# include <stdint.h>
#endif
+#define VTK_EXCLUDE_STRSTREAM_HEADERS
+
//--------------------------------------------------------------------
namespace clitk {
#include "itkPoint.h"
#include "clitkImageCommon.h"
#include "clitkCommon.h"
+#define VTK_EXCLUDE_STRSTREAM_HEADERS
#include <vtkMatrix4x4.h>
#include <vtkSmartPointer.h>
#include <itkObjectFactory.h>
#include <itkProcessObject.h>
+#define VTK_EXCLUDE_STRSTREAM_HEADERS
#include <vtkSmartPointer.h>
#include <vtkTransform.h>
/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
#include "clitkFilterBase.h"
#include "clitkCropLikeImageFilter.h"
#include "clitkSegmentationUtils.h"
-// #include "itkLabelOverlapMeasuresImageFilter.h"
// itk
#include <itkImageToImageFilter.h>
#include <itkLabelStatisticsImageFilter.h>
+#include <itkLabelOverlapMeasuresImageFilter.h>
#include <iomanip>
namespace clitk {
-
+
//--------------------------------------------------------------------
/*
Analyze the relative position of a Target (mask image) according
to some Object, in a given Support. Indicate the main important
- position of this Target according the Object.
+ position of this Target according the Object.
*/
//--------------------------------------------------------------------
-
+
template <class ImageType>
class LabelImageOverlapMeasureFilter:
public virtual FilterBase,
typedef LabelImageOverlapMeasureFilter<ImageType> Self;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
-
+
/** Method for creation through the object factory. */
itkNewMacro(Self);
-
+
/** Run-time type information (and related methods). */
itkTypeMacro(LabelImageOverlapMeasureFilter, ImageToImageFilter);
/** Some convenient typedefs. */
typedef typename ImageType::ConstPointer ImageConstPointer;
typedef typename ImageType::Pointer ImagePointer;
- typedef typename ImageType::RegionType RegionType;
+ typedef typename ImageType::RegionType RegionType;
typedef typename ImageType::PixelType PixelType;
typedef typename ImageType::SpacingType SpacingType;
typedef typename ImageType::SizeType SizeType;
typedef typename ImageType::IndexType IndexType;
typedef typename ImageType::PointType PointType;
-
+
/** ImageDimension constants */
itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
FILTERBASE_INIT;
-
+
// Options
itkGetConstMacro(BackgroundValue, PixelType);
- itkSetMacro(BackgroundValue, PixelType);
+ //itkSetMacro(BackgroundValue, PixelType);
itkGetConstMacro(Label1, PixelType);
itkSetMacro(Label1, PixelType);
itkGetConstMacro(Label2, PixelType);
itkSetMacro(Label2, PixelType);
+ itkSetMacro(VerboseFlag, bool);
+ itkGetConstMacro(VerboseFlag, bool);
+ itkBooleanMacro(VerboseFlag);
+
+ itkSetMacro(LongFlag, bool);
+ itkGetConstMacro(LongFlag, bool);
+ itkBooleanMacro(LongFlag);
+
// I dont want to verify inputs information
virtual void VerifyInputInformation() { }
-
+
protected:
LabelImageOverlapMeasureFilter();
virtual ~LabelImageOverlapMeasureFilter() {}
-
+
PixelType m_BackgroundValue;
PixelType m_Label1;
PixelType m_Label2;
ImagePointer m_Input1;
ImagePointer m_Input2;
+ bool m_VerboseFlag;
+ bool m_LongFlag;
virtual void GenerateOutputInformation();
virtual void GenerateInputRequestedRegion();
private:
LabelImageOverlapMeasureFilter(const Self&); //purposely not implemented
void operator=(const Self&); //purposely not implemented
-
+
}; // end class
//--------------------------------------------------------------------
/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
this->SetNumberOfRequiredInputs(2);
SetLabel1(1);
SetLabel2(1);
- SetBackgroundValue(0);
+ m_BackgroundValue = 0;
+ SetVerboseFlag(false);
+ SetLongFlag(false);
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template <class ImageType>
-void
+void
clitk::LabelImageOverlapMeasureFilter<ImageType>::
-GenerateOutputInformation()
-{
+GenerateOutputInformation()
+{
// DD("GenerateOutputInformation");
//ImagePointer input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
// ImagePointer outputImage = this->GetOutput(0);
//--------------------------------------------------------------------
template <class ImageType>
-void
+void
clitk::LabelImageOverlapMeasureFilter<ImageType>::
-GenerateInputRequestedRegion()
+GenerateInputRequestedRegion()
{
// Call default
itk::ImageToImageFilter<ImageType, ImageType>::GenerateInputRequestedRegion();
//--------------------------------------------------------------------
template <class ImageType>
-void
+void
clitk::LabelImageOverlapMeasureFilter<ImageType>::
-GenerateData()
+GenerateData()
{
- // DD("GenerateData");
-
// Get input pointer
m_Input1 = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
m_Input2 = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
// Resize like the union
ImagePointer input1 = clitk::ResizeImageLike<ImageType>(m_Input1, bbo, GetBackgroundValue());
ImagePointer input2 = clitk::ResizeImageLike<ImageType>(m_Input2, bbo, GetBackgroundValue());
- //DD(input1->GetLargestPossibleRegion());
- //DD(input2->GetLargestPossibleRegion());
-
- // Compute overlap image
- ImagePointer image_union = clitk::Clone<ImageType>(input1);
- ImagePointer image_intersection = clitk::Clone<ImageType>(input1);
- clitk::Or<ImageType>(image_union, input2, GetBackgroundValue());
- clitk::And<ImageType>(image_intersection, input2, GetBackgroundValue());
-
- ImagePointer image_1NotIn2 = clitk::Clone<ImageType>(input1);
- clitk::AndNot<ImageType>(image_1NotIn2, input2, GetBackgroundValue());
-
- ImagePointer image_2NotIn1 = clitk::Clone<ImageType>(input2);
- clitk::AndNot<ImageType>(image_2NotIn1, input1, GetBackgroundValue());
-
- //writeImage<ImageType>(image_union, "union.mha");
- //writeImage<ImageType>(image_intersection, "intersection.mha");
- //writeImage<ImageType>(image_1NotIn2, "image_1NotIn2.mha");
- //writeImage<ImageType>(image_2NotIn1, "image_2NotIn1.mha");
-
- // Compute size
- typedef itk::LabelStatisticsImageFilter<ImageType, ImageType> StatFilterType;
- typename StatFilterType::Pointer statFilter = StatFilterType::New();
- statFilter->SetInput(image_union);
- statFilter->SetLabelInput(image_union);
- statFilter->Update();
- int u = statFilter->GetCount(GetLabel1());
-
- statFilter->SetInput(image_intersection);
- statFilter->SetLabelInput(image_intersection);
- statFilter->Update();
- int inter = statFilter->GetCount(GetLabel1());
-
- statFilter->SetInput(m_Input1);
- statFilter->SetLabelInput(m_Input1);
- statFilter->Update();
- int in1 = statFilter->GetCount(GetLabel1());
-
- statFilter->SetInput(m_Input2);
- statFilter->SetLabelInput(m_Input2);
- statFilter->Update();
- int in2 = statFilter->GetCount(GetLabel1());
-
- statFilter->SetInput(image_1NotIn2);
- statFilter->SetLabelInput(image_1NotIn2);
- statFilter->Update();
- int l1notIn2 = statFilter->GetCount(GetLabel1());
-
- statFilter->SetInput(image_2NotIn1);
- statFilter->SetLabelInput(image_2NotIn1);
- statFilter->Update();
- int l2notIn1 = statFilter->GetCount(GetLabel1());
-
- double dice = 2.0*(double)inter/(double)(in1+in2);
+ /*
+ if (GetVerboseFlag()) {
+ std::cout << "Resize images to the union of bounding boxes: "
+ << input1->GetLargestPossibleRegion().GetSize() << std::endl;
+ }
+ */
+
+ /*
int width = 6;
std::cout << std::setw(width) << in1 << " "
<< std::setw(width) << in2 << " "
<< std::setw(width) << l1notIn2 << " "
<< std::setw(width) << l2notIn1 << " "
<< std::setw(width) << dice << " "; //std::endl;
+ */
+
+ // Compute overlap, dice
+ typedef itk::LabelOverlapMeasuresImageFilter<ImageType> FilterType;
+ typename FilterType::Pointer diceFilter = FilterType::New();
+ diceFilter->SetSourceImage(input1);
+ diceFilter->SetTargetImage(input2);
+ diceFilter->Update();
+
+ // Display information
+ if (!GetLongFlag()) {
+ if (GetVerboseFlag()) {
+ std::cout << "Dice : ";
+ }
+ std::cout << diceFilter->GetDiceCoefficient() << std::endl;
+ }
+ else { // long options
+ if (GetVerboseFlag()) {
+ std::cout << "Dice Jaccard Source Target Inter Union SrComp TarComp" << std::endl;
+ }
+ typename FilterType::MapType m = diceFilter->GetLabelSetMeasures();
+ int width = 6;
+ std::cout << std::setw(width) << diceFilter->GetDiceCoefficient() << " "
+ << std::setw(width) << diceFilter->GetJaccardCoefficient() << " "
+ << std::setw(width) << m[m_Label1].m_Source << " "
+ << std::setw(width) << m[m_Label2].m_Target << " "
+ << std::setw(width) << m[m_Label1].m_Intersection << " "
+ << std::setw(width) << m[m_Label1].m_Union << " "
+ << std::setw(width) << m[m_Label1].m_SourceComplement << " "
+ << std::setw(width) << m[m_Label2].m_TargetComplement << " "
+ << std::endl;
+ }
+
}
//--------------------------------------------------------------------
-
+++ /dev/null
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelOverlapMeasuresImageFilter.h,v $
- Language: C++
- Date: $Date: $
- Version: $Revision: $
-
- 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 __itkLabelOverlapMeasuresImageFilter_h
-#define __itkLabelOverlapMeasuresImageFilter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkFastMutexLock.h"
-#include "itkNumericTraits.h"
-
-//#include "itk_hash_map.h"
-#include "itksys/hash_map.hxx"
-
-namespace itk {
-
-/** \class LabelOverlapMeasuresImageFilter
- * \brief Computes overlap measures between the set same set of labels of
- * pixels of two images. Background is assumed to be 0.
- *
- * \sa LabelOverlapMeasuresImageFilter
- *
- * \ingroup MultiThreaded
- */
-template<class TLabelImage>
-class ITK_EXPORT LabelOverlapMeasuresImageFilter :
- public ImageToImageFilter<TLabelImage, TLabelImage>
-{
-public:
- /** Standard Self typedef */
- typedef LabelOverlapMeasuresImageFilter Self;
- typedef ImageToImageFilter<TLabelImage,TLabelImage> Superclass;
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> ConstPointer;
-
- /** Method for creation through the object factory. */
- itkNewMacro( Self );
-
- /** Runtime information support. */
- itkTypeMacro( LabelOverlapMeasuresImageFilter, ImageToImageFilter );
-
- virtual void VerifyInputInformation() { }
-
-
- /** Image related typedefs. */
- typedef TLabelImage LabelImageType;
- typedef typename TLabelImage::Pointer LabelImagePointer;
- typedef typename TLabelImage::ConstPointer LabelImageConstPointer;
-
- typedef typename TLabelImage::RegionType RegionType;
- typedef typename TLabelImage::SizeType SizeType;
- typedef typename TLabelImage::IndexType IndexType;
-
- typedef typename TLabelImage::PixelType LabelType;
-
- /** Type to use form computations. */
- typedef typename NumericTraits<LabelType>::RealType RealType;
-
- /** \class LabelLabelOverlapMeasuress
- * \brief Metrics stored per label */
- class LabelSetMeasures
- {
- public:
- // default constructor
- LabelSetMeasures()
- {
- m_Source = 0;
- m_Target = 0;
- m_Union = 0;
- m_Intersection = 0;
- m_SourceComplement = 0;
- m_TargetComplement = 0;
- }
-
- // added for completeness
- LabelSetMeasures& operator=( const LabelSetMeasures& l )
- {
- m_Source = l.m_Source;
- m_Target = l.m_Target;
- m_Union = l.m_Union;
- m_Intersection = l.m_Intersection;
- m_SourceComplement = l.m_SourceComplement;
- m_TargetComplement = l.m_TargetComplement;
- }
-
- unsigned long m_Source;
- unsigned long m_Target;
- unsigned long m_Union;
- unsigned long m_Intersection;
- unsigned long m_SourceComplement;
- unsigned long m_TargetComplement;
- };
-
- /** Type of the map used to store data per label */
- typedef itksys::hash_map<LabelType, LabelSetMeasures> MapType;
- typedef typename MapType::iterator MapIterator;
- typedef typename MapType::const_iterator MapConstIterator;
-
- /** Image related typedefs. */
- itkStaticConstMacro( ImageDimension, unsigned int,
- TLabelImage::ImageDimension );
-
- /** Set the source image. */
- void SetSourceImage( const LabelImageType * image )
- { this->SetNthInput( 0, const_cast<LabelImageType *>( image ) ); }
-
- /** Set the target image. */
- void SetTargetImage( const LabelImageType * image )
- { this->SetNthInput( 1, const_cast<LabelImageType *>( image ) ); }
-
- /** Get the source image. */
- const LabelImageType * GetSourceImage( void )
- { return this->GetInput( 0 ); }
-
- /** Get the target image. */
- const LabelImageType * GetTargetImage( void )
- { return this->GetInput( 1 ); }
-
- /** Get the label set measures */
- MapType GetLabelSetMeasures()
- { return this->m_LabelSetMeasures; }
-
- /**
- * tric overlap measures
- */
- /** measures over all labels */
- RealType GetTotalOverlap();
- RealType GetUnionOverlap();
- RealType GetMeanOverlap();
- RealType GetVolumeSimilarity();
- RealType GetFalseNegativeError();
- RealType GetFalsePositiveError();
- /** measures over individual labels */
- RealType GetTargetOverlap( LabelType );
- RealType GetUnionOverlap( LabelType );
- RealType GetMeanOverlap( LabelType );
- RealType GetVolumeSimilarity( LabelType );
- RealType GetFalseNegativeError( LabelType );
- RealType GetFalsePositiveError( LabelType );
- /** alternative names */
- RealType GetJaccardCoefficient()
- { return this->GetUnionOverlap(); }
- RealType GetJaccardCoefficient( LabelType label )
- { return this->GetUnionOverlap( label ); }
- RealType GetDiceCoefficient()
- { return this->GetMeanOverlap(); }
- RealType GetDiceCoefficient( LabelType label )
- { return this->GetMeanOverlap( label ); }
-
-
-#ifdef ITK_USE_CONCEPT_CHECKING
- /** Begin concept checking */
- itkConceptMacro( Input1HasNumericTraitsCheck,
- ( Concept::HasNumericTraits<LabelType> ) );
- /** End concept checking */
-#endif
-
-protected:
- LabelOverlapMeasuresImageFilter();
- ~LabelOverlapMeasuresImageFilter(){};
- void PrintSelf( std::ostream& os, Indent indent ) const;
-
- /**
- * Pass the input through unmodified. Do this by setting the output to the
- * source this by setting the output to the source image in the
- * AllocateOutputs() method.
- */
- void AllocateOutputs();
-
- void BeforeThreadedGenerateData();
-
- void AfterThreadedGenerateData();
-
- /** Multi-thread version GenerateData. */
- void ThreadedGenerateData( const RegionType&, int );
-
- // Override since the filter needs all the data for the algorithm
- void GenerateInputRequestedRegion();
-
- // Override since the filter produces all of its output
- void EnlargeOutputRequestedRegion( DataObject *data );
-
-private:
- LabelOverlapMeasuresImageFilter( const Self& ); //purposely not implemented
- void operator=( const Self& ); //purposely not implemented
-
- std::vector<MapType> m_LabelSetMeasuresPerThread;
- MapType m_LabelSetMeasures;
-
- SimpleFastMutexLock m_Mutex;
-
-}; // end of class
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkLabelOverlapMeasuresImageFilter.txx"
-#endif
-
-#endif
+++ /dev/null
-/*=========================================================================
-
- Program: Insight Segmentation & Registration Toolkit
- Module: $RCSfile: itkLabelOverlapMeasuresImageFilter.txx,v $
- Language: C++
- Date: $Date: $
- Version: $Revision: $
-
- 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 _itkLabelOverlapMeasuresImageFilter_txx
-#define _itkLabelOverlapMeasuresImageFilter_txx
-
-#include "itkLabelOverlapMeasuresImageFilter.h"
-
-#include "itkImageRegionConstIterator.h"
-#include "itkProgressReporter.h"
-
-namespace itk {
-
-#if defined(__GNUC__) && (__GNUC__ <= 2) //NOTE: This class needs a mutex for gnu 2.95
-/** Used for mutex locking */
-#define LOCK_HASHMAP this->m_Mutex.Lock()
-#define UNLOCK_HASHMAP this->m_Mutex.Unlock()
-#else
-#define LOCK_HASHMAP
-#define UNLOCK_HASHMAP
-#endif
-
-template<class TLabelImage>
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::LabelOverlapMeasuresImageFilter()
-{
- // this filter requires two input images
- this->SetNumberOfRequiredInputs( 2 );
-}
-
-template<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GenerateInputRequestedRegion()
-{
- Superclass::GenerateInputRequestedRegion();
- if( this->GetSourceImage() )
- {
- LabelImagePointer source = const_cast
- <LabelImageType *>( this->GetSourceImage() );
- source->SetRequestedRegionToLargestPossibleRegion();
- }
- if( this->GetTargetImage() )
- {
- LabelImagePointer target = const_cast
- <LabelImageType *>( this->GetTargetImage() );
- target->SetRequestedRegionToLargestPossibleRegion();
- }
-}
-
-template<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::EnlargeOutputRequestedRegion( DataObject *data )
-{
- Superclass::EnlargeOutputRequestedRegion( data );
- data->SetRequestedRegionToLargestPossibleRegion();
-}
-
-
-template<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::AllocateOutputs()
-{
- // Pass the source through as the output
- LabelImagePointer image =
- const_cast<TLabelImage *>( this->GetSourceImage() );
- this->SetNthOutput( 0, image );
-
- // Nothing that needs to be allocated for the remaining outputs
-}
-
-template<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::BeforeThreadedGenerateData()
-{
- int numberOfThreads = this->GetNumberOfThreads();
-
- // Resize the thread temporaries
- this->m_LabelSetMeasuresPerThread.resize( numberOfThreads );
-
- // Initialize the temporaries
- for( int n = 0; n < numberOfThreads; n++ )
- {
- this->m_LabelSetMeasuresPerThread[n].clear();
- }
-
- // Initialize the final map
- this->m_LabelSetMeasures.clear();
-}
-
-template<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::AfterThreadedGenerateData()
-{
- // Run through the map for each thread and accumulate the set measures.
- for( int n = 0; n < this->GetNumberOfThreads(); n++ )
- {
- // iterate over the map for this thread
- for( MapConstIterator threadIt = this->m_LabelSetMeasuresPerThread[n].begin();
- threadIt != this->m_LabelSetMeasuresPerThread[n].end();
- ++threadIt )
- {
- // does this label exist in the cumulative stucture yet?
- MapIterator mapIt = this->m_LabelSetMeasures.find( ( *threadIt ).first );
- if( mapIt == this->m_LabelSetMeasures.end() )
- {
- // create a new entry
- typedef typename MapType::value_type MapValueType;
- mapIt = this->m_LabelSetMeasures.insert( MapValueType(
- (*threadIt).first, LabelSetMeasures() ) ).first;
- }
-
- // accumulate the information from this thread
- (*mapIt).second.m_Source += (*threadIt).second.m_Source;
- (*mapIt).second.m_Target += (*threadIt).second.m_Target;
- (*mapIt).second.m_Union += (*threadIt).second.m_Union;
- (*mapIt).second.m_Intersection +=
- (*threadIt).second.m_Intersection;
- (*mapIt).second.m_SourceComplement +=
- (*threadIt).second.m_SourceComplement;
- (*mapIt).second.m_TargetComplement +=
- (*threadIt).second.m_TargetComplement;
- } // end of thread map iterator loop
- } // end of thread loop
-}
-
-template<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::ThreadedGenerateData( const RegionType& outputRegionForThread,
- int threadId )
-{
- ImageRegionConstIterator<LabelImageType> ItS( this->GetSourceImage(),
- outputRegionForThread );
- ImageRegionConstIterator<LabelImageType> ItT( this->GetTargetImage(),
- outputRegionForThread );
-
- // support progress methods/callbacks
- ProgressReporter progress( this, threadId,
- 2*outputRegionForThread.GetNumberOfPixels() );
-
- for( ItS.GoToBegin(), ItT.GoToBegin(); !ItS.IsAtEnd(); ++ItS, ++ItT )
- {
- LabelType sourceLabel = ItS.Get();
- LabelType targetLabel = ItT.Get();
-
- // is the label already in this thread?
- MapIterator mapItS =
- this->m_LabelSetMeasuresPerThread[threadId].find( sourceLabel );
- MapIterator mapItT =
- this->m_LabelSetMeasuresPerThread[threadId].find( targetLabel );
-
- if( mapItS == this->m_LabelSetMeasuresPerThread[threadId].end() )
- {
- // create a new label set measures object
- typedef typename MapType::value_type MapValueType;
- LOCK_HASHMAP;
- mapItS = this->m_LabelSetMeasuresPerThread[threadId].insert(
- MapValueType( sourceLabel, LabelSetMeasures() ) ).first;
- UNLOCK_HASHMAP;
- }
-
- if( mapItT == this->m_LabelSetMeasuresPerThread[threadId].end() )
- {
- // create a new label set measures object
- typedef typename MapType::value_type MapValueType;
- LOCK_HASHMAP;
- mapItT = this->m_LabelSetMeasuresPerThread[threadId].insert(
- MapValueType( targetLabel, LabelSetMeasures() ) ).first;
- UNLOCK_HASHMAP;
- }
-
- (*mapItS).second.m_Source++;
- (*mapItT).second.m_Target++;
-
- if( sourceLabel == targetLabel )
- {
- (*mapItS).second.m_Intersection++;
- (*mapItS).second.m_Union++;
- }
- else
- {
- (*mapItS).second.m_Union++;
- (*mapItT).second.m_Union++;
-
- (*mapItS).second.m_SourceComplement++;
- (*mapItT).second.m_TargetComplement++;
- }
-
- progress.CompletedPixel();
- }
-}
-
-/**
- * measures
- */
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetTotalOverlap()
-{
- RealType numerator = 0.0;
- RealType denominator = 0.0;
- for( MapIterator mapIt = this->m_LabelSetMeasures.begin();
- mapIt != this->m_LabelSetMeasures.end(); ++mapIt )
- {
- // Do not include the background in the final value.
- if( (*mapIt).first == NumericTraits<LabelType>::Zero )
- {
- continue;
- }
- numerator += static_cast<RealType>( (*mapIt).second.m_Intersection );
- denominator += static_cast<RealType>( (*mapIt).second.m_Target );
- }
- return ( numerator / denominator );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetTargetOverlap( LabelType label )
-{
- MapIterator mapIt = this->m_LabelSetMeasures.find( label );
- if( mapIt == this->m_LabelSetMeasures.end() )
- {
- itkWarningMacro( "Label " << label << " not found." );
- return 0.0;
- }
- RealType value =
- static_cast<RealType>( (*mapIt).second.m_Intersection ) /
- static_cast<RealType>( (*mapIt).second.m_Target );
- return value;
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetUnionOverlap()
-{
- RealType numerator = 0.0;
- RealType denominator = 0.0;
- for( MapIterator mapIt = this->m_LabelSetMeasures.begin();
- mapIt != this->m_LabelSetMeasures.end(); ++mapIt )
- {
- // Do not include the background in the final value.
- if( (*mapIt).first == NumericTraits<LabelType>::Zero )
- {
- continue;
- }
- numerator += static_cast<RealType>( (*mapIt).second.m_Intersection );
- denominator += static_cast<RealType>( (*mapIt).second.m_Union );
- }
- return ( numerator / denominator );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetUnionOverlap( LabelType label )
-{
- MapIterator mapIt = this->m_LabelSetMeasures.find( label );
- if( mapIt == this->m_LabelSetMeasures.end() )
- {
- itkWarningMacro( "Label " << label << " not found." );
- return 0.0;
- }
- RealType value =
- static_cast<RealType>( (*mapIt).second.m_Intersection ) /
- static_cast<RealType>( (*mapIt).second.m_Union );
- return value;
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetMeanOverlap()
-{
- RealType uo = this->GetUnionOverlap();
- return ( 2.0 * uo / ( 1.0 + uo ) );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetMeanOverlap( LabelType label )
-{
- RealType uo = this->GetUnionOverlap( label );
- return ( 2.0 * uo / ( 1.0 + uo ) );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetVolumeSimilarity()
-{
- RealType numerator = 0.0;
- RealType denominator = 0.0;
- for( MapIterator mapIt = this->m_LabelSetMeasures.begin();
- mapIt != this->m_LabelSetMeasures.end(); ++mapIt )
- {
- // Do not include the background in the final value.
- if( (*mapIt).first == NumericTraits<LabelType>::Zero )
- {
- continue;
- }
- numerator += ( ( static_cast<RealType>( (*mapIt).second.m_Source ) -
- static_cast<RealType>( (*mapIt).second.m_Target ) ) );
- denominator += ( ( static_cast<RealType>( (*mapIt).second.m_Source ) +
- static_cast<RealType>( (*mapIt).second.m_Target ) ) );
- }
- return ( 2.0 * numerator / denominator );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetVolumeSimilarity( LabelType label )
-{
- MapIterator mapIt = this->m_LabelSetMeasures.find( label );
- if( mapIt == this->m_LabelSetMeasures.end() )
- {
- itkWarningMacro( "Label " << label << " not found." );
- return 0.0;
- }
- RealType value = 2.0 *
- ( static_cast<RealType>( (*mapIt).second.m_Source ) -
- static_cast<RealType>( (*mapIt).second.m_Target ) ) /
- ( static_cast<RealType>( (*mapIt).second.m_Source ) +
- static_cast<RealType>( (*mapIt).second.m_Target ) );
- return value;
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetFalseNegativeError()
-{
- RealType numerator = 0.0;
- RealType denominator = 0.0;
- for( MapIterator mapIt = this->m_LabelSetMeasures.begin();
- mapIt != this->m_LabelSetMeasures.end(); ++mapIt )
- {
- // Do not include the background in the final value.
- if( (*mapIt).first == NumericTraits<LabelType>::Zero )
- {
- continue;
- }
- numerator += static_cast<RealType>( (*mapIt).second.m_TargetComplement );
- denominator += static_cast<RealType>( (*mapIt).second.m_Target );
- }
- return ( numerator / denominator );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetFalseNegativeError( LabelType label )
-{
- MapIterator mapIt = this->m_LabelSetMeasures.find( label );
- if( mapIt == this->m_LabelSetMeasures.end() )
- {
- itkWarningMacro( "Label " << label << " not found." );
- return 0.0;
- }
- RealType value =
- static_cast<RealType>( (*mapIt).second.m_TargetComplement ) /
- static_cast<RealType>( (*mapIt).second.m_Target );
- return value;
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetFalsePositiveError()
-{
- RealType numerator = 0.0;
- RealType denominator = 0.0;
- for( MapIterator mapIt = this->m_LabelSetMeasures.begin();
- mapIt != this->m_LabelSetMeasures.end(); ++mapIt )
- {
- // Do not include the background in the final value.
- if( (*mapIt).first == NumericTraits<LabelType>::Zero )
- {
- continue;
- }
- numerator += static_cast<RealType>( (*mapIt).second.m_SourceComplement );
- denominator += static_cast<RealType>( (*mapIt).second.m_Source );
- }
- return ( numerator / denominator );
-}
-
-template<class TLabelImage>
-typename LabelOverlapMeasuresImageFilter<TLabelImage>::RealType
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::GetFalsePositiveError( LabelType label )
-{
- MapIterator mapIt = this->m_LabelSetMeasures.find( label );
- if( mapIt == this->m_LabelSetMeasures.end() )
- {
- itkWarningMacro( "Label " << label << " not found." );
- return 0.0;
- }
- RealType value =
- static_cast<RealType>( (*mapIt).second.m_SourceComplement ) /
- static_cast<RealType>( (*mapIt).second.m_Source );
- return value;
-}
-
-template<class TLabelImage>
-void
-LabelOverlapMeasuresImageFilter<TLabelImage>
-::PrintSelf( std::ostream& os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-
-}
-
-
-}// end namespace itk
-#endif
WRAP_GGO(clitkUnsharpMask_GGO_C clitkUnsharpMask.ggo)
ADD_EXECUTABLE(clitkUnsharpMask clitkUnsharpMask.cxx ${clitkUnsharpMask_GGO_C})
- TARGET_LINK_LIBRARIES(clitkUnsharpMask clitkCommon )
+ TARGET_LINK_LIBRARIES(clitkUnsharpMask clitkCommon )
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkUnsharpMask)
WRAP_GGO(clitkFooImage_GGO_C clitkFooImage.ggo)
ADD_EXECUTABLE(clitkFooImage clitkFooImage.cxx ${clitkFooImage_GGO_C})
- TARGET_LINK_LIBRARIES(clitkFooImage clitkCommon )
+ TARGET_LINK_LIBRARIES(clitkFooImage clitkCommon )
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkFooImage)
#WRAP_GGO(clitkMedianImageFilter_GGO_C clitkMedianImageFilter.ggo)
# ADD_EXECUTABLE(clitkExtractSlice clitkExtractSlice.cxx clitkExtractSliceGenericFilter.cxx ${clitkExtractSlice_GGO_C})
# TARGET_LINK_LIBRARIES(clitkExtractSlice clitkCommon)
#SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkExtractSlice)
-
+
WRAP_GGO(clitkFlipImage_GGO_C clitkFlipImage.ggo)
ADD_EXECUTABLE(clitkFlipImage clitkFlipImage.cxx clitkFlipImageGenericFilter.cxx ${clitkFlipImage_GGO_C})
TARGET_LINK_LIBRARIES(clitkFlipImage clitkCommon)
TARGET_LINK_LIBRARIES(clitkTransformLandmarks clitkCommon)
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkTransformLandmarks)
+ WRAP_GGO(clitkDice_GGO_C clitkDice.ggo)
+ ADD_EXECUTABLE(clitkDice clitkDice.cxx ${clitkDice_GGO_C})
+ TARGET_LINK_LIBRARIES(clitkDice clitkSegmentationGgoLib clitkCommon ${ITK_LIBRARIES} )
+ SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkDice)
+
WRAP_GGO(clitkMaskLandmarks_GGO_C clitkMaskLandmarks.ggo)
ADD_EXECUTABLE(clitkMaskLandmarks clitkMaskLandmarks.cxx ${clitkMaskLandmarks_GGO_C})
TARGET_LINK_LIBRARIES(clitkMaskLandmarks clitkCommon)
ADD_EXECUTABLE(clitkJacobianImage clitkJacobianImage.cxx clitkJacobianImageGenericFilter.cxx ${clitkJacobianImage_GGO_C})
TARGET_LINK_LIBRARIES(clitkJacobianImage clitkCommon)
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkJacobianImage)
-
+
WRAP_GGO(clitkPadImage_GGO_C clitkPadImage.ggo)
ADD_EXECUTABLE(clitkPadImage clitkPadImage.cxx clitkPadImageGenericFilter.cxx ${clitkPadImage_GGO_C})
TARGET_LINK_LIBRARIES(clitkPadImage clitkCommon)
INSTALL (TARGETS ${TOOLS_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
ENDIF(CLITK_BUILD_TOOLS)
-
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+// clitk
+#include "clitkIO.h"
+#include "clitkDice_ggo.h"
+
+#include "clitkLabelImageOverlapMeasureGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[]) {
+
+ // Init command line
+ GGO(clitkDice, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::LabelImageOverlapMeasureGenericFilter<args_info_clitkDice> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+
+ try {
+ filter->Update();
+ } catch(std::runtime_error e) {
+ std::cout << e.what() << std::endl;
+ return EXIT_FAILURE;
+ }
+
+ return EXIT_SUCCESS;
+} // This is the end, my friend
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkDice.ggo
+package "clitkDice"
+version "1.0"
+purpose "Compute Dice between labeled images. Background must be 0."
+
+section "General options"
+option "config" - "Config file" string no
+option "verbose" v "Verbose" flag off
+option "imagetypes" - "Display allowed image types" flag off
+option "long" l "Long display (not only dice)" flag off
+
+section "Input"
+option "input1" i "Input mask 1" string yes
+option "input2" j "Input mask 2" string yes
+
+option "label1" - "Label in input1" int no default="1"
+option "label2" - "Label in input2" int no default="1"
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+#ifndef CLITKLABELIMAGEOVERLAPMEASUREGENERICFILTER_H
+#define CLITKLABELIMAGEOVERLAPMEASUREGENERICFILTER_H
+
+// clitk
+#include "clitkImageToImageGenericFilter.h"
+#include "clitkLabelImageOverlapMeasureFilter.h"
+#include "clitkBoundingBoxUtils.h"
+#include "clitkCropLikeImageFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+ template<class ArgsInfoType>
+ class ITK_EXPORT LabelImageOverlapMeasureGenericFilter:
+ public ImageToImageGenericFilter<LabelImageOverlapMeasureGenericFilter<ArgsInfoType> >
+ {
+ public:
+ //--------------------------------------------------------------------
+ LabelImageOverlapMeasureGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef ImageToImageGenericFilter<LabelImageOverlapMeasureGenericFilter<ArgsInfoType> > Superclass;
+ typedef LabelImageOverlapMeasureGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ itkNewMacro(Self);
+ itkTypeMacro(LabelImageOverlapMeasureGenericFilter, LightObject);
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const ArgsInfoType & a);
+ template<class FilterType>
+ void SetOptionsFromArgsInfoToFilter(FilterType * f) ;
+
+ //--------------------------------------------------------------------
+ // Main function called each time the filter is updated
+ template<class ImageType>
+ void UpdateWithInputImageType();
+
+ protected:
+ template<unsigned int Dim> void InitializeImageType();
+ ArgsInfoType mArgsInfo;
+
+ private:
+ LabelImageOverlapMeasureGenericFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ };// end class
+ //--------------------------------------------------------------------
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkLabelImageOverlapMeasureGenericFilter.txx"
+#endif
+
+#endif // #define CLITKRELATIVEPOSITIONANALYZERGENERICFILTER_H
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ===========================================================================**/
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+clitk::LabelImageOverlapMeasureGenericFilter<ArgsInfoType>::
+LabelImageOverlapMeasureGenericFilter():
+ ImageToImageGenericFilter<Self>("LabelImageOverlapMeasure")
+{
+ // Default values
+ cmdline_parser_clitkDice_init(&mArgsInfo);
+ //InitializeImageType<2>();
+ InitializeImageType<3>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::LabelImageOverlapMeasureGenericFilter<ArgsInfoType>::
+InitializeImageType()
+{
+ ADD_IMAGE_TYPE(Dim, uchar);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::LabelImageOverlapMeasureGenericFilter<ArgsInfoType>::
+SetArgsInfo(const ArgsInfoType & a)
+{
+ mArgsInfo=a;
+ //this->SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+ if (mArgsInfo.input1_given) this->AddInputFilename(mArgsInfo.input1_arg);
+ if (mArgsInfo.input2_given) this->AddInputFilename(mArgsInfo.input2_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void clitk::LabelImageOverlapMeasureGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+ f->SetLabel1(mArgsInfo.label1_arg);
+ f->SetLabel2(mArgsInfo.label2_arg);
+ f->SetVerboseFlag(mArgsInfo.verbose_flag);
+ f->SetLongFlag(mArgsInfo.long_flag);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class ImageType>
+void clitk::LabelImageOverlapMeasureGenericFilter<ArgsInfoType>::
+UpdateWithInputImageType()
+{
+ // Reading input
+ typename ImageType::Pointer input1 = this->template GetInput<ImageType>(0);
+ typename ImageType::Pointer input2 = this->template GetInput<ImageType>(1);
+
+ // Create filter
+ typedef clitk::LabelImageOverlapMeasureFilter<ImageType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+
+ // Set global Options
+ filter->SetInput(0, input1);
+ filter->SetInput(1, input2);
+ SetOptionsFromArgsInfoToFilter<FilterType>(filter);
+
+ // Go !
+ filter->Update();
+
+ // Write/Save results
+ // typename ImageType::Pointer output = filter->GetOutput();
+ // this->template SetNextOutput<ImageType>(output);
+}
+//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff