[vtkusers] Extract a tube of data from DICOM series data
Vincent32160
vsh at magellium.fr
Mon Dec 8 12:15:55 EST 2014
I am still struggling to unwrap the cylinder using vtkCylindricalTransform
and vtkImageReslice2.
I tried to follow your advices but I do not see the result of the
transformation.
For now, I only see a slice of the cylinder (through the center along the
z-axis)
Here is the code:
Thanks again
David Gobbi wrote
> On Thu, Nov 13, 2014 at 9:35 AM, Vincent32160 <
> vsh@
> > wrote:
>
>> Hi David,
>> I am still trying to unwrapped my cylinder.
>> Unfortunately I don't get what you mean by "you can select one
>> "radius" slice for viewing". Should I use a vtkImageViewer2 to do it?
>>
>
> When the cylinder has been unwrapped (via vtkImageReslice and a
> vtkCylindricalTransform), you get a volume where the coordinates
> are (r,theta,z). So, yes, you could set the orientation of
> vtkImageViewer2
> so that it extracts slices along the first axis instead of along the third
> axis.
> Or you could set the OutputExtent of vtkImageReslice so that it only
> produces the single "r" slice that you want.
>
>
>
>> Another question: I would like also to unwrap cylinder which don't have
>> the
>> same center as the original cylinder. Is that possible with
>> vtkImageReslice?
>
>
> Yes. Use vtkImageChangeInformation's SetOutputOrigin() method to
> adjust the input image, instead of using CenterImageOn(). This will allow
> you
> to put the center of the cylinder anywhere you want. In VTK, the
> "Origin"
> of
> the image means the position, in physical coordinates, of the first voxel.
> So
> if you know what voxel you want to be at the center of the cylinder, you
> can
> use algebra to compute how to set the Origin so that the physical
> coordinates
> of that voxel are (0,0,0). Drawing diagrams helps.
>
> - David
>
>
>
>> David Gobbi wrote
>> > Hi Vincent,
>> >
>> > The input to vtkImageReslice should be the original image
>> > (before either stencil has been applied). In order for
>> > vtkImageReslice to do the interpolation properly, it must
>> > have neighbor voxels for each voxel it extracts. After it
>> > has unwrapped the whole cylinder, you can select one
>> > "radius" slice for viewing.
>> >
>> > With vtkImageReslice, you _must_ specify what output
>> > sampling you want. Use SetOutputSpacing() to set the
>> > radius, circumferential angle, and longitudinal sample
>> > spacings. Also use SetOutputExtent() to set the
>> > number of samples for each.
>> >
>> > I may have been wrong about having to invert the
>> > transform. Try feeding it in without GetInverse().
>> >
>> > Also, for the transform to work properly, the input image must
>> > be centered. After all, in cylindrical coordinates the assuption
>> > is that (0,0,0) is at the center of the cylinder. The filter
>> > vtkImageChangeInformation can center the image (i.e. put
>> > vtkImageChangeInformation with CenterImageOn() before
>> > vtkImageReslice).
>> >
>> > Good luck,
>> >
>> > - David
>> >
>> >
>> > On Fri, Nov 7, 2014 at 7:29 AM, Vincent32160 <
>>
>> > vsh@
>>
>> > > wrote:
>> >
>> >> I now have a tube of data. On the right, you see stencilFiltrer2, the
>> >> result
>> >> of two vtkROIStencilSource (the first to remove the outer voxels and
>> the
>> >> second the inner)
>> >> <http://vtk.1045678.n5.nabble.com/file/n5729402/output3.png>
>> >>
>> >> I try to use vtkCylindricalTransform and vtkImageReslice to unwrap the
>> >> tube
>> >> and I don't get the result I want. Could you help?
>> >>
>> >> //Image Reslice
>> >> vtkCylindricalTransform * cylTransform =
>> vtkCylindricalTransform::New();
>> >>
>> >> vtkImageReslice * imageReslice = vtkImageReslice::New();
>> >> imageReslice->SetInputConnection(stencilFilter2->GetOutputPort());
>> >> imageReslice->SetResliceTransform(cylTransform->GetInverse());
>> >> imageReslice->Update();
>> >>
>> >> // Create volume
>> >> vtkSmartPointer
>> >
> <vtkPiecewiseFunction>
>> > outputOpacity =
>> >> vtkSmartPointer
>> >
> <vtkPiecewiseFunction>
>> > ::New();
>> >> outputOpacity->AddPoint(-1000, 1.0);
>> >> outputOpacity->AddPoint(3000, 0.0);
>> >>
>> >> // Create volume mapper
>> >> vtkVolumeRayCastMapper * imageMapper3d =
>> vtkVolumeRayCastMapper::New();
>> >> imageMapper3d->SetInputConnection(imageReslice->GetOutputPort());
>> >> imageMapper3d->SetVolumeRayCastFunction(rayCastFunction);
>> >>
>> >> // Volume property
>> >> vtkSmartPointer
>> >
> <vtkVolumeProperty>
>> > outputVolumeProperty =
>> >> vtkSmartPointer
>> >
> <vtkVolumeProperty>
>> > ::New();
>> >> outputVolumeProperty->SetScalarOpacity(outputOpacity);
>> >> outputVolumeProperty->SetInterpolationTypeToLinear();
>> >> outputVolumeProperty->ShadeOn();
>> >>
>> >> // Displayed volume
>> >> vtkSmartPointer
>> >
> <vtkVolume>
>> > extractedVol =
>> >> vtkSmartPointer
>> >
> <vtkVolume>
>> > ::New();
>> >> extractedVol->SetMapper(imageMapper3d);
>> >> extractedVol->SetProperty(outputVolumeProperty);
>> >>
>> >> Thanks
>> >>
>> >>
>> >> David Gobbi wrote
>> >> > Hi Vincent,
>> >> >
>> >> > Use an opacity transfer function that makes the black voxels
>> >> transparent.
>> >> >
>> >> > You can unwrap the tube by reslicing it through an inverse
>> cylindrical
>> >> > transformation (e.g. vtkCylindricalTransform and vtkImageReslice).
>> >> >
>> >> > - David
>> >> >
>> >> > On Thu, Nov 6, 2014 at 7:05 AM, Vincent32160 <
>> >>
>> >> > vsh@
>> >>
>> >> > > wrote:
>> >> >
>> >> >> Thanks again David!
>> >> >>
>> >> >> As I want to keep a volume I chose solution 2.
>> >> >> I used a volume mapper and the result is pretty good.
>> >> >> The only problem is that I am not able to remove the black voxels
>> >> around
>> >> >> the
>> >> >> cylinder. (See picture)
>> >> >> <http://vtk.1045678.n5.nabble.com/file/n5729393/output2.png>
>> >> >>
>> >> >> The next step of my approach is to be able to keep only the voxels
>> on
>> >> the
>> >> >> edges (meaning on a tube or hollow cylinder of 1-voxel thickness).
>> And
>> >> >> after
>> >> >> that I would like to unfold the tube and have a flat surface of
>> >> pixels.
>> >> >> Let me know if you think that it is better to create a new thread
>> for
>> >> >> these
>> >> >> two next steps.
>> >> >>
>> >> >> Thanks for your help.
>> >> >>
>> >> >> Vincent
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> View this message in context:
>> >> >>
>> >>
>> http://vtk.1045678.n5.nabble.com/Extract-a-tube-of-data-from-DICOM-series-data-tp5729381p5729393.html
>> >> >> Sent from the VTK - Users mailing list archive at Nabble.com.
>> >> >> _______________________________________________
>> >> >> Powered by www.kitware.com
>> >> >>
>> >> >> Visit other Kitware open-source projects at
>> >> >> http://www.kitware.com/opensource/opensource.html
>> >> >>
>> >> >> Please keep messages on-topic and check the VTK FAQ at:
>> >> >> http://www.vtk.org/Wiki/VTK_FAQ
>> >> >>
>> >> >> Follow this link to subscribe/unsubscribe:
>> >> >> http://public.kitware.com/mailman/listinfo/vtkusers
>> >> >>
>> >> >
>> >> > _______________________________________________
>> >> > Powered by www.kitware.com
>> >> >
>> >> > Visit other Kitware open-source projects at
>> >> > http://www.kitware.com/opensource/opensource.html
>> >> >
>> >> > Please keep messages on-topic and check the VTK FAQ at:
>> >> > http://www.vtk.org/Wiki/VTK_FAQ
>> >> >
>> >> > Follow this link to subscribe/unsubscribe:
>> >> > http://public.kitware.com/mailman/listinfo/vtkusers
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >> View this message in context:
>> >>
>> http://vtk.1045678.n5.nabble.com/Extract-a-tube-of-data-from-DICOM-series-data-tp5729381p5729402.html
>> >> Sent from the VTK - Users mailing list archive at Nabble.com.
>> >> _______________________________________________
>> >> Powered by www.kitware.com
>> >>
>> >> Visit other Kitware open-source projects at
>> >> http://www.kitware.com/opensource/opensource.html
>> >>
>> >> Please keep messages on-topic and check the VTK FAQ at:
>> >> http://www.vtk.org/Wiki/VTK_FAQ
>> >>
>> >> Follow this link to subscribe/unsubscribe:
>> >> http://public.kitware.com/mailman/listinfo/vtkusers
>> >>
>> >
>> > _______________________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Please keep messages on-topic and check the VTK FAQ at:
>> > http://www.vtk.org/Wiki/VTK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/vtkusers
>>
>>
>>
>>
>>
>> --
>> View this message in context:
>> http://vtk.1045678.n5.nabble.com/Extract-a-tube-of-data-from-DICOM-series-data-tp5729381p5729459.html
>> Sent from the VTK - Users mailing list archive at Nabble.com.
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the VTK FAQ at:
>> http://www.vtk.org/Wiki/VTK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/vtkusers
>>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/vtkusers
--
View this message in context: http://vtk.1045678.n5.nabble.com/Extract-a-tube-of-data-from-DICOM-series-data-tp5729381p5729717.html
Sent from the VTK - Users mailing list archive at Nabble.com.
More information about the vtkusers
mailing list