Пример #1
0
static
void SaveSliceOrImageAsPNG(mitk::Image::Pointer image, mitk::Image::Pointer mask, std::string path, int index)
{
  // Create a Standalone Datastorage for the single purpose of saving screenshots..
  mitk::StandaloneDataStorage::Pointer ds = mitk::StandaloneDataStorage::New();
  QmitkRenderWindow renderWindow;
  renderWindow.GetRenderer()->SetDataStorage(ds);

  auto nodeI = mitk::DataNode::New();
  nodeI->SetData(image);
  auto nodeM = mitk::DataNode::New();
  nodeM->SetData(mask);
  ds->Add(nodeI);
  ds->Add(nodeM);

  auto geo = ds->ComputeBoundingGeometry3D(ds->GetAll());
  mitk::RenderingManager::GetInstance()->InitializeViews(geo);

  mitk::SliceNavigationController::Pointer sliceNaviController = renderWindow.GetSliceNavigationController();
  unsigned int numberOfSteps = 1;
  if (sliceNaviController)
  {
    numberOfSteps = sliceNaviController->GetSlice()->GetSteps();
    sliceNaviController->GetSlice()->SetPos(0);
  }

  renderWindow.show();
  renderWindow.resize(256, 256);

  for (unsigned int currentStep = 0; currentStep < numberOfSteps; ++currentStep)
  {
    if (sliceNaviController)
    {
      sliceNaviController->GetSlice()->SetPos(currentStep);
    }

    renderWindow.GetRenderer()->PrepareRender();

    vtkRenderWindow* renderWindow2 = renderWindow.GetVtkRenderWindow();
    mitk::BaseRenderer* baserenderer = mitk::BaseRenderer::GetInstance(renderWindow2);
    auto vtkRender = baserenderer->GetVtkRenderer();
    vtkRender->GetRenderWindow()->WaitForCompletion();

    vtkRenderLargeImage* magnifier = vtkRenderLargeImage::New();
    magnifier->SetInput(vtkRender);
    magnifier->SetMagnification(3.0);

    std::stringstream ss;
    ss << path << "_Idx-" << index << "_Step-"<<currentStep<<".png";
    std::string tmpImageName;
    ss >> tmpImageName;
    auto fileWriter = vtkPNGWriter::New();
    fileWriter->SetInputConnection(magnifier->GetOutputPort());
    fileWriter->SetFileName(tmpImageName.c_str());
    fileWriter->Write();
    fileWriter->Delete();
  }
}
Пример #2
0
//##Documentation
//## @brief Load image (nrrd format) and display it in a 2D view
int main(int argc, char *argv[])
{
  QApplication qtapplication(argc, argv);

  if (argc < 2)
  {
    fprintf(stderr, "Usage:   %s [filename] \n\n", itksys::SystemTools::GetFilenameName(argv[0]).c_str());
    return 1;
  }

  // Register Qmitk-dependent global instances
  QmitkRegisterClasses();

  mitk::StandaloneDataStorage::Pointer ds = mitk::StandaloneDataStorage::New();

  // Load datanode (eg. many image formats, surface formats, etc.)
  mitk::IOUtil::Load(argv[1], *ds);

  // Create a RenderWindow
  QmitkRenderWindow renderWindow;

  // Tell the RenderWindow which (part of) the datastorage to render
  renderWindow.GetRenderer()->SetDataStorage(ds);

  // Initialize the RenderWindow
  auto geo = ds->ComputeBoundingGeometry3D(ds->GetAll());
  mitk::RenderingManager::GetInstance()->InitializeViews(geo);
  // mitk::RenderingManager::GetInstance()->InitializeViews();

  // Add Overlays
  //![TextAnnotation2D]
  // Create a textAnnotation2D
  mitk::TextAnnotation2D::Pointer textAnnotation = mitk::TextAnnotation2D::New();

  textAnnotation->SetText("Test!"); // set UTF-8 encoded text to render
  textAnnotation->SetFontSize(40);
  textAnnotation->SetColor(1, 0, 0); // Set text color to red
  textAnnotation->SetOpacity(1);

  // The position of the Annotation can be set to a fixed coordinate on the display.
  mitk::Point2D pos;
  pos[0] = 10;
  pos[1] = 20;
  textAnnotation->SetPosition2D(pos);

  std::string rendererID = renderWindow.GetRenderer()->GetName();

  // The LayoutAnnotationRenderer can place the TextAnnotation2D at some defined corner positions
  mitk::LayoutAnnotationRenderer::AddAnnotation(
    textAnnotation, rendererID, mitk::LayoutAnnotationRenderer::TopLeft, 5, 5, 1);
  //![TextAnnotation2D]

  //![TextAnnotation3D]
  mitk::PointSet::Pointer pointset = mitk::PointSet::New();

  // This vector is used to define an offset for the annotations, in order to show them with a margin to the actual
  // coordinate.
  mitk::Point3D offset;
  offset[0] = .5;
  offset[1] = .5;
  offset[2] = .5;

  // save references to Annotations so that they do not get deregistered
  std::vector<mitk::TextAnnotation3D::Pointer> annotationReferences;

  // Just a loop to create some points
  for (unsigned long i = 0; i < 10; i++)
  {
    // To each point, a TextAnnotation3D is created
    mitk::TextAnnotation3D::Pointer textAnnotation3D = mitk::TextAnnotation3D::New();
    mitk::Point3D point;
    point[0] = i * 20;
    point[1] = i * 30;
    point[2] = i * -50;
    pointset->InsertPoint(i, point);
    textAnnotation3D->SetText("A Point");

    // The Position is set to the point coordinate to create an annotation to the point in the PointSet.
    textAnnotation3D->SetPosition3D(point);

    // move the annotation away from the actual point
    textAnnotation3D->SetOffsetVector(offset);

    annotationReferences.push_back(textAnnotation3D);
    mitk::ManualPlacementAnnotationRenderer::AddAnnotation(textAnnotation3D, rendererID);
  }

  // Get the MicroserviceID of the registered textAnnotation
  std::string serviceID = textAnnotation->GetMicroserviceID();

  // The AnnotationUtils can retrieve any registered annotations by their microservice ID
  mitk::Annotation *annotation = mitk::AnnotationUtils::GetAnnotation(serviceID);
  // This way, it is possible to change the properties of Annotations without knowing their implementation
  annotation->SetText("changed text!");

  // also show the created pointset
  mitk::DataNode::Pointer datanode = mitk::DataNode::New();
  datanode->SetData(pointset);
  datanode->SetName("pointSet");
  ds->Add(datanode);
  //! [TextAnnotation3D]
  renderWindow.show();
  renderWindow.resize(256, 256);

  renderWindow.show();
  renderWindow.resize(256, 256);

  // cleanup: Remove References to DataStorage. This will delete the object
  ds = nullptr;
}
Пример #3
0
//##Documentation
//## @brief Load image (nrrd format) and display it in a 2D view
int main(int argc, char* argv[])
{
  QApplication qtapplication( argc, argv );

  if (argc < 2)
  {
    fprintf( stderr, "Usage:   %s [filename] \n\n", itksys::SystemTools::GetFilenameName(argv[0]).c_str() );
    return 1;
  }

  // Register Qmitk-dependent global instances
  QmitkRegisterClasses();

  //*************************************************************************
  // Part I: Basic initialization
  //*************************************************************************

  // Create a DataStorage
  // The DataStorage manages all data objects. It is used by the
  // rendering mechanism to render all data objects
  // We use the standard implementation mitk::StandaloneDataStorage.
  mitk::StandaloneDataStorage::Pointer ds = mitk::StandaloneDataStorage::New();


  //*************************************************************************
  // Part II: Create some data by reading a file
  //*************************************************************************

  // Create a DataNodeFactory to read a data format supported
  // by the DataNodeFactory (many image formats, surface formats, etc.)
  mitk::DataNodeFactory::Pointer reader=mitk::DataNodeFactory::New();
  const char * filename = argv[1];
  try
  {
    reader->SetFileName(filename);
    reader->Update();
    //*************************************************************************
    // Part III: Put the data into the datastorage
    //*************************************************************************

    // Add the node to the DataStorage
    ds->Add(reader->GetOutput());
  }
  catch(...)
  {
    fprintf( stderr, "Could not open file %s \n\n", filename );
    exit(2);
  }

  //*************************************************************************
  // Part IV: Create window and pass the datastorage to it
  //*************************************************************************

  // Create a RenderWindow
  QmitkRenderWindow renderWindow;

  // Tell the RenderWindow which (part of) the datastorage to render
  renderWindow.GetRenderer()->SetDataStorage(ds);

  // Initialize the RenderWindow
  mitk::TimeGeometry::Pointer geo = ds->ComputeBoundingGeometry3D(ds->GetAll());
  mitk::RenderingManager::GetInstance()->InitializeViews( geo );
  //mitk::RenderingManager::GetInstance()->InitializeViews();

  // Select a slice
  mitk::SliceNavigationController::Pointer sliceNaviController = renderWindow.GetSliceNavigationController();
  if (sliceNaviController)
    sliceNaviController->GetSlice()->SetPos( 0 );

  //*************************************************************************
  // Part V: Qt-specific initialization
  //*************************************************************************
  renderWindow.show();
  renderWindow.resize( 256, 256 );

  // for testing
  #include "QtTesting.h"
  if (strcmp(argv[argc-1], "-testing") != 0)
    return qtapplication.exec();
  else
    return QtTesting();

  // cleanup: Remove References to DataStorage. This will delete the object
  ds = NULL;
}
Пример #4
0
//##Documentation
//## @brief Change the type of display to 3D
//##
//## As in Step2, load one or more data sets (many image, surface
//## and other formats), but display it in a 3D view.
//## The QmitkRenderWindow is now used for displaying a 3D view, by
//## setting the used mapper-slot to Standard3D.
//## Since volume-rendering is a (rather) slow procedure, the default
//## is that images are not displayed in the 3D view. For this example,
//## we want volume-rendering, thus we switch it on by setting
//## the Boolean-property "volumerendering" to "true".
int main(int argc, char* argv[])
{
  QApplication qtapplication( argc, argv );
  if(argc<2)
  {
    fprintf( stderr, "Usage:   %s [filename1] [filename2] ...\n\n", itksys::SystemTools::GetFilenameName(argv[0]).c_str() );
    return 1;
  }

  // Register Qmitk-dependent global instances
  QmitkRegisterClasses();

  //*************************************************************************
  // Part I: Basic initialization
  //*************************************************************************

  // Create a DataStorage
  mitk::StandaloneDataStorage::Pointer ds = mitk::StandaloneDataStorage::New();

  //*************************************************************************
  // Part II: Create some data by reading files
  //*************************************************************************
  int i;
  for(i=1; i<argc; ++i)
  {
    // For testing
    if(strcmp(argv[i], "-testing")==0) continue;

    // Create a DataNodeFactory to read a data format supported
    // by the DataNodeFactory (many image formats, surface formats, etc.)
    mitk::DataNodeFactory::Pointer nodeReader=mitk::DataNodeFactory::New();
    const char * filename = argv[i];
    try
    {
      nodeReader->SetFileName(filename);
      nodeReader->Update();

      //*********************************************************************
      // Part III: Put the data into the datastorage
      //*********************************************************************

      // Since the DataNodeFactory directly creates a node,
      // use the datastorage to add the read node
      mitk::DataNode::Pointer node = nodeReader->GetOutput();
      ds->Add(node);

      // *********************************************************
      // ****************** START OF NEW PART 1 ******************
      // *********************************************************

      //*********************************************************************
      // Part IV: We want all images to be volume-rendered
      //*********************************************************************

      // Check if the data is an image by dynamic_cast-ing the data
      // contained in the node. Warning: dynamic_cast's are rather slow,
      // do not use it too often!
      mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
      if(image.IsNotNull())
      {
        // Set the property "volumerendering" to the Boolean value "true"
        node->SetProperty("volumerendering", mitk::BoolProperty::New(true));

        // Create a transfer function to assign optical properties (color and opacity) to grey-values of the data
        mitk::TransferFunction::Pointer tf = mitk::TransferFunction::New();
        tf->InitializeByMitkImage ( image );

        // Set the color transfer function AddRGBPoint(double x, double r, double g, double b)
        tf->GetColorTransferFunction()->AddRGBPoint ( tf->GetColorTransferFunction()->GetRange() [0], 1.0, 0.0, 0.0 );
        tf->GetColorTransferFunction()->AddRGBPoint ( tf->GetColorTransferFunction()->GetRange() [1], 1.0, 1.0, 0.0 );

        // Set the piecewise opacity transfer function AddPoint(double x, double y)
        tf->GetScalarOpacityFunction()->AddPoint ( 0, 0 );
        tf->GetScalarOpacityFunction()->AddPoint ( tf->GetColorTransferFunction()->GetRange() [1], 1 );

        node->SetProperty ( "TransferFunction", mitk::TransferFunctionProperty::New ( tf.GetPointer() ) );
      }


      // *********************************************************
      // ******************* END OF NEW PART 1 *******************
      // *********************************************************
    }
    catch(...)
    {
      fprintf( stderr, "Could not open file %s \n\n", filename );
      exit(2);
    }
  }

  //*************************************************************************
  // Part V: Create window and pass the tree to it
  //*************************************************************************

  // Create a renderwindow
  QmitkRenderWindow renderWindow;

  // Tell the renderwindow which (part of) the datastorage to render
  renderWindow.GetRenderer()->SetDataStorage(ds);

  // *********************************************************
  // ****************** START OF NEW PART 2 ******************
  // *********************************************************
  // Use it as a 3D view!
  renderWindow.GetRenderer()->SetMapperID(mitk::BaseRenderer::Standard3D);

  // *********************************************************
  // ******************* END OF NEW PART 2 *******************
  // *********************************************************

  //*************************************************************************
  // Part VI: Qt-specific initialization
  //*************************************************************************
  renderWindow.show();
  renderWindow.resize( 256, 256 );

  mitk::RenderingManager::GetInstance()->RequestUpdateAll();

  // for testing
  #include "QtTesting.h"
  if(strcmp(argv[argc-1], "-testing")!=0)
    return qtapplication.exec();
  else
    return QtTesting();
}
Пример #5
0
//##Documentation
//## @brief Load one or more data sets (many image, surface
//## and other formats) and display it in a 2D view
int main(int argc, char* argv[])
{
    QApplication qtapplication( argc, argv );

    if(argc<2)
    {
        fprintf( stderr, "Usage:   %s [filename1] [filename2] ...\n\n",
                 itksys::SystemTools::GetFilenameName(argv[0]).c_str() );
        return 1;
    }

    // Register Qmitk-dependent global instances
    QmitkRegisterClasses();

    //*************************************************************************
    // Part I: Basic initialization
    //*************************************************************************

    // Create a data storage object. We will use it as a singleton
    mitk::StandaloneDataStorage::Pointer storage = mitk::StandaloneDataStorage::New();

    //*************************************************************************
    // Part II: Create some data by reading files
    //*************************************************************************
    int i;
    for(i=1; i<argc; ++i)
    {
        // For testing
        if(strcmp(argv[i], "-testing")==0) continue;

        // Create a DataNodeFactory to read a data format supported
        // by the DataNodeFactory (many image formats, surface formats, etc.)
        mitk::DataNodeFactory::Pointer nodeReader=mitk::DataNodeFactory::New();
        const char * filename = argv[i];
        try
        {
            nodeReader->SetFileName(filename);
            nodeReader->Update();
            //*********************************************************************
            // Part III: Put the data into the datastorage
            //*********************************************************************

            // Since the DataNodeFactory directly creates a node,
            // use the datastorage to add the read node
            storage->Add(nodeReader->GetOutput());
        }
        catch(...)
        {
            fprintf( stderr, "Could not open file %s \n\n", filename );
            exit(2);
        }
    }

    //*************************************************************************
    // Part IV: Create window and pass the datastorage to it
    //*************************************************************************

    // Create a RenderWindow
    QmitkRenderWindow renderWindow;

    // Tell the RenderWindow which (part of) the datastorage to render
    renderWindow.GetRenderer()->SetDataStorage(storage);

    // Initialize the RenderWindow
    mitk::TimeGeometry::Pointer geo = storage->ComputeBoundingGeometry3D(storage->GetAll());
    mitk::RenderingManager::GetInstance()->InitializeViews( geo );

    // Select a slice
    mitk::SliceNavigationController::Pointer sliceNaviController = renderWindow.GetSliceNavigationController();
    if (sliceNaviController)
        sliceNaviController->GetSlice()->SetPos( 2 );


    //*************************************************************************
    // Part V: Qt-specific initialization
    //*************************************************************************
    renderWindow.show();
    renderWindow.resize( 256, 256 );

    // for testing
#include "QtTesting.h"
    if(strcmp(argv[argc-1], "-testing")!=0)
        return qtapplication.exec();
    else
        return QtTesting();
}
Пример #6
0
//##Documentation
//## @brief Load image (nrrd format) and display it in a 2D view
int main(int argc, char* argv[])
{
  QApplication qtapplication( argc, argv );

  if (argc < 2)
  {
    fprintf( stderr, "Usage:   %s [filename] \n\n", itksys::SystemTools::GetFilenameName(argv[0]).c_str() );
    return 1;
  }

  // Register Qmitk-dependent global instances
  QmitkRegisterClasses();

  //*************************************************************************
  // Part I: Basic initialization
  //*************************************************************************

  // Create a DataStorage
  // The DataStorage manages all data objects. It is used by the
  // rendering mechanism to render all data objects
  // We use the standard implementation mitk::StandaloneDataStorage.
  mitk::StandaloneDataStorage::Pointer dataStorage = mitk::StandaloneDataStorage::New();


  //*************************************************************************
  // Part II: Create some data by reading a file
  //*************************************************************************

  // Create a DataNodeFactory to read a data format supported
  // by the DataNodeFactory (many image formats, surface formats, etc.)
  mitk::DataNodeFactory::Pointer reader=mitk::DataNodeFactory::New();
  const char * filename = argv[1];
  try
  {
    reader->SetFileName(filename);
    reader->Update();
    //*************************************************************************
    // Part III: Put the data into the datastorage
    //*************************************************************************

    // Add the node to the DataStorage
    dataStorage->Add(reader->GetOutput());
  }
  catch(...)
  {
    fprintf( stderr, "Could not open file %s \n\n", filename );
    exit(2);
  }

  //*************************************************************************
  // Part IV: Create window and pass the datastorage to it
  //*************************************************************************

  // Create a RenderWindow
  QmitkRenderWindow renderWindow;

  // Tell the RenderWindow which (part of) the datastorage to render
  renderWindow.GetRenderer()->SetDataStorage(dataStorage);

  // Initialize the RenderWindow
  mitk::TimeSlicedGeometry::Pointer geo = dataStorage->ComputeBoundingGeometry3D(dataStorage->GetAll());
  mitk::RenderingManager::GetInstance()->InitializeViews( geo );
  //mitk::RenderingManager::GetInstance()->InitializeViews();

  // Select a slice
  mitk::SliceNavigationController::Pointer sliceNaviController = renderWindow.GetSliceNavigationController();
  if (sliceNaviController)
    sliceNaviController->GetSlice()->SetPos( 0 );

  //*************************************************************************
  // Part V: Qt-specific initialization
  //*************************************************************************

  //! [CreateOverlayManager]
  mitk::OverlayManager::Pointer OverlayManagerInstance = mitk::OverlayManager::New();
  mitk::BaseRenderer* renderer = mitk::BaseRenderer::GetInstance(renderWindow.GetVtkRenderWindow());
  renderer->SetOverlayManager(OverlayManagerInstance);
  //! [CreateOverlayManager]


  //! [GetOverlayManagerInstance]
  //The id that is passed identifies the correct mitk::OverlayManager and is '0' by default.
  mitk::BaseRenderer* renderer2D = mitk::BaseRenderer::GetInstance(renderWindow.GetVtkRenderWindow());
  mitk::OverlayManager::Pointer overlayManager = renderer2D->GetOverlayManager();
  //! [GetOverlayManagerInstance]


  //! [AddLayouter]
  //This creates a 2DLayouter that is only active for the recently fetched axialRenderer and positione
  mitk::Overlay2DLayouter::Pointer topleftLayouter = mitk::Overlay2DLayouter::CreateLayouter(mitk::Overlay2DLayouter::STANDARD_2D_TOPLEFT(), renderer2D);

  //Now, the created Layouter is added to the OverlayManager and can be referred to by its identification string.
  overlayManager->AddLayouter(topleftLayouter.GetPointer());

  //Several other Layouters can be added to the overlayManager
  mitk::Overlay2DLayouter::Pointer bottomLayouter = mitk::Overlay2DLayouter::CreateLayouter(mitk::Overlay2DLayouter::STANDARD_2D_BOTTOM(), renderer2D);
  overlayManager->AddLayouter(bottomLayouter.GetPointer());
  //! [AddLayouter]


  //! [TextOverlay2D]
  //Create a textOverlay2D
  mitk::TextOverlay2D::Pointer textOverlay = mitk::TextOverlay2D::New();

  textOverlay->SetText("Test!"); //set UTF-8 encoded text to render
  textOverlay->SetFontSize(40);
  textOverlay->SetColor(1,0,0); //Set text color to red
  textOverlay->SetOpacity(1);

  //The position of the Overlay can be set to a fixed coordinate on the display.
  mitk::Point2D pos;
  pos[0] = 10,pos[1] = 20;
  textOverlay->SetPosition2D(pos);

  //Add the overlay to the overlayManager. It is added to all registered renderers automaticly
  overlayManager->AddOverlay(textOverlay.GetPointer());

  //Alternatively, a layouter can be used to manage the position of the overlay. If a layouter is set, the absolute position of the overlay is not used anymore
  //The Standard TopLeft Layouter has to be registered to the OverlayManager first
  overlayManager->AddLayouter(mitk::Overlay2DLayouter::CreateLayouter(mitk::Overlay2DLayouter::STANDARD_2D_TOPLEFT(), renderer2D).GetPointer());
  //! [TextOverlay2D]

  //! [SetLayouterToOverlay]
  //Because a Layouter is specified by the identification string AND the Renderer, both have to be passed to the call.
  overlayManager->SetLayouter(textOverlay.GetPointer(),mitk::Overlay2DLayouter::STANDARD_2D_TOPLEFT(),renderer2D);
  //! [SetLayouterToOverlay]


  //! [TextOverlay3D]
  mitk::PointSet::Pointer pointset = mitk::PointSet::New();

  // This vector is used to define an offset for the annotations, in order to show them with a margin to the actual coordinate.
  mitk::Point3D offset;
  offset[0] = .5;
  offset[1] = .5;
  offset[2] = .5;

  //Just a loop to create some points
  for(int i=0 ; i < 10 ; i++){
    //To each point, a TextOverlay3D is created
    mitk::TextOverlay3D::Pointer textOverlay3D = mitk::TextOverlay3D::New();
    mitk::Point3D point;
    point[0] = i*20;
    point[1] = i*30;
    point[2] = -i*50;
    pointset->InsertPoint(i, point);
    textOverlay3D->SetText("A Point");

    // The Position is set to the point coordinate to create an annotation to the point in the PointSet.
    textOverlay3D->SetPosition3D(point);

    // move the annotation away from the actual point
    textOverlay3D->SetOffsetVector(offset);

    overlayManager->AddOverlay(textOverlay3D.GetPointer());
  }

  // also show the created pointset
  mitk::DataNode::Pointer datanode = mitk::DataNode::New();
  datanode->SetData(pointset);
  datanode->SetName("pointSet");
  dataStorage->Add(datanode);
  //! [TextOverlay3D]
  renderWindow.show();
  renderWindow.resize( 256, 256 );

  return qtapplication.exec();

  // cleanup: Remove References to DataStorage. This will delete the object
  dataStorage = NULL;
}