ENH: Add sparse threader for ANTS CC metric

Add support to use sparse sampling of a point set with ANTS
CC metric. The implementation of the dense metric is integrated
with this sparse metric, by overloading corresponding functions.

ENH: Remove files of the dense threader class of ANTS CC.

The implementation of both dense and sparse threaders for ANTS CC
metric are now integrated in one class template by specialing different
domain threader types. A helper class is added for overloading by
different threader partitioner type.

ENH: Add test for sparse threader in ANTS registration test

ENH: Add test for sparse threader in ANTS CC metric test

ENH: moved the InitializeScaning from metric class to threader

Since all computation are now in the threader, it makes sense
to move InitializaScanning and all related types to the threader
class. The ANTS CC metric class is more like a wrapper class
to encapsulate the threader class and store metric options.

STYLE: updated with detailed comments for function overloading

Function overloading is used here to intergrate sparse and dense
threaers under the same class.

STYLE: indentation etc.

COMP: add a missing header file

Change-Id: I9c2c01f813030d7db8be30ef221b8d3cb015b54d

Modules/Core/Common/include/itkDomainThreader.h

@@ -55,7 +55,7 @@ namespace itk
  *
  *  \tparam TDomainPartitioner A class that inherits from
  *  ThreadedDomainPartitioner.
- *  \tparam TAssociate  The asssociated class that uses a derived version of
+ *  \tparam TAssociate  The associated class that uses a derived version of
  *  this class as a "threaded method".  The associated class usually declares
  *  derived version of this class as nested classes so there is easy access to
  *  its protected and private members in ThreadedExecution.

Modules/Registration/Metricsv4/include/itkANTSNeighborhoodCorrelationImageToImageMetricv4.h

@@ -19,9 +19,7 @@
 #define __itkANTSNeighborhoodCorrelationImageToImageMetricv4_h
 
 #include "itkImageToImageMetricv4.h"
-#include "itkConstNeighborhoodIterator.h"
-
-#include "itkANTSNeighborhoodCorrelationImageToImageMetricv4DenseGetValueAndDerivativeThreader.h"
+#include "itkANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader.h"
 
 #include <deque>
 
@@ -177,59 +175,13 @@ class ITK_EXPORT ANTSNeighborhoodCorrelationImageToImageMetricv4 :
   ANTSNeighborhoodCorrelationImageToImageMetricv4();
   virtual ~ANTSNeighborhoodCorrelationImageToImageMetricv4();
 
-  // interested values here updated during scanning
-  typedef InternalComputationValueType                 QueueRealType;
-  typedef std::deque<QueueRealType>                    SumQueueType;
-  typedef ConstNeighborhoodIterator<VirtualImageType>  ScanIteratorType;
-
-  // one ScanMemType for each thread
-  typedef struct ScanMemType {
-    // queues used in the scanning
-    // sum of the fixed value squared
-    SumQueueType QsumFixed2;
-    // sum of the moving value squared
-    SumQueueType QsumMoving2;
-    SumQueueType QsumFixed;
-    SumQueueType QsumMoving;
-    SumQueueType QsumFixedMoving;
-    SumQueueType Qcount;
-
-    QueueRealType fixedA;
-    QueueRealType movingA;
-    QueueRealType sFixedMoving;
-    QueueRealType sFixedFixed;
-    QueueRealType sMovingMoving;
-
-    FixedImageGradientType  fixedImageGradient;
-    MovingImageGradientType movingImageGradient;
-
-    FixedImagePointType     mappedFixedPoint;
-    MovingImagePointType    mappedMovingPoint;
-    VirtualPointType        virtualPoint;
-  } ScanMemType;
-
-  typedef struct ScanParametersType {
-    // const values during scanning
-    ImageRegionType scanRegion;
-    SizeValueType   numberOfFillZero; // for each queue
-    SizeValueType   windowLength; // number of voxels in the scanning window
-    IndexValueType  scanRegionBeginIndexDim0;
-
-    typename FixedImageType::ConstPointer   fixedImage;
-    typename MovingImageType::ConstPointer  movingImage;
-    typename VirtualImageType::ConstPointer virtualImage;
-    RadiusType radius;
-
-  } ScanParametersType;
-
-  friend class ANTSNeighborhoodCorrelationImageToImageMetricv4DenseGetValueAndDerivativeThreader< Superclass, Self >;
-  typedef ANTSNeighborhoodCorrelationImageToImageMetricv4DenseGetValueAndDerivativeThreader< Superclass, Self >
+  friend class ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader< ThreadedImageRegionPartitioner< VirtualImageDimension >, Superclass, Self >;
+  typedef ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader< ThreadedImageRegionPartitioner< VirtualImageDimension >, Superclass, Self >
     ANTSNeighborhoodCorrelationImageToImageMetricv4DenseGetValueAndDerivativeThreaderType;
 
-  /** Create an iterator over the virtual sub region */
-  void InitializeScanning(const ImageRegionType &scanRegion,
-    ScanIteratorType &scanIt, ScanMemType &scanMem,
-    ScanParametersType &scanParameters ) const;
+  friend class ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader< ThreadedIndexedContainerPartitioner, Superclass, Self >;
+  typedef ANTSNeighborhoodCorrelationImageToImageMetricv4GetValueAndDerivativeThreader< ThreadedIndexedContainerPartitioner, Superclass, Self >
+    ANTSNeighborhoodCorrelationImageToImageMetricv4SparseGetValueAndDerivativeThreaderType;
 
   virtual void PrintSelf(std::ostream & os, Indent indent) const;
 

Modules/Registration/Metricsv4/include/itkANTSNeighborhoodCorrelationImageToImageMetricv4.hxx

@@ -34,8 +34,7 @@ ANTSNeighborhoodCorrelationImageToImageMetricv4<TFixedImage, TMovingImage,TVirtu
   // We have our own GetValueAndDerivativeThreader's that we want
   // ImageToImageMetricv4 to use.
   this->m_DenseGetValueAndDerivativeThreader  = ANTSNeighborhoodCorrelationImageToImageMetricv4DenseGetValueAndDerivativeThreaderType::New();
-  // not implemented
-  //this->m_SparseGetValueAndDerivativeThreader =
+  this->m_SparseGetValueAndDerivativeThreader = ANTSNeighborhoodCorrelationImageToImageMetricv4SparseGetValueAndDerivativeThreaderType::New();
 }
 
 template<class TFixedImage, class TMovingImage, class TVirtualImage>
@@ -49,51 +48,9 @@ void
 ANTSNeighborhoodCorrelationImageToImageMetricv4<TFixedImage, TMovingImage, TVirtualImage>
 ::Initialize(void) throw ( itk::ExceptionObject )
 {
-  if( this->GetUseFixedSampledPointSet() )
-    {
-    itkExceptionMacro("UseFixedSampledPointSet is set, but not supported in this metric.");
-    }
   Superclass::Initialize();
 }
 
-template<class TFixedImage, class TMovingImage, class TVirtualImage>
-void
-ANTSNeighborhoodCorrelationImageToImageMetricv4<TFixedImage, TMovingImage, TVirtualImage>
-::InitializeScanning( const ImageRegionType &scanRegion, ScanIteratorType &scanIt,
-                      ScanMemType & scanMem, ScanParametersType &scanParameters ) const
-{
-  scanParameters.scanRegion   = scanRegion;
-  scanParameters.fixedImage   = this->m_FixedImage;
-  scanParameters.movingImage  = this->m_MovingImage;
-  scanParameters.virtualImage = this->GetVirtualImage();
-  scanParameters.radius       = this->GetRadius();
-
-  OffsetValueType numberOfFillZero = this->GetVirtualRegion().GetIndex(0)
-      - (scanRegion.GetIndex(0) - scanParameters.radius[0]);
-
-  if (numberOfFillZero < NumericTraits<OffsetValueType>::ZeroValue())
-    {
-    numberOfFillZero = NumericTraits<OffsetValueType>::ZeroValue();
-    }
-
-  scanParameters.numberOfFillZero = numberOfFillZero;
-
-  scanIt = ScanIteratorType(scanParameters.radius, scanParameters.virtualImage, scanRegion);
-  scanParameters.windowLength = scanIt.Size();
-  scanParameters.scanRegionBeginIndexDim0 = scanIt.GetBeginIndex()[0];
-
-  scanMem.fixedA = NumericTraits< QueueRealType >::Zero;
-  scanMem.movingA = NumericTraits< QueueRealType >::Zero;
-  scanMem.sFixedMoving = NumericTraits< QueueRealType >::Zero;
-  scanMem.sFixedFixed = NumericTraits< QueueRealType >::Zero;
-  scanMem.sMovingMoving = NumericTraits< QueueRealType >::Zero;
-
-  scanMem.fixedImageGradient.Fill(0.0);
-  scanMem.movingImageGradient.Fill(0.0);
-  scanMem.mappedMovingPoint.Fill(0.0);
-}
-
-
 template<class TFixedImage, class TMovingImage, class TVirtualImage>
 void
 ANTSNeighborhoodCorrelationImageToImageMetricv4<TFixedImage, TMovingImage, TVirtualImage>