Hello,
First of all congrats for the update of RTK and the new Python integration.
This is really great for Python users who don't want the whole
C++ armada to test a small reconstruction principle!
I could easily run the first reconstruction and it worked perfectly! However, I
tried then to first save the images using these method within
a simulator python class:
def buildGeometry(self, offsetZ, offsetY):
geometry = rtk.ThreeDCircularProjectionGeometry.New()
for x in range(0, self.param['numberOfProjections']):
angle = self.param['firstAngle'] + x * self.param['angularArc'] /
self.param['numberOfProjections']
geometry.AddProjection(self.param['sid'] + offsetZ,
self.param['sdd'], angle, self.param['isox'],
self.param['isoy'], self.param['outOfPlaneAngle'],
self.param['inPlaneAngle'], self.param['sourceOffsetX'],
offsetY)
return geometry
def runCBCT(self, filename, offsetZ, offsetY):
geometry = self.buildGeometry(offsetZ, offsetY)
constantImageSource =
rtk.ConstantImageSource[self.param['TImageType']].New()
constantImageSource.SetOrigin( self.param['origin'] )
constantImageSource.SetSpacing( self.param['spacing'] )
constantImageSource.SetSize( self.param['sizeOutput'] )
constantImageSource.SetConstant(0.0)
source = constantImageSource.GetOutput()
self.rei.SetGeometry(geometry)
self.rei.SetInput(source)
projections = self.rei.GetOutput()
writer = itk.ImageFileWriter[self.param['TImageType']].New()
writer.SetFileName(filename)
writer.SetInput(projections)
writer.Update()
This parts works perfectly and the generated images are OK (checked with
IMageJ).
The problems start when I want to reconstruct the volume.
def buildVolumeFromFile(self, file, fileOUT, CBCT):
geometry = CBCT.buildGeometry(0, 0)
print("Performing reconstruction")
TImageType = self.param['TImageType']
reader = itk.ImageFileReader[TImageType].New()
reader.SetFileName(file)
reiImage = reader.GetOutput()
# Create reconstructed image
constantImageSource2 = rtk.ConstantImageSource[TImageType].New()
origin = [ -63.5, -63.5, -63.5 ]
sizeOutput = [ 128, 128, 128 ]
constantImageSource2.SetOrigin( origin )
constantImageSource2.SetSpacing( [1, 1, 1] )
constantImageSource2.SetSize( sizeOutput )
constantImageSource2.SetConstant(0.0)
source2 = constantImageSource2.GetOutput()
print("Performing reconstruction")
feldkamp = rtk.FDKConeBeamReconstructionFilter[TImageType].New()
feldkamp.SetGeometry( geometry )
feldkamp.SetInput(0, source2)
feldkamp.SetInput(1, reiImage)
image = feldkamp.GetOutput()
print("Masking field-of-view")
fov = rtk.FieldOfViewImageFilter[TImageType, TImageType].New()
fov.SetGeometry(geometry)
fov.SetProjectionsStack(reiImage)
fov.SetInput(image)
image = fov.GetOutput()
writer = itk.ImageFileWriter[TImageType].New()
writer.SetFileName ( fileOUT )
writer.SetInput(image)
writer.Update()
I cannot run this script. It generates a criptic segfault... What am I doing
wrong here?
If one of you RTK gurus could help me, I would greatly appreciate it!
Thanks,
Pierre
Disclaimer | Use of IBA e-communication<https://iba-worldwide.com/disclaimer>
The contents of this e-mail message and any attachments are intended solely for
the recipient (s) named above. This communication is intended to be and to
remain confidential and may be protected by intellectual property rights. Any
use of the information contained herein (including but not limited to, total or
partial reproduction, communication or distribution of any form) by persons
other than the designated recipient(s) is prohibited. Please notify the sender
immediately by e-mail if you have received this e-mail by mistake and delete
this e-mail from your system. E-mail transmission cannot be guaranteed to be
secure or error-free. Ion Beam Applications does not accept liability for any
such errors. Thank you for your cooperation.
_______________________________________________
Rtk-users mailing list
[email protected]
https://public.kitware.com/mailman/listinfo/rtk-users
