This notebook contains a few examples of how to call wrapped methods in itk and ITKTubeTK.
ITK, ITKTubeTK, and ITKWidgets must be installed on your system for this notebook to work.
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import os
import sys
import numpy
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import itk
from itk import TubeTK as ttk
from itkwidgets import view
Initialization
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PixelType = itk.F
Dimension = 3
ImageType = itk.Image[PixelType, Dimension]
# Read tre file
TubeFileReaderType = itk.SpatialObjectReader[Dimension]
tubeFileReader = TubeFileReaderType.New()
tubeFileReader.SetFileName("data/Normal071-VascularNetwork.tre")
tubeFileReader.Update()
tubes = tubeFileReader.GetGroup()
# Read template image
TemplateImageType = itk.Image[PixelType, Dimension]
TemplateImageReaderType = itk.ImageFileReader[TemplateImageType]
templateImageReader = TemplateImageReaderType.New()
templateImageReader.SetFileName("data/Normal071-MRA.mha")
templateImageReader.Update()
templateImage = templateImageReader.GetOutput()
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view(templateImage)
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TubesToImageFilterType = ttk.ConvertTubesToImage[TemplateImageType]
tubesToImageFilter = TubesToImageFilterType.New()
tubesToImageFilter.SetUseRadius(True)
tubesToImageFilter.SetTemplateImage(templateImageReader.GetOutput())
tubesToImageFilter.SetInput(tubes)
tubesToImageFilter.Update()
outputImage = tubesToImageFilter.GetOutput()
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TTKImageMathType = ttk.ImageMath[ImageType,ImageType]
imMath = TTKImageMathType.New(Input = outputImage)
imMath.AddImages(templateImage, 2048, 1)
combinedImage = imMath.GetOutput()
view(combinedImage)
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