<div dir="ltr"><div>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...</div><div>Simon<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Mar 15, 2023 at 8:51 PM Eldridge, Bryce D <<a href="mailto:bdeldri@sandia.gov">bdeldri@sandia.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg6133853441285447243">
<div style="overflow-wrap: break-word;" lang="EN-US">
<div class="m_6133853441285447243WordSection1">
<p class="MsoNormal">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):<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><img style="width: 7.802in; height: 3.4687in;" id="m_6133853441285447243Picture_x0020_5" src="cid:186fec575b0855d351" width="749" height="333"><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><img style="width: 7.875in; height: 5.1458in;" id="m_6133853441285447243Picture_x0020_6" src="cid:186fec575b29374b62" width="756" height="494"><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div style="border-color:rgb(225,225,225) currentcolor currentcolor;border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in">
<p class="MsoNormal"><b>From:</b> Eldridge, Bryce D <br>
<b>Sent:</b> Wednesday, March 15, 2023 10:48 AM<br>
<b>To:</b> Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>><br>
<b>Cc:</b> <a href="mailto:rtk-users@openrtk.org" target="_blank">rtk-users@openrtk.org</a><br>
<b>Subject:</b> RE: [EXTERNAL] Re: [Rtk-users] Help modifying first reconstruction example to read TIFF projections<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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.
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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.
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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. <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">A couple of spot check values in the image:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Background, X=1458,Y=919, Original pixel value= 60751, ProjectionReader value = 0.0758<u></u><u></u></p>
<p class="MsoNormal">Object, X=855,Y=1952, Original pixel value= 64512, ProjectionReader value = 0.0157<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><img style="width: 4.2395in; height: 3.5625in;" id="m_6133853441285447243Picture_x0020_3" src="cid:186fec575b2a18c373" width="407" height="342"><img style="width: 5.8333in; height: 3.552in;" id="m_6133853441285447243Picture_x0020_4" src="cid:186fec575b3afa3b84" width="560" height="341"><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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. <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Bryce<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<div style="border-color:rgb(225,225,225) currentcolor currentcolor;border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in">
<p class="MsoNormal"><b>From:</b> Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>>
<br>
<b>Sent:</b> Wednesday, March 1, 2023 8:33 AM<br>
<b>To:</b> Eldridge, Bryce D <<a href="mailto:bdeldri@sandia.gov" target="_blank">bdeldri@sandia.gov</a>><br>
<b>Cc:</b> <a href="mailto:rtk-users@openrtk.org" target="_blank">rtk-users@openrtk.org</a><br>
<b>Subject:</b> Re: [EXTERNAL] Re: [Rtk-users] Help modifying first reconstruction example to read TIFF projections<u></u><u></u></p>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">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
<a href="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" target="_blank">
here</a>)?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">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 <a href="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" target="_blank">
rtkfdk</a>.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Simon<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">On Wed, Mar 1, 2023 at 3:46 PM Eldridge, Bryce D <<a href="mailto:bdeldri@sandia.gov" target="_blank">bdeldri@sandia.gov</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border-color:currentcolor currentcolor currentcolor rgb(204,204,204);border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt">
<div>
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<div>
<p class="MsoNormal">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:<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"><img style="width: 8.2083in; height: 5.8645in;" id="m_6133853441285447243m_-469813464391934069Picture_x0020_1" src="cid:186fec575b3bdbb395" width="788" height="563" border="0"><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">But the reconstruction volume still does not look right:<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"><img style="width: 8.2083in; height: 5.8645in;" id="m_6133853441285447243m_-469813464391934069Picture_x0020_2" src="cid:186fec575b31f3c04f6" width="788" height="563" border="0"><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<div style="border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in;border-color:currentcolor">
<p class="MsoNormal"><b>From:</b> Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>>
<br>
<b>Sent:</b> Tuesday, February 28, 2023 10:49 PM<br>
<b>To:</b> Eldridge, Bryce D <<a href="mailto:bdeldri@sandia.gov" target="_blank">bdeldri@sandia.gov</a>><br>
<b>Cc:</b> <a href="mailto:rtk-users@openrtk.org" target="_blank">rtk-users@openrtk.org</a><br>
<b>Subject:</b> Re: [EXTERNAL] Re: [Rtk-users] Help modifying first reconstruction example to read TIFF projections<u></u><u></u></p>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">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...<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Simon<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">On Wed, Mar 1, 2023 at 12:38 AM Eldridge, Bryce D <<a href="mailto:bdeldri@sandia.gov" target="_blank">bdeldri@sandia.gov</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt;border-color:currentcolor currentcolor currentcolor rgb(204,204,204)">
<div>
<div>
<div>
<p class="MsoNormal">I will try writing out the projections and see what I get.
<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">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. <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">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.
<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<div style="border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in;border-color:currentcolor">
<p class="MsoNormal"><b>From:</b> Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>>
<br>
<b>Sent:</b> Tuesday, February 28, 2023 4:33 PM<br>
<b>To:</b> Eldridge, Bryce D <<a href="mailto:bdeldri@sandia.gov" target="_blank">bdeldri@sandia.gov</a>><br>
<b>Cc:</b> <a href="mailto:rtk-users@openrtk.org" target="_blank">rtk-users@openrtk.org</a><br>
<b>Subject:</b> [EXTERNAL] Re: [Rtk-users] Help modifying first reconstruction example to read TIFF projections<u></u><u></u></p>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">Hi,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">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.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Simon<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">On Tue, Feb 28, 2023 at 11:53 PM Eldridge, Bryce D <<a href="mailto:bdeldri@sandia.gov" target="_blank">bdeldri@sandia.gov</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt;border-color:currentcolor currentcolor currentcolor rgb(204,204,204)">
<div>
<div>
<div>
<p class="MsoNormal">Hi,<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">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. <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">It runs without errors, but the reconstructed volume looks very strange which makes me think I am doing something wrong.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">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.
<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"># Defines the image type<u></u><u></u></p>
<p class="MsoNormal">ImageType = itk.Image[itk.F,3]<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"># Defines the RTK geometry object<u></u><u></u></p>
<p class="MsoNormal">geometry = rtk.ThreeDCircularProjectionGeometry.New()<u></u><u></u></p>
<p class="MsoNormal">numberOfProjections = 37<u></u><u></u></p>
<p class="MsoNormal">firstAngle = 0.<u></u><u></u></p>
<p class="MsoNormal">angularArc = 185.<u></u><u></u></p>
<p class="MsoNormal">sid = 914 # source to isocenter distance (mm)<u></u><u></u></p>
<p class="MsoNormal">sdd = 1219 # source to detector distance (mm)<u></u><u></u></p>
<p class="MsoNormal">for x in range(0,numberOfProjections):<u></u><u></u></p>
<p class="MsoNormal"> angle = firstAngle + x * angularArc / numberOfProjections<u></u><u></u></p>
<p class="MsoNormal"> geometry.AddProjection(sid,sdd,angle)<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Skipping some code … (file name list setup, geometry output writing) …<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">tiffio = itk.TIFFImageIO.New()<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">ProjectionsReaderType = rtk.ProjectionsReader[ImageType]<u></u><u></u></p>
<p class="MsoNormal">projectionsSource = ProjectionsReaderType.New()<u></u><u></u></p>
<p class="MsoNormal">projectionsSource.SetImageIO(tiffio)<u></u><u></u></p>
<p class="MsoNormal">projectionsSource.SetFileNames(fileNameList)<u></u><u></u></p>
<p class="MsoNormal">projOrigin = [ -0.14*(3072-1)/2, -0.14*(2560-1)/2, 0 ] #input images are 3072x2560 pixels with a 0.14mm pixel size<u></u><u></u></p>
<p class="MsoNormal">projSpacing = [ 0.14, 0.14, 1.0 ]<u></u><u></u></p>
<p class="MsoNormal">projectionsSource.SetOrigin( projOrigin )<u></u><u></u></p>
<p class="MsoNormal">projectionsSource.SetSpacing( projSpacing )<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">ConstantImageSourceType = rtk.ConstantImageSource[ImageType]<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"># Create reconstructed image<u></u><u></u></p>
<p class="MsoNormal">constantImageSource2 = ConstantImageSourceType.New()<u></u><u></u></p>
<p class="MsoNormal">sizeOutput = [ 512, 512, 512 ]<u></u><u></u></p>
<p class="MsoNormal">origin = [ -255.5, -255.5, -255.5 ]<u></u><u></u></p>
<p class="MsoNormal">spacing = [ 1.0, 1.0, 1.0 ]<u></u><u></u></p>
<p class="MsoNormal">constantImageSource2.SetOrigin( origin )<u></u><u></u></p>
<p class="MsoNormal">constantImageSource2.SetSpacing( spacing )<u></u><u></u></p>
<p class="MsoNormal">constantImageSource2.SetSize( sizeOutput )<u></u><u></u></p>
<p class="MsoNormal">constantImageSource2.SetConstant(0.)<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"># FDK reconstruction<u></u><u></u></p>
<p class="MsoNormal">print("Reconstructing...")<u></u><u></u></p>
<p class="MsoNormal">FDKCPUType = rtk.FDKConeBeamReconstructionFilter[ImageType]<u></u><u></u></p>
<p class="MsoNormal">feldkamp = FDKCPUType.New()<u></u><u></u></p>
<p class="MsoNormal">feldkamp.SetInput(0, constantImageSource2.GetOutput()) # this is the template for the output image type<u></u><u></u></p>
<p class="MsoNormal">feldkamp.SetInput(1, projectionsSource.GetOutput()) # this is the projection stack from rtk.ProjectionsReader<u></u><u></u></p>
<p class="MsoNormal">feldkamp.SetGeometry(geometry)<u></u><u></u></p>
<p class="MsoNormal">feldkamp.GetRampFilter().SetTruncationCorrection(0.0)<u></u><u></u></p>
<p class="MsoNormal">feldkamp.GetRampFilter().SetHannCutFrequency(0.0)<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"># Writer<u></u><u></u></p>
<p class="MsoNormal">print("Writing output image...")<u></u><u></u></p>
<p class="MsoNormal">WriterType = rtk.ImageFileWriter[ImageType]<u></u><u></u></p>
<p class="MsoNormal">writer = WriterType.New()<u></u><u></u></p>
<p class="MsoNormal">writer.SetFileName(sys.argv[1])<u></u><u></u></p>
<p class="MsoNormal">writer.SetInput(feldkamp.GetOutput())<u></u><u></u></p>
<p class="MsoNormal">writer.Update()<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Thanks<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
</div>
<p class="MsoNormal">_______________________________________________<br>
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