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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hello,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal">C++ armada to test a small reconstruction principle!<o:p></o:p></p>
<p class="MsoNormal">I could easily run the first reconstruction and it worked perfectly! However, I tried then to first save the images using these method within<o:p></o:p></p>
<p class="MsoNormal">a simulator python class:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> def buildGeometry(self, offsetZ, offsetY):<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> geometry = rtk.ThreeDCircularProjectionGeometry.New()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> for x in range(0, self.param['numberOfProjections']):<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> angle = self.param['firstAngle'] + x * self.param['angularArc'] / self.param['numberOfProjections']<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> geometry.AddProjection(self.param['sid'] + offsetZ,
<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> self.param['sdd'], angle, self.param['isox'],
<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> self.param['isoy'], self.param['outOfPlaneAngle'],
<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> self.param['inPlaneAngle'], self.param['sourceOffsetX'], offsetY)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> return geometry<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> def runCBCT(self, filename, offsetZ, offsetY):<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> geometry = self.buildGeometry(offsetZ, offsetY)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> constantImageSource = rtk.ConstantImageSource[self.param['TImageType']].New()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> constantImageSource.SetOrigin( self.param['origin'] )<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> constantImageSource.SetSpacing( self.param['spacing'] )<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> constantImageSource.SetSize( self.param['sizeOutput'] )<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> <span lang="FR-BE">constantImageSource.SetConstant(0.0)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR-BE"> source = constantImageSource.GetOutput()<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR-BE"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="FR-BE"> </span>
self.rei.SetGeometry(geometry)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> self.rei.SetInput(source)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> <o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> projections = self.rei.GetOutput()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> writer = itk.ImageFileWriter[self.param['TImageType']].New()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> writer.SetFileName(filename)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> writer.SetInput(projections)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> writer.Update()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal">This parts works perfectly and the generated images are OK (checked with IMageJ).<o:p></o:p></p>
<p class="MsoNormal">The problems start when I want to reconstruct the volume.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt">def buildVolumeFromFile(self, file, fileOUT, CBCT):<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> geometry = CBCT.buildGeometry(0, 0)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> print("Performing reconstruction")<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> TImageType = self.param['TImageType']<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> reader = itk.ImageFileReader[TImageType].New()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> reader.SetFileName(file)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> reiImage = reader.GetOutput()
<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> <o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> # Create reconstructed image<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> constantImageSource2 = rtk.ConstantImageSource[TImageType].New()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> origin = [ -63.5, -63.5, -63.5 ]<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> sizeOutput = [ 128, 128, 128 ]<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> constantImageSource2.SetOrigin( origin )<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> constantImageSource2.SetSpacing( [1, 1, 1] )<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> constantImageSource2.SetSize( sizeOutput )<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> constantImageSource2.SetConstant(0.0)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> source2 = constantImageSource2.GetOutput()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> print("Performing reconstruction")<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> feldkamp = rtk.FDKConeBeamReconstructionFilter[TImageType].New()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> feldkamp.SetGeometry( geometry )<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> feldkamp.SetInput(0, source2)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> feldkamp.SetInput(1, reiImage)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> image = feldkamp.GetOutput()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> print("Masking field-of-view")<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> fov = rtk.FieldOfViewImageFilter[TImageType, TImageType].New()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> fov.SetGeometry(geometry)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> fov.SetProjectionsStack(reiImage)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> fov.SetInput(image)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> image = fov.GetOutput()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> writer = itk.ImageFileWriter[TImageType].New()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> writer.SetFileName ( fileOUT )<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> writer.SetInput(image)<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> writer.Update()<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal">I cannot run this script. It generates a criptic segfault… What am I doing wrong here?<o:p></o:p></p>
<p class="MsoNormal">If one of you RTK gurus could help me, I would greatly appreciate it!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Pierre<o:p></o:p></p>
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