Hi Tobi,
I tried the code, but get nothing in rendering window.
I am not sure what is going wrong. The data source is in raw format,
309*547*478 (load it through opening mhd file). I read the Geometry Overview in
MITK docs and your last mail, it seems I have to convert the index coordinate
(I think my data are in index coordinate) to world coordinate for reslice.
Here are my code.
QString fileName = QFileDialog::getOpenFileName(this, "Open File", "",
mitk::CoreObjectFactory::GetInstance()->GetFileExtensions());
if (fileName != "")
{
mitk::DataNodeFactory::Pointer nodeReader = mitk::DataNodeFactory::New();
nodeReader->SetFileName(fileName.toUtf8().constData());
nodeReader->Update();
mitk::DataNode::Pointer m_node = nodeReader->GetOutput();
if ( m_node->GetData() = NULL )
{
QMessageBox::critical(this, "Error", "Could not open file");
return;
}
QmitkRenderWindow* m_renderWindow = new QmitkRenderWindow(this); // this
pointer is QMainWindow
mitk::StandaloneDataStorage::Pointer m_DataStorage =
mitk::StandaloneDataStorage::New();
mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(m_node->GetData());
if(!image->IsVolumeSet())
{
QMessageBox::critical(this, "Error", "Fail to get vol");
return;
}
mitk::Vector3D spacing;
spacing[0]=spacing[1]=spacing[2]=1.0;
mitk::PlaneGeometry::Pointer m_planeGeo = mitk::PlaneGeometry::New();
m_planeGeo->Initialize();
m_planeGeo->InitializeStandardPlane(500.0, 500.0, spacing,
mitk::PlaneGeometry::Sagittal, 40, true, false);
m_planeGeo->ChangeImageGeometryConsideringOriginOffset(true);
// I delete your rotation code for test only
mitk::ExtractDirectedPlaneImageFilterNew::Pointer m_extractFilter =
mitk::ExtractDirectedPlaneImageFilterNew::New();
m_extractFilter->SetInput(image);
m_extractFilter->SetCurrentWorldGeometry2D(m_planeGeo);
m_extractFilter->Update();
mitk::Image::Pointer slice = m_extractFilter->GetOutput();
if(!slice->IsValidSlice())
{
QMessageBox::critical(this, "Error", "fail to get slice");
return;
}
mitk::DataNode::Pointer m_node_slice = mitk::DataNode::New();
m_node_slice->SetData(slice);
m_DataStorage->Add(m_node_slice);
m_renderWindow->GetRenderer()->SetDataStorage(m_DataStorage);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
Thanks and have a good weekend
Li
________________________________
发件人: Schröder, Tobias [[email protected]]
发送时间: 2012年3月7日 6:49
收件人: Liu, Li; [email protected]
主题: Re: [mitk-users] extract 2D slice from a 3D image volume along arbitrary
directions
Hi Li,
mitk::PlaneGeometry::InitializePlane is right, but you have to make sure that
it actually is a worldGeometry. As these have some special characteristic you
have do something like this:
mitk::PlaneGeometry::Pointer obliquePlane = mitk::PlaneGeometry::New();
obliquePlane->InitializeStandardPlane(planeSizeX, planeSizeY, spacing,
mitk::PlaneGeometry::Sagittal, zPosition, true, false);//or one of the other
initialize mehtods
obliquePlane->ChangeImageGeometryConsideringOriginOffset(true);
origin = obliquePlane->GetOrigin();
normal = obliquePlane->GetNormal();
normal.Normalize();
origin += normal * spacingInDerectionOfNormal * 0.5;
obliquePlane->SetOrigin(origin);
//that’s the thing about the worldGeometries, they are surrounding the pixel in
two directions but are located in center of the third.
//you have to do this after the initialization, if you are constructing one
from scratch, as an plane is not worldGeometry.
mitk::Vector3D rotationVector;
rotationVector[0] = 0.2;
rotationVector[1] = 0.4;
rotationVector[2] = 0.62;
float degree = 37.0;
//here you have calculate the rotation you need, to define the oblique plane
mitk::RotationOperation* op = new mitk::RotationOperation(mitk::OpROTATE,
obliquePlane->GetCenter(), rotationVector, degree);
obliquePlane->ExecuteOperation(op);
delete op;
Also the origin, the spacing and the size/bounding box should be considered to
be right (proper).
But instead if want to reslice at what the display is showing you can also
retrieve a worldGeometry from the renderer.
I recommend the second version.
The workflow with the filter is:
mitk::ExtractDirectedPlaneImageFilterNew::Pointer extractFilter =
mitk::ExtractDirectedPlaneImageFilterNew::New();
extractFilter::SetInput(yourVolume);
extractFilter::SetCurrentWorldGeometry(yourPlane);
extractFilter:: SetActualInputTimestep(yourTimeStep); //if you are dealing with
4D images
extractFilter::Update();
Image::Pointer slice = newExtractor->GetOutput();
That’s it. Now You can use the slice.
I hope it helps.
Best Regards
Tobi
>-----Ursprüngliche Nachricht-----
>Von: Liu, Li [mailto:[email protected]]<mailto:[mailto:[email protected]]>
>Gesendet: Mittwoch, 7. März 2012 05:54
>An: Schröder, Tobias
>Cc: [email protected]<mailto:[email protected]>
>Betreff: 答复: [mitk-users] extract 2D slice from a 3D image volume along
>arbitrary directions
>Hi Tobi,
>Thanks for your quick reply. Here are some questions about your answer.
>What is a proper initialization for PlaneGeometry? I think you mean
>mitk::PlaneGeometry::InitializePlane, right?
>Setting the position of plane is through
>mitk::BaseRenderer::SetCurrentWorldGeometry2D or
>mitk::ExtractDirectedPlaneImageFilterNew::SetCurrentWorldGeometry2D?
>Now, I load the volume data into mitk::StandaloneDataStorage, but how can I
>set volume data as the input of ExtractDirectedPlaneImageFilterNew.
>Thanks
Li
________________________________________
发件人: Schröder, Tobias [[email protected]]
发送时间: 2012年3月6日 2:11
收件人: Liu, Li;
[email protected]<mailto:[email protected]>
主题: Re: [mitk-users] extract 2D slice from a 3D image volume along arbitrary
directions
Hi Li,
there is a mitk class called ExtractDirectedPlaneImageFilterNew which meets
your needs.
A PlaneGeometry specifies the axes where to reslice at. The plane can be
arbitrary oriented and is set via SetCurrentWorldGeometry2D.
So just initialize a proper PlaneGeometry and set it together with your volume
as the input for the filter.
If this won't help provide me some further infos.
Regards
Tobi
>Von: Liu, Li [mailto:[email protected]]<mailto:[mailto:[email protected]]>
>Gesendet: Montag, 5. März 2012 20:14
>An: [email protected]<mailto:[email protected]>
>Betreff: [mitk-users] extract 2D slice from a 3D image volume along arbitrary
>directions
>Hi,
> I am new to MITK and got a problem. Currently, I am using MITK to construct a
> platform to implement extract arbitrary 2D slice from a 3D image volume (raw
> data format). I looked at the tutorial examples and ext app and all of them
> are only to extract 2D slice along transversal, sagittal and coronal
> direction. For me, they are x,y,z axes. If I want to extract 2D slices along
> other directions than transversal, sagittal and coronal direction, how can I
> do that?
>Thanks
>Li
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