This notebook contains a few examples of how to call wrapped methods in itk and tubeTK ITK. The primary aim is to show a bug in TubeTK python wrapping for itk::SpatialObjects.
If ITK is not installed in your python environment, you need to define the environment variable ITK_BUILD_DIR that contains the path to where ITK was built.
We need to find the directory in which TubeTK was build. This is required to find the path to the testing data, and may be also required to find the TubeTK library paths if your python environment does not include it.
The environment variable TubeTK_BUILD_DIR needs to be defined.
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import os
import sys
import numpy
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# Path for TubeTK libs and bin
#Values takend from TubeTK launcher
sys.path.append("C:/src/TubeTK_Python_ITK/TubeTK-build/lib/")
sys.path.append("C:/src/TubeTK_Python_ITK/TubeTK-build/lib/Release")
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# Setting TubeTK Build Directory
TubeTK_BUILD_DIR=None
if 'TubeTK_BUILD_DIR' in os.environ:
TubeTK_BUILD_DIR = os.environ['TubeTK_BUILD_DIR']
else:
print('TubeTK_BUILD_DIR not found!')
print(' Set environment variable')
os.environ["TubeTK_BUILD_DIR"] = "C:/src/TubeTK_Python_ITK/TubeTK-build"
TubeTK_BUILD_DIR = os.environ["TubeTK_BUILD_DIR"]
#sys.exit( 1 )
if not os.path.exists(TubeTK_BUILD_DIR):
print('TubeTK_BUILD_DIR set by directory not found!')
print(' TubeTK_BUILD_DIR = ' + TubeTK_BUILD_DIR )
sys.exit(1)
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try:
import itk
except:
ITK_BUILD_DIR = None
if 'ITK_BUILD_DIR' in os.environ:
ITK_BUILD_DIR = os.environ['ITK_BUILD_DIR']
else:
print('ITK_BUILD_DIR not found!')
print(' Set environment variable')
os.environ["ITK_BUILD_DIR"] = "C:/src/TubeTK_Python_R/ITK-build"
ITK_BUILD_DIR = os.environ["ITK_BUILD_DIR"]
#sys.exit( 1 )
if not os.path.exists(ITK_BUILD_DIR):
print('ITK_BUILD_DIR set by directory not found!')
print(' ITK_BUIDL_DIR = ' + ITK_BUILD_DIR )
sys.exit(1)
# Append ITK libs
sys.path.append("C:/src/TubeTK_Python_ITK/ITK-build/Wrapping/Generators/Python/Release")
sys.path.append("C:/src/TubeTK_Python_ITK/ITK-build/lib/Release")
sys.path.append("C:/src/TubeTK_Python_ITK/ITK-build/lib")
# Append TubeTK libs
sys.path.append("C:/src/TubeTK_Python_ITK/TubeTK-build/ITKModules/TubeTKITK-build/Wrapping/Generators/Python/Release")
import itk
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from itk import TubeTKITK as itktube
Initialization
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Dimension = 3
PixelType = itk.UC
sampleTubeFileName = os.path.join(TubeTK_BUILD_DIR, 'MIDAS_Data\Branch-truth.tre')
templateImageFileName = os.path.join(TubeTK_BUILD_DIR, 'MIDAS_Data\Branch.n010.mha')
outputImageFileName = os.path.join(TubeTK_BUILD_DIR, 'Temporary\\testOutput.mha')
ImageType = itk.Image[PixelType, Dimension]
SpatialObjectType = itk.SpatialObject[Dimension]
Reading the sample tube file and creating a sample spatial object group object
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TubeFileReaderType = itk.SpatialObjectReader[Dimension]
tubeFileReader = TubeFileReaderType.New()
tubeFileReader.SetFileName(sampleTubeFileName)
tubeFileReader.Update()
sampleSpatialObjectGroup = tubeFileReader.GetGroup()
Reading the sample image file and creating an image object
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ImageReaderType = itk.ImageFileReader[ImageType]
imageReader = ImageReaderType.New()
imageReader.SetFileName(templateImageFileName)
imageReader.Update()
image = imageReader.GetOutput()
Testing ITK filter using itk spatial object. There are two such filters
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# ITK Filter using ITK Spatial Object: OK
s2iType = itk.SpatialObjectToImageFilter[SpatialObjectType, ImageType]
s2i = s2iType.New()
s2i.SetInput(sampleSpatialObjectGroup)
s2i.Update()
#Save the output image
ImageWriterType = itk.ImageFileWriter[ImageType]
imageWriter = ImageWriterType.New()
imageWriter.SetInput(s2i.GetOutput())
imageWriter.SetFileName(outputImageFileName)
imageWriter.Update()
Testing TubeTK filter using itk Spatial Object
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# TubeTK Filter using ITK Spatial Object: NOT OK
SpatialObject = SpatialObjectType.New()
#verify sampleSpatialObjectGroup
print (isinstance(sampleSpatialObjectGroup, SpatialObjectType))
TubesToImageFilterType = itktube.ConvertTubesToImage[Dimension, PixelType]
tubesToImageFilter = TubesToImageFilterType.New()
tubesToImageFilter.SetUseRadius(True)
tubesToImageFilter.SetTemplateImage(image)
#tubesToImageFilter.SetInput(sampleSpatialObjectGroup) # //Expected to work, but is not working
tubesToImageFilter.SetInput(SpatialObject) # //Expected to work, but is not working
tubesToImageFilter.Update()
# Another TubeTK Filter
FilterType = itktube.ComputeTubeFlyThroughImage[PixelType, Dimension]
Filter = FilterType.New()
Filter.SetInputImage(image)
Filter.SetTubeId(0)
Filter.SetInput(sampleSpatialObjectGroup) # //Expected to work, but is not working
Filter.Update()
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