[vtkusers] vtkPolyDataToImageStencil with partial volume
Jonathan Morra
jonmorra at gmail.com
Thu Feb 24 12:32:33 EST 2011
I've never used vtkTransformPolyDataFilter, how would I use that filter in
my situation?
On Thu, Feb 24, 2011 at 9:17 AM, David Gobbi <david.gobbi at gmail.com> wrote:
> Hi Jonathan,
>
> I still recommend that you add a vtkTransformPolyDataFilter like in the
> ImageTracerWidget example. Right now your image slice is right on the
> top edge of the extruded contour, so the smallest amount of roundoff error
> might cause it to miss. By shifting the extruded contour up by half a
> voxel,
> you can preemptively guard against such errors.
>
> - David
>
>
> On Thu, Feb 24, 2011 at 10:09 AM, Jonathan Morra <jonmorra at gmail.com>
> wrote:
> > Actually, after setting the marching squares value to 0.5 and changing
> the
> > linear extrusion filter it's working now. Thanks!!!
> >
> > On Thu, Feb 24, 2011 at 9:02 AM, Bill Lorensen <bill.lorensen at gmail.com>
> > wrote:
> >>
> >> Also, the stencil algorithm and marching squares use different
> >> criteria to determine whether a "pixel" is inside or outside.
> >>
> >> For the stencil, the pixel is considered a point and checked within a
> >> tolerance for inside/outside. I'm guessing here).
> >> For marching squares, a "square" is composed of four pixels. If at
> >> least one of the four pixels is of the opposite state(inside/outside)
> >> then a contour will be generated.
> >>
> >> On Thu, Feb 24, 2011 at 11:53 AM, Bill Lorensen <
> bill.lorensen at gmail.com>
> >> wrote:
> >> > Definitely set the isovalue to .5 if you have binary 0/1 images.
> >> >
> >> > On Wed, Feb 23, 2011 at 2:59 PM, David Gobbi <david.gobbi at gmail.com>
> >> > wrote:
> >> >> I've never used marching squares, but I have a guess as
> >> >> to what the problem might be. If your binary image has
> >> >> values "0" and "1" then you should contour it at "0.5".
> >> >>
> >> >> - David
> >> >>
> >> >>
> >> >> On Wed, Feb 23, 2011 at 12:27 PM, Jonathan Morra <jonmorra at gmail.com
> >
> >> >> wrote:
> >> >>> 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.
> >> >>>> >> > _______________________________________________
> >> >>>> >> > 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
> >> >>>> >> >
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> >> >>>> >> >
> >> >>>> >> >
> >> >>>> >
> >> >>>> >
> >> >>>
> >> >>>
> >> >> _______________________________________________
> >> >> 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
> >> >>
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> >> >>
> >> >
> >
> >
>
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