[vtkusers] vtkPolyDataToImageStencil with partial volume

[Jonathan Morra]

If that's the case, then maybe I could have issues on the other side
(converting binary images to contours, I do both).  For this I'm using
vtkMarchingSquares followed by vtkStripper

int[] extent = binaryOrgan.GetExtent();
        switch (orientation) {
            case OrthoPanel.ORIENTATION_XY:
                extent[4] = slice;
                extent[5] = slice;
                break;
            case OrthoPanel.ORIENTATION_XZ:
                extent[2] = slice;
                extent[3] = slice;
                break;
            case OrthoPanel.ORIENTATION_YZ:
                extent[0] = slice;
                extent[1] = slice;
                break;
        }

vtkMarchingSquares marching = new vtkMarchingSquares();
        marching.SetInput(binaryOrgan);
        marching.SetImageRange(extent);
        marching.SetValue(0, 1);
        marching.Update();
        vtkPolyData marchingOutput = marching.GetOutput();

        vtkStripper stripper = new vtkStripper();
        stripper.SetInput(marchingOutput);
        stripper.Update();

Does anything look like it could be causing my issues there?

On Wed, Feb 23, 2011 at 11:18 AM, David Gobbi <david.gobbi at gmail.com> wrote:

> The value "1e-6" is a common tolerance because it is larger than
> most roundoff errors that are likely to occur in the calculations,
> but still small enough that it won't appreciably increase size of the
> region.
>
> Setting the tolerance to zero does exactly what you noted.  If the
> pixel is exactly on the edge, then it is considered to be inside if the
> edge is a leading edge, or outside if the edge is a trailing edge.
> This is done so that if you have two contours which are adjacent
> (i.e. share an edge), the edge voxels will be considered to be in
> just one of the two contours instead of in both.  If the tolerance is
> set larger than zero, then the edge pixels would always be considered
> to be in both contours.
>
> If you are dealing with rectangular contours, then the contour
> lines should be made so that they lie halfway between pixels, instead
> of lying directly on top of the pixels.  Then there is no uncertainty
> about whether a pixel lies inside or outside.
>
>  - David
>
>
> On Wed, Feb 23, 2011 at 11:58 AM, Jonathan Morra <jonmorra at gmail.com>
> wrote:
> > I had the tolerance set to 0, and setting it to 1e-6 didn't fix the
> problem.
> >  How did you come up with that number?  What's wrong with setting it to
> 0?
> >  In my case usually the left and top side of the vtkImageData is being
> > eroded, such that if I call the filter many times, the vtkImageData will
> > eventually be blank because it will all be eroded.   However, sometimes
> the
> > bottom and right grow in size, I haven't figured out which situations
> cause
> > which.
> >
> > On Wed, Feb 23, 2011 at 10:54 AM, David Gobbi <david.gobbi at gmail.com>
> wrote:
> >>
> >> Hi Jonathan,
> >>
> >> Whether a pixel is set depends on whether the center of the pixel
> >> is inside or outside the contour, irregardless of what proportion of
> >> the pixel's volume is inside or outside.
> >>
> >> The only adjustment is the Tolerance, which should be set to
> >> around 1e-6 so that pixels right on the edge of the contour
> >> are considered to be inside.  The tolerance cannot be negative.
> >>
> >>  - David
> >>
> >>
> >> On Wed, Feb 23, 2011 at 11:22 AM, Jonathan Morra <jonmorra at gmail.com>
> >> wrote:
> >> > I am currently using vtkPolyDataToImageStencil to successfully convert
> >> > contours represented as vtkPolyData to binary vtkImageData's.
>  However,
> >> > I'm
> >> > noticing a problem with the output sometimes.  Sometimes the resulting
> >> > binary images are slightly smaller or slightly bigger than the poly
> data
> >> > they were made from.  I assume this is the result of partial volume
> >> > effects.
> >> >  I would like to know 2 things
> >> > 1.  How does vtkPolyDataToImageStencil handle partial volume.
> >> > 2.  Is there a way to tune partial volume in
> vtkPolyDataToImageStencil?
> >> >  For
> >> > instance, a parameter which says if the contour includes less than x
> >> > percentage of the pixel then that pixel is 0.
> >> > Thanks,
> >> > Jon
> >> > PS If my assumption about partial volume effects is wrong, please let
> me
> >> > know.
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