[vtkusers] image island removal and hole filling
Jonathan Morra
jonmorra at gmail.com
Mon Dec 6 16:09:07 EST 2010
My data is all either 0 or 1. I'm not sure why I have to know seed points
in the other islands. I don't know if I'm going to be able to get those
points. Basically I want to keep the one island that has the mouse on it,
that's how I know the one point I'm interested in.
On Mon, Dec 6, 2010 at 12:11 PM, David Gobbi <david.gobbi at gmail.com> wrote:
> Hi Jonathan,
>
> If you are setting the FloodExtent to a size that is larger than the region
> that will be selected by the fill, then it shouldn't have any effect. As it
> says in the documentation, SetFloodExtent() is meant to restrict the flood
> fill to e.g. one slice of a 3D volume.
>
> This filter will not automatically remove islands, it just floods each
> connected region that contains a seed. For island removal, you would have
> to invert the threshold and then put a seed inside every island that you
> want to remove.
>
> I suspect that the thresholds are not set correctly. What is the data
> range of your image? Is it [0,1]? Or [0,255]?
>
> David
>
>
> On Mon, Dec 6, 2010 at 12:38 PM, Jonathan Morra <jonmorra at gmail.com>wrote:
>
>> While, I'd love to use ITK, I haven't had luck getting ITK, VTK, and Java
>> to play together, so I'd like to stick with VTK for now.
>>
>> David -- I'm still having issues with the filter.
>> 1. The filter has to run in real time because this is called on a mouse
>> move event. However, I know a bounding box outside of which all voxels are
>> guaranteed to have a value of 0. Therefore I went ahead and used the
>> SetFloodExtent method and set it to my known bounding box, is this OK?
>> 2 I'm still seeing islands in the resulting binary mask, here is the
>> latest version of what I'm doing, any ideas?
>>
>> vtkPoints seedPoints = new vtkPoints();
>>
>> seedPoints.InsertNextPoint(panel.getPicker().GetPickPosition());
>> vtkImageFloodFill fill = new vtkImageFloodFill();
>> fill.SetInput(binaryImage);
>> fill.SetSeedPoints(seedPoints);
>> fill.ThresholdByLower(1);
>> fill.SetFloodExtent(bounds);
>> fill.Update();
>> binaryImage = fill.GetOutput();
>>
>> On Mon, Dec 6, 2010 at 10:34 AM, Karthik Krishnan <
>> karthik.krishnan at kitware.com> wrote:
>>
>>> Or you could process the pipeline in ITK, if you are willing to
>>> incorporate another toolkit..
>>>
>>> itk::ConnectedThresholdImageFilter ->
>>> VotingBinaryHoleFillingImageFilter (or its iterative version)
>>>
>>>
>>> On Mon, Dec 6, 2010 at 11:49 PM, David Gobbi <david.gobbi at gmail.com>
>>> wrote:
>>> > I think I made a mistake... I should have told you to use
>>> > ThresholdByLower(1). Other than that, your code looks fine.
>>> > David
>>> >
>>> > On Mon, Dec 6, 2010 at 11:13 AM, Jonathan Morra <jonmorra at gmail.com>
>>> wrote:
>>> >>
>>> >> I just got your class in my version of vtk and up and running in Java,
>>> and
>>> >> it's not working for me. I was wondering what I'm doing wrong, could
>>> you
>>> >> help me out?
>>> >> Thanks
>>> >> // We have to remove all the islands not connected to the
>>> >> center
>>> >> // and then fill the holes in the resulting mask
>>> >> vtkPoints seedPoints = new vtkPoints();
>>> >>
>>> >> seedPoints.InsertNextPoint(panel.getPicker().GetPickPosition());
>>> >> vtkImageFloodFill fill = new vtkImageFloodFill();
>>> >> fill.SetInput(binaryImage);
>>> >> fill.SetSeedPoints(seedPoints);
>>> >> fill.ThresholdByUpper(1);
>>> >> fill.Update();
>>> >> binaryImage = fill.GetOutput();
>>> >> On Fri, Dec 3, 2010 at 11:27 AM, Jonathan Morra <jonmorra at gmail.com>
>>> >> wrote:
>>> >>>
>>> >>> Fantastic, thanks for your help!
>>> >>>
>>> >>> On Fri, Dec 3, 2010 at 11:13 AM, David Gobbi <david.gobbi at gmail.com>
>>> >>> wrote:
>>> >>>>
>>> >>>> Hi Jonathan,
>>> >>>> I put my flood-fill filter on github, and tested it to make sure it
>>> >>>> still works:
>>> >>>> http://github.com/dgobbi/VTK/tree/flood-fill/Imaging/
>>> >>>>
>>> >>>> The interface is just like the vtkThresholdFilter, except that it
>>> >>>> has a method called SetSeedPoints() to allow you to set your
>>> >>>> seeds. For a binary image, call ThresholdByUpper(1) so that
>>> >>>> you can set seeds inside any non-zero islands that you want
>>> >>>> to keep in your output.
>>> >>>> I'll probably contribute this class to VTK after I have brought
>>> >>>> it up-to-date (it was originally written for VTK 4).
>>> >>>> David
>>> >>>>
>>> >>>> On Thu, Dec 2, 2010 at 3:39 PM, Jonathan Morra <jonmorra at gmail.com>
>>> >>>> wrote:
>>> >>>>>
>>> >>>>> Thanks, let me know where I can download it from.
>>> >>>>>
>>> >>>>> On Thu, Dec 2, 2010 at 2:36 PM, David Gobbi <david.gobbi at gmail.com
>>> >
>>> >>>>> wrote:
>>> >>>>>>
>>> >>>>>> For Step 1, I have a VTK flood-fill class that do the job. I'll
>>> >>>>>> upload it to
>>> >>>>>> gerrit so that you can try it out. I don't think anything exists
>>> for
>>> >>>>>> your
>>> >>>>>> Step 2, though.
>>> >>>>>> David
>>> >>>>>>
>>> >>>>>> On Thu, Dec 2, 2010 at 3:14 PM, Jonathan Morra <
>>> jonmorra at gmail.com>
>>> >>>>>> wrote:
>>> >>>>>>>
>>> >>>>>>> I have a binary vtkImageData class and I want to do 2 things with
>>> it,
>>> >>>>>>> and I don't know how.
>>> >>>>>>> 1. I want to remove all islands from the image except one. I
>>> want
>>> >>>>>>> to identify the island not to be removed by a pixel location. I
>>> have seen
>>> >>>>>>> vtkImageIslandRemoval2D, and I don't think that'll work for me,
>>> because I do
>>> >>>>>>> not know anything about the island's size that I want to keep (it
>>> could be
>>> >>>>>>> big, small, or in the middle), all that I know is one point which
>>> >>>>>>> is guaranteed to be interior to one island, and that's the island
>>> I want to
>>> >>>>>>> keep.
>>> >>>>>>> 2. I want to do hole filling on the output of step 1 and I don't
>>> >>>>>>> know how to do that. I saw vtkFillHolesFilter but that appears
>>> only to work
>>> >>>>>>> on poly data. I'd like something analogous to that for
>>> vtkImageData.
>>> >>>>>>> If anyone knows how to do these things, I'd appreciate it. Also,
>>> if
>>> >>>>>>> it matters, I'm coding in Java.
>>> >>>>>>> Thanks
>>> >>>>>>> _______________________________________________
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>>> >>>>>>
>>> >>>>>
>>> >>>>
>>> >>>
>>> >>
>>> >
>>> >
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>>> > Powered by www.kitware.com
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>>
>>
>
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