Addressing warnings

.clang-format

@@ -48,7 +48,7 @@ DerivePointerAlignment: false
 DisableFormat:   false
 ExperimentalAutoDetectBinPacking: false
 ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
-IncludeCategories: 
+IncludeCategories:
   - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
     Priority:        2
   - Regex:           '^(<|"(gtest|isl|json)/)'

include/itkRLEImage.h

@@ -70,6 +70,8 @@ class RLEImage :
   * or other operations. */
   typedef TPixel PixelType;
 
+  typedef CounterType RLCounterType;
+
   /** Typedef alias for PixelType */
   typedef TPixel ValueType;
 
@@ -180,7 +182,7 @@ class RLEImage :
   * Returns difference in line length which happens due to merging or splitting segments.
   * This method is used by iterators directly. */
   int
-  SetPixel( RLLine& line, IndexValueType& segmentRemainder, IndexValueType& m_RealIndex, const TPixel& value );
+  SetPixel( RLLine& line, IndexValueType& segmentRemainder, SizeValueType& m_RealIndex, const TPixel& value );
 
   /** \brief Get a pixel. SLOW! Better use iterators for pixel access. */
   const TPixel&
@@ -312,4 +314,4 @@ class RLEImage :
 #include "itkRLEImage.hxx"
 #endif
 
-#endif // itkRLEImage_h
+#endif // itkRLEImage_h

include/itkRLEImage.hxx

@@ -139,7 +139,7 @@ RLEImage< TPixel, VImageDimension, CounterType >
 template < typename TPixel, unsigned int VImageDimension, typename CounterType >
 int
 RLEImage< TPixel, VImageDimension, CounterType >
-::SetPixel( RLLine& line, IndexValueType& segmentRemainder, IndexValueType& m_RealIndex, const TPixel& value )
+::SetPixel( RLLine& line, IndexValueType& segmentRemainder, SizeValueType& m_RealIndex, const TPixel& value )
 {
   // complete Run-Length Lines have to be buffered
   itkAssertOrThrowMacro( this->GetBufferedRegion().GetSize( 0 ) == this->GetLargestPossibleRegion().GetSize( 0 ), "BufferedRegion must contain complete run-length lines!" );
@@ -237,7 +237,7 @@ RLEImage< TPixel, VImageDimension, CounterType >
   typename BufferType::IndexType bi = truncateIndex( index );
   RLLine&        line = m_Buffer->GetPixel( bi );
   IndexValueType t = 0;
-  for ( IndexValueType x = 0; x < line.size(); x++ )
+  for ( SizeValueType x = 0; x < line.size(); x++ )
     {
     t += line[x].first;
     if ( t > index[0] - bri0 )
@@ -261,7 +261,7 @@ RLEImage< TPixel, VImageDimension, CounterType >
   typename BufferType::IndexType bi = truncateIndex( index );
   RLLine&        line = m_Buffer->GetPixel( bi );
   IndexValueType t = 0;
-  for ( IndexValueType x = 0; x < line.size(); x++ )
+  for ( SizeValueType x = 0; x < line.size(); x++ )
     {
     t += line[x].first;
     if ( t > index[0] - bri0 )
@@ -299,4 +299,4 @@ RLEImage< TPixel, VImageDimension, CounterType >
   os.precision( prec );
 } // >::PrintSelf
 } // end namespace itk
-#endif // itkRLEImage_hxx
+#endif // itkRLEImage_hxx

include/itkRLEImageConstIterator.h

@@ -388,7 +388,7 @@ friend class ::MultiLabelMeshPipeline;
 
   const RLLine* m_RunLengthLine;
 
-  mutable IndexValueType m_RealIndex;        // index into line's segment
+  mutable SizeValueType  m_RealIndex;        // index into line's segment
   mutable IndexValueType m_SegmentRemainder; // how many pixels remain in current segment
 
   IndexValueType m_BeginIndex0; // index to first pixel in region in relation to buffer start
@@ -474,4 +474,4 @@ class ImageConstIteratorWithOnlyIndex< RLEImage< TPixel, VImageDimension, Counte
 }; // no additional implementation required
 } // end namespace itk
 
-#endif // itkRLEImageConstIterator_h
+#endif // itkRLEImageConstIterator_h

include/itkRLEImageIterator.h

@@ -171,4 +171,4 @@ class ImageIteratorWithIndex< RLEImage< TPixel, VImageDimension, CounterType > >
 }; // no additional implementation required
 } // end namespace itk
 
-#endif // itkRLEImageIterator_h
+#endif // itkRLEImageIterator_h

include/itkRLEImageRegionConstIterator.h

@@ -251,4 +251,4 @@ class ImageRegionConstIteratorWithOnlyIndex< RLEImage< TPixel, VImageDimension,
 }; // no additional implementation required
 } // end namespace itk
 
-#endif // itkRLEImageRegionConstIterator_h
+#endif // itkRLEImageRegionConstIterator_h

include/itkRLEImageRegionIterator.h

@@ -158,4 +158,4 @@ class ImageRegionIteratorWithIndex< RLEImage< TPixel, VImageDimension, CounterTy
 }; // no additional implementation required
 } // end namespace itk
 
-#endif // itkRLEImageRegionIterator_h
+#endif // itkRLEImageRegionIterator_h

include/itkRLEImageScanlineConstIterator.h

@@ -177,4 +177,4 @@ class ImageScanlineConstIterator< RLEImage< TPixel, VImageDimension, CounterType
 };
 } // end namespace itk
 
-#endif // itkRLEImageScanlineConstIterator_h
+#endif // itkRLEImageScanlineConstIterator_h

include/itkRLEImageScanlineIterator.h

@@ -100,4 +100,4 @@ class ImageScanlineIterator< RLEImage< TPixel, VImageDimension, CounterType > >
 };
 } // end namespace itk
 
-#endif // itkRLEImageScanlineIterator_h
+#endif // itkRLEImageScanlineIterator_h

include/itkRLERegionOfInterestImageFilter.h

@@ -131,6 +131,105 @@ class RegionOfInterestImageFilter< RLEImage< TPixel, VImageDimension, CounterTyp
   RegionType m_RegionOfInterest;
 };
 
+template < typename TPixelIn, typename TPixelOut, unsigned int VImageDimension, typename CounterTypeIn, typename CounterTypeOut >
+class RegionOfInterestImageFilter< RLEImage< TPixelIn, VImageDimension, CounterTypeIn >, RLEImage< TPixelOut, VImageDimension, CounterTypeOut > >
+  : public ImageToImageFilter< RLEImage< TPixelIn, VImageDimension, CounterTypeIn >, RLEImage< TPixelOut, VImageDimension, CounterTypeOut > >
+{
+public:
+  /** Standard class typedefs. */
+  typedef RegionOfInterestImageFilter                            Self;
+  typedef RLEImage< TPixelIn, VImageDimension, CounterTypeIn >   RLEImageTypeIn;
+  typedef RLEImage< TPixelOut, VImageDimension, CounterTypeOut > RLEImageTypeOut;
+  typedef RLEImageTypeOut                                        ImageType;
+  typedef ImageToImageFilter< RLEImageTypeIn, RLEImageTypeOut >  Superclass;
+  typedef SmartPointer< Self >                                   Pointer;
+  typedef SmartPointer< const Self >                             ConstPointer;
+  typedef typename Superclass::InputImageRegionType              InputImageRegionType;
+
+  /** Method for creation through the object factory. */
+  itkNewMacro( Self );
+
+  /** Run-time type information (and related methods). */
+  itkTypeMacro( RegionOfInterestImageFilter, ImageToImageFilter );
+
+  /** Typedef to describe the input image region types. */
+  typedef typename RLEImageTypeIn::RegionType RegionType;
+  typedef typename RLEImageTypeIn::IndexType  IndexType;
+  typedef typename RLEImageTypeIn::SizeType   SizeType;
+
+  /** Typedef to describe the type of pixel. */
+  typedef typename RLEImageTypeOut::PixelType OutputImagePixelType;
+  typedef typename RLEImageTypeIn::PixelType  InputImagePixelType;
+
+  /** Set/Get the output image region. */
+  itkSetMacro( RegionOfInterest, RegionType );
+  itkGetConstMacro( RegionOfInterest, RegionType );
+
+  /** ImageDimension enumeration */
+  itkStaticConstMacro( ImageDimension, unsigned int, VImageDimension );
+  itkStaticConstMacro( OutputImageDimension, unsigned int, VImageDimension );
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+  // Begin concept checking
+  itkConceptMacro( SameDimensionCheck, (Concept::SameDimension< ImageDimension, OutputImageDimension >));
+  itkConceptMacro( InputConvertibleToOutputCheck, (Concept::Convertible< InputImagePixelType, OutputImagePixelType >));
+// End concept checking
+#endif
+
+protected:
+  RegionOfInterestImageFilter() {}
+  ~RegionOfInterestImageFilter() {}
+  void
+  PrintSelf( std::ostream& os, Indent indent ) const;
+
+  virtual void
+  GenerateInputRequestedRegion();
+
+  virtual void
+  EnlargeOutputRequestedRegion( DataObject* output );
+
+  /** RegionOfInterestImageFilter can produce an image which is a different
+   * size than its input image.  As such, RegionOfInterestImageFilter
+   * needs to provide an implementation for
+   * GenerateOutputInformation() in order to inform the pipeline
+   * execution model.  The original documentation of this method is
+   * below.
+   *
+   * \sa ProcessObject::GenerateOutputInformaton()  */
+  virtual void
+  GenerateOutputInformation();
+
+  /** RegionOfInterestImageFilter can be implemented as a multithreaded filter.
+   * Therefore, this implementation provides a ThreadedGenerateData()
+   * routine which is called for each processing thread. The output
+   * image data is allocated automatically by the superclass prior to
+   * calling ThreadedGenerateData().  ThreadedGenerateData can only
+   * write to the portion of the output image specified by the
+   * parameter "outputRegionForThread"
+   * \sa ImageToImageFilter::ThreadedGenerateData(),
+   *     ImageToImageFilter::GenerateData()  */
+  void
+  ThreadedGenerateData( const RegionType& outputRegionForThread, ThreadIdType threadId );
+
+private:
+  RegionOfInterestImageFilter( const Self& ); // purposely not implemented
+  void
+  operator=( const Self& ); // purposely not implemented
+
+  RegionType m_RegionOfInterest;
+};
+
+//not implemented on purpose, so it will produce a meaningful error message
+template < unsigned int VImageDimensionIn, unsigned int VImageDimensionOut >
+class InputAndOutputImagesMustHaveSameDimension;
+
+//input and output images must have the same dimension (e.g. both 2D or both 3D)
+//so disallow this by inheriting from unimplemented base class
+template < typename TPixelIn, typename TPixelOut, unsigned int VImageDimensionIn, unsigned int VImageDimensionOut, typename CounterTypeIn, typename CounterTypeOut >
+class RegionOfInterestImageFilter< RLEImage< TPixelIn, VImageDimensionIn, CounterTypeIn >, RLEImage< TPixelOut, VImageDimensionOut, CounterTypeOut > >
+  : InputAndOutputImagesMustHaveSameDimension< VImageDimensionIn, VImageDimensionOut >
+{};
+
 template < typename TPixel, unsigned int VImageDimension, typename CounterType >
 class RegionOfInterestImageFilter< Image< TPixel, VImageDimension >, RLEImage< TPixel, VImageDimension, CounterType > >
   : public ImageToImageFilter< Image< TPixel, VImageDimension >, RLEImage< TPixel, VImageDimension, CounterType > >
@@ -312,4 +411,4 @@ class RegionOfInterestImageFilter< RLEImage< TPixel, VImageDimension, CounterTyp
 #include "itkRLERegionOfInterestImageFilter.hxx"
 #endif
 
-#endif // itkRLERegionOfInterestImageFilter_h
+#endif // itkRLERegionOfInterestImageFilter_h