[vtkusers] image island removal and hole filling
David Gobbi
david.gobbi at gmail.com
Mon Dec 6 16:26:22 EST 2010
Hi Jonathan,
In your original email you said that you need to select one island in your
image (i.e. to keep only that island), and then fill the holes in that
island. When I said "island removal" in my last email, I actually just
meant fill the holes. I didn't mean to refer to the other islands.
If your data is 0 and 1, then you should be able to select white with:
ThresholdBetween(1,1) // only fill pixels that have a value of 1
SetOutValue(0) // set all other pixels black
ThresholdBetween(0,0) // only fill pixels that have a value of 0
SetOutValue(1) // set all other pixels white
David
On Mon, Dec 6, 2010 at 2:09 PM, Jonathan Morra <jonmorra at gmail.com> wrote:
> 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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