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

[David Gobbi]

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 at magellium.fr> 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
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> --
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