[Insight-users] shape label map trouble

Fri May 10 10:57:20 EDT 2013

Hi, 
I found that the example in the paper does not match the example in the code. The example in the code works correctly 

> -----Original Message-----
> From: insight-users-bounces at itk.org [mailto:insight-users-
> bounces at itk.org] On Behalf Of Robert.Atwood at diamond.ac.uk
> Sent: 30 April 2013 17:59
> To: insight-users at itk.org
> Subject: [Insight-users] shape label map trouble
> 
> 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() ); 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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Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom