[Insight-users] Commentary on community
Dženan Zukić
dzenanz at gmail.com
Wed Feb 13 12:55:12 EST 2013
It feels even better if you were the initiator :D
On Wed, Feb 13, 2013 at 12:01 PM, Matt McCormick <matt.mccormick at kitware.com
> wrote:
> 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)
> >>>>
> >>>>
> >>>
> >>_____________________________________
> >>Powered by www.kitware.com
> >>
> >>Visit other Kitware open-source projects at
> >>http://www.kitware.com/opensource/opensource.html
> >>
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> >>http://www.kitware.com/products/protraining.php
> >>
> >>Please keep messages on-topic and check the ITK FAQ at:
> >>http://www.itk.org/Wiki/ITK_FAQ
> >>
> >>Follow this link to subscribe/unsubscribe:
> >>http://www.itk.org/mailman/listinfo/insight-users
> >
> >
> >
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> >
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> >
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>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
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