[Insight-users] Commentary on community

[Johnson, Hans J]

All,

I wanted to pontificate on the virtues of living a good clean coding life
:) .

A need was identified on the user mailing list,
--February 8th, a SimpleITK suggestions was made
--February 12th, a re-implementation of that was provided in C++
--February 13th, an insight-journal article with illustrations,
alternative approaches, AND implementation files was submitted and is
available to the community
--Future these tools are being deployed TODAY for advancing our
understanding of human diseasee

It is wonderful to be part of such a distinguished community.

GO TEAM ITK!

Hans

On 2/13/13 4:34 AM, "Richard Beare" <richard.beare at gmail.com> wrote:

>The parallel classes for this are now on InsightJournal. Article
>includes some comparisons - hope it helps:
>
>http://hdl.handle.net/10380/3399
>
>
>On Tue, Feb 12, 2013 at 8:20 AM, Dženan Zukić <dzenanz at gmail.com> wrote:
>> Today I finally managed to try it myself, and it works. Below is
>> implementation in ITK, if anyone needs it.
>>
>> typedef itk::Image<unsigned char, 3> VisualizingImageType;
>> typedef itk::Image<float, 3> InternalImageType;
>>
>> //function call example
>> std::vector<VisualizingImageType::IndexType> centers;
>> for (int i=0; i<vertebra.size(); i++)
>> centers.push_back(vertebra[i]->centerIndex);
>> VisualizingImageType::Pointer vInfluence=multilabelDilation(region, 50,
>> centers);
>>
>>
>> VisualizingImageType::Pointer multilabelDilation(itk::ImageRegion<3>
>>region,
>> float radius, std::vector<VisualizingImageType::IndexType> points)
>> {
>>     typedef
>> itk::BinaryBallStructuringElement<VisualizingImageType::PixelType,3>
>> BallType;
>>     BallType ball;
>>     ball.SetRadius(radius);
>>     ball.CreateStructuringElement();
>>     typedef itk::BinaryDilateImageFilter<VisualizingImageType,
>> VisualizingImageType, BallType> growType;
>>     growType::Pointer grow=growType::New();
>>     grow->SetKernel(ball); //grow->SetRadius(radius);
>>
>>     VisualizingImageType::Pointer image=VisualizingImageType::New();
>>     image->SetRegions(region);
>>     image->Allocate();
>>     image->FillBuffer(0);
>>     for (int i=0; i<points.size(); i++)
>>         image->SetPixel(points[i], grow->GetDilateValue());
>>
>>     grow->SetInput(image);
>>     grow->Update();
>>     writeImage(grow->GetOutput(), "1dilate.nrrd"); //debug
>>
>>     typedef
>>itk::SignedMaurerDistanceMapImageFilter<VisualizingImageType,
>> InternalImageType> DistanceMapType;
>>     DistanceMapType::Pointer dm=DistanceMapType::New();
>>     dm->SetInput(image);
>>     dm->SetUseImageSpacing(true);
>>     dm->InsideIsPositiveOff();
>>     dm->Update();
>>     writeImage(dm->GetOutput(), "2distanceMap.nrrd"); //debug
>>
>>     for (int i=0; i<points.size(); i++)
>>         image->SetPixel(points[i], i+1); //now set index+1
>>
>>     typedef
>> itk::MorphologicalWatershedFromMarkersImageFilter<InternalImageType,
>> VisualizingImageType> morphoWSfMType;
>>     morphoWSfMType::Pointer ws=morphoWSfMType::New();
>>     ws->SetInput1(dm->GetOutput());
>>     ws->SetInput2(image);
>>     ws->Update();
>>     writeImage(ws->GetOutput(), "3watershed.nrrd"); //debug
>>
>>     typedef itk::AndImageFilter<VisualizingImageType> AndType;
>>     AndType::Pointer and=AndType::New();
>>     and->SetInput1(ws->GetOutput());
>>     and->SetInput2(grow->GetOutput());
>>     and->Update();
>>     writeImage(and->GetOutput(), "4multiplied.nrrd"); //debug
>>
>>     return and->GetOutput();
>> }
>>
>>
>> On Fri, Feb 8, 2013 at 11:36 AM, Bradley Lowekamp
>><blowekamp at mail.nih.gov>
>> wrote:
>>>
>>> Unfortunately, my helpful e-mail was too big to make it to the list. So
>>> here is the important bit, which defines a function in Python with
>>> SimpleITK:
>>>
>>>
>>> def MultilabelDilation(img,
>>> radius=1,kernel=sitk.BinaryDilateImageFilter.Ball):
>>>
>>>     distImg = sitk.SignedMaurerDistanceMap(img != 0,
>>> insideIsPositive=False, squaredDistance=False, useImageSpacing=False)
>>>
>>>     dilatImg = sitk.BinaryDilate(img!=0, radius, kernel)
>>>
>>>     wsImg = sitk.MorphologicalWatershedFromMarkers(distImg, img)
>>>
>>>     return dilatImg*wsImg
>>>
>>>
>>>
>>>
>>> On Feb 8, 2013, at 9:42 AM, Dženan Zukić <dzenanz at gmail.com> wrote:
>>>
>>> Thanks for the interest and the provided code Brad. Hopefully I will
>>>get
>>> to work today to try it out myself :D (Blizzard warning in Boston,
>>>where I
>>> am for a couple months)
>>>
>>>
>>
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