Hi Mathias,
I have tried your code and could indeed get a somewhat curved intersection
plane that way.
Unfortunately, the constructed vtkThinSplineTransform does not describe the
curved plane that I would like to obtain. I would like to define a curved
intersection plane that is planar in one direction and curved only in the other.
I therefore tried to use mitk::ExternAbstractTransformGeometry to define my own
transform. I tried to understand the MITK code in order to mimick
mitk::ThinPlateSplineCurvedGeometry.
To my understanding, the mapper request an intensity value at a 2D coordinate
which is mapped by a plane geometry to a 3D coordinate which is mapped by the
VTK transform to another 3D coordinate from which the image intensity is
obtained. Still it is not clear to me, what the ranges of the respective
coordinates should be and how to set up the plane in order to get a correctly
rendered result.
Right now, I can only see parts of the curved plane and if I rotate the 3D
view, things vanish and reappear. If, in the data manager, I click the "global
reinit" button the rendering is right again but the additional plane in the 3D
view is straight again and at the bottom of the image. Apparently, I am doing
something wrong.
If you have any idea from the above description what I am doing wrong, I would
appreciate any hint. I would also be happy, if you could give me a
description/example on how to use mitk::ExternAbstractTransformGeometry.
Thank you,
Michael Kelm.
________________________________
From: Seitel Mathias [mailto:[email protected]]
Sent: Friday, November 13, 2009 4:39 PM
To: Kelm, Michael; [email protected]
Subject: RE: Curved MPR
Hi Michael,
It seems a few things are still missing in your code. In your initialization
code, could you try the following:
// Set a reference 3D geometry (e.g. Geometry3D of an existing image volume)
tpsGeometry->SetFrameGeometry(imagegeometry)
// Set stiffness of spline (optional)
tpsGeometry->SetSigma(sigma);
// 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)
planeLandmarkProjector = mitk::PlaneLandmarkProjector::New();
planeLandmarkProjector ->SetProjectionPlane( plane );
// Initialize TPS geometry with projector
tpsGeometry->SetLandmarkProjector(m_PlaneLandmarkProjector);
For rebuilding the TPS surface, call
m_TPSGeometry->ComputeGeometry();
Also, you need to use a properly initialized and rendered GeometryData. The
easiest way is to use an existing GeometryData object from one of the render
windows. The 3D render window (widget4) can be used, since changing its 2D
Geometry has no other effect. Of course, a new separate plane can also be
created with a bit more work, but this would help you getting started:
// Get renderer from widget4 (3D render window)
m_MappingRenderer =
mitk::BaseRenderer::GetInstance(multiWidget->mitkWidget4->GetRenderWindow());
// Get geometry2DData from it and set necessary properties
mitk::DataTreeNode::Pointer tpsGeometryDataNode =
m_MappingRenderer->GetCurrentWorldGeometry2DNode();
tpsGeometryDataNode ->SetIntProperty("xresolution", 200); // x-resolution for
rendering the curved plane
tpsGeometryDataNode ->SetIntProperty("yresolution", 200); // y-resolution for
rendering the curved plane
tpsGeometryDataNode ->SetProperty( "name", mitk::StringProperty::New( "curved
plane" ) );
// For convenience: exclude extent of this plane when calculating DataTree
bounding box
tpsGeometryDataNode ->SetProperty("includeInBoundingBox",
mitk::BoolProperty::New(false));
child->Add(tpsGeometryDataNode);
// Set new 2D geometry for this mapper (required for the
Geometry2DDataVtkMapper3D)
m_MappingRenderer->SetWorldGeometry(m_TPSGeometry);
Hope that helps, please let us know if you run into further issues.
Regards,
Mathias
From: Kelm, Michael [mailto:[email protected]]
Sent: Thursday, November 12, 2009 5:26 PM
To: Seitel Mathias; [email protected]
Subject: RE: Curved MPR
Hi Mathias,
thank you for your quick help. I tried the following:
// setup TPS transform
mitk::ThinPlateSplineCurvedGeometry::Pointer pTPS =
mitk::ThinPlateSplineCurvedGeometry::New();
pTPS->SetTargetLandmarks(m_pSelectedPntSet->GetPointSet()->GetPoints());
// create mitk::GeometryData
mitk::GeometryData::Pointer pGeometryData = mitk::GeometryData::New();
pGeometryData->SetGeometry(pTPS);
// replace data tree node
mitk::DataTreeHelper::RemoveNode("CurvedMPR");
mitk::DataTreeNode::Pointer pNode = mitk::DataTreeNode::New();
pNode->SetData(pGeometryData);
mitk::DataTreeHelper::AddNode("CurvedMPR",pNode);
The node appears in the data tree but does not have any effect. Is there a
special way I have to insert the node?
Does it matter whether it is in front of or behind the image volume? Added to
the root or to the image node?
Thank you,
Michael.
________________________________
From: Seitel Mathias [mailto:[email protected]]
Sent: Thursday, November 12, 2009 10:05 AM
To: Kelm, Michael; [email protected]
Subject: RE: Curved MPR
Hi Michael,
MITK does support curved MPRs. They integrate nicely into the geometry
framework of MITK: The class mitk::ThinPlateSplineCurvedGeometry derives from
mitk::Geometry2D and thus represents a curved 2D plane in space. The spline
geometry is defined by landmarks in 3D space.
Curved MPRs can be visualized using the mappers mitk::Geometry2DDataMapper2D
(for flat mappings in 2D views) and mitk::Geometry2DDataVtkMapper3D (for curved
mappings in 3D views). To do so, an mitk::GeometryData object containing a
properly initialized instance of mitk::ThinPlateSplineCurvedGeometry needs to
be created and inserted into the DataStorage. The mapper then reslices all
visible data with this curved 2D plane (in the same way as the "normal" 2D
geometries for transversal, sagittal and coronal directions are displayed).
Regards,
Mathias
From: Kelm, Michael [mailto:[email protected]]
Sent: Thursday, November 12, 2009 9:44 AM
To: [email protected]
Subject: [mitk-users] Curved MPR
Hi,
Does MITK support curved MPRs?
If not, what would be the best way to implement that? Would I have to write a
new Mapper2D?
How could I use of such a new 2D mapper for volume data?
Thanks,
Michael.
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