[Rtk-users] error on build rtk in visual studio 2012 when rtk use cuda

Fri Jun 26 01:52:39 EDT 2015

Hi Cyril Mory
I am using example dataset for Varian from RTK website.
But i am using  86 projections insted of 686:
Proj_00000.hnd  , Proj_00008.hnd , Proj_00012.hnd +(steps : 8) ...,
Proj_00280.hnd,  Proj_00288.hnd, ....,Proj_00672.hnd, Proj_00680.hnd
and my geometry file is atached to mail

On Thu, Jun 25, 2015 at 8:25 PM, Yang K Park <theday79 at gmail.com> wrote:

> Hi Safdary,
>
>
>
> I’m a bit confused because the attached source code is not original rtkfdk
> source code.
>
>
>
> So, my point about genuine rtkfdk means,
>
> 1.       Update your rtk source
>
> 2.       Don’t change any source code and just compile them.
>
> 3.       Use the example dataset for Varian from RTK website.
>
> 4.       In the command prompt, run the command line (“rtkfdk …”)
>
>
>
> I guess you already did the above things, and then you could see something
> with CPU option but nothing in your cuda-based reconstruction.
>
>
>
> If that is the case, I’m suspecting your CUDA/Graphic driver and cuda
> implementation such as CUDA-compute_10 error you might have faced during
> RTK compiling.
>
> To be honest, I have no idea how to deal with such issues.(Sorry about
> that)
>
>
>
> Yang
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *From:* safdary mohsen [mailto:ieee.safdary at gmail.com]
> *Sent:* Thursday, June 25, 2015 1:28 AM
> *To:* Yang-Kyun Park
> *Cc:* rtk-users at openrtk.org; Cyril Mory
>
> *Subject:* Re: [Rtk-users] error on build rtk in visual studio 2012 when
> rtk use cuda
>
>
>
> Hi
>
>
>
>  what is genuine rtkfdk.exe ?
>
>
>
> source code is attached to mail and command line is:
>
> rtkfdk --geometry geometry.xml --regexp .*.hnd --path Scan0  --output
> slice30.mha  --verbose  --spacing 0.25,0.25,0.25 --dimension 1024,1,1024
> --origin -127.875,30,-127.875  --hardware cuda
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Wed, Jun 24, 2015 at 5:51 PM, Yang-Kyun Park <theday79 at gmail.com>
> wrote:
>
> Hi Safdary,
>
> So you might have tried the genuine rtkfdk.exe for your recon. Would you
> give me your command line you used?
>
> Yang
>
> On Jun 24, 2015 3:48 AM, "safdary mohsen" <ieee.safdary at gmail.com> wrote:
>
> Hi
>
>
>
> I cheched projectionreader and i abtained that all projection are readed.
>
> ( by using:
>
> typedef itk::ImageFileWriter<OutputImageType> WriterType;
>
> WriterType::Pointer writer = WriterType::New();
>
> writer->SetFileName( "reader.mha" );
>
> writer->SetInput( reader->GetOutput() );
>
> writer->Update();
>
> )
>
>
>
> and
>
>
>
> geometry is work for cpu mode means outputs are ok .
>
>
>
>
>
> I am confused for solving this problem!!!!!!!!!!!!!!!!!
>
>
>
> On Tue, Jun 16, 2015 at 11:09 AM, Cyril Mory <
> cyril.mory at creatis.insa-lyon.fr> wrote:
>
> Hi Safdary,
>
> Just to be sure: have you tried reconstructing in a larger volume
> (something really huge), just to make sure you are not trying to
> reconstruct some portion of space where, indeed, there is nothing ?
> You can try that easily, just replace your spacing, dimension and origin
> with
> --spacing 16,16,16 --dimension 256,256,256 --origin -2040,-2040,-2040
> in your rtkfdk command line.
>
> Cyril
>
>
>
> On 06/15/2015 05:19 PM, safdary mohsen wrote:
>
> Hi Yang
>
>
>
>
>
> I am use rtkfdk.exe but the results are same as  my code,
>
> means all pixels are zero!!!
>
>
>
> regards
>
>
>
> safdari
>
>
>
> On Mon, Jun 15, 2015 at 7:10 PM, Yang K Park <theday79 at gmail.com> wrote:
>
> Hi Safdary,
>
>
>
> Again, please cc rtk-users at openrtk.org when you send your email, since
> other users (much better experts than me!) can give us any suggestions.
>
>
>
> Thanks.
>
>
>
> Yang
>
>
>
> *From:* Yang K Park [mailto:theday79 at gmail.com]
> *Sent:* Monday, June 15, 2015 10:37 AM
> *To:* 'safdary mohsen'
> *Cc:* rtk-users at openrtk.org
> *Subject:* RE: [Rtk-users] error on build rtk in visual studio 2012 when
> rtk use cuda
>
>
>
> Hi Safdary,
>
>
>
> I recommend you to try rtkfdk.exe first (with cuda option) to see if it
> works for you.
>
>
>
> The example of the command line would be:
>
>
>
> rtkfdk --geometry geom.xml --path proj_dir --regexp .*.his --output
> test_output.mha --verbos  --spacing 1,1,1 --dimension 512,10,512 --origin
> -127.875,29.5,-127.875 --hardware cuda
>
>
>
> If it works for your image, then you can mimic the original rtkfdk code to
> make your own one.
>
>
>
> Good luck!
>
>
>
> Yang
>
>
>
>
>
>
>
>
>
> *From:* safdary mohsen [mailto:ieee.safdary at gmail.com
> <ieee.safdary at gmail.com>]
> *Sent:* Saturday, June 13, 2015 11:58 PM
> *To:* Yang K Park
> *Subject:* Re: [Rtk-users] error on build rtk in visual studio 2012 when
> rtk use cuda
>
>
>
> Hi Yang
>
>
>
> I have tried to adjust the window/level to see something inside of the
> image but all pixels set to zero.
>
> *My code is:*
>
> #define USE_CUDA
>
> int main(int , char **)
>
> {
>
> //// variable
>
> const unsigned int Dimension = 3;
>
> typedef float OutputPixelType;
>
> #ifdef USE_CUDA
>
> typedef itk::CudaImage< OutputPixelType, Dimension > OutputImageType;
>
> #else
>
> typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>
> #endif
>
>
> ////////////////////////////////////////////////////////////////////////////////////////////////////
>
> // Generate file names of projections
>
> itk::RegularExpressionSeriesFileNames::Pointer names = itk::
> RegularExpressionSeriesFileNames::New();
>
> names->SetDirectory(std::string("d://RTK/build/bin/Release/Scan1/"));
>
> names->SetRegularExpression(std::string("Proj_.*.hnd"));
>
>
> ////////////////////////////////////////////////////////////////////////////////////////////////////
>
> //// geometry
>
> // Defines the RTK geometry object
>
> typedef rtk::ThreeDCircularProjectionGeometry GeometryType;
>
> GeometryType::Pointer geometry = GeometryType::New();
>
> // Projection matrices
>
> unsigned int numberOfProjections = 86;
>
> unsigned int firstAngle = 0;
>
> unsigned int angularArc = 360;
>
> unsigned int sid = 1000;
>
> unsigned int sdd = 1200;
>
> int isox = 0;
>
> int isoy = 0 ;
>
> for(unsigned int noProj=0; noProj<numberOfProjections; noProj++)
>
> {
>
> double angle = (float)firstAngle + (float)noProj * angularArc / (float
> )numberOfProjections;
>
> geometry->AddProjection(sid,
>
> sdd,
>
> angle,
>
> isox,
>
> isoy);
>
> }
>
>
> /////////////////////////////////////////////////////////////////////////////////////////////////////
>
>
> ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
> // Projections reader
>
> typedef rtk::ProjectionsReader< OutputImageType > ReaderType;
>
> ReaderType::Pointer reader = ReaderType::New();
>
> reader->SetFileNames(names->GetFileNames());
>
> ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
>
> // Create reconstructed image ////////////////////////////////////
>
> typedef rtk::ConstantImageSource< OutputImageType >
> ConstantImageSourceType;
>
> ConstantImageSourceType::Pointer ImageSource = ConstantImageSourceType
> ::New();
>
> ConstantImageSourceType::PointType origin;
>
> ConstantImageSourceType::SizeType sizeOutput;
>
> ConstantImageSourceType::SpacingType spacing;
>
> origin[0] = -127.75;
>
> origin[1] = -127.75;
>
> origin[2] = -127.75;
>
>
>
> sizeOutput[0] = 512;
>
> sizeOutput[1] = 512;
>
> sizeOutput[2] = 512;
>
> spacing[0] = .5;
>
> spacing[1] = .5;
>
> spacing[2] = .5;
>
> ImageSource->SetOrigin( origin );
>
> ImageSource->SetSpacing( spacing );
>
> ImageSource->SetSize( sizeOutput );
>
> ImageSource->SetConstant( 0. );
>
> // getchar(); //////////////////////////////////////
>
> /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
>
>
> std::cout << "Performing reconstruction" << std::endl;
>
> // FDK reconstruction filtering
>
> // FDK reconstruction filtering
>
> #ifdef USE_CUDA
>
> typedef rtk::CudaFDKConeBeamReconstructionFilter FDKType;
>
> #elif USE_OPENCL
>
> typedef rtk::OpenCLFDKConeBeamReconstructionFilter FDKType;
>
> #else
>
> typedef rtk::FDKConeBeamReconstructionFilter< OutputImageType > FDKType;
>
> #endif
>
> FDKType::Pointer feldkamp = FDKType::New();
>
> feldkamp->SetInput( 0, ImageSource->GetOutput() );
>
> feldkamp->SetInput( 1, reader->GetOutput());
>
> feldkamp->SetGeometry( geometry);
>
> TRY_AND_EXIT_ON_ITK_EXCEPTION( feldkamp->Update() );
>
> std::cout << "Writing output image" << std::endl;
>
> // Writer
>
> typedef itk::Image< float, 3 > ImageType;
>
> typedef itk::ImageFileWriter<ImageType> WriterType;
>
> WriterType::Pointer writer = WriterType::New();
>
> writer->SetFileName( "output11.mha" );
>
> writer->SetInput( feldkamp->GetOutput() );
>
> writer->Update();
>
>
>
> getchar();
>
> return 0;
>
> }
>
>
>
>
>
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>
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>
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>
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