Re: [mitk-users] Points from segmentation

[Dinkelacker, Stefan]

Hi Hannes,

in addition to Tobias' answer, multilabel segmentation images are of type 
mitk::LabelSetImage [1].

Best,
Stefan

[1] http://docs.mitk.org/2016.11/classmitk_1_1LabelSetImage.html


Von: Stein, Tobias [mailto:t.st...@dkfz-heidelberg.de]
Gesendet: Monday, June 18, 2018 4:05 PM
An: hannes.bene...@gmx.de
Cc: mitk-users@lists.sourceforge.net
Betreff: Re: [mitk-users] Points from segmentation

Hi Hannes,

you can check the type of your image by using image->GetPixelType()
You should use the same return type of readAccess.GetPixelByIndex(idx) as you 
chose for the ImagePixelReadAccessor.

Best,

Tobias


Von: hannes.bene...@gmx.de<mailto:hannes.bene...@gmx.de> 
[mailto:hannes.bene...@gmx.de]
Gesendet: Montag, 18. Juni 2018 15:40
An: Stein, Tobias 
<t.st...@dkfz-heidelberg.de<mailto:t.st...@dkfz-heidelberg.de>>
Betreff: AW: [mitk-users] Points from segmentation

Hey Tobias,

so i tried to get the segmentation points, but i couldn't achieve it at all. I 
figuered out how to access the data storage and get the data node of a new 
segmentation node (labelsetimage). But when i try to acces the image, my 
program crashes. I'm trying with two attempts but none oft hem works. Only the 
second attempt gets through point 2.1 but the crashes as well.

So wich is the right pixeltype for a labelsetimage? What am i doing wrong in 
here?

Best regards,

Hannes



void DrillHoleSegmentation::GetRawSegmentation()
{
    // acces the data storage
    QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
    if (nodes.empty())
      return;

    mitk::DataNode *node = nodes.front();

    if (!node)
    {
      // Nothing selected. Inform the user and return
      QMessageBox::information(NULL, "Template", "Please load and select an 
image before starting image processing.");
      return;
    }

    mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());

    // access the raw image data

    try
    {
      itk::Index<3> idx = {{ 1, 1, 1 }};

      mitk::ImagePixelReadAccessor<uint16_t,3> readAccess(image, 
image->GetSliceData(2));
      std::cout << "step 1.1..OK  "  << std::endl;
      double value = readAccess.GetPixelByIndex(idx);
      std::cout << "step 1.2..OK...value:  " << value << std::endl;
    }
    catch(mitk::Exception& e)
    {
      // deal with the situation not to have access
        std::cout << "no acces to image data " << std::endl;
    }

    // another attempt
    try
    {
      float coords[3]={1.0,1.0,1.0};
      mitk::Point3D position(coords);

      mitk::ImagePixelReadAccessor<uint16_t,3> readAccess(image);
      std::cout << "step 2.1..OK " << std::endl;
      double value = readAccess.GetPixelByWorldCoordinates(position);
      std::cout << "step 2.2..OK..value 2: " << value << std::endl;
    }
    catch(mitk::Exception& e)
    {
      // deal with the situation not to have access
        std::cout << "no acces to image data v 2 " << std::endl;
    }

    // iterate through all pixels and check if the value is 0 or 1 (binary 
image)
}

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