[vtkusers] Problem with vtkPolyDataToImageStencil in 5.8
Jothybasu Selvaraj
jothybasu at gmail.com
Fri Mar 9 16:24:19 EST 2012
Hi David,
Some stunning revelation here!
The problem is because of the inconsistence between the DICOM tags Slice
thickness and ImagePositionPatient
Slice thickness says it's 3mm, but the z difference between two slices
according to their IPP is 2.5 mm.
If I set the extrude->SetVector(0,0,-2.5).
It works perfectly!
How can it happen in DICOM? Probably, that's the reason why other datasets
worked form me with the new vtkPolydataToImageStencil.
Can someone shed light on this?
Many thanks again
Jothy
On Fri, Mar 9, 2012 at 8:36 PM, David Gobbi <david.gobbi at gmail.com> wrote:
> Hi Jothy,
>
> Remove the extrude filter from the pipeline.
>
> - David
>
>
> On Fri, Mar 9, 2012 at 1:29 PM, Jothybasu Selvaraj <jothybasu at gmail.com>
> wrote:
> > Hi David,
> >
> > I am still not able to fix this issue.
> >
> > This is how I create the polydata and other pipeline.
> >
> > vtkSmartPointer<vtkPoints> points =
> >
> > vtkSmartPointer<vtkPoints>::New();
> >
> > vtkSmartPointer<vtkCellArray> cells =
> >
> > vtkSmartPointer<vtkCellArray>::New();
> >
> > points->SetNumberOfPoints(npts+1);
> >
> > cells->InsertNextCell(npts+1);
> >
> > for(int p=0;p<npts;p++)
> >
> > {
> >
> >
> >
> > points->SetPoint( p, Xp, Yp,Zp );
> >
> > cells->InsertCellPoint( p );
> >
> > }
> >
> > cells->InsertCellPoint(npts);
> >
> > points->SetPoint(npts,pts[0],pts[1],pts[2]);//close
> contour
> >
> >
> > vtkSmartPointer<vtkPolyData>polydataContour=
> >
> > vtkSmartPointer<vtkPolyData>::New();
> >
> > polydataContour->Initialize();
> >
> > polydataContour->SetLines(cells);
> >
> > polydataContour->SetPoints(points);
> >
> >
> > //Here all contours are appended to vtkAppendPolydataFilter
> >
> > vtkSmartPointer<vtkPolyDataToImageStencil> sts=
> > vtkSmartPointer<vtkPolyDataToImageStencil>::New();
> > sts->SetTolerance(1e-6);//very important
> > sts->SetInformationInput(binary_image);
> > vtkSmartPointer<vtkLinearExtrusionFilter> extrude=
> > vtkSmartPointer<vtkLinearExtrusionFilter>::New();
> > extrude->SetInput(appender->GetOutput());
> > extrude->CappingOff();//also tried ON
> > extrude->SetVector(0, 0,-zSpacing);//Correct Z spacing is
> > important
> > //qDebug()<<-zSpacing<<"-ve zSpacing";
> > sts->SetInput(extrude->GetOutput());
> >
> >
> > //qDebug()<<t->currentTime()<<"Stencil start";
> > vtkSmartPointer<vtkImageStencil> stencil=
> > vtkSmartPointer<vtkImageStencil>::New();
> > stencil->SetStencil(sts->GetOutput());
> > stencil->SetInput(binary_image);
> > stencil->ReverseStencilOn();
> > stencil->Update();
> >
> >
> > I am able to visualize the contour by setting appendFilter->GetOutput()
> to a
> > vtkPolyDataMapper.
> >
> > Is there any thing wrong.
> >
> > Thanks very much!
> >
> > Jothy
> >
> >
> >
> >
> > On Tue, Mar 6, 2012 at 3:48 PM, David Gobbi <david.gobbi at gmail.com>
> wrote:
> >>
> >> You'd have to use SetLines() instead of SetPolys(). And for
> >> polylines, the final point in the polyline has to connect to the first
> >> line to create a closed loop, so polylines cell arrays need an extra
> >> entry as compared to polygon cell arrays.
> >>
> >> On Tue, Mar 6, 2012 at 8:36 AM, Jothybasu Selvaraj <jothybasu at gmail.com
> >
> >> wrote:
> >> > I ma creating the polydat per conoutr like this
> >> >
> >> > vtkSmartPointer<vtkPolyData>polydataContour=
> >> >
> >> > vtkSmartPointer<vtkPolyData>::New();
> >> >
> >> > polydataContour->Initialize();
> >> >
> >> > polydataContour->SetPolys( cells );//vtkCellArray
> >> >
> >> > polydataContour->SetPoints( points);//vtkPoints
> >> >
> >> >
> >> > How should I do that?
> >> >
> >> > Thanks very much
> >> >
> >> > Jothy
> >> >
> >> >
> >> > On Tue, Mar 6, 2012 at 3:31 PM, David Gobbi <david.gobbi at gmail.com>
> >> > wrote:
> >> >>
> >> >> The contours must be polylines, not polygons, or it won't work.
> >> >>
> >> >> On Tue, Mar 6, 2012 at 6:29 AM, Jothybasu Selvaraj
> >> >> <jothybasu at gmail.com>
> >> >> wrote:
> >> >> > Yes, I have one contour for each z slice as a vtkPolyData. I will
> try
> >> >> > removing that.
> >> >> >
> >> >> > Thanks
> >> >> >
> >> >> >
> >> >> > On Tue, Mar 6, 2012 at 1:26 PM, David Gobbi <david.gobbi at gmail.com
> >
> >> >> > wrote:
> >> >> >>
> >> >> >> Do you have one contour for each Z slice? If so, then try
> removing
> >> >> >> the Extrude filter from your pipeline.
> >> >> >>
> >> >> >>
> >> >> >> On Tue, Mar 6, 2012 at 2:51 AM, Jothybasu Selvaraj
> >> >> >> <jothybasu at gmail.com>
> >> >> >> wrote:
> >> >> >> > Another point here,
> >> >> >> >
> >> >> >> > I am creating a vtkPolyData for each contour and then adding it
> to
> >> >> >> > the
> >> >> >> > vtkAppendPolydataFilter, then the output of
> vtkAppenPolydataFilter
> >> >> >> > is
> >> >> >> > set as
> >> >> >> > input to vtkPolydataToImageStencil.
> >> >> >> >
> >> >> >> > Could this make any difference?
> >> >> >> >
> >> >> >> > Thanks
> >> >> >> >
> >> >> >> > Jothy
> >> >> >> >
> >> >> >> >
> >> >> >> > On Mon, Mar 5, 2012 at 7:49 PM, Jothybasu Selvaraj
> >> >> >> > <jothybasu at gmail.com>
> >> >> >> > wrote:
> >> >> >> >>
> >> >> >> >> No, it doesn't fix the problem.
> >> >> >> >>
> >> >> >> >> But it seems to work fine for contours with z-spacing in steps
> of
> >> >> >> >> 1mm.
> >> >> >> >>
> >> >> >> >> It is working well for a dataset with 3mm spacing but fails for
> >> >> >> >> 2.5
> >> >> >> >> mm.
> >> >> >> >>
> >> >> >> >> Maybe I need to test it thoroughly. Can I use those cxx and .h
> >> >> >> >> from
> >> >> >> >> 5.6
> >> >> >> >> in
> >> >> >> >> 5.8, that would be a easy workaround.
> >> >> >> >>
> >> >> >> >> Thanks
> >> >> >> >>
> >> >> >> >> Jothy
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> On Mon, Mar 5, 2012 at 4:01 PM, David Gobbi
> >> >> >> >> <david.gobbi at gmail.com>
> >> >> >> >> wrote:
> >> >> >> >>>
> >> >> >> >>> Hi Jothy,
> >> >> >> >>>
> >> >> >> >>> It underwent significant changes, but the only change I can
> >> >> >> >>> think
> >> >> >> >>> of that might have affected your pipeline is the way that it
> >> >> >> >>> does
> >> >> >> >>> rounding, it used to use a Floor() method that provided a
> small
> >> >> >> >>> tolerance even if you did SetTolerance(0). Try calling
> >> >> >> >>> SetTolerance(1e-6) on your PolyDataToImageStencil object, it
> >> >> >> >>> might help.
> >> >> >> >>>
> >> >> >> >>> - David
> >> >> >> >>>
> >> >> >> >>> On Mon, Mar 5, 2012 at 3:17 AM, Jothybasu Selvaraj
> >> >> >> >>> <jothybasu at gmail.com>
> >> >> >> >>> wrote:
> >> >> >> >>> > Hi all,
> >> >> >> >>> >
> >> >> >> >>> > I was able to create a mesh using the following pipeline in
> >> >> >> >>> > 5.6
> >> >> >> >>> > and
> >> >> >> >>> > it
> >> >> >> >>> > worked well
> >> >> >> >>> >
> >> >> >> >>> >
> >> >> >> >>> >
> >> >> >> >>> >
> >> >> >> >>> >
> >> >> >> >>> >
> vtkPolyDataToImageStencil->vtkLinearExtrusionFilter->vtkImageStencil->vtkDiscreteMarchingCubes
> >> >> >> >>> >
> >> >> >> >>> > Now, I have updated vtk to 5.8 and I am getting gaps in the
> >> >> >> >>> > mesh
> >> >> >> >>> > along
> >> >> >> >>> > the z
> >> >> >> >>> > axis. I am really puzzled, I have tried with different data
> >> >> >> >>> > sets
> >> >> >> >>> > as
> >> >> >> >>> > well.
> >> >> >> >>> >
> >> >> >> >>> > I have read somewhere that vtkPolyDataToImageStencil had
> some
> >> >> >> >>> > changes
> >> >> >> >>> > in
> >> >> >> >>> > 5.8, does it has anything to do with this problem, or am I
> >> >> >> >>> > doing
> >> >> >> >>> > anything wrong?
> >> >> >> >>> >
> >> >> >> >>> > I have contours of constant z-spacing.
> >> >> >> >>> >
> >> >> >> >>> > Any hints?
> >> >> >> >>> >
> >> >> >> >>> > Thanks
> >> >> >> >>> >
> >> >> >> >>> > --
> >> >> >> >>> > Jothy
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> Jothy
> >> >> >> >>
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > --
> >> >> >> > Jothy
> >> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > Jothy
> >> >> >
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > Jothy
> >> >
> >
> >
> >
> >
> > --
> > Jothy
> >
>
--
Jothy
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