Problem with reconstruction on Python

[Ruslan1541]

Hello for everyone,

I have a some problems with reconstruction of real data. If I use the code below, then the resulting reconstructions are of very poor quality. It seems to me that I don't understand something fundamental.

Some info about my data: I have a 7201 projections in .tiff format, angle between projections — 0.05. Detector pixel size — 85.0 micrometer. I also already have a reconstruction of this data (1490x1490x1408) from different company, but i also want to try to reconstruct and compare the quality of resulting images.

Here is the basic python code I am trying to use (modified from the example), if anyone can see what I might be doing wrong I would appreciate it:

(some code of import modules) tiffio = itk.TIFFImageIO.New() ImageType = itk.Image[itk.F,3]

ProjectionsReaderType = rtk.ProjectionsReader[ImageType] projectionsSource = ProjectionsReaderType.New() projectionsSource.SetImageIO(tiffio) projectionsSource.SetFileNames(data_names) projectionsSource.GetOrigin() # output — itkVectorD3 ([1.79769e+308, 1.79769e+308, 1.79769e+308]) projectionsSource.GetSpacing() # output — itkPointD3 ([1.79769e+308, 1.79769e+308, 1.79769e+308]) geometry = rtk.ThreeDCircularProjectionGeometry.New()

projOffsetX=0.0375 projOffsetY=-27.965 numberOfProjections = 7201 firstAngle = 0. angularArc = 360. sid = 17.2 # source to isocenter distance sdd = 795 # source to detector distance for x in range(0,numberOfProjections): angle = firstAngle + x * angularArc / numberOfProjections geometry.AddProjection(sid,sdd,angle, projOffsetX, projOffsetY)

ConstantImageSourceType = rtk.ConstantImageSource[ImageType] constantImageSource2 = ConstantImageSourceType.New() origin = [-0.003677988(1490-1)/2, -0.003677988(1490-1)/2, 0] sizeOutput = [1490, 1490, 1410] spacing = [ 0.003677988, 0.003677988, 0.003677988] # Image pixel size — 3.677988 micrometers, so I convert to mm constantImageSource2.SetOrigin(origin) constantImageSource2.SetSpacing( spacing ) constantImageSource2.SetSize( sizeOutput ) constantImageSource2.SetConstant(0.)

print("Reconstructing...") FDKCPUType = rtk.FDKConeBeamReconstructionFilter[ImageType] feldkamp = FDKCPUType.New() feldkamp.SetInput(0, constantImageSource2.GetOutput()) feldkamp.SetInput(1, projectionsSource.GetOutput()) feldkamp.SetGeometry(geometry) feldkamp.GetRampFilter().SetTruncationCorrection(0.0) feldkamp.GetRampFilter().SetHannCutFrequency(0.0)

feldkamp.Update() output = feldkamp.GetOutput()

print("Writing output image...") WriterType = rtk.ImageFileWriter[ImageType] writer = WriterType.New() writer.SetFileName("rec.tif") writer.SetInput(feldkamp.GetOutput()) writer.Update()

Regards, Ruslan

[SimonRit]

Hi Ruslan, Thanks for your interest. Can you please post your question on the mailing list? GitHub issues are used to track bugs or feature requests. Thanks, Simon

[Ruslan1541]

Hi, Simon Actually I have already sent a message to rtk-users@public.kitware.com, but I dont know what the status of my question is. Maybe the e-mail address is incorrect? Thank you,

Regards, Ruslan.

[SimonRit]

This mailing list is no longer in use, it's been transferred to my lab CREATIS. Please use rtk-users@openrtk.org which is always redirected to the correct one.