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

Mon Mar 20 12:30:41 CET 2023

I don't know if it is the problem but according to your geometry, if I
haven't done any mistake, you need ~200° of angular coverage
(180+np.arctan(3072*0.14*0.5/1219)*2*180/np.pi) and you only have 185°.
That will be a problem in my opinion...
Simon

On Wed, Mar 15, 2023 at 8:51 PM Eldridge, Bryce D <bdeldri at sandia.gov>
wrote:

> More progress: Added some cropping, and called SetIO(0) on the projection
> reader, this seems to enable the IO estimation filter to run properly. I
> also went back to the non-inverted input projections, and now the filtered
> projections from the reader look like this (which looks correct to me):
>
>
>
>
>
> Added the PSSF filter, although I’m not sure if that is correct or not,
> and I’m still getting a very strange looking reconstructed volume:
>
>
>
>
>
> *From:* Eldridge, Bryce D
> *Sent:* Wednesday, March 15, 2023 10:48 AM
> *To:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Cc:* rtk-users at openrtk.org
> *Subject:* RE: [EXTERNAL] Re: [Rtk-users] Help modifying first
> reconstruction example to read TIFF projections
>
>
>
> Ok, so I finally got to the point where I can run some of this with the
> debugger (had to switch from python to c++ because of various issues), but
> now I can try to figure out why the projections don’t look right.
>
>
>
> I did verify that the projection reader is using unsigned short, which is
> correct, and is writing out float, which also seems correct, and looks like
> it is setting up a scatter correction, IO estimation, and raw to
> attenuation filter. However, I agree it is strange that the air is still
> non-zero, and I also don’t understand why the objects are still darker than
> the air, it seems backwards.
>
>
>
> Here's a picture of the raw projection vs the copy written out by the
> projection reader, I inverted the source (maybe not needed? Got the same
> results with non-inverted input images though) so that white was the dense
> part, but that results in the background being really high.
>
>
>
> A couple of spot check values in the image:
>
>
>
> Background, X=1458,Y=919, Original pixel value= 60751, ProjectionReader
> value = 0.0758
>
> Object, X=855,Y=1952, Original pixel value= 64512, ProjectionReader value
> = 0.0157
>
>
>
>
>
>
>
> If you have any ideas what I should be doing differently let me know,
> otherwise next I’m digging more into the projection reader to see exactly
> how that conversion is happening. Once I get the projections to look right
> I’ll move on to the Parker short scan filtering too.
>
>
>
> Bryce
>
>
>
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Wednesday, March 1, 2023 8:33 AM
> *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
>
>
>
> Is this image the output of the rtk::ProjectionsReader? If so, it does not
> look right because the air seems to be non zero (assuming that white is non
> zero). That should have been done automatically for unsigned short
> projections, I'm not sure what's wrong here. Maybe set the component type
> of your TIFFImageIO (see doxygen here
> <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fitk.org%2FDoxygen%2Fhtml%2Fclassitk_1_1TIFFImageIO-members.html&data=05%7C01%7Cbdeldri%40sandia.gov%7Cf4c94675eb5d4d0d0e2108db1a6a43ee%7C7ccb5a20a303498cb0c129007381b574%7C1%7C0%7C638132815945551072%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iu0GcpIs8y8QTUnsrUyl7zXbSy6d4vamQBwmwiYCNEM%3D&reserved=0>
> )?
>
> The next thing is that the sinogram seems to be incomplete (~180°
> coverage?) which is a problem for FDK and the probable cause for the bright
> streaks. You might want to add a ParkerShortScanImageFilter between the
> output of the ProjectionsReader and the FDK reconstruction, as in rtkfdk
> <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSimonRit%2FRTK%2Fblob%2Fmaster%2Fapplications%2Frtkfdk%2Frtkfdk.cxx%23L101-L115&data=05%7C01%7Cbdeldri%40sandia.gov%7Cf4c94675eb5d4d0d0e2108db1a6a43ee%7C7ccb5a20a303498cb0c129007381b574%7C1%7C0%7C638132815945551072%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OUoVD38udOdOLZtBH8r4zUIq7UzCMOOFDwJcudRchEo%3D&reserved=0>
> .
>
> Simon
>
>
>
> On Wed, Mar 1, 2023 at 3:46 PM Eldridge, Bryce D <bdeldri at sandia.gov>
> wrote:
>
> 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:
>
>
>
>
>
> But the reconstruction volume still does not look right:
>
>
>
>
>
> *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>
> 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>
> *Sent:* Tuesday, February 28, 2023 4:33 PM
> *To:* Eldridge, Bryce D <bdeldri at sandia.gov>
> *Cc:* 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>
> 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
>
>
>
>
>
> _______________________________________________
> Rtk-users mailing list
> rtk-users at openrtk.org
> https://www.creatis.insa-lyon.fr/mailman/listinfo/rtk-users
> <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.creatis.insa-lyon.fr%2Fmailman%2Flistinfo%2Frtk-users&data=05%7C01%7Cbdeldri%40sandia.gov%7Cf4c94675eb5d4d0d0e2108db1a6a43ee%7C7ccb5a20a303498cb0c129007381b574%7C1%7C0%7C638132815945551072%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yZqwWp2Hp%2BS4wdNz5DU%2B2dbuk1nq6QjNEEeFUrXVkeI%3D&reserved=0>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230320/03df0a5c/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image005.png
Type: image/png
Size: 170359 bytes
Desc: not available
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230320/03df0a5c/attachment-0006.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image006.png
Type: image/png
Size: 147701 bytes
Desc: not available
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230320/03df0a5c/attachment-0007.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image007.png
Type: image/png
Size: 279499 bytes
Desc: not available
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230320/03df0a5c/attachment-0008.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image008.png
Type: image/png
Size: 256185 bytes
Desc: not available
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230320/03df0a5c/attachment-0009.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image009.png
Type: image/png
Size: 120376 bytes
Desc: not available
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230320/03df0a5c/attachment-0010.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image010.png
Type: image/png
Size: 298786 bytes
Desc: not available
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230320/03df0a5c/attachment-0011.png>