Hi Andreas,
Thank you for your suggestions.
Sadly, not setting the bounds of the plane gives me a 1 voxel "plane" [1]
and not setting the spacing in the plane initialization gives me
the exact same problem (holes). In the mean time, I wrote my own plane
writer using PlaneGeometry, Geometry3D and ITK (AccessByItk*). Although, I
really want to know why it doesn't work with the mitkVtkImageOverwrite.
[1]: http://imgur.com/64dc1
-F
On Mon, Jan 14, 2013 at 11:42 AM, Fetzer, Andreas <
[email protected]> wrote:
> 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
> > >
> ------------------------------------------------------------------------------
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> http://p.sf.net/sfu/learnmore_122812_______________________________________________
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> >
> >
> >
> >
> > --
> > --
> > 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
>
>
--
--
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
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