In [1]:

    

import itk
from itk import TubeTK as ttk

from itkwidgets import view

import numpy as np


    

In [2]:

    

ImageType = itk.Image[itk.F, 3]

im1 = itk.imread("data/mra.mha",itk.F)


    

In [3]:

    

res = ttk.ResampleImage[ImageType].New()
res.SetInput(im1)
res.SetMakeHighResIso(True)
res.Update()
im1iso = res.GetOutput()


    

In [4]:

    

xp1=[-3.9,-54.8,12.3]
xp2=[18.4,-16,-21]
xp3=[-46,-15,-13]

vSeg = ttk.SegmentTubes[ImageType].New()
vSeg.SetInput(im1iso)
vSeg.SetVerbose(False)
vSeg.SetRadiusInObjectSpace( 0.33 )
vSeg.SetMinRoundness(0.2)
vSeg.SetVerbose(True)
tube = vSeg.ExtractTubeInObjectSpace( xp1, 1 )
tube = vSeg.ExtractTubeInObjectSpace( xp2, 2 )
tube = vSeg.ExtractTubeInObjectSpace( xp3, 3 )
tubeG = vSeg.GetTubeGroup()


    

In [10]:

    

# Example of accessing data in a tube
p = list(map(lambda x: tube.GetPoint(x).GetPositionInObjectSpace(), range(tube.GetNumberOfPoints())))
r = list(map(lambda x: tube.GetPoint(x).GetNormal1InObjectSpace()[0], range(tube.GetNumberOfPoints())))
print(r)


    

    




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In [6]:

    

TubesToImageFilterType = ttk.ConvertTubesToImage[ImageType]
tubesToImageFilter = TubesToImageFilterType.New()
tubesToImageFilter.SetUseRadius(True)
tubesToImageFilter.SetColorByRidgeness(True)
tubesToImageFilter.SetTemplateImage(im1)
tubesToImageFilter.SetInput(tubeG)
tubesToImageFilter.Update()

outputImage = tubesToImageFilter.GetOutput()
view(outputImage)


    

In [13]:

    

writer = itk.SpatialObjectWriter[3].New()
writer.SetFileName("vessels.tre")
writer.SetInput(tubeG)
writer.Update()


    

In [ ]: