[vtkusers] DICOM data resolution reduction

Amy Squillacote amy.squillacote at kitware.com
Thu Oct 5 09:06:50 EDT 2006


Actually, the latest version of "The VTK User's Guide", updated for VTK 
5 and available as of last week, devotes a whole chapter to the new 
pipeline architecture. There's also some more discussion of the pipeline 
in the chapter about writing a vtkAlgorithm.

- Amy

Glen Lehmann wrote:
> 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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