[Rtk-users] Error Result by using FDK algorithm to Reconstruction 2D X- ray Scan projection images into 2D CT Slice image
何明哲
m10512067 at yuntech.org.tw
Thu Jan 19 09:49:43 CET 2023
HI Simon
thanks a lot for suggestion .
this helped me a lot
Artefact have been removed so much
Thank you very much for your reply
Simon Rit <simon.rit at creatis.insa-lyon.fr> 於 2023年1月13日 週五 下午5:05寫道：
> Hi,
> So this is the same thing for the projections, you probably want to center
> them and set origin to (1152-1)*0.25*-0.5=-143.875. This can be set with
> reader->SetOrigin. The third coordinate of the origin vector is not used
> in the projections images, you can leave it at 0.
> Next is the angular arc. It is less than 360°. You will need to use the
> Parker short scan weighting to reduce these artefacts, see here
> <https://github.com/SimonRit/RTK/blob/master/applications/rtkfdk/rtkfdk.cxx#L100-L115>
> a code example in C++.
> Best regards,
> Simon
>
> On Fri, Jan 13, 2023 at 9:30 AM 何明哲 <m10512067 at yuntech.org.tw> wrote:
>
>> Hi Simon
>>
>> Sure, here is those information for reader->Getoutput()
>>
>> Size(XYZ)-> 1152,1152,270
>> Spacing(XYZ)-> 0.25,025,0.25.
>> Origin(XYZ)-> 143.875,143.875,143.875
>>
>> but your suggestion inspires me a lot ,
>>
>> I was use add TiffimageIO to set size spacing origin to projectionreader
>> source
>>
>> finally ,I can get this (see attached file )
>>
>> Although the image still has a lot of artifact and is not clear enough,
>>
>> Did you have any suggestion for this?
>>
>> but finally it is a huge breakthrough for me
>>
>> thanks for help and reply again
>>
>>
>>
>>
>> Simon Rit <simon.rit at creatis.insa-lyon.fr> 於 2023年1月12日 週四 下午10:57寫道：
>>
>>> Can you provide the size, origin and spacing of reader->GetOutput()?
>>> It's a bit hard to help you without this information.
>>> Simon
>>>
>>> On Thu, Jan 12, 2023 at 11:01 AM 何明哲 <m10512067 at yuntech.org.tw> wrote:
>>>
>>>>
>>>> Dear Simon
>>>>
>>>> Thanks for your reply .Its great help for me!
>>>>
>>>> 1.)I was refer your suggestion and modified the code,
>>>> but the result will be a large blank area and I don't understand why
>>>>
>>>> here is the code and result
>>>>
>>>> sizeOutput[0] = Imagewidth;
>>>> sizeOutput[1] = 1;
>>>> sizeOutput[2] = numberOfProjections;
>>>> spacing[0] = 0.25;
>>>> spacing[1] = 0.25;
>>>> spacing[2] = 0.25;
>>>> origin[0] = (Imagewidth-1)*0.5*spacing[0];
>>>> origin[1] = (Imageheigh-1)*0.5*spacing[1];
>>>> origin[2] = spacing[2]*SliceN*-1;
>>>>
>>>> recoVolume->SetSize(sizeOutput);
>>>> recoVolume->SetSpacing(spacing);
>>>> recoVolume->SetOrigin(origin);
>>>> recoVolume->SetConstant(0.);
>>>>
>>>>
>>>>
>>>> 2.)if you're doing 2D reconstruction, be careful that your projections
>>>> should not be 1D because the backprojection uses a 2D interpolation. It
>>>> should have at least 2 lines.
>>>> --> Yes , I hope I can eventually reconstruct a 2D CT Slice, if my
>>>> read projection step or setting have any problem please let me know,
>>>>
>>>> thanks for your reply
>>>>
>>>> BR,
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Simon Rit <simon.rit at creatis.insa-lyon.fr> 於 2023年1月12日 週四 下午4:30寫道：
>>>>
>>>>> Hi,
>>>>> I'm not sure I have enough information to answer... What I can say is:
>>>>> - that the origin is not set to center your volume, for centering, you
>>>>> should use (size-1)*0.5*spacing
>>>>> - if you're doing 2D reconstruction, be careful that your projections
>>>>> should not be 1D because the backprojection uses a 2D interpolation. It
>>>>> should have at least 2 lines.
>>>>> I hope it helps,
>>>>> Simon
>>>>>
>>>>> On Thu, Jan 12, 2023 at 8:46 AM 何明哲 <m10512067 at yuntech.org.tw> wrote:
>>>>>
>>>>>>
>>>>>> HI Everyone ,
>>>>>>
>>>>>> I have a question
>>>>>> that When I was refer to the official example
>>>>>> "Firstcudareconstruction.cpp",
>>>>>> then I tried to modify the code and reconstruction 2D x ray
>>>>>> projection image to 2D ct slice,
>>>>>> the code is worked but I got the wrong result too,
>>>>>> I don't understand what the problem I'm have ?
>>>>>> it's possible that the setting of reconstruction output image size
>>>>>> or origin is wrong?
>>>>>>
>>>>>> here is my code and result (I was tried to only reconstruction just
>>>>>> a slice NO.100 of the whole volume)
>>>>>>
>>>>>> --------------------------------------------------------------------------------------------
>>>>>> using GeometryType = rtk::ThreeDCircularProjectionGeometry;
>>>>>> GeometryType::Pointer geometry = GeometryType::New();
>>>>>> unsigned int numberOfProjections = 280;
>>>>>> double firstAngle = 0;
>>>>>> double angularArc = 280;
>>>>>> unsigned int sid = 510;
>>>>>> unsigned int sdd = 690;
>>>>>>
>>>>>> for (unsigned int noProj = 0; noProj < numberOfProjections;
>>>>>> noProj++)
>>>>>> {
>>>>>> double angle = firstAngle + noProj * angularArc /
>>>>>> numberOfProjections;
>>>>>> geometry->AddProjection(sid, sdd, angle);
>>>>>> }
>>>>>>
>>>>>> rtk::ThreeDCircularProjectionGeometryXMLFileWriter::Pointer
>>>>>> xmlWriter;
>>>>>> xmlWriter =
>>>>>> rtk::ThreeDCircularProjectionGeometryXMLFileWriter::New();
>>>>>> xmlWriter->SetFilename(".\\RTK_Geometry.xml");
>>>>>> xmlWriter->SetObject(geometry);
>>>>>> xmlWriter->WriteFile();
>>>>>>
>>>>>> using NameGeneratorType = itk::NumericSeriesFileNames;
>>>>>> NameGeneratorType::Pointer nameGenerator = NameGeneratorType::New();
>>>>>>
>>>>>> nameGenerator->SetSeriesFormat(ProjectionInage +"\\%d.tif");
>>>>>> nameGenerator->SetStartIndex(1);
>>>>>> nameGenerator->SetEndIndex(280);
>>>>>> nameGenerator->SetIncrementIndex(1);
>>>>>>
>>>>>> using IutputImageType = itk::CudaImage<float, 3>;
>>>>>> using ReaderType = rtk::ProjectionsReader<IutputImageType>;
>>>>>> ReaderType::Pointer reader = ReaderType::New();
>>>>>> reader->SetFileNames(nameGenerator->GetFileNames());
>>>>>> reader->Update();
>>>>>>
>>>>>> using ConstantImageSourceType =
>>>>>> rtk::ConstantImageSource<OutputImageType>;
>>>>>> ConstantImageSourceType::PointType origin;
>>>>>> ConstantImageSourceType::SpacingType spacing;
>>>>>> ConstantImageSourceType::SizeType sizeOutput;
>>>>>> ConstantImageSourceType::Pointer recoVolume =
>>>>>> ConstantImageSourceType::New();
>>>>>>
>>>>>> sizeOutput[0] = Imagewidth;
>>>>>> sizeOutput[1] = Imageheigh;
>>>>>> sizeOutput[2] = numofproj;
>>>>>> spacing[0] = 0.25;
>>>>>> spacing[1] = 0.25;
>>>>>> spacing[2] = 0.25;
>>>>>> origin[0] = Imagewidth*spacing[0]*0.5*-1;
>>>>>> origin[1] = Imageheigh*spacing[0]*0.5*-1;
>>>>>> origin[2] = spacing[2]*SliceN*-1;
>>>>>>
>>>>>> recoVolume->SetSize(sizeOutput);
>>>>>> recoVolume->SetSpacing(spacing);
>>>>>> recoVolume->SetOrigin(origin);
>>>>>> recoVolume->SetConstant(0);
>>>>>>
>>>>>> using FDKGPUType = rtk::CudaFDKConeBeamReconstructionFilter;
>>>>>> FDKGPUType::Pointer feldkamp = FDKGPUType::New();
>>>>>>
>>>>>> feldkamp->SetInput(0, recoVolume->GetOutput());
>>>>>> feldkamp->SetInput(1, reader->GetOutput());
>>>>>> feldkamp->SetGeometry(geometry);
>>>>>> feldkamp->SetNumberOfThreads(7);
>>>>>> feldkamp->Update();
>>>>>>
>>>>>> using WriterType = itk::ImageFileWriter<OutputImageType>;
>>>>>> WriterType::Pointer writer = WriterType::New();
>>>>>> writer->SetFileName("C:\\RTK.mhd");
>>>>>> writer->SetInput(feldkamp->GetOutput());
>>>>>> writer->Update();
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> it should be look like this
>>>>>>
>>>>>>
>>>>>> thanks for your reply
>>>>>>
>>>>>> BR,
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> rtk-users at openrtk.org
>>>>>> https://www.creatis.insa-lyon.fr/mailman/listinfo/rtk-users
>>>>>>
>>>>>
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