[vtkusers] Problem with vtkPolyDataToImageStencil in 5.8
Jothybasu Selvaraj
jothybasu at gmail.com
Fri Mar 9 16:26:49 EST 2012
And vtkDICOMImageReader depends on the slice thickness tag it seems, that's
why the imageData->GetSpacing()
give 3.0 mm, which is wrong in this case.
Jothy
On Fri, Mar 9, 2012 at 9:24 PM, Jothybasu Selvaraj <jothybasu at gmail.com>wrote:
> 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
>
>
--
Jothy
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.vtk.org/pipermail/vtkusers/attachments/20120309/1079dc14/attachment.htm>
More information about the vtkusers
mailing list