diff --git a/Utilities/ITK/Code/Review/itkBinaryImageToLabelMapFilter.h b/Utilities/ITK/Code/Review/itkBinaryImageToLabelMapFilter.h
index 49c20b056664248c5df1864dcd3dff3ff64a038d..8835e6d8cf208bbc81923c9248a67ca31e21010f 100644
--- a/Utilities/ITK/Code/Review/itkBinaryImageToLabelMapFilter.h
+++ b/Utilities/ITK/Code/Review/itkBinaryImageToLabelMapFilter.h
@@ -26,8 +26,6 @@
#include "itkProgressReporter.h"
#include "itkBarrier.h"
-//patch OTB
-#include "itkLabelMap.h"
namespace itk
{
diff --git a/Utilities/InsightJournal/itkAttributeKeepNObjectsLabelMapFilter.h b/Utilities/InsightJournal/itkAttributeKeepNObjectsLabelMapFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..4c212e8f37dfc5fcd13dbb34b61c71d217c10be3
--- /dev/null
+++ b/Utilities/InsightJournal/itkAttributeKeepNObjectsLabelMapFilter.h
@@ -0,0 +1,141 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkAttributeKeepNObjectsLabelMapFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkAttributeKeepNObjectsLabelMapFilter_h
+#define __itkAttributeKeepNObjectsLabelMapFilter_h
+
+#include "itkInPlaceLabelMapFilter.h"
+#include "itkAttributeLabelObject.h"
+
+namespace itk {
+/** \class AttributeKeepNObjectsLabelMapFilter
+ * \brief keep N objects according to their attribute
+ *
+ * AttributeKeepNObjectsLabelMapFilter keep the N objects in a label collection image
+ * with the highest (or lowest) attribute value. The attribute is provide by an
+ * attribute accessor given in template parameter.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TImage, class TAttributeAccessor=
+ typename Functor::AttributeLabelObjectAccessor< typename TImage::LabelObjectType > >
+class ITK_EXPORT AttributeKeepNObjectsLabelMapFilter :
+ public InPlaceLabelMapFilter<TImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef AttributeKeepNObjectsLabelMapFilter Self;
+ typedef InPlaceLabelMapFilter<TImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TImage ImageType;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::PixelType PixelType;
+ typedef typename ImageType::IndexType IndexType;
+ typedef typename ImageType::LabelObjectType LabelObjectType;
+
+ typedef TAttributeAccessor AttributeAccessorType;
+ typedef typename AttributeAccessorType::AttributeValueType AttributeValueType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TImage::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(AttributeKeepNObjectsLabelMapFilter,
+ InPlaceLabelMapFilter);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+/* itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));*/
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the ordering of the objects. By default, the ones with the
+ * highest value are kept. Turming ReverseOrdering to true make this filter
+ * keep the objects with the smallest values
+ */
+ itkSetMacro( ReverseOrdering, bool );
+ itkGetConstReferenceMacro( ReverseOrdering, bool );
+ itkBooleanMacro( ReverseOrdering );
+
+ /**
+ * Set/Get the number of objects to keep
+ */
+ itkSetMacro( NumberOfObjects, unsigned long );
+ itkGetConstReferenceMacro( NumberOfObjects, unsigned long );
+
+protected:
+ AttributeKeepNObjectsLabelMapFilter();
+ ~AttributeKeepNObjectsLabelMapFilter() {};
+
+ void GenerateData();
+
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ class ReverseComparator
+ {
+ public:
+ bool operator()( const typename LabelObjectType::Pointer & a, const typename LabelObjectType::Pointer & b )
+ {
+ return accessor( a ) < accessor( b );
+ }
+ AttributeAccessorType accessor;
+ };
+
+ class Comparator
+ {
+ public:
+ bool operator()( const typename LabelObjectType::Pointer & a, const typename LabelObjectType::Pointer & b )
+ {
+ return accessor( a ) > accessor( b );
+ }
+ AttributeAccessorType accessor;
+ };
+
+private:
+ AttributeKeepNObjectsLabelMapFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ bool m_ReverseOrdering;
+ unsigned long m_NumberOfObjects;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkAttributeKeepNObjectsLabelMapFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkAttributeKeepNObjectsLabelMapFilter.txx b/Utilities/InsightJournal/itkAttributeKeepNObjectsLabelMapFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..347283692150ea4ec429bef0256e8918a2653a61
--- /dev/null
+++ b/Utilities/InsightJournal/itkAttributeKeepNObjectsLabelMapFilter.txx
@@ -0,0 +1,102 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkAttributeKeepNObjectsLabelMapFilter.txx,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkAttributeKeepNObjectsLabelMapFilter_txx
+#define __itkAttributeKeepNObjectsLabelMapFilter_txx
+
+#include "itkAttributeKeepNObjectsLabelMapFilter.h"
+#include "itkProgressReporter.h"
+
+
+namespace itk {
+
+template <class TImage, class TAttributeAccessor>
+AttributeKeepNObjectsLabelMapFilter<TImage, TAttributeAccessor>
+::AttributeKeepNObjectsLabelMapFilter()
+{
+ m_ReverseOrdering = false;
+ m_NumberOfObjects = 1;
+}
+
+
+template <class TImage, class TAttributeAccessor>
+void
+AttributeKeepNObjectsLabelMapFilter<TImage, TAttributeAccessor>
+::GenerateData()
+{
+ // Allocate the output
+ this->AllocateOutputs();
+
+ ImageType * output = this->GetOutput();
+
+ typedef typename ImageType::LabelObjectContainerType LabelObjectContainerType;
+ const LabelObjectContainerType & labelObjectContainer = output->GetLabelObjectContainer();
+ typedef typename std::vector< typename LabelObjectType::Pointer > VectorType;
+
+ ProgressReporter progress( this, 0, 2 * labelObjectContainer.size() );
+
+ // get the label objects in a vector, so they can be sorted
+ VectorType labelObjects;
+ labelObjects.reserve( labelObjectContainer.size() );
+ for( typename LabelObjectContainerType::const_iterator it = labelObjectContainer.begin();
+ it != labelObjectContainer.end();
+ it++ )
+ {
+ labelObjects.push_back( it->second );
+ progress.CompletedPixel();
+ }
+
+ // instantiate the comparator and sort the vector
+ if( m_NumberOfObjects < labelObjectContainer.size() )
+ {
+ typename VectorType::iterator end = labelObjects.begin() + m_NumberOfObjects;
+ if( m_ReverseOrdering )
+ {
+ ReverseComparator comparator;
+ std::nth_element( labelObjects.begin(), end, labelObjects.end(), comparator );
+ }
+ else
+ {
+ Comparator comparator;
+ std::nth_element( labelObjects.begin(), end, labelObjects.end(), comparator );
+ }
+// progress.CompletedPixel();
+
+ // and remove the last objects of the map
+ for( typename VectorType::const_iterator it = end;
+ it != labelObjects.end();
+ it++ )
+ {
+ output->RemoveLabelObject( *it );
+ progress.CompletedPixel();
+ }
+ }
+}
+
+
+template <class TImage, class TAttributeAccessor>
+void
+AttributeKeepNObjectsLabelMapFilter<TImage, TAttributeAccessor>
+::PrintSelf(std::ostream& os, Indent indent) const
+{
+ Superclass::PrintSelf(os,indent);
+
+ os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
+ os << indent << "NumberOfObjects: " << m_NumberOfObjects << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkAttributeLabelObject.h b/Utilities/InsightJournal/itkAttributeLabelObject.h
new file mode 100644
index 0000000000000000000000000000000000000000..bf666318c9308d355c0bbbab2c5b40709047685f
--- /dev/null
+++ b/Utilities/InsightJournal/itkAttributeLabelObject.h
@@ -0,0 +1,138 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelObject.h,v $
+ Language: C++
+ Date: $Date: 2005/01/21 20:13:31 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkAttributeLabelObject_h
+#define __itkAttributeLabelObject_h
+
+#include "itkLabelObject.h"
+
+namespace itk
+{
+
+
+namespace Functor {
+
+template< class TLabelObject >
+class ITK_EXPORT AttributeLabelObjectAccessor
+{
+public:
+ typedef TLabelObject LabelObjectType;
+ typedef typename LabelObjectType::AttributeValueType AttributeValueType;
+
+ inline const AttributeValueType operator()( const LabelObjectType * labelObject )
+ {
+ return labelObject->GetAttribute();
+ }
+
+ inline void operator()( LabelObjectType * labelObject, AttributeValueType value )
+ {
+ labelObject->SetAttribute( value );
+ }
+};
+
+}
+
+
+/** \class AttributeLabelObject
+ * \brief A LabelObject with a generic attribute
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ *\sa LabelObject, ShapeLabelObject, StatisticsLabelObject
+ *
+ * \ingroup DataRepresentation
+ */
+template < class TLabel, unsigned int VImageDimension, class TAttributeValue >
+class ITK_EXPORT AttributeLabelObject : public LabelObject< TLabel, VImageDimension >
+{
+public:
+ /** Standard class typedefs */
+ typedef AttributeLabelObject Self;
+ typedef LabelObject< TLabel, VImageDimension > Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+ typedef WeakPointer<const Self> ConstWeakPointer;
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(AttributeLabelObject, LabelObject);
+
+ typedef LabelMap< Self > LabelMapType;
+
+ itkStaticConstMacro(ImageDimension, unsigned int, VImageDimension);
+
+ typedef typename Superclass::IndexType IndexType;
+
+ typedef TLabel LabelType;
+
+ typedef typename Superclass::LineType LineType;
+
+ typedef typename Superclass::LengthType LengthType;
+
+ typedef typename Superclass::LineContainerType LineContainerType;
+
+ typedef TAttributeValue AttributeValueType;
+
+ void SetAttribute( const AttributeValueType & v )
+ {
+ m_Attribute = v;
+ }
+
+ const AttributeValueType & GetAttribute() const
+ {
+ return m_Attribute;
+ }
+
+ AttributeValueType GetAttribute()
+ {
+ return m_Attribute;
+ }
+
+
+ virtual void CopyAttributesFrom( const Self * src )
+ {
+ Superclass::CopyAttributesFrom( src );
+ m_Attribute = src->m_Attribute;
+ }
+
+protected:
+ AttributeLabelObject()
+ {
+ // how to initialize the attribute ?
+ }
+
+
+ void PrintSelf(std::ostream& os, Indent indent) const
+ {
+ Superclass::PrintSelf( os, indent );
+
+ os << indent << "Attribute: " << m_Attribute << std::endl;
+ }
+
+private:
+ AttributeLabelObject(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ AttributeValueType m_Attribute;
+
+
+};
+
+} // end namespace itk
+
+#endif
diff --git a/Utilities/InsightJournal/itkAttributeOpeningLabelMapFilter.h b/Utilities/InsightJournal/itkAttributeOpeningLabelMapFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..1b3e9dfa0c961757453edac220f3d623037a1143
--- /dev/null
+++ b/Utilities/InsightJournal/itkAttributeOpeningLabelMapFilter.h
@@ -0,0 +1,134 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkAttributeOpeningLabelMapFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkAttributeOpeningLabelMapFilter_h
+#define __itkAttributeOpeningLabelMapFilter_h
+
+#include "itkInPlaceLabelMapFilter.h"
+#include "itkAttributeLabelObject.h"
+
+namespace itk {
+/** \class AttributeOpeningLabelMapFilter
+ * \brief remove the objects according to the value of their attribute
+ *
+ * AttributeOpeningLabelMapFilter removes the objects in a label collection image
+ * with an attribute value smaller or greater than a threshold called Lambda.
+ * The attribute is provide by an attribute accessor given in template parameter.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa AttributeLabelObject
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TImage, class TAttributeAccessor=
+ typename Functor::AttributeLabelObjectAccessor< typename TImage::LabelObjectType > >
+class ITK_EXPORT AttributeOpeningLabelMapFilter :
+ public InPlaceLabelMapFilter<TImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef AttributeOpeningLabelMapFilter Self;
+ typedef InPlaceLabelMapFilter<TImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TImage ImageType;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::PixelType PixelType;
+ typedef typename ImageType::IndexType IndexType;
+
+ typedef TAttributeAccessor AttributeAccessorType;
+ typedef typename AttributeAccessorType::AttributeValueType AttributeValueType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TImage::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(AttributeOpeningLabelMapFilter,
+ InPlaceLabelMapFilter);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+/* itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));*/
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the threshold used to keep or remove the objects.
+ */
+ itkGetConstMacro(Lambda, AttributeValueType);
+ itkSetMacro(Lambda, AttributeValueType);
+
+ /**
+ * Set/Get the ordering of the objects. By default, the objects with
+ * an attribute value smaller than Lamba are removed. Turning ReverseOrdering
+ * to true make this filter remove the object with an attribute value greater
+ * than Lambda instead.
+ */
+ itkGetConstMacro( ReverseOrdering, bool );
+ itkSetMacro( ReverseOrdering, bool );
+ itkBooleanMacro( ReverseOrdering );
+
+ AttributeAccessorType & GetAccessor()
+ {
+ return m_Accessor;
+ }
+
+ void SetAccessor(const AttributeAccessorType& accessor)
+ {
+ m_Accessor = accessor;
+ this->Modified();
+ }
+
+protected:
+ AttributeOpeningLabelMapFilter();
+ ~AttributeOpeningLabelMapFilter() {};
+
+ void GenerateData();
+
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+private:
+ AttributeOpeningLabelMapFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ AttributeValueType m_Lambda;
+ bool m_ReverseOrdering;
+ AttributeAccessorType m_Accessor;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkAttributeOpeningLabelMapFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkAttributeOpeningLabelMapFilter.txx b/Utilities/InsightJournal/itkAttributeOpeningLabelMapFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..e26d8c377c3939f56b6dbae58edc818b1a31ea09
--- /dev/null
+++ b/Utilities/InsightJournal/itkAttributeOpeningLabelMapFilter.txx
@@ -0,0 +1,85 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkAttributeOpeningLabelMapFilter.txx,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkAttributeOpeningLabelMapFilter_txx
+#define __itkAttributeOpeningLabelMapFilter_txx
+
+#include "itkAttributeOpeningLabelMapFilter.h"
+#include "itkProgressReporter.h"
+
+
+namespace itk {
+
+template <class TImage, class TAttributeAccessor>
+AttributeOpeningLabelMapFilter<TImage, TAttributeAccessor>
+::AttributeOpeningLabelMapFilter()
+{
+ m_Lambda = NumericTraits< AttributeValueType >::Zero;
+ m_ReverseOrdering = false;
+}
+
+
+template <class TImage, class TAttributeAccessor>
+void
+AttributeOpeningLabelMapFilter<TImage, TAttributeAccessor>
+::GenerateData()
+{
+ // Allocate the output
+ this->AllocateOutputs();
+
+ ImageType * output = this->GetOutput();
+
+ const typename ImageType::LabelObjectContainerType & labelObjectContainer = output->GetLabelObjectContainer();
+
+ ProgressReporter progress( this, 0, labelObjectContainer.size() );
+
+ typename ImageType::LabelObjectContainerType::const_iterator it = labelObjectContainer.begin();
+ while( it != labelObjectContainer.end() )
+ {
+ typedef typename ImageType::LabelObjectType LabelObjectType;
+ typename LabelObjectType::LabelType label = it->first;
+ LabelObjectType * labelObject = it->second;
+
+ if( ( !m_ReverseOrdering && m_Accessor( labelObject ) < m_Lambda )
+ || ( m_ReverseOrdering && m_Accessor( labelObject ) > m_Lambda ) )
+ {
+ // must increment the iterator before removing the object to avoid invalidating the iterator
+ it++;
+ output->RemoveLabel( label );
+ }
+ else
+ {
+ it++;
+ }
+
+ progress.CompletedPixel();
+ }
+}
+
+
+template <class TImage, class TAttributeAccessor>
+void
+AttributeOpeningLabelMapFilter<TImage, TAttributeAccessor>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
+ os << indent << "Lambda: " << static_cast<typename NumericTraits<AttributeValueType>::PrintType>(m_Lambda) << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkAttributeRelabelImageFilter.h b/Utilities/InsightJournal/itkAttributeRelabelImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..02250f14e974cc7261a2060eb7043ec8e74bb313
--- /dev/null
+++ b/Utilities/InsightJournal/itkAttributeRelabelImageFilter.h
@@ -0,0 +1,152 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkAttributeRelabelImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkAttributeRelabelImageFilter_h
+#define __itkAttributeRelabelImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkLabelMap.h"
+#include "itkLabelImageToLabelMapFilter.h"
+#include "itkAttributeRelabelLabelMapFilter.h"
+#include "itkLabelMapToLabelImageFilter.h"
+#include "itkAttributeLabelObject.h"
+
+
+namespace itk {
+
+/** \class AttributeRelabelImageFilter
+ * \brief relabel objects according to their shape attributes
+ *
+ * AttributeRelabelImageFilter relabel a labeled image according to the attribute of
+ * the objects. The label produced are always consecutives.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa AttributeLabelObject, RelabelComponentImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor=
+ typename Functor::AttributeLabelObjectAccessor< typename TImage::LabelObjectType > >
+class ITK_EXPORT AttributeRelabelImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef AttributeRelabelImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+
+ typedef TLabelObject LabelObjectType;
+ typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef typename itk::LabelImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
+ typedef TLabelObjectValuator LabelObjectValuatorType;
+ typedef TAttributeAccessor AttributeAccessorType;
+ typedef typename AttributeAccessorType::AttributeValueType AttributeValueType;
+ typedef typename itk::AttributeRelabelLabelMapFilter< LabelMapType, AttributeAccessorType > RelabelType;
+ typedef typename itk::LabelMapToLabelImageFilter< LabelMapType, OutputImageType > BinarizerType;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(AttributeRelabelImageFilter,
+ ImageToImageFilter);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the order of labeling of the objects. By default, the objects with
+ * the highest attribute values are labeled first. Set ReverseOrdering to true
+ * make the one with the smallest attributes be labeled first.
+ */
+ itkGetConstMacro( ReverseOrdering, bool );
+ itkSetMacro( ReverseOrdering, bool );
+ itkBooleanMacro( ReverseOrdering );
+
+protected:
+ AttributeRelabelImageFilter();
+ ~AttributeRelabelImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** AttributeRelabelImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** AttributeRelabelImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+ virtual void CustomizeInternalFilters( LabelizerType *, LabelObjectValuatorType *, RelabelType *, BinarizerType* ) {};
+
+private:
+ AttributeRelabelImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ OutputImagePixelType m_BackgroundValue;
+ bool m_ReverseOrdering;
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkAttributeRelabelImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkAttributeRelabelImageFilter.txx b/Utilities/InsightJournal/itkAttributeRelabelImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..6eb1494d74ba55027907a11f6c641299e5aee756
--- /dev/null
+++ b/Utilities/InsightJournal/itkAttributeRelabelImageFilter.txx
@@ -0,0 +1,115 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkAttributeRelabelImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/08/01 19:16:18 $
+ Version: $Revision: 1.7 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkAttributeRelabelImageFilter_txx
+#define __itkAttributeRelabelImageFilter_txx
+
+#include "itkAttributeRelabelImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+
+namespace itk {
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+AttributeRelabelImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::AttributeRelabelImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+ m_ReverseOrdering = false;
+}
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+AttributeRelabelImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+AttributeRelabelImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+AttributeRelabelImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::GenerateData()
+{
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Allocate the output
+ this->AllocateOutputs();
+
+ typename LabelizerType::Pointer labelizer = LabelizerType::New();
+ labelizer->SetInput( this->GetInput() );
+ labelizer->SetBackgroundValue( m_BackgroundValue );
+ labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(labelizer, .3f);
+
+ typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
+ valuator->SetInput( labelizer->GetOutput() );
+ valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(valuator, .3f);
+
+ typename RelabelType::Pointer opening = RelabelType::New();
+ opening->SetInput( valuator->GetOutput() );
+ opening->SetReverseOrdering( m_ReverseOrdering );
+ opening->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(opening, .2f);
+
+ typename BinarizerType::Pointer binarizer = BinarizerType::New();
+ binarizer->SetInput( opening->GetOutput() );
+ binarizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(binarizer, .2f);
+
+ this->CustomizeInternalFilters( labelizer, valuator, opening, binarizer );
+
+ binarizer->GraftOutput( this->GetOutput() );
+ binarizer->Update();
+ this->GraftOutput( binarizer->GetOutput() );
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+AttributeRelabelImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkAttributeRelabelLabelMapFilter.h b/Utilities/InsightJournal/itkAttributeRelabelLabelMapFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..23dda370cf9e6f7edd242ed5d8bcc48ae4ecf39e
--- /dev/null
+++ b/Utilities/InsightJournal/itkAttributeRelabelLabelMapFilter.h
@@ -0,0 +1,135 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkAttributeRelabelLabelMapFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkAttributeRelabelLabelMapFilter_h
+#define __itkAttributeRelabelLabelMapFilter_h
+
+#include "itkInPlaceLabelMapFilter.h"
+#include "itkAttributeLabelObject.h"
+
+namespace itk {
+/** \class AttributeRelabelLabelMapFilter
+ * \brief relabel objects according to their shape attributes
+ *
+ * AttributeRelabelLabelMapFilter relabel a label collection image according to the
+ * attribute of the objects.
+ * The attribute is provide by an attribute accessor given in template parameter.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa AttributeLabelObject, RelabelComponentImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TImage, class TAttributeAccessor=
+ typename Functor::AttributeLabelObjectAccessor< typename TImage::LabelObjectType > >
+class ITK_EXPORT AttributeRelabelLabelMapFilter :
+ public InPlaceLabelMapFilter<TImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef AttributeRelabelLabelMapFilter Self;
+ typedef InPlaceLabelMapFilter<TImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TImage ImageType;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::PixelType PixelType;
+ typedef typename ImageType::IndexType IndexType;
+ typedef typename ImageType::LabelObjectType LabelObjectType;
+
+ typedef TAttributeAccessor AttributeAccessorType;
+ typedef typename AttributeAccessorType::AttributeValueType AttributeValueType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TImage::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(AttributeRelabelLabelMapFilter,
+ InPlaceLabelMapFilter);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+/* itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));*/
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the order of labeling of the objects. By default, the objects with
+ * the highest attribute values are labeled first. Set ReverseOrdering to true
+ * make the one with the smallest attributes be labeled first.
+ */
+ itkSetMacro( ReverseOrdering, bool );
+ itkGetConstReferenceMacro( ReverseOrdering, bool );
+ itkBooleanMacro( ReverseOrdering );
+
+protected:
+ AttributeRelabelLabelMapFilter();
+ ~AttributeRelabelLabelMapFilter() {};
+
+ void GenerateData();
+
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ class ReverseComparator
+ {
+ public:
+ bool operator()( const typename LabelObjectType::Pointer & a, const typename LabelObjectType::Pointer & b )
+ {
+ return accessor( a ) < accessor( b );
+ }
+ AttributeAccessorType accessor;
+ };
+
+ class Comparator
+ {
+ public:
+ bool operator()( const typename LabelObjectType::Pointer & a, const typename LabelObjectType::Pointer & b )
+ {
+ return accessor( a ) > accessor( b );
+ }
+ AttributeAccessorType accessor;
+ };
+
+private:
+ AttributeRelabelLabelMapFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ bool m_ReverseOrdering;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkAttributeRelabelLabelMapFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkAttributeRelabelLabelMapFilter.txx b/Utilities/InsightJournal/itkAttributeRelabelLabelMapFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..3ba46f5afa205f43c141c3382dd3f4ee5e723b01
--- /dev/null
+++ b/Utilities/InsightJournal/itkAttributeRelabelLabelMapFilter.txx
@@ -0,0 +1,108 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkAttributeRelabelLabelMapFilter.txx,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkAttributeRelabelLabelMapFilter_txx
+#define __itkAttributeRelabelLabelMapFilter_txx
+
+#include "itkAttributeRelabelLabelMapFilter.h"
+#include "itkProgressReporter.h"
+
+
+namespace itk {
+
+template <class TImage, class TAttributeAccessor>
+AttributeRelabelLabelMapFilter<TImage, TAttributeAccessor>
+::AttributeRelabelLabelMapFilter()
+{
+ m_ReverseOrdering = false;
+}
+
+
+template <class TImage, class TAttributeAccessor>
+void
+AttributeRelabelLabelMapFilter<TImage, TAttributeAccessor>
+::GenerateData()
+{
+ // Allocate the output
+ this->AllocateOutputs();
+
+ ImageType * output = this->GetOutput();
+
+ typedef typename ImageType::LabelObjectContainerType LabelObjectContainerType;
+ const LabelObjectContainerType & labelObjectContainer = output->GetLabelObjectContainer();
+ typedef typename std::vector< typename LabelObjectType::Pointer > VectorType;
+
+ ProgressReporter progress( this, 0, 2 * labelObjectContainer.size() );
+
+ // get the label objects in a vector, so they can be sorted
+ VectorType labelObjects;
+ labelObjects.reserve( labelObjectContainer.size() );
+ for( typename LabelObjectContainerType::const_iterator it = labelObjectContainer.begin();
+ it != labelObjectContainer.end();
+ it++ )
+ {
+ labelObjects.push_back( it->second );
+ progress.CompletedPixel();
+ }
+
+ // instantiate the comparator and sort the vector
+ if( m_ReverseOrdering )
+ {
+ ReverseComparator comparator;
+ std::sort( labelObjects.begin(), labelObjects.end(), comparator );
+ }
+ else
+ {
+ Comparator comparator;
+ std::sort( labelObjects.begin(), labelObjects.end(), comparator );
+ }
+// progress.CompletedPixel();
+
+ // and put back the objects in the map
+ typedef typename ImageType::LabelObjectType LabelObjectType;
+ output->ClearLabels();
+ unsigned int label = 0;
+ for( typename VectorType::const_iterator it = labelObjects.begin();
+ it != labelObjects.end();
+ it++ )
+ {
+ // avoid the background label if it is used
+ if( label == output->GetBackgroundValue() )
+ {
+ label++;
+ }
+ (*it)->SetLabel( label );
+ output->AddLabelObject( *it );
+
+ // go to the nex label
+ label++;
+ progress.CompletedPixel();
+ }
+}
+
+
+template <class TImage, class TAttributeAccessor>
+void
+AttributeRelabelLabelMapFilter<TImage, TAttributeAccessor>
+::PrintSelf(std::ostream& os, Indent indent) const
+{
+ Superclass::PrintSelf(os,indent);
+
+ os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkAttributeSelectionLabelMapFilter.h b/Utilities/InsightJournal/itkAttributeSelectionLabelMapFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..b680477e23434dbdb47cb20641e7d5154d980d6a
--- /dev/null
+++ b/Utilities/InsightJournal/itkAttributeSelectionLabelMapFilter.h
@@ -0,0 +1,162 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkAttributeSelectionLabelMapFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkAttributeSelectionLabelMapFilter_h
+#define __itkAttributeSelectionLabelMapFilter_h
+
+#include "itkInPlaceLabelMapFilter.h"
+#include "itkAttributeLabelObject.h"
+#include <set>
+
+
+namespace itk {
+/** \class AttributeSelectionLabelMapFilter
+ * \brief remove the objects according to the value of their attribute
+ *
+ * AttributeSelectionLabelMapFilter removes the objects in a label collection image
+ * with an attribute value inside or outside a set of attribute values passed by
+ * the user.
+ * The attribute is provide by an attribute accessor given in template parameter.
+ * Contrary to the other filters made to remove some object of a LabelMap, no
+ * ordering relation for the attribute is needed in that filter.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa AttributeLabelObject
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TImage, class TAttributeAccessor=
+ typename Functor::AttributeLabelObjectAccessor< typename TImage::LabelObjectType > >
+class ITK_EXPORT AttributeSelectionLabelMapFilter :
+ public InPlaceLabelMapFilter<TImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef AttributeSelectionLabelMapFilter Self;
+ typedef InPlaceLabelMapFilter<TImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TImage ImageType;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::PixelType PixelType;
+ typedef typename ImageType::IndexType IndexType;
+
+ typedef TAttributeAccessor AttributeAccessorType;
+ typedef typename AttributeAccessorType::AttributeValueType AttributeValueType;
+
+ typedef typename std::set<AttributeValueType> AttributeSetType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TImage::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(AttributeSelectionLabelMapFilter,
+ InPlaceLabelMapFilter);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+/* itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));*/
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the threshold used to keep or remove the objects.
+ */
+ const AttributeSetType & GetAttributeSet() const
+ {
+ return m_AttributeSet;
+ }
+ void SetAttributeSet( const AttributeSetType & set )
+ {
+ m_AttributeSet = set;
+ this->Modified();
+ }
+
+ /**
+ * Set/Get the ordering of the objects. By default, the objects with
+ * an attribute value smaller than Lamba are removed. Turning ReverseOrdering
+ * to true make this filter remove the object with an attribute value greater
+ * than Lambda instead.
+ */
+ itkGetConstMacro( Exclude, bool );
+ itkSetMacro( Exclude, bool );
+ itkBooleanMacro( Exclude );
+
+ /** Clear the attribute set, and add the attribute passed in parameter */
+ void SetAttribute( const AttributeValueType & attr )
+ {
+ this->ClearAttributeSet();
+ this->AddAttribute( attr );
+ }
+
+ void ClearAttributeSet()
+ {
+ if( ! m_AttributeSet.empty() )
+ {
+ m_AttributeSet.clear();
+ this->Modified();
+ }
+ }
+
+ void AddAttribute( const AttributeValueType & attr )
+ {
+ unsigned long size = m_AttributeSet.size();
+ m_AttributeSet.insert( attr );
+ if( size != m_AttributeSet.size() )
+ {
+ this->Modified();
+ }
+ }
+
+protected:
+ AttributeSelectionLabelMapFilter();
+ ~AttributeSelectionLabelMapFilter() {};
+
+ void GenerateData();
+
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+private:
+ AttributeSelectionLabelMapFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ AttributeSetType m_AttributeSet;
+ bool m_Exclude;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkAttributeSelectionLabelMapFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkAttributeSelectionLabelMapFilter.txx b/Utilities/InsightJournal/itkAttributeSelectionLabelMapFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..fe2de08981984ea32bd1f40ec222b8d01e9fa533
--- /dev/null
+++ b/Utilities/InsightJournal/itkAttributeSelectionLabelMapFilter.txx
@@ -0,0 +1,86 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkAttributeSelectionLabelMapFilter.txx,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkAttributeSelectionLabelMapFilter_txx
+#define __itkAttributeSelectionLabelMapFilter_txx
+
+#include "itkAttributeSelectionLabelMapFilter.h"
+#include "itkProgressReporter.h"
+
+
+namespace itk {
+
+template <class TImage, class TAttributeAccessor>
+AttributeSelectionLabelMapFilter<TImage, TAttributeAccessor>
+::AttributeSelectionLabelMapFilter()
+{
+ m_AttributeSet.clear();
+ m_Exclude = false;
+}
+
+
+template <class TImage, class TAttributeAccessor>
+void
+AttributeSelectionLabelMapFilter<TImage, TAttributeAccessor>
+::GenerateData()
+{
+ // Allocate the output
+ this->AllocateOutputs();
+
+ ImageType * output = this->GetOutput();
+
+ AttributeAccessorType accessor;
+
+ const typename ImageType::LabelObjectContainerType & labelObjectContainer = output->GetLabelObjectContainer();
+
+ ProgressReporter progress( this, 0, labelObjectContainer.size() );
+
+ typename ImageType::LabelObjectContainerType::const_iterator it = labelObjectContainer.begin();
+ while( it != labelObjectContainer.end() )
+ {
+ typedef typename ImageType::LabelObjectType LabelObjectType;
+ typename LabelObjectType::LabelType label = it->first;
+ LabelObjectType * labelObject = it->second;
+ bool notInSet = m_AttributeSet.find( accessor( labelObject ) ) == m_AttributeSet.end();
+ if( m_Exclude != notInSet ) // no xor in c++, use != instead
+ {
+ // must increment the iterator before removing the object to avoid invalidating the iterator
+ it++;
+ output->RemoveLabel( label );
+ }
+ else
+ {
+ it++;
+ }
+
+ progress.CompletedPixel();
+ }
+}
+
+
+template <class TImage, class TAttributeAccessor>
+void
+AttributeSelectionLabelMapFilter<TImage, TAttributeAccessor>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "AttributeSet: " << &m_AttributeSet << std::endl;
+ os << indent << "Exclude: " << m_Exclude << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryAttributeKeepNObjectsImageFilter.h b/Utilities/InsightJournal/itkBinaryAttributeKeepNObjectsImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..6ec667805d426042ac7bf9dab66f4ad6c099fe01
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryAttributeKeepNObjectsImageFilter.h
@@ -0,0 +1,183 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryAttributeKeepNObjectsImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryAttributeKeepNObjectsImageFilter_h
+#define __itkBinaryAttributeKeepNObjectsImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkLabelMap.h"
+#include "itkBinaryImageToLabelMapFilter.h"
+#include "itkAttributeKeepNObjectsLabelMapFilter.h"
+#include "itkLabelMapToBinaryImageFilter.h"
+#include "itkAttributeLabelObject.h"
+
+
+namespace itk {
+
+/** \class BinaryAttributeKeepNObjectsImageFilter
+ * \brief keep N objects according to a generic attribute
+ *
+ * BinaryAttributeKeepNObjectsImageFilter keep the N objects in a binary image
+ * with the highest (or lowest) attribute value. The attribute is valued with
+ * and attribute valuator given in template parameter and is accessed with a
+ * attribute accessor also given in template parameter.
+ *
+ * Used in combination with AttributeLabelObject, and a specilized attribute valuator,
+ * this class is the most efficient way to keep N objects in a binary image.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa AttributeLabelObject, InPlaceLabelMapFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor=
+ typename Functor::AttributeLabelObjectAccessor< typename TImage::LabelObjectType > >
+class ITK_EXPORT BinaryAttributeKeepNObjectsImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryAttributeKeepNObjectsImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+
+ typedef TLabelObject LabelObjectType;
+ typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef typename itk::BinaryImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
+ typedef TLabelObjectValuator LabelObjectValuatorType;
+ typedef TAttributeAccessor AttributeAccessorType;
+ typedef typename AttributeAccessorType::AttributeValueType AttributeValueType;
+ typedef typename itk::AttributeKeepNObjectsLabelMapFilter< LabelMapType, AttributeAccessorType > KeepNObjectsType;
+ typedef typename itk::LabelMapToBinaryImageFilter< LabelMapType, OutputImageType > BinarizerType;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryAttributeKeepNObjectsImageFilter,
+ ImageToImageFilter);
+
+ /**
+ * Set/Get whether the connected components are defined strictly by
+ * face connectivity or by face+edge+vertex connectivity. Default is
+ * FullyConnectedOff. For objects that are 1 pixel wide, use
+ * FullyConnectedOn.
+ */
+ itkSetMacro(FullyConnected, bool);
+ itkGetConstReferenceMacro(FullyConnected, bool);
+ itkBooleanMacro(FullyConnected);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the value used as "foreground" in the output image.
+ * Defaults to NumericTraits<PixelType>::max().
+ */
+ itkSetMacro(ForegroundValue, OutputImagePixelType);
+ itkGetConstMacro(ForegroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the number of objects to keep
+ */
+ itkGetConstMacro(NumberOfObjects, unsigned long);
+ itkSetMacro(NumberOfObjects, unsigned long);
+
+ /**
+ * Set/Get the ordering of the objects. By default, the ones with the
+ * highest value are kept. Turming ReverseOrdering to true make this filter
+ * keep the objects with the smallest values
+ */
+ itkGetConstMacro( ReverseOrdering, bool );
+ itkSetMacro( ReverseOrdering, bool );
+ itkBooleanMacro( ReverseOrdering );
+
+protected:
+ BinaryAttributeKeepNObjectsImageFilter();
+ ~BinaryAttributeKeepNObjectsImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** BinaryAttributeKeepNObjectsImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** BinaryAttributeKeepNObjectsImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+ virtual void CustomizeInternalFilters( LabelizerType *, LabelObjectValuatorType *, KeepNObjectsType *, BinarizerType* ) {};
+
+private:
+ BinaryAttributeKeepNObjectsImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ bool m_FullyConnected;
+ OutputImagePixelType m_BackgroundValue;
+ OutputImagePixelType m_ForegroundValue;
+ unsigned long m_NumberOfObjects;
+ bool m_ReverseOrdering;
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryAttributeKeepNObjectsImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryAttributeKeepNObjectsImageFilter.txx b/Utilities/InsightJournal/itkBinaryAttributeKeepNObjectsImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..d4b0735f21be8c01f90779b748aedc48a94a1854
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryAttributeKeepNObjectsImageFilter.txx
@@ -0,0 +1,126 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryAttributeKeepNObjectsImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/08/01 19:16:18 $
+ Version: $Revision: 1.7 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryAttributeKeepNObjectsImageFilter_txx
+#define __itkBinaryAttributeKeepNObjectsImageFilter_txx
+
+#include "itkBinaryAttributeKeepNObjectsImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+
+namespace itk {
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+BinaryAttributeKeepNObjectsImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::BinaryAttributeKeepNObjectsImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+ m_ForegroundValue = NumericTraits<OutputImagePixelType>::max();
+ m_FullyConnected = false;
+ m_ReverseOrdering = false;
+}
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+BinaryAttributeKeepNObjectsImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+BinaryAttributeKeepNObjectsImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+BinaryAttributeKeepNObjectsImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::GenerateData()
+{
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Allocate the output
+ this->AllocateOutputs();
+
+ typename LabelizerType::Pointer labelizer = LabelizerType::New();
+ labelizer->SetInput( this->GetInput() );
+ labelizer->SetForegroundValue( m_ForegroundValue );
+ labelizer->SetBackgroundValue( m_BackgroundValue );
+ labelizer->SetFullyConnected( m_FullyConnected );
+ labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(labelizer, .3f);
+
+ typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
+ valuator->SetInput( labelizer->GetOutput() );
+ valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(valuator, .3f);
+
+ typename KeepNObjectsType::Pointer opening = KeepNObjectsType::New();
+ opening->SetInput( valuator->GetOutput() );
+ opening->SetNumberOfObjects( m_NumberOfObjects );
+ opening->SetReverseOrdering( m_ReverseOrdering );
+ opening->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(opening, .2f);
+
+ typename BinarizerType::Pointer binarizer = BinarizerType::New();
+ binarizer->SetInput( opening->GetOutput() );
+ binarizer->SetForegroundValue( m_ForegroundValue );
+ binarizer->SetBackgroundValue( m_BackgroundValue );
+ binarizer->SetBackgroundImage( this->GetInput() );
+ binarizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(binarizer, .2f);
+
+ this->CustomizeInternalFilters( labelizer, valuator, opening, binarizer );
+
+ binarizer->GraftOutput( this->GetOutput() );
+ binarizer->Update();
+ this->GraftOutput( binarizer->GetOutput() );
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+BinaryAttributeKeepNObjectsImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_ForegroundValue) << std::endl;
+ os << indent << "NumberOfObjects: " << m_NumberOfObjects << std::endl;
+ os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryAttributeOpeningImageFilter.h b/Utilities/InsightJournal/itkBinaryAttributeOpeningImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..a9017243bc100ee8e26cc00800f67efca03386ee
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryAttributeOpeningImageFilter.h
@@ -0,0 +1,186 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryAttributeOpeningImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryAttributeOpeningImageFilter_h
+#define __itkBinaryAttributeOpeningImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkLabelMap.h"
+#include "itkBinaryImageToLabelMapFilter.h"
+#include "itkAttributeOpeningLabelMapFilter.h"
+#include "itkLabelMapToBinaryImageFilter.h"
+#include "itkAttributeLabelObject.h"
+
+
+namespace itk {
+
+/** \class BinaryAttributeOpeningImageFilter
+ * \brief remove the objects in a binary image according to a generic attribute
+ *
+ * BinaryAttributeOpeningImageFilter remove the objects in a binary image
+ * with an attribute value smaller or greater than a threshold called Lambda.
+ * The attribute is valued with and attribute valuator given in template parameter
+ * and is accessed with an attribute accessor also given in template parameter.
+ *
+ * Used in combination with AttributeLabelObject, and a specilized attribute valuator,
+ * this class is the most efficient way to perform an attribute opening in a binary
+ * image.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa AttributeLabelObject, InPlaceLabelMapFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor=
+ typename Functor::AttributeLabelObjectAccessor< typename TImage::LabelObjectType > >
+class ITK_EXPORT BinaryAttributeOpeningImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryAttributeOpeningImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+
+ typedef TLabelObject LabelObjectType;
+ typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef typename itk::BinaryImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
+ typedef TLabelObjectValuator LabelObjectValuatorType;
+ typedef TAttributeAccessor AttributeAccessorType;
+ typedef typename AttributeAccessorType::AttributeValueType AttributeValueType;
+ typedef typename itk::AttributeOpeningLabelMapFilter< LabelMapType, AttributeAccessorType > OpeningType;
+ typedef typename itk::LabelMapToBinaryImageFilter< LabelMapType, OutputImageType > BinarizerType;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryAttributeOpeningImageFilter,
+ ImageToImageFilter);
+
+ /**
+ * Set/Get whether the connected components are defined strictly by
+ * face connectivity or by face+edge+vertex connectivity. Default is
+ * FullyConnectedOff. For objects that are 1 pixel wide, use
+ * FullyConnectedOn.
+ */
+ itkSetMacro(FullyConnected, bool);
+ itkGetConstReferenceMacro(FullyConnected, bool);
+ itkBooleanMacro(FullyConnected);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the value used as "foreground" in the output image.
+ * Defaults to NumericTraits<PixelType>::max().
+ */
+ itkSetMacro(ForegroundValue, OutputImagePixelType);
+ itkGetConstMacro(ForegroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the threshold used to keep or remove the objects.
+ */
+ itkGetConstMacro(Lambda, AttributeValueType);
+ itkSetMacro(Lambda, AttributeValueType);
+
+ /**
+ * Set/Get the ordering of the objects. By default, the objects with
+ * an attribute value smaller than Lamba are removed. Turning ReverseOrdering
+ * to true make this filter remove the object with an attribute value greater
+ * than Lambda instead.
+ */
+ itkGetConstMacro( ReverseOrdering, bool );
+ itkSetMacro( ReverseOrdering, bool );
+ itkBooleanMacro( ReverseOrdering );
+
+protected:
+ BinaryAttributeOpeningImageFilter();
+ ~BinaryAttributeOpeningImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** BinaryAttributeOpeningImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** BinaryAttributeOpeningImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+ virtual void CustomizeInternalFilters( LabelizerType *, LabelObjectValuatorType *, OpeningType *, BinarizerType* ) {};
+
+
+private:
+ BinaryAttributeOpeningImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ bool m_FullyConnected;
+ OutputImagePixelType m_BackgroundValue;
+ OutputImagePixelType m_ForegroundValue;
+ AttributeValueType m_Lambda;
+ bool m_ReverseOrdering;
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryAttributeOpeningImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryAttributeOpeningImageFilter.txx b/Utilities/InsightJournal/itkBinaryAttributeOpeningImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..c5bb494870b230fff1baed1ed74280ceb2b7d78a
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryAttributeOpeningImageFilter.txx
@@ -0,0 +1,126 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryAttributeOpeningImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/08/01 19:16:18 $
+ Version: $Revision: 1.7 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryAttributeOpeningImageFilter_txx
+#define __itkBinaryAttributeOpeningImageFilter_txx
+
+#include "itkBinaryAttributeOpeningImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+
+namespace itk {
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+BinaryAttributeOpeningImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::BinaryAttributeOpeningImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+ m_ForegroundValue = NumericTraits<OutputImagePixelType>::max();
+ m_FullyConnected = false;
+ m_ReverseOrdering = false;
+}
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+BinaryAttributeOpeningImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+BinaryAttributeOpeningImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+BinaryAttributeOpeningImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::GenerateData()
+{
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Allocate the output
+ this->AllocateOutputs();
+
+ typename LabelizerType::Pointer labelizer = LabelizerType::New();
+ labelizer->SetInput( this->GetInput() );
+ labelizer->SetForegroundValue( m_ForegroundValue );
+ labelizer->SetBackgroundValue( m_BackgroundValue );
+ labelizer->SetFullyConnected( m_FullyConnected );
+ labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(labelizer, .3f);
+
+ typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
+ valuator->SetInput( labelizer->GetOutput() );
+ valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(valuator, .3f);
+
+ typename OpeningType::Pointer opening = OpeningType::New();
+ opening->SetInput( valuator->GetOutput() );
+ opening->SetLambda( m_Lambda );
+ opening->SetReverseOrdering( m_ReverseOrdering );
+ opening->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(opening, .2f);
+
+ typename BinarizerType::Pointer binarizer = BinarizerType::New();
+ binarizer->SetInput( opening->GetOutput() );
+ binarizer->SetForegroundValue( m_ForegroundValue );
+ binarizer->SetBackgroundValue( m_BackgroundValue );
+ binarizer->SetBackgroundImage( this->GetInput() );
+ binarizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(binarizer, .2f);
+
+ this->CustomizeInternalFilters( labelizer, valuator, opening, binarizer );
+
+ binarizer->GraftOutput( this->GetOutput() );
+ binarizer->Update();
+ this->GraftOutput( binarizer->GetOutput() );
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+BinaryAttributeOpeningImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_ForegroundValue) << std::endl;
+ os << indent << "Lambda: " <<m_Lambda << std::endl;
+ os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryClosingByReconstructionImageFilter.h b/Utilities/InsightJournal/itkBinaryClosingByReconstructionImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..272e76ddc2fd572e42c27e67ddd1568ddcb1a4d9
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryClosingByReconstructionImageFilter.h
@@ -0,0 +1,132 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryClosingByReconstructionImageFilter.h,v $
+ Language: C++
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryClosingByReconstructionImageFilter_h
+#define __itkBinaryClosingByReconstructionImageFilter_h
+
+#include "itkImageToImageFilter.h"
+
+namespace itk {
+
+/**
+ * \class BinaryClosingByReconstructionImageFilter
+ * \brief binary morphological closing of an image.
+ *
+ * This filter removes small (i.e., smaller than the structuring
+ * element) holes in the image. It is defined as:
+ * Closing(f) = ReconstructionByErosion(Dilation(f)).
+ *
+ * The structuring element is assumed to be composed of binary
+ * values (zero or one). Only elements of the structuring element
+ * having values > 0 are candidates for affecting the center pixel.
+ *
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa MorphologyImageFilter, ClosingByReconstructionImageFilter, BinaryOpeningByReconstructionImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+
+template<class TInputImage, class TKernel>
+class ITK_EXPORT BinaryClosingByReconstructionImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryClosingByReconstructionImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage> Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryClosingByReconstructionImageFilter,
+ ImageToImageFilter);
+
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+
+ /** Declaration of pixel type. */
+ typedef typename TInputImage::PixelType InputPixelType ;
+ typedef typename TInputImage::PixelType OutputPixelType ;
+
+ /** Kernel typedef. */
+ typedef TKernel KernelType;
+
+ /** Set kernel (structuring element). */
+ itkSetMacro(Kernel, KernelType);
+
+ /** Get the kernel (structuring element). */
+ itkGetConstReferenceMacro(Kernel, KernelType);
+
+ /** Set the value in the image to consider as "foreground". Defaults to
+ * maximum value of InputPixelType. */
+ itkSetMacro(ForegroundValue, InputPixelType);
+
+ /** Get the value in the image considered as "foreground". Defaults to
+ * maximum value of InputPixelType. */
+ itkGetMacro(ForegroundValue, InputPixelType);
+
+ /**
+ * Set/Get whether the connected components are defined strictly by
+ * face connectivity or by face+edge+vertex connectivity. Default is
+ * FullyConnectedOff. For objects that are 1 pixel wide, use
+ * FullyConnectedOn.
+ */
+ itkSetMacro(FullyConnected, bool);
+ itkGetConstReferenceMacro(FullyConnected, bool);
+ itkBooleanMacro(FullyConnected);
+
+protected:
+ BinaryClosingByReconstructionImageFilter();
+ ~BinaryClosingByReconstructionImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** BinaryClosingByReconstructionImageFilter need to make sure they request enough of an
+ * input image to account for the structuring element size. The input
+ * requested region is expanded by the radius of the structuring element.
+ * If the request extends past the LargestPossibleRegion for the input,
+ * the request is cropped by the LargestPossibleRegion. */
+ void GenerateInputRequestedRegion() ;
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleDilateImageFilter GrayscaleErodeImageFilter. */
+ void GenerateData ();
+
+private:
+ BinaryClosingByReconstructionImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ /** kernel or structuring element to use. */
+ KernelType m_Kernel ;
+
+ InputPixelType m_ForegroundValue;
+
+ bool m_FullyConnected;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryClosingByReconstructionImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryClosingByReconstructionImageFilter.txx b/Utilities/InsightJournal/itkBinaryClosingByReconstructionImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..cb1efeb9606bb7ce8a63d2854da54a6bf73a7a29
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryClosingByReconstructionImageFilter.txx
@@ -0,0 +1,123 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryClosingByReconstructionImageFilter.txx,v $
+ Language: C++
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryClosingByReconstructionImageFilter_txx
+#define __itkBinaryClosingByReconstructionImageFilter_txx
+
+#include "itkBinaryClosingByReconstructionImageFilter.h"
+#include "itkBinaryReconstructionByErosionImageFilter.h"
+#include "itkBinaryDilateImageFilter.h"
+#include "itkProgressAccumulator.h"
+#include "itkCropImageFilter.h"
+#include "itkConstantPadImageFilter.h"
+#include "itkConstNeighborhoodIterator.h"
+#include "itkNeighborhoodIterator.h"
+#include "itkProgressReporter.h"
+
+namespace itk {
+
+template<class TInputImage, class TKernel>
+BinaryClosingByReconstructionImageFilter<TInputImage, TKernel>
+::BinaryClosingByReconstructionImageFilter()
+ : m_Kernel()
+{
+ m_ForegroundValue = NumericTraits<InputPixelType>::max();
+ m_FullyConnected = false;
+}
+
+template <class TInputImage, class TKernel>
+void
+BinaryClosingByReconstructionImageFilter<TInputImage, TKernel>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+template<class TInputImage, class TKernel>
+void
+BinaryClosingByReconstructionImageFilter<TInputImage, TKernel>
+::GenerateData()
+{
+ // Allocate the outputs
+ this->AllocateOutputs();
+
+ // let choose a background value. Background value should not be given by user
+ // because closing is extensive so no background pixels will be added
+ // it is just needed for internal erosion filter and constant padder
+ InputPixelType backgroundValue = NumericTraits<InputPixelType>::Zero;
+ if ( m_ForegroundValue == backgroundValue )
+ {
+ // current background value is already used for foreground value
+ // choose another one
+ backgroundValue = NumericTraits<InputPixelType>::max();
+ }
+
+ /** set up erosion and dilation methods */
+ typename BinaryDilateImageFilter<TInputImage, TInputImage, TKernel>::Pointer
+ dilate = BinaryDilateImageFilter<TInputImage, TInputImage, TKernel>::New();
+
+ typename BinaryReconstructionByErosionImageFilter<OutputImageType>::Pointer
+ erode = BinaryReconstructionByErosionImageFilter<OutputImageType>::New();
+
+ // create the pipeline without input and output image
+ dilate->ReleaseDataFlagOn();
+ dilate->SetKernel( this->GetKernel() );
+ dilate->SetDilateValue( m_ForegroundValue );
+ dilate->SetBackgroundValue( backgroundValue );
+ dilate->SetInput( this->GetInput() );
+ dilate->SetNumberOfThreads( this->GetNumberOfThreads() );
+
+ erode->ReleaseDataFlagOn();
+ erode->SetForegroundValue( m_ForegroundValue );
+ erode->SetBackgroundValue( backgroundValue );
+ erode->SetMarkerImage( dilate->GetOutput() );
+ erode->SetFullyConnected( m_FullyConnected );
+ erode->SetMaskImage( this->GetInput() );
+ erode->SetNumberOfThreads( this->GetNumberOfThreads() );
+
+
+ /** set up the minipipeline */
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+ progress->RegisterInternalFilter(erode, .8f);
+ progress->RegisterInternalFilter(dilate, .2f);
+
+ /** execute the minipipeline */
+ erode->GraftOutput( this->GetOutput() );
+ erode->Update();
+ this->GraftOutput( erode->GetOutput() );
+}
+
+template<class TInputImage, class TKernel>
+void
+BinaryClosingByReconstructionImageFilter<TInputImage, TKernel>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "Kernel: " << m_Kernel << std::endl;
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<InputPixelType>::PrintType>(m_ForegroundValue) << std::endl;
+ os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryFillholeImageFilter.h b/Utilities/InsightJournal/itkBinaryFillholeImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..edc217f84fcaa95c0786a9680790b6ce591c7d7b
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryFillholeImageFilter.h
@@ -0,0 +1,137 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryFillholeImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.5 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkFillholeImageFilter_h
+#define __itkFillholeImageFilter_h
+
+#include "itkImageToImageFilter.h"
+
+namespace itk {
+
+/** \class BinaryFillholeImageFilter
+ * \brief Remove holes not connected to the boundary of the image.
+ *
+ * BinaryFillholeImageFilter fills holes in a binary image.
+ *
+ * Geodesic morphology and the Fillhole algorithm is described in
+ * Chapter 6 of Pierre Soille's book "Morphological Image Analysis:
+ * Principles and Applications", Second Edition, Springer, 2003.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa GrayscaleFillholeImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage>
+class ITK_EXPORT BinaryFillholeImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryFillholeImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ OutputImageType::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryFillholeImageFilter,
+ ImageToImageFilter);
+
+ /**
+ * Set/Get whether the connected components are defined strictly by
+ * face connectivity or by face+edge+vertex connectivity. Default is
+ * FullyConnectedOff. For objects that are 1 pixel wide, use
+ * FullyConnectedOn.
+ */
+ itkSetMacro(FullyConnected, bool);
+ itkGetConstReferenceMacro(FullyConnected, bool);
+ itkBooleanMacro(FullyConnected);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /** Set the value in the image to consider as "foreground". Defaults to
+ * maximum value of InputPixelType. */
+ itkSetMacro(ForegroundValue, InputImagePixelType);
+
+ /** Get the value in the image considered as "foreground". Defaults to
+ * maximum value of InputPixelType. */
+ itkGetMacro(ForegroundValue, InputImagePixelType);
+
+
+protected:
+ BinaryFillholeImageFilter();
+ ~BinaryFillholeImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** BinaryFillholeImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** BinaryFillholeImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+
+private:
+ BinaryFillholeImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ InputImagePixelType m_ForegroundValue;
+
+ bool m_FullyConnected;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryFillholeImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryFillholeImageFilter.txx b/Utilities/InsightJournal/itkBinaryFillholeImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..c999f6cb9cdb3934d4a53ff60b614f5010a73ad5
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryFillholeImageFilter.txx
@@ -0,0 +1,147 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryFillholeImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/12/15 21:41:24 $
+ Version: $Revision: 1.10 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryFillholeImageFilter_txx
+#define __itkBinaryFillholeImageFilter_txx
+
+#include "itkBinaryFillholeImageFilter.h"
+#include "itkBinaryReconstructionByErosionImageFilter.h"
+#include "itkImageRegionExclusionIteratorWithIndex.h"
+#include "itkProgressAccumulator.h"
+
+namespace itk {
+
+template <class TInputImage>
+BinaryFillholeImageFilter<TInputImage>
+::BinaryFillholeImageFilter()
+{
+ m_FullyConnected = false;
+ m_ForegroundValue = NumericTraits<InputImagePixelType>::max();
+}
+
+template <class TInputImage>
+void
+BinaryFillholeImageFilter<TInputImage>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template <class TInputImage>
+void
+BinaryFillholeImageFilter<TInputImage>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage>
+void
+BinaryFillholeImageFilter<TInputImage>
+::GenerateData()
+{
+ // Allocate the output
+ this->AllocateOutputs();
+
+ // construct a marker image to manipulate using reconstruction by
+ // erosion. the marker image will have the same pixel values as the
+ // input image on the boundary of the image and will have the
+ // maximum pixel value from the input image for all the pixels in
+ // the interior
+ //
+
+ // let choose a background value. Background value should not be given by user
+ // because closing is extensive so no background pixels will be added
+ // it is just needed for internal erosion filter and constant padder
+ InputImagePixelType backgroundValue = NumericTraits<InputImagePixelType>::Zero;
+ if ( m_ForegroundValue == backgroundValue )
+ {
+ // current background value is already used for foreground value
+ // choose another one
+ backgroundValue = NumericTraits<InputImagePixelType>::max();
+ }
+
+ // allocate a marker image
+ InputImagePointer markerPtr = InputImageType::New();
+ markerPtr->SetRegions( this->GetInput()->GetRequestedRegion() );
+ markerPtr->CopyInformation( this->GetInput() );
+ markerPtr->Allocate();
+
+ // fill the marker image with the maximum value from the input
+ markerPtr->FillBuffer( m_ForegroundValue );
+
+ // set the border of the marker to the background value
+ //
+ ImageRegionExclusionIteratorWithIndex<TInputImage>
+ markerBoundaryIt( markerPtr, this->GetInput()->GetRequestedRegion() );
+ markerBoundaryIt.SetExclusionRegionToInsetRegion();
+
+ // copy the boundary pixels
+ markerBoundaryIt.GoToBegin();
+ while ( !markerBoundaryIt.IsAtEnd() )
+ {
+ markerBoundaryIt.Set( backgroundValue );
+ ++markerBoundaryIt;
+ }
+
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Delegate to a geodesic erosion filter.
+ //
+ //
+ typename BinaryReconstructionByErosionImageFilter<TInputImage>::Pointer
+ erode
+ = BinaryReconstructionByErosionImageFilter<TInputImage>::New();
+ erode->SetMarkerImage( markerPtr );
+ erode->SetForegroundValue( m_ForegroundValue );
+ erode->SetBackgroundValue( backgroundValue );
+ erode->SetMaskImage( this->GetInput() );
+ erode->SetFullyConnected( m_FullyConnected );
+ erode->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(erode,1.0f);
+
+ erode->GraftOutput( this->GetOutput() );
+ erode->Update();
+ this->GraftOutput( erode->GetOutput() );
+}
+
+
+template<class TInputImage>
+void
+BinaryFillholeImageFilter<TInputImage>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<InputImagePixelType>::PrintType>(m_ForegroundValue) << std::endl;
+ os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryGrindPeakImageFilter.h b/Utilities/InsightJournal/itkBinaryGrindPeakImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..3fd056fb9cca1dc688ba39c7b245f05d51e7f557
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryGrindPeakImageFilter.h
@@ -0,0 +1,145 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryGrindPeakImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.5 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryGrindPeakImageFilter_h
+#define __itkBinaryGrindPeakImageFilter_h
+
+#include "itkImageToImageFilter.h"
+
+namespace itk {
+
+/** \class BinaryGrindPeakImageFilter
+ * \brief Remove the objects not connected to the boundary of the image.
+ *
+ * BinaryGrindPeakImageFilter ginds peaks in a grayscale image.
+ *
+ * Geodesic morphology and the grind peak algorithm is described in
+ * Chapter 6 of Pierre Soille's book "Morphological Image Analysis:
+ * Principles and Applications", Second Edition, Springer, 2003.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa GrayscaleGrindPeakImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage>
+class ITK_EXPORT BinaryGrindPeakImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryGrindPeakImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ OutputImageType::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryGrindPeakImageFilter,
+ ImageToImageFilter);
+
+ /**
+ * Set/Get whether the connected components are defined strictly by
+ * face connectivity or by face+edge+vertex connectivity. Default is
+ * FullyConnectedOff. For objects that are 1 pixel wide, use
+ * FullyConnectedOn.
+ */
+ itkSetMacro(FullyConnected, bool);
+ itkGetConstReferenceMacro(FullyConnected, bool);
+ itkBooleanMacro(FullyConnected);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /** Set the value in the image to consider as "foreground". Defaults to
+ * maximum value of InputPixelType. */
+ itkSetMacro(ForegroundValue, InputImagePixelType);
+
+ /** Get the value in the image considered as "foreground". Defaults to
+ * maximum value of InputPixelType. */
+ itkGetMacro(ForegroundValue, InputImagePixelType);
+
+ /** Set the value in eroded part of the image. Defaults to zero */
+ itkSetMacro(BackgroundValue, InputImagePixelType);
+
+ /** Set the value in eroded part of the image. Defaults to zero */
+ itkGetMacro(BackgroundValue, InputImagePixelType);
+
+
+protected:
+ BinaryGrindPeakImageFilter();
+ ~BinaryGrindPeakImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** BinaryGrindPeakImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** BinaryGrindPeakImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+
+private:
+ BinaryGrindPeakImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ InputImagePixelType m_ForegroundValue;
+
+ InputImagePixelType m_BackgroundValue;
+
+ bool m_FullyConnected;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryGrindPeakImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryGrindPeakImageFilter.txx b/Utilities/InsightJournal/itkBinaryGrindPeakImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..e74e45dd086651a888d4d5265e5d616ab0c12984
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryGrindPeakImageFilter.txx
@@ -0,0 +1,138 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryGrindPeakImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/12/15 21:41:24 $
+ Version: $Revision: 1.10 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryGrindPeakImageFilter_txx
+#define __itkBinaryGrindPeakImageFilter_txx
+
+#include "itkBinaryGrindPeakImageFilter.h"
+#include "itkBinaryReconstructionByDilationImageFilter.h"
+#include "itkImageRegionExclusionIteratorWithIndex.h"
+#include "itkProgressAccumulator.h"
+
+namespace itk {
+
+template <class TInputImage>
+BinaryGrindPeakImageFilter<TInputImage>
+::BinaryGrindPeakImageFilter()
+{
+ m_FullyConnected = false;
+ m_ForegroundValue = NumericTraits<InputImagePixelType>::max();
+ m_BackgroundValue = NumericTraits<InputImagePixelType>::Zero;
+}
+
+template <class TInputImage>
+void
+BinaryGrindPeakImageFilter<TInputImage>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template <class TInputImage>
+void
+BinaryGrindPeakImageFilter<TInputImage>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage>
+void
+BinaryGrindPeakImageFilter<TInputImage>
+::GenerateData()
+{
+ // Allocate the output
+ this->AllocateOutputs();
+
+ // construct a marker image to manipulate using reconstruction by
+ // erosion. the marker image will have the same pixel values as the
+ // input image on the boundary of the image and will have the
+ // maximum pixel value from the input image for all the pixels in
+ // the interior
+ //
+
+ // allocate a marker image
+ InputImagePointer markerPtr = InputImageType::New();
+ markerPtr->SetRegions( this->GetInput()->GetRequestedRegion() );
+ markerPtr->CopyInformation( this->GetInput() );
+ markerPtr->Allocate();
+
+ // fill the marker image with the maximum value from the input
+ markerPtr->FillBuffer( m_BackgroundValue );
+
+ // set the border of the marker to the background value
+ //
+ ImageRegionExclusionIteratorWithIndex<TInputImage>
+ markerBoundaryIt( markerPtr, this->GetInput()->GetRequestedRegion() );
+ markerBoundaryIt.SetExclusionRegionToInsetRegion();
+
+ // copy the boundary pixels
+ markerBoundaryIt.GoToBegin();
+ while ( !markerBoundaryIt.IsAtEnd() )
+ {
+ markerBoundaryIt.Set( m_ForegroundValue );
+ ++markerBoundaryIt;
+ }
+
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Delegate to a geodesic erosion filter.
+ //
+ //
+ typename BinaryReconstructionByDilationImageFilter<TInputImage>::Pointer
+ dilate
+ = BinaryReconstructionByDilationImageFilter<TInputImage>::New();
+ dilate->SetMarkerImage( markerPtr );
+ dilate->SetForegroundValue( m_ForegroundValue );
+ dilate->SetBackgroundValue( m_BackgroundValue );
+ dilate->SetMaskImage( this->GetInput() );
+ dilate->SetFullyConnected( m_FullyConnected );
+ dilate->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(dilate,1.0f);
+
+ dilate->GraftOutput( this->GetOutput() );
+ dilate->Update();
+ this->GraftOutput( dilate->GetOutput() );
+}
+
+
+template<class TInputImage>
+void
+BinaryGrindPeakImageFilter<TInputImage>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<InputImagePixelType>::PrintType>(m_ForegroundValue) << std::endl;
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<InputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryNotImageFilter.h b/Utilities/InsightJournal/itkBinaryNotImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..366bca57dc5f8ef3d560be64c3ab00288f6c9641
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryNotImageFilter.h
@@ -0,0 +1,143 @@
+#ifndef __itkBinaryNotImageFilter_h
+#define __itkBinaryNotImageFilter_h
+
+#include "itkUnaryFunctorImageFilter.h"
+#include "itkNumericTraits.h"
+
+
+namespace itk
+{
+
+/** \class BinaryNotImageFilter
+ * \brief Implements the BinaryNot logical operator pixel-wise between two images.
+ *
+ * This class is parametrized over the types of the two
+ * input images and the type of the output image.
+ * Numeric conversions (castings) are done by the C++ defaults.
+ *
+ *
+ * The total operation over one pixel will be
+ *
+ * output_pixel = static_cast<PixelType>( input1_pixel != input2_pixel )
+ *
+ * Where "!=" is the equality operator in C++.
+ *
+ * \ingroup IntensityImageFilters Multithreaded
+ */
+namespace Functor {
+
+template< class TPixel >
+class BinaryNot
+{
+public:
+ BinaryNot() {};
+ ~BinaryNot() {};
+ bool operator!=( const BinaryNot & ) const
+ {
+ return false;
+ }
+ bool operator==( const BinaryNot & other ) const
+ {
+ return !(*this != other);
+ }
+ inline TPixel operator()( const TPixel & A )
+ {
+ bool a = ( A == m_ForegroundValue );
+ if( !a )
+ {
+ return m_ForegroundValue;
+ }
+ return m_BackgroundValue;
+ }
+
+ TPixel m_ForegroundValue;
+ TPixel m_BackgroundValue;
+};
+
+}
+template <class TImage>
+class ITK_EXPORT BinaryNotImageFilter :
+ public
+UnaryFunctorImageFilter<TImage, TImage,
+ Functor::BinaryNot< typename TImage::PixelType > >
+
+
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryNotImageFilter Self;
+ typedef UnaryFunctorImageFilter<TImage, TImage,
+ Functor::BinaryNot< typename TImage::PixelType> > Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryNotImageFilter,
+ ImageToImageFilter);
+
+ typedef typename TImage::PixelType PixelType;
+
+ /** Set the value in the image to consider as "foreground". Defaults to
+ * maximum value of PixelType.*/
+ itkSetMacro(ForegroundValue, PixelType);
+
+ /** Get the value in the image considered as "foreground". Defaults to
+ * maximum value of PixelType. */
+ itkGetConstMacro(ForegroundValue, PixelType);
+
+ /** Set the value used as "background". Defaults to
+ * NumericTraits<PixelType>::NonpositiveMin(). */
+ itkSetMacro(BackgroundValue, PixelType);
+
+ /** Get the value used as "background". Defaults to
+ * NumericTraits<PixelType>::NonpositiveMin(). */
+ itkGetConstMacro(BackgroundValue, PixelType);
+
+
+protected:
+ BinaryNotImageFilter()
+ {
+ m_ForegroundValue = NumericTraits<PixelType>::max();
+ m_BackgroundValue = NumericTraits<PixelType>::NonpositiveMin();
+ }
+ virtual ~BinaryNotImageFilter() {}
+
+ void PrintSelf(std::ostream& os, Indent indent) const
+ {
+ Superclass::PrintSelf(os,indent);
+
+ typedef typename NumericTraits<PixelType>::PrintType
+ PixelPrintType;
+
+ os << indent << "ForegroundValue: "
+ << static_cast< PixelPrintType > (m_ForegroundValue)
+ << std::endl;
+
+ os << indent << "BackgroundValue: "
+ << static_cast< PixelPrintType > (m_BackgroundValue)
+ << std::endl;
+ }
+
+ void GenerateData()
+ {
+ this->GetFunctor().m_ForegroundValue = m_ForegroundValue;
+ this->GetFunctor().m_BackgroundValue = m_BackgroundValue;
+ Superclass::GenerateData();
+ }
+
+private:
+ BinaryNotImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ PixelType m_ForegroundValue;
+ PixelType m_BackgroundValue;
+
+};
+
+} // end namespace itk
+
+
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryOpeningByReconstructionImageFilter.h b/Utilities/InsightJournal/itkBinaryOpeningByReconstructionImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..22725730c128f7ccacae5b4c229a96678ded544c
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryOpeningByReconstructionImageFilter.h
@@ -0,0 +1,140 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryOpeningByReconstructionImageFilter.h,v $
+ Language: C++
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryOpeningByReconstructionImageFilter_h
+#define __itkBinaryOpeningByReconstructionImageFilter_h
+
+#include "itkImageToImageFilter.h"
+
+namespace itk {
+
+/**
+ * \class BinaryOpeningByReconstructionImageFilter
+ * \brief binary morphological closing of an image.
+ *
+ * This filter removes small (i.e., smaller than the structuring
+ * element) objects in the image. It is defined as:
+ * Opening(f) = ReconstructionByDilatation(Erosion(f)).
+ *
+ * The structuring element is assumed to be composed of binary
+ * values (zero or one). Only elements of the structuring element
+ * having values > 0 are candidates for affecting the center pixel.
+ *
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa MorphologyImageFilter, OpeningByReconstructionImageFilter, BinaryClosingByReconstructionImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+
+template<class TInputImage, class TKernel>
+class ITK_EXPORT BinaryOpeningByReconstructionImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryOpeningByReconstructionImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage> Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryOpeningByReconstructionImageFilter,
+ ImageToImageFilter);
+
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+
+ /** Declaration of pixel type. */
+ typedef typename TInputImage::PixelType PixelType ;
+
+ /** Kernel typedef. */
+ typedef TKernel KernelType;
+
+ /** Set kernel (structuring element). */
+ itkSetMacro(Kernel, KernelType);
+
+ /** Get the kernel (structuring element). */
+ itkGetConstReferenceMacro(Kernel, KernelType);
+
+ /** Set the value in the image to consider as "foreground". Defaults to
+ * maximum value of PixelType. */
+ itkSetMacro(ForegroundValue, PixelType);
+
+ /** Get the value in the image considered as "foreground". Defaults to
+ * maximum value of PixelType. */
+ itkGetMacro(ForegroundValue, PixelType);
+
+ /** Set the value in eroded part of the image. Defaults to zero */
+ itkSetMacro(BackgroundValue, PixelType);
+
+ /** Set the value in eroded part of the image. Defaults to zero */
+ itkGetMacro(BackgroundValue, PixelType);
+
+ /**
+ * Set/Get whether the connected components are defined strictly by
+ * face connectivity or by face+edge+vertex connectivity. Default is
+ * FullyConnectedOff. For objects that are 1 pixel wide, use
+ * FullyConnectedOn.
+ */
+ itkSetMacro(FullyConnected, bool);
+ itkGetConstReferenceMacro(FullyConnected, bool);
+ itkBooleanMacro(FullyConnected);
+
+
+protected:
+ BinaryOpeningByReconstructionImageFilter();
+ ~BinaryOpeningByReconstructionImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** BinaryOpeningByReconstructionImageFilter need to make sure they request enough of an
+ * input image to account for the structuring element size. The input
+ * requested region is expanded by the radius of the structuring element.
+ * If the request extends past the LargestPossibleRegion for the input,
+ * the request is cropped by the LargestPossibleRegion. */
+ void GenerateInputRequestedRegion() ;
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleDilateImageFilter GrayscaleErodeImageFilter. */
+ void GenerateData ();
+
+private:
+ BinaryOpeningByReconstructionImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ /** kernel or structuring element to use. */
+ KernelType m_Kernel ;
+
+ PixelType m_ForegroundValue;
+
+ PixelType m_BackgroundValue;
+
+ bool m_FullyConnected;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryOpeningByReconstructionImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryOpeningByReconstructionImageFilter.txx b/Utilities/InsightJournal/itkBinaryOpeningByReconstructionImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..935c8c49119c4a7a739b8d06d02a5dd5aa060f0a
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryOpeningByReconstructionImageFilter.txx
@@ -0,0 +1,105 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryOpeningByReconstructionImageFilter.txx,v $
+ Language: C++
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryOpeningByReconstructionImageFilter_txx
+#define __itkBinaryOpeningByReconstructionImageFilter_txx
+
+#include "itkBinaryOpeningByReconstructionImageFilter.h"
+#include "itkBinaryErodeImageFilter.h"
+#include "itkBinaryReconstructionByDilationImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+namespace itk {
+
+template<class TInputImage, class TKernel>
+BinaryOpeningByReconstructionImageFilter<TInputImage, TKernel>
+::BinaryOpeningByReconstructionImageFilter()
+ : m_Kernel()
+{
+ m_ForegroundValue = NumericTraits<PixelType>::max();
+ m_BackgroundValue = NumericTraits<PixelType>::Zero;
+ m_FullyConnected = false;
+}
+
+template <class TInputImage, class TKernel>
+void
+BinaryOpeningByReconstructionImageFilter<TInputImage, TKernel>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+template<class TInputImage, class TKernel>
+void
+BinaryOpeningByReconstructionImageFilter<TInputImage, TKernel>
+::GenerateData()
+{
+ // Allocate the outputs
+ this->AllocateOutputs();
+
+ /** set up erosion and dilation methods */
+ typename BinaryErodeImageFilter<InputImageType, OutputImageType, TKernel>::Pointer
+ erode = BinaryErodeImageFilter<InputImageType, OutputImageType, TKernel>::New();
+ erode->SetErodeValue( m_ForegroundValue );
+ erode->SetBackgroundValue( m_BackgroundValue );
+ erode->SetKernel( this->GetKernel() );
+ erode->SetInput( this->GetInput() );
+ erode->ReleaseDataFlagOn();
+ erode->SetNumberOfThreads( this->GetNumberOfThreads() );
+
+ typename BinaryReconstructionByDilationImageFilter<OutputImageType>::Pointer
+ dilate = BinaryReconstructionByDilationImageFilter<OutputImageType>::New();
+ dilate->SetForegroundValue( m_ForegroundValue );
+ dilate->SetBackgroundValue( m_BackgroundValue );
+ dilate->SetMarkerImage( erode->GetOutput() );
+ dilate->SetMaskImage( this->GetInput() );
+ dilate->SetFullyConnected( m_FullyConnected );
+ dilate->ReleaseDataFlagOn();
+ dilate->SetNumberOfThreads( this->GetNumberOfThreads() );
+
+ /** set up the minipipeline */
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+ progress->RegisterInternalFilter(erode, .8f);
+ progress->RegisterInternalFilter(dilate, .2f);
+
+ /** execute the minipipeline */
+ dilate->GraftOutput( this->GetOutput() );
+ dilate->Update();
+ this->GraftOutput( dilate->GetOutput() );
+}
+
+template<class TInputImage, class TKernel>
+void
+BinaryOpeningByReconstructionImageFilter<TInputImage, TKernel>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "Kernel: " << m_Kernel << std::endl;
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<PixelType>::PrintType>(m_ForegroundValue) << std::endl;
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<PixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryReconstructionByDilationImageFilter.h b/Utilities/InsightJournal/itkBinaryReconstructionByDilationImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..fe126f73510a5efd176a2de557adadfb666cf3ad
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryReconstructionByDilationImageFilter.h
@@ -0,0 +1,192 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryReconstructionByDilationImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryReconstructionByDilationImageFilter_h
+#define __itkBinaryReconstructionByDilationImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkAttributeLabelObject.h"
+#include "itkLabelMap.h"
+#include "itkBinaryImageToLabelMapFilter.h"
+#include "itkBinaryReconstructionLabelMapFilter.h"
+#include "itkAttributeOpeningLabelMapFilter.h"
+#include "itkLabelMapToBinaryImageFilter.h"
+
+
+namespace itk {
+
+/** \class BinaryReconstructionByDilationImageFilter
+ * \brief Identify local maxima whose height above the baseline is greater than h.
+ *
+* \brief binary reconstruction by dilation of an image
+ *
+ * Reconstruction by dilation operates on a "marker" image and a "mask"
+ * image, and is defined as the dilation of the marker image with
+ * respect to the mask image iterated until stability.
+ *
+ * Geodesic morphology is described in Chapter 6.2 of Pierre Soille's
+ * book "Morphological Image Analysis: Principles and Applications",
+ * Second Edition, Springer, 2003.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa MorphologyImageFilter, ReconstructionByDilationImageFilter, BinaryReconstructionByErosionImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage>
+class ITK_EXPORT BinaryReconstructionByDilationImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryReconstructionByDilationImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+
+ typedef AttributeLabelObject<unsigned long, ImageDimension, bool> LabelObjectType;
+ typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef typename itk::BinaryImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
+ typedef typename itk::BinaryReconstructionLabelMapFilter< LabelMapType, InputImageType > ReconstructionType;
+ typedef typename itk::AttributeOpeningLabelMapFilter< LabelMapType > OpeningType;
+ typedef typename itk::LabelMapToBinaryImageFilter< LabelMapType, OutputImageType > BinarizerType;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryReconstructionByDilationImageFilter,
+ ImageToImageFilter);
+
+ /**
+ * Set/Get whether the connected components are defined strictly by
+ * face connectivity or by face+edge+vertex connectivity. Default is
+ * FullyConnectedOff. For objects that are 1 pixel wide, use
+ * FullyConnectedOn.
+ */
+ itkSetMacro(FullyConnected, bool);
+ itkGetConstReferenceMacro(FullyConnected, bool);
+ itkBooleanMacro(FullyConnected);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the value used as "foreground" in the output image.
+ * Defaults to NumericTraits<PixelType>::max().
+ */
+ itkSetMacro(ForegroundValue, OutputImagePixelType);
+ itkGetConstMacro(ForegroundValue, OutputImagePixelType);
+
+ /** Set the marker image */
+ void SetMarkerImage(InputImageType *input)
+ {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput( 0, const_cast<InputImageType *>(input) );
+ }
+
+ /** Get the marker image */
+ InputImageType * GetMarkerImage()
+ {
+ return static_cast<InputImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(0)));
+ }
+
+ /** Set the mask image */
+ void SetMaskImage( const InputImageType *input)
+ {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput( 1, const_cast<InputImageType *>(input) );
+ }
+
+ /** Get the mask image */
+ InputImageType * GetMaskImage()
+ {
+ return static_cast<InputImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(1)));
+ }
+
+
+protected:
+ BinaryReconstructionByDilationImageFilter();
+ ~BinaryReconstructionByDilationImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** BinaryReconstructionByDilationImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** BinaryReconstructionByDilationImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+
+private:
+ BinaryReconstructionByDilationImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ bool m_FullyConnected;
+ OutputImagePixelType m_BackgroundValue;
+ OutputImagePixelType m_ForegroundValue;
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryReconstructionByDilationImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryReconstructionByDilationImageFilter.txx b/Utilities/InsightJournal/itkBinaryReconstructionByDilationImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..90a99a5e4e02df64d24d5c15dee1eef74a5d99a0
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryReconstructionByDilationImageFilter.txx
@@ -0,0 +1,129 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryReconstructionByDilationImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/08/01 19:16:18 $
+ Version: $Revision: 1.7 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryReconstructionByDilationImageFilter_txx
+#define __itkBinaryReconstructionByDilationImageFilter_txx
+
+#include "itkBinaryReconstructionByDilationImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+
+namespace itk {
+
+template<class TInputImage>
+BinaryReconstructionByDilationImageFilter<TInputImage>
+::BinaryReconstructionByDilationImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+ m_ForegroundValue = NumericTraits<OutputImagePixelType>::max();
+ m_FullyConnected = false;
+ this->SetNumberOfRequiredInputs(2);
+}
+
+template<class TInputImage>
+void
+BinaryReconstructionByDilationImageFilter<TInputImage>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetMarkerImage());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+
+ input = const_cast<InputImageType *>(this->GetMaskImage());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template<class TInputImage>
+void
+BinaryReconstructionByDilationImageFilter<TInputImage>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage>
+void
+BinaryReconstructionByDilationImageFilter<TInputImage>
+::GenerateData()
+{
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Allocate the output
+ this->AllocateOutputs();
+
+ typename LabelizerType::Pointer labelizer = LabelizerType::New();
+ labelizer->SetInput( this->GetMaskImage() );
+ labelizer->SetForegroundValue( m_ForegroundValue );
+ labelizer->SetBackgroundValue( m_BackgroundValue );
+ labelizer->SetFullyConnected( m_FullyConnected );
+ labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(labelizer, .25f);
+
+ typename ReconstructionType::Pointer reconstruction = ReconstructionType::New();
+ reconstruction->SetInput( labelizer->GetOutput() );
+ reconstruction->SetMarkerImage( this->GetMarkerImage() );
+ reconstruction->SetForegroundValue( m_ForegroundValue );
+ reconstruction->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(reconstruction, .25f);
+
+ typename OpeningType::Pointer opening = OpeningType::New();
+ opening->SetInput( reconstruction->GetOutput() );
+ opening->SetLambda( true );
+ opening->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(opening, .25f);
+
+ typename BinarizerType::Pointer binarizer = BinarizerType::New();
+ binarizer->SetInput( opening->GetOutput() );
+ binarizer->SetForegroundValue( m_ForegroundValue );
+ binarizer->SetBackgroundValue( m_BackgroundValue );
+ binarizer->SetBackgroundImage( this->GetMaskImage() );
+ binarizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(binarizer, .5f);
+
+ binarizer->GraftOutput( this->GetOutput() );
+ binarizer->Update();
+ this->GraftOutput( binarizer->GetOutput() );
+}
+
+
+template<class TInputImage>
+void
+BinaryReconstructionByDilationImageFilter<TInputImage>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_ForegroundValue) << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryReconstructionByErosionImageFilter.h b/Utilities/InsightJournal/itkBinaryReconstructionByErosionImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..da1deaf1d7bc9d4063527a8811513a45b79d6ea6
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryReconstructionByErosionImageFilter.h
@@ -0,0 +1,192 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryReconstructionByErosionImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryReconstructionByErosionImageFilter_h
+#define __itkBinaryReconstructionByErosionImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkAttributeLabelObject.h"
+#include "itkLabelMap.h"
+#include "itkBinaryNotImageFilter.h"
+#include "itkBinaryImageToLabelMapFilter.h"
+#include "itkBinaryReconstructionLabelMapFilter.h"
+#include "itkAttributeOpeningLabelMapFilter.h"
+#include "itkLabelMapMaskImageFilter.h"
+
+
+namespace itk {
+
+/** \class BinaryReconstructionByErosionImageFilter
+ * \brief binary reconstruction by erosion of an image
+ *
+ * Reconstruction by erosion operates on a "marker" image and a "mask"
+ * image, and is defined as the erosion of the marker image with
+ * respect to the mask image iterated until stability.
+ *
+ * Geodesic morphology is described in Chapter 6.2 of Pierre Soille's
+ * book "Morphological Image Analysis: Principles and Applications",
+ * Second Edition, Springer, 2003.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa MorphologyImageFilter, ReconstructionByErosionImageFilter, BinaryReconstructionByDilationImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage>
+class ITK_EXPORT BinaryReconstructionByErosionImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryReconstructionByErosionImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+
+ typedef BinaryNotImageFilter< InputImageType > NotType;
+ typedef AttributeLabelObject<unsigned long, ImageDimension, bool> LabelObjectType;
+ typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef typename itk::BinaryImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
+ typedef typename itk::BinaryReconstructionLabelMapFilter< LabelMapType, InputImageType > ReconstructionType;
+ typedef typename itk::AttributeOpeningLabelMapFilter< LabelMapType > OpeningType;
+ typedef typename itk::LabelMapMaskImageFilter< LabelMapType, OutputImageType > BinarizerType;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryReconstructionByErosionImageFilter,
+ ImageToImageFilter);
+
+ /**
+ * Set/Get whether the connected components are defined strictly by
+ * face connectivity or by face+edge+vertex connectivity. Default is
+ * FullyConnectedOff. For objects that are 1 pixel wide, use
+ * FullyConnectedOn.
+ */
+ itkSetMacro(FullyConnected, bool);
+ itkGetConstReferenceMacro(FullyConnected, bool);
+ itkBooleanMacro(FullyConnected);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the value used as "foreground" in the output image.
+ * Defaults to NumericTraits<PixelType>::max().
+ */
+ itkSetMacro(ForegroundValue, OutputImagePixelType);
+ itkGetConstMacro(ForegroundValue, OutputImagePixelType);
+
+ /** Set the marker image */
+ void SetMarkerImage(InputImageType *input)
+ {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput( 0, const_cast<InputImageType *>(input) );
+ }
+
+ /** Get the marker image */
+ InputImageType * GetMarkerImage()
+ {
+ return static_cast<InputImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(0)));
+ }
+
+ /** Set the mask image */
+ void SetMaskImage(const InputImageType *input)
+ {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput( 1, const_cast<InputImageType *>(input) );
+ }
+
+ /** Get the mask image */
+ InputImageType * GetMaskImage()
+ {
+ return static_cast<InputImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(1)));
+ }
+
+
+protected:
+ BinaryReconstructionByErosionImageFilter();
+ ~BinaryReconstructionByErosionImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** BinaryReconstructionByErosionImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** BinaryReconstructionByErosionImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+
+private:
+ BinaryReconstructionByErosionImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ bool m_FullyConnected;
+ OutputImagePixelType m_BackgroundValue;
+ OutputImagePixelType m_ForegroundValue;
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryReconstructionByErosionImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryReconstructionByErosionImageFilter.txx b/Utilities/InsightJournal/itkBinaryReconstructionByErosionImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..471b56394add333f127931b5c5ed28163f4ffb1a
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryReconstructionByErosionImageFilter.txx
@@ -0,0 +1,145 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryReconstructionByErosionImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/08/01 19:16:18 $
+ Version: $Revision: 1.7 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryReconstructionByErosionImageFilter_txx
+#define __itkBinaryReconstructionByErosionImageFilter_txx
+
+#include "itkBinaryReconstructionByErosionImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+
+namespace itk {
+
+template<class TInputImage>
+BinaryReconstructionByErosionImageFilter<TInputImage>
+::BinaryReconstructionByErosionImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+ m_ForegroundValue = NumericTraits<OutputImagePixelType>::max();
+ m_FullyConnected = false;
+ this->SetNumberOfRequiredInputs(2);
+}
+
+template<class TInputImage>
+void
+BinaryReconstructionByErosionImageFilter<TInputImage>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetMarkerImage());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+
+ input = const_cast<InputImageType *>(this->GetMaskImage());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template<class TInputImage>
+void
+BinaryReconstructionByErosionImageFilter<TInputImage>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage>
+void
+BinaryReconstructionByErosionImageFilter<TInputImage>
+::GenerateData()
+{
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Allocate the output
+ this->AllocateOutputs();
+
+ typename NotType::Pointer notMask = NotType::New();
+ notMask->SetInput( this->GetMaskImage() );
+ notMask->SetForegroundValue( m_ForegroundValue );
+ notMask->SetBackgroundValue( m_BackgroundValue );
+ notMask->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(notMask, .1f);
+
+ typename NotType::Pointer notMarker = NotType::New();
+ notMarker->SetInput( this->GetMarkerImage() );
+ notMarker->SetForegroundValue( m_ForegroundValue );
+ notMarker->SetBackgroundValue( m_BackgroundValue );
+ notMarker->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(notMarker, .1f);
+
+ typename LabelizerType::Pointer labelizer = LabelizerType::New();
+ labelizer->SetInput( notMask->GetOutput() );
+ labelizer->SetForegroundValue( m_ForegroundValue );
+ labelizer->SetBackgroundValue( m_BackgroundValue );
+ labelizer->SetFullyConnected( m_FullyConnected );
+ labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(labelizer, .2f);
+
+ typename ReconstructionType::Pointer reconstruction = ReconstructionType::New();
+ reconstruction->SetInput( labelizer->GetOutput() );
+ reconstruction->SetMarkerImage( notMarker->GetOutput() );
+ reconstruction->SetForegroundValue( m_ForegroundValue );
+ reconstruction->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(reconstruction, .2f);
+
+ typename OpeningType::Pointer opening = OpeningType::New();
+ opening->SetInput( reconstruction->GetOutput() );
+ opening->SetLambda( true );
+ opening->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(opening, .2f);
+
+ // invert the image during the binarization
+ typename BinarizerType::Pointer binarizer = BinarizerType::New();
+ binarizer->SetInput( opening->GetOutput() );
+ binarizer->SetLabel( m_BackgroundValue );
+ binarizer->SetNegated( true );
+ binarizer->SetBackgroundValue( m_ForegroundValue );
+ binarizer->SetFeatureImage( this->GetMaskImage() );
+ binarizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(binarizer, .2f);
+
+ binarizer->GraftOutput( this->GetOutput() );
+ binarizer->Update();
+ this->GraftOutput( binarizer->GetOutput() );
+}
+
+
+template<class TInputImage>
+void
+BinaryReconstructionByErosionImageFilter<TInputImage>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_ForegroundValue) << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryReconstructionLabelMapFilter.h b/Utilities/InsightJournal/itkBinaryReconstructionLabelMapFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..755d99bcca80ca8fba7105903847f82d7ab7b72a
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryReconstructionLabelMapFilter.h
@@ -0,0 +1,135 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryReconstructionLabelMapFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryReconstructionLabelMapFilter_h
+#define __itkBinaryReconstructionLabelMapFilter_h
+
+#include "itkInPlaceLabelMapFilter.h"
+#include "itkAttributeLabelObject.h"
+
+namespace itk {
+/** \class BinaryReconstructionLabelMapFilter
+ * \brief
+ *
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TImage, class TMarkerImage, class TAttributeAccessor=
+ typename Functor::AttributeLabelObjectAccessor< typename TImage::LabelObjectType > >
+class ITK_EXPORT BinaryReconstructionLabelMapFilter :
+ public InPlaceLabelMapFilter<TImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryReconstructionLabelMapFilter Self;
+ typedef InPlaceLabelMapFilter<TImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TImage ImageType;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::PixelType PixelType;
+ typedef typename ImageType::IndexType IndexType;
+ typedef typename ImageType::LabelObjectType LabelObjectType;
+
+ typedef TMarkerImage MarkerImageType;
+ typedef typename MarkerImageType::Pointer MarkerImagePointer;
+ typedef typename MarkerImageType::ConstPointer MarkerImageConstPointer;
+ typedef typename MarkerImageType::PixelType MarkerImagePixelType;
+
+ typedef TAttributeAccessor AttributeAccessorType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TImage::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryReconstructionLabelMapFilter,
+ InPlaceLabelMapFilter);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+/* itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<PixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, PixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<PixelType>));*/
+ /** End concept checking */
+#endif
+
+ /** Set the marker image */
+ void SetMarkerImage(TMarkerImage *input)
+ {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput( 1, const_cast<TMarkerImage *>(input) );
+ }
+
+ /** Get the marker image */
+ MarkerImageType * GetMarkerImage()
+ {
+ return static_cast<MarkerImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(1)));
+ }
+
+ /** Set the input image */
+ void SetInput1(TImage *input)
+ {
+ this->SetInput( input );
+ }
+
+ /** Set the marker image */
+ void SetInput2(TMarkerImage *input)
+ {
+ this->SetMarkerImage( input );
+ }
+
+ /**
+ * Set/Get the value used as "foreground" in the output image.
+ * Defaults to NumericTraits<MaskPixelType>::max().
+ */
+ itkSetMacro(ForegroundValue, PixelType);
+ itkGetConstMacro(ForegroundValue, PixelType);
+
+protected:
+ BinaryReconstructionLabelMapFilter();
+ ~BinaryReconstructionLabelMapFilter() {};
+
+ virtual void ThreadedGenerateData( LabelObjectType * labelObject );
+
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+private:
+ BinaryReconstructionLabelMapFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ MarkerImagePixelType m_ForegroundValue;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryReconstructionLabelMapFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryReconstructionLabelMapFilter.txx b/Utilities/InsightJournal/itkBinaryReconstructionLabelMapFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..62be887941b24b14f026f1255a7df2075ddf4700
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryReconstructionLabelMapFilter.txx
@@ -0,0 +1,83 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryReconstructionLabelMapFilter.txx,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryReconstructionLabelMapFilter_txx
+#define __itkBinaryReconstructionLabelMapFilter_txx
+
+#include "itkBinaryReconstructionLabelMapFilter.h"
+#include "itkProgressReporter.h"
+
+
+namespace itk {
+
+template <class TImage, class TMarkerImage, class TAttributeAccessor>
+BinaryReconstructionLabelMapFilter<TImage, TMarkerImage, TAttributeAccessor>
+::BinaryReconstructionLabelMapFilter()
+{
+ this->SetNumberOfRequiredInputs(2);
+ m_ForegroundValue = NumericTraits< MarkerImagePixelType >::max();
+}
+
+
+template <class TImage, class TMarkerImage, class TAttributeAccessor>
+void
+BinaryReconstructionLabelMapFilter<TImage, TMarkerImage, TAttributeAccessor>
+::ThreadedGenerateData( LabelObjectType * labelObject )
+{
+ AttributeAccessorType accessor;
+
+ const MarkerImageType * maskImage = this->GetMarkerImage();
+
+ typename LabelObjectType::LineContainerType::const_iterator lit;
+ typename LabelObjectType::LineContainerType & lineContainer = labelObject->GetLineContainer();
+
+ // iterate over all the lines to find a pixel inside the object
+ for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
+ {
+ const IndexType & firstIdx = lit->GetIndex();
+ unsigned long length = lit->GetLength();
+
+ long endIdx0 = firstIdx[0] + length;
+ for( IndexType idx = firstIdx; idx[0]<endIdx0; idx[0]++ )
+ {
+ const MarkerImagePixelType & v = maskImage->GetPixel( idx );
+ if( v == m_ForegroundValue )
+ {
+ // keep the object
+ accessor( labelObject, true );
+ return;
+ }
+ }
+ }
+
+ // remove the object
+ accessor( labelObject, false );
+
+}
+
+
+template <class TImage, class TMarkerImage, class TAttributeAccessor>
+void
+BinaryReconstructionLabelMapFilter<TImage, TMarkerImage, TAttributeAccessor>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<MarkerImagePixelType>::PrintType>(m_ForegroundValue) << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryShapeKeepNObjectsImageFilter.h b/Utilities/InsightJournal/itkBinaryShapeKeepNObjectsImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..aed66974f853b43b53ef099b8fc2fa97034295d0
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryShapeKeepNObjectsImageFilter.h
@@ -0,0 +1,188 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryShapeKeepNObjectsImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryShapeKeepNObjectsImageFilter_h
+#define __itkBinaryShapeKeepNObjectsImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkShapeLabelObject.h"
+#include "itkLabelMap.h"
+#include "itkBinaryImageToLabelMapFilter.h"
+#include "itkShapeLabelMapFilter.h"
+#include "itkShapeKeepNObjectsLabelMapFilter.h"
+#include "itkLabelMapToBinaryImageFilter.h"
+
+
+namespace itk {
+
+/** \class BinaryShapeKeepNObjectsImageFilter
+ * \brief keep N objects according to their shape attributes
+ *
+ * BinaryShapeKeepNObjectsImageFilter keep the N objects in a binary image
+ * with the highest (or lowest) attribute value. The attributes are the ones
+ * of the ShapeLabelObject.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa ShapeLabelObject, LabelShapeKeepNObjectsImageFilter, BinaryStatisticsKeepNObjectsImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage>
+class ITK_EXPORT BinaryShapeKeepNObjectsImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryShapeKeepNObjectsImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+
+ typedef ShapeLabelObject<unsigned long, ImageDimension> LabelObjectType;
+ typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef typename itk::BinaryImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
+ typedef typename itk::ShapeLabelMapFilter< LabelMapType > LabelObjectValuatorType;
+ typedef typename LabelObjectType::AttributeType AttributeType;
+ typedef typename itk::ShapeKeepNObjectsLabelMapFilter< LabelMapType > KeepNObjectsType;
+ typedef typename itk::LabelMapToBinaryImageFilter< LabelMapType, OutputImageType > BinarizerType;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryShapeKeepNObjectsImageFilter,
+ ImageToImageFilter);
+
+ /**
+ * Set/Get whether the connected components are defined strictly by
+ * face connectivity or by face+edge+vertex connectivity. Default is
+ * FullyConnectedOff. For objects that are 1 pixel wide, use
+ * FullyConnectedOn.
+ */
+ itkSetMacro(FullyConnected, bool);
+ itkGetConstReferenceMacro(FullyConnected, bool);
+ itkBooleanMacro(FullyConnected);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the value used as "foreground" in the output image.
+ * Defaults to NumericTraits<PixelType>::max().
+ */
+ itkSetMacro(ForegroundValue, OutputImagePixelType);
+ itkGetConstMacro(ForegroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the number of objects to keep
+ */
+ itkGetConstMacro(NumberOfObjects, unsigned long);
+ itkSetMacro(NumberOfObjects, unsigned long);
+
+ /**
+ * Set/Get the ordering of the objects. By default, the ones with the
+ * highest value are kept. Turming ReverseOrdering to true make this filter
+ * keep the objects with the smallest values
+ */
+ itkGetConstMacro( ReverseOrdering, bool );
+ itkSetMacro( ReverseOrdering, bool );
+ itkBooleanMacro( ReverseOrdering );
+
+ /**
+ * Set/Get the attribute to use to select the object to keep. The default
+ * is "Size".
+ */
+ itkGetConstMacro( Attribute, AttributeType );
+ itkSetMacro( Attribute, AttributeType );
+ void SetAttribute( const std::string & s )
+ {
+ this->SetAttribute( LabelObjectType::GetAttributeFromName( s ) );
+ }
+
+protected:
+ BinaryShapeKeepNObjectsImageFilter();
+ ~BinaryShapeKeepNObjectsImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** BinaryShapeKeepNObjectsImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** BinaryShapeKeepNObjectsImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+private:
+ BinaryShapeKeepNObjectsImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ bool m_FullyConnected;
+ OutputImagePixelType m_BackgroundValue;
+ OutputImagePixelType m_ForegroundValue;
+ unsigned long m_NumberOfObjects;
+ bool m_ReverseOrdering;
+ AttributeType m_Attribute;
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryShapeKeepNObjectsImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryShapeKeepNObjectsImageFilter.txx b/Utilities/InsightJournal/itkBinaryShapeKeepNObjectsImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..e1029c723d2156513427238ca9a30c79b892dc5a
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryShapeKeepNObjectsImageFilter.txx
@@ -0,0 +1,135 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryShapeKeepNObjectsImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/08/01 19:16:18 $
+ Version: $Revision: 1.7 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryShapeKeepNObjectsImageFilter_txx
+#define __itkBinaryShapeKeepNObjectsImageFilter_txx
+
+#include "itkBinaryShapeKeepNObjectsImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+
+namespace itk {
+
+template<class TInputImage>
+BinaryShapeKeepNObjectsImageFilter<TInputImage>
+::BinaryShapeKeepNObjectsImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+ m_ForegroundValue = NumericTraits<OutputImagePixelType>::max();
+ m_FullyConnected = false;
+ m_ReverseOrdering = false;
+ m_Attribute = LabelObjectType::SIZE;
+}
+
+template<class TInputImage>
+void
+BinaryShapeKeepNObjectsImageFilter<TInputImage>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template<class TInputImage>
+void
+BinaryShapeKeepNObjectsImageFilter<TInputImage>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage>
+void
+BinaryShapeKeepNObjectsImageFilter<TInputImage>
+::GenerateData()
+{
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Allocate the output
+ this->AllocateOutputs();
+
+ typename LabelizerType::Pointer labelizer = LabelizerType::New();
+ labelizer->SetInput( this->GetInput() );
+ labelizer->SetForegroundValue( m_ForegroundValue );
+ labelizer->SetBackgroundValue( m_BackgroundValue );
+ labelizer->SetFullyConnected( m_FullyConnected );
+ labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(labelizer, .3f);
+
+ typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
+ valuator->SetInput( labelizer->GetOutput() );
+ valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
+ if( m_Attribute == LabelObjectType::PERIMETER || m_Attribute == LabelObjectType::ROUNDNESS )
+ {
+ valuator->SetComputePerimeter( true );
+ }
+ if( m_Attribute == LabelObjectType::FERET_DIAMETER )
+ {
+ valuator->SetComputeFeretDiameter( true );
+ }
+ progress->RegisterInternalFilter(valuator, .3f);
+
+ typename KeepNObjectsType::Pointer opening = KeepNObjectsType::New();
+ opening->SetInput( valuator->GetOutput() );
+ opening->SetNumberOfObjects( m_NumberOfObjects );
+ opening->SetReverseOrdering( m_ReverseOrdering );
+ opening->SetAttribute( m_Attribute );
+ opening->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(opening, .2f);
+
+ typename BinarizerType::Pointer binarizer = BinarizerType::New();
+ binarizer->SetInput( opening->GetOutput() );
+ binarizer->SetForegroundValue( m_ForegroundValue );
+ binarizer->SetBackgroundValue( m_BackgroundValue );
+ binarizer->SetBackgroundImage( this->GetInput() );
+ binarizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(binarizer, .2f);
+
+ binarizer->GraftOutput( this->GetOutput() );
+ binarizer->Update();
+ this->GraftOutput( binarizer->GetOutput() );
+}
+
+
+template<class TInputImage>
+void
+BinaryShapeKeepNObjectsImageFilter<TInputImage>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_ForegroundValue) << std::endl;
+ os << indent << "NumberOfObjects: " << m_NumberOfObjects << std::endl;
+ os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
+ os << indent << "Attribute: " << LabelObjectType::GetNameFromAttribute(m_Attribute) << " (" << m_Attribute << ")" << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryShapeOpeningImageFilter.h b/Utilities/InsightJournal/itkBinaryShapeOpeningImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..4b14f53983b241ed3b0d4be489ba252d6a586780
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryShapeOpeningImageFilter.h
@@ -0,0 +1,191 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryShapeOpeningImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryShapeOpeningImageFilter_h
+#define __itkBinaryShapeOpeningImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkShapeLabelObject.h"
+#include "itkLabelMap.h"
+#include "itkBinaryImageToLabelMapFilter.h"
+#include "itkShapeLabelMapFilter.h"
+#include "itkShapeOpeningLabelMapFilter.h"
+#include "itkLabelMapToBinaryImageFilter.h"
+
+
+namespace itk {
+
+/** \class BinaryShapeOpeningImageFilter
+ * \brief remove the objects according to the value of their shape attribute
+ *
+ * BinaryShapeOpeningImageFilter removes the objects in a binary image
+ * with an attribute value smaller or greater than a threshold called Lambda.
+ * The attributes are the ones of the ShapeLabelObject.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa ShapeLabelObject, LabelShapeOpeningImageFilter, BinaryStatisticsOpeningImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage>
+class ITK_EXPORT BinaryShapeOpeningImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryShapeOpeningImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+
+ typedef ShapeLabelObject<unsigned long, ImageDimension> LabelObjectType;
+ typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef typename itk::BinaryImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
+ typedef typename itk::ShapeLabelMapFilter< LabelMapType > LabelObjectValuatorType;
+ typedef typename LabelObjectType::AttributeType AttributeType;
+ typedef typename itk::ShapeOpeningLabelMapFilter< LabelMapType > OpeningType;
+ typedef typename itk::LabelMapToBinaryImageFilter< LabelMapType, OutputImageType > BinarizerType;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryShapeOpeningImageFilter,
+ ImageToImageFilter);
+
+ /**
+ * Set/Get whether the connected components are defined strictly by
+ * face connectivity or by face+edge+vertex connectivity. Default is
+ * FullyConnectedOff. For objects that are 1 pixel wide, use
+ * FullyConnectedOn.
+ */
+ itkSetMacro(FullyConnected, bool);
+ itkGetConstReferenceMacro(FullyConnected, bool);
+ itkBooleanMacro(FullyConnected);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the value used as "foreground" in the output image.
+ * Defaults to NumericTraits<PixelType>::max().
+ */
+ itkSetMacro(ForegroundValue, OutputImagePixelType);
+ itkGetConstMacro(ForegroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the threshold used to keep or remove the objects.
+ */
+ itkGetConstMacro(Lambda, double);
+ itkSetMacro(Lambda, double);
+
+ /**
+ * Set/Get the ordering of the objects. By default, the objects with
+ * an attribute value smaller than Lamba are removed. Turning ReverseOrdering
+ * to true make this filter remove the object with an attribute value greater
+ * than Lambda instead.
+ */
+ itkGetConstMacro( ReverseOrdering, bool );
+ itkSetMacro( ReverseOrdering, bool );
+ itkBooleanMacro( ReverseOrdering );
+
+ /**
+ * Set/Get the attribute to use to select the object to remove. The default
+ * is "Size".
+ */
+ itkGetConstMacro( Attribute, AttributeType );
+ itkSetMacro( Attribute, AttributeType );
+ void SetAttribute( const std::string & s )
+ {
+ this->SetAttribute( LabelObjectType::GetAttributeFromName( s ) );
+ }
+
+
+protected:
+ BinaryShapeOpeningImageFilter();
+ ~BinaryShapeOpeningImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** BinaryShapeOpeningImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** BinaryShapeOpeningImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+
+private:
+ BinaryShapeOpeningImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ bool m_FullyConnected;
+ OutputImagePixelType m_BackgroundValue;
+ OutputImagePixelType m_ForegroundValue;
+ double m_Lambda;
+ bool m_ReverseOrdering;
+ AttributeType m_Attribute;
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryShapeOpeningImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryShapeOpeningImageFilter.txx b/Utilities/InsightJournal/itkBinaryShapeOpeningImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..6ff29cc87372cda52a8503ace15847a43b24a44c
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryShapeOpeningImageFilter.txx
@@ -0,0 +1,135 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryShapeOpeningImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/08/01 19:16:18 $
+ Version: $Revision: 1.7 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryShapeOpeningImageFilter_txx
+#define __itkBinaryShapeOpeningImageFilter_txx
+
+#include "itkBinaryShapeOpeningImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+
+namespace itk {
+
+template<class TInputImage>
+BinaryShapeOpeningImageFilter<TInputImage>
+::BinaryShapeOpeningImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+ m_ForegroundValue = NumericTraits<OutputImagePixelType>::max();
+ m_FullyConnected = false;
+ m_ReverseOrdering = false;
+ m_Attribute = LabelObjectType::SIZE;
+}
+
+template<class TInputImage>
+void
+BinaryShapeOpeningImageFilter<TInputImage>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template<class TInputImage>
+void
+BinaryShapeOpeningImageFilter<TInputImage>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage>
+void
+BinaryShapeOpeningImageFilter<TInputImage>
+::GenerateData()
+{
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Allocate the output
+ this->AllocateOutputs();
+
+ typename LabelizerType::Pointer labelizer = LabelizerType::New();
+ labelizer->SetInput( this->GetInput() );
+ labelizer->SetForegroundValue( m_ForegroundValue );
+ labelizer->SetBackgroundValue( m_BackgroundValue );
+ labelizer->SetFullyConnected( m_FullyConnected );
+ labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(labelizer, .3f);
+
+ typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
+ valuator->SetInput( labelizer->GetOutput() );
+ valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
+ if( m_Attribute == LabelObjectType::PERIMETER || m_Attribute == LabelObjectType::ROUNDNESS )
+ {
+ valuator->SetComputePerimeter( true );
+ }
+ if( m_Attribute == LabelObjectType::FERET_DIAMETER )
+ {
+ valuator->SetComputeFeretDiameter( true );
+ }
+ progress->RegisterInternalFilter(valuator, .3f);
+
+ typename OpeningType::Pointer opening = OpeningType::New();
+ opening->SetInput( valuator->GetOutput() );
+ opening->SetLambda( m_Lambda );
+ opening->SetReverseOrdering( m_ReverseOrdering );
+ opening->SetAttribute( m_Attribute );
+ opening->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(opening, .2f);
+
+ typename BinarizerType::Pointer binarizer = BinarizerType::New();
+ binarizer->SetInput( opening->GetOutput() );
+ binarizer->SetForegroundValue( m_ForegroundValue );
+ binarizer->SetBackgroundValue( m_BackgroundValue );
+ binarizer->SetBackgroundImage( this->GetInput() );
+ binarizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(binarizer, .2f);
+
+ binarizer->GraftOutput( this->GetOutput() );
+ binarizer->Update();
+ this->GraftOutput( binarizer->GetOutput() );
+}
+
+
+template<class TInputImage>
+void
+BinaryShapeOpeningImageFilter<TInputImage>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_ForegroundValue) << std::endl;
+ os << indent << "Lambda: " << m_Lambda << std::endl;
+ os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
+ os << indent << "Attribute: " << LabelObjectType::GetNameFromAttribute(m_Attribute) << " (" << m_Attribute << ")" << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryStatisticsKeepNObjectsImageFilter.h b/Utilities/InsightJournal/itkBinaryStatisticsKeepNObjectsImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..27bdfbc6b5bf6396d26b86ad74e8b8c804c94490
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryStatisticsKeepNObjectsImageFilter.h
@@ -0,0 +1,219 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryStatisticsKeepNObjectsImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryStatisticsKeepNObjectsImageFilter_h
+#define __itkBinaryStatisticsKeepNObjectsImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkStatisticsLabelObject.h"
+#include "itkLabelMap.h"
+#include "itkBinaryImageToLabelMapFilter.h"
+#include "itkStatisticsLabelMapFilter.h"
+#include "itkStatisticsKeepNObjectsLabelMapFilter.h"
+#include "itkLabelMapToBinaryImageFilter.h"
+
+
+namespace itk {
+
+/** \class BinaryStatisticsKeepNObjectsImageFilter
+ * \brief keep N objects according to their statistics attributes
+ *
+ * BinaryStatisticsKeepNObjectsImageFilter keep the N objects in a binary image
+ * with the highest (or lowest) attribute value. The attributes are the ones
+ * of the StatisticsLabelObject.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa StatisticsLabelObject, LabelStatisticsKeepNObjectsImageFilter, BinaryShapeKeepNObjectsImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage, class TFeatureImage>
+class ITK_EXPORT BinaryStatisticsKeepNObjectsImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryStatisticsKeepNObjectsImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ typedef TFeatureImage FeatureImageType;
+ typedef typename FeatureImageType::Pointer FeatureImagePointer;
+ typedef typename FeatureImageType::ConstPointer FeatureImageConstPointer;
+ typedef typename FeatureImageType::PixelType FeatureImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+
+ typedef StatisticsLabelObject<unsigned long, ImageDimension> LabelObjectType;
+ typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef typename itk::BinaryImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
+ typedef typename itk::StatisticsLabelMapFilter< LabelMapType, TFeatureImage > LabelObjectValuatorType;
+ typedef typename LabelObjectType::AttributeType AttributeType;
+ typedef typename itk::StatisticsKeepNObjectsLabelMapFilter< LabelMapType > KeepNObjectsType;
+ typedef typename itk::LabelMapToBinaryImageFilter< LabelMapType, OutputImageType > BinarizerType;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryStatisticsKeepNObjectsImageFilter,
+ ImageToImageFilter);
+
+ /**
+ * Set/Get whether the connected components are defined strictly by
+ * face connectivity or by face+edge+vertex connectivity. Default is
+ * FullyConnectedOff. For objects that are 1 pixel wide, use
+ * FullyConnectedOn.
+ */
+ itkSetMacro(FullyConnected, bool);
+ itkGetConstReferenceMacro(FullyConnected, bool);
+ itkBooleanMacro(FullyConnected);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the value used as "foreground" in the output image.
+ * Defaults to NumericTraits<PixelType>::max().
+ */
+ itkSetMacro(ForegroundValue, OutputImagePixelType);
+ itkGetConstMacro(ForegroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the number of objects to keep
+ */
+ itkGetConstMacro(NumberOfObjects, unsigned long);
+ itkSetMacro(NumberOfObjects, unsigned long);
+
+ /**
+ * Set/Get the ordering of the objects. By default, the ones with the
+ * highest value are kept. Turming ReverseOrdering to true make this filter
+ * keep the objects with the smallest values
+ */
+ itkGetConstMacro( ReverseOrdering, bool );
+ itkSetMacro( ReverseOrdering, bool );
+ itkBooleanMacro( ReverseOrdering );
+
+ /**
+ * Set/Get the attribute to use to select the object to keep. The default
+ * is "Mean".
+ */
+ itkGetConstMacro( Attribute, AttributeType );
+ itkSetMacro( Attribute, AttributeType );
+ void SetAttribute( const std::string & s )
+ {
+ this->SetAttribute( LabelObjectType::GetAttributeFromName( s ) );
+ }
+
+
+ /** Set the feature image */
+ void SetFeatureImage(TFeatureImage *input)
+ {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput( 1, const_cast<TFeatureImage *>(input) );
+ }
+
+ /** Get the feature image */
+ FeatureImageType * GetFeatureImage()
+ {
+ return static_cast<FeatureImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(1)));
+ }
+
+ /** Set the input image */
+ void SetInput1(InputImageType *input)
+ {
+ this->SetInput( input );
+ }
+
+ /** Set the feature image */
+ void SetInput2(FeatureImageType *input)
+ {
+ this->SetFeatureImage( input );
+ }
+
+protected:
+ BinaryStatisticsKeepNObjectsImageFilter();
+ ~BinaryStatisticsKeepNObjectsImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** BinaryStatisticsKeepNObjectsImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** BinaryStatisticsKeepNObjectsImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+private:
+ BinaryStatisticsKeepNObjectsImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ bool m_FullyConnected;
+ OutputImagePixelType m_BackgroundValue;
+ OutputImagePixelType m_ForegroundValue;
+ unsigned long m_NumberOfObjects;
+ bool m_ReverseOrdering;
+ AttributeType m_Attribute;
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryStatisticsKeepNObjectsImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryStatisticsKeepNObjectsImageFilter.txx b/Utilities/InsightJournal/itkBinaryStatisticsKeepNObjectsImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..8a309c19050c4e13f4afe763c3336dcd3f047b5b
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryStatisticsKeepNObjectsImageFilter.txx
@@ -0,0 +1,138 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryStatisticsKeepNObjectsImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/08/01 19:16:18 $
+ Version: $Revision: 1.7 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryStatisticsKeepNObjectsImageFilter_txx
+#define __itkBinaryStatisticsKeepNObjectsImageFilter_txx
+
+#include "itkBinaryStatisticsKeepNObjectsImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+
+namespace itk {
+
+template<class TInputImage, class TFeatureImage>
+BinaryStatisticsKeepNObjectsImageFilter<TInputImage, TFeatureImage>
+::BinaryStatisticsKeepNObjectsImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+ m_ForegroundValue = NumericTraits<OutputImagePixelType>::max();
+ m_FullyConnected = false;
+ m_ReverseOrdering = false;
+ m_Attribute = LabelObjectType::MEAN;
+ this->SetNumberOfRequiredInputs(2);
+}
+
+template<class TInputImage, class TFeatureImage>
+void
+BinaryStatisticsKeepNObjectsImageFilter<TInputImage, TFeatureImage>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template<class TInputImage, class TFeatureImage>
+void
+BinaryStatisticsKeepNObjectsImageFilter<TInputImage, TFeatureImage>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage, class TFeatureImage>
+void
+BinaryStatisticsKeepNObjectsImageFilter<TInputImage, TFeatureImage>
+::GenerateData()
+{
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Allocate the output
+ this->AllocateOutputs();
+
+ typename LabelizerType::Pointer labelizer = LabelizerType::New();
+ labelizer->SetInput( this->GetInput() );
+ labelizer->SetForegroundValue( m_ForegroundValue );
+ labelizer->SetBackgroundValue( m_BackgroundValue );
+ labelizer->SetFullyConnected( m_FullyConnected );
+ labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(labelizer, .3f);
+
+ typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
+ valuator->SetInput( labelizer->GetOutput() );
+ valuator->SetFeatureImage( this->GetFeatureImage() );
+ valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
+ valuator->SetComputeHistogram( false );
+ if( m_Attribute == LabelObjectType::PERIMETER || m_Attribute == LabelObjectType::ROUNDNESS )
+ {
+ valuator->SetComputePerimeter( true );
+ }
+ if( m_Attribute == LabelObjectType::FERET_DIAMETER )
+ {
+ valuator->SetComputeFeretDiameter( true );
+ }
+ progress->RegisterInternalFilter(valuator, .3f);
+
+ typename KeepNObjectsType::Pointer opening = KeepNObjectsType::New();
+ opening->SetInput( valuator->GetOutput() );
+ opening->SetNumberOfObjects( m_NumberOfObjects );
+ opening->SetReverseOrdering( m_ReverseOrdering );
+ opening->SetAttribute( m_Attribute );
+ opening->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(opening, .2f);
+
+ typename BinarizerType::Pointer binarizer = BinarizerType::New();
+ binarizer->SetInput( opening->GetOutput() );
+ binarizer->SetForegroundValue( m_ForegroundValue );
+ binarizer->SetBackgroundValue( m_BackgroundValue );
+ binarizer->SetBackgroundImage( this->GetInput() );
+ binarizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(binarizer, .2f);
+
+ binarizer->GraftOutput( this->GetOutput() );
+ binarizer->Update();
+ this->GraftOutput( binarizer->GetOutput() );
+}
+
+
+template<class TInputImage, class TFeatureImage>
+void
+BinaryStatisticsKeepNObjectsImageFilter<TInputImage, TFeatureImage>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_ForegroundValue) << std::endl;
+ os << indent << "NumberOfObjects: " << m_NumberOfObjects << std::endl;
+ os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
+ os << indent << "Attribute: " << LabelObjectType::GetNameFromAttribute(m_Attribute) << " (" << m_Attribute << ")" << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkBinaryStatisticsOpeningImageFilter.h b/Utilities/InsightJournal/itkBinaryStatisticsOpeningImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..74b267497ca8124f0c67392f0d0a394894c418b2
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryStatisticsOpeningImageFilter.h
@@ -0,0 +1,221 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryStatisticsOpeningImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryStatisticsOpeningImageFilter_h
+#define __itkBinaryStatisticsOpeningImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkStatisticsLabelObject.h"
+#include "itkLabelMap.h"
+#include "itkBinaryImageToLabelMapFilter.h"
+#include "itkStatisticsLabelMapFilter.h"
+#include "itkStatisticsOpeningLabelMapFilter.h"
+#include "itkLabelMapToBinaryImageFilter.h"
+
+
+namespace itk {
+
+/** \class BinaryStatisticsOpeningImageFilter
+ * \brief remove the objects according to the value of their statistics attribute
+ *
+ * BinaryStatisticsOpeningImageFilter removes the objects in a binary image
+ * with an attribute value smaller or greater than a threshold called Lambda.
+ * The attributes are the ones of the StatisticsLabelObject.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa StatisticsLabelObject, LabelStatisticsOpeningImageFilter, BinaryShapeOpeningImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage, class TFeatureImage>
+class ITK_EXPORT BinaryStatisticsOpeningImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef BinaryStatisticsOpeningImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ typedef TFeatureImage FeatureImageType;
+ typedef typename FeatureImageType::Pointer FeatureImagePointer;
+ typedef typename FeatureImageType::ConstPointer FeatureImageConstPointer;
+ typedef typename FeatureImageType::PixelType FeatureImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+
+ typedef StatisticsLabelObject<unsigned long, ImageDimension> LabelObjectType;
+ typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef typename itk::BinaryImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
+ typedef typename itk::StatisticsLabelMapFilter< LabelMapType, TFeatureImage > LabelObjectValuatorType;
+ typedef typename LabelObjectType::AttributeType AttributeType;
+ typedef typename itk::StatisticsOpeningLabelMapFilter< LabelMapType > OpeningType;
+ typedef typename itk::LabelMapToBinaryImageFilter< LabelMapType, OutputImageType > BinarizerType;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(BinaryStatisticsOpeningImageFilter,
+ ImageToImageFilter);
+
+ /**
+ * Set/Get whether the connected components are defined strictly by
+ * face connectivity or by face+edge+vertex connectivity. Default is
+ * FullyConnectedOff. For objects that are 1 pixel wide, use
+ * FullyConnectedOn.
+ */
+ itkSetMacro(FullyConnected, bool);
+ itkGetConstReferenceMacro(FullyConnected, bool);
+ itkBooleanMacro(FullyConnected);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the value used as "foreground" in the output image.
+ * Defaults to NumericTraits<PixelType>::max().
+ */
+ itkSetMacro(ForegroundValue, OutputImagePixelType);
+ itkGetConstMacro(ForegroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the threshold used to keep or remove the objects.
+ */
+ itkGetConstMacro(Lambda, double);
+ itkSetMacro(Lambda, double);
+
+ /**
+ * Set/Get the ordering of the objects. By default, the objects with
+ * an attribute value smaller than Lamba are removed. Turning ReverseOrdering
+ * to true make this filter remove the object with an attribute value greater
+ * than Lambda instead.
+ */
+ itkGetConstMacro( ReverseOrdering, bool );
+ itkSetMacro( ReverseOrdering, bool );
+ itkBooleanMacro( ReverseOrdering );
+
+ /**
+ * Set/Get the attribute to use to select the object to remove. The default
+ * is "Mean".
+ */
+ itkGetConstMacro( Attribute, AttributeType );
+ itkSetMacro( Attribute, AttributeType );
+ void SetAttribute( const std::string & s )
+ {
+ this->SetAttribute( LabelObjectType::GetAttributeFromName( s ) );
+ }
+
+
+ /** Set the feature image */
+ void SetFeatureImage(TFeatureImage *input)
+ {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput( 1, const_cast<TFeatureImage *>(input) );
+ }
+
+ /** Get the feature image */
+ FeatureImageType * GetFeatureImage()
+ {
+ return static_cast<FeatureImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(1)));
+ }
+
+ /** Set the input image */
+ void SetInput1(InputImageType *input)
+ {
+ this->SetInput( input );
+ }
+
+ /** Set the feature image */
+ void SetInput2(FeatureImageType *input)
+ {
+ this->SetFeatureImage( input );
+ }
+
+protected:
+ BinaryStatisticsOpeningImageFilter();
+ ~BinaryStatisticsOpeningImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** BinaryStatisticsOpeningImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** BinaryStatisticsOpeningImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+
+private:
+ BinaryStatisticsOpeningImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ bool m_FullyConnected;
+ OutputImagePixelType m_BackgroundValue;
+ OutputImagePixelType m_ForegroundValue;
+ double m_Lambda;
+ bool m_ReverseOrdering;
+ AttributeType m_Attribute;
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkBinaryStatisticsOpeningImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkBinaryStatisticsOpeningImageFilter.txx b/Utilities/InsightJournal/itkBinaryStatisticsOpeningImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..b1bfdb5ad8235f9b228738c34c949c990ffe11fb
--- /dev/null
+++ b/Utilities/InsightJournal/itkBinaryStatisticsOpeningImageFilter.txx
@@ -0,0 +1,138 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkBinaryStatisticsOpeningImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/08/01 19:16:18 $
+ Version: $Revision: 1.7 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkBinaryStatisticsOpeningImageFilter_txx
+#define __itkBinaryStatisticsOpeningImageFilter_txx
+
+#include "itkBinaryStatisticsOpeningImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+
+namespace itk {
+
+template<class TInputImage, class TFeatureImage>
+BinaryStatisticsOpeningImageFilter<TInputImage, TFeatureImage>
+::BinaryStatisticsOpeningImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+ m_ForegroundValue = NumericTraits<OutputImagePixelType>::max();
+ m_FullyConnected = false;
+ m_ReverseOrdering = false;
+ m_Attribute = LabelObjectType::MEAN;
+ this->SetNumberOfRequiredInputs(2);
+}
+
+template<class TInputImage, class TFeatureImage>
+void
+BinaryStatisticsOpeningImageFilter<TInputImage, TFeatureImage>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template<class TInputImage, class TFeatureImage>
+void
+BinaryStatisticsOpeningImageFilter<TInputImage, TFeatureImage>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage, class TFeatureImage>
+void
+BinaryStatisticsOpeningImageFilter<TInputImage, TFeatureImage>
+::GenerateData()
+{
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Allocate the output
+ this->AllocateOutputs();
+
+ typename LabelizerType::Pointer labelizer = LabelizerType::New();
+ labelizer->SetInput( this->GetInput() );
+ labelizer->SetForegroundValue( m_ForegroundValue );
+ labelizer->SetBackgroundValue( m_BackgroundValue );
+ labelizer->SetFullyConnected( m_FullyConnected );
+ labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(labelizer, .3f);
+
+ typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
+ valuator->SetInput( labelizer->GetOutput() );
+ valuator->SetFeatureImage( this->GetFeatureImage() );
+ valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
+ valuator->SetComputeHistogram( false );
+ if( m_Attribute == LabelObjectType::PERIMETER || m_Attribute == LabelObjectType::ROUNDNESS )
+ {
+ valuator->SetComputePerimeter( true );
+ }
+ if( m_Attribute == LabelObjectType::FERET_DIAMETER )
+ {
+ valuator->SetComputeFeretDiameter( true );
+ }
+ progress->RegisterInternalFilter(valuator, .3f);
+
+ typename OpeningType::Pointer opening = OpeningType::New();
+ opening->SetInput( valuator->GetOutput() );
+ opening->SetLambda( m_Lambda );
+ opening->SetReverseOrdering( m_ReverseOrdering );
+ opening->SetAttribute( m_Attribute );
+ opening->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(opening, .2f);
+
+ typename BinarizerType::Pointer binarizer = BinarizerType::New();
+ binarizer->SetInput( opening->GetOutput() );
+ binarizer->SetForegroundValue( m_ForegroundValue );
+ binarizer->SetBackgroundValue( m_BackgroundValue );
+ binarizer->SetBackgroundImage( this->GetInput() );
+ binarizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(binarizer, .2f);
+
+ binarizer->GraftOutput( this->GetOutput() );
+ binarizer->Update();
+ this->GraftOutput( binarizer->GetOutput() );
+}
+
+
+template<class TInputImage, class TFeatureImage>
+void
+BinaryStatisticsOpeningImageFilter<TInputImage, TFeatureImage>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "FullyConnected: " << m_FullyConnected << std::endl;
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "ForegroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_ForegroundValue) << std::endl;
+ os << indent << "Lambda: " << m_Lambda << std::endl;
+ os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
+ os << indent << "Attribute: " << LabelObjectType::GetNameFromAttribute(m_Attribute) << " (" << m_Attribute << ")" << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkConnectedComponentAlgorithm.h b/Utilities/InsightJournal/itkConnectedComponentAlgorithm.h
new file mode 100644
index 0000000000000000000000000000000000000000..d97cdafdbe8d0321e65675d5cf5fb78a202c91aa
--- /dev/null
+++ b/Utilities/InsightJournal/itkConnectedComponentAlgorithm.h
@@ -0,0 +1,138 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkConnectedComponentAlgorithm.h,v $
+ Language: C++
+ Date: $Date: 2006/12/14 10:27:37 $
+ Version: $Revision: 1.2 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+
+#ifndef __itkConnectedComponentAlgorithm_h
+#define __itkConnectedComponentAlgorithm_h
+
+#include "itkImage.h"
+#include "itkConstShapedNeighborhoodIterator.h"
+#include "itkShapedNeighborhoodIterator.h"
+
+namespace itk
+{
+template< class TIterator >
+TIterator*
+setConnectivity( TIterator* it, bool fullyConnected=false )
+{
+ typename TIterator::OffsetType offset;
+ it->ClearActiveList();
+ if( !fullyConnected)
+ {
+ // only activate the neighbors that are face connected
+ // to the current pixel. do not include the center pixel
+ offset.Fill( 0 );
+ for( unsigned int d=0; d < TIterator::Dimension; ++d )
+ {
+ offset[d] = -1;
+ it->ActivateOffset( offset );
+ offset[d] = 1;
+ it->ActivateOffset( offset );
+ offset[d] = 0;
+ }
+ }
+ else
+ {
+ // activate all neighbors that are face+edge+vertex
+ // connected to the current pixel. do not include the center pixel
+ unsigned int centerIndex = it->GetCenterNeighborhoodIndex();
+ for( unsigned int d=0; d < centerIndex*2 + 1; d++ )
+ {
+ offset = it->GetOffset( d );
+ it->ActivateOffset( offset );
+ }
+ offset.Fill(0);
+ it->DeactivateOffset( offset );
+ }
+ return it;
+}
+
+template< class TIterator >
+TIterator*
+setConnectivityPrevious( TIterator* it, bool fullyConnected=false )
+{
+ // activate the "previous" neighbours
+ typename TIterator::OffsetType offset;
+ it->ClearActiveList();
+ if( !fullyConnected)
+ {
+ // only activate the neighbors that are face connected
+ // to the current pixel. do not include the center pixel
+ offset.Fill( 0 );
+ for( unsigned int d=0; d < TIterator::Dimension; ++d )
+ {
+ offset[d] = -1;
+ it->ActivateOffset( offset );
+// offset[d] = 1;
+// it->ActivateOffset( offset );
+ offset[d] = 0;
+ }
+ }
+ else
+ {
+ // activate all neighbors that are face+edge+vertex
+ // connected to the current pixel. do not include the center pixel
+ unsigned int centerIndex = it->GetCenterNeighborhoodIndex();
+ for( unsigned int d=0; d < centerIndex; d++ )
+ {
+ offset = it->GetOffset( d );
+ it->ActivateOffset( offset );
+ }
+ offset.Fill(0);
+ it->DeactivateOffset( offset );
+ }
+ return it;
+}
+
+template< class TIterator >
+TIterator*
+setConnectivityLater( TIterator* it, bool fullyConnected=false )
+{
+ // activate the "later" neighbours
+ typename TIterator::OffsetType offset;
+ it->ClearActiveList();
+ if( !fullyConnected)
+ {
+ // only activate the neighbors that are face connected
+ // to the current pixel. do not include the center pixel
+ offset.Fill( 0 );
+ for( unsigned int d=0; d < TIterator::Dimension; ++d )
+ {
+ offset[d] = 1;
+ it->ActivateOffset( offset );
+ offset[d] = 0;
+ }
+ }
+ else
+ {
+ // activate all neighbors that are face+edge+vertex
+ // connected to the current pixel. do not include the center pixel
+ unsigned int centerIndex = it->GetCenterNeighborhoodIndex();
+ for( unsigned int d=centerIndex+1; d < 2*centerIndex+1; d++ )
+ {
+ offset = it->GetOffset( d );
+ it->ActivateOffset( offset );
+ }
+ offset.Fill(0);
+ it->DeactivateOffset( offset );
+ }
+ return it;
+}
+
+}
+
+
+#endif
diff --git a/Utilities/InsightJournal/itkLabelAttributeKeepNObjectsImageFilter.h b/Utilities/InsightJournal/itkLabelAttributeKeepNObjectsImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..099070239940f85da71fa80beb11d7a6fdd44d1a
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelAttributeKeepNObjectsImageFilter.h
@@ -0,0 +1,164 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelAttributeKeepNObjectsImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelAttributeKeepNObjectsImageFilter_h
+#define __itkLabelAttributeKeepNObjectsImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkLabelMap.h"
+#include "itkLabelImageToLabelMapFilter.h"
+#include "itkAttributeKeepNObjectsLabelMapFilter.h"
+#include "itkLabelMapToLabelImageFilter.h"
+#include "itkAttributeLabelObject.h"
+
+
+namespace itk {
+
+/** \class LabelAttributeKeepNObjectsImageFilter
+ * \brief keep N objects according to a generic attribute
+ *
+ * LabelAttributeKeepNObjectsImageFilter keep the N objects in a labeled image
+ * with the highest (or lowest) attribute value. The attribute is valued with
+ * and attribute valuator given in template parameter and is accessed with a
+ * attribute accessor also given in template parameter.
+ *
+ * Used in combination with AttributeLabelObject, and a specilized attribute valuator,
+ * this class is the most efficient way to keep N objects in a labeled image.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa AttributeLabelObject, InPlaceLabelMapFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor=
+ typename Functor::AttributeLabelObjectAccessor< typename TImage::LabelObjectType > >
+class ITK_EXPORT LabelAttributeKeepNObjectsImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef LabelAttributeKeepNObjectsImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+
+ typedef TLabelObject LabelObjectType;
+ typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef typename itk::LabelImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
+ typedef TLabelObjectValuator LabelObjectValuatorType;
+ typedef TAttributeAccessor AttributeAccessorType;
+ typedef typename AttributeAccessorType::AttributeValueType AttributeValueType;
+ typedef typename itk::AttributeKeepNObjectsLabelMapFilter< LabelMapType, AttributeAccessorType > KeepNObjectsType;
+ typedef typename itk::LabelMapToLabelImageFilter< LabelMapType, OutputImageType > BinarizerType;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(LabelAttributeKeepNObjectsImageFilter,
+ ImageToImageFilter);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the number of objects to keep
+ */
+ itkGetConstMacro(NumberOfObjects, unsigned long);
+ itkSetMacro(NumberOfObjects, unsigned long);
+
+ /**
+ * Set/Get the ordering of the objects. By default, the ones with the
+ * highest value are kept. Turming ReverseOrdering to true make this filter
+ * keep the objects with the smallest values
+ */
+ itkGetConstMacro( ReverseOrdering, bool );
+ itkSetMacro( ReverseOrdering, bool );
+ itkBooleanMacro( ReverseOrdering );
+
+protected:
+ LabelAttributeKeepNObjectsImageFilter();
+ ~LabelAttributeKeepNObjectsImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** LabelAttributeKeepNObjectsImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** LabelAttributeKeepNObjectsImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+ virtual void CustomizeInternalFilters( LabelizerType *, LabelObjectValuatorType *, KeepNObjectsType *, BinarizerType* ) {};
+
+private:
+ LabelAttributeKeepNObjectsImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ OutputImagePixelType m_BackgroundValue;
+ unsigned long m_NumberOfObjects;
+ bool m_ReverseOrdering;
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkLabelAttributeKeepNObjectsImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkLabelAttributeKeepNObjectsImageFilter.txx b/Utilities/InsightJournal/itkLabelAttributeKeepNObjectsImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..a403922ecb0200c47f9924b627398019383f6132
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelAttributeKeepNObjectsImageFilter.txx
@@ -0,0 +1,118 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelAttributeKeepNObjectsImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/08/01 19:16:18 $
+ Version: $Revision: 1.7 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelAttributeKeepNObjectsImageFilter_txx
+#define __itkLabelAttributeKeepNObjectsImageFilter_txx
+
+#include "itkLabelAttributeKeepNObjectsImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+
+namespace itk {
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+LabelAttributeKeepNObjectsImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::LabelAttributeKeepNObjectsImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+ m_NumberOfObjects = 1;
+ m_ReverseOrdering = false;
+}
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+LabelAttributeKeepNObjectsImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+LabelAttributeKeepNObjectsImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+LabelAttributeKeepNObjectsImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::GenerateData()
+{
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Allocate the output
+ this->AllocateOutputs();
+
+ typename LabelizerType::Pointer labelizer = LabelizerType::New();
+ labelizer->SetInput( this->GetInput() );
+ labelizer->SetBackgroundValue( m_BackgroundValue );
+ labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(labelizer, .3f);
+
+ typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
+ valuator->SetInput( labelizer->GetOutput() );
+ valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(valuator, .3f);
+
+ typename KeepNObjectsType::Pointer opening = KeepNObjectsType::New();
+ opening->SetInput( valuator->GetOutput() );
+ opening->SetNumberOfObjects( m_NumberOfObjects );
+ opening->SetReverseOrdering( m_ReverseOrdering );
+ opening->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(opening, .2f);
+
+ typename BinarizerType::Pointer binarizer = BinarizerType::New();
+ binarizer->SetInput( opening->GetOutput() );
+ binarizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(binarizer, .2f);
+
+ this->CustomizeInternalFilters( labelizer, valuator, opening, binarizer );
+
+ binarizer->GraftOutput( this->GetOutput() );
+ binarizer->Update();
+ this->GraftOutput( binarizer->GetOutput() );
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+LabelAttributeKeepNObjectsImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "NumberOfObjects: " << m_NumberOfObjects << std::endl;
+ os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkLabelAttributeOpeningImageFilter.h b/Utilities/InsightJournal/itkLabelAttributeOpeningImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..149fc3ed34cef2741845bd72c41f6c5b1731ada8
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelAttributeOpeningImageFilter.h
@@ -0,0 +1,167 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelAttributeOpeningImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelAttributeOpeningImageFilter_h
+#define __itkLabelAttributeOpeningImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkLabelMap.h"
+#include "itkLabelImageToLabelMapFilter.h"
+#include "itkAttributeOpeningLabelMapFilter.h"
+#include "itkLabelMapToLabelImageFilter.h"
+#include "itkAttributeLabelObject.h"
+
+
+namespace itk {
+
+/** \class LabelAttributeOpeningImageFilter
+ * \brief remove the objects in a labeled image according to a generic attribute
+ *
+ * LabelAttributeOpeningImageFilter remove the objects in a labeled image
+ * with an attribute value smaller or greater than a threshold called Lambda.
+ * The attribute is valued with and attribute valuator given in template parameter
+ * and is accessed with an attribute accessor also given in template parameter.
+ *
+ * Used in combination with AttributeLabelObject, and a specilized attribute valuator,
+ * this class is the most efficient way to perform an attribute opening in a labeled
+ * image.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa AttributeLabelObject, InPlaceLabelMapFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor=
+ typename Functor::AttributeLabelObjectAccessor< typename TImage::LabelObjectType > >
+class ITK_EXPORT LabelAttributeOpeningImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef LabelAttributeOpeningImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+
+ typedef TLabelObject LabelObjectType;
+ typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef typename itk::LabelImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
+ typedef TLabelObjectValuator LabelObjectValuatorType;
+ typedef TAttributeAccessor AttributeAccessorType;
+ typedef typename AttributeAccessorType::AttributeValueType AttributeValueType;
+ typedef typename itk::AttributeOpeningLabelMapFilter< LabelMapType, AttributeAccessorType > OpeningType;
+ typedef typename itk::LabelMapToLabelImageFilter< LabelMapType, OutputImageType > BinarizerType;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(LabelAttributeOpeningImageFilter,
+ ImageToImageFilter);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /**
+ * Set/Get the threshold used to keep or remove the objects.
+ */
+ itkGetConstMacro(Lambda, AttributeValueType);
+ itkSetMacro(Lambda, AttributeValueType);
+
+ /**
+ * Set/Get the ordering of the objects. By default, the objects with
+ * an attribute value smaller than Lamba are removed. Turning ReverseOrdering
+ * to true make this filter remove the object with an attribute value greater
+ * than Lambda instead.
+ */
+ itkGetConstMacro( ReverseOrdering, bool );
+ itkSetMacro( ReverseOrdering, bool );
+ itkBooleanMacro( ReverseOrdering );
+
+protected:
+ LabelAttributeOpeningImageFilter();
+ ~LabelAttributeOpeningImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** LabelAttributeOpeningImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** LabelAttributeOpeningImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+ virtual void CustomizeInternalFilters( LabelizerType *, LabelObjectValuatorType *, OpeningType *, BinarizerType* ) {};
+
+
+private:
+ LabelAttributeOpeningImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ OutputImagePixelType m_BackgroundValue;
+ AttributeValueType m_Lambda;
+ bool m_ReverseOrdering;
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkLabelAttributeOpeningImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkLabelAttributeOpeningImageFilter.txx b/Utilities/InsightJournal/itkLabelAttributeOpeningImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..cd7b693895c24aaab91dd981d23238173e515960
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelAttributeOpeningImageFilter.txx
@@ -0,0 +1,118 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelAttributeOpeningImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/08/01 19:16:18 $
+ Version: $Revision: 1.7 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelAttributeOpeningImageFilter_txx
+#define __itkLabelAttributeOpeningImageFilter_txx
+
+#include "itkLabelAttributeOpeningImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+
+namespace itk {
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+LabelAttributeOpeningImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::LabelAttributeOpeningImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+ m_Lambda = NumericTraits< AttributeValueType >::Zero;
+ m_ReverseOrdering = false;
+}
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+LabelAttributeOpeningImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+LabelAttributeOpeningImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+LabelAttributeOpeningImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::GenerateData()
+{
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Allocate the output
+ this->AllocateOutputs();
+
+ typename LabelizerType::Pointer labelizer = LabelizerType::New();
+ labelizer->SetInput( this->GetInput() );
+ labelizer->SetBackgroundValue( m_BackgroundValue );
+ labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(labelizer, .3f);
+
+ typename LabelObjectValuatorType::Pointer valuator = LabelObjectValuatorType::New();
+ valuator->SetInput( labelizer->GetOutput() );
+ valuator->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(valuator, .3f);
+
+ typename OpeningType::Pointer opening = OpeningType::New();
+ opening->SetInput( valuator->GetOutput() );
+ opening->SetLambda( m_Lambda );
+ opening->SetReverseOrdering( m_ReverseOrdering );
+ opening->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(opening, .2f);
+
+ typename BinarizerType::Pointer binarizer = BinarizerType::New();
+ binarizer->SetInput( opening->GetOutput() );
+ binarizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(binarizer, .2f);
+
+ this->CustomizeInternalFilters( labelizer, valuator, opening, binarizer );
+
+ binarizer->GraftOutput( this->GetOutput() );
+ binarizer->Update();
+ this->GraftOutput( binarizer->GetOutput() );
+}
+
+
+template<class TInputImage, class TLabelObject, class TLabelObjectValuator, class TAttributeAccessor>
+void
+LabelAttributeOpeningImageFilter<TInputImage, TLabelObject, TLabelObjectValuator, TAttributeAccessor>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "Lambda: " << m_Lambda << std::endl;
+ os << indent << "ReverseOrdering: " << m_ReverseOrdering << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkLabelMapMaskImageFilter.h b/Utilities/InsightJournal/itkLabelMapMaskImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..9e8c8426fd1baeb9a6a9d916d0f867ed14ffdc5d
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelMapMaskImageFilter.h
@@ -0,0 +1,190 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelMapMaskImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.4 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelMapMaskImageFilter_h
+#define __itkLabelMapMaskImageFilter_h
+
+#include "itkLabelMapFilter.h"
+#include "itkBarrier.h"
+
+namespace itk {
+
+/** \class LabelMapMaskImageFilter
+ * \brief Mask and image with a LabelMap
+ *
+ * LabelMapMaskImageFilter mask the content of an input image according
+ * to the content of the input LabelMap. The masked pixel of the input image
+ * are set to the BackgroundValue.
+ * LabelMapMaskImageFilter can keep the input image for one label only, with
+ * Negated = false (the default) or it can mask the input image for a single label, when
+ * Negated equals true. In Both cases, the label is set with SetLabel().
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa LabelMapToBinaryImageFilter, LabelMapToLabelImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage, class TOutputImage>
+class ITK_EXPORT LabelMapMaskImageFilter :
+ public LabelMapFilter<TInputImage, TOutputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef LabelMapMaskImageFilter Self;
+ typedef LabelMapFilter<TInputImage, TOutputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TOutputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename InputImageType::LabelObjectType LabelObjectType;
+ typedef typename LabelObjectType::LabelType LabelType;
+
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+ typedef typename OutputImageType::IndexType IndexType;
+ typedef typename OutputImageType::SizeType SizeType;
+ typedef typename OutputImageType::RegionType RegionType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TOutputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TOutputImage::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(LabelMapMaskImageFilter,
+ ImageToImageFilter);
+
+ /** Set the feature image */
+ void SetFeatureImage(const TOutputImage *input)
+ {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput( 1, const_cast<TOutputImage *>(input) );
+ }
+
+ /** Get the feature image */
+ OutputImageType * GetFeatureImage()
+ {
+ return static_cast<OutputImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(1)));
+ }
+
+ /** Set the input image */
+ void SetInput1(TInputImage *input)
+ {
+ this->SetInput( input );
+ }
+
+ /** Set the feature image */
+ void SetInput2(TOutputImage *input)
+ {
+ this->SetFeatureImage( input );
+ }
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::Zero.
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /**
+ * The label to mask or to not mask, depending on the value of the Negated ivar.
+ */
+ itkSetMacro(Label, InputImagePixelType);
+ itkGetConstMacro(Label, InputImagePixelType);
+
+ /**
+ * Set/Get whether the Label should be masked or not.
+ */
+ itkSetMacro(Negated, bool);
+ itkGetConstReferenceMacro(Negated, bool);
+ itkBooleanMacro(Negated);
+
+ /**
+ * Set/Get whether the image size should be adjusted to the masked image or not.
+ */
+ itkSetMacro(Crop, bool);
+ itkGetConstReferenceMacro(Crop, bool);
+ itkBooleanMacro(Crop);
+
+ /**
+ * Set/Get the boder added to the mask before the crop. The default is 0 on
+ * all the axes.
+ */
+ itkSetMacro(CropBorder, SizeType);
+ itkGetConstReferenceMacro(CropBorder, SizeType);
+
+protected:
+ LabelMapMaskImageFilter();
+ ~LabelMapMaskImageFilter() {};
+
+ /** LabelMapMaskImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** LabelMapMaskImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ virtual void GenerateOutputInformation();
+
+ virtual void BeforeThreadedGenerateData();
+
+ virtual void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, int threadId );
+
+ virtual void ThreadedGenerateData( LabelObjectType * labelObject );
+
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+private:
+ LabelMapMaskImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ InputImagePixelType m_Label;
+ OutputImagePixelType m_BackgroundValue;
+ bool m_Negated;
+ bool m_Crop;
+ SizeType m_CropBorder;
+
+ TimeStamp m_CropTimeStamp;
+
+ typename Barrier::Pointer m_Barrier;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkLabelMapMaskImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkLabelMapMaskImageFilter.txx b/Utilities/InsightJournal/itkLabelMapMaskImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..7d5143d91aaa814809c9885ce513722d3631387c
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelMapMaskImageFilter.txx
@@ -0,0 +1,442 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelMapMaskImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelMapMaskImageFilter_txx
+#define __itkLabelMapMaskImageFilter_txx
+
+#include "itkLabelMapMaskImageFilter.h"
+#include "itkNumericTraits.h"
+#include "itkProgressReporter.h"
+#include "itkImageRegionConstIterator.h"
+#include "itkImageRegionIterator.h"
+
+namespace itk {
+
+template <class TInputImage, class TOutputImage>
+LabelMapMaskImageFilter<TInputImage, TOutputImage>
+::LabelMapMaskImageFilter()
+{
+ this->SetNumberOfRequiredInputs(2);
+ m_Label = NumericTraits< InputImagePixelType >::One;
+ m_BackgroundValue = NumericTraits< OutputImagePixelType >::Zero;
+ m_Negated = false;
+ m_Crop = false;
+ m_CropBorder.Fill( 0 );
+}
+
+template <class TInputImage, class TOutputImage>
+void
+LabelMapMaskImageFilter<TInputImage, TOutputImage>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if ( !input )
+ { return; }
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+}
+
+template <class TInputImage, class TOutputImage>
+void
+LabelMapMaskImageFilter<TInputImage, TOutputImage>
+::GenerateOutputInformation()
+{
+
+ if( m_Crop )
+ {
+ const InputImageType * input = this->GetInput();
+
+ if( !(input->GetMTime() > m_CropTimeStamp) && !(this->GetMTime() > m_CropTimeStamp) )
+ {
+ // early exit, crop sizes already computed
+ // std::cout << "Don't recompute the output size again." << std::endl;
+ // std::cout << "LargestPossibleRegion: " << this->GetOutput()->GetLargestPossibleRegion() << std::endl;
+ // std::cout << "BufferedRegion: " << this->GetOutput()->GetBufferedRegion() << std::endl;
+ // std::cout << "RequestedRegion: " << this->GetOutput()->GetRequestedRegion() << std::endl;
+ return;
+ }
+
+ // first, call the default implementation, to be sure to forgot nothing
+ Superclass::GenerateOutputInformation();
+
+ // update the input if needed
+ if( input->GetSource())
+ {
+ ProcessObject * upstream = input->GetSource();
+ if (upstream)
+ {
+ // this->SetInput(NULL);
+ // std::cout << "Update the input (again?)." << std::endl;
+ upstream->Update();
+ // this->SetInput(input);
+ }
+ }
+
+ // Prefetch image region and size
+ InputImageRegionType cropRegion = input->GetLargestPossibleRegion();
+
+ // now the output image size can be computed
+ if( m_Negated )
+ {
+ if( input->GetBackgroundValue() != m_Label )
+ {
+ // the "bad" case - the zone outside the object is at least partially
+ // covered by the background, which is not explicitely defined.
+
+ // simply do nothing for now
+ // TODO: implement that part
+ itkWarningMacro( << "Cropping according to background label is no yet implemented. The full image will be used." );
+
+ }
+ else
+ {
+ // compute the bounding box of all the objects which don't have that label
+ IndexType mins;
+ mins.Fill( NumericTraits< long >::max() );
+ IndexType maxs;
+ maxs.Fill( NumericTraits< long >::NonpositiveMin() );
+ typename InputImageType::LabelObjectContainerType container = this->GetInput()->GetLabelObjectContainer();
+ for( typename InputImageType::LabelObjectContainerType::const_iterator loit = container.begin();
+ loit != container.end();
+ loit++ )
+ {
+ if( loit->first != m_Label )
+ {
+ typename LabelObjectType::LineContainerType::const_iterator lit;
+ typename LabelObjectType::LineContainerType & lineContainer = loit->second->GetLineContainer();
+ // iterate over all the lines
+ for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
+ {
+ const IndexType & idx = lit->GetIndex();
+ unsigned long length = lit->GetLength();
+
+ // update the mins and maxs
+ for( int i=0; i<ImageDimension; i++)
+ {
+ if( idx[i] < mins[i] )
+ {
+ mins[i] = idx[i];
+ }
+ if( idx[i] > maxs[i] )
+ {
+ maxs[i] = idx[i];
+ }
+ }
+ // must fix the max for the axis 0
+ if( idx[0] + (long)length > maxs[0] )
+ {
+ maxs[0] = idx[0] + length - 1;
+ }
+ }
+ }
+ }
+
+ // final computation
+ SizeType regionSize;
+ for( int i=0; i<ImageDimension; i++ )
+ {
+ regionSize[i] = maxs[i] - mins[i] + 1;
+ }
+ cropRegion.SetIndex( mins );
+ cropRegion.SetSize( regionSize );
+
+ }
+ }
+ else
+ {
+ if( input->GetBackgroundValue() == m_Label )
+ {
+ // the other "bad" case - the label we want is not defined as a label object,
+ // but implicitely, in the zones not defined.
+
+ // simply do nothing for now
+ // TODO: implement that part
+ itkWarningMacro( << "Cropping according to background label is no yet implemented. The full image will be used." );
+
+ }
+ else
+ {
+ // just find the bounding box of the object with that label
+
+ const LabelObjectType * labelObject = input->GetLabelObject( m_Label );
+ typename LabelObjectType::LineContainerType::const_iterator lit;
+ const typename LabelObjectType::LineContainerType & lineContainer = labelObject->GetLineContainer();
+ IndexType mins;
+ mins.Fill( NumericTraits< long >::max() );
+ IndexType maxs;
+ maxs.Fill( NumericTraits< long >::NonpositiveMin() );
+ // iterate over all the lines
+ for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
+ {
+ const IndexType & idx = lit->GetIndex();
+ unsigned long length = lit->GetLength();
+
+ // update the mins and maxs
+ for( int i=0; i<ImageDimension; i++)
+ {
+ if( idx[i] < mins[i] )
+ {
+ mins[i] = idx[i];
+ }
+ if( idx[i] > maxs[i] )
+ {
+ maxs[i] = idx[i];
+ }
+ }
+ // must fix the max for the axis 0
+ if( idx[0] + (long)length > maxs[0] )
+ {
+ maxs[0] = idx[0] + length - 1;
+ }
+ }
+ // final computation
+ SizeType regionSize;
+ for( int i=0; i<ImageDimension; i++ )
+ {
+ regionSize[i] = maxs[i] - mins[i] + 1;
+ }
+ cropRegion.SetIndex( mins );
+ cropRegion.SetSize( regionSize );
+
+ }
+ }
+
+ // pad by the crop border, but take care to not be larger than the largest
+ // possible region of the input image
+ cropRegion.PadByRadius( m_CropBorder );
+ cropRegion.Crop( input->GetLargestPossibleRegion() );
+
+ // finally set that region as the largest output region
+ this->GetOutput()->SetLargestPossibleRegion( cropRegion );
+
+ m_CropTimeStamp.Modified();
+
+ }
+ else
+ {
+ // no crop -> use the default implementation
+ Superclass::GenerateOutputInformation();
+ }
+
+ // std::cout << "LargestPossibleRegion: " << this->GetOutput()->GetLargestPossibleRegion() << std::endl;
+ // std::cout << "BufferedRegion: " << this->GetOutput()->GetBufferedRegion() << std::endl;
+ // std::cout << "RequestedRegion: " << this->GetOutput()->GetRequestedRegion() << std::endl;
+
+}
+
+template <class TInputImage, class TOutputImage>
+void
+LabelMapMaskImageFilter<TInputImage, TOutputImage>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template <class TInputImage, class TOutputImage>
+void
+LabelMapMaskImageFilter<TInputImage, TOutputImage>
+::BeforeThreadedGenerateData()
+{
+ m_Barrier = Barrier::New();
+ m_Barrier->Initialize( this->GetNumberOfThreads() );
+
+ Superclass::BeforeThreadedGenerateData();
+
+}
+
+
+template <class TInputImage, class TOutputImage>
+void
+LabelMapMaskImageFilter<TInputImage, TOutputImage>
+::ThreadedGenerateData( const OutputImageRegionType& outputRegionForThread, int threadId )
+{
+ OutputImageType * output = this->GetOutput();
+ InputImageType * input = const_cast<InputImageType *>(this->GetInput());
+ const OutputImageType * input2 = this->GetFeatureImage();
+
+ // we will keep the values from the feature image if the same pixel in the label image
+ // equals the label given by the user. The other pixels are set to the background value.
+ if( ( input->GetBackgroundValue() == m_Label ) ^ m_Negated )
+ {
+ // the user want the mask to be the background of the label collection image
+ // copy the feature image to the output image
+ ImageRegionConstIterator< OutputImageType > featureIt( input2, outputRegionForThread );
+ ImageRegionIterator< OutputImageType > outputIt( output, outputRegionForThread );
+
+ for ( featureIt.GoToBegin(), outputIt.GoToBegin();
+ !featureIt.IsAtEnd();
+ ++featureIt, ++outputIt )
+ {
+ outputIt.Set( featureIt.Get() );
+ }
+ }
+ else
+ {
+ ImageRegionIterator< OutputImageType > outputIt( output, outputRegionForThread );
+
+ for ( outputIt.GoToBegin(); !outputIt.IsAtEnd(); ++outputIt )
+ {
+ outputIt.Set( m_BackgroundValue );
+ }
+ }
+
+ // wait for the other threads to complete that part
+ m_Barrier->Wait();
+
+ if( input->GetBackgroundValue() == m_Label )
+ {
+ // and delegate to the superclass implementation to use the thread support for the label objects
+ Superclass::ThreadedGenerateData( outputRegionForThread, threadId );
+ }
+ else
+ {
+ // need only one thread - take the first one
+ if( threadId == 0 )
+ {
+ const LabelObjectType * labelObject = this->GetLabelMap()->GetLabelObject( m_Label );
+ ProgressReporter progress( this, 0, labelObject->GetLineContainer().size() );
+
+ if( !m_Negated )
+ {
+ typename InputImageType::LabelObjectType::LineContainerType::const_iterator lit;
+ const typename InputImageType::LabelObjectType::LineContainerType & lineContainer = labelObject->GetLineContainer();
+
+ for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
+ {
+ IndexType idx = lit->GetIndex();
+ unsigned long length = lit->GetLength();
+ for( unsigned int i=0; i<length; i++)
+ {
+ output->SetPixel( idx, input2->GetPixel( idx ) );
+ idx[0]++;
+ }
+ progress.CompletedPixel();
+ }
+ }
+ else
+ {
+ // and mark the label object as background
+
+ // should we take care to not write outside the image ?
+ bool testIdxIsInside = m_Crop && ( input->GetBackgroundValue() == m_Label ) ^ m_Negated;
+ RegionType outputRegion = output->GetLargestPossibleRegion();
+
+ typename InputImageType::LabelObjectType::LineContainerType::const_iterator lit;
+ const typename InputImageType::LabelObjectType::LineContainerType & lineContainer = labelObject->GetLineContainer();
+
+ for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
+ {
+ IndexType idx = lit->GetIndex();
+ unsigned long length = lit->GetLength();
+ for( unsigned int i=0; i<length; i++)
+ {
+ if( !testIdxIsInside || outputRegion.IsInside( idx ) )
+ {
+ output->SetPixel( idx, m_BackgroundValue );
+ }
+ idx[0]++;
+ }
+ progress.CompletedPixel();
+ }
+ }
+
+ }
+ }
+}
+
+
+template<class TInputImage, class TOutputImage>
+void
+LabelMapMaskImageFilter<TInputImage, TOutputImage>
+::ThreadedGenerateData( LabelObjectType * labelObject )
+{
+ OutputImageType * output = this->GetOutput();
+ InputImageType * input = const_cast<InputImageType *>(this->GetInput());
+ const OutputImageType * input2 = this->GetFeatureImage();
+
+ if( !m_Negated )
+ {
+ // we will keep the values from the feature image if the same pixel in the label image
+ // equals the label given by the user. The other pixels are set to the background value.
+
+ // should we take care to not write outside the image ?
+ bool testIdxIsInside = m_Crop && ( input->GetBackgroundValue() == m_Label ) ^ m_Negated;
+ RegionType outputRegion = output->GetLargestPossibleRegion();
+
+ // the user want the mask to be the background of the label collection image
+ typename InputImageType::LabelObjectType::LineContainerType::const_iterator lit;
+ typename InputImageType::LabelObjectType::LineContainerType & lineContainer = labelObject->GetLineContainer();
+
+ for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
+ {
+ IndexType idx = lit->GetIndex();
+ unsigned long length = lit->GetLength();
+ for( unsigned int i=0; i<length; i++)
+ {
+ if( !testIdxIsInside || outputRegion.IsInside( idx ) )
+ {
+ output->SetPixel( idx, m_BackgroundValue );
+ }
+ idx[0]++;
+ }
+ }
+ }
+ else
+ {
+ // we will keep the pixels from the feature image if the same pixel from the label image
+ // is not equal to the label provided by the user. The pixels with the label provided by the
+ // user are set to the background value
+
+ // and copy the feature image where the label objects are
+ typename InputImageType::LabelObjectType::LineContainerType::const_iterator lit;
+ typename InputImageType::LabelObjectType::LineContainerType & lineContainer = labelObject->GetLineContainer();
+
+ for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
+ {
+ IndexType idx = lit->GetIndex();
+ unsigned long length = lit->GetLength();
+ for( unsigned int i=0; i<length; i++)
+ {
+ output->SetPixel( idx, input2->GetPixel( idx ) );
+ idx[0]++;
+ }
+ }
+ }
+}
+
+
+template<class TInputImage, class TOutputImage>
+void
+LabelMapMaskImageFilter<TInputImage, TOutputImage>
+::PrintSelf(std::ostream& os, Indent indent) const
+{
+ Superclass::PrintSelf(os,indent);
+
+ os << indent << "Label: " << static_cast<typename NumericTraits<LabelType>::PrintType>(m_Label) << std::endl;
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+ os << indent << "Negated: " << m_Negated << std::endl;
+ os << indent << "Crop: " << m_Crop << std::endl;
+ os << indent << "CropBorder: " << m_CropBorder << std::endl;
+}
+
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkLabelMapOverlayImageFilter.h b/Utilities/InsightJournal/itkLabelMapOverlayImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..e4431da5028f65f91a03ea6e9ab65b939f7c988d
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelMapOverlayImageFilter.h
@@ -0,0 +1,163 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelMapOverlayImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.4 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelMapOverlayImageFilter_h
+#define __itkLabelMapOverlayImageFilter_h
+
+#include "itkLabelMapFilter.h"
+#include "itkBarrier.h"
+#include "itkLabelOverlayFunctor.h"
+
+namespace itk {
+
+/** \class LabelMapOverlayImageFilter
+ * \brief Mask and image with a LabelMap
+ *
+ * LabelMapOverlayImageFilter mask the content of an input image according
+ * to the content of the input LabelMap. The masked pixel of the input image
+ * are set to the BackgroundValue.
+ * LabelMapOverlayImageFilter can keep the input image for one label only, with
+ * Negated = false (the default) or it can mask the input image for a single label, when
+ * Negated equals true. In Both cases, the label is set with SetLabel().
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa LabelMapToBinaryImageFilter, LabelMapToLabelImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage, class TFeatureImage, class TOutputImage=Image< RGBPixel< typename TFeatureImage::PixelType >, TFeatureImage::ImageDimension > >
+class ITK_EXPORT LabelMapOverlayImageFilter :
+ public LabelMapFilter<TInputImage, TOutputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef LabelMapOverlayImageFilter Self;
+ typedef LabelMapFilter<TInputImage, TOutputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename InputImageType::LabelObjectType LabelObjectType;
+ typedef typename LabelObjectType::LabelType LabelType;
+
+ typedef TFeatureImage FeatureImageType;
+ typedef typename FeatureImageType::Pointer FeatureImagePointer;
+ typedef typename FeatureImageType::ConstPointer FeatureImageConstPointer;
+ typedef typename FeatureImageType::RegionType FeatureImageRegionType;
+ typedef typename FeatureImageType::PixelType FeatureImagePixelType;
+
+ typedef TOutputImage OutputImageType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+ typedef typename OutputImageType::IndexType IndexType;
+ typedef typename OutputImageType::SizeType SizeType;
+ typedef typename OutputImageType::RegionType RegionType;
+
+ typedef typename Functor::LabelOverlayFunctor<FeatureImagePixelType, InputImagePixelType, OutputImagePixelType> FunctorType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TOutputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TOutputImage::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(LabelMapOverlayImageFilter,
+ ImageToImageFilter);
+
+ /** Set the feature image */
+ void SetFeatureImage(TFeatureImage *input)
+ {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput( 1, const_cast<TFeatureImage *>(input) );
+ }
+
+ /** Get the feature image */
+ FeatureImageType * GetFeatureImage()
+ {
+ return static_cast<FeatureImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(1)));
+ }
+
+ /** Set the input image */
+ void SetInput1(TInputImage *input)
+ {
+ this->SetInput( input );
+ }
+
+ /** Set the feature image */
+ void SetInput2(TFeatureImage *input)
+ {
+ this->SetFeatureImage( input );
+ }
+
+ /** Set/Get the opacity of the colored label image. The value must be
+ * between 0 and 1
+ */
+ itkSetMacro( Opacity, double );
+ itkGetConstReferenceMacro( Opacity, double );
+
+protected:
+ LabelMapOverlayImageFilter();
+ ~LabelMapOverlayImageFilter() {};
+
+ /** LabelMapOverlayImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** LabelMapOverlayImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ virtual void BeforeThreadedGenerateData();
+
+ virtual void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, int threadId );
+
+ virtual void ThreadedGenerateData( LabelObjectType * labelObject );
+
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+
+private:
+ LabelMapOverlayImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ double m_Opacity;
+ typename Barrier::Pointer m_Barrier;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkLabelMapOverlayImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkLabelMapOverlayImageFilter.txx b/Utilities/InsightJournal/itkLabelMapOverlayImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..b6d844fb9667ee261234fb214ee1b2b30174e74c
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelMapOverlayImageFilter.txx
@@ -0,0 +1,150 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelMapOverlayImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelMapOverlayImageFilter_txx
+#define __itkLabelMapOverlayImageFilter_txx
+
+#include "itkLabelMapOverlayImageFilter.h"
+#include "itkNumericTraits.h"
+#include "itkProgressReporter.h"
+#include "itkImageRegionConstIterator.h"
+#include "itkImageRegionIterator.h"
+
+namespace itk {
+
+template<class TInputImage, class TFeatureImage, class TOutputImage>
+LabelMapOverlayImageFilter<TInputImage, TFeatureImage, TOutputImage>
+::LabelMapOverlayImageFilter()
+{
+ this->SetNumberOfRequiredInputs(2);
+ m_Opacity = 0.5;
+}
+
+template<class TInputImage, class TFeatureImage, class TOutputImage>
+void
+LabelMapOverlayImageFilter<TInputImage, TFeatureImage, TOutputImage>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if ( !input )
+ { return; }
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+}
+
+template <class TInputImage, class TFeatureImage, class TOutputImage>
+void
+LabelMapOverlayImageFilter<TInputImage, TFeatureImage, TOutputImage>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage, class TFeatureImage, class TOutputImage>
+void
+LabelMapOverlayImageFilter<TInputImage, TFeatureImage, TOutputImage>
+::BeforeThreadedGenerateData()
+{
+ m_Barrier = Barrier::New();
+ m_Barrier->Initialize( this->GetNumberOfThreads() );
+
+ Superclass::BeforeThreadedGenerateData();
+
+}
+
+
+template<class TInputImage, class TFeatureImage, class TOutputImage>
+void
+LabelMapOverlayImageFilter<TInputImage, TFeatureImage, TOutputImage>
+::ThreadedGenerateData( const OutputImageRegionType& outputRegionForThread, int threadId )
+{
+ OutputImageType * output = this->GetOutput();
+ InputImageType * input = const_cast<InputImageType *>(this->GetInput());
+ const FeatureImageType * input2 = this->GetFeatureImage();
+
+ FunctorType function;
+ function.SetBackgroundValue( input->GetBackgroundValue() );
+ function.SetOpacity( m_Opacity );
+
+ ImageRegionConstIterator< FeatureImageType > featureIt( input2, outputRegionForThread );
+ ImageRegionIterator< OutputImageType > outputIt( output, outputRegionForThread );
+
+ for ( featureIt.GoToBegin(), outputIt.GoToBegin();
+ !featureIt.IsAtEnd();
+ ++featureIt, ++outputIt )
+ {
+ outputIt.Set( function( featureIt.Get(), input->GetBackgroundValue() ) );
+ }
+
+ // wait for the other threads to complete that part
+ m_Barrier->Wait();
+
+ // and delegate to the superclass implementation to use the thread support for the label objects
+ Superclass::ThreadedGenerateData( outputRegionForThread, threadId );
+}
+
+
+template<class TInputImage, class TFeatureImage, class TOutputImage>
+void
+LabelMapOverlayImageFilter<TInputImage, TFeatureImage, TOutputImage>
+::ThreadedGenerateData( LabelObjectType * labelObject )
+{
+ OutputImageType * output = this->GetOutput();
+ InputImageType * input = const_cast<InputImageType *>(this->GetInput());
+ const FeatureImageType * input2 = this->GetFeatureImage();
+
+ FunctorType function;
+ function.SetBackgroundValue( input->GetBackgroundValue() );
+ function.SetOpacity( m_Opacity );
+
+ const typename LabelObjectType::LabelType & label = labelObject->GetLabel();
+
+ // the user want the mask to be the background of the label collection image
+ typename InputImageType::LabelObjectType::LineContainerType::const_iterator lit;
+ typename InputImageType::LabelObjectType::LineContainerType & lineContainer = labelObject->GetLineContainer();
+
+ for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
+ {
+ IndexType idx = lit->GetIndex();
+ unsigned long length = lit->GetLength();
+ for( unsigned int i=0; i<length; i++)
+ {
+ output->SetPixel( idx, function( input2->GetPixel(idx), label ) );
+ idx[0]++;
+ }
+ }
+
+}
+
+
+template<class TInputImage, class TFeatureImage, class TOutputImage>
+void
+LabelMapOverlayImageFilter<TInputImage, TFeatureImage, TOutputImage>
+::PrintSelf(std::ostream& os, Indent indent) const
+{
+ Superclass::PrintSelf(os,indent);
+
+ os << indent << "Opacity: " << m_Opacity << std::endl;
+}
+
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkLabelMapToAttributeImageFilter.h b/Utilities/InsightJournal/itkLabelMapToAttributeImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..34161c5d41a13ac49b0dda4fcffa57204153bc4f
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelMapToAttributeImageFilter.h
@@ -0,0 +1,120 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelMapToAttributeImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.4 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelMapToAttributeImageFilter_h
+#define __itkLabelMapToAttributeImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkAttributeLabelObject.h"
+
+namespace itk {
+
+/** \class LabelMapToAttributeImageFilter
+ * \brief Convert a LabelMap to a labeled image
+ *
+ * LabelMapToAttributeImageFilter converts a LabelMap to an
+ * Image where all the pixels get the attribute value of the label object they belong.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa LabelMapToBinaryImageFilter, LabelMapMaskImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage, class TOutputImage, class TAttributeAccessor=
+ typename Functor::AttributeLabelObjectAccessor< typename TInputImage::LabelObjectType > >
+class ITK_EXPORT LabelMapToAttributeImageFilter :
+ public ImageToImageFilter<TInputImage, TOutputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef LabelMapToAttributeImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TOutputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TOutputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+ typedef typename OutputImageType::IndexType IndexType;
+
+ typedef TAttributeAccessor AttributeAccessorType;
+ typedef typename AttributeAccessorType::AttributeValueType AttributeValueType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TOutputImage::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(LabelMapToAttributeImageFilter,
+ ImageToImageFilter);
+
+ /**
+ * Set/Get the value used as "background" in the output image, if the input
+ * LabelMap use a background.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+protected:
+ LabelMapToAttributeImageFilter();
+ ~LabelMapToAttributeImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** LabelMapToAttributeImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** LabelMapToAttributeImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+
+private:
+ LabelMapToAttributeImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ OutputImagePixelType m_BackgroundValue;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkLabelMapToAttributeImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkLabelMapToAttributeImageFilter.txx b/Utilities/InsightJournal/itkLabelMapToAttributeImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..5f26a24b9f7416184f1f5d57a7c5e0edb0365aef
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelMapToAttributeImageFilter.txx
@@ -0,0 +1,111 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelMapToAttributeImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelMapToAttributeImageFilter_txx
+#define __itkLabelMapToAttributeImageFilter_txx
+
+#include "itkLabelMapToAttributeImageFilter.h"
+#include "itkNumericTraits.h"
+#include "itkProgressReporter.h"
+#include "itkImageRegionConstIteratorWithIndex.h"
+
+namespace itk {
+
+template <class TInputImage, class TOutputImage, class TAttributeAccessor>
+LabelMapToAttributeImageFilter<TInputImage, TOutputImage, TAttributeAccessor>
+::LabelMapToAttributeImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+}
+
+template <class TInputImage, class TOutputImage, class TAttributeAccessor>
+void
+LabelMapToAttributeImageFilter<TInputImage, TOutputImage, TAttributeAccessor>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetInput());
+ if ( !input )
+ { return; }
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+}
+
+
+template <class TInputImage, class TOutputImage, class TAttributeAccessor>
+void
+LabelMapToAttributeImageFilter<TInputImage, TOutputImage, TAttributeAccessor>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage, class TOutputImage, class TAttributeAccessor>
+void
+LabelMapToAttributeImageFilter<TInputImage, TOutputImage, TAttributeAccessor>
+::GenerateData()
+{
+ // Allocate the output
+ this->AllocateOutputs();
+ OutputImageType * output = this->GetOutput();
+ const InputImageType * input = this->GetInput();
+ ProgressReporter progress( this, 0, output->GetRequestedRegion().GetNumberOfPixels() );
+
+ AttributeAccessorType accessor;
+
+ output->FillBuffer( m_BackgroundValue );
+
+ typename InputImageType::LabelObjectContainerType::const_iterator it;
+ const typename InputImageType::LabelObjectContainerType & labelObjectContainer = input->GetLabelObjectContainer();
+ for( it = labelObjectContainer.begin(); it != labelObjectContainer.end(); it++ )
+ {
+ const typename InputImageType::LabelObjectType * labeObject = it->second;
+ const AttributeValueType & attribute = accessor( labeObject );
+
+ typename InputImageType::LabelObjectType::LineContainerType::const_iterator lit;
+ const typename InputImageType::LabelObjectType::LineContainerType & lineContainer = labeObject->GetLineContainer();
+
+ for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
+ {
+ IndexType idx = lit->GetIndex();
+ unsigned long length = lit->GetLength();
+ for( unsigned int i=0; i<length; i++)
+ {
+ output->SetPixel( idx, static_cast<OutputImagePixelType>( attribute ) );
+ idx[0]++;
+ progress.CompletedPixel();
+ }
+ }
+ }
+}
+
+
+template<class TInputImage, class TOutputImage, class TAttributeAccessor>
+void
+LabelMapToAttributeImageFilter<TInputImage, TOutputImage, TAttributeAccessor>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkLabelMapToRGBImageFilter.h b/Utilities/InsightJournal/itkLabelMapToRGBImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..da3d6b3a58ff2aaf2b4630d4fffa197e30396495
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelMapToRGBImageFilter.h
@@ -0,0 +1,100 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelMapToRGBImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.4 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelMapToRGBImageFilter_h
+#define __itkLabelMapToRGBImageFilter_h
+
+#include "itkLabelMapFilter.h"
+#include "itkLabelToRGBFunctor.h"
+#include "itkImage.h"
+#include "itkRGBPixel.h"
+
+
+namespace itk {
+
+/** \class LabelMapToRGBImageFilter
+ * \brief Convert a LabelMap to a colored image
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa LabelMapToBinaryImageFilter, LabelMapMaskImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage, class TOutputImage=Image< RGBPixel<unsigned char>, TInputImage::ImageDimension > >
+class ITK_EXPORT LabelMapToRGBImageFilter :
+ public LabelMapFilter<TInputImage, TOutputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef LabelMapToRGBImageFilter Self;
+ typedef LabelMapFilter<TInputImage, TOutputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TOutputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename InputImageType::LabelObjectType LabelObjectType;
+
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+ typedef typename OutputImageType::IndexType IndexType;
+
+ typedef typename Functor::LabelToRGBFunctor< InputImagePixelType, OutputImagePixelType > FunctorType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TOutputImage::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(LabelMapToRGBImageFilter,
+ ImageToImageFilter);
+
+protected:
+ LabelMapToRGBImageFilter();
+ ~LabelMapToRGBImageFilter() {};
+
+ virtual void BeforeThreadedGenerateData();
+
+ virtual void ThreadedGenerateData( LabelObjectType * labelObject );
+
+private:
+ LabelMapToRGBImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkLabelMapToRGBImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkLabelMapToRGBImageFilter.txx b/Utilities/InsightJournal/itkLabelMapToRGBImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..c41ba09bbe159bae8576a94cf43a092c8b89aef7
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelMapToRGBImageFilter.txx
@@ -0,0 +1,77 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelMapToRGBImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelMapToRGBImageFilter_txx
+#define __itkLabelMapToRGBImageFilter_txx
+
+#include "itkLabelMapToRGBImageFilter.h"
+#include "itkNumericTraits.h"
+#include "itkProgressReporter.h"
+#include "itkImageRegionConstIteratorWithIndex.h"
+
+namespace itk {
+
+template <class TInputImage, class TOutputImage>
+LabelMapToRGBImageFilter<TInputImage, TOutputImage>
+::LabelMapToRGBImageFilter()
+{
+}
+
+
+template<class TInputImage, class TOutputImage>
+void
+LabelMapToRGBImageFilter<TInputImage, TOutputImage>
+::BeforeThreadedGenerateData()
+{
+ OutputImageType * output = this->GetOutput();
+ const InputImageType * input = this->GetInput();
+
+ FunctorType function;
+ function.SetBackgroundValue( input->GetBackgroundValue() );
+ output->FillBuffer( function( input->GetBackgroundValue() ) );
+
+ Superclass::BeforeThreadedGenerateData();
+
+}
+
+
+template<class TInputImage, class TOutputImage>
+void
+LabelMapToRGBImageFilter<TInputImage, TOutputImage>
+::ThreadedGenerateData( LabelObjectType * labelObject )
+{
+ const typename LabelObjectType::LabelType & label = labelObject->GetLabel();
+
+ FunctorType function;
+ function.SetBackgroundValue( this->GetInput()->GetBackgroundValue() );
+
+ typename InputImageType::LabelObjectType::LineContainerType::const_iterator lit;
+ typename InputImageType::LabelObjectType::LineContainerType & lineContainer = labelObject->GetLineContainer();
+
+ for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
+ {
+ IndexType idx = lit->GetIndex();
+ unsigned long length = lit->GetLength();
+ for( unsigned int i=0; i<length; i++)
+ {
+ this->GetOutput()->SetPixel( idx, function( label ) );
+ idx[0]++;
+ }
+ }
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkLabelObjectUtils.h b/Utilities/InsightJournal/itkLabelObjectUtils.h
new file mode 100644
index 0000000000000000000000000000000000000000..6be33ba3a1666bf1ed07e0e42afe70ac5d528982
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelObjectUtils.h
@@ -0,0 +1,89 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelObject.h,v $
+ Language: C++
+ Date: $Date: 2005/01/21 20:13:31 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelObjectUtils_h
+#define __itkLabelObjectUtils_h
+
+#include <deque>
+#include <itkLightObject.h>
+#include "itkLabelMap.h"
+#include "itkLabelObjectLine.h"
+
+namespace itk
+{
+
+
+namespace Functor {
+
+template< class TLabelObject >
+class ITK_EXPORT LabelLabelObjectAccessor
+{
+public:
+ typedef TLabelObject LabelObjectType;
+ typedef typename LabelObjectType::LabelType AttributeValueType;
+
+ inline const AttributeValueType operator()( const LabelObjectType * labelObject )
+ {
+ return labelObject->GetLabel();
+ }
+};
+
+template< class TLabelObject >
+class ITK_EXPORT NumberOfLinesLabelObjectAccessor
+{
+public:
+ typedef TLabelObject LabelObjectType;
+ typedef int AttributeValueType;
+
+ inline const AttributeValueType operator()( const LabelObjectType * labelObject )
+ {
+ return labelObject->GetNumberOfLines();
+ }
+};
+
+template< class TLabelObject, class TAttributeAccessor >
+class LabelObjectComparator
+{
+public:
+ typedef TLabelObject LabelObjectType;
+ typedef TAttributeAccessor AttributeAccessorType;
+ bool operator()( const LabelObjectType * a, const LabelObjectType * b )
+ {
+ return accessor( a ) > accessor( b );
+ }
+private:
+ AttributeAccessorType accessor;
+};
+
+template< class TLabelObject, class TAttributeAccessor >
+class LabelObjectReverseComparator
+{
+public:
+ typedef TLabelObject LabelObjectType;
+ typedef TAttributeAccessor AttributeAccessorType;
+ bool operator()( const LabelObjectType * a, const LabelObjectType * b )
+ {
+ return accessor( a ) < accessor( b );
+ }
+private:
+ AttributeAccessorType accessor;
+};
+
+}
+
+} // end namespace itk
+
+#endif
diff --git a/Utilities/InsightJournal/itkLabelReconstructionByDilationImageFilter.h b/Utilities/InsightJournal/itkLabelReconstructionByDilationImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..d62dc10d0056ebb15a0f1f3853765b18bc4dbc61
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelReconstructionByDilationImageFilter.h
@@ -0,0 +1,174 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelReconstructionByDilationImageFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelReconstructionByDilationImageFilter_h
+#define __itkLabelReconstructionByDilationImageFilter_h
+
+#include "itkImageToImageFilter.h"
+#include "itkAttributeLabelObject.h"
+#include "itkLabelMap.h"
+#include "itkLabelImageToLabelMapFilter.h"
+#include "itkLabelReconstructionLabelMapFilter.h"
+#include "itkAttributeOpeningLabelMapFilter.h"
+#include "itkLabelMapToLabelImageFilter.h"
+
+
+namespace itk {
+
+/** \class LabelReconstructionByDilationImageFilter
+ * \brief Identify local maxima whose height above the baseline is greater than h.
+ *
+* \brief label reconstruction by dilation of an image
+ *
+ * Reconstruction by dilation operates on a "marker" image and a "mask"
+ * image, and is defined as the dilation of the marker image with
+ * respect to the mask image iterated until stability.
+ *
+ * Geodesic morphology is described in Chapter 6.2 of Pierre Soille's
+ * book "Morphological Image Analysis: Principles and Applications",
+ * Second Edition, Springer, 2003.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa MorphologyImageFilter, ReconstructionByDilationImageFilter, LabelReconstructionByErosionImageFilter
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TInputImage>
+class ITK_EXPORT LabelReconstructionByDilationImageFilter :
+ public ImageToImageFilter<TInputImage, TInputImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef LabelReconstructionByDilationImageFilter Self;
+ typedef ImageToImageFilter<TInputImage, TInputImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TInputImage InputImageType;
+ typedef TInputImage OutputImageType;
+ typedef typename InputImageType::Pointer InputImagePointer;
+ typedef typename InputImageType::ConstPointer InputImageConstPointer;
+ typedef typename InputImageType::RegionType InputImageRegionType;
+ typedef typename InputImageType::PixelType InputImagePixelType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::PixelType OutputImagePixelType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(InputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(OutputImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TInputImage::ImageDimension);
+
+ typedef AttributeLabelObject<unsigned long, ImageDimension, bool> LabelObjectType;
+ typedef typename itk::LabelMap< LabelObjectType > LabelMapType;
+ typedef typename itk::LabelImageToLabelMapFilter< InputImageType, LabelMapType > LabelizerType;
+ typedef typename itk::LabelReconstructionLabelMapFilter< LabelMapType, InputImageType > ReconstructionType;
+ typedef typename itk::AttributeOpeningLabelMapFilter< LabelMapType > OpeningType;
+ typedef typename itk::LabelMapToLabelImageFilter< LabelMapType, OutputImageType > BinarizerType;
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(LabelReconstructionByDilationImageFilter,
+ ImageToImageFilter);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+ itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));
+ /** End concept checking */
+#endif
+
+ /**
+ * Set/Get the value used as "background" in the output image.
+ * Defaults to NumericTraits<PixelType>::NonpositiveMin().
+ */
+ itkSetMacro(BackgroundValue, OutputImagePixelType);
+ itkGetConstMacro(BackgroundValue, OutputImagePixelType);
+
+ /** Set the marker image */
+ void SetMarkerImage(InputImageType *input)
+ {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput( 0, const_cast<InputImageType *>(input) );
+ }
+
+ /** Get the marker image */
+ InputImageType * GetMarkerImage()
+ {
+ return static_cast<InputImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(0)));
+ }
+
+ /** Set the mask image */
+ void SetMaskImage( const InputImageType *input)
+ {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput( 1, const_cast<InputImageType *>(input) );
+ }
+
+ /** Get the mask image */
+ InputImageType * GetMaskImage()
+ {
+ return static_cast<InputImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(1)));
+ }
+
+
+protected:
+ LabelReconstructionByDilationImageFilter();
+ ~LabelReconstructionByDilationImageFilter() {};
+ void PrintSelf(std::ostream& os, Indent indent) const;
+
+ /** LabelReconstructionByDilationImageFilter needs the entire input be
+ * available. Thus, it needs to provide an implementation of
+ * GenerateInputRequestedRegion(). */
+ void GenerateInputRequestedRegion() ;
+
+ /** LabelReconstructionByDilationImageFilter will produce the entire output. */
+ void EnlargeOutputRequestedRegion(DataObject *itkNotUsed(output));
+
+ /** Single-threaded version of GenerateData. This filter delegates
+ * to GrayscaleGeodesicErodeImageFilter. */
+ void GenerateData();
+
+
+private:
+ LabelReconstructionByDilationImageFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ OutputImagePixelType m_BackgroundValue;
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkLabelReconstructionByDilationImageFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkLabelReconstructionByDilationImageFilter.txx b/Utilities/InsightJournal/itkLabelReconstructionByDilationImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..ef731666e8a16724bcc0a16a51abb2cf39f193bd
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelReconstructionByDilationImageFilter.txx
@@ -0,0 +1,119 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelReconstructionByDilationImageFilter.txx,v $
+ Language: C++
+ Date: $Date: 2006/08/01 19:16:18 $
+ Version: $Revision: 1.7 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelReconstructionByDilationImageFilter_txx
+#define __itkLabelReconstructionByDilationImageFilter_txx
+
+#include "itkLabelReconstructionByDilationImageFilter.h"
+#include "itkProgressAccumulator.h"
+
+
+namespace itk {
+
+template<class TInputImage>
+LabelReconstructionByDilationImageFilter<TInputImage>
+::LabelReconstructionByDilationImageFilter()
+{
+ m_BackgroundValue = NumericTraits<OutputImagePixelType>::NonpositiveMin();
+ this->SetNumberOfRequiredInputs(2);
+}
+
+template<class TInputImage>
+void
+LabelReconstructionByDilationImageFilter<TInputImage>
+::GenerateInputRequestedRegion()
+{
+ // call the superclass' implementation of this method
+ Superclass::GenerateInputRequestedRegion();
+
+ // We need all the input.
+ InputImagePointer input = const_cast<InputImageType *>(this->GetMarkerImage());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+
+ input = const_cast<InputImageType *>(this->GetMaskImage());
+ if( input )
+ {
+ input->SetRequestedRegion( input->GetLargestPossibleRegion() );
+ }
+}
+
+
+template<class TInputImage>
+void
+LabelReconstructionByDilationImageFilter<TInputImage>
+::EnlargeOutputRequestedRegion(DataObject *)
+{
+ this->GetOutput()
+ ->SetRequestedRegion( this->GetOutput()->GetLargestPossibleRegion() );
+}
+
+
+template<class TInputImage>
+void
+LabelReconstructionByDilationImageFilter<TInputImage>
+::GenerateData()
+{
+ // Create a process accumulator for tracking the progress of this minipipeline
+ ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+ progress->SetMiniPipelineFilter(this);
+
+ // Allocate the output
+ this->AllocateOutputs();
+
+ typename LabelizerType::Pointer labelizer = LabelizerType::New();
+ labelizer->SetInput( this->GetMaskImage() );
+ labelizer->SetBackgroundValue( m_BackgroundValue );
+ labelizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(labelizer, .25f);
+
+ typename ReconstructionType::Pointer reconstruction = ReconstructionType::New();
+ reconstruction->SetInput( labelizer->GetOutput() );
+ reconstruction->SetMarkerImage( this->GetMarkerImage() );
+ reconstruction->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(reconstruction, .25f);
+
+ typename OpeningType::Pointer opening = OpeningType::New();
+ opening->SetInput( reconstruction->GetOutput() );
+ opening->SetLambda( true );
+ opening->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(opening, .25f);
+
+ typename BinarizerType::Pointer binarizer = BinarizerType::New();
+ binarizer->SetInput( opening->GetOutput() );
+ binarizer->SetNumberOfThreads( this->GetNumberOfThreads() );
+ progress->RegisterInternalFilter(binarizer, .5f);
+
+ binarizer->GraftOutput( this->GetOutput() );
+ binarizer->Update();
+ this->GraftOutput( binarizer->GetOutput() );
+}
+
+
+template<class TInputImage>
+void
+LabelReconstructionByDilationImageFilter<TInputImage>
+::PrintSelf(std::ostream &os, Indent indent) const
+{
+ Superclass::PrintSelf(os, indent);
+
+ os << indent << "BackgroundValue: " << static_cast<typename NumericTraits<OutputImagePixelType>::PrintType>(m_BackgroundValue) << std::endl;
+}
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkLabelReconstructionLabelMapFilter.h b/Utilities/InsightJournal/itkLabelReconstructionLabelMapFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..1417de17406ca271779d9087da3593f3d6f52ab6
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelReconstructionLabelMapFilter.h
@@ -0,0 +1,124 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelReconstructionLabelMapFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelReconstructionLabelMapFilter_h
+#define __itkLabelReconstructionLabelMapFilter_h
+
+#include "itkInPlaceLabelMapFilter.h"
+#include "itkAttributeLabelObject.h"
+
+namespace itk {
+/** \class LabelReconstructionLabelMapFilter
+ * \brief
+ *
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TImage, class TMarkerImage, class TAttributeAccessor=
+ typename Functor::AttributeLabelObjectAccessor< typename TImage::LabelObjectType > >
+class ITK_EXPORT LabelReconstructionLabelMapFilter :
+ public InPlaceLabelMapFilter<TImage>
+{
+public:
+ /** Standard class typedefs. */
+ typedef LabelReconstructionLabelMapFilter Self;
+ typedef InPlaceLabelMapFilter<TImage>
+ Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TImage ImageType;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::PixelType PixelType;
+ typedef typename ImageType::IndexType IndexType;
+ typedef typename ImageType::LabelObjectType LabelObjectType;
+
+ typedef TMarkerImage MarkerImageType;
+ typedef typename MarkerImageType::Pointer MarkerImagePointer;
+ typedef typename MarkerImageType::ConstPointer MarkerImageConstPointer;
+ typedef typename MarkerImageType::PixelType MarkerImagePixelType;
+
+ typedef TAttributeAccessor AttributeAccessorType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TImage::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(LabelReconstructionLabelMapFilter,
+ InPlaceLabelMapFilter);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+/* itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<PixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, PixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<PixelType>));*/
+ /** End concept checking */
+#endif
+
+ /** Set the marker image */
+ void SetMarkerImage(TMarkerImage *input)
+ {
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput( 1, const_cast<TMarkerImage *>(input) );
+ }
+
+ /** Get the marker image */
+ MarkerImageType * GetMarkerImage()
+ {
+ return static_cast<MarkerImageType*>(const_cast<DataObject *>(this->ProcessObject::GetInput(1)));
+ }
+
+ /** Set the input image */
+ void SetInput1(TImage *input)
+ {
+ this->SetInput( input );
+ }
+
+ /** Set the marker image */
+ void SetInput2(TMarkerImage *input)
+ {
+ this->SetMarkerImage( input );
+ }
+
+protected:
+ LabelReconstructionLabelMapFilter();
+ ~LabelReconstructionLabelMapFilter() {};
+
+ virtual void ThreadedGenerateData( LabelObjectType * labelObject );
+
+private:
+ LabelReconstructionLabelMapFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+} ; // end of class
+
+} // end namespace itk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkLabelReconstructionLabelMapFilter.txx"
+#endif
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkLabelReconstructionLabelMapFilter.txx b/Utilities/InsightJournal/itkLabelReconstructionLabelMapFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..ca1945a155a3c437c8b4b7c611843b2bdc1c8056
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelReconstructionLabelMapFilter.txx
@@ -0,0 +1,73 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelReconstructionLabelMapFilter.txx,v $
+ Language: C++
+ Date: $Date: 2005/08/23 15:09:03 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelReconstructionLabelMapFilter_txx
+#define __itkLabelReconstructionLabelMapFilter_txx
+
+#include "itkLabelReconstructionLabelMapFilter.h"
+#include "itkProgressReporter.h"
+
+
+namespace itk {
+
+template <class TImage, class TMarkerImage, class TAttributeAccessor>
+LabelReconstructionLabelMapFilter<TImage, TMarkerImage, TAttributeAccessor>
+::LabelReconstructionLabelMapFilter()
+{
+ this->SetNumberOfRequiredInputs(2);
+}
+
+
+template <class TImage, class TMarkerImage, class TAttributeAccessor>
+void
+LabelReconstructionLabelMapFilter<TImage, TMarkerImage, TAttributeAccessor>
+::ThreadedGenerateData( LabelObjectType * labelObject )
+{
+ AttributeAccessorType accessor;
+
+ const MarkerImageType * maskImage = this->GetMarkerImage();
+ const PixelType & label = labelObject->GetLabel();
+
+ typename LabelObjectType::LineContainerType::const_iterator lit;
+ typename LabelObjectType::LineContainerType & lineContainer = labelObject->GetLineContainer();
+
+ // iterate over all the lines to find a pixel inside the object
+ for( lit = lineContainer.begin(); lit != lineContainer.end(); lit++ )
+ {
+ const IndexType & firstIdx = lit->GetIndex();
+ unsigned long length = lit->GetLength();
+
+ long endIdx0 = firstIdx[0] + length;
+ for( IndexType idx = firstIdx; idx[0]<endIdx0; idx[0]++ )
+ {
+ const MarkerImagePixelType & v = maskImage->GetPixel( idx );
+ if( v == label )
+ {
+ // keep the object
+ accessor( labelObject, true );
+ return;
+ }
+ }
+ }
+
+ // remove the object
+ accessor( labelObject, false );
+
+}
+
+
+}// end namespace itk
+#endif
diff --git a/Utilities/InsightJournal/itkLabelSelectionLabelMapFilter.h b/Utilities/InsightJournal/itkLabelSelectionLabelMapFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..d476cc4bf20b477037d589a6bfdb988e51e9cf1b
--- /dev/null
+++ b/Utilities/InsightJournal/itkLabelSelectionLabelMapFilter.h
@@ -0,0 +1,126 @@
+/*=========================================================================
+
+ Program: Insight Segmentation & Registration Toolkit
+ Module: $RCSfile: itkLabelSelectionLabelMapFilter.h,v $
+ Language: C++
+ Date: $Date: 2006/03/28 19:59:05 $
+ Version: $Revision: 1.6 $
+
+ Copyright (c) Insight Software Consortium. All rights reserved.
+ See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#ifndef __itkLabelSelectionLabelMapFilter_h
+#define __itkLabelSelectionLabelMapFilter_h
+
+#include "itkAttributeSelectionLabelMapFilter.h"
+#include "itkLabelObject.h"
+#include <set>
+
+
+namespace itk {
+/** \class LabelSelectionLabelMapFilter
+ * \brief remove the objects according to the value of their attribute
+ *
+ * LabelSelectionLabelMapFilter removes the objects in a label collection image
+ * with an attribute value inside or outside a set of attribute values passed by
+ * the user.
+ * The attribute is provide by an attribute accessor given in template parameter.
+ * Contrary to the other filters made to remove some object of a LabelMap, no
+ * ordering relation for the attribute is needed in that filter.
+ *
+ * \author Ga�tan Lehmann. Biologie du D�veloppement et de la Reproduction, INRA de Jouy-en-Josas, France.
+ *
+ * \sa AttributeLabelObject
+ * \ingroup ImageEnhancement MathematicalMorphologyImageFilters
+ */
+template<class TImage>
+class ITK_EXPORT LabelSelectionLabelMapFilter :
+ public AttributeSelectionLabelMapFilter<TImage, typename Functor::LabelLabelObjectAccessor< typename TImage::LabelObjectType > >
+{
+public:
+ /** Standard class typedefs. */
+ typedef LabelSelectionLabelMapFilter Self;
+ typedef AttributeSelectionLabelMapFilter<TImage, typename Functor::LabelLabelObjectAccessor< typename TImage::LabelObjectType > > Superclass;
+ typedef SmartPointer<Self> Pointer;
+ typedef SmartPointer<const Self> ConstPointer;
+
+ /** Some convenient typedefs. */
+ typedef TImage ImageType;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::PixelType PixelType;
+ typedef typename ImageType::IndexType IndexType;
+
+ typedef typename Superclass::AttributeAccessorType AttributeAccessorType;
+ typedef typename Superclass::AttributeValueType AttributeValueType;
+
+ typedef typename Superclass::AttributeSetType AttributeSetType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int,
+ TImage::ImageDimension);
+
+ /** Standard New method. */
+ itkNewMacro(Self);
+
+ /** Runtime information support. */
+ itkTypeMacro(LabelSelectionLabelMapFilter,
+ AttributeSelectionLabelMapFilter);
+
+#ifdef ITK_USE_CONCEPT_CHECKING
+ /** Begin concept checking */
+/* itkConceptMacro(InputEqualityComparableCheck,
+ (Concept::EqualityComparable<InputImagePixelType>));
+ itkConceptMacro(IntConvertibleToInputCheck,
+ (Concept::Convertible<int, InputImagePixelType>));
+ itkConceptMacro(InputOStreamWritableCheck,
+ (Concept::OStreamWritable<InputImagePixelType>));*/
+ /** End concept checking */
+#endif
+
+ const AttributeSetType & GetLabelSet() const
+ {
+ return this->GetAttributeSet();
+ }
+
+ void SetLabelSet( const AttributeSetType & set )
+ {
+ this->SetAttributeSet( set );
+ }
+
+ /** Clear the attribute set, and add the attribute passed in parameter */
+ void SetLabel( const AttributeValueType & attr )
+ {
+ this->SetAttribute( attr );
+ }
+
+ void ClearLabelSet()
+ {
+ this->ClearAttributeSet();
+ }
+
+ void AddLabel( const AttributeValueType & attr )
+ {
+ this->AddAttribute( attr );
+ }
+
+protected:
+ LabelSelectionLabelMapFilter() {};
+ ~LabelSelectionLabelMapFilter() {};
+
+private:
+ LabelSelectionLabelMapFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+} ; // end of class
+
+} // end namespace itk
+
+#endif
+
+
diff --git a/Utilities/InsightJournal/itkScaleInvariantFeatureImageFilter.h b/Utilities/InsightJournal/itkScaleInvariantFeatureImageFilter.h
new file mode 100644
index 0000000000000000000000000000000000000000..2453e9aef53593f60532b2a875764e7d9e32f5b4
--- /dev/null
+++ b/Utilities/InsightJournal/itkScaleInvariantFeatureImageFilter.h
@@ -0,0 +1,325 @@
+/*=========================================================================
+Program: ITK nSIFT Implemention (Header)
+Module: $RCSfile: itkScaleInvariantFeatureImageFilter.h,v $
+Language: C++
+Date: $Date: 2007/11/25 15:51:48 $
+Version: $Revision: 1.0 $
+Copyright (c) 2005,2006,2007 Warren Cheung
+All rights reserved.
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+* Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+* The name of the Insight Consortium, nor the names of any consortium members,
+nor of any contributors, may be used to endorse or promote products derived
+from this software without specific prior written permission.
+* Modified source versions must be plainly marked as such, and must not be
+misrepresented as being the original software.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+=========================================================================*/
+
+//#define VERBOSE
+//#define DEBUG
+//#define DEBUG_VERBOSE
+
+//#define GENERATE_KEYS
+//#define REORIENT
+
+//#define SIFT_FEATURE
+
+//Generate histograms
+//compare gradient histograms
+//
+
+// Min DoG value for keypoints
+// Fix Gaussian Scale
+// Only iterate through the region up to 3 sigma from the point
+
+//More advanced features for better matching?
+//Simple quadrant system?
+
+
+/* Based on example code from the ITK Toolkit
+ * TODO: Use resampler+identity transform+spacing change instead of scaling
+ * arbitrary downscale between pyramid levels
+ * may need to have a threshold
+ * Gaussian filtration may fail if input image format is integer
+ * Generate Pointset
+ * Get Orientation
+ * Generate Features
+
+ * Test vs Noise (no need to for orientation)
+ * vs Stretch
+ * vs Scale
+ */
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#ifndef SIFTKEY_H
+#define SIFTKEY_H
+
+#include "itkImageRegistrationMethod.h"
+
+#include "itkLinearInterpolateImageFunction.h"
+#include "itkNearestNeighborInterpolateImageFunction.h"
+#include "itkImage.h"
+
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+
+#include "itkAffineTransform.h"
+#include "itkIdentityTransform.h"
+#include "itkResampleImageFilter.h"
+
+#include "itkDiscreteGaussianImageFilter.h"
+#include "itkSubtractImageFilter.h"
+#include "itkGradientImageFilter.h"
+#include "itkGradientMagnitudeImageFilter.h"
+#include "itkMultiplyImageFilter.h"
+
+#include "itkGaussianImageSource.h"
+
+#include "itkConstNeighborhoodIterator.h"
+
+#include "itkPointSet.h"
+#include "itkVector.h"
+
+#include <cstdio>
+
+
+namespace itk
+{
+
+/** \class ScaleInvariantFeatureImageFilter
+ * \brief Generate and match scale invariant features from an image input.
+ *
+ * This class takes the input image and locates scale invariant features in
+ * the image. The result is a set of keypoints, each with an associated
+ * vector of values (the corresponding feature). Two sets of keypoints
+ * can then be matched, to determine which points in the sets are likely
+ * to correspond, by comparing feature vectors.
+ *
+ * Three different features can be compiled from this source using
+ * preprocessor \#define commands:
+ *
+ * - default (no special \#define)
+ * - Histogram Feature
+ * - \#define REORIENT
+ * - Histogram Feature with reoriented to the highest magnitude histogram bin
+ * - \#define SIFT_FEATURE
+ * - n-Dimensional adaptation of the SIFT feature.
+ */
+
+ template <class TFixedImageType, unsigned int VDimension=2>
+ class ITK_EXPORT ScaleInvariantFeatureImageFilter
+ {
+ public:
+
+ /** typedefs to facilitate access to the image-related types */
+ typedef typename TFixedImageType::PixelType PixelType;
+ typedef typename TFixedImageType::Pointer FixedImagePointer;
+ typedef typename TFixedImageType::IndexType IndexType;
+
+ /** used for validating results from synthetic images */
+ typedef typename itk::ScalableAffineTransform< double, VDimension > TransformType;
+
+#ifdef GENERATE_KEYS
+ /** multidimensional histogram for the features */
+ typedef Array< float > FeatureType;
+ /** keypoints, storing the associated feature as well */
+ typedef PointSet< FeatureType, VDimension,
+ DefaultStaticMeshTraits< FeatureType, VDimension, VDimension, double > > PointSetType;
+#else
+ typedef PointSet< float, VDimension,
+ DefaultStaticMeshTraits< FeatureType, VDimension, VDimension, double > > PointSetType;
+#endif
+ typedef typename PointSetType::PointType PointType;
+ typedef typename PointSetType::Pointer PointSetTypePointer;
+
+ /** Filters for scaling and resampling images for the multiple scales */
+ typedef ResampleImageFilter< TFixedImageType, TFixedImageType > ResampleFilterType;
+ typedef typename ResampleFilterType::Pointer ResampleFilterPointerType;
+
+ /** Constructor to set default values */
+ ScaleInvariantFeatureImageFilter();
+
+ /** Used for debugging. Writes an image to disk */
+ void writeImage(FixedImagePointer fixedImage, const char *filename);
+
+ /** Create a filter that resamples the image (scale up or down) */
+ ResampleFilterPointerType getScaleResampleFilter ( FixedImagePointer fixedImage, float scale );
+
+ void SetDoubling (bool tmp);
+ void SetNumBins( unsigned int tmp);
+ void SetSigma( double tmp);
+ void SetNumScales ( unsigned int tmp);
+ void SetMatchRatio ( float tmp);
+
+ /** Generate and return the scale invariant keypoints and features */
+ PointSetTypePointer getSiftFeatures(FixedImagePointer fixedImage);
+
+ /** Match keypoints purely based on position. Upper bounds
+ * the performance when matching using features. Supply
+ * the inverse transform to get performance measures.
+ * Mainly used with synthetic tests.
+ */
+ void MatchKeypointsPos(PointSetTypePointer keypoints1, PointSetTypePointer keypoints2,
+ typename TransformType::Pointer inverse_transform);
+
+#ifdef GENERATE_KEYS
+ /** Match keypoints based on similarity of features. Matches are printed
+ * to standard out. Supply the inverse transform to get performance
+ * measures.
+ */
+ void MatchKeypointsFeatures(PointSetTypePointer keypoints1, PointSetTypePointer keypoints2,
+ typename TransformType::Pointer inverse_transform);
+#endif
+
+
+ private:
+
+ /** Filter to obtain gradient directions and magnitudes */
+ typedef itk::GradientImageFilter<TFixedImageType> GradientFilterType;
+ typedef typename GradientFilterType::OutputImageType GradientImageType;
+ typedef itk::GradientMagnitudeImageFilter<TFixedImageType, TFixedImageType> GradientMagFilterType;
+
+ /** Shorthand for an identity transform */
+ typedef IdentityTransform< double, VDimension > IdentityTransformType;
+ typename IdentityTransformType::Pointer m_IdentityTransform;
+
+ /** Scale up the original image by a factor of 2 before processing */
+ bool m_DoubleOriginalImage;
+ /** Number of image pyramid levels (scales) to test */
+ unsigned int m_ImageScalesTestedNumber;
+ /** Factor by which the images are scaled between pyramid levels */
+ float m_ScalingFactor;
+
+ /** The range of Gaussian sigma that will be tested */
+ float m_GaussianSigma;
+ /** Number of Gaussian Images that will be used to sample the range of
+ * sigma values ...
+ */
+ unsigned int m_GaussianImagesNumber;
+ /** ... determining the number of difference of gaussian images ... */
+ unsigned int m_DifferenceOfGaussianImagesNumber;
+ /** ... determining the number of sets of images we can test for
+ * feature points
+ */
+ unsigned int m_DifferenceOfGaussianTestsNumber;
+
+ /** Number of bins to cover 2pi radians
+ * Note that the multidimensional histogram has this many bins
+ * for each dimension when describing the angle in hyperspherical
+ * coordinates
+ */
+ unsigned int m_HistogramBinsNumber;
+ /** Minimum voxel intensity for a feature point */
+ float m_MinKeypointValue;
+ /** When looking for difference of Gaussian extrema in the images,
+ * consider a voxel to be extremal even if there are voxels
+ * that are this much more extreme.
+ */
+ float m_ErrorThreshold;
+
+ /** When matching points, reject a match if the ratio:
+ * \f[
+ * \frac{\textrm{distance to best match}}{\textrm{distance to second-best match}}
+ * \f]
+ * is greater than this value
+ */
+ float m_MaxFeatureDistanceRatio;
+
+ PointSetTypePointer m_KeypointSet;
+ long m_PointsCount;
+
+ /** Distance from the centre to the edge of the hypercube
+ * summarised by the nSIFT feature
+ */
+ unsigned int m_SIFTHalfWidth;
+ /** The hypercube edge length (in voxels) of the subregion summarised
+ * by each multidimensional histogram of the nSIFT feature
+ */
+ unsigned int m_SIFTSubfeatureWidth;
+ /** Number of bin used to summarise the hyperspherical coordinates
+ * of the voxels in each subregion
+ */
+ unsigned int m_SIFTSubfeatureBins;
+
+ /** The sigma for the Gaussian filtering for the j-th image on a level
+ * of the image pyramid
+ */
+ double GetGaussianScale( int j );
+
+ /** The total size of the (reoriented) histogram feature */
+ unsigned int HistFeatureSize();
+
+ /** Returns an image where all gradients are converted to hyperspherical
+ * coordinates
+ */
+ typename GradientImageType::Pointer GetHypersphericalCoordinates(typename GradientImageType::Pointer inputImg);
+
+ /** Convert a histogram bin number into an angle in hyperspherical
+ * coordinates
+ */
+ typename GradientImageType::PixelType BinToVector (unsigned int maxbin);
+
+ /** Size of the nSIFT feature */
+ unsigned int SiftFeatureSize();
+
+ /** Used when generating nSIFT features to figure out what portion
+ * of the nSIFT feature vector the current summary histogram starts at
+ */
+ unsigned int DeltaToSiftIndex (int delta[]);
+
+#ifdef GENERATE_KEYS
+ /** Generate nSIFT feature for pixel at pixelIndex */
+ FeatureType GetSiftKey(typename GradientImageType::Pointer inputImg,
+ FixedImagePointer multImg,
+ IndexType pixelIndex);
+
+
+ /** Generate weighted histogram feature for voxel at pixelIndex
+ * Feature point is weighted due to the Gaussian.
+ */
+ FeatureType GetHistogram(typename GradientImageType::Pointer inputImg,
+ FixedImagePointer multImg);
+#endif
+
+
+ /** Determine whether voxel at pixelIndex with intensity
+ * pixelvalue is the local max/min
+ */
+ void CheckLocalExtrema(FixedImagePointer image, IndexType pixelIndex,
+ PixelType pixelValue,
+ bool &isMax, bool &isMin,
+ bool checkCentre);
+
+#ifdef GENERATE_KEYS
+ /** Generate the (reoriented)histogram/nSIFT feature at a point
+ */
+ FeatureType GetFeatures( FixedImagePointer fixedImage,
+ typename GradientImageType::Pointer hgradImage,
+ PointType &point, float currScale);
+#endif
+
+ };
+}
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkScaleInvariantFeatureImageFilter.txx"
+#endif
+
+#endif /* SIFTKEY_H */
diff --git a/Utilities/InsightJournal/itkScaleInvariantFeatureImageFilter.txx b/Utilities/InsightJournal/itkScaleInvariantFeatureImageFilter.txx
new file mode 100644
index 0000000000000000000000000000000000000000..0723f3a202f561a27778e8365c6db68768bdbc1a
--- /dev/null
+++ b/Utilities/InsightJournal/itkScaleInvariantFeatureImageFilter.txx
@@ -0,0 +1,1335 @@
+/*=========================================================================
+Program: ITK nSIFT Implemention (Template Source)
+Module: $RCSfile: itkScaleInvariantFeatureImageFilter.txx,v $
+Language: C++
+Date: $Date: 2007/11/25 15:51:48 $
+Version: $Revision: 1.0 $
+Copyright (c) 2005,2006,2007 Warren Cheung
+All rights reserved.
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+* Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+* The name of the Insight Consortium, nor the names of any consortium members,
+nor of any contributors, may be used to endorse or promote products derived
+from this software without specific prior written permission.
+* Modified source versions must be plainly marked as such, and must not be
+misrepresented as being the original software.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+=========================================================================*/
+
+//#define VERBOSE
+//#define DEBUG
+//#define DEBUG_VERBOSE
+
+//#define GENERATE_KEYS
+//#define REORIENT
+
+//#define SIFT_FEATURE
+
+//TODO: Migrate the histogram reorientation code to the SIFT feature
+// Make histogram feature special case of the sift feature with
+// a single histogram.
+//REORIENT NSIFT: Keep a "global histogram" in addition to the specific ones.
+// Or maybe do the global histogram/reorient phase first?
+
+// Granularity of the Histogram causing cycles in reorientation accuracy?
+// Or maybe we need to shift all the angles by half a bin width?
+
+//Generate histograms
+//compare gradient histograms
+//
+
+// Min DoG value for keypoints
+// Fix Gaussian Scale
+// Only iterate through the region up to 3 sigma from the point
+
+//More advanced features for better matching?
+//Simple quadrant system?
+
+
+/* Based on example code from the ITK Toolkit
+ * TODO: Use resampler+identity transform+spacing change instead of scaling
+ * arbitrary downscale between pyramid levels
+ * may need to have a threshold
+ * Gaussian filtration may fail if input image format is integer
+ * Generate Pointset
+ * Get Orientation
+ * Generate Features
+
+ * Test vs Noise (no need to for orientation)
+ * vs Stretch
+ * vs Scale
+ */
+#if defined(_MSC_VER)
+#pragma warning ( disable : 4786 )
+#endif
+
+#include "itkScaleInvariantFeatureImageFilter.h"
+#include <cstdio>
+#include "vnl/vnl_math.h"
+
+#ifndef SIFTKEY_CLASS
+#define SIFTKEY_CLASS
+
+
+const float PI=3.14159265;
+
+namespace itk
+{
+
+ template <class TFixedImageType, unsigned int VDimension>
+
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::ScaleInvariantFeatureImageFilter()
+ {
+#ifdef DO_DOUBLE
+ m_ImageScalesTestedNumber = 4;
+#else
+ m_ImageScalesTestedNumber = 3;
+#endif
+ m_ScalingFactor = 2.0;
+ m_DifferenceOfGaussianTestsNumber = 3;
+#ifdef DO_DOUBLE
+ m_DoubleOriginalImage = true;
+#else
+ m_DoubleOriginalImage = false;
+#endif
+ m_HistogramBinsNumber = 36;
+ m_ErrorThreshold = 0.0;
+ m_MaxFeatureDistanceRatio = 0.8;
+ m_GaussianSigma = 1.5;
+ m_MinKeypointValue = 0.0075;
+ m_SIFTHalfWidth = 8; // This MUST be a multiple of m_SIFTSubfeatureWidth
+ m_SIFTSubfeatureWidth = 4;
+ m_SIFTSubfeatureBins = 8;
+
+ // Derived from above
+ m_DifferenceOfGaussianImagesNumber = m_DifferenceOfGaussianTestsNumber+2;
+ m_GaussianImagesNumber = m_DifferenceOfGaussianImagesNumber+1;
+ m_IdentityTransform = IdentityTransformType::New();
+ }
+
+
+ template <class TFixedImageType, unsigned int VDimension>
+ double
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::GetGaussianScale( int j )
+ {
+ return (vcl_pow(2, (double) j / (double) m_DifferenceOfGaussianTestsNumber) * m_GaussianSigma);
+ }
+
+ template <class TFixedImageType, unsigned int VDimension>
+ unsigned int
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::HistFeatureSize()
+ {
+ unsigned int size = 1;
+ // Have m_HistogramBinsNumber for each of the (VDimension-1) Orientation dimensions
+ for (unsigned int i = 1; i < VDimension; ++i)
+ {
+ size *= m_HistogramBinsNumber;
+ }
+ return size;
+ }
+
+ template <class TFixedImageType, unsigned int VDimension>
+ typename ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>::GradientImageType::Pointer
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::GetHypersphericalCoordinates(typename GradientImageType::Pointer inputImg)
+ {
+ typedef itk::ImageRegionIteratorWithIndex< GradientImageType > ImageIteratorType;
+ typedef itk::ImageRegionConstIteratorWithIndex< GradientImageType > ConstImageIteratorType;
+ typedef itk::ImageRegionConstIteratorWithIndex< TFixedImageType > ConstFixedImageIteratorType;
+ typename GradientImageType::Pointer outputImg = GradientImageType::New();
+ // Copy attributes
+ outputImg->SetRegions(inputImg->GetLargestPossibleRegion());
+ outputImg->CopyInformation( inputImg );
+ outputImg->Allocate();
+
+ ConstImageIteratorType inputIt(inputImg, inputImg->GetLargestPossibleRegion());
+ ImageIteratorType outputIt(outputImg, inputImg->GetLargestPossibleRegion());
+
+ for ( inputIt.GoToBegin(), outputIt.GoToBegin(); !inputIt.IsAtEnd();
+ ++inputIt, ++outputIt)
+ {
+ typename GradientImageType::PixelType x = inputIt.Get();
+ typename GradientImageType::PixelType p;
+
+ // position 0 is the norm
+ p[0] = x.GetNorm();
+
+ // position 1 is arctan (x0 / x1)
+ p[1] = atan2( x[0],x[1] );
+
+ // Iterate over all the positions
+ // position k is arctan (x_k-1 / (x_k * cos p_k))
+ for (unsigned int k = 2; k < x.Size(); ++k)
+ {
+ p[k] = atan2( x[k-1], x[k] * cos(p[k-1]));
+ }
+ outputIt.Set(p);
+ }
+
+ return outputImg;
+ }
+
+ // Generates a vector with positions 1 to VDimension-1 filled with
+ // histogram bin numbers from a single bin number
+
+ template <class TFixedImageType, unsigned int VDimension>
+ typename ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>::GradientImageType::PixelType
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::BinToVector (unsigned int maxbin)
+ {
+ // convert maxpos to orientation bin vector
+ typename GradientImageType::PixelType maxp;
+ for (unsigned int i = 1; i < VDimension; ++i) {
+ maxp[i] = maxbin % m_HistogramBinsNumber;
+ maxbin /= m_HistogramBinsNumber;
+ }
+ return maxp;
+ }
+
+ template <class TFixedImageType, unsigned int VDimension>
+ unsigned int
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::SiftFeatureSize()
+ {
+ unsigned int size = 1;
+ // Have m_HistogramBinsNumber for each of the (VDimension-1) Orientation dimensions
+ for (unsigned int i = 0; i < VDimension; ++i)
+ {
+ size *= (m_SIFTHalfWidth * 2 / m_SIFTSubfeatureWidth );
+ if (i > 0)
+ size *= m_SIFTSubfeatureBins;
+ }
+
+ return size;
+ }
+
+ // Convert the delta iterator into index to the
+ // start of the SIFT histogram
+ template <class TFixedImageType, unsigned int VDimension>
+ unsigned int
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::DeltaToSiftIndex (int delta[])
+ {
+ unsigned int bin = 0;
+ unsigned int binpos = 1;
+#ifdef DEBUG_VERBOSE
+ std::cerr << "Converting delta: ";
+#endif
+ for (unsigned int i = 0; i < VDimension; ++i) {
+#ifdef DEBUG_VERBOSE
+ std::cerr << delta[i];
+#endif
+ unsigned int tmp = (delta[i] + m_SIFTHalfWidth) / m_SIFTSubfeatureWidth;
+
+ bin += tmp * binpos;
+ binpos *= (m_SIFTHalfWidth * 2 / m_SIFTSubfeatureWidth );
+ }
+ for (unsigned int i = 1; i < VDimension; ++i)
+ bin *= m_SIFTSubfeatureBins;
+
+#ifdef DEBUG_VERBOSE
+ std::cerr << "\n";
+#endif
+ return bin;
+ }
+
+
+#ifdef GENERATE_KEYS
+ template <class TFixedImageType, unsigned int VDimension>
+ typename ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>::FeatureType
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::GetSiftKey(typename GradientImageType::Pointer inputImg,
+ FixedImagePointer multImg,
+ IndexType pixelIndex)
+ {
+#ifdef DEBUG_VERBOSE
+ std::cerr << "GetSiftKey..." << std::endl;
+#endif
+ FeatureType sifthistogram(this->SiftFeatureSize());
+ sifthistogram.Fill(0);
+
+ // delta iterates from -m_SIFTHalfWidth to m_SIFTHalfWidth-1
+ // in each dimensions
+ int delta[VDimension];
+ for (unsigned int k = 0; k < VDimension; ++k) {
+ delta[k] = -m_SIFTHalfWidth;
+ }
+
+ typename GradientImageType::SizeType regionSize =
+ inputImg->GetLargestPossibleRegion().GetSize();
+
+ while(1) {
+ unsigned int siftbin = this->DeltaToSiftIndex(delta);
+
+#ifdef DEBUG_VERBOSE
+ std::cerr << "Siftbin:" << siftbin << std::endl;
+#endif
+
+ // Get pixel index
+ // Clamp to image edges
+ IndexType tmpIndex;
+ for (unsigned int k=0; k < VDimension; ++k) {
+ if ((pixelIndex[k] + delta[k]) < 0) {
+ tmpIndex[k] = 0;
+ } else {
+ tmpIndex[k] = pixelIndex[k] + delta[k];
+ if (static_cast<unsigned int>(tmpIndex[k]) >= regionSize[k] )
+ tmpIndex[k] = regionSize[k]-1;
+ }
+ }
+
+#ifdef DEBUG_VERBOSE
+ std::cerr << "Pixel:" << tmpIndex << std::endl;
+#endif
+ typename GradientImageType::PixelType x =
+ inputImg->GetPixel(tmpIndex);
+
+ // Get histogram bin
+ // Iterate over all the positions
+ unsigned int bin = 0;
+ unsigned int binpos = 1;
+ for (unsigned int k = 1; k < x.Size(); ++k)
+ {
+ // Rescale from -PI to PI -> 0 to m_HistogramBinsNumber-1
+ float p;
+ p = (x[k] + PI) * (float) m_SIFTSubfeatureBins / (2.0 * PI);
+
+
+ if (p < 0 || p >= m_SIFTSubfeatureBins)
+ p = 0;
+ bin += (unsigned int) p * binpos;
+
+#ifdef DEBUG_VERBOSE
+ std::cout << " " << p;
+#endif
+ binpos *= m_SIFTSubfeatureBins;
+ }
+
+ bin += siftbin;
+
+ // Fill Sift Index bin
+ if (bin > this->SiftFeatureSize()) {
+ // VERY BAD
+ std::cerr << bin << " > " << this->SiftFeatureSize() << " Warning -- Overload2\n";
+ }
+ sifthistogram[bin] += x[0] * multImg->GetPixel(tmpIndex);
+
+#ifdef DEBUG_VERBOSE
+ std::cerr << "Incrementing\n";
+#endif
+ // Increment delta
+ bool resetdelta=false;
+ for(unsigned int k=0; k <= VDimension; ++k) {
+#ifdef DEBUG_VERBOSE
+ std::cerr << delta[k];
+#endif
+ if (k == VDimension) {
+#ifdef DEBUG_VERBOSE
+ std::cerr << "done\n";
+#endif
+ resetdelta = true;
+ break; // done
+ }
+ // Don't want to go past m_SIFTHalfWidth-1
+ if (++delta[k] < (int) m_SIFTHalfWidth) {
+ break;
+ }
+ delta[k] = -m_SIFTHalfWidth; // reset and increment the next pos
+ }
+ if(resetdelta) break;
+ }
+
+#ifdef DEBUG_VERBOSE
+ std::cerr << "SIFT key: " << sifthistogram << "\n";
+#endif
+ return(sifthistogram);
+ }
+
+
+ // Takes a hyperspherical coordinate gradient and gaussian weights
+ // returns a histogram
+ // Each orientation divides the 2PI angles into m_HistogramBinsNumber
+ // The value in each bin is the weighted magnitude
+ template <class TFixedImageType, unsigned int VDimension>
+ typename ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>::FeatureType
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::GetHistogram(typename GradientImageType::Pointer inputImg,
+ FixedImagePointer multImg)
+ {
+
+#ifdef ERROR_CHECK
+ std::cerr << "GetHistogram ... ";
+#endif
+
+ FeatureType histogram(this->HistFeatureSize());
+
+ histogram.Fill(0);
+
+ typedef itk::ImageRegionConstIteratorWithIndex< GradientImageType > ConstImageIteratorType;
+ typedef itk::ImageRegionConstIteratorWithIndex< TFixedImageType > ConstFixedImageIteratorType;
+
+ ConstImageIteratorType inputIt(inputImg, inputImg->GetLargestPossibleRegion());
+ ConstFixedImageIteratorType multIt( multImg, inputImg->GetLargestPossibleRegion());
+
+ for ( inputIt.GoToBegin(), multIt.GoToBegin(); !inputIt.IsAtEnd();
+ ++inputIt, ++multIt)
+ {
+ typename GradientImageType::PixelType x = inputIt.Get();
+ typename TFixedImageType::PixelType m = multIt.Get();
+ unsigned int bin = 0;
+ unsigned int binpos = 1;
+ typename GradientImageType::PixelType p;
+
+ // position 0 is the norm
+ p[0] = x[0];
+
+ if (vnl_math_isnan(p[0]) || (p[0] == 0.0))
+ continue;
+
+ // multiply by m
+ p[0] *= m;
+
+#ifdef DEBUG_VERBOSE
+ std::cout << "Bin: ";
+#endif
+ // Iterate over all the positions
+ for (unsigned int k = 1; k < x.Size(); ++k)
+ {
+ // Rescale from -PI to PI -> 0 to m_HistogramBinsNumber-1
+ p[k] = (x[k] + PI) * (float) m_HistogramBinsNumber / (2.0 * PI);
+
+
+ if (p[k] < 0 || p[k] >= m_HistogramBinsNumber)
+ p[k] = 0;
+ bin += (unsigned int) p[k] * binpos;
+
+#ifdef DEBUG_VERBOSE
+ std::cout << " " << p[k];
+#endif
+ binpos *= m_HistogramBinsNumber;
+ }
+#ifdef DEBUG_VERBOSE
+ std::cout << " Value: " << p[0] << std::endl;
+#endif
+ if (bin > this->HistFeatureSize()) {
+ // VERY BAD
+ std::cerr << x << " -> " << p << "\n";
+ std::cerr << bin << " > " << this->HistFeatureSize() << " Warning -- Overload2\n";
+ }
+ histogram[bin] += p[0];
+ }
+#ifdef DEBUG
+ // Print the Histogram
+ std::cout << histogram << std::endl;
+#endif
+
+ // Since we are going to use this as a feature
+ // Normalise
+ float hmag = 0.0;
+#ifdef REORIENT
+ float maxmag = -1;
+ unsigned int maxbin;
+#endif
+ for (unsigned int i = 0; i < this->HistFeatureSize(); ++i) {
+ float mag = histogram[i]*histogram[i];
+ hmag += mag;
+#ifdef REORIENT
+ if (maxmag < 0 || mag > maxmag) {
+ maxmag = mag;
+ maxbin = i;
+ }
+#endif
+ }
+ hmag = sqrt(hmag);
+
+#ifdef REORIENT
+ typename GradientImageType::PixelType maxp = this->BinToVector(maxbin);
+
+ FeatureType histogram2(this->HistFeatureSize());
+ histogram2.Fill(0);
+#endif
+
+ for (unsigned int i = 0; i < this->HistFeatureSize(); ++i) {
+ histogram[i] /= hmag;
+
+#ifdef REORIENT
+ typename GradientImageType::PixelType bini = this->BinToVector(i);
+
+ unsigned int bin = 0;
+ unsigned int binpos = 1;
+ for (unsigned int k = 1; k < VDimension; ++k) {
+ bini[k] = ((int) (bini[k] - maxp[k] + m_HistogramBinsNumber)) % m_HistogramBinsNumber;
+ if (bini[k] < 0 || bini[k] >= m_HistogramBinsNumber)
+ bini[k] = 0;
+ bin += (int) bini[k] * binpos;
+ binpos *= m_HistogramBinsNumber;
+ }
+ histogram2[bin] = histogram[i];
+#endif
+ }
+
+
+#ifdef DEBUG
+ std::cout << histogram << std::endl;
+#ifdef REORIENT
+ std::cout << "Max Bin: " << maxbin << " Max Mag: " << maxmag << std::endl;
+ std::cout << "Reoriented: " << histogram2 << std::endl;
+#endif
+#endif
+#ifdef ERROR_CHECK
+ std::cerr << "OK\n ";
+#endif
+
+#ifdef REORIENT
+ return histogram2;
+#else
+ return histogram;
+#endif
+ }
+#endif
+
+ template <class TFixedImageType, unsigned int VDimension>
+ void
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::CheckLocalExtrema(FixedImagePointer image, IndexType pixelIndex,
+ PixelType pixelValue,
+ bool &isMax, bool &isMin,
+ bool checkCentre)
+ {
+#ifdef ERROR_CHECK
+ std::cerr << "CheckLocalExtrema ... ";
+#endif
+ int delta[VDimension];
+ for (unsigned int k = 0; k < VDimension; ++k) {
+ delta[k] = -1;
+ }
+ while(1) {
+ bool isZero=true;
+ if (!checkCentre) {
+ for (unsigned int k=0; k < VDimension; ++k) {
+ if(delta[k] != 0) {
+ isZero = false;
+ break;
+ }
+ }
+ }
+
+ if (checkCentre || !isZero) {
+ // Check if not the centre
+ IndexType tmpIndex;
+ for (unsigned int k=0; k < VDimension; ++k) {
+ tmpIndex[k] = pixelIndex[k] + delta[k];
+ }
+
+ typename TFixedImageType::PixelType tmpValue =
+ image->GetPixel(tmpIndex);
+
+#ifdef DEBUG_VERBOSE
+ std::cout << "...Comparing to ( ";
+ for (unsigned int k = 0; k < VDimension; ++k)
+ std::cout << tmpIndex[k] << " ";
+ std::cout << ") = " << tmpValue << "\n";
+#endif
+ // Treat as equality if within the error bound
+ if (((tmpValue - pixelValue) <= m_ErrorThreshold) &&
+ ((tmpValue - pixelValue) >= -m_ErrorThreshold)) {
+ isMax = false;
+ isMin = false;
+ } else
+ if (tmpValue > pixelValue) {
+ isMax = false;
+ } else
+ if (tmpValue < pixelValue) {
+ isMin = false;
+ }
+ if (!isMax && !isMin) break;
+ }
+ // Increment delta
+ bool resetdelta=false;
+ for(unsigned int k=0; k <= VDimension; ++k) {
+ if (k == VDimension) {
+ resetdelta = true;
+ break; // done
+ }
+ if (delta[k] < 1) {
+ ++delta[k];
+ break;
+ }
+ delta[k] = -1; // reset and increment the next pos
+ }
+ if(resetdelta) break;
+ }
+#ifdef ERROR_CHECK
+ std::cerr << "OK\n";
+#endif
+ }
+
+#ifdef GENERATE_KEYS
+ // Input: Image, Gradient Image, Point
+ // Output: Vector of direction
+ template <class TFixedImageType, unsigned int VDimension>
+ typename ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>::FeatureType
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::GetFeatures( FixedImagePointer fixedImage,
+ typename GradientImageType::Pointer hgradImage,
+ PointType &point, float currScale)
+ {
+#ifdef ERROR_CHECK
+ std::cerr << "GetFeatures ... ";
+#endif
+
+ // Generate the Gaussian
+ typedef GaussianImageSource<TFixedImageType> GaussianImageSourceType;
+ typename GaussianImageSourceType::Pointer gaussImgSource;
+ typename GaussianImageSourceType::ArrayType sigma;
+
+ gaussImgSource = GaussianImageSourceType::New();
+ gaussImgSource->SetNormalized(true);
+ //gaussImgSource->SetNormalized(false);
+ //gaussImgSource->SetScale(255);
+ gaussImgSource->SetSpacing(fixedImage->GetSpacing());
+ gaussImgSource->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
+ gaussImgSource->SetMean(point);
+
+#if 0
+ // If we wanted to find the orientation, we would use this
+ for (unsigned int i = 0; i < VDimension; ++i)
+ sigma[i] = 3.0 * currScale;
+ gaussImgSource->SetSigma(sigma);
+#endif
+
+ // Simulate the 16x16 Gaussian window descriptor
+ // use sigma equal to half the descriptor window width
+ for (unsigned int i = 0; i < VDimension; ++i)
+ sigma[i] = 8.0;
+ gaussImgSource->SetSigma(sigma);
+
+ gaussImgSource->Update();
+
+ IndexType pixelIndex;
+ fixedImage->TransformPhysicalPointToIndex(point, pixelIndex);
+
+#if 0
+ // Only iterate through the region that is within 3 sigma of the mean
+
+ IndexType regionStart;
+ for (unsigned int k=0; k < VDimension; ++k)
+ {
+ if ((pixelIndex[k] - 3*sigma[k]) > 0)
+ regionStart[k] = (int) floor(pixelIndex[k] - 3*sigma[k]);
+ else
+ regionStart[k] = 0;
+ }
+
+ typename TFixedImageType::SizeType regionSize =
+ fixedImage->GetLargestPossibleRegion().GetSize();
+
+ // Avoid far edge
+ for (unsigned int k=0; k < VDimension; ++k) {
+ if ( ceil(regionStart[k] + 6*sigma[k]) < regionSize[k])
+ regionSize[k] = (int) ceil(6*sigma[k]);
+ else
+ regionSize[k] -= regionStart[k];
+ }
+
+ typename TFixedImageType::RegionType itregion;
+ itregion.SetIndex(regionStart);
+ itregion.SetSize(regionSize);
+#endif
+
+ // return the Gaussian weighted Histogram
+#ifdef SIFT_FEATURE
+ return this->GetSiftKey(hgradImage, gaussImgSource->GetOutput(),
+ pixelIndex);
+#else
+ return this->GetHistogram(hgradImage, gaussImgSource->GetOutput());
+#endif
+ }
+
+#endif
+
+ template <class TFixedImageType, unsigned int VDimension>
+ void
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::writeImage(FixedImagePointer fixedImage, const char *filename)
+ {
+
+ if (VDimension != 2) return;
+
+ typedef itk::Image< unsigned char, VDimension > OutImageType;
+ typedef typename itk::ImageFileWriter< OutImageType > FixedWriterType;
+ typedef itk::ResampleImageFilter< TFixedImageType, OutImageType >
+ OutResampleFilterType;
+
+
+ typename OutResampleFilterType::Pointer resampler =
+ OutResampleFilterType::New();
+
+ resampler->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
+ resampler->SetOutputSpacing( fixedImage->GetSpacing() );
+ resampler->SetTransform(m_IdentityTransform);
+ resampler->SetInput(fixedImage);
+
+ typename FixedWriterType::Pointer fixedWriter = FixedWriterType::New();
+
+ fixedWriter->SetFileName(filename);
+ fixedWriter->SetInput( resampler->GetOutput() );
+
+ std::cout << "[Writing file << " << filename << "]";
+
+ try
+ {
+ fixedWriter->Update();
+ }
+ catch( itk::ExceptionObject & excep )
+ {
+ std::cerr << "Exception caught !" << std::endl;
+ std::cerr << excep << std::endl;
+ }
+
+ }
+
+ // create a filter that resamples the image (scale up or down)
+ template <class TFixedImageType, unsigned int VDimension>
+ typename ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>::ResampleFilterPointerType
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::getScaleResampleFilter ( FixedImagePointer fixedImage, float scale )
+ {
+ ResampleFilterPointerType scaler = ResampleFilterType::New();
+
+ scaler->SetInput( fixedImage );
+
+
+ // Change the size of the image
+ typename TFixedImageType::SizeType size =
+ fixedImage->GetLargestPossibleRegion().GetSize();
+ for (unsigned int k = 0; k < VDimension; ++k)
+ size[k] = (unsigned int) floor(size[k] * scale);
+ scaler->SetSize( size );
+
+ // Change the spacing
+ typename TFixedImageType::SpacingType spacing =
+ fixedImage->GetSpacing();
+ for (unsigned int k = 0; k < VDimension; ++k)
+ spacing[k] = (spacing[k] / scale);
+ scaler->SetOutputSpacing( spacing );
+
+ scaler->SetTransform( m_IdentityTransform );
+ scaler->SetDefaultPixelValue( 100 );
+ scaler->Update();
+
+ return scaler;
+ }
+
+ template <class TFixedImageType, unsigned int VDimension>
+ void
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::SetDoubling (bool tmp)
+ {
+ m_DoubleOriginalImage = tmp;
+ }
+
+ template <class TFixedImageType, unsigned int VDimension>
+ void
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::SetNumBins( unsigned int tmp)
+ {
+ m_HistogramBinsNumber = tmp;
+ }
+
+ template <class TFixedImageType, unsigned int VDimension>
+ void
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::SetSigma( double tmp)
+ {
+ m_GaussianSigma = tmp;
+ }
+
+ template <class TFixedImageType, unsigned int VDimension>
+ void
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::SetNumScales ( unsigned int tmp)
+ {
+ m_ImageScalesTestedNumber = tmp;
+ }
+
+ template <class TFixedImageType, unsigned int VDimension>
+ void
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::SetMatchRatio ( float tmp)
+ {
+ m_MaxFeatureDistanceRatio = tmp;
+ }
+
+
+ template <class TFixedImageType, unsigned int VDimension>
+ typename ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>::PointSetTypePointer
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::getSiftFeatures(FixedImagePointer fixedImage)
+ {
+ unsigned int numMin = 0, numMax = 0, numReject = 0;
+
+ m_KeypointSet = PointSetType::New();
+
+ m_PointsCount = 0;
+
+ // Declare Gaussian
+ typedef itk::DiscreteGaussianImageFilter<TFixedImageType, TFixedImageType >
+ GaussianFilterType;
+
+ std::vector<typename GaussianFilterType::Pointer> gaussianFilter(m_GaussianImagesNumber);
+
+ std::vector<typename TFixedImageType::Pointer>
+ gaussianImage(m_GaussianImagesNumber);
+
+ // Declare DoG
+ typedef itk::SubtractImageFilter<TFixedImageType, TFixedImageType,
+ TFixedImageType> DifferenceFilterType;
+ std::vector<typename DifferenceFilterType::Pointer> dogFilter(m_DifferenceOfGaussianImagesNumber);
+ std::vector<typename TFixedImageType::Pointer> dogImage(m_DifferenceOfGaussianImagesNumber);
+
+ // Resampled image filters
+ std::vector<typename ResampleFilterType::Pointer> scaler(m_ImageScalesTestedNumber);
+ std::vector<typename TFixedImageType::Pointer> scaleImage(m_ImageScalesTestedNumber);
+
+#ifdef GENERATE_KEYS
+ // Declare Gradient
+ std::vector<typename GradientFilterType::Pointer> gradFilter(m_ImageScalesTestedNumber);
+ std::vector<typename GradientImageType::Pointer> gradImage(m_ImageScalesTestedNumber);
+ std::vector<typename GradientImageType::Pointer> hgradImage(m_ImageScalesTestedNumber);
+
+ std::vector<typename GradientMagFilterType::Pointer> gradMagFilter(m_ImageScalesTestedNumber);
+ std::vector<FixedImagePointer> gradMagImage(m_ImageScalesTestedNumber);
+#endif
+
+
+ float currScale = 0.5;
+
+ // For each scale
+ for (unsigned int i = 0; i < m_ImageScalesTestedNumber; ++i) {
+ std::cout << "Computing Scale Level " << i << "... (";
+
+ if (i == 0 && !m_DoubleOriginalImage) {
+ scaleImage[0] = fixedImage;
+ } else {
+ if (i == 0) {
+ // Input is the fixed Image.
+ scaler[i] = getScaleResampleFilter ( fixedImage, m_ScalingFactor );
+ } else {
+ // Input is the 2*sigma smoothed image from the previous octave
+ scaler[i] = getScaleResampleFilter ( gaussianImage[m_DifferenceOfGaussianTestsNumber] , 1.0 / m_ScalingFactor );
+ }
+ scaleImage[i] = scaler[i]->GetOutput();
+ }
+
+ {
+ typename TFixedImageType::SizeType gsize =
+ scaleImage[i]->GetLargestPossibleRegion().GetSize();
+ for (unsigned int j = 0; j < VDimension; ++j)
+ std::cout << gsize[j] << " ";
+ }
+
+ std::cout << ") Done\n";
+
+#ifdef DEBUG
+ char filename[256];
+ sprintf(filename, "gauss-%d-0.png", i);
+ this->writeImage(scaleImage[i], filename);
+#endif
+
+#ifdef GENERATE_KEYS
+ // ...Compute Gradient
+ std::cout << "...Computing Gradient...";
+ gradFilter[i] = GradientFilterType::New();
+ gradFilter[i]->SetInput(scaleImage[i]);
+ // Do this in pixel space
+ gradFilter[i]->SetUseImageSpacing(false);
+ gradFilter[i]->Update();
+ gradImage[i] = gradFilter[i]->GetOutput();
+ hgradImage[i] = this->GetHypersphericalCoordinates(gradImage[i]);
+
+ gradMagFilter[i] = GradientMagFilterType::New();
+ gradMagFilter[i]->SetInput(scaleImage[i]);
+ // Do this in pixel space
+ gradMagFilter[i]->SetUseImageSpacing(false);
+ gradMagFilter[i]->Update();
+ gradMagImage[i] = gradMagFilter[i]->GetOutput();
+ std::cout << "...Done\n";
+#endif
+
+ // ...Compute Gaussians
+ for (unsigned int j = 0; j < m_GaussianImagesNumber; ++j) {
+#ifdef VERBOSE
+ std::cout << "Setting Up Gaussian Filter " << i << "-" << j << "...";
+ std::cout.flush();
+#endif
+ gaussianFilter[j] = GaussianFilterType::New();
+
+ /* Variance is square of the sigma
+ * sigma = (2^(j/s)*sigma)
+ */
+
+ double variance = this->GetGaussianScale(j);
+ variance *= variance;
+ gaussianFilter[j]->SetVariance(variance);
+ gaussianFilter[j]->SetInput( scaleImage[i] );
+ // pixel-wise smoothing
+ gaussianFilter[j]->SetUseImageSpacing(false);
+ try {
+ gaussianFilter[j]->Update();
+ }
+ catch( itk::ExceptionObject & excep ) {
+ std::cerr << "Exception caught !" << std::endl;
+ std::cerr << excep << std::endl;
+ }
+
+ gaussianImage[j] = gaussianFilter[j]->GetOutput();
+
+#ifdef DEBUG
+ char filename[256];
+ sprintf(filename, "gauss-%d-%d.png", i, j);
+ this->writeImage(gaussianImage[j], filename);
+#endif
+
+#ifdef VERBOSE
+ std::cout << "Done\n";
+ std::cout.flush();
+#endif
+ }
+
+ // ...Compute Difference of Gaussians
+ for (unsigned int j = 0; j < (m_DifferenceOfGaussianImagesNumber); ++j) {
+#ifdef VERBOSE
+ std::cout << "Setting Up DoG Filter " << i << "-" << j << "...";
+ std::cout.flush();
+#endif
+ dogFilter[j] = DifferenceFilterType::New();
+ dogFilter[j]->SetInput1( gaussianImage[j] );
+ dogFilter[j]->SetInput2( gaussianImage[j+1] );
+ dogFilter[j]->Update();
+ dogImage[j] = dogFilter[j]->GetOutput();
+
+#ifdef DEBUG
+ char filename[256];
+ sprintf(filename, "dog-%d-%d.png", i, j);
+ this->writeImage(dogImage[j], filename);
+#endif
+
+#ifdef VERBOSE
+ std::cout << "Done\n";
+ std::cout.flush();
+#endif
+ }
+
+ for (unsigned int j=1; j < (m_DifferenceOfGaussianImagesNumber - 1); ++j) {
+ // Search the dogImages for local maxima, w.r.t. corresponding
+ // point in the scale above and below
+ // level 0 is the "doubled" image
+ // Iterate over the various doG filters
+ // Only use the middle dogs (ones with both neighbours above and below)
+ // Iterate over each position in the dog filter
+ typedef itk::ImageRegionIteratorWithIndex< TFixedImageType >
+ ImageIteratorType;
+
+ IndexType regionStart;
+ // Avoid the edges
+ for (unsigned int k=0; k < VDimension; ++k)
+ regionStart[k] = 1;
+
+ typename TFixedImageType::SizeType regionSize =
+ dogImage[j]->GetLargestPossibleRegion().GetSize();
+
+#ifdef VERBOSE
+ std::cout << "Searching for Extrema in DoG Image " << i << "-" << j;
+ std::cout << " ( ";
+ for (unsigned int k=0; k < VDimension; ++k)
+ std::cout << regionSize[k] << " ";
+ std::cout << ") Scale " << currScale << "\n";
+ std::cout.flush();
+#endif
+
+ // Avoid far edge
+ for (unsigned int k=0; k < VDimension; ++k)
+ regionSize[k] -= 2;
+
+ typename TFixedImageType::RegionType itregion;
+ itregion.SetIndex(regionStart);
+ itregion.SetSize(regionSize);
+
+ ImageIteratorType pixelIt(dogImage[j],
+ itregion);
+
+ for ( pixelIt.GoToBegin(); !pixelIt.IsAtEnd(); ++pixelIt) {
+ // Make sure to start sufficiently into the image so that all
+ // neighbours are present
+ IndexType pixelIndex = pixelIt.GetIndex();
+ typename TFixedImageType::PixelType pixelValue = pixelIt.Get();
+
+ PointType point;
+ dogImage[j]->TransformIndexToPhysicalPoint (pixelIndex, point);
+
+#ifdef ERROR_CHECK
+ std::cerr << "Checking ( ";
+ for (unsigned int k = 0; k < VDimension; ++k)
+ std::cerr << pixelIndex[k] << " ";
+ std::cerr << ") = " << pixelValue <<"\n";
+#endif
+
+ // Compare to the 8 immediate neighbours
+ bool isMax=true;
+ bool isMin=true;
+
+ this->CheckLocalExtrema(dogImage[j],
+ pixelIndex, pixelValue, isMax, isMin, false);
+
+ if (!isMax && !isMin) continue;
+
+ // Compare to scale above
+ if (j < (m_GaussianImagesNumber-1)) {
+#ifdef DEBUG_VERBOSE
+ std::cout << "...Checking Scale Above\n";
+#endif
+ //dogImage[i+1][j]->TransformPhysicalPointToIndex (point, tmpIndex);
+
+ this->CheckLocalExtrema(dogImage[j+1],
+ pixelIndex, pixelValue, isMax, isMin, true);
+ }
+ if (!isMax && !isMin) continue;
+
+ // Compare to scale below
+ if (j > 0) {
+#ifdef DEBUG_VERBOSE
+ std::cout << "...Checking Scale Below\n";
+#endif
+ //dogImage[i-1][j]->TransformPhysicalPointToIndex (point, tmpIndex);
+
+ this->CheckLocalExtrema(dogImage[j-1],
+ pixelIndex, pixelValue, isMax, isMin, true);
+ }
+ if (!isMax && !isMin) continue;
+
+ // Check if it is sufficiently large (absolute value)
+ if (fabs(pixelValue) < m_MinKeypointValue) {
+ ++numReject;
+ continue;
+ }
+
+
+ // Passed all checks:
+
+#ifdef DEBUG
+ std::cout << point << std::endl;
+#endif
+ m_KeypointSet->SetPoint( m_PointsCount, point);
+#ifdef GENERATE_KEYS
+ // Generate features
+ // Space used is the (smoothed) original image)
+ m_KeypointSet->SetPointData( m_PointsCount,
+ this->GetFeatures( gaussianImage[0],
+ hgradImage[i], point,
+ this->GetGaussianScale(j)));
+#else
+ m_KeypointSet->SetPointData( m_PointsCount, currScale);
+#endif
+ ++m_PointsCount;
+
+ if (isMax) {
+ // Maxima detected.
+ ++numMax;
+#ifdef DEBUG
+ std::cout << "Found Maxima! ";
+#endif
+ }
+ if (isMin) {
+ // Minima detected.
+ ++numMin;
+#ifdef DEBUG
+ std::cout << "Found Minima! ";
+#endif
+ }
+ }
+#ifdef VERBOSE
+ std::cout << "Acc. Num Max: " << numMax
+ << "\nAcc. Num Min: " << numMin
+ << "\nAcc. Num Reject: " << numReject
+ << std::endl;
+ std::cout.flush();
+#endif
+ }
+ currScale *= m_ScalingFactor;
+ }
+
+#ifdef VERBOSE
+ std::cout << "Total Num Max: " << numMax
+ << "\nTotal Num Min: " << numMin
+ << "\nTotal Num Reject: " << numReject
+ << std::endl;
+ std::cout.flush();
+#endif
+ return m_KeypointSet;
+ }
+
+ template <class TFixedImageType, unsigned int VDimension>
+ void
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::MatchKeypointsPos(PointSetTypePointer keypoints1, PointSetTypePointer keypoints2,
+ typename TransformType::Pointer inverse_transform)
+ {
+ // Compare Keypoints. Check Coverage and Accuracy
+ // This does the comparison based on position of the keypoints
+ // Find:
+ // # of points that match which will tell us
+ // # of points that did not scale
+ // # of points created by the scale
+ unsigned int numMatches;
+ unsigned int numMatches2;
+ unsigned int numMatches5;
+ const double MATCH_THRESHOLD = 1.5;
+ typename PointSetType::PointsContainer::Pointer keyps1, keyps2;
+
+ unsigned long numpoints1, numpoints2;
+ numpoints1 = keypoints1->GetNumberOfPoints();
+ std::cout << "Keypoints1 Found: " << numpoints1 << std::endl;
+ numpoints2 = keypoints2->GetNumberOfPoints();
+ std::cout << "Keypoints2 Found: " << numpoints2 << std::endl;
+
+ if (!inverse_transform)
+ return;
+
+ numMatches = 0;
+ numMatches2 = 0;
+ numMatches5 = 0;
+ for (unsigned int i = 0; i < numpoints2; ++i) {
+ PointType pp2;
+ keypoints2->GetPoint(i, &pp2);
+
+ bool match = false;
+ bool match2 = false;
+ bool match5 = false;
+ for (unsigned int j = 0; j < numpoints1; ++j) {
+ PointType tmpp, pp;
+ keypoints1->GetPoint(j, &tmpp);
+ pp = inverse_transform->TransformPoint(tmpp);
+ // for (int k = 0; k < VDimension; ++k)
+ // pp[k] *= scale_test;
+ if(!match && pp.EuclideanDistanceTo(pp2) <= MATCH_THRESHOLD)
+ {
+ ++numMatches;
+ match = true;
+ }
+ if(!match2 && pp.EuclideanDistanceTo(pp2) <= 2*MATCH_THRESHOLD)
+ {
+ ++numMatches2;
+ match2 = true;
+ }
+ if(!match5 && pp.EuclideanDistanceTo(pp2) <= 5*MATCH_THRESHOLD)
+ {
+ ++numMatches5;
+ match5 = true;
+ }
+ if (match && match2 && match5)
+ break;
+ }
+ }
+
+ std::cout << "Keypoints 2 Matching to Keypoints 1 (<" << MATCH_THRESHOLD << "): " << numMatches << std::endl;
+ std::cout << "% of Keypoints 2 Matching (<" << MATCH_THRESHOLD << "): " << (float) numMatches / numpoints2 << std::endl;
+ std::cout << "Keypoints 2 Matching to Keypoints 1 (<" << 2*MATCH_THRESHOLD << "): " << numMatches2 << std::endl;
+ std::cout << "% of Keypoints 2 Matching (<" << 2*MATCH_THRESHOLD << "): " << (float) numMatches2 / numpoints2 << std::endl;
+ std::cout << "Keypoints 2 Matching to Keypoints 1 (<" << 5*MATCH_THRESHOLD << "): " << numMatches5 << std::endl;
+ std::cout << "% of Keypoints 2 Matching (<" << 5*MATCH_THRESHOLD << "): " << (float) numMatches5 / numpoints2 << std::endl;
+
+
+ numMatches = 0;
+ numMatches2 = 0;
+ numMatches5 = 0;
+ for (unsigned int j = 0; j < numpoints1; ++j) {
+ PointType tmpp, pp;
+ keypoints1->GetPoint(j, &tmpp);
+ pp = inverse_transform->TransformPoint(tmpp);
+ // for (int k = 0; k < VDimension; ++k)
+ // pp[k] *= scale_test;
+
+ bool match = false;
+ bool match2 = false;
+ bool match5 = false;
+ for (unsigned int i = 0; i < numpoints2; ++i) {
+ PointType pp2;
+ keypoints2->GetPoint(i, &pp2);
+
+ if(!match && pp.EuclideanDistanceTo(pp2) <= MATCH_THRESHOLD)
+ {
+ ++numMatches;
+ match = true;
+ }
+ if(!match2 && pp.EuclideanDistanceTo(pp2) <= 2*MATCH_THRESHOLD)
+ {
+ ++numMatches2;
+ match2 = true;
+ }
+ if(!match5 && pp.EuclideanDistanceTo(pp2) <= 5*MATCH_THRESHOLD)
+ {
+ ++numMatches5;
+ match5 = true;
+ }
+ if (match && match2 && match5)
+ break;
+ }
+ }
+
+ std::cout << "Keypoints 1 Matching to Keypoints 2 (<" << MATCH_THRESHOLD << "): " << numMatches << std::endl;
+ std::cout << "% of Keypoints 1 Matching (<" << MATCH_THRESHOLD << "): " << (float) numMatches / numpoints1 << std::endl;
+ std::cout << "Keypoints 1 Matching to Keypoints 2 (<" << 2*MATCH_THRESHOLD << "): " << numMatches2 << std::endl;
+ std::cout << "% of Keypoints 1 Matching (<" << 2*MATCH_THRESHOLD << "): " << (float) numMatches2 / numpoints1 << std::endl;
+ std::cout << "Keypoints 1 Matching to Keypoints 2 (<" << 5*MATCH_THRESHOLD << "): " << numMatches5 << std::endl;
+ std::cout << "% of Keypoints 1 Matching (<" << 5*MATCH_THRESHOLD << "): " << (float) numMatches5 / numpoints1 << std::endl;
+ }
+
+#ifdef GENERATE_KEYS
+ template <class TFixedImageType, unsigned int VDimension>
+ void
+ ScaleInvariantFeatureImageFilter<TFixedImageType,VDimension>
+ ::MatchKeypointsFeatures(PointSetTypePointer keypoints1, PointSetTypePointer keypoints2,
+ typename TransformType::Pointer inverse_transform)
+ {
+ // Compare Keypoints. Check Coverage and Accuracy
+ // This does the comparison based on position of the keypoints
+ // Find:
+ // # of points that match which will tell us
+ // # of points that did not scale
+ // # of points created by the scale
+ unsigned int numMatches;
+ unsigned int numMatchesTried;
+ unsigned int numMatches2;
+ unsigned int numMatches5;
+ const double MATCH_THRESHOLD = 1.5;
+ typename PointSetType::PointsContainer::Pointer keyps1, keyps2;
+
+ unsigned long numpoints1, numpoints2;
+ numpoints1 = keypoints1->GetNumberOfPoints();
+ std::cout << "Keypoints1 Found: " << numpoints1 << std::endl;
+ numpoints2 = keypoints2->GetNumberOfPoints();
+ std::cout << "Keypoints2 Found: " << numpoints2 << std::endl;
+
+ std::cout << "***Keypoint Matches***\n";
+
+ numMatches = 0;
+ numMatches2 = 0;
+ numMatches5 = 0;
+ numMatchesTried = 0;
+ for (unsigned int i = 0; i < numpoints2; ++i) {
+ PointType pp2;
+ keypoints2->GetPoint(i, &pp2);
+ FeatureType ft2;
+ keypoints2->GetPointData(i, &ft2);
+
+ FeatureType bestft;
+ float bestdist = -1.0;
+ float nextbestdist = -1.0;
+ unsigned int bestj = 0;
+ for (unsigned int j = 0; j < numpoints1; ++j) {
+ PointType pp;
+ keypoints1->GetPoint(j, &pp);
+ FeatureType ft;
+ keypoints1->GetPointData(j, &ft);
+
+ float dist = 0.0;
+ for (unsigned int k = 0; k < ft.Size(); ++k)
+ dist += (ft[k] - ft2[k])*(ft[k] - ft2[k]);
+
+ if (nextbestdist < 0.0 || dist < bestdist)
+ {
+ nextbestdist = bestdist;
+ bestdist=dist;
+ bestft = ft;
+ bestj = j;
+ }
+ }
+
+ /* Reject "too close" matches */
+ if ((bestdist / nextbestdist) > m_MaxFeatureDistanceRatio)
+ continue;
+
+ /* NEW IDEA -- look to make sure it is a reciprocal best match */
+ /* Take the best feature found, see if pp2 makes the cut */
+ bestdist = -1.0;
+ nextbestdist = -1.0;
+ FeatureType bestft2;
+ unsigned int bestj2 = 0;
+
+ for (unsigned int j = 0; j < numpoints2; ++j) {
+ PointType pp;
+ keypoints2->GetPoint(j, &pp);
+ FeatureType ft;
+ keypoints2->GetPointData(j, &ft);
+
+ float dist = 0.0;
+ for (int unsigned k = 0; k < ft.Size(); ++k)
+ dist += (ft[k] - bestft[k])*(ft[k] - bestft[k]);
+
+ if (nextbestdist < 0.0 || dist < bestdist)
+ {
+ nextbestdist = bestdist;
+ bestdist=dist;
+ bestft2 = ft;
+ bestj2 = j;
+ }
+ }
+
+ /* Reject if not reciprocal best hit or "too close" matches */
+ if ( bestft2 != ft2 || ((bestdist / nextbestdist) > m_MaxFeatureDistanceRatio))
+ continue;
+ /* END NEW IDEA */
+
+ ++numMatchesTried;
+
+ // Check goodness of best feature
+ PointType tmpp, pp;
+ keypoints1->GetPoint(bestj, &tmpp);
+
+ // Print the match
+ std::cout << tmpp << " => " << pp2 << std::endl;
+
+ if (!inverse_transform)
+ continue;
+ pp = inverse_transform->TransformPoint(tmpp);
+
+ if(pp.EuclideanDistanceTo(pp2) <= MATCH_THRESHOLD)
+ ++numMatches;
+ if(pp.EuclideanDistanceTo(pp2) <= (2*MATCH_THRESHOLD))
+ ++numMatches2;
+ if(pp.EuclideanDistanceTo(pp2) <= (5*MATCH_THRESHOLD))
+ ++numMatches5;
+ }
+
+ std::cout << "\n***Features 2 Matches Attempted: " << numMatchesTried << std::endl;
+ std::cout << "Features 2 Matching to Features 1 (<" << MATCH_THRESHOLD << "): " << numMatches << std::endl;
+ std::cout << "% of Features 2 Matching (<" << MATCH_THRESHOLD << "): " << (float) numMatches / numMatchesTried << std::endl;
+ std::cout << "Features 2 Matching to Features 1 (<" << 2*MATCH_THRESHOLD << "): " << numMatches2 << std::endl;
+ std::cout << "% of Features 2 Matching (<" << 2*MATCH_THRESHOLD << "): " << (float) numMatches2 / numMatchesTried << std::endl;
+ std::cout << "Features 2 Matching to Features 1 (<" << 5*MATCH_THRESHOLD << "): " << numMatches5 << std::endl;
+ std::cout << "% of Features 2 Matching (<" << 5*MATCH_THRESHOLD << "): " << (float) numMatches5 / numMatchesTried << std::endl;
+
+ }
+#endif
+
+} // end namespace itk
+
+#endif