[Rtk-users] [EXTERNAL] Re: Help modifying first reconstruction example to read TIFF projections

Wed Mar 1 15:46:05 CET 2023

Ok, thanks. Writing out the projections like you suggested looks ok, I can load the written projection stack into slicer and the image data looks correct as far as I can tell:

[cid:image001.png at 01D94C11.DB58B880]

But the reconstruction volume still does not look right:

[cid:image002.png at 01D94C11.DB58B880]

From: Simon Rit <simon.rit at creatis.insa-lyon.fr>
Sent: Tuesday, February 28, 2023 10:49 PM
To: Eldridge, Bryce D <bdeldri at sandia.gov>
Cc: rtk-users at openrtk.org
Subject: Re: [EXTERNAL] Re: [Rtk-users] Help modifying first reconstruction example to read TIFF projections

The ProjectionsReader usually takes integer projections as input and convert them to float with the appropriate conversions. So I don't think it is the problem here. To be checked...
Simon

On Wed, Mar 1, 2023 at 12:38 AM Eldridge, Bryce D <bdeldri at sandia.gov<mailto:bdeldri at sandia.gov>> wrote:
I will try writing out the projections and see what I get.

Could it be a data type issue? The images are unsigned short (16-bit grayscale), but I’m using the itk.Image[itk.F,3] type so I’m not sure if the projection reader is defaulting to unsigned short and doing the appropriate conversions or not.

It looks like ITK doesn’t include wrapping support for unsigned short by default, so I’d have to rebuild it to try to test that.

From: Simon Rit <simon.rit at creatis.insa-lyon.fr<mailto:simon.rit at creatis.insa-lyon.fr>>
Sent: Tuesday, February 28, 2023 4:33 PM
To: Eldridge, Bryce D <bdeldri at sandia.gov<mailto:bdeldri at sandia.gov>>
Cc: rtk-users at openrtk.org<mailto:rtk-users at openrtk.org>
Subject: [EXTERNAL] Re: [Rtk-users] Help modifying first reconstruction example to read TIFF projections

Hi,
Maybe you can first check whether the projections are read adequately by adding a line itk.imwrite(projectionsSource)? The ProjectionsReader tries to automatically convert the projections to line integral and it might do something wrong... I don't see what could be wrong in your code.
Simon

On Tue, Feb 28, 2023 at 11:53 PM Eldridge, Bryce D <bdeldri at sandia.gov<mailto:bdeldri at sandia.gov>> wrote:
Hi,

I am trying to modify the first reconstruction example to read a set of 16-bit grayscale TIFF projections that I captured, run the 3D reconstruction, and save the output. The projects are taken at 5 degree increments over a 180 degree arc.

It runs without errors, but the reconstructed volume looks very strange which makes me think I am doing something wrong.

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.

# Defines the image type
ImageType = itk.Image[itk.F,3]

# Defines the RTK geometry object
geometry = rtk.ThreeDCircularProjectionGeometry.New()
numberOfProjections = 37
firstAngle = 0.
angularArc = 185.
sid = 914 # source to isocenter distance (mm)
sdd = 1219 # source to detector distance (mm)
for x in range(0,numberOfProjections):
  angle = firstAngle + x * angularArc / numberOfProjections
  geometry.AddProjection(sid,sdd,angle)

Skipping some code … (file name list setup, geometry output writing) …

tiffio = itk.TIFFImageIO.New()

ProjectionsReaderType = rtk.ProjectionsReader[ImageType]
projectionsSource = ProjectionsReaderType.New()
projectionsSource.SetImageIO(tiffio)
projectionsSource.SetFileNames(fileNameList)
projOrigin = [ -0.14*(3072-1)/2, -0.14*(2560-1)/2, 0 ] #input images are 3072x2560 pixels with a 0.14mm pixel size
projSpacing = [ 0.14, 0.14, 1.0 ]
projectionsSource.SetOrigin( projOrigin )
projectionsSource.SetSpacing( projSpacing )

ConstantImageSourceType = rtk.ConstantImageSource[ImageType]

# Create reconstructed image
constantImageSource2 = ConstantImageSourceType.New()
sizeOutput = [ 512, 512, 512 ]
origin = [ -255.5, -255.5, -255.5 ]
spacing = [ 1.0, 1.0, 1.0 ]
constantImageSource2.SetOrigin( origin )
constantImageSource2.SetSpacing( spacing )
constantImageSource2.SetSize( sizeOutput )
constantImageSource2.SetConstant(0.)

# FDK reconstruction
print("Reconstructing...")
FDKCPUType = rtk.FDKConeBeamReconstructionFilter[ImageType]
feldkamp = FDKCPUType.New()
feldkamp.SetInput(0, constantImageSource2.GetOutput()) # this is the template for the output image type
feldkamp.SetInput(1, projectionsSource.GetOutput()) # this is the projection stack from rtk.ProjectionsReader
feldkamp.SetGeometry(geometry)
feldkamp.GetRampFilter().SetTruncationCorrection(0.0)
feldkamp.GetRampFilter().SetHannCutFrequency(0.0)

# Writer
print("Writing output image...")
WriterType = rtk.ImageFileWriter[ImageType]
writer = WriterType.New()
writer.SetFileName(sys.argv[1])
writer.SetInput(feldkamp.GetOutput())
writer.Update()

Thanks

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