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Fix joint fusion bugs multi modal data #1302

Merged
merged 2 commits into from
Feb 5, 2022
Merged

Fix joint fusion bugs multi modal data #1302

merged 2 commits into from
Feb 5, 2022

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hjmjohnson
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Two bugs were identified when using uncommon parameters for ants joint fusion.

@hjmjohnson
BUG: Multi-modal atlas data causes duplicate atlases
653f13e 
For multiple modality images, the atlases were incorrectly
doubled.

For example, 3 atlases with T1 & T2 modalities should result in
a list of lists like

0: [A1-T1, A1-T2]
1: [A2-T1, A2-T2]
2: [A3-T1, A3-T2]

but instead resulted in

0: [A1-T1, A1-T2]
1: [A1-T1, A1-T2]
2: [A2-T1, A2-T2]
3: [A2-T1, A2-T2]
4: [A3-T1, A3-T2]
5: [A3-T1, A3-T2]

Only the first 3 elements are processed, so about 1/2
the atlases are not used.
@hjmjohnson
BUG: MSE requires both images are scaled similarly
2d85646 
Scaling the target, but not the atlases results in invalid
MSE minimized results when searching local regions.

TARGET[i] = [ 1, 1, 1, 1]
NORMALIZED_TARGET[i]=[ 0, 0, 0 ,0]

ATLAS[i]  = [ 1, 1, 1, 1]
ATLAS[i+1]= [ 0, 1, 1, 1]

MSE (NORMALIZED_TARGET[i], ATLAS[i])   = 4
MSE (NORMALIZED_TARGET[i], ATLAS[i+1]) = 3
@hjmjohnson hjmjohnson self-assigned this Feb 5, 2022
@ntustison
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Thanks again, @hjmjohnson . This is great.

@ntustison ntustison merged commit b9a1b74 into ANTsX:master Feb 5, 2022
@ntustison
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@hjmjohnson , I'm seeing the same thing on the failed Circle-CI build and on my local machine. Any suggestions?

(base) ntustison@Histograms ANTS-build % make antsJointFusion
[ 66%] Built target antsUtilities
Scanning dependencies of target l_antsJointFusion
[ 66%] Building CXX object Examples/CMakeFiles/l_antsJointFusion.dir/antsJointFusion.cxx.o
In file included from <built-in>:408:
<command line>:3:9: warning: 'vtkRenderingCore_AUTOINIT' macro redefined [-Wmacro-redefined]
#define vtkRenderingCore_AUTOINIT 3(vtkInteractionStyle,vtkRenderingFreeType,vtkRenderingOpenGL2)
        ^
<command line>:2:9: note: previous definition is here
#define vtkRenderingCore_AUTOINIT 2(vtkRenderingFreeType,vtkRenderingOpenGL2)
        ^
In file included from /Users/ntustison/Pkg/ANTs/Examples/antsJointFusion.cxx:8:
In file included from /Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.h:390:
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:528:80: error: expected ':' after 'case'
        case NonLocalPatchBasedImageFilterEnums::SimilarityMetric::MEAN_SQUARES):
                                                                               ^
                                                                               :
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:528:80: error: expected expression
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:533:87: error: expected ':' after 'case'
        case NonLocalPatchBasedImageFilterEnums::SimilarityMetric::PEARSON_CORRELATION):
                                                                                      ^
                                                                                      :
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:533:87: error: expected expression
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:539:11: error: use of undeclared identifier 'itkGenericException'
          itkGenericException("Invalid SimilarityMetric Chosen.");
          ^
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:542:10: error: expected ';' at end of declaration
        }
         ^
         ;
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:524:24: error: no viable conversion from '(lambda at /Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:524:42)' to 'const itk::WeightedVotingFusionImageFilter::RealType' (aka 'const double')
        const RealType patchSimilarity = [&] () -> RealType {
                       ^                 ~~~~~~~~~~~~~~~~~~~~
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:409:11: note: in instantiation of member function 'itk::WeightedVotingFusionImageFilter<itk::Image<float, 2>, itk::Image<unsigned int, 2>>::ThreadedGenerateDataForWeightedAveraging' requested here
    this->ThreadedGenerateDataForWeightedAveraging( region, threadId );
          ^
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.h:316:3: note: in instantiation of member function 'itk::WeightedVotingFusionImageFilter<itk::Image<float, 2>, itk::Image<unsigned int, 2>>::ThreadedGenerateData' requested here
  WeightedVotingFusionImageFilter();
  ^
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.h:67:16: note: in instantiation of member function 'itk::WeightedVotingFusionImageFilter<itk::Image<float, 2>, itk::Image<unsigned int, 2>>::WeightedVotingFusionImageFilter' requested here
  itkNewMacro( Self );
               ^
/Users/ntustison/Pkg/ANTs/Examples/antsJointFusion.cxx:142:71: note: in instantiation of member function 'itk::WeightedVotingFusionImageFilter<itk::Image<float, 2>, itk::Image<unsigned int, 2>>::New' requested here
  typename FusionFilterType::Pointer fusionFilter = FusionFilterType::New();
                                                                      ^
/Users/ntustison/Pkg/ANTs/Examples/antsJointFusion.cxx:1013:14: note: in instantiation of function template specialization 'ants::antsJointFusion<2>' requested here
      return antsJointFusion<2>( parser );
             ^
In file included from /Users/ntustison/Pkg/ANTs/Examples/antsJointFusion.cxx:8:
In file included from /Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.h:390:
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:524:24: error: no viable conversion from '(lambda at /Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:524:42)' to 'const itk::WeightedVotingFusionImageFilter::RealType' (aka 'const double')
        const RealType patchSimilarity = [&] () -> RealType {
                       ^                 ~~~~~~~~~~~~~~~~~~~~
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:409:11: note: in instantiation of member function 'itk::WeightedVotingFusionImageFilter<itk::Image<float, 3>, itk::Image<unsigned int, 3>>::ThreadedGenerateDataForWeightedAveraging' requested here
    this->ThreadedGenerateDataForWeightedAveraging( region, threadId );
          ^
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.h:316:3: note: in instantiation of member function 'itk::WeightedVotingFusionImageFilter<itk::Image<float, 3>, itk::Image<unsigned int, 3>>::ThreadedGenerateData' requested here
  WeightedVotingFusionImageFilter();
  ^
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.h:67:16: note: in instantiation of member function 'itk::WeightedVotingFusionImageFilter<itk::Image<float, 3>, itk::Image<unsigned int, 3>>::WeightedVotingFusionImageFilter' requested here
  itkNewMacro( Self );
               ^
/Users/ntustison/Pkg/ANTs/Examples/antsJointFusion.cxx:142:71: note: in instantiation of member function 'itk::WeightedVotingFusionImageFilter<itk::Image<float, 3>, itk::Image<unsigned int, 3>>::New' requested here
  typename FusionFilterType::Pointer fusionFilter = FusionFilterType::New();
                                                                      ^
/Users/ntustison/Pkg/ANTs/Examples/antsJointFusion.cxx:1018:14: note: in instantiation of function template specialization 'ants::antsJointFusion<3>' requested here
      return antsJointFusion<3>( parser );
             ^
In file included from /Users/ntustison/Pkg/ANTs/Examples/antsJointFusion.cxx:8:
In file included from /Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.h:390:
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:524:24: error: no viable conversion from '(lambda at /Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:524:42)' to 'const itk::WeightedVotingFusionImageFilter::RealType' (aka 'const double')
        const RealType patchSimilarity = [&] () -> RealType {
                       ^                 ~~~~~~~~~~~~~~~~~~~~
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.hxx:409:11: note: in instantiation of member function 'itk::WeightedVotingFusionImageFilter<itk::Image<float, 4>, itk::Image<unsigned int, 4>>::ThreadedGenerateDataForWeightedAveraging' requested here
    this->ThreadedGenerateDataForWeightedAveraging( region, threadId );
          ^
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.h:316:3: note: in instantiation of member function 'itk::WeightedVotingFusionImageFilter<itk::Image<float, 4>, itk::Image<unsigned int, 4>>::ThreadedGenerateData' requested here
  WeightedVotingFusionImageFilter();
  ^
/Users/ntustison/Pkg/ANTs/ImageSegmentation/itkWeightedVotingFusionImageFilter.h:67:16: note: in instantiation of member function 'itk::WeightedVotingFusionImageFilter<itk::Image<float, 4>, itk::Image<unsigned int, 4>>::WeightedVotingFusionImageFilter' requested here
  itkNewMacro( Self );
               ^
/Users/ntustison/Pkg/ANTs/Examples/antsJointFusion.cxx:142:71: note: in instantiation of member function 'itk::WeightedVotingFusionImageFilter<itk::Image<float, 4>, itk::Image<unsigned int, 4>>::New' requested here
  typename FusionFilterType::Pointer fusionFilter = FusionFilterType::New();
                                                                      ^
/Users/ntustison/Pkg/ANTs/Examples/antsJointFusion.cxx:1023:14: note: in instantiation of function template specialization 'ants::antsJointFusion<4>' requested here
      return antsJointFusion<4>( parser );
             ^
1 warning and 9 errors generated.
make[3]: *** [Examples/CMakeFiles/l_antsJointFusion.dir/antsJointFusion.cxx.o] Error 1
make[2]: *** [Examples/CMakeFiles/l_antsJointFusion.dir/all] Error 2
make[1]: *** [Examples/CMakeFiles/antsJointFusion.dir/rule] Error 2
make: *** [antsJointFusion] Error 2

@hjmjohnson
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@ntustison I'm looking right now. I think I may have compiled the wrong ant's directory with a different codebase for testing, and then pre-maturely pushed.

@hjmjohnson
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@ntustison I fixed the obvious syntax errors. I don't usually build with VTK, so those errors are going to take me a few minutes to build VTK and identify.

PR arriving shortly (at least for the non VTK mistakes).

@cookpa cookpa mentioned this pull request Mar 7, 2022
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@ntustison ntustison Awaiting requested review from ntustison

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