Hi Felix,
I noticed two thing in your code:
First of all you are setting the spacing of your original image to the plane.
This could be a problem since the spacing is recalculated in case of a rotated
image volume.
Next thing is that you are setting the bounds of the original image which also
could be a problem since the bounds of the plane are changed either after a
rotation.
You can try the following for plane initialization:
cutterPlaneTopRight->InitializeStandardPlane(rightToCenter, down);
cutterPlaneTopRight->SetOrigin(p1);
without setting the bounds.
Regards
Andreas
On 14.01.2013, at 16:11, Félix C. Morency wrote:
> Andreas,
>
> Thank you for your anwser, The solution in WriteBackSegmentationResult is
> great if you PlaneGeometry is aligned with the current axis. However, this is
> not my case.
>
> I define my PlaneGeometry from a T-shaped targed placed in the sagittal view
> [1]. The plane you see is created using
>
> mitk::Point3D p1 = figure->GetWorldControlPoint(0);
> mitk::Point3D p2 = figure->GetWorldControlPoint(1);
> mitk::Point3D center2D = figure->GetWorldControlPoint(2);
>
> //1.1 Setup direction vectors
> mitk::Vector3D rightToCenter = p2 - p1;
> mitk::Vector3D centerToTop = p1 - center2D;
> centerToTop.Normalize();
> rightToCenter.Normalize();
>
> mitk::Vector3D down = itk::CrossProduct(centerToRight,
> centerToTop);
> down.Normalize();
>
> //1.2 Initialize the planes
> mitk::PlaneGeometry::Pointer cutterPlaneTopRight =
> mitk::PlaneGeometry::New();
>
> cutterPlaneTopRight->InitializeStandardPlane(rightToCenter,
> down, &image->GetGeometry()->GetSpacing());
> cutterPlaneTopRight->SetOrigin(p1);
> cutterPlaneTopRight->SetBounds(image->GetGeometry()->GetBounds());
>
>
> where center2D is the top-most point in the image, p2 is the right-most
> point and p1 is the intersection point of the T. As you can see, the plane
> creation works just fine. The plane creation also works if the target is
> rotated [2].
>
> However, if the axis of the volume are rotated, the plane has holes in it [3]
> even if the target itself is not rotated. The plane creation is done using
>
> mitk::ExtractSliceFilter::Pointer slicer =
> mitk::ExtractSliceFilter::New();
> slicer->SetInput(image);
> slicer->SetWorldGeometry(cutterPlaneTopRight);
> slicer->SetVtkOutputRequest(true);
> slicer->Modified();
> slicer->Update();
>
> vtkSmartPointer<vtkImageData> sliceTopRight =
> vtkSmartPointer<vtkImageData>::New();
> sliceTopRight = slicer->GetVtkOutput();
>
> int* dims = sliceTopRight->GetDimensions();
> for (int z = 0; z < dims[2]; ++z)
> {
> for (int y = 0; y < dims[1]; ++y)
> {
> for (int x = 0; x < dims[0]; ++x)
> {
> sliceTopRight->SetScalarComponentFromDouble(x,y,z,0,1.0);
> }
> }
> }
>
> vtkSmartPointer<mitkVtkImageOverwrite> resliceIdx =
> vtkSmartPointer<mitkVtkImageOverwrite>::New();
> resliceIdx->SetOverwriteMode(true);
> resliceIdx->SetInputSlice(sliceTopRight);
> resliceIdx->Modified();
>
> mitk::ExtractSliceFilter::Pointer overwriter =
> mitk::ExtractSliceFilter::New(resliceIdx);
> overwriter->SetInput(image);
> overwriter->SetWorldGeometry(cutterPlaneTopRight);
> overwriter->SetVtkOutputRequest(true);
> overwriter->Modified();
> overwriter->Update();
>
> [1]: http://imgur.com/RPTo2
> [2]: http://imgur.com/JXFyx
> [3]: http://imgur.com/j05lH
>
> Regards,
> -F
>
>
> On Mon, Jan 14, 2013 at 3:43 AM, Fetzer, Andreas
> <[email protected]> wrote:
> Hi Felix,
>
> how do you get the PlaneGeometry which is set for writing the slice? You
> should retrieve the according PlaneGeometry like it is done e.g. in the
> mitkSegTool2D::WriteBackSegmentationResult. If this doesn't solve your
> problem it would be helpful if you could post your code here.
>
> Regards
> Andreas
>
> On 11.01.2013, at 21:15, Félix C. Morency wrote:
>
> > Hi list,
> >
> > I am trying to overwrite a slice of arbitrary orientation in a volume and
> > I'm facing some issues. I based my code on the
> > mitkOverwriteSliceFilterObliquePlaneTest. When my axis planes are oriented
> > by default (axial/coronal/sagittal), everything's going fine and the slice
> > is written properly [1].
> >
> > However, if I change the plane orientations using the coupled crosshair
> > rotation tool, my slice is full of holes [2]. I tried playing with
> > SetInPlaneResampleExtentByGeometry and with SetResliceTransformByGeometry
> > without any luck. My initial guess is that it has something to do with
> > slice sampling and current geometry. Does anyone have a clue on how to
> > solve my problem? The objective is to fill the entire slice with the same
> > value.
> >
> > [1]: http://imgur.com/Ru4Nm
> > [2]: http://imgur.com/FzCwx
> >
> > Regards,
> > --
> > Félix C. Morency, M.Sc.
> > Plateforme d’analyse et de visualisation d’images
> > Centre Hospitalier Universitaire de Sherbrooke
> > Centre de recherche clinique Étienne-Le Bel
> > Local Z5-3031 | 819.346.1110 ext 16634
> > ------------------------------------------------------------------------------
> > Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and
> > much more. Get web development skills now with LearnDevNow -
> > 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts.
> > SALE $99.99 this month only -- learn more at:
> > http://p.sf.net/sfu/learnmore_122812_______________________________________________
> > mitk-users mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/mitk-users
>
>
>
>
> --
> --
> Félix C. Morency, M.Sc.
> Plateforme d’analyse et de visualisation d’images
> Centre Hospitalier Universitaire de Sherbrooke
> Centre de recherche clinique Étienne-Le Bel
> Local Z5-3031 | 819.346.1110 ext 16634
------------------------------------------------------------------------------
Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
MVPs and experts. SALE $99.99 this month only -- learn more at:
http://p.sf.net/sfu/learnmore_122412
_______________________________________________
mitk-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/mitk-users
