Re: [mitk-users] Cropped planes with curved MPR

Daphné Wallach Fri, 21 Apr 2017 06:24:00 -0700

Dear Stefan,

Thank you for this code snippet!


What is m_TubeSurface?


Le 20/04/2017 à 13:23, Dinkelacker, Stefan a écrit :

Hi again, maybe I actually did something similar. Found a code snippetin my Dropbox, which I called “InitViewWithoutCameraReset”:


typedef mitk::RenderingManager::RenderWindowVector RenderWindowVector;

mitk::RenderingManager* renderingManager =mitk::RenderingManager::GetInstance();

const RenderWindowVector& renderWindows =renderingManager->GetAllRegisteredRenderWindows();


RenderWindowVector::const_iterator end = renderWindows.end();

for (RenderWindowVector::const_iterator it = renderWindows.begin(); it!= end; ++it)


{

      mitk::BaseRenderer* renderer = mitk::BaseRenderer::GetInstance(*it);

mitk::SliceNavigationController* sliceNavigationController =renderer->GetSliceNavigationController();


sliceNavigationController->SetInputWorldGeometry(m_TubeSurface->GetGeometry());

sliceNavigationController->Update();

if (renderer->GetMapperID() == mitk::BaseRenderer::Standard2D)

{

mitk::Stepper* slice = sliceNavigationController->GetSlice();

slice->SetPos(slice->GetSteps() / 2);

}

renderer->GetDisplayGeometry()->Fit();

}

*From:*Dinkelacker, Stefan [mailto:s.dinkelac...@dkfz-heidelberg.de]
*Sent:* Mittwoch, 19. April 2017 12:55
*To:* 'Daphné Wallach'; mitk-users@lists.sourceforge.net
*Subject:* Re: [mitk-users] Cropped planes with curved MPR

Hi, sorry, never did this. Maybe you can look into InitializeViews()and isolate the code that you actually want to execute from the slicereset? Best,


Stefan

*From:*Daphné Wallach [mailto:daphne.wall...@hrv-simulation.com]
*Sent:* Mittwoch, 19. April 2017 11:41

*To:* Dinkelacker, Stefan; mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>

*Subject:* [mitk-users] Cropped planes with curved MPR

Dear Stefan,

I am now using something very similar to the code you sent, andeverything is working perfectly except for one thing: the planar viewsare cropped.

I implemented a class similar to QmitkStdMultiWidget, where eachindividual viewer belongs to a class inheriting QmitkRenderWindow. Ireimplemented the wheelEvent method to scroll along a curve. Theplanes in the 3D viewer are normal, but the images in the individualviewers are cropped (see attached image).

I tried to call a reinit, which solves the cropping problem, but thisunfortunately also resets the slicing to the default one.


This is the code I use to reinitialize the views:

mitk::DataNode::Pointer originalImageNode =_dataStorage->GetNamedNode("originalImage");mitk::RenderingManager::GetInstance()->InitializeViews(originalImageNode->GetData()->GetTimeGeometry(),mitk::RenderingManager::REQUEST_UPDATE_ALL, true);

Do you know how I could recenter the views on my image, withoutresetting the slicing?


Best regards,

Daphné




--
Daphné Wallach
Ingénieur de recherche
http://www.hrv-simulation.com




Le 07/03/2017 à 15:54, Dinkelacker, Stefan a écrit :

    Hi Daphné,

    Sorry for the late answer. We asked around to check if really
    nobody is/was using the curved geometry stuff. Unfortunately not.
    However, I remember that I once implemented a slider in a plugin
    which was supposed to slide through slices along a curved path.
    The path was defined by points (center + 2 points for axes) per
    slice. And here is the snippet (quite old, but shouldn’t be too
    hard to adapt, if necessary at all):

    #include <QmitkRenderWindow.h>

    void QmitkMyPrototypeView::OnSliderValueChanged(int value)

    {

    if (value >= m_SliceOrientations.size())

    return;

    vtkSmartPointer<vtkSphereSource> originSource =
    vtkSmartPointer<vtkSphereSource>::New();

    originSource->SetCenter(

    m_SliceOrientations[value].Origin[0],

    m_SliceOrientations[value].Origin[1],

    m_SliceOrientations[value].Origin[2]);

    originSource->SetRadius(1.0);

    originSource->SetThetaResolution(32);

    originSource->SetPhiResolution(32);

    vtkSmartPointer<vtkSphereSource> xAxisSource =
    vtkSmartPointer<vtkSphereSource>::New();

    xAxisSource->SetCenter(

    m_SliceOrientations[value].Origin[0] +
    m_SliceOrientations[value].XAxis[0] * (0.5 * m_TubeMajorAxis),

    m_SliceOrientations[value].Origin[1] +
    m_SliceOrientations[value].XAxis[1] * (0.5 * m_TubeMajorAxis),

    m_SliceOrientations[value].Origin[2] +
    m_SliceOrientations[value].XAxis[2] * (0.5 * m_TubeMajorAxis));

    xAxisSource->SetRadius(0.5);

    xAxisSource->SetThetaResolution(32);

    xAxisSource->SetPhiResolution(32);

    vtkSmartPointer<vtkSphereSource> zAxisSource =
    vtkSmartPointer<vtkSphereSource>::New();

    zAxisSource->SetCenter(

    m_SliceOrientations[value].Origin[0] +
    m_SliceOrientations[value].ZAxis[0] * (0.5 * m_TubeMinorAxis),

    m_SliceOrientations[value].Origin[1] +
    m_SliceOrientations[value].ZAxis[1] * (0.5 * m_TubeMinorAxis),

    m_SliceOrientations[value].Origin[2] +
    m_SliceOrientations[value].ZAxis[2] * (0.5 * m_TubeMinorAxis));

    zAxisSource->SetRadius(0.5);

    zAxisSource->SetThetaResolution(32);

    zAxisSource->SetPhiResolution(32);

    vtkSmartPointer<vtkAppendPolyData> appendPolyData =
    vtkSmartPointer<vtkAppendPolyData>::New();

    appendPolyData->AddInputConnection(originSource->GetOutputPort(0));

    appendPolyData->AddInputConnection(xAxisSource->GetOutputPort(0));

    appendPolyData->AddInputConnection(zAxisSource->GetOutputPort(0));

    appendPolyData->Update();

    
m_Surface->SetVtkPolyData(static_cast<vtkPolyData*>(appendPolyData->GetOutputDataObject(0)));

    // this->RequestRenderWindowUpdate();

    
this->GetRenderWindowPart()->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SelectSliceByPoint(

    m_SliceOrientations[value].Origin +
    mitk::Vector3D(m_Surface->GetGeometry()->GetOrigin().GetDataPointer()));

    
this->GetRenderWindowPart()->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()->SelectSliceByPoint(

    m_SliceOrientations[value].Origin +
    mitk::Vector3D(m_Surface->GetGeometry()->GetOrigin().GetDataPointer()));

    
this->GetRenderWindowPart()->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()->ReorientSlices(

    m_SliceOrientations[value].Origin +
    mitk::Vector3D(m_Surface->GetGeometry()->GetOrigin().GetDataPointer()),

    m_SliceOrientations[value].XAxis,

    m_SliceOrientations[value].ZAxis);

    }

    *From:*Daphné Wallach [mailto:daphne.wall...@hrv-simulation.com]
    *Sent:* Freitag, 3. März 2017 16:50
    *To:* mitk-users@lists.sourceforge.net
    <mailto:mitk-users@lists.sourceforge.net>
    *Subject:* Re: [mitk-users] Curved MPR

    Dear Mitk users,

    I am still struggling with displaying a curved MPR, based on a set
    of points placed on the axial view by the user.

    I wrote a piece of code similar to the one presented in a quite
    old thread
    
(http://mitk-users.1123740.n5.nabble.com/Curved-MPR-is-cropped-for-some-reason-td2823.html,
    dating back from 2011). The workflow is the following:
     - create a ThinPlateSplineCurvedGeometry
     - give a frameGeometry (the same one as the dicom image) and a
    referenceGeometry to it
     - create a PlaneLandmarkProjector
     - give a projection plane and the landmarks to it
     - give the projector and the landmark to the
    ThinPlateSplineCurvedGeometry
     - compute the geometry of the ThinPlateSplineCurvedGeometry
     - give the ThinPlateSplineCurvedGeometry to the multiWidget
    through SetWorldGeometry3D.

    However, the code crashes on the last instruction
    (SetWorldGeometry3D) with a cryptic message ("0xC0000005: /Access
    violation reading..."/).

    First, is this workflow correct? I saw other examples, where the
    ThinPlateSplineCurvedGeometry was also added to the datastorage (I
    tried it, and the same crash appears).

    Second, I also looked at the code for the curvedmpr pluging (at
    
http://mitk.org/git/?p=MITK.git;a=shortlog;h=refs/heads/bug-10719-curved-mpr-master-integration),
    and I have the impression that the main difference with the
    workflow I use is that the ThinPlateSplineCurvedGeometry is added
    to the datastorage. Moreover, it seems like development was
    stopped in 2014, is that correct?

    I would greatly appreciate any help about the correct workflow to
    display a curved MPR, or comments about my code below.

    Best regards,
    Daphné

    Code snippet:
        mitk::DataNode::Pointer originalImageNode =
    _ds->GetNamedNode("originalImage");
        const mitk::PointSet::DataType::PointsContainer::Pointer
    splineLandmarks = mitk::PointSet::DataType::PointsContainer::New();
    // Get landmarks...

        if (splineLandmarks->Size() != 0 && originalImageNode->GetData())
        {
            mitk::ThinPlateSplineCurvedGeometry::Pointer tpsGeometry =
    mitk::ThinPlateSplineCurvedGeometry::New();
            const mitk::PlaneGeometry *plane =
    
_dataView->GetRenderWindow2()->GetSliceNavigationController()->GetCurrentPlaneGeometry();

            // Set a reference 3D geometry (e.g. Geometry3D of an
    existing image volume)
    tpsGeometry->SetFrameGeometry(originalImageNode->GetData()->GetGeometry());
    tpsGeometry->SetReferenceGeometry(plane->GetReferenceGeometry());

            // Create projector class; target landmarks will be
    projected on
            // a plane to create source landmarks for thin plate spline
            // (plane is a mitk::PlaneGeometry, e.g. one of the standard
            // coronal, sagittal, or transversal planes)
            mitk::PlaneLandmarkProjector::Pointer
    planeLandmarkProjector = mitk::PlaneLandmarkProjector::New();

    planeLandmarkProjector->SetProjectionPlane(plane);
    planeLandmarkProjector->ProjectLandmarks(splineLandmarks);

            // Initialize TPS geometry with projector
    tpsGeometry->SetLandmarkProjector(planeLandmarkProjector);
            tpsGeometry->SetTargetLandmarks(splineLandmarks);
            tpsGeometry->ComputeGeometry();

            mitk::BaseRenderer* mappingRenderer =
    mitk::BaseRenderer::GetInstance(_dataView->mitkWidget2->GetRenderWindow());
            mappingRenderer->SetWorldGeometry3D(tpsGeometry); // Crash
    happens here
        }

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





    Le 02/03/2017 à 14:44, Daphné Wallach a écrit :

        Dear MITK users,

        I am developping an application using MITK as a library, and I
        am currently trying to display a curved MPR, based on a set of
        points placed on the axial view by the user.

        I saw two related questions in the mailing list, but both
        answers were quite dated (2010 and 2014), so things might have
        changed since then. The most recent answer referred to a
        "Curved MPR" plugin, and mentionned it was under developpement.

        Does anybody have news about this plugin?

        Best regards,
        Daphné

--

    Daphné Wallach

    Ingénieur de recherche

    http://www.hrv-simulation.com




--
Daphné Wallach
Ingénieur de recherche
http://www.hrv-simulation.com


--
Daphné Wallach
Ingénieur de recherche
http://www.hrv-simulation.com

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Re: [mitk-users] Cropped planes with curved MPR

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