc
def loadImageData(filename, spacing=[]):
if not os.path.isfile(filename):
vc.printc('File not found:', filename, c=1)
return None
if '.tif' in filename.lower():
reader = vtk.vtkTIFFReader()
elif '.slc' in filename.lower():
reader = vtk.vtkSLCReader()
if not reader.CanReadFile(filename):
vc.printc('Sorry bad SLC/TIFF file ' + filename, c=1)
exit(1)
reader.SetFileName(filename)
reader.Update()
image = reader.GetOutput()
if len(spacing) == 3:
image.SetSpacing(spacing[0], spacing[1], spacing[2])
vc.printc('voxel spacing is', image.GetSpacing(), c='b', bold=0)
return image
def loadImageData(filename, spacing=[]):
if not os.path.isfile(filename):
colors.printc('File not found:', filename, c=1)
return None
if '.tif' in filename.lower():
reader = vtk.vtkTIFFReader()
elif '.slc' in filename.lower():
reader = vtk.vtkSLCReader()
if not reader.CanReadFile(filename):
colors.printc('Sorry bad slc file ' + filename, c=1)
exit(1)
elif '.vti' in filename.lower():
reader = vtk.vtkXMLImageDataReader()
reader.SetFileName(filename)
reader.Update()
image = reader.GetOutput()
if len(spacing) == 3:
image.SetSpacing(spacing[0], spacing[1], spacing[2])
return image
def load_image_data():
'''
Used to load the knee image data. It is possible to choose if we want to downsample it with the write_file
boolean declared above
'''
# Loading image data from file
reader = vtk.vtkSLCReader()
reader.SetFileName('vw_knee.slc')
reader.Update()
spacing = reader.GetDataSpacing()
# resampling if we want to
if low_res:
resample = vtk.vtkImageResample()
resample.SetMagnificationFactors(0.2, 0.2, 0.2)
resample.SetInputConnection(reader.GetOutputPort())
resample.Update()
reader = resample
# return the space between each point too
return (reader, spacing)
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Simple volume rendering example.
reader = vtk.vtkSLCReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/sphere.slc")
reader.Update()
# Create transfer functions for opacity and color
opacityTransferFunction = vtk.vtkPiecewiseFunction()
opacityTransferFunction.AddPoint(20,0.0)
opacityTransferFunction.AddPoint(255,1.0)
colorTransferFunction = vtk.vtkColorTransferFunction()
# Improve coverage
colorTransferFunction.SetColorSpaceToRGB()
colorTransferFunction.AddRGBPoint(100,1,1,1)
colorTransferFunction.AddRGBPoint(0,0,0,0)
colorTransferFunction.AddRGBPoint(200,1,0,1)
colorTransferFunction.AddRGBPoint(100,0,0,0)
colorTransferFunction.RemovePoint(100)
colorTransferFunction.RemovePoint(0)
colorTransferFunction.RemovePoint(200)
colorTransferFunction.AddHSVPoint(100,1,1,1)
colorTransferFunction.AddHSVPoint(0,0,0,0)
colorTransferFunction.AddHSVPoint(200,1,0,1)
colorTransferFunction.AddHSVPoint(100,0,0,0)
colorTransferFunction.RemovePoint(0)
colorTransferFunction.RemovePoint(200)
colorTransferFunction.RemovePoint(100)
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Simple volume rendering example.
reader = vtk.vtkSLCReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/sphere.slc")
# Create transfer functions for opacity and color
opacityTransferFunction = vtk.vtkPiecewiseFunction()
opacityTransferFunction.AddPoint(0,0.0)
opacityTransferFunction.AddPoint(30,0.0)
opacityTransferFunction.AddPoint(80,0.5)
opacityTransferFunction.AddPoint(255,0.5)
colorTransferFunction = vtk.vtkColorTransferFunction()
colorTransferFunction.AddRGBPoint(0.0,0.0,0.0,0.0)
colorTransferFunction.AddRGBPoint(64.0,1.0,0.0,0.0)
colorTransferFunction.AddRGBPoint(128.0,0.0,0.0,1.0)
colorTransferFunction.AddRGBPoint(192.0,0.0,1.0,0.0)
colorTransferFunction.AddRGBPoint(255.0,0.0,0.2,0.0)
# Create properties, mappers, volume actors, and ray cast function
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(colorTransferFunction)
volumeProperty.SetScalarOpacity(opacityTransferFunction)
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.ShadeOn()
compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
def __init__(self):
vtkImageReaderBase.vtkImageReaderBase.__init__(self)
self.SetImageReader(vtk.vtkSLCReader())
def SetUp(self):
'''
Set up cursor3D
'''
def OnClosing():
self.root.quit()
def ViewerDown(tkvw):
viewer = tkvw.GetImageViewer()
ViewerSetZSlice(tkvw, viewer.GetZSlice() - 1)
def ViewerUp(tkvw):
viewer = tkvw.GetImageViewer()
ViewerSetZSlice(tkvw, viewer.GetZSlice() + 1)
def ViewerSetZSlice(tkvw, z):
viewer = tkvw.GetImageViewer()
viewer.SetZSlice(z)
txt = 'slice: ' + str(z)
sliceLabel.configure(text=txt)
tkvw.Render()
def SetCursorFromViewer(event):
x = int(event.x)
y = int(event.y)
# We have to flip y axis because tk uses upper right origin.
self.root.update_idletasks()
height = int(self.tkvw.configure()['height'][4])
y = height - y
z = self.tkvw.GetImageViewer().GetZSlice()
SetCursor(x / IMAGE_MAG_X, y / IMAGE_MAG_Y, z / IMAGE_MAG_Z)
def SetCursor(x, y, z):
CURSOR_X = x
CURSOR_Y = y
CURSOR_Z = z
axes.SetOrigin(CURSOR_X, CURSOR_Y, CURSOR_Z)
imageCursor.SetCursorPosition(CURSOR_X * IMAGE_MAG_X,
CURSOR_Y * IMAGE_MAG_Y,
CURSOR_Z * IMAGE_MAG_Z)
self.viewer.Render()
self.tkrw.Render()
# Pipeline stuff.
reader = vtk.vtkSLCReader()
reader.SetFileName(VTK_DATA_ROOT + "/Data/neghip.slc")
# Cursor stuff
magnify = vtk.vtkImageMagnify()
magnify.SetInputConnection(reader.GetOutputPort())
magnify.SetMagnificationFactors(IMAGE_MAG_X, IMAGE_MAG_Y, IMAGE_MAG_Z)
imageCursor = vtk.vtkImageCursor3D()
imageCursor.SetInputConnection(magnify.GetOutputPort())
imageCursor.SetCursorPosition(CURSOR_X * IMAGE_MAG_X,
CURSOR_Y * IMAGE_MAG_Y,
CURSOR_Z * IMAGE_MAG_Z)
imageCursor.SetCursorValue(255)
imageCursor.SetCursorRadius(50 * IMAGE_MAG_X)
axes = vtk.vtkAxes()
axes.SymmetricOn()
axes.SetOrigin(CURSOR_X, CURSOR_Y, CURSOR_Z)
axes.SetScaleFactor(50.0)
axes_mapper = vtk.vtkPolyDataMapper()
axes_mapper.SetInputConnection(axes.GetOutputPort())
axesActor = vtk.vtkActor()
axesActor.SetMapper(axes_mapper)
axesActor.GetProperty().SetAmbient(0.5)
# Image viewer stuff.
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(imageCursor.GetOutputPort())
viewer.SetZSlice(CURSOR_Z * IMAGE_MAG_Z)
viewer.SetColorWindow(256)
viewer.SetColorLevel(128)
# Create transfer functions for opacity and color.
opacity_transfer_function = vtk.vtkPiecewiseFunction()
opacity_transfer_function.AddPoint(20, 0.0)
opacity_transfer_function.AddPoint(255, 0.2)
color_transfer_function = vtk.vtkColorTransferFunction()
color_transfer_function.AddRGBPoint(0, 0, 0, 0)
color_transfer_function.AddRGBPoint(64, 1, 0, 0)
color_transfer_function.AddRGBPoint(128, 0, 0, 1)
color_transfer_function.AddRGBPoint(192, 0, 1, 0)
color_transfer_function.AddRGBPoint(255, 0, .2, 0)
# Create properties, mappers, volume actors, and ray cast function.
volume_property = vtk.vtkVolumeProperty()
volume_property.SetColor(color_transfer_function)
# volume_property.SetColor(color_transfer_function[0],
# color_transfer_function[1],
# color_transfer_function[2])
volume_property.SetScalarOpacity(opacity_transfer_function)
volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
volume_mapper.SetInputConnection(reader.GetOutputPort())
volume = vtk.vtkVolume()
volume.SetMapper(volume_mapper)
volume.SetProperty(volume_property)
# Create outline.
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outline_mapper)
outlineActor.GetProperty().SetColor(1, 1, 1)
# Create the renderer.
ren = vtk.vtkRenderer()
ren.AddActor(axesActor)
ren.AddVolume(volume)
ren.SetBackground(0.1, 0.2, 0.4)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(256, 256)
# Create the GUI: two renderer widgets and a quit button.
self.root = tkinter.Tk()
self.root.title("cursor3D")
# Define what to do when the user explicitly closes a window.
self.root.protocol("WM_DELETE_WINDOW", OnClosing)
# Help label, frame and quit button
helpLabel = tkinter.Label(
self.root,
text=
"MiddleMouse (or shift-LeftMouse) in image viewer to place cursor")
displayFrame = tkinter.Frame(self.root)
quitButton = tkinter.Button(self.root, text="Quit", command=OnClosing)
# Pack the GUI.
helpLabel.pack()
displayFrame.pack(fill=BOTH, expand=TRUE)
quitButton.pack(fill=X)
# Create the viewer widget.
viewerFrame = tkinter.Frame(displayFrame)
viewerFrame.pack(padx=3,
pady=3,
side=LEFT,
anchor=N,
fill=BOTH,
expand=FALSE)
self.tkvw = vtkTkImageViewerWidget(viewerFrame,
iv=viewer,
width=264,
height=264)
viewerControls = tkinter.Frame(viewerFrame)
viewerControls.pack(side=BOTTOM, anchor=S, fill=BOTH, expand=TRUE)
self.tkvw.pack(side=TOP, anchor=N, fill=BOTH, expand=FALSE)
downButton = tkinter.Button(viewerControls,
text="Down",
command=[ViewerDown, self.tkvw])
upButton = tkinter.Button(viewerControls,
text="Up",
command=[ViewerUp, self.tkvw])
sliceLabel = tkinter.Label(viewerControls,
text="slice: " +
str(CURSOR_Z * IMAGE_MAG_Z))
downButton.pack(side=LEFT, expand=TRUE, fill=BOTH)
upButton.pack(side=LEFT, expand=TRUE, fill=BOTH)
sliceLabel.pack(side=LEFT, expand=TRUE, fill=BOTH)
# Create the render widget
renderFrame = tkinter.Frame(displayFrame)
renderFrame.pack(padx=3,
pady=3,
side=LEFT,
anchor=N,
fill=BOTH,
expand=TRUE)
self.tkrw = vtkTkRenderWidget(renderFrame,
rw=renWin,
width=264,
height=264)
self.tkrw.pack(side=TOP, anchor=N, fill=BOTH, expand=TRUE)
# Bindings
self.tkvw.BindTkImageViewer()
self.tkrw.BindTkRenderWidget()
# Lets add an extra binding of the middle button in the image viewer
# to set the cursor location.
self.tkvw.bind('<Button-2>', SetCursorFromViewer)
self.tkvw.bind('<Shift-Button-1>', SetCursorFromViewer)
# Associate the functions with the buttons and label.
#
downButton.config(command=partial(ViewerDown, self.tkvw))
upButton.config(command=partial(ViewerUp, self.tkvw))
def loadVolume(filename, c, alpha, wire, bc, edges, legend, texture, smoothing,
threshold, connectivity, scaling):
'''Return vtkActor from a TIFF stack or SLC file'''
if not os.path.exists(filename):
vc.printc(('Error in loadVolume: Cannot find file', filename), c=1)
return None
print('..reading file:', filename)
if '.tif' in filename.lower():
reader = vtk.vtkTIFFReader()
elif '.slc' in filename.lower():
reader = vtk.vtkSLCReader()
if not reader.CanReadFile(filename):
vc.printc('Sorry bad SLC file ' + filename, 1)
exit(1)
reader.SetFileName(filename)
reader.Update()
image = reader.GetOutput()
if smoothing:
print(' gaussian smoothing data with volume_smoothing =', smoothing)
smImg = vtk.vtkImageGaussianSmooth()
smImg.SetDimensionality(3)
vu.setInput(smImg, image)
smImg.SetStandardDeviations(smoothing, smoothing, smoothing)
smImg.Update()
image = smImg.GetOutput()
scrange = image.GetScalarRange()
if not threshold:
threshold = (2 * scrange[0] + scrange[1]) / 3.
a = ' isosurfacing volume with automatic iso_threshold ='
else:
a = ' isosurfacing volume with iso_threshold ='
print(a, round(threshold, 2), scrange)
cf = vtk.vtkContourFilter()
vu.setInput(cf, image)
cf.UseScalarTreeOn()
cf.ComputeScalarsOff()
cf.SetValue(0, threshold)
cf.Update()
clp = vtk.vtkCleanPolyData()
vu.setInput(clp, cf.GetOutput())
clp.Update()
image = clp.GetOutput()
if connectivity:
print(' applying connectivity filter, select largest region')
conn = vtk.vtkPolyDataConnectivityFilter()
conn.SetExtractionModeToLargestRegion()
vu.setInput(conn, image)
conn.Update()
image = conn.GetOutput()
if scaling:
print(' scaling xyz by factors', scaling)
tf = vtk.vtkTransformPolyDataFilter()
vu.setInput(tf, image)
trans = vtk.vtkTransform()
trans.Scale(scaling)
tf.SetTransform(trans)
tf.Update()
image = tf.GetOutput()
return vu.makeActor(image, c, alpha, wire, bc, edges, legend, texture)
def testContour2DAll(self):
# Create the RenderWindow, Renderer and both Actors
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.SetMultiSamples(0)
renWin.AddRenderer(ren)
# create pipeline
#
slc = vtk.vtkSLCReader()
slc.SetFileName(VTK_DATA_ROOT + "/Data/nut.slc")
slc.Update()
types = ["Char", "UnsignedChar", "Short", "UnsignedShort", "Int", "UnsignedInt", "Long", "UnsignedLong", "Float", "Double"]
i = 3
clip = list()
cast = list()
iso = list()
mapper = list()
actor = list()
for idx, vtkType in enumerate(types):
clip.append(vtk.vtkImageClip())
clip[idx].SetInputConnection(slc.GetOutputPort())
clip[idx].SetOutputWholeExtent(-1000, 1000, -1000, 1000, i, i)
i += 2
cast.append(vtk.vtkImageCast())
eval("cast[idx].SetOutputScalarTypeTo" + vtkType)
cast[idx].SetInputConnection(clip[idx].GetOutputPort())
cast[idx].ClampOverflowOn()
iso.append(vtk.vtkContourFilter())
iso[idx] = vtk.vtkContourFilter()
iso[idx].SetInputConnection(cast[idx].GetOutputPort())
iso[idx].GenerateValues(1, 30, 30)
mapper.append(vtk.vtkPolyDataMapper())
mapper[idx].SetInputConnection(iso[idx].GetOutputPort())
mapper[idx].SetColorModeToMapScalars()
actor.append(vtk.vtkActor())
actor[idx].SetMapper(mapper[idx])
ren.AddActor(actor[idx])
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(slc.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineActor.VisibilityOff()
#
# Add the actors to the renderer, set the background and size
#
ren.AddActor(outlineActor)
ren.ResetCamera()
ren.GetActiveCamera().SetViewAngle(30)
ren.GetActiveCamera().Elevation(20)
ren.GetActiveCamera().Azimuth(20)
ren.GetActiveCamera().Zoom(1.5)
ren.ResetCameraClippingRange()
ren.SetBackground(0.9, .9, .9)
renWin.SetSize(200, 200)
# render and interact with data
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin);
renWin.Render()
img_file = "contour2DAll.png"
vtk.test.Testing.compareImage(iRen.GetRenderWindow(), vtk.test.Testing.getAbsImagePath(img_file), threshold=25)
vtk.test.Testing.interact()
# Create the standard renderer, render window
# and interactor
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
iren.SetDesiredUpdateRate(3)
# Create the reader for the data
# This is the data the will be volume rendered
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/ironProt.vtk")
# create a reader for the other data that will
# be contoured and displayed as a polygonal mesh
reader2 = vtk.vtkSLCReader()
reader2.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/neghip.slc")
# convert from vtkImageData to vtkUnstructuredGrid, remove
# any cells where all values are below 80
thresh = vtk.vtkThreshold()
thresh.ThresholdByUpper(80)
thresh.AllScalarsOff()
thresh.SetInputConnection(reader.GetOutputPort())
# make sure we have only tetrahedra
trifilter = vtk.vtkDataSetTriangleFilter()
trifilter.SetInputConnection(thresh.GetOutputPort())
# Create transfer mapping scalar value to opacity
opacityTransferFunction = vtk.vtkPiecewiseFunction()
opacityTransferFunction.AddPoint(80,0.0)
opacityTransferFunction.AddPoint(120,0.2)
opacityTransferFunction.AddPoint(255,0.2)
# Create the standard renderer, render window
# and interactor
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
iren.SetDesiredUpdateRate(3)
# Create the reader for the data
# This is the data the will be volume rendered
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/ironProt.vtk")
# create a reader for the other data that will
# be contoured and displayed as a polygonal mesh
reader2 = vtk.vtkSLCReader()
reader2.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/neghip.slc")
# convert from vtkImageData to vtkUnstructuredGrid, remove
# any cells where all values are below 80
thresh = vtk.vtkThreshold()
thresh.ThresholdByUpper(80)
thresh.AllScalarsOff()
thresh.SetInputConnection(reader.GetOutputPort())
# make sure we have only tetrahedra
trifilter = vtk.vtkDataSetTriangleFilter()
trifilter.SetInputConnection(thresh.GetOutputPort())
# Create transfer mapping scalar value to opacity
opacityTransferFunction = vtk.vtkPiecewiseFunction()
opacityTransferFunction.AddPoint(80,0.0)
opacityTransferFunction.AddPoint(120,0.2)
opacityTransferFunction.AddPoint(255,0.2)
def testContour2DAll(self):
# Create the RenderWindow, Renderer and both Actors
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.SetMultiSamples(0)
renWin.AddRenderer(ren)
# create pipeline
#
slc = vtk.vtkSLCReader()
slc.SetFileName(VTK_DATA_ROOT + "/Data/nut.slc")
slc.Update()
types = [
"Char", "UnsignedChar", "Short", "UnsignedShort", "Int",
"UnsignedInt", "Long", "UnsignedLong", "Float", "Double"
]
i = 3
clip = list()
cast = list()
iso = list()
mapper = list()
actor = list()
for idx, vtkType in enumerate(types):
clip.append(vtk.vtkImageClip())
clip[idx].SetInputConnection(slc.GetOutputPort())
clip[idx].SetOutputWholeExtent(-1000, 1000, -1000, 1000, i, i)
i += 2
cast.append(vtk.vtkImageCast())
eval("cast[idx].SetOutputScalarTypeTo" + vtkType)
cast[idx].SetInputConnection(clip[idx].GetOutputPort())
cast[idx].ClampOverflowOn()
iso.append(vtk.vtkContourFilter())
iso[idx] = vtk.vtkContourFilter()
iso[idx].SetInputConnection(cast[idx].GetOutputPort())
iso[idx].GenerateValues(1, 30, 30)
mapper.append(vtk.vtkPolyDataMapper())
mapper[idx].SetInputConnection(iso[idx].GetOutputPort())
mapper[idx].SetColorModeToMapScalars()
actor.append(vtk.vtkActor())
actor[idx].SetMapper(mapper[idx])
ren.AddActor(actor[idx])
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(slc.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineActor.VisibilityOff()
#
# Add the actors to the renderer, set the background and size
#
ren.AddActor(outlineActor)
ren.ResetCamera()
ren.GetActiveCamera().SetViewAngle(30)
ren.GetActiveCamera().Elevation(20)
ren.GetActiveCamera().Azimuth(20)
ren.GetActiveCamera().Zoom(1.5)
ren.ResetCameraClippingRange()
ren.SetBackground(0.9, .9, .9)
renWin.SetSize(200, 200)
# render and interact with data
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin)
renWin.Render()
img_file = "contour2DAll.png"
vtk.test.Testing.compareImage(
iRen.GetRenderWindow(),
vtk.test.Testing.getAbsImagePath(img_file),
threshold=25)
vtk.test.Testing.interact()
import vtk from vtk.util.colors import tan ## Load in knee model kneeFile = r"./assets/vw_knee.slc" kneeReader = vtk.vtkSLCReader() kneeReader.SetFileName(kneeFile) ## Apply contourfilter to knee skin model kneeSkinContourFilter = vtk.vtkContourFilter() kneeSkinContourFilter.SetInputConnection(kneeReader.GetOutputPort()) kneeSkinContourFilter.SetValue(0, 50) ## Clip the knee skin sphere = vtk.vtkSphere() sphere.SetCenter(0, 0, 50) sphere.SetRadius(100) sphereClip = vtk.vtkClipPolyData() sphereClip.SetInputConnection(kneeSkinContourFilter.GetOutputPort()) sphereClip.GenerateClippedOutputOn() sphereClip.GenerateClipScalarsOn() sphereClip.SetClipFunction(sphere) ## Apply contour filter to knee itself kneeContourFilter = vtk.vtkContourFilter() kneeContourFilter.SetInputConnection(kneeReader.GetOutputPort()) kneeContourFilter.SetValue(0, 80) ## Smoothen everything up by sampling less kneeExtractVOI = vtk.vtkExtractVOI()
def SetUp(self):
"""
Set up cursor3D
"""
def OnClosing():
self.root.quit()
def ViewerDown(tkvw):
viewer = tkvw.GetImageViewer()
ViewerSetZSlice(tkvw, viewer.GetZSlice() - 1)
def ViewerUp(tkvw):
viewer = tkvw.GetImageViewer()
ViewerSetZSlice(tkvw, viewer.GetZSlice() + 1)
def ViewerSetZSlice(tkvw, z):
viewer = tkvw.GetImageViewer()
viewer.SetZSlice(z)
txt = "slice: " + str(z)
sliceLabel.configure(text=txt)
tkvw.Render()
def SetCursorFromViewer(event):
x = int(event.x)
y = int(event.y)
# We have to flip y axis because tk uses upper right origin.
self.root.update_idletasks()
height = int(self.tkvw.configure()["height"][4])
y = height - y
z = self.tkvw.GetImageViewer().GetZSlice()
SetCursor(x / IMAGE_MAG_X, y / IMAGE_MAG_Y, z / IMAGE_MAG_Z)
def SetCursor(x, y, z):
CURSOR_X = x
CURSOR_Y = y
CURSOR_Z = z
axes.SetOrigin(CURSOR_X, CURSOR_Y, CURSOR_Z)
imageCursor.SetCursorPosition(CURSOR_X * IMAGE_MAG_X, CURSOR_Y * IMAGE_MAG_Y, CURSOR_Z * IMAGE_MAG_Z)
self.viewer.Render()
self.tkrw.Render()
# Pipeline stuff.
reader = vtk.vtkSLCReader()
reader.SetFileName(VTK_DATA_ROOT + "/Data/neghip.slc")
# Cursor stuff
magnify = vtk.vtkImageMagnify()
magnify.SetInputConnection(reader.GetOutputPort())
magnify.SetMagnificationFactors(IMAGE_MAG_X, IMAGE_MAG_Y, IMAGE_MAG_Z)
imageCursor = vtk.vtkImageCursor3D()
imageCursor.SetInputConnection(magnify.GetOutputPort())
imageCursor.SetCursorPosition(CURSOR_X * IMAGE_MAG_X, CURSOR_Y * IMAGE_MAG_Y, CURSOR_Z * IMAGE_MAG_Z)
imageCursor.SetCursorValue(255)
imageCursor.SetCursorRadius(50 * IMAGE_MAG_X)
axes = vtk.vtkAxes()
axes.SymmetricOn()
axes.SetOrigin(CURSOR_X, CURSOR_Y, CURSOR_Z)
axes.SetScaleFactor(50.0)
axes_mapper = vtk.vtkPolyDataMapper()
axes_mapper.SetInputConnection(axes.GetOutputPort())
axesActor = vtk.vtkActor()
axesActor.SetMapper(axes_mapper)
axesActor.GetProperty().SetAmbient(0.5)
# Image viewer stuff.
viewer = vtk.vtkImageViewer()
viewer.SetInputConnection(imageCursor.GetOutputPort())
viewer.SetZSlice(CURSOR_Z * IMAGE_MAG_Z)
viewer.SetColorWindow(256)
viewer.SetColorLevel(128)
# Create transfer functions for opacity and color.
opacity_transfer_function = vtk.vtkPiecewiseFunction()
opacity_transfer_function.AddPoint(20, 0.0)
opacity_transfer_function.AddPoint(255, 0.2)
color_transfer_function = vtk.vtkColorTransferFunction()
color_transfer_function.AddRGBPoint(0, 0, 0, 0)
color_transfer_function.AddRGBPoint(64, 1, 0, 0)
color_transfer_function.AddRGBPoint(128, 0, 0, 1)
color_transfer_function.AddRGBPoint(192, 0, 1, 0)
color_transfer_function.AddRGBPoint(255, 0, 0.2, 0)
# Create properties, mappers, volume actors, and ray cast function.
volume_property = vtk.vtkVolumeProperty()
volume_property.SetColor(color_transfer_function)
# volume_property.SetColor(color_transfer_function[0],
# color_transfer_function[1],
# color_transfer_function[2])
volume_property.SetScalarOpacity(opacity_transfer_function)
volume_mapper = vtk.vtkFixedPointVolumeRayCastMapper()
volume_mapper.SetInputConnection(reader.GetOutputPort())
volume = vtk.vtkVolume()
volume.SetMapper(volume_mapper)
volume.SetProperty(volume_property)
# Create outline.
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(reader.GetOutputPort())
outline_mapper = vtk.vtkPolyDataMapper()
outline_mapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outline_mapper)
outlineActor.GetProperty().SetColor(1, 1, 1)
# Create the renderer.
ren = vtk.vtkRenderer()
ren.AddActor(axesActor)
ren.AddVolume(volume)
ren.SetBackground(0.1, 0.2, 0.4)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(256, 256)
# Create the GUI: two renderer widgets and a quit button.
self.root = tkinter.Tk()
self.root.title("cursor3D")
# Define what to do when the user explicitly closes a window.
self.root.protocol("WM_DELETE_WINDOW", OnClosing)
# Help label, frame and quit button
helpLabel = tkinter.Label(self.root, text="MiddleMouse (or shift-LeftMouse) in image viewer to place cursor")
displayFrame = tkinter.Frame(self.root)
quitButton = tkinter.Button(self.root, text="Quit", command=OnClosing)
# Pack the GUI.
helpLabel.pack()
displayFrame.pack(fill=BOTH, expand=TRUE)
quitButton.pack(fill=X)
# Create the viewer widget.
viewerFrame = tkinter.Frame(displayFrame)
viewerFrame.pack(padx=3, pady=3, side=LEFT, anchor=N, fill=BOTH, expand=FALSE)
self.tkvw = vtkTkImageViewerWidget(viewerFrame, iv=viewer, width=264, height=264)
viewerControls = tkinter.Frame(viewerFrame)
viewerControls.pack(side=BOTTOM, anchor=S, fill=BOTH, expand=TRUE)
self.tkvw.pack(side=TOP, anchor=N, fill=BOTH, expand=FALSE)
downButton = tkinter.Button(viewerControls, text="Down", command=[ViewerDown, self.tkvw])
upButton = tkinter.Button(viewerControls, text="Up", command=[ViewerUp, self.tkvw])
sliceLabel = tkinter.Label(viewerControls, text="slice: " + str(CURSOR_Z * IMAGE_MAG_Z))
downButton.pack(side=LEFT, expand=TRUE, fill=BOTH)
upButton.pack(side=LEFT, expand=TRUE, fill=BOTH)
sliceLabel.pack(side=LEFT, expand=TRUE, fill=BOTH)
# Create the render widget
renderFrame = tkinter.Frame(displayFrame)
renderFrame.pack(padx=3, pady=3, side=LEFT, anchor=N, fill=BOTH, expand=TRUE)
self.tkrw = vtkTkRenderWidget(renderFrame, rw=renWin, width=264, height=264)
self.tkrw.pack(side=TOP, anchor=N, fill=BOTH, expand=TRUE)
# Bindings
self.tkvw.BindTkImageViewer()
self.tkrw.BindTkRenderWidget()
# Lets add an extra binding of the middle button in the image viewer
# to set the cursor location.
self.tkvw.bind("<Button-2>", SetCursorFromViewer)
self.tkvw.bind("<Shift-Button-1>", SetCursorFromViewer)
# Associate the functions with the buttons and label.
#
downButton.config(command=partial(ViewerDown, self.tkvw))
upButton.config(command=partial(ViewerUp, self.tkvw))
def main():
InputFilename, iso_value = get_program_parameters()
colors = vtk.vtkNamedColors()
# vtkSLCReader to read.
reader = vtk.vtkSLCReader()
reader.SetFileName(InputFilename)
reader.Update()
# Create a mapper.
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(reader.GetOutputPort())
# Implementing Marching Cubes Algorithm to create the surface using vtkContourFilter object.
contourFilter = vtk.vtkContourFilter()
contourFilter.SetInputConnection(reader.GetOutputPort())
# Change the range(2nd and 3rd Paramater) based on your
# requirement. recomended value for 1st parameter is above 1
# contourFilter.GenerateValues(5, 80.0, 100.0)
contourFilter.SetValue(0, iso_value)
outliner = vtk.vtkOutlineFilter()
outliner.SetInputConnection(reader.GetOutputPort())
outliner.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(contourFilter.GetOutputPort())
mapper.SetScalarVisibility(0)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetDiffuse(0.8)
actor.GetProperty().SetDiffuseColor(colors.GetColor3d('Ivory'))
actor.GetProperty().SetSpecular(0.8)
actor.GetProperty().SetSpecularPower(120.0)
# Create a rendering window and renderer.
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindow.SetSize(500, 500)
# Create a renderwindowinteractor.
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
# Assign actor to the renderer.
renderer.AddActor(actor)
renderer.SetBackground(colors.GetColor3d('SlateGray'))
# Pick a good view
cam1 = renderer.GetActiveCamera()
cam1.SetFocalPoint(0.0, 0.0, 0.0)
cam1.SetPosition(0.0, -1.0, 0.0)
cam1.SetViewUp(0.0, 0.0, -1.0)
cam1.Azimuth(-90.0)
renderer.ResetCamera()
renderer.ResetCameraClippingRange()
renderWindow.SetWindowName('ReadSLC')
renderWindow.SetSize(640, 512)
renderWindow.Render()
# Enable user interface interactor.
renderWindowInteractor.Initialize()
renderWindow.Render()
renderWindowInteractor.Start()
def main():
ren_win = vtk.vtkRenderWindow()
ren_win.SetWindowName("The good knee")
ren_win.SetSize(1000, 1000)
# Watch for events
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(ren_win)
# Set the interactor style
style = vtk.vtkInteractorStyleTrackballCamera()
interactor.SetInteractorStyle(style)
# Create an SLC reader
reader = vtk.vtkSLCReader()
reader.SetFileName(SLC_FILENAME)
reader.Update()
# Create contours
bone_contour = contour(reader, 0, 72.0)
skin_contour = contour(reader, 0, 50)
# Create actors
knee_outline = outline(reader)
knee_bone = create_actor(bone_contour)
knee_skin = create_actor(skin_contour)
knee_skin.GetProperty().SetColor(0.9, 0.69, 0.56)
# Cut knee for top left visualization
cut_skin = repeated_cuts(skin_contour, 19)
cut_skin.GetProperty().SetColor(0.9, 0.69, 0.56)
# Clipped knee for top right and bottom left visualizations
knee_clipped = create_sphere_clipping(skin_contour, 48, (80, 40, 110))
knee_clipped.GetProperty().SetColor(0.9, 0.69, 0.56)
knee_clipped_transparent = create_sphere_clipping(skin_contour, 48,
(80, 40, 110))
knee_clipped_transparent.GetProperty().SetColor(0.9, 0.69, 0.56)
knee_clipped_transparent.GetProperty().SetOpacity(0.5)
knee_clipped_backside = create_sphere_clipping(skin_contour, 48,
(80, 40, 110))
knee_clipped_backside.GetProperty().SetColor(0.9, 0.69, 0.56)
knee_clipped_backside.GetProperty().FrontfaceCullingOn()
sphere_transparent = get_sphere_actor((80, 40, 110), 48)
sphere_transparent.GetProperty().SetOpacity(0.4)
# Colored bone for bottom right visualization
# This will generate the file if it doesn't exist (computationally expensive)
bone_color = distance_color(bone_contour, skin_contour,
"bone_distance_color.vtk")
# Set up a single camera for all the viewports
camera = vtk.vtkCamera()
camera.SetPosition(0, 0, 100)
camera.SetFocalPoint(0, 0, 0)
# Move the camera in the right position
camera.Elevation(-90)
camera.OrthogonalizeViewUp()
camera.Roll(180)
# Define viewport ranges
viewports = [(0, 0, 0.5, 0.5), (0.5, 0, 1, 0.5), (0, 0.5, 0.5, 1),
(0.5, 0.5, 1, 1)]
# Actors for the four viewports
actors_per_viewport = [[
knee_clipped, sphere_transparent, knee_bone, knee_outline
], [bone_color, knee_outline], [cut_skin, knee_bone, knee_outline],
[
knee_clipped_transparent, knee_clipped_backside,
knee_bone, knee_outline
]]
# Background colors for the four viewports
bg_colors = [(0.82, 0.82, 1), (0.82, 0.82, 0.82), (1, 0.82, 0.82),
(0.82, 1, 0.82)]
# Create the viewports and generate the visualizations
for idx, actors in enumerate(actors_per_viewport):
# Set up the renderer for this viewport
ren = vtk.vtkRenderer()
ren.SetActiveCamera(camera)
ren_win.AddRenderer(ren)
ren.SetViewport(viewports[idx])
# Add appropriate actors
for actor in actors:
ren.AddActor(actor)
ren.SetBackground(bg_colors[idx])
ren.ResetCamera()
# Move the camera around the focal point to turn around the objects
for _ in range(360):
camera.Azimuth(1)
ren_win.Render()
sleep(FRAMERATE)
interactor.Start()
