[vtkusers] Extract a tube of data from DICOM series data

[Vincent32160]

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?

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?

Thanks a lot.


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.