[vtkusers] [ITK-users] Reading DICOM series and visualize the volume with VTK
Jon Haitz Legarreta Gorroño
jon.haitz.legarreta at gmail.com
Fri Mar 15 13:52:11 EDT 2019
In fact, VTK also transitioned to discourse a few weeks ago:
https://discourse.vtk.org
So for a better experience and to increase your chances of getting an
answer, you'd better post your question at discourse rather than to
the mailing lists.
HTH,
JON HAITZ
On Fri, Mar 15, 2019 at 12:58 PM Dženan Zukić <dzenanz at gmail.com> wrote:
>
> Hi Marco,
>
> that is more of a VTK question than ITK one, best directed at vtkusers at vtk.org. Also, ITK has migrated to a new forum. Please post further ITK-related questions there instead of this mailing list.
>
> Regards,
> Dženan
>
> On Fri, Mar 15, 2019 at 12:54 PM Marco Festugato <marco.festugato at outlook.it> wrote:
>>
>> Hi Dzenan and thank u for your answer I've tried to do as u suggested, but i receive an error telling me that my mapper doesnt accept ''scalar cells''...maybe this connector doesnt work with my mapper? i've tried to simply add the 'connector' to my pipeline:
>>
>> reader -> connector -> mapper -> volume -> renderer -> window
>>
>> Here's my code if u want to check it (it still needs a bit of cleaning)...i would appreciate it a lot!! I need this to work for my project :'(
>>
>> // VTK includes
>> #include "vtkDICOMImageReader.h"
>> #include "vtkImageData.h"
>> #include "vtkRenderer.h"
>> #include "vtkRenderWindow.h"
>> #include "vtkRenderWindowInteractor.h"
>> #include "vtkVolume.h"
>> #include <vtkInteractorStyleTrackballCamera.h>
>> #include <vtkVolumeProperty.h>
>> #include <vtkSmartPointer.h>
>> #include <vtkPiecewiseFunction.h>
>> #include <vtkVolumeRayCastCompositeFunction.h>
>> #include <vtkFixedPointVolumeRayCastMapper.h>
>> #include <itkImage.h>
>> #include <itkImageFileReader.h>
>> #include <itkImageToVTKImageFilter.h>
>> #include "vtkVersion.h"
>> #include "vtkImageViewer.h"
>> #include "vtkImageMapper3D.h"
>> #include "vtkRenderWindowInteractor.h"
>> #include "vtkSmartPointer.h"
>> #include "vtkImageActor.h"
>> #include "vtkInteractorStyleImage.h"
>> #include "vtkRenderer.h"
>> #include "itkImage.h"
>> #include "itkGDCMImageIO.h"
>> #include "itkGDCMSeriesFileNames.h"
>> #include "itkImageSeriesReader.h"
>> #include "itkImageFileWriter.h"
>>
>> int main(int argc, char *argv[])
>> {
>> // Verify the number of parameters in the command line
>> if( argc < 2)
>> {
>> std::cerr << "Usage: " << std::endl;
>> std::cerr << argv[0] << " DICOMimagesDirectory " << std::endl;
>> return EXIT_FAILURE;
>> }
>> // Software Guide : BeginCodeSnippet
>> typedef signed short PixelType;
>> const unsigned int Dimension = 3;
>> typedef itk::Image< PixelType, Dimension > ImageType;
>> typedef itk::ImageToVTKImageFilter<ImageType> ConnectorType;
>>
>> ConnectorType::Pointer connector = ConnectorType::New();
>>
>> // We use the image type for instantiating the type of the series reader and
>> // for constructing one object of its type.
>>
>> typedef itk::ImageSeriesReader< ImageType > ReaderType;
>> ReaderType::Pointer reader = ReaderType::New();
>>
>> // A GDCMImageIO object is created and connected to the reader. This object is
>> // the one that is aware of the internal intricacies of the DICOM format.
>> //
>>
>> typedef itk::GDCMImageIO ImageIOType;
>> ImageIOType::Pointer dicomIO = ImageIOType::New();
>>
>> reader->SetImageIO( dicomIO );
>>
>> using NamesGeneratorType = itk::GDCMSeriesFileNames;
>> NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
>>
>> nameGenerator->SetUseSeriesDetails( true );
>> nameGenerator->SetDirectory( argv[1] );
>>
>> try
>> {
>> std::cout << std::endl << "The directory: " << std::endl;
>> std::cout << std::endl << argv[1] << std::endl << std::endl;
>> std::cout << "Contains the following DICOM Series: ";
>> std::cout << std::endl << std::endl;
>>
>>
>> // Software Guide : BeginLatex
>> //
>> // The GDCMSeriesFileNames object first identifies the list of DICOM series
>> // present in the given directory. We receive that list in a reference
>> // to a container of strings and then we can do things like print out all
>> // the series identifiers that the generator had found. Since the process of
>> // finding the series identifiers can potentially throw exceptions, it is
>> // wise to put this code inside a \code{try/catch} block.
>> //
>>
>>
>> typedef std::vector< std::string > SeriesIdContainer;
>>
>> const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
>>
>> // Given that it is common to find multiple DICOM series in the same directory,
>> // we must tell the GDCM classes what specific series we want to read. In
>> // this example we do this by checking first if the user has provided a series
>> // identifier in the command line arguments. If no series identifier has been
>> // passed, then we simply use the first series found during the exploration of
>> // the directory.
>>
>>
>> std::string seriesIdentifier;
>>
>> seriesIdentifier = seriesUID.begin()->c_str();
>>
>> std::cout << std::endl << std::endl;
>> std::cout << "Now reading series: " << std::endl << std::endl;
>> std::cout << seriesIdentifier << std::endl;
>> std::cout << std::endl << std::endl;
>>
>>
>> // We pass the series identifier to the name generator and ask for all the
>> // filenames associated to that series. This list is returned in a container of
>> // strings by the \code{GetFileNames()} method.
>>
>>
>> typedef std::vector< std::string > FileNamesContainer;
>> FileNamesContainer fileNames;
>>
>> fileNames = nameGenerator->GetFileNames( seriesIdentifier );
>>
>> //
>> // The list of filenames can now be passed to the \doxygen{ImageSeriesReader}
>> // using the \code{SetFileNames()} method.
>>
>>
>> reader->SetFileNames( fileNames );
>>
>> // Finally we can trigger the reading process by invoking the \code{Update()}
>> // method in the reader. This call as usual is placed inside a \code{try/catch}
>> // block.
>>
>> try
>> {
>> reader->Update();
>> }
>> catch (itk::ExceptionObject &ex)
>> {
>> std::cout << ex << std::endl;
>> return EXIT_FAILURE;
>> }
>> }
>> catch (itk::ExceptionObject &ex)
>> {
>> std::cout << ex << std::endl;
>> return EXIT_FAILURE;
>> }
>>
>> // Visualization pipeline
>>
>> // Create the renderer, render window and interactor
>> vtkRenderer *renderer = vtkRenderer::New();
>> vtkRenderWindow *renWin = vtkRenderWindow::New();
>> renWin->AddRenderer(renderer);
>>
>> vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
>> iren->SetRenderWindow(renWin);
>>
>> // Read the data
>> vtkImageData *input = nullptr;
>>
>> /* vtkDICOMImageReader *reader = vtkDICOMImageReader::New();
>> // vtkTIFFReader *reader = vtkTIFFReader::New();
>> reader->SetFileName(argv[1]); */
>> // reader->Update(); // read data
>>
>>
>> connector->SetInput(reader->GetOutput());
>>
>> // Create our volume and mapper
>> vtkVolume *volume = vtkVolume::New();
>> vtkFixedPointVolumeRayCastMapper *mapper = vtkFixedPointVolumeRayCastMapper::New();
>> // vtkVolumeRayCastCompositeFunction *compositeFunction = vtkVolumeRayCastCompositeFunction::New();
>> vtkInteractorStyleTrackballCamera *styleCamera = vtkInteractorStyleTrackballCamera::New();
>>
>> // connect up the volume to the property and the mapper
>> mapper -> SetInputData( connector -> GetOutput() );
>> mapper -> SetSampleDistance( 0.1 );
>>
>> vtkSmartPointer<vtkVolumeProperty> volumeProperty = vtkSmartPointer<vtkVolumeProperty>::New();
>>
>>
>> volumeProperty->SetInterpolationTypeToLinear(); // better image quality but computation's longer
>>
>>
>> vtkSmartPointer<vtkPiecewiseFunction> scalarOpacity = vtkSmartPointer<vtkPiecewiseFunction>::New();
>> vtkSmartPointer<vtkPiecewiseFunction> gradientOpacity = vtkSmartPointer<vtkPiecewiseFunction>::New();
>>
>> scalarOpacity->AddPoint(0, 0.00);
>> scalarOpacity->AddPoint(500, 0.15);
>> scalarOpacity->AddPoint(1000, 0.15);
>> scalarOpacity->AddPoint(1150, 0.85);
>>
>>
>> gradientOpacity->AddPoint(0, 0.0);
>> gradientOpacity->AddPoint(90, 0.5);
>> gradientOpacity->AddPoint(100, 1.0);
>>
>>
>> //set the transfer functions to the property
>> volumeProperty->SetScalarOpacity(scalarOpacity);
>> volumeProperty->SetGradientOpacity(gradientOpacity);
>>
>> //set the property to the volume
>>
>> volume->SetProperty(volumeProperty);
>>
>> volume->SetMapper( mapper );
>> iren -> SetInteractorStyle(styleCamera);
>> // Set the default window size
>> renWin->SetSize(600,600);
>>
>> // Add the volume to the scene
>> renderer->AddVolume( volume );
>>
>> // interact with data
>> renWin->Render();
>> iren -> Start();
>>
>>
>> return EXIT_SUCCESS;
>> }
>>
>>
>>
>> Inviato da Outlook
>> ________________________________
>> Da: Dženan Zukić <dzenanz at gmail.com>
>> Inviato: venerdì 15 marzo 2019 17:19
>> A: Marco Festugato
>> Cc: insight-users at itk.org
>> Oggetto: Re: [ITK-users] Reading DICOM series and visualize the volume with VTK
>>
>> Hi Marco,
>>
>> you could combine that example with VTK VolumeRendering example and connect them using ITKVTKGlue.
>>
>> Regards,
>> Dženan
>>
>> On Fri, Mar 15, 2019 at 7:00 AM Marco Festugato <marco.festugato at outlook.it> wrote:
>>
>> Hi guys! I'm very new to ITK-VTK...what i have to do is reading 199 dicom
>> images using ITK and visualize the volume using VTK.
>> Using the example "DicomSeriesReadImageWrite2" im able to read the series
>> and create a 3D volume but i dont know how to visualize it with VTK!
>> Any help? :)
>> Thank u for your time!
>>
>> Inviato da Outlook
>> The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
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