COMP: Address warnings

Fixed unused variables, functions hidden by derived classes, and
variable types.

Also fixed lurking bugs related to variables being used before being set.

src/Filtering/itktubeAnisotropicDiffusionTensorFunction.h

@@ -259,6 +259,7 @@ class AnisotropicDiffusionTensorFunction
 
   TimeStepType    m_TimeStep;
   bool            m_UseImageSpacing;
+  SpacingType     m_Spacing{1};
 
 }; // End class AnisotropicDiffusionTensorFunction
 

src/Filtering/itktubeAnisotropicDiffusionTensorFunction.hxx

@@ -90,6 +90,7 @@ AnisotropicDiffusionTensorFunction< TImageType >
 {
   DiffusionTensorNeighborhoodType tensorNeighborhood;
   SpacingType                     spacing;
+  spacing = m_Spacing;
   return this->ComputeUpdate( neighborhood,
                               tensorNeighborhood,
                               spacing,
@@ -314,6 +315,7 @@ AnisotropicDiffusionTensorFunction<TImageType>
   if( useImageSpacing )
     {
     minSpacing = input->GetSpacing()[0];
+    m_Spacing = input->GetSpacing();
     for( unsigned int i = 1; i < ImageDimension; i++ )
       {
       if( input->GetSpacing()[i] < minSpacing )
@@ -325,6 +327,7 @@ AnisotropicDiffusionTensorFunction<TImageType>
   else
     {
     minSpacing = 1.0;
+    m_Spacing.Fill(1.0);
     }
 
   // TODO plus 1?

src/Filtering/itktubeShrinkWithBlendingImageFilter.hxx

@@ -161,7 +161,7 @@ ShrinkWithBlendingImageFilter< TInputImage, TOutputImage >
   // We wish to perform the following mapping of outputIndex to
   // inputIndex on all points in our region
   outputPtr->TransformIndexToPhysicalPoint( outputIndex, tempPoint );
-  bool isInside = inputPtr->TransformPhysicalPointToIndex( tempPoint, inputIndex );
+  std::ignore = inputPtr->TransformPhysicalPointToIndex( tempPoint, inputIndex );
 
   // Support progress methods/callbacks
   ProgressReporter progress( this, threadId,
@@ -205,7 +205,7 @@ ShrinkWithBlendingImageFilter< TInputImage, TOutputImage >
         curMipPoint[i] = inputMipPointItPtr->Get()[i];
         }
 
-      isInside = inputPtr->TransformPhysicalPointToIndex( curMipPoint, inputIndex );
+      std::ignore = inputPtr->TransformPhysicalPointToIndex( curMipPoint, inputIndex );
 
       // set output pixel intensity as intensity of input pixel at mip point
       outIt.Set( inputPtr->GetPixel( inputIndex ) );
@@ -225,7 +225,7 @@ ShrinkWithBlendingImageFilter< TInputImage, TOutputImage >
     outputIndex = outIt.GetIndex();
 
     outputPtr->TransformIndexToPhysicalPoint( outputIndex, tempPoint );
-    isInside = inputPtr->TransformPhysicalPointToIndex( tempPoint, inputIndex );
+    std::ignore = inputPtr->TransformPhysicalPointToIndex( tempPoint, inputIndex );
 
     for( unsigned int i = 0; i < ImageDimension; ++i )
       {
@@ -484,7 +484,7 @@ ShrinkWithBlendingImageFilter< TInputImage, TOutputImage >
 
   outputPtr->TransformIndexToPhysicalPoint( outputRequestedRegionStartIndex,
     tempPoint );
-  bool isInside = inputPtr->TransformPhysicalPointToIndex( tempPoint,
+  std::ignore = inputPtr->TransformPhysicalPointToIndex( tempPoint,
     inputRequestedRegionStartIndex );
   for( unsigned int i = 0; i < TInputImage::ImageDimension; i++ )
     {

src/Filtering/itktubeSpatialObjectFilter.h

@@ -63,10 +63,14 @@ class SpatialObjectFilter
   SpatialObjectFilter( void );
   virtual ~SpatialObjectFilter( void ) {}
 
-  // To remove warning "was hidden [-Woverloaded-virtual]"
-  void SetInput( const typename Superclass::DataObjectIdentifierType &,
+    // from itkProcessObject
+  virtual void SetInput( const
+    itk::ProcessObject::DataObjectIdentifierType &,
     itk::DataObject * ) override {};
 
+  virtual void SetInput( unsigned int, const SpatialObjectType *
+    ) override {};
+
 private:
   // purposely not implemented
   SpatialObjectFilter( const Self & );

src/Filtering/itktubeSpatialObjectToSpatialObjectFilter.h

@@ -70,6 +70,10 @@ class SpatialObjectToSpatialObjectFilter
   SpatialObjectToSpatialObjectFilter( void );
   virtual ~SpatialObjectToSpatialObjectFilter( void ) {}
 
+  // To remove warning "was hidden [-Woverloaded-virtual]"
+  //void SetInput( const typename Superclass::DataObjectIdentifierType &,
+    //itk::DataObject * ) override {};
+
 private:
   // purposely not implemented
   SpatialObjectToSpatialObjectFilter( const Self & );

src/Filtering/itktubeSymmetricEigenVectorAnalysisImageFilter.h

@@ -66,6 +66,7 @@ class SymmetricEigenVectorAnalysisFunction
   inline TMatrix operator()( const TInput & x )
     {
     TOutput      eigenValues;
+    eigenValues.Fill(0);
     TMatrix eigenVectorMatrix;
     m_Calculator.ComputeEigenValuesAndVectors( x, eigenValues,
       eigenVectorMatrix );

src/MetaIO/itktubeMetaClassPDF.cxx

@@ -169,7 +169,7 @@ PrintInfo( void ) const
   if( ! m_ObjectId.empty() )
     {
     std::cout << m_ObjectId[0];
-    for( int i = 1; i < m_ObjectId.size(); i++ )
+    for( std::vector<double>::size_type i = 1; i < m_ObjectId.size(); i++ )
       {
       std::cout << ", " << m_ObjectId[i];
       }
@@ -878,9 +878,6 @@ M_Read( void )
       }
     }
 
-  unsigned int nFeatures = static_cast< unsigned int >(
-    MetaImage::NDims() );
-
   MET_FieldRecordType * mF = MET_GetFieldRecord( "NObjects",
     &m_Fields );
   unsigned int nObjects = ( unsigned int )mF->value[0];

src/ObjectDocuments/itktubeObjectDocumentToImageFilter.hxx

@@ -137,10 +137,16 @@ ObjectDocumentToImageFilter< TObjectDocument, TImageType >
   PointType & origin ) const
 {
   SizeType size = image->GetLargestPossibleRegion().GetSize();
+  PointType point;
   PointType maximum;
 
-  // Fill origin ( minimum value with large number ).
-  origin.Fill( 9999999 );
+  typename ImageType::IndexType index;
+  index.Fill(0);
+  image->TransformIndexToPhysicalPoint( index, point );
+  point = transform->TransformPoint( point );
+
+  origin = point;
+  maximum = point;
 
   // Transform all of the image corners and determine the minimum bounding
   // box.
@@ -150,14 +156,11 @@ ObjectDocumentToImageFilter< TObjectDocument, TImageType >
       {
       for( unsigned int z = 0; z <= size[2]; z += size[2] )
         {
-        typename ImageType::IndexType index;
 
         index[0] = x;
         index[1] = y;
         index[2] = z;
 
-        PointType point;
-
         image->TransformIndexToPhysicalPoint( index, point );
         point = transform->TransformPoint( point );
 

src/Registration/itkBSplineImageToImageRegistrationMethod.hxx

@@ -472,11 +472,6 @@ BSplineImageToImageRegistrationMethod<TImage>
   fixedPyramid->SetNumberOfLevels( numberOfLevelsUsing );
   movingPyramid->SetNumberOfLevels( numberOfLevelsUsing );
 
-  typename ImageType::SpacingType fixedSpacing =
-    this->GetFixedImage()->GetSpacing();
-  typename ImageType::SpacingType movingSpacing =
-    this->GetFixedImage()->GetSpacing();
-
   typename PyramidType::ScheduleType fixedSchedule =
     fixedPyramid->GetSchedule();
   typename PyramidType::ScheduleType movingSchedule =

src/Registration/itktubeMergeAdjacentImagesFilter.hxx

@@ -220,7 +220,7 @@ MergeAdjacentImagesFilter< TImage >
     pointX = m_InitialTransform->GetInverseTransform()->TransformPoint( pointX );
     }
 
-  bool isInside = m_Input1->TransformPhysicalPointToIndex( pointX, minX2 );
+  std::ignore = m_Input1->TransformPhysicalPointToIndex( pointX, minX2 );
 
   typename ImageType::SizeType size2 =
     m_Input2->GetLargestPossibleRegion().GetSize();
@@ -243,7 +243,7 @@ MergeAdjacentImagesFilter< TImage >
     {
     pointX = m_InitialTransform->GetInverseTransform()->TransformPoint( pointX );
     }
-  isInside = m_Input1->TransformPhysicalPointToIndex( pointX, maxX2 );
+  std::ignore = m_Input1->TransformPhysicalPointToIndex( pointX, maxX2 );
 
   // compute min-max coord and size of output
   for( unsigned int i = 0; i < ImageDimension; i++ )

src/Segmentation/itktubeRadiusExtractor2.hxx

@@ -303,7 +303,6 @@ RadiusExtractor2<TInputImage>
   int tempI;
   while( pntIter != m_KernelTube->GetPoints().end() )
     {
-    IndexType kernelPointI;
     if( !m_InputImage->TransformPhysicalPointToIndex(
       pntIter->GetPositionInObjectSpace(), kernelPointI ) )
       {

src/Segmentation/itktubeRadiusExtractor3.hxx

@@ -400,7 +400,7 @@ RadiusExtractor3<TInputImage>
   while( pntIter != m_KernelTube->GetPoints().end() )
     {
     p = pntIter->GetPositionInObjectSpace();
-    bool isInside = m_InputImage->TransformPhysicalPointToIndex( p, kernelPointIndex );
+    isInside = m_InputImage->TransformPhysicalPointToIndex( p, kernelPointIndex );
     if( !isInside )
       {
       ++pntIter;

test/Filtering/itktubeSubSampleSpatialObjectFilterTest.cxx

@@ -39,7 +39,6 @@ int itktubeSubSampleSpatialObjectFilterTest( int argc, char * argv[] )
   const char * outputTubeNetwork = argv[2];
 
   enum { Dimension = 3 };
-  typedef itk::TubeSpatialObject< Dimension >   TubeSpatialObjectType;
   typedef itk::GroupSpatialObject< Dimension >  GroupSpatialObjectType;
 
   // Read input tube tree.

test/Registration/itktubeSpatialObjectToImageRegistrationTest.cxx

@@ -55,7 +55,6 @@ int itktubeSpatialObjectToImageRegistrationTest( int argc, char * argv[] )
   enum { ObjectDimension = 3 };
   typedef double            FloatType;
 
-  typedef itk::TubeSpatialObject< ObjectDimension >            TubeType;
   typedef itk::GroupSpatialObject< ObjectDimension >           GroupType;
   typedef itk::SpatialObjectReader< ObjectDimension >          SOReaderType;
   typedef itk::Image< FloatType, ObjectDimension >             ImageType;

test/Segmentation/itktubeRidgeExtractorTest2.cxx

@@ -187,7 +187,7 @@ int itktubeRidgeExtractorTest2( int argc, char * argv[] )
     if( ridgeOp->LocalRidge( xRidgePnt ) != RidgeOpType::SUCCESS )
       {
       RidgeOpType::ContinuousIndexType xRidgeContI;
-      bool isInside = im->TransformPhysicalPointToContinuousIndex( xRidgePnt,
+      std::ignore = im->TransformPhysicalPointToContinuousIndex( xRidgePnt,
         xRidgeContI );
       std::cout << "*** FAILURE: Local ridge test failed.  No ridge found."
         << std::endl;
@@ -205,7 +205,7 @@ int itktubeRidgeExtractorTest2( int argc, char * argv[] )
       continue;
       }
     RidgeOpType::ContinuousIndexType xRidgeContI;
-    bool isInside = im->TransformPhysicalPointToContinuousIndex( xRidgePnt,
+    std::ignore = im->TransformPhysicalPointToContinuousIndex( xRidgePnt,
       xRidgeContI );
 
     double diff = 0;