[vtkusers] DICOM data resolution reduction
Glen Lehmann
glehmann at atamai.com
Thu Oct 5 08:35:00 EDT 2006
Hi Aonghus,
To be honest, I don't know if any of the user guides currently cover
the new pipeline architecture. This was covered on the mailing list
numerous times in the recent past, you should be able to search the
mailing list to find this topic.
Personally, I prefer to look through the VTK example and testing code
and search the mailing list archives. Regardless of how you choose to
learn VTK, it is a significant undertaking: there's just a lot of
stuff to know and often there's more than one way to accomplish the
task at hand.
Cheers,
Glen
On 05/10/06, O'Connor, Aonghus <A.OConnor at ucc.ie> wrote:
> Thanks Glen,
> That saved me so much hassle.
> Would you recommend the VTK Users guide for solving these kind of problems?
> Aonghus.
>
>
>
> -----Original Message-----
> From: glehmann.atamai at gmail.com [mailto:glehmann.atamai at gmail.com] On Behalf
> Of Glen Lehmann
> Sent: 05 October 2006 13:10
> To: O'Connor, Aonghus
> Cc: vtkusers at vtk.org
> Subject: Re: [vtkusers] DICOM data resolution reduction
>
> Hi Aonghus,
>
> The simplist way to reduce the size of our input vtkImageData is to
> use vtkImageResample:
>
> vtkImageResample *resample = vtkImageResample::New();
> resample->SetInputConnection( vtkImporter->GetOutputPort() );
> resample->SetAxisMagnificationFactor(0, 0.25);
> resample->SetAxisMagnificationFactor(1, 0.25);
> resample->SetAxisMagnificationFactor(2, 0.25);
>
> Since your data is already in unsigned char format, vtkImageShiftScale
> will not reduce the footprint of your data any further (otherwise it
> could be used to cast your data to unsigned char).
>
> At this point, you still have the original vtkImageData in memory.
> You may also want to do something like:
>
> vtkImageData *resampledData = resample->GetOutput();
> resampledData->Update();
> resampledData->Register(NULL); // break the pipeline
>
> // clean up any objects before the break in the pipeline
> reader->Delete();
> vtkImporter->Delete();
>
> Also note that instead of reducing the size of the vtkImageData, you
> could also reduce the size of the vtkPolyData that's output from your
> contour filter by running vtkDecimatePro.
>
> HTH,
>
> Glen
>
> On 05/10/06, O'Connor, Aonghus <A.OConnor at ucc.ie> wrote:
> >
> >
> >
> >
> > Hi,
> >
> > I have been having difficulty reducing the dataset size of a 512*512*87
> > DICOM dataset.
> >
> >
> >
> > The memory requirement for such a large set are too demanding on my
> > computer. I've set the extent of the dataset to 1 / 4 of the original size
> > and found that I can render this.
> >
> > For the whole set I've been messing with vtkImageShiftScale and
> > vtkImageShrink3D.
> >
> > Here are the steps I take:
> >
> >
> >
> > The following works
> >
> > 1. Read the source files into itk::ImageSeriesReader
> >
> > 2. Connect to vtk Importer via ConnectPipeline
> >
> > 3 Set extent to 1 / 4 of original data set
> >
> > 4. Extract Countour
> >
> > 5. Map to polydata
> >
> > 6. render image
> >
> >
> >
> > The following does not due to memory shortages
> >
> > 1. Read the source files into itk::ImageSeriesReader
> >
> > 2. Connect to vtk Importer via ConnectPipeline
> >
> > 3. Extract Countour
> >
> > 4. Map to polydata
> >
> > 5. render image
> >
> >
> >
> > Attempt to reduce dataset resolution using vtkImageShiftScale (not
> working)
> >
> > 1. Read the source files into itk::ImageSeriesReader
> >
> > 2. Connect to vtk Importer via ConnectPipeline
> >
> > 3 reduce using vtkImageShiftScale
> >
> > 4. Extract Countour
> >
> > 5. Map to polydata
> >
> > 6. render image
> >
> >
> >
> > Attempt to reduce dataset resolution using vtkImageShrink3D (not working)
> >
> > 1. Read the source files into itk::ImageSeriesReader
> >
> > 2. Connect to vtk Importer via ConnectPipeline
> >
> > 3 reduce using vtkImageShrink3D
> >
> > 4. Extract Countour
> >
> > 5. Map to polydata
> >
> > 6. render image
> >
> >
> >
> > Any help is appreciated.
> >
> > Regards Aonghus.
> >
> >
> >
> >
> >
> >
> >
> > typedef signed short PixelType;
> >
> > typedef itk::Image< PixelType, 3> ImageType;
> >
> > typedef itk::ImageSeriesReader< ImageType > ReaderType;
> >
> > typedef std::vector< std::string > FileNamesContainer;
> >
> > typedef itk::GDCMSeriesFileNames NamesGeneratorType;
> >
> > typedef std::vector< std::string > SeriesIdContainer;
> >
> > typedef std::vector< unsigned int> NumSeriesFilesContainer;
> >
> > typedef itk::GDCMImageIO ImageIOType;
> >
> >
> >
> > ReaderType::Pointer *reader;
> >
> > NamesGeneratorType::Pointer *nameGenerator;
> >
> > SeriesIdContainer *SeriesVector;
> >
> > NumSeriesFilesContainer *NumFilesVector;
> >
> >
> >
> > nameGenerator = new NamesGeneratorType::Pointer;
> >
> > (*nameGenerator) = NamesGeneratorType::New();
> >
> > (*nameGenerator)->SetUseSeriesDetails( true );
> >
> > (*nameGenerator)->SetDirectory(
> > "C:\\AOC\\Images\\Bassalt\\06151353" );
> >
> > const SeriesIdContainer & seriesUID =
> > (*nameGenerator)->GetSeriesUIDs();
> >
> >
> >
> > SeriesVector = new SeriesIdContainer();
> >
> > NumFilesVector = new NumSeriesFilesContainer();
> >
> >
> >
> > SeriesIdContainer::const_iterator seriesItr =
> > seriesUID.begin();
> >
> > SeriesIdContainer::const_iterator seriesEnd =
> > seriesUID.end();
> >
> > int counter = 0;
> >
> > while( seriesItr != seriesEnd )
> >
> > {
> >
> > SeriesVector->push_back(seriesUID[counter]);
> >
> > FileNamesContainer fileNames;
> >
> > fileNames = (*nameGenerator)->GetFileNames( seriesUID[counter]
> > );
> >
> > NumFilesVector->push_back(fileNames.size());
> >
> > seriesItr++;
> >
> > counter++;
> >
> > }
> >
> >
> >
> > reader = new ReaderType::Pointer;
> >
> > *reader = ReaderType::New();
> >
> > ImageIOType::Pointer dicomIO = ImageIOType::New();
> >
> > (*reader)->SetImageIO( dicomIO );
> >
> >
> >
> > std::string seriesIdentifier;
> >
> > seriesIdentifier = (*SeriesVector)[1];
> >
> > FileNamesContainer fileNames;
> >
> > fileNames = (*nameGenerator)->GetFileNames( seriesIdentifier );
> >
> > (*reader)->SetFileNames( fileNames );
> >
> > try
> >
> > {
> >
> > (*reader)->Update();
> >
> > }
> >
> > catch (itk::ExceptionObject &ex)
> >
> > {
> >
> > std::cout << ex << std::endl;
> >
> > return EXIT_FAILURE;
> >
> > }
> >
> >
> >
> > // ITK Export
> >
> > typedef itk::VTKImageExport< ImageType > ITKExportType;
> >
> >
> > ITKExportType::Pointer itkVTKExporter= ITKExportType::New();
> >
> > vtkImageImport *vtkImporter = vtkImageImport::New();
> >
> > itkVTKExporter->SetInput((*reader)->GetOutput());
> >
> > ConnectPipelines(itkVTKExporter, vtkImporter);
> >
> > vtkImporter->Update();
> >
> >
> >
> > int ext[6];
> >
> > vtkImporter->GetOutput()->GetWholeExtent(ext);
> >
> >
> > vtkImporter->GetOutput()->SetWholeExtent(ext[0],ext[0]+(ext[1]-ext[0])/4,
> > ext[2],ext[2]+(ext[3]-ext[2])/4,ext[4],ext[4]+(ext[5]-ext[4])/4);
> >
> > vtkImporter->GetOutput()->GetWholeExtent(ext);
> >
> >
> > vtkImporter->GetOutput()->SetScalarTypeToUnsignedChar();
> >
> >
> >
> >
> >
> > /*vtkImageShiftScale *shiftscale = vtkImageShiftScale::New();
> >
> > shiftscale->SetInput(readerDataToCheck);
> >
> > shiftscale->Update();*/
> >
> >
> >
> > /*vtkImageShrink3D* mask = vtkImageShrink3D::New();
> >
> > mask->SetInputConnection(grad->GetOutputPort());
> >
> > mask->SetShrinkFactors(15, 5, 5);*/
> >
> >
> >
> >
> >
> > vtkContourFilter *skinExtractor = vtkContourFilter::New();
> >
> > skinExtractor->SetInputConnection(vtkImporter
> > ->GetOutputPort());
> >
> > skinExtractor->SetValue(0, 500);
> >
> >
> >
> > vtkPolyDataMapper *skinMapper = vtkPolyDataMapper::New();
> >
> > skinMapper->SetInputConnection(skinExtractor->GetOutputPort());
> >
> >
> >
> > vtkActor *skin = vtkActor::New();
> >
> > skin->SetMapper(skinMapper);
> >
> >
> >
> > aRenderer->AddActor(skin);
> >
> > aRenderer->SetActiveCamera(aCamera);
> >
> > aRenderer->Render();
> >
> > aRenderer->ResetCamera ();
> >
> > aCamera->Dolly(1.5);
> >
> > aRenderer->SetBackground(1,1,1);
> >
> > renWin->SetSize(640, 480);
> >
> > aRenderer->ResetCameraClippingRange ();
> >
> > iren->Initialize();
> >
> > iren->Start();
> > _______________________________________________
> > This is the private VTK discussion list.
> > Please keep messages on-topic. Check the FAQ at:
> > http://www.vtk.org/Wiki/VTK_FAQ
> > Follow this link to subscribe/unsubscribe:
> > http://www.vtk.org/mailman/listinfo/vtkusers
> >
> >
> >
>
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