[vtkusers] image island removal and hole filling

David Gobbi david.gobbi at gmail.com
Mon Dec 6 16:45:00 EST 2010 

Good to hear.  I will probably contribute this class to VTK after I have
cleaned it up a bit.

  David


On Mon, Dec 6, 2010 at 2:29 PM, Jonathan Morra <jonmorra at gmail.com> wrote:

> Thanks, the first suggestion worked exactly like I expected and the speed
> is totally fine.
>
> Thanks again.
>
>
> On Mon, Dec 6, 2010 at 1:26 PM, David Gobbi <david.gobbi at gmail.com> wrote:
>
>> 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
>>>>>> >>>>>>> _______________________________________________
>>>>>> >>>>>>> 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
>>>>>> >>>>>>>
>>>>>> >>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>> >>>>>>> http://www.vtk.org/mailman/listinfo/vtkusers
>>>>>> >>>>>>>
>>>>>> >>>>>>
>>>>>> >>>>>
>>>>>> >>>>
>>>>>> >>>
>>>>>> >>
>>>>>> >
>>>>>> >
>>>>>> > _______________________________________________
>>>>>> > 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
>>>>>> >
>>>>>> > Follow this link to subscribe/unsubscribe:
>>>>>> > http://www.vtk.org/mailman/listinfo/vtkusers
>>>>>> >
>>>>>> >
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.vtk.org/pipermail/vtkusers/attachments/20101206/f8e06431/attachment.htm>

More information about the vtkusers mailing list