[Insight-users] Commentary on community

[Matt McCormick]

Thanks for explicitly recognizing this, Hans.  It is important to
acknowledge how outstanding this is!

Go team,
Matt

On Wed, Feb 13, 2013 at 7:56 AM, Johnson, Hans J <hans-johnson at uiowa.edu> wrote:
> 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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>
>
>
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