Hi,
You should use SetTruncationCorrection:
http://www.openrtk.org/Doxygen/classrtk_1_1FFTProjectionsConvolutionImageFilter.html#a4115316de11dee455c74ceb96ce40426
ZeroPadFactors only set the amount of zero padding in both directions.
Simon
On Tue, Apr 6, 2021 at 7:53 PM Benjamin W. Maloney <
benjamin.w.maloney...@dartmouth.edu> wrote:
> Hi Simon,
>
> Thanks. This is almost certainly what the issue is
> It's not obvious to me how to do this in C++
>
> I tried:
> feldkamp->GetRampFilter()->SetZeroPadFactors(1);
> and
> feldkamp->GetRampFilter()->SetZeroPadFactors(2);
> but neither seemed to make a difference.
>
> I didn't see any other pad functions though
>
> Thanks!
> Ben
> ------------------------------
> *From:* Simon Rit <simon....@creatis.insa-lyon.fr>
> *Sent:* Friday, April 2, 2021 4:51 PM
> *To:* Benjamin W. Maloney <benjamin.w.maloney...@dartmouth.edu>
> *Cc:* rtk-users@public.kitware.com <rtk-users@public.kitware.com>
> *Subject:* Re: [Rtk-users] Ring artifact even with homogenous valued
> projection
>
> Hi,
> If you pass homogeneous non-zero images, you expect such a ring artefact.
> The reason is that FDK assumes non-truncated projections, i.e., the
> projections should be 0 at the border. If not, then the ramp filtering will
> make a transition from the value to 0.
> Probably, your projections are non-zero on the borders either. This can be
> because they have not been calibrated to line integrals by taking the log
> of the flat field divided by the measure, because they have not been well
> calibrated or because they are truncated (detector too small for the
> object). You can then mitigate the effect by padding with data, see the
> --pad option in rtkfdk.
> Simon
>
> On Fri, Apr 2, 2021 at 7:35 PM Benjamin W. Maloney <
> benjamin.w.maloney...@dartmouth.edu> wrote:
>
> Hi all,
>
> I'm running into an issue where I'm getting a large ring artifact at the
> edge of my reconstructions. It is in the same place regardless of the input
> images (including homogeneous images), so it is something I'm doing wrong
> on the reconstruction side rather than a defective pixel on the detector.
>
> I'm happy to share my input images and output reconstructions if that helps
>
>
> Relevant code:
>
> using GeometryType = rtk::ThreeDCircularProjectionGeometry;
> GeometryType::Pointer geometry = GeometryType::New();
> unsigned int numberOfProjections = (steps_taken+1);
> float firstAngle = 0.;
> float angularArc = 360.132;
>
> const double sid = 306.6; // source to isocenter distance, 306.6mm, 0.3
> pixel size, image binned by 4 in x and y
> const double sdd = 561.3; // 561.3 source to detector distance
>
> const double offsetX_d = 0.;
> const double offsetY_d = 0.;
> const double outOfPlaneAngle = -2.55;
> const double inPlaneAngle = 0.0;
> const double offsetX_s = 0.;
> const double offsetY_s = 0.;
>
>
> for (unsigned int noProj = 0; noProj < numberOfProjections; noProj++)
> {
> double angle = 205 + ((double)noProj * ((double)angularArc /
> ((double)steps_taken + 1))); //Adjust the first number (23 before +) to
> rotate output of reconstruction
>
> geometry->AddProjection(sid, sdd, angle, offsetX_d, offsetY_d,
> outOfPlaneAngle, inPlaneAngle, offsetX_s, offsetY_s);
> }
>
> // Write the geometry to disk
> rtk::ThreeDCircularProjectionGeometryXMLFileWriter::Pointer xmlWriter;
> xmlWriter = rtk::ThreeDCircularProjectionGeometryXMLFileWriter::New();
> xmlWriter->SetFilename("..\\..\\..\\data\\geometry_newSystem_full.xml");
> xmlWriter->SetObject(geometry);
> xmlWriter->WriteFile();
> // Defines the image type
> using ImageType = itk::CudaImage< float, 3 >;
> // Projection Images
>
> using ConstantImageSourceType = rtk::ConstantImageSource< ImageType >;
> ConstantImageSourceType::PointType origin;
> ConstantImageSourceType::SpacingType spacing;
> ConstantImageSourceType::SizeType sizeOutput;
>
> int size_x = 3072 / binn;
> int size_y = 864 / binn;
> int size_z = numberOfProjections;
>
> //Binned x4
> origin[0] = -0.5 * (size_x - 1) * 0.3/4.*binn;
> origin[1] = -0.5 * (size_y - 1) * 0.3/4.*binn;
> origin[2] = 0.;
>
> sizeOutput[0] = size_x;
> sizeOutput[1] = size_y;
> sizeOutput[2] = numberOfProjections;
>
> spacing.Fill(0.3/4.*binn);
>
> // Load in my data
> typedef float PixelType;
> const unsigned char Dimension = 3;
> typedef itk::CudaImage< PixelType, Dimension > ImageType;
> ImageType::Pointer image;
>
> typedef itk::ImageFileReader< ImageType > ReaderType;
> ReaderType::Pointer reader;
> reader = ReaderType::New();
>
> reader->SetFileName(projection_file_r); // bin x4
> reader->Update();
> reader->GetOutput()->SetOrigin(origin);
> reader->GetOutput()->SetSpacing(spacing);
>
> // Create reconstructed image
> ConstantImageSourceType::Pointer constantImageSource2 =
> ConstantImageSourceType::New();
>
> // x4
> sizeOutput.Fill(size_x);
> sizeOutput[1] = size_y;
> origin.Fill(-0.5 * (size_x - 1) * 0.3/4.*binn*sid / sdd);
> origin[1] = (-0.5 * (size_y - 1) * 0.3/4.*binn*sid / sdd);
>
> spacing.Fill(0.3/4.*binn*sid / sdd);
> constantImageSource2->SetOrigin(origin);
> constantImageSource2->SetSpacing(spacing);
> constantImageSource2->SetSize(sizeOutput);
> constantImageSource2->SetConstant(0.);
>
> // FDK reconstruction
> //GPU
> using FDKGPUType = rtk::CudaFDKConeBeamReconstructionFilter;
> FDKGPUType::Pointer feldkamp = FDKGPUType::New();
>
> feldkamp->SetInput(0, constantImageSource2->GetOutput());
> feldkamp->SetInput(1, reader->GetOutput());
> feldkamp->SetGeometry(geometry);
>
>
> using WriterType = itk::ImageFileWriter< ImageType >;
> WriterType::Pointer writer = WriterType::New();
>
> writer->SetFileName(reconstruction_file_w);
>
> writer->SetInput(feldkamp->GetOutput());
> writer->Update();
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