[Insight-users] shape label map trouble

[Robert.Atwood at diamond.ac.uk]

Hi, everyone and Gaetan:

I was recoding some old itk applets I did before itk label map was introduced to use label map  and shape label object classes, I followed the example in Gaetan's paper
http://hdl.handle.net/1926/584

and used itk3.2 to try to be sure of compatibility and avoid issues of updating my old code too. 

However, I find 535 ojects but they all have size of zero. 
Somehow , the very simple example, translated for my code, virtually nothing changed except that the input is at the end of another pipeline , the objects always have zero size and centroid. 
The label map output image looks correct. 

Thanks
Robert



.... page 26 of the paper....

typedef itk::ShapeLabelMapFilter< LabelMapType > ShapeFilterType;
ShapeFilterType::Pointer shape = ShapeFilterType::New();
shape->SetInput( converter->GetOutput() );
shape->Update();
LabelMapType::Pointer labelMap = converter->GetOutput();
for( unsigned int label=1; label<=labelMap->GetNumberOfLabelObjects(); label++ )
{
// we don't need a SmartPointer of the label object here, because the reference is kept in
// in the label map.
const LabelObjectType * labelObject = labelMap->GetLabelObject( label );
std::cout << label << "\t" << labelObject->GetPhysicalSize() << "\t" << labelObject->GetCentroid()
}




Translated for my code:

220   makelabel->SetInputForegroundValue(1);
221   std::cout << makelabel << std::endl; // debugging .. dump the object
222
223   /* set the pipeline for finding the shapes */
224   std::cerr << "Now finding labelled components" << std::endl;
225   makelabel->SetInput(output);
226   getshapes->SetInput(makelabel->GetOutput());
227
228   try {
229       getshapes->Update();
230   }catch( itk::ExceptionObject & exp ) {
231      std::cerr << "ERROR: itkException caught during getshapes update !" << std::endl;
232      std::cerr << exp << std::endl;
233      std::cerr << "getshapes: " << std::endl << getshapes<< std::endl;
234      exit(0);
235   }
236
237   /* assign label map for convenience */
238
239   labelmap=makelabel->GetOutput();
240
241   std::cout<< " Number of Objects Found:  " << labelmap->GetNumberOfLabelObjects() << std::endl;
242
243   //for (onum=1;onum<labelmap->GetNumberOfLabelObjects(); onum++)
244   for (onum=1;onum<3; onum++) /* degugging .. just stop after a couple of objects */
245   {
246      const ShapeType * cshape=labelmap->GetLabelObject(onum); /* I tried using predefined smartpoitner, same result*/
247      std::cout<< onum<<" "<< cshape->GetPhysicalSize() << " "<< cshape->GetCentroid() << std::endl;
248      //std::cout << cshape << std::endl;
249      cshape->Print(std::cout);
250
251   }
252
253   /* make an image of the labels */
254   l2label->SetInput(makelabel->GetOutput());
255   mwriter1->SetInput(l2label->GetOutput());
256   mwriter1->SetFileName("labelmap.tif");
257   mwriter1->Update();


  ____________________
 
  Dr. Robert C. Atwood
  Senior Support Scientist
  Beamline I12-JEEP
  The Joint Engineering and Environmental Processing Beamline
  Diamond Light Source
  The Harwell Science and Innovation Campus
  Didcot,OXON
  OX11 0DE
  +44 (0) 1235 778 670
 



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