Hey everyone,
I'm trying to get the coordinates of all pixels from a fresh created
segmentation. What I achieved so far is to get the node from the data
manager and I also could iterate through all the points oft the segmentation
to check if its 0 or not. However this takes quite a lot of time and even
gives me wrong values or NaN, wich means something must be wrong. So now I
try to get only the shown segmentation where only the existing points are
included. My problem is, that i cant acces the label properly.
Does anyone have an idea how to achieve my goal? Anything that I could do
better? Thanks for your time anyway!
My attempts so far:
// 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;
}
// get the label with the stored points
mitk::LabelSetImage *lsi =
dynamic_cast<mitk::LabelSetImage*>(node->GetData());
unsigned int labels = lsi->GetTotalNumberOfLabels();
std::cout << "Total number of Labels: " << labels << std::endl; // 2
labels
std::cout << "number of Labels layer 0: " << lsi->GetNumberOfLabels(0)
<< std::endl; // 2
std::cout << "number of Labels layer 1: " << lsi->GetNumberOfLabels(1)
<< std::endl; // >1000000 (changes with every new segmentation)
//std::cout << "number of labels layer 2: " << lsi->GetNumberOfLabels(2)
<< std::endl; // crash
std::cout << "number of layer: " << lsi->GetNumberOfLayers() <<
std::endl; // 1
std::cout << "number of channels " << lsi->GetNumberOfChannels() <<
std::endl; // 1
const mitk::PixelType type = lsi->GetPixelType();
std::cout << "image type: " << type.GetPixelTypeAsString() << std::endl;
//nothing
mitk::Label *lab = lsi->GetActiveLabel();
mitk::Point3D cent = lab->GetCenterOfMassIndex();
std::cout << "label 0 center of mass index " << cent << std::endl; //
nothing
//read in all of the points and write to matrix
uint32_t neuerzaehlerb = 0;
mitk::Image *layerfive = lsi->GetLayerImage(lsi->GetActiveLayer()); //
try till 5
unsigned int maxx = layerfive->GetDimension(0); //lsi
unsigned int maxy = layerfive->GetDimension(1);
unsigned int maxz = layerfive->GetDimension(2);
Eigen::MatrixXd matb(1,3);
double point[3];
for (unsigned int a = 0; a < maxx; a++){
for (unsigned int b = 0; b < maxy; b++){
for (unsigned int c = 0; c < maxz; c++){
itk::Index<3> idx = {{ a, b, c }};
double pt = layerfive->GetPixelValueByIndex(idx);
if (pt != 0){
point[0] = static_cast<double>(a);
point[1] = static_cast<double>(b);
point[2] = static_cast<double>(c);
if ( isnan(point[0]) == false || isnan(point[1]) ==
false || isnan(point[2] == false) ) {
matb.resize(neuerzaehlerb+2,3);
matb(neuerzaehlerb,0)=point[0];
matb(neuerzaehlerb,1)=point[1];
matb(neuerzaehlerb,2)=point[2];
std::cout << "mat zeile: " << neuerzaehlerb << " : "
<< matb.row(neuerzaehlerb) << std::endl;
neuerzaehlerb++;
}
}
}
}
}
neuerzaehlerb = neuerzaehlerb - 5;
matb.resize(neuerzaehlerb,3);
QString outputpoints="Points: ";
outputpoints +=QString::number(neuerzaehlerb);
outputpoints.append(" ...succesfull loaded from the selected
segmentation.");
m_Controls.displaybottom->append(outputpoints + "\n");
Setmatrix(matb);
Pca();
/*
//attempt 2
mitk::Image::Pointer image =
dynamic_cast<mitk::Image*>(node->GetData());
const mitk::PixelType &type = image->GetPixelType();
std::string types = type.GetPixelTypeAsString();
std::cout << "image type: " << types << std::endl; // nothing
// access the raw image data
try
{
itk::Index<3> idx = {{ 1, 1, 1 }};
mitk::ImagePixelReadAccessor<short,3> readAccess(image,
image->GetSliceData(2));
std::cout << "step 1.1..OK " << std::endl;
short 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;
short 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)
*/
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
mitk-users mailing list
mitk-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mitk-users
